ABSTRACT: We performed microRNA sequencing (miRNA-seq) according to Illumina sequencing protocols. Total RNA extracted from ZR75.1 cells expressing or not human ER-beta in absence of estrogen stimuli was subjected to size selection library preparation and retrotranscribed. Obtained DNA was sequenced with the Illumina HiSeq 1500 sequencer .
Project description:We performed microRNA sequencing (miRNA-seq) according to Illumina sequencing protocols. Total RNA extracted from MCF-7 cells expressing or not human Erbeta in absence of estrogen stimuli was subjected to size selection labrary preparation ond retrotranscribed. Obtained DNA was sequenced with the Illumina/Solexa Genome Analyzer (GAIIX).
Project description:We performed microRNA sequencing (miRNA-seq) according to Illumina sequencing protocols. Total RNA extracted from MCF-7 cells expressing human ER-beta in absence of estrogen stimuli was subjected to size selection labrary preparation ond retrotranscribed. Obtained DNA was sequenced with the Illumina/Solexa Genome Analyzer (GAIIX).
Project description:We performed microRNA sequencing (miRNA-seq) according to Illumina sequencing protocols. Platelet-rich plasma (PRP) has been obtained by centrifuging whole blood at 160 x g for 15 min at room temperature. Platelets have been activated with 3 different physiologic agonists, namely ADP (20uM), collagen (60ug/mL), or Thrombin Receptor Activating Peptide (TRAP 25uM) under continuous stirring. An aliquot of platelets has been obtained at 120 minutes following ADP, collagen and TRAP and then processed to determine miRNA expression profiles. Time 0, indicating samples before any agonist treatment, was used as baseline. Total RNA was extracted by using mirVana Paris kit (life technologies) and then was subjected to size selection library preparation and retrotranscribed. Obtained cDNA was sequenced with the Illumina HiSeq 1000 sequencer .
Project description:Human estrogen-responsive breast cancer cell line MCF7 and ZR75.1 were treated with 10 nM of17beta-estradiol, or vehicle (ETOH). miRNA expression was analyzed on total RNA extracted before and after 6, 12, 24, and 72 hours of hormone stimulation. Total RNA was fluorescently labelled, amplified in triplicate, to be, than, pooled for the Hybridization, for MCF7 cells, while for ZR75.1, total RNA was fluorescently labelled, amplified in duplicate. Pools and duplicate, were hybridized for 18 hours on Illumina v2 MicroRNA Expression BeadChips, and after scanning, analysis was performed with GenomeStudio v.2010.1 software, for quality control and miRNA expression analysis.
Project description:miRNA sequencing of mammary tumor RNA from 18 [AKXD subline(n) x PyMT]F1. The PyMT strain was FVB/N-TgN(MMTV-PyVT)634Mul. Mammary tumor total small RNA from mice representing each of the 18 AKXD RI strains was pooled to represent each strain and sequenced using the Illumina Genome Analyzer IIx sequencer.
Project description:To identify QKI targets, we performed QKI knockdown in BEAS2B cells and analyzed alternative splicing patterns by high-throughput RNA sequencing. The mRNA profiles of control- and QKI-knockdown BEAS2B cells were generated by deep sequencing using Illumina GAIIx sequencer.
Project description:Despite clear evidence that exosomal microRNAs (miRNAs) are able to modulate the cellular microenvironment and that exosomal RNA cargo selection is often deregulated in pathological conditions, the mechanisms controlling specific RNA sorting into extracellular vescicles are still poorly understood. We identified here the RNA binding protein SYNCRIP (Synaptotagmin-binding Cytoplasmic RNA-Interacting Protein, also known as hnRNP-Q or NSAP1) as a component of the hepatocyte exosomal miRNA sorting machinery. SYNCRIP was found to bind directly a subset of miRNAs enriched in exosomes, sharing a common extra-seed sequence that we named hEXO motif. In vivo knock-down of SYNCRIP impaired microRNA sorting in exosomes and the hEXO motif was proven to play a role in the regulation of miRNA localization, as its embedment into a poorly exported miRNA enhanced its loading into exosomes. These results provide a new insight in the mechanisms of miRNA exosomal sorting process, that ca be exploited to further understand the role of these extracellular vescicles in cell-to-cell communications and the control of tissue micoenvironments.
Project description:To analyse the transcriptional response of Rhodococcus aetherivornas BCP1 to arsenic, RNA was extracted from BCP1 cultures exposed to arsenite [As(III)] 5 mM and arsenate [As(V)] 30 mM for 18 hours in the presence of glucose as only carbon and energy source. Control cultures were carried out without adding any arsenic oxyanions. Illumina Truseq stranded mRNA libraries were constructed after rRNA depletion via Illumina Ribozero and sequenced on Illumina HiSeq 1500 system 2 x 70nt PE rapid mode.
Project description:RNA-seq data from short term cultivated fibroblasts were sequenced on an Illumina HiSeq 2000 sequencer. Donors were differentiated by age (Years) and gender (F=female; M=male). Two samples were obtained from each individual from different locations (B=buttock, not UV exposed; S=shoulder, UV exposed).