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Schema
Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
476
ChIP-seq
19
ATAC-seq
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 genome editing followed by sgRNA sequencing
1
MPRA
WGBS
1
shRNA RNA-seq
1
siRNA RNA-seq
1
whole genome sequencing assay
Assay category
476
DNA binding
21
DNA accessibility
4
3D chromatin structure
2
Transcription
1
DNA sequencing
Target of assay
356
transcription factor
89
recombinant protein
80
control
65
RNA binding protein
38
histone
38
histone modification
30
chromatin remodeller
19
broad histone mark
19
narrow histone mark
3
nucleotide modification
2
other context
2
other post-translational modification
Date released
315
November, 2017
60
November, 2018
28
December, 2018
27
August, 2021
26
October, 2019
February, 2021
18
January, 2019
17
May, 2021
15
November, 2019
6
February, 2023
6
November, 2020
2
March, 2020
2
March, 2023
1
January, 2018
1
October, 2022
Available data
486
bam
438
bigWig
426
fastq
390
bed narrowPeak
355
bigBed narrowPeak
59
bed broadPeak
59
bigBed broadPeak
tsv
12
tagAlign
3
tar
2
bed bed3+
2
bedpe bed3+
2
hic
1
hdf5
1
txt
1
vcf
Organism
520
Homo sapiens
Biosample type
1581
tissue
736
primary cell
524
cell line
259
in vitro differentiated cells
6
stem cell
Organ
383
liver
61
blood
61
bodily fluid
58
pancreas
44
epithelium
13
kidney
Project
515
AMP
7
T1D
2
community
Genome assembly (visualization)
410
hg19
345
GRCh38
Lab
486
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:
53
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
month_released!
February, 2021
files.file_type!
tsv
assay_title!
WGBS
BIOSAMPLE
ASSAY
524 results
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ChIP-seq
ATAC-seq
MeRIP-seq
STARR-seq
Hi-C
CRISPR genome editing followed by DNA sequencing
Capture-C
DNase-seq
HiChIP
CRISPR genome editing followed by sgRNA sequencing
MPRA
shRNA RNA-seq
siRNA RNA-seq
whole genome sequencing assay
cell line
HepG2
378
2
2
1
GM12878
60
1
EndoC_BH1
15
18
6
1
3
2
2
1
Panc1
13
1
1
RCC 7860 HIF1a re-expression
4
RCC 7860 HIF2a over-expression
3
RCC 7860 vector
3
EndoC-BH1
1
1
HEK293T
2
MIN6
1
Synthesized DNA
1
glomerular visceral epithelial cell
1
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