|
| Status |
Public on Jul 02, 2014 |
| Title |
FP |
| Sample type |
SRA |
| |
|
| Source name |
Microdissected lens cortical fibers
|
| Organism |
Gallus gallus |
| Characteristics |
age: Embryonic day 13
tissue: Lens
tissue (differentiation state-specific region): cortical fibers
#pooled microdissections: 100
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The following protocol was performed in replicate. 100 Lenses were removed, microdissected (lens central epithelium, equatorial epithelium, cortical fibers, and central fiber core), pooled, and RNA was harvested using Trizol reagent. illumina directional mRNA-Seq Sample Preparation was performed under manufacturer guidelines for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Description |
Sample 5
|
| Data processing |
Prepared libraries were sequenced uni-directionally with the illumina Genome Analyzer IIx.
Reads aligned to ENSEMBLE; Galgal4; GCA_000002315.2.
Data was then processed using the cufflinks pipeline with replicates under default parameters. (http://cufflinks.cbcb.umd.edu/)
Differential expression analysis performed by cuffdiff version 2.1.1
Genome_build: Gallus_gallus-4.0 (Synonym: galGal4)
Supplementary_files_format_and_content: Tab-delimited text files including FPKM values and/or statistical analysis for the final assembled dataset
|
| |
|
| Submission date |
Jan 10, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Marc Kantorow |
| E-mail(s) |
mkantoro@fau.edu
|
| Phone |
5612973806
|
| Organization name |
Florida Atlantic University
|
| Street address |
777 Glades Rd
|
| City |
Boca Raton |
| State/province |
Florida |
| ZIP/Postal code |
33431 |
| Country |
USA |
| |
|
| Platform ID |
GPL13797 |
| Series (1) |
| GSE53976 |
Differentiation state-specific mitochondrial dynamic regulatory networks are revealed by global transcriptional analysis of the developing chicken lens. |
|
| Relations |
| BioSample |
SAMN02581121 |
| SRA |
SRX424599 |
