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| Status |
Public on Dec 24, 2016 |
| Title |
HET.18_2 |
| Sample type |
SRA |
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| Source name |
HET.18_hemi-forebrain
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| Organism |
Mus musculus |
| Characteristics |
strain background: C57BL/6
genotype/variation: heterozygous APP23 (+/-)
age: 18 months
tissue: brain; Hemi-forebrain
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| Extracted molecule |
total RNA |
| Extraction protocol |
The brain was harvested and dissected on ice into three parts: 2 hemi-forebrains and the cerebellum (olfactory bulbs were discarded). The frozen hemi-forebrains were lysed in QIAzol (Qiagen), followed by total RNA isolation using the RNeasy Lipid Tissue Mini Kit (Qiagen, 74804).
Sequence libraries were generated with the TruSeq RNA sample prep kit V2 (Illumina) using the Sciclone NGS liquid handler (Perkin Elmer).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Data processing |
The data was inspected with FASTQC (v0.10.1) and trimmed when necessary with FASTX trimmer
Alignment was performed with STAR (2.3.1l) (Dobin et al., 2013) with 2 mismatches allowed to the ensemble reference genome version 37 of the 1000Genome project.
Data was quantified with HT-Seq count (0.5.4) (Anders et al., 2015)
Genome_build: ensemble reference genome version 37 of the 1000Genome project
Supplementary_files_format_and_content: txt-file containing the HT-Seq count for the individual samples; raw counts of sequencing reads
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| Submission date |
Apr 20, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Peter Paul De Deyn |
| Organization name |
University of Antwerp
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| Street address |
universiteitsplein 1
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| City |
Wilrijk (Antwerp) |
| State/province |
Antwerpen |
| ZIP/Postal code |
2610 |
| Country |
Belgium |
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| Platform ID |
GPL17021 |
| Series (1) |
| GSE80465 |
Aging, microglia and cytoskeletal regulation are key factors in the pathological evolution of the APP23 mouse model for Alzheimer’s disease |
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| Relations |
| BioSample |
SAMN04874660 |
| SRA |
SRX1715811 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2127875_sample_22.htseq.txt.gz |
150.1 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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