Type I and type II interferon responses in two human liver cell lines (Huh-7 and HuH6)
In this study, we used microarray-based gene expression profiling to compare the response of Huh-7 and HuH6 cells to stimulation with IFN-α and IFN-γ. Furthermore, we determined whether the resistance of HCV replication in HuH6 cells can be linked to differences in the expression profile of IFN-regulated genes. Although both cells lines responded to IFNs with rapid changes in gene expression, thereby demonstrating functional type I and type II signaling pathways, differences were observed for a number of genes. Raw and normalized expression data have been deposited in GEO under accession number GSE68927. (Source: Genomics Data)
Source: Genomics Data - January 12, 2016 Category: Genetics & Stem Cells Source Type: research
Transcriptomic analysis of mouse EL4 T cells upon T cell activation and in response to protein synthesis inhibition via cycloheximide treatment
Publication date: March 2016 Source:Genomics Data, Volume 7 Author(s): Pek Siew Lim, Kristine Hardy, Kaiman Peng, Frances M. Shannon T cell activation involves the recognition of a foreign antigen complexed to the major histocompatibility complex on the antigen presenting T cell to the T cell receptor. This leads to activation of signaling pathways, which ultimately leads to induction of key cytokine genes responsible for eradication of foreign antigens. We used the mouse EL4 T cell as a model system to study genes that are induced as a result of T cell activation using phorbol myristate acetate (PMA) and calci...
Source: Genomics Data - January 11, 2016 Category: Genetics & Stem Cells Source Type: research
Cultivation-independent comprehensive investigations on bacterial communities in serofluid dish, a traditional Chinese fermented food
In this study, bacterial community of the fermented serofluid dish was assessed by Illumina amplicon sequencing. The metagenome comprised of 49,589 average raw reads with an average 11,497,917bp and G+C content is 52.46%. This is the first report on V4 hyper-variable region of the 16S rRNA metagenome sequence employing Illumina platform to profile the microbial community of this little known fermented food from Gansu Province, China. The metagenome sequence can be accessed at NCBI, SRA database accession no. SRP065370. (Source: Genomics Data)
Source: Genomics Data - January 11, 2016 Category: Genetics & Stem Cells Source Type: research
Transcriptional profiling of the epigenetic regulator Smchd1
Publication date: March 2016 Source:Genomics Data, Volume 7 Author(s): Ruijie Liu, Kelan Chen, Natasha Jansz, Marnie E. Blewitt, Matthew E. Ritchie Smchd1 is an epigenetic repressor with important functions in healthy cellular processes and disease. To elucidate its role in transcriptional regulation, we performed two independent genome-wide RNA-sequencing studies comparing wild-type and Smchd1 null samples in neural stem cells and lymphoma cell lines. Using an R-based analysis pipeline that accommodates observational and sample-specific weights in the linear modeling, we identify key genes dysregulated by Sm...
Source: Genomics Data - January 11, 2016 Category: Genetics & Stem Cells Source Type: research
Complete metagenome sequencing based bacterial diversity and functional insights from basaltic hot spring of Unkeshwar, Maharashtra, India
Publication date: March 2016 Source:Genomics Data, Volume 7 Author(s): Gajanan T. Mehetre, Aditi S. Paranjpe, Syed G. Dastager, Mahesh S. Dharne Unkeshwar hot springs are located at geographical South East Deccan Continental basalt of India. Here, we report the microbial community analysis of this hot spring using whole metagenome shotgun sequencing approach. The analysis revealed a total of 848,096 reads with 212.87Mbps with 50.87% G+C content. Metagenomic sequences were deposited in SRA database with accession number (SUB1242219). Community analysis revealed 99.98% sequences belonging to bacteria and 0.01% to...
