GEO DataSets

(Submitter supplied) Here we describe a method for purifying nuclei from specific tissues of animal models that allows simultaneous analysis of both expression and chromatin profiles. The method is based on in vivo labeling of the nuclear envelope and subsequent affinity purification. We describe the use of the method to isolate nuclei from muscle.

Organism:

Caenorhabditis elegans

Type:

Expression profiling by genome tiling array; Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL7098 GPL13657

18 Samples

Download data: BAM, BEDGRAPH, GFF, PAIR, PDF, TXT, WIG

(Submitter supplied) modENCODE_submission_2762 This submission comes from a modENCODE project of Steven Henikoff. For full list of modENCODE projects, see http://www.genome.gov/26524648 Project Goal: poly A+ RNA was isolated and used to synthesize single-stranded cDNA probes. Labeled cDNA and labeled genomic DNA were hybridized to NimbleGen microarrays (2-color hybridizations). These experiments are used as controls for nucleosome salt fractionations. more...

Organism:

Caenorhabditis elegans

Type:

Expression profiling by genome tiling array

Platform:

GPL7098

2 Samples

Download data: BEDGRAPH, PAIR

(Submitter supplied) We describe an in vivo chromatin purification system for genome-wide epigenetic profiling in C. elegans. In this system, we coexpressed the E. coli biotin ligase enzyme (BirA), together with the C. elegans H3.3 gene fused to BioTag, a 23-amino acid peptide serving as a biotinylation substrate for BirA, in vivo in worms. We developed methods to isolate chromatin under different salt extraction conditions, followed by affinity purification of biotinylated chromatin with streptavidin and genome-wide profiling with microarrays. more...

Organism:

Caenorhabditis elegans

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL7098

18 Samples

Download data: BEDGRAPH, GFF, PAIR, TXT

(Submitter supplied) In many species, a dosage compensation complex (DCC) is targeted to X chromosomes of one sex to equalize levels of X gene products between males (1X) and females (2X). Here we identify cis-acting regulatory elements that target the C. elegans X chromosome for repression by the DCC. The DCC binds to discrete, dispersed sites on X of two types. rex sites recruit the DCC in an autonomous, DNA sequence-dependent manner using a 12 bp consensus motif that is enriched on X. more...

Organism:

Caenorhabditis elegans

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL7098

1 Sample

Download data: GFF, PAIR

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Caenorhabditis elegans

Type:

Expression profiling by array; Genome binding/occupancy profiling by genome tiling array

5 related Platforms

42 Samples

Download data: CEL, GFF, PAIR, PDF, TXT

(Submitter supplied) Tiling array using NimbleGen platform (DesignID=6112). WormBase release WS170. Complete tiling of pseudo-chromosomes; no filtering; isothermal (target tm=76); mean probe length=54 (range=50 to 75); mean distance between probes=-6 (range=-18 to 1111); all probes on forward strand. Protocol: http://www.nimblegen.com/products/chip/index.html

Organism:

Caenorhabditis elegans

5 Series

35 Samples

Download data: GFF, NDF, TXT