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Sample GSM5492504 Query DataSets for GSM5492504
Status Public on Nov 20, 2023
Title TP73 ex2-3del_DOX_8wkcoculture_rep1
Sample type SRA
 
Source name TL-Om1 cells
Organism Homo sapiens
Characteristics cell line: ATL
knockdown: deletion (8 weeks co-culture)
treatment: Dox
Treatment protocol TL-Om1 cells were induced with doxycycline for 3 days to induce deletion. The cells were also cultured with control cells in the same flask for 8 weeks. In each condition, total RNA were harvested from sorted cells.
Growth protocol TL-Om1 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).
Strand-specific library construction and sequencing of paired-end, 100-bp-long reads by the DNBseq were performed at the BGI Biotech Solutions (Hong Kong) Co Ltd (Hong Kong).
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model DNBSEQ-T7
 
Description Replicate 1
Data processing RNA-seq reads were mapped to curated RefSeq transcripts (NM and NR transcripts) using salmon (version 1.1.0) with the options “--gcBias --seqBias –validateMappings”.
The salmon index file was created with default settings.
Transcript-level read counts were converted to gene-level read counts using tximport (version 1.18.0).
Differentially expressed genes were estimated using DESeq2 (version 1.30.0).
Supplementary_files_format_and_content: txt file for differentially expressed genes
 
Submission date Jul 30, 2021
Last update date Nov 20, 2023
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 GPL29480
Series (2)
GSE181212 RNA-seq analysis after TP73 exons 2-3 deletion in TL-Om1 cells
GSE181215 Requirement for TP73 in cancer cell maintenance and genetic alterations originating from its intragenic super-enhancer
Relations
BioSample SAMN20504912
SRA SRX11611558

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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