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Schema
Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
498
ChIP-seq
133
total RNA-seq
92
ATAC-seq
74
single cell RNA-seq
48
WGBS
8
Hi-C
6
MeRIP-seq
3
DNase-seq
2
Capture-C
2
STARR-seq
2
pCHi-C
1
CRISPR genome editing followed by sgRNA sequencing
1
RRBS
1
whole genome sequencing assay
Assay category
498
DNA binding
207
Transcription
95
DNA accessibility
49
DNA methylation
8
3D chromatin structure
1
DNA sequencing
Target of assay
301
transcription factor
111
histone
111
histone modification
86
control
82
recombinant protein
57
RNA binding protein
57
narrow histone mark
54
broad histone mark
21
chromatin remodeller
3
nucleotide modification
2
other context
2
other post-translational modification
Date released
315
November, 2017
80
May, 2022
72
September, 2018
46
November, 2018
41
August, 2017
38
February, 2023
37
August, 2021
37
July, 2018
34
February, 2021
33
April, 2018
24
May, 2021
19
September, 2020
16
November, 2019
16
October, 2019
15
December, 2017
7
August, 2020
6
November, 2020
5
December, 2019
5
January, 2019
5
March, 2020
5
September, 2017
3
August, 2018
3
October, 2022
2
July, 2019
2
June, 2019
2
October, 2018
1
December, 2018
1
June, 2018
1
May, 2020
Available data
653
bam
640
fastq
607
bigWig
419
bed narrowPeak
338
bigBed narrowPeak
162
tsv
80
zippedFastqFolder
61
bed broadPeak
61
bigBed broadPeak
19
tagAlign
9
bed bed3+
5
bedpe bed3+
5
hic
3
cool
3
tar
2
bed bedMethyl
2
bigBed bedMethyl
2
hdf5
1
bed bed3
1
vcf
Organism
870
Homo sapiens
Biosample type
tissue
493
cell line
360
primary cell
18
in vitro differentiated cells
Organ
509
epithelium
441
pancreas
430
liver
137
connective tissue
103
vasculature
97
blood vessel
80
heart
69
blood
69
bodily fluid
68
artery
55
kidney
37
embryo
22
vein
21
brain
14
musculature of body
5
eye
3
adipose tissue
1
bone element
1
bone marrow
1
mammary gland
1
pericardium
Project
715
AMP
152
HPAP
4
T1D
Genome assembly (visualization)
602
hg19
542
GRCh38
Lab
682
AMP-T2D consortium
152
Klaus Kaestner, Upenn
31
Bing Ren, UCSD
6
Rohit N. Kulkarni, M.D., Ph.D.
Audit category:
82
inconsistent ontology term
3
audit script error
1
inconsistent replicate
Audit category:
57
missing controlled_by
Audit category:
30
inconsistent control read length
8
inconsistent control run_type
1
inconsistent assembly
assay_title!
HiChIP
biosample_type!
tissue
organ_slims!
adrenal gland
BIOSAMPLE
ASSAY
871 results
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ChIP-seq
total RNA-seq
ATAC-seq
single cell RNA-seq
WGBS
Hi-C
MeRIP-seq
DNase-seq
Capture-C
STARR-seq
pCHi-C
CRISPR genome editing followed by sgRNA sequencing
RRBS
whole genome sequencing assay
cell line
HepG2
378
14
1
1
2
2
2
1
EndoC_BH1
15
33
19
1
6
2
1
Panc1
13
1
1
primary cell
pancreatic alpha cell
13
52
35
12
31
1
pancreatic beta cell
13
21
23
12
16
1
pancreatic acinar cell
8
4
9
12
1
pancreatic ductal cell
13
4
4
10
pancreatic endocrine cell
23
+ See 9 more…
in vitro differentiated cells
hepatocyte
15
pancreatic PP cell
3
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