|
| Status |
Public on Nov 01, 2016 |
| Title |
MG12_VR_E16_314 |
| Sample type |
SRA |
| |
|
| Source name |
E16 germinal zone of cortex
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
genotype: Uhrf1 -/-
age: E16
tissue: germinal zone of cortex
|
| Growth protocol |
dissection of the entire cortex in E16 embryos; further microdissection of the germinal zones: this involved using a tissue cutter to slice the cortex into several slices and micro dissecting each slice for the germinal zone
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol and RNA clean and concentrator kit (Zymo research), Clontech - RiboGone-Mammalian(634846 )
Clontech- SMARTer Stranded RNA-Seq Kit-(634837)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 1500 |
| |
|
| Data processing |
Trimming of 3 bases from the 5' end of each read using FastqFilter (Galaxy); Paired end RNA-seq reads were mapped to the mouse genome (mm10) using tophat2 (Kim et al., 2013). Expression of genes in FPKM was calculated with cuffdiff and cummerbund (Trapnell et al., 2013).
Genome_build: mm10
Supplementary_files_format_and_content: Uhrf1_E16VZ_repFpkmMatrix.txt file
|
| |
|
| Submission date |
Jul 19, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Gunnar Schotta |
| E-mail(s) |
gunnar.schotta@bmc.med.lmu.de
|
| Phone |
089218075422
|
| Organization name |
LMU Munich
|
| Department |
Biomedical Center
|
| Street address |
Grosshaderner Strasse 9
|
| City |
Planegg-Martinsried |
| ZIP/Postal code |
82152 |
| Country |
Germany |
| |
|
| Platform ID |
GPL18480 |
| Series (2) |
| GSE84547 |
Loss of Uhrf1 in neural stem cells leads to activation of retroviral elements and delayed neurodegeneration [E16VZ] |
| GSE84550 |
Loss of Uhrf1 in neural stem cells leads to activation of retroviral elements and delayed neurodegeneration |
|
| Relations |
| BioSample |
SAMN05415199 |
| SRA |
SRX1959622 |
