|
| Status |
Public on Apr 22, 2021 |
| Title |
Mouse, RABID.transcriptome.EAE |
| Sample type |
SRA |
| |
|
| Source name |
CNS
|
| Organism |
Mus musculus |
| Characteristics |
strain: C567Bl/6
Sex: Male
cell type: mCherry+ cells from Gfap-Cre;TVA-G(f/+) mice labeled with RabDG-mCherry-EnvA
treatment: Induction of EAE
|
| Treatment protocol |
Induction of EAE in mice. EAE was induced by injecting 150 µg of MOG35-55 diluted in 100 µL of PBS emulsified in 100 µL of CFA per mouse.
|
| Growth protocol |
N/A
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Each CNS was isolated per mouse. A cell suspension was generated by papain digestion, neutralization, and 70um filtration of cell extract. Cells were centrifuged, labeled with Miltenyi anti-Dead Cell and anti-myelin kits, then magnetically purified and washed. Cells were sorted by flow cytometry based on mCherry fluorescence. Post-sort, cells were washed then processed by inDrop
Libraries were created according to the InDrop v3 protocol derived from Klein et al. Cell 2015.
inDrop scRNA-Seq
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 550 |
| |
|
| Data processing |
R1: biological (all 61bp)
R2: technical -- part 1 of cell barcode (all 8bp)
R3: technical -- library barcode (all 8bp)
R4: technical -- part 2 of cell barcode (1-8bp) and UMI (9-14bp)
The data was demultiplexed using the inDrop pipeline (https://github.com/indrops/indrops) using the library index.
The reads were trimmed using Trimmomatic (v0.39) and the cell barcodes were checked against the cell barcode whitelist provided by the inDrop pipeline.
Reads were aligned to mouse (GRCm38) genome by bowtie.
The reads were quantified and expression of genes was calculated using the inDrop pipeline.
Genome_build: GRCm38
Supplementary_files_format_and_content: 10X format output including sparse matrix, barcode.tsv and gene.tsv
|
| |
|
| Submission date |
Aug 20, 2020 |
| Last update date |
Apr 22, 2021 |
| Contact name |
Michael Wheeler |
| E-mail(s) |
mwheeler0@bwh.harvard.edu
|
| Organization name |
Brigham and Women's Hospital
|
| Department |
Neurology
|
| Street address |
60 Fenwood Rd.
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02115 |
| Country |
USA |
| |
|
| Platform ID |
GPL21626 |
| Series (2) |
| GSE150858 |
Barcoded viral tracing of single-cell interactions in CNS inflammation |
| GSE156583 |
RABID transcriptome from peak EAE astrocyte networks |
|
| Relations |
| BioSample |
SAMN15869184 |
| SRA |
SRX8979487 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4734082_S501_EAE_transcriptome.tar.gz |
14.3 Mb |
(ftp)(http) |
TAR |
| GSM4734082_S502_EAE_transcriptome.tar.gz |
23.1 Mb |
(ftp)(http) |
TAR |
| GSM4734082_S503_EAE_transcriptome.tar.gz |
24.0 Mb |
(ftp)(http) |
TAR |
| GSM4734082_S504_EAE_transcriptome.tar.gz |
23.0 Mb |
(ftp)(http) |
TAR |
| GSM4734082_S505_EAE_transcriptome.tar.gz |
23.5 Mb |
(ftp)(http) |
TAR |
| GSM4734082_S506_EAE_transcriptome.tar.gz |
24.9 Mb |
(ftp)(http) |
TAR |
| GSM4734082_S507_EAE_transcriptome.tar.gz |
13.4 Mb |
(ftp)(http) |
TAR |
| GSM4734082_S508_EAE_transcriptome.tar.gz |
21.8 Mb |
(ftp)(http) |
TAR |
| GSM4734082_S510_EAE_transcriptome.tar.gz |
14.9 Mb |
(ftp)(http) |
TAR |
| GSM4734082_S511_EAE_transcriptome.tar.gz |
21.8 Mb |
(ftp)(http) |
TAR |
| GSM4734082_S513_EAE_transcriptome.tar.gz |
9.2 Mb |
(ftp)(http) |
TAR |
| GSM4734082_S515_EAE_transcriptome.tar.gz |
8.9 Mb |
(ftp)(http) |
TAR |
| GSM4734082_S516_EAE_transcriptome.tar.gz |
7.9 Mb |
(ftp)(http) |
TAR |
| GSM4734082_S517_EAE_transcriptome.tar.gz |
2.1 Mb |
(ftp)(http) |
TAR |
| GSM4734082_S518_EAE_transcriptome.tar.gz |
5.5 Mb |
(ftp)(http) |
TAR |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
