title: The Transcription Factor ATF7 Controls Adipocyte Differentiation and Thermogenic Gene Programming.

status: Public on Nov 09 2018

first: Yang

last: LIU

summary: The adipocytes functions as a central organ in the regulation of metabolic homeostasis. Factors which contribute to the adipocyte differentiation and function would be the promising targets to combat the obesity and associated metabolic disorders. The activating transcription factor 7 (ATF7), a stress-responsive chromatin regulator, has recently been shown to be involved in the energy metabolism; however, the underlying mechanisms are still unknown. Here, we show that ATF7 is required for adipocyte differentiation and it interacts with histone dimethyltransferase G9a in adipocyte to repress the interferon-stimulated genes (ISGs) expression, which suppresses adipogenesis. Ablation of ATF7 promotes the beige biogenesis and browning of inguinal white adipose tissue (iWAT). ATF7 binds to the transcription regulatory regions of Ucp1 gene, and silences it by maintaining the histone H3K9 dimethylation level. These results establish the multifunction of ATF7 in adipocyte and provide molecular insights into the epigenetic control of development and function of adipose tissues.

overall_design: Beige adipocytes derived from WT and ATF7 KO inguinal WAT preadipocytes with rosiglitazone treatment, in duplicate; white adipocytes derived from WT and ATF7 KO inguinal WAT preadipocytes without rosiglitazone treatment, in duplicate; beige adipocytes derived from control and ATF7 overexpressing C3H10t1/2 with rosiglitazone treatment, in duplicate, using NextSeq500 Illumina.

first: Toshio

last: Maekawa

first: Keisuke

last: Yoshida

first: Masafumi

last: Muratani

first: Bruno

last: Chatton

first: Shunsuke

last: Ishii


title: Single-nucleotide-resolution sequencing of human N6-methyldeoxyadenosine reveals strand-asymmetric clusters associated with SSBP1 in the mitochondrial genome

city: Shenzhen

first: Wee Siong Sho

last: Goh

state: Guangdong

address: Shenzhen Bay Laboratory, No. 5, Kelian Road, Goh Lab, A1819, Guangming District

department: Institute of Molecular Physiology

country: China

institute: Shenzhen Bay Laboratory

summary: N6-methyldeoxyadenosine (6mA) is a well-characterized DNA modification in prokaryotes but reports on its presence and function in mammals have been controversial. To address this issue, we established the capacity of 6mA-Crosslinking-Exonuclease-sequencing (6mACE-seq) to detect genome-wide 6mA at single-nucleotide-resolution, demonstrating this by accurately mapping 6mA in synthesized DNA and bacterial genomes. Using 6mACE-seq, we generated a human-genome-wide 6mA map that accurately reproduced known 6mA enrichment at active retrotransposons and revealed mitochondrial chromosome-wide 6mA clusters asymmetrically enriched on the heavy-strand. We identified a novel putative 6mA-binding protein in single stranded DNA binding protein 1 (SSBP1), a mitochondrial DNA (mtDNA) replication factor known to coat the heavy-strand, linking 6mA with the regulation of mtDNA replication. Finally, we characterized AlkB homolog 1 (ALKBH1) as a mitochondrial protein with 6mA demethylase activity and showed that its loss decreases mitochondrial oxidative phosphorylation. Our results show that 6mA clusters play a previously unappreciated role in regulating human mitochondrial function, despite 6mA being an uncommon DNA modification in the human genome.

sample_organism: Salmonella enterica subsp. enterica serovar Typhimurium

overall_design: UV crosslinking, immunoprecipitation and exonuclease treatment with anti-6mA antibodies was used to map 6mA in DNA at single-nucleotide-resolution

first: Wee Siong

middle: S


title: Widespread conservation of chromatin accessibility and transcription factor binding in human and chimpanzee induced pluripotent stem cells

city: Chicago

first: Irene

last: Gallego Romero

state: IL

address: 920 E 58th St, CLSC 317

department: Human Genetics

country: USA

institute: University of Chicago

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Changes in gene regulation have been shown to contribute to phenotypic differences between closely related species, most notably in primates. It is likely that a subset of inter-species regulatory differences can be explained by changes in chromatin accessibility and transcription factor binding, yet there is a paucity of comparative data sets with which to investigate this. Using ATAC-seq, we profiled genome-wide chromatin accessibility in a matched set of 6 human and 6 chimpanzee (Pan troglodytes, our closest living relative) induced pluripotent stem cells from which we have previously collected gene expression data. We examined chromatin accessibility patterns near 20,745 orthologous transcriptions start sites and used a footprinting algorithm to predict transcription factor binding activity in each species. We found that the majority of chromatin accessibility patterns and transcription factor activity are conserved between these two closely related species. Interestingly, interspecies divergence in chromatin accessibility and transcription factor binding in pluripotent cells appear to contribute not to differences in the pluripotent state, but to downstream developmental processes. Put together, our findings suggest that the pluripotent state is extremely stable and potentially subject to stronger evolutionary constraint than other somatic tissues.

sample_organism:
Pan troglodytes
Homo sapiens

platform_organism:
Pan troglodytes
Homo sapiens

overall_design: ATAC-seq of 6 chimpanzee iPSC lines (biological reps) and 6 human iPSC lines (biological reps)

first: Shyam

last: Gopalakhrisnan

first: Yoav

last: Gilad


title: Cleavage mapping in rps3

city: St Louis

first: Hani

last: Zaher

state: MO

address: 1 Brookings Drive

department: Biology

institute: Washington University in St Louis

summary: Mapping 3'ends of mRNAs from a reporter subject to no-go decay in an rps3 mutant background.

overall_design: Libraries were constructed from RNA collected from various S. cerevisiae strains expressing a PGK-stall sequence reporter gene (either a stem loop, (CGA)12 or (AAA)12.

first: Carrie

middle: L

last: Simms


title: Transcriptome-wide identification of transient RNA G-quadruplexes in human cells

city: Vancouver

first: Sunny

middle: Y

last: Yang

state: British Columbia

address: 2405 Wesbrook Mall

department: Faculty of Pharmaceutical Sciences

country: Canada

institute: University of British Columbia

type: Expression profiling by high throughput sequencing

summary: We report here on G4RP-seq, which comprises of a cross-linking step, followed by chemical-affinity capture with the G4-specific small-molecule, BioTASQ and target identification using sequencing. This allows for capturing global snapshots of relative average levels of transiently folded G4-RNAs. We observed widespread G4-RNA targets indicative of transient G4 formation in several RNA entities in living human cells. G4RP-seq has also demonstrated that G4-stabilizing ligands (BRACO-19 and RHPS4) can change the G4 transcriptomic landscape, most notably in long non-coding RNAs. G4RP-seq thus provides a proof-of-principle for studying the G4-RNA landscape, as well as new ways of considering the mechanisms underlying G4-RNA formation and the activity of G4-stabilizing ligands.

overall_design: Two BioTASQ-enriched samples and one input control for three different conditions (Untreated, BRACO-19-treated, and RHPS4-treated) in MCF7 cells

first: Pauline

last: Lejault

first: Sandy

last: Chevrier

first: Romain

last: Boidot

first: Gordon

last: Robertson

first: Judy

middle: M

last: Wong

first: David

last: Monchaud


title: Joint single-cell chromatin and protein profiling reveals environmental regulation of epigenomic heterogeneity [K562_GATA2]

city: Stanford

first: Howard

last: Chang

state: CA

address: 269 Campus Drive

department: Dermatology

institute: Stanford University

summary: A novel scATAC-seq approach, Multi-Index single cell ATAC-seq (MI-ATAC), in which we not only index the accessible chromatin of individual cells, but also index their protein expression using index Fluorescence Activated Cell Sorting (FACS).

overall_design: K562 cells were fixed, nuclei isolated and then permeabilized. Nuclei were then stained for GATA2 and transposed, then sorted into single wells of a 96 well plate for MI-ATAC

first: Xingqi

last: Chen

first: Ulrike

last: Litzenburger

first: Yuning

last: Wei

first: Alicia

middle: N

last: Schep

first: Edward

last: LaGory

first: Amato

middle: J

last: Giaccia

first: William

last: Greenleaf


title: Joint single-cell chromatin and protein profiling reveals environmental regulation of epigenomic heterogeneity [GM_MI-ATAC_unstained]

overall_design: GM12878 cells were fixed, permeabilized and transposed, then sorted into single wells of a 96 well plate for MI-ATAC


title: Joint single-cell chromatin and protein profiling reveals environmental regulation of epigenomic heterogeneity [GM_single_cell_unstimulated]

overall_design: GM12878 cells were fixed, permeabilized and stained against CD19 and pNFkB, then sorted into single wells of a 96 well plate for MI-ATAC


title: Joint single-cell chromatin and protein profiling reveals environmental regulation of epigenomic heterogeneity [Tumor_stained_for_EpCam_HIF1a]

overall_design: Freshly isolated cells from a breast tumor were fixed, permeabilized and stained against EpCam and HIF1a , then sorted into single wells of a 96 well plate for MI-ATAC


title: Gene expression and ChIP profiles of Setd2 fl/fl BMSCs infected with lentivirus expressing GFP and Cre

status: Public on Nov 08 2018

city: ShangHai

first: Lijun

last: Wang

state: China

address: 320 Yueyang Road

department: Institute of Biochemistry and Cell Biology

institute: Chinese Academy of Sciences

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

overall_design: Refer to individual Series


summary: During the aging process, bone marrow mesenchymal stem cells (BMSCs) exhibit declined osteogenesis accompanied by excess adipogenesis, which will lead to osteoporosis. Here we report that the H3K36 trimethylation, catalyzed by histone methyltransferase SETD2 regulates lineage commitment of BMSCs. Deletion of Setd2 in mBMSCs, through conditional Cre expression driven by Prx1 promoter, resulted in bone loss and marrow adiposity. Loss of Setd2 in BMSCs in vitro facilitated differentiation propensity to adipocytes rather than to osteoblasts. Through conjoint analysis of RNA-seq and ChIP-seq data, we identified a SETD2 functional target gene, Lbp, on which H3K36me3 was enriched, and its expression was affected by Setd2 deficiency. Furthermore, overexpression of LBP could partially rescue the lack of osteogenesis and enhanced adipogenesis resulted from the absence of Setd2 in BMSCs. Further mechanism study demonstrated that the trimethylation level of H3K36 could regulate Lbp transcriptional initiation and elongation. These findings suggest that H3K36 trimethylation mediated by SETD2 could regulate the cell fate of mesenchymal stem cells in vitro and in vivo, indicating that the regulation of H3K36me3 level by targeting SETD2 and/or the administration of downstream LBP protein may represent potential therapeutic way for new treatment in metabolic bone diseases, such as osteoporosis.

overall_design: H3K36me3 ChIP profiles of Setd2 fl/fl BMSCs infected with lentivirus expressing GFP and Cre, two repeats

first: Weiguo

last: Zou


overall_design: Gene expression profiles of Setd2 fl/fl BMSCs infected with lentivirus expressing GFP and Cre respectively,two repeats.


title: PS19 and PS19/C3aR KO RNAseq data

city: Houston

first: Hui

last: Zheng

state: Texas

address: One Baylor Plaza

department: Huffington Ceter on Aging

institute: Baylor College of Medicine

summary: Hippocampal tissue from 9 month old WT, C3aR KO, PS19 and PS19/C3aR KO mice was processed

first: Alexandra

last: Litvinchuk


title: MYC protein interactome profiling reveals functionally distinct regions that cooperate to drive tumorigenesis (ChIP-Seq)

city: Toronto

first: Diana

last: Resetca

state: ON

department: Medical Biophysics

institute: University of Toronto

summary: MYC is a potent oncogene associated with aggressive disease in many distinct tumor types. Transforming members of the MYC family (MYC, MYCL1, MYCN) encode transcription factors containing six highly conserved regions, termed MYC homology Boxes (MBs). Here, we conduct proteomic profiling of the MB interactomes, demonstrating that half of MYC interactors require one or more MBs for binding. Comprehensive phenotypic analyses revealed that two MBs are universally required for transformation. MBII interaction with acetyltransferase-containing complexes results in histone hyperacetylation and is essential for MYC-dependent tumor initiation. By contrast, MB0 interacts with transcription elongation factors through direct binding to the general transcription factor TFIIF, and deletion of MB0 severely inhibits tumor growth but is dispensable for tumor initiation. Notably, the full transforming activity of MYC can be restored upon co-expression of MB0 and MBII deletion mutants, indicating that these two regions confer unique biological functions, each required for oncogenic MYC activity.

