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Sample GSM5073643 Query DataSets for GSM5073643
Status Public on Jun 03, 2024
Title KO-rep1 [ncRNA-seq]
Sample type SRA
 
Source name bone marrow cells
Organism Mus musculus
Characteristics tag: bone marrow
genotype: Mat KO
Extracted molecule total RNA
Extraction protocol Total RNA was isolated using Trizol (Invitrogen).
1~3 μg total RNA per sample was used for library construction, which was generated using NEBNext Multiplex Small RNA Library Prep Set for Illumina (NEB) following manufacturer’s instructions. After synthesis of first strand cDNA, PCR amplification was performed using LongAmp Taq 2X Master Mix, SR Primer for illumina and index primer. PCR products were purified on a 8% polyacrylamide gel (100V, 80 min). DNA fragments corresponding to 170~370 bp (the length of snoRNA plus adaptors) were recovered and dissolved in 8 μL elution buffer. At last, library quality was assessed on the Agilent Bioanalyzer 2100 system using DNA High Sensitivity Chips. After clustering of the index-coded samples, the library preparations were sequenced on an Illumina NovaSeq platform.
 
Library strategy ncRNA-Seq
Library source transcriptomic
Library selection size fractionation
Instrument model Illumina HiSeq 2500
 
Data processing Illumina Casava1.8 software used for basecalling.
The raw reads were trimmed for adaptor sequences and low quality bases using trimmomatic (0.38)
The trimmed reads length less than 17 bp were removed. Clean reads for each sample were aligned by bowtie2 (2.3.4.1) with parameter “--very-sensitive-local” to the artificial small ncRNA reference which include ENSEMBL annotated small ncRNAs (miRNA, misc_RNA, Mt_rRNA, Mt_tRNA, snoRNA, snRNA, tRNA) and 45S pre-rRNA (NR_046233.2).
Read counts per ncRNA were calculated by a perl script.
Genome_build: GRCm38
Supplementary_files_format_and_content: Comma separated text files with raw gene counts for every gene and every sample
 
Submission date Feb 10, 2021
Last update date Jun 03, 2024
Contact name Jiang Penglei
E-mail(s) jpl3982233@zju.edu.cn
Organization name Zhejiang University
Department School of basic medicine science
Street address Yuhangtang Road 866
City Hangzhou
ZIP/Postal code 310058
Country China
 
Platform ID GPL17021
Series (2)
GSE166517 Small Nucleolar RNAs in the Dlk1-Gtl2 Imprinting Locus Maintains LT-HSC Self-renewal by Regulation of rRNA Modification and Translation [ncRNA-seq]
GSE166518 Small Nucleolar RNAs in the Dlk1-Gtl2 Imprinting Locus Maintains LT-HSC Self-renewal by Regulation of rRNA Modification and Translation
Relations
BioSample SAMN17850072
SRA SRX10064681

Supplementary file Size Download File type/resource
GSM5073643_KO1.ncRNA.counts.txt.gz 12.0 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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