title: ChIP-seq of histone marks H3K36, H3K27, and H3K9 in JMJD1C knockout or mutated MLL-AF9 leukemia cells

summary: We performed genome-wide profiling of H3K9me3, H3K9me1, H3K27me3, and H3K36me3 by ChIP-seq in JMJD1C knockout or mutated MLL-AF9 leukemia cells. For ChIP-seq in JMJD1C mutated cells, we transduced sgRNA targeting the zinc finger,  jumonji domain of JMJD1C or Renilla control and sorted on day 6 for GFP (MLL-AF9) Tdtomato (sgRNA) double positive cells. For ChIP-seq in JMJD1C knockout cells, we transduced Jmjd1c flox/flox MLL-AF9 leukemia cells with CRE TdTomato and sorted on day 6 for GFP (MLL-AF9) Tdtomato (CRE) double positive cells. These cells were subjected to ChIP-seq analysis with either  H3K27me3, H3K9me3, H3K9me1 (JMJD1C knockout cells) or H3K36me3 (both knockout and mutated cells) antibody. We found  increased H3K36me3 level at promoters of differentially expressed genes between control and JMJD1C loss or mutated leukemia cells.

overall_design: We performed ChIP-seq in mouse MLL-AF9 cells harboring JMJD1C sgRNA targeting zinc finger, jumonji domain or renilla control sgRNAs.

first: Luke

last: Christiansen

first: Jesus

last: Izaguirre-Carbonell


title: Transcriptomic profiling of head and neck squamous cell carcinoma cell lines

status: Public on Feb 26 2019

city: Ann Arbor

first: Chad

last: Brenner

state: Michigan

address: 1500 E Medical Center Drive / Cancer Center 6430

country: USA

institute: University of Michigan

type: Expression profiling by high throughput sequencing

summary: Head and neck squamous cell carcinoma (HNSCC) is the sixth most common cancer world wide, and survival rates range from 40-80% depending on subsite.  As novel treatment strategies are investigated, comprehensively characterized cell lines representative of the diversity seen in patients will be crucial to correlating genetic and phenotypic features with therapeutic response.  The University of Michigan has generated a large panel of HNSCC cell lines that are utilized in laboratories worldwide.  Here, we provide transcriptome sequencing of 36 of these cell lines in addition to 5 HNSCC lines derived elsewhere to inform selection of model systems for future studies.

overall_design: Analysis of 41 HNSCC cell lines by 75 nucleotide paired end sequencing to >100x depth on an Illumina HiSEQ4000.


title: Epigenome analysis of normal and schizophrenic samples

status: Public on Mar 21 2019

city: Uppsala

first: Lars

last: Feuk

address: Husargatan 3

department: Immunology, Genetics and Pathology

country: Sweden

institute: Uppsala University

summary: We analyzed fresh frozen post-mortem brain tissue from a cohort of 73 schizophrenic and 52 control samples, using the Illumina Infinium HumanMethylation450 Bead Chip, to investigate genome-wide DNA methylation patterns in patients diagnosed with schizophrenia.

overall_design: Bisulphite converted DNA from the 125 samples were hybridised to the Illumina Infinium 450k Human Methylation Beadchip v1.2


title: Critical Role of Jumonji Domain of JMJD1C in MLL-rearranged leukemia

status: Public on Apr 12 2019

city: Milwaukee

last: Zhu

state: WI

address: 8733 W Watertown Plank Rd

institute: Versiti Blood Research Institute Milwaukee

type: Genome binding/occupancy profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Gene expression profiling in mouse fibroblast tumors with overexpression of the homeoprotein SIX1

status: Public on Feb 12 2019

city: Madrid

first: Ignacio

last: Palmero

state: Madrid

address: Arturo Duperier, 4.

country: Spain

institute: CSIC

summary: Six1 is a developmental transcriptional regulator frequently overexpressed in human tumors. Recent results also show that SIX1 acts as a repressor of cell senescence, an antiproliferative response with key roles in tumor suppression, among other physiological and pathological settings. Here, we set to study the impact of SIX1 gain of function in transformation and tumorigenesis of fibroblasts, in connection with senescence. Using transcriptomic, histological, and functional analyses in murine cells and tumors of fibroblast origin, we show that SIX1 has a strong pro-tumorigenic action in this model, linked to the repression of a senescence-related gene signature and the activation of cellular plasticity, mediated at least in part by direct transcriptional regulation of the stemness factor Sox2. Moreover, functional analyses with human glioma cell lines also show that SIX1 controls SOX2 expression, senescence and self-renewal in this model. Collectively, our results support a general link of SIX1 with senescence and SOX2-mediated cell plasticity in tumors.

overall_design: mRNA profiles were obtained from SIX1-overexpressing tumors and controls in triplicate by RNA-Seq using Illumina HiSeq.


title: Cyclin C Regulated Oxidative Stress Responsive Transcriptome

status: Public on Feb 13 2019

city: Stratford

first: David

last: Stieg

state: NJ

address: 42 E. Laurel Rd

department: Molecular Biology

institute: Rowan Graduate School of Biomedical Sciences

summary: We report the findings from RNA-seq analysis in oxidatively stressed cells, in addition to findings from RNA-seq analysis in cells deleted for cyclin C. A total of 20-30% of genes regulated by cyclin C are responsive to oxidative stress.

overall_design: Cyclin C-Cdk8 is a conserved kinase that associates with the RNA polymerase II Mediator complex that stimulates or represses transcription depending on the locus. In response to oxidative stress, cyclin C, but not Cdk8, displays partial translocation into the cytoplasm. These findings open the possibility that cyclin C relocalization is a regulatory mechanism governing oxidative stress-induced transcriptional changes. In the present study, the cyclin C-dependent transcriptome was determined and compared to transcriptional changes occurring in oxidatively stressed mouse embryonic fibroblasts. We observed a similar number (~2000) of genes up or downregulated in oxidatively stressed cells. Induced genes include cellular repair/survival factors while repressed loci were generally involved in proliferation or differentiation. Depleting cyclin C in unstressed cells produced an approximately equal number of genes (~2400) that were repressed by, or whose transcription required, cyclin C. Consistent with the possibility that cyclin C nuclear release contributes to transcriptional remodeling in response to oxidative stress, we found that 37% cyclin C-dependent genes were downregulated following stress. Moreover, 20% of cyclin C-repressed genes were induced in response to stress.

middle: C

first: Randy

last: Strich


title: RNA-seq study on MLL-AF9 leukemia cells harboring JMJD1C sgRNAs targeting jumonji and zinc finger domains.

summary: We transduced clonally MLL-AF9 leukemia cells expressing cas9 with sgRNA targeting the jumonji and zinc finger domains of JMJD1C. GFP (MLL-AF9) and TdTomato (sgRNA) double positive cells were sorted on Day 6 after transduction. Total RNA was isolated followed by mRNA selection. cDNA libraries were generated and NextGen Sequencing was performed.

overall_design: We performed RNA-seq in mouse MLL-AF9 cas9 cells harboring sgRNA against jumonji and zinc finger domains of JMJD1C or renilla.

first: Robert

last: Burns


title: An unstructured MET-2/SETDB1 cofactor ensures H3K9me2, focus formation and perinuclear anchoring [RNA-seq]

status: Public on Feb 06 2019

city: Mainz

first: Jan

last: Padeken

address: Ackermannweg 4

country: Germany

institute: Institute of Molecular Biology

summary: The segregation of the genome into accessible euchromatin and histone H3 lysine 9 methylated (H3K9me) heterochromatin is essential for the repression of repetitive elements and tissue-specific genes. In C. elegans, the SETDB1 homolog MET-2 catalyzes H3K9me1 and me2. In worms as in vertebrates, the regulation of this crucial enzyme remains enigmatic. Contrary to the localization of overexpressed MET-2, we find endogenous MET-2 to be nuclear throughout development, enriched in perinuclear foci in a cell cycle-dependent manner. We show by mass spectrometry that MET-2 associates with a highly unstructured protein, LIN-65, and a conserved GTPase effector ARLE-14. All three colocalize at heterochromatic foci. Ablation of lin-65, but not arle-14, mislocalizes and destabilizes MET-2, resulting in decreased H3K9me2, derepression of MET-2 targets, and loss of fertility. Importantly, mutation of met-2 or lin-65 is sufficient to disrupt the perinuclear clustering of heterochromatin genome-wide. Thus, LIN-65 is an essential cofactor of MET-2 required for H3K9me2 deposition, heterochromatin clustering, perinuclear anchoring, and transcriptional repression.

overall_design: Total RNAseq of RNA isolated from early C. elegans embryos (~1-300 cell stage) in N2 (Bristol), met-2(n4256) III, lin-65(delta) I and lin-65(delta) I;met-2(n4256) III mutants. Extraction of RNA was performed according to the WormBook protocol (Stiernagle, 2006). Total RNA was purified using RNeasy kit (QIAGEN 74104) including DNase treatment. Depletion of ribosomal RNA was done for 5 ľg of total RNA with Ribo-Zero Margnetic Gold Kit (Epicentre MRGZG12324) and further concentrated with RNA Clean & Concentrator kit (Zymo Research R1015) according to corresponding manufacturers instructions.

first: Colin

last: Delaney

first: Stephen

last: Methot

first: Iskra

last: Katic

first: Susan

middle: M

last: Gasser


title: An unstructured MET-2/SETDB1 cofactor ensures H3K9me2, focus formation and perinuclear anchoring


title: An unstructured MET-2/SETDB1 cofactor ensures H3K9me2, focus formation and perinuclear anchoring [ChIP-seq]

overall_design: Chromatin was isolated from early embryos (before bean stage) grown after L1 synchronization (60–65 h depending on each strain) in three independent biological replicates and Lem-2 immunoprecipitation was performed using a rabbit anti Lem-2 antibody (Novus Biologicals 48540002). Libraries were prepared from chromatin IP and input samples using the TruSeq ChIP Library Preparation Kit (Illumina IP-202-1012), according to the manufacturer’s recommendations. No size selection was performed during sample preparation and the libraries were indexed and amplified using 12 PCR cycles, using the recommended conditions. After a final cleanup with Agencourt AmPure XP beads (Beckman # A63881), the library size distribution and concentrations were determined using a BioAnalyzer 2100 (Agilent technologies) and Qubit (Invitrogen) instrument, respectively. The final pools were prepared by mixing equimolar amounts of all individual indexed libraries and then sequenced on a HiSeq 2500 (Illumina) in Rapid mode (Paired-End 50).


title: Profiling the DNA methylation pattern in naïve induced Pluripotent Stem cells and somatic cells

status: Public on Dec 31 2018

city: Padua

first: Graziano

last: Martello

address: viale Colombo 3

department: Department of Biology

country: Italy

institute: University of Padua

type: Methylation profiling by high throughput sequencing

summary: We analysed by Reduced Representation Bisulfite Sequencing (RRBS) the genome methylation pattern in human fibroblast and in naïve induced pluripoent stem cells (niPSCs)

overall_design:
Three different fibroblast lines were reprogrammed to naïve pluripotency by transfection of modified messanger RNAs in microfluidics. Five niPSC lines have been generated and expanded under standard conditions before profiling by RBBS. An isogenic primed iPSC line (HPD00) has been also generated and analysed, as well as a naive PSC line (H9 Reset NK2), obtained by expression of NANOG-KLF2 transgenes in H9 primed hESCs.
We analyze 10 samples (human fibroblast and niPSCs) by RRBS (BioProject PRJNA381757).