overall_design: RNA-seq analysis was conducted in TET21 cells (n=4, for each of the MYC deletion mutant ectopycally expressed) to determine the nature of the MB transcriptomes, and ChIPseq was conducted on WT-MYC TET21-expressing cells to determine MYC binding (n=1).

first: Manpreet

last: Kalkat

first: Corey

last: Lourenco

first: Pak-Kei

last: Chan

first: Yong

first: Yu-Jia

last: Shiah

first: Natasha

last: Vitkin

first: Yufeng

last: Tong

first: Maria

last: Sunnerhagen

first: Susan

last: Done

first: Paul

middle: C

last: Boutros

first: Brian

last: Raught

first: Linda

middle: Z

last: Penn


title: SPI1/PU.1 controls fibroblast polarization and tissue fibrosis

city: Erlangen

first: Steffen

last: Uebe

address: Kussmaulallee 4

department: Humangenetisches Institut

country: Germany

institute: Uniklinikum Erlangen

summary:
Fibroblasts are polymorphic cells with pleiotropic roles in organ morphogenesis, tissue homeostasis and immune responses. In fibrotic diseases, fibroblasts synthesize abundant amounts of extracellular matrix which lead to scaring and organ failure. In sharp contrast, the hallmark feature of fibroblasts in arthritis is matrix degradation by the release of metalloproteinases and degrading enzymes, and subsequent tissue destruction. The mechanisms driving these functionally opposing pro-fibrotic and pro-inflammatory phenotypes of fibroblasts are enigmatic.
We have compared resting, fibrotic, and inflammatory fibroblasts; PU.1 was overexpressed in dermal fibroblasts and compared to scr-transfected controls. Fibrotic fibroblasts isolated from the skin of patients with systemic sclerosis were treated with PU.1 inhibitor and compared to untreated fibrotic fibroblasts and respective healthy controls.
Through this, we identified the transcription factor PU.1 as an essential orchestrator of the pro-fibrotic gene expression program. The interplay between transcriptional and post-transcriptional mechanisms which normally control PU.1 expression is perturbed in fibrotic diseases such as pulmonary fibrosis, systemic sclerosis, liver cirrhosis, kidney fibrosis and chronic graft-versus-host disease, resulting in upregulation of PU.1, the induction of fibrosis-associated gene sets, and a phenotypic switch in matrix-producing pro-fibrotic fibroblasts.
In contrast, inactivation of PU.1 disrupts the fibrotic network and enables re-programming of fibrotic fibroblasts into resting fibroblasts with regression of fibrosis in different organs. Targeting of PU.1 may thus represent a novel therapeutic approach for the treatment of a wide range of fibrotic diseases.

overall_design: The 21 analyzed samples belong to 6 different groups with 3 to 4 biological replicates per group. Two of the groups consisted of control samples.

first: Andreas

last: Ramming

first: Thomas

last: Wohlfahrt

first: Arif

middle: B

last: Ekici


title: Genome-Wide Localization of a Cell Penetrating Peptide, SVS-1

status: Public on Nov 07 2018

city: Frederick

first: Zhi-Ming

last: Zheng

state: Maryland

department: Center for Cancer Research

institute: National Cancer Institute

summary: Chem-seq analysis was conducted to reveal genome-wide localization of a cell penetrating peptide, SVS-1. A549 cells treated with 15 mM of biotin-PEG-GG-SVS-1 for 1 hour were passaged once to remove dead cell debris. After 24 hours incubation from the passage, the treated cells were fixed with formaldehyde to crosslink SVS-1 and chromatin, and total chromatin was subjected to fragmentation by sonication. Chromatin bound by the biotin-PEG-GG-SVS-1 was isolated with avidin-conjugated resin, followed by DNA purification. The input DNAs were also purified and employed as controls for the peak callings. The purified DNAs were subjected to library preparation for deep sequencing by the illumina platform. Sequencing was run by the NextSeq with paired end sequencing (2x76), 100 million clusters /sample.

overall_design: Two biological replicates (for a total of 2 IP and 2 input controls) using chemical affinity capture followed by deep sequencing (Chem-seq)

first: Ken

last: Ishikawa

first: Alexei

middle: V

last: Lobanov

first: Maggie

last: Cam

first: Joel

middle: P

last: Schneider


title: Molecular and functional heterogeneity of IL-10-producing CD4+ T cells [Human 10x]

city: Hamburg

first: Babett

last: Steglich

address: Martinistrasse 52

institute: Universitätsklinikum Hamburg-Eppendorf

summary: IL-10 is a prototypical anti-inflammatory cytokine, which is fundamental to the maintenance of immune homeostasis, especially in the intestine. There is an assumption that cells producing IL-10 have an immunoregulatory function. However, here we report that IL-10-producing CD4+ T cells are phenotypically and functionally heterogeneous. By combining single cell transcriptome and functional analyses, we identified a subpopulation of IL-10-producing Foxp3Neg CD4+ T cells that displays regulatory activity unlike other IL-10-producing CD4+ T cells, which are unexpectedly pro-inflammatory. The combinatorial expression of co-inhibitory receptors is sufficient to discriminate IL-10-producing CD4+ T cells with regulatory function from others and to identify them across different tissues and disease models in mice and humans. These regulatory IL-10-producing Foxp3Neg CD4+ T cells have a unique transcriptional program, which goes beyond the regulation of IL-10 expression. Finally, we found that patients with Inflammatory Bowel Disease (IBD), demonstrate a deficiency in this specific regulatory T-cell subpopulation.

overall_design: We performed scRNA-seq analysis of IL-10-producing CD4+ T cells isolated from the blood (PBMCs) of two healthy donors

first: Leonie

last: Brockmann

first: Shiwa

last: Soukou

first: Paulo

last: Czarnewski

first: Ergen

last: Can

first: Eduardo

last: Villablanca

first: Nicola

last: Gagliani

first: Samuel

last: Huber


title: An AKBA derivative (CKBA) regulates mRNA expression of naive mouse CD4+ T cells in vitro under TH17-polarizing conditions

city: Shanghai

first: Jing

last: Bai

state: Shanghai

address: 280# South Chongqing Road

department: School of Medicine

institute: Shanghai Jiao Tong University

summary: The goal of this study was to determine the effects of CKBA on mRNA expression of naive mouse CD4+ T cells under TH17-polarizing conditions in vitro.

overall_design: mRNA of CKBA treated and DMSO treated naive mouse CD4+ T cells under TH17-polarizing conditions were sequenced using Illumina Hiseq.

first: Honglin

last: Wang


title: Joint single-cell chromatin and protein profiling reveals environmental regulation of epigenomic heterogeneity [Tumor_stained_for_EpCam_CD45]

first: Howard

last: Chang

overall_design: Freshly isolated cells from a breast tumor were fixed, permeabilized and stained against EpCam and CD45,  then sorted into single wells of a 96 well plate for MI-ATAC

first: Xingqi

last: Chen

first: Ulrike

last: Litzenburger

first: Yuning

last: Wei

first: Alicia

last: Schep

first: Edward

last: LaGory

first: Amato

last: Giaccia

first: William

last: Greenleaf


title: Joint single-cell chromatin and protein profiling reveals environmental regulation of epigenomic heterogeneity

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: chrRNA-seq in wild-type, SmcHD1 MommeD1mut and somKO MEFs

city: Oxford

first: Michal

middle: R.

last: Gdula

address: South Parks Road

country: United Kingdom

institute: Oxford University

summary: In this study we investigate the role of the non-canonical SMC family protein, SmcHD1in the X inactivation.

overall_design: Set of allele-specific chromatin RNA-seq experiments on female clonal inter-specific (M.m.domesticus FVB x M.m.Castaneus) MEF cell lines: wild-type MEFs, SmcHD1 MomeD1 mut MEFs (SmcHD1 null) and  SmcHD1 CRISPR KO MEFs (derived from wild-type MEFs after establishemnt of X inactivation).

middle: R

first: Tatyana

last: Nesterova

first: Greta

last: Pintacuda

first: Jonathan

last: Godwin

first: Michael

last: McClellan

first: Skirmantas

last: Kriaucionis

first: Felix

last: Krueger

first: Wolf

last: Reik

first: Ye

last: Zhan

first: Hakan

last: Ozadam

first: Job

last: Dekker

first: Catherine

last: Green

first: Daniela

last: Moralli

first: Edith

last: Heard

first: Neil

last: Brockdorff


title: Joint single-cell chromatin and protein profiling reveals environmental regulation of epigenomic heterogeneity [GM12878]

first: Howard

last: Chang

overall_design: MI-ATAC-seq and bulk fixed ATAC-seq of GM12878 cells using different crosslinking reversal protocols.

first: Xingqi

last: Chen

first: Ulrike

last: Litzenburger

first: Yuning

last: Wei

first: Alicia

last: Schep

first: Edward

last: LaGory

first: Amato

last: Giaccia


title: Joint single-cell chromatin and protein profiling reveals environmental regulation of epigenomic heterogeneity [4T1-Splenocyte]

overall_design: Freshly isolated splenocytes were fixed, permeabilized and stained against CD45, then sorted into single wells of a 96 well plate for MI-ATAC

first: William

last: Greenleaf


title: Hi-C in wild-type, SmcHD1 MommeD1mut and somKO MEFs

first: Michal

last: Gdula

overall_design: Allele-specific Hi-C experiments were done in two replicates of wild-type and SmcHD1mut (SmcHD1 null) interspecific MEFs

first: Tatyana

last: Nesterova

first: Greta

last: Pintacuda

first: Jonathan

last: Godwin

first: Michael

last: McClellan

first: Skirmantas

last: Kriaucionis

first: Felix

last: Krueger


title: small RNA profiling of breast cancer cell lines [knockdowns]

city: San Francisco

first: Hani

last: Goodarzi

department: Biochemistry and Biophysics

institute: UCSF

type: Non-coding RNA profiling by high throughput sequencing

summary: We performed small RNA sequencing in breast cancer cells treated with siRNA for Control, DCGR8, DROSHA, TARBP2, DICER

overall_design: We used the NEXTflex Small RNA Sequencing Kit v3 (Biooscientific) per the manufacturer's protocol: small RNA samples were extracted using microRNA Purification Kit (Norgen) and subjected to library preparation.

first: L

last: Fish

first: S

last: Zhang

first: H


title: Analysis of gene expression in naïve T cells stimulated by cross-linking with both anti-CD3 and anti-CD155 antibodies

city: Tokyo

first: Naoko

last: Negishi

address: 2-1-1 Hongo, Bunkyo-ku

department: Atopy (Allergy) Research Center

country: Japan

institute: Juntendo University Graduate School of Medicine

summary: we have focused T-cell immunoreceptor with Ig and ITIM domains (TIGIT) as a responsible molecule for serial tolansfer if the tolerant state. When naïve T cells were co-cultured with tolerant T cells, stimulated naïve T cells showed higher and earlier TIGIT expression in comparison to that of their single culture without the tolerant T cells. We also showed that TIGIT expression in naïve T cells become high promptly/quickly by cross-linking of TCR and poliovirus receptor (PVR; CD155), a partner/ligand of TIGIT, which is accompanied by reduced IL-2 expression.

overall_design: Gene expression in activated naïve T cells that were stimulated by cross-linking with both anti-CD3 and anti-CD155 antibodies in comparison to that treated with anti-CD3 alone.

