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Escherichia coli cells: sorted vs. non-sorted

ABSTRACT: Transcription profile of sorted Escherichia coli cells was compared to that of non-sorted cells to evaluate the effect of sorting process on transcriptome of E. coli. E. coli cells were harvest from planktonic cultures in annular reactor and stored in RNAlater. Sorting includes 2-min homogenization with OMNI TH homogenizer on ice for E. coli cells pre-stored in RNAlater and then resuspended in nuclease free phosphate buffered saline for sorting with one-step immuno-magnetic separation with anti-E. coli antibody and microbeads on a MACS separator (Miltenyi, Auburn, CA).

ORGANISM(S): Escherichia coli

PROVIDER: GSE22885 | GEO | 2010/07/13

SECONDARY ACCESSION(S): PRJNA128143

REPOSITORIES: GEO

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Escherichia coli cells: sorted vs. non-sorted

Project description:Transcription profile of sorted Escherichia coli cells was compared to that of non-sorted cells to evaluate the effect of sorting process on transcriptome of E. coli. E. coli cells were harvest from planktonic cultures in annular reactor and stored in RNAlater. Sorting includes 2-min homogenization with OMNI TH homogenizer on ice for E. coli cells pre-stored in RNAlater and then resuspended in nuclease free phosphate buffered saline for sorting with one-step immuno-magnetic separation with anti-E. coli antibody and microbeads on a MACS separator (Miltenyi, Auburn, CA). Two condition experiments: sorted vs non-sorted. Two biological replicates with individually grown and harvested E. coli cells. Each biological replicate has two technical replicates of labeling and hybridization on microarray slides. Each slide has three built-in replicates for each probe.

2010-07-13 | E-GEOD-22885 | biostudies-arrayexpress

RNA-Seq of sorted and unsorted prophage-induced subpopulations in Corynebacterium glutamicum

Project description:Cells were treated as described in the material and methods section of the manuscript. Briefly, RNA-seq experiments were performed with sorted populations with an size of about 10_E6 Corynebacterium glutamicum cells. As a reference data set RNA-Seq. analysis of unsorted cells were conducted (n=3, induced vs uninduced =2, 2 x 3 = 6 data sets). For the sorting and the counter-silencer based prophage induction, RNAprotect and RNAlater were used and for each agent data sets with two biological relicates were generated (n = 2, RNAprotect + RNAlater = 2, induced vs uninduced = 2, 2 x 2 x 2 = 8 data sets). One data set was generated using 10_E5 cells (n = 1, induced vs uninduced =2, 2 x 1 = 2 data sets) For the subpopulation caused by iron-shift experiments RNAprotect was used (n = 3, positive vs negative, 3 x 2 = 6 data sets). In sum 26 data sets are uploaded. Each consist of two fastq files (due to paired-end sequencing).

2018-09-15 | E-MTAB-6809 | biostudies-arrayexpress

Project description:Tap water biofilms grown in annular reactor Metagenome

| PRJNA715820 | ENA

LC-MS/MS of mouse hepatocytes sorted by lobule layers

Project description:Hepatocytes of the mammalian liver are organized in liver lobules and operate in a spatially-dependent manner. Cells in different positions along the lobule’s porto-cenrtal axis, defined by the directionality of blood flow, express different genes and perform different liver tasks. Gradients of the transcriptome along liver lobule axis has been recently established, yet not for the hepatocyte proteome. We used two surface markers whose levels are inversely zonated – CD73 with a decreasing gradient from pericentral to periportal hepatocytes and E-cadherin with increasing gradient from portal to central hepatocytes. By staining for both surface markers, we efficiently isolated bulk populations of hepatocytes from distinct lobule layers by Fluorescence Activated Cell Sorting (FACS). Over all, we sorted 100,000 hepatocytes from each of eight spatially distinct populations, from five different mice. Cells were washed, digested by trypsin and subjected to LC-MS/MS. More cells from same populations from the same mice were also collected for mRNA sequencing and microRNA microarray profiling, to achieve a multi-omic view on spatially sorted hepatocytes, for better understanding of the transcriptomic and post-transcriptomic levels of regulation of liver zonation.

