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Sample GSM4089363 Query DataSets for GSM4089363
Status Public on Sep 23, 2021
Title 2DRG24H
Sample type RNA
 
Source name gene expression at 24h in cultured DRG neurons
Organism Rattus norvegicus
Characteristics strain: Sprague-Dawley
gender: male
tissue: Cultured DRG neurons
timepoint: 24h
gender: male
Treatment protocol At 0h, 1.5h, 3h, 6h, 12h, 18h, 24h, 30h, 36h after neurons planted, the total RNA was isolated from these cells
Growth protocol DRG neurons were obtained from the adult male Sprague-Dawley rats (180–220 g). After isolated from spinal cord, DRGs were rinsed twice in CMF-HBSS and then primary digesting with 0.1% collagenase type I and 0.25% trypsin. The single-cell suspension was spun for 5 min at 900 rpm with 15% BSA after triturated 3 times with 1 ml pipette tip. After discarding the supernatant, the cells were resuspended and planted with DMEM/F12 (Invitrogen) medium.
Extracted molecule total RNA
Extraction protocol Total RNA was isolated using TRIzol (Invitrogen) and miRNeasy mini kit (QIAGEN) according to manufacturer’s instructions, which efficiently recovered all RNA species, including miRNAs. RNA quality and quantity was measured by using nanodrop spectrophotometer (ND-1000, Nanodrop Technologies) and RNA Integrity was determined by gel electrophoresis.
Label Cy3
Label protocol Sample labeling and array hybridization were performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology). Briefly, total RNA from each sample was linearly amplified and labeled with Cy3-UTP.
 
Hybridization protocol The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000. 1 μg of each labeled cRNA was fragmented by adding 11 μl 10 × Blocking Agent and 2.2 μl of 25 × Fragmentation Buffer, then heated the mixture at 60 °C for 30 min, finally 55 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 100 μl of hybridization solution was dispensed into the gasket slide and assembled to the gene expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven. The hybridized arrays were washed, fixed and scanned with using the Agilent DNA Microarray Scanner (part number G2505C).
Scan protocol Then the slides were scanned immediately with the Agilent DNA Microarray Scanner (part number G2505C).
Data processing Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v11.5.1 software package (Agilent Technologies)
Quantile normalization was performed with using the GeneSpring GX v11.5.1 software package (Agilent Technologies)
 
Submission date Sep 23, 2019
Last update date Sep 23, 2021
Contact name Lili Zhao
E-mail(s) zhaoll@nicemice.cn
Organization name Nantong university
Street address 19 Qixiu
City Nantong
ZIP/Postal code 226000
Country China
 
Platform ID GPL14746
Series (2)
GSE137838 Altered mRNA expression of cultured dorsal root ganglia neurons at different times of rat
GSE137839 Altered miRNA and mRNA expression of cultured dorsal root ganglia neurons at different times of rat

Data table header descriptions
ID_REF
VALUE normalized

Data table
ID_REF VALUE
A_64_P002176 8.942224
A_42_P664913 9.241795
A_64_P126523 6.4614425
A_64_P038045 2.9554455
A_43_P11804 13.286916
A_44_P808710 4.3223352
A_64_P142111 9.758604
A_64_P095642 7.161542
A_42_P735279 12.34439
A_44_P902822 6.4962344
A_42_P610788 14.203657
A_44_P242429 10.141525
A_64_P020571 8.167312
A_42_P518462 12.721661
A_42_P469751 7.4823055
A_44_P209459 14.571089
A_64_P018547 11.581682
A_42_P493925 9.826998
A_64_P049828 9.901866
A_64_P137927 6.5719795

Total number of rows: 26011

Table truncated, full table size 572 Kbytes.




Supplementary file Size Download File type/resource
GSM4089363_2DRG24H.txt.gz 2.1 Mb (ftp)(http) TXT
Processed data included within Sample table
Processed data are available on Series record

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