title: Anticancer potential of UDCA on GBM

city: Jinan

first: Zhong

last: Yao

state: shandong province

address: No. 107 west Wenhua road

institute: Shandong University

summary: Glioblastoma multiforme (GBM) is the deadliest form of brain tumor with a median survival time of 15 months due to drug resistance. Ursodeoxycholic acid (UDCA) is approved of cancer suppressive potential in several tumors. Here we researched on the antitumor potential of UDCA on GBM. The CCK-8 and colony formation was used for detecting cell viability. RNA sequencing hinted transcriptional profile and pathways. PCR and western blot tested the change of related markers. Phenotype changes as cell cycle, apoptosis, MMP and ROS were measured. UDCA inhibited GBM cell viability in a dose- and time-dependent way. RNA sequencing results exhibited UDCA treatment was related to glioma progression and located on mitochondria and endoplasmic reticulum (ER). Cell cycle was arrested in G1 phase followed by caspase-independent apoptosis. UDCA led to decreased MMP, overproduction of ROS and ER stress. Three main stress sensors ATF6, IRE1αand PERK were activated in acute phase. Combining UDCA with bortezomib achieved a synergistic effect via enhancing PERK/ATF4/CHOP pathway and alleviating IRE1α activation. UDCA inhibited GBM progression and the combination with bortezomib achieved a synergistic effect via protracted ER stress. UDCA, alone or with combination of BTZ, presented a promising drug for GBM.

overall_design: a total of 6 samples were analyzed including 3 control group (LN229-NC1,LN229-NC2,LN229-NC3) and 3 treatment group (LN229-U1,LN229-U2,LN229-U3)

first: Xingang

last: Li


title: MGA represses MYC-target genes

status: Public on Jan 18 2020

city: Salt Lake City

first: Xiaoyang

last: Zhang

address: 1950 CIrcle of Hope

country: USA

institute: University of Utah

type: Expression profiling by high throughput sequencing

type: Genome binding/occupancy profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Knocking out C9ORF72 exacerbates axonal trafficking defects associated with hexanucleotide repeat expansion and reduces levels of heat shock proteins I

status: Public on Jan 17 2020

city: Dresden

first: Jared

last: Sterneckert

state: Saxony

address: Fetscherstraße 105

department: Center for Molecular and Cellular Bioengineering (CMCB)

country: Germany

institute: TU Dresden

summary: iPSCs with mutant C9ORF72 were edited using CRISPR/Cas9 (1) to knockout C9ORF72 or, alternatively, (2) to correct the ALS mutation, followed by differentiation into motor neurons.

overall_design: We tested the effects of mutations in C9ORF72 on iPSC-derived MNs by comparing to isogenic gene-corrected controls. In addition, we generated a knockout in MNs containing mutant C9ORF72 to test if this would exacerbate MN degeneration.

first: Masin

last: Abo-Rady


title: Single-cell analysis of neuroinflammatory responses following intracranial injection of G-deleted rabies viruses

city: Boston

first: Kee Wui

last: Huang

state: MA

address: 200 Longwood Ave, WAB 347

department: Neurobiology

institute: Harvard Medical School

summary: Viral vectors are essential tools for the study of neural circuits, with glycoprotein-deleted rabies viruses being widely used for monosynaptic retrograde tracing to map connectivity between specific cell types in the nervous system. However, the use of rabies virus is limited by the cytotoxicity and the inflammatory responses these viruses trigger. While components of the rabies virus genome contribute to its cytotoxic effects, the function of other neuronal and non-neuronal cells within the vicinity of the infected host neurons in either effecting or mitigating virally-induced tissue damage are still being elucidated. Here we analyzed 60,212 single-cell RNA profiles to assess both global and cell type-specific transcriptional responses in the mouse dorsal raphe nucleus following intracranial injection of glycoprotein-deleted rabies viruses and axonal infection of dorsal raphe serotonergic neurons. Gene pathway analyses revealed a down-regulation of genes involved in metabolic processes and neurotransmission following infection. We also identified several transcriptionally diverse leukocyte populations that infiltrate the brain and are distinct from resident immune cells. Cell type-specific patterns of cytokine expression showed that antiviral responses were likely orchestrated by Type I and Type II interferon signaling from microglia and infiltrating CD4+ T cells, respectively. Additionally, we uncovered transcriptionally distinct states of microglia along an activation trajectory that may serve different functions, which range from surveillance to antigen presentation and cytokine secretion. Intercellular interactions inferred from transcriptional data suggest that CD4+ T cells facilitate microglial state transitions during the inflammatory response. Our study uncovers the heterogeneity of immune cells mediating neuroinflammatory responses, and provides a critical evaluation of the compatibility between rabies-mediated connectivity mapping and single-cell transcriptional profiling. These findings provide additional insights into the distinct contributions of various cell types in mediating different facets of antiviral responses in the brain, and will facilitate the design of strategies to circumvent immune responses to improve the efficacy of viral gene delivery.

overall_design: Single cell RNA sequencing of live dissociated cells (unsorted) from mouse brain tissue containing the dorsal raphe nucleus using the inDrops v3 platform.

first: Kee

middle: W

first: Bernardo

middle: L

last: Sabatini


title: Knocking out C9ORF72 exacerbates axonal trafficking defects associated with hexanucleotide repeat expansion and reduces levels of heat shock proteins II

summary: wild type iPSCs were edited using CRISPR/Cas9 to knockout C9ORF72 followed by differentiation into neurons.

overall_design: We assessed the contribution of C9ORF72 to MN degeneration by knocking out the start codon and comparing the transcriptome.


title: High-throughput sequencing after immunization with pep27 mutant

city: Newark

first: GyuLee

last: Kim

state: NJ

address: South orange ave 205

institute: Rutgers University

summary: Purpose; The aim of this study is to find out the difference of gene expression by immunization with the pep27 mutant vaccine. Method; After immunization with the pep27 mutant vaccine, mRNA was extracted from lung and spleen. Result; Both B and T cells were activated by the pep27 mutant vaccine.

overall_design: mRNA profiles of immunized group in lung and spleen were compared to the non-immunized group.

first: Gyu-Lee

first: Dong-kwon

last: Rhee


title: Expression data from in vitro keratinocytes exposed to extracellular vesicles from UVA-irradiated melanocytes

status: Public on Jan 16 2020

city: Linköping

first: Petra

middle: Karolin

last: Wäster

address: Linköpings Universitet

country: Sweden

institute: Linköping University

summary: Analysis of altered gene expression in keratinocytes exposed to extracellular vesicles. In this dataset we include the respective expression data.

overall_design: 8 samples in total, 4 samples from control keratinocyte culture and 4 samples from keratinocyte culture exposed to extracellular vesicle from the same donor, respectively. The samples were RNA isolated, purified and subsequent analysed on the Affymetrix using the WT GenetTitan ST1.1.

first: K

last: Öllinger

first: P


title: Involvement of transcription elongation factor GreA in Mycobacterium tuberculosis viability, antibiotic susceptibility, and intracellular fitness

city: Guang zhou

first: siyuan

last: feng

address: 74 zhongshan 2nd road

country: China

institute: Sun Yat-Sen University

summary:
To understand how GreA may affect gene expression at the transcriptional level, we performed whole-transcriptome RNA-seq analyses.
To examine whether GreA binds to specific chromosomal regions, we performed chromatin immunoprecipitation followed by deep sequencing (ChIP-seq) and then sought to verify the binding mode of GreA. ChIP-seq experiments were performed by using M. smegmatis strains producing GreA proteins fused with two repeats of the FLAG epitope (FLAG2). GreA-FLAG2-DNA nucleoprotein complexes fixed with formaldehyde in the log phase of growth were immunoprecipitated using magnetic beads. To exclude unspecific interactions with magnetic beads, we used a WT strain lacking the FLAG epitope as a negative control for our ChIP-seq experiments. Enriched regions were determined by comparison to the background noise level, which was estimated versus the input DNA of each ChIP-Seq replicate.
Disrupting greA resulted in the differential regulation of 195 genes in M. smegmatis during the exponential growth. Among these, 28 were positively regulated and 167 were negatively regulated.
The identified GreA-FLAG2 binding sites included 1005 ChIP-seq peaks that were confirmed in two biological replicates and absent in WT strain.

overall_design:
For RNA-seq: Examination of 2 strains (Wild type VS ΔgreA).
For ChIP-seq: Examination of 2 strains (Wild type VS greA-flag).

first: Siyuan

last: Feng

first: Guobao

last: Tian


title: circSamd4 represses myogenic transcriptional activity of PUR proteins

city: Baltimore

first: Supriyo

last: De

state: Maryland

address: 251 Bayview Blvd

department: Laboratory of Genetics and Genomics

institute: NIA-IRP, NIH

type: Non-coding RNA profiling by high throughput sequencing

summary: By interacting with proteins and nucleic acids, the vast family of mammalian circRNAs is proposed to influence many biological processes. Here, RNA sequencing analysis of circRNAs differentially expressed during myogenesis revealed that circSamd4 expression increased robustly in mouse C2C12 myoblasts differentiating into myotubes. Moreover, silencing circSamd4, which is conserved between human and mouse, delayed myogenesis and lowered the expression of myogenic markers in cultured myoblasts from both species. Affinity pulldown followed by quantitative mass spectrometry revealed that circSamd4 associated with PURA and PURB, two repressors of myogenesis that function by impairing transcription of the myosin heavy chain (MYH) protein family. Supporting the hypothesis that circSamd4 might complex with PUR proteins thereby preventing their interaction with DNA, silencing circSamd4 enhanced the association of PUR proteins with the Myh promoter, while overexpressing circSamd4 interfered with the binding of PUR proteins to the MYH promoter. These effects were abrogated when using a mutant circSamd4 lacking the PUR binding site. Our results indicate that the association of PUR proteins with circSamd4 directly contributes to myogenesis by derepressing MYH transcription.

overall_design: RNA sequencing followed by circular RNA detection.

first: Poonam

middle: R

last: Pandey

first: Amaresh

middle: C

last: Panda

first: Jen

middle: H

last: Yang

first: Ji

last: Noh

first: Kyoung

middle: M

first: Dimitrios

last: Tsitsipatis

first: Rachel

last: Munk

first: Xiaoling

first: Jennifer

last: Martindale

first: Ming

last: Chang

first: Kotb

last: Abdelmohsen

first: Myriam

last: Gorospe


title: Inhibition of cytoplasmic cap methylation identifies 5’ TOP mRNAs as recapping targets and reveals recapping sites downstream of native 5’ ends

city: Columbus

first: Ralf

last: Bundschuh

state: OH

address: 191 West Woodruff Avenue

department: Department of Physics

institute: The Ohio State University

summary: Cap homeostasis is the cyclical process of decapping and recapping that maintains the translation and stability of a subset of the transcriptome. Previous work showed levels of some recapping targets decline following transient expression of an inactive form of RNMT (ΔN-RNMT), likely due to degradation of mRNAs with improperly methylated caps. The current study examined transcriptome-wide changes following inhibition of cytoplasmic cap methylation. This identified mRNAs with 5’-terminal oligopyrimidine (TOP) sequences as the largest single class of recapping targets. Cap end mapping of several TOP mRNAs identified recapping events at native 5’ ends and downstream of the TOP sequence of EIF3K and EIF3D. This provides the first direct evidence for downstream recapping. Inhibition of cytoplasmic cap methylation was also associated with mRNA abundance increases for a number of transcription, splicing, and 3’ processing factors. Previous work suggested a role for alternative polyadenylation in target selection, but this proved not to be the case. However, inhibition of cytoplasmic cap methylation resulted in a shift of upstream polyadenylation sites to annotated 3’ ends. Together, these results solidify cap homeostasis as a fundamental process of gene expression control and show cytoplasmic recapping can impact regulatory elements present at the ends of mRNA molecules.

