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| Status |
Public on Feb 10, 2021 |
| Title |
BCAS-IgG-R3 |
| Sample type |
SRA |
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| Source name |
Brain cortex
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| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6J
tissue: Brain cortex
age: 3 months
Sex: Male
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| Treatment protocol |
The mice are treated on day 1, 4, 7, 10, 13, 20, 27 after BCAS surgery
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| Extracted molecule |
nuclear RNA |
| Extraction protocol |
Cortical tissue was dissected from mice perfused with cold PBS buffer with a transcription inhibitor cocktail at a speed of 6 mL/min for 8 minutes and flash frozen in liquid nitrogen. The frozen tissue was subsequently placed into a tissue dounce for homogenization with homogenization buffer (0.25M sucrose, 25mM KCl, 5mM MgCl2, 20mM Tricine-KOH pH7.8 with freshly added 1mM DTT, 0.15mM spemine (Sigma), 0.5mM spermidine (Sigma), 0.04% BSA (Sigma) and RNase inhibitors (Promega)). 5% IGEPAL (Sigma) stock solution was added to the homogenization buffer to a final concentration of 0.32% for 20 strokes with tight pestle. The homogenate was visually inspected, passed through 40-µm filter (BD Falcon) and layered onto an OptiPrep (Sigma) gradient, as previously described. The gradient was centrifuged at 10,000g for 18 minutes, and nuclei were collected between the 30% and 40% OptiPrep gradient layers. Single nucleic suspension was visually confirmed under microscope and diluted to 80,000 nuclei/mL for nuclei encapsulation and sequencing library preparation following an inDrop protocol as previously described. Approximately about 1,500 nuclei per mouse cortex were encapsulated and passed the quality controls. The prepared libraries are sequenced on Illumina Nova-seq at Broad Institute Walk-up sequencing facility, at a coverage of about 7 billion reads for ~15,000 droplets (~450,000 reads per nuclei).
Sequencing libraries were prepared following an inDrop protocol as previously described (Klein et al, Cell, 2015)
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
Transcripts were mapped to the mouse transcriptome following an established bioinformatics pipeline (https://github.com/indrops/indrops) for inDrop experiments to create a raw gene-cell counts matrix (Klein et al, Cell, 2015)
The file Unique_barocde_sequences.txt contains the barcode sequenes for each cell ID and is available on the series record.
Genome_build: GRCm38.81
Supplementary_files_format_and_content: text files include Gene_vs_Cell raw counts matrix (single cell matrix)
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| Submission date |
Feb 20, 2019 |
| Last update date |
Feb 11, 2021 |
| Contact name |
Chenxi Qiu |
| E-mail(s) |
cqiu@bidmc.harvard.edu
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| Organization name |
Harvard Medical School
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| Street address |
NRB 858, 77 Avenue Louis Pasteur
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| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02115 |
| Country |
USA |
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| Platform ID |
GPL24247 |
| Series (1) |
| GSE126815 |
Antibody-neutralizable major early driver of Alzheimer’s disease and vascular dementia |
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| Relations |
| BioSample |
SAMN10910736 |
| SRA |
SRX5360226 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3613875_BCAS-IgG_3.counts.tsv.gz |
13.7 Mb |
(ftp)(http) |
TSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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