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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At BMC Research Notes, we recognise that valuable data often go unpublished when instead they could be helping to progress science.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?

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. The availability of matched sequencing data for the same sample across different sequencing platforms is a necessity for validation and effective comparison of sequencing platforms. A commonly sequenced sample...

    Authors: Shannon N. Fenlon, Yuemin Celina Chee, Jacqueline Lai Yuen Chee, Yeen Hui Choy, Alexis Jiaying Khng, Lu Ting Liow, Kurosh S. Mehershahi, Xiaoan Ruan, Stephen W. Turner, Fei Yao and Swaine L. Chen

    Citation: BMC Research Notes 2020 13:487

    Content type: Data note

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  2. The data herein represents multiple gauge sets and multiple radar sites of like-type Doppler data sets combined to produce populations of ordered pairs. Publications spanning decades yet specific to Doppler ra...

    Authors: Jesse W. Lansford, Tyson H. Walsh, T. V. Hromadka II and P. Rao

    Citation: BMC Research Notes 2020 13:482

    Content type: Data note

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  3. Respiratory tract diseases (RTDs) are among the top five leading causes of death worldwide. Mortality rates due to respiratory tract diseases (MRRTDs) follow a spatial pattern and this may suggest a potential ...

    Authors: Elahe Pishgar, Alireza Mohammadi, Nasser Bagheri and Behzad Kiani

    Citation: BMC Research Notes 2020 13:469

    Content type: Data note

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  4. Colorectal cancer (CRC) is the third most common cancer across the world that multiple risk factors together contribute to CRC development. There is a limited research report on impact of nutritional risk fact...

    Authors: Neda Firouraghi, Nasser Bagheri, Fatemeh Kiani, Ladan Goshayeshi, Majid Ghayour-Mobarhan, Khalil Kimiafar, Saeid Eslami and Behzad Kiani

    Citation: BMC Research Notes 2020 13:466

    Content type: Data note

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  5. The data presented herein represents the simulated datasets of a recently conducted larger study which investigated the behaviour of Bayesian indices of significance and effect size as alternatives to traditio...

    Authors: Riko Kelter

    Citation: BMC Research Notes 2020 13:452

    Content type: Data note

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  6. Maranhão State—Northeast Brazil–has the world’s highest incidence of penile cancer. This study describes the epidemiological, histopathological and clinical profile of patients stricken across that Brazilian s...

    Authors: Ciro Bezerra Vieira, Antonio Teixeira-Júnior, Laisson Feitoza, Jaqueline Pinho, José Calixto, Francisco Sérgio Moura Silva do Nascimento, Marcos Adriano Garcia Campos, Joyce Lages, Antonio Machado Alencar Junior, Fernando Soares, Isabela Cunha and Gyl Eanes Barros Silva

    Citation: BMC Research Notes 2020 13:442

    Content type: Data note

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  7. Phytohormones are small signaling molecules with crucial roles in plant growth, development, and environmental adaptation to biotic and abiotic stress responses. Despite several previously published molecular ...

    Authors: Junesung Lee, Jae-Young Nam, Hakgi Jang, Nayoung Kim, Yong-Min Kim, Won-Hee Kang and Seon-In Yeom

    Citation: BMC Research Notes 2020 13:440

    Content type: Data note

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  8. Patients with end-stage heart failure (ESHF) treated with ventricular assist devices (VADs) tend to gain weight after implantation, which is associated with higher complication rates and is a contraindication ...

    Authors: Adrian daSilva-deAbreu, Kiran Garikapati, Bader Aldeen Alhafez, Sapna Desai, Clement Eiswirth, Selim Krim, Hamang Patel, Carl J. Lavie, Hector O. Ventura, Juan Francisco Loro-Ferrer and Stacy A. Mandras

    Citation: BMC Research Notes 2020 13:439

    Content type: Data note

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  9. Nuclear Factor One X (NFIX) is a transcription factor expressed by neural stem cells within the developing mouse brain and spinal cord. In order to characterise the pathways by which NFIX may regulate neural s...

    Authors: Elise Matuzelski, Alexandra Essebier, Lachlan Harris, Richard M. Gronostajski, Tracey J. Harvey and Michael Piper

    Citation: BMC Research Notes 2020 13:437

    Content type: Data note

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  10. The data provided herein represent the whole-genome resequencing data related to three wolves and three Iranian local dogs. The understanding of genome evolution during animal domestication is an interesting s...

    Authors: Zeinab Amiri Ghanatsaman, Guo-Dong Wang, Masood Asadi Fozi, Ya-Ping Zhang and Ali Esmailizadeh

    Citation: BMC Research Notes 2020 13:436

    Content type: Data note

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  11. Clostridium species of the order Clostridiales are mostly strictly anaerobic rod-shaped bacteria. They can be detected in a variety of environments, including the intestines of humans and animals, soil, water, an...

