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Schema
Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
459
ChIP-seq
77
total RNA-seq
4
STARR-seq
4
pCHi-C
3
CRISPR genome editing followed by DNA sequencing
3
Hi-C
2
HiChIP
CRISPR genome editing followed by sgRNA sequencing
1
MPRA
1
WGBS
1
shRNA RNA-seq
1
siRNA RNA-seq
1
whole genome sequencing assay
Assay category
459
DNA binding
79
Transcription
DNA accessibility
3
3D chromatin structure
1
DNA methylation
1
DNA sequencing
Target of assay
353
transcription factor
82
recombinant protein
75
control
64
RNA binding protein
30
chromatin remodeller
26
histone
26
histone modification
13
broad histone mark
13
narrow histone mark
2
other context
2
other post-translational modification
Date released
315
November, 2017
61
February, 2021
61
November, 2018
41
August, 2021
28
December, 2018
23
January, 2019
15
October, 2019
5
February, 2023
4
March, 2020
2
March, 2023
1
May, 2020
1
October, 2022
Available data
509
bam
461
bigWig
427
fastq
372
bed narrowPeak
353
bigBed narrowPeak
80
tsv
58
bed broadPeak
58
bigBed broadPeak
20
tagAlign
3
tar
2
bed bed3+
1
bed bedMethyl
1
bedpe bed3+
1
bigBed bedMethyl
1
hdf5
1
hic
1
txt
1
vcf
Organism
554
Homo sapiens
Biosample type
2218
tissue
761
primary cell
557
cell line
246
in vitro differentiated cells
9
stem cell
Organ
400
liver
60
blood
60
bodily fluid
58
artery
58
blood vessel
58
heart
58
vasculature
14
pancreas
8
embryo
3
kidney
1
epithelium
1
mammary gland
Project
550
AMP
5
T1D
2
community
Genome assembly (visualization)
458
hg19
396
GRCh38
Lab
517
AMP-T2D consortium
33
Bing Ren, UCSD
5
Kyle Gaulton, UCSD
2
Anna Gloyn, Oxford
Audit category:
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
assay_slims!
DNA accessibility
assay_title!
CRISPR genome editing followed by sgRNA sequencing
audit.ERROR.category!
inconsistent ontology term
BIOSAMPLE
ASSAY
557 results
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ChIP-seq
total RNA-seq
STARR-seq
pCHi-C
CRISPR genome editing followed by DNA sequencing
Hi-C
HiChIP
MPRA
WGBS
shRNA RNA-seq
siRNA RNA-seq
whole genome sequencing assay
cell line
HepG2
378
14
2
2
2
1
1
GM12878
60
smooth muscle cell of the coronary artery
6
52
Panc1
13
1
H1-hESC
8
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