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Sample GSM1335293 Query DataSets for GSM1335293
Status Public on May 19, 2014
Title hMe-SEAL: 48 Hypoxia_Rep1
Sample type SRA
Source name SK-N-BE(2)
Organism Homo sapiens
Characteristics cell line: SK-N-BE(2)
treatment: hypoxia
Treatment protocol 1% O2 or 20% O2 for 48 hours
Growth protocol DMEM with 10% FBS
Extracted molecule genomic DNA
Extraction protocol hMe-SEAL followed previously described methods(Song et al., Nature Biotechnology, 2011). RNA extracted with Trizol reagent.
Standard Illumina protocols
Library strategy OTHER
Library source genomic
Library selection other
Instrument model Illumina HiSeq 2500
Description hMe-SEAL
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 SAMN02665663
SRA SRX476314

Supplementary file Size Download File type/resource
GSM1335293_H03_PFPeaks_treat_afterfiting_all.wig.gz 365.2 Mb (ftp)(http) WIG
SRA Run SelectorHelp
Processed data provided as supplementary file
Raw data are available in SRA

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