overall_design: Human U2OS osteosarcoma cells stably expressing the tetracycline repressor (U2OS-TR) were described previously in (Otsuka et al., 2009). To generate cells with tetracycline-inducible ΔN-RNMT stably integrated, U2OS-TR cells were transfected with pcDNA3/TO-ΔN-RNMT.  U2OS-TR/ΔN-RNMT (n=10) and parental U2OS-TR (n=6) were grown in 10cm dishes. After 48 hr half of the samples were induced with doxycycline.  24 hours later the cells were lysed,  RNA extracted , and QuantSeq REV 3' mRNA-Seq libraries prepared. Induced (+doxycycline) vs uninduced (-doxycycline) gene expression was separately compared for the U2OS-TR/ΔN-RNMT and parental U2OS-TR  cell lines. See also BioProject PRJNA547607 and SRA project SRP201120.

first: Daniel

last: del Valle Morales

first: Jackson

middle: B

last: Trotman

last: Schoenberg


title: RNA Sequencing of postnatal mouse Math1-Cre; Sufu flox/- cerebellum

status: Public on Jan 15 2020

city: Toronto

first: Norman

middle: D

last: Rosenblum

address: 686 Bay Street

country: Canada

institute: The Hospital for Sick Children

summary: Transcriptional profiling to identify genes differentially regulated by Sufu during cerebellum development. Sufu was specifically deleted from the granule neuron compartment using Math1-driven Cre recombinase.

overall_design: Whole cerebella were collected from 4 Math1-Cre; Sufu (flox/-) mice and 4 control littermates (Sufu flox/+) at 2 days postnatal, followed by RNA extraction and next generation RNA sequencing

first: Tayyaba

last: Jiwani


title: miRNA expession data in breast cancer and adjacent normal tissues

city: Wuhan

first: balu

last: wu

address: Donghu Road

institute: Wuhan University

summary:
We select 3 pairs of tissue samples, including 3 breast tissues and 3 adjacent tissues, and then perform miRNA chip detection to find differential miRNAs.
We used microarrays to identify differential expressed miRNAs in breast cancer and paired normal breast tissue

overall_design: Normal breast tissue is represented by N, and breast cancer tissue is represented by T.

first: Yunbao

last: Pan


title: C/EBPα is crucial determinant of epithelial maintenance by preventing epithelial-to-mesenchymal transition

city: Utrecht

first: Ana

last: Lourenço

address: Uppsalalaan 8

country: Netherlands

institute: UMC Utrecht

summary: RNA-sequencing of human mammary epithelial cells (HMLEs) that were lentivirally transduced with vector that constitutively expresses C/EBPα and its respective empty vector control. Both lines were analyzed with and without TGF-β treatment.

overall_design:
RNA-sequencing of human mammary epithelial cells (HMLEs) engineered to express either pLZRS EV or pLZRS-C/EBPα with and without TGF-β (2.5ng/ml) for 24 hours.
Through RNA-sequencing we analysed the differentially TGF-β regulated genes that were also regulated by C/EBPα

first: M

middle: G

last: Roukens

first: A

first: P

middle: J

last: Coffer


title: Transcriptional profiling of 5 days post LPC lesion after microglia ablation

city: Calgary

first: Jeff

last: Biernaskie

state: Alberta

address: 3330 Hospital Drive NW

department: Comparative Biology and Experimental Medicine

institute: University of Calgary

summary: Following all types of neurological injury, resident macrophages are activated locally, and blood-derived macrophages are recruited. Distinguishing the role of resident and blood-derived macrophages is complicated by the difficulty in distinguishing between these cell types because they mostly express the same molecular markers in a diseased state. To begin to understand the complexity of functions of resident and blood-derived macrophages following acute injury in the central nervous system (CNS) we ablated microglia, but not infiltrating macrophages, to determine their contribution following lysolecithin-induced demyelination .

overall_design: RNAseq experiment was performed on LCM collected tissue from CX3CR1CreER; Rosa-iDTR mice or CX3CR1CreER; Rosa-wt controls. Mice received tamoxifent for three days (~12-15) and then LPC demyelination of the ventral spinal cord 4-6 weeks later. Mice recieved daily diphtheria toxin injections until 5 days post-LPC when spinal cords were collected. Lesion tissue or distal control tissue was microdissected in microglia ablated and control mice. We have 3 control groups and 4 microglia ablated groups each containing 3-5 pooled mice.

first: Jason

last: Plemel

first: V

last: Yong


title: RNAseq analysis of intestinal epithelial cells in stopFlox and stopdIEC mice

city: Providence

first: Shipra

last: Vaishnava

state: Rhode Island

address: 171 Meeting street, Box G-B5, MMI dept

department: Molecular Microbiology and Immunology

institute: Brown University

summary: RNAseq analysis of laser capture microdissected ileal epithelial cells from stopFlox(control) and stopdIEC (epithelium-specific vitamin A signaling knockdown) mice

overall_design: 3 mice per group. All mice were littermates and age matched. Frozen OCT blocks of distal ileum were used for sectioning and laser capture microdissection. NuGEN Ovation Mouse kit used for Library preparation. Sequencing done on Illumina platform

first: Namrata

last: Iyer


title: Quantitative Analysis of Transcriptomes between Negative control, UBR5 depleted and MYC depleted HeLa cells

city: Turku

first: Jukka

last: Westermarck

address: Tykistokatu 6

department: Turku Bioscience Centre

country: Finland

institute: University of Turku

summary:
Purpose: The goal of this study is to compare the transcriptome changes between Negative control, UBR5 depleted and MYC depleted HeLa cells
Methods: Gene expression profiles of Negative control, UBR5 depleted and MYC depleted HeLa cells were generated by deep sequencing, in triplicate.
Results:The data were analyzed, and we sucessfully detected global differences in the gene expression between the given groups.
Conclusions: UBR5 depletion induces gene expression changes that are partly overlapping with gene expression changes induced by MYC depletion

overall_design: mRNA profiles of  Negative control, UBR5 depleted and MYC depleted HeLa cells were generated by deep sequencing, in triplicate.

first: Xi

last: Qiao


title: Whole transcriptome analysis of human kidney cells after exposure to Ochratoxin A

city: Halle (Saale)

first: Virginie

last: Dubourg

address: Magdeburger Str. 6

department: Julius Bernstein Institute for Physiology

institute: Martin Luther University - Halle-Wittenberg

summary: Ochratoxin A (OTA) is a nephrotoxin that has been associated with kidney damages. The goal of this project was to identified which impact had nanomolar concentrations of this toxin on cells derived from human kidney in order to identify putative key regulators and underlying mechanisms of the already described phenotypes (e.g. increased apoptosis, dysregulated cell cycle)

overall_design:
RNASequencing of HK-2 and HEK293-T cells after 48 hours exposure to OTA (final concentrations: 0,10,100nM)
Raw RNASequencing data were treated successively with Cutadapt (adaptor removal), Tophat (mapping) and featureCounts (counting).

first: Alexander

last: Nolze

first: Michael

last: Kopf

last: Gekle

first: Gerald

last: Schwerdt


title: RNA sequencing of murine C2C12 cell treated with high-throughput screening hit compound 6,8-dimethyl-3-(4-phenyl-1H-imidazol-5-yl)quinolin-2(1H)-one.

city: New York

first: Brandoch

last: Cook

state: NY

address: 1300 York Ave LC-711

department: Surgery

institute: Weill Cornell Medicine

summary: The hit compound promotes expression and acitivity of alkaline phosphatase in murine cells that are bipotential for myogenic and osteoblastogenic differentiaion. RNA sequecing was performed to assess global transcript expression, with particular attention to genes indicative of osteoblast and bone differentiation.

overall_design: For RNA-Sequencing total RNA was isolated with Trizol reagent (Invitrogen 15596026) from murine C2C12 cells cultured for two days in DMSO (1% in culture medium) or 10 μM 6,8-dimethyl-3-(4-phenyl-1H-imidazol-5-yl)quinolin-2(1H)-one (n=3 each).

first: Cook

last: Brandoch


title: Single-cell transcriptomics of Cx3cr1 fate mapped cells following lysolecithin-induced demyelination in the spinal cord

summary: To isolate Cx3cr1 fate mapped cells following lysolecithin-induced demyelination in the spinal cord, we performed stereotaxic injection of lysolecithin into the ventral white matter tract of the thoracic spinal cord in adult Cx3cr1-CreER:Rosa26-tdTomato+ve mice treated with tamoxifen 4 weeks previously. We FACS collected viable tdTomato+ve cells from uninjured mice and from mice at 5 days post-injury. All samples were processed according to 10X Genomics ChromiumTM Single Cell 3’ Reagent Guidelines v2 Chemistry as per the manufacturer’s protocol. In brief, single cells were sorted into 1% BSA–PBS and partitioned into Gel Bead-In-EMulsions (GEMs) using 10xTM GemCodeTM Technology. This process lysed cells and enabled barcoded reverse transcription of RNA, generating full-length cDNA from poly-adenylated mRNA. DynaBeads® MyOneTM Silane magnetic beads were used to remove leftover biochemical reagents, then cDNA was amplified by PCR. Quality control size gating was used to select cDNA amplicon size prior to library construction. Read 1 primer sequences were added to cDNA during GEM incubation. P5 primers, P7 primers, i7 sample index, and Read 2 primer sequences were added during library construction. Quality control and cDNA quantification was performed using Agilent High Sensitivity DNA Kit. Sequencing was performed first using Illumina MiSeq SR50 to approximate the number of recovered cells in each sample. We recovered 705 and 580 cells for Uninjured and Injured conditions, respectively. Based on this, we determined lane distributions for sequencing using Illumina HiSeq 4000 PE (75 bp paired-end reads) with a targeted sequencing depth of ~100,000-150,000 reads/cell.

overall_design: Single-cell RNA-seq of Uninjured and injuired spinal cord Cx3cr1 fate mapped cells

first: Jo

middle: A

last: Stratton


title: Regulation of the RNAPII Pool Is Integral to the DNA Damage Response [RNA-seq]

status: Public on Jan 14 2020

city: London

first: Richard

middle: James

last: Mitter

state: LONDON

address: 1 Midland Road

department: Bioinformatics & Biostatistics

country: United Kingdom

institute: The Francis Crick Institute

summary: In response to transcription-blocking DNA damage, cells orchestrate a multi-pronged  reaction, involving transcription-coupled DNA repair, degradation of RNAPII and  genome-wide transcription shutdown. How these responses are connected has  remained unclear. Here we show that damage-induced ubiquitylation of RNAPII itself,  at a single lysine (RPB1 K1268), is the focal point for DNA damage response  coordination. K1268-ubiquitylation affects DNA repair and signals RNAPII degradation,  essential for surviving genotoxic insult. It is also crucial for transcriptional shutdown,  in the absence of which cells display dramatic transcriptome alterations. Additionally,  regulation of RNAPII stability is central to transcription recovery – indeed, depletion of  the RNAPII pool underlies the failure of this process in Cockayne syndrome B cells.  These data expose regulation of global RNAPII levels as integral to the cellular DNA  damage response, and open the intriguing possibility that RNAPII pool size generally  affects cell-specific transcription programmes, in genome instability disorders and  even normal cells.

