refine.bio
  • Search
      • Normalized Compendia
      • RNA-seq Sample Compendia
  • Docs
  • About
  • My Dataset
github link
Showing
of 17273 results
Sort by

Filters

Organism

Technology

Platform

accession-icon DRP003981
Combinatory use of the distinct single cell RNA-seq analytical platforms reveals heterogeneous transcriptome response to an anti-cancer drug in lung adenocarcinoma cell lines
  • organism-icon Homo sapiens
  • sample-icon 548 Downloadable Samples
  • Technology Badge IconIlluminaHiSeq2500

Description

Single cell RNA-seq (scRNA-seq) is a powerful tool to reveal the heterogeneity in cancer cells. Cancer heterogeneity would provide crucial information to understand eventual development of drug resistant cells or metastatic disseminations in cancers. In our study, we particularly focused on transcriptomic heterogeneity in response to an anti-cancer drug in five lung adenocarcinoma-derived cell lines. We generated single-cell RNA-seq by the two different platforms, the micro-droplet based platform and the micro-chamber platform, then we attempted to combine those datasets to complete information of datasets.

Publication Title

No associated publication

Alternate Accession IDs

None

Sample Metadata Fields

No sample metadata fields

View Samples
accession-icon DRP003241
Full-parasites: database of full-length cDNAs of apicomplexa parasites, 2014 update
  • organism-icon Homo sapiens
  • sample-icon 16 Downloadable Samples
  • Technology Badge IconIllumina Genome Analyzer IIx

Description

Full-Parasites (http://fullmal.hgc.jp/) is a transcriptome database of apicomplexa parasites, which include Plasmodium and Toxoplasma species

Publication Title

No associated publication

Alternate Accession IDs

None

Sample Metadata Fields

Cell line

View Samples
accession-icon DRP002586
Single cell analysis of lung adenocarcinoma cell lines and the response to an anti-cancer drug stimulation
  • organism-icon Homo sapiens
  • sample-icon 255 Downloadable Samples
  • Technology Badge IconIllumina HiSeq 2500

Description

To understand heterogeneous behaviors of individual cancer cells, it should be important to investigate gene expression levels as well as their divergences between individual cells. Here we conducted a single cell RNA Seq analysis of a series of lung adenocarcinoma cell lines. We analyzed a total of 337 RNA Seq libraries of single cells and found gene expression diversities between individual cells are characteristic depending on genes. The genes showing highly variable expressions were enriched in particular pathways. Particularly, the EGFR pathway genes originally showed wider variations and further diversity was induced in response to an anticancer-drug stimulation. We also observed that cancer-related genes, which were identified from recent clinical cancer sequencing projects, showed potential expression variations, which firstly became apparent on the anti-cancer drug stimulation.

Publication Title

No associated publication

Alternate Accession IDs

None

Sample Metadata Fields

Cell line

View Samples
accession-icon DRP000987
Interactive Transcriptome Analysis of Malaria Patients and Infecting Plasmodium falciparum in Indonesia
  • organism-icon Homo sapiens
  • sample-icon 122 Downloadable Samples
  • Technology Badge IconIlluminaGenomeAnalyzerIIx

Description

To understand the mutual association of the transcriptomes between host humans and infecting malaria parasites, Plasmodium falciparum (Pf), in vivo, we conducted the RNA-Seq analysis of 116 Indonesian malaria patients. Using RNAs extracted from peripheral blood of the patients as the mixture of the human and Pf transcripts, we generated a total of 3 billion RNA-Seq tags. Analysis of these tags allowed us to identify genes and pathways which were associated with clinical symptoms both on human and parasite sides. Particularly, we observed characteristic expression changes in the human innate immune response pathway genes depending on severity of malaria. We also identified a group of transcription regulatory factors and signaling molecule genes which have positive or negative correlations between humans and Pfs. These genes may change their expression patterns to accommodate the respective organisms to mutually conflicting environments. Furthermore, it was possible to utilize the RNA-Seq data for genotyping of the parasites to identify possible drug resistant genetic variations. By bypassing technical difficulty in preparing samples in field, this approach should provide a practically useful mean to describe mutually interacting transcritpomes of humans and parasites, which should eventually explain diverse malaria symptoms.

