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Illumina Inc bp single end sequencing
Bp Single End Sequencing, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 99/100, based on 22 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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Average 99 stars, based on 22 article reviews
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bp single end sequencing - by Bioz Stars, 2020-02
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Centrifugation:

Article Title: A high-resolution map of transcriptional repression
Article Snippet: Sonicated chromatin was recovered as supernatant after centrifugation at 25,000 rcf for 15 min at 4°C and incubated with antibodies to histone H3 (Abcam AB1791), acetylated histone H3 (Abcam AB47915), acetylated histone H4 (Millipore 06–866), RNAP2 (Santa Cruz sc-899), TFIIB (Santa Cruz sc-225), CHD4 (Abcam AB70469), MBD3 (Bethyl A302-528A) or Brg1 (Millipore, 07–478) on a rotating platform at 4°C overnight, washed sequentially in 140 mM NaCl, 50 mM HEPES, 1 mM EDTA, 1% Triton X-100, 0.1% SDS, 0.1% sodium deoxycholate, pH 7.9 followed by 500 mM NaCl, 50 mM HEPES, 1 mM EDTA, 1% Triton X-100, 0.1% SDS, 0.1% sodium deoxycholate, pH 7.9 followed by 250 mM LiCl, 50 mM HEPES, 1 mM EDTA, 0.5% NP-40, 0.5% sodium deoxycholate, pH 8.0 and finally 10 mM Tris-HCl, 1 mM EDTA, pH 7.5. .. After 50 bp single-end sequencing (Hi-seq 2500, Illumina, ~155 M reads per condition), reads were aligned to mm9 using BWA version 0.7.5.

Amplification:

Article Title: Autoimmune disease-associated gene expression is reduced by BET-inhibition
Article Snippet: .. Removal of rRNA and globin-encoding mRNA, RNA fragmentation, cDNA generation, adapter ligation and PCR amplification was done using the TruSeq stranded total RNA with ribo-zero globin sample preparation kit (Illumina) and 75 bp single-end sequencing was performed using an Illumina NextSeq 500 platform through the Utrecht DNA sequencing facility. .. 2.3 Quality control Read quality assessment, sample demultiplexing, and adapter trimming was performed by Utrecht DNA sequencing facility using BaseSpace (Illumina) software.

Article Title: Genomic signatures of environmental selection despite near‐panmixia in summer flounder. Genomic signatures of environmental selection despite near‐panmixia in summer flounder
Article Snippet: Pooled samples were size selected to 273 ± 27 bp using a Pippin Prep (Sage Science; Beverly, MA) and then amplified with PCR using read 1 and read 2 primers (Table ) designed to only amplify DNA with both P1 and P2 adapters. .. An initial 10 nM library composed of two pools containing 20 individuals each was sent to the Rutgers Genome Cooperative (New Brunswick, NJ, USA) for 200 bp single‐end sequencing on the Illumina Miseq platform.

Article Title: High-throughput mRNA and miRNA profiling of epithelial-mesenchymal transition in MDCK cells
Article Snippet: Amplified cDNA libraries were size fractionated on a 2 % low-melt agarose gel and fragments with a length between 90 to 110 nucleotides were excised. .. 36 bp single-end sequencing was performed according to the manufacturer’s protocols (Illumina).

Article Title: Cell type-specific epigenetic links to schizophrenia risk in the brain
Article Snippet: Second-strand cDNA was adenylated, ligated, and cleaned up twice by EpiNext beads. cDNA libraries were amplified by PCR and cleaned up twice by EpiNext beads. cDNA library quality was quantified by a 2100 Bioanalyzer using an Agilent High Sensitivity DNA Kit (#5067-4626, Agilent). .. Barcoded libraries were pooled and underwent 75 bp single-end sequencing on an Illumina NextSeq 500.

Synthesized:

Article Title: HSB-1 Inhibition and HSF-1 Overexpression Trigger Overlapping Transcriptional Changes To Promote Longevity in Caenorhabditis elegans
Article Snippet: RNA-Seq Library Preparation TRIzol reagent (Thermo Fisher) was used to extract total RNA from ∼1,000 age-synchronized young adults of N2 , EQ150 and EQ140 strains (three biological replicates per genotype) using the manufacturer’s protocol and DNase-treatment was performed using TURBO DNA-free kit (Themo Fisher). mRNA was isolated from the DNase-treated total RNA using oligo(dT) and cDNA was synthesized by reverse transcription using TruSeq RNA Library Prep Kit v2 (Illumina). .. All samples were multiplexed for 50 bp single-end sequencing on a HiSeq 2500 platform (Illumina).

Cytometry:

Article Title: Autoimmune disease-associated gene expression is reduced by BET-inhibition
Article Snippet: 2.2 RNA sample preparation and sequencing CD4+ CD45RO+ cells (ranging between 600.000–1.200.000 cells per sample) were isolated from frozen HC PBMCs and JIA SFMCs using flow cytometry, activated with human T-activator CD3/CD28 dynabeads (1 cell: 3 beads) and cultured for 16 h in the presence of 300 nM JQ1(+) or JQ1(−). .. Removal of rRNA and globin-encoding mRNA, RNA fragmentation, cDNA generation, adapter ligation and PCR amplification was done using the TruSeq stranded total RNA with ribo-zero globin sample preparation kit (Illumina) and 75 bp single-end sequencing was performed using an Illumina NextSeq 500 platform through the Utrecht DNA sequencing facility.

Concentration Assay:

Article Title: Genomic signatures of environmental selection despite near‐panmixia in summer flounder. Genomic signatures of environmental selection despite near‐panmixia in summer flounder
Article Snippet: Qubit Fluorometric Quantitation (Thermo Fisher Scientific; Waltham, MA, USA) was used to quantify the final concentration of each pool. .. An initial 10 nM library composed of two pools containing 20 individuals each was sent to the Rutgers Genome Cooperative (New Brunswick, NJ, USA) for 200 bp single‐end sequencing on the Illumina Miseq platform.

Real-time Polymerase Chain Reaction:

Article Title: DNA methylome and transcriptome sequencing in human ovarian granulosa cells links age-related changes in gene expression to gene body methylation and 3ʹ-end GC density
Article Snippet: The enrichment of captured DNA after MethylCap kit was confirmed by comparison to the input DNA with qPCR using human H19 and UBE primer pairs (Eurofins MWG Operon). .. For each MethylCap sequencing library, one to two lanes of 36 bp single-end sequencing were performed on the Illumina Genome Analyzer II according to the manufacturer's protocol at NIH Intramural Sequencing Center (Rockville, MD).

Incubation:

Article Title: A high-resolution map of transcriptional repression
Article Snippet: Sonicated chromatin was recovered as supernatant after centrifugation at 25,000 rcf for 15 min at 4°C and incubated with antibodies to histone H3 (Abcam AB1791), acetylated histone H3 (Abcam AB47915), acetylated histone H4 (Millipore 06–866), RNAP2 (Santa Cruz sc-899), TFIIB (Santa Cruz sc-225), CHD4 (Abcam AB70469), MBD3 (Bethyl A302-528A) or Brg1 (Millipore, 07–478) on a rotating platform at 4°C overnight, washed sequentially in 140 mM NaCl, 50 mM HEPES, 1 mM EDTA, 1% Triton X-100, 0.1% SDS, 0.1% sodium deoxycholate, pH 7.9 followed by 500 mM NaCl, 50 mM HEPES, 1 mM EDTA, 1% Triton X-100, 0.1% SDS, 0.1% sodium deoxycholate, pH 7.9 followed by 250 mM LiCl, 50 mM HEPES, 1 mM EDTA, 0.5% NP-40, 0.5% sodium deoxycholate, pH 8.0 and finally 10 mM Tris-HCl, 1 mM EDTA, pH 7.5. .. After 50 bp single-end sequencing (Hi-seq 2500, Illumina, ~155 M reads per condition), reads were aligned to mm9 using BWA version 0.7.5.

Article Title: A DNMT3A PWWP mutation leads to methylation of bivalent chromatin and growth retardation in mice
Article Snippet: Antibodies for H3K4me3 (250 ng per reaction, Diagenode C15410003), H3K27me3 (125 ng per reaction, Millipore 07-449), or H3K36me3 (250 ng per reaction, Diagenode C15410192) were pre-bound to Protein A/G beads and incubated with chromatin for immunoprecipitation. .. Libraries were sequenced using 75 bp single-end sequencing on the Illumina NextSeq500 platform at the Babraham Institute Sequencing Facility.

Modification:

Article Title: A high-resolution map of transcriptional repression
Article Snippet: For RNAP2, chromatin remodeler and histone modification ChIP ( ) cells were fixed as described for MNase, lysed in 25 mM HEPES, 1.5 mM MgCl2, 10 mM KCl, 0.1% NP-40, pH 7.9 at 50 × 106 cells/ml on ice for 15 min, centrifuged at 900 rcf for 10 min at 4°C, resuspended in 140 mM NaCl, 50 mM HEPES, 1 mM EDTA, 1% Triton X-100, 0.1% SDS, 0.1% sodium deoxycholate, pH 7.9 and sonicated for 25 min at 4°C with 30 s on, and 30 s off (Bioruptor, Diagenode). .. After 50 bp single-end sequencing (Hi-seq 2500, Illumina, ~155 M reads per condition), reads were aligned to mm9 using BWA version 0.7.5.

Article Title: Quantitative trait loci and differential gene expression analyses reveal the genetic basis for negatively associated β-carotene and starch content in hexaploid sweetpotato [Ipomoea batatas (L.) Lam.]
Article Snippet: Next-generation sequencing 64-plex libraries were made based on the GBSpoly protocol (Wadl et al. ), while 125 bp single-end sequencing was performed on a total of 40 sequencing lanes (8 lanes for each of the 5 libraries) of the Illumina HiSeq 2500 platform. .. We aligned the GBS tags against the diploid relatives of sweetpotato, I. trifida and I. triloba reference genomes (Wu et al. ) using Bowtie2 (Langmead and Salzberg ), and obtained the allele read counts per locus using the Tassel-GBS pipeline (Glaubitz et al. ) modified for polyploids (Pereira et al. ).

