 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on May 20, 2015 |
| Title |
P14 mouse retina 5 |
| 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.
For replicates 4-6, 0.5% human HEK cells were included.
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. For replicates 4-6, human reads from spiked-in HEK cells (0.5%) were removed from BAMs and digital expression files. 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 four separate days -- were merged together into a single matrix. 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 |
| E-mail(s) |
emacosko@genetics.med.harvard.edu
|
| 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 |
|
| Relations |
| Reanalyzed by |
GSE110623 |
| BioSample |
SAMN03393379 |
| SRA |
SRX907223 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1626797_P14Retina_5.bam |
12.0 Gb |
(ftp)(http) |
BAM |
| GSM1626797_P14Retina_5.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 |
|
|
|
|
 |
