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accession-icon ERP005988
Single cell mRNA -sequencing reveals cell-to-cell variation in three mouse ES cell culture conditions
  • organism-icon Mus musculus
  • sample-icon 717 Downloadable Samples
  • Technology Badge IconIlluminaHiSeq2000

Description

We sequence mRNA from single mESCs from three culture conditions: serum + LIF, 2i + LIF and “alternative 2i” + LIF. We extensively analysed population and single cell gene expression to identify differences and similarities between conditions. This is a subset of data from ArrayExpress accession E-ERAD-186 (ENA: ERP003293)

Publication Title

No associated publication

Alternate Accession IDs

None

Sample Metadata Fields

No sample metadata fields

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accession-icon ERP001942
RNA-sequencing of 465 lymphoblastoid cell lines from the 1000 Genomes
  • organism-icon Homo sapiens
  • sample-icon 535 Downloadable Samples
  • Technology Badge IconIlluminaHiSeq2000

Description

The data is under embargo until the first publication by the investigators in early 2013. This RNA sequencing data set of 465 human lymphoblastoid cell line samples from the CEU, FIN, GBR, TSI and YRI populations from the 1000 Genomes sample collection was created by the Geuvadis consortium.

Publication Title

No associated publication

Alternate Accession IDs

None

Sample Metadata Fields

No sample metadata fields

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accession-icon ERP003613
HPA RNA-seq normal tissues
  • organism-icon Homo sapiens
  • sample-icon 171 Downloadable Samples
  • Technology Badge IconIlluminaHiSeq2000

Description

RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes.

Publication Title

No associated publication

Alternate Accession IDs

None

Sample Metadata Fields

No sample metadata fields

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accession-icon ERP001982
Transcriptional networks controlling the cell cycle (RNA-seq)
  • organism-icon Drosophila melanogaster
  • sample-icon 146 Downloadable Samples
  • Technology Badge IconIllumina Genome Analyzer IIx

Description

Transcription profiling by RNA-seq of Drosophila S2 cells after knock down of strongest cell cycle regulators to map their genome-wide transcriptional targets (155 assays). RNA samples used for this experiment are a subset of the 200 samples used in Affymetrix microarray experiment E-MTAB-453.

Publication Title

No associated publication

Alternate Accession IDs

None

Sample Metadata Fields

Cell line

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accession-icon ERP003917
Identification of putative target genes of the transcription factor RUNX2
  • organism-icon Homo sapiens
  • sample-icon 102 Downloadable Samples
  • Technology Badge IconIlluminaGenomeAnalyzerII

Description

We overexpress RUNX2 in ten human cell lines and identify genes that are affected by RUNX2 expression. These target genes provide a valuable resource into pathways regulated by RUNX2

Publication Title

No associated publication

Alternate Accession IDs

None

Sample Metadata Fields

No sample metadata fields

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accession-icon ERP005640
Th single cell RNA-Seq
  • organism-icon Mus musculus
  • sample-icon 95 Downloadable Samples
  • Technology Badge IconIllumina HiSeq 2000

Description

Th2 cells regulate helminth infections, allergic disorders, tumor immunity and pregnancy by secreting various cytokines. It is likely that there are undiscovered Th2-signaling molecules. While steroids are known to be immunoregulators, de novo steroid production from immune cells has not been previously characterised. We demonstrate production of the steroid pregnenolone by Th2 cells in vitro, and in vivo in a helminth infection model. To identify gene-expression identify of these steroidogenic-Th2 cells, we performed single-cell RNA-sequencing.

Publication Title

No associated publication

Alternate Accession IDs

None

Sample Metadata Fields

No sample metadata fields

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accession-icon ERP001908
CIT_VADS_BW_OMICS
  • organism-icon Homo sapiens
  • sample-icon 63 Downloadable Samples
  • Technology Badge IconIllumina HiSeq 2000

Description

A Cartes d'Identite des Tumeurs (CIT) project from the french Ligue Nationale Contre le Cancer (http://cit.ligue-cancer.net); Integrative study based on 89 patients with Head and Neck Squamous Cell Carcinoma (HNSCC); 89 Affymetrix HG-U133 Plus 2.0 GeneChips arrays; 88 samples on HumanCNV370-Quad GeneChips arrays; 84 samples on Illumina Human Methylation 27K arrays;Micro-RNA sequencing of 64 tumors. Please note: Characteristics[MetastasisFreeSurvivalEvent] indicates if there is a metastasis-free survival for a particular sample / patient (it is like an event-free survival variable where the event considered is a metastasis). Characteristics[MetastasisFreeSurvivalDelay] - whenever the MetastasisFreeSurvivalEvent is 1, gives the duration of the metastasis-free survival period in months.