overall_design: To study the role of the RPB1 K1268-ubiquitylation in human cells, we generated switchover model systems (in HEK293 TRex flp In background) whereby an endogenous RPB1 transcript is depleted by highly efficient siRNAs, and simultaneously, expression of a transgenic, siRNA-resistant RPB1 is induced by doxycycline (Dox) - thus "switching over" from endogenous to transgenic RPB1. Transgenic RPB1 is expressed at near-endogenous levels, and is either WT or carries the K1268R mutation to prevent ubiquitylation at this position. Samples were UV irradiated (20 J/m2) 2 days after inducing the switchover (siRNA + Dox treatment), and collected 3h, 8h, 24h and 48 h. Untreated sample was collected at t=0 (just before UV irradiation of other samples).

first: Ana

middle: T

last: Vidakovic

first: Jesper

middle: Q

last: Svejstrup


title: Fluoride alters Ca2+ signaling and mitochondrial function in enamel cells

city: Abu dhabi

first: Youssef

last: Idaghdour

state: Abu dhabi

address: Saadiyat Marina District

department: Biology

country: United Arab Emirates

institute: NYUAD

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: Regulation of the RNAPII Pool Is Integral to the DNA Damage Response


title: Fluoride alters Ca2+ signaling and mitochondrial function in enamel cells [Mouse]

summary: We analyzed the effects of fluoride exposure in mouse enamel cells to assess its impact on cell Ca2+ signaling

overall_design: Treatment of cells using NaF for 24 hrs to test differences between mouse enamel cell lines and HEK-293 cells on the effects of fluoride

first: Francisco

last: Aulestia

first: Johnny

last: Groeling

first: Guilherme

last: Bomfim

first: Veronica

last: Costiniti

first: Vinu

last: Manikandan

first: Ariya

last: Chaloemtoem

first: Axel

last: Concepcion

first: Yi

last: Li

first: Larry

middle: E

last: Wagner II

first: David

middle: I

last: Yule

first: Rodrigo

middle: S

last: Lacruz


title: Regulation of the RNAPII Pool Is Integral to the DNA Damage Response [TT-seq CSBKO]

overall_design: To study the effects of the cellular RPB1 pool on transcription in  WT and CSB KO human cells, we generated switchover model systems (in HEK293 TRex flp In background) whereby an endogenous RPB1 transcript is depleted by highly efficient siRNAs, and simultaneously, expression of a transgenic, siRNA-resistant RPB1 is induced by doxycycline (Dox) - thus "switching over" from endogenous to transgenic RPB1. Transgenic RPB1 is expressed at near-endogenous levels, and is either WT or carries the K1268R mutation to prevent ubiquitylation at this position. Samples were UV irradiated (5 J/m2) 2 days after inducing the switchover (siRNA + Dox treatment), and collected 24h later . Untreated samples were collected at t=0 (just before UV irradiation of other samples). 4SU was added to cells 15 min prior to harvesting in all cases.


title: Base J binding protein (JBP3) is a Component of a Novel Trypanosomatid PNUTS-PP1 Phosphatase Complex involved in RNA Pol II Transcription Termination

city: Athens

first: Robert

last: Schmitz

state: GA

address: B416 Davison Life Sciences

department: Genetics

institute: University of Georgia

summary: Base J is a modified DNA base that is enriched at RNA polymerase II termination sites and telomeres. We previously found that base J functions to prevent readthrough transcription within gene clusters in T. brucei. We now identify a complex in Leishmania and T. brucei composed of PNUTS, PP1, Wdr82 and a J-binding protein (JBP3). We show the RNAi ablation of PNUTS in T. brucei leads to readthrough transcription and expression of downstream genes.

overall_design: The role of PNUTS in regulating transcription termination was investigated using RNAi ablation in T. brucei cell lines. We used 6 RNA seq libraries to determine gene expression changes following the loss of PNUTS. As a control we used 4 RNA seq libraries to determine changes following the loss of TbVAa protein.

last: Sabatini

first: Rudo

last: Kieft

first: Alexandre

middle: P

last: Marand

first: Jose

last: Moran

last: Bridger

first: Lance

last: Wells


title: Gene expression profiles of control IgG and anti-Dll4 Ab treated retinal endothelial cells (ECs) in EC-specific RiboTag mouse (Cdh5-CreERT2 Rpl22 tm1.1Psam)

city: Daejeon

first: Injune

last: Kim

address: Daehak-ro 291, Biomedical Building (E7) 8102

department: Graduate School of Medical Science and Engineering

country: South Korea

institute: Korea Advanced Institute of Science and Technology

summary: We report the gene expression profiles of control IgG and anti-Dll4 Ab treated retinal endothelial cells (ECs) in EC-specific RiboTag mouse (Cdh5-CreERT2 Rpl22 tm1.1Psam )

overall_design: Examination of gene expression profiles in anti-Dll4 Ab treated retinal endothelial cells by RiboTag analysis


title: Genome-wide analysis of mRNA polyadenylation and translation during vertebrate oocyte maturation

city: Boston

first: Michael

middle: Demian

last: Blower

address: 185 Cambridge St CPZN-7250

department: Molecular Biology

institute: Massachusetts General Hospital

summary: Changes in gene expression are required to orchestrate changes in cell state during development. Most cells change patterns of gene expression through transcriptional regulation. In contrast, oocytes are transcriptionally silent and use changes in mRNA poly-A tail length to control protein production. Recent technical advances have enabled genome-wide measurement of poly-A tail length. Poly-A tail lengthening is correlated with translational activation and poly-A tail shortening is correlated with translational repression at a global level during early development. However, it is not clear how poly-A tail changes affect mRNA translation at a global level during vertebrate oocyte maturation. We used TAIL-seq and polyribosome analysis to measure poly-A tail and translational changes during oocyte maturation in Xenopus laevis. We found that the transcriptome undergoes large-scale poly-A and translational changes during oocyte maturation and that poly-A tail length and translation are well-correlated. Interestingly, we found that poly-A tail changes precede translation changes. Additionally, we identified a family of U-rich sequence elements that are enriched near the polyadenylation signal of polyadenylated and translationally activated mRNAs. Interestingly, we found that cytoplasmic polyadenylation is not sufficient to activate translation, which requires a specific density and spacing of U-rich elements. Collectively, our data shows that changes in mRNA polyadenylation are the dominant mechanism controlling protein expression during vertebrate oocyte maturation and that these changes are controlled by a group of cis-acting sequence elements. Our results provide insight into mechanisms of translational control in oocytes and identify novel proteins important for the completion of meiosis.

overall_design: poly-A tail lengths and polysome fractions were measured for genome-wide during oocyte maturation in Xenopus laevis


title: Regulation of the RNAPII Pool Is Integral to the DNA Damage Response [TT-seq]

first: Richard

last: Mitter

overall_design: To study the role of the RPB1 K1268-ubiquitylation in human cells, we generated switchover model systems (in HEK293 TRex flp In background) whereby an endogenous RPB1 transcript is depleted by highly efficient siRNAs, and simultaneously, expression of a transgenic, siRNA-resistant RPB1 is induced by doxycycline (Dox) - thus "switching over" from endogenous to transgenic RPB1. Transgenic RPB1 is expressed at near-endogenous levels, and is either WT or carries the K1268R mutation to prevent ubiquitylation at this position. Samples were UV irradiated (20 J/m2) 2 days after inducing the switchover (siRNA + Dox treatment), and collected 45 min and 3h later . Untreated samples were collected at t=0 (just before UV irradiation of other samples). 4SU was added to cells 15 min prior to harvesting in all cases.

first: Ana

last: Tufegdzic Vidakovic

first: Jesper

last: Svejstrup


title: Fluoride alters Ca2+ signaling and mitochondrial function in enamel cells [Human]

first: Youssef

last: Idaghdour

overall_design: Treatment of cells using NaF for 24 hrs to test differences between enamel cell lines and HEK-293 cells on the effects of fluoride

first: Francisco

last: Aulestia

first: Johnny

last: Groeling

first: Guilherme

last: Bomfim

first: Veronica

last: Costiniti

first: Vinu

last: Manikandan

last: Chaloemtoem

middle: R

last: Concepcion


title: The single cell transcriptional landscape of lung adenocarcinoma metastasis

city: NEW YORK

first: Ashley

last: Laughney

state: New York

address: 413 East 69th Street

department: Physiology, Biophysics and Systems Biology


title: Impact of HSF1 and HSF2 on gene expression in normal growth conditions and upon proteotoxic stress.

first: Jenny

middle: Maaria

last: Joutsen

state: Varsinais-Suomi

address: Tykistökatu 6A

department: Cell Biology

institute: Åbo Akademi University

summary: RNA sequencing (RNA-seq) was used to study the impact of heat shock factors 1 and 2 (HSF1 and HSF2) on gene expression in normal growth conditions, upon Bortezomib-induced proteasome inhibition (25 nM, 6 h or 10 h), and upon heat shock (42∘C, 1 h).

overall_design: U2OS WT, HSF1 KO, and HSF2 KO were treated with 25 nM of Bortezomib for 6 h or 10 h, or heat shocked at 42 degrees for 1 h. Samples were prepared in biological quadruplets.

first: Alejandro

last: Da Silva

first: Jens

middle: C

last: Luoto

first: Marek

last: Budzynski

first: Anna

last: Nylund

first: Aurelie

last: de Thonel

first: Jean-Paul

last: Concordet

first: Valérie

last: Mezger

first: Délara

last: Sabéran-Djoneidi

first: Eva

last: Henriksson

first: Lea

last: Sistonen


title: The single cell transcriptional landscape of a mouse model of lung cancer metastasis

middle: M

summary: Transcriptionally profiling of single cells isolated from progressive stages of metastatic outbreak in a mouse model of lung cancer metastasis.

overall_design: Single-cell RNA sequencing was performed on 6 spontaneous and 6 NK cell-depleted metastasis; spontaneous lesions include disseminated tumor cells isolated from BLI-negative organs, incipient lesions, and macrometastatic outbreaks.

first: Jing

last: Hu

first: Nathaniel

last: Campbell

first: Samuel

middle: F

last: Bakhoum

first: Manu

last: Setty

first: Vincent-Philippe

last: Lavallée

first: Yubin

last: Xie

first: Ignas

last: Masilonis

first: Ambrose

last: Carr

first: Viola

last: Allaj

first: Marissa

last: Mattar

first: Joao

last: Xavier

first: Linas

last: Mazutis

first: John

last: Poirier

first: Charles

last: Rudin

first: Dana

last: Pe'er

first: Joan

last: Massagué


title: The single cell transcriptional landscape of human lung adenocarcinoma (primary tumours and metastases)

first: Ashley

last: Laughney

summary: By transcriptionally profiling single cells from patients spanning different stages of lung adenocarcinoma progression, we provide evidence of epithelial regeneration in untreated primary tumours and a continuum of phenotypic states spanning key stages of embryonic development and lung morphogenesis in metastases. We transcriptionally profiled 41,384 single cells obtained from fresh surgical human samples taken from non-tumour-involved lung (n = 4), primary lung adenocarcinomas (n = 8; 7 untreated and 1 post neo-adjuvant chemotherapy), as well as brain (n = 3), bone (n = 1), and adrenal (n = 1) lung adenocarcinoma metastases. These samples were derived from patients spanning various stages of tumour progression without enrichment for a specific cell type, such that the entire tumour and its microenvironment were sampled in an unbiased manner. Data from all patients were merged to create a global cell atlas of the normal lung, primary tumours, and metastases.

