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Sample GSM5100474 Query DataSets for GSM5100474
Status Public on Jun 01, 2021
Title s1_2_pbmc_10x_esat
Sample type SRA
Source name Peripheral blood mononuclear cells
Organism Equus caballus
Characteristics age: 6
Sex: Male
breed: Warmblood
time-point: Peak-viremia
tissue: Peripheral blood mononuclear cells
Extracted molecule total RNA
Extraction protocol Periperal blood mononuclear cells were isolated 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: gene-cell barcode matrices
Submission date Feb 22, 2021
Last update date Jun 01, 2021
Contact name Gerlinde Van de Walle
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)
GSE167260 Pathogenesis, miR-122 gene-regulation, and protective immune responses after acute equine hepacivirus infection
BioSample SAMN18027903
SRA SRX10151072

Supplementary file Size Download File type/resource
GSM5100474_equineSample_s1_2.gene.txt.gz 6.8 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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