|
| Status |
Public on Nov 29, 2017 |
| Title |
Patient 7 needle core biopsy - pre treatment |
| Sample type |
SRA |
| |
|
| Source name |
breast carcinoma
|
| Organism |
Homo sapiens |
| Characteristics |
disease state: TNBC
individual: Patient 7
protocol: pre-treatment needle core biospy
tumor sample subtype: normal breast
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA was isolated with Qiagen RNeasy Mini kit.
mRNA libraries were made with Illumina TruSeq RNA Sample Prep Kit starting with 0.5-1 micrograms of total RNA.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
150501_UNC15-SN850_0404_AC5JF0ACXX_2_TTAGGC_L002
LCCC1122_rawRSEM.txt
LCCC1122_normalizedLog2RSEM.txt
|
| 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.
For DESeq differential expression analysis comparing pre-treatment and post-treatment patient tumors: 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 post-treatment conditions. 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.
Genome_build: hg19
Supplementary_files_format_and_content: Processed files contain raw or log2-transformed upper-quartile normalized RSEM transcript abundance estimates, organized by official gene symbol and Entrez Gene ID.
|
| |
|
| Submission date |
Nov 29, 2017 |
| Last update date |
Dec 04, 2017 |
| 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 |
GPL11154 |
| Series (2) |
| GSE87424 |
Enhancer Remodeling During Adaptive Bypass to MEK Inhibition Is Attenuated by Pharmacological Targeting of the P-TEFb Complex |
| GSE107502 |
Defining the Triple Negative Breast Cancer Kinome Response to GSK1120212 (RNA-Seq) |
|
| Relations |
| BioSample |
SAMN08110972 |