first: Sonoko

last: Habu


title: MYC protein interactome profiling reveals functionally distinct regions that cooperate to drive tumorigenesis

first: Diana

last: Resetca


title: MYC protein interactome profiling reveals functionally distinct regions that cooperate to drive tumorigenesis (RNA-Seq)

first: Manpreet

last: Kalkat

first: Corey

last: Lourenco

first: Pak-Kei

last: Chan

first: Yong

last: Wei

first: Yu-Jia

last: Shiah

first: Natasha

last: Vitkin

first: Yufeng

last: Tong

first: Maria

last: Sunnerhagen

first: Susan

last: Done

first: Paul

last: Boutros

first: Brian

last: Raught

first: Linda

last: Penn


title: The non-canonical SMC protein SmcHD1 antagonises TAD formation on the inactive X chromosome

first: Michal

last: Gdula

type: Methylation profiling by high throughput sequencing


title: Analysis of gene expression in OVA-specific tolerant T cell and  naive T cell after stimulation with OVA.

summary: In this study, in order to analyze molecular mechanism for serial anergy transfer, we compared specific gene expressed on the anergy T cells compared with naïve T cells after both are co-culture with OVA. Microarray analysis showed extremely higher expression of TIGIT in the anergy T cells than naïve T cells in the presence of OVA. Moreover, when naïve T cells and anergy T cells are co-culture with OVA, the naive T cells showed the increase of TIGIT+ T cells in comparison to activated naïve T cells. In conclusion, TIGIT+ anergy T cells induce a suppressor function to naïve T cells in a cell to cell contanct-dependent manner.

overall_design: Gene expression in naïve T cell cocultured with anergic T cell and naïve CD4 T celll was measured at 24 hours after stimulation of OVA


title: SmcHD1,H3k27me3,CTCF and RAd21 ChIP-seq

overall_design: Set of allele-specific ChIP-seq experiments on female clonal inter-specific (M.m.domesticus FVB x M.m.Castaneus) MEF cell lines: wild-type MEFs, SmcHD1 MomeD1 mut MEFs (SmcHD1 null) and  SmcHD1 CRISPR KO MEFs (derived from wild-type MEFs after establishemnt of X inactivation). Each ChIP library was accompanied with respective input library and each experiment was done in biological replicates (2-4).

first: Tatyana

last: Nesterova

first: Greta

last: Pintacuda

first: Jonathan

last: Godwin

first: Michael

last: McClellan

first: Skirmantas

last: Kriaucionis

first: Felix

last: Krueger

first: Wolf

last: Reik

first: Ye

last: Zhan

first: Hakan

last: Ozadam

first: Job

last: Dekker

first: Catherine

last: Green

first: Daniela

last: Moralli

first: Edith

last: Heard

first: Neil

last: Brockdorff


title: Molecular and functional heterogeneity of IL-10-producing CD4+ T cells [Mouse 10x]

first: Babett

last: Steglich

overall_design: We isolated T-cells from the spleen and small intestine of mice treated with anti-CD3. We sorted the IL-10+ CD4+ T-cells and loaded them onto the 10X Genomics Chromium platform for single-cell capture. cDNA libraries were constructed and subsequently sequenced on the Illumina platform.

first: Leonie

last: Brockmann

first: Shiwa

last: Soukou

first: Paulo

last: Czarnewski

first: Ergen

last: Can

first: Eduardo

last: Villablanca

first: Nicola

last: Gagliani

first: Samuel

last: Huber


title: WGBS in wild-type and MommeD1mut MEFs

first: Michal

last: Gdula

overall_design: Allele-specific whole genome bisulfite sequencing (WGBS) experiments were done in wild-type and SmcHD1mut (SmcHD1 null MommeD1 mutant cells) interspecific MEFs

first: Tatyana

last: Nesterova

first: Greta

last: Pintacuda

first: Jonathan

last: Godwin

first: Michael

last: McClellan

first: Skirmantas

last: Kriaucionis

first: Felix

last: Krueger


title: Transcriptome differences between  brown adipose tissues of wildtype and UCP1-KO mice

status: Public on Nov 06 2018

city: Freising

first: Tobias

last: Fromme

address: Gregor-Mendel-Str. 2

department: Molecular Nutritional Medicine

institute: Technical University of Munich

summary: We analyzed coding transcript abundance in murine, interscapular brown adipose tissue from wildtype and UCP1-KO mice.

overall_design: We prepared the interscapular brown fat from wildtype C57BL/6J mice and UCP1-KO mice on the same strain background. We sequenced total RNA and determined transcript abundance.

first: Yongguo

last: Li

first: Sabine

last: Schweizer

first: Martin

last: Klingenspor


title: Molecular and functional heterogeneity of IL-10-producing CD4+ T cells [Mouse Bulk-seq]

first: Babett

last: Steglich

overall_design: We carried out high troughput RNA sequencing of RNA isolated from IL-10 producing Foxp3- CD4+ T-cells, which were isolated from the spleen of mice treated with anti-CD3 antibody.

first: Leonie

last: Brockmann

first: Shiwa

last: Soukou


title: O-GlcNAc Homeostasis Controls Cell Fate Decisions During Hematopoiesis

city: Kansas City

first: Stefan

middle: Hannes

last: Graw

address: 3901 Rainbow Blvd

department: Biostatistics

institute: University of Kansas Medical Center

summary: The addition of O-GlcNAc (a single β-D-N-acetylglucosamine sugar at serine and threonine residues) by O-GlcNAc transferase (OGT) and removal by O-GlcNAcase (OGA) maintains homeostatic levels of O-GlcNAc. We investigated the role of OGlcNAc homeostasis in hematopoiesis utilizing G1E-ER4 cells carrying a GATA-1 transcription factor fused to the estrogen receptor (GATA-1ER) that undergo erythropoiesis following the addition of β-estradiol (E2) and myeloid leukemia cells that differentiate into neutrophils in the presence of all-trans retinoic acid. During G1E-ER4 differentiation, a decrease in overall O-GlcNAc levels and an increase in GATA-1  interactions with OGT and OGA were observed. Transcriptome analysis on G1E-ER4 cells differentiated in the presence of Thiamet-G (TMG), an OGA inhibitor, identified expression changes in 433 GATA-1 target genes. Chromatin immunoprecipitation demonstrated that the occupancy of GATA-1, OGT, and OGA at Laptm5 gene GATA site was decreased with TMG. Myeloid leukemia cells showed a decline in O-GlcNAc levels during differentiation and TMG reduced the expression of genes involved in differentiation. Sustained treatment with TMG in G1E-ER4 cells prior to differentiation caused a reduction of hemoglobin positive cells during differentiation. Our results show that alterations in O-GlcNAc homeostasis disrupt transcriptional programs causing differentiation errors suggesting a vital role of O-GlcNAcylation in control of cell fate.

overall_design: To determine whether the erythroid gene transcription network was altered by disruptions in O-GlcNAc homeostasis during G1E-ER4 differentiation. We performed Next Generation RNAsequence analysis on G1E-ER4 cells without treatment (Ctrl), with TMG or E2 treatment only, and E2+TMG treatment for 30 hrs.  Thiamet G (TMG) is a highly selective inhibitor of OGA that blocks the enzymes ability to remove the O-GlcNAc moiety. Cells treated with TMG lose the ability to remove the O-GlcNAc moiety leading to increased cellular O-GlcNAc levels, and ultimately alters O-GlcNAc cycling. Cells were harvest and total RNA was isolated by TRI Reagent (Sigma) for library preparation. Briefly, cDNA library was prepared using Illumina TruSeq Stranded mRNA sample preparation kit (Illumina) as manufacturer’s instruction. 800 ng of the total RNA was used for each library preparation. The quality of total RNA was evaluated by Agilent 2100 Expert bioanalyzer and RNA with RIN ≥ 9.80 was used. The libraries were sequenced paired-end using Illumina HiSeq2500. FastQC (0.11.2) and RSEM (1.2.22) software were used to assess the quality of the RNA sequencing results, align the reads to the mouse genome reference GRCm38/mm10, and calculate the gene expression values. R (3.2.2) and EdgeR (3.14.0) software were used to normalize the expression values using the TMM-method (weighted trimmed mean of M-values), followed by differential expression analysis. To reduce the burden of multiple testing in differential gene expression analyses, a filter was initially applied to reduce the number of genes. Genes were removed if they did not present a meaningful gene expression across all samples; only genes with cpm (counts per million) of >10 in least two samples were considered in differential expression analyses. The Benjamini and Hochberg procedure was used to control the false discovery rate (FDR).

first: Zhen

last: Zhang

first: Matt

last: Parker

first: Lesya

last: Novikova

first: Halyna

last: Fedosyuk

first: Joseph

middle: D

last: Fontes

first: Devin

last: Koestler

first: Kenneth

last: Peterson

first: Chad

last: Slawson


title: Genome-wide transcription factor binding and histone mark profiling in pluripotent and lineage-committed cells

first: Anthony

middle: E

last: Oro

address: 269 Campus Dr, CCSR 2140

summary:
Purpose: Assess changes in p63 binding in human embryonic stem cells and surface ectoderm; evaluate differences in the following histone marks: H3K27me3, H3K27ac, H3K4me1, and H3K4me3 in the surface ectoderm with and without p63; and examine changes in H3K27me3 between human embyronic stem cells and surface ectoderm with and without p63.
Methods: p63 ChIP-seq libraries were generated in p63 gain-of-function human embryonic stem cells and wild-type surface ectoderm. H3K27me3 ChIP-seq libraries were generated in wild-type and p63 gain-of-function human embryonic stem cells as well as wild-type and p63 knockout surface ectoderm. H3K27ac, H3K4me1, and H3K4me3 ChIP-seq libraries were generated in wild-type and p63 knockout surface ectoderm. All ChIP-seq experiments were performed in duplicate and sequenced on Illumina NextSeq 500 sequencer.  To ensure quality reads, fastq files were analyzed using FASTQC. Bowtie was used for read mapping and the parameters were as follows: -p 24 -S -a -m 1 --best --strata. For peak calling using MACS2, default settings were specified with a p-value of 0.05. To ensure quality peaks, IDR was run on all files, specifying FDR of 1% or 5% (or 10% for some broadPeak histone marks).
Results: Limited changes in p63 binding in human embryonic stem cells and surface ectoderm; global loss of H3K37me3 without p63 in the surface ectoderm; limited differences in H3K27ac, H3K4me1, and H3K4me3 +/- p63 in the surface ectoderm; and increase in H3K27me3 with ectopic expression of p63 in human embryonic stem cells.
Conclusion: p63 is able to bind it's surface ectoderm target sites regardless of the epigenetic landscape; p63 promotes H3K27me3 accumulation;  and p63 does not regulate histone marks H3K27ac, H3K4me1, or H3K4me3

overall_design: p63, H3K27me3, H3K27ac, H3K4me1, and H3K4me3 ChIP-seq profiles were generated in duplicate by deep sequencing on Illumina NextSeq 500 sequencer

first: Sandra

last: Melo

first: Jillian

last: Pattison

first: Samantha

last: Piekos


title: Hi-C in wild-type and SmcHD1 MommeD1 MEFs, first set

first: Michal

last: Gdula

first: Tatyana

last: Nesterova

first: Greta

last: Pintacuda

first: Jonathan

last: Godwin

first: Michael

last: McClellan

first: Skirmantas

last: Kriaucionis

first: Felix

last: Krueger

first: Wolf

last: Reik

first: Ye

last: Zhan

first: Hakan

last: Ozadam

first: Job

last: Dekker

first: Catherine

last: Green

first: Daniela

last: Moralli

first: Edith

last: Heard

first: Neil

last: Brockdorff


title: Multidimensional Assessment of the Host Response in Mechanically Ventilated Patients with Suspected Pneumonia

first: Ziyou

last: Ren

address: 303 E Chicago Ave

institute: Northwestern University

summary:
Rationale: Patients in the intensive care unit (ICU) are frequently exposed to unnecessary antibiotics. Markers of the host response to infection may aid pneumonia diagnosis and avoid antibiotic-induced complications.
Objective: To assess the host response to suspected bacterial pneumonia through assessment of alveolar neutrophilia and transcriptomic profiling of alveolar macrophages.
Methods: We determined the test characteristics of BAL neutrophilia for the diagnosis of bacterial pneumonia in 3 cohorts of mechanically ventilated patients. In one cohort, we also isolated alveolar macrophages from BAL fluid and used the transcriptome to identify signatures of bacterial pneumonia. Finally, we developed a humanized mouse model of Pseudomonas aeruginosa pneumonia to determine if pathogen-specific signatures can be identified in human alveolar macrophages.
Measurements and Main Results: BAL neutrophilia was highly sensitive for bacterial pneumonia in both the retrospective (N = 851) and validation cohorts (N = 76 and N = 79) with a negative predictive value of over 90% when BAL neutrophil percentage was less than 50%. A transcriptional signature of bacterial pneumonia was present in both resident and recruited macrophages. Gene signatures from both cell types identified patients with bacterial pneumonia with test characteristics similar to BAL neutrophilia.
Conclusions: A BAL neutrophil percentage of less than 50% is highly sensitive for bacterial pneumonia. Informative transcriptomic signatures can be generated from BAL fluid obtained during routine clinical care in the ICU. The identification of novel host response biomarkers is a promising approach to aid the diagnosis and treatment of pneumonia.

