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| Status |
Public on Nov 06, 2024 |
| Title |
hNSC shSCR KD 72h #3: I21-1460-09 |
| Sample type |
SRA |
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| Source name |
hNSCs
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| Organism |
Homo sapiens |
| Characteristics |
cell line: hNSCs
cell type: H9 human embryonic stem cell-derived neural stem cells
genotype: WT, Control knockdown
time: 72h after transfection
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| Growth protocol |
hNSCs were cultured on Geltrex-coated dishes (GeltrexÔ LDEV-free reduced growth factor membrane matrix, A1413202, Thermo Fisher Scientific) in KnockOutÔ DMEM/F12 (12660012, Invitrogen) supplemented with 2 mM L-Glutamine (25030024, Thermo Fisher Scientific), 20 ng/ml EGF (315-09, Peprotech), 20 ng/ml FGF (100-18B, Peprotech) and 2% of StemProÒ Neural Supplement (A1050801, Thermo Fisher Scientific)
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated using the GenElute™ Mammalian Total RNA Miniprep Kit (Sigma-Aldrich, RTN350-1KT)
Total RNA was prepped using the Illumina TruSEq Stranded mRNA library Prep kit according to the manufacturer's protocol
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Description |
I21-1460-09
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| Data processing |
The Illumina adapter and poly-A sequences were removed from the reads.
The trimmed reads were alligned to the reference genome GRCh38 using HISAT2.
Quantification of the reads was performed using HT-seq count.
Differential gene expression was calculated using EdgeR.
Assembly: GRCh38
Supplementary files format and content: Tab-delimited file including raw counts for each sample
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| Submission date |
Nov 06, 2023 |
| Last update date |
Nov 06, 2024 |
| Contact name |
Raymond A Poot |
| E-mail(s) |
r.poot@erasmusmc.nl
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| Organization name |
Erasmus MC
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| Department |
Cell Biology
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| Street address |
Wytemaweg 80
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| City |
Rotterdam |
| ZIP/Postal code |
3015 GE |
| Country |
Netherlands |
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| Platform ID |
GPL16791 |
| Series (2) |
| GSE247131 |
A CHD8-TRRAP axis facilitates MYC and E2F target gene regulation in human neural stem cells. [RNA-Seq] |
| GSE247133 |
A CHD8-TRRAP axis facilitates MYC and E2F target gene regulation in human neural stem cells. |
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| Relations |
| BioSample |
SAMN38122782 |
| SRA |
SRX22385529 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7884005_I21-1460-09.htseq.txt.gz |
189.1 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
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