title: Assessment of the impact of the TLR3 L412F variant in terms of TLR3-sensitive transcript induction

first: Gaspard

summary: we assessed the impact of TLR3 L412F at endogenous cellular levels upon double stranded RNA (dsRNA) stimulation, by performing RNA-sequencing in primary fibroblasts from individuals homozygous for the ancestral allele (n =2) or homozygous for TLR3 L412F (n = 4) upon extracellular Poly(I:C) stimulation that activates the TLR3 pathway. The average response of TLR3 L412F homozygotes was significantly decreased (mean Δ log2 fold-change = 0.93; Wilcoxon p <10-16) compared to that of cells with the ancestral allele, approaching that of TLR3-deficient cells, used as negative control.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for primary human fibroblasts of individuals with the TLR3 412F derived allele and its ancestral complementary allele at the same genomic position

first: Kerrouche

last: Nacim

first: Rinchai

last: Darawan


title: RNA-seq of primary mouse hepatocyte, primary mouse adipocyte, and C2C12 cell line treated with olanzapine and/or either calcifediol or calcitriol

status: Public on Jan 13 2023

city: Kyoto

first: Kazuki

last: Nagayasu

address: 46-29 Yoshidashimoadachicho, Sakyo

department: Graduate School of Pharmaceutical Sciences

country: Japan

institute: Kyoto University

type: Expression profiling by high throughput sequencing

summary: Olanzapine is considered to induce dyslipidemia as an adversary effect in clinical practice. Critically, raised low-density lipoprotein levels and lowered high-density lipoprotein levels in the blood of patients are detected. The present study utilized three independent sources of clinical big data to analyze the drugs potent to prevent olanzapine-induced dyslipidemia, and vitamin D was found to be effective. To clarify the molecular mechanism of the influence of olanzapine and vitamin D, the culture of three cholesterol metabolism-related cells of mice, primary hepatocyte, primary adipocyte, and C2C12 cells (myocyte) were introduced to treat with olanzapine and vitamin D primary metabolites like calcifediol and calcitriol. RNA-seq was performed on these three types of cells to uncover the direct effects of olanzapine and vitamin D in cholesterol metabolism.

overall_design: mRNA profiles of primary mouse hepatocytes, primary mouse adipocytes, and C2C12 cell line under vehicle(DMSO), olanzapine, olanzapine + calfediol, or olanzapine + calcitriol treatment

first: ZIJIAN

last: Zhou

first: Shuji

last: Kaneko


title: Coordinated histone variant H2A.Z eviction and H3.3 deposition control plant thermomorphogenesis

city: Beijing

first: Fengyue

last: Zhao

address: No. 1 West Beichen Road, Chaoyang District

country: China

institute: Institute of Genetics and Developmental Biology Chinese Academy of Sciences

type: Genome binding/occupancy profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Coordinated histone variant H2A.Z eviction and H3.3 deposition control plant thermomorphogenesis [RNA-seq I]

summary: Plants can sense temperature changes and adjust their development and morphology accordingly in a process called thermomorphogenesis. This phenotypic plasticity implies complex mechanisms regulating gene expression reprogramming in response to environmental alteration. Histone variants contribute to the chromatin dynamics and transcriptional control, yet how their deposition/eviction modulates transcriptional changes induced by environmental cues remains elusive. In Arabidopsis thaliana, temperature elevation-induced transcriptional activation at thermo-responsive genes entails the chromatin eviction of a histone variant H2A.Z by INO80, which is recruited to these loci via interacting with a key thermomorphogenesis regulator PHYTOCHROME-INTERACTING FACTOR 4 (PIF4). Here, we show that both INO80 and the deposition chaperones of another histone variant H3.3 associate with EARLY FLOWERING7 (ELF7), a critical component of the transcription elongation factor polymerase-associated factor 1 complex (PAF1c). H3.3 promotes thermomorphogenesis and the high temperature-enhanced RNA Pol II transcription at PIF4 targets, and it is broadly required for the H2A.Z removal-induced gene activation. Reciprocally, INO80 and ELF7 regulate H3.3 deposition, and are necessary for the high temperature-induced H3.3 enrichment at PIF4 targets. Our findings demonstrate close coordination between H2A.Z eviction and H3.3 deposition in gene activation induced by high temperature, and pinpoint the importance of histone variants dynamics in transcriptional regulation.

overall_design: Transcriptome profiles were examined by RNA-seq in WT (Col), h3.3kd and elf7-3 at 21°C or 27°C

first: Danhua

last: Jiang


status: Public on Jan 17 2023

city: Boston

first: Kasper

last: Lage

state: MA

address: 185 Cambridge St

country: USA

institute: Massachusetts General Hospital

summary:
Pintacuda G*, Hsu YH*, Tsafou K, Li KW, Martín JM, Riseman J, Biagini JC, Ching JKT, Mena D, Gonzalez-Lozano MA, Egri SB, Jaffe J, Smit AB, Fornelos N, Eggan KC, Lage K. Protein interaction studies in human induced neurons indicate convergent biology underlying autism spectrum disorders. Cell Genomics (2023). [DOI: https://doi.org/10.1016/j.xgen.2022.100250]

Autism spectrum disorders (ASD) have been linked to genes with enriched expression in the brain, but it is unclear how these genes converge into cell-type-specific networks. We built a protein-protein interaction network for 13 ASD-associated genes in human excitatory neurons derived from induced pluripotent stem cells (iPSCs). The network contains newly reported interactions and is enriched for genetic and transcriptional perturbations observed in individuals with ASDs. We leveraged the network data to show that the ASD-linked brain-specific isoform of ANK2 is important for its interactions with synaptic proteins and to characterize a PTEN-AKAP8L interaction that influences neuronal growth. The IGF2BP1-3 complex emerged as a convergent point in the network that may regulate a transcriptional circuit of ASD-associated genes. Our findings showcase cell-type-specific interactomes as a framework to complement genetic and transcriptomic data, and illustrate how both individual and convergent interactions can lead to biological insights into ASDs.

overall_design: RNA-seq of human iPSC-derived induced neurons at 3 differentiation time points (days 0, 21, and 51)


title: scRNA-Seq to study the impact of HIV-1 on DC biology [PreDC_Single_Cell_Patient]

city: Paris

first: Philippe

last: Benaroch

address: 12, rue Lhomond

department: INSERM U932 Immunity and Cancer

country: France

institute: Institut Curie

summary: Primary DC from HIV-1-infected patient during primo-infection were isolated to study their transcriptom by scRNA-seq

overall_design: Cells were sorted from PMBCs to obtain pre-DC, cDC1, cDC2 and pDC. The 4 population were mixed and run onto the Chromium (10X Genomics)

last: BENAROCH

first: Nicolas

last: RUFFIN

first: Francesca

last: Nadalin


title: Programming to S1PR1+ Endothelial Cell Promotes Restoration of Lung Vascular Integrity

status: Public on Jan 15 2023

city: Chicago

first: Md Zahid

last: Akhter

state: IL

address: 835 S Wolcott Ave

department: Pharmacology

institute: University of Illinois at Chicago

summary: Increased endothelial permeability and failure to repair is the hallmark of several vascular diseases including acute lung injury (ALI).  However, little is known about the intrinsic pathways that activate endothelial cell (EC) regenerative programs and thereby tissue repair. Studies have invoked a crucial role of sphingosine-1-phosphate (S1P) in resolving endothelial hyperpermeability through activation of the G-protein coupled receptor, sphingosine-1-phosphate receptor 1 (S1PR1). Here, we addressed mechanisms of generation of S1PR1+ EC, which may prevent endothelial injury. Studies were made using inducible EC-S1PR1-/- (iEC-S1PR1-/-) mice and S1PR1-GFP reporter mice to trace the generation of S1PR1+ EC. We observed in a mouse model of endotoxemia that S1P generation induced the programming of S1PR1lo to S1PR1+ EC, which comprised 80% of lung EC. The transition of these cells was required for reestablishing the endothelial barrier. We also observed that conditional deletion of S1PR1 in EC increased vascular permeability. RNA-seq analysis of S1PR1+ EC showed enrichment of genes regulating S1P synthesis and transport, sphingosine kinase 1 (SPHK1) and SPNS2, respectively. The activation of transcription factors EGR1 and STAT3 were essential for transcribing SPHK1 and SPNS2, respectively, to increase S1P production that served to amplify S1PR1+ EC transition. Transplantation of S1PR1+ EC into injured lung vasculature restored endothelial integrity. Our findings show that generation of a S1PR1+ EC population activates the endothelial regenerative program mediating vascular endothelial repair, thus raising the possibility of harnessing this pathway to restore vascular homeostasis in inflammatory injury.

overall_design: 4 samples, RNA-seq

first: Jagdish

middle: C

last: Chandra

first: A

middle: R

last: Vijay

first: Richard

middle: L

last: Proia

first: Asrar

middle: B

last: Malik

first: Dolly

last: Mehta


title: scRNA-Seq to study the impact of HIV-1 on DC biology [PreDC_Single_Cell_Exp2]

summary: Pre-DC have been initially described through their ontogeny. Our lab reported for the first time a pre-DC functional specificity in the context of HV-1 capture, infection and in vitro transmission as a consequence of their constitutive expression of Siglec-1. However, pre-DC immune response to viral exposure remained to be studied. This study aim to decipher innate immune response of pre-DC and cDC2 when exposed to HIV-1 in the presence or not of Vpx.

overall_design: Pre-DC and cDC2 were cultured with HIV-1 NL-AD8 complemented or not with Vpx for 24h. Pre-DC cultured in mock medium were used as controls.


title: scRNA-Seq to study the impact of HIV-1 on pre-DC biology [PreDC_Single_Cell_Exp1]

summary: Pre-DC have been initially described through their ontogeny. Our lab reported for the first time a pre-DC functional specificity in the context of HV-1 capture, infection and in vitro transmission as a consequence of their constitutive expression of Siglec-1. However, pre-DC immune response to viral exposure remained to be studied. This study aim to decipher innate immune response of pre-DC when exposed to HIV-1.

overall_design: Pre-DC were cultured with HIV-1 NL-AD8 complemented with Vpx for 12 or 24h. Pre-DC cultured in mock medium were used as controls, as well as pre-DC exposed to HIV-1 in the presence of  azidothymidine and neverapin to inhibit retrotranscription. A CpG-A stimulated sample was also included as control.


title: NSD2 E1099K drives relapse in pediatric acute lymphoblastic leukemia by disrupting 3D chromatin organization

city: New York

first: Sonali

last: Narang

state: NY

address: 435 east 30th street

institute: NYU Langone

summary: The NSD2 p.E1099K (EK) mutation has been shown to be enriched in patients with relapsed ALL indicating a role in clonal evolution and drug resistance. We previously demonstrated that the impact of EK is highly cell context dependent. To uncover 3D chromatin architecture-related mechanisms underlying drug resistance, we performed Hi-C on three B-ALL cell lines heterozygous for NSD2 EK (RS4;11, RCH-ACV, SEM) and assessed changes upon knockdown.

overall_design: We performed Hi-C on three B-ALL cell lines heterozygous for NSD2 EK (RS4;11, RCH-ACV, SEM) and assessed changes upon knockdown for a total of 6 cell lines.

first: Nikki

middle: A

last: Evensen

first: Jason

last: Saliba

first: Joanna

last: Pierro

first: Mignon

last: Loh

first: Patrick

last: Brown

first: Pandurang

last: Kolekar

first: Heather

last: Mulder

first: Ying

last: Shao

first: John

last: Easton

first: Xiaotu

last: Ma

first: Aristotelis

last: Tsirigos

first: William

last: Carroll


title: Epigenetic modules governing skin epidermal homeostasis [Dlx3 WT and KO primary cells]

city: Bethesda

first: Stephen

last: Brooks

state: MD

address: 50 SOUTH DR, RM 1140

department: Biodata Mining and Discovery Section

institute: NIAMS/NIH

summary: Skin homeostasis is guided by spatiotemporal regulation of gene expression, establishing each stage of keratinocyte differentiation. The current study presents transcriptomic and chromatin profiling for the proliferating (basal) and differentiated (suprabasal) cell populations derived from neonate mice (p0-p2) skin epidermis. This multi-omic approach will enable idenitification of cell specific epidermal cross-talk central to the equlibirum.

