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Sample GSM688733 Query DataSets for GSM688733
Status Public on Nov 21, 2011
Title B cells WT vs CCR7-/- Replicate 1 (Pool1)
Sample type RNA
 
Channel 1
Source name B cells
Organism Mus musculus
Characteristics strain: C57BL/6J
genotype/variation: wildtype
tissue: peripheral lymph nodes
Treatment protocol The cells were sorted on a FACSAria (BD Biosciences) and immediately subjected to total RNA isolation.
Growth protocol The cells were not cultured after isolation.
Extracted molecule total RNA
Extraction protocol Total RNA from sorted cell samples was extracted by use of the Nucleospin RNA XS kit (Macherey & Nagel).
Label Cy3
Label protocol 20ng of total RNA per condition were used to prepare Cy3-, or Cy5-labeled cRNA (Amino Allyl MessageAmp™ II Kit; Ambion) as directed by the company.
 
Channel 2
Source name B cells
Organism Mus musculus
Characteristics tissue: peripheral lymph nodes
strain: B6.129P2(C)-Ccr7tm1Rfor/J
genotype/variation: Ccr7 knock-out
Treatment protocol The cells were sorted on a FACSAria (BD Biosciences) and immediately subjected to total RNA isolation.
Growth protocol The cells were not cultured after isolation.
Extracted molecule total RNA
Extraction protocol Total RNA from sorted cell samples was extracted by use of the Nucleospin RNA XS kit (Macherey & Nagel).
Label Cy5
Label protocol 20ng of total RNA per condition were used to prepare Cy3-, or Cy5-labeled cRNA (Amino Allyl MessageAmp™ II Kit; Ambion) as directed by the company.
 
 
Hybridization protocol cRNA fragmentation, hybridization, and washing steps were carried out according to Agilent’s Two-Color Microarray-Based Gene Expression Analysis Protocol V5.7 (for details see http://www.agilent.com) except that 500ng of each labeled cRNA sample were used for hybridization. Microarrays were co-hybridized with differently-labeled material from CCR7 -/- versus wildtype animals in a dual-color setting.
Scan protocol Slides were scanned on the Agilent Micro Array Scanner G2505 B at two different PMT settings (100 % and 5 %) to increase the dynamic range of the measurements (extended dynamic range mode).
Data processing Data extraction and normalization were performed with the “Feature Extraction Software V9.5.3.1” by using the recommended default extraction protocol file: GE2-v5_95_Feb07.xml. To correct for systematic bias at the high end of the fluorescence intensity measurements, the highest ranking 2% of Processed Signals in the green channel (gPS) were further normalized according to an intensity-dependent, non-linear scaling strategy, to optimize fitting to their respective counterparts in the red channel.
 
Submission date Mar 10, 2011
Last update date Nov 21, 2011
Contact name Oliver Dittrich-Breiholz
E-mail(s) dittrich.oliver@mh-hannover.de
Organization name Medical School Hannover
Department Research Core Unit Genomics
Street address Carl-Neuberg-Str. 1
City Hannover
ZIP/Postal code 30625
Country Germany
 
Platform ID GPL4134
Series (1)
GSE27885 Transcription profile of B cells isolated from peripheral lymph nodes of wild-type vs CCR7-/- mice

Data table header descriptions
ID_REF
VALUE Corrected log2 ratios (wiltype / Ccr7 knock-out)

Data table
ID_REF VALUE
1 0.177051545
2 0
3 -0.442917397
4 0.001993951
5 0
6 0
7 0
8 -0.939468515
9 0
10 -0.782598846
11 -1.131210474
12 -1.326637429
13 -0.041469109
14 0.19345407
15 -0.826178609
16 -0.413499218
18 -0.452372088
19 0
20 -0.487517335
21 -0.269037635

Total number of rows: 45018

Table truncated, full table size 709 Kbytes.




Supplementary file Size Download File type/resource
GSM688733_M2461-M2462_rH100L5gH100L5_251486814428_S01_GE2-v5_95_Feb07_1_1.txt.gz 15.5 Mb (ftp)(http) TXT
Processed data included within Sample table

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