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Illumina Inc input dna input
Input Dna Input, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/result/input dna input/product/Illumina Inc
Average 86 stars, based on 1 article reviews
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input dna input - by Bioz Stars, 2021-07
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Concentration Assay:

Article Title: Global Analysis of Transcription Factor-Binding Sites in Yeast Using ChIP-Seq
Article Snippet: When ready to use, dilute adapters to the working concentration of Illumina genomic DNA adapters generating successful input DNA or ChIP DNA libraries. .. To determine adapter concentrations quickly, just compare DNA concentration measurements obtained on a Nanodrop spectrophotometer for Illumina genomic DNA adapter mix and custom-made adapters. .. 15 This gel extraction get rids of adapter-adapter dimers.

Article Title: T Oligo-Primed Polymerase Chain Reaction (TOP-PCR): A Robust Method for the Amplification of Minute DNA Fragments in Body Fluids
Article Snippet: Comparison between TOP-PCR and Illumina’s library construction using loop adaptor It would be interesting to compare TOP-PCR to Illumina’s amplification method. .. Here, TOP-PCR (using half adaptor) was compared to the Illumina PCR amplification procedure using loop adaptor, which was randomly chosen, and the comparison was conducted for both low (with unknown concentration) and high (20 ng) initial DNA inputs. .. TOP-PCR vs. Illumina’s protocol at low DNA concentration As shown in , TOP-PCR was able to rescue the DNA fragments from a sample with a DNA concentration far below the undetectable level by regular devices.

Spectrophotometry:

Article Title: Global Analysis of Transcription Factor-Binding Sites in Yeast Using ChIP-Seq
Article Snippet: When ready to use, dilute adapters to the working concentration of Illumina genomic DNA adapters generating successful input DNA or ChIP DNA libraries. .. To determine adapter concentrations quickly, just compare DNA concentration measurements obtained on a Nanodrop spectrophotometer for Illumina genomic DNA adapter mix and custom-made adapters. .. 15 This gel extraction get rids of adapter-adapter dimers.

Sequencing:

Article Title: Transcriptome Analysis of the Portunus trituberculatus: De Novo Assembly, Growth-Related Gene Identification and Marker Discovery
Article Snippet: .. The pooling samples were then used to prepare one separate Illumina sequencing libraries. cDNA libraries were generated using Illumina TruSeq RNA Sample Preparation Kit (Illumia, San Diego, USA) following manufacturer's recommendations. .. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads.

Article Title: Comprehensive Analysis of DNA Methylation Data with RnBeads
Article Snippet: .. Data import RnBeads supports a broad range of DNA methylation assays, comprising the Illumina Infinium microarray platform (in both its 450k and 27k version), various types of bisulfite sequencing (including WGBS and RRBS) and other sequencing-based methods that can be used to bioinformatically infer DNA methylation measurements at the level of single CpGs (such as MeDIP, MDB-seq and MRE-seq). ..

Generated:

Article Title: Transcriptome Analysis of the Portunus trituberculatus: De Novo Assembly, Growth-Related Gene Identification and Marker Discovery
Article Snippet: .. The pooling samples were then used to prepare one separate Illumina sequencing libraries. cDNA libraries were generated using Illumina TruSeq RNA Sample Preparation Kit (Illumia, San Diego, USA) following manufacturer's recommendations. .. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads.

Sample Prep:

Article Title: Transcriptome Analysis of the Portunus trituberculatus: De Novo Assembly, Growth-Related Gene Identification and Marker Discovery
Article Snippet: .. The pooling samples were then used to prepare one separate Illumina sequencing libraries. cDNA libraries were generated using Illumina TruSeq RNA Sample Preparation Kit (Illumia, San Diego, USA) following manufacturer's recommendations. .. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads.

