|
| Status |
Public on Jan 01, 2017 |
| Title |
RNA-seq on Dox-treated Tet-On HEXIM1-inducible A375 cells-3 |
| Sample type |
SRA |
| |
|
| Source name |
A375 melanoma cell line - HEXIM1-inducible
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: A375
|
| Treatment protocol |
One million HEXIM1-inducible A375 cells per condition were treated with DMSO or 1 μg/mL doxycycline. Drugs used were DMSO (Sigma) and doxycycline (Sigma).
|
| Growth protocol |
Human HEXIM1-inducible A375 malignant melanoma cells (ATCC) are grown on standard tissue culture plates in filter sterilized DMEM (Life Technologies) with 10% heat-inactivated FBS (Atlanta Biologicals), 1X GlutaMAX (Life Technologies) and 1% Penicillin-Streptomycin (Life Technologies).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
After 48 hrs, RNA was isolated using the RNeasy Plus Kit (Qiagen) and treated with the RiboZero Gold Kit (EpiCentre) to remove rRNAs.
The NEBNext multiplex oligos for Illumina Kit (NEB) was used to make the samples suitable for multiplexing. The PCR reaction was run for 15 cycles. The indexed libraries were size-selected for 300 bp fragments using Agencourt Ampure XP beads (Beckman Coulter). The concentration of the isolated libraries was estimated with a high-sensitivity DNA chip from Agilent according to manufacturer’s protocol and libraries were mixed in equal quantities and sequenced on Illumina Hi-Seq2000. Index sequences from multiplexed primers were used to identify treatment group and reads were demultiplexed using a perl script.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
HEXIM1-inducible Dox-3
|
| Data processing |
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using cutadapt, then mapped to hg19 whole genome using Tophat 2.0.11 without novel splicing form calls
Transcript abundance and differential expression were calculated with Cufflinks 2.2.1. FPKM values were used to normalize and quantify each transcripts
Genome_build: hg19
Supplementary_files_format_and_content: excel files include RPKM values for each Sample ...
|
| |
|
| Submission date |
Apr 20, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Leonard Zon |
| E-mail(s) |
zon@enders.tch.harvard.edu
|
| Organization name |
Boston Children's Hospital
|
| Department |
Oncology/Hematology
|
| Street address |
1 Blackfan Circle
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02115 |
| Country |
USA |
| |
|
| Platform ID |
GPL16791 |
| Series (2) |
| GSE68040 |
Nucleotide stress induction of HEXIM1 suppresses melanoma by modulating cancer cell-specific gene transcription [RNA-Seq2] |
| GSE68053 |
Nucleotide stress induction of HEXIM1 suppresses melanoma by modulating cancer cell-specific gene transcription |
|
| Relations |
| BioSample |
SAMN03492282 |
| SRA |
SRX1000215 |
