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Illumina Inc transcriptome library
Distribution of Opisthopappus Shih populations. The blue dot represents the distribution of O. longilobus . The red dot represents the distribution of O. taihangensis . The black oval represents the sampling sites of <t>transcriptome</t> sequencing. The black arrow represents the sampling sites of SNP analysis.
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Images

1) Product Images from "De novo Assembly and Transcriptome Characterization of Opisthopappus (Asteraceae) for Population Differentiation and Adaption"

Article Title: De novo Assembly and Transcriptome Characterization of Opisthopappus (Asteraceae) for Population Differentiation and Adaption

Journal: Frontiers in Genetics

doi: 10.3389/fgene.2018.00371

Distribution of Opisthopappus Shih populations. The blue dot represents the distribution of O. longilobus . The red dot represents the distribution of O. taihangensis . The black oval represents the sampling sites of transcriptome sequencing. The black arrow represents the sampling sites of SNP analysis.
Figure Legend Snippet: Distribution of Opisthopappus Shih populations. The blue dot represents the distribution of O. longilobus . The red dot represents the distribution of O. taihangensis . The black oval represents the sampling sites of transcriptome sequencing. The black arrow represents the sampling sites of SNP analysis.

Techniques Used: Sampling, Sequencing

2) Product Images from "Microarray Analysis in Glioblastomas"

Article Title: Microarray Analysis in Glioblastomas

Journal: Methods in molecular biology (Clifton, N.J.)

doi: 10.1007/7651_2015_245

A representative heatmap of gene expression obtained by microarray analysis. Shown is an unpublished heatmap showing differentially expressed genes in a glioblastoma cell engineered to express shRNA targeting autophagy gene ATG7
Figure Legend Snippet: A representative heatmap of gene expression obtained by microarray analysis. Shown is an unpublished heatmap showing differentially expressed genes in a glioblastoma cell engineered to express shRNA targeting autophagy gene ATG7

Techniques Used: Expressing, Microarray, shRNA

A representative microarray-based experimental workflow. Shown are the typical steps taken in microarray analysis from sample processing to data analysis
Figure Legend Snippet: A representative microarray-based experimental workflow. Shown are the typical steps taken in microarray analysis from sample processing to data analysis

Techniques Used: Microarray

3) Product Images from "An essential domain of an early-diverged RNA polymerase II functions to accurately decode a primitive chromatin landscape"

Article Title: An essential domain of an early-diverged RNA polymerase II functions to accurately decode a primitive chromatin landscape

Journal: Nucleic Acids Research

doi: 10.1093/nar/gkx486

Mutations in the CTD of T. brucei RPB1 cause varied phenotypes. ( A ) Schematic of T. brucei RPB1. The conserved A-H domains, characteristic of eukaryotic RNA pol II, make up the body of the polypeptide. They are followed by a 284-amino acid-long non-canonical CTD (gray) in place of the canonical CTD found in most model eukaryotes. Clusters of serine residues (red, numbered on top) in the WT Ty1 CTD that were substituted with alanine residues (blue) in the cell lines M2 Ty1 , M9 Ty1 and M3 Ty1 are shown. Drawing is not to scale. ( B ) Schematic of genetic background in four transgenic cell lines. Endogenous RPB1 (endoRPB1) mRNAs, encoded by allelic pairs within chromosomes 4 and 8, contain similar 3΄UTRs (open bar) that are targeted for RNAi-mediated destruction in the presence of tetracycline. N-terminally tagged (black box) proteins are produced from RNAi-resistant mRNA containing a different 3΄UTR (closed bar), also in the presence of tetracycline. Red boxes mark regions containing the serine-to-alanine mutations. ( C ) Schematic of experimental design for growth and expression analyses. Stable transgenic cell lines were induced with tetracycline on Day 0. Time points indicate days after induction. The gray and black ramps indicate the corresponding decrease of endogenous RPB1 and increase of tagged proteins. ( D ) Growth curves of WT Ty1 , M2 Ty1 , M9 Ty1 and M3 Ty1 cells in the absence (black squares) and presence (gray/red squares) of tetracycline. Tetracycline addition caused endogenous RPB1 depletion and concomitant production of tagged proteins. ( E ) Immunoblot analyses of whole cell extracts prepared before (Day 0) and after (Days 1–3) tetracycline induction. Anti-RPB1 antibodies detect both endogenous RPB1 and exogenous wild-type, or mutant, Ty1-tagged RPB1 proteins. Anti-Ty1 antibodies detect only the tagged proteins. Robust expression of tagged protein in each of the cell lines is visible on Day 1. As RPB1 is predicted to have multiple and dynamic modifications, it often appears as a doublet. Anti-EF2 immunoblots are loading controls.
Figure Legend Snippet: Mutations in the CTD of T. brucei RPB1 cause varied phenotypes. ( A ) Schematic of T. brucei RPB1. The conserved A-H domains, characteristic of eukaryotic RNA pol II, make up the body of the polypeptide. They are followed by a 284-amino acid-long non-canonical CTD (gray) in place of the canonical CTD found in most model eukaryotes. Clusters of serine residues (red, numbered on top) in the WT Ty1 CTD that were substituted with alanine residues (blue) in the cell lines M2 Ty1 , M9 Ty1 and M3 Ty1 are shown. Drawing is not to scale. ( B ) Schematic of genetic background in four transgenic cell lines. Endogenous RPB1 (endoRPB1) mRNAs, encoded by allelic pairs within chromosomes 4 and 8, contain similar 3΄UTRs (open bar) that are targeted for RNAi-mediated destruction in the presence of tetracycline. N-terminally tagged (black box) proteins are produced from RNAi-resistant mRNA containing a different 3΄UTR (closed bar), also in the presence of tetracycline. Red boxes mark regions containing the serine-to-alanine mutations. ( C ) Schematic of experimental design for growth and expression analyses. Stable transgenic cell lines were induced with tetracycline on Day 0. Time points indicate days after induction. The gray and black ramps indicate the corresponding decrease of endogenous RPB1 and increase of tagged proteins. ( D ) Growth curves of WT Ty1 , M2 Ty1 , M9 Ty1 and M3 Ty1 cells in the absence (black squares) and presence (gray/red squares) of tetracycline. Tetracycline addition caused endogenous RPB1 depletion and concomitant production of tagged proteins. ( E ) Immunoblot analyses of whole cell extracts prepared before (Day 0) and after (Days 1–3) tetracycline induction. Anti-RPB1 antibodies detect both endogenous RPB1 and exogenous wild-type, or mutant, Ty1-tagged RPB1 proteins. Anti-Ty1 antibodies detect only the tagged proteins. Robust expression of tagged protein in each of the cell lines is visible on Day 1. As RPB1 is predicted to have multiple and dynamic modifications, it often appears as a doublet. Anti-EF2 immunoblots are loading controls.

Techniques Used: Transgenic Assay, Produced, Expressing, Mutagenesis, Western Blot

mRNA-Seq shows reduced expression of TSS-proximal genes in M2 Ty1 and M9 Ty1 cells. ( A and B ) Heat map views of gene expression changes (Fragments Per Kilobase of transcript per Million mapped reads, log 2 -fold change) in WT Ty1 and M2 Ty1 cells on chromosomes 3 (A) and 7 (B) after 1 day (Day 1), 2 days (Day 2) and three days (Day 3) of tetracycline induction (compared to untreated cells). Data are shown using the IGV™ browser. Yellow and black show increases and decreases in expression, respectively. Black arrows indicate the length and direction of polycistronic transcription units. Black bars show coding sequences. Pre-ribosomal RNA gene clusters, tRNAs and snoRNAs are shown by asterisks (*). ( C ) Volcano plots for WT Ty1 , M2 Ty1 , M9 Ty1 and M3 Ty1 cells, showing gene expression (log 2- fold changes) versus adjusted significance P -values (log 10 ) for all protein coding genes, before and after two days of tetracycline addition. The set of 482 TSS-proximal genes is highlighted in blue; all other genes (∼8000) are shown in red.
Figure Legend Snippet: mRNA-Seq shows reduced expression of TSS-proximal genes in M2 Ty1 and M9 Ty1 cells. ( A and B ) Heat map views of gene expression changes (Fragments Per Kilobase of transcript per Million mapped reads, log 2 -fold change) in WT Ty1 and M2 Ty1 cells on chromosomes 3 (A) and 7 (B) after 1 day (Day 1), 2 days (Day 2) and three days (Day 3) of tetracycline induction (compared to untreated cells). Data are shown using the IGV™ browser. Yellow and black show increases and decreases in expression, respectively. Black arrows indicate the length and direction of polycistronic transcription units. Black bars show coding sequences. Pre-ribosomal RNA gene clusters, tRNAs and snoRNAs are shown by asterisks (*). ( C ) Volcano plots for WT Ty1 , M2 Ty1 , M9 Ty1 and M3 Ty1 cells, showing gene expression (log 2- fold changes) versus adjusted significance P -values (log 10 ) for all protein coding genes, before and after two days of tetracycline addition. The set of 482 TSS-proximal genes is highlighted in blue; all other genes (∼8000) are shown in red.

