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Schema
Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
458
ChIP-seq
26
total RNA-seq
20
ATAC-seq
5
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
458
DNA binding
26
Transcription
22
DNA accessibility
3
3D chromatin structure
1
DNA methylation
Target of assay
345
transcription factor
89
recombinant protein
73
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
February, 2021
61
November, 2018
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
487
bam
427
fastq
425
bigWig
376
bed narrowPeak
355
bigBed narrowPeak
59
bed broadPeak
59
bigBed broadPeak
32
tsv
12
tagAlign
3
tar
2
bed bed3+
1
bed bedMethyl
1
bedpe bed3+
1
bigBed bedMethyl
1
hdf5
1
hic
1
txt
Organism
517
Homo sapiens
Biosample type
1798
tissue
519
cell line
507
primary cell
314
in vitro differentiated cells
8
stem cell
Organ
368
liver
61
blood
61
bodily fluid
60
pancreas
47
epithelium
17
kidney
8
embryo
1
mammary gland
Project
515
AMP
4
T1D
Genome assembly (visualization)
422
hg19
372
GRCh38
Lab
519
AMP-T2D consortium
34
Bing Ren, UCSD
6
Rohit N. Kulkarni, M.D., Ph.D.
5
Kyle Gaulton, UCSD
2
Anna Gloyn, Oxford
Audit category:
59
inconsistent ontology term
1
inconsistent control
Audit category:
13
missing controlled_by
Audit category:
26
inconsistent control read length
8
inconsistent control run_type
1
inconsistent assembly
organ_slims!
musculature of body
month_released!
February, 2021
BIOSAMPLE
ASSAY
519 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
1
1
GM12878
60
1
EndoC_BH1
15
7
19
1
2
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
MCF-7
1
MIN6
1
RCC 7860 VHL
1
fibroblast cell line
1
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