Publication Title

No associated publication

Alternate Accession IDs

None

Sample Metadata Fields

No sample metadata fields

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accession-icon ERP003263
A methyltransferase EHMT1 controls brown adipose cell fate and adaptive thermogenesis through a PRDM16 complex
  • organism-icon Mus musculus
  • sample-icon 55 Downloadable Samples
  • Technology Badge IconIllumina HiSeq 2500

Description

Brown adipose tissue (BAT) dissipates chemical energy in the form of heat, as a defense against hypothermia and obesity. Current evidence indicates that brown adipocytes arise from Myf5+-dermotomal precursors through the action of a PRDM16-C/EBP-_ transcriptional complex; however, the underlying mechanisms that determine lineage specification and maintenance of brown adipose cells remain poorly understood. Here we study the role of euchromatic histone-lysine N-methyltransferase 1 (EHMT1), a brown fat-enriched lysine methyltransferase, as an essential enzymatic component of the PRDM16 transcriptional complex and controls brown adipose cell fate. To identify targets and function of EHMT1, we performed genome-wide gene expression profiling of BAT from control mouce (Ehmt1flox/flox), Ehmt1Myf5 KO mouse (Myf5-Cre+/-; Ehmt1flox/flox) and Ehmt1adipo KO mouse (Adipo-Cre+/-; Ehmt1flox/flox). Loss of EHMT1 in Myf5+ lineage causes a near total loss of brown fat characteristics and induces muscle-selective gene program in vivo. In addition, adipose-specific deletion of EHMT1 by Adipo-Cre leads to a marked reduction of the thermogenic and fat oxidation genes.

Publication Title

No associated publication

Alternate Accession IDs

None

Sample Metadata Fields

No sample metadata fields

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accession-icon ERP005336
NEUROMESO
  • organism-icon Mus musculus
  • sample-icon 32 Downloadable Samples
  • Technology Badge IconIllumina HiSeq 2500

Description

Exposure of mouse ESCs to a sequence of extrinsic signals, which recapitulates in vivo development, generates a bipotential neuromesodermal precursor (NMP) that can be directed to differentiate into either spinal cord or paraxial mesodermal tissue. To induce differentiation,mouse ES cells were plated on CellBINDSurface dishes (Corning) precoated with 0.1% gelatin (Sigma) at a density of 5x10^3 cells cm-2 in N2B27 medium. Cells were grown in N2B27 supplemented with 10ng/ml bFGF (R&D) for 3 days (D1-D3) and then were transferred into serum free media without bFGF (D3-D5). To induce ventral hindbrain identity NPCs (NH) 100nM RA (Sigma) and 500nM SAG (Calbiochem) was added from D3-D5. Spinal cord identity (NP) was induced by the addition of 5nM CHIR 99021 (Axon) from D2 to D3 followed by 100nM RA, 500nM SAG from D3-D5. To induce mesodermal differentiation the cells were treated with CHIR99021 from D2-D5.

Publication Title

No associated publication

Alternate Accession IDs

None

Sample Metadata Fields

No sample metadata fields

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accession-icon ERP004640
RNA_seq_Salmonella_pig
  • organism-icon Sus scrofa
  • sample-icon 27 Downloadable Samples
  • Technology Badge IconIllumina HiScanSQ

Description

Salmonella enterica serovar Typhimurium is a gram-negative bacterium that can colonize the gut of humans and several species of food producing farm animals to cause enteric or septicaemic salmonellosis. Besides compromising public health and food safety, sub-clinical salmonellosis is also believed to be a major problem affecting the profitability of the pig industry. Distinct responses to Salmonella infection have been observed in pigs, some recovering faster and shedding lower levels of Salmonella in faeces than others (low shedders, LS versus persistent shedders, PS). This trait variation could indicate the existence of a genetic component to Salmonella shedding and resistance that may be exploited in animal breeding and disease diagnostics. The study aimed to identify porcine genes and gene co-expression networks that differentiate distinct responses to Salmonella infection with respect to faecal Salmonella shedding.

Publication Title

No associated publication

Alternate Accession IDs

None

Sample Metadata Fields

Specimen part, Time

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refine.bio is a repository of uniformly processed and normalized, ready-to-use transcriptome data from publicly available sources. refine.bio is a project of the Childhood Cancer Data Lab (CCDL)

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Cite refine.bio

Casey S. Greene, Dongbo Hu, Richard W. W. Jones, Stephanie Liu, David S. Mejia, Rob Patro, Stephen R. Piccolo, Ariel Rodriguez Romero, Hirak Sarkar, Candace L. Savonen, Jaclyn N. Taroni, William E. Vauclain, Deepashree Venkatesh Prasad, Kurt G. Wheeler. refine.bio: a resource of uniformly processed publicly available gene expression datasets.
URL: https://www.refine.bio

Note that the contributor list is in alphabetical order as we prepare a manuscript for submission.

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