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| Status |
Public on Mar 16, 2016 |
| Title |
P_0018 |
| Sample type |
SRA |
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| Source name |
prefrontal cortex (BA9)
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| Organism |
Homo sapiens |
| Characteristics |
tissue: brain
location: prefrontal cortex
strain: BA9
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| Extracted molecule |
total RNA |
| Extraction protocol |
QIAzol Lysis Reagent, miRNeasy purification
Illumina TruSeq Small RNA Preparation Kit
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| Library strategy |
miRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 1000 |
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| 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
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| Submission date |
Sep 11, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Adam Labadorf |
| E-mail(s) |
labadorf@bu.edu
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| Organization name |
Boston University Medical School
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| Department |
Neurology
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| Street address |
72 East Concord Street E301
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| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02118 |
| Country |
USA |
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| Platform ID |
GPL15433 |
| Series (1) |
| GSE72962 |
microRNA profiles in Parkinson’s disease prefrontal cortex |
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| Relations |
| BioSample |
SAMN04054351 |
| SRA |
SRX1225499 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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