overall_design: Transcriptomic profiling for adeno-virus transduced (either Ad-GFP or Ad-Dlx3) primary cells cultured from transgenic Dlx3 wild-type and knock-out pups (p0-p1)

first: Subhashree

last: Nayak

first: Stefania

last: Dell O'rso

first: Maria

middle: I

last: Morasso


title: Epigenetic modules governing skin epidermal homeostasis [neonate skin epidermis]

overall_design: Transcriptomic profiling for basal and suprabasal cells in mouse neonate skin epidermis (Fvb/N strain and Dlx3 transgenic mice)


title: Transcriptome analysis of Zeugodacus cucurbitae in response to 60Cobalt gamma radiation.

city: Haikou

first: Shakil

last: Ahmad

state: Hainan

address: Hainan University, Haikou, Hainan Province, 570228

department: School of Plant Protection

institute: Hainan University

summary: The goal of the current study is to know the possible molecular mechanism of the effects of 60Co radiation stress when eggs of Z. cucurbitae were exposed to the radiation dose of 50 Gy. A comparative transcriptome analysis was performed to investigate the global gene expression changes in 3rd instar of Z. cucurbitae emerged from the irradiated eggs. Hence we described the Transcriptome of Z. cucurbitae using Illumina Hiseq 4000 platform. To identify the DEGs between irradiated and non-irradiated flies, we performed a DGE (Digital Gene Expression) analysis in the non-irradiated group and compared this analysis with flies after the irradiation. This approach was a shortcut to identify the genes involved in the irradiation-induced developmental defects and growth regulation in Z. cucurbitae. Based on searches against databases, deferentially expressed genes (DEGs) were classified and enriched in different functional categories and pathways.

overall_design: Cobalt-60 radiation effects on gene expression profile of melon fly, Z. cucurbitae.

first: Momana

last: Jamil

first: Coline C.

last: Jaworski

first: Yanping

last: Luo


title: RNA-Seq to study the response of HIV-1 infection

first: Philippe

last: Benaroch


title: Bulk RNA-Seq to study the response of CD11c+ and CD11c- Axl+DC to HIV-1 infection

summary: Determine if dual responses observed in Axl+DC are due to CD11c heterogeneity

overall_design: CD11c+ and CD11c- Axl+DC cells were cultured with HIV-1 NL-AD8 complemented with Vpx for 24h. Cells cultured in mock medium were used as a control, as well as cells exposed to HIV-1 in the presence of  azidothymidine (Azt) and neverapin (Nvp) to inhibit retrotranscription.

last: BENAROCH

first: Ouardia

last: Ait-Mohamed

first: Nicolas

last: RUFFIN

first: Flavien

last: BROUILLER


title: Bulk RNA-Seq to study the response of cDC2 and Axl+DC to HIV-1 infection

summary: Axl+DC have been initially described through their ontogeny. Our lab reported for the first time an Axl+ DC functional specificity in the context of HV-1 capture, infection and in vitro transmission as a consequence of their constitutive expression of Siglec-1. However, Axl+DC immune responses to viral exposure remained to be studied. This study aim to decipher innate immune response of Axl+DC  when exposed to HIV-1 in comparison to other DC subtypes.

overall_design: cDC2 and Axl+DC cells were cultured with HIV-1 NL-AD8 complemented with Vpx for 24h. Cells cultured in mock medium were used as a control, as well as cells exposed to HIV-1 in the presence of  azidothymidine (Azt) and neverapin (Nvp) to inhibit retrotranscription. Cells stimulated with TLR-L were also included .


title: Autoantibodies are highly prevalent in non-SARS-CoV-2 respiratory infections and critical illness [CTD]

status: Public on Jan 12 2023

city: Stanford

first: Allan

last: Feng

state: CA

address: 269 Campus Dr

department: Imm/Rheum

institute: Stanford School of Medicine

summary: We used protein arrays to measure IgG autoantibodies associated with Connective Tissue Diseases (CTDs) and Anti-Cytokine Antibodies (ACA) in patients with non-COVID-19 infections such as influenza

platform_organism:
Escherichia coli
Triticum aestivum
Spodoptera frugiperda
Homo sapiens
Sus scrofa
Bos taurus
Capra hircus

overall_design: Protein arrays were constructed by coupling antigens to carboxylated magnetic beads. Arrays consisting of conjugated beads were then used to probe patient serum or plasma samples, healthy control samples, and autoimmune prototype samples. Samples were run in duplicate except one sample (UP67 D7) which was run in quadruplicate. for A Luminex FLEXMAP 3D® system was used to quantitatively measure autoantibody reactivity in each sample in units of mean flourescent intensity (MFI). Positive antibody hits were statistically identified by a 5 standard deviation cutoff calculated from the MFI of healthy controls.

first: Emily

middle: Y

last: Yang

first: Andrew

last: Moore

first: Shaurya

last: Dhingra

first: Sarah

middle: E

last: Chang

first: Xihui

last: Yin

first: Ruoxi

last: Pi

first: Elisabeth

last: Mack

first: Sara

last: Völkel

first: Reinhard

last: Geßner

first: Margrit

last: Gündisch

first: Andreas

last: Neubauer

first: Harald

last: Renz

first: Sotirios

last: Tsiodras

first: Paraskevi

last: Fragkou

first: Adijat

last: Asuni

first: Joseph

last: Levitt

first: Jennifer

middle: G

last: Wilson

first: Michelle

middle: W

last: Leong

middle: H

last: Lumb

first: Rong

last: Mao

first: Kassandra

last: Pinedo

first: Jonasel

last: Roque

first: Christopher

middle: M

last: Richards

first: Mikayla

last: Stabile

first: Gayathri

last: Swaminathan

last: Salagianni

first: Vasiliki

last: Triantafyllia

first: Wilhelm

last: Bertrams

first: Catherine

last: Blish

first: Jan

last: Carette

last: Frankovich

first: Eric

last: Meffre

first: Kari

last: Nadeau

first: Upinder

last: Singh

first: Taia

middle: T

last: Wang

first: Eline

last: Luning Prak

first: Susanne

last: Herold

first: Evangelos


title: Autoantibodies are highly prevalent in non-SARS-CoV-2 respiratory infections and critical illness

first: Allan

last: Feng


title: Multimodal single nuclei profiling of human macular and peripheral retinal pigment epithelial cells

city: Iowa City

first: Nathaniel

middle: Kevin

last: Mullin

state: IA

address: 375 Newton Road

institute: University of Iowa

summary: We sought to understand how the RPE confers region-specific disease susceptibility in the retina by examining heterogeneity within human donor RPE. We profiled RPE nuclei from the macular and peripheral retina using joint single-cell RNA and ATAC sequencing.

overall_design: RPE nuclei were isolated from macular and peripheral regions of the posterior pole from four healthy human donors. Joint profiling of nuclear chromatin and transcript abundance was performed.

middle: K

first: Robert

middle: F

last: Mullins


title: Autoantibodies are highly prevalent in non-SARS-CoV-2 respiratory infections and critical illness [ACA]

platform_organism:
Escherichia coli
Homo sapiens

first: Emily

last: Yang

first: Andrew

last: Moore

first: Shaurya

last: Dhingra

first: Sarah

last: Chang

first: Xihui

last: Yin

first: Ruoxi

last: Pi

first: Elisabeth

last: Mack

first: Sara

last: Völkel

first: Reinhard

last: Geßner

first: Margrit

last: Gündisch

first: Andreas

last: Neubauer

first: Harald

last: Renz

first: Sotirios

last: Tsiodras

first: Paraskevi

last: Fragkou

first: Adijat

last: Asuni

first: Joseph

last: Levitt

first: Jennifer

last: Wilson

first: Michelle

last: Leong

last: Lumb

first: Rong

last: Mao

first: Kassandra

last: Pinedo

first: Jonasel

last: Roque

first: Christopher

last: Richards

last: Stabile

first: Maria


title: Impact of post-lysis stopping point prior to reverse transcription

city: Berkeley

first: Iain

middle: Christopher

last: Clark

address: 374 Stanley Hall

institute: University of California, Berkeley

summary: We used human + mouse cell mixtures to demonstrate the purity of PIP-seq single cell RNA-sequencing

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: PIP-seq of HEK/3T3 cells

first: Kristina

last: Fontanez


title: Analysis of hashing quality in a PBMC sample

summary: We used PIP-seq single cell RNA-sequencing to understand hashing efficiency in a standard set of healthy human PBMCs

overall_design: PIP-seq of PBMCs with hashing

first: Pabodha

last: Hettige

first: Trinity

last: Smithers

first: Corey

last: Hayford

first: Adam

last: Abate


title: The little skate genome and the evolutionary emergence of wing-like fin appendages [Hi-C Skate stage 31]

city: Sevilla

first: Juan

middle: J.

last: Tena

address: Univ. Pablo Olavide, Ctra. Utrera km1

country: Spain

institute: CABD/CSIC

summary: While retaining ancestral morphological and genomic traits, skates evolved a novel body plan with remarkably enlarged wing-like fins that allowed skates to thrive in benthic environments, but their molecular underpinnings remain elusive. Here we investigate the origin of this phenotypical innovation by assembling a high-quality chromosome-scale genome sequence for the little skate Leucoraja erinacea and by generating extensive regulatory profiling datasets in developing fins (gene expression, chromatin occupancy and conformation). We show that despite their derived morphology, the skate genome retains multiple features of the ancestral jawed vertebrate genome.

overall_design: HiC experiments in skate fins samples

first: Ferdinand

last: Marlétaz

first: Elisa

last: de la Calle-Mustienes

first: Rafael

middle: D

last: Acemel

first: Tetsuya

last: Nakamura

first: Christina

last: Paliou

first: Silvia

last: Naranjo

first: Pedro

last: Manuel Martínez-García

first: Ildefonso

last: Cases

first: Victoria

last: Sleight

first: Christine

last: Hirschberger

first: Ali

last: Andrescavage

first: Marina

last: Marcet-Houben

first: Ozren

last: Bogdanovic

first: Liyan

last: Yang

first: Lourdes

last: Gallardo-Fuentes

first: Ismael

last: Sospedra

first: Javier

last: Lopez-Rios

first: Fabrice

last: Darbellay

first: Axel

last: Visel

first: Job

last: Dekker

first: Neil

last: Shubin

first: J

last: Gillis

first: Toni

last: Gabaldón

middle: J

first: Dario

last: Lupianez

first: Daniel

middle: S

last: Rokhsar

first: José

last: Luis Gómez-Skarmeta


title: Cross-Platform Comparison

first: Iain

last: Clark

first: Kristina

last: Fontanez


title: Analysis of cell type heterogeneity in a large PBMC sample

summary: We used PIP-seq single cell RNA-sequencing to study single cells from a standard set of healthy human PBMCs

overall_design: PIP-seq of PBMCs

first: Ahmad

last: Osman

first: Chris

last: D'Amato

first: Corey

last: Hayford

first: Adam

last: Abate


title: Single-cell RNA based phenotyping reveals a pivotal role of thyroid hormone receptor alpha for hypothalamic development

city: Lübeck

first: Varun

middle: K A

last: Sreenivasan

state: Schleswig Holstein

address: Gebaude 67, BMF, 1.OG Links, Marie-Curie-Strasse,

department: Institute of Human Genetics

country: Germany

summary: Here we used single-nucleus RNA sequencing to obtain an unbiased view on the importance of TRɑ1 for hypothalamic development and cellular diversity. Sc-RNA-seq of Hypothalamus from wild type (WT) and TRɑ1R384C (TRɑ1+m) were performed.

