title: Clinical spectrum of multi-locus imprinting disturbances associated with maternal-effect variants range from overt Beckwith-Wiedemann syndrome to apparently healthy phenotype

status: Public on Oct 01 2019

first: Ankit

last: Verma

summary: Multi-locus imprinting Disturbances (MLID) are methylation defects affecting germline-derived Differentially Methylated Regions (gDMRs) and they have been associated with maternal-effect variants causing imprinting disorders in the offspring. In a family with multiple pregnancy losses, a child with Beckwith-Wiedemann syndrome (BWS) and a further child without any features of imprinting disorders, novel compound heterozygous variants in the NLRP5 gene of the mother were found.  Locus-specific and whole-genome methylation analysis by using Infinium MethylationEPIC BeadChip (WG-317-1001, Illumina) revealed MLID with different methylation profiles in both the siblings. The proband and the normal sibling were found to cluster with other MLID cases as shown by principal component analysis and unsupervised hierarchical clustering and remain distinct from controls. However, we were unable to cluster MLID cases associated with specific clinical phenotypes.  The identification of two novel maternal-effect variants of NLRP5 associated with poly-abortivity and MLID add further evidence to the role of NLRP5 in the maintenance of genomic imprinting in early embryos. Furthermore, our results demonstrate that within these pedigrees MLID can also be present in the progeny with healthy phenotype, indicating that some sort of compensation occurs between altered imprinted loci in these individuals.

overall_design: DNA samples extracted from Blood were subjected to methylation analysis using Infinium MethylationEPIC 850K Bead Chip and pyrosequencing. We also included 6 closely-related individuals from family as control samples. The methylation profile was further correlated with publicaly available MLID and BWS datasets.

first: Angela

last: Sparago

first: Maria

last: Patricelli

first: Laura

last: Pignata

last: Russo

first: Luciano

last: Calzari

first: Naomi

last: De Francesco

first: Rosita

last: Del Prete

first: Orazio

last: Palumbo

first: Massimo

last: Carella

first: Deborah

last: Mackay

first: Faisal

last: Rezwan

first: Claudia

last: Angelini

first: Flavia

last: Cerrato

middle: V

last: Cubellis

first: Andrea

last: Riccio


title: Transcriptomic analysis of plant  Cd-regulated genes in the ericoid mycorrhizal symbiosis

status: Public on Feb 12 2020

city: Champenoux

first: Annegret

last: Kohler

address: Centre Grand Est Nancy

country: France

institute: INRAE

type: Expression profiling by high throughput sequencing

summary: Illumina HiSeq2000 technology was used to generate mRNA profiles from Vaccinium myrtillus mycorrhizal and non-mycorrhizal roots with or without Cadmium treatment.  150bp reads were generated and aligned to a Vaccinium myrtillus de novo assembly as reference using CLC Genomics Workbench 8.

sample_organism:
Vaccinium myrtillus
Oidiodendron maius Zn

overall_design: To analyse the effect of Cadmium, total RNA from V. myrtillus mycorrhizal and non-mycorrhizal roots with or without Cadmium treatment were generated and sequenced by Illumina HiSeq2000. Three biological replicates from each treatment were sequenced.

first: Salvatore

last: Casarrubia

first: Stefania

last: Daghino

first: Vasanth

last: Singan

first: Erika

last: Lindquist

first: Francis

last: Martin

first: Elena

last: Martino

first: Silvia

last: Perotto


title: Whole Genome Bisulfite Sequencing of Female Zebrafish Embryos Treated with Atrazine

status: Public on Jan 24 2020

city: West Lafayette

first: Chongli

last: Yuan

state: IN

address: 480 Stadium Mall Drive

country: USA

institute: Purdue University

type: Methylation profiling by high throughput sequencing

summary: We exposed zebrafish embryos to 0.3, 3, and 30 ppb (µg/L) of ATZ for 72 hours post fertilization. We performed whole-genome bisulfite sequencing (WGBS) to assess the effects of developmental ATZ exposure on DNA methylation in female fish brains

overall_design: Next generation sequencing was performed using NovaSeq (Illumina, US) at Purdue Genomics Core Facility. All sequencing was performed at a sequencing depth of 30x coverage on the 1.5 billion base zebrafish genome

first: Chris

last: Bryan

first: Jennifer

last: Freeman


title: Long noncoding RNA INCA1 regulates tumor interferon signaling

status: Public on Jul 29 2020

city: Boston

first: Marco

last: Mineo

state: MA

address: 60 Fenwood Rd, BTM 8016N

institute: Brigham and Women's Hospital

type: Non-coding RNA profiling by high throughput sequencing

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

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

first: E

middle: A

last: Chiocca


title: Single cell sequencing of mouse heart immune infiltrate in pressure overload-driven heart failure reveals extent of immune activation

status: Public on Oct 12 2019

city: Pieve Emanuele (MI)

first: Bioinformatics

last: Unit

address: Via Rita Levi Montalcini 4

country: Italy

institute: IRCCS Humanitas Research Hospital

summary: Single-cell RNA sequencing is revolutionizing the mapping of tissues in physiology and pathology. Whilst immune responses are emerging as key mediators of heart failure, no thorough immune mapping of the ailing heart has been performed so far. Here we examined, at single-cell level, the cardiac immune composition after transverse aortic constriction, the standard murine model of non-ischemic heart failure. We identified the presence of most major immune cell subpopulations in the myocardium of both healthy and cardiopathic mice. Despite the absence of infectious agents or an autoimmune trigger, the ailing heart, especially at late-stage disease, is characterized by an immune activation that is both drastic and far more wide-ranging in the immune cell types involved than previously thought. The molecular-level detail we uncover in the cells undergoing activation in response to cardiac stress may enable the identification of novel biomarkers and therapeutic targets for heart failure.

overall_design: 4 experimental condtions, two time points

first: Paolo

last: Kunderfranco

first: Marinos

last: Kallikourdis

first: Gianluigi

last: Condorelli


title: Whole Genome Bisulfite Sequencing of Rett Syndrome and Control Human BA9 Cortex

status: Public on Sep 17 2019

city: Vancouver

first: Annie

middle: Vogel

last: Ciernia

state: British Columbia

address: 2215 Wesbrook Mall room 4550, Centre for Brain Health

country: Canada

institute: University of British Columbia

summary: Rett syndrome (RTT) is an X-linked neurodevelopmental disorder caused by mutations in the gene encoding methyl CpG binding protein 2 (MeCP2) that occur sporadically in 1:10,000 female births. RTT is characterized by a period of largely normal development followed by regression in language and motor skills at 6-18 months of age. To investigate alterations in DNA methylation in RTT, we performed whole genome bisulfite sequencing on brodmann area 9 of human cortex from RTT and matched controls.

overall_design: Whole Genome Bisulfite Sequencing of Human BA9 Cortex

first: Janine

last: LaSalle


status: Public on Aug 20 2019

city: Chapel Hill

first: Alessandro

last: Porrello

state: NC

address: 450 West Drive

department: Lineberger Comprehensive Cancer Center

institute: University of North Carolina at Chapel Hill

summary:
Expression data from 4T1 subclones derived from mammary fat pad tumors (MFP), axillary lymph node tumors (AxLN), and axillary lymph node-derived lung metastases (AxLN-LuM). In parallel, expression data, in the same subclones, of tail vein-derived (TV) lung metastases.
The mechanism of how lymph node metastases seed distant metastases is unknown. We used the 4T1 breast cancer cell line, which is an immune competent model of triple negative breast cancer and spontaneously metastasizes in balb/c mice.
4T1-GFP/fLuc cells were injected into MFP to form tumors and 4T1-mCherry/rLuc cells were injected into axillary lymph nodes to form tumors and then allowed to metastasize to lung. TV cells were allowed to metastasize in the lung. Cells were harvested at different time intervals after the injection. Tumors were extracted, dissociated, and then expanded in vitro to obtain MFP, AxLN, AxLN-LuM and TV-LuM subclones isolated after different time lags with respect to the injection.

overall_design: Subclones were grown to 60-80% confluence for RNA extraction and hybridization on Affymetrix microarrays. Then, differentially expressed genes were assessed amongst the aforementioned subclones.

first: Chad

last: Pecot


title: Human Cortical DNA methylation by WGBS in Autism Spectrum Disorders and Rett Syndrome

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

overall_design: Refer to individual Series


title: A Single-Cell Atlas of the Multicellular Ecosystem of Primary and Metastatic Hepatocellular Carcinoma

status: Public on Apr 30 2020

city: Beijing

first: Yiming

last: Lu

address: Taiping Road

country: China

institute: State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine

summary: Hepatocellular carcinoma (HCC) represents a paradigm of the relation between tumor microenvironment and tumor development. Here, we generated > 70,000 single-cell transcriptomes for 10 HCC patients from four relevant sites: primary tumor, portal vein tumor thrombus (PVTT), metastatic lymph node and non-tumor liver. We discovered a cluster of antitumor central memory T cells enriched in intratumoral tertiary lymphoid structures (TLSs) of HCC. We found chronic HBV/HCV infection increases the infiltration of CD8+ T cells in tumors but aggravates the exhaustion of tumor-infiltrating lymphocytes. We identified MMP9+ macrophages to be terminally differentiated tumor-associated macrophages (TAMs) and two distinct differentiation trajectories are related to their accumulation. We further demonstrated MMP9+ TAMs can promote HCC cells migration, invasion and angiogenesis. Our data also revealed the heterogeneous population of malignant hepatocytes and found they might play multifaceted roles in shaping the immune microenvironment of HCC. Finally, we identified seven TME subtypes of HCC that can predict patient prognosis. Collectively, this large-scale, single-cell atlas deepens our understanding of the ecosystem in primary and metastatic HCCs, might facilitating identification of new immune therapy strategies for this malignancy.

overall_design:
Single-cell suspensions were converted to barcoded scRNA-seq libraries by using the Chromium Single Cell 3’ Library, Gel Bead & Multiplex Kit and Chip Kit (10x Genomics), aiming for an estimated 5,000 cells per library and following the manufacturer’s instructions. Samples were processed using kits pertaining to V2 barcoding chemistry of 10x Genomics. Single samples are always processed in a single well of a PCR plate, allowing all cells from a sample to be treated with the same master mix and in the same reaction vessel. For each patient, all samples (NTL, PT, PVTT and MLN) were processed in parallel in the same thermal cycler. The generated scRNA-seq libraries were sequenced on an Illumina NovaSeq sequencer. The Cell Ranger software (version 2.2.0) was used to perform sample demultiplexing, barcode processing and single-cell 3’ counting. Cell Ranger’s mkfastq function was used to demultiplex raw base call files from the sequencer, into sample-specific fastq files. Afterward, fastq files for each sample were processed with Cell Ranger’s count function, which was used to align reads to human genome (build hg38) and quantify gene expression levels in single cells.

