|
| Status |
Public on Jan 12, 2023 |
| Title |
SCC10-PDX2 |
| Sample type |
SRA |
| |
|
| Source name |
sorted cSCC-PDX cells
|
| Organism |
Homo sapiens |
| Characteristics |
group: Control
disease state: Cutaneous squamous cell carcinoma
tissue: Tumor
|
| Treatment protocol |
When tumors were detectable (approximately 380 mm3), mice were randomly assigned to a control or inhibitor treatment group, and were orally treated with gefitinib, or vehicle every 48 hours. Intrinsically resistant cSCC34-PDXs were continuously treated with gefitinib. Mice carrying cSCC10-, cSCC16- and cSCC24-PDXs received 21 doses of gefitinib, which showed a stable and significant reduction of tumor growth. Then, treatment was halted in these mice, allowing tumor relapse. Samples of relapsed tumors were engrafted in new NSG mice, and when they were detectable were again treated with gefinitib for one or two cycles more to test the acquisition of gefitinib resistance.
|
| Growth protocol |
cSCC-PDX samples were engrafted on NOD-scid IL2Rgamma null (NSG) mice and tumor volume was monitored every 2 days during the treatment
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from FACS-sorted tumor cells by using RNAesay Mini Kit (Qiagen). RNA quality was assessed by Agilent 2100 Bioanalyzer (Agilent Technologies).
RNA libraries were prepared for sequencing using standard Illumina TruSeq protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
H10B
2018-08-01_PMunoz_RNAseq_hg38_allsamples_raw_counts
|
| Data processing |
Strand-specific 50-bp paired-end reads were generated using a HiSeq 2500 sequencer (Illumina).
The quality of the fastq files was checked using the FastQC and the Qualimap (rnseq module – version 2.2.1) software
An estimation of ribosomal RNA in the raw data was obtained with riboPicker (version 0.4.3)
Reads were aligned with the STAR mapper (version 2.5.2a) to release 88 of the Homo sapiens ENSEMBL version of the genome (GRCh38/hg38 assembly).
A raw count of reads per gene was also obtained with STAR (quantMode GeneCounts option).
Genome_build: GRCh38/hg38
Supplementary_files_format_and_content: From the fastq files were generated two excel files that contain the number of counts for each gene in the different analyzed samples. The file "2018-08-01_PMunoz_RNAseq_hg38_allsamples_raw_counts" contains the counts corresponding to the cSCC10-, cSCC16- and cSCC24-PDXs, and the file "2019-10-11_PMunoz_RNAseq_hg38_allsamples_raw_counts" contains the counts corresponding to the cSCC34-PDX. The RNA-seq of all the models analysed has been carried out by the same laboratory located at the Genomic Unit in the Genomic Regulation Center (CRG), Barcleona. All data was generated and processed under the same criteria and using the same tools as the models were generated
|
| |
|
| Submission date |
Jan 13, 2020 |
| Last update date |
Jan 12, 2023 |
| Contact name |
Purificación Muñoz |
| E-mail(s) |
p.munoz@idibell.cat
|
| Organization name |
IDIBELL
|
| Street address |
Av Gran Vía de L'Hospitalet 199-203
|
| City |
Barcelona |
| ZIP/Postal code |
08908 |
| Country |
Spain |
| |
|
| Platform ID |
GPL16791 |
| Series (1) |
| GSE143588 |
Characterization of the mechansims involved in resistance to EGFR inhibitors |
|
| Relations |
| BioSample |
SAMN13839612 |
| SRA |
SRX7551070 |
