title: Long noncoding RNA INCA1 regulates tumor interferon signaling [CLIP-seq]

status: Public on Jul 29 2020

city: Boston

first: Marco

last: Mineo

state: MA

address: 60 Fenwood Rd, BTM 8016N

institute: Brigham and Women's Hospital

summary: Tumor interferon signaling regulates the expression of immunosuppressive molecules and promotes cancer immune evasion. Although the role of long noncoding RNAs (lncRNAs) in the regulation of gene expression is now emerging, their function in tumor interferon signaling remains unexplored.  We have identified the interferon-γ (IFNγ)-stimulated non-coding RNA 1 (INCA1) as a novel lncRNA expressed form the PD-L1 locus. INCA1 is expressed in multiple tumor types and its levels increase after IFNγ stimulation. Silencing INCA1 decreased the expression of several interferon-stimulated genes (ISGs). We discovered that the transcripts of some ISGs are negatively regulated by HNRNPH1. We demonstrate that binding of INCA1 to HNRNPH1 is required for ISG expression. Overall, our findings reveal a mechanism of tumor interferon signaling regulation mediated by the lncRNA INCA1.

overall_design: Melanoma cell line was stimulated with interferon gamma for 6 hours. RNAs bound to HNRNPH1 were identified by CLIP-seq using Illumina HiSeq4000.

first: E

last: Chiocca


title: Control of osteoblast regeneration by a train of Erk activity waves

status: Public on Sep 23 2020

city: Madison

first: Jianhong

last: Ou

state: Wisconsin

address: 330 N Orchard Street

country: USA

institute: Morgridge Institute For Research

type: Expression profiling by high throughput sequencing

summary: We report here a dataset regarding the transcriptome of Erk active osteoblasts in regenerating zebrafish scales. We recently discovered that the marker osx:Venus-hGeminin anti-correlates with Erk activity in those cells. Thus, by sorting (using FACS) cells based on both the expression of an osteoblast marker (osx::H2A-mCherry) and the levels of hGeminin, we could sort osteoblasts into separate Erk+ and Erk- populations and perform RNAsequence (in triplicates). We found that dusp and sprouty transcripts are elevated in osteoblasts with high Erk activity. Specifically, dusp2, dusp5 and spry4 transcripts are predominant in scales and consistently present at higher levels in the population enriched for Erk+ cells.

overall_design: Comparison of the transcriptome of osteoblasts of regenerating zebrafish scales with high and low Erk activity. Cells are sorted on the basis of their osx:Venus-hGeminin signal, which anti-correlates with Erk activity.

first: Alessandro

last: De Simone

first: Stefano

last: Di Talia


title: Long noncoding RNA INCA1 regulates tumor interferon signaling.

summary: This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: RNA-seq of primary human aortic smooth muscle cells treated with AEA

status: Public on Apr 21 2020

city: bad nauheim

first: Stefan

last: Günther

address: ludwigtr. 43

country: Germany

institute: MPI for heart and lung research

summary: Primary human aortic smooth muscle cells (HAoSMC) were starved over night in 1% FCS. On the next day cells were treated with 100nM Anandamide (AEA) or EtOH as control for 4h in presence of 10µM diclofenac. Subsequently cells were treated with or without 10ng/mL IL-1β for last 1.5h.

overall_design: RNA Seq analysis of human aortic smooth muscle cells after treatment with the endocannabinoid anandamide (AEA) with or without IL-1β.

first: Beatrice

last: Pflüger-Müller

first: Matthias

middle: S

last: Leisegang

first: Ralf

middle: P

last: Brandes


title: Tp53 suppression promotes cardiomyocyte proliferation during zebrafish heart regeneration

status: Public on Sep 21 2020

summary: Transcriptome sequencing of uninjured and regenerating (7dpi) tp53M214K and tp53WT ventricles.

overall_design: 4 experimental groups were analyzed in triplicates: 1) uninjured ventricle of tp53 mutant fish; 2) injured ventricle of tp53 mutant fish; 3) uninjured ventricle of tp53 wild type fish; 4) injured ventricle of tp53 wild type fish.

first: V

last: Cigliola

first: A

last: Shoffner

first: K

middle: D

last: Poss


title: Single cell sequencing facilitates the identification of colonic epithelial Tcf4 Lin-  stem cells that give rise to absortive and secretory precursor populations.

status: Public on Apr 01 2020

city: Salt Lake City

first: Mario

middle: R.

