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Sample GSM6568563 Query DataSets for GSM6568563
Status Public on Mar 13, 2024
Title REST_PAN_pd_rep_1
Sample type SRA
 
Source name NA
Organism Mus musculus
Characteristics tissue: NA
cell line: NA
cell type: primary neuronal culture (cortical)
lentivirus: Pan-TurboID
fraction: pulldown
genotype: NA
treatment: Chx
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 Pan-TurboID proximal protein-bound RNAs in resting neurons, replicate 2
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 SAMN30752275
SRA SRX17504627

Supplementary file Size Download File type/resource
GSM6568563_rest_cyto_pd_2_quant.sf.gz 732.4 Kb (ftp)(http) SF
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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