Expression data from endpoint mammary gland tumours from Ezh2 +/+ or Ezh2 -/- Tet ON PyVmT mice
Ontology highlight
ABSTRACT:
ORGANISM(S): Mus musculus
PROVIDER: GSE108861 | GEO | 2018/02/26
REPOSITORIES: GEO
Similar Datasets
Project description:We report the application of single-molecule-based sequencing technology for high-throughput profiling of histone modifications in endpoint tumours from Ezh2+/+ or Ezh2-/- Tet ON PyVmT mammary gland tumours. In order to understand the H3K27me3 targets in the context of mouse mamamry gland tumorigenesis, data were generated by deep sequencing a pool of 5 tumours per genoype, in duplicate using Illumina HiSeq2500. Using an optimized data analysis workflow, we mapped about 30 million sequence reads per sample to the mouse genome (build mm10). Raw reads were trimmed for length (n>=32), quality (phred score >= 30) and adaptor sequence using fastx v0.0.13.1.Trimmed reads were (pools of 5 different tumors per genotype) then aligned to the mouse reference genome mm10 using BWA v0.5.9 Broad peaks were called using MACS v1.4.1 software (mfold=10,30; bandwith=300; pvalue cutoff=1E-5) using sequenced libraries of input DNA as control. Peak list intersections were done using BEDTools v2.12.0. Binding peaks were considered overlapping if at least 1 base of the peaks overlapped. Our study demonstrated the first mapping of H3K27me3 in the endpint tumours of tetracycline ducible PyVmT mouse mamary tumours.
2018-03-01 | GSE108899 | GEO
Project description:Expression data from endpoint mammary gland tumours from Ezh2 +/+ or Ezh2 -/- Tet ON PyVmT mice
| PRJNA428969 | ENA
Project description:Genome-wide maps of H3K27me3 in endpoint Ezh2+/+ or Ezh2-/- Tet ON PyVmT mouse mammary gland tumours
| PRJNA429046 | ENA
Project description:This study set out to globally compare the liver transcriptomes from 24-week old wild type (WT) and FBP1-deficient mice. Total RNA was isolated from 10 snap frozen liver tissue samples using RNeasy Mini Kit (Qiagen). 250~300 bp insert eukaryotic mRNA derived cDNA non-directional libraryRNA libraries were prepared using standard Illumina protocols. The sequencing were performed on Illumina Platform PE150, with 20M raw reads/sample.
2019-08-10 | GSE135616 | GEO
Project description:This series represents a group of five samples (from sigmoid colon biopsies of clinically normal Patients A-E) profiled by a publicly available cDNA-based platform (GPL284) and a commercial oligonucleotide-based platform (GPL91). Sample RNA extraction: Biopsies taken during endoscopic analysis were immediately snap-frozen in liquid nitrogen and at no time prior to or during subsequent sample manipulation were the samples allowed to thaw. Standard laboratory procedures to eliminate the presence of RNases, including the use of RNase free plastic-ware, heat baked glassware, molecular biology grade chemicals and DEPC-treated solutions, were adopted. Frozen biopsies were crushed to a fine powder under liquid nitrogen using a manual crusher with a teflon head (Omnilab) and total RNA was isolated using the RNeasy Mini Kit (Qiagen) according to the manufacturers protocol, with minor modifications that improved RNA yields and purity in our hands. In brief, crushed biopsy samples were lysed in an appropriate volume of Buffer RLT (typically 600 µL/20 mg tissue). To facilitate complete lysis, samples were allowed to stand at room temperature for 5-10 min before vortexing. The lysate was homogenized by addition to a QIA shredder column (Qiagen) and centrifuged at 14,000 rpm for 2 min. The resulting supernatant was centrifuged at 14,000 rpm for 3 min to pellet any cell debris. One volume of 70% ethanol was added to the cleared lysate, added to the RNeasy column and centrifuged at 10,000 rpm for 15 sec. Bound RNA was washed with the addition of RW1 buffer to the column and allowed to stand at room temperature for 10 min followed by centrifugation at 10,000 rpm for 15 sec. DNase 1 incubation mix (Stock: 273 kunits; RNase-free DNase Set, Qiagen) was added directly to the spin column membrane and digestion of any contaminating genomic DNA was carried out at room temperature for 30 min. The column was washed with RWI buffer and the DNase treatment step was repeated. The bound RNA was washed with RW1 buffer and centrifuged at 10,000 rpm for 15 sec three times, followed by two additional wash and centrifugation steps with RPE buffer. Finally, purified RNA was eluted off the column with RNase-free water. RNA concentration and purity was determined spectrophotometrically at A260/A280 and was determined to be intact as assessed by formaldehyde gel electrophoresis. The presence of genomic DNA contamination was assessed by PCR amplification of GAPDH using standard PCR conditions and the following primers: GAPDH_F2-5’- ACCCACTCCTCCACCTTTGAC-3’, GAPDH_R2- 5’-CTGTTGCTGTAGCCAAATTCGT-3’. RNA was re-treated with DNase if necessary. Upon confirming the quality of the RNA (intact and free of genomic DNA), 15 µg of total RNA from each of the five biological replicates was used for expression screening on either the Affymetrix or the clone-based filter platform. Keywords: parallel sample
