|
| Status |
Public on Mar 07, 2021 |
| Title |
MCH_PDX_CTRL_2 (RNA-seq) |
| Sample type |
SRA |
| |
|
| Source name |
glioma
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: glioma patient-derived xenograft
location: orthotopic
treatment: DMSO
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Tissue blocks were lysed in TRIzol reagent (Sigma-Aldrich). The lysate was well mixed with chloroform and spun for 15 min at 13000 g at 4 °C. RNA in top aqueous phase was collected and mixed with propan-2-ol to precipitate total RNA.
RNA libraries were prepared for sequencing using MGIEasymRNA Library Prep Kit V2.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
BGISEQ-500 |
| |
|
| Data processing |
Basecalls performed using BGISEQ-500.
SOAPnuke was used to get the "clean reads".
Mapping clean reads to hg19 whole genome using HISAT2
Bowtie2 was used to get the mapping ratio.
Fragments Per Kilobase Million (FPKM) was calculated based on the RSEM.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include fpkm values for each Sample
|
| |
|
| Submission date |
Mar 12, 2018 |
| Last update date |
Mar 08, 2021 |
| Contact name |
Jinquan Cai |
| E-mail(s) |
caijinquan666777@126.com
|
| Organization name |
Harbin Medical University
|
| Street address |
Xuefu Road
|
| City |
Harbin |
| ZIP/Postal code |
150086 |
| Country |
China |
| |
|
| Platform ID |
GPL23227 |
| Series (2) |
| GSE111673 |
RNA-seq of glioma patient-derived xenografts treated by DMSO or LY2109761 |
| GSE111676 |
Mesenchymal glioblastoma constitutes a major ceRNA signature in the TGF-Beta pathway |
|
| Relations |
| BioSample |
SAMN08685772 |
| SRA |
SRX3781628 |
