title: RNA sequencing of K562 and MOLT4 cell lines

city: West Haven

first: Sarah

last: Slavoff

state: Connecticut

address: Yale University West Campus-Building 600

department: Chemistry

institute: Yale University- West Campus

summary: Here, we present global microprotein quantitation in two human leukemia cell lines, K562 and MOLT4. We identify unannotated microproteins that are differentially expressed in these cell lines. The expression of six microproteins was validated biochemically, and two were found to localize to the nucleus. Thus, we demonstrate that label-free comparative proteomics enables quantitation of microprotein expression between human cell lines, and that differentially expressed microproteins have properties, like subcellular localization, consistent with functionality.

overall_design: Gene expression changes between three biological replicates from K562 cells and MOLT4 cells are quantified.

first: Alexandra

last: Khitun


title: The KMT2D Kabuki syndrome histone methylase controls neural crest cell differentiation and facial morphology

status: Public on Jun 01 2020

city: Chapel Hill

first: Karl

middle: B.

last: Shpargel

state: NC

address: 120 Mason Farm Road

department: Genetics

country: USA

institute: University of North Carolina

type: Expression profiling by high throughput sequencing

summary: We report RNA-seq from mouse E14.25 WT and KMT2D neural crest cell knockout palatal shelves

overall_design: RNA-seq from 3 biological replicates of paired palatal shelves from WT and KMT2D neural crest cell knockout embryos

middle: B

first: Terry

last: Magnuson


title: Identification of RUNX1 targets in iLSCs

status: Public on Jun 03 2020

city: New York

first: Hanzhi

last: Luo

state: New York

address: 417 E 68th street

department: Molecular Pharmacology

institute: MSKCC

type: Genome binding/occupancy profiling by high throughput sequencing

summary: We identified 2 phenotypically and functionally distinct populations in our AML-iPSC line upon hematopoietic differentiation. One population is phenotypically and functionally a leukemia stem cell population (iLSCs = Samples A) and the second is more differentiated (iBlasts = Samples S). We found RUNX1 to be critical for iLSC maintenance and used gene expression and chromatin accessibility analyses after RUNX1 KD in iLSCs and iBlasts to identify the molecular mechanism of RUNX1 in iLSCs.

overall_design: examination of RUNX1 KD in iLSCs vs iBlasts using RNAseq and ATACseq, triplicates per group

first: Josephine

last: Wesely

first: Andriana

middle: G

last: Kotini

first: Franco

last: Izzo

first: Han

last: Yuan

first: Jun

last: Sun

first: Maria

last: Georgomanoli

first: Asaf

last: Zviran

first: Andre

last: Deslauriers

first: Neville

last: Dusaj

first: Stephen

middle: D

last: Nimer

first: Christina

last: Leslie

first: Dan

middle: A

last: Landau

first: Michael

last: Kharas

first: Eirini

middle: P

last: Papapetrou


title: Tobacco RNA Dependent RNA Polymerase 1 affects the expression of defence related genes in Nicotiana benthamiana during geminivirus infection

city: Cambridge

first: Archana

last: Singh

state: England

address: Downing Street

department: Plant Science

country: United Kingdom

institute: Cambridge University

type: Non-coding RNA profiling by high throughput sequencing

summary: RNA dependent RNA Polymerase 1 of Nicotiana tabacum modulates ToLCV pathogenesis by influencing a number of defence related genes in N. benthamiana plants.

overall_design: To understand the reduced susceptibility of NtRDR1 N. benthamiana plants during ToLCV infection, NGS of sRNAs was carried out from wild-type N. benthamiana (Mock) wild-type N. benthamiana-ToLCV infected, NtRDR1 N. benthamiana (Mock), NtRDR1 N. benthamiana-ToLCV infected plants. All samples were in triplicates.

first: Ved

last: Prakash

first: Ashish

last: Kumar Singh

first: Tamas

last: Dalmay

first: Supriya

last: Chakraborty


title: Hippocampal Gene Expression in bred High Responder (bHR) vs. bred Low Responder (bLR) Rats: RNA-Seq Data from Generation F29

status: Public on Jun 02 2020

city: Ann Arbor

first: Megan

middle: Hastings

last: Hagenauer

state: MI

address: 205 Zina Pitcher Pl.

department: MBNI

institute: University of Michigan

summary: The strong pattern of comorbidity amongst psychiatric disorders is believed to be generated by a spectrum of latent liability, arising from a complex interplay of genetic risk and environmental factors, such as stress and childhood adversity. At one end of this spectrum are internalizing disorders, which are associated with neuroticism, anxiety, and depression. At the other end of the spectrum are externalizing disorders, which are associated with risk-taking and novelty-seeking, as seen in mania, substance abuse, and impulse-control disorders. We model the genetic contributions underlying both extremes of this spectrum by selectively breeding rats that react differently to a novel environment. “Bred high responder” (bHR) rats are highly exploratory with a disinhibited, novelty-seeking temperament, including hyperactivity, aggression, and drug-seeking. “Bred low responder” (bLR) rats are highly-inhibited, exhibiting reduced locomotor activity and anxious and depressive-like behavior. These behavioral propensities are robust and stable, beginning early in development similar to temperament in humans.   This RNA-sequencing study examined gene expression in the hippocampus, a region critical for emotional regulation, in generation F29 male bHR rats and bLR rats from two ages: P14 and adulthood (n=2/group).

overall_design: Overall Design: This RNA-sequencing study examined gene expression in the hippocampus in generation F29 male bHR rats and bLR rats from two ages: P14 and adulthood (n=2/group).     Sacrifice & RNA Extraction: Rats were sacrificed through rapid decapitation, followed by immediate brain extraction. The whole hippocampus was rapidly dissected on ice, fast-frozen at –40°C, and stored at –80°C before processing. TRIzol reagent (Invitrogen, Calsbad, CA) was used to extract total RNA, followed by purification using RNeasy RNA purification columns (Qiagen, Valencia, CA). The quality and concentration of the RNA was determined using an Agilent bioanalyzer (Palo Alto, CA) and wavelength absorbance (260/280 nm ratio) by Nanodrop.  RNA Sequencing: Purified RNA was shipped to the Genomic Services Laboratory at HudsonAlpha (https://gsl.hudsonalpha.org/index) for short-read (50 bp length) single-end sequencing. RNA Qubit was used to assess concentration (range: 720-1120 ng/uL). The dilutions were denatured through heat application at 70˚C for two minutes and then checked for quality with a RNA Nano bioanalysis chip. Indexed non-stranded cDNA libraries were then prepared using standard Illumina procedures and a TruSeq library preparation kit (Illumina) after which they were pooled for sequencing with four samples per pool. The pooled libraries were clustered on a HiSeq flowcell (Illumina) and sequenced using a first generation HiSeq 2000 sequencer.    RNA-Seq Data Preprocessing: Reads were mapped to the rat reference genome (RGSC v3.4) using Tophat2 and Bowtie2 with default parameters and a standard sequence read output. Only reads that aligned with the genome once were maintained for later differential expression analysis. Transcript assembly was collected using Cufflinks and Cuffmerge (Trapnell et al. 2012; Nat Protoc. 7: 562–578), and bHR vs. bLR differential expression was assessed for each age group (P14 and adult) using CuffDiff (Trapnell et al. 2012; Nat Protoc. 7: 562–578).

middle: H

first: Sarah

middle: M

last: Clinton

first: Fan

last: Meng

first: Isabelle

last: Birt

first: Stanley

middle: J

last: Watson Jr

first: Huda

last: Akil


title: Hippocampal Gene Expression in bred High Responder (bHR) vs. bred Low Responder (bLR) Rats: Affymetrix Microarray Data from Generation F4

summary: The strong pattern of comorbidity amongst psychiatric disorders is believed to be generated by a spectrum of latent liability, arising from a complex interplay of genetic risk and environmental factors, such as stress and childhood adversity. At one end of this spectrum are internalizing disorders, which are associated with neuroticism, anxiety, and depression. At the other end of the spectrum are externalizing disorders, which are associated with risk-taking and novelty-seeking, as seen in mania, substance abuse, and impulse-control disorders. We model the genetic contributions underlying both extremes of this spectrum by selectively breeding rats that react differently to a novel environment. “Bred high responder” (bHR) rats are highly exploratory with a disinhibited, novelty-seeking temperament, including hyperactivity, aggression, and drug-seeking. “Bred low responder” (bLR) rats are highly-inhibited, exhibiting reduced locomotor activity and anxious and depressive-like behavior. These behavioral propensities are robust and stable, beginning early in development similar to temperament in humans.   This Affymetrix (Rat Expression Set 230 A) microarray study examined gene expression in the hippocampus in generation F4 adult male bHR rats and bLR rats (n=6 per group).

overall_design: Overall Design: This microarray study examined gene expression in the hippocampus in generation F4 adult male bHR rats and bLR rats (n=6 per group).   Behavioral testing: Locomotor response to a novel environment was assessed between age P50–75 as part of our selective breeding paradigm (protocol: Stead et al., 2006, Behav Genet. 36: 697–712).  Sacrifice & RNA Extraction: The rats were sacrificed in adulthood (between P102-P108) via rapid decapitation followed by immediate brain extraction. The whole hippocampus, frontal cortex, and hypothalamus samples were rapidly dissected on ice, fast-frozen at –40°C, and stored at –80°C before processing. TRIzol reagent (Invitrogen, Calsbad, CA) was used to extract total RNA, followed by purification using RNeasy RNA purification columns (Qiagen, Valencia, CA). The quality and concentration of the RNA was determined using an Agilent bioanalyzer (Palo Alto, CA) and wavelength absorbance (260/280 nm ratio) by Nanodrop.  Microarray: The samples were transcriptionally profiled using Affymetrix Rat Expression Set 230 A (RAE230A) microarray according to standard manufacturer’s procedures. The samples were run in two batches: the first included the hippocampus and cortex samples and the second included the hypothalamus samples. Each brain region was run on a separate chip. Only data from the hippocampal samples are included in this data release.  Microarray Data Preprocessing: For our current analyses, the ReadAffy() function (from R package affy version 1.54.0; Gautier et al. 2004, Bioinformatics. 20: 307–315) was used to read the data from the hippocampal Affymetrix .CEL files into R studio (R Studio v.1.0.153, R v.3.2.2). An expression set was generated using the Robust Multi-Array Average method (RMA: Irizarry et al. 2003, Biostatistics. 4: 249–264). Using a custom .cdf (Dai et al. 2005, Nucleic Acids Res. 33: e175) we summarized the probe signals into probesets for the RAE230A chip (“rae230arnentrezgcdf_19.0.0”) which mapped the probe sequences to Entrez Gene IDs (downloaded from http://nmg-r.bioinformatics.nl/NuGO_R.html on Jan 2017, release date Nov 2015). We re-annotated the data according to Official Gene Symbol using the function org.Rn.egSYMBOL() from the R package org.Rn.eg.db (version 3.4.1; Carlson 2017, http://bioconductor.org/packages/org.Rn.eg.db/), and then removed rows lacking annotation (leaving 9,959 gene symbols). Quality control identified two samples with low sample-sample correlation values (around 0.66: 13F4-H07M1.1-HPC-HR-1 and 22F4-L08M2.0-HPC-LR-5), leaving a final sample size of n=5 per group. The full analysis code is available at: https://github.com/isabellie4/PhenotypeProject and https://github.com/hagenaue/bHRbLR_MetaAnalysisProject.