title: RNA-seq profiling of human somatic, primed and naïve induced Pluripotent Stem cells

summary: RNA-seq based transcriptome analysis of human fibroblast, primed and naïve induced pluripoent stem cells

overall_design:
Three different fibroblast lines were reprogrammed to naïve pluripotency by transfection of modified messanger RNAs in microfluidics. Eight niPSC lines have been generated and expanded under standard conditions before profiling by RNAseq. An isogenic primed iPSC line (HPD00) has been also generated and analysed, as well as a naive PSC line (H9 Reset), obtained by expression of NANOG-KLF2 transgenes in H9 primed hESCs.
RNAseq data of 13 samples (human fibroblast, niPSCs and primed induced pluripotent stem cell) BioProject PRJNA381757; SRA study Accession SRP103188.


title: Genetic AMPK activation in liver protects against diet-induced obesity and NAFLD

status: Public on Feb 05 2019

city: San Diego

first: April

middle: Elizabeth

last: Williams

state: California

address: 10010 N Torrey Pines Rd

department: IGC

institute: Salk Institute for Biological Studies

summary: We developed a GEMM in which AMPK can be inducibly activated in vivo (iAMPK mice). We provide here the data (RNA seq) on the transcriptional changes induced by AMPK activation in livers from mice fed a high-fat diet.

overall_design: iAMPK and L-iAMPK mice were fed a high-fat diet (45% calories from fat), plus or minus doxycycline, for eight weeks before collection of liver samples. Doxycycline-treated L-iAMPK mice activate AMPK in liver.

first: Daniel

last: Garcia

first: Maxim

middle: N

last: Shokhirev

first: Reuben

middle: J

last: Shaw


title: RNA-seq profiling and DNA methylation of human somatic, primed and naïve induced Pluripotent Stem cells


title: RNA-sequencing in irradiated and normal A549 cells.

status: Public on Dec 27 2018

city: chengdu

first: Ting

last: Zhang

address: Chengdu Medical College, The First Affiliated Hospital, No. 278, Baoguang Road, Chengdu, Sichuan 610500, China.

department: The First Affiliated Hospital of Chengdu Medical College

country: China

institute: Clinical Laboratory

summary: The aim of this study is to investigate the role of circRNAs/miRNAs/lncRNAs in radioresistance in A549 cells. For irradiation, A549 cells were exposed to a single fraction 2 GY or 4GY X-ray dose using an X-RAD 160-225 instrument (Precision X-Ray, Inc., Branford, CT, USA; filter: 2 mm AI; 42 cm, 225 kV/s, 12.4 mA, 2.0 Gy/min). The irradiated A549 cells (after a single dose of irradiation) and normal A549 cells  were cultured for further 48h and then collected its total RNA for high-throughput sequencing.

overall_design: Examing 3 conditions, each with 3 replicates. The three groups were 0GY group (control),  2GY group (treatment-1) and  4GY group (treatment-2).

first: ying

last: xu


title: Comparison of microRNA expression profiling in pig spleens among three time points after infection by Chinese I genotype strain of Toxoplasma gondii

city: Yangzhou

first: Hou

last: Zhaofeng

state: Jiangsu

address: No. 12, Wenhui East Road

institute: Yangzhou University

type: Non-coding RNA profiling by high throughput sequencing

summary: The objectives of the present study were to analyze the changes on miRNA expression profile in swine spleen using next-generation sequencing (NGS) technology and bioinformatic analysis at 10, 25 and 50 days post inoculation (DPI) with Chinese I genotype strain of T. gondii. Compared to control group, 34, 6 and 86 differentially expressed miRNAs (DEMs) were respectively found in spleens of infected pigs at 10, 25 and 50 DPI. The results not only showed that the miRNA expression of the host can be changed by the invasion of T. gondii, but also revealed the differences on the regulation of the key biological processes or pathways involved in host responses between the acute and chronic T. gondii infection.

overall_design: Differential expression of porcine microRNAs at three time points after infection with Chinese I genotype strain of Toxoplasma gondii were analyzed by deep sequencing

first: Zhaofeng

last: Hou

first: Jianping

last: Tao


title: Bias-minimized quantification of microRNA reveals widespread alternative processing and 3′ end modification

status: Public on Dec 12 2018

city: Seoul

first: Haedong

last: Kim

address: 1 Gwanak-ro, Gwanak-gu

department: Biological Sciences

country: South Korea

institute: Seoul National University

summary: MicroRNAs (miRNAs) modulate diverse biological and pathological processes via post-transcriptional gene silencing. High-throughput small RNA sequencing (sRNA-seq) has been widely adopted to investigate the functions and regulatory mechanisms of miRNAs. However, accurate quantification of miRNAs has been limited owing to the severe ligation bias in conventional sRNA-seq methods. Here we quantify miRNAs and their variants (known as isomiRs) by an improved sRNA-seq protocol, termed AQ-seq (accurate quantification by sequencing), that utilizes adapters with terminal degenerate sequences and a high concentration of polyethylene glycol (PEG), which minimize the ligation bias during library preparation. Measurement using AQ-seq allows us to correct the previously misannotated 5′ end usage and strand preference in public databases. Importantly, the analysis of 5′ terminal heterogeneity reveals widespread alternative processing events which have been underestimated. We also identify highly uridylated miRNAs originating from the 3p strands, indicating regulations mediated by terminal uridylyl transferases at the pre-miRNA stage. Taken together, our study reveals the complexity of the miRNA isoform landscape, allowing us to refine miRNA annotation and to advance our understanding of miRNA regulation. Furthermore, AQ-seq can be adopted to improve other ligation-based sequencing methods including crosslinking-immunoprecipitation-sequencing (CLIP-seq) and ribosome profiling (Ribo-seq).

overall_design: Total RNA was isolated from HEK293T and HeLa cells, mixed with thirty synthetic miRNA-like spike-in oligos, and subjected to small RNA-seq library preparation using TruSeq (Illumina) or the AQ-seq method.

first: Jimi

first: Kijun

first: Hyeshik

last: Chang

first: Kwontae

last: You

first: V


title: The effect of sample splitting and technical replication on mRNA-seq and sRNA-seq quantification

status: Public on Dec 15 2018

city: Oxford

first: Irina

last: Mohorianu

address: Headington

department: Medical Sciences Division

country: United Kingdom

institute: University of Oxford

summary: RNA sequencing (RNA-seq) is a widely used method for quantifying RNA levels across the environmental, biological and medical sciences. The accuracy of the output from an RNA-seq experiment is known to vary due to sequencing biases or errors in quantification. These have the potential to lead to false calls of differential expression (DE), and hence, to affect the accuracy of the biological inference. A proposed solution to reduce the number of false positives and increase confidence in the quality of results from such experiments is to increase the number of biological replicates. In addition, more recent suggestions are to create additional technical replicates within biological replicates (i.e. to split samples across sequencing lanes). The optimal strategy for analysing and normalizing such data, and for maximising accuracy as a function of cost, biological and technical replication is important to understand, yet currently unclear. The aim of this study was to test the effect of technical replication and sample splitting on the overall outcome of gene expression profiling for RNA-seq data.

overall_design: To compare the effect of introducing technical replicates, and as a result, reducing the sequencing depth allocated per sample, we sequenced 3 samples both full and split approaches. The full approach is equivalent to sequencing the whole sample on one lane. The split approach is equivalent to creating two technical replicates, 50% each. The full samples corresponding to this study are presented in GSE55839. The samples are from wild type Dahomey D. melanogaster males that were exposed to rival males ('R') for 2 or 26 hours and split into Head-Thorax 'H' or Abdomen 'A' samples. Males were reared under standardised conditions and snap frozen at the same time of day. The mRNA-seq was single end, 50nt reads, standard Illumina adapters and using the HiSeq-2500 platform. Samples 2RA3_1 and 2 (2h, Rivals, Abdomen) are samples of the same biological sample that were split and sequenced on different lanes of the same flow cell, 2RH2_1 and 2 similarly for the 2h, Rivals, Head-Thorax sample and 26RH3_1 and 2 similarly for the 26h Rivals Head-Thorax sample.

first: Rachel

last: Rusholme-Pilcher

first: Tracey

last: Chapman


title: Genome-wide analysis of RNAs associated with Populus euphratica Oliv. heterophyll morphogenesis

status: Public on Nov 28 2018

city: Alar

first: Shaowei

last: Qin

state: Xinjiang

address: Hongqiao Road 705

department: College of Life Sciences

institute: Tarim University


title: Genome-wide analysis of RNAs associated with Populus euphratica Oliv. heterophyll morphogenesis [RNA-Seq]

summary: The desert plant Populus euphratica Oliv. has typical heterophylly; linear (Li), lanceolate (La), ovate (Ov) and broad-ovate (Bo) leaves grow in turn from young to adult trees. It is therefore a potential model organism for leaf development. To investigate the roles of RNAs (including mRNAs, miRNAs, lncRNAs and circRNAs) in the morphogenesis of P. euphratica heterophyll, the juvenile heterophyll were respectively sampled, and then their expression patterns were analyzed by small RNA sequencing and strand-specific RNA sequencing. We found that 1374 mRNAs, 19 miRNAs, 71 lncRNAs and 2 circRNAs were P. euphratica heterophyll morphogenesis associated (PHMA) RNAs, among them, 17 PHMA miRNAs could disturb the expression of 46 PHMA mRNAs, furthermore, 11 lncRNAs and 2 circRNAs interacted with 27 PHMA mRNAs by ceRNA hypothesis, respectively. According to GO and KEGG pathway analysis, PHMA RNAs were mainly involved in metabolic, response to stimulus and developmental processes. Our results indicated that both external environmental factors and genetic factors of P. euphratica co-regulated the expression of PHMA RNAs, caused the cell division was repressed, while cell growth was reinforced, and resulted in the morphogenesis of P. euphratica heterophyll, ultimately.

overall_design: RNA-seq of linear (Li), lanceolate (La), ovate (Ov) and broad-ovate (Bo) leaf groups of Populus euphratica, every group including three biology replicates, were named  Li1, Li2, Li3, La1, La2, La3, Ov1, Ov2, Ov3, Bo1, Bo2 and Bo3, respectively.And all the raw data of RNA-seq have been submitted to Sqeuence Read Archive(SRA) of NCBI under accession number SRP163216.

first: L

middle: F

last: Zhao

first: S

middle: W

first: C

middle: L

last: Li

first: Z

middle: Z

last: Guo

middle: H

last: Bao


title: MicroRNA-seq of cell lines expressing pri-miR-9 paralog constructs

status: Public on Dec 10 2018

city: Frederick

first: Xavier

last: Bofill-De Ros

state: MD

address: 1050 Boyles St., blg 560

department: RNA Biology Laboratory

institute: National Cancer Institute

summary: MicroRNA (miRNA) biogenesis begins with Drosha cleavage, the fidelity of which is critical for downstream processing and mature miRNA target specificity. To understand how pri-miRNA sequence and structure influence Drosha cleavage, we studied the processing of three pri-miR-9 paralogs (pri-miR-9-1, pri-miR-9-2 and pri-miR-9-3), which encode the same miRNA but differ in the surrounding scaffold. We show that pri-miR-9-1 has a unique Drosha cleavage profile due to its kinked tertiary structure. Cleavage of pri-miR-9-1, but not pri-miR-9-2 or pri-miR-9-3, generates an alternative-miR-9 with a shifted seed sequence that expands the scope of its target RNAs. Here, we report the the miRNA-seq data of HEK293T and HeLa cell lines transfected with different pri-miR-9 constructs.

