 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Jul 15, 2023 |
| Title |
Tree shrew2 |
| Sample type |
SRA |
| |
|
| Source name |
whole brain
|
| Organism |
Tupaia belangeri |
| Characteristics |
tissue: whole brain
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The entire brains of the tree shrew embryos were immediately transferred to ice-cold DMEM solution with 10% FBS (DMEM/FBS) after dissection. Centrifugation of the samples was performed at 4°C. After transferring the whole brains of tree shrew embryos to ice-cold DMEM solution with 10% FBS (DMEM/FBS), the dura mater and blood vessels were removed from the brains. Brain tissues were dissociated using a modified protocol from the Worthington Papain Dissociation System. In brief, the dissected brains were cut into small pieces of less than 1mm3. The small pieces were then digested with 1mg/ml papain and 0.4% DNaseI at 37°C for 30min, shaking once every 5 minutes. After 40 minutes, the digestion process was blocked with DMEM/FBS. Cell suspensions were filtered through a 100 µm cell strainer and pelleted in a benchtop centrifuge at 200×g for 5 minutes. Pellets were re-suspended in DMEM and strained through a 40 µm filter. To remove cell debris, 2ml cell suspension were layered onto a gradient composed of 1ml layers of 11%, 20% and 35% Optiprep1.32 pH 7.4 in DMEM and centrifuged for 5 min at 430×g with no brake. The bottom 1ml of the gradient was collected and mixed with 1ml DMEM. The cells were then pelleted at 550×g for 5min before being re-suspended in 100-200 µl DMEM with 0.2% BSA.
The input cells were loaded onto the channel of Single Cell B Chip (v3 chemistry, PN-1000153). The 10x library was constructed using 10x Chromium Controller and Chromium Single Cell 3’ Reagent Kits (v3 chemistry CG000183) following the detailed protocol of the manufacturer. In brief, single-cell suspensions in each channel of the chip were loaded on a Chromium Controller (10x Genomics, Pleasanton, CA) to generate single-cell GEMs (gel beads in the emulsion). The 10x libraries of each channel were then prepared using the Chromium Single Cell 3’Gel Bead and Library Kit v3 (PN-1000153, 1000075, 120262; 10x Genomics).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
10x Genomics
|
| Data processing |
We used fastp software to perform basic statistics on the quality of the raw reads, ensuring the raw reads of Read1 and Read2 were adequate for subsequent analyses.
The raw data were analyzed by cellranger 3.1.0. In brief, the cellranger mkfastq transformed raw base call (BCL) files generated by Illumina sequencers into FASTQ files and decoded the multiplexed samples. Cellranger count took FASTQ files from cellranger mkfastq and performed sequencing alignment, filtering, barcode counting and UMI counting using the default parameters. The reference genome and annotation files of the tree shrew were downloaded from the Tree Shrew Database (TS_2.0 long-read assembly, http://www.treeshrewdb.org/). The standard output files generated by cellranger count served as input data for further analyses with Seurat v3.
Assembly: TS_2.0 long-read assembly (From: http://www.treeshrewdb.org/)
Supplementary files format and content: Tab-separated values files and matrix files
|
| |
|
| Submission date |
May 30, 2023 |
| Last update date |
Jul 15, 2023 |
| Contact name |
Xiao-Lin Zhuang |
| E-mail(s) |
zhuangxiaolin@mail.kiz.ac.cn
|
| Organization name |
ology, Kunming Institute of Zoology, Chinese Academy of Sciences
|
| Street address |
Longxin Road
|
| City |
Kunming |
| ZIP/Postal code |
650201 |
| Country |
China |
| |
|
| Platform ID |
GPL33447 |
| Series (1) |
| GSE233757 |
Gene expression profile at single cell level from the whole brain of two tree shrew fetus |
|
| Relations |
| BioSample |
SAMN35533417 |
| SRA |
SRX20542706 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7434218_Tree-shrew2-barcodes.tsv.gz |
40.2 Kb |
(ftp)(http) |
TSV |
| GSM7434218_Tree-shrew2-features.tsv.gz |
153.9 Kb |
(ftp)(http) |
TSV |
| GSM7434218_Tree-shrew2-matrix.mtx.gz |
34.3 Mb |
(ftp)(http) |
MTX |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
|
|
|
|
 |
