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accession-icon SRP153147
Inter-tumoral heterogeneity in SCLC is influenced by the cell-type of origin
  • organism-icon Mus musculus
  • sample-icon 41 Downloadable Samples
  • Technology Badge IconIllumina HiSeq 2500, Illumina HiSeq 4000

Description

We describe two different routes of SCLC metastatic progression Overall design: We performed RNA-seq on primary tumors and metastasis from SCLC mouse model (Rb/p53/p130/mTmG) transduced by Ad-CMV-Cre or Ad-CGRP-Cre

Publication Title

Axon-like protrusions promote small cell lung cancer migration and metastasis.

Sample Metadata Fields

Specimen part, Subject

View Samples
accession-icon GSE72406
Identification and targeting of long-term tumor propagating cells in small cell lung cancer
  • organism-icon Mus musculus
  • sample-icon 6 Downloadable Samples
  • Technology Badge Icon Affymetrix Mouse Genome 430 2.0 Array (mouse4302)

Description

FACS sorted TPCs (CD24HighCD44LowEpCAMHigh) and non-TPCs (CD24Low, CD24HighCD44High, and CD24HighCD44LowEpCAMLow) from mouse primary SCLC tumors

Publication Title

Identification and Targeting of Long-Term Tumor-Propagating Cells in Small Cell Lung Cancer.

Sample Metadata Fields

Specimen part

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accession-icon GSE17179
Definition of the Pseudomonas aeruginosa Anr and Dnr Regulons
  • organism-icon Pseudomonas aeruginosa
  • sample-icon 8 Downloadable Samples
  • Technology Badge Icon Affymetrix Pseudomonas aeruginosa Array (paeg1a)

Description

The anaerobic metabolism of the opportunistic pathogen Pseudomonas aeruginosa is important for growth and survival during persistent infections. The two Fnr-type transcription factors Anr and Dnr regulate different parts of the underlying network. Both are proposed to bind to a non-distinguishable DNA sequence named Anr box.

Publication Title

Anaerobic adaptation in Pseudomonas aeruginosa: definition of the Anr and Dnr regulons.

Sample Metadata Fields

No sample metadata fields

View Samples
accession-icon GSE44765
Global profiling of human hair follicle scalp dermal papilla cells using Affymetrix microarrays
  • organism-icon Homo sapiens
  • sample-icon 17 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)

Description

Dermal papilla cells isolated from the human hair follicle are capable of inducing hair growth in recipient epithelia. However, demonstrating disparity from rodent dermal papilla, human cells lose this inductive competance immediately upon growth in culture under normal growth conditions. We grew dermal papilla cells in hanging drop cultures that are morphologically akin to intact dermal papilla, and found that by enhancing the environment for aggregation, we could restore the inductive capacity of human dermal papilla cells in culture. The underlying genes that regulate the inductive potential of dermal papilla cells is not well understood, and we sought to use global profiling to identify key genes and pathways related to inductive competance within dermal papilla cells.

Publication Title

Microenvironmental reprogramming by three-dimensional culture enables dermal papilla cells to induce de novo human hair-follicle growth.

Sample Metadata Fields

Sex, Specimen part, Subject

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accession-icon GSE69091
Expression data from a mouse small cell lung cancer (SCLC) cell line, KP1, transfected with Notch-ICD
  • organism-icon Mus musculus
  • sample-icon 6 Downloadable Samples
  • Technology Badge Icon Affymetrix Mouse Gene 2.0 ST Array (mogene20st)

Description

Transient transfection of activated Notch1 (Notch1-ICD) decreases cellular proliferation and reduces the expression of a subset of neuroendocrine genes.

Publication Title

Comprehensive genomic profiles of small cell lung cancer.

Sample Metadata Fields

Specimen part, Cell line, Time

View Samples
accession-icon GSE148778
Expression data of whole kidneys from fetuses subjected to chronix hypoxia or caloric restriction vs controls
  • organism-icon Mus musculus
  • sample-icon 9 Downloadable Samples
  • Technology Badge Icon Affymetrix Mouse Gene 1.0 ST Array (mogene10st)

Description

Reduced oxygen availability during embryogenesis leads to intra-uterine growth restriction (IUGR), increasing the risk for hypertension, cardiovascular and chronic kidney disease (CKD) in adults. Although this association has long been recognized, underlying mechanisms still require extensive research.

Publication Title

Fetuin-A is a HIF target that safeguards tissue integrity during hypoxic stress.

Sample Metadata Fields

Specimen part, Treatment

View Samples
accession-icon GSE24904
Snail regulates MyoD binding-site occupancy to direct enhancer switching and differentiation-specific transcription in myogenesis
  • organism-icon Mus musculus
  • sample-icon 9 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

Snail regulates MyoD binding-site occupancy to direct enhancer switching and differentiation-specific transcription in myogenesis.

Sample Metadata Fields

Specimen part, Disease, Time

View Samples
accession-icon GSE24811
Time Series of gene expression during the course of myogenic differentiation in mouse skeletal muscle cells
  • organism-icon Mus musculus
  • sample-icon 9 Downloadable Samples
  • Technology Badge Icon Affymetrix Mouse Gene 1.0 ST Array (mogene10st)

Description

In skeletal myogenesis, the transcription factor MyoD activates distinct transcriptional programs in progenitors compared to terminally differentiated cells. Using ChIP-seq and gene expression analyses, we show that in primary myoblasts, Snail-HDAC1/2 repressive complex bind and exclude MyoD from its targets. Notably, Snail binds E-box motifs that are G/C-rich in their central dinucleotides, and such sites are almost exclusively associated with genes expressed during differentiation. By contrast, Snail does not bind the A/T-rich E-boxes associated with MyoD targets in myoblasts. Thus, Snai1-HDAC1/2 prevents MyoD occupancy on differentiation-specific regulatory elements and the change from Snail- to MyoD-binding often results in enhancer switching during differentiation. Furthermore, we show that a regulatory network involving Myogenic Regulatory Factors (MRFs), Snail/2, miR-30a and miR-206 acts as a molecular switch that controls entry into myogenic differentiation. Together, these results reveal a regulatory paradigm that directs distinct gene expression programs in progenitors versus terminally differentiated cells.

Publication Title

Snail regulates MyoD binding-site occupancy to direct enhancer switching and differentiation-specific transcription in myogenesis.

Sample Metadata Fields

Specimen part, Time

View Samples
accession-icon GSE58095
Dissecting the heterogeneity of skin gene expression patterns in systemic sclerosis.
  • organism-icon Homo sapiens
  • sample-icon 59 Downloadable Samples
  • Technology Badge IconIllumina HumanHT-12 V4.0 expression beadchip

Description

We identified fibro-inflammatory and keratin gene expression signatures in systemic sclerosis skin.

Publication Title

Dissecting the heterogeneity of skin gene expression patterns in systemic sclerosis.

Sample Metadata Fields

Age, Specimen part, Race, Subject, Time

View Samples
accession-icon GSE49782
Gene expression profiles of CD4 T cells and CD45+ HLA-DR+ cells during experimental allergic rhinitis in humans.
  • organism-icon Homo sapiens
  • sample-icon 20 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Gene 1.1 ST Array (hugene11st)

Description

Six patients with seasonal allergic rhinitis were challenged daily for 8 days with birch pollen extract. A mucosal biopsy was obtained from one nostril at basline (day 0) and from the other nostril after allergen challenge (day 9).

Publication Title

Rapid recruitment of CD14(+) monocytes in experimentally induced allergic rhinitis in human subjects.

Sample Metadata Fields

Specimen part, Treatment, Subject

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

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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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