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Sample GSM1579213 Query DataSets for GSM1579213
Status Public on Jan 07, 2018
Title Control_747 (sncRNA)
Sample type SRA
Source name lung
Organism Homo sapiens
Characteristics tissue: lung
cell type: bronchial smooth muscle (BSM) cells
disease state: control
Growth protocol BSM cells were established and grown in RPMI 1640 (Lonza, Basel, Switzerland) supplemented with 5% fetal calf serum (FCS), 8 mM L-glutamine, 20 mM hydroxyethyl piperazine ethane sulfonic acid and 1% modified Eagle’s medium vitamin mix (Gibco, Paisley, UK). Neither antibiotics nor antimycotics were added at any time.
Extracted molecule total RNA
Extraction protocol RNA isolation was performed with mirVana miRNA isolation kit (Ambion, Life Science, Zug, Switzerland). RNA concentration of each sample was evaluated with a ND-1000 spectrophotometer (NanoDrop) and its quality was analysed with the Agilent 2100 Bioanalyzer using Agilent RNA 6000 nano kit (Agilent Technologies, Milano, Italy).
For small RNA profiling, 1 µg of total RNA was used for library preparation according to the Illumina TruSeq small RNA sample preparation protocol. Sized microRNA libraries were gel purified and sequenced on a Illumina HiSeq1500 sequencer. For polyA RNA sequencing, an equimolar RNA pool was prepared from all 14 RNA samples extracted from both asthmatic and normal primary BSM cells. 1 µg of total RNA was used for library preparation according to the Illumina TruSeq stranded mRNA sample preparation protocol. Resulting mRNA library was sequenced on a Illumina NextSeq sequencer.
Library strategy ncRNA-Seq
Library source transcriptomic
Library selection size fractionation
Instrument model Illumina HiSeq 1500
Description sncRNA
processed data file: all_sncRNA_RPM_normalized.txt
Data processing Basecalls was performed using CASAVA version 1.8
iMir was used to identify members of the following sncRNA families: microRNAs, tRNAs or rRNAs, piRNAs RFam and tiRNAs with Minimum Read Count of 3, Minimum Read Length of 17, minReadlengthTrans of 32 and maxReadLength of 32. Reads were normalized using reads per million method (RPM). ToAdaptor sequences and low-quality terminal nucleotide positions within the reads were removed using Trimmomatic software
Sequenced reads for RNA-Seq libraries were aligned to human reference genome with TopHat (v 2.0.10) using the -G (GTF file of Ensembl release 75) option. Further, the aligned reads are used to quantify mRNA expression by using the HTSeq-count (v 0.6.1) with hg19 GTF (Ensembl release 75).The pre-processed reads were mapped to the human genome, using the software Bowtie2.
Genome_build: hg 19
Supplementary_files_format_and_content: all_sncRNA_RPM_normalized.txt file includes RPM normalized sncRNA expression values for each Sample
Supplementary_files_format_and_content: mRNA-Seq_read_count.txt file contains read counts for genes that have read count ≥10
Submission date Jan 07, 2015
Last update date May 15, 2019
Contact name Elena Alexandrova
Phone +393661595308
Organization name University of Salerno
Department Faculty of Medicine and Surgery
Lab Laboratory of Molecular Medicine and Genomics
Street address Viale Stazione, 22
City Portici
State/province Napoli
ZIP/Postal code 80055
Country Italy
Platform ID GPL18460
Series (1)
GSE64744 Small RNA profiling reveals deregulated PTEN/PI3K/Akt pathway in asthmatic bronchial smooth muscle cells
BioSample SAMN03277040
SRA SRX835537

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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