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| Status |
Public on Jun 03, 2024 |
| Title |
KO mouse [Polysome RNA RNA-seq] |
| Sample type |
SRA |
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| Source name |
bone marrow cells
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| Organism |
Mus musculus |
| Characteristics |
tissue: bone marrow
genotype: Mat KO
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| Extracted molecule |
total RNA |
| Extraction protocol |
WT/KO BM cells (4× 107) were incubated with 100 μg/ml of cycloheximide(Cell Signaling Technology) for 10 minutes at 37°C, washed with cold PBS containing100 μg/ml of cycloheximideand lysed as 50 mM HEPES, 2mM MgCl2, 100 mM KCl, 1% Triton X-100, 1mM DTT, 100 μg/ml cycloheximide, 20U/ml RNase Inhibitor(EDTA free) and 1× Complete Protease Inhibitor, EDTA-free (Roche). Polysomal RNA was separated on 10.5mL 10%-50% linear sucrose gradients containing 10mM Tris-HCl (pH 7.5), 5mM MgCl2, and 100mM NaCl, and centrifuged in a SW41 rotor at 38,000rpm for 3 hours. Gradients were then measured of absorbance at 254 nm and fractionated using a Gradient Station fractionator.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
Illumina Casava1.8 software used for basecalling.
Raw data were trimmed with trimmomatic and then were filtered out any reads could map to rRNA (Genebank: BK000964.3) using SortMeRNA (2.1b)
Clean data were aligned to the mouse reference genome GRCm38 by HISAT2 (2.1.0) with default setting.
Genes counts were quantified by HTSeq (0.11.2)[9] with parameter “--mode intersection-strict --stranded no --minaqual 1”.
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited 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 |
GPL24247 |
| Series (2) |
| GSE166514 |
Small Nucleolar RNAs in the Dlk1-Gtl2 Imprinting Locus Maintains LT-HSC Self-renewal by Regulation of rRNA Modification and Translation [Polysome RNA RNA-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 |
SAMN17850034 |
| SRA |
SRX10064670 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5073632_KO1.geneCounts.txt.gz |
131.4 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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