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Expression analysis of doxycycline inducible secondary fibroblasts reprogramming under adherent and suspension conditions

ABSTRACT: Samples of adherent and suspension cells undergoing reprogramming were collected at day 0, day2, day6, day15 (with doxycycline) and day25 (without doxycycline).

ORGANISM(S): Mus musculus

PROVIDER: GSE35422 | GEO | 2012/03/25

SECONDARY ACCESSION(S): PRJNA152585

REPOSITORIES: GEO

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Expression analysis of doxycycline inducible secondary fibroblasts reprogramming under adherent and suspension conditions

Project description:Samples of adherent and suspension cells undergoing reprogramming were collected at day 0, day2, day6, day15 (with doxycycline) and day25 (without doxycycline). Reprogramming under adherent and suspension conditions was compared by PCC analysis, non-hierarchical clustering and by functional criteria for differentially expressed genes.

2012-03-25 | E-GEOD-35422 | biostudies-arrayexpress

Identifying differences in differentiation between adherent and suspension culture for iPSC derived beta cells

Project description:Stage 3 cells from a suspension environment and adherent culture were compared and evaluated through RNA sequencing. RNA sequencing data in heatmap and volcano plot evaluation of core endocrine genes showed that expression levels in adherent cells were lower than those expressed in 3D environment. Several genes that are essential for insulin transcription such as NEUROD1, MAFA, PPARGC1A and NKX2.2 along with INS were expressed with higher transcript levels in bioreactor samples. It was observed that genes usually expressed in earlier stages such as FOXA2 and HNF1b had higher expression levels in adherent culture indicating that 2D environment differentiation might be lagging.

2024-04-26 | GSE264176 | GEO

RNA-seq of suspension-grown vs. adherent Neisseria gonorrhoeae under conditions of zinc sequestration or zinc excess

Project description:Deep sequencing of cDNA of Neisseria gonorrhoeae bacteria that were grown in suspension or adherent to acid-washed glass coverslips, in media where zinc was sequestered or available in excess.

2022-12-12 | GSE191020 | GEO

RNA-sequencing and CRISPR/Cas9 Screen of PEO1 cells grown in suspension.

Project description:RNA-sequencing of PEO1 cells grown in suspension (SUS1 and SUS3) was performed to evaluate transcriptional reprogramming during anokis escape. CRISPR/Cas9 screen of PEO1 cells grown in adherent and suspension culture settings for 5 days or 10 days. GeCKO v2 library transduced in PEO1 cell line and cells were selected with puromycin. PEO1 line was authenticated prior to sequencing. PEO1 parental were confirmed to be BRCA2-mutated (5139C>G).

2018-12-04 | GSE123290 | GEO

Adherent and suspension baby hamster kidney cells have a different cytoskeleton and surface receptor repertoire

Project description:Adherent and suspension baby hamster kidney cells have a different cytoskeleton and surface receptor repertoire

| PRJEB44757 | ENA

Cell line adaptation Changes in the proteome level during a step-wise adaptation of an adherent Madin Darby canine kidney (MDCK) cell line

Project description:In this work, changes in the proteome level during a step-wise adaptation of an adherent Madin Darby canine kidney (MDCK) cell line to suspension growth and chemically defined medium were analyzed.

2015-04-22 | PXD001306 | Pride

Murine uterus expression profile during Peri-implantation: Pre-implantation vs. Post-implantation

Project description:Anaylsis differentially expressed genes of mouse peri-implanted uteri comparing pre-implantation uteri (Day2, Day3 and Day4) with post-implantation uteri (Day6, Day7 and Day8) by microassay. This study has built a meaningful basis for future investigation in elucidating the molecular nature of maternal-fetal interactions during pregnancy establishment and maintenance. Pre-implantation uteri VS. Post-implantation uteri. Three biological replicates of each experiments: pre-implantation uteri (Day2, Day3 and Day4): 234, 234①, 234②; 3 mixture of post-implantation uteri (Day6, Day7 and Day8): 678, 678①, 678②. Two hybridizations were performed by using a reverse fluorescence strategy (Cy3, Cy5) for each sample.

2011-06-30 | E-GEOD-26615 | biostudies-arrayexpress

Murine uterus expression profile during Peri-implantation: Pre-implantation vs. Post-implantation

2011-06-30 | GSE26615 | GEO

Mouse Embryonic Stem Cells Resist c-Jun induced Differentiation in Suspension

Project description:The oncogene c-Jun plays a key role in development and cancer. Yet, its role in cell fate decision remains poorly understood at the molecular level. Here we report that c-Jun confers different fate decisions upon mouse embryonic stem cells (mESCs) in adhesion vs suspension. We developed a Tet-on system for temporal induction of c-Jun expression by Doxycycline treatment in mESCs. We show that mESCs carrying the inducible c-Jun TetOn remain pluripotent and grow slowly in suspension with induction of c-Jun, while undergoing differentiation with normal proliferative potentials in adherence upon c-Jun induction. Apparently, c-Jun pushes mESCs in suspension into cell cycle arrest at G1/S, through the induction of Cdkn1a/b and Cdkn2/a/b/c. Despite cell cycle arrest, they can re-enter cell cycle upon plating on adhesive surface and grow into typical mESC colonies albeit at lower efficiency. These results demonstrate that mESCs respond to c-Jun differently in suspension or adherence. Our results suggest that cells in suspension may be more resistant to differentiation than in adherence.

2019-02-19 | GSE114381 | GEO

Effects of RELA and RELB in spheroid and adherent ovarian cancer

Project description:Purpose: To understand the role of NF-kB signaling in tumor-initiating cell (TIC) and non-TIC populations in ovarian cancer. Methods: OV90 cells with inducible shRNA against RelA and RelB, and a non-targeting shRNA control were induced by doxycycline treatment and were grown in adherent (non-TIC) or spheroid (TIC) conditions. Total RNA was extracted from each condtion and RNAseq was performed and analysed for differential gene expression between the conditions.

2023-04-28 | GSE230678 | GEO

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