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Schema
Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
427
ChIP-seq
113
total RNA-seq
28
ATAC-seq
10
pCHi-C
6
MeRIP-seq
5
STARR-seq
4
Hi-C
3
CRISPR genome editing followed by DNA sequencing
2
Capture-C
2
DNase-seq
2
HiChIP
1
CRISPR RNA-seq
1
CRISPR genome editing followed by sgRNA sequencing
1
CRISPRi RNA-seq
1
GRO-seq
1
MPRA
1
WGBS
1
shRNA RNA-seq
1
siRNA RNA-seq
1
whole genome sequencing assay
Assay category
427
DNA binding
117
Transcription
30
DNA accessibility
4
3D chromatin structure
1
DNA methylation
1
DNA sequencing
Target of assay
310
transcription factor
89
recombinant protein
78
control
55
RNA binding protein
39
histone
39
histone modification
20
broad histone mark
20
chromatin remodeller
19
narrow histone mark
3
nucleotide modification
2
other context
2
other post-translational modification
Date released
315
November, 2017
96
February, 2021
46
November, 2018
44
August, 2021
30
October, 2019
21
May, 2021
16
November, 2019
15
March, 2020
6
February, 2023
6
November, 2020
5
January, 2019
4
March, 2023
3
December, 2017
1
December, 2018
1
January, 2018
1
May, 2020
1
October, 2022
Available data
525
bam
470
bigWig
371
fastq
352
bed narrowPeak
301
bigBed narrowPeak
123
tsv
59
bed broadPeak
59
bigBed broadPeak
20
tagAlign
6
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
605
Homo sapiens
Biosample type
2737
tissue
1080
primary cell
601
cell line
394
in vitro differentiated cells
10
stem cell
Organ
401
liver
92
pancreas
79
epithelium
66
artery
66
blood vessel
66
heart
66
vasculature
blood
61
bodily fluid
19
kidney
8
embryo
1
connective tissue
1
mammary gland
Project
598
AMP
9
T1D
4
community
Genome assembly (visualization)
478
hg19
413
GRCh38
1
hg18
Lab
562
AMP-T2D consortium
34
Bing Ren, UCSD
6
Rohit N. Kulkarni, M.D., Ph.D.
5
Kyle Gaulton, UCSD
4
Anna Gloyn, Oxford
Audit category:
93
inconsistent ontology term
1
inconsistent replicate
Audit category:
13
missing controlled_by
Audit category:
28
inconsistent control read length
8
inconsistent control run_type
1
inconsistent assembly
organ_slims!
blood
BIOSAMPLE
ASSAY
611 results
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Clear Filters
ChIP-seq
total RNA-seq
ATAC-seq
pCHi-C
MeRIP-seq
STARR-seq
Hi-C
CRISPR genome editing followed by DNA sequencing
Capture-C
DNase-seq
HiChIP
CRISPR RNA-seq
CRISPR genome editing followed by sgRNA sequencing
CRISPRi RNA-seq
GRO-seq
MPRA
WGBS
shRNA RNA-seq
siRNA RNA-seq
whole genome sequencing assay
cell line
HepG2
378
14
1
2
2
2
1
1
EndoC_BH1
15
33
19
6
1
3
2
2
1
smooth muscle cell of the coronary artery
6
52
8
Panc1
13
1
1
H1-hESC
8
+ See 13 more…
stem cell
hESC
3
1
SB Ad3.1
1
1
mesenchymal stem cell
1
mesendoderm
1
neural progenitor cell (neural stem cell)
1
+ See 1 more…
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