|
| Status |
Public on Feb 28, 2017 |
| Title |
3CTR |
| Sample type |
SRA |
| |
|
| Source name |
control cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: human glioblastoma stem cell
tissue type: brain
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The RNA sequencing libraries were constructed using the Illumina mRNA-Seq Prep Kit, and they were sequenced on the Illumina HiSeq 2000 platform in paired-end reads with 150 bp length
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer |
| |
|
| Data processing |
Basecalls performed using CASAVA version 1.8
Data were filtered using GSQCToolkitv2.3.3 with parameters –pe -cutOffReadLen4HQ 70 –cutOffQualScore 20 N 5.
RNA-seq reads were aligned to the human genome assembly using Tophat-2.1.0 with read-mismatches=2.
The fragments per kilobase of transcript per million fragments (FPKM) of the genes were calculated using express cufflinks2.2.1, --max-multiread-fraction 0.75, Cuffnorm all samples from different stages, –library-norm-method is genometric. Then raw data was transform into logarithm, log2(FPKM +1).
|
| |
|
| Submission date |
Feb 27, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Junjun Hao |
| E-mail(s) |
haojunjun@mail.kiz.ac.cn
|
| Organization name |
Kunming Institute of Zoology
|
| Street address |
32 Jiaochang Donglu Kunming
|
| City |
Kunming |
| ZIP/Postal code |
650223 |
| Country |
China |
| |
|
| Platform ID |
GPL9052 |
| Series (1) |
| GSE95392 |
3alpha-acetonyltabersonine induces glioblastoma apoptosis via the inhibition of DNA damage repair |
|
| Relations |
| SRA |
SRX2592104 |
| BioSample |
SAMN06472380 |
