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accession-icon SRP170733
Using RNA Seq to investigate adaptation mechanisms in P. aeruginosa
  • organism-icon Pseudomonas aeruginosa
  • sample-icon 26 Downloadable Samples
  • Technology Badge IconIllumina HiSeq 2500

Description

We demonstrate that the versatile environmental bacterium Pseudomonas aeruginosa adapts a virulence phenotype after serial passage in Galleria mellonella as an invertebrate model host. The virulence phenotype was not linked to the acquisition of genetic variations and was sustained for several generations, despite cultivation of the ex vivo virulence-adapted P. aeruginosa cells under non-inducing rich medium conditions. Transcriptional reprogramming seemed to be induced by a host-specific food source as reprogramming was also observed upon cultivation of P. aeruginosa in medium supplemented with polyunsaturated long-chain fatty acids. Methods : mRNA profiles were generated for Pseudomonas aerugionsa samples derived from LB-cultures grown to an OD600 =2. The removal of ribosomal RNA was performed using the Ribo-Zero Bacteria Kit (Illumina) and cDNA libraries were generated with the ScriptSeq v2 Kit (Illumina) . The samples were sequenced in single end mode on an Illumina HiSeq 2500 device and mRNA reads were trimmed and mapped to the NC_008463.1 (PA14) reference genome from NCBI using Stampy pipeline with defaut settings. Overall design: Isolate CH2658 was subjected to in vivo and in vitro evolution experiments in this study. This isolate was obtained from the lab of G. Gastmeier, Charite Berlin, Germany. The in vivo passages (using G. mellonella) are named CH2658 I-IV corresponding to passages 1 4. The last passage CH2658 IV corresponds to the “evolved strain” and was passaged in LB (four days, two passages a day) to generate revertants which are referred to as CH2658 Rev1-4 corresponding to samples from day1-4. The last passage CH2658 Rev4 is called “revertant”. Additionally, the clinical isolate was passaged under in vitro conditions in the presence of linolenic acid (Roth) with (CH2658 Lil+P) and without paraffin (CH2658 Lil). As controls, CH2658 was passaged in LB (CH2658 LB) and in LB supplemented with paraffin (CH2658 LB+P). The in vitro passage experiment was conducted for four days and two passages a day.

Publication Title

Establishment of an induced memory response in Pseudomonas aeruginosa during infection of a eukaryotic host.

Sample Metadata Fields

Subject

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accession-icon SRP159291
Using RNA Seq to identify a CF habitat specific transcriptional profile
  • organism-icon Pseudomonas aeruginosa
  • sample-icon 10 Downloadable Samples
  • Technology Badge IconIllumina HiSeq 2500

Description

Purpose: The goal of this study was to use RNA Seq to explore whether and to what extent genetic heterogeneity would shape the transcriptional profile in the environment of the CF lung Methods : mRNA profiles were generated for Pseudomonas aerugionsa samples derived from explanted lung tissue or pure cultures isolated from the same lung regions by deep sequencing. To enrich the bacterial RNA MicrobeEnrich Kit (Ambion) was used. The removal of ribosomal RNA was performed using the Ribo-Zero Bacteria Kit (Illumina) and cDNA libraries were generated with the ScriptSeq v2 Kit (Illumina) . The samples were sequenced in single end mode on an Illumina HiSeq 2500 device and mRNA reads were trimmed and mapped to the PAO1 NC_002516 reference genome from NCBI using Stampy pipeline with defaut settings. Overall design: mRNA profiles either from Pseudomonas aeruginosa containing explanted lung tissue from a single patient from various regions of the lung or pure P. aeruginosa liquid cultures grown in LB at 37C from the same lung regions as the ex vivo samples were generated and deep sequenced using Illumina HiSeq 2500.

Publication Title

Genetically diverse Pseudomonas aeruginosa populations display similar transcriptomic profiles in a cystic fibrosis explanted lung.

Sample Metadata Fields

Subject

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accession-icon GSE25067
Gene expression in response to genetic and chemical perturbations of chromatin structure
  • organism-icon Arabidopsis thaliana
  • sample-icon 12 Downloadable Samples
  • Technology Badge Icon Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)

Description

Microarray expression profiling was used to identify genes expressed misexpressed in wild-type Arabidopsis seedlings treated with 5-aza-2 deoxyctidine (5AC) or trichostatin A (TSA), and in decrease in dna methylation1 (ddm1) mutant seedlings.

Publication Title

Changes in global gene expression in response to chemical and genetic perturbation of chromatin structure.

Sample Metadata Fields

Specimen part

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accession-icon SRP214490
RNA-seq of P. aeruginosa clinical isolate collection under biofilm growth conditions
  • organism-icon Pseudomonas aeruginosa
  • sample-icon 167 Downloadable Samples
  • Technology Badge IconIllumina NovaSeq 6000, Illumina HiSeq 2500

Description

Purpose : The goal of this study was to use RNA-seq to compare transcriptional profiles under biofilm conditions with planktonic growth and explore the correlation of gene expression of a collection of clinical P. aeruginosa isolates to various phenotypes, such as biofilm structure or virulence. Methods : mRNA profiles were generated for Pseudomonas aeruginosa clinical samples derived from various geographical locations by deep sequencing. The removal of ribosomal RNA was performed using the Ribo-Zero Bacteria Kit (Illumina) and cDNA libraries were generated with the ScriptSeq v2 Kit (Illumina). The samples were sequenced in single end mode on an Illumina HiSeq 2500 device or paired end mode on an Illumina Novaseq 6000. mRNA reads were trimmed and mapped to the NC_008463.1 (PA14) reference genome from NCBI using bowtie2 with default settings. Overall design: mRNA profiles from Pseudomonas aeruginosa derived from static biofilm cultures grown for 12h to 48h in 96-well microtiter plates or planktonic LB cultures grown to an OD600 = 2 and deep sequenced using Illumina HiSeq 2500/NovaSeq 6000.

