title: The effect of curcumin/ZNPs hydrogel on the transcription of gingiva in rats with periodontitis

status: Public on Jan 01 2022

city: CHENGDU

first: CHENGCHENG

last: LIU

state: SICHUAN

address: No. 14, Section 3, Renminnan Road

institute: Sichuan University

summary:
Purpose: The goals of this study are to compare NGS-derived gingiva transcriptome profiling (RNA-seq)  of rats with or without experimental periodontitis and to explore the effect of  curcumin/ZNPs hydrogel on the transcription of gingiva in rats with periodontitis.
Methods:  Six-week-old male Sprague-Dawley rats weighing 250–300 g (Dashuo company, China) were randomly divided into five groups (n = 5 per group): i) healthy control (Sham); ii) experimental periodontitis (EP); iii) experimental periodontitis treated by curcumin hydrogel (EP+Cur); iv) experimental periodontitis treated by ZNPs hydrogel (EP+ZNPs); v) experimental periodontitis treated by curcumin/ZNPs hydrogel (EP+Cur/ZNPs). Animals were anesthetized with isoflurane (5% induction, 2% maintenance, sealed until euthanized) and intramuscularly administered 0.1 mL penicillin (40,000 U/mL) for 7 days. EP was established by ligature with 4–0 silk thread around the bilateral maxillary first molars. Three days after ligature, P. gingivalis ATCC 33277 (107 CFU/mL) was smeared onto silk twice. Rats in the EP+Cur group were treated by curcumin hydrogel (Dalian Meilun Biotech Co., Ltd), EP+ZNPs group were treated by ZNPs hydrogel (Shanghai aladdin Biochemical Technology Co., Ltd), and EP+Cur/ZNPs group were treated by curcumin/ZNPs hydrogel.   Total RNA was extracted with TRIzol® reagent (Thermo Fisher Scientific, Inc.). The TruSeq Stranded total RNA with RiboZero Plus kit (IIlumina, San Diego, CA) was used to obtain a sequencing library from 1μg of total RNA. Eukaryotic mRNA sequencing was performed on Illumina Novaseq 6000 by Shanghai Majorbio Bio-pharm Technology Co., Ltd. Raw gene counts with a minimum of two counts per million in at least one sample were used for downstream analyses. Differentially expressed genes were determined by the DESeq2 Bioconductor/R package. qRT–PCR validation was performed using TaqMan and SYBR Green assays.
Results: Transcriptome analysis of 25 samples was completed in this project, and a total of 184.45 Gb Clean Data was obtained. The Clean Data of each sample reached 5.92 Gb and above, and the Q30 base percentage was above 92.75%. The Clean Reads of each sample were compared with the designated reference genome, and the comparison rate ranged from 93.38% to 95.1%. A total of 26188 expressed genes were detected in this analysis, including 22736 known genes and 3452 new genes; 57,961 expressed transcripts, including 29332 known transcripts and 28629 new transcripts.
Conclusions: Our study represents the first detailed analysis of gingival transcriptomes of rats treated by Cur/ZnO gel, with biologic replicates, generated by RNA-seq technology.

overall_design: Gingival mRNA profiles of six-week old  Sprague-Dawley rats in Sham, EP, EP+Cur, EP+ZnO and EP+Cur/ZnO groups.

first: Chengcheng

last: Liu


title: MAP2K2 Role in Acute Lung Injury

status: Public on Jan 14 2022

city: Seattle,

first: Stephanie

last: Osmond

state: WA

address: 1201 9th Ave

country: USA

institute: Benaroya Research Institute

type: Expression profiling by high throughput sequencing

summary: To determine how MEK2 may be driving altered inflammatory and repair processes in ALI, we analyzed lung tissue from wildtype and MEK2-knockout mice for gene expression using RNAseq during naïve state (day 0), and at days 2 and 4 post-infection.

overall_design: Lung tissue from mice was analyzed before or following P. aeruginosa infection. Samples were collected at 3 time-points across 2 genotypes (n=5/group for n=30 samples total)

first: Anne

last: Manicone

first: Sina

last: Gharib

first: Matthew

last: Long

first: Ke-Qin

last: Gong


title: scRNA of preadipocytes and mature adipocytes from mice exposed to a mouse model of early life stress

status: Public on Dec 31 2021

city: Lexinton

first: Analia

middle: S

last: Loria

state: KY

address: 900 S Limestone

department: Pharmacology

institute: U of Kentucky

summary:
Background: Adipose tissue homeostasis is a complex process influenced by many mechanisms that become dysregulated with obesity. We have previously shown that Maternal Separation and Early Weaning (MSEW), a mouse model of early life stress, exacerbates high-fat diet (HF)-induced fat deposition in female mice, but not male mice. In addition, we have shown that this exacerbated adiposity is due to an increase in visceral adipose tissue, and fat depot known to be linked with cardio-metabolic dysfunction.
Purpose: The aim of this study was to determine differential gene expression patterns in gonadal white adipose tissue (gWAT), a visceral fat, in female mice exposed to MSEW compared to controls. Adipose tissue is composed of many different stromal cell types including preadipocytes, mature adipocytes, and immune cells. Preadipocytes are the precursor stem cells that differentiate into mature adipocytes that can uptake and store lipids and have a more predominte endocrine function.
Methods: Control and MSEW mice were weaned onto either a low-fat diet (LF) or a high-fat diet (HF) for 20 weeks. Fresh gonadal white adipose tissue was harvested after euthanasia and subjected to collagenase digestion. Tissue was centrifuged and filtered to separate the mature fraction from the stromal vascular fraction. Magnetic Activated Cell Sorting (MACs) was used to further isolate adipocytes from other cell types. Pre-and mature adipocytes were collected and saved in Purezol at -80oC for later RNA extraction using the Promega ReliaPrep RNA miniprep systems. Total RNA was sent to Novogene for scRNAseq analysis.

