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Schema
Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
476
ChIP-seq
59
total RNA-seq
20
ATAC-seq
6
MeRIP-seq
6
pCHi-C
5
STARR-seq
2
Capture-C
2
DNase-seq
2
Hi-C
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
476
DNA binding
61
Transcription
22
DNA accessibility
2
3D chromatin structure
1
DNA methylation
1
DNA sequencing
Target of assay
357
transcription factor
89
recombinant protein
81
control
65
RNA binding protein
36
histone
36
histone modification
30
chromatin remodeller
19
broad histone mark
17
narrow histone mark
3
nucleotide modification
2
other context
2
other post-translational modification
Date released
315
November, 2017
61
November, 2018
43
August, 2021
30
February, 2021
30
October, 2019
28
December, 2018
23
January, 2019
20
May, 2021
15
November, 2019
8
March, 2020
6
November, 2020
2
March, 2023
1
February, 2023
January, 2018
1
May, 2020
1
October, 2022
Available data
512
bam
461
bigWig
427
fastq
390
bed narrowPeak
355
bigBed narrowPeak
65
tsv
59
bed broadPeak
59
bigBed broadPeak
14
tagAlign
3
bed bed3+
3
tar
2
bedpe bed3+
hic
1
bed bed3
1
bed bedMethyl
1
bigBed bedMethyl
1
hdf5
1
txt
1
vcf
Organism
580
Homo sapiens
Biosample type
2660
tissue
876
primary cell
584
cell line
386
in vitro differentiated cells
9
stem cell
Organ
400
liver
87
pancreas
74
epithelium
artery
66
blood vessel
66
heart
66
vasculature
60
blood
60
bodily fluid
19
kidney
8
embryo
1
mammary gland
Project
582
AMP
T1D
2
community
Genome assembly (visualization)
459
hg19
396
GRCh38
Lab
543
AMP-T2D consortium
33
Bing Ren, UCSD
6
Rohit N. Kulkarni, M.D., Ph.D.
2
Anna Gloyn, Oxford
Audit category:
87
inconsistent ontology term
1
inconsistent control
1
inconsistent replicate
Audit category:
13
missing controlled_by
Audit category:
26
inconsistent control read length
8
inconsistent control run_type
1
inconsistent assembly
organ_slims!
artery
files.file_type!
hic
month_released!
January, 2018
award.project!
T1D
BIOSAMPLE
ASSAY
584 results
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ChIP-seq
total RNA-seq
ATAC-seq
MeRIP-seq
pCHi-C
STARR-seq
Capture-C
DNase-seq
Hi-C
CRISPR genome editing followed by sgRNA sequencing
MPRA
WGBS
shRNA RNA-seq
siRNA RNA-seq
whole genome sequencing assay
cell line
HepG2
378
14
1
2
2
1
1
1
EndoC_BH1
13
31
19
6
2
1
GM12878
60
Panc1
13
1
1
H1-hESC
8
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