modENCODE

modMine

Release #32

Explore a hierarchical view of regulatory networks for fly and worm.

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View Fly Regulatory Network

View Worm Regulatory Network

Regions

Maps

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amazon

The entire modENCODE data set available for analysis in the Amazon compute cloud.

Dataset

Find, view and download datasets in bulk.

FTP

Download released data using the traditional FTP interface.

Choose an organism below to see GBrowse, Dataset Search links:

OICR GBrowse

C. elegans
C. brenneri
C. briggsae
C. japonica
C. remanei
D. melanogaster
D. ananassae
D. mojavensis
D. pseudoobscura
D. simulans
D. virilis
D. yakuba

Browse Projects

D. melanogaster
C. elegans

Histone Variants

Genome-wide Chromatin Profiling in Drosophila

Pi: Steven Henikoff

Labs: Kamran Ahmad

Submissions: 7

Experimental factors: biochemical fraction, cell line, extraction time, sodium chloride concentration

GBrowse Tracks: 2
Histone Variants

Genome-wide Chromatin Profiling

Pi: Steven Henikoff

Labs: Kamran Ahmad, Steven Henikoff

Submissions: 32

Experimental factors: developmental stage, biochemical fraction, cell line, extraction time, sodium chloride concentration

GBrowse Tracks: 32

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Jason Lieb
Steven Henikoff

Chromatin Function

Nucleosome mapping

Pi: Jason Lieb

Labs: Jason Lieb

Submissions: 3

Experimental factors: developmental stage, strain, temperature

GBrowse Tracks: 3
Histone Variants

Genome wide chromatin profiling in C. elegans

Pi: Steven Henikoff

Labs: Steven Henikoff

Submissions: 8

Experimental factors: developmental stage, biochemical fraction, extraction time, sodium chloride concentration, strain

GBrowse Tracks: 8

D. melanogaster

Origins of Replication

CGH drosophila cell lines

Pi: David MacAlpine

Labs: David MacAlpine

Submissions: 1

Experimental factors: cell line

GBrowse Tracks: 1
Origins of Replication

CNV in Drosophila cell lines

Pi: David MacAlpine

Labs: David MacAlpine

Submissions: 7

Experimental factors: cell line

GBrowse Tracks: 7
Origins of Replication

Differential Replication of Polytene Chromosomes

Pi: David MacAlpine

Labs: Terry Orr-Weaver

Submissions: 7

Experimental factors: developmental stage, strain, tissue

Features: CopyNumberVariation: 149

GBrowse Tracks: 7

D. melanogaster
C. elegans

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Kevin White
Sue Celniker

Regulatory Elements in Drosophila

Systematic evaluation of factors influencing ChIP-seq fidelity using ultra-deep sequencing

Pi: Kevin White

Labs: Kevin White

Submissions: 2

Experimental factors: antibody, cell line
The Drosophila Transcriptome

RNA made in Bloomington

Pi: Sue Celniker

Labs: Peter Cherbas, Tom Gingeras

Submissions: 16

Experimental factors: developmental stage, cell line, compartment, compound, strain, tissue

GBrowse Tracks: 40

Browse Projects

Cell-type-specific nuclei purification from whole animals for genome-wide expression and chromatin profiling.

modMine: flexible access to modENCODE data

Epigenome characterization at single base-pair resolution

Identification and experimental validation of splicing regulatory elements in Drosophila melanogaster reveals functionally conserved splicing enhancers in metazoans

The modENCODE Data Coordination Center: lessons in harvesting comprehensive experimental details

The developmental transcriptome of Drosophila melanogaster.

Comprehensive analysis of the chromatin landscape in Drosophila melanogaster.

A cis-regulatory map of the Drosophila genome.

Plasticity in patterns of histone modifications and chromosomal proteins in Drosophila heterochromatin.

Chromatin signatures of the Drosophila replication program.

Developmental control of the DNA replication and transcription programs.

Genome-wide analysis of promoter architecture in Drosophila melanogaster.

Conservation of an RNA regulatory map between Drosophila and mammals.

Deep annotation of Drosophila melanogaster microRNAs yields insights into their processing, modification, and emergence.

Polycomb preferentially targets stalled promoters of coding and noncoding transcripts.

Broad chromosomal domains of histone modification patterns in C. elegans.

High nucleosome occupancy is encoded at X-linked gene promoters in C. elegans.

Diverse transcription factor binding features revealed by genome-wide ChIP-seq in C. elegans.

A global analysis of C. elegans trans-splicing.

Multimodal RNA-seq using single-strand, double-strand, and CircLigase-based capture yields a refined and extended description of the C. elegans transcriptome.

Prediction and characterization of noncoding RNAs in C. elegans by integrating conservation, secondary structure, and high-throughput sequencing and array data.

Computational and experimental identification of mirtrons in Drosophila melanogaster and Caenorhabditis elegans.

The transcriptional diversity of 25 Drosophila cell lines.

The Drosophila melanogaster transcriptome by paired-end RNA sequencing.

A spatial and temporal map of C. elegans gene expression.

Genome-wide analysis of alternative splicing in Caenorhabditis elegans.

Integrative analysis of the Caenorhabditis elegans genome by the modENCODE project.

Identification of Functional Elements and Regulatory Circuits by Drosophila modENCODE.

Caenorhabditis elegans chromosome arms are anchored to the nuclear membrane via discontinuous association with LEM-2.

A Comprehensive Map of Insulator Elements for the Drosophila Genome.

Unlocking the secrets of the genome.

Genome-wide profiling of salt fractions maps physical properties of chromatin.