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| Status |
Public on Nov 15, 2023 |
| Title |
Biol rep 1 - GFP-HI |
| Sample type |
SRA |
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| Source name |
Lung
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| Organism |
Sus scrofa |
| Characteristics |
tissue: Lung
cell type: GFP-HI
genotype: LGR5-H2B-GFP knock-in
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| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were isolated from lungs of adult or fetal LGR5 pigs. 2-3 cm2 pieces of lung were collected in cold PBS and moved into a sterile hood. Lung tissue was then minced using scissors or razor blade and then washed twice with cold PBS to remove blood and immune cells. Minced tissues were then incubated for 1 hour in a roller incubator at 37℃ in an enzymatic digest buffer containing 10 mg/mL Dispase (Invitrogen), 2 mg/mL DNase I (STEMCELL Technologies), and 5mg/mL (adult) or 2mg/mL (fetal) Collagenase Type II (Sigma). The digestion mixture was then strained using a 70 μM cell strainer and washed with a wash buffer (PBS, 5% FBS, 1% antibiotic-antimycotic) and centrifuged. For adult tissue, pellets were incubated in Red Blood Cell Lysis Buffer (Invitrogen) for 10 minutes at room temperature with gentle agitation. For fluorescent activated cell sorting, cells from porcine lung or dissociated organoids were suspended in MACS buffer (Miltenyi) and incubated with 10μl/ml anti-EpCAM-APC (Thermo Scientific, 17-5791-83) and/or anti-NGFR-PE (eBioscience, 12-9400-41). Propidium iodide was added for dead cell exclusion immediately before fluorescence activated cell sorting (Beckman Coulter MoFlo XPD).
Illumina Nextera XT library was used for sequencing library preparation.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
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| Description |
GFP FACS sorted
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| Data processing |
Unique gene hit counts were calculated by using feature Counts from the Subread package v.1.5.2. Only unique reads that fell within exon regions were counted.
Using DESeq2 (v1.37.6), a comparison of gene expression between the groups of samples was performed. The Wald test was used to generate p-values and Log2 fold changes.
Assembly: Sus scrofa 11.1
Supplementary files format and content: Comma delimited text files contain count values for each sample.
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| Submission date |
Nov 23, 2022 |
| Last update date |
Nov 15, 2023 |
| Contact name |
Jorge Piedrahita |
| E-mail(s) |
japiedra@ncsu.edu
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| Organization name |
North Carolina State University
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| Lab |
Piedrahita Lab
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| Street address |
1060 William Moore Drive, BPC Suite 200
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| City |
Raleigh |
| State/province |
NORTH CAROLINA |
| ZIP/Postal code |
27607 |
| Country |
USA |
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| Platform ID |
GPL22475 |
| Series (2) |
| GSE218657 |
Transgenic porcine model reveals two roles for LGR5 during lung development and homeostasis [Bulk RNA-seq] |
| GSE218658 |
Transgenic porcine model reveals two roles for LGR5 during lung development and homeostasis |
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| Relations |
| BioSample |
SAMN31853101 |
| SRA |
SRX18366914 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM6754175_Rep1_counts_GFP-Hi.csv.gz |
118.9 Kb |
(ftp)(http) |
CSV |
SRA Run Selector |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
| Raw data are available in SRA |
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