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| Status |
Public on Jan 29, 2018 |
| Title |
SHEP21_4HR_RNA-seq_rep2 |
| Sample type |
SRA |
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| Source name |
SHEP21_4HR
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| Organism |
Homo sapiens |
| Characteristics |
cell line: SHEP-21N
cell type: neuroblastoma cell line
treated with: doxycycline (0.2 ug/ml) for 4hrs
bar code: AGTTCC
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| Treatment protocol |
TET-off MYCN shutdown was performed by addition of doxycycline (0.2 micrograms/mL) to the growth media for the inidicated timepoints.
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| Growth protocol |
SHEP-21N cells were cultured in RPMI supplemented with 10% Tetracycline-Free FBS (Clontech).
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| 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)
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| Description |
RNA-seq of SHEP-21N, 4hr, rep2
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| 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: SHEP21_all_fpkm_exprs_raw.txt: Tab-delimited text file matix containing raw FPKM values for each transcript. Please note that the rep0, rep1, rep2 in the *txt files corresponds to rep1, rep2 and rep3 in the sample title, respectively.; SHEP21_all_fpkm_exprs_norm.txt: Tab-delimited text file matix containing ERCC cell count normalized FPKM values for each transcript. Please note that the rep0, rep1, rep2 in the *txt files corresponds to rep1, rep2 and rep3 in the sample title, respectively.
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| Submission date |
Apr 11, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
James Bradner |
| E-mail(s) |
[email protected]
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| Organization name |
Dana-Farber Cancer Institute
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| Department |
Medical Oncology
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| Lab |
Bradner Lab
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| Street address |
450 Brookline
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| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02215 |
| Country |
USA |
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| 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 |
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| Relations |
| BioSample |
SAMN04632536 |
| SRA |
SRX1690240 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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