title: Continuous transcription initiation guarantees robust repair of all transcribed genes and regulatory regions

status: Public on Feb 14 2020

city: Vari

first: Maria

last: Fousteri

address: 34 Fleming Street

department: Institute for Fundamental Biomolecular Research

country: Greece

institute: Biomedical Sciences Research Center "Alexander Fleming"

summary: Inhibition of transcription caused by DNA damage-impaired RNA polymerase II (Pol II) elongation conceals a local increase in de novo transcription, slowly progressing from Transcription Start Sites (TSSs) to gene ends. Although associated with accelerated repair of Pol II-encountered lesions and limited mutagenesis, it is still unclear how this mechanism is maintained during genotoxic stress-recovery. Here we uncover a widespread gain in chromatin accessibility and preservation of the active H3K27ac mark after UV-irradiation. The concomitant increase in Pol II escape from promoter-proximal pause (PPP) sites of most active genes, PROMPTs and enhancer RNAs favors unrestrained initiation, as evidenced by the synthesis of nascent RNAs including start RNAs. Accordingly, drug-inhibition of PPP-release replenishes levels of pre-initiating Pol II at TSSs after UV. Our data show that such continuous engagement of Pol II molecules ensures maximal transcription-driven repair throughout expressed genes and regulatory loci. Importantly, revealing this unanticipated regulatory layer of UV-response provides physiological relevant traction to the emerging concept that Pol II initiation rate is determined by pause-release dynamics.

overall_design: ChIP-seq and ATAC-seq experiments were performed in human VH10 cells before and following DNA damage induced by low doses (15 or 20 J/m2) of UV-C irradiation. Inhibitor of transcription DRB was used as indicated in the protocols section.

first: Anastasios

last: Liakos

first: Dimitris

last: Konstantopoulos

first: Matthieu

middle: D

last: Lavigne


title: Single cell RNAseq analysis of undifferentiated skeletal cells in the murine limb bud

status: Public on Jan 29 2020

city: Houston

first: Noriaki

last: Ono

state: Texas

department: School of Dentistry

country: USA

institute: University of Texas Health Science Center at Houston

type: Expression profiling by high throughput sequencing

summary: A single cell transcriptional profile of undifferentiated skeletal cells in the murine limb bud marked by Prrx1-cre at E11.5

overall_design: tdTomato+ cells were FACS-isolated from embryonic day 11.5 (E11.5) hind limbs of Prrx1-cre; R26R-tdTomato+ mice. 15,000 cells were loaded onto 10X Genomic Chromium Single Cell Expression Solution version 3 platform. cDNA was sequenced by Illumina NovaSeq 6000


title: MYC and Twist1 cooperate to drive metastasis by eliciting crosstalk between cancer and innate immunity

status: Public on Jan 21 2020

city: Stanford

first: Renumathy

last: Dhanasekaran

state: CA

address: 300 Pasteur Drive, Alway M211

institute: Stanford University

summary: Comparative transcriptional profiling of MYC driven HCC and MYC/Twist1 driven HCC during tumor progression, regression and recurrence.

overall_design: RNA sequencing of MYC-HCC and MYC/Twist1-HCC was performed.

first: Renu

first: Dean

last: Felsher


title: OCaMIR a non-invasive early diagnostic test for ovarian cancer: A multi-cohort retrospective and prospective analysis

status: Public on Mar 06 2020

city: Chengdu

first: Shentao

last: Zhou

address: Chengdu

country: China

institute: West China Second University Hospital

type: Non-coding RNA profiling by high throughput sequencing

summary: Owing to the lack of effective screening tools and early detection biomarkers, ovarian cancer (OC) still remains as a deadly disease with highest mortality among other gynecological cancers. So far there have been no attempts to discover biomarkers using early stage OC patients. MicroRNAs (miRNAs) have been recognized as great tool to develop non-invasive biomarkers in various cancers including ovarian cancer.

overall_design: We have performed small RNA sequencing in fresh-frozen primary tissue samples collected from stage I OC (n=31) and identified a panel of eight miRNAs (OCaMIR) for the early detection of OC.

first: Ajay

last: Goel


title: MYC drives temporal evolution of small cell lung cancer subtypes by reprogramming neuroendocrine fate [Bulk RNA-seq of RPM and RPR2 tumors]

status: Public on May 28 2020

city: Durham

first: Trudy

last: Oliver

email: tgo@duke.edu, trudy.oliver@duke.edu

state: NC

address: Duke University, Box 3813, LSRC Room C138B, 308 Research Drive

department: Pharmacology & Cancer Biology

institute: Duke University

summary: Distinct SCLC molecular subtypes have been defined based on expression of lineage-related transcription factors: ASCL1, NEUROD1, POU2F3 or YAP1, but their origins remain unknown. We perform bulk RNA-sequencing on SCLC tumors from RPM and Rb1/Trp53/Rbl2 (RPR2) GEMMs, initiated by CGRP-Cre, to complement time-series analysis of single-cell transcriptome profiling and reveal that MYC drives the dynamic evolution of SCLC subtypes. MYC promotes a temporal shift from an ASCL1-to-NEUROD1-to-YAP1+ state from a neuroendocrine cell of origin. MYC activates Notch signaling to dedifferentiate tumor cells to non-neuroendocrine fates. Sequenced RPM tumors driven by MycT58A, in comparison to RPR2 tumors associated with high Mycl, have increased intratumoral subtype heterogeneity by bulk-seq, single-cell RNA seq, and IHC compared to RPR2 tumors. In RPM tumors with high MYC, tumors are able to proceed to non-NE subtypes resembling the NEUROD1+ and YAP1+ human SCLC subtypes. These findings support our overall conclusions that genetics, cell of origin, and tumor cell plasticity determine SCLC subtype.

overall_design: Bulk RNA-sequencing on 10 invasive tumors from the RPM GEMM and 5 invasive tumors from the RPR2 GEMM all infected by CGRP-Cre to study heterogeneity within RPM tumors and gene expression across models.

first: Abbie

middle: S

last: Ireland

middle: G


title: Expression data from children and adolescents treated with Fluoxetine

status: Public on Dec 31 2019

city: Barcelona

first: Teresa

last: Torres Moral

address: Casanova, 143

country: Spain

institute: Universitat de Barcelona

summary:
It is well-known that between  40 and 50% of patients taking antidepressants do not respond to treatment or relapse. Genome wide gene expression studies can help us to understand better the response to antidepressants, revealing the effects of both genetic background and environmental/epigenetic factors.
We used microarrays to detail the response to Fluoxetine in children and adolescents, analysing the expression just before intake of drug and 8 weeks after starting the treatment.

overall_design: RNA extraction was done from blood of patients. Two samples of each patient were obtained, one previous to treatment and another 8 weeks later.  The samples with better quality were selected for hybridization and Affymetrix microarrays.

last: Torres

first: Daniel

last: Boloc

first: Natalia

last: Rodrigez

first: Ana

last: Blázquez

middle: T

last: Plana

first: Eva

last: Varela

first: Albert

last: Martinez-Pinteño

first: Patricia

last: Gassó

first: Amalia

last: Lafuente

first: Joan

middle: A

last: Arnaiz

first: Luisa

last: Lazaro

first: Sergi

last: Mas


title: Divergences of sperm DNA methylomes between monozygotic twin seed bulls reveal fertility-related genes (WGBS)

status: Public on Jan 01 2020

city: Beijing

first: Shengli

last: Zhang

address: 2rd, Yuanmingyuan West Road

department: Colledge of Animal Science and Techonology

institute: China Agricultural University

type: Methylation profiling by high throughput sequencing

summary: The sperm DNA methylomes of the MZ twin bulls were investigated by WGBS at single-base resolution. We detected DMRs between the twin bulls with divergent sperm qualities. We also conducted transcriptome sequencing for the MZ twin bulls in three replicates. We investigated the relationship between methylation and gene expression.

overall_design: Comparison of sperm DNA methylomes between monozygotic twin bulls with divergent male fertility

first: Shuli

last: Liu

first: Ying

last: Yu


title: MYC drives temporal evolution of small cell lung cancer subtypes by reprogramming neuroendocrine fate [SuperSeries]

last: Oliver

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: Divergences of sperm DNA methylomes between monozygotic twin seed bulls reveal fertility-related genes


title: Nanog affects establishment of chromatin marks at zebrafish Zygotic Genome Activation

status: Public on May 07 2020

city: Freiburg

first: Daria

last: Onichtchouk

address: Hauptstrasse 1

country: Germany

institute: University of Freiburg

type: Genome binding/occupancy profiling by high throughput sequencing

summary: In zebrafish embryos, the maternal  transcription factors (TFs)Nanog,  Pou5f3 and Sox19b activate the early zygotic gene expression. To evaluate the  role of Nanog,   we examined the changes in H3K27ac and H3K4me3 chromatin modifications in the MZnanog embryos mutant by maternal and zygotic Nanog.

overall_design: We performed ChIP-seq for H3K27ac and H3K4me3 chromatin modifications in  the embryos mutant by Nanog transcription factor (MZnanog). Experiments were performed at dome stage (4.3 hours post-fertilization (hpf).

first: Anna

last: Gebhard


title: Genome-wide localisation of histone H3S57ph in proliferating and hydroxyurea pre-treated cells

city: Montpellier

last: Fisher

address: 1919 Route de Mende

department: IGMM

country: France

institute: CNRS

summary: We identified a species of histone H3 phosphorylated on serine 57 and showed that it is involved in responses to DNA replication stress. Here we asked whether it is specifically localised in the human genome by ChIP-seq from human osteosarcoma cells (U2OS) growing exponentially or treated with 2mM hydroxyurea for 2 hours to stall DNA replication forks

overall_design: Two condition experiment. 2 biological replicates of each condition

first: Nikolaos

last: Parisis


title: ChIP-chip data for identifying target genes and consensus binding sequences of mutant p53 in MDA-MB-468 breast cancer cells

status: Public on Dec 08 2019

city: Changsha

first: Jianlin

last: Zhou

state: Hunan

address: 36 Lushan road

department: College of Life Science

institute: Hunan Normal University

type: Genome binding/occupancy profiling by genome tiling array

summary: The tumor suppressor p53 exerts its role mainly as a transcription factor. The TP53 gene, which encodes the p53 protein, is the most commonly mutated gene in human cancers, particularly triple negative breast cancer (TNBC). Variations in the TP53 gene occur mainly in exons 5–8 and result in missense mutations in the DNA-binding domain of the p53 protein that alter DNA binding specificity. To identify the target genes of mutant p53, we performed chromatin immunoprecipitation followed by DNA microarray (ChIP-chip). Briefly, the TNBC cell line MDA-MB-468 containing the endogenous p53-R273H mutation (the arginine residue at position 273 is mutated to a histidine) was cross-linked with 1% formaldehyde and ultrasonically sheared to generate chromatin fragments in a range of 200∼1000 bp. An aliquot of the sheared chromatin was kept as input, and the other chromatin was precipitated with a p53 monoclonal antibody. DNA was purified from the precipitated chromatin and the unprecipitated chromatin (i.e., input), amplified, and labeled with Cy5 (ChIP DNA) or Cy3 (input DNA). Cy5- and Cy3-labeled DNA samples were cohybridized with the NimbleGen Human ChIP-chip 2.1 M Deluxe Promoter Array. The raw and analyzed data are described in this article. They are useful for identifying target genes and consensus binding motifs of the p53 R273H mutant and for further clarifying the molecular mechanism underlying the oncogenic activity of the p53 mutant.

overall_design: Identify the target genes and the binding-motif of p53-R724H mutant.

first: Mai Nhu Uyen

last: Le

first: Yichong

last: Ning


title: Identification of Potential Biomarkers for Improving the Precision of Early Detection of Steroid-induced Osteonecrosis of the Femoral Head

first: Yanqiong

address: No 16, Nanxiaojie, Dongzhimennei

institute: Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences

summary:
Early diagnosis and prompt treatment are the key to prevent collapse and delay Steroid-induced Osteonecrosis of the Femoral Head(SONFH) progression.The aim of this study was to identify potential biomarkers for the diagnosis of SONFH, so to improve the efficiency of early diagnosis.
Microarray analysis based on the 30 SONFH patients and 10 non-SONFH patients(following steroid administration) was performed to screen SONFH-related genes.