last: Capecchi

state: UT

address: 15 North 2030 East

institute: University of Utah

summary: We report the Single Cell analysis of Tcf4 Lin- cells isolated from the mouse colon.

overall_design: Isolation and single cell sequencing of Tcf4 Lin- cells to define the Tcf4 Lin- populations within the colon

first: Melinda

middle: L

last: Angus-Hill

first: Tim

last: Mosbruger

first: Annika

middle: V

last: Thorpe

first: Saher

last: Hammoud


title: Whole blood transcriptomic analysis of beef cattle at arrival identifies potential predictive molecules and mechanisms that indicate animals that naturally resist bovine respiratory disease

status: Public on Jan 14 2020

city: Canyon

first: Matthew

last: Scott

state: TX

address: 3201 Russell Long Blvd

institute: Texas A&M University

summary:
Objectives: Identify gene products that characterize the biological status of typical calves which have been recently weaned, transported, and co-mingled prior to arrival at stocker facilities in order to identify gene products associated with BRD resistance.
Methods: Whole blood RNA profiles were generated via NGS approach, using an Illumina HiSeq 3000. Individual samples were processed using an adaptation of the Revised Tuxedo Suite protocol (Tuxedo 2), then analyzed in R using edgeR and DESeq2 with likelihood-ratio testing. Genes were considered differentially expressed with an FDR cutoff of 0.10. qRT-PCR validation was performed using a SYBR green assay.
Results: 135 differentially expressed genes were identified between healthy and BRD animals; 36 were shared between edgeR and DESeq2. Biological processes, using the 36 DEGs, were identified to be involved with inflammation, defense response, macrophage function, and lipoxin metabolism/biosynthesis. Enriched pathways of the 36 DEGs were involving SPM synthesis and angiotensinogen metabolism to angiotensins. Genes increased in diseased animals had known function towards anitmicrobial activity.
Conlusions: Our analysis has provided, for the first time, a list of whole blood molecular biomarkers that may predict disease risk in the first 28 days of stocker cattle arrival. We identified pathways related to immune response, inflammatory mediation, metabolic processes, and stress regulation. Using whole blood transcriptomic analysis, this study provides an insight to host immunity in response to BRD.

overall_design: Whole blood mRNA of stocker cattle at facility arrival were generated through next-generation sequencing utilizing an Illumina HiSeq 3000.


title: Stable knockdown of PLAGL2 in hepatocellular carcinoma cells

status: Public on Oct 11 2018

city: Nanjing

first: Hu

last: Weiwei

address: No. 639, long Mian Road, Jiangning District, Nanjing

country: China

institute: China Pharmaceutical University

summary: Pleomorphic adenoma gene like-2 (PLAGL2), along with PLAG1 and PLAGL1, belong to PLAGL gene family of zinc-finger transcription factors, PLAG proteins are highly homologous, and with the structures of the seven C2H2 zinc finger domain on the N-terminal. PLAG proteins recognize similar GC rich consensus DNA-binding sequences, that these family members function as regulators of transcription target genes and pathways. PLAGL2 has been shown to have both oncogenic and tumor suppressor activities, PLAGL2 is mainly consided as a transcription factor, other functions which may contribute to its oncogenic potential are not clear. So it is meaningful to study the role of PLAGL2 in different diseases. To our knowledge, there is no report about the PLAGL2 in the development process of HCC.

overall_design: mRNA profile of Hepatocarcinoma cell line HCC-LM3 with shctrl and shPLAGL2 were generated by deep sequencing

first: Yong

last: Yang

first: Weiwei

last: Hu


title: Genetic interaction mapping (GIM) for factors involved in RNA and protein synthesis and degradation

status: Public on Dec 31 2019

city: Paris

first: Cosmin

last: Saveanu

address: 25-28 rue du docteur Roux

department: Genomes and Genetics

country: France

institute: Institut Pasteur

summary:
A S. cerevisiae strain a gene of interest mutated or deleted was combined with two collections of yeast mutants: one in which non-essential genes were deleted and one in which an long 3' UTR extension has been added to the mRNA of essential genes (GIM method, Decourty et al., 2008). Combined double-mutant deletion cells growth was quantified using barcodes that are specific for each gene mutation. A reference population was obtained by mixing the results of 15 GIM screens DNA prior to barcode amplification and labeling (Decourty et al., in preparation).
The identification of genetic interactions between genes involved in different cellular pathways indicate new functions for previously characterized genes and new links between

