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SRP048842
Homo sapiens
2 Downloadable Samples
Illumina HiSeq 2000
Description
Unraveling complexity of DNA methylome is essential to decipher DNA methylation mechanism in life. However, this has been subjected to technological constraints to balance between cost and accurate measurement of the DNA methylation level. In this study, by innovatively introducing C-hydroxylmethylated adapters, we have developed MeDIP-Bisulfite sequencing (MB-seq), which could obtain DNA methylome of repertoire CpGs at single-base resolution. We found MB-seq only costs 10% of MethylC-seq, but covers 85% of total CpGs in human genome. Unlike absolute methylation levels determined by MethylC-seq and RRBS, MB-seq presented relative methylation levels that are linearly inflated. This has enlightened us to develop a MB-seq corresponding correction method for methylation level based on ridge regression, which integrates the data of MB-seq and RRBS to predict the methylation level of total 28.2 million CpGs on human genome with high accuracy (Pearson correlation coefficient, PCC=0.90). Moreover, by employing MB-seq, we generated the DNA methylome of an ovarian epithelial cell line (T29) and its oncogenic counterpart (T29H), respectively. After ridge regression, we identified 131,790 differential methylation regions (DMRs) with high accuracy between T29 and T29H, far more than 7,567 obtained from RRBS. Taken together, our result demonstrated that the MB-seq combined with ridge regression is a wide applicable approach for profiling of DNA methylome. Overall design: Total RNAs were extracted from T29 and T29H with RNeasy Mini Kit (QIAGEN, Germany). RNA quality was quality-controlled by Bioanalyser 2100 (RNA nano kits, Agilent). mRNA-Seq libraries were generated from total RNA with polyA+ selection of mRNA using the TruSeq RNA Sample Prep Kit v2 (Illumina, San Diego, CA), and then subjected to transcriptome sequencing on the Illumina Hiseq 2000
Publication Title
MBRidge: an accurate and cost-effective method for profiling DNA methylome at single-base resolution.
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 4 Downloadable Samples
- Illumina HiSeq 2000
Description
By using NGS-derived retinal transcriptome profiling (RNA-seq) to compare the gene expression profiling between 4 differently treated NPC cells Overall design: Examination of different gene expression in EBV-miRNA-BART1/3/7 lentivirus and their control infected nasopharyngeal carcinoma cells.
Publication Title
Epstein-Barr virus-encoded microRNA BART1 induces tumour metastasis by regulating PTEN-dependent pathways in nasopharyngeal carcinoma.
Sample Metadata Fields
Specimen part, Cell line, Subject
View Samples- Gallus gallus, Eimeria tenella
- 6 Downloadable Samples
Affymetrix Chicken Genome Array (chicken)
Description
Relative expression levels of mRNAs in chicken cecal epithelia experimentally infected with Eimeria tenella were measured at 4.5 days post-infection. Two weeks old chickens were uninfected (negative control) or were orally inoculated with sporulated oocysts of Eimeria tenella. Cecal epithelia samples were collected from >12 birds in infected or uninfected group at 4.5 d following infections, in which samples from 4 birds were pooled together to form a total 3 biological replicates in each group. Parasite merozoites were also collected from four infected chickens at 5 d after infections. Uninfected control samples, merozoites and infection group samples were selected for RNA extraction and hybridization on Affymetrix microarrays.
Publication Title
Transcriptome analysis in chicken cecal epithelia upon infection by Eimeria tenella in vivo.
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 6 Downloadable Samples
- Affymetrix Human Gene 2.0 ST Array (hugene20st)
Description
Affymetrix Human Gene 2.0 ST microarray (ThermoFisher Scientific, Waltham, MA, USA) was used to select differentially expressed genes.
Publication Title
BRD2 induces drug resistance through activation of the RasGRP1/Ras/ERK signaling pathway in adult T-cell lymphoblastic lymphoma.
Sample Metadata Fields
Sex, Age
View Samples- Sus scrofa
- 3 Downloadable Samples
- Illumina HiSeq 2000
Description
To gain insight into the role of testosterone in modulating hepatic fat accumulation, we collected liver tissues from high fat diet-fed intact male pigs, castrated male pigs, and castrated male pigs with testosterone replacement. RNA-Seq was employed to profile hepatic gene expression in pigs with different testosterone levels. Overall design: Liver mRNA profiles of intact male pigs fed a HFC diet, castrated male pigs fed a HFC diet, and castrated male pigs treated with testosterone fed a HFC diet were generated by deep sequencing, using Illumina HiSeq 2000.
