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Sample GSM3106838 Query DataSets for GSM3106838
Status Public on Jun 15, 2019
Title PCHiC_human primary fetal astrocytes_rep1
Sample type SRA
Source name human primary fetal astrocytes
Organism Homo sapiens
Characteristics cell type: human primary fetal astrocytes
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 HiSeq 4000
Description JC005
library strategy: In situ Hi-C followed by promoter capture Hi-C
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 Apr 20, 2018
Last update date Jun 17, 2019
Contact name Yin Shen
Phone 4155023403
Organization name UCSF
Department Department of Neurology
Lab Shen Lab
Street address 513 Parnassus Ave
State/province CALIFORNIA
ZIP/Postal code 94143-0410
Country USA
Platform ID GPL20301
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
BioSample SAMN08965073
SRA SRX3981953

Supplementary file Size Download File type/resource
GSM3106838_JC005.chinput.txt.gz 257.1 Mb (ftp)(http) TXT
GSM3106838_astrocyte.cutoff.5.washU.txt.gz 854.6 Kb (ftp)(http) TXT
GSM3106838_astrocyte.ibed.txt.gz 949.9 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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