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Sample GSM1703070 Query DataSets for GSM1703070
Status Public on Jun 04, 2015
Title CA894
Sample type SRA
 
Source name children with diarrhea_DAEC
Organism Homo sapiens
Characteristics age: 2 year-old or older
group: Diarrhea
organisms: DAEC
severity: mild
tissue: Whole blood
flowcell: A
lane: 4
Extracted molecule polyA RNA
Extraction protocol Total RNA was isolated using MagMax for Stabilized Blood Tubes RNA Isolation Kit (Ambion, TX) and RNA sample was globin reduced wit GLOBINclear (Ambion, TX) according to manufacturer’s instructions.
Libraries were prepared from globin reduced RNA samples using the Illumina TrueSeq RNA Sample Preparation kit according to manufacturer's instructions.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
 
Data processing Base-calling was performed automatically in Illumina BaseSpace after sequencing; FASTQ reads were trimmed in Galaxy in two steps: 1) hard-trimming to remove 1 3'-end base (FASTQ Trimmer tool, v.1.0.0); 2) quality trimming from both ends until minimum base quality for each read >= 30 (FASTQ Quality Trimmer tool, v.1.0.0).
Reads were aligned in Galaxy using bowtie and TopHat (Tophat for Illumina tool, v.1.5.0).
Read counts per Ensembl gene ID were estimated in Galaxy using htseq-count (htseq-count tool, v.0.4.1).
Sequencing, alignment, and quantitation metrics were obtained for FASTQ, BAM/SAM, and count files in Galaxy using FastQC, Picard, TopHat, Samtools, and ht-seq-count.
Non-protein coding and mitochondrial genes were filtered out.
Samples were selected for further analysis by using these criteria: unpaired reads examined/FASQ total read >0.75 and median CV coverage <1. Samples that had total counts less than one million were excluded.
Genes expressed (counts per million >1) in less than 3 samples were removed. Data normalization (TMM) and differential expression analysis were performed in R using "edgeR" package.
Genome_build: GRCh38
Supplementary_files_format_and_content: (1) mexico_processed_data_for_GEO.csv: comma-separated matrix – first 6 columns contain Ensembl gene ID, Ensembl transcript ID, HGNC symbol, location information and chromosome name, remaining columns include read counts assigned for each library; data represents all processing steps up to and including "sample QC and filtering" but not downstream processing/normalization for analysis. (2) mexico_combined_metrics.csv: comma-separated matrix – the first column contains library ID, remaining columns include RNA sequencing and alignment metrics.
 
Submission date Jun 03, 2015
Last update date May 15, 2019
Contact name Scott Presnell
E-mail(s) SPresnell@benaroyaresearch.org
Organization name Benaroya Research Institute
Street address 1201 Ninth Avenue
City Seattle
State/province WA
ZIP/Postal code 98101
Country USA
 
Platform ID GPL16791
Series (1)
GSE69529 Elucidating the etiology and molecular pathogenicity of infectious diarrhea by high throughput RNA sequencing
Relations
BioSample SAMN03759942
SRA SRX1047708

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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