overall_design: Eight mRNA profiles of flow sorting of alveolar macrophages from humanized mouse model of P. aeruginosa pneumonia were generated by standard Illumina RNA-seq protocols.

first: Nikita

last: Joshi

first: Alexandra

last: McQuattie-Pimentel

first: Alexander

last: Misharin

first: James

last: Walter

first: Ziyan

last: Lu

first: Alan

last: Hauser

first: Scott

last: Budinger

first: Richard

last: Wunderink


title: Cohesin HiChIP datasets of pluripotent and surface ectoderm cells with and without p63

first: Anthony

last: Oro

summary:
Purpose: Assess changes in the three-dimensional (3D) chromatin architecture during surface ectoderm commitment and evaluate changes in 3D chromatin architecture in human embryonic stem cells and surface ectoderm cells with and without p63.
Methods: Cohesin HiChIP profiles for human embryonic stem cells and surface ectoderm cells with and without p63 were generated in triplicate with deep sequencing on the Illumina HiSeq 4000 sequencer. Using HiC-Pro, paired end reads were aligned to hg19, duplicate reads were removed, and then were assigned to MboI restriction fragments, filtered for valid interactions, and used to generate binned interaction matrices of 10 kb resolution. Contacts were called using FitHiC and filtered for counts >= 10 and FDR < 0.001.
Results: The greatest change in 3D chromatin architecture was observed between human embryonic stem cells and surface ectoderm cells, while moderate changes were observed in human embryonic stem cells with and without p63, and limited changes were observed in surface ectoderm cells with and without p63.
Conclusion: Both p63 and the surface ectoderm morphogens direct changes in chromatin folding to establish the 3D chromatin landscape in the surface ectoderm.

overall_design: Cohesin HiChIP datasets of human embryonic stem cells and surface ectoderm cells with and without p63 were deep sequenced in triplicate on the Illumina HiSeq 4000 sequencer.

first: Sandra

last: Melo

first: Jillian

last: Pattison

first: Samantha

last: Piekos


title: Simultaneous epitope and epigenetic profile measurements with multi-index single-cell ATAC-sequencing [4T1]

first: Howard

last: Chang

summary: A novel scATAC-seq approach, Multi-Index single cell ATAC-seq (MI-ATAC), in which we not only index the accessible chromatin of individual cells, but also index their protein expression using index Fluorescence Activated Cell Sorting (FACS).

overall_design: scATAC-seq performed on 4T1 cells in normoxia or hypoxic conditions for 6h, 12h, 24h, 48h, 36h, 48h or 72h.

first: Xingqi

last: Chen

first: Ulrike

last: Litzenburger

first: Yuning

last: Wei

first: Alicia

last: Schep

first: Edward

last: LaGory

first: Amato

last: Giaccia

first: William

last: Greenleaf


title: Molecular and functional heterogeneity of IL-10-producing CD4+ T cells

first: Babett

last: Steglich

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

overall_design: Refer to individual Series


title: Genome-wide chromatin accessibility in pluripotent and surface ectoderm cells with and without p63

summary:
Purpose: Evaluate changes in chromatin accessibility between human embryonic stem cells and surface ectoderm cells with and without the transcription factor p63.
Method: Chromatin accessibility profiles for human embryonic stem cells and surface ectoderm with and without p63 were generated by deep sequencing, in duplicate, with the Illumina NextSeq sequencer. Quality reads were assessed by fastq. Reads were aligned using Bowtie2, PCR duplicates and mitochondrial DNA were discarded, and peak calling was completed using MACS2. Non-reproducible peaks were filtered out by IDR with an FDR of 5%.
Results: p63 fails to modify chromatin accessibility when ectopically expressed in human embryonic stem cells; differentiation of human embryonic stem cells to surface ectoderm results in the closure of some regions open in pluripotent cells and the opening of new regions; and loss of p63 in the surface ectoderm results in increased accessibility of 1/3 of the regions opened during surface ectoderm differentiation.
Conclusion: p63's ability to modify chromatin accessibility is dependent upon the underlying epigenetic landscape, and when it can modify the landscape, it does so by closing regions that become open during ectoderm differentiation.

overall_design: Chromatin accessibility profiles for human embryonic stem cells and surface ectoderm with and without p63 were generated by deep sequencing, in duplicate, with Illumina NextSeq sequencer.


title: RA and BMP4 cooperate with p63 to alter chromatin dynamics during surface epithelial commitment


title: Gene expression analysis of Ovol2-deficent newborn keratinocytes

city: Irvine

first: Daniel

last: Haensel

state: California

address: Medical Sciences D288

institute: UC Irvine

summary: We report the differential gene expression differences between control and Ovol2-deficent newborn keratinocytes

overall_design: Two control and two Ovol2-deficent samples were isolated

first: Xing

last: Dai


title: UMI-4C in wild-type and p63-null surface ectoderm cells

summary:
Purpose: Validate HiChIP-identified long-range chromatin interactions at the TFAP2C locus, in a viewpoint-specific manner.
Methods: UMI-4C libraries targeting 3 individual viewpoints at the TFAP2C locus were generated in duplicate, in surface ectoderm cells with and without p63. Replicates were sequenced on Illumina NextSeq sequencer, and reads were aligned and filtered for valid long-range interactions using HiCPro.
Results: Dynamic long-range interactions at the TFAP2C locus were detected with and without p63 in surface ectoderm cells.
Conclusion: Long-range interactions detected via HiChIP were confirmed in the surface ectoderm by this technique, validating the HiChIP method through an orthogonal approach.

overall_design: UMI-4C libraries, generated using DpnII digestion and TFAP2C locus primer viewpoints, were sequenced in duplicate on Illumina NextSeq sequencer.


title: Identification of ADAR1 adenosine deaminase dependency in a subset of cancer cells

city: Boston

first: Tao

last: Zou

address: 450 Brookline Avenue

institute: Dana-Farber Cancer Institute

summary: Using RNA-seq to identify gene expression changes after genetic deletion of ADAR

overall_design: RNA-seq of A549, HCC366, NCI-H1650, and NCI-H196 cells after CRISPR-Cas9-mediated deletion of ADAR as compared to a control gene. A549 cells were also treated with vehicle or interferon-β for 24 hours prior to collection for RNA-seq.


title: Quantitative profiling of drug-responsive regulatory activity at the human genome scale

city: Durham

first: Charles

middle: A

last: Gersbach

state: North Carolina

address: 101 science drive rm 2323

institute: Duke University

summary: Environmental stimuli commonly act via changes in gene regulation. Human-genome-scale assays to measure such responses are indirect or require knowledge of the transcription factors (TFs) involved. Here, we present the first use of genome-wide high-throughput reporter assays to measure environmentally-responsive regulatory element activity. We focused on responses to glucocorticoids (GCs), an important class of pharmaceuticals and a standard model for gene regulation. Our assay library contains >108 unique fragments and covers the human genome at >50x. Changes in regulatory element activity correlated with changes in gene expression, histone modifications and transcription factor occupancy. We also detected allele-specific environmental responses. Notably, the assays did not require knowledge of the TFs that mediate GC responses, thus can be used to agnostically quantify genomic responses to environmental signals for which the underlying mechanism remains unknown.

overall_design: 12 input STARR-seq input libraries and 25 STARR-seq output libraries (five replicates of five different durations of 100 nM dexamethasone exposure).

first: Graham

last: Johnson

first: Alejandro

last: Barrera

first: Ian

last: McDowell

last: D'Ippolito

middle: H

last: Majoros

first: Christopher

last: Vockley

first: Xingyan

last: Wang

first: Andrew

last: Allen

first: Timothy

last: Reddy


title: Genome-wide screening of NEAT1 regulators reveals mito-paraspeckle communication

first: Li

last: Yang

address: 131 Dong-An Road

department: Institutes of Biological Sciences

institute: Fudan University

summary: The long non-coding RNA NEAT1 (nuclear enriched abundant transcript 1) nucleates the formation of paraspeckles, which constitute a type of nuclear body that has multiple roles in gene expression. How the NEAT1 gene itself is regulated and how paraspeckles communicate with other cell compartments remains poorly understood. Here we identify regulators of NEAT1 transcription using an endogenous NEAT1 promoter-driven EGFP reporter in human cells coupled with genome-wide RNAi screens. In addition to transcription factors and chromatin modulators, the screens unexpectedly yielded gene candidates involved in mitochondrial functions as essential regulators of NEAT1 expression and paraspeckle formation. Mitochondrial defects altered NEAT1 transcription via ATF2 and subsequently uncoupled 3’ end processing of NEAT1_1 from its long isoform to favour NEAT1_2 production, which is key for generating elongated paraspeckles that have different features from the regular, globular bodies. Correspondingly, NEAT1 depletion has profound effects on mitochondrial dynamics and function by altering sequestration of mRNAs of mitochondrial genes enriched in paraspeckles. Overall, our data provided a rich resource for understanding NEAT1 and paraspeckle regulation, and revealed an unexpected crosstalk between cytoplasmic organelles and nuclear bodies.

overall_design: Examination of differential expressed genes between wild type and NEAT1 KO by poly(A)+ RNA-Seq and identifying RNAs that interact with NEAT1 by NEAT1 CHART (capture hybridization analysis of RNA targets) assays followed by RNA-sequencing (CHART RNA-seq) from HeLa cells.

first: Ling-Ling

last: Chen

first: Shi-Bin

last: Hu

first: Yang

first: Meng-Ran

first: Di

last: Wu

first: Run-Wen

last: Yao


title: 10x Genomics Drop-seq single-cell RNA-seq of isolated Adult human spermatogonia, spermatocytes, spermatids & steady-state spermatogenic cells

city: San Antonio

first: Brian

middle: P.

last: Hermann

state: TX

address: 1 UTSA Circle

department: Department of Biology

institute: University of Texas at San Antonio

summary: To reveal distinct transcriptomes associated with various spermatogenic cells, including spermatogonial stem cells and all of their subsequent progeny, single-cell transcriptomes from Adult human spermatogonia, StaPut-enriched spermatocytes and spermatids, or unselected steady-state spermatogenic cells were used for Drop-Seq analysis. We used the 10x Genomics Chromium (Drop-Seq) to perform single-cell RNA-seq

overall_design: Sorted Adult Human spermatogonia, three replicate preparations of steady-state unselected spermatogenic cells, and isolated adult spermatocytes and spermatids were used for this study. In one experiment, a 1:1 mixture of human and mouse steady-state spermatogenic cells were evaluated together to establish a multiplet rate. Data are from a total of 36,451 cells.

first: Keren

last: Cheng

first: Anukriti

last: Singh

first: Lorena

last: Roa-de-la-Cruz

first: Kazadi

last: Mutoji

first: Heidi

last: Gildersleeve

first: I-Chung

first: Max

last: Mayo

first: Birgit

last: Westernströer

first: Nate

last: Law

first: Melissa

last: Oatley

first: Ellen

middle: K

last: Velte

first: Bryan

last: Niedenberger

first: Danielle

last: Fritze

first: Sherman

last: Silber

last: Geyer

first: Jon

first: John

last: McCarrey


title: RNA-seq profiles of pluripotent and surface ectoderm cells with and without p63

city: Stanford

first: Anthony

last: Oro

institute: Stanford University

summary:
Purpose: Evaluate p63 regulation of gene expression in human embryonic stem cells and the surface ectoderm
Methods: RNA profiles for human embyronic stem cells and surface ectoderm cells with and without p63 using deep sequencing, in duplicate, on Illumina NextSeq 500 sequencer. Quality of reads were checked by fastqc. Reads were aligned to hg19 genome using tophat and FPKM values were generated using Homer.
Results: p63 is largely unable to regulate gene expression in pluripotent cells, but acts primarily as a repressor in the surface ectoderm.
Conclusion: p63 regulation of gene expression is dependent on the changes the cell undergoes during surface ectoderm commitment

overall_design:
RNA-seq profiles of human embryonic stem cells and surface ectoderm cells with and without p63 were generated in duplicate by deep sequencing on Illumina NextSeq 500 sequencer.

