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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Nov 27, 2019 |
| Title |
CrVg2dCD45CD90R1 |
| Sample type |
SRA |
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| Source name |
Mouse retina, 6-8 wk old
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| Organism |
Mus musculus |
| Characteristics |
tissue: retina
age: 6-8 wk old
cell type: retinal ganglion cells
time point: 2d_afterCrush
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| Treatment protocol |
Vglut2:cre;Stp15 and C57BL/6J mice were used. Retinas were dissected in Ames solution (Sigma-Aldrich; equilibrated with 95% O2/5% CO2 for all use) immediately following enucleation.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Retinas were dissected in oxygenated AMES, digested in papain, and dissociated to single cell suspensions using manual trituration in ovomucoid solution. Single cell suspensions were incubated with 0.5ul of anti-CD90, CD45 and CD140a (conjugated to various fluorophores) (Thermo Fisher Scientific) for 10 million cells per 100µl. Cells were sorted using a MoFlo Astrios. Cellular debris, doublets, and dead cells were excluded, and RGCs were collected based on high CD90 and GFP co-expression. Collected cells were loading into 10X Chromium Single Cell A Chips at ~1,000 cells/ul.
Single cell libraries were made with Chromium 3’ v2 platform (10X Genomics, Pleasanton, CA) following the manufacturer’s protocol. Briefly, single cells were partitioned into Gel bead in EMulsion (GEMs) in the GemCode instrument with cell lysis and barcoded reverse transcription of RNA, followed by amplification, shearing and 5’ adaptor and sample index attachment. On average, approximately 10,000 single cells were loaded on each channel and approximately 6,000 cells were recovered. Libraries were sequenced on Illumina HiSeq 2500.
Chromium 3’ v2 platform (10X Genomics, Pleasanton, CA)
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Description |
ONCRGCs_2d_afterCrush_count_mat.csv
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| Data processing |
Sample demultiplexing with the mkfastq function from Cell Ranger software(version 2.1.0, 10X Genomics)
Sample alignment to mouse genome GRCm38 with a costumized transcriptome reference using the count function from Cell Ranger software(version 2.1.0, 10X Genomics)
Genome_build: GRCm38
Supplementary_files_format_and_content: Csv files including gene expression matrix from all samples at each time point
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| Submission date |
Sep 13, 2019 |
| Last update date |
Nov 27, 2019 |
| Contact name |
Wenjun Yan |
| E-mail(s) |
wey334@g.harvard.edu
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| Organization name |
Harvard University
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| Department |
Department of Molecular and Cellular Biology
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| Lab |
Joshua Sanes
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| Street address |
52 Oxford Street
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| City |
Cambridge |
| State/province |
MA |
| ZIP/Postal code |
02138 |
| Country |
USA |
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| Platform ID |
GPL17021 |
| Series (2) |
| GSE137398 |
Single-cell profiles of retinal neurons differing in resilience to injury reveal neuroprotective genes - Time course of transcriptomic changes in single retinal ganglion cells following optic nerve crush |
| GSE137400 |
Single-cell profiles of retinal neurons differing in resilience to injury reveal neuroprotective genes |
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| Relations |
| BioSample |
SAMN12742355 |
| SRA |
SRX6843288 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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