|
| Status |
Public on May 30, 2024 |
| Title |
700_NoDox_Plastic |
| Sample type |
SRA |
| |
|
| Source name |
Small intestine
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Small intestine
cell type: Organoid
genotype: Smad4KO;BRAFV600E/+;pINDUCER-SMAD4
treatment: Untreated
|
| Treatment protocol |
Vehicle or 4ug/mL doxycycline
|
| Growth protocol |
Organoids were passaged and cultured in 1x CCM for 48 hours prior to collection for RNA-Seq.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Organoids were collected and resuspended in Trizol. RNA was extracted using the RNeasy Kit (QIAGEN).
1ug of RNA was submitted to BGI for library construction
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
BGISEQ-500 |
| |
|
| Data processing |
Files were processed using Kallisto and DESeq2 for differential gene expression analysis. Genes were filtered for significantly regulated genes (Log2FC > 1.0 or < -1.0, adjp-value <0.05)
Assembly: mm9
Supplementary files format and content: TXT files include FPKM and DESeq readouts (Dox vs. NoDox) for samples
|
| |
|
| Submission date |
May 10, 2023 |
| Last update date |
May 30, 2024 |
| Contact name |
Kevin Tong |
| E-mail(s) |
kevin.tong@hmh-cdi.org
|
| Organization name |
Hackensack Meridian Health
|
| Department |
CDI
|
| Street address |
111 Ideation Way
|
| City |
Nutley |
| State/province |
NJ |
| ZIP/Postal code |
07110 |
| Country |
USA |
| |
|
| Platform ID |
GPL23479 |
| Series (2) |
| GSE232137 |
In vitro organoid-based assays reveal SMAD4 tumor-suppressive mechanisms for serrated colorectal cancer invasion [RNA-seq] |
| GSE232138 |
In vitro organoid-based assays reveal SMAD4 tumor-suppressive mechanisms for serrated colorectal cancer invasion |
|
| Relations |
| BioSample |
SAMN35021415 |
| SRA |
SRX20276840 |