Chromatin Immunoprecipitation:

Article Title: Epigenomic annotation of enhancers predicts transcriptional regulators of human neural crest
Article Snippet: All antibodies used in this study have been previously reported as suitable for ChIP and/or ChIP-seq: p300 (sc-585, Santa Cruz Biotechnology), H3K4me1 (ab8895, Abcam), H3K27ac (ab4729, Abcam), H3K4me3 (39159, Active Motif), H3K27me3 (39536, Active Motif), NR2F1 (PP-H8132-00, Perseus Proteomics), NR2F2 (PP-H7147-00, Perseus Proteomics), TFAP2A (sc-184, Santa Cruz Biotechnology). .. DNA libraries were prepared from hNCC p300 ChIP, hNCC FAIRE, hNCC H3K4me3 ChIP, hNCC H3K4me1 ChIP, hNCC H3K27me3 ChIP, hNCC H3K27ac ChIP, hNCC NR2F1 ChIP, hNCC NR2F2 ChIP, hNCC TFAP2A ChIP, hNCC input DNA, St11-14 Chicken H3K27ac ChIP, St20 Chicken H3K27ac ChIP, St11-14 Chicken input DNA, St20 Chicken input DNA ChIP-seq, FAIRE-seq and input libraries were prepared according to Illumina protocol and sequenced using Illumina Genome Analyzer. .. All sequences were mapped by ELAND software (Illumina Inc) and analyzed by QuEST 2.4 software ( ).

ChIP-sequencing:

Article Title: Epigenomic annotation of enhancers predicts transcriptional regulators of human neural crest
Article Snippet: All antibodies used in this study have been previously reported as suitable for ChIP and/or ChIP-seq: p300 (sc-585, Santa Cruz Biotechnology), H3K4me1 (ab8895, Abcam), H3K27ac (ab4729, Abcam), H3K4me3 (39159, Active Motif), H3K27me3 (39536, Active Motif), NR2F1 (PP-H8132-00, Perseus Proteomics), NR2F2 (PP-H7147-00, Perseus Proteomics), TFAP2A (sc-184, Santa Cruz Biotechnology). .. DNA libraries were prepared from hNCC p300 ChIP, hNCC FAIRE, hNCC H3K4me3 ChIP, hNCC H3K4me1 ChIP, hNCC H3K27me3 ChIP, hNCC H3K27ac ChIP, hNCC NR2F1 ChIP, hNCC NR2F2 ChIP, hNCC TFAP2A ChIP, hNCC input DNA, St11-14 Chicken H3K27ac ChIP, St20 Chicken H3K27ac ChIP, St11-14 Chicken input DNA, St20 Chicken input DNA ChIP-seq, FAIRE-seq and input libraries were prepared according to Illumina protocol and sequenced using Illumina Genome Analyzer. .. All sequences were mapped by ELAND software (Illumina Inc) and analyzed by QuEST 2.4 software ( ).

DNA Methylation Assay:

Article Title: Comprehensive Analysis of DNA Methylation Data with RnBeads
Article Snippet: .. Data import RnBeads supports a broad range of DNA methylation assays, comprising the Illumina Infinium microarray platform (in both its 450k and 27k version), various types of bisulfite sequencing (including WGBS and RRBS) and other sequencing-based methods that can be used to bioinformatically infer DNA methylation measurements at the level of single CpGs (such as MeDIP, MDB-seq and MRE-seq). ..

Microarray:

Article Title: Comprehensive Analysis of DNA Methylation Data with RnBeads
Article Snippet: .. Data import RnBeads supports a broad range of DNA methylation assays, comprising the Illumina Infinium microarray platform (in both its 450k and 27k version), various types of bisulfite sequencing (including WGBS and RRBS) and other sequencing-based methods that can be used to bioinformatically infer DNA methylation measurements at the level of single CpGs (such as MeDIP, MDB-seq and MRE-seq). ..

