|
| Status |
Public on Jul 14, 2021 |
| Title |
TBI180_1 (cep135 null E14.5 cortex) |
| Sample type |
SRA |
| |
|
| Source name |
Dorsal telencephalon from E14.5 embryonic cortex
|
| Organism |
Mus musculus |
| Characteristics |
cell type: Dorsal telencephalon (tissue)
culture time (hours): n/a
genotype: Cep135 (-/-)
|
| Treatment protocol |
no pharmacological treatment
|
| Growth protocol |
All mice were generated and maintained at the Animal Facility of the Spanish National Cancer Research Centre (CNIO) under specific pathogen-free conditions in accordance with the recommendation of the Federation of European Laboratory Animal Science Associations (FELASA)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA samples were used (300 ng on average, with five samples under 60 ng). Sample RNA Integrity numbers were 9.4 on average (range 8.6-9.4) when assayed on an Agilent 2100 Bioanalyzer. Sequencing libraries were prepared with the "QuantSeq 3‘ mRNA-Seq Library Prep Kit (FWD) for Illumina" (Lexogen, Cat.No. 015) by following manufacturer instructions. Library generation is initiated by reverse transcription with oligodT priming, and a second strand synthesis is performed from random primers by a DNA polymerase. Primers from both steps contain Illumina-compatible sequences. Libraries are completed by PCR {This kit generates directional libraries stranded in the sense orientation (the read1 (the only read in single read format) has the sense orientation (--library-type fr-secondstrand in TopHat, --stranded=yes in HTSeq).} cDNA libraries are purified, applied to an Illumina flow cell for cluster generation and sequenced on an Illumina instrument (see below) by following manufacturer's protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 550 |
| |
|
| Description |
sacrifice at embryonic day E14.5
TBI180_1
|
| Data processing |
Read adapters and polyA tails were removed with bbduk.sh, following the Lexogen recommendations. Processed reads were analysed with the nextpresso pipeline, as follows: Sequencing quality was checked with FastQC v0.11.7 (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). Reads were aligned to the mouse reference genome (GRCm38) with TopHat-2.0.10 using Bowtie 1.0.0 and Samtools 0.1.19 (--library-type fr-secondstrand in TopHat), allowing three mismatches and twenty multihits. Read counts were obtained with HTSeq-count v0.6.1 (--stranded=yes), using the mouse gene annotation from GENCODE (gencode.vM20.GRCm38.Ensembl95). Differential expression was performed with DESeq2, using a 0.05 FDR. GSEAPreranked was used to perform gene set enrichment analysis for several gene signatures on a pre-ranked gene list, setting 1000 gene set permutations. Only those gene sets with significant enrichment levels (FDR q-value < 0.25) were considered.
Genome_build: GRCm38
Supplementary_files_format_and_content: Normalized counts obtained with DESeq2
|
| |
|
| Submission date |
Mar 24, 2020 |
| Last update date |
Jul 14, 2021 |
| Contact name |
Osvaldo Graña |
| Organization name |
CNIO
|
| Department |
Structural Biology
|
| Lab |
Bioinformatics Unit
|
| Street address |
C/ Melchor Fernández Almagro, 3
|
| City |
Madrid |
| State/province |
Comunidad de Madrid |
| ZIP/Postal code |
28029 |
| Country |
Spain |
| |
|
| Platform ID |
GPL21626 |
| Series (1) |
| GSE147491 |
Cep135 deficiency promotes cell cycle de-regulation, p53 accumulation and cell deah of neural progenitors |
|
| Relations |
| BioSample |
SAMN14442225 |
| SRA |
SRX7988155 |
