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accession-icon SRP055967
human embryonic and mesenchymal stem cells
  • organism-icon Homo sapiens
  • sample-icon 10 Downloadable Samples
  • Technology Badge IconIlluminaHiSeq2500

Description

Mesenchymal stem cells (MSC) are self-renewing multipotent cells which hold great potential in stem cell-based therapy. MSC can be derived from multiple adult tissues but require invasive harvesting and imply donor-to-donor differences. MSC derived from embryonic stem cells (ESC) may provide an alternative source not suffering from those limitations, but to what extend they correspond to the adult counterpart is not known. Here we characterized human ESC-derived MSC in-depth and compared them to human adult tissue-derived MSC (bone marrow BM-MSC) as well as to hESC using next-generation RNA sequencing. In MSC we observed enrichment of proteins involved in cell adhesion, wound healing, extracellular matrix generation, as well as vesicle-mediated transport and exosomes, with the latter pointing towards paracrine signaling. The enrichment and variety of developmental terms associated with MSC further suggest the support function in tissue regeneration. The observed differences between ESC-and adult tissue derived-MSC are similar in magnitude to those reported for MSC of different origin and the former may thus represent an alternative source for therapeutic applications.

Publication Title

No associated publication

Sample Metadata Fields

No sample metadata fields

View Samples
accession-icon SRP067373
Bos taurus Raw sequence reads
  • organism-icon Bos taurus
  • sample-icon 220 Downloadable Samples
  • Technology Badge IconIllumina HiSeq 2000, Illumina MiSeq, Illumina HiSeq 3000

Description

Bovine RNA sequences

Publication Title

No associated publication

Sample Metadata Fields

Sex, Specimen part, Disease, Disease stage, Cell line, Treatment

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accession-icon SRP198932
Homo sapiens Transcriptome or Gene expression
  • organism-icon Homo sapiens
  • sample-icon 5 Downloadable Samples
  • Technology Badge IconIllumina HiSeq 2000

Description

AGO1 RIP-Seq from chromatin associated RNAs

Publication Title

No associated publication

Sample Metadata Fields

Sex, Specimen part, Cell line

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accession-icon GSE35935
Rituximab plus chlorambucil as initial treatment for elderly patients with chronic lymphocytic leukemia: effect of pretreatment biologic characteristics and gene expression patterns on response to treatment
  • organism-icon Homo sapiens
  • sample-icon 62 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)

Description

Evaluation of pretreatment gene expression profiling features in elderly CLL patients; correlation with clinical outcome

Publication Title

No associated publication

Sample Metadata Fields

Sex, Age, Specimen part

View Samples
accession-icon GSE15777
Spontaneous regression of chronic lymphocytic leukemia: clinical and biological features of 9 cases
  • organism-icon Homo sapiens
  • sample-icon 25 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Genome U133A 2.0 Array (hgu133a2)

Description

We describe 9 CLL patients who underwent a spontaneous clinical regression. CD38 and ZAP-70 were negative in all cases. Immunoglobulin heavy chain variable region (IgVH) genes, mutated in all 7 evaluable patients, were restricted to the VH3 family in 6, with the usage of VH3-30 gene in 2. The light chain variable region genes were mutated in 6/8 cases, with the usage of V4-1 gene in 3. Microarray analysis of CLL cells revealed a distinctive genomic profile. The number of activated T lymphocytes expressing IFN-, TNF- and IL-4 was similar between CLL in spontaneous regression and healthy individuals.

Publication Title

Spontaneous regression of chronic lymphocytic leukemia: clinical and biologic features of 9 cases.

Sample Metadata Fields

Specimen part

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accession-icon E-MEXP-1094
Transcription profiling of leaves from wild type and AtFAAH over-expressing Arabidopsis plants after inoculation with non-host pathogen Pseudomonas syringae pv. syringae for 0, 6 and 12 hours
  • organism-icon Arabidopsis thaliana
  • sample-icon 12 Downloadable Samples
  • Technology Badge Icon Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)

Description

Compare expression profiles between Col-0 and transgenic lines overexpressing AtFAAH(At5g64440) after inoculated with nonhost pathogen Pseudomonas syringae pv. syringae at 0, 6 and 12 hours.

