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Sample GSM1055163 Query DataSets for GSM1055163
Status Public on Dec 19, 2014
Title Vv homokaryon strain PYd15
Sample type SRA
 
Source name Mushroom
Organism Volvariella volvacea
Characteristics strain: PYd15
nuclear condition: homokaryotic
tissue: Mycelia
Growth protocol V. volvacea strains were routinely grown at 32 °C on potato dextrose agar medium (PDA) (200 g.L-1 of potato tissue, 20 g.L-1 glucose,20 g.L-1 agar). Liquid cultures were prepared in potato dextrose broth by shaking at 150 rpm for 7 days.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted from mycelia using pBIOZOL Plant Total RNA Extraction Reagent, according to the manufacturer’s protocol (BioFlux). The isolated RNA was treated with RNeasy plant mini kit to remove potential genomic DNA contamination, according to the manufacturer’s protocol (QIAGEN, Germany). RNA integrity and concentration were evaluated using an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA). RNA (6 μg) from each of the three strains was submitted to BGI-Shenzhen (Shenzhen, China) for library construction and sequencing.
Sequence tag preparation was carried out using the Illumina Gene Expression Sample Prep Kit according to the manufacturer’s protocol.
library strategy: 3'-tag digital gene expression (DGE)
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
 
Description Sample 2
Data processing Illumina Cluster Station and Illumina HiSeq™ 2000 instrument used for basecalling.
Raw sequences have 3' adaptor fragments as well as a few low-quality sequences and several types of impurities. Raw sequences are transformed into Clean Tags after certain steps of data-processing.
A virtual libraries containing all the possible CATG+17 bases length sequences of the reference gene sequences. All clean tags were mapped to the reference sequences and only 1bp mismatch is considered. Clean tags mapped to reference sequences from multiple genes were filtered. Remainder clean tags were designed as unambiguous clean tags. The number of unambiguous clean tags for each gene was calculated and then normalized to TPM (number of transcripts per million clean tags). ('t Hoen, Ariyurek, et al. 2008; Morrissy, Morin, et al. 2009).
Genome_build: V.volvacea strain PYd21 genome data
Supplementary_files_format_and_content: tab-delimited text files include tag sequences,tag number and TPM values for each strain.
 
Submission date Dec 19, 2012
Last update date May 15, 2019
Contact name Baogui Xie
E-mail(s) mrcfafu@163.com
Phone +86-591-83789277
Fax +86-591-83789277
Organization name mrcfafu
Department Mycological Research Center
Street address Shangdian Road
City Fuzhou
State/province Fujian
ZIP/Postal code 350002
Country China
 
Platform ID GPL16412
Series (1)
GSE43019 Composition and expression of genes encoding carbohydrate-active enzymes in the straw-degrading mushroom Volvariella volvacea
Relations
SRA SRX212029
BioSample SAMN01832040

Data table header descriptions
SEQUENCE
COUNT
TPM Transcript Per Million

Data table
SEQUENCE COUNT TPM
CATGTAGATGCTTGGTGGGCA 2 0.35
CATGGGTCGTGTCTTACGTGG 2 0.35
CATGACATCGTGACGGTGGGG 2 0.35
CATGCAGACTCTATCTTTGAT 2 0.35
CATGTTCTCTAAAAAAAAAAA 2 0.35
CATGTATCAACTGAAAAAAAA 2 0.35
CATGAACTAGCCACGAGTTTC 2 0.35
CATGATGACCTACCGATTACT 2 0.35
CATGCGAACCACGCGGCATCA 2 0.35
CATGTTGATGCTGGGAATGAG 2 0.35
CATGAGGGTTGGGTGGAGGGG 2 0.35
CATGCAACCTGAACAAAAAAA 2 0.35
CATGATACGTGTAATTGTGCA 2 0.35
CATGGTCGCGGTCGTTTGGAT 2 0.35
CATGTTGGGTTTTTGCTGGAG 2 0.35
CATGCTTTGTTATACTTCAAA 2 0.35
CATGGCAGGTAGTGGGGGAGG 2 0.35
CATGGGGTTCGTCGTCAAAAA 2 0.35
CATGGAGAGTGGTGGAGGGTC 2 0.35
CATGTCCTTAGGTACCTCTGG 2 0.35

Total number of rows: 86772

Table truncated, full table size 2504 Kbytes.




Supplementary file Size Download File type/resource
GSM1055163_PYd15_TagCopyNumber.txt.gz 557.8 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data included within Sample table

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