Techniques Used: Expressing

4) Product Images from "Transcriptome profiling provides new insights into the formation of floral scent in Hedychium coronarium"

Article Title: Transcriptome profiling provides new insights into the formation of floral scent in Hedychium coronarium

Journal: BMC Genomics

doi: 10.1186/s12864-015-1653-7

Gene expression comparisons.  a  Venn diagram of number of DEGs. Genes in overlapping sets show the differential expression in two or three comparison pairs.  b  Changes in gene expression profile. The numbers of up-regulated and down-regulated genes between D1 and D4, D1 and D6, D4 and D6 are summarized
Figure Legend Snippet: Gene expression comparisons. a Venn diagram of number of DEGs. Genes in overlapping sets show the differential expression in two or three comparison pairs. b Changes in gene expression profile. The numbers of up-regulated and down-regulated genes between D1 and D4, D1 and D6, D4 and D6 are summarized

Techniques Used: Expressing

5) Product Images from "Reversal of Pathologic Lipid Accumulation in NPC1-Deficient Neurons by Drug-Promoted Release of LAMP1-Coated Lamellar Inclusions"

Article Title: Reversal of Pathologic Lipid Accumulation in NPC1-Deficient Neurons by Drug-Promoted Release of LAMP1-Coated Lamellar Inclusions

Journal: The Journal of Neuroscience

doi: 10.1523/JNEUROSCI.0900-16.2016

Gene expression profiling by RNAseq of RGCs acutely purified from wild-type and NPC1-deficient mice. A , Left, false-color micrographs of RGCs acutely purified from 1-week-old mice by immunopanning and subjected to nuclear staining with DAPI (blue) and to immunocytochemical staining for Thy1 (green). Scale bar, 20 μm. Right, percentage of Thy1+ cells after isolation from retinae of 1-week-old ( n = 9) and 2-week-old mice ( n = 5; t test). Immunopanning delivered ∼73,000 ± 8,000 Thy1-positive cells per 1-week-old mouse ( n = 5). B , Quantity of total RNA in purified RGCs per mouse ( n = 4 mice per genotype corresponding to biological replicates; t test). C , Heat map of Pearson's correlation coefficient showing the reproducibility of transcript counts among biological replicates. D , First factorial plane resulting from a correspondence analysis of variance-stabilized data with the x -axis and y -axis explaining 23 and 22% of the variability of the whole dataset, respectively. E , Mean fold changes of transcript counts in RGCs from 1-week-old mutant mice compared to wild-type littermates plotted against normalized mean counts of each transcript as revealed by RNAseq. Red dots indicate genes with an adjusted p value of
Figure Legend Snippet: Gene expression profiling by RNAseq of RGCs acutely purified from wild-type and NPC1-deficient mice. A , Left, false-color micrographs of RGCs acutely purified from 1-week-old mice by immunopanning and subjected to nuclear staining with DAPI (blue) and to immunocytochemical staining for Thy1 (green). Scale bar, 20 μm. Right, percentage of Thy1+ cells after isolation from retinae of 1-week-old ( n = 9) and 2-week-old mice ( n = 5; t test). Immunopanning delivered ∼73,000 ± 8,000 Thy1-positive cells per 1-week-old mouse ( n = 5). B , Quantity of total RNA in purified RGCs per mouse ( n = 4 mice per genotype corresponding to biological replicates; t test). C , Heat map of Pearson's correlation coefficient showing the reproducibility of transcript counts among biological replicates. D , First factorial plane resulting from a correspondence analysis of variance-stabilized data with the x -axis and y -axis explaining 23 and 22% of the variability of the whole dataset, respectively. E , Mean fold changes of transcript counts in RGCs from 1-week-old mutant mice compared to wild-type littermates plotted against normalized mean counts of each transcript as revealed by RNAseq. Red dots indicate genes with an adjusted p value of

Techniques Used: Expressing, Purification, Mouse Assay, Staining, Isolation, Mutagenesis

6) Product Images from "Expression of the Phosphatase Ppef2 Controls Survival and Function of CD8+ Dendritic Cells"

Article Title: Expression of the Phosphatase Ppef2 Controls Survival and Function of CD8+ Dendritic Cells

Journal: Frontiers in Immunology

doi: 10.3389/fimmu.2019.00222

RNA-sequencing reveals changes in RNA-expression of Ppef2 −/− CD8 + cDC1. (A) CD8 + DCs were purified by flow cytometry from cell suspensions of 3 pooled spleens as live MHCII + CD11c + CD11b − CD8 + cells to purity of > 95%. 15 spleens from Ppef2 +/+ or Ppef2 −/− mice were used to generate 5 samples each for RNA-sequencing. Shown is the volcano plot analysis of sorted CD8 + DCs. Fold change of−2 (a, blue) and +2 (a, red), and a p -value ≤ 0.01 were chosen as cut-off. Ppef2, protein phosphatase EF-hands 2; LOC100503496, uncharacterized transcript LOC100503496; Xlr4c, X-linked lymphocyte-regulated 4C; Dll4, delta-like ligand 4; Trim2, tripartite motif-containing 2; Npcd, neuronal pentraxin chromo domain; Mfsd2b, major facilitator superfamily domain containing 2B; Cmah, cytidine monophospho-N-acetylneuraminic acid hydroxylase; Xntrpc, Xndc1-transient receptor potential cation channel, subfamily C, member 2; A530064D06Rik, Riken cDNA A530064D06 gene; 1810014B01Rik, Riten cDNA 1810014B01 gene; Triqk, triple QxxK/R motif containing; Nptxr, neuronal pentraxin receptor; Rasd1, RAS, dexamethasone-induced 1; Gfra2, glial cell line derived neurotrophic factor family receptor alpha 2; Rmi2, RMI2, RecQ mediated genome instability 2; Thsd1, thrombospondin, type I, domain 1; Ccl2, chemokine (C-C motif) ligand 2; Zfp772, zinc finger protein 772; Cenpw, centromere protein W. (B) Boxplots represent normalized expression with 0,1 quantile, 0.9 quantile and all single points (each group n = 5) ** p
Figure Legend Snippet: RNA-sequencing reveals changes in RNA-expression of Ppef2 −/− CD8 + cDC1. (A) CD8 + DCs were purified by flow cytometry from cell suspensions of 3 pooled spleens as live MHCII + CD11c + CD11b − CD8 + cells to purity of > 95%. 15 spleens from Ppef2 +/+ or Ppef2 −/− mice were used to generate 5 samples each for RNA-sequencing. Shown is the volcano plot analysis of sorted CD8 + DCs. Fold change of−2 (a, blue) and +2 (a, red), and a p -value ≤ 0.01 were chosen as cut-off. Ppef2, protein phosphatase EF-hands 2; LOC100503496, uncharacterized transcript LOC100503496; Xlr4c, X-linked lymphocyte-regulated 4C; Dll4, delta-like ligand 4; Trim2, tripartite motif-containing 2; Npcd, neuronal pentraxin chromo domain; Mfsd2b, major facilitator superfamily domain containing 2B; Cmah, cytidine monophospho-N-acetylneuraminic acid hydroxylase; Xntrpc, Xndc1-transient receptor potential cation channel, subfamily C, member 2; A530064D06Rik, Riken cDNA A530064D06 gene; 1810014B01Rik, Riten cDNA 1810014B01 gene; Triqk, triple QxxK/R motif containing; Nptxr, neuronal pentraxin receptor; Rasd1, RAS, dexamethasone-induced 1; Gfra2, glial cell line derived neurotrophic factor family receptor alpha 2; Rmi2, RMI2, RecQ mediated genome instability 2; Thsd1, thrombospondin, type I, domain 1; Ccl2, chemokine (C-C motif) ligand 2; Zfp772, zinc finger protein 772; Cenpw, centromere protein W. (B) Boxplots represent normalized expression with 0,1 quantile, 0.9 quantile and all single points (each group n = 5) ** p

Techniques Used: RNA Sequencing Assay, RNA Expression, Purification, Flow Cytometry, Cytometry, Mouse Assay, Derivative Assay, Expressing

7) Product Images from "The developmental dynamics of the Populus stem transcriptome"

Article Title: The developmental dynamics of the Populus stem transcriptome

Journal: Plant Biotechnology Journal

doi: 10.1111/pbi.12958

K‐means clustering and enrichment analysis of transcripts differentially expressed between the apex and IN 1‐5. (a) K‐means clustering showing the transcriptome expression profiles. Nine clusters were identified based on expression levels in six developmental zones (Apex, IN 1, IN 2, IN 3, IN 4 and IN 5). (b) Gene Ontology enrichment among the nine clusters. Yellow to red, significant enrichment; white, not significant.
Figure Legend Snippet: K‐means clustering and enrichment analysis of transcripts differentially expressed between the apex and IN 1‐5. (a) K‐means clustering showing the transcriptome expression profiles. Nine clusters were identified based on expression levels in six developmental zones (Apex, IN 1, IN 2, IN 3, IN 4 and IN 5). (b) Gene Ontology enrichment among the nine clusters. Yellow to red, significant enrichment; white, not significant.

Techniques Used: Expressing

8) Product Images from "Impact of genomic polymorphisms on the repertoire of human MHC class I-associated peptides"

Article Title: Impact of genomic polymorphisms on the repertoire of human MHC class I-associated peptides

Journal: Nature Communications

doi: 10.1038/ncomms4600

Integrative view of the genomic landscape of the MIP repertoire of HLA-identical siblings. Circos plot showing similar proportions of sequenced genomic and transcriptomic regions in both siblings (tracks 1–3) and the small number of identified MiHAs (track 7) relative to the number of MS-detected MIPs (track 6) and sequenced polymorphic regions (tracks 4–5). From outermost to innermost tracks: (1) ideogram indicating chromosomal positions for each chromosome, (2) histogram depicting the number of genes for 500 kb windows, (3) heat map showing the fraction of bases of 500 kb windows covered by exome (outer circle) or transcriptome (inner circle) sequencing of subjects 1 (orange) and 2 (blue), (4) tile graph of 4,833 ns-SNP between siblings (purple), (5) tile graph of 3,774 heterozygous loci where both alleles are shared by the two subjects and lead to non-synonymous amino-acid changes (green), (6) tile graph representing genomic regions that give rise to 4,468 MIPs, (7) each dot represents one single gene-encoded MiHA deriving from regions containing ns-SNPs and detected by MS in subjects 1 (orange), 2 (blue) or both (green).
Figure Legend Snippet: Integrative view of the genomic landscape of the MIP repertoire of HLA-identical siblings. Circos plot showing similar proportions of sequenced genomic and transcriptomic regions in both siblings (tracks 1–3) and the small number of identified MiHAs (track 7) relative to the number of MS-detected MIPs (track 6) and sequenced polymorphic regions (tracks 4–5). From outermost to innermost tracks: (1) ideogram indicating chromosomal positions for each chromosome, (2) histogram depicting the number of genes for 500 kb windows, (3) heat map showing the fraction of bases of 500 kb windows covered by exome (outer circle) or transcriptome (inner circle) sequencing of subjects 1 (orange) and 2 (blue), (4) tile graph of 4,833 ns-SNP between siblings (purple), (5) tile graph of 3,774 heterozygous loci where both alleles are shared by the two subjects and lead to non-synonymous amino-acid changes (green), (6) tile graph representing genomic regions that give rise to 4,468 MIPs, (7) each dot represents one single gene-encoded MiHA deriving from regions containing ns-SNPs and detected by MS in subjects 1 (orange), 2 (blue) or both (green).

Techniques Used: Mass Spectrometry, Sequencing

9) Product Images from "Transcriptomic responses of corpuscle of Stannius gland of Japanese eels (Anguilla japonica) to Changes in Water Salinity"

Article Title: Transcriptomic responses of corpuscle of Stannius gland of Japanese eels (Anguilla japonica) to Changes in Water Salinity

Journal: Scientific Reports

doi: 10.1038/srep09836

Workflow of Illumina deep sequencing and bioinformatic analyses. It includes sample preparation, cDNA library construction, Illumina sequencing, and data analyses including transcriptome assembly, BLAST search, GO annotation, and gene expression analysis.
Figure Legend Snippet: Workflow of Illumina deep sequencing and bioinformatic analyses. It includes sample preparation, cDNA library construction, Illumina sequencing, and data analyses including transcriptome assembly, BLAST search, GO annotation, and gene expression analysis.

