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Sample GSM7695747

Query DataSets for GSM7695747

Status

Public on Apr 03, 2024

Title

N103, RNA-seq

Sample type

SRA

Source name

proliferative zone of the acetabular cartilage

Organism

Rattus norvegicus

Characteristics

tissue: proliferative zone of the acetabular cartilage
treatment: control
time: ten days after birth

Extracted molecule

total RNA

Extraction protocol

The total RNA was extracted according to the instruction manual of the TRlzol Reagent (Life technologies, California, USA).
Library preparation for mRNA sequencing: A total amount of 1.5 μg RNA per sample was used as input material for rRNA removal using the Ribo-Zero rRNA Removal Kit (Epicentre, Madison, WI, USA). Sequencing libraries were generated using NEBNextR UltraTM Directional RNA Library Prep Kit for IlluminaR (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.
Library preparation for miRNA sequencing: A total amount of 2.5 ng RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNextR UltraTM small RNA Sample Library Prep Kit for IlluminaR(NEB, USA) folloing manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina NovaSeq 6000

Description

All_mRNA_fpkm.txt

Data processing

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 ploy-N and low quality reads from raw data.
The adaptor sequences and low-quality sequence reads were removed from the data sets. Raw sequences were transformed into clean reads after data processing. These clean reads were then mapped to the reference genome sequence. Only reads with a perfect match were further analyzed and annotated based on the reference genome. HISAT2 soft were used to map with reference genome.
Gene expression levels were estimated by fragments per kilobase of transcript per million fragments mapped
Differential expression analysis of two conditions/groups was performed using the DESeq2.
Assembly: Rnor_6.0
Supplementary files format and content: TXT files include FPKM values for each Sample

Submission date

Aug 07, 2023

Last update date

Apr 03, 2024

Contact name

Jiahui Liu

E-mail(s)

ljh0706@zju.edu.cn

Organization name

Children's Hospital, Zhejiang University School of Medicine

Street address

3333 Binsheng Rd