|
| Status |
Public on Jun 15, 2019 |
| Title |
pcHi-C_human primary fetal astrocytes batch 2_rep2 |
| Sample type |
SRA |
| |
|
| Source name |
pcHi-C_human primary fetal astrocytes batch 2
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: human primary fetal astrocytes batch 2
|
| Growth protocol |
Human primary fetal astrocytes were cultured according to the ScienCell protocol (catalog #1801).
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were harvested, fixed in 1% formaldehyde, snap frozen in dry ice, then stored at -80C. Nuclei extraction was performed prior to further processing.
In situ Hi-C was performed using the standard protocol, then 500 ng of the resulting libraries were used to prepare pcHi-C using a custom biotinylated RNA probe set.
In situ Hi-C followed by pcHi-C
|
| |
|
| Library strategy |
Hi-C |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
MS128
processed data file: wtc_PASS_hg19.phased.vcf.txt.gz
|
| Data processing |
All reads were quality trimmed using fastp.
Reads were mapped, filtered, and deduplicated using HiCUP 0.7.1 running bowtie2 and retaining ditags with lengths between 100 and 1200 bp.
Paired-end BAM files from HiCUP were converted to CHiCAGO input format and interactions were called using CHiCAGO with minNPerBaits=250 and a score cutoff of 5.
Genome_build: hg19
Supplementary_files_format_and_content: CHiCAGO input files for each biological replicate, CHiCAGO interaction data in IBED format, and WashU interaction files
|
| |
|
| Submission date |
Feb 11, 2019 |
| Last update date |
Jun 15, 2019 |
| Contact name |
Yin Shen |
| E-mail(s) |
Yin.Shen@ucsf.edu
|
| Phone |
4155023403
|
| Organization name |
UCSF
|
| Department |
Department of Neurology
|
| Lab |
Shen Lab
|
| Street address |
513 Parnassus Ave
|
| City |
SAN FRANCISCO |
| State/province |
CALIFORNIA |
| ZIP/Postal code |
94143-0410 |
| Country |
USA |
| |
|
| Platform ID |
GPL24676 |
| Series (2) |
| GSE113481 |
Mapping cis-regulatory chromatin contacts in neural cells links neuropsychiatric disorder risk variants to target genes [PCHiC] |
| GSE113483 |
Mapping cis-regulatory chromatin contacts in neural cells links neuropsychiatric disorder risk variants to target genes |
|
| Relations |
| BioSample |
SAMN10912736 |
| SRA |
SRX5360629 |
