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| Status |
Public on Dec 20, 2020 |
| Title |
Functional genomics atlas of synovial fibroblasts defining rheumatoid arthritis heritability |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Other
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| Summary |
Genome-wide association studies have reported more than 100 risk loci for rheumatoid arthritis, and there loci have been shown to be enriched in immune cell-specific enhancers, we add Synovial fibroblasts (FLS), the local stromal cells of joints to this analysis. We integrated ChIP-seq, Hi-C, Capture Hi-C, ATAC-seq and RNA-seq datasets from FLS , with genetic fine-mapping of RA loci. From this we identified putative casual variants, enhancers and genes for 30-60% of RA loci and demonstrated that FLS regulatory elements accounts for up to 24% of RA heritability. We also examined the effects of TNF stimulation on the chromatin landscape of FLS, and we found there are significant alterations in the organization of topologically associated domains, chromatin interactions and the expression of several putative causal genes.
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| Overall design |
Examine the enrichment of RA signals in FLS functional elements, assign putative gene targets for these RA signals in FLS, and quantify the effects of TNF stimulation on FLS.
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| Contributor(s) |
Ge X, Frank-Bertoncelj M, Klein K, Mcgovern A, Kuret T, Houtman M, Burja B, Micheroli R, Marks M, Filer A, Buckley CD, Orozco G, Distler O, Morris AP, Martin P, Eyre S, Ospelt C |
| Citation(s) |
34433485 |
| |
| Submission date |
Dec 19, 2020 |
| Last update date |
Aug 31, 2021 |
| 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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| Platforms (3) |
| GPL16791 |
Illumina HiSeq 2500 (Homo sapiens) |
| GPL20301 |
Illumina HiSeq 4000 (Homo sapiens) |
| GPL24676 |
Illumina NovaSeq 6000 (Homo sapiens) |
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| Samples (142)
|
| GSM4981433 |
335: Input DNA ChIP-seq, Primary FLS, Unstimulated |
| GSM4981434 |
335: Input1 DNA ChIP-seq, Primary FLS, Unstimulated |
| GSM4981435 |
335: H3K27ac ChIP-seq, Primary FLS, Unstimulated |
| GSM4981436 |
335: H3K36me3 ChIP-seq, Primary FLS, Unstimulated |
| GSM4981437 |
335: H3K4me3 ChIP-seq, Primary FLS, Unstimulated |
| GSM4981438 |
335: H3K27me3 ChIP-seq, Primary FLS, Unstimulated |
| GSM4981439 |
335: H3K4me1 ChIP-seq, Primary FLS, Unstimulated |
| GSM4981440 |
335: H3K9me3 ChIP-seq, Primary FLS, Unstimulated |
| GSM4981441 |
368: Input DNA ChIP-seq, Primary FLS, Unstimulated |
| GSM4981442 |
368: Input1 DNA ChIP-seq, Primary FLS, Unstimulated |
| GSM4981443 |
368: H3K27ac ChIP-seq, Primary FLS, Unstimulated |
| GSM4981444 |
368: H3K36me3 ChIP-seq, Primary FLS, Unstimulated |
| GSM4981445 |
368: H3K4me3 ChIP-seq, Primary FLS, Unstimulated |
| GSM4981446 |
368: H3K27me3 ChIP-seq, Primary FLS, Unstimulated |
| GSM4981447 |
368: H3K4me1 ChIP-seq, Primary FLS, Unstimulated |
| GSM4981448 |
368: H3K9me3 ChIP-seq, Primary FLS, Unstimulated |
| GSM4981449 |
384: Input DNA ChIP-seq, Primary FLS, Unstimulated |
| GSM4981450 |
384: Input1 DNA ChIP-seq, Primary FLS, Unstimulated |
| GSM4981451 |
