|
| Status |
Public on Jun 28, 2022 |
| Title |
Scrambled Rep#1 |
| Sample type |
SRA |
| |
|
| Source name |
Osteosarcoma
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: 143B
cell type: Osteosarcoma
treatment: scrambled-siRNA control
harvest time: 48 hour
|
| Treatment protocol |
143B cells were grown in 6-well plates and transfected with with either scrambled-siRNA or ALKBH5-siRNAs (Sigma-Aldrich) for 48 hours. Transfection was carried out using the RNAiMAX Reagent (Thermofisher) according to the manufacturer’s protocol.
|
| Growth protocol |
143B cells were cultured in minimum essential medium (Eagle) supplemented with 10% fetal bovine serum and 1% penicillin/streptamycin. Cells were maintained in a humidified incubator at 37°C and 5% CO2.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from 143B cell lines 48 hours after transfection , using RNeasy Mini Kit (Qiagen)
RNA-seq library preparation by following the Illumina TruSeq stranded mRNA sample preparation guide
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 3000 |
| |
|
| Data processing |
Illumina Casava v1.8.2 software used for base-calling
All RNA-seq FastQ reads were aligned with the reference genome (UCSC human genome build hg19) using TopHat2 default settings. The aligned BAM files sorted (SAMTools) and then processed using HTSeq-count to obtain the counts per gene
gene count measurements were obtained using HTSeq-count
Genome_build: hg19
Supplementary_files_format_and_content: The processed data files are in tabular format. The first column contains the gene symbols and the second column contain the read counts of the gene using htseq-count
|
| |
|
| Submission date |
Jul 15, 2020 |
| Last update date |
Jun 28, 2022 |
| Contact name |
Yidong Chen |
| E-mail(s) |
cheny8@uthscsa.edu
|
| Phone |
2105629163
|
| Organization name |
UT Health Science Center at San Antonio
|
| Department |
Population Health Sciences
|
| Street address |
8403 Floyd Curl Drive, MSC 7784
|
| City |
San Antonio |
| State/province |
Texas |
| ZIP/Postal code |
78229 |
| Country |
USA |
| |
|
| Platform ID |
GPL21290 |
| Series (2) |
| GSE154528 |
Gene regulation by m6A demethylase ALKBH5 in osteosarcoma [RNA-seq] |
| GSE154530 |
Gene regulation by m6A demethylase ALKBH5 in osteosarcoma |
|
| Relations |
| BioSample |
SAMN15546683 |
| SRA |
SRX8741392 |