first: John

last: Stead


title: Development of a gene expression-based prognostic signature for IDH wild-type glioblastoma [GLARIUS]

city: South San Francisco

first: Radia

last: Johnson

state: CA

address: 1 DNA Way

institute: Genentech

summary:
Background. We aimed to develop a gene expression-based prognostic signature for isocitrate dehydrogenase (IDH) wild-type glioblastoma using clinical trial datasets representative of glioblastoma clinical trial populations.
Results. NanoString data were available from 512 patients in the discovery ATE dataset. Elastic net identified a prognostic signature of nine genes (CHEK1, GPR17, IGF2BP3, MGMT, MTHFD1L, PTRH2, SOX11, S100A9, and TFRC). Translating weighted elastic net scores to an average z-score signature conserved the prognostic value of the ATE signature. The z-score signature was prognostic for OS in the ATE dataset (P < 0.0001), as expected, and in the validation cohorts (AVAglio, P < 0.0001; GLARIUS, P = 0.021; UCLA, P = 0.0037). The signature remained prognostic following adjustment for MGMT promoter methylation status or corticosteroid use at baseline. A positive correlation between the signature and proneural/proliferative subtypes was observed in patients with MGMT non-methylated promoter status.
Conclusions. The ATE signature showed prognostic value and may enable clinical trial stratification for IDH wild-type glioblastoma.

overall_design: Methods. Samples were collected from newly diagnosed patients with IDH wild-type glioblastoma in the ARTE, TAMIGA, EORTC 26101 (collectively referred to as ‘ATE’), AVAglio, and GLARIUS trials, or treated at UCLA. Transcriptional profiling was achieved with the NanoString gene expression platform. To identify genes prognostic for overall survival (OS), we built an elastic net Cox-penalized regression model using the ATE dataset for discovery. For validation in independent datasets (AVAglio, GLARIUS, UCLA), we combined elastic net-selected genes into a robust z-score signature to overcome gene expression platform differences between the discovery and validation cohorts.

first: Christoph

last: Mancao

first: Richard

last: Bourgon

first: Josep

last: Garcia


title: γδ T Cells Promote Steatohepatitis by Orchestrating Innate and Adaptive Immune Programming

first: Varshini

last: Vasudevaraja

state: NY

address: 550 1st Avenue

department: Pathology

institute: NYU Langone Health

summary: Gene ontology analysis suggests that MCD diet induced changes in CD4+ T cells and γδ Tcells

overall_design: Compare the transcriptome of γδ Tcells in WT Mice fed Ctl or MCD diet, and CD4+ T cells in WT and γδTCR-/- mice and fed Ctl or MCD diet

first: Alejandro

last: Torres-Hernandez

first: George

last: Miller


title: A novel method for genome-wide profiling of poly(A)-tail lengths

status: Public on Jun 04 2020

city: Wuhan

first: Dong

last: Chen

state: Hubei

address: 388 GaoXin 2nd Road, East Lake Hi-Tech Development Zone

department: Center for Genome Analysis

country: China

institute: ABLife, Inc.

summary: Polyadenylation at the 3’ end of eukaryotic messenger RNAs enhances mRNA stability and translational efficiency. Global analysis for poly(A) tail lengths may shed lights on various aspects of gene regulation studies. Two NGS-based methods have been introduced for genome-wide poly(A) profiling, and they have shown human poly(A) profiles with shorter than previously conceived tail lengths. However, both methods are technically challenging and difficult to be repeated or widely adapted. Here we present a more straightforward method for poly(A) profiling. Poly(A)-seq performed on Illumina NextSeq 500 produces single-end 300 nt reads that covers the entirety of poly(A) tails, and poly(A) lengths can be directly calculated from base call data. With Poly(A)-seq we report that the global poly(A) lengths of several human cell lines may be longer than previously reported. We also show that the size selection step during Poly(A)-seq library preparation may greatly affect the sequencing profile, and thus cautions should be taken for comparisons between samples. As a convenient tool, we hope wide applications of Poly(A)-seq helps to bring better understanding of poly(A) tail properties and functions.

overall_design: The poly(A) length profiles of human HeLa (wild-type and siPTB), HEK293T and HCT116 cells were examined.

first: Wenqing

last: Wang

first: Fengyun

last: Yu

first: Zisong

last: Zhou

first: Yu

last: Zhang

first: Chao

last: Cheng

first: Wenliang

last: Rang

first: Qijia

last: Wu

first: Yi


title: Hippocampal Gene Expression in bred High Responder (bHR) vs. bred Low Responder (bLR) Rats

first: Megan

last: Hagenauer

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

overall_design: Refer to individual Series


title: Insights into olfactory ensheathing cell development from a laser-microdissection and transcriptome-profiling approach

first: Clare

last: Baker

state: Cambridgeshire

department: Dept. Physiology, Development & Neuroscience (PDN)

institute: University of Cambridge

summary: Olfactory ensheathing cells (OECs) are neural crest-derived glia that ensheath bundles of olfactory axons from their peripheral origins in the olfactory epithelium to their central targets in the olfactory bulb. We took an unbiased laser microdissection and differential RNA-seq approach, validated by in situ hybridisation, to identify candidate molecular mechanisms underlying mouse OEC development and differences with the neural crest-derived Schwann cells developing on other peripheral nerves. We identified 25 novel markers for developing OECs in the olfactory mucosa and/or the olfactory nerve layer surrounding the olfactory bulb, of which 15 were OEC-specific, i.e., not expressed by Schwann cells. One pan-OEC-specific gene, Ptprz1, encodes a receptor-like tyrosine phosphatase that blocks oligodendrocyte differentiation. Mutant analysis suggests Ptprz1 may also act as a brake on OEC differentiation, and that its loss disrupts olfactory axon targeting. Overall, our results provide new insights into OEC development and the diversification of neural crest-derived glia.

overall_design: Embryonic mouse olfactory nerve regions (at E11.5, E13.5 and E16.5) and trigeminal nerve (at E16.5) were isolated in situ by laser microdissection of 8 μm cryosections of flash-frozen embryos. mRNA profiles were generated by sequencing using the Illumina NextSeq 500 platform (multiplex paired-end). At least 3 replicates were analysed per sample type.

first: C

middle: V


title: Hippocampal Gene Expression in bred High Responder (bHR) vs. bred Low Responder (bLR) Rats: Illumina Microarray Data from Generation F15

summary: The strong pattern of comorbidity amongst psychiatric disorders is believed to be generated by a spectrum of latent liability, arising from a complex interplay of genetic risk and environmental factors, such as stress and childhood adversity. At one end of this spectrum are internalizing disorders, which are associated with neuroticism, anxiety, and depression. At the other end of the spectrum are externalizing disorders, which are associated with risk-taking and novelty-seeking, as seen in mania, substance abuse, and impulse-control disorders. We model the genetic contributions underlying both extremes of this spectrum by selectively breeding rats that react differently to a novel environment. “Bred high responder” (bHR) rats are highly exploratory with a disinhibited, novelty-seeking temperament, including hyperactivity, aggression, and drug-seeking. “Bred low responder” (bLR) rats are highly-inhibited, exhibiting reduced locomotor activity and anxious and depressive-like behavior. These behavioral propensities are robust and stable, beginning early in development similar to temperament in humans.   This Illumina (RatRef-12v1 Beadchip) microarray study examined gene expression in the hippocampus in generation F15 male bHR rats and bLR rats at age postnatal day 14 (P14, n=6 per group).

overall_design: Overall Design: This microarray study examined gene expression in the hippocampus in generation F15 male bHR rats and bLR rats at age postnatal day 14 (P14, n=6 per group).  Sacrifice & RNA Extraction: The rats were sacrificed at postnatal day 14 (P14) via rapid decapitation followed by immediate brain extraction. The whole hippocampus was rapidly dissected on ice, fast-frozen at –40°C, and stored at –80°C before processing. TRIzol reagent (Invitrogen, Calsbad, CA) was used to extract total RNA, followed by purification using RNeasy RNA purification columns (Qiagen, Valencia, CA). The RNA was divided into two aliquots earmarked for transcriptional profiling using different microarray platforms. The quality and concentration of the RNA was determined using an Agilent bioanalyzer (Palo Alto, CA) and wavelength absorbance (260/280 nm ratio) by Nanodrop.  Microarray: One aliquot from each sample was transcriptionally profiled using Illumina (RatRef-12v1 Beadchip) microarray according to standard manufacturer’s procedures.   Microarray Data Preprocessing: To extract the AVG_Signal for all probes for each of the samples, we used the read.idat() function (R package limma version 3.28.21; Ritchie et al. 2015, Nucleic Acids Res. 43: e47). We performed a log2 transformation and then quantile normalized the data using the normalize.quantiles() function in the R package preprocessCore (version 1.34.0; Bolstad 2016 https://github.com/bmbolstad/preprocessCore). During quality control, a potential outlier was noted during principal components analysis (PCA). However, due to the strong sample-sample correlations among all samples (>0.98), removing the outlier was deemed unnecessary. The full analysis code is available at: https://github.com/isabellie4/PhenotypeProject and https://github.com/hagenaue/bHRbLR_MetaAnalysisProject.

first: Sarah

last: Clinton

first: Isabelle

last: Birt

first: Stanley

last: Watson Jr

first: Huda

last: Akil


title: Critical roles of translation initiation and RNA uridylation in endogenous retroviral expression and neural differentiation in pluripotent stem cells

city: Kyoto

first: Kazutoshi

last: Takahashi

address: 53 Kawahara-cho, Shogoin, Sakyo-ku

department: Center for iPS Cell Research and Application

country: Japan

institute: Kyoto University

summary: Previous studies have suggested that the loss of the translation initiation factor eIF4G1 homolog NAT1 induces excessive self-renewability of naïve pluripotent stem cells (PSCs). Yet the role of NAT1 in the self-renewal and differentiation of primed PSCs, is still unclear. Here we generated conditional knockout of NAT1 in primed PSCs and used the cells for the functional analyses of NAT1. Our results showed that NAT1 is required for the self-renewal and neural differentiation of primed PSCs. In contrast, NAT1 deficiency in naïve pluripotency attenuated the differentiation to all cell types. We also found that NAT1 is involved in efficient protein expression of an RNA uridyltransferase TUT7. TUT7 is involved in the neural differentiation of primed PSCs via the regulation of human endogenous retrovirus accumulation. These data demonstrated the essential roles of NAT1 and TUT7 in the precise transition of stem cell fate.

overall_design:
Conditional knockout of NAT1 gene in primed human iPSCs, N=6
Conditional knockout of NAT1 gene in naïve-like human iPSCs, N=6
Conditional knockout of NAT1 gene in human NPCs, N=12

first: K

first: M

last: Narita


title: Deciphering the molecular effects of non-ablative Er:YAG laser treatment in an in vitro model of the non-keratinized mucous membrane

city: Aachen

first: Sebastian

last: Huth

address: Pauwelsstr. 30

country: Germany

institute: Uniklinik RWTH Aachen

summary: This study aimed to investigate the molecular effects of non-ablative Er:YAG laser treatment using an in vitro model of the non-keratinized mucous membrane and to compare its molecular effects with other ablative and non-ablative laser systems. In dermatology, the use of non-ablative and ablative fractional lasers has become the gold standard treatment for a number of indications. Each of the individual laser types is advantageous for different types of indications due to its respective properties, but new technologies open up new fields of application for individual laser systems. Performing a comprehensive gene expression profiling we compared the gene regulatory effects of non-ablative Er:YAG laser with other non-ablative and ablative laser systems. In vitro 3D models have proven to be a reliable and reproducible tool to study the molecular biological effects of different laser settings.

overall_design: Eight samples were analyzed: Er:YAG (non-ablative) treated vs. Er:YAG (non-ablative) control; CO2 (ablative) treated vs. CO2 (ablative) control; Er:YAG (ablative) treated vs. Er:YAG (ablative) control; Er:Glass (non-ablative) treated vs.  Er:Glass (non-ablative) control.

