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Sample GSM6689141 Query DataSets for GSM6689141
Status Public on Nov 03, 2022
Title MF_Gm_csfKO_treated_pnd9_3
Sample type RNA
 
Source name Lung
Organism Mus
Characteristics strain: C57BL/6
metadata info: metaData_microarrays.txt
Extracted molecule total RNA
Extraction protocol Cells were sorted into 500ul RLT buffer (QIAGEN). RNA was isolated using the RNeasy micro kit (QIAGEN) and sent to the Nucleomics facility, VIB Leuven, Belgium where the microarrays were performed using the GeneChip Mouse Gene 1.0 ST arrays (Affymetrix).
Label biotin
Label protocol standard Affymetrix protocol
 
Hybridization protocol standard Affymetrix protocol
Scan protocol Affymetrix Gene ChIP Scanner 3000 7G
Description GM-CSF KO macrophages on post natal day 9 treated with GM-CSF
GM-CSF KO macrophages on post natal day 9 treated with GM-CSF
Data processing Samples were analyzed using R/limma: Robust Multi-array Average (RMA) procedure was used to normalize data within arrays (probeset summarization, background correction and log2-transformation) and between arrays (quantile normalization). Only probesets that uniquely mapped to an EntrezID were kept.
 
Submission date Oct 27, 2022
Last update date Nov 03, 2022
Contact name Liesbet Martens
E-mail(s) liesbet.martens@irc.vib-ugent.be
Organization name VIB-University of Ghent
Department VIB Inflammation Research Center
Street address Technologiepark 927
City Zwijnaarde
ZIP/Postal code 9052
Country Belgium
 
Platform ID GPL6246
Series (2)
GSE216701 Loss of evolutionary conserved GM-CSF-dependent signature in pulmonary macrophages in COVID-19 provides a rationale for inhaled GM-CSF treatment (microarray)
GSE216705 Loss of GM-CSF-dependent instruction of alveolar macrophages in COVID-19 provides a rationale for inhaled GM-CSF treatment

Data table header descriptions
ID_REF
VALUE All samples passed quality control, and the Robust Multi-array Average (RMA) procedure was used to normalize data within arrays (probeset summarization, background correction and log2-transformation) and between arrays (quantile normalization).

Data table
ID_REF VALUE
10338001 12.79412471
10338002 5.787588838
10338003 11.06506027
10338004 9.892414699
10338005 2.27712455
10338006 2.44559648
10338007 2.751565199
10338008 3.378783649
10338009 7.423083283
10338010 2.315163263
10338011 5.130419523
10338012 2.395355492
10338013 2.154081596
10338014 2.187124255
10338015 2.187616663
10338016 6.899093021
10338017 13.30593831
10338018 6.037976414
10338019 4.50438942
10338020 7.474353753

Total number of rows: 35556

Table truncated, full table size 725 Kbytes.




Supplementary file Size Download File type/resource
GSM6689141_MF_Gm_csfKO_treated_pnd9_3.CEL.gz 3.9 Mb (ftp)(http) CEL
Processed data included within Sample table

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