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Schema
Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
387
ChIP-seq
35
total RNA-seq
20
ATAC-seq
6
MeRIP-seq
5
STARR-seq
5
pCHi-C
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
387
DNA binding
37
Transcription
22
DNA accessibility
4
3D chromatin structure
1
DNA methylation
1
DNA sequencing
Target of assay
356
transcription factor
recombinant protein
80
control
65
RNA binding protein
38
histone
38
histone modification
30
chromatin remodeller
19
broad histone mark
19
narrow histone mark
3
nucleotide modification
2
other context
2
other post-translational modification
Date released
249
November, 2017
February, 2021
45
November, 2018
44
August, 2021
28
December, 2018
23
January, 2019
23
October, 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
398
bam
351
bigWig
345
fastq
302
bed narrowPeak
274
bigBed narrowPeak
59
bed broadPeak
59
bigBed broadPeak
41
tsv
12
tagAlign
3
tar
2
bed bed3+
2
bedpe bed3+
2
hic
1
bed bedMethyl
1
bigBed bedMethyl
1
hdf5
1
txt
1
vcf
Organism
473
Homo sapiens
Biosample type
2192
tissue
1040
primary cell
477
cell line
368
in vitro differentiated cells
10
stem cell
Organ
317
liver
66
pancreas
61
blood
61
bodily fluid
53
epithelium
12
kidney
8
embryo
1
mammary gland
Project
466
AMP
9
T1D
2
community
Genome assembly (visualization)
352
hg19
284
GRCh38
Lab
430
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:
59
inconsistent ontology term
1
inconsistent control
Audit category:
12
missing controlled_by
Audit category:
25
inconsistent control read length
8
inconsistent control run_type
1
inconsistent assembly
month_released!
February, 2021
target.investigated_as!
recombinant protein
BIOSAMPLE
ASSAY
477 results
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ChIP-seq
total RNA-seq
ATAC-seq
MeRIP-seq
STARR-seq
pCHi-C
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
296
14
2
1
2
1
1
GM12878
60
1
EndoC_BH1
15
7
19
6
1
3
2
2
1
Panc1
13
1
1
H1-hESC
8
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