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Schema
Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
479
ChIP-seq
total RNA-seq
20
ATAC-seq
9
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
479
DNA binding
22
DNA accessibility
4
3D chromatin structure
4
Transcription
1
DNA methylation
1
DNA sequencing
Target of assay
356
transcription factor
89
recombinant protein
81
control
65
RNA binding protein
40
histone
40
histone modification
30
chromatin remodeller
20
broad histone mark
20
narrow histone mark
3
nucleotide modification
2
other context
2
other post-translational modification
Date released
315
November, 2017
61
November, 2018
28
December, 2018
27
August, 2021
26
October, 2019
February, 2021
18
January, 2019
17
May, 2021
15
November, 2019
11
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
464
bam
426
fastq
416
bigWig
392
bed narrowPeak
355
bigBed narrowPeak
59
bed broadPeak
59
bigBed broadPeak
12
tagAlign
10
tsv
5
bed bed3+
3
tar
2
bedpe bed3+
2
hic
1
bed bedMethyl
1
bigBed bedMethyl
1
hdf5
1
txt
1
vcf
Organism
535
Homo sapiens
Biosample type
1645
tissue
794
primary cell
531
cell line
254
in vitro differentiated cells
10
stem cell
Organ
385
liver
61
blood
61
bodily fluid
59
pancreas
45
epithelium
15
kidney
1
connective tissue
1
mammary gland
Project
530
AMP
7
T1D
4
community
Genome assembly (visualization)
414
hg19
349
GRCh38
1
hg18
Lab
501
AMP-T2D consortium
25
Bing Ren, UCSD
6
Rohit N. Kulkarni, M.D., Ph.D.
5
Kyle Gaulton, UCSD
4
Anna Gloyn, Oxford
Audit category:
57
inconsistent ontology term
1
inconsistent control
Audit category:
13
missing controlled_by
Audit category:
28
inconsistent control read length
8
inconsistent control run_type
1
inconsistent assembly
month_released!
February, 2021
assay_title!
total RNA-seq
BIOSAMPLE
ASSAY
541 results
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ChIP-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
378
1
2
2
1
1
GM12878
60
1
EndoC_BH1
15
19
6
1
3
2
2
1
Panc1
13
1
1
RCC 7860 HIF1a re-expression
4
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stem cell
hESC
3
1
SB Ad3.1
1
1
mesenchymal stem cell
1
mesendoderm
1
neural progenitor cell (neural stem cell)
1
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