|
| Status |
Public on Mar 26, 2019 |
| Title |
IMR_THZ_2h_2 |
| Sample type |
SRA |
| |
|
| Source name |
IMR32 cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: IMR32
treatment: THZ531 2h
cancer: Neuroblastoma
|
| Treatment protocol |
Cells were incubated for 30min and 2 hours in the presence of DMSO or THZ531 (400nM) and labeled in media for 10 min with 500 μM 4-thiouridine before performing RNA extraction.
|
| Growth protocol |
IMR-32 cells were grown in RPMI-1640 media supplemented with 10% fetal bovine serum and 1% penicillin/streptomycin
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA extraction was performed with TRIzol (Ambion) following the manufacturers’ instructions. Total RNA was treated with DNase I (Invitrogen). Subsequently, the purified RNA was fragmented on a BioRuptor Next Gen (Diagenode) at high power for one cycle of 30’’/30’’ ON/OFF.
Sequencing libraries were prepared with the RNA-seq library kit (TruSeq Stranded Total RNA RiboZero Gold, Illumina)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
nascent RNA
processed data files:
IMR_THZ_2h_forwardCov.bw
IMR_THZ_2h_reverseCov.bw
IMR_THZ_2h_2_forwardCov.bw
IMR_THZ_2h_2_reverseCov.bw
|
| Data processing |
Paired-end 75bp reads were mapped to the human genome (GRCh38) concatenated with ERCC spike-in sequences using STAR (v2.5.1b) and default parameters.
Properly mapped reads were extracted using samtools (v1.3.1) and parameters “-q 7 and –f 83,99,147,163”.
Library size normalization was based on individual spike-in reads counted with samtools idxstats and used as input for estimateSizeFactorsForMatrix (DESeq2).
Strand specific coverage files were created with bamCoverage (DeepTools v2.5.4) with previously calculated sizefactors and parameters “--scaleFactor --normalizeUsingRPKM –filterRNAstrand –bs 100".
Biological replicates were merged using "samtools merge" and processed as described for the individual replicates.
Genome_build: GRCh38
Supplementary_files_format_and_content: bigWig coverage files for both individual replicates and merged replicates.
|
| |
|
| Submission date |
Apr 18, 2018 |
| Last update date |
Mar 26, 2019 |
| Contact name |
Ruben Dries |
| E-mail(s) |
[email protected]
|
| Organization name |
DFCI
|
| Department |
Computational Biology
|
| Lab |
Longwood Center
|
| Street address |
360 Longwood Ave
|
| City |
Boston |
| ZIP/Postal code |
02215 |
| Country |
USA |
| |
|
| Platform ID |
GPL18573 |
| Series (2) |
| GSE113313 |
Nascent RNA sequencing in IMR-32 cells treated with THZ531 or DMSO |
| GSE113314 |
Gene expression profiling in neuroblastoma cell lines treated with THZ531 or DMSO |
|
| Relations |
| BioSample |
SAMN08947178 |
| SRA |
SRX3960752 |
