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| Status |
Public on Jul 11, 2022 |
| Title |
bulk RNA NPCTKO #3 |
| Sample type |
SRA |
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| Source name |
GBM cells
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| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
tissue: GBM
age: 3 months
model: NPCTKO
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNA isolation was performed using the TRIZOL reagent (Invitrogen) according to manufacturer’s instructions. Tissue or cells were homogenized using a glass-Teflon in 1 ml or 500 µl TRIZOL reagent on ice and phase separation was achieved with 200 µl or 100 µl chloroform. After centrifugation at 12,000× g for 15 min at 4°C, RNA was precipitated by mixing aqueous phase with equal volumes of isopropyl alcohol and 0.5 µl 20 mg/ml glycogen. Precipitation were dissolved in DNase/RNase-free water (not diethylpyrocarbonate treated, Ambion).
Total RNA was extracted as described above. The concentration and quality of RNA was measured with Nanodrop 2000c (Thermo Fisher Scientific) and an Agilent 2100 Bioanalyzer (Agilent Technologies), respectively. RNA-seq libraries were constructed by NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB E7490) and NEBNext Ultra II Non-Directional RNA Second Strand Synthesis Module (NEB E6111). Briefly, mRNA was extracted by poly-A selected with magnetic beads with poly-T and transformed into cDNA by first and second strand synthesis. Newly synthesized cDNA was purified by AMPure XP beads (1:1) and eluted in 50 μl nucleotide-free water. RNA-seq libraries were sequenced by Illumina NovaSeq 6000 platform with pair-end reads of 150 bp. The sequencing depth was 60 million reads per library.
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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 |
Cutadapt (version 1.16, http://cutadapt.readthedocs.io/en/stable/guide.html) was used for adaptor sequence remove with the parameters -u 0 -u -30 -U 0 -U -30 -m 30
Cleaned reads were mapped to the mouse reference genome (UCSC mm10) using TopHat (version 2.1.1, http://ccb.jhu.edu/software/tophat/index.shtml) with default settings.
Principal component analysis (PCA) of the quality control matrices was employed to determine the presence of RNA-Seq sample outliers.
The gene expression level was calculated by Cufflinks (version 2.2.1, http://cole-trapnell-lab.github.io/ cufflinks) and normalized by fragments per kilobase of bin per million mapped reads (FPKM).
Genome_build: UCSC mm10 (GRCm38)
Supplementary_files_format_and_content: RNA-seq_Model1_NPCTKO_and_Model2_NSCHRas_shP53_raw_count.txt: Tab-delimited text file includes raw counts for each Sample.
Supplementary_files_format_and_content: RNA-seq_Model1_NPCTKO_and_Model2_NSCHRas_shp53_FPKM.txt: Tab-delimited text file includes FPKM values for each Sample.
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| Submission date |
Nov 24, 2021 |
| Last update date |
Jul 11, 2022 |
| Contact name |
Xuan Liu |
| E-mail(s) |
lx2014@whu.edu.cn
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| Organization name |
Wuhan university
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| Street address |
Donghu Road, No. 115, Wuchang District, Wuhan, Hubei Province, P.R. China
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| City |
Wuhan |
| ZIP/Postal code |
430071 |
| Country |
China |
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| Platform ID |
GPL24247 |
| Series (2) |
| GSE189541 |
Bulk RNA-Seq on GBM cells from NPCTKO and NSCHRas-shp53 mouse models |
| GSE190155 |
Bulk RNA-Seq and single-cell RNA-Seq on GBM cells from NPCTKO and NSCHRas-shp53 mouse models |
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| Relations |
| BioSample |
SAMN23428515 |
| SRA |
SRX13224717 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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