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RNAseq transcriptome data from reprogramming human CD34+ cells to iPS

ABSTRACT: We reprogrammed human CD34+ cells from cord blood using a lentiviral vector encoding OCT4, SOX2 and KLF4.We collected RNA from parental CD34+ cells (3samples), reprogramming timepoints (9 timepoints), iPS clones derived from this experiment (6 clones), and human ES cell lines (9 samples). All samples were sequenced at 100bp reads.

ORGANISM(S): Homo sapiens

PROVIDER: GSE57866 | GEO | 2014/05/24

SECONDARY ACCESSION(S): PRJNA248289

REPOSITORIES: GEO

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RNAseq transcriptome data from reprogramming human CD34+ cells to iPS

Project description:We reprogrammed human CD34+ cells from cord blood using a lentiviral vector encoding OCT4, SOX2 and KLF4.We collected RNA from parental CD34+ cells (3samples), reprogramming timepoints (9 timepoints), iPS clones derived from this experiment (6 clones), and human ES cell lines (9 samples). All samples were sequenced at 100bp reads. Endogenous retroelement expression during reprogramming

2014-05-24 | E-GEOD-57866 | biostudies-arrayexpress

RNA-seq of CD34+CD43+ cells derived from CMML-iPS clones and Control-iPS clones

Project description:RNA-seq of CD34+CD43+ cells derived from CMML-iPS clones and Control-iPS clones for integration with eRRBS analysis

2020-04-30 | E-MTAB-7850 | biostudies-arrayexpress

RNA-seq of CD34+CD43+ cells derived from CMML-iPS clones and Control-iPS clones

Project description:RNA-seq of CD34+CD43+ cells derived from CMML-iPS clones and Control-iPS clones

| PRJEB32099 | ENA

Global transcriptome profiling of Oct4/Klf4/Sox2 (3Factor, 3F) + IL6 iPS clones derived from mouse embryonic fibroblasts.

2013-08-28 | GSE46104 | GEO

Global transcriptome profiling of Oct4/Klf4/Sox2 (3Factor, 3F) + IL6 iPS clones derived from mouse embryonic fibroblasts.

Project description:We used heterokaryon cell fusion based reprogramming and identified the cytokine IL6 as a potential regulator of reprogramming to pluripotency. We generated iPS clones using the four reprogramming factors (4F) Oct4, Klf4, Sox2, and c-Myc. In addition, iPS clones were generated using only three factors (3F: Oct4, Klf4, amd Sox2) with the addition of the cytokine IL6 to reprogramming culture conditions. Global RNA-Seq of the 3F + IL6 derived iPS clones was done for comparison with 4F-derived iPS clones, mouse embryonic stem cells and mouse embryonic fibroblasts. This study includes 8 samples: 2 independently derived 3F + IL6 iPS clones, 2 independently derived 4F iPS clones, 2 biological replicates of mouse D3-GFP ES cells, and 2 biological replicates of mouse embryonic fibroblasts (MEFs). The latter 6 samples are provided as references for the 3F + IL6 iPS clones. Poly-A RNA was isolated and prepared for sequencing using the Illumina TruSeq RNA kit (v2) to generate 50bp reads. Reads were aligned to mm10.

2013-08-28 | E-GEOD-46104 | biostudies-arrayexpress

mRNA expression in iPS cells generated by a synthetic self-replicative RNA

Project description:We generated iPS cells with a synthetic self-replicative RNA that expresses four independent reprogramming factors (OCT4, KLF4, SOX2 and either c-MYC or GLIS1). We performed whole genome RNA sequencing (RNA-seq) of iPS cell clones, parental BJ and HUES9 ES cell controls. All iPS cell clones analyzed by RNA-seq showed unsupervised hierarchical clustering and expression signatures characteristic of human HUES9 ES cells that were highly divergent from parental human fibroblasts. RNA-seq in two OKS-iM iPS clones (generated from OCT4, KLF4, SOX2 and cMYC expressing RNA replicon), two OKS-iG clones (generated from OCT4, KLF4, SOX2 and GLIS1 expressing RNA replicon), HUES9 and BJ cells.

2014-04-25 | E-GEOD-38265 | biostudies-arrayexpress

Gene expression profiles of murine fibroblasts and iPS

Project description:We reprogrammed adult murine fibroblasts obtained from p14f/f (wt version of conditional loxP-flanked p14 knockout (KO); C57/Bl6) by transduction of a lentiviral vector (pRRL.PPT.SF.hOKSMco.idTom.PRE) overexpressing the four Yamanaka factors (c-Myc, Klf-4, Oct-4, Sox-2). After successful reprogramming and establishment of stable iPS clones we performed gene expression profiling of three different murine iPS clones (#2, #2EX, #3) and their parental fibroblasts.

2018-03-01 | GSE97152 | GEO

mRNA expression in iPS cells generated by a synthetic self-replicative RNA

2014-04-25 | GSE38265 | GEO

Reprogramming human fat cells into iPS cells

Project description:This study determined whether human adipose stem cells (hASCs) could be reprogrammed into induced pluripotent stem (iPS) cells using the 4 factors OCT4, SOX2, KLF4, and cMYC. We showed successfull reprogramming could be achieved in which fat/adipose cells were able to assume embryonic-like phenotypes after lentiviral transduction with the 4 factors. Further, we believe these fat cells are intrinsically better-suited for reprogramming compared to fibroblasts, and result in higher yields of iPS cells.

2009-02-27 | GSE14982 | GEO

DNA microarrays of three shRNA control iPS clones (Ctrl 2,3,4) and shECAD iPS clones (shECAD 4,8,9)

Project description:E-cadherin upregulation is an early event of reprogramming of fibroblasts to induce pluripotent stem cells (iPS). Knocking down of E-cadherin by shRNA impairs iPS generation, though some colonies with great morphorlogical difference to shRNA control colonies remain. To illustrate the molecular and functional difference between shECAD iPS clones and shRNA control iPS clones, three respective iPS clones (shECAD 4,8,9 and Ctrl 2,3,4) were derived and DNA microarrays were run to analyze the transcriptional profile of these clones. OG2 MEFs were infected with Sox2, Klf4, Oct4 and c-Myc (SKOM) plus either Luciferase shRNA (shLUC) or E-cadherin shRNA (shECAD) retrovirus. At Day 6 post infection cells were split onto feeder cells. Several colonies from SKOM+shLuc and SKOM+shECAD were picked out at Day 14 post infection respectively and three cell lines were established, namely Ctrl 2,3,4 for SKOM+shLuc iPS and shECAD 4,8,9 for SKOM+shECAD iPS. All clones were maintained on feeder cells in mESC medium. RNA were extracted from these six cell lines and DNA microarrays were run to analyze the transcriptional profile.

2010-06-08 | E-GEOD-21062 | biostudies-arrayexpress

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