title: Flura-Seq Identifies In Situ Transcriptomes of Micrometastases

first: Danilo

last: Macalinao

address: 1275 York Avenue

institute: MSKCC

summary: Understanding the biology of rare cell populations in the context of their microenvironment requires an accurate analysis of the transcriptomes of these cells as expressed in situ. We developed fluorouracil-tagged RNA sequencing (Flura-seq) to characterize the transcriptomes of small cell subpopulations from a whole organ in model systems. The method utilizes cytosine deaminase (CD), which converts the non-natural pyrimidine base fluorocytosine to fluorouracil. Expression of S. cerevisiae CD in cells of interest and exposure to fluorocytosine generates fluorouracil, which is metabolically incorporated into newly synthesized RNAs. The fluorouracil-tagged RNAs can then be immunopurified and sequenced. We applied Flura-seq to define the transcriptome of human breast cancer xenografts, representing as few as 0.003% of host organ cell population during the early stages of metastatic colonization of mouse lungs. The robustness, simplicity and lack of toxicity of Flura-seq make this tool broadly applicable to many studies in developmental, regenerative, and cancer biology.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design:
RNAs were tagged withfluorouracil, and the tagged RNAs were immunopurified before sequencing.
MDA_Con-Dox = MDA231 control cells that does not express CD/UPRT
MDA_FC50uM4hr = MDA231 cells treated with Doxycycline for 24 hours to express CD/UPRT and further treated with 50 uM 5-fluorocytosine for 4 hours.
MDA_FC50uM12hr = MDA231 cells treated with Doxycycline for 24 hours to express CD/UPRT and further treated with 50 uM 5-fluorocytosine for 12 hours.
MDA_FC250uM4hr = MDA231 cells treated with Doxycycline for 24 hours to express CD/UPRT and further treated with 250 uM 5-fluorocytosine for 4 hours.
MDA_FC250uM4hr = MDA231 cells treated with Doxycycline for 24 hours to express CD/UPRT and further treated with 250 uM 5-fluorocytosine for 12 hours.
MDA_SBCon = MDA231 cells treated with 2.5 uM SB-505124 for 150minutes.
MDA_TGFBCon = MDA231 cells treated with 200 pM TGFB for 150minutes.
MDA_SB_IP = MDA231 cells treated with Doxycyline for 24 hours to express CD/UPRT, then with 250 uM of 5-fluorocytosine for 30 minutes before adding 2.5 uM of SB-505124 for additional 150 minutes, and the mRNAs from the cells were immunoprecipitated with anti-BrdU antibody.
MDA_TGFB_IP = MDA231 cells treated with Doxycyline for 24 hours to express CD/UPRT, then with 250 uM of 5-fluorocytosine for 30 minutes before adding 200 pM of TGFB for additional 150 minutes, and the mRNAs from the cells were immunoprecipitated with anti-BrdU antibody.
MDA_msLung_4h Input = MDA231 cells injected in mouse lung through tail vien, and 4 weeks after the injection CD/UPRT was induced by feeding Doxycycline diet for 2-3 days, and 250 mg/kg 5-fluorocytosine was injected intraperitoneally and 125 mg/kg thymine subcutaneously, and 4 hours later mouse lungs were harvested, homogenized, mRNAs were isolated and sequenced.
MDA_msLung_4h IP = MDA231 cells injected in mouse lung through tail vien, and 4 weeks after the injection CD/UPRT was induced by feeding Doxycycline diet for 2-3 days, and 250 mg/kg 5-fluorocytosine was injected intraperitoneally and 125 mg/kg thymine subcutaneously, and 4 hours later mouse lungs were harvested, homogenized, mRNAs were isolated, immunopurified with anti-BrdU antibody and sequenced.
MDA_msLung_12h Input = MDA231 cells injected in mouse lung through tail vien, and 4 weeks after the injection CD/UPRT was induced by feeding Doxycycline diet for 2-3 days, and 250 mg/kg 5-fluorocytosine was injected intraperitoneally and 125 mg/kg thymine subcutaneously, and 12 hours later mouse lungs were harvested, homogenized, mRNAs were isolated and sequenced.
MDA_msLung_12h IP = MDA231 cells injected in mouse lung through tail vien, and 4 weeks after the injection CD/UPRT was induced by feeding Doxycycline diet for 2-3 days, and 250 mg/kg 5-fluorocytosine was injected intraperitoneally and 125 mg/kg thymine subcutaneously, and 12 hours later mouse lungs were harvested, homogenized, mRNAs were isolated, immunopurified with anti-BrdU antibody and sequenced.

first: Harihar

last: Basnet

first: Joan

last: Massagué


title: DNA Methylation profile in hypothalamus for mouse offspring with maternal high fat (HF), low protein (LP) and control (CO) diets

status: Public on Jan 01 2019

city: Los Angeles

first: Xia

last: Yang

state: CA

address: 2000 Terasaki Life Sciences Bldg, 610 Charles E. Young Drive East

department: IBP

country: USA

institute: UCLA

type: Methylation profiling by high throughput sequencing

summary: To investigate the materal dietary effects (HF, LP) on affecting DNA methylations in the mouse offspring hypothalamus.

overall_design: C57BL/6 mice of breeding age (5-8 week of age) were put on either a normal Chow diet (CO), a low protein diet (LP) , or a high fat diet (HF) for 5-6 weeks from the time breeding began to gestation.  Upon birth of new litters, all breeders (multiple breeders for each diet) were switched to the normal Chow diet before weaning.  Offspring remained with their birth mothers except that female pups were removed from breeder cages 4-7 days after birth. At weaning, all male pups from breeders on the same diet were pooled and randomized into large cages in groups of n=3 and received either a Chow diet or a DIO diet for 12 weeks. All diets with the exception of the HF are isocaloric and closely balanced to ensure that potential differences result simply from the differences in protein and fat content. For each pup diet group, 6-9 males were studied. At the end of the diet period, liver, mesenteric adipose, and hypothalamus were collected and flash froze in liquid nitrogen. The diet experiments and tissue collection were completed at Taconic Farms, Inc.

first: Qingying

last: Meng


title: miR941 overexpression experiment

city: Shanghai

first: Haiyang

last: Hu

address: 320 Yueyang Road

country: China

institute: PICB

type: Expression profiling by high throughput sequencing

summary: miRNA sponge, a special class of miRNA target,  has been emerging as a pivotal player in miRNA mediated regulatory network. Currently, the identified miRNA sponge genes mostly act on sequestering conserved miRNAs (e.g. miR-7, miR-145), however, the existence, potential function and evolutionary process of miRNA sponge genes for species-specific miRNA, especially for human specific miRNA, are largely unknown. In this study, we conducted a systematic analysis including sponge gene identification and subsequent function and evolutionary analyses for an authentic human-specific miRNA, miR-941.

overall_design: Total RNA after miR-941 duplex or mock control transfection in 293T cells  were generated by deep sequencing using Illumina HiSeq 2000

first: Philipp

last: Khaitovich


title: Wiskott-Aldrich Syndrome-causative mutations disrupt alternative splicing and promote gene networks predisposed to hematologic malignancies

city: La Jolla

first: Christopher

last: Benner

state: California

address: 9500 Gilman Dr. MC 0640

department: Medicine

institute: University of California, San Diego (UCSD)

summary: Wiskott-Aldrich syndrome (WAS) is characterized by X-linked thrombocytopenia, eczema, immunodeficiency, recurrent infections and increased risk of autoimmunity and malignancies. WAS is caused by mutations in the WAS gene, which encodes the exclusively hematopoietic WAS protein (WASp) that is classically characterized as aν actin nucleator. However, disruption of F-actin polymerization by WAS mutations can not account for many aspects of WAS pathogenesis. Ignorance of other functions of WASP precludes in-depth understanding of the pathogenic effects of mutant WASP, and therefore hampers development of effective therapy. Here we generated induced pluripotent stem cells (iPSCs) from WAS patients (WAS-iPSC) bearing different mutations and corresponding isogenic iPSCs in which the pathogenic mutations had been corrected by targeted genome editing. Hematopoietic cells differentiated from WAS-iPSCs not only recapitulated known disease phenotypes, but also revealed novel defects of WASP deficient cells. WASP co-localized with nuclear pores, nucleoli, nuclear speckles and PML bodies by immunocytochemistry and/or serial block face scanning microscopy (SBF-SEM). MudPIT (multi-dimensional protein identification technology) analysis revealed that WASP physically interacted with nuclear body components, nuclear structural proteins, chromatin modifying complexes, and many RNA-binding proteins including major components of the spliceosome. Next-generation sequencing captured a dramatic global change of alternative splicing in WAS patient cells. WAS mutation impacted splicing of multiple genes frequently mutated in myelodysplastic syndrome and other cancers. RNA sequencing showed that WAS-iPSC derived immune cells misregulated many cell cycle regulators, tumor suppressors, immune function genes and splicing factors, and activated gene networks that drive cancer development and inflammatory diseases. Together these data uncovered previously unappreciated functions of the WASP and provided a mechanistic understanding of the pathogenesis of malignancy and autoimmunity in the most severe form of WAS. These new knowledge could help develop targeted therapy for WAS in the future.

overall_design: Human WAS-iPSC derived from two WAS patients (genotype: p.Phe35* and p.Leu425Profs*70, respectively) and gene corrected WAS-iPSCs (cWAS-iPSC) were differentiated into macrophages. Human cord blood progenitor cells were differentiated into macrophages as a control. Total RNAs were extracted and been analyzed by RNA-seq.

first: Mo

last: Li

first: Chris

first: Juan

middle: C

last: Belmonte


title: Transcriptomic analysis of gene expression in adult Drosophila hemocytes

city: College Park

first: Stephen

middle: M.

last: Mount

state: MD

address: HJP, 4065 Campus Dr.

department: Cell Biol. & Mol. Genetics

institute: Univ. Maryland

summary: Hemocytes are phagocytic blood cells that act as the first line of defense against bacterial pathogens in the fruit fly, Drosophila melanogaster. To gain insight into the immune-regluated transcriptional response in this cell type, we sequenced uninfected, mock (PBS) infected, and Staphylococcus aureus infected hemocytes collected from adult flies. Wildtype and A2bp1 RNAi hemocytes expressing a mouse-CD8-GFP fusion protein were isolated using immunselection and sequenced using 50bp single end reads on an Illumina HiSeq platform. A2bp1 RNAi hemocytes express the TRiP short hairpin RNA HMS00478 (which targets all isoforms of Ataxin-2 binding protein 1) under the hemolectinΔGAL4 promoter.

overall_design: Examination of gene expression profiles in phagocytic blood cells from adult fruit flies. 18 RNA samples were analyzed by RNAseq (3 replicates x 3 treatments x 2 genotypes). Treatments were uninfected, mock-infected and S. aureus-infected.  Genotypes were wild-type and RNAi vs. A2BP1.

first: Ashley

last: Nazario-Toole

first: Louisa

last: Wu

middle: M


title: RNA deep sequencing analysis of human brain microvascular endothelial cells (ECs) treated with glioma-conditioned medium (glioma-CM)

status: Public on Dec 31 2018

city: Philadelphia

first: Yi

last: Fan

state: PA

address: 3400 Civic Center Blvd

department: Department of Radiation Oncology

institute: University of Pennsylvania Perelman School of Medicine

summary: To determine the effects of glioma-conditioned medium on global gene expression in ECs.

overall_design: Three lines of human microvascular ECs were treated with or without glioma-CM, followed by RNA extraction and RNA-seq.