384: H3K27ac ChIP-seq, Primary FLS, Unstimulated |
| GSM4981452 |
384: H3K36me3 ChIP-seq, Primary FLS, Unstimulated |
| GSM4981453 |
384: H3K4me3 ChIP-seq, Primary FLS, Unstimulated |
| GSM4981454 |
384: H3K27me3 ChIP-seq, Primary FLS, Unstimulated |
| GSM4981455 |
384: H3K4me1 ChIP-seq, Primary FLS, Unstimulated |
| GSM4981456 |
384: H3K9me3 ChIP-seq, Primary FLS, Unstimulated |
| GSM4981457 |
341: Input DNA ChIP-seq, Primary FLS, Unstimulated |
| GSM4981458 |
341: Input1 DNA ChIP-seq, Primary FLS, Unstimulated |
| GSM4981459 |
341: H3K27ac ChIP-seq, Primary FLS, Unstimulated |
| GSM4981460 |
341: H3K36me3 ChIP-seq, Primary FLS, Unstimulated |
| GSM4981461 |
341: H3K4me3 ChIP-seq, Primary FLS, Unstimulated |
| GSM4981462 |
341: H3K27me3 ChIP-seq, Primary FLS, Unstimulated |
| GSM4981463 |
341: H3K4me1 ChIP-seq, Primary FLS, Unstimulated |
| GSM4981464 |
341: H3K9me3 ChIP-seq, Primary FLS, Unstimulated |
| GSM4981465 |
343: Input DNA ChIP-seq, Primary FLS, Unstimulated |
| GSM4981466 |
343: Input1 DNA ChIP-seq, Primary FLS, Unstimulated |
| GSM4981467 |
343: H3K27ac ChIP-seq, Primary FLS, Unstimulated |
| GSM4981468 |
343: H3K36me3 ChIP-seq, Primary FLS, Unstimulated |
| GSM4981469 |
343: H3K4me3 ChIP-seq, Primary FLS, Unstimulated |
| GSM4981470 |
343: H3K27me3 ChIP-seq, Primary FLS, Unstimulated |
| GSM4981471 |
343: H3K4me1 ChIP-seq, Primary FLS, Unstimulated |
| GSM4981472 |
343: H3K9me3 ChIP-seq, Primary FLS, Unstimulated |
| GSM4981473 |
316: Input DNA ChIP-seq, Primary FLS, Unstimulated |
| GSM4981474 |
316: Input1 DNA ChIP-seq, Primary FLS, Unstimulated |
| GSM4981475 |
316: H3K27ac ChIP-seq, Primary FLS, Unstimulated |
| GSM4981476 |
316: H3K36me3 ChIP-seq, Primary FLS, Unstimulated |
| GSM4981477 |
316: H3K4me3 ChIP-seq, Primary FLS, Unstimulated |
| GSM4981478 |
316: H3K27me3 ChIP-seq, Primary FLS, Unstimulated |
| GSM4981479 |
316: H3K4me1 ChIP-seq, Primary FLS, Unstimulated |
| GSM4981480 |
316: H3K9me3 ChIP-seq, Primary FLS, Unstimulated |
| GSM4981481 |
88: Input DNA ChIP-seq, Primary FLS, Unstimulated |
| GSM4981482 |
88: Input1 DNA ChIP-seq, Primary FLS, Unstimulated |
| GSM4981483 |
88: H3K27ac ChIP-seq, Primary FLS, Unstimulated |
| GSM4981484 |
88: H3K36me3 ChIP-seq, Primary FLS, Unstimulated |
| GSM4981485 |
88: H3K4me3 ChIP-seq, Primary FLS, Unstimulated |
| GSM4981486 |
88: H3K27me3 ChIP-seq, Primary FLS, Unstimulated |
| GSM4981487 |
88: H3K4me1 ChIP-seq, Primary FLS, Unstimulated |
| GSM4981488 |
88: H3K9me3 ChIP-seq, Primary FLS, Unstimulated |
| GSM4981489 |
412: Capture Hi-C, Primary FLS, unstimulated |
| GSM4981490 |
415A: Capture Hi-C, Primary FLS, unstimulated |
| GSM4981491 |
415B: Capture Hi-C, Primary FLS, unstimulated |
| GSM4981492 |
424: Capture Hi-C, Primary FLS, unstimulated |
| GSM4981493 |
420: Capture Hi-C, Primary FLS, unstimulated |
| GSM4981494 |
429: Capture Hi-C, Primary FLS, unstimulated |
| GSM4981495 |
427: Capture Hi-C, Primary FLS, unstimulated |
| GSM4981496 |
412_TNF: Capture Hi-C, Primary FLS, TNF stimulated |
| GSM4981497 |
415A_TNF: Capture Hi-C, Primary FLS, TNF stimulated |
| GSM4981498 |
415B_TNF: Capture Hi-C, Primary FLS, TNF stimulated |
| GSM4981499 |
424_TNF: Capture Hi-C, Primary FLS, TNF stimulated |
| GSM4981500 |
420_TNF: Capture Hi-C, Primary FLS, TNF stimulated |
| GSM4981501 |