Techniques Used: Sequencing, Sample Prep, cDNA Library Assay, Expressing

10) Product Images from "An essential domain of an early-diverged RNA polymerase II functions to accurately decode a primitive chromatin landscape"

Article Title: An essential domain of an early-diverged RNA polymerase II functions to accurately decode a primitive chromatin landscape

Journal: Nucleic Acids Research

doi: 10.1093/nar/gkx486

Mutations in the CTD of T. brucei RPB1 cause varied phenotypes. ( A ) Schematic of T. brucei RPB1. The conserved A-H domains, characteristic of eukaryotic RNA pol II, make up the body of the polypeptide. They are followed by a 284-amino acid-long non-canonical CTD (gray) in place of the canonical CTD found in most model eukaryotes. Clusters of serine residues (red, numbered on top) in the WT Ty1 CTD that were substituted with alanine residues (blue) in the cell lines M2 Ty1 , M9 Ty1 and M3 Ty1 are shown. Drawing is not to scale. ( B ) Schematic of genetic background in four transgenic cell lines. Endogenous RPB1 (endoRPB1) mRNAs, encoded by allelic pairs within chromosomes 4 and 8, contain similar 3΄UTRs (open bar) that are targeted for RNAi-mediated destruction in the presence of tetracycline. N-terminally tagged (black box) proteins are produced from RNAi-resistant mRNA containing a different 3΄UTR (closed bar), also in the presence of tetracycline. Red boxes mark regions containing the serine-to-alanine mutations. ( C ) Schematic of experimental design for growth and expression analyses. Stable transgenic cell lines were induced with tetracycline on Day 0. Time points indicate days after induction. The gray and black ramps indicate the corresponding decrease of endogenous RPB1 and increase of tagged proteins. ( D ) Growth curves of WT Ty1 , M2 Ty1 , M9 Ty1 and M3 Ty1 cells in the absence (black squares) and presence (gray/red squares) of tetracycline. Tetracycline addition caused endogenous RPB1 depletion and concomitant production of tagged proteins. ( E ) Immunoblot analyses of whole cell extracts prepared before (Day 0) and after (Days 1–3) tetracycline induction. Anti-RPB1 antibodies detect both endogenous RPB1 and exogenous wild-type, or mutant, Ty1-tagged RPB1 proteins. Anti-Ty1 antibodies detect only the tagged proteins. Robust expression of tagged protein in each of the cell lines is visible on Day 1. As RPB1 is predicted to have multiple and dynamic modifications, it often appears as a doublet. Anti-EF2 immunoblots are loading controls.
Figure Legend Snippet: Mutations in the CTD of T. brucei RPB1 cause varied phenotypes. ( A ) Schematic of T. brucei RPB1. The conserved A-H domains, characteristic of eukaryotic RNA pol II, make up the body of the polypeptide. They are followed by a 284-amino acid-long non-canonical CTD (gray) in place of the canonical CTD found in most model eukaryotes. Clusters of serine residues (red, numbered on top) in the WT Ty1 CTD that were substituted with alanine residues (blue) in the cell lines M2 Ty1 , M9 Ty1 and M3 Ty1 are shown. Drawing is not to scale. ( B ) Schematic of genetic background in four transgenic cell lines. Endogenous RPB1 (endoRPB1) mRNAs, encoded by allelic pairs within chromosomes 4 and 8, contain similar 3΄UTRs (open bar) that are targeted for RNAi-mediated destruction in the presence of tetracycline. N-terminally tagged (black box) proteins are produced from RNAi-resistant mRNA containing a different 3΄UTR (closed bar), also in the presence of tetracycline. Red boxes mark regions containing the serine-to-alanine mutations. ( C ) Schematic of experimental design for growth and expression analyses. Stable transgenic cell lines were induced with tetracycline on Day 0. Time points indicate days after induction. The gray and black ramps indicate the corresponding decrease of endogenous RPB1 and increase of tagged proteins. ( D ) Growth curves of WT Ty1 , M2 Ty1 , M9 Ty1 and M3 Ty1 cells in the absence (black squares) and presence (gray/red squares) of tetracycline. Tetracycline addition caused endogenous RPB1 depletion and concomitant production of tagged proteins. ( E ) Immunoblot analyses of whole cell extracts prepared before (Day 0) and after (Days 1–3) tetracycline induction. Anti-RPB1 antibodies detect both endogenous RPB1 and exogenous wild-type, or mutant, Ty1-tagged RPB1 proteins. Anti-Ty1 antibodies detect only the tagged proteins. Robust expression of tagged protein in each of the cell lines is visible on Day 1. As RPB1 is predicted to have multiple and dynamic modifications, it often appears as a doublet. Anti-EF2 immunoblots are loading controls.

Techniques Used: Transgenic Assay, Produced, Expressing, Mutagenesis, Western Blot

mRNA-Seq shows reduced expression of TSS-proximal genes in M2 Ty1 and M9 Ty1 cells. ( A and B ) Heat map views of gene expression changes (Fragments Per Kilobase of transcript per Million mapped reads, log 2 -fold change) in WT Ty1 and M2 Ty1 cells on chromosomes 3 (A) and 7 (B) after 1 day (Day 1), 2 days (Day 2) and three days (Day 3) of tetracycline induction (compared to untreated cells). Data are shown using the IGV™ browser. Yellow and black show increases and decreases in expression, respectively. Black arrows indicate the length and direction of polycistronic transcription units. Black bars show coding sequences. Pre-ribosomal RNA gene clusters, tRNAs and snoRNAs are shown by asterisks (*). ( C ) Volcano plots for WT Ty1 , M2 Ty1 , M9 Ty1 and M3 Ty1 cells, showing gene expression (log 2- fold changes) versus adjusted significance P -values (log 10 ) for all protein coding genes, before and after two days of tetracycline addition. The set of 482 TSS-proximal genes is highlighted in blue; all other genes (∼8000) are shown in red.
Figure Legend Snippet: mRNA-Seq shows reduced expression of TSS-proximal genes in M2 Ty1 and M9 Ty1 cells. ( A and B ) Heat map views of gene expression changes (Fragments Per Kilobase of transcript per Million mapped reads, log 2 -fold change) in WT Ty1 and M2 Ty1 cells on chromosomes 3 (A) and 7 (B) after 1 day (Day 1), 2 days (Day 2) and three days (Day 3) of tetracycline induction (compared to untreated cells). Data are shown using the IGV™ browser. Yellow and black show increases and decreases in expression, respectively. Black arrows indicate the length and direction of polycistronic transcription units. Black bars show coding sequences. Pre-ribosomal RNA gene clusters, tRNAs and snoRNAs are shown by asterisks (*). ( C ) Volcano plots for WT Ty1 , M2 Ty1 , M9 Ty1 and M3 Ty1 cells, showing gene expression (log 2- fold changes) versus adjusted significance P -values (log 10 ) for all protein coding genes, before and after two days of tetracycline addition. The set of 482 TSS-proximal genes is highlighted in blue; all other genes (∼8000) are shown in red.

Techniques Used: Expressing

11) Product Images from "LIX1 regulates YAP activity and controls gastrointestinal cancer cell plasticity, et al. LIX1 regulates YAP activity and controls gastrointestinal cancer cell plasticity"

Article Title: LIX1 regulates YAP activity and controls gastrointestinal cancer cell plasticity, et al. LIX1 regulates YAP activity and controls gastrointestinal cancer cell plasticity

Journal: Journal of Cellular and Molecular Medicine

doi: 10.1111/jcmm.15569

LIX1 down‐regulation reduces the proliferative and invasive capacities of GIST cells. A, RT‐qPCR analysis of  LIX1  transcript level in GIST‐T1 cells upon  LIX1  silencing. Data were normalized to the mean  GAPDH  and  RPLPO  expression. Normalized expression levels were converted into fold changes. Values are presented as the mean ± SEM of n = 20 samples of GIST‐T1‐ Scrambled , n = 15 for GIST‐T1‐ ShLIX1#1  and n = 12 for‐ ShLIX1#2  cells. * P
Figure Legend Snippet: LIX1 down‐regulation reduces the proliferative and invasive capacities of GIST cells. A, RT‐qPCR analysis of LIX1 transcript level in GIST‐T1 cells upon LIX1 silencing. Data were normalized to the mean GAPDH and RPLPO expression. Normalized expression levels were converted into fold changes. Values are presented as the mean ± SEM of n = 20 samples of GIST‐T1‐ Scrambled , n = 15 for GIST‐T1‐ ShLIX1#1 and n = 12 for‐ ShLIX1#2 cells. * P

Techniques Used: Quantitative RT-PCR, Expressing

LIX1  silencing reduces GIST aggressive phenotype in vivo. A, Schematic representation of the approach. GIST‐T1‐ Scrambled , GIST‐T1‐ ShLIX1#1  or ‐ ShLIX1#2  cells were grafted in the ChorioAllantoic Membrane (CAM) of E7 chicken embryos and grafts were allowed to grow for 5 d when individual grafts were removed and analysed. B, Representative images (left panels) and dry weight (right panel) of GIST‐T1‐ Scrambled  and GIST‐T1‐ ShLIX1  cell grafts at E12. Scale bars, 2 mm. Values are the mean ± SEM of GIST‐T1‐ Scrambled  (n = 11), GIST‐T1‐ ShLIX1#1  (n = 8) and GIST‐T1‐ ShLIX1#2  cell grafts (n = 7). * P
Figure Legend Snippet: LIX1 silencing reduces GIST aggressive phenotype in vivo. A, Schematic representation of the approach. GIST‐T1‐ Scrambled , GIST‐T1‐ ShLIX1#1 or ‐ ShLIX1#2 cells were grafted in the ChorioAllantoic Membrane (CAM) of E7 chicken embryos and grafts were allowed to grow for 5 d when individual grafts were removed and analysed. B, Representative images (left panels) and dry weight (right panel) of GIST‐T1‐ Scrambled and GIST‐T1‐ ShLIX1 cell grafts at E12. Scale bars, 2 mm. Values are the mean ± SEM of GIST‐T1‐ Scrambled (n = 11), GIST‐T1‐ ShLIX1#1 (n = 8) and GIST‐T1‐ ShLIX1#2 cell grafts (n = 7). * P