first: Laura

first: Yvonne

last: Marquardt

first: Philipp

last: Winterhalder

first: Timm

last: Steiner

first: Frank

last: Hölzle

first: Reinhard

last: Gansel

first: Jens

last: Baron

first: Laurenz

last: Schmitt


title: Genome-wide maps of O-GlcNAc proteins in human breast cancer cells by next generation sequencing

city: panjin

first: bo

middle: yu

last: liu

state: liaoning

address: Dagong Road 2

institute: Dalian University of Technology

summary: We applied the chemical reporter-based metabolic labeling method to acquire O-GlcNAc modified proteins chromatin loci. Human breast cancer cell line MCF-7, as well as the genotoxic stress (Adriamycin) adapted cells MCF-7/ADR, were fed with 1 mM GalNAz. Metabolic labeled O-GlcNAz chromatin were crosslinked, sonicated and enriched by bioorthogonal chemistry. Then, the genomic DNA fragments bounded by O-GlcNAc mark were de-crosslinked, and constructed into libraries following by next-generation sequencing (Chemoselective O-GlcNAc chromatin sequencing, COGC-seq). To verify the robustness of this chemical reporter-based metabolic labeling method, we compared the results in MCF-7 and MCF-7/ADR cells with classical lectin succinylated wheat germ agglutinin (sWGA) ChIP-seq strategy. We also analyzed gene expression MCF-7 and MCF-7/ADR cells by RNA-seq.

overall_design: Examination O-GlcNAc protein bound chromatin loci in human breast cancer cells MCF-7 and MCF-7/ADR cells. Gene expression profiling of MCF-7 and MCF-7/ADR cells were performed by RNA-seq.

first: Yubo

last: Liu

first: Nana

last: Zhang

first: Yu

last: Cao

first: Tongyi

last: Dou

first: Jianing


title: Age-resolved ribosome profiling and RNA-Seq data of mice liver and kidney samples

city: Vienna

first: Aleksandra

middle: S

last: Anisimova

address: Dr. Bohr Gasse 9

country: Austria

institute: Max Perutz Labs, Vienna BioCenter, University of Vienna, Medical University of Vienna

summary: We report ribosome profiling and RNA-Seq data of liver and kidney samples taken from C57BL/6 mice of different ages

overall_design: Ribosome profiling and transcriptome sequencing of liver and kidney samples of C57BL/6 mice of different ages. Liver samples were collected from mice of six (1, 3, 11, 20, 26 and 32 months) different ages, whereas kidney samples were collected from the same mice of three (3, 20 and 32 months) ages. Samples from three animals were taken for each age, except for 32 months old mice (2 animals).

first: Mark

last: Meerson

first: Maxim

last: Gerashchenko

first: Ivan

last: Kulakovskiy

first: Sergey

middle: E

last: Dmitriev

first: Vadim

middle: N

last: Gladyshev


title: E proteins orchestrate dynamic transcriptional cascades implicated in the suppression of the differentiation of group 2 innate lymphoid cells [RNA-Seq]

status: Public on May 31 2020

city: Oklahoma City

first: Jonathan

last: Wren

state: OK

address: 825 N.E. 13th Street

department: Genes & Human Disease Research Program

institute: OMRF

summary: Group 2 innate lymphoid cells (ILC2s) represent a subset of newly discovered immune cells that are involved in immune reactions against microbial pathogens, host allergic reactions as well as tissue repair.  The basic helix-loop-helix transcription factors collectively called E proteins powerfully suppress the differentiation of ILC2s from bone marrow and thymic progenitors while promoting the development of B and T lymphocytes.  How E proteins exert the suppression is not well understood.  Here we investigated the underlying molecular mechanisms using inducible gain and loss of function approaches in ILC2s and their precursors, respectively.  Cross-examination of RNA sequencing and ATAC sequencing data obtained at different time points reveals a set of genes which are likely direct targets of E proteins.  Consequently, a widespread down-regulation of chromatin accessibility occurs at a later time point, possibly due to the activation of transcriptional repressor genes such as Cbfa2t3 and Jdp2.  The large number of genes repressed by gain of E protein function leads to the down-regulation of a transcriptional network important for ILC2 differentiation.

overall_design: RNA-seq was performed on thymic ILC2 cells isolated from Id1 transgenic mice, which were transduced with retroviruses expressing either GFP alone or together with an E47-ER fusion protein after stimulation with ILC2, IL-7, IL-25 and IL-33.  Transduced cells were sorted for GFP and expanded in ILC2, IL-7, IL-25 and IL-33.  The cells were then treated with 4-hydroxy-Tamoxifen for 4 or 16 hours before harvested for RNA isolation.

first: Xiao-Hong

last: Sun

first: Constantin

last: Georgescu


title: Development of a gene expression-based prognostic signature for IDH wild-type glioblastoma [UCLA]

first: Radia

last: Johnson

first: Christoph

last: Mancao

first: Richard

last: Bourgon

first: Josep

last: Garcia


title: Development of a gene expression-based prognostic signature for IDH wild-type glioblastoma [AVAglio]


title: STIM1-mediated gene expression in non-pathogenic and pathogenic CD4+ Th17 cells

first: Stefan

last: Feske

address: 550 First Avenue

institute: New York University School of Medicine

summary: Immunity to fungal infections is mediated by cells of the innate and adaptive immune system. Activation of immune cells requires Ca2+ influx through the Ca2+ channel ORAI1, which is activated by stromal interaction molecule 1 (STIM1). Th17 cells are essential for immunity to C. albicans infection and require Ca2+ influx for expression of IL-17A and other Th17 cytokines. In mice, deletion of STIM1 and thus Ca2+ influx in all immune cells enhanced susceptibility to mucosal C. albicans infection, whereas T cell-specific deletion of STIM1 impaired immunity to systemic C. albicans infection. STIM1 deletion in CD4 T cells had different effects on gene expression programs in pathogenic (proinflammatory) and non-pathogenic Th17 cells. STIM1 deletion in non-pathogenic Th17 cells, which are required for antifungal immunity, compromised the expression of genes in several metabolic pathways including Foxo and HIF-1a signaling as well as the TCA cycle and oxidative phosphorylation (OXPHOS). Consequently, STIM1 deficient non-pathogenic Th17 cells had impaired glycolysis and mitochondrial respiration. By contrast, STIM1 deletion in pathogenic Th17 cells showed only attenuated mitochondrial function but normal glycolysis.

overall_design: Comparing transcriptome of WT and Stim1fl/fl Cd4Cre Th17 cells

first: Sascha

last: Kahlfuss

first: Ulrike

last: Kaufmann


title: Development of a gene expression-based prognostic signature for IDH wild-type glioblastoma


title: Development of a gene expression-based prognostic signature for IDH wild-type glioblastoma [ATE]


title: RNA-seq analysis in NRG1 and enzalutamide treated 22Pc-EP cell line

city: New York City

first: Zeda

last: Zhang

address: 1275 York Aveune

institute: Memorial Sloan Kettering Cancer Center

summary: Transcriptome prolifing analysis was performed in 22Pc-EP cells to identify differentially regulated genes by enzalutamide and NRG1

overall_design: 22Pc-EP cells were treated with androgen receptor inhibition (enzalutamide) or a HER3 ligand NRG1 for 48hrs.

first: Charles

middle: L

last: Sawyers


title: Solar UVR and exosomal miRNAs effect pre-mature senescence in melanocytes [microarray]

city: Cleveland

first: Nikki

last: Harter

state: Ohio

address: 10900 Euclid Avenue

department: Biochemistry

institute: Case Western Reserve University

summary: The selection of specific miRNAs by exosomes and their release from cultured melanocytes after exposure to solar UVR (UVA+UVB) have activities in inducing these cells into a premature senescence.

overall_design: In this analysis, Affymetrix's GeneChip miRNA 4.0 array was used to measure changes in the levels of miRNAs in exosomes from un-irradiated and irradiated melanocytes

first: M


title: Transcriptional profiling of macrophages derived from young and aged injured nerves at 3 days post-injury

city: Montreal

first: Jo Anne

last: Stratton

state: Quebec

address: 3801 University Road

department: Neurology and Neurosurgery

country: Canada

institute: McGill University

summary: Pro-regenerative macrophages are well known for their role in promoting tissue repair, however in aging macrophage numbers are reduced acutely and repair following nerve injury deminished. Macrophage-targeted RNAseq revealed that macrophages expressed an array of ligands post nerve injury, and several of these ligands are downregulated in aging.

overall_design: RNAseq experiment was performed on FACS-collected cells obtained from the nerves of adult and aged female mice (n=7-8 per time point at Day 3 nerve injury) from a double macrophage reporter (Cx3cr1-GFP/Ccr2-RFP) mouse line (stock no.: 017586; stock No.: 005582, Jackson Laboratories). Samples were pooled to obtain 2 RNAseq sample replicates per time point.

first: Jo

first: Jeff

last: Biernaskie


title: High-throughput sequencing reveals induction of drug metabolism in various cholestatic livers

city: Urbana

first: Waqar

last: Arif

state: IL

address: 506 S. Mathews Avenue

institute: UIUC

summary: Cholestasis is a multifactorial disorder that compromises liver function. We wanted to examine Phase I and II drug metabolism in cholestatic livers. We performed high-throughput sequencing on livers from Fxr-/- Shp-/- double knockout mice, which mimic juvenile cholestasis. Next, we used comparative transcriptomic approach to test if the induction in drug metabolism is also seen in models of liver injury, including steatosis, regeneration and bile acid-stressed livers.

overall_design: Hepatic mRNA expression profiles of adult wild type, CAR-activated (TCPOBOP injected) (n=2), Fxr-/- Shp-/- (n=3), high fat diet-fed (n=2), partial hepatectomized (n=3) and bile acid diet-fed (n=3) mice.

first: Bhoomika

last: Mathur

first: Megan

last: Patton

first: Faiyaz

last: Rahiman

first: Auinash

last: Kalsotra

first: Anthony

last: Wheatley

first: Sayeepriyadarshini

last: Anakk


title: NKL homeobox gene activity in normal and malignant myeloid cells

city: Braunschweig

first: Claudia

last: Pommerenke

address: Inhoffenstraße 7B

institute: Leibniz Institute DSMZ

summary: Recently, we have reported a hematopoietic NKL-code which describes normal expression patterns of NKL homeobox genes in early hematopoiesis and lymphopoiesis including T-cell, B-cell and NK-cell development. This code allows the identification of deregulated NKL homeobox genes in lymphoid malignancies. Here, we report normal activities of NKL homeobox genes in myelopoiesis, thus, extending the NKL-code for the hematopoietic system. Analysis of public expression profiling data for developing and mature granulocytes, mast cells, monocytes, macrophages, megakaryocytes and erythrocytes revealed seven active myeloid NKL homeobox genes including DLX2, HHEX, HLX, HMX1, NANOG, NKX3-1 and VENTX. Furthermore, we analyzed public expression profiling data of 251 acute myeloid leukemia (AML) patients identifying 18 deregulated genes. These results indicated that NKL homeobox genes are frequently deregulated in this myeloid malignancy. For detailed analysis we focused on NKL homeobox gene NANOG which acts as stem cell factor and was accordingly expressed just in hematopoietic stem/progenitor cells. We detected aberrant NANOG expression in a small subset of AML patients and in AML cell line NOMO-1 which served as model to investigate upstream and downstream factors of this gene. Karyotyping and genomic profiling excluded rearrangements of the NANOG locus at 12p13. Analysis of NOMO-1 cells treated for NANOG knockdown, expression profiling analyses of HL-60 cells lentivirally transfected for NANOG overexpression, and of public AML patient data revealed regulators and target genes of NANOG. NKL homeobox genes HHEX and MSX1 and the NOTCH-pathway were located upstream of NANOG and HHEX, HLX, VENTX, MYB, CDK6, MAML2 and MIR17HG represented target genes of NANOG in the myeloid context. In conclusion, we described a myeloid NKL-code and several deregulated NKL homeobox genes in AML. We identified for NKL homeobox gene NANOG deregulating factors and downstream activities in AML. These data indicate a common oncogenic role of NKL homeobox genes in myeloid malignancies.

