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Schema
Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
359
ChIP-seq
28
total RNA-seq
6
pCHi-C
5
STARR-seq
3
CRISPR genome editing followed by DNA sequencing
2
ATAC-seq
2
Hi-C
2
HiChIP
1
DNase-seq
1
MPRA
1
WGBS
1
shRNA RNA-seq
1
siRNA RNA-seq
1
whole genome sequencing assay
Assay category
359
DNA binding
30
Transcription
3
DNA accessibility
2
3D chromatin structure
1
DNA methylation
1
DNA sequencing
Target of assay
356
transcription factor
recombinant protein
70
control
64
RNA binding protein
30
chromatin remodeller
19
histone
19
histone modification
10
narrow histone mark
9
broad histone mark
other context
2
other post-translational modification
Date released
247
November, 2017
45
November, 2018
42
August, 2021
28
December, 2018
23
January, 2019
8
October, 2019
6
March, 2020
5
February, 2023
4
February, 2021
2
March, 2023
1
January, 2018
1
May, 2020
1
October, 2022
Available data
362
bam
343
fastq
320
bigWig
281
bed narrowPeak
265
bigBed narrowPeak
57
bed broadPeak
57
bigBed broadPeak
33
tsv
14
tagAlign
3
tar
1
bed bed3
1
bed bed3+
1
bed bedMethyl
1
bedpe bed3+
1
bigBed bedMethyl
1
hic
1
txt
1
vcf
Organism
410
Homo sapiens
Biosample type
2136
tissue
711
primary cell
413
cell line
391
in vitro differentiated cells
10
stem cell
Organ
317
liver
pancreas
79
epithelium
66
artery
blood vessel
66
heart
66
vasculature
61
blood
61
bodily fluid
12
kidney
8
embryo
1
mammary gland
Project
406
AMP
5
T1D
2
community
Genome assembly (visualization)
321
hg19
255
GRCh38
Lab
372
AMP-T2D consortium
34
Bing Ren, UCSD
5
Kyle Gaulton, UCSD
2
Anna Gloyn, Oxford
Audit category:
9
inconsistent ontology term
1
inconsistent control
1
inconsistent replicate
Audit category:
12
missing controlled_by
Audit category:
25
inconsistent control read length
8
inconsistent control run_type
organ_slims!
blood vessel
pancreas
target.investigated_as!
other context
recombinant protein
BIOSAMPLE
ASSAY
413 results
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ChIP-seq
total RNA-seq
pCHi-C
STARR-seq
CRISPR genome editing followed by DNA sequencing
ATAC-seq
Hi-C
HiChIP
DNase-seq
MPRA
WGBS
shRNA RNA-seq
siRNA RNA-seq
whole genome sequencing assay
cell line
HepG2
294
14
2
2
1
2
1
1
GM12878
60
1
H1-hESC
8
EndoC_BH1
3
2
RCC 7860 vector
1
1
1
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