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| Status |
Public on Apr 15, 2024 |
| Title |
Single-cell 5’ RNA-seq of Bactrian camel: C2 PBMC |
| Sample type |
SRA |
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| Source name |
blood
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| Organism |
Camelus bactrianus |
| Characteristics |
tissue: blood
cell type: PBMC
treatment: pre-immunization
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
For each camel, 50 ml peripheral blood was collected from the jugular vein and placed in sodium citrate anticoagulation tubes after disinfection treatment. The collections were made following the guidelines from the Camel Protection Association of Inner Mongolia. PBMCs were isolated from the peripheral blood with density gradient centrifugation using the Ficoll-Paque medium. 3ml PBMCs were transferred into 5ml cryotubes with 2ml cell freezing medium. Cells were stored frozen at -80°C for one day and then transported to sequencing lab on dry ice.
The viability of thawed cells was examined to exceed 80% with trypan blue staining. Single-cell libraries were constructed using the Chromium Next GEM Single Cell V(D)J Reagent Kits v1.1 (10x Genomics, 5’ Library Kit) according to the manufacturer’s instructions. Specifically, cells, barcoded gel beads and partitioning oil were combined on a microfluidic chip to form Gel Beads-in-Emulsion (GEMs). Within each GEM, a single cell was lysed and the transcripts were identically barcoded through reverse transcription. The cDNA libraries were sequenced on an Illumina NovaSeq platform to generate 2×150-bp paired-end reads.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
Sequencing reads were processed by the Cell Ranger pipeline (v6.1.2, 10x Genomics), including demultiplexing, barcoded processing, UMI counting and aggregation.
Single-cell BCR sequences were constructed using TRUST4 (v1.0.6) and annotated with IgBLAST (v1.10.0), taking known IGHV/D/J/C sequences of Bactrian camels as the reference (Ming et al. Mol Ecol Resour 2020, 20:770).
Assembly: BCGSAC_Cfer_1.0 (GCF_009834535.1)
Supplementary files format and content: Filtered single-cell gene expression matrix, cell barcodes and gene features using Cell Ranger
Supplementary files format and content: BCR sequences constructed using TRUST4 and annotated using IgBLAST (AIRR format)
Supplementary files format and content: BCR assignment to cell barcodes (tab-seperated values)
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| Submission date |
Jul 24, 2023 |
| Last update date |
Apr 15, 2024 |
| Contact name |
Zhen Wang |
| E-mail(s) |
zwang01@sibs.ac.cn
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| Organization name |
Shanghai Institute of Nutrition and Health
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| Street address |
320 Yueyang Road
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| City |
Shanghai |
| ZIP/Postal code |
200031 |
| Country |
China |
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| Platform ID |
GPL33602 |
| Series (1) |
| GSE238082 |
Single-cell 5' RNA sequencing of Bactrian camel PBMCs |
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| Relations |
| BioSample |
SAMN36682594 |
| SRA |
SRX21127784 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7658338_C2_BCR_barcode.tsv.gz |
173.0 Kb |
(ftp)(http) |
TSV |
| GSM7658338_C2_BCR_seq_AIRR.tsv.gz |
10.9 Mb |
(ftp)(http) |
TSV |
| GSM7658338_C2_barcodes.tsv.gz |
28.4 Kb |
(ftp)(http) |
TSV |
| GSM7658338_C2_features.tsv.gz |
161.3 Kb |
(ftp)(http) |
TSV |
| GSM7658338_C2_matrix.mtx.gz |
29.6 Mb |
(ftp)(http) |
MTX |
SRA Run Selector |
| Raw data not provided for this record |
| Processed data provided as supplementary file |
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