title: The acute transcriptome response of the midbrain/diencephalon to injury in the adult mummichog (Fundulus heteroclitus)

status: Public on Jun 03 2020

city: Charleston

first: Gary

last: Hardiman

state: SC

address: 135 Cannon Street

department: Medicine

country: USA

institute: Medical University of South Carolina

summary: Adult fish produce new cells throughout their central nervous system during the course of their lives. Furthermore, they maintain a tremendous capacity to repair damaged neural tissue. Much of the focus on understanding brain repair and regeneration in fish has been directed at regions of the brainstem and forebrain; however, the mesencephalon (midbrain) and diencephalon have received comparatively little attention. We sought to characterize differential gene expression in the midbrain/diencephalon in response to injury in the adult fish using RNA-seq. Using the mummichog (Fundulus heteroclitus), we administered a mechanical lesion traversing the midbrain optic tectum, tegmentum and underlying hypothalamus of the diencephalon and examined differential gene expression at an acute recovery time of 1hr post-injury. Comparisons of whole transcriptomes derived from isolated RNA of intact and injured midbrain/diencephalic tissue identified over 400 differentially expressed genes with the vast majority being upregulated. Using qPCR, we validated the upregulation of three differentially expressed genes, pim-2-like, syndecan-4-like, and cd83. Based on genes both familiar and novel regarding the adult brain response to injury, these data provide an extensive molecular profile giving insight into a range of cellular processes putatively involved in the injury response of a brain regenerative-capable vertebrate.

overall_design: 10 subjects x 2 samples of midbrain/diencephalon tissue from each subject = 20 samples total: 10 Lesioned (L) hemispheres and 10 contralateral Intact (I) hemispheres

first: Ellie

middle: C

last: Bisese

first: Chandler

last: Ciuba

first: Amelia

last: Davidson

first: Akanksha

last: Kaushik

first: Sabrina

last: Mullen

first: E

last: Hazard

first: Bob

last: Wilson

first: Jamie

last: Barth

first: David

last: Hollis


title: Dissecting transcriptomic signatures of genotype x genotype interactions during the initiation of plant-rhizobium symbiosis

status: Public on Jun 04 2020

city: Sesto Fiorentino

first: Giovanni

last: Bacci

state: FI

address: via Madonna del Piano, 6

department: Department of Biology

country: Italy

institute: University of Florence

type: Expression profiling by high throughput sequencing

summary: The genome X  genome interactions between rhizobium and plant in the early interaction phase was evaluated using RNA-sequencing

overall_design: Analysis of the trascriptional patterns of three strains of S. meliloti exposed to root exudates derived from three M. sativa varieties.

first: Camilla

last: Fagorzi

first: Rui

last: Huang

first: Lisa

last: Cangioli

first: Alice

last: Checcucci

first: Margherita

last: Fini

first: Elena

last: Perrin

first: Chiara

last: Natali

first: George

last: diCenzo

first: Alessio

last: Mengoni


title: Expression data from rosettes and roots of Arabidopsis  Col-0 and rpt2 grown under sulfur deficiency.

status: Public on Jun 09 2020

city: Warsaw

first: Anna

middle: Katarzyna

last: Wawrzyńska

address: Pawinskiego 5A

department: Plant Biochemistry

country: Poland

institute: Institute of Biochemistry and Biophysics Polish Academy of Sciences

summary:
Bearing in mind the prevalent occurrence of sulfur deficiency in soils, it is highly essential to comprehend the molecular processes of plant response to the changing conditions of sulfur nutrition. As there is an increasing understanding of ubiquitin-proteasomal protein degradation system participation in nutrient deficiency response, we could predict its input to the sulfur metabolism as well. Therefore, we decided to investigate the consequences of proteasome malfunction in Arabidopsis in sulfur deficient conditions.
This study presents the transcriptomic response profiles of sulfur-deficient rosettes and roots of Arabidopsis thaliana mutant plants with proteasomal malfunction.

overall_design: Arabidopsis thaliana plants (Col-0 and rpt2-3a mutant) were grown hydroponically under short-day conditions (8h light / 16h dark cycles) under full nutrient supply for 5 weeks. After that the plants were either grown as previously or transferred to sulfur deficient nutrients for 5 days. Arabidopsis rosette and root material was harvested separately and used for RNA extraction and hybridization on Affymetrix microarrays. Three biological replicates from each condition were analyzed.

last: Wawrzynska

first: Agnieszka

last: Sirko


title: Tumor reliance on cytosolic versus mitochondrial one-carbon flux depends on folate availability

status: Public on Jun 24 2020

city: Haifa

first: Tomer

last: Shlomi

address: 7-2 Emerson Building, Technion

country: Israel

institute: Technion - Israel Institute of Technology

summary: The goal of this analysis is to detect the differentially expressed genes between cells cultured in high or low folate condition.

overall_design:
RNA from 6 samples was sequenced and analyzed.
The samples can be divided into 2 groups:
Low folate condition (0.2mM) – 3 biological replicates (samples:1,3,5)
High folate condition (2mM) – 3 biological replicates (samples:2,4,6)

first: Won

middle: D

last: Lee

first: Shachar

last: Raz


title: High fat diet inhibits EV-Mediated angiogenisis

status: Public on Jul 09 2020

city: Providence

first: Guangbin

last: Shi

state: RI

address: 1 Hoppin street

department: Surgery

institute: Rhode Island Hospital

summary:
Mesenchymal stem cell-derived extracellular vesicles (EVs) have been shown to promote angiogenesis in the ischemic myocardium. This study examines the difference in vascular density, myocardial perfusion, molecular signaling, and gene expression between normal diet (ND) and high fat diet (HFD) groups at baseline and following intra-myocardial injection of EVs
We used GeneChip Gene Arrays for whole-transcriptome analysis between normal diet and high fat diet groups at baseline and following intra-myocardial injection of Evs.

overall_design: Intact male Yorkshire swine fed either Normal diet (ND) or High fat diet (HFD) underwent placement of an ameroid constrictor on their left circumflex coronary artery. Subsequently ND and HFD animals received either intra-myocardial injection of vehicle-daline as controls or EVs into the ischemic territory. Five weeks later, myocardial tissue were harvest for RNA isolation and gene array.

first: Christoph

last: Schorl


title: Oral Regeneration Is the Default Pathway Triggered by Injury in Hydra

status: Public on Jul 01 2020

city: Davis

first: Jack

last: Cazet

state: CA

address: 1 Shields Ave.

department: MCB

institute: University of California, Davis

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Animals capable of whole-body regeneration can fully restore any tissue lost due to injury. Because different types of injury may require the regeneration of different structures, transcription during whole-body regeneration needs to dynamically adapt to meet the requirements specific to any given injury. However, the regulatory mechanisms responsible for modulating the transcriptional response to injury are poorly understood at the molecular level. We therefore used the highly regenerative cnidarian polyp, Hydra vulgaris, to better understand how transcription in wounded tissue responds to its surrounding tissue environment to enable the restoration of the original body plan. We comprehensively characterized changes in transcript abundance and chromatin accessibility during two types of regeneration, oral and aboral regeneration, and found that the initial transcriptional response to injury was the same regardless of the injury’s tissue environment. This initial response included the activation of the canonical Wnt signaling pathway, which specifies oral tissue in cnidarians, likely through the direct upregulation of Wnt ligands by conserved injury responsive bZIP transcription factors. The duration of the injury-induced increase in Wnt signaling depended on the injury’s tissue context, as Wnt signaling was activated only transiently during aboral regeneration but showed sustained activation during oral regeneration. Inhibiting TCF, the transcription factor downstream of canonical Wnt signaling, delayed the onset of oral- and aboral-specific transcription genome-wide, suggesting that proper regulation of canonical Wnt signaling is critical for both types of regeneration. Finally, we found that Wnt signaling was also activated by puncture wounds, and that removing pre-existing organizers induced these injuries to undergo ectopic head regeneration. These findings suggest that head regeneration is the default response to injury in Hydra, and that other wound repair outcomes are the result of inhibitory signals produced by the surrounding tissue environment. Furthermore, our work raises the possibility that Wnt signaling may be part of an ancient and conserved wound response program that predates the split of bilaterians and cnidarians over 500 million years ago.

overall_design: Hydra vulgaris polyps were transversely bisected at the midpoint of their oral/aboral axis and allowed to regenerate for 0, 3, 8, or 12 hours. During regeneration, Hydra were either left untreated or were exposed to 5µM iCRT14, a TCF/β-catenin inhibitor. The iCRT14 treatment also included a 2 hour pre-incubation in iCRT14 prior to amputation. Head and foot regenerating tips corresponding to ~1/3 of the total length of each regenerate were then isolated and used to prepare either RNA-seq or ATAC-seq libraries. ATAC-seq replicates were made up of ~15 pooled regenerating tips and RNA-seq replicates were made up of ~30 regenerating tips. Each ATAC-seq treatment group is made up of 3-5 biological replicates. Each RNA-seq treatment group is made up of 3 biological replicates.  There are a total of 71 ATAC-seq samples and 42 RNA-seq samples.

middle: F

first: Celina

middle: E

last: Juliano


title: Transcriptomic analysis of short-term 17α-ethynylestradiol exposure in two Californian sentinel fish species sardine (Sardinops sagax) and mackerel (Scomber japonicus)

first: Gary

last: Hardiman

summary: In this study, we carried out RNA sequencing (RNAseq) of liver RNA harvested from wild sardine and mackerel exposed under laboratory conditions to EE2 and developed an analytical framework for transcriptomic analyses of species with limited genomic information. EE2 exposure altered expression patterns of key genes involved in important metabolic and physiological processes. The systems approach presented here provides a powerful tool for obtaining a comprehensive picture of endocrine disruption in aquatic organisms.

sample_organism:
Scomber japonicus
Sardinops sagax

platform_organism:
Scomber japonicus
Sardinops sagax

overall_design: Examination of transcriptome changes in sentinel species exposed to a common, environmental compound (EE2).


title: Gene expression of hypertrophic scar fibroblasts treated with glucocorticoids under mechanical stretch environment

status: Public on May 28 2020

city: Xi’an

first: Huayu

last: Zhu

state: Shaanxi

address: Changle Xilu 15

department: Department of Burns and Cutaneous Surgery, Xijing Hospital

country: China

institute: Fourth Military Medical University

summary:
After disruption of the skin, fibroblasts along wound edges are constantly exposed to high levels of stress, resulting in increased collagen synthesis and decreased apoptosis. Emerge evidences shows that, the hypertrophic scars tissue fibrosis phenomena are original from the intrinsic cellular mechanical stretch.
Traditional glucocorticoids on hypertrophic scarring have been performed for 30 years, utilizing for their anti-inflammatory, anti-allergenic and immunomodulatory effects and for their well-established, pro-apoptotic effects on hematological malignancies. To explore effects of glucocorticoid triamcinolone acetonide for responses to mechanical stress in hypertrophic scars fibroblasts (HSFB), we performed microarrays to explore the differential gene expression.

overall_design: Our protocol included hypertrophic scars fibroblasts treated with glucocorticoid were seeded in the chambers and subjected to mechanical stretch. Paired HSFBs in the control groups were treated with solvent and subjected to mechanical stretch. Then we analyzed using human gene expression arrays.

first: Dahai

last: Hu

first: Jun

last: Li


title: URT1-mediated uridylation prevents the production of spurious siRNAs targeting mRNAs in Arabidopsis thaliana

city: Strasbourg

first: Dominique

last: Gagliardi

address: 12, rue du General Zimmer

department: IBMP

country: France

institute: CNRS

type: Non-coding RNA profiling by high throughput sequencing

summary: To determine whether the developmental defects of urt1-1 xrn4-3 are linked to the biogenesis of spurious siRNAs, we analyzed small RNA libraries and indeed detected the accumulation of 21 nt siRNAs originating from mRNA loci in urt1-1 xrn4-3.

