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Sample GSM7720322

Query DataSets for GSM7720322

Status

Public on May 05, 2024

Title

YFF_1

Sample type

SRA

Source name

Heart

Organism

Mus musculus

Characteristics

tissue: Heart
genotype: Ythdc1flox/flox

Extracted molecule

total RNA

Extraction protocol

Ythdc1flox/flox and Ythdc1-CKO mice were fed with normal chow for 15 days.Total RNA was extracted using Tripure Isolation Reagent (Roche, Mannheim, Germany). Three independent biological replicates for each group were used for RNA-seq.
mRNA was purified from total RNA by using poly-T oligo-attached magnetic beads.Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction uffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase, then use RNaseH to degrade the RNA. Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and dNTP. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then PCR amplification, the PCR product was purified by AMPure XP beads, and the library was finally obtained.
After the library is qualified, the different libraries are pooling according to the effective concentration and the target amount of data off the machine, then being sequenced by the Illumina NovaSeq 6000. The end reading of 150bp pairing is generated. The basic principle of sequencing is to synthesize and sequence at the same time (Sequencing by Synthesis). Four fluorescent labeled dNTP, DNA polymerase and splice primers were added to the sequenced flowcell and amplified. When the sequence cluster extends the complementary chain, each dNTP labeled by fluorescence can release the corresponding fluorescence. The sequencer captures the fluorescence signal and converts the optical signal into the sequencing peak by computer software, so as to obtain the sequence information of the fragment to be tested.

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina NovaSeq 6000

Data processing

The image data measured by the high-throughput sequencer are converted into sequence data (reads) by CASAVA base recognition. Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data(clean reads) were obtained by removing reads containing adapter, reads containing Nbase and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2(v2.0.5) and paired-end clean reads were aligned to the mouse reference genome(GRCm38.p6) using Hisat2 (v2.0.5). We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
featureCounts (v1.5.0-p3) was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs equenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.20.0). DESeq2 provide statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate . padj<=0.05 and |log2(foldchange)| >= 0 were set as the threshold for significantly differential expression.
Assembly: mouse reference genome(GRCm38.p6)
Supplementary files format and content: Processed data files; txt; fpkm of each gene

Submission date

Aug 21, 2023

Last update date

May 05, 2024

Contact name

lei shi

E-mail(s)

shilei2021@yeah.net

Organization name

jilin university

Street address

changchun