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Sample GSM1080945 Query DataSets for GSM1080945
Status Public on Oct 22, 2013
Title prp4-1
Sample type SRA
 
Source name Yeast cells
Organism Saccharomyces cerevisiae
Characteristics genotype: prp4-1 (MATalpha prp4-1 ade2- leu2-3,112 ura3-52 his3-delta-200)
growth conditions: 26ÂșC YPD OD=0.5
Extracted molecule polyA RNA
Extraction protocol total RNA was extracted according to Rio et al., Cold Spring Harb Protoc, 2010 "Method 1"
strand-specific libraries (dUTP/USER) were made from polyA selected mRNA; adaptors, end repair through enrichment steps using Illumina DNA Sample Prep kit V2
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
 
Description spliceosomal mutant (prp4-1)
Data processing Illumina Casava1.8.2 software used for basecalling.
Sequenced reads (100bp read1, 58bp read2) were mapped to sacCer3 using tophat, allowing for a maximum intron size of 1200bp, with an estimated mean distance between the read pairs of 85bp (std dev 100bp).
A gtf file of previously known splice sites was supplied to tophat. Tophat's coverage search and segment search intron-finding algorithms were also enabled. In the case of multiply-mapped reads, the single best hit as scored by bowtie was kept.
Expression values (i.e., reads per exon or per gene) are calculated by summing the coverage at each position and dividing by read length.
Genome_build: sacCer3
Supplementary_files_format_and_content: spreadsheet containing summarized gene expression, intron and exon2 read counts, as well as calculated Intron Accumulation Indexes
 
Submission date Feb 11, 2013
Last update date May 15, 2019
Contact name Lily Shiue
E-mail(s) lshiue@ucsc.edu
Phone 831-459-2612
Organization name UCSC
Department MCD Biology
Lab Ares
Street address 1156 High Street
City Santa Cruz
State/province CA
ZIP/Postal code 95064
Country USA
 
Platform ID GPL13821
Series (1)
GSE44219 Competition between pre-mRNAs for a limiting splicing machinery drives global changes in splicing
Relations
SRA SRX233535
BioSample SAMN01919387

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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