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Human NTERA2 (NT2/D1) cells lines: shZRF1 vs. shRandom during Retinoic Acid (RA) administration

ABSTRACT: Transcriptional profiling of human NT2 cell lines comparing control cells (shRandom) with ZRF1 knockdown cells (shZRF1) both either untreated (0 h) or treated with Retinoic Acid (3 h) at 0.01 µM. The cell lines were established by retroviral infection allowing for the transcription of either a random shRNA (shRandom) or a shRNA specific for ZRF1 (shZRF1). The goal was to determine the effect of ZRF1 on transcriptional activation at the onset of differentiation.

ORGANISM(S): Homo sapiens

PROVIDER: GSE16858 | GEO | 2010/12/24

SECONDARY ACCESSION(S): PRJNA122657

REPOSITORIES: GEO

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Human NTERA2 (NT2/D1) cells lines: shZRF1 vs. shRandom during Retinoic Acid (RA) administration

Project description:Transcriptional profiling of human NT2 cell lines comparing control cells (shRandom) with ZRF1 knockdown cells (shZRF1) both either untreated (0 h) or treated with Retinoic Acid (3 h) at 0.01 M-BM-5M. The cell lines were established by retroviral infection allowing for the transcription of either a random shRNA (shRandom) or a shRNA specific for ZRF1 (shZRF1). The goal was to determine the effect of ZRF1 on transcriptional activation at the onset of differentiation. Four-condition experiment, shRandom vs. shZRF1 cells either uninduced (0 h) or RA induced (3 h). Biological replicates: 6 replicates (shRandom) taken on 3 different days without or with RA administration. 6 shZRF1 replicates taken on three different days with or without RA administration.

2010-12-24 | E-GEOD-16858 | biostudies-arrayexpress

Human NTERA2 (NT2/D1) cells lines: Genomewide distribution of ZRF1 at gene promoters during RA administration

Project description:Chip-on-chip experiment with NT2 wildtype cells untreated (0 h) or treated with Retinoic Acid (1h and 3 h) at 0.01 µM. The goal was to determine the genome-wide occupancy of ZRF1 at gene promoters in undifferentiated cells and at the onset of differentiation. Three-condition experiment. Biological replicates: NT2 cells were treated with or without RA on three different days from cycling NT2 cells (0h, 1h and 3h of RA). Chromatin was prepared and a triplicate of IPs was performed with specific ZRF1 antibodies for every condition. A triplicate of control IPs was performed with IgGs.

2010-12-24 | E-GEOD-16878 | biostudies-arrayexpress

Human NTERA2 (NT2/D1) cells lines

Project description:This SuperSeries is composed of the following subset Series: GSE16858: Human NTERA2 (NT2/D1) cells lines: shZRF1 vs. shRandom during Retinoic Acid (RA) administration GSE16878: Human NTERA2 (NT2/D1) cells lines: Genomewide distribution of ZRF1 at gene promoters during RA administration Refer to individual Series

2010-12-24 | E-GEOD-16891 | biostudies-arrayexpress

Human NTERA2 (NT2/D1) cells lines: Genomewide distribution of ZRF1 at gene promoters during RA administration

2010-12-24 | GSE16878 | GEO

Distribution of macroH2A1 and macroH2A2 at gene promoters in NT2/D1 cells

Project description:Chip-on-chip experiment with NT2 wildtype cells and cells treated with shRNA for macroH2A1 and macroH2A2 The goal was to determine the genome-wide occupancy of macroH2A1 and macroH2A2 at gene promoters in undifferentiated cells

2009-09-06 | GSE17531 | GEO

Human NTERA2 (NT2/D1) cells lines

Project description:This SuperSeries is composed of the SubSeries listed below.

2010-12-24 | GSE16891 | GEO

NT2 DMSO vs. RA

Project description:NT2 cells were treated with DMSO (control) or 10uM Retinoic Acid (RA). Total RNA was isolated using TriReagent, and subsequent cleanup with RNeasy columns (Qiagen) according to the manufacturer's directions. Hybridizations were performed according to Affymetrix guidelines using the Human HG-U133A chip containing 22,500 unique genetic elements. Double-stranded cDNA was synthesized using Superscript II RT (Invitrogen). In vitro transcription labeling was performed with biotin labeled nucleotides using the Bioarray High Yield RNA Labeling Kit (ENZO). 20 ul of labeled RNA per sample was added to the hybridization cocktail, with a total of 15 ug hybridized to the chip (16 hours, 45C). RMA analysis was performed using Gene Traffic software (Iobion), where raw data for each hybridization was normalized, background corrected and filtered for signal intensity of 50 or greater in at least one comparison. Keywords: other

2005-10-18 | GSE2448 | GEO

Transcriptome analysis of PRMT6 knock-out in NT2/D1 cells

Project description:Whole transcriptome for PRMT6 knock-out and control NT2/D1 cells with and without ATRA (all-trans retinoic acid) was sequenced. These samples were compared to each other to find differentially regulated genes and PRMT6-dependent transcriptome in pluripotency and differentiating cells.

2018-09-27 | GSE107611 | GEO

Transcriptome analysis of SOX9 over-expressing NT2/D1 cells

Project description:To identify novel downstream target genes of SOX9, transcriptome analysis of SOX9 transfected human embryonic testicular cell line, NT2/D1, was carried out.

2015-04-30 | E-MTAB-3378 | biostudies-arrayexpress

Differentially expressed genes in human hippocampus and Tera-1 cell line versus HepG2, A549, NT2/D1 and NGP127 cells.

Project description:We discovered a new tissue specific enhancer originated from the human spesific endogenous retrovirus (hsERV). This enhancer displayed its activity in hippocampus and Tera-1 cell line as opposed to HepG2, A549, NT2/D1 and NGP127 cells. The aim of this study was to find transcription factors responsible for the hsERV enhancer activity. So we attempted to identify a fraction of transcription factor genes that were upregulated in enhancer-positive cells. Total RNA obtained from human hippocampus and Tera-1, HepG2, A549, NT2/D1 and NGP127 cell lines.

2013-01-26 | E-GEOD-43773 | biostudies-arrayexpress

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