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| Status |
Public on Apr 25, 2024 |
| Title |
AD 11 |
| Sample type |
SRA |
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| Source name |
Grey matter SFG
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| Organism |
Homo sapiens |
| Characteristics |
tissue: Grey matter SFG
condition: AD
Sex: M
batch: B
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated with RNeasy Mini Kit RNA (Qiagen, Valencia, CA, USA) in combination with Trizol (3 ml Trizol per 100 mg tissue; Life Technologies, Grand Island, NY, USA).
NEBNext Ultra II Directional RNA Library Prep Kit for Illumina was used to process 35 samples (GenomeScan, Leiden, The Netherlands). Briefly, rRNA was depleted from total RNA using the rRNA depletion kit (NEB #E6310). After fragmentation of the depleted rRNA, a cDNA synthesis was performed for ligation with the sequencing adapters and PCR amplification. The size of the resulting products was consistent with the expected size distribution (a broad peak between 300-500 bp). Clustering and DNA sequencing using the NovaSeq6000 was performed according to manufacturer's protocols. A concentration of 1.1 nM of DNA was used. At least 15 Gb, yielding ~30-40 million read pairs, was generated per sample with a quality score of ≥30.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
104397-001-006
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| Data processing |
Sequence reads were trimmed to remove possible adapter sequences using cutadapt v 2.10. Reads were aligned to the human genome (GRCh38.p13) using STAR (2.7.10a) with default settings. Feature counting was performed with HTSeq v0.11.0. Samples were sequenced in two batches, with a minimal batch effect between runs. Sequence reads were trimmed to remove possible adapter sequences using cutadapt v 2.10. Reads were aligned to the human genome (GRCh38.p13) using STAR (2.7.10a) with default settings. Feature counting was performed with HTSeq v0.11.0. Samples were sequenced in two batches, with a minimal batch effect between runs.
Assembly: GRCh38.p13
Supplementary files format and content: Raw counts for each sample
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| Submission date |
Mar 18, 2024 |
| Last update date |
Apr 25, 2024 |
| Contact name |
Luuk Elard de Vries |
| Organization name |
Netherlands Institute for Neuroscience
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| Department |
Neuroregeneration
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| Street address |
Meibergdreef 47
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| City |
Amsterdam |
| ZIP/Postal code |
1105 BA |
| Country |
Netherlands |
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| Platform ID |
GPL24676 |
| Series (1) |
| GSE261817 |
Gene-expression profiling of individuals resilient to Alzheimer's disease reveals higher expression of genes related to metallothionein and mitochondrial processes and no changes in the unfolded protein response |
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| Relations |
| BioSample |
SAMN40528744 |
| SRA |
SRX23980595 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
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