|
| Status |
Public on Jan 27, 2022 |
| Title |
FGF control and mutant |
| Sample type |
SRA |
| |
|
| Source name |
Peripheral retina
|
| Organism |
Mus musculus |
| Characteristics |
developmental stage: E14
genotype: Control: a-Cre; FgfR1 f/+ ; FgfR2 f/+ Mutant: a-Cre; FgfR1 f/f ; FgfR2 f/f; Rosa26-TdTomato
strain: Mixed
|
| Extracted molecule |
total RNA |
| Extraction protocol |
E14 retinal tissue was harvested and pooled from 3 embryos each for mutant and control. Cells were dissociated using a Papain protocol. Cells were sorted according to fluorescent reporters and single cell suspension was transferred to the Columbia genome center for further processing.
Barcoded cDNA library was contructed using the 10X Genomics Chromium controller.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
XR001
|
| Data processing |
Approximately 11,000 cells were sequenced on the 10X platform. cDNA Libraries were sequenced on an Illumina NovaSeq 6000 sequencer. The data alignment, barcode processing and generation of cell gene matrices was performed by the Single Cell Analysis core facility at Columbia Genome Center using cellranger pipeline v2.0.0.
Count matrices were aggregated and filtered for further processing using Seurat v3.
Supplementary_files_format_and_content: There is no barcode file. The control and mutant cells are sequenced together. During processing and analysis, they can be separated based on TdTomato reporter expression. The manuscript (in preparation) details how the separate matrices were constructed using Seurat workflow in R.
|
| |
|
| Submission date |
Nov 04, 2019 |
| Last update date |
Aug 07, 2023 |
| Contact name |
Revathi Balasubramanian |
| E-mail(s) |
rb3132@columbia.edu
|
| Organization name |
Columbia University
|
| Department |
Ophthalmology
|
| Street address |
635 West 165th street
|
| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10032 |
| Country |
USA |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE139904 |
Single cell RNA sequencing of peripheral retina in control and FGF signaling mutant mouse embryonic tissue |
|
| Relations |
| Reanalyzed by |
GSE240316 |
| BioSample |
SAMN13191890 |
| SRA |
SRX7099188 |