overall_design: Briefly, HEK293 and HeLa cells were transfected with several wild-type and chimeric pri-miR-9 constructs. Transfections were performed using PolyJet™ DNA Transfection Reagent (SignaGen) according to the manufacturer's instructions. 48 hours after transfection total RNA was obtained using a chloroform-isopropanol extraction. 5µg of total RNA was ligated with RNA 3’ adaptor using T4 RNA Ligase 2 - truncated (NEB), in the presence of RNase Inhibitor (NEB). RNA 5’ adaptor was ligated using T4 RNA Ligase 1 - high concentration (NEB) and 10 mM ATP. Ligated small RNAs were reverse transcribed using SuperScript® IV Reverse Transcriptase (Thermo-Fisher). Small RNA library cDNA was amplified and indexed using Phusion® High-Fidelity DNA polymerase (NEB). Constructs were purified in a 6% (w/v) native acrylamide gel based on the expected product size and purified by ethanol precipitation. Libraries quality was assessed by using Qubit dsDNA HS Assay Kit (ThermoFisher) and Agilent High Sensitivity DNA kit (Agilent). Libraries were pulled together, denaturalized and prepared at a final concentration of 12pM and run on MiSeq Reagent Kit v3 (Illumina) according to the manufacturer specifications. Adaptors, primers sequences and detailed protocol temperatures can be found at Supplementary Table S2. Fastq files were analyzed using a Python-based custom software, QuagmiR (https://github.com/Gu-Lab-RBL-NCI/QuagmiR) designed for the optimal mapping and analysis of isomiRs.

first: Shuo

last: Gu


title: Transcriptome analysis of Chrdl1-treated RGCs

status: Public on Oct 29 2018

first: April

last: Williams

summary: Chrdl1 treatment promotes formation of synapses and GluA2-AMPAR recruitment in Retinal ganglion cell (RGC) cultures. Analysis of the transcriptome of RGCs with or without Chrdl1 treatment let us determine potential alterations in the expression of genes related to BMP signaling, or genes involved in excitatory synaptogenesis and AMPAR trafficking.

overall_design: RNA was isolated from RGC cultures treated for 12 hours with 1ug/ml Chrdl1, and compared to RNA isolated from buffer-treated (vehicle) RGCs as a control.

first: Elena

last: Blanco-Suarez

first: Maxim

last: Shokhirev

first: Nicola

last: Allen


title: Predicting age from the transcriptome of human dermal fibroblasts

status: Public on Nov 16 2018

summary: There is a marked heterogeneity in human lifespan and health outcomes for people of the same chronological age. Thus, one fundamental challenge is to identify molecular and cellular biomarkers of aging that could predict lifespan and be useful in evaluating lifestyle changes and therapeutic strategies in the pursuit of healthy aging. Here, we developed a computational method to predict biological age from gene expression data in skin fibroblast cells using an ensemble of machine learning classifiers. We generated an extensive RNA-seq dataset of fibroblast cell lines derived from 133 healthy individuals whose ages range from 1 to 94 years, and 10 patients with Hutchinson-Gilford Progeria Syndrome (HGPS), a premature aging disease. On this dataset, our method predicted chronological age with a median error of 4 years, outperforming algorithms proposed by prior studies that predicted age from DNA methylation [4–8] and gene expression data [6,9] for fibroblasts. Importantly, our method consistently predicted higher ages for Progeria patients compared to age-matched controls, suggesting that our algorithm can identify accelerated aging in humans. These results show that the transcriptome of skin fibroblasts retains important age-related signatures. Our computational tool may also be applicable to predicting age from other genome-wide datasets.

overall_design: Single end stranded RNA-Seq

first: Jason

middle: G

last: Fleischer

first: Roberta

last: Schulte

first: Hsiao

last: Tsai

first: Swati

last: Tyagi

first: Arkaitz

last: Ibarra

first: Ling

last: Huang

first: Martin

last: Hetzer

first: Saket

last: Navlakha


title: DNA methylation profiles of Purified Blood Cell types

status: Public on Sep 30 2018

city: Exeter

first: Jonathan

last: Mill

address: RILD Building, RD&E Hospital

department: Medical School

institute: University of Exeter

overall_design: DNA methylation profiles for CD4 T cells, CD8 T cells, B cells, Monocytes and Granulocytes purified from 28 individuals (140 samples in total).  145 samples are submitted. 5 samples ("Patient 0") failed quality control and were not included in the analysis. The raw data for these samples are provided but there are no accompanying processed data.

first: Eilis

last: Hannon

first: Joe

last: Burrage


title: Transcriptome of the visual cortex in WT or Chrdl1 KO mice at post-natal day 14

summary: Chrdl1, a BMP antagonist, is an astrocyte-secreted factor that promotes synapse maturation in the upper layers of the visual cortex at P14. We analyzed the transcriptome of the visual cortex of WT and Chrdl1 KO mice at P14 in order to determine if genes related to BMP signaling, astrocyte development or synapse formation were altered.

overall_design: RNA was isolated from visual cortex of WT or KO mice at post-natal day 14.


title: Specifying the Anterior Primitive Streak by Modulating YAP1 Levels in Human Pluripotent Stem Cells

status: Public on Nov 14 2018

summary: Specifying the primitive streak (PS) guides stem cell differentiation in vitro, however much remains to be learned about the transcription networks that direct anterior and posterior PS cells (APS and PPS, respectively) to differentiate to distinct mesendodermal subpopulations. Here, we show that APS genes are predominantly induced in YAP1-/- hESCs in response to ACTIVIN. This finding establishes the Hippo effector YAP1 as a master regulator of PS specification, functioning to repress ACTIVIN-regulated APS genes in hESCs. Moreover, transient exposure of wild-type hESCs to dasatinib, a potent C-SRC/YAP1 inhibitor, enables differentiation to APS-derived endoderm and cardiac mesoderm in response to ACTIVIN. Importantly, these cells can differentiate efficiently to normal beating cardiomyocytes without the cytoskeletal defect seen in YAP1-/- hESC-derived cardiomyocytes. Overall, we uncovered an induction mechanism to generate APS cells using a cocktail of ACTIVIN and YAP1i molecules that holds practical implications for hESC and iPSC differentiation into distinct mesendodermal lineages.

overall_design: Our data strongly indicate that combined treatment of ACTIVIN and YAP1i during the first 24h of differentiation in WT hESCs and hiPSCs is sufficient to generate APS cells that efficiently differentiate into cardiac mesoderm. Thus, we reasoned that transient ACTIVIN+YAP1i exposure might provide an alternative strategy to generate cardiomyocytes in WT  hESCs.We then compared the transcriptomes of cardiomyocytes generated from WT H1 hESC by YAPi+ACTIVIN treament to the GiWi protocol at Day 30 of differentiation.

first: Conchi

last: Estaras

first: Hui-Ting

last: Hsu


title: Plasmodium falciparum intraerythrocytic stage transcription time course for NF54 and isogenic mutant line with altered K13 expression I.

status: Public on Oct 28 2018

city: Notre Dame

first: Michael

middle: T

last: Ferdig

state: IN

address: 100 Galvin Life Sciences Center

institute: University of Notre Dame

summary: Plasmodium falciparum intraerythrocytic stage transcription four hour time course for NF54 and PB58 (an isogenic line with a piggyBac transposon in the 5’ UTR of K13  of K13 that alters K13 expression).

overall_design: The parasite strains NF54 and PB58  (the K13 mutant) were maintained in identical standard culture conditions and synchronized by 3 rounds of sorbitol synchronization. A four hour time-course was collected at 2, 6, 10, 14, 18, 22, 26, 30, 34, 38, 42, and 46 hours post invasion (hpi) with triplicate samples at 6, 26 and 38 hpi.

first: Katrina

middle: A

last: Button-Simons


title: Mutation analysis of parental and 10 avirulent C. rodentium isolates from the feces of C3H/HeJ mice

status: Public on Sep 21 2018

first: April

last: Williams

summary: We report that dietary iron protects mice from infection by Citrobacter rodentium. Iron induces a state of insulin resistance and increases glucose availability in the gut, thereby attenutating C. rodentium virulence. Additionally the pathogen appears to be driven towards a long-term commensal state. Here, we identify mutations in persistent and avirulent Citrobacter rodentium isolates from mice given an iron supplemented diet.

overall_design: 10 isolates of avirulent C. rodentium from the feces of C3H/HeJ mice and the parental strain were sequenced, then compared to identify mutations in the isolates.

first: Janelle

middle: S

last: Ayres

first: Grischa

middle: Y

last: Chen


title: RNA-seq analysis to assess transcriptional effects of Rp mutations in wing imaginal discs and their dependence on Xrp1

status: Public on Aug 20 2018

city: bronx

first: Nicholas

last: Baker

state: NY

address: 1300 Morris Park Avenue

department: genetics

institute: albert einstein college of medicine

summary: Since the putative transcription factor Xrp1 gene is required for many aspects of Rp+/- phenotypes, we sought to define what transcriptional changes occur in Rp+/- wing discs and their dependence on Xrp1.   We identified 257 genes whose transcripts were significantly altered in the same direction in two Rp+/- genotypes, most of which depended on Xrp1. The results show that Xrp1 regulates a significant transcriptional response in Rp+/- genotypes.

overall_design: 12 samples with wildtype (named as frt82_w) in triplicate, one type of Rp+/- (named as M67_w) in triplicate, and the other type of Rp+/- (named as M95_w) in triplicate, as well as RpS3+/- Xrp1+/- (named as M2-73_M95) in triplicate

first: Marianthi

last: Kiparaki

first: Jorge

last: Blanco

first: Virginia

last: Folgado

first: Zhejun

last: Ji

first: Amit

last: Kumar

first: Gerard

last: Rimesso


title: Identification of the ER-beta cistrome in ER-beta expressing MDA-MB-231 cells [ChIP-seq]

status: Public on Aug 23 2018

city: Cambridge

first: Jason

last: Carroll

address: Li Ka Shing Centre, Robinson Way

institute: Cancer Research UK, Cambridge Institute

summary: We have utilized ChIPseq to identify the ER-beta cistrome in ER-beta expressing MDA-MB-231 triple negative breast cancer cells.  ER-beta has been identified as a tumor suppressor in breast cancer and recent reports have demonstrated that ER-beta protein is detectable at moderate to high levels in approximately 30% of triple negative breast tumors.  Increased expression of ER-beta in triple negative breast cancer has also been reported to be associated with improved recurrence-free survival.  Treatment of ER-beta expressing triple negative breast cancer cells with estrogen, or the ER-beta selective agonist, LY500307, results in decreased cell proliferation, invasion and migration.  To begin to identify the molecular mechanisms by which ER-beta elicits tumor suppressive effects in triple negative breast cancer, we performed ChIPseq studies and identified the genome-wide binding sites for ER-beta following exposure to 1nM estrogen or 10nM LY500307 for 3 hours.  Over 28,000 and 10,000 unique ER-beta binding sites were identifed in response to these two ligands respectively.  The top transcription factor motifs identified under both treatment conditions were estrogen response elements and AP1 response elements.  The majority of ER-beta binding sites were found at enhancer regions located within introns or intergenic chromatin regions followed by gene promoters.

overall_design: Examination of ER-beta binding sites in ER-beta expressing MDA-MB-231 cells.  ER-beta immunoprecipitations were carried out using a Flag-specific antibody (M2).  All treatment conditions were conducted in triplicate and data were normalized using input controls and compared to vehicle treated cells.

first: John

middle: R

last: Hawse

first: Adam

last: Nelson


title: Dietary iron drives conversion of an enteric pathogen to commensalism via host metabolic alteration

