|
| Status |
Public on Jan 26, 2024 |
| Title |
Lung, Sample 6 |
| Sample type |
SRA |
| |
|
| Source name |
Lung
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Lung
cell line: N/A
cell type: Small cell lung cancer
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
2% Agarose gel electrophoresis followed by DNA purification
one-step PCR
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
raw_cell_number_for_6_samples.csv
|
| Data processing |
Quality controls of fastq files (fastqc software).
Merge paired-end reads (PANDA-seq software)
Reads filtering and trimming for barcode clustering (DADA2 software)
Training of error model on known sequences (DADA2 software)
Downstream analysis (GC correction, tumor size, tumor number and other quantifications - tuba-seq package )
Assembly: mm39
Supplementary files format and content: Cell numbers accumulated across all six samples used in tuba sequencing.
Library strategy: Tuba-seq (Tumor barcoding sequencing)
|
| |
|
| Submission date |
Jul 27, 2023 |
| Last update date |
Jan 26, 2024 |
| Contact name |
Pawel Karol Mazur |
| E-mail(s) |
pkmazur@mdanderson.org
|
| Organization name |
University of Texas MD Anderson Cancer Center
|
| Street address |
1515 Holcombe Blvd.
|
| City |
Houston |
| State/province |
TX |
| ZIP/Postal code |
77030 |
| Country |
USA |
| |
|
| Platform ID |
GPL21103 |
| Series (2) |
| GSE239440 |
In vivo multiplexed screen reveals a critical role of Keap1/Nrf2 pathway in small cell lung cancer [TUBAseq] |
| GSE239441 |
In vivo multiplexed screen reveals a critical role of Keap1/Nrf2 pathway in small cell lung cancer |
|
| Relations |
| BioSample |
SAMN36730712 |
| SRA |
SRX21173449 |