Raw data access provided at: European Genome-phenome Archive (EGA) under accession EGAS00001004468.

first: Aiqing

last: Yang

first: Cheng

last: Quan

first: Haoyun

last: Zhang

first: Yingwei

last: Pan

first: Yuanfeng

last: Li

first: Chengming

last: Gao

first: Hao

first: Pengbo

last: Cao

first: Hongxia

last: Chen

first: Shichun

first: Gangqiao

last: Zhou


title: Gene expression profiling of sarcoma T cells deriving from Csf3r WT and KO mice

status: Public on Jun 24 2019

first: Bioinformatics

last: Unit

summary: Recently, tumor-associated neutrophils (TANs) are considered as an important component of the tumor microenvironment. Here, we show that a specific genetic deficiency of neutrophils induced accelerated mesenchymal carcinogenesis associated with a deficient production of IFN-γ in the tumor microenvironment. Unexpectedly, increased susceptibility to cancer of neutropenic mice was associated with impaired type 1 polarization of unconventional T cell (UTC) subsets, namely mucosal-associated invariant T (MAIT) cells and double CD4 and CD8 negative TCRβ+ T (DNT) cells, resulting in reduced expression of T-bet and IFN-γ and increased expression of Rorγt and IL-17A. Here, we uncovered a new mechanism by which neutrophils induced an IL-12-dependent type 1 polarization of MAIT and DNT cells characterized by the upregulation of T-bet expression. Therefore, a systemic reconstitution of Csf3r-/- mice with functional naïve neutrophils was sufficient to restore UTCs activation state and to slow down sarcoma growth. Finally, in patients with undifferentiated pleomorphic sarcoma, TAN infiltration signature was associated with better overall survival and increased expression of IFN-γ and type 1 inflammatory response signature.

overall_design: Transcriptome profiling of sarcoma associated T cells (CD4, CD8, UTCs, γδ) in Csf3r WT and KO mice

first: R

last: Carriero

first: A

last: Ponzetta

first: S

last: Jaillon


title: Embryonic day 13.5 mRNA profiles for wildtype and MIDEAS and DNTTIP1 knockout MEFs

status: Public on May 26 2020

city: Leicester

first: John

last: Schwabe

state: Leicestershire

address: Lancaster Road

department: Molecular and Cell Biology

country: United Kingdom

institute: University of Leicester

summary:
Objective: Perform deep sequencing on mouse embryonic fibroblasts from e13.5 embryos with wildtype, MIDEAS-/- and DNTTIP1-/- genotypes to provide insights into observed embryonic lethality with associated haemolytic anaemia and heart defects.
Method: Heterozygous mates of MIDEAS or DNTTIP1 set up and pregnant females culled at e13.5. MEFs were created from embryos and cultured for 4-6 passages before total RNA extraction and deep sequencing (novogene) to obtain mRNA pofiles. FastQ files processed using TRIMGALORE!, STAR,  Picards remove duplicates and SAM Tools. R was used for DESeq2 analysis to find differentially regulated genes
Results: A large number of both up and down regulated genes were found for both MIDEAS and DNTTIP1 knockout MEFs compared to wildtype. Of these a significant amount were common to both knockouts suggesting a role in the same complex and shared gene targets. A number of these transcripts were associated with angiogenesis and haematopoiesis as well as neual development.
Conclusion: Whilst further biological experiments are required to confirm reason for haemolytic anaemia present in knockout embryos there is a strong indication this could be caused by changes in gene regulation cause by the loss of the MIDAC compex

overall_design: MEF mRNA profiles of wildtype and DNTTIP1-/- (duplicate) or wildtype and MIDEAS-/- (triplicate) from e13.5 embryos were generated by deep sequencing using Ilumina novo-seq platform

first: Robert

middle: E

last: Turnbull

first: Emma

last: Kelsall

first: Aditya

last: Chandru

first: Shaun

middle: M

last: Cowley

middle: W


title: Single-cell RNA-seq of UTCαβ population in sarcoma mice models

summary: Neutrophils represent a fundamental mechanism of antimicrobial resistance and inflammation 1. Moreover, neutrophils have emerged as important players in the activation, orchestration and regulation of adaptive immune responses2,3. Neutrophils are a component of the tumor microenvironment (TME) and have been prevalently shown to promote progression 4-6. On the other hand, unleashed neutrophilic effectors have also been reported to mediate anti-cancer resistance7-11. Antibody-mediated depletion used to investigate the role of neutrophils in tumor progression suffers from limitations, including duration, specificity and perturbation of the system12. We therefore used a genetic approach to investigate the role of neutrophils in primary 3-methylcholanthrene (3-MCA)-induced sarcomagenesis. Neutrophils were found to play an essential role in resistance against primary carcinogenesis by driving an interferon-γ dependent type 1 immune response. Neutrophil-dependent macrophage production of IL-12p70 led to type 1 polarization of CD4- CD8- unconventional αβ T cells (UTCαβ) in the TME. Single cell RNAseq analysis and in vivo evidence from two preclinical sarcoma models highlight the antitumor potential of a UTCαβ subset. In the TCGA cohort of human undifferentiated pleomorphic sarcomas (UPS), unlike other sarcomas, granulocyte-colony stimulating factor receptor (CSF3R) expression and a neutrophil signature were associated with better outcome and with a type 1 immune response. The positive association between high neutrophil infiltration and improved clinical outcome was confirmed in an independent UPS cohort by immunohistochemistry. Thus, neutrophils, by driving a type 1 immune response and polarization of UTCαβ, mediate resistance against murine and human sarcomas.

overall_design: two experimental conditions, two biological replicates for each condition

last: Mantovani


title: Regulation of hypoxia-inducible factor activity by ZMYND8

status: Public on Apr 10 2019

city: Dallas

first: Weibo

last: Luo

state: Texas

address: 5323 Harry Hines Blvd.

department: Pathology

institute: UT Southwestern Medical Center

type: Genome binding/occupancy profiling by high throughput sequencing

summary: ZMYND8 coactivates the global HIF target genes in breast cancer MDA-MB-231 cells.

overall_design: MDA-MB-231 cells were exposed to 20% or 1% O2 for 24 hrs and subjected to mRNA-seq. MDA-MB-231 cells were exposed to 1% O2 for 24 hrs and subjected to ChIP-seq.

first: Yan


title: Gene expression data from human left and right atrial tissues in patients with degenerative MR in SR and AFib.

status: Public on Feb 04 2019

city: Ankara

first: Gunseli

last: Cubukcuoglu Deniz

address: Ceyhun Atuf Kansu Cad. No: 169

department: Stem Cell Institute

country: Turkey

institute: Ankara University

summary: We aimed to compare the gene expression profiles of patients with degenerative MR in SR and AFib. We used Affymetrix human gene expression microarrays for each atrium sample. We chose most homogenous groups to compare, cause of the noise overshadows in high-throughput analysis when investigating complex diseases.

overall_design: Left and right atrial tissue samples were obtained from patients with chronic primary severe MR in permanent AFib (n=15) and sinus rhythm (n=15). Transcriptomic analysis and bioinformatics have been done on all atrial tissues. Independent datasets from GEO were included in the analysis to confirm our findings. Real-time qPCR used to validate microarray results. Atrial tissues investigated via transmission electron microscopy for ultrasutructural changes.

middle: C

last: Deniz

first: Serkan

last: Durdu

first: Hilal

last: Özdağ

first: Rüçhan

last: Akar


title: Analysis of promoter-associated chromatin interactions reveals biologically relevant candidate target genes at endometrial cancer risk loci

status: Public on Apr 13 2020

city: Brisbane

first: Tracy

last: O'Mara

state: QLD

address: 300 Herston Road

country: Australia

institute: QIMR Berghofer Medical Research Institute

summary: The identification of target genes at genome-wide association study (GWAS) loci is a major obstacle for GWAS follow-up. To identify candidate target genes at the 16 known endometrial cancer GWAS risk loci, we performed HiChIP chromatin looping analysis of endometrial cell lines. To enrich for enhancer-promoter interactions, a mechanism through which GWAS variation may target genes, we captured loops associated with H3K27Ac histone, characteristic of promoters and enhancers. Analysis of HiChIP loops contacting promoters revealed enrichment for endometrial cancer GWAS heritability and intersection with endometrial cancer risk variation identified 103 HiChIP target genes at 13 risk loci. Expression of four HiChIP target genes (SNX11, SRP14, HOXB2 and BCL11A) was associated with risk variation, providing further evidence for their regulation. Network analysis functionally prioritized a set of proteins that interact with those encoded by HiChIP target genes, and this set was enriched for pan-cancer and endometrial cancer drivers. Lastly, HiChIP target genes and prioritized interacting proteins were over-represented in pathways related to endometrial cancer development. In summary, we have generated the first global chromatin looping data from endometrial cells, enabling analysis of all known endometrial cancer risk loci and identifying biologically relevant candidate target genes.

overall_design: We performed H3K27Ac HiChIP on 4 endometrial cell lines

first: Dylan

last: Glubb


title: The downstream gene expression of Notch signal in tumor associated endothelial cells

status: Public on Feb 26 2019

city: Xi'an

first: Xian-Chun

last: Yan

address: Chang-Le Xi street #169

institute: fourth military medical university

summary: To study the effects of Notch signal in tumor associated endothelial cells ,we conducted a RNA sequence assay. Briefly, TECs were isolatedas described above from LLC tumors 14 days after inoculation in 3 pairs of NICeCA and control mice. Total RNA was extracted using Trizol, and RNA integrity was evaluated using the Agilent 2200 Tape Station (Agilent Technologies, Santa Clara, California, USA) and each sample had the RINe above 7.0. rRNA was removed using the EpicentreRibo-Zero rRNARemoval Kit ( Illumina, San Diego, CA). Remaining RNA was fragmented into approximately 200bp fragments. Subsequently, the sample was subjected to first and second strand cDNA synthesis followed by adaptor ligation and enrichment with a low-cycle PCR usingTruSeq® RNA LT/HT Sample Prep Kit (Illumina). The purified library products were evaluated using the Agilent 2200 TapeStation and Qubit®2.0 (Life Technologies) and then diluted to 10 pM for cluster generation in situ on the HiSeq3000 pair-end flow cell followed by sequencing (2×150 bp) on HiSeq 3000.

overall_design: LLC tumor endothelial cells mRNA profile of endothelial specific Notch signal activation mice and control mice were generated by deep sequencing, in triplicate,using Illumina 3000

first: Xianchun

first: Hua

last: Han


title: Profiling of villi transcriptome in Trpm7 gene deficient mice and control littermates.

status: Public on Feb 01 2019

city: Munich

first: Vladimir

last: Chubanov

state: Non-US/Canada

address: Goethestraße 33

department: Walther-Straub-Institut

country: Germany

institute: Ludwig-Maximilians-Universität München

summary:
To attain deeper insight into metabolic alterations in Trpm7 gene deficient mice we used microarrays for profiling of transcripts in villi of Trpm7 ko and control mice.
We identified a set of gene networks up- or down-regulated in villi of Trpm7 gene deficient mice.

overall_design: Villi were isolated from intestines obtained from 5 days old Trpm7 deficient (n=3) and control (n=3) littermates.

first: Lorenz

last: Mittermeier

first: Thomas

last: Gudermann


title: Gymnopus androsaceus growth on pine needles

status: Public on Nov 28 2019

first: Annegret

last: Kohler

summary: Illumina HiSeq2500 technology was used to generate mRNA profiles from Gymnopus androsaceus grown on pine needles for 2, 5 and 10 months.    Paired-end reads of 125 bp were generated and aligned to Gymnopus androsaceus reference transcripts using  CLC Genomics Workbench 9.

overall_design: mRNA profiles from Gymnopus androsaceus grown on pine needles for 2, 5 and 10 months were generated by Illumina HiSeq2500 sequencing (2x125bp). Three biological replicates from 2, 5 and 10 months were sequenced.

first: Laure

last: Fauchery

first: Preetisri

last: Baskaran

first: Björn

last: Lindahl

first: Francis

last: Martin


title: Gene expression changes in galls at 21 dai and corresponding uninfected roots from Poplar CAD and WT lines

status: Public on Jan 15 2019

summary: Illumina  technology was used to generate mRNA profiles of galls from root-knot nematodes infected and corresponding uninfected roots from Poplar CAD and WT lines.   RNA was extracted from 3 replicates.TruSeq mRNA Stranded libraries were constructed and after pooling and normalization of libraries, sequencing was done on a NextSeq500 Sequencing System.  Raw reads were trimmed for quality and mapped to the substituted genome sequence of P. tremula x P. alba 717-1B4  using CLC Genomics Workbench v9.5.2 and the primary transcripts only.

overall_design: mRNA profiles of galls and uninfected roots from Poplar CAD and WT lines were generated by NextSeq500 sequencing (2x75bp). Three biological replicates were sequenced.

first: Fabien

last: Baldacci-Cresp

first: Marie

last: Baucher


title: Optimal-transport analysis of single-cell gene expression identifies developmental trajectories in reprogramming

status: Public on Jan 31 2019

city: Warsaw

first: Marcin

last: Tabaka

address: Kasprzaka 44/52

country: Poland

institute: International Centre for Translational Eye Research


title: Chalara longipesis growth on pine needles

summary: Illumina HiSeq2500 technology was used to generate mRNA profiles from Chalara longipesis grown on pine needles for 2, 5 and 10 months.    Paired-end reads of 125 bp were generated and aligned to Chalara longipesis reference transcripts using CLC Genomics Workbench 9.

overall_design: mRNA profiles from Chalara longipesis grown on pine needles for 2, 5 and 10 months were generated  by Illumina HiSeq2500 sequencing (2x125bp).Two biological replicates from 2 and 5 months and Three biological replicates from 10 months were sequenced.

last: Lindah


title: Circular non-coding LRP6 is a tissue-enriched circular RNA which regulates smooth muscle cell biology acting as a sponge for miR-145

status: Public on Dec 05 2018

first: Bioinformatics

last: Unit

summary:
Rationale: microRNAs (miRNAs) modulate gene expression by repressing translation of targeted genes. Previous work has established a role for miRNAs in regulating vascular smooth muscle cell (VSMC) activity. Whether circular RNAs (circRNA) are involved in the modulation of miRNA activity in VSMCs is unknown.

