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Sample GSM3301798 Query DataSets for GSM3301798
Status Public on Jul 23, 2021
Title NR8383 - Pass Nu 20 - rep4
Sample type RNA
 
Source name NR8383_Passage Number 20
Organism Rattus norvegicus
Characteristics cell line: NR8383
tissue origin: lung
cell type: alveolar macrophage cell line
passage number: low (passage 20)
Treatment protocol Cells were seeded in 25 cm2 flasks at a density of 3 x 105 cells / mL for 48 h. Cells were at two different passage numbers 20 and 200 in four biological replicates.
Growth protocol NR8383 cell line were established from normal rat by lung lavage and was obtained from American Type Culture Collection (ATCC® CRL-2192™, Manassas, VA, USA). Cells, with a 50% adherent and 50% floating cell phenotype, were grown in DMEM medium supplemented with 15 % of heat-inactivated fetal bovine serum, 2 mM of L-glutamine, as well as 100 U/mL of penicillin, 100 µg/mL of streptomycin and 0.25 µg/mL of amphotericin B (all from Sigma Aldrich). Cells were incubated at 37°C in an atmosphere composed of 95 % air, 5 % CO2 and medium are changed every 2-3 days.
Extracted molecule total RNA
Extraction protocol The quality of the RNA extracted by RNA-Solv Reagent (Omega Bio-tek, USA) was determined by spectrophotometry (A260nm/A280nm, A260nm/A230nm > 1.8, BioSpec-nano, Shimadzu) and by capillary electrophoresis using RNA 6000 Nano® (RIN > 7.5, Agilent 2100 Bioanalyzer, Santa Clara, CA, USA).
Label CTP-Cy3
Label protocol CTP-cyanine-3 (Cy3) labeled cRNA was prepared from 100 ng RNA using the One-Color Microarray-Based Gene Expression Analysis (Agilent) according to manufacturer's instructions, followed by chromatographic purification (RNeasy Mini kit, QIAGEN). Dye incorporation and cRNA yield and quality were checked by spectrophotometry (specific activity > 10 pmol Cy3 / µg cRNA, BioSpec-nano, Shimadzu) and by electrophoresis (Agilent 2100 Bioanalyzer).
 
Hybridization protocol Six hundred ng of CTP-Cy3-labelled cRNA were fragmented at 60°C for 30 min in a reaction volume of 25 µL following the manufacturer’s instructions. 25 µL of 2x Agilent hybridization buffer were added to the fragmentation mixture and cRNA were hybridized to SurePrint G3 Rat GE v2 8x60K (Agilent) for 17 h at 65°C in a rotating hybridization oven. After hybridization, microarrays were washed 1 min at room temperature with GE Wash Buffer 1TM and 1 min with 37°C GE Wash buffer 2TM (Agilent).
Scan protocol Slides were scanned immediately after washing using Agilent DNA Microarray Scanner (G2505C) by setting: (i) one color scan channel for 8x60k array slides, (ii) scan area of 61x21.6 mm, (iii) scan resolution of 3 µm, (iv) dye channel to Green, (v) Tiff file dynamic range of 20 bits and (vi) Green PMT to 100 %.
Description Gene expression in NR8383 cells after 20 passages
Data processing The scanned images were analyzed by Feature Extraction version 11.0.1.1 (Agilent) using default parameters (protocol GE1_1100_Jul11 and Grid: 074036_D_F_20150914) to subtract background and to obtain spatially detrended processed signal intensities. Features flagged in Feature Extraction as Non-uniform outliers Feature were excluded.
 
Submission date Jul 23, 2018
Last update date Jul 23, 2021
Contact name Olivier Joubert
E-mail(s) olivier.joubert@univ-lorraine.fr
Phone 0372742694
Organization name Université de lorraine
Department Dpt 4
Lab Nanomatériaux et santé
Street address 2 allée guinier
City nancy
ZIP/Postal code 54011
Country France
 
Platform ID GPL22145
Series (1)
GSE117487 Effect of cell passage number on gene expression in NR8383 macrophages

Data table header descriptions
ID_REF
VALUE Non-Normalized signal intensity (medians of each sample).

Data table
ID_REF VALUE
1 6492
2 48
3 48.5
4 59
5 78
6 57
7 57
8 1479
9 180
10 250
11 64
12 81768.5
13 564.5
14 102.5
15 215.5
16 61
17 50
18 134120
19 55
20 48

Total number of rows: 62976

Table truncated, full table size 625 Kbytes.




Supplementary file Size Download File type/resource
GSM3301798_P_20-4_Feature_extraction.txt.gz 12.4 Mb (ftp)(http) TXT
Processed data included within Sample table

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