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| Status |
Public on Jun 13, 2021 |
| Title |
8month_KITpos_rep1 |
| Sample type |
SRA |
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| Source name |
Spermatogonial progenitor cell
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| Organism |
Mus musculus |
| Characteristics |
strain: B6;CBA-Tg(Pou5f1-EGFP)2Mnn/J
cell source: Oct4-GFP+ germ cells
age: 8 months
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| 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.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
KIT+ cells from 8-month-old mice
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| 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.
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| Submission date |
Jan 11, 2021 |
| Last update date |
Jun 14, 2021 |
| Contact name |
Jinyue Liao |
| E-mail(s) |
liaojinyue@cuhk.edu.hk
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| Organization name |
The Chinese University of Hong Kong
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| Department |
Department of Chemical Pathology
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| Street address |
Room 38016, 1/F Lui Che Woo Clinical Sciences Building
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| City |
Hong Kong |
| ZIP/Postal code |
000000 |
| Country |
Hong Kong |
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| 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 |
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| Relations |
| BioSample |
SAMN17284728 |
| SRA |
SRX9823198 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5014769_8month_kitpos1.txt.gz |
254.0 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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