GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Sample GSM1626794 Query DataSets for GSM1626794
Status Public on May 20, 2015
Title P14 mouse retina 2
Sample type SRA
Source name Mus musculus retina, P14
Organism Mus musculus
Characteristics strain/background: C57BL/6
genotype/variation: wild-type
tissue: retina
age: P14
Extracted molecule total RNA
Extraction protocol Single-cell suspensions were processed through Drop-Seq to generate single-cell cDNA libraries attached to microbeads.
Microbeads were counted, and amplified by PCR, and the 3' end of the cDNA prepared for sequencing using a modified Nextera XT protocol.
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
Description Drop-Seq
Data processing Base calls performed with bcl2fastq2.15.
Read 2 was aligned with Star v2.4.0.
Each aligned read was tagged with its mate-pair UMI and cell barcode.
Each aligned exonic read was tagged with a gene name.
A digital expression matrix was built by counting the number of unique UMIs per gene within each cell; columns are cells, and rows are genes.
The first inflection point was estimated on a cumulative sum plot of the digital expression matrix to determine the number of cells in the sample.
Samples 1-7 -- prepared from P14 mouse retinas on multiple separate days -- were merged together into a single matrix. Merged DGE file from all 7 samples generated. log(1+10,000*(DGE normalized to total transcripts per cell)) calculated on DGE.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: Digital expression matrices. Compressed, flat text files with tab delimiters.
Submission date Mar 06, 2015
Last update date May 15, 2019
Contact name Evan Macosko
Organization name Harvard Medical School
Department Genetics
Lab McCarroll Lab
Street address 77 Avenue Louis Pasteur, NRB 260
City Boston
State/province MA
ZIP/Postal code 02115
Country USA
Platform ID GPL19057
Series (2)
GSE63472 Drop-Seq analysis of P14 mouse retina single-cell suspension
GSE63473 Highly parallel genome-wide expression profiling of individual cells using nanoliter droplets
BioSample SAMN03393380
SRA SRX907220

Supplementary file Size Download File type/resource
GSM1626794_P14Retina_2.bam 15.6 Gb (ftp)(http) BAM
GSM1626794_P14Retina_2.digital_expression.txt.gz 9.1 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap