|
| Status |
Public on Jan 01, 2020 |
| Title |
SHSY5Y_SOX9-GFP_1108 |
| Sample type |
SRA |
| |
|
| Source name |
Neuroblasotma cell line
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: SH-SY5Y
cell type: Neuroblasotma cell line
genotype/variation: SOX9 overexpression
plasmid: pCMV6-SOX9-GFP
|
| Growth protocol |
Cell lines were culture in DMEM/F-12 medium(Thermo Fisher Scientific) supplemented with 10% fetal bovine serum(Dutscher), 1X L-glutamine(Thermo Fisher Scientific), 1X sodium pyruvate(Thermo Fisher Scientific), and 1X MEM non-essential amino acids(Thermo Fisher Scientific), and maintained in a humidified incubator at 37°C, 5% CO2.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA of harvested cells was extracted by RNeasy Kit (QIAGEN) according to manufacturer's instruction
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
SH-SY5Y cell was transfected with pCMV6-SOX9-GFP, and GFP+ cells were sorted
|
| Data processing |
bcl2Fastq v2.19 software used for demultiplexing + basecalling.
reads trimmed with trimmomatic, options: ILLUMINACLIP:adapters.fa:1:20:7:5:true AVGQUAL:10 MINLEN:20
reads mapped with STAR v2.5.4b, options: --sjdbOverhang 150 --twopassMode None --runThreadN 8 --outFilterType BySJout --outFilterMatchNmin 30 --outFilterMismatchNmax 10 --outFilterMismatchNoverLmax 0.05 --outMultimapperOrder Random --alignSJDBoverhangMin 1 --alignSJoverhangMin 8 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outFilterMultimapNmax 50 --chimSegmentMin 15 --chimJunctionOverhangMin 15 --chimScoreMin 15 --chimScoreSeparation 10 --outSAMstrandField intronMotif --outSAMattributes All --outStd BAM_Unsorted --outSAMtype BAM Unsorted
count: FeatureCounts (Bioconductor), options: allowMultiOverlap = true; countPrimaryAlignmentsOnly= true; minFeatureOverlap=10; minMapQuality= 10 ; keepMultiHits=true
differential expression analysis: EdgeR, options: normMethod = TMM; backgroundExpression =10; testMethod = glm; deTest =QL
Genome_build: Homo_sapiens/Ensembl/GRCh38.p10/Annotation/Release_91-2018-02-26
Supplementary_files_format_and_content: tad-delimited, raw counts
|
| |
|
| Submission date |
Jun 19, 2019 |
| Last update date |
Jan 02, 2020 |
| Contact name |
giancarlo russo |
| E-mail(s) |
[email protected]
|
| Organization name |
ETH/University of Zurich
|
| Department |
Functional Genomics Center Zurich
|
| Street address |
winterthurerstrasse 190
|
| City |
Zurich |
| State/province |
Schweiz |
| ZIP/Postal code |
8057 |
| Country |
Switzerland |
| |
|
| Platform ID |
GPL24676 |
| Series (1) |
| GSE133014 |
Distinct SOX signature determines neuroblastoma origin and predicts clinical outcome |
|
| Relations |
| BioSample |
SAMN12096309 |
| SRA |
SRX6095306 |
