|
| Status |
Public on May 06, 2022 |
| Title |
SG_1L1D |
| Sample type |
SRA |
| |
|
| Source name |
silk gland cells
|
| Organism |
Bombyx mori |
| Characteristics |
strain: B. mori (Nistari strain)
cell type: Eukaryotic cell
in vivo &in vitro: In vitro expansion
developmental stage: day 1 of first-instar larvae, 1L1D
|
| Treatment protocol |
SG samples from each developmental stage were composed of a mixture of ~2000 intact SGs to ensure sufficient materials for subsequent cell dissociation. Tissues were dissociated and then resuspended in 1 mL PBS containing 0.04% BSA.Wash the tissue with medium (1640). Cut the tissue into pieces in the culture medium, add an appropriate amount of enzyme and digest it in a constant temperature incubator for 30-60min. Over 40 after digestion μ M cell sieve.Wash the culture medium for more than two times (centrifugation for 5min at 300g at 4 ℃). Wash the culture medium for more than two times (centrifugation for 5min at 300g at 4 ℃).
|
| Growth protocol |
B. mori (Nistari strain) embryos developed to E8D, 1L1D larvae, and 1LM larvae were maintained under standard laboratory conditions and collected to obtain SG samples.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Single cells were suspended in calcium- and magnesium-free PBS containing 0.04% weight/volume BSA. Then Cells were added to each channel. After generation of GEMs, reverse transcription reactions were engaged barcoded full-length cDNA followed by the disruption of emulsions using the recovery agent and cDNA clean up with DynaBeads Myone Silane Beads (Thermo Fisher Scientific). Subsequently, the amplified cDNA was fragmented, end-repaired, A-tailed, and index adaptor ligated and library amplification.
After the cell viability test, single-cell separation, complementary DNA amplification and library construction were performed according to the manufacturer’s protocol for Chromium Single-cell 3’ Kits (10× Genomics).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
The Cell Ranger software pipeline (version 3.1.0) provided by 10× Genomics was applied to demultiplex the cellular barcodes, map reads to the reference genome and transcriptome by using the STAR aligner, and downsample reads as required to generate normalized aggregate data across samples, generating a matrix of gene counts versus cells.
Genome_build: GCF_000151625.1_ASM15162v1
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every cell
|
| |
|
| Submission date |
Jan 08, 2022 |
| Last update date |
May 08, 2022 |
| Contact name |
Hanfu Xu |
| E-mail(s) |
xuhf@swu.edu.cn
|
| Organization name |
State Key Laboratory of Silkworm Genome Biology Southwest University
|
| Street address |
2 Tiansheng Road, Beibei District
|
| City |
Chongqing |
| ZIP/Postal code |
400715 |
| Country |
China |
| |
|
| Platform ID |
GPL29210 |
| Series (1) |
| GSE193279 |
A single-cell transcriptomic atlas characterizes the silk-producing organ in the silkworm |
|
| Relations |
| BioSample |
SAMN24744555 |
| SRA |
SRX13669317 |
