{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Thomas MERCHER"],"organism":["Homo sapiens"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-14189"],"description":["Cells lines expressing the ETO2-GLIS2 oncogene (M07e and WSU-AML) were transduced with an shRNA against Renilla or DLX3 and a GFP reporter. After 48H, cells were sorted on GFP and RNA was extracted. Then library were prepared follow by sequencing."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Sequencing - 50-bp paired-end sequencing was performed using the Illumina technology.","Nucleic Acid Extraction - Cells were lysed and RNA extract using RNeasy MiniKit (Qiagen).","Sample Collection - GFP positive cells were sorted 48H after doxycycline induction (500 ng/mL).","Library Construction - cDNA libraries were synthesized from 250 ng total RNA using TruSeq Strandard mRNA Kit (Illumina). Libraries were verified for their amount and quality by capillary electrophoresis using a 2100 Bioanalyzer (Agilent Technologies)."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Sequence Alignment - Poor quality reads removal and reads trimming were performed using Trim Galore (v0.6.6) with the command : trim_galore --output_dir ${pathrepertorytrimmgalore}/output_fastq_trimmgalore \\\\ --basename $basefastqpref \\\\ --phred33 \\\\ --fastqc \\\\ --quality 20 \\\\ --paired \\\\ --cores $NbThread \\\\ $fastqpref$suffixeR1 $fastqpref$suffixeR2  Then, the quantification of reads was performed using Salmon (v0.14.2). The following code was used to performed this task : salmon quant -i $salmon_index \\\\ --threads $nbThread \\\\ --seqBias \\\\ --gcBias \\\\ -l A \\\\ -1 ${arrayfastq[$i]}$extR1 \\\\ -2 ${arrayfastq[$i]}$extR2 \\\\ -o ${pathresults}/${arrayfastq[$i]} \\\\ --validateMappings  Of note, the index was generated using the following code : Salmon index -t gentrome.fa -i human_97_ensembl_salmon_0142_decoys_index --decoys decoys.txt  -k 31 The decoy-aware transcriptome file used to generate the salmon index was downloaded at the following adress : https://drive.google.com/drive/folders/1SW3hO_pnxcTWm7OZHYA9P9qPirevodjU (Ensembl, release 97 human).","Data Transformation - The normalization was performed using the R software (v4.2.1). Transcript abundance files (.sf files) were imported in R with tximport using the following code line : txi <- tximport(files,type = \\\\\"salmon\\\\\",txOut = FALSE,tx2gene=tx2gene,ignoreTxVersion=TRUE)  Of note the tx2gene dataframe used as value of the argument tx2gene has been generated using the function makeTxDbFromGFF (package GenomicFeatures) with the GTF file Homo_sapiens.GRCh38.97.gtf.  The DESeqDataSet class object used for the DESeq2 analysis was generated using the function DESeqDataSetFromTximport. Only genes with at least 10 associated counts were kept for the DESeq2 analysis.   Normalization was performed with the following code lines : dds <- estimateSizeFactors(dds) normalized_counts <- counts(dds, normalized=TRUE)  VST transformation was performed using the code : vst(dds, blind=FALSE)"],"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["Illumina HiSeq 4000"],"study_type":["RNA-seq of coding RNA"],"species":["Homo sapiens"],"pubmed_authors":["Thomas MERCHER","Elie ROBERT"],"additional_accession":[]},"is_claimable":false,"name":"Transcriptional effect of DLX3 transcription factor inhibition by shRNA in ETO2-GLIS2 cell lines","description":"Cells lines expressing the ETO2-GLIS2 oncogene (M07e and WSU-AML) were transduced with an shRNA against Renilla or DLX3 and a GFP reporter. After 48H, cells were sorted on GFP and RNA was extracted. Then library were prepared follow by sequencing.","dates":{"release":"2025-07-09T00:00:00Z","modification":"2025-07-09T16:01:36.849Z","creation":"2024-06-20T16:11:59.574Z"},"accession":"E-MTAB-14189","cross_references":{"ENA":["ERP161323"],"Biostudies":["E-MTAB-14190","E-MTAB-14188"],"EFO":["EFO_0002944","EFO_0004170","EFO_0004917","EFO_0005518","EFO_0003816","EFO_0003738","EFO_0004184"]}}