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Sample GSM572410 Query DataSets for GSM572410
Status Public on Jul 13, 2011
Title Stem cell memory (TSCM) cells from Donor#1 [exon-level]
Sample type RNA
Source name CD8+ T cells
Organism Homo sapiens
Characteristics cell type: CD8+ T cells
cd8+ t cell subset: TSCM
donor: 1
Treatment protocol N/A
Growth protocol Peripheral blood mononuclear cells (PBMC) were isolated from lymphocyte-enriched apheresis blood (provided by the NIH Blood Bank) according to standard techniques and used immediately for cell sorting. CD8+ T cells were enriched from PBMC by using the EasySep CD8+ T cell enrichment kit (Stem Cell Technologies), stained with different combinations of fluorescent-labeled monoclonal antibodies and sorted with a FACSAria (BD Biosciences) in different live (Live/Dead-; Invitrogen) CD8+ T cell subsets, as follows: TN (CD45RO-, CD45RA+, CCR7+, CD27+, CD62L+, CD11a dull, CD95-), TSCM (CD45RO-, CD45RA+, CCR7+, CD27+, CD62L+, CD11a dull, CD95+), TCM (CD45RO+, CD62L+, CCR7+) and TEM (CD45RO+, CD62L-, CCR7-), generating 12 samples total.
Extracted molecule total RNA
Extraction protocol RNEasy Micro kit (Qiagen), following manufatcturer's instructions
Label biotin
Label protocol WT expression kit (Ambion), WT Terminal Labeling Kit (Affymetrix), according to the manufatcturer's instructions
Hybridization protocol Samples were hybridized to WT Human Gene 1.0 ST arrays using Affymetrix hybridization kit materials, according to the manufacturrer's instructions. Sample cocktails were heated at 99°C for 5 minutes, then 45°C for 5 minutes, centrifuged at max speed for 1 minute. Eighty ul of hyb solution was transferred to each array, and hybridized 17 hours at 45°C at 60rpm. Fluidics washing protocol used was FS450_0007.
Scan protocol Arrays were scanned on a GeneChip Scanner 3000 7G (Affymetrix).
Description FACS-sorted CD8+ T cell subset derived from healthy blood donor
Donor#1 TSCM
Donor#1 Tcd95_(HuGene-1_0-st-v1).CEL
Data processing In all processing steps, samples were processed at the same time as a single batch. Raw data from the generated .CEL files were imported into Partek Genomincs Suite using the RMA method.
For exon-level analysis, exons differentially expressed between groups (i.e. genes subject of alternative splicing) were identified using Partek's Alternative Splicing ANOVA (p<0.05) supported by the Benjamini-Hochberg correction method for multiple comparisons allowing for a false discovery rate of <0.05.
For gene-level analyses, probeset level data were merged into gene-level datasets based on median probeset signal level.
Differentially expressed genes (DEGs) were identified by One-Way Repeated Measures ANOVA (p<0.01) corrected by Benjamini-Hochberg's False Discovery Rate method (p<0.05), resulting in a gene list of 900 DEGs. For pair wise comparisons between all possible sample pairs (e.g. TN vs. TSCM, etc), this gene list was further filtered for between-group alpha levels of p<0.01 and a fold change criterion of >2.0. By additional filtration of the 900 significant genes, a separate list of DEGs, displaying gradually changing expression levels along with the process of memory cell differentiation, i.e. in the TN -> TSCM -> TCM -> TEM direction, direction, was also identified. Finally, a limited list of common DEGs significant when comparing T naive CD95+ cells with all three other T cell populations individually was also described using slightly modified selection criteria; One-Way Repeated Measures ANOVA (p<0.05) corrected by Benjamini-Hochberg's False Discovery Rate method (p<0.05).
Exon-level analysis_probe group file: HuGene-1_0-st-v1.r4.pgf
Transcript-level analysis_meta-probeset file: HuGene-1_0-st-v1.r4.mps
Submission date Jul 29, 2010
Last update date Jul 13, 2011
Contact name Zoltan Pos
Phone +(36)12102930-56435
Organization name Semmelweis University
Department Dept. of Genetics, Cell- and Immunobiology
Street address 4 Nagyvarad ter
City Budapest
ZIP/Postal code H-1089
Country Hungary
Platform ID GPL10739
Series (1)
GSE23321 Expression data from human naïve (TN), stem cell memory (TSCM), central memory (TCM) and effector memory (TEM) CD8+ T cells
Affiliated with GSM572422

Data table header descriptions
VALUE Log 2-transformed RMA signal intensities from Partek GS

Data table
7896737 6.95951
7896739 5.31664
7896741 6.09317
7896743 9.28223
7896745 7.01222
7896747 9.24872
7896749 9.77752
7896751 4.48358
7896753 9.9493
7896755 8.48428
7896757 6.37598
7896758 6.48062
7896760 7.59427
7896762 11.0156
7896763 6.26738
7896764 5.78025
7896765 3.85785
7896766 7.91035
7896767 6.30586
7896768 10.1012

Total number of rows: 253002

Table truncated, full table size 3925 Kbytes.

Supplementary data files not provided
Processed data included within Sample table

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