Annelida
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ABSTRACT:
PROVIDER: PRJDB14830 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:We performed Chromatin Isolation by RNA Purification (ChIRP) of SRA and ChIP of p68 following by high-throughput sequencing in NTERA2 cell line. We find that SRA localizes with p68 genome-wide at genes whose function is involved in embryonic development.
2014-06-18 | GSE58641 | GEO
Project description:PPARγ is a master transcriptional regulator of adipogenesis. Hence, the identification of PPARγ coactivators should help reveal mechanisms controlling gene expression in adipose tissue development and physiology. We show that the non-coding RNA Steroid receptor RNA Activator, SRA, associates with PPARγ and coactivates PPARγ-dependent reporter gene expression. Overexpression of SRA in ST2 adipocyte precursor cells promotes their differentiation into adipocytes. Conversely, knockdown of endogenous SRA inhibits 3T3-L1 preadipocyte differentiation. Microarray analysis reveals hundreds of SRA-responsive genes in adipocytes, including genes in cell cycle, insulin and TNFα signaling pathways. Some functions of SRA may involve mechanisms other than coactivation of PPARγ. SRA increases insulin-stimulated glucose uptake in adipocytes. SRA promotes S-phase entry during mitotic clonal expansion, decreases expression of cyclin-dependent kinase inhibiters p21Cip1 and p27Kip1, and increases phosphorylation of Cdk1/Cdc2. SRA also inhibits the TNFα-induced phosphorylation of c-Jun NH2-terminal kinase. In conclusion, SRA enhances adipogenesis and adipocyte function through multiple pathways.
2013-05-07 | GSE21594 | GEO
Project description:We introduce FACIL (http://www.cmbi.ru.nl/FACIL), a fast, reliable tool to evaluate nucleic acid sequences for non-standard codes that detects alternative genetic codes even in species distantly related to known organisms. Results are visualized in a Genetic Code Logo. To illustrate the use of our method, we analysed several contigs derived from the mitochondrial genome of the foraminifer Globobulimina pseudospinescens. These are particularly challenging data, as the genome is highly fragmented and incomplete. Approximately 10,000 single-cell Globobulimina pseudospinescens organisms were isolated by hand from Gullmar Fjord Sweden sediment. After washing, total DNA was extracted and sequenced by Illumina sequencing. The reads were assembled using Edena. To illustrate the use of our method, we analysed several contigs derived from the mitochondrial genome of the foraminifer Globobulimina pseudospinescens, an organism without any sequenced relatives in the databases. These are particularly challenging data, as the genome is highly fragmented and incomplete. DNA isolated from approximately 10,000 single-cell Globobulimina pseudospinescens organisms
2011-06-20 | E-GEOD-26664 | biostudies-arrayexpress
Project description:Rhizophora mucronata Lam., a prevalent mangrove variety of Indo-Pacific region is reported to defy saline stress up to 40 ppt, but the genome or transcriptome behind this tolerance is yet to be investigated. As an initiative to create a reference sequence database, we have forged a set of 46,366,348 paired end RNA-Seq raw reads of Rhizophora mucronata Lam. leaf tissues from Illumina HiSeq 2500 platform (SRA study accession SRP093200 ; Bioproject accession PRJNA345155). All possible gene transcripts were then reconstructed from the RNA raw seq data and 93960 Trinity assembled, annotated transcripts that are being actively expressed at a given time is proposed (TSA accession GGEC00000000). To estimate gene transcript expression, we used Bowtie 2 programme and successfully aligned back up to 95.14% of the filtered reads to the assembled transcriptome. We allowed up to 1-mismatches in the seed region (length =31bp) and all multiple mapped position were reported. Of all filtered reads about 95.14% of reads from each sample were properly aligned back to the assembled transcriptome. Overall we found 52,153 unique transcripts which have expression >=1 FPKM.