first: Tianrun

last: Liu

first: Wenjuan

last: Ma

first: Haineng

last: Xu


title: Cold acclimation of the thermoacidophilic red alga Galdieria sulphuraria - changes in gene expression and involvement of horizontally acquired genes

city: Düsseldorf

first: Andreas

middle: PM

last: Weber

address: Universitätsstr. 1

department: Institute for Plant Biochemistry

country: Germany

institute: Heinrich-Heine-University

summary:
Purpose: We aimed at i) obtaining insight into how a thermophile organism reacts to cold stress, and ii) evaluating the impact of HGT candidates on the acclimation process to temperature decrease.
Methods: The experimental design followed a temperature shift timeline: after two weeks of cultivation at 42°C, constant illumination (90 μE) and constant shaking (160 rpm) in photoautotrophic conditions the first sampling took place (Hot_T48_1) and the cultures of G.sulphuraria were swiftly moved to 28°C ( = cold temperature). "Cold" samples were taken after 3h (Cold_T3_2), 12h (Cold_T12_3) and 48h (Cold_T48_4). After cold treatment at 28°C for 48 hours, the G. sulphuraria was then switched to 46°C for 48 hours (="Hot"). Again, samples were taken after 3h (Hot_T3_5), 12h (Hot_T12_6) and 48h (Hot_T48_7). Altogether, a 48h temperature timeshift at 28°C  and successive recovery at 46°C were targeted for sampling.
Results: Galdieria sulphuraria is a unicellular red alga that lives in hot, acidic, toxic metal-rich, volcanic environments, where few other organisms survive. Its genome harbours up to 5% of genes most likely acquired through horizontal gene transfer. These genes probably contributed to G. sulphuraria’s adaptation to its extreme habitats, resulting in today’s polyextremophilic traits. Here, we applied RNA-sequencing to obtain insights into the acclimation of a thermophilic organism towards temperatures below its growth optimum and to study how horizontally acquired genes contribute to cold acclimation. A decrease in growth temperature from 42 °C/46 °C to 28 °C resulted in an upregulation of ribosome biosynthesis, while excreted proteins, probably components of the cell wall, were downregulated. Photosynthesis was suppressed at cold temperatures, and transcript abundances indicated that C-metabolism switched from gluconeogenesis to glycogen degradation. Folate cycle and S-adenosylmethionine cycle (one-carbon metabolism) were transcriptionally upregulated, probably to drive the biosynthesis of betaine. All these cold-induced changes in gene expression were reversible upon temperature increase. Numerous genes acquired by horizontal gene transfer displayed pronounced temperature-dependent expression changes, corroborating the view that these genes contributed to adaptive evolution in G. sulphuraria.

overall_design: mRNA reads of a temperature-shift timecourse were generated by sequencing, using Illumina HiSeq2000, PE-Reads, 2x100bp.

first: Alessandro

middle: W

last: Rossoni

first: Gerald

last: Schoenknecht

first: Hyun

middle: J

last: Lee

first: Ryan

middle: L

last: Rupp

first: Samantha

last: Flachbart

first: Tabea

last: Mettler-Altmann

middle: P

first: Marion

last: Eisenhut


title: RNA sequencing of ICR and Gerbil wounded skin 3 days after  wound

city: Seoul

first: Eun-Jung

last: Kim

address: 50 Yonsei-ro

department: Department of Oral Biology

country: South Korea

institute: Yonsei Universiry

summary: RNA sequencing was used to examine RNA expression changes in gerbil wounded skin.

sample_organism:
Meriones unguiculatus
Mus musculus

platform_organism:
Meriones unguiculatus
Mus musculus

overall_design: RNA sequencing was performed with RNAs of the wounded dermis at 3 days after wound between ICR and gerbil.

first: Min-Jung

first: Dong-Joon

first: Han-Sung

last: Jung


title: High-throughput sequencing of small RNAs and mRNA transcriptome during Brassica rapa seed development

city: London

first: Jun

last: Wang

address: Charterhouse Square

country: United Kingdom

institute: Barts Cancer Institute, Queen Mary, London

type: Non-coding RNA profiling by high throughput sequencing

summary: We sequenced small RNAs and mRNA transcriptome for 15 and 30 days after pollination during B. rapa seed development. We wanted to identify differential expressed small RNAs and mRNAs between the two stage and link small RNA and RNA expression profiles.

overall_design: 2 time-points examined: 15 days and 30 days after pollination (DAP)

first: Andrew

last: Stoute

first: Priyanka

last: Srivastava

first: Smita

last: Kurup

first: Graham

last: King


title: Comparison of the transcriptome and chromatin state between human cord blood HSC and human iPSC derived hematopoietic progenitor using next-generation sequencing

first: Christopher

last: Benner

type: Genome binding/occupancy profiling by high throughput sequencing

summary: We analyzed the transcriptome and transposase accessible chromatin–using RNAseq and ATAC-seq, respectively–of human cord blood hematopoietic stem cells and human iPSC derived hematopoietic progenitors. iPSC-derived HPCs were FACS sorted CD34+/CD43+ cells. We also examined the effect of inhibiting Wnt signaling during the second week of hematopoietic differentiation of hiPSC. The integrated transcriptomic, epigenomic and functional analyses not only uncovered novel molecular differences between hPSC- HPCs and native HSCs, but also enabled us to target these differences with small molecules to improve derivation and function of hPSC derived HPCs. The strategies here delineated could also be useful for increasing the production of blood cell types such as erythrocytes for therapeutic purposes. Given the existence of a multitude of small molecules specifically targeting a wide range of molecular pathways, our approach could provide a comprehensive strategy for reconstituting the authentic HSC regulatory program and thus open up new avenues for de novo generation of HSCs from hPSCs.

overall_design: Examination of the whole transcriptome and transposase accessible chromatin in 2 cell types.

first: Mo

last: Li

first: Juan

middle: I

last: Belmonte


title: Arginine methylation regulates widespread alternative polyadenylation

city: Beijing

first: xiaofeng

last: cao

address: West Lincui Road, Chaoyang District

department: State Key Laboratory of Plant Genomics

institute: Institute of Genetics and Developmental Biology

summary: Alternative polyadenylation (APA) has recently been recognized as a universal mechanism for gene regulation, but it remains unclear how APA is controlled. Here we report that the Arabidopsis thaliana Protein Arginine Methyltransferase 10 (AtPRMT10) regulates global APA with its protein partner HLP1, a conserved hnRNP A/B protein. HLP1 binds preferentially to A-rich and U-rich cis-elements around polyadenylation sites, thereby linking AtPRMT10 to the control of APA through protein-protein interactions. AtPRMT10 mutations cause significant proximal-to-distal poly(A) site shifts largely overlapping with those in hlp1-1 mutants. Proximal polyadenylation is maintained by AtPRMT10-directed methylation and is mediated in part by methylation of HLP1 at specific arginine residues. Our findings demonstrate that arginine methylation of an RNA-binding protein adds a novel layer of regulation to widespread alternative polyadenylation.

overall_design: Investigate the role of PRMT10 in alternative polyadenylation.

first: Xiaofeng

last: Cao


title: TRIM9-mediated resolution of neuroinflammation confers neuroprotection against ischemic stroke in mice

first: Zhifei

last: Luo

address: 1450 Biggy Street, NRT 6514

institute: University of Southern California

summary: Excessive and unresolved neuroinflammation is part of the pathological cascade in brain injuries such as acute ischemia, as well as neurodegenerative diseases, including multiple sclerosis and Alzheimer’s disease. Particularly, timely resolution of inflammation is critical for the recovery and repair after brain injury. The nuclear factor-κB (NF-κB) signaling plays a central role in neuroinflammation through transcriptional induction of proinflammatory genes. Here, we report that TRIM9, a brain-specific member of the TRIpartite motif (TRIM) family with ubiquitin E3 ligase activity, is upregulated in the peri-infarct cortical areas of mouse brain upon ischemic stroke, and governs the resolution of NF-κB-mediated neuroinflammation. Mechanistically, neuronal TRIM9 sequestered β-TrCP, a component of the Skp-Cullin-F-box (SCF) E3 ligase complex, from ubiquitinating IκBα, thereby mitigating NF-κB-dependent inflammatory responses including production of proinflammatory mediators and infiltration of immune cells. Consequently, Trim9 deficient mice were highly vulnerable to ischemia, manifesting uncontrolled neuroinflammation and exacerbated neuropathological and neurological outcomes. Systemic administration of recombinant adeno-associated virus (AAV)-PHP.B, allowing brain-wide enriched TRIM9 expression, effectively resolved neuroinflammation and alleviated neuronal death in aging mice. This reveals that TRIM9 is essential for fine tuning of NF-κB-dependent neuroinflammation, and TRIM9-potentiation based therapy may offer a new approach for the treatment of stroke and inflammation-related neurological disorders.

overall_design: RNA-seq

first: Jianxiong

last: Zeng

first: Yaoming

first: Lin-Chun

last: Chang

first: Xiaochun

last: Xie

first: Shiwei

last: Duan

first: Qinwen

first: Benjamin

middle: E

last: Deverman

first: Viviana

last: Gradinaru

first: Stephanie

last: Gupton

first: Berislav

middle: V

last: Zlokovic

first: Zhen

last: Zhao

first: Jae

middle: U


title: Transcriptomic analysis of liver of WT and p21KO mice upon 24h fasting

city: Madrid

first: Elena

last: López-Guadamillas

state: Madrid

address: Calle Melchor Fdez Almagro

department: Molecular Oncology

country: Spain

institute: CNIO

summary: We profiled total liver mRNA  of WT and p21KO mice that were fed ad libitum or fasted for 24 hours

overall_design: 2-3 mice of each genotype were either fed or fasted for 24 hours, sacrificed and total mRNA was extracted from liver (we mapped >12M reads per sample)

first: Manuel

last: Serrano

last: Lopez-Guadamillas


title: Regulation of gene expression during formation of nodule-like structures (NLS) in rice roots

city: Conway

first: Arijit

last: Mukherjee

state: AR

address: 201 Donaghey Avenue, UCA

department: Biology

institute: University of Central Arkansas

summary: Several studies have shown that plant hormones play key roles during legume-rhizobia symbiosis. For instance, auxins can induce formation of nodule-like structures (NLS) on legume roots in the absence of rhizobia. Furthermore, these NLS can be colonized by nitrogen-fixing bacteria, which favor nitrogen fixation compared to regular roots and subsequently increase plant yield. Interestingly, auxin also induces similar NLS in cereal roots. While several genetic studies have identified plant genes controlling NLS formation in legumes, no studies have investigated the genes involved in NLS formation in cereals. In this study, we performed a comprehensive RNA sequencing experiment to identify genes differentially expressed during NLS formation in rice at different stages and identified several promising genes for control of NLS based on their biological and molecular functions.

overall_design: Examination of RNA transcripts in rice roots with or without nodule-like structures 1, 7, and 14 days post treatment with auxin, 50μM 2,4-D. Three biological replicates from each samples were included.


