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Data Notes

At BMC Research Notes, we recognise that valuable data often go unpublished when instead they could be helping to progress science. This is why we launched data notes: a short article type allowing researchers to describe their data, sharing them with the research community and receiving credit for all their work - not just a finished article.

We present here all the data notes published in the journal, a free and open resource for the scientific community. Why not join them and free your data too?

Do you have questions about publishing data notes? Try out our data note query form!

Featured data: Effect of CFIm68 knockdown on RNA pol II transcription

Recent research suggests that the cleavage and polyadenylation (CPA) complex plays a role in regulating RNA polymerase II (pol II) turnover after transcription initiation. To explore this possibility, Tellier et al. at the University of Oxford knocked-down a subunit of the cleavage factor I (CFIm), CFIm68, which is part of the CPA complex and involved in alternative polyadenylation, and performed pol II ChIP-seq in absence or presence of a transcription elongation inhibitor. The data they produced are described here as October's featured data note, and available through the listed repository links.

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  1. Pabda (Ompok bimaculatus) is a freshwater catfish, largely available in Asian countries, especially in Bangladesh, India, Pakistan and Nepal. This fish is highly valued for its fabulous taste and high nutritional...

    Authors: Ruby Dhar, Karthikeyan Pethusamy, Sunil Singh, Indrani Mukherjee, Ashikh Seethy, Bharoti Sengupta, Tryambak Srivastava, Sajib Sarkar, Vikramjit Mandal, Madhumita Karmakar, Sandipan Gupta, Arpita Ghosh and Subhradip Karmakar

    Citation: BMC Research Notes 2019 12:825

    Content type: Data note

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  2. Early-onset severe preeclampsia is associated with significant maternal and perinatal morbidity and mortality especially in low-resource settings, where women have limited access to antenatal care. This datase...

    Authors: Solwayo Ngwenya, Brian Jones, Desmond Mwembe, Cladnos Mapfumo, Akinbowale Familusi, Hausitoe Nare and Alexander Edward Patrick Heazell

    Citation: BMC Research Notes 2019 12:822

    Content type: Data note

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  3. Text classification is a recurrent goal in machine learning projects and a typical task in crowdsourcing platforms. Hybrid approaches, leveraging crowdsourcing and machine learning, work better than either in ...

    Authors: Jorge Ramírez, Marcos Baez, Fabio Casati and Boualem Benatallah

    Citation: BMC Research Notes 2019 12:820

    Content type: Data note

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  4. File fragment classification of audio file formats is a topic of interest in network forensics. There are a few publicly available datasets of files with audio formats. Therewith, there is no public dataset fo...

    Authors: Atieh Khodadadi and Mehdi Teimouri

    Citation: BMC Research Notes 2019 12:819

    Content type: Data note

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  5. We report a transcriptome acquisition for the bath sponge Spongia officinalis, a non-model marine organism that hosts rich symbiotic microbial communities. To this end, a pipeline was developed to efficiently sep...

    Authors: Tereza Manousaki, Vasiliki Koutsouveli, Jacques Lagnel, Spyridon Kollias, Costas S. Tsigenopoulos, Christos Arvanitidis, Antonios Magoulas, Costas Dounas and Thanos Dailianis

    Citation: BMC Research Notes 2019 12:813

    Content type: Data note

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  6. Salmonella bacteria can induce the unfolded protein response, a cellular stress response to misfolding proteins within the endoplasmic reticulum. Salmonella can exploit the host unfolded protein response leading ...

    Authors: Antony N. Antoniou, Simon J. Powis and Janos Kriston-Vizi

    Citation: BMC Research Notes 2019 12:808

    Content type: Data note

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  7. Classification of textual file formats is a topic of interest in network forensics. There are a few publicly available datasets of files with textual formats. Therewith, there is no public dataset for file fra...

    Authors: Fatemeh Mansouri Hanis and Mehdi Teimouri

    Citation: BMC Research Notes 2019 12:801

    Content type: Data note

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  8. File fragment classification of image file formats is a topic of interest in network forensics. There are a few publicly available datasets of files with image formats. Therewith, there is no public dataset fo...

    Authors: Reyhane Fakouri and Mehdi Teimouri

    Citation: BMC Research Notes 2019 12:774

    Content type: Data note

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  9. The data presented here is part of a study that was aimed at characterizing the molecular mechanisms of polyunsaturated fatty acid metabolism by CYP2J2, the main cytochrome P450 enzyme active in the human card...

