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BaM-seq and TBaM-seq, highly multiplexed and targeted RNA-seq protocols for rapid, low-cost library generation from bacterial samples [TBaM-seq]

ABSTRACT: Here, we report the development of two RNA-seq library preparation protocols that increase the throughput and decrease the cost of converting RNA to cDNA libraries compatible for sequencing on high-throughput platforms. BaM-seq allows for early barcoding of samples such that many biological samples can be processed simultaneously. TBaM-seq allows for enrichment of target RNAs to decrease the required sequencing depth. Both methods are able to accurately measure gene expression changes with high technical reproducibility and agreement with gold standard, lower throughput approaches.

ORGANISM(S): Bacillus subtilis

PROVIDER: GSE206424 | GEO | 2023/02/01

REPOSITORIES: GEO

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BaM-seq and TBaM-seq, highly multiplexed and targeted RNA-seq protocols for rapid, low-cost library generation from bacterial samples [BaM-seq]

Project description:Here, we report the development of two RNA-seq library preparation protocols that increase the throughput and decrease the cost of converting RNA to cDNA libraries compatible for sequencing on high-throughput platforms. BaM-seq allows for early barcoding of samples such that many biological samples can be processed simultaneously. TBaM-seq allows for enrichment of target RNAs to decrease the required sequencing depth. Both methods are able to accurately measure gene expression changes with high technical reproducibility and agreement with gold standard, lower throughput approaches.

2023-02-01 | GSE206423 | GEO

Hungarian BAM files

Project description:Hungarian BAM files

| PRJEB20905 | ENA

Sequencing coliphage Bam

Project description:Sequencing coliphage Bam

| PRJEB49062 | ENA

Transcription profiling of Drosophila ovaries from bam mutant and stwl bam double mutant females

Project description:Abstract: During Drosophila oogenesis, germline stem cell (GSC) identity is maintained largely by preventing the expression of factors that promote differentiation. This is accomplished via the activity of several genes acting either in the GSC or its niche. The translational repressors, Nanos and Pumilio, act in GSCs to prevent differentiation, likely by inhibiting translation of early differentiation factors, while niche signals prevent differentiation by silencing transcription of the differentiation factor Bam. We have found that the DNA-associated protein Stonewall (Stwl) is also required for GSC maintenance. stwl is required cell-autonomously; clones of stwl- germ cells were lost by differentiation, and ectopic Stwl caused an expansion of GSCs. stwl mutants acted as Suppressors of Variegation, indicating stwl normally acts in chromatin-dependent gene repression. In contrast to several previously described GSC maintenance factors, Stwl likely functions epigenetically to prevent GSC differentiation. Stwl-dependent transcriptional repression does not target bam, but rather Stwl represses the expression of many genes, including those that may be targeted by Nanos/Pumilio translational inhibition. Experiment Overall Design: Genetic variation comparison between germ cells of Drosophila ovaries from bam mutant and stwl bam double mutant females. Six total samples were analyzed, with each genotype performed in triplicates.

2008-03-13 | E-GEOD-6928 | biostudies-arrayexpress

XL-MS data of BAM and SurA binding

Project description:We present XL-MS data of the BAM:SurA complex to define the interaction sites for SurA on BAM

2022-07-12 | PXD030209 | Pride

HDX-MS data of BAM and SurA binding

Project description:We present HDX-MS data of the BAM:SurA complex to define the interaction sites for SurA on BAM and vice versa.

2022-07-12 | PXD030268 | Pride

OnePot-seq and OPT-seq, highly multiplexed and targeted RNA-seq protocols for rapid, low-cost library generation

Project description:This SuperSeries is composed of the SubSeries listed below.

2023-02-01 | GSE206425 | GEO

Low-cost, low-input RNA-seq protocols perform nearly as well as high-input protocols.

Project description: Not available

| S-EPMC4380159 | biostudies-literature

The bovine alveolar macrophage (bAM) DNA methylome is resilient to infection with Mycobacterium bovis

Project description:Whole genome bisulfite sequencing (WGBS) was used to assess the effect of M. bovis infection on the bAM DNA methylome (5-methylcytosine). The methylomes of bAM infected with M. bovis (n = 8) were compared to those of non-infected control bAM (n = 8) at 24 hours post-infection (hpi). No differences in DNA methylation (CpG or non-CpG) were observed between control and infected bAM. Analysis of DNA methylation at proximal promoter regions uncovered >250 genes harbouring intermediately methylated (IM) promoters (average methylation = 33–66%). Gene ontology (GO) analysis, focusing on genes with low, intermediate or highly methylated promoters, revealed that genes with IM promoters were enriched for immune-related GO categories; this enrichment was not observed for genes in the high or low methylation groups. Targeted analysis of two non-imprinted genes in the IM category, C1QB and IL2RA, confirmed the WGBS observation. This study is the first in cattle to examine genome-wide DNA methylation at single nucleotide resolution in an important bovine cellular host-pathogen interaction model and provides evidence for intermediate promoter methylation in bAM.

2019-02-13 | GSE110412 | GEO

Transcription profiling of Drosophila melanogaster BAM over expressing germline stem cells vs controls

Project description:Gene expression is tested for an association with GSCs by comparing expression levels in ovary tips of c587-GAL4; hs-bam UAS-dpp females at 0 hr, 20 hr and 50 hr after heat shock ; results of two independent experiments are given as expt 1 and expt 2 Experiment Overall Design: 0 hr ovary tips contain many GSCs Experiment Overall Design: 20 hr hs-bam has induced differentiation of all GSCs Experiment Overall Design: 50 hr Bam has turned over and cystocytes have reverted to become GSCs again Experiment Overall Design: see Kai et al. (2005) Dev. Biol, in press.

2007-11-02 | E-GEOD-2784 | biostudies-arrayexpress

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