|
| Status |
Public on Feb 04, 2020 |
| Title |
WT_Tumor_Control2 |
| Sample type |
SRA |
| |
|
| Source name |
CD104+ SCC Tumors
|
| Organism |
Mus musculus |
| Characteristics |
cell type: Primary tumor cells
marker: CD104+
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Zymoresearch RNA Extraction Kit.
RNA libraries were prepared for sequencing using standard Illumina protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
processed data file: Tumors_Adam10_KO_deseq2.xlsx
|
| Data processing |
Reads were aligned to mm10 using Hisat2 (2.1.0).
Raw reads obtained from bam files using featureCounts and mm10 annotation file from Ensembl (Mus_musculus.GRCm38.94.gtf).
DESeq2 package in R was used to determine differentially expressed genes between samples.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: *_deseq2.xlsx: Differential gene expression analysis
|
| |
|
| Submission date |
Nov 15, 2019 |
| Last update date |
Feb 04, 2020 |
| Contact name |
Daniel Schramek |
| E-mail(s) |
schramek@lunenfeld.ca
|
| Organization name |
Lunenfeld- Tanenbaum Research Institute
|
| Lab |
Schramek Lab
|
| Street address |
600 University Ave, Room 1080
|
| City |
Toronto |
| State/province |
ON |
| ZIP/Postal code |
M5G 1X5 |
| Country |
Canada |
| |
|
| Platform ID |
GPL19057 |
| Series (2) |
| GSE140495 |
In vivo CRISPR screens reveal NOTCH regulators suppressing Head and Neck Squamous Cell Carcinoma in mice [RNA-seq] |
| GSE140497 |
In vivo CRISPR screens reveal NOTCH regulators suppressing Head and Neck Squamous Cell Carcinoma in mice |
|
| Relations |
| BioSample |
SAMN13293634 |
| SRA |
SRX7157612 |
