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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Aug 13, 2020 |
| Title |
KO-P7-1 |
| Sample type |
SRA |
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| Source name |
corneal endothelium
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| Organism |
Mus musculus |
| Characteristics |
cell type: immortalized mouse corneal endothelial cells
passage: P7
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| Growth protocol |
All MCEnC lines were cultured on flasks coated with a mixture of 40 µg/cm2 chondroitin sulfate (Sigma-Aldrich) and 40 ng/ cm2 laminin (Sigma-Aldrich). The cells were grown at 33°C in OptiMEM-I medium (Thermo Fisher Scientific) supplemented with 8% fetal bovine serum (Atlanta Biologicals), 10 ng/mL recombinant human FGF, pituitary extract 50 μg/mL (Sigma-Aldrich), CaCl2 200 mg/L, 0.08% chondroitin sulfate (G6737, Sigma-Aldrich), gentamicin 50 μg/mL (Thermo Fisher Scientific), 100 µg/mL penicillin (Thermo Fisher Scientific), and 100 µg/mL streptomycin (Thermo Fisher Scientific).
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA from cultured MCEnC was isolated and purified using the RNeasy Plus Mini Kit (Qiagen).
UCLA TCGB protocol
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 3000 |
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| Description |
Slc4a11-/-
MCEC-KO-P7-1_S35_L004_R1_001
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| Data processing |
Alignment - HISAT2, --no-unal
Assemble and Quantify - HTSeq-count
DGE analysis - LIMMA and VOOM
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: txt - list of DGE
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| Submission date |
Dec 26, 2019 |
| Last update date |
Aug 13, 2020 |
| Contact name |
Wenlin Zhang |
| E-mail(s) |
w.zhang@jsei.ucla.edu
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| Organization name |
UCLA, Jules Stein Eye Institute
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| Street address |
200 Stein Plaza, Dserc 3-143
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| City |
Los Angeles |
| State/province |
CA |
| ZIP/Postal code |
90095 |
| Country |
USA |
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| Platform ID |
GPL21493 |
| Series (1) |
| GSE142635 |
Transcriptome of Immortalized Mouse Corneal Endothelial Cells with SLC4A11 deficiency |
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| Relations |
| BioSample |
SAMN13683657 |
| SRA |
SRX7443218 |
| 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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