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Sample GSM3720882 Query DataSets for GSM3720882
Status Public on Sep 02, 2019
Title aged_CD31_3
Sample type SRA
Source name BM CD45-CD31+ endothelial cells_aged
Organism Mus musculus
Characteristics strain: Nes-GFP
sample group: aged
age: > 20 months
cell type: BM CD45-CD31+ endothelial cells
replicate: 3
Extracted molecule polyA RNA
Extraction protocol Young and aged bone marrow CD45- CD31 endothelial cells were sorted from endosteal preparations and frozen in IMDM + 20% FCS + 10% DMSO.
Endothelial cells were thawed, washed once in warm PBS, and subjected immediately to encapsulation in oil droplets using the Chromium system by 10X Genomics. cDNA synthesis and library preparation were done according to the manufacturer’s instructions for 3’ end counting. PCR cycles for both cDNA synthesis and amplification were adjusted for each sample individually to the number of cells loaded cDNA yield respectively.
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 3000
Data processing Read filtering, alignment, barcode counting and UMI counting was performed using the Cellranger pipeline of 10X Genomics (version 2.1.1; cellranger count with default settings).
Single cell data were filtered based on total number of UMIs (>= 1000), total number of detected genes (>= 1000, at least one read) and percentage of mitochondrial reads (< 10%) using the scater toolkit (version 1.10.1, R 3.5.2).
Counts were normalized using the calcNormFunction of the edgeR package (version 3.24.3, R 3.5.2) using the "upperquartile" method. Highly variable genes were selected from log-transformed and normalized data using the M3Drop package (version 1.8.1, R 3.5.2).
Differential expression analysis was performed on hypervariable genes using DESeq2 (version 1.22.2, R 3.5.2). The analysis was performed on raw counts and the likelihood ratio test with the experimental batches as covariables was used. Dispersions were estimated using a local fit and size factors were estimated using the “poscounts” setting. "minmu" was set to "1e-6" and "minReplicatesForReplace" was set to "Inf".
Genome_build: mm10
Supplementary_files_format_and_content: Tab delimited txt files contain raw feature counts for all detected barcodes and all genes as obtained by the Cellranger pipeline. Row names show ENSEMBL gene IDs, column names show barcodes.
Submission date Apr 12, 2019
Last update date Sep 03, 2019
Contact name Johannes Pospiech
Organization name Ulm University
Street address Albert-Einstein Allee 11
City Ulm
ZIP/Postal code 89081
Country Germany
Platform ID GPL21493
Series (2)
GSE129726 Hematopoietic stem cells in perisinusoidal niches are protected from ageing [young and aged BM CD45-CD31+ endothelial cells]
GSE130299 Hematopoietic stem cells in perisinusoidal niches are protected from ageing
BioSample SAMN11405803
SRA SRX5675019

Supplementary file Size Download File type/resource
GSM3720882_aged_cd31_3_matrix.tsv.txt.gz 1.2 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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