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Sample GSM2339238 Query DataSets for GSM2339238
Status Public on May 23, 2018
Title Dicer KO BMDMs, Replicate 3
Sample type RNA
 
Source name Dicer knockout bone marrow-derived macrophages
Organism Mus musculus
Characteristics tissue: bone marrow
cell type: macrophages
genotype: LysM-Cre/Dicerflox/flox/Apoe–/–
age: 6-8 weeks
Sex: Male
Growth protocol mouse bone marrow-derived macrophages were cultured in DMEM-F12/10% FCS/10% L929-conditioned medium, at 37°C in a humidified atmosphere of 5% CO2
Extracted molecule total RNA
Extraction protocol mirVana miRNA Isolation Kit, see manufacturer's web site
Label FAM
Label protocol cDNA was obtained by TaqMan MicroRNA Reverse Transcription Kit (Applied Biosystems) and amplified by TaqMan PreAmp Master Mix (Applied Biosystems)
 
Hybridization protocol N/A
Scan protocol N/A
Description Biological replicate 3. of 3 BMDMs from LysM-Cre/Dicerflox/flox/Apoe–/– mice
Sample name: Macrophage-KO3
Data processing The Applied Biosystems TaqMan Rodent miRNA A+B Cards Set v3.0 (catalog number 4444909) was used for this study. Taqman low density arrays were run on the 7900HT Fast Real-Time PCR System. The ABI TaqMan SDS v2.4 software was utilized to obtain raw CT values. To review results, the raw CT data (SDS file format) were exported from the Plate Centric View into the ABI TaqMan RQ manager software. Automatic baseline and manual CTs were calculated with the RQ Manager Software for all samples. Statistical analysis: The global data set of miRNAs from card A and B was used for analysis. Data were calculated using qBase software. Input data for analysis consisted of all samples. CT values were normalized to multiple endogenous controls (snoRNA202, snoRNA135 and MammU6 for Card A, snoRNA202, snoRNA135, MammU6 and snoRNA429 for Card B).
normalization: qBase-software computed signal (target gene signal normalized to endogenous controls and then scaled to WT group); Fold_Change: KO/WT
 
Submission date Oct 06, 2016
Last update date May 23, 2018
Contact name Andreas Schober
E-mail(s) aschober@med.lmu.de
Organization name Ludwig-Maximilians-University
Department Institute for Cardiovascular Prevention
Street address Pettenkoferstr. 9
City Munich
State/province Bavaria
ZIP/Postal code 80336
Country Germany
 
Platform ID GPL18082
Series (2)
GSE87718 miRNA expression profiles in Dicer WT and KO bone marrow-derived macrophages
GSE87721 Ago2-RIP-chip and miRNA expression profile in Dicer WT and KO macrophages from bone marrow or aorta

Data table header descriptions
ID_REF
VALUE qBase-software computed normalized and scaled signal

Data table
ID_REF VALUE
mmu-let-7a-4373169 0.099925729
mmu-let-7b-4373168 0.212077969
mmu-let-7c-4373167 0.179991415
mmu-let-7d-4395394 0.181956648
mmu-let-7e-4395517 0.3561771
mmu-let-7f-4373164 0.297095776
mmu-let-7g-4395393 0.326238737
mmu-let-7i-4395332 0.118969748
mmu-miR-1-4395333 0.231272666
mmu-miR-100-4373160 0.530343871
mmu-miR-101a-4395364 0.253958852
mmu-miR-103-4373158 0.13530934
mmu-miR-105-4395595 0.530343871
mmu-miR-106a-4395589 0.45638818
mmu-miR-106b-4373155 0.227457146
mmu-miR-107-4373154 0.07162796
mmu-miR-10a-4373153 0.309712174
mmu-miR-10b-4395329 0.046145486
mmu-miR-122-4395356 0.530343871
mmu-miR-124-4373295 0.0330013

Total number of rows: 596

Table truncated, full table size 18 Kbytes.




Supplementary data files not provided
Raw data are available on Series record
Processed data included within Sample table
Processed data are available on Series record

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