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Sample GSM4594235 Query DataSets for GSM4594235
Status Public on Jul 01, 2021
Title scRNAseq_ThrbPos_rep1
Sample type SRA
Source name scRNAseq_ThrbPos
Organism Gallus gallus
Characteristics cell type: Retina Progentor Cell
treatment/condition: ThrbPos
Treatment protocol N/A
Growth protocol Retina progenitor cells were cultured in DMEM with 10% FBS
Extracted molecule total RNA
Extraction protocol Total RNA is extracted using Direct-zol RNA Kits (Zymo Research)
1ug of RNA is used to make the library using NEBNext® Ultra™ RNA Library Prep Kit for Illumina®
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina MiSeq
Data processing For 10X Chromium libraries, sequencing output was demultiplexed by Cell Ranger (version 3.0.0), then mapped with dropEst (Petukhov et al, Genome Biology 2018) pipeline
Quality score above 0.9 were filtered and then any cells more than 4,000 features filtered out for doublet removal and cells above 15% mitochondrial content removed
Genome_build: galGal5 (Ensembl, release 94, only protein coding and lincRNA with two additional transgenes MCHERRY and EGFP)
Supplementary_files_format_and_content: Seurat (v3.1.5) object with meta information; equivalent text file in market matrix format (MTX) with rownames (features) and colnames (barcodes)
Submission date Jun 07, 2020
Last update date Jul 01, 2021
Contact name CHANGHEE LEE
Phone 617-432-6534
Organization name Harvard Medical School
Department Genetics
Lab Clifford Tabin
Street address 77 AVENUE LOUIS PASTEUR
State/province MA
ZIP/Postal code 02115
Country USA
Platform ID GPL19064
Series (1)
GSE151947 Onecut1 and Otx2 directly regulate multiple genes expressed early in cone and horizontal cell development [scRNA-seq]
BioSample SAMN15159189
SRA SRX8487943

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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