|
| Status |
Public on Sep 28, 2019 |
| Title |
CC_P34_7 |
| Sample type |
SRA |
| |
|
| Source name |
Tam4_Crx
|
| Organism |
Mus musculus |
| Characteristics |
tissue: retina
genotype/variation: Otx2 KO
cell type in which ablation occurs: photoreceptor
days after ko induction: 4
|
| Treatment protocol |
A single dose of a solution tamoxifen/corn oil was injected intraperitonally (5ul/gram of weight of a 10mg/ul stock solution) to promote an efficient KO
|
| Growth protocol |
All mice used for this experiment were raised according to the EUROPEAN COMMUNITIES COUNCIL DIRECTIVE of the 22 September 2010 (2010/63/EEC) and to the guideline declared in our Project of Aniaml Experimentation
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted by full retinas using a Tri Reagent (T9424 Sigma) solution according to the manufacturer's protocol
RNA-Seq libraries were generated from 500 ng of total RNA using TruSeq Stranded mRNA LT Sample Preparation Kit (Illumina, San Diego, CA), according to manufacturer's instructions. Briefly, following purification with poly-T oligo attached magnetic beads, the mRNA was fragmented using divalent cations at 94oC for 2 minutes. The cleaved RNA fragments were copied into first strand cDNA using reverse transcriptase and random primers. Strand specificity was achieved by replacing dTTP with dUTP during second strand cDNA synthesis using DNA Polymerase I and RNase H. Following addition of a single 'A' base and subsequent ligation of the adapter on double stranded cDNA fragments, the products were purified and enriched with PCR (30 sec at 98oC; [10 sec at 98oC, 30 sec at 60oC, 30 sec at 72oC] x 12 cycles; 5 min at 72oC) to create the cDNA library. Surplus PCR primers were further removed by purification using AMPure XP beads (Beckman-Coulter, Villepinte, France) and the final cDNA libraries were checked for quality and quantified using capillary electrophoresis.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
Alignment : Reads were mapped onto mm10 assembly of mouse genome using STAR v.2.5.3a
Quantification : Gene Expression was quantified using HTSeq v.0.6.1p1 (union mode) and Ensembl release 93 annotations.
Genome_build: mm10
Supplementary_files_format_and_content: Tabulated text file containing raw read counts in each sample.
|
| |
|
| Submission date |
Sep 27, 2019 |
| Last update date |
Sep 28, 2019 |
| Contact name |
PASQUALE PENSIERI |
| E-mail(s) |
ppensieri@unice.fr
|
| Phone |
+33603960714
|
| Organization name |
INSTITUT BIOLOGIE VALROSE
|
| Department |
SCIENCES NATURELLES
|
| Lab |
NEURODEVELOPMENT , LAMONERIE'S TEAM
|
| Street address |
PARC VALROSE
|
| City |
NICE |
| ZIP/Postal code |
06108 |
| Country |
France |
| |
|
| Platform ID |
GPL21103 |
| Series (1) |
|
| Relations |
| BioSample |
SAMN12860863 |
| SRA |
SRX6914913 |
