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Sample GSM7695748 Query DataSets for GSM7695748
Status Public on Apr 03, 2024
Title D101, 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: DDH
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
City Hangzhou
State/province Zhejiang
ZIP/Postal code 310000
Country China
 
Platform ID GPL25947
Series (1)
GSE240299 miRNA and mRNA transcriptome profiling of chondrocytes in proliferative zone of acetabular cartilage in developmental dysplasia of the hip
Relations
BioSample SAMN36877418
SRA SRX21286090

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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