|
| Status |
Public on Dec 14, 2012 |
| Title |
100% Human Replicate 3A |
| Sample type |
SRA |
| |
|
| Source name |
human breast
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: MDA-MB-231
human portion (%): 100
mouse portion (%): 0
|
| Growth protocol |
MDA-MB-231 human breast carcinoma cell line was obtained from the American Type Culture Collection, and maintained according to the supplier’s instructions. RNA was isolated from three independent cultures of sub-confluent MDA-MB-231 cells in the exponential phase of growth.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted from cultured MDA-MB-231 cells and normal lung tissue using Trizol Reagent (Invitrogen) according to the manufacturer’s instructions. Concentration and yield of RNA samples were determined using a NanoDrop ND-1000 Spectrophotometer (NanoDrop Technologies). RNA integrity was determined by analysis on an Agilent 2100 Bioanalyzer (Agilent Technologies) following the manufacturer’s recommendations.
RNA libraries were prepared for sequencing using standard Illumina protocols. Briefly, mRNA (200ng) was fragmented at 70 uC for 5 minutes in a fragmentation buffer (Ambion), and converted to first-strand cDNA using Superscript III (Invitrogen); followed by second-strand cDNA synthesis using Escherichia coli DNA pol I (Invitrogen). The double stranded cDNA library was further processed by illumina Genomic DNA Sample Prep Kit.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Data processing |
Basecalls performed using CASAVA version 1.3
RNA-Seq reads were aligned to the Ensembl human (hg19) and mouse (mm9) assemblies using the TopHat 1.4.1 spliced-read aligner.
Alignments were filtered based on their MAPQ values (MAPQ=30).
Read counts were calculated for genes of interest (GTF files) using the MAPQ filtered alignments that mapped to the gene's genomic interval.
Genome_build: hg19, mm9
Supplementary_files_format_and_content: Read Counts. Tab delimited read counts for the gene in column 1. Column 2 contains the read counts in the genomic interval. Column 3 is an alternate gene name if one is available, otherwise it is the same as column 1. Column 4 is the chromosome. Columns 5 and 6 are the start and end positions (genomic coordinates).
Supplementary_files_format_and_content: GTF. Standard format GTF files describing the genes for Ensembl (Ensembl GTF) and CCDS (CCDS GTF).
|
| |
|
| Submission date |
Sep 14, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Camilo Valdes |
| Organization name |
University of Miami
|
| Department |
Center for Computational Science
|
| Lab |
Bioinformatics and Computational Biology
|
| Street address |
Locator C-213. 1120 NW 14 Street
|
| City |
Miami |
| State/province |
FL |
| ZIP/Postal code |
33136 |
| Country |
USA |
| |
|
| Platform ID |
GPL10999 |
| Series (2) |
| GSE40890 |
Characteristics of Cross-Hybridization and Cross-Alignment in Pseudo-Xenograft samples by RNA-Seq and Microarrays [RNA-Seq] |
| GSE40892 |
Characteristics of Cross-Hybridization and Cross-Alignment in Pseudo-Xenograft samples by RNA-Seq and Microarrays |
|
| Relations |
| SRA |
SRX187125 |
| BioSample |
SAMN01177825 |
