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Sample GSM6761340 Query DataSets for GSM6761340
Status Public on Dec 01, 2023
Title 10X_tdT_pnx_1w
Sample type SRA
 
Source name Pneumonectomy 2 weeks lung EC
Organism Mus musculus
Characteristics strain: c57bl/6
cell sorting: FACS sorted
cell type: lung EC
developmental stage: Adult
genotype: control
treatment: Pneumonectomy 2 weeks
Treatment protocol Mice were pre-treated with tamoxifen to induced tdTomato expression in Apln expressing cells
Growth protocol 10x single cell RNA sequencing 3' NEXT GEM v3.1
Extracted molecule total RNA
Extraction protocol FACS sorted lung tdTomato+ cells and endothelial cells were processed on the 10X chromium system following the manufacturer's protocols
Using 10x single cell RNA sequencing 3' NEXT GEM v3.1 reagent Kit (10X genomics), cDNA libraries were constructed
 
Library strategy RNA-Seq
Library source transcriptomic single cell
Library selection cDNA
Instrument model HiSeq X Ten
 
Description tdT_pnx_1w
Data processing Cell Ranger (v3.0.0) was used to process single cell 3' RNA-seq ouput. First, cell ranger mkfastq demultiplexed illumina BCLs into fastq files.
Then, using cell ranger count, reads were aligned to mm10 mouse reference genome.
Aligned reads were then read by Seurat (v4.0.4) and cell-gene raw expression matrices were made. Then, low quality cells (expressing less than 800 genes), potential doublets (expressing more than 6000 genes),potential dead cells (>10% mitochondrial gene percentage) and contaminating CD31- cells were removed. Also, genes that are only expressed in less than 3 cells were discarded.
Expression matrices were made after quality control. Matrices were log normalized and variables such as number of UMIs and mitochondrial gene percentage were regressed out and scaled with Seurat to produce processed data files.
Dimensionality reduction, clustering and differential expression testing were performed using R package Seurat
Assembly: mm10
Supplementary files format and content: Cell-gene expression matrix of log normalized UMI counts for ECs following bleomycin administration (bleo_2w & bleo4w) or pneumonectomy (pnx_1w & pnx_4w) in WT(tdT mouse) or Kitl deleted mouse
 
Submission date Nov 29, 2022
Last update date Dec 01, 2023
Contact name Myung Jin Yang
E-mail(s) mjyang@kaist.ac.kr
Organization name Institute for Basic Science
Street address 34141
City Daejeon
ZIP/Postal code 34141
Country South Korea
 
Platform ID GPL21273
Series (1)
GSE218972 Transcriptomic changes of lung ECs following bleomycin induced pulmonary fibrosis, unilateral pneumonectomy, in WT mouse and the effect of Kitl deletion in Apln+ cells
Relations
BioSample SAMN31926810
SRA SRX18413504

Supplementary file Size Download File type/resource
GSM6761340_tdT_pnx_1w_normalized_expression_matrix.csv.gz 68.8 Mb (ftp)(http) CSV
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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