|
| Status |
Public on Jun 13, 2014 |
| Title |
Rna_Ascl1_het_2 |
| Sample type |
SRA |
| |
|
| Source name |
E11.5 Neural Tube
|
| Organism |
Mus musculus |
| Characteristics |
developmental stage: E11.5
genotype/variation: Ascl1GFP/+
strain: ICR
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Mouse E11.5 neural tubes were dissected from Ascl1 GFP knockin or 12.4kbPtf1a::mCherry;Ptf1a Cre knockin embryos into DMEM/F12 on ice and dissociated in 0.25% trypsin for 15 minutes at 37°C. Trypsin activity was quenched with 2% fetal bovine serum, and GFP positive cells were purified from the resulting single cell suspension by fluorescence activated cell sorting. Total RNA from the sorted cells was extracted and purified with Zymo’s Mini RNA Isolation Kit.
Neural tube libraries were made according to Illumina’s mRNA-seq sample prep protocol.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
mRNA from FACS sorted GFP cells
|
| Data processing |
Basecalls performed using CASAVA
Sequence reads were aligned to the mm9 build of the mouse genome using TopHat v2.0.8.
Biological replicate were specified and used to build an expression level model determined by the FPKM method of Cuffdiff v2.1.1 . Upper quartile normalization (-N option) was performed to more accurately estimate levels of low-abundance transcripts, and multiple read correction (-u option) was selected to better distribute reads mapping to multiple genomic locations. To correct any sequence-specific bias introduced during the library preparation option –b was used. All other settings were left at default values.
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited .txt file showing FPKM values for each sample type
|
| |
|
| Submission date |
Mar 12, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Jane E Johnson |
| E-mail(s) |
jane.johnson@utsouthwestern.edu
|
| Organization name |
UT Southwestern Medical Center
|
| Department |
Neuroscience
|
| Street address |
5323 Harry Hines Blvd
|
| City |
Dallas |
| State/province |
TX |
| ZIP/Postal code |
75390-9111 |
| Country |
USA |
| |
|
| Platform ID |
GPL13112 |
| Series (2) |
| GSE55831 |
Transcription Factor Network Specifying Inhibitory versus Excitatory Neurons in the Dorsal Spinal Cord [RNA-Seq] |
| GSE55841 |
Transcription Factor Network Specifying Inhibitory versus Excitatory Neurons in the Dorsal Spinal Cord |
|
| Relations |
| BioSample |
SAMN02688095 |
| SRA |
SRX485253 |
