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Schema
Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
474
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
474
DNA binding
37
Transcription
22
DNA accessibility
4
3D chromatin structure
1
DNA methylation
1
DNA sequencing
Target of assay
356
transcription factor
89
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
other context
2
other post-translational modification
Date released
313
November, 2017
February, 2021
61
November, 2018
44
August, 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
485
bam
437
bigWig
425
fastq
388
bed narrowPeak
353
bigBed narrowPeak
58
bed broadPeak
58
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
560
Homo sapiens
Biosample type
2189
tissue
1040
primary cell
564
cell line
368
in vitro differentiated cells
10
stem cell
Organ
397
liver
66
pancreas
61
blood
61
bodily fluid
53
epithelium
19
kidney
8
embryo
1
mammary gland
Project
553
AMP
9
T1D
2
community
Genome assembly (visualization)
435
hg19
370
GRCh38
Lab
517
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:
66
inconsistent ontology term
1
inconsistent control
Audit category:
13
missing controlled_by
Audit category:
26
inconsistent control read length
8
inconsistent control run_type
1
inconsistent assembly
month_released!
February, 2021
target.investigated_as!
other context
BIOSAMPLE
ASSAY
564 results
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Clear Filters
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
376
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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