overall_design: Small RNA libraries were produced from 24 day-old in vitro grown seedlings for WT, urt1-1,  xrn4-3 and urt1-1 xrn4-3 plants.

first: Hélène

last: Zuber


title: Chromatin looping links target genes with genetic risk loci for dermatological traits

status: Public on May 27 2020

city: Manchester

first: chenfu

last: shi

address: AV Hill Building, Upper Brook Street, room 1.023

country: United Kingdom

institute: the university of manchester

summary: Chromatin looping between regulatory elements and gene promoters presents a potential mechanism whereby disease risk variants affect their target genes. Here we use H3K27ac HiChIP, a method for assaying the active chromatin interactome in two cell lines: keratinocytes and skin derived CD8+ T cells. We integrate public datasets for a lymphoblastoid cell line and primary CD4+ T cells and identify gene targets at risk loci for skin-related disorders. Interacting genes enrich for pathways of known importance in each trait, such as cytokine response (psoriatic arthritis, psoriasis) and replicative senescence (melanoma). We show examples of how our analysis can inform changes in the current understanding of multiple psoriasis associated risk loci. For example, the variant rs10794648, which is generally assigned to IFNLR1, was linked to GRHL3 in our dataset, a gene essential in skin repair and development. Our findings, therefore, indicate a renewed importance of skin related factors in the risk of disease.

overall_design: HiChIP and Hi-C data was generated for Keratinocytes (HaCaT) and CD8+ T cells (MyLa). Keratinocytes were also stimulated with IFN-?. We generated biological 2 replicates for each HiChIP sample and 1 replicate for each Hi-C sample. Accompanying RNA-seq data was also generated with 4 libraries for naive HaCaT, 3 for stimulated HaCaT, 1 for MyLa and 2 for GM12878 cells. The data was also uploaded to GSE68257 for a previous study but the processed files here are updated to reflect the new study.

first: Chenfu

first: Helen

last: Ray-Jones

first: James

last: Ding

first: Kate

last: Duffus

first: Yao

last: Fu

first: Vasanthi

middle: P

last: Gaddi

first: Oliver

last: Gough

first: Jenny

last: Hankinson

first: Paul

last: Martin

first: Amanda

last: McGovern

first: Annie

last: Yarwood

first: Patrick

last: Gaffney

first: Steve

last: Eyre

first: Magnus

last: Rattray

first: Richard

middle: B

last: Warren

first: Gisela

last: Orozco


status: Public on Jun 30 2020

city: Ann Arbor

middle: Katherine

last: Huber

state: MI

address: 1000 Wall Street

department: Computational Medicine and Bioinformatics

institute: University of Michigan

summary: scRNA and snATAC sequencing of cells harvested from the tendon injury site after a severe burn/tenotomy injury in Hoxa11 lineage traced mice allowed for differentation tracing of MSCs located in zeugopod after severe heterotopic ossification inducing injury. The use of immobilization also allowed us to determine the effects of limb immoblization on MSCs during aberrant wound healing.

overall_design: Burn and tenotomy was performed as previously described (PMID 26274052) in Hoxa11CreERt2 +/- TdTom/tom mice. Mice were allowed to ambulate normally or had their injured hindlimb immobilized.Tenotomy injury site was harvested from Day 0 (no injury baseline), Day 7 mobile (normal ambulation), Day 7 immobile, and Day 42 mobile mice. Tissue samples were digested for 20 minutes in 750U/ml Type 1 Collagenase and 7U/ml Dispase II (Gibco) in Roswell Park Memorial Institute (RPMI) medium at 37°C under constant agitation of 160rpm. Digestions were subsequently quenched with 2% FBS in PBS and filtered through 40μm sterile strainers. Cells were then washed in 2% FBS in PBS, counted and resuspended at a concentration of 1000-1200 cells/ul. Cell viability was assessed with Trypan blue exclusion on a Countess II (Thermo Fisher Scientific) automated counter and only samples with >85% viability were used for scRNA sequencing. Enough reagent was taken to sequence the transcriptome of 5000 cells according to 10x guidelines. 100,000 remaining cells were used for nuclei isolation according to the 10X Nuclei Isolation for Single Cell ATAC Sequencing protocol (available on their website).

middle: K

first: Simone

last: Marini

first: Karthik

last: Padmanabhan

first: Chase

last: Pagani

first: Benjamin

last: Levi


title: Non-biased genome-wide mRNA profiling of triazoloacridone C-1305 effects in human cell lines

status: Public on May 26 2020

city: GDANSK

first: Rafal

middle: A

last: Bartoszewski

address: Hallera 107

institute: Medical University of Gdansk

summary: In this study we used unbiased approach in the lung cancer and colon cell lines (A549 and HTC 116 respectively) to identify universal early transcriptomic signatures of C-1305 cytotoxicity, and to highlight novel pathways responsible for its biological activity. The data obtained with real time analysis was used to select appropriate doses for subsequent RNAseq and biochemical analysis. Furthermore, the RNA samples prior RNA-seq analysis were pre-verified for transcriptomic activation of apoptosis related pathways via qPCR . Since our real time analysis of cell growth have shown that 24 h exposure to C-1305 (at IC50 concentrations) is sufficient to significantly alter A549 and HTC 116 cells growth and to activate apoptosis-related transcriptional signals, we determined genome wide transcriptomic alterations in A549 and HTC 116 upon C-1305 treatment. In brief, A549 and HTC 116 cells were exposed to 3 µM or 10 µM of C-1305, respectively for 24 h day after plating. Furthermore, since our data have shown that 24 h exposure of noncancer cells epithelial lung cells 16HBE14o- to 3 µM C-1305 resulted in minimal cellular damage and loss of viability, we have included this treatment of 16HBE14o- as a negative control in our analysis. Finally, since genomic instabilities were reported for A549 cells  to avoid related artifacts, DMSO vehicle treated cells (controls) were obtained after 24 h and after 8 h of cell culture. Total RNA was extracted from the cells after 24 h exposure to C-1305 and 24 h and/or 8 h exposure to vehicle and subjected to RNA sequencing.

overall_design: Examination of C-1305 in 2 human cancer cell lines and one human normal imortalized cell line


title: Non-monotonic regulation of gene expression, neural progenitor fate and brain growth by the chromatin remodeller CHD8

city: London

first: Albert

last: Basson

address: Floor 27, Tower Wing, Guy's Hospital

department: Craniofacial Development and Stem Cell Biology

institute: King's College London

summary: Heterozygous CHD8 mutations are associated with autism and macrocephaly with high penetrance in the human population. The reported mutations may have loss-of-function (haploinsufficient), hypomorphic or dominant negative effects on protein function. To determine the effects of reducing CHD8 protein function below haploinsufficient levels on brain development, we established a Chd8 allelic series in the mouse. Chd8 heterozygous mice exhibited relatively subtle brain overgrowth and little gene expression changes in the embryonic neocortex. In comparison, mild Chd8 hypomorphs displayed significant postnatal lethality, with surviving animals exhibiting more pronounced brain hyperplasia, and significantly altered expression of over 2000 genes. Autism-associated genes were downregulated and neural progenitor proliferation genes upregulated. Severe Chd8 hypomorphs displayed even greater transcriptional dysregulation, affecting genes and pathways that largely overlapped with those dysregulated in the mild hypomorphs. By contrast, homozygous, conditional deletion of Chd8 in early neuronal progenitors resulted in the induction of p53 target genes, cell cycle exit, apoptosis and pronounced brain hypoplasia. Intriguingly, increased progenitor proliferation in hypomorphs was primarily restricted to TBR2+ intermediate progenitors, suggesting critical roles for CHD8 in regulating the expansion of this population. Given the importance of these progenitors in human cortical growth, this observation suggests that human brain development might be more sensitive to CHD8 deficiency than the mouse. We conclude that brain development is acutely sensitive to CHD8 dosage and that the varying sensitivities of different progenitor populations and cellular processes to CHD8 dosage can result in non-linear effects on gene transcription and brain growth.

overall_design: Cortical mRNA profiles of control and Chd8 heterozygous mice at E12.5, and control and Chd8 conditional knockout mice at E10.5, were generated by sequencing on the Hiseq 4000

first: Shaun

last: Hurley

first: Conor

last: Mohan

first: Philipp

last: Suetterlin

first: Jacob

last: Ellegood

first: Fabrizio

last: Rudari

first: Jason

last: Lerch

first: Cathy

last: Fernandes


title: Expression data from  TCQA-treated hAECs

status: Public on Jul 02 2020

city: Tsukuba,

first: Meriem

last: Bejaoui

state: Ibaraki

address: 1 Chome-1-1 Tennodai

country: Japan

institute: University of Tsukuba

summary:
Gene expression profiling reveals a potential role of TCQA in  neuronal and pigment cell differentiation of hAECs.
hAECs were isolated from discarded term placenta and were treated with 20 μM TCQA for seven days. Microarray gene expression profiling was conducted for biological replicates of TCQA-treated (T7) and untreated control cells on day 0 (D0) and day 7 (D7).

overall_design: RNA was extracted using Isogen (Nippon Gene Co. Ltd., Toyama, Japan). The integrity of RNA was quantified using NanoDrop 2000 spectrophotometer (Thermo Scientific, Wilmington, DE, USA). RNA samples were prepared for gene expression profiling analysis with GeneChip® 3' Expression Arrays using 3' IVT PLUS Reagent Kit (Affymetrix Inc., Santa Clara, CA, USA). Two hundred and fifty ng of total RNA from each sample was used to generate amplified and biotinylated complementary RNA (cRNA) from poly (A) RNA in a total RNA sample according to the user manual. IVT Incubation time was 16 hour. GeneAtlas® Hybridization, Wash and Stain Kit was used for hybridizing 3' IVT Array Strips according to the user manual (P/N 08-0306). Human genome array strips (HG-U219) were hybridized for 16 hours in a 45oC incubator, washed and stained and finally imaging was done with the GeneAtlas Fluidics and Imaging Station.


title: Roles of Nr4a family transcription factors in Th and Treg cell differentiation from Tnaive cells

status: Public on Jul 08 2020

city: Ichikawa

first: Takashi

last: Sekiya

state: Chiba

address: 1-7-1 Kohnodai

institute: National Center for Global Health and Medicine

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

overall_design: Refer to individual Series


title: Endogenous suppression of WNT signalling in human embryonic stem cells leads to low differentiation propensity towards definitive endoderm

status: Public on Jun 29 2020

city: Gent

first: Laurentijn

last: Tilleman

address: Ottergemsesteenweg 460

country: Belgium

institute: Ghent University

summary: We compared a transcriptome of hESC line VUB04 which has a low differentiation propensity towards definitive endoderm with transcriptomes of control hESC lines at the undifferentiated stage and after the 24-hour differentiation towards mesendoderm. The results showed that endogenous suppression of WNT signalling in VUB04 results in an inefficient switch from self-renewal to commitment during the definitive endoderm differentiation. Subsequenlty, we demonstrated that this differentiation disruption can be overcome by increasing the WNT stimulation or by inhibiting the PI3K/AKT signalling at the onset of differentiation.

overall_design: Four experimental groups (1- undifferentiated VUB01, VUB02 and VUB03, 2- undifferentiated VUB04, 3- 24h mesendoderm VUB01 and VUB02, 4- 24h mesendoderm VUB04); each experimental group conists of at least 5 samples/replicates; group 1 was compared to group 2, group 3 was compared to group 4.

