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Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
474
ChIP-seq
33
total RNA-seq
20
ATAC-seq
5
STARR-seq
5
pCHi-C
4
Hi-C
2
Capture-C
2
DNase-seq
1
CRISPR genome editing followed by sgRNA sequencing
1
MPRA
1
WGBS
1
whole genome sequencing assay
Assay category
474
DNA binding
33
Transcription
22
DNA accessibility
4
3D chromatin structure
1
DNA methylation
1
DNA sequencing
Target of assay
356
transcription factor
89
recombinant protein
77
control
65
RNA binding protein
36
histone
36
histone modification
30
chromatin remodeller
19
broad histone mark
17
narrow histone mark
2
other context
2
other post-translational modification
Date released
315
November, 2017
February, 2021
61
November, 2018
44
August, 2021
30
October, 2019
28
December, 2018
23
January, 2019
20
May, 2021
16
November, 2019
8
March, 2020
1
February, 2023
1
January, 2018
1
May, 2020
1
October, 2022
Available data
483
bam
435
bigWig
427
fastq
388
bed narrowPeak
355
bigBed narrowPeak
59
bed broadPeak
59
bigBed broadPeak
39
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
547
Homo sapiens
Biosample type
2131
tissue
556
primary cell
549
cell line
368
in vitro differentiated cells
8
stem cell
Organ
399
liver
61
blood
61
bodily fluid
56
pancreas
43
epithelium
19
kidney
8
embryo
1
mammary gland
Project
549
AMP
9
T1D
2
community
Genome assembly (visualization)
433
hg19
368
GRCh38
Lab
515
AMP-T2D consortium
34
Bing Ren, UCSD
Rohit N. Kulkarni, M.D., Ph.D.
Audit category:
56
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
lab.title!
Rohit N. Kulkarni, M.D., Ph.D.
month_released!
February, 2021
BIOSAMPLE
ASSAY
549 results
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ChIP-seq
total RNA-seq
ATAC-seq
STARR-seq
pCHi-C
Hi-C
Capture-C
DNase-seq
CRISPR genome editing followed by sgRNA sequencing
MPRA
WGBS
whole genome sequencing assay
cell line
HepG2
378
14
2
1
2
1
1
GM12878
60
1
EndoC_BH1
13
5
19
1
2
1
Panc1
13
1
1
H1-hESC
8
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