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

sample_organism:
Mus musculus
Citrobacter rodentium

platform_organism:
Mus musculus
Citrobacter rodentium

overall_design: Refer to individual Series


title: Identification of the ERβ transcriptome in ER-beta expressing MDA-MB-231 cells


title: Shared molecular targets in the glomerular transcriptome from patients with nephrotic syndrome and ANCA-associated vasculitis

status: Public on May 17 2018

city: Ann Arbor

first: Sean

last: Eddy

state: MI

address: 1150 West Medical Center Drive

institute: University of Michigan

summary: Glomerular transcriptome from human kidney biopsies in Neptune and ERCB. A subset of samples profiled in this analysis were also profiled in Series GSE68127, and in GSE104066. Corresponding tubulointerstitial transcriptome data is submitted under GEO ID: GSE108113.

overall_design: RNA from the glomerular compartment was extracted and processed for hybridization on Affymetrix ST 2.1 microarrays, annotated using Human Entrez Gene ID custom CDF version 19.

first: Viji

last: Nair

first: Sebastian

last: Martini

first: Laura

last: Mariani

first: Matt

last: Sampson

first: Felix

last: Eichinger

first: Brad

last: Godfrey

first: Matthias

last: Kretzler


title: Shared molecular targets in the glomerular and tubulointerstitial transcriptomes from patients with nephrotic syndrome and ANCA-associated vasculitis

summary: This SuperSeries is composed of the SubSeries listed below. A subset of samples profiled in this analysis were also profiled in Series GSE68127, and GSE104066. Corresponding glomerular transcriptome data can be found under GEO ID: GSE108109.


title: Transcriptional profiling of Drosophila photoreceptors in response to blue light

status: Public on Jun 20 2018

city: WEST LAFAYETTE

first: Vikki

last: Weake

state: INDIANA

address: 175 S. University St.

department: Biochemisty

institute: Purdue University

summary: Purpose: The goal of this study was to characterize the transcript levels of genes in Drosophila photoreceptor neurons in response to blue light. Using transcriptome profiling of isolated photoreceptor nuclei, we analyzed the changes in gene expression that occur in response to 3h of blue light exposure at 1 or 6 days post-eclosion. We identified sets of genes with both up-regulated and down-regulated expression in response to blue light at either age.

overall_design: Method: Flies were exposed to 3h blue light (465nm; 8000 lux; 2mW/cm2) or dark control at 1 or 6 days post-eclosion. RNA extracted from photoreceptor nuclei of flies was used to generate cDNA libraries using NuGen Ovation Drosophila RNA seq system. Samples were sequenced using  Illumina HiSeq2500 next generation sequencer (three biological replicates per age/treatment). As a control, total RNA isolated from the pre-isolation (head homogenate) from the day 1 dark sample was sequenced.

first: Hana

last: Hall

first: Jingqun

last: Ma


title: Gene expression analyses of mouse mesenchymal cells, keratinocytes and induced stratified epithelial progenitor cells.

status: Public on Jul 16 2018

first: April

last: Williams

summary: We report the method for generating epithelial tissues from bottom of ulcer by lineage conversion. Both in vitro and in vitro, mesenchymal cells can be converted to the cells having ability to form stratified epithelium by transduction of lineage-specific transcription factors. We named the converted cells as induced stratified epithelial progenitor cells (iSEPs). Gene expression signatures of mesenchymal cells, in vitro generated iSEPs, in vivo generated iSEPs, and primary keratinocytes are analyzed.

overall_design: Three sets of Pdgfra (+) adipose derived stromal cells (ADSCs), in vitro iSEPs, in vivo iSEPs, and primary keratinocytes are prepared from 3 nimals.

first: Juan

middle: I

last: Belmonte

first: Maxim

last: Shokhirev

first: Masakazu

last: Kurita


title: ARID2 promotes clear cell renal cell carcinoma in the absence of functional PBRM1

status: Public on Aug 14 2018

city: New Haven

first: David

middle: Aaron

last: Schoenfeld

state: CT

address: 20 York Street

department: Medical Oncology

institute: Yale Cancer Center

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: Shared molecular targets in the tubulointerstitial transcriptome from patients with nephrotic syndrome and ANCA-associated vasculitis

summary: Tubulointerstitial transcriptome from human kidney biopsies in Neptune and ERCB. A number of samples profiled in this analysis were also profiled in Series GSE68127.

overall_design: RNA from the tubulointerstitial compartment was extracted and processed for hybridization on Affymetrix ST 2.1 microarrays, annotated using Human Entrez Gene ID custom CDF version 19.


summary: Glomerular Transcriptome from subjects in the NEPTUNE cohort. A number of samples profiled in this analysis were also profiled in Series GSE68127, and Series GSE108113.

overall_design:
RNA from the glomerular compartment of was extracted and processed for hybridization on Affymetrix microarrays.

Contributor: NEPTUNE Consortium


title: Longitudinal dataset: An optimized library for reference-based deconvolution of whole-blood biospecimens assayed using the Illumina HumanMethylationEPIC BeadArray (I)

status: Public on May 08 2018

city: Lebanon

first: Lucas

middle: A.

last: Salas

state: NH

address: 1 Medical Center Dr, DHMC

department: Epidemiology

institute: Geisel School of Medicine at Dartmouth

type: Methylation profiling by genome tiling array

summary: DNA methylation assessments of peripheral blood DNA can be used to accurately estimate the relative proportions of underlying leukocyte subtypes. Such cell deconvolution analysis relies on libraries of discriminating differentially methylated regions that are developed for each specific cell type measured. The relationship between estimated cell type proportions can then be tested for their association with phenotypes, disease states, and subject outcomes, or used in multivariable models as terms for adjustment in epigenome-wide association studies (EWAS). We obtained purified neutrophils, monocytes, B-lymphocytes, natural killer (NK) cells, CD4+ T-cells, and CD8+ T-cells from healthy subjects and measured DNA methylation with the Illumina HumanMethylationEPIC array platform. In addition, we measured DNA methylation with the EPIC array in two sets of artificial DNA mixtures comprising the above cell types. We compared three separate approaches to select reference differentially methylated region libraries (DMR library), for cell type proportion inference. The IDOL algorithm identified an optimal DMR library consisting of 450 CpG sites for inferring leukocyte subtype proportions (average R2=99.2). Importantly, the majority of CpG sites (69%) in the IDOL DMR library were unique to the new EPIC methylation array, in that they were not present on the 450K array. Our new reference DMR library is available as a Bioconductor package, has the potential to reduce any unintended technical differences arising from the combination of different generations of array platforms, and may be helpful in generating larger DMR libraries that include novel cell subtypes. A longitudinal dataset of 12 measurements in a single healthy subject (age 33 at the beginning of the blood collection) was used to apply our new DMR library. The subject was followed up for approximately 400 days with samples collected every 40 days. One of the samples was excluded from the final analysis due to a potential mix-up.

overall_design: Bisulphite converted DNA from whole blood draw from a healthy male subject at 12 different times (every 40 days during about 400 days) were hybridised to the Illumina Infinium HumanMethylationEPIC Beadchip v1.0_B4.

first: Devin

middle: C

last: Koestler

first: Rondi

last: Butler

first: Helen

middle: M

last: Hansen

first: John

middle: K

last: Wiencke

first: Karl

last: Kelsey

first: Brock

last: Christensen


title: Molecular signature of human cerebral organoids glioma model

status: Public on Apr 25 2018

middle: Elizabeth

summary: We have developed a cancer model of gliomas in human cerebral organoids by CRISPR/Cas9 technology to target a Harvey-Ras (H-RAS) G12V-IRES-tdTomato construct by homologous recombination into the TP53 locus. 16 weeks after electrporation, these tdTomato positive transduced cells were sorted and compared to nontransduced cellls by RNA-seq and gene expression profiles were compared to each other and with human glioma Verhaak subtype signatures.

overall_design: tdTomato positive and negative cell fractions of transduced organoids for four independent batches were sorted and analyzed by RNA-seq. Transcriptome data was then evaluated against the Verhaak defined glioblastoma subtypes based on clinical samples (Verhaak et al., 2011).

first: Junko

last: Ogawa

middle: N


title: Sequencing of microglia during focal remyelination of the corpus callosum

status: Public on May 24 2019

city: Edinburgh

first: Veronique

last: Miron

address: 49 Little France Crescent

department: UK DRI

institute: The University of Edinburgh

summary: The goal of the study was to determine the gene expression of microglia prior to the onset of remyelination (3 days post lysolecithin injection) and pro-regenerative microglia at the onset of remyelination (10 days post remyelination).

overall_design: 3 mice were used per time point (3 dpl, 10 dpl). 10 week-old male C57Bl/6J mice were anaesthetised with isoflurane before being stereotaxically injected with 2 μl of 1% lysolecithin (LPC; vol/vol) into the corpus callosum. Mice were perfused with ice cold phosphate buffered saline with 10% sodium citrate. Lesioned corpus callosum was homogenised using a 2 ml Dounce and filtrated (250 µm filter; Pierce). Following a spin at 600 g for 5 min (with brake), cells were resuspended in 100 % fetal bovine serum (FBS) and 33 % Percoll (1:10), overlaid with 1 ml of 10 % FBS, and spun for 15 min at 800 g at 4 °C without brake. The cell pellet was washed in FACS buffer and spun for 10 min at 600 g at 4 °C, and incubated in anti-mouse CD16/32 Fc-block (Clone 93, BioLegend, 1:200) on ice for 10 min. Fluorescently-conjugated antibodies CD11b-PeCy7 (Clone M1/70, Invitrogen, 1:100), CD45-BV605 (Clone 30D11, Biolegend, 1:200), Ly6G-PerCP Cy5 (Clone 1A8, BioLegend, 1:200), and CD3-APC (Clone 17A2, BioLegend, 1:200) were applied on ice for 30 min. Following centrifugation and filtration (30 μm), cells were sorted by flow cytometry into FBS-coated Eppendorf tubes on ice. Cells were spun at 800 g for 5 min, resuspended in RLT Plus buffer with β-mercaptoethanol, and centrifuged at 10,000 rpm for 2 min in QIAshredder tubes (Qiagen). RNA was extracted using the AllPrep DNA/RNA/miRNA kit (Qiagen) as per the manufacturer’s instructions, and quantity/quality analysed using the Bioanalyser 2100 (Agilent) and RNA 6000 Pico kit (Agilent) as per the manufacturer’s instructions. cDNA production/ library preparation was performed using the NuGEN Ovation RNAseq System v2 kit (NuGEN) by BGI (Hong Kong). End Repair Mix was added to the amplified cDNA and incubated at 20°C for 30 min. AxyPrep Mag PCR clean up kit (Axygen) was used to purify the end-repaired DNA, which was then combined with A-tailing Mix (Enzymatic) and incubated at 37°C for 30 min. Adaptors (Invitrogen) were ligated to the Adenylate 3’ ends DNA, and incubated at 16°C for 16 h. Insert size was used to select the adaptor-ligated DNA fragments. Several rounds of PCR amplification with PCR Primer cocktail (Invitrogen) and PCR Master Mix (New England Biolabs) were performed to enrich the adaptor-ligated DNA fragments to produce the final library, purified using AxyPrep Mag PCR clean up kit (Axygen). The final library average molecule length was determined using the Bioanalyser 2100 using the DNA 1000 kit (Agilent) and was quantified by real-time qPCR (TaqMan probe). cBot (Illumina) was used to amplify the libraries to generate the cluster on the Flow Cell (HiSeq 4000, Illumina). An average of 40 million clean 100 paired-end reads (read lengths approximately 100 bp) were achieved per sample. Data was processed to remove adaptors and low quality reads from raw reads.