Flow Cytometry:

Article Title: Autoimmune disease-associated gene expression is reduced by BET-inhibition
Article Snippet: 2.2 RNA sample preparation and sequencing CD4+ CD45RO+ cells (ranging between 600.000–1.200.000 cells per sample) were isolated from frozen HC PBMCs and JIA SFMCs using flow cytometry, activated with human T-activator CD3/CD28 dynabeads (1 cell: 3 beads) and cultured for 16 h in the presence of 300 nM JQ1(+) or JQ1(−). .. Removal of rRNA and globin-encoding mRNA, RNA fragmentation, cDNA generation, adapter ligation and PCR amplification was done using the TruSeq stranded total RNA with ribo-zero globin sample preparation kit (Illumina) and 75 bp single-end sequencing was performed using an Illumina NextSeq 500 platform through the Utrecht DNA sequencing facility.

Ligation:

Article Title: DNA methylome and transcriptome sequencing in human ovarian granulosa cells links age-related changes in gene expression to gene body methylation and 3ʹ-end GC density
Article Snippet: After ligation, the DNA was enriched by 18 cycles of PCR with primers complementary to the single ended adaptor sequences followed by agarose gel size selection and purification. .. For each MethylCap sequencing library, one to two lanes of 36 bp single-end sequencing were performed on the Illumina Genome Analyzer II according to the manufacturer's protocol at NIH Intramural Sequencing Center (Rockville, MD).

Article Title: Autoimmune disease-associated gene expression is reduced by BET-inhibition
Article Snippet: .. Removal of rRNA and globin-encoding mRNA, RNA fragmentation, cDNA generation, adapter ligation and PCR amplification was done using the TruSeq stranded total RNA with ribo-zero globin sample preparation kit (Illumina) and 75 bp single-end sequencing was performed using an Illumina NextSeq 500 platform through the Utrecht DNA sequencing facility. .. 2.3 Quality control Read quality assessment, sample demultiplexing, and adapter trimming was performed by Utrecht DNA sequencing facility using BaseSpace (Illumina) software.

Cell Culture:

Article Title: Autoimmune disease-associated gene expression is reduced by BET-inhibition
Article Snippet: 2.2 RNA sample preparation and sequencing CD4+ CD45RO+ cells (ranging between 600.000–1.200.000 cells per sample) were isolated from frozen HC PBMCs and JIA SFMCs using flow cytometry, activated with human T-activator CD3/CD28 dynabeads (1 cell: 3 beads) and cultured for 16 h in the presence of 300 nM JQ1(+) or JQ1(−). .. Removal of rRNA and globin-encoding mRNA, RNA fragmentation, cDNA generation, adapter ligation and PCR amplification was done using the TruSeq stranded total RNA with ribo-zero globin sample preparation kit (Illumina) and 75 bp single-end sequencing was performed using an Illumina NextSeq 500 platform through the Utrecht DNA sequencing facility.

Generated:

Article Title: A high-resolution map of transcriptional repression
Article Snippet: After 50 bp single-end sequencing (Hi-seq 2500, Illumina, ~155 M reads per condition), reads were aligned to mm9 using BWA version 0.7.5. .. SAM files were generated, aligned, sorted and indexed with samtools version 0.1.18.

Article Title: Autoimmune disease-associated gene expression is reduced by BET-inhibition
Article Snippet: The quality of the RNA was assessed based on the RNA profile generated by the bioanalyzer using the picochip. .. Removal of rRNA and globin-encoding mRNA, RNA fragmentation, cDNA generation, adapter ligation and PCR amplification was done using the TruSeq stranded total RNA with ribo-zero globin sample preparation kit (Illumina) and 75 bp single-end sequencing was performed using an Illumina NextSeq 500 platform through the Utrecht DNA sequencing facility.

Article Title: Targeted degradation of BRD9 reverses oncogenic gene expression in synovial sarcoma
Article Snippet: Libraries were generated using the NEBNext Ultra RNA Library Prep kit for Illumina (NEB, E7530L) in accordance with the manufacturer’s instructions. .. Pooled libraries were diluted and processed for 75 bp single-end sequencing on an Illumina NextSeq instrument using the NextSeq 500 High Output v2 kit (75 cycle) (Illumina, FC-404–2005) in accordance with the manufacturer’s instructions.

DNA Sequencing:

Article Title: Autoimmune disease-associated gene expression is reduced by BET-inhibition
Article Snippet: .. Removal of rRNA and globin-encoding mRNA, RNA fragmentation, cDNA generation, adapter ligation and PCR amplification was done using the TruSeq stranded total RNA with ribo-zero globin sample preparation kit (Illumina) and 75 bp single-end sequencing was performed using an Illumina NextSeq 500 platform through the Utrecht DNA sequencing facility. .. 2.3 Quality control Read quality assessment, sample demultiplexing, and adapter trimming was performed by Utrecht DNA sequencing facility using BaseSpace (Illumina) software.

Article Title: Targeted degradation of BRD9 reverses oncogenic gene expression in synovial sarcoma
Article Snippet: ChIP purified DNA was quantified using a Qubit fluorimeter (Invitrogen), and 2–50 ng of DNA/ChIP was used to generate ChIP-seq libraries with the ThruPLEX DNA-seq kit (Rubicon Genomics, R400427). .. Pooled libraries were diluted and processed for 75 bp single-end sequencing on an Illumina NextSeq instrument using the NextSeq 500 High Output v2 kit (75 cycle) (Illumina, FC-404–2005) in accordance with the manufacturer’s instructions.

Sequencing:

Article Title: A high-resolution map of transcriptional repression
Article Snippet: .. After 50 bp single-end sequencing (Hi-seq 2500, Illumina, ~155 M reads per condition), reads were aligned to mm9 using BWA version 0.7.5. .. SAM files were generated, aligned, sorted and indexed with samtools version 0.1.18.

Article Title: Whole transcriptome profiling of patient-derived xenograft models as a tool to identify both tumor and stromal specific biomarkers
Article Snippet: .. These libraries were then submitted for 50 bp single-end sequencing on the Illumina HiSeq 2000 platform using eight samples per lane. ..

Article Title: DNA methylome and transcriptome sequencing in human ovarian granulosa cells links age-related changes in gene expression to gene body methylation and 3ʹ-end GC density
Article Snippet: .. For each MethylCap sequencing library, one to two lanes of 36 bp single-end sequencing were performed on the Illumina Genome Analyzer II according to the manufacturer's protocol at NIH Intramural Sequencing Center (Rockville, MD). .. Reduced representation bisulfite sequencing (RRBS) We based our RRBS method on two previously published protocols [ , ].

Article Title: Autoimmune disease-associated gene expression is reduced by BET-inhibition
Article Snippet: .. Removal of rRNA and globin-encoding mRNA, RNA fragmentation, cDNA generation, adapter ligation and PCR amplification was done using the TruSeq stranded total RNA with ribo-zero globin sample preparation kit (Illumina) and 75 bp single-end sequencing was performed using an Illumina NextSeq 500 platform through the Utrecht DNA sequencing facility. .. 2.3 Quality control Read quality assessment, sample demultiplexing, and adapter trimming was performed by Utrecht DNA sequencing facility using BaseSpace (Illumina) software.

Article Title: Targeted degradation of BRD9 reverses oncogenic gene expression in synovial sarcoma
Article Snippet: .. Pooled libraries were diluted and processed for 75 bp single-end sequencing on an Illumina NextSeq instrument using the NextSeq 500 High Output v2 kit (75 cycle) (Illumina, FC-404–2005) in accordance with the manufacturer’s instructions. .. Total RNA was isolated from cells using the RNeasy Mini Kit (Qiagen, 74106) in accordance with the manufacturer’s instructions.

Article Title: HSB-1 Inhibition and HSF-1 Overexpression Trigger Overlapping Transcriptional Changes To Promote Longevity in Caenorhabditis elegans
Article Snippet: .. All samples were multiplexed for 50 bp single-end sequencing on a HiSeq 2500 platform (Illumina). .. RNA-Seq Data Analysis Quality control and adaptor trimming of raw sequencing reads were performed using Trim Galore version 0.4.5 (available at https://github.com/FelixKrueger/TrimGalore ) ( ).

Article Title: Genomic signatures of environmental selection despite near‐panmixia in summer flounder. Genomic signatures of environmental selection despite near‐panmixia in summer flounder
Article Snippet: .. An initial 10 nM library composed of two pools containing 20 individuals each was sent to the Rutgers Genome Cooperative (New Brunswick, NJ, USA) for 200 bp single‐end sequencing on the Illumina Miseq platform. .. A subsequent 10 nM library of five pools containing 48 individuals each was sent to the Princeton Core Facility (Princeton, NJ, USA) for 141 bp single‐end sequencing on a single lane run using the Illumina HiSeq 2500 platform.

Article Title: High-throughput mRNA and miRNA profiling of epithelial-mesenchymal transition in MDCK cells
Article Snippet: .. 36 bp single-end sequencing was performed according to the manufacturer’s protocols (Illumina). .. miRNA-Seq reads quality control, alignment, miRNA detection and prediction, expression profiling and analysis of differential expression Quality of reads was checked with FASTQC ( http://www.bioinformatics.babraham.ac.uk/projects/fastqc ), during which an overrepresentation of “Illumina Small RNA 3p Adapter 1” was found.

Article Title: Evaluation of experimental design and computational parameter choices affecting analyses of ChIP-seq and RNA-seq data in undomesticated poplar trees
Article Snippet: .. Sequencing libraries were prepared with Illumina TrueSeq DNA Sample PrepKit and submitted for ultra-high-throughput Solexa (Illumina) 50 bp single-end sequencing. .. Input libraries were prepared with approximately 10 ng whole genomic DNA purified from sonicated chromatin used for ChIP reactions.

Article Title: Genome-wide mapping of 8-oxo-7,8-dihydro-2′-deoxyguanosine reveals accumulation of oxidatively-generated damage at DNA replication origins within transcribed long genes of mammalian cells
Article Snippet: .. 50 bp single-end sequencing was performed using Illumina HiSeq 2000 platform. ..

