A67723a1-b956-40e8-bfbd-c56dab390005 - samples
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ABSTRACT:
PROVIDER: EGAD00001007813 | EGA |
REPOSITORIES: EGA
Similar Datasets
Project description:RNAseq was performed using 200 ng of total RNA by GATC Biotech. Directional libraries were performed after mRNA selection by polyA selection using UTP method. RNA-seq libraries were sequenced on HiSeq2500 Illumina machine using 100bp paired-end reads. Reads alignment was performed using the STAR aligner (version 2.4.0f1) and human genome hg19 as reference.
| EGAS00001004347 | EGA
Project description:Transcriptome profiling (RNA-Seq) to evaluate the connection the metabolic enzyme UGDH on gene expression. The RNA libraries were prepared and sequenced at University of Houston Seq-N-Edit Core per protocols. Total libraries were prepared with Ovation® Universal Plus mRNA-Seq (NuGen) using 200 ng input RNA. The size selection for libraries were performed using SPRIselect beads (Beckman Coulter) and purity of the libraries were analyzed using the High Sensitivity DNA chip on Bioanalyzer 2100 (Agilent). The prepared libraries pooled and sequenced using NextSeq 500 (Illumina), generating ~15 million 2×76 bp paired-end reads per samples. The RNA-seq raw fastq data were processed with RNA-Seq Express app within the Illumina BaseSpace app suite (www.basespace.illumina.com), which performed alignment with STAR aligner, assignment of aligned reads to genes, and differential gene expression with DESeq2 Analysis was performed comparing controls (shNT) against individual knockdowns (shU1 or shU2). Then, results from both analyses were compared for the intersection to identify commonly altered genes.
2018-08-21 | GSE118772 | GEO
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:Total RNA-seq was performed on HeLa cells to investigate transcriptomic changes associated with physiological protein condensates. rRNA was depleted using NEBNext rRNA Depletion Kit. Strand-specific libraries were prepared using QIAseq FastSelect and NEBNext Ultra II Directional RNA Library Prep Kit. Sequencing was performed on Illumina NovaSeq X Plus with 2x150 paired-end configuration. Reads were trimmed with Trimmomatic, mapped to human reference genome (ENSEMBL) using STAR, and gene counts generated with featureCounts.
2026-06-13 | E-MTAB-17121 | biostudies-arrayexpress
Project description:Evaluation of modulation of the innate immune response during H1N1 infection. The modulatory effect of Single-stranded oligonucleotides (ssON) on monocyte-derived dendritic cells (MoDCs) are evaluated. RNAseq data are used to study the effect on the transcriptome of MoDCs, during infection with simultaneous addition of ssON. Further mechanistic information are added via RNAseq data on poly I:C stimulated MoDCs (Toll-Like Receptor 3 agonist). Control samples are included to perform differential expression analysis. Provided are the fastq files, obtained in the following manner: The RNA sequencing was performed with the TruSeq RiboZero kit from Illumina, 25 M reads per sample and 2x125bp. Read quality were assessed using FastQC (Version 0.11.5) Trim Galore (Version 0.3.6) was used for adapter removal and quality trimming with a quality threshold of 20 on the Phred scale. Count files was created out of the trimmed fastq by mapping high-quality reads to Homo sapiens UCSC hg38 (GRCh38.77) reference genome using STAR aligner (version 2.5) with default values and the parameter out Reads Unmapped set to Fastx in order to extract the unmapped reads. After STAR alignment, the count data for the aligned reads were generated with HTSeq-count (version 0.6.1). The-m parameter was set to union.
2019-05-03 | E-MTAB-7803 | biostudies-arrayexpress
Project description:H3K9Ac enrichment in intestinal epithelial cells from the intestine of WT mice treated with vehicle or buytrate for 7 days. Intestinal epithelial cells were harvested from the terminal ileum of vehicle or butyrate treated mice. Chromatin immunoprecipitation was performed with anti-H3K9Ac. Sequencing was performed using the Illumina and reads were mapped to mm10 genome using STAR Aligner.
