GEO DataSets

(Submitter supplied) modENCODE_submission_3154 This submission comes from a modENCODE project of Jason Lieb. For full list of modENCODE projects, see http://www.genome.gov/26524648 Project Goal: To complement our extensive ChIP-chip characterization of chromosomal regulators in C. elegans, in select experiments we also isolate total RNA from parallel cultures of staged animals. Labeled cDNA will be prepared and used to probe either gene-specific microarrays, or genomic tiling microarrays to assess the transcriptional state of genomic sequences flanking the protein-binding regions localized by ChIP-chip and ChIP-seq. more...

Organism:

Caenorhabditis elegans

Type:

Expression profiling by genome tiling array

Platform:

GPL8673

4 Samples

Download data: GFF, TXT

(Submitter supplied) For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf This SuperSeries is composed of the SubSeries listed below.

Organism:

Caenorhabditis elegans

Type:

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

Platforms:

GPL8647 GPL8673 GPL9269

31 Samples

Download data: BED, GFF, GFF3, PAIR, SAM, TXT, WIG

(Submitter supplied) The two major methods for growing C. elegans are liquid and plate culture. Differences in oxygenation and other environmental variables could affect many experimentally relevant biological processes, such as metabolism, cellular structure, and gene regulation. Worms on solid support move with deliberate sinusoidal movements, while worms in liquid thrash rapidly and almost constantly, often appearing elongated. more...

Organism:

Caenorhabditis elegans

Type:

Expression profiling by array

Platform:

GPL8673

6 Samples

Download data: CALLS, PAIR

(Submitter supplied) We profiled nucleosome occupancy of different developmental stages in C. elegans. Mononucleosomal DNA was sequenced by Illumina paired-end sequencing. We used embryos, germlineless adults, germ line containing adults, and XO hermaphrodites at L3 larval stage. RNA abundance is determined by microarray analysis. We also digested naked DNA with MNase. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

Organism:

Caenorhabditis elegans

Type:

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

Platforms:

GPL9269 GPL8673

12 Samples

Download data: CALLS, PAIR, WIG

(Submitter supplied) In C. elegans, a condensin-like protein complex associates specifically with both X chromosomes of XX animals to execute dosage compensation. Dosage Compensation Complex (DCC) reduces the level of transcripts arising from each of the two X chromosomes. Recruitment to X is specified in part by discrete DNA sequence motifs, but following recruitment, the DCC is targeted to the promoters of individual active genes by an unknown mechanism. more...

Organism:

Caenorhabditis elegans

Type:

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

7 related Platforms

39 Samples

Download data: CALLS, PAIR

(Submitter supplied) NimbleGen 4 plex expression array. Array contains three probes per gene and is based on WS170. ***A different version of this platform with the ORF or SEQ_ID in the ID column is assigned accession number GPL18855 and GPL18856, respectively. Protocol: Details on the manufacture protocol can be found on http://www.nimblegen.com/technology/index.html

Organism:

Caenorhabditis elegans

5 Series

26 Samples

Download data: NDF