first: Amy

middle: F

last: Lloyd

first: Claire

middle: L

last: Davies

first: Rebecca

last: Holloway

first: Yasmin

last: Labrak

first: Graeme

last: Ireland

first: Dario

last: Carradori

first: Alessandra

last: Dillenburg

first: Eva

last: Borger

first: Daniel

last: Soong

first: Jill

last: Richardson

first: Tanja

last: Kuhlmann

first: Anna

first: Jeffrey

middle: W

last: Pollard

first: Anne

last: des Rieux

first: Josef

last: Priller

middle: E


title: Identification of the ERβ transcriptome in MDA-MB-231 cells [microarray]

first: Jason

last: Carroll

summary: The goal of this study was to identify ERβ regulated genes in the triple negative MDA-MB-231 cell line which was engineered to express ERβ in a doxycycline inducible manner

overall_design: ERβ expressing MDA-MB-231 cells were treated with either vehicle control or 17-beta estradiol for 5 days.  Treatments were conducted in replicates of 3.  Upon original analysis, replicate 3 from each treatment showed a slight variation from the other two replicates.  For this reason, a second sample of RNA from replicate 3 was submitted and the values between the original sample (#3) and the resubmitted sample (#3 rpt) were averaged together and analyzed along with the other two replicates for each treatment.

first: John

last: Hawse


title: Expression data from human breast cancer cells MCF-7 before and after ATP treatment

status: Public on Apr 28 2018

city: Beijing

first: Ying

last: Liu

state: State...

address: Xueyuan Road 38, Haidian District, Beijing, China

department: Department of pathology

institute: Peking University Health Science Center

summary: We used microarrays to explore gene expression fold change in breast cancer cells before and after ATP treatment.

overall_design: MCF-7 cells before and after 100μM ATP treatment (24h) were for RNA extraction and hybridization on Affymetrix microarrays.

first: Weigang

last: Fang

first: Xinxia

last: Tian


title: Transcriptome analysis of infected and uninfected mice with Citrobacter rodentium

city: San Diego

first: April

last: Williams

address: 10010 N Torrey Pines Rd

institute: Salk Institute for Biological Studies

overall_design: Mice were orally infected with C. rodentium. At day 8 the livers were harvested for RNAseq analysis

first: Janelle

last: Ayres

first: Maxim

last: Shokhirev


title: Efficient generation of human CA3 neurons and modeling hippocampal neuronal connectivity in vitro (bulk)

status: Public on May 02 2018

summary: Despite widespread interest in using human stem cells in neurological disease modeling, a suitable model system to study human neuronal connectivity is lacking. Here, we report a protocol for efficient differentiation of hippocampal pyramidal neurons and an in vitro model for hippocampal neuronal connectivity. We developed an embryonic stem cell (ESC)- and induced pluripotent stem cell (iPSC)-based protocol to differentiate human CA3 pyramidal neurons from patterned hippocampal neural progenitor cells (NPCs). This differentiation induces a comprehensive patterning and generates multiple CA3 neuronal subtypes. The differentiated CA3 neurons are functionally active and readily form neuronal connection with dentate granule (DG) neurons in vitro, recapitulating the synaptic connectivity within the hippocampus. When we applied this neuronal co-culture approach to study connectivity in schizophrenia, we found deficits in spontaneous activity in patient iPSC derived DG–CA3 co-culture by multi-electrode array recording. In addition, both multi-electrode array recording and whole cell patch clamp electrophysiology revealed a reduction in spontaneous and evoked neuronal activity in CA3 neurons derived from schizophrenia patients. Altogether these results underscore the relevance of this new model in studying diseases with hippocampal vulnerability.

overall_design: 8 samples, 2-3 technical replicates per sample

first: Anindita

last: Sarkar

first: Arianna

last: Mei

first: Apua

last: Paquola

first: Shani

last: Stern

first: Cedric

last: Bardy

last: Klug

first: Stacy

last: Kim

first: Neda

last: Neshat

first: Hyung

middle: J

first: Manching

last: Ku

first: David

last: Adamowicz

first: Maria

last: Marchetto

first: Roberto

last: Jappeli

first: Jennifer

last: Erwin

first: Krishnan

last: Padmanabhan

first: Matthew

last: Shtrahman

first: Xin

last: Jin

first: Fred

middle: H

last: Gage


title: Efficient generation of human CA3 neurons and modeling hippocampal neuronal connectivity in vitro

first: April

last: Williams


title: Transcriptome analyses of three Zymoseptoria tritici isolates during infection of Triticum aestivum

city: Kiel

first: Janine

last: Haueisen

address: Am Botanischen Garten 1-9

department: Botanical Institute

institute: Christian-Albrechts University of Kiel

summary: We collected infected wheat leaf material at up to nine time points per Z. tritici isolate and conducted confocal microscopy analyses to select samples for RNA extraction and transcriptome sequencing based on the morphological infection stage.  Thereby, we generated stage-specific RNA-seq datasets corresponding to the four core infection stages allowing us to compare the isolate-specific expression profiles at the same developmental stage of infection. Our final dataset comprises four stage-specific transcriptomes per isolate with two biological replicates per sample. Comparative transcriptome analyses reveal that the expression phenotypes of the three isolates differ significantly.

sample_organism:
Triticum aestivum
Zymoseptoria tritici

platform_organism:
Triticum aestivum
Zymoseptoria tritici

overall_design: Comparative analyses of stage-specific and isolate-specific expression profiles of three Z. tritici isolates

first: Eva

last: Stukenbrock


title: Efficient generation of human CA3 neurons and modeling hippocampal neuronal connectivity in vitro (single cells)

overall_design: 4 technical replicates were used and later pooled together for the bioinformatic analysis.

first: Anindita

last: Sarkar

first: Arianna

last: Mei

first: Apua

last: Paquola

first: Shani

last: Stern

first: Jason

first: Maxim

last: Shokhirev

middle: A


title: ETV1 and FOXF1 cistrome in wildtype GIST48, GIST-T1, MDA-PCa2b, and ETV1 or FOXF1 knocked-down GIST48 cells

status: Public on Feb 01 2018

city: New York

first: Yuedan

last: Chen

department: HOPP

institute: Memorial Sloan Kettering Cancer Center

summary: ChIP profiles were generated by deep sequencing using Illumina HiSeq.

overall_design:
To examine the specific binding pattern of ETV1 and FOXF1 in different cell lineages, we performed performed ETV1 and FOXF1 ChIP-sequencing in GIST48 and MDA-PCa2b
To directly examine whether FOXF1 can modulate binding of other transcription factors in GIST, we performed ETV1 and FOXF1 ChIP-sequencing in GIST48 cells with ETV1 or FOXF1 knockdown.

first: Ping

last: Chi


title: PDGF-driven glioblastoma mouse model scRNA-Seq

status: Public on Feb 23 2018

city: Tucson

first: Hongxu

last: Ding

state: AZ

address: The University of Arizona

institute: University of Arizona

summary: Generate scRNA-Seq profiles for PDGF-driven glioblastoma mouse model.

overall_design: Obtain 85 scRNA-Seq profiles from a de novo tumor-derived cell line.

first: Sayantan

last: Bose

first: Christian

last: Gonzalez

first: Angeliki

last: Mela

first: Peter

middle: D

last: Canoll

last: Sims


title: Gene-by-sex interactions in mitochondrial functions and tissue-specific gene expression in cardio-metabolic traits

status: Public on Apr 10 2018

city: Los Angeles

first: Calvin

last: Pan

address: 675 Charles Young Dr South

institute: UCLA

summary: We report a multi-omic study of sex differences and gene-by-sex interactions across a panel of 100 inbred strains of mice (the Hybrid Mouse Diversity Panel, HMDP), with a focus on metabolic and cardiovascular traits.  For all traits examined, including obesity, insulin resistance, fatty liver, atherosclerosis, and gut microbiota composition, sex differences were influenced by genetic background.  Loci identified by genome-wide association studies (GWAS) of the traits were frequently influenced by sex.  Lyplal1, a gene implicated in human obesity, was shown to underlie a sex-specific locus for diet induced obesity.  Many of the sex-dependent traits showed interdependencies as judged by correlation and shared gene expression patterns, indicating higher order regulation.  Global gene expression analyses of tissues across the HMDP indicated that sex differences in mitochondrial functions in adipose contributed to many of the traits.  Consistent with this, we observed that females tended to be more resistant to the adverse effects of a high fat diet, with smaller adipocytes and increased “browning” of white adipose tissue as compared to males.  Sex-specific differences in mitochondrial activity were confirmed by examining respiration of isolated mitochondria.  Gonadectomy experiments revealed thousands of genes influenced by sex hormones.  In liver, a tissue exhibiting particularly strong differences in gene expression between tissues, sex hormones appeared to be the primary driver of the differences, whereas in adipose organizational effects of sex appeared to be more important.

overall_design: Sixteen male and sixteen female C57BL/6J were purchased from The Jackson Laboratory (Bar Harbor). Mice were either maintained on a chow diet (Ralston Purina Company) or placed on an HF/HS diet (Research Diets D12266B) at 8 weeks of age until 16 weeks of age. At 6 weeks of age the mice were gonadectomized under isoflurane anesthesia. Scrotal regions of male mice were bilaterally incised, testes removed, and the incisions closed with wound clips. Ovaries of female mice were removed through an incision just below the rib cage. There were four mice per group. The muscle layer was sutured, and the incision closed with wound clips. In sham-operated control mice, incisions were made and closed as described above. The gonads were briefly manipulated, but remained intact.  Gonadal fat and liver samples were taken for RNASeq expression profiling.

first: Aldons

last: Lusis

first: Brian

last: Parks

first: Margarete

last: Mehrabian


title: Chromatin accessibility of GIST48, GIST882 and GIST-T1 cells with ETV1 or FOXF1 knockdown

summary: ATAC profiles were generated by deep sequencing using Illumina HiSeq.

overall_design: To directly examine whether FOXF1 can modulate chromatin accessibility and help guide binding of other transcription factors, we performed assay for transposase-accessible chromatin coupled with next generation sequencing (ATAC-seq) in GIST48, GIST882, and GIST-T1 cells


title: Genome-wide analysis of gefitinib-tolerant gene expression in single cell-derived clones

status: Public on Jan 11 2018

city: Boston

first: Wen Cai

last: Zhang

state: MASSACHUSETTS

address: 330 BROOKLINE AVENUE, CLS417

department: Pathology

institute: Beth Israel Deaconess Medical Center

summary: Analysis of gene expression profiles for gefitinib-tolerant cells derived from single cells. The hypothesis tested here was that a small population of cancer cells contribute to tolerance status in a bulk of EGFR mutated lung cancer cells. Results provide important infromnation of the tolerance to the EGFR tyrosine kinase inhibitor, gefitinib, such as upregualtion of cancer-stemness related genes.

overall_design: A single cell was sorted by FACS into four 96-well plates. Two plates of the cells were treated with 0.4 uM and 2 uM gefitinib for 14 days. The other two plates were treated with DMSO. The suriviving clones treated and untreated were validated by IC50 assay. One growing clone sensitive to gefitinbi and five clones tolerant to gefitinib were randomly selected and used  for RNA extraction.

first: Wencai


title: mRNA sequencing to assess RfxCasR and matching shRNA specificity

status: Public on Mar 21 2018

first: April

last: Williams

summary: Matching sets of RfxCasR and shRNAs targeting ANXA4 and B4GALNT1 plus non-targeting (NT) controls were profiled by mRNA sequencing to compare non-specific transcriptome perturbations  for both shRNA and RfxCasR technologies.

overall_design: Three biological replicates for 3 shRNAs and 2 RfxCasR guide RNAs plus 2 RfxCasR arrays expresssed in HEK 293FT cells

first: Patrick

last: Hsu

first: Silvana

last: Konermann


title: ChIPseq in Mouse Hematopoietic Progenitor Cells (HPCs)

status: Public on Apr 11 2018

summary: ChIPseq to detect binding of Nup98, SET1A to chromatin and to observe H3K4me3 on chromatin under various conditions

overall_design:
Extract DNA from BALB/c mouse HPCs, immunopurify protein complexed and associated DNA, deep sequence to identify genomic binding sites.

