|
| Status |
Public on Dec 21, 2022 |
| Title |
WT_Ventral_rep3 |
| Sample type |
SRA |
| |
|
| Source name |
hESC_derived NPCs
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: hESC_derived NPCs
genotype: wild type
cell line: WA09
cell fate: Ventral
|
| Treatment protocol |
For ventralization, SHH and the smoothened activator purmorphamine were added into the neural induction medium during day10 to day17. To re-introduce ASCL1 expression in ASCL1-RE cell line, Dox was added during day22 to day25.
|
| Growth protocol |
hESCs were broken into small clumps and suspended in hESCM for 4 days to form EBs. The EBs were then switched to neural induction medium to direct cells toward a neuroectoderm (NE) fate for 2 days. At day 6, cell aggregates were plated on laminin-coated culture surface and neural tube-like rosettes could be seen at days 14-17.The neural progenitors were maintained in suspension culture as neurospheres in neural induction medium at day 18 through 25. All samples were collected at day25.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA was isolated using a TRIzol kit (Invitrogen) and used to prepare a library.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
ASCL1_WT_Ventral_D25_NPCs_rep3
|
| Data processing |
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using histat2 with parameters -p 4 --no-unal --dta-cufflinks -k 1
Samtools with -bh -q 50 were used to filter mapping reads
Cuffdiff2 was used for generated the expression level.The expression level of each gene was normalized to Reads Per Kilobase of exon per Megabase of library size (RPKM)
For differential expression analysis, sequencing counts at the gene level were obtained using HTSeq v0.9.1. R package DESeq2 was then used to identify DEGs between different conditions. To assess the significance of differential gene expression, the P-value threshold was set at 0.05 and the fold change was set at 2.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample
|
| |
|
| Submission date |
Apr 22, 2020 |
| Last update date |
Dec 21, 2022 |
| Contact name |
yanhua du |
| E-mail(s) |
yhdu@shsmu.edu.cn
|
| Organization name |
Shanghai Jiaotong University School of Medicine
|
| Department |
Shanghai Institute of Immunology
|
| Street address |
227 South Chongqing Road, Huangpu District
|
| City |
Shanghai |
| ZIP/Postal code |
200025 |
| Country |
China |
| |
|
| Platform ID |
GPL16791 |
| Series (1) |
| GSE149096 |
Role of ASCL1 in human neural development |
|
| Relations |
| BioSample |
SAMN14668232 |
| SRA |
SRX8155328 |
