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Schema
Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
474
ChIP-seq
113
total RNA-seq
29
ATAC-seq
10
pCHi-C
6
MeRIP-seq
5
STARR-seq
4
Hi-C
3
CRISPR genome editing followed by DNA sequencing
2
Capture-C
2
DNase-seq
2
HiChIP
1
CRISPR RNA-seq
1
CRISPR genome editing followed by sgRNA sequencing
1
CRISPRi RNA-seq
1
GRO-seq
1
MPRA
1
WGBS
1
shRNA RNA-seq
1
siRNA RNA-seq
1
whole genome sequencing assay
Assay category
474
DNA binding
117
Transcription
31
DNA accessibility
4
3D chromatin structure
1
DNA methylation
1
DNA sequencing
Target of assay
349
transcription factor
88
recombinant protein
84
control
63
RNA binding protein
39
histone
39
histone modification
24
chromatin remodeller
20
broad histone mark
19
narrow histone mark
3
nucleotide modification
2
other context
2
other post-translational modification
Date released
305
November, 2017
96
February, 2021
58
November, 2018
44
August, 2021
30
October, 2019
28
December, 2018
23
January, 2019
21
May, 2021
16
November, 2019
15
March, 2020
6
February, 2023
6
November, 2020
4
March, 2023
3
December, 2017
2
January, 2018
1
May, 2020
1
October, 2022
Available data
572
bam
513
bigWig
418
fastq
394
bed narrowPeak
343
bigBed narrowPeak
123
tsv
59
bed broadPeak
59
bigBed broadPeak
20
tagAlign
6
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
653
Homo sapiens
Biosample type
2671
tissue
1013
primary cell
649
cell line
388
in vitro differentiated cells
10
stem cell
Organ
388
liver
92
pancreas
79
epithelium
66
artery
66
blood vessel
66
heart
66
vasculature
61
blood
61
bodily fluid
19
kidney
8
embryo
1
connective tissue
1
mammary gland
Project
646
AMP
9
T1D
4
community
Genome assembly (visualization)
521
hg19
462
GRCh38
1
hg18
Lab
610
AMP-T2D consortium
34
Bing Ren, UCSD
6
Rohit N. Kulkarni, M.D., Ph.D.
5
Kyle Gaulton, UCSD
4
Anna Gloyn, Oxford
Audit category:
93
inconsistent ontology term
1
inconsistent control
1
inconsistent replicate
Audit category:
missing controlled_by
Audit category:
23
inconsistent control read length
2
inconsistent control run_type
1
inconsistent assembly
assay_title!
snDrop-seq
audit.NOT_COMPLIANT.category!
missing controlled_by
month_released!
July, 2019
BIOSAMPLE
ASSAY
659 results
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Clear Filters
ChIP-seq
total RNA-seq
ATAC-seq
pCHi-C
MeRIP-seq
STARR-seq
Hi-C
CRISPR genome editing followed by DNA sequencing
Capture-C
DNase-seq
HiChIP
CRISPR RNA-seq
CRISPR genome editing followed by sgRNA sequencing
CRISPRi RNA-seq
GRO-seq
MPRA
WGBS
shRNA RNA-seq
siRNA RNA-seq
whole genome sequencing assay
cell line
HepG2
365
14
1
2
2
2
1
1
EndoC_BH1
15
33
19
6
1
3
2
2
1
smooth muscle cell of the coronary artery
6
52
8
GM12878
60
1
Panc1
13
1
1
+ See 14 more…
stem cell
hESC
3
1
SB Ad3.1
1
1
mesenchymal stem cell
1
mesendoderm
1
neural progenitor cell (neural stem cell)
1
+ See 1 more…
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