Publication Title

No associated publication

Alternate Accession IDs

None

Sample Metadata Fields

No sample metadata fields

View Samples
accession-icon DRP002315
Long Noncoding RNA NEAT1-Dependent SFPQRelocation from Promoter Region to ParaspeckleMediates IL8 Expression upon Immune Stimuli
  • organism-icon Homo sapiens
  • sample-icon 8 Downloadable Samples
  • Technology Badge IconIlluminaHiSeq2500

Description

Although thousands of long noncoding RNAs(lncRNAs) are localized in the nucleus, only a fewdozen have been functionally characterized. Herewe show that nuclear enriched abundant transcript1 (NEAT1), an essential lncRNA for the formation ofnuclear body paraspeckles, is induced by influenzavirus and herpes simplex virus infection as well asby Toll-like receptor3-p38 pathway-triggered polyI:C stimulation, resulting in excess formation ofparaspeckles. We found that NEAT1 facilitates theexpression of antiviral genes including cytokinessuch as interleukin-8 (IL8). We found that splicingfactor proline/glutamine-rich (SFPQ), a NEAT1-bindingparaspeckle protein, is a repressor of IL8 transcription,and that NEAT1 induction relocates SFPQfrom the IL8 promoter to the paraspeckles, leadingto transcriptional activation of IL8. Together, ourdata show that NEAT1 plays an important role inthe innate immune response through the transcriptionalregulation of antiviral genes by the stimulusresponsivecooperative action of NEAT1 and SFPQ.

Publication Title

No associated publication

Alternate Accession IDs

None

Sample Metadata Fields

No sample metadata fields

View Samples
accession-icon E-MEXP-1329
Transcription profiling of shoot apices from Arabidopsis wild type, teb, atr, and teb atr mutant plants
  • organism-icon Arabidopsis thaliana
  • sample-icon 6 Downloadable Samples
  • Technology Badge Icon Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)

Description

Global gene expression patterns were compared among wild-type Col-0, teb, atr, teb atr of A. thaliana using shoot apices.

Publication Title

No associated publication

Alternate Accession IDs

None

Sample Metadata Fields

Age, Specimen part, Time

View Samples
accession-icon E-ATMX-1
Transcription profiling of Arabidopsis wild type seeds grown under sulfur-deficient conditions
  • organism-icon Arabidopsis thaliana
  • sample-icon 4 Downloadable Samples
  • Technology Badge Icon Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)

Description

Comparison of Arabidopsis wild-type developing seeds grown under sulfur-deficient condition vs Arabidopsis wild-type developing seeds grown under control condition.

Publication Title

No associated publication

Alternate Accession IDs

None

Sample Metadata Fields

Specimen part

View Samples
accession-icon DRP003745
Examination of gene expression in sunitinib resistant cells and its HIF2a knock out cells
  • organism-icon Homo sapiens
  • sample-icon 4 Downloadable Samples
  • Technology Badge IconIllumina HiSeq 2500

Description

Next Generation Sequencing Facilitates Quantitative Analysis of sunitinib resistant cells and its HIF2a knock out cells.

Publication Title

No associated publication

Alternate Accession IDs

None

Sample Metadata Fields

Cell line

View Samples
accession-icon GSE41804
Hepatic gene expression of HCV related Hepatocellular carcinoma and non-cancerous tissue with Il28B rs8099917 TT genotype and TG/GG genotype
  • organism-icon Homo sapiens
  • sample-icon 37 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)

Description

IL28B genotype was shown to be associated with treatment outcome of antiviral thearpy for HCV infection. We tried to clarify the molecular feature that was asocciated with IL2B genotype by comparing Hepatic gene expression of HCV related Hepatocellular carcinoma and non-cancerous tissue with Il28B rs8099917 TT genotype and TG/GG genotype.

Publication Title

Association of interleukin-28B genotype and hepatocellular carcinoma recurrence in patients with chronic hepatitis C.

Alternate Accession IDs

E-GEOD-41804

Sample Metadata Fields

Specimen part

View Samples
accession-icon GSE97494
Endogenous Muscle Atrophy F-box is Involved in the Development of Cardiac Rupture After Myocardial Infarction
  • organism-icon Mus musculus
  • sample-icon 8 Downloadable Samples
  • Technology Badge Icon Affymetrix Mouse Gene 1.0 ST Array (mogene10st)

Description

Muscle atrophy F-box (MAFbx/atrogin-1), an E3 ubiquitin ligase, is a crucial mediator of skeletal muscle atrophy and cardiac hypertrophy in response to pressure overload and exercise.

Publication Title

No associated publication

Alternate Accession IDs

E-GEOD-97494

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
Version 1.42.67-hotfix - .0.0