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GEO help: Mouse over screen elements for information. |
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Status |
Public on Jun 30, 2023 |
Title |
Adult lung [MY-21] |
Sample type |
SRA |
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Source name |
adult lung
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Organism |
Mus musculus |
Characteristics |
cell type: mouse adult lung cells passages: N/A strain: C57BL/6
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Extracted molecule |
total RNA |
Extraction protocol |
For total RNA extraction of MEFs (iPUL cells), matrigel blocks containing differentiated cells and fibroblasts were digested using dispase (Corning) at 37°C for 120 minutes. The clusters of the cells were separated using 70 μm cell strainer and lysed and total RNA was harvested using RNA easy kit (Quiagen).For total RNA extraction of adult lung, lungs were removed, flash frozen on dry ice, and total RNA was harvested using RNA easy kit (Quiagen). For total RNA extraction of SP-C+ cells in 3D culture, matrigel blocks containing differentiated cells and fibroblasts were digested using dispase (Corning) at 37°C for 120 minutes. To prepare the single cell suspension of iPUL cells, cells were incubated in 0.25% Tripsin/EDTA at 37°C for 5 min. GFP+/SP-C+ cells were sorted by flow cytometry. The sorted GFP+/SP-C+ cells were lysed and total RNA was harvested using RNA easy kit (Quiagen). Total RNA obtained from each sample was subjected to a sequencing library construction using NEBNext Ultra Directional RNA Library Prep Kit for Illumina (New England Biolabs, MA) with NEBNext Poly(A) mRNA Magnetic Isolation Module according to the manufacturer’s protocols. The quality of the libraries was assessed with an Agilent 2200 TapeStation High Sensitivity D1000 (Agilent Technologies, Santa Clara, CA). The pooled libraries of the samples were sequenced using the illumina HiSeq 1500 system (Illumina, Inc., San Diego, CA) in 50-base-pair (bp) single-end reads.
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 1500 |
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Description |
MY-21
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Data processing |
Sequenced reads were pseudoaligned to the reference mouse transcriptome (GRCm38) and quantified transcripts abundance using kallisto (v0.43.0) with parameters --single -l 380 -s 70 Genome_build: GRCm38 assembly, release 90 Supplementary_files_format_and_content: Concatenated abundances.tsv from kallisto
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Submission date |
Jan 29, 2018 |
Last update date |
Jun 30, 2023 |
Contact name |
Hideo Watanabe |
E-mail(s) |
hideo.watanabe@mssm.edu
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Organization name |
Icahn School of Medicine at Mount Sinai
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Department |
Department of Medicine, Division of Pulmonary, Critical Care and Sleep Medicine
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Lab |
Hideo Watanabe
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Street address |
One Gustave L. Levy Place
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City |
New York |
State/province |
NY |
ZIP/Postal code |
10029 |
Country |
USA |
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Platform ID |
GPL18480 |
Series (1) |
GSE109810 |
RNA-seq analyses of mouse embryonic fibloblasts (MEFs) reprogrammed into induced pulmonary epithelial cell-like cells |
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Relations |
BioSample |
SAMN08435711 |
SRA |
SRX3630160 |
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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