|
| Status |
Public on Mar 26, 2019 |
| Title |
IMR_CDK13_sh701_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
IMR_CDK13_sh701
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: IMR-32
cell type: neuroblastoma cells
treatment: CDK13 sh701
|
| Treatment protocol |
pLKO.1 plasmids containing shRNA sequences targeting CDK12 and CDK13 were obtained from the RNAi Consortium of the Broad Institute (Broad Institute, Cambridge, MA); Briefly, the constructs were transfected into HEK293T cells with helper plasmids: pCMV-dR8.91 and pMD2.G-VSV-for virus production. Cells were then transduced with virus, followed by puromycin selection for two days.
|
| 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 file:
all_IMR_CDK_KD_sub_peaks.narrowPeak
IMR_polyA_CDK13_sh_forwardRawCov.bw
IMR_polyA_CDK13_sh_reverseRawCov.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 merged replicates.
|
| |
|
| Submission date |
Nov 08, 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) |
| GSE113314 |
Gene expression profiling in neuroblastoma cell lines treated with THZ531 or DMSO |
| GSE122304 |
PolyA-sequencing in IMR-32 neuroblastoma cells with shRNA mediated depletion of CDK12, CDK13 or GFP. |
|
| Relations |
| BioSample |
SAMN10395182 |
| SRA |
SRX4995115 |
