Homo sapiens
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA109095 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:We performed miRNA microarray profiling on samples prepared from two different cell lines by three widely-used total RNA sample prep methods.
2008-08-19 | GSE11840 | GEO
Project description:This SuperSeries is composed of the following subset Series: GSE11806: miRNA Microarray Profiling of Nine Different Normal Human Tissues GSE11840: miRNA Microarray Profiling with Three Different Total RNA Prep Methods Refer to individual Series
2008-08-19 | E-GEOD-11879 | biostudies-arrayexpress
Project description:Microarray Based Comparison of three Amplification Methods For Nanogram Amounts of Total RNA
| PRJNA91841 | ENA
Project description:We performed miRNA microarray profiling on samples prepared from two different cell lines by three widely-used total RNA sample prep methods. miRNA microarrays were manufactured by Agilent Technologies (Santa Clara, CA), and contain 20-40 features targeting each of 470 human miRNAs (Agilent design ID 016436). Sequences of the 470 miRNAs were obtained from the Sanger miRBase, release 9.1. Labeling and hybridization of total RNA samples were performed according to the manufacturer’s protocol. 100ng total RNA was used as input into the labeling reaction, and the entire reaction was hybridized to the array for 20 hours at 55°C. For total RNA preps, frozen cell pellets were resuspended in phosphate buffered saline and divided into equal aliquots of 5x106 (HeLa) or 1x107 (ZR-75-1) cells and refrozen. Individual aliquots were subsequently thawed just before use.
2008-08-19 | E-GEOD-11840 | biostudies-arrayexpress
Project description:<p>We have deeply sequenced total RNA and whole exome of six different post-mortem human snap-frozen tissues (brain, liver, lung, striated muscle, kidney, heart) from three unrelated healthy Caucasian individuals (males, aged 47-54) with the aim to characterize post-transcriptional events due to alternative splicing and RNA editing. In addition, to facilitate the detection of RNA editing sites we have also resequenced the entire genome of each individual. Data are also used to investigate tissue-specific abundance of mitochondrial DNA from exomes and its correlation with mitochondrial transcription, mass and respiratory activity.</p> <p>Tissues were obtained from Cureline (South San Francisco, CA, USA). DNA and RNA were purified using the DNeasy Blood and Tissue Kit (Qiagen, Hilden, Germany) and the RNeasy Plus Mini Kit (Qiagen, Hilden, Germany), respectively.</p> <p>Exome capture was performed using the TruSeq Exome Enrichment Kit (Illumina, San Diego, CA) and the sequencing was carried out at IGA Technology Services in Udine (Italy) on Illumina HiSeq 2000 (generating for each tissue approximately 40 millions of 100bp paired-end reads). </p> <p>Strand-oriented RNA reads (2x100bp) were generated using the TruSeq Stranded Total RNA Sample Prep Kit (Illumina, San Diego, CA, USA) and sequenced at IGA Technology Services in Udine (Italy) on Illumina HiSeq 2000 platform.</p> <p>Whole genome resequencing was performed at Personal Genomics in Italy on an Illumina HiSeq 2000 platform (2x100bp) with a mean coverage of 30X.</p> <p>MiRNA-Seq was instead performed at IBBE Institute (Italy) using the TruSeq Small RNA Sample Prep Kit on Illumina MiSeq platform.</p> <p>Preliminary bioinformatics analyses have been performed to check quality using FASTQC software and inconsistent read regions have been trimmed using trim_galore. All reads were mapped onto the human reference genome (version hg19) using GSNAP.</p>
| phs000870 | dbGaP
Project description:We compared 3 small RNA library prep kits (CleanTag, NEXTflex, QIAseq) and two RNA extraction methods (miRNeasy and MagnaZol) on plasma. We report that library preparation has a significant effect upon the miRNA profile detected, with QIAseq libraries exhibiting the least sequencing bias of the three library kits. RNA extraction methods also contribute, to a lesser extent, to the miRNA profile detected, with MagnaZol RNA extraction increasing the percentage of reads mapping to miRNAs and the number of individual miRNAs detected.
2019-05-21 | GSE118125 | GEO
Project description:Microarray Based Comparison of two Amplification Methods For Nanogram Amounts of Total RNA
| PRJNA89973 | ENA
Project description:miRNA Microarray Profiling of Nine Different Normal Human Tissues
| PRJNA109089 | ENA
Project description:Purpose: The aim of this study is to compare the plasma miRNA profile between healthy control and sepsis patients Methods: Plasma from healthy control and sepsis patients were used in the study. Total RNA was isolated from equal volume of plasma using Trizol LS. NGS cDNA libraries were prepared using Norgen Biotek Small RNA Library Prep Kit. Library quality was validated prior to sequencing on an Illumina NextSeq 500 platform.
2020-05-04 | GSE149764 | GEO
Project description:Purpose: The aim of this study is to build up a transcriptomic data analysis pipeline and test its performance using synthetic "sequins" controls and lung cancer cell lines. Methods - Cell Culture: Lung adenocarcinoma cell lines NCI-H1975 and HCC827 from a range of passages (2-4) were grown on 3 separate occasions in Roswell Park Memorial Institute (RPMI) 1640 medium with 10% fetal calf serum and 1% penicillin-streptomycin. Methods - RNA preparation: Total RNA was extracted using the TRIzol reagent. 6 ng of sequins were added to 1 ug of total RNA (mix A with H1975, mix B with HCC827). Methods - Library prep: the sequin+total RNA mixtures were subjected to polyA selection (NEBNext PolyA E7490) and library prep (NEBNext Ultra II Directional RNA Library Prep Kit for Illumina) following manufacturer's instructions; we performed 9 PCR cycles
2021-01-12 | GSE164598 | GEO