NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM3959511 Query DataSets for GSM3959511
Status Public on Jul 20, 2020
Title NGP_ARID1A_mut#2
Sample type SRA
 
Source name Neuroblastoma
Organism Homo sapiens
Characteristics cell line: NGP
cell type: ARID1A-/- #2
Growth protocol The NGP neuroblastoma cell line was maintained in RPMI 1640 Medium (GIBCO) supplemented with 10% fetal bovine serum (Sigma) and 1X penicillin-streptomycin (GIBCO),and 0.5ug/ml puromycin (Sigma #P8833).
Extracted molecule polyA RNA
Extraction protocol Total RNA was depleted of ribosomal RNA with the SMARTer Universal Low Input RNA Kit (Clontech). Enriched mRNA was then applied to library preparation according to manufacturer’s protocol (NEBNext Ultra). After repeated quality control for average DNA input size of 300 bp, the samples were sequenced on aIllumina NextSeq 500 with 75bp single-end reads.
RNA libraries were prepared for sequencing using standard Illumina protocols
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
 
Data processing Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using HISAT2 version 2.1.0 with defalt parameters for single end reads.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using GFold version 1.1.2
Genome_build: hg19
 
Submission date Jul 22, 2019
Last update date Jul 20, 2020
Contact name Ting Tao
E-mail(s) taot@zju.edu.cn
Organization name Children's Hospital, Zhejiang University School of Medicine
Lab Ting Tao
Street address 3333 Binsheng Road
City Hangzhou
State/province Zhejiang
ZIP/Postal code 310052
Country China
 
Platform ID GPL18573
Series (2)
GSE134631 ARID1A Loss in Neuroblastoma Promotes the Adrenergic-to-Mesenchymal Transition by Regulating Enhancer-Mediated Gene Expression [RNA-seq]
GSE134632 ARID1A Loss in Neuroblastoma Promotes the Adrenergic-to-Mesenchymal Transition by Regulating Enhancer-Mediated Gene Expression
Relations
BioSample SAMN12335353
SRA SRX6483145

Supplementary file Size Download File type/resource
GSM3959511_Mut2_RNASeq.RPKM.txt.gz 339.4 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap