refine.bio
  • Search
      • Normalized Compendia
      • RNA-seq Sample Compendia
  • Docs
  • About
  • My Dataset
github link
Showing
of 639 results
Sort by

Filters

Technology

Platform

accession-icon GSE44708
Optic nerve crush induces spatial and temporal gene expression patterns in optic nerve and retina of BALB/cJ mice
  • organism-icon Mus musculus
  • sample-icon 24 Downloadable Samples
  • Technology Badge Icon Affymetrix Mouse Gene 1.0 ST Array (mogene10st)

Description

This SuperSeries is composed of the SubSeries listed below.

Publication Title

Optic nerve crush induces spatial and temporal gene expression patterns in retina and optic nerve of BALB/cJ mice.

Sample Metadata Fields

Specimen part, Time

View Samples
accession-icon GSE44705
Optic nerve crush induces spatial and temporal gene expression patterns in optic nerve of BALB/cJ mice
  • organism-icon Mus musculus
  • sample-icon 12 Downloadable Samples
  • Technology Badge Icon Affymetrix Mouse Gene 1.0 ST Array (mogene10st)

Description

Central nervous system (CNS) trauma and neurodegenerative disorders trigger a cascade of cellular and molecular events resulting in neuronal apoptosis and regenerative failure. The pathogenic mechanisms and gene expression changes associated with these detrimental events can be effectively studied using a rodent optic nerve crush (ONC) model. The purpose of this study was to use a mouse ONC model to: (a) evaluate changes in optic nerve (ON) gene expression, (b) identify neurodegenerative pathogenic pathways and (c) discover potential new therapeutic targets.

Publication Title

Optic nerve crush induces spatial and temporal gene expression patterns in retina and optic nerve of BALB/cJ mice.

Sample Metadata Fields

Specimen part, Time

View Samples
accession-icon GSE44707
Optic nerve crush induces spatial and temporal gene expression patterns in retina of BALB/cJ mice
  • organism-icon Mus musculus
  • sample-icon 12 Downloadable Samples
  • Technology Badge Icon Affymetrix Mouse Gene 1.0 ST Array (mogene10st)

Description

Central nervous system (CNS) trauma and neurodegenerative disorders trigger a cascade of cellular and molecular events resulting in neuronal apoptosis and regenerative failure. The pathogenic mechanisms and gene expression changes associated with these detrimental events can be effectively studied using a rodent optic nerve crush (ONC) model. The purpose of this study was to use a mouse ONC model to: (a) evaluate changes in retina gene expression, (b) identify neurodegenerative pathogenic pathways and (c) discover potential new therapeutic targets.

Publication Title

Optic nerve crush induces spatial and temporal gene expression patterns in retina and optic nerve of BALB/cJ mice.

Sample Metadata Fields

Specimen part, Time

View Samples
accession-icon GSE38512
Placental gene expression in pregnancies established after the transfer of day 7 blastocysts derived from in vitro (IVP), somatic cell nuclear transfer (SCNT) and in vivo (AI) embryos
  • organism-icon Bos taurus
  • sample-icon 12 Downloadable Samples
  • Technology Badge Icon Affymetrix Bovine Genome Array (bovine)

Description

Aberrant placental gene expression associated with culture condition and/or deficiencies in transcriptome reprogramming are hypothesized to be the major cause of SCNT and IVP inefficiencies. Therefore, the main objective of this study was to invesitgate the dysregulated genes, molecular pathways and functional alteration in bovine placentas derived from SCNT and IVP pregnancies compared to their AI counterparts

Publication Title

Aberrant placenta gene expression pattern in bovine pregnancies established after transfer of cloned or in vitro produced embryos.

Sample Metadata Fields

Specimen part, Treatment

View Samples
accession-icon GSE84516
PBMC transcriptome profiles identifies potential candidate genes and functional networks controlling the innate and the adaptive immune response to PRRSV vaccine in Pietrain pig
  • organism-icon Sus scrofa
  • sample-icon 18 Downloadable Samples
  • Technology Badge Icon Porcine Gene 1.0 ST Array (porgene10st)

Description

In vivo microarray study of global gene expression changes in peripheral blood mononuclear cells (PBMCs) of Pietrain pigs during the stage of inatte immune and adaptive immune response to porcine reproductive and respiratory syndrome virus vaccination.