title: Post-transcriptional regulation of the epithelial cell response to colitis

city: Piscataway

first: Premal

last: Shah

state: NJ

address: 145 Bevier Road, Rm 326

department: Genetics

institute: Rutgers University

summary:
Aim: RNA binding proteins (RBPs) are emerging as critical regulators of gut homeostasis via post-transcriptional control of key growth and repair pathways. IMP1 (IGF2 mRNA Binding Protein 1) is ubiquitously expressed during embryonic development and Imp1 hypomorphic mice exhibit severe gut growth defects. In the present study, we investigated the mechanistic contribution of intestinal epithelial IMP1 to gut homeostasis and response to injury.
Method: We evaluated IMP1 expression in patients with Crohn’s disease followed by unbiased ribosome profiling in IMP1 knockout cells. Concurrently, we measured differences in histology and cytokine expression in mice with intestinal epithelial-specific Imp1 deletion (Imp1ΔIEC) following dextran sodium sulfate (DSS)- colitis. Based on ribosome profiling analysis, we evaluated changes in autophagy in Imp1ΔIEC mice as well as in silico and in vitro approaches to evaluate direct protein:RNA interactions. Finally, we analyzed the consequence of genetic deletion of Atg7 in Imp1ΔIEC mice using colitis and irradiation models.
Results: IMP1 was robustly upregulated in Crohn’s disease patients and Imp1 loss lessened DSS-colitis severity. Unbiased ribosome-profiling revealed that IMP1 may coordinate translation of multiple pathways important for intestinal homeostasis, including cell cycle and autophagy, which we verified by Western blotting. Mechanistically, we observed evidence for increased autophagy flux in Imp1ΔIEC mice, reinforced through in silico and biochemical analyses revealing direct binding of IMP1 to autophagy transcripts. Finally, we found genetic deletion of Atg7 reversed the phenotype observed in DSS- or irradiation-challenged Imp1ΔIEC mice.
Conclusions: IMP1 acts as a post-transcriptional regulator of gut epithelial repair, in part through modulation of autophagy. This study highlights the need for examining post-transcriptional regulation as a critical mechanism in inflammatory bowel disease.

overall_design: Ribosome-footprinting and RNA-seq samples from WT SW480 cells and IMP1-/- knockout cells

first: P

last: Chatterji

first: K

middle: A

last: Whelan

first: S

middle: F

last: Andres

first: F

last: Samper

first: L

last: Simon

first: R

last: Mizuno

first: E

middle: T

last: Lundsmith

first: D

middle: S

last: Lee

last: Liang

first: H

middle: R

last: Wijeratne

last: Marti

last: Chau

first: V

last: Giroux

first: G

middle: D

last: Wu

middle: G

last: Tartaglia

last: Hamilton


title: Low incubation temperature during early development negatively affects survival and related innate immune processes in zebrafish larvae exposed to lipopolysaccharide

city: Bodø

first: Jorge

last: Fernandes

address: Universitetsalleen 11

department: Faculty of Biosciences and Aquaculture

country: Norway

institute: Nord University

overall_design: Zebrafish embryos were collected from 28 °C, and divided into three temperature groups (24 °C, 28 °C, 32 °C) for incubation. At the first-feeding stage, larvae from each incubation temperature group were further split into three temperature groups in a full-factorial way for LPS challenge. In total, nine temperature groups (three incubation temperatures x three challenge temperatures) were generated. At 24 h post LPS challenge, mortality of larvae were recorded. Larvae originating from 24 °C incubation temperature group had higher mortality rate than larvae from the other two temperature groups. LPS-treated larvae from three temperature groups, incubation 24 °C x challenge 24 °C, incubation 24 °C x challenge 32 °C, and incubation 32 °C x challenge 24 °C, together with their respective control were chosen for transcriptomic analyses using mRNA sequencing. A total of 722 genes were determined differentially expressed (DEGs) by DESeq2 (adjusted p-value < 0.05) in LPS-challenged larvae compared to control, and 605 of them had a fold change greater than 1.5, including 294 DEGs (144 up-/150 down-regulated) in larvae incubated and challenged with LPS at 24 °C; 33 DEGs (20 up-/13 down-regulated) in larvae incubated at 32 °C and challenged at 24 °C; and 278 DEGs (190 up-/88 down-regulated) in larvae incubated at 24 °C and challenged at 32 °C. Larvae incubated and challenged with LPS at 24 °C had stimulated innate immune response compared to control, while they also showed down-regulated innate immune processes and genes. In larvae incubated at 32 °C and challenged at 24 °C, the innate immune processes were up-regulated in larvae exposed to LPS compared to control, and theses processes were even much stronger (with higher enrichment values) than larvae from incubation and challenge temperature of 24 °C. In larvae incubated at 24 °C and challenged with LPS at 32 °C, limited innate immune response were up-regulated, and additional hypoxia and oxidative processes were observed. Genes annexin A2a, S100 calcium binding protein A10b, and lymphocyte antigen-6, epidermis were identified as promising candidates for LPS recognition and signal transduction.

first: Qirui

last: Zhang

first: Martina

last: Kopp

first: Igor

last: Babiak

middle: M


title: miRNA profile of duck duodenum mucosa damage caused by transportation stress

city: Wuhan

first: Hao

state: Hubei

address: Nanhu Road 7#

department: Institute of Animal Husbandry and Veterinary Sciences

institute: Hubei Academy of Agricultural Sciences

summary: We deep sequenced and analyzed  miRNAs using deep RNA sequencing (RNA-seq) in transported and control duck's duodenum sample of Jingjiang duck.  We analyzed the miRNA data with 9467248 reads and 9808143 million reads, obtained 9338224 and 9677777 clean reads in transported and control duck's by high-throughput sequencing, respectively. we respectively gained 4636135 and 4759049 miRNAs sequences in two groups by filtering the known non-miRNA reads, such as rRNA, tRNA, snRNA, and snoRNA by screening against ncRNA deposited in the GenBank and Rfam databases. These findings provided insights into the expression profiles of miRNAs in duck duodenum, and deepened our understanding of miRNAs in transportation injury of duck.

overall_design: Examination of miRNA expression profile in transported duck's duodenum and control duck's duodenum samples

first: Zhenhua


title: Response of murine lymphatic endothelial cells to stimulation with vascular enothelial growth factor-C (VEGF-C)

city: Chicago

first: Shann

last: Yu

state: IL

address: 5640 S Ellis Ave, Eckhardt Research Center

department: PME-Immunoengineering Center

institute: University of Chicago

summary:
The goal of this study is to investigate changes in gene expression profile of lymphatic endothelial cells (LECs) following stimulation with VEGF-C. Primary murine LECs from C57Bl/6 mice were expanded ex vivo from five individual mice (taken from digests of axillary, brachial, cervical, inguinal, popliteal lymph nodes), and stimulated with media only or supplemented with 10 or 100 ng/mL of murine VEGF-C (recombinant, expressed in HEK-293E cells) for 72 h (3 d). This timepoint was chosen because we had detected no significant changes in cell number or density in a daily check up to this timepoint, and ELISAs/Luminex assays detected no significant changes in most chemokine/cytokine biomarkers before 72 h. At this time, LECs were lysed and mRNA isolated for RNAseq analysis to determine differences in gene expression as a function of VEGF-C stimulation. Unstimulated, 10 ng/mL VEGFC-stimulated, and 100 ng/mL VEGFC-stimulated LEC transcriptomes (n = 5 per condition) are provided here.

Grant ID - AdG-323053
Agency - European Research Council (ERC)
Grant Title - LYMPHIMMUNE - Flow in the tumor microenvironment: Linking mechanobiology with immunology

overall_design: lymphatic endothelial cells, unstimulated vs. 10 ng/mL VEGF-C vs. 100 ng/mL VEGF-C for 72h (3d)

first: Petra

last: Aigner

first: Elena

last: Cabello

first: Bastien

last: Mangeat

first: Melody

last: Swartz


title: Dynamics of Proteo-Transcriptomic Response to HIV-1 Infection

city: Basel

first: Monica

last: Golumbeanu

address: Mattenstrasse 26

department: D-BSSE

country: Switzerland

institute: ETH Zürich

summary: Throughout HIV-1 replication cycle, a complex interplay of host-pathogen interactions takes place in the infected cell, leading to production of new virions. The virus modulates the host cellular machinery in order to support its life cycle, while controlling intracellular defense. We have investigated the dynamic host response to HIV-1 infection by systematically measuring transcriptome, proteome and phosphoproteome expression changes in infected and uninfected SupT1 CD4+ T cells at 5 time-points throughout the HIV-1 replication cycle. Genome-wide transcript levels were assessed by RNA-Seq, while protein and phosphoprotein relative abundances were obtained using SILAC mass spectrometry. By the means of a Gaussian mixed-effects model, we stratified host genes based on their gene expression temporal patterns at the three levels, showing how HIV may affect regulation of certain host genes. The results of the implemented integrative analysis of time-series omics data offers a catalogue of dynamic host response to HIV infection allowing a more comprehensive understanding of host-virus interactions. Furthermore, it facilitates identifying novel host factors potentially promoting or restricting HIV replication.

overall_design: Host-HIV interactions in CD4+T-cells. Time-series RNA-Seq was performed in mock-treated and HIV-infected CD4+ T-cells at 6h, 12h, 18h, 24h and 30h.

first: Sébastien

last: Desfarges

first: Céline

last: Hernandez

first: Manfredo

last: Quadroni

first: Sylvie

last: Rato

first: Pejman

last: Mohammadi

first: Amalio

last: Telenti

first: Niko

last: Beerenwinkel

first: Angela

last: Ciuffi


title: Transcriptome analysis on TDP43 and SRSF3 downstream genes and binding RNAs in MDA-MB231 cells by Next Generation Sequencing

city: Kunming

first: Baowei

last: Jiao

state: Yunnan

address: 32 Jiaochang Donglu Kunming

department: Kunming Institute of Zoology

institute: Chinese Academy of Sciences

summary: TDP43 and SRSF3 has been reported to be RNA-binding proteins; however their roles in breast cancer progression has not been  examined previously. Here, we performed RNA-seq on MDA-MB231 cells stably expressed sh-control, shTDP43, shSRSF3 or sh-TDP43 and sh-SRSF3 using lentivirus in duplicates. In addition, MDA-MB231 cells with stable expression of flag-TDP43 or flag-SRSF3 were also generated by using lentivirus. RIP-seq was also applied to identify binding RNA against Flag antibodies.

overall_design: Kncoking down TDP43 or SRSF3 in these cells was achieved using stable expression of shRNA specific for TDP43 or SRSF3 gene using lentivirus. Stable infected cells were selected and harvested for RNA isolation in duplicates. RNA-seq was performed to study the effect of TDP43 or TDP43-knowdown in MDA-MB231. Examination of RNA immunoprecipitation in Flag-TDP43 and Flag-SRSF3 wtih Flag antibodies.

last: Ke

first: Limin

last: Zhao


title: Ribosome profiling in wild-type and APOBEC1-deficient BMDMs

city: New York

first: F.

middle: Nina

last: Papavasiliou

state: New York

address: 1230 York Ave.

institute: Rockefeller University

summary: APOBEC1 wildtype (WT) and Apobec1-/- (KO) unstimulated bone marrow-derived macrophages (BMDMs) were subject to ribosome profiling (n=6 for each genotype) in order to investigate the effect of APOBEC1 on translation

overall_design: Examination of effect of functional APOBEC1 on translation

first: Dewi

last: Harjanto

first: Violeta

last: Rayon-Estrada

first: Claire

last: Hamilton

first: F

middle: N


title: Genome-wide expression of HD-Zip genes in cassava

city: HaiKou

first: Zehong

last: Ding

state: HaiNan

address: No.4 XueYuan Rd

institute: ITBB

summary: To reveal the expression of HD-Zip genes in different tissues of cassava, samples from leaf (90 days after planting), stem (90 days after planting), early storage root (ESR, 90 days after planting), middle storage root (MSR, 150 days after planting) and last storage root (LSR, 210 days after planting) were collected for RNA-seq analysis. In addition, their expression was also examined in folded leaf (FL), full expanded leaf (FEL) and bottom leaf (BL), as well as root (RT) at 0, 3, 24 h after the treatment of PEG 6000.