Article Title: Single base resolution analysis of 5-hydroxymethylcytosine in 188 human genes: implications for hepatic gene expression
Article Snippet: Only CpG sites with merged read depth above 25× were used for cross-validation purposes; TAB-450K combines TAB-Seq with Illumina Infinium HumanMethylation450 BeadChip assay ( , ). .. The latter is a microarray-based technique which allows to interrogate a defined set of CpG sites (n = 485 463); TrueMethyl-450K employs the same Illumina HumanMethylation450 microarray platform together with the oxidative bisulfite (OxBS-Seq) methodology ( , ). .. This alternative approach for hmC detection involves the oxidation of input DNA by potassium perruthenate followed by bisulfite conversion ( ); Regarding TrueMethyl-WGBS (whole-genome oxidative bisulfute sequencing), we sequenced one liver gDNA sample with 4× median read depth.

Methylation Sequencing:

Article Title: Comprehensive Analysis of DNA Methylation Data with RnBeads
Article Snippet: .. Data import RnBeads supports a broad range of DNA methylation assays, comprising the Illumina Infinium microarray platform (in both its 450k and 27k version), various types of bisulfite sequencing (including WGBS and RRBS) and other sequencing-based methods that can be used to bioinformatically infer DNA methylation measurements at the level of single CpGs (such as MeDIP, MDB-seq and MRE-seq). ..

Methylated DNA Immunoprecipitation:

Article Title: Comprehensive Analysis of DNA Methylation Data with RnBeads
Article Snippet: .. Data import RnBeads supports a broad range of DNA methylation assays, comprising the Illumina Infinium microarray platform (in both its 450k and 27k version), various types of bisulfite sequencing (including WGBS and RRBS) and other sequencing-based methods that can be used to bioinformatically infer DNA methylation measurements at the level of single CpGs (such as MeDIP, MDB-seq and MRE-seq). ..

Polymerase Chain Reaction:

Article Title: T Oligo-Primed Polymerase Chain Reaction (TOP-PCR): A Robust Method for the Amplification of Minute DNA Fragments in Body Fluids
Article Snippet: Comparison between TOP-PCR and Illumina’s library construction using loop adaptor It would be interesting to compare TOP-PCR to Illumina’s amplification method. .. Here, TOP-PCR (using half adaptor) was compared to the Illumina PCR amplification procedure using loop adaptor, which was randomly chosen, and the comparison was conducted for both low (with unknown concentration) and high (20 ng) initial DNA inputs. .. TOP-PCR vs. Illumina’s protocol at low DNA concentration As shown in , TOP-PCR was able to rescue the DNA fragments from a sample with a DNA concentration far below the undetectable level by regular devices.

Amplification:

Article Title: T Oligo-Primed Polymerase Chain Reaction (TOP-PCR): A Robust Method for the Amplification of Minute DNA Fragments in Body Fluids
Article Snippet: Comparison between TOP-PCR and Illumina’s library construction using loop adaptor It would be interesting to compare TOP-PCR to Illumina’s amplification method. .. Here, TOP-PCR (using half adaptor) was compared to the Illumina PCR amplification procedure using loop adaptor, which was randomly chosen, and the comparison was conducted for both low (with unknown concentration) and high (20 ng) initial DNA inputs. .. TOP-PCR vs. Illumina’s protocol at low DNA concentration As shown in , TOP-PCR was able to rescue the DNA fragments from a sample with a DNA concentration far below the undetectable level by regular devices.

Oxidative Bisulfite Sequencing:

Article Title: Single base resolution analysis of 5-hydroxymethylcytosine in 188 human genes: implications for hepatic gene expression
Article Snippet: Only CpG sites with merged read depth above 25× were used for cross-validation purposes; TAB-450K combines TAB-Seq with Illumina Infinium HumanMethylation450 BeadChip assay ( , ). .. The latter is a microarray-based technique which allows to interrogate a defined set of CpG sites (n = 485 463); TrueMethyl-450K employs the same Illumina HumanMethylation450 microarray platform together with the oxidative bisulfite (OxBS-Seq) methodology ( , ). .. This alternative approach for hmC detection involves the oxidation of input DNA by potassium perruthenate followed by bisulfite conversion ( ); Regarding TrueMethyl-WGBS (whole-genome oxidative bisulfute sequencing), we sequenced one liver gDNA sample with 4× median read depth.

