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| Status |
Public on Aug 18, 2016 |
| Title |
E16 retina replicate 2 |
| Sample type |
SRA |
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| Source name |
Retina cells
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| Organism |
Gallus gallus |
| Characteristics |
age: E16
tissue: Retina
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| Treatment protocol |
no treatments were used
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| Growth protocol |
tissue was harvested from chicken embryos grown under normal incubation conditions
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| Extracted molecule |
total RNA |
| Extraction protocol |
Qiagen all prep min kit was used to extract nucleic acids
cDNA libraries were prepared from poly A+ RNAs according to Illumina's instructions accompanying the Illumina TruSeq kit.
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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 |
Basecalls performed using CASAVA
Data were aligned to the Galgal4 genome using STAR with the following parameters: --outSAMstrandField intronMotif --outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.04 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000
Aligned reads were counted against genes from the Ensembl Galgal4 annotation using the featureCounts program in the subread package.
Data were normalized for library size using the DESeq2 median ratio normalization procedure described in Ander and Huber (2010).
Differential gene expression was assessed using the DESeq2 package in R.
Genome_build: Galgal4
Supplementary_files_format_and_content: DESeq-normalized count matrix text file
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| Submission date |
Feb 13, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Stephen Turner |
| Organization name |
Signature Science, LLC
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| Street address |
1670 Discovery Drive
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| City |
Charlottesville |
| State/province |
VA |
| ZIP/Postal code |
22911 |
| Country |
USA |
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| Platform ID |
GPL19787 |
| Series (1) |
| GSE65938 |
RNA-seq analysis of the developing chicken retina |
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| Relations |
| BioSample |
SAMN03344788 |
| SRA |
SRX877995 |
| 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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