overall_design: Single-cell RNA sequencing was performed on 17 donors using the 10X Genomics protocol. For each donor, all viable cells (identified by forward and side scatter and DAPI exclusion) were assayed for trancriptome-wide RNA-sequence.

first: A

first: J

first: N

first: S

first: M

first: V

first: Y

first: I

first: L

first: C

first: D


title: Rewiring of cell cycle regulated gene expression by calcineurin

city: Worcester

first: Jennifer

last: Benanti

address: 364 Plantation St., LRB 525

department: Molecular, Cell and Cancer Biology

institute: University of Massachusetts Medical School


title: Dynamics of calcineurin-regulated gene expression in the absence of Hog1 in S. cerevisiae

summary: Gene expression was quantified in crz1 hog1 delete S. cerevisae cells over a time course following calcineurin activation by CaCl2. Cells were pretreated with buffer or the calcineurin inhibitor FK506 to allow the identification of calcineurin-regulated genes. We show that calcineurin-dependent downregulation of G1/S genes is partly dependent on the osmostress-activated kinase Hog1.

overall_design: For each strain/condition four samples were collected at intervals through 60 minutes following the addition of CaCl2. Duplicate time course experiments were performed for each strain/condition.

first: Cassadra

last: Leech

first: Heather

last: Arsenault

first: Jianhong

last: Ou

first: Haibo

last: Liu

first: Lihua

last: Zhu


title: Dynamics of calcineurin-regulated gene expression in S. cerevisiae

summary: Gene expression was quantified in crz1 delete S. cerevisae cells over a time course following calcineurin activation by CaCl2. Cells were pretreated with buffer or the calcineurin inhibitor FK506 to allow the identification of calcineurin-regulated genes. A strain with a calcineurin-resistant mutation in the transcription factor Hcm1 was also examined. We show that calcineurin activation leads to downregulation of a many clusters of cell cycle-regulated genes, including those expressed at the G1/S and G2/M transitions.

overall_design: For each strain/condition seven samples were collected at 10-30 minute intervals through 90 minutes following the addition of CaCl2. Duplicate time course experiments were performed for each strain/condition.


title: A maple syrup extract alleviates liver injury in type 2 diabetic model mice

status: Public on Jan 13 2020

city: Gunma

first: Tsudoi

last: Toyoda

address: 54 Nakaorui-machi, Takasaki-shi

country: Japan

institute: Tkasaki University of Health and Welfare

summary: A recent study showed that 54% of type 2 diabetes (T2D) patients have nonalcoholic fatty liver disease, which is a risk factor for aggravation diabetic symptoms. Previous studies suggested components in maple syrup alleviated liver injury and found polyphenols as food components to improve the symptoms and complications of diabetes. Therefore, we hypothesized that a polyphenol fraction in maple syrup improves the symptoms and complications of diabetes. To address the hypothesis, we investigated the effects of a polyphenol-rich maple syrup extract (MSE) on a T2D model mice. KK-Ay mice were fed a normal or 0.1% MSE-supplemented diet for 43 days. The results showed that the levels of serum alanine aminotransferase and aspartate aminotransferase were significantly reduced in mice that ingested MSE. Hepatic genes related to lipogenesis and lipolysis were down- and upregulated, respectively, in mice that ingested MSE. These results suggest that MSE intake alleviates liver injury and suppresses lipid accumulation in the livers of T2D mice.

overall_design: Male KK-Ay mice 4 weeks of age were purchased from CLEA Japan (Tokyo, Japan). The mice were individually housed in a room maintained at 21–23°C with 50–70% relative humidity and a 12:12-h light/dark cycle. Normal and 0.1% MSE-supplemented diets were prepared based on the AIN-93G formula by Oriental Yeast Co. (Tokyo, Japan). The supplemented dose of MSE was decided on the basis of polyphenol content in our previous study. In the study, we showed that a liver injury marker decreased in healthy rat fed maple syrup-supplemented diet which had almost the same amount of polyphenol as the diet in this study. After one week of acclimation, the mice were divided into two groups (n = 8 each) with approximately equal mean body weights and nonfasting blood glucose levels. The mice were fed normal or MSE diets (the control or MSE group) with a pair-feeding technique for 43 days and allowed free access to ultrapure water. The food intake and body weight were measured every two and four days, respectively. After 16 h of food deprivation, the mice were sacrificed under sodium pentobarbital anesthesia. The liver was treated with RNAlater (Thermo Fisher Scientific Inc., Waltham, MA, USA). The samples were stored at −80°C until use.

first: Kota

last: Iida

first: Tomoko

last: Ishijima

first: Keiko

last: Abe

first: Shinji

last: Okada

first: Yuji

last: Nakai


title: Analysis for transcriptome profiling changes in 4'-O-methylpyridoxine (OMP) treated leukemic cells

first: Yu-Jui

last: Ho

address: 417 E 68th St

department: Cancer Biology & Genetics Program

institute: Memorial Sloan Kettering Cancer Center

summary: To validate the transcriptome profiling changes upon pharmacologic inhibition of PDXK, a key enzyme in vitamin B6 metabolism pathway, mouse leukemic cells were treated with PDXK inhibitor OMP. mRNA was extracted and purified for RNA_seq.

overall_design: There are 3 replicates for vehicle or OMP treatment and 6 samples in total.

first: Bo

last: Li

first: Lingbo

last: Zhang

first: ChiChao

last: Chen

first: Scott

last: Lowe


title: Regulation of embryonic and adult neurogenesis by Ars2

city: Beijing

first: Yang

last: Yu

address: Dong Dan San Tiao #5

institute: Chinese Academy of Medical Sciences

summary: Neural development is tightly controlled at multiple levels to orchestrate appropriate choices of cell fate and differentiation. While more attention has been paid to the roles of neural-restricted factors, broadly-expressed factors can have compelling impacts on tissue-specific development. Here, we describe in vivo genetic analysis of Ars2, which has mostly been studied as a general RNA processing factor in yeast and cultured cells. Ars2 protein exhibits a dynamic expression pattern during neural lineage progression, and conditional knockout analyses demonstrated that Ars2 is required for proliferation of embryonic neural stem cells (NSCs). In addition, Ars2 null neural stem cells can still transition into post-mitotic neurons, but fail to undergo terminal differentiation. Ars2 is similarly required for neurogenesis in the adult brain. We next generated Ars2 ChIP-seq data to broaden evidence for a distinct role for Ars2 as a transcriptional regulator in neural development. Notably, Ars2 preferentially occupies DNA enhancers in NSCs, and broadly colocalizes with the NSC regulator SOX2, but exhibits markedly reduced association with chromatin following differentiation. Finally, we demonstrate a continuous requirement for Ars2 during adult neurogenesis, since adult-specific deletion of Ars2 compromises hippocampal neurogenesis and results in specific behavioral defects. Together, we provide evidence for Ars2 as an essential neural regulator that interacts dynamically with DNA and controls neural lineage development.

overall_design: ChIP-seq of three proteins in primary mouse neural stem cells and differentiating neurospheres

first: Eric

last: Lai


title: ATAC-seq profile of zebrafish periderm at 4-somite stage

city: Iowa City

first: Robert

last: Cornell

state: Iowa

address: 1-400 D Bowen Science Bldg. 51 Newton Road

department: Anatomy and Cell Biology

institute: University of Iowa

summary: In order to profile periderm-specific nucleosome free regions of zebrafish periderm cells at 4-somite stage, we isolated the equal number of GFP-positive cells and GFP-negative cells from Tg(krt4:GFP) embryos and perform ATAC-seq. This study revealed the landscape of zebrafish periderm-specific nucleosome free regions at 4-somite stage.

overall_design: GFP-positive embryos were harvested from two independent incross of Tg(krt4:GFP). Embryos were dissociated and sorted with FACS. For each batch, 50000 GFP-positive and 50000 GFP-negative cells were collected and subjected to ATAC-seq.

first: Huan


title: mRNA profile of zebrafish periderm at 4-somite stage

summary: In order to compare the transcriptome and tissue-specific nucleosome free regions of zebrafish periderm cells at 4-somite stage, we isolated the RNA from sorted GFP-positive cells of Tg(krt4:GFP) embryos and perform low-input RNA-seq. This study revealed periderm-specific transcriptome at 4-somite stage. Moreover, comparing with ATAC-seq from the same tissue, we confirmed the correlation between gene expression and nearby chromatin accessibility.

overall_design: GFP-positive embryos were harvested from three independent incross of Tg(krt4:GFP). Embryos were dissociated and sorted with FACS. For each batch, 2000 GFP-positive and 2000 GFP-negative cells were collected and subjected to RNA-seq.


title: Zebrafish periderm at 4-somite stage

overall_design: Refer to individual Series


title: Transcriptome upon PDXK knock-out in mouse and human leukemic cells

summary: To study transcriptomic changes upon PDXK knock-out in mouse and human leukemic cells

overall_design: For RNA-seq analysis of the transcriptional profiles of mouse MLLAF9-NrsG12D and human MOLM13 leukemic cells transduced with PDXK targeting sgRNA, total RNA was extracted from bulk tissue using the RNeasy Mini Kit (Qiagen). Purified polyA mRNA was subsequently fragmented, and first and second strand cDNA synthesis performed using standard Illumina mRNA TruSeq library preparation protocols. Double stranded cDNA was subsequently processed for TruSeq dual-index Illumina library generation.

first: Chichao


title: Monocyte-derived alveolar macrophages induced by influenza infection confer long-term antibacterial protection [ATAC-seq]

first: Andreas

last: Wack

summary: To investigate differences in the chromatin accessibility using ATAC-seq. This was done in macrophages from a BM origin (CD45.1) and embryonic origin (CD45.2) in influenza-experienced, and naive lungs -  at baseline and following Pam3CSK4 stimulation

overall_design: In this experiment we sorted alveolar macrophages from naïve, and post-influenza mice using congenic markers to indicate origin. Cells were then stimulated ex vivo for 2 hours with Pam3CSk4 to investigate differences in stimulated cells, but also at steady state (Mock stimulated). This was done in parallel with RNA-sequencing, to identify changes at both the transcriptional, and chromatin level in the same cells.

first: H

last: Aegerter

first: S

last: Crotta

first: J

last: Kulikauskaite

last: Patel

first: E

last: Hessel

last: Beinke

first: A


title: Treatment-induced tumor dormancy through YAP-mediated transcriptional reprogramming of the apoptotic pathway [scRNASeq]

first: Kari

last: Kurppa

address: 450 Brookline Ave

institute: Dana-Farber Cancer Institute

summary: Eradicating tumor dormancy that develops following oncogene-targeted therapy, including after epidermal growth factor receptor (EGFR) tyrosine kinase inhibitor (TKI) treatment of EGFR-mutant non-small cell lung cancer (NSCLC), is an attractive therapeutic strategy but the mechanisms governing the establishment of tumor dormancy are poorly understood. We observe that blockade of ERK1/2 reactivation following EGFR TKI treatment by combined EGFR/MEK inhibition uncovers cells that survive by entering a senescence-like dormant state, characterized by extensive epigenetic remodeling and high YAP/TEAD activity. YAP/TEAD trigger an epithelial-to-mesenchymal transition (EMT) program and engage the EMT transcription factor SLUG to directly repress pro-apoptotic BMF, limiting drug-induced apoptosis. Pharmacological co-inhibition of YAP or TEAD, or genetic deletion of YAP1, all deplete dormant cells by enhancing EGFR/MEK induced apoptosis. Thus, YAP activation can promote the survival of EGFR-mutant NSCLC cells in the chronic absence of EGFR signaling. Eradicating this population enhances the efficacy of targeted therapies which could ultimately lead to prolonged treatment responses in cancer patients.

