 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Jul 11, 2022 |
| Title |
RNA-seq analysis of human TNBC cells overexpressing three splicing factor genes (SRSF2-SRSF3-SRSF7) or MYC |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
|
| Summary |
We profiled gene expression and splicing changes in HCC1806 human TNBC cells overexpressing three splicing factor genes (SRSF2-SRSF3-SRSF7), all three splicing factors (called 3xSR) or MYC. We performed RNA-seq, in triplicate on 3xSR, MYC-OE, triple plasmid control, SRFS2, SRSF3, SRSF7, or single plasmid control HCC1806 cells.
|
| |
|
| Overall design |
2D-grown HCC1806 cells were harvested by scraping adherent cells in PBS once ~90% confluence was reached. Total RNA was extracted using the RNeasy kit (Qiagen) including DNase I treatment per manufacturer instructions. Barcoded RNA libraries were prepared starting with 500ng of total RNA using the TrueSeq stranded mRNA kit with polyA selection (Illumina), and quantified using a Bioanalyzer DNA 1000 chip (Agilent). Libraries were sequenced as 150bp paired-end reads at 100-200 million reads per library on an Illumina NovaSeq, equal amounts of 18 libraries were pooled per lane.
|
| |
|
| Contributor(s) |
Urbanski L, Brugiolo M, Park S, Angarola BL, Leclair NK, Yurieva M, Palmer P, Sahu SK, Anczuków O |
| Citation(s) |
36417849 |
| |
| Submission date |
Aug 12, 2021 |
| Last update date |
Jan 17, 2023 |
| Contact name |
Olga Anczukow |
| Organization name |
The Jackson Laboratory for Genomic Medicine
|
| Street address |
10 Discovery Drive
|
| City |
Farmington |
| State/province |
CT |
| ZIP/Postal code |
06032 |
| Country |
USA |
| |
|
| Platforms (1) |
| GPL24676 |
Illumina NovaSeq 6000 (Homo sapiens) |
|
| Samples (21)
|
|
| Relations |
| BioProject |
PRJNA754051 |
| SRA |
SRP332238 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE181956_HCC1806_01-08-21_gene_count_matrix_revision.csv.gz |
992.4 Kb |
(ftp)(http) |
CSV |
| GSE181956_HCC1806_01-08-21_gene_count_matrix_subset.csv.gz |
809.0 Kb |
(ftp)(http) |
CSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
|
|
|
|
 |
Less...
More...