Objective: We aimed to identify circRNAs interacting with miRNAs enriched in VSMCs and modulating the cells' activity.

Methods and Results: RNA sequencing and bioinformatics identified several circRNAs enriched in VSMCs; however, only one, possessing multiple putative binding sites for miR-145, was highly conserved between mouse and man. This circRNA gemmed from alternative splicing of lipoprotein receptor 6 (Lrp6), a gene highly expressed in vessels and implicated in vascular pathologies, and was thus named circ_Lrp6. Its role as a miR-145 sponge was confirmed by determining reciprocal interaction through RNA immunoprecipitation, stimulated emission depletion microscopy, and competitive luciferase assays; functional inhibition of miR-145 was assessed by measuring expression of the target genes ITGβ8, FASCIN, KLF4, Yes1, and Lox. The interaction was preferentially localized to P-bodies, sites of mRNA degradation. Using loss- and gain-of-function approaches, we found that circ_Lrp6 hindered miR-145-mediated regulation of VSMC migration, proliferation, and differentiation. Differential expression of miR-145 and circ_Lrp6 in murine and human vascular diseases suggests that the ratio of circ_Lrp6 bound to miR145 vs. unbound could play a role in vascular pathogenesis. Viral delivery of circ_Lrp6 shRNA prevented intimal hyperplasia in mouse carotids.

Conclusions: circ_Lrp6 is an intracellular modulator and a natural sponge for miR-145, counterbalancing the functions of the miRNA in VSMCs.

overall_design:
mouse circular RNA
DCC_circRNAs_Mouse.txt: circular RNAs detected with DCC package in Mouse Aorta


title: Expression analysis of inguinal white adipose tissue

status: Public on Nov 01 2018

city: San Francisco

first: Biao

last: Wang

address: 555 Mission Bay Blvd South

department: CVRI

institute: University of California, San Francisco

summary: We use microarray to analyze gene expression after adipocyte constitutively active HDAC4 expression in inguinal white adipose tissue

overall_design: We extracted RNA from inguinal white adipose tissues of ~8-week-old wild-type and H4-TG mice. We pooled RNAs from 4 animals from the same genotype for microarray analysis.

first: Dongmei

last: Wu


title: Whole Genome Bisulfite Sequencing of Autism and Control Human BA9 Cortex

first: Annie

last: Ciernia

summary: Autism spectrum disorders (ASD), characterized by lack of social and communicative behaviors, have complex etiologies involving multiple genetic and environmental risk factors. Epigenetic information, such as brain DNA methylation patterns, is predicted to reveal insight into the gene networks, cell types, and developmental timing of ASD etiology, but prior methylation studies in ASD have been limited by platform or data integration. Here, we used whole genome bisulfite sequencing (WGBS) to examine DNA methylation genome wide in Brodmann Area 9 of dorsal lateral prefrontal cortex of ASD and Control samples.

overall_design: Whole Genome Bisulfite Sequencing of Human BA9 Cortex

first: Janine

last: LaSalle


title: Neonatal and adult human testis defined at the single-cell level

status: Public on Dec 22 2018

city: La Jolla

first: Miles

middle: F

last: Wilkinson

state: CA

address: 2880 Torrey Pines Scenic Dr. Room 4811

department: Reproductive Medicine

institute: University of California

summary: Spermatogenesis has been well studied in rodents and invertebrates, but remains poorly understood in humans. As a step towards illuminating human spermatogenesis, we used single-cell RNA-sequencing (scRNAseq) analysis to analyze neonatal and adult human testes. Clustering analysis of neonatal testes revealed 3 germ subsets, including cells with characteristics of primordial germ cells (PGCs), and more differentiated cells with gene expression profiles similar with adult spermatogonial stem cells (SSCs). We identified markers for these neonatal subsets, including protein markers for the PGC-like (PGCL) subset. Clustering analysis of the adult testis revealed 9 germ and 3 somatic cell subsets. Among the germ cell clusters are 4 undifferentiated spermatogonia (SPG) states, each marked by specific genes. One of the SPG states has characteristics suggesting it is enriched for SSCs. We identified protein markers specific for this state, including cell-surface proteins that we used to enrich for these cells. We mapped the timeline of male germ cell development from PGCs through fetal germ cells to differentiating adult SPG stages. We also defined somatic cell subsets in the human testis and traced their developmental trajectories.  Together, our data provides a blueprint for understanding the development of the male germline and supporting somatic cells in humans. The germ cell subset markers we identified are candidates to be used for clinical applications, including SSC therapy for treating infertility.

overall_design: Single cell sequencing from two neonatal and two adult testicular cells was performed. Cells were either enriched for ITGA6 expression or unfractionated before GEM capture

first: Abhishek

last: Sohni

first: Kun

last: Tan

first: Hye-Won

last: Song

first: Dana

last: Burow


title: Expression data from DC1 purified from spleens of WT, WT Irf8VENUS+, and Batf3-/- Irf8VENUS+ mice.

status: Public on Nov 30 2018

city: St Louis

first: Theresa

last: Murphy

state: MO

address: 4940 Parkview Place

institute: washington university school of medicine

summary: Batf3-/- mice have impaired development of DC1 . However, DC1 development is restored in Batf3-/- mice containing an Irf8VENUS transgene. Even though DC1 development was restored in these mice, they were still unable to reject a transplanted immunogenic fibrosarcoma, indicating that there are some functions of Batf3-dependent dendritic cells that are not restored by the Irf8VENUS transgene.

overall_design: Microarray analysis was performed on DC1 sorted from skin draining lymph nodes of WT Irf8VENUS, and Batf3-/- Irf8VENUS mice, all on C57Bl/6j background. Migratory and resident DC1 were analyzed for both genotypes.

first: Kenneth


title: Estrogen receptor beta enhances chemotherapy response of GBM cells by down regulating DNA damage response pathways

status: Public on May 02 2019

city: SAN ANTONIO

first: YI

last: ZOU

state: TX

address: 8403 Floyd Curl Drive

institute: UTHSA-GCCRI

summary: We examined the transcriptional changes modulated by estrogen receptor beta (ERβ) by performing global transcriptome analysis. U87 cells were transduced with lentiviral particles carrying either empty vector or ERβ-FLAG expression vector and the RNA was isolated and utilized for RNA-seq analysis. Our results demonstrated that ERβ modulated genes were related to homologous recombination, DNA damage response, ATM signaling and cell cycle pathways.

overall_design: Total RNA was isolated from U87 cells expressing either empty vector or ERβ expression vector. Illumina TruSeq RNA Sample Preparation was performed following manufacturer's protocol. Samples were run on an Illumina HiSeq 2000 in duplicate. The combined raw reads were aligned to UCSC hg19 and genes were annotated by Tophat2. Genes were annotated and quantified by HTSeq-DESeq pipeline.

first: Gangadhara

middle: R

last: Sareddy

first: Yidong

last: Chen

first: Ratna

middle: K

last: Vadlamudi


title: TNFα-stimulated gene 6 (TSG-6) is a key molecule for stemness and a predictive marker for biological properties of mesenchymal stem cells

status: Public on Apr 21 2019

summary: The major aim is to decipher the functional biological activity of TSG6 by transcriptional profiling on mouse Mesenchymal stem cells in the presence and abesence of TSG6. Here, we investigate, by approaching with functional validations of the data set generated by RNA-sequencing data, how the lack of TSG-6 may impact MSCs in terms of their stemness and/or biological, immunomodulatory, tumorigenic properties. In light of this, we identify TSG-6 as a biomarker useful in predicting MSCs biology and efficacy.

overall_design: Profiling of the transcriptome of Wildtype and TSG6 knockout MSCs population in  mice. Two biological replicates were profiled for each cell type.

first: Paolo

last: Kunderfranco

first: Luca

last: Massimino

first: Sudharshan

last: Elangovan

first: Stefania

last: Vetrano


title: The Human Testis Cell Atlas via Single-cell RNA-seq

status: Public on Oct 15 2018

city: Salt Lake City

first: Jingtao

last: Guo

state: UT

address: 2000 Circle of Hope

department: Department of Surgery Division of Urology

institute: University of Utah School of Medicine

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

overall_design: Refer to individual Series


title: Optimized ChIP-seq procedure facilitates hormone receptor profiling in human tumors

status: Public on Dec 27 2018

city: Amsterdam

last: Singh

address: Plesmanlaan

country: Netherlands

institute: Netherlands Cancer Institute

summary: Performing ChIP-seq analyses in clinical specimens has remained largely challenging due to multiple technical limitations and low quantities of starting material, resulting in low enrichments and poor signal-to-noise ratio. Here, we refined the original protocols for transcription factor ChIP-seq analyses in breast, prostate, and endometrial tumor tissue. In addition to the standard fixative formaldehyde, a second crosslinker Disuccinimidyl glutarate (DSG) was included in the procedure.

overall_design: AR, FOXA1, ERα, H3K27ac & H3K4me3 ChIP-seq data with and without double croslinking in celllines (LNCAP & MCF-7) and in human tissues (Prostate, Breast, Endometrium and Prostate samples from core needle biopsies).

first: Wilbert

last: Zwart

first: Suzan

last: Stello

first: Karianne

last: Schuurman

first: Simon

last: Linder

first: Marjolein

last: Droog


title: Lifecycle progression and sexual development of the apicomplexan parasite Cryptosporidium parvum

status: Public on Sep 03 2019

city: Philadelphia

first: Boris

last: Striepen

state: PA

address: 380 S University Ave

department: Department of Pathobiology

institute: University of Pennsylvania

summary: The apicomplexan parasite Cryptosporidium is a leading global cause of severe diarrheal disease and an important contributor to early childhood mortality. Currently there are no fully effective treatments or vaccines available. Transmission of the disease occurs through ingestion of oocysts, through direct contact or contaminated water or food. Oocysts are meiotic spores and the product of parasite sex. Cryptosporidium has a single host lifecycle where both asexual and sexual processes unfold in the intestine of infected hosts. Here we use the new-found ability to genetically engineer Cryptosporidium to make life cycle progression and parasite sex tractable. We derive reporter strains to follow parasite development in culture and infected mice and define the genes that orchestrate sex and oocyst formation through mRNA sequencing of sorted cells. After two days, parasites in cell culture show pronounced sexualization, but productive fertilization does not occur and infection falters. In contrast in infected mice, male gametes successfully fertilize females, leading to meiotic division and sporulation. To rigorously test for fertilization, we devised a two-component genetic crossing assay employing a Cre recombinase activated reporter. Our findings suggest obligate developmental progression towards sex in Cryptosporidium, which has important implications for the treatment and prevention of the infection.