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  • 86
    Illumina Inc input dna libraries
    Comparison of <t>DNA</t> methylation state in FGSCs and MGSCs. a A snapshot of the IGV depicting DNA methylation in FGSCs and MGSCs. b Comparison of methylation at promoter regions (−2 kb to 500 bp) between FGSCs and MGSCs. We divided UCSC transcript promoters into 500-bp windows and showed that the absolute methylation signals from mean whole-genome bisulfite sequencing (MGSCs) and the mean <t>MethylCap-seq</t> normalized relative methylation levels (FGSCs) have a correlation of 0.229. c The number of genes methylated at TSS regions (−2 kb to 500 bp) in FGSCs and MGSCs. d Functional annotation of genes with FGSC-specific ( left ) or MGSC-specific methylation ( right ) ( p
    Input Dna Libraries, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/input dna libraries/product/Illumina Inc
    Average 86 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    input dna libraries - by Bioz Stars, 2021-07
    86/100 stars
      Buy from Supplier

    99
    Illumina Inc input total rna
    TCAIM-dependent expression of metabolism controlling genes in activated CD8 + T cells. ( a ) Myc and Hif1α <t>mRNA</t> expression of naïve and polyclonally activated CD8 + T cells with TCAIM KI, KO or wt gene expression (KI and wt: n = 3; KO: n = 2). <t>RNA-seq</t> raw count data of protein-coding genes were normalized and log 2 -transformed after adding a pseudocount to each value. Cells had been stimulated with 5 µg/ ml plate-bound αCD3 and 2 µg/ ml soluble αCD28 at a density of 6 x 10 5 cells/ 200 µl culture medium. Quantitative data represents means ± SEM. ( b ) Overview of the differentially expressed enzymes controlling the glycolysis, TCA cycle and glutaminolysis pathway between 24 to 48 h polyclonally activated TCAIM KI and wt CD8 + T cells (log 2 fold change). P-values have been adjusted to either 0.05 or 0.3 as indicated (n = 3). White areas indicate p-values exceeding the adjusted ones. Cells had been stimulated with 5 µg/ ml plate-bound αCD3 and 2 µg/ ml soluble αCD28 at a density of 6 x 10 5 cells/ 200 µl culture medium (a-b).
    Input Total Rna, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 99/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/input total rna/product/Illumina Inc
    Average 99 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    input total rna - by Bioz Stars, 2021-07
    99/100 stars
      Buy from Supplier

    86
    Illumina Inc low input mrna
    Datasets in this study. a The GSE50856 dataset was divided into 6 groups: SFM-Smart, SFM-DP, SFM-CEL, AA100-Smart, AA100-DP and AA100-CEL. Each group had four low input <t>mRNA</t> levels, 1000 pg, 100 pg, 50 pg and 25 pg, and each level had two technical replicates. b The GSE17565 dataset was divided into 2 groups: Raji and MCF-7. Each group had four low input total <t>RNA</t> levels, 1000 pg, 250 pg, 50 pg and 10 pg, and each level had two technical replicates
    Low Input Mrna, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/low input mrna/product/Illumina Inc
    Average 86 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    low input mrna - by Bioz Stars, 2021-07
    86/100 stars
      Buy from Supplier

    99
    Illumina Inc dna input
    Coverage of the microbial genomes, Olsenella profusa (62% GC) (left) and Bacillus megaterium (38% GC) (right) with (A) <t>MGIEasy</t> PCR-Free <t>DNA</t> Library Pre Set and (B) MGIEasy FS PCR-Free DNA Library Pre Set. Read coverage across the range of the GC content, calculated in 100 bp windows (pink bars) and normalized coverage (colored dots). 3 replicates (red, blue and green dots) were included in the normalized coverage VS GC content analysis.
    Dna Input, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 99/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/dna input/product/Illumina Inc
    Average 99 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    dna input - by Bioz Stars, 2021-07
    99/100 stars
      Buy from Supplier

