8f45984e-eaaa-441b-b595-8e0fd0c75d9a - samples
Ontology highlight
ABSTRACT:
PROVIDER: EGAD00001009047 | EGA |
REPOSITORIES: EGA
Similar Datasets
Project description:RNAseq was done on Breast cancer PDX samples uisng Library protocol =llumina TruSeq Stranded Total RNA Kit with Ribo-Zero Gold , HiSeq 125 Cycle Paired-End Sequencing v4
2018-05-24 | GSE113476 | GEO
Project description:RNAseq was done on Breast cancer PDX samples uisng Library protocol =llumina TruSeq Stranded Total RNA Kit with Ribo-Zero Gold , HiSeq 50 Cycle Single-Read Sequencing v4
2019-03-01 | GSE113986 | GEO
Project description:Male C3H/HeOuJ mice are susceptible to spontaneous liver neoplasms. We collected liver samples from young, tumour-free mice for control experiments. Liver tissue samples were snap frozen in liquid nitrogen and total RNA was extracted using the AllPrep 96 DNA/RNA Kit (Qiagen) according to the manufacturer’s instructions. Libraries were prepared using the TruSeq Stranded Total RNA Library Prep Kit with Ribo-Zero Gold (Illumina) and sequenced in an Illumna HiSeq4000 to produce 150bp paired-end reads.
2018-07-29 | E-MTAB-6972 | biostudies-arrayexpress
Project description:Male C3H/HeOuJ and CAST/EiJ mice were treated with diethylnitrosamine to induce liver tumours. We collected liver samples from untreated P15 mice for control experiments. Liver tissue samples were snap frozen in liquid nitrogen and total RNA was extracted using the AllPrep 96 DNA/RNA Kit (Qiagen) according to the manufacturer’s instructions. Libraries were prepared using the TruSeq Stranded Total RNA Library Prep Kit with Ribo-Zero Gold (Illumina) and sequenced on an Illumna HiSeq4000 to produce 150bp paired-end reads.
2020-06-18 | E-MTAB-8518 | biostudies-arrayexpress
Project description:CTCF is a highly conserved and ubiquitously expressed protein involved in several fundamental processes such as fine-tuning gene expression, imprinting, X-chromosome inactivation and 3D chromatin organisation. To understand the impact of differences in the concentration of CTCF abundance on these processes, we exploit a CTCF hemizygous mouse model with a stable reduction in the concentration of this protein. We derived twelve independent primary lines of mouse embryonic fibroblasts (MEFs) from six wildtype and six CTCF-hemizygous mouse E13.5 embryos. Total RNA from each MEF line was purified using QIAzol Lysis Reagent (Qiagen); DNase treatment and removal was performed using the TURBO DNA-freeTM Kit (Ambion, Life Technologies). Libraries were prepared using the TruSeq Stranded Total RNA Library Prep Kit with Ribo-Zero Gold (Illumina) and sequenced in an Illumna HiSeq4000 to produce 150bp paired-end reads. On the same MEF lines we have performed ChIPseq for CTCF, H3K4me3 and H3K27ac and HiC.
2018-07-29 | E-MTAB-6259 | biostudies-arrayexpress
Project description:Male C3H/HeOuJ mice are susceptible to spontaneous liver neoplasms. We aged a cohort of mice for up to 76 weeks and isolated liver tumours. Tumours were bisected: one half was snap frozen in liquid nitrogen for RNA extraction and the other half of the tumour was processed for histological examination. Total RNA was extracted using the AllPrep 96 DNA/RNA Kit (Qiagen) according to the manufacturer’s instructions. Libraries were prepared using the TruSeq Stranded Total RNA Library Prep Kit with Ribo-Zero Gold (Illumina) and sequenced in an Illumina HiSeq4000 to produce 50bp paired-end reads.
2018-07-29 | E-MTAB-6971 | biostudies-arrayexpress
Project description:Purpose: transcriptome analysis of CPSF5 dependent starvation response Methods: Total RNA was extracted from larval fat body using TRIzol® reagent (Invitrogen). After assessing RNA quality with an Agilent Bioanalyzer, libraries constructed with an Illumina TruSeq Stranded Total RNA Library Prep Kit with Ribo-Zero Gold were sequenced using an Illumina HiSeq 4000 at the Columbia Genome Center (http://systemsbiology.columbia.edu/genome-center). Results: Using an optimized data analysis workflow, we identified 1933 genes responding to starvation and 585 genes were found to be CPSF5-dependent. The gene set enrichment analyses and qPCR confirmation further suggested autophagy, changes of lipid, protein and energy metabolism is requlated by CPSF5 during starvation. Conclusions: our study identified the regulatory role of CPSF5 in autophagy and metabolisms during starvation.
