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Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
451
ChIP-seq
25
total RNA-seq
4
STARR-seq
3
CRISPR genome editing followed by DNA sequencing
3
Hi-C
3
pCHi-C
2
DNase-seq
2
HiChIP
1
ATAC-seq
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
451
DNA binding
27
Transcription
3
3D chromatin structure
3
DNA accessibility
1
DNA methylation
1
DNA sequencing
Target of assay
348
transcription factor
82
recombinant protein
72
control
64
RNA binding protein
30
chromatin remodeller
26
histone
26
histone modification
13
broad histone mark
13
narrow histone mark
2
other context
2
other post-translational modification
Date released
315
November, 2017
February, 2021
61
November, 2018
41
August, 2021
28
December, 2018
23
January, 2019
17
October, 2019
6
February, 2023
4
March, 2020
2
March, 2023
1
January, 2018
1
May, 2020
1
October, 2022
Available data
451
bam
427
fastq
407
bigWig
369
bed narrowPeak
355
bigBed narrowPeak
59
bed broadPeak
59
bigBed broadPeak
28
tsv
12
tagAlign
3
tar
2
bed bed3+
1
bed bedMethyl
1
bedpe bed3+
1
bigBed bedMethyl
1
hdf5
1
hic
1
txt
1
vcf
Organism
496
Homo sapiens
Biosample type
2185
tissue
986
primary cell
500
cell line
271
in vitro differentiated cells
9
stem cell
Organ
399
liver
61
blood
61
bodily fluid
16
pancreas
8
embryo
4
kidney
3
epithelium
1
mammary gland
Project
493
AMP
5
T1D
2
community
Genome assembly (visualization)
403
hg19
341
GRCh38
Lab
460
AMP-T2D consortium
33
Bing Ren, UCSD
5
Kyle Gaulton, UCSD
2
Anna Gloyn, Oxford
Audit category:
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
audit.ERROR.category!
inconsistent ontology term
month_released!
February, 2021
BIOSAMPLE
ASSAY
500 results
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ChIP-seq
total RNA-seq
STARR-seq
CRISPR genome editing followed by DNA sequencing
Hi-C
pCHi-C
DNase-seq
HiChIP
ATAC-seq
CRISPR genome editing followed by sgRNA sequencing
MPRA
WGBS
shRNA RNA-seq
siRNA RNA-seq
whole genome sequencing assay
cell line
HepG2
378
14
2
2
1
1
1
GM12878
60
1
Panc1
13
1
1
H1-hESC
8
EndoC_BH1
3
2
1
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