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Schema
Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
19
ATAC-seq
11
ChIP-seq
6
pCHi-C
5
STARR-seq
4
Hi-C
3
CRISPR genome editing followed by DNA sequencing
3
MeRIP-seq
2
Capture-C
2
HiChIP
1
CRISPR genome editing followed by sgRNA sequencing
1
MPRA
1
WGBS
1
whole genome sequencing assay
Assay category
Transcription
19
DNA accessibility
11
DNA binding
4
3D chromatin structure
1
DNA methylation
1
DNA sequencing
Target of assay
control
8
transcription factor
3
histone
3
histone modification
3
nucleotide modification
2
RNA binding protein
2
broad histone mark
1
narrow histone mark
Date released
16
May, 2021
10
November, 2017
9
August, 2021
6
February, 2023
6
March, 2020
3
November, 2020
2
October, 2019
1
December, 2018
1
February, 2021
1
January, 2018
1
May, 2020
1
November, 2018
1
November, 2019
1
October, 2022
Available data
393
bigWig
bed narrowPeak
389
bam
347
fastq
343
bigBed narrowPeak
59
bed broadPeak
59
bigBed broadPeak
16
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
57
Homo sapiens
Biosample type
357
tissue
313
primary cell
81
in vitro differentiated cells
59
cell line
5
stem cell
Organ
27
pancreas
25
epithelium
18
liver
4
kidney
1
blood
1
bodily fluid
1
mammary gland
Project
54
AMP
5
T1D
Genome assembly (visualization)
13
hg19
2
GRCh38
Lab
44
AMP-T2D consortium
7
Bing Ren, UCSD
5
Kyle Gaulton, UCSD
3
Rohit N. Kulkarni, M.D., Ph.D.
Audit category:
27
inconsistent ontology term
Audit category:
missing controlled_by
Audit category:
2
inconsistent control read length
1
inconsistent assembly
assay_slims!
Transcription
audit.NOT_COMPLIANT.category!
missing controlled_by
files.file_type!
bed narrowPeak
target.investigated_as!
control
BIOSAMPLE
ASSAY
59 results
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ATAC-seq
ChIP-seq
pCHi-C
STARR-seq
Hi-C
CRISPR genome editing followed by DNA sequencing
MeRIP-seq
Capture-C
HiChIP
CRISPR genome editing followed by sgRNA sequencing
MPRA
WGBS
whole genome sequencing assay
cell line
EndoC_BH1
18
1
3
3
2
2
1
HepG2
10
2
2
2
1
1
HEK293T
2
Panc1
1
1
GM12878
1
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