overall_design: Examination of gene expression in different tissues of three genotypes, or in leaves and root in response to PEG treatment in cassava

first: Wenquan

last: Wang


title: Identification of microRNAs and Their Targets in Ulmus pumila under Salt Stress by High-Throughput Sequencing

first: Zhu

last: Jianfeng

address: Haidian District, Xiang Shan Road

department: Research Center of Saline and Alkali Land of State Forestry Administration

institute: Chinese Academy of Forestry

summary: MicroRNAs (miRNAs) are a class of endogenous small RNAs that play important roles in growth, development, and environmental stress response processes in plants. Ulmus pumila is a typical deciduous broadleaved tree species of north temperate, and is widely distributed in central and northern Asia, which has important economic and ecological value. With the  spread and aggravate of soil salinisation, salt stress has become a major abiotic stress that highly affects the normal growth and development of U. pumila. However, to date, no investigation into the influence of salt stress on U. pumila miRNAs has been reported. To identify miRNAs and predict their target mRNA genes under salt stress, three small RNA libraries were generated and sequenced from CK (without salt stress), LSS (light salt stress for a short time) and MSL (medium-heavy salt stress for a long time) roots of U. pumila seedlings. Through integrative analysis, 245 conserved miRNAs representing 30 families and 64 novel miRNAs were identified, of which 89 exhibited altered expression level under salt stress, and 232 potential targets for the miRNAs were predicted and annotated in U. pumila. The expressions of six differentially expressed miRNAs were validated by qRT-PCR. These salt responsive miRNAs may play crucial roles in U. pumila defense against salt stress, and our miRNA data provides valuable information regarding further functional analysis of miRNAs involved in salt tolerance of U. pumila and other forest tree species.

overall_design: Examination of small RNA expression profilings in Ulmus pumila seeding root under different salt stress.

first: Jianfeng

last: Zhu

first: Huaxin

last: Zhang


title: Transcriptomic changes mediated by β-amyloid in human aortic endothelial cells (HAOEC)

city: Milan

first: Fabio

last: Martelli

address: via morandi 30

country: Italy

institute: IRCCS-Policlinico San Donato

summary: We found that β-amyloid accumulation is modulated in HAOEC cells by overexpression or blocking of lncRNA BACE1-AS, which in turn regulates both BACE1 mRNA and protein expression. BACE1 is key-enzyme in the synthesis of β-amyloid from Amyloid Precursor Protein (APP). The transcriptomic changes mediated by 400nM  β-amyloid was investigated in HAOEC cells.

overall_design: HAOEC cells stimulated or not with 400nM β-amyloid

first: Simona

last: Greco

first: Matteo

last: Carrara


title: ctDNA methylation markers in diagnosis and prognosis of hepatocellular carcinoma

city: La Jolla

first: Kang

address: 9500 Gilman Dr

institute: UCSD

summary: To develop diagnostic and prognostic biomarkers, we compared methylation profiles of HCC tissues and normal blood by analyzing 485,000 CpG markers and identified a HCC enriched methylation marker panel compared to that of normal blood. We found there was a highly correlation of methylation profiles between DNA from HCC cancer tissue and matched plasma ctDNA within the same patient. We then selected 10 markers from this panel and created a combined diagnosis score (cd-score) which showed high diagnostic specificity and sensitivity in both a training cohort and an independent validation cohort. We also showed the cd-score correlate highly with tumor load, treatment response and stage and is superior to that by AFP.  We also showed the cd-score correlate highly with tumor load, treatment response and stage and is superior to that by AFP.  Additional, we generated 8 markers from unicox and LASSO-cox analysis and created a combined prognosis score (cp-score) which could predict prognosis and survival.  Together, these findings demonstrated the utility of ctDNA methylation markers in the diagnosis, treatment evaluation and prognosis of HCC.

overall_design: Base-pair resolution DNA methylation across 467 genomic ~100bp regions was analyzed in circulating tumor DNA (ctDNA) extracted from serum of 1221 hepatocellular carcinoma patients and from 970 healthy controls

first: Michal

last: Krawczyk

first: Wenqiu

first: Ken

last: Flagg


title: Cytoplasmic Control of Plastid Retrograde Signaling by SCFDIF-Mediated Degradation of DIFFERENTIATION AND GREENING-LIKE

city: Athens

first: Zhihua

last: Hua

state: Ohio

address: 22 Richland Ave

department: Department of Environmental and Plant Biology

institute: Ohio University

summary:
Purpose: In plants, chloroplasts not only fix energy through photosynthesis, but they synthesize numerous metabolites which can act as important growth regulators by impacting nuclear gene expression.  Upon developmental and external stimuli, signaling between the nucleus and chloroplasts is essential for maintaining plant cellular homeostasis.  In this study, we applied an Illumina HiSeq 2500 platform to investigate the transcriptome changes of 2 Arabidopsis thaliana mutant lines, a T-DNA knock out muant allele of DIFFERENTIAL AND GREENING-LIKE (DAL), termed dal-2, and a dexmathasone (Dex)-induced overexpression line of DAL-INTERACTING F-BOX  (termed DIF-OX2).
Methods: Total RNA was isolated from 12-d-old Col-0 (wild type control) and DIF-OX2 seedlings grown on Gamborg’s B-5 (GM) medium containing 1% sucrose (GM-Suc), with or without 10 μM Dex, and 20-d-old dal-2 plants also grown on GM-Suc medium, and deep sequenced as 100-mers using the Illumina HiSeq 2500 platform (DNA Sequencing Facility, University of Wisconsin Biotechnology Center).  Raw image files for each library were converted to FASTQ files by the standard Illumina pipeline and processed for quality control by Trimmomatic (http://www.usadellab.org/cms/?page=trimmomatic) to remove adapter and low quality sequences (phred=33, minimum length=36).  Processed sequences were aligned to the A. thaliana Col-0 genomic sequence (from The Arabidopsis Information Resource (TAIR) version 10 at www.arabidopsis.org) via TOPHAT2 to identify accepted hits, which were then used to generate an absolute expression level (counts) of each locus by HTSeq (http://www-huber.embl.de/users/anders/HTSeq/).  The resulting counts per locus were normalized to counts per million reads (CPM) among all 10 libraries and used to generate the list of differentially expressed (DE) genes between treatments or genotypes by edgeR (FDR < 5% or ABS[log2FoldChange (FC)] ≥ 1).
Results: In total, 6,743 differentially expressed (DE) RNAs were identified using edgeR (FDR < 5%) in either dal-2 or DIF-OX2 (+Dex) seedlings, as compared to Dex-untreated or Dex-treated wild-type seedlings, respectively.  Among these DE genes, the expression levels of 2,606 loci in dal-2 changed at a level greater than or equal to 2 fold compared to those in the Dex-untreated wild type control, but showed a strong positive correlation with their expression levels in DIF-OX2 (+Dex) (Spearman’s rank correlation rho = 0.72, p < 2.2e-16; Figure 5B-C).
Conclusions: The similar transcriptome changes in both DIF-OX2 (+Dex) and dal-2 plants suggests that the DIF and DAL proteins are involved in the same pathway, which controls a retrograde signaling from chloroplasts to the nucleus, based on further biochemical analysis, cellular localization, and transcriptome comparisons with other public available microarray data from mutants impacting chloroplast retrograde signaling.

overall_design: Transcriptome profiles of 12-d-old Col-0 and DIF-OX2 seedlings grown on GM-Suc medium with or without 10 μM Dex, and 20-d-old dal-2 plants grown on GM-Suc medium, under LD conditions (see below) were generated by deep sequencing, in duplicate, using Illumina HiSeq 2500 platform.

first: Richard

last: Marshall

last: Vierstra


title: Methylome, hydroxymethylome, and integrative transcriptome profiling in human CRC tissue and paired normal tissues

city: Hangzhou

first: Yimin

state: Zhejiang

address: Yuhangtang Road

institute: Zhejiang university

summary: DNA methylation (5-mC) and hydroxymethylation (5-hmC) are regarded as important epigenetic hallmarks in the carcinogenesis of colorectal cancer by transcriptional regulation. 5hmC is an intermediate during active demethylation and maintains the equilibrium of DNA methylation. Previous studies on DNA methylation don’t differentiate 5-hmC from 5-mC. Here, in order to elucidate the epigenetic mechanisms of carcinogenesis of colorectal cancer, we integrate genome wide levels of 5-mC, 5-hmC and Transcriptional expression. 12 samples, including six colorectal tumor tissues and corresponding normal colonic tissues were recruited after surgery. Genome-wide DNA methylation was determined by methylated DNA immune- precipitation sequencing (MeDIP-seq), and hydroxymethylation by hydroxyl- methylated DNA immune-precipitation sequencing (hMedip-seq). Transcriptional expression was determined by RNA-seq. Group-wise different methylation region (DMR), different hydroxyl methylation region (DhMR) and different expressed gene (DEG) were identified. Epigenetic biomarkers were screened by integrating DMR, DhMR and DEG. We found that a genome-scale distinct hydroxymethylation pattern could be used as epigenetic biomarker for clearly differentiating colorectal cancer from normal tissues. 59249 differentially methylated regions (DMR), 187172 differentially hydroxymethylated region (DhMR) and 948 differentially expressed genes (DEGs) were identified. After cross-matched genes containing DMRs or DhMRs with DEGs, seven genes were screened. Furthermore, hypermethylation of HADHB was persistently found to be correlated with its down-regulation of transcription in CRC, potentially suggesting its role as TSG. The differences of methylation, hydroxymethylation and transcriptional expression in HADHB between cancerous and normal tissues were validated among additional colorectal cancer patients. To further validate this assumption, we also performed functional analysis and found that the expression of HADHB obviously reduced cancer cells migration and invasiveness. This study provided valuable basic data for screening epigenetic biomarkers and elucidated the epigenetic mechanisms of carcinogenesis of colorectal cancer.

overall_design: 12 samples, including six colorectal tumor tissues and corresponding normal colonic tissues were recruited after surgery and subjected to MeDIP-seq, hMeDIP-seq and RNA-seq.

first: Maode

last: Lai

first: Fei

last: Gao


title: Whole blood RNA sequencing in idiopathic pneumonia syndrome reveals a unique transcriptomic profile compared to ARDS

city: Philadelphia

first: Blanca

last: Himes

address: 423 Guardian Dr

department: Department of Biostatistics, Epidemiology and Informatics

institute: University of Pennsylvania

summary:
The acute respiratory distress syndrome (ARDS) is a highly lethal syndrome characterized by hypoxemia and bilateral lung infiltrates in response to an inciting event such as sepsis. Allogeneic bone marrow transplantation (BMT) is a life-saving treatment for patients with hematologic malignancies that can be complicated by ARDS. We sought to identify blood gene expression signatures that distinguish whether ARDS in BMT may be a distinct pathobiologic entity from ARDS in non-BMT patients.
RNA-Seq was used to measure whole blood transcript expression differences between 26 patients meeting the Berlin definition of ARDS: 8 patients without BMT and 5 BMT patients with ARDS from the Brigham and Women’s Registry of Critical Illness (RoCI), as well as 7 non-BMT patients with sepsis and 6 BMT patients with sepsis. RNA was globin cleared using the Ambion GLOBINclear kit prior to preparation of poly(A)-selected RNA-Seq libraries with the Illumina TruSeq method. An Illumina HiSeq 2500 instrument was used to generate 75 base pair paired-end reads, which were aligned to the hg38 reference genome using STAR. Differential expression analysis was performed using DESeq2.