overall_design:
Groups (6 total): C_HF_P; MS_HF_P; C_HF_A; MS_HF_A; C_LF_P; MS_LF_P.
C=control; MS=maternal separation and early weaning; HF=high-fat diet; LF= low-fat diet; P=preadipocyte; A=mature adipocyte.

first: Jacqueline

middle: R

last: Leachman


title: Single cell RNA sequencing on PyMT mammary gland tumor cells

status: Public on Jan 13 2022

city: Bronx

first: Rachel

last: Hazan

state: NY

address: 1300 Morris Park Avenue

department: Pathology

institute: Albert Einstein College of Medicine

summary: We labeled PyMT control cells versus PyMT-GPx2 KD with GFP in vitro and then injected into mammary fat pad of mice for incubating 45 days. We then generated single cell suspension by FACS sorting from PyMT-control, GPx2 KD. 10X Genomics was used to make cDNA library. We then sequenced the samples with Illumina high throughput sequencing.

overall_design: Investigating how GPx2 loss affects mammary tumor heterogeneity and metastasis.

first: Zuen

last: Ren

middle: B

first: Malindrie

last: Dharmaratn

first: Ameya

last: Kulkarni

first: Jessica

middle: C

last: Mar

first: Atefeh

last: Taherian Fard


title: Differential roles of TSLP and IL-33 in regulation of Treg cells in progression of colorectal cancer

status: Public on Dec 22 2021

summary: Recruitment of regulatory T cells (Tregs) to tumors is a hallmark of cancer progression.  However, the role of epithelial cell-derived cytokines in regulation of Treg cells in colorectal cancers is not fully understood.  We found a subset of Tregs co-expressing the receptors for thymic stromal lymphopoietin (TSLP) and IL-33 (TSLPR+ST2+ Tregs) was increased in colorectal tumors in humans and mice.  This Treg subset expressed high levels of CTLA-4 and PD-1, and TSLPR signaling regulated the expression of CTLA-4 and number of TSLPR+ST2+ Tregs. Treg-specfic deletion of TSLPR resulted in a reduction in tumor number and size, with concomitant increase of Th1 cells in tumors.  Similarly, blockade of TSLP effectively inhibited progression of colorectal tumors.  On the other hand, TSLPR-ST2+ Tregs highly express Tgfb1 and Pdcd,1 which have been shown to suppress CD8+ T cell immune responses.  Collectively, TSLP and IL-33 differentially regulate subsets of Tregs in the progression of colorectal tumor.  These data suggest that TSLPR+ST2+ Treg cells are potentially a biomarker, and a therapeutic target for CRC.

overall_design: 33 samples total. 4 mice with tumors, 5 without. 4 T-cell populations defined by ST2 and TSLP positivity for 8 mice, 1 naive T-cell population for 1 mouse

first: Kazushige

last: Obata-Ninomiya

first: Steven

last: De Jesus Carrion

last: Ziegler

first: Alex

last: Hu


title: Expression profiling of WT and aSMA-TK wounds

status: Public on Jan 10 2022

city: Houston

first: Kalluri

last: Lab

state: Texas

address: 1901 East Rd

institute: UT MD Anderson Cancer Center

summary: RNA was isolated from WT and aSMA-TK wounds at day 6 and day 17 post-wounding

overall_design:
Profiled 3 day 6 WT and aSMA-TK wounds (technical duplicates of each wound), 2 day 17 WT and aSMA-TK wounds (technical triplicates of each wound)

316a,b: Day 6 WT
319a,b: Day 6 WT
320a,b: Day 6 WT
p34a,b: Day 6 aSMA-TK
p35a,b: Day 6 aSMA-TK
p36a,b: Day 6 aSMA-TK
TK7-1,2,3: Day 17 aSMA-TK
TK37-1,2,3: Day 17 aSMA-TK
22W-1,2,3: Day 17 WT
38W-1,2,3: Day 17 WT

first: Raghu

last: Kalluri


title: Expression data from aortic dissection patients and the healthy controls

status: Public on Dec 12 2021

city: Beijing

first: Xiaohan

last: Fan

address: Beilishi Road 167

country: China

institute: Fuwai Hospital

summary:
The mechanisms of acute aortic dissection are not well understood. Transcriptomic strategy has been proven to be an effective way to find the potential mechanisms and also the reliable biomarkers for a specific disease.
The whole-genome expression profiling was assayed in a panel of aortic tissues from 4 male acute aortic dissection patients and 4 male healthy controls.

overall_design: Whole-genome expression profiling of the aortic tissues samples of aortic dissection patients and the healthy controls was assayed using Affymetrix HG-U133 Plus 2.0 GeneChip. We sought to find the differentially expressed genes between aortic dissection patients and the healthy control, which were helpful to potential aortic dissection biomarkers in clinical practice.

