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Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
432
ChIP-seq
19
total RNA-seq
6
pCHi-C
3
CRISPR genome editing followed by DNA sequencing
2
ATAC-seq
2
HiChIP
1
DNase-seq
1
Hi-C
1
MPRA
1
WGBS
1
shRNA RNA-seq
1
siRNA RNA-seq
Assay category
432
DNA binding
21
Transcription
3
DNA accessibility
1
3D chromatin structure
1
DNA methylation
Target of assay
345
transcription factor
89
recombinant protein
66
control
63
RNA binding protein
30
chromatin remodeller
16
histone
16
histone modification
8
broad histone mark
8
narrow histone mark
2
other context
2
other post-translational modification
Date released
315
November, 2017
61
November, 2018
28
December, 2018
23
January, 2019
15
October, 2019
8
August, 2021
6
March, 2020
5
February, 2023
4
February, 2021
2
March, 2023
1
January, 2018
1
May, 2020
1
October, 2022
Available data
453
bam
427
fastq
396
bigWig
357
bed narrowPeak
348
bigBed narrowPeak
58
bed broadPeak
58
bigBed broadPeak
24
tsv
14
tagAlign
3
tar
1
bed bed3
1
bed bed3+
1
bed bedMethyl
1
bigBed bedMethyl
1
txt
Organism
467
Homo sapiens
Biosample type
2139
tissue
705
primary cell
470
cell line
391
in vitro differentiated cells
10
stem cell
Organ
370
liver
pancreas
79
epithelium
66
artery
66
blood vessel
66
heart
vasculature
61
blood
61
bodily fluid
17
kidney
8
embryo
1
mammary gland
Project
463
AMP
5
T1D
2
community
Genome assembly (visualization)
393
hg19
345
GRCh38
Lab
463
AMP-T2D consortium
Bing Ren, UCSD
5
Kyle Gaulton, UCSD
2
Anna Gloyn, Oxford
Audit category:
15
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
organ_slims!
vasculature
pancreas
lab.title!
Bing Ren, UCSD
BIOSAMPLE
ASSAY
470 results
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ChIP-seq
total RNA-seq
pCHi-C
CRISPR genome editing followed by DNA sequencing
ATAC-seq
HiChIP
DNase-seq
Hi-C
MPRA
WGBS
shRNA RNA-seq
siRNA RNA-seq
cell line
HepG2
360
5
2
1
1
1
GM12878
60
1
H1-hESC
8
EndoC_BH1
3
2
RCC 7860 HIF1a re-expression
4
1
RCC 7860 vector
3
1
1
RCC 7860 HIF2a over-expression
3
1
EndoC-BH1
1
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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