|
| Status |
Public on Mar 26, 2019 |
| Title |
RNA-seq_THZ_2h_1 |
| 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 2 and 6 hours in the presence of DMSO or THZ531 (400nM) 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 |
polyA RNA |
| Extraction protocol |
Biological duplicated were collected and RNA extraction was performed with TRIzol (Ambion) following the manufacturers’ instructions. Total RNA was treated with DNase I (Invitrogen).
Sequencing libraries were prepared with the RNA-seq library kit (QuantSeq 3’ mRNA Sequencing REV, Lexogen) following the manufacturers’ instructions.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
processed data files:
all_quantseq_peaks.narrowPeak
IMR_quantseq_THZ_2h.selected_forwardCov.bw
IMR_quantseq_THZ_2h.selected_reverseCov.bw
|
| Data processing |
Single-end 100bp reads were filtered with bbduk.sh and parameters “k=13 ktrim=r useshortkmers=t mink=5 qtrim=r trimq=20 minlength=75 ref=truseq_rna.fa.gz”
STAR (v2.5.1b) was used to align reads to the human genome (GRCh38) with the following parameters “--outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.1 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outSAMattributes NH HI NM MD --outSAMtype BAM SortedByCoordinate”.
Strand specific coverage profiles were created with the bamCoverage command (DeepTools v2.5.4) with parameters “--normalizeUsingRPKM –filterRNAstrand –bs 50".
Biological replicates were merged using "samtools merge" and processed as described for the individual replicates.
PolyA-seq peaks were called using MACS2 (v 2.1.1) and parameters “--nomodel --extsize 100 --shift 0”.
Genome_build: GRCh38
Supplementary_files_format_and_content: Peaks and 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) |
| GSE113312 |
PolyA-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 |
SAMN08947187 |
| SRA |
SRX3960759 |