first: Xiaojian

last: Wang


title: Transcriptomic profile of non-alcoholic fatty liver disease in rat induced by high-fat diet

status: Public on Dec 02 2021

city: Nanning

first: xing

last: lin

address: Shuangyong Road

institute: Guangxi medical university

summary: This study aimed to investigate the effect and underlying mechanism of Smilax china L. Saponins (SCS) on lipid metabolic disturbance in rats with non-alcoholic fatty liver disease (NAFLD). Rats were administrated with a high-fat diet (HFD) for 8 weeks to induce NAFLD, followed by SCS treatment for further 8 weeks.

overall_design: Rats were randomly devided into three groups, including normal group, model group (high-fat diets for 8 weeks) and SCS group

first: Cuiyu

last: Li

first: bin

last: Fang

first: yuanyuan

last: Wei

first: Rou

last: Mo

first: Xing

last: Lin

first: Quanfang

last: Huang


title: Comparison of the root tip transcriptome of 2 pearl millet lines with contrasted primary root growth

status: Public on Oct 10 2021

city: Montpellier

first: Laurent

last: Laplaze

address: 911 avenue Agropolis

department: DIADE

country: France

institute: IRD

summary: We analysed global gene expression in the primary root tip of 2 pearl millet (Pennisetum glaucum) inbred lines with high (line 249) and low (line 337) primary root growth using RNAseq. The objective was to identify genes potentially associated with changes in root growth.

overall_design: Two pearl millet lines with contrasted root soil aggregation were grown in hydropony for 15 days. 3 biological replicates were produced per line. RNA was extracted from the primary root tip (2 cm apex). RNA-seq was performed by the Montpellier GenomiX Platform (MGX, https://www.mgx.cnrs.fr/). Sequencing was performed on an Illumina HiSeq 2500.

first: Marilyne

last: Debieu

first: Alexandre

last: Grondin


title: Permutational immune analysis reveals architectural similarities between inflammaging, Down syndrome and autoimmunity

status: Public on Sep 11 2021

first: Stephanie

last: Osmond

summary: Permutational analysis of immune landscape reveals advanced immune aging in people with Down syndrome and in people with type 1 diabetes.

overall_design: Perumtative comparison of Typical Control individuals to those with Down Syndrome and/or other auto-immune diseases

first: Katharina

last: Lambert

first: Keagan

middle: G

last: Moo

first: Azlann

last: Arnett

first: Gautam

last: Goel

first: Kaitlin

middle: J

last: Flynn

first: Cate

last: Speake

first: Alice

middle: E

last: Wiedeman

first: Carla

last: Greenbaum

first: S

middle: A

last: Long

first: Rebecca

last: Partridge

first: Jane

middle: H

last: Buckner

first: Bernard

last: Khor


title: Human skeletal muscle transcriptome in response to high-intensity interval training

status: Public on Sep 01 2021

city: Stockholm

first: Eric

last: Rullman

address: C1:82 Karolinska University Hospital, Huddinge

department: Laboratory Medicine

country: Sweden

institute: Karolinska Institutet

summary: Skeletal muscle tissue is a highly adaptable tissue, responding to the specific demands it is subjected to. High-intensity interval training (HIIT) has been shown to generate similar, or even greater, molecular changes in skeletal muscle as that of constant load longer-lasting endurance-type training at moderate intensities. Despite shorter exposure times, the higher intensity provided by HIIT training leads to greater metabolic perturbations and thereby larger improvements in mitochondrial content and maximal oxygen uptake. During a period of regular exercise training, the performance improvements follow a non-linear pattern with a relatively faster pace initially and a gradual ‘plateauing-off’ after weeks and months. It is believed that this ‘plateau effect’ is due to a blunting of the molecular responses to acute exercise with exercise training. In the present study we utilised an explorative global transcriptomic approach to investigate the phenomenon of transcriptional-level blunting of the acute exercise response in human skeletal muscle over the course of a three-week HIIT intervention. We hypothesize that the blunting of transcription at this time-point is specific to certain pathways, including metabolic regulation and that these genes have communal transcriptional regulation.

overall_design: Eleven healthy men with mean age of 24.8 years and VO2peak of 51.9 ±  1.9 ml O2x kg-1 x min-1 performed nine sessions of HIIT (10 x 4 minutes of cycling at 91 % of HRmax) over three weeks. Before and 3 h after the 1st and 9th exercise bout, skeletal muscle biopsies were obtained, and RNA sequencing was performed.

first: Alen

last: Lovric


title: Genome-wide profiling of histone H1 variants and H3K9me3 in T47D-MTVL cells upon multiple H1 depletion

status: Public on Aug 16 2021

city: Barcelona

first: Albert

last: Jordan

address: Baldiri Reixac 4

department: Molecular Genomics

country: Spain

institute: IBMB-CSIC

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Human somatic cells may contain up to seven members of the histone H1 family contributing to chromatin compaction and regulation of nuclear processes, apparently with certain subtype specificities. In breast cancer cells, the combined depletion of H1.2 and H1.4 has a strong deleterious effect, deregulates many genes, promotes the appearance of accessibility sites genome-wide, and triggers an interferon response via activation of heterochromatic repeats. We have further analyzed the consequences of multiple H1 variants depletion by profiling the occupancy of five somatic histone H1 variants and H3K9me3 post-translational modification in T47D-MTVL cancer cells. Specifically, stable breast cancer-derived cell lines expressing an shRNA against multiple histone H1 isoforms in response to doxycycline (Dox) were grown for six days in the presence or absence of Dox. ChIP-Seq experiments were subsequently performed to analyze the genome-wide localization of histone H1 variants and H3K9me3.

