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Schema
Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
424
ChIP-seq
27
ATAC-seq
6
MeRIP-seq
5
STARR-seq
4
Hi-C
3
CRISPR genome editing followed by DNA sequencing
2
Capture-C
2
DNase-seq
2
HiChIP
1
WGBS
1
pCHi-C
1
whole genome sequencing assay
Assay category
424
DNA binding
29
DNA accessibility
4
3D chromatin structure
1
DNA methylation
1
DNA sequencing
Target of assay
310
transcription factor
89
recombinant protein
77
control
55
RNA binding protein
37
histone
37
histone modification
20
chromatin remodeller
19
broad histone mark
18
narrow histone mark
3
nucleotide modification
2
other context
2
other post-translational modification
Date released
315
November, 2017
46
November, 2018
27
August, 2021
26
October, 2019
18
February, 2021
17
May, 2021
15
November, 2019
6
November, 2020
5
February, 2023
2
March, 2020
1
December, 2018
Available data
522
bam
467
bigWig
367
fastq
350
bed narrowPeak
301
bigBed narrowPeak
tsv
59
bed broadPeak
59
bigBed broadPeak
20
tagAlign
3
bed bed3+
3
tar
2
bedpe bed3+
2
hic
1
bed bed3
1
bed bedMethyl
1
bigBed bedMethyl
1
hdf5
1
vcf
Organism
478
Homo sapiens
Biosample type
1692
tissue
810
primary cell
478
cell line
263
in vitro differentiated cells
4
stem cell
Organ
386
liver
blood
61
bodily fluid
57
pancreas
43
epithelium
14
artery
14
blood vessel
14
heart
14
vasculature
13
kidney
Project
471
AMP
7
T1D
Genome assembly (visualization)
370
hg19
306
GRCh38
Lab
442
AMP-T2D consortium
25
Bing Ren, UCSD
6
Rohit N. Kulkarni, M.D., Ph.D.
5
Kyle Gaulton, UCSD
Audit category:
53
inconsistent ontology term
1
inconsistent replicate
Audit category:
13
missing controlled_by
Audit category:
26
inconsistent control read length
8
inconsistent control run_type
1
inconsistent assembly
organ_slims!
blood
files.file_type!
tsv
BIOSAMPLE
ASSAY
478 results
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ChIP-seq
ATAC-seq
MeRIP-seq
STARR-seq
Hi-C
CRISPR genome editing followed by DNA sequencing
Capture-C
DNase-seq
HiChIP
WGBS
pCHi-C
whole genome sequencing assay
cell line
HepG2
378
1
2
2
1
1
1
EndoC_BH1
15
18
6
1
3
2
2
Panc1
13
1
1
smooth muscle cell of the coronary artery
6
8
RCC 7860 HIF1a re-expression
4
RCC 7860 HIF2a over-expression
3
RCC 7860 vector
3
HEK293T
2
iPSC derived cell line
2
Synthesized DNA
1
glomerular visceral epithelial cell
1
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