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Academic Journal

Whole transcriptome analysis to identify non-coding RNA regulators and hub genes in sperm of non-obstructive azoospermia by microarray, single-cell RNA sequencing, weighted gene co-expression network analysis, and mRNA-miRNA-lncRNA interaction analysis.

  • Authors : Karoii DH; Department of Cell and Molecular Biology, School of Biology, College of Science, University of Tehran, Tehran, Iran.; Faculty of Biotechnology, Amol University of Special Modern Technologies, Amol, Iran.

Subjects: Azoospermia*/Azoospermia*/Azoospermia*/genetics ; Azoospermia*/Azoospermia*/Azoospermia*/metabolism ; Single-Cell Analysis* Azoospermia, Nonobstructive

  • Source: BMC genomics [BMC Genomics] 2024 Jun 11; Vol. 25 (1), pp. 583. Date of Electronic Publication: 2024 Jun 11.Publisher: BioMed Central Country of Publication: England NLM ID: 100965258 Publication Model: Electronic Cited Medium: Internet ISSN: 1471-2164

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Academic Journal

Identification of circRNAs expression profiles and functional networks in parotid gland of type 2 diabetes mouse.

  • Authors : Huang Y; Department of Oral and Maxillofacial Surgery, Peking University School and Hospital of Stomatology & National Center of Stomatology & National Clinical Research Center for Oral Diseases & National Engineering Research Center of Oral Biomaterials and Digital Medical Devices & Beijing Key Laboratory of Digital Stomatology & Research Center of Engineering and Technology for Computerized Dentistry Ministry of Health & NMPA Key Laboratory for Dental Materials, 100081, Beijing, P.R. China.; Department of Oral and Maxillofacial Surgery, Stomatological Hospital of Xiamen Medical College, Xiamen Key Laboratory of Stomotalogical Disease Diagnosis and Treatment, 361006, Xiamen, P.R. China.

Subjects: RNA, Circular*/RNA, Circular*/RNA, Circular*/genetics ; Diabetes Mellitus, Type 2*/Diabetes Mellitus, Type 2*/Diabetes Mellitus, Type 2*/genetics ; Diabetes Mellitus, Type 2*/Diabetes Mellitus, Type 2*/Diabetes Mellitus, Type 2*/metabolism

  • Source: BMC genomics [BMC Genomics] 2024 May 07; Vol. 25 (1), pp. 450. Date of Electronic Publication: 2024 May 07.Publisher: BioMed Central Country of Publication: England NLM ID: 100965258 Publication Model: Electronic Cited Medium: Internet ISSN: 1471-2164

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Academic Journal

FastCAR: fast correction for ambient RNA to facilitate differential gene expression analysis in single-cell RNA-sequencing datasets.

  • Authors : Berg M; Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands. .; University of Groningen, University Medical Center Groningen, Groningen Research Institute, for Asthma and COPD (GRIAC), Groningen, The Netherlands. .

Subjects: RNA*/RNA*/RNA*/metabolism ; Gene Expression Profiling*/Gene Expression Profiling*/Gene Expression Profiling*/methods; Humans

  • Source: BMC genomics [BMC Genomics] 2023 Nov 29; Vol. 24 (1), pp. 722. Date of Electronic Publication: 2023 Nov 29.Publisher: BioMed Central Country of Publication: England NLM ID: 100965258 Publication Model: Electronic Cited Medium: Internet ISSN: 1471-2164

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Academic Journal

RNA-seq analysis reveals changes in mRNA expression during development in Daphnia mitsukuri.

  • Authors : Zhang X; MOE Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Science, Fudan University, Songhu Road 2005, Shanghai, China.; Yang W

Subjects: Daphnia*/Daphnia*/Daphnia*/metabolism ; Gene Expression Profiling*; Humans

  • Source: BMC genomics [BMC Genomics] 2024 Mar 21; Vol. 25 (1), pp. 302. Date of Electronic Publication: 2024 Mar 21.Publisher: BioMed Central Country of Publication: England NLM ID: 100965258 Publication Model: Electronic Cited Medium: Internet ISSN: 1471-2164

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Academic Journal

A single workflow for multi-species blood transcriptomics.

