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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Mar 24, 2024 |
| Title |
NP-Plp Tumor 9 Grade UD |
| Sample type |
SRA |
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| Source name |
Tumor tissue
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| Organism |
Mus musculus |
| Characteristics |
strain: B6.129
mouse line: NP-Plp
diagnosis: GEM PNST/UD (grade undetermined)
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using the Direct-zol RNA Miniprep kit (Zymo), quantified by Qubit 3.0 Fluorometer, and quality checked by 4200 TapeStation High Sensitivity RNA ScreenTape assay (Agilent).
Libraries were prepared from 350 ng of total RNA using the TruSeq Stranded Total RNA Library Prep Kit (Illumina 20020599)
Libraries were sequenced on Illumina NovaSeq 6000, obtaining 100 million 100-bp paired-end reads.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
T3538T1
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| Data processing |
Total stranded RNA sequencing data were processed by the internal AutoMapper pipeline.First the raw reads were firs trimmed (Trim-Galore version 0.60), mapped to mouse (GRCm38, mm10) or human (GRCh38, hg38) genome assembly (STAR v2.7).
The gene level expression values were quantified (RSEM v1.31) based on GENCODE annotations (vM22 for GRCm38, v31 for GRCh38)
Supplementary_files_format_and_content: gene-level RSEM raw count, TPM, FPKM txt files
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| Submission date |
Apr 16, 2021 |
| Last update date |
Mar 24, 2024 |
| Contact name |
Hongjian Jin |
| E-mail(s) |
hongjian.jin@STJUDE.ORG
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| Organization name |
St Jude Children's Research Hospital
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| Department |
Center for Applied Bioinformatics
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| Street address |
262 Danny Thomas Place
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| City |
Memphis |
| State/province |
TN |
| ZIP/Postal code |
38015 |
| Country |
USA |
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| Platform ID |
GPL24247 |
| Series (1) |
| GSE172221 |
A genetic mouse model of malignant peripheral nerve sheath tumor with postnatal Nf1 and p53 loss recapitulates the histology and transcriptome of human tumors |
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| Relations |
| BioSample |
SAMN18757409 |
| SRA |
SRX10615771 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5244247_1966715_SJMMMPNST067347_D1-T3538T1.RSEM.genes.counts.txt.gz |
625.6 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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