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accession-icon SRP140536
Single Cell RNA sequencing of Adult Human Breast Epithelial Cells [C1_Individual_3]
  • organism-icon Homo sapiens
  • sample-icon 287 Downloadable Samples
  • Technology Badge IconIllumina HiSeq 2500

Description

Breast cancer arises from breast epithelial cells that acquire genetic alterations leading to subsequent loss of tissue homeostasis. Several distinct epithelial subpopulations have been proposed, but complete understanding of the spectrum of heterogeneity and differentiation hierarchy in the human breast remains elusive. Here, we used single-cell mRNA sequencing (scRNAseq) to profile the transcriptomes of 25,790 primary human breast epithelial cells isolated from reduction mammoplasties of seven individuals. Unbiased clustering analysis reveals the existence of three distinct epithelial cell populations, one basal and two luminal cell types, which we identify as secretory L1- and hormone-responsive L2-type cells. Pseudotemporal reconstruction of differentiation trajectories produc one continuous lineage hierarchy that closely connects the basal lineage to the two differentiated luminal branches. Our comprehensive cell atlas provides novel insights into cellular blueprint of the human breast epithelium and will form the foundation to understand how the system goes awry during breast cancer. Overall design: Microfluidics-enabled Single Cell RNA sequencing libraries were generated for 3 adult human women using the Fluidigm C1 and sequenced on the Illumina HighSeq 2500

Publication Title

Single-cell landscape in mammary epithelium reveals bipotent-like cells associated with breast cancer risk and outcome.

Alternate Accession IDs

GSE113198

Sample Metadata Fields

Sex, Specimen part, Subject

View Samples
accession-icon SRP140488
Single Cell RNA sequencing of Adult Human Breast Epithelial Cells [C1_Individual_1]
  • organism-icon Homo sapiens
  • sample-icon 294 Downloadable Samples
  • Technology Badge IconIllumina HiSeq 2500

Description

Breast cancer arises from breast epithelial cells that acquire genetic alterations leading to subsequent loss of tissue homeostasis. Several distinct epithelial subpopulations have been proposed, but complete understanding of the spectrum of heterogeneity and differentiation hierarchy in the human breast remains elusive. Here, we used single-cell mRNA sequencing (scRNAseq) to profile the transcriptomes of 25,790 primary human breast epithelial cells isolated from reduction mammoplasties of seven individuals. Unbiased clustering analysis reveals the existence of three distinct epithelial cell populations, one basal and two luminal cell types, which we identify as secretory L1- and hormone-responsive L2-type cells. Pseudotemporal reconstruction of differentiation trajectories produc one continuous lineage hierarchy that closely connects the basal lineage to the two differentiated luminal branches. Our comprehensive cell atlas provides novel insights into cellular blueprint of the human breast epithelium and will form the foundation to understand how the system goes awry during breast cancer. Overall design: Microfluidics-enabled Single Cell RNA sequencing libraries were generated for 3 adult human women using the Fluidigm C1 and sequenced on the Illumina HighSeq 2500

Publication Title

Single-cell landscape in mammary epithelium reveals bipotent-like cells associated with breast cancer risk and outcome.

Alternate Accession IDs

GSE113099

Sample Metadata Fields

Sex, Specimen part, Subject

View Samples
accession-icon SRP140489
Single Cell RNA sequencing of Adult Human Breast Epithelial Cells [C1_Individual_2]
  • organism-icon Homo sapiens
  • sample-icon 159 Downloadable Samples
  • Technology Badge Icon

Description

Breast cancer arises from breast epithelial cells that acquire genetic alterations leading to subsequent loss of tissue homeostasis. Several distinct epithelial subpopulations have been proposed, but complete understanding of the spectrum of heterogeneity and differentiation hierarchy in the human breast remains elusive. Here, we used single-cell mRNA sequencing (scRNAseq) to profile the transcriptomes of 25,790 primary human breast epithelial cells isolated from reduction mammoplasties of seven individuals. Unbiased clustering analysis reveals the existence of three distinct epithelial cell populations, one basal and two luminal cell types, which we identify as secretory L1- and hormone-responsive L2-type cells. Pseudotemporal reconstruction of differentiation trajectories produc one continuous lineage hierarchy that closely connects the basal lineage to the two differentiated luminal branches. Our comprehensive cell atlas provides novel insights into cellular blueprint of the human breast epithelium and will form the foundation to understand how the system goes awry during breast cancer. Overall design: Microfluidics-enabled Single Cell RNA sequencing libraries were generated for 3 adult human women using the Fluidigm C1 and sequenced on the Illumina HighSeq 2500

Publication Title

Single-cell landscape in mammary epithelium reveals bipotent-like cells associated with breast cancer risk and outcome.

Alternate Accession IDs

GSE113127

Sample Metadata Fields

No sample metadata fields

View Samples
accession-icon GSE45136
Identification of the chemokine CCL28 as a growth and survival factor for human hematopoietic stem- and progenitor cells
  • organism-icon Homo sapiens
  • sample-icon 9 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)

Description

To discover novel growth factors for hematopoietic stem- and progenitor cells (HSPCs), we have assessed cytokine responses of cord blood (CB)-derived CD34+ cells in a high-content growth factor screen. We identify the immunoregulatory chemokine (C-C motif) ligand 28 (CCL28) as a novel growth factor that directly stimulates proliferation of primitive hematopoietic cells from different ontogenetic origins.

Publication Title

Identification of the chemokine CCL28 as a growth and survival factor for human hematopoietic stem and progenitor cells.