2017-06-01 | GSE99509 | GEO
Project description:Purpose: Using a C57BL6/J mouse model of diet-induced obesity, we observed that mannose supplementation of high fat diet-fed mice prevents weight gain, lowers adiposity, reduces liver steatosis, and improves glucose tolerance and insulin sensitivity. Mannose increases Bacteroidetes to Firmicutes ratio of the gut microbiota, a signature previously associated with the lean phenotype. These beneficial effects of mannose are observed when supplementation is started early (3 weeks post weaning) but are lost when started later in life (8 weeks post weaning). We profiled transcriptomes of gut microbiota from high fat diet mice supplemented with or without mannose to understand the functional differences of supplementation at 3 weeks post weaning and 8 weeks post weaning. Method: Mice were weaned on high fat diet (HFD) or high fat diet with 2% mannose in drinking water (HFDM). RNA from each mouse for each diet group was isolated individually using Ambion RiboPure Bacteria kit (ThermoFisher Scientific). 1 mg cecal RNA each from 8 mice/diet group was pooled to generate 1 pool/diet for library preparation. The quality of total RNA was assessed by the Agilent Bioanalyzer Nano chip (Agilent Technologies). Total RNA was Ribo-depleted using Ribo-Zero Gold rRNA kit (Epidemiology) (Illumina). RNA-Seq library was constructed from the recovered non-ribosomal RNAs using Truseq Stranded total RNA library preparation kit (Illumina) as per the instructions. Multiplexed libraries were pooled and single-end 50-bp sequencing was performed using an Illumina Hiseq 1500. Results: The comparison of transcriptome profiles of mice supplemented with mannose at 3 weeks post weaning and 8 weeks post weaning shows mannose reduced transcript abundance for glycosyl hydrolases and carbohydrate metabolism when supplied at 3 weeks post weaning. Conclusion: The beneficial effects of mannose in responsive mice (3 weeks post weaning) are at least in part due to reduced energy harvest by gut microbes.
2018-11-06 | GSE110794 | GEO
Project description:Purpose: We report the coding and non-coding transcriptomic changes in primary cutaneous squamous cell carcinoma Methods: 4 mm punch biopsies were collected from 7 unmatched healthy and 9 cSCC patients and snap frozen. The library preparation was done using Illumina TruSeq® Stranded Total RNA (with Ribo-Zero Gold) preparation kit. 100 ng of total RNA was depleted of rRNAs using ribo-zero gold magnetic bead based capture-probe system (Illumina Inc.). The remaining RNA was subsequently purified (RNAcleanXP, Beckman Coulter) and fragmented using enzymatic fragmentation. Then first strand synthesis and second strand synthesis were performed and the double stranded cDNA was purified (AMPure XP, Beckman Coulter). The cDNA was end repaired, 3’ adenylated and Illumina sequencing adaptors ligated onto the fragments ends, and the library was purified (AMPure XP). The stranded libraries were amplified with PCR and purified (AMPure XP). The libraries size distribution was validated and quality inspected on a Bioanalyzer. Sequencing was performed on NextSeq 500 instrument using v2 reagent kits according to the manufacturer instructions (Illumina Inc.). Results: On average 49.8 million 100 base pair (bp) paired-end reads were obtained from each sample and genome mapping was on average 55% for all samples. Altered expression of 5,352 protein-coding genes, 908 lncRNAs and 55 circular RNAs was identified. Conclusions: Here, we report the coding and non-coding transcriptomic changes from cSCC samples, along with identification of skin specific transcripts and novel deregulated circRNAs.
2020-03-09 | GSE139505 | GEO
Project description:C2H2 zinc finger proteins represent the largest and most enigmatic class of human transcription factors. Their C2H2 arrays are highly variable, indicating that most will have unique DNA binding motifs. However, most of the binding motifs have not been directly determined. We have determined the binding sites and motifs of 119 C2H2 zinc finger proteins and the expression pattern of 80 cell lines overexpressing C2H2 zinc finger proteins in order to study the role of C2H2 zinc finger proteins in gene regulation. We expressed GFP-tagged C2H2-ZF proteins in stable transgenic HEK293 cells. Total RNA was isolated using Trizol and sequencing libraries were constructed using TruSeq Stranded Total RNA Library Prep Kit with Ribo-Zero Gold or TruSeq RNA Library Preparation Kit v2.
2016-10-25 | E-GEOD-76495 | biostudies-arrayexpress