|
| Status |
Public on Dec 10, 2023 |
| Title |
RNASEQ_GFP_control_biorep_1 |
| Sample type |
SRA |
| |
|
| Source name |
kidney
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: kidney
cell line: HEK293T
cell type: epithelial
treatment: Lipofectamine 2000 transfected GFP Plasmid
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
RNeasy RNA extraction ployA library prep with TruSeq mRNA library prep, sequenced with NovaSeq 6000
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
GFP_RNASEQ_control_1
|
| Data processing |
For RNA-seq, FASQC was used for quality check filtering reqd quality scores below 30, reads mapped with HISAT2 and counted across aligned genome with featureCounts. DEG analysis performed with limma-voom, which filtered gened with a conts-per-million value below 0.5
Assembly: chr38
Supplementary files format and content: RNA-seq, .csv files are provided in "Processed GEO data.csv" with logFC expression for all genes as well as counts-per-million values for genes of interest in desired KEGG pathways
|
| |
|
| Submission date |
Oct 30, 2023 |
| Last update date |
Dec 10, 2023 |
| Contact name |
Pablo Pinera |
| E-mail(s) |
angelom3@illinois.edu
|
| Organization name |
University of Illinois at Urbana-Champaign
|
| Department |
Bioengineering
|
| Lab |
Perez
|
| Street address |
2332 West John Street, Apt. D
|
| City |
Champaign |
| State/province |
Illinois |
| ZIP/Postal code |
61821 |
| Country |
USA |
| |
|
| Platform ID |
GPL24676 |
| Series (2) |
| GSE246587 |
SPLICER: A Highly Efficient Base Editing Toolbox That Enables in vivo Exon Skipping For Targeting Alzheimer’s Disease [RNA-seq] |
| GSE246588 |
SPLICER: A Highly Efficient Base Editing Toolbox That Enables in vivo Exon Skipping For Targeting Alzheimer’s Disease |
|
| Relations |
| BioSample |
SAMN38042668 |
| SRA |
SRX22289588 |
