|
| Status |
Public on Jan 17, 2020 |
| Title |
1br4Â |
| Sample type |
SRA |
| |
|
| Source name |
CD4+ Beta-synuclein reactive T cell
|
| Organism |
Rattus norvegicus |
| Characteristics |
strain: LEW/Crl
genotype: b-syn TCR Tg
tissue: Brain parenchyma
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Blood and brain were were removed, beta-synuclein T cells were sorted out and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
NEBNext® Single Cell/Low Input RNA Library Prep Kit for Illumina
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
FastQ files generating by demultiplexing using bcl2fastq v2.17.1.14
Quality control of sequences calculated using FastQC 0.11.5
Read alignment using STAR 2.5 using no more than 2 mismatches
Count reads within genes in Rattus norvegicus v87 using FeatureCounts v1.5.0-p1
Differential expression analysis run using DESeq2 v1.14.1 in R v3.4.2
Genome_build: rn6
|
| |
|
| Submission date |
Jan 17, 2019 |
| Last update date |
Jan 17, 2020 |
| Contact name |
Gabriela Salinas |
| E-mail(s) |
Gabriela.Salinas-Riester@medizin.uni-goettingen.de
|
| Organization name |
Universitaetsmedizin Goettingen
|
| Department |
Department of Pathology
|
| Lab |
NGS Integrative Genomics
|
| Street address |
Kreuzbergring 57
|
| City |
Goettingen |
| State/province |
Lower-Saxony |
| ZIP/Postal code |
37075 |
| Country |
Germany |
| |
|
| Platform ID |
GPL22396 |
| Series (1) |
| GSE125298 |
Next Generation Sequencing Analysis of wild-type and transgenic beta-synuclein reactive T cells |
|
| Relations |
| BioSample |
SAMN10768132 |
| SRA |
SRX5260136 |