overall_design: mRNA profiles obtained via RNA-Seq for whole blood samples from ARDS patients with and without BMT

first: Joshua

last: Englert

first: Michael

middle: H

last: Cho

first: Rebecca

last: Baron


title: Time-serialized expression profile of MeJA induced Andrographis paniculata leaves

first: Tong

last: Chen

address: No 16 Nan-xiao-jie Dong-zhi-men-nei

department: State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica

institute: China Academy of Chinese Medical Sciences

summary: To shed light on the biosynthesis mechanisms of these diterpenes, we performed the first high-throughput RNA-seq for A. paniculata leaves with time-serialized MeJA treatments. The transcriptomic approach not only defined a comprehensive transcriptome (comprised of 20,629 highly expressed genes), but also profiled time-serialized gene expression patterns with 4,463 up-regulated genes and 6,517 down-regulated genes responding to MeJA induction. These up-regulated genes significantly enriched in biological processes like stress responses, metabolic pathways, and secondary metabolites biosynthesis, especially terpene/terpenoid metabolic process. Consistent with the gradual accumulation of andrographolide, the expression of most genes involved in MEP pathway showed progressive increase. In the hypothetical terpenoid metabolism pathway, ApCPS2, which was putatively involved in andrographolide synthesis, dramatically increased its expression. Among other co-regulated genes, 154 genes encode cytochrome P450s (CYP450s); 42 genes were predicted as UDP glycosyltransferases (UGTs); and 363 genes belong to transcription factors.

overall_design: Strand-specific paired-end mRNA-seq data were generated in MeJA treated leaf samples including 0 hours past induction (hpi), 12 hpi, 24 hpi and 48 hpi with three biological replicates each to ensure the veracity.

first: Huixin

last: Lin


title: Investigation of Rsf1 genomic distribution and effect on gene expression

city: Richmond

first: Hengbin

last: Wang

state: VA

address: 401 College Street

department: Massey Cancer Institute

institute: Virginia Commonwealth University

summary: We report the effect of Rsf1 knockdown or deletion on gene expression in human and mouse cells.  We also report the genomic distribution of Rsf1 in mouse embryonic stem cells and nucleosome positioning in wild type and RSF1 knockout mouse ESC.

overall_design: Examination of Rsf1 regulated gene expression, genomic distribution, and chromatin structure in human and mouse cells.

first: Wang

last: Hengbin


title: miRNA regulatory networks in male and female mouse ESC-to-EpiSC differentiation

city: Lyngby

first: Federico

last: De Masi

address: Kemitorvet 208

department: Institute of Systems Biology

country: Denmark

institute: Technical University of Denmark

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

overall_design: Refer to individual Series


title: BS-seq of ros1-3, ros1-4 with wildtype col-0

city: Seoul

first: Jin Hoe

last: Huh

address: Gwanak-gu

department: Dept Plant Science

institute: Seoul National University

summary:
To servey the methylome changes by mutation of a DNA demethylase ROS1, we performed the Next-gen sequencing (NGS) associated whole genome bisulfite sequencing (BS-seq) analysis.
Two ROS1 knockout lines (ros1-3 and ros1-4; Penterman et al. 2007 [PMID: 17409185]) were subjected in this study.

overall_design: Whole genome bisulfite sequencing of ros1-3 and ros1-4 with the wildtype col-0 plants at 12-d-old, using Illumina HiSeq 2000 system

first: June-Sik

last: Kim

first: Hosub

last: Shin

first: Jin


title: Novel genes differentiating Eosinophilic Esophagitis (EoE) from GERD identified by RNA Sequencing

city: Durham

first: Integrative

last: Bioinformatics

state: NC

address: 111 TW Alexander Drive

department: BCBB

institute: NIEHS

summary: RNA sequencing analysis of proximal and distal esophageal biopsies from a small cohort of EoE, GERD, and control patients was performed to identify differentially expressed genes.

overall_design: Proximal and distal esophageal biopsies from three patients with EoE, GERD, and control esophagus, 18 samples total

first: Curt

last: Hagedorn

first: Kathy

last: Peterson


title: Screen of differential expression genes on bat hibernating regulation

city: Guangzhou

first: Lihong

last: Yuan

state: Guangdong

address: 105 Xin-gang Xi road

institute: Guangdong Entomological Institute

summary: We report the application of the Illumina/Solexa sequencing-by-synthesis platform to analysis differential expression genes of two key tissues (brain and adipose tissue) during hibernation vs. aroused state, with a hibernating bat species (Myotis ricketti) as model. Total of 12272 genes were identified including 11291 genes in brain and 10691 genes in adipose tissue. Chi-square test indicated that 1943 and 3673 genes in brain and adipose tissues respectively reached the significant level (P â¤ 0.01), including 1243 up-regulated and 700 down-regulated genes in hibernating brain and 2621 up-regulated and 1052 down-regulated genes in hibernating adipose tissue. This study provide opportunity to in-deep analysis the molecular mechanism of hibernating regualtion.

overall_design: Screening the differential expressed genes of 2 different tissues in 2 states.

first: Haibo

last: Sun

first: Benfu

first: Shuyi

last: Zhang


title: miRNA regulatory networks in male and female mouse ESC-to-EpiSC differentiation [miRNA]

summary: Early stem cell differentiation programmes are tightly controlled by coordinated pre- and post-transcriptional regulatory networks. In this study, we investigate and characterise miRNA networks responsible for the post-translational gene regulation in early differentiation in both female and male mouse embryonic stem cells. We obtained miRNA-Seq and RNA-Seq profiles of male and female cells from day 0 (D0; 2i) to days 4, 10, 20 and 30. Interestingly, we observed a significant difference in gene expression profiles between females and males, both in terms of identity of regulated genes and of temporal characteristics. Similarly, we observed differences between miRNA species playing significant regulatory roles in female and male cells.

overall_design: mESC small RNA profiles during differentiation were generated by deep sequencing using Illumina.

first: Christel

last: Picard

first: Constance

last: Ciaudo

first: Christopher

last: Workman

first: Edith

last: Heard


title: Rage null mice exposed to cigarette smoke demonstrate attenuated inflammatory, oxidative and ER stress responses in alveolar macrophages

summary: Analysis of alveolar macrophage gene expression in C57BL6 wild-type and RAGE null mice exposed to cigarette smoke

overall_design: 4 groups of 3-4 mice at two exposure time points (7-day and 4 month), 31 samples total

first: John

last: Hoidal

first: Karl

last: Sanders


title: miRNA regulatory networks in male and female mouse ESC-to-EpiSC differentiation [mRNA]

first: Federico

overall_design: mESC mRNA profiles during differentiation were generated by deep sequencing using Illumina.


title: RNA m6A-Ythdf1 in dendritic cells triggers anti-tumor immunity (RNA-seq and RIP-seq in in GMDCs)

status: Public on Dec 29 2018

city: Bethesda

first: Chuanyuan

last: Chen

address: 9000 Rockville Pike, Building 37

department: National Cancer Institute

institute: National Institutes of Health

summary: Emerging evidence emphasizes the important role of tumor neoantigen in generating the spontaneous antitumor immune response and predicting the clinical response to immunotherapies. Despite the presence of numerous neoantigens, complete tumor elimination rarely occurs in majority of patients due to failures in mounting a sufficient and lasting antitumor immunity. Here we show that the durable neoanitgen-specific immunity is regulated by a m6A-binding protein, Ythdf1. In contrast to wild-type mice, Ythdf1-deficient (Ythdf1-/-) mice generate more antigen-specific CD8+ T cell response for persistent tumor control. Loss of Ythdf1 in dendritic cell (DC) results in an enhanced cross-presentation of tumor antigen and cross-priming of CD8+ T cell in vivo. To confirm our observations, we performed RNA-Seq to analyze the transcriptional level of genes in DCs and performed RNA Immunoprecipitation (RIP-seq) to locate the binding sites of Ythdf1.

overall_design: To confirm our observations about the functional influence of Ythdf1 on DCs, we performed RNA-Seq to analyze the transcriptional level of genes in DCs from WT and Ythdf1-/- mice.  To indentify the mRNA that recognized by Ythdf1, we performed profiling of RNA Immunoprecipitation (RIP-seq) to locate the binding sites of Ythdf1. GMCSF-induced bone marrow DCs (GMDCs) were used for library preparation.

first: Dali

last: Han

first: Meng

last: Xu

first: Chuan

last: He


title: FOXO1 Regulates Attachment of the Implanting Blastocyst to the Endometrium at the Window of Receptivity [ChIP-seq]

city: Houaton

first: Rainer

middle: B

last: Lanz

state: TX

address: One Baylor Plaza

department: Molecular and Cellular biology

institute: Baylor College of Medicine

summary: We report the whole genome binding profile of the Forkhead Box O1

overall_design: ChIP-seq in murine endometrium

first: Franscesco

middle: J

last: DeMayo

first: Yasmin

last: Vasquez


title: Hair follicle stem cells sense niche integrity and recruit immune cells to contain barrier breaches

status: Public on Dec 28 2018

first: Kenneth

last: Lay

state: NY

address: 1230 York Avenue

institute: The Rockefeller University

summary: We demonstrated that hair follicle stem cells (HFSCs) are able to sense the integrity of their epithelial niche. By ablating a core cell junction component E-cadherin (encoded by Cdh1), the epithelial niche no longer maintains proper barrier function, leading to microbial infiltration through the hair follicle.  The surrounding HFSCs respond by increasing its expression of immune associated genes and recruiting immune cells to their niche so as to cope with compromised tissue function.

overall_design:
Transcriptomes of hair follicle stem cells (HFSCs) FACS-purified from Cdh1 cKO and Het mice non-treated or treated with the immunosuppressant dexamethasone (Dex) were subjected to Ilumina HiSeq4000 next-generation sequencing.
Transcriptomes of cells comprising the HFSC bulge niche were FACS-purified from Cdh1 cKO and Het mice and subjected to Ilumina HiSeq4000 next-generation sequencing.

first: Elaine

last: Fuchs


title: RNA m6A-Ythdf1 in dendritic cells triggers anti-tumor immunity

state: MD


title: Differential lipid synthesis in the developing seeds of Jatropha and Vernicia: a comparative transcriptomic study

city: Changsha

first: Dangquan

address: South Shaoshan Road

institute: Central South University of Forestry and Technology

summary: Two Euphorbiaceae oil trees, Vernicia and Jatropha, were chosen to make a comparative transcriptomic study, with a focus on the differential oil accumulation process. Transcriptome sequencing was conducted with seeds at the initial- and fast- stage of oil accumulation from both.

sample_organism:
Vernicia fordii
Jatropha curcas

platform_organism:
Vernicia fordii
Jatropha curcas

overall_design: Seeds of three-year-old Jatropha or Vernicia trees were collected, with the former from a natural farmland in southern Guizhou province of China and the later from northwest Hunan province. Samples collected at two distinct developing stages: the early stage of oil accumulation (S1, Jcu_29DAP, Vfo_90 DAP) and the fast accumulation stage (S2, Jcu_37DAP, Vfo_135DAP). To eliminate the sampling error, total RNAs were extracted independently from three seeds, equally mixed and used for illumina library preparation.

first: Huaiyun

first: Dan

last: Yang

first: Kuan

last: Peng


title: Roles of Staphylococcus aureus alternative sigma factor B in staphylococcal bovine mastitis

city: bangkok

first: Sirirak

last: Supa-amornkul

address: 272 Payatai

department: Microbiology

country: Thailand

institute: Mahidol University

summary:
A sigB null (∆sigB) mutant was constructed and analyzed for its phenotypes and transcriptome along with those of the parental RF122 strain.
Method: Duplicate samples of rRNA depleted RNA from wild type and mutants were used to study transcriptomes by ion torrent platform.

overall_design: rRNA-depleted RNA samples from stationary phase wilde type and sigB null mutant cultures were used to compare transcriptomes.  Some affected genes from RNAseq result were selected for confirmation by quantitative reverse transcriptase PCR.