first: D

last: Dziedzicka

first: M

last: Geens

first: K

last: Sermon

first: L

first: F

last: Van Nieuwerburgh


title: Ectopic expression of URT1 remodels poly(A) tail profiles in Nicotiana benthamiana

first: Dominique

last: Gagliardi

summary: 3’RACE-seq experiments were conducted to determine the impact of URT1 ectopic expression on the poly(A) tail length profile of both a GFP reporter mRNA co-expressed in Nicotiana benthamiana leaves and an endogenous mRNA encoding PATHOGENESIS-RELATED PROTEIN 2 (PR2)

overall_design: 3’RACE-seq method was used to measure poly(A) tail sizes and analyze uridylation level. This protocol is based on the ligation of a primer at the 3’ end of RNAs, and the subsequent targeted amplification by PCR of amplicons suitable for Illumina sequencing.

first: Caroline

last: de Almeida

first: Hélène

last: Scheer

last: Zuber


title: Long noncoding RNA (lncRNA) expression profiles of hypertrophic scar fibroblasts treated with glucocorticoids under mechanical stretch environment

first: Huayu

last: Zhu

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

summary:
After disruption of the skin, fibroblasts along wound edges are constantly exposed to high levels of stress, resulting in increased collagen synthesis and decreased apoptosis. Emerge evidences shows that, the hypertrophic scars tissue fibrosis phenomena are original from the intrinsic cellular mechanical stretch.
Traditional glucocorticoids on hypertrophic scarring have been performed for 30 years, utilizing for their anti-inflammatory, anti-allergenic and immunomodulatory effects and for their well-established, pro-apoptotic effects on hematological malignancies. To explore effects of glucocorticoid triamcinolone acetonide (TA) for responses to mechanical stress in hypertrophic scars fibroblasts (HSFB), we performed microarrays to explore long noncoding RNA expression.

overall_design: Our protocol included hypertrophic scars fibroblasts treated with glucocorticoid were seeded in the chambers and subjected to mechanical stretch. Paired HSFBs in the control groups were treated with solvent and subjected to mechanical stretch. LncRNA expression profiles were evaluated by customized Agilent human microarray (OE Biotech Human ceRNA Microarray, Design ID:086188).

first: Dahai

last: Hu

first: Jun

last: Li


status: Public on May 23 2020

city: Stanford

first: Zhiyong

last: Wang

state: California

address: 260 panama street

department: Plant Biology

institute: Carnegie Institute for Science

summary: RNA-seq analysis of revealed differential expression changes and alternative splicing events in acinus-2 pnn compared to WT

overall_design: RNA-seq analysis of acinus-2 pnn vs WT Arabidopsis seedlings, in triplicates, using illumina Hiseq 2000

first: Yang

last: Bi


title: Apple peel and flesh contain pro-neurogenic compounds

status: Public on May 19 2020

city: Dresden

first: Gerd

last: Kempermann

state: Saxony

address: Tatzberg 41

country: Germany

institute: German Center for Neurodegenerative Diseases (DZNE)

summary: As mammals evolved exposed to particular diets, naturally abundant compounds may have become part of the set of environmental co-determinants that shaped brain structure and function. Here we investigated whether bioactive factors found in apples directly affect hippocampal neural stem cells and promote neurogenesis in the adult. Whereas the consumption of apple juice per se neither altered adult hippocampal neurogenesis nor improved learning and memory, we did find specific direct effects of apple-derived factors on neural stem cell survival and differentiation. Our results revealed that quercetin, the most abundant flavanol in apple peel, was anti-proliferative at high concentrations but acted pro-neurogenically at low concentrations. This was confirmed in vivo, with intraperitoneally-delivered quercetin promoting survival and neuronal differentiation, without affecting proliferation, likely via the PI3 kinase-Akt and Nrf2-Keap1 pathways, respectively. Using a bio-assay-guided fractionation approach with high-resolution collision induced dissociation mass spectroscopy, we also identified additional pro-neurogenic compounds in apple flesh that were not related to flavonoids. In particular, we found that 3,5-dihydroxybenzoic acid, a weak agonist to the lactate receptor, significantly increased both in vitro and in vivo neural precursor cell proliferation and neurogenesis. Altogether, this work shows that both flavonoids and 3,5-dihydroxybenzoic acid are pro-neurogenic, not only by activating precursor cell proliferation but also through promoting cell cycle exit, cellular survival, and neuronal differentiation.

overall_design: Two experiments in different conditions both contain three replicates each of control and treated samples. Thus 12 samples in four groups.

first: Muhammad

last: Ichwan

first: Rupert

middle: W

last: Overall

first: Giannino

last: Patone

first: Kathrin

last: Saar

first: Norbert

last: Hübner


title: The transcriptomic profile of wild-type and Sur7-deletion Beauveria bassiana grown on nutrient-distinct media

city: Fuzhou

first: Long-Bin

last: zhang

state: Fujian

address: Jianping Road

department: College of Biological Science and Engineering

institute: Fuzhou University

summary: We report the application of RNA sequencing with Next Generation Sequencing technology for high-throughput status of transcripts in wild-type and Sur7-deletion Beauveria bassiana grown on nutrient-sufficient media (SDAY) or nutrient-limiting media (CDA), respectively

overall_design: The transcriptomic status of wild-type (WT) and Sur7-deletion (ΔSur7) strains grown on SDAY or CDA media, respectively

last: Zhang


title: Adaptive evolution provides a high-light stress tolerance in Synechocystis sp. PCC 6803

status: Public on May 06 2020

city: Suita

first: Kenichi

last: Ogawa

state: Osaka

address: 1-5, Yamadaoka

institute: Osaka University

summary: we obtained a HL tolerant (Tol) strain Synechocystis sp. PCC 6803 by adaptive evolution experiment that the cells were repeatedly subcultured for prolonged periods of time (52 days) under high light stress condition (7000 to 9000 μmol m-2 s-1). Although the growth of the parental strain almost stopped under 9000 μmol m-2 s-1, no growth inhibition was observed in the Tol strain. Furthermore, the growth rate was identical to that of parental strain under low light condition (40 μmol m-2 s-1). To further investigate the high light tolerant mechanisms in the Tol strain, the transcriptome was performed. The transcriptome data suggests the increase of isiA expression in the Tol strain under HL condition. The overexpression of isiA successfully enhanced the HL stress tolerance in the parental strain. The HL tolerant mechanism was different from previous reported mechanisms, such as a reduction of the light-harvesting antenna size. The tolerant strain would be an attractive host for bio-production under high light conditions.

overall_design: Microarray data were obtained from the PCC6803 and Tol grown under 4000 and 7000 μmol m-2 s-1. Three independent experiments were performed under each conditions.

first: Kenchi

first: Hiroshi

last: Shimizu


title: Joint probabilistic modeling of paired transcriptome and proteome measurements in single cells [CITE-seq of mouse spleen and lymph nodes]

status: Public on May 15 2020

city: Berkeley

first: Zoë

last: Steier

address: 378 Stanley Hall

institute: UC Berkeley

summary: The paired measurement of RNA and surface protein abundance in single cells with CITE-seq is a promising approach to connect transcriptional variation with cell phenotypes and functions. However, each data modality exhibits unique technical biases, making it challenging to conduct a joint analysis and combine these two views into a unified representation of cell state. Here we present Total Variational Inference (totalVI), a framework for the joint probabilistic analysis of paired RNA and protein data from single cells. totalVI probabilistically represents the data as a composite of biological and technical factors such as limited sensitivity of the RNA data, background in the protein data, and batch effects. To evaluate totalVI, we performed CITE-seq on immune cells from murine spleen and lymph nodes with biological replicates and with different antibody panels measuring over 100 surface proteins. With this dataset we demonstrate that totalVI provides a cohesive solution for common analysis tasks like the integration of datasets with matched or unmatched protein panels, dimensionality reduction, clustering, evaluation of correlations between molecules, and differential expression testing. totalVI enables scalable, end-to-end analysis of paired RNA and protein data from single cells and is available as open-source software.

overall_design: CITE-seq was performed on cells from the spleen and lymph nodes of two wild-type mice (biological replicates) that were processed in separate experimental runs of 10x Chromium over two days. Cells from each mouse were stained with either 111 antibodies or 208 antibodies, resulting in four samples across which 39,875 cells were captured.

first: Adam

last: Gayoso

first: Romain

last: Lopez

first: Jeffrey

last: Regier

first: Kristopher

middle: L

last: Nazor

first: Aaron

last: Streets

first: Nir

last: Yosef


title: Dual Relief of T-Lymphocyte Proliferation and Effector Function Underlies Response to PD-1 Blockade in Epithelial Malignancies

status: Public on May 01 2020

city: Toulouse

first: Clara-Maria

last: Scarlata

state: toulouse

address: 2 avenue Hubert Curien

institute: INSERM

summary: Although understanding of T-cell exhaustion is widely based on mouse models, its analysis in cancer patients could provide clues indicating tumor sensitivity to immune checkpoint blockade (ICB). Data suggests a role for costimulatory pathways, particularly CD28, in exhausted T-cell responsiveness to PD-1/PD-L1 blockade. Here, we used single-cell transcriptomic, phenotypic, and functional approaches to dissect the relation between CD8+ T-cell exhaustion, CD28 costimulation, and tumor specificity in head and neck, cervical, and ovarian cancers. We found that memory tumor-specific CD8+ T cells, but not bystander cells, sequentially express immune checkpoints once they infiltrate tumors leading, in situ, to a functionally exhausted population. Exhausted T cells were nonetheless endowed with effector and tumor residency potential but exhibited loss of the costimulatory receptor CD28 in comparison to their circulating memory counterparts. Accordingly, PD-1 inhibition improved proliferation of circulating tumor-specific CD8 T cells and reversed functional exhaustion of specific T cells at tumor sites. In agreement with their tumor specificity, high infiltration of tumors by exhausted cells was predictive of response to therapy and survival in ICB-treated head and neck cancer patients. Our results showed that PD-1 blockade–mediated proliferation/reinvigoration of circulating memory T cells and local reversion of exhaustion occur concurrently to control tumors.

overall_design: 4 head and neck, cervical, and ovarian cancers

first: Camille-Charlotte

last: Balança

first: Marie

last: Michelas

last: Tosolini

first: Maha

last: Ayyoub


title: Gene expression profiling of SARS-CoV-1/2 infected human cell lines at bulk and single-cell level

status: Public on May 04 2020

city: Berlin

first: Emanuel

last: Wyler

address: Robert Roessle Str 10

department: Berlin Institute for Medical Systems Biology

institute: Max Delbrück Center for Molecular Medicine

summary: To identify human genes and cellular pathways influencing SARS-CoV-1 and SARS-CoV-2 infection, we performed genome-wide measurements of different aspects of gene expression at the bulk and single-cell level.

overall_design:
Different human cell lines were infected with SARS-CoV-1 and SARS-CoV-2 and harvested at different time points. Gene expression profiling was measured using bulk and single-cell polyA RNA-sequencing, smallRNA sequencing, and totalRNA sequencing.

