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Sample GSM3039872 Query DataSets for GSM3039872
Status Public on Mar 14, 2018
Title rep5_wt_aPDL1 [Lexogen_47]
Sample type SRA
 
Source name Tumour infiltrating lymphocytes
Organism Mus musculus
Characteristics strain: C57BL/6
cell type: Tumour infiltrating lymphocytes
genotype: wild type
treatment: aPDL1
Treatment protocol Ab treatment with 0.5 mg anti-mouse PD-L1 (Clone10F.9G2; BE0101) or control Ab IgG2b (LTF-2; BE0090) was injected i.p. starting on d3 twice a week.
Growth protocol 5×10^5 B16-OVA tumor cells were injected s.c. into wild-type or Nr2f6-deficient mice.
Extracted molecule total RNA
Extraction protocol RNA was isolated using the RNeasy® Mini Kit. (205113, Qiagen). RNA integrity was verified with the Agilent Bioanalyzer. Ion TorrentTM compatible libraries were generated from 20 ng total RNA input
QuantSeq 3' mRNA-Seq Library Prep Kit from Lexogen was used for library construction
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Ion Torrent Proton
 
Description therapy_normalized_counts.txt
Lexogen_47
Data processing The reads were first preprocessed through a high stringency quality control pipeline consisting of adapter removal with Cutadapt and quality trimming with Trimmomatic to remove bases with bad quality scores. All reads shorter than 22 nucleotides were removed.
The quality-trimmed reads were mapped to the mm10 reference genome using a two-step alignment method; alignment with STAR followed by alignment of the unmapped reads with Bowtie2.
Gene-specific read counts were calculated using HTSeq-count. Differential expression analyses were performed using the R package DESeq2.
Genome_build: mm10
Supplementary_files_format_and_content: count matrix with normalized counts, where rows are genes and columns are samples
 
Submission date Mar 13, 2018
Last update date Mar 14, 2018
Contact name Dietmar Rieder
E-mail(s) dietmar.rieder@i-med.ac.at
Phone +43512900371402
Organization name Innsbruck Medical University
Department Biocenter
Lab Division of Bioinformatics
Street address Innrain 80
City Innsbruck
ZIP/Postal code 6020
Country Austria
 
Platform ID GPL18635
Series (1)
GSE111796 Nuclear Receptor NR2F6 as an Alternative Cancer Immune Checkpoint in the T Cell Compartment
Relations
BioSample SAMN08706802
SRA SRX3786392

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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