  • Authors : Orcel E; BIOASTER, 40 Avenue Tony Garnier, Lyon, 69007, France.; Hage H

Subjects: Gene Expression Profiling* ; Vaccines*; Humans

  • Source: BMC genomics [BMC Genomics] 2024 Mar 16; Vol. 25 (1), pp. 282. Date of Electronic Publication: 2024 Mar 16.Publisher: BioMed Central Country of Publication: England NLM ID: 100965258 Publication Model: Electronic Cited Medium: Internet ISSN: 1471-2164

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Academic Journal

Genome-wide analysis of acid tolerance genes of Enterococcus faecalis with RNA-seq and Tn-seq.

  • Authors : Chen Z; Department of Endodontics and Operative Dentistry, Ninth People's Hospital, College of Stomatology, Shanghai Jiao Tong University School of Medicine, Shanghai, China.; National Clinical Research Center for Oral Diseases, Shanghai, China.

Subjects: Enterococcus faecalis*/Enterococcus faecalis*/Enterococcus faecalis*/genetics ; Gene Expression Profiling*; RNA-Seq

  • Source: BMC genomics [BMC Genomics] 2024 Mar 08; Vol. 25 (1), pp. 261. Date of Electronic Publication: 2024 Mar 08.Publisher: BioMed Central Country of Publication: England NLM ID: 100965258 Publication Model: Electronic Cited Medium: Internet ISSN: 1471-2164

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Academic Journal

The forgotten variable? Does the euthanasia method and sample storage condition influence an organisms transcriptome - a gene expression analysis on multiple tissues in pigs.

  • Authors : Chakkingal Bhaskaran B; Department of Biosystems, Centre for Animal Breeding and Genetics, KU Leuven, Kasteelpark Arenberg 30, Box 2472, Leuven, 3001, Belgium. .; Meyermans R

Subjects: Transcriptome* ; Gene Expression Profiling*/Gene Expression Profiling*/Gene Expression Profiling*/methods; Animals

  • Source: BMC genomics [BMC Genomics] 2023 Dec 14; Vol. 24 (1), pp. 769. Date of Electronic Publication: 2023 Dec 14.Publisher: BioMed Central Country of Publication: England NLM ID: 100965258 Publication Model: Electronic Cited Medium: Internet ISSN: 1471-2164

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Academic Journal

A new and effective two-step clustering approach for single cell RNA sequencing data.

  • Authors : Li R; Translational Medical Center for Stem Cell Therapy, Shanghai East Hospital, and School of Medicine, Tongji University, 1239 Siping Road, 200092, Shanghai, China.; Department of Computer Science and Technology, Tongji University, 4800 Caoan Road, 201804, Shanghai, China.

Subjects: Gene Expression Profiling*/Gene Expression Profiling*/Gene Expression Profiling*/methods ; Single-Cell Analysis*/Single-Cell Analysis*/Single-Cell Analysis*/methods; Sequence Analysis, RNA/Sequence Analysis, RNA/Sequence Analysis, RNA/methods

  • Source: BMC genomics [BMC Genomics] 2023 Nov 09; Vol. 23 (Suppl 6), pp. 864. Date of Electronic Publication: 2023 Nov 09.Publisher: BioMed Central Country of Publication: England NLM ID: 100965258 Publication Model: Electronic Cited Medium: Internet ISSN: 1471-2164

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Academic Journal

Application of the 3' mRNA-Seq using unique molecular identifiers in highly degraded RNA derived from formalin-fixed, paraffin-embedded tissue.

  • Authors : Jang JS; Genome Analysis Core, Medical Genome Facility, Center for Individualized Medicine, Mayo Clinic, Stabile Research Building, 200 First Street SW, Rochester, MN, 55905, USA. .; Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA. .

Subjects: Gene Expression Profiling* ; RNA*; Formaldehyde

  • Source: BMC genomics [BMC Genomics] 2021 Oct 24; Vol. 22 (1), pp. 759. Date of Electronic Publication: 2021 Oct 24.Publisher: BioMed Central Country of Publication: England NLM ID: 100965258 Publication Model: Electronic Cited Medium: Internet ISSN: 1471-2164

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Academic Journal

scQCEA: a framework for annotation and quality control report of single-cell RNA-sequencing data.

  • Authors : Nassiri I; Oxford Genomics Centre, Nuffield Department of Medicine, Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK. .; Fairfax B

Subjects: Software* ; Gene Expression Profiling*; Animals

  • Source: BMC genomics [BMC Genomics] 2023 Jul 06; Vol. 24 (1), pp. 381. Date of Electronic Publication: 2023 Jul 06.Publisher: BioMed Central Country of Publication: England NLM ID: 100965258 Publication Model: Electronic Cited Medium: Internet ISSN: 1471-2164

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