overall_design: Genome-wide analysis of H1.0, H1.2, H1.4, H1.5, and H1X linker histones, and H3K9me3 epigenetic modification in T47D-MTVL cells expressing a Dox-inducible shRNA against multiple H1 variants.

first: A

first: N

last: Serna

first: M

last: Salinas


title: Molecular Profiling of COVID-19 Autopsies Uncovers Novel Disease Mechanisms [Digital Spatial Profiling data]

status: Public on Sep 03 2021

city: New York

first: Robert

last: Sebra

address: One Gustave L. Levy Place

department: Genetics and Genomic Sciences

institute: Icahn School of Medicine at Mount Sinai

summary: Our work illustrates how high-resolution molecular and spatial profiling of COVID-19 patient tissues collected during rapid autopsies can serve as a hypothesisgenerating tool to identify key mediators driving the pathophysiology of COVID-19 for diagnostic and therapeutic target testing. Here we employ bulk RNA sequencing to identify key regulators of COVID-19 and list specific mediators for further study as potential diagnostic and therapeutic targets. We use single-nuclei RNA sequencing to highlight the diversity and heterogeneity of coronavirus receptors within the brain, suggesting that it will be critical to expand the focus from ACE2 to include other receptors, such as BSG and ANPEP, and we perform digital spatial profiling of lung and lymph node tissue to compare two patients with different clinical courses and symptomatology.

overall_design:
Total 120 regions of interest from 10 scans (five per patient).

*** FASTQ raw data files have been requested. ***

first: Carlos

last: Cordon-Cardo


title: Transcriptional profiling of circulatory monocytes in community-acquired pneumonia

status: Public on Aug 05 2021

city: Msida

first: Brendon

last: Scicluna

address: Msida campus

country: Malta

institute: University of Malta

summary: In this study, we sought to broaden our understanding of circulatory monocyte functions captured during the acute (on hospital admission; day0) and recovery (one month follow-up) stages of patients diagnosed with community-acquired pneumonia (CAP).

overall_design: Examination of RNA expression in circulating CD14+ monocytes obtained from CAP patients on hospital admission (CAP; day0), from the same patients after one month recovery (CAP_D28; one month), and age and sex-matched control participants (Healthy_Volunteer; HV).

middle: P

first: Tom

last: van der Poll

first: Xanthe

last: Brands


title: Vaccine driven lung TRM cells provide immunity against Klebsiella via fibroblast IL-17R signaling [scRNA-Seq]

status: Public on Aug 01 2021

city: New Orleans

first: Jay

last: Kolls

state: LA

address: 1430 Tulane Ave

department: Medicine

institute: Tulane University

summary: Subunit vaccine elicits lung tissue resident memmory CD4+ T-cells and confers lung protection against heterologous strain

overall_design:
I. We immunized WT C57BL/6 mice oropharyngealy with 1ug OmpX+10ug LTA1 or 40ug heat-killed Klebsiella pneumoniae (ATCC 43816) twice 3 weeks apart, and 1 more week later we euthanized and removed the lungs for single cell suspensions as well as spleen cells from naïve WT C57BL/6 mice. Then, the CD4+ T-cells were sorted from the cell suspensions by magnetic beads. Recombinant OmpX were generated from K. pneumoniae-43816 and purified by using E. coli expression systems. The adjuvant LTA1 was A1 subunit of the heat-labiled enterotoxin from E.coli and purified from E. coli expression systems.
II. We immunized IL-17F-Thy1.1 reporter mice oropharyngealy with 1ug OmpX+10ug LTA1 twice 3 weeks apart, and 1 more week later we euthanized and removed the lungs for single cell suspensions as well as naive spleen cells. Then, the CD4+ T-cells were sorted from the cell suspensions by magnetic beads. Recombinant OmpX were generated from K. pneumoniae-43816 and purified by using E. coli expression systems. The adjuvant LTA1 was A1 subunit of the heat-labiled enterotoxin from E.coli and purified from E. coli expression systems.

middle: K

first: Naoki

last: Iwanaga


title: An epigenetic and transcriptomic signature of immune tolerance in human monocytes by multi-omic integration

type: Methylation profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Genome-wide profiling of histone H1 variants in T47D-MTVL cells

summary: Human somatic cells may contain up to seven members of the histone H1 family contributing to chromatin compaction and regulation of nuclear processes, apparently with certain subtype specificities. Previous studies in T47D breast cancer cells determined that H1 variants are distributed in a variant-specific manner throughout the genome, although only H1.2 and H1X endogenous variants were mapped. Now, we performed ChIP-seq of five endogenous H1 variants (H1.0, H1.2, H1.4, H1.5, H1X) in T47D cells.

