GEO Accession viewer

NCBI > GEO > Accession Display

Not logged in | Login

GEO help: Mouse over screen elements for information.

Sample GSM7910940

Query DataSets for GSM7910940

Status

Public on Aug 14, 2024

Title

Control5

Sample type

SRA

Source name

Atrium

Organism

Canis lupus familiaris

Characteristics

tissue: Atrium

Extracted molecule

total RNA

Extraction protocol

For the extraction of total RNA, 1 ml TRIzol (Magen (R4801-02)) was added to the sample ground in liquid nitrogen, and total RNA was extracted by the TRIzol method. Then, the sample concentration and 260/280, 260/230 ratio were measured and recorded by Nanodrop (ThermoFisher (ND-2000)), and the integrity of RNA was checked by Agilent 4150 (Agilent Technologies Inc).
For the library construction, oligo (DT) beads were used to enrich eukaryotic mRNA, fragmentation buffer was added to randomly interrupt mRNA, mRNA was used as template to synthesize two strands of cDNA, and double-stranded cDNA was purified by AMPure XP beads. The purified double-stranded cDNAs were end-repaired and A-tailed, and then the fragment size was selected by AMPure XP beads. Finally, the final cDNA library was obtained by PCR enrichment.

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

DNBSEQ-T7

Description

control

Data processing

The raw image data files obtained by high-throughput sequencing were transformed into the original sequencing sequence by CASAVA Base Calling analysis(Sequenced Reads)
The sequencing quality value Phred.The conversion formula between Quality Score (Q-phred) and Probability of Incorrect Base Call (P) is:Q-phred= -10log10 (P)
The original sequencing sequence contains Low Quality reads with connectors. To ensure the quality of subsequent analysis, it is necessary to remove the connectors and filter out low quality reads. The number of bases with base quality value less than or equal to 25 accounted for more than 60% of the whole reads) and the proportion of N (N means that base information could not be determined) was greater than 5% to obtain clean reads that could be used for subsequent analysis
In this project, the HISAT2 software was used to sequence align CleanReads with the designated genome to obtain information about their position on the reference genome.
The expected number of Fragments PerKilobase of transcript sequence per Millions (FPKM) was calculated for each gene in each sample using featureCounts software base pairs sequenced)
Assembly: canFam3.1
Supplementary files format and content: Include FPKM values for each Sample with xls files.

Submission date

Nov 20, 2023

Last update date

Aug 14, 2024

Contact name

Yinglong Hou

E-mail(s)

yinglonghou@hotmail.com

Organization name

Qianfoshan Hospital of Shandong Province

Street address

No. 16766, Jingshi Road, Lixia District, Jinan City, Shandong Province, China