Source: Genomics Data - January 11, 2016 Category: Genetics & Stem Cells Source Type: research
Metagenomic data of fungal internal transcribed spacer from serofluid dish, a traditional Chinese fermented food
Publication date: March 2016 Source:Genomics Data, Volume 7 Author(s): Peng Chen, Yang Zhao, Zhengrong Wu, Ronghui Liu, Ruixiang Xu, Lei Yan, Hongyu Li Serofluid dish (or Jiangshui, in Chinese), a traditional food in the Chinese culture for thousands of years, is made from vegetables by fermentation. In this work, microorganism community of the fermented serofluid dish was investigated by the culture-independent method. The metagenomic data in this article contains the sequences of fungal internal transcribed spacer (ITS) regions of rRNA genes from 12 different serofluid dish samples. The metagenome compr...
Source: Genomics Data - January 11, 2016 Category: Genetics & Stem Cells Source Type: research
Gene expression profile of Musculus longissimus dorsi in bulls of a Charolais×Holstein F2-cross with divergent intramuscular fat content
Publication date: March 2016 Source:Genomics Data, Volume 7 Author(s): Katrin Komolka, Siriluck Ponsuksili, Elke Albrecht, Christa Kühn, Klaus Wimmers, Steffen Maak Transcriptomes of Musculus longissimus dorsi (MLD) were compared between bulls from a F2-cross derived from Charolais and Holstein Friesian. Two groups of 10 bulls were selected which differed significantly in intramuscular fat (IMF) deposition despite standardized husbandry and feeding conditions and identical sires in both groups. Consequently, genetic factors underlying the different capability of IMF deposition should be identified. A total...
Source: Genomics Data - January 11, 2016 Category: Genetics & Stem Cells Source Type: research
Mapping transcriptome profiles of in vitro iPSC-derived cardiac differentiation to in utero heart development
Publication date: March 2016 Source:Genomics Data, Volume 7 Author(s): Xing Li, Katherine A. Campbell, Sherri M. Biendarra, Andre Terzic, Timothy J. Nelson The dataset includes microarray data (Affymetrix Mouse Genome 430 2.0 Array) from WT and Nos3−/− mouse embryonic heart ventricular tissues at 14.5days post coitum (E14.5), induced pluripotent stem cells (iPSCs) derived from WT and Nos3−/− mouse tail tip fibroblasts, iPSC-differentiated cardiomyocytes at Day 11, and mouse embryonic stem cells (mESCs) and differentiated cardiomyocytes as positive controls for mouse iPSC differentiation. Both in utero...
Source: Genomics Data - January 11, 2016 Category: Genetics & Stem Cells Source Type: research
Androgen receptor DNA binding and chromatin accessibility profiling in prostate cancer
Publication date: March 2016 Source:Genomics Data, Volume 7 Author(s): Ekaterina Nevedomskaya, Suzan Stelloo, Henk G. van der Poel, Jeroen de Jong, Lodewyk F.A. Wessels, Andries M. Bergman, Wilbert Zwart Prostate cancer (PCa) is the second most common cancer in men. The Androgen Receptor (AR) is the major driver of PCa and the main target of therapy in the advanced setting. AR is a nuclear receptor that binds the chromatin and regulates transcription of genes involved in cancer cell proliferation and survival. In a study by Stelloo et al. (1) we explored prostate cancer on the level of transcriptional reg...
Source: Genomics Data - January 11, 2016 Category: Genetics & Stem Cells Source Type: research
Genome Sequencing and Annotation of Mycobacterium tuberculosis PR08 strain
Publication date: March 2016 Source:Genomics Data, Volume 7 Author(s): Mohammad Maaruf Jaafar, Mohd Zakihalani A. Halim, Mohamad Izwan Ismail, Lee Lian Shien, Teh Lay Kek, Ngeow Yun Fong, Norazmi Mohd Nor, Zainul Fadziruddin Zainuddin, Tang Thean Hock, Mohd Nazalan Mohd Najimudin, Mohd Zaki Salleh Mycobacterium tuberculosis is an acid fast bacterial species in the family Mycobacteriaceae and is the causative agent of most cases of tuberculosis. Here, we report the genomic features of Mycobacterium tuberculosis isolated from the cerebrospinal fluid (CSF) of a patient diagnosed with both pulmonary ...
