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| Status |
Public on Jul 01, 2014 |
| Title |
Tumor RNA BT55 |
| Sample type |
SRA |
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| Source name |
Primary breast cancer
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| Organism |
Homo sapiens |
| Characteristics |
tissue: breast cancer tumor
breast cancer subtype: Luminal B
library id: RHB001
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using the AllPrep DNA/RNA Mini kit (Qiagen) and enriched for poly(A) mRNA using a μMACS™ poly(T) kit (Life Technologies). 500 ng of purified poly(A) RNA was used for library preparation.
RNA libraries were prepared for sequencing using a SOLiD™ Total RNA-Seq Kit (Applied Biosystems), according to the manufacturer's instructions.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
AB SOLiD 4 System |
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| Data processing |
Sequenced reads were aligned to the human genome hg18 assembly using BioScope v1.3.1
Fragments Per Kilobase of transcript per Million fragments mapped (FPKM) were calculated using Cufflinks, version 1.0.3 (Trapnell et al., Nature Biotechnology, 2010) and the hg18 RefSeq Genes track downloaded from the UCSC genome browser as the gene annotation file. Gene-based values were generated as the sum of the FPKM of all of the transcripts correspoding to the same gene.
Genome_build: hg18
Supplementary_files_format_and_content: Tab-delimited text files include trasncript- and gene-based FPKM values for each sample
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| Submission date |
May 22, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Edison Liu |
| E-mail(s) |
ed.liu@jax.org
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| Organization name |
The Jackson Laboratory
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| Street address |
600 Main Street
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| City |
Bar Harbor |
| State/province |
Maine |
| ZIP/Postal code |
04609 |
| Country |
USA |
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| Platform ID |
GPL13393 |
| Series (1) |
| GSE57914 |
Chromosome as oncogenic organizer: functional consequences of structural mutations in breast cancer (RNA-Seq) |
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| Relations |
| BioSample |
SAMN02798186 |
| SRA |
SRX551038 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1397344_BT55.FPKM.txt.gz |
555.5 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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