|
| Status |
Public on Jan 11, 2024 |
| Title |
171R-NIC/p66Low (Parental) |
| Sample type |
SRA |
| |
|
| Source name |
Mammary fat pad
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Mammary fat pad
strain: FVB/N
disease state: mammary tumor
genotype: NIC/p66Low
phenotype: Parental
Sex: female
|
| Treatment protocol |
Orthotopic injections were performed in 8- to 12-week-old FVB/N mice for NIC cells, using 250,000 NIC cells per mouse suspended in a 1:1 mixture of PBS and matrigel (VWR, CACB354234). The area of the fourth mammary fat pad was depilated and sterilized before suspended cells were injected into the fat pad itself through a small incision. Subcutaneous carpofen and topical lidocaine were applied as analgesics.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using RNeasy Midi Kit (QIAGEN).
Library preparation was performed using the rRNA-depleted stranded (HMR) kit according to instruction from the manufacturer
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
171R-NIC_p66Low_parental
|
| Data processing |
Raw reads were trimmed using Trimmomatic v0.32. First, adaptors and other Illumina-specific sequences from each read were removed using palindrome mode. Then, a four-nucleotide sliding window removes the bases once the average quality within the window falls below 30. Next, the first four bases at the start of each read were removed. Finally, reads shorter than 30 base pairs were dropped.
Cleaned reads were aligned to the mouse reference genome build mm10 using STAR v2.3.0e with default settings. Reads mapping to more than 10 locations in the genome (MAPQ < 1) were discarded.
Gene expression levels were estimated by quantifying primary alignments mapping to at most 2 locations (MAPQ >= 3) to exonic regions (the maximal genomic locus of each gene and its known isoforms) using featureCounts v1.4.4 and the mm10 ensGene annotation set from Ensembl.
Assembly: mm10
Supplementary files format and content: tab separated file containing the raw exonic counts for each sample using the mm10 Ensembl annotation set.
|
| |
|
| Submission date |
May 31, 2023 |
| Last update date |
Jan 11, 2024 |
| Contact name |
Claudia L Kleinman |
| E-mail(s) |
claudia.kleinman@mcgill.ca
|
| Phone |
514-340-8222 25139
|
| Organization name |
Lady Davis Institute for Medical Research
|
| Department |
Human Genetics
|
| Street address |
3999 Côte Ste-Catherine Road
|
| City |
Montréal |
| State/province |
Québec |
| ZIP/Postal code |
H3T 1E2 |
| Country |
Canada |
| |
|
| Platform ID |
GPL21103 |
| Series (1) |
|
| Relations |
| BioSample |
SAMN35540138 |
| SRA |
SRX20546971 |