Article Title: Cell type-specific epigenetic links to schizophrenia risk in the brain
Article Snippet: .. Barcoded libraries were pooled and underwent 75 bp single-end sequencing on an Illumina NextSeq 500. .. RNA-seq mapping, QC, and expression quantification Reads were aligned to the human hg19 (GRCh37) reference genome using STAR 2.5.2b [ ] with the following parameters: --outFilterMultimapNmax 10 --alignSJoverhangMin 10 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 3 --twopassMode Basic .

Article Title: A DNMT3A PWWP mutation leads to methylation of bivalent chromatin and growth retardation in mice
Article Snippet: .. Libraries were sequenced using 75 bp single-end sequencing on the Illumina NextSeq500 platform at the Babraham Institute Sequencing Facility. .. ChIP data analysis ChIP-seq data was trimmed using Trim Galore 0.5.0 and mapped against Mus Musculus GRCm38 genome with Bowtie 1.2.2 .

Article Title: Isolation of Open Chromatin Identifies Regulators of Systemic Acquired Resistance 1Isolation of Open Chromatin Identifies Regulators of Systemic Acquired Resistance 1 [OPEN]
Article Snippet: .. Briefly, isolated FAIRE-DNA was subjected to two rounds of 50 bp single-end sequencing using an Illumina HiSeq 2000 platform. .. FAIRE-DNA of a later repeat experiment was sequenced using 125 bp paired ends and an Illumina HiSeq 2500 platform to allow for the explicit detection of DNA fragment size.

Sonication:

Article Title: A high-resolution map of transcriptional repression
Article Snippet: Sonicated chromatin was recovered as supernatant after centrifugation at 25,000 rcf for 15 min at 4°C and incubated with antibodies to histone H3 (Abcam AB1791), acetylated histone H3 (Abcam AB47915), acetylated histone H4 (Millipore 06–866), RNAP2 (Santa Cruz sc-899), TFIIB (Santa Cruz sc-225), CHD4 (Abcam AB70469), MBD3 (Bethyl A302-528A) or Brg1 (Millipore, 07–478) on a rotating platform at 4°C overnight, washed sequentially in 140 mM NaCl, 50 mM HEPES, 1 mM EDTA, 1% Triton X-100, 0.1% SDS, 0.1% sodium deoxycholate, pH 7.9 followed by 500 mM NaCl, 50 mM HEPES, 1 mM EDTA, 1% Triton X-100, 0.1% SDS, 0.1% sodium deoxycholate, pH 7.9 followed by 250 mM LiCl, 50 mM HEPES, 1 mM EDTA, 0.5% NP-40, 0.5% sodium deoxycholate, pH 8.0 and finally 10 mM Tris-HCl, 1 mM EDTA, pH 7.5. .. After 50 bp single-end sequencing (Hi-seq 2500, Illumina, ~155 M reads per condition), reads were aligned to mm9 using BWA version 0.7.5.

Article Title: Evaluation of experimental design and computational parameter choices affecting analyses of ChIP-seq and RNA-seq data in undomesticated poplar trees
Article Snippet: The nuclei were isolated with CelLytic PN extraction kit (Sigma-Aldrich) and sonicated in a Lysis buffer (50 mM Tris-HCI, pH 8.0, 10 mM EDTA, 0.5% DOC, 0.3% SDS, proteinase inhibitor and 1 mM PMSF) until the majority of chromatin was fragmented to a size range of 200-500 bp. .. Sequencing libraries were prepared with Illumina TrueSeq DNA Sample PrepKit and submitted for ultra-high-throughput Solexa (Illumina) 50 bp single-end sequencing.

Binding Assay:

Article Title: Evaluation of experimental design and computational parameter choices affecting analyses of ChIP-seq and RNA-seq data in undomesticated poplar trees
Article Snippet: Sequencing libraries were prepared with Illumina TrueSeq DNA Sample PrepKit and submitted for ultra-high-throughput Solexa (Illumina) 50 bp single-end sequencing. .. MACS1.4 software ( http://liulab.dfci.harvard.edu/MACS/00README.html ) was used to call peaks representing enriched binding sites as discussed in the Results and Discussion sections.

ChIP-sequencing:

Article Title: A high-resolution map of transcriptional repression
Article Snippet: For ChIP-seq, 10 ng ChIP and input DNA were used to prepare libraries (Next Ultra, NEB) with size selection for fragments between 100 and 300 bp. .. After 50 bp single-end sequencing (Hi-seq 2500, Illumina, ~155 M reads per condition), reads were aligned to mm9 using BWA version 0.7.5.

Article Title: Targeted degradation of BRD9 reverses oncogenic gene expression in synovial sarcoma
Article Snippet: Paragraph title: ChIP-seq library preparation and sequencing ... Pooled libraries were diluted and processed for 75 bp single-end sequencing on an Illumina NextSeq instrument using the NextSeq 500 High Output v2 kit (75 cycle) (Illumina, FC-404–2005) in accordance with the manufacturer’s instructions.

Article Title: Evaluation of experimental design and computational parameter choices affecting analyses of ChIP-seq and RNA-seq data in undomesticated poplar trees
Article Snippet: Paragraph title: ChIP-seq and data analysis ... Sequencing libraries were prepared with Illumina TrueSeq DNA Sample PrepKit and submitted for ultra-high-throughput Solexa (Illumina) 50 bp single-end sequencing.

Article Title: Genome-wide mapping of 8-oxo-7,8-dihydro-2′-deoxyguanosine reveals accumulation of oxidatively-generated damage at DNA replication origins within transcribed long genes of mammalian cells
Article Snippet: Paragraph title: γH2AX ChIP-sequencing ... 50 bp single-end sequencing was performed using Illumina HiSeq 2000 platform.

Article Title: A DNMT3A PWWP mutation leads to methylation of bivalent chromatin and growth retardation in mice
Article Snippet: Paragraph title: Ultra-low input native ChIP-seq library preparation ... Libraries were sequenced using 75 bp single-end sequencing on the Illumina NextSeq500 platform at the Babraham Institute Sequencing Facility.

RNA Sequencing Assay:

Article Title: HSB-1 Inhibition and HSF-1 Overexpression Trigger Overlapping Transcriptional Changes To Promote Longevity in Caenorhabditis elegans
Article Snippet: Paragraph title: RNA-Seq Library Preparation ... All samples were multiplexed for 50 bp single-end sequencing on a HiSeq 2500 platform (Illumina).

Article Title: Targeted degradation of BRD9 reverses oncogenic gene expression in synovial sarcoma
Article Snippet: Paragraph title: Cell count RNA-seq library prep and sequencing ... Pooled libraries were diluted and processed for 75 bp single-end sequencing on an Illumina NextSeq instrument using the NextSeq 500 High Output v2 kit (75 cycle) (Illumina, FC-404–2005) in accordance with the manufacturer’s instructions.

Article Title: Cell type-specific epigenetic links to schizophrenia risk in the brain
Article Snippet: Paragraph title: RNA sequencing ... Barcoded libraries were pooled and underwent 75 bp single-end sequencing on an Illumina NextSeq 500.

Fluorescence:

Article Title: Quantitative trait loci and differential gene expression analyses reveal the genetic basis for negatively associated β-carotene and starch content in hexaploid sweetpotato [Ipomoea batatas (L.) Lam.]
Article Snippet: In summary, the concentration of DNA samples was normalized after quality check on 1% agarose gel and quantification based on the PicoGreen fluorescence-based assay. .. Next-generation sequencing 64-plex libraries were made based on the GBSpoly protocol (Wadl et al. ), while 125 bp single-end sequencing was performed on a total of 40 sequencing lanes (8 lanes for each of the 5 libraries) of the Illumina HiSeq 2500 platform.

Methylation:

Article Title: DNA methylome and transcriptome sequencing in human ovarian granulosa cells links age-related changes in gene expression to gene body methylation and 3ʹ-end GC density
Article Snippet: Paragraph title: Methylated DNA capture followed by next-gen sequencing (MethylCap-seq) ... For each MethylCap sequencing library, one to two lanes of 36 bp single-end sequencing were performed on the Illumina Genome Analyzer II according to the manufacturer's protocol at NIH Intramural Sequencing Center (Rockville, MD).

Isolation:

Article Title: Autoimmune disease-associated gene expression is reduced by BET-inhibition
Article Snippet: 2.2 RNA sample preparation and sequencing CD4+ CD45RO+ cells (ranging between 600.000–1.200.000 cells per sample) were isolated from frozen HC PBMCs and JIA SFMCs using flow cytometry, activated with human T-activator CD3/CD28 dynabeads (1 cell: 3 beads) and cultured for 16 h in the presence of 300 nM JQ1(+) or JQ1(−). .. Removal of rRNA and globin-encoding mRNA, RNA fragmentation, cDNA generation, adapter ligation and PCR amplification was done using the TruSeq stranded total RNA with ribo-zero globin sample preparation kit (Illumina) and 75 bp single-end sequencing was performed using an Illumina NextSeq 500 platform through the Utrecht DNA sequencing facility.

Article Title: HSB-1 Inhibition and HSF-1 Overexpression Trigger Overlapping Transcriptional Changes To Promote Longevity in Caenorhabditis elegans
Article Snippet: RNA-Seq Library Preparation TRIzol reagent (Thermo Fisher) was used to extract total RNA from ∼1,000 age-synchronized young adults of N2 , EQ150 and EQ140 strains (three biological replicates per genotype) using the manufacturer’s protocol and DNase-treatment was performed using TURBO DNA-free kit (Themo Fisher). mRNA was isolated from the DNase-treated total RNA using oligo(dT) and cDNA was synthesized by reverse transcription using TruSeq RNA Library Prep Kit v2 (Illumina). .. All samples were multiplexed for 50 bp single-end sequencing on a HiSeq 2500 platform (Illumina).

Article Title: Targeted degradation of BRD9 reverses oncogenic gene expression in synovial sarcoma
Article Snippet: ERCC spike-in controls were added to isolated RNA to facilitate cell count normalization of RNA-sequencing data. .. Pooled libraries were diluted and processed for 75 bp single-end sequencing on an Illumina NextSeq instrument using the NextSeq 500 High Output v2 kit (75 cycle) (Illumina, FC-404–2005) in accordance with the manufacturer’s instructions.

