Ena-DATASET-CRCL-23-12-2016-14:08:28:414-551 - samples
Ontology highlight
ABSTRACT:
PROVIDER: EGAD00001003121 | EGA |
REPOSITORIES: EGA
Similar Datasets
Project description:Purpose: Identification of genes regulated by NasT during denitrifying growth in B. diazoefficiens. Methods: Two biological replications were processed for each strain (wild-type USDA 110 and ΔnasT mutant). Sequencing was performed in an Illumina HiSeq 2000 Sequencing System in paired-end mode running 100x2 cycles (performed by Hokkaido System Science Co., Ltd.). Mapping of reads to the reference genome, read counting, normalization to RPKM (reads per kilobase per million mapped reads), and calculations of expression values were performed with default values with the CLC Genomic Workbench software 9.5.3. From the total reads that were generated, ~85% were trimmed, and from those, ~42% could be mapped onto the B. diazoefficiens genome. Genes with fewer than 10 reads per 1 million mRNA reads were omitted from the following analysis. A gene with a fold change ≥2 or ≤‒2 and a q value (estimate of false discovery rate) ≤0.05 was considered up- or down- regulated, respectively. The results were validated by qRT–PCR. Conclusion: A total of 77 genes were differentially expressed in the ∆nasT mutant compared to those of the wild-type strain, with 38 genes decreased and 37 genes increased in the ∆nasT mutant. Most of these genes were related to nitrogen metabolism.
2019-04-26 | GSE130301 | GEO
Project description:Undamaged utricular sensory epithelia from P2, P4, and P6 mice were isolated using FACS and underwent Smartseq-2 protocol for single cell RNA seq. Data was generated using Illumina NextSeq 500, paired end, 75-150bp reads with median depth of ~0.5 million reads per cell.
2020-12-27 | GSE155966 | GEO
Project description:we analyzed globally the effect of exosome processing on the nuclear pre-mRNA transcripts by inactivating either the RRP41 or DIS3 subunit of the exosome. Using SOLiD RNA sequencing technology, we report 30-120 million mapped cellular compartment specific reads per sample allowing the detection of unspliced pre-mRNAs. We show that RRP41 and DIS3 knockdowns stabilize an overlapping set of U12-type introns.
2014-05-26 | GSE52539 | GEO
Project description:To understand the role of Cklf1 in the proliferation of vascular smooth muscle cells (VSMC), we quantified the whole genome transcriptomes of VSMC that were treated by Cklf1 adenovirus (n=3) or control (n=3) for 24 h using RNA-seq. In total, we obtained over 82 million clean reads from each library after trimming adaptor sequences, low quality reads and multiple mapped reads. The clean reads were mapped to 29330 genes annotated in the rat reference genome (Rattus_norvegicus 6.0). We then identified differentially expressed genes (DEGs) between Cklf1-associated adenovirus and controls by comparing RNA-Seq data between the two groups. A total of 238 DEGs for Ad-GFP vs. Ad-Cklf1 and 468 DEGs for shRNA Scramble vs. shRNA Cklf1 were defined using the thresholds of FDR ≤ 0.05, difference ratio of FPKM (fragments per kilobase of exon model per million mapped fragments) ≥ 2 and diverge probability ≥ 0.8. The increased CKLF1 resulted in 34 up-regulated and 204 down-regulated genes while knockdown of Cklf1 led to 358 up-regulated and 110 down-regulated genes.
2021-03-05 | GSE111398 | GEO
Project description:RNA was isolated from livers of DIO mice treated with IXA4 or vehicle (n=4 per condition) using the Zymo Research Quick-RNA Miniprep Kit according to the manufacturer’s instructions. RNA sequencing was performed by BGI Americas on the BGI proprietary platform (DNBseq), providing single-end 50 bp reads at 20 million reads per sample. Alignment of the sequencing data to the Mus musculus MGSCv37 NCBI build 37.2 was performed using DNAstar Lasergene SeqManPro. Assembled data were then imported into ArrayStar 12.2 with QSeq (DNAStar Inc) to quantify gene expression and normalized reads per kilobase million (RPKM). Differential expression analysis and statistical significance calculations between conditions were assessed using DESeq in R using a standard negative binomial fit for the aligned counts data and are described relative to the indicated control
2022-01-08 | GSE162567 | GEO
Project description:Purpose: Analysing gene expression changes along mose spermatogenesis Method:The novel method of the isolation of 6 populations of cells at sequantial developmental stages -from undifferentiated spermatogonia (Undiff.Spg), differentiating spermatogonia (Diff.Spg), preleptotene (PreL), leptotene/zygotene (LZ), pachytene/diplotene (PD) and round spermatids (RS) was developed. Results: Median sequencing depth was ~18 million reads per sample. Sequencing depth was homogenous across samples in the experiment. We found a profound shift in gene expression between LZ and PD populations.
