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Sample GSM2985449

Query DataSets for GSM2985449

Status

Public on Jun 07, 2019

Title

SC5314

Sample type

SRA

Source name

cells

Organism

Candida albicans

Characteristics

tissue: cells
strain: SC5314

Extracted molecule

total RNA

Extraction protocol

Cells of the JL01 and SC5314 were inoculated from overnight cultures by 1% into liquid YPD plus 10% serum medium at 37°C for 3 h. Cells were collected and total RNA was extracted as described. RNA-Seq analysis was performed by the company Majorbio (Shanghai, China). mRNA was purified, fragmented and used to synthesize cDNA. The library products were sequenced on the HisSeq 4000 platform using the HisSeq 4000 PE Cluster Kit and HisSeq 4000 SBS Kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina HiSeq 4000

Data processing

Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.

Submission date

Feb 07, 2018

Last update date

Jun 07, 2019

Contact name

Chengzhen Zhang

E-mail(s)

782369857@qq.com

Organization name

Nanjing University

Street address

22 Han-kou road