|
| Status |
Public on Dec 16, 2020 |
| Title |
AL609-CL |
| Sample type |
SRA |
| |
|
| Source name |
Liver tumors
|
| Organism |
Mus musculus |
| Characteristics |
protocol: Hydrodynamic tail-vein injection method
strain: C57BL/6
mutations: MYC;sg-Axin1
tissue: Cell line
passage: 8-10 passages
|
| Treatment protocol |
no treatment
|
| Growth protocol |
hydrodynamic tail vein delivery
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Trizol® (Invitrogen) followed by digestion with DNase I (Roche) and purification with the RNeasy Kit (Qiagen).
TruSeq RNA Sample Preparation
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
RNA-seq
|
| Data processing |
We first assessed the quality of paired-end reads with FASTQC (version 0.11.8). Next, we filtered reads with BBDUK from BBTOOLS (version 37.53) to remove adapters, known artefacts and then quality trimmed (PHRED quality score < 10). Reads that became too short after trimming (N < 60 bp) were discarded. We did not retain singleton reads (i.e., reads whose mate has been discarded). We estimated the transcript-level quantification of cleaned RNA-seq data using SALMON (version 1.0.0) by a quasi-mapping on Mus musculus GRCm38. We estimated the gene-level quantification using tximport library and converted mouse gene expression to human gene expression using biomaRt library.
Genome_build: GRCm38
Genome_build: Mus_musculus.GRCm38.cds.all.fa.gz (ENSEMBL)
|
| |
|
| Submission date |
Apr 09, 2020 |
| Last update date |
Dec 16, 2020 |
| Contact name |
Tiphaine Christiane Martin |
| E-mail(s) |
tiphaine.martin@mssm.edu
|
| Phone |
2128248403
|
| Organization name |
Icahn School of Medicine at Mount Sinai, Tisch Cancer Institute
|
| Department |
Oncological Sciences
|
| Lab |
Parsons
|
| Street address |
1470 Madison Ave
|
| City |
New York |
| State/province |
75459 |
| ZIP/Postal code |
10029 |
| Country |
USA |
| |
|
| Platform ID |
GPL21103 |
| Series (1) |
| GSE148379 |
Cooperation between distinct cancer drivers dictates inter-tumor heterogeneity in hepatocellular carcinoma |
|
| Relations |
| BioSample |
SAMN14567549 |
| SRA |
SRX8090121 |
