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| Scope: Self Platform Samples Series Family Format: HTML SOFT MINiML Amount: Brief Quick GEO accession: |  |
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| Sample GSM2992310 | Query DataSets for GSM2992310 |
| | Status | Public on Dec 03, 2018 | | Title | G29T1 | | Sample type | SRA | | Source name | Responder T1 patient8 | | Organism | Homo sapiens | | Characteristics | tissue: Whole blood cells collected from patient after septic shockpatient: G29timepoint: T1clinical classification: R | | Extracted molecule | total RNA | | Extraction protocol | Peripheral blood was collected in EDTA tubes at T1 and T2 and stored at -20°C after adding 400µl of 2X Denaturing solution (Ambion, USA).Total RNA was extracted from 800 µl of blood with MirVana Paris Kit and treated with Turbo DNA-free Kit (Ambion, USA). RNA Quality was assessed on Agilent Bioanalyzer with the RNA 6000 Nano Kit (Agilent, Santa Clara, CA) and samples were considered suitable for processing if RNA Integrity Number was greater than 7.5Sequencing libraries were prepared with the TruSeq Stranded Total RNA with Ribo-Zero Globin Kit (Illumina, San Diego, CA) using 800 ng of total RNA | | Library strategy | RNA-Seq | | Library source | transcriptomic | | Library selection | cDNA | | Instrument model | Illumina HiSeq 2500 | | Description | Ribo and Globin depleted library | | Data processing | Basecalls performed using CASAVA version 1.8.2Trimming performed with Trimmomatic v0.35, with following parameters: MINLEN:40, AVGQUAL:25 and TRAILING:15Trimmed reads aligned to GRCh38 using STAR v.2.5.2b using as reference transcript the gencode (v.25) primary assembly gene transfer file (GTF).Gene counting performed on files including only uniquely mapped fragments using featurecounts v1.5.1 with custom parameters: --minOverlap 5; only both reads, no multimapping.Genome_build: GRCh38Supplementary_files_format_and_content: excel file including raw counts for each sample (columns) across 58906 genes (rows) [counts matrix] | | Submission date | Feb 12, 2018 | | Last update date | May 17, 2019 | | Contact name | Matteo Barcella | | E-mail(s) | [email protected] | | Organization name | SR-TIGET | | Street address | Via Olgettina 60 | | City | Milano | | ZIP/Postal code | 20132 | | Country | Italy | | Platform ID | GPL16791 | | Series (1) | | GSE110487 | Whole blood transcriptome analysis of Septic shock patients according to early therapy response |
| | Relations | | Reanalyzed by | GSM3775741 | | BioSample | SAMN08519054 | | SRA | SRX3683518 |
| Supplementary data files not provided | SRA Run Selector | | Raw data are available in SRA | | Processed data are available on Series record |
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