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Effects of fixation on natural microbial community metatranscriptomes

ABSTRACT: Testing the short term and long term effects of fixation on natural marine microbial community metatranscriptomes

PROVIDER: PRJEB23003 | ENA |

REPOSITORIES: ENA

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Metatranscriptomes

Project description:Metatranscriptomes

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AR in metatranscriptomes

Project description:Mining microbial metatranscriptomes for expression of antibiotic resistance genes under natural conditions

| PRJEB7599 | ENA

Metatranscriptomes of phytoplankton blooms from an ocean acidification mesocosm experiment

Project description:Sequencing the metatranscriptome can provide information about the response of organisms to varying environmental conditions. We present a methodology for obtaining random whole-community mRNA from a complex microbial assemblage using Pyrosequencing. The metatranscriptome had, with minimum contamination by ribosomal RNA, significant coverage of abundant transcripts, and included significantly more potentially novel proteins than in the metagenome. Keywords: metatranscriptome, mesocosm, ocean acidification This experiment is part of a much larger experiment. We have produced 4 454 metatranscriptomic datasets and 6 454 metagenomic datasets. These were derived from 4 samples. The experiment is an ocean acidification mesocosm set up in a Norwegian Fjord in 2006. We suspended 6 bags containing 11,000 L of sea water in a Coastal Fjord and then we bubbled CO2 through three of these bags to simulate ocean acidification conditions in the year 2100. The other three bags were bubbled with air. We then induced a phytoplankton bloom in all six bags and took measurements and performed analyses of phytoplankton, bacterioplankton and physiochemical characteristics over a 22 day period. We took water samples from the peak of the phytoplankton bloom and following the decline of the phytoplankton bloom to analyses using 454 metagenomics and 454 metatranscriptomics. Day 1, High CO2 Bag and Day 1, Present Day Bag, refer to the metatranscriptomes from the peak of the bloom. Day 2, High CO2 Bag and Day 2, Present Day Bag, refer to the metatranscriptomes following the decline of the bloom. Obviously High CO2 refers to the ocean acidification mesocosm and Present Day refers to the control mesocosm. Raw data for both the metagenomic and metatranscriptomic components are available at NCBI's Short Read Archive at ftp://ftp.ncbi.nlm.nih.gov/sra/Studies/SRP000/SRP000101

2008-02-08 | E-GEOD-10119 | biostudies-arrayexpress

Natural Orifice Transluminal Endoscopic Surgery for Colorectal Cancer

Project description:The purpose of this study is to assess different hybrid natural orifice transluminal endoscopic surgery techniques in management of colorectal cancer as regard: feasibility of the technique, short term oncologic outcome and functional outcome.

| 2198083 | ecrin-mdr-crc

Single-Cell Transcriptome Analysis of Acute Myeloid Leukemia Cells Using Methanol Fixation and Cryopreservation

Project description:Introduction: The application of single-cell RNA sequencing has greatly improved our under-standing of various cellular and molecular mechanisms involved in physiological and pathophysi-ological processes. However, obtaining living cells for this technique can be difficult under certain conditions. To solve this problem, the methanol fixation method appeared as a promising alternative for routine clinical use. Materials and Methods: In this study, we selected two AML samples that had been fixed in methanol for 12–18 months. Once the cells were rehydrated, these samples were subjected to single-cell RNA sequencing. We then compared the results obtained from these samples with those obtained from the same samples cryopreserved in DMSO. Results: We used a previously validated methanol fixation protocol to perform scRNA-seq on DMSO cryopreserved cells and cells fixed in methanol for more than one year. Preliminary results show that methanol fixation induces some genetic and transcriptional modification compared with DMSO cryopreservation but remains a valuable method for single-cell analysis of primary human leukemia cells. Conclusions: The initial findings from this study highlight certain resemblances in methanol fixation over a 12-month period and cryopreservation with DMSO, along with associated transcriptional level modifications. However, we observed genetic degradation in the fixation condition when extending beyond one year. Despite certain study limitations, it is evident that short-term methanol fixation can be effec-tively used for leukemia blast samples. Its ease of implementation holds the potential to simplify the integration of this technique into routine clinical practice.

2023-08-17 | GSE237239 | GEO

CO2-fixation bacterial

Project description:CO2-fixation bacterial Metagenome

| PRJNA757792 | ENA

Red Sea coral metatranscriptomes

Project description:Red Sea coral metatranscriptomes

| PRJNA638633 | ENA

Aspo HRL metatranscriptomes

Project description:Aspo HRL metatranscriptomes Raw sequence reads

| PRJNA541524 | ENA

Anode respiration-dependent biological nitrogen fixation by Geobacter sulfurreducens

Project description:Our study revealed a synergistic effect between biological nitrogen fixation and current generation by G. sulfurreducens, providing a green nitrogen fixation alternative through shifting the nitrogen fixation field from energy consumption to energy production and having implications for N-deficient wastewater treatment.

2021-10-09 | GSE185414 | GEO

Transcriptional profile of Escherichia coli K12 strain DH10B harboring A1501 nitrogen fixation island (NFI) under nitrogen fixation conditions

Project description:A1501 NFI is a genomic island derived from Pseudomonas stutzeri A1501. To study the molecular interactions of the P. stutzeri nif genes with the E. coli genome during nitrogen fixation, the NIF of A1501 was transferred into E. coli and comparative transcriptomics analyses were performed between nitrogen fixation conditions and nitrogen excess conditions.

2015-08-05 | GSE37780 | GEO

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