2024-03-06 | GSE249959 | GEO
Project description:The goal of this study is to perform RNAseq in different sub-types of the zebrafish embryonic dorsal aorta (DA) at 28-30 hpf using TgBAC(runx1P2:Citrine);Tg(kdrl:mCherry) double-transgenic zebrafish embryos. A min. of 3000 cells per population were collected via FACS. RNA was isolated with the RNeasy Plus Micro Kit (QIAGEN, Cat No. 74034). High quality RNA (RIN > 8.0) was sent for RNAseq to the Wellcome Trust Centre for Human Genetics (WTCHG). 2.2 ng of total RNA was used to generate SMARTer libraries for low-input RNA. Sequencing was performed on an Illumina HiSeq4000 machine with a 75 bp paired end protocol. Sequenced reads were checked for base qualities, trimmed where 20% of the bases were below quality score 20, and filtered to exclude adapters using Trimmomatic (Version 0.32). Sequences were aligned to the Zebrafish Genome Zv10 with STAR with default parameters. Aligned read features were counted using Subread tool: featureCounts method (version 1.4.5-p1). To determine number of mapped reads we used the trimmed data. The alignment has been performed using STAR with default parameters. The number of mapped reads (QC-passed reads count) has been obtain using Samtools mapping statistics (flagstat tool).
2019-06-06 | GSE132259 | GEO
Project description:LSEC fom WT and Bmp9-KO 25-weeks female mice were isolated using collagenase and treated for bulk RNAsequencing. The objective was to determine the biological processes that are altered in Bmp9-KO compared to WT, as BMP9 is know to be a vascular quiescence factor produced by hepatic stellate cells. RNAseq reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36 16. The trimmed reads were mapped to the Mus Musculus MM10 reference genome available on ENSEMBL using the STAR aligner v.2.5.2b 17. Unique gene hit counts were calculated by using ‘featureCounts’ from the Subread package v.1.5.2 WT samples are F126, F121, F120, F119, F135 KO samples are F131, F132, F124 and F133
2024-04-30 | E-MTAB-14012 | biostudies-arrayexpress
Project description:To investigate a potential role for RNF5 in AML, we monitored changes in gene expression profiles in multiple AML cell lines after RNF5 knock-down. PolyA RNA was isolated using the NEBNext Poly(A) mRNA Magnetic Isolation Module, and bar-coded libraries were constructed using the NEBNext Ultra™ Directional RNA Library Prep Kit for Illumina (NEB, Ipswich, MA). Libraries were pooled and single end-sequenced (1×75) on the Illumina NextSeq 500 using the High output V2 kit (Illumina, San Diego, CA). Quality control was performed using Fastqc (v0.11.5, Andrews S. 2010)), reads were trimmed for adapters, low quality 5′ bases, and minimum length of 20 using CUTADAPT (v1.1). The number of reads per sample and the number of aligned reads suggested that read quality and number were good and that the data were valid for analysis. High-quality data were then mapped to human reference genome (hg19) using STAR mapping algorithm (version 2.5.2a). FeatureCounts implemented in Subread (v1.50) was used to count the sequencing reads from mapped BAM files. Analyses of differentially expressed genes (DEGs) were subsequently performed using a negative binomial test method (edgeR) implemented using SARTools R Package. A list of the DEGs was observed and pathway analysis was performed using IPA (http://www.ingenuity.com) based on the following criteria: |log2(fold change)| >0.4 and p value < 0.05.
2021-07-25 | GSE155929 | GEO
Project description:To identify the molecular mechanisms of reduced pain response in Twik-1 knockout mice, we performed bulk RNA-sequencing on lumbar DRGs from WT and Twik-1 knockout mice. Thirty days after sciatic nerve injury, the ipsilateral L4-L6 DRGs were manually sectioned into ~150 µm slices using a razor blade. RNAs were extracted from the sliced DRGs using PicoPure™ RNA Isolation Kit. RNA libraries were constructed using the SMART-Seq v4 Ultra Low Input RNA Kit. High-quality libraries were pooled and sequenced on the Illumina NovaSeq 6000 platform with 150 bp paired-end reads. Image analysis was performed using the NovaSeq 6000 Control Software (v1.8.2), and base calling data were demultiplexed using bcl2fastq (v2.20.0.422), generating FASTQ files. Raw sequencing reads were aligned to the Mus musculus reference genome (GRCm39) using STAR aligner (version 2.7.11a). The genome index was built from the primary assembly FASTA file (Mus_musculus.GRCm39.dna.primary_assembly.fa.gz) and the corresponding gene annotation file (Mus_musculus.GRCm39.113.gtf.gz), ensuring accurate mapping across exon–intron boundaries. Resulting SAM/BAM files were then processed, sorted, and indexed with Samtools (version 1.18). Gene-level counts were generated using htseq-count (version 2.0.3) with the corresponding GTF annotation file.
2026-04-14 | GSE316192 | GEO