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| Status |
Public on Jul 19, 2015 |
| Title |
86_FCX |
| Sample type |
SRA |
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| Source name |
brain
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| Organism |
Homo sapiens |
| Characteristics |
tissue: Frontal Cortex
genotype: Healthy
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted from frozen human postmortem samples of cerebellum and frontal cortex using 20-30 mg of tissue. A two-step tissue homogenization method was performed using pestle tips and 21G syringes. Total RNA was extracted using the RNAeasy Plus Mini Kit (QIAGEN, Germantown, MD, USA), as per manufacturer’s instructions. RNA integrity (RIN) was verified on an Agilent 2100 bioanalyzer (Agilent Technologies, Santa Clara, CA, USA) and 100-200 ng of RNA (RIN ≥ 7.0) in a 5 μl volume was used for library preparation and RNA sequencing (RNAseq).
Paired-end sequencing libraries were prepared using the TruSeq Stranded Total Sample Preparation kit (Illumina) by the Mayo Clinic sequencing core facilities (Rochester, MN) followed by quality control, cluster generation and sequencing on the Illumina HiSeq 2000 platform. The reads were de-multiplexed and converted to FASTQ format using CASAVA software from Illumina (by the Mayo Clinic core).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Data processing |
alignment TopHat v2.0.6
htseq-count
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited gene counts
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| Submission date |
Mar 24, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Hu Li |
| E-mail(s) |
li.hu@mayo.edu
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| Organization name |
Mayo Clinic
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| Department |
Molecular Pharmacology & Experimental Therapeutics
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| Lab |
Systems Biology and Pharmacology
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| Street address |
200 First Street, Gonda Building G19-408
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| City |
Rochester |
| State/province |
MN |
| ZIP/Postal code |
55904 |
| Country |
USA |
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| Platform ID |
GPL11154 |
| Series (1) |
| GSE67196 |
Distinct brain transcriptome profiles in c9orf72-associated and sporadic ALS |
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| Relations |
| BioSample |
SAMN03444542 |
| SRA |
SRX966660 |
| 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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