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Sample GSM6507555

Query DataSets for GSM6507555

Status

Public on Aug 01, 2024

Title

T3 (Ribo-seq)

Sample type

SRA

Source name

Thyroid

Organism

Homo sapiens

Characteristics

sample pair: pair 3
tissue: Thyroid tumor tissue
tumor stage: T3bN1aM0, I
Sex: male
age: 54

Extracted molecule

total RNA

Extraction protocol

Thyroid cancer and adjacent normal tissue were collected, physiological saline cleaning, liquid nitrogen quick freezing.
After obtaining ribosome footprints above, Ribo-seq libraries were constructed using NEBNext® Multiple Small RNA Library Prep Set for Illumina® (catalog no.E7300S, E7300L). Briefly, adapters were added to both ends of RFs, followed by reverse transcription and PCR amplification. The 140-160bp size PCR products were enriched to generate a cDNA library and sequenced using Illumina HiSeqTM 2500 by Gene Denovo Biotechnology Co. (Guangzhou, China).

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina HiSeq 2500

Data processing

Raw reads containing over 50% of low quality bases or over 10% of N bases were removed. Adapter sequences were trimmed. Reads with length between 10-50bp were retained for subsequent analysis.
Short reads alignment tool Bowtie2 [1]was used for mapping reads to ribosome RNA (rRNA) database. The rRNA mapped reads will be removed. The remaining reads were further used in downstream analysis.
The rRNA removed reads of each sample were mapped to reference genome by Bowtie2 allowing no mismatches. RFs were assigned to different genomic features (5’UTR, CDS, 3’UTR and others) based on the position of the 5’ end of the alignment.
To monitor sequencing reliability, RFs density at different codon positions was calculated. Generally speaking, RFs have the highest density at the first base of codon.
Reads number in the open reading frame of coding genes was calculated by software RiboTaper[2], and the gene expression level was normalized by using FPKM (Fragments Per Kilobase of transcript per Million mapped reads) method.
Assembly: GRCh38.release 94
Supplementary files format and content: tab-delimited text file includes FPKM and count values for each Sample

Submission date

Aug 25, 2022

Last update date

Aug 01, 2024

Contact name

lv chengzhou

E-mail(s)

yidalcz@126.com

Phone

13390159116

Organization name

the first hospital of china medical university