|
Status |
Public on Jan 17, 2020 |
Title |
1mb3Â |
Sample type |
SRA |
|
|
Source name |
CD4+ Beta-synuclein reactive T cell
|
Organism |
Rattus norvegicus |
Characteristics |
strain: LEW/Crl genotype: b-syn TCR Tg tissue: Meninges Brain
|
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 |
SAMN10768129 |
SRA |
SRX5260139 |