overall_design: 4 biological replicates each of 3 sorted life stages, or 3 biological replicates each of 3 infection time points

first: Jayesh

last: Tandel

first: Elizabeth

middle: D

last: English

first: Adam

last: Sateriale

first: Jodi

last: Gullicksrud

first: Daniel

last: Beiting


title: Effect of Oak extractives on the gene expression of Phanerochaete chrysosporium

status: Public on Oct 01 2018

city: Champenoux

first: Annegret

last: Kohler

address: Centre Grand Est Nancy

institute: INRAE

summary: Illumina HiSeq2500 technology was used to generate mRNA profiles from Phanerochaete chrysosporium treated with oak extractives for 1, 3 and 6h. 125bp pair-end reads were generated and aligned to the P.chrysosporium reference transcripts. (https://genome.jgi.doe.gov/Phchr2/Phchr2.home.html) using CLC Genomics Workbench 9.

overall_design: To analyse the effect of oak extractives, total RNA from P. chrysosporium treated for 1,3 or 6h were extracted and sequenced by Illumina HiSeq2500. Three biological replicates from each treatment were generated.

first: Nicolas

last: Valette

first: Melanie

last: Morel-Rouhier


title: The transcriptome of Oak roots associated with truffles

status: Public on Jul 01 2018

summary: Illumina HiSeq technology was used to generate mRNA profiles from mycorrhizal Quercus robur roots.   Tuber melanosporum, T. aestivum and T.magnatum mycorrhizal root tips were harvested and used for RNA extraction.   Paired-end reads of 100 bp were generated and aligned to Quercus robur CDS using CLC Genomics Workbench 9.

overall_design: mRNA profiles from Tuber-Oak mycorrhizas were generated  by Illumina HiSeq2000 sequencing (2x100bp). Three biological replicates were sequenced from Tuber melanosporum, T. aestivum and T.magnatum mycorrhizal root tips .

first: Laure

last: Fauchery

first: Claude

last: Murat

first: Francis

last: Martin


title: Gene expression changes in Cenococcum geophilum 1.58-Pinus sylvestris ectomycorrhizal roots, sclerotia and extramatrical mycelium compared to Cenococcum geophilum free-living mycelium

status: Public on Mar 01 2018

summary: Illumina HiSeq technology was used to generate mRNA profiles from Cenococcum geophilum ectomycorrhizal Pine roots, sclerotia and extramatrical mycelium compared to free-living mycelium . Ectomycorrhizal pine roots, sclerotia, extramatrical mycelium and control mycelium were harvested after 90 days and used for RNA extraction. Reads of 150bp were generated and aligned to the C. geophilum reference genome (https://genome.jgi.doe.gov/Cenge3/Cenge3.home.html).

sample_organism:
Pinus sylvestris
Cenococcum geophilum 1.58

overall_design: mRNA profiles from Cenococcum geophilum ectomycorrhizal roots, sclerotia, extramatrical mycelium and free-living mycelium were generated by 150bp Illumina HiSeq2000/2500 sequencing. Three biological replicates were sequenced for mycorrhizal, sclerotia and mycelium samples.

first: Maira

last: de Freitas Pereira

first: Vasanth

last: Singan

first: Martina

last: Peter

first: Igor

last: Grigoriev


title: Gene expression changes in Cenococcum geophilum 1.58-Populus tremulaxalba INRA 717-1B4 ectomycorrhizal roots compared to Cenococcum geophilum free-living mycelium

summary: Illumina HiSeq technology was used to generate mRNA profiles from Cenococcum geophilum ectomycorrhizal poplar roots compared to free-living mycelium . Ectomycorrhizal poplar roots and control mycelium were harvested after 60  days and used for RNA extraction. Reads of 150bp were generated and aligned to the C. geophilum reference genome (https://genome.jgi.doe.gov/Cenge3/Cenge3.home.html).

overall_design: mRNA profiles from Cenococcum geophilum ectomycorrhizal roots and free-living mycelium were generated by 150bp Illumina HiSeq2000/2500 sequencing. Three biological replicates were sequenced for mycorrhizal and mycelium samples.


title: RNA-seq differential expression analysis of Komagataella phaffii CBS2612 under mating conditions

status: Public on Apr 27 2018

city: Vienna

first: Nadine

middle: Elpida

last: Tatto

address: Muthgasse 18

department: Department of Biotechnology

country: Austria

institute: University of Natural Resources and Life Sciences

summary: We used RNA sequencing to analyse the differences in gene expression between the homothallic K. phaffii CBS2612 wild type and heterothallic a- and α-type strains during growth in rich medium and under mating conditions. This data was used to investigate mating-type specific gene expression and allowed the identification of the K. phaffii a-factor genes.

overall_design: Examination of expression levels in two different media with wild type and heterothallic a- and α-type cells.

first: Lina

last: Heistinger

first: Josef

last: Moser

first: Minoska

last: Valli

first: Brigitte

last: Gasser

first: Diethard

last: Mattanovich


title: Enhancer analysis of rat cardiac myocytes and fibroblasts reveals a collaborative control by transcription factor families [RNA-Seq]

status: Public on Feb 06 2018

city: Haifa

first: Izhak

last: Kehat

address: Efron St.

country: Israel

institute: Technion - Israel's Institute of Technology

summary: We used a differential open chromatin approach, coupled with active enhancer mark ,transcriptomic and computational TFs binding analysis to map cell-type-specific active enhancers in cardiac fibroblasts and cardiomyocytes, and outline the TFs that control them.  We identified Tead, Sox9, Smad, Tcf, Meis, Rbpj, and Runx1 as the main cardiac fibroblasts TF groups. Our analysis shows that in cardiomyocytes and cardiac fibroblasts, distal enhancers, containing concentrated combinatorial clusters of multiple tissue expressed TFs recognition motifs, are combinatorically clustered around tissue specific genes.

overall_design: We examine 4 different biological samples ('cardioPE', 'cardioSFM', 'cardiaFibro-SFM' and 'cardiacFibro-PE' (cardiomyocytes and cardiac fibroblasts in different conditions)), in duplicates/triplicates, to compare gene expression by using RNA-seq.

first: Tal

last: Golan-Lagziel

first: Yair

last: Lewis

first: Guy

last: Douvdevany

first: Lilac


title: Enhancer analysis of rat cardiac myocytes and fibroblasts reveals a collaborative control by transcription factor families


title: Enhancer analysis of rat cardiac myocytes and fibroblasts reveals a collaborative control by transcription factor families [ChIP-Seq]

overall_design: We examined 3 different biological samples ('cardioPE', 'cardioSFM' (cardiomyocytes in different conditions) and 'cardiacFibro'), in duplicates, to identify histone modification by using ChIP-seq assay.


title: Optimal-transport analysis of single-cell gene expression identifies developmental trajectories in reprogramming II

first: Marcin

last: Tabaka

summary: We collected duplicate samples at the various time points, generated single cell suspensions and performed scRNA-Seq. We also collected samples from established iPSC lines reprogrammed from the same MEFs, maintained in either 2i or serum conditions. Overall, we profiled ~250,000 cells.

overall_design: We collected scRNA-seq profiles of 250,00 cells across a 18-day time course of iPSC induction, under two conditions: 2i and serum

first: Jian

last: Shu


title: UHRF1-mediated epigenetic regulation of smooth muscle cell modulates development of vascular pathologies

city: Pieve Emanuele (MI)

first: Bioinformatics

last: Unit

address: Via Rita Levi Montalcini 4

institute: IRCCS Humanitas Research Hospital

summary: Adult vascular smooth muscle cells (VSMCs) dedifferentiate in response to extracellular cues such as vascular damage and inflammation. Dedifferentiated VSMCs are proliferative, migratory, less contractile, and can contribute to vascular repair as well as to cardiovascular pathologies such as intimal hyperplasia/restenosis in coronary artery and arterial aneurysm. We here demonstrate the role of ubiquitin-like containing PHD and RING finger domains 1 (UHRF1) as an epigenetic master regulator of VSMC plasticity. UHRF1 expression correlated with the development of vascular pathologies associated with modulation of noncoding RNAs, such as microRNAs. miR-145 — pivotal in regulating VSMC plasticity, which is reduced in vascular diseases — was found to control Uhrf1 mRNA translation. In turn, UHRF1 triggered VSMC proliferation, directly repressing promoters of cell-cycle inhibitor genes (including p21 and p27) and key prodifferentiation genes via the methylation of DNA and histones. Local vascular viral delivery of Uhrf1 shRNAs or Uhrf1 VSMC-specific deletion prevented intimal hyperplasia in mouse carotid artery and decreased vessel damage in a mouse model of aortic aneurysm. Our study demonstrates the fundamental role of Uhrf1 in regulating VSMC phenotype by promoting proliferation and dedifferentiation. UHRF1 targeting may hold therapeutic potential in vascular pathologies.

overall_design: 4 samples analyzed in duplicate, 2 scramble shRNA and 2 Uhrf1 shRNA

first: Paolo

last: Kunderfranco

first: Manuela

last: Quintavalle

first: Leonardo

last: Elia

first: Gianluigi

last: Condorelli


title: RNAseq in Pax7-reprogrammed corticotropes AtT-20 cells

status: Public on Jan 24 2018

city: LAUSANNE

first: ALEXANDRE

last: MAYRAN

state: Waadt

address: Station 19

country: Switzerland

institute: EPFL

summary:
Deployment of a cell-specifying enhancer repertoire by the pioneer factor Pax7
The establishment and maintenance of cell identity depends on implementation of stable cell-specific chromatin landscapes. Pioneer transcription factors establish new cell fate competences by triggering chromatin remodeling during development. Here, we used pituitary cell specification to define the salient features of pioneer action. Comparison of purified pituitary cells of different lineages showed that chromatin accessibility differs at enhancers rather than promoters. The pioneer factor Pax7 specifies one pituitary lineage identity by opening a specific repertoire of enhancers that are distinct from the myogenic targets of Pax7. Pax7 binds its pioneer targets rapidly and days before chromatin remodeling and gene activation. Finally, enhancers opened by Pax7-dependent chromatin remodeling exhibit loss of DNA methylation and they acquire long term epigenetic memory. The present work identifies enhancer pioneering as a critical feature for cell fate specification and maintenance.

overall_design: RNA extraction followed by high throughput sequencing (RNA-seq)

first: Alexandre

last: Mayran

first: Jacques

last: Drouin


title: Pioneer factor Pax7 deploys a stable enhancer repertoire for specification of cell fate


title: ChIPseq in Pax7-reprogrammed corticotropes AtT-20 cells

overall_design: ChIP assay followed by high throughput sequencing (ChIP-seq)

first: Yves

last: Gauthier


title: ATACseq in Pax7-reprogrammed corticotropes AtT-20 cells

overall_design: Transposase assay followed by high throughput sequencing (ATACseq)

first: Fadi

last: Hariri


title: The transcriptome landscape of Tuber magnatum

first: Annegret

last: Kohler

summary: Illumina HiSeq technology was used to generate mRNA profiles from Tuber magnatum truffles, free-living mycelium and oak mycorrhizal root tips.    Paired-end reads of 100 bp were generated and aligned to Tuber magnatum reference transcripts using CLC Genomics Workbench 9.

