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Schema
Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
487
ChIP-seq
total RNA-seq
29
ATAC-seq
10
pCHi-C
6
MeRIP-seq
5
STARR-seq
4
Hi-C
3
CRISPR genome editing followed by DNA sequencing
2
Capture-C
2
DNase-seq
2
HiChIP
1
CRISPR RNA-seq
1
CRISPR genome editing followed by sgRNA sequencing
1
CRISPRi RNA-seq
1
GRO-seq
1
MPRA
1
WGBS
1
shRNA RNA-seq
1
siRNA RNA-seq
1
whole genome sequencing assay
Assay category
487
DNA binding
31
DNA accessibility
4
3D chromatin structure
4
Transcription
1
DNA methylation
1
DNA sequencing
Target of assay
361
transcription factor
89
recombinant protein
84
control
65
RNA binding protein
40
histone
40
histone modification
30
chromatin remodeller
20
broad histone mark
20
narrow histone mark
3
nucleotide modification
2
other context
2
other post-translational modification
Date released
315
November, 2017
61
November, 2018
28
December, 2018
27
August, 2021
26
October, 2019
18
February, 2021
18
January, 2019
17
May, 2021
15
November, 2019
11
March, 2020
6
February, 2023
6
November, 2020
4
March, 2023
3
December, 2017
2
January, 2018
1
May, 2020
1
October, 2022
Available data
481
bam
426
fastq
421
bigWig
406
bed narrowPeak
355
bigBed narrowPeak
59
bed broadPeak
59
bigBed broadPeak
20
tagAlign
10
tsv
6
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
553
Homo sapiens
Biosample type
1690
tissue
836
primary cell
549
cell line
258
in vitro differentiated cells
10
stem cell
Organ
387
liver
61
blood
61
bodily fluid
59
pancreas
45
epithelium
15
kidney
14
artery
14
blood vessel
14
heart
14
vasculature
1
connective tissue
1
mammary gland
Project
548
AMP
7
T1D
4
community
Genome assembly (visualization)
429
hg19
363
GRCh38
1
hg18
Lab
519
AMP-T2D consortium
25
Bing Ren, UCSD
6
Rohit N. Kulkarni, M.D., Ph.D.
5
Kyle Gaulton, UCSD
4
Anna Gloyn, Oxford
Audit category:
57
inconsistent ontology term
1
inconsistent control
1
inconsistent replicate
Audit category:
13
missing controlled_by
Audit category:
28
inconsistent control read length
8
inconsistent control run_type
1
inconsistent assembly
assay_title!
total RNA-seq
award.project!
LungMap
organ_slims!
eye
BIOSAMPLE
ASSAY
559 results
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ChIP-seq
ATAC-seq
pCHi-C
MeRIP-seq
STARR-seq
Hi-C
CRISPR genome editing followed by DNA sequencing
Capture-C
DNase-seq
HiChIP
CRISPR RNA-seq
CRISPR genome editing followed by sgRNA sequencing
CRISPRi RNA-seq
GRO-seq
MPRA
WGBS
shRNA RNA-seq
siRNA RNA-seq
whole genome sequencing assay
cell line
HepG2
378
1
2
2
2
1
1
GM12878
60
1
EndoC_BH1
15
19
6
1
3
2
2
1
Panc1
13
1
1
smooth muscle cell of the coronary artery
6
8
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stem cell
hESC
3
1
SB Ad3.1
1
1
mesenchymal stem cell
1
mesendoderm
1
neural progenitor cell (neural stem cell)
1
+ See 1 more…
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