overall_design: Genomic distribution of H1.0, H1.2, H1.4, H1.5, and H1X linker histones  in T4LD-MTVL cells (ChIP-seq)


title: Spatial proteogenomics reveals distinct and evolutionarily-conserved hepatic macrophage niches

status: Public on Jan 11 2022

city: Zwijnaarde

first: Liesbet

last: Martens

address: Technologiepark 927

department: VIB Inflammation Research Center

country: Belgium

institute: VIB-University of Ghent

summary:
This SuperSeries is composed of the SubSeries listed below.
For metadata files please visit https://livercellatlas.org

sample_organism:
Danio rerio
Gallus gallus
Macaca mulatta
Homo sapiens
Sus scrofa
Mesocricetus auratus
Mus musculus


title: Characterization of hormone-producing cell types in the medaka pituitary gland using single-cell RNA-seq

status: Public on Jul 29 2021

city: Oslo

first: Khadeeja

last: siddique

address: Karl Staaffs vei 75, house 7

country: Norway

institute: Norwegian University of Life sciences (NMBU))

summary: The pituitary is the vertebrate endocrine gland responsible for the production and secretion of several essential peptide hormones. These, in turn, control many aspects of an animal’s physiology and development, including growth, reproduction, homeostasis, metabolism and stress responses. In teleost fish, each hormone is presumably produced by a specific cell type. However, key details on the regulation of, and communication between these cell types are still poorly understood. We have therefore generated gene expression profiles for 2592 and 3804 individual cells from the pituitaries of female and male adult medaka (Oryzias latipes), respectively. Based on expression profile clustering, we define 15 and 16 distinct cell types in the female and male pituitary, respectively, of which nine are involved in the exclusive production of a single peptide hormone.  Collectively, our data provide a high-quality reference for studies on pituitary biology and the regulation of hormone production, both in fish and in vertebrates in general.

overall_design: Single cell sequencing (scRNA-seq) of the medaka pituitary.

last: Siddique

first: Eirill

last: Ager-Wick

first: Romain

last: Fontaine

first: Finn-Arne

last: Weltzien

first: Christiaan

last: Henkel


title: Mutation of a schizophrenia risk gene SETD1A alters neuronal network activity in human neurons through cAMP/PKA pathway

status: Public on Jul 23 2021

first: Ibrahim

last: Akkouh

address: Kirkeveien 166

department: Institute of Clinical Medicine

institute: University of Oslo

summary: Using CRISPR/Cas9 to generate an hiPSC line with SETD1A haploinsufficiency and differentiating it into glutamatergic and GABAergic neurons, we found that SETD1A haploinsufficiency resulted in altered neuronal network activity, which was predominantly defined by increased network burst frequency, whereas unchanged global firing activity.  In individual neurons, this network phenotype was reflected functionally by increased synchronized synaptic inputs and structurally by increased somatodendritic complexity in both glutamatergic and GABAergic neurons. The transcriptome profile in SETD1A haploinsufficient neurons demonstrated perturbations in gene sets associated with schizophrenia, synaptic transmission, and glutamatergic synaptic function. In addition, transcriptomic data suggested cAMP/PKA pathway might be disturbed in SETD1A haploinsufficient networks, which was further verified by pharmacological experiments.

overall_design: Functional and transcriptional analysis of 3 wildtype neuronal hiPSC lines and 3 lines with induced SETD1A haploinsufficiency.

first: Shan

last: Wang

first: Srdjan

last: Djurovic

first: Dirk

last: Schubert


title: Primary cilia are required for the persistence of memory and stabilization of perineuronal nets

status: Public on Jun 05 2021

city: Göttingen

first: Andre

last: Fischer

state: NDS

address: Von-Siebold-Str. 3a

department: Epigenetics and Systems Medicine in Neurodegenerative Diseases

country: Germany

institute: DZNE Göttingen

summary: We investigate the gene expression changes occurring during the transition of aversive episodic memories from recent to remote. Early mechanisms of memory formation (synaptic consolidation) have been extensively characterized. However, delayed mechanisms (systems consolidation), which maintain hippocampal activity as memories stabilize in cortical circuits, are not well understood. Transcriptomic analysis reveals that, contrary to the transient expression of early- and delayed-response genes, the expression of cytoskeleton- and extracellular matrix- associated genes remains dynamic even at remote time points. The most profound expression changes clustered around primary cilium-associated and collagen genes.

overall_design: Total RNA extract from the dorsal hippocampus of mice subjected to contextual fear conditioning (3 min context, 2 s electric shock 0.7 mA) 20 min after vehicle or gaboxadol intrahippocampal infusion. Dorsal hippocampi collected 4 or 21 days after conditioning.

first: Vladimir

last: Jovasevic

first: Jelena

last: Radulovic


title: A new epithelial cell subpopulation predicts response to surgery, chemotherapy, and immunotherapy in bladder cancer

status: Public on Jun 04 2021

city: Los Angeles

first: Kenneth

middle: Howard

last: Gouin III

state: CA

address: 8700 Beverly Blvd

institute: Cedars-Sinai Medical Center

summary: The advent of neoadjuvant chemotherapy (NAC) prior to surgery and immune checkpoint therapy (ICT) have revolutionized bladder cancer management1-7. However, stratification of patients that would benefit most from these modalities remains a major clinical challenge. Here, we combine single nuclei RNA sequencing with spatial transcriptomics and single cell resolution spatial proteomic analysis of human bladder cancer to identify a novel epithelial subpopulation with therapeutic response prediction ability. These cells were defined by expression of Cadherin 12 (CDH12, N-Cadherin 2), catenins and other epithelial markers. CDH12-enriched tumors define patients with poor outcome following surgery with or without NAC. In contrast, CDH12-enriched tumors had a superior response to ICT. In all settings, patient stratification by tumor CDH12 enrichment offered better prediction of outcome than currently established bladder cancer subtypes. Molecularly, the CDH12 population resembles an undifferentiated state with inherent chemoresistance mediated through ALDH1A1 expression and fibroblast activation potential. Furthermore, CDH12-enriched cells express PD-L1 and PD-L2 and co-localize with exhausted T-cells, possibly mediated through CD49a (ITGA1), providing one explanation for ICT efficacy in these tumors. Altogether, this study describes a new cancer cell population with an intriguing diametric response to the major therapeutic modalities in bladder cancer. Importantly, it also provides a compelling rationale for the design of novel biomarker guided therapeutic clinical trials.

