title: Single cell transcriptomic analysis reveals cellular diversity of murine esophageal epithelium and age-associated mitochondrial dysfunction [scRNA-seq]

first: Kelly

middle: A

last: Whelan

address: 3307 N Broad St. PAHB Rm 203

department: Fels Institute

country: USA

institute: Temple University

summary: We have performed single cell RNA-sequencing to characterize the murine esophageal epithelium in young and aged mice.

overall_design: We used peeled esophageal epithelium from young (≤4 months) and aged (≥18 months) mice to investigate the molecular heterogeneity of the esophageal epithelium at single cell resolution.

first: Adam

middle: L

last: Karami

first: Mohammad

last: Kabir

first: Kelsey

last: Keith

first: Jozef

last: Madzo

first: Jaroslav

last: Jelenik

first: Kumaraswam

last: Chitrala


title: Expression data from gastric cancer

status: Public on Jan 14 2022

city: nanjing

first: lei

last: he

address: hanzhongmen

country: China

institute: The Second Affiliated Hospital of Nanjing Medical University

summary:
Gastric cancer is a most prevalent cancer with high mortality and strong invasiveness. Presently, there are many kinds of diagnosis and treatment methods, but the diagnosis rate of early gastric cancer is still not high, with a low five-year survival rate. Although the gastric cancer mechanism has been extensively studied, but the entire regulatory networks of gastric cancer is still unclear.
We used microarrays to detect gene expression in NOL6 normal and knockdown gastric cancer cells a, and to identify differentially expressed genes in this program.

overall_design: In order to explore the mechanism of NOL6 in the progression of gastric cancer, gastric cancer cells were isolated by RNA extraction and Affymetrix microarray hybridization. The experiment was divided into normal expression group of NOL6 and low expression group of NOL6, with three microarrays in each group, and the differentially expressed genes were screened using microarray data

first: Lei

last: He

first: Ping

middle: P

last: Ge

first: Dong

last: Fan

first: Xiang

last: Ma

first: Qiong

last: Wu

first: Jin

last: Sun

first: Li

middle: J

last: Xu


title: Maternal High-Fructose Intake Activates Myogenic Program In Fetal Brown Fat And Predisposes Offspring to Diet-Induced Metabolic Dysfunctions In Adulthood

status: Public on Jan 15 2022

city: Nanning City

first: Wang

last: Peng

address: Nanning City College Road and XiXiangTang District

institute: Guangxi University

type: Expression profiling by high throughput sequencing

summary: We performed RNA-seq analysis for evaluating the effect of maternal high-fructose intake on fetal brown fat development. We find that maternal high-fructose intake induces myogenic signature in fetal brown fat, indicating impairment of brown fat development by maternal high-fructose intake.

overall_design: The pregnant mice were randomly assigned to either sterilized tap water or 20% (w/v) fructose (sigma, F3510) water until delivery. At E18.5, a subset of pregnant mice were killed and the BAT of male fetuses were collected for RNA-seq analysis.

first: Peng

last: Wang

first: Ziyi

last: Song

first: Tian


title: Chromatin profiling in human neurons reveals aberrant roles for histone acetylation and BRD4 in schizophrenia

status: Public on Jan 12 2022

city: New York

first: Aarthi

last: Ramakrishnan

state: New York

address: 1425 Madison Avenue

department: Neuroscience

institute: Icahn School of Medicine at Mount Sinai

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Schizophrenia (SZ) is a psychiatric disorder with complex genetic risk dictated by interactions between hundreds of risk variants. Epigenetic factors, such as histone posttranslational modifications (PTMs), have been shown to play critical roles in many neurodevelopmental processes, and when perturbed may also contribute to the precipitation of disease. Here, we applied an unbiased proteomics approach to evaluate combinatorial histone PTMs in human induced pluripotent stem cell (hiPSC)-derived forebrain neurons from individuals with SZ. We observed hyper-acetylation of H2A.Z and H4 in neurons derived from SZ cases, results that were confirmed in postmortem human brain. We demonstrated that the bromodomain containing protein, BRD4, is a bona fide ‘reader’ of H2A.Z acetylation, and further provide evidence that BRD4 inhibition ameliorates transcriptional abnormalities in patient-derived neurons and improves sensorimotor gating behavior in mice. Thus, treatments aimed at alleviating BRD4 interactions with hyperacetylated histones may aid in the prevention or treatment of SZ.

overall_design:
Human induced pluripotent stem cell (hiPSC)-derived forebrain neurons from control individuals or individuals with schizophrenia were treated with vehicle (PBS) or JQ1, and RNA-seq was performed.

H2A.Zac ChIP-seq in HeLa cells (n=3, plus 3 respective inputs)

first: Lorna

last: Farrelly

first: Shuangping

last: Zhang

first: Nadine

last: Schrode

first: Kristen

last: Brennand

first: Ian

last: Maze


title: Single cell transcriptomic analysis reveals cellular diversity of murine esophageal epithelium and age-associated mitochondrial dysfunction

city: Philadelphia

first: Kelly

last: Whelan

state: PA

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

overall_design: Refer to individual Series


title: Gibbin (AHDC1) regulates the mesoderm to pattern epithelial development

status: Public on Jan 17 2022

city: Stanford

first: Anthony

last: Oro

state: CA

address: 269 Campus Drvie

department: Dermatology

institute: Stanford University

type: Methylation profiling by genome tiling array


title: Profiling Mouse embryonic fibroblasts from wt and SARAF KO animals

status: Public on Jan 13 2022

city: Rehovot

first: Eitan

last: Reuveny

state: Please Select

address: Dept. Biomolecular Sciences, 234 Hertzl St.

country: Israel

institute: Weizmann Inst. of Science

summary: comparing SARAF KO transcription profile in MEF, comparing to cell from wt animals

overall_design: Total RNA was taken from MEFs grown in culture to 75% confluency

first: Diana

last: Gataulin


title: Effects of sub-acute exposure of NOAEL-dose neonicotinoid clothianidin on the gene expression profiles of cerebral cortex and hippocampus in male mice

status: Public on Jan 08 2022

city: Toyama

first: Tetsushi

last: Hirano

state: Toyama

address: 2630 sugitani

country: Japan

institute: University of Toyama

summary:
Neonicotinoid pesticides cause behavioral abnormalities in mammals, raising concerns about their effects on neural function.
We investigated effects of sub-acute exposure to a neonicotinoid pesticide, clothianidin (CLO) on gene expression profiles of the cerebral cortex and hippocampus in male mice

overall_design: Male mice were administrated no observed adverse effect level (NOAEL; 50 mg/kg/day) of CLO or vehicle (1% DMSO) for 2 weeks.

first: Misaki

last: Nishi

first: Nobuhiko

last: Hoshi

first: Yoshiaki

last: Tabuchi


title: QPCTL deletion results in a rewiring of the tumor microenvironment

status: Public on Jan 03 2022

city: Amsterdam

first: Kaspar

last: Bresser

address: Plesmanlaan 125

department: Hematopoeisis

country: Netherlands

institute: Sanquin


title: Rhesus macaque early-gestation trophoblast cells are permissive to Zika virus infection and viral exposure altered extracellular vesicle cargo

status: Public on Jan 01 2022

city: Madison

first: Thaddeus

last: Golos

state: Wisconsin

address: 1223 Capitol Court

department: WNPRC

institute: UW Madison

summary: Zika virus (ZIKV) infection of maternal and placental cells at the maternal-fetal interface is associated with a spectrum of adverse pregnancy outcomes including fetal demise and pregnancy loss. Trophoblast cell types that comprise the placenta include cytotrophoblasts, syncytiotrophoblasts (STs), and extravillous trophoblasts (EVTs). To determine which trophoblast cells are permissive to ZIKV and to understand how infection impacts cellular gene expression, we utilized a macaque in vitro trophoblast stem cell (TSC) model. TSCs were derived from primary cytotrophoblasts and represent a proliferative trophoblast that can be differentiated into STs and EVTs. TSCs and ST3Ds (STs grown in suspension) were highly permissive to infection with ZIKV strain DAK AR 41524, whereas EVTs maintained a level of resistance to productive infection. The impact of ZIKV on cellular gene expression was determined by transcriptomic and miRNAome analysis. Infection of TSCs and ST3Ds results in increased expression of immune related genes, including those in the type I and type III interferon response. ZIKV exposure impacts EV protein, mRNA, and miRNA cargo, regardless of productive infection. Altogether, these findings suggest TSCs and STs of the macaque are permissive to ZIKV infection and that EV analysis has the potential to identify ZIKV infection. These findings provide a foundation for further ZIKV study and allow for potential ZIKV infection biomarker identification in a highly translational model.

overall_design: 4 biological replicates per cell type (3 cell types total) were sequenced. The 3 cell types include trophoblast stem cells (TSCs), syncytiotrophoblasts (ST3Ds), and extravillous trophoblasts (EVTs). Each biological replicate was exposed to ZIKV or left as uninfected controls, for a total of 24 samples.

first: Lindsey

middle: N

last: Block

middle: G


title: QPCTL deletion results in a rewiring of the tumor microenvironment [bulk RNA-seq]

summary: bulk RNA sequencing performed on the FACS sorted CD45-negative cells from QPCTL-proficient and -deficient TMEs; and, base-line comparison of lymphoid organs from QPCTL-KO and QPCTL-WT animals

overall_design: The effects of QPCTL-deficiency were assessed in this study. To this end, a QPCTL-KO mouse strain was used. Mice homozygous for the QPCTL-KO allele or wild-type littermates were innoculated with either QPCTL-KO or QPCTL B16F10 tumor cells, respectively. After 14 days tumors were harvested, single cell suspensions were made and live CD45-negative cells were isolated by FACS, after which cells were processed for RNA sequencing. For baseline samples, whole organs were harvested from mice, snapfrozen and used for mRNA isolations.

first: Meike

last: Logtenberg

first: Ton

last: Schumacher


title: The Drosophila functional Smad suppressing element fuss, a homologue of the human Skor genes, retains prooncogenic properties of the Ski/Sno family

status: Public on Jan 05 2022

city: Regensburg

first: Mathias

last: Rass

address: Universitätsstraße 31

department: Developmental Biology

country: Germany

institute: University of Regensburg

summary: To detect dysregulated genes upon overexpression of the functional smad suppressing element (fuss) in Drosophila melanogaster, we overexpressed fuss with the GMR-Gal4 line in developing eye discs and with the nub-Gal4 driverline in developing wing discs. The offspring of crossings of the driver lines GMR-Gal4 or nub-Gal4 with w1118 were used as controls.  Libraries were generated from total RNA and sequenced on a Illumina HiSeq 1000. Via differential gene expression analysis we discovered the genes which are dysregulated by fuss overexpression compared to controls.

overall_design: Analysis of effects of functional smad suppressing element overexpression in wing and eye discs of Drosophila melanogaster larvae

first: Stephan

last: Schneuwly


title: Zika virus impacts extracellular vesicle composition and cellular gene expression in macaque early gestation trophoblasts [miRNA-seq]

status: Public on Jan 10 2022

type: Non-coding RNA profiling by high throughput sequencing

summary: Zika virus (ZIKV) infection at the maternal-placental interface is associated with adverse pregnancy outcomes including fetal demise and pregnancy loss. To determine how infection impacts placental trophoblasts, we utilized rhesus macaque trophoblast stem cells (TSC) that can be directed to differentiate into early gestation syncytiotrophoblasts (ST) and extravillous trophoblasts (EVT). TSCs and STs, but not EVTs, were highly permissive to productive infection with ZIKV strain DAK AR 41524. The impact of ZIKV on the cellular transcriptome showed that infection of TSCs and STs increased expression of immune related genes, including those involved in type I and type III interferon responses. ZIKV exposure altered extracellular vesicle (EV) protein, mRNA, and miRNA cargo, regardless of productive infection. These findings suggest that early gestation macaque TSCs and STs are permissive to ZIKV infection, and that EV analysis may provide a foundation for identifying non-invasive biomarkers of placental infection in a highly translational model.

