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| Status |
Public on Sep 19, 2023 |
| Title |
PL4, rep3 |
| Sample type |
SRA |
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| Source name |
prefrontal cortex
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| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6/SJL
age: 16-18 months
cognitive test: poor learner or impaired
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| Extracted molecule |
total RNA |
| Extraction protocol |
Frontal cortex were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols
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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 quality of the samples was verified using FastQC v0.11.5 software.
FASTQ files were mapped to hg38 human assembly using STAR v2.5.3a with default parameters.
featureCounts v1.6.0 software and Gencode M18 release were used to obtain read counts at gene level considering only those genes aligned to exonic regions
Obtained gene counts were normalized using edgeR and voom function of limma
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include gene counts obtained with featureCounts for each sample.
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| Submission date |
Jul 27, 2021 |
| Last update date |
Sep 19, 2023 |
| Contact name |
Ana Garcia Osta |
| E-mail(s) |
agosta@unav.es
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| Phone |
9481947002023
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| Organization name |
Cima
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| Department |
neuroscience
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| Lab |
2.06
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| Street address |
Juslarrocha 10, 3H
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| City |
Pamplona |
| State/province |
Navarra |
| ZIP/Postal code |
31540 |
| Country |
Spain |
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| Platform ID |
GPL17021 |
| Series (1) |
| GSE180968 |
Identifying main functional pathways associated with cognitive resilience to Alzheimer ´s Disease |
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| Relations |
| BioSample |
SAMN20441706 |
| SRA |
SRX11579451 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5481556_PL4.counts.txt.gz |
3.6 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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