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Sample GSM1639326 Query DataSets for GSM1639326
Status Public on Jun 30, 2019
Title FAPLung3
Sample type SRA
 
Source name FAP Lung
Organism Mus musculus
Characteristics tissue: Lung
cell type: FAP
Extracted molecule total RNA
Extraction protocol Total RNA extracted with Trizol Lysis Reagent (Invitrogen, Carlsbad, CA, USA) and purified using RNeasy Micro kit (Qiagen) per manufacturer's instructions. The RNA integrity (RNA Integrity Score >= 7) and quantity determined on the Agilent 2100 Bioanalyzer (Agilent; Palo Alto, CA, USA) per manufacturer's recommendation and subjected to Illumina library prep for RNAseq.
RNA libraries were prepared for sequencing using standard Illumina protocols
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 1500
 
Data processing Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the mm10 genome using Bowtie version 2.1.0.0 (Phred 33)
Count files generated using HTSeq: http://bioinformatics.oxfordjournals.org/content/31/2/166 and EdgeR: Empirical analysis of digital gene expression data in R, see http://www.bioconductor.org/packages/release/bioc/html/edgeR.html
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file includes raw count values for each sample
 
Submission date Mar 20, 2015
Last update date Jun 30, 2019
Contact name Paul A Wilson
E-mail(s) paul.a.wilson@gsk.com
Organization name GSK
Department Target Sciences
Lab Computational Biology
Street address GlaxoSmithKline Medicine Research Centre
City Stevenage
State/province Hertfordshire
ZIP/Postal code SG1 2NY
Country United Kingdom
 
Platform ID GPL18480
Series (1)
GSE67117 Identifying signals from the skeletal muscle niche that regulate satellite cell function
Relations
BioSample SAMN03435911
SRA SRX962809

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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