|
| Status |
Public on Apr 08, 2021 |
| Title |
HF-3177_RNAseq_rep2 |
| Sample type |
SRA |
| |
|
| Source name |
Glioblastoma neurosphere cell suspensions
|
| Organism |
Homo sapiens |
| Characteristics |
source: Glioblastoma
|
| Growth protocol |
Tumor specimens were dissociated and cultured as neurospheres in DMEM/F12 medium (11330-032, Gibco) supplemented with N-2 supplement (17502-048, Gibco) and growth factors (EGF and FGF-basic). Cells with passages between 15 and 26 were used for experiments.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA was isolated in biological replicates using AllPrep DNA/RNA Mini Kit (80204, QIAGEN).
Strand-specific RNA libraries were generated from 300 ng of total RNA following the manuals of KAPA Stranded mRNA Sequencing Kit (KK8502, KAPA Biosystems). Libraries were sequenced on Illumina platform with 75 bp paired-end sequencing.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
genes.fpkm_tracking
|
| Data processing |
The raw sequencing reads were trimmed using Trim Galore version 0.4.3 (options: --stringency 3 -q 20 -e .20 --length 15 --paired) and aligned to the hg19 genome using hisat 2.1.0 (options: --dta-cufflinks). The transcripts were assembled using Cufflinks 2.2.1. and the final expression level were quantified using Cuffdiff (options: --library-type fr-firststrand).
Illumina RTA-1.18 software used for basecalling
Genome_build: hg19
|
| |
|
| Submission date |
Jan 07, 2019 |
| Last update date |
Apr 08, 2021 |
| Contact name |
Chia-Lin Wei |
| E-mail(s) |
[email protected]
|
| Organization name |
University of Washington
|
| Department |
The Northwest Genomics Center (NWGC)
|
| Lab |
Genome Sciences
|
| Street address |
3720 15th Ave NE
|
| City |
Seattle |
| State/province |
WA |
| ZIP/Postal code |
98195-5065 |
| Country |
USA |
| |
|
| Platform ID |
GPL18573 |
| Series (1) |
| GSE124769 |
Oncogenic extrachromosomal DNA functions as mobile enhancers to globally amplify chromosomal transcription |
|
| Relations |
| BioSample |
SAMN10711825 |
| SRA |
SRX5222977 |
