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| Status |
Public on Oct 12, 2022 |
| Title |
Week 70 male brain |
| Sample type |
SRA |
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| Source name |
whole brain
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| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6J
tissue: whole brain
age: week 70
Sex: male
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from postnatal day 5 and week 70 old male and female mice using an AllPrep DNA/RNA Mini Kit (Qiagen, Cat No./ID: 80204) following the manufacturer’s instruction.
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
W70M
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| Data processing |
The quality of raw sequences was checked with FastQC followed by trimming the adaptors from the sequence reads by cutadapt. The trimmomatic tool was used to perform base quality trimming (Phred score >30) by sliding window scan (4 nucleotides). The quality reads were then mapped to the mouse reference genome GRCm38 using Hisat2 aligner.
Read counting from the alignment data was performed by FeatureCounts. The feature count data was then analyzed by edgeR to determine significance of differential expression of KO compared to WT brain.
Assembly: GRCm39
Supplementary files format and content: comma separated file
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| Submission date |
Oct 10, 2022 |
| Last update date |
Oct 12, 2022 |
| Contact name |
Susanta K. Behura |
| E-mail(s) |
behuras@missouri.edu
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| Organization name |
Univeristy of Missouri
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| Department |
Division of Animal Sciences
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| Street address |
920 East Campus Drive
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| City |
Columbia |
| State/province |
Missouri |
| ZIP/Postal code |
65211 |
| Country |
USA |
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| Platform ID |
GPL24247 |
| Series (1) |
| GSE215138 |
Fetal origin of sex-bias brain aging [RNA-seq] |
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| Relations |
| BioSample |
SAMN31228289 |
| SRA |
SRX17839655 |
| 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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