sample_organism:
Quercus robur
Tuber magnatum

platform_organism:
Quercus robur
Tuber magnatum

overall_design: mRNA profiles from truffles, free-living mycelium and oak mycorrhizal root tips of T. magnatum were generated  by Illumina HiSeq2000 sequencing (2x100bp).   Three biological replicates from each tissue were sequenced.

first: Laure

last: Fauchery

first: Claude

last: Murat

first: Francesco

last: Paolocci

first: Francis

last: Martin


title: The Human Testis Cell Atlas via Single-cell RNA-seq (Healthy men scRNA-seq data set)

first: Jingtao

last: Guo

summary: Human adult spermatogenesis involves a balance of spermatogonial stem cell self renewal and differentiation, alongside complex germline-niche interactions. To better understand, we performed single cell RNA sequencing of ~7000 testis cells from three healthy men of peak reproductive age. Our analyses revealed multiple distinctive transcriptional ‘states’ of self-renewing and differentiating spermatogonia, the cellular stages of gametogenesis, five niche cells (Leydig, Myoid, Sertoli, Endothelial, macrophage) and insights into germline-niche communication. Spermatogenesis was reconstructed computationally, which identified sequential coding, noncoding, and repeat-element transcriptional signatures. A new, developmentally early and likely quiescent spermatogonial state is identified (GFRA1-/ETV5-/ID4+/UTF1+/FGFR3+). Notably, certain epigenetic features combined with nascent transcription analyses suggest considerable plasticity within certain spermatogonial populations/states. Key findings were validated via RNA and protein staining. Taken together, we provided the first “Cell Atlas” of the adult human testis, and provide multiple new insights into germ cell development and germ cell – niche interaction.

overall_design: We isolated single testicular cell from three healthy men of peak reproductive age. Two technical replicates were performed for each individual.

first: Bradley

last: Cairns


title: Gene expression in Tuber melanosporum fruiting bodies at different developmental stages

status: Public on Jan 15 2018

summary: This study characterizes the transcriptomic alterations of Tuber melanosporum during fruiting body development. Stage III, IV, V and VI were analyzed. For images and description of stages see Zarivi et al.2015 (https://doi.org/10.1016/j.phytochem.2015.02.024)

overall_design: We performed 4 hybridizations (NimbleGen) with samples derived from different stages of T.melanosporum fruiting body.   All samples were labeled with Cy3.

first: O

last: Zarivi

first: M

last: Miranda

first: G

last: Pacioni

first: A

first: F


title: Gene expression changes in Rhizoscyphus ericae UMAH 7357- Vaccinium myrtillus mycorrhizal roots compared to Rhizoscyphus ericae UMAH 7357 free-living mycelium

status: Public on Jan 01 2018

summary: Illumina HiSeq technology was used to generate mRNA profiles fromRhizoscyphus ericae UMAH 7357 mycorrhizal roots compared to free-living mycelium . Mycorrhizal roots and control mycelium were harvested after 75 days and used for RNA extraction. Reads of 150bp were generated and aligned to Rhizoscyphus ericae UMAH 7357 transcripts (https://genome.jgi.doe.gov/Rhier1/Rhier1.home.html) using CLC Genomics Workbench 8.

overall_design: mRNA profiles from Rhizoscyphus ericae UMAH 7357 mycorrhizal roots and free-living mycelium were generated by 150bp Illumina HiSeq2500 sequencing. Three biological replicates were sequenced for mycorrhizal and mycelium samples.

first: Elena

last: Martino

first: Stefania

last: Daghino

first: Silvia

last: Perotto

first: Vasanth

last: Singan

first: Igor

last: Grigoriev


title: Transcriptome analyses of the Laccaria bicolor-Populus trichocarpa mycorrhiza

status: Public on Apr 03 2017

first: Annegret

summary: Illumina HiSeq2000 technology was used to generate mRNA profiles from the ectomycorrhizal fungi Laccaria bicolor colonizing roots of Populus trichocarpa. Samples were taken after 3 months of contact in order to identify mycorrhiza-regulated transcripts. 100bp reads were generated and aligned to the Populus trichocarpa (http://www.phytozome.net/poplar.php) reference genome.

sample_organism:
Populus trichocarpa
Laccaria bicolor

platform_organism:
Populus trichocarpa
Laccaria bicolor

overall_design: mRNA profiles from Populus trichocarpa roots colonized by Laccaria bicolor for three months as well as from control roots were generated by using one lane of 1X100bp Illumina HiSeq2000 sequencing per sample.

first: Jonathan

last: Plett

first: Emilie

last: Tisserant


title: An autofluorescence-based method for the isolation of highly purified ventricular cardiomyocytes

status: Public on Dec 08 2017

first: Bioinformatics

last: Unit

summary: Profiling of the transcriptome of FITChigh/FSCdim and FITCdim/FSChigh sub-populations. Three biological replicates were profiled for each cell type.

first: Paolo

last: Kunderfranco

first: Veronica

last: Larcher

first: Gianluigi

last: Condorelli


title: The transcriptional landscape of basidiosporogenesis in mature Pisolithus microcarpus basidiocarp

status: Public on Mar 01 2017

last: Kohler

summary: Illumina HiSeq technology was used to generate mRNA profiles from Pisolithus microcarpus basidiocarp compartments.   Unconsolidated, young, and mature peridioles, as well as internal and free spores from three basidiocaps were harvested and used for RNA extraction.   Paired-end reads of 100 bp were generated and aligned to Pisolithus microcarpus (http://genome.jgi.doe.gov/Pismi1/Pismi1.home.html) reference transcripts using CLC Genomics Workbench 7.

overall_design: mRNA profiles from Pisolithus microcarpus basidiocarp compartments were generated  by Illumina HiSeq2000 sequencing (2x100bp). Three biological replicates were sequenced from unconsolidated, young, and mature peridioles, as well as internal and free spores.

first: Maira

last: de Freitas Pereira

first: Mauricio

last: Dutra Costa

first: Francis

last: Martin


title: Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and Nrl-/- Retinal Transcriptomes

status: Public on Jun 08 2017

city: 上海

first: Bo

last: Jing

state: 上海

address: 同济大学医学院713

institute: 同济大学医学院

summary:
Purpose: To identify the role of glycosylation of dentin matrix protein1 (DMP1), S89G-DMP1 point mutation mouse model was created with changing S89 to glycine(S89G). RNA sequencing were performed to compare the transcriptome differences between the neural stem cells or astrocytes separated form S89G-DMP1 and WT mice.
Methods: mRNA profiles of astrocytes and neural stem cell separated from S89G-DMP1 and WT were generated by RNA sequencing. The sequence reads that passed quality filters were analyzed at the transcript isoform level with TopHat2(for astrocytes) or with HISAT2o (for neural stem cells).
Results: Differential expression analyses with DESeq2 use raw read counts: 762 transcripts were downregulated and 991 transcripts were up-regulated in S89G-DMP1 astrocytes; 475 transcripts were downregulated and 343 transcripts were up-regulated in S89G-DMP1 neural stem cells. All the differential expressed genes were used for Heatmap analysis and KEGG or GO enrichment analyses.
Conclusions: Our study represents the detailed transcriptome changes of astrocytes and neural stem cells with deglycosylated DMP1.

overall_design: mRNA profiles of astrocytes and neural stem cells separated from adult (10-week-old) S89G-DMP1 or WT mice were generated by RNA sequencing using Illumina.

first: Jiping

last: Liu


title: The ectomycorrhizal basidiomycete Hebeloma cylindrosporum undergoes early waves of transcriptional reprogramming prior to symbiotic structures differentiation

status: Public on Feb 01 2017

summary: Illumina HiSeq2000 technology was used to generate mRNA profiles from Hebeloma cylindrosporum pre-infectious stages (2 and 4 days) compared to control mycelium. Pre-infectious and control mycelia were harvested after 2 and 4 days and used for RNA extraction. Reads of 150 bp were generated and aligned to Hebeloma cylindrosporum reference transcripts  (http://genome.jgi-psf.org/Hebcy2) using CLC Genomics Workbench 8.5.1.

overall_design: mRNA profiles from Hebeloma cylindrosporum pre-infectious and control mycelium were generated by Illumina HiSeq2000 sequencing (150bp). Three biological replicates were sequenced for Hebeloma cylindrosporum mycelium in contact for 2 and 4 days with Pinus pinaster seedlings as well as for control mycelium at the same time-points.

first: Gilles

last: Gay

first: Jeanne

last: Doré


title: Gene expression changes in Tulasnella calospora - Serapias vomeracea mycorrhizal protocorms at stage P2 compared to asymbiotic, achlorophyllous Serapias vomeracea protocorms

status: Public on Dec 01 2016

summary: Illumina HiSeq technology was used to generate mRNA profiles from  Serapias vomeracea-Tulasnella calospora mycorrhizal protocorms compared to asymbiotic protocorms . Protocorms were harvested at stage P2 and used for RNA extraction. Reads of 150bp were generated and aligned to a de novo transcriptome assembly from Serapias vomeracea using CLC Genomics Workbench 9.

sample_organism:
Serapias vomeracea
Tulasnella calospora

platform_organism:
Serapias vomeracea
Tulasnella calospora

overall_design:
mRNA profiles from Serapias vomeracea-Tulasnella calospora mycorrhizal protocorm and asymbiotic, achlorophyllous  Serapias vomeracea protocorms were generated by 150bp Illumina HiSeq2500  sequencing. Three biological replicates were sequenced for mycorrhizal and asymbiotic samples. Asymbiotic samples (containing only plant-derived reads) were used to generate a reference de novo assembly (Trinity software) and reads from all samples were then aligned to this reference.
Please note that the raw data for Mycorrhizal protocorm_plantP2* samples are same as GSM2311257-GSM2311259 raw data, but re-analyzed on the plant side in the current study as they are dual transcriptome from symbiotic tissue containing both fungal and plant reads.

first: Valeria

last: Fochi

first: Silvia

last: Perotto


title: Enhancer analysis of rat cardiac myocytes and fibroblasts reveals a collaborative control by transcription factor families [ATAC-Seq]

first: Izhak

last: Kehat

overall_design: We examined 4 different biological samples ('cardioPE', 'cardioSFM', 'cardioGata4' (cardiomyocytes in 3 different conditions) and 'cardiacFibro'), in duplicates, to identify the 'open' chromatin regions of each by using ATAC-seq assay.

first: Tal

last: Golan-Lagziel

first: Yair

last: Lewis

first: Guy

last: Douvdevany

first: Lilac


title: Gene expression changes in Tulasnella calospora- Serapias vomeracea mycorrhizal protocorms at stage P2 compared to Tulasnella calospora free-living mycelium

first: Annegret

summary: Illumina HiSeq technology was used to generate mRNA profiles from Tulasnella calospora mycorrhizal protocorms at stage P2 compared to free-living mycelium  grown on Modified Melin-Norkrans medium with two different N sources, ammonium (AL13M) and glutamine (AL1 G) . Protocorms were harvested at stage P2 and mycelium after 15 days and used for RNA extraction. Reads of 150bp were generated and aligned to Tulasnella calospora  transcripts (http://genome.jgi-psf.org/Tulca1) using CLC Genomics Workbench 9.

overall_design: mRNA profiles from Tulasnella calospora mycorrhizal protocorms stage P2 and free-living mycelium grown on Modified Melin-Norkrans medium with two different N sources, ammonium (AL13M) and glutamine (AL13 G) were generated by 150bp Illumina HiSeq2500  sequencing. Three biological replicates were sequenced for mycorrhizal and mycelium samples.

