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Schema
Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
19
ChIP-seq
9
total RNA-seq
4
STARR-seq
4
pCHi-C
3
CRISPR genome editing followed by DNA sequencing
3
Hi-C
2
HiChIP
1
ATAC-seq
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 binding
11
Transcription
3
3D chromatin structure
1
DNA accessibility
1
DNA sequencing
Target of assay
12
transcription factor
4
control
3
histone
3
histone modification
2
narrow histone mark
1
RNA binding protein
1
broad histone mark
Date released
33
August, 2021
6
February, 2023
2
March, 2020
2
March, 2023
1
December, 2018
1
February, 2021
1
January, 2018
1
May, 2020
1
November, 2017
1
October, 2019
1
October, 2022
Available data
bam
464
bigWig
427
fastq
383
bed narrowPeak
355
bigBed narrowPeak
80
tsv
59
bed broadPeak
59
bigBed broadPeak
20
tagAlign
3
bed bed3+
3
tar
1
bed bed3
1
bed bedMethyl
1
bedpe bed3+
1
bigBed bedMethyl
1
hdf5
1
hic
1
txt
1
vcf
Organism
46
Homo sapiens
Biosample type
734
tissue
468
primary cell
55
in vitro differentiated cells
50
cell line
6
stem cell
Organ
35
liver
2
kidney
2
pancreas
1
blood
1
bodily fluid
1
epithelium
1
mammary gland
Project
43
AMP
5
T1D
2
community
Genome assembly (visualization)
18
hg19
1
GRCh38
Lab
33
Bing Ren, UCSD
10
AMP-T2D consortium
5
Kyle Gaulton, UCSD
2
Anna Gloyn, Oxford
Audit category:
inconsistent ontology term
Audit category:
1
inconsistent assembly
files.file_type!
bam
audit.ERROR.category!
inconsistent ontology term
organ_slims!
connective tissue
BIOSAMPLE
ASSAY
50 results
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Clear Filters
ChIP-seq
total RNA-seq
STARR-seq
pCHi-C
CRISPR genome editing followed by DNA sequencing
Hi-C
HiChIP
ATAC-seq
CRISPR genome editing followed by sgRNA sequencing
MPRA
shRNA RNA-seq
siRNA RNA-seq
whole genome sequencing assay
cell line
HepG2
19
9
2
2
2
1
EndoC_BH1
3
2
1
EndoC-BH1
1
1
HEK293T
2
GM12878
1
MCF-7
1
MIN6
1
Panc1
1
fibroblast cell line
1
See all biosamples
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