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Sample GSM1080942

Query DataSets for GSM1080942

Status

Public on Oct 22, 2013

Title

BY-Rapa10'-Rep2

Sample type

SRA

Source name

Yeast cells

Organism

Saccharomyces cerevisiae

Characteristics

genotype: BY4741
growth conditions: 30ºC YPD OD=0.5
treatment: 200ng/mL rapamycin for 10 min

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

treated with 200ng/mL rapamycin for 10 min

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)

[email protected]

Phone

831-459-2612

Organization name

UCSC