first: Vasanth

last: Singan

first: Igor

last: Grigoriev


title: Whole Genome Bisulfite Sequencing in Pax7-reprogrammed corticotropes AtT-20 cells

first: ALEXANDRE

last: MAYRAN

overall_design: Bisulfite conversion of genomic DNA followed by high throughput sequencing (WGBS)

first: Alexandre

last: Mayran

first: Jacques

last: Drouin


title: Gene expression changes in Cenococcum geophilum-Pinus sylvestris  ectomycorrhizal roots compared to Cenococcum geophilum free-living mycelium

status: Public on Aug 01 2016

last: Kohler

summary: Illumina HiSeq technology was used to generate mRNA profiles from Cenococcum geophilum ectomycorrhizal roots compared to free-living mycelium . Mycorrhizal roots were harvested after 3 months, pooled and used for RNA extraction. Reads of 2X100bp were generated and aligned to Cenococcum geophilum (http://genome.jgi.doe.gov/Cenge3/Cenge3.home.html) reference transcripts using CLC Genomics Workbench 6.

overall_design: mRNA profiles from Cenococcum geophilum ectomycorrhizal roots and free-living mycelium were generated by paired-end (2x100bp) Illumina HiSeq2000 sequencing. Three biological replicates were sequenced for mycorrhizal and mycelium samples.

first: M

last: Peter

first: A

first: F


title: Mapping interactions for the TNIP2 hub protein

status: Public on Oct 24 2016

city: Kansas City

first: Gaye

middle: L

last: Hattem

state: Missouri

address: 1000 E. 50th Street

department: Proteomics

institute: Stowers Institute

summary: This experiment analyzes the set of RNAs copurifying with the protein TNIP2 (amino acids 196-346)

overall_design: HEK293 cells were transfected with constructs expressing either Halo tag (controls) or Halo-TNIP2 196-346. Total RNA was purified from an aliquot of the whole cell extract (Input samples). Halo-tagged proteins were purified from the remainder of the whole cell extract, and RNA subsequently purified from the Halo purified samples (Pulldown samples).

first: Charles

last: Banks

first: Gina

last: Boanca

first: Mike

middle: P

last: Washburn


title: Scots pine (Pinus sylvestris) differentially interacts with Cenococcum geophilum and other simultaneously inoculated mycorrhizal (ECM) fungi

summary: To identify specific gene networks induced in host roots by C. geophilum, we inoculated seedlings of Scots pine simultaneously with C. geophilum and either Suillus granulatus or Rhizopogon roseolus, two common ECM fungi associated to pines. We then measured the differential expression of Scots pine genes in the respective mycorrhizas using oligoarrays.

platform_organism:
Pinus sylvestris
Cenococcum geophilum

overall_design: We performed 14 hybridizations (NimbleGen) with samples derived from Pinus sylvestris mycorrhiza with Cenococcum geophilum, Rhizopogon roseolus or Suillus granulatus (3 biological replicates each), as well as from non-mycorrhizal control roots (two replicates). Only the Pinus-derived sequences from the array were considered for this analysis. All samples were labeled with Cy3.

first: E

last: Tisserant

last: Martin


title: RNAseq in primary pituitary cells

overall_design: RNA extraction followed by high throughput sequencing (RNA-seq)

first: Konstantin

last: Khetchoumian


title: Genome-wide map of DNA 5-Hydroxymethylcytosine in cardiomyocytes isolated from E14.5, Neonatal, Adult, pressure-overload (TAC), sh-control and sh-TET2 isolated cardiomyocytes

status: Public on Jun 21 2016

first: Bioinformatics

last: Unit

summary:
Methylation at 5-cytosine (5-mC) is a fundamental epigenetic DNA modification associated recently with cardiac disease. In contrast, the role of 5-hydroxymethylcytosine (5-hmC) – 5-mC’s oxidation product – is unknown in the context of the heart. Here, we assess the hydroxymethylome in embryonic, neonatal, adult and hypertrophic mouse cardiomyocytes, showing that dynamic modulation of hydroxymethylated DNA is associated with specific transcriptional networks during heart development and failure. DNA hydroxymethylation marks gene bodies of highly expressed genes and distal regulatory regions with enhanced activity. Pathological hypertrophy is characterized by a partial shift towards a fetal-like distribution pattern.
We further demonstrate a regulatory function of TET2 and provide evidence that the expression of key cardiac genes, such as Myh7 is modulated by TET2-mediated 5-hmC deposition on the gene body and at enhancers in cardiac cells.
We thus provide the first genome-wide analysis of 5-hmC in the cardiomyocyte, and establish the role of this epigenetic modification in heart development and disease

overall_design: Profiling of 5hmC in E14.5, Neonatal, Adult, pressure-overload (TAC), sh-control and sh-TET2 isolated cardiomyocytes

first: Paolo

last: Kunderfranco

first: Carolina

last: Greco

first: Gianluigi

last: Condorelli


title: A Stringent Systems Approach Uncovers Gene-Specific Mechanisms Regulating Inflammation [ATAC-seq]

status: Public on Jan 18 2016

city: Los Angeles

first: Stephen

last: Smale

state: Ca

address: 6-730 MRL 675 Charles E. Young Drive South

department: MIMG

institute: University of California Los Angeles

summary: Much has been learned about transcriptional cascades and networks from large-scale systems analyses of high-throughput data sets. However, analysis methods that optimize statistical power through simultaneous evaluation of thousands of ChIP-seq peaks or differentially expressed genes possess substantial limitations in their ability to uncover mechanistic principles of transcriptional control. By examining nascent transcript RNA-seq, ChIP-seq, and binding motif data sets from lipid A-stimulated macrophages with increased attention to the quantitative distribution of signals, we identified unexpected relationships between the in vivo binding properties of inducible transcription factors, motif strength, and transcription. Furthermore, rather than emphasizing common features of large clusters of co-regulated genes, our results highlight the extent to which unique mechanisms regulate individual genes with key biological functions. Our findings demonstrate the mechanistic value of stringent interrogation of well-defined sets of genes as a complement to broader systems analyses of transcriptional cascades and networks.

overall_design: Bone marrow-derived macrophages were stimulated with lipid A for 0 or 120 minutes. Chromatin was treated with Tn5 transposase to measure DNA accessibility

first: Ann-Jay

last: Tong

first: Brandon

middle: J

last: Thomas


title: Compared gene expression profile of gastric and intestinal progenitors grown as spheroids in the ex vivo culture system

status: Public on May 11 2016

city: Brussels

first: Frederick

last: Libert

address: 808 route de Lennik

department: IRIBHM

country: Belgium

institute: ULB

summary: In adult stomach, Lgr5 is a marker of epithelial glandular stem cells that grow in the three dimensional ex vivo culture system as organoids. However, little is known about the markers that characterize fetal progenitors before cytodifferentiation and their potential involvement in regenerative processes in adults. Using the ex vivo culture system, we isolated epithelial progenitors from the fetal stomach. These cells generated stable undifferentiated immortal spheroids showing lower growth factor requirements as compared to the adult-type gastric Lgr5-expressing organoids. Although very similar in their gene expression profiles, cultured fetal gastric and intestinal spheroids differentially expressed Sox2/Cdx2 genes involved in regional pre-patterning. Accordingly, gastric but not intestinal spheroids, spontaneously converted into the cell lineages of the adult glandular stomach ex vivo. In vivo, the Trop2 marker enriched in the fetal gastric spheroids was transiently expressed in the gastric epithelium before cytodifferentiation while it remained barely detectable under glandular homeostasis in adults. However, upon specific ablation of the Lgr5 stem cell pool, highly proliferative Trop2-expressing cells rapidly emerged in the adult epithelium, qualifying Trop2 as a marker of Lgr5-independent gastric stem cells. Together, these data indicate that the Trop2 receptor identifies gastric fetal progenitors and adult stem/progenitor cells involved in regeneration of glandular stomach.

overall_design:
1. Mouse E15.5 stomach and small intestine epithelial progenitors were isolated from same pool of embryos and cultured ex vivo, growing as undifferentiated immortal spheroids. At  passage 2 day 6 or passage 3 day 2 or day3 , spheroid-generating cells were harvested;

2. Mouse small intestine organoids were derived from E15.5 embryos and adult (3 month-old) mice cultures. Cells were isolated at passage 4 day5 (embryos) and passage 1 day5 (adult);

3. Trop2-expressing cells from mouse E14.5 proximal or distal stomach and intestine were isolated by flow cytometry;

4. Trop2-expressing or Lgr5-expressing cells from adult (2 month-old) Lgr5-DTR heterozygous mice pre-treated with or without diphtheria toxin were  isolated by flow cytometry; and the the mRNA profiles of these cells were determined

first: Valeria

last: Fernandez-Vallone

first: Morgane

last: Leprovots

first: Sandra

last: Strollo

first: Gabriela

last: Vasile

first: Anne

last: Lefort

first: Frédérick

first: Gilbert

last: Vassart

first: Marie

last: Isabelle Garcia


title: ATACseq in primary pituitary cells

first: ALEXANDRE

last: MAYRAN

summary:
Deployment of a cell-specifying enhancer repertoire by the pioneer factor Pax7
The establishment and maintenance of cell identity depends on implementation of stable cell-specific chromatin landscapes. Pioneer transcription factors establish new cell fate competences by triggering chromatin remodeling during development. Here, we used pituitary cell specification to define the salient features of pioneer action. Comparison of purified pituitary cells of different lineages showed that chromatin accessibility differs at enhancers rather than promoters. The pioneer factor Pax7 specifies one pituitary lineage identity by opening a specific repertoire of enhancers that are distinct from the myogenic targets of Pax7. Pax7 binds its pioneer targets rapidly and days before chromatin remodeling and gene activation. Finally, enhancers opened by Pax7-dependent chromatin remodeling exhibit loss of DNA methylation and they acquire long term epigenetic memory. The present work identifies enhancer pioneering as a critical feature for cell fate specification and maintenance.

overall_design: Transposase assay followed by high throughput sequencing (ATACseq)

first: Alexandre

last: Mayran

first: Fadi

last: Hariri

first: Jacques

last: Drouin


title: Gene expression profiling during cardiac maturation, hypertrophy and after KD of TET2

first: Bioinformatics

last: Unit

overall_design: Profiling of the transcriptome of embryonic, neonatal, adult, 1 week hypertrophic cardiomyocytes, sh-control and sh-TET2 cardiomyocytes. Two biological replicates were profiled for each cell type.

first: Paolo

last: Kunderfranco

first: Carolina

last: Greco

first: Gianluigi


title: Circulating microRNA screening of high-risk individuals enrolled in COSMOS lung cancer screening trial.

status: Public on Feb 29 2016

city: San Giovanni Rotondo (FG)

first: Fabrizio

last: Bianchi

state: Outside U.S. & Canada

address: Viale Padre Pio 7

institute: Fondazione IRCCS Casa Sollievo della Sofferenza

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

summary: Lung cancer is the leading cause of cancer death worldwide. Low-dose computed tomography screening (LDCT) was recently shown to anticipate the time of diagnosis, thus reducing lung cancer mortality. We identifed a serum microRNA signature (the miR-Test) that could identify the optimal target population for LDCT screening. Here, we performed a large-scale validation study of the miR-Test in high-risk individuals enrolled in the Continuous Observation of Smoking Subjects (COSMOS) lung cancer screening program.

overall_design: RT-qPCR of circulating microRNA purified from serum samples. Trizol-LS and miRNEASY Mini kit (Qiagen) were used for miRNA purification. Custom TaqMan® Low Density Array microRNA Custom Panel (Life Technologies) was used to screen serum circulating microRNA.

first: Pier

last: Di Fiore

first: Matteo

last: Marzi

first: Francesca

last: Montani

first: Francesco

last: Nicassio


title: A Stringent Systems Approach Uncovers Gene-Specific Mechanisms Regulating Inflammation

first: Stephen

last: Smale

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

overall_design: Refer to individual Series


title: Heterobasidion annosum gene expression during saprotrophic growth  on topsoil (organic layer) from mineral soil, drained and undrained peatland forests.

