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Sample GSM4716852

Query DataSets for GSM4716852

Status

Public on Aug 11, 2020

Title

CLG_3: M. truncatula root with Gongronella sp. w5 inoculation_rep3

Sample type

SRA

Source name

M. truncatula root

Organism

Medicago truncatula

Characteristics

tissue: Root
treatment: Treated with Gongronella sp. w5 for 16 day

Extracted molecule

total RNA

Extraction protocol

Total RNA of root samples was extracted using the TransZol Plant RNA Kit (Transgen, Beijing, China). Paired-end cDNA sequencing libraries were carried out according to the manufacturer’s protocol of Illumina TruSeq Stranded Total RNA Library Preparation Kit.
Libraries were sequenced with the Illumina HiSeq 2000 platform (Shanghai Personal Biotechnology Co., Ltd)

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina HiSeq 2000

Data processing

FASTQ files are coded with Illumina 1.8+ version
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 the default parameters.
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.
Genome_build: Medicago truncatula Genome Database:http://www.medicagogenome.org/
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample.

Submission date

Aug 10, 2020

Last update date

Aug 11, 2020

Contact name

Wang Xiaojie

E-mail(s)

[email protected]

Phone

18756074074

Organization name

Anhui University