|
| Status |
Public on Apr 05, 2018 |
| Title |
spm24 |
| Sample type |
SRA |
| |
|
| Source name |
microglia
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: microglia
age: 63
gender: M
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from flow cytometry-sorted microglia cells using an RNeasy and AllPrep Micro Kit (Qiagen) and from whole brain tissue using RNeasy Lipid Tissue Mini kit (Qiagen), according to the manufacturer's protocol. Illumina TruSeq RNA Sample Prep Kit was used with 60 ng of total RNA for the construction of sequencing libraries of 23 samples. Clontech SMARTer Stranded Total RNA-Seq Kit - Pico Input (Takara Bio, Japan) cDNA libraries were prepared for 16 samples starting with 500 pg of total RNA.
Human RNA libraries were prepared for sequencing using standard Illumina and Clontech protocols. Mouse RNA samples were prepared with a Quantseq 3’mRNA-Seq kit. (Lexogen, USA)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
Illumina TruSeq RNA Sample Prep Kit
|
| Data processing |
Illumina Casava1.9 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, then mapped to hg38 whole genome using STAR v2.5.2_b with parameters --outFilterMultimapNmax 20 --outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.04 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --alignEndsType EndToEnd --sjdbScore 1
counts were generated by featureCounts v1.5.1 with parameters -p -t exon -g gene_id -B -T8 -M -O --fraction
normalized log2-transformed count table was generated by the voom function from the R/Bioconductor limma package
mouse data was processed according to lexogen proprietary software
Genome_build: hg38/mm10
Supplementary_files_format_and_content: tab-delimited matrices including raw counts and log2-normalized counts for all samples.
|
| |
|
| Submission date |
Apr 04, 2018 |
| Last update date |
Jun 24, 2021 |
| Contact name |
Antonio Marcondes Lerario |
| E-mail(s) |
alerario@umich.edu
|
| Phone |
7347737640
|
| Organization name |
University of Michigan
|
| Department |
MEND
|
| Lab |
Hammer Lab
|
| Street address |
109 Zina Pitcher Place, 1528 BSRB
|
| City |
Ann Arbor |
| State/province |
MI |
| ZIP/Postal code |
48109 |
| Country |
USA |
| |
|
| Platform ID |
GPL16791 |
| Series (1) |
| GSE99074 |
Transcriptomic analysis of purified human cortical microglia reveals age-associated changes |
|
| Relations |
| Reanalyzed by |
GSE178846 |
| BioSample |
SAMN08864861 |
| SRA |
SRX3884765 |
