title: TET enzymes augment AID expression via 5hmC modifications at the Aicda superenhancer [Tet2-ChIP-seq]

city: La Jolla

first: Anjana

last: Rao

address: 9420 Athena Cir

department: Signaling and Gene Expression

institute: La Jolla Institute for Allergy and Immunology

summary: TET enzymes are dioxygenases that promote DNA demethylation by oxidizing the methyl group of 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC). Here we report a close correspondence between 5hmC-marked regions, chromatin accessibility and enhancer activity in B cells, and a strong enrichment for consensus binding motifs for basic region-leucine zipper (bZIP) transcription factors at TET-responsive genomic regions. Functionally, Tet2 and Tet3 regulate class switch recombination (CSR) in murine B cells by enhancing expression of Aicda, encoding the cytidine deaminase AID essential for CSR. TET enzymes deposit 5hmC, demethylate and maintain chromatin accessibility at two TET-responsive elements, TetE1 and TetE2, located within a superenhancer in the Aicda locus. Transcriptional profiling identified BATF as the bZIP transcription factor involved in TET-dependent Aicda expression. 5hmC is not deposited at TetE1 in activated Batf-deficient B cells, indicating that BATF recruits TET proteins to the Aicda enhancer. Our data emphasize the importance of TET enzymes for bolstering AID expression, and highlight 5hmC as an epigenetic mark that captures enhancer dynamics during cell activation.

overall_design: 5hmC mapping by CMS-IP, ATAC-seq, RNA-seq, ChIP-seqs using B cells unstimulated or activated as a function time. Cells were either from WT or with Tet2/3 acutely deleted.

first: Chan-Wang

last: Lio

first: Vipul

last: Shukla

first: Edahi

last: Gonzalez-Avalos

first: Daniela

last: Samaniego-Castruita

first: Abhijit

last: Chakraborty

first: Xiaojing

last: Yue

first: David

last: Schatz

first: Ferhat

last: Ay


title: TET enzymes augment AID expression via 5hmC modifications at the Aicda superenhancer [H3K27ac_ChIP-seq]

status: Public on Apr 29 2019

state: California

country: USA

type: Genome binding/occupancy profiling by high throughput sequencing

middle: J

middle: G


title: TET enzymes augment AID expression via 5hmC modifications at the Aicda superenhancer [BATF_ChIP-seq]


title: CUT&Tag for efficient epigenomic profiling of small samples and single cells.

city: Seattle

first: Jorja

last: Henikoff

state: WA

address: 1100 Fairview AV N, A1-162

department: Basic Sciences

institute: Fred Hutchinson Cancer Research Center

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

overall_design: Refer to individual Series


title: TET enzymes augment AID expression via 5hmC modifications at the Aicda superenhancer [RNA-seq]

type: Expression profiling by high throughput sequencing


title: TET enzymes augment AID expression via 5hmC modifications at the Aicda superenhancer

type: Methylation profiling by high throughput sequencing


title: TET enzymes augment AID expression via 5hmC modifications at the Aicda superenhancer [BS-seq]


title: TET enzymes augment AID expression via 5hmC modifications at the Aicda superenhancer [CMS-IP]


title: Fungal acetylome comparative analysis identifies an essential role of acetylation in human fungal pathogen virulence

status: Public on Apr 26 2019

city: ShenYang

first: Li

last: Hailong

state: Liaoning

address: NO. 3-11, Wenhua Road, Heping District

country: China

institute: Northeastern University

summary: Lysine acetylation is critical in regulating important biological processes in many organisms, yet little is known about acetylome evolution and its contribution to phenotypic diversity. Here, we compare the acetylomes of baker’s yeast and the three deadliest human fungal pathogens, Cryptococcus neoformans, Candida albicans, and Aspergillus fumigatus. Using mass spectrometry enriched for acetylated peptides together with public data from Saccharomyces cerevisiae, we show that fungal acetylomes are characterized by dramatic evolutionary dynamics and limited conservation in core biological processes. Notably, the levels of protein acetylation in pathogenic fungi correlate with their pathogenicity. Using gene knockouts and pathogenity assays in mice, we identify deacetylases with critical roles in virulence and protein translation elongation. Finally, through mutational analysis of deactylation motifs we find evidence of positive selection at specific acetylation motifs in fungal pathogens. These results shed new light on the pathogenicity regulation mechanisms underlying the evolution of fungal acetylomes.

overall_design: The paired-end RNA-seq and ChIP-seq of Cryptococcus neoformans H99s were performed using three biological replicates

first: Chen

last: Ding

first: Yanjian

last: Li

first: Hailong

first: Mingfei

last: Sui

first: Minghui

first: Jiamei

last: Wang

first: Yanag

last: Meng

first: Tianshu

last: Sun

first: Qiaojing

last: Liang

first: Chenhao

last: Suo

first: Xindi

last: Gao

first: Chao

first: Zhuoran

first: Wei

last: Du

first: Baihua

last: Zhang

first: Sixiang

last: Sai

first: Zhang

first: Jing

last: Ye

first: Hongchen

first: Shang

first: Jiayi

first: Manli

last: Zhong

first: Changbin

last: Chen

first: Shouliang

last: Qi

first: Ling

last: Lu

first: Dancheng


title: Tbet regulates the transcriptional programming of Be1 B cells.

city: Atlanta

first: Chris

last: Scharer

state: GA

address: 1510 Clifton Rd, Suite 3086A

department: Microbiology and Immunology

institute: Emory University

summary: To investigate the role of Tbet in B cell differentiation to "effector-like" antibody secreting cells (ASC's) we utilized an ex vivo culture system to differentiate B cells (Be1 cells) in the presence of Th1 polarized T cells. To determine the role of Tbet in Be1 cell differentiation we performed RNA-seq on Wt Be1 and Tbet negative (TbetNeg) Be1 cells.  Collectively, these data show that T-bet serves as master regulator for the Be1 cell fate and is required for induction of genes required for ASC differentiation in Be1 cells.

overall_design: Three biological replicates of Wt Be1 and Tbet negative Be1 cells were anazlyed by RNA-seq.

first: Frances

middle: E

last: Lund

first: Sara

middle: L

last: Stone

first: Betty

last: Mousseau

first: Christopher

middle: D


title: TET enzymes augment AID expression via 5hmC modifications at the Aicda superenhancer [ATAC-seq]

first: Anjana

last: Rao

first: Chan-Wang

last: Lio

first: Vipul

last: Shukla

first: Edahi

last: Gonzalez-Avalos

first: Daniela

last: Samaniego-Castruita

first: Abhijit

last: Chakraborty

first: Xiaojing

last: Yue

first: David

last: Schatz

first: Ferhat

last: Ay


title: Self-organization and symmetry breaking in intestinal organoid development

city: Basel

first: Denise

last: Serra

address: Maulbeerstrasse 14

country: Switzerland

institute: FMI


title: “Transcriptomics Analysis Of SOCS3-deficient keratinocytes: Reveled Insights Into Progression of Chronic Skin Disease

status: Public on Apr 28 2019

city: Tsurumi-ku, Yokohama City,

first: Archana

last: Bajpai

state: Kanagawa,

address: 1-7-22 Suehiro-cho,

department: IMS

country: Japan

institute: RIKEN Yokohama

summary: We analyzed time series transcriptomics data of SOCS3 conditional knockout keratinocytes mice at 2, 8 and 10 week by using RNA-Sequencing technology to gain a basic understanding on the role of SOCS3 in epidermal homeostasis and what are the key regulatory genes and interactions that are important for skin hemostasis. We identified the top altered genes profile and associated biological pathways and investigated how loss of SOCS3 from keratinocytes leads to chronic skin diseases. We also validated our RNA-seq analysis results on a human derived cultured keratinocyte cells. Our results suggest a novel function of SOCS3 gene that not only controls immune hemostasis but also plays an important role in epidermal hemostasis. We believe that establishing a regulatory model to explain the dynamics of SOCS3 that controls multiple cellular processes in keratinocyte will provide a detailed knowledge to elucidate the molecular mechanisms underlying epidermal homeostasis and the development of chronic epidermal diseases.

overall_design: Socs3 cKO mice mRNA profiles of 2, 8 and 10 week wild type (WT)  C57BL/6 mice were generated by sequencing using HiSeq 1000 system (Illumina) machine  which could read a 50 bp sequence.

first: Takashi

last: Ishii

first: Kosuke

last: Miyauchi

last: Gupta

first: Yuki

last: Shimizu-Yoshida

first: Masato

last: Kubo

first: Hiroaki

last: Kitano


title: In vivo generation of post-infarct human cardiac muscle by laminin-promoted cardiovascular progenitors [LN-521 or LN-521+LN-221]

city: Singapore

first: Aida

last: Moreno-Moral

address: 8 College Road

country: Singapore

institute: Duke-NUS Medical School

summary: Regeneration of injured human heart muscle is limited and an unmet clinical need. There are no methods for the reproducible generation of clinical quality stem-cell-derived cardiovascular progenitors (CVPs). We identified laminin-221 (LN-221) as the most likely expressed cardiac laminin. We produced it as human recombinant protein, and showed that LN-221 promotes differentiation of pluripotent hESCs towards cardiomyocyte lineage and downregulates pluripotency and teratoma associated genes. We developed a chemically defined, xeno-free laminin-based differentiation protocol to generate CVPs. We show high reproducibility of the differentiation protocol using time-course bulk RNA sequencing developed from different hESC lines. Single-cell RNA sequencing of CVPs derived from hESC lines supported reproducibility and identified three main progenitor subpopulations. These CVPs were transplanted into myocardial infarction mice, where heart function was measured by echocardiogram and human heart muscle bundle formation was identified histologically. This method may provide clinical quality cells for use in regenerative cardiology.

overall_design: Human embryonic stem cells were cultured in wells coated with LN-521 or LN-521+LN-221 using nutristem medium. RNA is extracted when cells reached confluence.

first: Lynn

last: Yap

first: Enrico

last: Petretto

first: Karl

last: Tryggvason


title: In vivo generation of post-infarct human cardiac muscle by laminin-promoted cardiovascular progenitors [H1 differentiation protocol]

overall_design: Human embryonic stem cells were cultured in wells coated with LN-521 and LN-221 using RPMI1460 supplemented with B21 without insulin medium. Differentiation commenced when cells reached confluency. Small molecule inhibitor CHIR99021 (inhibitor of GSK3) was added at day 0 followed by IWP2 (inhibiot of Wnt production) at day 3. Cells continue to be cultured in RPMI1460 supplemented with B21 without insulin medium for 10 days with medium change every other day. After day 10, medium was changed to RPMI1460 supplemented with B21 CTS grade medium. RNA was extracted from triplicates wells at day 0, 1, 3, 11, 14, 20, 30 and 90 and from 5 wells at day 5, 7 and 9.


title: Expression data from young and old mouse ovarian secondary follicles

status: Public on Apr 25 2019

city: Wuhan

first: Shixuan

last: Wang

state: Hubei

address: No.1095 Jie Fang Avenue

institute: Huazhong University of Science and Technology

summary: The ovarian function decreases in parallel with aging. So do the quantity of follicles, which is about 1-2 million at birth, while only about 1000 primordial follicles are left at menopause. Folliculogenesis is vital for ovary function, no matter the synthesis of female hormones or ovulation, yet the mechanisms for its changing with increasing age are not fully understood. To further understand the age-related molecular changes in the process of folliculogenesis, we performed microarray gene expression profile analysis using total RNA extracted from young (9 weeks old) and old (32 weeks old) mouse ovarian secondary follicles. The results of our current microarray study revealed that there were 371 (≥2 fold, q-value ≤0.05) genes differentially expressed in which 174 genes were up-regulated and 197 genes were down-regulated in old mouse ovarian secondary follicles compared to young mouse ovarian secondary follicles. The gene ontology and KEGG pathway analysis of differentially expressed genes uncovered critical biological functions such as immune system process, aging, transcription, DNA replication, DNA repair, protein stabilization and apoptotic process were affected in the process of aging. The considerable changes in gene expression profile may have an adverse influence on follicle quality and folliculogenesis. Our study provided information on the processes that may contribute to age-related decline in ovarian function.

