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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Transcription profiling by array of Taf10 KO livers

ABSTRACT: Transcriptional profiling of Taf10-/- livers as compared to age-matched wild_type controls.

ORGANISM(S): Mus musculus

SUBMITTER: George Garinis

PROVIDER: E-MEXP-3442 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Defective transcription initiation causes postnatal growth failure in a mouse model of nucleotide excision repair (NER) progeria.

Kamileri Irene I Karakasilioti Ismene I Sideri Aria A Kosteas Theodoros T Tatarakis Antonis A Talianidis Iannis I Garinis George A GA

Proceedings of the National Academy of Sciences of the United States of America 20120208 8

Nucleotide excision repair (NER) defects are associated with cancer, developmental disorders and neurodegeneration. However, with the exception of cancer, the links between defects in NER and developmental abnormalities are not well understood. Here, we show that the ERCC1-XPF NER endonuclease assembles on active promoters in vivo and facilitates chromatin modifications for transcription during mammalian development. We find that Ercc1(-/-) mice demonstrate striking physiological, metabolic and ...[more]

PMID: 22323595

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E-IMBB-Mm-1

Project description:Transcription profiling of mouse livers in adult males and embryos with wild-type and TAF10 -/- hepatocytes.

2008-11-08 | E-MTAB-3 | biostudies-arrayexpress

Transcriptome profiling of NER progeroid animals treated with an NF-kB inhibitor.

Project description:NBD treatment of animals: Sibling pairs of Ercc1-/delta mice housed in a single cage were treated with 8K-NBD or 8K-mNBD 10 mg/kg three times per week intraperitoneally by an investigator blinded as to the treatment group. Treatment began at 5 weeks of age before the animals were symptomatic and continued throughout their lifespan. Mice were euthanized via CO2 inhalation at 12 or 18-20 weeks of age and tissues isolated. 8K-NBD (KKKKKKKKGGTALDWSWLQTE) and inactive 8K-mutant NBD (8K-mNBD) (KKKKKKKKGGTALDASALQTE) were synthesized at the University of Pittsburgh Peptide facility. Peptides were dissolved in DMSO at 40uM and stored at -80 C until dilution in PBS directly before use.

2012-07-01 | E-MEXP-3615 | biostudies-arrayexpress

High throughput RNA sequencing of hepatocellular carcinoma and pre tumor samples from Tdg fl/-; UBC-cre/ERT2+ mice livers and their age/sex matched Tdg fl/fl controls livers

Project description:We isolated whole livers from male TDG knockout livers (4-month post tamoxifen injection) and HCC, along with their age matched male control livers. RNA was extracted from the samples as per RNAzol manufacturer guidelines with DNase treatment. RNA was then analyzed by bioanalyzer and subjected to sequencing using the Illumina NextSeq 500 platform.

2020-03-06 | GSE146401 | GEO

TAF8 MUTATION CAUSES INTELLECUAL DISABILITY, TFIID DISASSEMBLY WITH NO EFFECT ON RNA POLYMERASE II TRANSCRIPTION

Project description:The human general transcription factor TFIID is composed of the TATA-binding protein (TBP) and 13 TBP-associated factors (TAFs). In eukaryotic cells, TFIID nucleates RNA Polymerase II (Pol II) preinitiation complex formation on gene promoters and thus, is crucial for Pol II transcription. Germline knock out of several mouse TFIID subunits (Tbp, Taf7, Taf8, and Taf10) results in lethality at embryonic day 4.0, demonstrating the fundamental role of holo-TFIID in transcription. We identified a child harboring a splice-site mutation in TAF8, who has intellectual disability, poor growth, progressive spasticity and microcephaly. The c.781-G>A TAF8 mutation in this patient resulted in a frame shift, which affected the final 50 carboxy terminal amino acids of TAF8. We found that the mutant TAF8 protein is unstable and the patient c.781-G>A TAF8 primary fibroblasts did not form canonical TFIID complexes. Astonishingly however, genome-wide RNA pol II occupancy and pre-mRNA transcription on the tested genes was unaffected in the patient’s primary fibroblasts. This study indicates that perturbed TFIID function is less deleterious for transcription in human cells than originally anticipated.

2018-04-16 | PXD008084 | Pride

The gene expression profiles of WT and NML-KO livers

Project description:To examine whether energy starvation caused by the increase in rRNA transcription affects liver metabolism, we compared the gene expression profiles of WT and NML-KO livers using Affymetrix microarray technology. We analyzed 5 livers of WT mice and 5 livers of NML-KO mice.

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SUPT3H-less SAGA coactivator can assemble and function without significantly perturbing RNA polymerase II transcription in mammalian cells

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Metabolic reprogramming in livers from LKB1 KO mice

Project description:Metabolic reprogramming in livers from LKB1 KO mice

| PRJNA791350 | ENA

The gene expression profiles of WT and NML-KO livers

2013-06-22 | GSE48191 | GEO

TAF10 interacts with the GATA1 transcription factor and controls mouse erythropoiesis

Project description:We have ablated TAF10 in the erythroid compartment only by crossing the TAF10lox mice with the EpoR-Cre mice and we have studied the development of the erythroid cells in vivo. TAF10 ablation led to embryonic death at E13.5 while at E12.5 there was a clear developmental defect which was reflected in the transcriptional profile of the fetal liver cells. Gata1-target genes were mostly affected and were responsible for the lethal phenotype. mRNA from E12.5 fetal livers of TAF10lox/KO:EpoR-Cre+/- (TAF10KO) mice, TAF10HET and WT mice was profiled by NGS (Illumina).

2015-04-21 | E-GEOD-68083 | biostudies-arrayexpress

Gene expression analysis of PiZ mouse livers

Project description:Transgenic PiZ mice have been genetically engineered to express ATZ and have been a valuable experimental model for studing liver disease associated with AAT deficiency. ATZ accumulates in these mice within the ER of hepatocytes in a nearly identical manner to livers of affected patients. To investigate the pathogenesis of liver damage induced by ATZ, we performed gene expression analysis in livers of 6-week-old PiZ mice and strain-, age-, and gender-matched wild-type mouse controls. All samples were processed on Affymetrix Mouse 430A 2.0 arrays using GeneChip 3’-IVT Plus and Hybridization Wash and Stain kits by means of Affymetrix’s standard protocols. The analysis indicated that most genes upregulated in PiZ livers were associated with response to unfolded proteins, ER nuclear signaling pathway, and response to protein stimulus.

2017-03-23 | GSE93115 | GEO

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