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| Status |
Public on Oct 20, 2020 |
| Title |
Human-10K-13 |
| Sample type |
SRA |
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| Source name |
Brain
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| Organism |
Homo sapiens |
| Characteristics |
tissue: Temporal and inferior parietal cortex
treatment: 10,000 x g pellet from digested tissue
disease state: Alzheimer's Disease
apoe genotype: E3/3
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted by miRNeasy Mini Kit (Qiagen 217004) according to the manufacturer’s instructions.
Small RNA libraries were constructed using the Ion Total RNA-Seq Kit V2 (Life Technologies 4475936).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Ion Torrent S5 |
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| Description |
Human_combined_raw_counts-AD.xlsx
IonXpressRNA_022_rawlib.basecaller_A6_10K
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| Data processing |
FASTQC run before and after adapter trimming. The reads were aligned to the reference transcriptomes in a sequential manner. First, all reads were mapped to RNA species with low sequence complexity and/or high number of repeats: rRNA, tRNA, RN7S, snRNA, snoRNA, scaRNA, VT-RNA, Y-RNA as well as mitochondrial chromosome (mtRNA). All reads that did not map to the above RNAs were aligned to premiRNA reference, then to protein coding mRNA transcripts (pc) and long non-coding RNAs (lncRNAs). Please note that some % of reads always overlaps between pc and lncRNAs. The reads which did not map to premiRNA, protein coding (pc) transcripts and lncRNAs were aligned to the remaining transcriptome [other ncRNAs containing mostly pseudogenes and non-protein coding parts of mRNAs]. Finally, all reads which did not map to human transcriptome were aligned to the hg38 genome reference (rest_hg38).
The mapping was performed with bowtie2 default settings for all references except premiRNA. PremiRNA were sequential mapping with bowtie using settings with: 0 mismatch tolerance, then 1 mismatch tolerance and finally 2 mismatches tolerance.
Genome_build: Hg38
Supplementary_files_format_and_content: Excel with raw counts
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| Submission date |
Oct 19, 2020 |
| Last update date |
Oct 20, 2020 |
| Contact name |
Kenneth W. Witwer |
| E-mail(s) |
kwitwer1@jhmi.edu
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| Phone |
4109559770
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| Organization name |
Johns Hopkins University School of Medicine
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| Department |
Department of Molecular and Comparative Pathobiology
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| Street address |
733 N. Broadway
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| City |
Baltimore |
| State/province |
MD |
| ZIP/Postal code |
21205 |
| Country |
USA |
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| Platform ID |
GPL23934 |
| Series (1) |
| GSE159541 |
Small RNA sequencing of brain-derived extracellular vesicles from post-mortem brain tissue of controls and Alzheimer's disease patients with different APOE genotypes |
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| Relations |
| BioSample |
SAMN16474762 |
| SRA |
SRX9296556 |
| 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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