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Schema
Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
408
ChIP-seq
108
total RNA-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
WGBS
1
shRNA RNA-seq
1
siRNA RNA-seq
1
whole genome sequencing assay
Assay category
408
DNA binding
110
Transcription
DNA accessibility
4
3D chromatin structure
1
DNA methylation
1
DNA sequencing
Target of assay
303
transcription factor
89
recombinant protein
80
control
55
RNA binding protein
23
histone
23
histone modification
20
chromatin remodeller
12
narrow histone mark
11
broad histone mark
3
nucleotide modification
1
other context
1
other post-translational modification
Date released
257
November, 2017
87
February, 2021
61
November, 2018
44
August, 2021
28
December, 2018
28
October, 2019
January, 2019
15
November, 2019
9
March, 2020
6
February, 2023
6
November, 2020
5
May, 2021
2
March, 2023
1
May, 2020
1
October, 2022
Available data
547
bam
497
bigWig
404
fastq
377
bed narrowPeak
338
bigBed narrowPeak
113
tsv
58
bed broadPeak
bigBed broadPeak
20
tagAlign
3
tar
2
bed bed3+
2
bedpe bed3+
2
hic
1
bed bedMethyl
1
bigBed bedMethyl
1
hdf5
1
txt
1
vcf
Organism
546
Homo sapiens
Biosample type
2300
tissue
779
primary cell
550
cell line
347
in vitro differentiated cells
9
stem cell
Organ
337
liver
72
pancreas
59
epithelium
58
artery
58
blood vessel
58
heart
58
vasculature
42
blood
42
bodily fluid
18
kidney
8
embryo
1
mammary gland
Project
539
AMP
9
T1D
2
community
Genome assembly (visualization)
437
hg19
388
GRCh38
Lab
503
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:
73
inconsistent ontology term
1
inconsistent control
Audit category:
13
missing controlled_by
Audit category:
13
inconsistent control read length
8
inconsistent control run_type
1
inconsistent assembly
assay_slims!
DNA accessibility
assembly!
hg18
files.file_type!
bigBed broadPeak
month_released!
January, 2019
BIOSAMPLE
ASSAY
550 results
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ChIP-seq
total RNA-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
WGBS
shRNA RNA-seq
siRNA RNA-seq
whole genome sequencing assay
cell line
HepG2
320
9
2
2
2
1
1
EndoC_BH1
15
33
6
1
3
2
2
1
smooth muscle cell of the coronary artery
6
52
GM12878
42
Panc1
13
1
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