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Schema
Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
420
ChIP-seq
61
total RNA-seq
21
ATAC-seq
6
MeRIP-seq
6
pCHi-C
5
STARR-seq
4
Hi-C
3
CRISPR genome editing followed by DNA sequencing
2
Capture-C
2
HiChIP
1
CRISPR genome editing followed by sgRNA sequencing
1
DNase-seq
1
MPRA
1
WGBS
1
shRNA RNA-seq
1
siRNA RNA-seq
1
whole genome sequencing assay
Assay category
420
DNA binding
63
Transcription
22
DNA accessibility
4
3D chromatin structure
1
DNA methylation
1
DNA sequencing
Target of assay
313
transcription factor
89
recombinant protein
81
control
61
RNA binding protein
26
chromatin remodeller
24
histone
24
histone modification
13
narrow histone mark
11
broad histone mark
3
nucleotide modification
1
other context
1
other post-translational modification
Date released
257
November, 2017
61
November, 2018
44
August, 2021
30
February, 2021
29
October, 2019
28
December, 2018
23
January, 2019
21
May, 2021
16
November, 2019
11
March, 2020
6
February, 2023
6
November, 2020
2
March, 2023
1
January, 2018
1
May, 2020
1
October, 2022
Available data
516
bam
466
bigWig
427
fastq
392
bed narrowPeak
355
bigBed narrowPeak
67
tsv
bed broadPeak
59
bigBed broadPeak
14
tagAlign
3
bed bed3+
3
tar
2
bedpe bed3+
2
hic
1
bed bed3
1
bed bedMethyl
1
bigBed bedMethyl
1
hdf5
1
txt
1
vcf
Organism
533
Homo sapiens
Biosample type
2436
tissue
943
primary cell
537
cell line
393
in vitro differentiated cells
10
stem cell
Organ
343
liver
91
pancreas
79
epithelium
66
artery
blood vessel
66
heart
66
vasculature
61
blood
61
bodily fluid
19
kidney
8
embryo
1
mammary gland
Project
526
AMP
9
T1D
2
community
Genome assembly (visualization)
407
hg19
355
GRCh38
Lab
490
AMP-T2D consortium
34
Bing Ren, UCSD
6
Rohit N. Kulkarni, M.D., Ph.D.
5
Kyle Gaulton, UCSD
2
Anna Gloyn, Oxford
Audit category:
92
inconsistent ontology term
1
inconsistent control
1
inconsistent replicate
Audit category:
13
missing controlled_by
Audit category:
13
inconsistent control read length
8
inconsistent control run_type
1
inconsistent assembly
month_released!
September, 2018
organ_slims!
blood vessel
files.file_type!
bed broadPeak
BIOSAMPLE
ASSAY
537 results
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ChIP-seq
total RNA-seq
ATAC-seq
MeRIP-seq
pCHi-C
STARR-seq
Hi-C
CRISPR genome editing followed by DNA sequencing
Capture-C
HiChIP
CRISPR genome editing followed by sgRNA sequencing
DNase-seq
MPRA
WGBS
shRNA RNA-seq
siRNA RNA-seq
whole genome sequencing assay
cell line
HepG2
320
14
1
2
2
2
1
1
EndoC_BH1
15
33
19
6
1
3
2
2
1
GM12878
60
1
Panc1
13
1
H1-hESC
8
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