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Schema
Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
395
ChIP-seq
25
total RNA-seq
4
STARR-seq
4
pCHi-C
3
CRISPR genome editing followed by DNA sequencing
3
Hi-C
2
ATAC-seq
2
HiChIP
1
CRISPR genome editing followed by sgRNA sequencing
1
DNase-seq
1
MPRA
1
WGBS
1
shRNA RNA-seq
1
siRNA RNA-seq
1
whole genome sequencing assay
Assay category
395
DNA binding
27
Transcription
3
3D chromatin structure
3
DNA accessibility
1
DNA methylation
1
DNA sequencing
Target of assay
305
transcription factor
82
recombinant protein
73
control
60
RNA binding protein
26
chromatin remodeller
12
histone
12
histone modification
7
narrow histone mark
5
broad histone mark
1
other context
1
other post-translational modification
Date released
257
November, 2017
61
November, 2018
41
August, 2021
28
December, 2018
23
January, 2019
16
October, 2019
6
February, 2023
4
February, 2021
4
March, 2020
2
March, 2023
1
January, 2018
1
May, 2020
1
October, 2022
Available data
454
bam
427
fastq
408
bigWig
371
bed narrowPeak
355
bigBed narrowPeak
bed broadPeak
59
bigBed broadPeak
28
tsv
14
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
441
Homo sapiens
Biosample type
2188
tissue
983
primary cell
445
cell line
277
in vitro differentiated cells
9
stem cell
Organ
343
liver
66
artery
66
blood vessel
heart
66
vasculature
61
blood
61
bodily fluid
15
pancreas
8
embryo
4
kidney
3
epithelium
1
mammary gland
Project
438
AMP
5
T1D
2
community
Genome assembly (visualization)
347
hg19
298
GRCh38
Lab
405
AMP-T2D consortium
33
Bing Ren, UCSD
5
Kyle Gaulton, UCSD
2
Anna Gloyn, Oxford
Audit category:
inconsistent ontology term
1
inconsistent control
1
inconsistent replicate
Audit category:
13
missing controlled_by
Audit category:
13
inconsistent control read length
8
inconsistent control run_type
1
inconsistent assembly
audit.ERROR.category!
inconsistent ontology term
files.file_type!
bed broadPeak
organ_slims!
heart
BIOSAMPLE
ASSAY
445 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
ATAC-seq
HiChIP
CRISPR genome editing followed by sgRNA sequencing
DNase-seq
MPRA
WGBS
shRNA RNA-seq
siRNA RNA-seq
whole genome sequencing assay
cell line
HepG2
320
14
2
2
2
1
1
1
GM12878
60
1
Panc1
13
1
H1-hESC
8
EndoC_BH1
3
2
1
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