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Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
460
ChIP-seq
52
total RNA-seq
21
ATAC-seq
6
pCHi-C
3
Hi-C
2
Capture-C
2
DNase-seq
1
CRISPR genome editing followed by sgRNA sequencing
1
MPRA
1
WGBS
Assay category
460
DNA binding
52
Transcription
23
DNA accessibility
3
3D chromatin structure
1
DNA methylation
Target of assay
346
transcription factor
89
recombinant protein
74
control
64
RNA binding protein
35
histone
35
histone modification
30
chromatin remodeller
18
broad histone mark
17
narrow histone mark
2
other context
2
other post-translational modification
Date released
315
November, 2017
61
November, 2018
30
February, 2021
30
October, 2019
28
December, 2018
23
January, 2019
21
May, 2021
16
November, 2019
11
March, 2020
10
August, 2021
1
February, 2023
1
January, 2018
1
May, 2020
1
October, 2022
Available data
516
bam
452
bigWig
427
fastq
378
bed narrowPeak
355
bigBed narrowPeak
59
bed broadPeak
59
bigBed broadPeak
58
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
Organism
547
Homo sapiens
Biosample type
2292
tissue
549
cell line
487
primary cell
340
in vitro differentiated cells
8
stem cell
Organ
370
liver
86
pancreas
73
epithelium
66
artery
66
blood vessel
66
heart
vasculature
61
blood
61
bodily fluid
17
kidney
8
embryo
1
mammary gland
Project
545
AMP
4
T1D
Genome assembly (visualization)
451
hg19
400
GRCh38
Lab
549
AMP-T2D consortium
33
Bing Ren, UCSD
6
Rohit N. Kulkarni, M.D., Ph.D.
5
Kyle Gaulton, UCSD
2
Anna Gloyn, Oxford
Audit category:
85
inconsistent ontology term
1
inconsistent control
1
inconsistent replicate
Audit category:
13
missing controlled_by
Audit category:
26
inconsistent control read length
8
inconsistent control run_type
1
inconsistent assembly
organ_slims!
vasculature
assay_title!
whole genome sequencing assay
BIOSAMPLE
ASSAY
549 results
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ChIP-seq
total RNA-seq
ATAC-seq
pCHi-C
Hi-C
Capture-C
DNase-seq
CRISPR genome editing followed by sgRNA sequencing
MPRA
WGBS
cell line
HepG2
360
5
1
2
1
1
EndoC_BH1
15
33
19
1
2
1
GM12878
60
1
Panc1
13
1
1
H1-hESC
8
RCC 7860 HIF1a re-expression
4
1
RCC 7860 vector
3
1
1
RCC 7860 HIF2a over-expression
3
1
early embryonic cell
2
glomerular visceral epithelial cell
1
1
iPSC derived cell line
2
MCF-7
1
MIN6
1
RCC 7860 VHL
1
fibroblast cell line
1
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