|
| Status |
Public on Sep 23, 2015 |
| Title |
Donor 3-Control |
| Sample type |
SRA |
| |
|
| Source name |
Human peripheral bloood
|
| Organism |
Homo sapiens |
| Characteristics |
individual: Donor 3
factor inducing monocyte differentiation: M-CSF
resulting cell type: macrophage
protocol: No treatment
|
| 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 (http://www.ncbi.nlm.nih.gov/), UniProt (http://www.uniprot.org/) and the Gene Ontology (http://www.geneontology.org/). 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 |
| E-mail(s) |
zhangwuchang104@hotmail.com
|
| 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) |
|
| Relations |
| BioSample |
SAMN03580657 |
| SRA |
SRX1016110 |