2003-12-14 | GSE405 | GEO
Project description:Ampicillin treatment casues dysbiosis that persists until study endpoint [RNA-seq]
| PRJNA575802 | ENA
Project description:Enhancer of zeste homolog 2 (EZH2) is a core component of polycomb repressive complex 2 that plays a vital role in transcriptional repression of gene expression. Conditional ablation of EZH2 using progesterone receptor (Pgr)-Cre in the mouse uterus has uncovered its roles in regulating uterine epithelial cell growth and stratification, suppressing decidual myofibroblast activation, and maintaining normal female fertility. However, it is unclear whether EZH2 plays a role in the development of uterine glands, which are required for pregnancy success. Herein, we created mice with conditional deletion of Ezh2 using anti-Mullerian hormone receptor type 2 (Amhr2)-Cre recombinase that is expressed in mesenchyme-derived cells of the female reproductive tract. Strikingly, these mice showed marked defects in uterine adenogenesis. Unlike Ezh2 Pgr-Cre conditional knockout mice, deletion of Ezh2 using Amhr2-Cre did not lead to the differentiation of basal-like cells in the uterus. The deficient uterine adenogenesis was accompanied by impaired uterine function and pregnancy loss. Transcriptomic profiling using next generation sequencing revealed dysregulation of genes associated with signaling pathways that play fundamental roles in development and disease. In summary, this study has identified an unrecognized role of EZH2 in uterine gland development, a postnatal event critical for pregnancy success and female fertility.
| S-EPMC9779349 | biostudies-literature
Project description:Purpose: The goal of this study is to identify differentially expressed genes (DEGs) in immature ears between Barren inflorescence3 (Bif3) mutant and its wild-type siblings in maize. Methods: the 3-4 mm ear primordia of maize wild-type and Bif3 mutant were dissected from maize plant at the reproductive stage, and samples were snap freeze using liquid nitrogen. The total RNAs were prepared using RNeasy mini kit (Qiagen). All those RNA samples of wild-type and Bif3 mutant were submitted for RNA-Seq. Conclusions: Our RNA-seq experiments identified 1380 up- and 242 down-regulated genes (P < 0.05, FDR < 0.1, fold-change > 1.5).
2021-03-17 | GSE158330 | GEO
Project description:We demonstrate that the catalytic subunit of Polycomb Repressive Complex 2, EZH2, is targeted by the MELK-FOXM1 complex, which in turn promotes resistance to radiation in GSCs. Clinically, EZH2 and MELK are co-expressed in GBM and significantly induced in post-irradiation recurrent tumors whose expression inversely correlated with patient prognosis. Through gain-and loss-of-function study, our data show that MELK or FOXM1 contributes on GSC radioresistance by regulation of EZH2. We used microarrays to validate EZH2 target gene expression. GSCs were treated with shNT (control), shMELK, shFOXM1, and EZH2 overexpression. Total RNA was isolated using the Qiagen RNeasy kit (Qiagen).
2015-04-16 | E-GEOD-63963 | biostudies-arrayexpress
Project description:<p>We have deeply sequenced total RNA and whole exome of six different post-mortem human snap-frozen tissues (brain, liver, lung, striated muscle, kidney, heart) from three unrelated healthy Caucasian individuals (males, aged 47-54) with the aim to characterize post-transcriptional events due to alternative splicing and RNA editing. In addition, to facilitate the detection of RNA editing sites we have also resequenced the entire genome of each individual. Data are also used to investigate tissue-specific abundance of mitochondrial DNA from exomes and its correlation with mitochondrial transcription, mass and respiratory activity.</p> <p>Tissues were obtained from Cureline (South San Francisco, CA, USA). DNA and RNA were purified using the DNeasy Blood and Tissue Kit (Qiagen, Hilden, Germany) and the RNeasy Plus Mini Kit (Qiagen, Hilden, Germany), respectively.</p> <p>Exome capture was performed using the TruSeq Exome Enrichment Kit (Illumina, San Diego, CA) and the sequencing was carried out at IGA Technology Services in Udine (Italy) on Illumina HiSeq 2000 (generating for each tissue approximately 40 millions of 100bp paired-end reads). </p> <p>Strand-oriented RNA reads (2x100bp) were generated using the TruSeq Stranded Total RNA Sample Prep Kit (Illumina, San Diego, CA, USA) and sequenced at IGA Technology Services in Udine (Italy) on Illumina HiSeq 2000 platform.</p> <p>Whole genome resequencing was performed at Personal Genomics in Italy on an Illumina HiSeq 2000 platform (2x100bp) with a mean coverage of 30X.</p> <p>MiRNA-Seq was instead performed at IBBE Institute (Italy) using the TruSeq Small RNA Sample Prep Kit on Illumina MiSeq platform.</p> <p>Preliminary bioinformatics analyses have been performed to check quality using FASTQC software and inconsistent read regions have been trimmed using trim_galore. All reads were mapped onto the human reference genome (version hg19) using GSNAP.</p>
| phs000870 | dbGaP