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SRP100788
Mus musculus
422 Downloadable Samples
NextSeq 500
Description
Mammary glands were collected from 8 pubescent (4.7-4.9 week-old) female mice and 8 adult (10 week old) female mice. Freshly sorted epithelial cells were submitted to a Fluidigm C1 System machine for single cell capture and cDNA synthesis. Cells were visualized under the microscope to ensure integrity of the captured single cells prior to cDNA preparation. Libraries were prepared using the Nextera XT kit and sequencing was carried out on an Illumina NextSeq 500 to achieve paired-end 75 bp reads. Overall design: RNA-seq profiling was completed for 221 cells from pubescent mice and 223 cells from adult mice.
Publication Title
Construction of developmental lineage relationships in the mouse mammary gland by single-cell RNA profiling.
Sample Metadata Fields
Cell line, Subject
View Samples- Mus musculus
- 346 Downloadable Samples
- Illumina HiSeq 2000
Description
Mammary glands were collected from pre-pubescent (2 weeks old), pubescent (4.7- 4.9 weeks old) and adult (10 week-old) female mice. Freshly sorted epithelial cells were submitted to a Fluidigm C1 System machine for single cell capture and cDNA synthesis. Cells were visualized under a microscope to ensure integrity of the captured single cells prior to cDNA preparation. Libraries were prepared using the Nextera XT kit and sequencing was carried out on an Illumina Hiseq 2000 to achieve 100 bp paired-end reads. Overall design: RNA-seq profiling was completed for 144 cells from 8 pre-puberty (2 week old) mice, 136 cells from 8 pubescent (4.7-4.9 week old) mice and 66 cells from 8 adult (10 week old) mice.
Publication Title
Construction of developmental lineage relationships in the mouse mammary gland by single-cell RNA profiling.
Sample Metadata Fields
Cell line, Subject
View Samples- Mus musculus
- 311 Downloadable Samples
- NextSeq 500
Description
Mammary glands were collected from 8 pregnant (12.5 day) mice and 8 adult (10 week old) female mice. Basal epithelial cells were FACS sorted. Freshly sorted cells were submitted to a Fluidigm C1 System machine for single cell capture and cDNA synthesis. Cells were visualized under the microscope to ensure integrity of the captured single cells prior to cDNA preparation. Libraries were prepared using the Nextera XT kit and sequencing was carried out on an Illumina NextSeq 500 to achieve paired-end 75 bp reads. Overall design: RNA-seq profiling was completed for 75 cells from pregnant mice and 237 cells from adult mice.
Publication Title
Construction of developmental lineage relationships in the mouse mammary gland by single-cell RNA profiling.
Sample Metadata Fields
Cell line, Subject
View Samples- Mus musculus
- 278 Downloadable Samples
- NextSeq 500
Description
Mammary glands were collected from 8 pregnant (12.5 day) mice and 8 non-pregnant adult (10 week old) female mice. Epithelial cells were FACS sorted from the pregnant mice. Cells from the adult mice were FACS sorted as basal or luminal. Freshly sorted cells were submitted to a Fluidigm C1 System machine for single cell capture and cDNA synthesis. Cells were visualized under the microscope to ensure integrity of the captured single cells prior to cDNA preparation. Libraries were prepared using the Nextera XT kit and sequencing was carried out on an Illumina NextSeq 500 to achieve 75 bp paired-end reads. Overall design: 112 basal cells and 43 luminal cells were profiled from the adult mice. 123 total epithelial cells were profiled from the pregnant mice.
Publication Title
Construction of developmental lineage relationships in the mouse mammary gland by single-cell RNA profiling.
Sample Metadata Fields
Cell line, Subject
View Samples- Mus musculus
- 169 Downloadable Samples
- Illumina HiSeq 2000
Description
Mammary glands of 8 adult (10 week-old) female mice were collected. Freshly sorted basal and luminal epithelial cells were submitted to a Fluidigm C1 System machine for single cell capture and cDNA synthesis. Cells were visualized under the microscope to ensure integrity of the captured single cells prior to cDNA preparation. Libraries were prepared using the Nextera XT kit and sequencing was carried out on an Illumina Hiseq 2000 to achieve 100bp paired-end reads. Overall design: 96 basal and 90 luminal cells were profiled from 8 mice.
Publication Title
Construction of developmental lineage relationships in the mouse mammary gland by single-cell RNA profiling.
