Rattus norvegicus
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA195545 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:In order to establish a rat embryonic stem cell transcriptome, mRNA from rESC cell line DAc8, the first male germline competent rat ESC line to be described and the first to be used to generate a knockout rat model was characterized using RNA sequencing (RNA-seq) analysis.
2016-09-02 | GSE44150 | GEO
Project description:Whole transcriptome profiling of the rat pineal gland during development from embryonic day 21 to adult
| PRJNA197305 | ENA
Project description:The rat pineal gland is a highly dynamic tissue with many hundreds of genes changing more than two-fold in a 24-hr daily rhythm as measured by Affymetrix GeneChip analysis. We sought to more completely understand this dynamic transcriptome using RNA-Seq in order to capture information regarding alternative splicing, novel exons, unannotated mRNAs, non-coding RNAs, etc. We also wished to identify transcripts that were selectively expressed in the pineal glands relative to other tissues. Toward this end we performed RNA-Seq on three types of samples; 1) a pool of pineal glands sampled at mid-day (ZT7); 2) a pool of pineal glands sampled at mid-night (ZT19); and a pool of 15 different tissues collected from 3 animals at mid-day (ZT7). Animals were housed in a 14:10 light:dark lighting cycle. PolyA-selected RNA was fragmented and sequenced on an Illumina GAII machine, yielding paired-end 51-mer reads.
2015-03-23 | GSE45654 | GEO
Project description:Knee osteoarthritis (KOA), as a degenerative multifactorial disease, affects the quality of life and mental health of patients, and also brings a huge socioeconomic burden. Treating synovitis have shown promise as anti-inflammatory therapeutics in mitigating OA symptoms and disease progression. Here, by analysing synovial single-cell sequencing (scRNA-seq) data from KOA, we found that synovial fibroblasts (FLS) in OA synovium showed a distinct pro-inflammatory phenotype. We collected synovial tissue from patients with clinical OA as well as from healthy donors, and histological examination was consistent with findings in scRNA-seq. Inspired by recent cross-tissue fibroblast lineage studies, we identified by sequencing that healthy FLS in synovial tissues share transcriptome-level similarities with dermal fibroblasts (DFb). Subsequently, we revealed the local as well as systemic distribution of intra-articular injected DFbs by constructing/extracting two types of rat fibroblasts (luciferase DFbs as well as GFP DFbs). The results demonstrate that DFbs can be locally retained in the synovium for up to three weeks following targeted engrafting on it. And intra-articular injection does not result in DFbs migration to vital organs or the occurrence of histological changes in these organs. A rat model of KOA was constructed by anterior cruciate ligament transection (ACLT) in order to study the therapeutic effect of DFbs on KOA. After injection, the rats showed improvement in painful gait. In addition, histological as well as imaging results showed reduced synovitis and improvement in articular cartilage. Finally we verified the protective effect of DFbs on cytokine-stimulated chondrocytes in a co-culture system.
2026-06-24 | GSE304724 | GEO
Project description:PacBio SMRT sequencing of Ttc8 isoforms expressed in the rat pineal gland at night
| PRJNA320100 | ENA
Project description:Development of daily rhythmicity in the rat pineal transcriptome interrogated using RNA-Seq
| PRJNA68829 | ENA
Project description:The rat pineal transcriptome is highly dynamic, with many hundreds of transcripts changing more than two-fold on a 24-hr basis, as revealed earlier using Affymetrix GeneChip analysis. The retina is evolutionally related to the pineal gland so these two tissues share many gene expression patterns. This study more completely characterizes the temporally dynamic transcriptomes of these tissues using RNA-Seq to capture information regarding alternative splicing, novel exons, unannotated mRNAs, non-coding RNAs, and coding transcripts not represented on the Affymetrix chips. We also identified transcripts that were selectively expressed in the pineal gland relative to other tissues by comparing pineal samples to a sample of pooled non-pineal tissues. The transcriptomes of the rat pineal gland and retina were sequenced using samples collected at 6 time points throughout a 24-hour cycle to identify rhythmically expressed transcripts. The transcriptomes of pools of mixed tissues collected at mid-day (ZT7) and mid-night (ZT19) were also sequenced for comparison to aid in determining pineal-enriched transcripts. Contributor: NISC, Comparative Sequencing Program
2014-02-05 | E-GEOD-46069 | biostudies-arrayexpress
Project description:RNA-Seq of the rat pineal transcriptome, with in-vivo and in-vitro samples, under various treatment and surgical conditions
| PRJNA267246 | ENA
Project description:The rat pineal transcriptome is highly dynamic, with many hundreds of transcripts changing more than two-fold on a 24-hr basis, as revealed earlier using Affymetrix GeneChip analysis. The retina is evolutionally related to the pineal gland so these two tissues share many gene expression patterns. This study more completely characterizes the temporally dynamic transcriptomes of these tissues using RNA-Seq to capture information regarding alternative splicing, novel exons, unannotated mRNAs, non-coding RNAs, and coding transcripts not represented on the Affymetrix chips. We also identified transcripts that were selectively expressed in the pineal gland relative to other tissues by comparing pineal samples to a sample of pooled non-pineal tissues.
2014-02-05 | GSE46069 | GEO
Project description:The transcriptome of the rat pineal gland is highly dynamic, with many hundreds of genes changing more than two-fold on a 24-hr daily rhythm, as revealed earlier using Affymetrix GeneChip analysis. Several key transcription factors and enzymes are known to change dramatically during development of the pineal gland. Studies on a small number of genes indicate that the onset of rhythmic expression generally occurs later in development. This study characterizes this temporally dynamic transcriptome using RNA-Seq to capture information regarding alternative splicing, novel exons, unannotated mRNAs, non-coding RNAs and coding transcripts not represented on the Affymetrix chips. The rat pineal transcriptome was sequenced in samples from four ages, from embryonic day 21 through adult. At each age, samples were taken at mid-day and mid-night. Data were collected to describe the changes in the developing pineal transcriptome and to identify transcripts that exhibit day/night differences in expression at each age.
2014-10-24 | E-GEOD-46127 | biostudies-arrayexpress