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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
  • Transcription
    720
Target of assay
  • RNA binding protein
    478
  • transcription factor
    86
  • control
    55
Date released
  • August, 2015
    88
  • October, 2014
    85
  • March, 2016
    84
  • December, 2014
    78
  • July, 2013
    69
  • November, 2014
    59
  • February, 2016
    50
  • January, 2016
    44
  • September, 2016
    32
  • January, 2017
    30
  • June, 2016
    29
  • June, 2014
    25
  • July, 2016
    18
  • August, 2017
    13
  • December, 2017
    7
  • August, 2016
    3
  • February, 2017
    2
  • February, 2018
    2
  • September, 2018
    2
Available data
  • fastq
    717
  • bam
    715
  • bigWig
    715
  • tsv
    715
  • tar
    440
  • sra
    65
Experiment status
  • released
    707
  • archived
    10
  • revoked
    3
Organism
  • Homo sapiens
    642
  • Mus musculus
    78
Biosample type
  • cell line
    548
  • tissue
    130
  • primary cell
    37
  • in vitro differentiated cells
    5
Organ
  • blood
    288
  • bodily fluid
    288
  • liver
    266
  • brain
    29
  • embryo
    24
  • epithelium
    16
  • extraembryonic component
    15
  • heart
    13
  • limb
    11
  • penis
    11
  • skin of body
    11
  • mammary gland
    7
  • musculature of body
    6
  • lung
    5
  • connective tissue
    4
  • intestine
    4
  • kidney
    4
  • pancreas
    4
  • stomach
    4
  • adrenal gland
    3
  • gonad
    3
  • placenta
    3
  • prostate gland
    2
  • testis
    2
  • thyroid gland
    2
  • uterus
    2
  • vagina
    2
  • large intestine
    1
  • ovary
    1
  • thymus
    1
  • urinary bladder
    1
Cell
  • cancer cell
    538
  • epithelial cell
    268
  • stem cell
    7
  • hematopoietic cell
    6
  • leukocyte
    6
  • fibroblast
    5
  • melanocyte
    5
  • T cell
    3
  • keratinocyte
    3
  • lymphoblast
    3
  • neural cell
    2
  • induced pluripotent stem cell
    1
  • smooth muscle cell
    1
Project
  • ENCODE
    651
  • Roadmap
    69
Genome assembly
  • GRCh38
    628
  • hg19
    591
  • mm10
    78
Lab
  • Brenton Graveley, UConn
    533
  • Ali Mortazavi, UCI
    118
  • Joseph Costello, UCSF
    67
  • Bing Ren, UCSD
    2
Audit category:
  • missing possible_controls
    2
Audit category:
  • missing controlled_by
    2
  • missing documents
    2
  • missing RNA fragment size
    1
Audit category:
  • inconsistent platforms
    1
  • missing analysis_step_run
    1
BIOSAMPLE
ASSAY

720 results

Clear Filters
shRNA RNA-seq
microRNA-seq
cell line
K5622762
HepG2257
GM128783
H1-hESC3
GM232481
tissue
forebrain9
heart9
midbrain8
hindbrain7
liver7
primary cell
neurosphere8
foreskin melanocyte5
foreskin fibroblast3
foreskin keratinocyte3
peripheral blood mononuclear cell3
in vitro differentiated cells
bipolar neuron1
hepatocyte1
myocyte1
neural progenitor cell1
smooth muscle cell1
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