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    Comparison of DNA methylation state in FGSCs and MGSCs. a A snapshot of the IGV depicting DNA methylation in FGSCs and MGSCs. b Comparison of methylation at promoter regions (−2 kb to 500 bp) between FGSCs and MGSCs. We divided UCSC transcript promoters into 500-bp windows and showed that the absolute methylation signals from mean whole-genome bisulfite sequencing (MGSCs) and the mean MethylCap-seq normalized relative methylation levels (FGSCs) have a correlation of 0.229. c The number of genes methylated at TSS regions (−2 kb to 500 bp) in FGSCs and MGSCs. d Functional annotation of genes with FGSC-specific ( left ) or MGSC-specific methylation ( right ) ( p

    Journal: Genome Biology

    Article Title: Integrative epigenomic analysis reveals unique epigenetic signatures involved in unipotency of mouse female germline stem cells

    doi: 10.1186/s13059-016-1023-z

    Figure Lengend Snippet: Comparison of DNA methylation state in FGSCs and MGSCs. a A snapshot of the IGV depicting DNA methylation in FGSCs and MGSCs. b Comparison of methylation at promoter regions (−2 kb to 500 bp) between FGSCs and MGSCs. We divided UCSC transcript promoters into 500-bp windows and showed that the absolute methylation signals from mean whole-genome bisulfite sequencing (MGSCs) and the mean MethylCap-seq normalized relative methylation levels (FGSCs) have a correlation of 0.229. c The number of genes methylated at TSS regions (−2 kb to 500 bp) in FGSCs and MGSCs. d Functional annotation of genes with FGSC-specific ( left ) or MGSC-specific methylation ( right ) ( p

    Article Snippet: MethylCap and input DNA libraries were sequenced with an Illumina HiSeq 2000.

    Techniques: DNA Methylation Assay, Methylation, Methylation Sequencing, Functional Assay

    TCAIM-dependent expression of metabolism controlling genes in activated CD8 + T cells. ( a ) Myc and Hif1α mRNA expression of naïve and polyclonally activated CD8 + T cells with TCAIM KI, KO or wt gene expression (KI and wt: n = 3; KO: n = 2). RNA-seq raw count data of protein-coding genes were normalized and log 2 -transformed after adding a pseudocount to each value. Cells had been stimulated with 5 µg/ ml plate-bound αCD3 and 2 µg/ ml soluble αCD28 at a density of 6 x 10 5 cells/ 200 µl culture medium. Quantitative data represents means ± SEM. ( b ) Overview of the differentially expressed enzymes controlling the glycolysis, TCA cycle and glutaminolysis pathway between 24 to 48 h polyclonally activated TCAIM KI and wt CD8 + T cells (log 2 fold change). P-values have been adjusted to either 0.05 or 0.3 as indicated (n = 3). White areas indicate p-values exceeding the adjusted ones. Cells had been stimulated with 5 µg/ ml plate-bound αCD3 and 2 µg/ ml soluble αCD28 at a density of 6 x 10 5 cells/ 200 µl culture medium (a-b).

    Journal: bioRxiv

    Article Title: TCAIM controls effector T cell generation by preventing Mitochondria-Endoplasmic Reticulum Contact Site-initiated Cholesterol Biosynthesis

