|
| Status |
Public on Feb 09, 2015 |
| Title |
SF3_LPS_rep2 |
| Sample type |
SRA |
| |
|
| Source name |
macrophages
|
| Organism |
Mus musculus |
| Characteristics |
cell type: RAW 264.7 macrophages
strain: BALB/c
lps addition: 20 ng/ml for 4 h
sirna: targeting SF3A1 for 24 h
|
| Treatment protocol |
siRNAs were transfected using the Amaxa nucleofector shuttle; 24 hours later, cells were treated with LPS for 4 hours
|
| Growth protocol |
RAW264.7 cells were maintained in DMEM supplemented with 10% FBS
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was harvested with the RNAeasy kit (Qiagen). PolyA RNA was then isolated using the Dynabeads mRNA Direct Purification kit (Life Technologies).
polyA-RNA-seq library construction was prepared using the Ion Total RNA-Seq kit v2, for next generation sequencing using an Ion Proton platform (Life Technologies).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Ion Torrent Proton |
| |
|
| Data processing |
Basecalling, barcode demultiplexing and adapter trimming by Ion Torrent Suite 3.6
Mapping with GSNAP 2013-11-27 using SNP137 (after removal of reads <30 nt).
Counting reads per gene using htseq-count (from HTSeq version 0.5.4p) and Ensembl annotation (downloaded from UCSC table browser July 29, 2013)
Counting reads per (partial) exon using scripts from DEXSeq version 1.6.0 (and libraries from HTSeq version 0.5.4p)
Genome_build: mm10
Supplementary_files_format_and_content: htseq-genecounts_uniq.txt: reads per gene for each gene and sample (consolidated from htseq-count output); *DEXSeq-counts.txt files: reads per (partial) exon (for DEXSeq).
|
| |
|
| Submission date |
Jun 12, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Scott Alper |
| E-mail(s) |
alpers@njhealth.org
|
| Organization name |
National Jewish Health
|
| Department |
Integrated Center for Genes Environment & Health
|
| Street address |
1400 Jackson St.
|
| City |
Denver |
| State/province |
CO |
| ZIP/Postal code |
80206 |
| Country |
USA |
| |
|
| Platform ID |
GPL18635 |
| Series (1) |
| GSE58432 |
Effect of SF3A1 inhibition on pre-mRNA splicing |
|
| Relations |
| BioSample |
SAMN02851661 |
| SRA |
SRX591905 |
