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Sample GSM4981461 Query DataSets for GSM4981461
Status Public on Dec 20, 2020
Title 341: H3K4me3 ChIP-seq, Primary FLS, Unstimulated
Sample type SRA
 
Source name Primary FLS
Organism Homo sapiens
Characteristics sample id: 341
stimulation: None
joint: Shoulder
disease state: Rheumatoid Arthritis
Extracted molecule genomic DNA
Extraction protocol Chromatin was prepared on pellets of fixed cells using the iDeal ChIP seq kit for Histones (Diagenode). ChIP assays were performed using 1 million cells per IP and the following antibodies: H3K4me3 (0.5 μg, C15411003, Diagenode), H3K27me3 (1 μg, C15410195, Diagenode) and H3K27ac (1 μg, C15410196, Diagenode). A control library was processed in parallel using the same amount of control Diagenode ChIP’d DNA.
Libraries were prepared from 1 ng of IP and input DNA using the MicroPLEX v2 protocol, quantified by BioAnalyzer, purified (AMPure beads) and eluted in TE.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 2500
 
Description processed_data_file: 341_H3K4me3_RA_SH_peaks.narrowPeak
Data processing CHiC were mapped to GRCh38 using HICUP, CHiCAGO was applied to the stimulatory conditions, treating each sample as a replicate. Interactions with CHiCAGO score over 5 were picked up and corresponding counts data were extracted from CHiCAGO results, for downstream differential interaction analysis using DESeq2.
Individual ATAC-seq reads were mapped to GRCh38 by Bowtie2. Duplicates were removed by Picard. Bam files of the stimulatory conditions were merged and MACS2 were applied to call peaks on each merged bam file.
RNA-seq data were mapped to GRCh38 by STAR. Gene expression quantification was done by RSEM, downstream normalizatioin and differential analysis was performed by DESeq2.
Hi-C reads were mapped to GRCh38 and processed by the HiC-Pro pipeline, the .hic files produced were then used for downstream TAD analysis using the R package TADCompare.
Hi-C reads were mapped to GRCh38 by HiCUP and then converted to HOMER format, runHiCpca.pl and findHiCCompartments.pl from HOMER were used to identify A/B compartments.
Genome_build: GRCh38
Supplementary_files_format_and_content: HGNC_FLS_norm_exp.txt: RNA-seq expression counts normalized by DESeq2.
Supplementary_files_format_and_content: narrowPeak/broadPeak: ATAC/ChIP-seq peaks as identified by MACS2 (chromosome, start, end, id, score, strand, signalValue, pValue, qValue, peak point-source)
Supplementary_files_format_and_content: allValidPairs.hic : Hi-C data processed by HiC-Pro.
Supplementary_files_format_and_content: Chicago_washU_text.txt : Significant Chi-C interactions (bait location, prey location, ChiCAGO score)
Supplementary_files_format_and_content: 18_segment.sorted.bed : ChromHMM state inference from 18 states based on 6 histone marks. (Segment_chr, segment_start, Segment_end, Inferred state)
Supplementary_files_format_and_content: All_stim/unstim_A/B.bed : Merged A/B compartments as identified by HOMER. (A/B compartment chr, A/B compartment start, A/B compartment end)
Supplementary_files_format_and_content: All_TADs_extended.sorted.bed : TADs identified with TADCompare, and their differential TAD status. (TAD chr, TAD start, TAD end, basal TAD score, stim TAD score, differential TAD score, differential status, enriched in condition, differential TAD type)
 
Submission date Dec 19, 2020
Last update date Dec 22, 2020
Contact name Xiangyu Jack Ge
E-mail(s) xiangyuge123@hotmail.co.uk
Organization name University of Manchester
Street address Oxford road
City Manchester
ZIP/Postal code M13 9PL
Country United Kingdom
 
Platform ID GPL16791
Series (1)
GSE163548 Functional genomics atlas of synovial fibroblasts defining rheumatoid arthritis heritability
Relations
BioSample SAMN17120453
SRA SRX9706019

Supplementary file Size Download File type/resource
GSM4981461_341_H3K4me3_RA_SH_peaks.narrowPeak.gz 858.4 Kb (ftp)(http) NARROWPEAK
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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