|
| Status |
Public on May 15, 2024 |
| Title |
7053-GB-3 |
| Sample type |
SRA |
| |
|
| Source name |
breast adenocarcinoma cell line
|
| Organism |
Mus musculus |
| Characteristics |
tissue: breast adenocarcinoma cell line
cell line: D2.OR
cell type: murine mammary gland adenocarcinoma
treatment: one week culture in 2% FBS prior to sorting CTFR+/-
|
| Treatment protocol |
D2.0R cells were labeled with cell trace far red and 2e6 were plated in each T150 flask with 20 mL of DMEM with 2% FBS and 1x glutamax and cultured for 1 week before CTFR+ quiescent cells and CTFR- proliferative cells were FACS sorted.
|
| Growth protocol |
D2.0R cells were maintained in DMEM with 10% FBS and 1x glutamax
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
RNA was isolated using the Rneasy Qiagen kit
Libraries were prepared by the University of Michigan Advanced Genomics Core
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
CTFRpos-1, -2, -3, bulk-1, -2, -3, CTFRneg -1,-2,-3
|
| Data processing |
Reads were trimmed using Cutadapt v2.3
FastQC v0.11.8 was used to ensure quality of data
Fastq Screen was used to screen for various types of contamination
Reads were mapped to the reference genome GRCm38 using STAR v2.7.8a and assigned count estimates to genes with RSEM v1.3.3. Alignment options followed ENCODE standards for RNA-seq
Multiqc v2.7 compiled the results from several of these tools and provided a detailed and comprehensive quality control report
Assembly: GRCm38
Supplementary files format and content: txt file is the expected counts for each gene
|
| |
|
| Submission date |
May 15, 2024 |
| Last update date |
May 15, 2024 |
| Contact name |
Grace Bushnell |
| E-mail(s) |
ggb@umich.edu
|
| Organization name |
University of Michigan
|
| Department |
Internal Medicine
|
| Lab |
Wicha Lab
|
| Street address |
2800 Plymouth Rd NCRC B26
|
| City |
Ann Arbor |
| State/province |
MI |
| ZIP/Postal code |
48109 |
| Country |
USA |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE267583 |
Natural killer cell regulation of breast cancer stem cells mediates metastatic dormancy |
|
| Relations |
| BioSample |
SAMN41407031 |
| SRA |
SRX24567501 |
