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| Status |
Public on Jun 06, 2019 |
| Title |
LHX4::GFP- |
| Sample type |
SRA |
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| Source name |
Retinal cells
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| Organism |
Mus musculus |
| Characteristics |
strain: Tg(Lhx4::EGFP)KN199Gsat/Mmucd
cell type: Retinal cells (LHX4::GFP-)
developmental stage: E14.5
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| 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).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
PolyA RNAseq
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| 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.
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| Submission date |
Jun 05, 2019 |
| Last update date |
Apr 03, 2020 |
| Contact name |
Mark Monroe Emerson |
| E-mail(s) |
memerson@ccny.cuny.edu
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| Phone |
212-650-8417
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| Organization name |
The City College of New York
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| Department |
Biology
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| Street address |
160 Convent Ave
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| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10031 |
| Country |
USA |
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| Platform ID |
GPL24247 |
| Series (1) |
| GSE132272 |
Identification of genes with enriched expression in early developing mouse cone photoreceptors |
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| Relations |
| 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 Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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