Techniques Used: In Vivo, Chick Chorioallantoic Membrane Assay

LIX1 down‐regulation reprogrammes KIT‐positive GIST cells to the SMC lineage. A, Transcriptional profiling of GIST‐T1‐ Scrambled  and GIST‐T1‐ ShLIX1  cells. Gene ontology enrichment analysis of up‐regulated genes and biological processes common to GIST‐T1‐ ShLIX1#1  and ‐ ShLIX1#2  in smooth muscle development. Data were from n = 3 GIST‐T1‐ Scrambled , n = 3 GIST‐T1‐ ShLIX1#1  and n = 3 ‐ ShLIX1#2  (n = 3) independent samples. B, Transcript fold change of SMC‐restricted genes in GIST‐T1‐ ShLIX1  vs GIST‐T1‐ Scrambled  cells. The SMC gene list is based on previously published work (Table   S5 );  P
Figure Legend Snippet: LIX1 down‐regulation reprogrammes KIT‐positive GIST cells to the SMC lineage. A, Transcriptional profiling of GIST‐T1‐ Scrambled and GIST‐T1‐ ShLIX1 cells. Gene ontology enrichment analysis of up‐regulated genes and biological processes common to GIST‐T1‐ ShLIX1#1 and ‐ ShLIX1#2 in smooth muscle development. Data were from n = 3 GIST‐T1‐ Scrambled , n = 3 GIST‐T1‐ ShLIX1#1 and n = 3 ‐ ShLIX1#2 (n = 3) independent samples. B, Transcript fold change of SMC‐restricted genes in GIST‐T1‐ ShLIX1 vs GIST‐T1‐ Scrambled cells. The SMC gene list is based on previously published work (Table  S5 ); P

Techniques Used:

12) Product Images from "IreA Controls Endoplasmic Reticulum Stress-Induced Autophagy and Survival through Homeostasis Recovery"

Article Title: IreA Controls Endoplasmic Reticulum Stress-Induced Autophagy and Survival through Homeostasis Recovery

Journal: Molecular and Cellular Biology

doi: 10.1128/MCB.00054-18

Sequence analysis of Dictyostelium IreA protein and its subcellular localization. (A) Diagram of the IreA predicted protein structure. The signal peptide (residues 1 to 26), the transmembrane region (residues 437 to 457), the kinase domain (residues 575 to 851), and kinase extension nuclease (KEN) domain (residues 854 to 984) are highlighted. (B) Pairwise alignments between Dictyostelium IreA and the H. sapiens , A. thaliana , and S. cerevisiae orthologues. Protein sequences of Ire1 orthologues were analyzed with SIM alignment tool, and results were visualized with LALNVIEW. (C) Percent identity between Ire1 orthologues obtained from a multiple alignment analysis. (D) Confocal microscopy of WT cells expressing an IreA-GFP hybrid protein, prepared for immunofluorescence detection of PDI (labeled with a secondary antibody conjugated to Alexa Fluor red 546) and DAPI-stained nuclei (scale bar, 10 μm). (E) Diagrams of the WT ireA locus, the ireA ::BST construct, and the generated ireA − BST-interrupted locus. Gray boxes represent coding sequences; lines between boxes are introns. Arrows represent primers used for PCR amplification. A 998-bp deletion was generated in the ireA chromosomal locus by homologous recombination of a blasticidin (BST) resistance cassette. The insertion of BST in the ireA locus was corroborated by PCR with the indicated oligonucleotides. (F) Table presenting the expected sizes of the PCR amplification products that would be obtained with the respective oligonucleotide pairs depicted in panel E. (G and H) PCR products obtained using DNA (G) or cDNA (H) as the template. RNA was used as a negative control for DNA contamination. The asterisk denotes a control PCR amplification of an unrelated gene. M, molecular size marker.
Figure Legend Snippet: Sequence analysis of Dictyostelium IreA protein and its subcellular localization. (A) Diagram of the IreA predicted protein structure. The signal peptide (residues 1 to 26), the transmembrane region (residues 437 to 457), the kinase domain (residues 575 to 851), and kinase extension nuclease (KEN) domain (residues 854 to 984) are highlighted. (B) Pairwise alignments between Dictyostelium IreA and the H. sapiens , A. thaliana , and S. cerevisiae orthologues. Protein sequences of Ire1 orthologues were analyzed with SIM alignment tool, and results were visualized with LALNVIEW. (C) Percent identity between Ire1 orthologues obtained from a multiple alignment analysis. (D) Confocal microscopy of WT cells expressing an IreA-GFP hybrid protein, prepared for immunofluorescence detection of PDI (labeled with a secondary antibody conjugated to Alexa Fluor red 546) and DAPI-stained nuclei (scale bar, 10 μm). (E) Diagrams of the WT ireA locus, the ireA ::BST construct, and the generated ireA − BST-interrupted locus. Gray boxes represent coding sequences; lines between boxes are introns. Arrows represent primers used for PCR amplification. A 998-bp deletion was generated in the ireA chromosomal locus by homologous recombination of a blasticidin (BST) resistance cassette. The insertion of BST in the ireA locus was corroborated by PCR with the indicated oligonucleotides. (F) Table presenting the expected sizes of the PCR amplification products that would be obtained with the respective oligonucleotide pairs depicted in panel E. (G and H) PCR products obtained using DNA (G) or cDNA (H) as the template. RNA was used as a negative control for DNA contamination. The asterisk denotes a control PCR amplification of an unrelated gene. M, molecular size marker.

Techniques Used: Sequencing, Confocal Microscopy, Expressing, Immunofluorescence, Labeling, Staining, Construct, Generated, Polymerase Chain Reaction, Amplification, Homologous Recombination, Negative Control, Marker

13) Product Images from "Comparative transcriptome analysis revealed genes involved in the fruiting body development of Ophiocordyceps sinensis"

Article Title: Comparative transcriptome analysis revealed genes involved in the fruiting body development of Ophiocordyceps sinensis

Journal: PeerJ

doi: 10.7717/peerj.8379

qPCR validation of the expressed genes in Illumina sequencing. (A) Bars represent the fold change in expression of each candidate gene identified in FB relative to DF. (B) Bars represent the fold change in expression of each candidate gene identified in CM relative to DF Black bars represent qRT-PCR result (2 −ΔΔ Ct ). Error bars indicate the standard error. White bars represent the RNA-seq results (log 2 fold change). Histone H2A gene (MSTRG. 2474) was the internal reference. FB represents the mature fruiting body. CM represents the asexual mycelium. DF represents the developing fruiting body. * represents significant difference in gene expression between FB/CM and DF, respectively, with qRT-PCR measured by paired t -test at p
Figure Legend Snippet: qPCR validation of the expressed genes in Illumina sequencing. (A) Bars represent the fold change in expression of each candidate gene identified in FB relative to DF. (B) Bars represent the fold change in expression of each candidate gene identified in CM relative to DF Black bars represent qRT-PCR result (2 −ΔΔ Ct ). Error bars indicate the standard error. White bars represent the RNA-seq results (log 2 fold change). Histone H2A gene (MSTRG. 2474) was the internal reference. FB represents the mature fruiting body. CM represents the asexual mycelium. DF represents the developing fruiting body. * represents significant difference in gene expression between FB/CM and DF, respectively, with qRT-PCR measured by paired t -test at p

Techniques Used: Real-time Polymerase Chain Reaction, Sequencing, Expressing, Quantitative RT-PCR, RNA Sequencing Assay

14) Product Images from "Transfer of clinically relevant gene expression signatures in breast cancer: from Affymetrix microarray to Illumina RNA-Sequencing technology"

Article Title: Transfer of clinically relevant gene expression signatures in breast cancer: from Affymetrix microarray to Illumina RNA-Sequencing technology

Journal: BMC Genomics

doi: 10.1186/1471-2164-15-1008

Gene expression signatures
Figure Legend Snippet: Gene expression signatures

Techniques Used: Expressing

Correlation values for the evaluated subtype classifiers and gene expression signatures. A:  Cohen’s Kappa coefficients for subtype classifiers (orange: SCMs; purple: SSPs).  B:  Spearman correlation values for prognostic (orange), immune (green), stroma (blue) and pathway (purple) signature scores as computed using Affymetrix microarray and Illumina RNA-Seq platforms.
Figure Legend Snippet: Correlation values for the evaluated subtype classifiers and gene expression signatures. A: Cohen’s Kappa coefficients for subtype classifiers (orange: SCMs; purple: SSPs). B: Spearman correlation values for prognostic (orange), immune (green), stroma (blue) and pathway (purple) signature scores as computed using Affymetrix microarray and Illumina RNA-Seq platforms.

Techniques Used: Expressing, Microarray, RNA Sequencing Assay

15) Product Images from "The Draft Genome and Transcriptome of Amaranthus hypochondriacus: A C4 Dicot Producing High-Lysine Edible Pseudo-Cereal"

Article Title: The Draft Genome and Transcriptome of Amaranthus hypochondriacus: A C4 Dicot Producing High-Lysine Edible Pseudo-Cereal

Journal: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes

doi: 10.1093/dnares/dsu021

Comparative proteome analysis of A. hypochondriacus , V. vinifera and S. lycopersicum . The pie chart shows the source of evidence for proteins from the assembled transcriptome and genome. 17,770 proteins find evidence in both homology and presence in the transcriptome, 3,880 are ab initio predicted with presence in the transcriptome, and 3,179 are those with only evidence from homology to known plant proteins. The Venn diagram compares the total numbers of A. thaliana genes that are orthologous to the respective genomic scaffolds of A. hypochondriacus , V. vinifera and S. lycopersicum with 14,590 proteins common to all the three species representing three major clades under dicots. This figure appears in colour in the online version of DNA Research .
Figure Legend Snippet: Comparative proteome analysis of A. hypochondriacus , V. vinifera and S. lycopersicum . The pie chart shows the source of evidence for proteins from the assembled transcriptome and genome. 17,770 proteins find evidence in both homology and presence in the transcriptome, 3,880 are ab initio predicted with presence in the transcriptome, and 3,179 are those with only evidence from homology to known plant proteins. The Venn diagram compares the total numbers of A. thaliana genes that are orthologous to the respective genomic scaffolds of A. hypochondriacus , V. vinifera and S. lycopersicum with 14,590 proteins common to all the three species representing three major clades under dicots. This figure appears in colour in the online version of DNA Research .