overall_design: 24 cell and 24 EV samples were submitted for miRNAseq


title: Zika virus impacts extracellular vesicle composition and cellular gene expression in macaque early gestation trophoblasts

overall_design: 8 extracellular vesicle (EV) samples were analyzed for poly(A) mRNAs. 5 were control and 3 were ZIKV-exposed cells.


title: MYCN mediates cysteine addiction and sensitizes neuroblastoma to ferroptosis

city: Heidelberg

first: Hamed

last: Alborzinia

address: Im Neuenheimer Feld 280

department: Stem cells and Cancer (DFKZ)

institute: DKFZ

summary: Analysis of ferroptosis markers from cells isolated from neuroblastoma orthotopic xenograft mouse model. We combine simultaneous inhibition of cysteine uptake and transsulfuration in xenograft model using SK-N-DZ cell line. We treated the mice with IKE and PPG together with genetic targeting of GPX4 activity. At the end of the treatment, transcriptional profiling of residual small tumors revealed induction of ferroptosis markers after combined inhibition of cystine uptake/cysteine synthesis and GPX4 as compared to tumors treated with vehicle control.

overall_design: 5 samples were analyzed in each group

first: Andrés

middle: F

last: Flórez

first: Andreas

last: Trumpp


title: X chromosome by high throughput sequencing

city: Tsukuba, Ibaraki

first: Ken

last: Nishimura

address: 1-1-1 Tennodai

institute: University of Tsukuba


title: Transcriptomic profiling of mouse lung endothelial cells associated with metastasis of Tenascin C-depleted breast cancer cells

status: Public on Dec 31 2021

first: Tsunaki

last: Hongu

state: Baden-Württemberg

department: Junior Research Group Metastatic Niches

institute: German Cancer Research Center (Deutsches Krebsforschungszentrum, DKFZ)

summary:
In cancer progression to metastasis, disseminated cancer cells frequently lodge near vasculature in secondary organs. However, our understanding of the cellular crosstalk evoked at perivascular sites is still rudimentary. In this study, we identified an inter-cellular machinery governing formation of a pro-metastatic vascular niche during breast cancer colonization in lungs. Transcriptomic analysis of endothelial cells (ECs) isolated from mouse lungs with metastases revealed a marked upregulation of genes linked to proliferation, inflammation and numerous secreted proteins. We showed that four secreted factors, INHBB, SCGB3A1, OPG and LAMA1, induced in ECs form a supportive niche that promotes metastasis in mice, by enhancing stem cell properties and survival ability of cancer cells. Interestingly, the blocking vascular endothelial cell growth factor (VEGF), a major cytokine regulating EC behaviors, dramatically suppressed EC proliferation whereas no impact was observed on the expression of the four vascular niche factors in lung ECs. We found that the formation of a vascular niche is correlated with inflammation, and revealed that metastasis-associated macrophages are essential for production of all of four niche factors in lung ECs. Macrophages are activated via TNC-TLR4 at perivasculature and sequentially stimulate ECs to produce the four niche factors. Thus, our findings provide mechanistic insights into the formation of a perivascular niche and offer the possibility that targeting macrophages may synergize with existing anti-angiogenic drugs to effectively suppress vascular function in metastatic colonization.
We used microarrays to analyze the global changes of gene expression in mouse lung endothelial cells associated with metastasis of Tenascin C-depleted breast cancer cells

overall_design: For profiling of lung endothelial cells (ECs) associating with metastasis, NSG mice (6-8 weeks of age) were intravenously injected with MDA-MB-231-LM2 (MDA-LM2) breast cancer cells expressing control shRNA or shRNA for Tenascin C (TNC).  Lungs from mice were harvested on day 20 post cancer cell injection, and ECs were isolated from whole lungs by fluorescence-activated cell sorting (FACS) using a panel of negative selection markers and CD31 as positive endothelial cell marker. For each group, 3 biological replicates were analyzed.

first: Thordur

last: Oskarsson


title: QPCTL deletion results in a rewiring of the tumor microenvironment [scRNA-seq]

summary: single cell RNA sequencing performed on the FACS sorted tumor microenvironment of (QPCTL-proficient and -deficient) B16F10 tumors

overall_design: C57/Bl6JR mice that were QPCTL-WT or QPCTL-KO were innoculated with either QPCTL-proficient or deficient B16F10 tumor cells, respectively (n=3 each). After 14 days tumors were harvested, single cell suspensions were made and live cells were isolated by FACS, after which cells were processed for scRNA-seq (10X Chromium 3' kit), and sequenced on Illumina NextSeq


title: Transcriptomic profiling of SUM159 human breast cancer cells with ectopic expression of SCGB3A1

summary:
In cancer progression to metastasis, disseminated cancer cells frequently lodge near vasculature in secondary organs. However, our understanding of the cellular crosstalk evoked at perivascular sites is still rudimentary. In this study, we identified an inter-cellular machinery governing formation of a pro-metastatic vascular niche during breast cancer colonization in lungs. Transcriptomic analysis of endothelial cells (ECs) isolated from mouse lungs with metastases revealed a marked upregulation of genes linked to proliferation, inflammation and numerous secreted proteins. We showed that four secreted factors, INHBB, SCGB3A1, OPG and LAMA1, induced in ECs form a supportive niche that promotes metastasis in mice, by enhancing stem cell properties and survival ability of cancer cells. Interestingly, the blocking vascular endothelial cell growth factor (VEGF), a major cytokine regulating EC behaviors, dramatically suppressed EC proliferation whereas no impact was observed on the expression of the four vascular niche factors in lung ECs. We found that the formation of a vascular niche is correlated with inflammation, and revealed that metastasis-associated macrophages are essential for production of all of four niche factors in lung ECs. Macrophages are activated via TNC-TLR4 at perivasculature and sequentially stimulate ECs to produce the four niche factors. Thus, our findings provide mechanistic insights into the formation of a perivascular niche and offer the possibility that targeting macrophages may synergize with existing anti-angiogenic drugs to effectively suppress vascular function in metastatic colonization.
We used microarrays to analyze the global changes of gene expression in SUM159 human breast cancer cells with ectopic expression of SCGB3A1.

overall_design: SUM159 human breast cancer cells were infected with lentivirus harboring pLVX-puro empty vector (control) or pLVX-puro-hSCGB3A1 and selected with 2 μg/ml puromycin (Invitrogen) for 7days. Cells were seeded into ultra-low attachment cell culture dishes with HuMEC-medium (Invitrogen) supplemented 0.1% BSA, B27 Supplement (Gibco), 50 U/ml penicillin (Sigma-Aldrich) and 50 μg/ml streptomycin (Sigma-Aldrich). After 5 days, cells were harvested and total RNA was isolated. RNA from three biological replicates was analyzed using Affymetrix Gene Chip human U133 Plus 2.0 Arrays.


title: Differential transcription in cell sorted paired TLR9hi and TLR9lo CLL samples

city: Falmer

first: Andrea

last: Pepper

address: University of Sussex

country: United Kingdom

institute: Brighton and Sussex Medical School

summary: This study set out to establish whether sub-populations of chronic lymphocytic leukaemia (CLL) cells, with different expression of cell surface TLR9 expression, have altered gene transcription signatiures.

overall_design: Primary CLL cells were labelled with fluorescence-tagged antibodies recognising CD5, CD19 and TLR9. Tumour sub-populations were identified by co-expression of CD5 and CD19 together with TLR9hi or TLR9lo expression. CD5+/CD19+/TLR9hi and CD5+/CD19+/TLR9lo fractions were high speed cell sorted using a FACSMelody cell sorter. RNA was the extracted using a Qiagen RNeasy kit followed by RNA-sequencing. Anyalysis revealed that TLR9hi CLL cells showed gene set enrichment for pathways involved in immune cell activation, cell-cell adhesion and leukeocyte migration.

first: Chris


title: Genome-wide Kdm1a binding in X chromosome by high throughput sequencing [ChIP-Seq]

summary: We analyzed KDM1A (LSD1) occupancy in the Xi during somatic cell reprogramming of female mouse cells. We use MEFs from hybrid embryos by crossing male Mus spretus and female Mus musculus domesticus C57BL/6J to distiguish genome DNA from the Xi. We found a possible physical and/or functional regulation of KDM1A during the X chromosome reactivation in the intiation site on the Xi.

overall_design: Chromatins were isolated from MEF, and cells reprogrammed by SeVdp(fKOSMaB) with or without 30 nM Shield1 at day 20. ChIP was performed using anti-LSD1 antibody (ab17721, abcam). Libraries were sequenced on an Illumina NovaSeq 6000 and data was analyzed allele-specifically by variantcall using bcftools mpileup.

first: Akihiro

last: Kuno

first: Eiji

last: Sugihara


title: Transcriptomic profiling of bone marrow-derived macrophages upon treatment with recombinant Tenascin-C and TLR4 inhibitor

summary:
In cancer progression to metastasis, disseminated cancer cells frequently lodge near vasculature in secondary organs. However, our understanding of the cellular crosstalk evoked at perivascular sites is still rudimentary. In this study, we identified an inter-cellular machinery governing formation of a pro-metastatic vascular niche during breast cancer colonization in lungs. Transcriptomic analysis of endothelial cells (ECs) isolated from mouse lungs with metastases revealed a marked upregulation of genes linked to proliferation, inflammation and numerous secreted proteins. We showed that four secreted factors, INHBB, SCGB3A1, OPG and LAMA1, induced in ECs form a supportive niche that promotes metastasis in mice, by enhancing stem cell properties and survival ability of cancer cells. Interestingly, the blocking vascular endothelial cell growth factor (VEGF), a major cytokine regulating EC behaviors, dramatically suppressed EC proliferation whereas no impact was observed on the expression of the four vascular niche factors in lung ECs. We found that the formation of a vascular niche is correlated with inflammation, and revealed that metastasis-associated macrophages are essential for production of all of four niche factors in lung ECs. Macrophages are activated via TNC-TLR4 at perivasculature and sequentially stimulate ECs to produce the four niche factors. Thus, our findings provide mechanistic insights into the formation of a perivascular niche and offer the possibility that targeting macrophages may synergize with existing anti-angiogenic drugs to effectively suppress vascular function in metastatic colonization.
We used microarrays to analyze the global changes of gene expression in bone marrow-derived macrophages upon treatment with Tenascin-C and TLR4 inhibitor

overall_design: For profiling of bone marrow-derived macrophages (BMDMs), bone marrow cells were obtained from BALB/c mice (8-10 weeks old) and cultured for 7 days in DMEM (ThermoFisher Scientific) supplemented with 10% FBS and 20 μg/ml macrophage-colony stimulating factor (M-CSF, Peprotech). Differentiated BMDMs were further cultured overnight with DMEM containing 1% FBS and 20 μg/ml M-CSF. BMDMs were then treated with 3 μM TAK-242 (TLR4i, Merck) or vehicle control (0.1% DMSO in final) for 1 hr, and stimulated with 2 μg/ml recombinant Tenascin-C (TNC, Merck) for 6 hrs.  Total RNA from three biological replicates was isolated and analyzed using Affymetrix Gene Chip Mouse Genome U430 2.0 Arrays.