Article Title: High-throughput mRNA and miRNA profiling of epithelial-mesenchymal transition in MDCK cells
Article Snippet: miRNA Sequencing- library preparation and Illumina sequencing Quality and quantity of total RNA from MDCK and MDCK-Ras cells isolated with peqGOLD TriFast (Peqlab) were checked on an Agilent Bioanalyzer using the Agilent RNA 6000 Nano Kit (Agilent). .. 36 bp single-end sequencing was performed according to the manufacturer’s protocols (Illumina).

Article Title: Evaluation of experimental design and computational parameter choices affecting analyses of ChIP-seq and RNA-seq data in undomesticated poplar trees
Article Snippet: The nuclei were isolated with CelLytic PN extraction kit (Sigma-Aldrich) and sonicated in a Lysis buffer (50 mM Tris-HCI, pH 8.0, 10 mM EDTA, 0.5% DOC, 0.3% SDS, proteinase inhibitor and 1 mM PMSF) until the majority of chromatin was fragmented to a size range of 200-500 bp. .. Sequencing libraries were prepared with Illumina TrueSeq DNA Sample PrepKit and submitted for ultra-high-throughput Solexa (Illumina) 50 bp single-end sequencing.

Article Title: Isolation of Open Chromatin Identifies Regulators of Systemic Acquired Resistance 1Isolation of Open Chromatin Identifies Regulators of Systemic Acquired Resistance 1 [OPEN]
Article Snippet: .. Briefly, isolated FAIRE-DNA was subjected to two rounds of 50 bp single-end sequencing using an Illumina HiSeq 2000 platform. .. FAIRE-DNA of a later repeat experiment was sequenced using 125 bp paired ends and an Illumina HiSeq 2500 platform to allow for the explicit detection of DNA fragment size.

Purification:

Article Title: A high-resolution map of transcriptional repression
Article Snippet: Reverse crosslinked DNA was purified by phenol-chloroform extraction. .. After 50 bp single-end sequencing (Hi-seq 2500, Illumina, ~155 M reads per condition), reads were aligned to mm9 using BWA version 0.7.5.

Article Title: DNA methylome and transcriptome sequencing in human ovarian granulosa cells links age-related changes in gene expression to gene body methylation and 3ʹ-end GC density
Article Snippet: After ligation, the DNA was enriched by 18 cycles of PCR with primers complementary to the single ended adaptor sequences followed by agarose gel size selection and purification. .. For each MethylCap sequencing library, one to two lanes of 36 bp single-end sequencing were performed on the Illumina Genome Analyzer II according to the manufacturer's protocol at NIH Intramural Sequencing Center (Rockville, MD).

Article Title: Targeted degradation of BRD9 reverses oncogenic gene expression in synovial sarcoma
Article Snippet: ChIP purified DNA was quantified using a Qubit fluorimeter (Invitrogen), and 2–50 ng of DNA/ChIP was used to generate ChIP-seq libraries with the ThruPLEX DNA-seq kit (Rubicon Genomics, R400427). .. Pooled libraries were diluted and processed for 75 bp single-end sequencing on an Illumina NextSeq instrument using the NextSeq 500 High Output v2 kit (75 cycle) (Illumina, FC-404–2005) in accordance with the manufacturer’s instructions.

Article Title: Evaluation of experimental design and computational parameter choices affecting analyses of ChIP-seq and RNA-seq data in undomesticated poplar trees
Article Snippet: Sequencing libraries were prepared with Illumina TrueSeq DNA Sample PrepKit and submitted for ultra-high-throughput Solexa (Illumina) 50 bp single-end sequencing. .. Input libraries were prepared with approximately 10 ng whole genomic DNA purified from sonicated chromatin used for ChIP reactions.

Article Title: A DNMT3A PWWP mutation leads to methylation of bivalent chromatin and growth retardation in mice
Article Snippet: Bound DNA was purified by SPRI purification. .. Libraries were sequenced using 75 bp single-end sequencing on the Illumina NextSeq500 platform at the Babraham Institute Sequencing Facility.

Polymerase Chain Reaction:

Article Title: DNA methylome and transcriptome sequencing in human ovarian granulosa cells links age-related changes in gene expression to gene body methylation and 3ʹ-end GC density
Article Snippet: After ligation, the DNA was enriched by 18 cycles of PCR with primers complementary to the single ended adaptor sequences followed by agarose gel size selection and purification. .. For each MethylCap sequencing library, one to two lanes of 36 bp single-end sequencing were performed on the Illumina Genome Analyzer II according to the manufacturer's protocol at NIH Intramural Sequencing Center (Rockville, MD).

Article Title: Autoimmune disease-associated gene expression is reduced by BET-inhibition
Article Snippet: .. Removal of rRNA and globin-encoding mRNA, RNA fragmentation, cDNA generation, adapter ligation and PCR amplification was done using the TruSeq stranded total RNA with ribo-zero globin sample preparation kit (Illumina) and 75 bp single-end sequencing was performed using an Illumina NextSeq 500 platform through the Utrecht DNA sequencing facility. .. 2.3 Quality control Read quality assessment, sample demultiplexing, and adapter trimming was performed by Utrecht DNA sequencing facility using BaseSpace (Illumina) software.

Article Title: HSB-1 Inhibition and HSF-1 Overexpression Trigger Overlapping Transcriptional Changes To Promote Longevity in Caenorhabditis elegans
Article Snippet: The samples were subsequently end-repaired, poly(A)-tailed, ligated to barcoded oligo adapters (Illumina) and PCR-amplified using Apollo 324 library preparation system (Wafergen Bio-systems) to prepare non-stranded poly(A)-based cDNA libraries with 120 bp insert size. .. All samples were multiplexed for 50 bp single-end sequencing on a HiSeq 2500 platform (Illumina).

Article Title: Genomic signatures of environmental selection despite near‐panmixia in summer flounder. Genomic signatures of environmental selection despite near‐panmixia in summer flounder
Article Snippet: Read 2 PCR primers contained one of 12 Illumina indices so that pools could be distinguished from one another. .. An initial 10 nM library composed of two pools containing 20 individuals each was sent to the Rutgers Genome Cooperative (New Brunswick, NJ, USA) for 200 bp single‐end sequencing on the Illumina Miseq platform.

Article Title: Cell type-specific epigenetic links to schizophrenia risk in the brain
Article Snippet: Second-strand cDNA was adenylated, ligated, and cleaned up twice by EpiNext beads. cDNA libraries were amplified by PCR and cleaned up twice by EpiNext beads. cDNA library quality was quantified by a 2100 Bioanalyzer using an Agilent High Sensitivity DNA Kit (#5067-4626, Agilent). .. Barcoded libraries were pooled and underwent 75 bp single-end sequencing on an Illumina NextSeq 500.

cDNA Library Assay:

Article Title: Cell type-specific epigenetic links to schizophrenia risk in the brain
Article Snippet: Second-strand cDNA was adenylated, ligated, and cleaned up twice by EpiNext beads. cDNA libraries were amplified by PCR and cleaned up twice by EpiNext beads. cDNA library quality was quantified by a 2100 Bioanalyzer using an Agilent High Sensitivity DNA Kit (#5067-4626, Agilent). .. Barcoded libraries were pooled and underwent 75 bp single-end sequencing on an Illumina NextSeq 500.

Agarose Gel Electrophoresis:

Article Title: DNA methylome and transcriptome sequencing in human ovarian granulosa cells links age-related changes in gene expression to gene body methylation and 3ʹ-end GC density
Article Snippet: After ligation, the DNA was enriched by 18 cycles of PCR with primers complementary to the single ended adaptor sequences followed by agarose gel size selection and purification. .. For each MethylCap sequencing library, one to two lanes of 36 bp single-end sequencing were performed on the Illumina Genome Analyzer II according to the manufacturer's protocol at NIH Intramural Sequencing Center (Rockville, MD).

Article Title: High-throughput mRNA and miRNA profiling of epithelial-mesenchymal transition in MDCK cells
Article Snippet: Amplified cDNA libraries were size fractionated on a 2 % low-melt agarose gel and fragments with a length between 90 to 110 nucleotides were excised. .. 36 bp single-end sequencing was performed according to the manufacturer’s protocols (Illumina).

Article Title: Quantitative trait loci and differential gene expression analyses reveal the genetic basis for negatively associated β-carotene and starch content in hexaploid sweetpotato [Ipomoea batatas (L.) Lam.]
Article Snippet: In summary, the concentration of DNA samples was normalized after quality check on 1% agarose gel and quantification based on the PicoGreen fluorescence-based assay. .. Next-generation sequencing 64-plex libraries were made based on the GBSpoly protocol (Wadl et al. ), while 125 bp single-end sequencing was performed on a total of 40 sequencing lanes (8 lanes for each of the 5 libraries) of the Illumina HiSeq 2500 platform.

Chromatin Immunoprecipitation:

Article Title: A high-resolution map of transcriptional repression
Article Snippet: Paragraph title: Chromatin accessibility by MNase and chromatin immunoprecipitation (ChIP) ... After 50 bp single-end sequencing (Hi-seq 2500, Illumina, ~155 M reads per condition), reads were aligned to mm9 using BWA version 0.7.5.

Article Title: Targeted degradation of BRD9 reverses oncogenic gene expression in synovial sarcoma
Article Snippet: ChIP purified DNA was quantified using a Qubit fluorimeter (Invitrogen), and 2–50 ng of DNA/ChIP was used to generate ChIP-seq libraries with the ThruPLEX DNA-seq kit (Rubicon Genomics, R400427). .. Pooled libraries were diluted and processed for 75 bp single-end sequencing on an Illumina NextSeq instrument using the NextSeq 500 High Output v2 kit (75 cycle) (Illumina, FC-404–2005) in accordance with the manufacturer’s instructions.

Article Title: Evaluation of experimental design and computational parameter choices affecting analyses of ChIP-seq and RNA-seq data in undomesticated poplar trees
Article Snippet: Chromatin immunoprecipitations were performed using CHIP-IT Express kit (Active Motif) following manufacturer's instruction. .. Sequencing libraries were prepared with Illumina TrueSeq DNA Sample PrepKit and submitted for ultra-high-throughput Solexa (Illumina) 50 bp single-end sequencing.