Alternate Accession IDs

E-GEOD-45136

Sample Metadata Fields

Specimen part

View Samples
accession-icon GSE56273
leukemia propagating cells rebuild an evolving niche in response to therapy
  • organism-icon Homo sapiens
  • sample-icon 6 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)

Description

Residence of cancer-propagating cells (CPCs) within preferential microenvironmental niches has a major part in evading therapy. However, the nature of niches involved and the mechanisms protecting CPCs remain largely unknown. We addressed these issues in mouse transplantation models of acute lymphoblastic leukemia (ALL). When the engrafted leukemic cells substantially damaged adjacent vascular structures and endosteal linings in the bone marrow (BM), after chemotherapy small foci of CPCs were retained, surrounded by sheaths of supporting cells that comprise a novel niche. We investigated patients BM biopsies and found evidence of a similar process in patients receiving induction-therapy. The efficacy of chemotherapy was enhanced by interfering with the niche formation or niche-CPC interaction. We therefore identified a therapy-induced niche that protects CPCs.

Publication Title

Leukemia propagating cells rebuild an evolving niche in response to therapy.

Alternate Accession IDs

E-GEOD-56273

Sample Metadata Fields

Specimen part, Treatment

View Samples
accession-icon SRP024272
The tetraspanin CD9 affords high purity capture of all murine hematopoietic stem cells.
  • organism-icon Mus musculus
  • sample-icon 4 Downloadable Samples
  • Technology Badge IconIllumina Genome Analyzer

Description

Prospective isolation is critical to understand the cellular and molecular aspects of stem cell heterogeneity. Here we identify the cell surface antigen CD9 as a novel positive marker that provides a simple alternative for hematopoietic stem cell-isolation at high purity Overall design: mRNA profiles of LT and ST HSCs

Publication Title

The tetraspanin CD9 affords high-purity capture of all murine hematopoietic stem cells.

Alternate Accession IDs

GSE47707

Sample Metadata Fields

Subject

View Samples
accession-icon GSE7302
Expression data from bone marrow hematopoietic stem cell CD34 Flt3 subfractions
  • organism-icon Mus musculus
  • sample-icon 6 Downloadable Samples
  • Technology Badge Icon Affymetrix Mouse Genome 430 2.0 Array (mouse4302)

Description

Lineage negativ Sca1+ Kit+ bone marrow cells (containing putative hematopoietic stem cells) subfractionation based on CD34 and FLT3 identifies three functionally destinc subpopulations (LSKCD34-FLT3-, LSKCD34+FLT3- & LSKCD34+FLT3+).

Publication Title

Molecular evidence for hierarchical transcriptional lineage priming in fetal and adult stem cells and multipotent progenitors.

Alternate Accession IDs

E-GEOD-7302

Sample Metadata Fields

No sample metadata fields

View Samples
accession-icon GSE52075
Expression data of the endothelial-to-hematopoietic transition in E8.5 concepti
  • organism-icon Mus musculus
  • sample-icon 9 Downloadable Samples
  • Technology Badge Icon Affymetrix Mouse Genome 430 2.0 Array (mouse4302)

Description

During development a specialised subset of endothelial cells, the haemogenic endothelium, undergo an endothelial-to-haematopoietic transition. This process critically involves the transcription factor Runx1. Here we have isolated a specific subpopulation of endothelial cells using a Runx1 enhancer-reporter transgenic mouse line (23GFP). We have compared the gene expression profile of this population to non-23GFP expressing endothelial cells and CD41 expressing haematopoietic progenitor cells to assess whether 23GFP expression marks a biologically distinct subset of endothelium.

Publication Title

Early dynamic fate changes in haemogenic endothelium characterized at the single-cell level.

Alternate Accession IDs

E-GEOD-52075

Sample Metadata Fields

Specimen part

View Samples
accession-icon SRP076334
Identification of rare, dormant and therapy resistant stem cells in acute lymphoblastic leukemia
  • organism-icon Homo sapiens
  • sample-icon 228 Downloadable Samples
  • Technology Badge IconIllumina HiSeq 1500

Description

Tumor relapse is associated with dismal prognosis, but responsible biological principles remain incompletely understood. To isolate and characterize relapse-inducing cells, we used genetic engineering and proliferation-sensitive dyes in patient-derived xenografts of acute lymphoblastic leukemia (ALL). We identified a rare subpopulation that resembled relapse-inducing cells with combined properties of long-term dormancy, treatment resistance, and stemness. Single-cell and bulk expression profiling revealed their similarity to primary ALL cells isolated from pediatric and adult patients at minimal residual disease (MRD). Therapeutically adverse characteristics were reversible, as resistant, dormant cells became sensitive to treatment and started proliferating when dissociated from the in vivo environment. Our data suggest that ALL patients might profit from therapeutic strategies that release MRD cells from the niche. Overall design: Gene expression profiles from two PDX ALL Samples (ALL-199 & ALL-265) were generated for either dormant (LRC) vs. dividing (non-LRC) cells or drug treated vs. non-treated cells. For single cell analysis one mouse were analyzed for each condition.

Publication Title

Characterization of Rare, Dormant, and Therapy-Resistant Cells in Acute Lymphoblastic Leukemia.

Alternate Accession IDs

GSE83142

Sample Metadata Fields

Specimen part, Treatment, Subject

View Samples
accession-icon GSE29382
Characterisation of early thymic progenitors and thymus seeding progenitors
  • organism-icon Mus musculus
  • sample-icon 36 Downloadable Samples
  • Technology Badge Icon Affymetrix Mouse Genome 430 2.0 Array (mouse4302)

Description

Gene expression analysis of early thymic progenitors and thymus seeding progenitors

Publication Title

The earliest thymic T cell progenitors sustain B cell and myeloid lineage potential.

Alternate Accession IDs

E-GEOD-29382

Sample Metadata Fields

Sex, Age, Specimen part, Disease

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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