overall_design: 312 independent experiments were tested using Agilent microarrays


title: Massively Parallel Reporter Assay of human-specific substitutions in neurodevelopmental enhancers

status: Public on Nov 26 2019

city: New Haven

first: James

middle: Patrick

last: Noonan

state: CT

address: 333 Cedar Street

department: Genetics

institute: Yale University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: We performed a Massively Parallel Reporter Assay (MPRA) to screen >30,000 human-specific substitutions in ChIP-seq-identified Human Gain Enhancers (HGEs) and Human Accelerated Regions (HARs), highly conserved non-coding regions that show accelerated sequence evolution in humans. After comparing human and chimpanzee reference alleles, we used a second MPRA to deconvolute individual substitutions within differentially active enhancers from substitutions in the same fragment and from other variants (human segregating variants or chimpanzee-specific variants) to isolate their specific effects on enhancer activity.

sample_organism:
Pan troglodytes
Homo sapiens

platform_organism:
Pan troglodytes
Homo sapiens

overall_design: This submission contains data for two MPRA experiments. MPRA1 contains data for an inert library, a competent library, and four experimental replicates. MPRA2 contains data for an inert library and two experimental replicates. This submission also contains ATAC-seq data for hNSCs (three replicates).

first: Severin

last: Uebbing

first: Jake

last: Gockley


title: MBD1 activates neuronal developmental genes through modulating chromatin structure during neuronal maturation

status: Public on May 15 2018

first: Xinyu

last: Zhao

state: WI

address: 1500 HIGHLAND AVE, T513 Waisman Center

department: Department of Neuroscience

institute: University of Wisconsin-Madison


title: Tissue Regeneration Enhancer Element Discovery by Chromatin Accessibility Profiling of Regenerating Zebrafish Fins

status: Public on Jul 19 2020

first: Jianhong

last: Ou

summary: Mammalian genomes likely encode all gene products required to regenerate an amputated limb, yet they lack the correct instructions for strategically modulating those gene products to accomplish limb regeneration. Zebrafish and many other non-mammalian vertebrates possess these instructions, which exist as gene cis-regulatory elements. Here, to identify candidate tissue regeneration enhancer elements (TREEs) important for zebrafish fin regeneration, we performed ATAC-seq from bulk tissue or purified fibroblasts of uninjured and regenerating caudal fins.  We identified thousands of DNA regions from each tissue type with dynamic accessibility during regeneration, and assigned these regions to proximal genes with corresponding changes in RNA levels. To determine whether these profiles revealed bona fide TREEs, we tested the sufficiency of several sequences in stable transgenic and mutant lines. These experiments identified new regulatory sequences near several induced and/or required genes, including fgf20a, cx43, and mdka, with unique expression domains for each confirmed TREE.  Deletion of TREE sequences from the zebrafish genome revealed requirements and redundancies surrounding cis-regulatory regions. Our study generates a novel resource for dissecting the regulatory mechanisms of appendage regeneration.

overall_design: Samples were enzymatically dissociated with Liberase and collected in biological triplicates for RNA and ATAC library preparation. Corresponding sample pools include: whole fin 0 dpa and whole fin 4 dpa whole fin 0 dpa and whole fin 1 dpa, and fibroblast 0 dpa and fibroblast 4 dpa.

first: John

last: Thompson

first: Kenneth


title: Long noncoding RNA INCA1 regulates tumor interferon signaling

first: Marco

last: Mineo

type: Non-coding RNA profiling by high throughput sequencing

summary: Tumor interferon signaling regulates the expression of immunosuppressive molecules and promotes cancer immune evasion. Although the role of long noncoding RNAs (lncRNAs) in the regulation of gene expression is now emerging, their function in tumor interferon signaling remains unexplored.  We have identified the interferon-γ (IFNγ)-stimulated non-coding RNA 1 (INCA1) as a novel lncRNA expressed form the PD-L1 locus. INCA1 is expressed in multiple tumor types and its levels increase after IFNγ stimulation. In this study we performed transcriptome analysis (RNA-seq) of INCA1 knockdown cells and show that INCA1 regulates the expression of several interferon-stimulated genes. Overall, our findings reveal INCA1 as a critical component of the tumor interferon signaling.

overall_design: Tumor cell lines stable expressing shRNA control or shRNA targeting INCA1 were stimulated with interferon gamma for 24 hours. RNA expression profiles were generated by RNA-seq, in triplicate, using Illumina NovaSeq6000.

