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Schema
Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
465
ChIP-seq
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
465
DNA binding
31
DNA accessibility
4
3D chromatin structure
2
Transcription
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
broad histone mark
19
narrow histone mark
3
nucleotide modification
2
other context
2
other post-translational modification
Date released
307
November, 2017
61
November, 2018
28
December, 2018
26
August, 2021
22
October, 2019
18
February, 2021
18
January, 2019
17
May, 2021
9
November, 2019
7
March, 2020
6
February, 2023
6
November, 2020
2
March, 2023
1
January, 2018
1
May, 2020
1
October, 2022
Available data
460
bam
414
fastq
400
bigWig
387
bed narrowPeak
345
bigBed narrowPeak
51
bed broadPeak
51
bigBed broadPeak
14
tagAlign
6
tsv
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
526
Homo sapiens
Biosample type
1418
tissue
719
primary cell
530
cell line
202
in vitro differentiated cells
9
stem cell
Organ
378
liver
61
blood
61
bodily fluid
49
pancreas
39
epithelium
15
kidney
14
artery
14
blood vessel
14
heart
14
vasculature
1
mammary gland
Project
521
AMP
7
T1D
2
community
Genome assembly (visualization)
408
hg19
344
GRCh38
Lab
493
AMP-T2D consortium
24
Bing Ren, UCSD
6
Rohit N. Kulkarni, M.D., Ph.D.
5
Kyle Gaulton, UCSD
2
Anna Gloyn, Oxford
Audit category:
50
inconsistent ontology term
1
inconsistent control
1
inconsistent replicate
Audit category:
13
missing controlled_by
Audit category:
20
inconsistent control read length
8
inconsistent control run_type
1
inconsistent assembly
award.project!
LungMap
assay_title!
total RNA-seq
target.investigated_as!
broad histone mark
BIOSAMPLE
ASSAY
530 results
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ChIP-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
369
1
2
2
2
1
1
GM12878
60
1
EndoC_BH1
9
19
6
1
3
2
2
1
smooth muscle cell of the coronary artery
6
8
Panc1
9
1
1
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