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accession-icon SRP092010
Hit-and-run'' programing of CAR-T cells using mRNA nanocarriers
  • organism-icon Homo sapiens
  • sample-icon 27 Downloadable Samples
  • Technology Badge IconIllumina HiSeq 2500

Description

RNAseq of ex vivo CD8 T cell lineages and in vitro differentiated CD8 T cells treated with nanocarriers encapsulating control or Foxo1-3A transcription factor mRNA Overall design: Gene expression in central memory CD8 and in vitro Foxo1-3A nanoparticle treated CD8 were compared to control cells cultured in vitro with eGFP mRNA encapsulating nanoparticles.

Publication Title

Hit-and-run programming of therapeutic cytoreagents using mRNA nanocarriers.

Alternate Accession IDs

GSE89134

Sample Metadata Fields

Specimen part, Subject

View Samples
accession-icon GSE74600
Transcriptomic analysis and ChIP-seq in CCE-Rx cells to identify SOX2 transcription factor target genes
  • organism-icon Mus musculus
  • sample-icon 8 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

Targeted resequencing identifies PTCH1 as a major contributor to ocular developmental anomalies and extends the SOX2 regulatory network.

Alternate Accession IDs

E-GEOD-74600

Sample Metadata Fields

Specimen part, Time

View Samples
accession-icon GSE74598
Transcriptomic analysis after transfection in murine genetically modified stem cells overexpressing the RAX gene (CCE-Rx cells) of either a siRNA against SOX2 or a scramble siRNA
  • organism-icon Mus musculus
  • sample-icon 8 Downloadable Samples
  • Technology Badge Icon Affymetrix Mouse Gene 1.0 ST Array (mogene10st)

Description

SOX2 is the main gene involved in anophthalmia. In order to identify genes regulated by SOX2 transcription factors (genes that could be good candidates to also be involved in ocular development), we studied transcriptomic profiles of murine genetically modified stem cells overexpressing the RAX gene (CCE-Rx cells) after transfection by a siRNA against SOX2 or a scramble siRNA.

Publication Title

Targeted resequencing identifies PTCH1 as a major contributor to ocular developmental anomalies and extends the SOX2 regulatory network.

Alternate Accession IDs

E-GEOD-74598

Sample Metadata Fields

Specimen part, Time

View Samples
accession-icon GSE8318
Expression from control subplate neurons with few synapses and cocultured subplate neurons with induced synaptogenesis
  • organism-icon Rattus norvegicus
  • sample-icon 20 Downloadable Samples
  • Technology Badge Icon Affymetrix Rat Genome 230 2.0 Array (rat2302)

Description

The transcriptional events accompanying synaptogenesis are largely unknown, or have been studied in systems in which synapse formation occurs gradually over time. With a system in which synaptogenesis is synchronized and controllable, molecular or biochemical techniques can be used to examine cellular events across cultures on a wide scale, as synapses develop.

Publication Title

Synaptogenesis in purified cortical subplate neurons.

Alternate Accession IDs

E-GEOD-8318

Sample Metadata Fields

No sample metadata fields

View Samples
accession-icon SRP009043
Genome-wide Analysis of Nascent Transcription in Saccharomyces cerevisiae
  • organism-icon Saccharomyces cerevisiae
  • sample-icon 22 Downloadable Samples
  • Technology Badge IconIllumina Genome Analyzer II

Description

We combined the nuclear run-on (NRO) assay which labels and captures nascent transcripts with high throughput DNA sequencing to examine transcriptional activity in Saccharomyces cerevisiae. Overall design: Examination of nascent transcripts and steady-state transcripts in exponentially growing and heat-shock treated yeast.

Publication Title

Genome-Wide Analysis of Nascent Transcription in Saccharomyces cerevisiae.

Alternate Accession IDs

GSE33136

Sample Metadata Fields

Cell line, Treatment, Subject

View Samples
accession-icon GSE6765
Aeromonas caviae infection, 24 hours
  • organism-icon Mus musculus
  • sample-icon 9 Downloadable Samples
  • Technology Badge Icon Affymetrix Mouse Genome 430 2.0 Array (mouse4302)

Description

Aeromonas caviae has been associated with human gastrointestinal disease. Strains of this species typically lack virulence factors (VFs) such as enterotoxins and hemolysins that are produced by other human pathogens of the Aeromonas genus. Microarray profiling of murine small intestinal extracts, 24 hours after oral infection with an A. caviae strain, provides evidence of a Th1 type immune response. A large number of gamma-interferon (-IFN) induced genes are up-regulated as well as several tumor necrosis factor-alpha (TNF-) transcripts. A. caviae has always been considered an opportunistic pathogen because it lacks obvious virulence factors. This current effort suggests A. caviae colonizes murine intestinal tract and causes what has been described by others as a dysregulatory cytokine response leading to an irritable bowel-like syndrome. This response would explain why a number of diarrheal waterborne outbreaks have been attributed to A. caviae even though it lacks obvious enteropathogenic properties.

Publication Title

Aeromonas caviae strain induces Th1 cytokine response in mouse intestinal tract.

