|
| Status |
Public on Jan 30, 2023 |
| Title |
Experiment 2_LacZsg_1 |
| Sample type |
SRA |
| |
|
| Source name |
SAOS2 cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: osteosarcoma cells
treatment: cells transduced with CRISPR-Cas9 and LacZ sg (replicate 1)
cell line: SAOS2
|
| Treatment protocol |
Experiment 1: cells were treated with either DMSO or ponatinib (250 nM) for 24 hours before collection. Experiment 2: Cells were transduced with lentiviral particules containing desired plasmids, and then selected with puromycin for at least 7 days before collection.
|
| Growth protocol |
SAOS2 and T1000 cells were cultured in DMEM and RPMI media, respectively, supplemented with 10% FBS and 1% PS
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using Qiagen RNeasy Mini kit (experiment 1) or Promega Reliaprep RNA cell miniprep kit (experiment 2).
Poly-A mRNAs enrichment
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Experiment 1: 100 bp paired-end reads were pseudo-aligned and quantified to Gencode (hg38) transcripts using the Kallisto program.
Experiment 2: Paired-end reads were aligned to the reference genome using Hisat2 v2.0.5. FeatureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene and subsequently, FPKM values were calculated for every gene.
Supplementary_files_format_and_content: Expression abundances in terms of FPKM or TPM as measured by DESeq2 or Kallisto respectively.
|
| |
|
| Submission date |
Dec 08, 2021 |
| Last update date |
Jan 30, 2023 |
| Contact name |
Maya Jeitany |
| E-mail(s) |
maya.jeitany@gmail.com
|
| Organization name |
Nanyang Technological University
|
| Street address |
60 Nanyang Dr
|
| City |
Singapore |
| ZIP/Postal code |
637551 |
| Country |
Singapore |
| |
|
| Platform ID |
GPL24676 |
| Series (1) |
| GSE190438 |
Signalling inhibition by ponatinib disrupts alternative lengthening of telomeres (ALT) |
|
| Relations |
| BioSample |
SAMN23778222 |
| SRA |
SRX13351551 |
