|
| Status |
Public on Mar 13, 2024 |
| Title |
DEP_PSD95_in_rep_2 |
| Sample type |
SRA |
| |
|
| Source name |
NA
|
| Organism |
Mus musculus |
| Characteristics |
tissue: NA
cell line: NA
cell type: primary neuronal culture (cortical)
lentivirus: PSD95-TurboID
fraction: input
genotype: NA
treatment: Chx + KCl depolarization
|
| Treatment protocol |
Primary cortical neurons were treated with cycloheximide for 2 minutes before biotinylation for 30 minutes. Depolarization was performed by incubating the cells with tetrodotoxin and DL-AP5 for 2 hours before 55 mM KCl addition for 1 hour, followed by resting for 30 minutes before harvest.
|
| Growth protocol |
Primary cortical neurons were grown in Neurobasal media supplemented with B27 and Glutamax.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA from inputs and streptavidin pulldowns was extracted using the TRIzol protocol.
RNA (input and pulldown, ~100 ng) was used as the starting material and first treated with DNAse on columns. TruSeq stranded RNA sample protocol was followed using RiboZero to get rid of ribosomal RNAs. For unique adapters, IDT Illumina Truseq RNA UD Indexes were used. The samples were then pooled and sequenced on the Illumina NovaSeq 6000 sequencer.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
RNA-seq of all protein-bound RNAs in resting neurons transduced with PSD95-TurboID, replicate 3
|
| Data processing |
Prepare transcriptome indices: The transcripts sequences were built based on Txdb.Mmusculus.Ucsc.mm10.knownGene. Then the transcripts were indexed with index function of Salmon.
Alignment and counting: The fastq files were mapped to transcriptome indices and counted by using Salmon quant.
Differential gene expression: The count results of all samples were loaded into DESeq object by using tximport. Then, the differential gene expression between groups were analyzed using limma.
Assembly: Genome version: mm10; reference genome: BSgenome.Mmusculus.UCSC.mm10; annotation database: Txdb.Mmusculus.Ucsc.Mm10.Knowngene.
Supplementary files format and content: Tab-delimited text files include raw counts values for each sample.
|
| |
|
| Submission date |
Sep 09, 2022 |
| Last update date |
Mar 13, 2024 |
| Contact name |
Caryn R Hale |
| E-mail(s) |
chale@rockefeller.edu, carynhale@gmail.com
|
| Organization name |
Rockefeller University
|
| Street address |
1230 York Avenue
|
| City |
New York |
| State/province |
New York |
| ZIP/Postal code |
10065 |
| Country |
USA |
| |
|
| Platform ID |
GPL24247 |
| Series (2) |
| GSE213012 |
Total and dendritic RNA-sequencing from primary mouse cortical neurons |
| GSE213083 |
Profiling data from primary mouse cortical neurons |
|
| Relations |
| BioSample |
SAMN30752264 |
| SRA |
SRX17504638 |
