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Schema
Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
424
ChIP-seq
total RNA-seq
29
ATAC-seq
6
MeRIP-seq
6
pCHi-C
5
STARR-seq
4
Hi-C
3
CRISPR genome editing followed by DNA sequencing
2
Capture-C
2
DNase-seq
2
HiChIP
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
424
DNA binding
31
DNA accessibility
4
3D chromatin structure
2
Transcription
1
DNA sequencing
Target of assay
304
transcription factor
80
control
73
recombinant protein
44
RNA binding protein
38
histone
38
histone modification
23
chromatin remodeller
19
broad histone mark
19
narrow histone mark
3
nucleotide modification
2
other context
2
other post-translational modification
Date released
315
November, 2017
November, 2018
28
December, 2018
27
August, 2021
26
October, 2019
18
February, 2021
18
January, 2019
17
May, 2021
15
November, 2019
7
March, 2020
6
February, 2023
6
November, 2020
2
March, 2023
1
January, 2018
1
May, 2020
1
October, 2022
Available data
417
bam
361
bigWig
361
fastq
348
bed narrowPeak
299
bigBed narrowPeak
59
bed broadPeak
59
bigBed broadPeak
20
tagAlign
6
tsv
3
bed bed3+
3
tar
2
bedpe bed3+
2
hic
1
bed bed3
1
hdf5
1
txt
1
vcf
Organism
484
Homo sapiens
Biosample type
1637
tissue
809
primary cell
488
cell line
256
in vitro differentiated cells
10
stem cell
Organ
341
liver
59
pancreas
46
blood
46
bodily fluid
45
epithelium
15
kidney
14
artery
14
blood vessel
14
heart
14
vasculature
1
mammary gland
Project
479
AMP
7
T1D
2
community
Genome assembly (visualization)
372
hg19
303
GRCh38
Lab
450
AMP-T2D consortium
25
Bing Ren, UCSD
6
Rohit N. Kulkarni, M.D., Ph.D.
5
Kyle Gaulton, UCSD
2
Anna Gloyn, Oxford
Audit category:
56
inconsistent ontology term
1
inconsistent control
1
inconsistent replicate
Audit category:
10
missing controlled_by
Audit category:
21
inconsistent control read length
4
inconsistent control run_type
1
inconsistent assembly
assay_title!
total RNA-seq
audit.ERROR.category!
audit script error
month_released!
November, 2018
October, 2018
BIOSAMPLE
ASSAY
488 results
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ChIP-seq
ATAC-seq
MeRIP-seq
pCHi-C
STARR-seq
Hi-C
CRISPR genome editing followed by DNA sequencing
Capture-C
DNase-seq
HiChIP
CRISPR genome editing followed by sgRNA sequencing
MPRA
shRNA RNA-seq
siRNA RNA-seq
whole genome sequencing assay
cell line
HepG2
333
1
2
2
2
1
EndoC_BH1
15
19
6
1
3
2
2
1
GM12878
45
1
Panc1
13
1
1
smooth muscle cell of the coronary artery
6
8
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