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Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
458
ChIP-seq
42
total RNA-seq
21
ATAC-seq
6
MeRIP-seq
6
pCHi-C
3
Hi-C
2
DNase-seq
1
CRISPR genome editing followed by sgRNA sequencing
1
MPRA
1
WGBS
Assay category
458
DNA binding
42
Transcription
23
DNA accessibility
3
3D chromatin structure
1
DNA methylation
Target of assay
346
transcription factor
89
recombinant protein
77
control
64
RNA binding protein
33
histone
33
histone modification
30
chromatin remodeller
18
broad histone mark
15
narrow histone mark
3
nucleotide modification
2
other context
2
other post-translational modification
Date released
315
November, 2017
61
November, 2018
August, 2021
30
February, 2021
30
October, 2019
28
December, 2018
23
January, 2019
20
May, 2021
16
November, 2019
8
March, 2020
6
November, 2020
1
February, 2023
1
January, 2018
1
May, 2020
1
October, 2022
Available data
504
bam
440
bigWig
427
fastq
376
bed narrowPeak
355
bigBed narrowPeak
59
bed broadPeak
59
bigBed broadPeak
48
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
539
Homo sapiens
Biosample type
2324
tissue
541
cell line
524
primary cell
352
in vitro differentiated cells
8
stem cell
Organ
370
liver
86
pancreas
73
epithelium
66
artery
blood vessel
66
heart
66
vasculature
61
blood
61
bodily fluid
17
kidney
1
mammary gland
Project
541
AMP
9
T1D
2
community
Genome assembly (visualization)
439
hg19
388
GRCh38
Lab
535
AMP-T2D consortium
6
Rohit N. Kulkarni, M.D., Ph.D.
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!
blood vessel
month_released!
August, 2021
BIOSAMPLE
ASSAY
541 results
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ChIP-seq
total RNA-seq
ATAC-seq
MeRIP-seq
pCHi-C
Hi-C
DNase-seq
CRISPR genome editing followed by sgRNA sequencing
MPRA
WGBS
cell line
HepG2
360
5
1
2
1
1
EndoC_BH1
13
31
19
6
1
1
GM12878
60
1
Panc1
13
1
1
RCC 7860 HIF1a re-expression
4
1
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