Raw data are not provided for AEC samples due to patient privacy concerns.

first: Kirstin

last: Mösbauer

first: Vedran

last: Franke

first: Asija

last: Diag

first: Lina

middle: T

last: Gottula

first: Roberto

last: Arsie

first: Filippos

last: Klironomos

first: David

last: Koppstein

first: Salah

last: Ayoub

first: Christopher

last: Buccitelli

first: Anja

last: Richter

first: Ivano

last: Legnini

first: Andranik

last: Ivanov

first: Tommaso

last: Mari

first: Simone

last: Del Giudice

first: Jan

last: Papies

first: Samantha

last: Praktiknjo

first: Marcel

last: Müller

first: Daniela

last: Niemeyer

first: Matthias

last: Selbach

first: Altuna

last: Akalin

first: Nikolaus

last: Rajewsky

first: Christian

last: Drosten

first: Markus

last: Landthaler


title: SYSTEMS ANALYSIS OF THE LIVER TRANSCRIPTOME IN ADULT MALE ZEBRAFISH EXPOSED TO THE NON-IONIC SURFACTANT NONYLPHENOL (NP).

status: Public on Jun 03 2020

city: Charleston

first: Gary

last: Hardiman

address: 135 Cannon Street

institute: Medical University of South Carolina

summary: We report the effects of exposure to the endocrine disruptor nonylphenol (NP) on transcriptome modification in the livers of  in vivo Zebrafish. Our data indicate changes in fatty acid metabolism and inflammation, pathways associated with the development of Non-Alcoholic Fatty Liver Disease (NAFLD).

overall_design: Examination of transcriptome changes in an in vivo model organism exposed to a common, environmental compound.

first: Matthew

last: Huff


title: Transcriptomic fingerprints of C. elegans exposed to sodium perchlorate.

status: Public on Apr 30 2020

first: Stephen

last: Sturzenbaum

address: 150 Stamford Street

department: Analytical, Environmental and Forensic Sciences

summary: The excessive perchlorate utilization as an oxidizer in rocket propellants and blasting agents had led to the contamination of surface and ground waters. This chemical is known to compete with iodine for binding to the thyroid membrane receptors potentially causing hypothyroidism and fetal retardation in pregnant women. Nevertheless, to date, its biological effects are not completely understood. We have investigated the molecular mechanisms responsive to perchlorate in the nematode C. elegans to nominate a candidate gene for further peruse in the development of a C.elegans perchlorate biosensor. Perchlorate (1 mg/mL) affected the transcriptional response of Regulation of developmental process, growth, defense mechanisms and stress response, among other biological processes.

overall_design: The global transcriptome was compared in wild type N2 raised in the presence or absence of sodium perchlorate at the concentration of 1 mg/mL for  for 48 hours from L1 stage.

first: Sana

last: AlSaleh

first: Leon

last: Barron

middle: R


title: Molecular connection between the TUTase URT1 and decapping activators

first: Dominique

last: Gagliardi

address: 12, rue du General Zimmer

sample_organism:
Arabidopsis thaliana
Nicotiana benthamiana


title: URT1-mediated uridylation shapes poly(A) tails in Arabidopsis

summary: Using 3' RACE-seq method, we show that the Arabidopsis TUTase URT1 shapes poly(A) tail profiles by reducing the accumulation of short-tailed mRNAs in planta. We took advantage of the depth of this method to precisely compare polyadenylation and uridylation profiles for 22 mRNAs analyzed in two biological replicates of wild-type and urt1 plants in Arabidopsis

overall_design: 3’ RACE-seq method was used to measure poly(A) tail sizes and analyze uridylation levels. This protocol is based on the ligation of a primer at the 3’ end of RNA, and the subsequent targeted amplification by PCR of amplicons suitable for Illumina sequencing.

first: Caroline

last: de Almeida

first: Hélène

last: Zuber


title: Identification of genes regulated by Foxc1,  which is a host target of miR-138

status: Public on Apr 27 2020

city: Hangzhou

first: Dongli

last: Pan

state: Zhejiang

address: 866 Yuhangtang Road

institute: Zhejiang University

summary: In other parts of this study we identified Foxc1 as a host target of miR-138 and found that Foxc1 can promote herpes simplex virus-1 (HSV-1) replication. To understand the mechanisms of this function, we performed an RNAseq experiment comparing vector (pcDNA) and pFoxchuman transfected Neuro-2a cells. After transfection, these cells were infected with HSV-1 for 5 hours at an MOI of 1 to identify viral genes regulated by Foxc1 as well as host genes.

sample_organism:
Mus musculus
Human alphaherpesvirus 1

platform_organism:
Mus musculus
Human alphaherpesvirus 1

overall_design: We transfected Neuro-2a cells with pFoxc1human for 40 hours and then infected with KOS for 5 hours at an MOI of 1 before RNAseq analysis of these cells. This dataset contain three replicates for pcDNA transfected cells and three replicates for pFoxc1human transfected cells.

first: Donald

middle: M

last: Coen


title: Whole Genome DNA Methylation Analysis of Active Pulmonary Tuberculosis Disease Identifies Novel Epigenotypes: PARP9/miR-505/RASGRP4/GNG12 Gene Methylation and Clinical Phenotypes

city: Hsinchu

first: Tingwen

last: Chen

address: No. 75, Boat Street, East District

country: Taiwan

institute: National Yang Ming Chiao Tung University

summary: We hypothesized that DNA methylation patterns may contribute to the development of active pulmonary tuberculosis (TB). Illumina’s DNA methylation 450 K assay was used to identify differentially methylated loci (DML) in a discovery cohort of 12 active pulmonary TB patients and 6 healthy subjects (HS). DNA methylation levels were validated in an independent cohort of 64 TB patients and 24 HS. Microarray analysis identified 1028 DMLs in TB patients versus HS, and 3747 DMLs in TB patients after versus before anti-TB treatment, while autophagy was the most enriched signaling pathway. In the validation cohort, PARP9 and miR505 genes were hypomethylated in the TB patients versus HS, while RASGRP4 and GNG12 genes were hypermethylated, with the former two further hypomethylated in those with delayed sputum conversion, systemic symptoms, or far advanced lesions. MRPS18B and RPTOR genes were hypomethylated in TB patients with pleural involvement. RASGRP4 gene hypermethylation and RPTOR gene down-regulation were associated with high mycobacterial burden. TB patients with WIPI2/GNG12 hypermethylation or MRPS18B/FOXO3 hypomethylation had lower one-year survival. In vitro ESAT6 and CFP10 stimuli of THP-1 cells resulted in DNA de-methylation changes of the PARP9, RASGRP4, WIPI2, and FOXO3 genes. In conclusions, aberrant DNA methylation over the PARP9/miR505/RASGRP4/GNG12 genes may contribute to the development of active pulmonary TB disease and its clinical phenotypes, while aberrant DNA methylation over the WIPI2/GNG12/MARPS18B/FOXO3 genes may constitute a determinant of long-term outcomes.

overall_design:
Bisulphite converted DNA from the 21 samples were hybridised to the Illumina Infinium HumanMethylation450 BeadChip

Genome wide DNA methylation profiling of Tuberculosis (TB) patients and healthy subjects. The Illumina Infinium HumanMethylation450 BeadChip was used to obtain DNA methylation profiles across in peripheral blood mononuclear cell samples.
Samples included 6 normal subjects and 12 TB patients among which 3 of them have 2nd samples from follow-up examination.

first: Yung-Che

first: Ting-Wen


title: Effects of host miR-138 on herpes simplex virus 1 gene expression in Neuro-2a cells and their dependence of the binding sites on ICP0 mRNA

summary: We previously showed that miR-138 can repress herpes simplex virus 1 (HSV-1) ICP0 expression by binding to ICP0 mRNA. However, in this study we found that miR-138 can also repress viral gene expression independent of ICP0. Therefore we conducted this RNAseq experiment to assess the effects of miR-138 on expression of each individual viral gene to search for other viral targets of miR-138

overall_design: We transfected Neuro-2a cell with a miR-138 mimic or a scrambled control, and then infected them with wild-type or M138 mutant virus (which contains mutations in the miR-138 binding sites in ICP0 mRNA). For both wild-type and mutant viruses, miR-138 transfected cells were compared with scrambled control transfected cells. Three biological replicates for each condition.


title: Identification of targets of miR-138 in Neuro-2a and 293T cells by RNAseq

summary: We previously showed that miR-138 can repress herpes simplex virus 1 (HSV-1) ICP0 expression by binding to ICP0 mRNA. However, in this study we found that miR-138 can also repress viral gene expression independent of ICP0. We did not find other confirmed viral targets of miR-138. Therefore we conducted these RNAseq experiments (in combination with PAR-CLIP experiments whose results are uploaded separately) to identify host targets of miR-138 in two cell lines to explain the ICP0-independent effects on HSV-1 gene expression.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: We transfected Neuro-2a cells or 293T cells with a miR-138 mimic or a scrambled control mimic, and compared miR-138 transfected with control transfected cells. Three biological replicates for each condition.


title: Discrete regulation of β-catenin-mediated transcription governs identity of intestinal epithelial stem cells [RNA-Seq]

status: Public on Apr 21 2020

city: Zurich

first: Tomas

last: Valenta

address: Winterthurerstrasse 190

department: Institute of Molecular Life Sciences

country: Switzerland

institute: University of Zurich

summary: The homeostasis of the gut epithelium relies upon continuous renewal and proliferation of crypt-resident intestinal epithelial stem cells (IESCs). Wnt/β-catenin signaling is required for IESC maintenance, however, it remains unclear how this pathway selectively governs the identity and proliferative decisions of IESCs. Here, we demonstrate that C-terminally-recruited transcriptional co-factors of β-catenin act as all-or-nothing regulators of Wnt-target gene expression. Blocking their interactions with β-catenin rapidly induces loss of IESCs and intestinal homeostasis. Conversely, N-terminally recruited co-factors fine-tune β-catenin’s transcriptional output to ensure proper self-renewal and proliferative behaviour of IESCs. Impairment of N-terminal interactions triggers transient hyperproliferation of IESCs, resulting in exhaustion of the self-renewing stem cell pool. IESC mis-differentiation, accompanied by intrinsic and extrinsic stress signalling results in a process resembling aberrant "villisation" of intestinal crypts. Our data suggest that IESC-specific Wnt/β-catenin output requires discrete regulation of transcription by transcriptional co-factors.

overall_design: RNA sequencing of bulk extracts of murine small intestinal epithelium of betacatenin-mutant mice (4xcontrol, 3xD164A, 2xDeltaC, 2xdm, 2xKO)

first: Costanza

last: Borrelli


title: Cardiac organoid model of human myocardial infarction (batch2)

status: Public on Apr 14 2020

summary: While human organoid systems have provided a powerful platform in modeling diseases caused by genetic disorders, non-genetic factors, such as lifestyle and environment, are the largest attributable factors to devastating diseases like cardiovascular disease (CVD), the leading cause of death worldwide. Specifically, myocardial infarction (MI) (i.e., heart attack) makes up ~8.5% of CVD and is a common cause of heart failure with a 40% five-year mortality after the first MI. This highlights an urgent need to develop relevant human heart failure models for drug development. This is further evidenced by the disappointing performance of heart failure drugs in clinical trials during the last decade, which has been partially attributed to the distinct differences between human patient hearts and animal heart failure models. Here, we combined major non-genetic causal factors of MI with our previously established cardiac organoids to create the first human organoid model of cardiac infarction. In particular, we leveraged the diffusion limitation in 3D microtissues to recreate the nutrient diffusion gradient across infarcted hearts (i.e., infarct-border-remote zones) in human cardiac organoids to induce cardiac organotypic response to infarction. This enabled the recapitulation of major MI hallmarks in human cardiac organoids at the transcriptomic, structural and functional level.

overall_design: Three Control Organoid replicates versus Three Infarct Organoid replicates

first: Dylan

middle: J

last: Richards

first: Yang

last: Li

first: Jenny

last: Yao

first: Robert

last: Coyle

first: Jia

last: Jia

first: Brooke

last: Damon

first: E

middle: S

last: Hazard

last: Menick

first: Hai

first: Tong

last: Ye

first: Ying

last: Mei


title: Global investigation by TAILseq of mRNA 3' ends in Arabidopsis thaliana flowers

status: Public on May 28 2020

city: Strasbourg

first: Dominique

last: Gagliardi

institute: CNRS

summary: To estimate mRNA uridylation levels at a transcriptome-wide level, TAIL-seq libraries were generated for three biological replicates of Col-0 plants.

