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Sample GSM2756729 Query DataSets for GSM2756729
Status Public on May 27, 2020
Title NSTEMI_14
Sample type SRA
 
Source name Peripheral blood
Organism Homo sapiens
Characteristics tissue: Whole blood
Sex: Male
age (years): 58
country of origin: Italy
Growth protocol Blood samples were collected and mantained into Tempus Blood RNA tubes until processing following manufacturer's instructions.
Extracted molecule total RNA
Extraction protocol Total RNA was isolated using the Tempus Spin RNA Isolation Kit (Applied Biosystems) and was treated with RNase-free DNase-I to eliminate genomic contamination, following the manufacturer’s instructions.
Five µg of total RNA were precipitated, α- and β-globin mRNAs were depleted with GLOBINclear Whole Blood Globin Reduction kit (Applied Biosystems), and poly(A)+ RNA was enriched following MicroPoly(A) Purist kit protocol (Applied Biosystems). Libraries were prepared and pooled together using the multiplex SOLiD System Sequencing and Barcoding kits. Complementary DNA (cDNA) amplification reaction was conducted with 20 µL template in 100 µl end-volume reaction and with 16 PCR cycles. Clonally amplification of library templates was performed on SOLiD p1 DNA beads by emulsion PCR (ePCR) using 0.5 pM library template and E120 EZbeads scale.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model AB 5500xl Genetic Analyzer
 
Description 12081
Data processing We used XSQTools (Applied Biosystems) with default parameters to remove reads with low quality base values and to generate .csfasta and .QV.qual files for each samples.
Using TopHat v2.0.11 with Bowtie 1 to handle colour space reads, we mapped all reads to the human genome version HG38/GRCh38.76 downloaded from the Ensembl database. We excluded 'haplotypes' and 'patches' sequences from the reference, in order to focus on primary assembly and to avoid under-estimation of gene expression.
We implemented the reference annotation based transcript (RABT) procedure, using Cufflinks suite v2.1.1 to create a new assembly for downstream analysis, integrating the information about known genes and transcripts position in the genome (Ensemble GTF release 76) with those reads mapped in intergenic or intronic regions.
We estimated genes and transcripts expression levels by Cuffquant (using default parameters, apart from -multi-read-correct -frag-bias-correct 'reference.fasta' and -mux-bundle-frags 100000000) and then Cuffnorm (with default parameters, apart from -total-hits-norm).
For each feature we computed both reads counts and fragments per kilobase of transcript per million fragments mapped (FPKM) values. Genes with a FPKM value ≥ 0.046 in at least 60% of samples were considered expressed. This threshold was obtained correlating RNA-Seq data with those from a qPCR gene expression array in preliminary experiments.
Genome_build: HG38/GRCh38.76
Supplementary_files_format_and_content: Tab-delimited text files include raw counts or FPKM values for each Sample. The header of the files reports gene name, Ensemble gene ID, chromosome location, gene length, biotype, biotype class and sample identifiers.
Supplementary_files_format_and_content: txt file containing raw expression measurements
Supplementary_files_format_and_content: txt file containing expression measurements expressed as fragments per kilobase of transcript per million fragments mapped (FPKM) values
Supplementary_files_format_and_content: txt file containing expression measurements as filtered and normalized counts
 
Submission date Aug 28, 2017
Last update date Nov 21, 2022
Contact name Gualtiero Ivanoe Colombo
E-mail(s) gualtiero.colombo@cardiologicomonzino.it
Phone +39 0258002464
Organization name Centro Cardiologico Monzino IRCCS
Lab Immunology and Functional Genomics
Street address Via Carlo Parea, 4
City Milano
ZIP/Postal code 20138
Country Italy
 
Platform ID GPL16288
Series (1)
GSE103182 Whole blood transcriptional profiling by RNA sequencing in patients with ST-elevation and non-ST elevation myocardial infarction
Relations
Reanalyzed by GSM6745978
BioSample SAMN07568106
SRA SRX3141112

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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