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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
E-mail(s) biren@ucsd.edu
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
Relations
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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