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| Status |
Public on Mar 01, 2017 |
| Title |
CDH1+/THY1+ WT1 |
| Sample type |
SRA |
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| Source name |
male germline stem cells
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| Organism |
Mus musculus |
| Characteristics |
cell type: CDH1+/THY1+
passage: 6 to 8
strain: C57BL/6
age: 5 weeks
gender: male
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| 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.
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| 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.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| 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
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| Submission date |
Nov 30, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Aaron Buechlein |
| E-mail(s) |
abuechle@indiana.edu
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| Organization name |
Indiana University
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| Department |
Center for Genomics and Bioinformatics
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| Street address |
1001 E 3rd St
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| City |
Bloomington |
| State/province |
IN |
| ZIP/Postal code |
47405 |
| Country |
USA |
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| Platform ID |
GPL19057 |
| Series (1) |
| GSE90712 |
RNA sequencing of CDH1+/THY1+ and CDH1-/THY1+ germline stem cells |
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| Relations |
| BioSample |
SAMN06077134 |
| SRA |
SRX2384328 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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