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Sample GSM1079825 Query DataSets for GSM1079825
Status Public on Apr 10, 2013
Title KO_12.2_U
Sample type RNA
Source name Mesencymal stem cell line
Organism Mus musculus
Characteristics cell type: Mesencymal stem cell line clone 12.2
genotype: Dicer-/-
differentiation status: undifferentiated
Treatment protocol To determine gene expression alterations induced Dicer loss, the cells were infected with Adeno-Cre-GFP, sorted for GFP to enrich for infected cells, and plated at low density for monoclonal isolation. Homozygous deletion within clones was confirmed by genotyping PCR. For isolation of total RNA, cells were passaged under normal culture conditions.
Growth protocol Primary mesenchymal stem cells were isolated from the hindlimb bone marrow of a one-year old Dicerflox/flox mouse, transduced with retrovirus encoding SV40 Large T Antigen for immortalization, and then plated at low density for monoclonal isolation. Cells were cultured in Alpha-MEM supplemented with pen/strep and 10% fetal bovine serum. The MIT Institutional Animal Care and Use Committee approved all animal studies and procedures.
Extracted molecule total RNA
Extraction protocol RNA was extracted using Qiazol (Qiagen).
Label biotin
Label protocol Affymetrix GeneChip® WT Sense Target Labeling
Hybridization protocol Performed according to manufacturer's instructions (Affymetrix) for Affymetrix Mouse Exon 1.0 ST arrays.
Scan protocol Affymetrix Gene ChIP Scanner 3000 7G; GeneChip® Command Console.
Data processing Data processing was done using Partek Genomics Suite 6.5 software. RMA was used to summarize and normalize the probe data into probe set expression values. The list of utilized probe sets was defined by custom .ps and .mps files. The RMA procedure used included the options adjust for GC content, probe sequence, RMA background correction, Quantile Normalization and median polish probe set summarization. Expression values for probesets were summarized to a single value per gene based on the custom file MoEx-1_0-st-v1._core+miRNA+RfSq+UCSC_.SH.2916.mps. The outlier excluded mean method was used. This procedure excludes probe set values that are more than 3 standard deviations above the mean or more and 2 standard deviations below the mean.
probe group file: MoEx-1_0-st-v1.r2.pgf
probe set file:
meta-probeset file: MoEx-1_0-st-v1._core+miRNA+RfSq+UCSC_.SH.2916.mps
Submission date Feb 07, 2013
Last update date Apr 10, 2013
Contact name A Bhutkar
Organization name MIT
Street address 77 Massachusetts Avenue
City Cambridge
State/province MA
ZIP/Postal code 02139
Country USA
Platform ID GPL6096
Series (2)
GSE44161 Let-7 represses Nr6a1 and a mid-gestation developmental program in adult fibroblasts [Exon array]
GSE44163 Let-7 represses Nr6a1 and a mid-gestation developmental program in adult fibroblasts

Data table header descriptions
VALUE Quantile normalized gene level expression values in log2 space from Partek Genomics Suite 6.5.

Data table
7008252 3.64593
6898252 2.58444
6823768 7.05448
6823769 2.41262
6898253 3.25996
6933677 10.6351
6958212 2.61316
6933678 7.73287
6933679 9.63985
6848296 2.24619
6958215 2.64329
6983639 2.61525
6958216 8.66593
6788351 6.62593
6788352 3.25507
6823777 6.85803
6898262 2.04455
6763829 2.35514
6823778 2.66798
6898263 2.48483

Total number of rows: 44343

Table truncated, full table size 688 Kbytes.

Supplementary file Size Download File type/resource
GSM1079825_AA124_KO_12.2_U.CEL.gz 21.8 Mb (ftp)(http) CEL
Processed data included within Sample table

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