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Sample GSM1673634 Query DataSets for GSM1673634
Status Public on Sep 23, 2015
Title Donor 1-NaCl
Sample type SRA
Source name Human peripheral bloood
Organism Homo sapiens
Characteristics individual: Donor 1
factor inducing monocyte differentiation: M-CSF
resulting cell type: macrophage
protocol: Additional 51mM NaCl for 24 hours
Treatment protocol mature macrophages were treated with or without additional 51mM NaCl for 24 hours.
Growth protocol monocyte differentiation into macrophages were induced by 6-day treatment of 100ng/ml M-CSF.
Extracted molecule total RNA
Extraction protocol RNA was harvested using Trizol reagent.
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.
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Ion Torrent Proton
Data processing Clean reads were obtained from the raw reads by removing the adaptor sequences, reads with >5% ambiguous bases (noted as N) and low-quality reads containing more than 20 percent ofbases with qualities of <13.
The clean reads were then aligned to human genome (version: GRCH37) 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
Gene ontology (GO) analysis was performed to facilitate elucidating the biological implications of unique genes in the significant or representative profiles of the differentially expressed gene in the experiment [4]. We downloaded the GO annotations from NCBI (, UniProt ( and the Gene Ontology ( Fisher’s exact test was applied to identify the significant GO categories and FDR was used to correct the p-values.
Genome_build: GRCH37
Supplementary_files_format_and_content: Tab-delimited text file including raw counts for each Sample
Submission date May 03, 2015
Last update date May 15, 2019
Contact name WUCHANG ZHANG
Phone 4243853408
Organization name UCLA
Department School of Dentistry
Street address CHS 56-200, 650 Charles E. Young Dr. So
City Los Angeles
State/province California
ZIP/Postal code 90095
Country USA
Platform ID GPL17303
Series (1)
GSE68482 High salt primes a specific activation state of macrophages, M(Na)
BioSample SAMN03580654
SRA SRX1016107

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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