Publication Title

PBMC transcriptome profiles identifies potential candidate genes and functional networks controlling the innate and the adaptive immune response to PRRSV vaccine in Pietrain pig.

Sample Metadata Fields

Sex

View Samples
accession-icon SRP133834
Transcriptome of microbiome for the nematode Caenorhabditis elegans
  • organism-icon Caenorhabditis elegans
  • sample-icon 72 Downloadable Samples
  • Technology Badge IconIllumina HiSeq 2000

Description

Host-microbe associations underlie many key processes of host development, immunity, and life history. Yet, none of the current research on the central model species Caenorhabditis elegans considers the worm's natural microbiome. Instead, almost all laboratories exclusively use the canonical strain N2 and derived mutants, maintained through routine bleach sterilization in monoxenic cultures with an E. coli strain as food. Here, we characterize for the first time the native microbiome of C. elegans and assess its influence on nematode life history characteristics via transcriptomics. Overall design: mRNA profiles of wild type (WT) C.elegans fed to either Ochrobactrum strain MYb65, MYb71, mixture of MYb65 and MYb71 or standard lab food E. coli OP50 at different life stages (from L2 to adults) were generated by deep sequencing, in triplicate, using Illumina HiSeq2000.

Publication Title

The Inducible Response of the Nematode <i>Caenorhabditis elegans</i> to Members of Its Natural Microbiota Across Development and Adult Life.

Sample Metadata Fields

Cell line, Treatment, Subject, Time

View Samples
accession-icon SRP040273
Differential expression of miRNAs in granulosa cells of bovine preovulatory dominant and subordinate follicles
  • organism-icon Bos taurus
  • sample-icon 6 Downloadable Samples
  • Technology Badge IconIllumina HiSeq 2000

Description

The study aimed to uncover differential expression pattern of regulatory microRNAs in bovine granulosa cells derived from preovulatory dominant and subordinate follicles. Overall design: We used ovarian follicle samples of experimental heifers slaughtered at day 19 of the estrous cycle . Follicles were catagorized as preovulatory dominant follicles (PDF) and anovulatory subordinate follicles (SF). The granulosa cells were collected from each follicle and subjected to microRNA enriched total RNA isolation and used for miRNAs deep sequencing. A total of 6 samples (three biological replicated from PDF and 3 biological replicates from SF) were used for miRNA deep sequencing.

Publication Title

MicroRNA Expression Profile in Bovine Granulosa Cells of Preovulatory Dominant and Subordinate Follicles during the Late Follicular Phase of the Estrous Cycle.

Sample Metadata Fields

Subject

View Samples
accession-icon GSE77080
Neuroblastoma cells depend on HDAC11 for mitotic cell cycle progression and survival
  • organism-icon Homo sapiens
  • sample-icon 36 Downloadable Samples
  • Technology Badge IconIllumina HumanHT-12 V4.0 expression beadchip

Description

The number of long-term survivors of high-risk neuroblastoma remains discouraging, with 10-year survival as low as 20%, despite decades of considerable international efforts to improve outcome. Major obstacles remain and include managing resistance to induction therapy, which causes tumor progression and early death in high-risk patients, and managing chemotherapy-resistant relapses, which can occur years after the initial diagnosis. Identifying and validating novel therapeutic targets is essential to improve treatment. Delineating and deciphering specific functions of single histone deacetylases in neuroblastoma may support development of targeted acetylome-modifying therapeutics for patients with molecularly defined high-risk neuroblastoma profiles. We show here that HDAC11 depletion in MYCN-driven neuroblastoma cell lines strongly induces cell death, mostly mediated by apoptotic programs. Genes necessary for mitotic cell cycle progression and cell division were most prominently enriched in at least two of three time points in whole-genome expression data combined from two cell systems, and all nine genes in these functional categories were strongly repressed, including CENPA, KIF14, KIF23 and RACGAP1. Enforced expression of one selected candidate, RACGAP1, partially rescued the induction of apoptosis caused by HDAC11 depletion. High-level expression of all nine genes in primary neuroblastomas signicantly correlated with unfavorable overall and event-free survival in patients, suggesting a role in mediating the more aggressive biological and clinical phenotype of these tumors. Our study identied a group of cell cycle-promoting genes regulated by HDAC11, being both predictors of unfavorable patient outcome and essential for tumor cell viability. The data indicates a signicant role of HDAC11 for mitotic cell cycle progression and survival of MYCN-amplified neuroblastoma cells, and suggests that HDAC11 could be a valuable drug target.

