|
| Status |
Public on Sep 30, 2020 |
| Title |
4T1 |
| Sample type |
SRA |
| |
|
| Source name |
tumor
|
| Organism |
Mus musculus |
| Characteristics |
genotype: Rosa26-LSL-EWSR1-ATF1
|
| Treatment protocol |
no pharmacological treatments
|
| Growth protocol |
genetically induced tumors
|
| Extracted molecule |
total RNA |
| Extraction protocol |
harvested and snap frozen at primary tumor morbidity
Illumina TruSeq Stranded RNA Kit with Ribo-Zero Gold
ribosomal RNA depletion
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
16216X7: 4T1 (column header information in raw counts file)
|
| Data processing |
RTA v1.18.61 used for basecalling.
Trim adapters with cutadapt, Align to mm10 with STAR -2.7.5a
Generate count matrices with featureCounts and RSEM
Perform differential expression with DESeq2
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
|
| |
|
| Submission date |
Sep 29, 2020 |
| Last update date |
Sep 30, 2020 |
| Contact name |
Jinxiu Li |
| Organization name |
China Agricutural University
|
| Department |
College of biological sciences
|
| Lab |
State key laboratories of Agrobiotechnology
|
| Street address |
Yuanmingyuan west road 2#
|
| City |
Beijing |
| State/province |
Beijing |
| ZIP/Postal code |
100193 |
| Country |
China |
| |
|
| Platform ID |
GPL24247 |
| Series (2) |
| GSE158725 |
RNAseq comparing mouse Cre-loxP-induced EWSR1-ATF1 expression from Rosa26 versus Ewsr1-Atf1 translocation |
| GSE158726 |
Cre-loxP-induced Ewsr1-Atf1 translocation tumors |
|
| Relations |
| BioSample |
SAMN16288728 |
| SRA |
SRX9212198 |
