|
| Status |
Public on Dec 02, 2017 |
| Title |
LAN1.DMSO.day5.rep1 |
| Sample type |
SRA |
| |
|
| Source name |
Neuroblastoma cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: LAN-1
treatment: DMSO
time: 5 days
replicate: 1
|
| Treatment protocol |
Kelly and LAN-1 cells were treated in duplicate with 2 uM GSK126 (Excess Biosciences M60071-2) or DMSO for 2 or 5 days.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted from cells with the RNeasy Kit (Qiagen).
RNA libraries were prepared for sequencing using standard Illumina protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
Sample name: Sample 11
|
| Data processing |
Samples were sequenced using Illumina TruSeq strand specific library. The pool of sixteen samples was sequenced on two lanes of an Illumina HiSeq, generating single end reads of 32-76 bp length.
Quality control tests for the mapped reads were performed using the FASTQC software (Babraham Lab, http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). Read coverage per sample ranged between 17 Mbp to 24 Mbp.
The sequenced reads were aligned to the GRCh37/hg19 human genome by using the tophat2 mapper for single end alignment. Quality control tests for the aligned reads and for the replicate consistency were performed by using the qualimap v2.2 (Garcia-Alcalde et al, 2012) and the SARTools (Hugo Varet, 2015) pipelines. The average percentage of uniquely mapped reads in the aligned data was 86.50% with a standard deviation 2.3%.
Transcript abundance (reads and FPKM scores) at the GRCh37/hg19 RefSeq gene level was computed with the Feature Counts method implemented in the Bioconductor v3.2 Rsubread package (Liao et al., 2014).
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files include the gene level reads for each sample.
|
| |
|
| Submission date |
Aug 10, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Gabriela Alexe |
| E-mail(s) |
[email protected]
|
| Organization name |
Broad Institute
|
| Department |
Computational Biology and Bioinformatics
|
| Street address |
415 Main St.
|
| City |
Cambridge |
| State/province |
MA |
| ZIP/Postal code |
02142 |
| Country |
USA |
| |
|
| Platform ID |
GPL11154 |
| Series (2) |
| GSE85431 |
Targeting EZH2 in MYCN-amplified Neuroblastoma [RNA-seq] |
| GSE85432 |
Targeting EZH2 in MYCN-amplified Neuroblastoma |
|
| Relations |
| BioSample |
SAMN05558687 |
| SRA |
SRX2011532 |