status: Public on Oct 01 2015

first: Annegret

last: Kohler

summary: Transcript profiles of H. annosum from different tissues and mycelium grown on different substrates and under different stresses were analyzed. The array probes were designed from gene models taken from the Joint Genome Institute (JGI, department of energy) H. irregulare genome sequence version 1.  One aim of this study was to compare gene expression profiles  of H. annosum  during saprotrophic growth  on topsoil from mineral soil, drained and undrained peatland.

overall_design: The Heterobasidion irregulare custom-exon expression array (4 x 72K) manufactured by Roche NimbleGen Systems Limited (Madison, WI) (http://www.nimblegen.com/products/exp/index.html) contained five independent, non-identical, 60-mer probes per gene model coding sequence. For 12,199 of the 12,299 annotated protein-coding gene models probes could be designed. For 19 gene models no probes could be generated and 81 gene models shared all five probes with other gene models. Included in the array were 916 random 60-mer control probes and labelling controls. For 2032 randomly chosen gene models, technical duplicates were included on the array. We performed 12 hybridizations (NimbleGen) with samples derived from H. annosum grown in either liquid Malt Extract Medium (three biological replicates), on Pine-dominated mineral forest topsoil (three biological replicates), on Pine-dominated pristine peatland forest topsoil (three biological replicates) or  on Pine-dominated drained peatland forest topsoil (three biological replicates).

first: H

last: Sun

first: T

last: Raffaello

last: Chen

first: A

first: F

last: Martin

middle: O

last: Asiegbu


title: A Stringent Systems Approach Uncovers Gene-Specific Mechanisms Regulating Inflammation [ChIP-seq]

summary: Much has been learned about transcriptional cascades and networks from large-scale systems analyses of high-throughput data sets. However, analysis methods that optimize statistical power through simultaneous evaluation of thousands of ChIP-seq peaks or differentially expressed genes possess substantial limitations in their ability to uncover mechanistic principles of transcriptional control. By examining nascent transcript RNA-seq, ChIP-seq, and binding motif data sets from lipid A-stimulated macrophages with increased attention to the quantitative distribution of signals, we identified unexpected relationships between the in vivo binding properties of inducible transcription factors, motif strength, and transcription. Furthermore, rather than emphasizing common features of large clusters of co-regulated genes, our results highlight the extent to which unique mechanisms regulate individual genes with key biological functions. Our findings demonstrate the mechanistic value of stringent interrogation of well- defined sets of genes as a complement to broader systems analyses of transcriptional cascades and networks.

overall_design: Bone marrow-derived macrophages were stimulated with lipid A for 0, 15, 30, 60, and 120 minutes. Chromatin was immunoprecipitated with antibodies against RelA, SRF, or IRF3.

first: Ann-Jay

last: Tong


title: Analysis of wound-induced transcripts in poplar leaf disks versus whole leaves

summary: Expression of defense response-related transcripts could be affected upon leaf wounding such as after excision of leaf disks. In this experiment, transcripts were isolated from whole leaves and 5-cm2 excised leaf disks samples from interaction assays between leaves of the 'Beaupré' poplar cultivar (Poplus trichocarpa x Poplus deltoides) and virulent (98AG31, compatible interaction) and avirulent (93ID6, incompatible interaction) urediniospores of Melampsora larici-populina, the fungus responsible for the foliar rust disease in poplar. For each type of interaction, three samples were collected in a time-course series (18, 21 and 24 hpi for strain 93ID6, and 18, 24 and 48 hpi for strain 98AG31). Both leaf disks and whole leaves were inoculated in strictly similar conditions, so differential transcript expression is likely attributable to the wounding effect in leaf disks. The aim of this study is to identify genes that are induced by wounding in leaf disks compared with whole leaves. For this purpose, cDNA templates were used for hybridization on poplar oligoarrays.

overall_design: We performed 12 hybridizations (NimbleGen oligoarrays) with samples derived from incompatible (18, 21 and 24hpi) and compatible (18, 24 and 48hpi) interactions of Melampsora larici-populina with P. trichocarpa x P. deltoides poplar cultivar 'Beaupré' leaf disks (6 conditions) and whole leaves (6 conditions). All samples were labeled with Cy3.

first: Benjamin

last: Petre

first: Sébastien

last: Duplessis

first: Francis

first: Nicolas

last: Rouhier


title: Gene expression changes in Meliniomyces bicolor- Vaccinium myrtillus mycorrhizal roots compared to Meliniomyces bicolor free-living mycelium

summary: Illumina HiSeq technology was used to generate mRNA profiles from Meliniomyces bicolor mycorrhizal roots compared to free-living mycelium . Mycorrhizal roots and control mycelium were harvested after 113 days and used for RNA extraction. Reads of 150bp were generated and aligned to Meliniomyces bicolor transcripts (https://genome.jgi.doe.gov/Melbi2/Melbi2.home.html) using CLC Genomics Workbench 8.

overall_design: mRNA profiles from Meliniomyces bicolor mycorrhizal roots and free-living mycelium were generated by 150bp Illumina HiSeq2500 sequencing. Three biological replicates were sequenced for mycorrhizal and mycelium samples.

first: Elena

last: Martino

first: Stefania

last: Daghino

first: Silvia

last: Perotto

first: Vasanth

last: Singan

first: Igor

last: Grigoriev


title: A Stringent Systems Approach Uncovers Gene-Specific Mechanisms Regulating Inflammation [RNA-Seq]

overall_design: Bone marrow-derived macrophages derived from C57Bl/6, Myd88-/-, Trif-/-, Irf3-/-, Ifnar-/-, and RelA-/- mice were stimulated with lipid A; C57Bl/6 macrophages were stimulated with lipid A in the presence of MAPK inhibitors or cycloheximide, or stimulated with PAM3CSK4 for 0, 15, 30, 60, and 120 minutes, or stimulated with lipid A for 0, 5, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, and 60 minutes. Two biological replicates were generated for each time point for each treatment type.


title: Cumulative Impact of Polychlorinated Biphenyl and Large Chromosomal Duplications on DNA Methylation, Chromatin, and Expression of Autism Candidate Genes.

status: Public on Dec 13 2016

city: Davis

first: Keith

last: Dunaway

address: 3318 Tupper Hall

department: MMI

institute: UC Davis

summary: Rare variants enriched for functions in chromatin regulation and neuronal synapses have been linked to autism. How chromatin and DNA methylation interact with environmental exposures at synaptic genes in autism etiologies is currently unclear. Using whole-genome bisulfite sequencing in brain tissue and a neuronal cell culture model carrying a 15q11.2-q13.3 maternal duplication, we find that significant global DNA hypomethylation is enriched over autism candidate genes and affects gene expression. The cumulative effect of multiple chromosomal duplications and exposure to the pervasive persistent organic pollutant PCB 95 altered methylation of more than 1,000 genes. Hypomethylated genes were enriched for H2A.Z, increased maternal UBE3A in Dup15q corresponded to reduced levels of RING1B, and bivalently modified H2A.Z was altered by PCB 95 and duplication. These results demonstrate the compounding effects of genetic and environmental insults on the neuronal methylome that converge upon dysregulation of chromatin and synaptic genes.

overall_design:
Examination of DNA Cytosine methylation in human brain and cell culture;
Brain_Control: 11 different post-mortem human brains with no diagnosed neurological disorders
Brain_Dup15: 9 different post-mortem human brains diagnosed with Dup15q Syndrome
Brain_PWS: 5 different post-mortem human brains diagnosed with Prader-Willi Syndrome
Brain_Angelman: 3 different post-mortem human brains diagnosed with Angelman Syndrome
Brain_Downs: 4 different post-mortem human brains diagnosed with Downs Syndrome
Brain_IdioAut: 6 different post-mortem human brains diagnosed with Idiopathic Autism
BraindfBA_Control: 2 different post-mortem human Control brains that are the same biological sample as those found in Brain_Control but a different Brodmann Area
BraindfBA_Dup15: A post-mortem human Dup15q brain that are the same biological sample as that found in Brain_Dup15 but a different Brodmann Area
Culture_SH: SH-SY5Y human neuroblastoma cell line treated with DMSO for 10 days.
Culture_SHPCB: SH-SY5Y human neuroblastoma cell line treated with PCB 95 in DMSO for 10 days.
Culture_SH15M: SH-SY5Y human neuroblastoma cell line with a duplication of part of chromosome 15 treated with DMSO for 10 days.
Culture_SH15MPCB: SH-SY5Y human neuroblastoma cell line with a duplication of part of chromosome 15 treated with PCB 95 in DMSO for 10 days.
Culture_SHclone: SH-SY5Y human neuroblastoma cell line treated with DMSO for 40 days. Then, single cell cloned and grown for 21 generations.
Culture_SHPCBclone: SH-SY5Y human neuroblastoma cell line treated with PCB 95 in DMSO for 40 days. Then, single cell cloned and grown for 21 generations.
Culture_SH15Mdup22: SH-SY5Y human neuroblastoma cell line with a duplication of part of chromosome 15 treated with DMSO for 40 days. Then, single cell cloned and grown for 21 generations.
Culture_SH15Mdup22PCB: SH-SY5Y human neuroblastoma cell line with a duplication of part of chromosome 15 treated with PCB 95 in DMSO for 40 days. Then, single cell cloned and grown for 21 generations.

first: Janine

last: LaSalle


title: Epigenetic inflexibility of exhausted T cells limits durability of reinvigoration by PD-1 blockade

status: Public on Oct 31 2016

first: E

middle: JOHN

last: WHERRY

address: 421 Curie Blvd,354 BRB II/III

department: Systems Pharmacology       and Translational Therapeutics,Institute for Immunology

summary: Upon PD-1 pathway blockade,the epigenetic landscape of exhausted cells was only minimally remodeled consistent with lineage commitment and re-exhaustion of these cells over time.

overall_design: Epigenetic profiling of Exhausted T cells & examinaton of epigenetic changes associated with PD-pathway blockade by  ATAC-seq using the mouse model of chronic infection with lymphocytic choriomeningitis virus (LCMV)

first: Kristen

last: Pauken

first: Omar

last: Khan

first: Morgan

last: Sammons

first: Sasi

last: Manne

last: Wherry


title: Poplar-Laccaria Mycorrhizal Roots

status: Public on Jun 22 2015

first: Annegret

last: Kohler

summary: This study characterizes the transcriptomic alterations of P. tremula x P. alba at three weeks after inoculation with the ectomycorrhizal fungus Laccaria bicolor.

overall_design: We performed 6 hybridizations (NimbleGen) with samples derived from Populus tremula x P. alba control roots and mycorrhizal root tips. Samples were taken after 3 weeks of interaction (three biological replicates).  All samples were labeled with Cy3.

first: A

last: Vayssières

first: F

last: Martin

first: V

last: Legué


title: Gene expression changes in greenhouse Hebeloma cylindrosporum-Pinus pinaster ectomycorrhizal root tips compared to Hebeloma cylindrosporum free-living mycelium

status: Public on Jul 01 2015

summary: Illumina HiSeq technology was used to generate mRNA profiles from Hebeloma cylindrosporum ectomycorrhizal root tips compared to free-living mycelium . Ectomycorrhizal root tips  were harvested after 6 months and used for RNA extraction. Reads of 100 bp were generated and aligned to Hebeloma cylindrosporum transcripts (http://genome.jgi-psf.org/Hebcy2) using CLC Genomics Workbench 6.

overall_design: mRNA profiles from Hebeloma cylindrosporum ectomycorrhizal root tips and  free-living mycelium were generated by Illumina HiSeq2000 sequencing (100bp). Ttwo biological replicates were sequenced for mycorrhizal and mycelium samples.