overall_design: The aim of this study was to identify potential biomarkers for the diagnosis of SONFH. The gene expression profile was detected by microarray analysis based on the 30 SONFH patients and 10 non-SONFH patients. Then, a list of candidate gene biomarkers of SONFH were identified by integrating differential expression data analysis and gene signal transduction network analysis.


title: Adipose tissue NAD+ biosynthesis is required for regulating adaptive thermogenesis and whole-body energy homeostasis in mice

status: Public on Nov 14 2019

city: Izumo

first: Jun

last: Yoshino

state: Shimane

address: 89-1 Enya-cho

country: Japan

institute: Faculty of Medicine, Shimane University

summary: We evaluated the effects of NAMPT (nicotinamide phosphoribosyltransferase) knockout on transcriptome in brown adipose tissue (BAT) by analyzing BAT obtained from control (Nampt-flox/flox, F1-F4) and adipocyte-specific Nampt knockout (ANKO, A1-A4) mice.

overall_design: We analzyed BAT obtained from 4 control mice and 4 ANKO mice.

first: Michael

last: Franczyk


title: Next Generation Sequencing provides insights into pancreas tumor-educated adipocytes

status: Public on Nov 12 2019

city: Shanghai

first: Zhiwei

last: Cai

state: Shanghai

address: Yan'an Road 221

department: Department of Surgery

institute: Huadong Hospital of Fudan University

summary: We performed RNA sequencing to compare the transcriptomes of 3T3-L1 mature adipocytes alone and cocultured with PC cell line Panc-1 cells for 5.

overall_design: Eight days after induction, mature 3T3-L1 adipocytes were cocultured with Panc-1 for another 5 days using a transwell indirect coculture system,  adipocytes cultivated alone at the same time points were as controls.

first: Chongyi

last: Jiang


title: Whole genome transcriptomics of pre-access veins and hemodialysis arteriovenous fistula (AVF) samples from two-stage AVF patients with different maturation outcomes (matured vs. failed)

status: Public on Jan 28 2020

city: Miami

first: Anthony

last: Griswold

state: FL

address: 1501 NW 10th Ave, BRB 318

institute: University of Miami

summary: We report the RNA expression profiles of native veins used for AVF creation and of remodeled AVF samples obtained 6-15 weeks later at the time of transposition (if vein matured) or salvage procedure (if vein failed). We perfomed RNA-seq on native veins and AVFs with different maturation outcomes (matured vs. failed). The "matured" and "failed" subgroups were similar in terms of demographics (age range, sex distribution, ethnicity distribution), clinical characteristics (proportion of diabetes mellitus and coronary artery disease, previous hemodialysis access history), and time interval between first-stage and second-stage surgeries. We uncovered a battery of pro-inflammatory genes upregulated in native veins that failed compared to those that matured.

overall_design: This case-control study was designed to 1) identify differentially expressed genes in native veins that matured or failed after AVF creation, 2) find differentially expressed genes in remodeled AVFs with distinct maturation outcomes, and 3) evaluate longitudinal changes in gene expression during the vein to AVF transformation.

first: Roberto

middle: I

last: Vazquez-Padron

first: Laisel

last: Martinez

middle: J


title: Single-nuclei RNAseq (NucSeq) of human eyes

status: Public on Jan 22 2020

city: South San Francisco

first: Luz

last: Orozco

address: 1 DNA Way

department: Bioinformatics

institute: Genentech Inc.

summary: 11 samples total with libraries prepared on 10X Chromium. Corresponding to 4 control eyes.

overall_design:
**Raw Data not provided due to patient privacy concerns**

Methods: Donor eyes with no retinal disease diagnosis from the Lions Eye Institute (Tampa, FL) were enucleated and flash frozen in LN2 within 5 h postmortem or less, shipped on dry ice and stored at -80C. The eye globes were cryosectioned at 60 μm starting at the base of the optic nerve and at a plane perpendicular to the optic nerve. Posterior sections with visible RPE layers were collected in batches of 8 for NucSeq (see below). Additional sections of more anterior eye regions were used to assess overall RNA quality. 108955 (right eye) is from a 78 year old female donor, PMI = 3:40 hours, RNA integrity number (RIN) = 8.0; 120974 (left eye) is from a 79 year old male donor, PMI = 2:40 hours, RIN = 8.0; 109829 (left eye) is from a 77 year old female donor, PMI = 4:08 hours, RIN = 8.4; 109373 (right eye) is from a 70 year old male donor, PMI = 4:40 hours RIN = 8.6; 110814 (right eye) is from a 65 year old male donor, PMI = 4:25 hours, RIN = 8.5. For donor eye 108955, sections 1-8 (region 1, most poterior) and 9-18 (region 2) are separately subjected to nuclei extraction and library construction with the 10X Chromium single cell 3’ gene expression kit v2. For the remaining 4 donor eyes, only region 2 was used for NucSeq with the v3 kit.  Nuclei were isolated and processed based on methods in (Krishnaswami et al., 2016). Briefly, sections were thawed directly in ice cold homogenization buffer (250 mM sucrose, 25 mM KCl, 5 mM MgCl2, 10 mM Tris buffer pH 8.0, 1 μM DTT, 1X cOmpleteTM protease inhibitors with EDTA (Roche), 0.1% v/v Triton X 100, 0.4U/μL recombinant RNAse Inhibitor (Ambion), 0.2U/μL SUPERas-In (Ambion), 0.2 μg/ml DAPI) and dounced 15X with a loose pestle in a glass tissue homogenizer (Wheaton). Nuclei released were washed once in homogenization buffer and sorted for 2N DNA content gated on DAPI (linear scale) on a FACS-ARIA II (BD) with cooled chamber. Sorted single nuclei were collected in 1% BSA/1X PBS with 0.2U/μL RNase Inhibitor, concentrated, resuspended in ~50 μL residual buffer, counted manually with a hemocytometer, and immediately processed with 10X Chromium single cell 3’ gene expression kit v2 or v3 (10X Genomics) at ~16000 nuclei per library and 2-3 libraries per region, following manufacturer’s protocol.

first: Hsu-Hsin

last: Chen


title: Integration of eQTL and single-cell transcriptomics in the human eye identifies causal genes for age-related macular degeneration

summary: Bulk RNAseq of retina and RPE/choroid tissue, each from the macula or non-macula (peripheral) regions of human donor eyes.

overall_design:
**Raw Data not provided due to patient privacy concerns**

Postmortem eyes from 129 human donors for bulk RNA seq and 5 donors for single-nucleus RNAseq (see below) were procured by the Florida Lions Eye Bank (Tampa, FL). Donors profiled in this study were 43 females and 76 males, ranging from 59 to 98 years of age. From these, 99 donors had no history of ocular diseases and 23 donors were previously diagnosed with AMD. Eyes were enucleated 4 h postmortem or less and preserved in RNAlater immediately after collection. The macula is fully contained within the boundaries of superior and inferior temporal vascular arcades and is easily visualized. After the macula was dissected out from the peripheral fundus using dissecting scissors, the macular retina was separated from the RPE and choroid underneath the retina. Total RNA was isolated from tissues using RNeasy Mini kit (QIAGEN) including the on-column DNase digestion.

Quality control of samples was done to determine RNA quantity and quality prior to their processing by RNA-seq. The concentration of RNA samples was determined using NanoDrop 8000 (Thermo Scientific) and the integrity of RNA was determined by Fragment Analyzer (Advanced Analytical Technologies). Samples with RNA integrity number (RIN) below 8 were excluded from further analysis. 0.5 ug of total RNA was used as an input material for library preparation using TruSeq RNA Sample Preparation Kit v2 (Illumina). Size of the libraries was confirmed using 2200 TapeStation and High Sensitivity D1000 screen tape (Agilent Technologies) and their concentration was determined by qPCR-based method using Library quantification kit (KAPA). The libraries were multiplexed and then sequenced on Illumina HiSeq2500 (Illumina) to generate 30M of single end 50 base pair reads. Sequencing data analysis was performed as previously described (Durinck et al., 2015). Sequencing reads were mapped to the reference human genome (GRCh38), using the GSNAP short read aligner (Wu and Nacu, 2010). Expression was quantified using HTSeqGenie as reads per kilobase of gene model per million total reads (RPKM), and normalized using size factors computed using DESeq2 (nRPKM).

first: Yanli

last: Hou


title: Divergences of sperm DNA methylomes between monozygotic twin seed bulls reveal fertility-related genes (RNA-Seq)

first: Shengli

last: Zhang

summary: Semen quality is extremely important for fertility, and it is easily influenced by environmental factors and can induce subfertility of the next generations. The sperm DNA methylomes of the MZ twin bulls were investigated by WGBS at single-base resolution. We detected DMRs between the twin bulls with divergent sperm qualities. We also conducted transcriptome sequencing for the MZ twin bulls in three replicates. We investigated the relationship between methylation and gene expression.

overall_design: Comparison of sperm transcriptome profiles between monozygous twin bulls with divergent male fertility.

first: Shuli

last: Liu

first: Ying

last: Yu


title: Genomic Resolution of DLX-orchestrated Transcriptional Circuits Driving Development of Forebrain GABAergic Neurons

status: Public on Aug 20 2019

city: Davis

first: Alex

middle: S.

last: Nord

address: 1544 Newton Court

department: Center for Neuroscience

institute: University of California Davis

summary: DLX transcription factors (TFs) are master regulators of the developing vertebrate brain, driving forebrain GABAergic neuronal differentiation. Ablation of Dlx1&2 alters expression of genes that are critical for forebrain GABAergic development. We integrated epigenomic and transcriptomic analyses, complemented with in situ hybridization (ISH), and in vivo and in vitro studies of regulatory element (RE) function. This elucidated the DLX-organized gene regulatory network at genomic, cellular, and spatial level in mouse embryonic basal ganglia. DLX TFs perform dual activating and repressing functions; the consequences of their binding were determined by the sequence and genomic context of target loci. Our results reveal and, in part, explain the paradox of widespread DLX binding contrasted with a limited subset of target loci that are sensitive at the epigenomic and transcriptomic level to Dlx1&2 ablation. The regulatory properties identified here for DLX TFs suggest general mechanisms by which TFs orchestrate dynamic expression programs underlying neurodevelopment.

overall_design: Regulatory wiring of early telencephalic GABAergic neuron development organized by DLX family transcription factors, integrating in situ hybridization, transcriptomic, and epigenomic data from wild-type and Dlx1/2 knockout ganglionic eminences (embryonic mouse basal ganglia (BG))

first: Susan

last: Lindtner

first: Rinaldo

last: Catta-Preta

first: Hua

last: Tian

first: Linda

last: Su-Feher

first: James

last: Price

first: Diane

middle: E

last: Dickel

first: Vanille

last: Greiner

first: Shanni

middle: N

last: Silberberg

first: Gabriel

middle: L

last: McKinsey

last: McManus

first: Axel

last: Visel

first: Len

last: Pennacchio

first: John

middle: R

last: Rubenstein


title: miRNA expression profiles of macrophages (cell line: RAW264.7) and endothelial cells (cell line: TIME)

status: Public on Aug 22 2019

city: Halle (Saale)

first: Julia

last: Schumann

address: Franzosenweg 1a

institute: University Medicine Halle (Saale)

summary: We report the miRNA profiles of  macrophages (cell line: RAW264.7) and endothelial cells (cell line: TIME) after supplementation with polyunsaturated fatty acids (PUFA) and stimulation with LPS/pro-inflammatory cytokines. The fatty acids docosahexaenoic acid (DHA, C22:6n3) or arachidonic acid (AA, C20:4n6) were included in the culture medium in concentrations of 15 µmol/L using ethanol as a vehicle (0.2 % v/v final ethanol concentration). Cells were cultured in the enriched media totaling either 72 h (RAW264.7) or 144 h (TIME). Stimulation of cells was performed in the last 24 h of fatty acid supplementation by addition of either LPS (1 µg/mL; from E. coli serotype 0111:B4) for cell line RAW264.7 or the cytokines IL-1β, TNF-α, and IFN-γ each in a concentration of 5 ng/ml for cell line TIME.

