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GEO help: Mouse over screen elements for information. |
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| Status |
Public on May 04, 2023 |
| Title |
p53-wt-CB5232-Ad-Cre |
| Sample type |
SRA |
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| Source name |
lung
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| Organism |
Mus musculus |
| Characteristics |
tissue: lung
cell line: CB5232
cell type: LUAD cancer cells
genotype: p53-wt
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| Treatment protocol |
LUAD cell lines were maintained in Dulbecco’s Modified Eagle Medium (Gibco) supplemented with 10% Fetal Bovine Serum (FCS and incubated at 37°C in a carbon dioxide incubator. To reactivate p53, LUAD cell lines were treated with Ad5-CMV-Cre (University of Iowa Viral Vector Core), or cell lines were treated with Ad5-CMV-Empty (University of Iowa Viral Vector Core) to remains p53 null. Cell lines were infected at an MOI of 100. Cells were harvested for immunofluorescence, Western blotting, and RT-qPCR between 24-96 hours after infection.
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| Extracted molecule |
total RNA |
| Extraction protocol |
For RNA-sequencing, LUAD cells were harvested, pelleted, and flash frozen in liquid directly after sorting.
Once all samples were collected, RNA was harvested and library prepared with TruSeq RNA Library Prep Kit v2 for sequencing on a HiSeq4000 (Illumina).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
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| Description |
wt-2
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| Data processing |
RNA-seq reads were aligned to the mouse genome (mm10) using HISAT2 (version 2.0.5, https://github.com/DaehwanKimLab/hisat2), sorted based on genomic location and indexed using Samtools (version 1.3.1, https://github.com/samtools/samtools), and counted and mapped to each gene using HTSeq-Count (version 0.6.1, https://github.com/simon-anders/htseq). Differentially expressed genes (DEGs) were identified using DESeq2 with a cutoff of a p-adjusted value of < 0.05 (version 1.24.0, https://github.com/mikelove/DESeq2).
Assembly: mm10
Supplementary files format and content: counts file, each column is a sample
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| Submission date |
May 04, 2023 |
| Last update date |
May 04, 2023 |
| Contact name |
Laura D Attardi |
| E-mail(s) |
[email protected]
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| Organization name |
Stanford University
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| Lab |
Attardi
|
| Street address |
269 Campus Drive
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| City |
Stanford |
| State/province |
CA |
| ZIP/Postal code |
94305 |
| Country |
USA |
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| Platform ID |
GPL21103 |
| Series (2) |
| GSE231678 |
p53 governs an alveolar type 1 differentiation program in lung cancer suppression [in_vitro_RNA_seq] |
| GSE231681 |
p53 governs an alveolar type 1 differentiation program in lung cancer suppression |
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| Relations |
| BioSample |
SAMN34591343 |
| SRA |
SRX20229018 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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