|
|
GEO help: Mouse over screen elements for information. |
|
Status |
Public on Mar 16, 2016 |
Title |
P_0034 |
Sample type |
SRA |
|
|
Source name |
prefrontal cortex (BA9)
|
Organism |
Homo sapiens |
Characteristics |
tissue: brain location: prefrontal cortex strain: BA9
|
Extracted molecule |
total RNA |
Extraction protocol |
QIAzol Lysis Reagent, miRNeasy purification Illumina TruSeq Small RNA Preparation Kit
|
|
|
Library strategy |
miRNA-Seq |
Library source |
transcriptomic |
Library selection |
size fractionation |
Instrument model |
Illumina HiSeq 1000 |
|
|
Data processing |
Basecalls from CASAVA 1.7 QUALITY FILTERING: FASTX-toolkit version 0.0.13.2 fastq_quality filter with -Q 33 -q 20 -p 80; ADAPTER REMOVAL: cutadapt 1.2.1 with --minimum-length 15 option, READ COLLAPSING: FASTX-toolkit version 0.0.13.2 fastx_collapser READ ALIGNMENT: bowtie-1.0.0 with no mismatches and 200 multimap limit using -v 0 -k 200; ANNOTATION: bedtools v2.2 intersectBed and miRBase v20 COUNTING: custom R-script counting miRNAs ±4 nucleotides from 5' annotated start location DIFFERENTIAL EXPRESSION ANALYSIS: Using R: DESeq2 v1.40 for variance stabilizing transformation counts, ComBat (R package sva 3.10) for batch effect correction, LIMMA v3.20.8 with adjustment for death at death for statistical comparison between conditions Genome_build: hg19 Supplementary_files_format_and_content: Processed files contain normalized counts for all samples, covariates file with additional sample information and differential expression results from LIMMA, in comma separated value format
|
|
|
Submission date |
Sep 11, 2015 |
Last update date |
May 15, 2019 |
Contact name |
Adam Labadorf |
E-mail(s) |
labadorf@bu.edu
|
Organization name |
Boston University Medical School
|
Department |
Neurology
|
Street address |
72 East Concord Street E301
|
City |
Boston |
State/province |
MA |
ZIP/Postal code |
02118 |
Country |
USA |
|
|
Platform ID |
GPL15433 |
Series (1) |
GSE72962 |
microRNA profiles in Parkinson’s disease prefrontal cortex |
|
Relations |
BioSample |
SAMN04054364 |
SRA |
SRX1225512 |
Supplementary data files not provided |
SRA Run Selector |
Raw data are available in SRA |
Processed data are available on Series record |
|
|
|
|
|