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| Status |
Public on Sep 08, 2011 |
| Title |
embryonic digit stage 31 LH3_mRNAseq |
| Sample type |
SRA |
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| Source name |
Embryonic chicken digit
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| Organism |
Gallus gallus |
| Characteristics |
embryonic stage: Stage 31
tissue: embryonic digit
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| Growth protocol |
Fertilized chicken eggs were obtained from Charles River Laboratories International, Inc. and incubated between 37.5-39C at high relative humidity (>50%).
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using RNeasy Mini Kit (Qiagen, Cat. No. 74106, Maryland, USA), and treated with DNase I using RNase-Free DNase Set (Qiagen, Cat. No. 79254, Hilden, Germany). Extracted total RNA of the 14 samples was submitted to Yale Center for Genome Analysis for mRNA sequencing (mRNA-seq) using Illumina Genome Analyzer. mRNA-seq 8-Sample Prep Kit (Illumina, Cat. No. RS-100-0801, San Diego, USA), Standard Cluster Generation Kit (Illumina, Cat. No. GD-103-4001, San Diego, USA) and Illumina Sequencing Kit (Illumina, Cat. No. FC-104-1001, San Diego, USA) were used for constructing libraries for single-read sequencing, cluster amplification and final sequencing-by-synthesis.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer |
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| Description |
N/A
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| Data processing |
txt: Reads from mRNA-seq data were aligned to Ensembl chicken genome (Gallus gallus WASHUC2) using GERALD module of Illumina CASAVA v1.6 software. After alignment, gene raw counts (gene expression levels) were counted by Illumina CASAVA v1.6 software, and then normalized using TMM method performed using the edgeR package.
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| Submission date |
Mar 24, 2011 |
| Last update date |
Jun 11, 2013 |
| Contact name |
Zhe Wang |
| Organization name |
Yale University
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| Street address |
300 Heffernan Drive, B31-RA269
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| City |
West Haven |
| State/province |
CT |
| ZIP/Postal code |
06516-4150 |
| Country |
USA |
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| Platform ID |
GPL10223 |
| Series (1) |
| GSE28156 |
mRNA-seq data of embryonic chicken digits |
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| Relations |
| BioSample |
SAMN02198637 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM697431_LH3.txt.gz |
267.0 Kb |
(ftp)(http) |
TXT |
| GSM697431_LH3_export.txt.gz |
1.5 Gb |
(ftp)(http) |
TXT |
| Processed data provided as supplementary file |
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