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Schema
Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
131
ChIP-seq
113
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
HiChIP
1
CRISPR genome editing followed by sgRNA sequencing
1
MPRA
1
shRNA RNA-seq
1
siRNA RNA-seq
1
whole genome sequencing assay
Assay category
131
DNA binding
115
Transcription
29
DNA accessibility
4
3D chromatin structure
1
DNA sequencing
Target of assay
83
control
33
transcription factor
18
histone
18
histone modification
9
broad histone mark
9
narrow histone mark
8
recombinant protein
4
RNA binding protein
3
nucleotide modification
Date released
96
February, 2021
66
November, 2017
44
August, 2021
22
October, 2019
21
May, 2021
16
November, 2019
11
March, 2020
8
January, 2019
6
February, 2023
6
November, 2020
4
November, 2018
2
March, 2023
1
December, 2018
1
January, 2018
1
May, 2020
1
October, 2022
Available data
581
bam
521
bigWig
426
fastq
403
bed narrowPeak
bigBed narrowPeak
119
tsv
59
bed broadPeak
59
bigBed broadPeak
20
tagAlign
3
bed bed3+
3
tar
2
bedpe bed3+
2
hic
1
bed bed3
1
bed bedMethyl
bigBed bedMethyl
1
hdf5
1
txt
1
vcf
Organism
302
Homo sapiens
Biosample type
2191
tissue
969
primary cell
377
in vitro differentiated cells
306
cell line
10
stem cell
Organ
107
liver
85
pancreas
78
epithelium
66
artery
66
blood vessel
66
heart
66
vasculature
18
kidney
8
embryo
7
blood
7
bodily fluid
1
mammary gland
Project
295
AMP
9
T1D
2
community
Genome assembly (visualization)
179
hg19
140
GRCh38
Lab
259
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:
92
inconsistent ontology term
1
inconsistent replicate
Audit category:
1
missing controlled_by
Audit category:
2
inconsistent control read length
1
inconsistent assembly
audit.ERROR.category!
inconsistent control
files.file_type!
bigBed bedMethyl
bigBed narrowPeak
BIOSAMPLE
ASSAY
306 results
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ChIP-seq
total RNA-seq
ATAC-seq
MeRIP-seq
pCHi-C
STARR-seq
Hi-C
CRISPR genome editing followed by DNA sequencing
Capture-C
HiChIP
CRISPR genome editing followed by sgRNA sequencing
MPRA
shRNA RNA-seq
siRNA RNA-seq
whole genome sequencing assay
cell line
HepG2
85
14
1
2
2
2
1
EndoC_BH1
15
33
19
6
1
3
2
2
1
smooth muscle cell of the coronary artery
6
52
8
H1-hESC
8
Panc1
7
1
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