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Schema
Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
484
ChIP-seq
28
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
484
DNA binding
30
DNA accessibility
4
3D chromatin structure
1
DNA methylation
1
DNA sequencing
Target of assay
361
transcription factor
89
recombinant protein
83
control
65
RNA binding protein
38
histone
38
histone modification
30
chromatin remodeller
19
broad histone mark
19
narrow histone mark
3
nucleotide modification
2
other context
2
other post-translational modification
Date released
315
November, 2017
61
November, 2018
28
December, 2018
27
August, 2021
26
October, 2019
18
February, 2021
18
January, 2019
17
May, 2021
15
November, 2019
6
November, 2020
5
February, 2023
2
March, 2020
1
January, 2018
Available data
582
bam
522
bigWig
427
fastq
404
bed narrowPeak
355
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
539
Homo sapiens
Biosample type
1690
tissue
787
primary cell
539
cell line
263
in vitro differentiated cells
4
stem cell
Organ
386
liver
61
blood
61
bodily fluid
57
pancreas
43
epithelium
14
artery
14
blood vessel
14
heart
14
vasculature
13
kidney
Project
532
AMP
7
T1D
Genome assembly (visualization)
425
hg19
360
GRCh38
Lab
503
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 control
1
inconsistent replicate
Audit category:
13
missing controlled_by
Audit category:
26
inconsistent control read length
8
inconsistent control run_type
1
inconsistent assembly
files.file_type!
tsv
audit.ERROR.category!
audit script error
BIOSAMPLE
ASSAY
539 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
GM12878
60
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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