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Sample GSM3427165 Query DataSets for GSM3427165
Status Public on Oct 12, 2018
Title PreIPSN_R1
Sample type SRA
 
Source name This sample is the synaptoneurosome band of a sucrose percoll gradient without any TRAP, from an Rbp4 TRAP mouse.
Organism Mus musculus
Characteristics age: p21
strain: Rbp4 TRAP
tissue: Cortex
Extracted molecule total RNA
Extraction protocol Five replicates of RBP4-TRAP and VGAT-TRAP were harvested by rapid forebrain dissection at 21 days post birth as described (Ouwenga et al. 2017; Westmark et al. 2011). Each replicate contained a pool of two to three forebrains of both sexes as available. Four samples were collected from each replicate in parallel: whole cell homogenate (WCH) was RNA isolated from an aliquot of the initial homogenization of the tissue, TRAP was the capture of GFP-tagged ribosomes from an aliquot of WCH. RNA isolated from a fraction of the WCH subjected to synaptoneurosomal fractionation (SNF), and SynapTRAP (ST) is TRAP performed on the SNF, as described (Ouwenga et al. 2017). RNA concentration for all was measured using a Nanodrop and diluted to <5ng/µL before being assessed for quality and concentration using an Agilent TapeStation 4200
Library preparation was performed with 30ng of total RNA from each sample. ds-cDNA was prepared using the SMARTer Ultra Low RNA kit for Illumina Sequencing (Clontech #634936) per manufacturer’s protocol. cDNA was fragmented using a Covaris E220 sonicator using peak incident power 18, duty factor 20%, cycles/burst 50, time 120 seconds at 18 degrees. cDNA was blunt ended, had an A base added to the 3’ends, and then had Illumina sequencing adapters ligated to the ends. Ligated fragments were then amplified for 13 cycles using primers incorporating unique index tags.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 3000
 
Data processing RNA-seq reads were aligned to the Ensembl top-level assembly with STAR version 2.0.4b (Dobin et al. 2013) (RRID:SCR_015899).
Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 1.4.5. Sequencing performance was assessed with RSeQC version 2.3 (L. Wang, Wang, and Li 2012) (RRID:SCR_005275) for total number of aligned reads, total number of uniquely aligned reads, genes and transcripts detected, ribosomal fraction, known junction saturation, and read distribution over known gene models.
Mouse: Ensembl76
Supplementary_files_format_and_content: Gene Counts
 
Submission date Oct 12, 2018
Last update date Oct 13, 2018
Contact name Joseph D Dougherty
Organization name Washington University
Department Genetics and Psychiatry
Street address 4566 Scott Ave, box 8232
City St Louis
State/province Missouri
ZIP/Postal code 63110
Country USA
 
Platform ID GPL21493
Series (1)
GSE121162 The differences in local translatome across distinct neuron types is mediated by both baseline cellular differences and post-transcriptional mechanisms
Relations
BioSample SAMN10234722
SRA SRX4870844

Supplementary file Size Download File type/resource
GSM3427165_PreIPSN_R1_gene_counts.txt.gz 2.6 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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