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Sample GSM3855434 Query DataSets for GSM3855434
Status Public on Jun 06, 2019
Title LHX4::GFP-
Sample type SRA
Source name Retinal cells
Organism Mus musculus
Characteristics strain: Tg(Lhx4::EGFP)KN199Gsat/Mmucd
cell type: Retinal cells (LHX4::GFP-)
developmental stage: E14.5
Extracted molecule total RNA
Extraction protocol Live cells were collected after dissociation and flow sorting for GFP signal. 3 Samples were extracted from 2 litters of E14.5 LHX4::GFP mice, pooled into one sorting solution during dissociation.
For each sample (GFP+ and GFP-), approx. 4000 cells were individually lysed, and their RNA transcribed and sequenced by the Columbia University Single Cell Analysis Core.
They were prepared using the 10X Chromium Single Cell 3’ Reagent Kits v2 according to manufacturer's instructions (cDNA amplification cycles = 12, library amplification cycles = 12).
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
Description PolyA RNAseq
Data processing Sequencing and alignment were provided by the Columbia Genome Center Single Cell Core. In brief, raw sequencing data from NovaSeq6000 were processed using the 10x Genomics Cell Ranger pipeline (v2.1.1) using default parameters and the reference genome was refdata-cellranger-mm10-2.1.0, distributed by 10X.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: Files include barcode.tsv, genes.tsv and matrix.mtx that are produced as CellRanger output.
Submission date Jun 05, 2019
Last update date Apr 03, 2020
Contact name Mark Monroe Emerson
Phone 212-650-8417
Organization name The City College of New York
Department Biology
Street address 160 Convent Ave
City New York
State/province NY
ZIP/Postal code 10031
Country USA
Platform ID GPL24247
Series (1)
GSE132272 Identification of genes with enriched expression in early developing mouse cone photoreceptors
BioSample SAMN11963761
SRA SRX5979386

Supplementary file Size Download File type/resource
GSM3855434_LHX4-GFPnegative_barcodes.tsv.gz 18.2 Kb (ftp)(http) TSV
GSM3855434_LHX4-GFPnegative_genes.tsv.gz 217.5 Kb (ftp)(http) TSV
GSM3855434_LHX4-GFPnegative_matrix.mtx.gz 39.5 Mb (ftp)(http) MTX
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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