    Authors: K. K. Abelak, D. Bishop-Bailey and I. Nobeli

    Citation: BMC Research Notes 2019 12:760

    Content type: Data note

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  10. In frame of a study to characterize the interaction of human macrophage-like cells with pathogenic corynebacteria, Corynebacterium diphtheriae and Corynebacterium ulcerans, live cell imaging experiments were carr...

    Authors: Dulanthi Weerasekera, Jonas Hahn, Martin Herrmann and Andreas Burkovski

    Citation: BMC Research Notes 2019 12:695

    Content type: Data note

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  11. Corynebacterium ulcerans can colonize a wide variety of animals and also humans are infected, typically by zoonotic transmission. Symptoms range from skin ulcers or systemic infections to diphtheria-like illness....

    Authors: Anne Busch, Jens Möller, Andreas Burkovski and Helmut Hotzel

    Citation: BMC Research Notes 2019 12:692

    Content type: Data note

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  12. Like many other proteins, those belonging to the signal transduction cascade initiating sporulation (Spo0 pathway) have conserved protein domains (Capra and Laub in Annu Rev Microbiol 66:325–47, 2012). Improvemen...

    Authors: Paola Martinez-Amador, Nori Castañeda, Antonio Loza, Lizeth Soto, Enrique Merino and Rosa Maria Gutierrez-Rios

    Citation: BMC Research Notes 2019 12:686

    Content type: Data note

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  13. The purpose of this experiment is to analyze the changes of transcriptome in Pseudomonas aeruginosa under the action of sodium houttuyfonate (SH) to reveal the possible mechanism of SH inhibiting P. aeruginosa. W...

    Authors: Yeye Zhao, Yuanqing Si, Longfei Mei, Jiadi Wu, Jing Shao, Changzhong Wang and Daqiang Wu

    Citation: BMC Research Notes 2019 12:685

    Content type: Data note

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  14. Persian walnut (Juglans regia L.), the walnut species cultivated for nut production, is grown worldwide in temperate areas. In this work, chronological phenotypic data have been collected regarding a part of the ...

    Authors: Anthony Bernard, Teresa Barreneche, Marine Delmas, Sophie Durand, Cyril Pommier, Fabrice Lheureux, Eloïse Tranchand, Marianne Naudin and Elisabeth Dirlewanger

    Citation: BMC Research Notes 2019 12:662

    Content type: Data note

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  15. Basal stem rot disease causes severe economic losses to oil palm production in South-east Asia and little is known on the pathogenicity of the pathogen, the basidiomyceteous Ganoderma boninense. Our data presente...

    Authors: Mui Yun Wong, Nisha T. Govender and Chia Sui Ong

    Citation: BMC Research Notes 2019 12:631

    Content type: Data note

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  16. Transcription of eukaryotic protein-coding genes by RNA polymerase II (pol II) is highly regulated at initiation, elongation and termination. Transcription is also coordinated with co-transcriptional processin...

    Authors: Michael Tellier, Jessica G. Hardy, Chris J. Norbury and Shona Murphy

    Citation: BMC Research Notes 2019 12:554

    Content type: Data note

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    The Data note to this article has been published in BMC Research Notes 2018 11:894

  17. Crop production is an important variable in social, economic and environmental analyses. There is an abundance of crop data available for the United States, but we lack a typology of county-level crop producti...

    Authors: Courtney R. Hammond Wagner, Meredith T. Niles and Eric D. Roy

    Citation: BMC Research Notes 2019 12:552

    Content type: Data note

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  18. Label-free quantitative proteomics has emerged as a powerful strategy to obtain high quality quantitative measures of the proteome with only a very small quantity of total protein extract. Because our research...

    Authors: Gaëlle Lelandais, Thomas Denecker, Camille Garcia, Nicolas Danila, Thibaut Léger and Jean-Michel Camadro

    Citation: BMC Research Notes 2019 12:470

    Content type: Data note

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  19. Aspergillus flavus isolate TERIBR1 was isolated from tannery sludge highly contaminated with chromium. During characterization process, it exhibited capability to adapt and grow in fungal growth media amended wit...

    Authors: Pushplata Prasad Singh, Akanksha Jaiswar, Divya Srivastava and Alok Adholeya

    Citation: BMC Research Notes 2019 12:443

    Content type: Data note

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  20. The data presented herein represents the raw genotype data of a recently conducted larger study which investigated the association of single nucleotide polymorphisms (SNPs) in breast cancer related genes with ...

    Authors: Nirmala Dushyanthi Sirisena, Nilakshi Samaranayake and Vajira H. W. Dissanayake

    Citation: BMC Research Notes 2019 12:435

    Content type: Data note

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    The Data note to this article has been published in BMC Research Notes 2018 11:643

    The Research article to this article has been published in BMC Cancer 2018 18:180

  21. In humanitarian settings, children of pastoralists usually are the increased risk of malnutrition and its related complications. Consequently, as part of the program’s targeted response to the burgeoning malnu...

