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Schema
Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
466
ChIP-seq
total RNA-seq
29
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
WGBS
1
shRNA RNA-seq
1
siRNA RNA-seq
1
whole genome sequencing assay
Assay category
466
DNA binding
31
DNA accessibility
4
3D chromatin structure
2
Transcription
1
DNA methylation
1
DNA sequencing
Target of assay
347
transcription factor
89
recombinant protein
80
control
59
RNA binding protein
37
histone
37
histone modification
24
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
61
November, 2018
28
December, 2018
27
August, 2021
26
October, 2019
18
February, 2021
January, 2019
17
May, 2021
15
November, 2019
7
March, 2020
6
February, 2023
6
November, 2020
2
March, 2023
1
January, 2018
1
May, 2020
1
October, 2022
Available data
460
bam
404
fastq
403
bigWig
389
bed narrowPeak
340
bigBed narrowPeak
59
bed broadPeak
59
bigBed broadPeak
20
tagAlign
6
tsv
3
bed bed3+
3
tar
2
bedpe bed3+
2
hic
1
bed bed3
1
bed bedMethyl
1
bigBed bedMethyl
1
hdf5
1
txt
1
vcf
Organism
527
Homo sapiens
Biosample type
1693
tissue
841
primary cell
531
cell line
258
in vitro differentiated cells
10
stem cell
Organ
387
liver
59
pancreas
45
epithelium
43
blood
43
bodily fluid
15
kidney
14
artery
14
blood vessel
14
heart
14
vasculature
1
mammary gland
Project
522
AMP
7
T1D
2
community
Genome assembly (visualization)
411
hg19
345
GRCh38
Lab
493
AMP-T2D consortium
25
Bing Ren, UCSD
6
Rohit N. Kulkarni, M.D., Ph.D.
5
Kyle Gaulton, UCSD
2
Anna Gloyn, Oxford
Audit category:
56
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
month_released!
January, 2019
assay_title!
total RNA-seq
BIOSAMPLE
ASSAY
531 results
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ChIP-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
WGBS
shRNA RNA-seq
siRNA RNA-seq
whole genome sequencing assay
cell line
HepG2
378
1
2
2
2
1
1
EndoC_BH1
15
19
6
1
3
2
2
1
GM12878
42
1
Panc1
13
1
1
smooth muscle cell of the coronary artery
6
8
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