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| Status |
Public on May 11, 2021 |
| Title |
QuantSeq_RNAseq_MM1S_NCOR1_sgRNA2_DMSO_6hours_replicate2 |
| Sample type |
SRA |
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| Source name |
Multiple Myeloma
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| Organism |
Homo sapiens |
| Characteristics |
cell line: MM1.S
timepoint: 6 hours
treatment+dose: DMSO
ectopic expression: FU-Cas9-Cherry + NCOR1 sgRNA
rna library prep: 3'-mRNA (QuantSeq)
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| Treatment protocol |
Samples were treated in biological duplicate or triplicate in the presence of small molecule inhibitors, as indicated.
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| Growth protocol |
Cells were grown in vitro under standard culture conditions
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| Extracted molecule |
total RNA |
| Extraction protocol |
For 3'-mRNA-seq (QuantSeq), Cells were collected and washed once with ice-cold PBS prior to resuspension in TRIzol™ (ThermoFisher Scientific, 15596026). RNA was isolated using the Direct-zol RNA MiniPrep kit (Zymo Research, R2052) according to the manufacturers instructions. Sequencing libraries were prepared from 500ng RNA using the QuantSeq 3’-mRNA Seq Library Prep Kit for Ilumina (Lexogen, Vienna, Austria). Libraries were sequenced on the Illumina NextSeq 500 to obtain 75 b.p. single-end reads.
For Total RNA-seq, Total RNA was immediately extracted using TRIzol reagent (ThermoFisher Scientific, 15596026) and isolated using the Direct-zol RNA MiniPrep kit (Zymo Research, R2052). Libraries were prepared with NEBNext Ultra II Directional RNA Library Prep Kit for Ilumina (NEB, E7760S) with ribosomal RNA depletion and sequenced on an Ilumina NextSeq 500 with 75 b.p. single-end reads.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| Description |
RNAseq_Counts_MM1S_NCOR1_KO_featureCounts_unnormalized.txt
MM1-NCOR1-2-DMSO-2
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| Data processing |
For 3'-mRNA-seq (QuantSeq), Sequencing files were demultiplexed using Bcl2fastq (v2.17.1.14) to generate FASTQ files on which QC was performed using FASTQC (v0.11.5). Sequencing reads were trimmed using cutadapt (v1.7) and aligned to the human reference genome (Hg19) using HISAT2 (v2.1.0).
Fo 3'-mRNA-seq (QuantSeq), Read counting across genomic features was performed using featureCounts prior to differential gene expression analysis using limma voom. Gene set enrichment analyses were performed using GSEA software (Broad Institute) and enrichment plots were plotted using replotGSEA.R.
For Total RNA-seq, Sequencing files were demultiplexed using Bcl2fastq (v2.17.1.14) to generate FASTQ files on which QC was performed using FASTQC (v0.11.5). Sequencing reads were trimmed using cutadapt (v1.7) and aligned to the human reference genome (Hg19) using HISAT2 (v2.1.0). Read counting across genomic features was performed using featureCounts v1.5.0 (Liao et al., 2014) prior to differential gene expression analysis using limma voom (Law et al., 2014).
For Total RNA-seq, Pre-ranked gene set enrichment analyses were performed using GSEA software (Broad Institute) against the Molecular Signatures Database (MSigDB) collection, and enrichment plots were plotted using replotGSEA.R (part of the Rtoolbox R package).Analysis of core transcriptional regulatory circuitries was performed by using MM1.S and HeLa specific gene sets previously described (Huang et al., 2018) and normalized RNA-seq count (normalized CPM) values in Rstudio.
Genome_build: HG19
Supplementary_files_format_and_content: Gene Expression Counts
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| Submission date |
May 11, 2021 |
| Last update date |
May 12, 2021 |
| Contact name |
Simon J Hogg |
| Organization name |
AbbVie
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| Department |
Oncology Discovery Research
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| Street address |
1000 Gateway Boulevard
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| City |
South San Francisco |
| State/province |
California |
| ZIP/Postal code |
94080 |
| Country |
USA |
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| Platform ID |
GPL18573 |
| Series (2) |
| GSE172051 |
Targeting P300/CBP reveals discrete regulation of transcription and chromatin accessibility by histone acetylation |
| GSE174266 |
Targeting P300/CBP reveals discrete regulation of transcription and chromatin accessibility by histone acetylation [RNAseq] |
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| Relations |
| BioSample |
SAMN19109143 |
| SRA |
SRX10844146 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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