overall_design: PC-9 EGFR-mutant NSCLC cells were treated in vitro and in vivo with EGFR-inhibitor osimertinib and MEK inhibitor trametinib until minimal residual disease-state, followed by single-cell RNA-sequencing. In vitro, the cells were treated for three weeks, followed sample preparation for single-cell RNA-seq. Control cells were treated with DMSO for 2 days. PC-9 In vivo tumors (3 mice / group) were treated with either single-agent osimertinib or with the combination of osimertinib and trametinib for three weeks, followed sample preparation for single-cell RNA-seq. Control tumors were treated with vehicle for three weeks.

first: Pasi

last: Jänne


title: Monocyte-derived alveolar macrophages induced by influenza infection confer long-term antibacterial protection [ATAC-seq 2]

summary: To investigate differences in the chromatin accessibility using ATAC-seq. This was done in macrophages isolated from a busulfan chimera, using congenic markers (CD45.1 for a BM origin, and CD45.2 for a host origin) in influenza-experienced, and naive lungs -  at baseline and following Pam3CSK4 stimulation


title: Treatment-induced tumor dormancy through YAP-mediated transcriptional reprogramming of the apoptotic pathway [DMSO vs DORMANT]

overall_design: PC-9, HCC827 and HCC4006 cells were plated at 15 x 104 cells / cm2 into 10 cm plates (DMSO treated control cells) or into 15 cm plates (dormant cells) in duplicate. The next day, cells were treated either with DMSO or with the combination of 100 nM osimertinib and 30nM trametinib. DMSO-treated control cells were harvested 24h later, and the dormant cells after 2 weeks of treatment. At these timepoints, cells were lysed into TRIzol and RNA extraction was performed according to the manufacturer’s protocol.


title: Monocyte-derived alveolar macrophages induced by influenza infection confer long-term antibacterial protection

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


title: Treatment-induced tumor dormancy through YAP-mediated transcriptional reprogramming of the apoptotic pathway [YAP1 KO vs CTRL]

overall_design: PC-9 and HCC4006 CTRL and YAP1 KO cells were plated into 10 cm dishes at 15 x 104 cells / cm2 in triplicate. The next day, the cells were treated with DMSO or with the combination of 100 nM osimertinib and 30 nM trametinib (OT). After 24 hours, the cells were lysed into TRIzol and RNA extraction was performed according to the manufacturer’s protocol


title: Recapitulating the Human Segmentation Clock with Pluripotent Stem Cells - RNAseq analysis of in vitro induced murine presomitic mesoderm (PSM) and identification of components of the in vitro mouse segmentation clock [Oscillation_Mm]

city: Kyoto

first: Cantas

last: Alev

address: Medical Faculty Bldg. B, Yoshida-Konoe-cho, Sakyo-ku

department: Institute for the Advanced Study of Human Biology (ASHBi)

institute: Kyoto University

summary: Pluripotent stem cells (PSCs) have increasingly been used to model different aspects of embryogenesis and organ formation. Despite recent advances in the in vitro induction of major mesodermal lineages and mesoderm-derived cell types, experimental model systems that can recapitulate more complex biological features of human mesoderm development and patterning are largely missing. Here, we utilized induced pluripotent stem cells (iPSCs) for the stepwise in vitro induction of presomitic mesoderm (PSM) and its derivatives to model distinct aspects of human somitogenesis. We focused initially on modeling the human segmentation clock, a major biological concept believed to underlie the rhythmic and controlled emergence of somites, which give rise to the segmental pattern of the vertebrate axial skeleton. We succeeded to observe oscillatory expression of core segmentation clock genes, including HES7 and DKK1, and identified novel oscillatory genes in human and mouse PSC-derived PSM. We furthermore determined the period of the human segmentation clock to be around five hours and showed the presence of dynamic traveling wave-like gene expression within in vitro induced human PSM. Utilizing CRISPR/Cas9-based genome editing technology, we then targeted genes, for which mutations in patients with abnormal axial skeletal development such as spondylocostal dysostosis (HES7, LFNG and DLL3)  have been reported. Subsequent analysis of patient-like iPSC knock-out lines as well as patient-derived iPSCs together with their genetically corrected isogenic controls revealed gene-specific alterations in oscillation, synchronization or differentiation properties, validating the overall utility of our model system, to recapitulate not only key features of human somitogenesis but also to provide novel insights into diseases associated with the formation and patterning of the human axial skeleton.

overall_design: In order to identify the molecular components of the mouse segmentation clock, mouse epiblast stem cell (EpiSCs)-derived presomitic mesoderm (PSM) samples were collected in timely manner utilizing a luciferase reporter line of the key oscillatory segmentation clock gene Hes7 (Hes7-reporter). Two independent sets of 16 samples each of entrained oscillating mouse in vitro induced PSM samples were analyzed using RNAseq.

first: Mitsuhiro

last: Matsuda* (equal contribution)

first: Yoshihiro

last: Yamanaka* (equal contribution)

first: Maya

last: Uemura

first: Satoko

last: Sakurai

first: Miki

last: Ebisuya

first: Takuya

last: Yamamoto


title: Treatment-induced tumor dormancy through YAP-mediated transcriptional reprogramming of the apoptotic pathway [ChIP + ATAC]

overall_design: For ChIP-seq, PC-9 cells were plated at 15 x 104 cells / cm2 into 15 cm plates in duplicate, and treated the next day either with DMSO or with the combination of 100 nM osimertinib and 30nM trametinib. Cells were trypsinized at after 48h of treamtent, and cryopreserved in FBS + 8% DMSO in -80C until processing. For ATAC-seq, PC-9 cells were plated at 15 x 104 cells / cm2 into 15 cm plates in triplicate, and treated the next day with DMSO, 100 nM osimertinib or with the combination of 100 nM osimertinib and 30nM trametinib. DMSO-treated control cells were harvested 24h later. Osimertinib and osimertinib/trametinib treated cells were harvested after 2 weeks of treatment. Rebound samples were obtained by withdrawing drugs from three additional osimertinib/trametinib-treated plates and harvesting the cells once the plates reached 60-70% confluence. Cells were trypsinized at timepoints, and cryopreserved in FBS + 8% DMSO in -80C until processing.


title: Monocyte-derived alveolar macrophages induced by influenza infection confer long-term antibacterial protection [RNA-seq]

summary: To investigate transcriptomic differences using RNA-seq in macrophages from a BM origin (CD45.1) and embryonic origin (CD45.2) in influenza-experienced, and naive lungs - at baseline and following stimulation

overall_design: In this experiment we sorted alveolar macrophages from naïve, and post-influenza mice using congenic markers to indicate origin. Cells were then stimulated ex vivo for 16 hours with Pam3CSk4 to investigate differences in stimulated cells, but also at steady state (Mock stimulated). This was done in parallel with ATAC-sequencing, to identify changes at both the transcriptional, and chromatin level in the same ells.


title: Recapitulating the Human Segmentation Clock with Pluripotent Stem Cells - RNAseq analysis of healthy control (WT) and knock-out reporter lines of segmentation clock genes HES7, DLL3, LFNG and MESP2.

summary: Pluripotent stem cells (PSCs) have increasingly been used to model different aspects of embryogenesis and organ formation. Despite recent advances in the in vitro induction of major mesodermal lineages and mesoderm-derived cell types experimental model systems that can recapitulate more complex biological features of human mesoderm development and patterning are largely missing. Here, we utilized induced pluripotent stem cells (iPSCs) for the stepwise in vitro induction of presomitic mesoderm (PSM) and its derivatives to model distinct aspects of human somitogenesis. We focused initially on modeling the human segmentation clock, a major biological concept believed to underlie the rhythmic and controlled emergence of somites, which give rise to the segmental pattern of the vertebrate axial skeleton. We succeeded to observe oscillatory expression of core segmentation clock genes, including HES7 and DKK1, determined the period of the human segmentation clock to be around five hours and showed the presence of dynamic traveling wave-like gene expression within in vitro induced human PSM. We furthermore identified and compared oscillatory genes in human and murine PSC-derived PSM, which revealed species-specific as well as common molecular components and novel pathways associated with the mouse and human segmentation clocks. Utilizing CRISPR/Cas9-based genome editing technology, we then targeted genes, for which mutations in patients with segmentation defects of vertebrae (SDV) such as spondylocostal dysostosis (SCD) have been reported (e.g. HES7, LFNG, DLL3 and MESP2 DLL3). Subsequent analysis of patient-like knock-out and point-mutation lines as well as patient-derived iPSCs together with their genetically corrected isogenic controls revealed gene-specific alterations in oscillation, synchronization or differentiation properties, validating the overall utility of our model system, to provide novel insights into the human segmentation clock as well as diseases associated with the formation of the human axial skeleton.

overall_design: RNAseq analysis of iPSC and presomitic mesoderm (PSM) samples derived from either control (WT) or knock-out (KO) lines generated in the Hes7-reporter background. At least two different knock-out clones for each targeted gene (HES7, DLL3, LFNG and MESP2) were analyzed. Original iPSC line from which the Hes7-reporter is derived (201B7) was analyzed and used for comparison.

last: Yamanaka


title: Monocyte-derived alveolar macrophages induced by influenza infection confer long-term antibacterial protection [RNA-seq 2]

last: Wack

summary: To investigate transcriptomic differences using RNA-seq. This was done in macrophages isolated from a busulfan chimera, using congenic markers (CD45.1 for a BM origin, and CD45.2 for a host origin) in influenza-experienced, and naive lungs -  at baseline and following Pam3CSK4 stimulation

overall_design: In this experiment we sorted alveolar macrophages from naïve, and post-influenza mice using congenic markers to indicate origin. Cells were then stimulated ex vivo for 16 hours with Pam3CSk4 to investigate differences in stimulated cells, but also at steady state (Mock stimulated). This was done in parallel with ATAC-sequencing, to identify changes at both the transcriptional, and chromatin level in the same cells.


title: Recapitulating the Human Segmentation Clock with Pluripotent Stem Cells - RNAseq analysis of in vitro induced human presomitic mesoderm (PSM) and identification of components of the human segmentation clock [Oscillation_Hs]

overall_design: In order to identify the molecular components of the human segmentation clock, human induced pluripotent stem cell (iPSC)-derived presomitic mesoderm (PSM) samples were collected in timely manner utilizing a luciferase reporter line of the key oscillatory segmentation clock gene Hes7 (Hes7-reporter). Two independent sets of 16 samples each of entrained oscillating human PSM samples were analyzed using RNAseq.


