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Schema
Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
476
ChIP-seq
27
total RNA-seq
6
MeRIP-seq
5
STARR-seq
5
pCHi-C
4
Hi-C
3
CRISPR genome editing followed by DNA sequencing
2
Capture-C
2
HiChIP
1
CRISPR genome editing followed by sgRNA sequencing
1
MPRA
1
WGBS
1
shRNA RNA-seq
1
siRNA RNA-seq
whole genome sequencing assay
Assay category
476
DNA binding
29
Transcription
DNA accessibility
4
3D chromatin structure
1
DNA methylation
Target of assay
356
transcription factor
89
recombinant protein
80
control
65
RNA binding protein
38
histone
38
histone modification
30
chromatin remodeller
19
broad histone mark
19
narrow histone mark
3
nucleotide modification
2
other context
2
other post-translational modification
Date released
315
November, 2017
February, 2021
61
November, 2018
35
August, 2021
28
December, 2018
28
October, 2019
23
January, 2019
15
November, 2019
9
March, 2020
6
February, 2023
6
November, 2020
5
May, 2021
2
March, 2023
1
May, 2020
1
October, 2022
Available data
476
bam
427
fastq
426
bigWig
387
bed narrowPeak
353
bigBed narrowPeak
58
bed broadPeak
58
bigBed broadPeak
32
tsv
12
tagAlign
3
tar
2
bedpe bed3+
2
hic
1
bed bed3+
1
bed bedMethyl
1
bigBed bedMethyl
1
hdf5
1
txt
Organism
531
Homo sapiens
Biosample type
1770
tissue
780
primary cell
535
cell line
300
in vitro differentiated cells
10
stem cell
Organ
398
liver
60
blood
60
bodily fluid
46
pancreas
33
epithelium
18
kidney
embryo
1
mammary gland
Project
524
AMP
9
T1D
2
community
Genome assembly (visualization)
423
hg19
361
GRCh38
Lab
489
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:
47
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
assay_slims!
DNA accessibility
assay_title!
whole genome sequencing assay
month_released!
February, 2021
organ_slims!
embryo
BIOSAMPLE
ASSAY
535 results
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Clear Filters
ChIP-seq
total RNA-seq
MeRIP-seq
STARR-seq
pCHi-C
Hi-C
CRISPR genome editing followed by DNA sequencing
Capture-C
HiChIP
CRISPR genome editing followed by sgRNA sequencing
MPRA
WGBS
shRNA RNA-seq
siRNA RNA-seq
cell line
HepG2
378
14
2
1
2
1
GM12878
60
EndoC_BH1
15
7
6
1
3
2
2
1
Panc1
13
1
RCC 7860 HIF1a re-expression
4
1
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