2018-03-22 | GSE112162 | GEO
Project description:We employed next generation sequencing to examine whether knocking down the steroid receptor RNA activator (SRA) gene significantly affect the expression levels of certain genes in MCF-7 cells. MCF-7 cells were transfected with either a pool of four non-target control siRNAs or a pool of four SRA siRNAs for 32 hrs. 157 million reads were generated from triplicate samples of the control group; 151 million reads were generated from triplicate samples of the SRA knockdown group. Six genes were identified as significantly changed in the expression levels with the cutoff of q value ≤ 0.05, fold change ≤ 0.5 or ≥ 2, and reads per kilobase per million mapped reads (RPKM) ≥ 1. However, except for SRA itself, the other five genes were shown by real-time PCR to be only affected by one siRNA in the SRA siRNA pool. Further analysis of this dataset with different cuttoff setting may reveal true SRA-regulated genes in MCF-7.
2014-01-23 | GSE52385 | GEO
Project description:The human steroid receptor RNA activator (SRA) gene encodes both non-coding RNAs (ncRNAs) and protein-generating isoforms. However, the breadth of endogenous target genes that might be regulated by SRA RNAs remains largely unknown. To address this, we depleted SRA RNA in two human cancer cell lines (HeLa and MCF-7) with small interfering RNAs, then assayed for changes in gene expression by microarray analyses using Affymetrix HGU133+2 arrays. We also tested if SRA depletion affects estradiol-regulated genes in MCF-7 breast cancer cells.
2010-02-01 | GSE20081 | GEO
Project description:We performed Chromatin Isolation by RNA Purification (ChIRP) of SRA and ChIP of p68 following by high-throughput sequencing in NTERA2 cell line. We find that SRA localizes with p68 genome-wide at genes whose function is involved in embryonic development. SRA ChIRP and p68 ChIP of triplicate samples.
2014-06-18 | E-GEOD-58641 | biostudies-arrayexpress
Project description:We report a novel function of the lncRNA SRA in regulation of global gene expression through direct chromatin binding in human erythroleukemia cell line K562 and in primary human proerythroblasts derived from HSCs. We demonstrate that SRA, together with CTCF, H3K4me3, and H3K27me3, occupies various genomic regions. Further, SRA facilitates transcriptome-wide expression of erythroid program and expression of erythroid markers in K562 and in primary human proerythroblasts. Hence, a possible function of the lncRNA SRA during erythroid development is to promote transcription of erythroid genes and therefore erythropoiesis.
2020-07-04 | GSE151926 | GEO
Project description:In order to elucidate the general rules for gene localization and regulation mediated by CpG islands, we reanalyzed published ChIP-seq data of CXXC domain, H3K9me3, KDM2A, SUV39H1, ATF4, MYBL1, MYOD1, SPI1, and CTCF. Raw data were downloaded from Sequence Read Archive (SRA) in National Center for Biotechnology Information (NCBI) database. FASTQ files were extracted with the SRA Toolkit version 2.5.5 and aligned using Bowtie 2.2.5 onto the mouse and human genome (mm9 and hg19, respectively). For the identification of factor binding sites, model-based analysis for ChIP-seq peak caller (MACS 1.4.2) was used with a p-value cutoff of 1e-5.
2018-02-15 | GSE80791 | GEO
Project description:Earthworms show a wide spectrum of regenerative potential with certain species like Eisenia fetida, a terrestrial redworm, capable of regenerating more than two-thirds of their body while other closely related species, such as Paranais litoralis seem to have lost this ability. Earthworms belong to the phylum annelida, in which the genomes of the marine oligochaete Capitella telata, and the freshwater leech Helobdella robusta have been sequenced and studied. Herein, we report the de novo assembled transcriptome of Eisenia fetida (Indian isolate), along with an analysis of the transcriptomic changes during regeneration. We also used de novo assembled RNAseq data to identify genes that are differentially expressed during regeneration, both in the newly regenerating cells and in the adjacent tissue.
2018-07-03 | GSE101310 | GEO