Article Title: Genome-wide mapping of 8-oxo-7,8-dihydro-2′-deoxyguanosine reveals accumulation of oxidatively-generated damage at DNA replication origins within transcribed long genes of mammalian cells
Article Snippet: 10 ng of ChIP (or Input) DNA were used to prepare ChIP-Seq libraries with TruSeq ChIP Sample Prep Kit (Illumina) according to the manufacturer's instructions. .. 50 bp single-end sequencing was performed using Illumina HiSeq 2000 platform.

Software:

Article Title: Evaluation of experimental design and computational parameter choices affecting analyses of ChIP-seq and RNA-seq data in undomesticated poplar trees
Article Snippet: Sequencing libraries were prepared with Illumina TrueSeq DNA Sample PrepKit and submitted for ultra-high-throughput Solexa (Illumina) 50 bp single-end sequencing. .. MACS1.4 software ( http://liulab.dfci.harvard.edu/MACS/00README.html ) was used to call peaks representing enriched binding sites as discussed in the Results and Discussion sections.

Article Title: Quantitative trait loci and differential gene expression analyses reveal the genetic basis for negatively associated β-carotene and starch content in hexaploid sweetpotato [Ipomoea batatas (L.) Lam.]
Article Snippet: Next-generation sequencing 64-plex libraries were made based on the GBSpoly protocol (Wadl et al. ), while 125 bp single-end sequencing was performed on a total of 40 sequencing lanes (8 lanes for each of the 5 libraries) of the Illumina HiSeq 2500 platform. .. The read counts were ultimately used for dosage calling in the software SuperMASSA (Serang et al. ) with the help of VCF2SM script (Pereira et al. ).

Multiplex Assay:

Article Title: Targeted degradation of BRD9 reverses oncogenic gene expression in synovial sarcoma
Article Snippet: This information was used to calculate pooling ratios for multiplex library sequencing. .. Pooled libraries were diluted and processed for 75 bp single-end sequencing on an Illumina NextSeq instrument using the NextSeq 500 High Output v2 kit (75 cycle) (Illumina, FC-404–2005) in accordance with the manufacturer’s instructions.

Selection:

Article Title: A high-resolution map of transcriptional repression
Article Snippet: For ChIP-seq, 10 ng ChIP and input DNA were used to prepare libraries (Next Ultra, NEB) with size selection for fragments between 100 and 300 bp. .. After 50 bp single-end sequencing (Hi-seq 2500, Illumina, ~155 M reads per condition), reads were aligned to mm9 using BWA version 0.7.5.

Article Title: Whole transcriptome profiling of patient-derived xenograft models as a tool to identify both tumor and stromal specific biomarkers
Article Snippet: RNA libraries were made with the Illumina TruSeq Stranded mRNA Sample Preparation kit with oligo dT selection according to the manufacturer's protocol. .. These libraries were then submitted for 50 bp single-end sequencing on the Illumina HiSeq 2000 platform using eight samples per lane.

Article Title: DNA methylome and transcriptome sequencing in human ovarian granulosa cells links age-related changes in gene expression to gene body methylation and 3ʹ-end GC density
Article Snippet: After ligation, the DNA was enriched by 18 cycles of PCR with primers complementary to the single ended adaptor sequences followed by agarose gel size selection and purification. .. For each MethylCap sequencing library, one to two lanes of 36 bp single-end sequencing were performed on the Illumina Genome Analyzer II according to the manufacturer's protocol at NIH Intramural Sequencing Center (Rockville, MD).

Sample Prep:

Article Title: Whole transcriptome profiling of patient-derived xenograft models as a tool to identify both tumor and stromal specific biomarkers
Article Snippet: RNA libraries were made with the Illumina TruSeq Stranded mRNA Sample Preparation kit with oligo dT selection according to the manufacturer's protocol. .. These libraries were then submitted for 50 bp single-end sequencing on the Illumina HiSeq 2000 platform using eight samples per lane.

Article Title: Autoimmune disease-associated gene expression is reduced by BET-inhibition
Article Snippet: .. Removal of rRNA and globin-encoding mRNA, RNA fragmentation, cDNA generation, adapter ligation and PCR amplification was done using the TruSeq stranded total RNA with ribo-zero globin sample preparation kit (Illumina) and 75 bp single-end sequencing was performed using an Illumina NextSeq 500 platform through the Utrecht DNA sequencing facility. .. 2.3 Quality control Read quality assessment, sample demultiplexing, and adapter trimming was performed by Utrecht DNA sequencing facility using BaseSpace (Illumina) software.

Article Title: High-throughput mRNA and miRNA profiling of epithelial-mesenchymal transition in MDCK cells
Article Snippet: The miRNA sequencing libraries were prepared from four biological replicates per experimental condition with the Illumina Small RNA Sample Prep v1.5 (Illumina, San Diago, CA USA) as described in the corresponding protocol. .. 36 bp single-end sequencing was performed according to the manufacturer’s protocols (Illumina).

Article Title: Genome-wide mapping of 8-oxo-7,8-dihydro-2′-deoxyguanosine reveals accumulation of oxidatively-generated damage at DNA replication origins within transcribed long genes of mammalian cells
Article Snippet: 10 ng of ChIP (or Input) DNA were used to prepare ChIP-Seq libraries with TruSeq ChIP Sample Prep Kit (Illumina) according to the manufacturer's instructions. .. 50 bp single-end sequencing was performed using Illumina HiSeq 2000 platform.

Next-Generation Sequencing:

Article Title: Quantitative trait loci and differential gene expression analyses reveal the genetic basis for negatively associated β-carotene and starch content in hexaploid sweetpotato [Ipomoea batatas (L.) Lam.]
Article Snippet: .. Next-generation sequencing 64-plex libraries were made based on the GBSpoly protocol (Wadl et al. ), while 125 bp single-end sequencing was performed on a total of 40 sequencing lanes (8 lanes for each of the 5 libraries) of the Illumina HiSeq 2500 platform. .. We aligned the GBS tags against the diploid relatives of sweetpotato, I. trifida and I. triloba reference genomes (Wu et al. ) using Bowtie2 (Langmead and Salzberg ), and obtained the allele read counts per locus using the Tassel-GBS pipeline (Glaubitz et al. ) modified for polyploids (Pereira et al. ).

Article Title: Isolation of Open Chromatin Identifies Regulators of Systemic Acquired Resistance 1Isolation of Open Chromatin Identifies Regulators of Systemic Acquired Resistance 1 [OPEN]
Article Snippet: Isolated DNA elements were sequenced using next-generation sequencing (see “Materials and Methods“). .. Briefly, isolated FAIRE-DNA was subjected to two rounds of 50 bp single-end sequencing using an Illumina HiSeq 2000 platform.

Quantitation Assay:

Article Title: Genomic signatures of environmental selection despite near‐panmixia in summer flounder. Genomic signatures of environmental selection despite near‐panmixia in summer flounder
Article Snippet: Qubit Fluorometric Quantitation (Thermo Fisher Scientific; Waltham, MA, USA) was used to quantify the final concentration of each pool. .. An initial 10 nM library composed of two pools containing 20 individuals each was sent to the Rutgers Genome Cooperative (New Brunswick, NJ, USA) for 200 bp single‐end sequencing on the Illumina Miseq platform.

Article Title: A DNMT3A PWWP mutation leads to methylation of bivalent chromatin and growth retardation in mice
Article Snippet: Libraries were quantitated and quality control checked using Agilent High Sensitivity DNA kit and Kapa Illumina library quantitation kit, as per manufacturer’s instructions. .. Libraries were sequenced using 75 bp single-end sequencing on the Illumina NextSeq500 platform at the Babraham Institute Sequencing Facility.

Produced:

Article Title: Isolation of Open Chromatin Identifies Regulators of Systemic Acquired Resistance 1Isolation of Open Chromatin Identifies Regulators of Systemic Acquired Resistance 1 [OPEN]
Article Snippet: Briefly, isolated FAIRE-DNA was subjected to two rounds of 50 bp single-end sequencing using an Illumina HiSeq 2000 platform. .. This sequencing run produced almost 548 million reads totaling 68.5 billion bases.

Immunoprecipitation:

Article Title: A DNMT3A PWWP mutation leads to methylation of bivalent chromatin and growth retardation in mice
Article Snippet: MicroPlex Library Preparation kit v2 (Diagenode) was used as per manufacturer’s instructions to generate libraries of inputs and immunoprecipitated samples. .. Libraries were sequenced using 75 bp single-end sequencing on the Illumina NextSeq500 platform at the Babraham Institute Sequencing Facility.

Cell Counting:

Article Title: Targeted degradation of BRD9 reverses oncogenic gene expression in synovial sarcoma
Article Snippet: Paragraph title: Cell count RNA-seq library prep and sequencing ... Pooled libraries were diluted and processed for 75 bp single-end sequencing on an Illumina NextSeq instrument using the NextSeq 500 High Output v2 kit (75 cycle) (Illumina, FC-404–2005) in accordance with the manufacturer’s instructions.

Lysis:

Article Title: Evaluation of experimental design and computational parameter choices affecting analyses of ChIP-seq and RNA-seq data in undomesticated poplar trees
Article Snippet: The nuclei were isolated with CelLytic PN extraction kit (Sigma-Aldrich) and sonicated in a Lysis buffer (50 mM Tris-HCI, pH 8.0, 10 mM EDTA, 0.5% DOC, 0.3% SDS, proteinase inhibitor and 1 mM PMSF) until the majority of chromatin was fragmented to a size range of 200-500 bp. .. Sequencing libraries were prepared with Illumina TrueSeq DNA Sample PrepKit and submitted for ultra-high-throughput Solexa (Illumina) 50 bp single-end sequencing.

