NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM2970294 Query DataSets for GSM2970294
Status Public on Jun 30, 2023
Title MEFs transduced 4 foctors (Nkx2-1, Foxa1, Foxa2, Gata6) [MY-6]
Sample type SRA
 
Source name embryonic fibroblast
Organism Mus musculus
Characteristics cell type: mouse embryonic fibroblast (E13.5)
passages: 2 to 5
strain: CBA/Ca x C57BL/6
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.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 1500
 
Description MY-6
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
 
Submission date Jan 29, 2018
Last update date Jun 30, 2023
Contact name Hideo Watanabe
E-mail(s) hideo.watanabe@mssm.edu
Organization name Icahn School of Medicine at Mount Sinai
Department Department of Medicine, Division of Pulmonary, Critical Care and Sleep Medicine
Lab Hideo Watanabe
Street address One Gustave L. Levy Place
City New York
State/province NY
ZIP/Postal code 10029
Country USA
 
Platform ID GPL18480
Series (1)
GSE109810 RNA-seq analyses of mouse embryonic fibloblasts (MEFs) reprogrammed into induced pulmonary epithelial cell-like cells
Relations
BioSample SAMN08435716
SRA SRX3630155

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap