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Sample GSM1826487 Query DataSets for GSM1826487
Status Public on Feb 14, 2019
Title BMDM_3_PBS
Sample type RNA
 
Source name Primary mouse bone marrow-derived macrophages
Organism Mus musculus
Characteristics treatment: PBS
cell type: BMDM
Treatment protocol Hepcidin (Peptide International) was added to the wells at 10µg/ml. The BMDMs were incubated for one hour and lysed with Trizol.
Growth protocol Bone marrow-derived macrophages (BMDMs) were obtained from bone marrow (BM) precursor cells. In brief, total BM was obtained from 8-10 week old WT by flushing femur and tibiae BM with Dulbecco’s modified Eagle’s medium (DMEM). Cells were cultured in plastic tissue culture dishes (150 mm) in 25 ml of DMEM containing 20% FBS (Fetal Bovine Serum) and 30% L cell-conditioned medium as a source of M-CSF. They were then incubated at 37°C in a humidified 5% CO2 atmosphere. After 7 days of culture, a homogeneous population of adherent BMDMs was obtained. BMDMs were scrapped and seeded at 150 000 cells per well into 24-well plate in 0,5 ml of DMEM containing 15% L cell-conditioned medium and 10% FBS. The following day, hepcidin (Peptide International) was added to the wells at 10µg/ml. The BMDMs were incubated for one hour and lysed with Trizol.
Extracted molecule total RNA
Extraction protocol Trizol extraction of total RNA was performed according to the manufacturer's instructions.
Label Biotin
Label protocol Biotinylated cDNA were prepared according to the standard Affymetrix protocol from total RNA (Following the GeneChip whole transcript (WT) Sense Target labelling assay kit Affymetrix)
 
Hybridization protocol Following fragmentation, cDNA were hybridized for 16 hr at 45C on GeneChip murine Gene from Affymetrix GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
Scan protocol GeneChips were scanned using the GCS 3000 scanner (Affymetrix)
Description Gene expression data from BMDM with PBS
JM_5
Data processing The data were RMA normalized with package affy_1.36.1 of Bioconductor (BiocInstaller_1.8.3)
 
Submission date Jul 20, 2015
Last update date Feb 14, 2019
Contact name Florent Dumont
E-mail(s) florent.dumont@u-psud.fr
Organization name Université Paris-Saclay
Street address 17 avenue des sciences
City 91400 Orsay
State/province Ile de France
ZIP/Postal code 91400
Country France
 
Platform ID GPL20710
Series (1)
GSE71073 Gut hepcidin: a key regulator of inflammation

Data table header descriptions
ID_REF
VALUE log2 RMA signal

Data table
ID_REF VALUE
100009600 4.114232176
100009609 2.231595076
100009614 4.054520135
100009664 3.337272493
100012 2.534717296
100017 9.12337714
100019 7.534646026
100033459 3.43070103
100034251 9.317050253
100034675 3.63500074
100034729 2.894133823
100034739 4.381994003
100034748 3.88226914
100036518 2.805195954
100036520 4.870628546
100036521 5.492170991
100036523 5.916341312
100036537 3.853114826
100036569 2.397502484
100036768 5.629801377

Total number of rows: 24973

Table truncated, full table size 454 Kbytes.




Supplementary file Size Download File type/resource
GSM1826487_JM_5_MoGene-2_0-st_.CEL.gz 8.6 Mb (ftp)(http) CEL
Processed data included within Sample table

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