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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Oct 12, 2018 |
| Title |
PreIPSN_R5 |
| Sample type |
SRA |
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| Source name |
This sample is the synaptoneurosome band of a sucrose percoll gradient without any TRAP, from an Rbp4 TRAP mouse.
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| Organism |
Mus musculus |
| Characteristics |
age: p21
strain: Rbp4 TRAP
tissue: Cortex
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| 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.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 3000 |
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| 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
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| Submission date |
Oct 12, 2018 |
| Last update date |
Oct 13, 2018 |
| Contact name |
Joseph D Dougherty |
| Organization name |
Washington University
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| Department |
Genetics and Psychiatry
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| Street address |
4566 Scott Ave, box 8232
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| City |
St Louis |
| State/province |
Missouri |
| ZIP/Postal code |
63110 |
| Country |
USA |
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| 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 |
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| Relations |
| BioSample |
SAMN10234718 |
| SRA |
SRX4870848 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3427169_PreIPSN_R5_gene_counts.txt.gz |
2.6 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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