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accession-icon GSE27973
Human airway epithelial responses to rhinovirus infection and cigarette smoke extract alone and in combination
  • organism-icon Homo sapiens
  • sample-icon 16 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)

Description

This study was performed to test the hypothesis that cigarette smoke extract would alter the responses of primary cultures of human bronchial epithelial cells to infection with purified human rhinovirus 16.

Publication Title

Cigarette smoke modulates expression of human rhinovirus-induced airway epithelial host defense genes.

Sample Metadata Fields

Specimen part, Subject

View Samples
accession-icon SRP052856
Genome-wide expression profiling of an in vitro model for studying esophageal epithelial differentiation
  • organism-icon Homo sapiens
  • sample-icon 9 Downloadable Samples
  • Technology Badge IconIlluminaHiSeq2000

Description

We used RNA sequencing to identify differentially expressed genes during esophageal epithelial differentiation and in the presence of interleukin 13 using an air-liquid interface culture system. Overall design: RNA sequencing was performed on a human esophageal epithelial cell line (EPC2-hTERT) grown submerged (day 8) or at the air-liquid interface (ALI) (day 14, untreated or treated with interleukin 13 [100 ng/mL])

Publication Title

Eosinophilic esophagitis-linked calpain 14 is an IL-13-induced protease that mediates esophageal epithelial barrier impairment.

Sample Metadata Fields

No sample metadata fields

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accession-icon GSE57997
Gene expression changes in Itpr triple conditional knockout T cell progenitors
  • organism-icon Mus musculus
  • sample-icon 4 Downloadable Samples
  • Technology Badge Icon Affymetrix Mouse Gene 1.0 ST Array (mogene10st)

Description

Calicum plays critical roles in developing T cells, promoting survival, proliferation, and differentiation at multiple stages of maturation. Calcium release from intracellular stores due to T cell receptor and pre-T cell receptor signaling is thought to require the inositol triphosphate receptors (Itpr), however the requirement for these receptors has not been investigated. We used microarrays to examine gene expression differences between control and Itpr deficient T cell progenitors.

Publication Title

Loss of IP3R-dependent Ca2+ signalling in thymocytes leads to aberrant development and acute lymphoblastic leukemia.

Sample Metadata Fields

Sex, Age, Specimen part

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accession-icon SRP073381
Transcriptome analysis of 6 hours post fertilization mecp2-null versus wild type zebrafish embryos
  • organism-icon Danio rerio
  • sample-icon 6 Downloadable Samples
  • Technology Badge IconIlluminaHiSeq4000

Description

RNA sequencing was performed on RNA isolated from groups of 6 hpf wild type and mecp2-null embryos (n=3 biological replicates per condition with 30 embryos pooled per replicate). DESeq2 analysis was performed using https://usegalaxy.org/ Overall design: Whole embryo mRNA profile of 30 pooled mecp2-null or wild type 6 hpf zebrafish embryos, in triplicate, using the Illumina HiSeq4000 platform

Publication Title

Mecp2 regulates <i>tnfa</i> during zebrafish embryonic development and acute inflammation.

Sample Metadata Fields

No sample metadata fields

View Samples
accession-icon GSE44181
A systems biology approach for defining the molecular framework of the hematopoietic stem cell niche
  • organism-icon Mus musculus
  • sample-icon 51 Downloadable Samples
  • Technology Badge Icon Affymetrix Mouse Gene 1.0 ST Array (mogene10st)

Description

Hematopoietic stem/progenitor cells (HSPCs) are at the basis of the hematopoietic hierarchy. Their ability to self-renew and differentiate is strictly controlled by molecular signals produced by their surrounding micorenvironments composed of stromal cells. HSPCs first emerge in the AGM (Aorta Gonads Mesonephros) region, amplify in the fetal liver (FL) and are maintained in the adult bone marrow (BM). To further characterize the molecular program of the HSPC niches, we have compared the global transcriptome of HSPC-supportive and non/less-supportive stromal clones established from the AGM, FL and BM.

Publication Title

A systems biology approach for defining the molecular framework of the hematopoietic stem cell niche.

Sample Metadata Fields

Specimen part

View Samples
accession-icon GSE97743
Host transcription profile in nasal epithelium and blood of hospitalized children under two years old with Respiratory Syncitial Virus infection
  • organism-icon Homo sapiens
  • sample-icon 332 Downloadable Samples
  • Technology Badge IconIllumina HumanHT-12 V4.0 expression beadchip

Description

This SuperSeries is composed of the SubSeries listed below.

Publication Title

Host Transcription Profile in Nasal Epithelium and Whole Blood of Hospitalized Children Under 2 Years of Age With Respiratory Syncytial Virus Infection.

Sample Metadata Fields

Sex, Age, Specimen part, Disease, Disease stage

View Samples
accession-icon GSE17447
Expression data using esophageal epithelia from 3 month old-mice lacking the transcription factor Klf4
  • organism-icon Mus musculus
  • sample-icon 6 Downloadable Samples
  • Technology Badge Icon Affymetrix Mouse Gene 1.0 ST Array (mogene10st)

Description

Using the ED-L2 promoter of Epstein-Barr virus to drive Cre, we obtained tissue specific ablation of Klf4 in the squamous epithelia of the esophagus.

Publication Title

Esophageal squamous cell dysplasia and delayed differentiation with deletion of krüppel-like factor 4 in murine esophagus.

Sample Metadata Fields

Sex, Age, Specimen part

View Samples
accession-icon GSE28422
Effects of resistance exercise and resistance training on the skeletal muscle transcriptome in young and old adults
  • organism-icon Homo sapiens
  • sample-icon 109 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)

Description

Global microarray (HG U133 Plus 2.0) was used to investigate the effects of resistance exercise and resistance training on the skeletal muscle transcriptome profile of 28 young and old adults. Vastus lateralis muscle biopsies were obtained pre and 4hrs post resistance exercise in the beginning (untrained state) and at the end (trained state) of a 12 wk progressive resistance training program.

Publication Title

Transcriptome signature of resistance exercise adaptations: mixed muscle and fiber type specific profiles in young and old adults.

Sample Metadata Fields

Sex, Specimen part, Time

View Samples
accession-icon GSE28392
Effects of resistance exercise on the transcriptome in MHC I and MHC IIa muscle fibers of young and old women
  • organism-icon Homo sapiens
  • sample-icon 70 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)

Description

Global microarray (HG U133 Plus 2.0) was used for the first time to investigate the effects of resistance exercise on the transcriptome in slow-twitch myosin heavy chain (MHC) I and fast-twitch MHC IIa muscle fibers of young and old women. Vastus lateralis muscle biopsies were obtained pre and 4hrs post resistance exercise in the beginning (untrained state) and at the end (trained state) of a 12 wk progressive resistance training program.

Publication Title

Transcriptome signature of resistance exercise adaptations: mixed muscle and fiber type specific profiles in young and old adults.

Sample Metadata Fields

Sex, Specimen part, Subject, Time

View Samples
accession-icon GSE25941
Effects of age on the skeletal muscle transcriptome
  • organism-icon Homo sapiens
  • sample-icon 34 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)

Description

Global microarray (HG U133 Plus 2.0) was used to investigate the basal level skeletal muscle transcriptome profile of young and old adults. One vastus lateralis muscle biopsy was obtained in the basal state from 36 different subjects.

Publication Title

Transcriptome signature of resistance exercise adaptations: mixed muscle and fiber type specific profiles in young and old adults.

Sample Metadata Fields

Sex, Specimen part

View Samples
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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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Developed by the Childhood Cancer Data Lab

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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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