|
| Status |
Public on Oct 25, 2021 |
| Title |
NGP_DMSO_1 |
| Sample type |
SRA |
| |
|
| Source name |
Neuroblastoma
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: NGP
treatment protocol: DMSO, 6 days
|
| Growth protocol |
Cells were grown in 6-well plates in RPMI media containing 10% FBS and 1% pen-strep. Cells were treated with DMSO or ATRA (5uM) for 6 days.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Libraries were prepared using Illumina TruSeq stranded specific sample preparation kits from 500ng of purified total RNA according to the manufacturer’s protocol. Finished dsDNA libraries were quantified by Qubit fluorometer, Agilent TapeStation 4200, and RT-qPCR using the Roche Kapa Biosystems library quantification kit according to manufacturer’s protocols. Indexed libraries were pooled in equimolar ratios and sequenced on an Illumina NextSeq 550 with single-end 75bp reads by the Dana-Farber Cancer Institute Molecular Biology Core Facilities.
Cells were collected directly into Trizol and ERCC-spike in RNA was added directly to the suspension, normalized to cell number. RNA from the aqueous phase was then purified using QIAgen RNeasy columns according to the manufacturer’s protocol, and eluted in 30 uL RNase-free water.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Reads were aligned to a reference genome containing the non-random chromosomes from hg19 and the sequences of ERCC probes using hisat2 with parameters --no-novel-juncs and -G set to a gene database file downloaded from RefSeq on 7/5/2017 to which positions of the ERCC probes were added. Coverage of the genes in this list was calculated using htseq-count with parameters -i gene_id --stranded=reverse -f bam -m intersection-strict.
Supplementary_files_format_and_content: Counts files represent the number of reads quantified for each gene using htseq-count
|
| |
|
| Submission date |
Jul 23, 2020 |
| Last update date |
Oct 25, 2021 |
| Contact name |
Richard A Young |
| E-mail(s) |
young_computation@wi.mit.edu
|
| Phone |
617-258-5219
|
| Organization name |
Whitehead Institute for Biomedical Research
|
| Lab |
Young Lab
|
| Street address |
9 Cambridge Center
|
| City |
Cambridge |
| State/province |
MA |
| ZIP/Postal code |
02142 |
| Country |
USA |
| |
|
| Platform ID |
GPL18573 |
| Series (2) |
| GSE155000 |
Retinoic acid rewires the adrenergic core regulatory circuitry of neuroblastoma but can be subverted by enhancer hijacking of MYC or MYCN (RNA-Seq) |
| GSE155002 |
Retinoic acid rewires the adrenergic core regulatory circuitry of neuroblastoma but can be subverted by enhancer hijacking of MYC or MYCN |
|
| Relations |
| BioSample |
SAMN15630027 |
| SRA |
SRX8814894 |
