GEO DataSets

(Submitter supplied) Transcription Start Site analysis in Mouse Ter119+ erythroid cells

Organism:

Mus musculus

Type:

Other

Platform:

GPL13112

1 Sample

Download data: WIG

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

Organism:

Mus musculus

Type:

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

Platforms:

GPL13112 GPL11002

6 Samples

Download data: WIG

(Submitter supplied) Genome-wide identification of active regions in the mouse erythroid genome using DNase-seq.

Organism:

Mus musculus

Type:

Other

Platform:

GPL13112

1 Sample

Download data: WIG

(Submitter supplied) Analysis of gene expression in Mouse Ter119+ erythroid cells

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13112

1 Sample

Download data: WIG

(Submitter supplied) Analysis of Non-Polyadenylated gene expression in Mouse Ter119+ erythroid cells

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11002

1 Sample

Download data: WIG

(Submitter supplied) Regions of chromatin modified by H3K4me1 and H3K4me3 were identified in mouse erythroid cells using ChIP-seq.

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL13112

2 Samples

Download data: WIG

(Submitter supplied) Recent discovery that much of the mammalian genome does not encode protein-coding genes (PCGs) has brought widespread attention to long noncoding RNAs (lncRNAs) as a novel layer of biological regulation. Enhancer lnc (elnc) RNAs from the enhancer regions of the genome carry the capacity to regulate PCGs in cis or in trans. Spotted fever rickettsioses represent the consequence of host infection with Gram-negative, obligate intracellular bacteria in the Genus Rickettsia. more...

Organism:

Mus musculus

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL18480

6 Samples

Download data: XLSX

(Submitter supplied) Mammalian genomes are pervasively transcribed to produce thousands of spliced long noncoding RNAs (lncRNAs), whose functions remain poorly understood. Because recent evidence has implicated several specific lncRNA loci in the local regulation of gene expression, we sought to determine whether such local regulation is a property of many lncRNA loci. We used genetic manipulations to dissect 12 genomic loci that produce lncRNAs and found that 5 of these loci influence the expression of a neighboring gene in cis. more...

Organism:

Mus musculus

Type:

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

Platform:

GPL17021

462 Samples

Download data: BED, TDF

(Submitter supplied) We examined the subcellular localization of long noncoding RNAs (lncRNAs) in mouse embryonic stem cells.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17021

6 Samples

Download data: BIGWIG

(Submitter supplied) We designed a custom microarray to profile the expression and used it to measure the expression of 9929 human lncRNAs manually-annotated by the GENCODE group as part of the ENCODE consortium.

Organism:

Homo sapiens

Type:

Non-coding RNA profiling by array

Platform:

GPL15094

31 Samples

Download data: TXT

(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

(Submitter supplied) This data was generated by ENCODE. If you have questions about the data, contact the submitting laboratory directly (Jonathan Preall jpreall@cshl.edu (Generation 0 Data from Hannon Lab), Carrie Davis davisc@cshl.edu (experimental), Alex Dobin dobin@cshl.edu (computational), Wei Lin wlin@cshl.edu (computational), Tom Gingeras gingeras@cshl.edu (primary investigator)). If you have questions about the Genome Browser track associated with this data, contact ENCODE (mailto:genome@soe.ucsc.edu). more...

Organism:

Homo sapiens

Type:

Non-coding RNA profiling by high throughput sequencing

Platforms:

GPL10999 GPL9052 GPL11154

87 Samples

Download data: BAM, BEDRNAELEMENTS, BIGWIG, GTF, PDF, TXT

(Submitter supplied) Purpose:The purpose of this study is to create unbiased, stage-specific transcriptomes by RNA-seq analyses of pure populations of both murine and human erythroblasts at distinct developmental stages. Methods: Recently developed FACS-based methods (Chen et al, PNAS, Liu et al, Blood, Hu et al Blood) were employed to purify morphologically and functionally discrete populations of cells, each representing specific stages of terminal erythroid differentiation. more...

Organism:

Homo sapiens; Mus musculus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL13112 GPL11154

27 Samples

Download data: TXT

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

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing; Third-party reanalysis; Expression profiling by array; Non-coding RNA profiling by array

Platform:

GPL17864

19 Samples

Download data: TXT

(Submitter supplied) Mammals express thousands of long noncoding (lnc) RNAs, a few of which are shown to function in tissue development. However, the entire repertoire of lncRNAs and the extent to which they regulate biological processes in different tissues and species are not defined. Indeed, most lncRNAs are not conserved between species, raising questions about function. We used RNA-Seq to identify lncRNAs in primary murine fetal liver erythroblasts expressing the lineage marker TER119, megakaryocytes (CD41+) cultured from embryonic day (E) 14.5 murine fetal liver and megakaryocyte erythroid progenitors (MEPs) isolated from mouse bone marrow. more...

Organism:

Mus musculus

Type:

Expression profiling by array; Non-coding RNA profiling by array

Platform:

GPL17864

19 Samples

Download data: TXT

(Submitter supplied) Mammals express thousands of long noncoding (lnc) RNAs, a few of which are shown to function in tissue development. However, the entire repertoire of lncRNAs and the extent to which they regulate biological processes in different tissues and species are not defined. Indeed, most lncRNAs are not conserved between species, raising questions about function. We used RNA-Seq to identify lncRNAs in primary murine fetal liver erythroblasts expressing the lineage marker TER119, megakaryocytes (CD41+) cultured from embryonic day (E) 14.5 murine fetal liver and megakaryocyte erythroid progenitors (MEPs) isolated from mouse bone marrow. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing; Third-party reanalysis

Download data: GTF, TXT

(Submitter supplied) 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

Platforms:

GPL11154 GPL16791

34 Samples

Download data

(Submitter supplied) While long noncoding RNAs (lncRNAs) and mRNAs share similar biogenesis pathways, these two transcript classes differ in many regards. LncRNAs are less conserved, less abundant, and more tissue specific than mRNAs, implying that our understanding of lncRNA transcriptional regulation is incomplete. Here, we perform an in depth characterization of numerous factors contributing to this regulation. We find that lncRNA promoters contain fewer transcription factor binding sites than do those of mRNAs, with some notable exceptions. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing

Platform:

GPL16791

30 Samples

Download data: TXT

(Submitter supplied) While long noncoding RNAs (lncRNAs) and mRNAs share similar biogenesis pathways, these two transcript classes differ in many regards. LncRNAs are less conserved, less abundant, and more tissue specific than mRNAs, implying that our understanding of lncRNA transcriptional regulation is incomplete. Here, we perform an in depth characterization of numerous factors contributing to this regulation. We find that lncRNA promoters contain fewer transcription factor binding sites than do those of mRNAs, with some notable exceptions. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing

Platform:

GPL11154

4 Samples

Download data: TXT

(Submitter supplied) To explore the circadian regulations of Bmal1, we examined the transcriptome changes in mouse livers upon Bmal1 knock out at two circadian time points, CT0 and CT12. To explore the circadian regulations of Nr1d1, we examined the transcriptome changes in mouse livers upon Nr1d1 knock out at two circadian time points, CT0 and CT12. To explore interactome of lnc-Crot, 4C-seq was performed with lnc-Crot as bait region at CT6 and CT18.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL13112

26 Samples

Download data: TXT