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Sample GSM1446142 Query DataSets for GSM1446142
Status Public on May 01, 2022
Title PMNs sorted from spleen, low_vehicle2
Sample type SRA
 
Source name PMNs sorted from spleen
Organism Mus musculus
Characteristics strain: KPC
tissue: myeloid cell
treatment: vehicle control
days after treatment: N/A
Extracted molecule total RNA
Extraction protocol Whole tumours were frozen in RNAlater and RNA was extracted using Qiagen RNeasy mini kit. The RNA library was prepared using TruSeq Stranded Total RNA library preparation with Ribozero Gold and quality measured on Agilent BioAnalyzer. The NGS was performed on HiSeq 2000 TM using V3 flow cells on one lane at 100bp paired-end. whole RNA was extracted from pellets of sorted myeloid cells using Qiagen RNeasy mini kit and stored in -80 until analysis. Libraries were made by using either IlluminaTrue Seq kits or Nugen Library Construction kits. Samples were multiplexed in 4 lanes and sequenced via the Illumina HiSeq2000 platform. 100 base-pair, paired-end data sequence data were then generated and subsequently analysed.
RNA libraries were prepared for sequencing using standard Illumina protocols
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
 
Description low_vehicle2
Data processing Illumina Casava1.9 software used for basecalling.
Raw reads were aligned to the reference genome (mm10) using Tophat2 or STAR aligner (for myeloid cells). Number of reads aligned to the exonic region of each gene were counted using the Rsamtools Bioconductor package based on the genome annotation from UCSC ‘ensGene’ table. Genes on the sex chromosomes were excluded from the following analysis.
Only genes that achieved at least two read count per million reads (CPM) in at least three samples were kept. Read counts were further normalized using the conditional quantile normalization (cqn) method accounting for gene length and GC content.
This generated normalized log2 RPKM values for each filtered gene across all samples. Differential expression analysis was performed using LIMMA, with the array quality weights function applied
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include log2 transformed RPKM values for each sample
 
Submission date Jul 25, 2014
Last update date May 01, 2022
Contact name Jun Wang
E-mail(s) j.a.wang@qmul.ac.uk
Organization name Barts Cancer Institute, Queen Mary, London
Street address Charterhouse Square
City London
ZIP/Postal code EC1M 6BQ
Country United Kingdom
 
Platform ID GPL13112
Series (1)
GSE59757 PI3Kδ Inhibition Modulates the Innate Inflammatory Response in Pancreatic Ductal Adenocarcinoma and Normalizes Aberrant Metabolism Associated with Cachexia
Relations
BioSample SAMN02940883
SRA SRX661305

Supplementary file Size Download File type/resource
GSM1446142_low_vehicle2.log2RPKM.txt.gz 161.2 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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