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Sample GSM3239678 Query DataSets for GSM3239678
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

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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