Publication Title
Transcriptomic analysis of hepatic responses to testosterone deficiency in miniature pigs fed a high-cholesterol diet.
Sample Metadata Fields
Specimen part, Cell line, Subject
View Samples- Mus musculus
- 17 Downloadable Samples
Description
Mammalian preimplantation development is a complex process involving dramatic changes in the transcriptional architecture. Through single-cell RNA-sequencing (RNA-seq), we report here a comprehensive analysis of transcriptome dynamics from oocyte to morula in both human and mouse embryos. Based on single nucleotide variants (SNVs) in blastomere mRNAs and paternal-specific SNPs, we identify novel stage-specific monoallelic expression patterns for a significant portion of polymorphic gene transcripts (25-53%). By weighted gene co-expression network analysis (WGCNA), we find that each developmental stage can be concisely delineated by a small number of functional modules of co-expressed genes. This result indicates a sequential order of transcriptional changes in pathways of cell cycle, gene regulation, translation, and metabolism in a step-wise fashion from cleavage to morula. Cross-species comparisons reveal that the majority of human stage-specific modules (7 out of 9) are remarkably preserved, only to diverge in developmental specificity and timing in mice. We further identify conserved key members (or hub genes) of the human and mouse networks. These genes represent novel candidates that are likely key players in driving mammalian preimplantation development. Collectively, we demonstrate that mammalian preimplantation development is orchestrated by evolutionarily conserved genetic programs that diverge in developmental timing. Our results provide a valuable resource to dissect gene regulatory mechanism underlying progressive development of early mammalian embryos. Overall design: single-cell RNA-seq of human and mouse blastomeres
Publication Title
Genetic programs in human and mouse early embryos revealed by single-cell RNA sequencing.
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 4 Downloadable Samples
- Affymetrix Mouse Gene 1.0 ST Array (mogene10st)
Description
Using Tbx18Cre to target embryonic DP precursors, we ablate Sox2 early and efficiently, resulting in diminished hair shaft outgrowth. Transcriptional profiling of Sox2 null DPs reveals increased Bmp6 and decreased Bmp inhibitor Sostdc1, a direct Sox2 transcriptional target.
Publication Title
Sox2 in the dermal papilla niche controls hair growth by fine-tuning BMP signaling in differentiating hair shaft progenitors.
Sample Metadata Fields
Specimen part
View Samples- Homo sapiens
- 4 Downloadable Samples
- Illumina HiSeq 2500
Description
Human adult spermatogenesis involves a balance of spermatogonial stem cell self renewal and differentiation, alongside complex germline-niche interactions. To better understand, we performed single cell RNA sequencing of ~7000 testis cells from three healthy men of peak reproductive age. Our analyses revealed multiple distinctive transcriptional 'states' of self-renewing and differentiating spermatogonia, the cellular stages of gametogenesis, five niche cells (Leydig, Myoid, Sertoli, Endothelial, macrophage) and insights into germline-niche communication. Spermatogenesis was reconstructed computationally, which identified sequential coding, noncoding, and repeat-element transcriptional signatures. A new, developmentally early and likely quiescent spermatogonial state is identified (GFRA1-/ETV5-/ID4+/UTF1+/FGFR3+). Notably, certain epigenetic features combined with nascent transcription analyses suggest considerable plasticity within certain spermatogonial populations/states. Key findings were validated via RNA and protein staining. Taken together, we provided the first “Cell Atlas” of the adult human testis, and provide multiple new insights into germ cell development and germ cell – niche interaction. Overall design: We isolated single testicular cell from two infant (13 months old). Two technical replicates were performed for each individual.
Publication Title
The adult human testis transcriptional cell atlas.
Sample Metadata Fields
Sex, Age, Specimen part, Subject
View Samples- Arabidopsis thaliana
- 7 Downloadable Samples
- Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)
Description
RNA prepared from specialized replum cells within siliques provided targets for profiling the Arabidopsis genome during replum cell development.
Publication Title
Laser capture microdissection of plant cells from tape-transferred paraffin sections promotes recovery of structurally intact RNA for global gene profiling.
Sample Metadata Fields
Specimen part
View Samples- Mus musculus
- 22 Downloadable Samples
Affymetrix Mouse Gene 1.0 ST Array (mogene10st)
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
Vitamin C enhances the generation of mouse and human induced pluripotent stem cells.
Sample Metadata Fields
Specimen part, Treatment, Time
View Samples