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Sample GSM433817 Query DataSets for GSM433817
Status Public on Dec 31, 2009
Title Control (WT) A
Sample type RNA
 
Source name mouse lung
Organism Mus musculus
Characteristics strain: C57BL/6
genotype/variation: wild type
age: 6-8 wks old
gender: male
tissue: whole lung
treatment: Control
time: n/a
Extracted molecule total RNA
Extraction protocol RNA was extracted with Trizol reagent followed by purification and DNase I treatment using QIAGEN RNeasy mini kit according to manufacturer's protocol. Quality control was performed with an Agilent Bioanalyzer.
Label biotin
Label protocol Biotinylated cRNA was prepared using the Ambion MessageAmp kit for Illumina arrays.
 
Hybridization protocol Standard Illumina hybridization protocol
Scan protocol Standard Illumina scanning protocol
Description replicate 1
Data processing The data were normalized using in-house software described in Grigoryev et, Identification of candidate genes in scleroderma-related pulmonary arterial hypertension. Transl Res 151(4):197-207. Briefly, the significance (P>0.95) of hybridization signals were tested and “Present” and “Absent” transcripts identified. The chip background and brightness were computed using high quartile and whole set of “Absent” hybridization signals, respectively. The expression data was stratified by experimental conditions (n=3) and hybridization of each transcript was evaluated. The transcripts that had P>0.95 and produced signal at least twice as high as that of background in at least 75% of hybridizations in any given group of mice were considered Present. The signal intensity values of these transcripts from each chip were background adjusted and divided by a chip brightness coefficient for normalization. Only Present values are reported and used for Significance Analysis of Microarrays (SAM) analysis.
 
Submission date Jul 27, 2009
Last update date Oct 19, 2010
Contact name Dmitry N Grigoryev
E-mail(s) dgrigor1@jhmi.edu
Phone 410 550 1557
Organization name JHU
Lab HopGene
Street address
City Baltimore
State/province MD
ZIP/Postal code 21224
Country USA
 
Platform ID GPL4865
Series (1)
GSE17355 Regulatory T cell-mediated resolution of lung injury: Identification of potential target genes via expression profiling

Data table header descriptions
ID_REF
VALUE log2 normalized signal

Data table
ID_REF VALUE
18S_rRNA_X00686_523-S 4.064
GI_21070949-S 4.716
GI_21746160-S -0.46
GI_23346428-S -1.086
GI_23592945-S 5.159
GI_28476905-S 4.327
GI_31982339-S -0.9611
GI_46909570-S 1.517
GI_6671508-S 5.659
GI_6679936-S 2.991
GI_7106304-S -0.9811
IGHA_J00475$V00785_Ig_heavy_constant_alpha_135-S -0.7404
IGHM_V00818_Ig_heavy_constant_mu_941-S 0.6713
IGHV1S114_L33955_Ig_heavy_variable_1S114_205-S -0.8026
IGHV1S119_L33961_Ig_heavy_variable_1S119_14-S -0.7501
IGHV1S136_AF304557_Ig_heavy_variable_1S136_154-S -0.9697
IGHV1S63_L26853_Ig_heavy_variable_1S63_4-S -1.256
IGHV3S2_M12435_Ig_heavy_variable_3S2_32-S -0.9956
IGHV5S17_U04227_Ig_heavy_variable_5S17_185-S -1.299
IGHV5S18_AF290972_Ig_heavy_variable_5S18_125-S -0.7138

Total number of rows: 13029

Table truncated, full table size 322 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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