overall_design: In total, there are 4 sequenced samples (2 x WT and 2 x TRɑ1+m). Each of these samples contains nuclei pooled from 3 mice (of the same genotype) in order to average out some of the biological variability between mice.

middle: A

first: Riccardo

last: Dore

first: Julia

last: Resch

last: Maier

first: Carola

last: Dietrich

first: Jana

last: Henck

first: Saranya

last: Balachandran

first: Jens

last: Mittag

first: Malte

last: Spielmann


title: Combinatorial treatment rescues tumour-microenvironment-mediated attenuation of MALT1 inhibitors in B-cell lymphomas

city: Ithaca

first: Lauren

last: Walter

address: 161 Weill Hall

department: Biomedical Engineering

institute: Cornell University

summary: Activated B cell-like diffuse large B cell lymphomas (ABC-DLBCLs) arise from B cell follicles of secondary lymphoid organs and are among the most aggressive DLBCLs. ABC-DLBCLs are characterized by constitutive activation of NF-ĸB driven by activation of the B cell receptor (BCR) and toll-like receptor (TLR) pathways, often due to activating mutations. The goal of the current RNA Sequencing study was to understand the role of select bioadhesive extracellular matrix ligands and cell-based ligands in regulating the gene expression in ABC-DLBCL cells.

overall_design: Samples are bulk RNA-sequencing libraries from organoids fabricated with 40,000 HBL1 cells with or without 40,000 CD40L presenting stromal cells. The control matrix is REDV and the tested conditions were REDV+CD40L and GFOGER. There are three biological replicates per condition.

first: Ankur

last: Singh

first: Zhe

last: Zhong

first: Benjamin

last: Cosgrove


title: SMAD3 promotes the expression and activity of androgen receptor in prostate cancer [CUT&RUN]

city: Baltimore

first: Jianfei

last: Qi

address: 655W baltimore street

department: Biochemistry and Molecular Biology

institute: University of Maryland

summary: Overexpression of androgen receptor (AR) is the primary cause of castration-resistant prostate cancer, although mechanisms upregulating AR transcription in this context are not well understood. Our RNAseq studies revealed that SMAD3 knockdown decreased levels of AR and AR target genes, whereas SMAD4 or SMAD2 knockdown had little or no effect. ChIP-seq analysis showed that SMAD3 knockdown decreased global binding of AR to chromatin. Mechanistically, we show that SMAD3 binds to intron 3 of the AR gene to promote AR expression. Targeting these binding sites by CRISPRi reduced transcript levels of AR and AR targets. In addition, ~50% of AR and SMAD3 ChIP-seq peaks overlapped, and SMAD3 may also cooperate with or co-activate AR for AR target expression. Functionally, AR re-expression in SMAD3-knockdown cells partially rescued AR target expression and cell growth defects. The SMAD3 peak in AR intron 3 overlapped with H3K27ac ChIP-seq and ATAC-seq peaks in datasets of prostate cancer. AR and SMAD3 mRNAs were upregulated in datasets of metastatic prostate cancer and CRPC compared with primary prostate cancer. A SMAD3 PROTAC inhibitor reduced levels of AR, AR-V7 and AR targets in prostate cancer cells. This study suggests that SMAD3 could be targeted to inhibit AR in prostate cancer.

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for SMAD3, AR, H3K4me1, and H3K27ac in control or SMAD3-KD RV1 cells.

first: Hee-Young

last: Jeon


title: SMAD3 promotes the expression and activity of androgen receptor in prostate cancer.

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

overall_design: Refer to individual Series


title: Analysis of mixed phenotype acute leukemia

first: Iain

last: Clark

summary: We used PIP-seq single cell RNA-sequencing to study MPAL from two patients before and after treatment

overall_design: PIP-seq of dissociated breast tissue

first: Cathy

last: Smith


title: SMAD3 promotes the expression and activity of androgen receptor in prostate cancer [RNA-seq]

overall_design: Comparative gene expression profiling analysis of RNA-seq data for pLKO.1, sh-SMAD3, sh-SMAD2, sh-SMAD4 in RV1 cells


title: CROP-seq + PIP-seq

summary: We used PIP-seq with a CROP-seq library to evaluate the feability of PIP-seq for large pooled CRISPR screens

overall_design: K562 CRISPRi cells were cultured in RPMI-1640 (Gibco #11875093) with 10% FBS (Thermo Fisher Scientific, #10438026) and 1% penicillin/streptomycin (Thermo Fisher Scientific, #15140148) in an incubator at 37°C with 5% CO2. K562 CRISPRi cells were transduced with a lentivirus library containing 138 sgRNA (Jost et al 2020) at a multiplicity of infection of 0.1. Lentivirus infected cells (BFP+) were sorted to high purity using a BD FACS Aria III (100 µMnozzle) and processed according to the PIP-seq scRNA-seq workflow.


title: Mouse Human Purity mixing studies

first: Kristina

last: Fontanez


title: RhoJ controls EMT associated resistance to chemotherapy

city: Bruxelles

first: Yura

last: Song

address: 808, route de Lennik

country: Belgium

institute: Université Libre de Bruxelles

summary: To identify potential mechanisms by which EMT tumour cells are resistant to  chemotherapy, we assessed the expression of putative mediators of resistance to  therapy in Epcam+ and Epcam- tumour cells from skin squamous cell carcinoma.                                                                                To determine how RhoJ impacts the transcriptional landscape of Epcam- tumour cells, we performed RNA seq of sh-RNA RhoJ knock-down Epcam- tumour cells.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for FACS isolated Epcam+ or Epcam- YFP+ tumour cells from Lgr5CreER/KRasG12D/p53cKO/ Rosa-YFP mice; Comparative gene expression profiling analysis of RNA-seq data for Epcam- cells grown in culture and transduced with RhoJ sh-RNA or control sh-RNA. 2 cell lines were studied in each condition.

first: Maud

last: Debaugnies

first: Cédric

last: Blanpain


title: PIPseq on Gefitinib sensitive and resistant cell lines

summary: We used PIP-seq single cell RNA-sequencing to study the response of PC9 and H1975 to Gefitinib

first: Chris

last: D’Amato


title: Analysis of cell type heterogeneity in breast tissue.

summary: We used PIP-seq single cell RNA-sequencing to study single cells from dissociated breast tissue

first: Jesse

middle: Q

last: Zhang

first: Kiet

last: Phong

first: Zev

last: Gartner

first: Adam

last: Abate


title: Microfluidics-free single-cell genomics with templated emulsification


title: The little skate genome and the evolutionary emergence of wing-like fin appendages

first: Juan

last: Tena


title: Analysis of cell type heterogeneity in breast tissue


title: The little skate genome and the evolutionary emergence of wing-like fin appendages [Hi-C]

overall_design: ATACseq, RNAseq, HiC and HiChIP experiments in skate fins samples


title: The little skate genome and the evolutionary emergence of wing-like fin appendages [HiChIP]

first: Ferdinand

last: Marlétaz

first: Elisa

last: de la Calle-Mustienes

first: Rafael

last: Acemel

first: Tetsuya

last: Nakamura

first: Christina

last: Paliou

first: Silvia

last: Naranjo

first: Pedro

last: Martínez-García

first: Ildefonso

last: Cases

first: Victoria

last: Sleight

first: Christine

last: Hirschberger

first: Ali

last: Andrescavage

first: Marina

last: Marcet-Houben

first: Ozren

last: Bogdanovic

first: Liyan

last: Yang

first: Lourdes

last: Gallardo-Fuentes

first: Ismael

last: Sospedra

first: Javier

last: Lopez-Rios

first: Fabrice

last: Darbellay

first: Axel

last: Visel

first: Job

last: Dekker

first: Neil

last: Shubin

first: J

last: Gillis

first: Toni

last: Gabaldón

first: Dario

last: Lupianez

first: Daniel

last: Rokhsar

first: José

middle: L

last: Gómez-Skarmeta


title: The little skate genome and the evolutionary emergence of wing-like fin appendages [RNA-seq, st31]

first: Juan

last: Tena

first: Ferdinand

last: Marlétaz

first: Elisa

last: de la Calle-Mustienes

first: Rafael

last: Acemel

first: Tetsuya

last: Nakamura

first: Christina

last: Paliou

first: Silvia

last: Naranjo

first: Pedro

last: Martínez-García

first: Ildefonso

last: Cases

first: Victoria

last: Sleight

first: Christine

last: Hirschberger


title: The little skate genome and the evolutionary emergence of wing-like fin appendages [ATAC-seq]

first: Ali

last: Andrescavage

first: Marina

last: Marcet-Houben

first: Ozren

last: Bogdanovic

first: Liyan

last: Yang

first: Lourdes

last: Gallardo-Fuentes

first: Ismael

last: Sospedra

first: Javier

last: Lopez-Rios

first: Fabrice

last: Darbellay

first: Axel

last: Visel

first: Job

last: Dekker

first: Neil

last: Shubin


title: Lysine methyltransferase Kmt2d regulates naive CD8+ T cell activation-induced survival

status: Public on Jan 11 2023

first: Nan-ping

last: Weng

state: Maryland

address: 251 Bayview Blvd

institute: National Institute on Aging

summary: Lysine specific methyltransferase 2D (Kmt2d) catalyzes the mono-methylation of histone 3 lysine 4 (H3K4me1) and plays a critical role in regulatory T cell generation via modulating Foxp3 gene expression. We utilized ChIPseq, RNAseq, and scRNAseq to show the role of Kmt2d in naive CD8+ T cell generation and survival.

overall_design: Generated T-cell specific Kmt2d knock out mice to investrigate the role of Kmt2d in CD8+ T cell function. Isolated naive CD8+ T cells from Kmt2d KO and Kmt2d WT mice to investigate the function of Kmt2d.

first: Jaekwan

last: Kim

first: Thomas

last: Nguyen

first: Jeffrey

last: Cifello

first: Raheel

last: Ahmad

first: Yongqing

last: Zhang

first: Qian

first: Ji-Eun

last: Lee

first: Xiang

last: Li

first: Yan

last: Kai

first: Supriyo

last: De

first: Weiqun

last: Peng

first: Kai

last: Ge


title: Combined Time Restricted Feeding and Cisplatin Enhance the Anti-tumor Effects in Cisplatin Resistant and -Sensitive Lung Cancer Cells

city: chongqing

first: Qianyao

last: Chen

address: No.1 Yixueyuan Rd, Yuzhong District

institute: chongqing medical university

summary: Combination therapy as an important treatment option for lung cancer has been attracting attention due to the primary and acquired resistance of chemotherapeutic drugs in the clinical application. In the present study, as a new therapy strategy, concomitant treatment with time-restricted feeding (TRF) plus cisplatin (DDP) on lung cancer growth was investigated in DDP-resistant and DDP-sensitive lung cancer cells. We first found that TRF significantly enhanced the drug susceptibility of DDP in DDP-resistant A549 (A549/DDP) cell line, illustrated by reversing the inhibitory concentration 50 (IC50) values of A549/DDP cells to normal level of parental A549 cells. We also found that TRF markedly enhanced DDP inhibition on cell proliferation, migration, as well as promoted apoptosis compared to the DDP-alone group in A549, H460 and A549/DDP cells lines. We further revealed that the synergistic anti-tumor effect of combined DDP and TRF was greater than that of combined DDP and simulated fasting condition (STS), a known anti-tumor cellular medium. Moreover, mRNA sequence analysis from A549/DDP cell line demonstrated the synergistic anti-tumor effect involved in upregulated pathways in p53 signaling pathway and apoptosis. Notably, compared with the DDP-alone group, combination of TRF and DDP robustly upregulated the P53 protein expression without mRNA level change by regulating its stability via promoting protein synthesis and inhibiting degradation, revealed by cycloheximide and MG132 experiments. Collectively, our results suggested that TRF in combination with cisplatin might be an additional novel therapeutic strategy for patients with lung cancer

overall_design: The three different interventions were as follows: RPMI-1640 medium (Gibco, USA) continually supplemented with 2 g/L glucose and 10% FBS as a normal control (CON) diet for 24h cycles; Normal control RPMI-1640 medium for 6 h followed with serum-free and glucose-free RPMI-1640 medium for 18 h for 24h cycles as a TRF mimicking group; 0.5 g/L glucose and 1% FBS were continuously added to glucose-free RPMI-1640 medium as a simulated fasting condition (STS) for 24h cycles. When changing the medium, cells were washed twice with PBS and then switched to another medium.