first: Paninee

last: Mongkolsuk

first: Soraya

last: Chaturongakul


title: Next Generation Sequencing Facilitates Quantitative Analysis of floral-fruit Transcriptomes

city: Beijing

first: Jing

last: Li

address: xiangshan street

institute: Beijing institute of botany

summary:
Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of plants. The goals of this study are to compare omparatively evaluated both sequence variation and gene expression at the transcriptomic level between two species.
Methods: Pooled total RNA of P. floridana flower buds and young fruits, in triplicate, using Illumina HiSeqTM 2000.  The sequence reads remove reads with adaptors or unknown nucleotides larger than 5% and low-quality reads using . qRT–PCR validation was performed using TaqMan and SYBR Green assays
Results:  Sequencing the Physalis transcriptome revealed 147,118 unigenes. When aligned to the tomato genome, we estimated that around 30,121 genes were expressed in the Physalis floral-fruit transcriptome, and 10,498 orthologous gene pairs were identified between P. floridana and S. pimpinellifolium.with a fold change ≥1.5 and FER value <0.001,  0.68% of the unigenes in the Physalis floral-fruit transcriptome were developmentally regulated at the floral-fruit transition, and Altered expression of 15 genes was confirmed with qRT–PCR, demonstrating the high degree of sensitivity of the RNA-seq method.
Conclusions: Our study represents the first detailed analysis of floral-fruit transcriptomes, with biologic replicates, generated by RNA-seq technology.The optimized data analysis workflows reported here should provide a framework for comparative investigations of expression profiles. Our results show that NGS offers a comprehensive and more accurate quantitative and qualitative evaluation of mRNA content within a organ or tissue. We conclude that RNA-seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions.

overall_design: total mRNA profiles of flower and fruit were generated by deep sequencing, in triplicate, using HiSeqTM 2000.

first: Chaoying


title: Expression data from Wild-type (WT) and Astrocyte elevated gene-1 (AEG-1) knockout (KO) bone marrow derived macrophages (BMDM)

status: Public on Dec 27 2018

first: Mikhail

last: Dozmorov

address: 830 E Main St

department: Biostatistics

summary: AEG-1 is overexpressed in human hepatocellular carcinoma (HCC) and positively regulates inflammation and development and progression of HCC. An AEG-1KO mouse was generated to understand the function of AEG-1 in inflammatory processes in HCC.

overall_design: BMDMs were isolated from WT and AEG-1KO mice for RNA extraction and RNA-sequencing.

first: Devanand

last: Sarkar


title: Nicotinamide Nucleotide Transhydrogenase as a novel treatment target in adrenocortical carcinoma

status: Public on Feb 01 2019

city: Birmingham

first: Wiebke

last: Arlt

address: Edgbaston

department: Institute of Metabolism and Systems Research  (IMSR)

institute: University of Birmingham

summary: RNA-seq samples used to support a study in to the understanding of antioxidant targeting in adrenocortical carcinoma

overall_design: Pairwise comparison of knockdown samples against controls (scrambled si/sh-RNA)

first: Vasileios

last: Chortis

first: Angela

last: Taylor

first: Craig

middle: L

last: Doig

first: Mark

last: Walsh

first: Eirini

last: Meimaridou

first: Carl

last: Jenkinson

first: Giovanny

last: Rodriguez-Blanco

first: Cristina

last: Ronchi

first: Alisha

last: Jafri

first: Louise

last: Metherell

first: Daniel

last: Hebenstreit

first: Warwick

last: Dunn

first: Paul

last: Foster


title: CDK4/6 inhibition sensitizes myeloma to lenalidomide by reducing the MEIS2 to CRBN ratio that accelerates IKZF1 and IKZF3 degradation

city: New York

first: Selina

last: Chen-Kiang

address: 1300 York Avenue

department: Pathology and Laboratory Medicine

institute: Weill Cornell Medical College

summary: The RNA-seq data presented in this study include libraries from bone marrow plasma cells (BMPC), primary myeloma cells (BMMCs) from 7 patients, and myeloma cell line MM1.S and KMS12

overall_design: RNA-Seq on BMPC, BMMCs and cell line samples

first: Xiangao

last: Huang

first: David

last: Jalabalan

first: Maurizio

last: Di Liberto


title: Fatty Acid Oxidation and Glycolysis Regulate Skin ECM Homeostasis by Shifting Fibroblasts between Catabolism and Anabolism (RNA-Seq)

city: Toronto

first: Benjamin

last: Haibe-Kains

state: Ontario

address: 610 University Avenue

department: Princess Margaret Research

country: Canada

institute: Princess Margaret Cancer Centre

summary:
Transcriptome profiling of murine skin fibrosis, and its treatment through CD36highCD90+ fibroblast transplantation revealed the most significant alterations to be involved in fatty acid metabolism and glycolysis.

The paper has been published: https://www.nature.com/articles/s42255-018-0008-5?WT.feed_name=subjects_metabolism

overall_design: Transcriptome profiling via RNA-seq of murine skin fibrosis +/- CD36highCD90+ fibroblast transplantation

first: Fei

last: Liu


title: RNAseq of drought treated  Populus trichocarpa

city: Raleigh

first: Vincent

last: Chiang

address: 840 Main Campus Drive

department: Forestry and Environmental Resources

institute: North Carolina State University

summary: To identify genes that are drought-responsive we conducted drought (soil water depletion) experiments on 3-month-old *P*. *trichocarpa *clonal plants. The plants undergo five different stages based on the appearance of their shoots and leaves during the drought experiments. Stage I: The shoot and leaves are green, and the leaves are well-spread. Stage II: The leaves are droopy. Stage III: The shoot is droopy, and the leaves are partially dry. Stage IV: The leaves are brown and totally dry. Stage V: The shoot is brown. With fully irrigation, the soil water content is 74% and the xylem water content is 80.6%. Plants in Stage III (Day 5) are under a mild drought state. The soil and xylem water content in Stage III dropped to 33% and 75.3%, respectively. Stage IV (Day 6-10) is a severe drought state where the soil and xylem water content continued decreasing to 29% and 74.3%, respectively in Day 7. The stressed plants from Stage I-IV could all recover in 3 days after rehydration, but the plants in Stage V could not recover after rehydration.

overall_design: We collected the xylem tissue from plants (1) without drought treatment (Control, Day 0), (2) under mild drought stress (Stage III, Day 5), (3) under severe drought stress (Stage IV, Day 7) followed by RNA-seq analysis.

first: V


title: SCL establishes a global repressive environment and cooperates with Polycomb RYBP-PRC1 to suppress alternative lineages in blood-fated cells [SCL ChIP-seq]

city: Oxford

first: Hedia

last: Chagraoui

address: john radcliffe hospital headley way headington

department: Molecular Hematology Unit

institute: Weatherall Institute of Molecular Medicine

summary: Understanding the molecular basis of cell fate decision is critical to shed light onto biological processes supporting tissue formation. In particular, whether lineage-fated cells derive from multi-primed progenitors and need to establish active fate restriction mechanisms to engage in a differentiation pathway is still matter of debate. To characterise the mechanisms underlying specification of blood-fated cells from mesodermal precursors, we studied the transcriptional activity of the key hematopoietic regulator SCL/TAL1. Scl-null mouse embryos die at embryonic day E9.5 from absence of blood formation, and exhibit mis-specification of mesodermal cells into cardiomyocytes, thus offering an excellent entry point for mechanistic studies of fate determination. Using high-throughput assays from mouse ES cell-derived mesodermal cells, we showed that, in parallel with activating the blood program and repressing the cardiac and paraxial programs, SCL strongly activates expression of repressors, such as ETO2 (known partner of SCL) and RYBP (member of Polycomb repressive complex PRC1). ETO2’s association with chromatin reflects SCL’s overall genomic binding, pointing to ETO2’s modulatory, rather than purely repressive, transcriptional activities. In contrast, SCL/RYBP chromatin co-occupancy is preferentially enriched at genes normally repressed in blood-fated cells and involved in early developmental processes and alternative lineages, highlighting a relationship between SCL and RYBP/PRC1 in repressive processes. Remarkably, SCL is critical for maintaining high levels of PRC1-associated repressive histone mark H2AK119ub genome-wide. It is also required for maximal levels of repressive mark H3K27me3 on genes normally repressed. Finally, Rybp knock-down in differentiating ES cells phenocopies the cardiac phenotype of Scl-null cells, supporting a functional interaction between SCL and a critical repressive chromatin remodeling complex. Altogether, these data unveil the establishment of a repressive environment in mesodermal progenitors by a hematopoietic-specific transcriptional regulator. This leads to restriction of expression of regulators of alternative fates and uncompromised commitment towards a hematopoietic identity.

overall_design: SCL Chip sequencing was performed from two independent wild type ES cell differentiation where we isolated at day 3.5 of EB formation FLK1+ mesodermal cells.

first: Catherine

last: Porcher


title: SCL establishes a global repressive environment and cooperates with Polycomb RYBP-PRC1 to suppress alternative lineages in blood-fated cells [RNA-seq]

overall_design: RNA  sequencing was performed from three independent  ES cell differentiation where we isolated at day 3.5 of EB formation FLK1+ mesodermal cells from WT and Scl -/- background.


title: Integrative analysis of genome-wide histone H3 lysine 9 acetylation and gene expression in *Populus trichocarpa* under drought stress reveals that AREB1 transcription factors recruit the GCN5-ADA2b complexes to activate drought-inducible gene expression

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

overall_design: Refer to individual Series


title: Differential expression of pancreatic cancer  PANC1 cells treated with pilocarpine

status: Public on Dec 26 2018

first: Timothy

middle: Cragin

last: Wang

address: 1130 St. Nicholas Ave

department: Medicine- Liver and Digestive Diseases

institute: Columbia University Medical Center

summary: Human Panc1 cells were treated with 1mM  Pilocarpine and the differential expression measured by RNASeq

overall_design:
a. PANC1 cells untreated (n=4)
b. PANC1 cells treated with 1 mM pilocarpine for 72 hours (n=4)

first: Takayuki

last: Tanaka

first: Bernhard

middle: W

last: Renz

first: Masaki

last: Sunagawa

first: Ryota

last: Takahashi

first: Zhengyu

last: Jiang

first: Marina

last: Macchini

first: Giovanni

last: Valenti

first: Ruth

last: White

first: Moritz

last: Middelhoff

middle: E

last: Oberstein

first: Xiaowei

last: Chen

first: Huan

last: Deng

first: Yoku

last: Hayakawa

first: Yagnesh

last: Tailor

first: Karan

last: Nagar

last: Chu

first: Richard

last: Friedman

first: Kenneth

middle: P

last: Olive

middle: C


title: Genome-wide analysis of histone H3 lysine 9 acetylation in Populus trichocarpa under drought stress

first: Vincent

last: Chiang

summary: We report on the genome-wide distribution pattern of histone H3 lysine 9 acetylation (H3K9ac) and the pattern’s association with whole genome expression profiles in Populus trichocarpa subjected to soil-water depletion. We identified a set of drought responsive genes whose expression is directly regulated by differential modification of H3K9ac.

overall_design: We treated 3-month-old Populus trichocarpa plants by no watering. Plants were under a mild drought state without watering after 5 days (Day5) and under a severe drought state after 7 days (Day7), and plants fully irrigated were as a control (Day0). Differential H3K9ac enrichments under mild and severe drought treatments were examined in stem differentiating xylem (SDX) of the Populus trichocarpa plants.


