|
| Status |
Public on Dec 06, 2017 |
| Title |
IW2158 |
| Sample type |
SRA |
| |
|
| Source name |
Unique mouse tranduced with multiplexed lentiviral library for Tuba-seq analysis
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Whole Lung Extract
cell type: Lung Epithelium, heterogenous progression to adenocarcinoma
weeks of tumor growth: 15
genotype: KPTC
treatment: Tranduced with Lenti-sgTS/Pool
|
| Treatment protocol |
n.a.
|
| Growth protocol |
Tumors were transduced in mice via Cre & Cas9-mediated genome editing via intratracheal intubation of lentivirus
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Mice were humanely sacrificed, then barcodes were PCR-amplified from DNA extract derived from whole lungs harboring multiplexed tumors
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit and multiplexed by mouse sample.
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
Library strategy: Tuba-seq
Data was processed using the Tuba-seq analysis pipeline developed for the novel method detailed in this publication
See https://github.com/petrov-lab/tuba-seq
Fastq files were filtered & trimmed using preprocess.py
Barcode pileups were clustered using DADA2_clustering.R, trained via DADA2_error_training.R, and merged with postprocess.py
Bias of sizes by GC-content of barcode was corrected using a 4th-order polynomial, as described in manuscript
Tumors were called using a minimum cell size of 500 cells (unless otherwise specified in the manuscript) and a clustering proclivity of OMEGA_A = 1e-10
Genome_build: Custom Lentiviral Amplicon
|
| |
|
| Submission date |
Dec 05, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Christopher Dennis McFarland |
| E-mail(s) |
cdm286@gmail.com
|
| Phone |
518-860-2834
|
| Organization name |
Stanford University
|
| Department |
Cancer Systems Biology
|
| Lab |
Dmitri Petrov & Monte Winslow
|
| Street address |
2647 Alpine RD
|
| City |
Menlo Park |
| State/province |
CA |
| ZIP/Postal code |
94025 |
| Country |
USA |
| |
|
| Platform ID |
GPL21103 |
| Series (1) |
| GSE107716 |
The fitness landscape of tumor suppression in lung adenocarcinoma in vivo |
|
| Relations |
| BioSample |
SAMN08133974 |
| SRA |
SRX3445539 |
