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Sequencing-based assays (Page 124)
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GSE79470: Next Generation Sequencing Analysis of human embryonic stem cells derived MESP1-mTomato reporter cells
Purpose: To compare the transcriptome of MESP1-mTomato reporter cells at undifferentiated state, mes...
GSE71505: SMARCB1-mediated SWI/SNF complex function is essential for enhancer regulation [cell line_RNA-seq]
SMARCB1 (SNF5/INI1/BAF47), a core subunit of the SWI/SNF (BAF) chromatin remodeling complex, is inac...
GSE69092: ELAVL2-regulated transcriptional networks in human neurons link atlernative splicing, autism and human neocortical evolution
The role of post-transcriptional gene regulation in human brain development and cognitive diseases r...
GSE98393: Selective expression of long non-coding RNAs in a breast cancer cell progression model
Long non-coding RNAs are emerging as key regulators of cancer cell activities. In this study, our go...
GSE148985: Mapping of hydrogen sulfide molecular targets in human keratinocytes
In the present paper, we report on the pan-genomics and pan-proteomics analysis of cultured epitheli...
GSE66744: Decoding breast cancer tissue-stroma interactions using species-specific sequencing
Decoding genome-wide effects of experimental tissue-tissue or cell-cell interactions is important, f...
GSE70089: Whole genome analysis of the methylome and hydroxymethylome in normal and malignant lung and liver [RNA-Seq]
DNA methylation at the 5-postion of cytosine (5mC) is a well-established epigenetic modification whi...
GSE65991: Transcriptomic analysis of cultured corneal endothelial cells as a validation for their use in cell-replacement therapy
The corneal endothelium plays a primary role in maintaining corneal homeostasis and clarity, and mus...
GSE66777: RNA-seq analysis of gene expression patterns responding to TSA treatment during hESC neural differentiation
We report the differential roles of an HDAC inhibitor-TSA during hESC nerual commitment. In the init...
GSE66086: m6A level and isoform characterization sequencing (m6A-LAIC-seq) reveal the census and complexity of the m6A epitranscriptome
N6-methyladenosine (m6A) is a widespread reversible chemical modification of RNAs, implicated in man...
GSE148562: A functional link between miR-200a and ELK3 regulates the metastatic nature of breast cancer
The ectopic expression of miR-200a impaired the migration and invasion of TNBC cells by reducing the...
GSE69239: Long non-coding RNA profiling of human lymphoid progenitors reveals transcriptional divergence of B cell and T cell lineages
To elucidate the transcriptional landscape that regulates human lymphoid commitment during postnatal...
GSE67196: Distinct brain transcriptome profiles in c9orf72-associated and sporadic ALS
Increasing evidence suggests that defective RNA processing contributes to the development of amyotro...
GSE68180: Unbiased evaluation of cell-free amniotic fluid transcriptome of term and preterm infants to detect fetal maturity
Objective: Amniotic fluid (AF) is a proximal fluid to the fetus containing higher amounts of cell-fr...
GSE66217: Single Cell Analysis Reveals Unexpected Transcriptional Heterogeneity of Neural Progenitors in the Developing Human Cortex
The human cerebral cortex depends for its normal development and size on a precisely controlled bala...
GSE66207: mRNA and small RNA associated with Crohn's disease behavior [RNA-Seq]
There is a need for reliable prognostic markers that can guide therapeutic intervention in Crohns di...
GSE74977 (human): The LRF/ZBTB7A transcription factor is a BCL11A-independent repressor of fetal hemoglobin
Hemoglobinopathies, including sickle cell disease and _-thalassemia, are global public health concer...
GSE98386: Expression profile of early and mid-secretory healthy human endometrium revealed by RNA-seq
Inner uterine lining or endometrium is a unique constantly self-renewed adult tissue that is vital f...
GSE67070: Transcriptome profiling links intrinsic stem cell and proneural properties of basal epithelial cells to human prostate tumorigenesis
The prostate gland mainly contains basal and luminal cells constructed as a pseudostratified epithel...
GSE135873: Effect of zinc chelation in Caco-2 cells
To identify the molecular pathways that are perturbed due to transient zinc chelation; Zinc is known...
GSE98547: RAP2 Mediates Mechanotransduction to Hippo pathway
Mammalian cells are surrounded by the extracellular matrix (ECM), which regulates intercellular sign...
