|
| Status |
Public on Jun 17, 2021 |
| Title |
Early lesions #4 |
| Sample type |
SRA |
| |
|
| Source name |
Indolent lesions
|
| Organism |
Mus musculus |
| Characteristics |
source name abbreviation: EL
strain: FVB
tissue: Mammary gland
pool: 4
batch (sample prep): 2
sequence id: 18042R-01-09
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Tumor cells were homogenized using a Bullet Blender (Next Advance) and RNA extracted (Qiagen RNeasy Kit). RNA was treated with DNase (Turbo DNA-Free Kit), and then cleaned and concentrated (Zymo RNA Cleanup Kit), per manufacturers’ instructions
RNA libraries were prepared according to manufacturer's instructions for NEBNext® Ultra™ RNA Library Prep Kit for Illumina, NEBNext® Poly(A) mRNA Magnetic Isolation Module
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
HiSeq X Ten |
| |
|
| Description |
9
|
| Data processing |
alignment and gene count by STAR (version 2.6.0b)
gene annotation used GENCODE M19 (Ensembl 94)
differential expression analysis carried out in R (3.6.0) using Bioconductor package DESeq2
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-deliminated data matrix of normalized gene counts
|
| |
|
| Submission date |
Nov 23, 2020 |
| Last update date |
Jun 17, 2021 |
| Contact name |
Yuan Qi |
| E-mail(s) |
[email protected]
|
| Organization name |
University of Texas M.D. Anderson Cancer Center
|
| Department |
Bioinformatics & Computational Biology
|
| Street address |
1400 Pressler St
|
| City |
Houston |
| State/province |
TX |
| ZIP/Postal code |
77030-4008 |
| Country |
USA |
| |
|
| Platform ID |
GPL21273 |
| Series (2) |
| GSE162005 |
Transcriptional profiling of indolent and aggressive mammary lesions |
| GSE162006 |
Profiling of indolent and aggressive mammary lesions |
|
| Relations |
| BioSample |
SAMN16873947 |
| SRA |
SRX9556832 |