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    Illumina Inc 100 bp single end
    Ancestry results for samples from the southeastern portion of the range. Ancestry proportions were determined using Structure with 50,000 and <t>100,000</t> burn‐in and MCMC iterations and the previously determined optimal K ‐value of 2
    100 Bp Single End, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 83/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/100 bp single end/product/Illumina Inc
    Average 83 stars, based on 1 article reviews
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    100 bp single end - by Bioz Stars, 2020-02
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    79
    Illumina Inc 100 bp paired single end
    Decreased human endothelial TSP1. (A) Immunofluorescent staining of TSP1 (red) and collagen IV (green) of human CCM and lesion-free brain tissue. Arrowheads, capillary; arrows, venule; asterisks, vascular lumen of CCM lesions. Bar, <t>100</t> µm ( n = 2). (B and C) HUVECs were transduced with shKrit1 or shControl using lentivirus. (B) KRIT1-depleted HUVECs expressed ∼50% as much TSP1 protein as control cells (SEM, n = 3). (C) KRIT1 shRNA 55% decrease in KRIT1 mRNA as determined by RT-qPCR (SEM, n = 4). **, P
    100 Bp Paired Single End, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 79/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/100 bp paired single end/product/Illumina Inc
    Average 79 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    100 bp paired single end - by Bioz Stars, 2020-02
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    Image Search Results


    Ancestry results for samples from the southeastern portion of the range. Ancestry proportions were determined using Structure with 50,000 and 100,000 burn‐in and MCMC iterations and the previously determined optimal K ‐value of 2

    Journal: Evolutionary Applications

    Article Title: Population assignment and local adaptation along an isolation‐by‐distance gradient in Pacific cod (Gadus macrocephalus). Population assignment and local adaptation along an isolation‐by‐distance gradient in Pacific cod (Gadus macrocephalus)

    doi: 10.1111/eva.12639

    Figure Lengend Snippet: Ancestry results for samples from the southeastern portion of the range. Ancestry proportions were determined using Structure with 50,000 and 100,000 burn‐in and MCMC iterations and the previously determined optimal K ‐value of 2

    Article Snippet: Libraries were pooled within samples in 10 nM concentrations and sequenced in 100‐bp single‐end reads on a HiSeq2000 (Illumina, Inc., San Diego, CA) at the University of Oregon Genomics and Cell Characterization Core Facility (GC3F, Eugene, Oregon).

    Techniques:

    LD decay (mean r 2 ) estimated in three populations (as defined by population genetic structure) using 3321 desi (A) and 8592 kabuli (B) SNPs, respectively . For LD decay, the r 2 -value of the marker physical distance of 0 kb is considered 1. The plotted curved lines indicate the mean r 2 -values among markers spaced with uniform 100 kb physical intervals from 0 to 1000 kb. The plotted line in uppermost panel I indicate the mean r 2 -values among markers spaced with uniform 10 kb physical intervals from 0 to 100 kb. The marked line in panels I, II indicate the mean r 2 -values among markers spaced with uniform 10 and 20 kb physical intervals from 0 to 100 kb and 0 to 200 kb, respectively. “All” includes the LD decay across entire three populations.

    Journal: Frontiers in Plant Science

    Article Title: Employing genome-wide SNP discovery and genotyping strategy to extrapolate the natural allelic diversity and domestication patterns in chickpea

    doi: 10.3389/fpls.2015.00162

    Figure Lengend Snippet: LD decay (mean r 2 ) estimated in three populations (as defined by population genetic structure) using 3321 desi (A) and 8592 kabuli (B) SNPs, respectively . For LD decay, the r 2 -value of the marker physical distance of 0 kb is considered 1. The plotted curved lines indicate the mean r 2 -values among markers spaced with uniform 100 kb physical intervals from 0 to 1000 kb. The plotted line in uppermost panel I indicate the mean r 2 -values among markers spaced with uniform 10 kb physical intervals from 0 to 100 kb. The marked line in panels I, II indicate the mean r 2 -values among markers spaced with uniform 10 and 20 kb physical intervals from 0 to 100 kb and 0 to 200 kb, respectively. “All” includes the LD decay across entire three populations.

    Article Snippet: These libraries were pooled together (following Elshire et al., ; Spindel et al., ) and sequenced (100-bp single end) using Illumina HiSeq 2000.

    Techniques: Marker

    A genome scan plot depicting the density of SNPs physically mapped across eight chromosomes of desi (A) and kabuli (B) genomes at 100-kb sliding window . The SNP density is represented by the number of SNPs mapped within 1-Mb physical intervals across chromosomes.

    Journal: Frontiers in Plant Science

    Article Title: Employing genome-wide SNP discovery and genotyping strategy to extrapolate the natural allelic diversity and domestication patterns in chickpea

    doi: 10.3389/fpls.2015.00162

    Figure Lengend Snippet: A genome scan plot depicting the density of SNPs physically mapped across eight chromosomes of desi (A) and kabuli (B) genomes at 100-kb sliding window . The SNP density is represented by the number of SNPs mapped within 1-Mb physical intervals across chromosomes.

    Article Snippet: These libraries were pooled together (following Elshire et al., ; Spindel et al., ) and sequenced (100-bp single end) using Illumina HiSeq 2000.

    Techniques:

    Gene Correlation Network Analysis (A) Hierarchical cluster dendrogram groups 21,143 genes into distinct co-expression modules identified using weighted gene correlation network analysis. Six major modules are indicated as colored boxes (Mod1, black; Mod2, salmon; Mod3, brown; Mod4, yellow; Mod5, midnight blue; Mod6, blue). (B) Heatmap showing relative expression of genes in the six major modules across ten samples of two sexes. The color values are the standardized Z scores of gene expression. (C) Percentage of genes that are previously known to be enriched in specific cells or tissues across different modules. Previously known gene lists include for panneural enriched ( Spencer et al., 2011 ), sperm and oocyte enriched ( Reinke et al., 2004 ), and cuticle collagen enriched ( Page and Johnstone, 2007 ). Number of genes was normalized in order to avoid the effect of different module sizes (y axis). (D and E) Tissue-specific expression of reporter transgenes for two C-type lectin domain ( clec ) genes chosen from Mod1 (D) and Mod3 (E) in both sexes. Arrow indicates expression in head neurons in (D) or in vas deferens of male in (E). The magnified view of the arrowed region is shown at the bottom of each image. In all images, anterior is left and posterior is right. The scale bars represent 100 μm.

    Journal: Cell reports

    Article Title: Gene Function Prediction Based on Developmental Transcriptomes of the Two Sexes in C. elegans

    doi: 10.1016/j.celrep.2016.09.051

    Figure Lengend Snippet: Gene Correlation Network Analysis (A) Hierarchical cluster dendrogram groups 21,143 genes into distinct co-expression modules identified using weighted gene correlation network analysis. Six major modules are indicated as colored boxes (Mod1, black; Mod2, salmon; Mod3, brown; Mod4, yellow; Mod5, midnight blue; Mod6, blue). (B) Heatmap showing relative expression of genes in the six major modules across ten samples of two sexes. The color values are the standardized Z scores of gene expression. (C) Percentage of genes that are previously known to be enriched in specific cells or tissues across different modules. Previously known gene lists include for panneural enriched ( Spencer et al., 2011 ), sperm and oocyte enriched ( Reinke et al., 2004 ), and cuticle collagen enriched ( Page and Johnstone, 2007 ). Number of genes was normalized in order to avoid the effect of different module sizes (y axis). (D and E) Tissue-specific expression of reporter transgenes for two C-type lectin domain ( clec ) genes chosen from Mod1 (D) and Mod3 (E) in both sexes. Arrow indicates expression in head neurons in (D) or in vas deferens of male in (E). The magnified view of the arrowed region is shown at the bottom of each image. In all images, anterior is left and posterior is right. The scale bars represent 100 μm.

    Article Snippet: Library preparation followed the protocol described at http://wasp.einstein.yu.edu/index.php/Main_Page , and sequences were determined for 100-bp single-end reads using the Illumina HiSeq2500.

    Techniques: Expressing, Polyacrylamide Gel Electrophoresis

    Identification of Semen Protein Genes (A) Schematic of procedure to identify and validate semen protein genes from the RNA-seq data. (B) The anatomical location of seminal vesicle, valve region, and vas deferens in male gonad (gray). (C) Tissue-specific expression of reporter transgenes for three semen candidate genes in male. Arrows indicate expression in seminal vesicle ( ins-31 ), vas deferens ( F59B2.12 ), and the valve region of vas deferens ( B0207.5 ). Arrowhead indicates signal from co-injection marker ttx-3::GFP . In all images, anterior is left and posterior is right. (D) Protein localization identified using translational reporters for ins-31 and F59B2.12 . The Nomarski images show localization within the vesicular structures in the seminal vesicle region for INS-31 and in vas deferens for F59B2.12 protein. (E) Time course images showing transfer of INS-31 from male to hermaphrodite during mating. To facilitate observation of mating behavior, slower-moving unc-119 mutant hermaphrodites were used. INS-31::sfGFP (green) is visible within the seminal vesicle of a male before spicule insertion (a) and moves into the lumen of vas deferens after insertion until ejaculation (b). During ejaculation, INS-31::sfGFP is transferred into the vulva region of the hermaphrodite (c) and remains diffused in the uterus after mating (d). (F) A Venn diagram showing the comparison of semen candidate gene lists obtained from this study, SPELL, and WormNet. The numbers of candidate genes and genes belonging to Mod3 (parentheses) are indicated. The scale bars represent 100 μm in (C) and 20 μm in (D).

    Journal: Cell reports

    Article Title: Gene Function Prediction Based on Developmental Transcriptomes of the Two Sexes in C. elegans

    doi: 10.1016/j.celrep.2016.09.051

    Figure Lengend Snippet: Identification of Semen Protein Genes (A) Schematic of procedure to identify and validate semen protein genes from the RNA-seq data. (B) The anatomical location of seminal vesicle, valve region, and vas deferens in male gonad (gray). (C) Tissue-specific expression of reporter transgenes for three semen candidate genes in male. Arrows indicate expression in seminal vesicle ( ins-31 ), vas deferens ( F59B2.12 ), and the valve region of vas deferens ( B0207.5 ). Arrowhead indicates signal from co-injection marker ttx-3::GFP . In all images, anterior is left and posterior is right. (D) Protein localization identified using translational reporters for ins-31 and F59B2.12 . The Nomarski images show localization within the vesicular structures in the seminal vesicle region for INS-31 and in vas deferens for F59B2.12 protein. (E) Time course images showing transfer of INS-31 from male to hermaphrodite during mating. To facilitate observation of mating behavior, slower-moving unc-119 mutant hermaphrodites were used. INS-31::sfGFP (green) is visible within the seminal vesicle of a male before spicule insertion (a) and moves into the lumen of vas deferens after insertion until ejaculation (b). During ejaculation, INS-31::sfGFP is transferred into the vulva region of the hermaphrodite (c) and remains diffused in the uterus after mating (d). (F) A Venn diagram showing the comparison of semen candidate gene lists obtained from this study, SPELL, and WormNet. The numbers of candidate genes and genes belonging to Mod3 (parentheses) are indicated. The scale bars represent 100 μm in (C) and 20 μm in (D).

