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Sample GSM2339236 Query DataSets for GSM2339236
Status Public on May 23, 2018
Title Dicer KO BMDMs, Replicate 1
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 1. of 3 BMDMs from LysM-Cre/Dicerflox/flox/Apoe–/– mice
Sample name: Macrophage-KO1
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
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
VALUE qBase-software computed normalized and scaled signal

Data table
mmu-let-7a-4373169 0.117467481
mmu-let-7b-4373168 0.107618649
mmu-let-7c-4373167 0.144219018
mmu-let-7d-4395394 0.174584817
mmu-let-7e-4395517 0.181998694
mmu-let-7f-4373164 0.167047852
mmu-let-7g-4395393 0.110210481
mmu-let-7i-4395332 0.160873656
mmu-miR-1-4395333 0.230206424
mmu-miR-100-4373160 6.747407684
mmu-miR-101a-4395364 0.111259467
mmu-miR-103-4373158 0.05842245
mmu-miR-105-4395595 6.747407684
mmu-miR-106a-4395589 0.166854982
mmu-miR-106b-4373155 0.185694115
mmu-miR-107-4373154 0.43951978
mmu-miR-10a-4373153 0.118202572
mmu-miR-10b-4395329 0.005882588
mmu-miR-122-4395356 6.747407684
mmu-miR-124-4373295 0.419865746

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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