overall_design: Expression profiling analyses of HL-60 cells lentivirally transfected for NANOG overexpression.

first: Stefan

last: Nagel


title: The Tug1 locus is required for male fertility and comprised of DNA, RNA and Protein regulatory elements

status: Public on May 27 2020

city: Boulder

first: Audrey

middle: Renee

last: Watson

state: Colorado

address: 3415 Colorado Avenue

institute: University of Colorado Boulder

summary: We have sequenced mouse embryonic fibroblasts (MEFs) and 6 organs (testes, prostate, liver, heart, spleen, and eye) harvested from adult male wild type and Tug1 knockout (Tug1_tm1.1Vlcg) mice in a C57BL/6J/129S6 (N3-C57BL/6J, no Neo) background.  Additional sequencing was done on the testes of a Tug1 rescue mouse, which contains a doxycycline inducible allele for Tug1 (tg(Tug1)) and CAGs-rtTA3 in the Tug1 knockout background (Tug1_tmn1.1Vlcg).

overall_design: Comparison between wild type and Tug1 knockout (Tug1_tm1.1Vlcg) organs and primary cell transcriptomes. Additional comparisons of the transcriptomes of wildtype, knockout, and rescue testes.

first: Jordan

last: Lewandowski

first: Gabrijela

last: Dumbovic

middle: R

first: Emily

last: Jacobs-Palmer

first: Taeyoung

last: Hwang

first: Nydia

last: Chang

first: Christian

last: Much

first: Kyle

last: Turner

first: Christopher

last: Kirby

first: Nimrod

last: Rubinstein

first: Abigail

middle: F

last: Groff

first: Steve

middle: C

last: Liapis

first: Chiara

last: Gerhardinger

first: Catherine

last: Dulac

first: Hopi

last: Hoekstra

first: Martin

last: Sauvageau

first: John

last: Rinn


title: Multifaceted rewiring of the hepatic lipidome during proliferation and carcinogenesis

status: Public on May 28 2020

first: Davide

last: Chiarugi

address: Box 289, Addenbrooke’s Hospital

department: Metabolic Research Laboratories

institute: WT-MRC Institute of Metabolic Science

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: Distinct Notch1 and BCL11B requirements mediate human γδ/αβ T cell development

status: Public on May 26 2020

city: Ghent

first: Tom

last: Taghon

address: Corneel Heymanslaan 10

department: Diagnostic Sciences

country: Belgium

institute: Ghent University

type:
Expression profiling by array
Expression profiling by RT-PCR


title: Sam68 regulation of alternative splicing in the developing cerebellum

city: TORONTO

first: Robert

last: Weatheritt

state: Ontario

address: 160 College Street, Room 1030

institute: University of Toronto

summary: We uncover a Sam68-dependent splicing program during cerebellar development. These events direct proper isoform expression of the genes required to guarantee the establishment of the correct spatial/temporal neural circuitry. The dysregulation in Sam68 null mice leads to functional defects in adult neurons

overall_design: Examination of 3 different RNA from P1, P10 and P30 wild type cerebella of mouse, and 2 from P1 and P10 Sam68 null cerebella

first: Claudio

last: Sette

first: Donatella

last: Farini


title: Distinct Notch1 and BCL11B requirements mediate human γδ/αβ T cell development [BCL11B_coculture]

summary:
Notch-dependent BCL11B induction converts thymus seeding precursor cells into committed T cell progenitors that subsequently differentiate into T cells bearing either the γδ or αβ T cell receptor. In human, strong Notch activation favors γδ T cell development at the expense of αβ-lineage differentiation, but the underlying molecular mechanism has remained unclear. Therefore, we performed paired mRNA and miRNA profiling across 11 stages of human T cell development, including developing γδ T cells. We identify the miR-17-92 cluster as a direct Notch target and show that miR-17 promotes human TCRγδ T cell development by targeting BCL11B, a gene required for αβ but not for γδ T cell development. Thus, following its role as a licensing factor to induce BCL11B expression in early T cell precursors, Notch activation limits BCL11B expression through miR-17 until thymocytes have passed the β-selection checkpoint when Notch activation is turned off. Hereby Notch prevents premature BCL11B upregulation that is required for αβ-lineage differentiation and this results in preferential γδ-lineage differentiation. Our work unravels a dual role for Notch in controlling BCL11B expression during intrathymic differentiation and provides a unique resource for understanding the mRNA/miRNA interactions that control human T cell development.
We used microarrays in order to profile gene expression in CD34+ thymocytes before culture and after 5 or 10 days culture on OP9 stromal cells expressing Notch ligands JAG1, JAG2, DLL1 or DLL4.

overall_design: Gene expression was profiled in CD34+ thymocytes before and after culture on OP9 stromal cells expressing JAG1, JAG2, DLL1 or DLL4. Cultured cells were harvested after 5 days or 10 days of culture and sorted for CD45+. 2 independent experiments were performed, using 2 different thymus donors (2 replicates for each experimental setup).

first: Anne-Catherine

last: Dolens

first: Kaat

last: Durinck

first: Marieke

last: Lavaert

first: Joni

last: Van der Meulen

first: Frank

last: Speleman


title: Solar UVR and exosomal miRNAs effect pre-mature senescence in melanocytes

first: Nikki

last: Harter

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

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

platform_organism:
Homo sapiens
synthetic construct

overall_design: Refer to individual Series


title: Diffusible signaling factor interferes with and is toxic towards Bdellovibrio bacteriovorus 109J

status: Public on May 22 2020

city: CLEVELAND

first: MOHAMMED

last: DWIDAR

state: OHIO

address: 2111 E96th street

department: Center for Microbiome and Human Health

institute: Cleveland Clinic Lerner Research Institute

summary: Bdellovibrio bacteriovorus 109J is a predatory bacterium which lives by predating on other Gram-negative bacteria to obtain the nutrients it needs for replication and survival. Here, we evaluated the effects a bacterial signaling molecule called diffusible signaling factor (DSF) have on B. bacteriovorus 109J transcriptomics.

overall_design: Bdellovibrio bacteriovorus 109J was exposed to DSF during both its attack, and intraperiplasmic growth phases, and its transcriptomics were compared to those cells which were not exposed.

first: Mohammed

last: Dwidar

first: Naseer

last: Sangwan

first: Sora

last: Yoon

first: Dougu

last: Nam

last: Mitchell


title: Multifaceted rewiring of the hepatic lipidome during proliferation and carcinogenesis - PART 2 (Human HCC - "Fatty Liver" background)

city: Cambridge

last: Chiarugi

summary: The scope of this project is to study, using state-of-the-art systems biology approaches integrating the changes in metabolomics, lipidomics and transcriptomics, changes in hepatocytes' metabolism occurring in human HCC. We focused on altered metabolic pathways including lipogenesis, fatty acid desaturation, and generation of phosphatidylcholine (PC) occurring in HCC vs. paired HCC-free tissue.

overall_design: HCC samples and paired HCC-free tissues were collected during hepatectomy or transplant.

first: Matthew

last: Hoare

first: Michael

last: Allison

first: Michele

last: Vacca

first: Zoe

last: Hall


title: Multifaceted rewiring of the hepatic lipidome during proliferation and carcinogenesis - PART 1 (Liver Regeneration)

first: Davide

summary: The scope of this project is to study, using state-of-the-art systems biology approaches integrating the changes in metabolomics, lipidomics and transcriptomics, changes in hepatocytes' metabolism occurring in liver regeneration. We focused on altered metabolic pathways including lipogenesis, fatty acid desaturation, and generation of phosphatidylcholine (PC) occurring in the liver following partial hepatectomy (PH) or carbon-tetrachloride (CCl4) injection.

overall_design: Male C57BL/6J mice were challenged with A) IP injection of 2ul/g body weight of olive oil (OO) or CCl4:olive oil [1:1 (v/v)] mix; Mice were culled 3 days after IP injection. B) Partial Hepatectomy; Mice were culled 3 days after surgery.


title: Distinct Notch1 and BCL11B requirements mediate human γδ/αβ T cell development [miRNA BCL11B_ex vivo]

first: Tom

last: Taghon

summary:
Notch-dependent BCL11B induction converts thymus seeding precursor cells into committed T cell progenitors that subsequently differentiate into T cells bearing either the γδ or αβ T cell receptor. In human, strong Notch activation favors γδ T cell development at the expense of αβ-lineage differentiation, but the underlying molecular mechanism has remained unclear. Therefore, we performed paired mRNA and miRNA profiling across 11 stages of human T cell development, including developing γδ T cells. We identify the miR-17-92 cluster as a direct Notch target and show that miR-17 promotes human TCRγδ T cell development by targeting BCL11B, a gene required for αβ but not for γδ T cell development. Thus, following its role as a licensing factor to induce BCL11B expression in early T cell precursors, Notch activation limits BCL11B expression through miR-17 until thymocytes have passed the β-selection checkpoint when Notch activation is turned off. Hereby Notch prevents premature BCL11B upregulation that is required for αβ-lineage differentiation and this results in preferential γδ-lineage differentiation. Our work unravels a dual role for Notch in controlling BCL11B expression during intrathymic differentiation and provides a unique resource for understanding the mRNA/miRNA interactions that control human T cell development.
The expression of 756 miRNAs and 3 small RNA controls was determined using the Taqman stem-loop RT-qPCR method as previously described (Mets E. Leukemia. 2015, Mavrakis KJ. Nat Genet. 2011).

overall_design: miRNA expression was profiled in 11 T cell subsets isolated from human thymus. 2 independent experiments were performed, using 2 different thymus donors (2 replicates for each experimental setup).

last: Dolens

first: Jo

last: Vandesompele

first: Pieter

last: Mestdagh


title: Solar UVR and exosomal miRNAs effect pre-mature senescence in melanocytes [RT-PCR]

summary:
The selection of specific miRNAs by exosomes and their release from cultured melanocytes after exposure to solar UVR (UVA+UVB) have activities in inducing these cells into a premature senescence.
In this analysis, human TaqMan microRNA array cards A+B were used to measure the relative expression of miRNAs in exosomes isolated from the irradiated and un-irradiated melanocytes.

overall_design: QM-0 mJ and QMa, b, c- 25mJ, represent experimental replicates for both Card A and B. Experiments were performed using Applied Biosystems TaqMan Array Human microRN A A+B cards v3.0, catalog # 444913

first: M


title: SP8 promotes an aggressive phenotype in hepatoblastoma via FGF8 activation

status: Public on May 29 2020

city: Munich

first: Roland

last: Kappler

address: Lindwurmstr. 2a

department: Pediatric Surgery

institute: University Munich

summary: Purpose: Despite an overall good outcome of hepatoblastoma patients, prognosis is still poor if associated with metastatic disease. Transcriptomic profiling enables a global view on deregulated cellular pathways. The goal of this study was to compare RNAseq data of metastasized and non-metastasized specimens to identify new molecular players for high-risk hepatoblastoma patients.