overall_design: Single-nuclei RNA-sequencing of human treatment-naïve muscle-invasive bladder cancer (n = 25 patients) and human histologically-normal bladder (n = 3 patients) tissue.

first: Nathan

last: Ing

first: Simon

last: Knott

first: Dan

last: Theodorescu


title: Ventral parafacial inhibitory neurons regulate baseline breathing by a mechanism involving disinhibition

status: Public on May 12 2021

city: Farmington

first: William

middle: F

last: Flynn

state: CT

address: 10 Discovery Drive

institute: The Jackson Laboratory

summary: A parafacial region of the medulla called the retrotrapezoid nucleus (RTN) is an important respiratory control center. A group of glutamatergic neurons in this region function as respiratory  chemoreceptors by regulating breathing in response to changes in tissue CO2/H+. Cellular mechanisms underlying this function involve H+-inhibition of TASK2 channels and -activation of  GPR4 receptors. Evidence also suggests the RTN and greater parafacial region functions as a CO2/H+ sensing network where CO2/H+-activated and -inhibited neurons talk to each other through  excitatory and inhibitory interactions. However, contributions of parafacial inhibitory neurons to control of breathing are unknown, and synaptic properties of RTN chemorecpetors have not been  characterized. Here, we show the ventral parafacial region contains parvalbumin (Pvalb), cholecystokinin (CCK), neuron-derived neurotrophic factor (Ndnf) and somatostatin (SST) subtypes of interneurons including a subset strongly inhibited by CO2/H+. We also show that chemosensitive RTN neurons receive tonic inhibitory input under control conditions that is withdrawn in a CO2/H+-dependent manner, and chemogenetic inhibition of ventral parafacial inhibitory neurons increases baseline respiratory activity. These results suggest ventral parafacial inhibitory neurons are important determinants of respiratory activity under baseline conditions when the respiratory system is most prone to failure.

overall_design: Examination of cells from ventral parafacial brain slices from two batches of B6 mice

first: Colin

middle: M

last: Cleary

first: Fu-Shan

last: Kuo

first: Shaun

middle: D

last: James

first: Paul

last: Robson

first: Daniel

last: Mulkey


title: An autoimmune pleiotropic SNP modulates IRF5 alternative promoter usage through ZBTB3-mediated chromatin looping

status: Public on Mar 03 2021

city: Tianjin

first: Mulin Jun

last: Li

state: Tianjin

address: No.22, Qixiangtai Road, Hepin

department: Basic Medical Research Center

institute: Tianjin Medical University

summary: Genetic sharing is extensively observed for many autoimmune diseases, but the causal variants and their underlying molecular mechanisms remain largely unknown. Through systematic investigation of known autoimmune disease pleiotropic loci, we found that most of these genetic effects are transmitted from regulatory code and colocalize with hematopoietic lineage-specific expression quantitative trait loci. We used an evidence-based strategy to functionally prioritize known pleiotropic variants and identify their target genes. A top-ranked pleiotropic variant, rs4728142, yielded many lines of evidence as being causal, and regulates IRF5 transcript expression. Mechanistically, the rs4728142-containing region interacts with the IRF5 downstream alternative promoter in an allele-specific manner and orchestrates its upstream enhancer to regulate IRF5 alternative promoter usage through chromatin looping. A putative structural regulator, ZBTB3, mediates the allele-specific chromatin looping to promote IRF5 short transcript expression at the rs4728142 risk allele, resulting in IRF5 overactivation and M1 macrophage polarization. Together, our findings establish a causal mechanism between the regulatory variant and fine-scale molecular phenotype underlying the dysfunction of pleiotropic genes in human autoimmunity.

overall_design: Examination of ATAC-seq, 6 different ChIP-seq, and 2 different 4C-seq in SC cells, and RNA-Seq in the rs4728142 locus destruction (sKO) and unedited (control) SC-Cas9 cells

first: Zhao


overall_design: Visium spatial transcriptomics of human treatment-naïve muscle-invasive bladder cancer (n=4) fresh-frozen tissue.


