|
| Status |
Public on Jul 10, 2024 |
| Title |
X3i |
| Sample type |
SRA |
| |
|
| Source name |
Sprague-Dawley
|
| Organism |
Rattus norvegicus |
| Characteristics |
strain: Sprague-Dawley
age: Embryonic day 18, 19 DIV
source: Striatum
treatment: lacZ sgRNA
|
| Treatment protocol |
Primary rat striatal neurons were transduced with lentiviruses expressing CRISPRi machinery on DIV12 with a multiplicity of infection (MOI) per cell of 2000 for each virus.
|
| Growth protocol |
Neurons were removed from rat striatal tissue at embryonic day 18, and maintained in vitro for 12 days prior transduction with CRISPRi lentivirus components. RNA was extracted at DIV 19 and RNA-seq was performed using mRNA.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA from was extracted, DNase-treated, and purified (RNeasy, Qiagen). 1µg of total RNA underwent quality control (Bioanalyzer; all RIN values > 7.0) and library construction for polyA+ RNA sequencing.
1 μg of total RNA underwent quality control (Bioanalyzer) and was prepared for directional RNA sequencing using NEBNext reagents (New England Biolabs) according to manufacturer’s recommendations. Specifically, the NEBNext Poly(A) mRNA manetic isolation module was used to enrich polyadenylated RNA. RNA-seq libraries underwent sequencing (100 bp paired-end directional reads) on an Illumina sequencing platform (NovaSeq6000).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
3i_S61
|
| Data processing |
Raw FASTQ files were processed using nf-core/rnaseq v3.10 (doi: https://doi.org/10.5281/zenodo.1400710) of the nf-core collection of workflows using a pipeline executed with Nextflow v23.04.1.
Splice-aware alignment to the mRatBn7.2/Rn7 genome assembly was conducted using STAR v2.7.9a with the associated Ensembl gene transfer format (gtf) file (version 105).
Binary alignment map files were indexed with SAMtools (v1.16.1). Gene-level counts were generated using featureCounts (Rsubread v2.0.1)
QC metrics were collected and reviewed with MultiQC (v1.13), and a minimum of 20M mapped reads were obtained per sample (range: 22.6M to 121.4M)
Differential expression testing was conducted using DESeq2 (v1.38.3). DEG testing p-values were adjusted with the Benjamini–Hochberg method, and DEGs were designated as those genes with an adjusted p-value <0.05. Genes with unreliable/low expression estimates (basemean <50) were excluded from subsequent analysis.
Assembly: Rn7 (Ensemble gtf version 105)
Supplementary files format and content: Count_matrix.txt contains RNA-seq count values for annotated gene for each sample
|
| |
|
| Submission date |
Jun 07, 2024 |
| Last update date |
Jul 10, 2024 |
| Contact name |
Jeremy Jason Day |
| E-mail(s) |
jjday@uab.edu
|
| Phone |
205-996-8960
|
| Organization name |
UAB
|
| Department |
Neurobiology
|
| Lab |
Day
|
| Street address |
1825 University Blvd
|
| City |
Birmingham |
| State/province |
AL |
| ZIP/Postal code |
35294 |
| Country |
USA |
| |
|
| Platform ID |
GPL25947 |
| Series (1) |
| GSE269366 |
RNA-seq dataset for "Reelin marks cocaine-activated striatal ensembles, promotes neuronal excitability, and regulates cocaine reward" |
|
| Relations |
| BioSample |
SAMN41748866 |
| SRA |
SRX24839477 |
