|
Status |
Public on Jul 18, 2019 |
Title |
Renca Responder rep12 [RZ71] |
Sample type |
SRA |
|
|
Source name |
Renca_Responder
|
Organism |
Mus musculus |
Characteristics |
host strain: balb/c host mouse age: 8-9 weeks host mouse gender: female tumor cells: Renca tumor type: kidney cancer treatment: anti-CTLA4 plus anti-PDL-1 timepoint: day 0 - pretreatment response to immunotherapy: Responder rna 260/280: 2 rna 260/230: 2.1
|
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 |
RZ71_CAPNMANXX_ACTGAT_L003
|
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 2.18.0.12 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 |
E-mail(s) |
emma.dejong@uwa.edu.au
|
Organization name |
University of Western Australia
|
Street address |
35 Stirling Hwy
|
City |
Crawley, 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 |
|
Relations |
Alternative to |
GSM4658951 |
BioSample |
SAMN09691424 |
SRA |
SRX4408146 |