|
| Status |
Public on Jun 21, 2021 |
| Title |
case10_Substantia_Nigra_compacta_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
midbrain dopamine neurons
|
| Organism |
Homo sapiens |
| Characteristics |
case number (refer to table in paper): 10
disease status: Control
neurons: SNc
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Lysis buffer is directly added to the cells after laser capture. No RNA extraction is conducted. The cell lysate is direcly used for library preparation.
Libraries for RNA-seq were prepared by using SMART-seq2 combined with Tn5 tagementation.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
GEO_RPKMS_LCMseq_human_SNc_VTA.txt
|
| Data processing |
Base-calling using Illumina Cassava 1.7
Alignment to the human genome (hg38) performed using STAR with default parameters. RPKM were estimated using ¨rpkmforgenes¨ (Ramsköld et al., 2009).
For cases having more than 1 replicate per group, corresponding samples were averaged before the analysis so that each Case have only 1 SNc and 1 VTA.
Differential gene expression analysis was performed on the read counts using DESeq version 1.16.1. Only genes with reads in at least one third of the samples or more were considered in the analysis.
Genome_build: hg38
Supplementary_files_format_and_content: One processed data file is added providing abundance measurements (RPKM) organized as a matrix for all samples (tab-delimited txt).
|
| |
|
| Submission date |
May 25, 2018 |
| Last update date |
Jun 21, 2021 |
| Contact name |
Eva Hedlund |
| E-mail(s) |
eva.hedlund@dbb.su.se
|
| Phone |
0046761130911
|
| Organization name |
Stockholm University
|
| Department |
Department of Biochemistry and Biophysics
|
| Lab |
Hedlund
|
| Street address |
Svante Arrhenius v. 16C
|
| City |
Stockholm |
| ZIP/Postal code |
106 91 |
| Country |
Sweden |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE114918 |
RNAseq of human SNc and VTA midbrain dopamine neurons isolated from post mortem material of control subjects and Parkinson's Disease patients using laser capture microdisection. |
|
| Relations |
| BioSample |
SAMN09260288 |
| SRA |
SRX4124847 |