overall_design: TAILseq method (Chang et al. 2014, https://doi.org/10.1016/j.molcel.2014.02.007) was used to measure poly(A) tail sizes and analyze uridylation levels.

first: Caroline

last: de Almeida

first: Hélène


title: Discrete regulation of β-catenin-mediated transcription governs identity of intestinal epithelial stem cells [ATAC-Seq]

overall_design: bulk ATAC sequencing of small intestinal crypts of betacatenin-mutant mice (3xcontrol, 3xD164A)


title: Discrete regulation of β-catenin-mediated transcription governs identity of intestinal epithelial stem cells

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

overall_design: Refer to individual Series


title: Cell and molecular transitions during efficient dedifferentiation: population timecourses

status: Public on Apr 07 2020

first: Jonathan

last: Chubb

address: Gower Street

department: MRC Laboratory for Molecular Cell Biology

institute: University College London

summary: Transcriptomic analysis of dedifferentiation in Dictyostelium discoideum, with comparison to forward development

overall_design: RNAseq timecourses sampling the dedifferentiation of 14h developed cells in two different nutrient conditions; liquid growth media (Media, 0 to 18 h) and Klebsiella bacteria (Bacteria, 0 to 24 h), compared with mock dedifferentiation in phosphate buffer (Buffer, 0 to 6 h), a reference sample of undifferentiated cells (Undifferentiated) and a timecourse of forward development (Development, 0 to 14 h). All timecourses performed in duplicate.

first: John

last: Nichols

first: Vlatka

last: Antolovic

first: Jacob

last: Reich

first: Sophie

last: Brameyer

first: Peggy

last: Paschke


title: Cell and molecular transitions during efficient dedifferentiation


title: Discrete regulation of β-catenin-mediated transcription governs identity of intestinal epithelial stem cells [scRNA-Seq]

first: Tomas

last: Valenta

overall_design: single cell RNA sequencing of small intestinal crypts of betacatenin-mutant mice (3xcontrol, 3xD164A)

first: Costanza

last: Borrelli


title: RNA-Seq analysis of murine pro-B BAF3 cells transfected with oncogenic form of receptor tyrosine kinases

status: Public on Apr 10 2020

city: Shanghai

first: Min

last: Huang

address: 555, Zuchongzhi Road

institute: Shanghai Institute of Materia Medica

summary: To identify gene expression changes associated with receptor tyrosine kinase (RTK) activation, we performed RNA-Seq analysis of murine pro-B BAF3 cells over-expressing the oncogenic form of EGFR (EGFR-L858R-T790M), FGFR (TEL-FGFR1 fusion), MET (TPR-MET fusion) or RET (CCDC6-RET fusion) genes. We reported the RTK-driven transcriptional reprogramming of metabolic genes.

overall_design: Murine pro-B BAF3 cells were stably transfected with EGFR-L858R-T790M, TEL-FGFR1 fusion, TPR-MET fusion or CCDC6-RET fusion. The gene expression change versus BAF3 parental cells were analyzed using RNA-seq analysis. Numbers of significantly activated genes in different RTK-driven cells had been identified.

last: Jin

first: Aiwei

last: Bi

first: Xiaojing

last: Lan

first: Jun

last: Xu

first: Minjia

last: Tan

first: Jing

last: Ai

first: Hua

last: xie

first: Tao

last: Zhang

first: Dandan

last: Liu

first: Ruimin

first: Yue

last: Song

first: Elaine

last: Leung

first: Jian

last: Ding

first: Meiyu

last: Geng

first: Shuhai

last: Lin


title: Super-enhancer redistribution as a mechanism of broad gene dysregulation in repeatedly drug-treated cancer cells [dataset 3]

status: Public on Apr 01 2020

city: San Diego

first: Qi

last: Ma

address: 9500 Gilman Dr,

institute: UCSD

summary: We provide a series of chromatin and transcriptomic profiles to establish the short-term and long-term effects of cisplatin treatment in ovarian cancer A2780 cells.

overall_design: All ChIP-Seq, GRO-seq, RNA-seq, and ribosome-profiling experiments were designed to understand the effects of cisplatin on 6 different layers of gene-expression regulation in cancer cells.

first: Ivan

last: Garcia-Bassets


title: Differentially expressed miRNAs in mice renal tubular epithelial cells which co-cultured with mesenchymal stem cells vs controls

city: suzhou

first: shouli

last: wang

address: renai road 199, suzhou industrial park

department: pathology

institute: soochow university school of medicine

summary: In order to study the effect of mesenchymal stem cells on miRNAs in renal tubular epithelial cells during renal fibrosis, and to find new treatment methods for renal fibrosis, we used TGF-β1 to stimulate mouse tubular epithelial cells, co-cultured with mesenchymal stem cells for 48 hours, and collected renal tubular epithelial cells .The renal tubular epithelial cells that were only stimulated by TGF-β1 were used as a control group. High-throughput miRNA sequencing was used to detect the increased and decreased miRNAs after co-culture.

overall_design: C57 / BL6 mouse renal tubular epithelial cells were stimulated with TGF-β1 for 48 hours and divided into two groups. One group was used as the experimental group for co-culture with mouse mesenchymal stem cells for 24 hours, and the other group was used as the control group without treatment, each with 3 replicates.

first: Shouli

last: Wang

first: Lei

last: Wu

first: Maomin

last: Sun


title: Transcriptional profile of the CNS of pups from Zika virus-infected SJL mothers treated with nanoliposomes loaded with AHR antagonist CH223191

status: Public on Apr 13 2020

city: Boston

first: Francisco

middle: Javier

last: Quintana

state: MA

address: 60 Fenwood Road

department: Neurology

institute: Brigham and Women's Hospital

summary: SJL pregnant mice were infected with Zika virus and treated with nanoliposomes loaded with AHR antagonist CH223191 or control nanoliposomes. RNA-Seq analysis was performed in CNS samples from the pups.

overall_design: CNS was obtained from pups from Zika virus-infected mothers treated with empty nanoliposomes  (control, n=4 pups) and pups from Zika virus-infected mothers treated with CH223191-loaded nanoliposomes (n=3). RNA was extracted and RNA-Seq analysis was performed.

first: Federico

last: Giovannoni

first: Carolina

last: Polonio

first: Zhaorong

last: Li

first: Jean-Pierre

last: Peron


title: Super-enhancer redistribution as a mechanism of broad gene dysregulation in repeatedly drug-treated cancer cells [dataset 2]


title: Tuberculosis biomarker identification cohort

status: Public on Mar 30 2020

city: Borstel/Suelfeld

first: Maja

last: Reimann

state: Schleswig Holstein

address: Parkallee 35

department: Clinical infectious disease

institute: Research Center Borstel

summary: Sample collection and  identification of biomarker for personalized therapy in tuberculosis patients

overall_design: 329 Samples of 80 patients with non MDR and MDR TB, repeated measurements after therapy start (14 days, culture conversion, sputum conversion, 6 months, 10 months, 15 months and therapy end); one time measurements of 10 healthy controls

first: Jan

last: Heyckendorf

first: Sebastian

last: Marwitz


title: Genome-wide analysis of the transcriptional profile of Zika virus-infected HepG2 cells

summary: We report the identification of pathways upregulated by Zika virus infection in HepG2 cells 48 h post infection

overall_design: We obtained a list of  diferentially expressed genes by comparing HepG2 cells infected with Zika virus (n=3 independent experiments) to mock-infected HepG2 cells (n=3 independent experiements). This list was later used for pathway overrepresentaion analysis.

first: Emily

middle: C

last: Tjon


title: Romanian MDR tuberculosis cohort

summary: Validation Cohort for Biomarker for personalized therapy for Tuberculosis

overall_design: 262 samples of 52 at different measurement times during TB-treatment (0 days, 14 days, 28 days, 6 months, 10 months, 15 months and 20 months)


title: Integrated small RNA genomics of mosquito cells reveal dynamic evolutionary responses to viruses and transposons.

status: Public on Apr 11 2020

city: BOSTON

first: NELSON

last: LAU

address: 72 E Concord St K219, Dept of Biochemistry

department: Biochemistry and Cell Biology

institute: Boston University Chobanian & Avedisian School of Medicine

summary: We present an integrated resource of profiling and analysis of small RNAs from mosquiot cells and tissues from 4 main species to determine how the viruses and transposons compare in the production of small regulatory RNAs.

sample_organism:
Aedes aegypti
Aedes albopictus
Anopheles gambiae
Culex quinquefasciatus

overall_design: Various mosquito cell lines and tissues were cultured or obtained, dissected to separate gonads from soma, and then total RNA was extracted and the small RNAs were purified and converted to Illumina libraries for high throughput sequencing.

first: Nelson

last: Lau

first: Qicheng

first: Satyam

last: Srivastav

first: Stephanie

last: Gamez


title: AMPKα1 deletion in myofibroblasts exacerbates post myocardial infarction fibrosis by a miR-125b and Connexin 43 mechanism

status: Public on Mar 25 2020

city: Woluwé

first: Jérôme

last: Ambroise

address: Avenue Hippocrate 54

department: Institut de Recherche Expérimentale et Clinique

institute: Université catholique de Louvain

summary: Myofibroblasts (MFs) are crucial components of the fibrotic remodeling after myocardial infarction (MI). We have previously demonstrated the centrality of AMPKα1 in post-MI remodeling. Here, we investigate the effects of MF-specific deletion of AMPKα1 on left ventricular (LV) adaptation following MI, and the underlying molecular mechanisms. Importantly, MF-restricted AMPKα1 conditional knockout (cKO) hearts exhibit exacerbated post-MI adverse LV remodeling and are characterized by exaggerated fibrotic response, compared to wild-type (WT) hearts. Myofibroblast proliferation significantly increases in cKO infarcted hearts, coincident with a significant reduction of Connexin 43 (Cx43) expression in MFs. Mechanistically, lack of AMPKα1 in MFs enhances miR-125b expression, which, in turn, downregulates Cx43. Collectively, our data demonstrate a cardinal role for MF-AMPKα1 in cardiac remodeling, as its lineage-specific inactivation accentuates fibrosis and LV dilatation following MI. The deleterious effects of MF-specific AMPKα1 deletion are mediated via Cx43, and its post-transcriptional regulation by miR-125b.

overall_design: We investigated the impact of AMPKa1 invalidation on mRNA profile in cultured human cardiac fibroblasts. We used 5 replicates per group,

first: Cécile

last: Dufeys

first: Sandrine

last: Horman


title: PHOTOTROPIN 1 and 2 regulate photosynthesis and UV-induced oxidative stress and cell death

status: Public on Mar 26 2020

city: Gent

first: Patrick

last: Willems

address: Technologiepark 927

department: PSB

institute: Ghent University

summary: Phototropins are plasma membrane‐associated photoreceptors of blue light. Arabidopsis thaliana genome has two genes, PHOT1 and PHOT2, encoding two phototropins that mediate phototropism, chloroplast positioning and stomatal opening. They are well characterized in terms of photomorphogenetic processes, but so far little was known about their involvement in photosynthesis and response to stress factors triggering oxidative stress and cell death. This work fills the gap in our understanding of PHOT1 and PHOT2 involvement in these processes. We used UV-C treatment to promote oxidative stress and cell death in Arabidopsis thaliana wild-type (Col-0 gl1), phot1, phot2 and phot1/phot2 mutants. Using RNAseq we identified genes differentially expressed in phot mutants, in comparison to the wild-type, in both non-stress conditions and after UV-C stress.

