|
| Status |
Public on Dec 08, 2020 |
| Title |
equineSample_bone_marrow_derived_MSC_s2 |
| Sample type |
SRA |
| |
|
| Source name |
Peripheral blood mononuclear cells
|
| Organism |
Equus caballus |
| Characteristics |
age: 10 year old
Sex: Female
breed: Warmblood
|
| Growth protocol |
Equine mesenchymal stromal cells (MSCs) were isolated and cultured from the adipose tissue (AT), bone marrow (BM) and peripheral blood (PB), of a healthy adult research warmblood mare, euthanized for reasons unrelated to this study, exactly as described in Pennington et al. 2016 (10.1089/ten.TEC.2015.0403)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Libraries were prepared with 10X Genomics 3' end single cell RNA sequencing library prepration protocol, version 2
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
fastq files were aligned to version 95 of the horse genome reference (with manually annotated immunoglobulins (adapted from Wagner B. Immunoglobulins and immunoglobulin genes of the horse. Developmental & Comparative Immunology. 2006;30: 155–164. doi:10.1016/j.dci.2005.06.008)) from ensembl using the count function in the cellranger suite (10X Genomics, v3.0.1)
Alignments were extracted from intermediate BAM files and modified by appending cell barcode and unique molecular identifiers to their read names
The End Sequence Analysis Toolkit(v0.1.1) was applied on the resulting BAM files to obtain gene-cell barcode expression matrices (Derr A, Yang C, Zilionis R, Sergushichev A, Blodgett DM, Redick S, et al. End Sequence Analysis Toolkit (ESAT) expands the extractable information from single-cell RNA-seq data. Genome Res. 2016;26: 1397–1410. doi:10.1101/gr.207902.116)
Custom script was applied to identify duplicated genes and scale their expression proportionally
Genome_build: EquCab3.0
Supplementary_files_format_and_content: gene-cell barcode matrices
|
| |
|
| Submission date |
Aug 19, 2020 |
| Last update date |
Dec 09, 2020 |
| Contact name |
Gerlinde Van de Walle |
| E-mail(s) |
grv23@cornell.edu
|
| Organization name |
Cornell University
|
| Department |
Microbiology and Immunology
|
| Lab |
Gerlinde Van de Walle
|
| Street address |
235 Hungerford Hill Road
|
| City |
Ithaca |
| State/province |
NY |
| ZIP/Postal code |
14853 |
| Country |
USA |
| |
|
| Platform ID |
GPL21401 |
| Series (1) |
| GSE156467 |
Single-cell RNA sequencing of mesenchymal stromal cells from primary donor-matched tissue sources reveals functional heterogeneity in immune activity and cell motility |
|
| Relations |
| BioSample |
SAMN15856844 |
| SRA |
SRX8970460 |
