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| Status |
Public on May 02, 2018 |
| Title |
Normal_wt4 |
| Sample type |
SRA |
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| Source name |
tissue
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| Organism |
Mus musculus |
| Characteristics |
tissue: supratentorial ependymoma
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted from cell cultures every two weeks during the exponential growth phase; RNA was isolated from 0.5-1.0×106 cells. Total RNA was prepared using RNeasy Mini Kit with DNase I (Qiagen). RNA concentration and quality (A260/A280) was measured using a NanoDrop 1000 Spectrophotometer (Thermo Scientific)
RNA libraries were prepared for sequencing using standard Illumina protocols
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Description |
Normal_wt4
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| Data processing |
Sequencing was performed using an Illumina HiSeq 2500 in Rapid Run mode and employed a paired-end, 50 base read length (PE50) sequencing strategy.
RNA-seq reads were aligned to the UCSC mm10 assembly using Tophat2 and counted for gene associations against the UCSC genes database with HTSeq
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include raw values for each Sample.
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| Submission date |
Jan 30, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Sonali Arora |
| E-mail(s) |
sarora@fredhutch.org
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| Organization name |
FHCRC
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| Street address |
1100 Fairview Ave N,
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| City |
Seattle |
| State/province |
WA |
| ZIP/Postal code |
98109 |
| Country |
USA |
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| Platform ID |
GPL17021 |
| Series (1) |
| GSE93765 |
A de novo mouse model of C11orf95-RELA fusion-driven ependymoma identifies driver functions in addition to NFκB |
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| Relations |
| BioSample |
SAMN06282519 |
| SRA |
SRX2528316 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2472448_raw_TO13_H271NL_data.txt.gz |
103.2 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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