NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM2265845 Query DataSets for GSM2265845
Status Public on Aug 15, 2017
Title P [251911910877_S01_1_2]
Sample type RNA
 
Source name CD4 T cells (pDCs)
Organism Mus musculus
Characteristics origin: CD4 T cells after coculture with pDCs in the absence of OVA
cell type: Primary CD4 T cells
Treatment protocol T cells were cocultured with the corresponding subset of DCs (8:1 T cell/DC ratio) in the presence or absence of chicken ovalbumin (OVA) 323-339 peptide for 18 h. CD4+ T cells from the coculture were sorted on a flow cytometer.
Growth protocol Mouse naive CD4+ T cells were isolated from cell suspensions of lymph nodes or spleen. Cell suspensions were incubated with biotinylated antibodies (BD Biosciences) against CD8, CD19, CD25, CD11b, CD11c, CD45R, MHC-II (I-Ab), DX5, IgM, Gr-1 and F4/80 and subsequently with streptavidin microbeads (MACS; Miltenyi Biotec). CD4+ T cells were negatively selected in auto-MACS Pro Separator (Miltenyi Biotec) according to the manufacturer's instructions. At this point DC preparations were characterized as CD11c+ MHCII+ Ly6G-. To obtain both pDCs and cDCs, bone marrow cell suspensions were cultured with 100 ng ml-1 Flt3-ligand for 8 d and maturation was subsecuently induced by 6 µg ml-1 of CpG. pDCs and cDCs were isolated using MACS system B220-labeled beads and auto-MACS Pro Separator (Miltenyi Biotec) being pDCs B220+ fraction and cDCs B220- fraction.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted with Quiazol reagent and the miRNeasy® mini kit (Quiagen),
Label Cy3
Label protocol miRNA Labeling Kit (Agilent Technologies) was used to label RNA. Basically, 100 ng of total RNA were dephosphorylated and Cyanine 3-pCp molecule was ligated to the 3´ end of each RNA molecule by using T4 RNA ligase.
 
Hybridization protocol 100 ng of Cy3 labelled RNA were hybridized for 20 hours at 55ºC in a hybridization oven (G2545A, Agilent) set to 15 rpm in a final concentration of 1X GE Blocking Agent and 1X Hi-RPM Hybridization Buffer, according to manufacturer's instructions (miRNA Microarray System Protocol, Agilent Technologies).
Scan protocol Arrays were scanned at 5mm resolution on an Agilent DNA Microarray Scanner (G2565BA, Agilent Technologies) using the default settings for miRNA Microarray v2.0 (miRNA Microarray System Protocol, Agilent Technologies).
Description Expression of miRNAs from CD4 T cells sorter from coculture with pDCs
Data processing Images provided by the scanner were analyzed using Agilent´s software Feature Extraction version 10.7.3.1 and protocol miRNA_105_Jan09
 
Submission date Aug 09, 2016
Last update date Aug 15, 2017
Contact name Fatima Sanchez-Cabo
E-mail(s) fscabo@cnic.es
Phone +34 91 4531200
Organization name CNIC
Street address Melchor Fernandez Almagro
City Madrid
ZIP/Postal code 28029
Country Spain
 
Platform ID GPL8824
Series (1)
GSE85363 microRNA profiles of CD4 T cells after cognate antigen specfic stimulation

Data table header descriptions
ID_REF
VALUE vsn2-invariant normalized intensities

Data table
ID_REF VALUE
DarkCorner 2.707225374
NC1_00000197 3.533679156
NC1_00000215 3.542697823
NC2_00079215 3.534567566
NC2_00092197 3.537105524
NC2_00106057 3.545410064
NC2_00122731 3.534281964
NegativeControl 5.401276481
SCorner3 1.846050056
dmr_285 2.26378292
dmr_3 2.264461167
dmr_308 2.263820609
dmr_316 2.265214406
dmr_31a 2.264142636
dmr_6 2.265009016
hur_1 11.50661728
hur_2 15.45948047
hur_4 10.7927202
hur_5 2.086684824
hur_6 12.27211134

Total number of rows: 598

Table truncated, full table size 14 Kbytes.




Supplementary file Size Download File type/resource
GSM2265845_251911910877_S01_1_2_GeneView.txt.gz 5.5 Kb (ftp)(http) TXT
GSM2265845_US22502514_251911910877_S01_miRNA_105_Jan09_1_2.txt.gz 713.2 Kb (ftp)(http) TXT
Processed data included within Sample table

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap