|
| Status |
Public on Aug 25, 2016 |
| Title |
P17 Vsx2-GFP mouse retina 2 (Batch 1) |
| Sample type |
SRA |
| |
|
| Source name |
Mus musculus retina, P17
|
| Organism |
Mus musculus |
| Characteristics |
tissue: retina
developmental stage: P17
genotype: Vsx2-GFP
|
| 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 |
Bipolar2
|
| 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 Bipolar1-6 -- prepared from P17 Vsx2-GFP mouse retinas on two separate days (Bipolar1-4 and Bipolar5-6)--were merged together into a single matrix.
Genome_build: mm10
Supplementary_files_format_and_content: compressed, flat text file with tab delimiters
|
| |
|
| Submission date |
May 25, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Karthik Shekhar |
| E-mail(s) |
karthik@broadinstitute.org
|
| Phone |
217-979-9852
|
| Organization name |
Broad Institute
|
| Street address |
415 Main St.
|
| City |
Cambridge |
| State/province |
MA |
| ZIP/Postal code |
02142 |
| Country |
USA |
| |
|
| Platform ID |
GPL19057 |
| Series (2) |
| GSE81904 |
Drop-Seq analysis of P17 FACS sorted retinal cells from the Tg(Chx10-EGFP/cre,-ALPP)2Clc or Vsx2-GFP transgenic line |
| GSE81905 |
Single cell RNA-sequencing of retinal bipolar cells |
|
| Relations |
| BioSample |
SAMN05177286 |
| SRA |
SRX1800076 |