    doi: 10.1101/2021.04.20.440500

    Figure Lengend Snippet: TCAIM-dependent expression of metabolism controlling genes in activated CD8 + T cells. ( a ) Myc and Hif1α mRNA expression of naïve and polyclonally activated CD8 + T cells with TCAIM KI, KO or wt gene expression (KI and wt: n = 3; KO: n = 2). RNA-seq raw count data of protein-coding genes were normalized and log 2 -transformed after adding a pseudocount to each value. Cells had been stimulated with 5 µg/ ml plate-bound αCD3 and 2 µg/ ml soluble αCD28 at a density of 6 x 10 5 cells/ 200 µl culture medium. Quantitative data represents means ± SEM. ( b ) Overview of the differentially expressed enzymes controlling the glycolysis, TCA cycle and glutaminolysis pathway between 24 to 48 h polyclonally activated TCAIM KI and wt CD8 + T cells (log 2 fold change). P-values have been adjusted to either 0.05 or 0.3 as indicated (n = 3). White areas indicate p-values exceeding the adjusted ones. Cells had been stimulated with 5 µg/ ml plate-bound αCD3 and 2 µg/ ml soluble αCD28 at a density of 6 x 10 5 cells/ 200 µl culture medium (a-b).

    Article Snippet: Briefly, mRNA-Seq libraries were prepared from 100 ng of input total RNA samples using TruSeq stranded mRNA kit (Illumina).

    Techniques: Expressing, RNA Sequencing Assay, Transformation Assay

    TCAIM interacts with MERC promoting proteins. ( a ) GFP co-immunoprecipitates of cell lysates from HEK293T cells transfected with pTCAIM-EGFP-N1 or mito-PAGFP control plasmid were analyzed for TCAIM interaction partner by LC-MS/MS. Volcano plot showing 14 proteins (FDR 0.05, S0 0.7) being significantly enriched only in pTCAIM-EGFP-N1 cell lysate fractions (n = 3). ( b-c ) mRNA expression of selected TCAIM interaction partners of naïve and polyclonally activated TCAIM KI, KO or wt CD8 + T cells (KI and wt: n = 3; KO: n = 2). RNA-seq raw count data of protein-coding genes were normalized and log 2 -transformed after adding a pseudocount to each value. Cells had been stimulated with 5 µg/ ml plate-bound αCD3 and 2 µg/ ml soluble αCD28 at a density of 6 x 10 5 cells/ 200 µl culture medium. ( d ) Representative dot plots from one out of two BiFC assay experiments for validation of TCAIM interaction with TOM40 measured by flow cytometry. As indicated HEK293T cells were transfected with plasmids encoding for the split eGFP fusion proteins TCAIM-eGFPc + TOM40-eGFPn, TOM40-eGFPn + MIC60-eGFPc as positive control or TCAIM-eGFPc alone as negative control. Quantitative data represents means ± SEM (b-c).

    Journal: bioRxiv

    Article Title: TCAIM controls effector T cell generation by preventing Mitochondria-Endoplasmic Reticulum Contact Site-initiated Cholesterol Biosynthesis

    doi: 10.1101/2021.04.20.440500

    Figure Lengend Snippet: TCAIM interacts with MERC promoting proteins. ( a ) GFP co-immunoprecipitates of cell lysates from HEK293T cells transfected with pTCAIM-EGFP-N1 or mito-PAGFP control plasmid were analyzed for TCAIM interaction partner by LC-MS/MS. Volcano plot showing 14 proteins (FDR 0.05, S0 0.7) being significantly enriched only in pTCAIM-EGFP-N1 cell lysate fractions (n = 3). ( b-c ) mRNA expression of selected TCAIM interaction partners of naïve and polyclonally activated TCAIM KI, KO or wt CD8 + T cells (KI and wt: n = 3; KO: n = 2). RNA-seq raw count data of protein-coding genes were normalized and log 2 -transformed after adding a pseudocount to each value. Cells had been stimulated with 5 µg/ ml plate-bound αCD3 and 2 µg/ ml soluble αCD28 at a density of 6 x 10 5 cells/ 200 µl culture medium. ( d ) Representative dot plots from one out of two BiFC assay experiments for validation of TCAIM interaction with TOM40 measured by flow cytometry. As indicated HEK293T cells were transfected with plasmids encoding for the split eGFP fusion proteins TCAIM-eGFPc + TOM40-eGFPn, TOM40-eGFPn + MIC60-eGFPc as positive control or TCAIM-eGFPc alone as negative control. Quantitative data represents means ± SEM (b-c).