title: Recapitulating the Human Segmentation Clock with Pluripotent Stem Cells


title: Genome wide gene expression analysis of acutely injured primary mouse neurons

city: Jena

first: Marco

last: Groth

address: Beutenbergstraße 11

department: Core Facility - Next Generation Sequencing

institute: Leibniz Institute on Aging - FLI

summary: We aimed at identifying a common transcriptional response of neurons to acute injury by conducting a RNA-Seq analysis on primary mouse neurons. We performed parallel damaging of cultured neurons by applying oxygen-glucose deprivation (OGD) as model for cerebral ischemia as well as excitotoxicity induced by the glutamate receptor agonist kainic acid (KA) as an in vitro model amyotrophic lateral sclerosis and epilepsy. For each of the assays, we determined the experimental conditions in which 20% of the cultured cells died due to an 8-hour treatment. In suggesting a convergence of insult-specific upstream factors on shared downstream signals, we assessed the intersection of the conditions and identified 318 statistically significant transcripts with similar regulation in the two in vitro assays

overall_design: 12 samples in total: 3 OGD; 3 OGD control; 3 KA; 3 KA control

first: Alex

last: Schulz


title: Estrogen Receptor α (ERα)-mTOR signaling crosstalk rewires cancer cell metabolism providing a mechanism underlying obesity-associated postmenopausal breast cancer

status: Public on Jan 11 2020

city: Urbana

first: Karen

last: Chen

state: IL

address: 1201 W Gregory St

department: Division of Nutritional Sciences

institute: University of Illinois at Urbana-Champaign


title: Estrogen Receptor α (ERα)-mTOR signaling crosstalk rewires cancer cell metabolism providing a mechanism underlying obesity-associated postmenopausal breast cancer [RNA-seq]

summary: Obesity is a risk factor for postmenopausal ERα (+) breast cancer. The metabolites from serum that contribute to this risk and how these factors affect ERα signaling are not known. Using whole metabolite profiling and a detection panel for proteins, we identified biomarkers that were differentially present in serum from obese vs. non-obese postmenopausal women, and we validated these factors in two separate cohorts of postmenopausal women who either developed breast cancer or those who were obese and lost weight after the onset of menopause. In vitro assays identified free fatty acids (FFAs), in particular oleic acid (OA) as serum factors that correlate with increased proliferation and aggressiveness in ERα(+) breast cancer cells by. FFAs activated both ERα and mTOR pathways and rewired metabolism in breast cancer cells. Pathway preferential estrogen-1 (PaPE-1), which target ERα and mTOR signaling, was able to block changes induced by FFAs. In fact, PaPEs were more effective in the presence of FFAs, suggesting a role for obesity-associated gene and metabolic rewiring in providing new targetable vulnerabilities for ERα-(+) breast cancer in postmenopausal women. Our findings provide a basis for preventing or inhibiting obesity-associated breast cancer by using PaPEs that would reverse these newly appreciated metabolic vulnerabilities of breast tumors in obese postmenopausal women.

overall_design: Examination of metabolic pathways in MCF-7 cells upon OA exposure and PaPE-1 treatmnent

first: Zeynep

last: Madak-Erdogan


title: Estrogen Receptor α (ERα)-mTOR signaling crosstalk rewires cancer cell metabolism providing a mechanism underlying obesity-associated postmenopausal breast cancer [ChIP-seq]


title: The Xenobiotic Transporter Mdr1 Enforces T Cell Homeostasis in the Presence of Intestinal Bile Acids

status: Public on Jan 10 2020

city: Jupiter

first: Mark

last: Sundrud

state: FL

address: 120 Scripps Way

department: Immunology and Microbiology

institute: The Scripps Research Institute

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

CD4+ T cells are tightly regulated by microbiota in the intestine, but whether intestinal T cells interface with host-derived metabolites is less clear. Here, we show that CD4+ T effector (Teff) cells upregulated the xenobiotic transporter, Mdr1, in the ileum to maintain homeostasis in the presence of bile acids. Whereas wild-type Teff cells upregulated Mdr1 in the ileum, those lacking Mdr1 displayed mucosal dysfunction and induced Crohn?s disease-like ileitis following transfer into Rag1-/- hosts. Mdr1 mitigated oxidative stress and enforced homeostasis in Teff cells exposed to conjugated bile acids (CBAs), a class of liver-derived emulsifying agents that actively circulate through the ileal mucosa. Blocking ileal CBA reabsorption in transferred Rag1-/- mice restored Mdr1-deficient Teff cell homeostasis and attenuated ileitis. Further, a subset of ileal Crohn?s disease patients displayed MDR1 loss of function. Together, these results suggest that coordinated interaction between mucosal Teff cells and CBAs in the ileum regulate intestinal immune homeostasis.


title: Airway Smooth Muscle Differentiation is Essential for Promoting Airway Size, Tracheal Cartilage Segmentation, but Dispensable for Epithelial Branching

first: Randee

last: Young

address: 4 Blackfan st

department: Pediatrics

institute: Boston Children's Hospital

summary: The goals of this study are to evalute the role of airway smooth muscle during mouse lung development. We have compared Tbx4rtTA;tetOcre;Mycocdf/f (MyocdCKO) mutants to control mice and generated next generation sequencing transcriptome profiling (RNA-seq) to compare the transcriptomes of each genotype.

overall_design: Methods: Lung and trachea mRNA profiles of E18.5 and E13.5 control and MyocdCKO mice were generated by deep sequencing using Illumina HiSeq4000. Sequences in FASTQ files were aligned to the mouse reference genome using STAR (Dobin et al., 2013). Reads were counted using featureCounts and differential expression analysis was performed using DeSeq2 (Liao et al.,  2014; Love et al., 2014).

first: Xin

last: Sun


title: The Xenobiotic Transporter Mdr1 Enforces T Cell Homeostasis in the Presence of Intestinal Bile Acids [Rh123hi-lo RNA-Seq]

summary: CD4+ T cells are tightly regulated by microbiota in the intestine, but whether intestinal T cells interface with host-derived metabolites is less clear. Here, we show that CD4+ T effector (Teff) cells upregulated the xenobiotic transporter, Mdr1, in the ileum to maintain homeostasis in the presence of bile acids. Whereas wild-type Teff cells upregulated Mdr1 in the ileum, those lacking Mdr1 displayed mucosal dysfunction and induced Crohn’s disease-like ileitis following transfer into Rag1-/- hosts. Mdr1 mitigated oxidative stress and enforced homeostasis in Teff cells exposed to conjugated bile acids (CBAs), a class of liver-derived emulsifying agents that actively circulate through the ileal mucosa. Blocking ileal CBA reabsorption in transferred Rag1-/- mice restored Mdr1-deficient Teff cell homeostasis and attenuated ileitis. Further, a subset of ileal Crohn’s disease patients displayed MDR1 loss of function. Together, these results suggest that coordinated interaction between mucosal Teff cells and CBAs in the ileum regulate intestinal immune homeostasis.

overall_design:
RNAseq of sorted Rh123hi (Mdr1-) or Rh123lo (Mdr1+) CD4+ Teff cells isolated from mesenteric lymph nodes of Rag deficient hosts 6 weeks post T cell transfer
6 samples, 3 replicates each

first: M


title: Transcriptional profilling of In vitro-primed C.rodentium-specific WT or Caspase-1 deficient Th cells

city: Cincinnati

first: Chandrashekhar

last: Pasare

address: 3333 Burnet Ave

institute: Cininnati Children's Hospital Medical Center

summary:
Introduction: We reported that caspase-1 is highly expressed in in vitro-primed C.rodentium-specific Th cells. Caspase-1 deficient (Casp1d10) naïve T cells differentiate into pathogen-specific Th17 cells at an suboptimal level and fail to protect against C.rodentium infection. To gain insight into the regulatory pathways exerted by caspase-1 in Th cells, we performed RNA-seq on in vitro-primed WT and Casp1d10 Th cells.
Method: We stimulated WT C57/BL6J splenic CD11c+ DCs with 10ug/ml C.rodentium lysate for 5 hours. Then DCs are washed and co-cultured in 1:5 ratio with naïve WT C57/BL6J or Casp1d10 CD4 T cells for 10 days. CFSE-CD90+ (pathogen-specific Th cells) were FACS-sorted and subjected to mRNA-seq analysis.
Conclusion: We found that WT Cr-specific Th cells have higher expression of Th17 genes, including Il17a,f,Il22 and Rorc. Casp1Δ10 Cr-specific Th cells exhibited higher expression of iNOS genes and exogenous lipid metabolism genes such as Cd36, suggesting a distinct cellular metabolism potentially regulated by Caspase-1.

overall_design: mRNA profiles of WT and Casp1d10 Cr-specific Th cells.

first: Yajing

last: Gao


title: Transcriptomic and proteomic response of the organohalide respiring bacterium Desulfoluna spongiiphila to growth with 2,6-dibromophenol as electron acceptor

city: New Brunswick,

first: Jie

last: Liu

address: 76 Lipman Drive

department: Department of Biochemistry and Microbiology

institute: Rutgers University

summary: We compared the global transcriptomic analysis of Desulfoluna spongiiphila strain AA1, an organohalide-respiring Desulfobacterota isolated from a marine sponge, with 2,6-dibromophenol or with sulfate as electron acceptor. The most significant difference of the transcriptomic analysis was the expression of one reductive dehalogenase gene cluster (rdh16), which was significantly upregulated with 2,6-dibromophenol.

overall_design: Desulfoluna spongiiphila AA1 was pregrown on sulfate and then amended with either 2,6-dibromophenol or sulfate. Gene expression was compared for cultures under these two conditions. Each condition was established in triplicate.

first: Max

last: Häggblom


title: Transcriptional profilling of In vitro-primed C.rodentium-specific Th17 cells, cytokine-differentiated Th17 cells and ex vivo Th17 cells following C.rodentium infection

summary:
Introduction: We reported a in vitro pathogen-specific priming system to using pathogen lysate stimulated splenic CD11c+ DCs to differentiate pathogen-specific murine T helper cells. This method allowed us to compare side-by-side transcriptional profiles of bulk T helper cells  that are specific to distinct pathogens and to study their composition and functionality. Moreover, we can utilize cytokine reporter mice to isolate specific Th subtypes from these in vitro-primed T cells and study their transcriptional regulation.
Method: We isolate commited Th17 cells by utilizing IL-17A fate-mapping mice (Il17aCRE; R26tdT). We generated Th17 cells in 3 conditions: 1. We used Cr-stimulated DCs to prime Th17 cells and sorted CD90+CFSE-tdT+ population, dubbed 'ppTh17' cells. CFSE+CD90+ naive T cells from the same culture as controls. 2. We polarized naive Il17aCRE; R26tdT CD4 T cells to Th17 lineage using previously defined cytokine and antibody cocktail (IL-6+TGFb1+IL-1b+IL-23; plate bound anti-CD3+anti-CD28). We sorted CD90+tdT+ population, dubbed 'cdTh17' cells. 3. We intragastrically infected Il17aCRE; R26tdT mice with 5x10^8 C.rodentium and harvested mesenteric lymph nodes at 10 days post infection (dpi). We sorted tdT+ CD4 T cells from mesenteric lymph nodes, dubbed "ex vivo Th17' cells. The four sorted populations were subjected to mRNA-sequencing analysis.
Conclusion: We found that compared to cdTh17 cells, ppTh17 cells and ex vivo Th17 cells resemble each other. These two physiologically relevant Th17 populations maintain high levels of heterogeneity and plasticity, as well as posess ability to upregulate memory T cell related genes. cdTh17 cells highly express glycolysis and one-carbon metabolism genes, correlate with their expression of cell cycle genes, suggesting a highly activated state.

overall_design: mRNA profiles of ppTh17, cdTh17 and ex vivo Th17 cells  were generated by Illumina sequencing in duplicate or triplicate. CFSE+CD90+ naïve T cell from Cr-primed cultures served as control.


title: Single Cell RNA Sequencing of Monocyte Derived Endothelial Cells

city: Buffalo

first: Stylianos

last: Andreadis

address: 908 Furnas Hall

department: Department of Chemical and Biological Engineering

institute: University at Buffalo

summary: We examined the global transcriptome of individual cells in the three cell populations, starting MC from three donors after 1hr adherence to FN pooled, MC-derived EC subjected to shear stress, and HCAEC subjected to shear stress using single cell RNA-sequencing (scRNA-Seq). Analysis showed that the initial population of MC clustered separately from HCAEC, while the resulting MCEC overlapped with HCAEC and not MC. Co-expression analysis reveals that only the resulting MCEC contain cells co-expressing KDR and PROM1 (CD133), whereas our starting MC population contained only one cell expressing KDR and a separate cell expressing PROM1 suggesting that our initial MC population did not contain any EPC/ECFCs. Interestingly, heatmaps constructed using EC and MC associated genes revealed that the resulting MCEC cells expressed predominantly EC genes but also some MC genes.