first: E

middle: A

last: Chiocca


title: RNAseq analysis on E14.5 cortical material from mouse, Tcf4-ko line vs WT littermates.

status: Public on Jul 01 2020

city: Amsterdam

first: Marten

middle: Piet

last: Smidt

state: NH

address: Sciencepark 904

department: SILS

country: Netherlands

institute: UVA

summary: Tcf4 encodes cortical differentiation during development

overall_design: examination of 2 groups form TCF4ko and WT littermates, N=3 form both. RNA samples from E14.5 Cortical dissected material.

first: M

first: S

last: Mesman


title: mRNA and miRNA expression data from human Ewing's sarcoma (ES)

status: Public on Jul 14 2015

city: Yufu

first: Masanori

last: Kawano

address: 1-1 Idaigaoka, Hasama-machi

country: Japan

institute: Oita University

type:
Non-coding RNA profiling by array
Expression profiling by array

platform_organism:
Homo sapiens
synthetic construct


title: Granulosa cell expression data from five different time points before and up to 36 hours after induction of ovulation in women receiving fertility treatment

status: Public on Mar 01 2020

city: Køge

first: Liv

middle: la Cour

last: Poulsen

address: Lykkebækvej 14

department: Gynaecology and Obstetrics

country: Denmark

institute: Zealand University Hospital

summary:
The process of ovulation includes oocyte meiotic maturation, follicle rupture and transformation of the follicle into a corpus luteum. These events are initiated by the midcycle surge of gonadotropins and require the coordinated regulation of thousands of genes. The aim of the study was to monitor the changes in granulosa cell gene expression across five different time points during the first 36 hours of ovulation until follicle rupture, in order to increase our understanding of the events of human ovulation.
We conducted a prospective cohort study including women undergoing ovarian stimulation for fertility treatment. Women were treated in a standard antagonist protocol with individually dosed human menopausal gonadotropin (hMG) or recombinant follicle stimulating hormone (rFSH). Ovulation was induced with either recombinant hCG (rhCG) or gonadotropin releasing hormone agonist (GNRHa). The granulosa cells were collected by transvaginal ultrasound-guided follicle puncture of one follicle at two specific time points during ovulation (repeated measurements), and the study covered a total of five time points: before ovulation induction (OI), 12, 17, 32 and 36 hours after OI.

overall_design: Fifty patients were included resulting in 100 samples of granulosa cells (two repeated samples per patient). 17 out of 100 samples were excluded from further analysis because of either insufficient RNA or bad quality of RNA resulting in outliers. The 83 remaining samples represented time points 0h (n=17), 12h (n=7), 17h (n=6), 32h (n=9) and 36h (n=44).

first: Olga

last: Østrup

first: Claus

last: Yding Andersen

first: Marie

last: Grøndahl

first: Anne

middle: M

last: Englund


title: Transcriptomes of the hybrid mouse diversity panel subjected to Isoproterenol challenge

status: Public on Jul 10 2013

city: Los Angeles

first: Christoph

middle: Daniel

last: Rau

state: United States

address: 675 Charles E Young Drive S

institute: UCLA

summary: Transcriptomes performed on left ventricular heart samples from mice of the hybrid mouse diversity panel, a set of over a hundred inbred strains of mice.  In this project, the strains were challenged with Isoproterenol, a beta-adrenergic agonist to induce cardiac hypertrophy and failure.  Results are useful for the analysis of heart-related traits in mice

overall_design: Mice were given three weeks of ISO @ 20ug/g/day for three weeks, then sacrificed.  Left ventricles from these mice and matched controls were used for transcripome analysis.

first: Jessica

last: Wang

first: Yibin

first: Aldons

middle: J

last: Lusis


title: High throughput analysis of three human adipose cell lines PAZ6, SGBS and SW872

status: Public on Jan 01 2015

city: Doha

first: Andrea

last: Guennoun

address: PO Box 24144

department: Genetic Medicine

country: Qatar

institute: Weill Cornell Medical College in Qatar

summary: We report molecular characterization of human brown and white adipocytes. We showed that PAZ6 and SW872 cells exhibit classical molecular and phenotypic markers of brown and white adipocytes, respectively. However, SGBS cells presented a versatile phenotype of adipocyte

overall_design: Sequencing of three human adipocytes cell lines (SGBS, SW872 and PAZ6) in undifferentiated and differentiated stages.