overall_design: Ovarian secondary follicles from young and old mouse were selected for RNA extraction and hybridization on Affymetrix microarrays. The gene expression profile were analyzed to found what changed in the process of mouse ovarian aging.

first: Wenlei

last: Ye

first: Wei

last: Shen

first: Su

last: Zhou

last: Yan

first: Jing

last: Cheng

first: Guangxin

last: Pan

first: Aiyue

last: Luo


title: CGH array used to identify de novo copy number variations in offspring of BaP exposed parents.

city: Ottawa

first: Matthew

last: Meier

state: Ontario

address: 251 Sir Frederick Banting Driveway

department: Health Canada

country: Canada

institute: Government of Canada

summary: CGH arrays were used to detect de novo CNVs in the litters produced from mating MutaMouse sires with C57Bl/6J dams.

overall_design: Specifically, high molecular weight DNA was extracted from the liver of each animal. One µg of offspring DNA was labelled with Cy5 dye. Five hundred ng of DNA from each respective parent were mixed together and labelled with Cy3 dye. As positive controls, and to identify existing strain differences, two additional arrays were used to compare MutaMouse with C57BL/6J DNA. DNA labelled with Cy3 and Cy5 were mixed together for hybridization onto the CGH array.

first: Marc

middle: A

last: Beal

first: Andrew

last: Williams

first: Andrea

last: Rowan-Carroll

first: Remi

last: Gagne

first: Sarah

last: Lindsay

first: Tomas

last: Fitzgerald

last: Hurles

first: Franscesco

last: Marchetti

first: Carole

last: Yauk


title: In vivo generation of post-infarct human cardiac muscle by laminin-promoted cardiovascular progenitors [HS1001 differentiation protocol]

first: Aida

last: Moreno-Moral

overall_design: Human embryonic stem cells HS1001 were cultured in wells coated with LN-521 and LN-221 using RPMI1460 supplemented with B21 without insulin medium. Differentiation commenced when cells reached confluency. Small molecule inhibitor CHIR99021 (inhibitor of GSK3) was added at day 0 followed by IWP2 (inhibiot of Wnt production) at day 3. Cells continue to be cultured in RPMI1460 supplemented with B21 without insulin medium for 10 days with medium change every other day. After day 10, medium was changed to RPMI1460 supplemented with B21 CTS grade medium. RNA was extracted from triplicates wells at day 0, 1, 3, 11, 14, 20, 30 and 90 and from 5 wells at day 5, 7 and 9.

first: Lynn

last: Yap

first: Enrico

last: Petretto

first: Karl

last: Tryggvason


title: Identification of metabolically distinct adipocyte progenitor cells in human adipose tissues

city: Clayton

first: Stuart

middle: Kenneth

last: Archer

state: VIC

address: 15 Innovation Walk, Monash University

department: Monash Bioinformatics Platform

country: Australia

institute: Monash University

summary: Adipocyte progenitor cells (APCs) provide the reservoir of regenerative cells to produce new adipocytes, although their identity in humans remains elusive. Using FACS analysis, gene expression profiling and metabolic and proteomic analyses, we identified three APCs subtypes in human white adipose tissues. The APC subtypes are molecularly distinct but possess similar proliferative and adipogenic capacities. Adipocytes derived from APCs with high CD34 expression exhibit exceedingly high rates of lipid flux compared with APCs with low or no CD34 expression, while adipocytes produced from CD34- APCs display beige-like adipocyte properties and a unique endocrine profile. APCs were more abundant in gluteofemoral compared with abdominal subcutaneous and omental adipose tissues, and the distribution of APC subtypes varies between depots and in patients with type 2 diabetes. These findings provide a mechanistic explanation for the heterogeneity of human white adipose tissue and a potential basis for dysregulated adipocyte function in type 2 diabetes.

overall_design: Molecular, biochemical and clinical examination of three cell types wthin the stromal vascular fraction of human adipose tissue.

first: Arthe

last: Raajendiran

first: Paul

middle: O

last: Brien

first: Renea

last: Taylor

middle: S

last: Rodeheffer

middle: R

last: Burton

last: Watt

middle: K


title: Medium pH influences citric acid and lipid production in oleaginous yeast Yarrowia lipolytica

city: Urbana

first: Christopher

middle: V

last: Rao

state: IL

address: 600 S Mathews Ave

department: Chemical and Biomolecular Engineering

institute: University of Illinois Urbana Champaign

summary: The goal of this study is to find out how Yarrowia lipolytica W29’s transcriptome changes in response to different pHs in certain medium, where the production of citric acid and lipid vary significantly at different pHs. The changes in transcriptome will give us insight about the mechanism of citric acid and/or lipid production are regulated. We harvested Y. lipolytica cells from bioreactor cultures from three different pHs: 2.0, 4.0 and 6.0 in triplicates. We sequenced the mRNA by Illumina HiSeq 2500 and generated an average of 20 million reads for each sample. We did not find distinct gene expression changes for the enzymes right downstream the intersection where citrate is cleaved into acetyl-CoA. Instead, from gene ontology enrichment analysis, we observed proteins with transport activities were overrepresented in gene groups that were up-regulated higher pH conditions, where citric acid secretion is favored.

overall_design: mRNA profiling of Yarrowia lipolytica W29 cells in pH 2.0, 4.0 and 6.0 bioreactors in triplicates, harvested at hour 50, sequenced by Illumina HiSeq 2500

first: Shuyan

last: Zhang

first: Christpher


title: Relationship between growth and gene expression in papaya treated with freeze-thaw awakening method

status: Public on Apr 24 2019

city: Tokyo

first: Minaho

last: Kawamura

address: BLICK GATE Suidobashi F2, Chiyodaku-kandamisakicho

summary: The freeze-thaw awakening is a method in which seeds or germ cells prior to germination are slowly cooled, stored, and thawed to promote growth. To further test the validity of this method, we applied freeze-thaw awakening treatment on papaya seeds. When the seed was grown under room temperature (15-25C), the germination rate increased by more than 40% compared to those that were not subjected to the method.  At 60 days post germination, the plant’s height was about 1.4 times as high as that of the untreated control. In addition, when both samples were grown in the field for about a year and a half, the treated showed darker green leaf color and an increase of seedlings per seed compared to the control. No significant difference in weight per fruit was observed. Comprehensive gene expression analysis of papaya leaves using RNA-seq showed more than 1000 differentially expressed genes, of which had genes involved in plant hormone synthase and environmental stress response. From these results, we show here that freeze-thaw-awakening is an effective method in promoting papaya growth.

overall_design: Total RNA-seq data was performed between Freeze-thaw-awakening method-treated and untreated (control) Carica Papaya Linn leaves (n=1).

first: Setsuzo

last: Tanaka


title: Self-organization and symmetry breaking in intestinal organoid development [scRNA-Seq]

first: Denise

last: Serra

summary: Intestinal organoids are complex three-dimensional structures that mimic cell type composition and tissue organization of the intestine by recapitulating the self-organizing capacity of cell populations derived from a single stem cell. Crucial in this process is a first symmetry-breaking event, in which only a fraction of identical cells in a symmetrical cyst differentiate into Paneth cells, which in turn generates the stem cell niche and leads to asymmetric structures such as crypts and villi. We here combine a quantitative single-cell gene expression and imaging approach to characterize the development of intestinal organoids from a single cell. We show that intestinal organoid development follows a regeneration process driven by transient Yap1 activation.  Cell-to-cell variability in Yap1, emerging in symmetrical cysts, initiates a Notch/Dll1 lateral inhibition event driving the symmetry-breaking event and the formation of the first Paneth cell. Our findings reveal how single cells exposed to a uniform growth-promoting environment have the intrinsic ability to generate emergent, self-organized behavior resulting in the formation of complex multicellular asymmetric structures.

overall_design: Single cell RNA sequencing of single cells isolated from intestinal organoids day3 and intestinal organoids day 5

first: Urs

last: Mayr

first: Andrea

last: Boni

first: Ilya

last: Lukonin

first: Markus

last: Rempfler

first: Ludivine

last: Challet Meylan

first: Michael

middle: B

last: Stadler

first: Petr

last: Strnad

first: Panagiotis

last: Papasaikas

first: Dario

last: Vischi

first: Annick

last: Waldt

first: Guglielmo

last: Roma

first: Prisca

last: Liberali


title: Self-organization and symmetry breaking in intestinal organoid development [bulk RNA-Seq]

overall_design: Intestinal organoids mRNA profiles for each day of organoid development (day 0 – day 5) in triplicate. Three different organoid lines C57BL/6 wild type have been used.


title: RNA-seq and ATAC-seq analysis of the role of PBRM1 under stress conditions

city: Bethesda

first: Benjamin

last: Carter

state: MD

address: 10 Center Drive

department: NHLBI

institute: National Institutes of Health

summary: We used RNA-seq to characterize the contributions of PBRM1 to gene expression in NmuMG cells with and without oxidative or low-glucose stress conditions. Further, we used ATAC-seq to characterize the effects of PBRM1 on chromatin accessibility in HK-2 and NMuMG cell lines. Our analyses reveal a role for PBRM1 in expression of genes associated with stress responses and with specific transcription factor families, such as the FOXO family.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Libraries prepared for RNA-seq or ATAC-seq were sequenced using Illumina HiSeq technology. Sequencing was performed in biological triplicate.

first: Emily

last: Dykhuizen

first: Basudev

last: Chowdhury


title: Transitions in cell potency during early mouse development are driven by Notch

city: Madrid

first: Manuel

last: Gomez

state: Madrid

address: Melchor Fernández Almagro, 3

country: Spain

institute: CNIC

summary: The Notch signalling pathway plays fundamental roles in diverse developmental processes in metazoans, where it is important in driving cell fate and directing differentiation of various cell types. However, we still have limited knowledge about the role of Notch in early preimplantation stages of mammalian development, or how it interacts with other signalling pathways active at these stages such as Hippo. By using genetic and pharmacological tools in vivo, together with image analysis of single embryos and pluripotent cell culture, we have found that Notch is active from the 4-cell stage. Transcriptomic analysis in single morula identified novel Notch targets, such as early naïve pluripotency markers or transcriptional repressors such as TLE4. Our results reveal a previously undescribed role for Notch in driving transitions during the gradual loss of potency that takes place in the early mouse embryo prior to the first lineage decisions.

overall_design: Transcriptomic analysis comparing single Rbpj mutant and control mouse morulae. RNA was isolated from individual E2.5 embryos from two litters. 3 mutant and 3 control embryos were used for analysis.

