|
| Status |
Public on Jun 14, 2021 |
| Title |
BoC69 5dC1 |
| Sample type |
SRA |
| |
|
| Source name |
human colorectal tumor tissue, mouse stroma (PDX)
|
| Organisms |
Homo sapiens; Mus musculus |
| Characteristics |
treatment: 5 d cetuximab
|
| Treatment protocol |
Nude mice were treated with cetuximab (Merck Serono) by intra peritoneal (i.p.) injection twice per week and dosed at 25mg/kg, treatment was initiated when tumor size reached approx. 100-200 mm³
|
| Growth protocol |
Three 1-3 mm tumor pieces of early passage xenograft tumor soaked in matrigel were implanted via standard technology subcutaneously on the dorsal flanks of nude mice (two implantation sites per mouse; nu/nu NMRI) to establish treatment and control tumor cohorts.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA isolation from 25-30 (20mm) frozen xenograft tumor sections were isolates using the mirVana™ PARIS™ Kit (Applied Biosystems) according to the manufacture`s protocol. RNA integrity was analysed using standard RNA-gel electrophoresis. Total-RNA concentration and purity of total-RNA samples was measured with the NanoDrop 1000 spectrophotometer (NanoDrop Technologies/Thermo Scientific).
Sequencing libraries have been prepared with Lexogen QuantSeq 3' mRNA-Seq Library Prep Kit FWD for Illumina following the manufacturer's handbook.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Basecalling of raw sequencing output was performed with Illumina bcl2fast2 version 2.19.1.
For adapter sequence trimming in FASTQ files, fastp version 0.20.0 was used.
Cleaned read sequences were aligned with STAR version 2.7.3a.
Read assignment for exonic regions was performed with subread featureCounts version 2.0.0.
Fragment counts were generated with UMI-tools version 1.0.0.
Genome_build: GRCh37 and GRCm38
Supplementary_files_format_and_content: Raw fragment count data in tabular text file format.
|
| |
|
| Submission date |
Dec 11, 2019 |
| Last update date |
Jun 14, 2021 |
| Contact name |
Jakob Admard |
| Organization name |
Universitätsklinikum Tübingen
|
| Department |
Institut für Medizinische Genetik und Angewandte Genomik
|
| Street address |
Calwerstr. 7
|
| City |
Tübingen |
| ZIP/Postal code |
72076 |
| Country |
Germany |
| |
|
| Platform ID |
GPL25526 |
| Series (1) |
| GSE141861 |
Secondary Resistance to Anti-EGFR Therapy by Transcriptional Reprogramming in Patient-Derived Colorectal Cancer Models |
|
| Relations |
| BioSample |
SAMN13542062 |
| SRA |
SRX7348260 |
