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Sample GSM298997 Query DataSets for GSM298997
Status Public on Jun 20, 2008
Title LLsh4_2
Sample type RNA
 
Source name LL-sh4
Organism Homo sapiens
Characteristics LL-sh4
Treatment protocol The cells were activated with plate bound anti-CD3 and anti-CD28 for 48 hours.
Growth protocol Human primary CD4+ T cells were isolated from peripheral blood and cultured in IL-2 containing medium.
Extracted molecule total RNA
Extraction protocol RNA was isolated with RNeasy columns (Qiagen)
Label biotin
Label protocol labelling was performed according to the Affymetrix (Santa Clara, CA) GeneChip Whole Transcript (WT) Sense Target Labelling Assay manual
 
Hybridization protocol microarrays were hybridized overnight with 5 mg biotin labelled ss-cDNA, and washed in fluidics station wash protocol: MES_EukGE-WS2v5_450
Scan protocol Genechip scanner 3000 7G
Description FileNumber: 1
Data processing The input files were normalized with full quantile normalization (Irizarry et al 2003). For each input array, for each probe expression value, the array ith percentile probe value was replaced with the average of all array ith percentile points. Next, the 6,553,590 probes were manipulated into the analysis values as follows. Probes with GC count less than 6 and greater than 17 were excluded from the analysis. Probe scores were then transformed by taking the Natural Logarithm of 0.1 plus the probe score. Background CorrectionExon arrays do not use individual mis-match probes. Background is established from a pool of probes designed for that purpose. Background probes are stratified by CG content and are defined in the Human Exon 1.0 ST_antigenomic.bgp file. BGP files can also be downloaded from www.affymetrix.com. Each probe score was corrected for background by subtracting the median expression score of background probes with similar GC content. The Human Exon 1.0 ST array contains 1,404,693 probe-sets (typically, but not always, groups of four probes). Probe-set Expression Scores and Annotation FilteringThe expression score for a probe-set was defined to be the median of its probe expression scores and probe-sets with fewer than 1 probes (that pass all of the tests defined above) are excluded from further analysis. Exon Array Probes are designed off of genomic sequence and hence the reliability of probes and probe-sets correspond to the quality of their parent genomic annotations. Probe-set reliability is ranked from more to less reliable as Core, Extended, or Full. For example 'Core' probe-sets include probe-sets that correspond to high quality genomic features like RefSeq (www.ncbi.nlm.nih.gov) or Ensembl (www.ensembl.org) transcripts while 'full' and 'extended' probe-sets match less reliable annotations like EST hits and gene prediction algorithms. For this analysis, only 'Core' probe-sets were analyzed.
 
Submission date Jun 19, 2008
Last update date Jun 19, 2008
Contact name Shalini Oberdoerffer
E-mail(s) shalini.oberdoerffer@nih.gov
Phone 301-846-7104
Organization name National Cancer Institute
Street address 1050 Boyles Street
City Frederick
State/province MD
ZIP/Postal code 21702
Country USA
 
Platform ID GPL5188
Series (2)
GSE11833 LL-sh4/uninfected/shGFP ANOVA group
GSE11834 HnRNPLL is a global regulator of alternative splicing in activated T cells

Data table header descriptions
ID_REF
VALUE Expression values derived as described above in data processing

Data table
ID_REF VALUE
2390602 2.71380803704415
2390601 3.81539391819931
2390600 3.85086221065101
2390599 3.90725843495392
2390598 2.87729872286098
2390597 3.56944751330729
2390596 4.47078328070496
2390595 3.95618671989427
2315374 4.5818635126202
2315375 3.83585918264868
2315376 5.0741116604681
2315377 4.27711730786221
2390982 5.30285619906805
2390981 4.42537343377686
2390980 3.93887650833437
2390979 4.58070418569957
2390978 4.96747868572366
2390977 4.37734878900591
4054626 2.27433395901765
4054625 2.96088648495726

Total number of rows: 272678

Table truncated, full table size 6601 Kbytes.




Supplementary file Size Download File type/resource
GSM298997.CEL.gz 21.2 Mb (ftp)(http) CEL
Processed data included within Sample table

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