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Sample GSM4148508 Query DataSets for GSM4148508
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
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
Reanalyzed by GSE240316
BioSample SAMN13191890
SRA SRX7099188

Supplementary file Size Download File type/resource
GSM4148508_filtered_feature_bc_matrix-barcodes.tsv.gz 55.4 Kb (ftp)(http) TSV
GSM4148508_filtered_feature_bc_matrix-features.tsv.gz 272.8 Kb (ftp)(http) TSV
GSM4148508_filtered_feature_bc_matrix-matrix.mtx.gz 103.8 Mb (ftp)(http) MTX
GSM4148508_molecule_info.h5 501.5 Mb (ftp)(http) H5
GSM4148508_raw_feature_bc_matrix-barcodes.tsv.gz 20.0 Mb (ftp)(http) TSV
GSM4148508_raw_feature_bc_matrix-features.tsv.gz 272.8 Kb (ftp)(http) TSV
GSM4148508_raw_feature_bc_matrix-matrix.mtx.gz 148.7 Mb (ftp)(http) MTX
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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