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Status |
Public on Jun 12, 2021 |
Title |
PE1 - RNA Sequencing |
Sample type |
SRA |
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Source name |
placenta
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Organism |
Homo sapiens |
Characteristics |
tissue: placenta disease: early-onset preeclampsia
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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
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina NovaSeq 6000 |
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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
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Submission date |
Jun 11, 2021 |
Last update date |
Jun 12, 2021 |
Contact name |
Tao Duan |
E-mail(s) |
duan_taotongji@aliyun.com
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Organization name |
shanghai first maternity and infant hospital , tongji university school of medicine
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Department |
obstetrics
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Street address |
NO.2699, West Gao ke Road, Pudong New District
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City |
shanghai |
ZIP/Postal code |
201204 |
Country |
China |
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Platform ID |
GPL24676 |
Series (1) |
GSE177049 |
Integrative Analysis of miRNA and gene Expression Profiles of Early-Onset Preeclampsia |
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Relations |
BioSample |
SAMN19670504 |
SRA |
SRX11122127 |
Supplementary data files not provided |
SRA Run Selector |
Raw data are available in SRA |
Processed data are available on Series record |
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