Project description:Mammalian genomes contain thousands of genes for long non-coding RNA (lncRNAs) that affect expression of other genes through diverse mechanisms. The lncRNA transcripts are longer than 200 nucleotides and are often capped, spliced and polyadenylated, but they are not translated into protein. Nuclear lncRNAs modify chromatin structure and transcription in trans or cis by interacting with the DNA, forming R-loops, and recruiting regulatory proteins. Not much is known about the role of lncRNA in pituitary gland differentiation and function. To develop a research resource for the study of lncRNA, we used cell-type specific cre transgenes to tag individual pituitary cell types in adult mice with fluorescent markers and enriched for thyrotropes, gonadotropes and somatotropes using fluorescence activated cell sorting. We determined the transcriptome of each cell population using RNA sequencing and mined the data for lncRNA. We detected hundreds of lncRNA in adult pituitary cells, and some were cell-type specific, and located immediately nearby genes that encode pituitary hormones or lineage-specific transcription factors. We also mined transcriptome data from mouse pituitary glands collected at embryonic days 12.5 and 14.5 and identified 351 unique lncRNAs, many of which are exclusively expressed during development. The location of many of these lncRNA suggests a cis-acting regulatory role for them in pituitary development or physiological function. This research resource sets the foundation examining the actions of lncRNAs on expression of their nearby genes during development and in response to physiological demand.
Project description:Methods: RNA profiles of 12 tissues were generated by deep sequencing using Illumina HiSeq 2000. The sequence reads that passed quality filters were analyzed at the transcript isoform level with TopHat followed by Cufflinks. Results: This work has focused on identification of non-coding RNAs expressed in human tissues. We have identified a set of non-coding RNAs that are both expressed and conserved, as described in the manuscript accompagnying this work.
Project description:This SuperSeries is composed of the following subset Series: GSE32898: Comprehensive identification of long non-coding RNAs expressed during zebrafish embryogenesis [RNA_seq] GSE32899: Comprehensive identification of long non-coding RNAs expressed during zebrafish embryogenesis [ChIP_Seq] Refer to individual Series
Project description:Methods: RNA profiles of 12 tissues were generated by deep sequencing using Illumina HiSeq 2000. The sequence reads that passed quality filters were analyzed at the transcript isoform level with TopHat followed by Cufflinks. Results: This work has focused on identification of non-coding RNAs expressed in human tissues. We have identified a set of non-coding RNAs that are both expressed and conserved, as described in the manuscript accompagnying this work. total RNA profiles of 12 normal human tissues, no replicates.
Project description:Interventions: Case series:Nil
Primary outcome(s): intestinal microecological disorders;blood non-coding RNAs and immune status
Study Design: Randomized parallel controlled trial
Project description:We investigated the transcriptome of B. cenocepacia under infection of the nematode Caenorhabditis elegans. RNAs fractions extracted from C. elegans infected with B. cenocepacia were used for Illumina high throughput sequencing using the CappableSeq method. The main objective of this work was to identify small non-coding RNAs (sRNAs) expressed by B. cenocepacia under infection conditions.
Project description:Using RNA CaptureSeq we annotated non-coding RNAs transcribed from genome intervals surrounding breast cancer risk signals in a range of mammary-derived tissue and cell lines.