2022-05-31 | GSE162740 | GEO
Project description:The goal of this study was to investigate molecular pathways associated with PDE10A in ovarian cancer. We used CRISPR/Cas9 to knockout PDE10A in SKOV3 cells. We used the Illumina NextSeq500 to generate between 30-35 million paired end 75bp sequencing reads per sample for transcript level abundance.
2022-01-10 | GSE164474 | GEO
Project description:We present a high-resolution network of gene expression during meiosis and its regulatory control elements in polyploid wheat. MeioCapture method (Shunmugam et al. 2018 BMC Plant Biology 18: 293) was used for isolating high-purity sporogenous archesporial columns of synchronized male meiocytes from wheat anthers in different meiotic stages. Total RNA extracted from three independent biological replicates per developmental stage of the meiocytes, as well as vegetative flag leaf, young leaves, and reproductive anthers and pollen, was sequenced using Illumina platform, generating 548 million paired-end short mRNA reads. Filtered reads were aligned to the wheat reference genome (IWGSC v1.0) using STAR. Transcript abundance was estimated using the RSEM (v1.3.3) and the IWGSC v1.1 annotation, and read counts and transcripts per million (TPM) values that normalize counts to a consistent number per library (1 million) to facilitate the comparison of relative expression across various samples were generated.
2023-01-31 | GSE182171 | GEO
Project description:To study cell type- and HTT CAG length-dependent transcriptional and alternative splicing changes associated with HD, we conducted deep RNA-sequencing analysis on human embryonic stem cells (hESC), NPC and neuron cell lines (ESC and NPC, NEU) expressing wild-type (27/ and 30 CAG repeats), 45 CAG (45Q; representing 45 polyQ mutant HTT protein) and 81 CAG (81Q) repeat expansion HTT gene (n=3). The cell lines were derived from an isogenic HTT CAG repeat expansion allelic cell line panel (IsoHD) where hESC H9 cells were genetically modified with monoallelic knockin of expanded CAG tract in exon 1 of HTT representing early onset (45Q) and late onset (81Q) HD, with the 27Q/30Q genotype as healthy control phenotype (Ooi et al., 2019). The sequencing experiment generated 2.9 billion pairs of 150 bp paired-end reads from 27 samples (3 clones, 3 genotypes, 3 cell lines), with 80 to 110 million read pairs per sample. Transcriptome alignment yielded 75 to 100 million uniquely mapped read pairs across all samples.
2024-09-17 | GSE217469 | GEO
Project description:To understand the whole genome transcriptome of in vivo Treg cells and ex vivo TGF-beta induced Treg cells from WT and Aim2 knockout mice, the total RNA was extracted from indicated Treg cells using the Direct-zol miniprep kit (Zymo Research, R2060). The RNA samples were firstly enriched by Oligo(dT) magnetic beads and used to construct BGISEQ-500 libraries. RNA-seq libraries sequenced using the 50bp single-end protocol (in vivo isolated Treg cells) or 100bp paired-end protocol (TGF-β induced Treg cells) via the BGISEQ-500 sequencer per the manufacturer’s protocol. After filtering of adaptors and low quality reads, clean reads (>26 Million reads per sample for in vivo isolated Treg cells and >40 Million reads per sample for TGF-β induced Treg cells) are mapped to mouse reference genome using HISAT /Bowtie2 tool. Mapping results are stored in BAM files using SAMtools. Total read counts in gene level were summarized using featureCounts function in the Rsubread in R environment, with the R package biomaRt for gene and transcripts mapping. The differential expression (DE) genes were analyzed by DESeq2 package with default setting using total read counts as input, and the adjusted p value (padj) less than 0.05.
2020-12-04 | GSE133019 | GEO