Techniques Used:

16) Product Images from "Genomic Appraisal of the Multifactorial Basis for In Vitro Acquisition of Miltefosine Resistance in Leishmania donovani"

Article Title: Genomic Appraisal of the Multifactorial Basis for In Vitro Acquisition of Miltefosine Resistance in Leishmania donovani

Journal: Antimicrobial Agents and Chemotherapy

doi: 10.1128/AAC.00478-16

HePC uptake by Leishmania promastigotes. (A) Confocal fluorescence images were obtained from WT and resistant parasites (R30 line) incubated with 2.5 μM HePC-BODIPY (green fluorescence). The cells were stained with 10 μg/ml DAPI (4′,6-diamidino-2-phenylindole)
Figure Legend Snippet: HePC uptake by Leishmania promastigotes. (A) Confocal fluorescence images were obtained from WT and resistant parasites (R30 line) incubated with 2.5 μM HePC-BODIPY (green fluorescence). The cells were stained with 10 μg/ml DAPI (4′,6-diamidino-2-phenylindole)

Techniques Used: Fluorescence, Incubation, Staining

Abundances of metacyclic promastigotes in different lines and their association with HePC resistance. Promastigotes resistant to HePC exhibit decreased metacyclogenesis, as determined by Ficoll enrichment (left) and qRT-PCR of SHERP expression using GAPDH
Figure Legend Snippet: Abundances of metacyclic promastigotes in different lines and their association with HePC resistance. Promastigotes resistant to HePC exhibit decreased metacyclogenesis, as determined by Ficoll enrichment (left) and qRT-PCR of SHERP expression using GAPDH

Techniques Used: Quantitative RT-PCR, Expressing

17) Product Images from "Reversible switching between epigenetic states in honeybee behavioral subcastes"

Article Title: Reversible switching between epigenetic states in honeybee behavioral subcastes

Journal: Nature neuroscience

doi: 10.1038/nn.3218

DNA methylation distinguishes nurses, foragers and reverted nurses Two examples of CHARM DMRs. a-b , Top panels show percent methylation for both CHARM and WGBS data sets, with points representing individual samples, and the smoothed lines representing the average for the phenotype. The t-test panel displays the top 1% differentially methylated CpGs by t-test. Color of the point indicates which phenotype has greater methylation at that CpG ( n =6 per phenotype). The RNAseq expression panel is a t-statistic based on the number or reads detected within the annotated exons, with the color indicating the higher expressed phenotype. The Exon junctions panel is a t-statistic based on the number or reads detected spanning the exon junctions, as predicted by the TopHat program, with the color indicating the higher expressed phenotype. Switching between higher expressed nurse and forager exon junctions is indicative of alternative splicing events. The RNA reads panels indicate the number of reads per phenotype as compiled by TopHat program ( n =6 per phenotype). The bottom two panels show the CpG density, and the relative position of the gene. c . Plot of relative gene expression comparing foragers to reverted nurses. 26 genes associated with DMRs were tested for gene expression differences by real-time PCR ( n =12 per phenotype). The plot depicts the difference in average log2 expression versus average difference in methylation as determined by CHARM. Correlation analysis results in a P -value of 0.001.
Figure Legend Snippet: DNA methylation distinguishes nurses, foragers and reverted nurses Two examples of CHARM DMRs. a-b , Top panels show percent methylation for both CHARM and WGBS data sets, with points representing individual samples, and the smoothed lines representing the average for the phenotype. The t-test panel displays the top 1% differentially methylated CpGs by t-test. Color of the point indicates which phenotype has greater methylation at that CpG ( n =6 per phenotype). The RNAseq expression panel is a t-statistic based on the number or reads detected within the annotated exons, with the color indicating the higher expressed phenotype. The Exon junctions panel is a t-statistic based on the number or reads detected spanning the exon junctions, as predicted by the TopHat program, with the color indicating the higher expressed phenotype. Switching between higher expressed nurse and forager exon junctions is indicative of alternative splicing events. The RNA reads panels indicate the number of reads per phenotype as compiled by TopHat program ( n =6 per phenotype). The bottom two panels show the CpG density, and the relative position of the gene. c . Plot of relative gene expression comparing foragers to reverted nurses. 26 genes associated with DMRs were tested for gene expression differences by real-time PCR ( n =12 per phenotype). The plot depicts the difference in average log2 expression versus average difference in methylation as determined by CHARM. Correlation analysis results in a P -value of 0.001.

Techniques Used: DNA Methylation Assay, Methylation, Expressing, Real-time Polymerase Chain Reaction

18) Product Images from "Reversal of Pathologic Lipid Accumulation in NPC1-Deficient Neurons by Drug-Promoted Release of LAMP1-Coated Lamellar Inclusions"

Article Title: Reversal of Pathologic Lipid Accumulation in NPC1-Deficient Neurons by Drug-Promoted Release of LAMP1-Coated Lamellar Inclusions

Journal: The Journal of Neuroscience

doi: 10.1523/JNEUROSCI.0900-16.2016

Gene expression profiling by RNAseq of RGCs acutely purified from wild-type and NPC1-deficient mice. A , Left, false-color micrographs of RGCs acutely purified from 1-week-old mice by immunopanning and subjected to nuclear staining with DAPI (blue) and to immunocytochemical staining for Thy1 (green). Scale bar, 20 μm. Right, percentage of Thy1+ cells after isolation from retinae of 1-week-old ( n = 9) and 2-week-old mice ( n = 5; t test). Immunopanning delivered ∼73,000 ± 8,000 Thy1-positive cells per 1-week-old mouse ( n = 5). B , Quantity of total RNA in purified RGCs per mouse ( n = 4 mice per genotype corresponding to biological replicates; t test). C , Heat map of Pearson's correlation coefficient showing the reproducibility of transcript counts among biological replicates. D , First factorial plane resulting from a correspondence analysis of variance-stabilized data with the x -axis and y -axis explaining 23 and 22% of the variability of the whole dataset, respectively. E , Mean fold changes of transcript counts in RGCs from 1-week-old mutant mice compared to wild-type littermates plotted against normalized mean counts of each transcript as revealed by RNAseq. Red dots indicate genes with an adjusted p value of
Figure Legend Snippet: Gene expression profiling by RNAseq of RGCs acutely purified from wild-type and NPC1-deficient mice. A , Left, false-color micrographs of RGCs acutely purified from 1-week-old mice by immunopanning and subjected to nuclear staining with DAPI (blue) and to immunocytochemical staining for Thy1 (green). Scale bar, 20 μm. Right, percentage of Thy1+ cells after isolation from retinae of 1-week-old ( n = 9) and 2-week-old mice ( n = 5; t test). Immunopanning delivered ∼73,000 ± 8,000 Thy1-positive cells per 1-week-old mouse ( n = 5). B , Quantity of total RNA in purified RGCs per mouse ( n = 4 mice per genotype corresponding to biological replicates; t test). C , Heat map of Pearson's correlation coefficient showing the reproducibility of transcript counts among biological replicates. D , First factorial plane resulting from a correspondence analysis of variance-stabilized data with the x -axis and y -axis explaining 23 and 22% of the variability of the whole dataset, respectively. E , Mean fold changes of transcript counts in RGCs from 1-week-old mutant mice compared to wild-type littermates plotted against normalized mean counts of each transcript as revealed by RNAseq. Red dots indicate genes with an adjusted p value of

Techniques Used: Expressing, Purification, Mouse Assay, Staining, Isolation, Mutagenesis

19) Product Images from "LIX1 regulates YAP activity and controls gastrointestinal cancer cell plasticity, et al. LIX1 regulates YAP activity and controls gastrointestinal cancer cell plasticity"

Article Title: LIX1 regulates YAP activity and controls gastrointestinal cancer cell plasticity, et al. LIX1 regulates YAP activity and controls gastrointestinal cancer cell plasticity

Journal: Journal of Cellular and Molecular Medicine

doi: 10.1111/jcmm.15569

LIX1 down‐regulation reduces the proliferative and invasive capacities of GIST cells. A, RT‐qPCR analysis of LIX1 transcript level in GIST‐T1 cells upon LIX1 silencing. Data were normalized to the mean GAPDH and RPLPO expression. Normalized expression levels were converted into fold changes. Values are presented as the mean ± SEM of n = 20 samples of GIST‐T1‐ Scrambled , n = 15 for GIST‐T1‐ ShLIX1#1 and n = 12 for‐ ShLIX1#2 cells. * P
Figure Legend Snippet: LIX1 down‐regulation reduces the proliferative and invasive capacities of GIST cells. A, RT‐qPCR analysis of LIX1 transcript level in GIST‐T1 cells upon LIX1 silencing. Data were normalized to the mean GAPDH and RPLPO expression. Normalized expression levels were converted into fold changes. Values are presented as the mean ± SEM of n = 20 samples of GIST‐T1‐ Scrambled , n = 15 for GIST‐T1‐ ShLIX1#1 and n = 12 for‐ ShLIX1#2 cells. * P

Techniques Used: Quantitative RT-PCR, Expressing

LIX1 silencing reduces GIST aggressive phenotype in vivo. A, Schematic representation of the approach. GIST‐T1‐ Scrambled , GIST‐T1‐ ShLIX1#1 or ‐ ShLIX1#2 cells were grafted in the ChorioAllantoic Membrane (CAM) of E7 chicken embryos and grafts were allowed to grow for 5 d when individual grafts were removed and analysed. B, Representative images (left panels) and dry weight (right panel) of GIST‐T1‐ Scrambled and GIST‐T1‐ ShLIX1 cell grafts at E12. Scale bars, 2 mm. Values are the mean ± SEM of GIST‐T1‐ Scrambled (n = 11), GIST‐T1‐ ShLIX1#1 (n = 8) and GIST‐T1‐ ShLIX1#2 cell grafts (n = 7). * P
Figure Legend Snippet: LIX1 silencing reduces GIST aggressive phenotype in vivo. A, Schematic representation of the approach. GIST‐T1‐ Scrambled , GIST‐T1‐ ShLIX1#1 or ‐ ShLIX1#2 cells were grafted in the ChorioAllantoic Membrane (CAM) of E7 chicken embryos and grafts were allowed to grow for 5 d when individual grafts were removed and analysed. B, Representative images (left panels) and dry weight (right panel) of GIST‐T1‐ Scrambled and GIST‐T1‐ ShLIX1 cell grafts at E12. Scale bars, 2 mm. Values are the mean ± SEM of GIST‐T1‐ Scrambled (n = 11), GIST‐T1‐ ShLIX1#1 (n = 8) and GIST‐T1‐ ShLIX1#2 cell grafts (n = 7). * P

