|
| Status |
Public on Aug 25, 2023 |
| Title |
SG32 PDX dBET6 treated 2 |
| Sample type |
SRA |
| |
|
| Source name |
Adenoid cystic carcinoma PDX
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Adenoid cystic carcinoma PDX
treatment: 5 mg/kg dBET6
|
| Treatment protocol |
Once tumours reached 100-200mm3, animals were allocated to receive either 5 mg/kg of dBET6 or vehicle, twice daily by IP injection for at least 4 days.
|
| Growth protocol |
ACC sample SG32 single cells were injected subcutaneously into the flank of NSG mice.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Snap frozen tissue was homogenised in Trizol using the Precellys cyrolysis system. The aqueous phase was isolated and transferred to a Qiagen Mini kit column following which kit protocol was followed. At least 500ng of RNA was used for library prep.
RNA libraries for RNA-seq were prepared usingUltra II Directional RNA Library Prep Kit for Illumina (New England Biolabs) following manufacturer's protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 2000 |
| |
|
| Data processing |
Read mapping was performed using the STAR alignment software (v.2.7.6a) to Ensembl Human and Mouse reference genomes (Ensembl Human reference genome version GRCh38.92 and Ensembl Mouse reference genome version GRCm38.83)
Once the reads were mapped, XenofilteR R package was used to remove mouse reads from human alignments.
After the filtering, HTSeq-count (HTSeq v2.0.2) was used to count the number of reads mapping unambiguously to genomic features in each sample.
Assembly: Ensembl Human reference genome version GRCh38.92
Supplementary files format and content: tab deliminated text files; normalised counts from DESeq in excel format
|
| |
|
| Submission date |
Jul 14, 2023 |
| Last update date |
Aug 25, 2023 |
| Contact name |
Amanda Swain |
| E-mail(s) |
amanda.swain@icr.ac.uk
|
| Organization name |
The Institute of Cancer Research
|
| Street address |
237 Fulham Road, 3n17
|
| City |
London |
| State/province |
London |
| ZIP/Postal code |
SW36JB |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL30173 |
| Series (1) |
| GSE237382 |
Cell-type-specific tumour sensitivity identified with a bromodomain targeting PROTAC in adenoid cystic carcinoma. |
|
| Relations |
| BioSample |
SAMN36451761 |
| SRA |
SRX21024187 |
