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Schema
Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
452
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
DNase-seq
2
HiChIP
1
CRISPR genome editing followed by sgRNA sequencing
1
MPRA
1
WGBS
1
shRNA RNA-seq
1
siRNA RNA-seq
1
whole genome sequencing assay
Assay category
452
DNA binding
63
Transcription
23
DNA accessibility
4
3D chromatin structure
1
DNA methylation
1
DNA sequencing
Target of assay
342
transcription factor
88
recombinant protein
81
control
59
RNA binding protein
27
histone
27
histone modification
19
chromatin remodeller
14
narrow histone mark
13
broad histone mark
3
nucleotide modification
2
other context
2
other post-translational modification
Date released
294
November, 2017
56
November, 2018
44
August, 2021
30
February, 2021
30
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
490
bam
440
bigWig
401
fastq
368
bed narrowPeak
331
bigBed narrowPeak
67
tsv
46
bed broadPeak
46
bigBed broadPeak
3
bed bed3+
3
tagAlign
3
tar
2
bedpe bed3+
2
hic
1
bed bed3
1
bed bedMethyl
1
bigBed bedMethyl
1
hdf5
1
txt
1
vcf
Organism
566
Homo sapiens
Biosample type
2598
tissue
1052
primary cell
570
cell line
377
in vitro differentiated cells
8
stem cell
Organ
375
liver
92
pancreas
79
epithelium
66
artery
blood vessel
66
heart
66
vasculature
61
blood
61
bodily fluid
19
kidney
8
embryo
1
mammary gland
Project
559
AMP
9
T1D
2
community
Genome assembly (visualization)
440
hg19
378
GRCh38
Lab
523
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:
8
missing controlled_by
Audit category:
inconsistent control read length
8
inconsistent control run_type
1
inconsistent assembly
audit.WARNING.category!
inconsistent control read length
organ_slims!
blood vessel
BIOSAMPLE
ASSAY
570 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
DNase-seq
HiChIP
CRISPR genome editing followed by sgRNA sequencing
MPRA
WGBS
shRNA RNA-seq
siRNA RNA-seq
whole genome sequencing assay
cell line
HepG2
352
14
1
2
2
2
1
1
EndoC_BH1
15
33
19
6
1
3
2
2
1
GM12878
60
1
Panc1
13
1
1
H1-hESC
8
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