    Article Snippet: Library preparation followed the protocol described at http://wasp.einstein.yu.edu/index.php/Main_Page , and sequences were determined for 100-bp single-end reads using the Illumina HiSeq2500.

    Techniques: RNA Sequencing Assay, Expressing, Injection, Marker, Mutagenesis

    Decreased human endothelial TSP1. (A) Immunofluorescent staining of TSP1 (red) and collagen IV (green) of human CCM and lesion-free brain tissue. Arrowheads, capillary; arrows, venule; asterisks, vascular lumen of CCM lesions. Bar, 100 µm ( n = 2). (B and C) HUVECs were transduced with shKrit1 or shControl using lentivirus. (B) KRIT1-depleted HUVECs expressed ∼50% as much TSP1 protein as control cells (SEM, n = 3). (C) KRIT1 shRNA 55% decrease in KRIT1 mRNA as determined by RT-qPCR (SEM, n = 4). **, P

    Journal: The Journal of Experimental Medicine

    Article Title: Thrombospondin1 (TSP1) replacement prevents cerebral cavernous malformations

    doi: 10.1084/jem.20171178

    Figure Lengend Snippet: Decreased human endothelial TSP1. (A) Immunofluorescent staining of TSP1 (red) and collagen IV (green) of human CCM and lesion-free brain tissue. Arrowheads, capillary; arrows, venule; asterisks, vascular lumen of CCM lesions. Bar, 100 µm ( n = 2). (B and C) HUVECs were transduced with shKrit1 or shControl using lentivirus. (B) KRIT1-depleted HUVECs expressed ∼50% as much TSP1 protein as control cells (SEM, n = 3). (C) KRIT1 shRNA 55% decrease in KRIT1 mRNA as determined by RT-qPCR (SEM, n = 4). **, P

    Article Snippet: RNA libraries were multiplexed and sequenced with 100-bp paired single-end reads (SR100) to a depth of ∼30 million reads per sample on an Illumina HiSeq2500.

    Techniques: Staining, Transduction, shRNA, Quantitative RT-PCR

    TSP1 replacement does not suppress the rise in KLF2 and KLF4 after loss of KRIT1. (A and B) Analysis of TSP1, ZO-1, KLF2, and KLF4 mRNA levels by RT-qPCR in freshly isolated microvasculature from mice at P5 and P7 as indicated. Krit1 fl/fl littermate controls, at each developmental stage, were used to calculate percentage increase or decrease in Krit1 ECKO mice using the following formulas: % increase = 100 × ( X − F )/ F and % decrease = 100 × ABS[( F − X )/ F ], where X and F = mRNA abundance in Krit1 ECKO and Krit1 fl/fl BMECs, respectively (SEM, n = 4 or 6). (C) Representative confocal images of retinal vasculature stained for KLF4 (green), TSP1 (red), or isolectin B4 (turquoise). TSP1 is decreased and KLF4 is increased at areas of condensed vasculature ( n = 5 or 6 mice in each group). Bar, 25 µm. (D and E) Analysis of levels of KLF2 and KLF4 mRNA by RT-qPCR from Krit1 ECKO BMEC (D) or cerebellar tissue from Krit1 ECKO mice (E) treated with 3TSR, TSP1, or vehicle compared with Krit1 fl/fl BMEC or Krit1 fl/fl controls. Data are expressed as percentage increase or decrease in Krit1 ECKO using the same formulas as in A and B (SEM, n = 3 or 4 in each group). (F) HUVECs were transduced with lentivirus encoding shKrit1, KLF2, or KLF4, and the increase in KLF2 or KLF4 mRNA relative to cells transduced with lentivirus encoding GFP was measured by RT-qPCR (SEM, n = 4). (G) HUVECs were transduced with lentivirus encoding ShKrit1, KLF2, or KLF4 as described in F, and the decrease of TSP1 mRNA levels was measured relative to cells transduced with EGFP control lentivirus (SEM, n = 4 or 5). (H) Analysis of TSP1 protein levels in HUVECs transduced with lentivirus encoding KLF2 or KLF4 as assessed by Western blot analysis; lentivirus encoding GFP was used as a control (SEM, n = 4). White lines indicate intervening lanes have been spliced out. (I) Loss of endothelial KRIT1 increases expression of KLF2 and KLF4 transcription factors, contributing to CCM formation by downstream effects including suppressed TSP1 expression. 3TSR (TSP1 derivative) reduces CCM lesion formation by replacing functions of TSP1 such as blocking VEGF signaling. Loss of KRIT1 also leads to ROCK activation in a KLF2-dependent manner, and blocking ROCK can also ameliorate CCMs. Thus, blockade of these and other downstream targets of KLF2 and KLF4 may offer a general strategy to reduce CCM formation in humans. *, P

    Journal: The Journal of Experimental Medicine

    Article Title: Thrombospondin1 (TSP1) replacement prevents cerebral cavernous malformations

    doi: 10.1084/jem.20171178

    Figure Lengend Snippet: TSP1 replacement does not suppress the rise in KLF2 and KLF4 after loss of KRIT1. (A and B) Analysis of TSP1, ZO-1, KLF2, and KLF4 mRNA levels by RT-qPCR in freshly isolated microvasculature from mice at P5 and P7 as indicated. Krit1 fl/fl littermate controls, at each developmental stage, were used to calculate percentage increase or decrease in Krit1 ECKO mice using the following formulas: % increase = 100 × ( X − F )/ F and % decrease = 100 × ABS[( F − X )/ F ], where X and F = mRNA abundance in Krit1 ECKO and Krit1 fl/fl BMECs, respectively (SEM, n = 4 or 6). (C) Representative confocal images of retinal vasculature stained for KLF4 (green), TSP1 (red), or isolectin B4 (turquoise). TSP1 is decreased and KLF4 is increased at areas of condensed vasculature ( n = 5 or 6 mice in each group). Bar, 25 µm. (D and E) Analysis of levels of KLF2 and KLF4 mRNA by RT-qPCR from Krit1 ECKO BMEC (D) or cerebellar tissue from Krit1 ECKO mice (E) treated with 3TSR, TSP1, or vehicle compared with Krit1 fl/fl BMEC or Krit1 fl/fl controls. Data are expressed as percentage increase or decrease in Krit1 ECKO using the same formulas as in A and B (SEM, n = 3 or 4 in each group). (F) HUVECs were transduced with lentivirus encoding shKrit1, KLF2, or KLF4, and the increase in KLF2 or KLF4 mRNA relative to cells transduced with lentivirus encoding GFP was measured by RT-qPCR (SEM, n = 4). (G) HUVECs were transduced with lentivirus encoding ShKrit1, KLF2, or KLF4 as described in F, and the decrease of TSP1 mRNA levels was measured relative to cells transduced with EGFP control lentivirus (SEM, n = 4 or 5). (H) Analysis of TSP1 protein levels in HUVECs transduced with lentivirus encoding KLF2 or KLF4 as assessed by Western blot analysis; lentivirus encoding GFP was used as a control (SEM, n = 4). White lines indicate intervening lanes have been spliced out. (I) Loss of endothelial KRIT1 increases expression of KLF2 and KLF4 transcription factors, contributing to CCM formation by downstream effects including suppressed TSP1 expression. 3TSR (TSP1 derivative) reduces CCM lesion formation by replacing functions of TSP1 such as blocking VEGF signaling. Loss of KRIT1 also leads to ROCK activation in a KLF2-dependent manner, and blocking ROCK can also ameliorate CCMs. Thus, blockade of these and other downstream targets of KLF2 and KLF4 may offer a general strategy to reduce CCM formation in humans. *, P

    Article Snippet: RNA libraries were multiplexed and sequenced with 100-bp paired single-end reads (SR100) to a depth of ∼30 million reads per sample on an Illumina HiSeq2500.

    Techniques: Quantitative RT-PCR, Isolation, Mouse Assay, Staining, Transduction, Western Blot, Expressing, Blocking Assay, Activation Assay

    TSP1 derivative, 3TSR, prevents CCMs and retinal vascular lesions in Krit1 ECKO mice. (A) Experimental protocol: vehicle or 3TSR (1.6 mg/Kg) was administered by retroorbital plexus injection at P5 and P6, and brains and retinas were analyzed at P7. (B) Prominent lesions are present in the cerebellum of Krit1 ECKO mice, whereas administration of 3TSR suppressed lesion formation. (C) Hematoxylin and eosin staining of cerebellar sections from Krit1 ECKO mice after treatment with 3TSR or vehicle ( n = 4 mice in each group). (D) Representative image of whole-mount P7 retinal vasculature at the angiogenic growth front. The marked area in Krit1 ECKO whole-mount retina shows decreased areas of condensed vascular plexus in Krit1 ECKO treated with 3TSR compared with vehicle-treated Krit1 ECKO littermates (SEM, n = 8 mice in each group). (E) Quantification of lesion coverage in Krit1 ECKO mice treated with 3TSR or Vehicle (SEM, n = 8 mice in each group). (F) Administered 3TSR is present in CCM. 3TSR was injected retroorbitally into a Krit1 ECKO ;Thbs1 −/− mouse. After 30 min, the mouse was killed, and its cerebellar cortex was stained for 3TSR (red, using anti-TSP1 antibodies) and endothelial marker PECAM1 (green); DAPI staining (blue) was used to reveal nuclei. 3TSR is observed in CCM. (G) Higher-magnification images of boxed areas in F. (F and G) Asterisks, vascular lumen of CCM. Bars: (B) 1 mm; (C and F) 100 µm; (D) 200 µm; (G) 50 µm. ***, P