overall_design: miRNA profiles of macrophages (cell line: RAW264.7) and endothelial cells (cell line: TIME) supplemented with unsaturated fatty acids and exposed to an inflammatory milieu were generated by deep sequencing, in triplicate, using Illumina HiScanSQ.

first: Claudia

last: Roessler

first: Knut

last: Krohn


title: The conjunctival transcriptome in Ethiopians after trichiasis surgery: associations with the development of eyelid contour abnormalities and the effect of oral doxycycline treatment

status: Public on Aug 21 2019

city: london

first: Tamsyn

middle: Ruth

last: Derrick

address: keppel street

country: United Kingdom

institute: london school of hygiene and tropical medicine

summary: Surgery to correct trichiasis is a key component of the WHO trachoma control strategy, however unfavourable outcomes such as eyelid contour abnormalities (ECA) following surgery are relatively common. This study aimed to understand the transcriptional changes associated with the early development of ECA and the impact of doxycycline, which has anti-inflammatory and anti-fibrotic properties, upon these transcription patterns. One thousand Ethiopians undergoing trichiasis surgery were enrolled in a randomised controlled trial following informed consent. Equal groups of individuals were orally administered with 100mg/day of doxycycline or placebo for 28 days. Conjunctival swabs were collected immediately prior to surgery and at one- and six-months post-surgery. 3’ mRNA sequencing was performed on paired baseline and one-month samples from 48 individuals; 24 from each treatment group. Within each treatment group, 12 individuals developed ECA. Treatment and outcome groups were matched by age, sex and baseline disease severity. qPCR validation was then performed for 46 genes of interest in 145 individuals who developed ECA at one month and 145 matched controls, using samples from baseline, one and six months. All treatment/outcome groups upregulated genes associated with wound healing pathways at one month relative to baseline, however no differences were detected between groups. The summed expression of a highly coexpressed cluster of pro-fibrotic genes was higher in patients that developed ECA in the placebo group relative to controls. qPCR validation revealed that all genes in this cluster and a number of other pro-inflammatory genes were strongly associated with ECA, however these associations were not modulated by trial arm. The development of post-operative ECA is associated with overexpression of pro-inflammatory and pro-fibrotic genes including growth factors, matrix metalloproteinases, collagens and extracellular matrix proteins. There was no evidence that doxycycline modulated the association between gene expression and ECA.

first: Esmael

last: Habtamu

first: Zerihun

last: Tadesse

first: E

middle: K

last: Callahan

first: Abebaw

last: Worku

first: Bizuayehu

last: Gashaw

first: David

last: Macleod

middle: C

last: Mabey

first: Martin

last: Holland

first: Matthew

last: Burton


title: STAT3 MODULATION AS A PROMISING THERAPEUTIC OPTION IN A PRECLINICAL MOUSE MODEL OF ULCERATIVE COLITIS

status: Public on Jul 24 2019

first: Prema

last: Robinson

address: 6767 Bertner Ave

department: Infectious Diseases

institute: University of Texas MD Anderson Cancer Center

summary:
Ulcerative colitis (UC) is a form of inflammatory bowel disease (IBD) that predisposes to colorectal cancer (CRC) and is modeled in mice by administration of dextran sodium sulfate (DSS) in drinking water. There are two isoforms of STAT3, STAT3α is pro-inflammatory and anti-apoptotic, while STAT3β has opposing effects on STAT3α. We examined the severity of DSS-induced colitis in transgenic-mice expressing only STAT3α (  /  ) and in wild-type (WT) mice administered C188-9, a small molecule direct-inhibitor of STAT3. While manifestations of DSS-induced UC, such as mortality, weight-loss, rectal-bleeding, diarrhea, and colon-shortening, were exacerbated in   /   transgenic versus cage-control WT mice, all were prevented by C188-9 treatment of WT mice. C188-9 treatment also increased apoptosis of pathogenic CD4+T-cells, reduced colon-levels of IL17-positive cells, down-modulated mRNA-levels of STAT3-genes involved in inflammation, apoptosis-prevention, and colorectal-cancer-metastases. These are the only studies showing efficacy of Thus small-molecule targeting of STAT3 may be a useful novel approach in treating UC and preventing UC-associated colorectal-cancer.
We performed genome-wide microarray expression profiling to gain greater understanding of the mechanisms involved in the protective effect of C188-9 in DSS-induced colitis, we examined mRNA levels in the colon of mice receiving DSS or plain water, without or with C188-9 treatment.

overall_design: After the mice were euthanized, their colons were harvested and length measured; a portion was flash frozen in liquid nitrogen to isolate RNA for microarray analyse.


title: Hippocampal and neocortex transcriptome sequencing data from 17 mesial temporal lobe epilepsy patients and 2 neocortex samples from neurologically healthy controls

city: Copenhagen

first: Guido

last: Barzaghi

address: Strandlodsvej 19B, st TH

country: Denmark

institute: University of Copenhagen

summary: Comparative analysis of gene expression differences (DEGs) between the amygdalohippocampal complex  (most often the region of seizure onset in mesial temporal lobe epilepsy (mTLE)) and  neocortex from mTLE patients who undergo epilepsy surgery can be used to illuminate pathophysiological events involved in epileptogenises. Transcriptome analysis was performed on freshly resected  amygdalohippocampal and temporal lobe cortex tissue obtained after surgery of 17 patients with drug-resistant temporal lobe epilepsy from Copenhagen University Hospital.

overall_design: Hippocampal and neocortex  samples from 17 mesial temporal lobe epilepsy patients (paired data), and neocortex from 2 patients without epilepsy results in a total of 36 samples. The tissue was surgically removed en bloc and cut to 50 mg pieces. After a short rinse in RNAlater tissue sample 1-13 was placed in Rnase-free eppendorf tubes and flash frozen in liquid nitrogen. Sample 14-17 was placed in RNAlater.

first: Christina

last: Kjaer

first: Lasse

last: Bak

first: Jens

middle: P

last: Goetze

middle: W

last: Yde

last: Woldbye

first: Lars

middle: H

last: Pinborg

last: Jensen


title: EGFR and hair shaft differentiation

status: Public on Jul 23 2019

city: Wien

first: Gerwin

last: Heller

address: Währinger Gürtel 18-20

department: Medicine I

country: Austria

institute: Medical University of Vienna

summary: EGFR signaling controls skin development and homeostasis in mice and humans and its deficiency causes severe skin inflammation, which might affect epidermal stem cell behaviour. Here, we describe the inflammation-independent effects of EGFR-deficiency during skin morphogenesis and in adult HFSCs. Expression and alternative splicing analysis of RNAseq data from interfollicular epidermis and outer root sheath indicate that EGFR controls genes involved in epidermal differentiation, but also in centrosome function, DNA damage, cell cycle and apoptosis. Genetic experiments employing p53-deletion in EGFR–deficient epidermis reveal that EGFR signalling exhibits p53-dependent functions in proliferative epidermal compartments, as well as p53–independent functions in differentiated hair shaft keratinocytes. Loss of EGFR leads to absence of Lef1 protein specifically in the innermost epithelial hair layers, resulting in disorganization of medulla cells. Thus, our results uncover important spatial and temporal features of cell-autonomous EGFR functions in the epidermis.

overall_design: 150bp PE RNA-seq, EGFR knock out vs controls

first: Nicole

last: Amberg


title: Rapid and Inexpensive Preparation of Genome-Wide Nucleosome Footprints from Model and Non-Model Organisms

status: Public on Dec 10 2019

city: Eugene

first: Jeffrey

last: McKnight

state: OR

address: 1229 University of Oregon, 1318 Franklin Blvd, Rm 273 Onyx Bridge

department: Institute of Molecular Biology

institute: University of Oregon

summary: We report the development of a versatile strategy to map nucleosomes in multiple model organisms

sample_organism:
Schizosaccharomyces pombe
Saccharomyces cerevisiae
Neurospora crassa

overall_design: Nucleosome positoining data (MNase-seq) from S. cerevisiae (exponentially-growing, quiescent, solid patches), N. crassa, and S. pombe


title: ELICITOM

status: Public on Nov 13 2019

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

institute: IPMC/CNRS

summary: ELICITOM project aims to decipher the complex regulation of tomato induced resistance to pathogens. Here, we use a classical elicitor of tomato defenses, ie beta-aminobutyric acid (BABA). This unusual amino acid triggers a strong resistance to the oomycete pathogen Phytophthora parasitica as well as to Oidium neolycopersici (powdery mildew) to a lesser extent. No resistance could be observed towards the grey mold (Botrytis cinerea). Transcriptomic data were generated from RNA extracted from tomato leaves (Solanum lycopercum cv "Marmande") sprayed with 10 mM BABA compared to control organs treated with water, 24 h after treatment. Mapping was achieved on Solanum lycopersicum cv Heinz1706 genome (release ITAG2,3).

overall_design: BABA (10 mM) and water were sprayed on non senescent fully expanded leaves (2 stages) of 5 weeks old tomato plants. Each treatment was carried out on 3 plants and sampling was achieved  after 24h. From each plant (the biological triplicates), treated  leaflets were sampled randomly. Grinding was peformed under liquid nitrogen and from the obtained homogeneous powder, an aliquot was TRIzol extracted to give total RNA.

first: M

last: Da-Rocha

first: C

last: Rancurel

first: V

last: Magnone

first: K

first: P

last: Barbry

last: Ponchet


title: GSK-J4 and suppression of the H3K27 demethylase UTX specifically activates expression of ATF4 and its target genes independently of PERK-eIF2α phosphorylation

city: Singapore

first: Kian Leong

last: LEE

state: Singapore

address: #07-21, 8 College Road

department: Duke-NUS Medical School

country: Singapore

institute: National University of Singapore (NUS)

summary: UTX/KDM6A encodes a major histone H3 lysine 27 (H3K27) demethylase which is frequently mutated in various types of cancers. Although UTX appears to play a crucial role in cancer, its mechanisms remain poorly understood. Here we found that a specific pharmacological inhibitor of H3K27 demethylases, GSK-J4, induces expression of the ATF4 (transcription activating factor 4) protein and its downstream target genes (e.g. PCK2, CHOP, REDD1, CHAC1 and TRIB3), and activates autophagy-related gene products (LC3A, LC3B and ATG5-ATG12). ATF4 induction by GSK-J4 did not entail either ATF6α processing or an increase of PERK and eIF2α serine 51 phosphorylation, indicating that this action is not triggered by canonical endoplasmic reticulum (ER) stress. No changes in expression levels of the endogenous ATF4 mRNA and exogenously expressed ATF4 proteins driven by the CMV promoter were detected, suggesting that the induction is not due to either transcriptional or post-translational regulation of ATF4. Although GSK-J4 efficiently induces apoptosis, it is unlikely that the induction is due to activation of the ATF4-CHOP axis. By using gene expression profiling experiments in conjunction with CRISPR editing and stable re-expression of UTX, we found that UTX specifically suppresses expression of ATF4 target genes. These findings highlight not only that GSK-J4, which has been considered an anti-cancer drug, is a strong inducer of ATF4, but also that UTX is an important component of this regulation and may contribute to oncogenesis via ATF4 regulation.

overall_design: Stable wild type UTX expressing and empty vector control (CSII-CMV-IRES2-puro) clones were derived from two independent UTX CRISPR-Cas9 mutated HCT116 cell-lines CR1 and CR2. Total RNA was extracted from all 4 conditions in biological triplicates and subjected to Illumina HumanHT-12 v4.0 microarray profiling for identification of UTX-regulated target genes.

