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Sample GSM1152263 Query DataSets for GSM1152263
Status Public on Sep 11, 2014
Title Purified lung lavage macrophages Scnn1b-Tg, PND 42 germ-free, biological replicate 2
Sample type RNA
 
Source name Scnn1b-Tg, macrophages, germ-free facility
Organism Mus musculus
Characteristics strain: C57Bl/6N Tac
animal facility type: germ-free
genotype: Scnn1b-Transgenic
age (postnatal day): 42
Treatment protocol Mice are either wildtype or Scnn1b-transgenic and were harvested at post natal days 0, 3, 10, and 42. At PND 42 macrophages were also isolated from wildtype and Scnn1b-transgenic mice grown in a germ-free environment.
Growth protocol Mouse lung lavage macrphages purified by negative selection through from a Lys-6G column; mice grown either under specific-pathogen-free conditions in micro-isolator cages or in a germ-free environment
Extracted molecule total RNA
Extraction protocol Magnetic activated cell sorting uas used to purify macrophages from lung lavage samples using Ant-Ly-6G MicroBeads (Miltenyi Biotec, MA). Ly-6G negative cells (macrophages) were pelleted, snap-frozen and stored at -80 C. Frozen macrophage pellets were lysed and homogenized in lysis buffer and QIAshedder (Qiagen). Genomic DNA was eliminated using gDNA eliminator spin columns; RNA was isolated using Purelink RNA mini kits (Invitrogen).
Label biotin
Label protocol 12 ng of RNA was used to generate cDNA using Ovation Pico WTA system V2 kig (NuGEN Technologies, CA).
 
Hybridization protocol Hybridization was performed at 48 degrees using the GeneTitan plate system.
Scan protocol Affymetrix GeneChip Scanner 3000 7G
Description purified macrophages
Data processing CEL files were imported into Partek Genomics Suite v6.5, and exon-level log2 intensities were obtained through RMA background correction, GC content and sequence adjustment, quantile normalization, and median polish probeset summarization. Gene-level log2 intensity were summarized as the mean of exon probesets.
MoGene-1_1-st-v1.r4.pgf
MoGene-1_1-st-v1.r4.mps
 
Submission date May 31, 2013
Last update date Sep 12, 2014
Contact name Hong Dang
E-mail(s) dangh@email.unc.edu
Organization name UNC Chapel Hill
Department CF Center
Street address 7027 Thurston-Bowles Bldg. CB#7248
City Chapel Hill
State/province NC
ZIP/Postal code 27599
Country USA
 
Platform ID GPL11533
Series (2)
GSE47548 Gene expression in whole lung and pulmonary macrophages reflects the dynamic pathology associated with airway surface dehydration
GSE47551 mRNA expression data from either wild-type mice or Scnn1b-transgenic mice at post-natal days 0, 3, 10, and 42

Data table header descriptions
ID_REF
VALUE Mean log2 intensity from exon-level probesets, normalized by RMA background correction, GC content and sequence adjustment, quantile normalization, and median polish probeset summarization (Partek Genomics Suite v6.5).

Data table
ID_REF VALUE
10605884 4.57911
10411593 3.98518
10351644 5.56723
10461553 3.03951
10436128 3.26399
10411595 8.23288
10485979 2.64899
10545940 7.28791
10521515 2.94679
10486081 3.39366
10595900 6.87775
10485982 3.27276
10606001 8.62617
10461558 10.1622
10411609 8.75304
10595892 3.03628
10571467 2.97735
10411611 7.82632
10595895 3.31474
10546047 3.34157

Total number of rows: 35556

Table truncated, full table size 586 Kbytes.




Supplementary file Size Download File type/resource
GSM1152263_MAC_Scnn1b-Tg_PND42GF_rep2_HP391.CEL.gz 4.0 Mb (ftp)(http) CEL
Processed data included within Sample table

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