first: Jianling


title: Intra-pituitary follicle-stimulating hormone signaling regulates hepatic lipid metabolism

city: Saarbrücken

first: Kathrin

last: Kattler-Lackes

state: non-US Resident

address: Campus A2.4 Raum 0.13

department: Epigenetics

institute: Saarland University

summary: Inter-organ communication is a major hallmark of health and is often orchestrated by hormones released by the anterior pituitary gland. Pituitary gonadotropes secrete follicle-stimulating hormone (FSH) and luteinizing hormone (LH) to regulate gonadal function and control fertility. Whether FSH and LH also act on organs other than the gonads is debated. Here, we found that gonadotrope depletion in adult female mice triggers profound hypogonadism, obesity, glucose intolerance, fatty liver, and bone loss. The absence of sex steroids precipitates these phenotypes, with the notable exception of fatty liver, which results from ovary-independent actions of FSH. We uncover paracrine FSH action on pituitary corticotropes as a novel mechanism to restrain the production of corticosterone and prevent hepatic steatosis. Our data demonstrate that functional communication of two distinct hormone-secreting cell populations in the pituitary regulates hepatic lipid metabolism.

overall_design: Total RNA from liver tissue was purified by using the RNeasy Plus Mini kit (QIAGEN) according to the manufacturer's instructions. RNA samples with RNA integrity number greater than 8 were used to build RNA-seq libraries. 1000 ng total RNA for each sample was used to build libraries employing the NEB Next Ultra RNA Library preparation kit (Ipswich). The library was sequenced in the Illumina Hiseq2500 platform with 2× 100-bp paired-end reads. After alignment, transcripts with an absolute value of log2 (fold change) larger than 1 and q value below 0.05 were considered to be differentially expressed. Gene Set Enrichment Analysis (GSEA) was performed to functionally study the transcriptomic changes.

first: Sen

last: Qiao

first: Samer

last: Alasmi

first: Amanda

last: Wyatt

first: Hongmei

last: Wang

first: Michael

last: Candlish

first: Debajyoti

last: Das

first: Mari

last: Aoki

first: Ramona

last: Grünewald

first: Ziyue

last: Zhou

first: Qinghai

last: Tian

first: Philipp

last: Wartenberg

first: Qiang

last: Yu

first: Anouar

last: Belkacemi

first: Ahsan

last: Raza

first: Fabien

last: Ectors

last: Kattler

first: Gilles

last: Gasparoni

first: Jörn

last: Walter

first: Peter

last: Lipp

first: Patrice

last: Mollard

first: Daniel

last: Bernard

first: Ersin

last: Karatayli

first: Senem

middle: C

first: Frank

last: Lammert

first: Ulrich

last: Boehm


title: Gene expression in 832/13 INS1 beta-cells transduced with lentiviral vector conferring expression of GFP or Pax5

city: Malmö

first: Charlotte

last: Ling

address: Jan Waldenstroms gata 35

country: Sweden

institute: Lund Univesity

summary: We found PAX5 to be overexpressed in human pancreatic islets of donors from donors with type 2 diabetes compared to islets from non-diabetic individuals. Functional follow-up showed that Pax5 overexpression in rat clonal beta-cells (832/13 INS1) results in impaired insulin secretion. Microarrays were used to investigate if overexpression of Pax5 alters the gene expression profile of 832/13 INS1 beta-cells.

overall_design: 16 samples, 8 from cells transduced with a control (GFP) virus and 8 transduced with a Pax5 virus. Cells were transdcued with a MOI of 1.25 and samples were collected 72h post transduction

first: Karl

last: Bacos

first: Alexander

last: Perfilyev

first: Alexandros

last: Karagiannopoulos

first: Elaine

last: Cowan

first: Jones

last: Ofori

first: Ludivine

last: Bertonnier-Brouty

first: Tina

last: Rönn

first: Andreas

last: Lindqvist

first: Cheng

last: Luan

first: Sabrina

last: Ruhrmann

first: Mtakai

last: Ngara

first: Åsa

last: Nilsson

first: Sevda

last: Gheibi

first: Claire

last: Lyons

first: Jens

middle: O

last: Lagerstedt

first: Mohammad

last: Barghouth

first: Jonathan

last: Esguerra

first: Petr

last: Volkov

first: Malin

last: Fex

first: Hindrik

last: Mulder

first: Nils

last: Wierup

first: Ulrika

last: Krus

first: Isabella

last: Artner

first: Lena

last: Eliasson

first: Rashmi

last: Prasad

first: Luis

middle: R

last: Cataldo


title: Emergent dynamics of adult stem cell lineages from single cell RNA-Seq of Drosophila testes

status: Public on Jan 10 2023

city: Cambridge

first: Amelie

last: Raz

state: Ma

address: 455 Main St

institute: Whitehead Institute for Biomedical Research

summary: Here we provide a single cell RNA-seq resource covering all of spermatogenesis in Drosophila starting from in-depth analysis of adult testis single nucleus RNA-seq . Proper differentiation of sperm from germline stem cells, essential for production of the next generation, requires dramatic changes in gene expression that drive remodeling of almost all cellular components, from chromatin to organelles to cell shape itself.  Here we provide a single nucleus and single cell RNA-seq resource covering all of spermatogenesis in Drosophila starting from in-depth analysis of adult testis single nucleus RNA-seq (snRNA-seq) data from the Fly Cell Atlas (FCA) study (Li et al., 2022).  With over 44,000 nuclei and 6,000 cells analyzed, the data provide identification of rare cell types, mapping of intermediate steps in differentiation, and the potential to identify new factors impacting fertility or controlling differentiation of germline and supporting somatic cells.  We justify assignment of key germline and somatic cell types using combinations of known markers, in situ hybridization, and analysis of extant protein traps.  Comparison of single cell and single nucleus datasets proved particularly revealing of dynamic developmental transitions in germline differentiation.  To complement the web-based portals for data analysis hosted by the FCA, we provide datasets compatible with commonly used software such as Seurat and Monocle.  The foundation provided here will enable communities studying spermatogenesis to interrogate the datasets to identify candidate genes to test for function in vivo.

overall_design: This dataset was collected from testes of adult Drosophila males.

first: Yukiko

last: Yamashita

first: Margaret

last: Fuller

first: Stephen

last: Dinardo


title: A Systemic and Integrated Analysis of p63-Driven Regulatory Networks in Mouse Oral Squamous Cell Carcinoma

city: Buffalo

first: Satrajit

last: Sinha

address: 955 Main Street

institute: University at Buffalo

summary: Oral squamous cell carcinoma (OSCC) is the most common malignancy of the oral cavity and despite therapeutic advances, late-stage diagnoses continue to negatively affect survival, presenting a continuing challenge for clinicians. Detailed molecular characterization by recent bulk and single-cell RNA-sequencing datasets from OSCC suggest that identification of prognostic biomarkers may lead to more targeted therapies, improving  patient outcomes. Development of OSCC is associated with exposure to tobacco, alcohol consumption, and infection with human papillomavirus. The mouse model of 4-Nitroquinoline 1-oxide (4NQO) carcinogenesis produces a spectrum of neoplastic lesions that are a robust model of tobacco-induced OSCC. Specifically, studies have shown that similar to human OSCC, mouse OSCC shows upregulation of the oncogenic master transcription factor p63. We performed complementary loss- and gain-of-function experiments of p63 in mouse 4NQO-transformed OSCC cell lines and utilized RNA-sequencing and ChIP-sequencing to uncover the p63 oncogenic network. By combining our signature with publicly available bulk and scRNA-seq data, we generated a murine p63 signature that we have utilized to better understand the role of p63 in mOSCC. Our analyses have identified several potential biomarkers and conserved pathways that are relevant to hOSCC, as well as highlighted the dynamic role of p63 in migration and invasion.

overall_design: RNA-seq of mOSCC 4NQO-generated cell lines (B7E3, B4B8, B7E11), RNA-seq of p63 knockdown cells in the B7E11 cell line, RNA-seq of B7E3 p63 overexpression cell lines

first: Alexandra

last: Glathar

first: Akinsola

last: Oyelakin

first: Kasturi

middle: B

last: Nayak

first: Jennifer

last: Sosa


overall_design: ChIP-seq of master TF p63 in B7E11  cells utilizing 2 independent p63 antibodies


title: Spontaneously Evolved Progenitor Niches Escape Yap Oncogene Addiction in Advanced Pancreatic Ductal Adenocarcinomas [Cut&Tag]

city: Washington

first: Chunling

last: Yi

state: DC

address: 3700 O St NW

department: Oncology

institute: Georgetown University

summary: Lineage plasticity has been proposed as a major source of intratumoral heterogeneity and therapeutic resistance. Employing an inducible genetic engineered mouse model, we illustrate that lineage plasticity enables advanced Pancreatic Ductal Adenocarcinoma (PDAC) tumors to develop spontaneous relapse following elimination of the central oncogenic driver - Yap. Transcriptomic and immunohistochemistry analysis of a large panel of PDAC tumors reveals that within high-grade tumors, small niches of PDAC cells gradually evolve to re-activate pluripotent transcription factors (PTFs), which lessen their dependency on Yap. Comprehensive Cut&Tag analysis demonstrate that although acquisition of PTF expression is coupled with the process of epithelial-to-mesenchymal transition (EMT), PTFs form a core transcriptional regulatory circuitry (CRC) with Jun to overcome Yap dependency, which is distinct from the classic TGFb-induced EMT-TF network.  A chemical-genetic screen and follow-up functional studies establish Brd4 as an epigenetic gatekeeper for the PTF-Jun CRC, and strong synergy between BET and Yap inhibitors in blocking PDAC growth.

overall_design: Cut&Tag of Histone Marks: BRD4, H3K27ac, and H3K4me3, as well as TFs: Yap, Sox2, Sox5, and Twist2 of Murine Primary Pancreatic Ductal Carcinoma (PDAC) Cells, organized by line morphology

first: Shigekazu

last: Murakami

first: Shannon

middle: M

last: White

first: Alec

middle: T

last: McIntosh

first: Chan

last: Nguyen


title: Time-resolved assessment of single-cell protein secretion by sequencing

city: Singapore

first: Tongjin

last: WU

address: MD6, 14 Medical Drive

department: Institute for Health Innovation and Technology

country: Singapore

institute: National University of Singapore

summary: Secreted proteins play critical roles in cellular communication. Methods enabling concurrent measurement of cellular protein secretion, phenotypes and transcriptomes are still unavailable. Here, we describe Time-Resolved Assessment of Protein Secretion from single cells by sequencing (TRAPS-seq). Released proteins are trapped onto cell surface and probed by oligonucleotide-barcoded antibodies before simultaneously sequenced with transcriptomes in single cells. TRAPS-seq unravels the phenotypic and transcriptional determinants of the secretion of pleiotropic Th1 cytokines (IFN-γ, IL-2 and TNF-α) in activated T cells. We further demonstrate the use of TRAPS-seq to track dynamic secretion of multiple cytokines over time, uncovering unique molecular signatures that govern the preservation or transition of single-cell cytokine secretions. Our results revealed that early central memory T cells with CD45RA expression (TCMRA) are important in both the production and maintenance of polyfunctional cytokines. TRAPS-seq presents a unique tool for seamless integration of secretomics measurement with multi-omics profiling in single cells.

