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| Status |
Public on Jun 03, 2024 |
| Title |
KO-rep3 [ncRNA-seq] |
| Sample type |
SRA |
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| Source name |
bone marrow cells
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| Organism |
Mus musculus |
| Characteristics |
tag: bone marrow
genotype: Mat KO
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| 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.
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| Library strategy |
ncRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 2500 |
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| 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
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| Submission date |
Feb 10, 2021 |
| Last update date |
Jun 03, 2024 |
| Contact name |
Jiang Penglei |
| E-mail(s) |
jpl3982233@zju.edu.cn
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| Organization name |
Zhejiang University
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| Department |
School of basic medicine science
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| Street address |
Yuhangtang Road 866
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| City |
Hangzhou |
| ZIP/Postal code |
310058 |
| Country |
China |
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| 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 |
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| Relations |
| BioSample |
SAMN17850070 |
| SRA |
SRX10064683 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5073645_KO3.ncRNA.counts.txt.gz |
12.5 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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