scholarly journals Improved Search of Large Transcriptomic Sequencing Databases Using Split Sequence Bloom Trees

2018 ◽  
Vol 25 (7) ◽  
pp. 755-765 ◽  
Author(s):  
Brad Solomon ◽  
Carl Kingsford
Keyword(s):  
Split Sequence ◽  
Transcriptomic Sequencing

scholarly journals Improved Search of Large Transcriptomic Sequencing Databases Using Split Sequence Bloom Trees

2016 ◽  
Author(s):  
Brad Solomon ◽  
Carl Kingsford
Keyword(s):  
Population Variation ◽  
Rna Seq ◽  
Specific Expression ◽  
Short Read ◽  
Short Read Sequencing ◽  
Split Sequence ◽  
Transcriptomic Sequencing ◽  
And Storage ◽  
Expressed Sequence ◽  
Over Time

AbstractEnormous databases of short-read RNA-seq sequencing experiments such as the NIH Sequencing Read Archive (SRA) are now available. These databases could answer many questions about the condition-specific expression or population variation, and this resource is only going to grow over time. However, these collections remain difficult to use due to the inability to search for a particular expressed sequence. While some progress has been made on this problem, it is still not feasible to search collections of hundreds of terabytes of short-read sequencing experiments. We introduce an indexing scheme called Split Sequence Bloom Tree (SSBT) to support sequence-based querying of terabyte-scale collections of thousands of short-read sequencing experiments. SSBT is an improvement over the SBT [1] data structure for the same task. We apply SSBT to the problem of finding conditions under which query transcripts are expressed. Our experiments are conducted on a set of 2,652 publicly available RNA-seq experiments contained in the NIH for the breast, blood, and brain tissues. We demonstrate that this SSBT index can be queried for a 1000 nt sequence in under 4 minutes using a single thread and can be stored in just 39 GB, a five-fold improvement in search and storage costs compared to SBT. We further report that SSBT can be further optimized by pre-loading the entire index to accomplish the same search in 30 seconds.

scholarly journals Suppression of steroid 5α-reductase type I promotes cellular apoptosis and autophagy via PI3K/Akt/mTOR pathway in multiple myeloma

2021 ◽  
Vol 12 (2) ◽  
Author(s):  
Renjie Dou ◽  
Jinjun Qian ◽  
Wei Wu ◽  
Yanxin Zhang ◽  
Yuxia Yuan ◽  
...  
Keyword(s):  
Multiple Myeloma ◽  
Type I ◽  
Disease Course ◽  
Mtor Signaling Pathway ◽  
Hairpin Rna ◽  
Aberrant Expression ◽  
Transcriptomic Sequencing ◽  
Family Protein ◽  
Cellular Apoptosis ◽  
Autophagic Process

AbstractSteroid 5α-reductase type I (SRD5A1) is a validated oncogene in many sex hormone-related cancers, but its role in multiple myeloma (MM) remains unknown. Based on gene expression profiling (GEP) of sequential MM samples during the disease course, we found that the aberrant expression of SRD5A1 was correlated with progression and poor prognosis in MM patients. In this study, the oncogenic roles of SRD5A1 were validated in human MM cell lines (ARP1 and H929) and the xenograft MM model as well as the 5TMM mouse model. MTT and flow cytometry were used to assess MM cell proliferation, cell cycle, and apoptosis post inducible knockdown SRD5A1 by lentivirus-mediated short-hairpin RNA (shRNA). Transcriptomic sequencing, immunofluorescence, and western blot were used to investigate the effects of SRD5A1 suppression on cell apoptosis and autophagy. Mechanistically, SRD5A1 downregulation simultaneously regulated both the Bcl-2 family protein-mediated apoptosis and the autophagic process via PI3K/Akt/mTOR signaling pathway in MM cells. Meanwhile, the autophagy inhibitor (3-methyladenine) and SRD5A1 inhibitor (Dutasteride) were utilized to evaluate their anti-myeloma effect. Thus, our results demonstrated that SRD5A1 downregulation simultaneously regulated both the apoptosis and the autophagic process in MM cells. The dual autophagy–apoptosis regulatory SRD5A1 may serve as a biomarker and potential target for MM progression and prognosis.

scholarly journals Physiological and Transcriptional Characterization of Persistent and Nonpersistent Listeria monocytogenes Isolates

2011 ◽  
Vol 77 (18) ◽  
pp. 6559-6569 ◽  
Author(s):  
Edward M. Fox ◽  
Nola Leonard ◽  
Kieran Jordan
Keyword(s):  
Listeria Monocytogenes ◽  
Antimicrobial Agents ◽  
Cetylpyridinium Chloride ◽  
Phenotype Microarray ◽  
Content Type ◽  
Benzethonium Chloride ◽  
Transcriptomic Sequencing ◽  
Ammonium Compounds ◽  
Compare Gene Expression

