|
| Status |
Public on Sep 30, 2024 |
| Title |
HBC530 Replicate 2 |
| Sample type |
SRA |
| |
|
| Source name |
HEK293T
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HEK293T
group: HBC530
|
| Treatment protocol |
Cells were treated with 10 µM ligand/DMSO for 5h.
|
| Growth protocol |
HEK293T cells were maintained in DMEM/F-12 supplemented with 10% FBS and GlutaMAX (1x) in humidified atmosphere with 5% CO2 at 37C.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted with innuPREP RNA Mini Kit 2.0 (analytikjena) followed by DNA digestion (NEB), phenol chloroform extraction and isopropanol precipitation.
NEBNext Ultra II RNA Library Preparation Kit
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq X Plus |
| |
|
| Description |
2_530
|
| Data processing |
Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36. The trimmed reads were mapped to the Homo sapiens GRCh38 reference genome available on ENSEMBL using the STAR aligner v.2.5.2b. BAM files were generated as a result of this step.
Unique gene hit counts were calculated by using featureCounts from the Subread package v.1.5.2. The hit counts were summarized and reported using the gene_id feature in the annotation file. Only unique reads that fell within exon regions were counted.
After extraction of gene hit counts, the gene hit counts table was used for downstream differential expression analysis. Using DESeq2, a comparison of gene expression between the customer-defined groups of samples was performed. The Wald test was used to generate p-values and log2 fold changes. Genes with an adjusted p-value < 0.05 and absolute log2 fold change > 1 were called as differentially expressed genes for each comparison.
Assembly: Homo sapiens GRCh38
Supplementary files format and content: hit-counts: hit count for all the genes, log2 fold change and (adjusted) p-value table: Differential_expression_analysis_table_DMSO_530.csv, Differential_expression_analysis_table_DMSO_C3Ms.csv
|
| |
|
| Submission date |
Jul 08, 2024 |
| Last update date |
Sep 30, 2024 |
| Contact name |
Kamila Nykiel |
| E-mail(s) |
[email protected]
|
| Organization name |
Medical University of Innsbruck
|
| Street address |
Innrain 52
|
| City |
Innsbruck |
| ZIP/Postal code |
6020 |
| Country |
Austria |
| |
|
| Platform ID |
GPL34284 |
| Series (1) |
| GSE271728 |
Engineering covalent small molecule–RNA complexes in living cells |
|
| Relations |
| BioSample |
SAMN42390945 |
| SRA |
SRX25261495 |