    Authors: Emmanuel Nene Odjidja and Sonia Hakizimana

    Citation: BMC Research Notes 2019 12:434

    Content type: Data note

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  22. Black Bengal goat (Capra hircus), a member of the Bovidae family with the unique traits of high prolificacy, skin quality and low demand for food is the most socioeconomically significant goat breed in Bangladesh...

    Authors: Amam Zonaed Siddiki, Abdul Baten, Masum Billah, Mohammad Atique Ul Alam, Kazi Shefaul Mulk Shawrob, Sourav Saha, Muntaha Chowdhury, Atif Hasan Rahman, Michael Stear, Gous Miah, Mahadia Kumkum, Mohammad Sirazul Islam, Mohammad Alamgir Hossain, A. K. M. Moniruzzaman Mollah and Md. Kabirul Islam Khan

    Citation: BMC Research Notes 2019 12:362

    Content type: Data note

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  23. Mycolicibacterium peregrinum, a rapidly growing mycobacterial species, can opportunistically infect humans and other animals. Although M. peregrinum infections in animals have been reported, the infection sources...

    Authors: Tetsuya Komatsu, Kenji Ohya, Kotaro Sawai, Justice Opare Odoi, Keiko Otsu, Atsushi Ota, Toshihiro Ito, Mikihiko Kawai and Fumito Maruyama

    Citation: BMC Research Notes 2019 12:341

    Content type: Data note

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  24. Soybean aphid (Aphis glycines Matsumura; SBA) is the most economically damaging insect of soybean (Glycine max) in the United States. One previous study demonstrated that avirulent (biotype 1) and virulent (bioty...

    Authors: Surendra Neupane, Adam J. Varenhorst and Madhav P. Nepal

    Citation: BMC Research Notes 2019 12:325

    Content type: Data note

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  25. The present database contains information on patient falls in the hospital setting. Data were collected in January 2018 with of describing in-hospital falls reported from 1st January 2012 to 31 December 2017 i...

    Authors: Aline Brenner de Souza, Vania Röhsig, Rubia Natasha Maestri, Mohamed Fayeq Parrini Mutlaq, Elisiane Lorenzini, Belisa Marin Alves, Daniela Oliveira and Danusa Cristina Gatto

    Citation: BMC Research Notes 2019 12:284

    Content type: Data note

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  26. The objective of this experiment was to identify transcripts in baker’s yeast (Saccharomyces cerevisiae) that could have originated from previously non-coding genomic regions, or de novo. We generated this data t...

    Authors: William R. Blevins, Lucas B. Carey and M. Mar Albà

    Citation: BMC Research Notes 2019 12:250

    Content type: Data note

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  27. Voltage-gated Ca2+ channels (VGCCs) are of central relevance in regulating Ca2+ influx into living cells. The low-voltage activated (LVA) Cav3 T-type Ca2+ channels are widely distributed throughout the brain incl...

    Authors: Andreas Lundt, Christina Henseler, Carola Wormuth, Julien Soos, Robin Seidel, Ralf Müller, Muhammad Imran Arshaad, Karl Broich, Jürgen Hescheler, Agapios Sachinidis, Dan Ehninger, Anna Papazoglou and Marco Weiergräber

    Citation: BMC Research Notes 2019 12:157

    Content type: Data note

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  28. Enterococci are Gram-positive lactic acid bacteria and common inhabitants of the gastrointestinal tract of mammals, including humans. They are also widely distributed in diverse environments such as soil, wate...

    Authors: Fauzia Aziz, Muhammad Nasim Khan, Safia Ahmed and Simon Colin Andrews

    Citation: BMC Research Notes 2019 12:99

    Content type: Data note

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  29. Hilsa shad (Tenualosa ilisha), is a popular fish of Bangladesh belonging to the Clupeidae family. An anadromous species, like the salmon and many other migratory fish, it is a unique species that lives in the sea...

    Authors: Avizit Das, Peter Ianakiev, Abdul Baten, Rifath Nehleen, Tasneem Ehsan, Oly Ahmed, Mohammad Riazul Islam, M. Niamul Naser, Mong Sano Marma and Haseena Khan

    Citation: BMC Research Notes 2018 11:921

    Content type: Data note

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  30. Cardiovascular risk factor burden was recently reported to be high in the Caribbean country Suriname. However, historical data for comparison were lacking. We report here rediscovered and hitherto unpublished ...

