|
| Status |
Public on Jan 15, 2014 |
| Title |
MCF7 mRNAseq library |
| Sample type |
SRA |
| |
|
| Source name |
MCF7 cell culture
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: MCF7
purification: oligo(dT) beads
|
| Growth protocol |
MCF-7 cells were grown in D-MEM high glucose with 10% (v/v) fetal bovine serum, 1% (v/v) 2 mM L-glutamine, 1% (v/v) 10,000 U/ml penicillin/10,000 µg/ml streptomycin.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
oligodT-purified RNA converted into cDNA by TruSeq™ RNA Sample Preparation Kit
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Read demultiplexing, read filtering and adapter trimming was done using flexbar (Dodt et al, 2012).
We used TopHat2 (version 2.06) (Trapnell et al., 2009 and Kim et al. 2013) for spliced alignment of reads to the human reference genome sequence (hg18).
We used Cuffdiff (version 2.0.2)(Trapnell et al., 2010) to generate FPKM values
Genome_build: hg18
Supplementary_files_format_and_content: FPKM table
|
| |
|
| Submission date |
Jan 14, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Markus Landthaler |
| E-mail(s) |
markus.landthaler@mdc-berlin.de
|
| Phone |
+49-30-9406-3026
|
| Organization name |
Max-Delbrück-Center for Molecular Medicine
|
| Department |
Berlin Institute for Medical Systems Biology
|
| Street address |
Robert-Rössle-Straße 10
|
| City |
Berlin |
| ZIP/Postal code |
13125 |
| Country |
Germany |
| |
|
| Platform ID |
GPL16791 |
| Series (1) |
| GSE49831 |
Differential Protein Occupancy Profiling of the mRNA Transcriptome |
|
| Relations |
| BioSample |
SAMN02584019 |
| SRA |
SRX426377 |