first: Sergio

last: Menchero

first: Miguel

last: Manzanares


title: Mapping the chemotherapy-induced RNA interactome in Glioblastoma

city: Luxembourg

first: Arnaud

last: Muller

address: 84 Val Fleuri

department: DONC

country: Luxembourg

institute: LIH

type: Non-coding RNA profiling by high throughput sequencing


title: Mapping the chemotherapy-induced RNA interactome in Glioblastoma [RNA-Seq]

summary: Long non-coding RNAs (lncRNAs) are increasingly recognized as important players in transcription and epigenetic-driven cell diversification. So far, lncRNA function in more dynamic transcriptional reprogramming, i.e drug response, has been largely unexplored. Here, we investigated the regulatory circuits induced by chemotherapy in glioblastoma, the most aggressive and clinically refractory brain cancer. We performed a detailed characterization of the cellular and transcriptional response of glioblastoma stem-like cells to the alkylating agent temozolomide (TMZ). We found that in addition to mRNAs, TMZ affects the expression of a large number of non-coding RNAs (miRNAs, snoRNAs, lncRNAs). Our global transcriptome analysis provides a comprehensive characterization of regulatory circuits involving transcription factors, mRNAs, miRNAs and lncRNAs. To analyse the putative functions of these largely unknown RNA molecules, we developed a pipeline to integrate small and large RNA-seq data from multiple public databases and our own experiments. This led to the identification of the RNA interactome of glioblastoma and allowed us to define regulatory loops mediated by lncRNAs. We identified 22 key lncRNAs involved in transcriptional regulatory motifs, and three lncRNAs associated with patient prognosis, independent of other known response predictors. The investigation of TMZ-induced molecular networks in glioblastoma highlights novel coding and non-coding RNA-based predictors of glioblastoma chemoresistance, as well as potential targets to counteract such resistance.

overall_design:
RNA and small RNA profiling of 3 GBM stem-like cells and neural stem cells under TMZ treatment or vehicle in triplicate.
This Series represents the RNA profiling dataset.

first: Sabrina

last: Fritah

first: Wei

last: Jiang

first: Ramkrishna

last: Mitra

first: Anna

last: Golebiewska

first: Tao

last: Ye

first: Laurent

last: Vallar

first: Eric

last: Van Dyck

first: Christel

last: Herold-Mende

first: Zhongming

last: Zhao

first: Francisco

last: Azuaje

first: Simone

middle: P

last: Niclou


title: Mapping the chemotherapy-induced RNA interactome in Glioblastoma [smallRNA-Seq]

overall_design:
RNA and small RNA profiling of 3 GBM stem-like cells and neural stem cells under TMZ treatment or vehicle in triplicate.
This Series represents the small RNA profiling dataset.


title: ETV4 is necessary for estrogen signaling and growth in endometrial cancer cells [RNA-seq]

status: Public on Apr 23 2019

city: Salt Lake City

first: Jason

last: Gertz

state: UT

address: 2000 Circle of Hope

department: Oncological Sciences

institute: University of Utah

summary: Estrogen signaling through estrogen receptor alpha (ER) plays a major role in endometrial cancer risk and progression; however, the molecular mechanisms underlying ER’s regulatory role in endometrial cancer are poorly understood. In breast cancer cells, ER genomic binding is enabled by FOXA1 and GATA3, but the transcription factors that control ER genomic binding in endometrial cancer cells remain unknown. We previously identified ETV4 as a candidate factor controlling ER genomic binding in endometrial cancer cells and here we explore the functional importance of ETV4. Homozygous deletion of ETV4, using CRISPR/Cas9, led to greatly reduced ER binding at the majority of loci normally bound by ER. Consistent with the dramatic loss of ER binding, the gene expression response to estradiol was dampened for most genes. ETV4 contributes to estrogen signaling in two distinct ways; ETV4 loss impacts chromatin accessibility at some ER bound loci and impairs ER nuclear translocation. The diminished estrogen signaling upon ETV4 deletion led to decreased growth, particularly in 3D culture where hollow organoids were formed. Our results show that ETV4 plays a necessary role in estrogen signaling in endometrial cancer cells.

overall_design: RNA-seq was used to study the effects of ETV4 knock out on gene expression

first: Adriana

middle: C

last: Rodriguez


title: Identification of HIF-1 signaling pathway in Pelteobagrus vachelli using RNA-Seq: effects of acute hypoxia and reoxygenation on oxygen sensings, respiratory metabolism and hematology indices

status: Public on Apr 21 2019

city: Nanjing

first: Shaowu

last: Yin

state: jiangsu

address: College of Life Sciences, Nanjing Normal University, 1 Wenyuan Road,  210023, China.

institute: Nanjing Normal University

summary: we used next-generation sequencing technology to characterise mRNA-seq from five mixed tissues (heart, liver, brain, spleen and kidney) to generate a large amount of P. vachelli transcriptomic reads from multiple tissues.

overall_design: Examination of 2 different oxygen-treated in Pelteobagrus vachelli (Repeat each treatment has three biology).

first: Guosong

last: Zhang


title: CellTag Indexing: genetic barcode-based sample multiplexing for single-cell genomics

status: Public on Apr 20 2019

city: St Louis

first: Samantha

last: Morris

state: Missouri

address: Department of Developmental Biology, Washington University School of

institute: Washington University in St Louis

summary: High-throughput single-cell assays increasingly require special consideration in experimental design, sample multiplexing, batch effect removal, and data interpretation. Here, we describe a lentiviral barcode-based multiplexing approach, CellTag Indexing, which uses predefined genetic barcodes that are also heritable, enabling cell populations to be tagged, pooled, and tracked over time in the same experimental replicate. We demonstrate the utility of CellTag Indexing by sequencing transcriptomes using a variety of cell types, including long-term tracking of cell engraftment and differentiation in vivo. Together, this presents CellTag Indexing as a broadly applicable genetic multiplexing tool that is complementary with existing single-cell technologies.

overall_design: RNA sequencing of single transcriptomes and detection of sample identity by CellTag barcodes in 2-tag species mixing of MEF and HEK293T cells, 5-tag species mixing of MEF and HEK293T cells, and iEP-engrafted mouse colon.

first: Chuner

last: Guo


title: Defining reprogramming checkpoints from single cell analysis of induced pluripotency

city: Madison

first: Rupa

last: Sridharan

state: WI

address: 330 N. Orchard Street

department: Wisconsin Institute for Discovery

institute: University of Wisconsin

summary: Elucidating the mechanism of reprogramming is confounded by heterogeneity due to the low efficiency and differential kinetics of obtaining induced pluripotent stem cells (iPSCs) from somatic cells. Therefore we increased the efficiency with a novel combination of epigenetic and signaling molecules and profiled the transcriptomes of individual reprogramming cells. Contrary to the established temporal order, somatic gene inactivation and upregulation of cell cycle, epithelial and early pluripotency genes can be triggered independently such that any combination of these events co-occurs in single cells. Sustained pluripotency requires the co-expression of Nanog, Oct4 and Sox2 with specific cohorts of genes. We uncover functional roles for Ehf, Phlda2, and translation initiation factor Eif4a1 for robust iPSC generation. Using regulatory network analysis we identify a critical role for signaling inhibition by 2i in repressing somatic expression, and synergy between the epigenetic modifiers ascorbic acid and a Dot1L inhibitor for pluripotency gene activation.

overall_design: Single cell RNA sequencing of mouse embryonic fibroblast during reprogramming and embryonic stem cells.

first: Khoa

last: Tran


title: Transcriptomic analysis reveals the early signaling events of narciclasine in Arabidopsis root apex

status: Public on Apr 19 2019

city: yinchuan

last: Xiaofan

state: Ningxia

address: Helanshan west road

department: school of life science

institute: Ningxia univertisty

summary: we report the application of high throughput sequencing technology for digital gene expression profiling of the gene expression pattern in Arabidopsis root tips treated with 0.5 µM narciclasine at 2 and 12 hr.Compared with controls, 236 genes were upregulated and 54 genes were downregulated with 2 hrs of narciclasine treatment, while 968 genes were upregulated and 835 genes were down-regulated with 12 hrs of treatment. The Gene Ontology analysis revealed that the differentially expressed genes were highly enriched during oxidative stress, including those involved in the 'regulation of transcription', 'response to oxidative stress', 'plant-pathogen interaction', 'ribonucleotide binding', 'plant cell wall organization', and 'ribosome biogenesis'. Moreover, Kyoto Encyclopedia of Genes and Genomes pathway enrichment statistics suggested that carbohydrate metabolism, amino acid metabolism, amino sugar and nucleotide sugar metabolism, and biosynthesis of phenylpropanoid and secondary metabolites were significantly inhibited by 12 hrs of narciclasine exposure.

overall_design: Examination of the gene expression profiles at 2 and 12 hr of narciclasine treatment in Arabidopsis root tips

first: Xiaofan


title: PAD2-mediated citrullination contributes to efficient oligodendrocyte differentiation and myelination

city: Stockholm

first: Eneritz

last: Agirre

address: Solnavägen 9

department: MBB

country: Sweden

institute: Karolinska Institutet

summary: Citrullination, the deimination of arginine residues into citrulline, has been implicated in the aetiology of several diseases. In multiple sclerosis (MS), citrullination is thought to be a major driver of pathology, through hypercitrullination and destabilization of myelin. As such, inhibition of citrullination has been suggested as a therapeutical strategy for MS. Here we show that citrullination by peptidylarginine deiminase 2 (PADI2) is in contrast required for normal oligodendrocyte differentiation, myelination and motor function. We identify several targets for PADI2, including not only myelin-related proteins, but also several chromatin-associated proteins, implicating PADI2 in epigenetic regulation. Accordingly, we observe that PADI2 inhibition and its knockdown affect chromatin accessibility and prevent the upregulation of genes involved in oligodendrocyte differentiation. Moreover, mice lacking PADI2, display motoric dysfunction and a decreased number of myelinated axons in the corpus callosum. Our study demonstrates that citrullination is required for oligodendrocyte lineage progression and myelination and thus its targeted activation in the oligodendrocyte lineage might be beneficial in the context of remyelination in diseases as MS.

overall_design: ATAC-seq of siPadi2 and control differentiating oli-neu. 3 n's for scrambled siRNA and siRNA targeting Padi2 exon2 in differentiating oli-neu, performed ATAC-seq according to Buenrostro et al 2013. H3K27ac ChIP-seq of proliferating and differentiating oli-neu.

first: Ana

middle: M

last: Falcao

first: Mandy

last: Meijer

first: Antonella

last: Scaglione

first: Puneet

last: Rinwa

first: Jialiang

last: Liang

first: Sara

last: Larsen

first: Abeer

last: Heskol

first: Rebecca

last: Frawley

first: Michael

last: Klingener

first: Manuel

last: Varas-Godoy

first: Alexandre ASF

last: Raposo

first: Patrik

last: Ernfors

first: Diogo

last: Castro

last: Nielsen

first: Patrizia

last: Casaccia

first: Gonçalo

last: Castelo-Branco


title: Genomic binding of RUNX1 in MCF10A cells

status: Public on Apr 18 2019

first: Jing

last: Huang

institute: National Cancer Institute

summary: The overall goal of this study is to identify the genomic binding of RUNX1 in MCF10A cells. We used ChIPseq (chromatin immunoprecipitation assay followed by deep sequencing) to identify the binding sites of RUNX1 in MCF10A cells. We performed ChIPseq of RUNX1 using parental MCF10A cells and did not identify high confident binding sites. To overcome this hurdle, we first generated a RUNX1 deleted MCF10A cell line using CRISPR-Cas9. We then transduced this RUNX1 KO MCF10A cells with lentiviruses that inducibly expresses RUNX1. After treating RUNX1 inducible MCF10A cells with 1 ug/ml doxycycline for 24 hours, we performed ChIPseq of RUNX1.