429_TNF: Capture Hi-C, Primary FLS, TNF stimulated |
| GSM4981502 |
427_TNF: Capture Hi-C, Primary FLS, TNF stimulated |
| GSM4981503 |
412: Hi-C, Primary FLS, unstimulated |
| GSM4981504 |
415A: Hi-C, Primary FLS, unstimulated |
| GSM4981505 |
415B: Hi-C, Primary FLS, unstimulated |
| GSM4981506 |
424: Hi-C, Primary FLS, unstimulated |
| GSM4981507 |
420: Hi-C, Primary FLS, unstimulated |
| GSM4981508 |
429: Hi-C, Primary FLS, unstimulated |
| GSM4981509 |
427: Hi-C, Primary FLS, unstimulated |
| GSM4981510 |
412_TNF: Hi-C, Primary FLS, TNF stimulated |
| GSM4981511 |
415A_TNF: Hi-C, Primary FLS, TNF stimulated |
| GSM4981512 |
415B_TNF: Hi-C, Primary FLS, TNF stimulated |
| GSM4981513 |
424_TNF: Hi-C, Primary FLS, TNF stimulated |
| GSM4981514 |
420_TNF: Hi-C, Primary FLS, TNF stimulated |
| GSM4981515 |
429_TNF: Hi-C, Primary FLS, TNF stimulated |
| GSM4981516 |
427_TNF: Hi-C, Primary FLS, TNF stimulated |
| GSM4981517 |
SF_346: ATAC-seq, Primary FLS, unstimulated |
| GSM4981518 |
SF_346_TNF: ATAC-seq, Primary FLS, TNF stimulated |
| GSM4981519 |
SF_415B: ATAC-seq, Primary FLS, unstimulated |
| GSM4981520 |
SF_415B_TNF: ATAC-seq, Primary FLS, TNF stimulated |
| GSM4981521 |
SF_420: ATAC-seq, Primary FLS, unstimulated |
| GSM4981522 |
SF_420_TNF: ATAC-seq, Primary FLS, TNF stimulated |
| GSM4981523 |
SF_424: ATAC-seq, Primary FLS, unstimulated |
| GSM4981524 |
SF_424_TNF: ATAC-seq, Primary FLS, TNF stimulated |
| GSM4981525 |
SF_427: ATAC-seq, Primary FLS, unstimulated |
| GSM4981526 |
SF_427_TNF: ATAC-seq, Primary FLS, TNF stimulated |
| GSM4981527 |
SF_429: ATAC-seq, Primary FLS, unstimulated |
| GSM4981528 |
SF_429_TNF: ATAC-seq, Primary FLS, TNF stimulated |
| GSM4981529 |
SF_292: RNA-seq, Primary FLS, unstimulated |
| GSM4981530 |
SF_292_TNF: RNA-seq, Primary FLS, TNF stimulated |
| GSM4981531 |
SF_336: RNA-seq, Primary FLS, unstimulated |
| GSM4981532 |
SF_336_TNF: RNA-seq, Primary FLS, TNF stimulated |
| GSM4981533 |
SF_346: RNA-seq, Primary FLS, unstimulated |
| GSM4981534 |
SF_346_TNF: RNA-seq, Primary FLS, TNF stimulated |
| GSM4981535 |
SF_407: RNA-seq, Primary FLS, unstimulated |
| GSM4981536 |
SF_407_TNF: RNA-seq, Primary FLS, TNF stimulated |
| GSM4981537 |
SF_415B: RNA-seq, Primary FLS, unstimulated |
| GSM4981538 |
SF_415B_TNF: RNA-seq, Primary FLS, TNF stimulated |
| GSM4981539 |
SF_435: RNA-seq, Primary FLS, unstimulated |
| GSM4981540 |
SF_435_TNF: RNA-seq, Primary FLS, TNF stimulated |
| GSM4981541 |
230: RNA-seq, Primary FLS, unstimulated |
| GSM4981542 |
230_TNF: RNA-seq, Primary FLS, TNF stimulated |
| GSM4981543 |
387: RNA-seq, Primary FLS, unstimulated |
| GSM4981544 |
387_TNF: RNA-seq, Primary FLS, TNF stimulated |
| GSM4981545 |
285: RNA-seq, Primary FLS, unstimulated |
| GSM4981546 |
285_TNF: RNA-seq, Primary FLS, TNF stimulated |
| GSM4981547 |
379: RNA-seq, Primary FLS, unstimulated |
| GSM4981548 |
379_TNF: RNA-seq, Primary FLS, TNF stimulated |
| GSM4981549 |
331: RNA-seq, Primary FLS, unstimulated |
| GSM4981550 |
331_TNF: RNA-seq, Primary FLS, TNF stimulated |
| GSM4981551 |
430: RNA-seq, Primary FLS, unstimulated |
| GSM4981552 |
430_TNF: RNA-seq, Primary FLS, TNF stimulated |
| GSM4981553 |
466: RNA-seq, Primary FLS, unstimulated |
| GSM4981554 |
466_TNF: RNA-seq, Primary FLS, TNF stimulated |
| GSM4981555 |
438: RNA-seq, Primary FLS, unstimulated |
