|
| Status |
Public on Sep 30, 2020 |
| Title |
KO2 |
| Sample type |
SRA |
| |
|
| Source name |
PFC
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
age: 8-10 weeks
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Micro punch from PFC region was collected using mouse brain slicer.Total RNA was exctracted from the punches using LEV simply and RNA Tissue Kit (Promega, USA). RNA quality was checked using Agilent RNA 6000 Nano Kit and Agilent 2100 Bioanalyzer.
BGISeq-500 Library preparation kit
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
BGISEQ-500 |
| |
|
| Data processing |
BGISeq-500 platform was used to perfrom Single-end read RNA sequencing .
Sequence data were filtered to remove the adaptor sequence and low-quality sequence.
The first 5 bases were removed from the start of the read using using Trimmomatic
Reads that passed the quality control are mapped using HISAT2 to the mouse genome (Mus_musculus.GRCm.38.95).
Transcript assembly and quantification was performed using StringTie. Number of transcripts are normalized by gene length and sequencing depth (in millions) in the sample to produce Transcripts Per Kilobase Million (TPM).
Genome_build: mm10
Supplementary_files_format_and_content: TPM values for each sample
|
| |
|
| Submission date |
Mar 19, 2020 |
| Last update date |
Sep 30, 2020 |
| Contact name |
Abdel-Rahman Al-Absi |
| E-mail(s) |
[email protected]
|
| Organization name |
Aarhus University
|
| Street address |
Palle Juul Jensens Boulevard 99
|
| City |
Aarhus |
| ZIP/Postal code |
8200 |
| Country |
Denmark |
| |
|
| Platform ID |
GPL23479 |
| Series (1) |
| GSE147233 |
Df(h15q13)/+ mouse model reveals loss of astrocytes and synaptic-related changes of the excitatory and inhibitory circuits in the medial prefrontal cortex. |
|
| Relations |
| BioSample |
SAMN14405000 |
| SRA |
SRX7953445 |
