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Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
484
ChIP-seq
total RNA-seq
29
ATAC-seq
5
STARR-seq
5
pCHi-C
3
CRISPR genome editing followed by DNA sequencing
3
Hi-C
2
Capture-C
2
HiChIP
1
CRISPR genome editing followed by sgRNA sequencing
1
DNase-seq
1
MPRA
1
WGBS
1
shRNA RNA-seq
1
siRNA RNA-seq
1
whole genome sequencing assay
Assay category
484
DNA binding
30
DNA accessibility
3
3D chromatin structure
2
Transcription
1
DNA methylation
1
DNA sequencing
Target of assay
361
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
2
other context
2
other post-translational modification
Date released
315
November, 2017
61
November, 2018
28
December, 2018
27
August, 2021
24
October, 2019
18
January, 2019
17
February, 2021
17
May, 2021
15
November, 2019
7
March, 2020
6
February, 2023
2
March, 2023
1
January, 2018
1
May, 2020
1
October, 2022
Available data
478
bam
422
fastq
418
bigWig
404
bed narrowPeak
355
bigBed narrowPeak
59
bed broadPeak
59
bigBed broadPeak
20
tagAlign
6
tsv
bed bed3+
3
tar
2
bedpe bed3+
2
hic
1
bed bed3
1
bed bedMethyl
1
bigBed bedMethyl
1
hdf5
1
txt
1
vcf
Organism
536
Homo sapiens
Biosample type
1491
tissue
806
primary cell
540
cell line
233
in vitro differentiated cells
7
stem cell
Organ
386
liver
61
blood
61
bodily fluid
51
pancreas
39
epithelium
15
kidney
14
artery
14
blood vessel
14
heart
14
vasculature
1
mammary gland
Project
531
AMP
7
T1D
2
community
Genome assembly (visualization)
423
hg19
358
GRCh38
Lab
508
AMP-T2D consortium
25
Bing Ren, UCSD
Rohit N. Kulkarni, M.D., Ph.D.
5
Kyle Gaulton, UCSD
2
Anna Gloyn, Oxford
Audit category:
50
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
files.file_type!
bed bed3+
lab.title!
Rohit N. Kulkarni, M.D., Ph.D.
assay_title!
total RNA-seq
BIOSAMPLE
ASSAY
540 results
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ChIP-seq
ATAC-seq
STARR-seq
pCHi-C
CRISPR genome editing followed by DNA sequencing
Hi-C
Capture-C
HiChIP
CRISPR genome editing followed by sgRNA sequencing
DNase-seq
MPRA
WGBS
shRNA RNA-seq
siRNA RNA-seq
whole genome sequencing assay
cell line
HepG2
378
1
2
1
2
1
1
GM12878
60
1
EndoC_BH1
15
19
3
1
2
2
1
smooth muscle cell of the coronary artery
6
8
Panc1
13
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