GSE141698: Genome-wide maps of O-GlcNAc proteins in human breast cancer cells by next generation sequencing
We applied the chemical reporter-based metabolic labeling method to acquire O-GlcNAc modified protei...
GSE71401: Tumor hypoxia causes DNA hypermethylation by reducing TET activity (RNA-Seq)
Hypermethylation of tumor suppressor gene (TSG) promoters confers growth advantages to cancer cells,...
GSE66182: Oncogenic MYC induces a dependency on the spliceosome in human cancer
c-MYC (MYC) overexpression or hyperactivation is one of the most common drivers of human cancer. Des...
GSE69312: Genome-wide maps of human OEC innate immune responses to Burkholderia
We report a transcriptional response in human OECs that encompasses multiple innate immune networks ...
GSE67848: Characterization of Type I Interferon pathway during Hepatic Differentiation of Human Pluripotent Stem Cells and hepatitis C virus infection
Pluripotent stem cells are being actively studied as a cell source for regenerating damaged liver. ...
GSE69597: Refining brucellosis diagnosis by blood transcriptional profiling.
Diagnosis of brucellosis remains challenging for several reasons, including lack of culture sensitiv...
GSE67844: PANCR, the PITX2 adjacent noncoding RNA, is specifically expressed in human left atria and regulates PITX2c expression
Purpose: Common genetic variation at chromosome 4q25 lead to the strongest locus associated with atr...
GSE67427: Mycobacterial infection induces a specific human innate immune response
The innate immune system provides the first response to pathogen infection and orchestrates the acti...
GSE84346: Transcriptional response to hepatitis C virus infection and interferon alpha treatment in the human liver
Hepatitis C virus (HCV) is widely used to investigate host-virus interactions and cellular responses...
GSE67447: The MEF2B Regulatory Network - RNA-seq data
Myocyte enhancer factor 2B (MEF2B) is a transcription factor with somatic mutation hotspots at K4, Y...
GSE69114: Somatic cell fusions reveal extensive heterogeneity in basal-like breast cancer [RNA-Seq]
Basal-like and luminal breast tumors have distinct clinical behavior and molecular profiles, yet the...
GSE69637: RNA-seq identifies novel lncRNAs involved in vascular smooth muscle cell proliferation
Smooth muscle cell (SMC) phenotypic switching from a contractile to a synthetic state is implicated ...
GSE68795: Reprogrammed myeloid cell transcriptomes in NSCLC
Lung cancer is the leading cause of cancer related mortality worldwide, with non-small cell lung can...
GSE69383: The apoptotic network and expression of BH3-containing proteins predict phenotypic response to BET bromodomain inhibitors
Small molecule inhibitors of the bromodomain and extraterminal (BET) family of proteins are in clini...
GSE85083: Control of gene expression in senescence through transcriptional read-through of convergent protein-coding genes [RNA-Seq siRNA H2A.Z]
Antisense RNAs are non-coding RNAs, which can regulate their corresponding sense RNAs and are genera...
GSE67892: CTCF and CohesinSA-1 Mark Active Promoters and Boundaries of Repressive Chromatin Domains in Primary Human Erythroid Cells [RNA-Seq]
CTCF and cohesinSA-1 are regulatory proteins involved in a number of critical cellular processes inc...
GSE73121: Single-cell transcriptome profiling for metastatic renal cell carcinoma patient-derived cells [RNA-seq]
Clear cell renal cell carcinoma (ccRCC) initiated from the renal epithelium is the most prevalent hi...
GSE69110: Distinct regulatory programs for Sox9 in transcriptional regulation of the developing mammalian chondrocyte [RNA-seq]
We compared Sox9-association at chondrocyte targets to a broad catalogue of regulatory indicators of...
GSE70909: The impact of oil spill to lung health insights from an RNA-seq study of human airway epithelial cells
To reveal the potential effects of oil and oil dispersants on the respiratory system at the molecula...
GSE69604: Identification of CEBPD regulated genes in MCF7 cells
Purpose: To determine which genes are regulated by CEBPD in MCF-7 cells.; Methods: MCF7 cells were t...
