refine.bio
  • Search
      • Normalized Compendia
      • RNA-seq Sample Compendia
  • Docs
  • About
  • My Dataset
    0
github link
Showing
of 302 results
Sort by

Filters

Technology

Platform

accession-icon GSE15238
Expression data from human embryonic (9-12w) and post-natal livers
  • organism-icon Homo sapiens
  • sample-icon 12 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)

Description

The liver is a multifunctional organ, which undergoes rapid changes during the developmental period and relies on tightly-regulated gene expression. Little is known regarding the complex expression patterns of mRNAs during the early stages of human liver development in comparison to post-natal livers.

Publication Title

Comprehensive gene and microRNA expression profiling reveals a role for microRNAs in human liver development.

Sample Metadata Fields

Specimen part

View Samples
accession-icon GSE16674
Analysis of gene expression in miR-34a overexpressing K562 cells
  • organism-icon Homo sapiens
  • sample-icon 2 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)

Description

miR-34a is strongly induced upon TPA-induced megakaryocyte differentiation of K562 cells. To investigate the gene networks regulated by this miRNA during the process of differentiation we performed gene microarray analysis in K562 cells overexpressing miR-34a or a control sequence.

Publication Title

miR-34a contributes to megakaryocytic differentiation of K562 cells independently of p53.

Sample Metadata Fields

Cell line

View Samples
accession-icon SRP159668
The Lysosomal Transcription Factor TFEB regulates myelination downstream of the Rag-Ragulator complex.
  • organism-icon Danio rerio
  • sample-icon 2 Downloadable Samples
  • Technology Badge IconIllumina HiSeq 2000

Description

Purpose: To identify genes that are differentially expressed in oligodendrocytes between control and rraga mutant zebrafish, we performed RNA seq using the Illumina platform Overall design: Oligodendrocytes were isolated from control and rraga mutant zebrafish at 5 days post fertilization using FACS sorting of Cldnk:GFP positive cells. RNA was extracted from these cells and sequenced using standard Illumina protocol.

Publication Title

The Lysosomal Transcription Factor TFEB Represses Myelination Downstream of the Rag-Ragulator Complex.

Sample Metadata Fields

Cell line, Subject

View Samples
accession-icon GSE13460
Effect of wt versus mutant hsa-miR-122 overexpression on spontaneous hESC differentiation
  • organism-icon Homo sapiens
  • sample-icon 5 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Genome U133A 2.0 Array (hgu133a2)

Description

We aimed to determine whether overexpression of endoderm-specific miRNA may affect hESC differentiation. To this end, we analyzed the effect of lentiviral-based overexpression of liver-specific miR-122 on hESC differentiation, using genomewide gene microarrays. Stable overexpression of endoderm-specific miR-122 in hESC resulted in increased expression of a few endodermal markers in spontaneously-differentiating hESC, but had no clear effect on directing differentiation towards an endodermal fate; rather, it delayed the general differentiation of hESC.

Publication Title

MicroRNA expression patterns and function in endodermal differentiation of human embryonic stem cells.

Sample Metadata Fields

Cell line

View Samples
accession-icon SRP026382
A miR-155-ruled microRNA hierarchy in dendritic cell maturation and macrophage activation
  • organism-icon Mus musculus
  • sample-icon 20 Downloadable Samples
  • Technology Badge IconIllumina HiSeq 1000

Description

MicroRNAs (miRNAs) are small RNAs that play important regulatory roles in many cellular pathways. MiRNAs associate with members of the Argonaute (Ago) protein family and bind to partially complementary sequences on mRNAs and induce translational repression or mRNA decay. MiRNA expression can be controlled by transcription factors and can therefore be cell type- or tissue-specific. Here we have analyzed miRNA expression profiles in murine monocyte-derived dendritic cells (DCs) and macrophages upon stimulation with LPS, LDL, eLDL and oxLDL to identify not only stimuli-specific miRNA, but also to identify a hierarchical miRNA system involving miR-155. For this, miR-155 knockout dendritic cells and macrophages were also sequenced using the same stimuli. Overall design: Sequencing of murine monocyte-derived dendritic cells and macrophages (each wild type and miR-155 knock out cells) matured and stimulated, respectively, by LPS, oxLDL, eLDL or LDL.

