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| Status |
Public on Jun 01, 2021 |
| Title |
s1_2_pbmc_10x_esat |
| Sample type |
SRA |
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| Source name |
Peripheral blood mononuclear cells
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| Organism |
Equus caballus |
| Characteristics |
age: 6
Sex: Male
breed: Warmblood
time-point: Peak-viremia
tissue: Peripheral blood mononuclear cells
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| 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
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| 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
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| Submission date |
Feb 22, 2021 |
| Last update date |
Jun 01, 2021 |
| Contact name |
Gerlinde Van de Walle |
| E-mail(s) |
grv23@cornell.edu
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| Organization name |
Cornell University
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| Department |
Microbiology and Immunology
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| Lab |
Gerlinde Van de Walle
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| Street address |
235 Hungerford Hill Road
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| City |
Ithaca |
| State/province |
NY |
| ZIP/Postal code |
14853 |
| Country |
USA |
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| Platform ID |
GPL21401 |
| Series (1) |
| GSE167260 |
Pathogenesis, miR-122 gene-regulation, and protective immune responses after acute equine hepacivirus infection |
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| Relations |
| 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 Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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