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accession-icon GSE30166
Cell-type, developmental stage, and whole root responses to low pH and sulfur deficiency
  • organism-icon Arabidopsis thaliana
  • sample-icon 78 Downloadable Samples
  • Technology Badge Icon Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)

Description

This SuperSeries is composed of the SubSeries listed below.

Publication Title

Cell identity regulators link development and stress responses in the Arabidopsis root.

Sample Metadata Fields

Age, Specimen part, Treatment

View Samples
accession-icon GSE30095
Expression analysis of root cell types after treatment with low pH
  • organism-icon Arabidopsis thaliana
  • sample-icon 25 Downloadable Samples
  • Technology Badge Icon Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)

Description

Cell-type specific transcriptional profiles were generated by FACS (Fluorescence Activated Cell Sorting) sorting of roots that express cell-type specific GFP-reporters. Five different GFP-reporter lines were used. FACS cell populations were isolated from roots grown under standard pH (pH 5.7) or roots that had been transfered to low pH (pH 4.6) media for 24 hours.

Publication Title

Cell identity regulators link development and stress responses in the Arabidopsis root.

Sample Metadata Fields

Specimen part

View Samples
accession-icon GSE30096
Expression analysis of developmental stages of Arabidopsis roots exposed to low pH
  • organism-icon Arabidopsis thaliana
  • sample-icon 16 Downloadable Samples
  • Technology Badge Icon Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)

Description

To understand the effect of low pH on developmental stages in the root, we dissected the root into four developmental zones after exposure to low pH and expression profiled each zone.

Publication Title

Cell identity regulators link development and stress responses in the Arabidopsis root.

Sample Metadata Fields

Age

View Samples
accession-icon GSE30099
Expression analysis of root cell types after treatment with sulfur deficient media
  • organism-icon Arabidopsis thaliana
  • sample-icon 14 Downloadable Samples
  • Technology Badge Icon Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)

Description

Cell-type specific transcriptional profiles were generated by FACS (Fluorescence Activated Cell Sorting) sorting of roots that express cell-type specific GFP-reporters. Five different GFP-reporter lines were used. FACS cell populations were isolated from roots grown under sulfur deficient conditions for 3 hours.

Publication Title

Cell identity regulators link development and stress responses in the Arabidopsis root.

Sample Metadata Fields

Specimen part

View Samples
accession-icon GSE30098
Expression analysis time-course of Arabidopsis roots to sulfur deficiency
  • organism-icon Arabidopsis thaliana
  • sample-icon 12 Downloadable Samples
  • Technology Badge Icon Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)

Description

We preformed at time-course of the expression of whole Arabidopsis roots for 3H, 12H, 24H, 48H and 72H after transfer to media lacking sulfur. We combined these data with 13 other datasests and performed a meta-analysis to ask whether a universal stress response exists in Arabidopsis roots.

Publication Title

Cell identity regulators link development and stress responses in the Arabidopsis root.

Sample Metadata Fields

No sample metadata fields

View Samples
accession-icon GSE30100
Expression analysis of developmental stages of Arabidopsis roots exposed to sulfur deficient media
  • organism-icon Arabidopsis thaliana
  • sample-icon 8 Downloadable Samples
  • Technology Badge Icon Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)

Description

To understand the effect of sulfur deficiency on developmental stages in the root, we dissected the root into four developmental zones after exposure to sulfur deficiency and expression profiled each zone.

Publication Title

Cell identity regulators link development and stress responses in the Arabidopsis root.

Sample Metadata Fields

No sample metadata fields

View Samples
accession-icon GSE30091
Expression analysis of the effect of protoplasting and sorting in roots exposed to low pH
  • organism-icon Arabidopsis thaliana
  • sample-icon 3 Downloadable Samples
  • Technology Badge Icon Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)

Description

To estimate the effect of protoplasting and sorting on low pH-regulated gene expression, we generated expression profiles for whole roots treated with low pH for 24 hours and whole roots that had been protoplasted and FACS sorted after 24 hours of exposure to low pH.

Publication Title

Cell identity regulators link development and stress responses in the Arabidopsis root.

Sample Metadata Fields

Treatment

View Samples
accession-icon SRP004637
Transcriptome sequencing across a prostate cancer cohort identifies PCAT-1, an unannotated lincRNA implicated in disease progression (RNA-Seq data)
  • organism-icon Homo sapiens
  • sample-icon 58 Downloadable Samples
  • Technology Badge IconIlluminaGenomeAnalyzerII, IlluminaGenomeAnalyzer

Description

Noncoding RNAs (ncRNAs) are emerging as key molecules in human cancer, with the potential to serve as novel markers of disease and to reveal uncharacterized aspects of tumor biology. Here we discover 121 unannotated prostate cancer–associated ncRNA transcripts (PCATs) by ab initio assembly of high-throughput sequencing of polyA+ RNA (RNA-Seq) from a cohort of 102 prostate tissues and cells lines. We characterized one ncRNA, PCAT-1, as a prostate-specific regulator of cell proliferation and show that it is a target of the polycomb repressive complex 2 (PRC2). We further found that patterns of PCAT-1 and PRC2 expression stratified patient tissues into molecular subtypes distinguished by expression signatures of PCAT-1–repressed target genes. Taken together, our findings suggest that PCAT-1 is a transcriptional repressor implicated in a subset of prostate cancer patients. These findings establish the utility of RNA-Seq to identify disease-associated ncRNAs that may improve the stratification of cancer subtypes. Overall design: 21 prostate cell lines sequenced on the Illumina Genome Analyzer and GAII. Variable number of replicates per sample. RNA-Seq data from prostate cancer tissues used in this study will be made available on dbGAP.

Publication Title

Transcriptome sequencing across a prostate cancer cohort identifies PCAT-1, an unannotated lincRNA implicated in disease progression.

Sample Metadata Fields

No sample metadata fields

View Samples
accession-icon GSE64616
Genome-wide hsa-miR-503, hsa-miR-103, and hsa-miR-494 target profiles
  • organism-icon Homo sapiens
  • sample-icon 10 Downloadable Samples
  • Technology Badge IconIllumina HumanHT-12 V4.0 expression beadchip

Description

This SuperSeries is composed of the SubSeries listed below.

Publication Title

miR-503 represses human cell proliferation and directly targets the oncogene DDHD2 by non-canonical target pairing.

Sample Metadata Fields

Cell line

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accession-icon SRP119333
Expression profiling of differentiating emerin-null myogenic progenitor identifies molecular pathways implicated in their impaired differentiation
  • organism-icon Mus musculus
  • sample-icon 34 Downloadable Samples
  • Technology Badge IconIllumina HiScanSQ

Description

RNA sequencing was performed on proliferating and differentiating wildtype and emerin-null myogenic progenitors to identify molecular pathways implicated in Emery-Dreifuss Muscular Dystrophy. Overall design: Total RNA was isolated from 2 million wildtype or emerin-null H2Ks during proliferation and at each day of differentiation using the miRNeasy Mini Kit (Qiagen, product #217004) and processed according to manufacturer's protocol. RNA was isolated from three independent cell culture plates for each sample.

Publication Title

Expression Profiling of Differentiating Emerin-Null Myogenic Progenitor Identifies Molecular Pathways Implicated in Their Impaired Differentiation.

Sample Metadata Fields

Specimen part, Cell line, Subject

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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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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