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Sample GSM4693033 Query DataSets for GSM4693033
Status Public on Oct 25, 2021
Title NBLS_DMSO_1
Sample type SRA
 
Source name Neuroblastoma
Organism Homo sapiens
Characteristics cell type: NBL-S
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 SAMN15630033
SRA SRX8814888

Supplementary file Size Download File type/resource
GSM4693033_NBLS_DMSO_1.counts.txt.gz 107.1 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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