|
| Status |
Public on Nov 02, 2023 |
| Title |
GC-2 cells, DMSO, normoxia 24h, 3 [ND3] |
| Sample type |
SRA |
| |
|
| Source name |
mouse type B spermatogonia
|
| Organism |
Mus musculus |
| Characteristics |
tissue: mouse type B spermatogonia
cell line: GC-2 cells
cell type: mouse type B spermatogonia GC-10 cells
genotype: WT
treatment: DMSO, normoxia 24h
|
| Treatment protocol |
GC-2 cells were incubated with MLN4924 (1 μM) or DMSO as control, and then the cells were cultured under normoxia or hypoxia for 24 hours. GC-2 Cells were incubated under the hypoxic condition (1% O2, 5% CO2, and balanced with N2) in an NBS Galaxy 48R incubator.
|
| Growth protocol |
GC-2 cells, originally from the National Collection of Authenticated Cell Cultures, China, were cultivated in Dulbeccos’ modified Eagle medium (DMEM) (VivaCell) with 10% fetal bovine serum (FBS) at 37℃ in an incubator containing 5% CO2.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNAs were extracted using RNAiso Plus (TaKaRa Bio),and then purified using the RNeasy Mini Kit (QIAGEN, 74104).
Sequencing libraries were prepared using the NEBNext Ultra RNA Library Prep Kit for Illumina (NEB, USA, #E7530L) according to the manufacturer’s protocol. Qualified libraries were pooled and sequenced on Illumina NovaSeq platforms using PE150 strategy at Wuhan Benagen Technology Co., Ltd. (Wuhan, China).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Fastp version 0.21.0 (https://github.com/OpenGene/fastp) was used to perform basic statistics on the quality of the raw reads. The data processing steps were as follows: discard a paired reads if either one read contains adapter contamination; discard a paired reads if more than 10% of bases are uncertain in either read; discard a paired reads if the proportion of low quality (Phred quality <5) bases is over 50% in either one read.
The clean reads were mapped to the mouse reference genome (http://ftp.ensembl.org/pub/current_fasta/mus_musculus/) using Star version 2.7.9a (https://github.com/alexdobin/STAR).
RSEM version 1.3.3 (https://github.com/deweylab/RSEM) was used to calculate read counts of genes and transcripts.
Assembly: mm39
Supplementary files format and content: tab-delimited text file includes FPKM values for each Sample
|
| |
|
| Submission date |
Oct 22, 2023 |
| Last update date |
Nov 02, 2023 |
| Contact name |
Hongyan Deng |
| E-mail(s) |
dhy0917@126.com
|
| Organization name |
Wuhan University
|
| Street address |
299 Bayi Road, Wuchang District
|
| City |
Wuhan |
| ZIP/Postal code |
430000 |
| Country |
China |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE245989 |
Inhibiting neddylation with MLN4924 potentiates hypoxia-induced apoptosis of mouse type B spermatogonia GC-2 cells |
|
| Relations |
| BioSample |
SAMN37920523 |
| SRA |
SRX22167725 |
