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Sample GSM3263092 Query DataSets for GSM3263092
Status Public on Jul 09, 2019
Title day00.ctrl.RNA.Rep2
Sample type SRA
Source name Embryonic stem cell
Organism Homo sapiens
Characteristics tissue: Embryonic stem cell
differentiation time: day00
genotype: H9 MLC2v:H2B
Extracted molecule total RNA
Extraction protocol Total RNA was extracted with Trizol according to protocol (Thermo Scientific, 15596-026). All libraries were constructed using standard illumina TruSeq LT library prep.
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 4000
Data processing base-calling use bcl2fastq version 2.17
alignment was performed using bowtie2 for ATAC-seq, BWA for ChIP-seq and Hi-C, rnaSTAR for RNA-seq. Contacts for Hi-C data were stored in the juicer Hi-C format (could be opened with juicebox.jar provided by Aiden lab).
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files for ChIP-seq and input, juicer hic format for Hi-C data and normalized read per million kilobases (RPKM) for RNA-seq.
Submission date Jul 10, 2018
Last update date Jul 11, 2019
Contact name Bing Ren
Organization name Ludwig Institute for Cancer Research
Street address 9500 Gilman Dr.
City San Diego
State/province CA
ZIP/Postal code 92093
Country USA
Platform ID GPL20301
Series (2)
GSE116862 Chromatin structure dynamics during human cardiomyocyte differention reveals a role of HERV-H in demarcating TAD boundaries.
GSE186958 Chromatin structure dynamics during human cardiomyocyte differention
BioSample SAMN09637504
SRA SRX4377151

Supplementary file Size Download File type/resource
GSM3263092_RYZ2-chrM.rpkm.gz 4.7 Mb (ftp)(http) RPKM
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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