GEO Accession viewer

NCBI > GEO > Accession Display

Not logged in | Login

GEO help: Mouse over screen elements for information.

Sample GSM3534322

Query DataSets for GSM3534322

Status

Public on Feb 28, 2019

Title

lib4716 [TN02_9043986_11]

Sample type

SRA

Source name

whole blood

Organism

Homo sapiens

Characteristics

subject: TN02_9043986
rate of c-peptide change: -1.92805499120608
visit day: 190
age at enrollment: 12.3
Sex: male
race: White
ethnicity: Not Hispanic or Latino
library batch: Fisher_UPITT
lymphocyte percent: 40.7
neutrophil percent: 46.4

Extracted molecule

total RNA

Extraction protocol

RNA was isolated from whole blood samples preserved in Tempus blood RNA tubes (Applied Biosystems, CA) using the Total RNA Isolation chemistry on an ABI Prism 6100 (Applied Biosystems, CA) or a Thermo Scientific KingFisher (Thermo Fisher Scientific, MA).
Samples were globin-reduced with the GLOBINclear kit (Ambion, CA), and libraries were constructed from globin-reduced RNA using the Illumina TruSeq RNA Sample Preparation kit v2. Libraries were clustered on flow cells using the TruSeq Single Read Cluster Kit v3.

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina HiSeq 2500

Description

lib4716

Data processing

Base-calling was performed automatically by Illumina real time analysis software and demultiplexing was performed on Illumina BaseSpace.
Hard trimming was performed in Galaxy; 1 3'-end base was removed from all reads using the FASTQ Trimmer tool (v1.0.0)
Quality-based trimming was performed in Galaxy; reads were trimmed from both ends using the FASTQ Quality Trimmer tool (v1.0.0) until minimum base quality for each read was >= 30.
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 htseq-count.
Genome_build: GRCh38
Supplementary_files_format_and_content: T1D_placebos_raw_counts.csv is a comma-delimited matrix. The first column ("ensgene") contains Ensembl gene IDs. The remaining columns include raw read counts assigned for each library. All samples that passed SNP-based identity checks are included, with 3 samples of uncertin provenance excluded. Data have not otherwise been filtered or normalized.

Submission date

Dec 28, 2018

Last update date

Mar 06, 2024

Contact name

Stephanie Osmond

E-mail(s)

[email protected]

Organization name

Benaroya Research Institute

Street address

1201 9th Ave