|
| Status |
Public on Jan 03, 2019 |
| Title |
BT-28_WT-Tag_RNA-seq |
| Sample type |
SRA |
| |
|
| Source name |
Mouse brainstem tumor
|
| Organism |
Mus musculus |
| Characteristics |
full genotype: Nestin-creERT2; H3f3aLSL-WT-Tag/+; LSL-PDGFRαV544ins; Trp53flox/flox
gender: female
|
| Extracted molecule |
total RNA |
| Extraction protocol |
1 ml of Trizol (Invitrogen, 15596-018) was added to 2 x 106 dissociated neurosphere cells. 2 ul of 1:20 diluted ERCC spike in (Ambion Cat #4456740, Lot # 1412017) was added directly to the Trizol. For tumor tissue, a piece of snap frozen tissue was mechanically dissociated in Trizol. RNA was extracted following the standard Trizol protocol except the final 70% EtOH wash was repeated three times.
Libraries were prepared from total RNA with the TruSeq Stranded Total RNA Library Prep Kit (Illumina.)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
Basecalls performed using CASAVA
fastq files werer mapped with internal pipeline that employs Tophat2 and STAR
reads were counted using an internal pipeline and converted to FPKM using mm9
Genome_build: mm9
Supplementary_files_format_and_content: matrix txt file with FPKM for each gene symbol for each sample
|
| |
|
| Submission date |
Dec 20, 2017 |
| Last update date |
Jan 03, 2019 |
| Contact name |
Hongjian Jin |
| E-mail(s) |
hongjian.jin@STJUDE.ORG
|
| Organization name |
St Jude Children's Research Hospital
|
| Department |
Center for Applied Bioinformatics
|
| Street address |
262 Danny Thomas Place
|
| City |
Memphis |
| State/province |
TN |
| ZIP/Postal code |
38015 |
| Country |
USA |
| |
|
| Platform ID |
GPL21103 |
| Series (2) |
| GSE108362 |
Spontaneous DIPG Modeling Reveals Novel H3.3 K27M-Mediated Oncogenic Mechanisms Acting Through Epigenetic Effects [RNA-seq] |
| GSE108364 |
Spontaneous DIPG Modeling Reveals Novel H3.3 K27M-Mediated Oncogenic Mechanisms Acting Through Epigenetic Effects |
|
| Relations |
| BioSample |
SAMN08214594 |
| SRA |
SRX3491027 |