title: Effects of miR-26a expression and miRNA-sponge-mediated miR-26 family knockdown on the transcriptome of B cell precursors

city: Innsbruck

first: Sebastian

last: Herzog

address: Innrain 80-82

department: Institute of Developmental Immunology

country: Austria

institute: Medical University of Innsbruck, Biocenter

summary: Here, we have screened a miRNA expression library in a pre-B cell expression system to identify miRNAs with a potential oncogenic activity in early lymphocytes. We show that miR-26a is sufficient to transform B cell precursors in vitro as defined by growth factor independence, and demonstrate that its continuous expression is necessary to keep cells in the transformed state. Mechanistically, we find that expression of miR-26a protects against apoptosis induced by growth factor withdrawal as well as DNA damage, provides a competitve advantage  and interferes with the differentiation of pre-B to immature B cells. In consequence, transformed cells express the pre-BCR on the cell surface, which appears to provide signals for ongoing proliferation and survival. Using microarray analysis, we identified several previously known and novel putative target genes of miR-26a in B cell precursors. A key target appears to be PTEN, a well established tumor suppressor and regulator of PI3K signaling, as knockdown of Pten mRNA by shRNA at least partially phenocopies miR-26a overexpression. To gain inside into the physiological role of miR-26 in early B cell develobment, in contrast to the oncogenic situation if aberrantly overexpressed, we further more sequestered endogenous miR-26a and b by expression of a miRNA sponge. This functional knockdown indeed induced the reciprocal phenotype relative to the overexpression, i.e. cells had a proliferative disadvantage and differentiated more efficient into immature B cells. Surprisingly, however, transcriptional changes induced by miR-26 sequestration were very mild. We therefoer hypothesize that most of the sponge-mediated deregulation is below detection level while still being functional relevant.

overall_design: Gene expression in cells expressing a control vector or a vector encoding miR-26a overexpression or miR-26 sponge constructs was measured either in the presencel of the growth factor IL-7. Two independent experiments were performed, using independently generated cell clones for each repetition.


title: The histone H3K27 demethylase REF6/JMJ12 Promotes thermomorphogenesis in Arabidopsis

city: Beijing

first: Xiaofeng

last: Cao

state: Beijing

address: No.1 West Beichen Road, Chaoyang District

department: National Key Lab of Plant Genomics

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

summary: Dynamic trimethylation of histone H3 at Lys27 (H3K27me3) affects gene expression and controls plant development and environmental responses. In Arabidopsis thaliana, RELATIVE OF EARLY FLOWERING 6/JUMONJI DOMAIN-CONTAINING PROTEIN 12 (REF6/JMJ12) demethylates H3K27me3 by recognizing a specific DNA motif; however, little is known about how REF6 activates target gene expression after recognition, especially in environmental responses. In response to warm ambient temperature, plants undergo thermomorphogenesis, which involves accelerated growth, early flowering, and changes in morphology. Here we show that REF6 regulates thermomorphogenesis and cooperates with the transcription factor PHYTOCHROME INTERACTING FACTOR 4 (PIF4) to synergistically activate thermo-responsive genes under warm ambient temperature. The ref6 loss-of-function mutants exhibited attenuated hypocotyl elongation at warm temperature, partially due to down-regulation of GIBBERELLIN 20-OXIDASE2 (GA20ox2) and BASIC HELIX-LOOP-HELIX 87 (bHLH87). REF6 enzymatic activity is necessary for warm ambient temperature responses. Together, our results provide direct evidence of an epigenetic modifier and a transcription factor working together to respond to the environment.

overall_design: All mutant lines used in this study were in the Columbia ecotype background. H3K27me3 ChIP-Seq was performed at 22℃ and 28℃ in wild type and ref6 KO Arabidopsis (Col). REF6 ChIP-Seq were performed at 22℃ and 28℃ in wild type. RNA-seq were performed at 22℃ and 28℃ in wild type and ref6 KO Arabidopsis (Col).

first: Kaixuan

last: He

first: Xian

last: Deng

first: Hailiang

last: Mei


title: Histone H3K4me3 signal breadth reveals constitutive and hypoxia stress responsive endometrial functions linked to endometriosis

city: West Haven

first: Kalle

middle: T

last: Rytkönen

state: CT

address: 840 West Campus Drive

department: EEB, Systems Biology institute

institute: Yale University

summary: We report sequening of chromatin immunoprecipitated DNA (ChIP-Seq) of histone H3 at lysine 4 (H3K4me3) normoxic and hypoxia treated endometrial stromal fibroblasts (ESF) and hypoxia treated differentiated decidual stromal cells (DSC),

overall_design: We conducted H3K4me3 ChIP-seq in hypoxia treated (16 h, 1% O2) undifferentiated endometrial stromal fibroblasts (ESF) and differentiated decidual stromal cells (DSC) and compared the H3K4me3 marks to those in normoxia. For DSC, before hypoxia treatment ESF were in vitro decidulized with cAMP and progesterone (MPA) for 2 days.

first: Mauris

middle: C

last: Nnamani


title: Reduced chromatin accessibility correlates with resistance to Notch activation

status: Public on Jan 07 2022

city: Cambridge

last: Brand

address: Tennis Court Rd

institute: The Gurdon Institute

summary: The Notch signalling pathway is a master regulator of cell fate transitions in development and disease. In the brain, Notch promotes neural stem cell (NSC) proliferation, regulates neuronal migration and maturation and can act as an oncogene or tumour suppressor. How NOTCH and its transcription factor RBPJ activate distinct gene regulatory networks in closely related cell types in vivo remains to be determined. Here we use Targeted DamID (TaDa), requiring only thousands of cells, to identify NOTCH and RBPJ binding in NSCs and their progeny in the mouse embryonic cerebral cortex in vivo. We find that NOTCH and RBPJ associate with a broad network of NSC genes. Repression of NSC-specific Notch target genes in intermediate progenitors and neurons correlates with decreased chromatin accessibility, suggesting that chromatin compaction may contribute to restricting NOTCH-mediated transactivation.

overall_design: Notch and RBPJ targeted DamID and chromatin accessibility DamID from mouse embryonic cortex. Between 3 and 7 replicates per experimental condition. For Notch and RBPJ binding, data are normalized to Dam-only samples (see protocol).

first: Jelle

last: van den Ameele

first: Robert

last: Krautz

first: Seth

middle: W

last: Cheetham

first: Alex

last: Donovan

first: Oriol

last: Llorà-Battle

first: Rebecca

last: Yakob

middle: H


title: Induction of human trophoblast stem-like cells from primed pluripotent stem cells

city: Austin

first: Yu Jin

last: Jang

state: Texas

address: 2506 Speedway, NMS 4.246

department: Molecular Biosciences

institute: University of Texas at Austin

summary: The placenta is a transient but important multifunctional organ crucial for healthy pregnancy for both mother and fetus. Nevertheless, limited access to human placenta samples and the paucity of a proper in vitro model system has hampered our understanding of the mechanisms underlying early human placental development and placenta-associated pregnancy complications. To overcome these constraints, we established a simple procedure with a short-term treatment of bone morphogenetic protein 4 (BMP4) in trophoblast stem cell culture medium (TSCM) to convert human primed pluripotent stem cells (PSCs) to trophoblast stem-like cells (TSLCs). These TSLCs show not only comparable morphology and gene expression profile to bona fide human trophoblast stem cells (TSCs) but also long-term self-renewal capacity with bipotency that allows the cells to differentiate into extravillous trophoblasts (EVT) and syncytiotrophoblasts (ST). These indicate that TSLCs are equivalent to genuine human TSCs. Our data suggest a straightforward approach to make human TSCs directly from pre-existing primed PSCs and provide a valuable opportunity to study human placenta development and pathology even from patients with placenta-related diseases.

overall_design: RNA-seq was performed on the following cells: primary hTSCs (CT27), undifferentiated hESCs (H9), undifferentiated hiPSCs, hTSLCs (TS-like cells) derived from hESCs (ES-TSLCs), hTSLCs derived from hiPSCs (iPS-TSLCs), EVT differentiated from hTSCs, EVT differentiated from ES-TSLCs (ES-EVT), EVT differentiated from iPS-TSLCs (iPS-EVT), ST differentiated from hTSCs, ST differentiated from ES-TSLCs (ES-ST), and ST differentiated from iPS-TSLCs (iPS-ST). Two biological replicates were used for each cell type.

first: Jonghwan

last: Kim


title: Sox2 levels configure the WNT response of epiblast progenitors responsible for vertebrate body formation [EXP5_ChIPSeq]

city: London

first: James

last: Briscoe

address: 1 Midland Road

institute: The Francis Crick Institute

summary: In this experiment the binding of SOX2, B-catenin, and LEF1 was assayed using ChIP-seq following differentiation of WT, T/Bra mutant, and Cdx1,2,4 triple mutant embryonic stem cells to caudal ebiblast progenitors. SOX2 binding in epiblast cells was assayed for comparison.

overall_design: Triplicate chromatin immunoprecipitations from independent biological replicates were performed for each factor analyzed in three genetic backgrounds. Binding of each factor was compared between WT caudal epiblast progenitor cells , T/Bra mutant, and Cdx1,2,4 triple mutant progenitors differentiated in the presence of the WNT agonist CHIR99021. SOX2 binding was also compared between caudal epiblast progenitors and epiblast progenitors differentiated in the absence of CHIR99021.

last: Blassberg

first: Harshil

last: Patel

first: Thomas

last: Watson

first: Mina

last: Gouti

first: Vicki

last: Metzis

first: M

last: Delas


title: Prrx1 is a Master Transcription Factor of myofibroblastic Cancer-Associated Fibroblasts [Human_CAF_RNA_seq]

city: Gangnam-gu

first: Seok-Hyung

state: Seoul

address: 81, Irwon-ro

department: Department of Pathology

country: South Korea

institute: Samsung Medical Center

summary: Although cancer associated fibroblasts (CAF) play a critical role in cancer progression, their identities are still unknown. Because cells’ own identity is determined by core regulatory circuit (CRC) comprising master transcription factors (TFs), it is critical to find CAF’s master TF. Therefore, we attempt to find master TF of CAF through the extensive screening of single cell RNA-seq database of cancer tissues, and discovered Prrx1, master regulator of embryonic mesenchymal cells, as candidate for master TF of CAF. Prrx1 was abundantly expressed in CAFs with significant correlation with unfavorable clinical outcomes. Furthermore, Prrx1 in fibroblasts dramatically enhanced tumor progression and metastasis in fibroblast-specific Prrx1 inducible mice. On the other hand, tumor formation was severely inhibited in conditional Prrx1 knock-down mice. Finally, we confirmed that Prrx1 is a master TF of CAF and normal fibroblast executing wound healing program using ChIP-SEQ, CRC modeling, and in vivo validation. Furthermore we also revealed that targeting Prrx1 in fibroblast alone induced complete remission of chemotherapy-resistant cancer in preclinical mouse experiments.

overall_design: First, three murine fibroblasts such as mouse embryonic fibroblast, wound healing fibroblast, and MMTV CAF are obtained from C57BL/6, FVB strains. The ChIP-seq were performed in these fibroblasts using H3K27ac, H3K4me3, and Prrx1 antibody and the RNA-seq also were performed. Second, single cells of murine wound tissue obtained from BALB/c were performed using 10X platform. Third, nine ex vivo cultured human CAFs isolated from advanced colorectal cancer tissue were established. we performed H3K27ac ChIP-seq and RNA-seq from these human CAFs.

