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Status |
Public on Dec 01, 2023 |
Title |
10X_tdT_pnx_1w |
Sample type |
SRA |
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Source name |
Pneumonectomy 2 weeks lung EC
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Organism |
Mus musculus |
Characteristics |
strain: c57bl/6 cell sorting: FACS sorted cell type: lung EC developmental stage: Adult genotype: control treatment: Pneumonectomy 2 weeks
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Treatment protocol |
Mice were pre-treated with tamoxifen to induced tdTomato expression in Apln expressing cells
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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
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Library strategy |
RNA-Seq |
Library source |
transcriptomic single cell |
Library selection |
cDNA |
Instrument model |
HiSeq X Ten |
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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
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|
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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 |
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Relations |
BioSample |
SAMN31926810 |
SRA |
SRX18413504 |