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Sample GSM3143531 Query DataSets for GSM3143531
Status Public on Jun 11, 2019
Title adult_mac_cx3cr1low_rep1
Sample type RNA
Source name mouse dermis, CX3CR1low
Organism Mus musculus
Characteristics strain: C57Bl/6
genotype: Cx3cr1+/gfp
tissue: ear skin
cell type: macrophage
Treatment protocol untreated
Growth protocol SPF animal facility, no earclipping
Extracted molecule total RNA
Extraction protocol Total RNA was extracted from sorted cells with the Rneasy Micro Kit (Qiagen) as per manufacturer's instructions.
Label Biotin
Label protocol Sample preparation for microarray hybridization was carried out as described in the Affymetrix GeneChip WT Pico Reagent Kit User Guide (Affymetrix, Inc., Santa Clara, CA, USA).
Hybridization protocol Purified ss cDNA was fragmented using a combination of uracil DNA glycosylase (UDG) and apurinic/apyrimidinic endonuclease 1 (APE 1) at the dUTP residues followed by a terminal labeling with biotin. 3,8 µg of fragmented and labeled ss cDNA were hybridized to Affymetrix Mouse Gene 2.1 ST Array Plates. For hybridization, washing, staining and scanning an Affymetrix GeneTitan system, controlled by the Affymetrix GeneChip Command Console software v4.2, was used.
Scan protocol For scanning an Affymetrix GeneTitan system, controlled by the Affymetrix GeneChip Command Console software v4.2, was used.
Data processing Summarized probe set signals in log2 scale were calculated by using the RMA (1) algorithm with the Affymetrix GeneChip Expression Console v1.4 Software. After exporting into Microsoft Excel, average signal values, comparison fold changes and significance P values were calculated. Probe sets with a fold change above 2.0 fold and a student’s t test P value lower than 0.05 were considered as significantly regulated.
Submission date May 16, 2018
Last update date Jun 11, 2019
Contact name Philipp Henneke
Organization name Universitätsklinikum Freiburg
Department CCI
Street address Breisacher Str. 115
City Freiburg
ZIP/Postal code 79106
Country Germany
Platform ID GPL17400
Series (2)
GSE114525 Genome-wide expression study of macrophage subsets in the adult murine dermis
GSE114526 Genome-wide expression study of macrophage subsets in mouse skin

Data table header descriptions
VALUE log 2 RMA Signal

Data table
17532268 3.632084
17311551 3.250865
17219362 5.131051
17289549 2.602547
17321951 3.786334
17371800 4.233054
17269358 4.449913
17302594 5.870647
17367216 5.554736
17269415 5.268921
17550332 5.042966
17550360 5.042966
17302136 2.138968
17212724 3.941371
17541721 2.676955
17473292 3.508018
17488032 7.89307
17520073 4.013534
17438584 6.109092
17280749 5.809448

Total number of rows: 34390

Table truncated, full table size 600 Kbytes.

Supplementary file Size Download File type/resource
GSM3143531_adult_mac_cx3cr1low_rep1.CEL.gz 4.9 Mb (ftp)(http) CEL
Processed data included within Sample table

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