GSE70050: Lack of allergy to timothy grass pollen is not a passive phenomenon but associated with allergen specific modulation of immune reactivity
Timothy grass (TG) pollen is a common seasonal airborne allergen associated with symptoms ranging fr...
GSE68836: BRCA1, R-loops and Recombination defects in Ewing's sarcoma (RNA-seq)
Ewings sarcoma family of tumors (ESFT) is an aggressive pediatric bone and soft tissue cancer. It is...
GSE68452: Role of cervicovaginal microbiota in genital inflammation
We performed gene expression analysis using the SCRB-Seq method from cervical and peripheral blood a...
GSE69932: Comparison of the transcriptome and chromatin state between human cord blood HSC and human iPSC derived hematopoietic progenitor using next-generation sequencing
We analyzed the transcriptome and transposase accessible chromatinusing RNAseq and ATAC-seq, respect...
GSE71204: Comprehensive analysis of microRNA expression in regionalized human neural progenitor cells reveals microRNA-10 as a caudalizing factorl
MicroRNAs (miRNAs) have been implicated in regulating multiple processes during brain development in...
GSE145783: Transcriptional regulators of the amino acid response pathway in leukemia
CRISPR/Cas9-based genetic screening revealed ZBTB1 as a critical mediator of the response of T-ALL c...
GSE68925: RNAi profiling of primary human AML cells identifies ROCK1 as a therapeutic target and nominates Fasudil as an anti-leukemic drug.
Acute myeloid leukemia (AML) is characterized by a marked genetic heterogeneity, which complicates t...
GSE69738: Gene body H2B1ub regulates RNA Polymerase II pause release and is not needed for transcription elongation
Histone H2B monoubiquitylation (H2Bub1) is localized to transcribed regions of genes and spread in p...
GSE71326: A Surveillance System of Active Enhancers by a RACK7-histone Demethylase Complex (RNA-Seq II)
Primed enhancers are marked by histone H3K4 mono-methylation (H3K4me1), and the conversion to active...
GSE69626: Integrated Transcriptomic and Epigenomic Comparison of Human Induced Pluripotent Stem Cells Generated from Various Reprogramming Methods
Within the last decade, multiple reprogramming methods have been developed to generate human induced...
GSE69549: Transcriptome analysis of CD4+ T cells reveals imprint of BACH2 and IFN regulation
We used RNA sequencing to profile over 70 transcriptomes of CD4+ T cells, a cell type crucial for Co...
GSE80554: Accelerated functional evolution of regulatory lncRNAs in the human lineage
Long noncoding RNA sequences evolve relatively rapidly, but it is unclear whether this is due to rel...
GSE69692: 3D regulatory landscape of human naive pluripotency [RNA-Seq]
The control of cell identity is orchestrated by transcriptional and chromatin regulators in the cont...
GSE69678: TALENs-mediated gene disruption of FLT3 in leukemia cells: Using genome-editing approach for exploring the molecular basis of gene abnormality
Novel analytic tools are needed to elucidate the molecular basis of leukemia-relevant gene mutations...
GSE69656: An Alternative Splicing Event Amplifies Evolutionary Differences Between Vertebrates
Alternative splicing (AS) generates extensive transcriptomic and proteomic complexity. However, the ...
GSE113698: Precise and Predictable CRISPR Chromosomal Rearrangement Editing Reveals Principles of Cas9-mediated Nucleotide Insertion
Chromosomal rearrangements including large DNA-fragment inversions, deletions, and duplications by C...
GSE69021: Gene target specificity of the Super Elongation Complex (SEC) family: How HIV-1 Tat employs selected SEC members to activate viral transcription
The AF4/FMR2 proteins AFF1 and AFF4 act as a scaffold to assemble the Super Elongation Complex (SEC)...
GSE68611: RC3H1 posttranscriptionally regulates A20 mRNA and modulates the activity of the IKK/NF-kB pathway [RNA-Seq]
The RNA-binding protein RC3H1 (also known as ROQUIN) promotes TNFalpha mRNA decay via a 3'UTR consti...
GSE71456: Derivation and differentiation of haploid human embryonic stem cells [RNA-Seq 1]
Diploidy is a fundamental genetic feature in mammals, in which haploid cells normally arise only as ...