    Authors: Lizzy M. Brewster and Jules Brewster

    Citation: BMC Research Notes 2018 11:919

    Content type: Data note

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  31. The Chars Tobacco Assessment Project 2018 is a holistic survey conducted in the chars (riverine islands) of Gaibandha in Northern Bangladesh, covering 985 households over 24 clusters. The survey was conducted wit...

    Authors: Adnan M. S. Fakir, Mustahsin Aziz, Mutasim Billah Mubde, Afraim Karim, Ashraf S. Khan, Rifayat Raisa, Lubaba Ferdous Alim and Mayeesha Fahmin

    Citation: BMC Research Notes 2018 11:914

    Content type: Data note

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  32. Plasmodium berghei ANKA infection in mice is a model for human cerebral malaria, the most severe complication of Plasmodium falciparum infection. Responses of brain microglia have been little investigated, and ma...

    Authors: Carlos Talavera-López, Barbara Capuccini, Richard Mitter, Jing-wen Lin and Jean Langhorne

    Citation: BMC Research Notes 2018 11:913

    Content type: Data note

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    The Correction to this article has been published in BMC Research Notes 2019 12:48

  33. Leber’s hereditary optic neuropathy (LHON) is a mitochondrial genetic disease characterized by a variable and reduced penetrance. Individuals carrying a primary LHON-causing mitochondrial DNA (mtDNA) mutation ...

    Authors: Angelica Bianco, Alessio Valletti, Giovanna Longo, Luigi Bisceglia, Julio Montoya, Sonia Emperador, Silvana Guerriero and Vittoria Petruzzella

    Citation: BMC Research Notes 2018 11:911

    Content type: Data note

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  34. This paper presents magnetic resonance images of the dorsi- and plantar flexor muscles for individual young and older healthy adults. Also included are measurements of the volume, proportion, and longitudinal ...

    Authors: Christopher J. Hasson, Jane A. Kent and Graham E. Caldwell

    Citation: BMC Research Notes 2018 11:910

    Content type: Data note

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  35. Corals, the building blocks of reef ecosystems, have been severely threatened by climate change. Coral bleaching, the loss of the coral’s endosymbiotic algae, occurs as a consequence of increasing ocean temper...

    Authors: Maha J. Cziesielski, Yi Jin Liew and Manuel Aranda

    Citation: BMC Research Notes 2018 11:905

    Content type: Data note

    Published on:

  36. crAssphage is a newly found phage described as the most abundant virus in the human gut microbiome. The majority of the crAssphage proteins are unknown in sequences databases, and its pathogenicity and epidemi...

    Authors: Melany Cervantes-Echeverría, Edgar Equihua-Medina, Fernanda Cornejo-Granados, Abigail Hernández-Reyna, Filiberto Sánchez, Blanca Estela López-Contreras, Samuel Canizales-Quinteros and Adrián Ochoa-Leyva

    Citation: BMC Research Notes 2018 11:902

    Content type: Data note

    Published on:

  37. Transcription of eukaryotic protein-coding genes by RNA polymerase II (pol II) is a highly regulated process. Most human genes have multiple poly(A) sites, which define different possible mRNA ends, suggesting...

    Authors: Michael Tellier, Jessica G. Hardy, Chris J. Norbury and Shona Murphy

    Citation: BMC Research Notes 2018 11:894

    Content type: Data note

    Published on:

    The Data note to this article has been published in BMC Research Notes 2019 12:554

  38. Biomedical research is gaining ground on human disease through many types of “omics”, which is leading to increasingly effective treatments and broad applications for precision medicine. The majority of diseas...

    Authors: Jeremy J. Jay, Alexa Sanders, Robert W. Reid and Cory R. Brouwer

    Citation: BMC Research Notes 2018 11:883

    Content type: Data note

    Published on:

  39. The oomycete Pythium insidiosum infects humans and animals worldwide, and causes the life-threatening condition, called pythosis. Most patients lose infected organs or die from the disease. Comparative genomic an...

    Authors: Theerapong Krajaejun, Weerayuth Kittichotirat, Preecha Patumcharoenpol, Thidarat Rujirawat, Tassanee Lohnoo and Wanta Yingyong

    Citation: BMC Research Notes 2018 11:880

    Content type: Data note

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  40. There is a dearth of research into the quality of assessments based on Multiple Choice Question (MCQ) items in Massive Open Online Courses (MOOCs). This dataset was generated to determine whether MCQ item writ...

    Authors: Eamon Costello, Jane C. Holland and Colette Kirwan

    Citation: BMC Research Notes 2018 11:849

    Content type: Data note

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