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| Status |
Public on Jul 09, 2019 |
| Title |
day00.HERV2.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 HERV2-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 |
SAMN09637491 |
| SRA |
SRX4377155 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3263096_RYZ6-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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