first: Wendi

last: Sun

first: Shojiro

last: Kitajima

first: Kian

last: Lee

first: Jolene

last: Ho

first: Lorenz

last: Poellinger

first: Hiroyuki

last: Kato


title: CDK12 catalytic activity is rate-limiting for RNAPII processivity on core DNA replication genes and G1/S progression (nuclear RNA)

status: Public on Jul 22 2019

city: München

first: Caroline

last: Friedel

address: Amalienstr. 17

department: Institut für Informatik

institute: Ludwig-Maximilians-Universität München

summary: In this study we characterized the importance of CDK12-kinase activity in cell cycle regulation, using CDK12 anolog-sentive cells. Inhibition of analog-sensitive CDK12 reveals its catalytic activity is necessary for optimal G1/S progression. Mechanistically, CDK12 regulates transcription of core DNA replication genes and affects timely assembly of pre-replication DNA complex on chromatin. We have performed 3’-end RNA-sequencing after CDK12 inhibition and identified that the expression of core DNA replication genes were affected. To investigate further, we carried out nuclear RNA-seq coupled with ChIP-seq,  and demonstrated that CDK12 regulates RNAPII processivity of core DNA replication genes and optimal G1/S progression.

overall_design: Nuclear RNA seq. was performed in three biological replicates, after treatment with or without 5 µM 3-MB-PP1 for 4.5 h in serum synchronised AS CDK12 HCT116 cells. Total number of samples analyzed were six.

first: Anil

last: Manavalan

first: Kveta

last: Pilarova

first: Michael

last: Kluge

first: Koen

last: Bartholomeeusen

first: Jan

last: Oppelt

first: Kamil

last: Paruch

first: Lumir

last: Krejci

first: Dalibor

last: Blazek


title: CDK12 catalytic activity is rate-limiting for RNAPII processivity on core DNA replication genes and G1/S progression (3' RNA)

overall_design: 3'end RNA seq was performed in three biological replicates, after treatment with or without 5 µM 3-MB-PP1 for 5 h in serum synchronised AS CDK12 HCT116 cells. Total number of samples analyzed were six.


title: CDK12 catalytic activity is rate-limiting for RNAPII processivity on core DNA replication genes and G1/S progression

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

overall_design: Refer to individual Series


title: Analysis of Fusarium verticillioides gene expression in response to lactam and lactone compounds

status: Public on Jun 25 2019

city: Athens

first: Anthony

middle: E.

last: Glenn

state: GA

address: 950 College Station Rd

department: Toxicology & Mycotoxin Research Unit

institute: USDA, ARS, USNPRC, R.B. Russell Research Center

summary: Investigation of whole transcriptional changes in F. verticillioides FRC M-3125 when exposed to 5 μg/ml pyrrocidine A (PA), 20 μg/ml pyrrocidine B (PB), 50 μg/ml 2-benzoxazolinone (BOA), 50 μg/ml 2-oxindole (OXD), 50 μg/ml 2-coumaranone (CMN), or 50 μg/ml chlorzoxazone (CZX).  Cultures were harvested one hour after exposure.  Assessed in reference to control cultures of M-3125 exposed to DMSO (0.5% final concentration) since all the above compounds were dissolved in DMSO.

overall_design: Two milliliters of PDB cultures in sterile snap-cap tubes, with caps loose, were seeded with 10000 FRC M-3125 wild-type F. verticillioides conidia and grown at 27 °C, 250 rpm for 47 hours, at which time the respective cultures were treated [10 μL DMSO containing 100 μg of either BOA, OXD, CMN, or CZX (final concentrations of 50 μg/mL); or 10 μg of PA (5 μg/m final); or 40 μg of PB (20 μg/m final)]. Ten microliters of DMSO was added to control samples. All culture tubes were incubated for a final one-hour induction. After induction, total RNA was extracted.

first: Gao

last: Minglu

first: Scott

last: Gold


title: CDK12 catalytic activity is rate-limiting for RNAPII processivity on core DNA replication genes and G1/S progression (ChIP-Seq)

overall_design: After treatment with or without 5 µM 3-MB-PP1 for 4.5 h in serum synchronised AS CDK12 HCT116 cells, ChIP-seq was performed in three biological replicates with RNAPII, P-Ser2 RNAPII and P-Ser5 RNAPII antibodies. Total number of samples analyzed were twenty, including two no antibody control samples


title: MYC-driven small-cell lung cancer is metabolically distinct and vulnerable to arginine depletion

status: Public on Dec 22 2019

city: Durham

first: Trudy

last: Oliver

address: Duke University, Box 3813, LSRC Room C138B, 308 Research Drive

institute: Duke University

summary: We report ChIP-Seq analyses for MYC and H3K27Ac in tumors from our MYC-driven genetically engineered mouse model of small cell lung cancer (SCLC) infected with Ad-Cgrp-Cre

overall_design: Individual lung tumors from mice were micro-dissected, flash frozen and stored at -80°C until chromatin immunoprecipitation

middle: G

first: Milind

middle: D

last: Chalishazar


title: CDK12 catalytic activity is rate-limiting for RNAPII processivity on core DNA replication genes and G1/S progression (ChIP-Seq II)

overall_design: After treatment with or without 5 µM 3-MB-PP1 for 4.5 h in serum synchronised AS CDK12 HCT116 cells, ChIP-seq was performed in three biological replicates with SPT6 antibodies. Total number of samples analyzed were seven, including one no antibody control sample

first: Michal

last: Rajecky


title: RNA sequencing of human macrophages treated with iron chelator deferiprone (DEF), with and without lipopolysaccharide (LPS)

status: Public on Jul 09 2019

city: London, United Kingdom

first: Norzawani

middle: Binti

last: Buang

state: London

address: 9N15 Commonwealth Buidling, Ducane Road

institute: Imperial College London

summary: In order to identify transcript changes in response to DEF , we used human macrophages with or without DEF treatment.  In order to study the effect of iron chelation on LPS-polarized macrophage transcriptome, we exposed DEF-treated or control macrophages to short time exposure to LPS. We then performed whole-genome transcriptome sequencing by RNA-sequencing  (RNA-seq).

overall_design: Macrophages from 3 healthy donors were either treated with DEF (500 µM - designated as DEF) or left unstimulated (CONTROL). LPS treatment (100 ng/ml, 3 hours) was performed in cells with DEF (designated as LPS+DEF) or without  (LPS). RNA-seq was performed on Illumina Hiseq 2500

first: Jacques

middle: V

last: Behmoaras


title: Transcriptomes of rat hearts after kidney transplantation in chronic kidney disease model

status: Public on Oct 01 2019

city: Utrecht

last: Mokry

address: Lundlaan 6

country: Netherlands

institute: Wilhelmina Children's Hospital, University Medical Center Utrecht

summary: Transcriptomes from hearts of control and CKD rats after transplantation of healthy kidney and kidney from CKD animal.


title: A transcriptional signature associated with non-Hodgkin lymphoma in the blood of patients with Q fever

status: Public on Jun 05 2019

city: marseille

first: Amira

last: Ben Amara

address: 27  Boulevard Leï Roue

institute: IHU-CRCM

summary: Coxiella burnetii, the agent causing Q fever, has been associated with B-cell non-Hodgkin lymphoma (NHL). To better clarify this link, we analysed the genetic transcriptomic profile of peripheral blood leukocytes from patients with C. burnetii infection to identify possible links to lymphoma. Microarray analyses revealed that 1189 genes were expressed differently (p <.001 and fold change ≥4) in whole blood of patients with C. burnetii infection compared to controls. In addition, 95 genes expressed in patients with non-Hodgkin lymphoma (NHL) and in patients with C. burnetii persistent infection have allowed us to establish the ‘C. burnetii-associated NHL signature’. Among these, 33 genes previously found modulated in C. burnetii-associated -NHL by the microarray analysis were selected and their mRNA expression levels were measured in distinct C. burnetii-induced pathologies, namely, acute Q fever, focalized persistent infection, lymphadenitis and C.burnetii-associated NHL. Specific genes involved in anti-apoptotic process were found highly expressed in leukocytes from patients with C. burnetii associated-NHL: MIR17HG, REL and SP100. This signature differed from that found for NHL-control group. Patients with C. burnetii lymphadenitis presented significant elevated levels of BCL2 and ETS1 mRNAs. Altogether, we identified a specific transcriptionnal signature for NHL during C. burnetii infection reflecting the up-regulation of anti-apoptotic processes and the fact that lymphadenitis might constitute a critical step towards lymphomagenesis.

overall_design: RNAs were extracted from whole blood (PAXgene tubes, Qiagen, Courtaboeuf, France) with PAXgene kit with a DNase I treatment to eliminate DNA contaminants and according to the recommendations of the manufacturer (Qiagen, Courtaboeuf, France)

first: Cléa

last: Melenotte

first: Soraya

last: Mezouar

first: Simon

last: Benatti

last: Chiaroni

first: Christian

last: Devaux

first: Guido

last: Kroemer

first: Jean-Louis

last: Mege

first: Didier

last: Raoult


title: Single Cell RNA Sequencing Identifies Subsets of Hepatic Stellate Cells and Myofibroblasts in Liver Fibrosis

status: Public on Jun 14 2019

city: Cologne

first: Ali

middle: T

last: Abdallah

address: Joseph Stelzmann Str. 26

department: Medical Faculty

institute: University of Cologne

summary: Hepatic stellate cells and activated myofibroblasts display a high heterogeneity in healthy and fibrotic liver characterized by differential expression of collagens and chemokines.

overall_design: Hepatic stellate cells and myofibroblasts were isolated from healthy and early fibrotic liver (3 weeks CCl4) and subjected to single cell RNA sequencing analysis. In vivo activated fibroblasts were then compared with in vitro generated.

first: Oliver

last: Krenkel

first: Jana

last: Hundertmark

first: Thomas

last: Ritz

first: Ralf

last: Weiskirchen

first: Frank

last: Tacke


title: Expression profiling of mouse primary prostate cells from WT mice

status: Public on Sep 02 2019

city: Manchester

first: Esther

last: Baena

address: The University of Manchester, Wilmslow Road

department: Prostate Oncobiology

institute: Cancer Research UK Manchester Institute

summary: By single-cell expression profiling and validation, here we report that both basal and luminal-localized cells, particularly the latter, are molecularly heterogeneous. We validate LY6D as a marker linking CR luminal cells to luminal progenitors.

overall_design: Primary prostate cells were isolated and luminal prostate cells were FACS-sorted by LY6D+/- SCA1High/Int/low from the lineage (CD31, CD45, Ter119) negative fraction.  Total RNA was extracted from two biological replica test. Lexogen Quantseq RNA Sample Prep Kit was used with 10-20 ng of total RNA for the construction of sequencing libraries.


title: genome-wide mapping of Fra-1 and Fra-2 binding sites in MDA-MB-231 cell line

status: Public on Sep 01 2019

city: Montpellier

first: Isabelle

last: Jariel-Encontre

state: Montpellier Cedex5

address: 208 Avenue des Apothicaires

institute: IRCM-U1194- INSERM

summary: we report the mapping of Fra-1 and Fra-2 binding site on MDA-MB-231 cell line  genome

overall_design: identification of Fra-1 and Fra-2 binding sites on MDA-MB-231 cell genome

first: Claire

last: Tolza

first: Fabienne

last: Bejjani

first: Muhammad

last: A. Maqbool

first: Marc

last: Piechaczyk


title: Variovorax enforce stereotypic root development

status: Public on May 15 2019

city: Chapel Hill

first: Isai

last: Salas Gonzalez

address: 250 Bell Tower Drive, Room 4244

institute: The University of North Carolina at Chapel Hill


title: The role of MAGI1 (membrane-associated guanylate kinase with inverted domain structure-1) in regulating disturbed flow-induced changes of gene expression

status: Public on May 09 2019

city: Houston

first: Jun-ichi

last: Abe

address: 2121 W Holcombe Blvd. IBT8 803e

institute: University of Texas MD Anderson Cacer Center

summary: To understand the function of MAGI1 in ECs, we isolated total RNAs from human umblical vein endothelial cells (HUVECs) transfected with control or Magi1 siRNA and transcriptionally profiled them. Ingenuity pathway Analysis (IPA) demonstrated activation of antiviral responses, including interferon signaling, without affecting NF-κB expression and inhibition of ER stress gene expression induced by the reduction of MAGI1 expression. Because activation of interferon signaling tends to increase NF-κB activation, the finding that depletion of MAGI1 promotes antiviral responses without increasing NF-κB activation is unique, suggesting that MAGI1 is an incomparable molecular switch for pro-viral and pro-inflammatory responses.

