GEO Accession viewer

NCBI > GEO > Accession Display

Not logged in | Login

GEO help: Mouse over screen elements for information.

Sample GSM7233673

Query DataSets for GSM7233673

Status

Public on May 31, 2023

Title

WL_NNCON_L_1

Sample type

SRA

Source name

leaf

Organism

Hordeum vulgare

Characteristics

tissue: leaf
varity: Nasonijo
treatment: Waterlogging stress was carried out on barley seedlings with three leaves at one stage
time: 0 hour

Extracted molecule

total RNA

Extraction protocol

After qualified RNA samples were detected, magnetic beads with Oligo(dT) were used to enrich mRNA of eukaryotes
mRNA was divided into fragments by fragmentation buffer. cDNA was synthesized by six-base random hexamers based on mRNA template. Buffer solution, dNTPs, and DNA polymerase I and RNaseH were then added to synthesize the two-strand cDNA, which was then purified using AMPure XP beads. The purified double-stranded cDNA was first end-repaired with A tail and connected with sequencing connectors, and then AMPure XPbeads were used for segment size selection. After that, USER enzyme was used to degrade the second strand of cDNA containing U, so that the final sequencing information came from the first strand cDNA, thus preserving the strand orientation of mRNA. Finally, PCR products were amplified and purified by AMPure XP beads to obtain chain specific cDNA libraries.

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina HiSeq 2000

Description

NNCON_L_1
WL_AllSamplesFPKMValue.xlsx

Data processing

Fastp V0.20
1. Remove the Adapter sequence; 2. Reads with low quality (mass value less than 15) whose base number exceeded 40% of the Read length ratio were removed; 3. Reads with more than 5 bases of "N" were removed; 4. From the 5 'end of Reads (i.e., the beginning of Reads), sliding window quality filtering was carried out, and the sliding window whose average base quality was lower than the threshold value (20) was cut out (sliding window size 4); 5. Reads less than 36 in length were removed after filtering.
Using Hisat2 software, select the reference genome and annotation file of barley in NCBI or ENSEMBL and find the comparison with default parameters. Then evaluate the comparison of reads (read segments) obtained by sequencing.
The number of reads for each gene is calculated by using featureCounts v1.5.0, including the SAM recounts produced by Hisat and the GTF recounts of the genome. Then the FPKM value of the gene is calculated using the formula to represent its expression, depending on the length of the exon.
Assembly: Morex v1.0
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

Submission date

Apr 27, 2023

Last update date

May 31, 2023

Contact name

zhenxiang zhou

E-mail(s)

zzx526560938@outlook.com

Phone

17694804542

Organization name

Yangzhou University