overall_design: Liver mRNA profiles of hepatoblastoma patients


title: Analysis of circulating-miRNA expression in lactating Holstein cows under summer heat stress

status: Public on May 21 2020

city: Cheonan

first: Jihwan

last: Lee

address: Sinbang 1Gil 114, NIAS

country: South Korea

institute: National Institute of Animal Science

summary: Korean peninsular weather is rapidly becoming subtropical due to global warming. In summer 2018, South Korea experienced the highest temperatures since the meteorological observations recorded in 1907. Heat stress has a negative effect on Holstein cows, the most popular breed of dairy cattle in South Korea, which is susceptible to heat. To examine physiological changes in dairy cows under heat stress conditions, we analyzed the profiles circulating microRNAs isolated from whole blood samples collected under heat stress and non-heat stress conditions using small RNA sequencing. We compared the expression profiles in lactating cows under heat stress and non-heat stress conditions to understand the regulation of biological processes in heat-stressed cows. Moreover, we measured several heat stress indicators, such as rectal temperature, milk yield, average daily gain, and progesterone concentration. All these assessments showed that pregnant cows were more susceptible to heat stress than non-pregnant cows. Particularly, progesterone concentrations known to have maternal warming effects were at similar levels in non-pregnant cows but significantly increased in pregnant cows under heat stress conditions. The differentially expressed miRNAs and their putative target genes were analyzed in pregnant cows. Interestingly, we found that differentially expressed miRNAs (bta-miR-146b, bta-miR-20b, bta-miR-29d-3p, bta-miR-1246) specifically targeted progesterone biosynthesis (StAR) and the function of corpus luteum-related genes (CCL11, XCL), suggesting that pregnant cows with elevated progesterone concentrations are more susceptible to heat stress. In addition, we found the differential expression of 11 miRNAs (bta-miR-19a, bta-miR-19b, bta-miR-30a-5p, and several from the bta-miR-2284 family) in both pregnant and non-pregnant cows under heat stress conditions. In target gene prediction and gene set enrichment analysis, these miRNAs were found to be associated with the cytoskeleton, cell junction, vasculogenesis, cell proliferation, ATP synthesis, oxidative stress, and immune responses involved in heat response. These miRNAs can be used as potential biomarkers for heat stress.

overall_design: Discovery of biomarkers associated with heat stress in dairy cows.

first: Suhyun

first: Seunghwan

first: Inchul

last: Choi


title: Chromatin accessibility analysis of induced trophoblast stem cells.

status: Public on May 15 2020

city: Melbourne

first: Fernando

last: Rossello

state: VIC

address: L 10, 305 Grattan Street

country: Australia

institute: The University of Melbourne

summary: We report chromatin accessibility time-course profiling (ATAC-seq) of induced trophoblast stem cells (iTSCs) derived directly from human fibroblasts and naïve reprogramming intermediates.

overall_design: ATAC-seq of iTSCs

first: Xiaodong

last: Liu

first: Jia

last: Tan

first: Jose

last: Polo


title: Single-cell RNA sequencing of day 21 reprogramming intermediates cultured under fibroblast condition, naïve pluripotent and trophoblast stem cell conditions.

status: Public on May 16 2020

summary: We report single-cell RNA profiling of intermediate populations of reprogramming conducetd in the fibroblast condition, naïve pluripotent and trophoblast stem cell conditions to reveal cellular heterogeneity under these conditions.

overall_design: scRNA-seq of day 21 fibroblast, naïve pluripotent and trophoblast stem cell intermediates.

first: John

last: Ouyang

first: Owen

last: Rackham


title: Transcriptional analysis of induced trophoblast stem cells and their derived placenta subtypes.

summary: We report the transcriptional analysis of induced trophoblast stem cells (iTSCs) and their derived plancenta subtypes including syncytiotrophoblasts (STs) and extravillous trophoblasts (EVTs).

overall_design: RNA-seq of iTSCs, STs and EVTs with control cell types.

first: Jan

last: Schroder


title: Co-culturing Bacillus subtilis and wastewater microbial community in a bio-electrochemical system enhances denitrification and butyrate formation

city: Goteborg

first: Shadi

last: Rahimi

address: Kemivägen 10

department: Department of Biology and Biological Engineering

country: Sweden

institute: Chalmers University of Technology

summary: Bio-augmentation could be a promising strategy to improve processes for treatment and resource recovery from wastewater. In this study, the Gram-positive bacterium Bacillus subtilis was co-cultured with the microbial communities present in wastewater samples with high concentrations of nitrate or ammonium. Glucose supplementation (1%) was used to boost biomass growth in all wastewater samples. In anaerobic conditions, the indigenous microbial community bio-augmented with B. subtilis was able to rapidly remove nitrate from wastewater. In these conditions, B. subtilis overexpressed nitrogen assimilatory and respiratory genes including NasD, NasE, NarG, NarH, and NarI, which arguably accounted for the observed boost in denitrification. Next, we attempted to use the the ammonium- and nitrate-enriched wastewater samples bio-augmented with B. subtilis in the cathodic compartment of bioelectrochemical systems (BES) operated in anaerobic condition. B. subtilis only had low relative abundance in the microbial community, but bio-augmentation promoted the growth of Clostridium butyricum and C. beijerinckii, which became the dominant species. Both bio-augmentation with B. subtilis and electrical current from the cathode in the BES promoted butyrate production during fermentation of glucose. A concentration of 3.4 g/L butyrate was reached with a combination of cathodic current and bio-augmentation in ammonium-enriched wastewater. With nitrate-enriched wastewater, the BES effectively removed nitrate reaching 3.2 mg/L after 48 h. In addition, 3.9 g/L butyrate was produced. We propose that bio-augmentation of wastewater with B. subtilis in combination with bioelectrochemical processes could both boost denitrification in nitrate-containing wastewater and enable commercial production of butyrate from carbohydrate- containing wastewater, e.g. dairy industry discharges. These results suggest that B. subtilis bio-augmentation in our BES promotes simultaneous wastewater treatment and butyrate production.

sample_organism:
Clostridium butyricum
Clostridium beijerinckii

overall_design: Examination of 8 different samples in MEC cells and each sample was sequenced four times to ensure sufficient sequencing depth.


title: Distinct Notch1 and BCL11B requirements mediate human γδ/αβ T cell development [BCL11B_ex vivo]

first: Tom

summary:
Notch-dependent BCL11B induction converts thymus seeding precursor cells into committed T cell progenitors that subsequently differentiate into T cells bearing either the γδ or αβ T cell receptor. In human, strong Notch activation favors γδ T cell development at the expense of αβ-lineage differentiation, but the underlying molecular mechanism has remained unclear. Therefore, we performed paired mRNA and miRNA profiling across 11 stages of human T cell development, including developing γδ T cells. We identify the miR-17-92 cluster as a direct Notch target and show that miR-17 promotes human TCRγδ T cell development by targeting BCL11B, a gene required for αβ but not for γδ T cell development. Thus, following its role as a licensing factor to induce BCL11B expression in early T cell precursors, Notch activation limits BCL11B expression through miR-17 until thymocytes have passed the β-selection checkpoint when Notch activation is turned off. Hereby Notch prevents premature BCL11B upregulation that is required for αβ-lineage differentiation and this results in preferential γδ-lineage differentiation. Our work unravels a dual role for Notch in controlling BCL11B expression during intrathymic differentiation and provides a unique resource for understanding the mRNA/miRNA interactions that control human T cell development.
We used microarrays in order to profile the gene expression in 11 ex vivo T cell subsets, isolated from human thymus. Cord blood CD34+Lin- HPCs were used as a reference subset for extrathymic HPCs.

overall_design: Gene expression was profiled in 11 T cell subsets isolated from human thymus and cord blood CD34+Lin- HPCs (used as a reference subset for extrathymic HPCs). 2 independent experiments were performed, using 2 different thymus or cord blood donors (2 replicates for each experimental setup).

first: Anne-Catherine

first: Kaat

last: Durinck

first: Marieke

last: Lavaert

first: Joni

last: Van der Meulen

first: Frank

last: Speleman


title: Integrative Analysis Identifies Key Molecular Signatures Underlying Neurodevelopmental Deficits in Fragile X Syndrome

status: Public on May 24 2020

city: Singapore

first: Kagistia

middle: Hana

last: Utami

address: 8A Biomedical Grove

country: Singapore

institute: Translational Laboratory in Genetic Medicine

summary: We report the generation of isogenic hPSC model of FXS and characterize the neurodevelopmental capacity of these cells, performed transcriptome profiling in FXS neurons and identified key pathways

overall_design: Transcriptome profiling of FXS-derived neurons from hESC generated by RNA-seq in four replicates per genotype for using Illumina HiSeq4000. Control and FXS-derived neurons from hiPSC were generated by RNA-seq in 3 replicates per genotype.

first: Mahmoud

last: Pouladi


title: Influence of the Muc1 on Gene Expression Profiles in Helicobacter Pylori Infection in Mice

status: Public on May 30 2020

city: Brisbane

first: yong

middle: hua

last: sheng

state: QLD

address: 37 Kent St

department: Inflammatory Disease Biology

institute: Mater Research Institute – The University of Queensland

summary:
The cell surface mucin MUC1 is an important host factor limiting Helicobacter pylori (H. pylori) pathogenesis in both humans and mice by providing a protective barrier and modulating mucosal epithelial and leukocyte responses.
We used microarrays to detail the global programme of gene expression in Wild type and MUC1- deficient mice in response to H. pylori infection.

overall_design: We elucidate the time-course of molecular events and dynamic networks in gastric tissue from Muc1-/- and wild type  (WT) mice in response to the very early stages of H. pylori infection.

first: Yong

last: Sheng

first: Garrett

middle: Z

last: Ng

first: Kim

last: Summers

first: Alison

last: Every

first: Gareth

last: Price

first: Sumaira

last: Hasnain

first: Philip

last: Sutton

first: Michael

middle: A

last: McGuckin


title: Single-nucleus RNA sequencing of intermediates during human primed and naïve reprogramming.

first: Fernando

last: Rossello

summary: We report single-nucleus RNA time-course profiling of intermediate populations of reprogramming of human fibroblasts into primed and naïve pluripotent states

overall_design: Time-course snRNA-seq of human primed and naïve reprogramming intermedaites

first: Xiaodong

last: Liu

first: Jia

middle: P

last: Tan

first: Luciano

middle: G

last: Martelotto

first: John

last: Ouyang

first: Owen

last: Rackham

first: Jose

last: Polo


title: Overexpression of MtHSFA9 in hairy roots of Medicago truncatula

status: Public on May 20 2020

city: Beaucouze

first: Julia

last: Buitink

address: 42 rue Georges Morel

department: BAP

country: France

institute: INRAE

summary: HSFA9 (Medtr4g126070) is a seed-specific heat shock transcription factor that is upregulated during the later stages of seed maturation. To identify genes that are regulated by this transcription factor in the model legume Medicago truncatula, Medicago hairy roots were generated using Agrobacterium rhizogenes transformed with the genomic sequence of the genomic HSFA9 gene of Medicago. Using the Medicago NimbleGen chip, a transciptomic analysis was performed to identify differentially expressed genes compared to the GUS expressed control

overall_design: Two-condition experiment, gus versus genomic. Biological replicates: 3 control (35s :: GUS-GFP), 3 treatment (35s :: Genomic-GFP), independently grown and harvested. One replicate per array.

