|
| Status |
Public on Dec 04, 2015 |
| Title |
oNTa10 |
| Sample type |
SRA |
| |
|
| Source name |
E8.5 embryo, open neural tube at anterior boundary of closure 1
|
| Organism |
Mus musculus |
| Characteristics |
strain: FVB
morphology: open neural tube
tissue: neural tube
|
| Treatment protocol |
Cryosections of embryos at 8.5 days of gestation were used to prepare neural tube tissue by Laser microdissection. The anterior boundary of neural tube closure site 1 was determined and used as reference point to collect sections immediately anterior (open neural tube) of closure site 1. Teratogenic protrusions were microdissected from the open neural plate.
|
| Growth protocol |
Diabetic dams were mated, and the morning where presence of a vaginal plug was detected was designated as day 0.5 of gestation. Pregnant dams were single housed, and embryos were prepared at 8.5 days of gestation.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was prepared using Trizol, RNA concentration was determined on a Qbit fluorometer, and 7-12ng RNA per sample was used for sequencing library construction.
Libraries were prepared using the Applied Biosystems SOLiDSAGE kit, according to AB's instructions for the SOLiD 4 System (except a 1:100 of Adaptor B dilution was used).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
AB 5500xl Genetic Analyzer |
| |
|
| Description |
SOLiD SAGE Kit with Barcoding Adaptor Module (#4452811) and SOLiD RNA Barcode Kit (#4427046)
|
| Data processing |
conversion of SOLiD 5500 XSQ files to csfasta/qual files was performed using perl and bash shell scripts that were developed in-house. These scripts make use of Life Technologies XSQ conversion tools, version 1.5.
alignment of sequence tags back to a mouse reference genome was performed using a modified version of the Applied Biosystems SOLiD™ SAGE™ Analysis Software v1.10 that was developed in-house.
filtering non-unique tags, and establishing counts per RefSeq gene was performed using a modified version of the Applied Biosystems SOLiD™ SAGE™ Analysis Software v1.10 that was developed in-house.
Genome_build: The following version of RefSeg RNA was used for mapping sequence tags: Mouse (mm9): ftp://ftp.ncbi.nlm.nih.gov/genomes/M_musculus/ARCHIVE/BUILD.37.2/RNA/rna.fa.gz
Supplementary_files_format_and_content: processed data files contain the counts per gene for 26608 mouse RefSeq genes
|
| |
|
| Submission date |
Dec 06, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
J. Michael Salbaum |
| Organization name |
Pennington Biomedical Research Center
|
| Department |
Regulation of Gene Expression
|
| Street address |
6400 Perkins Road
|
| City |
Baton Rouge |
| State/province |
LA |
| ZIP/Postal code |
70808 |
| Country |
USA |
| |
|
| Platform ID |
GPL15907 |
| Series (1) |
| GSE53075 |
Perturbed gastrulation in embryos from diabetic pregnancies. |
|
| Relations |
| BioSample |
SAMN02437597 |
| SRA |
SRX388153 |