Sample Metadata Fields
Cell line, Subject
View Samples- Homo sapiens
- 8 Downloadable Samples
Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
CSNK1a1 Regulates PRMT1 to Maintain the Progenitor State in Self-Renewing Somatic Tissue.
Sample Metadata Fields
Specimen part, Treatment
View Samples- Homo sapiens
- 8 Downloadable Samples
Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
Here we determine the target gene sets controlled by PRMT1 or CSNK1a1 in maintaining the undifferentiated state of primary human keratinocytes.
Publication Title
CSNK1a1 Regulates PRMT1 to Maintain the Progenitor State in Self-Renewing Somatic Tissue.
Sample Metadata Fields
Treatment
View Samples- Mus musculus
- 2 Downloadable Samples
- NextSeq 500
Description
Epithelial cells were isolated by FACS from the mammary glands of adult (10 week old) female mice. A basal subpopulation of the epithelial cells was also isolated. Freshly sorted cells were submitted to a 10X Genomics Chromium System for single cell capture. cDNA synthesis and library preparation was done according to the protocol supplied by the manufacturer. Sequencing was carried out on an Illumina NextSeq500 sequencer to achieve 75 bp paired-end reads. Overall design: Transcriptional profiling was completed for 4771 basal cells and 3302 total epithelial cells from 8 mice.
Publication Title
Construction of developmental lineage relationships in the mouse mammary gland by single-cell RNA profiling.
Sample Metadata Fields
Cell line, Subject
View Samples- Mus musculus
- 12 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
Despite substantial investments, tuberculosis remains one of the biggest challenges in public health.
Publication Title
Synergy of chemotherapy and immunotherapy revealed by a genome-scale analysis of murine tuberculosis.
Sample Metadata Fields
Sex, Specimen part
View Samples- Macaca mulatta
- 12 Downloadable Samples
- Affymetrix Rhesus Macaque Genome Array (rhesus)
Description
CD8+ T-cells inhibit virus replication in SIV-infected rhesus macaques (RM). However, it is not clear how SIV infection is controlled in germinal center during chronic SIV infection and limited information exists on the characteristics of CXCR5+ CD8 T cells during chronic SIV/HIV infection. In this study, we used functional genomics to investigate characteristic features and potential mechanisms of CXCR5+ and CXCR5- SIV specific CD8 T cells for the control of pathogenic SIV infection. Six chronically SIV infected RMs, three SIVE660 infected and three SIV mac251 infected that are positive for Mamu A01 allele were selected and SIV-specific CXCR5+ and CXCR5- CD8 T cells were sorted based on CXCR5 expression. RNA from sorted cells were extracted and microarray were performed and analysed. Principal component analysis demonstrated that overall gene expression difference between CXCR5+ and CXCR5- SIV-specific CD8 T cells. Interestingly, the CXCR5+ CD8 T cells revealed a distinct gene signature pattern when compared to CXCR5- CD8 T cells. Unlike the CXCR5- CD8 T cells, the CXCR5+ CD8 T cells expressed higher levels of genes associated with Tfh CD4 T cells such as the master transcription factor Bcl6, CD200, and CTLA4 as well as markers associated with Th2 CD4 T cells such as IL-4R (CD124), CCR4, STAT6, NFATC, and IL-10. Effector molecules typically observed in cytotoxic CD8 T cells such as granzyme A, B, and K were expressed at lower levels on CXCR5+ CD8 T cells compared to their CXCR5- counterparts. CXCR5+ CD8 T cells also expressed higher levels of molecules associated with co-stimulation/antigen presentation such as CD40, CD83, 41BBL and MAMU-DRA. The CXCR5+ CD8 also expressed higher levels of inhibitory receptors such as CD200 and SPRY2 but lower levels of other inhibitory receptors CD160 and CD244. The functional consequence of the expression of these molecules is yet to be determined. Additionally, CXCR5+ CD8 T cells expressed higher levels of the anti-apoptotic gene Bcl-2 and lower levels of the pro-apoptotic gene annexin, suggestive of their better survival potential during chronic SIV infection. Collectively, these results demonstrate that SIV specific CXCR5+ CD8 T cells possess a unique gene expression signature compared to SIV-specific CXCR5- CD8 T cells.
Publication Title
Dynamics of SIV-specific CXCR5+ CD8 T cells during chronic SIV infection.
Sample Metadata Fields
Specimen part
View Samples