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Experiment matrix

Enter search terms to filter the experiments included in the matrix.

Assay
  • ChIP-seq
    9242
  • DNase-seq
    880
  • polyA RNA-seq
    831
  • shRNA RNA-seq
    533
  • total RNA-seq
    491
  • eCLIP
    469
  • RNA microarray
    291
  • WGBS
    268
  • DNAme array
    257
  • RRBS
    218
  • small RNA-seq
    216
  • microRNA-seq
    187
  • ATAC-seq
    180
  • RAMPAGE
    168
  • RNA Bind-n-Seq
    161
  • genotyping array
    142
  • single cell RNA-seq
    137
  • CAGE
    121
  • Repli-seq
    119
  • microRNA counts
    115
  • siRNA RNA-seq
    113
  • CRISPRi RNA-seq
    77
  • RIP-seq
    73
  • MRE-seq
    68
  • Repli-chip
    63
  • ChIA-PET
    62
  • Hi-C
    55
  • MeDIP-seq
    55
  • CRISPR RNA-seq
    50
  • PAS-seq
    47
  • genetic modification DNase-seq
    46
  • FAIRE-seq
    37
  • RIP-chip
    32
  • polyA depleted RNA-seq
    32
  • RNA-PET
    31
  • whole genome sequencing assay
    21
  • genotyping HTS
    17
  • MS-MS
    14
  • 5C
    13
  • TAB-seq
    8
  • iCLIP
    7
  • DNA-PET
    6
  • 5' RLM RACE
    2
  • MNase-seq
    2
  • Switchgear
    2
  • Circulome-seq
    1
Assay category
  • DNA methylation
    268
  • RNA binding
    73
Target of assay
  • RNA binding protein
    66
  • recombinant protein
    29
  • transcription factor
    23
  • chromatin remodeller
    17
  • control
    6
  • other post-translational modification
    1
  • tag
    1
Date released
  • July, 2013
    134
  • May, 2016
    36
  • March, 2014
    30
  • June, 2014
    28
  • December, 2017
    14
  • January, 2018
    14
  • June, 2015
    12
  • March, 2018
    12
  • March, 2016
    11
  • December, 2018
    10
  • December, 2014
    9
  • August, 2011
    8
  • August, 2015
    8
  • October, 2016
    6
  • October, 2015
    3
  • July, 2014
    2
  • April, 2018
    1
  • February, 2016
    1
  • June, 2016
    1
  • September, 2014
    1
Available data
  • fastq
    326
  • bam
    248
  • bigWig
    182
  • bed bedMethyl
    175
  • bigBed bedMethyl
    175
  • sra
    53
  • bed bedGraph
    30
  • tsv
    30
  • bed broadPeak
    6
  • bigBed broadPeak
    6
Experiment status
  • released
    246
  • archived
    90
  • revoked
    5
Organism
  • Homo sapiens
    227
  • Mus musculus
    84
  • Drosophila melanogaster
    30
Biosample type
  • tissue
    196
  • cell line
    94
  • primary cell
    37
  • in vitro differentiated cells
    14
Organ
  • embryo
    60
  • blood
    59
  • bodily fluid
    59
  • brain
    39
  • heart
    17
  • epithelium
    16
  • intestine
    16
  • liver
    15
  • limb
    13
  • lung
    13
  • stomach
    12
  • musculature of body
    11
  • connective tissue
    10
  • skin of body
    10
  • extraembryonic component
    9
  • large intestine
    7
  • mammary gland
    7
  • adipose tissue
    6
  • spleen
    6
  • adrenal gland
    5
  • esophagus
    5
  • gonad
    5
  • kidney
    5
  • pancreas
    5
  • small intestine
    5
  • ovary
    3
  • penis
    3
  • thymus
    3
  • arterial blood vessel
    2
  • blood vessel
    2
  • nerve
    2
  • placenta
    2
  • testis
    2
  • thyroid gland
    2
  • urinary bladder
    2
  • vasculature
    2
  • bone element
    1
  • bone marrow
    1
  • prostate gland
    1
  • spinal cord
    1
  • uterus
    1
Cell
  • cancer cell
    35
  • lymphoblast
    16
  • hematopoietic cell
    14
  • leukocyte
    13
  • stem cell
    12
  • epithelial cell
    11
  • T cell
    8
  • fibroblast
    5
  • neural cell
    3
  • induced pluripotent stem cell
    2
  • smooth muscle cell
    2
  • B cell
    1
  • keratinocyte
    1
  • melanocyte
    1
  • monocyte
    1
  • myeloid cell
    1
  • myoblast
    1
  • neuroblastoma cell
    1
Project
  • ENCODE
    177
  • Roadmap
    134
  • modENCODE
    30
Genome assembly
  • GRCh38
    106
  • mm10
    72
  • dm3
    30
  • hg19
    15
Lab
  • Joe Ecker, Salk
    132
  • Joseph Costello, UCSF
    50
  • Richard Myers, HAIB
    50
  • John Rinn, Broad
    35
  • Bradley Bernstein, Broad
    34
  • Brenton Graveley, UConn
    30
  • Scott Tenenbaum, SUNY-Albany
    8
  • John Stamatoyannopoulos, UW
    2
Audit category:
  • extremely low coverage
    7
  • inconsistent ontology term
    1
Audit category:
  • partially characterized antibody
    19
  • insufficient read length
    14
  • uncharacterized antibody
    6
  • insufficient coverage
    4
  • antibody not characterized to standard
    3
  • missing possible_controls
    1
Audit category:
  • missing genetic modification characterization
    30
  • low coverage
    4
  • high lambda C methylation ratio
    3
  • inconsistent platforms
    2
BIOSAMPLE
ASSAY

341 results

Clear Filters
WGBS
RIP-seq
tissue
liver11
heart10
stomach10
forebrain8
hindbrain8
cell line
K562129
S2R+30
GM12878214
H1-hESC3
GM232482
primary cell
neurosphere4
sperm4
CD8-positive, alpha-beta T cell3
myoepithelial cell of mammary gland3
CD4-positive, alpha-beta T cell2
in vitro differentiated cells
ectodermal cell2
endodermal cell2
mesodermal cell2
neural stem progenitor cell2
smooth muscle cell2
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