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Sample GSM4468657 Query DataSets for GSM4468657
Status Public on Jan 25, 2021
Title s7_pbmc_10x_esat
Sample type SRA
 
Source name Peripheral blood mononuclear cells
Organism Equus caballus
Characteristics cell type: Peripheral blood mononuclear cells
age: 10
Sex: Female
breed: Warmblood
Extracted molecule total RNA
Extraction protocol Periperal blood mononuclear cells were isolated from healthy horses by Ficoll gradient separation
Libraries were prepared in accordance to the 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)
Intermediate BAM files were extracted 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: ESAT processed gene-cell barcode matrix
 
Submission date Apr 09, 2020
Last update date Jan 26, 2021
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)
GSE148416 Single cell resolution landscape of equine peripheral blood mononuclear cells reveals diverse immune cell subtypes including T-bet+ B cells
Relations
BioSample SAMN14569676
SRA SRX8092699

Supplementary file Size Download File type/resource
GSM4468657_s7_pbmc_10x_esat.txt.gz 6.3 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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