|
| Status |
Public on Jan 20, 2017 |
| Title |
SUM159xenograft_mouse3_control_48h |
| Sample type |
SRA |
| |
|
| Source name |
SUM159 breast carcinoma cell line: xenograft
|
| Organism |
Homo sapiens |
| Characteristics |
xenograft: SUM159 breast carcinoma cell line xenograft
treatment: control
time: 48h
|
| 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 libraries 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 or Illumina TruSeq RNA library kit v2.
library preparation kit: KAPA Stranded mRNAseq kit
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| 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.
Differential expression analysis was performed as follows: RSEM gene-level expected read counts were imported into R version 3.2.2 and were analyzed using DESeq2 v1.12.3 to detect genes that were differentially expressed between pre-treatment and trametinib-treated conditions for claudin-low cell lines (DESeq2_Figure2_claudin.xlsx) or basal-like cell lines (DESeq2_Figure2_basal.xlsx), or to detect genes that were differentially expressed between claudin-low and basal-like cell line groups (DESeq2_Figure2_subtype_group_comparison.xlsx). DESeq2 v1.12.3 was also used to detect differentially expressed transcripts in response to trametinib among biological replicates of an individual cell line (DESeq2_SUM159replicates.xlsx). Default DESeq2 parameters were used for the analysis, specifying sample ID in addition to pre and post treatment status to account for pairing between samples in the specification of the model design matrix. Significantly differentially expressed genes were selected based on adjusted p-values, utilizing a threshold of 0.05 for significance.
Genome_build: hg19 or mm9
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 |
Sep 28, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Gary L Johnson |
| E-mail(s) |
[email protected]
|
| 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 |
SAMN05832147 |
| SRA |
SRX2194345 |
