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Sample GSM1051521 Query DataSets for GSM1051521
Status Public on Dec 21, 2013
Title Sca-1+ PDC, replicate 1
Sample type RNA
 
Source name Sca-1+ PDC collected from in vitro culture of differentiated bone marrow precursor cells using mFlt3-L
Organism Mus musculus
Characteristics strain: BALB/c
gender: female
cell type: plasmacytoid dendritic cells (PDC)
genotype/variation: Sca-1+
Treatment protocol Cells were directly lysed in RA1 buffer (Macherey-Nagel).
Growth protocol Cells were directly isolated from indicated cell culture sources by magnetic and flow cytometric cell sorting.
Extracted molecule polyA RNA
Extraction protocol RNA was isolated using the NucleoSpin® RNA II kit (Macherey-Nagel) following manufacturer's instructions.
Label Cy3
Label protocol 100 ng of each RNA was used as template to produce Cy3- labeled cRNA. The RNA samples were amplified and labeled using the Low Input Quick Amp Labeling Kit (Agilent Technologies) following the manufacturer’s protocol.
 
Hybridization protocol Cy3 labeled cRNAs were hybridized overnight (17 hours, 65°C) to an Agilent Whole Mouse Genome Oligo Microarrays (8x60K) using Agilent’s recommended hybridization chamber and oven.Finally, microarrays were washed once with wash buffer 1 for 1 min at RT followed by a second wash with wash buffer 2 for 1 min at 37°C and a final wash step with acetonitrile for 30 sec at RT.
Scan protocol Fluorescence signals of the hybridized Agilent Microarrays were detected using Agilent’s Microarray Scanner System (G2505C, Agilent Technologies, Palo Alto, USA).
Description 1+_0h_1
gene expression analysis of SuperAmplified™ polyA RNA
Data processing The Agilent Feature Extraction Software (FES 10.7.3.1 ) was used to read out and process the microarray image files.
FES derived output data files were further analyzed using the Rosetta Resolver gene expression data analysis system (Rosetta Biosoftware, Rosetta error model; Lee Weng et al 2006).
 
Submission date Dec 12, 2012
Last update date Dec 22, 2013
Contact name Stefan Tomiuk
E-mail(s) stefant@miltenyibiotec.de
Organization name Miltenyi Biotec GmbH
Department Bioinformatics
Street address Friedrich-Ebert-Str. 68
City Bergisch-Gladbach
ZIP/Postal code 51429
Country Germany
 
Platform ID GPL10787
Series (1)
GSE42860 Sca-1 expression defines different developmental stages of mouse PDC that show functional heterogeneity in the endosomal but not lysosomal TLR9 response

Data table header descriptions
ID_REF
VALUE Quantile normalized signal intensity data in log2 space.

Data table
ID_REF VALUE
A_30_P01017425 5.580
A_30_P01017426 6.966
A_30_P01017427 5.660
A_30_P01017428 6.909
A_30_P01017429 2.800
A_30_P01017430 2.084
A_30_P01017431 4.049
A_30_P01017432 5.823
A_30_P01017433 4.661
A_30_P01017434 6.447
A_30_P01017435 1.749
A_30_P01017436 1.625
A_30_P01017437 7.240
A_30_P01017438 1.714
A_30_P01017439 5.276
A_30_P01017440 1.735
A_30_P01017441 1.882
A_30_P01017442 8.168
A_30_P01017443 8.434
A_30_P01017444 2.272

Total number of rows: 55681

Table truncated, full table size 1096 Kbytes.




Supplementary file Size Download File type/resource
GSM1051521_252800511864_S01_GE1_105_Jan09_1_2.txt.gz 11.9 Mb (ftp)(http) TXT
Processed data included within Sample table

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