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Sample GSM5956754 Query DataSets for GSM5956754
Status Public on Apr 03, 2022
Title CybbKO RPM F4/80low 1
Sample type RNA
Source name Mouse resident peritoneal macrophage (B220-CD115+ F4/80low MHCIIhigh)
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
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
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
VALUE Normalized signal intensity

Data table
A_51_P366061 191.2187256
A_55_P2173827 29.75643937
A_55_P2146590 26.06117092
A_55_P2030790 84.74932661
A_55_P2059352 24.39781424
A_55_P2073024 22.43749947
A_55_P2007389 495.4480562
A_55_P2016842 27.55610356
A_55_P2174203 98.20945365
A_55_P2173825 47.96233528
A_55_P1969650 1518.677687
A_52_P574668 24.85372173
A_55_P2086825 326.2807357
A_55_P1992617 24.65656635
A_55_P1988183 71.1326497
A_55_P2124751 23.84987831
A_55_P1970910 65.95499414
A_55_P2193512 9380.180701
A_51_P269792 343.4937408
A_51_P246066 61687.90368

Total number of rows: 31176

Table truncated, full table size 776 Kbytes.

Supplementary file Size Download File type/resource
GSM5956754_252665510859_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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