title: Transcriptome Analysis of Human Induced Excitatory Neurons Supports a Strong Effect of Clozapine on Cholesterol Biosynthesis

status: Public on Feb 11 2021

city: Baltimore

first: Dimitrios

last: Avramopoulos

state: Maryland

address: 733 North Broadway

department: Genetic Medicine

institute: Johns Hopkins University

summary: Antipsychotics are known to modulate dopamine and other neurotransmitters which is often thought to be the mechanism underlying their therapeutic effects. Nevertheless, other less studied consequences of antipsychotics on neuronal function may contribute to their efficacy. Revealing the complete picture behind their action is of paramount importance for precision medicine and accurate drug selection. Progress in cell engineering allows the generation of induced pluripotent stem cells (iPSCs) and their differentiation to a variety of neuronal types, providing new tools to study antipsychotics. Here we use excitatory cortical neurons derived from iPSCs to explore their response to therapeutic levels of Clozapine as measured by their transcriptomic output, a proxy for neuronal homeostasis. To our surprise, but in agreement with the results of many investigators studying glial-like cells, Clozapine had a very strong effect on cholesterol metabolism. More than a quarter (12) of all annotated cholesterol genes (46) in the genome were significantly changed at FDR<0.1, all upregulated. This is a 35-fold enrichment with an adjusted p = 8 x10-11. Notably no other functional category showed evidence of enrichment. Cholesterol is a major component of the neuronal membrane and myelin but it does not cross the blood brain barrier, it is produced locally mostly by glia but also by neurons. By singling out increased expression of cholesterol metabolism genes as the main response of cortical excitatory neurons to antipsychotics, our work supports the hypothesis that cholesterol metabolism may be a contributing mechanism to the beneficial effects of Clozapine and possibly other antipsychotics.

overall_design: One Induced pluripotent stem cell line was differentiated in 10 replicates to excitatory neurons by induction with Ngn2 expression. Four  to six replicates were exposed to 300 ng/ul clozapine and the remaining to methanol which was the solvent of clozapine. After RNA extraction they were subjected to RNA sequencing


title: Temperature-dependent induction of browning in retrobulbar fat

status: Public on Jan 15 2021

first: Dong Won

middle: Thomas

last: Kim

address: 733 N.Broadway, MRB building (Rm 332)

department: Neuroscience

summary: Bulk RNA-Seq of mouse and human adipose tissue

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Orbital fat, inguinal fat, epididymal fat, and brown fat from CD1 mice (9 weeks); and orbital fat from human were collected for bulk RNA-Sequencing.

first: Fatemeh

last: Rajaii

first: Dong

middle: W

first: Jianbo

last: Pan

first: Nicholas

last: Mahoney

first: Charles

last: Eberhart

first: Jiang

last: Qian

first: Seth

last: Blackshaw


title: Chromatin Accessibility Maps Provide Evidence of Multilineage Gene Priming in Hematopoietic Stem Cells

status: Public on Jan 06 2021

city: Santa Cruz

first: Camilla

last: Forsberg

state: California

address: 1156 High Street

institute: Institute for the Biology of Stem Cells, University of California Santa Cruz

summary: Hematopoietic stem cells (HSCs) have the capacity to differentiate into vastly different types of mature blood cells. The epigenetic mechanisms regulating the multilineage ability, or multipotency of HSCs are not well understood. To test the hypothesis that cis regulatory elements that control fate decisions for all lineages are primed in HSCs, we used ATAC-seq to compare chromatin accessibility of HSCs with five unipotent cell types. We observed the highest similarity in accessibility profiles between Megakaryocyte Progenitors and HSCs, whereas B cells had the greatest number of regions with de novo gain in accessibility during differentiation. Despite these differences, we identified cis regulatory elements from all lineages that displayed epigenetic priming in HSCs. These findings provide new insights into the regulation of stem cell multipotency, as well as a resource to identify functional drivers of lineage fate.

overall_design: ATAC-seq of Hematopoieitc stem cells and unipotent lineage cells, total of 6 cell types.

first: Eric

last: Martin

first: Jana

last: Krietsch

first: Roman

last: Reggiardo

first: Rebekah

last: Sousae

first: E


title: DNA methylation and hydroxymethylation assessment through Illumina EPIC array analysis of paired bisulfite and oxidative-bisulfite conversion

status: Public on Jan 04 2021

city: Atlanta

first: Carmen

last: Marsit

state: GA

address: 1518 Clifton Road

department: Environmental Health

institute: Rollins School of Public Health at Emory University

type: Methylation profiling by genome tiling array

summary:
Analysis of genome-wide hydroxymethylation within infant placenta tissue collected at term.
These samples have been collected from the Rhode Island Child Health Study (RICHS) cohort.

overall_design: Bisulfite and oxidative bisulfite converted DNA was hybridized to the Illumina EPIC platform and processed at the Emory University Integrated Genomics Core.


title: Epithelial miR-141 regulates IL-13-induced airway mucus production [single-cell RNA-seq]

status: Public on Dec 30 2020

city: San Francisco

first: Srilaxmi

last: Nerella

address: HSE1355A, 513 Parnassus ave

department: Department of Medicine

institute: UCSF

summary: We performed single cell RNA sequencing on bronchial cells from human bronchoalveolar lavage fluid from 4 independent study participants who had asthma and who underwent lung segmental allergen challenge with diluent or allergen (either house duse mite or cat). The goal was to assess total mRNAs in single cell preparations of bronchoalveolar lavage cells.

