|
| Status |
Public on Jan 01, 2016 |
| Title |
Lesion I |
| Sample type |
SRA |
| |
|
| Source name |
Brain
|
| Organism |
Homo sapiens |
| Characteristics |
condition: Multiple sclerosis
tissue: brain
gender: female
age: 36 years-old
|
| Extracted molecule |
total RNA |
| Extraction protocol |
total RNA from homogenized brain tissue was extracted using RNeasy Micro (QIAGEN, Hilden, Germany) following manufacturer’s instructions.
Library preparation for RNA-Seq was performed using the TruSeq Stranded Total RNA with Ribo-Zero Gold removing both cytoplasmic and mitochondrial rRNA (Illumina, Cat N° RS-122-2201). 200 ng of total RNA were used as start material . Accurate quantitation of cDNA libraries was performed by using the QuantiFluor™ dsDNA System (Promega). The size range of final cDNA libraries was determined applying the DNA 1000 chip on the Bioanalyzer 2100 from Agilent (280 bp). cDNA libraries were amplified and sequenced by using the cBot and HiSeq2000 from Illumina (SR; 1x50 bp;5- 6 GB ca. 30-35 million reads per sample).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
Demyelinated brain lesion
|
| Data processing |
Sequence images were transformed with Illumina software BaseCaller to bcl files, which were demultiplexed to fastq files with CASAVA v1.8.2.
Quality check was done via fastqc (v. 0.10.0, Babraham Bioinformatics).
Read alignment was performed using Bowtie2 v2.1.0 to the h19 human reference genome.
SAMfiles were converted and sorted by samtools 0.1.19
reads per gene were counted via htseq version 0.5.4.p3.
Differential expression analysis was performed using R/Bioconductor (3.0.2/2.12) loading DESeq, gplots and goseq packages. Candidate genes were filtered to a minimum of 2 x fold change and FDR-corrected pvalue<0.05. For functional analysis gene ontology enrichment was tested accounting for gene length via R-package goseq.
Genome_build: hg19
Supplementary_files_format_and_content: Original fastq files and gene counts
|
| |
|
| Submission date |
Aug 29, 2014 |
| Last update date |
May 15, 2019 |
| 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 |
GPL11154 |
| Series (2) |
| GSE60942 |
Next Generation Sequencing of Pattern II Demyelinating Brain Lesions from a Multiple Sclerosis Patient |
| GSE60943 |
Multiple Sclerosis Pattern II Demyelinating Lesions |
|
| Relations |
| BioSample |
SAMN03013621 |
| SRA |
SRX690027 |
