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| Status |
Public on May 20, 2015 |
| Title |
P14 mouse retina 1 |
| Sample type |
SRA |
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| Source name |
Mus musculus retina, P14
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| Organism |
Mus musculus |
| Characteristics |
strain/background: C57BL/6
genotype/variation: wild-type
tissue: retina
age: P14
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| 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.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| Description |
Drop-Seq
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| 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.
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| Submission date |
Mar 06, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Evan Macosko |
| E-mail(s) |
emacosko@genetics.med.harvard.edu
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| Organization name |
Harvard Medical School
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| Department |
Genetics
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| Lab |
McCarroll Lab
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| Street address |
77 Avenue Louis Pasteur, NRB 260
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| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02115 |
| Country |
USA |
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| 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 |
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| Relations |
| BioSample |
SAMN03393378 |
| SRA |
SRX907219 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1626793_P14Retina_1.bam |
14.9 Gb |
(ftp)(http) |
BAM |
| GSM1626793_P14Retina_1.digital_expression.txt.gz |
7.6 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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