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Sample GSM5956753 Query DataSets for GSM5956753
Status Public on Apr 03, 2022
Title CybbKO RPM F4/80high 3
Sample type RNA
 
Source name Mouse resident peritoneal macrophage (B220-CD115+ F4/80high MHCII-)
Organism Mus musculus
Characteristics genotype: CGD
tissue: Peritoneal lavage
gender: Male
age: 9wks
Extracted molecule total RNA
Extraction protocol Qiagen RNAeasy micro plus
Label Cy5
Label protocol RNA samples were amplified using SIGMA WTA2 RNA amplification system. Amplified cDNAs were chemically labeled with Kreatech ULS RNA labeling kit (Kreatech Diagnostics). Per reaction, 3ug of each RNA (+water=16ul) was mixed with Kreatech 10x labeling buffer (2ul) and Kreatech cy5/DY-ULS (2ul). The reactions were incubated at 85C for 15 minutes in the dark and placed on ice for 3 minutes. Labeled cDNA was purified with Qiagen PCR purification columns according to manufacturer’s protocol. cDNAs were quantitated on a Nanodrop spectrophotometer. Detailed protocol can be found at http://www.kreatech.com/fileadmin/user_upload/Documenten/PDF/12_man_EA-021-022-023__D0.6.pdf
 
Hybridization protocol The balanced aRNAs were suspended in Agilent 2X Gene Expression buffer (55ul), Agilent 10X Blocking agent (11ul), and Kreablock (6ul). The hybridization solutions were applied to Agilent Mouse v2 4x44K microarrays (G4846A-026655). Hybridization was carried out at 65C for 20 hours. Washing procedures were carried out according to Agilent gene expression protocols.
Scan protocol Slides were scanned on an Agilent C-class Microarray scanner to detect Cy5 fluorescence, according to manufacturer's specifications.
Description No treatment
Data processing Gridding and analysis of images was performed using Feature Extraction (v11.5.1.1, Agilent Technologies). The extracted signal was quantile-normalizated using Partek.
 
Submission date Mar 16, 2022
Last update date Apr 03, 2022
Contact name Mary C Dinauer
E-mail(s) mdinauer@wustl.edu
Organization name Washington University In St Louis
Department Pathology & Immunology
Street address 660 South Euclid Ave
City St Louis
State/province Missouri
ZIP/Postal code 63110
Country USA
 
Platform ID GPL11202
Series (2)
GSE198771 Analysis of resident peritoneal macrophage's transcriptome in WT and CGD mice
GSE198778 The leukocyte NADPH oxidase 2 (NOX2) plays a key role in pathogen killing and immunoregulation

Data table header descriptions
ID_REF
VALUE Normalized signal intensity

Data table
ID_REF VALUE
A_51_P366061 18674.73305
A_55_P2173827 777.3982232
A_55_P2146590 389.6648533
A_55_P2030790 2055.110141
A_55_P2059352 1803.020394
A_55_P2073024 2200.018591
A_55_P2007389 49.3387753
A_55_P2016842 1211.76985
A_55_P2174203 383.156508
A_55_P2173825 9739.284009
A_55_P1969650 33.60700331
A_52_P574668 658.6964662
A_55_P2086825 2500.845125
A_55_P1992617 214.3374298
A_55_P1988183 2672.918252
A_55_P2124751 278.607445
A_55_P1970910 1368.424383
A_55_P2193512 23.21121278
A_51_P269792 3656.632691
A_51_P246066 3513.273071

Total number of rows: 31176

Table truncated, full table size 776 Kbytes.




Supplementary file Size Download File type/resource
GSM5956753_252665510857_S01_GE1_107_Sep09_red_only_1_4.txt.gz 9.1 Mb (ftp)(http) TXT
Processed data included within Sample table

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