Source: Genomics Data - January 11, 2016 Category: Genetics & Stem Cells Source Type: research
Genome-wide localization of Rrm3 and Pif1 DNA helicases at stalled active and inactive DNA replication forks of Saccharomyces cerevisiae
We present datasets deposited in the gene expression omnibus (GEO) database under accession number GSE68214, which show how the DNA helicases Rrm3 and Pif1 (8) associate to active and inactive DNA replication forks. (Source: Genomics Data)
Source: Genomics Data - January 11, 2016 Category: Genetics & Stem Cells Source Type: research
Microarray studies on the effect of silencing tynA in Escherichia coli K-12
Publication date: March 2016 Source:Genomics Data, Volume 7 Author(s): Heli Elovaara To study the biological role of the tynA gene product of Escherichia coli, a primary amine oxidase (ECAO, E.C. 1.4.3.21), the tynA gene was genetically silenced by conjugation with a kanamycin resistance cassette. We used a microarray method to compare the mRNA expression in the modified strain (ΔtynA) to that in the wild type (wt) strain at the time of induction of ECAO expression (0h) as well as 1h and 4h after the induction. These data in brief describe the different experimental conditions, sample preparation, data collection an...
Source: Genomics Data - January 11, 2016 Category: Genetics & Stem Cells Source Type: research
Identification of genes responsible for RelA-dependent proliferation arrest in human mammary epithelial cells conditionally expressing RelA
Publication date: March 2016 Source:Genomics Data, Volume 7 Author(s): Bose S. Kochupurakkal, J. Dirk Iglehart The molecular mechanisms responsible for opposing oncogenic and tumor-suppressor activities of NF-kB are obscure. Semi-quantitative immunohistochemistry of primary breast tumors using antibodies to RelA, the pleiotropic NF-kB factor, and Ki67 revealed a negative correlation between RelA levels and Ki67-index among ER+/HER2− tumors [1]. Similarly, expression of AURKA, a marker for proliferation, negatively correlates with expression of NFKBIA, a surrogate for RelA expression and activity, in ER+/HER2− t...
Source: Genomics Data - December 25, 2015 Category: Genetics & Stem Cells Source Type: research
De novo assembly and comparison of the ovarian transcriptomes of the common Chinese cuttlefish (Sepiella japonica) with different gonadal development
Publication date: Available online 21 December 2015 Source:Genomics Data Author(s): Zhenming Lü, Wan Liu, Liqin Liu, Huilai Shi, Hongling Ping, Tianming Wang, Changfeng Chi, Changwen Wu, Ching-Hung Chen, Kang-Ning Shen, Chung-Der Hsiao The common Chinese cuttlefish (Sepiella japonica) has been considered one of the most economically important marine Cephalopod species in East Asia and seed breeding technology has been established for massive aquaculture and stock enhancement. In the present study, we used Illumina HiSeq2000 to sequence, assemble and annotate the transcriptome of the ovary tissues...
Source: Genomics Data - December 22, 2015 Category: Genetics & Stem Cells Source Type: research
Transcriptome profiling of Musculus longissimus dorsi in two cattle breeds with different intramuscular fat deposition
Publication date: Available online 19 December 2015 Source:Genomics Data Author(s): Elke Albrecht, Katrin Komolka, Siriluck Ponsuksili, Takafumi Gotoh, Klaus Wimmers, Steffen Maak Intramuscular fat (IMF) deposition is a physiological process in cattle and is highly variable among breeds suggesting a large influence of genetic factors besides environmental factors. In order to elucidate molecular pathways underlying the genetic variation in this trait we compared transcriptomes of Musculus longissimus dorsi (MLD) in steers of Japanese Black and Holstein Friesian cattle breeds fed a high energy diet typically...
Source: Genomics Data - December 20, 2015 Category: Genetics & Stem Cells Source Type: research