overall_design: Two samples from MCF10A cells: one input control and one RUNX1 ChIPseq.


title: RNA binding of CBFB and hnRNPK

summary: RNA immunoprecipitation assay followed by next generation sequencing (RIPseq) to identify RNAs bound by CBFB and hnRNPK in breast cells.

overall_design: One repeat for RIPseq of CBFB and two repeats for hnRNPK. A stable cell line derived from MCF10A cells (ATCC, Cat: CRL-10317) expressing FLAG tagged CBFB was used for CBFB RIP using the FLAG antibody (Sigma, Cat: A2220). Parental MCF10A cells were used for hnRNPK RIP using hnRNPK antibody (Bethyl Laboratory, Cat: A300-674A).

first: Navdeep

last: Malik


title: Notch signalling mediates secondary senescence

city: Providence

first: Nicola

last: Neretti

state: RI

address: 70 Ship St

department: Department of Molecular Biology, Cell Biology & Biochemistry

institute: Brown University

summary: Oncogene induced senescence (OIS) is a tumour suppressive response to oncogene activation that can be transmitted to neighbouring cells through secreted factors of the senescence associated secretory phenotype (SASP). Using single-cell transcriptomics we observed two distinct endpoints, a primary marked by Ras and a secondary by Notch. We find that secondary senescence in vitro and in vivo requires Notch, rather than SASP alone as previously thought. Currently, primary and secondary senescent cells are not thought of as functionally distinct endpoints. A blunted SASP response and the induction of fibrillar collagens in secondary senescence compared to OIS point towards a functional diversification.

overall_design: (Smart-seq2 Time course experiment): ER:RasG12V -expressing cells were induced into senescence for 7 days with 4-hydroxytamoxifen (4-OHT) and were isolated as single cells using FACS. Single cells that were not induced with 4-OHT were used as control. Single cells were also collected at another two time points, day 2 and day 4, before they became fully senescent on day 7. (10x Co-culture experiment): GFP cells are co-cultured with ER:Ras expressing cells and were induced into senescence with 4-OHT. Single cell 3' gene expression data was generated using 10x Genomics Chromium.  (Smart-seq2 Hepatocyte experiment): Ex vivo primary hepatocytes were isolated using a modified retrograde perfusion technique as previously described[27]. Briefly, following perfusion with Perfusion Medium (Gibco) for 5 min, and Liver Digest Medium (Gibco) for 10 min, the liver was excised and the capsule disrupted to yield a cell suspension that was collected in Williams' E Medium supplemented with 2% FCS. Hepatocytes were purified by pelleting through a 40% (v:v) percoll gradient prior to FACS analysis.  (10x dnMAML1 experiment): We used normal diploid human female lung fibroblasts IMR90 isolated at 16 weeks of gestation for all in vitro assays (ATCC® CCL-186™). pLNCX2 ER:rasG12V-expressing IMR90 were maintained and senescence induced as described under 5% O2 conditions. ER:IMR90 cells were co-cultured with IMR90:GFP (an empty vector fused with mVenus  or with a dominant negative form of MAML1 fused with mVenus  cells at 1:10 ratio. (Transwell bulk-RNA-seq): ER:RasG12V-expressing cells were co-cultured with IMR90:GFP. The co-cultured cells were placed into the lower chamber of a transwell system (density 5x103 cells/well). Another pure population of IMR90:GFP cells were cultured in the upper chamber of the transwell system. All cells were maintained in 4-hydroxytamoxifen (Sigma) for 7 days. All experiments were performed in triplicate.

first: Y

last: Teo

first: Tamir

last: Chandra


title: An siRNA screen identifies CHD4 as a target for epigenetic therapy

city: Philadelphia

first: yasuyuki

last: okamoto

state: pa

address: 3307 N. Broad Street

department: fels

institute: temple university

summary:
AIM: We performed RNA-sequencing experiments seeking genes whose expression changed after siCHD4 treatment.
METHOD: We generated cDNA libraries from RNA purified from SW48 treated by siNegative control, siCHD4, siNegative control plus siDNMT1, siCHD4 plus siDNMT1, siCHD4 plus Decitabine and siNegative control plus Decitabine. We sequenced the cDNA libraries generating single end 50 bp reads on the illumina HiSeq 2500 platform. Sequencing reads were aligned to the human genome hg19 using TopHat
RESULTS: We were able to map 23600 genes.  284 genes in siCHD4, 289 genes in  siDNMT1, 309 genes in DAC, 1090 genes in siCHD4 plus siDNMT1 and 468 genes in siCHD4 plus siDNMT1 were significantly  upregulated at least two fold compared  to siNegative control.

first: Matteo

last: Cesaroni

first: Yasuyuki

last: Okamoto


title: RNAseq of ribosomal fractionation to assess the effect of CBFB on translation regulation

summary: Five million wild type (WT) and CBFB knockout (CBFB_KO) MCF10A cells were subject to ribosomal fractination. Total RNA from each fraction was extracted using Trizol followed by Qiagen RNAeasy kit. Polyribosomal fractions were polled as one sample. RNAs in the free, mono- (mono) and polyribosomal (poly) fractions were used for RNAseq.

overall_design:
Two replicates for each sample
Sequenced on Illumina NextSeq 500


title: Gene expression regulated by warm temperature in C. elegans

city: Chongqing

first: lei

last: Zhou

address: No.55, South University Road, Shapingba District

institute: Chongqing University

summary: Stress resistance induced by mild environmental stress protects animals against aging-associated cellular damages and promotes longevity. Here, we reveal that mild heat triggers innate immune and detoxification responses that confers longevity at warm temperatures. We compared the transcriptome of 25°C-cultivated animals to that of 15°C controls through RNA-seq analysis. A total of 1958 transcripts were differentially regulated, with 1143 up-regulations and 815 down-regulations.

overall_design: RNA from 15°C and 25°C-cultivated wild type C. elegans developed to the L4 stage was extracted and analyzed by RNA sequencing. Genes having a fold change of > 2 (either up or down) and FDR of < 0.01 were considered as high temperature-regulated genes.

first: Haiqing

last: Tang

first: Lei

first: Bin

last: He

first: Shanshan

last: Pang


title: 6mA-DNA-binding factor Jumu controls maternal-to-zygotic transition upstream of Zelda

city: Beijing

first: Shunmin

address: 1 Beichen West Road,  Chaoyang District

institute: Institute of Zoology, Chinese Academy of Sciences

summary: A long-standing question in the field of embryogenesis is how the zygotic genome is precisely activated by maternal factors, allowing normal early embryonic development. We have previously shown that N6-methyladenine (6mA) DNA modification is highly dynamic in early Drosophila embryos and forms an epigenetic mark. However, little is known about how 6mA-formed epigenetic information is decoded. Here we report that the Fox-family protein Jumu binds 6mA-marked DNA and acts as a maternal factor to regulate the maternal-to-zygotic transition. We find that zelda encoding the pioneer factor Zelda is marked by 6mA. Our genetic assays suggest that Jumu controls the proper zygotic genome activation (ZGA) in early embryos, at least in part, by regulating zelda expression. Thus, our findings not only support that the 6mA-formed epigenetic can be read by specific transcription factors, but also uncover a mechanism by which the Jumu regulates ZGA partially through Zelda in early embryos.

overall_design: Different stages 6mA, mRNA profiles of jumu mutant embryos were generated by deep sequencing, using Illumina Hiseq250 and NovaSeq platform

first: Guoqiang

last: Zhang

first: Jiajia

last: Wang

first: Yajie

last: Gao

first: Ruidi

last: Sun

first: Zhijie

last: Cao

first: Zhenping

last: Chen

first: Xiudeng

last: Zheng

first: Jiao

last: Yuan

first: Yuewan

last: Luo

first: Xiaona

first: Wenxin

first: Peng

first: Yi

last: Zhao

first: Chuan

last: Tao

first: Qinmiao

first: Dahua


title: Identifying transcripts that are transcriptinoally regulated by CBFB and RUNX1 using RNAseq

first: Jing

last: Huang

summary: Using RNAseq to identify differentially expressed transcripts between CBFB wild type (WT) and knockout (KO) or between RUNX1 wild type (WT) and knockout (KO) MCF10A cells.

overall_design: Three repeats for CBFB KO and CBFB WT MCF10A cells. Four repeats for RUNX1 KO and RUNX1 WT MCF10A cells. One CBFB KO clone (#751) and two RUNX1 KO clones (5008 and 5010) were used.

first: Navdeep

last: Malik


title: Genome-wide profiling of γH2AX in Arabidopsis

status: Public on Apr 17 2019

first: Jincong

last: Zhou

address: Tsinghua Yuan

institute: Tsinghua University

summary: The R-loop, composed of a DNA-RNA hybrid and the displaced single-stranded DNA, regulates diverse cellular processes. However, how cellular R-loops are sensed remain poorly understood. Here we report the discovery of the evolutionally conserved ALBA proteins (AtALBA1&2) functioning as the R-loops sensor of genic regions in higher plant Arabidopsis thaliana. AtALBA1 and 2 form a heterodimer protein complex and localize in the nucleus. While AtALBA1 binds to the DNA-RNA hybrid strand, AtALBA2 associates with single-stranded DNA in the R-loops. AtALBA1&2 preferentially binds to the genic R-loop regions that are associated with active epigenetic marks. Depletion of AtALBA1 or AtALBA2 results in hypersensitivity of plants to DNA damaging agents. Our results demonstrate the unprotected R-loops by loss of AtALBA1&2 are main source of DNA damage through γH2AX ChIP-seq.

overall_design: We conducted γH2AX ChIP-seq with Arabidopsis wild-type (Col-0) and double mutant (alba1-1/alba2-1) seedlings to proflie the DNA damage .

first: Wei

first: Jinjin

last: Tong

first: Qianwen

first: Weiqiang

last: Qian


title: Epigenetic dysregulation of enhancers in neurons is associated with Alzheimer’s disease pathology and cognitive symptoms (RNA-Seq)

city: Grand Rapids

first: Peipei

last: Li

state: MI

address: 333 Bostwick Ave N.E.

department: Center for Neurodegenerative Science

institute: Van Andel Research Institute

summary: Epigenetic control of enhancers alters neuron functions and may be involved in Alzheimer’s disease (AD). Here, we identify enhancers in neurons contributing to AD by comprehensive fine-mapping of DNA methylation at enhancers, genome-wide. We examine 1.2 million CpG and CpH sites in enhancers in prefrontal cortex neurons of individuals with no/mild, moderate, and severe AD pathology (n=101). We identify 1,224 differentially methylated enhancer regions; most of which are hypomethylated at CpH sites in AD neurons. CpH methylation losses occur in normal aging neurons, but are accelerated in AD. Integration of epigenetic and transcriptomic data demonstrates a pro-apoptotic reactivation of the cell cycle in post-mitotic AD neurons. Furthermore, AD neurons have a large cluster of significantly hypomethylated enhancers in the DSCAML1 gene that targets BACE1. Hypomethylation of these enhancers in AD is associated with an upregulation of BACE1 transcripts and an increase in amyloid plaques, neurofibrillary tangles, and cognitive decline.

overall_design: In order to identify enhancers involved in AD, we comprehensively mapped DNA methylation at enhancers, genome-wide, in neurons isolated from the prefrontal cortex of 106 individuals with no/mild, moderate and severe AD pathology (Braak stage: I-II n=38, III-IV n=32, and V-VI n=36). We first isolated neuronal nuclei using an established antibody (NeuN+) and flow cytometry-based approach. We then fine-mapped DNA methylation at enhancer elements using a targeted bisulfite sequencing strategy, known as bisulfite padlock probe sequencing.

