|
| Status |
Public on Sep 14, 2016 |
| Title |
miR-155-/- BMM, Mtb 8h, rep 1, val |
| Sample type |
RNA |
| |
|
| Source name |
miR-155-/- BMM, Mtb 8h
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
genotype/variation: miR-155-/- (B6.Cg-MiR-155tm1.1Rsky/J)
cell type: BMM
infection: Mtb H37Rv strain (MOI 5)
timepoint: 8h
series: validation
|
| Treatment protocol |
On day 7, BMM were infected with Mtb H37Rv strain (MOI 5), followed by washing 2X with PBS. BMM were infected with H37Rv for 8 hours prior to RNA extraction.
|
| Growth protocol |
Bone marrow-derived macrophages (BMM) were cultured in complete RPMI (cRPMI; plus 10% FBS, 2 mM l-glutamine, penicillin and streptomycin) with recombinant human CSF-1 (50 ng/ml) for 6 days.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from cells using TRIzol (Invitrogen) according to manufacturer's instructions. Prior to labeling, sample integrity was checked using an Agilent 2100 Bioanalyzer.
|
| Label |
biotin
|
| Label protocol |
Total RNA samples were labeled as described in the Whole Transcript Sense Target Labeling protocol (Affymetrix)
|
| |
|
| Hybridization protocol |
Samples were hybridized according to the Whole Transcript Sense Target Labeling protocol: Heat cocktail mix at 99°C for 5 minutes, 45°C for 5 minutes, and then centrifuge at 13,200g for 1 minute. Transfer 200uL of hyb solution to each array. Hybridize 16 hours at 45°C at 60rpm. Wash and stain using fluidics protocol FS450_0001.
|
| Scan protocol |
Affymetrix Gene ChIP Scanner 3000 7G
|
| Description |
Mtb-infected miR-155-/- BMM
|
| Data processing |
Microarrays were normalized at the gene level using the BrainArray custom CDF (Entrez Gene, Version 14) for probeset definitions and RMA as implemented in the justRMA function of the Bioconductor package affy for background adjustment, quantile normalization and summarization.
BrainArray version 14: MoEx10stv1_Mm_ENTREZG
|
| |
|
| Submission date |
Mar 30, 2016 |
| Last update date |
Sep 14, 2016 |
| Contact name |
Aderem Lab |
| E-mail(s) |
[email protected]
|
| Organization name |
Seattle Children's Research Institute
|
| Lab |
Aderem Lab
|
| Street address |
307 Westlake Avenue North, Suite 500
|
| City |
Seattle |
| State/province |
WA |
| ZIP/Postal code |
98109 |
| Country |
USA |
| |
|
| Platform ID |
GPL13712 |
| Series (2) |
| GSE79732 |
Gene expression data from Mycobacterium tuberculosis-infected WT and miR-155-/- bone-marrow derived macrophages [validation] |
| GSE79733 |
Gene expression data from Mycobacterium tuberculosis-infected WT and miR-155-/- bone-marrow derived macrophages |
|
