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Sample GSM5373522

Query DataSets for GSM5373522

Status

Public on Jun 12, 2021

Title

PE5 - RNA Sequencing

Sample type

SRA

Source name

placenta

Organism

Homo sapiens

Characteristics

tissue: placenta
disease: early-onset preeclampsia

Extracted molecule

total RNA

Extraction protocol

Total RNA was extracted from the frozen human placentas using TRIZOL reagent following the manufacturer’s protocol. The RNA yield and purity were determined using Agilent 2100 Bio-analyzer (Agilent Technologies, Santa Clara, CA, United States) and NanoDrop 1000 Spectrophotometer (Thermo Fisher Scientific, Waltham, MA, United States). All RNA samples passed quality control.
RNA libraries were prepared for sequencing using standard Illumina protocols

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina NovaSeq 6000

Data processing

The overall quality of raw reads was evaluated using program FastQC, and then raw reads were trimmed to remove adapter sequences using Cutadapt script
As for microRNA sequencing, the cleaned reads were mapped to human genomes GRCh38 by bowtie.
As for RNA sequencing, the cleaned reads were mapped to human genome hg19/GRCh37 using the Hisat2 with perfect matches (0 mismatches).
miRDeep2 was used to quantify the expression level of known mature miRNAs curated in the human miRBase database.
RNA-level quantification was performed using StringTie, which is a reads summarization program to efficiently count the mapped reads for genomic features
The miRNA-seq and RNA-seq data were analyzed by Edge R package, which employs a negative binomial generalized linear model with likelihood ratio test (glmLRT) to compare read counts of each miRNA or gene between two conditions
Differentially expressed miRNAs and genes were classified using a significance of log2 fold change > 1.5 or <-1.5 and a p -value < 0.05.
The count-per-million (CPM) at log2 scale, denoted as LogCPM, was computed for visualization of miRNA/gene abundance, heatmap-clustering analysis.
Genome_build: hg19/GRCh38/GRCh37
Supplementary_files_format_and_content: tab-delimited excel files include FPKM values for each Sample
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

Submission date

Jun 11, 2021

Last update date

Jun 12, 2021

Contact name

Tao Duan

E-mail(s)

duan_taotongji@aliyun.com

Organization name

shanghai first maternity and infant hospital , tongji university school of medicine

Department

obstetrics