first: David

last: Lalanne

last: Zinsmeister


title: Two Doublesex1 mutants revealed a tunable gene network underlying intersexuality in Daphnia magna

city: Suita

first: Hajime

last: Watanabe

address: Yamadaoka 2-1

institute: Osaka University

summary:
Purpose: To justify whether sex is strictly binary or variable along a spectrum, exhaustive investigation into intersexuality is necessary. In this study, by mutating the sex determining locus Doublesex1, we generated two Daphnia magna strains from which two different forms of feminized males could be obtained. mRNA sequencing of these intersex males was carried out to explore the transcritomic shift responsible for the changes in sexual phenotype.
Methods: Two Doublesex1 mutants, namely Line A and Line B, were generated by microinection of designed TALENs into Daphnia magna eggs. Line A males showed severe, while Line B males showed minor bodywide feminization. Whole body mRNA profiles of 40 hour post oviposition embryos were generated for wildtype female, Line A male, Line B male and wildtype male using Illumina sequencing (mRNA sequencing service provided by Novogene). Data analysis was done using CLC Genomics Workbench software.
Results: Among 731 sex-biased genes identified in this dataset, more than half (449 genes) showed non-binary expression profile in which their expression in the mutant males was at an intermediate level between wildtype female and wildtype male.
Conclusions: Downstream genes of Doublesex1 cascade may fluctuate in activity and give rise to a spectrum of sexual phenotypes in Daphnia magna.

overall_design: mRNA profile comparison of four groups: wildtype female, Line A male, Line B male, and wildtype male. Triplicates for each group (total 12 samples). Same age (40 hour post oviposition).

first: Quang

middle: D

last: Nong

first: Tomoaki

last: Matsuura

first: Yasuhiko

last: Kato


title: Comparative analysis between effects of thalidomide and environmental chemicals on neuronal differentiations in human sphere

city: Yokohama

first: Hideko

last: Sone

address: 601 Matanocho Totsuka

institute: Yokohama University of Pharmacy

summary: To develop molecular indicators of neurodevelopmental disorders related to the exposure to external chemicals, we have employed whole genome microarray expression profiling as a discovery platform to identify genes with the potential to influence neuronal differentiation from embryonic stem cells. Thalidomide (TMD), bisphenol A (BPA), 4-hydroxy-2,2',3,4',5,5',6-heptachlorobiphenyl (4OH-PCB187) and 2,2',4,4'-tetrabromodiphenyl ether (BDE-47) were exposed to human embryonic stem (ES) cell-derived sphere on day 3 after starting sphere formation for 72 hours. Gene expression analysis on the stage of sphere development showed chemical specific characteristics.

overall_design: Thalidomide and three environmental chemicals induced gene expression in human embryonic derived neuroprogenitor spheres were measured on day 3 after exposure to doses of  thalidomide, bisphenol A, 4OH-PCB187 and BDE47.  Eight experiments were performed using cultured cells for each experiment.

first: Tomohiro

last: Ito


title: Interleukin-33 contributes to anemia of chronic inflammation by inhibiting differentiation of erythroid progenitors

city: Oxford

first: Stephen

last: Sansom

state: Oxfordshire

address: Roosevelt Drive

department: NDORMS

institute: Kennedy Institute of Rheumatology

summary: Mature blood cells are produced continuously from hematopoietic stem and progenitor cells (HSPCs) in the bone marrow (BM).  During chronic inflammation, this process may be perturbed by inflammatory cytokines acting on HSPCs to cause anemia of inflammatory disease.  Among BM HSPCs, we found the receptor for interleukin (IL)-33, ST2, was expressed preferentially and highly on erythroid progenitors.  Induction of inflammatory spondyloarthritis in mice increased IL-33 in BM plasma, and IL-33 was required for inflammation-dependent suppression of erythropoiesis in BM.  Conversely, administration of IL-33 in healthy mice suppressed erythropoiesis, decreased hemoglobin expression, and caused anemia.  Using purified erythroid progenitors in vitro, we showed that IL-33 directly inhibited terminal maturation.  This effect was dependent on NF-kB activation and was associated with altered signalling events downstream of the erythropoietin receptor.  Accordingly, IL-33 also suppressed erythropoietin-induced stress erythropoiesis in vivo.  These results reveal a role for IL-33 in regulation of erythropoiesis during inflammatory disease and define a new target for its treatment.

overall_design: RNA-seq of purified erythroid progenitors treated with IL33 or vehicle.

first: James

middle: W

last: Swann

first: Thibault

last: Griseri

first: Lada

last: Koneva


title: Reversible mitochondrial dysfunction drives terminal T-cell exhaustion

city: New York

first: Bryan

last: King

department: Cancer Biology and Genetics

institute: Memorial Sloan Kettering Cancer Center

summary: The failure of T-cells to control tumor growth has been associated with several functional defects that collectively lead to T-cell “exhaustion.”  This phenotype results from chronic antigen stimulation within the tumor microenvironment, but how repetitive antigenic stimulation leads to T-cell exhaustion remains poorly defined.  Here we show that persistent antigen stimulation induces mitochondrial oxidative stress that reduces tricarboxylic acid (TCA) cycle activity.  The resultant bioenergetic compromise impairs nucleotide triphosphate synthesis, induces endoplasmic reticulum (ER) stress, and activates an exhaustion-associated gene expression program.  Reversal of oxidative stress with N-acetylcysteine effectively restores T-cell proliferation, effector function, and memory-associated gene expression and enhances anti-tumor T-cell efficacy in vivo.  These data reveal that induction of mitochondrial oxidative stress is a critical component of terminal T-cell dysfunction.  Furthermore, treatments that restore mitochondrial redox are sufficient to prevent T-cell exhaustion and enhance anti-tumor immunity.

overall_design: RNA-sequencing of polyclonal or OT-I transgenic CD8+ T cells following acute or chronic TCR stimulation ex vivo, +/- N-acetylcysteine

first: Santosha

last: Vardhana

first: Craig

middle: B

last: Thompson


title: Distinct Notch1 and BCL11B requirements mediate human γδ/αβ T cell development [miRNA BCL11B_coculture]

first: Tom

last: Taghon

summary:
Notch-dependent BCL11B induction converts thymus seeding precursor cells into committed T cell progenitors that subsequently differentiate into T cells bearing either the γδ or αβ T cell receptor. In human, strong Notch activation favors γδ T cell development at the expense of αβ-lineage differentiation, but the underlying molecular mechanism has remained unclear. Therefore, we performed paired mRNA and miRNA profiling across 11 stages of human T cell development, including developing γδ T cells. We identify the miR-17-92 cluster as a direct Notch target and show that miR-17 promotes human TCRγδ T cell development by targeting BCL11B, a gene required for αβ but not for γδ T cell development. Thus, following its role as a licensing factor to induce BCL11B expression in early T cell precursors, Notch activation limits BCL11B expression through miR-17 until thymocytes have passed the β-selection checkpoint when Notch activation is turned off. Hereby Notch prevents premature BCL11B upregulation that is required for αβ-lineage differentiation and this results in preferential γδ-lineage differentiation. Our work unravels a dual role for Notch in controlling BCL11B expression during intrathymic differentiation and provides a unique resource for understanding the mRNA/miRNA interactions that control human T cell development.
The expression of 756 miRNAs was determined using the Taqman stem-loop RT-qPCR method as previously described (Mets E. Leukemia. 2015, Mavrakis KJ. Nat Genet. 2011).

overall_design: miRNA expression was profiled in CD34+ thymocytes before and after culture on OP9 stromal cells expressing JAG1, JAG2, DLL1 or DLL4. Cultured cells were harvested after 5 days or 10 days of culture and sorted for CD45+. 2 independent experiments were performed, using 2 different thymus donors (2 replicates for each experimental setup).

first: Anne-Catherine

last: Dolens

first: Kaat

last: Durinck

first: Marieke

last: Lavaert

first: Joni

last: Van der Meulen

first: Jo

last: Vandesompele

first: Pieter

last: Mestdagh

first: Frank

last: Speleman


title: Effects of Single and Combined Low Concentrations of Neuroactive Drugs on Daphnia magna Reproduction and Transcriptomic Responses

city: Barcelona

first: Inmaculada

last: Fuertes

state: Barcelona

address: Calle Jordi Girona, 18-26

department: Department of Environmental Chemistry

country: Spain

institute: CSIC

summary:
Transcriptomic profiling of Daphnia magna samples exposed to carbamazepine (CBZ), diazepan (DZP), propranolol (PR) and to an equitoxic mixture of them (M).
Assessing the risks of emerging contaminants such as neuro-active pharmaceuticals in the environment requires an understanding of their joint effects at low concentrations across species. Here, we assessed reproductive and transcriptional effect of propranolol, diazepam and carbamazepine on the crustacean Daphnia magna at environmentally relevant concentrations.  The three compounds enhanced reproductive parameters in adults, and induced specific transcriptome changes in pre-adolescent individuals. Comparing results from single exposures and of ternary equi-effective mixtures showed additive action for both effects. Transcriptomic analyses identified 3248 genes affected by at least one of the treatment, which were grouped into four clusters.  Two clusters included 1897 gene transcripts in total, that behaved similarly (appearing either over- or underrepresented relative to control) in single and mixture treatments. The third and fourth clusters grouped genes differently transcribed upon exposure to diazepam and propranolol, respectively. Functional transcriptomics indicated that the four clusters shared major de-regulated signalling pathways implicated on energy, growth, reproduction, and neurologically- related processes,  which may be responsible for the observed reproductive effects. Our study, thus, showed additive effects at the transcriptional and physiological level and is providing a novel  approach to the analysis of environmental relevant mixtures of neuro-active compounds

overall_design: In total, 15 samples were analysed, all corresponding to 4-day Daphnias, just after the third molt, including 3 control-solvent samples, 3 exposed to 1 µg/L  of carbamazepine, 3 exposed to 0.1 µg/L of diazepan, 3 exposed to  0.1 µg/L of propranolol and 3 exposed to a 1/3 mixture of them, with ratio proportional to LOEC.

first: Bruno

last: Campos

first: Claudia

last: Rivetti

first: Benjamín

last: Piña

first: Carlos

last: Barata


title: Transcriptome analysis to UHRF1 depletion in MUTU I cells

status: Public on May 04 2020

city: Boston

first: Rui

last: Guo

state: Massachusetts

address: 150 Harrison Ave.

department: School of Medicine

institute: Tufts University

summary: RNAseq was used to identify host and viral transcriptome changes in UHRF1 knock-out MUTU I cells.  UHRF1 KO MUTU I cells were subjected to FACSort for ICAM1+/GP350- and ICAM1-/GP350+ subpopulations, which were further used for RNAseq analysis. The MUTU I cells expressing control sgRNA was used as the control.

first: Benjamin

last: Gewurz

first: Yuchen

last: Zhang


title: Decoding SARS-CoV-2 coding capacity

status: Public on May 08 2020

city: Rehovot

first: Noam

last: Stern-Ginossar

address: 234 herzel

department: Molecular Genetics

country: Israel

institute: Weizmann Institute

summary: SARS-CoV-2 is a coronavirus responsible for the COVID-19 pandemic. Although the SARS-CoV-2 trascriptome was reported recently, its coding capacity and the relative production of different viral proteins remained unclear. Utilizing a suit of ribosome profiling techniques, we present a high resolution map of the SARS-CoV-2 coding regions.

sample_organism: Severe acute respiratory syndrome coronavirus 2

overall_design: To capture the SARS-CoV-2 coding capacity, we applied a suits of ribosome profiling approaches to two types of infected cells, Vero 6 and Calu 3. The Vero 6 cells were infected for 5 and 24 hours with BavPat1/2020 EPI_ISL_406862, and the Calu 3 cells were infected for 7 hours with BavPat1/2020 Ref-SKU: 026V-03883. For each time point we mapped genome-wide translation events by preparing three different ribosome-profiling libraries. Two libraries facilitate mapping of translation initiation sites, by treating cells with lactimidomycin (LTM) or harringtonine (Harr), drugs that inhibit translation initiation, and the third library was prepared from cells treated with the translation elongation inhibitor cycloheximide (CHX). In parallel, we used a tailored RNA-seq protocol which on top of quantification of RNA levels allows identification of transcription start sites (TSSs).

