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| Status |
Public on Jul 01, 2021 |
| Title |
scRNAseq_ThrbNeg_rep2 |
| Sample type |
SRA |
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| Source name |
scRNAseq_ThrbNeg
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| Organism |
Gallus gallus |
| Characteristics |
cell type: Retina Progentor Cell
treatment/condition: ThrbNeg
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| Treatment protocol |
N/A
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| Growth protocol |
Retina progenitor cells were cultured in DMEM with 10% FBS
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| 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®
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| 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)
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| Submission date |
Jun 07, 2020 |
| Last update date |
Jul 01, 2021 |
| Contact name |
CHANGHEE LEE |
| E-mail(s) |
chlee@genetics.med.harvard.edu
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| Phone |
617-432-6534
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| Organization name |
Harvard Medical School
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| Department |
Genetics
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| Lab |
Clifford Tabin
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| Street address |
77 AVENUE LOUIS PASTEUR
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| City |
BOSTON |
| State/province |
MA |
| ZIP/Postal code |
02115 |
| Country |
USA |
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| Platform ID |
GPL19787 |
| Series (1) |
| GSE151947 |
Onecut1 and Otx2 directly regulate multiple genes expressed early in cone and horizontal cell development [scRNA-seq] |
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| Relations |
| BioSample |
SAMN15159186 |
| SRA |
SRX8487946 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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