Antibodies used:

Nup98 (P671) - Cell Signaling Technology - #2292
H3K4me3 - Abcam - ab8580
SET1A - Abcam - ab70378
Flag - Sigma - Flag M2 affinity gel #A2220

first: Tobias

last: Franks

first: Maxim

last: Shokhirev

first: Martin

last: Hetzer


title: Cytosolic calcium and nuclear calcium-regulated transcription networks in response to ABA and JA

status: Public on Jan 25 2018

first: Fei

middle: fei

last: Huang

state: Beijing

address: No 19 Xin Jie Kou Wai Da Jie

department: Beijing Normal University

institute: College of Life Sciences,

summary:
Calcium acts as a universal second messenger to regulate gene expression in both developmental processes and responses to environmental stresses. Previous studies showed that a number of stimuli can induce calcium increases in the cytoplasm and nucleus, independently. However, the gene expression network deciphering [Ca2+]cyt  and/or [Ca2+]nuc signaling pathway remain obscure.
Using transgenic Arabidopsis containing a fusion protein, comprising rat parvalbumin (PV) with either a nuclear export sequence (PV-NES) or a nuclear localization sequence (NLS-PV), to selectively buffer the cytosolic or nucleosolic calcium, we identified the [Ca2+]cyt- or /and [Ca2+]nuc-regulated ABA- and MeJA-responsible genes with the Arabidopsis Genome Oligo array.

overall_design: Three day-old seedlings of wild type (Col-0) , the transgenic plants PV-NES and NLS-PV  were transferred onto medium with or without 10 μM ABA or 50 μM MeAJ for growing additional 5 days. Then RNA was extracted from those seedlings .

first: Feifei

first: Pengcheng

last: Yan

first: Yanli

last: Nie

first: Jin

last: Luo

first: Lvli

last: Chen

first: Shengcheng

last: Han


title: YAP Repression of the WNT3 Gene Controls hESC Differentiation Along the Cardiac Mesoderm Lineage

status: Public on Jan 08 2018

department: IGC

summary: In hESCs, Wnt3/β-catenin activity is low and Activin/SMAD signaling ensures NANOG expression to sustain pluripotency. In response to exogenous Wnt3 effectors, Activin/SMADs switch to cooperate with β-catenin and induce mesendodermal differentiation genes. We show here that the HIPPO effector YAP binds to the WNT3 gene enhancer and prevents the gene from being induced by Activin in proliferating hESCs. In the absence of YAP, Activin signaling is sufficient to induce expression of the endogenous Wnt3 cytokine, which stabilizes β-catenin and selectively activates genes required for cardiac mesoderm (ME) formation. Interestingly, Activin-stimulated YAP-knockout hESCs strongly express β-catenin-dependent cardiac mesoderm markers (BAF60c and HAND1), but unlike WT hESCs, fail to express cardiac inhibitor genes (CDX2, MSX1).  Accordingly, YAP-/- cells treated with Activin alone can differentiate efficiently to beating cardiomyocytes in culture, bypassing the need for sequential treatment with exogenous Wnt ligand and Wnt inhibitors.  Similarly, Activin in combination with small-molecule YAP inhibitors generates beating cardiomyocytes from wild-type hESCs following a one- step protocol. Our findings highlight an unanticipated role of YAP as an upstream regulator of WNT3 to maintain hESC pluripotency in the presence of Activin, and uncover a direct route for the development of human embryonic cardiac mesoderm.

overall_design: We performed a set of sequencing experiments to identify the role of YAP in hESCs and whether YAP influences the activity of the Activin and Wnt signaling pathways during the mesoderm differentiation. We performed transcriptional profile of WT and YAP-KO cells under different Wnt or Activin treatments and performed ChIP-seq analysis of the Wnt and Activin effectors beta-catenin and Smad2,3. In parallel we also mapped the binding of the YAP protein together with TEAD4 DNA-binding protein in hESCs. As a read-out of transcriptional activity under the different treatments we performed ChIP-seq of the active elongation mark CTD-Ser7P RNAPII.

first: Conchi

last: Estaras

first: Ling


title: The influence of transcript assembly on the proteogenomics discovery of microproteins

status: Public on Dec 20 2017

summary: Proteogenomics methods have identified many non-annotated protein-coding genes in the human genome. Many of the newly discovered protein-coding genes encode peptides and small proteins, referred to collectively as microproteins. Microproteins are produced through ribosome translation of small open reading frames (smORFs). The discovery of many smORFs reveals a blind spot in traditional gene-finding algorithms for these genes. Biological studies have found roles for microproteins in cell biology and physiology, and the potential that there exists additional bioactive microproteins drives the interest in detection and discovery of these molecules. A key step in any proteogenomics workflow is the assembly of RNA-Seq data into likely mRNA transcrips that are then used to create a searchable protein databases. Here we demonstrate that specific features of the assembled transcriptome impact microprotein detection by shotgun proteomics. By tailoring transcript assembly for downstream mass spectrometry searching, we show  that we can detect more than double the number of high-quality microprotein candidates and introduce a novel open-source mRNA assembler for proteogenomics (MAPS) that incorporates all of these features. By integrating our specialized assembler, MAPS, and a popular generalized assembler into our proteogenomics pipeline, we detect 45 novel human microproteins from a high quality proteogenomics dataset of a human cell line. We then characterize the features of the novel microproteins, identifying two classes of microproteins. Our work highlights the importance of specialized transcriptome assembly upstream of proteomics validation when searching for short and potentially rare and poorly conserved proteins.

overall_design: Paired End High Throughput RNA Sequencing

first: Jiao

last: Ma

first: Alan

last: Saghatelian


title: Targeted CpG island methylation in human pluripotent stem cells

status: Public on Dec 01 2017

first: April

summary: In our manuscript, we describe novel methodologies for bidirectional DNA methylation editing at targeted genomic loci through homologous recombination (HR) in human pluripotent stem cells. In order to gain insights on the applicability of these methodologies towards modeling epigenetic alterations, as well as for the development of platforms for cell transplantation upon epigenetic correction.

overall_design: Analysis of targeted CpG island methylation

first: Yuta

last: Takahashi

first: Chris

last: Benner


title: Next-Generation Sequencing Facilitates Quantitative Analysis of Transcriptomes in PB- and PB-TERRA-transfected 46C Mouse Embryonic Stem Cells

status: Public on Sep 18 2017

city: Hefei

first: Xiaojuan

last: Xu

state: Anhui

address: 350 Shushanhu Road

institute: Hefei Institutes of Physical Science

summary: Next-generation sequencing facilitates quantitative analysis of transcriptomes in 46C mouse embryonic stem cells overexpressing PB-TERRA or PB empty vector at gene expression level. Results provide important information of the response of up-regulating TERRA, such as specific mechano-responsive genes, up- or down-regulated genes that were mainly enriched in signaling pathways regulating pluripotency of stem cells.

overall_design: Total RNA obtained from TERRA-overexpressed 46C ESCs compared to empty vector-transfected control 46C ESCs.

first: Shoudong

last: Ye


title: AKR1C enzymes sustain therapy resistance in pediatric T-ALL

status: Public on Sep 30 2017

city: padova

first: silvia

last: bresolin

state: padova

address: via giustiniani 3

department: department of women's and children's health

institute: università di padova

summary:
Although intensification of chemotherapy approaches considerably increased the outcome of pediatric T-cell Acute Lymphoblastic Leukemia (T-ALL) patients, a subgroup of them still experience treatment failure and relapse. In this context, we hypothesized that the Nrf2 signalling and its downstream effectors could be involved in sustain therapy resistance in T-ALL, as previously reported in other cancers. Indeed, in this study we identified the Aldo-Keto Reductase (AKR) enzymes AKR1C1-3, as over-expressed in T-ALL samples from therapy-resistant patients, demonstrating their fundamental role in the control of the response to vincristine (VCR) treatment. In particular, we evidence that the modulation of AKR1C1-3 gene expression and activity is sufficient to strongly affect the sensitivity of T-ALL cell lines and primary cells to VCR treatment, but not to daunorubicin, cytarabine or L-asparaginase. Moreover, we found a correlation between the degree of VCR response and the amount of AKR1Cs expression in patient-derived T-ALL xenografts. Interestingly, we show that daunorubicin and cytarabine are able to induce the over-activation of AKR1C enzymes, thus establishing a potential resistance loop generated by the combination of these drugs during T-ALL treatment.
In this study, we demonstrate a clear involvement of AKR1C enzymes in controlling the response to chemotherapics in T-ALL, suggesting the possibility of considering AKR1Cs as reliable targets for the setup of novel combination treatments for T-ALL patients who do not respond to therapy

overall_design: Gene expression was measured on Affymetrix in 48 T-ALL pediatric patients and 6 T-ALL xenografts in NOD/SCID mouse

first: Silvia

last: Bresolin

first: Luca

last: Persano


title: Effects of two weeks of intermittent hypoxia on liver and adipose tissue in lean mice,

status: Public on Sep 23 2017

city: paris

first: veronique

last: PELLOUX

address: 50-52 bld Vincent Auriol

department: UMR 1166 eq 6

country: France

institute: INSERM

summary: Lean mice were submitted to either normoxia (controls) or CIH (CIH+) for 14 days. We analyzed liver and epidydimal adipose tissue signatures using transcriptomic analysis.

overall_design: Total RNA obtained from liver of 7 mice CIH+ and  8 mice controls to liver and 8 mice CIH+ and  8 mice controls to epidydimal adipose tissue .  An Illumina RNA amplification kit (Ambion) was used according to the manufacturer’s instructions to obtain biotin-labeled complementary RNA from 250 ng total RNA.

first: Judith

last: Pelloux

first: Karine

last: Clement


title: Oxidative stress elicits a rapid and global RNA polymerase II transcriptional response in human cells

status: Public on Aug 07 2017

city: Iowa City

first: David

last: Price

state: IA

address: 500 Newton Road

department: Biochemistry

institute: University of Iowa

summary:
In GSE93931, we used ChIP-Seq to show that hydrogen peroxide causes rapid accumulation of Pol II at promoters and enhancers. Over time, a fraction of accumulated Pol II loses NELF and creeps downstream. In GSE100740, we also compared nuclear walk-on results with PRO-Seq, both of which were performed using nuclei from DMSO- and flavopiridol-treated cells.

This SuperSeries is composed of the SubSeries listed below.

overall_design:
ChIP-Seq in HeLa cells
PRO-Seq using nuclei from HeLa cells

Refer to individual Series


title: Transcriptome analysis by expression microarrays  of colorectal cancer derived from the Cancer Institute Hospital of Japanese Foundation for Cancer Research.

status: Public on Aug 31 2017

city: Tokyo

first: Norio

last: Tanaka

address: Ariake 3-8-31, Koto

country: Japan

institute: Japanese Foundation Cancer Research

summary: We performed the expression microarray experiments for mRNA of colorectal cancer tissue.

overall_design:
Messenger RNA were extracted from primary tumor of 60 colorectal cancer patients, hybridized and scanned with Affymetrix Human Genome GeneChip U133 Plus 2.0 array.

