|
| Status |
Public on Feb 09, 2021 |
| Title |
MIA.e12.5.1623.2.S51.L005 |
| Sample type |
SRA |
| |
|
| Source name |
dorsal telencephalon/pallium or developing cortex
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
age: E12.5
treatment: PolyIC
response to polyic: med
sex by xist counts: F
sex by xist counts: 8
tissue: dorsal telencephalon/pallium or developing cortex
|
| Treatment protocol |
Pregnant mice at gestational day E12.5 were injected intraperitoneally (IP) with 30 mg/kg poly(I:C) dsRNA from Sigma Aldrich (St. Louis, MO, cat #P0913) or with vehicle control (sterile 0.9% saline) injected at 5ul per gram of body weight. Pregnancy was determined to be E12.5 by visualizing vaginal seminal plug, noted as embryonic day 0.5 (E0.5) and by an increase in body weight.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using Ambion RNAqueous total RNA Isolation Kit and assayed using Agilent RNA 6000 Nano Bioanalyzer kit/instrument.
Stranded mRNA libraries were prepared using TruSeq Stranded mRNA kits. 8–12 samples per lane were pooled and sequenced on an Illumina HiSeq 4000 instrument using a single-end 50-bp protocol.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
Reads from RNA-seq were aligned to the mouse genome (mm9) using STAR (version 2.4.2a).
Aligned reads mapping to genes were counted at the gene level using subreads featureCounts.
The mm9 knownGene annotation track and aligned reads were used to generate quality control information using the full RSeQC tool suite.
Samples that exhibited strong 3′ _bias using geneBody_coverage.py or poor exon distribution using read_distribution.py were discarded.
Unaligned reads were quality checked by FastQC to ensure high quality datasets.
Genome_build: mm9
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
|
| |
|
| Submission date |
Feb 08, 2021 |
| Last update date |
Feb 10, 2021 |
| Contact name |
Alexander Star Nord |
| E-mail(s) |
asnord@ucdavis.edu
|
| Organization name |
University of California Davis
|
| Department |
Center for Neuroscience
|
| Lab |
Nord Neurogenomics lab
|
| Street address |
1544 Newton Court
|
| City |
Davis |
| State/province |
CA |
| ZIP/Postal code |
95618 |
| Country |
USA |
| |
|
| Platform ID |
GPL21103 |
| Series (1) |
| GSE166376 |
A temporal map of maternal immune activation-induced changes reveals a shift in neurodevelopmental timing and perturbed cortical development in mice |
|
| Relations |
| BioSample |
SAMN17834568 |
| SRA |
SRX10049158 |
