|
Status |
Public on Aug 22, 2018 |
Title |
Thalamus [P60THRep4P2] |
Sample type |
SRA |
|
|
Source name |
P60-70 Male Mice
|
Organism |
Mus musculus |
Characteristics |
strain/background: C57Blk6/N gender: Male age: P60-70 tissue: Thalamus
|
Treatment protocol |
Acute brain slices digested for 3 hrs with a protease cocktail before titration, centrifugation to isolate debris-depleted single cells.
|
Extracted molecule |
total RNA |
Extraction protocol |
Drop-seq (Macosko et al. 2014 Cell).
|
|
|
Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina NextSeq 500 |
|
|
Description |
P60THRep4P2 Single-cell gene expression data based on 3' transcript counts. mRNA (cDNA) processed data file: F_GRCm38.81.P60Thalamus.raw.dge.txt
|
Data processing |
Sequencing was performed on an Illumina NextSeq500 using a 75 cycle kit (Read1: 20bp; Read2: 50 bp). Sequencing Reads were aligned against the GRCm38.81 mouse genome draft using STAR. Aligned Reads within a gene were collapsed to UMI(XM)-Gene Pairs and associated with single-cells through a cell barcode (XC) shared on Read 1. A count matrix - called the digital gene expression (DGE) matrix - was output. Columns belong to STAMPs (cells) and transcript counts (rows). Genome_build: GRCm38.81 Supplementary_files_format_and_content: *.raw.dge.txt: Digital gene expression matrix; comma-delimited file with columns = cells, and rows = transcript counts. Supplementary_files_format_and_content: metacells.BrainCellAtlas_Saunders_version_2018.04.01.csv: Comma-delimited digital gene expression matrix (ncol = 565, nrow =32307).
|
|
|
Submission date |
Jun 29, 2018 |
Last update date |
Aug 22, 2018 |
Contact name |
Arpiar Saunders |
E-mail(s) |
arpiar.saunders@gmail.com
|
Organization name |
Harvard Medical School
|
Department |
Genetics
|
Lab |
McCarroll Lab
|
Street address |
77 Avenue Louis Pasteur
|
City |
Boston |
State/province |
MA |
ZIP/Postal code |
02115 |
Country |
USA |
|
|
Platform ID |
GPL19057 |
Series (1) |
GSE116470 |
A Single-Cell Atlas of Cell Types, States, and Other Transcriptional Patterns from Nine Regions of the Adult Mouse Brain |
|
Relations |
BioSample |
SAMN09521021 |
SRA |
SRX4327785 |