|
| Status |
Public on Dec 31, 2014 |
| Title |
E16 Sorted callosal projection neurons replicate 1 |
| Sample type |
SRA |
| |
|
| Source name |
Callosal projection neurons
|
| Organism |
Mus musculus |
| Characteristics |
developmental stage: E16
neuron subtype: CPN
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 |
E16_a_cpn
|
| 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 |
| E-mail(s) |
loyalgoff@jhmi.edu
|
| 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 |
|
| Relations |
| BioSample |
SAMN03203499 |
| SRA |
SRX765212 |
