|
| Status |
Public on Nov 26, 2024 |
| Title |
EXP_ 9.11_D_Tumor_only_timepoint 2_3_R1 |
| Sample type |
SRA |
| |
|
| Source name |
D
|
| Organism |
Mus musculus |
| Characteristics |
cell line: D
treatment: Tumor_only
|
| Growth protocol |
Cells were cultured in RPMI medium (Gibco) supplemented with 100 U/ml penicillin and 100 µg/ml streptomycin (Gibco), 10% fetal bovine serum (FBS) (Capricorn Scientific), 50 µM β-mercaptoethanol (Sigma-Aldrich) and 2500 U/ml Interleukin-2 (Miltenyi Biotec)
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
AllPrep DNA/RNA Mini Kit (Qiagen)
DNA barcodes were amplified with a three nested PCR step protocol
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
The analysis workflow took place in R v.4.0.3. Reads were loaded into R environment as DNAStringSet object and barocodes were located with the aid of vmatchPattern() from Biostrings v.2.58.0. Differentiall abundance was carried out using DESeq2 v.1.30.0.
Assembly: n/a
Supplementary files format and content: Excel worksheet file containing barcode counts tables per cell line and experiment.
Library strategy: DNA amplicon sequencing
|
| |
|
| Submission date |
Sep 25, 2024 |
| Last update date |
Nov 26, 2024 |
| Contact name |
Aleksandr Bykov |
| E-mail(s) |
[email protected]
|
| Organization name |
CCRI
|
| Department |
BiCU
|
| Street address |
Zimmermannpl. 10
|
| City |
Vienna |
| ZIP/Postal code |
1090 |
| Country |
Austria |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE278011 |
NK cell cytotoxicity shapes the clonal evolution of B cell leukemia [DNA barcoding] |
|
| Relations |
| BioSample |
SAMN43929289 |
| SRA |
SRX26200525 |