overall_design: Four genotypes (wild-type, phot1, phot2, phot1/phot2) x two conditions (non-treated and UV-treated)

first: Weronika

last: Czarnocka

first: Frank

last: Van Breusegem

first: Stanislaw

last: Karpinski


title: Super-enhancer redistribution as a mechanism of broad gene dysregulation in repeatedly drug-treated cancer cells [dataset 1]

first: Qi

last: Ma

first: Ivan

last: Garcia-Bassets


title: Novel Model for Vertical Zika Virus Transmission via Decidual Cell-mediated Infection of Anchoring Villi

status: Public on Mar 14 2020

city: Tampa

first: Ozlem

last: Guzeloglu Kayisli

state: FL

address: 12901 Bruce B Down Blvd

department: Ob and Gyn

institute: University of South Florida

summary: Vertical transmission of Zika virus (ZIKV) causes severe fetal defects, but the exact pathogenic mechanism is unclear. We identified up to a 10480-fold higher expression of viral attachment factors AXL, GAS6 and PROS1 and 3880-fold increase in ZIKV infectiousness/propagation in decidual cells (DCs) versus trophoblasts. Moreover, levels of viral attachment factors and ZIKV are significantly increased while expression of innate immune response genes are significantly decreased in first trimester versus term DCs. ZIKV-infected DC supernatants increased cytotrophoblast infection up to 252-fold compared to directly infected cytotrophoblasts. Tizoxanide treatment efficiently inhibited ZIKV infection in both cell types. We conclude that decidual cells may act as reservoirs for trimester-dependent placental transmission of ZIKV, accounting for the higher ZIKV infection susceptibility and more severe fetal sequelae observed in early versus late pregnancy. Moreover, tizoxanide is a promising agent in preventing perinatal ZIKV transmission.

overall_design: Primary cultured decidualized term decidual cells (TDC), cytotrophoblasts (CTB) and syncytiotrophoblasts (STB) obtained from term placental samples were subjected to RNA extraction, quantification, and evaluation, followed by hybridization on Illumina BeadChip. Three biological replicates were used (N=9 total samples).

first: O

last: Guzeloglu-Kayisli

first: X

last: Guo

first: Z

last: Tang

first: N

last: Semerci

first: A

last: Ozmen

first: K

last: Larsen

first: D

last: Mutluay

first: S

last: Guller

first: F

last: Schatz

first: U

last: Kayisli

first: C

last: Lockwood


title: Redefining the heterogeneity of peripheral nerve cells in health and autoimmunity

city: Muenster

first: Michael

last: Heming

address: Albert-Schweitzer-Campus 1, Bldg A1

department: Department of Neurology with Institute of Translational Neurology

institute: University Hospital Muenster

summary: Peripheral nerves contain axons and their enwrapping glia cells named Schwann cells (SC) that are either myelinating or non-myelinating (nmSC). Our understanding of other cells in the peripheral nervous system (PNS) remains limited.   Here, we provide an unbiased single-cell transcriptomic characterization of the non-diseased rodent PNS. We identified and independently confirmed novel markers of previously underappreciated nmSC and nerve-associated fibroblasts. We also found and characterized two distinct populations of nerve-resident homeostatic myeloid cells that transcriptionally differed from central nervous system microglia. In a model of chronic autoimmune neuritis, homeostatic myeloid cells were outnumbered by infiltrating lymphocytes which modulated the local cell-cell interactome and induced a specific transcriptional response in glia cells. This response was partially shared between the peripheral and central nervous system glia identifying common immunological features across different parts of the nervous system. Our study thus identifies novel subtypes and cell-type markers of PNS cells and a partially conserved autoimmunity module induced in glia cells.

sample_organism:
Mus musculus
Rattus norvegicus

platform_organism:
Mus musculus
Rattus norvegicus

overall_design: Single cell RNA sequencing of undiseased C57BL/6 mice and naive Lewis rats to explore the healthy PNS. ScRNA-seq of NOD control and ICAM-1-/-NOD mice was performed to analyze chronic autoimmune neuritis.

first: Jolien

last: Wolbert

first: Xiaolin

last: Li

first: Gerd

last: Meyer zu Hörste


title: Genome-wide transcriptional responses to nucleotides in zebrafish (Danio rerio) embryos

status: Public on Mar 23 2020

first: Gary

last: Hardiman

state: SC

address: 135 Cannon Street

department: Medicine

summary:
Purpose:To investigate the transcriptomic profiles in zebrafish embryos exposed externally to nucleotides at a critical develpomental window (3-7 days post fertilization) determine biological processes and pathways based on differentially expressed gene transcripts using High Throughput Sequencing (HTS).
Methods:Total mRNA profiles of 7 dpf zebraifsh embryos after exposure to 10-5M ATP, AMP, adenosine and adenine were generated by deep sequencing, in triplicate, using Illumina HiSeq2500
Results: There were many differentially expressed genes; including ubiquitin-, actin-, and tubulin-related, showing that the cytoskeleton was altered; other DEGs involved with purine binding, specifically guanine, which was expected as the mixture was composed of purines; DEGs involved with GTP binding were also upregulated, suggesting increased cell signaling,

overall_design: Total mRNA profiles of 7 dpf zebraifsh embryos after nucelotide exposure were generated by deep sequencing, in triplicate, using Illumina HiSeq2500.

first: Angela

last: Shamchuk

first: Brian

last: Blunt

first: Danielle

middle: D

last: Lyons

first: Mo

middle: Q

last: Wang

first: Anastasia

last: Gasheva

first: Carlie

last: Lewis

first: Kirsten

last: Tomlin

first: Starr

last: Hazard

first: Gerard

first: Keith

last: Tierney


title: Super-enhancer redistribution as a mechanism of broad gene dysregulation in repeatedly drug-treated cancer cells

first: Qi

last: Ma


title: Tuberculosis biomarker validation cohort

first: Maja

last: Reimann

summary: Sample collection and identification of biomarker for personalized therapy in tuberculosis patients

overall_design: 335 Samples of 60 patients with non MDR and MDR TB, repeated measurements after therapy start (14 days, culture conversion, sputum conversion, 6 months, 10 months, 15 months and therapy end)

first: Jan

last: Heyckendorf

first: Sebastian

last: Marwitz


title: Quantitative Analysis of  Wild Type and CTGF-/- Retinal Transcriptomes During Postnatal Vascular Development

status: Public on Mar 13 2020

city: Brooklyn

first: Brahim

last: Chaqour

state: NY

address: 450 Clarkson Avenue

department: Cell Biology

institute: SUNY Downstate Medical Center

summary:
Purpose:  The goal of this study is to compare the retinal transcriptomes of wild-type and CTGF-/- mice during postnatal development of the retinal vasculature.
Results:  The results from principal component analysis (PCA) showed a distinguishable gene expression profiling among the samples. The expression level (FPKM value) of known genes and transcripts were calculated using ballgown through the transcript abundances estimated with StringTie. The number of identified genes and transcripts per group was calculated based on the mean of FPKM in group > 0.5. We have identified 24,818 transcripts for 12946 gene count in WT mouse retinas and 24708 transcripts for 12852 gene count in knockout mouse retinas. The significantly enriched GO terms of the differentially expressed genes include those involved in protein, lipid and DNA metabolism, neurogenesis and signal transduction and gene regulation.

overall_design: Methods: Retinal mRNA profiles of 7-day-old wild-type (WT) and connective tissue growth factor-deficient (CTGF-/-) mice (obtained using inducible Cre/lox system) were generated by deep sequencing, in triplicate. Total RNA from each sample was enriched by oligo (dT) magnetic beads  to remove rRNA. RNA-seq libraries were prepared using KAPA Stranded RNA-Seq Library Prep Kit (Illumina). The completed libraries were qualified with Agilent 2100 Bioanalyzer and quantified by absolute quantification qPCR method. To sequence the libraries on the Illumina HiSeq 4000 instrument, the barcoded libraries were mixed, denatured to single stranded DNA in NaOH, captured on Illumina flow cell, amplified in situ, and subsequently sequenced for 150 cycles for both ends on Illumina HiSeq instrument.  Image analysis and base calling were performed using Solexa pipeline v1.8 (Off-Line Base Caller software, v1.8). Sequence quality was examined using the FastQC software. The trimmed reads (trimmed 5’, 3’-adaptor bases using cutadapt) were aligned to reference genome using Hisat2 software. The transcript abundance for each sample was estimated with StringTie, and the FPKM value for gene and transcript level was calculated with R package Ballgown. The differentially expressed genes and transcripts were filtered using R package Ballgown. The novel genes and transcripts were predicted from assembled results by comparing to  the reference annotation using StringTie and Ballgown, then use CPAT to assess the coding potential of those sequences.

first: Sangmi

last: Lee


title: Interaction with Cholangiocytes and Neutrophils

city: NEW HAVEN

first: Michael

last: Nathanson

state: CONNECTICUT

address: 300 Cedar Street, TAC, S230

department: Internal medicine

institute: Yale university

summary: Alcoholic hepatitis (AH) is a life-threatening disease with limited treatment options. The presence of cholestasis worsens prognosis but the responsible mechanism is unknown. AH results in infiltration of polymorphonuclear neutrophils (PMNs) in the liver, and cholestasis often reflects bile duct pathology, so we investigated whether and how PMNs interact with cholangiocytes in AH.

overall_design: RNA was isolated from NHC with non-coculture condition and after coculture condition.

first: Masahiro

last: Takeuchi

middle: H


title: A single-cell RNA-seq atlas of the pathogenic stage of Schistosoma mansoni identifies a key regulator of blood feeding

status: Public on Mar 11 2020

city: Dallas

first: George

last: Wendt

state: TX

address: 6001 Forest Park Road, ND7.300

department: Pharmacology

institute: University of Texas Southwestern Medical Center

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

overall_design: Refer to individual Series


title: Comparison of age-related changes in gene expression of 2 rat skeletal muscles

city: Lausanne

first: Jerome

last: Feige

address: EPFL Innovation Park, Building H

department: Musculo-Skeletal Health

institute: Nestle Institute Of Health Sciences

overall_design: 5 groups of age (8 months, 18 months, 20 months, 22 months and 24 months) were analyzed, with 9-10 replicates per group. Gastrocnemius and Triceps were collected for each animal.


title: Development of gene expression signatures for oral cancer

status: Public on Mar 06 2020

city: Chiba　City

first: Yutaro

last: Kase

state: Chiba Prefecture

address: 1-8-1 Inohana, Chuo-ku, Chiba, 260–8670, Japan

institute: Department of Oral Science, Graduate School of Medicine, Chiba University

summary: To further development of gene expression approach to squamous carcinoma, we have employed whole genome microarray expression profiling as a discovery platform to identify genes with the potential to reveal the relation between oral squamous carcinoma (OSCC) and human normal oral mucosal epithelial keratinocytes.

overall_design: 11 Samples: 8 OSCC and 3 human normal oral mucosal epithelial keratinocytes.


title: Role of MPK4 in pathogen-associated molecular pattern-triggered alternative splicing in Arabidopsis

status: Public on Mar 03 2020

city: Thuwal

first: Prof. Heribert

last: HIRT

address: 4700 KAUST

country: Saudi Arabia

institute: KAUST

summary: Alternative splicing (AS) of pre-mRNAs in plants is an important mechanism of gene regulation in environmental stress tolerance but plant signals involved are essentially unknown. Pathogen-associated molecular pattern (PAMP)-triggered immunity (PTI) is mediated by mitogen-activated protein kinases and the majority of PTI defense genes are regulated by MPK3, MPK4 and MPK6. These responses have been mainly analyzed at the transcriptional level, however many splicing factors are direct targets of MAPKs. Here, we studied alternative splicing induced by the PAMP flagellin in Arabidopsis.

