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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Feb 21, 2024 |
| Title |
onc+msc.ev 2w |
| Sample type |
SRA |
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| Source name |
Retina
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| Organism |
Mus musculus |
| Characteristics |
cell type: Retina immune cells
tissue: Retina
strain: C57BL/6
age: 6-8 weeks old
treatment: MSC-sEV
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| Extracted molecule |
total RNA |
| Extraction protocol |
Retinas from 6 mice per group were pooled together and cut into small pieces to be digested in Ames’ Medium containing 15 U/mL papain (Worthington) and 0.1 mg/mL DNase I (Sigma) at 34 ℃for fifteen minutes. After centrifugation in 300 g for 8 min at 4 ℃, cell pellets were resuspended and incubated with 10 µL of CD45 Microbeads (Miltenyi Biotec) in 90 µl MACS buffer (0.5% BSA in PBS) per 107 total cells at 4 ℃ for 15 min according to the manufacture instruction. After washed with MACS buffer, single cell suspension was applied onto the column (Miltenyi Biotec), which was placed in the magnetic field of a MACS Separator (Miltenyi Biotec).Magnetically labeled CD45+ cells were immediately flushed out into the collection tube by firmly pushing the plunger into the column with 1 ml MACS buffer.
ScRNA-seq libraries were prepared using the Chromium Single Cell 30 Reagent Kits v3 (10x Genomics; Pleasanton, CA, USA) according to the manufacturer’s instructions. Briefly, single cells were partitioned with Gel beads in EMulsion (GEMs) using the Chromium instrument. Then, cells lysis, reverse transcription, cDNA amplification, enzymatic fragmentation, adaptor attachment, and sample indexing were performed sequentially. Generated libraries were sequenced on an Illumina NovaSeq 6000, at a sequencing depth of 50K-100K reads per cell and followed by de-multiplexing and mapping to the mouse genome (build mm10) using CellRanger (10x Genomics, version 3.0.2) with default parameter.
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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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| Description |
10x Genomics
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| Data processing |
10X Genomics Cellranger 3.0.2
Supplementary files format and content: mm10
Supplementary files format and content: Tab-separated values files and matrix files
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| Submission date |
Jan 23, 2023 |
| Last update date |
Feb 21, 2024 |
| Contact name |
xialin liu |
| E-mail(s) |
yangziqi@gzzoc.com
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| Organization name |
Zhongshan Opythalmic Center, Sun yat-sen University
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| Street address |
Jinsui Road
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| City |
Guangzhou |
| ZIP/Postal code |
510000 |
| Country |
China |
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| Platform ID |
GPL24247 |
| Series (2) |
| GSE223530 |
Single-cell profiling identifies a specific monocyte subset for neuroregeneration |
| GSE224068 |
MSC-sEV regulates Ly6Clow Mo/MΦ in neural restoration |
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| Relations |
| BioSample |
SAMN32878319 |
| SRA |
SRX19144170 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM6958393_onc+msc.ev.2w.barcodes.tsv.gz |
14.0 Kb |
(ftp)(http) |
TSV |
| GSM6958393_onc+msc.ev.2w.features.tsv.gz |
272.8 Kb |
(ftp)(http) |
TSV |
| GSM6958393_onc+msc.ev.2w.matrix.mtx.gz |
17.0 Mb |
(ftp)(http) |
MTX |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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