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| Status |
Public on Dec 20, 2020 |
| Title |
438_TNF: RNA-seq, Primary FLS, TNF stimulated |
| Sample type |
SRA |
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| Source name |
Primary FLS
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| Organism |
Homo sapiens |
| Characteristics |
sample id: 438_TNF
stimulation: 10 ng/ml TNF for 24 hours
joint: shoulder
disease state: Rheumatoid Arthritis
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| 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 generated using the Illumina TruSeq Stranded total RNA protocol with the TruSeq Stranded total RNA Sample Preparation Kit
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
processed_data_file: 438_TNF.txt
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| 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)
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| Submission date |
Dec 19, 2020 |
| Last update date |
Dec 22, 2020 |
| Contact name |
Xiangyu Jack Ge |
| E-mail(s) |
xiangyuge123@hotmail.co.uk
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| Organization name |
University of Manchester
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| Street address |
Oxford road
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| City |
Manchester |
| ZIP/Postal code |
M13 9PL |
| Country |
United Kingdom |
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| Platform ID |
GPL24676 |
| Series (1) |
| GSE163548 |
Functional genomics atlas of synovial fibroblasts defining rheumatoid arthritis heritability |
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| Relations |
| BioSample |
SAMN17120402 |
| SRA |
SRX9705988 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4981556_438_TNF.txt.gz |
104.1 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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