overall_design: Using RNA-seq to study the Col-0 and summ2 mpk4 Transcriptomes

first: Jeremie

last: Bazin

first: Kiruthiga

last: Mariappan

first: Yunhe

last: Jiang

first: Thomas

last: Blein

first: Ronny

last: Voelz

first: Martin

last: crespi

first: Heribert

last: Hirt


title: tRNA quantification of five human cell lines by hydro-tRNAseq and small RNA-seq

status: Public on Feb 28 2020

city: Barcelona

first: Luis

last: Serrano

address: C/ Dr. Aiguader, 88

department: Systems Biology

country: Spain

institute: Centre for Genomic Regulation (CRG)

summary: We analyze whether tRNA quantifications based on small RNA-seq data are informative enough to distinguish between different human cell lines covering multiple tissue types. We therefore apply both small RNA-seq and Hydro-tRNAseq to HEK293 (kidney), HCT116 (colon), HeLa (cervix), MDA-MB-231 (breast), and BJ fibroblasts. First, the correlations between the two methods of identical samples and computational mapping pipeline range between 0.93 and 0.96 for all cell lines. tRNA quantifications from both protocols are compared and significantly higher Spearman correlations are obtained within matching samples versus mismatching cell lines. In consequence, we demonstrate that small RNA-seq quantifications of sample-specific tRNA profiles show a good agreement with conventional tRNA-seq.

overall_design: This study contains 30 samples.  Three replicates for each of the five cell lines. For HCT116, BJ fibroblasts and MDA-MB-232, both hydro-tRNAseq and small RNA-seq are determined. For HEK293 and HELA, the  hydro-tRNAseq raw files have already been published (ArrayExpress under accession number E-MTAB-8144).

first: Xavier

last: Hernandez-Alias

first: Hannah

last: Benisty

last: Schaefer


title: A Time-series transcriptome analysis of Rosiglitazone effects in mice neonatal cardiomyocytes.

status: Public on Feb 26 2020

city: Charleston

first: Gary

last: Hardiman

institute: Medical University of South Carolina

summary: Rosiglitazone is a member of the thiazolidinedione class of drugs, an anti-diabetic drug known for being a ligand of peroxisome proliferation activating receptors γ (PPARγ), a group of nuclear hormone receptors that are involved in the regulation of genes related to glucose and lipid metabolism. The use of Rosiglitazone has been shown to increase the risk of congestive heart failure in type II diabetes patients due to increased fluid retention and plasma volume. Our data show that the effects of Rosiglitazone on cardiomyocytes occur really early within a great increase in magnitude in time but consistent in the pathways affected. Also, the initial deleterious effect triggers a protective molecular response at 24 hours of exposure that is maintained at 48h but also accompanied by further activation of the system that can damage the heart.

overall_design: Neonatal rat ventricular myocytes (NRVMs) were harvested from 1-day old Harlan Sprague-Dawley Rats (Rattus norvegicus albinus) and cultured as described by Sprenkle et al 1995. The cultured cells were divided In four Groups, control and exposure time of Half-hour, 24-Hours, 48-Hours.

first: Willian

last: da Silveira


title: Voltage-gated sodium channel (VGSC) beta1 subunit-intracellular domain (Beta1-ICD) overexpression in Chinese hamster lung cells

status: Public on Feb 08 2020

city: Ann Arbor

first: Bioinformatics

last: Core

state: MI

address: BRCF Bioinformatics Core, 2800 Plymouth Rd

institute: University of Michigan

summary: Overexpression of hypothesized transcriptional regulator in a cell line to compare gene expression changes to in vivo knockout of upstream signaling pathway component.  All samples are from Chinese hamster lung cells.

overall_design: RNA-Seq, 2 groups with 4 samples each.  Four samples have stable overexpression of human VGSC beta1 subunit-intracellular domain (Beta1-ICD) tagged with V5 followed by a 2A peptide and eGFP (WTICD) and four controls have overexpression of eGFP alone (eGFP).

first: Lori

last: Isom

first: Alexandra

last: Bouza

first: Rebecca

last: Tagett

first: Dana

last: King


title: Differential gene expression in postnatal day 10 Scn1b+/+ vs. Scn1b -/- cardiac ventricle

summary: Scn1b null mice are a model of a severe developmental and epileptic encephalopathy called Dravet Syndrome (DS). The goal of this study was to identify changes in gene expression between Scn1b wild-type and Scn1b null mice before seizure onset (postnatal day 10)

overall_design: RNA-Seq in postnatal day 10 Scn1b+/+ vs. Scn1b -/- mouse cardiac ventricle


title: Strand-specific single-cell methylomics reveals distinct modes of DNA demethylation dynamics in preimplantation mouse and human embryos

status: Public on Feb 13 2020

city: Utrecht

first: Maya

last: Sen

address: 8 Uppsalalaan

country: Netherlands

institute: Hubrecht Institute

type: Methylation profiling by high throughput sequencing

summary: DNA methylation (5mC) is central to cellular identity and the global erasure of 5mC from the parental genomes during preimplantation mammalian development. This process is critical to reset the methylome of terminally differentiated gametes to the become pluripotent cells in the blastocyst. While active and passive modes of demethylation have both been suggested to play a role in this process, the relative contribution of these two mechanisms to genome-wide 5mC erasure remains unclear. Here, we report a new high-throughput single-cell method (scMspJI-seq) that enables strand-specific quantification of 5mC, thereby allowing us to systematically probe the dynamics of global demethylation. First, when applied to hybrid mouse embryonic stem cells, we identified substantial cell-to-cell strand-specific 5mC heterogeneity with a small group of cells displaying asymmetric levels of 5mCpG between the two DNA strands of a chromosome and suggesting loss of maintenance methylation. Next, using scMspJI-seq in preimplantation mouse development, we discovered that maintenance methylation is active till the 16-cell stage followed by passive demethylation in a fraction of cells within 2 the early blastocyst at the 32-cell stage of development. Finally, we found that human preimplantation embryos qualitatively show slower yet similar demethylation dynamics as mouse preimplantation embryos. Collectively, these results demonstrate that scMspJI-seq is a sensitive and cost effective method to map the strand-specific genome- wide patterns of 5mC in single cells, thereby enabling quantitative investigation of methylation dynamics in developmental systems.

overall_design: 72 libraries

first: Dylan

last: Mooijman

first: Jean-Charles

last: Boisset

first: Alex

last: Chialastri

first: Mina

last: Popovic

first: Björn

last: Heindryckx

first: Susana

last: Chuva de Sousa Lopes

first: Siddharth

last: Dey

first: Alexander

last: van Oudenaarden


title: SELEX and ChIP/CLIP-Seq identification of nucleic acid sequences bound by the DDX43 KH domain (89 aa)

status: Public on Feb 03 2020

city: Saskatoon

first: Yuliang

last: Wu

state: Saskatchewan

address: Rm 4D01.1, HSB, 107 Wiggins Road

department: BMI

country: Canada

institute: University of Saskatchewan

summary: SELEX (systematic evolution of ligands by exponential enrichment), chromatin immunoprecipitation (ChIP)-seq, and crosslinking immunoprecipitation (CLIP)-seq showed that the DDX43 KH domain binds C/T rich DNA and U rich RNA.

sample_organism:
Homo sapiens
synthetic construct

platform_organism:
Homo sapiens
synthetic construct

overall_design: Using purified recombinant DDX43-KH-89 protein to pull down ssDNA from a oligonucleotides library (TriLink Biotechnologies, O-32001-20), the bound DNA was Illumina sequenced. DDX43 KH domain (89 aa) was overexpressed in HEK293T cells, bound DNA and RNA were pulled down by Co-IP, and isolated, and illumina sequenced.

first: Manisha

last: Yadav

first: Shizhuo

last: Yang

first: Daniel

last: Hogan

first: Venkatasubramanian

last: Vidhyasagar

first: Ravi

last: Singh

first: Ivy

middle: Y

last: Chung

first: Anthony

last: Kusalik

first: Oleg

last: Dmitriev

first: Miroslaw

last: Cygler


title: Diachasmimorpha longicaudata venom gland transcriptome

city: Hilo

first: Kelsey

last: Coffman

state: HI

address: 64 Nowelo St

department: Tropical Pest Genetics and Molecular Biology Research Unit

institute: USDA-ARS

summary: Diachasmimorpha longicaudata parasitoid wasps carry a symbiotic poxvirus, known as DlEPV, within the female wasp venom gland. We sequenced RNA from venom gland tissue to identify DlEPV orthologs for 3 conserved poxvirus core genes. The DlEPV ORFs identified from this transcriptome were used to design primers for downstream RT-qPCR analysis and RNAi knockdown experiments.

overall_design: Total RNA from the pooled venom gland tissue of 3 unemerged adult female wasps was sequenced.

first: Gaelen

last: Burke


title: RNY4 in circulating exosomes of patients with pediatric Anaplastic Large Cell Lymphoma: an active player?

status: Public on Feb 21 2020

city: Padova

first: Stefania

last: Bortoluzzi

address: via G. Colombo 3

department: Department of Molecular Medicine

institute: University of Padova

summary: Emerging evidence indicates that extracellular vesicles, particularly exosomes, play a role in several biological processes and actively contribute to cancer development and progression, by carrying and delivering proteins, transcripts and small RNAs (sRNAs). We profiled by RNA-seq the sRNA content of circulating exosomes of 20 pediatric patients with Anaplastic Large Cell Lymphoma (ALCL), 5 healthy controls and of 5 ALCL cell lines. Our analysis disclosed that non-miRNA derived sRNAs constitute the prominent fraction of sRNA loaded in exosomes. A fragment of RNY4 was the most abundant of 180 sRNAs significantly enriched in exosomes of ALCL patients compared to controls. Further investigation by qRT-PCR of RNY4 fragments and full-length sequence disclosed that the latter is massively loaded into exosomes of ALCL patients with more advanced and aggressive disease. Since recent findings supported a role of RNY4 in the modulation of tumor microenvironment, our data open new possibilities to understand how tumor derived exosomes can facilitate disease spread in ALCL patients.

overall_design: Tumor biopsies and plasmatic exosomes from ALCL pediatric patients; plasmatic exosomes from healthy donors; exosomes from ALCL cell lines culture surnatants.

first: Federica

last: Lovisa

first: Piero

last: Di Battista

first: Enrico

last: Gaffo

first: Carlotta

last: Damanti

first: Anna

last: Garbin

first: Ilaria

last: Gallingani

first: Elisa

last: Carraro

first: Marta

last: Pillon

first: Alessandra

last: Biffi

first: Lara

last: Mussolin


title: Single-nucleus RNA-seq in the post-mortem brain in major depressive disorder

status: Public on Feb 25 2020

city: Montreal

first: Gustavo

last: Turecki

state: Quebec

address: 6875 Boulevard LaSalle

department: Psychiatry

institute: McGill University

summary: We performed high-throughput snRNA-seq using the 10X Genomics Chromium platform on archived post-mortem dorsolateral prefrontal cortex (BA9) tissue in MDD subjects who died by suicide and in control subjects to identify cell-type specific differentially expressed genes.