| GSM4981556 |
438_TNF: RNA-seq, Primary FLS, TNF stimulated |
| GSM4981557 |
427: RNA-seq, Primary FLS, unstimulated |
| GSM4981558 |
427_TNF: RNA-seq, Primary FLS, TNF stimulated |
| GSM4981559 |
217: RNA-seq, Primary FLS, unstimulated |
| GSM4981560 |
217_TNF: RNA-seq, Primary FLS, TNF stimulated |
| GSM4981561 |
429: CAGE-seq, Primary FLS, unstimulated |
| GSM4981562 |
429_TNF: CAGE-seq, Primary FLS, TNF stimulated |
| GSM4981563 |
427: CAGE-seq, Primary FLS, unstimulated |
| GSM4981564 |
427_TNF: CAGE-seq, Primary FLS, TNF stimulated |
| GSM4981565 |
424: CAGE-seq, Primary FLS, unstimulated |
| GSM4981566 |
424_TNF: CAGE-seq, Primary FLS, TNF stimulated |
| GSM4981567 |
420: CAGE-seq, Primary FLS, unstimulated |
| GSM4981568 |
420_TNF: CAGE-seq, Primary FLS, TNF stimulated |
| GSM4981569 |
415B: CAGE-seq, Primary FLS, unstimulated |
| GSM4981570 |
415B_TNF: CAGE-seq, Primary FLS, TNF stimulated |
| GSM4981571 |
276: CAGE-seq, Primary FLS, unstimulated |
| GSM4981572 |
276_TNF: CAGE-seq, Primary FLS, TNF stimulated |
| GSM4981573 |
460: CAGE-seq, Primary FLS, unstimulated |
| GSM4981574 |
460_TNF: CAGE-seq, Primary FLS, TNF stimulated |
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| Relations |
| BioProject |
PRJNA686662 |
| SRA |
SRP298566 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE163548_316_18_segments.sorted.bed.gz |
3.1 Mb |
(ftp)(http) |
BED |
| GSE163548_335_18_segments.sorted.bed.gz |
3.1 Mb |
(ftp)(http) |
BED |
| GSE163548_341_18_segments.sorted.bed.gz |
3.0 Mb |
(ftp)(http) |
BED |
| GSE163548_343_18_segments.sorted.bed.gz |
3.2 Mb |
(ftp)(http) |
BED |
| GSE163548_368_18_segments.sorted.bed.gz |
2.8 Mb |
(ftp)(http) |
BED |
| GSE163548_384_18_segments.sorted.bed.gz |
2.9 Mb |
(ftp)(http) |
BED |
| GSE163548_88_18_segments.sorted.bed.gz |
3.0 Mb |
(ftp)(http) |
BED |
| GSE163548_All_TADs_extended.sorted.bed.gz |
143.5 Kb |
(ftp)(http) |
BED |
| GSE163548_All_stim_A.bed.gz |
146.8 Kb |
(ftp)(http) |
BED |
| GSE163548_All_stim_B.bed.gz |
167.4 Kb |
(ftp)(http) |
BED |
| GSE163548_All_unstim_A.bed.gz |
148.1 Kb |
(ftp)(http) |
BED |
| GSE163548_All_unstim_B.bed.gz |
166.6 Kb |
(ftp)(http) |
BED |
| GSE163548_Basal.merged_peaks.narrowPeak.gz |
2.1 Mb |
(ftp)(http) |
NARROWPEAK |
| GSE163548_HGNC_FLS_norm_exp.txt.gz |
1.8 Mb |
(ftp)(http) |
TXT |
| GSE163548_Knee_TNF_clusters_tpm.txt.gz |
444.6 Kb |
(ftp)(http) |
TXT |
| GSE163548_Knee_clusters_tpm.txt.gz |
478.1 Kb |
(ftp)(http) |
TXT |
| GSE163548_MCP_TNF_clusters_tpm.txt.gz |
624.2 Kb |
(ftp)(http) |
TXT |
| GSE163548_MCP_clusters_tpm.txt.gz |
606.9 Kb |
(ftp)(http) |
TXT |
| GSE163548_RAW.tar |
59.6 Mb |
(http)(custom) |
TAR (of BROADPEAK, NARROWPEAK, TXT) |
| GSE163548_Shoulder_TNF_clusters_tpm.txt.gz |
436.6 Kb |
(ftp)(http) |
TXT |
| GSE163548_Shoulder_clusters_tpm.txt.gz |
475.5 Kb |
(ftp)(http) |
TXT |
| GSE163548_Stim.merged_peaks.narrowPeak.gz |
2.5 Mb |
(ftp)(http) |
NARROWPEAK |
| GSE163548_Stim_Chicago_washU_text.txt.gz |
363.0 Kb |
(ftp)(http) |
TXT |
| GSE163548_Unstim_Chicago_washU_text.txt.gz |
365.3 Kb |
(ftp)(http) |
TXT |
| GSE163548_basal.allValidPairs.hic |
2.0 Gb |
(ftp)(http) |
HIC |
| GSE163548_stim.allValidPairs.hic |
2.6 Gb |
(ftp)(http) |
HIC |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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