|
| Status |
Public on Jul 10, 2024 |
| Title |
DNTCF4-Vector-2 (RNA-seq) |
| Sample type |
SRA |
| |
|
| Source name |
breast tumor
|
| Organism |
Mus musculus |
| Characteristics |
tissue: breast tumor
cell line: CCN6KOT
cell type: Breast Cancer cell line
condition: Spindle Metaplastic
treatment: Lentivirus-DNTCF4
|
| Treatment protocol |
treatment with puromycin
|
| Growth protocol |
CCN6KOT primary Cells were growth in DMEM/F12 10%FBS and transduced with lentivirus of DNTCF4 construct and control followed by puromycin selection
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were collected trypsin and then RNA extracted using QIAGEN RNA protocol.
Qiagen RNA protocol for cells.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
7975-MG-5
|
| Data processing |
The reads were trimmed using Cutadapt v2.3
FastQC v0.11.8 was used to ensure the quality of data
Reads were mapped to the reference genome GRCm38 (ENSEMBL), using STAR v2.7.8a and assigned count estimates to genes with RSEM v1.3.3
Data were pre-filtered to remove genes with 0 counts in all samples.
Differential gene expression analysis was performed using DESeq2
Assembly: GRCm38
Supplementary files format and content: tab delimited text file containing raw counts
Supplementary files format and content: tab delimited text file containing rlog normalized counts
|
| |
|
| Submission date |
Dec 19, 2023 |
| Last update date |
Jul 10, 2024 |
| Contact name |
Bioinformatics Core |
| E-mail(s) |
bioinformatics@umich.edu
|
| Organization name |
University of Michigan
|
| Street address |
BRCF Bioinformatics Core, 2800 Plymouth Rd
|
| City |
Ann Arbor |
| State/province |
Mi |
| ZIP/Postal code |
48109-2800 |
| Country |
USA |
| |
|
| Platform ID |
GPL24247 |
| Series (2) |
| GSE250538 |
CCN6/WISP3 suppresses metaplastic breast carcinoma by antagonizing a WNT/b-catenin/EZH2 cascade [RNA-seq] |
| GSE250575 |
CCN6/WISP3 suppresses metaplastic breast carcinoma by antagonizing a WNT/b-catenin/EZH2 cascade |
|
| Relations |
| BioSample |
SAMN38931834 |
| SRA |
SRX22969569 |