overall_design: 10X Genomics Chromium snRNA-seq was performed on nuclei extracted from BA9 of the post-mortem brain tissue of 17 control subjects and 17 MDD cases who died by suicide. All subjects were male. Cell-types were identified by unsupervised clustering and diffrential gene expression was performed between cases and controls for each cell-type cluster. The library preparation was performed with the Chromium Singel Cell 3’ Reagent Kits v2. Paired-end sequencing was performed on the HiSeq Illumina 4000. FastQ files were produced with Cellranger v2.1.0 mkfastq. Alignments and gene counts were generated with Cellranger v2.1.0 count.


title: miR-146 connects stem cell identity with metabolism and pharmacological resistance in breast cancer

status: Public on Jan 21 2020

city: Milano

first: Francesco

last: Nicassio

address: Via Adamello 16

department: Center for genomic science

institute: Istituto Italiano di Tecnologia

summary: Although ectopic overexpression of miRNAs can influence mammary normal and cancer stem cells (SCs/CSCs), their physiological relevance remains uncertain. Here, we found that the miR-146 family is linked to SC identity, since: i) their expression is very high in SCs/CSCs from human/mouse primary mammary tissues; correlates with the basal-like breast cancer subtype, which typically has a high CSC content; and specifically distinguishes cells with SC/CSC identity; ii) miR-146 depletion reduces SC/CSC self-renewal in vitro and the number of tumor-initiating cells in vivo. Analysis of the transcriptional effects of miR-146 in breast SC-like cells revealed a complex network of highly connected miR-146 targets related to quiescence, transcription and metabolic pathways (one-carbon pool, purine synthesis and folate metabolism). As predicted by our analysis, SCs/CSCs display innate resistance to anti-folate therapy that can be reversed by miR-146 depletion, unmasking a “hidden vulnerability” that could be exploited for the development of anti-CSC therapies.

overall_design: total RNA expression by deep-sequencing in HMLE sorted for different levels of miR-146 activity

first: Chiara

last: Tordonato

first: Matteo

last: Marzi

first: Pier

middle: P

last: Di Fiore


title: Microarray profiling analysis ofcircular RNAs expression in osteosarcoma

status: Public on Jan 14 2020

city: Shenyang

first: Ming

last: He

state: Liaoning

address: No. 36 Sanhao Street

institute: Shengjing Hospital of China Medical University

summary:
Strategies targeted vascular endothelial growth factor (VEGF)-dependent osteosarcoma progression are limited although important progress has been made in illustrating the mechanisms. Here we identified circ_001621 as one of the significantly upregulated circular RNAs (circRNAs) by circRNAs microarrays. We found that patients with high circ_001621 expression had a shorter survival time. Moreover, we found several potential sponge micro RNAs (miRNA) of circ_001621 with Circular RNA Interactome database. Among the candidate sponge, we elucidated the association of circ_001621 and miR-578. In addition, we demonstrated that miR-578 targeted circ_001621 directly. Functionally, we set up the experimental system to investigate the effects of circ_001621/miR-578/VEGF interaction in vitro and in vivo. Results indicated circ_001621 promoted osteosarcoma proliferation and migration via attenuating the inhibition of cyclin-dependent kinase 4 (CDK4) and matrix metallopeptidase 9 (MMP9) by miR-578, respectively. Nude mice experiment was further performed to estimate the promotion of metastasis by circ_001621. The present study evaluated the mechanisms underlying circ_001621 enhanced osteosarcoma progression and provided novel therapeutic targets for advanced osteosarcoma.
Circular RNAs profiling by array

overall_design: Three primary osteosarcoma patients who underwent complete resection without pre- or postoperative chemotherapies were recruited in the present study. Microarray based circRNA expression profiles were gain with Qiagen custom RT2 PCR Arrays


title: Gene Network Transitions in Embryos Depend Upon Interactions between a Pioneer Transcription Factor and Core Histones [RNA-Seq]

status: Public on Jan 22 2020

city: Philadelphia

first: Gregory

last: Donahue

state: PA

address: 3400 Civic Center Blvd, Bldg 421

department: Cell & Developmental Biology

institute: The University of Pennsylvania

summary: Gene network transitions in embryos and fate-changing contexts involve combinations of transcription factors.  A subset of fate-changing transcription factors act as pioneers; they scan and target nucleosomal DNA and initiate cooperative events that can open the local chromatin.  But a gap has remained in understanding how molecular interactions with the nucleosome, beyond interactions with the DNA helix, contribute to the chromatin opening phenomenon.  Here we identified a short alpha-helical region, conserved among FoxA pioneer factors and separated from the DNA binding domain, that interacts with core histones and is necessary for chromatin opening in vitro. The same domain is necessary for chromatin opening in early mouse embryos and for normal embryonic development and viability.  Thus, local opening of chromatin by interactions between pioneer factors and core histones is crucial for genetic programming.

overall_design: Single-end RNA-seq of mouse embryo cells (E7.5) which were FACS-sorted on FoxA2-tag-RFP into RFP-high, RFP-middle, and RFP-negative cell populations. FoxA2 WT mice were compared to mice with a homozygous DHx mutation that removes an alpha helix from FoxA2 critical for the activation of gene targets. Three replicates were sequenced for each (genetic background, RFP level) condition.

first: Makiko

last: Iwafuchi-Doi

first: Isabel

last: Cuesta

first: Greg

first: Naomi

last: Takenaka

last: Osipovich

first: Mark

last: Magnuson

first: Heinrich

last: Roder

first: Steven

last: Seeholzer

first: Pilar

last: Santisteban

first: Kenneth

last: Zaret


title: Comparison of age-related changes in gene expression of 2 rat skeletal muscles (20 months, 22 months)

first: Jerome

last: Feige

summary: In this study we compared Gastrocnemius and Triceps gene expression with age. Our results show that gene expression is massively modulated with age in Gastroc but on the contrary very stable in Triceps, suggesting that Triceps is resistant to age-related defects.

overall_design: 2 groups of age (20 months, 22 months) were analyzed, with 10 replicates per group. Gastrocnemius and Triceps were collected for each animal.

first: Alice

last: Pannérec

first: Eugenia

last: Migliavacca

first: Anastasiya

last: Börsch

first: Frédéric

last: Raymond

first: Descombes

last: Patrick

middle: N


title: Gene Network Transitions in Embryos Depend Upon Interactions between a Pioneer Transcription Factor and Core Histones [ATAC-Seq]

overall_design: Paired-end ATAC-seq of mouse embryo cells (E7.5) which were FACS-sorted on FoxA2-tag-RFP into RFP-high, RFP-middle, and RFP-negative cell populations. FoxA2 WT mice were compared to mice with a homozygous DHx mutation that removes an alpha helix from FoxA2 critical for the activation of gene targets. Two replicates were sequenced for each (genetic background, RFP level) condition.

first: Anna


title: Gene Network Transitions in Embryos Depend Upon Interactions between a Pioneer Transcription Factor and Core Histones

status: Public on Jan 20 2020

first: Gregory

overall_design: Refer to individual Series


title: PRC1 catalytic activity is central to Polycomb system function.

status: Public on Jan 08 2020

city: Oxford

first: Nadezda

last: Fursova

address: South Parks Rd

department: Department of Biochemistry

institute: University of Oxford


title: Transcriptome Effects of the knockout of Intraflagellar Transport 88 gene in mitral leaflets and in mitral leaflets with mutations in Dzip1

first: Gary

last: Hardiman

address: 135 Cannon Street

summary: The genes Ift88 and Dzip1 are critical for primary cilium biogenesis, the objective this study was to determine the transcriptome changes in Mitral leaflets in these genetic deficiencies.

overall_design: Examination of transcriptome changes in  in vivo model organism knockout of the gene Ift88 or in the context of a pathogenic Dzip1 mutation.

first: Katelynn

last: Toomer

first: Mengyao

last: Yu

first: Diana

last: Fulmer

first: Lilong

last: Guo

first: Neal

last: Peterson

first: Alex

last: Drohan

first: Breiona

last: Catching

first: Andy

last: Wessels

first: Joshua

last: Lipschutz

first: Francesca

last: Delling

first: Xavier

last: Jeunmaitre

first: Christian

last: Dina

first: Ryan

last: Collins

first: Harrison

last: Brand

first: Mike

last: Talkowski

first: Rupak

last: Mukherjee

first: Simon

last: Body

first: Willian

last: da Silveira

first: Starr

last: Hazard

first: Baolin

last: Wang

first: Maire

last: Leyne

first: Ronen

last: Durst

first: Roger

last: Markwald

first: Solena

last: Le Scouranec

first: Albert

last: Hagege

first: David

last: Milan

first: Jean-Jacques

last: Schott

first: Thierry

last: Le Tourneau

first: Robert

last: Levine

first: Nabila

last: Bouatia-Naji

first: Susan

last: Slaugenhaupt

first: Russell

last: Norris


title: A single-cell RNA-seq atlas of the pathogenic stage of Schistosoma mansoni identifies a key regulator of blood feeding [RNA-Seq]

first: George

last: Wendt

summary: The schistosome homolog of hnf4 is involved in parasite blood feeding and stem cell biology. In order to understand the function of hnf4, we performed RNAseq on either control(RNAi) or hnf4(RNAi) parasites to see the transcriptional consequences of hnf4 RNAi

overall_design: Adult male parasites were treated with either control dsRNA or hnf4-targeting dsRNA then subjected to RNAseq

first: Lu

last: Zhao

first: James

last: Collins


title: Prospective isolation of radiation induced erythroid stress progenitors reveals unique transcriptomic and epigenetic signatures enabling increased erythroid output

status: Public on Jan 03 2020

city: Lund

first: Johan

last: Flygare

address: Sölvegatan 19

country: Sweden

institute: Lund University

summary: Massive expansion of erythroid progenitor cells is essential for surviving anemic stress.   Research towards understanding this critical process, referred to as stress-erythropoiesis, has been hampered due to lack of specific marker-combinations enabling analysis of the distinct stress-progenitor cells capable of providing radioprotection and enhanced red blood cell production. Here we present a method for precise identification and in vivo validation of progenitor cells contributing to both steady-state and stress-erythropoiesis, enabling for the first time in-depth molecular characterization of these cells. Differential expression of surface markers CD150, CD9 and Sca1 defines a hierarchy of splenic stress-progenitors during irradiation-induced stress recovery in mice, and provides high-purity isolation of the functional stress-BFU-Es with a 100-fold improved enrichment compared to state-of-the-art. By transplanting purified stress-progenitors expressing the fluorescent protein Kusabira Orange, we have for the first time determined their kinetics in vivo and demonstrated that CD150+CD9+Sca1- stress-BFU-Es provide a massive but transient radioprotective erythroid wave, followed by multi-lineage reconstitution from CD150+CD9+Sca1+ multi-potent stem/progenitor cells. Whole genome transcriptional analysis revealed that stress-BFU-Es express gene signatures more associated with erythropoiesis and proliferation compared to steady-state BFU-Es, and are BMP-responsive. Evaluation of chromatin accessibility through ATAC sequencing reveals enhanced and differential accessibility to binding sites of the chromatin-looping transcription factor CTCF in stress-BFU-Es compared to steady-state BFU-Es. Our findings offer molecular insight to the unique capacity of stress-BFU-Es to rapidly form erythroid cells in response to anemia and constitute an important step towards identifying novel erythropoiesis stimulating agents.

overall_design: For RNA-seq, one steady-state BFU-E population in bone marrow and one from irradiation-induced stress erythropoiesis in spleen were sorted and sequenced in triplicates together with one stressed splenic MPP and one CFU-E population for internal comparison. For ATAC-seq, one steady-state BFU-E population in bone marrow and one from irradiation-induced stress erythropoiesis in spleen were sorted and sequenced in triplicates.

first: Sofie

last: Singbrant

first: Alexander

last: Mattebo

first: Tobias

last: Strid

first: Mikael

last: Sigvardsson