overall_design: HUVECs were transfected by control siRNA or MAGI1 siRNA, and after 48 hrs of transfection HUVECs were exposed to disturbed flow (d-flow). After 24 hrs of disturbed flow RNA was extracted for futher microarray processing. We have the following four groups (1. Control siRNA under static condition (siCont), 2. Control siRNA under d-flow (siCont + DF), 3. MAGI1 siRNA under static condition (siMAGI1), and 4. MAGI1 siRNA under d-flow (siMAGI1 + DF), and each group have three samples and total twelve samples were analyzed.

first: Nhat-Tu

last: Le


title: P2 receptor expression in different tissue-resident phagocyte populations isolated from peritoneal tissues of Cx3cr1gfp/+Ccr2rfp/+ mice

status: Public on Apr 04 2019

city: New Haven

first: Andrew

last: Martins

state: Connecticut

address: 100 College Street Rm 1155

department: Immunobiology

institute: Yale School of Medicine

summary: In support of the investigation into the response of tissue resident phagocytes to sterile tissue damage in the peritoneal wall, different phagocyte populations were isolated from this tissue and RNA expression was measured using RNAseq.

overall_design: Peritoneal wall phagocytes from three Cx3cr1gfp/+Ccr2rfp/+ animals were sorted into Cx3cr1-Ccr2rfp-, Cx3cr1-Ccr2rfp+, and Cx3cr1+Ccr2rfp- groups. Cells from three mice were sorted, and carried through the RNAseq protocol as three replicates per group.

first: Stefan

last: Uderhardt

middle: J

first: Tim

last: Lämmermann

first: Ronald

last: Germain


title: miRNAs expression in four breast cancer cells

status: Public on Mar 19 2019

city: Beijing

first: yongmei

last: song

institute: State Key Laboratory of Molecular Oncology

summary: To determine the miRNAs’ roles in the tumorigenesis behavior of TNBC, we profiled the global miRNA expression in 2 highly aggressive TNBC cell lines (MDA-MB-231 and CAL-51) in comparison with that in 2 non-aggressive luminal-type breast cancer cell lines (ZR-75-1 and MCF-7).

first: Yongmei

last: Song

first: Zitong

last: Zhao


title: JAK1/2 inhibitor therapy-associated lymphomas in myelofibrosis arising from a pre-existing B-cell clone

status: Public on Feb 05 2019

city: Wien

first: Gerwin

last: Heller

institute: Medical University of Vienna

summary: In this study, we elucidated differential gene expression between transformed and untransformed murine Stat1 -/- B cells by RNA sequencing. In addition, clinical samples from 2 lymphoma patients were analyzed. Key results are that 1) JAK1/2 inhibitor treatment in myelofibrosis is associated with an increased risk for aggressive B-cell lymphomas and 2) patients at risk can be identified by screening for pre-existing B-cell clones in peripheral blood or bone marrow.

overall_design: Differential gene expression between 2 murine groups.  Clinical samples from 2 lymphoma patients.

first: Veronika

last: Sexl

first: Gewin


title: VenomSeq - 25 venoms vs. IMR-32

status: Public on Feb 15 2019

city: New York

first: Nicholas

last: Tatonetti

state: New York

address: 622 W 168th Street

department: Department of Biomedical Informatics

institute: Columbia University

summary: We report the perturbational effects of 25 crude venoms on human IMR-32 (neuroblastoma) cells. These data are used to evaluate the VenomSeq transcriptomic data analysis workflow, and to provide the first dataset generated by this workflow. By comparison with data published by the Connectivity Map team, and other free sources of genetic perturbation in the context of disease or drug exposure, we use these data to discover several novel associations between venoms and specific therapeutic actions.

overall_design: 192 samples total, corresponding to 2 96-well plates of samples. These 192 samples are treated with each of 25 venoms, where extraction takes place at each of 3 time points with 2 replicates per time point (6 samples per venom). 24  samples were treated with water only, and 18 were left untreated. Dosages per venom were determined experimentally as the concentration at which cell growth was inhibited by 20%.

first: Joseph

last: Romano

last: Realubit

first: Hai

last: Li

first: Charles

last: Karan


title: Integrated metabolome and transcriptome analyses provide novel insight into colon cancer modulation by the gut microbiota

status: Public on Dec 29 2018

city: Columbia

first: Susheel Bhanu

last: Busi

state: MO

address: 4011 Discovery Drive

institute: UNIVERSITY OF MISSOURI - COLUMBIA

summary: Colon cancer onset and progression is strongly associated with the presence, absence, or relative abundances of certain microbial taxa in the gastrointestinal tract. However, specific mechanisms affecting disease susceptibility related to complex bacterial mixtures are poorly understood. We used a multi-omics approach to determine how differences in the complex gut microbiome (GM) influence the metabolome and host transcriptome and ultimately affect susceptibility to adenoma development. Fecal samples collected from Pirc rats harboring two distinct complex GMs were analyzed using ultra-high performance liquid chromatography mass spectrometry (UHPLC-MS). We identified putative metabolite profiles that predicted future disease severity from samples collected prior to observable disease onset. Transcriptome analyses performed after disease onset on normal epithelium and tumor tissues suggests that the GM also alters the host transcriptome. Integrated pathway (IP) analyses of the metabolome and transcriptome based on putatively identified metabolic features indicate that bile acid biosynthesis was enriched in rats with high tumors (GM:F344)  along with increased fatty acid metabolism and mucin biosynthesis. These data emphasize the utility of using untargeted metabolomics to identify metabolites for revealing signatures of susceptibility and resistance.

overall_design: Examination of host transcriptome of the Pirc rat model of human colon cancer, under two gut microbiota conditions

first: Susheel

middle: B

first: James

last: Amos-Landgraf


title: Role of SIPA1 in chemotherapy resistance in breast cancer cells

status: Public on Dec 25 2018

city: Wuhan

first: Li

last: Su

state: -- None selected --

address: 1037 Luoyu Road

department: College of Life Science and Technology

institute: Huazhong University of Science and Technology

summary: SIPA1 is a potential transcriptional modulator of tumor metastasis and recurrence. Here we showed that the breast cancer patients with higher SIPA1 expression have a higher relapse rate and worse prognosis, especially for triple-negative breast cancer (TNBC) patients. Moreover, SIPA1 expression was found positively correlated with relapse of breast cancer patients receiving adjuvant chemotherapy. In a TNBC cell line MDA-MB-231, we identified the possible tumorigenesis and metastasis processes regulated by SIPA1, and demonstrated that SIPA1 promoted cancer stem-like feature to form tumourspheres. Tumoursphere-formed MDA-MB-231 cells were shown to be resistant to epirubicin. Then we confirmed that SIPA1 could particularly activate the CD44 promoter and upregulate CD44 expression. Furthermore, SIPA1 could promote ABCB1 expression and strengthen chemoresistance of MDA-MB-231 cells to epirubicin. In conclusion, SIPA1 is a risk factor for highly-relapse in TNBC patients and a transcriptional regulator to maintain cancer stem-like features and promote chemoresistance in breast cancer cells.

overall_design: Detection of DNA sequences bound to SIPA1 by ChIP-Seq in MDA-MB-231 cells.

first: Ang

last: Lu


title: Interrogation of human hematopoiesis at single-cell and single-variant resolution

status: Public on Mar 11 2019

first: Caleb

last: Lareau

address: 417 E 68th St, Zuckerman - ZRC 1132

institute: Memorial Sloan Kettering

summary: Incomplete annotation of cell-to-cell state variation and widespread linkage disequilibrium in the human genome represent significant challenges to elucidating mechanisms of trait-associated genetic variation. Here, using data from the UK Biobank, we perform genetic fine-mapping for 16 blood cell traits to quantify posterior probabilities of association while allowing for multiple independent signals per region. We observe an enrichment of fine-mapped variants in genes encoding for trait-relevant biological pathways and in accessible chromatin of lineage-committed hematopoietic progenitor cells. For fine-mapped regulatory variants, we gain insights into patterns of developmental enhancer activity and identify putative molecular mechanisms, including several regulatory elements that contain independent functional variants, as well as target genes. Across diverse blood cell lineages, we observe 172 fine-mapped pleiotropic variants, finding that ~90% of these tune the production of distinct lineages in consistent directions, whereas ~10% favor the production of a single lineage at the expense of others. Finally, we develop a novel analytic framework that takes advantage of fine-mapping to identify “core gene” cell type enrichments and show that this approach uniquely resolves relevant cell types within closely related populations. Applying our approach to single cell chromatin accessibility data, we discover significant heterogeneity within classically defined multipotential progenitor populations. In total, our study provides an analytic framework for single-variant and single-cell analyses and represents one of the most comprehensive maps of variant to function to date.

overall_design: Biological replicates (2 per population) were processed across 1 biological donor for bulk ATAC-seq

first: Jacob

last: Ulirsch

first: Erik

last: Bao


title: ChIP-Chip tiling array for H3k27ac in mouse MV+ (lens epithelium) and RAG cells ( renal adenocarcinoma) over panel of genes including Pax6, Sox2, Otx2, Sox9.

status: Public on Oct 18 2018

city: Edinburgh

first: nick

last: gilbert

address: Crewe Rd

department: MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine

institute: University of Edinburgh

summary:
Enhancer identification using H3k27ac ChIP-ChIP in mouse MV+ and RAG, using custom tilling array covering a 66 Mb region around Pax6 (Chr2:75,000,000-141,000,000) mm9.
Additional loci and regions, Sox2 (chr3:32,000,000-37,000,000),  Otx2 (chr14:48,500,000-50,500,000), Rax (chr18:65,500,000-68,000,000), Hba a-globin (chr11:32,050,000-32,450,000), Six3 (chr17:85,200,000-86,700,000), Sox1 (chr8:11,800,000-12,800,000), Mab21L2 (chr3:85,850,000-86,850,000), Bmp4 (chr14:46,500,000-47,500,000), NeuroD1 (chr2:79,050,000-79,600,000), Prox1 (chr1:191,700,000-192,700,000), Hmx1 (chr5:34,700,000-36,200,000), H19-Igf2 (chr7:149500000-150500000), Sox9 (chr11:110000000-116000000).

overall_design: Two cell lines, with two biological replicates of MV+ and RAG H3K27ac ChIP hybrisdised verus input DNA.

first: Adam

last: Buckle

first: Chris

last: Brackley

first: Shelagh

last: Boyle

first: Davide

last: Marenduzzo

first: Nick

last: Gilbert


first: Isai

last: Salas Gonzalez

summary: This study evaluated the transcriptomic profiles of  Arabidopsis thaliana (Col-0) plants grown along four SynCom treatments that induced differential primary root growth. Treatments Dropout Variovorax and DropoutVariovoraxBurkholderia induced primary root growth inhibition (RGI), while treatments Full and DropoutBurkholderia mantained a stereotypical long primary root.

overall_design:
All seeds were surface-sterilized with 70% bleach, 0.2% Tween-20 for 8 min, and rinsed three times with sterile distilled water to eliminate any seed-borne microbes on the seed surface. Seeds were stratified at 4 °C in the dark for two days. Plants were germinated on vertical square 10 X 10 cm agar plates with JM containing 0.5% sucrose, for 7 days. Then, 10 plants were transferred to each of the bacteria-inoculated agar plates  containg JM without sucrose
RNA-seq of Arabidopsis thaliana seedlings growing axenically, or in the presence of different bacterial Synthetic Community treatments that induced different root morphology

first: Omri

last: Finkel

first: Gabriel

last: Castrillo

first: Jeff

last: Dangl


title: RNA sequencing of genetically engineered mouse model lung tumors and normal mouse lung.