***Please note that the submitters no longer have access to the fastq or all of the original bam files (i.e. no raw data). The text files used for all downstream analyses were provided.

first: Sandra

last: Melo

first: Jillian

middle: M

last: Pattison

first: Samantha

last: Piekos


title: C1 single-cell RNA-seq of Adult ID4-EGFP mouse spermatoognia

first: Brian

last: Hermann

summary: To reveal distinct transcriptomes associated with spermatogonial stem cell renewal vs. initiation of differentiation, single-cell transcriptomes from Adult ID4-EGFP+ spermatogonia were subdivided into subpopulations that displayed distinct fates when assayed by transplantation, with ID4-EGFPbright cells highly enriched for SSCs, and ID4-EGFPdim cells enriched for progenitors. We used the Fluidigm C1 instrument to capture individual spermatogonia for SMART-Seq2 single-cell RNA-seq.

overall_design: Four replicate preparations of Adult mouse ID4-EGFP+ spermatogonia were used for this study. Data are from a total of 300 cells. Cells were binned into quartiles according to EGFP epifluorescence intensity (Q1 = EGFP-bright, Q4=EGFP-dim, Q2 and Q3 have intermediate EGFP fluorescence) to facilitate comparisons.

first: Keren

last: Cheng

first: Anukriti

last: Singh

first: Lorena

last: Roa-de-la-Cruz

first: Kazadi

middle: N

last: Chen

first: Brya

first: Christopher


title: C1 single-cell RNA-seq of immature (P6) ID4-EGFP mouse spermatoognia

summary: To reveal distinct transcriptomes associated with spermatogonial stem cell renewal vs. initiation of differentiation, single-cell transcriptomes from P6 ID4-EGFP+ spermatogonia were subdivided into subpopulations that displayed distinct fates when assayed by transplantation, with ID4-EGFPbright cells highly enriched for SSCs, and ID4-EGFPdim cells enriched for progenitors. We used the Fluidigm C1 instrument to capture individual spermatogonia for SMART-Seq2 single-cell RNA-seq.

overall_design: Five replicate preparations of mouse P6 ID4-EGFP+ spermatogonia were used for this study. Data are from a total of 278 cells. Cells were binned into quartiles according to EGFP epifluorescence intensity (Q1 = EGFP-bright, Q4=EGFP-dim, Q2 and Q3 have intermediate EGFP fluorescence) to facilitate comparisons.

last: Mutoji

first: Heidi

last: Gildersleeve

first: I-Chung

first: Max

last: Mayo

first: Birgit

last: Westernströer

first: Nate

last: Law

first: Melissa

middle: J

first: Ellen


title: 10x Genonics Drop-seq single-cell RNA-seq of isolated Adult ID4-EGFP mouse spermatogonia, spermatocytes, spermatids & steady-state spermatogenic cells

summary: To reveal distinct transcriptomes associated with various spermatogenic cells, including spermatogonial stem cells and all of their subsequent progeny, single-cell transcriptomes from Adult ID4-EGFP+ spermatogonia (sorted for brightest or dimmest), StaPut-enriched spermatocytes and spermatids, or unselected steady-state spermatogenic cells were used for 10x Genomics analysis. The GFP-bright and dim phenotypes exhibit distinct fates when assayed by transplantation, with ID4-EGFPbright cells highly enriched for SSCs, and ID4-EGFPdim cells enriched for progenitors. We used the 10x Genomics Chromium (Drop-Seq) to perform single-cell RNA-seq

overall_design: Unselected or sorted Adult ID4-EGFP+ spermatogonia (sorted separately as EGFP-bright or EGFP-dim), three replicate preparations of steady-state unselected spermatogenic cells, and isolated adult spermatocytes and spermatids were used for this study. Data are from a total of 17,491 cells.

middle: C

last: Oatley

last: Velte

last: Niedenberger

first: Danielle

last: Fritze

first: Sherman

last: Silber

first: Jon

first: John


title: small RNA profiling of extracellular RNA from breast cancer cell lines

status: Public on Nov 05 2018

first: Hani

last: Goodarzi

summary: We performed small RNA sequencing of conditioned media collected from breast cancer cells as well as human mammary epithelial cells (HUMEC) in biological replicates.

overall_design: BRCA-lines_CM_smRNA: Eight breast cancer lines and human mammary epithelial cells were cultured in biological replicates. RNA was then extracted from conditioned media (CM) and subjected to small RNA sequencing. The number of unique orphan non-coding RNAs were then recorded for each sample.

first: L

last: Fish

first: S

last: Zhang

first: H


title: Discovery and annotation of intracellular and extracellular orphan non-coding RNAs in breast cancer


title: Haploinsufficiency of the intellectual disability-gene SETD5 disturbs developmental gene expression and cognition

city: Wien

first: Christoph

last: Dotter

address: Zimmermannplatz 10

country: Austria

institute: St. Anna Children’s Cancer Research Institute (St. Anna CCRI)

summary: SETD5 gene mutations have been identified as a frequent cause of idiopathic intellectual disability. Here we show that Setd5 haploinsufficient mice present developmental defects such as abnormal brain to body weight ratio and neural crest defect associated phenotypes. Furthermore, Setd5 mutant mice show impairments in cognitive tasks, enhanced long-term potentiation, delayed ontogenetic profile of ultrasonic vocalisation and behavioural inflexibility. Behavioural issues are accompanied by abnormal expression of postsynaptic density proteins previously associated with cognition. Our data suggest that Setd5 might regulate RNA polymerase II dynamics and gene transcription during development and learning via its interaction with the Hdac3 and Paf1 complexes. Our results emphasize the decisive role of Setd5 in a biological pathway found to be disrupted in intellectual disability and autism spectrum disorder patients.

overall_design: RNA-sequencing for wild type and Setd5 heterozygous knockout mice in two settings. First, in whole embryo samples (age E9.5), three biological replicates each. Second, gene expression changes due to contextual fear conditioning (CFC) was studied by comparing baseline transcription in homecage (HC) mice with transcription one hour (CFC_1h) or three hours (CFC_3h) after fear conditioning (4-5 biological replicates per time point and genotype).

first: Elena

last: Deliu

first: Jasmin

last: Morandell

first: Gaia

last: Novarino


title: Reliability of 3D Cortical Spheroids Generation from Human Pluripotent Stem Cells

city: Los Angeles

first: Aaron

last: Gordon

address: Gonda Building, 695 Charles E. Young Drive South

department: Neurology

institute: UCLA

summary: Here we assess the reliability of human cortical spheroid differentiation cultured in xeno-free, feeder-free conditions. We find high reliability in differentiation across multiple hiPSC lines as well as across experiments, and we anticipate that this directed differentiation approach will be useful for large scale generation of brain-region specific spheroids and disease modeling.

overall_design:
Differentiation was performed across 7 iPSC lines each sampled at 4 time points during differentiation.
Due to HIPPA compliance issues, submitters are unable to provide raw data.

first: Daniel

last: Geschwind

first: Sergiu

last: Pasca


title: small RNA profiling of extracellular RNA from breast cancer cell lines [EV]

summary: We performed small RNA sequencing of exosomes and extracellular vesicles collected from breast cancer cells as well as human mammary epithelial cells (HUMEC) in biological replicates (using Norgen's cell culture media exosme purification and RNA isoaltion kits).

overall_design: BRCA-lines_EV_smRNA: Eight breast cancer lines and human mammary epithelial cells were cultured in biological replicates. Exosomes/small extracellular vesicles (EV) were then collected from the conditioned media using the Cell Culture Media Exosome Purification Mini Kit (Norgen). Samples were then subjected to small RNA sequencing. The number of unique orphan non-coding RNAs were then recorded for each sample.


title: Transcript analysis of multi-locus sampled tumor tissue in patients with non-small cell lung cancer

status: Public on Nov 04 2018

city: Chongqing

first: Qingzhu

last: Jia

address: Xinqiao

department: Department of Onoclogy

institute: XinQiao Hospital

summary: we investigated the spatial features of surgically-removed biopsies from multiple loci in tumor masses of 15 patients with non-small cell lung cancer (NSCLC). We observed that the immune microenvironment is highly spatial heterogeneous such that intra-tumoral regional variation is as large as inter-personal variation. While the local mutational burden was associated with local T cell clonal expansion, observed local anti-tumor cytotoxicity is strongly associated with local tumoral circumstance rather than TMB alone

overall_design: We recruited 15 newly-diagnosed NSCLC patients who had surgery with curative intent, and multiple biopsy samples were collected from each individual tumor mass according to previously method. For each sample, we performed multiple genomic and immunogenomic assays including whole exome sequencing (WES), transcriptome profiling (RNA-Seq), and T cell repertoire sequencing (TCR-Seq).

first: Wei

last: Wu

first: Yuqi

last: Wang

first: Peter

last: Alexander

first: Chengdu

last: Sun

first: Zhihua

last: Gong

first: Jia’nan

last: Cheng

first: Huaibo

first: Yanfang

last: Guan

first: Xuefeng

last: Xia

first: Ling

last: Yang

first: Xin

last: Yi

first: Yisong

middle: Y

last: Wan

first: Haidong

first: P

last: Futreal

first: Qi-Jing

last: Li

first: Bo

last: Zhu


title: Folliculin regulates mTORC1/2 and WNT pathways in early human pluripotency

status: Public on Nov 03 2018

city: Seattle

first: Hannele

last: Ruohola-Baker

state: WA

address: 850 Republican Street

institute: Institute for Stem Cell and Regenerative Medicine

summary: It is important to understand how cells can maintain and exit human pluripotency. We exploited the metabolic and epigenetic differences between naïve and primed pluripotent cells to design a CRISPR-Cas9 screen for identifying genes that promote the exit from naïve pluripotency. Among the known and novel regulators of this early step of human development, we identified the tumor suppressor folliculin (FLCN). Flcn is important for implantation of the mouse embryo into the uterus and has been shown to regulate the exit of pluripotency in mouse through activation of Esrrb. However, the function of FLCN is unknown in human embryonic stem cells (hESC). Knock-out (KO) of FLCN revealed that it is not essential to maintain the naïve pluripotent state but is required for the exit of that state, in part by controlling the localization of the transcription factor TFE3. While mainly found in the cytoplasm of cells exiting the naïve state, FLCN KO resulted in TFE3 nuclear localization. TFE3 targets up-regulated in FLCN KO exit assay were members of Wnt pathway and ESRRB. Treatment of FLCN KO hESC with a Wnt inhibitor rescued the phenotype and allowed the cells to exit the naïve state. In contrast, the lack of rescue in ESRRB/FLCN double KO lines suggested that ESRRB was not responsible for the FLCN mutant phenotype. Using co-immunoprecipitation and mass spectrometry analysis we identified unique FLCN binding partners, in addition to known FLCN interactors, at various stages of pluripotency. The interactions of FLCN with components of the mTOR pathway (mTORC1 and mTORC2) revealed a mechanism of FLCN function during exit from naïve pluripotency.

