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Sample GSM786290 Query DataSets for GSM786290
Status Public on Mar 27, 2012
Title 2UWTC
Sample type RNA
 
Source name Resting naïve CD4+ T cells (N) were purified to 95% purity from the spleens and lymph nodes of 4-6 week old WT Balb/c mice (Wt) using CD4+CD62L+ T cell Purification Kit II per manufacturer’s instructions (Miltenyi).
Organism Mus musculus
Characteristics cell type: Resting Th2 cells
strain: Balb/c
genotype/variation: wild type
Treatment protocol Resting Th2 cells (2U) were used.
Growth protocol Resting Th2 cells were prepared from resting naive cells by plating onto anti-CD3 (1ug/ml), anti-CD28 (2 ug/ml) coated plates at 1-2 x 106/ml in the presence of 10ng/ml IL-4, 10ug/ml anti-IFN-gamma. IL-2 (100U/ml) was added 24 hours later. Cultures were expanded in IL-2 (100U/ml) three days after initial culture.
Extracted molecule total RNA
Extraction protocol RNA was isolated using RNeasy Kit (Qiagen). Quality and quantity of the total RNA was checked with the Agilent 2100 bioanalyzer using RNA 6000 Nano chips.
Label Streptavidin-Cy3 bound to biotin-labeled cRNA.
Label protocol standard Illumina protocol using Illumina TotalPrep RNA Amplification Kit (Ambion; Austin, TX, cat # IL1791) In short, 0.5g of total RNA was first converted into single-stranded cDNA with reverse transcriptase using an oligo-dT primer containing the T7 RNA polymerase promoter site and then copied to produce double-stranded cDNA molecules. The double stranded cDNA was cleaned and concentrated with the supplied columns and used in an overnight in-vitro transcription reaction where single-stranded RNA (cRNA) was generated and labeled by incorporation of biotin-16-UTP.
 
Hybridization protocol standard Illumina protocol. In short, a total of 0.75ug of biotin-labeled cRNA was hybridized at 58 degrees C for 16 hours to Illumina's Sentrix HumanRef-8,v2 Expression BeadChips (Illumina, San Diego, CA). Each BeadChip has 24,000 well-annotated RefSeq transcripts with approximately 30-fold redundancy. The arrays were washed, blocked and the labeled cRNA was detected by staining with streptavidin-Cy3.
Scan protocol Arrays were scanned at a resolution of 0.8um using the Beadstation 500 X from Illumina.
Description Resting Th2 cells, wild type, replicate C
Data processing Data was extracted using the Illumina GenomeStudio software(v1.6.0). Any spots at or below the background intensity were filtered out using an Illumina detection p value of 0.02 and above. The natural log of all remaining scores were used to find the avg and std of each array and the z-score normalization was calculated and presented below. Z-score = (raw value - avg)/std. Complete data including detection p-values will be included in the supplemental file.
 
Submission date Aug 25, 2011
Last update date Jun 22, 2020
Contact name Supriyo De
Organization name NIA-IRP, NIH
Department Laboratory of Genetics and Genomics
Lab Computational Biology & Genomics Core
Street address 251 Bayview Blvd
City Baltimore
State/province Maryland
ZIP/Postal code 21224
Country USA
 
Platform ID GPL6885
Series (1)
GSE31676 IL-10 transcription is negatively regulated by BAF180, a component of the SWI/SNF chromatin remodeling enzyme

Data table header descriptions
ID_REF
RAW_VALUE raw intensity value from Beadstudio software
VALUE Z transformation of the natural log of the raw intensity values

Data table
ID_REF RAW_VALUE VALUE
ILMN_1212607
ILMN_1212612
ILMN_1212619
ILMN_1212628
ILMN_1212632 40 -0.535483396
ILMN_1212636 553.1 2.490122874
ILMN_1212637 78.4 0.239670416
ILMN_1212645 43.3 -0.444169906
ILMN_1212648 74.2 0.176247952
ILMN_1212653 46 -0.374493884
ILMN_1212672 74.9 0.187063842
ILMN_1212682
ILMN_1212683
ILMN_1212685
ILMN_1212692 47 -0.349721236
ILMN_1212693 51.6 -0.24216516
ILMN_1212695 40.3 -0.526876504
ILMN_1212698
ILMN_1212702 47.9 -0.327872416
ILMN_1212703 46.7 -0.357097251

Total number of rows: 25697

Table truncated, full table size 593 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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