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| Status |
Public on Jan 24, 2022 |
| Title |
HLKLYBBXX_15803806_S63_L007 |
| Sample type |
SRA |
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| Source name |
RM04_RPE-Choroid_Peripheral_OS8
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| Organism |
Macaca mulatta |
| Characteristics |
tissue: RPE-Choroid
location: Peripheral
eye (od/os): OS8
macaque number: RM04
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| Treatment protocol |
Postmorterm rhesus
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| Extracted molecule |
total RNA |
| Extraction protocol |
Two-millimeter punch biopsies were removed from macular/foveal, perimacular, temporal, and nasal regions of the retina. Following the biopsy, the tissues were separated into layers of neural retina and RPE/choroid using microdissection techniques. otal RNA was isolated from fresh tissues using the PicoPure™ RNA Isolation Kit (Applied Biosystems, Waltham, Massachusetts, USA) following mortar and pestle tissue homogenization. Extracted RNA samples were checked for quality using the 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA) and only samples with RIN value > 6.5 were used (Range 1 – 10).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
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| Data processing |
Macaca_mulatta.Mmul_8.0.1.90.gtf.gz used as reference for Salmon index build
Quantified with Salmon 0.13
Imported into R with tximport (lengthScaledTPM)
HCOP annotation information used to align gene names with ensembl ID
TPM values scaled for library size with edgeR calcNormFactors
Genome_build: Macaca_mulatta.Mmul_8.0.1.90.gtf.gz
Supplementary_files_format_and_content: TSV
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| Submission date |
Jan 24, 2022 |
| Last update date |
Jan 24, 2022 |
| Contact name |
David McGaughey |
| E-mail(s) |
mcgaugheyd@mail.nih.gov
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| Organization name |
NIH
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| Department |
NEI
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| Street address |
10 Center Dr
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| City |
Bethesda |
| State/province |
MD |
| ZIP/Postal code |
20892 |
| Country |
USA |
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| Platform ID |
GPL23949 |
| Series (1) |
| GSE194285 |
Transcriptional mapping of the macaque retina and RPE-choroid reveals conserved inter-tissue transcription drivers and signaling pathways |
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| Relations |
| BioSample |
SAMN25227238 |
| SRA |
SRX13883809 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5832423_HLKLYBBXX_15803806_S63_L007.tsv.gz |
891.5 Kb |
(ftp)(http) |
TSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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