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29 series

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Accession	Title	Series type(s)	Organism(s)	Samples	Supplementary	Contact	Release date
Filter		Expression profiling by high throughput sequencing	Escherichia coli		TSV
GSE155677	Multimodal profiling of the transcriptional regulatory landscape of the developing mouse cortex identifies Neurog2 as a key epigenome remodeler	Expression profiling by high throughput sequencing Genome binding/occupancy profiling by high throughput sequencing Methylation profiling by high throughput sequencing Other	Escherichia coli Mus musculus	36	BED BEDGRAPH BW FA MTX PICKLE TAR TSV TXT SRA Run Selector	Boyan Bonev	Jan 27, 2022
GSE174575	Bacterial Heterochromatin Formation Through Liquid-Liquid Phase Separation	Expression profiling by high throughput sequencing Genome binding/occupancy profiling by high throughput sequencing	Escherichia coli	36	BED CSV TSV SRA Run Selector	Lydia Freddolino	Dec 23, 2021
GSE211736	Joint epigenome profiling reveals cell-type-specific gene regulatory programs in human cortical organoids	Expression profiling by high throughput sequencing Other	Escherichia coli Homo sapiens Mus musculus	27	BW FA PICKLE TAB TSV TXT SRA Run Selector	Boyan Bonev	Aug 23, 2023
GSE164308	Landscape of transcriptional and translational changes over 22 years of bacterial adaptation	Expression profiling by high throughput sequencing Other	Escherichia coli	8	CSV TSV SRA Run Selector	Premal Shah	Jan 12, 2021
GSE188639	A single-cell massively parallel reporter assay detects cell type specific cis-regulatory activity	Expression profiling by high throughput sequencing Other	Escherichia coli Homo sapiens Mus musculus	19	CSV MTX TSV	SIQI ZHAO	Nov 11, 2021
GSE216481	A Transcription Factor Atlas of Directed Differentiation	Expression profiling by high throughput sequencing Genome binding/occupancy profiling by high throughput sequencing Other	Escherichia coli Homo sapiens Lentivirus	281	CSV MTX TSV	Julia Joung	Jan 05, 2023
GSE271571	Decoding the Escherichia coli epitranscriptome	Expression profiling by high throughput sequencing	Escherichia coli Escherichia coli str. K-12 substr. MG1655	4	FASTA TSV TXT	Kirsten Jung	Feb 21, 2025
GSE142291	Dynamic landscape of protein occupancy across the Escherichia coli chromosome	Expression profiling by high throughput sequencing Genome binding/occupancy profiling by high throughput sequencing	Escherichia coli Escherichia coli str. K-12 substr. MG1655	52	GR TSV SRA Run Selector	Lydia Freddolino	Jun 15, 2021
GSE96573	Reduced protein expression in a virus attenuated by codon deoptimization	Expression profiling by high throughput sequencing	Escherichia coli	27	TSV SRA Run Selector	Claus Wilke	Jul 30, 2017
GSE104303	Chaperone saturation mediates translation and protein folding efficiency	Other Expression profiling by high throughput sequencing	Escherichia coli Escherichia coli str. K-12 substr. MG1655	30	TSV SRA Run Selector	Vincent J Hilser	Oct 27, 2024
GSE111874	Escherichia coli Lrp regulates one-third of the genome via direct, cooperative, and indirect paths	Genome binding/occupancy profiling by high throughput sequencing Expression profiling by high throughput sequencing	Escherichia coli	108	TSV SRA Run Selector	Peter Freddolino	Nov 28, 2018
GSE123854	Transcript degradation and codon usage as gene regulation in a lytic phage	Expression profiling by high throughput sequencing	Escherichia coli Escherichia phage T7	30	TSV SRA Run Selector	Claus Wilke	May 01, 2019
GSE125110	Complete genome sequence of Escherichia coli C - old model organism with a new application in biofilm research	Expression profiling by high throughput sequencing	Escherichia coli	6	TSV TXT SRA Run Selector	Joshua P Earl	Jan 01, 2020
GSE126081	Transcriptome profiling in an Escherichia coli strain collection	Expression profiling by high throughput sequencing	Escherichia coli	252	TSV SRA Run Selector	Pedro Beltrao	Mar 01, 2022
GSE132637	RNAseq transcriptome analysis of K. pneumoniae MS6671 and E. coli MS8345 treated with PBT2	Expression profiling by high throughput sequencing	Escherichia coli Klebsiella pneumoniae	12	TSV TXT SRA Run Selector	David Manuel Pereira De Oliveira	Jun 13, 2019
GSE161708	Differential transcription in E. coli WT vs. fum null mutants in response to DNA damage induction	Expression profiling by high throughput sequencing Non-coding RNA profiling by high throughput sequencing	Escherichia coli	45	TSV ZIP SRA Run Selector	Ophry Pines	Nov 19, 2020
GSE180237	Bacterial droplet-based single-cell RNA-seq reveals antibiotic-associated heterogeneous cellular states	Expression profiling by high throughput sequencing	Enterococcus faecalis Escherichia coli Klebsiella pneumoniae Pseudomonas aeruginosa	35	TSV TXT SRA Run Selector	Peijun Ma	Jan 27, 2023
GSE205240	Transcriptional profiling of extraintestinal Escherichia coli exposed to cranberry pomace extracts alone or in combination with ceftriaxone	Expression profiling by high throughput sequencing	Escherichia coli	12	TSV	Dion Lepp	Jun 01, 2023
GSE215798	Stress response in Escherichia coli following sublethal phenalene-1-one mediated antimicrobial photodynamic therapy: an RNA-Seq study	Expression profiling by high throughput sequencing	Escherichia coli	20	TSV	Stefan Czemmel	Sep 23, 2024
GSE223493	Plasticity and stereotypic rewiring of the transcriptome upon bacterial evolution of antibiotic resistance	Expression profiling by high throughput sequencing	Escherichia coli	27	TSV	Gabor Grezal	Jan 26, 2023