|
| Status |
Public on May 23, 2021 |
| Title |
THP-1 sgSCR untreated replicate 2 |
| Sample type |
SRA |
| |
|
| Source name |
Acute myeloid leukemia cell line expressing Cas9 and non-targeting (Scramble) sgRNA
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: THP-1 cell line
genotype: expressing Cas9 and non-targeting (Scramble) sgRNA
treatment: Untreated control
|
| Treatment protocol |
THP-1 cells were treated with LPS (1µg/mL) over a time-course and HT-29 cells were treated with CDK9i (AZ5576, 170nM, 2 hours), DBK-1154 (10µM, 2 hours 15 minutes) or a combination of both
|
| Growth protocol |
Cells were cultured in RPMI-1640 supplemented with 10-20 percent heat-inactivated fetal bovine serum, 100U/mL penicillin, 100µg/mL streptomycin and 2mM GlutaMAX at 37 degrees celciuus and 5 percent carbon dioxide
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were lysed in TriZol reagent and total DNAse-treated RNA isolated using the Zymogen RNA mini-prep kit. For HT-29 cells, total RNA (5 percent) from Drosophila S2 cells was spiked into each human RNA sample.
RNA libraries were prepared using the Lexogen QuantSeq 3'-mRNA Seq Library Prep kit (015)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
SCR-UT-2_S37
LPS_WT_vs_KO_normalizedcounts.csv
counts_LPS.txt
|
| Data processing |
Sequenced reads were demultiplexed using bcl2fastq (v2.17.1.14)
Basic QC performed on fastq files using FASTQC (v0.11.6)
Sequencing reads were trimmed using cutadapt (v2.1) and aligned to the Hg19 or a combined Hg19/dm3 reference genome using HISAT 2 (v2.1.0)
Read counting across genomic regions was performed using the Subread (v2.0.0) featureCounts function and differential gene expression analysis was performed in Rstudio (v3.6.1) using Voom-Limma (v3.42.2)
Genome_build: Hg19 and dm3
Supplementary_files_format_and_content: Tag density files (TDF) of 3'UTR RNA coverage across the Hg19 genome; text files of featureCounts counts; text file of normalized (voom) and normalized (voom and S2 spike-in) counts
|
| |
|
| Submission date |
Dec 24, 2020 |
| Last update date |
May 23, 2021 |
| Contact name |
Stephin J Vervoort |
| E-mail(s) |
[email protected]
|
| Organization name |
Peter MacCallum Cancer Centre
|
| Street address |
305 Grattan Street
|
| City |
Melbourne |
| ZIP/Postal code |
3000 |
| Country |
Australia |
| |
|
| Platform ID |
GPL18573 |
| Series (2) |
| GSE163802 |
A PP2A-Integrator complex fine-tunes transcription by opposing CDK9 [3UTR-seq] |
| GSE163805 |
A PP2A-Integrator complex fine-tunes transcription by opposing CDK9 |
|
| Relations |
| BioSample |
SAMN17151440 |
| SRA |
SRX9730696 |
