 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Mar 05, 2016 |
| Title |
Z899_41R |
| Sample type |
SRA |
| |
|
| Source name |
brain
|
| Organism |
Chlorocebus sabaeus |
| Characteristics |
mptp treatment: MPTP treated
transplant type: Low cell dose
monkey id: Z899
brain region: Substantia Nigra
tissue: brain
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using the miRVANA miRNA Isolation Kit (Life Tecnhnologies) using the total RNA protocol
RNAseq libraries were constructed using the TruSeq Stranded Total RNA Library Prep Kit (Illumina)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
illumina
FASTQC followed by trimming to remove 10 nucleotides on each end, and removal of reads with a paired read quality score < 30
STAR mapping to hg19
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated
Annotated using Human reference genome version Ensembl GRCh37
Genes without at least one sample with at least ten reads were removed from the analysis
2 Putamen samples with low reads were removed
The count data for the remaining samples were normalized using the R package DESeq2
One-way ANOVA (analysis of variance) with post-hoc Tukey HSD (honestly significant difference) was performed
Genome_build: hg19
Supplementary_files_format_and_content: comma separated file containing normalized read counts and metrics used to perform the comparison for each brain region separately: ("low cell dose" AND "high cell dose") to "buffer injection". These metrics include: average counts per comparison group, q-value, and fold-change.
|
| |
|
| Submission date |
Mar 04, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Marwa Khater |
| E-mail(s) |
marwa.f.khater@gmail.com
|
| Organization name |
UCSD
|
| Street address |
11990 cypress valley dr
|
| City |
san diego |
| ZIP/Postal code |
92131 |
| Country |
USA |
| |
|
| Platform ID |
GPL21566 |
| Series (1) |
| GSE78921 |
Whole transcriptome profiles of different brain regions from a Chlorocebus sabaeus model of Parkinson's disease with and without human parthenogenetic stem cell derived neural stem cell transplantation. |
|
| Relations |
| BioSample |
SAMN04532675 |
| SRA |
SRX1613630 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
|
|
|
|
 |
