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Sample GSM1410888 Query DataSets for GSM1410888
Status Public on Feb 09, 2015
Title 24_LPS_rep3
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: nontargeting 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 SAMN02851666
SRA SRX591900

Supplementary file Size Download File type/resource
GSM1410888_24_LPS_sample3_run1_mima0.08_ensGene.mm10.splicesites_snp137.unpaired_uniq_DEXSeq-counts.txt.gz 1.3 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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