first: Orel

last: Mizrahi

first: Yaara

last: Finkel

first: Aharon

last: Nachshon

first: Michal

last: Schwartz


title: Transcriptome analysis of MUTU I and MUTU III cells

summary: RNAseq was used to identify host and viral transcriptome changes in MUTU I and MUTU III cells.

overall_design: Total RNA extracted from MUTU I and MUTU III cells were used for RNAseq analysis.

first: Jiang

last: Chang


title: Native molecule sequencing by nano-ID reveals synthesis and stability of RNA isoforms

status: Public on May 06 2020

city: Göttingen

first: Björn

last: Schwalb

address: Fassberg 11

institute: MPI

summary: Eukaryotic genes often generate a variety of RNA isoforms that can lead to functionally distinct protein variants. The synthesis and stability of RNA isoforms is however poorly characterized. The reason for this is that current methods to quantify RNA metabolism use short-read sequencing that cannot detect RNA isoforms. Here we present nanopore sequencing-based Isoform Dynamics (nano-ID), a method that detects newly synthesized RNA isoforms and monitors isoform metabolism. nano-ID combines metabolic RNA labeling, long-read nanopore sequencing of native RNA molecules and machine learning. nano-ID derived RNA stability estimates enable a distinctive evaluation of stability determining factors such as sequence, poly(A)-tail length, RNA secondary structure, translation efficiency and RNA binding proteins. Application of nano-ID to the heat shock response in human cells reveals that many RNA isoforms change their stability. nano-ID also shows that the metabolism of individual RNA isoforms differs strongly from that estimated for the combined RNA signal at a specific gene locus. nano-ID enables studies of RNA metabolism on the level of single RNA molecules and isoforms in different cell states and conditions.

sample_organism:
Homo sapiens
synthetic construct

overall_design: Direct RNA nanopore sequencing in human cells

first: Kerstin

last: Maier

first: Saskia

last: Gressel

first: Patrick

last: Cramer


title: Single-cell RNA sequencing of intermediates during human primed and naïve reprogramming.

first: Fernando

last: Rossello

summary: We report single-cell RNA time-course profiling of intermediate populations of reprogramming of human fibroblasts into primed and naïve t2iLGoY and RSeT pluripotent states

overall_design: Profiling of pooled single cell reporgramming trajectories.

first: Xiaodong

last: Liu

first: Christian

middle: M

last: Nefzger

middle: J

first: John

last: Ouyang

first: Owen

last: Rackham

first: Jose

last: Polo


title: Transcriptional analysis of intermediates during human primed and naïve reprogramming.

summary: We report transcriptional time-course profiling (RNA-seq) of intermediate populations of reprogramming of human fibroblasts into primed and naïve pluripotent states

overall_design: Time-course RNA-seq of human primed and several naïve reprogramming intermediates


title: Genome-wide gene expression prolifing post GNL3 knockdown in human neural progenitor cells

city: Hengyang

first: Qingtuan

last: Meng

state: Hunan

address: 69 Chuanshan Road

institute: The First Affiliated Hospital of University of South China

summary: We used two siRNAs to knock down GNL3 in human neural progenitor cells which were derived from normal human induced pluripotent stem cells (ATCC, ACS-1011). GNL3 knockdown experiments were done in three biological replicates. Total RNA was extracted from GNL3 knockdown and control groups for RNA sequencing (Illumina Hiseq2000, paired-end 100 bp). Genes that affected by both siRNAs were considered differentially expressed genes between GNL3 knockdown and control groups (adjusted P value < 0.05). Using Gene Ontology and KEGG pathway analysis, we found that those differentially exrepssed genes were mainly related to immune response, response to cytokine, cell cycle, and p53 signaling pathway.

overall_design: GNL3 was knocked down in human neural progenitor cells by using two siRNAs. RNA-seq was then used to identify genes affected by GNL3 knockdown.

first: Chuan

last: Jiao


title: NTP4 modulates miRNA accumulation via asymmetric modification of miRNA-3p/5p duplex

status: Public on May 23 2020

city: Shenzhen

first: Wenwen

last: Kong

state: Guangdong

address: 1066 Xueyuan Avenue, Nanshan District

department: College of Life Sciencesand Oceanography

institute: Shenzhen University

summary: Arabidopsis uridylyltransferase on unmethylated sRNAs and directed their degradation. Here, the small RNA deep sequencing of the uridylyltransferase mutants of Arabidopsis were performed, which include Col-0, heso1-1, urt1-1, ntp4-1.

overall_design: Col-0, heso1-1, urt1-1, ntp4-1 each include 3 bioreplicates. In total, there are 12 samples.


title: Chromatin accessibility analysis of intermediates during human primed and naïve reprogramming.

summary: We report chromatin accessibility time-course profiling (ATAC-seq) of intermediate populations of reprogramming of human fibroblasts into primed and naïve pluripotent states

overall_design: Time-course ATAC-seq of human primed and naïve reprogramming intermedaites


title: Small RNA sequencing of human and macaque brain tissue and brain-derived extracellular vesicles separated by size exclusion chromatography

status: Public on May 14 2020

city: Baltimore

first: Kenneth

middle: W.

last: Witwer

state: MD

address: 733 N. Broadway

department: Department of Molecular and Comparative Pathobiology

institute: Johns Hopkins University School of Medicine

summary: Extracellular vesicles (EVs) are involved in a wide range of physiological and pathological processes by shuttling material out of and between cells. Tissue EVs may thus lend insights into disease mechanisms and also betray disease when released into easily accessed biological fluids. Since brain-derived EVs (bdEVs) and their cargo may serve as biomarkers of neurodegenerative diseases, we evaluated modifications to a published, rigorous protocol for separation of EVs from brain tissue and studied effects of processing variables on quantitative and qualitative outcomes. To this end, size exclusion chromatography (SEC) and sucrose density gradient ultracentrifugation were compared as final separation steps in protocols involving stepped ultracentrifugation. bdEVs were separated from brain tissues of human, macaque. Effects of post-mortem interval (PMI) before final bdEV separation were probed. MISEV2018-compliant EV characterization was performed, and both small RNA and protein profiling were done. We conclude that the modified, SEC-employing protocol achieves EV separation efficiency roughly similar to a protocol using gradient density ultracentrifugation, while decreasing operator time and, potentially, variability. The protocol appears to yield bdEVs of higher purity for human tissues compared with macaque, suggesting opportunities for optimization. The interval between death/tissue storage/processing and final bdEV separation can also affect bdEV populations and composition and should thus be recorded for rigorous reporting. Different populations of EVs obtained through the modified method reported herein display characteristic RNA and protein content that hint at biomarker potential. To conclude, this study finds that the automatable and increasingly employed technique of SEC can be applied to tissue EV separation, and also reveals more about the importance of species-specific and technical considerations when working with tissue EVs. These results are expected to enhance the use of bdEVs in revealing and understanding brain disease.

sample_organism:
Macaca nemestrina
Homo sapiens

platform_organism:
Macaca nemestrina
Homo sapiens

overall_design: Total RNA was extracted from brain tissue (BH), a minimally processed 10,000 x g centrifuge pellet (10K) following tissue extraction, and size exclusion chromatography-based separation of extracellular vesicles from 10K supernatant (EVs). Macaque brain tissues were also placed at room temperature for 2 hours and 6 hours before EV separation to assess the effect of time on EV separation.

first: Yiyao

last: Huang

first: Andrew

last: Hill

first: Lesley

last: Cheng

first: Andrey

last: Turchinovich


title: Liquid-infused structured titanium surfaces for dental implants: antiadhesive mechanism to repel bacterial biofilms

status: Public on May 10 2020

city: Hannover

first: Katharina

last: Doll

address: Carl-Neuberg-Str. 1

institute: Hannover Medical School

summary: To combat dental implant-associated infections, there is a need for novel materials which effectively inhibit bacterial biofilm formation. In the present study, a titanium surface functionalization based on the “slippery liquid-infused porous surfaces” (SLIPS) principle was analyzed in an oral flow chamber system. The immobilized liquid layer was stable over 13 days of continuous flow. With increasing flow rates, the surface exhibited a significant reduction in attached biofilm of both the oral initial colonizer Streptococcus oralis and an oral multi-species biofilm composed of S. oralis, Actinomyces naeslundii, Veillonella dispar and Porphyromonas gingivalis. Using single cell force spectroscopy, reduced bacterial adhesion forces on the lubricant layer could be measured. Gene expression patterns in biofilms on SLIPS, on control surfaces and planktonic cultures were also compared. For this purpose, the genome of S. oralis strain ATCC® 9811TM was sequenced using PacBio Sequel technology. Even though biofilm cells showed clear changes in gene expression compared to planktonic cells, no differences could be detected between bacteria on SLIPS and on control surfaces. Therefore, it can be concluded that the ability of liquid-infused titanium to repel biofilms is solely due to weakened bacterial adhesion to the underlying liquid interface.

overall_design: Examination of Streptococcus oralis gene expression  in biofilms on SLIPS and titanium control surfaces and in planktonic cultures

first: Szymon

last: Szafrański

first: Ines

last: Yang

first: Gesa

last: Bei der Wieden


title: Quant-seq analysis of differential gene expression and polyadenylation site usages in caused by inhibition of CDK12 and CDK13 using THZ531 in THP-1 cells (3’ Quant-seq)

status: Public on Apr 29 2020

city: Melbourne

first: Zheng

last: Fan

state: Victoria

address: 305 Grattan Street

institute: Peter MacCallum Cancer Centre

summary: We used 3' RNA-Seq to determine effect of dual inhibition of CDK12 and CDK13 on gene expression and polyadenatltion site usages in THP-1 cells

overall_design: we performed 3’RNA-seq (Quantseq) on 6 hours THZ531 or DMSO reatment on parental THP-1 cells

first: Jennifer

last: Devlin

first: Stephin

last: Vervoort

first: Ricky

last: Johnstone


title: Transcriptome analysis to UHRF1 depletion in RaeL cells

first: Rui

last: Guo

summary: RNAseq was used to identify host and viral transcriptome changes in UHRF1 knock-out RaeL cells.  UHRF1 KO RaeL cells were subjected to FACSort for ICAM1+ subpopulations, which were further used for RNAseq analysis. The RaeL cells expressing control sgRNA was used as the control.

first: Benjamin

middle: E

last: Gewurz

first: Yuchen

last: Zhang


title: Global transcriptional patterns in irr and wild-type plants

status: Public on May 03 2020

city: La Jolla

first: Keini

last: Dressano

state: California

address: 9500 Gilman Drive #0116

department: Biology

institute: UC San Diego

summary: To better understand potential mechanisms underlying rrm (rrm=irr) hypersensitivity to Pep treatment, global transcriptional patterns in irr-1 and wild-type plants were profiled by RNA-seq 24 h post-treatment with either water or 1 µM AtPep1. Genes  that were differentially regulated in irr-1 compared to wild-type were analyzed, as well as changes in gene splicing patterns.

overall_design: Three biological replicates per genotype (Wt and rrm/irr) per treatment were used. Treatments were: water (untreated) or 1 µM AtPep1 (treated) for 24 hours.

first: Elly

last: Porestky

first: Alisa

last: Huffaker


title: Characterization of RNAs in soybean (Glycine max)

status: Public on May 09 2020

city: St. Louis

first: Blake

middle: C.

last: Meyers

state: MO

address: 975 N Warson Road

institute: Donald Danforth Plant Science Center

summary: RNA-seq was used to characterize gene expression in soybean from a wide range of tissues. The primary focus of the project was small RNAs, and the identification of microRNAs and phased siRNA-generating loci, but RNA-seq data were generated from the same samples. This project was supported by the United Soybean Board.

