NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM4083364 Query DataSets for GSM4083364
Status Public on Mar 23, 2020
Title MS CP 5
Sample type SRA
 
Source name Choroid Plexus
Organism Homo sapiens
Characteristics condition: Multiple Sclerosis
gender: Male
age (years): 63
Treatment protocol Frozen postmortem tissue
Growth protocol N/A
Extracted molecule total RNA
Extraction protocol Up to 30 mg of tissue was disrupted from the whole lateral CP by cutting slices approximately 10 µm thick using a cryotome at -20oC. Tissue was homogenized with a POLYTRON PT 1200 (Kinematica). Total RNA from the CP was extracted with the RNeasy mini kit (Qiagen, 74104), following the manufacturer's instructions (using 600 µL of lysis buffer).
RNA libraries were prepared according to the manufacturer’s instructions using TruSeq stranded mRNA Library Prep Kit including an rRNA depletion step (RiboMinus, ThermoFisher).
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 3000
 
Data processing Ilumina 1.9
FASTQ files were checked for quality control metrics using FastQC (version 0.11.5) and Qualimap (version 2.2.1)
Post-Quality control, raw reads were mapped to the reference genome using TopHat2 (version 2.1.1) proceeded by exon-counting using HTSeq-count (version 0.6.1)
Genome_build: Ensembl GRCh38, build 84
Supplementary_files_format_and_content: Tab-delimeted files containing the Ensembl gene id and the RLE normalized counts
 
Submission date Sep 17, 2019
Last update date Mar 25, 2020
Contact name Helga E de Vries
E-mail(s) he.devries@amsterdamumc.nl
Organization name Amsterdam UMC
Department MCBI
Street address De Boelelaan 1108
City Amsterdam
ZIP/Postal code 1007 MB
Country Netherlands
 
Platform ID GPL21290
Series (1)
GSE137619 The choroid plexus in progressive multiple sclerosis presents hypoxia and secretory changes that may be related to neuroprotection
Relations
BioSample SAMN12776802
SRA SRX6862766

Supplementary file Size Download File type/resource
GSM4083364_m5.txt.gz 220.3 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap