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Sample GSM3602074 Query DataSets for GSM3602074
Status Public on Feb 13, 2019
Title 17927_WT rep1
Sample type SRA
Source name WT_lung
Organism Mus musculus
Characteristics strain background: C57BL/6
age: post natal day 14
genotype/variation: wild type; Gli1creERT:mTmG
tissue: Lung
cell type: GFP+ cells; secondary crest myofibroblasts (SCMF)
Extracted molecule total RNA
Extraction protocol Lungs were dissected from mouse pups at PN14; cells were separated using gentleMACS dissociator; GFP+ cells were collected by FACs; RNA was extracted using Qiagen RNeasy micro kit; total RNA was sent to the sequencing facility at Caltech for sequencing.
RNA libraries were prepared for sequencing using standard Illumina protocols
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
Description 17927_CAGATC_L00*
Data processing The unaligned raw reads were processed on PartekFlow platform.
Reads alignment and gene annotation & quantification were based on mouse genome (mm10) and transcriptome (GENECODE genes-release 7); Tophat2 and Upper Quartile were algorithms used for mapping and normalization; Differential Gene Expression was done with PartekFlow’s Gene Specific Analysis (GSA).
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include gene ID, total counts, FDR, Fold change
Submission date Feb 12, 2019
Last update date Feb 13, 2019
Contact name Fremont Gao
Organization name USC
Street address 2011 Zonal Ave, HMR 903
City Los Angeles
State/province California
ZIP/Postal code 90033
Country USA
Platform ID GPL17021
Series (1)
GSE126457 The Secondary Crest Myofibroblast PDGFRa Controls Elastogenesis Pathway via a Secondary Tier of Signaling Networks During Alveogenesis
BioSample SAMN10921472
SRA SRX5369380

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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