|
| Status |
Public on Jun 26, 2019 |
| Title |
HDN 3 |
| Sample type |
SRA |
| |
|
| Source name |
Neutrophils isolated from peripheral blood
|
| Organism |
Mus musculus |
| Characteristics |
strain: Balb/c
gender: Female
age: 8 weeks
|
| Extracted molecule |
total RNA |
| Extraction protocol |
TriZol + RNeasy mini Kit (Qiagen, #74106)
KAPA Stranded RNA-Seq PolyA (KAPA Biosystems)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
Neutrophil_Cnts_070109.csv
|
| Data processing |
Base calling was performed with Illumina RTA 1.17.21.3. Base calls were then demultiplexed and converted to FASTQ using Illumina Casava 1.8.2.
Read trimmer was done by Trimmomatic
Alignment was performed by using STAR
Read counter was analyzed using STAR counts
Differential gene expression was analyzed using DESeq2 (version 1.16.1)
Genome_build: h19 genome
|
| |
|
| Submission date |
Dec 11, 2018 |
| Last update date |
Jun 26, 2019 |
| Contact name |
Brian Hsu |
| E-mail(s) |
brian.hsu@mail.mcgill.ca
|
| Phone |
5149935989
|
| Organization name |
McGill University
|
| Department |
Medicine
|
| Lab |
Peter Siegel
|
| Street address |
1160 Pine Avenue West
|
| City |
Montréal |
| State/province |
QC |
| ZIP/Postal code |
H3A1A3 |
| Country |
Canada |
| |
|
| Platform ID |
GPL13112 |
| Series (1) |
| GSE123669 |
Immature low-density neutrophils exhibit metabolic flexibility that facilitates breast cancer liver metastasis |
|
| Relations |
| BioSample |
SAMN10581964 |
| SRA |
SRX5126325 |
