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| Status |
Public on May 01, 2022 |
| Title |
KPC tumour, vehicle7 |
| Sample type |
SRA |
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| Source name |
KPC tumour
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| Organism |
Mus musculus |
| Characteristics |
strain: KPC
tissue: tumour
treatment: vehicle control
days after treatment: N/A
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| 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
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
MJ_04
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| 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
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| Submission date |
Jul 25, 2014 |
| Last update date |
May 01, 2022 |
| Contact name |
Jun Wang |
| E-mail(s) |
j.a.wang@qmul.ac.uk
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| Organization name |
Barts Cancer Institute, Queen Mary, London
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| Street address |
Charterhouse Square
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| City |
London |
| ZIP/Postal code |
EC1M 6BQ |
| Country |
United Kingdom |
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| Platform ID |
GPL13112 |
| Series (1) |
| GSE59757 |
PI3Kδ Inhibition Modulates the Innate Inflammatory Response in Pancreatic Ductal Adenocarcinoma and Normalizes Aberrant Metabolism Associated with Cachexia |
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| Relations |
| BioSample |
SAMN02940876 |
| SRA |
SRX661298 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1446135_MJ_04.log2RPKM.txt.gz |
185.9 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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