|
Status |
Public on Jul 09, 2019 |
Title |
HERV2-ins-clone1.HiC.Rep2 |
Sample type |
SRA |
|
|
Source name |
Embryonic stem cell
|
Organism |
Homo sapiens |
Characteristics |
tissue: Embryonic stem cell differentiation time: day00 genotype: H9 MLC2v:H2B HERV2-ins-clone1
|
Extracted molecule |
genomic DNA |
Extraction protocol |
Briefly, 2 million cells were cross-linked with 1% formaldehyde for 10min at RT and reaction was quenched using 125 mM of Glycine for 5 min at RT. Nuclei were isolated and directly applied for digestion using 4 cutter restriction enzyme MboI (NEB) at 37 °C o/n. All libraries were constructed using standard illumina TruSeq LT library prep.
|
|
|
Library strategy |
Hi-C |
Library source |
genomic |
Library selection |
other |
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.
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|
|
Submission date |
Apr 24, 2019 |
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 |
SAMN11491136 |
SRA |
SRX5730034 |