GSE69567: Combinatorial Regulation Mediated by Biochemically Distinct Forms of SWI/SNF [RNA-Seq]
The precise makeup of chromatin remodeling complexes is important for determining cell type and cell...
GSE71100: LIN28B/let-7 Axis Regulates Multiple Myeloma Proliferation by Enhancing MYC and RAS Survival Pathways
We report that LIN28B is overexpressed and associated with an adverse outcome in MM patients. LIN28B...
GSE155241: Identification of Drugs Blocking SARS-CoV-2 Infection using hPSC-derived Lung and Colonic Organoids
The SARS-CoV-2 has already caused over twelve million COVID-19 cases and half a million deaths world...
GSE70810: A network-based strategy for prioritizing hits from chemical screening data by leveraging genetic, epigenetic and transcriptional datasets
Small molecule screens are widely used to prioritize compounds for development of pharmaceuticals an...
GSE73982: A Primate lncRNA Mediates Notch Signaling During Neuronal Development by Sequestering miRNA [SHSY5Y cells]
Long non-coding RNAs (lncRNAs) are a diverse category of transcripts with poor conservation and have...
GSE71520: Synergistic gene expression signature observed in TK6 cells upon co-exposure to UVC-irradiation and protein kinase C-activating tumor promoters, a dosage study (study 2/2)
The purpose of this study, including this dosage series and another time course series, was to esta...
GSE81475: Zika Virus Disrupts Phospho-TBK1 Localization and Mitosis in Human Neural Stem Cell Model Systems
Purpose: Use single cell RNA-seq technology on neural epithelial stem cell culture to understand the...
GSE70874: Spontaneous single-copy loss of TP53 in human embryonic stem cells markedly increases cell proliferation and survival [RNA-Seq]
The potential safety issues related to the acquisition of common genomic aberrations in hPSC culture...
GSE74999: HDAC inhibitors cause site-specific chromatin remodeling at PU.1-bound enhancers in K562 cells
We used the myelogenous leukemia line K562 as a model of HDACi-induced differentiation to investigat...
GSE71238: Deciphering H3K4me3 Broad Domains Associated With Gene Regulatory Networks and Conserved Epigenomic Landscapes in the Human Brain
ChIP-seq and RNA-seq datasets newly generated for this manuscript are included in the SubSeries list...
GSE72577: Circular RNAs are down-regulated in KRAS mutant colon cancer cells and can be transferred to exosomes
Recent studies have shown that circular RNAs (circRNAs) are abundant, widely expressed in mammals, a...
GSE99209: Microvesicle-mediated delivery of miR-1343: impact on markers of fibrosis
We previously identified miR-1343 as a potent repressor of TGF-b signaling and fibrosis through the ...
GSE70685: Musashi-2 attenuates AHR signalling to expand human haematopoietic stem cells
A greater understanding of the molecular pathways that underpin the unique human hematopoietic stem ...
GSE71275: CRISPR Inversion of CTCF Sites Alters Genome Topology and Enhancer/Promoter Function
CTCF/cohesin play a central role in insulator function and higher-order chromatin organization of ma...
GSE71284: Truncation of LOC100288798 (SLC38A4-AS) lncRNA in human haploid KBM7 cell line
Many thousand long non-coding (lnc) RNAs are mapped in the human genome. Time consuming studies usin...
GSE71289: Transcriptome profiling of human neural progenitor cells and neurons with DISC1 interruption
Purpose: Genetic and clinical association studies have identified disrupted-in-schizophrenia 1 (DISC...
GSE79280: Parental allele specific single-cell transcriptome dynamics reveal incomplete epigenetic reprogramming in human female germ cells
In contrast to mouse, human female germ cells develop asynchronously. Germ cells transition to meios...
GSE76023: LncPRESS1 is a p53-regulated lncRNA that safeguards pluripotency by disrupting SIRT6 mediated de-acetylation of histone H3K56
Recent evidence suggests that lncRNAs play an integral regulatory role in numerous functions, includ...
GSE80131: Topoisomerase 1 inhibition suppresses inflammatory genes and protects from death by inflammation (RNA-Seq)
The host innate immune response is the first line of defense against pathogens and is orchestrated ...
GSE69896: Cellular androgen content influences enzalutamide agonism of F877L mutant androgen receptor
Prostate cancer is the most commonly diagnosed and second-most lethal cancer among men in the United...
