|
| Status |
Public on Jun 29, 2018 |
| Title |
RD_33-31015047 |
| Sample type |
SRA |
| |
|
| Source name |
cortex, WT, 4m
|
| Organism |
Mus musculus |
| Characteristics |
strain/background: C57BL/6
genotype/variation: WT
age: 4m
gender: male
tissue: cortex
sample id: 33
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The hippocampus and cortex were dissected from the left hemisphere of each mouse brain, and snap frozen in liquid nitrogen. Tissues were homogenized in Qiazol reagent and total RNA isolated using the RNeasy Plus Universal Mini Kit according to the manufacturer's protocol (Qiagen). RNA integrity (RIN) was measured for all samples using the Bioanalyser Agilent 2100 series using RNA nano chip. All sequencing libraries analyzed were generated from RNA samples measuring a RIN score >= 8.9.
The Illumina TruSeq mRNA stranded protocol was used to obtain poly-A mRNA from all samples. 100ng of isolated mRNA was used to construct RNA-seq libraries. Libraries were quantified and normalized using the NEBNext® mRNA Library prep kit for Illumina.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Illumina NextSeq 500 platform 76bp reads.
RNA-seq reads were aligned to the mouse GRCm38 rel 79 reference transcriptome using Kallisto version 0.42.4.
Genome_build: GRCm38.rel79
Supplementary_files_format_and_content: *tsv: Tab-delimited text files include TPM values and counts for each Sample.
|
| |
|
| Submission date |
Sep 28, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Guillermo Carbajosa |
| E-mail(s) |
guillermo.carbajosa_antona@kcl.ac.uk
|
| Phone |
+44 (0) 7511295922
|
| Organization name |
King's College London
|
| Department |
Medical and Molecular Genetics
|
| Lab |
Bioinformatics and Population Genomics Group
|
| Street address |
Guy’s Hospital, St Thomas Street
|
| City |
London |
| ZIP/Postal code |
SE1 9RT |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL19057 |
| Series (1) |
| GSE104381 |
Loss of Trem2 in microglia leads to widespread disruption of cell coexpression networks in mouse brain |
|
| Relations |
| BioSample |
SAMN07715720 |
| SRA |
SRX3228236 |