first: Keun-Woo

last: Lee

first: So-Young

last: Yeo

first: Jeong-Ryeol

last: Gong

first: Kwang-Hyun

last: Cho


title: Prrx1 is a Master Transcription Factor of myofibroblastic Cancer-Associated Fibroblasts [Murine_Fibroblast_ChIP_seq]

overall_design: First, three murine fibroblasts such as mouse embryonic fibroblast, wound healing fibroblast, and MMTV CAF are obtained from C57BL/6, FVB strains. The ChIP-seq were performed in these fibroblasts using H3K27ac, H3K4me3, and Prrx1 antibody and the RNA-seq also were performed. Second, single cells of murine wound tissue obtained from C57BL/6 were performed using 10X platform. Third, nine ex vivo cultured human CAFs isolated from advanced colorectal cancer tissue were established. we performed H3K27ac ChIP-seq and RNA-seq from these human CAFs.


title: Sox2 levels configure the WNT response of epiblast progenitors responsible for vertebrate body formation [EXP5_RNASeq]

summary: In this experiment the transcriptional changes accompanying differentiation of WT, T/Bra mutant, and Cdx1,2,4 mutant embryonic stem cells to caudal epiblast-like cells was assayed using RNA-seq.

overall_design: Transcriptional profiles were generated from three independent biological replicates in three genetic backgrounds. WT caudal epiblast progenitor cells were compared to T/Bra mutant and Cdx1,2,4 triple mutant progenitors differentiated in the presence of the WNT agonist CHIR99021.

first: Robert


title: Prrx1 is a Master Transcription Factor of myofibroblastic Cancer-Associated Fibroblasts [Murine_Wound_Tissue_scRNAseq]


title: Genome-wide transcripts from X chromosome by high throughput sequencing [RNA-Seq]

first: Ken

last: Nishimura

summary: We analyzed a transcriptional landscape of the Xi during somatic cell reprogramming of female mouse cells. We use MEFs from hybrid embryos by crossing male Mus spretus and female Mus musculus domesticus C57BL/6J to monitor allele-specific transcripts from the Xi. We could capture the earliest phase of X chromosome reactivation and found that a subset of genes clustered near the centromere display an early reactivation on the Xi.

overall_design: RNA were isolated from MEF, and cells reprogrammed by SeVdp(fKOSMaB) with or without 30 nM Shield1. Libraries were sequenced on an Illumina NextSeq500 with paired-end mode for 2x76-base reads. Data was analyzed allele-specifically by variantcall using Basic Variant Call tool in CLC-Genomic Workbench.

first: Masafumi

last: Muratani


title: Prrx1 is a Master Transcription Factor of myofibroblastic Cancer-Associated Fibroblasts

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: Comparative gene expression profiles of NOS1-KO and WT A375 melanoma cell lines

city: Guangzhou

first: Liu

last: Qiuzhen

address: No.1023,South Shatai Road, Baiyun District

country: Zimbabwe

institute: Southern Medical University

summary: NOS1 plays a vital role in tumor. A cell model of NOS1 gene knockout in human melanoma cell line A375 was constructed using CRISPR/Cas9 technique for the study of its function. We used microarrays to detail the Global gene expression underlying NOS1-knockout compare to wild type A375 cell.

overall_design: NOS1-KO and WT A375 cells for RNA extraction and hybridization on Affymetrix microarrays. There were three biological replicates performed for each cell lines.

first: Qiuzhen

last: Liu

first: Xi

last: Chen


title: Prrx1 is a Master Transcription Factor of myofibroblastic Cancer-Associated Fibroblasts [Murine_co-culture_RNA_seq]

last: Kim


title: Prrx1 is a Master Transcription Factor of myofibroblastic Cancer-Associated Fibroblasts [Human_CAF_ChIP_seq]


title: Sox2 levels configure the WNT response of epiblast progenitors responsible for vertebrate body formation. [EXP4_RNASeq]

first: James

last: Briscoe

summary: In this experiment the transcriptional changes accompanying differentiation of embryonic stem cell to epiblast-like cells was assayed using RNA-seq.

overall_design: Transcriptional profiles were generated from three independent biological replicates in two experimental conditions. Serum cultured ES cells were compared to epiblast progenitor cells differentiated in the presence of FGF.


title: Sox2 levels configure the WNT response of epiblast progenitors responsible for vertebrate body formation. [EXP2 ChIPSeq]

summary: In this experiment the relationship between SOX2 levels and the binding of B-catenin, TCF/LEF factors, and SOX2 to chromatin was assayed using ChIP-seq during embryonic stem cell differentiation and in naive pluripotency.  A doxycycline inducible cell line (SOX2 TetON) was employed to experimentally control SOX2 expression.

overall_design: Triplicate chromatin immunoprecipitations from independent biological replicates were performed for each factor analysed in four experimental conditions. Sox2 TetON ES cells differentiated in the presence or absence of 1ug/ml doxycycline were compared to differentiated WT epiblast progenitor cells and naive pluripotent embryonic stem cells.

last: Blassberg

first: Harshil


title: Sox2 levels configure the WNT response of epiblast progenitors responsible for vertebrate body formation. [EXP1_ATACSeq]

summary: In this experiment the relationship between SOX2 levels and chromatin accessibility was assayed using ATAC-seq during embryonic stem cell differentiation.  A doxycycline inducible cell line (SOX2 TetON) was employed to experimentally control SOX2 expression.

overall_design: Transposase accessible chromatin profiles were generated at high read depth in three experimentall conditions. Sox2 TetON ES cells differentiated in the presence or absence of 1ug/ml doxycycline were compared to differentiated WT epiblast progenitor cells.

last: Patel

first: Thomas


title: Transcriptomic profiling of SUM-LM1 human breast cancer cells upon treatment with recombinant Activin B or vehicle

first: Tsunaki

last: Hongu

summary:
In cancer progression to metastasis, disseminated cancer cells frequently lodge near vasculature in secondary organs. However, our understanding of the cellular crosstalk evoked at perivascular sites is still rudimentary. In this study, we identified an inter-cellular machinery governing formation of a pro-metastatic vascular niche during breast cancer colonization in lungs. Transcriptomic analysis of endothelial cells (ECs) isolated from mouse lungs with metastases revealed a marked upregulation of genes linked to proliferation, inflammation and numerous secreted proteins. We showed that four secreted factors, INHBB, SCGB3A1, OPG and LAMA1, induced in ECs form a supportive niche that promotes metastasis in mice, by enhancing stem cell properties and survival ability of cancer cells. Interestingly, the blocking vascular endothelial cell growth factor (VEGF), a major cytokine regulating EC behaviors, dramatically suppressed EC proliferation whereas no impact was observed on the expression of the four vascular niche factors in lung ECs. We found that the formation of a vascular niche is correlated with inflammation, and revealed that metastasis-associated macrophages are essential for production of all of four niche factors in lung ECs. Macrophages are activated via TNC-TLR4 at perivasculature and sequentially stimulate ECs to produce the four niche factors. Thus, our findings provide mechanistic insights into the formation of a perivascular niche and offer the possibility that targeting macrophages may synergize with existing anti-angiogenic drugs to effectively suppress vascular function in metastatic colonization.
We used microarrays to analyze the global changes of gene expression in SUM-LM1 human breast cancer cells upon treatment with Activin B

overall_design: For profiling of Activin B-treated or vehicle-treated breast cancer cells, SUM-LM1 cells were seeded into ultra-low attachment cell culture dishes with HuMEC-medium (Invitrogen) supplemented 0.1% BSA, 50 U/ml penicillin (Sigma-Aldrich) and 50 μg/ml streptomycin (Sigma-Aldrich) with or without 50 ng/ml recombinant Activin B (R&D systems). 0.1% BSA/PBS was used as vehicle control. After 6 hrs stimulation, cells were harvested and total RNA was isolated. RNA from three biological replicates was analyzed using Affymetrix Gene Chip human U133 Plus 2.0 Arrays.

first: Thordur

last: Oskarsson


title: Sox2 levels configure the WNT response of epiblast progenitors responsible for vertebrate body formation.


title: Prrx1 is a Master Transcription Factor of myofibroblastic Cancer-Associated Fibroblasts [Murine_Fibroblast_RNA_seq]


title: Transcriptomic profiling of metastasis-associated lung endothelial cells from mice with treatment for macrophage-depletion

summary:
In cancer progression to metastasis, disseminated cancer cells frequently lodge near vasculature in secondary organs. However, our understanding of the cellular crosstalk evoked at perivascular sites is still rudimentary. In this study, we identified an inter-cellular machinery governing formation of a pro-metastatic vascular niche during breast cancer colonization in lungs. Transcriptomic analysis of endothelial cells (ECs) isolated from mouse lungs with metastases revealed a marked upregulation of genes linked to proliferation, inflammation and numerous secreted proteins. We showed that four secreted factors, INHBB, SCGB3A1, OPG and LAMA1, induced in ECs form a supportive niche that promotes metastasis in mice, by enhancing stem cell properties and survival ability of cancer cells. Interestingly, the blocking vascular endothelial cell growth factor (VEGF), a major cytokine regulating EC behaviors, dramatically suppressed EC proliferation whereas no impact was observed on the expression of the four vascular niche factors in lung ECs. We found that the formation of a vascular niche is correlated with inflammation, and revealed that metastasis-associated macrophages are essential for production of all of four niche factors in lung ECs. Macrophages are activated via TNC-TLR4 at perivasculature and sequentially stimulate ECs to produce the four niche factors. Thus, our findings provide mechanistic insights into the formation of a perivascular niche and offer the possibility that targeting macrophages may synergize with existing anti-angiogenic drugs to effectively suppress vascular function in metastatic colonization.
We used microarrays to analyze the global changes of gene expression in metastasis-associated lung endothelial cells upon macrophage-depleted conditions

overall_design: For profiling of lung endothelial cells (ECs) associating with metastasis, NSG mice (6-8 weeks of age) were injected with MDA-MB-231-LM2 (MDA-LM2) breast cancer cells via the tail vein. On the day 14, 16 and 18 post cancer cell injection, mice were intravenously injected with PBS-loaded liposomes or clodronate-loaded liposomes (100 ul per mouse), and lungs from mice were harvested on day 20. ECs were isolated from whole lungs by fluorescence-activated cell sorting (FACS) using a panel of negative selection markers and CD31 as positive endothelial cell marker. For each group, 3 biological replicates were analyzed.


title: Transcriptomic profiling of metastasis-associated lung endothelial cells from mice treated with anti-VEGFR2 antibody (DC101)

summary:
In cancer progression to metastasis, disseminated cancer cells frequently lodge near vasculature in secondary organs. However, our understanding of the cellular crosstalk evoked at perivascular sites is still rudimentary. In this study, we identified an inter-cellular machinery governing formation of a pro-metastatic vascular niche during breast cancer colonization in lungs. Transcriptomic analysis of endothelial cells (ECs) isolated from mouse lungs with metastases revealed a marked upregulation of genes linked to proliferation, inflammation and numerous secreted proteins. We showed that four secreted factors, INHBB, SCGB3A1, OPG and LAMA1, induced in ECs form a supportive niche that promotes metastasis in mice, by enhancing stem cell properties and survival ability of cancer cells. Interestingly, the blocking vascular endothelial cell growth factor (VEGF), a major cytokine regulating EC behaviors, dramatically suppressed EC proliferation whereas no impact was observed on the expression of the four vascular niche factors in lung ECs. We found that the formation of a vascular niche is correlated with inflammation, and revealed that metastasis-associated macrophages are essential for production of all of four niche factors in lung ECs. Macrophages are activated via TNC-TLR4 at perivasculature and sequentially stimulate ECs to produce the four niche factors. Thus, our findings provide mechanistic insights into the formation of a perivascular niche and offer the possibility that targeting macrophages may synergize with existing anti-angiogenic drugs to effectively suppress vascular function in metastatic colonization.
We used microarrays to analyze the global changes of gene expression in metastasis-associated lung endothelial cells upon VEGFR2 inhibition

overall_design: For profiling of lung endothelial cells (ECs) associating with metastasis, NSG mice (6-8 weeks of age) were injected with MDA-MB-231-LM2 (MDA-LM2) breast cancer cells via the tail vein. On the day 21 and 24 post cancer cell injection, mice were treated with rat IgG or anti-VEGFR2 antibody (DC101, 40 mg/kg, i.p. injection), and lungs from mice were harvested on day 25. Lungs from age-matched healthy mice treated with rat IgG were used as control group. ECs were isolated from whole lungs by fluorescence-activated cell sorting (FACS) using a panel of negative selection markers and CD31 as positive endothelial cell marker. For each group, 3 biological replicates were analyzed.


