81780fc1-ce52-4e64-8658-0b2dc6b6049b - samples
Ontology highlight
ABSTRACT:
PROVIDER: EGAD00001009639 | EGA |
REPOSITORIES: EGA
Similar Datasets
Project description:we employed RNA-Seq to examine transcriptome profiles of male and female mouse gonads at 12.5dpc, 13.5dpc, 16.5dpc and 6dpp. Methods: Gonadal mRNA profiles of 12.5dpc,13.5dpc, 16.5dpc and 6dpp mice were generated by deep sequencing, in triplicate, using Illumina Hiseq 2500. The cDNA library was constructed with a SMARTer® Ultra Low Input RNA for lllumina® Sequencing kit (Clontech Laboratories) and sequenced on an Illumina HiSeq 2500.After sequencing, clean reads were obtained by removing reads containing the adaptor sequences, reads with > 5% ambiguous bases, and low-quality reads, then mapped to the mouse genome (version: mm10_GRCm38) using TopHat software. Gene expression level was calculated using the fragments per kilobase per million mapped reads method.
2019-10-29 | GSE117590 | GEO
Project description:Library preparation for ATAC-Seq was performed on 1000-5000 cells with Nextera DNA Sample Preparation kit (Illumina), according to previously reported protocol55. 4 ATAC-seq libraries were sequenced per lane in HiSeq 2500 System (Illumina) to generate paired-end 50-bp reads. Reads were mapped to hg38 using BWA (0.7.15) using default parameters. Duplicate reads, reads mapped to mitochondria, an ENCODE blacklisted region or an unspecified contig were removed (Encode Project Consortium, 2012). MACS (2.2.5) was used to call peaks in mapped reads.
2025-03-10 | GSE285437 | GEO
Project description:Total RNA, greater than 100ng, from cultured cells was isolated in TRIzol L and purified using Qiagen RNeasy Mini Kit per manufacturer’s protocols. Agilent Technologies 2100 Bioanalyzer was used to assess the RNA quality. RNA libraries were prepared and multiplexed using Illumina TruSeq RNA Library Preparation Kit v2 (non-stranded and poly-A selection) and 10 nM of cDNA was used as the input for high-throughput sequencing via Illumina’s HiSeq 2500 platform, producing 50 bp paired end reads.
2021-03-02 | GSE167959 | GEO
Project description:RNA was isolated from Vehicle/Entacapone(ENT) treated mouse inguinal White Adipose Tissue using the TRIzol (Invitrogen) reagent by following the company manual. mRNA was isolated by using Dynabeads mRNA Purification Kit (Invitrogen). For all samples the RNA integrity was checked using an Agilent Bioanalyzer 2100. Approximately 5 µg of mRNA was used for m6A-IP. The immunoprecipitated m6A modified mRNAs were then used for library preparation using a TruSeq™ RNA Sample Prep Kit v2 (Illumina, San Diego, CA, USA) according to the manufacturer’s protocol.The libraries were sequenced using HiSeq 2500(Illumina) in paired-read mode, creating reads with a length of 101 bp. Sequencing chemistry v2 (Illumina) was used.
2020-11-16 | GSE106996 | GEO
Project description:Purpose: The aim of this study is to determine the absolute and relative expresson levels of mRNA transcripts across two purbred (Angus and Brahman) cattle and their receipicalcross. Methods: Total RNA was extracted and purified from five tissues using the RiboZero Gold kit. Sequencing libraries were prepared with a KAPA Stranded RNA-Seq Library Preparation Kit following the Illumina paired-end library preparation protocol. Completed libraries were sequenced on HiSeq 2000 as 100 bp paired-end reads at the Australian Cancer Research Foundation (ACRF) Cancer Genomics Facility, Adelaide, Australia and USDA-ARS-US Meat Animal Research Center, Clay Center, USA. Approximately 60 million 100 bp single-end reads were obtained for each sample. Reads were aligned to the cattle reference genome UOA_brahman_1/UOA_angus_1 and mapped to known genomic features at the gene level using the Hisat2. Single reads were then summarized into gene-level counts using FeatureCounts.
2021-06-09 | GSE148909 | GEO
Project description:To understand the genetic regulation of gene expression and patterns of gene co-expression, we sequenced the transcriptome of the hippocampus of founder mice of both sexes. Mice were sacrificed between 6-8 weeks of age and hippocampus dissected. Total hippocampal RNA was isolated using a TRIzol Plus RNA purification kit (Life Technologies) and mRNA sequencing library was prepared using a TruSeq kit (Illumina), both according to manufacturer's protocols. Paired-end 100bp reads were obtained using the Illumina HiSeq 2000.
2025-09-30 | GSE278035 | GEO
Project description:The DIO mouse were treated with Vehicle/Entacapone for 3 weeks. Total RNA was isolated from White Adipose Tissue using the TRIzol (Invitrogen) reagent by following the company manual. For all samples the RNA integrity was checked using an Agilent Bioanalyzer 2100. Approximately 2.5 µg of total RNA was then used for library preparation using a TruSeq™ RNA Sample Prep Kit v2 (Illumina, San Diego, CA, USA) according to the manufacturer’s protocol.The libraries were sequenced using HiSeq 2500 (Illumina) in paired-read mode, creating reads with a length of 101 bp. Sequencing chemistry v2 (Illumina) was used.
2020-11-16 | GSE106995 | GEO
Project description:The goal of this study was to find the differentially expressed circRNAs/linear RNA in AKI mice model compared to normal mice. We established cisplatin-induced AKI mice models and then extracted RNAs from isolated renal tubular tissues for Next Generation Sequencing(NGS) at different time points during early stage of AKI. CircRNA library was constructed by NEB Next®Ultra™ small RNA Sample Library Prep Kit for Illumina®. NGS was performed by using Illumina HiSeq 2500 Genome Sequencers.The original image data file was transformed into Raw Data by Base Calling. Clean Data was obtained by removing reads that containing joints and more than 5% N (undetermined base information). Mapped Reads were obtained by sequence alignment between Clean Reads and reference genome sequenced using BWA software package. CIRI software was used to predict circRNAs. Finally, we identified 2162 circRNAs and our study represents the first detailed analysis of AKI mice circRNA transcriptomes, which provide a framework for investigations of circRNAs expression profiles in AKI
2020-02-01 | GSE130814 | GEO
Project description:CD3+ T cells were isolated by FACS from primary tumour tissues of two triple-negative breast cancer patients. Sorted cells were submitted to a 10X Genomics Chromium System for single cell capture. cDNA synthesis and library preparation were done according to the protocol supplied by the manufacturer. Libraries were sequenced on an Illumina HiSeq 2500 High Output Mode using V4 clustering and sequencing chemistry to achieve 100 bp paired-end reads.
2018-06-24 | GSE110686 | GEO
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