overall_design: RNA-seq of 2 biological replicates in 6 conditions: Elf 2iLIF, Elf 2iLIF FLCN KO, Elf 2iLIF FLCN AAVS1-FLCN-GFP no Dox, Elf 2iLIF FLCN KO AAVS1-FLCN-GFP with Dox, Elf FLCN KO in TeSR 7 day, and Elf in TeSR 7 day; RNA-seq of Elf FLCN KO treated with IWP2 and DMOS; ChIP-seq of H3K27me3 for NNMT CRISPR mutant 6.2.4

first: Yuliang

first: Julie

last: Mathieu


title: MYOD1 functions as a clock amplifier as well as a critical co-factor for downstream circadian gene expression in muscle

status: Public on Nov 02 2018

city: MILL VALLEY

first: Brian

last: Hodge

address: 338 EDGEWOOD AVE, A

institute: Buck Institute

summary: In the present study we show that the master myogenic regulatory factor, MYOD1, is a positive modulator of molecular clock amplitude and functions with the core clock factors for expression of clock-controlled genes in skeletal muscle. We demonstrate that MYOD1 directly regulates the expression and circadian amplitude of the positive core clock factor Bmal1. We identify a non-canonical E-box element in Bmal1 and demonstrate that is required for full MYOD1-responsiveness. Bimolecular fluorescence complementation assays demonstrate that MYOD1 colocalizes with both BMAL1 and CLOCK throughout myonuclei. We demonstrate that MYOD1 and BMAL1:CLOCK work in a synergistic fashion through a tandem Ebox to regulate the expression and amplitude of the muscle specific clock-controlled gene, Titin-cap (Tcap). In conclusion, these findings reveal mechanistic roles for the muscle specific transcription factor MYOD1 in the regulation of amplitude of the molecular clock as well as  synergistic regulation of clock-controlled genes in skeletal muscle.

overall_design: Gastrocnemius muslce from male mice (C57bl6) were collected every 4hrs for 24 hrs and pooled into one sample.

first: Yi

last: Cao


title: Cap-specific terminal N6-methylation of RNA by an RNA polymerase II-associated methyltransferase.

city: Wako

first: Shintaro

last: Iwasaki

state: Saitama

address: 2-1, Hirosawa

department: Center for Pioneering Research

institute: RIKEN

summary: N6-methyladenosine (m6A), a major modification of messenger RNAs (mRNAs), plays critical roles in RNA metabolism and function. In addition to the internal m6A, N6, 2'-O-dimethyladenosine (m6Am) is present at the transcription start nucleotide of capped mRNAs in vertebrates. However, its biogenesis and functional role remain elusive. Using a reverse genetics approach, we identified PCIF1, a factor that interacts with the serine-5-phosphorylated carboxyl-terminal domain of RNA polymerase II, as a cap-specific adenosine methyltransferase (CAPAM) responsible for N6-methylation of m6Am. The crystal structure of CAPAM in complex with substrates revealed the molecular basis of cap-specific m6A formation. A transcriptome-wide analysis revealed that N6-methylation of m6Am promotes the translation of capped mRNAs. Thus, a cap-specific m6A writer promotes translation of mRNAs starting from m6Am.

overall_design: Ribosome profiling and RNA-seq

first: Shinichiro

last: Akichika

first: Seiichi

last: Hirano

first: Yuichi

last: Shichino

first: Takeo

last: Suzuki

first: Hiroshi

last: Nishimasu

first: Ryuichiro

last: Ishitani

first: Yutaka

last: Hirose

first: Osamu

last: Nureki

first: Tsutomu


title: DEGs in the bone marrow of Esr1Nkx2-1Cre females

first: Candice

last: Herber

address: 1550 4th Street

institute: UCSF

summary: Disrupting central estrogen signaling exposes a powerful sex-dependent brain-to-bone axis in female mice triggering massive increases in bone density.

overall_design: Comparison of wild type bone marrow from female (Esr1flox/flox) mice compared to the bone marrow of mutant (Esr1fl/fl;Nkx2-1Cre) female mice at 4 weeks of age.

first: Matthew

last: Schmitz

first: Holly

last: Ingraham


title: OGT binds a conserved C-terminal domain of TET1 to regulate TET1 activity and function in development

city: Chicago

first: Xiaolong

last: Cui

address: 680 N Lake Shore Drive

department: Department of Preventive Medicine

summary: TET enzymes convert 5-methylcytosine to 5-hydroxymethylcytosine and higher oxidized derivatives. TETs stably associate with and are post-translationally modified by the nutrient-sensing enzyme OGT, suggesting a connection between metabolism and the epigenome. Here, we show for the first time that modification by OGT enhances TET1 activity in vitro. We identify a a domain of TET1 domain that is responsible necessary and sufficient for binding to OGT and report a point mutation that disrupts the TET1-OGT interaction.  We show that the TET1-OGTthis interaction is necessary for TET1 to rescue hematopoetic stem cell production in tet mutant zebrafish embryos, suggesting that OGT promotes TET1’s function during development. Finally, we show that disrupting the TET1-OGT interaction in mouse embryonic stem cells changes the abundance of TET-containing high molecular weight complexesTET2 and 5-methylcytosine, which is accompanied by alterations in gene expression and causes widespread gene expression changes. These results link metabolism and epigenetic control, which may be relevant to the developmental and disease processes regulated by these two enzymes.

overall_design: 5hmC-Seal was performed in WT and C2018A samples, respectively.

first: Joel

last: Hrit

first: Ji

last: Nie

first: Chuan

last: He

first: Barbara

last: Panning


title: Identification of grade and origin specific cell populations in serous epithelial ovarian cancer by single cell RNA-seq

city: Mahasset

first: Andrew

last: Shih

state: NY

address: 350 Community Dirive

institute: Feinstein Institute - Northwell Health

summary: Here we investigated different cell populations within ovarian cancer using single-cell RNA seq: fourteen samples from nine patients with differing grades (high grade, low grade and benign) as well as different origin sites (primary and metastatic tumor site, ovarian in origin and fallopian in origin).

overall_design: Examination of cellular heterogeneity of primary and metastatic tumor samples from nine patients with differing stage of serous epithelial ovarian cancer.

first: Annette

middle: T

last: Lee


title: C1 single-cell RNA-seq of Adult Human spermatoognia

first: Brian

last: Hermann

summary: To reveal distinct transcriptomes associated with spermatogonial stem cell renewal vs. initiation of differentiation, single-cell transcriptomes from Adult Human spermatogonia were subdivided into subpopulations based on the levels of ID4 mRNA (determined in this experiment). This correlates with distinct fates of corresponding mouse spermatogonia when assayed by transplantation, with ID4-EGFPbright cells highly enriched for SSCs, and ID4-EGFPdim cells enriched for progenitors. We used the Fluidigm C1 instrument to capture individual spermatogonia for SMART-Seq2 single-cell RNA-seq.

overall_design: Nine replicate preparations of Adult Human spermatogonia were used for this study. Data are from a total of 635 cells. Cells were binned into quartiles according to ID4 mRNA levels (Q1 = ID4-high, Q4=ID4-low, Q2 and Q3 have intermediate ID4 mRNA levels) to facilitate comparisons.

first: Keren

last: Cheng

first: Anukriti

last: Singh

first: Lorena

last: Roa-de-la-Cruz

first: Kazadi

last: Mutoji

first: Heidi

last: Gildersleeve

first: I-Chung

last: Chen

first: Max

last: Mayo

first: Birgit

last: Westernströer

first: Nate

last: Law

first: Melissa

last: Oatley

first: Ellen

last: Velte

first: Brya

last: Niedenberger

first: Danielle

last: Fritze

first: Sherman

last: Silber

first: Christopher

middle: B

last: Geyer

first: Jon

first: John

last: McCarrey


title: Exploiting Mouse Models to Understand Female Hypersensitivity to Cocaine

city: Farmington

first: Richard

last: Mains

state: CT

address: 263 Farmington Ave, Neuroscience Dept., Neuroscience Dept.

department: Neuroscience

institute: University of Connecticut Health Center

summary: Male mice, female mice, ovariectomized female mice given placebo pellets, and ovariectomized female mice given extradiol pellets were treated with experimenter-administered saline or cocaine for 7 days, and behaviorally monitored. After a 28 day withdrawal period, RNA samples were prepared from nucleus accumbens and subjected to RNA-Seq, followed by differential expression analyses using Cuffdiff, Limma and DESeq2. Selected transcripts were further investigated using quantitative polymerase chain reaction.

overall_design: After surgeries and non-operated controls, mice were administered saline or cocaine, and behaviorally analyzed. After withdrawal from drugs, nucleus accumbens RNA was used for RNA-Seq and qPCR analyses.

first: Bruce

last: Rheaume


title: scFTD-seq: freeze-thaw lysis based, portable approach toward highly distributed single-cell 3’ mRNA profiling

city: New Haven

first: Burak

last: Dura

state: Connecticut

address: 55 Prospect St

department: Biomedical Engineering

institute: Yale University

summary: We present sc-FTDseq, a microchip platform for single-cell freeze-thaw lysis directly toward 3’ mRNA sequencing. It offers format flexibility with a much simplified, widely adoptable workflow that reduces the number of preparation steps and hands-on time, with the quality of data and the cost per sample matching that of the state-of-the-art scRNA-seq platforms. Freeze-thaw, known as an unfavorable lysis method resulting in RNA fragmentation, turns out to be fully compatible with single-cell 3’ mRNA sequencing, which detects only ~50 bases at the 3’ end. We applied it to the profiling of mixed populations including whole tumors for distinguishing all major cell types and to the profiling of circulating follicular helper T cells implicated in systemic lupus erythematosus pathogenesis. Our results delineate the heterogeneity in the transcriptional programs and effector functions of these rare pathogenic T cells.

overall_design: mRNA sequencing libraries are prepared after lysing the cells using three cycles of freeze-thaw. Open-surface and closed-environment formats refer to how a microwell array is used for co-loading cells and uniquely barcoded beads for mRNA capture. In closed-environment format, the microwell array is bonded with a channel on top of the array, and the cells and beads are introduced into the microwells through the channel. In open-surface format, microwell arrays are used without a channel on top, and cells and beads are introduced onto the array using a pipette.

first: Rong

last: Fan


title: small RNA profiling of breast cancer cell lines

city: San Francisco

first: Hani

last: Goodarzi

summary: We performed small RNA sequencing in breast cancer cells as well as human mammary epithelial cells (HUMEC) in biological replicates.

overall_design: BRCA-lines_IC_smRNA: Small RNA samples were extracted from eight breast cancer lines in biological replicates and human mammary epithelial cells in triplicates (HUMEC). The samples were prepared for small RNA sequencing using NEXTflex Small RNA Sequencing Kit v3 (Biooscientific) per the manufacturer's protocol.

first: L

last: Fish

first: S

last: Zhang

first: H


title: Downstream Target Screening of TopBP1 in differentiated HPV-positive keratinocytes

status: Public on Nov 01 2018

first: Yan

last: Li

state: IL

address: 900 East 57th St.

department: Center for Research Informatics

institute: The University of Chicago

summary: TopBP1 is more than a DNA damage factor. The knockdown indicates it could have transcriptional regulatory function and we validated this by examining E2F1/p73 pathway.

overall_design: HPV-positive keratinocytes were transduced with viruses expressing TopBP1 shRNA and stably selected by puromysin.  The knockdown cells and the srcramble cells were compared to explore the potential targets for TopBP1 downstream.