Publication Title

A miR-155-dependent microRNA hierarchy in dendritic cell maturation and macrophage activation.

Sample Metadata Fields

Specimen part, Cell line, Subject

View Samples
accession-icon GSE18607
Type I IFN-signaling following Pneumocystis (PC)-infection and clearance in CD4 T cell-competent mice
  • organism-icon Mus musculus
  • sample-icon 12 Downloadable Samples
  • Technology Badge Icon Affymetrix Mouse Genome 430 2.0 Array (mouse4302)

Description

Type I IFN-signaling suppresses an excessive IFN-{gamma} response and prevents lung damage and chronic inflammation following Pneumocystis (PC)-infection and clearance in CD4 T cell-competent mice.

Publication Title

Type-I IFN signaling suppresses an excessive IFN-gamma response and thus prevents lung damage and chronic inflammation during Pneumocystis (PC) clearance in CD4 T cell-competent mice.

Sample Metadata Fields

Specimen part

View Samples
accession-icon GSE37714
Mammalian TRIM71 as repressor of mRNAs that inhibits translation and affects mRNA stability
  • organism-icon Mus musculus, Homo sapiens
  • sample-icon 12 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Gene 1.0 ST Array (hugene10st)

Description

This SuperSeries is composed of the SubSeries listed below.

Publication Title

The mammalian TRIM-NHL protein TRIM71/LIN-41 is a repressor of mRNA function.

Sample Metadata Fields

Specimen part, Cell line

View Samples
accession-icon GSE37713
Expression data from HEK293 Flp-In cells constitutivly expressing FLAG-HA-tagged TRIM71 and that of the parental cell line
  • organism-icon Homo sapiens
  • sample-icon 6 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Gene 1.0 ST Array (hugene10st)

Description

We identify mammalian TRIM71 as repressor of mRNAs that inhibits translation and affects mRNA stability.

Publication Title

The mammalian TRIM-NHL protein TRIM71/LIN-41 is a repressor of mRNA function.

Sample Metadata Fields

Cell line

View Samples
accession-icon SRP019990
miRNAs associated with the different human Argonaute proteins
  • organism-icon Homo sapiens
  • sample-icon 6 Downloadable Samples
  • Technology Badge IconIllumina Genome Analyzer IIx

Description

microRNAs (miRNAs) are small non-coding RNAs that function in literally all cellular processes. miRNAs interact with Argonaute (Ago) proteins and guide them to specific target sites located in the 3’ untranslated region (UTR) of target mRNAs leading to translational repression and deadenylation-induced mRNA degradation. Most miRNAs are processed from hairpin-structured precursors by the consecutive action of the RNase III enzymes Drosha and Dicer. However, processing of miR-451 is Dicer-independent and cleavage is mediated by the endonuclease Ago2. Here we have characterized miR-451 sequence and structure requirements for processing as well as sorting of miRNAs into different Ago proteins. Pre-miR-451 appears to be optimized for Ago2 cleavage and changes result in reduced processing. In addition, we show that the mature miR-451 only associates with Ago2 suggesting that mature miRNAs are not exchanged between different members of the Ago protein family. Based on cloning and deep sequencing of endogenous miRNAs associated with Ago1-3, we do not find evidence for miRNA sorting in human cells. However, Ago identity appears to influence the length of some miRNAs, while others remain unaffected. Overall design: Examination of miRNAs associated with endogenous human Ago1-4 in HeLa cells

Publication Title

microRNAs associated with the different human Argonaute proteins.

Sample Metadata Fields

No sample metadata fields

View Samples
accession-icon GSE37712
Expression data from mouse embryonic stem cells upon TRIM71 KD and parental ctrl cells
  • organism-icon Mus musculus
  • sample-icon 6 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Gene 1.0 ST Array (hugene10st)

Description

We identify mammalian TRIM71 as repressor of mRNAs that inhibits translation and affects mRNA stability. In this data set we compare the expression profile of mouse ES upon Trim71 KD versus that of the parental cells.

Publication Title

The mammalian TRIM-NHL protein TRIM71/LIN-41 is a repressor of mRNA function.

Sample Metadata Fields

Specimen part

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