Publication Title

No associated publication

Sample Metadata Fields

Age, Specimen part, Subject, Time

View Samples
accession-icon GSE22501
Functional Analysis and Gene Expression Profile of Umbilical Cord Blood Regulatory T Cells
  • organism-icon Homo sapiens
  • sample-icon 9 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)

Description

Since the role of cord blood (CB) regulatory T cells (Tregs) for the suppression of the allogeneic T-cell response is under investigation, we analyzed and compared the functional properties and gene expression profile of Tregs expanded from CB units or from the peripheral blood (PB) of helathy donors. Tregs were purified from 23 CB units and from the PB of 13 donors and expanded for 6 days with anti-CD3, anti-CD28 and IL-2. Immunophenotypic analyses were performed, and suppressor activity of expanded Tregs was measured in mixed lymphocyte reaction (MLR) cultures. The IL-10 production capacity was tested and gene expression profile experiments were performed on 6 Tregs from PB and 4 from CB. CB and PB Tregs had similar immunophenotypic features. Tregs from CB presented a higher expansion capacity and genomic characterization showed in CB-derived Tregs a significant enrichments of genes involved in cell proliferation, chromatin modification and regulation of gene expression in CB-derived Tregs. All samples were positive for the Foxp3 gene and protein after expansion. CB and PB expanded Tregs exerted a comparable and potent suppressive function of MLR and presented a high in vitro IL-10 production capacity. Gene profile analysis also revealed for PB Tregs a significant enrichments of genes involved in the adaptive immune response.

Publication Title

No associated publication

Sample Metadata Fields

Specimen part

View Samples
accession-icon E-MEXP-1310
Transcription profiling of Arabidopsis seedlings treated with NAE(12:0)
  • organism-icon Arabidopsis thaliana
  • sample-icon 6 Downloadable Samples
  • Technology Badge Icon Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)

Description

Transcript profiling and gene expression studies in NAE-treated seedlings: Seeds were germinated and seedlings maintained for 4 d in liquid MS media supplemented with 35 uM NAE(12:0)(N-lauroylethanolamine) prior to RNA isolation.

Publication Title

N-Acylethanolamine metabolism interacts with abscisic acid signaling in Arabidopsis thaliana seedlings.

Sample Metadata Fields

Age, Specimen part, Compound

View Samples
accession-icon E-TABM-255
Transcription profiling of bone marrow from children with T-cell acute lymphoblastic leukamia comparing those who remained in continuous complete remission with those that relapsed
  • organism-icon Homo sapiens
  • sample-icon 12 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Genome U133A Array (hgu133a)

Description

We compared the gene expression profile from a group of children with T-cell acute lymphoblastic leukamia who remained in continuous complete remission (CCR) (n = 7) with that from a group who relapsed (n = 5), using Affymetrix HG-U133A arrays. Using the decision-tree based supervised learning algorithm Random Forest (RF), genes were ranked with respect to their ability to discriminate between patients who remained in CCR and those who relapsed. From the 300 top-ranked probe sets 9 genes were selected for further investigation and validation in an independent cohort of 25 T-ALL patients using quantitative real time polymerase chain reaction.

Publication Title

Identification of novel molecular prognostic markers for paediatric T-cell acute lymphoblastic leukaemia.

Sample Metadata Fields

Sex, Age, Specimen part, Disease, Subject

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accession-icon SRP060446
Differential kinetics of host responses during infection with genetically distinct henipavirus strains in a lethal ferret model
  • organism-icon Mustela putorius furo
  • sample-icon 28 Downloadable Samples
  • Technology Badge IconIllumina HiSeq 2500

Description

RNA-seq analysis of lung and brain tissues from ferrets infected with Hendra virus and Nipah-Bangladesh virus

Publication Title

No associated publication

Sample Metadata Fields

Sex, Specimen part, Cell line, Time

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)

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Developed by the Childhood Cancer Data Lab

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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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