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Sample GSM1611660 Query DataSets for GSM1611660
Status Public on Feb 16, 2016
Title 5µM AGE-BSA with BMP2
Sample type SRA
 
Source name ligament cells_stimulated
Organism Homo sapiens
Characteristics cell type: Primary human posterior longitudinal ligament cells
stimulated with: 5µM AGE-BSA with BMP2
passage: 3
Treatment protocol AGE-BSA (1µM or 5µM) or BSA with or without 5µM of BMP2 were added to the medium, and cells were collected for further analysis after 3 days of treatment
Growth protocol Normal posterior longitudinal ligament were dissected during the surgery, all tissues were obtained with written informed consent signed by the donors voluntarily for research. Ligaments were further cut into pieces and cultured in DMEM supplemented with 20% fetal bovine serum, and cells of passage 3 were used for the experiments.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted from cell or animal tissue by Trizol reagent (Invitrogen) separately. The RNA quality was checked by Bioanalyzer 2200 (Aligent) and kept at -80℃.The RNA with RIN >8.0 is right for cDNA library construction.
The complementary DNA (cDNA) libraries for single-end sequencing were prepared using Ion Total RNA-Seq Kit v2.0 (Life Technologies) according to the manufacturer’s instructions. The cDNA libraries were then processed for the Proton Sequencing process according to the commercially available protocols. Samples were diluted and mixed, the mixture was processed on a OneTouch 2 instrument (Life Technologies) and enriched on a OneTouch 2 ES station (Life Technologies) for preparing the template-positive Ion PI™ Ion Sphere™ Particles (Life Technologies) according to Ion PI™ Template OT2 200 Kit v2.0 (Life Technologies). After enrichment, the mixed template-positive Ion PI™ Ion Sphere™ Particles of samples was loaded on to 1 P1v2 Proton Chip (Life Technologies) and sequenced on Proton Sequencers according to Ion PI Sequencing 200 Kit v2.0 (Life Technologies).
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Ion Torrent Proton
 
Data processing The complementary DNA (cDNA) libraries for single-end sequencing were prepared using Ion Total RNA-Seq Kit v2.0 (Life Technologies) according to the manufacturer’s instructions. The cDNA libraries were then processed for the Proton Sequencing process according to the commercially available protocols. Samples were diluted and mixed, the mixture was processed on a OneTouch 2 instrument (Life Technologies) and enriched on a OneTouch 2 ES station (Life Technologies) for preparing the template-positive Ion PI™ Ion Sphere™ Particles (Life Technologies) according to Ion PI™ Template OT2 200 Kit v2.0 (Life Technologies). After enrichment, the mixed template-positive Ion PI™ Ion Sphere™ Particles of samples was loaded on to 1 P1v2 Proton Chip (Life Technologies) and sequenced on Proton Sequencers according to Ion PI Sequencing 200 Kit v2.0 (Life Technologies).
The clean reads were then aligned to human genome (version: hg19) using the MapSplice program (v2.1.6). In alignment, preliminary experiments were performed to optimize the alignment parameters (-s 22 -p 15 --ins 6 --del 6 --non-canonical) to provide the largest information on the AS events.
We applied HTseq to calculate the mRNA counts based on the mapping result
Genome_build: hg19
Supplementary_files_format_and_content: fastq file and txt file
 
Submission date Feb 16, 2015
Last update date May 15, 2019
Contact name Chen Xu
E-mail(s) chenxu8836@hotmail.com
Phone +86-13774294166
Organization name The Second Military Medical University
Street address No, 800, Rd. Xiangyin
City Shanghai
ZIP/Postal code 200433
Country China
 
Platform ID GPL17303
Series (1)
GSE65952 Transcriptome analysis of Advanced glycation end products treated ligament cells
Relations
BioSample SAMN03349681
SRA SRX878527

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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