Mouse
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1225162 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| Other | ||||
| SRR32563500.fastq.gz | Fastqsanger.gz | |||
| SRR32563500_1.fastq.gz | Fastqsanger.gz | |||
| SRR32563500_2.fastq.gz | Fastqsanger.gz | |||
| SRR32563700.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 508 |
Similar Datasets
Project description:Pollen grains of Arabidopsis thaliana contain two haploid sperm cells enclosed in a haploid vegetative cell. Upon germination, the vegetative cell extrudes a pollen tube that carries the sperm to an ovule for fertilization. Knowing the identity, relative abundance, and splicing patterns of pollen transcripts will improve understanding of pollen and allow investigation of tissue-specific splicing in plants. Most Arabidopsis pollen transcriptome studies have used the ATH1 microarray, which does not assay splice variants and lacks specific probe sets for many genes. To investigate the pollen transcriptome, we performed high-throughput sequencing (RNA-Seq) of Arabidopsis pollen and seedlings for comparison. Gene expression was more diverse in seedling, and genes involved in cell wall biogenesis were highly expressed in pollen. RNA-Seq detected at least 4,172 protein coding genes expressed in pollen, including 289 assayed only by non-specific probe sets. Additional exons and previously unannotated 5’ and 3’ UTRs for pollen-expressed genes were revealed. We detected regions in the genome not previously annotated as expressed; 14 were tested and 12 confirmed by PCR. Gapped read alignments revealed 1,908 high-confidence new splicing events supported by 10 or more spliced read alignments. Alternative splicing patterns in pollen and seedling were highly correlated. For most alternatively spliced genes, the ratio of variants in pollen and seedling was similar, except for some encoding proteins involved in RNA splicing. This study highlights the robustness of splicing patterns in plants and the importance of on-going annotation and visualization of RNA-Seq data using interactive tools such as Integrated Genome Browser.
2013-05-25 | E-MTAB-4242 | biostudies-arrayexpress
Project description:Over 2000 publicly accessible human and mouse ChIP-Seq datasets for about 250 Transcription Factors and chromatin complexes from various databases (ENCODE, GEO) were mapped to custom-made human and mouse genomes containing a reference rDNA sequence of the appropriate species (Genbank U13369.1 for human, BK000964.3 for mouse). The read mapping density across the rDNA sequence was then extracted and normalized to the median in that dataset. Unbiased clustering and analysis, followed by curation, was performed to identify high-confidence patterns of rDNA occupancy for numerous hematopoietic TFs and TF families at canonical TF motif sequences. ************************ Data processing steps: FASTQs were trimmed using Trimmomatic with the following parameters: LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:30 Reads were mapped to customized genomes (containing additional rDNA sequence) using Bowtie2 using the following parameter: -X 2000 Read density across the rDNA sequence was extracted using igvtools ************************
2022-01-15 | GSE191272 | GEO
Project description:Bam files containing mitochondrial alignments, extracted from CPCGene Whole Genome Alignments
| EGAD00001003360 | EGA
Project description:The aim of this sequencing experiment was to make available tissue expression panels for selected fish species for comparative expression studies between the species. Tissue samples were collected for zebrafish (Danio rerio), medaka (Oryzias latipes), and rainbow trout (Oncorhynchus mykiss). Tissue types included liver, skin, muscle, heart, gut, gill, eye, brain for all three species, with additionally pyloric caeca, kidney, head kidney, and spleen for rainbow trout. Only liver samples were taken in replicate of four or three for rainbow trout. All fish were raised under standard rearing conditions for the species. Total RNA was extracted from the tissue samples and paired‐end sequencing of sample libraries was completed on an Illumina HiSeq 2500 with 125‐bp reads. Processed count tables per species as raw counts, FPKM, or TPM, were generated from read alignment to the Ensembl genomes of the respective species using STAR and gene level counting using RSEM and Ensembl gene annotation.
2020-04-30 | E-MTAB-8959 | biostudies-arrayexpress
Project description:The aim of this sequencing experiment was to make available liver tissue expression for selected fish species, northern pike (Esox lucius, Eluc), coho salmon (Oncorhynchus kisutch, Okis) and Arctic charr (Salvelinus alpinus, Salp), for comparative expression studies between the species. Samples in replicate of four were sacrificed according to protocols at each of the facilities from where samples were obtained. RNA was extracted from samples and Illumina TruSeq Stranded mRNA libraries were built. Sequencing was performed in two passes on an Illumina HiSeq2500, paired-end 125bp reads. Processed count tables per species as raw counts, FPKM, or TPM, were generated from read alignment to the NCBI genomes of the respective species using STAR and gene level counting using RSEM and NCBI gene annotation.
2020-04-30 | E-MTAB-8962 | biostudies-arrayexpress
Project description:C57BL/6 mice were maintained in specific pathogen-free conditions in accordance with the Institutional Animal Care and Use Committee. Listeria monocytogenes (clinical isolate 10403s) was from V. Boyartchuk (NTNU, Trondheim, Norway) and infected as previously described (PMID 24477914) for 24 hours before harvesting the spleen. PBS was used as control. . Single cell suspensions from spleens were used to make total RNA. 4 μg of total RNA was used to generate libraries for RNA-sequencing (Illumina unstranded mRNA kits). Samples were sized, quantified and validated on a Bioanalyzer. Libraries were sequenced on a High-Seq System (Illumina 2000, San Diego, CA) as paired-end 100 reads. Sequence reads were aligned to the mouse genome (assembly NCBI m37/mm9) using TopHat.Gene level read counts based on the resulting alignments were calculated using HTSeq. The DESeq R package was used to normalize gene counts, calculate fold change in gene expression, estimate p-values and adjusted p-values for change in gene expression values, and to perform a variance stabilized transformation on read counts.
2015-06-30 | E-MTAB-3315 | biostudies-arrayexpress
Project description:Long-read RNA sequencing (RNA-seq) holds great potential for characterizing transcriptome variation and full-length transcript isoforms, but the relatively high error rate of current long-read sequencing platforms poses a major challenge. We present ESPRESSO, a computational tool for robust discovery and quantification of transcript isoforms from error-prone long reads. ESPRESSO jointly considers alignments of all long reads aligned to a gene and uses error profiles of individual reads to improve the identification of splice junctions and the discovery of their corresponding transcript isoforms. On both a synthetic spike-in RNA sample and human RNA samples, ESPRESSO outperforms multiple contemporary tools in not only transcript isoform discovery but also transcript isoform quantification. In total, we generated and analyzed ~1.1 billion nanopore RNA-seq reads covering 30 human tissue samples and three human cell lines. ESPRESSO and its companion dataset provide a useful resource for studying the RNA repertoire of eukaryotic transcriptomes.
2022-10-14 | GSE192955 | GEO