Messenger RNA were extracted from primary tumor of 31 colorectal cancer patients, hybridized and scanned with Affymetrix Human Genome GeneChip U133 Plus 2.0 array.

Messenger RNA were extracted from primary tumor of 100 colorectal cancer patients, hybridized and scanned with Affymetrix Human Genome GeneChip U133 Plus 2.0 array.

first: Toshiharu

last: Yamaguchi


title: RNA Expression Profiling of CD8+ T Cell-Enriched Peripheral Blood Mononuclear Cells from Potentiated Sulfonamide-Treated Patients with a Range of Lymphocyte Cytotoxicity Phenotypes

status: Public on Jun 26 2017

city: Madison

first: Jennifer

last: Reinhart

state: WI

address: 2015 Linden Dr.

department: Medical Sciences

institute: University of Wisconsin-Madison

summary:
Hypersensitivity reactions are rare, but potentially severe adverse effects of sulfonamide antibiotics. Increased in vitro toxicity of lymphocytes, primarily CD8+ T cells, to sulfonamide drug metabolites as been proposed as a marker for sulfonamide hypersensitivity, but the mechanisms underlying this marker are unknown.
Therefore, we used microarrays to compare RNA expression of CD8+ T cell-enriched peripheral blood mononuclear cells of human patients who have had a hypersensitivity (HS) reaction to sulfonamide antibiotics vs. patients who have been tolerant (TOL) to a course of sulfonamide antibiotics.

overall_design: 40ml of heparinized blood was obtained from each patient, peripheral blood mononuclear cells were extracted and enriched for CD8+ T cells and RNA was extracted.

first: Daniel

last: Panyard

first: Michael

last: Newton

first: Lauren

last: Trepanier


title: Oxidative stress elicits a rapid and global RNA polymerase II transcriptional response in human cells [PRO-Seq]

summary: We compared nuclear walk-on results with PRO-Seq, both of which were performed using nuclei from DMSO- and flavopiridol-treated cells. In GSE93931, we also used ChIP-Seq to show that hydrogen peroxide causes rapid accumulation of Pol II at promoters and enhancers. Over time, a fraction of accumulated Pol II loses NELF and creeps downstream.

overall_design: PRO-Seq using nuclei from HeLa cells

first: Kyle

last: Nilson


title: Oxidative stress elicits a rapid and global RNA polymerase II transcriptional response in human cells [ChIP-Seq]

summary: Using ChIP-Seq, we show that hydrogen peroxide causes rapid accumulation of Pol II at promoters and enhancers. Over time, a fraction of accumulated Pol II loses NELF and creeps downstream. In GSE100740, we also compared nuclear walk-on results with PRO-Seq, both of which were performed using nuclei from DMSO- and flavopiridol-treated cells.

overall_design: ChIP-Seq in HeLa cells


title: The methylome of Burkitt Lymphoma

status: Public on Jul 24 2017

city: Bron

first: Hector

last: Hernandez-Vargas

state: Rhone

address: 36 bis Rue de la Batterie

institute: Genomics Consulting

summary: Burkitt Lymphoma cell lines were established and used for methylome profiling with Illumina HM450 beadchip

overall_design: Samples were classified into two groups according to EBV status: positive (n=10) and negative (n=9)

first: H

first: R

last: Accardi


title: Global transcriptional analysis and genome-wide analysis of chromatin state in extended pluripotent stem cells, primed pluripotent stem cells, and naïve pluripotent stem cells

status: Public on Apr 06 2017

first: Hongkui

last: Deng

address: this is for reviewer only

institute: Peking University

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

overall_design: Refer to individual Series


title: Global transcriptional analysis of human extended pluripotent stem cells, human primed pluripotent stem cells, mouse extended pluripotent stem cells, and mouse embryonic stem cells by RNA-seq

summary: All mammals develop from embryonic founder cells with the ability to generate all of the differentiated cells that constitute the organism. Capture of stem cells with such developmental potential in vitro has been a major challenge in stem cell biology. Here, we show that a chemical cocktail enables the derivation of a new stem cell type from both mice and humans, designated as extended pluripotent stem (EPS) cells. A single human or mouse EPS cell is able to contribute to both embryonic and extraembryonic lineages in inter- and intra-species chimeric mouse conceptuses respectively. Compared to known pluripotent stem cells, EPS cells show upregulation of gene modules marking embryonic cells from early preimplantation development. Further analysis shows that PARP1 inhibition is required for maintaining EPS potency. Our findings constitute a first step towards capturing authentic mammalian totipotency in vitro, and open new avenues for basic and translational research.

overall_design: Total of 10 samples were analyzed, which included human extended pluripotent stem cells, human primed pluripotent stem cells, mouse extended pluripotent stem cells, and mouse embryonic stem cells. For human primed pluripotent stem cells, one cell line H1 was analyzed, which included two samples. For human extended pluripotent stem cells, two cell lines were analyzed, which included ES1-EPS (2 samples) and H1-EPS (2 samples). For mouse extended pluripotent stem cells, two cell lines were analyzed, which included mc6-1 (1 sample) and OG6-3 (1 sample). For mouse embryonic stem cells, two cell lines were analyzed, which included mc2i (1 sample) and OG-2i (1 sample).

first: Yang

last: Yang

first: Bei

last: Liu

first: Jun

last: Xu

first: Jinlin

last: Wang


title: Integrative single-cell analysis of transcriptional and epigenetic states in the human adult brain [snDrop-seq]

status: Public on Dec 11 2017

city: La Jolla

first: Kun

last: Zhang

state: California

address: 9500 Gilman Drive

institute: UCSD

summary: Detailed characterization of the cell types in the human brain requires scalable experimental approaches to examine multiple aspects of the molecular state of individual cells, as well as computational integration of the data to produce unified cell-state annotations. Here we report improved high-throughput methods for single-nucleus droplet-based sequencing (snDrop-seq) and single-cell transposome hypersensitive site sequencing (scTHS-seq). We used each method to acquire nuclear transcriptomic and DNA accessibility maps for >60,000 single cells from human adult visual cortex, frontal cortex, and cerebellum. Integration of these data revealed regulatory elements and transcription factors that underlie cell-type distinctions, providing a basis for the study of complex processes in the brain, such as genetic programs that coordinate adult remyelination. We also mapped disease-associated risk variants to specific cellular populations, which provided insights into normal and pathogenic cellular processes in the human brain. This integrative multi-omics approach permits more detailed single-cell interrogation of complex organs and tissues.

overall_design:
Single DAPI+ nuclei (according to the Samples list) were isolated from the visual cortex (BA17), frontal cortex (BA6 or BA10), and cerebellar hemisphere from 6 different postmortem adult human brains and were processed for single-nucleus Drop-seq (snDrop-seq).

This series contains data only for snDrop-Seq.

first: Blue

middle: B

last: Lake

first: Song

last: Chen

first: Brandon

last: Sos

first: Jean

last: Fan

first: Yun

last: Yung

first: Jerold

last: Chun

first: Peter

middle: V

last: Kharchenko


title: Systematic identification of Ctr9 regulome in ERα-positive breast cancer

status: Public on Oct 10 2016

first: Xuehua

last: Zhong

address: 330 N. Orchard St.

department: Epigenetics

institute: Wisconsin Institute for Discovery

summary: Ctr9, the key scaffold subunit of the human RNA polymerase II (RNAPII) associated factor complex (PAFc), has been demonstrated as a positive regulator of ERα-positive breast cancer progression and ERα-target gene expression. Previously, we found that knockdown of Ctr9 reduces ERα protein stability and decreases the occupancy of ERα and RNAPII at select ERα-target genes. However, the genome-wide regulation of the occupancy of ERα and RNAPII mediated by Ctr9 is still unclear. Here, we determined the genome-wide ERα and RNAPII occupancy in response to estrogen induction and/or Ctr9 knockdown by performing chromatin immunoprecipitation coupled with high-throughput sequencing (ChIP-seq). We found that loss of Ctr9 dramatically decreases the global occupancy of ERα and RNAPII, highlighting the significance of Ctr9 in regulating estrogen signaling in ERα-positive breast cancer cells. Combining this resource with previously published genomic data sets, we identified a unique subset of ERα and Ctr9 target genes, and further delineates the possible independent function of Ctr9 from other subunits in PAFc.

overall_design: ChIP-seq experiments for ERα and RNAPII

first: Hao

last: Zeng

first: Li

last: Lu

first: Wei


title: Genome-wide analysis of the therapeutic effect of VND3207 on irradiation-induced intestinal injury

status: Public on Oct 18 2016

city: Suzhou

first: Ming

last: Li

address: No. 199 Ren'ai Road

institute: Soochow University

summary: The objective was to investigate the therapeutic effect of VND3207 on irradiation-induced intestinal injury at gene expression level. Gene expression profilings between VND3207 and vehicle treated mice which were received 9 Gy total body irradiation were compared.

overall_design: Mice were divided into two groups (3 mice per group) and administered intragastrically with 100mg/kg VND3207 or equivalent volume of vehicle respectively. Vehicle treated mice were served as controls. Half hours later, all mice were given 9 Gy radiation. 6 hours post radiation, mice jejunum tissues were isolated. Total RNA obtained from jejunum tissues and subjected to gene expression profiling assays.

first: Zengfu

last: Shang


title: mRNA expression data from overexpression or inhibition of miR-340 in 451 Lu melanoma cells

status: Public on Sep 06 2017

city: Madision

first: Ashley

last: Strong

address: 7418 1111 Highland Drive

department: Dermatology

institute: UW-Madison

summary: Characterizing miRNA function remains challenging due to an abundance of predicted targets and an experimental bottleneck in identifying biologically relevant direct targets. We developed a novel technique (miFAST) to identify direct miRNA target genes. Using miFAST, we confirmed several previously reported miR-340 target genes and identified five additional novel direct miR-340 targets in melanoma cells. This methodology can also be efficiently applied for the global characterization of miRNA targets.

overall_design: miR-340 inhibited or overexpressed 451 Lu melanoma cells were used for RNA extraction and hybridization onto Affymetrix microarrays.

last: Poenitzsch Strong

first: Scott

last: Berry

first: David

last: Beebe

first: Jian-Liang

first: Vladmir

middle: S

last: Spiegelman


title: Integrative single-cell analysis of transcriptional and epigenetic states in the human adult brain

first: Kun

last: Zhang

summary:
Detailed characterization of the cell types in the human brain requires scalable experimental approaches to examine multiple aspects of the molecular state of individual cells, as well as computational integration of the data to produce unified cell-state annotations. Here we report improved high-throughput methods for single-nucleus droplet-based sequencing (snDrop-seq) and single-cell transposome hypersensitive site sequencing (scTHS-seq). We used each method to acquire nuclear transcriptomic and DNA accessibility maps for >60,000 single cells from human adult visual cortex, frontal cortex, and cerebellum. Integration of these data revealed regulatory elements and transcription factors that underlie cell-type distinctions, providing a basis for the study of complex processes in the brain, such as genetic programs that coordinate adult remyelination. We also mapped disease-associated risk variants to specific cellular populations, which provided insights into normal and pathogenic cellular processes in the human brain. This integrative multi-omics approach permits more detailed single-cell interrogation of complex organs and tissues.