title: Sox2 levels configure the WNT response of epiblast progenitors responsible for vertebrate body formation. [EXP3 RNASeq]

summary: In this experiment the relationship between SOX2 levels and WNT-induced gene expression was assayed using RNA-seq during embryonic stem cell differentiation.  A doxycycline inducible cell line (SOX2 TetON) was employed to experimentally control SOX2 expression.

overall_design: Transcriptional profiles were generated from three independent biological replicates in four experimental conditions. Sox2 TetON ES cells differentiated in the presence or absence of 1ug/ml doxycycline were compared to differentiated WT epiblast progenitor cells cultured in the presence or absence of the WNT agonist CHIR99021.

last: Watson

first: Mina

last: Gouti

first: Vicki

last: Metzis

first: M


title: Inter-cellular machinery governing formation of a pro-metastatic vascular niche during breast cancer colonization in lungs


title: Transcriptomic profiling of lung endothelial cells at different stages of lung colonization by MDA-MB-231-LM2 cells

summary:
In cancer progression to metastasis, disseminated cancer cells frequently lodge near vasculature in secondary organs. However, our understanding of the cellular crosstalk evoked at perivascular sites is still rudimentary. In this study, we identified an inter-cellular machinery governing formation of a pro-metastatic vascular niche during breast cancer colonization in lungs. Transcriptomic analysis of endothelial cells (ECs) isolated from mouse lungs with metastases revealed a marked upregulation of genes linked to proliferation, inflammation and numerous secreted proteins. We showed that four secreted factors, INHBB, SCGB3A1, OPG and LAMA1, induced in ECs form a supportive niche that promotes metastasis in mice, by enhancing stem cell properties and survival ability of cancer cells. Interestingly, the blocking vascular endothelial cell growth factor (VEGF), a major cytokine regulating EC behaviors, dramatically suppressed EC proliferation whereas no impact was observed on the expression of the four vascular niche factors in lung ECs. We found that the formation of a vascular niche is correlated with inflammation, and revealed that metastasis-associated macrophages are essential for production of all of four niche factors in lung ECs. Macrophages are activated via TNC-TLR4 at perivasculature and sequentially stimulate ECs to produce the four niche factors. Thus, our findings provide mechanistic insights into the formation of a perivascular niche and offer the possibility that targeting macrophages may synergize with existing anti-angiogenic drugs to effectively suppress vascular function in metastatic colonization.
We used microarrays to analyze the global changes of gene expression in lung endothelial cells at different stages of lung colonization by MDA-MB-231-LM2 cells

overall_design: For profiling of lung endothelial cells (ECs) at different metastatic stages, NSG mice (6-8 weeks of age) were injected with MDA-MB-231-LM2 (MDA-LM2) breast cancer cells via the tail vein. At week 1, 2 and 3 post cancer cell injection, lungs from mice were harvested. Lungs from age-matched healthy mice were used as control group. Endothelial cells were isolated from whole lungs by fluorescence-activated cell sorting (FACS) using a panel of negative selection markers and CD31 as positive endothelial cell marker. For each time point, 3 biological replicates were analyzed.


title: RNAseq gene expression profiles of 87 pre-treatment biopsies of breast cancer patients to study neoadjuvant treatment response

status: Public on Dec 28 2021

first: Esther

last: Lips

address: Plesmanlaan 121

department: Molecular Pathology

institute: NKI-AVL

summary: When locally advanced breast cancer is treated with neoadjuvant chemotherapy, the recurrence risk is significantly higher if no complete pathologic response is achieved. Identification of the underlying resistance mechanisms is essential to select treatments with maximal efficacy and minimal toxicity. Here we employed gene expression profiles derived from 317 HER2-negative treatment-naïve breast cancer biopsies of patients who underwent neoadjuvant chemotherapy, deep whole exome and RNA-sequencing profiles of 22 matched pre- and post-treatment tumors, and treatment outcome data to identifiy biomarkers of response and resistance mechanims. Molecular profiling of treatment-naïve breast cancer samples revealed that expression levels of proliferation, immune response and extracellular matrix (ECM) organization combined predict response to chemotherapy. Triple negative patients with high proliferation, high immune response and low ECM expression had a significantly better treatment response and survival benefit (HR 0.29, 95% CI 0.10-0.85; p=0.02), while in ER+ patients the opposite was seen (HR 4.73, 95% CI 1.51-14.8; 0=0.008). The characterization of paired pre-and post-treatment samples revealed that aberrations of known cancer genes were either only present in the pre-treatmane sample (CDKN1B) or in the post-treatment sample(TP53, APC, CTNNB1). Proliferation-associated genes were frequently down-regulated in post-treatment ER+ tumors, but not in triple negative tumors. Genes involved in ECM were upregulated in the majority of post-chemotherapy samples. Genomic and transcriptomic differences between pre- and post-chemotherapy samples are common and may reveal potential mechanisms of therapy resistance. Our results show a wide range of distinct, but related mechanisms, with a prominent role for proliferation- and ECM-related genes.

overall_design:
Triple negative and luminal type breast cancer patients scheduled to receive neoadjuvant chemotherapy were included in this study. RNA was isolated from fresh-frozen biopsies. Illumina sequencing libraries were made and sequencing was performed on Illumina HiSeq 2000. Data was analyzed together with GSE34138, resulting in a larger dataset of n=317 neoadjuvant gene expression profiles.
**RAW data was deposited at EGA (EGAD00001008433)**

first: Marlous

last: Hoogstraat


title: NEK2 regulates triple negative breast cancer transcriptome.

status: Public on Dec 21 2021

city: Paris

first: Pierre

last: de la Grange

address: 29, rue du Faubourg Saint-Jacques

department: Paris Biotech Santé

country: France

institute: GenoSplice technology

summary: NEK2 is a mitotic kinase that is upregulated and mislocalized in the nucleus of human cancer cells. NEK2 modulates expression and activity of both transcription and splicing factors in cancer cells, nevertheless whether this kinase affects transcriptome regulation genome widely and whether this activity concurs to its oncogenic activity is still unknown. Herein,  by high-throughput RNA sequencing analysis of MDA-MB-231 cells transiently silenced for NEK2 we uncover an extensive modulation of triple-negative breast cancer cell transcriptome by this kinase.

overall_design: RNA‐Seq data for MDA-MB-231 cells, transiently silenced for NEK2

first: Chiara

last: Naro

last: de La Grange

first: Claudio

last: Sette


title: Transcriptome analysis of MCF10A-M2 cells upon the depletion of OVOL1 or OVOL2

status: Public on Dec 26 2021

city: Leiden

first: Hailiang

last: Mei

address: Einthovenweg 20

department: Sequencing Analysis Support Core

institute: Leiden University Medical Center

summary: OVOL1 protein was shown to be downregulated in breast cancer patient samples and was inversely correlated with the epithelial-to-mesenchymal transition (EMT) signature. To better dissect the downstream target genes and elucidate the signaling pathways altered by OVOL1, we deplete OVOL1 by the specific siRNA in MCF10A-M2 cells. To set as a control, OVOL2 was knockdown by the specific siRNA in the same cell line. The total RNA was collected and sent for RNA sequencing analysis. Afterwards, the differentially expressd genes were used for the pathway enrichment analysi and the gene set enrichment analysis (GSEA).

overall_design: OVOL1 or OVOL2 is depleted by siRNA in MCF10A-M2 cells. RNA from cells transfected with the non-targeting RNA siNT is set as a control. Three biological replicates are included in each group.

first: Chuannan

last: Fan

first: Cedrick

last: Agaser

first: Peter

last: ten Dijke


title: Transcriptomic profiling of metastasis-associated lung endothelial cells from mice treated with anti-VEGFA antibody (B20.4.1.1)

summary:
In cancer progression to metastasis, disseminated cancer cells frequently lodge near vasculature in secondary organs. However, our understanding of the cellular crosstalk evoked at perivascular sites is still rudimentary. In this study, we identified an inter-cellular machinery governing formation of a pro-metastatic vascular niche during breast cancer colonization in lungs. Transcriptomic analysis of endothelial cells (ECs) isolated from mouse lungs with metastases revealed a marked upregulation of genes linked to proliferation, inflammation and numerous secreted proteins. We showed that four secreted factors, INHBB, SCGB3A1, OPG and LAMA1, induced in ECs form a supportive niche that promotes metastasis in mice, by enhancing stem cell properties and survival ability of cancer cells. Interestingly, the blocking vascular endothelial cell growth factor (VEGF), a major cytokine regulating EC behaviors, dramatically suppressed EC proliferation whereas no impact was observed on the expression of the four vascular niche factors in lung ECs. We found that the formation of a vascular niche is correlated with inflammation, and revealed that metastasis-associated macrophages are essential for production of all of four niche factors in lung ECs. Macrophages are activated via TNC-TLR4 at perivasculature and sequentially stimulate ECs to produce the four niche factors. Thus, our findings provide mechanistic insights into the formation of a perivascular niche and offer the possibility that targeting macrophages may synergize with existing anti-angiogenic drugs to effectively suppress vascular function in metastatic colonization.
We used microarrays to analyze the global changes of gene expression in metastasis-associated lung endothelial cells upon VEGFA neutralization

overall_design: For profiling of lung endothelial cells (ECs) associating with metastasis, NSG mice (6-8 weeks of age) were injected with MDA-MB-231-LM2 (MDA-LM2) breast cancer cells via the tail vein. Mice were treated with control IgG or anti-VEGFA antibody (B20.4.1.1 provided from Genentech, 10 mg/kg, twice in a week, i.p. injection), and lungs from mice were harvested on day 21 after the injection of cancer cells. Lungs from age-matched healthy mice treated with control IgG were used as control group. ECs were isolated from whole lungs by fluorescence-activated cell sorting (FACS) using a panel of negative selection markers and CD31 as positive endothelial cell marker. For each group, 3 biological replicates were analyzed.


title: Comprehensive characterization of pre- and post-treatment samples of breast cancer reveal potential mechanisms of chemotherapy resistance

status: Public on Dec 18 2021

overall_design:
Here we employed gene expression profiles derived from 317 HER2-negative treatment-naïve breast cancer biopsies of patients who underwent neoadjuvant chemotherapy, deep whole exome and RNA-sequencing profiles of 22 matched pre- and post-treatment tumors, and treatment outcome data to identifiy biomarkers of response and resistance mechanims.
-----------------------------------
Authors state "The raw sequencing data files have been put on EGA (EGAD 00001008421)".


title: Insights into standards of care – dexamethasone and antibodies against COVID-19 in hamster models

city: Berlin

first: Emanuel

last: Wyler

address: Robert Roessle Str 10

department: Berlin Institute for Medical Systems Biology

institute: Max Delbrück Center for Molecular Medicine

summary: We describe the cellular response to SARS-CoV-2 infections combined with antibody and/or dexamethasone treatment in Syrian and Roborovski dwarf hamsters

sample_organism:
Mesocricetus auratus
Phodopus roborovskii

overall_design: Histopathology and bulk RNA-seq was performed from the lung of animals both species, single-cell RNA-sequencing was performed from lungs of Roborvski dwarf hamsters, upon SARS-CoV-2 infections combined with the indicated treatments.