Techniques Used: In Vivo, Chick Chorioallantoic Membrane Assay

LIX1 down‐regulation reprogrammes KIT‐positive GIST cells to the SMC lineage. A, Transcriptional profiling of GIST‐T1‐ Scrambled and GIST‐T1‐ ShLIX1 cells. Gene ontology enrichment analysis of up‐regulated genes and biological processes common to GIST‐T1‐ ShLIX1#1 and ‐ ShLIX1#2 in smooth muscle development. Data were from n = 3 GIST‐T1‐ Scrambled , n = 3 GIST‐T1‐ ShLIX1#1 and n = 3 ‐ ShLIX1#2 (n = 3) independent samples. B, Transcript fold change of SMC‐restricted genes in GIST‐T1‐ ShLIX1 vs GIST‐T1‐ Scrambled cells. The SMC gene list is based on previously published work (Table S5 ); P
Figure Legend Snippet: LIX1 down‐regulation reprogrammes KIT‐positive GIST cells to the SMC lineage. A, Transcriptional profiling of GIST‐T1‐ Scrambled and GIST‐T1‐ ShLIX1 cells. Gene ontology enrichment analysis of up‐regulated genes and biological processes common to GIST‐T1‐ ShLIX1#1 and ‐ ShLIX1#2 in smooth muscle development. Data were from n = 3 GIST‐T1‐ Scrambled , n = 3 GIST‐T1‐ ShLIX1#1 and n = 3 ‐ ShLIX1#2 (n = 3) independent samples. B, Transcript fold change of SMC‐restricted genes in GIST‐T1‐ ShLIX1 vs GIST‐T1‐ Scrambled cells. The SMC gene list is based on previously published work (Table S5 ); P

Techniques Used:

20) Product Images from "LIX1 regulates YAP activity and controls gastrointestinal cancer cell plasticity, et al. LIX1 regulates YAP activity and controls gastrointestinal cancer cell plasticity"

Article Title: LIX1 regulates YAP activity and controls gastrointestinal cancer cell plasticity, et al. LIX1 regulates YAP activity and controls gastrointestinal cancer cell plasticity

Journal: Journal of Cellular and Molecular Medicine

doi: 10.1111/jcmm.15569

LIX1 down‐regulation reduces the proliferative and invasive capacities of GIST cells. A, RT‐qPCR analysis of LIX1 transcript level in GIST‐T1 cells upon LIX1 silencing. Data were normalized to the mean GAPDH and RPLPO expression. Normalized expression levels were converted into fold changes. Values are presented as the mean ± SEM of n = 20 samples of GIST‐T1‐ Scrambled , n = 15 for GIST‐T1‐ ShLIX1#1 and n = 12 for‐ ShLIX1#2 cells. * P
Figure Legend Snippet: LIX1 down‐regulation reduces the proliferative and invasive capacities of GIST cells. A, RT‐qPCR analysis of LIX1 transcript level in GIST‐T1 cells upon LIX1 silencing. Data were normalized to the mean GAPDH and RPLPO expression. Normalized expression levels were converted into fold changes. Values are presented as the mean ± SEM of n = 20 samples of GIST‐T1‐ Scrambled , n = 15 for GIST‐T1‐ ShLIX1#1 and n = 12 for‐ ShLIX1#2 cells. * P

Techniques Used: Quantitative RT-PCR, Expressing

LIX1 silencing reduces GIST aggressive phenotype in vivo. A, Schematic representation of the approach. GIST‐T1‐ Scrambled , GIST‐T1‐ ShLIX1#1 or ‐ ShLIX1#2 cells were grafted in the ChorioAllantoic Membrane (CAM) of E7 chicken embryos and grafts were allowed to grow for 5 d when individual grafts were removed and analysed. B, Representative images (left panels) and dry weight (right panel) of GIST‐T1‐ Scrambled and GIST‐T1‐ ShLIX1 cell grafts at E12. Scale bars, 2 mm. Values are the mean ± SEM of GIST‐T1‐ Scrambled (n = 11), GIST‐T1‐ ShLIX1#1 (n = 8) and GIST‐T1‐ ShLIX1#2 cell grafts (n = 7). * P
Figure Legend Snippet: LIX1 silencing reduces GIST aggressive phenotype in vivo. A, Schematic representation of the approach. GIST‐T1‐ Scrambled , GIST‐T1‐ ShLIX1#1 or ‐ ShLIX1#2 cells were grafted in the ChorioAllantoic Membrane (CAM) of E7 chicken embryos and grafts were allowed to grow for 5 d when individual grafts were removed and analysed. B, Representative images (left panels) and dry weight (right panel) of GIST‐T1‐ Scrambled and GIST‐T1‐ ShLIX1 cell grafts at E12. Scale bars, 2 mm. Values are the mean ± SEM of GIST‐T1‐ Scrambled (n = 11), GIST‐T1‐ ShLIX1#1 (n = 8) and GIST‐T1‐ ShLIX1#2 cell grafts (n = 7). * P

Techniques Used: In Vivo, Chick Chorioallantoic Membrane Assay

LIX1 down‐regulation reprogrammes KIT‐positive GIST cells to the SMC lineage. A, Transcriptional profiling of GIST‐T1‐ Scrambled and GIST‐T1‐ ShLIX1 cells. Gene ontology enrichment analysis of up‐regulated genes and biological processes common to GIST‐T1‐ ShLIX1#1 and ‐ ShLIX1#2 in smooth muscle development. Data were from n = 3 GIST‐T1‐ Scrambled , n = 3 GIST‐T1‐ ShLIX1#1 and n = 3 ‐ ShLIX1#2 (n = 3) independent samples. B, Transcript fold change of SMC‐restricted genes in GIST‐T1‐ ShLIX1 vs GIST‐T1‐ Scrambled cells. The SMC gene list is based on previously published work (Table S5 ); P
Figure Legend Snippet: LIX1 down‐regulation reprogrammes KIT‐positive GIST cells to the SMC lineage. A, Transcriptional profiling of GIST‐T1‐ Scrambled and GIST‐T1‐ ShLIX1 cells. Gene ontology enrichment analysis of up‐regulated genes and biological processes common to GIST‐T1‐ ShLIX1#1 and ‐ ShLIX1#2 in smooth muscle development. Data were from n = 3 GIST‐T1‐ Scrambled , n = 3 GIST‐T1‐ ShLIX1#1 and n = 3 ‐ ShLIX1#2 (n = 3) independent samples. B, Transcript fold change of SMC‐restricted genes in GIST‐T1‐ ShLIX1 vs GIST‐T1‐ Scrambled cells. The SMC gene list is based on previously published work (Table S5 ); P

Techniques Used:

21) Product Images from "Poly(A)-ClickSeq: click-chemistry for next-generation 3΄-end sequencing without RNA enrichment or fragmentation"

Article Title: Poly(A)-ClickSeq: click-chemistry for next-generation 3΄-end sequencing without RNA enrichment or fragmentation

Journal: Nucleic Acids Research

doi: 10.1093/nar/gkx286

Schematic overview of Poly(A)ClickSeq (PAC-seq). ( A ) RT-PCR is launched from a non-anchored Poly(T) primer containing a portion of the Illumina p7 adaptor. RT-PCR is performed in the presence of AzATP, AzGTP and AzCTP, but not AzTTP, thus only allowing chain termination to occur upstream of the poly(A) tail in the 3΄UTR. ( B ) 3΄-Azido-blocked cDNA fragments are ‘click-ligated’ to 5΄-hexynyl–functionalised DNA oligos containing the p5 Illumina adaptor. This yields triazole-linked ssDNA which can be PCR-amplified using primers to the p5 and p7 Illumina adaptors. ( C ) The cDNA library is analysed by gel electrophoresis and should consist of a smear of DNA products centered ∼200–300 bp. Appropriate cDNA fragment sizes are cut out of the gel and purified to yield a final library. ( D ) The final library consists of DNA fragments containing the Illumina p5 adaptor, a portion of the 3΄UTR, a stretch of As derived from both the RNA template and the poly(T) primer, and finally the p7 Illumina Indexing primer.
Figure Legend Snippet: Schematic overview of Poly(A)ClickSeq (PAC-seq). ( A ) RT-PCR is launched from a non-anchored Poly(T) primer containing a portion of the Illumina p7 adaptor. RT-PCR is performed in the presence of AzATP, AzGTP and AzCTP, but not AzTTP, thus only allowing chain termination to occur upstream of the poly(A) tail in the 3΄UTR. ( B ) 3΄-Azido-blocked cDNA fragments are ‘click-ligated’ to 5΄-hexynyl–functionalised DNA oligos containing the p5 Illumina adaptor. This yields triazole-linked ssDNA which can be PCR-amplified using primers to the p5 and p7 Illumina adaptors. ( C ) The cDNA library is analysed by gel electrophoresis and should consist of a smear of DNA products centered ∼200–300 bp. Appropriate cDNA fragment sizes are cut out of the gel and purified to yield a final library. ( D ) The final library consists of DNA fragments containing the Illumina p5 adaptor, a portion of the 3΄UTR, a stretch of As derived from both the RNA template and the poly(T) primer, and finally the p7 Illumina Indexing primer.

Techniques Used: Reverse Transcription Polymerase Chain Reaction, Polymerase Chain Reaction, Amplification, cDNA Library Assay, Nucleic Acid Electrophoresis, Purification, Derivative Assay

22) Product Images from "Transcriptome Analysis of Portunus trituberculatus in Response to Salinity Stress Provides Insights into the Molecular Basis of Osmoregulation"

Article Title: Transcriptome Analysis of Portunus trituberculatus in Response to Salinity Stress Provides Insights into the Molecular Basis of Osmoregulation

Journal: PLoS ONE

doi: 10.1371/journal.pone.0082155

Schematic of Illumina deep sequencing and analysis. It includes sample preparation, cDNA library construction and Illumina sequencing, data analysis including assemble, blast, GO annotation, gene expression analysis, etc.
Figure Legend Snippet: Schematic of Illumina deep sequencing and analysis. It includes sample preparation, cDNA library construction and Illumina sequencing, data analysis including assemble, blast, GO annotation, gene expression analysis, etc.

