Derivation of Rhesus Monkey Parthenogenetic Embryonic Stem Cells and its MicroRNA Signature
ABSTRACT: We derived two novel rpESC lines and characterized their microRNA signature by Solexa deep sequencing. By characterizing their microRNA signature, we identified 91 novel microRNAs, except those are also detected in other primate ESCs. Moreover, these two novel rpESCs display a unique microRNA signature, comparing to their biparental counterpart ESCs. Examination of 2 different small RNA expression profilings in 2 rhesus parthenogenetic embryonic stem cell lines
Parthenogenetic embryonic stem cells are considered as a promising resource for regeneration medicine and powerful tools for developmental biology. A lot of studies have revealed that embryonic stem cells have distinct microRNA expression pattern and these microRNAs play important roles in self-renewal and pluripotency of embryonic stem cells. However, few studies concern about microRNA expression pattern in parthenogenetic embryonic stem cells, especially in non-human primate--the ideal model s ...[more]
Project description:We established three new rhesus embryonic stem cells lines and conducted their microRNA profilings by Solexa sequencing. Sequencing of small RNA libraries yielded 12.66 million, 13.12 million and 11.57 million raw reads from IVF1.2, IVF3.2 and IVF3.3, respectively. After filtering, we obtained 10.89 million (IVF1.2), 10.60 million (IVF3.2) and 9.26 million (IVF3.3) clean reads (18-30nt). Examination of 3 different small RNA expression profilings in 3 rhesus embryonic stem cell lines
Project description:miRNAs-mediated gene silencing pathway plays vital roles in plant development, abiotic and biotic stress responses. Here, we carried out a high-throughput sequencing approach to identify miRNAs in leaves and flowers of sweet orange. Consequently we identified genome-wide 183 known miRNAs and 38 novel miRNAs. Small RNA sequencing of the leaves and flowers in sweet orange
Project description:Parthenogenetic stem cells were derived from parthenotes, then differentiated to mesenchymal stem cells. These were further reprogrammed to induced pluripotent stem cells, which were finally differentiated to secondary mesenchymal stem cells. Transcriptional analysis was performed at all 4 states of potency to indetify changes in expression stability of partehnogenetic cells. Overall design: 4 samples for each stage of potency were analyzed, controls were biparental embryonic stem cells and their mesenchymal derivate, as well as biparental induced pluripotent stem cells
Project description:Parthenogenetic stem cells were derived from parthenotes, then differentiated to mesenchymal stem cells. These were further reprogrammed to induced pluripotent stem cells, which were finally differentiated to secondary mesenchymal stem cells. Transcriptional analysis was performed at all 4 states of potency to indetify changes in expression stability of partehnogenetic cells. 4 samples for each stage of potency were analyzed, controls were biparental embryonic stem cells and their mesenchymal derivate, as well as biparental induced pluripotent stem cells
Project description:We report the application of illumina deep sequencing technology for high-throughput profiling of microRNA in aflatoxin B1 treated rat liver tissue, as well as normal liver tissue. miRNAs of miR-17-92 cluster, thought to be tumor activating miRNAs, were down-regulated. miR-34a, considered to be a tumor suppressor, was up-regulated.Novel miRNAs and miRNA base alteration caused by SNP or editing were predicted and summarized. Examination of 2 microRNA profiles in 2 liver tissues under different treatments.
Project description:PD0325901 is involved in improving reprogramming efficiency during inducing pluripotent stem cells (iPSC) or maintain a blastocyst-like state in embryonic stem cells (ESC). However, the knowledge about this small molecule regulating miRNAs in ESC was limited. To understand the role of miRNAs during PD03-induced ESC maintenance and gain an insight how PD0325901 regulates miRNAs expression; we performed small RNA sequencing using Illumina HiSeq 2000 under the compounds treatment. The data show the miRNAs regulated by PD0325901. J1 mESCs maintained in medium containing 1000 U/mL LIF and supplemented with PD0325901 for 24 hours, J1 treated with DMSO was set as control. Then total RNA was extracted for analysis.
Project description:Two fiber tissues harvested 10 days post anthesis from upland cotton trees grown under the same green house conditions except for different seasons of the year were used for RNA extraction. Small RNA molecules under 30 bases were amplified and isolated from an agarose gel. The purified DNA was used directly for cluster generation and sequencing analysis using the Illumina Genome Analyzer according to the manufacturer's instructions. The 35nt sequence tags from sequencing went through data cleaning first, which included getting rid of the low-quality tags and several kinds of contaminants from the 35nt tags. All clean tag sequences with copy numbers were then summarized into a fasta format file. Fiber samples from different seasons were used for small RNA sequencing and data processing.
Project description:In order to discover novel small RNAs expressed in elongated spermatids, we isolated elongated spermatids from mouse testis. The small RNA fraction (18-40nt) was cloned and sequenced from total RNA. RNAs extracted from elongated spermatids were used for high throughput sequencing analysis
Project description:To understand how microRNA are involved in the complex biology of this zoonotic parasite, we describe our initial attempts to characterize small RNA in adult Dirofilaria immitis by using Illumina/Solexa deep-sequencing technology. Examination of 4 different adult Dirofilaria immitis (pooled)
Project description:In order to discover novel small RNAs expressed in mature sperm, we isolated mature sperm from mouse cauda epididymis, comparing with data from adult tesis and uterus. The small RNA fraction (18-40nt) was cloned and sequenced from total RNA of mature sperm, testis and uterus of mice. RNAs extracted from mature sperm, adult testis and uterus were used for high throughput sequencing analysis