overall_design: Examination of global transcriptome of 3 cell populations, initial monocytes, monocyte derived endothelial cells, and human endothelial cells as a control

first: Randall

last: Smith Jr

first: Julien

middle: V

last: Kann

first: Jonathan

last: Bard

first: Donald

last: Yergeau

first: Stelios


title: Recapitulating the Human Segmentation Clock with Pluripotent Stem Cells - RNAseq-based comparison of patient and isogenic rescue/healthy control iPSC lines during in vitro differentiation of human presomitic mesoderm and its derivatives

first: Cantas

last: Alev

overall_design: All stages of our stepwise in vitro induction and differentiation protocol were analyzed using spondylocostal dysostosis (SCD) patient iPSC lines (clones SCDP1-A and SCDP1-F) together with their corresponding isogenic controls (SCDP1-resA and SCDP1-resF) or healthy control iPSCs (201B7); identified heterozygous compound mutations in MESP2 of SCDP1-patient line were corrected via CRISPR/Cas9-based allele-specific genome editing. Two patient clones were utilized (SCDP1-A and SCDP1-F) together with three rescue clones (SCDP1-resA1, SCDP1-resF2 and SCDP1resF3). All stages of the induction protocol were targeted (induced pluripotent stem cell (iPSC), primitive streak (PS), presomitic mesoderm (PSM), somitic mesoderm (SM), sclerotome (SCL) and dermomyotome (DM))

first: Yoshihiro

last: Yamanaka

first: Maya

last: Uemura

first: Satoko

last: Sakurai

first: Takuya

last: Yamamoto


title: Recapitulating the Human Segmentation Clock with Pluripotent Stem Cells - RNAseq analysis of step-wise in vitro induction/differentiation of human presomitic mesoderm and its derivatives

overall_design: Induced pluripotent stem cells (iPSCs) of healthy controls (201B7 and 1231A3) were differentiated under defined feeder-free conditions in a step-wise manner into paraxial mesoderm and its major derivatives. Initially, iPSCs were induced into human primitive streak (PS), and subsequently into presomitic mesoderm (PSM) and somitic mesoderm (SM), followed by the induction of the two major derivatives of somitic mesoderm, sclerotome (SCL), which gives rise to bone and cartilage of the axial skeleton and dermomyotome (DM), which gives rise to skeletal muscle and dermis of the emerging embryo. Transcriptomes of three independent samples of each developmental stage derived from two different human healthy control iPSC lines were analyzed using RNAseq.


title: Single-cell RNA sequencing of human fallopian tubes from benign donors

city: Oxford

first: Zhiyuan

last: Hu

address: John Radcliffe Hospital/Headley Way

department: MRC Weatherall Institute of Molecular Medicine

institute: University of Oxford

summary: The inter-differentiation between cell states promotes cancer cell survival under stress and fosters non-genetic heterogeneity (NGH). NGH is, therefore, a surrogate of tumor resilience but its quantification is confounded by genetic heterogeneity. Here we show that NGH can be accurately measured when informed by the molecular signatures of the normal cells of origin. We surveyed the transcriptomes of ~ 4000 normal fallopian tube epithelial (FTE) cells, the cells of origin of serous ovarian cancer (SOC), and identified six FTE subtypes. We used subtype signatures to deconvolute SOC expression data and found substantial intra-tumor NGH that was previously unrecognized. Importantly, NGH-based stratification of ~1700 tumors robustly predicted survival. Our findings lay the foundation for accurate prognostic and therapeutic stratification of SOC.

overall_design: Sequenced cells, mainly epithelial cells, from normal fallopian tubes of five benign patients to study the cell populations in the human fallopian tube epithelium

first: Christopher

last: Yau

first: Ahmed

last: Ahmed


title: Transcript profile of Trichoderma-induced response in Zea mays against Fusarium verticillioides infection

city: Barcelona

first: Gabriel

middle: Eduardo

last: Rech

address: Passeig Marítim de la Barceloneta 37-49

country: Spain

institute: Consejo Superior de Investigaciones Cientificas - Institute of Evolutionary Biology (CSIC-UPF)

summary: In the present study we have assessed, by transcriptional profiling, the systemic defense response of Zea mays plants to the ear rotting pathogen Fusarium verticilioides induced by the beneficial fungus Trichoderma atroviride

overall_design: Four treatments with 3 samples (biological replicates): Maize silk samples were inoculated with one, two or none fungal species: Trichoderma (T) and/or Fusarium (F). Minus (m) means no inoculation and and Plus (p) means inoculation. Thus, we have four different treatments TmFm that correspond to silk samples without any inoculation, TmFp means without Trichoderma inoculation but with Fusarium infection, TpFm Trichoderma inoculation and absence of Fusarium, TpFp both fungi present in the sample .

first: Valeria

last: Campos-Bermudez

first: Sebastian

last: Rius

first: Romina

middle: B

last: Agostini

first: Agustina

last: Postigo

first: Walter

last: Vargas


title: An integrative view of the regulatory and transcriptional landscapes in mouse hematopoiesis [ATAC-seq]

status: Public on Jan 09 2020

city: University Park

first: Ross

last: Hardison

state: PA

address: 303 Wartik Lab

institute: Pennsylvania State University

summary: Thousands of epigenomic datasets have been generated in the past decade, but it is difficult for  researchers to effectively utilize all the data relevant to their projects. Systematic integrative  analysis can help meet this need, and the VISION project was established for ValIdated  Systematic IntegratiON of epigenomic data in hematopoiesis. Here, we systematically  integrated extensive data recording epigenetic features and transcriptomes from many sources,  including individual laboratories and consortia, to produce a comprehensive view of the  regulatory landscape of differentiating hematopoietic cell types in mouse. By employing IDEAS  as our Integrative and Discriminative Epigenome Annotation System, we identified and  assigned epigenetic states simultaneously along chromosomes and across cell types, precisely  and comprehensively. Combining nuclease accessibility and epigenetic states produced a set of  over 200,000 candidate cis-regulatory elements (cCREs) that efficiently capture enhancers and  promoters. The transitions in epigenetic states of these cCREs across cell types provided  insights into mechanisms of regulation, including decreases in numbers of active cCREs during  differentiation of most lineages, transitions from poised to active or inactive states, and shifts in  nuclease accessibility of CTCF-bound elements. Regression modeling of epigenetic states at  cCREs and gene expression produced a versatile resource to improve selection of cCREs  potentially regulating target genes. These resources are available from our VISION website  (usevision.org) to aid research in genomics and hematopoiesis.

overall_design: Twelve samples, each in replicate

first: Guanjue

last: Xiang

first: Cheryl

middle: A

last: Keller

first: Elisabeth

last: Heuston

first: Belinda

last: Giardine

first: Lin

last: An

first: Alexander

last: Wixom

first: Amber

last: Miller

first: April

last: Cockburn

first: Michael

last: Sauria

first: Kathryn

last: Weaver

first: Jens

last: Lichtenberg

first: Berthold

last: Göttgens

first: Qunhua

last: Li

first: David

last: Bodine

first: Shaun

last: Mahony

first: James

last: Taylor

first: Gerd

last: Blobel

first: Mitchell

middle: J

last: Weiss

first: Yong

last: Cheng

first: Feng

last: Yue

first: Jim

last: Hughes

first: Douglas

last: Higgs

first: Yu

last: Zhang


title: Two separate roles for the transcription coactivator SAGA and a set of genes redundantly regulated by TFIID and SAGA [RNA-Seq]

city: Oklahoma City

first: Rafal

last: Donczew

state: OK

address: 825 NE 13th St

department: Cell Cycle and Cancer Biology

institute: Oklahoma Medical Research Foundation

summary: Deletions within genes coding for subunits of the transcription coactivator SAGA caused strong genome-wide defects in transcription and SAGA-mediated chromatin modifications. In contrast, rapid SAGA depletion produced only modest transcription defects at 13% of protein-coding genes – genes that are generally more sensitive to rapid TFIID depletion. However, transcription of these “coactivator-redundant” genes is strongly affected by rapid depletion of both factors, showing the overlapping functions of TFIID and SAGA at this gene set. We suggest that this overlapping function is linked to TBP-DNA recruitment. The remaining 87% of expressed genes that we term “TFIID-dependent” are highly sensitive to rapid TFIID depletion and insensitive to rapid SAGA depletion. Genome-wide mapping of SAGA and TFIID found binding of both factors at many genes independent of gene class. DNA analysis suggests that the distinction between the gene classes is due to multiple components rather than any single regulatory factor or promoter sequence motif.

overall_design: Newly synthesized RNAs were labeled with 4-thioU, purified and analyzed with RNA-seq. Depletion of TFIID and/or SAGA subunits was achieved either thorugh targeted degradation (auxin-degron system) or SAGA subunits deletion. Corresponding control and treatment sample files are labeled DMSO and 3IAA, respectively. For SAGA subunit deletion strain BY4705 was used to construct spt20 and spt7 deletion strains and strain SHY565 was used to construct spt3 deletion strain. All experiments were done in two (A,B) or three replicates (A,B,C).

first: Linda

last: Warfield

first: Derek

last: Pacheco

first: Ariel

last: Erijman

first: Steven

last: Hahn


title: An integrative view of the regulatory and transcriptional landscapes in mouse hematopoiesis [histones]

first: Ross

last: Hardison

overall_design: Four samples each in replicate, with an input controls

first: Guanjue

last: Xiang

first: Cheryl

last: Keller

first: Elisabeth

last: Heuston

first: Belinda

last: Giardine

first: Lin

last: An

first: Alexander

last: Wixom

first: Amber

last: Miller

first: April

last: Cockburn

first: Michael

last: Sauria

first: Kathryn

last: Weaver

first: Jens

last: Lichtenberg

first: Berthold

last: Göttgens


title: Mouse transcriptome reveals potential signatures of protection and pathogenesis in human tuberculosis [lung array]

city: London

first: Anne

last: OGarra

address: 1 Midland Road

institute: Francis Crick Insititue

summary: Characterisation of blood and lung global transcriptional responses to Mycobacterium tuberculosis infection in distinct mouse models of Tuberculosis

overall_design: Microarray analysis of whole blood and lung samples obtained from BALB mice infected with low dose of Mycobacterium tuberculosis H37Rv, collected at different time points Day 14, 21 56, 129 after infection and uninfected control mice.

first: Lucia

last: Moreira-Teixeira

last: O'Garra


title: The taste receptor TAS1R3 regulates small intestinal tuft cell homeostasis

city: Boston

first: Adam

last: Haber

state: Massachusetts

address: 665 Huntington Ave, HSPH Building 1, Room 305

institute: Harvard T. H. Chan School of Public Health

summary: Tuft cells are an epithelial cell subset critical for initiating type 2 immune responses to parasites and protozoa in the small intestine. To respond to these stimuli, intestinal tuft cells use taste chemosensory signaling pathways, but the role of taste receptors in type 2 immunity is poorly understood. Here, we show that the taste receptor TAS1R3, which detects sweet and umami in the tongue, also regulates tuft cell responses in the distal small intestine. BALB/c mice, which have an inactive form of TAS1R3, as well as Tas1r3-deficient C57BL6/J mice both have severely impaired responses to tuft cell-inducing signals in the ileum including the protozoa Tritrichomonas muris and succinate. In contrast, TAS1R3 is not required to mount an immune response to the helminth Heligmosomoides polygyrus, which infects the proximal small intestine. Examination of uninfected Tas1r3-/- mice revealed a modest reduction in the number of tuft cells in the proximal small intestine but a severe decrease in the distal small intestine at homeostasis. Together, these results suggest that TAS1R3 influences intestinal immunity by shaping the epithelial cell landscape at steady state.

