|
| Status |
Public on Nov 15, 2017 |
| Title |
Control RNASeq 4 |
| Sample type |
SRA |
| |
|
| Source name |
bone marrow metastatic neuroblastoma
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: neuroblastoma cell line
cell line: SK-N-BE2
treatment: control
|
| Treatment protocol |
a 1:1 mix of lentiviral particles carrying empty TRC1 and TRC2 Plko.1-puro vectors was used as a negative control
|
| Growth protocol |
BE2 cell lines were maintained at 80 – 90% confluence in DMEM/F-12 supplemented with 10% FBS and antibiotics
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using Direct-zol RNA Miniprep kit (Zymo Research) according to manufacturer’s indications
We use poly-A pull-down to enrich mRNAs from total RNA samples (200ng-1ug per sample, RIN>8 required) and proceed on library preparation by using Illumina TruSeq. Libraries are then sequenced using Illumina HiSeq2500/HiSeq4000 at Columbia Genome Center. RNA prep kit. Libraries are then sequenced using Illumina HiSeq2500/HiSeq4000 at Columbia Genome Center. We multiplex samples in each lane, which yields targeted number of single-end/paired-end 100bp reads for each sample, as a fraction of 280-400 million reads for the whole lane.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
We use RTA (Illumina) for base calling and bcl2fastq2 (version 2.17) for converting BCL to fastq format, coupled with adaptor trimming.
We map the reads to a reference genome (Human: NCBI/build37.2) using STAR(2.5.2b) and featureCounts(v1.5.0-p3)
The data was then normalized using voom implemented in edgeR R Bioconductor package
Genome_build: hg19
Supplementary_files_format_and_content: txt files were generated containing gene level normalized expression values
|
| |
|
| Submission date |
Sep 21, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Gonzalo Lopez |
| Organization name |
Mount Sinai School of Medicine
|
| Department |
Genetics and Genomic Sciences
|
| Street address |
1399 Park avenue
|
| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10016 |
| Country |
USA |
| |
|
| Platform ID |
GPL16791 |
| Series (1) |
| GSE84389 |
Network-based, cross-cohort discovery of transcriptional mechanisms presiding over maintenance of high-risk neuroblastoma subtype state |
|
| Relations |
| BioSample |
SAMN07682861 |
| SRA |
SRX3204208 |