status: Public on Oct 16 2018

first: Trudy

last: Oliver

department: Pharmacology & Cancer Biology

institute: Duke University

summary: Genetically engineered mouse models (GEMM) of cancer are powerful tools to study multiple aspects of caner biology. We developed a novel GEMM for lung squamous cell carcinoma (LSCC) by genetically combining overexpression of Sox2 with loss of Lkb1: Rosa26LSL-Sox2-IRES-GFP;Lkb1fl/fl (SL). We compared gene expression profiles of SL lung tumors with normal mouse lung tissue, mouse lung adenocarcinoma (LADC) tumors from KrasLSL-G12D/+;Trp53fl/fl (KP), mouse LSCC tumors from Lkb1fl/fl;Ptenfl/fl (LP) model as well as Lenti-Sox2-Cre Lkb1fl/fl.

overall_design: Tumors were isolated from formalin-fixed paraffin-embedded (FFPE) tissue samples by microdissection and nucleic acid isolation was performed followed by single-read or paired-end RNA sequencing.

first: Gurkan

last: Mollaoglu

first: Anandaroop

last: Mukhopadhyay

first: Timothy

last: Mosbruger

first: Christopher

last: Stubben

last: Conley

first: Arjun

last: Bhutkar


title: ChIP-Chip tiling array for CTCF and Rad21 in mouse β-TC3 cells (pancreatic insulinoma) MV+ (lens epithelium) and RAG cells (renal adenocarcinoma) over panel of genes including Pax6, Sox2, Otx2, Sox9.

last: gilbert

summary:
CTCF and Rad21 ChIP-ChIP in mouse pancretic cells, pancreatic β-TC3 cells, lens epithelium MV+ cells and renal adenocarcinoma RAG cells, using custom tilling array covering a 66 Mb region around Pax6 (Chr2:75,000,000-141,000,000) mm9.
Additional loci and regions, Sox2 (chr3:32,000,000-37,000,000),  Otx2 (chr14:48,500,000-50,500,000), Rax (chr18:65,500,000-68,000,000), Hba a-globin (chr11:32,050,000-32,450,000), Six3 (chr17:85,200,000-86,700,000), Sox1 (chr8:11,800,000-12,800,000), Mab21L2 (chr3:85,850,000-86,850,000), Bmp4 (chr14:46,500,000-47,500,000), NeuroD1 (chr2:79,050,000-79,600,000), Prox1 (chr1:191,700,000-192,700,000), Hmx1 (chr5:34,700,000-36,200,000), H19-Igf2 (chr7:149500000-150500000), Sox9 (chr11:110000000-116000000).

overall_design: Three cell lines, with two biological replicates of  β-TC3, MV+ and RAG with both CTCF and Rad21 ChIP hybrisdised verus input DNA. CTCF (Antibody Cell signalling, D31H2) and Rad21 (Antibody Ab992).


title: Characterisation by Next generation Capture-C of Pax6 locus in three mouse cell lines (MV+, RAG and β-TC3 cells).

summary: NG-Capture-C profiling of chromatin interactions (using DpnII 3C and Oligo nucleotide sequence capture followed by Next generation sequencing) of enhancers, promoters and CTCF/Rad21 binding sites throughout a ~600kb region of the mouse Pax6 locus in three expression states, High (β-TC3), On (MV+) and OFF (RAG). β-TC3 cell are a mouse pancreatic β cell derived from mouse insulinoma, MV+ a lens epithelium cell line and RAG a mouse kidney adenocarcinoma cell line.

overall_design: Three cell lines where analysed and two biological replicates generated for each, with two separte panels of capture oligos.

last: Buckle


title: RNA-seq of Arabidopsis thaliana seedlings growing axenically or in the presence of Arthrobacter CL28, isolate Variovorax CL14, or both isolates together

summary: This study evaluated the transcriptomic profiles of  Arabidopsis thaliana (Col-0) plants grown along bacterial isolates whose interactions induce root morhology changes in the plant

overall_design:
All seeds were surface-sterilized with 70% bleach, 0.2% Tween-20 for 8 min, and rinsed three times with sterile distilled water to eliminate any seed-borne microbes on the seed surface. Seeds were stratified at 4 °C in the dark for two days. Plants were germinated on vertical square 10 X 10 cm agar plates with JM containing 0.5% sucrose, for 7 days. Then, 10 plants were transferred to each of the bacteria-inoculated agar plates  containg JM without sucrose.
RNA-seq of Arabidopsis thaliana seedlings growing axenically or in the presence of the primary root growth inhibitor (RGI) isolate Arthrobacter CL28, the RGI reverter isolate Variovorax CL14 or both isolates together


title: The Lineage-Defining Transcription Factors SOX2 and NKX2-1 Determine Lung Cancer Cell Fate and Shape the Tumor Immune Microenvironment

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

GSE118246 (RNA-seq)
GSE118245 (single cell RNA-seq by 10x Genomics)
GSE118244 (Chip-Seq)

overall_design: Refer to individual Series


title: ChIP-Chip tiling array for Rad21 in RAG cells (renal adenocarcinoma) over mouse Pax6 gene region. Agilent ChIP-chip, Agilent 4x180K.

summary: Rad21 ChIP-ChIP in renal adenocarcinoma RAG cells, using custom tilling array covering Pax6 mm9 (Chr2:103500000-107499954) mm9. This study is part of a large data set study gene regulotry mechnism in the Pax6 locus and complements other ChIP-ChIP data.

overall_design: RAG Rad21 ChIP hybrisdised verus input DNA using [Agilent ChIP-chip]

last: Brackley


title: Gene expression pattern of IFU5 deleted Candida albicans cells

status: Public on Feb 01 2019

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

address: 259, Apoorva 4th cross,80 feet Road,RMV 2ND STAGE

country: India

institute: Genotypic Technology

summary: To elucidate the impact of  IFU5 in Candida albicans, genome wide transcription profiling was performed in ifu5?/? mutant strain. Wild type and mutant cells were grown for 5 hours and RNA extracted from these cultures, followed by microarray profiling. Expression of six genes (EFG1, ALS3, SOD3, BMT4, COX2, NAD1) was validated by qPCR.

overall_design: Agilent Whole Genome Candida albicans 8x15k Gene Expression  (AMADID: 026377) designed by Genotypic Technology privatted Limited, Bangalore  , Labeling kit: Agilent Quick-Amp labeling Kit (p/n5190-0442)

first: Sneh

last: Panwwar


title: Heterogeneity within the PF-EPN-B subgroup

status: Public on Jul 17 2018

city: Toronto

first: Vijay

last: Ramaswamy

state: ON

address: 555 University Avenue

country: Canada

institute: Hospital for Sick Children

type: Methylation profiling by genome tiling array

summary:
Combined EPIC and 450k analysis across 212 posterior fossa ependymoma's classified as PFB using the Heidelberg Brain Tumour Classifier
Methylation profiling across 212 posterior fossa PFB ependymoma's to discern molecular heterogeneity

overall_design: 212 primary posterior fossa ependymoma's analysed by Illumina methylation arrays and processed as per manufacturers instructions

first: Marcel

last: Kool


title: Danger signals activate the innate immune system of a filamentous fungus during regeneration

status: Public on Aug 14 2018

city: IRAPUATO

first: ALFREDO

last: HERRERA ESTRELLA

state: GUANAJUATO

address: 9.6 KM CARR IRAPUATO LEON

department: LANGEBIO

country: Mexico

institute: CINVESTAV

summary: The ability to respond to injury is a biological process conserved across kingdoms, which in some cases results in regeneration of an organism’s lost part or structure.  Due to their immobility, multicellular fungi are prey to a variety of predators and are therefore constantly exposed to mechanical damage. Nevertheless, our current knowledge of how fungi respond to injury is scarce. Activation of injury responses and regeneration relies on the detection of danger or alarm signals known as Danger- or Damage-Associated Molecular Patterns. We show that Ca2+ influxes and extracellular ATP, two such signals, together with Mitogen-Activated Protein Kinases, play a key role in the control of hyphal regeneration in the filamentous fungus Trichoderma atroviride. We further show that these signaling cascades activate major transcriptional changes early after injury. We identified a set of regeneration genes related to cell signaling, stress responses, regulation of transcription, ribosome biogenesis/translation, replication and DNA repair. We uncovered the activation of an innate immune response, including HET domain genes, until now only known to participate in vegetative incompatibility. We show that fungal and animal regeneration share danger-signals, signaling cascades, and the activation of an immune system, challenging the current notion of the evolution of this process.

overall_design: Differential expression analysis of 8 conditions for triplicate. In all cases, an injured control without chemical treatment and a control without injury were included, and three biological replicates were analyzed per strain and/or treatment.

first: Elizabeth

last: Medina-Castellanos

first: José

middle: M

last: Villalobos-Escobedo

first: Meritxell

last: Riquelme

last: Read

first: Cei

last: Abreu-Goodger

first: Alfredo

last: Herrera-Estrella


title: ETV1 activates a rapid conduction transcriptional program in rodent and human cardiomyocytes

status: Public on Oct 15 2018

first: Akshay

last: Shekhar

state: NY

address: 564 1st Ave Apt 11S

department: Medicine - Cardiology

institute: NYU School of Medicine

summary: ETV1 (ER81) was identified as a highly enriched transcription factor in rapidly conducting atrial and His-Purkinje cardiomyocytes. Previous work has shown that ETV1 is a critical factor in determining fast conduction physiology in the heart. This high-throughput sequencing project aims to uncover ETV1-dependent gene networks in cardiomyocytes. These results provide insight into the role of ETV1 in the establishment of rapid conduction zones in the heart.

sample_organism:
Mus musculus
Rattus norvegicus

platform_organism:
Mus musculus
Rattus norvegicus

overall_design: Neonatal rat ventricular myocytes were isolated and purified from postnatal day 1 Sprague-Dawley wild type male and female rats using Miltenyi Biotec rat neonatal cardiomyocyte isolation kit (Miltenyi Biotec, 130-105-420) according to the manufacture's protocol. The final myocyte cultures contained enriched cardiomyocytes at a density of 3X10^6 cells per 35-mm dish. Myocytes cultures were transduced with either Ad-ETV1-GFP or Ad-GFP 24 hours after plating. RNA was extracted at day 4 post-transduction to analyze transcriptional differences with the overexpression of ETV1 in cardiomyocytes.

first: Xianming

last: Lin

first: Bin

first: Fang-Yu

last: Liu

first: Jie

last: Zhang

first: Alireza

last: Khodadadi-Jamayran

first: Aristotelis

last: Tsirigos

first: Lei

last: Bu

first: Glenn

middle: I

last: Fishman

first: David

middle: S

last: Park


title: Genome-wide methylation analysis of ependymoma using Infinium HumanMethylation 450 BeadChip

status: Public on May 17 2018

city: Chuo-ku

first: Kohei

last: Fukuoka

address: 5-1-1 Tsukiji

department: Division of Brain Tumor Translational Research

institute: National Cancer Center Research Institute

summary: Genome wide DNA methylation profiling of ependymomas. The Illumina Infinium 450k Human DNA methylation Beadchip was used to obtain DNA methylation profiles across approximately 485,500 CpGs. Samples included 83 ependymomas.

overall_design: Bisulphite converted DNA from the 83 samples were hybridised to the Illumina Infinium 450k Human Methylation Beadchip

first: Koichi

last: Ichimura


title: Clinical and genetic diversity and recurrent CXorf67 mutations across distinct molecular subgroups of posterior fossa type A (PFA) ependymoma.

