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Status |
Public on Jul 09, 2019 |
Title |
day00.HERV1.KO.RNA.Rep2 |
Sample type |
SRA |
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Source name |
Embryonic stem cell
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Organism |
Homo sapiens |
Characteristics |
tissue: Embryonic stem cell differentiation time: day00 genotype: H9 MLC2v:H2B HERV1-KO
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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.
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 4000 |
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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 |
Jul 10, 2018 |
Last update date |
Oct 22, 2024 |
Contact name |
Bing Ren |
E-mail(s) |
biren@ucsd.edu
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Organization name |
University of California, San Diego
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Street address |
9500 Gilman Drive
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City |
La Jolla |
ZIP/Postal code |
92093 |
Country |
USA |
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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 |
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Relations |
BioSample |
SAMN09637546 |
SRA |
SRX4377153 |
Supplementary file |
Size |
Download |
File type/resource |
GSM3263094_RYZ4-chrM.rpkm.gz |
4.7 Mb |
(ftp)(http) |
RPKM |
SRA Run Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |
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