first: Lee

last: Marshall

first: Gabriel

last: Oh

first: Jennifer

last: Jakubowski

first: Daniel

last: Groot

first: Yu

last: He

first: Ting

first: Arturas

last: Petronis

first: Viviane

last: Labrie


title: RNAseq Data of Neural Stem Cells, Glial progenitors and Sox1 positive Glial progenitors

city: Planegg-Martinsried

first: Valentin

middle: Claude Vincent

last: Baumann

address: Grosshaderner Strasse 9

department: Physiologicl Genomics

country: Germany

institute: Biomedical Center, LMU Munich

summary: With this study we aimed to characterize the changes invoked in glial progenitor cells by activation of the endogenous copy of the master transcription factor Sox1. For this study, a progenitor cell line was derived from ES cells carrying a heterozygous GFP knock-in in the Sox1 ORF. Sox1 positive cells were identified by GFP expression, and separated by FACS. As control population, Sox1 negative progenitors were used, as well as GFP sorted and unsorted, Sox1 positive Neuroepithelial cells derived from the same ES cell line.

overall_design: Samples were divided in four groups: Baseline (=Sox1 negative) glial progenitors, neural stem cells (unsorted neuroepithelial cells,NSCs), neural rosettes (GFP sorted neuroepithelial cells, NR), and Sox1 positive glial progenitors. For each group, three independent biological samples were generated on different days, resulting in a total of 12 samples;

first: Stefan

middle: H

last: Stricker


title: Transcriptome Analysis on Maternal Separation Rats with Depression-related Manifestations Ameliorated by Electroacupuncture

city: Guangzhou

first: Yongjun

last: Chen

state: Guangdong

address: 232 Wai Huan East Road, University Town,Panyu District

department: Medical College of Acu-Moxi and Rehabilitation

institute: Guangzhou University of Chinese Medicine

summary:
Objective: To investigate the mechanisms depression-related manifestations ameliorated by electroacupuncture on genome-wide transcriptomes of the frontal cortex at the molecular level, we evaluated unbiased genome-wide RNA sequencing of depression-related rats suffer from maternal separation (MS).
Methods: Rats were randomly divided into control, MS, electro-acupuncture treatment(EA) group  . We demonstrated depression-like behavior deficiencies in a sucrose preference test and a forced swimming test in a rat model with neonatal maternal separation. Repeated EA treatment at the acupoints Baihui (GV20) and Yintang (GV29) during the adult period was shown to be remarkably attenuated above behavioral deficits. Sequencing was performed using Hiseq Xten (Illumina, USA).
Results: Based on the data from RNA-seq analysis, for mRNA, 48 genes were significantly and differentially expressed in MS rats relative to control rats, with 39 up-regulated genes and 9 down-regulated genes. 40 genes in the EA rats relative to the MS rats show differential expression, with 21 genes up-regulated and 18 genes down-regulated. For lncRNA, 11 genes increased significantly in the MS rats relative and 4 genes decreased relative to controls. 31 genes increased in the EA rats relative to the MS rats while 1 gene decreased. For circRNA, 20 genes increased significantly in the MS rats relative to control rats and 17 genes decreased. 18 genes increased in the EA rats relative to the MS rats while 28 genes decreased. Using ceRNA, we narrowed the targets of mRNA from 31 to 17 genes with a circRNA_miRNA_mRNA network, and narrowed the targets of mRNA from 31 to 8 genes with an lncRNA_miRNA_mRNA network, pointing the way for further studies to verify the genes and describe their function.
Conclusions: Our investigation demonstrates the first analysis of the frontal cortex genome-wide transcriptomes in depression rats under maternal separation by RNA-seq technology. These results suggest that EA at GV20 and GV29 ameliorates depression-related manifestations by regulating the expression of multiple genes.

overall_design: The frontal cortex profiles of the Rats after behavior test were generated by deep sequencing, in triplicate, using Hiseq Xten (Illumina, USA).

first: Yuanjia

last: Zheng

first: Jiang


title: ALBA protein complex reads genic R-loops to maintain genome stability in Arabidopsis

first: Jincong

summary: The R-loop, composed of a DNA-RNA hybrid and the displaced single-stranded DNA, regulates diverse cellular processes. However, how cellular R-loops are sensed remain poorly understood. Here we report the discovery of the evolutionally conserved ALBA proteins (AtALBA1&2) functioning as the R-loops sensor of genic regions in higher plant Arabidopsis thaliana. AtALBA1 and 2 form a heterodimer protein complex and localize in the nucleus. While AtALBA1 binds to the DNA-RNA hybrid strand, AtALBA2 associates with single-stranded DNA in the R-loops. AtALBA1&2 preferentially binds to the genic R-loop regions that are associated with active epigenetic marks. Depletion of AtALBA1 or AtALBA2 results in hypersensitivity of plants to DNA damaging agents. Our results demonstrate the AtALBA1&2 protein complex is the Arabidopsis genic R-loops sensor for maintaining genome stability in Arabidopsis.

overall_design: We conducted ssDRIP-seq with Arabidopsis wild-type (Col-0) and double mutant (alba1-1/alba2-1) seedlings to proflie the genowide R-loop levels.

first: Wei

last: Yuan

first: Jinjin

last: Sun


title: Oct1/Pou2f1 is selectively required for gut regeneration and regulates gut malignancy

first: Dean

last: Tantin

address: 15 North Medical Drive East

department: Department of Pathology

summary: As part of a larger study focused on deletion of Oct1 (Pou2f1) in the mouse gut, we identify Oct1 target genes in HCT116 colon carcinomal cells, with H3K4me3 and input controls. Identified target genes are associated with mitotic stability, metabolism, stress response and malignancy.

overall_design: Oct1- or H3K4me3-enriched DNA fragments, and input controls, were sequenced in triplicate

first: Karina

last: Vázquez-Arreguín


title: Integrated high-throughput screen to identify novel treatment leads for pediatric acute myeloid leukemia (AML)

status: Public on Apr 16 2019

city: Memphis

first: Michael

last: Walsh

state: TN

address: 262 Danny Thomas Place

department: Clinical Applications Core Tech

institute: St. Jude's Childrens Research Hospital

summary: AML cell lines that underwent high throughput drug screening had baseline RNA sequencing done for the purpose of gene expression studies

overall_design: Untreated cells growing in logrithmic phase underwent RNA extraction and sequencing

first: Christina

last: Drenberg

first: Tanja

last: Gruber


title: Single-cell RNA sequencing-based CRISPRi screening resolves molecular drivers of early human endoderm development [set 1]

city: Worcester

first: Rene

last: Maehr

state: MA

address: 55 Lake Ave N

department: Program in Molecular Medicine

institute: UMass Medical School

summary: Studies in vertebrates have outlined conserved molecular control of definitive endoderm (END) development. Yet, recent work also shows that key molecular aspects of human END regulation differ even from rodents. Differentiation of human pluripotent stem cells (hPSCs) to END offers a tractable system to study the molecular basis of normal and defective human-specific END development. Here, we interrogated dynamics in chromatin accessibility during differentiation of hPSCs to END, predicting DNA-binding proteins that may drive this cell fate transition. We then combined single-cell RNA-seq with parallel CRISPR-perturbations to comprehensively define the loss-of-function phenotype of those factors in END development. Following a few candidates, we revealed distinct impairments in the differentiation trajectories for mediators of TGFβ signaling and expose a role for the FOXA2 transcription factor in priming human END competence for human foregut and hepatic endoderm specification. Together, this single-cell functional genomics study provides high-resolution insight on human END development.

overall_design: CRISPRi screen of endodermal differentiation with a single-cell RNA readout. This submission contains the chromatin data.

first: Ryan

last: Genga

first: Eric

last: Kernfeld

first: Krishna

last: Parsi

first: Teagan

last: Parsons

last: Ziller


title: RNA-seq of N2a cells treated with 100 nM Dexamethasone for 4 hours +/- siARGLU1

city: Toronto

first: Carolyn

last: Cummins

address: 144 College St.

institute: University of Toronto

summary: ARGLU1 was identified in a screen for new modulators of glucocorticoid signaling in the CNS. RNA-seq of neuronal cells ±siARGLU1 revealed significant changes in the expression and alternative splicing of distinct genes involved in neurogenesis. Treatment with dexamethasone, a GR activator, also induced changes in the pattern of alternatively spliced genes, highlighting an underappreciated global mechanism of glucocorticoid action in neuronal cells. Thus, in addition to its basal role, ARGLU1 links glucocorticoid-mediated transcription and alternative splicing in neural cells, providing new avenues from which to investigate the molecular underpinnings of cognitive stress disorders.

overall_design: N2a cells were transfected with non-targeting control and ARGLU1 siRNAs for 48 hrs followed by Vehicle (EtOH) or 100 nM Dexamethasone treatment for 4 hrs. RNA was extracted and pooled by treatment group (n=3/group) and mRNA enriched Illumina TruSeq V2 RNA libraries were prepared. Samples were sequenced on Illumina HiSeq2500.

first: Lilia

last: Magomedova

first: Serge

last: Gueroussov

first: Manuel

last: Irimia

first: Benjamin

middle: J

last: Blencowe


title: miRNA expression in a time-series EMT process of 0h, 24h and 96h via next-generation sequencing

city: Shanghai

first: Mengzhu

last: Xue

address: No.100, Haike Road

institute: Shanghai Advanced Research Institute

summary: The goal of this study is to explore miRNA expressions in a time-series EMT process of 0h, 24h and 96h.

overall_design: EMT was induced in A549 cells with TGFb in a time-series of 0h, 24h and 96h. RNA samples were collected and analyzed by deep sequencing in duplicate.

first: Yuwei

last: Liu


title: Epigenetic dysregulation of enhancers in neurons is associated with Alzheimer’s disease pathology and cognitive symptoms

first: Peipei

last: Li

summary:
Epigenetic control of enhancers alters neuron functions and may be involved in Alzheimer’s disease (AD). Here, we identify enhancers in neurons contributing to AD by comprehensive fine-mapping of DNA methylation at enhancers, genome-wide. We examine 1.2 million CpG and CpH sites in enhancers in prefrontal cortex neurons of individuals with no/mild, moderate, and severe AD pathology (n=101). We identify 1,224 differentially methylated enhancer regions; most of which are hypomethylated at CpH sites in AD neurons. CpH methylation losses occur in normal aging neurons, but are accelerated in AD. Integration of epigenetic and transcriptomic data demonstrates a pro-apoptotic reactivation of the cell cycle in post-mitotic AD neurons. Furthermore, AD neurons have a large cluster of significantly hypomethylated enhancers in the DSCAML1 gene that targets BACE1. Hypomethylation of these enhancers in AD is associated with an upregulation of BACE1 transcripts and an increase in amyloid plaques, neurofibrillary tangles, and cognitive decline.

