|
| Status |
Public on Jul 25, 2013 |
| Title |
BR5.7 |
| Sample type |
SRA |
| |
|
| Source name |
late stage_prefrontal cortex
|
| Organism |
Homo sapiens |
| Characteristics |
age: 79
gender: male
alzheimer's disease stage: late stage
tissue: brain
region: prefrontal cortex
molecule subtype: microRNA
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA were obtained by TRIzol homogeneization of prefrontal cortex tissues and purification on miRVana columns
Libraries were prepared according to Illumina's instructions accompanying the TruSeq Small RNA Sample Preparation Kit (Part# RS-200-0012).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
Sample 7
|
| Data processing |
Trimming of adaptor with Flicker v3.0
quality read filtering and contaminant removal
Manual removal of reads with N
Reads longer than 15 nucleotides were mapped to the hg19 build genome using the short-read aligner Bowtie2 (version 2.0.2) and allowing one mismatch
Reads were processed with HTSeq-counts (version 0.5.3p9)
Normalized expression was determined with DESeq (version 1.6.1) after discarding miRNAs with less than 30 counts over the 12 samples
Genome_build: hg19
Supplementary_files_format_and_content: count data
|
| |
|
| Submission date |
Jul 05, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Pierre Lau |
| E-mail(s) |
pierre.laupouicheung@cme.vib-kuleuven.be
|
| Phone |
+(32)16373105
|
| Organization name |
KUL-VIB
|
| Street address |
49 Herestraat
|
| City |
Leuven |
| ZIP/Postal code |
3000 |
| Country |
Belgium |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE48552 |
Alteration of the microRNA network during the progression of Alzheimer’s disease |
|
| Relations |
| BioSample |
SAMN02226052 |
| SRA |
SRX318173 |