overall_design: mRNA profiling was done by Illumina TruSeq sample preparation (not stranded) followed by high-throughput sequencing using an Illumina HiSeq 2500 at the Delaware Biotechnology Institute. The study focused on small RNA, with these RNA-seq libraries made from the same samples (see PMID: 25465409).


title: CDK12 and CDK13

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

sample_organism:
Drosophila melanogaster
Homo sapiens

platform_organism:
Drosophila melanogaster
Homo sapiens

overall_design: Refer to individual Series


title: RNA-Seq for validating the RNA expression of wild type and analog sensitive CDK12 and CDK13 in analog sensitive MV4;11 cell lines that generated by CRISPR HDR

summary: We used Poly-A enriched RNA-Seq to validate CDK12, CDK13 anlalog senstive mutationsand their expression level in the cell lines that has analog sensitive mutations that were introduced by CRISPR HDR

overall_design: we performed Poly-A enriched RNA-Seq to validate the expression of analog sensitive/wild-type CDK12 and CDK13 in WT, CDK12AS/NULL, CDK13AS/AS, #1CDK12AS/NULL;CDK13AS/NULL and #2CDK12AS/NULL;CDK13AS/AS MV4;11 clones.

middle: R


title: Specification of embryonic mesoderm by Pinhead signaling

first: Olga

last: Ossipova

state: NY

address: 1 Gustave L Levy Place Anbg 25-90 PO Box 1020

institute: Mount Sinai Hospital

summary: Among the three embryonic germ layers, mesoderm plays a central role in the establishment of the vertebrate body plan.  Mesoderm is specified by secreted signaling proteins from the FGF, Nodal, BMP and Wnt families.  No new classes of extracellular mesoderm-inducing factors have been identified in more than two decades.  Here we show that the Xenopus pinhead (pnhd) gene encodes a novel secreted protein that activates specific mesodermal markers in presumptive ectoderm.  We demonstrate that Pnhd is required for the specification of a subset of embryonic mesoderm in vivo. RNA sequencing revealed that many transcriptional targets of Pnhd are shared with those of the FGF pathway. Pnhd signaling involves active FGF but not Wnt receptors and is accompanied by Erk1 phosphorylation.  We propose that Pnhd operates in the marginal zone to specify mesodermal progenitors via an FGF receptor-dependent mechanism.

overall_design: Gain of function and loss of function study of Pinhead, a novel growth factor. Duplicate samples for control ectoderm explants (Cocaps1, Cocaps2) and Flag-Pinhead-expressing caps (FlagPin1, FlagPin2) at stage 11, gastrula were analyzed for Pinhead gain-of-function by RNAseq. For Pinhead loss-of-function, duplicate samples for control marginal zone explants (Co1, Co2) and Pinhead-depleted (Pinhead SpMo) marginal zone explants  (PhSpMo1, PhSpMo2) were studied at st.11 by RNAseq.

first: Keiji

last: Itoh

first: Aurelian

last: Radu

first: Ezan

last: Jerome

first: Sergei

middle: Y

last: Sokol


title: Gene expression changes of Pseudomonas syringae pv. actinidiae biovar 6 in various culture conditions

status: Public on May 02 2020

city: Tsukuba

first: Takashi

last: Fujikawa

state: Ibaraki

address: Fujimoto 2-1

department: Institute of Fruit Tree and Tea Sience

institute: National Agriculture and Food Research Organization

summary: Pseudomonas syringae pv. actinidiae biovar 6 (Psa6) is a causal agent of kiwifruit bacterial canker and is a unique plant pathogenic bacterium, producing two types of phytotoxins, coronatine and phaseolotoxin. We investigated the expression behavior of virulent genes of Psa6 under various culture conditions.

overall_design: Two milliliters of bacterial resuspension (in each medium) were inoculated into 15 mL of respective test media and the cultures were shaken at 160 rpm at 27 or 18 °C. As test media, HS medium and HSC medium were used. HS and HSC media have been reported to activate coronatine production of Pseudomonas syringae pv. glycinea. Additionally, it has been reported that cultures at 18 °C, compared to 27 °C, induce the production of phytotoxins such as coronatine and phaseolotoxin. After incubation at 3 h, 1 mL of each culture was taken and used for RNA-Seq. Sequence data by IonPGM sequencer were assembled and analyzed using the CLC Genomics Workbench and the statistical software R with various packages (edgeR, limma, and gplots). Namely, using high-quality sequence reads with the reference genome of Psa6 MAFF 212134 (accession no. MSBW00000000), the reads per kilobase of exon per million mapped reads (RPKM) values were obtained and normalized. Then, using R software, the gene expression values relative to the 27 °C HS medium were calculated to log2 values of fold change (log2FC) with FDR (false discovery rate) values under the four culture conditions.

first: Karin

last: Hirose


title: Genome-wide map of Pol II  and Ser2 phosphorylated Pol inoccupancy alteration on chromatin upon analog sensitive CDK12 and/or CDK13 inhibition (ChIP-Seq)

first: Zheng

last: Fan

summary: We performed ChIP-Seq on MV4;11  WT, CDK12AS/NULL, CDK13AS/AS, #1CDK12AS/NULL;CDK13AS/NULL and #2CDK12AS/NULL;CDK13AS/AS MV4;11 clones treated with 1-NM-PP1 or vehicle for 4 hours to determine the location of total Pol II and phosphorylated Ser2 of Pol II occupancy

overall_design: Analog senstive MV4;11 cells were treated with 1-NM-PP1/DMSO for 4 hours, then total Pol II or phosphorylated Pol II at Ser2 of the CTD bound chromatin were isolated from soniacated nuclear extracts using antibody angaist  RNA polymerase II, clone CTD4H8 mouse monoclonal or RNA polymerase II (phospho CTD Ser-2) respectively

first: Jennifer

last: Devlin


title: Transcriptome wide alternative splicing analysis to determine the effect of CDK12 and CDK13 inhibition by THZ531 in alternative splicing (Total RNA-Seq)

summary: We performed Total RNA-seq on MV4;11 cells after 6 hours treatment of THZ531 to determine whether CDK12 and CDK13 inhibtion to cause splicing defects.

overall_design: MV4;11 cells, 3 replicates, DMSO, 100nM, 200nM THZ531 treatment for 6 hours, then total RNA was extracted

first: Stephin

last: Vervoort

first: Ricky

last: Johnstone


title: Transcriptome wide analysis of differential gene expression and polyadenylation site usages caused by inhibition of CDK12 and/or CDK13 in MV4;11 cells (3’ Quant-seq)

summary: We used 3' RNA-Seq to determine the effects of analog senstive CDK12, CDK13 and dual inhibition on gene expression and polyadenatltion site usages, and to test the redundancy between CDK12 and CDK13 in maintaining global transcrition on the tramcrotpomte level.

overall_design: we performed 3’RNA-seq (Quantseq) on WT, CDK12AS/NULL, CDK13AS/AS, #1CDK12AS/NULL;CDK13AS/NULL and #2CDK12AS/NULL;CDK13AS/AS MV4;11 clones treated with 1-NM-PP1 or vehicle for 4 hours. 6 hours THZ531 or vehicle treatments were applied on parental MV4;11 cells


title: Transcriptional profiling of Pseudomonas aeruginosa ∆lasR in mono- and co-culture with wild type.

status: Public on Apr 28 2020

city: Farmington

first: Mark

last: Adams

state: CT

address: 10 Discovery Drive

institute: The Jackson Laboratory

summary: Pseudomonas aeruginosa is a troublesome opportunistic pathogen isolated from diverse environmental sources. An arsenal of degrading enzymes and antagonistic factors contribute to P. aeruginosa persistence and damage of a susceptible host. Largely through density-dependent regulation referred to as quorum sensing, the LasR, RhlR, and PqsR transcription factors collectively modulate hundreds of genes, including the expression of several virulence factors, in response to diffusible signals called autoinducers. LasR loss-of-function (LasR-) strains are commonly isolated from clinical samples and produce fewer toxins in monoculture, yet these strains are associated with worse clinical outcomes. We show that in co-culture with P. aeruginosa wild type where LasR loss-of-function strains are often found in vivo, ∆lasR hyperproduces RhlR/I dependent antagonistic factors. Specifically, we present a cyclic model of interaction between wild type and ∆lasR wherein the iron-scavenging siderophore pyochelin produced by the lasR mutant induces citrate release and cross-feeding from the wild type to ∆lasR to stimulate production of antagonistic factors with native functions involved in iron acquisition. Co-culture specific behaviors mediated by altered metabolite secretion and metabolism may explain complications associated with LasR loss-of-function strains. More broadly, this report illustrates how heterogenous behaviors within a mono-species community can promote antagonism associated with carbon and metal assimilation.

overall_design: Genome-wide transcriptional profiles of Pseduomonas aerguinosa ∆lasR colony biofilms physically separated from lawn of ∆lasR or WT P.a..

first: Dallas

middle: L

last: Mould

first: Deborah

last: Hogan


title: Assess the effects of antipsychotic use on gene expression changes in dementia

status: Public on Apr 30 2020

city: Exeter

first: Yasaman

last: Malekizadeh

address: Barrack Road

department: Biomedical and Clinical Science

institute: University of Exeter

summary: In order to elucidate mechanisms underlying adverse effects of antipsychotic use in dementia we generated gene expression signatures for three antipsychotics representing  a  range  of  mechanisms  of  action  relevant  to  the  current  landscape  of  drug development  and  clinical  use  in  dementia:  amisulpride  (primarily  a  D2/D3  antagonist), risperidone  (primarily  a  5HT2A/D2  antagonist)  and  volinanserin  (highly  selective  5HT2A inverse agonist). We  reported  that  the antipsychotic signatures would be score positively with conditions and diseases related to known side effects of their use in dementia such as cardiovascular and infectious diseases.

overall_design: Examining the effects of 3 antipsychotics on the gene expression changes using SH-SY5Y neuroblastoma cell line


title: The landscape of RNA polymerase II-associated chromatin interactions in prostate cancer

status: Public on Apr 27 2020

city: Dallas

first: Ram

last: Mani

state: Texas

address: 5323 Harry Hines Blvd NB6.444

department: Pathology

institute: UT Southwestern Medical Center

summary: The goal of the study is to profile the gene expression signatures in prosate cancer models.

overall_design: RNA -seq libraries were constucruted by extarcting total RNA from cells grown in culture, followed by mRNA enrichment by poly A capture.


title: Quant-seq analysis of differential polyadenylation site usages in caused by different Pol II mutants with slow elongation rates in  Flp-In-293 cells and dual inhibition of CDK12 and CDK13 by THZ531 HEK293T cells

summary: We used 3' RNA-Seq to determine the effects of slow elongating Pol II on polyadenatltion site usages, also the effects of CDK12 and CDK13 inhibition caused by THZ531 on alternative polyadenylation

overall_design: We performed 3’RNA-seq (Quantseq) on Flp-In-293 cells with slow elongating or wild-type a-amanitin resistant Pol II,  as well as THZ531/DMSO treated HEK293T cells to compare the the effect of slow elongating Pol II to CDK12 and CDK13 inhibtion.


title: Genome-wide map of Pol II occupancy alterations on chromatin upon CDK12 and CDK13 inhibition (ChIP-Seq)

summary: We performed ChIP-Seq on MV4;11 cells after 6 hours treatment of DMSO, 100nM and 200nM THZ531 to determine the location of Pol II occupancy

overall_design: MV4;11 cells,  DMSO, 100nM, 200nM THZ531 treatment for 6 hours, then Pol II bound chromatin where isolated from soniacated nuclear extracts using antibody angaist Pol II CTD (4H8)