|
| Status |
Public on Nov 10, 2019 |
| Title |
shGFP_dup1 |
| Sample type |
SRA |
| |
|
| Source name |
Kelly cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: Neuroblastoma
shRNA: control
|
| Treatment protocol |
Kelly cells were infected with the shRNA-expressing lentivirus. Puromycin selection was carried out 36 hours post infection, after which total RNA were harvested.
|
| Growth protocol |
Kelly cells were cultured in RPMI-1640 medium supplemented with 10% FBS and Pen/Strep.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was harvested using the miRNeasy Mini Kit (Qiagen).
Reverse stranded library construction and sequencing of paired-end, 100-bp-long reads by the BGISeq500 were performed at the BGI Biotech Solutions
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
BGISEQ-500 |
| |
|
| Description |
shGFP_dup1
|
| Data processing |
RNA-seq datasets of two control samples and two knockdown samples for LMO1 and MYCN were aligned to the hg19 human genome using STAR 2.5.2a with the parameter outFilterMultimapNmax set to 1.
htseq-count v0.6.1 was used for the mapped reads in .bam files to generate count tables based on the Ensembl gene annotation
Bioconductor package DESeq2 v1.12.4, with the intersection-strict mode, was used to analyze differential gene expression.
Genome_build: hg19
Supplementary_files_format_and_content: txt file for differentially expressed genes
Supplementary_files_format_and_content: htseq-count file
|
| |
|
| Submission date |
Aug 21, 2018 |
| Last update date |
Nov 18, 2019 |
| Contact name |
Tze King Tan |
| Organization name |
National University of Singapore
|
| Department |
Cancer Science Institute
|
| Lab |
Takaomi Sanda Lab
|
| Street address |
14 Medical Drive
|
| City |
Singapore |
| ZIP/Postal code |
117599 |
| Country |
Singapore |
| |
|
| Platform ID |
GPL23227 |
| Series (2) |
| GSE118823 |
RNA-seq analysis after LMO1 or MYCN knockdown in Kelly cells |
| GSE132760 |
ASCL1 is a MYCN- and LMO1-dependent member of the adrenergic neuroblastoma core regulatory circuitry |
|
| Relations |
| BioSample |
SAMN09867735 |
| SRA |
SRX4582011 |