title: Gene expression profile of neurons expressing protein kinase C δ (PKCδ) or somatostatin (SST) in the central amygdala (CEA) of mice

city: Vienna

first: Thomas

middle: Rainer

last: Burkard

address: Dr. Bohrgasse 7

country: Austria

institute: IMBA

summary: Circuit neuroscience has made great progress by linking neuronal function to marker gene expression, allowing the specific investigation of otherwise indistinguishable neuronal ensembles. Here, we performed next generation sequencing on two functionally and genetically distinct interneuronal populations marked by the expression of protein kinase C δ (PKCδ) or somatostatin (SST) in the central amygdala (CEA) of mice, which are known to play distinct and sometimes opposing roles in emotion processing. Making their gene expression profile known will aid in forming hypotheses of how different neurotransmitters or psychoactive drugs could alter information processing in these neurons.

overall_design: Unchallenged gene expression profile of two different neuronal populations in the central amygdala

first: Johannes

last: Griessner

first: Nadia

last: Kaouane

first: Barbara

last: Werner

first: Wulf

last: Haubensak


title: Primate fetal hepatic response to maternal obesity: epigenetic signaling pathways and lipid accumulation [miRNA-seq]

city: San Antonio

first: Sobha

last: Puppala

department: Genetics

institute: Texas Biomedical Research Institute

summary: The liver is a major site for synthesis, storage and redistribution of carbohydrates, proteins and lipids. In addition, it is well-known that maternal obesity (MO) increases risk of offspring cardiovascular disease (CVD), diabetes and obesity. However, the mechanisms by which the MO intrauterine environment predisposes offspring to CVD and metabolic dysregulation are unknown. The goal of this study was to assess the impact of MO on primate fetal liver and identify underlying molecular mechanisms by which MO increases disease risk. The goal of this study was to identify candidate molecular mechanisms underlying MO in the near-term NHP fetal liver. This is the first study of NHP fetal MO livers using unbiased transcriptome analysis to quantify hepatic gene expression, identify dysregulated signaling pathways and potential miRNAs regulating the disrupted metabolic processes. Unbiased gene (arrays) and microRNA (miRNA; small RNA-Seq) abundances were quantified in near-term (0.9 Gestation (0.9G)) baboon fetal livers (control (CON) = 6; MO = 5) and subjected to pathway and network analyses (GeneSifter, Ingenuity® Pathway Analysis (IPA)) to identify a coordinated molecular response to MO. Lipid and glycogen content (CON = 16; MO = 16) were quantified by Computer Assisted Stereology Toolbox (CAST) in 0.9G livers.Pairwise comparisons showed 933 differentially expressed genes between CON and MO livers: 350 genes were upregulated and 583 were downregulated. Pathway analysis revealed upregulation of Wnt/β-catenin signaling and downregulation of tricarboxylic acid (TCA) cycle, proteasome, oxidative phosphorylation and glycolysis pathways in MO fetal livers compared with CON. Inversely expressed miRNAs that target genes in these pathways provide additional support for the importance of these pathways in fetal liver metabolic regulation. Consistent with the observed pathway changes in MO, we found hepatic lipid content was threefold greater in MO than CON fetal livers (p=0.02). Molecular genetic analyses of CON and MO fetal baboon livers revealed dysregulation of Wnt/β-catenin signaling, TCA cycle, proteasome, oxidative phosphorylation and glycolysis pathways in MO livers, all of which are central to fatty acid metabolism and lipid storage. The marked lipid accumulation in MO fetal livers supports our hypothesis that dysregulation of these pathways detrimentally impacts lipid management. Furthermore, our findings demonstrate the detrimental impact of MO on fetal liver development and suggest impaired hepatic function prior to birth.

overall_design: MicroRNA (miRNA; small RNA-Seq) abundances were quantified in near-term (0.9 Gestation (0.9G)) baboon fetal livers (control (CON) = 6; MO = 5) and subjected to pathway and network analyses (GeneSifter, Ingenuity® Pathway Analysis (IPA)).

first: Cun

last: Li

first: Jeremy

last: Glenn

first: Amy

last: Quinn

first: Jennifer

last: Palarczyk

first: Edward

last: Dick Jr

first: Peter

last: Nathanielsz

first: Laura

middle: A

last: Cox


title: Biosynthesis of histone messenger RNA employs a specific 3' end endonuclease

first: Nicholas

last: Proudfoot

address: South Parks Road

institute: Sir William Dunn School of Pathology,  University of Oxford

summary: During S-phase of the cell cycle production of the core histone proteins is precisely balanced with DNA replication. Metazoan mRNAs encoding replication dependent (RD) histones lack polyA tail normally formed by 3’ end cleavage and coupled polyadenylation of the pre-mRNA. Instead, they undergoes to endonucleolytic cleavage on the 3ʹ side of an RNA hairpin (stem loop) producing mRNA with a 3´-stem loop (SL), which is exported from the nucleus for use in translation. The same endonuclease that is involved in normal protein-coding pre-mRNA cleavage, i.e. cleavage and poyladenylation specificity factor 73 (CPSF73), is proposed to catalyse RD pre-histone mRNA cleavage. Additional factors specific to RD pre-histone mRNA processing, including stem loop binding protein (SLBP) and the U7 small nuclear ribonucleoprotein (U7snRNP) that binds to a histone downstream element (HDE) are thought to be involved in CPSF73 targeting to RD pre-histone mRNA. We report that a different histone specific endonuclease (HSE), which like CPSF73 is a metallo β lactamase (MBL) fold protein, is specific for RD pre-histone mRNA cleavage10,11. Crystallographic and biochemical studies reveal HSE has a di-zinc ion containing active site related to that of CPSF73, but which has distinct overall fold. Notably HSE depletion from cells leads to the production of unprocessed RD pre-histone mRNA due to inefficient 3ʹ end processing. The consequent depletion of core histone proteins correlates with a cell cycle defect due to a delay in entering/progressing through S-phase. HSE thus may represent a new type of S-phase specific cancer target.

overall_design: Examination of chromatin mRNA profiles in HeLa cells after depletion of HSE or CPSF73 by siRNA treatment.

first: Ilaria

last: Pettinati

first: Claudia

last: Ribeiro de Almeida

first: Somdutta

last: Dhir

first: Christopher

last: Schofield


title: Transcriptome Analysis of miRNAs in Umbilical cord blood exosomes of Intrauterine Growth Restriction Pigs

city: chongqing

first: Jia

last: Luo

state: chongqing

address: tiansheng road

institute: Southwest University

summary: Dysfunctional umbilical cord blood (CB) is an important factor for the development of IUGR in utero. However, the genetic mechanism underlying the miRNAs in CB exosomes influence the development of IUGR is not well characterized. Herein, we present a comprehensive investigation of miRNA transcriptome of umbilical cord vein and artery between IUGR and normal littermate. We total identified 636 unique miRNAs. There were 116 significant differentially expressed (DE) miRNAs between umbilical vein of normal (NV) and IUGR (IV) and 226 DE miRNAs between umbilical artery of normal (NA) and IUGR (IA) (P < 0.001). Cluster analysis revealed that umbilical artery had the most striking divergence, implied it plays more prominent role in the development of IUGR. The miRNAs enriched in NA mainly participate in blood vessel development, regulation of transcription and growth. The miRNAs highly expressed in IA mainly enriched in apoptosis, cell death, embryonic development and immune system development Besides, miRNAs related to oxygen transfer (miR-210, miR-424), angiogenesis (miR-130a, miR-150, miR-34a) and immune system development (miR-181a, miR-155) were lower expressed in IUGR. Our findings demonstrate that CB derived miRNAs participate in fetal epigenetic regulation during pregnancy, which may supply a new explanation for abnormal embryologic development and some congenital diseases.

overall_design: Investigation of miRNA transcriptome of umbilical cord vein and artery between IUGR and normal littermate

first: Li

last: Zhu


title: Next generation sequencing facilitates quantitative transcriptomic comparison between HA107 conditioned and unconditioned germ-free small intestinal tissue.

city: Bern

first: Andrew

middle: J.

last: Macpherson

state: Bern

address: Murtenstrasse 35

department: Department for BioMedical Research

institute: University of Bern

summary: The goal of this study is to identify durable transcriptomic reprogramming after transient bacterial colonisation in germ-free mice.

overall_design: The HA107 conditioned mice were prepared by reversible colonisation (10^10 CFU bacterial gavage for four times on alternate days) two weeks prior to the small intestinal sampling. Unconditioned mice were trated similarly with PBS gavage.

first: Yasuhiro

last: Uchimura


title: RNA Methyltransferase METTL14 Promotes Breast Cancer Growth and Progression

first: Yidong

last: Chen

state: Texas

address: 8403 Floyd Curl Drive, MSC 7784

department: Population Health Sciences

institute: UT Health Science Center at San Antonio

summary: We investigated the role of RNA N6-adenosine methyltransferase protein METTL14 that supports breast cancer growth and progression, and we showed METTL14 knockdown inhibited long-term survival, migration as well as invasion of breast cancer cells.

overall_design: To understand the mechanism by which METTL14 may promote breast cancer growth, we performed RNA-seq analyses on METTL14 siRNA-transfected breast cancer cells (2x MDA-MB-231), comparing to cells transfected with scramble siRNAs (2 replicates). Interestingly, several genes known to be associated with oncogenic pathways were found to be significantly altered in METTL14-silenced breast cancer cells, including transforming growth factor beta1 (TGFβ1), smad3, cyclin D1 and cyclin E1.

first: Subbarayalu

last: Panneerdoss

first: Vijay

middle: K

last: Eedunuri

first: Manjeet

last: Rao


title: RNA-sequencing of milk cells extracted from pre-partum secretions and longitudinally from mature human milk across the first year of lactation

city: Crawley

first: Alecia-Jane

last: Twigger

state: WA

address: 35 Stirling Highway

department: Chemistry and Biochemistry

country: Australia

institute: The University of Western Australia

summary: Changes in mammary cell behavior mediating normal breast development during pregnancy and lactation are poorly understood due to limited availability of breast biopsies during this time. Human milk contains a hierarchy of cells including stem cells, mature milk producing cells (lactocytes) and myoepithelial cells. Here we non-invasively sampled the total epithelial cell population of the lactating mammary gland from mature HM collected from healthy mother/infant dyads during the first year postpartum, and explored temporal changes in the mammary cell transcriptome using RNA sequencing. Comparisons were done with mammary secretions from late pregnancy from the same women and with purchased resting mammary tissue. Distinct gene signatures were found for the different mammary developmental stages examined. Cell adhesion pathways were differentially regulated between the resting gland and pregnancy, whereas immune cell signaling and morphogenesis/cancer pathways differed between lactation and pregnancy or the resting gland, respectively. The transcriptome of lactation remained consistent in the first year postpartum in these successfully lactating women. The gene signatures characteristic of HM cells confirmed lactation genes previously reported in animal models and the HM fat globule. This study identifies key genes and molecular pathways undergoing controlled regulation as the mammary gland transitions from a quiescent into a functional organ, providing experimental targets for the molecular investigation of mammary gland pathologies.

overall_design: The human milk cell transcriptome was generated from cells extracted from pre-partum samples and mature milk at months 1, 3, 6 and 12 of lactation.