Techniques Used: Sequencing, Sample Prep, cDNA Library Assay, Expressing

23) Product Images from "SMARTcleaner: identify and clean off-target signals in SMART ChIP-seq analysis"

Article Title: SMARTcleaner: identify and clean off-target signals in SMART ChIP-seq analysis

Journal: BMC Bioinformatics

doi: 10.1186/s12859-018-2577-4

Strand-specific amplification of non-targeted sequences at poly(T/A) sites in the SMART ChIP-seq analysis. a ). b , c Modified flowcharts to show annealing of the SMART poly(dA) primers to non-tailed Ts within targeted ( b ) or non-targeted ( c ) DNA templates, leading to strand-specific amplification at poly(T) sites. For poly(A) sites, false amplification occurs to the opposite strand. d - f ] is used to show the ChIP-seq reads from paired-end (PE) or single-end (SE) sequencing. For PE, read1 and read2 are shown as pairs, with reads mapped to “+” and “-“strands in red and blue, respectively. For SE, only Read1 (extracted from PE data) is shown. g - i : Fig. S6) for the calculation of read distribution
Figure Legend Snippet: Strand-specific amplification of non-targeted sequences at poly(T/A) sites in the SMART ChIP-seq analysis. a ). b , c Modified flowcharts to show annealing of the SMART poly(dA) primers to non-tailed Ts within targeted ( b ) or non-targeted ( c ) DNA templates, leading to strand-specific amplification at poly(T) sites. For poly(A) sites, false amplification occurs to the opposite strand. d - f ] is used to show the ChIP-seq reads from paired-end (PE) or single-end (SE) sequencing. For PE, read1 and read2 are shown as pairs, with reads mapped to “+” and “-“strands in red and blue, respectively. For SE, only Read1 (extracted from PE data) is shown. g - i : Fig. S6) for the calculation of read distribution

Techniques Used: Amplification, Chromatin Immunoprecipitation, Modification, Sequencing

24) Product Images from "SMARTcleaner: identify and clean off-target signals in SMART ChIP-seq analysis"

Article Title: SMARTcleaner: identify and clean off-target signals in SMART ChIP-seq analysis

Journal: BMC Bioinformatics

doi: 10.1186/s12859-018-2577-4

Strand-specific amplification of non-targeted sequences at poly(T/A) sites in the SMART ChIP-seq analysis. a Flowchart of the SMART ChIP-seq procedure at non-poly(T/A) sites, adapted from the user manual of the kit ( https://www.takarabio.com/documents/User%20Manual/DNA%20SMART%20ChIP-Seq%20Kit%20User%20Manual_101617.pdf ). b , c Modified flowcharts to show annealing of the SMART poly(dA) primers to non-tailed Ts within targeted ( b ) or non-targeted ( c ) DNA templates, leading to strand-specific amplification at poly(T) sites. For poly(A) sites, false amplification occurs to the opposite strand. d - f ChIP-seq read densities at three randomly picked non-poly(T/A) and poly(T/A) sites. The data is from SRR3229031 (Additional file 1 : Table S1, Dataset 1), and Integrative Genomics Viewer (IGV) [ 32 ] is used to show the ChIP-seq reads from paired-end (PE) or single-end (SE) sequencing. For PE, read1 and read2 are shown as pairs, with reads mapped to “+” and “-“strands in red and blue, respectively. For SE, only Read1 (extracted from PE data) is shown. g - i . Aggregated read distribution at non-poly(T/A) and poly(T/A) sites. In h and i, poly(T/A) sites were defined as those with ≥12 consecutive T or A in the human reference genome. To define non-poly(T/A) sites, we first selected genomic regions that are > 4 kb in length and > 1 kb away from poly(T/A) sites, and then take the 2 kb regions around the middle points. In total, we got 301,474 non-poly(T/A) sites, 338,568 poly(T) sites, and 336,703 poly(A) sites. Refer to the Method section (SE mode, Additional file 2 : Fig. S6) for the calculation of read distribution
Figure Legend Snippet: Strand-specific amplification of non-targeted sequences at poly(T/A) sites in the SMART ChIP-seq analysis. a Flowchart of the SMART ChIP-seq procedure at non-poly(T/A) sites, adapted from the user manual of the kit ( https://www.takarabio.com/documents/User%20Manual/DNA%20SMART%20ChIP-Seq%20Kit%20User%20Manual_101617.pdf ). b , c Modified flowcharts to show annealing of the SMART poly(dA) primers to non-tailed Ts within targeted ( b ) or non-targeted ( c ) DNA templates, leading to strand-specific amplification at poly(T) sites. For poly(A) sites, false amplification occurs to the opposite strand. d - f ChIP-seq read densities at three randomly picked non-poly(T/A) and poly(T/A) sites. The data is from SRR3229031 (Additional file 1 : Table S1, Dataset 1), and Integrative Genomics Viewer (IGV) [ 32 ] is used to show the ChIP-seq reads from paired-end (PE) or single-end (SE) sequencing. For PE, read1 and read2 are shown as pairs, with reads mapped to “+” and “-“strands in red and blue, respectively. For SE, only Read1 (extracted from PE data) is shown. g - i . Aggregated read distribution at non-poly(T/A) and poly(T/A) sites. In h and i, poly(T/A) sites were defined as those with ≥12 consecutive T or A in the human reference genome. To define non-poly(T/A) sites, we first selected genomic regions that are > 4 kb in length and > 1 kb away from poly(T/A) sites, and then take the 2 kb regions around the middle points. In total, we got 301,474 non-poly(T/A) sites, 338,568 poly(T) sites, and 336,703 poly(A) sites. Refer to the Method section (SE mode, Additional file 2 : Fig. S6) for the calculation of read distribution

Techniques Used: Amplification, Chromatin Immunoprecipitation, Modification, Sequencing

25) Product Images from "Guanine Deaminase in Human Epidermal Keratinocytes Contributes to Skin Pigmentation"

Article Title: Guanine Deaminase in Human Epidermal Keratinocytes Contributes to Skin Pigmentation

Journal: Molecules

doi: 10.3390/molecules25112637

Keratinocyte (KC) guanine deaminase (GDA) expression is involved in the melanogenic property of UV-exposed normal human keratinocyte (NHK)-conditioned media. ( A ) Melanin content was increased when normal human melanocytes (NHMs) were treated with UVB-exposed NHK-conditioned media (CM) for 5 d. ( B ) Stem cell factor (SCF) and endothelin-1 (ET-1) mRNA expression levels in small interfering RNA for guanine deaminase (siGDA)-transfected NHKs were significantly lower than those in negative control siRNA (siNC)-transfected NHKs at 48 h. ( C ) ET-1 concentration was reduced in the conditioned media of siGDA-transfected NHKs at 48 h. ** p
Figure Legend Snippet: Keratinocyte (KC) guanine deaminase (GDA) expression is involved in the melanogenic property of UV-exposed normal human keratinocyte (NHK)-conditioned media. ( A ) Melanin content was increased when normal human melanocytes (NHMs) were treated with UVB-exposed NHK-conditioned media (CM) for 5 d. ( B ) Stem cell factor (SCF) and endothelin-1 (ET-1) mRNA expression levels in small interfering RNA for guanine deaminase (siGDA)-transfected NHKs were significantly lower than those in negative control siRNA (siNC)-transfected NHKs at 48 h. ( C ) ET-1 concentration was reduced in the conditioned media of siGDA-transfected NHKs at 48 h. ** p

Techniques Used: Expressing, Small Interfering RNA, Transfection, Negative Control, Concentration Assay

The use of small interfering RNA for guanine deaminase (siGDA) in keratinocytes (KCs) downregulates melanogenesis while guanine deaminase (GDA) overexpression promotes melanogenesis in the coculture. ( A ) Melanin content and ( B ) GDA and tyrosinase mRNA expression levels were decreased by siGDA in the coculture of normal human melanocytes (NHMs) and normal human keratinocytes (NHKs) for 5 d. ( C ) While UVB increased melanin content in the negative control siRNA (siNC)-transfected coculture of NHMs and NHKs, siGDA effectively reversed this accelerated melanin accumulation by UVB on day 5. ( D ) Melanin content was increased by a lentiviral-overexpressed GDA gene in the coculture of NHMs and HaCaT cells on day 5. * p
Figure Legend Snippet: The use of small interfering RNA for guanine deaminase (siGDA) in keratinocytes (KCs) downregulates melanogenesis while guanine deaminase (GDA) overexpression promotes melanogenesis in the coculture. ( A ) Melanin content and ( B ) GDA and tyrosinase mRNA expression levels were decreased by siGDA in the coculture of normal human melanocytes (NHMs) and normal human keratinocytes (NHKs) for 5 d. ( C ) While UVB increased melanin content in the negative control siRNA (siNC)-transfected coculture of NHMs and NHKs, siGDA effectively reversed this accelerated melanin accumulation by UVB on day 5. ( D ) Melanin content was increased by a lentiviral-overexpressed GDA gene in the coculture of NHMs and HaCaT cells on day 5. * p

Techniques Used: Small Interfering RNA, Over Expression, Expressing, Negative Control, Transfection

26) Product Images from "Expression of the Phosphatase Ppef2 Controls Survival and Function of CD8+ Dendritic Cells"

Article Title: Expression of the Phosphatase Ppef2 Controls Survival and Function of CD8+ Dendritic Cells