This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: Epigenetic dysregulation of enhancers in neurons is associated with Alzheimer’s disease pathology and cognitive symptoms (Bisulfite-Seq)

first: Lee

last: Marshall

first: Gabriel

last: Oh

first: Jennifer

last: Jakubowski

first: Daniel

last: Groot

first: Yu

last: He

first: Ting

last: Wang

first: Arturas

last: Petronis

first: Viviane

last: Labrie


title: Slow transcriptional elongation causes embryonic lethality and perturbs kinetic coupling of long neural genes

status: Public on Apr 15 2019

city: Edinburgh

first: Magdalena

middle: Maria

last: Maslon

address: Crewe Road

country: United Kingdom

institute: University of Edinburgh

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


title: De novo sequencing of transcriptome of Sf9 cells after Bm-15 overexpression and repression

city: Nanyang

first: Dandan

state: Henan

address: 1638 Wolong Road

institute: Nanyang Normal University

summary: Small nucleolar RNAs (snoRNA) function in guiding 2'-O-methylation and pseudouridylation of ribosomal RNAs. But we found that knock down of a C/D box snoRNA, Bm-15, can induce apoptosis of insect Spodoptera frugiperda Sf9 cells. For the genome sequence of Spodoptera frugiperda is incomplete, here with the de novo sequencing method, transcriptome of Spodoptera frugiperda cell line Sf9 were sequenced after being transfected with overexpression vector and repression probes of snoRNA Bm-15. Results showed that 21 apoptosis-related genes were up-regulated upon Bm-15 inhibition and down-regulated with Bm-15 overexpression.

overall_design: Examination of transcriptome of 3 different samples, normal Sf9 cells, cells with Bm-15 overexpression and repression.

first: Yunchao

last: Kan


title: Pax3 cooperates with Ldb1 to direct local chromosome architecture during lineage specification

city: Minneapolis

first: Alessandro

last: Magli

state: MN

address: 2231 6th St SE

department: Medicine

institute: University of Minnesota

summary: Chromatin looping allows enhancer-bound regulatory factors to influence transcription. Large domains, referred to as Topologically Associated Domains (TADs), participate in genome organization but the mechanisms underlining interactions within TADs, that actually control gene expression, are largely unknown. Here we report that activation of embryonic myogenesis is associated with establishment of long-range chromatin interactions centered on Pax3-bound loci. Using mass spectrometry and genomic studies, we identified the ubiquitously expressed LIM-domain binding protein 1 (Ldb1) as the mediator of looping interactions at a subset of Pax3 binding sites. Ldb1 is recruited to Pax3-bound elements independently of CTCF-Cohesin, and is necessary for efficient deposition of H3K4me1 at these sites and chromatin looping. When Ldb1 is deleted in Pax3-expressing cells in vivo, specification of migratory myogenic progenitors is severely impaired. These results highlight Ldb1 requirement for Pax3 myogenic activity and demonstrate how a transcription factor promotes formation of sub-TAD interactions associated with lineage specification.

overall_design: Pax3 doxycycline-inducible murine embryonic stem cells (iPax3) were used to investigate Pax3 function during myogenic lineage specification. ChIP-seq for histone marks was used to characterize the Pax3-bound loci and define enhancers. ChIP-seq for Ldb1, Smc1 and Ctcf was performed to test/validate Pax3-dependent recruitment of these proteins at Pax3-bound sites. HiChIP was used to study chromatin looping at Pax3 bound sites.

first: Rita

last: Perlingeiro

first: Pruthvi

last: Pota


title: Slow transcriptional elongation causes embryonic lethality and perturbs kinetic coupling of long neural genes [4sURDB-Seq]

summary: The rate of RNA Polymerase II (RNAPII) elongation has an important role in the control of Alternative splicing (AS); however, the in vivo consequences of an altered elongation rate are unknown. Here, we generated mouse embryonic stem cells (ESCs) knocked-in for a slow elongating form of RNAPII. We show that a reduced transcriptional elongation rate results in early embryonic lethality in mice and impairs the differentiation of ESCs into the neural lineage. This is accompanied by changes in splicing and in gene expression in ESCs and along the pathway of neuronal differentiation. In particular, we found a crucial role for RNAPII elongation rate in transcription and splicing of long neuronal genes involved in synapse signaling. The impact of the kinetic coupling of RNAPII elongation rate with AS is more predominant in ESC-differentiated neurons than in pluripotent cells. Our results demonstrate the requirement for an appropriate transcriptional elongation rate to ensure proper gene expression and to regulate AS during development.

overall_design: 4sURDB-Seq mouse wt and homozygous Polr2a[R749H] mutant embryonic stem cells in triplicates.

first: Ulrich

last: Braunschweig

first: Stuart

last: Aitken

first: Abigail

last: Mann

first: Fiona

last: Kilanowski

first: Chris

last: Hunter

first: Benjamin

last: Blencowe

first: Alberto

last: Kornblihtt

first: Ian

last: Adams

first: Javier

middle: F

last: Cáceres


title: Slow transcriptional elongation causes embryonic lethality and perturbs kinetic coupling of long neural genes [RNA-seq]

overall_design: RNA-Seq of mouse wt and homozygous Polr2a[R749H] mutant embryonic stem cells, and neural precursor cells, PSA-NCAM+ cells, and mature neurons differentiated from them in vitro, in triplicates.


title: Symbiont-mediated defense against Legionella pneumophila in amoebae

status: Public on Apr 14 2019

city: Vienna

first: Lena

last: König

address: Althanstrasse 14

country: Austria

institute: University of Vienna

summary: Legionella pneumophila are important opportunistic pathogens for which environmental reservoirs such as protists are crucial for the infection of humans. Free-living amoebae are considered key hosts providing nutrients and shelter for highly efficient intracellular proliferation of L. pneumophila, which eventually leads to lysis of the amoeba host cell. Yet, the significance of other bacterial players for L. pneumophila ecology is poorly understood. In this study we used a ubiquitous amoeba and their bacterial endosymbiont to investigate the impact of this common association on L. pneumophila infection. We demonstrate that Acanthamoeba castellanii harboring the chlamydial symbiont Protochlamydia amoebophila were able to erase L. pneumophila and, in contrast to symbiont-free amoebae, survived the infection and were able to resume growth. Environmental amoeba isolates harboring P. amoebophila were equally well-protected, and fresh environmental isolates of L. pneumophila were equally well-erased, suggesting ecological relevance of this symbiont-mediated protection. We further show that protection was not mediated by impaired L. pneumophila uptake. Instead, we observed reduced virulence of L. pneumophila released from symbiont-containing amoebae that is strongly supported by transcriptome data. Interference with transition to the transmissive phase is thus likely the basis for this protection. Finally, our data indicate that the defensive response of amoebae harboring P. amoebophila leaves the amoebae with superior fitness reminiscent of immunological memory. Given that mutualistic associations between bacteria and amoebae are widely distributed, P. amoebophila and potentially other amoeba endosymbionts could be key elements in shaping environmental survival, abundance and virulence of this important pathogen thereby affecting frequency of human infection.

sample_organism:
Legionella pneumophila
Acanthamoeba castellanii
Candidatus Protochlamydia amoebophila

overall_design: RNA-Seq of A. castellanii Neff amoebae infected with L. pneumophila Paris either in the presence of the amoeba endosymbiont P. amoebophila UWE25, or without the endosymbiont; in either case, 3 time points during L. pneumophila were sequenced: 24 hours post L. pneumophila infection (hpi), 96 hpi, and bacteria released at 96 hpi (extracellular bacteria); all in biological triplicates; in addition, amoebae only containing the endosymbionts at 24 hpi (biological duplicates) and 96 hpi (biological duplicates) were sequenced; in all conditions, total RNA (i.e. simulanteously from all organisms present) was extracted, DNase-treated, rRNA-depleted, libraries prepared, and sequenced on an Illumina HiSeq 2500;

first: Cecilia

last: Wentrup

first: Frederik

last: Schulz

first: Florian

last: Wascher

first: Sarah

last: Escola

first: Michele

last: Swanson

first: Carmen

last: Buchrieser

first: Matthias

last: Horn


title: Lamin B1 loss promotes lung cancer development and metastasis  by epigenetic derepression of RET [RNA-Seq]

city: Mannheim

first: Gergana

last: Dobreva

state: Baden Württemberg

address: Ludolf-Krehl-Str. 7-11

department: Cardiovascular Genomics and Epigenomics

institute: Medical Faculty Mannheim/University of Heidelberg

summary: Although abnormal nuclear structure is an important criterion for cancer diagnostics, remarkably little is known about its relationship to tumor development. Here we report that loss of lamin B1, a determinant of nuclear architecture, plays a key role in lung cancer.  We found that lamin B1 levels were reduced in lung cancer patients. Lamin B1 silencing in lung epithelial cells promoted epithelial-mesenchymal transition, cell migration, tumor growth and metastasis. Mechanistically, we show that lamin B1 recruits the polycomb repressive complex 2 (PRC2) to alter the H3K27me3 landscape and repress genes involved in cell migration and signaling. In particular, epigenetic derepression of the RET proto-oncogene by loss of PRC2 recruitment, and activation of the RET/p38 signaling axis, play a crucial role in mediating the malignant phenotype upon lamin B1 disruption. Importantly, loss of a single lamin B1 allele induced spontaneous lung tumor formation and RET activation. Thus, lamin B1 acts as a tumor suppressor in lung cancer, linking aberrant nuclear structure and epigenetic patterning with malignancy.

overall_design: RNA-seq analysis of control (n=2; Lmnb1_ctrl_MLE12_RNA_seq_rep1 and Lmnb1_ctrl_MLE12_RNA_seq_rep2) and lamin B1 knockdown (n=2; Lmnb1_KD_MLE12_RNA_seq_rep1 and Lmnb1_KD_MLE12_RNA_seq_rep2) MLE12 cells.

first: Yanhan

last: Jia

first: Julio

last: Cordero


title: DamID of Dam::EMR-1 in Caenorhabditis elegans L1 larvae

status: Public on Apr 12 2019

city: Seville

first: Peter

last: Askjaer

address: UPO Carretera de Utrera km 1

institute: Centro Andaluz de Biología del Desarrollo

summary: The execution of developmental programs of gene expression requires an accurate partitioning of the genome into distinct compartments, with heterochromatin enriched at the nuclear periphery. In C. elegans embryonic cells, the methylation of histone H3 lysine 9 (H3K9me) is critical for peripheral anchoring via the chromodomain protein CEC-4, while alternative, H3K9me-independent pathway(s) function in differentiated tissues. An RNAi screen unexpectedly identified the euchromatin factor MRG-1, which binds H3K36me2/me3 domains, as necessary for heterochromatin sequestration in differentiated cells. The data in this submission refer to the identification of chromatin enriched at the nuclear periphery (as measured by interaction with Dam::EMR-1) in intestinal cells of control, singly depleted cec-4 or mrg-1 or doubly depleted cec-4 mrg-1 animals.

overall_design: Comparison of Dam::EMR-1 DNA association in wild type, mrg-1(RNAi), cec-4(ok3124) and mrg-1(RNAi) cec-4(ok3124) backgrounds. Strains expressing a nuclear GFP::Dam fusion were used to normalise for changes in chromatin accessibility. Using a Pelt-2::FLP driver to induce genome recombination (Mu  oz-Jim  nez et al, PMID: 28646043), the Dam fusion proteins were expressed uniquely in intestine. Three biological replicas were prepared: all strains were grown in parallel in each replica. For technical reasons, we eliminated one replica of mrg-1 (RNAi), which was not included in this series.