Publication Title

Parallel evolutionary paths to produce more than one <i>Pseudomonas aeruginosa</i> biofilm phenotype.

Sample Metadata Fields

Subject

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accession-icon GSE33588
Human-specific patterns of gene expression in the brain
  • organism-icon Macaca mulatta, Pan troglodytes, Homo sapiens
  • sample-icon 29 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)

Description

This SuperSeries is composed of the SubSeries listed below.

Publication Title

Divergent whole-genome methylation maps of human and chimpanzee brains reveal epigenetic basis of human regulatory evolution.

Sample Metadata Fields

No sample metadata fields

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accession-icon GSE33010
Human-specific patterns of gene expression in the brain (Arrays)
  • organism-icon Macaca mulatta, Pan troglodytes, Homo sapiens
  • sample-icon 29 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)

Description

We identified human-specific gene expression patterns in the brain by comparing expression with chimpanzee and rhesus macaque

Publication Title

Divergent whole-genome methylation maps of human and chimpanzee brains reveal epigenetic basis of human regulatory evolution.

Sample Metadata Fields

No sample metadata fields

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accession-icon GSE97910
Epistatic interaction between the lipase-encoding genes Pnpla2 (ATGL) and Lipe (HSL) causes liposarcoma in mice
  • organism-icon Mus musculus
  • sample-icon 72 Downloadable Samples
  • Technology Badge IconIllumina MouseRef-8 v2.0 expression beadchip

Description

Liposarcoma is a poorly understood malignancy of fat cells. Lipolysis, a central pathway of adipose tissue metabolism, has been implicated in cancer. Here, we generated tissue-specific single- and combined knockout mice for the two major lipases ATGL and HSL. Notably, double knockout (DAKO) mice developed late onset liposarcoma with complete penetrance, while single knockout mice appeared normal. DAKO whole transcriptome profiles differed from those of single knockout mice, revealing an early-onset tissue-specific response that persisted until the late-onset development of liposarcoma. Cancer-associated markers Gpnmb and G0s2 were among the most highly dysregulated genes in DAKO mice and also in human liposarcomas, suggesting a potential role for these proteins as liposarcoma-specific biomarkers. Taken together, our results demonstrate a novel epistatic interaction linking lipolysis with cancer. DAKO mice provide a promising model for studying early premalignant changes that lead to late-onset disease.

Publication Title

Epistatic interaction between the lipase-encoding genes Pnpla2 and Lipe causes liposarcoma in mice.

Sample Metadata Fields

Age, Specimen part

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accession-icon SRP120487
Trnascriptome analysis of HeLa cells infected with rTHOV-wt, -dML, -SW mutant or mock-treated
  • organism-icon Homo sapiens
  • sample-icon 12 Downloadable Samples
  • Technology Badge IconIllumina HiSeq 2500

Description

The goal of the study was to compare transcriptome changes in HeLa cells after infection with recombinant Thogoto virus (wild-type, ML deletioin mutant or ML SW mutant not able to interact wiith TFIIB. While wild-type virus is able to inhibit inflammatory genes, ML deletion mutant and TFIIB-non-interacting mutant lose this effect on gene transcription. Overall design: Examination of transcriptome changes in HeLa cells under steady state or after THOV infection using Illumina HiSeq.

Publication Title

Viral targeting of TFIIB impairs de novo polymerase II recruitment and affects antiviral immunity.

Sample Metadata Fields

Cell line, Subject

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accession-icon SRP043364
Human cortical transcriptome informs brain imaging
  • organism-icon Homo sapiens
  • sample-icon 52 Downloadable Samples
  • Technology Badge IconIlluminaHiSeq2000

Description

We carried out RNA-sequencing (RNA-seq) of adult human postmortem neocortical brain tissue, and then correlated those expression values with the fMRI signal in each brain region Overall design: Ten cortical regions were included in the analysis: pre-motor cortex - PMV (BA6), dorsolateral prefrontal cortex – DLPFC (BA9), middle temporal gyrus – pMTG (BA21), superior temporal gyrus – pSTG (BA22), angular gyrus - AG (BA39), supramarginal gyrus - SMG (BA40), pars opercularis - POP (BA44), pars triangularis - PTr (BA45), middle frontal gyrus – MFG (BA46) and pars orbitalis - POrB (BA47). For each brain region, three or more samples from left adult brain hemispheres were collected (ages range from 33 to 49) and only males were included to avoid the effect of sex

Publication Title

Correspondence between Resting-State Activity and Brain Gene Expression.

Sample Metadata Fields

No sample metadata fields

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accession-icon SRP008930
Combinatorial role of two paralogous splicing factors, hnRNP L and L-like, in multiple-exon regulation of CD45 alternative splicing
  • organism-icon Homo sapiens
  • sample-icon 4 Downloadable Samples
  • Technology Badge IconIllumina Genome Analyzer IIx

Description

The goal of this study was to investigate the role of hnRNP L-like in alternative pre-mRNA splicing in human B-cells through an RNA-Seq approach. Overall design: RNA-Seq was performed in DG75 cell line with over expression of hnRNP L-like or GFP as control.

Publication Title

HnRNP L and L-like cooperate in multiple-exon regulation of CD45 alternative splicing.

Sample Metadata Fields

Cell line, Subject

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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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