    Journal: The Journal of Experimental Medicine

    Article Title: Thrombospondin1 (TSP1) replacement prevents cerebral cavernous malformations

    doi: 10.1084/jem.20171178

    Figure Lengend Snippet: TSP1 derivative, 3TSR, prevents CCMs and retinal vascular lesions in Krit1 ECKO mice. (A) Experimental protocol: vehicle or 3TSR (1.6 mg/Kg) was administered by retroorbital plexus injection at P5 and P6, and brains and retinas were analyzed at P7. (B) Prominent lesions are present in the cerebellum of Krit1 ECKO mice, whereas administration of 3TSR suppressed lesion formation. (C) Hematoxylin and eosin staining of cerebellar sections from Krit1 ECKO mice after treatment with 3TSR or vehicle ( n = 4 mice in each group). (D) Representative image of whole-mount P7 retinal vasculature at the angiogenic growth front. The marked area in Krit1 ECKO whole-mount retina shows decreased areas of condensed vascular plexus in Krit1 ECKO treated with 3TSR compared with vehicle-treated Krit1 ECKO littermates (SEM, n = 8 mice in each group). (E) Quantification of lesion coverage in Krit1 ECKO mice treated with 3TSR or Vehicle (SEM, n = 8 mice in each group). (F) Administered 3TSR is present in CCM. 3TSR was injected retroorbitally into a Krit1 ECKO ;Thbs1 −/− mouse. After 30 min, the mouse was killed, and its cerebellar cortex was stained for 3TSR (red, using anti-TSP1 antibodies) and endothelial marker PECAM1 (green); DAPI staining (blue) was used to reveal nuclei. 3TSR is observed in CCM. (G) Higher-magnification images of boxed areas in F. (F and G) Asterisks, vascular lumen of CCM. Bars: (B) 1 mm; (C and F) 100 µm; (D) 200 µm; (G) 50 µm. ***, P

    Article Snippet: RNA libraries were multiplexed and sequenced with 100-bp paired single-end reads (SR100) to a depth of ∼30 million reads per sample on an Illumina HiSeq2500.

    Techniques: Mouse Assay, Injection, Staining, Marker

    Altered tight junctions are an early phenotypic consequence of Krit1 inactivation. (A) Representative confocal images of ZO-1 (red), claudin5 (CLDN5; turquoise), and VE-cadherin (green) staining in primary BMEC Krit1 ECKO or control Krit1 fl/fl BMECs. Nuclei were counterstained with DAPI (blue; n = 4). Arrows indicate loss of tight junctions but not adherence junctions. (B) Quantification of brain endothelial ZO-1, claudin5, and VE-cadherin protein as assessed by Western blot analysis in Krit1 ECKO compared with Krit1 fl/fl BMEC controls (SEM, n = 3 or 4). (C) Confocal microscopy of cerebellar cortex at P7 stained with anti-PECAM1 (green). (D) Higher-magnification images of boxed areas in C stained for ZO-1 (red), claudin5 (turquoise), and PECAM1 (green). Arrows, staining of tight junction proteins ZO-1 and claudin5; asterisks, vascular lumen of CCM ( n = 3). (E) Quantification of brain endothelial ZO-1, claudin5, and VE-cadherin protein abundance in freshly isolated cerebellar microvasculature in Krit1 ECKO compared with Krit1 fl/fl littermate controls (SEM, n = 3 or 4). (F) Maximum-intensity projection of whole-mount P7 retinal vasculature at the angiogenic growth front stained for ZO-1 (red), claudin5 (turquoise), and an endothelial marker, isolectin B4 (green). (G) Higher-magnification images of boxed areas in F show staining for ZO-1 (red), claudin5 (turquoise), and isolectin B4 (green). (H) Quantification of ZO-1 and claudin5 protein expression in retinal vasculature at the angiogenic front in Krit1 ECKO compared with Krit1 fl/fl littermate controls (SEM, n = 6 mice per group). Bars: (A) 50 µm; (C) 100 µm; (D, F, and G) 25 µm. *, P

    Journal: The Journal of Experimental Medicine

    Article Title: Thrombospondin1 (TSP1) replacement prevents cerebral cavernous malformations

    doi: 10.1084/jem.20171178

    Figure Lengend Snippet: Altered tight junctions are an early phenotypic consequence of Krit1 inactivation. (A) Representative confocal images of ZO-1 (red), claudin5 (CLDN5; turquoise), and VE-cadherin (green) staining in primary BMEC Krit1 ECKO or control Krit1 fl/fl BMECs. Nuclei were counterstained with DAPI (blue; n = 4). Arrows indicate loss of tight junctions but not adherence junctions. (B) Quantification of brain endothelial ZO-1, claudin5, and VE-cadherin protein as assessed by Western blot analysis in Krit1 ECKO compared with Krit1 fl/fl BMEC controls (SEM, n = 3 or 4). (C) Confocal microscopy of cerebellar cortex at P7 stained with anti-PECAM1 (green). (D) Higher-magnification images of boxed areas in C stained for ZO-1 (red), claudin5 (turquoise), and PECAM1 (green). Arrows, staining of tight junction proteins ZO-1 and claudin5; asterisks, vascular lumen of CCM ( n = 3). (E) Quantification of brain endothelial ZO-1, claudin5, and VE-cadherin protein abundance in freshly isolated cerebellar microvasculature in Krit1 ECKO compared with Krit1 fl/fl littermate controls (SEM, n = 3 or 4). (F) Maximum-intensity projection of whole-mount P7 retinal vasculature at the angiogenic growth front stained for ZO-1 (red), claudin5 (turquoise), and an endothelial marker, isolectin B4 (green). (G) Higher-magnification images of boxed areas in F show staining for ZO-1 (red), claudin5 (turquoise), and isolectin B4 (green). (H) Quantification of ZO-1 and claudin5 protein expression in retinal vasculature at the angiogenic front in Krit1 ECKO compared with Krit1 fl/fl littermate controls (SEM, n = 6 mice per group). Bars: (A) 50 µm; (C) 100 µm; (D, F, and G) 25 µm. *, P

    Article Snippet: RNA libraries were multiplexed and sequenced with 100-bp paired single-end reads (SR100) to a depth of ∼30 million reads per sample on an Illumina HiSeq2500.

    Techniques: Staining, Western Blot, Confocal Microscopy, Isolation, Marker, Expressing, Mouse Assay

    Loss of KRIT1 inhibits the expression of TSP1. (A) Genome-wide RNA-seq from three independent biological replicates followed by gene ontology analysis of genes differentially expressed in Krit1 ECKO BMECs compared with Krit1 fl/fl BMECs. Each term listed was the top term in a cluster of related terms, and the corrected p-values were calculated according to Benjamini’s method ( Huang et al., 2009 ). (B) Expression levels of differentially expressed genes represented on a scatter plot; fragments per kilobase of transcript per million mapped reads (FPKM) of individual transcripts are represented on a log2 scale. A few of the most highly suppressed and up-regulated genes are labeled. (C) RT-qPCR confirmation of RNA-seq–identified marked decrease in mRNA of extracellular regulators of angiogenesis in Krit1 ECKO BMECs compared with Krit1 fl/fl BMECs (SEM, n = 3). (D) Quantification of TSP1 protein from three independent biological replicates in Krit1 ECKO (KO) and in Krit1 fl/fl (Flox) BMECs (SEM, n = 3). (E) RT-qPCR analysis of isolated brain microvasculature in Krit1 ECKO compared with Krit1 fl/fl littermate controls (SEM, n = 3). (F) Quantification of TSP1 protein from freshly isolated brain microvasculature in Krit1 ECKO (KO) compared with Krit1 fl/fl (Flox) littermate controls (SEM, n = 3). (G) Confocal microscopy of cerebellar cortex stained for TSP1 (red) and endothelial specific marker PECAM1 (green); DAPI staining (blue) was used to reveal nuclei ( n = 3). (H) Higher-magnification images of boxed areas in G. TSP1 protein expression was decreased in CCM from Krit1 ECKO mice (arrows). Asterisks, vascular lumen of CCM lesions. Bars: (G) 100 µm; (H) 25 µm. *, P

    Journal: The Journal of Experimental Medicine

    Article Title: Thrombospondin1 (TSP1) replacement prevents cerebral cavernous malformations

    doi: 10.1084/jem.20171178

    Figure Lengend Snippet: Loss of KRIT1 inhibits the expression of TSP1. (A) Genome-wide RNA-seq from three independent biological replicates followed by gene ontology analysis of genes differentially expressed in Krit1 ECKO BMECs compared with Krit1 fl/fl BMECs. Each term listed was the top term in a cluster of related terms, and the corrected p-values were calculated according to Benjamini’s method ( Huang et al., 2009 ). (B) Expression levels of differentially expressed genes represented on a scatter plot; fragments per kilobase of transcript per million mapped reads (FPKM) of individual transcripts are represented on a log2 scale. A few of the most highly suppressed and up-regulated genes are labeled. (C) RT-qPCR confirmation of RNA-seq–identified marked decrease in mRNA of extracellular regulators of angiogenesis in Krit1 ECKO BMECs compared with Krit1 fl/fl BMECs (SEM, n = 3). (D) Quantification of TSP1 protein from three independent biological replicates in Krit1 ECKO (KO) and in Krit1 fl/fl (Flox) BMECs (SEM, n = 3). (E) RT-qPCR analysis of isolated brain microvasculature in Krit1 ECKO compared with Krit1 fl/fl littermate controls (SEM, n = 3). (F) Quantification of TSP1 protein from freshly isolated brain microvasculature in Krit1 ECKO (KO) compared with Krit1 fl/fl (Flox) littermate controls (SEM, n = 3). (G) Confocal microscopy of cerebellar cortex stained for TSP1 (red) and endothelial specific marker PECAM1 (green); DAPI staining (blue) was used to reveal nuclei ( n = 3). (H) Higher-magnification images of boxed areas in G. TSP1 protein expression was decreased in CCM from Krit1 ECKO mice (arrows). Asterisks, vascular lumen of CCM lesions. Bars: (G) 100 µm; (H) 25 µm. *, P

    Article Snippet: RNA libraries were multiplexed and sequenced with 100-bp paired single-end reads (SR100) to a depth of ∼30 million reads per sample on an Illumina HiSeq2500.

    Techniques: Expressing, Genome Wide, RNA Sequencing Assay, Labeling, Quantitative RT-PCR, Isolation, Confocal Microscopy, Staining, Marker, Mouse Assay