|
| Status |
Public on Dec 01, 2020 |
| Title |
RNAseq_MCF7L_parental_rep3 |
| Sample type |
SRA |
| |
|
| Source name |
RNAseq_MCF7L_parental
|
| Organism |
Homo sapiens |
| Characteristics |
cell line background: MCF7L
cell type: breast cancer cell line
passages: 3-10
|
| Treatment protocol |
MCF7TR or T47DTR cells were cultured in phenol red free RPMI-1640 containing 10% charcoal-stripped FBS, 1% pen/strep and 100nM Tamoxifen (Sigma-Aldrich). Tamoxifen was replaced every 48 hours. All the cells were kept at cell culture incubator with 37 °C and 5% CO2 until they reach 90% confluence. The cells were treated with Sapitinib (AZD8931) at the concentrations at 0uM to 30uM, the gradient concentration is 5uM. Cells absorbance was recorded at day 1 and day 7.
|
| Growth protocol |
Human breast carcinoma cell lines MCF7 and T47D and their tamoxifen resistant (TR) cell lines were originated from Osborne et al (Osborne et al. 1994). MCF7 or T47D was cultured in RPMI-1640 supplemented with 10 % fetal bovine serum, 1% penicillin and streptomycin (pen/strep) until 90% confluent.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted by ZYMO Research Quick-RNA MiniPrep kit from the lysed 10 million of breast cancer cells in RNA Lysis Buffer, then removed most of gDNA with Spin-Away Filter. After that, the mixture of RNA was transferred with ethanol to Zymo-Spin IIICG column to remove trace DNA by DNase I on the column, then washed twice with RNA wash buffer followed by eluted with 50 μl DNase/RNase-free water.
RNA-seq library was prepared with NEBNext® Poly(A) mRNA Magnetic Isolation Module (NEB #E7490). Washed the Oligo dT Beads with RNA binding buffer incubated with total 1ug RNA to purify followed with washing by beads washing buffer. Then eluted mRNA with elution buffer and reverse transcripted. After that, the first and the second strand cDNA was synthesized with the synthesis reaction. After the purification of Double-stranded cDNA, do adaptor ligation and purification. Adaptor Ligated DNA was enriched by PCR followed by purification, then the DNA library was sequenced with Illumina HiSeq3000.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 3000 |
| |
|
| Data processing |
All raw reads were mapped to HG19 reference genome by using tophat2.
raw bam files were further processed by samtools and picard
Differentail genes were identified by DESeq2
Genome_build: hg19
Supplementary_files_format_and_content: xlsx;Differentiated expression genes
|
| |
|
| Submission date |
Jan 28, 2020 |
| Last update date |
Dec 01, 2020 |
| Contact name |
Victor Jin |
| E-mail(s) |
vjin@mcw.edu
|
| Phone |
+1 210 562 9209
|
| Organization name |
Medical college of Wisconsin
|
| Department |
IHE
|
| Street address |
8701 Watertown Plank Rd
|
| City |
Milwaukee |
| State/province |
WI |
| ZIP/Postal code |
53226 |
| Country |
USA |
| |
|
| Platform ID |
GPL21290 |
| Series (2) |
| GSE144378 |
The 3D Genomic Landscape of Differential Response to EGFR/HER2 Inhibition in Endocrine-Resistant Breast Cancer [RNA-seq] |
| GSE144380 |
The 3D Genomic Landscape of Differential Response to EGFR/HER2 Inhibition in Endocrine-Resistant Breast Cancer |
|
| Relations |
| BioSample |
SAMN13936271 |
| SRA |
SRX7642875 |
