|
| Status |
Public on Jan 24, 2017 |
| Title |
Tet2 deficient macrophage, biological replicate 2 |
| Sample type |
RNA |
| |
|
| Source name |
Tet2 deficient macrophage
|
| Organism |
Mus musculus |
| Characteristics |
strain background: C57BL/6J
genotype/variation: Tet2-/- mice
cell type: Thioglycollate-elicited macrophages from the peritoneal cavity of mice.
treated with: LPS and IFNg for 10 hr
|
| Treatment protocol |
Isolated macrophages were treated with a combination of 10 ng/ml LPS and 2 ng/ml IFNg for 10 hours.
|
| Growth protocol |
After 4-days of 1mL aged 4% Brewer's thyoglycollate injection (i.p.), peritoneal macrophages were isolated from C57BL/6J Tet2-deficient (Tet2-/-) mice or wildtype littermates, plated on standard cell culture plates in RPMI supplemented with antibiotics and 10% FBS.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted with an AllPrep DNA/RNA Mini Kit Print (Qiagen) and treated with Rnase-free Dnase I kit (Qiagen), according to manufacturer’s instructions.
|
| Label |
Biotin
|
| Label protocol |
Whole-transcript expresion profiling experiments were carried out by the Boston University Microarray Core Facility. Biotyinated DNA was prepared per manufactureer's recommendaton
|
| |
|
| Hybridization protocol |
Fragmented, biotinylated DNA samples were hybridized on 6 mouse Gene 2.0ST arrays.
|
| Scan protocol |
A total of 6 array images were acquired by GeneChip Scanner 3000TG and quality assesed bty Affymetrix Expression Console (Santa Clara, CA)
|
| Description |
KW_226
|
| Data processing |
Mouse Gene 2.0 ST CEL files were normalized to produce gene-level expression values using the implementation of the Robust Multiarray Average (RMA) [1] in the affy package (version 1.36.1) [2] included in the Bioconductor software suite (version 2.12) [3] and an Entrez Gene-specific probeset mapping (17.0.0) from the Molecular and Behavioral Neuroscience Institute (Brainarray) at the University of Michigan [4,5]. Array quality was assessed by computing Relative Log Expression (RLE) and Normalized Unscaled Standard Error (NUSE) using the affyPLM package (version 1.34.0)
References:
1. PMID 12925520; 2. PMID 14960456; 3. PMID 15461798; 4. PMID 16284200
5. http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF
6. Brettschneider J, Collin F, Bolstad BM, and Speed TP. Quality Assessment for Short Oligonucleotide Microarray Data. Technometrics 2008 50(3):241, doi:10.1198/004017008000000334
|
| |
|
| Submission date |
May 12, 2016 |
| Last update date |
Jan 25, 2017 |
| Contact name |
Chia-Ling Wu |
| E-mail(s) |
[email protected]
|
| Organization name |
Boston University
|
| Department |
Whitaker Cardiovascular Institute
|
| Lab |
Walsh
|
| Street address |
700Albany St
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02118 |
| Country |
USA |
| |
|
| Platform ID |
GPL17791 |
| Series (1) |
| GSE81398 |
Expression data from LPS/IFNgamma-treated Tet2-/- and Tet2+/+ mouse macrophages. |
|
