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Schema
Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
461
ChIP-seq
26
total RNA-seq
20
ATAC-seq
9
pCHi-C
6
MeRIP-seq
3
CRISPR genome editing followed by DNA sequencing
3
Hi-C
2
Capture-C
2
DNase-seq
2
HiChIP
1
CRISPR RNA-seq
1
CRISPR genome editing followed by sgRNA sequencing
1
CRISPRi RNA-seq
1
GRO-seq
1
MPRA
1
WGBS
1
shRNA RNA-seq
1
siRNA RNA-seq
Assay category
461
DNA binding
30
Transcription
22
DNA accessibility
3
3D chromatin structure
1
DNA methylation
Target of assay
345
transcription factor
89
recombinant protein
77
control
64
RNA binding protein
37
histone
37
histone modification
30
chromatin remodeller
19
broad histone mark
18
narrow histone mark
3
nucleotide modification
2
other context
2
other post-translational modification
Date released
315
November, 2017
February, 2021
61
November, 2018
30
October, 2019
28
December, 2018
23
January, 2019
21
May, 2021
16
November, 2019
15
March, 2020
10
August, 2021
6
February, 2023
6
November, 2020
4
March, 2023
3
December, 2017
2
January, 2018
1
May, 2020
1
October, 2022
Available data
490
bam
431
fastq
428
bigWig
378
bed narrowPeak
355
bigBed narrowPeak
59
bed broadPeak
59
bigBed broadPeak
36
tsv
12
tagAlign
5
bed bed3+
3
tar
1
bed bedMethyl
1
bedpe bed3+
1
bigBed bedMethyl
1
hdf5
1
hic
1
txt
Organism
536
Homo sapiens
Biosample type
2188
tissue
1040
primary cell
532
cell line
368
in vitro differentiated cells
10
stem cell
Organ
368
liver
66
pancreas
61
blood
61
bodily fluid
53
epithelium
17
kidney
8
embryo
1
connective tissue
1
mammary gland
Project
529
AMP
9
T1D
4
community
Genome assembly (visualization)
425
hg19
375
GRCh38
1
hg18
Lab
527
AMP-T2D consortium
Bing Ren, UCSD
6
Rohit N. Kulkarni, M.D., Ph.D.
5
Kyle Gaulton, UCSD
4
Anna Gloyn, Oxford
Audit category:
66
inconsistent ontology term
1
inconsistent control
Audit category:
13
missing controlled_by
Audit category:
28
inconsistent control read length
8
inconsistent control run_type
1
inconsistent assembly
lab.title!
Bing Ren, UCSD
month_released!
February, 2021
BIOSAMPLE
ASSAY
542 results
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Clear Filters
ChIP-seq
total RNA-seq
ATAC-seq
pCHi-C
MeRIP-seq
CRISPR genome editing followed by DNA sequencing
Hi-C
Capture-C
DNase-seq
HiChIP
CRISPR RNA-seq
CRISPR genome editing followed by sgRNA sequencing
CRISPRi RNA-seq
GRO-seq
MPRA
WGBS
shRNA RNA-seq
siRNA RNA-seq
cell line
HepG2
360
5
1
1
1
GM12878
60
1
EndoC_BH1
15
7
19
6
3
1
2
2
1
Panc1
13
1
1
H1-hESC
8
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stem cell
hESC
3
1
SB Ad3.1
1
1
mesenchymal stem cell
1
mesendoderm
1
neural progenitor cell (neural stem cell)
1
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