|
Status |
Public on Dec 06, 2017 |
Title |
IW2036 |
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 |
SAMN08133977 |
SRA |
SRX3445536 |