|
| Status |
Public on Jan 29, 2018 |
| Title |
BE2C_shT_3HR_rep2 |
| Sample type |
SRA |
| |
|
| Source name |
Neuroblastoma
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: BE(2)-C with tetracycline inducible shTWIST1
bar code: CAGATC
|
| Treatment protocol |
BE(2)-C cells were treated with 1μM JQ1 (DMSO stock solution) at the indicated timepoints. Tet-on shTWIST1 expression was performed by addition of doxycycline (0.5μg/mL) to growth media.
|
| Growth protocol |
BE(2)-C cells cultured in Dulbecco’s Modified Eagle Medium (DMEM) supplemented with 10% FBS. BE(2)-C engineered cells expressing inducible shTWIST1 cultured in DMEM supplemented with Tetracycline-Free FBS (Clontech).
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Prior to RNA isolation, cell numbers were determined and total RNA isolation was performed using the miRvana miRNA total RNA isolation kit (ThermoFisher Scientific, AM1560) according to manufacturers instructions. Following isolation, RNA was digested with DNase (Ambion). During isolation, external RNA spike-ins (ERCC, Ambion) were added at the time of cell lysis.
Total RNA was subject to polyA selection and adapter ligation in preparation for next-generation sequencing (Illumina stranded mRNA library prep)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
RNA-seq of BE(2)-C cells with a tetracycline inducible TWIST1 shRNA at 3 ,6, 12, 24, and 48 hours after induction with 0.5ug/ml doxycycline
|
| Data processing |
alignment: HiSat using default settings
expression levels: Gene-level expression measurements for RefSeq genes were reported in fragments per kilobase per million reads (FPKM) by Cufflinks 2.0.0 (http://cufflinks.cbcb.umd.edu/) (Trapnell et al., 2010). Cufflinks assembles transcripts, estimates their abundance, and tests for differential expression and regulation in RNA-Seq samples. FPKM values were ERCC normalized. See methods for further details
Genome_build: hg19
Supplementary_files_format_and_content: BE2C_TWIST_all_fpkm_exprs_raw.txt: Tab-delimited text file matix containing raw FPKM values for each transcript; BE2C_TWIST_all_fpkm_exprs_norm.txt: Tab-delimited text file matix containing ERCC cell count normalized FPKM values for each transcript
|
| |
|
| Submission date |
Apr 10, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
James Bradner |
| E-mail(s) |
bradner_computation@dfci.harvard.edu
|
| Organization name |
Dana-Farber Cancer Institute
|
| Department |
Medical Oncology
|
| Lab |
Bradner Lab
|
| Street address |
450 Brookline
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02215 |
| Country |
USA |
| |
|
| Platform ID |
GPL18573 |
| Series (2) |
| GSE80153 |
Enhancer invasion shapes MYCN dependent transcriptional amplification in neuroblastoma [RNA-seq] |
| GSE80154 |
Enhancer invasion shapes MYCN dependent transcriptional amplification in neuroblastoma |
|
| Relations |
| BioSample |
SAMN06704966 |
| SRA |
SRX2731808 |
