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Sample GSM948986 Query DataSets for GSM948986
Status Public on Jan 07, 2014
Title MGC_Placenta1_rep1
Sample type RNA
 
Source name MGC
Organism Homo sapiens
Characteristics cd14: NO
time [days of culture]: 9
cell type: MGC
source placenta: 1
biological replicate: 1
Treatment protocol MGC (9 days of culture) were compared with initial placental macrophages (CD14+).
Growth protocol Placentas from healthy at-term pregnancies and vaginal deliveries were collected in the Gynecology-Obstetrics Department of the Hôpital de la Conception (Marseille, France). Chorionic villi from the maternal interface were cut along their entire length without taking the membrane of the chorionic plate. They were then cut into small pieces of approximately 1 cm² and rinsed in PBS. Placenta samples were digested. Briefly, placenta samples were incubated in a solution consisting of HBSS, MgSO4, DNase I and 2.5% trypsin buffered with HEPES for 45 min and then for 30 min under gentle agitation at 37°C. The digestion products were filtered through 100-µm pores, incubated in 50 ml tubes containing 2 ml FCS and centrifuged at 1,000 × g for 15 min. The cells were counted, deposited on a Ficoll cushion and centrifuged at 700 × g for 20 min. Mononuclear cells were recovered, and the placental macrophages were isolated using magnetic beads coated with anti-CD14 Abs. The purity of the isolated CD14+ cells was verified by flow cytometry and was greater than 97%. Placental MGCs were obtained as follows. CD14+ macrophages (2 × 105 cells per assay) were seeded in 24-well plates containing glass coverslips (day 0) and cultured in DMEM-F12 containing 10% FCS and antibiotics for 9 days. The morphology of the placental macrophages and the percentage of MGCs were determined by May-Grünwald Giemsa staining using the HemaColor kit.
Extracted molecule total RNA
Extraction protocol RNA was extracted using an RNeasy Mini kit (Qiagen, Courtaboeuf, France). The quantity and quality of total RNA were assessed using the Nanodrop (Thermo Scientific, Illkirch, France) and a 2100 Bioanalyzer (Agilent Technologies, Massy, France). The RNA was eluted in 30 µl of water and stored at -20°C.
Label Cy3
Label protocol In brief, 400 ng RNA were labeled with cyanine-3-CTP using the Low RNA Input Fluorescent Amplification Kit from Agilent Technologies.
 
Hybridization protocol RNA was analyzed using microarray chips including 45,000 probes (4x44K Whole Human Genome, Agilent Technologies) and One-color Microarray Based Gene Expression Analysis. Hybridization was performed at 65°C using the in situ Hybridization Plus kit (Agilent Technologies) for 17 hours.
Scan protocol Arrays were scanned with a pixel size of 5 µm with the DNA Microarray Scanner G2505B. Image analysis and correction of intra-array signals were performed with the Feature Extraction Software A.9.1.3 (Agilent Technologies).
Data processing Microarray data analysis was performed using the R and the Bioconductor software suite. Raw data were filtered and normalized using the Agi4x44PreProcess library. Unsupervised and supervised analyses were done using hierarchical clustering, correspondence analysis (COA) (made4 library) and Significance Analysis of Microarray (SAM) algorithm (siggenes library). Supervised analysis was performed using SAM. Genes were considered to be differentially expressed when the false discovery rate was below 1% and absolute fold change (FC) was above 4.
 
Submission date Jun 15, 2012
Last update date Jan 07, 2014
Contact name Julien Textoris
E-mail(s) julien.textoris@gmail.com
Phone +33 472 119 546
Organization name bioMérieux
Department Medical Diagnostic Discovery Department (MD3)
Lab Joint Research Unit - bioMérieux / HCL
Street address Hôpital Edouard herriot - Pavillon P; 5 place d'Arsonval
City Lyon
ZIP/Postal code 69437
Country France
 
Platform ID GPL6480
Series (1)
GSE38747 Regulatory role of multinucleated giant cells derived from placental CD14+ macrophages: Pathophysiological implications

Data table header descriptions
ID_REF
VALUE Quantile normalized signal intensities (log2)

Data table
ID_REF VALUE
A_24_P66027 9.372021864
A_23_P212522 9.817843319
A_24_P9671 13.97646157
A_32_P29551 6.016763706
A_24_P801451 8.538397705
A_32_P30710 14.52251696
A_32_P89523 3.974757278
A_32_P86028 14.23739964
A_24_P470079 5.378721105
A_23_P65830 10.88785499
A_23_P109143 14.42452565
A_24_P595567 7.055311181
A_24_P391591 6.754686045
A_24_P835500 12.49182076
A_23_P54340 5.277855283
A_23_P67555 6.804744354
A_24_P286412 5.980753683
A_23_P202696 9.556591056
A_23_P124837 11.08351805
A_24_P329635 10.61502088

Total number of rows: 32397

Table truncated, full table size 776 Kbytes.




Supplementary file Size Download File type/resource
GSM948986_US84403583_251485064862_S01_GE1_105_Dec08_1_1.txt.gz 9.1 Mb (ftp)(http) TXT
Raw data provided as supplementary file
Processed data included within Sample table

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