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| Status |
Public on Jan 08, 2013 |
| Title |
fetal CEC 2 |
| Sample type |
SRA |
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| Source name |
corneal endothelial cells
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| Organism |
Homo sapiens |
| Characteristics |
cell type: corneal endothelial cells
age: gestation age 16-18wk
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| Growth protocol |
Adult cornea samples (age 31, 56, and 64 years old) were obtained from normal subjects who donated to the eye bank in UCLA Jules Stein Eye Institute. Fetal CEC samples were dissected from fetal ocular samples (16-18 weeks of gestation) provided by UCLA department of Pathology & laboratory and approved by UCLA IRB. The whole corneal endothelial layers were carefully peeled off under dissecting microscope and were immediately lyses in reagents for RNA purification.
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNA were extracted from those adult and fetal tissues using RNeasy Micro Kit (Qiagen, Cat. No. 74004, CA,USA). RNA concentration was detected by nanodrop spectrophotometer
RNA-Seq library construction followed the protocol described in illumina TruSeq™ RNA Sample Preparation Guide. Library construction was started with 100ng total RNA, via poly-T oligo-attached magnetic beads to purify the poly-A containing mRNA molecules. RNA fragments were reverse transcribed into first stand cDNA, follwed by synthesis second strand cDNA. After end repaired with a single ‘A’ base, cDNAs were ligated with different adapters for PCR amplification. After amplified for 15 cycles, the concentration of product was tested by the Qubit Fluorometer (Invitrogen, USA).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Data processing |
each sample was subjected to sequencing according to manufacturer’s instruction with Illumina Hiseq 2000. Reads were mapped to the hg19 genome using BWA.
For all datasets analyzed, we first transformed transcript read counts to the RPKM metric, and genes with an average RPKM<1 were filtered out, followed by quantile normalization.
Genome_build: hg19
Supplementary_files_format_and_content: filtered and normalized RPKM table
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| Submission date |
Oct 16, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Kevin Huang |
| Phone |
310-267-0438
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| Organization name |
UCLA
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| Department |
Human Genetics
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| Lab |
Guoping Fan
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| Street address |
Gonda BLDG Rm. 6554, P.O.Box 957088
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| City |
Los Angeles |
| State/province |
CA |
| ZIP/Postal code |
90095-7088 |
| Country |
USA |
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| Platform ID |
GPL11154 |
| Series (1) |
| GSE41616 |
Identification of Novel Molecular Markers through Transcriptomic Analysis in Human Fetal and Adult Corneal Endothelial Cells |
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| Relations |
| Reanalyzed by |
GSE81474 |
| SRA |
SRX195465 |
| BioSample |
SAMN01766531 |
| 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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