Journal: Frontiers in Immunology

doi: 10.3389/fimmu.2019.00222

RNA-sequencing reveals changes in RNA-expression of Ppef2 −/− CD8 + cDC1. (A) CD8 + DCs were purified by flow cytometry from cell suspensions of 3 pooled spleens as live MHCII + CD11c + CD11b − CD8 + cells to purity of > 95%. 15 spleens from Ppef2 +/+ or Ppef2 −/− mice were used to generate 5 samples each for RNA-sequencing. Shown is the volcano plot analysis of sorted CD8 + DCs. Fold change of−2 (a, blue) and +2 (a, red), and a p -value ≤ 0.01 were chosen as cut-off. Ppef2, protein phosphatase EF-hands 2; LOC100503496, uncharacterized transcript LOC100503496; Xlr4c, X-linked lymphocyte-regulated 4C; Dll4, delta-like ligand 4; Trim2, tripartite motif-containing 2; Npcd, neuronal pentraxin chromo domain; Mfsd2b, major facilitator superfamily domain containing 2B; Cmah, cytidine monophospho-N-acetylneuraminic acid hydroxylase; Xntrpc, Xndc1-transient receptor potential cation channel, subfamily C, member 2; A530064D06Rik, Riken cDNA A530064D06 gene; 1810014B01Rik, Riten cDNA 1810014B01 gene; Triqk, triple QxxK/R motif containing; Nptxr, neuronal pentraxin receptor; Rasd1, RAS, dexamethasone-induced 1; Gfra2, glial cell line derived neurotrophic factor family receptor alpha 2; Rmi2, RMI2, RecQ mediated genome instability 2; Thsd1, thrombospondin, type I, domain 1; Ccl2, chemokine (C-C motif) ligand 2; Zfp772, zinc finger protein 772; Cenpw, centromere protein W. (B) Boxplots represent normalized expression with 0,1 quantile, 0.9 quantile and all single points (each group n = 5) ** p
Figure Legend Snippet: RNA-sequencing reveals changes in RNA-expression of Ppef2 −/− CD8 + cDC1. (A) CD8 + DCs were purified by flow cytometry from cell suspensions of 3 pooled spleens as live MHCII + CD11c + CD11b − CD8 + cells to purity of > 95%. 15 spleens from Ppef2 +/+ or Ppef2 −/− mice were used to generate 5 samples each for RNA-sequencing. Shown is the volcano plot analysis of sorted CD8 + DCs. Fold change of−2 (a, blue) and +2 (a, red), and a p -value ≤ 0.01 were chosen as cut-off. Ppef2, protein phosphatase EF-hands 2; LOC100503496, uncharacterized transcript LOC100503496; Xlr4c, X-linked lymphocyte-regulated 4C; Dll4, delta-like ligand 4; Trim2, tripartite motif-containing 2; Npcd, neuronal pentraxin chromo domain; Mfsd2b, major facilitator superfamily domain containing 2B; Cmah, cytidine monophospho-N-acetylneuraminic acid hydroxylase; Xntrpc, Xndc1-transient receptor potential cation channel, subfamily C, member 2; A530064D06Rik, Riken cDNA A530064D06 gene; 1810014B01Rik, Riten cDNA 1810014B01 gene; Triqk, triple QxxK/R motif containing; Nptxr, neuronal pentraxin receptor; Rasd1, RAS, dexamethasone-induced 1; Gfra2, glial cell line derived neurotrophic factor family receptor alpha 2; Rmi2, RMI2, RecQ mediated genome instability 2; Thsd1, thrombospondin, type I, domain 1; Ccl2, chemokine (C-C motif) ligand 2; Zfp772, zinc finger protein 772; Cenpw, centromere protein W. (B) Boxplots represent normalized expression with 0,1 quantile, 0.9 quantile and all single points (each group n = 5) ** p

Techniques Used: RNA Sequencing Assay, RNA Expression, Purification, Flow Cytometry, Cytometry, Mouse Assay, Derivative Assay, Expressing

27) Product Images from "Guanine Deaminase in Human Epidermal Keratinocytes Contributes to Skin Pigmentation"

Article Title: Guanine Deaminase in Human Epidermal Keratinocytes Contributes to Skin Pigmentation

Journal: Molecules

doi: 10.3390/molecules25112637

Keratinocyte (KC) guanine deaminase (GDA) expression is involved in the melanogenic property of UV-exposed normal human keratinocyte (NHK)-conditioned media. ( A ) Melanin content was increased when normal human melanocytes (NHMs) were treated with UVB-exposed NHK-conditioned media (CM) for 5 d. ( B ) Stem cell factor (SCF) and endothelin-1 (ET-1) mRNA expression levels in small interfering RNA for guanine deaminase (siGDA)-transfected NHKs were significantly lower than those in negative control siRNA (siNC)-transfected NHKs at 48 h. ( C ) ET-1 concentration was reduced in the conditioned media of siGDA-transfected NHKs at 48 h. ** p
Figure Legend Snippet: Keratinocyte (KC) guanine deaminase (GDA) expression is involved in the melanogenic property of UV-exposed normal human keratinocyte (NHK)-conditioned media. ( A ) Melanin content was increased when normal human melanocytes (NHMs) were treated with UVB-exposed NHK-conditioned media (CM) for 5 d. ( B ) Stem cell factor (SCF) and endothelin-1 (ET-1) mRNA expression levels in small interfering RNA for guanine deaminase (siGDA)-transfected NHKs were significantly lower than those in negative control siRNA (siNC)-transfected NHKs at 48 h. ( C ) ET-1 concentration was reduced in the conditioned media of siGDA-transfected NHKs at 48 h. ** p

Techniques Used: Expressing, Small Interfering RNA, Transfection, Negative Control, Concentration Assay

The use of small interfering RNA for guanine deaminase (siGDA) in keratinocytes (KCs) downregulates melanogenesis while guanine deaminase (GDA) overexpression promotes melanogenesis in the coculture. ( A ) Melanin content and ( B ) GDA and tyrosinase mRNA expression levels were decreased by siGDA in the coculture of normal human melanocytes (NHMs) and normal human keratinocytes (NHKs) for 5 d. ( C ) While UVB increased melanin content in the negative control siRNA (siNC)-transfected coculture of NHMs and NHKs, siGDA effectively reversed this accelerated melanin accumulation by UVB on day 5. ( D ) Melanin content was increased by a lentiviral-overexpressed GDA gene in the coculture of NHMs and HaCaT cells on day 5. * p
Figure Legend Snippet: The use of small interfering RNA for guanine deaminase (siGDA) in keratinocytes (KCs) downregulates melanogenesis while guanine deaminase (GDA) overexpression promotes melanogenesis in the coculture. ( A ) Melanin content and ( B ) GDA and tyrosinase mRNA expression levels were decreased by siGDA in the coculture of normal human melanocytes (NHMs) and normal human keratinocytes (NHKs) for 5 d. ( C ) While UVB increased melanin content in the negative control siRNA (siNC)-transfected coculture of NHMs and NHKs, siGDA effectively reversed this accelerated melanin accumulation by UVB on day 5. ( D ) Melanin content was increased by a lentiviral-overexpressed GDA gene in the coculture of NHMs and HaCaT cells on day 5. * p

Techniques Used: Small Interfering RNA, Over Expression, Expressing, Negative Control, Transfection

28) Product Images from "Transcriptome Analysis of the Portunus trituberculatus: De Novo Assembly, Growth-Related Gene Identification and Marker Discovery"

Article Title: Transcriptome Analysis of the Portunus trituberculatus: De Novo Assembly, Growth-Related Gene Identification and Marker Discovery

Journal: PLoS ONE

doi: 10.1371/journal.pone.0094055

Schematic of Illumina deep sequencing and analysis. It includes sample preparation, cDNA library construction and Illumina sequencing, data analysis including assemble, blast, GO annotation, SSR and SNP analysis, etc.
Figure Legend Snippet: Schematic of Illumina deep sequencing and analysis. It includes sample preparation, cDNA library construction and Illumina sequencing, data analysis including assemble, blast, GO annotation, SSR and SNP analysis, etc.

Techniques Used: Sequencing, Sample Prep, cDNA Library Assay

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RNA Sequencing Assay:

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Article Snippet: .. Here, in the light of recent developments and progress in RNA-seq library protocols, we use human input samples to evaluate three different recently developed commercial kits used for RNA-seq library preparation: TruSeq (Illumina), SMARTer (Clontech/Takara Bio) and SMARTer Ultra-Low (Clontech/Takara Bio). .. Furthermore, we test these kits for unstranded and stranded conditions, mRNA and total RNA input selection and for three different quantities of input material: standard (1 μg), low (100 ng and 10 ng) and ultra-low ( < 1 ng).

Article Title: TSS-EMOTE, a refined protocol for a more complete and less biased global mapping of transcription start sites in bacterial pathogens
Article Snippet: .. Interestingly, we observe a slight shift of about 10 nt, between the rTSSs and the increase in coverage, which underlines that the TruSeq RNA sequencing protocol (used to prepare the RNAseq library for Illumina sequencing) does not preserve the native 5’-end of the RNA. ..

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Next-Generation Sequencing:

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Article Snippet: .. We compared 5 methods of library preparation for Illumina Next Generation sequencing: NuGEN Ovation RNA-Seq system V2 Kit, TaKaRa SMARTer Stranded Total RNA-Seq Kit, TaKaRa SMART-Seq v4 Ultra Low Input RNA Kit, Illumina TruSeq RNA Library Prep Kit v2 and NEBNext® Ultra™ Directional RNA Library Prep Kit using slightly modified protocols each with 4 ng of total RNA. ..

Sequencing:

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Article Snippet: .. Sequencing libraries Poly-A enriched strand-specific libraries were generated with the TruSeq mRNA V2 sample preparation kit (#RS-122-2001, Illumina), ribosomal RNA depleted strand-specific RNA libraries with the TruSeq Stranded Total RNA LT sample preparation kit with Ribo-Zero Gold (#RS-122-2301and (#RS-122-2302, Illumina), and transcriptome capture based libraries with the TruSeq RNA Access Library Prep Kit (#RS-301-2001, Illumina). ..

Article Title: TSS-EMOTE, a refined protocol for a more complete and less biased global mapping of transcription start sites in bacterial pathogens
Article Snippet: .. Interestingly, we observe a slight shift of about 10 nt, between the rTSSs and the increase in coverage, which underlines that the TruSeq RNA sequencing protocol (used to prepare the RNAseq library for Illumina sequencing) does not preserve the native 5’-end of the RNA. ..

Article Title: Decreasing miRNA sequencing bias using a single adapter and circularization approach
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Article Title: A comparative analysis of library prep approaches for sequencing low input translatome samples
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Generated:

Article Title: A comprehensive assessment of RNA-seq protocols for degraded and low-quantity samples
Article Snippet: .. Sequencing libraries Poly-A enriched strand-specific libraries were generated with the TruSeq mRNA V2 sample preparation kit (#RS-122-2001, Illumina), ribosomal RNA depleted strand-specific RNA libraries with the TruSeq Stranded Total RNA LT sample preparation kit with Ribo-Zero Gold (#RS-122-2301and (#RS-122-2302, Illumina), and transcriptome capture based libraries with the TruSeq RNA Access Library Prep Kit (#RS-301-2001, Illumina). ..

Modification:

Article Title: A comparative analysis of library prep approaches for sequencing low input translatome samples
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Sample Prep:

Article Title: A comprehensive assessment of RNA-seq protocols for degraded and low-quantity samples
Article Snippet: .. Sequencing libraries Poly-A enriched strand-specific libraries were generated with the TruSeq mRNA V2 sample preparation kit (#RS-122-2001, Illumina), ribosomal RNA depleted strand-specific RNA libraries with the TruSeq Stranded Total RNA LT sample preparation kit with Ribo-Zero Gold (#RS-122-2301and (#RS-122-2302, Illumina), and transcriptome capture based libraries with the TruSeq RNA Access Library Prep Kit (#RS-301-2001, Illumina). ..

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