first: Shiyuan

last: Hong


title: Translatome and transcriptome analysis of TMA20 (MCT-1) and TMA64 (eIF2D) knockout yeast strains

city: Pushchino

first: Ivan

middle: V

last: Kulakovskiy

address: Institutskaya 4

country: Russia

institute: Institute of Protein Research

summary: We report ribosome profiling and RNA-Seq data of S.cerevisiae strains with TMA20, TMA64 single- and TMA20/TMA64 double-gene knockouts, grown in the rich YPD or minimal SD medium.

overall_design: Yeast cells of 4 different S. cerevisiae strains, namely:  Δtma20, Δtma64, ΔΔtma20tma64 knockout strains and the wild-type BY4741, were maintained in YPD or SD media. Two biological replicates were performed for wild-type strain, maintained in YPD media. Ribosomal profiling experiments of the wild-type and knockout strains grown in different media were performed. The сDNA libraries were obtained from total 9 RNA samples and 9 ribosome-bound RNA samples.

first: Desislava

middle: S

last: Makeeva

first: Maria

last: Logacheva

first: Sergey

last: Dmitriev


title: Age-specific biological and molecular profiling distinguishes paediatric from adult acute myeloid leukaemias

city: St. Lucia

first: Othmar

last: Korn

state: Queensland

address: University of Queensland

country: Australia

institute: Australian Institute for Bioengineering and Nanotechnology

summary: Acute myeloid leukaemia (AML) affects children and adults of all ages. AML remains one of the major causes of death in children with cancer and for children with AML relapse is the most common cause of death. By modelling AML in vivo we demonstrate that AML is discriminated by the age of the cell of origin. Young cells give rise to myeloid, lymphoid or mixed phenotype acute leukaemia, whereas adult cells give rise exclusively to AML, with a shorter latency. Unlike adult, young AML cells do not remodel the bone marrow stroma. Transcriptional analysis distinguishes young AML by the upregulation of immune pathways. Analysis of human paediatric AML samples recapitulates a paediatric immune cell interaction gene signature, highlighting two genes, RGS10 and FAM26F as prognostically significant. This work advances our understanding of paediatric AML biology, and provides murine models that offer the potential for developing paediatric specific therapeutic strategies.

overall_design: Analysis of AML in adult and young mice

first: Shahzya

last: Chaudhury

first: Caitríona

last: O’Connor

first: Ana

last: Cañete

first: Joana

last: Bittencourt-Silvestre

first: Evgenia

last: Sarrou

first: Áine

last: Prendergast

first: Jarny

last: Choi

first: Pamela

last: Johnston

first: Christine

last: Wells

first: Brenda

last: Gibson

first: Karen

last: Keeshan


title: Downstream effects of YAP examined by RNA-Seq analysis of skin in YAP2-5SA-∆C transgenic mice

city: Sydney

first: Susan

last: Corley

state: NSW

address: D26, Kensignton Campus

department: Biotechnology & Biomolecular Sciences

institute: UNSW

summary: To obtain insights into the global changes of gene expression in the mouse skin in response to epidermal YAP activity, we performed whole transcriptome sequencing of skin tissue of YAP2-5SA-∆C transgenic mice.

overall_design: RNA was extracted from dorsal neck skin biopsies of three P33 female YAP2-5SA-∆C mice (TG) showing the early onset of the externally visible phenotype, and of three female wild type littermate mice (WT). The six RNA-Seq libraries were sequenced on the Illumina NextSeq platform to produce approximately 30 million, 75 nucleotide paired-end reads per sample. Differential expression analysis was performed using the Bioconductor packages, edgeR and  limma (Voom).

first: Veronica

last: Mendoza-Reinoso

first: Marc

middle: R

last: Wilkins

first: Annemiek

last: Beverdam


title: mRNA sequencing analysis of cultured human primary airway epithelial cells upon exposure to PMN exosomes

city: Birmingham

first: Derek

last: Russell

state: Alabama

address: LHRB 321, 700 19th St. South

institute: University of Alabama at Birmingham

summary: We analyzed the mRNA expression of monolayers of human primary airway epithelial cells after exposure to 1X10^5 exosomes from activated or quiescent PMNs along with PBS treated controls

overall_design: Activated PMN exosome (n=3), quiescent PMN exosome (n=3) or PBS (n=2) exposed primary human airway cells were grown and terminally differentiated to confluence under polarizing air-liquid interface conditions in a 5% CO2 incubator. Each 1.9 cm2 well containing approximately 100,000 cells was administered either 1μL of PBS, or 1X105 activated or quiescent exosomes (in 1 μL PBS) to the apical surface. After 24 hours, cells were scraped and lysed and total mRNA was harvested with RNEasy kit (Qiagen) per manufacturer’s instructions.

middle: W


title: Tumor-infiltrating immune cells of young and aged mice

city: Boston

first: Juhyun

last: Oh

address: 185 Cambridge Street

institute: Massachusetts General Hospital

summary: Macrophages, dendritic cells, conventional CD4+ T cells, CD8+ T cells, and regulatory T cells isolated from mouse colon cancer model MC38 tumors implanted subcutaneously to young (3 month) and aged (12 month) mice were sequenced using ImmGen's standard ultra-low input RNA-seq pipeline, in order to study age-dependent differences in intraltumoral immune cell functions and their impact on tumor control

overall_design: Samples collected at the Center for Systems Biology at Mass General Hospital, shipped frozen to a central location, and sequenced using ImmGen's standard RNA-seq pipeline

first: Ralph

last: Weissleder


title: Human induced pluripotent stem cell-derived astrocytes are differentially activated by multiple sclerosis-associated cytokines

city: Epalinges

first: Sylvain

last: Perriot

state: Vaud

address: Chemin des Boveresses 155, Building CLEC / Room C203

country: Switzerland

institute: CHUV

summary: Recent studies highlighted the importance of astrocytes in neuroinflammatory diseases, interacting closely with other CNS cells but also with the immune system. However, due to the difficulty in obtaining human astrocytes, their role in these pathologies is still poorly characterized. Here, we develop a new serum-free protocol to differentiate human iPSCs into astrocytes. Gene expression and functional assays show that our protocol consistently yields a highly enriched population of resting mature astrocytes across the thirteen hiPSC lines differentiated. Using this new model, we first highlight the importance of serum-free media for astrocyte culture to generate resting astrocytes. Second, we assess the astrocytic response to IL-1β, TNFα and IL-6, all cytokines important in neuroinflammation, such as multiple sclerosis. Our study reveals very specific profiles of reactive astrocytes depending on the triggering stimulus. This new model provides ideal conditions for in-depth and unbiased characterization of astrocyte reactivity in neuroinflammatory conditions.

overall_design: Comparison of resting astrocytes vs astrocytes exposed to serum, IL-1β, IL-6 and TNFα

first: Amandine

last: Mathias

first: Guillaume

last: Perriard

first: Mathieu

last: Canales

first: Nils

last: Jonkmans

first: Nicolas

last: Merienne

first: Cécile

last: Meunier

first: Lina

last: El Kassar

first: Anselme

middle: L

last: Perrier

first: David-Axel

last: Laplaud

first: Myriam

last: Schluep

first: Nicole

last: Déglon

first: Renaud

last: Du Pasquier


title: Targeting FOXA1-mediated repression of TGF-β signaling suppresses castration-resistant prostate cancer progression [RNA-Seq]

city: Atlanta

first: Jindan

last: Yu

state: GA

address: E330, 1760 Haygood Dr NE

department: Urology

institute: Emory University

summary: our study establishes FOXA1 as an important regulator of lineage plasticity mediated in part by TGF-β signaling and supports a novel therapeutic strategy to control lineage switching and potentially extend clinical response to antiandrogen therapies.

overall_design: RNA-seq examination of LNCaP cells with control and FOXA1 knockdown

first: Bing

last: Song


title: RNA Sequencing Gene Expression Profile of IEL Incubated In The Presence or Absence of Osteopontin

city: Nashville

first: Danyvid

last: Olivares-Villagomez

state: TN

address: 21 Ave and Garland, 811 Light Hall

institute: Vanderbilt University

summary: We report the application of RNA-Seq technology for high-throughput gene expression profiling of intestinal intraepithelial lymphocytes (IEL) that were incubated for 24 hrs in the presence or absence of recombinant osteopontin.

overall_design: Examination of gene expression profile of CD45+ IEL that were incubated for 24hrs in the presence or absence of recombinant osteopontin

first: Michael

last: Greer


title: Identification of Bmi1 regulated genes in pro-B cells

city: New York

first: David

last: Cantor

state: New York

address: 550 First Avenue

institute: NYU School of Medicine

summary: We report differences in gene expression between WT and Bmi1 KO pro-B cells.

overall_design: RNA profiles from WT and Bmi1 KO pro-B cells were generated in duplicate.

first: Gregory

last: David


title: N6-methyladenine DNA Modification in Glioblastoma [ChIP-seq, BiSulfite-seq, DIP-seq]

city: San Diego

first: Jeremy

last: Rich

state: CA

address: 9500 Gilman Drive #0695

institute: University of California, San Diego

summary: Genetic drivers of cancer can be dysregulated through epigenetic modifications of DNA. While the critical role of DNA 5-methylcytosine (5mC) in the regulation of transcription is recognized, the functions of other non-canonical DNA modifications remain obsure. Here, we report the  identification of novel N(6)-methyladenine (N6-mA) DNA modifications in human tissues and implicate this epigenetic regulation in human disease, the highly malignant brain cancer, glioblastoma. Glioblastoma upregulates N6-mA levels, which co-localize with heterochromatic histone modifications, namely H3K9me3. N6-mA levels are dynamically regulated by the DNA demethylase, ALKBH1, to transcriptionally silence oncogenic pathways through decreasing chromatin accessibility. Targeting the N6-mA regulator, ALKBH1, in patient-derived human glioblastoma models inhibited tumor cell proliferation and extended survival of tumor-bearing mice, supporting this novel DNA modification as a potential new molecular therapeutic target for glioblastoma. Collectively, our results uncover a novel epigenetic node in cancer through the DNA modification, N6-mA.

overall_design: ChIP-seq, DIPseq, and Methyl-seq of patient derived glioblastoma stem cells in hypoxia and normoxia

first: Qi

last: Xie

first: Tao

middle: P

last: Wu

first: Ryan

last: Gimple

first: Zheng

last: Li

first: Briana

last: Prager

first: Qiulian

first: Yang

first: Pengcheng

last: Wang

first: Yinsheng

middle: U

last: Gorkin

first: Cheng

last: Zhang

first: Alexis

last: Dowiak

first: Kaixuan

last: Lin

first: Chun

last: Zeng

first: Yinghui

last: Sui

first: Leo

last: Kim

first: Tyler

middle: E

last: Miller

first: Li

last: Jiang

first: Christine

last: HLee

first: Zhi

last: Huang

first: Xiaoguang

last: Fang

first: Kui

last: Zhai

first: Stephen

last: Mack

first: Maike

last: Sander

first: Shideng

last: Bao

first: Andrew

last: Sloan

middle: Z

last: Xiao


title: RNAseq analysis of Angiotensin II perfused Apolipoprotein E deficient mice reconstituted with Wild Type or Netrin-1 deficient hematopoietic stem cells

first: Bhama

last: Ramkhelawon

address: 435 East 30th - Science Building 416

department: Surgery

institute: NYU Langone Medical Center

summary: We report the transcriptomic analysis of RNA-seq of aortas isolated from WT ApoE-/- and Ntn1-/- ApoE-/- mice exposed to Ang II to uncover the mechanisms underlying the undefined role netrin-1 in AAA

overall_design: Comparison of mouse aortic samples of Apolipoprotein E deficient mice reconstituted with Wild Type or Netrin-1 deficient hematopoietic stem cells


title: Impact of Escherichia coli K12 and O18 on human platelets: effects on platelet activation, spliced platelet RNAs and proteins

city: Amsterdam

first: Myron

last: Best

address: De Boelelaan 1117

department: Neurosurgery

country: Netherlands

institute: VU University Medical Center

summary: We report RNA-sequencing data of 12 platelet samples isolated from four healthy individuals and incubated with either E. coli K12, E. coli O18 or no bacteria. This dataset highlights the differential effect of bacteria on spliced platelet RNA profiles.

