|
| Status |
Public on Jan 02, 2025 |
| Title |
RNAseq_KIT+_dSPG_Zbtb16_Null_rep2 |
| Sample type |
SRA |
| |
|
| Source name |
spermatogoniall stem cells
|
| Organism |
Mus musculus |
| Characteristics |
cell type: Mouse KIT+ dSPG at P7
genotype: Zbtb16 null
genotype: Zbtb16 null
|
| Growth protocol |
Testes from three mice were pooled for each cell isolation experiment. Single cells were isolated from testes at P7 using 0.25% Trypsin digestion and resuspended in MACS separation buffer (Miltenyi Biotec). Harvested cells used to purify undifferentiated SPG and differentiating SPG using immunomagnetic cell sorting (IMCS) with anti-THY1/CD90.2 (Miltenyi Biotec) and anti-KIT/CD117 (Miltenyi Biotec) antibodies conjugated with magnetic microbeads.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Purified cells were lysed in Trizol and then were purified using Direct-zol RNA mini-prep kit, including DNase I treatment to remove genomic DNA (Zymo research). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Illumina TruSeq Stranded RNA Kit with Ribo-Zero Gold Kit following manufacturer's protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
12223X4
|
| Data processing |
Novoalign
RNA-seq reads for each library were processed to Ensemble annotation NCBI38/mm10 using the Novoalign (http://novocraf.com), followed by trimming the adaptor sequence with the parameters: -o SAM -r All 50 -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCA.
Processed reads were mapped to the mouse mm10 genome using USeq8.9.6 packages, containing DESeq2 to generate FPKM value and analyze differential gene expression with the default parameter adding -x 50000000
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample
|
| |
|
| Submission date |
May 12, 2022 |
| Last update date |
Jan 02, 2025 |
| Contact name |
Bradley R. Carins |
| E-mail(s) |
brad.cairns@hci.utah.edu
|
| Phone |
8015851822
|
| Organization name |
University of Utah
|
| Department |
Oncological Sciences
|
| Lab |
Cairns Lab
|
| Street address |
2000 Circle of Hope
|
| City |
Salt Lake City |
| State/province |
UT |
| ZIP/Postal code |
84112 |
| Country |
USA |
| |
|
| Platform ID |
GPL17021 |
| Series (2) |
| GSE202817 |
ZBTB16/PLZF regulates self-renewal and differentiation of spermatogonial stem cells through an extensive transcription factor-chromatin poising network [RNA-Seq] |
| GSE202819 |
ZBTB16/PLZF regulates juvenile spermatogonial stem cell development via an extensive transcription factor poising network |
|
| Relations |
| BioSample |
SAMN28202695 |
| SRA |
SRX15241072 |
