{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Frances Marks"],"organism":["Mycobacterium tuberculosis"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-16124"],"description":["This experiment was performed to transriptioally profile bacteria with a whiA conditional knockdown using CRISPR interference (CRISPRi). A conditional knockdown strain was treated with 0 or 500 ng/mL anhydrotetracycline (ATC) for 4 days, which turns on the CRISPRi machinery. RNA extraction was performed using Zymo RNA miniprep kit. Libraries were constructed using NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs) using 150 ng of input RNA. Libraries were amplified using 8 cycles on the thermocycler. Post amplification libraries were size selected ay 250-450 bp in length using SparQ beads. Libraries were validated using Bioanalyzer high sensitivity DNA analysis."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Sample Collection - Samples were collected by combining with 5M GTC, pelleting cells, and resuspending in trizol.","Library Construction - Libraries were constructed using NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs) using 150 ng of input RNA. Libraries were amplified using 8 cycles on the thermocycler. Post amplification libraries were size selected ay 250-450 bp in length using SparQ beads. Libraries were validated using Bioanalyzer high sensitivity DNA analysis.","Sample Treatment - Cells were treated with either 0 or 500 ng/mL Anhydrotetracycline (ATC)","Nucleic Acid Extraction - RNA extraction was performed using Zymo RNA miniprep kit","Growth Protocol - 7H9, 0.2% glycerol 10% OADC, 0.05% tyloxapol, 25  µg/mL kanamycin. Cells were cultured at 37C with 5% CO2","Sequencing - Paired end sequencing was performed used Illumina NovaSeq 6000"],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Sequence Alignment - Trimmed a filtered sequencing reads were mapped to the H37Rv reference genome (GenBank AL123456.3; RefSeq NC_000962.3; GCF_000195955.2; Genome assembly ASM19595v2)","Data Transformation - Raw read counts were done using featureCounts and normalized read counts were done using DESeq2"],"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["NA","Illumina NovaSeq 6000","Rstudio"],"study_type":["RNA-seq of coding RNA"],"species":["Mycobacterium tuberculosis"],"pubmed_authors":["Frances Marks"],"additional_accession":[]},"is_claimable":false,"name":"RNA-seq of an inducible whiA CRISPRi strain grown with 0 or 500 ng/mL anhydrotetracycline","description":"This experiment was performed to transriptioally profile bacteria with a whiA conditional knockdown using CRISPR interference (CRISPRi). A conditional knockdown strain was treated with 0 or 500 ng/mL anhydrotetracycline (ATC) for 4 days, which turns on the CRISPRi machinery. RNA extraction was performed using Zymo RNA miniprep kit. Libraries were constructed using NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs) using 150 ng of input RNA. Libraries were amplified using 8 cycles on the thermocycler. Post amplification libraries were size selected ay 250-450 bp in length using SparQ beads. Libraries were validated using Bioanalyzer high sensitivity DNA analysis.","dates":{"release":"2026-08-06T00:00:00Z","modification":"2026-08-06T21:36:09.514Z","creation":"2025-11-14T12:43:12.157Z"},"accession":"E-MTAB-16124","cross_references":{"ENA":["ERP184441"],"EFO":["EFO_0002944","EFO_0004170","EFO_0003789","EFO_0004917","EFO_0005518","EFO_0003816","EFO_0003738","EFO_0004184","EFO_0003969"]}}