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| Status |
Public on Sep 02, 2019 |
| Title |
young_CD31_3 |
| Sample type |
SRA |
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| Source name |
BM CD45-CD31+ endothelial cells_young
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| Organism |
Mus musculus |
| Characteristics |
strain: Nes-GFP
sample group: young
age: 10-12 weeks
cell type: BM CD45-CD31+ endothelial cells
replicate: 3
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| 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.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 3000 |
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| 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.
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| Submission date |
Apr 12, 2019 |
| Last update date |
Sep 03, 2019 |
| Contact name |
Johannes Pospiech |
| E-mail(s) |
johannespospiech@gmail.com
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| Organization name |
Ulm University
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| Street address |
Albert-Einstein Allee 11
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| City |
Ulm |
| ZIP/Postal code |
89081 |
| Country |
Germany |
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| 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 |
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| Relations |
| BioSample |
SAMN11405766 |
| SRA |
SRX5675017 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3720880_young_cd31_3_matrix.tsv.txt.gz |
953.4 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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