first: Foteini

last: Kakulas


title: Groucho related gene 5 (GRG5) is required for the maintenance of embryonic and neural stem cells

status: Public on Dec 25 2018

city: Heraklion, Crete

first: KONSTANTINA

last: CHANOUMIDOU

address: Nikolaou Plastira 100

department: Institute of Molecular Biology and Biotechnology (IMBB)

country: Greece

institute: Foundation for research and technology - HELLAS (FORTH)

summary: Groucho related gene 5 (GRG5) is a multifunctional protein that has been implicated in late embryonic and postnatal mouse development. Here, we describe a previously unknown role of GRG5 in early developmental stages by analyzing its function in stem cell fate decisions. By both loss and gain of function approaches we demonstrate that ablation of GRG5 deregulates the Embryonic Stem Cell (ESC) pluripotent state whereas its overexpression leads to enhanced self-renewal and acquisition of cancer cell-like properties. A pro-oncogenic potential for GRG5 is revealed by the malignant behavior of teratomas generated from ESCs that overexpress it. Furthermore, transcriptomic analysis and cell differentiation approaches underline GRG5 as a multifaceted signaling regulator that represses mesendodermal-related genes. When ES cells exit pluripotency, GRG5 promotes neuroectodermal specification via Wnt and BMP signaling pathways suppression. Moreover, GRG5 promotes the neuronal reprogramming of fibroblasts and maintains the self-renewal of Neural Stem Cell (NSC) by sustaining the activity of Notch and Jak/Stat3 pathways. In summary, our results demonstrate that GRG5 has pleiotropic roles in stem cell biology functioning as a stemness factor and a neural fate specifier.

overall_design: Gene expression profiling of control and Grg5 knockdown (KD) embryonic stem cells with RNA-seq, in dublicate, using Ion Torrent Proton.

first: Konstantina

last: Chanoumidou

first: Christiana

last: Hadjimichael

first: Henrik

last: Ahlenius

first: Christoforos

last: Nikolaou

first: Antonis

last: Klonizakis

first: Elias

last: Drakos

last: Kostouros

first: Maria

last: Grigoriou

first: Androniki

last: Kretsovali


title: Transcriptomic analysis of Aspergillus flavus and its ASPES transcription factor deletion strains

city: Jinan

first: Guangshan

last: Yao

address: No 27 ShanDa nan road

department: School of life science

institute: Shandong university

summary: RNA-seq was used to compare differential gene expressions for Aspergillus flavus wild type strain and  ASPES transcription factor deletion strains.The goals of this study are to explore the aflatoxin regulation pathway in A. flavus.

overall_design: Examination of differential gene expressions by RNA-seq in Aspergillus flavus wild type strain under both YES and YEP, and two APSES transcription factor mutant strains(AfRafA knoutout strain and AfStuA)

first: Shihua

last: Wang


title: Identification of novel recurrent ETV6-IGH fusions in primary central nervous system lymphoma using high throughput RNA sequencing

city: Paris

first: Pierre

last: de la Grange

address: 29, rue du Faubourg Saint-Jacques

department: Paris Biotech Santé

country: France

institute: GenoSplice technology

summary: We provide a novel gene fusion (ETV6-IgH) involving a truncation of ETV6 and leading to haploinsuffiency of ETV6 expression. ETV6-IgH is a new potential surrogate marker of PCNSL with favorable prognosis

overall_design: We have performed RNA-Seq in 6 PCNSL patients and we have pinpointed several new chimeric transcripts

first: Aurelie

last: Bruno

first: Agusti

last: Alentorn


title: HIF-1α activation is sufficient for the development of MDS

city: Hachioji

first: Yoshihiro

last: Hayashi

state: Tokyo

address: 1432-1 Horinouchi

country: Japan

institute: Tokyo University of Pharmacy and Life Sciences

summary: Hypoxia inducible factor-1α (HIF-1α) is a critical transcription factor for the hypoxic response, angiogenesis, normal hematopoietic stem cell regulation, and cancer development. Importantly, HIF-1α is also a key regulator for immune cell activation. In order to determine whether HIF-1α is sufficient for developing MDS phenotypes, we generated blood specific inducible HIF-1α transgenic mice. Using Vav1-Cre/Rosa26-loxP-Stop-loxP (LSL) rtTA driver, stable HIF-1α can be induced in a doxycycline administration dependent manner. After induction, HIF-1α-induced mice developed thrombocytopenia, leukocytopenia, macrocytic anemia, and multi-lineage dysplasia. We also found activation of both innate and adaptive immunity in HIF-1α- induced mice compared to those from control mice. Taken together, these data suggest that HIF-1α is sufficient to trigger a variety of key MDS features

overall_design: Expression profiles of mRNA in HSPCs from constitutively active form of HIF1a protein induced mice and their control mice.

first: Gang

last: Huang


title: RNA-Seq analysis of human colorectal cancer with liver metastasis

city: Shanghai

first: DA

last: FU

state: Shanghai

address: Middle 301 Yanchang Road

institute: Shanghai Tenth People's Hospital

overall_design: Nine specimens from three colorectal cancer (CRC) patients including adjacent normal tissue, primary tumor, and lever metastasis tissue, and three specimens from 3 CRC patients without liver metastasis were collected for RNA sequencing analysis. The mRNA libraries were separately generated from total RNA and constructed according to the standard Illumina mRNA library preparation (Illumina Inc, USA). Sequencing was done on the Illumina Nextseq 500 platform according to the manufacturer’s instructions. Images generated by Nextseq 500 were converted into nucleotide sequences by a base calling pipeline and stored in FASTQ format and the dirty raw reads were filtered out prior to analyzing the data. Clean reads were mapped to reference Homo sapiens transcriptome sequences from the UCSC website (hg19) using Bowtie2 and Tophat 2.0.1 software. To annotate gene expression, reads per kilo bases per million reads (RPKM) values of each gene were calculated, and differentially expressed genes (DEGs) were extracted using this value.

first: Da

last: Fu


title: Neoplastic pancreas cells enter a quasi-mesenchymal state with increased oncogenic potential following transient TGF-β exposure

first: Dafna

last: Bar-Sagi

address: 550 First Avenue, SML 206

department: Biochemistry and Molecular Phamacology

country: USA

institute: NYU Langone Medical Center

summary: Pancreatic ductal adenocarcinoma (PDAC) is a deadly disease and a major health problem in the United States. While the cytokine TGF-β has been implicated in PDAC development, it can exert bot pro- and anti-tumorigenic effects that are highly context dependent and incompletely understood. To better characterize the responses of neoplastic pancreas cells to TGF-β, three-dimensional (3D) cultures of KrasG12D-expressing mouse pancreatic epithelial cells were employed. While active exposure to exogenous TGF-β caused the KrasG12D cells to growth arrest, its subsequent removal allowed the cells to enter a hyper-proliferative, quasi-mesenchymal (QM) and progenitor-like state. This transition was highly stable and maintained by autocrine TGF-β signaling. Transient pulses of TGF-β have been observed during pancreatitis, a major risk factor for PDAC, and may therefore serve to convert pre-existing KrasG12D-expressing cells into QM cells. While untreated KrasG12D cells formed simple cysts in vivo, QM cells formed ductal structures resembling human PanINs. Furthermore, markers of the QM state are expressed in human PDAC and are associated with worse outcomes. These data suggest that the QM state plays a role in PDAC development and may selectively contribute to more aggressive PDAC subtypes. This work therefore provides novel molecular insights into both PDAC development and the complex role of TGF-β in tumorigenesis.

overall_design: Three technical replicates per experimental group from one isolate were analyzed by RNA  sequencing

first: Jesse

last: Handler

first: Jane

last: Cullis

first: Emily

last: Vucic

first: Antonina

last: Avanzi


title: Transcriptomic study of soybean (Glycine max) leaves in response to short-term phosphorus deficiency

city: Hangzhou

first: Houqing

last: Zeng

address: NO.2318, Yuhangtang Rd, Yuhang District

country: China

institute: Hangzhou Normal University

summary: We conducted a genome-wide transcriptomic analysis in soybean leaves treated with a short-term (24 h) Pi-deficiency using RNA sequencing (RNA-seq) technology. Two biological replicates of RNA-seq were included for both Pi-sufficient leaves (PSL) and Pi-deficient leaves (PDL), and therefore a total of four libraries were constructed. Using a 2-fold change and a P-value ≤0.05 as the cut-off for selecting the differentially expressed transcripts, we globally identified short-term Pi-stress responsive genes. Some DEGs potentially involved in Pi sensing, signaling, and homeostasis were up-regulated by Pi deprivation, including five SPX-containing genes. Some DEGs possibly associated with water and nutrient uptake, hormonal and calcium signaling, protein phosphorylation and dephosphorylation, and cell wall modification were affected at the early stage of Pi deprivation. At least thirty-one transcription factor genes belonging to 10 diverse families were found to be responsive to Pi starvation.

overall_design: The first trifoliate true leaves of soybean were harvested after 24 h treatment with or without phosphate, and RNA was extracted and sequenced by paired-end sequencing. RNA sequencing reads were aligned against the soybean reference genome and differentially expressed genes between treatments were detected.


title: Regulatory divergence controlling wound-responsive gene expression in domesticated and wild tomatoes

city: Taipei

first: Ming-Jung

last: Liu

address: 128 Sec. 2, Academia Rd, Nankang

country: Taiwan

institute: Academia sinica

summary: We report the global wound-induced gene expression profile to compare the underlying transcriptional mechansims among S. lycopersicum, jasmonic acid–insensitive1 (jai1) and S. pennellii.

sample_organism:
Solanum lycopersicum
Solanum pennellii

platform_organism:
Solanum lycopersicum
Solanum pennellii

overall_design: We examined the mRNA abundances in response to mechanical wounding in the leaves of S. lycopersicum,  jai1 and S. pennellii.

first: Koichi

last: Sugimoto

first: Gregg

last: Howe

first: Shin-Han

last: Shiu


title: Transcriptome profiles of seminiferous tubes on different stage of spermatogenesis

city: Beijing

first: Xiaoyu

last: Li

address: 1 Beichen West Road, Chaoyang District

institute: Institute of Zoology, Chinese Academy of Sciences

summary: In order to get the different gene expression profiles of these seminiferous tubules on different stages of spermatogenesis, four groups of samples were taken in accordance with the differentiation stage of germ cells, namely: empty tubes before SSCs transplantation (named as “EmptBtrans”), empty tubes after SSCs transplantation (named as “EmptAtrans”), tubes which SSCs had successfully homed and differentiated into spermatocytes and round spermatids (named as “SM_and_RS”) and fluorescent tubes which were taken from recipient mice that already had offsprings to make sure these tubes had complete spermatogenesis (named as “sperm”).  Pairwise comparison was made between these four groups, the number of significantly differentially expressed genes increased with the differentiation of germ cells.

overall_design: Compare the gene expression profiles of different seminiferous tubules containing different kinds of germ cells

first: Yixun


title: FTO Regulates Activation of Rho GTPases Signaling as N6-methyladenosine RNA Demethylase and an Rhotekin Partner Protein

city: chicago

first: jun

last: liu

state: Illinois

institute: UoC

summary: Reversible RNA modification of N6-methyladenosine (m6A) plays a critical role in post-transcriptional gene regulation1-13. Although the fat mass and obesity-associated protein (FTO) has been previously shown to function as an m6A demethylase in nuclear RNA1,14, its exact function in disease pathogenesis remains a mystery. Here, we demonstrate that FTO suppresses the activation of Rho GTPase signaling via both its demethylation activity and specific interaction with Rho effector, Rhotekin (RTKN)15. The knockdown of FTO activates RhoA and RhoC, induces stress fibres, and accelerates cell migration. Endogenous RTKN is highly expressed in certain cancer and cancer-derived cell lines16,17 with overexpression of RTKN leading to moderate activation of Rho18. We further found that overexpression of RTKN blocks nuclear import of FTO and traps FTO in the cytoplasm to mediate m6A demethylation of cytosolic mRNA, thereby changing gene expression by preventing m6A-dependent mRNA decay and translation. Our results illustrate how FTO represses Rho activation through m6A demethylation and direct interaction with RTKN, and shed new light on FTO-dependent post-transcriptional gene regulation in RTKN overexpressed cancers, which may provide a new direction for developing anti-cancer therapies.

overall_design: RNA-seq in HeLa cells

first: Jun

first: Zhike

last: Lu

first: Guifang

last: Jia