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Schema
Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
399
ChIP-seq
9
ATAC-seq
4
STARR-seq
4
pCHi-C
3
CRISPR genome editing followed by DNA sequencing
3
Hi-C
2
DNase-seq
2
HiChIP
1
CRISPR genome editing followed by sgRNA sequencing
1
MPRA
1
WGBS
1
whole genome sequencing assay
Assay category
399
DNA binding
Transcription
11
DNA accessibility
3
3D chromatin structure
1
DNA methylation
1
DNA sequencing
Target of assay
302
transcription factor
82
recombinant protein
69
control
54
RNA binding protein
25
histone
25
histone modification
20
chromatin remodeller
13
broad histone mark
12
narrow histone mark
2
other context
2
other post-translational modification
Date released
315
November, 2017
46
November, 2018
24
August, 2021
18
February, 2021
16
October, 2019
6
February, 2023
2
March, 2020
1
December, 2018
1
May, 2020
1
October, 2022
Available data
392
bam
362
fastq
341
bigWig
329
bed narrowPeak
301
bigBed narrowPeak
59
bed broadPeak
59
bigBed broadPeak
20
tagAlign
3
bed bed3+
3
tar
3
tsv
1
bed bed3
1
bed bedMethyl
1
bedpe bed3+
1
bigBed bedMethyl
1
hdf5
1
hic
1
txt
1
vcf
Organism
428
Homo sapiens
Biosample type
1460
tissue
600
primary cell
430
cell line
232
in vitro differentiated cells
7
stem cell
Organ
387
liver
61
blood
bodily fluid
16
pancreas
14
artery
14
blood vessel
14
heart
14
vasculature
3
kidney
2
epithelium
1
mammary gland
Project
425
AMP
5
T1D
Genome assembly (visualization)
347
hg19
285
GRCh38
Lab
401
AMP-T2D consortium
24
Bing Ren, UCSD
5
Kyle Gaulton, UCSD
Audit category:
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
assay_slims!
Transcription
audit.ERROR.category!
inconsistent ontology term
organ_slims!
bodily fluid
bone marrow
BIOSAMPLE
ASSAY
430 results
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ChIP-seq
ATAC-seq
STARR-seq
pCHi-C
CRISPR genome editing followed by DNA sequencing
Hi-C
DNase-seq
HiChIP
CRISPR genome editing followed by sgRNA sequencing
MPRA
WGBS
whole genome sequencing assay
cell line
HepG2
378
1
2
2
2
1
1
Panc1
13
1
1
smooth muscle cell of the coronary artery
6
8
EndoC_BH1
3
2
1
HEK293T
2
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