|
| Status |
Public on Jul 01, 2015 |
| Title |
TCL1-AT monocytes 2 |
| Sample type |
RNA |
| |
|
| Source name |
Mouse spleen monocytes
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
age: 3 months
intervention: Transplantation with CLL
|
| Treatment protocol |
C57BL/6 mice transplanted with murine CLL cells and after 6 weeks total RNA from splenic monocytes (Lin- CD11b+ F4/80int CD11clow-int MHC-Iilow) from leukemic mice and WT controls was isolated.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted from sorted cells using the RNeasy Micro Kit (Qiagen) according to the manufacturer’s protocol
|
| Label |
biotin
|
| Label protocol |
The Illumina TotalPrep RNA Amplification Kit (life technologie) is used to generate single-stranded cRNA from input amounts of 150ng total RNA, Label: Biotin, Cy3-Streptavidin
|
| |
|
| Hybridization protocol |
Standard Illumina Hybridisation Protocol Part # 11322355 (Whole-Genome Gene Expression Direct Hybridization Assay Guide). 1,5 ug of cRNA were hybridized for 17 hr at 58°C on Illumina Mouse (WG-6)-Microarray.
|
| Scan protocol |
Gene Expression Microarrays were scanned using the Illumina iScan-Scanner according to Standard Illumina Scanning Protocol Part # 11322355 (Whole-Genome Gene Expression Direct Hybridization Assay Guide)
|
| Description |
Replicate 2
SAMPLE 2
|
| Data processing |
A cluster analysis using Euclidean distances and average linkage was performed to search for unwanted grouping effects. Intensity values were normexp-by-control background corrected and quantile normalized with control probes (Shi et al. 2010).
Probes that failed to reach a detection P-value of 0.05 on at least two arrays were filtered as not expressed. Linear regression models approach of Smyth (2004) was used to derive moderated statistics to compare WT with TCL1 monocytes. To correct for multiple testing p values were adjusted using the method of Benjamini and Hochberg (1995) to control the false discovery rate (FDR).
|
| |
|
| Submission date |
Mar 13, 2015 |
| Last update date |
Jul 01, 2015 |
| Contact name |
Bola Hanna |
| E-mail(s) |
[email protected]
|
| Organization name |
German Cancer Research Center
|
| Street address |
Im Neuenheimer Feld 280
|
| City |
Heidelberg |
| ZIP/Postal code |
69120 |
| Country |
Germany |
| |
|
| Platform ID |
GPL17543 |
| Series (1) |
| GSE66858 |
Gene expression profiling of splenic monocytes from TCL1-AT mice and WT controls |
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