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| Status |
Public on Dec 22, 2021 |
| Title |
MT1205_AGG2 |
| Sample type |
SRA |
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| Source name |
Neoplastic cells isolated from lung tumors by FACS
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| Organism |
Mus musculus |
| Characteristics |
virus: Lenti-sgCebpa/sgCebpb/sgCebpd/Cre
Sex: Female
label: sgCebpa/b/d#3
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| Growth protocol |
Lung tumors were initiated via intratracheal delivery of Lenti-sgRNA/Cre (sgNeo1/sgNT/sgNeo2/Cre (sgInert), Lenti-sgLkb1/Cre (sgLkb1), or Lenti-sgCebpa/sgCebpb/sgCebpd/Cre (sgCebpa/b/d)) in 60 µL PBS. Lung tumors were developed for 17 weeks.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Microdissected lung tumors were dissociated with collagenase IV, dispase, and trypsin at 37 °C for 30 min. After dissociation, the samples were maintained on ice, in the presence of 2 mM EDTA and 1 U/mL DNase to prevent aggregation. For the sorting of neoplastic cells, the dissociated cells were stained with antibodies against CD45 (BioLegened, 103112), CD31 (BioLegend, 303116), F4/80 (BioLegend, 123116), and Ter119 (BioLegend, 116212) to exclude hematopoietic and endothelial cells (lineage-positive (Lin+) cells). DAPI was used to exclude dead cells. FACSAria sorters (BD Biosciences) were used for cell sorting.RNA was purified using RNA/DNA Allprep kit (Qiagen, 80284). RNA quality was assessed using the RNA6000 PicoAssay for the Agilent 2100 Bioanalyzer.
Two to ten nanograms of total RNA served as input for the preparation of RNA-Seq libraries using the Trio RNA-Seq, Mouse rRNA kit (Tecan Genomics: 0507-32). Libraries were constructed per the manufacturer’s instructions. Purified libraries were assessed using the Agilent High Sensitivity DNA kit (Agilent Technologies: 5067-4626).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| Data processing |
Reads were aligned to mm10 via 2-pass mapping with the STAR aligner (v2.6.1d).
Estimates of gene expression were generated using RSEM (v1.2.30) with standard input parameters.
The differentially expressed genes between different tumor genotypes were called by DESeq2 (v1.26.0) using transcript abundance estimates imported via tximport.
Genome_build: mm10
Supplementary_files_format_and_content: Median of ratios normalized (DESeq2) counts across all samples; Differential expression analysis output from DESeq2; RSEM gene-level outputs for each library, which can be imported into R with tximport.
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| Submission date |
Jul 06, 2021 |
| Last update date |
Dec 23, 2021 |
| Contact name |
Christopher Murray |
| Organization name |
Stanford University
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| Department |
Genetics
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| Lab |
Winslow
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| Street address |
1291 Welch Rd. B261, Beckman Center
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| City |
Stanford |
| State/province |
California |
| ZIP/Postal code |
94305 |
| Country |
USA |
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| Platform ID |
GPL19057 |
| Series (2) |
| GSE179558 |
LKB1 drives stasis and C/EBP-mediated reprogramming to an alveolar type II fate in lung cancer [C/EBP Bulk RNA-seq] |
| GSE179560 |
LKB1 drives stasis and C/EBP-mediated reprogramming to an alveolar type II fate in lung cancer |
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| Relations |
| BioSample |
SAMN20081425 |
| SRA |
SRX11361518 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5420545_MT1205_AGG2.genes.results.gz |
2.5 Mb |
(ftp)(http) |
RESULTS |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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