|
| Status |
Public on Jun 30, 2024 |
| Title |
4T1 DAC replicate 2 [RNA-seq] |
| Sample type |
SRA |
| |
|
| Source name |
4T1
|
| Organism |
Mus musculus |
| Characteristics |
cell line: 4T1
treatment: DAC for 48 h
|
| Treatment protocol |
B16F10 and 4T1 cells (2x10^4/well in 24 well plates) were treated with 0.1 uM or 1 uM of DAC for 48 hours, respectively. Dead cells were removed with dead cell removal microbeads and live cells were used for RNAseq
|
| Growth protocol |
B16F10 cell line was a kind gift of Gordon Freeman (Dana-Farber Cancer Institute). 4T1 cells were provided by Fred Miller (Wayne State University). Cells were cultured with Dulbecco’s modified Eagle medium (DMEM) supplemented with 10% heat-inactivated fetal bovine serum (FBS, VWR), 6 mM HEPES, 1.6 mM L-glutamine, 50 mM 2-mercaptoethanol, 100 U/ml penicillin G and 100 mg/ml streptomycin sulfate (Sigma-Aldrich). All cell lines were verified to be free of mycoplasma by PCR and were authenticated by morphology.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
genomic DNA was isolated with Quick-DNA Microprep Kit (ZYMO RESEARCH).
12 groups were prepared for RNA-seq libraries using NEXTflex Illumina qRNA-Seq Library Prep Kit (Bioo Scientific)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Real-Time Analysis (RTA) software
sequencing reads were aligned to the mm10 genombe in RSEM pipeline
Differential analysis were conducted in EdgeR. The significant genes were deducted by computing NB exact genewise tests with corrected p < 0.05.
P-values of differential expression were adjusted for multiple-hypothesis testing using False Discovery Rate (FDR) method.
Assembly: mm10
Supplementary files format and content: Data matrix was generated by RSEM
|
| |
|
| Submission date |
Aug 25, 2022 |
| Last update date |
Jun 30, 2024 |
| Contact name |
Eric Greer |
| E-mail(s) |
Eric.Greer@childrens.harvard.edu
|
| Organization name |
Boston Children's Hospital/Harvard Medical School
|
| Department |
Newborn Medicine/Department of Pediatrics
|
| Lab |
Greer Lab
|
| Street address |
320 Longwood Avenue
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02115 |
| Country |
USA |
| |
|
| Platform ID |
GPL24247 |
| Series (2) |
| GSE212027 |
Transcriptome analysis in B16F10 and 4T1 cell lines with decitabine treatment [RNA-seq] |
| GSE212029 |
B16 and 4T1 cell lines with decitabine treatment |
|
| Relations |
| BioSample |
SAMN30497026 |
| SRA |
SRX17212186 |
