|
| Status |
Public on Feb 24, 2020 |
| Title |
HMLER2_HDAC7_siRNA_CC11 |
| Sample type |
SRA |
| |
|
| Source name |
non-stem breast cancer cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HMLER2
cell type: Breast primary epithelial cells
transforming gene: hTERT; SV40-LT/st; hRASV12
sirna: siHDAC7
|
| Treatment protocol |
BPLER and HMLER cells were plated in 10cm petri dish at 7.0x10e5 cell/plate respectively in BMI-T and MEGM (Lonza) medium 24h before transfection. Cells were transfected with pools, 50 nM each, of HDAC1 and HDAC7 specific double-stranded RNAs and non-specific (NS) siRNAs as control using Lipofectamine RNAiMAX (Invitrogen) in OptiMEM (GIBCO, Life Technologies) added directly to the medium. The cells were harvested 72h later for total RNA extraction.
|
| Growth protocol |
BPLER and HMLER cells were described before (Cancer Cell 12, 160-170, 2007). Both cell types and BPLER culture medium (BMI-T) are available from the Live Tissue Culture Service Center, University if Miami (contact LTCC@med.miami.edu).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA preparations were obtained with RNAzol® RT (Sigma) and cleaned with Turbo DNA-Free Kit (Ambion).
DNase I-treated total RNA preparations were qualitatively validated by Eukaryote Total RNA 6000 Nano analysis on 2100 Bioanalyzer (Agilent) and libraries were prepared using the KAPA RNA HyperPrep kit according to manufacturer instructions (KAPA).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
processed data files:
DESeq2_HMLER2_siHDAC7_vs_siNT.txt
HMLER2_siHDAC7_vs_siNT.txt
CC11
|
| Data processing |
Base calling and data filtering was performed on BaseSpace Illumina platform.
RNA-seq fastq files were uploaded to the Galaxy web platform and we used the public server at galaxy.org to analyze the data. RNA-seq data sets were paired and aligned using HISAT2 (version 2.1.0) to reference version NCBIv37/hs19 of the human genome; transcript assembly, quantification and merging was done with StringTie (version 1.3.4).
Number of reads per transcript was counted using featureCounts (version 1.6.3) and differential expression analysis was performed using DESeq2 (version 2.11.40.2).
A cutoff of 0.6<log2<-0.6, p<0.05 was applied for the identification of genes with significant differential expression.
Genome_build: hs19
Supplementary_files_format_and_content: Tab-delimited text files from DESeq2 differential expression analysis (DESeq2*.txt) and files with normalized counts
DESeq2_BPLER2_siHDAC7_vs_siNT.txt: differential measurements
BPLER2_siHDAC7_vs_siNT.txt: normalized counts
DESeq2_BPLER2_siHDAC1_vs_siNT.txt: differential measurements
BPLER2_siHDAC1_vs_siNT.txt: normalized counts
DESeq2_HMLER2_siHDAC7_vs_siNT.txt: differential measurements
HMLER2_siHDAC7_vs_siNT.txt: normalized counts
DESeq2_HMLER2_siHDAC1_vs_siNT.txt: differential measurements
HMLER2_siHDAC1_vs_siNT.txt: normalized counts
|
| |
|
| Submission date |
May 22, 2019 |
| Last update date |
Feb 24, 2020 |
| Contact name |
Corrado Caslini |
| E-mail(s) |
ccaslini@med.miami.edu
|
| Organization name |
University of Miami
|
| Street address |
1501 NW 10th Avenue
|
| City |
Miami |
| State/province |
FL |
| ZIP/Postal code |
33136 |
| Country |
USA |
| |
|
| Platform ID |
GPL18573 |
| Series (2) |
| GSE131631 |
Next Generation Sequencing and differential expression analysis in stem-like vs. non-stem breast cancer cells in response to HDAC1 and HDAC7 knockdown |
| GSE131632 |
Genome-wide analysis of histone 3 lysine K27 acetylation and differential expression analysis in stem-like breast cancer cells in response to HDAC1/3/7 inhibition or knockdown |
|
| Relations |
| BioSample |
SAMN11823159 |
| SRA |
SRX5883076 |