first: Celia

last: Muñoz-Jiménez


title: Antisense lncRNA transcription mediates DNA demethylation to drive stochastic Protocadherin α promoter choice

city: San Francisco

first: Daniele

last: Canzio

state: CA

address: 555 Mission Bay Boulevard South

department: Neurology

institute: University of California San Francisco

summary: Stochastic activation of clustered Protocadherin (Pcdh) α, β, and γ genes generates a cell-surface identity code in individual neurons that functions in neural circuit assembly. Here, we show that Pcdhα gene choice involves the activation of an antisense promoter located in the first exon of each Pcdhα alternate gene. Transcription of an antisense long noncoding RNA (lncRNA) from this antisense promoter extends through the sense promoter, leading to DNA demethylation of the CTCF binding sites proximal to each promoter. Demethylation-dependent CTCF binding to both promoters facilitates cohesin-mediated DNA looping with a distal enhancer (HS5-1), locking in the transcriptional state of the chosen Pcdhα gene. Uncoupling DNA demethylation from antisense transcription by Tet3 overexpression in mouse olfactory neurons promotes CTCF binding to all Pcdhα promoters, resulting in proximity-biased DNA looping of the HS5-1 enhancer. Thus, antisense transcription-mediated promoter demethylation functions as a mechanism for distance-independent enhancer/promoter DNA looping to ensure stochastic Pcdhα promoter choice.

overall_design: RNA-seq, ChIP-seq, and Hi-C

first: Tom

last: Maniatis


title: The different expression of long non-coding RNAs and messenger RNAs in temozolomide-resistant glioblastoma cells and parental glioblastoma cells

city: Harbin

first: Wu

last: Pengfei

state: Hei Longjiang

address: No.246, Xuefu Road, Nangang District

department: Department of Neurosurgery, The Second Affiliated Hospital

institute: Harbin medical university

summary: Temozolomide (TMZ) resistance may contribute to the treatment failure in patients with glioblastoma (GBM). Hence, understanding the underlying mechanisms and developing effective strategies against TMZ resistance are highly desired in the clinic. long non-coding RNAs (lncRNAs) have emerged as new regulatory molecules with diverse functions in biological processes and been deregulated in many pathologies, involved in the therapeutic resistance. It is urgent to elucidate the underlying lncRNA-based mechanisms of TMZ resistance in GBM patients.

overall_design: LN229 cells were seeded in 96 well plates with 6000 per hole and the half maximal inhibitory concentration (IC50) of TMZ was determined. Then, TMZ was added to the cell culture medium with IC50 1/50 concentration (0.83±0.26μM) to culture LN229 cells in 6 well plates. After cells grew stably, the drug dose was increased in multiples. Each dose was maintained for 15 days to the end of the fifth month. Induced TMZ-resistant cells were named as 229R. LN229 and 229R cells were used for lncRNA microarray

first: Jinquan

last: Cai

first: Pengfei

last: Wu


title: Epigenomic Landscape derived from ChIP-Seq of 1,000 mouse early embryonic cells

first: Yusi

last: Fu

address: biopic,PKU

institute: PKU

summary: Chromatin immunoprecipitation coupled with high-throughput sequencing (ChIP-Seq) is a powerful tool to dissect global epigenetic landscapes of cells. However, this method usually consumes millions of cells. Here we develop a robust technique for performing ChIP-Seq using as low as 1,000 cells. This method combines a semi-automatic nanoliter ChIP reaction with a carrier-based sequencing library preparation strategy without pre-amplification of the ChIP product. We used this method to investigate the pattern of trimethylation of histone 3 lysine 4 (H3K4me3) of mouse post-implantation epiblast cells at embryonic day 6.5 (E6.5) and showed that it is very similar to that of mEpiSCs. Together with the high similarity between the transcriptomes of EpiSCs and E6.5 epiblast cells, this suggests that EpiSCs is a reliable in vitro model for post-implantation epiblast cells in vivo.

overall_design: Use 1 million cells mEpiSC as the positive control,  1000 mEpiSC sample is used to validate the protocol. Embryo_exp1 and embryo_exp2 are two biological replicates

first: Yanyi

last: Huang

first: Fuchou

last: Tang


title: TBX5-Clover2/NKX2-5-TagRFP iPSCs for simultaneously isolating human lineage-specific cardiovascular cells

city: Stanford

first: Joseph

state: Carlifornia

address: Stanford University School of Medicine

institute: Stanford University School of Medicine

summary: We develop a method for purification of four discrete cardiovascular lineages derived from human indued pluriopotent stem cells. We used RNAseq to identify the gene signuature of different lineages at early differentiation stages.

overall_design: exmmination of transcriptome profile of different lineages

first: Joe

last: Zhang

first: Ning-Yi

last: Shao


title: Single cell lineage tracing by endogenous mitochondrial DNA mutations in ATAC-seq data [stem cells and blasts]

first: Howard

middle: Y.

last: Chang

state: CALIFORNIA

address: 269 Campus Drive, CCSR 2130

institute: Stanford

summary:
Simultaneous measurement of lineage relationship and information on cell fate is desireable for human tissues. Here we describe a new strategy to track cell lineage using endogenous mitochondrial DNA variants in ATAC-seq data, which simultaneously measures the chromatin profiling.
We first provide a proof of principle that somatic mutations in the mitochondrial genome can be used as a genetic marker to depict cellular lineage relationships and further quantified the power of lineage definition with these genetic markers.
Using this method, we demonstrated the genetic and epigenetic heterogeneity of hematopoietic stem cells from patient with acute myeloid leukemia.

overall_design: Single-cell ATAC-seq of leukemia stem cells and leukemic blasts from AML patients

first: Jin

last: Xu

middle: Y


title: Transcriptome analysis of Opium poppy using Illumina HiSeq X Ten platform [cultivars]

status: Public on Apr 11 2019

city: Nanjing

first: Yucheng

last: Zhao

address: Tongjiaxiang 24

institute: China pharmaceutical unoversity

summary:
Purpose: Opium poppy is one of the most important medical plants and remains the only commercial resource of morphinan-based painkillers. However, little is known about its regulation mechanism in benzylisoquinoline alkaloids (BIAs) biosynthesis. Herein, the Transcriptome dataset of Opium poppy was constructed to identify the gene involved in its regulation mechanism in BIAs biosynthesis.
Methods:  Using Illumina HiSeq X Ten platform, 33 samples of Illumina transcriptome data from different tissues, growth phases and cultivars were constructed.
Results: The high-quality transcripts were subsequent quantified with the short reads, and the expression of each unigenes among different samples was calculated by RPKM (the reads per kilobase per million mapped reads).
Conclusions: These data provide a foundation of opium poppy transcriptome which may contribute to understand the regulation of BIAs biosynthesis.

overall_design: This series includes samples from cultivars (BioProject accession No. PRJNA510279 and SRA study accession No.SRP173565).

first: Lingyi

last: Kong


title: Transcriptome analysis of Opium poppy using Illumina HiSeq X Ten platform [growth phases]

overall_design: This series includes samples from growth phases (BioProject accession No. PRJNA510248 and SRA study accession No.SRP173551)


title: Transcriptome analysis of Opium poppy using Illumina HiSeq X Ten platform [different tissues]

overall_design: This series includes samples from different tissues (BioProject accession No. PRJNA510228 and SRA study accession No.SRP173546)


title: Transcriptome analysis of Opium poppy using Illumina HiSeq X Ten platform


title: Small RNA sequencing in mutant strains of C. elegans infected by the Orsay virus

city: Cambridge

first: Tomas

last: Di Domenico

address: Gurdon Institute, Tennis Court Road

department: Gurdon Institute

institute: University of Cambirdge

summary:
Background information: According to our observations, cde-1 (tm1021) null C. elegans animals show increased susceptibility to the Orsay virus (which has a bipartite positive RNA genome), compared to WT (N2 strain). Viral infection seems limited to intestinal cells. CDE-1 is a terminal uridylyltransferase (TUT). TUTs have been shown to promote RNA decay by 3’ end uridylation in various contexts and organisms. We hypothesize that CDE-1 serves as an antiviral factor by uridylating the viral RNA genome.
Aims: We question small RNA populations in cde-1 mutants versus WT after two days of infection by the Orsay virus.
Methods: Approximately 200 C. elegans animals were infected for 48 hours from the L2 stage to the adult stage with 20 µl filtrate of the Orsay virus on 50mm plate seeded with HB101 bacteria, in biological duplicates, for the following genetic backgrounds: N2 (+), drh-1 (ok3495), rde-1 (ne219), cde-1 (mj414), cde-1 (tm1021), cde-1 (tm1021);drh-1 (ok3495), cde-1 (tm1021);rde-1 (ne219). Animals were then washed in M9 and resuspended in 1 ml TRIsure (Bioline). Samples were freeze-thaw three times using liquid nitrogen and RNA purification was performed according to Bioline’s guidelines. Purified RNA was either directly used for library preparation (5’ dependent libraries) or was first submitted to 5’ polyphosphatase treatment (5’ independent libraries) as in Ashe, et al. 2013. sRNA libraries were prepared using the TruSeq Small RNA Library Preparation Kit (Illumina) according to manufacturer’s instructions (with size selection between 20 and 35 nt, adapters excluded) and deep sequencing was produced with an Illumina HiSeq machine (single read 36).

overall_design: Examination of small RNA profiles in Orsay virus infected C. elegans animals from different genetic backgrounds

first: Jérémie

last: Le Pen

first: Tomás

first: Eric

middle: A

last: Miska


title: Single cell lineage tracing by endogenous mitochondrial DNA mutations in ATAC-seq data [HSC]

overall_design: Single-cell ATAC-seq of pre-leukemia  hematopoietic stem cells from AML patient


title: Active chromatin marks, H3K36me and MRG-1, drive spatial sequestration of heterochromatin

city: Basel

first: Dimos

last: Gaidatzis

address: Maulbeerstrasse 66

institute: Friedrich Miescher Institute

overall_design: Refer to individual Series


title: Single cell lineage tracing by endogenous mitochondrial DNA mutations in ATAC-seq data


title: Gene expression changes in mrg-1 mutant L1 larvae compared to wild type.

summary: We compared wild type N2 to mrg-1 mutants L1 larvae. Genes tend to be upregulated rather than downregulated in these mutants. Comparison to available ChIPseq datasets indicates that the upregulated genes are heterochromatic and are not enriched for H3K36 methylation, indicating that MRG-1 loss derepresses heterochromatin indirectly.

overall_design: 3 biological replicas

first: Daphne

last: Cabianca


title: Gene expression changes upon depletion of H3K36 methylation by mutating met-1 and RNAi depleting mes-4 in worm L1 larvae

summary: We compared wild type N2 fed L4440 control RNAi to met-1 mutants fed mes-4 RNAi food. Genes tend to be upregulated rather than downregulated in these mutants. Comparison to available ChIPseq datasets indicates that the upregulated genes are heterochromatic and are not enriched for H3K36 methylation, indicating that H3K36me loss derepresses heterochromatin indirectly.

overall_design: Comparison of 2 independent biological replicas


title: Campylobacter jejuni demonstrates conserved proteomic and transcriptomic responses when co-cultured with human INT 407 and Caco-2 epithelial cells

city: Pullman

first: Michael

middle: E

last: Konkel

state: WA

institute: Washington State University

summary: Major foodborne bacterial pathogens, such as Campylobacter jejuni, have devised complex strategies to establish and foster intestinal infections. For more than two decades researchers have used immortalized cell lines derived from human intestinal tissue to dissect C. jejuni-host cell interactions. Known from these studies is that C. jejuni virulence is multifactorial, requiring a coordinated response to produce virulence factors that facilitate the bacterium’s host-cell interactions. This study was initiated to identify C. jejuni proteins that contribute to adaptation to the host cell environment and cellular invasion. We demonstrated that C. jejuni responds to INT 407 and Caco-2 cells in a similar fashion at the cellular and molecular levels. Active protein synthesis was found to be required for C. jejuni to maximally invade these host cells. Proteomic and transcriptomic approaches were then used to define the protein and gene expression profiles of C. jejuni co-cultured with cells. By focusing on those genes showing increased expression by C. jejuni when co-cultured with epithelial cells, we discovered that C. jejuni quickly adapts to co-culture with epithelial cells by synthesizing gene products that enable it to acquire specific amino acids for growth, scavenge for inorganic molecules including iron, resist reactive oxygen/nitrogen species, and promote bacteria-host cell interactions. Based on these findings, we selected a subset of the genes involved in chemotaxis and the regulation of flagellar assembly and generated C. jejuni deletion mutants for phenotypic analysis. Binding and internalization assays revealed significant differences in the interaction of C. jejuni chemotaxis and flagellar regulatory mutants. The identification of genes involved in C. jejuni adaptation to culture with host cells provides new insights into the infection process.

