Ena-DATASET-UOC-08-05-2018-17:41:43:993-1591 - samples
Ontology highlight
ABSTRACT:
PROVIDER: EGAD00001004111 | EGA |
REPOSITORIES: EGA
Similar Datasets
Project description:Sheep total RNA was extracted from embryonic and adult tissues. Sequencing libraries were prepared from the RNA using the Illumina TruSeq stranded total RNA with the Ribo Zero gold option for the rRNA removal. The fragmentation in the standard protocol was modified to increase the average insert size in the library. Sequencing with 151 base paired end reads was performed on an Illumina HiSeq 2500 in rapid mode.
2014-12-04 | E-MTAB-3838 | biostudies-arrayexpress
Project description:E15.5 embryos were micro-disscted from Gata4 G295S mutant mice and littermate controls, RNA was isolated using Norgen total RNA isolation, and libraries were generated with the RNA TruSeq Stranded Total RNA kit. 50 base pair paired end reads were obtained on an illumina high seq 2500. Fastq files were aligned to the mouse genome using STAR aligner. QC was performed using RNASeQC and RSeQC. BAM files were processed using cufflinks pipeline.
2019-05-17 | GSE117621 | GEO
Project description:To assess expression of mtDNA genes in the canine transmissible venereal tumour (CTVT), biopsy tissue samples from 33 CTVT cases were subjected to total RNA extraction, and stranded RNA sequencing libraries generated with the Ribo-Zero ribosomal RNA removal kit (insert size 100–300 bp) were sequenced using 75-bp paired-end sequencing reads on an Illumina HiSeq4000 instrument. Gene transcript abundance was quantified using the Salmon software (v0.8.2).
2020-04-29 | E-MTAB-9037 | biostudies-arrayexpress
Project description:DNA mate pair and RNA sequencing data of conventional osteosarcomas. Mate pair libraries, with average insert sizes of 2-4 kb, were prepared for sequencing using the Nextera Mate Pair Library Preparation Kit. Paired-end 76 base pair reads were generated using an Illumina NextSeq 500 sequencing instrument. Total RNA was enriched for polyadenylated RNA using magnetic oligo(dT) beads. Enriched RNA was prepared for sequencing using the TruSeq RNA Sample Preparation Kit v2 and paired-end 151 base pair reads were generated from the cDNA libraries using an Illumina NextSeq 500 instrument.
| EGAS00001003842 | EGA
Project description:mRNAs of siCTRL, siNSUN2 and ALYREF-RIP HeLa cells, and multiple mouse tissues were purified using oligo (dT)-conjugated magnetic beads followed by RiboMinus treatement. mRNAs were fragmented to ~200 nt and treated by Sodium bisulfite solution (pH 5.1) containing Hydroquinone. Bisulfite treated mRNAs were reverse transcribed to cDNA using ACT random hexamer primers. The cDNAs were subjected to libraries construction using KAPA Stranded mRNA-Seq Kit (KAPA) and performed sequencing on HiSeq2500 (Illumina) in pair-end mode, creating reads with a length of 125 bp. Sequencing chemistry v4 (Illumina) was used and every sample was sequenced at one lane.
2017-04-19 | GSE93749 | GEO
Project description:RNA-Seq analysis of mouse cardiac transcriptome. RNA was isolated from the ventricles of 12-weeks-old male mice. Sequencing libraries were prepared using TrueSeq Stranded RNA LT Kit Ribo-Zero Gold (Illumina, 15032619). Libraries were pair-end sequenced on a MiSeq sequencer (Illumina) and mapped to the Mus musculus reference genome GRCm38 (https://support.illumina.com/sequencing/sequencing_software/igenome.html) using TopHat2 (Kim et al., 2013). Differential gene-expression analysis between controls and the EphB4 flox mice was performed using DESeq2 (Love et al., 2014). Read counts were obtained with HTSeq (Anders et al., 2015). Genes were considered as differentially expressed when the FDR-adjusted p-value was Ôëñ0.05.
2020-01-15 | E-MTAB-7686 | biostudies-arrayexpress
Project description:RNA-sequencing analysis from whole heart ribosome depleted RNA from the 2-week old WT and Lmna-/- mice (N=5) . Strand specific RNA seq libraries where prepared form ribosome-depleted cardiac RNA samples using the Illumina TruSeq stranded total RNA library preparation kit. The samples weresequenced on the Illumina HiSeq 4000 instrument using the paired-end sequencing reagents to generate100 base paired end reads.
2019-02-08 | GSE110341 | GEO
Project description:The goal of RNA-seq is to explore whether olfactory sensory neurons (OSNs) that display a specific olfactory receptor (OR) express a distinct transcriptional program from OSNs that display a different OR. The GFP knockin mice (Olfr73-IRES-GFP, Olfr1507-IRES-GFP, and Olfr160-IRES-mCherry) was used to label the OSN expressing specific OR. These cells was then isolate with fluorescence activated cell sorting. For each sample, at least 5000 cells are collected, there biological replicates were collected for each genotype and in total 9 samples were prepared for RNA-seq libraries with using NEBNext® Single Cell/Low Input RNA Library Prep Kit for Illumina® (NEB) following the manufacturer’s guidelines with one alteration, which was to increase the insert length to ~300 base pair. Libraries were sequenced using paired end 150 cycle reads on an Illumina Hiseq4000 (Novogene). The sequencing reads were processed using the DolphinNext RNAseq pipeline (https://dolphinnext.umassmed.edu/index.php?np=1&id=732). The default settings were employed except STAR v2.6.1 and RSEM v1.3.1 were used for alignment and quantification, respectively. Differential analysis were conducted in DESeq2. The significant genes were deducted by computing Wald test with corrected p < 0.05. Our results shows that different types of OSNs express significantly different patterns of genes, especially the genes involved in axonal guidance.
2022-01-31 | GSE169010 | GEO
Project description:Abstract: As part of the zebrafish genome annotation project the 3 prime ends of genes were pulled down on polyT beads and sequenced on the Illumina Genome Analyzer to identify alternative 3 prime ends in a range of tissues and developmental stages. <br> Study description: Total RNA from a range of developmental stages and adult tissues were chemically fragmented, pulled down on polyT magnetic beads and double stranded cDNA was synthesized. The cDNA was BpmI digested to release from the beads and to leave a 6 T base tail. Illumina sequencing libraries were made followed by 76 base paired-end sequencing.
2011-07-01 | E-MTAB-308 | biostudies-arrayexpress
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