Project description:Bulk RNA-sequencing experiments were performed to analyze the transcriptomic effects of such integrations into two newly established genomic safe harbor sites. Jurkat and HEK293T cells were edited to integrate CMV-mRuby expressing cassette into Rogi2 genomic safe harbor site using Cas9 RNP
Project description:Atlantic salmon (Salmo salar) move from fresh- to seawater environments following a seasonally timed preparative transition called smoltification, which takes place under photoperiodic control in the freshwater environment. In masu salmon (Oncorhynchus masou), coordination of photoperiodic sexual maturation is proposed to involve in a fish-specific circumventricular organ, the saccus vasculosus (SV), through its intrinsic opsin-based light sensitivity, thyrotrophin secretion and modulation of deiodinase activity (TSH-DIO cascade). The saccus vasculosus is a highly vascularized structure located on the ventral side of the hypothalamus and its interface between the blood and cerebrospinal fluid also hints at a role in ionic balance of the cerebrospinal fluid (CSF). Both the potential photoperiodic and ionic functions of the SV led us to perform transcriptome analysis of the SV in smoltification in Atlantic salmon. Our data show that SV response to seawater exposure is highly dependent on photoperiodic history and identifies ependymin as a major secretory output of the SV, consistent with a role in control of CSF composition. Conversely, we could not detect crucial elements of the opsin-TSH-DIO cascade suggesting that the photoperiodic history-dependence of the SV to seawater exposure is unlikely to stem from SV-intrinsic responses to photoperiod.
Project description:The soft coral Scleronephthya gracillimum is an azooxanthellate octocoral order Alcyonacea. In this study, stress responses to increased seawater temperature and marine acidification were investigated using a microarray. The S. gracillimum microarray was constructed. The S. gracillimum microarray was constructed after RNA-seq. Oligonucleotides were picked from UniGene of S. gracillimum and the clones were annotated using Blast.
Project description:This data was generated by ENCODE. If you have questions about the data, contact the submitting laboratory directly (Jonathan Preall jpreall@cshl.edu (Generation 0 Data from Hannon Lab), Carrie Davis davisc@cshl.edu (experimental), Alex Dobin dobin@cshl.edu (computational), Wei Lin wlin@cshl.edu (computational), Tom Gingeras gingeras@cshl.edu (primary investigator)). If you have questions about the Genome Browser track associated with this data, contact ENCODE (mailto:genome@soe.ucsc.edu). hg18: This data was produced by Hannon lab part of Cold Spring Harbor as part of the ENCODE Project. The series depicts NextGen sequencing information for RNAs between the sizes of 20-200 nt isolated from RNA samples from tissues or sub cellular compartments of cell lines. hg19: This track depicts NextGen sequencing information for RNAs between the sizes of 20-200 nt isolated from RNA samples from tissues or sub cellular compartments from ENCODE cell lines. The overall goal of the ENCODE project is to identify and characterize all functional elements in the sequence of the human genome. hg19: This cloning protocol generates directional libraries that are read from the 5' ends of the inserts, which should largely correspond to the 5' ends of the mature RNAs. The libraries were sequenced on a Solexa platform for a total of 36, 50 or 76 cycles however the reads undergo post-processing resulting in trimming of their 3' ends. Consequently, the mapped read lengths are variable. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf