|
| Status |
Public on May 03, 2016 |
| Title |
MD231 |
| Sample type |
SRA |
| |
|
| Source name |
Cell culture
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: Breast carcinoma
cell line: MDA-MB-231
cell number per plate: 1.40E+07
|
| Treatment protocol |
No experimental treatments
|
| Growth protocol |
All breast cell lines were obtained from the ATCC and grown as described (PMC3845839). Cells were plated in 15 cm dishes or 96 well plates, grown for 24 hours, starved in serum-free media for 18h, and starved again for an additional hour prior to treatment. NHDF cells (primary neonatal fibroblasts) were obtained from Lonza and cultivated according to manufactors instructions.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Cells were washed 2x with ice cold PBS, lysed in 1ml of RLT buffer (RNeasy Mini Kit, Qiagen) supplemented with 1:100 β-mercaptoethanol, transferred to a micro-centrifuge tube, and snap-frozen in liquid nitrogen.
Genomic DNA was removed from RNA samples using a Qiagen RNase-Free DNase Set kit. RNA integrity was ascertained with a Bioanalyzer and all samples had an RNA integrity number (RIN) between 9 or 10. Ribo-zero Gold rRNA removal kit was used to enrich transcripts and a SOLiD® Total RNA-Seq Kit was used to construct template cDNA for RNA-Seq. The ribosomal depleted mRNA was fragmented using hydrolysis, followed by ligation with strand specific adapters and reverse transcript to generate cDNA. Fragments > 150 bp were subsequently selected using Agencourt Ampure XP beads. The isolated cDNA went through 15 cycles of amplification to produce enough templates for the SOLiD™ EZ Bead™ system to generate a templated bead library for ligation-based sequencing on the 5500XL SOLiD™ platform using barcoding, with a minimum of 2.2 x 107 mapped reads per cell line.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
AB SOLiD System 3.0 |
| |
|
| Data processing |
Measurement of gene expression was performed in seven RNA-Seq experiments using a Life Technologies SOLiD 3 sequencer. The short read sequences produced by the SOLiD 3 sequencer were mapped in color space using the Life Technologies BioScope software version 1.3. (https://abcommunity.thermofisher.com/groups/solid-news/blog/2010/11/10/solid-bioscope-software-13-now-available). The default settings were used in the Life Technologies BioScope software. Precise BioScope version: bioscope-v1.3-rBS131_55029_20101119113500. The reference genome was the human genome UCSC hg19, released Feb 2009. (See https://genome.ucsc.edu/FAQ/FAQreleases.html)
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited gene rollup text files listing the gene counts for each sample
|
| |
|
| Submission date |
May 02, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Stephen R Lindemann |
| E-mail(s) |
lindems@purdue.edu
|
| Phone |
765-494-9207
|
| Organization name |
Purdue University
|
| Department |
Food Sciences
|
| Street address |
745 Agriculture Mall Drive
|
| City |
West Lafayette |
| State/province |
IN |
| ZIP/Postal code |
47907 |
| Country |
USA |
| |
|
| Platform ID |
GPL9442 |
| Series (1) |
| GSE81032 |
Comparative proteomics and transcriptomics study of signaling network proteins across multiple normal and cancer cell lines |
|
| Relations |
| BioSample |
SAMN04932462 |
| SRA |
SRX1738784 |
