|
| Status |
Public on Dec 16, 2018 |
| Title |
2240T |
| Sample type |
SRA |
| |
|
| Source name |
Spalax fibrosarcoma
|
| Organism |
Nannospalax ehrenbergi |
| Characteristics |
specimen_id: spalax_2240
diagnosis: fibrosarcoma
Sex: F
treatment: 3MCA
time of operation after treatment: 18 months
tissue: muscle
sample side: injected side
|
| Extracted molecule |
total RNA |
| Extraction protocol |
1ug of total RNA was used to construct the libraries using the TruSeq Small RNA Sample Prep kit (Illumina). The strand-specific RNAseq libraries were prepared with Illumina's 'TruSeq Stranded RNA Sample Prep kit'.
The libraries were pooled in equimolar concentration and the pool was quantitated by qPCR and sequenced on one lane (small RNAs) or two lanes (RNAseq) for 101 cycles on a Illumina HiSeq 2500 using a TruSeq SBS sequencing kit version 4. Fastq files were generated and demultiplexed with with the bcl2fastq v1.8.4 Conversion Software (Illumina)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
Sp2240T
Sp2240T_GGCTAC_L00M
processed data file: counts_spalax_16samples.csv
|
| Data processing |
FASTQ files were receiven from Mark Band, USA
repeated runs concatenated
Mapping of read pairs using TopHat (v1.4.1)
Read counting using HTSeq, annotation from BioMart mouse reference
Normalisation using R-package DESeq
Genome_build: Spalax genome: RefSeq/GenBank assembly accession GCF_000622305.1; mouse: GRCm38
Supplementary_files_format_and_content: comma seperated values (csv) with normalized read counts
|
| |
|
| Submission date |
Jul 23, 2018 |
| Last update date |
Dec 16, 2018 |
| Contact name |
Robert Altwasser |
| Organization name |
Max-Delbrück-centrum
|
| Department |
AG Di Virgilio
|
| Street address |
Robert-Rössle-Str. 10
|
| City |
Berlin |
| ZIP/Postal code |
13125 |
| Country |
Germany |
| |
|
| Platform ID |
GPL25363 |
| Series (2) |
| GSE117499 |
The transcriptome landscape of the carcinogenic treatment response in the blind mole rat: Insights into cancer resistance mechanisms [RNA-seq] |
| GSE117501 |
The transcriptome landscape of the carcinogenic treatment response in the blind mole rat: Insights into cancer resistance mechanisms |
|
| Relations |
| BioSample |
SAMN09703514 |
| SRA |
SRX4417148 |
