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Sample GSM4815401

Query DataSets for GSM4815401

Status

Public on Sep 30, 2023

Title

GM12878-RAD21-ChIA-Drop-Rep11

Sample type

SRA

Source name

GM12878

Organism

Homo sapiens

Characteristics

cell line: GM12878
method: RAD21-ChIA-Drop
antibody: RAD21 (Abcam, catalog# ab922)

Biomaterial provider

Coriell Cell Repositories https://catalog.coriell.org/0/Sections/Search/Sample_Detail.aspx?Ref=GM12878&Product=GM12878

Extracted molecule

genomic DNA

Extraction protocol

The overall chromatin sample preparation for ChIA-Drop is very similar to Hi-C, except without the proximity ligation step in ChIA-Drop. Similarly, CTCF, cohesin, and RNAPII ChIA-Drop chromatin samples are prepared as they are for respective ChIA-PET experiments but omitting proximity ligation step.
Fragmented chromatin sample was mixed with BSA to prevent chromatin aggregation. About 0.5ng of chromatin DNA material was loaded to microfluidics device, Chromium Controller with reagents from Chromium Genome v2 Library Kit & Gel Bead Kit for partitioning of single chromatin complex into individual droplets with unique gel beads according to the manufacturer’s protocol with modification. The barcoded DNA amplicons of each chromatin complex were released from all droplets.The purified DNA fragments were subjected for end repair, A-tailing, adaptor ligation, Sample Index PCR and size selection. The final ChIA-Drop library was sequenced (2× 150 bp) by NextSeq, HiSeq, or NovaSeq runs.
We applied microfluidics-based strategy for genome-wide analysis of multiplex chromatin interactions with single-molecule precision (ChIA-Drop). Here, individual chromatin complexes are isolated in droplets that contain a gel bead with unique DNA barcode, in which tethered chromatin DNA fragments are barcoded and amplified for sequencing and mapping to demarcate chromatin contacts.

Library strategy

OTHER

Library source

genomic

Library selection

other

Instrument model

Illumina NovaSeq 6000

Description

Sample 29
nuclear chromatin
RAD21-ChIA-Drop
GM12878-cohesin-pooled_comp.txt
GM12878-cohesin-pooled.bedgraph
GM12878-cohesin-pooled.hic

Data processing

Library strategy: ChIA-Drop
ChIA-Drop fastq files were mapped by longranger (version 2.1.5, 10X Genomics) with wgs command. ChIP-seq fastq files were mapped by BWA (version 0.7.7) with mem command. ChIA-PET fastq files were mapped by our in-house ChIA-PET processing pipeline, available in github (ChIA-PIPE).
After mapping and identifying barcords of ChIA-Drop using longranger, our in-house processing pipeline (available in github, ChIA-DropBox) generated putative complexes. These data sets were further filtered by MIA-Sig (available in github), and then generated tab-delimited txt file.
DNA-binding protein coverage files (bedgraph) were generated by bedtools (version 2.26.0) with genomecov command. Coverage files were sorted by chromosome and coordinate.
ChIA-PET loop files (bedpe) were generated by our in-house ChIA-PET processing pipeline, available in github (ChIA-PIPE).
Peaks (broadPeak, bed file type) were called by SPP (version 1.13) with our input control file (sample# 63, library ID: CHG0033).
2D contact map files (hic) were generated by Juicer Tools (Version 1.7.5) using chromatin interaction data from ChIA-PET and ChIA-Drop. In ChIA-Drop, we used all pairwise interactions from each GEM.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited txt format of ChIA-Drop, containing GEM_ID, GEM_coordinate, GEM_span, Fragment_number, List_of_fragment_coordinates. Each row represents one GEM.
Supplementary_files_format_and_content: bedgraph format of ChIA-Drop, ChIP-seq, and ChIA-PET, containing a DNA-binding protein coverage
Supplementary_files_format_and_content: bedpe format of ChIA-PET, containing ChIA-PET loop (long-range interaction data) data
Supplementary_files_format_and_content: broadPeak format of ChIP-seq and ChIA-PET, containing peaks called by SPP software
Supplementary_files_format_and_content: hic format of ChIA-Drop and ChIA-PET, 2D contact map file, visualized by Juicebox software

Submission date

Oct 01, 2020

Last update date

Sep 30, 2023

Contact name

Yijun Ruan

E-mail(s)

yijun.ruan@jax.org

Organization name

The Jackson Laboratory

Department

Ruan