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| Status |
Public on Feb 01, 2022 |
| Title |
T2 |
| Sample type |
SRA |
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| Source name |
PBMC
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| Organism |
Bos taurus |
| Characteristics |
breed: Holstein
age: 2 years old
treatment: LPS for 4 hours
cell type: PBMC
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
four whole blood samples included either no LPS treatment - control sample CO, or three treated samples with LPS (2 μg/ml, Product Number: L2880, Sigma Aldrich, Saint Louis, MO, USA) for 2 hours - T1, 4hours - T2, and 8 hours - T3 at 37°C. PBMCs were isolated by centrifugation of whole blood on Hanks' Balanced Salt Solution (Solarbio; Beijing, China) at 500 g for 20 min at roomtemperature.
scRNA-seq Library generation for 10x Genomics v2 chemistry was performed following the Chromium Single Cell 3′ Reagent Kits v3 User Guide: CG000183 Rev C.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
one sample from cattle PBMC
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| Data processing |
We first processed 10X Genomics raw data by the Cell Ranger Single-Cell Software Suite (release 3.1.0), including using Cell Ranger “mkfastq” to demultiplex raw base call files into FASTQ files followed by use of Cell Ranger “count” to perform alignment, filtering, barcode counting, and UMI counting. The raw reads were aligned to the ARS-UCD1.2 cattle reference genome by Cell Ranger “pipeline” using default parameters
Genome_build: ARS-UCD1.2
Supplementary_files_format_and_content: matrix.mtx.gz, features.tsv.gz, barcodes.tsv.gz
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| Submission date |
Feb 05, 2021 |
| Last update date |
Feb 01, 2022 |
| Contact name |
Yahui Gao |
| E-mail(s) |
yahuigao306@gmail.com
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| Organization name |
ARS, USDA
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| Street address |
10300 Baltimore Ave Bldg 306
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| City |
Beltsville |
| State/province |
Maryland |
| ZIP/Postal code |
20705 |
| Country |
USA |
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| Platform ID |
GPL26012 |
| Series (1) |
| GSE166245 |
Single-cell RNA analyses of cattle PBMC |
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| Relations |
| BioSample |
SAMN17808926 |
| SRA |
SRX10037051 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5066756_T2_barcodes.tsv.gz |
33.7 Kb |
(ftp)(http) |
TSV |
| GSM5066756_T2_features.tsv.gz |
157.4 Kb |
(ftp)(http) |
TSV |
| GSM5066756_T2_matrix.mtx.gz |
40.9 Mb |
(ftp)(http) |
MTX |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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