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Unknown,Transcriptomics,Genomics,Proteomics

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Systematic identification of transcription factors capable of inducing cell-type-specific transcriptional profiles

ABSTRACT: This SuperSeries is composed of the following subset Series: GSE29724: Unsupervised hierarchical clustering of iNPCs induced by 6 or 5 TFs GSE29726: The overexpression of Pax6 affects mesenchymal to epithelial transition (MET) pathway during iPS induction in NPC. GSE29728: Overexpression of each of the 6 interfering TFs and 5 non-interfering TFs GSE29729: Selection of NPC specific Transcription factors GSE29730: Unsupervised hierarchical clustering of iHPCs induced by 9 or 10 TFs Refer to individual Series

ORGANISM(S): Mus musculus

SUBMITTER: Takafusa Hikichi

PROVIDER: E-GEOD-29875 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Unsupervised hierarchical clustering of iHPCs induced by 9 or 10 TFs

Project description:To clarify the gene expression profile of iHep, microarray analysis was performed using iHeps induced by 10 TFs (Foxg1, Lcor, Hnf3b, Hnf4a, Foxo6, Cdx2, Tcf1, Foxa3 ,Tcf2, Onecut1) and 9 TFs (Onecut1 was omitted from 10 TFs). Unsupervised hierarchical clustering indicated that iHep is expressing a global transcriptional profile more similar to that of HPCs rather than that of NPCs, and suggested that TFs present in the pool acted as inducing TFs. HPC (HB1 and HNG2) were established from fetal liver (E13.5) of C57BL6J and STOCK Tg(Nanog-GFP, Puro)1 Yam, respectively. iHeps were induced from NPC (NSBAg2, established from an ES cell line BAg73C2 carrying beta-geo knock-in allele in Afp) using retroviral vectors (pMXs without drug-selection markers) of 9 or 10 transcription factors. Three weeks after the infection, G418 was added and cultured for 1 week before the harvest. NSBAg2 and NSEB5-2C were used for the data of NPC. GSM396240 and GSM336010 were used for the data of ESC.

2011-06-07 | E-GEOD-29730 | biostudies-arrayexpress

Unsupervised hierarchical clustering of iNPCs induced by 6 or 5 TFs

Project description:To clarify the gene expression profile of iNPC, microarray analysis was performed using iNPCs induced by 6 TFs (Pax6, Hmga2, Etv6, Gatad2b, Nfxl1, and Esx1) and 5 TFs (Esx1 was omitted from 6 TFs). Unsupervised hierarchical clustering indicated that iNPC is expressing a global transcriptional profile more similar to that of NPCs rather than that of MEFs, and suggested that the TFs present in the pool acted as inducing TFs. iNPCs were induced from MEF using 6 or 5 transcription factors. iNPCs were induced from MEF (MEFSH, derived from mice carrying IRES-Hygro in Sox allele) using retroviral vectors (pMXs-IRESNeo) of 6 or 5 transcription factors. Four weeks after the infection, Hygromycin was added and cultured for 1 week before the harvest. NSBAg2 and NSEB5-2C were used for the data of NPC. GSM396240 and GSM336010 were used for the data of ESC.GSM651349 and GSM336011 were used for the data of MEF.

2011-06-07 | E-GEOD-29724 | biostudies-arrayexpress

Selection of NPC specific Transcription factors

Project description:To construct a candidate pool of NPC specific transcription factor (TF), we selected the genes expressed at relatively high levels in NPCs by comparing them to mixed RNA derived from multiple organs, eliminating housekeeping genes. As result, 160 putative NPC specific TFs were selected. We used three independent NPC lines (NSEB5-2C, NS195R, NS21) established from different ES cell lines (EB5, 195R, 21, respectively). Genes exhibiting relatively higher expression (1.5 fold) in NSEB5-2C and NS195R (or, NSEB5-2C and NS21) were selected by comparing with Mixture (consisting of equal microgram of RNAs from heart, kidney, thymus, spleen, liver, lung, d11 embryo). Gene Ontology (GO) terms ‘DNA binding’ and ‘transcription activity’ were used to select TFs.

2011-06-07 | E-GEOD-29729 | biostudies-arrayexpress

Overexpression of each of the 6 interfering TFs and 5 non-interfering TFs

Project description:To clarify that the interfering effect in iPS induction was not because of extraordinary gene expression which was caused by overexpression of infected genes, transcriptional profile of the cells infected six genes were analysed using microarray analysis. As result, overexpression of each of the 6 interfering TFs in NSEB5-2C did not compromise transcriptional profile compared with the five non-interfering TFs. The cells were infected by retroviruses (carrying each ORF in pMXs-IRESNeo) at the titre in which around 95% of cells express the transgene. After 24hr of the infection, G418 was added to eliminate non-expressing cells. Each cells were harvested at 72hr after the infection.

2011-06-07 | E-GEOD-29728 | biostudies-arrayexpress

Mus musculus

Project description:Unsupervised hierarchical clustering of iNPCs induced by 6 or 5 TFs

| PRJNA153865 | ENA

Mus musculus

Project description:Unsupervised hierarchical clustering of iHPCs induced by 9 or 10 TFs

| PRJNA153851 | ENA

The overexpression of Pax6 affects mesenchymal to epithelial transition (MET) pathway during iPS induction in NPC.

Project description:We performed a microarray analysis to compare N31EGFP and N31Pax6 transcriptional profiles 24 h after iPS induction. Among 603 genes whose levels changed greater than two-fold (295 lower, 308 higher), we noticed a 10-fold decrease in the Cdh1 signal in N31Pax6, which was confirmed by reverse transcription-mediated quantitative polymerase chain reaction (RT-QPCR). iPS induction is known to require activation of the mesenchymal to epithelial transition (MET) pathway, which involves Cdh1 upregulation. In fact, Twist1 expression, repression of which is required for MET pathway activation was higher in N31Pax6. Dox-inducible iPS-NPC, N31, was established from the primary iPSC induced from NSEB5-2C by introducing dox-inducible Oct3/4, Sox2, Klf4 and c-Myc. EGFP or Pax6 were overexpressed in N31 by transfecting CAG-EGFP-IP or CAG-Pax6-IP by Tol2 transposon. Gene expression was measured at 24 hours after exposure to doxycycline, when apparent morphological change was observed only in N31EGFP.

2011-06-07 | E-GEOD-29726 | biostudies-arrayexpress

Unsupervised hierarchical clustering of iNPCs induced by 6 or 5 TFs

2011-06-07 | GSE29724 | GEO

Unsupervised hierarchical clustering of iHPCs induced by 9 or 10 TFs

2011-06-07 | GSE29730 | GEO

Mus musculus

Project description:Overexpression of each of the 6 interfering TFs and 5 non-interfering TFs

| PRJNA153869 | ENA