NHEK cells were plated at a density of 8 x 10 000/cm2 and the cell cultures were grown for 24 hours before addition of 2 mM N-Acetyl-L-Cystein. RNA obtained from cultures grown for 1, 12 and 24 hrs after NAC treatment were compared to RNA from untreated cells at the corresponding time points. I.e 1 hour NAC treated vs 1 hour untreated cells etc. Each EXTRACT represents an individual mRNA extraction and subsequent cDNA synthesis from a batch of totalRNA originating from one cellculture dish.
Global gene expression analysis in time series following N-acetyl L-cysteine induced epithelial differentiation of human normal and cancer cells in vitro.
Specimen part, Subject, Compound, Time
View SamplesCaco-2 human colon carcinoma cells were seeded at a density of 9 x 10 000 cells/cm2 and the cell cultures were grown for 24 hours before addition of 10 mM N-Acetyl-L-Cystein. RNA obtained from cultures grown for 1, 12 and 24 hrs after NAC treatment were compared to RNA from untreated cells at the corresponding time points. I.e 1 hour NAC treated vs 1 hour untreated cells etc. Each "SAMPLE" represents a biological replicate (i.e. separate cellcultures treated similarily) although I have given identical SAMPLE numbers in pairs.
Global gene expression analysis in time series following N-acetyl L-cysteine induced epithelial differentiation of human normal and cancer cells in vitro.
Specimen part, Cell line, Subject, Compound, Time
View SamplesThe aim of the dataset was to study on genome-wide level the effect of Notch inhibition in gene expression on neural crest differentiation of human embryonic stem cells under chemically defined conditions.
Notch signaling regulates the differentiation of neural crest from human pluripotent stem cells.
Specimen part
View SamplesWe extracted RNA from whole cells and RNA from the cytoplasm and performed RNA sequening to compare differences in gene expression level and investigate what is the most appropriate estimate of the amount of mRNA present in a given cell population. The study was based on three human cell lines. Overall design: Analyze of transcriptome in 3 human cell lines (U-2 OS, A-431, U-251MG). Each cell line was prepared with four biological replicates for total RNA and four for cytoplasmic RNA.
Comparison of total and cytoplasmic mRNA reveals global regulation by nuclear retention and miRNAs.
No sample metadata fields
View SamplesForkhead box class O (FoxO) transcription factors regulate whole body energy metabolism, skeletal muscle mass and substrate switching. To elucidate the role of FOXO in skeletal muscle, dominant negative (dn) constructs for FOXO1 (FOXO1dn) or FOXO3 (FOXO3dn) were transfected by electroporation into mouse tibialis anterior muscle and glucose uptake, signal transduction, and glucose stimulated gene expression profiles were assessed. Results were compared against contralateral control transfected muscle.
Regulation of glucose uptake and inflammation markers by FOXO1 and FOXO3 in skeletal muscle.
Sex, Age, Specimen part
View SamplesThe amount of RNA sequencing data on skeletal muscle is very limited. We have analyzed a large set of human muscle biopsy samples and provide extensive information on the baseline skeletal muscle transcriptome, including completely novel protein-coding transcripts. Overall design: Analyze of transcriptome in 23 skeletal muscle biopsy samples from six individuals. Four biopsies from each subject, two biopsies from each leg (except subject 6 which has only three biopsies in total).
The human skeletal muscle transcriptome: sex differences, alternative splicing, and tissue homogeneity assessed with RNA sequencing.
No sample metadata fields
View SamplesmRNA, sncRNA and lncRNA show a clear difference in expression between proliferative phase and 7–9 days after ovulation, thorough described together with lncRNA, snoRNA and snRNA not previously reported in healthy human endometrium Overall design: 7 small RNA and 7 total RNA samples sequenced from endmometrial tissue from two time points of the menstrual cycle. Gene expression from the two time points compared. Additionally 12 small RNA from stromal cells was sequenced.
Comprehensive RNA sequencing of healthy human endometrium at two time points of the menstrual cycle.
No sample metadata fields
View SamplesThis SuperSeries is composed of the SubSeries listed below.
Dual role of FoxA1 in androgen receptor binding to chromatin, androgen signalling and prostate cancer.
Specimen part, Cell line
View SamplesWe report the dual role of FoxA1 in androgen receptor recruitment to the chromatin of androgen responsive prostate cancer cell line LNCaP-1F5 using ChIP-sequencing. Depletion of FoxA1 reprograms both androgen and glucocorticoid receptor recruitment and subsequent gene expression. The ChIP-seq has been performed using AR, FoxA1, GR, H3K4me2 antibodies. We have also mapped the DNaseI-hypersensitive sites (DHS) using deep sequencing.
Dual role of FoxA1 in androgen receptor binding to chromatin, androgen signalling and prostate cancer.
Cell line
View SamplesA subpopulation of pericytes expressing the Glast-CreERT2 transgene (Type A pericytes) has recently been identified as the main source of stromal scar tissue that forms after SCI. Identification of molecules associated with pericyte-derived scarring may offer new therapeutic targets to facilitate axon regeneration following central nervous system (CNS) injury. We conducted genome-wide RNA sequencing of (i) uninjured spinal cord segments and (ii) lesion sites presenting full or attenuated pericyte-derived scarring 14 days after SCI. Overall design: Adult Glast-Rasless-YFP (Glast-CreERT2 x R26R-YFP x Rasless) mice receiving vehicle (Veh) or tamoxifen (Tam) underwent dorsal hemisection at high thoracic level. Fourteen days after SCI, injury sites were dissected out, homogenized and total RNA was isolated from lesions presenting (i) dense (Veh, n=4) and (ii) attenuated (Tam, n=4) pericyte-derived scarring. Age-matched Glast-Rasless-YFP mice served as uninjured controls (n=4).
Reducing Pericyte-Derived Scarring Promotes Recovery after Spinal Cord Injury.
Specimen part, Treatment, Subject, Time
View Samples