|
| Status |
Public on Nov 02, 2023 |
| Title |
MO-1065.1G.N |
| Sample type |
SRA |
| |
|
| Source name |
brain
|
| Organism |
Rattus norvegicus |
| Characteristics |
tissue: brain
cell line: brain primary cell line
cell type: Neural Progenitor Cell
strain: Sprague Dawley
treatment: 1Gy 5uM Noggin
|
| Treatment protocol |
The effect of radiation on NSp growth and differentiation was measured after 0 and 1 Gy photon radiation (day=3 after NPCs seeding) with a CellRad+ benchtop X-ray irradiator (Precision). 5uM of Noggin and 200uM Ascobic Acid as tretament pre and post radiation exposure
|
| Growth protocol |
Neural progenitor cells were isolated from the brain of E15 Sprague Dawley rat fetuses and cultured in NeuroCult basal medium supplemented with 1% Pen/Strep, 1X N-2 supplement, 1X B-27 supplement, 20ng/mL human epidermal growth factor, 20ng/mL human fibroblast growth factor, and 1:500 dilution of 0.2% heparin solution in ultra-low attachment microplates where they spontaneously form spheroids (neurospheres)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted from Neurospheres using TRIzol and pipet homogenization. Glycogen was added to the TRIzol sample after homogenization to aid in RNA recovery. RNA quantification was assessed using Epoch Biotek spectrophotometer (Biotek Instruments, Winooski, Vermont)
RNA was QC analyzed by Bioanalyzer (Agilent, Santa Clara, CA). To isolate polyA RNA for library preparation, NEBNext Poly(A) mRNA Magnetic Isolation Module (New England BioLabs, Ipswich, MA) was used with 1 µg good quality total RNA as input.
The polyA RNA was enriched using SMARTer Apollo automated NGS library prep system (Takara Bio USA, Mountain View, CA). Next, NEBNext Ultra II Directional RNA Library Prep kit (New England BioLabs) was used for library preparation under PCR cycle number of 8
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 2000 |
| |
|
| Description |
TPM_NPC.txt
TPM_NPC_outlierRemoved.txt
|
| Data processing |
Paired-end reads were aligned to rat genome build Rn7 with STAR v2.6.1
Kallisto was used to generate TPM which were then processed through NOISeq v2.42.0 for batch correction. One outlier sample was identified from the Control treatment group (MO2) and was removed from further analysis.
AltAnalyze v2.1.4.4 (EnsMart106 database) was then used for differential expression analysis on the batch corrected data matrix.
The AltAnalyze supplied empirical Bayes moderated t-test was performed followed by Benjamini-Hochberg adjustment for false discovery (FDR).
Final threshold cutoffs were an adjusted p-value < 0.05 (FDR) and fold change ≥ 1.5. GO and KEGG pathway enrichment was also performed in AltAnalyze using the integrated GO-Elite pathway analysis tool
Assembly: Rn7
Supplementary files format and content: TPM_NPC.txt tab delimited file containing Gene-level Transcript Per Million (TPM) estimates before outlier removal
Supplementary files format and content: TPM_NPC_outlierRemoved.txt tab delimited file containing Gene-level Transcript Per Million (TPM) estimates after outlier removal
|
| |
|
| Submission date |
Sep 11, 2023 |
| Last update date |
Nov 02, 2023 |
| Contact name |
Nathan Salomonis |
| E-mail(s) |
nathan.salomonis@cchmc.org
|
| Organization name |
Cincinnati Children's Hospital
|
| Department |
Biomedical Informatics
|
| Lab |
Nathan Salomonis
|
| Street address |
3333 Burnet Avenue
|
| City |
Cincinnati |
| State/province |
OH |
| ZIP/Postal code |
45229 |
| Country |
USA |
| |
|
| Platform ID |
GPL32190 |
| Series (1) |
| GSE242899 |
Effect of radiation exposure on gene expression in neurospheres |
|
| Relations |
| BioSample |
SAMN37352150 |
| SRA |
SRX21751781 |
