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Sample GSM5014763 Query DataSets for GSM5014763
Status Public on Jun 13, 2021
Title 6day_KITneg_rep1
Sample type SRA
 
Source name Spermatogonial stem cell (SSC)
Organism Mus musculus
Characteristics strain: B6;CBA-Tg(Pou5f1-EGFP)2Mnn/J
cell source: Oct4-GFP+ germ cells
age: 6 days
Extracted molecule total RNA
Extraction protocol 1 million primary cells of each population in two independent experiments were FACS-sorted as described above. Total RNA was isolated from each cell fraction using the AllPrep DNA/RNA Mini kit (Qiagen, Valencia, CA, USA) according to the manufacturer's instructions. RNA yield and purity were evaluated using a NanoDrop 1000 spectrophotometer (NanoDrop Technologies/Thermo Scientific, Waltham, MA). Quality and integrity were determined by RNA 6000 Nano kit with a Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA). The ratio of absorbance at 260 and 280 nm was ≥1.9 and the RNA integrity number (RIN) was >9 for all samples.
Sequencing libraries were prepared with ribosomal RNA (rRNA) depletion using a Ribo-Zero Gold kit (Epicentre) followed by Apollo 324 NGS Library Prep System (WaferGen Biosystems, Fremont, CA, USA).
Sequencing libraries were prepared with ribosomal RNA (rRNA) depletion using a Ribo-Zero Gold kit (Epicentre) followed by Apollo 324 NGS Library Prep System (WaferGen Biosystems, Fremont, CA, USA). The prepared libraries were sequenced on an Illumina HiSeq 2000 (Illumina, San Diego, CA) with 100 base pairs (bp) paired-end RNA-Seq reads.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
 
Description KIT- cells from 6-day-old mice
Data processing Raw reads were pre-processed with trim-galore for trimming Illumina adaptor sequences.
Counts were assigned to genes defined by the Ensembl (release 67) annotation using RSEM.
Genome_build: mm9
Supplementary_files_format_and_content: Text file with RPKM.
 
Submission date Jan 11, 2021
Last update date Jun 14, 2021
Contact name Jinyue Liao
E-mail(s) liaojinyue@cuhk.edu.hk
Organization name The Chinese University of Hong Kong
Department Department of Chemical Pathology
Street address Room 38016, 1/F Lui Che Woo Clinical Sciences Building
City Hong Kong
ZIP/Postal code 000000
Country Hong Kong
 
Platform ID GPL13112
Series (2)
GSE164604 Transcriptomic profiling of young and aged spermatogonial stem cells (RNA-Seq)
GSE164607 Transcriptomic and epigenomic profiling of young and aged spermatogonial stem cells reveals molecular targets regulating differentiation
Relations
BioSample SAMN17284734
SRA SRX9823192

Supplementary file Size Download File type/resource
GSM5014763_6dayneg1.txt.gz 218.9 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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