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Sample GSM1551767 Query DataSets for GSM1551767
Status Public on Dec 31, 2014
Title E18 Sorted corticothalamic projection neurons replicate 2
Sample type SRA
Source name Corticothalamic projection neurons
Organism Mus musculus
Characteristics developmental stage: E18
neuron subtype: Corticothal
strain: CD1
Treatment protocol N/A
Growth protocol N/A
Extracted molecule total RNA
Extraction protocol RNA was recovered from FACS-purified cells using the RecoverAll Total Nucleic Acid Isolation Kit (Ambion) according to manufacturer’s instructions except proteinase K digestion was performed at 50˚C for 3 hours. RNA concentration was quantified with Nanodrop 1000 and quality was determined with an Agilent 2100 Bioanalyzer. RNA Integrity Numbers (RIN) for all samples were between between 6.3 and 9. Typical yield was between 1 and 2 picograms RNA per sorted event, requiring approximately 100,000 cells to yield 200 ng RNA for library input.
Purified RNA served as input for the standard Illumina RNA-seq library preparation with poly(A) selection.
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
Description E18_b_corticothal
Data processing 100 base pair-paired end reads were mapped to the mouse genome (mm9) using Tophat2 (Kim et al., 2013) with an average of 1.09x108 mapped reads (range 7.62x107-1.33x108; s.d. 1.30x107) and assembled into transcripts using Cufflinks (Trapnell et al., 2010). Individual assemblies were merged using Cuffmerge and UCSC coding genes as a reference.
The merged assembly was used as input for our previously-described long non-coding RNA (lncRNA) identification pipeline (Cabili et al., 2011). Assembled lncRNAs were appended to the list of known UCSC protein-coding genes to establish a suitable reference transcriptome.
Differential expression testing was performed between all pairs of conditions using Cuffdiff2. Data was visualized using the cummeRbund package from Bioconductor (Gentleman et al., 2004; Trapnell et al., 2012b) and additionally integrated into the DeCoN interactive web resource.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text file with normalized expression estimates (FPKM) for each gene under each condition
Submission date Nov 21, 2014
Last update date May 15, 2019
Contact name Loyal A Goff
Organization name Johns Hopkins University
Department Institute of Genetic Medicine
Lab Goff
Street address 733 N. Broadway Avenue
City Baltimore
State/province MD
ZIP/Postal code 21205
Country USA
Platform ID GPL17021
Series (1)
GSE63482 Transcriptional Profiling of Sorted Mouse Cortical Projection Neuron Subtypes
BioSample SAMN03203509
SRA SRX765223

Supplementary data files not provided
SRA Run SelectorHelp
Processed data are available on Series record
Raw data are available in SRA

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