overall_design: 6 replicates of Ileal tuft cells from C57BL/6J mice

last: Howitt

first: Y

middle: G

last: Cao

first: Matthew

last: Gologorsky

first: Jessica

last: Li

middle: L

first: Moshe

last: Biton

last: Lang

first: Monia

last: Michaud

first: Aviv

last: Regev

first: Wendy

last: Garrett


title: Mouse transcriptome reveals novel signatures of protection and pathogenesis in human tuberculosis [blood]

overall_design: RNA-seq analysis of blood and whole lung samples obtained from C57Bl/6 and C3HeB/FeJ mice infected with low and high doses of Mycobacterium tuberculosis H37Rv or HN878 strains, and uninfected control mice.


title: Mouse transcriptome reveals signatures of protection and pathogenesis in human tuberculosis

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

overall_design: Refer to individual Series


title: Transcriptional profilling of pathogen-specific T helper cells

first: Chandrashekhar

last: Pasare

summary:
Introduction: We reported a in vitro pathogen-specific priming system to using pathogen lysate stimulated splenic CD11c+ DCs to differentiate pathogen-specific murine T helper cells. This method allowed us to compare side-by-side transcriptional profiles of bulk T helper cells  that are specific to distinct pathogens and to study their composition and functionality.
Method: We stimulated mouse splenic CD11c+ DCs with 10ug/ml Lm or Cr lysate for 5hours. The DCs were subsequently washed and co-cultured at 1:5 ratio to purified, CFSE-labeled CD62L+CD44- mouse naïve CD4 T cells. At day-7, CD90+CFSE- (Pathogen-specific Th cells) or CD90+CFSE+ (naive T cells) were sorted from the same culture and were subjected to RNA isolation, library prep and subsequent sequencing.
Conclusion: We found that Lm- and Cr-specific Th cells have distinct transcriptomes and contained distinct Th subtypes. Lm-specific Th cells contained higher expressions of Th1-associated cytokines, while  Cr-specific Th cells contained higher levels of Th17 associate cytokines and transcription factors. In addition, we have identified heterogeneity within the pathogen-specific Th cells, as they express various cytokines from multiple Th lineages. Lastly, we found a vast variety of genes differentially expressed between Lm- and Cr-specific Th cells, indicating that different pathogen-stimulated DCs denote distinct function and developmental cues to T cells during differentiation.

overall_design: mRNA profiles of Lm- or Cr-specific Th cells were generated by Illumina sequencing in duplicate. CFSE+CD90+ naïve T cell from Lm and Cr condition cultures served as control.

first: Yajing

last: Gao


title: ATAC-seq profiling of influenza-specific memory CD8 T cells in the lung airways (BAL), lung interstitium (LR), lung vasculature (LV), and spleen

city: Atlanta

first: Chris

last: Scharer

address: 1510 Clifton Rd, Suite 3086A

department: Microbiology and Immunology

institute: Emory University

summary: To examine differences in chromatin accessibility of resident memory CD8 T cells in the lung, influenza nucleoprotein-specific CD8 T cells from the airways , lung interstitium, and spleen were FACS sorted and ATAC-seq performed.

overall_design: C57Bl/6 mice were infected with influenza x31 and rested for 35 days to establish T cell memory. Five minutes prior to euthanasia mice were injected with anti-CD45.2-PE to discriminate between tissue resident and circulating cells, and cells were isolated from the airways by bronchoalveolar lavage, from the lung parechyma by enzymatic digestion, and from the spleen by mechanical disruption. Cells were sorted on CD8+ CD44Hi FluNP 366-374 Db tetramer+ populations, and cells from the airways and parenchyma were further sorted on intravital label negative (i.e. tissue resident) cells.  This cohort was used as a replicate cohort.

first: C

middle: D

first: J

middle: E

last: Kohlmeier


title: The Human ZC3H3 and RBM26/27 Proteins Are Critical for PAXT-mediated Nuclear RNA Decay

city: Aarhus C

first: Manfred

last: Schmid

address: CF Møllers Alle bldg 1130

department: Molecular Biology and Genetics

country: Denmark

institute: Aarhus University

summary: Recruitment of the human ribonucleolytic RNA exosome to nuclear polyadenylated (pA+) RNA is facilitated by the Poly(A) Tail eXosome Targeting (PAXT) connection. Besides its core dimer, formed by the exosome co-factor MTR4 and the ZFC3H1 protein, the PAXT connection remains poorly defined. By characterizing nuclear pA+-RNA bound proteomes as well as MTR4-ZFC3H1 containing complexes in conditions favoring PAXT assembly, we here uncover three additional proteins required for PAXT function: ZC3H3, RBM26 and RBM27 along with the known PAXT-associated protein, PABPN1. The zinc-finger protein ZC3H3 interacts directly with MTR4-ZFC3H1 and loss of any of the newly identified PAXT components results in the accumulation of PAXT substrates. Collectively, our results establish new factors involved in the turnover of nuclear pA+ RNA and suggest that these are limiting for PAXT activity.

overall_design: RNA from HeLa cells was analysed by next generation sequencing upon depletion of EGFP(control), ZC3H3 and co-depletion of RBM26+RBM27. Total RNA was collected for each condition in triplicates. Triplicate ZC3H3 depletion was carried out together with triplicate EGFP depletion (batchZC3H3) and RBM26+RBM27 depletions were performed in 2 separate batches (batch RBM with 2 samples; and batch RBM2 with 1 sample)  where each batch contained the same number of EGFP controls.

first: Toomas

last: Silla

first: Yuhui

last: Dou

first: Miha

last: Milek

first: Koshi

last: Imami

first: Dennis

last: Johnsen

first: Patrik

last: Polak

first: Jens

middle: S

last: Andersen

first: Mathias

last: Selbach

first: Markus

last: Landthaler

first: Torben

middle: H

last: Jensen

first: William

last: Garland


title: Skeletal Muscle Transcriptional Networks Linked to Motor Unit Remodeling in Human Parkinson’s Disease

city: New York

first: Yongchao

last: Ge

address: One Gustave L Levy Place #1137

department: Neurology

institute: Icahn School of Medicine at Mount Sinai

summary: We performed transcriptional profiling to test the hypothesis that type I grouping severity in Parksino's disease link to distinct gene expression networks

overall_design: Bulk mRNAseq was performed on 12 people with Parksin Disease, and 12 age and sex-matched old adults and 12 sex-matched young adults

first: Kaleen

last: Lavin

first: Stuart

last: Sealfon

first: Merry-Lynn

middle: N

last: McDonald

first: Brandon

last: Roberts

first: Katarzyna

last: Wilk

first: Venugopalan

last: Nair

first: Preeti

last: Kumar

first: Samuel

middle: T

last: Wndham

first: Marcas

last: Bamman


title: Epigenomics of vitamin K response to supplementation

first: Sarah

last: Booth

address: 711 Washington St.

institute: JM-USDA Human Nutrition Research Center on Aging at Tufts University

type: Methylation profiling by genome tiling array

summary: DNA methylation data were assayed using the Illumina MethylationEPIC microarray platform in blood samples from 48 individuals taking part in a vitamin K supplementation trial.

overall_design: case-control


title: Notch ligand Dll4 impairs the recruitment of hemogenic cells into intra-aortic clusters and limits hematopoietic stem cell production.

first: Anna

last: Bigas

state: Barcelona

address: Dr. Aiguader 88

department: Cancer Research

institute: Institut Hospital del Mar d'Investigacions Mèdiques

summary: Hematopoietic stem cells (HSCs) develop from the hemogenic endothelium in the embryonic aorta. In most vertebrates, hemogenic cells protrude into the aortic lumen forming clusters where the hematopoietic features are acquired. Although much is known about the molecular characteristics of the hematopoietic cells, we still lack basic understanding on the origin and 3D-organization of intraortic hematopoietic clusters (IAHC) in the mouse embryo and how they evolve over time. Here we use advanced live imaging techniques of organotypic slice cultures, clonal analysis, and mathematical modelling to show that IAHC formation is a two-step process. First, a hemogenic progenitor buds up from the endothelium and undergoes division forming the monoclonal core of the cluster. Next, cells from the surrounding hemogenic endothelium are recruited into the IAHCs, increasing their size and heterogeneity. We found that the recruitment phase of IAHC formation is negatively regulated by Notch signalling via the Delta-like-4 (Dll4) Notch ligand. We show that blocking of Dll4 promotes the entrance of new hemogenic Gfi1+ cells into the IAHC and increases the number of cells that acquire HSC activity.  Mathematical modelling based on our data provides estimation of the cluster lifetime and the average recruitment time of hemogenic cells to the cluster under physiologic and Dll4-inhibited conditions. Single cell transcriptomic analysis indicates that cell identities are preserved after Dll4 blockage. Our data provides for the first time a detailed characterization of the aortic hematopoietic stem cell niche and its maturation dynamics, identifying the Notch ligand Dll4 as a major molecular player governing dynamics of cluster formation and HSCs production.

overall_design: Detection of differentially expressed genes in three cell populations, treated or not with DII4 antibody

first: Cristina

last: Porcheri

last: Ruiz-Herguido

first: Yolanda

last: Guillén


title: Two separate roles for the transcription coactivator SAGA and a set of genes redundantly regulated by TFIID and SAGA [ChIP-Seq]

first: Rafal

last: Donczew

overall_design: Standard ChIP-seq approach including crosslinking, chromatin extraction, DNA fragmentation and immunoprecipitation. All experiments were done in two biological replicates (A and B).

first: Linda

last: Warfield

first: Derek

last: Pacheco

first: Ariel

last: Erijman

first: Steven

last: Hahn


title: An integrative view of the regulatory and transcriptional landscapes in mouse hematopoiesis [RNA-seq]

first: Ross

last: Hardison

overall_design: Two samples, each in replicate

first: Guanjue

last: Xiang

first: Cheryl

last: Keller

first: Elisabeth

last: Heuston

first: Belinda

last: Giardine

first: Lin

last: An

first: Alexander

middle: Q

last: Wixom

first: Amber

last: Miller

first: April

last: Cockburn

first: Michael

last: Sauria

first: Kathryn

last: Weaver

first: Jens

last: Lichtenberg

first: Berthold

last: Göttgens

first: Qunhua

last: Li

first: David

last: Bodine

first: Shaun

last: Mahony

first: James

last: Taylor

first: Gerd

last: Blobel

first: Mitchell

last: Weiss

first: Yong

last: Cheng

first: Feng

last: Yue

first: Jim

last: Hughes

first: Douglas

middle: R

last: Higgs

first: Yu

last: Zhang


title: Mouse transcriptome reveals potential signatures of protection and pathogenesis in human tuberculosis [blood array]

first: Anne

last: OGarra

overall_design: Microarray analysis of whole blood and lung samples obtained from BALB mice infected with low dose of Mycobacterium tuberculosis H37Rv, collected at different time points Day 14, 21 56, 138 after infection and uninfected control mice.

first: Lucia

last: Moreira-Teixeira

last: O'Garra


title: Mouse transcriptome reveals novel signatures of protection and pathogenesis in human tuberculosis [lung]