overall_design: C. jejuni were inoculated at an OD540 of 0.05 and grown for 18-20 hours in MH broth. The C. jejuni was then adjusted to an OD540 of 0.3 in MEM supplemented with 1% FBS. INT 407 or Caco-2 cells were first rinsed with MEM 1% FBS, 10 mL of the C. jejuni suspension was introduced, and the host cells were incubated for 2.5 or 4 at 37°C with 5% CO2. The supernatant was then collected and bacteria were recovered by centrifugation.

first: Nicholas

last: Negretti

first: Geremy

last: Clair

first: Prabhat

last: Talukdar

first: Christopher

last: Gourley

first: Steven

last: Huynh

first: Colby

last: Corneau

first: Joshua

middle: N

last: Adkins

first: Craig

last: Parker


title: Quantitative Analysis of JAK2V617F/+ Plek2+/+ and JAK2V617F/+ Plek2-/- erythroblast and hematopoietic stem cells/ progenitor cells Transcriptomes

city: CHCAGO

first: BAOBING

last: ZHAO

state: IL

address: 303 E CHICAGO AVENUE

institute: NORTHWESTERN UNIVERSITY

summary: V617F driver mutation of JAK2 is the leading cause of the Philadelphia-chromosome-negative myeloproliferative neoplasms (MPNs). Loss of Plek2 ameliorated JAK2V617F-induced myeloproliferative phenotypes including erythrocytosis, neutrophilia, thrombocytosis, and splenomegaly, thereby reverting the widespread vascular occlusions and lethality of JAK2V617F knockin mice. To reveal the role of Plek2 in the pathogenesis of JAK2V617F-induced MPNs and the detail mechanisms of its rescue, we performed RNA sequencing to analyze the gene expression profiles change between JAK2V617F/+ Plek2+/+ and JAK2V617F/+ Plek2-/- erythroblasts and hematopoietic stem/progenitor cells.

overall_design: mRNA profiles of bone marrow erythroblasts and hematopoietic stem/progenitor cells from 4-month JAK2V617F/+ Plek2+/+ and JAK2V617F/+ Plek2-/- mice were generated by deep sequencing, in duplicate, using an Illumina HiSEQ4000.

first: Baobing

first: Peng

last: Ji


title: Transcriptional and metabolomic analyses implicate cell wall changes are associated with drought tolerance in Brachypodium distachyon.

status: Public on Apr 10 2019

city: Aberystwyth

first: Maurice

last: Bosch

address: Gogerddan

department: Institute of Biological, Environmental & Rural Sciences

institute: Aberystwyth University

summary: Brachypodium distachyon as an annual species that colonises broken ground is a highly appropriate model to define drought tolerance mechanisms. We have previously identified accessions exhibiting drought tolerance, high susceptibility and intermediate tolerance to drought; respectively, ABR8, KOZ1 and ABR4, from a screen of 138 genotypes. To define the mechanisms of tolerance, the responses to drought were assessed using transcriptomic and metabolomic approaches. Analysis of RNA-seq before and following drought suggested relatively few differentially expressed genes in ABR8. Linking these to gene ontology (GO) terms revealed an enrichment for biological processes related to “regulated stress response”,  “plant cell wall” and “oxidative stress”. Interestingly, drought tolerance also appeared to correlate with pre-existing differences in gene expression linked to GO terms associated with the cell wall. These included glycoside hydrolases involved in cell wall remodelling, pectin methylesterases, expansins and a pectin acetylesterase. Metabolomic assessments of the same samples also indicated few statistically significant changes in ABR8 with drought.  Instead, pre-existing differences in the cell-wall associated metabolites appeared to correlate with drought tolerance. Our data suggests two different modes/levels at which  cell wall characteristics can play a role in conferring drought tolerance: (i) an active response mode/level which involves stress induced changes in cell wall features to help the plant cope with drought and (ii) an intrinsic mode in which innate differences in cell wall composition and architecture between genotypes are important in determining tolerance to drought stress. Both modes seem to contribute to the drought tolerance of ABR8. Identification of the exact mechanisms through which the cell wall confers drought tolerance will be important to fully exploit the contribution of the cell wall in the development of drought tolerant cereals and other grasses.

overall_design: For each of the ecotypes, leaf tissue was harvested at three time points for RNA extraction; at the start (T0, control (C)), after 4 days (T1, both C and treatment (D)) and after 8 days (T2, both C and D). In total 45 plants were harvested ((T0+T1C+T1D+T2C+T2D) * 3 ecotypes * 3 biological replicates).

first: Ingo

last: Lenk

first: Lorraine

last: Fisher

first: Martin

last: Vickers

first: Thomas

last: Didion

last: Swain

first: Christian

middle: S

last: Jensen

first: Klaus

last: Nielsen

first: Luis

last: Mur


title: Interrogating histone acetylation and BRD4 as mitotic bookmarks of transcription [TFs]

city: University Park

first: Ross

last: Hardison

state: PA

address: 303 Wartik Lab

institute: Pennsylvania State University

summary: Global changes in chromatin organization and the cessation of transcription during mitosis are thought to challenge the resumption of appropriate transcription patterns following mitosis. The acetyl-lysine binding protein BRD4 has been previously suggested to function as a transcriptional “bookmark” on mitotic chromatin. Here, genome-wide location analysis of BRD4 in erythroid cells, combined with novel data normalization and peak characterization approaches, reveals that BRD4 widely occupies mitotic chromatin. However, removal of BRD4 from mitotic chromatin does not impair post-mitotic activation of transcription. Additionally, histone mass spectrometry reveals global preservation of most posttranslational modifications (PTMs) during mitosis. In particular, H3K14ac, H3K27ac, H3K122ac, and H4K16ac widely mark mitotic chromatin, especially at lineage-specific genes, and predict BRD4 mitotic binding genome wide. Therefore, BRD4 is likely not a mitotic bookmark but only a “passenger”. Instead, mitotic histone acetylation patterns may constitute the actual bookmarks that restore lineage-specific transcription patterns after mitosis.

overall_design: Asynchronous vs nocodazole arrested mitotic cells in G1E ER4 cell line differentiated using 13h estradiol treatment

first: Vivek

last: Behera

first: Gerd

last: Blobel


title: TGF-beta signaling pathway and male disadvantage in the pathogenesis of the bronchial pulmonary dysplasia

city: Los Angeles

first: Brendan

last: Grubbs

address: 4661 W. Sunset Blvd.

department: Obstetrics and Gynecology

institute: University of Southern California

summary: Insufficient activation of the TGF-b signaling pathway leads to abnormalities in embryonic lung development. Herein, we determined the effect of the epithelial over-activation of the TGF-b signaling pathway in the embryonic lung development by expressing the constitutive active form of the Tgf-b receptor 1. Ectopic activation of the TGF-b signaling pathway in the lung embryonic epithelium resulted in a complex and lethal phenotype in male mice, but not in female mice. Mutant male embryos died at birth due to their inability to breathe, and showed a bronchial-pulmonary-dysplasia-like phenotype which included reduced lung size, increased alveolar wall thickness, increased cellular density of the lung parenchyma and diminished population of club cells. While the NOTCH signaling, pathway was not affected, we found that protein expression of the endodermal stem cell marker Ssea1 was strongly reduced in proximal lung airways of male lungs. In the distal lung epithelium, ectopic activation of the TGF-b signaling pathway resulted in the increased number of Sox9+ alveolar progenitor cells. Moreover, deletion of one Sox9 allele reduced the severity of the phenotype in mutant males, suggesting that TGF-b mediated over-expression of Sox9 protein is critical for the development of the bronchial pulmonary dysplasia-like phenotype displayed by the mutant male animals. Gene expression profiling identified 993 differentially expressed genes in the mutant male lungs compared to the control male lung. Several of these genes, such as Cbr2 and Hp, are expressed by the club cell and were downregulated by the TGF-b signaling pathway in the mutant male lung. Others such as Spock2, Adamtsl2 and Adamts18 were previous found to be linked to fetal lung disease and indispensable for proper lung development. Finally, we showed that injection of b-estradiol in the pregnant female rescued the phenotype in the mutant male embryos which suggests a critical role of the sex hormones in the pathogenesis of the bronchial pulmonary dysplasia disease. In conclusion, we have established a novel sex-specific mouse model that may be helpful in elucidating specific pathways by which sex adversely affects the well-known but obscure more adverse outcome of male patients.

overall_design: A total of 8 samples were analyzed: 2 control E17.5 lung female, 2 mutant E17.5 lung female, 2 control E17.5 lung male, 2 mutant E17.5 lung male.

first: Gianluca

last: Turcatel

first: Matthew

last: Thornton


title: Interrogating histone acetylation and BRD4 as mitotic bookmarks of transcription [Histones]


title: The emergent landscape of the mouse gut endoderm at single-cell resolution

city: Seattle

first: Manu

last: Setty

address: 1100 Fairview Ave N

department: Basic Sciences Division

institute: Fred Hutchinson Cancer Center

summary: To comprehensively delineate the ontogeny of an organ system, we generated 112,217 single- cell transcriptomes representing all endoderm populations within the mouse embryo until midgestation. We employed graph-based approaches to model differentiating cells for spatio- temporal characterization of developmental trajectories. Our analysis reveals the detailed architecture of the emergence of the first (primitive or extra-embryonic) endodermal population and pluripotent epiblast. We uncover an unappreciated relationship between descendants of these lineages, before the onset of gastrulation, suggesting that mixing of extra-embryonic and embryonic endoderm cells occurs more than once during mammalian development. We map the trajectories of endoderm cells as they acquire embryonic versus extra-embryonic fates, and their spatial convergence within the gut endoderm; revealing them to be globally similar but retaining aspects of their lineage history. We observe the regionalized localization of cells along the forming gut tube, reflecting their extra-embryonic or embryonic origin, and their coordinate patterning into organ-specific territories along the anterior-posterior axis.

overall_design: Total RNA was extracted from bulk tissue and dissociated cells of 13ss (~E8.75) gut tubes, from bulk tissue from anterior, anterior-midgut, midgut-posterior and posterior sections of 13ss gut tubes, as well as from extra-embryonic visceral endoderm and embryonic visceral endoderm of E7.5 embryos (see also table in section: Bulk RNA processing). The Trizol method (Invitrogen) was used for RNA extraction.

first: Sonja

last: Nowotschin

first: Ying-Yi

last: Kuo

first: Vincent

last: Lui

first: Vidur

last: Garg

first: Roshan

last: Sharma

first: Claire

last: Simon

first: Nestor

last: Saiz

first: Rui

last: Gardner

first: Stephane

last: Boutet

first: Deanna

last: Church

first: Pamela

last: Hoodless

first: Anna-Katerina

last: Hadjantonakis

first: Dana

last: Pe'er