ABSTRACTThis study aimed to characterize physiological differences between persistent and presumed nonpersistentListeria monocytogenesstrains isolated at processing facilities and to investigate the molecular basis for this by transcriptomic sequencing. Full metabolic profiles of two strains, one persistent and one nonpersistent, were initially screened using Biolog's Phenotype MicroArray (PM) technology. Based on these results, in which major differences from selected antimicrobial agents were detected, another persistent strain and two nonpersistent strains were characterized using two antimicrobial PMs. Resistance to quaternary ammonium compounds (QACs) was shown to be higher among persistent strains. Growth of persistent and nonpersistent strains in various concentrations of the QACs benzethonium chloride (BZT) and cetylpyridinium chloride (CPC) was determined. Transcriptomic sequencing of a persistent and a presumed nonpersistent strain was performed to compare gene expression among these strains in the presence and absence of BZT. Two strains, designated “frequent persisters” because they were the most frequently isolated at the processing facility, showed overall higher resistance to QACs. Transcriptome analysis showed that BZT induced a complex peptidoglycan (PG) biosynthesis response, which may play a key role in BZT resistance. Comparison of persistent and nonpersistent strains indicated that transcription of many genes was upregulated among persistent strains. This included three gene operons:pdu,cob-cbi, andeut. These genes may play a role in the persistence ofL. monocytogenesoutside the human host.

scholarly journals Transcriptome Analysis of Neuroendocrine Regulation of Ovine Hypothalamus-Pituitary-Ovary Axis during Ovine Anestrus and the Breeding Season

Genes ◽  
2021 ◽  
Vol 12 (12) ◽  
pp. 1861
Author(s):  
Yingjie Zhong ◽  
Ran Di ◽  
Yang Yang ◽  
Qiuyue Liu ◽  
Mingxing Chu
Keyword(s):  
Functional Analysis ◽  
Neuroendocrine Regulation ◽  
Regulation Mechanism ◽  
Sequencing Technology ◽  
Indigenous Sheep ◽  
Transcriptomic Sequencing ◽  
Molecular Studies ◽  
Isoleucine Biosynthesis ◽  
Tan Sheep ◽  
Key Genes

Most sheep are seasonal estrus, and they breed in autumn when the days get shorter. Seasonal estrus is an important factor that affects the productivity and fertility of sheep. The key point to solve this problem is to explore the regulation mechanism of estrus in sheep. Therefore, in this study, transcriptomic sequencing technology was used to identify differentially expressed mRNAs in the hypothalamus, pituitary and ovary of Small Tail Han sheep (year-round estrus) and tan sheep (seasonal estrus) among luteal, proestrus and estrus stages. There were 256,923,304,156 mRNAs being identified in the hypothalamus, pituitary and ovary, respectively. Functional analysis showed that the photosensor, leucine and isoleucine biosynthesis pathways were enriched significantly. It is speculated that photoperiod may initiate estrus by stimulating the corresponding pathways in hypothalamus. ODC1, PRLH, CRYBB2, SMAD5, OPN1SW, TPH1 are believed to be key genes involved in the estrogen process. In conclusion, this study expanded the database of indigenous sheep breeds, and also provided new candidate genes for future genetic and molecular studies on the seasonal estrus trait in sheep.

Transcriptomic sequencing reveals the response of Dunaliella salina to copper stress via the increased photosynthesis and carbon metabolisms

2021 ◽  
Author(s):  
Na Ling ◽  
Weilu Li ◽  
Guiguo Xu ◽  
Zheng Qi ◽  
Chen-Feng Ji ◽  
...  
Keyword(s):  
Heavy Metal ◽  
Green Algae ◽  
Environmental Conditions ◽  
Dunaliella Salina ◽  
Heavy Metal Stress ◽  
Metal Stress ◽  
Copper Stress ◽  
Low Concentration ◽  
Transcriptomic Sequencing

The green algae Dunaliella salina is known for its rich carotenoids. It is also resistant to various environmental conditions, particularly to heavy metal stress. The low concentration of copper can...

scholarly journals A method for isolating RNA from canine bone

BioTechniques ◽  
2020 ◽  
Vol 68 (6) ◽  
pp. 311-317
Author(s):  
Rebecca Nance ◽  
Payal Agarwal ◽  
Maninder Sandey ◽  
Dmytro Starenki ◽  
Jey Koehler ◽  
...  
Keyword(s):  
Gene Expression ◽  
Bone Marrow ◽  
Connective Tissue ◽  
Bone Cells ◽  
Transcriptomic Analysis ◽  
Unique Challenge ◽  
Downstream Application ◽  
Transcriptomic Sequencing ◽  
Mineralized Matrix

Extracting sufficient quantity and quality RNA from bone is essential for downstream application, such as transcriptomic sequencing, to evaluate gene expression. Isolation of RNA from bone presents a unique challenge owing to the hypocellular, brittle and mineralized matrix, which makes homogenizing the tissue difficult and provides little RNA to work with. Removal of contaminating tissue, such as bone marrow and connective tissue, is essential for isolating RNA that is unique to osteoblasts, osteoclasts and osteocytes. This study established a method to effectively isolate RNA from normal canine bone cells using the phalanges, without contamination from other tissue types, for downstream transcriptomic analysis.

scholarly journals Total infectomes of 162 SARS-CoV-2 cases using meta-transcriptomic sequencing

2020 ◽  
Author(s):  
Hong Zhou ◽  
Cixiu Li ◽  
Tao Hu ◽  
Ti Liu ◽  
Nan Ni ◽  
...  
Keyword(s):  
Transcriptomic Sequencing
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