status: Public on Jun 26 2018

city: Heidelberg

first: Martin

last: Sill

address: Im Neuenheimer Feld 280

department: Division of Pediatric Neurooncology

institute: DKFZ

summary: Ependymomas are neuroepithelial tumors of the central nervous system (CNS), presenting in both adults and children but accounting for almost 10% of all pediatric CNS tumors and up to 30% of CNS tumors in children under 3 years (Bouffet et al., 2009; McGuire et al., 2009; Rodriguez et al., 2009). In children, most ependymomas arise in the posterior fossa, while most adult ependymomas present around the lower spinal cord and spinal nerve roots. Ependymomas display a wide range of morphological features, and several variants are listed in the World Health Organization (WHO) classification (Ellison et al., 2016). These variants are assigned to three WHO grades (I-III), but the clinical utility of this classification is acknowledged to be limited (Ellison et al., 2011).     An increasing understanding of the genomic landscape of ependymoma and the discovery of distinct molecular groups by DNA methylation or gene expression profiling have begun to refine approaches to disease classification and prognostication, but have yet to be translated into clinical routine (Hoffman et al., 2014; Mack et al., 2014; Pajtler et al., 2017; Pajtler et al., 2015; Parker et al., 2014; Wani et al., 2012; Witt et al., 2011). Our comprehensive study of DNA methylation profiling across the entire disease demonstrated three molecular groups for each major anatomic compartment: supratentorial (ST), posterior fossa (PF), and spinal (SP) (Pajtler et al., 2015). In the ST compartment, two molecular groups (ST-EPN-RELA and ST-EPN-YAP1) align with tumors harboring specific genetic alterations, RELA and YAP1 fusion genes, which were initially discovered in a whole genome sequencing study (Parker et al., 2014). Among PF ependymomas, two of three molecular groups, PFA (PF-EPN-A) and PFB (PF-EPN-B), account for nearly all tumors; PF-SE tumors are rare, generally showing the morphology of a subependymoma (Pajtler et al., 2015).     PFA tumors are found mainly in infants and young children (median age ≈ 3yrs) and have a relatively poor outcome, while PFB tumors are generally found in young adults (median age ≈ 30yrs) and are associated with a better prognosis (Pajtler et al., 2015; Witt et al., 2011). PFA tumors show few copy number alterations (CNAs), while PFB tumors harbor multiple CNAs that tend to affect entire chromosomes. While recurrent structural variants (SVs) are found in ST ependymomas, recurrent SVs or other mutations, such as single nucleotide variants (SNVs) and insertions or deletions (indels), have not been identified in PF ependymomas to date (Mack et al., 2014; Parker et al., 2014).

overall_design: The Illumina Infinium HumanMethylation450 array and IlluminaHumanMethylationEPIC (Illumina, San Diego, USA) data from n=675 patients were used to obtain genome-wide assessment of DNA methylation, according to the manufacturer’s instructions at the Genomics and Proteomics Core Facility of the German Cancer Research Center (DKFZ) as described previously (Pajtler et al. Cancer Cell. 2015; 27 (5), 728-743)

first: Kristian

last: Pajtler

first: Ji

last: Wen

first: Tong

first: Wilda

last: Orisme

first: Vijay

last: Ramaswamy

first: Bo

last: Tang

first: Jens-Martin

last: Hübner

first: James

last: Dalton

first: Kelly

last: Haupfear

first: Sujuan

last: Jia

first: Hazel

last: Rogers

first: Chandanamali

last: Punchihewa

first: Ryan

last: Lee

first: John

last: Easton

first: Gang

last: Wu

first: Lukas

last: Chavez

first: Fredrick

middle: A

last: Boop

first: Paul

last: Klimo

first: Noah

last: Sabin

first: Robert

last: Ogg

first: Tanja

last: Mittag

last: Jones

first: Ruth

last: Tatevossian

first: Amar

last: Gajjar

first: Jinghui

first: J

last: Taylor

first: Thomas

middle: E

last: Merchant

first: Richard

last: Grundy

first: Michael

first: Stefan

last: Pfister

first: Andrey

last: Korshunov

first: Marcel

last: Kool

last: Ellison


title: Gene expression analysis after selective expression of coagulation factor FVII

status: Public on Sep 18 2018

city: Leiden

first: Henri

last: Versteeg

address: Albinusdreef 2

department: Einthoven Lab for Experimental Vascular Medicine

institute: Leiden University Medical Center

summary: Analysis of coagulation factor FVII-induced breast cancer cell transformation at gene expression level. The hypothesis tested in the present study was that expression of FVII upregulates genes involved in epithelial-to-mesenchymal transition and transformation. Results provide important information on the cellular response to tumor FVII expression with respect to pro-oncogenic programs .

overall_design: Total RNA obtained from an MDA-MB-231-based cell line (MDA-FRT; an MDA-MB-231 cell line containing a flp-in FRT site) containing human FVII cDNA (2A3-3-flTF)  compared to cells expressing an empty vector control (pcDNA).

first: Nathalie

last: Swier


title: Single-Cell RNA Sequencing Analysis Reveals Sequential Cell Fate Transition during Human Spermatogenesis

status: Public on Aug 30 2018

city: BeiJing

first: Yidong

last: Chen

address: Yiheyuan Road

institute: Peking University

summary: Spermatogenesis generates mature male gametes and is critical for the proper transmission of genetic information between generations. However, the developmental landscape and underlying molecular signals during human spermatogenesis remain unknown. Here, we examined human spermatogenesis using transcriptome-wide single-cell RNA sequencing of 2,854 individual testicular cells from donors with normal spermatogenesis (donors with normal fertility or OA) and 174 testicular cells from one donor diagnosed as having nonobstructive azoospermia (NOA). Systematic bioinformatics analyses enabled us to delineate the full developmental trajectories of human spermatogenesis. A hierarchical model was established, which was characterized by the sequential and step-wise development of three spermatogonia subtypes, seven spermatocyte subtypes, and four spermatid subtypes. Furthermore, we recapitulated key hallmarks of human spermatogenesis at the single-cell level, including spermatogonial development, mitosis-to-meiosis transition, meiotic recombination, meiotic sex chromosome inactivation, and histone-to-protamine exchange. Remarkably, BMPR1B and FGFR3 were identified as novel markers of human spermatogonial stem cells, indicating the potentially critical role of BMP and FGF signaling pathways for SSC maintenance. Further analysis identified several novel marker genes of specific cell type such as HMGA1, PIWIL4, TEX29, SCML1, and CCDC112, the expression patterns of which were confirmed via RNA FISH or immunostaining. We also demonstrated that scRNA-seq provided a platform to find differentially expressed genes correlated with one type of nonobstructive azoospermia (NOA) at the genome-wide transcriptional profiling level, which might pave way for further diagnosis and dissecting the underlying mechanisms of male infertility. Our work allows for the reconstruction of transcriptional programs inherent to sequential cell fate transition during human spermatogenesis and has implications for deciphering male-related reproductive disorders.

overall_design:
Here we performed scRNA sequencing for 2,854 individual human testicular cells including spermatogonia, spermatocytes, spermatids, and testicular somatic cells (soma) from donors with normal fertility and obstructive azoospermia.Besides, another 174 human testicular cells from one NOA male were included as an example of infertilty.

Some samples were sorted by FACS based on preliminary ploidy. These samples include "1N", "2N", or "4N" in the sample title. This information is also available in the sample characteristics.

first: Fuchou

last: Tang


title: Characterisation of three mouse cell lines by ATAC-seq (MV+, RAG and β-TC3 cells).

first: nick

last: gilbert

summary: Chromatin accessibility profiling using ATAC-seq to study and identify novel Cis-regulatory elements of MV+ a lens epithelium cell line, RAG a mouse kidney adenocarcinoma cell line and β-TC3 cell a mouse pancreatic β cell, derived from mouse insulinoma.

overall_design: Three cell lines where analysed and two biological replicates generated for each.

first: Adam

last: Buckle

first: Chris

last: Brackley

first: Shelagh

last: Boyle

first: Davide

last: Marenduzzo

first: Nick

last: Gilbert


title: Induction of genes encoding lignocellulolytic enzymes in the basidiomycete Dichomitus squalens strain FBCC312

status: Public on Apr 05 2018

city: Utrecht

first: Ronald

last: de Vries

address: Uppsalalaan 8

department: fungal physiology

institute: Centre of fungal biodiversity

summary: Expression of genes encoding plant biomass degrading enzymes in ascomycetes is controlled by transcriptional activators that respond to the presence of monomeric components of plant polymers. It can be expected that a similar system exists in basidiomycetes, but no homologs of the ascomycete regulators could be identified in basidiomycetes.

overall_design: To identify candidate regulators of plant biomass degradation in D. squalens, transcriptomics on monomeric carbon sources will be analyzed.

first: Sara

last: Casado López

first: Tedros

middle: Y

last: Issak

first: Mao

last: Peng

first: Paul

last: Daly

first: Miia

middle: R

last: Mäkelä


title: Single-cell RNA-sequencing of tumor associated neutrophils and control peripheral blood neutrophils in a novel lung squamous cell carcinoma mouse model

city: Durham

first: Trudy

last: Oliver

state: NC

address: Duke University, Box 3813, LSRC Room C138B, 308 Research Drive

summary: Tumor-associated neutrophils (TANs) can be conditioned to become “N2” pro-tumorigenic neutrophils in the tumor microenvironment. TANs have been shown to acquire N2 features and promote multiple aspects of tumor growth in mouse models of many cancers, including non-small cell lung cancer. We developed a novel mouse model for lung squamous cell carcinoma (LSCC): Rosa26LSL-Sox2-IRES-GFP;Nkx2-1fl/fl;Lkb1fl/fl (SNL). SNL mice develop tumors with short latency of ~3 months and SNL tumors have high neutrophil infiltration similar to other LSCC mouse models. We employed this novel model and single-cell RNA-sequencing to profile TANs in SNL lung tumors in comparison to peripheral blood neutrophils (PBNs) from tumor-bearing SNL mice.

overall_design: Flow cytometry sorted neutrophils (CD45+CD11B+LY6G+) from freshly isolated SNL lung tumors or peripheral blood from tumor-bearing mice were single-cell RNA sequenced with 10X Genomics.

first: Gurkan

last: Mollaoglu

first: Christopher

last: Conley


title: Targeted enhancer activation by a subunit of the integrator complex

status: Public on Mar 01 2018

city: London

first: Marco

last: Trizzino

state: UK

address: Imperial College Road

department: Life Sciences

institute: Imperial College London

summary: We investigated the genomic occupancy of INTS13 during monocytic differentiation, in in vitro differentiated monocytes and a leukemia-derived cell line. We produced genome wide data for steady state RNA (total RNA-seq) and chromatin-associated RNA (chromatin RNA-seq). Further, we used ChIP-seq to examine genome-wide distribution of INTS13, INTS11, EGR1 and NAB2, as well as the changes in occupancy of  RNAPII, H3K4me1 and H3K27ac.

overall_design: Analysis of genomic occupancy of INTS13 during monocytic differentiation

first: Elisa

last: Barbieri

first: Sarah

last: Welsh

first: Tori

last: Owens

first: Alessandro

last: Gardini


title: SOX2 genomic binding sites in lung squamous cell carcinoma GEMM tumor and cell lines

summary: SOX2 is a lineage specifier oncogene for lung squamous cell carcinoma (LSCC) and frequently amplified and overexpressed in human LSCC tumors (up to 90% of the cases). Our study demonstrated that SOX2 is a key determinant of neutrophil recruitment to tumors even in the absence of squamous histology. We generated cell lines from KrasLSL-G12D/+;Trp53fl/fl (KP) tumors that overexpress Sox2 (i.e. tumors from Lenti-Sox2-Cre infected KP mice that are validated to have Sox2 overexpression) (abbreviated as KPS) and employed chromatin immunoprecipitation sequencing (ChIP-seq) to identify genomic binding loci of SOX2 in KPS lines as well as Lkb1fl/fl;Ptenfl/fl (LP) LSCC tumors.