Publication Title

Neuroblastoma cells depend on HDAC11 for mitotic cell cycle progression and survival.

Sample Metadata Fields

Cell line, Time

View Samples
accession-icon SRP078433
Transcriptome Profile of Lung Dendritic Cells after In Vitro Porcine Reproductive and Respiratory Syndrome Virus (PRRSV) Infection
  • organism-icon Sus scrofa
  • sample-icon 12 Downloadable Samples
  • Technology Badge IconIllumina HiSeq 2000

Description

Investigation of the transcriptome profile of lung dendritic cells (DCs) of two genetically different pig breeds (Pietrain and Duroc) after PRRSV infection in vitro and determination of the temporal changes in transcriptional profiles. Overall design: Pietrain and Duroc lung DCs were isolated and infected in vitro with PRRSV. Total cellular mRNA from non-infected (0 hours) and infected (3, 6, 9, 12 and 24 hours post infection) lung DCs was extracted and 12 lung DCs samples were used for the global transcriptome profile analysis (RNA-Seq).

Publication Title

Transcriptome profile of lung dendritic cells after in vitro porcine reproductive and respiratory syndrome virus (PRRSV) infection.

Sample Metadata Fields

Sex, Specimen part, Subject

View Samples
accession-icon GSE54294
Gene Expression Profiling of Peri-implant Healing of PLGA-Li+ Implants Suggests an Activated Wnt Signaling Pathway in vivo
  • organism-icon Rattus norvegicus
  • sample-icon 24 Downloadable Samples
  • Technology Badge Icon Affymetrix Rat Gene 2.0 ST Array (ragene20st)

Description

Bone development and regeneration is associated with the Wnt signaling pathway that, according to literature, can be modulated by lithium ions (Li+). The aim of this study was to evaluate the gene expression profile during peri-implant healing of poly(lactic-co-glycolic acid) (PLGA) implants with incorporated Li+, while PLGA without Li+ was used as control, and a special attention was then paid to the Wnt signaling pathway. The implants were inserted in rat tibia for 7 or 28 days and the gene expression profile was investigated using a genome-wide microarray analysis. The results were verified by qPCR and immunohistochemistry. Histomorphometry was used to evaluate the possible effect of Li+ on bone regeneration. The microarray analysis revealed a large number of significantly differentially regulated genes over time within the two implant groups. The Wnt signaling pathway was significantly affected by Li+, with approximately 34% of all Wnt-related markers regulated over time, compared to 22% for non-Li+ containing (control; Ctrl) implants. Functional cluster analysis indicated skeletal system morphogenesis, cartilage development and condensation as related to Li+. The downstream Wnt target gene, FOSL1, and the extracellular protein-encoding gene, ASPN, were significantly upregulated by Li+ compared with Ctrl. The presence of -catenin, FOSL1 and ASPN positive cells was confirmed around implants of both groups. Interestingly, a significantly reduced bone area was observed over time around both implant groups. The presence of periostin and calcitonin receptor-positive cells was observed at both time points. This study is to the best of the authors knowledge the first report evaluating the effect of a local release of Li+ from PLGA at the fracture site. The present study shows that during the current time frame and with the present dose of Li+ in PLGA implants, Li+ is not an enhancer of early bone growth, although it affects the Wnt signaling pathway.

Publication Title

Gene expression profiling of peri-implant healing of PLGA-Li+ implants suggests an activated Wnt signaling pathway in vivo.

Sample Metadata Fields

Sex, Specimen part, Treatment, Time

View Samples
...

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)

fund-icon Fund the CCDL

Developed by the Childhood Cancer Data Lab

Powered by Alex's Lemonade Stand Foundation

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.

BSD 3-Clause LicensePrivacyTerms of UseContact