overall_design: For end-timepoint measurement of cytokine secretion by TRAPS-seq, human lymphocytes with depletion of CD19+ cells were enriched using Moflo Astrios cell sorter (Beckman Coulter) and kept in incubator overnight before stimulation. Cells were activated by anti-CD3/CD28 Dynabeads (Gibco, 11161D) at 2:1 bead-to-cell ratio for indicated time periods (0 hour, 1 hours, 6 hours and 16 hours) in 96-well U-bottom plate. Post beads removal, cells were subjected to TRAPS-seq. For secretion tracing, total T cells were enriched by immunomagnetic negative selection (STEMCELL Technologies, 19051) and loaded onto the nanowell array dropwise at 40,000 cells per array. The unloaded cells were gently rinsed off and 20 µl anti-CD3/CD28 Dynabeads (Gibco, 11161D) were loaded. The cells were activated in open array for 10 hours before subjected to TRAPS-seq-powered on-array secretion tracing.

last: Wu

first: Lih Feng

last: Cheow


title: Pyrimidine de novo synthesis inhibition selectively blocks effector but not memory T-cell development [scRNA-Seq 10x]

city: Freising

first: Gustavo

middle: P.

last: de Almeida

state: Bavaria

address: Liesel-Beckmann-Str. 1

department: Division of Animal Physiology and Immunology

institute: Technical University of Munich

summary: Blocking pyrimidine de novo synthesis via inhibiting Dihydroorotate dehydrogenase (DHODH) is clinically used to treat autoimmunity and to prevent the growth of rapidly dividing cells including activated T-cells. We identified a previously unrecognized resistance of precursors of memory T-cells to pyrimidine starvation. While the treatment effectively blocks effector T-cells, numbers, function and transcriptional profiles of memory T-cells and their precursors remain completely unaltered. We pinpoint this effect to a narrow time-window in the early T-cell expansion phase, when developing effector, but not memory T-cells are selectively vulnerable to pyrimidine starvation. This stems from a higher proliferative pace of early effector T-cells paired with lower pyrimidine synthesis capacity compared to memory precursors. This differential sensitivity constitutes a novel, drug-targetable checkpoint that efficiently diminishes effector T-cells without harming the memory compartment. We envision that knowledge of this pyrimidine synthesis-based cell fate-determining particularity opens up new means to safely manipulate effector T-cell responses.

overall_design: T-cells were isolated from control and Leflunomide treated host mice on day 4 after a Listeria monocytogenes infection (n=4).

first: D

last: Zehn

first: A

last: Schulz

first: G

middle: P


title: Defining the age-dependent and tissue-specific circadian transcriptome in male mice

city: Gainesville

first: Karyn

last: Esser

state: Florida

address: 1345 Center Drive

department: PHYSIOLOGY & FUNCTIONAL GENOMICS

institute: University of Florida

summary: Cellular circadian clocks direct a daily transcriptional program that supports homeostasis. Emerging evidence supports age-associated changes in circadian functions. To define age-dependent changes at the systems level, we profiled the circadian transcriptome in the hypothalamus, lung, heart, kidney, skeletal muscle, and adrenal gland in 3 age groups. We found age-dependent and tissue-specific clock output changes. Aging reduced the number of rhythmically expressed genes (REGs), indicative of weakened circadian control. Many genes gained rhythmicity in old tissues, reflecting an adaptive response. REGs were enriched for the hallmarks of aging, adding a new dimension to understanding aging. Differential gene expression analysis found that there were temporally distinct clusters of genes in tissue-specific manner. This novel analysis extends the landscape of the understanding of aging. Increased daily gene expression variability is a common feature of aged tissues. Our data highlight the impact of aging on circadian function and temporal changes in gene expression.

overall_design: Hypothalamus, lung, kidney, skeletal muscle, heart, and adrenal gland tissues from Young (6mo), Aged (18mo), and Old (27mo) male mice were collected every 4h for 48h to characterize the circadian transcriptome changes with age. Two samples per age were collected and pooled for RNAseq analysis.

first: Christopher

last: Wolff

first: Miguel

last: Gutierrez-Monreal

first: Lingsong

last: Meng

first: Xiping

last: Zhang

first: Lauren

last: Douma

first: Hannah

last: Costello

first: Collin

last: Douglas

first: Elnaz

last: Ebrahimi

first: Bryan

last: Alava

first: Andrew

last: Morris

first: Mehari

last: Endale

last: Crislip

first: Kit-yan

last: Cheng

first: Elizabeth

last: Schroder

first: Brian

last: Delisle

last: Bryant

first: Michelle

last: Gumz

first: Zhiguang

last: Huo

last: Liu


title: Pyrimidine de novo synthesis inhibition selectively blocks effector but not memory T-cell development [SCRB-seq]

first: Gustavo

last: de Almeida

overall_design: T-cells were isolated from control and Teriflunomide treated host mice on day 4 after a Listeria monocytogenes infection (n=3).

first: D

last: Zehn

first: A

last: Schulz

first: G


title: Transcriptome analysis of  inducible HOTAIR overexpression mouse breast cancer cells

city: Shenzhen

first: Qing

last: Ma

address: 1068 Xueyuan Avenue, Shenzhen University Town, Shenzhen, P.R.China

institute: Shenzhen Institutes of Advanced Technology

summary: HOTAIR is a 2.2 kb long noncoding RNA (lncRNA) whose dysregulation has been linked to oncogenesis, defects in pattern formation during early development, and irregularities during the process of epithelial-to-mesenchymal transition (EMT). However, the oncogenic transformation determined by HOTAIR in vivo and its impact on chromatin dynamics are incompletely understood. Here we generate a transgenic mouse model with doxycycline-inducible expression of human HOTAIR in the context of the MMTV-PyMT breast cancer-prone background (iHOT-PyMT mice) to systematically interrogate the cellular mechanisms by which human HOTAIR lncRNA acts to promote breast cancer progression. We isolated breast cancer cells from the primary tumors of iHOT-PyMT mice (named iHOT+ cells) and performed RNA-seq and ATAC-seq of iHOT+ cells treated with 3 conditions: Dox+, Dox- and DoxWD. We showed that HOTAIR overexpression altered both the cellular transcriptome and chromatin accessibility landscape of multiple metastasis-associated genes and promoted epithelial to mesenchymal transition. These alterations are abrogated within several cell cycles after HOTAIR expression is reverted to basal levels, indicating an erasable lncRNA-associated epigenetic memory. These results suggest that a continual role for HOTAIR in programming a metastatic gene regulatory program.

overall_design: The iHOT+ cells were treated with 3 conditions: Dox+ HOTAIR overexpressing cells which were consistently treated with Dox for several days; DoxWD cells which had been temporarily treated with Dox and later withdrawn from HOTAIR overexpression; and Dox- untreated control cells in which HOTAIR remained at baseline levels. Gene expression profiles in iHOT+ cells with different treatments were generated by RNA-seq using the Illumina Genome Analyzer IIX platform.

first: Karen

last: Tolentino

first: Yang

last: Zhao

first: Lingjie

last: Li


title: Gene expression profiles of oil palm leaves from different oil yields and genetic population: Transcriptomic dataset

city: Jakarta Timur

first: Ardha

last: Apriyanto

state: DKI Jakarta

address: Puloayang Raya Blok OR I

country: Indonesia

institute: Astra Agro Lestari

summary: Oil palm (Elaeis guineensis Jacq.) is one of the most important oil-producing crops in the world. However, the demand for oil from this crop will increase in the future. A comparative gene expression profile of the oil palm leaves was needed in order to understand the key factors that influence the oil production. Here, we reported an RNA-seq dataset from three different oil yields and three different genetic populations of oil palm. All raw sequencing reads were obtained from an Illumina NextSeq 500 platform. We also provide a list of the genes and their expression levels resulting from the RNA-sequencing. This transcriptomic dataset will provide a valuable resource for increasing oil yield.

overall_design: Comparative gene expression profiling analysis of RNA-seq data from different oil yield and genetic population


title: Pyrimidine de novo synthesis inhibition selectively blocks effector but not memory T-cell development.

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

overall_design: Refer to individual Series


title: Genome-wide screen in human plasma identifies multifaceted complement evasion of Pseudomonas aeruginosa

city: Grenoble

first: Manon

last: Janet-Maitre

address: 71 Avenue des Martyrs

institute: IBS


title: Analysis of difference in transcriptome of ILC2s derived from WT C57BL/6 and RAG1-/- mice

city: Bethesda

first: Jinfag

last: Zhu

address: 10 Center Drive

department: Laboratory of Immune System Biology

institute: NIAID/NIH

summary:
Purpose: To analyze the transcriptome difference of ILC2s isoalted from WT and RAG-/- mice under inflammaed condition
Method: Lung ILC2s from mice chronically challenged with papain (40 µg/20 µl PBS, 6 subsequest papain challenges, day 0, 1, 2, 13, 14, and 15)

overall_design: Total RNA from lung ILC2s (live lineage markers- CD127+ T1ST/2+) was used for RNA-seq library preparation

first: Rama

middle: K

last: Gurram

first: Kairong

last: Cui

first: Gangqing

last: Hu

first: Keji

first: Jinfang


title: Tissue resident iNKT17 cells facilitate cancer cell extravasation in liver metastasis via IL-22

city: Hamburg

first: Babett

last: Steglich

address: Martinistrasse 52

institute: Universitätsklinikum Hamburg-Eppendorf

summary: The crosstalk among the immune system, cancer cells and the tissue microenvironment is fundamental for the emergence of organ-specific niches that facilitate metastasis formation. Here, we studied the involvement of IL-22, which is known to be produced by immune cells and to act on the tissue, in mediating this crosstalk and thus metastasis formation. We found that Il22-deficient mice and mice treated with an IL-22 antibody are protected from liver and lung metastasis formation, while over expression of IL-22 promoted metastasis formation. Mechanistically, IL-22 acted on endothelial cells thereby promoting endothelial permeability and cancer cell transmigration via induction of endothelial aminopeptidase N. Finally, tissue resident iNKT17 cells were the key source of IL-22 in the liver. Thus, targeting tissue resident immune cells derived IL-22 represents a potential therapeutic target in metastasis formation.

overall_design: Liver metastasis can be induced in mice by intrasplenic injection of cancer cells. We used single cell sequencing to study IL-22 expression by leukocytes in the liver before and 12h after intrasplenic injection.

first: Anastasios

last: Giannou

first: Jan

last: Kempski

first: Ahmad

last: Shiri

first: Richard

last: Flavell

first: Nicola

last: Gagliani

first: Samuel

last: Huber


title: The immunocytokine PD1-IL2v overcomes resistance to tumor immunity, and synergizes with anti-PD-L1

city: Lausanne

first: Nadine

last: Fournier

state: Vaud

address: Agora Cancer Research Center, Bugon 25A

country: Switzerland

institute: Agora Cancer Research Center & Swiss Institute of Bioinformatics

summary: Immunotherapies have shown remarkable, albeit tumor-selective therapeutic benefits in the clinic. Here we evaluated the effects of the immunocytokine PD1-IL2v in a mouse model of de novo pancreatic neuroendocrine cancer resistant to checkpoint and other immunotherapies. PD1-IL2v is a bi-specific molecule based on a bivalent PD-1 antibody, serving as a targeting moiety, fused to an immuno-stimulatory IL-2 variant (IL2v) to precisely deliver IL2v to PD-1+ T-cells in the tumor microenvironment. PD1-IL2v elicited dramatic infiltration by CD8 T cells, notably stem-like and effector memory T cells, resulting in tumor regression and enhanced survival in mice. Furthermore, combining anti-PD-L1 with PD1-IL2v sustained the response phase, improving therapeutic efficacy both by reprogramming immunosuppressive tumor-associated macrophages and tumor endothelial cells , and by enhancing TCR immune repertoire diversity. The data motivate consideration of clinical trials to evaluate the combination therapy of PD1-IL2v and anti-PD-L1, especially in immunotherapy-resistant tumors infiltrated with PD-1+ T stem-like CD8 T cells.

