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Sample GSM2411057 Query DataSets for GSM2411057
Status Public on Mar 01, 2017
Title CDH1+/THY1+ WT1
Sample type SRA
Source name male germline stem cells
Organism Mus musculus
Characteristics cell type: CDH1+/THY1+
passage: 6 to 8
strain: C57BL/6
age: 5 weeks
gender: male
Growth protocol GSCs were cultured on DR4 MEFs. GSC medium was used for GSCs maintenance, including StemPro-34 (Gibco), StemPro supplement (1X, Gibco); MEM vitamin solution (1X, Gibco); non-essentialamino acid solution (1X, Gibco); Antibiotic-Antimycotic (1X, Gibco); L-glutamine (1X, Hyclone); estradiol (Sigma), 30 ng/ml; progesterone (Sigma), 60ng/ml; fetal bovine serum (Hyclone), 1%; transferrin (Sigma), 100 ug/ml; insulin (Gibco), 25 ug/ml; Rat GDNF (peprotech), 10 ng/ml; human FGF (peprotech), 10 ng/ml; putrescine (Sigma),60 um; selenite (Sigma), 30 nM; pyruvic acid (Sigma), 30 ug/ml; lactic acid, 0.06% (Sigma), b-mercaptoethanol (Sigma), 50 uM; ascorbic acid (Sigma), 100 uM; D-biotin (Sigma), 10 ug/ml; D-glucose (Sigma), 6 mg/ml; BSA (Calbiochem), 5 mg/ml.
Extracted molecule total RNA
Extraction protocol RNAs were isolated using RNeasy-plus micro kit (74034, Qiagen).
Libraries for each sample were constructed using the Illumina TruSeq Stranded Total RNA Library Prep Kit / Ribo-Zero Gold kit as per manufacturer’s instructions. Libraries were quantified using an Agilent 2200 TapeStation, pooled equimolar and sequenced on an Illumina NextSeq500 instrument using a NextSeq150-v2 Mid Output reagent kit and flowcells.
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
Data processing Sequenced reads were trimmed using Trimmomatic V 0.32 for adaptor sequence and low-quality sequence. Remaining paired reads were then mapped to GRCm38.p4 whole genome using tophat2 v2.1.1 with parameters --b2-very-sensitive --read-edit-dist 2 --max-multihits 100
Mapped reads were quantified using featureCounts from the Subread v1.5.0-p3 package, with the following parameters: -p -t exon -g gene_id -s 2 -T 32 and gencode vM9 as the annotation.
DESeq2 V1.12.3 (R version 3.3.1) was used to perform fold-change analysis on the raw counts table.
Genome_build: GRCm38.p4
Supplementary_files_format_and_content: tab-delimited text file includes the DESeq2 fold-change results
Submission date Nov 30, 2016
Last update date May 15, 2019
Contact name Aaron Buechlein
Organization name Indiana University
Department Center for Genomics and Bioinformatics
Street address 1001 E 3rd St
City Bloomington
State/province IN
ZIP/Postal code 47405
Country USA
Platform ID GPL19057
Series (1)
GSE90712 RNA sequencing of CDH1+/THY1+ and CDH1-/THY1+ germline stem cells
BioSample SAMN06077134
SRA SRX2384328

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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