|
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 |