first: Julia

middle: M

last: Adler

first: Kathrin

last: Eschke

first: Gustavo

last: Teixeira

first: Stefan

last: Peidli

first: Fabian

last: Pott

last: Kazmierski

first: Dylan

last: Postmus

first: Laura

last: Michalick

first: Olivia

last: Kershaw

first: Judith

last: Hoppe

first: Sandro

last: Andreotti

last: Pennitz

first: Christine

last: Goffinet

first: Jakob

last: Kreye

first: S

last: Reincke

first: Harald

last: Prüss

first: Nils

last: Blüthgen

first: Achim

middle: D

last: Gruber

first: Martin

last: Witzenrath

first: Markus

last: Landthaler

first: Geraldine

last: Nouailles

last: Trimpert


title: Integrative analysis of lncRNA-miRNA-mRNA regulatory network reveals candidate lncRNAs responsible for meat quality in goats

status: Public on Dec 25 2021

city: Chengdu

first: changsheng

last: he

address: No. 16, South Section, 1st Ring Roa

institute: southwest minzu university

summary: Our analysis revealed the unique and common lncRNA-miRNA-mRNA networks of two kinds of adipocytes. Several lncRNAs that regulate goat meat quality were identified, such as XR_001918647.1, XR_001917728.1, XR_001297263.2 and LNC_004191. Our study utilized RNA-seq analysis to predict the functions of lncRNA on goat meat quality. Furthermore, our findings of lncRNA-miRNA-mRNA network, may contribute to a better understanding of the molecular mechanisms underlying in goat meat quality and provide a theoretical basis for further goat molecular breeding.

overall_design:
Examining lncRNA and mRNA information related to the differentiation of 2 adipocyte species in goats
lncRNA sequencing of intramuscular and subcutaneous adipocytes from goats before and after differentiation

first: Yaqiu

last: Lin


title: On the genetic constitution of the Marquesas

status: Public on Dec 17 2021

city: Tartu

first: Tuuli

last: Reisberg

address: Riia 23

country: Estonia

institute: University of Tartu

summary: We combined new data with previously published data (PMID: 24297229, 21940856, 33753914, 27302840, 25877615, 18292342, 26811443, 30846778 and 29379068) to examine the genetic history of three groups from Marquesan Islands

overall_design:
32 samples were analysed with the Illumina HumanOmniExpress 24 Genotyping BeadChips and are described herein.
Please note that Tatte_1_*.txt and Tatte_2_*.txt files contains HumanOmniExpress-24 v1.1- and HumanOmniExpress-24 v1.2-generated data, respectively.

first: Rene

last: Herrera

first: Kai

last: Tätte

first: Ene

last: Metspalu

first: Mait


title: Transcriptome profiles of monocytes of Periodontal Ehlers–Danlos Syndrome patients

status: Public on Dec 16 2021

city: nanjing

first: Juan

last: Wu

state: jiangsu

address: Nanjing Stomatological Hospital, Gulou District, ZhongYang Road.

department: Department of Periodontology

institute: Nanjing Stomatological Hospital

summary: Periodontal Ehlers–Danlos syndrome (pEDS) is a rare, distinct hereditary disorder characterized by  early onset periodontal destruction, tissue fragility and joint hypermobility.  pEDS is caused by mutant variants of C1R (and C1S) genes, which encode the C1s (and C1s)  subunits of the first component of the classical complement pathway. Abberant serine protease  activation will result in C4 cleavage and local complement cascade activation, as well as other  possible consequences.  Although multiple studies have investigated the genetic variant analysis of pEDS, the  transcriptome profiles of pEDS remain unknown. To better understand the pathomechanism  underlying the clinical manifestation of pEDS and to identify novel molecular targets that may  expand treatment strategies, our study performed transcriptome profiling by RNA sequencing of  patient-derived monocytes from 2 pEDS patients and 3 normal controls.  Genes related to  periodontal host defense, inflammatory response, skin disease and vascular development were  significantly enriched. Furthermore, we identified genes that may be involved in the pathogenesis of  periodontal destruction and pretibial pigmentation of pEDS. Overall, our study presents the first  pEDS transcriptomics data, revealing distinct molecular features in monocytes of periodontal  Ehlers–Danlos syndrome, and serves as a tool to better understand the disease.

overall_design: RNA-seq of monocytes from 2 pEDS patients and 3 normal controls.

first: Tian

last: Zhao

first: Zhuoyi

last: Liao


title: Next Generation Sequencing Facilitates Quantitative Analysis  of DLD1 parental cells and DLD1 p85β K477A/R478A mutant cells [RNA-seq]

status: Public on Dec 15 2021

city: Shanghai

first: Baoyu

last: He

address: No. 25, Lane 2200, Xietu Road

institute: Renji Hospital

summary: To elucidate whether p85β nuclear translocation plays a role in  cancer tumorigenesis, a RNA-seq analysis was performed to compare the gene expression profiles of  DLD1 parental cells and DLD1 p85β K477A/R478A mutant cells

overall_design: RNA-seq was performed in DLD1 parental cells and DLD1 p85β K477A/R478A mutant cells

first: Yujun

last: Hao

first: Liping

first: Yamu

last: Li

first: Zhenghe

last: Wang


title: PAMP-triggered genetic reprogramming involves widespread alternative transcription initiation and an immediate transcription factor wave

city: Copenhagen

first: Axel

last: Thieffry

state: Hovedstaden

address: Lersø Parkallé 42-44

department: R&D

country: Denmark

institute: BioPhero-FMC

summary: Immune responses triggered by pathogen-associated molecular patterns (PAMPs) are key to pathogen defense, but drivers and stabilizers of the growth-to-defense genetic reprogramming remain incompletely understood in plants. Here, we report a time-course study of the establishment of PAMP-triggered immunity (PTI) using cap analysis of gene expression. We show that around 15% of all transcription start sites (TSSs) rapidly induced during PTI define alternative transcription initiation events. From these, we identify clear examples of regulatory TSS change via alternative inclusion of target peptides or domains in encoded proteins, or of upstream open reading frames in mRNA leader sequences. We also find that 60% of PAMP response genes respond earlier than previously thought. In particular, a cluster of rapidly and transiently PAMP-induced genes is enriched in transcription factors (TFs) whose functions, previously associated with biological processes as diverse as abiotic stress adaptation and stem cell activity, appear to converge on growth restriction. Furthermore, examples of known potentiators of PTI, in one case under direct mitogen-activated protein kinase control, support the notion that the rapidly induced TFs could constitute direct links to PTI signaling pathways and drive gene expression changes underlying establishment of the immune state.

overall_design: RNA-seq sequencing of 14-day old whole Arabidopsis thaliana Col-0 wild type seedlings that underwent flg22 peptide treatment at 0 minutes (control), 10, 30, and 60 minutes.

first: Diego

last: López-Márquez

first: Jette

last: Bornholdt

first: Mojgan

last: Malekroudi

first: Simon

last: Bressedorff

first: Andrea

last: Barghetti

first: Albin

last: Sandelin

first: Peter

last: Brodersen


title: Genome-wide maps of chromatin state of H3K27me3 in DLD1 parental cells and DLD1 p85β K477A/R478A mutant cells [ChIP-seq]

status: Public on Dec 11 2021

summary: We performed ChIP coupled with high-throughput sequencing (ChIP-seq) for H3K27me3 in DLD1 parental cells and DLD1 p85β K477A/R478A mutant cells

overall_design: Examination of H3K27me3 genomic bingding efficiency and histone modifications pattern change in DLD1 parental cells and DLD1 p85β K477A/R478A mutant cells


title: Lipid Metabolism (LiMe) genes and the genesis of estrogen receptor negative breast cancer [RNA-seq]

status: Public on Dec 12 2021

city: Chicago

first: Susan

middle: Elizabeth

last: Clare

state: IL

address: 303 E Superior, LURIE  4-105

department: Department of Surgery

institute: FEINBERG SCHOOL OF MEDICINE, Northwestern University

summary: MCF-12A breast epithelial cells were exposed to fatty acids to determine if lipids engender changes in gene expression associated with malignant transformation.

overall_design: MCF-12A breast epithelial cells were exposed to vehicle (PBS) or octanoic acid (OA) for 24 hours.

first: Mariana

last: Bustamante Eduardo

middle: E


title: Lipid Metabolism (LiMe) genes and the genesis of estrogen receptor negative breast cancer [ATAC-seq]

summary: MCF-10A breast epithelial cells were exposed to fatty acids to determine if lipids engender changes in gene expression associated with malignant transformation.

overall_design: MCF-10A breast epithelial cells were exposed to vehicle (BSA) or Linoleic acid (LA) for 24 hours.


overall_design: CAGE-seq sequencing of 12 days-old Arabidopsis thaliana whole seedlings (Col-0) for 3 different genotypes, a rrp4-2 mutant (hypomorphic allele), a hen2-4 mutant (T-DNA line), and a wild type. Additional samples of the same genotypes underwent a flg22 induction timecourse of 10 and 30 minutes.

last: Bressendorff


title: Lipid Metabolism (LiMe) genes and the genesis of estrogen receptor negative breast cancer

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

overall_design: Refer to individual Series


title: UPR induction in samples derived from OVCAR5 cancer cells treated with spirocyclic dimer SpiD7

status: Public on Dec 10 2021

city: Omaha

first: Amarnath

last: Natarajan

state: NE

address: 986805 Nebraska Medical Center

institute: University of Nebraska Medical Center

summary: The objective of this study was to evaluate the transcriptional changes in OVCAR5 cells upon treatment with a spirocyclic α-methylene-γ-butyrolactone dimer SpiD7. To assess if SpiD7 activates Unfolded Protein Response, OVCAR5 cells were treated with SpiD7 for different time points. A time dependent increase in the expression of genes in the hallmark UPR gene set was observed demonstrating induction of UPR.

overall_design: 6 total samples were analyzed- 2 negative controls, 2 from 2h SpiD7 treatment, 1 from 6h SpiD7 treatment, 1 from 12h SpiD7 treatment.

first: Smit

last: Kour

first: David

last: Klinkebiel


title: Genome-wide DNA-methylation analysis of fat-1 transgenic bovine fetal fibroblasts and wild-type

status: Public on Dec 09 2021

city: Hohhot

first: xueqiao

last: wang

address: No.24，zhaojun Street

institute: Inner Mongolia University

type: Methylation profiling by high throughput sequencing

summary:
Purpose:We found that fat-1 transgenic bovine fetal fibroblasts have changes in the expression of energy metabolism-related genes compared with wild-type, so whether this change is due to changes in DNA methylation needs to be determined.
Methods:Total DNA was extracted using QIAamp Fast DNA Tissue Kit (Qiagen, Dusseldorf, Germany) following the manufacturer's procedure. The quantity of DNA was measured by reading A260/280 ratios by spectrophotometer. When A260/280 ratios located range 1.8 to 2.0, DNA was available. The fragmented DNA samples by using sonication were subjected to bisulfite conversion. The Accel-NGS Methyl-Seq DNA Library Kit (Swift, MI, USA) was utilized for attaching adapters to single-stranded DNA fragments. Briefly, the Adaptase step is a highly efficient, proprietary reaction that simultaneously performs end repair, tailing of 3 ends, and ligation of the first truncated adapter complement to 3 ends. The Extension step is used to incorporate truncated adapter 1 by a primer extension reaction. The Ligation step is used to add the second truncated adapter to the bottom strand only. The Indexing PCR step increases yield and incorporates full length adapters. Bead-based SPRI clean-ups are used to remove both oligonucleotides and small fragments, as well as to change enzymatic buffer composition. Finally, we performed the pair-end 2 150bp sequencing on an illumina Hiseq 4000 platform housed in the LC Sciences.
Results:The results showed Genome-wide DNA-methylation analysis also showed differences between the two groups. KEGG analysis revealed that approximately 80% of the differential genes were enriched in metabolic pathways, and significant changes occurred in DNA methylation of genes related to thermogenesis, fatty acid elongation, TCA cycle and oxidative phosphorylation between FT and WT cells。
Conclusions：There are indeed differences between fat-1 transgenic bovine fetal fibroblasts and wild-type in genome-wide DNA methylation detection, and 80% of these differences are related to metabolism.