overall_design: SOX2 ChIP-seq in three KPS cell lines and one LP tumor

first: Jeffery

last: Vahrenkamp

first: Kristofer

middle: C

last: Berrett

first: Jason

last: Gertz


title: Global gene expression profile of dasatinib-resistant RCH-ACV cells

city: Stanford

first: Jesus

last: Duque-Afonso

state: CA

address: 265 Campus Drive

department: Pathology

institute: Stanford University

summary: Purpose: Several ALL subtypes have been described depending on their karyotype, cell type, immunophenotype and gene-expression profile. Recently, a novel ALL subtype has been described and is characterized by expression of the pre-B cell receptor (pre-BCR). Interestingly, half of the cases is associated with the chromosomal translocation t(1:19), coding for the chimeric fusion protein E2A-PBX1, which is present in about 5% of pediatric and adult ALL. Using preclinical models, we and other groups have shown very promising preclinical activity of dasatinib in pre-BCR+ ALL and early clinical evidence supports our observations. To study mechanism of acquired dasatinib resistance, we generated dasatinib-resistant pre-BCR+/E2A-PBX1+ cell lines through multiple passages in the presence of increasing drug concentrations. Whole transcriptome analysis of dasatinib-sensitive and resistant ALL cells were performed to detect systematically differentially expressed genes and enriched pathways involved in dasatinib resistance.

overall_design: RNA was isolated at three different time points (replicates) from two independent generated dasatinib-resistant RCH-ACV sublines. Replicates from control dasatinib-sensitive RCH-ACV cell sublines were used as controls.

first: Chiou-Hong

last: Lin

first: Kyuho

last: Han

first: David

middle: W

last: Morgens

first: Edwin

last: Jeng

first: Ziming

last: Weng

first: Johan

last: Jeong

first: Stephen

middle: H

last: Wong

first: Li

last: Zhu

first: Michael

last: Wei

first: Hee-Don

last: Chae

first: Kathleen

last: Sakamoto

last: Bassik

middle: L

last: Cleary


title: Genome-wide chromatin accessibility profiles of TET2-disrupted T cells from a chronic lymphocytic leukemia (CLL) patient.

status: Public on Mar 30 2018

city: Philadelphia

first: J

middle: Joseph

last: Melenhorst

state: PA

address: SPE 9-105, 3400 Civic Center Blvd.

department: Center for Cellular Immunotherapies

institute: University of Pennsylvania

summary: Following CD19-directed chimeric antigen receptor (CAR) T cell infusion, TET2 disrupted CAR+ T cells exhibited an epigenetic profile consistent with altered differentiation.

overall_design: Epigenetic profiling of CAR+ and CAR- CD8+ T cells and examination of chromatin landscape changes associated with TET2 dysfuction using lymphocytes expanded from a CLL patient.

first: Joseph

last: Fraietta

first: Morgan

last: Sammons

first: Shelley

last: Berger

first: Carl

last: June


title: Slc12a8 is a nicotinamide mononucleotide transporter that counteracts aging

status: Public on Jan 01 2019

city: Izumo

first: Jun

last: Yoshino

state: Shimane

address: 89-1 Enya-cho

institute: Faculty of Medicine, Shimane University

summary: NAD+ levels decline in multiple tissues over age, causing various age-associated pathophysiologies. Nicotinamide mononucleotide (NMN) is a key NAD+ intermediate that promotes NAD+biosynthesis and counteracts age-associated physiological decline. However, how NMN transport is regulated remains unknown. Here we report a novel NMN transporter encoded by the Slc12a8 gene. Slc12a8 is highly expressed and regulated by NAD+ in the small intestine. Knocking down this gene abrogates the transport of NMN in vitro and in vivo. Slc12a8 exhibits specificity to NMN and dependency on the sodium ion. Slc12a8 deficiency significantly decreases NAD+ levels in the jejunum and ileum, due to decreases in NMN uptake traced by doubly labeled isotopic NMN. Slc12a8 expression is upregulated in the aged ileum, contributing to the maintenance of NAD in aged mice. Thus, this newly identified NMN transporter plays a critical role in counteracting NAD+ decline during aging.

overall_design: To evaluate the effects of NAD depletion induced by FK866 treatment, we conducted microarray analyses and compared global gene expression profiles in control (DMSO 0.1%) and FK866-treated primary hepatocytes/islets.

first: Alessia

last: Grozio

first: Kathryn

middle: F

last: Mills

first: Santina

last: Bruzzone

first: Giovanna

last: Sociali

first: Kyohei

last: Tokizane

first: Hanyue

last: Lei

first: Richard

last: Cunningham

first: Yo

last: Sasaki

first: Marie

last: Migaud

first: Shin-ichiro

last: Imai


title: Mobilization of Pack-CACTA transposons in Arabidopsis suggests the mechanism of gene shuffling

status: Public on Nov 22 2018

city: Birmingham

first: Marco

last: Catoni

address: Edgbaston

department: School of Biosciences

institute: University of Birmingham

type: Genome variation profiling by high throughput sequencing

summary: Pack-TYPE transposons are a unique class of potentially mobile non-autonomous elements that can capture, merge and relocate fragments of chromosomal DNA. It has been postulated that their activity accelerates the evolution of host genes. However, this important presumption is based only on the sequences of currently inactive Pack-TYPE transposons and the acquisition of chromosomal DNA has not been recorded in real time. Analysing the DNA copy number variation in hypomethylated Arabidopsis lines, we have now for the first time witnessed the mobilization of novel Pack-TYPE elements related to the CACTA transposon family, over several plant generations. Remarkably, these elements can insert into genes as closely spaced direct repeats and they frequently undergo incomplete excisions, resulting in the deletion of one of the end sequences. These properties suggest a mechanism of efficient acquisition of genic DNA residing between neighbouring Pack-TYPE transposons and its subsequent mobilization. Our work documents crucial steps in the formation of in vivo novel Pack-TYPE transposons, and thus the possible mechanism of gene shuffling mediated by this type of mobile element.

overall_design: Genome wide sequencing of PCR-free DNA libraries from 67 Arabidopsis met1-derived epigenetic recombinant imbred lines (epiRILs) and parental controls


title: Induction of genes encoding lignocellulolytic enzymes in the basidiomycete Dichomitus squalens

first: Ronald

last: de Vries

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

overall_design: Refer to individual Series


title: Induction of genes encoding lignocellulolytic enzymes in the basidiomycete monokaryotic Dichomitus squalens strain CBS 464.89

first: Sara

last: López

first: Tedros

last: Issak

first: Mao

last: Peng

first: Paul

last: Daly

first: Miia

last: Mäkelä

middle: P


title: MEIS1 regulates hematopoiesis in hPSCs

status: Public on Jan 31 2018

city: Tianjin

first: Jiaxi

last: Zhou

state: Tianjin

address: 288# Nanjing Road, He ping district

institute: PUMC


title: RNA-sequencing of C.elegans isp-1 mutant and superoxide dismutase-isp-1 double mutants

status: Public on Aug 30 2017

city: Montreal

first: Jeremy

middle: Michael

last: Van Raamsdonk

state: QC

address: 1001 Decarie Boulevard

department: Neurology and Neurosurgery

institute: McGill University

summary: isp-1;sod double mutants have decreased lifespan, increased resistance to oxidative stress and slow physiologic rates. We performed RNA sequencing to compare gene expression between isp-1 mutants and isp-1;sod-3 and isp-1;sod-5 double mutants

overall_design: Nine biological replicates per genotype; mRNA was isolated individually from each replicate; three mRNA samples were pooled into one sample; three samples for WT, isp-1, isp-1;sod-3, isp-1;sod-5 were sequenced individually

first: Ben

middle: K

last: Johnson


title: Spotlight and whole-plant far-red enrichment at sub-organ-specific level

status: Public on Jun 26 2017

last: Pierik

address: Padualaan 8

department: Plant Ecophysiology

institute: Utrecht University

summary:
In dense stands,the earliest neighbor response is induced by touching,leading to shade avoidance. During light competion the R:FR distribution is not homogenous, leading to local differences in light quality (R:FR) within the same leaf. Hyponasty is induced by FR-signaling in the lamina tip,  which then induces local cell growth in the petiole base. Likewise, local touching of the leaf tip induces a similar phenoype.
We studied gene expression in Arabidopsis, exposed to supplemental-FR in the lamina tip and in whole rosette plant. We harvested the lamina tip and the petiole base after 5h of the treatments (white-light, supplemeted-FR in the lamina tip (local FR) and rossete plants exposed to low R:FR (whole plant FR))

overall_design: Plants were grown in single pots for 28 days (all light treatments). Gene expression measured in lamina tip and petiole base.

first: Chrysoula

last: Pantazopoulou


title: Gene signature profiles in respiratory epithelium infected with nontuberculous mycobacteria

status: Public on Oct 13 2017

city: New Haven

first: Andrew

last: Martins

address: 100 College Street Rm 1155

department: Immunobiology

institute: Yale School of Medicine

summary: The incidence of pulmonary nontuberculous mycobacterial (PNTM) disease is increasing, but host susceptibility factors are not fully understood. We infected air-liquid interface (ALI) primary respiratory epithelial cell cultures with Mycobacterium avium complex (MAC) or Mycobacterium abscessus (MAB) and performed transcriptome sequencing (RNA-Seq) to identify relevant gene expression differences. We used cells from 4 different donors in order to try to obtain generalizable data. The differentiated respiratory epithelial cells in ALI were infected with MAC or MAB at MOI of 100:1 or 1000:1, and RNA-seq was performed at 1 and 3 days after infection. We found downregulation of ciliary genes, including several identified with polymorphisms in previous PNTM cohorts. The cytokine IL-32, the superpathway of cholesterol biosynthesis and downstream targets within the IL-17 signaling pathway were all elevated. The integrin signaling pathway was more upregulated by MAB than MAC infection. Working with primary respiratory epithelial cells infected with nontuberculous mycobacteria at ALI, we identified ciliary function, cholesterol biosynthesis, chemokine production and the IL-17 pathway as major targets of host responses to infection. Some of these pathways may be amenable to therapeutic manipulation.

overall_design: 44 strand-specific RNA libraries for high-throughput sequencing were prepared (samples from 4 different donors, 57F, 75M, 69F, and 42F, for each condition) using the TruSeq Stranded mRNA Sample Preparation Kit with 750ng of total RNA according to manufacturer’s instructions.

first: Masashi

last: Matsuyama

middle: J

first: John

last: Tsang

first: Steven

last: Holland


title: RNA-seq profiling of mouse transformed culture cells as Pax6 locus cell models

status: Public on Oct 18 2018

city: Edinburgh

first: nick

last: gilbert

address: Crewe Rd

institute: University of Edinburgh

summary: Transcriptome profiling using RNA-seq of MV+, a mouse lens epithelium cell line expressing Pax6 and RAG renal adenocarcinoma cell line which does not express Pax6.

overall_design: Total RNA was collected and a Illumina sequencing libraries prepared from three biological replicates of cultured MV+ and RAG cells.

first: Adam

last: Buckle

first: Chris

last: Brackley

first: Shelagh

last: Boyle

first: Davide

last: Marenduzzo

first: Nick

last: Gilbert


title: Innate and adaptive lymphocytes sequentially shape the gut microbiota and lipid metabolism

status: Public on Nov 20 2017

summary: In support of our manuscript investigating the roles of ILCs and T cells in the maintenance of gut hoemostasis, we have performed RNAseq on terminal illeum of mice lacking either all adaptive immune cells (RAG1 -/-), deficient in T cells (TCRalpha -/-), or deficient in T cells but co-housed with wild-type mice and RAG1 -/- mice.

overall_design: Tissues from three mice per group were analysed, and the following comparisions were made: RAG1-/- vs. WT C57BL/6 and TCRa-/- co-housed vs TCRa-/- seperately housed. Differential expression genes were identified at 1% FDR using DESeq2.

first: Kairui

last: Mao

first: Ronald

middle: N

last: Germain