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SRP040145
Homo sapiens
13 Downloadable Samples
IlluminaHiSeq2000
Description
Induced pluripotent stem cells (iPSCs) offer opportunity for insight into the genetic requirements of the X chromosome for somatic and germline development. Turner syndrome is caused by complete or partial loss of the second sex chromosome; while more than 90% of Turner cases result in spontaneous fetal loss, survivors display an array of somatic and germline clinical characteristics. Here, we derived iPSCs from Turner syndrome and control individuals and examined germ cell development as a function of X chromosome composition. We analyzed gene expression profiles of derived iPSCs and in vitro differentiated cells by single cell qRT-PCR and RNA-seq. We whoed that two X chromosomes are not necessary for reprogramming or pluripotency maintenance. Genes that escape X chromosome inactivation (XCI) between control iPSCs and those with X chromosome aneuploidies revealed minimal expression differences relative to a female hESC line. Moreover, when we induced germ cell differentiation via murine xenotransplantation of iPSC lines into the seminiferous tubules of busulfan-treated mice, we observed that undifferentiated iPSCs, independent of X chromosome composition, when placed within the correct somatic environment, are capable of forming early germ cells in vivo. Results indicate that two intact X chromosomes are not required for germ cell formation; however, clinical data suggest that two sex chromosomes are required for maintenance of human germ cells. Overall design: RNA-seq of H9 cells, iPSCs from Turner syndrome and control individuals and in vitro differentiated cells
Publication Title
Human germ cell formation in xenotransplants of induced pluripotent stem cells carrying X chromosome aneuploidies.
Sample Metadata Fields
No sample metadata fields
View Samples- Macaca mulatta
- 25 Downloadable Samples
Affymetrix Rhesus Macaque Genome Array (rhesus)
Description
Pedigreed primate ESCs display homogeneous and reliable expression profiles.
Publication Title
Pedigreed primate embryonic stem cells express homogeneous familial gene profiles.
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 423 Downloadable Samples
- Illumina HiSeq 2500
Description
Spermatogonial stem cells (SSCs) are critical for maintaining spermatogenesis throughout adult life. Little is known about how SSCs are first generated. Here, we report the identification of a transcription factor—RHOX10—that promotes the initial establishment of SSCs. We were led to this discovery because we found that conditional loss of a large X-linked gene cluster comprised of 33 related homeobox genes, including Rhox10, causes defects predicted if SSCs fail to be generated or maintained. Remarkably, KO of only Rhox10 elicits SSC-related defects indistinguishable from KO of the entire gene cluster. Using a battery of approaches, including single cell-RNAseq analysis, we determined that loss of Rhox10 causes accumulation of undifferentiated germ cells—Pro-spermatogonia (ProSG)—at a time when they normally would form SSCs. The identification of a transcription factor that drives the initial generation of SSCs has potential therapeutic applications for infertility. Overall design: Single cell RNA-seq analysis of ID4-positive testicular cells from Wildtype and Rhox10 knockout mice (Postnatal day 3 and 7)
Publication Title
The Homeobox Transcription Factor RHOX10 Drives Mouse Spermatogonial Stem Cell Establishment.
Sample Metadata Fields
Specimen part, Subject
View Samples- Homo sapiens
- 5 Downloadable Samples
- Affymetrix Human Genome U219 Array (hgu219)
Description
Glioblastoma cells are characterized by a highly invasive behavior whose mechanisms are not yet understood. Using the wound healing and Boyden chamber assays we compared in the present study the migration and invasion abilities of 5 glioblastoma cell lines (DK-MG, GaMG, U87-MG, U373-MG, SNB19) differing in p53 and PTEN status. We also analyzed by Western blotting the expression of PTEN, p53, mTOR and several other marker proteins involved in cell adhesion, migration and invasion. Among 5 cell lines, GaMG cells exhibited the fastest rate of wound closure, whereas U87-MG cells showed the most rapid chemotactic migration in the Boyden chamber assay. In DK-MG and GaMG cells, F-actin mainly occurred in the numerous stress fibers spanning the cytoplasm, whereas U87-MG, U373-MG and SNB19 cells preferentially expressed F-actin in filopodia and lamellipodia. Moreover, the two glioblastoma lines mutated in both p53 and PTEN genes (U373-MG and SNB19) were found to exhibit the fastest invasion rates through the Matrigel matrix.
