|
Status |
Public on Feb 04, 2020 |
Title |
Adam10_Hom_Tumor_Rep2 |
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 |
SAMN13293629 |
SRA |
SRX7157617 |