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GEO help: Mouse over screen elements for information. |
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| Status |
Public on May 13, 2022 |
| Title |
Day 14 IRE1α KO 8 |
| Sample type |
SRA |
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| Source name |
Lung cancer cells
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| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
genotype: IRE1alpha KO
cell type: Lung cancer cells
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| Growth protocol |
IRE1α WT or KO cell lines were injected into immunocompetent C57BL/6 mice by tail vein injection. Tumor growth kinetics were measured using the IVIS in vivo imaging system and the luciferase reporter to ensure adequate growth kinetics. At day's 10 and 14 lungs were harvested, and tumor cells were isolated by flow cytometry.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Single cell suspensions were generated and stained with CD45, and Epcam, without fixation. Viable CD45- mCherry+ Epcam+ cells were sorted into Trizol. mRNA was extracted as previously described. mRNA concentration was then evaluated by Nanodrop (Thermo Fisher), and the quality of the mRNA was evaluated by Bioanalyzer (Agilent).
cDNA libraries were generated using the Illumina TruSeq RNA Sample Preparation kit V2 with non-stranded Poly A selection, in accordance with the manufacturers protocol. 2x50 bp single-end sequencing was performed on the HiSeq 4000 sequencer.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
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| Data processing |
Raw sequencing reads were aligned to the mm9 mouse reference genome using Tophat2.
Cufflinks was used to measure transcript abundances in Fragments per Kilobase of exon model per Million mapped reads (FPKM), with upper-quartile normalization and sequence-specific bias correction and non-normalized raw counts.
FPKM expression matrices were employed for heatmaps and Log2 transformed FPKM values were used for principal component analysis and visualized using ggplot2 in R.
Heatmaps were made using the Pheatmap and RColorBrewer packages, and the Venny web portal was used to make all venn diagrams. Differential gene expression (DGE) was performed on non-normalized counts using the standard DESeq2 package protocol in R,
Assembly: mm9
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| Submission date |
May 13, 2022 |
| Last update date |
May 13, 2022 |
| Contact name |
Olivier Elemento |
| E-mail(s) |
ole2001@med.cornell.edu
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| Organization name |
Weill Cornell Medicine
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| Department |
Biochemistry
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| Street address |
1305 York Ave
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| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10021 |
| Country |
USA |
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| Platform ID |
GPL21103 |
| Series (1) |
| GSE202939 |
Tumor-intrinsic IRE1α signaling controls protective immunity in lung cancer. |
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| Relations |
| BioSample |
SAMN28231000 |
| SRA |
SRX15251456 |
| 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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