overall_design: Blood platelets were isolated from whole blood in citrate-coated BD Vacutainers by standard centrifugation and multiple washing steps. Total RNA was extracted from the platelet pellet, subjected to cDNA synthesis and SMARTer amplification, fragmented by Covaris shearing, and prepared for sequencing using the TruSeq Nano DNA Sample Preparation Kit. Subsequently, pooled sample libraries were sequenced on the Illumina HiSeq 2500 platform. All steps were quality-controlled using Bioanalyzer 2100 with RNA 6000 Picochip, DNA 7500 and DNA High Sensitivity chips measurements. For further downstream analyses, reads were quality-controlled using Trimmomatic, mapped to the human reference genome using STAR, and intron-spanning reads were summarized using HTseq.

first: Aniko

last: Fejes

middle: G

first: Thomas

last: Wurdinger

last: Mannhalter


title: N6-methyladenine DNA Modification in Glioblastoma [ATAC-seq]

first: Jeremy

last: Rich

summary: Genetic drivers of cancer can be dysregulated through epigenetic modifications of DNA. While the critical role of DNA 5-methylcytosine (5mC) in the regulation of transcription is recognized, the functions of other non-canonical DNA modifications remain obscure. Here, we report the identification of novel N(6)-methyladenine (N6-mA) DNA modifications in human tissues and implicate this epigenetic regulation in human disease, the highly malignant brain cancer, glioblastoma. Glioblastoma upregulates N6-mA levels, which co-localize with heterochromatic histone modifications, namely H3K9me3. N6-mA levels are dynamically regulated by the DNA demethylase, ALKBH1, to transcriptionally silence oncogenic pathways through decreasing chromatin accessibility. Targeting the N6-mA regulator, ALKBH1, in patient-derived human glioblastoma models inhibited tumor cell proliferation and extended survival of tumor-bearing mice, supporting this novel DNA modification as a potential new molecular therapeutic target for glioblastoma. Collectively, our results uncover a novel epigenetic node in cancer through the DNA modification, N6-mA.

overall_design: ATAC-seq following knockdown of ALKBH1 in glioblastoma stem cells.

first: Qi

last: Xie

first: Tao

last: Wu

first: Ryan

last: Gimple

first: Zheng

last: Li

first: Briana

last: Prager

first: Qiulian

first: Yang

last: Yu

first: Pengcheng

last: Wang

first: Yinsheng

first: David

last: Gorkin

first: Cheng

last: Zhang

first: Alexis

last: Dowiak

first: Kaixuan

last: Lin

first: Chun

last: Zeng

last: Sui

last: Kim

middle: H

last: Lee


title: N6-methyladenine DNA Modification in Glioblastoma

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

overall_design: Refer to individual Series


title: Genome-wide RNA sequencing analysis  in Il10-/- bone marrow-derived macrophages stimulated by lipopolysaccharide

first: W. K. Eddie

last: Ip

address: 300 Cedar Street

department: Immunobiology

institute: Yale University School of Medicine

summary: We report the genome-wide RNA sequencing analysis  in Il10-/- bone marrow-derived macrophages (BMDMs) stimulated by lipopolysaccharide (LPS) where IL-10 effect in macrophage inflammatory response was examined in IL-10-deficient BMDMs upon LPS stimulation with addition of exogenous IL-10.

overall_design:
Examination of IL-10 effect in bone marrow-derived macrophages (BMDMs) in response to LPS stimulation.
To grow bone-marrow derived macrophages (BMDMs), bone marrow cells were flushed from femur and tibia bones of IL-10-deficient mice strain in C57BL/6 background between 6 and 12 weeks of age, and were grown at 37°C in a humidified incubator in RPMI-1640 medium containing L-glutamine, 10% FCS and 30% L929 supernatant (i.e. BMDM growth media) for 7-8 days.
The RNA sequencing analysis was performed separately in two groups of samples. Group 1: Il10-/- BMDMs were stimulated for 3 h without (control samples C1 and C2) or with 100 ng/ml of lipopolysaccharide (LPS)(samples C3 and C4), 100 ng/ml of IL-10 (samples D1 and D2) or both (samples D3 and D4). Group 2: Il10-/- BMDMs were stimulated without (control samples K1 and K2) or with 100 ng/ml of LPS (for 6 h: samples K3 and K4; for 12 h: samples K9 and K10), 100 ng/ml of IL-10 (for 6 h: samples K7 and K8; for 12 h: samples K13 and K14) or both (for 6 h: samples K5 and K6; for 12 h: samples K11 and K12).

first: Ruslan

last: Medzhitov


title: Combination immunotherapy can rescue CD8+ T cell dysfunction and maintain memory phenotype in cancer

city: Tarrytown

first: Wen

address: 777 Old Saw Mill River Road

institute: Regeneron Pharma.

summary: In this study we unveiled specific molecular and cellular mechanisms driving the potent synergism of a coinhibitory antagonist (anti-PD-1 Ab) and a costimulatory agonist (anti-GITR Ab), a modality currently in early clinical testing, and elucidated the parameters required for durable anti-tumor responses.

overall_design: Single cell sequencing on CD8 T cells sorted from MC38 mouse colon tumors and spleens treated with Isotype control, aGITR mono, aPD1 mono and aGITR+aPD1 combo on day 8 and 11. MC38 cells were injected subcutaneously into mice.

first: Bei


title: RNA-seq of CD11b DCs from mice with established pulmonary fibrosis

city: Hannover

middle: S.

last: DeLuca

address: Carl-Neuberg-Str 1

department: Biomedical Research in End-stage and Obstructive Lung Disease Hannover

institute: Hannover Medical School

summary: DNA-digested RNA samples were prepared from CD11b DCs which were purified from the lungs of control vector or AdTGF-β1 exposed WT mice (day 14 post-treatment) by high-speed cell sorting.

overall_design: Six control samples and six samples from AdTGF-β1 exposed  mice

first: Meritxell

last: Tort Tarrés

first: Ulrich

middle: A

last: Maus


title: Plasmodium-specific atypical memory B cells are short-lived activated B cells

city: London

first: Damián

last: Perez-Mazliah

address: 1 Midland Road

institute: The Francis Crick Institute

summary: Chronic infections such as HIV, tuberculosis and malaria in humans are associated with the appearance of atypical memory B cells in peripheral blood. It has been suggested that these B cells do not function normally as memory cells, and thus may be responsible for poor acquisition of immunity and maintenance of chronic infections. Studies on these cells in human infections are limited by the lack of accessibility to lymphoid organs, and relevant mouse models would be valuable to investigate their development, functional capacities, and role.      To investigate Plasmodium-specific memory B-cell responses during malaria, we generated an immunoglobin heavy chain knock-in mouse with a B-cell receptor that recognizes the merozoite surface protein (MSP)-1 of the rodent malaria parasite, Plasmodium chabaudi. Using this mouse and a P. chabaudi infection initiated by infected mosquito bites we show that antigen-specific B cells with many characteristics of human atypical memory B cells are generated. These cells are immunoglobulin class-switched and express, among others, the cell surface molecules CD11c, CD11b, FCRL5, and some inhibitory receptors including PD1 and LAIR-1, as well as the transcription factor T-bet. Antigen-specific atypical memory B cells are detected side-by-side with classical memory B cells during chronic blood-stage infection. Whereas classical memory B cells persist after complete infection clearance, atypical memory B cells are short-lived and disappear from the spleen at the resolution of chronic infection. Short-lived Plasmodium-specific atypical B cells also appear transiently after immunization with a TLR7/8 ligand and MSP-1.  Our data suggest that these atypical memory B cells are not a subset of memory B cells, but rather antigen-experienced activated cells, and part of a normal ongoing response. Their persistence over weeks in malaria and other infections may be a consequence of continued and chronic antigenic stimulation.

overall_design: Antigen-specific B cells (CD19+B220+) were flow cytometry sorted from the spleen of C57BL/6J mice infected with Plasmodium chabaudi at different time points post-infection. Total RNA was extracted, and submitted to mRNAseq analysis.

last: Pérez-Mazliah

first: Peter

middle: J

last: Gardner

first: Edina

last: Schweighoffer

first: Sarah

last: McLaughlin

first: Caroline

last: Hosking

first: Irene

last: Tumwine

first: Randall

last: Davis

first: Alexandre

last: Potocnik

first: Victor

last: Tybulewicz

first: Jean

last: Langhorne


title: N6-methyladenine DNA Modification in Glioblastoma [RNA-seq]

first: Jeremy

last: Rich

overall_design: RNA-seq of patient derived glioblastoma stem cells in hypoxia and normoxia

first: Qi

last: Xie

first: Tao

last: Wu

first: Ryan

middle: C

last: Gimple

first: Zheng

last: Li

first: Briana

last: Prager

first: Qiulian

first: Yang

last: Yu

first: Pengcheng

last: Wang

first: Yinsheng

first: David

last: Gorkin

first: Cheng

last: Zhang

first: Alexis

last: Dowiak

first: Kaixuan

last: Lin

first: Chun

last: Zeng

first: Yinghui

last: Sui

first: Leo

last: Kim

first: Tyler

last: Miller

first: Li

last: Jiang

first: Christine

last: HLee

first: Zhi

last: Huang

first: Xiaoguang

last: Fang

first: Kui

last: Zhai

first: Stephen

last: Mack

first: Maike

last: Sander

first: Shideng

last: Bao

first: Andrew

last: Sloan

last: Xiao

middle: N


title: Genome-wide maps of H3K27me3 in chromatin state in embryonic stem cells differentiated motor neurons

city: Taipei

first: Ya-Ping

last: Yen

address: 128 Academia Road, Section 2, Nankang

department: Institute of molecular biology

country: Taiwan

institute: Academia Sinica

summary: In this experiment, we sought to identify how the distribution of H3K27me3 upon Meg3 KD

overall_design: 2 lines (WT ESC, Meg3 KD ESC)

first: Jun-An

last: Chen


title: A stably self-renewing adult blood-derived induced neural stem cell exhibiting patternability and epigenetic rejuvenation

city: Bonn

first: Andreas

last: Till

state: NRW

address: Sigmund-Freud-Str. 25

department: Institute of Reconstructive Neurobiology

institute: University of Bonn

summary: Recent reports suggest that induced neurons (iNs), but not induced pluripotent stem cell (iPSC)-derived neurons largely preserve age-associated traits. Here we report on the extent of preserved epigenetic and transcriptional aging signatures in directly converted induced neural stem cells (iNSCs). Employing restricted and integration-free expression of SOX2 and c-MYC we generate a fully functional, bona fide NSC population from adult blood cells that remains highly responsive to regional patterning cues. Upon conversion, low passage iNSCs display a profound loss of age-related DNA methylation signatures, which further erode across extended passaging, thereby approximating the DNA methylation age of isogenic iPSC-derived neural precursors. This epigenetic rejuvenation is accompanied by a lack of age-associated transcriptional signatures and absence of cellular aging hallmarks. We find iNSCs to be competent for modeling pathological protein aggregation and for neurotransplantation, depicting blood-to-NSC conversion as a rapid alternative route for both disease modeling and neuroregeneration.

overall_design: 19 human cell samples representing either EPC, iNSC or smNPC were used for identification of differentially expressed genes by RNAseq

first: Chao

last: Sheng

first: Johannes

last: Jungverdorben

first: Hendrik

last: Wiethoff

first: Qiong

last: Lin

first: Lea

last: Flitsch

first: Daniela

last: Eckert

first: Matthias

last: Hebisch

first: Julia

last: Fischer

first: Jaideep

last: Kesavan

first: Beatrice

last: Weykopf

first: Linda

last: Schneider

first: Dominik

last: Holtkamp

first: Heinz

last: Beck

first: Ullrich

last: Wüllner

first: Michael

last: Ziller

first: Wolfgang

last: Wagner

last: Peitz

first: Oliver

last: Brüstle