    Authors: Elvira E. Ziganshina, Waleed S. Mohammed and Ayrat M. Ziganshin

    Citation: BMC Research Notes 2020 13:413

    Content type: Data note

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  12. Labeo catla (catla), one of the three Indian major carps, is native to the Indo-Gangetic riverine system of India as well as the rivers of Pakistan, Bangladesh, Nepal and Myanmar. Its higher growth rate and compa...

    Authors: Lakshman Sahoo, Paramananda Das, Bismay Sahoo, Gargee Das, Prem Kumar Meher, Uday Kumar Udit, Kanta Das Mahapatra and Jitendra Kumar Sundaray

    Citation: BMC Research Notes 2020 13:411

    Content type: Data note

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  13. Efforts to restore tropical peat swamp forests in Indonesia face huge challenges of potential failures due to socio-economic factors and ecological dynamics attributed to lack of knowledge on the adaptive mech...

    Authors: Iskandar Zulkarnaen Siregar, Fifi Gus Dwiyanti, Ulfah Juniarti Siregar and Deden Derajat Matra

    Citation: BMC Research Notes 2020 13:405

    Content type: Data note

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  14. Data was collected to evaluate the survival rates of head and neck (conjunctiva, oropharyngeal and non-oropharyngeal) squamous cell carcinomas in Ghana.

    Authors: Osei Owusu-Afriyie, W. K. B. A. Owiredu, Alexander Acheampong Oti, Emmanuel Acheampong, Kwabena Owusu-Danquah, Rita Larsen-Reindorf, Linda Ahenkorah Fondjo, Evans Asamoah Adu, Sampson Donkor and Peter Donkor

    Citation: BMC Research Notes 2020 13:392

    Content type: Data note

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  15. Patients with end-stage heart failure (ESHF) treated with ventricular assist devices (VADs) tend to gain weight, which may prevent them from receiving heart transplantation (HT) if their body mass index (BMI) ...

    Authors: Adrian daSilva-deAbreu, Bader Aldeen Alhafez, Yuhamy Curbelo-Pena, Carl J. Lavie, Hector O. Ventura, Juan Francisco Loro-Ferrer and Stacy A. Mandras

    Citation: BMC Research Notes 2020 13:382

    Content type: Data note

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  16. Pig pluripotent stem cells have tremendous potential because the pig is a valuable animal as both an agricultural resource and as a preclinical model of human therapy. To date, a lack of understanding of pig p...

    Authors: Kwang-Hwan Choi, Dong-Kyung Lee, Jong-Nam Oh, Seung-Hun Kim, Mingyun Lee, Sung Woo Kim and Chang-Kyu Lee

    Citation: BMC Research Notes 2020 13:144

    Content type: Data note

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  17. The leading factors of paediatric, pedestrian road traffic injuries (PPRTIs) are associated with the characteristics of immediate environment. Spatial analysis of data related to PPRTIs could provide useful kn...

    Authors: Parinaz Tabari, Hamidreza Shabanikiya, Nasser Bagheri, Robert Bergquist, Soheil Hashtarkhani, Fatemeh Kiani, Alireza Mohammadi and Behzad Kiani

    Citation: BMC Research Notes 2020 13:363

    Content type: Data note

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  18. Genome sequences are a vital resource for accelerating the biological exploration of an organism of interest. Pythium destruens (a synonym of Pythium insidiosum) causes a difficult-to-treat infectious disease cal...

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

    Citation: BMC Research Notes 2020 13:329

    Content type: Data note

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  19. Spiroplasma citri is a bacterium with a wide host range and is the causal agent of citrus stubborn and brittle root diseases of citrus and horseradish, respectively. S. citri is transmitted in a circulative, pers...

    Authors: Raymond Yokomi, Rachel Rattner, Fatima Osman, Yogita Maheshwari, Vijayanandraj Selvaraj, Deborah Pagliaccia, Jianchi Chen and Georgios Vidalakis

    Citation: BMC Research Notes 2020 13:320

    Content type: Data note

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  20. Mouse models have delivered variable recapitulation of Kyasanur Forest disease (KFD) pathology and consistently demonstrated neurological involvement which may be a limited feature of human disease. With the p...

    Authors: A. M. Nikiforuk, K. Tierny, T. A. Cutts, D. K. Kobasa, S. S. Theriault and B. W. M. Cook

    Citation: BMC Research Notes 2020 13:291

    Content type: Data note

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  21. Malaria is an infectious disease that annually presents around 200,000 cases in Brazil. The availability of data on malaria is crucial for enabling and supporting studies that can promote actions to prevent it...

