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Schema
Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
450
ChIP-seq
61
total RNA-seq
21
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
DNase-seq
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
450
DNA binding
63
Transcription
23
DNA accessibility
4
3D chromatin structure
DNA methylation
1
DNA sequencing
Target of assay
356
transcription factor
89
recombinant protein
79
control
65
RNA binding protein
30
chromatin remodeller
27
histone
27
histone modification
narrow histone mark
13
broad histone mark
3
nucleotide modification
2
other context
2
other post-translational modification
Date released
301
November, 2017
60
November, 2018
42
August, 2021
28
December, 2018
28
February, 2021
27
October, 2019
22
January, 2019
20
May, 2021
12
November, 2019
10
March, 2020
6
February, 2023
6
November, 2020
2
March, 2023
1
January, 2018
1
May, 2020
1
October, 2022
Available data
498
bam
446
bigWig
418
fastq
374
bed narrowPeak
345
bigBed narrowPeak
67
tsv
53
bed broadPeak
53
bigBed broadPeak
tagAlign
3
bed bed3+
3
tar
2
bedpe bed3+
2
hic
1
bed bed3
1
hdf5
1
txt
1
vcf
Organism
563
Homo sapiens
Biosample type
2174
tissue
834
primary cell
567
cell line
311
in vitro differentiated cells
9
stem cell
Organ
384
liver
83
pancreas
73
epithelium
60
artery
60
blood
60
blood vessel
60
bodily fluid
60
heart
vasculature
19
kidney
8
embryo
1
mammary gland
Project
558
AMP
7
T1D
2
community
Genome assembly (visualization)
439
hg19
377
GRCh38
Lab
522
AMP-T2D consortium
32
Bing Ren, UCSD
6
Rohit N. Kulkarni, M.D., Ph.D.
5
Kyle Gaulton, UCSD
2
Anna Gloyn, Oxford
Audit category:
86
inconsistent ontology term
1
inconsistent control
1
inconsistent replicate
Audit category:
12
missing controlled_by
Audit category:
15
inconsistent control read length
8
inconsistent control run_type
1
inconsistent assembly
assay_slims!
DNA methylation
files.file_type!
tagAlign
organ_slims!
vasculature
target.investigated_as!
narrow histone mark
BIOSAMPLE
ASSAY
567 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
DNase-seq
HiChIP
CRISPR genome editing followed by sgRNA sequencing
MPRA
shRNA RNA-seq
siRNA RNA-seq
whole genome sequencing assay
cell line
HepG2
362
14
1
2
2
2
1
EndoC_BH1
9
33
19
6
1
3
2
2
1
GM12878
59
1
Panc1
10
1
1
H1-hESC
8
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