|
| Status |
Public on Apr 20, 2019 |
| Title |
wdr12: GFP+ rep1 |
| Sample type |
SRA |
| |
|
| Source name |
optic tectum
|
| Organism |
Oryzias latipes |
| Characteristics |
line: Wdr12:GFP
age: 1 month
tissue: optic tectum
|
| Treatment protocol |
Thirty one-month optic tecta were quickly dissected out and placed in ice-cold calcium-free RINGER solution. Cells were dissociated in FACSmax Cell Dissociation Solution (AMS Biotechnology, Abingdon, UK; T200100). A mechanical dissociation step was performed with a plunger from a 1-mL syringe. Tectums were squished through a strainer (40-μm mesh) into a Petri dish and the cell suspension was transferred into another tube. Cells were sorted on a MoFlo Astrios (Beckman-Coulter) cytometer
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA isolation was performed using the PicoPureTM Isolation kit according to the manufacturer's protocol. Total RNA concentration and quality were checked in an Agilent Bioanalyser.
4ng of RNA were used for each library construction (Epicentre). Library construction was performed with TotalScript™ RNA-Seq Kit according to the manufacter’s protocol.
Libraries were sequenced on an Illumina Hiseq 1000 instrument, using a TruSeq SR Cluster Kit v3-cBot-HS (Illumina) and TruSeq SBS Kit v3-HS - 50 cycles (Illumina), using a Single Read 50 bp protocol. Libraries have been pooled in equimolar proportions and diluted to a final concentration of 12pM, according to Illumina recommandations.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 1000 |
| |
|
| Data processing |
Basecalls performed using Illumina script BclToFastq version 1.8.3
Data were demultiplexed using the distribution of CASAVA software (CASAVA-1.8.2)
Data quality was checked with FastQC 0.10.1
Reads were mapped to the genome of Oryzias latipes oryLat2 (downloaded from UCSC) using TopHat2
Differential expression analysis of RNA-seq and gene expression profiles with biological replication was performed using the Bioconductor package DESeq
Differential expression statistics classified each gene as up, down or not significant according a |log2-transformed fold change| >1, with adjusted p-values less than 0.05, and computed FDR from resulting p-values using a Benjamini Hochberg multiple test
DE statistics classified each gene as up/down/not significant according a |log2-transformed fold change| >1, with adjusted p-values less than 0.05
FDR from resulting p-values using a Benjamini Hochberg multiple test (FDR <= 0.05)
Selection of genes up regulated and downregulated in wdr12:GFP+ compared both to wdr12:GFP- and ebf3:GFP+ cells (refered as controls)
Genome_build: Oryzias latipes oryLat2
Supplementary_files_format_and_content: wdr12: GFP+ referred as wdr12GFP
Supplementary_files_format_and_content: wdr12: GFP- referred as wdr12GFPm
Supplementary_files_format_and_content: ebf3: GFP+ referred as ebf3GFP
Supplementary_files_format_and_content: ebf3: GFP+ union wdr12:GFP- referred as controls
Supplementary_files_format_and_content: raw counts: ebf3GFP_tot-count.xlsx
Supplementary_files_format_and_content: raw counts: wdr12GFPmvsebf3GFP.xls
Supplementary_files_format_and_content: raw counts: wdr12GFPmvswdr12GFP.xls
Supplementary_files_format_and_content: raw counts: wdr12GFPvsebf3GFP.xls
|
| |
|
| Submission date |
Apr 20, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Emilie Dambroise |
| E-mail(s) |
[email protected]
|
| Organization name |
Institut Imagine
|
| Department |
U1163
|
| Lab |
Molecular and physiopathological bases of osteochondrodysplasia
|
| Street address |
24 bd Montparnasse
|
| City |
Paris |
| ZIP/Postal code |
75015 |
| Country |
France |
| |
|
| Platform ID |
GPL21753 |
| Series (1) |
| GSE80497 |
Gene expression profiling of optic tectum neuroepithelial cells in adult medaka |
|
| Relations |
| BioSample |
SAMN04875729 |
| SRA |
SRX1716244 |