first: Gilles

last: Gay

first: Jeanne

last: Doré

first: Francis


title: Changes in gene expression in the bark of MIR15

status: Public on May 07 2015

summary: Illumina HiSeq technology was used to generate mRNA profiles of bark from MIR15 compared to wildtype plants. Wild type (WT) and transgenic poplars (Populus tremula x P. alba, clone INRA 717-1B4) were grown aseptically on Woody Plant Medium. Total RNA was extracted using Tri-Reagent according to the manufacturer’s instructions. Reads of 2X100bp were generated and aligned to Populus trichocarpa v3.0 reference transcripts (http://phytozome.jgi.doe.gov/pz/portal.html#!info?alias=Org_Ptrichocarpa; Ptrichocarpa_210_transcript_primaryTranscriptOnly) using CLC Genomics Workbench 7.

overall_design: mRNA profiles of bark from MIR15 compared to wildtype plants were generated by paired-end (2x100bp) Illumina HiSeq2000 sequencing. Two biological replicates were sequenced for MIR15 and WT samples.

first: Fabien

last: Baldacci-Cresp

first: Jean-Charles

last: Leplé

first: Marie

last: Baucher


title: Sepula lacrymans interacting with tree roots

status: Public on Feb 06 2015

summary: This study characterizes the transcriptomic alterations of Serpula lacrymans in contact with tree roots compared to the transcriptome of free-living mycelium.

overall_design: We performed 6 hybridizations (NimbleGen) with samples derived from Picea sylvestris root tips inoculated with Serpula lacrymans (three biological replicates).  These samples were compared to free-living mycelium from Serpula lacrymans (three biological replicates). All samples were labeled with Cy3.

first: N

last: Högberg


title: Batf3 maintains Irf8 autoactivation for commitment of a novel clonogenic progenitor of CD8+DCs

status: Public on Jun 08 2015

first: Gary

last: Grajales-Reyes

state: Mo

address: Room 7766, CSRB

department: Immunology

institute: Washington University in St. Louis

summary: The transcription factors Batf3 and IRF8 are required for development of CD8α+ conventional dendritic cells (cDCs), but the basis for their actions was unclear. Here, we identify two novel Zbtb46+ progenitors that separately generate CD8α+ and CD4+ cDCs and arise directly from the common DC progenitor (CDP).  Irf8 expression in the CDP depends on prior PU.1-dependent autoactivation, and specification of pre-CD8 DC progenitors requires IRF8 but not Batf3. However, upon pre-CD8 DC specification, Irf8 autoactivation becomes Batf3-dependent at a CD8α+ cDC-specific enhancer containing multiple AP1-IRF composite elements (AICEs) within the Irf8 superenhancer. CDPs from Batf3-/- mice that specify toward pre-CD8 DCs fail to complete CD8α+ cDC development due to decay of Irf8 autoactivation, and divert to the CD4+ cDC lineage.

overall_design: Examination of histone modifications (H3K27ac and H3K4me1) and 2 transcription factors (Batf3 and Irf8) and the p300 co-factor binding in 3 different dendritic cell subsets

first: Arifumi

last: Iwata

first: Kenneth

last: Murphy


title: Gene expression changes in Suillus luteus- Pinus sylvestris ectomycorrhizal roots compared to Suillus luteus free-living mycelium

summary: Illumina HiSeq technology was used to generate mRNA profiles from Suillus luteus ectomycorrhizal roots compared to free-living mycelium . Mycorrhizal roots were harvested after 40 days, pooled and used for RNA extraction. Reads of 2X100bp were generated and aligned to Suillus luteus (http://genome.jgi-psf.org/Suilu1/Suilu1.home.html) using CLC Genomics Workbench 6.

overall_design: mRNA profiles from Suillus luteus ectomycorrhizal roots and free-living mycelium were generated by paired-end (2x100bp) Illumina HiSeq2000 sequencing. Two biological replicates were sequenced for mycorrhizal and mycelium samples.

first: Francois

last: Rineau

first: Jan

last: Colpaert


title: Dynamics of 5-hmC in cardiac maturation and hypertrophy

first: Bioinformatics

last: Unit


title: Gene expression changes in Paxillus involutus- Betula pendula ectomycorrhizal roots compared to  Paxillus involutus mycelium patches

first: Annegret

summary: Illumina HiSeq technology was used to generate mRNA profiles from  Paxillus involutus ectomycorrhizal roots compared to mycelium patches . Mycorrhizal roots  were harvested after 4 weeks, pooled and used for RNA extraction. Reads of 2X100bp were generated and aligned to Paxillus involutus (http://genome.jgi-psf.org/Paxin1/Paxin1.home.html) using CLC Genomics Workbench 6.

overall_design: mRNA profiles from Paxillus involutus ectomycorrhizal roots and mycelium patches were generated by paired-end (2x100bp) Illumina HiSeq2000 sequencing. Two biological replicates were sequenced for mycorrhizal and mycelium samples.

first: Tomas

last: Johansson

first: Anders

last: Tunlid


title: Gene expression changes in Sebacina vermifera- Arabidopsis thaliana mycorrhizal roots compared to Sebacina vermifera free-living mycelium

last: Kohler

summary: Illumina HiSeq technology was used to generate mRNA profiles from Sebacina vermifera mycorrhizal roots compared to free-living mycelium . Mycorrhizal roots  were harvested after 3, 7 and 14 days, pooled and used for RNA extraction. Reads of 2X100bp were generated and aligned to Sebacina vermifera (http://genome.jgi-psf.org/Sebve1/Sebve1.home.html) using CLC Genomics Workbench 6.

overall_design: mRNA profiles from Sebacina vermifera mycorrhizal roots and free-living mycelium were generated by paired-end (2x100bp) Illumina HiSeq2000 sequencing. Three biological replicates were sequenced for mycorrhizal and mycelium samples.

first: Yi

last: Din

first: Urs

last: Lahrmann

first: Alga

last: Zuccaro


title: Gene expression changes in Oidiodendron maius- Vaccinium myrtillus mycorrhizal roots compared to Oidiodendron maius free-living mycelium

summary: Illumina HiSeq technology was used to generate mRNA profiles from Oidiodendron maius mycorrhizal roots compared to free-living mycelium . Mycorrhizal roots and control mycelium were harvested after 45 days and used for RNA extraction. Reads of 2X100bp were generated and aligned to Oidiodendron maius transcripts (http://genome.jgi-psf.org/Oidma1) using CLC Genomics Workbench 6.

overall_design: mRNA profiles from Oidiodendron maius mycorrhizal roots and free-living mycelium were generated by paired-end (2x100bp) Illumina HiSeq2000 sequencing. Three biological replicates were sequenced for mycorrhizal and mycelium samples.

first: Elena

last: Martino

first: Silvia

last: Perotto

first: Francis

last: Martin


title: Gene expression changes in Tulasnella calospora- Serapias vomeracea mycorrhizal protocorms compared to Tulasnella calospora free-living mycelium

summary: Illumina HiSeq technology was used to generate mRNA profiles from Tulasnella calospora mycorrhizal protocorms compared to free-living mycelium . Protocorms and control mycelium were harvested after 30 days and used for RNA extraction. Reads of 2X100bp were generated and aligned to Tulasnella calospora  transcripts (http://genome.jgi-psf.org/Tulca1) using CLC Genomics Workbench 6.

overall_design: mRNA profiles from Tulasnella calospora mycorrhizal protocorms and free-living mycelium were generated by paired-end (2x100bp) Illumina HiSeq2000 sequencing. Three biological replicates were sequenced for mycorrhizal and mycelium samples.

first: Mariangela

last: Girlanda


title: Gene expression changes in Piloderma croceum-Quercus robur ectomycorrhizal roots compared to Piloderma croceum free-living mycelium

summary: Illumina HiSeq technology was used to generate mRNA profiles from Piloderma croceum ectomycorrhizal roots compared to free-living mycelium . Mycorrhizal roots  were harvested after 8 weeks, pooled and used for RNA extraction. Reads of 2X100bp were generated and aligned to Piloderma croceum (http://genome.jgi-psf.org/Pilcr1/Pilcr1.home.html) using CLC Genomics Workbench 6.

overall_design: mRNA profiles from Piloderma croceum ectomycorrhizal roots and free-living mycelium were generated by paired-end (2x100bp) Illumina HiSeq2000 sequencing. Three biological replicates were sequenced for mycorrhizal and mycelium samples.

first: Mika

last: Tarrka

first: S

last: Herrmann

first: F

last: Buscot


title: Gene expression changes in Hebeloma cylindrosporum- Pinus pinaster ectomycorrhizal root tips compared to Hebeloma cylindrosporum free-living mycelium

summary: Illumina HiSeq technology was used to generate mRNA profiles from Hebeloma cylindrosporum ectomycorrhizal root tips compared to free-living mycelium . Ectomycorrhizal root tips and control mycelium were harvested after 3 weeks and used for RNA extraction. Reads of 150 bp were generated and aligned to Hebeloma cylindrosporum transcripts (http://genome.jgi-psf.org/Hebcy2) using CLC Genomics Workbench 7.

overall_design: mRNA profiles from Hebeloma cylindrosporum ectomycorrhizal root tips and  free-living mycelium were generated by Illumina HiSeq2000 sequencing (150bp). Three biological replicates were sequenced for mycorrhizal and mycelium samples.

first: Gilles

last: Gay

first: Jeanne

last: Doré

first: Igor

last: Grigoriev


title: Gene expression changes in Amanita muscaria- Populus tremula x tremuloides ectomycorrhizal root tips compared to Amanita muscaria free-living mycelium

summary: Illumina HiSeq technology was used to generate mRNA profiles from Amanita muscaria ectomycorrhizal root tips compared to free-living mycelium . Ectomycorrhizal root tips and control mycelium were harvested after 6 weeks and used for RNA extraction. Reads of 150 bp were generated and aligned to Amanita muscaria transcripts (http://genome.jgi-psf.org/Amamu1) using CLC Genomics Workbench 7.

overall_design: mRNA profiles from Amanita muscaria ectomycorrhizal root tips and free-living mycelium were generated by Illumina HiSeq2000 sequencing (150bp). Two biological replicates were sequenced for mycorrhizal and mycelium samples.

first: Uwe

last: Nehls


title: Transcriptome comparison of ectomycorrhizal, ericoid and orchid mycorrhizal fungi

first: Annegret

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

sample_organism:
Suillus luteus
Amanita muscaria
Paxillus involutus
Hebeloma cylindrosporum
Oidiodendron maius
Piloderma croceum
Serendipita vermifera
Tulasnella calospora

overall_design: Refer to individual Series


title: Genome-wide maps of chromatin histone methylation marks in neonatal and adult cardiomyocytes

status: Public on Dec 22 2014

first: Bioinformatics

last: Unit

summary: Epigenetic changes in DNA and chromatin are implicated in organogenesis and cell differentiation. Through a genome-wide chromatin-immunoprecipitation DNA-sequencing approach (ChIP-seq) we analyses the enrichment of H3K79me2 and H3K4me3 (histone methylation marks associated with transcriptional activation) and H3K27me3 and H3K9me3 (histone methylation marks associated with transcriptional repression) in neonatal and adult cardiomyocytes. The histone methylation profile obtained was correlated with an Illumina gene expression profile from the same samples. Our results demonstrate that histone methylation, and in particular the DOT1L-mediated H3K79me2 mark, drives cardiomyogenesis through the definition of a specific transcriptional landscape

overall_design: Profiling of H3K79me2, H3K4me3, H3K27me3 and H3K9me3 in neonatal and adult cardiomyocytes

first: Paola

last: Cattaneo

first: Roberto

last: Papait

first: Paolo

last: Kunderfranco

first: Gianluigi

last: Condorelli