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| Status |
Public on Mar 23, 2020 |
| Title |
Control CP 2 |
| Sample type |
SRA |
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| Source name |
Choroid Plexus
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| Organism |
Homo sapiens |
| Characteristics |
condition: Control
gender: Male
age (years): 55
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| Treatment protocol |
Frozen postmortem tissue
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| Growth protocol |
N/A
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| 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).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 3000 |
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| 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
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| Submission date |
Sep 17, 2019 |
| Last update date |
Mar 25, 2020 |
| Contact name |
Helga E de Vries |
| E-mail(s) |
he.devries@amsterdamumc.nl
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| Organization name |
Amsterdam UMC
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| Department |
MCBI
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| Street address |
De Boelelaan 1108
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| City |
Amsterdam |
| ZIP/Postal code |
1007 MB |
| Country |
Netherlands |
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| Platform ID |
GPL21290 |
| Series (1) |
| GSE137619 |
The choroid plexus in progressive multiple sclerosis presents hypoxia and secretory changes that may be related to neuroprotection |
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| Relations |
| BioSample |
SAMN12776811 |
| SRA |
SRX6862757 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4083355_c2.txt.gz |
218.5 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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