|
| Status |
Public on Jun 01, 2021 |
| Title |
1_LPS_Mse_BMDM [nanopore] |
| Sample type |
SRA |
| |
|
| Source name |
Primary Bone Marrow Derived Macrophages, Day 8
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
cell type: Primary BMDM
treatment: 100ng/ml LPS for 6hrs
age: 10 weeks
genotype: wild type
|
| Treatment protocol |
Treat cells with 100ng/ml LPS for 6hrs.
|
| Growth protocol |
Harvest bone marrow from mice, lyse all red blood cells and differentiate hematopoietic stem cells for 8 days using MCSF from L929 cell line. Grow cells in DMEM 10% FCS 10%MCSF, Pen/strep
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Remove all media, pipette in 400ul of TriReagent into cell culture dish. Isolate RNA using Zimogen kit.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
MinION |
| |
|
| Description |
counts_matrix
|
| Data processing |
ONT albacore version 2.1.0 was used to baseball Nanopore direct RNA raw signal
We used minimap2 with default parameters to align reads to the mm10 mouse genome reference
We used SAMtools to filter-out reads with mapping quality (MAPQ) less than 30
Genome_build: mm10
|
| |
|
| Submission date |
Dec 10, 2019 |
| Last update date |
Jun 01, 2021 |
| Contact name |
Sergio Covarrubias |
| E-mail(s) |
[email protected]
|
| Phone |
2132710156
|
| Organization name |
UCSC
|
| Department |
MCD
|
| Lab |
Carpenter
|
| Street address |
Thimann Receiving/Department Carpenter Lab/Biomed 125, 1156 High St., Thimann Labs
|
| City |
Santa Cruz |
| State/province |
CA |
| ZIP/Postal code |
95064 |
| Country |
USA |
| |
|
| Platform ID |
GPL24973 |
| Series (2) |
| GSE141750 |
Inflammation drives alternative first exon usage of critical immune genes including Aim2 [nanopore] |
| GSE141754 |
Inflammation drives alternative first exon usage of critical immune genes including Aim2 |
|
| Relations |
| BioSample |
SAMN13523047 |
| SRA |
SRX7299336 |
