|
| Status |
Public on Jul 18, 2019 |
| Title |
AB1 Non-responder rep1 [AB02] |
| Sample type |
SRA |
| |
|
| Source name |
AB1_Non-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: Non-responder
rna 260/280: 2.05
rna 260/230: 2.21
|
| 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 |
AB02_CAF66ANXX_CGATGT_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 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@telethonkids.org.au
|
| 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 |
|
| Relations |
| Alternative to |
GSM4658810 |
| BioSample |
SAMN09691421 |
| SRA |
SRX4408101 |
