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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
17
ChIP-seq
9
total RNA-seq
6
MeRIP-seq
5
STARR-seq
5
pCHi-C
4
Hi-C
2
Capture-C
1
CRISPR genome editing followed by sgRNA sequencing
1
MPRA
1
shRNA RNA-seq
1
siRNA RNA-seq
1
whole genome sequencing assay
Assay category
19
DNA accessibility
17
DNA binding
11
Transcription
4
3D chromatin structure
1
DNA sequencing
Target of assay
12
transcription factor
7
control
3
histone
3
histone modification
3
nucleotide modification
narrow histone mark
1
RNA binding protein
1
broad histone mark
Date released
34
August, 2021
16
May, 2021
6
November, 2020
5
March, 2020
2
March, 2023
1
December, 2018
1
February, 2021
1
February, 2023
1
January, 2018
1
May, 2020
1
November, 2017
1
November, 2019
1
October, 2019
1
October, 2022
Available data
bam
503
bigWig
419
fastq
386
bed narrowPeak
345
bigBed narrowPeak
118
tsv
53
bed broadPeak
53
bigBed broadPeak
15
tagAlign
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
68
Homo sapiens
Biosample type
761
tissue
418
primary cell
72
cell line
52
in vitro differentiated cells
7
stem cell
Organ
33
liver
29
pancreas
28
epithelium
4
kidney
1
blood
1
bodily fluid
mammary gland
Project
70
AMP
2
community
Genome assembly (visualization)
19
hg19
1
GRCh38
Lab
32
AMP-T2D consortium
32
Bing Ren, UCSD
6
Rohit N. Kulkarni, M.D., Ph.D.
Kyle Gaulton, UCSD
2
Anna Gloyn, Oxford
Audit category:
30
inconsistent ontology term
Audit category:
1
inconsistent assembly
files.file_type!
bam
lab.title!
Kyle Gaulton, UCSD
organ_slims!
mammary gland
target.investigated_as!
narrow histone mark
BIOSAMPLE
ASSAY
72 results
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Clear Filters
ATAC-seq
ChIP-seq
total RNA-seq
MeRIP-seq
STARR-seq
pCHi-C
Hi-C
Capture-C
CRISPR genome editing followed by sgRNA sequencing
MPRA
shRNA RNA-seq
siRNA RNA-seq
whole genome sequencing assay
cell line
HepG2
17
9
2
2
2
1
EndoC_BH1
18
6
1
2
1
EndoC-BH1
1
1
HEK293T
2
GM12878
1
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