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Sample GSM3291713 Query DataSets for GSM3291713
Status Public on Jul 18, 2019
Title AB1 Responder rep1 [AB01]
Sample type SRA
Source name AB1_Responder
Organism Mus musculus
Characteristics host strain: balb/c
host mouse age: 8-9 weeks
host mouse gender: female
tumor cells: AB1
tumor type: mesothelioma
treatment: anti-CTLA4 plus anti-PDL-1
timepoint: day 0 - pretreatment
response to immunotherapy: Responder
rna 260/280: 2.04
rna 260/230: 2.03
Growth protocol AB1 or Renca tumour cells were subcutaneously injected into Balb/c mice, and whole tumour surgically removed 8 or 10 days after (respectively)"
Extracted molecule total RNA
Extraction protocol Frozen tumours were dissociated in Trizol using a TissueRuptor, total RNA was extracted using chloroform and purified on Rneasy MiniElute columns.
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 AB01_CAF66ANXX_ATCACG_L004
Data processing Image analysis was performed in real time by the HiSeq Control Software (HCS) v2.2.68 and Real Time Analysis (RTA) v1.18.66.3. RTA performs real-time base calling on the HiSeq instrument computer
The Illumina bcl2fastq pipeline was used to generate the sequence data
Read libraries were mapped to the GRCh37 (hg19) Human genome using HISAT2 (v2.0.4)
Gene-level quantitation (counts) of HISAT2 alignments was performed using SummarizeOverlaps
Transcript discovery and quantification (FPKM) of HISAT2 alignments was performed using StringTie (v1.3.0) and Ballgown
Genome_build: hg19
Supplementary_files_format_and_content: genecounts.csv file contains a matrix of raw gene counts (unfiltered and un-normalised data)
Submission date Jul 19, 2018
Last update date Nov 17, 2020
Contact name Emma de Jong
Organization name Telethon Kids Institute
Street address 15 Hospital Ave
City Nedlands, Perth
State/province WA
ZIP/Postal code 6009
Country Australia
Platform ID GPL13112
Series (1)
GSE117358 RNA-sequencing of pretreatment AB1 (mesothelioma) and Renca (kidney cancer) tumours mice both respondant and non-respondant to immunotherapy with CTLA4 and PD-L1
Alternative to GSM4658809
BioSample SAMN09691422
SRA SRX4408100

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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