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Sample GSM4981539

Query DataSets for GSM4981539

Status

Public on Dec 20, 2020

Title

SF_435: RNA-seq, Primary FLS, unstimulated

Sample type

SRA

Source name

Primary FLS

Organism

Homo sapiens

Characteristics

sample id: SF_435
stimulation: None
joint: Shoulder
disease state: Rheumatoid Arthritis

Extracted molecule

total RNA

Extraction protocol

Cultured FLS were treated with 10 ng/ml human recombinant TNF (Roche) for 24 h or were left untreated. Total RNA was isolated using the RNeasy Mini kit (Qiagen) including on-column DNAase I digestion.
RNA-seq libraries were prepared using the NEB Next Ultra Directional RNAseq Protocol with ribosomal depletion.

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina HiSeq 4000

Description

processed_data_file: HGNC_FLS_norm_exp.txt

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