overall_design: Analysis of scRNAseq and scTCRseq from Rip-Tag5 PanNET mouse model (tumors and spleens) treated with PD1-IL2v, aPD-L1, PD1-IL2v + aPD-L1 or untreated for 10 days

first: Melanie

last: Tichet

first: Stephan

last: Wullschleger

first: Rachel

last: Marcone

first: Annamaria

last: Kauzlaric

first: Douglas

last: Hanahan


title: A program of successive gene expression in mouse one-cell embryos

status: Public on Jan 09 2023

first: Brian

middle: Yee Hong

last: Lam

address: Box 289 Addenbookes Hospital, Hills Road

department: Metabolic Research Laboratories

country: United Kingdom

institute: University of Cambridge

summary: At the moment of union in fertilization, sperm and oocyte are transcriptionally silent. The ensuing onset of embryonic transcription (embryonic genome activation, EGA) is critical for development, yet its timing and profile are unknown in any vertebrate species. We here dissect hitherto inaccessible transcription during EGA by high resolution single-cell RNA-sequencing of precisely synchronized mouse one-cell embryos. This reveals a program of embryonic gene expression (immediate EGA, iEGA) initiating within four hours of fertilization. Expression during iEGA produces canonically-spliced transcripts, occurs substantially from the maternal genome, and is mostly down-regulated at the two-cell stage. Transcribed genes predict regulation by transcription factors (TFs) associated with cancer, including c-Myc. Blocking c- Myc or other predicted regulatory TF activities disrupts iEGA and induces acute  developmental arrest. These findings illuminate intracellular mechanisms that regulate the onset of mammalian development and promise a new paradigm for the study of cancer

overall_design: RNASeq comparison of 10058-F4/alpha-amanitin treated  versus control untreated one-cell embryo

middle: Y

first: Maki

last: Asami

first: Marcella

last: Ma

first: Kara

last: Rainbow

first: Giles

last: Yeo

first: Anthony

last: Perry


title: Measurement of mRNA stability during  transcriptional memory  in mutants for RNA degradation

city: Solna

first: Vicent

last: Pelechano

address: Nobels väg 16

department: MTC

institute: ScilifeLab - Karolinska Institutet

summary: Transcriptional memory, by which cells respond faster to repeated stimuli, is key for cellular adaptation and organism survival. Factors related to chromatin organization and activation of transcription have been shown to play a role in the faster response of those cells previously exposed to a stimulus (primed). However, the contribution of post-transcriptional regulation is not yet explored. Here, we investigate the contribution of cytoplasmic RNA decay to this process, we investigate global changes in mRNA turnover in ski2∆ (component of the cytoplasmic 3’-5’exosome) and xrn1∆ (cytoplasmic 5’-3’exonuclease) strains in S. cerevisiae.

overall_design: We use S. cerevisiae as a model organism and investigate the gene expression changes associated to the change from rich media with glucose as carbon source (YPD) to rich media with galactose as carbon source (YPGal). We investigate naïve and primed cells in both wild type (BY4741), ski2∆  and xrn1∆ strains. For the wild-type strain we perform a pulse chase strategy (labeling for 1h prior to change to YPGal and measuring at t0,10 and 30 min). While for mutant strains we assume steady state for RNA turnover and measure in YPD (for naïve and primed cells). We perform 3 independent biological replicates.

first: Bingnan

last: Li

first: Yujie

last: Zhang

first: Yerma

last: Pareja Sanchez


title: Pyrimidine de novo synthesis inhibition selectively blocks effector but not memory T-cell development [bulk RNA-seq]

first: Gustavo

last: de Almeida

overall_design: Transferred OT-1 T-cells were isolated from host mice treated with Leflunomide or control on day 7 and day 28 post infection with OVA-expressing Listeria monocytogenes (n=5).

first: D

last: Zehn

first: A

last: Schulz

first: G


title: Chromatin profile-based identification of a novel ER-positive breast cancer subgroup with reduced ER-responsive element accessibility

city: Koto-ku

first: Reo

last: Maruyama

state: Tokyo

department: Cancer Institute

institute: Japanese Foundation For Cancer Research

summary: Estrogen receptor (ER) signaling–dependent cancer cell growth is one of the major features of ER-positive breast cancer (BC). Inhibition of ER function is a standard and effective treatment for ER-positive tumors; however, ~20% of patients with ER-positive BC experience early or late recurrence. In this study, we examined intertumor heterogeneity from an epigenetic perspective based on the hypothesis that the intrinsic difference in epigenetic states around ER signaling pathway underlies endocrine therapy resistance. We profiled chromatin accessibility data from 42 BC samples, including 35 ER-positive human epidermal growth factor receptor 2 (HER2)-negative and 7 triple-negative tumors, identifying a subgroup of ER-positive BCs with a distinctive chromatin accessibility pattern including reduced accessibility to ER-responsive elements (EREs). The same subgroup was also observed in The Cancer Genome Atlas BC cohort. Despite the reduced accessibility to EREs, the expression of ER and potential ER target genes were not decreased in these tumors. Our findings highlight the existence of a subset of ER-positive BCs with unchanged ER expression but reduced EREs accessibility that cannot be distinguished by conventional immunostaining for ER. Future studies should determine whether these tumors are associated with resistance to endocrine therapy.

overall_design:
42 breast cancer samples collected by core needle biopsies from surgical specimens were objected to ATAC-seq analysis.
***Please note that raw data is not provided since the submitter have obtained informed consent that does not presuppose registration of genomic sequence data in public databases.

first: Kohei

last: Kumegawa

first: Yoko

last: Takahashi

first: Sumito

last: Saeki


title: Retinoic acid-induced differentiation of porcine spermatogonia in vitro

city: Shaanxi

first: Xueni

last: You

state: 陕西省

address: 22 Xi-nong Road

department: College of Animal Science and Technology

institute: Northwest A&F University

type: Non-coding RNA profiling by high throughput sequencing

summary: Spermatogenesis is an intricate developmental process occurring in testes by which spermatogonial stem cells (SSCs) self-renew and differentiate into mature sperm. The molecular mechanisms for SSC self-renewal and differentiation, while have been well studied in mice, may differ between mice and domestic animals including pigs. To gain knowledge about the molecular mechanisms for porcine SSC self-renewal and differentiation that have to date been poorly understood, here we isolated and enriched primitive spermatogonia from neonatal porcine testes, and exposed the cells to retinoic acid, a direct inducer for spermatogonial differentiation. We then identified that retinoic acid could induce porcine primitive spermatogonial differentiation into leptotene spermatocyte-like cells, which was accompanied by a clear transcriptomic alteration, as revealed by the RNA-sequencing analysis. We also compared retinoic acid-induced in vitro porcine spermatogonial differentiation with the in vivo process, and compared retinoic acid-induced in vitro spermatogonial differentiation between pigs and mice. Furthermore, we analyzed retinoic acid-induced differentially expressed long non-coding RNAs (lncRNAs), and demonstrated that a pig-specific lncRNA, lncRNA-106504875, positively regulated porcine spermatogonial proliferation by targeting the core transcription factor ZBTB16. Taken together, these results would help to elucidate the roles of retinoic acid in porcine spermatogonial differentiation, thereby contributing to further knowledge about the molecular mechanisms underlying porcine SSC development and, in the long run, to optimization of both long-term culture and induced differentiation systems for porcine SSCs.

first: Tianjiao

first: Youjie

last: Cui

first: Wei

last: Liu


title: Conserved and plant-specific GCN5-containing complexes cooperate to regulate gene transcription and plant development [30d RNA-seq]

city: Beijing

first: xinjian

last: He

address: No. 7, zhongguancun life science park road, changping district

institute: National Institute of Biological Sciences

summary: Although a conserved SAGA complex containing the histone acetyltransferase GCN5 is known to mediate histone acetylation and transcriptional activation in eukaryotes, how to maintain different levels of histone acetylation and transcription at the whole-genome level remains to be determined. Here, we identify and characterize a plant-specific GCN5-containing complex, which we term PAGA, in Arabidopsis thaliana and Oryzae sativa. In Arabidopsis, the PAGA complex consists of two conserved subunits (GCN5 and ADA2A) and four plant-specific subunits (SPC, ING1, SDRL, and EAF6). Chromatin immunoprecipitation and sequencing indicate that PAGA and SAGA have both shared and specific target genes, and independently mediate moderate and high levels of histone acetylation, thereby promoting moderately and highly transcriptional activation, respectively. By combining RNA-seq and ChIP-seq data, we found that PAGA and SAGA antagonistically regulate histone acetylation and gene transcription. Genetically, PAGA mutations can partially rescue the developmental defects of the SAGA-specific mutant ada2b-c. Unlike SAGA, which regulates multiple biological processes, PAGA is specifically involved in plant height and branch growth by regulating the transcription of hormone biosynthesis and response related genes. These results reveal how PAGA and SAGA cooperate to regulate histone acetylation, transcription, and development. Given that the PAGA mutants show semi-dwarf and increased branching phenotypes without reduction in seed yield, the PAGA mutations could potentially be used for crop improvement.

overall_design: Examination of the mRNA expression of 30-day-old wild type and six mutants in Arabidopsis

first: Xin-Jian


title: Conserved and plant-specific GCN5-containing complexes cooperate to regulate gene transcription and plant development [H3K14Ac ChIP-seq]

overall_design: Examination of H3K14Ac levels in wild type and four mutants


title: Effect of deletion of ERRalpha, ERRbeta and/or ERRgamma on gene expression in soleus and extensor digitorum longus (EDL) skeletal muscles

city: Baltimore

first: Anastasia

last: Kralli

address: 725 N. Wolfe Street

department: Phys Physiology

institute: Johns Hopkins School of Medicine

summary:
The three estrogen related receptors (ERRs) are regulators of oxidative metabolism in many cell types, yet their roles in skeletal muscle have not been elucidated. To address the roles and significance of ERRs for skeletal muscle mitochondria and muscle function, we generated mice lacking combinations of ERRs specifically in skeletal muscle. We then compared the impact of ERR loss on the transcriptomes of EDL and soleus, i.e., muscles rich in glycolytic or oxidative fibers, respectively. Our findings highlight an essential role of ERRs for skeletal muscle oxidative metabolism and identify broad classes of ERR-dependent gene programs in muscle. They also suggest a high degree of functional redundancy among muscle ERR isoforms for the protection of oxidative capacity, with ERR isoform-specific phenotypes being driven primarily, but not exclusively, by their relative levels in different muscles.
To compare the relative contributions of ERRs for oxidative capacity in glycolytic and oxidative skeletal muscles, we generated mice lacking one or two ERRs specifically in skeletal muscle.  We then performed gene expression profiling analysis using data obtained from RNA-seq of soleus and EDL muscles of WT and ERR KO mice .

overall_design: Comparative gene expression profiling analysis of RNA-seq data from skeletal muscles of ERR muscle-specific KO mice and their WT littermates.  Three biological replicates of each KO class were compared to three WT replicates.

first: Elodie

last: Eury


title: The development of mouse trophoblast cells at the single cell level

first: Xiangxiang

last: Jiang

state: Beijing

address: 1 Beichen West Road, Chaoyang District

institute: Institute of Zoology, Chinese Academy of Sciences

summary: The placenta is a poorly understood yet vital support organ. Transcriptome analysis at single cell resolution can help us understand cell compositions, developmental processes, and physiological functions. Both mice and humans have the hemochorial placenta. Profiling the single cell transcriptome of the mouse placenta is necessary for deepening our knowledge of mammalian placentation.We systematically profiled single cell transcriptomes of mouse placentae every day from E7.5 to E14.5. After stringent filtering, 15682 mouse trophoblast cells were subjected to following transcriptome analysis. We noted that trophoblast cells underwent 3 main differentiation stages: E7.5-E8.5, E9.5-E10.5, and E11.5-E14.5. With the help of advanced computational technologies from Velocyto, PAGA, monocle, and SCENIC, we have updated the recognitions of several developmental events. Firstly, P-TGCs are suggested to only derive from EPC like cells. Secondary, sinusoid trophoblast and spongiotrophoblast all derived from EPC cells, and their cell fates have been determined before the chorioallantoic fusion. Sinusoid trophoblast cells were not derived from chorion. Thirdly, SpA-TGCs were suggested to be differentiated from spongiotrophoblast cells via Gly-T cells. Furthermore, new transcription factors have been found to play roles during the differentiation of trophoblast cells. Lastly, the expression of Ifnlr1 in chorion branch cells gradually increased during placentation, which reconfirmed that mature placenta can defend the Zika virus (ZIKV) through IFN signaling. We clarified the developmental histories of mouse trophoblast cells at the branch level, especially the differentiation of sinusoid branch trophoblast cells. Meanwhile, we offered a convincing data resource for the study of mammalian placentation and etiology analysis of pregnancy-associated diseases.

