|
| Status |
Public on Jan 20, 2017 |
| Title |
SUM159_DMSO_24h_500nMtrametinib_replicate1 |
| Sample type |
SRA |
| |
|
| Source name |
SUM159_DMSO_24h_500nMtrametinib
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: SUM159 breast carcinoma cell line
culture media: DMEM/F12 1:1 supplemented with 5% FBS, 5 µg/ml insulin, 1 µg/ml hydrocortisone
library preparation kit: KAPA Stranded mRNAseq kit
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA was isolated using Qiagen RNeasy Plus kit.
2 µg total RNA and 15 cycles of amplification were used for libaries constructed with Illumina TruSeq RNA Library Prep Kit v2. 4 µg total RNA and 10 cycles of amplification (using 0.5X recommended DNA template) were used for libraries constructed with KAPA Stranded mRNAseq kit.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
processed data file:
DESeq2_Figure2_claudin.xlsx
DESeq2_Figure2_subtype_group_comparison.xlsx
|
| Data processing |
Reads were aligned to the human reference genome hg19_M_rCRS using MapSplice v2.1.4; alignment profile was determined by Picard Tools v1.88.
Aligned reads were sorted and indexed using SAMtools v1.2 and translated to transcriptome coordinates and filtered for indels, large inserts, and zero mapping quality using UNC Bioinformatics Utilities v1.2.
Transcript abundance estimates were determined using RSEM and upper-quartile normalized.
Genome_build: hg19
Supplementary_files_format_and_content: Processed files (.xlsx and .normalized_results) contain upper-quartile normalized RSEM transcript abundance estimates, organized by official gene symbol and Entrez Gene ID.
|
| |
|
| Submission date |
Jan 18, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Gary L Johnson |
| E-mail(s) |
glj@med.unc.edu
|
| Organization name |
University of North Carolina School of Medicine
|
| Department |
Pharmacology
|
| Lab |
Gary L. Johnson Lab
|
| Street address |
4009 Genetic Medicine Building, 120 Mason Farm Road
|
| City |
Chapel Hill |
| State/province |
NC |
| ZIP/Postal code |
27599 |
| Country |
USA |
| |
|
| Platform ID |
GPL18573 |
| Series (2) |
| GSE87419 |
Enhancer Remodeling During Adaptive Bypass to MEK Inhibition Is Attenuated by Pharmacological Targeting of the P-TEFb Complex (RNA-seq) |
| GSE87424 |
Enhancer Remodeling During Adaptive Bypass to MEK Inhibition Is Attenuated by Pharmacological Targeting of the P-TEFb Complex |
|
| Relations |
| BioSample |
SAMN06239105 |
| SRA |
SRX2514227 |