This SuperSeries is composed of the SubSeries listed below.


title: CD86 regulates a pro-survival signal in myeloma cells

status: Public on Jan 01 2017

city: Atlanta

first: Benjamin

middle: G

last: Barwick

state: GA

address: 1365 Clifton Rd. NE WCI-C 4th Floor Benches 36-37

department: Hematology and Medical Oncology

institute: Emory University

summary: While multiple myeloma patient prognosis has improved over the past decade, research towards discovery of new therapeutic avenues is important, and could lead to a cure for this chronic plasma cell malignancy. Data analysis from a myeloma patient database shows that the CD28-CD86 signaling module may provide a survival advantage in myeloma cells that negatively impacts patient outcome. Here we show that blocking the CD28-CD86 pathway, by silencing or with CTLA-4-Ig, leads to myeloma cell death. Blockade of this pathway leads to downregulation of nutrient transporters, integrins, and IRF4, a known myeloma survival factor. Our data also indicate that CD86, the canonical "ligand" in this pathway, is mediating a pro-survival signal via the cytosolic domain that has not been previously described. These findings indicate that blockade of this pathway is a promising therapeutic avenue for myeloma, as it leads to modulation of different processes important in cell viability.

overall_design: The myeloma cell lines MM.1s, RPMI8226, KMS18, and RPMI8226 that overexpresses the anti-apoptotic protein Mcl1 were transfected with short hairpin RNAs targeting CD28, CD86, Gapdh (control), or empty vector (pLK0.1) control and gene expression analysis was performed by RNA-seq.

first: Catherine

last: Gavile

first: Boise

last: Lawrence


title: Evolution of a transcriptional regulator from a transmembrane nucleoporin

status: Public on Jun 24 2016

city: San Diego

first: April

last: Williams

address: 10010 N Torrey Pines Rd

institute: Salk Institute for Biological Studies


title: Microarray whole transcriptome profiling of Sepantronium bromide (YM-155) treated MDA-MB-231 cells

status: Public on Aug 26 2017

city: Tallahassee

first: Elizabeth

last: Mazzio

state: Florida

address: 1515 MLK Blvd

department: College of Pharmacy & Pharmaceutical Science

institute: Florida Agricultural & Mechanical University

summary: Sepantronium bromide (YM-155) is believed to trigger apoptosis in tumor cells by inducing a major reduction in baculoviral inhibitor of apoptosis repeat-containing 5 (BIRC 5) also known as survivin. In MDA-MB-231 cells, the toxic effects of YM-155 were equi potent to standard chemotherapy drugs , having an LC50 < 50ng/ml. In this study we investigate whole transcriptome changes occurring at 8 hours of incubation with YM-155, preceding apoptosis as well as at a 20 hour time point. Microarrays were acquired for mRNAs and long intergenic non-coding RNA transcripts using the GeneChip™ Human Gene 2.1 ST Arrays by Affymetrix Inc.

overall_design: MDA-MB-231 cells grown under variable experimental treatment; 2 time points; triplicates

first: Karam

last: Soliman


title: A restricted period for formation of Outer Subventricular Zone defined by Cdh1 and Trnp1 levels

status: Public on Jun 01 2016

city: San Juan de Alicante

first: Victor

last: Borrell

state: Alicante

address: Av Ramon y Cajal s/n

department: Institute of Neuroscience

institute: CSIC

summary: The Outer Subventricular Zone (OSVZ) is a germinal layer playing key roles in the development of the neocortex, with particular relevance in gyrencephalic species like human and ferret where it contains abundant basal Radial Glia Cells (bRGCs) that promote cortical expansion.  Here we identify a brief period in ferret embryonic development when apical RGCs generate a burst of bRGCs that become founders of the OSVZ.  After this period, bRGCs in the OSVZ proliferate and self-renew exclusively locally, thereby forming a self-sustained lineage independent from the other germinal layers.  The time window for the brief period of OSVZ bRGC production is delineated by the coincident down-regulation of Cdh1 and Trnp1, and their up-regulation reduces bRGC production and prevents OSVZ seeding.  This mechanism in cortical development may have key relevance in brain evolution and disease

overall_design: Samples were analyzed with 3 replicates of each of them (except E34SVZ that has 2 replicantes). Comparisons were done taking different reference sample depending on the comparison.

first: Maria

last: Martínez-Martínez

first: Camino

last: De Juan Romero

first: Virginia

last: Fernández

first: Adrián

last: Cárdenas

first: Magdalena

last: Götz

first: Víctor


title: Profiling of mouse muscle stem cells aging and activation upon skeletal muscle injury

status: Public on Jul 04 2016

city: Lausanne

first: Jerome

last: Feige

address: EPFL Innovation Park, Building H

department: Musculo-Skeletal Health

country: Switzerland

institute: Nestle Institute Of Health Sciences

summary: Utilizing glycerol intramuscular injections in M. musculus provide a models of skeletal muscle damage followed by skeletal muscle regeneration. In particular, glycerol-induced muscle injury triggers accute activation of skeletal muscle stem cells, called satellite cells. However, aging dramatically impairs the regenerative capacity of satellite cells. We characterized genome-wide expression profiles of young and old satellite cells in the non-proliferative and activated state, freshly isolated to non-injured or damaged muscles, respectively. Our goal was to uncover new regulatory signaling specific to satellite cells entry into the activation and myogenic program that are affected with age.

overall_design: Satellite cells were isolated in either quiescent / non-proliferative or activated state from uninjured or 3 days after glycerol-induced injury of tibialis anterior, gastrocnemius and quadriceps, respectively. Young (2-4 months old) and old (20-24 months old) wildtype C57BL/6J male were used, with five to six biological replicates per group.

first: Laura

last: Lukjanenko

first: Eugenia

last: Migliavacca

first: Sonia

last: Karaz

first: Sylviane

last: Metairon

first: Frederic

last: Raymond

first: Florian

last: Bentzinger


title: Identification of a nuclear exosome decay pathway for processed transcripts

status: Public on Nov 03 2016

city: Aarhus

first: Evdoxia

last: Karadoulama

address: C.F. Møllers Alle 3

department: Molecular Biology and Genetics

country: Denmark

institute: Aarhus University

summary: The   RNA   exosome   is   fundamental   for   the   degradation   of   RNA   in eukaryotic  nuclei.  Substrate  targeting   is  facilitated  by  its  co-factor Mtr4p/hMTR4,  which  links  to RNA-binding  protein  adaptors. One  such activity  is  the  human  Nuclear  EXosome  Targeting  (NEXT)  complex, composed  of  hMTR4,  the  Zn-finger  protein  ZCCHC8  and  the  RNA-binding  factor  RBM7.  NEXT  primarily  targets  early  and  unprocessed transcripts, demanding   a   rationale   for   how   the   nuclear exosome recognizes processed  RNAs. Here, we describe the  PolyA tail eXosome Targeting  (PAXT)  connection, comprising  the  hitherto  uncharacterized ZFC3H1 Zn-knuckle  protein  as  a  central  link  between  hMTR4  and  the nuclear  polyA  binding  protein  PABPN1.  Individual  depletion  of  ZFC3H1 and  PABPN1  results  in  the  accumulation  of  common  transcripts,  that are   generally   both   longer   and   more   3’polyadenylated   than   NEXT substrates. Importantly, ZFC3H1/PABPN1  and  ZCCHC8/RBM7  contact hMTR4  in  a  mutually  exclusive  manner,  revealing  that  the  exosome targets nuclear transcripts of different maturation status by substituting its hMTR4-associating adaptors.

overall_design: RNA from HeLa cells was analysed by next generation sequencing upon depletion of EGFP(control), RRP40, RBM7, ZCCHC8, PABPN1 and ZFC3H1. Both total and BrU RNA (one hour labeling) were collected for each condition in triplicates. The spike-in sequences used in the samples can be provided upon request.

first: Nicola

last: Meola

first: Michal

last: Domanski

first: Yun

last: Chen

first: Coline

last: Gentil

first: Dennis

last: Pultz

first: Kristoffer

last: Seerup

first: Søren

last: Andersen

first: Jens

first: Albin

last: Sandelin

first: Torben

last: Jensen


title: Rabbit Model of Fetal Tracheal Occlusion for Congenital Diaphragmatic Hernia

status: Public on Jul 26 2016

city: Cincinnati

first: Jing

state: OH

address: 3333 Burnet Ave

institute: CCHMC

summary: Analysis of embronic day 30.5 (E30.5) fetal rabbit left lung after creation of diapragmatic hernia (DH) at E25 and tracheal occlusion (TO) at E27.

overall_design: The fetuses of timed pregnant New Zealand rabbits were subjected to creation of a left diaphragmatic hernia at E25 with or without tracheal occlusion at E27. At E30.5, the fetuses were sacrificed with collection of the lateral aspect of the left upper lobe for NextGen mRNA sequencing.

first: Brian

last: Varisco


title: Transcriptional profiling of aged Drosophila photoreceptors

status: Public on Nov 10 2017

city: WEST LAFAYETTE

first: Vikki

last: Weake

state: INDIANA

address: 175 S. University St.

department: Biochemisty

institute: Purdue University

summary: Purpose: The goal of this study was to globally characterize the transcript levels of genes in Drosophila photoreceptor neurons during aging. Using transcriptome profiling of isolated photoreceptor nuclei we analyzed the changes in gene expression that occur during aging over 5 time-points from 10 to 40 days post-eclosion and identified sets of genes with both up-regulated and down-regulated expression.

overall_design: Method: RNA extracted from photoreceptor nuclei of flies aged from 10 to 40 days was used to generate cDNA libraries using NuGen Ovation Drosophila RNA seq system. Samples were sequenced using  Illumina HiSeq2500 next generation sequencer (five different age time points and three biological replicates per time point).

first: Hana

last: Hall

first: Patrick

last: Medina

first: Jeremiah

last: Rounds

first: Christopher

last: Vincent

first: Rebecca

last: Doerge

middle: M


title: Global Rebalancing of Cellular Resources by Pleiotropic Point Mutations Illustrates a Multi-scale Mechanism of Adaptive Evolution

status: Public on Apr 28 2016

city: Cuernavaca

first: Jose

last: Utrilla

state: Morelos

address: Av. Universidad sn

department: Centro de Ciencias Genómicas

country: Mexico

institute: Universidad Nacional Autonoma de México

summary:
Pleiotropic regulatory mutations affect diverse cellular processes, posing an explicit challenge to our multi-scale understanding of the genotype-phenotype relationships across multiple biological scales. Adaptive Laboratory Evolution (ALE) allows for such mutations to be found and characterized in the context of clear selection pressures. Here, several ALE-selected single-mutation variants in Escherichia coli’s RNA polymerase (RNAP) are detailed using an
integrated multi-scale experimental and computational approach. While these mutations increase cellular growth rates in steady environments, they reduce tolerance to stress and environmental fluctuations. We detail structural changes in the RNAP that rewire the transcriptional machinery to rebalance proteome and energy allocation towards growth and away from several hedging and stress functions.  SurprisinglyW, we find that while these mutations occur in diverse locations in the RNAP, they share a common adaptive mechanism. In turn, these findings highlight the resource allocation trade-offs organisms face and suggest
how the structure of the regulatory network enhances evolvability.

sample_organism: Escherichia coli str. K-12 substr. MG1655

overall_design: Samples were taken from mid-log phase of batch cultures or steady state phase in chemostat cultures. RNAseq was performed by paired end libraries in a modified dUTP method (see methods in paper)

first: Edward

last: O'Brien

first: Bernhard

middle: O

last: Palsson

first: Adam

last: Feist