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Sample GSM5568054 Query DataSets for GSM5568054
Status Public on Sep 11, 2021
Title lib55110
Sample type SRA
 
Source name Whole Blood
Organism Homo sapiens
Characteristics registry: Type 1 Diabetes
age at draw: 24
Sex: male
tissue: Whole Blood
Growth protocol Whole blood was collected in Tempus tubes (Ambion).
Extracted molecule total RNA
Extraction protocol Total RNA was isolated from whole blood samples using MagMax for Stabilized Blood Tubes RNA Isolation Kit (Ambion) and globin-reduced using GLOBINclear (Ambion) per manufacturer's instructions.
Globin-reduced RNA was used to construct libraries using SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Takara), with reverse transcription followed by PCR amplification to generate full length amplified cDNA. Sequencing libraries were constructed using the NexteraXT DNA sample preparation kit with unique dual indexes (Illumina) to generate Illumina-compatible barcoded libraries.
Libraries were pooled and quantified using a Qubit® Fluorometer (Life Technologies). Sequencing of pooled libraries was carried out on a NextSeq 2000 sequencer (Illumina) with paired-end 53-base reads, using NextSeq P2 sequencing kits (Illumina) with a target depth of 5 million reads per sample.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model NextSeq 2000
 
Description lib55110_AAAHMLVM5
66_rn118797159
Data processing Base calls were processed to FASTQs on BaseSpace (Illumina).
Reads were processed using workflows managed on the Galaxy platform; reads were trimmed by 1 base at the 3’ end, and then trimmed from both ends until base calls had a minimum quality score of at least 30 (Galaxy FASTQ Trimmer tool v1.0.0)
FastqMcf (v1.1.2, https://benthamopen.com/ ABSTRACT/TOBIOIJ-7-1) was used to remove any remaining adapter sequence.
Reads were aligned using the STAR aligner with the GRCh38 reference genome
Gene counts were generated using HTSeq-count (v0.4.1)29. Quality metrics were compiled from PICARD (v1.134, http://broadinstitute.github.io/picard/), FASTQC (v0.11.3, http://www.bioinformatics.babraham.ac.uk/projects/fastqc/), Samtools (v1.2)30, and HTSeq-count (v0.4.1).
Genome_build: GRCh38 reference genome and gene annotations from ensembl release 77
Supplementary_files_format_and_content: Processed data is in .csv format. Each row is a gene, each column is a sample.
 
Submission date Sep 08, 2021
Last update date Apr 25, 2024
Contact name Stephanie Osmond
E-mail(s) sosmond@benaroyaresearch.org
Organization name Benaroya Research Institute
Street address 1201 9th Ave
City Seattle,
State/province WA
ZIP/Postal code 98101
Country USA
 
Platform ID GPL30173
Series (1)
GSE183701 Permutational immune analysis reveals architectural similarities between inflammaging, Down syndrome and autoimmunity
Relations
BioSample SAMN21359889
SRA SRX12109250

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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