|
| Status |
Public on May 15, 2019 |
| Title |
BMDM_PBS_000 |
| Sample type |
RNA |
| |
|
| Source name |
BMDM_PBS
|
| Organism |
Mus musculus |
| Characteristics |
Sex: female
age: adult
cell type: bone marrow derived macrophages (BMDM)
treatment: PBS for 4hrs
|
| Treatment protocol |
BMDMs were exposed to LPS (1mg/ml), TcES (25ng/ml) or TcES plus LPS for 4 or 24 h. After these time points, total RNA was extracted using Qiazol and following the manufacters protocol.
|
| Growth protocol |
Bone marrow derived macrophages (BMDMs) were grown from bone marrow precursors incubated with M-CSF for 7 days.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
After a period of 4 or 24 h incubation with previously mention treatments, 500ul of Qiazol reagent (Qiagen) were added into the wells and upon 5 minutes at RT supernatants were transferred into new tubes with fresh cold chloroform (300 ul) gently mixed and left additional 10 min at RT. After samples were centrifugated (12,000 rpm 15 min), supernatants were mixed with 500 ul of ice cold isopropil alcohol and a final round of centrifugation conducted (12,000 rpm 5 min) pellets were left to dry, quantified by using nanodrop and normalized to 10 ng each sample. Quality was ensure with BioAnalyzer
|
| Label |
nanostring fluorescence barcode
|
| Label protocol |
n/a
|
| |
|
| Hybridization protocol |
n/a
|
| Scan protocol |
n/a
|
| Description |
BMDM_000
|
| Data processing |
Analysis of the NanoString data was done in R 3.2.5. Raw NanoString data was imported to R using NanoStringQCPro and normalized using NanoStringNorm. For technical variation was adjusted using the sum of positive controls, we then substracted the backgroung using the mean of negative controls and finally, we normalized RNA content using the geometric mean of the housekeeping genes.
|
| |
|
| Submission date |
Jan 16, 2019 |
| Last update date |
May 15, 2019 |
| Contact name |
Luis Ignacio Terrazas Valdes |
| E-mail(s) |
literrazas@unam.mx
|
| Organization name |
UNAM
|
| Street address |
Av. de los Barrios 1, colonia Los Reyes Iztacala
|
| City |
Tlalnepantla de Baz |
| State/province |
Estado de Mexico |
| ZIP/Postal code |
54090 |
| Country |
Mexico |
| |
|
| Platform ID |
GPL20885 |
| Series (2) |
| GSE125170 |
Taenia crassiceps excreted/secreted products alters the microRNA profile and regulates the pro-inflammatory response of M1 macrophages [mRNA] |
| GSE125172 |
Taenia crassiceps excreted/secreted products alters the microRNA profile and regulates the pro-inflammatory response of M1 macrophages |
|