overall_design: Examine the genome-wide DNA-methylation in 2 different genotypes of bovine fetal fibroblasts.

first: Xueqiao

first: Lei

last: Yang


title: PCB126 exposure induced DNA methylation and gene expression changes in adult zebrafish testis

city: Woods Hole

first: Neelakanteswar

last: Aluru

state: MA

address: 45 Water Street

department: Biology

institute: Woods Hole Oceanographic Institution

summary: The objective of this study is to determine the effects of pre-conceptional exposure to environmental chemicals on DNA methylation and gene expression in testis. We used a dioxin-like PCB (3, 3’, 4, 4’, 5-pentachlorobiphenyl; PCB126) as a model environmental chemical because the mechanism of action is well-characterized, involving activation of aryl hydrocarbon receptor, a ligand-activated transcription factor. Adult zebrafish were exposed to 3 and 10 nM PCB126 for 24 h (water-borne exposure) and testis tissue was sampled at 7 days post-exposure for histology, DNA methylation and gene expression profiling. We used enhanced Reduced Representation Bisulfite Sequencing (RRBS) and RNAseq to quantify DNA methylation and gene expression, respectively. RRBS revealed 37 and 92 differentially methylated regions (DMRs) in response to 3 and 10nM PCB126 exposures, respectively. We observed 19 DMRs to be common between the two PCB126 treatment groups. Among them 14 and 5 are hypomethylated and hypermethylated, respectively. Majority of these DMRs are hypomethylated and gene ontology analysis revealed that these regions are regulate genes associated with RNA processing, nucleoside metabolic process, iron-sulfur cluster assembly and gluconeogenesis. Dysregulation of all these pathways have been associated with spermatogenic defects such as infertility. RNAseq results revealed differential expression of genes related to xenobiotic metabolism, oxidative stress and immune function. There was very little correlation between differentially methylated regions and differentially expressed genes suggesting complex and multiple layers of regulation. Overall, the results from this study provide new understanding about the mechanisms of action of dioxin-like PCBs in affecting testicular function and potential multigenerational phenotypes.

overall_design: 5-6 biological replicates per treatment condition. Three treatment conditions (DMSO control,  3nM PCB126 and 10 nM PCB126)

first: Jan

last: Engelhardt


title: Epigenetic traits inscribed in chromatin accessibility in aged hematopoietic stem cells (CUT&TAG H3K27ac,H3K4me1)

status: Public on Dec 08 2021

city: Minato-ku

first: Atsushi

last: Iwama

state: Tokyo

address: 4-6-1, Shirokanedai

department: Center for Stem Cell Biology and Regenerative Medicine

institute: The Institute of Medical Science, The University of Tokyo

summary: Hematopoietic stem cells (HSCs) exhibit considerable cell-intrinsic changes with age. Here, we performed an integrated analysis of transcriptome and chromatin accessibility of aged HSCs and downstream progenitors. Alterations in chromatin accessibility preferentially took place in HSCs with aging, which gradually resolved with differentiation. Differentially open accessible regions (open DARs) in aged HSCs showed enrichment of binding motifs of the STAT, ATF, and CNC family transcription factors that are activated in response to external stresses, and most of them comprised active, primed , and inactive enhancers. Genes linked to open DARs showed significantly higher levels of basal expression and their expression reached significantly higher peaks after cytokine stimulation in aged HSCs than in young HSCs, suggesting that open DARs contribute to augmented transcriptional responses under stress conditions. These results indicate that the ongoing and/or history of exposure to external stresses is epigenetically inscribed in HSCs to augment their responses to external stimuli.

overall_design: H3K27ac and H3K4me1 profiling using CUT&TAG method

first: Naoki

last: Itokawa

first: Motohiko

last: Oshima

first: Wakako

last: Kuribayashi

first: Naoya

last: Takayama

first: Shuhei

last: Koide

first: Yaeko

last: Nakajima-Takagi

first: Aoyama

last: Kazumasa

first: Satoshi

last: Yamazaki

first: Koji

last: Eto


title: Epigenetic traits inscribed in chromatin accessibility in aged hematopoietic stem cells (RNA-seq of MPPs after cytokine stimulation)

overall_design: RNA-seq of MPPs before and after cytokine stimulation


title: Pcgf6 suppresses Myc-induced lymphomagenesis [RNA-seq]

status: Public on Dec 05 2021

city: Milan

first: Marco

last: Filipuzzi

address: Via Giuseppe Ripamonti, 435

country: Italy

institute: IEO

summary: Max is an obligate dimerization partner for the Myc transcription factors and for several repressors, such as Mnt, Mxd1-4 and Mga, collectively thought to antagonize Myc function in transcription and oncogenesis. Mga, in particular, is part of the variant Polycomb group repressive complex PRC1.6. Here, we show that ablation of the distinct PRC1.6 subunit Pcgf6 – but not Mga – accelerates Myc-induced lymphomagenesis in Eµ-myc transgenic mice. Unexpectedly, however, Pcgf6 loss shows no significant impact on transcriptional profiles, in neither pre-tumoral B-cells, nor lymphomas. Altogether, these data unravel an unforeseen, Mga- and PRC1.6-independent tumor suppressor activity of Pcgf6.

overall_design: Total RNA profiling of gene expression upon knock-out of Pcgf6 in pretumoral B-cells or bulk population of full blown Eμ-myc lymphomas

first: Nina

last: Tanaskovic


title: Pcgf6 suppresses Myc-induced lymphomagenesis [ChIP-seq]

overall_design: Mapping Pcgf6 and active/repressive histone marks (H3K4me3, H3K4me1, H3K27ac, H3K27me3, H2AK199Ub) genomic distribution in in vitro stabilized lymphomas wild type, Pcgf6-/- or Mga-/-


title: Epigenetic traits inscribed in chromatin accessibility in aged hematopoietic stem cells (single cell ATAC-seq)

overall_design: single-cell-ATAC of young HSCs and aged HSCs


title: Nuclear oligo hashing improves differential analysis of single-cell RNA-seq

status: Public on Dec 01 2021

city: Seattle

first: Hyeon-Jin

last: Kim

state: WA

address: 3720 15th Ave NE

department: Genome Sciences

institute: University of Washington

summary: Single-cell RNA sequencing (scRNA-seq) offers a high-resolution molecular view into complex tissues, but suffers from high levels of technical noise which frustrates efforts to compare the gene expression programs of different cell types. “Spike-in” RNA standards help control for technical variation in scRNA-seq, but using them with recently developed, ultra-scalable scRNA-seq methods based on combinatorial indexing is not feasible. Here, we describe a simple and cost-effective method for normalizing transcript counts and subtracting technical variability that improves differential expression analysis in scRNA-seq. The method affixes a ladder of synthetic single-stranded DNA oligos to each cell that appears in its RNA-seq library. With improved normalization we explore chemical perturbations with broad or highly specific effects on gene regulation, including RNA pol II elongation, histone deacetylation, and activation of the glucocorticoid receptor. Our methods reveal that inhibiting histone deacetylation prevents cells from executing their canonical program of changes following glucocorticoid stimulation.

overall_design: Single-cell RNA-seq libraries of untreated and drug treated HEK293T and A549 cells were generated using single-cell combinatorial indexing RNA sequencing (sci-RNA-seq) and the nuclear oligo hashing method (sci-plex). Along with hash labels unique to each experimental conditions, hash ladders were spiked into each sci-RNA-seq libraries for normalization. Hash ladders were designed by mixing various hash species at different concentration.

first: Greg

last: Booth

first: Lauren

last: Saunders

first: Sanjay

last: Srivatsan

first: José

last: McFaline-Figueroa

first: Cole

last: Trapnell


title: Pcgf6 suppresses Myc-induced lymphomagenesis


title: Nanopore sequencing and data analysis for base-resolution genome-wide 5-methylcytosine profiling

status: Public on Dec 03 2021

city: Sydney

first: Allegra

last: Angeloni

state: NSW

address: 384 Victoria St Darlinghurst

department: Genomics and Epigenetics Division

country: Australia

institute: Garvan Institute of Medical Research

summary: Whole-genome bisulfite sequencing (WGBS) is currently the gold standard for DNA methylation (5-methylcytosine, 5mC) profiling, however the destructive nature of sodium bisulfite results in DNA fragmentation and subsequent biases in sequencing data. Such issues have led to the development of bisulfite-free methods for 5mC detection. Nanopore sequencing is a long read non-destructive approach that directly analyzes DNA and RNA fragments in real time. Recently, computational tools have been developed that enable base-resolution detection of 5mC from Oxford Nanopore sequencing data. In this chapter we provide a detailed protocol for preparation, sequencing, read assembly and analysis of genome-wide 5mC using Nanopore sequencing technologies.

overall_design: Nanopore sequencing (PromethION FLO-PRO002): 24hpf (n=20 embryos); Whole-genome bisulfite sequencing (WGBS): 24hpf (n=20 embryos)

first: James

last: Ferguson

first: Ozren

last: Bogdanovic


title: RNA_Seq of AGOI_IP long (16:8), short (8:16) day heads

status: Public on Dec 04 2021

city: Liverpool

first: Mirko

last: Pegoraro

state: Liverpool

address: Byrom Street

department: School of Natural Science and Psychology

institute: Liverpool John Moores University

summary: Input and IP (AGO1_ab) RNA_seq libraries were prepared from long (2 libraries) and short (1 library) day heads

overall_design: The heads homogenate was fractioned in input and AGO1 immunoprecipitate. Input and IP was used to generate RNA_seq libraries to compare between long and short day AGO1 related RNAs

first: Eran

last: Tauber


title: Comparison of the transcriptome analysis of Tom[Low] and Tom[High] AT2 subpopulations in mice

city: Giessen

first: Jochen

last: Wilhelm

state: Hessen

address: Aulweg 132

department: Institute for Lung Health

institute: Justus-Liebig University Giessen

summary: Transgenic mice in two control (SftpCreERT2/+; Tomatoflox/flox) and Experimental (SftpCreERT2/+; Fgfr2bflox/flox; Tomatoflox/flox) groups were treated with tamoxifen (1mg/ml) in drinking water. The lungs were harvested at different time points (d4,d7 and d14) following tamoxifen treatment. RNA was isolated from AT2 cells sorted by FACS. FACS analysis showed two different Alveolar epithelial type 2 cells population with low and high RFP levels. RFP low and high populations showed different fgfr2b signaling gene expression in experimental versus control groups. The aim of the gene array experiment is to compare  RFP low and high populations transcriptome. Moreover, we aim to analyze FGf10/fgfr2b, AT1 and AT2 and Wnt signiture and obtain KEGG- Pathways targeted.

