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Schema
Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
469
ChIP-seq
10
ATAC-seq
5
STARR-seq
3
CRISPR genome editing followed by DNA sequencing
2
Hi-C
2
HiChIP
1
DNase-seq
1
MPRA
1
WGBS
1
pCHi-C
1
shRNA RNA-seq
1
siRNA RNA-seq
1
whole genome sequencing assay
Assay category
469
DNA binding
11
DNA accessibility
2
3D chromatin structure
2
Transcription
1
DNA methylation
1
DNA sequencing
Target of assay
360
transcription factor
89
recombinant protein
78
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
61
November, 2018
28
December, 2018
25
October, 2019
24
August, 2021
18
February, 2021
18
January, 2019
5
February, 2023
2
March, 2023
1
January, 2018
1
October, 2022
Available data
531
bam
472
bigWig
427
fastq
389
bed narrowPeak
354
bigBed narrowPeak
tsv
59
bed broadPeak
59
bigBed broadPeak
20
tagAlign
3
bed bed3+
3
tar
1
bed bed3
1
bed bedMethyl
bedpe bed3+
1
bigBed bedMethyl
1
hdf5
1
hic
1
txt
1
vcf
Organism
495
Homo sapiens
Biosample type
1679
tissue
528
primary cell
498
cell line
234
in vitro differentiated cells
6
stem cell
Organ
385
liver
61
blood
61
bodily fluid
57
pancreas
epithelium
14
artery
14
blood vessel
14
heart
14
vasculature
13
kidney
Project
491
AMP
5
T1D
2
community
Genome assembly (visualization)
407
hg19
345
GRCh38
Lab
467
AMP-T2D consortium
24
Bing Ren, UCSD
5
Kyle Gaulton, UCSD
2
Anna Gloyn, Oxford
Audit category:
11
inconsistent ontology term
1
inconsistent control
1
inconsistent replicate
Audit category:
13
missing controlled_by
Audit category:
26
inconsistent control read length
8
inconsistent control run_type
1
inconsistent assembly
files.file_type!
tsv
bedpe bed3+
organ_slims!
epithelium
BIOSAMPLE
ASSAY
498 results
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ChIP-seq
ATAC-seq
STARR-seq
CRISPR genome editing followed by DNA sequencing
Hi-C
HiChIP
DNase-seq
MPRA
WGBS
pCHi-C
shRNA RNA-seq
siRNA RNA-seq
whole genome sequencing assay
cell line
HepG2
378
1
2
1
1
1
1
GM12878
60
1
Panc1
13
1
1
smooth muscle cell of the coronary artery
6
8
EndoC_BH1
3
2
RCC 7860 HIF1a re-expression
4
RCC 7860 HIF2a over-expression
3
RCC 7860 vector
3
EndoC-BH1
1
1
HEK293T
2
iPSC derived cell line
2
MIN6
1
Synthesized DNA
1
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