last: Worschech

first: Melissa

last: Kazantzis

first: Remy

last: Thomas

first: Martin

last: Wabitsch

first: Daniel

last: Tews

first: Mouaadh

last: Abdelkarim

first: Vladimir

last: Zilberfarb

first: A

last: Strosberg

first: Lotfi

last: Chouchane


title: Long noncoding RNA expression profiles analysis in GBM patient-derived cells stimulated with interferon gamma

first: Marco

last: Mineo

summary: Long noncoding RNAs (lncRNAs) are key regulators of gene expression both in physiological and pathological conditions. Previous studies showed changes in lncRNA expression during tumorigenesis. To analyze the role of lncRNAs in tumor interferon signaling and cancer-mediated immunosuppression, we used RNA-seq technique to identify lncRNAs that are differentially expressed in GBM patient-derived cells stimulated with interferon gamma compared to unstimulated cells. 15,768 lncRNAs were surveyed in the analysis. RNA-seq data show upregulation of 113 lncRNAs upon interferon gamma treatment (p value < 0.01, fold change > 2). Our findings indicate that the expression of several lncRNAs is stimulated by interferon gamma suggesting a critical role of lncRNAs in tumor interferon signaling.

overall_design: Patient-derived GBM cells were stimulated with interferon gamma for 24 hours. Non stimulated cells were used as control. LncRNA expression profiles were generated by RNA-seq, in triplicate, using Illumina HiSeq 4000.

first: E

last: Chiocca


title: The effect of listening to music on human transcriptome

status: Public on Apr 13 2015

city: Helsinki

first: Irma

last: Jarvela

address: Biomedicum Helsinki, PO Box 63, Room B311b

department: Medical Genetics

country: Finland

institute: University of Helsinki

summary: The aim of the dataset was to study the effect of music exposure  on human blood transcriptome.

overall_design:
Total RNAs from peripheral blood of samples were compared before and after listening to a 20 minutes of classical music. Samples were collected from 48 samples before and after music exposure.

***On March 3, 2025, the submitter requested removal of the samples due to patient privacy concerns.***

first: Chakravarthi

last: Kanduri

first: Minna

last: Ahvenainen

first: Liisa

last: Ukkola-Vuoti

first: Pirre

last: Raijas

first: Harri

last: Lähdesmaki

last: Järvelä


title: A single nucleotide polymorphism in the promoter of a hairpin RNA contributes to Alternaria leaf spot resistance in apple (Malus × domestica Borkh.)

status: Public on Dec 25 2018

city: Beijing

first: Tianzhong

last: Li

address: Yuanmingyuan Street No.2

department: Horticulture

institute: China Agricultural University

summary: Apple leaf spot caused by the Alternaria alternata f. sp. mali (ALT1) fungus is one of the most devastating diseases of apple (Malus × domestica). We identified a hairpin RNA (hpRNA)-mediated small RNAs, MdhpRNA277, from apple (cv. ‘Golden Delicious’) that is induced by infection with ALT1. MdhpRNA277 produces mdm-siR277-1 and mdm-siR277-2, which target five R genes, MdRNL1, MdRNL2, MdRNL3, MdRNL4, and MdRNL5, that are expressed at high levels in the resistant apple variety ‘Hanfu’ and at low levels in the susceptible variety ‘Golden Delicious’ following ALT1 infection. MdhpRNA277 is strongly induced in ‘Golden Delicious’ but was not induced in ‘Hanfu’ following ALT1 inoculation. The promoter activity of MdhpRNA277 was much stronger in ‘Golden Delicious’ than in ‘Hanfu’ after ALT1 inoculation. We identified a single nucleotide polymorphism (SNP) in the MdhpRNA277 promoter region between the susceptible variety ‘Golden Delicious’ (pMdhpRNA277-GD) and resistant variety ‘Hanfu’ (pMdhpRNA277-HF). The transcription factor MdWHy binds to pMdhpRNA277-GD, but not to pMdhpRNA277-HF. Transgenic ‘GL-3’ apple lines expressing pMdhpRNA277-GD: MdhpRNA277 were more susceptible to ALT1 infection than were those expressing pMdhpRNA277-HF:MdhpRNA277 due to induced mdm-siR277 accumulation and low levels of expression of the five target R genes. The failure of MdWHy to bind to pMdhpRNA277-HF might contribute to the low levels of MdhpRNA277 and mdm-siR277-1/-2 expression and the high levels of R gene expression and resistance to Alternaria leaf spot in resistant apple varieties. We confirmed that the SNP in pMdhpRNA277 is associated with Alternaria leaf spot resistance by analyzing the progeny of three additional crosses. The SNP identified in this study could be used as a marker to distinguish between apple varieties that are resistant or susceptible to Alternaria leaf spot.

