|
| Status |
Public on Jan 14, 2013 |
| Title |
Substantia nigra dopaminergic neurons, Nurr1 cKO 4 |
| Sample type |
SRA |
| |
|
| Source name |
Substantia nigra TH1+ neurons, Nurr1 cKO
|
| Organism |
Mus musculus |
| Characteristics |
strain/background: 129Sv
genotype/variation: homozygous Nurr1-floxed, heterozygous BAC-DAT-CreER T2
tissue: substantia nigra
cell type: TH-positive neurons
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Pico RNA isolation kit (Arcturus Engineering, Inc.)
SMARTer Ultra Low Input RNA for Illumina Sequencing kit (Clontech #634935).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
~200 TH-positive neurons from SN of Nurr1-floxed DAT-Cre mice, sample 56.
PolyA+ RNA
|
| Data processing |
Alignment by Bowtie version 0.12.7 to mm9 genome (excluding small contigs in _random files) and Ensembl transcriptome (version 11 Apr 2012).
Removal of non-unique alignments.
Gene expression values from 'rpkmforgenes' (http://sandberg.cmb.ki.se/rnaseq/) version 29 Nov 2011.
Genome_build: MGSCv37 (mm9)
Supplementary_files_format_and_content: BED files containing aligned reads, and tab-delimited text files containing gene expression values (RPKM/FPKM).
|
| |
|
| Submission date |
Dec 13, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Daniel Ramsköld |
| E-mail(s) |
daniel.ramskold@ki.se
|
| Organization name |
Karolinska Institutet
|
| Lab |
Rickard Sandberg's group (rickard.sandberg@ki.se) (2008-2014, 2018-); Rheumatology unit (2014-2018)
|
| Street address |
Nobels väg 3
|
| City |
Stockholm |
| ZIP/Postal code |
17177 |
| Country |
Sweden |
| |
|
| Platform ID |
GPL13112 |
| Series (1) |
| GSE42912 |
Nurr1 maintains fiber integrity and nuclear-encoded mitochondrial gene expression in dopamine neurons |
|
| Relations |
| SRA |
SRX209902 |
| BioSample |
SAMN01831200 |
