|
| Status |
Public on Nov 04, 2021 |
| Title |
NI_40_rep2: non-infected 40hr post-infection replicate 2 |
| Sample type |
SRA |
| |
|
| Source name |
Neuronal progenitor cell-derived neurons
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: NPC-derived neuron
infection: non-infected
harvest time: 40hr post-infection
|
| Treatment protocol |
Neurons treated with viruses or mock-medium were harvested at 0, 8, 24, and 40hrs post-infection.
|
| Growth protocol |
iPSC-derived NPCs were maintained in DMEM/F12 medium with N-2 and B27 supplements, and bFGF on PLO and Laminin-coated plate until differentiation. The medium was changed to Neurobasal medium with B27 and Glutamax and refreshed every 2~3 days for 14 days for neuron differentiation.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNAs were prepared after Trizol extraction, DNase I treatment, second Trizol extraction and ethanol precipitation.
RNA libraries were prepared for sequencing using Illumina TruSeq Stranded mRNA library kit.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Reads were cleaned of adapter sequences and low-quality sequences using cutadapt version 1.11 . Only sequences at least 25 nucleotides (nt) in length were considered for further analysis.
STAR version 2.5.0a, with default parameters, was used for alignment against the reference genome (Human (GRCh38) from ENSEMBL version 98).
Genes were counted using featureCounts version 1.4.6-p3 from the Subreads package (parameters: -t gene -g gene_id -s 2 -p).
Count data were analyzed using R version 3.6.1 and the Bioconductor package DESeq2 version 1.24.0. The normalization and dispersion estimation were performed with DESeq2 using the default parameter and statistical tests for differential expression were performed applying the independent filtering algorithm. A generalized linear model was set in order to test for the differential expression between conditions. For each pairwise comparison, raw p-values were adjusted for multiple testing according to the Benjamini and Hochberg (BH) procedure and genes with both an absolute log2FC > 1 and an adjusted p-value lower than 0.05 were considered differentially expressed.
Genome_build: Human (GRCh38) from ENSEMBL version 98
Supplementary_files_format_and_content: Matrix from DESeq2
|
| |
|
| Submission date |
Jun 21, 2021 |
| Last update date |
Nov 04, 2021 |
| Contact name |
Rachel Legendre |
| E-mail(s) |
rachel.legendre@pasteur.fr
|
| Organization name |
Institut Pasteur
|
| Department |
Research and Resource Center for Scientific Informatics
|
| Lab |
Hub of Bioinformatics and Biostatistics
|
| Street address |
28, rue du docteur Roux
|
| City |
Paris |
| ZIP/Postal code |
75724 |
| Country |
France |
| |
|
| Platform ID |
GPL24676 |
| Series (1) |
| GSE178583 |
Early transcriptional changes in rabies virus-infected neurons and extended effects on neuronal functions |
|
| Relations |
| BioSample |
SAMN19797242 |
| SRA |
SRX11188559 |
