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Sample GSM3660644 Query DataSets for GSM3660644
Status Public on Jun 21, 2019
Title SC45NOR
Sample type SRA
 
Source name mix of upper + lower lobe lung_healthy donor
Organism Homo sapiens
Characteristics subject status: normal/healthy donor
tissue: lung
lung section/portion: mix of upper + lower lobe lung
Extracted molecule polyA RNA
Extraction protocol 10X Genomics 3 Prime V2 chemistry
Explanted lungs were finely diced and digested for 1 hour in a mix of collagenase A/DNAse I. A single cell suspension was generated by filtering lungs through 70 micron filters and resuspending cells in PBS containing 0.04% BSA. Cells were loaded into the 10X Genomics Chromium instrument per manufacturer's directions.
Libraries were constructed according to 10X Genomics' Single Cell 3’ Reagent Kits v2 User Guide
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
 
Data processing 10X Genomics' Cell Ranger 2.0 software's mkfastq command was used for basecalling. It is a wrapper for Illumina's bcl2fastq
Sequenced reads were then mapped to GRCh38 whole genome using 10X Genomics' Cell Ranger 2.0 software's cellranger count function
Cell Ranger output of raw_gene_bc_matrices were utilized for further downstream analysis in R with the package Seurat 2.3.4, only cells expressing at least 200 genes were kept for downstream analysis. Further filtration removed cells expressing greater than 50,000 UMI or 35% mitochondrial genes.
Genome_build: GRCh38
Supplementary_files_format_and_content: tsv files contain lists of genes and barcodes for each sample, mtx files count gene UMI couns for each sample
 
Submission date Mar 07, 2019
Last update date Mar 23, 2021
Contact name Tracy Tabib
Organization name University of Pittsburgh
Department Department of Medicine
Lab Laboratory of Robert Lafyatis
Street address 200 Lothrop Street
City Pittsburgh
State/province PA
ZIP/Postal code 15213
Country USA
 
Platform ID GPL18573
Series (1)
GSE128033 Proliferating SPP1/MERTK-expressing macrophages in idiopathic pulmonary fibrosis
Relations
Reanalyzed by GSM5206785
BioSample SAMN11086905

Supplementary file Size Download File type/resource
GSM3660644_SC45NOR_barcodes.tsv.gz 2.2 Mb (ftp)(http) TSV
GSM3660644_SC45NOR_genes.tsv.gz 258.6 Kb (ftp)(http) TSV
GSM3660644_SC45NOR_matrix.mtx.gz 27.1 Mb (ftp)(http) MTX
Processed data provided as supplementary file
Raw data not provided for this record

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