|
| Status |
Public on Jan 10, 2024 |
| Title |
Ire1af/f Emx1Cre cortex Polysome 1 |
| Sample type |
SRA |
| |
|
| Source name |
E18 Cerebral Cortex
|
| Organism |
Mus musculus |
| Characteristics |
genotype: Ire1aEmx1Cre
strain: C57BL/6J
developmental stage: E18
tissue: cerebral cortex
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Ribosome fractionation and polysome purification from E18.5 cortex was performed as published protocol (Kraushar et al., 2021). RNA was isolated using the Relia-prep RNA mini kit (Promega)
Stranded Total RNAseq libraries were prepared using TruSeq with Ribo-Zero Gold rRNA Removal
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
total RNA (polysome fraction)
|
| Data processing |
Raw reads were aligned to GRCm38.p5 using STAR 2.5.3a with parameters --outFilterMultimapNmax 100 --winAnchormultimapNmax 100 --outSamstrandField intronMotif and the gencode vM16 basic annotation transcriptome
Count table was generated from the resulting bam files using TETranscripts
Fit to a quasi-likelihood negative binomial generalized log-linear model and tested for differential expression using EdgeR
Genome_build: GRCm38.p5
|
| |
|
| Submission date |
Apr 21, 2021 |
| Last update date |
Jan 10, 2024 |
| Contact name |
Andrew Newman |
| Organization name |
Charité Universitätsmedizin Berlin
|
| Department |
Institute for Cell and Neurobiology
|
| Lab |
Andrew Newman
|
| Street address |
Charitéplatz 1
|
| City |
Berlin |
| ZIP/Postal code |
10117 |
| Country |
Germany |
| |
|
| Platform ID |
GPL21103 |
| Series (1) |
| GSE172489 |
Protein translation rate determines neocortical neuron fate |
|
| Relations |
| BioSample |
SAMN18821645 |
| SRA |
SRX10652567 |
