|
| Status |
Public on Sep 21, 2021 |
| Title |
G1 |
| Sample type |
SRA |
| |
|
| Source name |
PWBC scRNA-seq
|
| Organism |
Anas platyrhynchos |
| Characteristics |
cell type: peripheral white blood cells
|
| Treatment protocol |
Peripheral blood samples from 45-week-old male specific pathogen-free (SPF) ducks and removed erythrocytes from blood samples using erythrocyte lysis solution. Then, cells were first separated by density gradient centrifugation using a duck lymphocyte isolation kit.The peripheral blood mononuclear cells (PBMCs), which were located in the middle layer, were further separated by differential adhesion in culture dishes preloaded with sterilized glass coverslips according to the different adherent properties of PBMCs.
|
| Growth protocol |
Seperated cells were maintained in 1640 medium supplemented with 10% fetal bovine serum (FBS), 100 units/ml penicillin, 100 μg/ml streptomycin and 2 mM L_glutamine. Cell cultures were incubated at 37°C/5% CO2.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Seperated single_cell samples were treated by Smart_Seq2 protocol to get amplified cDNA.
RNA libraries were prepared for sequencing using standard Illumina scRNA-seq and 10 × Chromium platform protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
HiSeq X Ten |
| |
|
| Data processing |
Useful Perl script was used to filter the original raw data, to trim Smart_seq2 public primer sequence from the reads , remove the contaminated reads for adapters, remove the low quality reads and remove the reads whose N base more than 5% for total bases. scRNA-seq data was processed using stander CellRanger pipeline.
Bowtie2 v2.2.3 was used for building the genome index, and clean data was mapped to the reference genome using TopHat v2.0.12. scRNA-seq data was processed using stander CellRanger pipeline.
Transcript assemble, difference expression anlysis was finished by Cufflinks 2.2.1. scRNA-seq data was processed using stander CellRanger and Seurat pipeline.
Genome_build: Anas_platyrhynchos.BGI_duck_1.0.90
Genome_build: ftp://ftp.ensembl.org/pub/release-90/fasta/anas_platyrhynchos/dna/Anas_platyrhynchos.BGI_duck_1.0.dna.toplevel.fa.gz
Genome_build: ftp://ftp.ensembl.org/pub/release-90/gtf/anas_platyrhynchos/Anas_platyrhynchos.BGI_duck_1.0.90.gtf.gz
Supplementary_files_format_and_content: The BAM (Binary Alignment/Map) file format is a generic and highly compressed format for storing alignments.txt file could use as BAMs in Cuffquant to quantifies gene and transcript expression levels. Matrix file containing the transcription profiles of all single cells could be loaded to Seurat for further analysis.
|
| |
|
| Submission date |
Sep 21, 2020 |
| Last update date |
Sep 21, 2021 |
| Contact name |
Hai Li |
| E-mail(s) |
lihai@xjtu.edu.cn
|
| Organization name |
Xi'an Jiaotong University
|
| Department |
Department of Pathogenic Microbiology and Immunology
|
| Street address |
No.76 Yanta West Road
|
| City |
Xi'an |
| ZIP/Postal code |
710061 |
| Country |
China |
| |
|
| Platform ID |
GPL29169 |
| Series (1) |
| GSE153825 |
Characterization of duck peripheral blood cells at single-cell resolution |
|
| Relations |
| BioSample |
SAMN16231625 |
| SRA |
SRX9162662 |