    Article Snippet: Briefly, mRNA-Seq libraries were prepared from 100 ng of input total RNA samples using TruSeq stranded mRNA kit (Illumina).

    Techniques: Transfection, Plasmid Preparation, Liquid Chromatography with Mass Spectroscopy, Expressing, RNA Sequencing Assay, Transformation Assay, Bimolecular Fluorescence Complementation Assay, Flow Cytometry, Positive Control, Negative Control

    Reduced gene expression of mevalonate pathway and cholesterol biosynthesis controlling enzymes in TCAIM KI CD8 + T cells. mRNA expression of additional genes controlling the mevalonate pathway ( a ) and the cholesterol biosynthesis ( b ) of naïve and polyclonally activated CD8 + T cells with TCAIM KI, KO or wt gene expression (KI and wt: n = 3; KO: n = 2). RNA-seq raw count data of protein-coding genes were normalized and log 2 -transformed after adding a pseudocount to each value. Cells had been stimulated with 5 µg/ ml plate-bound αCD3 and 2 µg/ ml soluble αCD28 at a density of 6 x 10 5 cells/ 200 µl culture medium. Data represents means ± SEM.

    Journal: bioRxiv

    Article Title: TCAIM controls effector T cell generation by preventing Mitochondria-Endoplasmic Reticulum Contact Site-initiated Cholesterol Biosynthesis

    doi: 10.1101/2021.04.20.440500

    Figure Lengend Snippet: Reduced gene expression of mevalonate pathway and cholesterol biosynthesis controlling enzymes in TCAIM KI CD8 + T cells. mRNA expression of additional genes controlling the mevalonate pathway ( a ) and the cholesterol biosynthesis ( b ) of naïve and polyclonally activated CD8 + T cells with TCAIM KI, KO or wt gene expression (KI and wt: n = 3; KO: n = 2). RNA-seq raw count data of protein-coding genes were normalized and log 2 -transformed after adding a pseudocount to each value. Cells had been stimulated with 5 µg/ ml plate-bound αCD3 and 2 µg/ ml soluble αCD28 at a density of 6 x 10 5 cells/ 200 µl culture medium. Data represents means ± SEM.

    Article Snippet: Briefly, mRNA-Seq libraries were prepared from 100 ng of input total RNA samples using TruSeq stranded mRNA kit (Illumina).

    Techniques: Expressing, RNA Sequencing Assay, Transformation Assay

    Datasets in this study. a The GSE50856 dataset was divided into 6 groups: SFM-Smart, SFM-DP, SFM-CEL, AA100-Smart, AA100-DP and AA100-CEL. Each group had four low input mRNA levels, 1000 pg, 100 pg, 50 pg and 25 pg, and each level had two technical replicates. b The GSE17565 dataset was divided into 2 groups: Raji and MCF-7. Each group had four low input total RNA levels, 1000 pg, 250 pg, 50 pg and 10 pg, and each level had two technical replicates

    Journal: BMC Genomics

    Article Title: Robust transcriptional signatures for low-input RNA samples based on relative expression orderings

    doi: 10.1186/s12864-017-4280-7

    Figure Lengend Snippet: Datasets in this study. a The GSE50856 dataset was divided into 6 groups: SFM-Smart, SFM-DP, SFM-CEL, AA100-Smart, AA100-DP and AA100-CEL. Each group had four low input mRNA levels, 1000 pg, 100 pg, 50 pg and 25 pg, and each level had two technical replicates. b The GSE17565 dataset was divided into 2 groups: Raji and MCF-7. Each group had four low input total RNA levels, 1000 pg, 250 pg, 50 pg and 10 pg, and each level had two technical replicates

    Article Snippet: In contrast, we found that approximately 90% of REOs of gene pairs in high-input RNA samples were maintained in the diluted 1000 pg, low-input mRNA samples which were amplified and profiled by Smart-seq, DP-seq and CEL-seq techniques using the Illumina HiSeq 2000 platform.