    Authors: Lais Baroni, Marcel Pedroso, Christovam Barcellos, Rebecca Salles, Samella Salles, Balthazar Paixão, Alvaro Chrispino, Gustavo Guedes and Eduardo Ogasawara

    Citation: BMC Research Notes 2020 13:274

    Content type: Data note

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  22. The present database contains information on sociodemographic and clinical data as well as data from the Care Transition Measure (CTM 15-Brazil) of cancer patients undergoing clinical or surgical treatment. Da...

    Authors: Elisiane Lorenzini, Julia Estela Willrich Boell, Nelly D. Oelke, Caroline Donini Rodrigues, Letícia Flores Trindade, Vanessa Dalsasso Batista Winter, Michelle Mariah Malkiewiez, Gabriela Ceretta Flôres, Pâmella Pluta and Adriane Cristina Bernat Kolankiewicz

    Citation: BMC Research Notes 2020 13:267

    Content type: Data note

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  23. In order to characterize a river-associated, enriched microbiome capable of degrading an anthraquinone dye from the oil blue family, as well as assessing its functional potential, we performed a taxa-specific ...

    Authors: Ayixon Sánchez-Reyes, Luz Bretón-Deval, Hayley Mangelson and Alejandro Sanchez-Flores

    Citation: BMC Research Notes 2020 13:265

    Content type: Data note

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  24. UHRF1 is a multi-domain protein that recognizes both histone and DNA modification marks on chromatin. UHRF1 is involved in various cellular processes that lead to tumorigenesis and thus attracted considerable ...

    Authors: Debasis Patnaik

    Citation: BMC Research Notes 2020 13:254

    Content type: Data note

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  25. Although follicular thyroid carcinoma (FTC) generally has a good prognosis, it occasionally metastasises, leading to poor prognosis. Unfortunately, minimally invasive FTC (mi-FTC) and encapsulated angioinvasiv...

    Authors: Tomoo Jikuzono, Tomoko Ishikawa, Mitsuyoshi Hirokawa, Iwao Sugitani and Osamu Ishibashi

    Citation: BMC Research Notes 2020 13:241

    Content type: Data note

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  26. File fragment classification of video file formats is a topic of interest in network forensics. There are some publicly available datasets for file fragments of various file types such as textual, audio, and i...

    Authors: Narges Sadeghi, Mohadeseh Fahiminia and Mehdi Teimouri

    Citation: BMC Research Notes 2020 13:213

    Content type: Data note

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  27. The genus Bacillus comprises spore-forming rod-shaped Gram-positive bacteria, which usually grow aerobically or anaerobically. Members of this genus are common environmental microorganisms. Also, they can be moni...

    Authors: Waleed S. Mohammed, Elvira E. Ziganshina, Ramilya F. Akhmetova and Ayrat M. Ziganshin

    Citation: BMC Research Notes 2020 13:152

    Content type: Data note

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  28. In the bovine placenta, intimate fetomaternal contact is restricted to placentomes. Within the placentomes fetal chorionic villi interdigitate with corresponding maternal caruncular crypts. The trophoblast epi...

    Authors: Marina Polei, Juliane Günther, Dirk Koczan and Rainer Fürbass

    Citation: BMC Research Notes 2020 13:115

    Content type: Data note

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  29. Advanced tools and resources are needed to efficiently and sustainably produce food for an increasing world population in the context of variable environmental conditions. The maize genomes to fields (G2F) ini...

    Authors: Bridget A. McFarland, Naser AlKhalifah, Martin Bohn, Jessica Bubert, Edward S. Buckler, Ignacio Ciampitti, Jode Edwards, David Ertl, Joseph L. Gage, Celeste M. Falcon, Sherry Flint-Garcia, Michael A. Gore, Christopher Graham, Candice N. Hirsch, James B. Holland, Elizabeth Hood…

    Citation: BMC Research Notes 2020 13:71

    Content type: Data note

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  30. To show the body image of people over 50 in Spain using the Body Shape Questionnaire test (BSQ), taking into account attribute variables of great interest such as age, gender, sentimental status, habitat (rural o...

    Authors: Roberto Sánchez-Cabrero, Fernando Martínez-López and Reyna Guadalupe Euán-Ramírez

    Citation: BMC Research Notes 2020 13:50

    Content type: Data note

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  31. 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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  32. 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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  33. 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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  34. 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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  35. 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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  36. 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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  37. 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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  38. 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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  39. 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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  40. 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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  41. 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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  42. 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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  43. 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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  44. 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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  45. 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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