overall_design:
Single cell transcriptomes of mouse placentae that were collected at one-day intervals between E7.5 and E14.5

NOTE:

The MPL39603-*.csv,MTR15682-*.csv, UMAP-MPL39603.csv, UMAP-MTR15682.csv, UMAP-MTR-E78-3529.csv files (included in the 10x_V*_processed_data.tar.gz) belong to the GSM4725071 - GSM4725071, and V3MPL30518-*.csv, V3MTR8067-*.csv files belong to the GSM6744596 - GSM6744600 samples.

first: Yue

last: Wang

first: Hongmei


title: Single cell evaluation of endocardial HAND2 gene regulatory networks reveals critical HAND2 dependent pathways impacting cardiac morphogenesis.

city: Indianapolis

first: Anthony

last: Firulli

email: tfirulli@iupui.edu, tfirulli@iu.edu

state: IN

address: 1044 W Walnut R4302E

department: pediatrics

institute: IU school of medicine

summary: The basic-helix-loop-helix transcription factor HAND2 plays a critical role in endocardium to myocardium signaling during cardiac morphogenesis through its role within the NOTCH signaling pathway. Hand2 endocardial deletion (H2CKOs) results in embryonic lethality by E13.5 due to tricuspid atresia (TA) or double inlet left ventricle (DILV) with accompanying intraventricular septum defects, multiple septa, and hypo-trabeculated ventricles. In addition, H2CKOs also exhibit an increased density of coronary lumens. In order to understand the underlying regulatory mechanisms that cause these phenotypes, we undertook a single cell transcriptome analysis of E11.5 H2CKOs hearts.

overall_design: Hand2fx/+Nfatc1Cre males were crossed with Hand2fx/fxR262RmTmG/mTmG females to generate embryos at E11.5. Cre status determined by presence or absence of GFP fluorescence. Rapid genotyping used to adetermine the status of Hand2 conditional allele. Whole hearts from control and H2CKO embryos were dissociated for single cell sequencing.

first: Rajani

last: George


title: Differential regulation of mRNA stability modulates transcriptional memory and facilitates environmental adaptation

first: Vicent

last: Pelechano

summary: Transcriptional memory, by which cells respond faster to repeated stimuli, is key for cellular adaptation and organism survival. Factors related to chromatin organization and activation of transcription have been shown to play a role in the faster response of those cells previously exposed to a stimulus (primed). However, the contribution of post-transcriptional regulation is not yet explored. Here, we perform a genome-wide characterisation of this process and explore the contribution of the nuclear mRNA surveillance (RRP6) to this process. Using S. cerevisiae as a model organism, we investigate changes in mRNA abundance, mRNA stability and chromatin organization. Our results demonstrate that mRNA post-transcriptional regulation, and not only transcription regulation, should be considered when investigating gene expression memory.

overall_design: We use S. cerevisiae as a model organism and investigate the gene expression changes associated to the change from rich media with glucose as carbon source (YPD) to rich media with galactose as carbon source (YPGal). We investigate naïve and primed cells in both wild type (BY4741) and rrp6delta strains.  For mRNA abundance we measured mRNA abundance during exponential growth in YPD (t0, naïve) and 30 min, 1 hour and 3 hours after change to galactose (t30, t60 and t180). Then we transferred cells to YPD for 3 hours (t0’, primed) and measured galactose reinduction at 15 min, 30 min and 1 hour (t15’, t30’ and t60’). We perform 3 independent biological replicates.  For ChIP-Seq we compare naïve and primed cells. We Perform MNase treatment to map nucleosomes and investigate Input material (MNase treated) and after IP for H3, H3K4me2 and H3K4me2. We perform 3 independent biological replicates.  For RNA stability (nascent mRNA synthesis), we perform RNA metabolic labeling (SLAM-Seq) for naïve and primed cells. We investigate both prior to change to galactose (t0) and after 30 minutes in galactose (t30). We perform 2 independent biological replicates.

first: Bingnan

last: Li

first: Alisa

last: Alekseenko


title: SARS-CoV-2 mRNA Dual Immunization Induces Innate Transcriptional Signatures, Establishes T-Cell Memory and Coordinates the Response to Booster

city: Athens

first: Ioanna

last: Papadatou

state: Greece

address: Thivon & Papadiamantopoulou 1

department: "Agia Sophia" Children's Hospital

country: Greece

institute: National and Kapodistrian University of Athens

summary: Bulk mRNA sequencing of whole blood from health-care professionals aged 28-65 years was perfomed in samples collected before and three days after the second dose of BNT162b2, in order to analyze the human immune response to dual mRNA immunization with the mRNA BNT162b2 vaccine.

overall_design: 22 human whole blood samples before and after vaccination with the second dose of the mRNA BNT162b2 vaccine

first: I

first: M

last: Geropeppa

last: Verrou

last: Tzanoudaki

first: T

last: Lagousi

first: E

last: Liatsis

first: V

last: Spoulou


title: Conserved and plant-specific GCN5-containing complexes cooperate to regulate gene transcription and plant development [ChIP-Seq]

first: xinjian

last: He

summary: Although the conserved histone acetyltransferase HAG1/GCN5-containing complex SAGA (Spt-Ada-Gcn5 acetyltransferase) has been extensively studied in plants, whether HAG1 forms a plant-specific complex is unknown. Here, we identified a plant-specific GCN5-containing complex, PAGA (plant-ADA2A-GCN5-acetyltransferase), in Arabidopsis thaliana; the complex consists of two conserved subunits (HAG1/GCN5 and ADA2A) and four plant-specific subunits (SPC, ING1, SDRL, and EAF6). In the PAGA complex, SPC functions as a scaffold protein that is responsible for integrating the other subunits. SPC also enhances the binding of ING1 to histone H3 with methylated lysine 4 and promotes the histone acetylation activity of HAG1. Chromatin immunoprecipitation followed by sequencing indicated that PAGA not only shares target genes with SAGA but also has its specific target genes. While PAGA and SAGA promote transcription by mediating moderate and high levels of histone acetylation, respectively, at different sets of genes, PAGA can also function antagonistically against SAGA to prevent excessive transcription of PAGA- and SAGA-shared target genes. Unlike SAGA, which regulates multiple biological processes, PAGA is mainly involved in plant height and branch growth by regulating the transcription of genes involved in hormone biosynthesis and response. These results indicate that the HAG1-containing SAGA and PAGA complexes are coordinated to regulate gene transcription and development.

overall_design: Examination of the enrichment of ADA2A, ADA2B, HAG1, and ING1 on chromatin; Examination of H3K9Ac levels in wild type and two mutants

first: Xin-Jian


title: Conserved and plant-specific GCN5-containing complexes cooperate to regulate gene transcription and plant development [RNA-Seq]

overall_design: Examination of the mRNA expression of wild type and nine mutants in Arabidopsis


title: ABIN1 mutant (Q478H) contribute to progressive myelodysplastic syndromes liked diseases by type I IFNs signaling

status: Public on Jan 08 2023

city: shanghai

first: xuanhui

last: wu

state: shanghai

address: yueyang road 320

department: Institute of Nutrition

institute: Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences

summary: To understand the mechanism of MDS in  Abin1Q478H/Q478H mice, we performed RNA-seq analysis of  bone marrow lineage-negative cells from 5 months Abin1Q478H/Q478H mice and WT control mice to gain a global view of the transcriptome profile regulated by ABIN1(Q478H) mutation.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for bone marrow lineage-negative cells from 5 months Abin1Q478H/Q478H mice and WT control mice

first: Xuanhui

last: Wu

first: Haibing

last: Zhang


title: TCF7L2 is a key determinant of nonalcoholic fatty liver induced by carbohydrate intake I

city: Daejeon

first: Jaeeun

last: Jung

address: 125 Gwahak-ro, Youseong-gu

country: South Korea

institute: KRIBB

summary: Nonalcoholic fatty liver disease (NAFLD) associated with type 2 diabetes (T2D) easily progresses toward severe forms of nonalcoholic steatohepatitis (NASH) and fibrosis, and the underlying mechanism is under active investigation. Here, we established the role of transcription factor 7-like 2 (TCF7L2), the most significant T2D susceptibility gene, in NAFLD development and progression. Hepatic TCF7L2 expression was decreased in liver biopsies of patients with NAFLD. Based on the major risk factors for NAFLD development, liver-specific TCF7L2 knockout mice were subjected to a high-fat diet providing fatty acids (FAs) and refeeding/high-carbohydrate diet stimulating de novo lipogenesis. Hepatic TCF7L2 deficiency significantly increased the lipid synthetic pathways and hepatic TG accumulation by preferentially metabolizing carbohydrates than FAs. Mechanistically, TCF7L2 regulated miRNAs targeting SREBF1c and enhanced proteasome-mediated MLXIPL (ChREBP) degradation. Our findings will deepen the pathophysiological mechanism of NAFLD associated with dietary carbohydrate and diabetes, and will provide a potential target for treatment of NAFLD.

overall_design: Hepatic mRNA profiles of 12-week-old TCF7L2 wild type (TCF7L2 WT) and liver-specific TCF7L2 knockout (TCF7L2 LKO) mice refed a normal chow diet (NCD) for 24 h

first: Kyoung-Jin

last: Oh


title: Genome-wide tracking of DNA polymerase III in E. coli

city: Göteborg

first: Anders R.

last: Clausen

address: Box 440

institute: University of Gothenburg

summary: We used steric gate variants of DNA polymerase III that allows increased amounts of ribonucleotides to be incorporated. Ribonucleotides incorporated into genomic is hydrolyzed by alkali. The generated 5-ends are subsequently mapped.

overall_design: We map these ribonucleotides in the entire genome and determine if there is any strand bias.

first: Mahmood

last: Faraz

first: Roger

last: Woodgate

first: Anders


title: Multinucleation resets human macrophages for specialized functions at the expense of their identity

city: Singapore

first: Harry

last: Park

address: 8 College Rd

institute: Duke-NUS Medical School

summary: To investigate the effects of macrophage cell fusion and multinucleation, we have sorted mononuclear and multinucleated macrophages from 3 types of polykaryons: osteoclasts, foreign body giant cells (FBGCs) and Langhans giant cells (LGCs).

overall_design: Comparative gene expression profiling by RNA-seq between mononuclear and multinucleated osteoclasts, FBGCs and LGCs

first: Jacques

last: Behmoaras

first: Kourosh

last: Ahmadzadeh


title: Effect of MED23 R617Q mutation on enhancer activity and gene transcription in HEK293T cells [ChIP-Seq]

city: Shanghai

first: Gang

last: Wang

address: 2005 Songhu Rd

department: School of life sciences

institute: Fudan university

summary: To investigate the effect of MED23 R617Q mutation on gene regulation, we established MED23/R617Q mutant HEK293T cell line.

