|
| Status |
Public on Dec 31, 2022 |
| Title |
hNSC_cGP1 |
| Sample type |
SRA |
| |
|
| Source name |
Neural stem cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: Human fetal neural stem cells isolated from human cerebral cortex from male fetus at embryonic week 14
treatment: 1 mM cGP for 4 h
|
| Treatment protocol |
cGP and/or H2O2 treated to hfNSCs for 4h
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol reagents were used for the extraction of total RNA.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Sequencing data were analyzed using an open bioinformatics tool for the quick analysis of RNA-seq data RaNA-seq
FASTQ files are pre-processed with the Fastp tool, and the expression quantification is performed with Salmon
The quality of the raw date was represented some graphs produced by the package RJSplot
the distances between plots in the graphs are calculated with SERE
DEseq2 was used to identify the differentially expressed genes (DEGs) with more than two-fold changes in transcripts per million (TPM) between control and cGP, H2O2, or H2O2+cGP-treated groups
Genome_build: hg19
Supplementary_files_format_and_content: Excel files include differential expression analysis for comparision between two exerimental groups. Expression levels in mRNA are calculated as TPMs values using salmon (Patro et al., Nat Methods., 2017)
Supplementary_files_format_and_content: DE_cont_vs_cGP.xlsx: Comparision of abundance measurements between control and cGP
Supplementary_files_format_and_content: DE_cont_vs_H2O2.xlsx: Comparision of abundance measurements between control and H2O2
Supplementary_files_format_and_content: DE_cont_vs_H2O2+cGP.xlsx: Comparision of abundance measurements between control and H2O2+cGP
Supplementary_files_format_and_content: DE_H2O2_vs_H2O2+cGP.xlsx: Comparision of abundance measurements between H2O2 and H2O2+cGP
|
| |
|
| Submission date |
Oct 05, 2021 |
| Last update date |
Oct 10, 2023 |
| Contact name |
Kazutoshi Murotomi |
| E-mail(s) |
k-murotomi@aist.go.jp
|
| Organization name |
Advanced Industrial Science and Technology
|
| Street address |
1-1-1 Higashi
|
| City |
Tsukuba |
| ZIP/Postal code |
305-8566 |
| Country |
Japan |
| |
|
| Platform ID |
GPL24676 |
| Series (1) |
| GSE185324 |
RNA-seq data of cGP-treated human fetal neural stem cells |
|
| Relations |
| BioSample |
SAMN22060723 |
| SRA |
SRX12488038 |
