|
| Status |
Public on Jan 10, 2024 |
| Title |
IRE1aKO-Polysome-light-1 |
| Sample type |
SRA |
| |
|
| Source name |
Cortex
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Cortex
time: Postnatal Day 0
genotype: IRE1af/f Emx1Cre
treatment: Purified Polysome light Fraction RNA
|
| Treatment protocol |
Ribosome fractionation and polysome purification from P0 cortex was performed as published protocol (Kraushar et al., 2021 doi: 10.1016/j.molcel.2020.11.037). Seven brains (14 neocortex hemispheres) of each genotype were pooled per biological replicate.
|
| Growth protocol |
Primary Tissue from Mouse Postnatal Day 0 Cerebral Cortex
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Tools and work surfaces used for RNA work were thoroughly cleaned with 70% ethanol (Sigma) and rinsed with RNA-Zap (Thermo Fisher) before the procedure. Embryonic brains at E18.5 were dissected in DEPC-PBS and flash-frozen in liquid nitrogen until the purification procedure. RNA was isolated using RNeasy columns (RNeasy Mini Kit, Qiagen).
TruSeq Stranded total RNA libraries were made with Ribo-Zero Gold rRNA depletion and sequenced using Illumina Nextseq 500/550, and in later runs (batch 3) using Novaseq 6000.
Total RNAseq with rRNA depletion
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Reads were quantified with Salmon quant --validateMappings to GRCm39 using gene annotation: gencode comprehensive release M33
further analysis steps can be seen in github code
Assembly: GRCm39
Supplementary files format and content: Counts table provides transcript level counts from tximport using option ' countsFromAbundance="scaledTPM" ' across all samples and technical replicates.
|
| |
|
| Submission date |
Dec 13, 2023 |
| 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 |
GPL24247 |
| Series (1) |
| GSE172489 |
Protein translation rate determines neocortical neuron fate |
|
| Relations |
| BioSample |
SAMN38811116 |
| SRA |
SRX22879186 |
