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Sample GSM3488971 Query DataSets for GSM3488971
Status Public on Mar 29, 2020
Title Tmem_lvempty_B
Sample type RNA
 
Source name primary T lymphocytes derived from human peripheral blood mononuclear cells (PBMC)
Organism Homo sapiens
Characteristics cell type: memory T lymphocytes
culture conditions: transduced with lv-empty, supplemented with IL-2 (50 U/ml)
Treatment protocol Cells were selected for transduction with puromycin (2ug/ml, Sigma-Aldrich). Before collection, samples were treated for 3h with PMA/ionomycin.
Growth protocol memory T lymphocytes were isolated by magnetic enrichment for CD4 (Miltentyi Biotec) and sorted for CD4+CD25-CD45RA-CCR7+/-. Cells were activated with plate-bound aCD3 and aCD28 for 2 days, before removed from stimuli and transduced with the indicated lentiviral constructs. Cells were cultured another 10 days and from day 5 on IL-2 (50 U/ml, provided by the institute) was added to the media.
Extracted molecule total RNA
Extraction protocol Memory T cells were resuspended in Trizol and total RNA was extracted with Direct-Zol RNA mini Prep (Zymo Research)
Label biotin
Label protocol 50ng of total RNA were labelled with the nCounter® Immunology Panel (Human V2) codeset according to the manufacturers protocol
 
Hybridization protocol Samples were hybridized overnight at 65C
Scan protocol Samples were run on a Nanostring Sprint Profiler
Description Human peripheral blood mononuclear cells were separated from peripheral blood using Ficoll-Paque Plus (GE Healthcare). CD4+ T lymphocytes were further isolated by positive selection using magnetic microbeads (Miltenyi Biotec). Memory T cell subsets were then sorted based on the expression of the following surface markers: CD4+CD25–CD45RA-CCR7+-.
nCounter® Immunology Panel (Human V2)
Data processing Raw data was processed with nSolver 3.0 Software (Nanostring). Reads were normalized to internal postive & negative controls and to included housekeeping genes. Genes were considered expressed if the sum of reads in one of the transduction groups was >150. Differential expression and p-values were calculated within the nSolver 3.0 software
 
Submission date Nov 26, 2018
Last update date Mar 29, 2020
Contact name Chiara Balestrieri
E-mail(s) balestrieri.c@gmail.com
Organization name IRCCS San Raffaele Scientific Institute
Department Center for Omics Sciences
Street address Via Olgettina 58
City Milan
ZIP/Postal code 20132
Country Italy
 
Platform ID GPL21847
Series (2)
GSE122942 A molecular network regulating the pro-inflammatory phenotype of human memory T lymphocytes (Nanostring I)
GSE122946 A molecular network regulating the proinflammatory phenotype of human memory T lymphocytes

Data table header descriptions
ID_REF
VALUE normalized reads

Data table
ID_REF VALUE
ABCB1 99.13
ABL1 1.66
ADA 42.68
AHR 761.57
AICDA 12.8
AIRE 2.83
APP 27.74
ARG1 41.02
ARG2 4.49
ARHGDIB 77.55
ATG10 9.47
ATG12 41.02
ATG16L1 65.92
ATG5 104.11
ATG7 9.47
ATM 32.72
B2M 30350.56
B3GAT1 14.46
BATF 451.1
BATF3 1088.64

Total number of rows: 594

Table truncated, full table size 7 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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