Publication Title
Actin cytoskeleton organization, cell surface modification and invasion rate of 5 glioblastoma cell lines differing in PTEN and p53 status.
Sample Metadata Fields
Specimen part, Cell line
View Samples- Homo sapiens
- 64 Downloadable Samples
- IlluminaGenomeAnalyzerIIx
Description
56 breast cancer cell lines were profiled to identify patterns of gene expression associated with subtype and response to therapeutic compounds. Overall design: Cell lines were profiled in their baseline, unperturbed state.
Publication Title
Modeling precision treatment of breast cancer.
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 6 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
Stabilized Alpha-Helix peptides of BCL9 HD2 (SAH-BCL9) block BCL9 and B9L interactions with beta-catenin and specifically downregulate Wnt target gene expression.
Publication Title
Targeted disruption of the BCL9/β-catenin complex inhibits oncogenic Wnt signaling.
Sample Metadata Fields
Specimen part, Cell line, Treatment
View Samples- Mus musculus
- 16 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
Multiple myeloma (MM) evolves from highly prevalent premalignant condition termed Monoclonal Gammopathy of Undetermined Significance (MGUS). We report an MGUS-MM phenotype arising in transgenic mice with Emu-directed expression of the unfolded protein/ER stress response and plasma cell development spliced isoform factor XBP-1s. Emu-XBP-1s elicited elevated serum Ig and IL-6 levels, skin alterations and with advancing age, a significant proportion of Emu-xbp-1s transgenic mice develop features diagnostic of human MM including bone lytic lesions. Transcriptional profiles of Emu-xbp-1s B lymphoid and MM cells show aberrant expression of genes known to be dysregulated in human MM including Cyclin D1, MAF, MAFB, and APRIL. This genetic model coupled with documented frequent XBP-1s overexpression in human MM serve to implicate chronic XBP-1s dysregulation in the development of this common and lethal malignancy.
Publication Title
The differentiation and stress response factor XBP-1 drives multiple myeloma pathogenesis.
Sample Metadata Fields
No sample metadata fields
View Samples- Arabidopsis thaliana
- 10 Downloadable Samples
- Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)
Description
We also used microarray analysis to examine transcriptomic changes under moderate drought, identifying thousends of genes that potentially mediate moderate drought responses in the flower, including genes encoding transcription factors that likely play crucial regulatory roles.
Publication Title
Moderate drought causes dramatic floral transcriptomic reprogramming to ensure successful reproductive development in Arabidopsis.
Sample Metadata Fields
Specimen part
View Samples- Arabidopsis thaliana
- 6 Downloadable Samples
- Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)
Description
We performed microarray to determine transcriptomic changes upon anac019-1 under drought, identifying hundreds of genes that potentially function downstream of ANAC019 and mediate drought responses in the flower, including genes encoding transcription factors that likely play crucial regulatory roles.
Publication Title
ANAC019 is required for recovery of reproductive development under drought stress in Arabidopsis.
Sample Metadata Fields
Specimen part
View Samples- Homo sapiens
- 59 Downloadable Samples
- IlluminaHiSeq2000, IlluminaMiSeq
Description
Establishment and application of RNAseq based transcriptome analayis on an archivaed bladder cancer cohort. Overall design: Total RNA profilling 61 archived bladder cancer samples and comparison of 4 pairs of fresh frozen and FFPE bladder cancer samples.
Publication Title
Next-generation RNA sequencing of archival formalin-fixed paraffin-embedded urothelial bladder cancer.
Sample Metadata Fields
No sample metadata fields
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