    Techniques:

    Coverage of the microbial genomes, Olsenella profusa (62% GC) (left) and Bacillus megaterium (38% GC) (right) with (A) MGIEasy PCR-Free DNA Library Pre Set and (B) MGIEasy FS PCR-Free DNA Library Pre Set. Read coverage across the range of the GC content, calculated in 100 bp windows (pink bars) and normalized coverage (colored dots). 3 replicates (red, blue and green dots) were included in the normalized coverage VS GC content analysis.

    Journal: bioRxiv

    Article Title: Advanced Whole Genome Sequencing Using a Complete PCR-free Massively Parallel Sequencing (MPS) Workflow

    doi: 10.1101/2019.12.20.885517

    Figure Lengend Snippet: Coverage of the microbial genomes, Olsenella profusa (62% GC) (left) and Bacillus megaterium (38% GC) (right) with (A) MGIEasy PCR-Free DNA Library Pre Set and (B) MGIEasy FS PCR-Free DNA Library Pre Set. Read coverage across the range of the GC content, calculated in 100 bp windows (pink bars) and normalized coverage (colored dots). 3 replicates (red, blue and green dots) were included in the normalized coverage VS GC content analysis.

    Article Snippet: It should be noted that MGIEasy kit prepared libraries used 1 μg or 250ng DNA input, far less than the input amount of datasets downloaded from Illumina Basespace website.

    Techniques: Polymerase Chain Reaction

    DNBSEQTM WGS PCR vs PCR-free workflows and general performance of PCR-free libraries. (a) MPS library construction workflows of WGS PCR and PCR-free libraries. RCA ( r olling c ircle a mplification) is used to increase signal intensity during array formation, which is followed by sequencing DNBs with DNBSEQ TM technology. Individual copies from the same DNB are replicated independently using the same ssCir template. Therefore, amplification errors cannot accumulate. Black, genomic DNA; Gray rectangle, adapter; green, barcode; red, amplification errors. (b) Two sets of 9 replicates from 1 μg NA12878 DNA were processed with MGIEasy PCR-Free DNA Library Prep Set (blue) or MGIEasy FS PCR-Free DNA Library Prep Set (orange). The GC content, Duplication rate, Median Insert size, and regions with > 10x Coverage were calculated and plotted. The error bars represent the standard deviations across the replicates.

    Journal: bioRxiv

    Article Title: Advanced Whole Genome Sequencing Using a Complete PCR-free Massively Parallel Sequencing (MPS) Workflow

    doi: 10.1101/2019.12.20.885517

    Figure Lengend Snippet: DNBSEQTM WGS PCR vs PCR-free workflows and general performance of PCR-free libraries. (a) MPS library construction workflows of WGS PCR and PCR-free libraries. RCA ( r olling c ircle a mplification) is used to increase signal intensity during array formation, which is followed by sequencing DNBs with DNBSEQ TM technology. Individual copies from the same DNB are replicated independently using the same ssCir template. Therefore, amplification errors cannot accumulate. Black, genomic DNA; Gray rectangle, adapter; green, barcode; red, amplification errors. (b) Two sets of 9 replicates from 1 μg NA12878 DNA were processed with MGIEasy PCR-Free DNA Library Prep Set (blue) or MGIEasy FS PCR-Free DNA Library Prep Set (orange). The GC content, Duplication rate, Median Insert size, and regions with > 10x Coverage were calculated and plotted. The error bars represent the standard deviations across the replicates.

    Article Snippet: It should be noted that MGIEasy kit prepared libraries used 1 μg or 250ng DNA input, far less than the input amount of datasets downloaded from Illumina Basespace website.

    Techniques: Polymerase Chain Reaction, Sequencing, Amplification