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for histone modifications H3K4me3,H3K4me1,H3K27ac as well as the PolII binding in the WT and MED23/R617Q mutant HEK293T cells.

first: Yenan

last: Yang

first: Chonghui

last: Li


title: Effect of MED23 R617Q mutation on chromatin interactions in HEK293T cells [Hi-C]

overall_design: Comparative chromain interation analysis of Hi-C data for the WT and MED23/R617Q mutant HEK293T cells.


title: Effect of MED23 R617Q mutation on gene expression in HEK293T cells [RNA-seq]

overall_design: Comparative gene expression profiling analysis of RNA-seq data for the WT and MED23/R617Q mutant HEK293T cells.


title: Changes in gene expression profile caused by mechanical stress in the ligamentum flavum -long term rabbit model-

status: Public on Jan 07 2023

city: Osaka

first: Akinobu

last: Suzuki

state: Osaka

address: 1-4-3 Asahimachi, Abeno-ku

department: Department of Orthopaedic surgery

institute: Osaka Metropolitan University

summary: To identify the changes in gene expression profile caused by mechanical stress in the ligamentum flavum, we performed resection of the L3-4 supraspinal muscle and L2-3, L4-5 posterolateral fusion with instrumentation to concentrate the mechanical stress with segmental instability at the L3-4 level. The control group underwent only surgical exposure as a sham operation. Both groups of rabbits were sacrificed at 1 year after surgery and total RNA were extracted from ligamentum flavum.

overall_design: mRNA profiles of rabbit ligamentum flavum obtained at the intervertebral stress concentration level (ISC level) , the fused level and the control level were generated by deep sequencing using Illumina Miseq. Sequence data were mapped on the Rabbit genome (Apr. 2009 (Broad/oryCun2)) using Tophat and analyzed by Cufflinks.

first: Akito

last: Yabu

first: Yuuki

last: Imai


title: Large-scale study suggests effects of trisomy 21 on fetal neurodevelopment may be more subtle than variability between organoids and isogenic lines

city: Worcester

first: Jan

last: Czerminski

state: MA

address: 55 Lake Ave N

department: Neurology

institute: UMass Medical School

summary: This study examines cortical organoids generated from a panel of isogenic trisomic and disomic iPSC lines (subclones) as a model of early fetal brain development in Down syndrome. An initial experiment comparing organoids from one trisomic and one disomic line showed many genome-wide transcriptomic differences and modest differences in cell-type proportions, suggesting there may be a neurodevelopmental phenotype that is due to trisomy of chr 21. To better control for multiple sources of variation, we undertook a highly robust study of ∼1,200 organoids using an expanded panel of six all-isogenic lines, three disomic, and three trisomic. The power of this experimental design was indicated by strong detection of the ∼1.5- fold difference in chr21 genes. However, the numerous expression differences in non-chr21 genes seen in the smaller experiment fell away, and the differences in cell-type representation between lines did not correlate with trisomy 21. Results suggest that the initial smaller experiment picked up differences between small organoid samples and individual isogenic lines, which “averaged out” in the larger panel of isogenic lines. Our results indicate that even when organoid and batch variability are better controlled for, variation between isogenic cell lines (even subclones) may obscure, or be conflated with, subtle neurodevelopmental phenotypes that may be present in ∼2nd trimester DS brain development. Interestingly, despite this variability between organoid batches and lines, and the “fetal stage” of these organoids, an increase in secreted Aβ40 peptide levels—an Alzheimer-related cellular phenotype—was more strongly associated with trisomy 21 status than were neurodevelopmental shifts in cell-type composition.

overall_design: Comparison of RNA-seq gene expression data from trisomic (T21) versus disomic cerebral organoids. In the pilot study, each RNA-seq library was from an individual organoid, with 5 samples each from one trisomic and one isogenic disomic cell-line. In the expanded study, each RNA-seq library was from a pool of ~6 organoids, with 8 samples (4 separate experiments x 2 replicate pools) each from three trisomic and three disomic cell-lines, all isogenic.

first: Oliver

middle: D

last: King

first: Jeanne

last: Lawrence


title: Effect of MED23 R617Q mutation

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

overall_design: Refer to individual Series


title: Evaluation of safety and immuno-efficacy of a next generation live attenuated yellow fever vaccine in cynomolgus macaques

status: Public on Jan 06 2023

city: Marcy L'Etoile

first: Emilie

last: Chautard

address: 1541 Avenue Marcel Mérieux

institute: Sanofi

summary: 36 male NHPs were randomized into groups of nine to receive subcutaneous injection in the deltoid muscle region of the upper arm with a single commercial dose of Stamaril (4 LogCCID50) or YF-VAX (6 LogCCID50), or 4 or 5 LogCCID50 vYF at WSL stage. Nine months after vaccination, NHPs along with six additional unvaccinated controls were challenged by a single sub-cutaneous injection of 3.0 LogCCID50 wild-type YFV Asibi strain in the scapula region. Blood samples were obtained before vaccination (baseline) and at various time points after vaccination, and before and after challenge.

overall_design: Whole blood RNA-seq to assess the genes involved in the immune responses to vaccination and to challenge with the wild type YFV Asibi.

first: Fabienne

last: Piras-Douce

first: Karine

last: Broudic

first: Franck

last: Raynal

first: Virginie

last: Courtois

first: Sylviane

last: Gautheron

first: Nathalie

last: Mantel


title: Ribosome dynamics following arginine deprivation in colon cancer cells

city: Pittsburgh

first: Dennis

last: Hsu

state: PA

address: 5117 Centre Ave

institute: University of Pittsburgh

summary: To investigate ribosome localization and gene expression dynamics during starvation in cancer cells, we performed RNA sequencing and ribosome profiling in RKO cells under fed and starved (12.5 uM arginine) conditions.

overall_design: Cells were kept under fed (400 uM arginine) or starved (12.5 uM arginine) conditions for 24 hours. RNA sequencing and ribosome profiling were performed concurrently following previously published protocols (PMID 28579404)


title: In-depth profiling of transcriptional activity of Aire in mouse mTECs

city: Tsurumi-ku, Yokohama

first: Hideyuki

last: Yoshida

state: Kanagawa

address: 1-7-22 Suehiro-cho

institute: RIKEN IMS

summary: Aire, a transcriptional regulator whose defect results in the development of autoimmunity, controls the transcriptome in medullary thymic epithelial cells (mTECs) including the genes for self-antigens. Here, we utilized a technique for profiling transcriptome from a single cell (RamDA-seq) to investigate bulk populations in mTECs deeply.

overall_design: Bulk RNA-seq analysis of FACS-sorted mouse thymic epithelial cells (TECs, CD45-EpCAM+Ly51-) from wild-type and Aire knockout (KO) mice

first: Ryuichiro

last: Miyazawa

first: Jun-ichi

last: Nagao

first: Ken-ichi

last: Arita-Morioka

first: Minoru

last: Matsumoto

first: Junko

last: Morimoto

first: Masaki

first: Takeshi

last: Oya

first: Koichi

last: Tsuneyama

first: Yoshihiko

last: Tanaka

first: Mitsuru


title: Dysregulation of RNA Pol activity at CTCF binding sites in EBV LCL ΔCTCF mutant

city: Ithaca

first: Joel

last: Baines

state: NY

address: Hungerford Hill Rd

department: Baker Institute for Animal Health

institute: Cornell University

summary: We used Precision Nuclear Run-on followed by Deep Sequencing (PRO-Seq) to investigate RNA Polymerase (Pol) activity during Epstein-Barr Virus (EBV) reactivation and its link to CTCF in latently EBV infected ymphoblastoid cell lines (LCLs). Nuclei were harvested from WT LCLs or LCLs containing an 18bp deletion at the LMP CTCF binding site (DCTCF) treated with DMSO or induced to reactivate with the small molecule C60 for 24h. Relative to WT, DCTCF displayed disrupted transcriptional activity at other CTCF sites during latency and this phenotype correlated with an inability to reactivate from latency.

overall_design: PRO-Seq data from 14h DMSO or C60 treated WT EBV LCLs and DCTCF EBV LCLs containing 2 biological replicates per condition. All samples contain Drosophila spike-in.

first: Laura

middle: E

last: Dunn

first: Chenhe

last: Su

first: Fang

last: Lu

first: Paul

last: Lieberman


title: ATAC-seq profiling in CD14+ cells isolated from rhesus macaques vaccinated with V1-deleted DNA/ALVAC/gp120 vaccine [study 2]

city: Bethesda

first: Massimiliano

last: Bissa

state: MD

address: 9000 Rockville Pike, bldg 41/ room c303

department: NCI/CCR

institute: National Institutes of Health

summary: We analyzed innate and adaptive immune responses elicited by the V1-deleted DNA/ALVAC/gp120/alum vaccine in non-human primates. Following SIVmac251 challenge exposure, we observed reduced risk of SIV acquisition comparing vaccinated animals to controls, confirming th ability of this vaccine strategy in decreasing the risk of SIV acquisition against vaginal exposure. Transcriptome and chromatin accessibility in CD14+ cells were analyzed by RNA-seq and ATAC-seq. Epigenetic reprogramming in CD14+ cells of the cyclic AMP/CREB pathway correlated with vaccine efficacy. The efficacy of V1-delted DNA/ALVAC/gp120/alum vaccine, based on V2-specific antibodies mediating apoptosis of infected cells (V2-ADCC), is complemented by efferocytosis, a cyclic AMP (cAMP)-dependent antiphlogistic engulfment of apoptotic cells by CD14+ monocytes. Our data support the protective role for CREB1 expression in monocytes and posit that efferocytosis, through the prompt and effective removal of apoptotic infected cells, contributes to vaccine efficacy by decreasing inflammation and maintaining tissue homeostasis.

overall_design: Twelve juvenile (average age 3.91 years, 0.155 SD), female macaques were enrolled in the study. All twelve macaques were immunized twice with V1-deleted DNA-SIV at weeks 0 and 4. At weeks 8 and 12 all macaques were boosted with intramuscular inoculations of 10^8 Plaque Forming Units (PFU) of recombinant ALVAC (vCP2432). At week 12, vaccinated macaques also received 400 μg of v1-delted SIVmac251–M766 protein formulated in alum Alhydrogel. The isolation of CD14+ cells was performed from freshly isolated PBMCs collected at weeks 13. The chromatin accessibility of monocyte population was assessed by Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq).

first: Sohyoung

last: Kim

first: Ramona

last: Moles

first: Saori

last: Fujiwara

first: Gordon

last: Hager

first: Genoveffa

last: Franchini


title: Paternal exposure to methylphenidate induces ADHD-like behavioral phenotypes and altered gene expressions in mouse offspring.

city: Shinagawa-ku

first: Ryota

last: Nakano

address: Hatanodai 1-5-8

department: Showa University Graduate School of Pharmacy

institute: Showa university

summary:
To determine whether paternal methylpenidate exposure alters the behavior and gene expression of the offspring.
We administrated methylphenidate (15 mg/kg) or saline (10 ml/kg) to sire and performed gene expression profiling analysis using data obtained from RNA-seq of striatum of 6-week-old offspring.

overall_design: Comparative gene expression profiling analysis of 6-week-old striatum RNA-seq data from offspring born to methylphenidate- or saline-treated sires.


title: RNA-seq profiling in CD14+ cells isolated from rhesus macaques vaccinated with V1-deleted DNA/ALVAC/gp120 vaccine

overall_design: Twelve juvenile (average age 3.91 years, 0.155 SD), female macaques were enrolled in the study. All twelve macaques were immunized twice with V1-deleted DNA-SIV at weeks 0 and 4. At weeks 8 and 12 all macaques were boosted with intramuscular inoculations of 10^8 Plaque Forming Units (PFU) of recombinant ALVAC (vCP2432). At week 12, vaccinated macaques also received 400 μg of v1-delted SIVmac251–M766 protein formulated in alum Alhydrogel. The isolation of CD14+ cells was performed from freshly isolated PBMCs collected at weeks 13. The transcriptome was assessed by total RNA sequencing (RNA-seq)

first: Slim

last: Fourati

first: Sarkis

last: Sarkis

first: Rafick

last: Sekaly