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Schema
Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
400
ChIP-seq
113
total RNA-seq
29
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
400
DNA binding
115
Transcription
31
DNA accessibility
4
3D chromatin structure
1
DNA methylation
1
DNA sequencing
Target of assay
361
transcription factor
89
recombinant protein
83
control
RNA binding protein
38
histone
38
histone modification
30
chromatin remodeller
19
broad histone mark
narrow histone mark
3
nucleotide modification
2
other context
2
other post-translational modification
Date released
274
November, 2017
96
February, 2021
41
August, 2021
40
November, 2018
27
October, 2019
26
December, 2018
20
May, 2021
16
January, 2019
11
November, 2019
10
March, 2020
6
February, 2023
6
November, 2020
2
March, 2023
1
January, 2018
1
May, 2020
1
October, 2022
Available data
501
bam
440
bigWig
356
fastq
323
bed narrowPeak
284
bigBed narrowPeak
119
tsv
49
bed broadPeak
49
bigBed broadPeak
15
tagAlign
3
bed bed3+
2
bedpe bed3+
2
hic
2
tar
1
bed bed3
1
bed bedMethyl
1
bigBed bedMethyl
1
hdf5
1
txt
1
vcf
Organism
574
Homo sapiens
Biosample type
2251
tissue
912
primary cell
578
cell line
328
in vitro differentiated cells
9
stem cell
Organ
338
liver
82
pancreas
72
epithelium
66
artery
66
blood vessel
66
heart
66
vasculature
50
blood
50
bodily fluid
19
kidney
8
embryo
1
mammary gland
Project
569
AMP
7
T1D
2
community
Genome assembly (visualization)
449
hg19
390
GRCh38
Lab
534
AMP-T2D consortium
31
Bing Ren, UCSD
6
Rohit N. Kulkarni, M.D., Ph.D.
5
Kyle Gaulton, UCSD
2
Anna Gloyn, Oxford
Audit category:
85
inconsistent ontology term
1
inconsistent control
1
inconsistent replicate
Audit category:
10
missing controlled_by
Audit category:
15
inconsistent control read length
5
inconsistent control run_type
1
inconsistent assembly
month_released!
July, 2018
organ_slims!
eye
target.investigated_as!
RNA binding protein
narrow histone mark
BIOSAMPLE
ASSAY
578 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
315
14
1
2
2
2
1
1
EndoC_BH1
8
33
19
6
1
3
2
2
1
smooth muscle cell of the coronary artery
6
52
8
GM12878
49
1
Panc1
10
1
1
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