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Sample GSM5532039

Query DataSets for GSM5532039

Status

Public on Jun 30, 2023

Title

S94

Sample type

SRA

Source name

plasma

Organism

Homo sapiens

Characteristics

tissue: plasma
age: 57
gender: male
disease state: healthy

Extracted molecule

total RNA

Extraction protocol

Total RNA was extracted from plasma samples using the Qiagen miRNeasy Serum/Plasma Kit. Briefly, frozen plasma samples were thawed, vortexed and centrifuged for 16000 x g in 10 minutes and 50 µl was used for RNA extraction following the manufacturer’s protocol. Purified RNA was eluted in 50µl H2O and saved at -80C.
4 µl of purified RNA was used in a Small-seq protocol to construct the libraries (Hagemann-Jensen et al., 2018). Small RNA libraries were pooled and sequenced using an Illumina HiSeq 3000 platform for 100 bp single read.

Library strategy

ncRNA-Seq

Library source

transcriptomic

Library selection

size fractionation

Instrument model

Illumina HiSeq 3000

Description

94_S66_L001_R1_001

Data processing

Reads were mapped to 202,272 Ensembl transcript IDs using the Smallseq data analysis pipeline (Hagemann-Jensen et al., 2018), and to 4,121 transfer RNA fragments (tRF) using the MINTmap pipeline (Loher et al., 2017).
Only small RNA with read counts higher than 1 in more than 20% of samples were kept, resulting in a list of 4,767 small RNA.
Counts were rounded and data normalization and differential expression analysis was performed with the DESeq2 package (version 1.26.0) (Love et al. 2014). Small RNA levels were used as the dependent variable and chronological age as the explanatory variable. A local fit was used for estimating dispersions. Size factor normalized small RNA counts were obtained using the counts functions with arguments normalized = T.
After DESeq2 analysis, small RNA with unclear transcripts biotypes were removed from all analysis since they indicate potential degradation products (i.e. protein coding, lncRNA, processed transcript, retained intron, …). Transcript biotypes were defined using the biomaRt package (version 2.42.0) (Durinck et al. 2005). A total of 587 small RNA were kept after this filtering step, of which 276 were significantly associated with age at an FDR threshold of 0.2.
Genome_build: hg38
Supplementary_files_format_and_content: raw_counts_Smallseq_Ensembl.txt (raw counts)
Supplementary_files_format_and_content: raw_counts_MINTmap_tRF.txt (raw counts)
Supplementary_files_format_and_content: DESeq2_normalized_counts.xlsx (normalized counts)
Supplementary_files_format_and_content: DESeq2_small_RNA_association_with_age.xlsx (significance table)

Submission date

Aug 23, 2021

Last update date

Jun 30, 2023

Contact name

Christian Günter Riedel

E-mail(s)

christian.riedel@ki.se

Organization name

Karolinska Institute

Department

Biosciences and Nutrition