GSE71797: Genome-wide RNA-sequencing (RNA-seq) of benign and malignant prostate cell lines without and with androgen (R1881) stimulation.
RNA-seq data were obtained from hTERT immortalized human prostate transit amplifying EP156T cells (+...
GSE71569: Interactions of aCPs with Cytosine-rich Polypyrimidine Tracts Enhance Splicing of Cassette Exons
Alternative splicing comprises a robust generator of mammalian transcriptome complexity. Splice site...
GSE71594: Transcriptome of iPSC-derived Neural Cells with Heterozygous Knockout in CHD8
CHD8, encoding Chromodomain helicase DNA binding protein 8, is a top autism spectrum disorders (ASDs...
GSE71890: The Polycomb protein BMI1 induces an invasive gene expression signature in melanoma that promotes metastasis and chemoresistance.
The epigenetic regulator BMI1 is upregulated in many human malignancies and has been implicated in c...
GSE75140: Human cerebral organoids recapitulate gene expression programs of fetal neocortex development.
Cerebral organoids three-dimensional cultures of human cerebral tissue derived from pluripotent ste...
GSE71812: FUS KO mRNA sequencing and anti-FUS RNA immunoprecipitation sequencing
The aim of our study is to identify the role of FUS in shaping the transcriptome. RNA-seq of two FUS...
GSE71878: Transcript abundance in A-T-derived iPSC: Comparing isogenic cells to unrelated individual
Induced pluripotent stem cells (iPSC) were prepared from multiple subjects with Ataxia-telangiectasi...
GSE71613: RNA-Sequencing shows novel transcriptomic signatures in failing and non-failing human heart
The knowledge of an expression network signature in end-stage heart failure (HF) diseased hearts may...
GSE71900: AKT Inhibition Promotes Non-autonomous Cancer Cell Survival [RNA-Seq]
Small-molecule inhibitors of AKT signaling are being in evaluated in patients with various cancer ty...
GSE74958: Generation of Patient-Matched Malignant and Normal Primary Cell Cultures from Clear Cell Renal Cell Carcinoma Patients
Transcriptome profiling of de novo-derived ccRCC cell cultures and their matching parental tumours. ...
GSE72400: naive T cell heterogeneity after neonatal thymectomy
The generation of new naive T-cells is dependent on thymic output, but in adults the naive T-cell po...
GSE73313: TSLP acts on neutrophils to drive complement-mediated killing of methicillin-resistant Staphylococcus aureus
Staphylococcus aureus can cause serious skin, respiratory, and other life-threatening invasive infec...
GSE75270: The SPOP-containing Complex Functions as an E3 Ligase for SETD2 to Regulate Gene-Specific H3K36me3-Coupled Alternative Splicing
H3K36me3 has been reported to associate with active gene expression, and SETD2 is the mainly methylt...
GSE71862: Differential Gene Expression between MCF10A and MCF7 cells
These RNA-seq data were generated to correlate with genomic interaction data in a related Hi-C analy...
GSE72437: Effect of Hypoxia in Severe Preeclampsia through Epigenetic Regulation
Though the pathophysiology of preeclampsia (PE) is unclear worldwide, placental hypoxia has been imp...
GSE71960: Research resource: global identification of estrogen receptor target genes in triple negative breast cancer cells
The goal of this work was to identify all estrogen receptor beta target genes using RNA sequencing i...
GSE75146: Nudt3 is a mRNA Decapping Enzyme That Modulates Cell Migration
The Dcp2 and Nudt16 Nudix hydrolases, are mRNA decapping enzymes that preferentially modulate stabil...
GSE72259: Potent and targeted activation of HIV-1 using the CRISPR/Cas9 activator Complex
Integration of the HIV-1 provirus in the host genome ensures a persistent supply of latently infecte...
GSE71831: Deletion of DXZ4 on the human inactive X chromosome eliminates superdomains and impairs gene silencing
During interphase, the inactive X chromosome (Xi) adopts an unusual 3D configuration known as the Ba...
GSE72299: Gene expression in TAL1-driven T-cell ALL in response to TAL1-KD, UTX-KD, and GSKJ4 treatment
T-cell Acute Lymphoblastic Leukemia (T-ALL) is a heterogeneous group of hematological tumors compose...