|
| Status |
Public on Jan 25, 2021 |
| Title |
P56_2_Striatum |
| Sample type |
SRA |
| |
|
| Source name |
P56_Striatum
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
age: post natal day 56
tissue: striatum
replicate: 2
|
| Treatment protocol |
N/A
|
| Growth protocol |
N/A
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA including miRNA fractions were isolated using Qiagen miRNeasy mini kit according to the manufacturer’s protocol. RNA integrity was assessed with an Agilent 2100 Bioanalyzer using an Agilent Bioanalyzer 6000 Nano kit.
Input of 400ng of total RNA was used as starting material for each sample and libraries were prepared using 99 TruSeq Stranded Total RNA LT with Ribo-Zero Gold Depletion Kit from Illumina. Quantification was performed using KAPA Library Quantification Kit and the average size of 300 bp was determined by using a High Sensitivity DNA Kit. The libraries were pooled and diluted to 13 pM to load on an Illumina HiSeq 2500 Instrument.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
P56_2_Striatum
|
| Data processing |
Basecalling and sample de-multiplexing was performed with CASAVA-1.8.4 and default parameters
Reads were quality check with fastqc v0.11.5 default parameters
Reads for each sample/replicate were mapped against the mouse genome assembly and counted using STAR read aligner v2.7.3a
Antisense contigs were assembled using the Trinity platform v2.8.4
Genome_build: Ensembl GRCm38 with assembled antisense contigs
Supplementary_files_format_and_content: Read counts per gene/contig
|
| |
|
| Submission date |
Mar 09, 2020 |
| Last update date |
Jan 28, 2021 |
| Contact name |
Roland Schmucki |
| E-mail(s) |
roland.schmucki@roche.com
|
| Organization name |
F. Hoffmann - La Roche AG
|
| Street address |
Grenzacherstrase
|
| City |
Basel |
| ZIP/Postal code |
4058 |
| Country |
Switzerland |
| |
|
| Platform ID |
GPL17021 |
| Series (1) |
| GSE146628 |
Identification of Natural Antisense Transcripts in Mouse Brain and Their Association with Autism Spectrum Disorder Risk Genes |
|
| Relations |
| BioSample |
SAMN14336194 |
| SRA |
SRX7875172 |