2019-08-06 | PXD014512 | Pride

Homo sapiens

Project description:Prognostic gene signatures can be measured with samples stored in RNAlater

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Prognostic gene signatures can be measured with samples stored in RNAlater

Project description:A number of breast or colon specific genes predictive of the relapse status were used in comparing the outcome from matched fresh frozen and stored in RNAlater preservative. Keywords: disease state analysis

2005-12-06 | GSE3726 | GEO

RNA-seq of Escherichia coli MG1655 and SR under fluctuating ammonia availability (limitation-depletion)

Project description:In large-scale production processes, metabolic control is typically achieved by limited supply of essential nutrients like ammonia. With increasing bioreactor dimensions, microbial producers such as Escherichia coli are exposed to changing substrate availabilities due to limited mixing. In turn, cells sense and respond to these dynamic conditions leading to frequent activation of their regulatory programs which result in production yield losses. This study is focused on transcriptional changes due to fluctuating ammonia supply, while sampling a continuously running two-compartment bioreactor system comprising a stirred tank reactor (STR) and a plug flow reactor (PFR). A previously created mutant E.coli SR was used to limit the reaction to environmntal influences via knock-out of stringent response. E. coli WT revealed highly diverging short-term transcriptional responses in ammonia fluctuation compared E. coli SR.

2021-05-05 | GSE158198 | GEO

FACS sorted podocytes, mesangial cells

Project description:FACS sorted glomerular kidney cells from a single mouse were subjected to proteomics.

2022-10-13 | PXD016237 | Pride

RNA-seq of Escherichia coli under fluctuating ammonia availability (limitation-depletion)

Project description:In large-scale production processes, metabolic control is typically achieved by limited supply of essential nutrients like glucose or ammonia. With increasing bioreactor dimensions, microbial producers such as Escherichia coli are exposed to changing substrate availabilities due to limited mixing. In turn, cells sense and respond to these dynamic conditions leading to frequent activation of their regulatory programs. Previously, we characterized short- and long-term strategies of cells to adapt to glucose fluctuations. Here, we focused on fluctuating ammonia supply, while studying a continuously running two-compartment bioreactor system comprising a stirred tank reactor (STR) and a plug flow reactor (PFR). Genes were repeatedly switched on/off when E. coli returned to the STR. Moreover, E. coli revealed highly diverging long-term transcriptional responses in ammonia compared to glucose fluctuations. The identification of target genes may help to create robust cells and processes for large-scale application.

2017-03-27 | GSE90743 | GEO

Comparison of sample preservation methods for field collection of animal-microbe symbioses for metaproteomic analyses

Project description:When studying gene expression in microbe-animals symbioses collected in the field it is essential to quickly and efficiently preserve in situ symbiont and host gene expression patterns. One of the most commonly used sample preservation methods for samples targeted for proteomic analyses is flash freezing, however, liquid nitrogen or dry ice needed for flash freezing are often not available at remote field sites. We tested if RNAlater allows to preserve proteins in animal-microbe symbioses as efficiently as flash freezing and without introducing issues with downstream processing. We used the marine gutless oligochaete Olavius algarvensis as a model for testing. Olavius algarvensis lives in shallow water sediments off the coast of Elba, Italy. It has no digestive and excretory system and harbors five bacterial symbionts that fulfill its nutritional and waste recycling needs (Kleiner et al., 2012, PNAS 109(19):1173-82). We compared five RNAlater preserved and five flash frozen samples in terms of the number of identified proteins, abundances of individual proteins and potential biases against specific protein or taxonomic groups. Five worms were incubated in RNAlater for 24 hours. After incubation, RNAlater was removed and samples were stored at -80°C. The remaining five worms were preserved with liquid nitrogen and stored at -80 °C immediately after preservation.

2021-11-03 | PXD014591 | Pride

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