GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Sample GSM1335295 Query DataSets for GSM1335295
Status Public on May 19, 2014
Title RNA-Seq: 48h Normox
Sample type SRA
Source name SK-N-BE(2)
Organism Homo sapiens
Characteristics cell line: SK-N-BE(2)
treatment: normoxia
Treatment protocol 1% O2 or 20% O2 for 48 hours
Growth protocol DMEM with 10% FBS
Extracted molecule total RNA
Extraction protocol hMe-SEAL followed previously described methods(Song et al., Nature Biotechnology, 2011). RNA extracted with Trizol reagent.
Standard Illumina protocols
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
Description RNA-Seq
Data processing hMe-Seal: DNA reads were aligned using BWA aligner
hMe-SEAL: Peaks called using MACS1.4
RNA-Seq: Reads aligned with tophat2 and bowtie2
RNA-Seq: Cufflinks (cufflinks, cuffcompare, cuffdiff) for expression analysis
Genome_build: hg19
Supplementary_files_format_and_content: wig for DNA data; tab-delimited output of FPKM for RNA
Submission date Feb 26, 2014
Last update date May 15, 2019
Contact name Christopher Mariani
Organization name University of Chicago
Street address 900 E 57 St
City Chicago
State/province IL
ZIP/Postal code 60637
Country USA
Platform ID GPL16791
Series (1)
GSE55391 TET1-mediated hydroxymethylation facilitates hypoxic gene induction in neuroblastoma
BioSample SAMN02665662
SRA SRX476316

Supplementary file Size Download File type/resource
GSM1335295_SKNBE2_gene_exp_normoxia_and_hypoxia.txt.gz 382.1 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Processed data provided as supplementary file
Raw data are available in SRA

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