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| Status |
Public on Mar 30, 2019 |
| Title |
iPSC-RPE RPE008 RNA-seq |
| Sample type |
SRA |
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| Source name |
iPSC-RPE
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| Organism |
Homo sapiens |
| Characteristics |
cell type: iPSC-RPE
individual: e562a8bc-cc91-46fe-ba2f-aa8ab62fefe9
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA was isolated using the Quick-RNA Mini Prep Kit (Zymo) from frozen RTL plus pellets, including on-column DNAse treatment step. RNA was eluted in 40 µl RNAse-free water and run on a Bioanalyzer (Agilent) to determine integrity. Concentration was measured by Qubit. Illumina Truseq Stranded mRNA libraries were prepared and sequenced on HiSeq4000, to an average of 40 M 150 bp paired-end reads per sample.
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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 |
RNA-seq reads were aligned using STAR (Dobin et al., 2013) with a splice junction database built from the Gencode v19 gene annotation (Harrow et al., 2012a). Transcript and gene-based expression values were quantified using the RSEM package (1.2.20) (Li and Dewey, 2011) and normalized to transcript per million bp (TPM).
Genome_build: hg19
Supplementary_files_format_and_content: bigWig, tpm, FPKM
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| Submission date |
Feb 21, 2019 |
| Last update date |
Feb 26, 2024 |
| Contact name |
Kelly Ann Frazer |
| E-mail(s) |
kafrazer@health.ucsd.edu
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| Phone |
650 288-9391
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| Organization name |
UC San Diego
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| Department |
Pediatrics
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| Lab |
Frazer
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| Street address |
9500 Gilman Drive
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| City |
La Jolla |
| State/province |
CA |
| ZIP/Postal code |
92093 |
| Country |
USA |
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| Platform ID |
GPL20301 |
| Series (1) |
| GSE126847 |
Human iPSC-derived retinal pigment epithelium: a model system for identifying and functionally characterizing causal variants at AMD risk loci |
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| Relations |
| BioSample |
SAMN10979878 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3615273_045005d6-6ec1-467b-a549-174dd15822c8.tpm.tsv.gz |
1.5 Mb |
(ftp)(http) |
TSV |
| Raw data are available in SRA |
| Processed data are available on Series record |
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