overall_design: Small RNAs were induced  by  Alternaria alternaria f. sp. mali (ALT1) infection in apple by deep sequencing

first: Qiulei

last: Zhang


title: mRNA Expression data from human Ewing's sarcoma (ES)

first: Masanori

last: Kawano

summary:
To explore possible oncogenic factors in ES, we used a microarray-based approach to profile changes in the expression of mRNAs in five ES cell lines and human mesenchymal stem cells (hMSCs).
We used a microarray-based approach to profilein the mRNA expression of ES

overall_design: Human ES cell lines were analyzed with genome-wide expression arrays.

first: Kazuhiro

last: Tanaka


title: microRNA Expression data from human Ewing's sarcoma (ES)

summary:
To explore possible oncogenic factors in ES, we used a microarray-based approach to profile changes in the expression of miRNAs in five ES cell lines and human mesenchymal stem cells (hMSCs).
We used a microarray-based approach to profilein the mRNA expression of ES


title: Blood Transcriptional Endotypes in Women with Pelvic Inflammatory Disease

status: Public on Feb 06 2018

city: Chapel Hill

first: xiaojing

last: zheng

address: 111 Mason Farm Road

institute: UNC-CH

summary: By comparing blood mRNA responses of women with biopsy confimed Chlamydia trachomatis (CT) and/or Neisseria gonorrhoeae (GC) induced pelvic inflammatory disease (PID) to those from women with CT and/or GC infection limited to their cervix and asymptomatic uninfected women determined via microarray, we discovered important pathogenic mechanisms in PID and response differences that provide a pathway to biomarker discovery. Women with GC and/or CT-induced PID exhibit overexpression of myeloid cell genes and suppression of protein synthesis, mitochondrial oxidative phosphorylation, and T-cell specific genes. Coinfected women exhibited the greatest activation of cell death pathways and suppression of responses essential for adaptive immunity. Blood microarrays reveal discrete pathobiological endotypes in women with PID that are driven by pathogen invasion of the upper genital tract.

overall_design: Total RNA was extracted from whole blood collected in Tempus™ Blood RNA tubes of participants in this study at enrollment.

first: Xiaojing

last: Zheng

first: Catherine

last: O’Connell

first: Wujuan

last: Zhong

first: Toni

last: Darville


title: Hemicastration induced spermatogenesis related DNA methylation and gene expression changes in mice testis

status: Public on Jan 24 2018

city: chengdu

first: Yixin

last: Wang

state: sichuan

address: 211 huimin street

department: Institute of Animal Genetics and Breeding, College of Animal Science and Technology

institute: Sichuan Agricultural University

type: Methylation profiling by high throughput sequencing

summary: This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: Systematic identification of human SNPs affecting regulatory element activity

status: Public on Apr 05 2019

first: Bas

last: van Steensel

address: Plesmanlaan 121

department: division of Molecular Biology

institute: Netherlands Cancer Institute

summary: Most of the millions of single-nucleotide polymorphisms (SNPs) in the human genome are non-coding, and many overlap with putative regulatory elements. Genome-wide association studies have linked many of these SNPs to human traits or to gene expression levels, but rarely with sufficient resolution to identify the causal SNPs. Functional screens based on reporter assays have previously been of insufficient throughput to test the vast space of SNPs for possible effects on enhancer and promoter activity. Here, we have leveraged the throughput of the SuRE reporter technology to survey a total of 5.9 million SNPs, including 57% of the known common SNPs world-wide. We identified more than 30 thousand SNPs that alter the activity of putative regulatory elements, often in a cell-type specific manner. These data indicate that a large proportion of human non-coding SNPs may affect gene regulation. Integration of these SuRE data with genome-wide association studies may help to identify causal SNPs.

overall_design: SuRE-seq assays with 8 libraries obtained from four heterozygous genomes from the 1000-genome project, each in 2 biological replicates. Each library is transfected in K562, using 3 biological replicates, and in HepG2 cell-lines, using 2 biological replicates.

first: Joris

last: van Arensbergen

first: Ludo

last: Pagie

first: Marcel

last: de Haas