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Sample GSM775345 Query DataSets for GSM775345
Status Public on Aug 10, 2011
Title Mouse_sham_1
Sample type RNA
Source name whole liver RNA, control
Organism Mus musculus
Characteristics strain: CD1
tissue: liver
cell type: endothelial cells
treatment: sham surgery
phenoytpe: no cirrhosis
Treatment protocol Common bile duct ligation or sham surgery.
Growth protocol Standard mouse housing conditions.
Extracted molecule total RNA
Extraction protocol miR-VANA miRNA Isolation Kit (Ambion).
Label biotin
Label protocol GeneChip® One-Cycle Target Labeling.
Hybridization protocol GeneChip® Hybridization.
Scan protocol Affymetrix® GeneChip® Scanner.
Description miRNA expression.
Data processing Data were analyzed using the Affymetrix® miRNA QC Tool Software using the default analysis.

Probe-specific signal detection calls: Each probe on an array is assayed for detection. For miRNA probes, detection is based on a Wilcoxon Rank-Sum test of the miRNA probe set signals compared to the distribution of signals from GC-content-matched anti-genomic probes. If the resulting p-value for the probes is p=0.06, it is considered “detected above background”.

Background estimation and correction: The same set of anti-genomic probes used to determine detection calls are used to estimate GC-content-matched background signals. Each miRNA probe signal has a GC-content-matched background estimate subtracted from its value. This GC-specific background contribution is estimated by the median signal from the distribution of GC-matched anti-genomic probes. The resulting value may be negative at this stage, if the probe’s signal is less than the median value of the GC-matched anti-genomic probes. The same process can be applied using two other ways to match main content probes to background probes: a) by GC percent and b) by both GC content and probe length.

Constant Variance Stabilization on probes: Probe level constant variance stabilization is based on adding a small constant to all of the intensities. The default value of this constant is 16.

Normalization: Probe-level normalization is provided via quantile, mean array scaling, and mean array scaling (based on normalization probes) normalization algorithms.

Summarization: This process provides the quantification of probe intensities into probe set intensities (via mean, median or RMA methods).
Submission date Aug 09, 2011
Last update date Aug 10, 2011
Contact name Robert Christian Huebert
Organization name Mayo Clinic
Department Gastroenterology and Hepatology
Lab Vijay Shah
Street address 200 1st Street SW
City Rochester
State/province MN
ZIP/Postal code 55905
Country USA
Platform ID GPL8786
Series (1)
GSE31293 MicroRNA Expression Data From Sham or BDL CD1 Mouse Liver

Data table header descriptions
VALUE Quantification of normalized probe intensity

Data table
ID_REF VALUE p-value Detection
mmu-let-7a_st 12.56428 2.05E-08 TRUE
mmu-let-7a-star_st 4.11721 0.618265 FALSE
mmu-let-7b_st 13.74992 2.05E-08 TRUE
mmu-let-7b-star_st 5.274446 0.002168356 TRUE
mmu-let-7c_st 14.20574 2.05E-08 TRUE
mmu-let-7c-1-star_st 3.807348 0.8241195 FALSE
mmu-let-7c-2-star_st 3.574626 0.872807 FALSE
mmu-let-7d_st 13.15348 2.05E-08 TRUE
mmu-let-7d-star_st 6.117097 4.34E-05 TRUE
mmu-let-7e_st 12.43658 2.05E-08 TRUE
mmu-let-7f_st 8.967966 2.13E-08 TRUE
mmu-let-7f-star_st 4.672554 0.04387686 TRUE
mmu-let-7g_st 9.324127 2.05E-08 TRUE
mmu-let-7g-star_st 4.036801 0.1467868 FALSE
mmu-let-7i_st 11.47281 2.05E-08 TRUE
mmu-let-7i-star_st 5.386144 0.005003998 TRUE
mmu-miR-1_st 4.459149 0.1400978 FALSE
mmu-miR-100_st 9.172668 2.05E-08 TRUE
mmu-miR-101a_st 4.482809 0.1250967 FALSE
mmu-miR-101a-star_st 4.151904 0.2263308 FALSE

Total number of rows: 609

Table truncated, full table size 24 Kbytes.

Supplementary file Size Download File type/resource
GSM775345.CEL.gz 168.3 Kb (ftp)(http) CEL
Processed data included within Sample table

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