Alternate Accession IDs

E-GEOD-6765

Sample Metadata Fields

No sample metadata fields

View Samples
accession-icon SRP032999
Next generation sequencing of the transcriptome in MCF-7 cells with/without SRA knockdown
  • organism-icon Homo sapiens
  • sample-icon 6 Downloadable Samples
  • Technology Badge IconIlluminaHiSeq2000

Description

We employed next generation sequencing to examine whether knocking down the steroid receptor RNA activator (SRA) gene significantly affect the expression levels of certain genes in MCF-7 cells. MCF-7 cells were transfected with either a pool of four non-target control siRNAs or a pool of four SRA siRNAs for 32 hrs. 157 million reads were generated from triplicate samples of the control group; 151 million reads were generated from triplicate samples of the SRA knockdown group. Six genes were identified as significantly changed in the expression levels with the cutoff of q value = 0.05, fold change = 0.5 or = 2, and reads per kilobase per million mapped reads (RPKM) = 1. However, except for SRA itself, the other five genes were shown by real-time PCR to be only affected by one siRNA in the SRA siRNA pool. Further analysis of this dataset with different cuttoff setting may reveal true SRA-regulated genes in MCF-7. Overall design: MCF-7 cells were cultured in high glucose DMEM with 10% fetal bovine serum, 2 mM Glutamax-1, 100 units/ml penicillin and 100 µg/ml streptomycin. ON-TARGETplus SMARTpool for human SRA (Thermo Scientific, L-027192-00-0005) was used to knockdown SRA (siSRA) and ON-TARGETplus Non-targeting Pool Thermo Scientific, D-001810-10-05) was used as a negative control (siCtrl). A total of 25 nM siRNA was transfected in 6-well dishes using Lipofectamine™ RNAiMAX Reagent (Life Technologies, Invitrogen) following the manufacturer’s recommendations. Polyadenylated RNA was purified from the cells 32 hrs after transfection. cDNA libraries were prepared and double-stranded cDNA was fragmented using DNase I according to Illumina specifications, prior to adaptor ligation. Sequencing libraries were amplified and sequenced using an Illumina HiSeq 2000 sequencer.

Publication Title

Structure and function of steroid receptor RNA activator protein, the proposed partner of SRA noncoding RNA.

Alternate Accession IDs

GSE52385

Sample Metadata Fields

No sample metadata fields

View Samples
accession-icon GSE6928
Stonewalling Drosophila stem cell differentiation by epigenetic controls
  • organism-icon Drosophila melanogaster
  • sample-icon 6 Downloadable Samples
  • Technology Badge Icon Affymetrix Drosophila Genome 2.0 Array (drosophila2)

Description

Abstract: During Drosophila oogenesis, germline stem cell (GSC) identity is maintained largely by preventing the expression of factors that promote differentiation. This is accomplished via the activity of several genes acting either in the GSC or its niche. The translational repressors, Nanos and Pumilio, act in GSCs to prevent differentiation, likely by inhibiting translation of early differentiation factors, while niche signals prevent differentiation by silencing transcription of the differentiation factor Bam. We have found that the DNA-associated protein Stonewall (Stwl) is also required for GSC maintenance. stwl is required cell-autonomously; clones of stwl- germ cells were lost by differentiation, and ectopic Stwl caused an expansion of GSCs. stwl mutants acted as Suppressors of Variegation, indicating stwl normally acts in chromatin-dependent gene repression. In contrast to several previously described GSC maintenance factors, Stwl likely functions epigenetically to prevent GSC differentiation. Stwl-dependent transcriptional repression does not target bam, but rather Stwl represses the expression of many genes, including those that may be targeted by Nanos/Pumilio translational inhibition.

Publication Title

Stonewalling Drosophila stem cell differentiation by epigenetic controls.

Alternate Accession IDs

E-GEOD-6928

Sample Metadata Fields

No sample metadata fields

View Samples
accession-icon GSE14908
Global expression profiling of CD4 T-cell responses to house dust mite allergens in human atopics and nonatopics.
  • organism-icon Homo sapiens
  • sample-icon 88 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Gene 1.0 ST Array (hugene10st)

Description

The aim of this study was to employ a systems-level analysis to elucidate gene expression networks operating in the CD4 T-cell responses which underpin human atopic disease.

Publication Title

A network modeling approach to analysis of the Th2 memory responses underlying human atopic disease.

Alternate Accession IDs

E-GEOD-14908

Sample Metadata Fields

Time

View Samples
accession-icon GSE41058
Competition between viral-derived and endogenous small RNA pathways regulates gene expression in response to viral infection in C.elegans.
  • organism-icon Caenorhabditis elegans
  • sample-icon 20 Downloadable Samples
  • Technology Badge Icon Affymetrix C. elegans Genome Array (celegans)

Description

This SuperSeries is composed of the SubSeries listed below.

Publication Title

Competition between virus-derived and endogenous small RNAs regulates gene expression in Caenorhabditis elegans.

Alternate Accession IDs

E-GEOD-41058

Sample Metadata Fields

No sample metadata fields

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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