|
| Status |
Public on Jun 17, 2013 |
| Title |
AD sample 33 |
| Sample type |
SRA |
| |
|
| Source name |
whole blood
|
| Organism |
Homo sapiens |
| Characteristics |
group: alzheimer patient
gender: female
age: 57
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA including miRNA was isolated using the PAXgene Blood miRNA Kit (Qiagen) following the manufacturer’s recommendations.
For the library preparation, 200 ng of total RNA was used per sample. Preparation was performed following the protocol of the TruSeq Small RNA Sample Prep Kit (Illumina). Libraries were then pooled in batches of six samples in equal amounts and clustered with a concentration of 9 pmol in one lane each of a single read flowcell using the cBot (Illumina).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Demultiplexing of the raw sequencing data and generation of the fastq files was done using CASAVA v.1.8.2
The raw reads were preprocessed by cutting the 3' adapter sequence using the program fastx_clipper from the FASTX-Toolkit
mirbase v18 counts and counts for novel predicted miRNAs were collected using the miRDeep2 pipeline
miRNAs with less than 50 read counts summed up across all samples of each group (ad or control) were excluded from further analysis
the counts were normalized by quantile normalization
Genome_build: hg19
Supplementary_files_format_and_content: Excel table containing the raw mirbase and novel mirna counts and the quantile normalized counts
|
| |
|
| Submission date |
May 02, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Andreas Keller |
| Organization name |
Saarland University
|
| Street address |
Building 60
|
| City |
Homburg |
| ZIP/Postal code |
69112 |
| Country |
Germany |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE46579 |
A blood based 12-miRNA signature of Alzheimer patients |
|
| Relations |
| BioSample |
SAMN02116304 |
| SRA |
SRX273450 |
