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Sample GSM2101749 Query DataSets for GSM2101749
Status Public on Sep 14, 2016
Title WT BMM, Mtb 48h, rep 1
Sample type RNA
Source name WT BMM, Mtb 48h
Organism Mus musculus
Characteristics strain: C57BL/6
genotype/variation: WT
cell type: BMM
infection: Mtb H37Rv strain (MOI 5)
timepoint: 48h
series: timecourse
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 4, 8, 24, or 48 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 WT 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
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)
GSE79731 Gene expression data from Mycobacterium tuberculosis-infected WT and miR-155-/- bone-marrow derived macrophages [timecourse]
GSE79733 Gene expression data from Mycobacterium tuberculosis-infected WT and miR-155-/- bone-marrow derived macrophages

Data table header descriptions
VALUE log2, gene-level, RMA normalized signal

Data table
100008567_at 5.857941672
100009600_at 5.144548523
100009609_at 3.54173438
100009614_at 5.287752944
100009664_at 4.481853295
100012_at 4.808967744
100017_at 10.54862286
100019_at 8.034201378
100033459_at 9.456519986
100034251_at 12.24655873
100034739_at 5.136270743
100034748_at 5.777123198
100036520_at 6.438972872
100036521_at 7.055862284
100036523_at 6.934416131
100036537_at 4.57181761
100036768_at 5.973313919
100037258_at 9.743588417
100037260_at 4.675736106
100037262_at 6.462272575

Total number of rows: 23243

Table truncated, full table size 489 Kbytes.

Supplementary file Size Download File type/resource
GSM2101749_20130308_wt_bmm_Mtb_MOI5_48h_1.CEL.gz 22.6 Mb (ftp)(http) CEL
Raw data provided as supplementary file
Processed data included within Sample table

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