overall_design: 8 groups, each with 1 biological replicates

first: Negah

last: Ahmadvand

first: Saverio

last: Bellusci


title: VE-cadherin is essential for trophoblast migration and endovascular invasion

status: Public on Nov 30 2021

city: Philadelphia

first: Apoorva

last: Babu

state: PA

address: SCTR, 3400 Civic Center Blvd

department: Cardiovascular Institute

institute: University of Pennsylvania

summary: Vascular endothelial (VE-)cadherin is a homotypic adhesion protein that is expressed selectively by ECs in which it enables formation of tight vessels and regulation of vascular permeability. Since VE-cadherin is also strongly expressed in placental trophoblasts, it is a prime candidate for a molecular mechanism of vascular mimicry by those cells. Here, we show that the VE-cadherin is required for trophoblast migration and endovascular invasion into the maternal decidua. VE-cadherin deficiency results in loss of spiral artery remodeling due to a lack of invasive trophoblasts, leading to decreased flow of maternal blood into the placenta, fetal growth retardation and death. Loss of trophoblast invasion prevents decidualization, extracellular matrix remodeling, and immune cell clearance. These studies identify VE-cadherin as essential for trophoblast migration and coordination of decidual changes during endovascular invasion. They further suggest endothelial proteins such as VE-cadherin that are expressed by trophoblasts may play functionally distinct roles that do not simply mimic those in ECs.

overall_design: Examination of E12.5 deciduas from control and trophoblast-specific VE-cadherin knockout placentas

first: Sung

last: Derek C

first: Kahn

last: Mark L

first: Babu

last: Apoorva


title: A 3’-end capture sequencing method for high-throughput targeted gene expression profiling

city: Gent

first: Eric

middle: James

last: de Bony de Lavergne

state: <None>

address: 10 corneel heymanslaan, UZ Campus, building Block B, Entry 36

department: Biomolecular Medecine

country: Belgium

institute: University of Ghent

summary: We describe a 3'-end capture sequencing method allowing a maximization of read allocation towards genes of interest using biotynilated probes.

overall_design: Comparison of gene coverage in in reference datasets and capture dataset

last: de Bony

first: Fien

last: Gysens

first: Nurten

last: Yigit

first: Jasper

last: Anckaert

first: Celine

last: Everaert

first: Eveline

last: Vanden Eynde

first: Kimberly

last: Verniers

first: Willem

last: Van Snippenberg

first: Wim

last: Trypsteen

first: Pieter

last: Mestdagh


title: Transcriptome sequencing of fat-1 transgenic bovine fetal fibroblasts and wild-type

first: xueqiao

last: wang

summary:
Purpose:The fatty acid dehydrogenase fat-1 gene derived from Caenorhabditis elegans encodes n-3 polyunsaturated fatty acid dehydrogenase and catalyzes the 18-20 carbon n-6 polyunsaturated fatty acids to generate corresponding n-3 PUFA balance ratio between n-6 PUFA and n- 3 PUFA in fat-1 transgenic cells. Changes in fatty acid composition will affect the entire metabolic system. We used transcriptome sequencing to analyze the expression of which genes are altered by fat-1 transgenic cells, and which metabolic pathways these genes mainly aggregate in.
Methods:Total RNA of bovine fetal fibroblast cells was extracted witth Trizol reagent (Invitrogen, CA, USA). Poly (A) RNA was purified from total RNA (5μg) by poly-T oligo-attached magnetic beads and broken into small fragments. The spliced RNA fragments were reverse-transcribed to construct the final cDNA library and then the paired-end sequencing on IlluminaHiseq4000 (LC Sceiences, USA). The read values of the samples were aligned with the UCSC (http://genome.ucsc.edu/) reference genome using HISAT package, which initially removed a portion of the reads based on the quality information accompanying each read value, and then mapped the reads to the reference genome. All the transcripts in the samples were combined and a comprehensive transcriptome was reconstructed using Perl Scripts, and StringTie and edgeR to estimate expression levels of all transcripts. The differentially expressed mRNAs and genes with log2 (fold change) >1 or log2 (fold change) < -1 and with statistical significance (P value < 0.05) were screened by R package.
Results:Total of 27,366 differential genes were obtained, among which 1157 genes significantly up-regulated and 1,200 genes significantly down-regulated . KEGG pathway enrichment showed that ECM-receptor interaction, axon guidance, and MAPK signaling pathway were significantly upregulated . GO enrichment revealed the differential genes were associated with cell migration, positive regulation of cell migration and substrate adhesion-dependent cell spreading. Genes related to oxidative phosphorylation, thermogenesis, and TCA were down-regulated, and these genes were involved in oxidation-reduction process, single-stranded DNA binding. Interestingly, we found many items related to ATP synthesis, oxidation-reduction process, proton-transporting ATP synthase complex, coupling factor F(o), ATP synthesis coupled proton transport pathways were significantly changed between fat-1 transgenic cells and wild-type cells .
Conclusions:These results suggest that the transgenic fat-1genes not only change the fatty acid composition but also regulate and influence energy metabolism, possibly the ATP synthesis pathway.

overall_design: Transcriptome sequencing of two cell types and three samples of each type.

first: Xueqiao

last: Wang

first: Lei

last: Yang


title: Transcriptomic consequence of Fyn knock-out in glioblastoma

city: Daejeon

first: Haemin

last: Chon

address: Daehak-ro 291

department: Graduate school of medical science and engineering

institute: KAIST

summary: To investigate the role of Fyn in glioblastoma, transcriptomic comparison between WT and Fyn-KO glioblastoma was done by bulk RNA sequencing.

overall_design: 3 WT and 4 FYN-KO GBM mice cancer cells were sorted independently and RNA libraries were made independently.

first: Injune

last: Kim


title: MeRIP-Seq map HNRNPA2B1 maintains MM tumorigenicity by m6A dependent stabilizing of  mRNA

city: Nan jing

first: Feng

middle: Jie

last: Jiang

state: Jiangsu

address: Xianlin Avenue 138

department: School of Medicine&Holistic Integrative Medicine

institute: Nanjing University of Chinese Medicine

summary: To investigated the mechanism of HNRNPA2B1 in MM tumorigenesis, performed m6A IP seq analysis (MeRIP-Seq) to identify the expression changes in stable HNRNPA2B1-knockdown MM cells.60 genes m6A with over 2-fold expression change in shHNRNPA2B compared with control in both ARP1 and H929 cells.44 differentially expressed genes (P<0.05) in both m6A and transcription in shHNRNPA2B compared with control in ARP1 cell.

overall_design: Examination of HNRNPA2B1-KD  in 2 MM cells.

first: Fengjie

first: Chunyang

last: Gu

first: Ye


title: Explored the underlying mechanism by which ILF3 exerted carcinogenesis and its potential targets in MM

summary: An RIP experiment was performed in ARP1 cell following the instructions of the article. ~5-20 × 10^6 cells were harvested and lysed. Protein A/G MagBeads pre-coated with 5μg of the antibody of interest  (HNRNPA2B1/ILF3, Proteintech) and incubated with cell lysate supernatant overnight at 4°C.The beads containing immunoprecipitated RNA-protein complex were treated with 150μL of Proteinase K buffer to digest the proteins. Specific binding RNAs were isolated by using TRIzol.

overall_design: Examination  in ARP1 cell.


title: Acetylation-dependent Multimerization of SAGA Regulates Gene Transcription

status: Public on Nov 29 2021

city: Wuhan

first: Junhua

last: Huang

state: Hubei

address: NO. 368, Youyi Ave., Wuchang District

department: School of Life Sciences

institute: Hubei University

summary: In Saccharomyces cerevisiae, the SAGA complex regulates its own activity by undergoing multimerization. This multimerization is triggered by SAGA autoacetylation at three sites on its Ada3 subunit, allowing recognition of this acetylation by the bromodomain of the Gcn5/Spt7 SAGA subunit. Once multimerized, SAGA is capable of cooperatively acetylating chromatin, and an inability to autoacetylate Ada3 leads to transcriptional and phenotypic defects in a wide range of stress-activated genes. The SAGA multimerization increased significantly in media with Sucorse as the only carbon resource than that with Glucose. In this study, the  high-throughput sequence of wild type (WT) strain, Ada3 acetylation mutant (Ada3-3KR), Gcn5 bromodomain mutant (Gcn5m) and Spt7 bromodomain mutant (Spt7m) indicate a new function for Ada3 acetylation, show which genes transcription can be regulated by SAGA multimers.

overall_design: The wild type (WT) strain, Ada3 acetylation mutant (Ada3-3KR), Gcn5 bromodomain mutant (Gcn5m) and Spt7 bromodomain mutant (Spt7m) were cultured in media with Sucrose or Glucose as the carbon resource for 30 min, respectively. The total RNA were extracted and subjected to high-through sequence.

first: Wenjing

last: Dai

first: Xilan

last: Yu

first: Shanshan

last: Li


title: Absence of microglia promotes diverse pathologies andearly lethality in Alzheimer's disease mice

status: Public on Nov 24 2021

city: Irvine

first: Mathew

last: Blurton-Jones

state: CA

address: 3400 Bio Sci 3

department: Neurobiology and Behavior

institute: University of California, Irvine

summary: Microglia are strongly implicated in the development and progression of Alzheimer’s disease (AD), yet the precise mechanisms underlying their effects on neuropathology remain unclear.  To further define the influence of microglia on AD neuropathology, we generated a novel mouse model of AD that genetically lack microglia. The resulting microglial-deficient mice exhibit a profound shift from parenchymal amyloid plaques to cerebral amyloid angiopathy (CAA) that is further accompanied by transcriptional changes within multiple cell types, a dramatic induction of brain calcification and cerebral hemorrhages, and premature lethality. Importantly, adult microglia replacement fully rescues these comorbidities, supporting novel roles for microglia in maintaining vascular function and preventing brain calcification. We further examined the clinical implications of these findings in human tissue and hiPSC-derived microglia, finding evidence that calcification is inversely related to plaque pathology and that microglial interactions with calcifications are altered by genetic AD risk factors.

overall_design: An unbiased survey of the cellular landscape in genetic microglia loss in Alzheimer's Disease mice (5XFAD)

first: Samuel

last: Morabito

first: Vivek

last: Swarup


title: Epigenetic traits inscribed in chromatin accessibility in aged hematopoietic stem cells(ATAC-seq in cytokine and LPS:polyIpolyC experiments))

first: Atsushi

last: Iwama

summary: Aging of the hematopoietic system is associated with cytopenia and increased risk of hematological malignancies. To investigate cell-intrinsic factors underlying aging of hematopoiesis, we profiled transcriptome, chromatin accessibility, histone modifications in young and aged Hematopoietic stem cells (HSCs) and progenitors. Various differentially expressed genes were detected in each fraction. Changes of transcriptome were more drastic in progenitors than in HSCs. In contrast, aberrant chromatin accessible regions were accumulated particularly in aged HSCs without affecting steady-state transcriptions of nearest genes. These regions were enriched for motif of STAT3, STAT5, c-Jun-CRE, NF-E2, NRF2. We also found H3K27me3 marked genes and bivalent genes were substantially decreased in aged HSCs, some of which became active state and some of which became more repressive state with increased DNA methylation. Our data indicates that integrated analysis of epigenome and transcriptome provides more profound insights into aging of hematopoietic systems.

overall_design: ATAC-seq before and after cytokine stimulation(3h) and PBS treatments and LPS:polyIpolyC treatments.

first: Naoki

last: Itokawa

first: Motohiko

last: Oshima

first: Wakako

last: Kuribayashi

first: Naoya

last: Takayama

first: Shuhei

last: Koide

first: Yaeko

last: Nakajima-Takagi

first: Aoyama

last: Kazumasa

first: Satoshi

last: Yamazaki

first: Koji

last: Eto