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Items: 10

1.

ENCODE Cold Spring Harbor Labs Long RNA-seq (hg18)

(Submitter supplied) This track depicts high throughput sequencing of long RNAs (>200 nt) from RNA samples from tissues or subcellular compartments from ENCODE cell lines. The overall goal of the ENCODE project is to identify and characterize all functional elements in the sequence of the human genome. 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:
Homo sapiens
Type:
Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing
Platform:
GPL9052
3 Samples
Download data: BB
Series
Accession:
GSE32931
ID:
200032931
2.

Mammalian X upregulation

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Mus musculus; Mus musculus x Mus spretus
Type:
Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by genome tiling array; Expression profiling by array
9 related Platforms
60 Samples
Download data: BED, BIGWIG, CEL, GFF, PAIR, TXT
Series
Accession:
GSE30761
ID:
200030761
3.

Expression analysis in mouse female PGK12.1 ES cells by RNA-seq

(Submitter supplied) Many animal species employ a chromosome-based mechanism of sex determination, which has led to coordinate evolution of dosage compensation systems. Dosage compensation not only corrects the imbalance in the number of X-chromosomes between the sexes, but is also hypothesized to correct dosage imbalance within cells due to mono-allelic X expression and bi-allelic autosomal expression, by upregulating X-linked genes (termed ‘Ohno’s hypothesis’). more...
Organism:
Mus musculus
Type:
Expression profiling by high throughput sequencing
Platform:
GPL9185
1 Sample
Download data: TXT
Series
Accession:
GSE30690
ID:
200030690
4.

Enrichment profiles of Ser-5 phosphorylated RNA polymerase II (PolII S5p) in mouse female ES cells

(Submitter supplied) Many animal species employ a chromosome-based mechanism of sex determination, which has led to coordinate evolution of dosage compensation systems. Dosage compensation not only corrects the imbalance in the number of X-chromosomes between the sexes, but is also hypothesized to correct dosage imbalance within cells due to mono-allelic X expression and bi-allelic autosomal expression, by upregulating X-linked genes (termed ‘Ohno’s hypothesis’). more...
Organism:
Mus musculus
Type:
Genome binding/occupancy profiling by genome tiling array
Platform:
GPL9833
2 Samples
Download data: GFF, PAIR
Series
Accession:
GSE30689
ID:
200030689
5.

ENCODE Cold Spring Harbor Labs Long RNA-seq (hg19)

(Submitter supplied) This data was generated by ENCODE. If you have questions about the data, contact the submitting laboratory directly (Carrie Davis mailto:davisc@cshl.edu (experimental), Alex Dobin mailto:dobin@cshl.edu (computational), Felix Schlesinger mailto:schlesin@cshl.edu (computational), Tom Gingeras mailto:gingeras@cshl.edu (primary investigator), and Roderic Guigo's group mailto:rguigo@imim.es at the CRG). If you have questions about the Genome Browser track associated with this data, contact ENCODE (mailto:genome@soe.ucsc.edu). These tracks were generate by the ENCODE Consortium. They contain information about human RNAs > 200 nucleotides in length obtained as short reads off the Illumina GAIIx platform. Data is available from biological replicates of several cell lines. In addition to profiling Poly-A+ and Poly-A- RNA from whole cells, we have also gather data from various subcellular compartments. In many cases, there are Cap Analysis of Gene Expression (CAGE, RIKEN Institute) and Small RNA-Seq (<200 nucleotides, CSHL) and Pair-End di-TAG-RNA (PET-RNA, Genome Institute of Singapore) datasets available from the same biological replicates. 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:
Homo sapiens
Type:
Expression profiling by high throughput sequencing
Platforms:
GPL10999 GPL11154 GPL9115
99 Samples
Download data: BAM, BEDRNAELEMENTS, BIGWIG, GFF, GTF, PDF, TXT
Series
Accession:
GSE30567
ID:
200030567
6.

ENCODE Cold Spring Harbor Labs Long RNA-seq

(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:
Homo sapiens
Type:
Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing
4 related Platforms
84 Samples
Download data: BAM, BB, BEDRNAELEMENTS, BIGWIG, GFF, GTF, PDF
Series
Accession:
GSE26284
ID:
200026284
7.

High resolution analysis of genomic imprinting in the embryonic and adult mouse brain AND Sex-specific imprinting in the mouse brain

(Submitter supplied) Genomic imprinting results in the preferential expression of the paternal, or maternal allele of certain genes. We have performed a genome-wide characterization of imprinting in the mouse embryonic and adult brain using F1 hybrid mice generated from reciprocal crosses of CASTEiJ and C57BL/6J mice. We also uncovered genes associated with sex specific parental effects in the adult mouse brain. Our study identified preferential selection of the maternally inherited X chromosome in glutamatergic neurons of the female cortex.
Organism:
Mus musculus
Type:
Expression profiling by high throughput sequencing
Platform:
GPL9250
32 Samples
Download data: CSV, TXT
Series
Accession:
GSE22131
ID:
200022131
8.

Genome-wide nucleosome occupancy profiling by high throughput sequencing, and microarray analysis of RNA abundance

(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
9.

Dynamic regulation of alternative splicing and chromatin structure in Drosophila gonads revealed by RNA-seq

(Submitter supplied) Both transcription and post-transcriptional processes, such as alternative splicing, play crucial roles in controlling developmental programs in metazoans. Recently emerged RNA-seq method has brought our understanding of eukaryotic transcriptomes to a new level, because it can resolve both gene expression level and alternative splicing events simultaneously. To gain a better understanding of cellular differentiation in gonads, we analyzed mRNA profiles from Drosophila testes and ovaries using RNA-seq. more...
Organism:
Drosophila melanogaster
Type:
Expression profiling by high throughput sequencing
Platform:
GPL9061
4 Samples
Download data: GRAPH, TXT
Series
Accession:
GSE16960
ID:
200016960
10.

Polymorphic cis- and trans-regulation of human gene expression

(Submitter supplied) Expression levels of human genes vary extensive among individuals. Gene expression determines cell function and characteristics thus this variation likely contributes to phenotypic variation. Genetic studies have shown that there is a heritable component to gene expression variation, and have identified genomic regions that contain polymorphic regulators. However, most of these regions are quite large, and few regulators have been identified. more...
Organism:
Homo sapiens
Type:
Expression profiling by high throughput sequencing
Platform:
GPL9052
41 Samples
Download data: MAP, TXT
Series
Accession:
GSE16921
ID:
200016921
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