overall_design: Single cell RNA sequencing was performed on a total of 8 samples of airway epithelial (bronchial) brushings obtained at bronchoscopy from subjects (n=4); 4 samples of which were collected after diluent challenge, and 4 samples collected after allergen challenge (with either house dust mite or cat allergen)

first: Prescott

last: Woodruff

first: Sana

last: Siddiqui


title: Transcriptional profiles along cell programming into corneal epithelial differentiation

status: Public on Dec 29 2020

city: Mexico City

first: Federico

last: Castro-Muñozledo

address: Av Instituto Politecnico Nacional 2508, San Pedro Zacatenco

department: Cell Biology

country: Mexico

institute: CINVESTAV

summary: Corneal epithelial RCE1(5T5) cells follow a sequential process that leads to the formation of a 4-5 layered stratified epithelium with a gene expression pattern similar to that shown in primary cultures of corneal epithelial cells. We have identified three different developmental stages during the differentiation of the rabbit corneal epithelial cell line RCE1(5T5), and thus, analyzed the transcriptome of such different stages in order to understand the regulation of the corneal epithelial cell differentiation. This analysis has led to identify the global expression of gene signatures associated to such differentiation stages.

overall_design: We obtained the transcriptome of three samples of rabbit corneal epithelium formed by RCE1(5T5) cells at distinct stages of the differentiation program.

first: Maria-Teresa

last: Ortiz-Melo

first: María-Jimena

last: Garcia-Murillo

first: Victor

last: Salazar-Rojas

first: Jorge

last: Campos-Contreras

last: Castro-Munozledo


title: Chlorophyll content is a sensetive indicator of silver nanoparticle toxicity in Arabidopsis thaliana

status: Public on Dec 22 2020

city: Springfield

first: Laszlo

last: Kovacs

state: Missouri

address: 901 S  National Avenue

department: Biology

institute: Missouri State University

summary:
Purpose: Analyze changes in the transcriptome of Arabidopsis thaliana in response to sublethal concentrations of silver nanoparticles in order to gain insight into phytotoxicity caused by these nanomaterials.
Methods: mRNA was extracted from non-treated and silver nanoparticle-treated 14-day old Arabidopsis thaliana seedlings using the RNAeasy extraction kit (Qiagen). RNA-seq libraries (3 rep/treatment and 3 reps/control) constructed with the TruSeq Stranded mRNA Sample Preparation kit (Illumina) were single-end sequenced (100-nt read length) on an Illumina HiSeq2500 system. Reads were mapped to the A. thaliana TAIR10 reference genome sequence and transcript levels were analyzed using the softare CLC Genomics Workbench (version 7.0.40, Qiagen).
Results: Chronic exposure of A. thaliana plants to silver nanoparticles caused a change in abundance of transcripts involved in cell wall synhtesis and response to oxidative and biotic stress-related genes.
Conclusions: While exposure to silver nanoparticle lead to gene expression changes, the reduction in chlorophyll concentration and carbon assimilation rate measured in exposed plants cannot be attributed to a shift in photosynthesis-related gene regulation.

overall_design: mRNA profile comparison between non-treated and silver nanoparticle-treated 14-day old Arabidopsis thaliana (Col-0) seedlings.

first: Natalie

last: Smith

first: Vincent

last: Mays


title: Gene expression deregulation in ovarian cancer cells with acquired inverse resistance to paclitaxel and cisplatin

status: Public on Dec 15 2020

city: Poznan

first: Aleksandra

middle: Maria

last: Swiercz

address: Piotrowo 2

department: Institute of Computing Science

country: Poland

institute: Poznan University of Technology

summary: Resistance to anti-cancer drugs is the main challenge in oncology. In pre-clinical studies established cancer cell lines are primary tools in deciphering molecular mechanisms of this phenomenon. In this study we proposed a new approach, based on a model of isogenic cancer cell lines with gradually changing resistance. We analyzed trends in gene expression to find out a scaffold of resistance development process. Ovarian cancer cell line A2780 was treated with stepwise increased concentrations of paclitaxel (PTX) to generate a series of drug resistant sublines.  To monitor transcriptome changes we submitted them to mRNA-sequencing, followed by identification of differentially expressed genes (DEGs), principal component analysis (PCA) and hierarchical clustering. Functional interactions of proteins, encoded by DEGs, were analyzed by building protein-protein interaction (PPI) networks. We provided a model of human ovarian cancer cell lines with gradually developed resistance to PTX and collateral sensitivity to cisplatin (CDDP) (inverse resistance). In their transcriptomes we identified two groups of DEGs: 1) with fluctuations in expression in the course of resistance acquiring; and 2) with consistently changed expression in each stage of resistance development, constituting a scaffold of the process. In the scaffold PPI network, cell cycle regulator – PLK2; proteins belong to TNF ligand and receptor family as well as ephrin receptor family were found, but proteins linked to osteo- and chondrogenesis and nervous system development turned out to be key players. Our cellular model of drug resistance allowed for keeping track of trends in gene expression and studying this phenomenon as a process of evolution. This approach revealed that abrogation of osteomimic phenotype in ovarian cancer cells may occur during the development of inverse resistance to PTX and CDDP.

overall_design: Examination of genome-wide expression profile in series of A2780-derived  sublines with gradually increasing resistance to PTX and sensitivity to CDDP. Fourteen samples were analyzed, each one in two replicates. A2780 untreated cells were references samples.

first: Jolanta

last: Szenajch

first: Luiza

last: Handschuh

last: Świercz

first: Alicja

last: Szabelska-Beręsewicz

first: Joanna

last: Zyprych-Walczak

first: Idzi

last: Siatkowski

first: Michał

last: Góralski

first: Agnieszka

last: Synowiec


title: Integrator is a genome-wide attenuator of non-productive transcription

status: Public on Jan 03 2021

city: Aarhus C

first: Søren

last: Lykke-Andersen

address: C.F.Møllers Allé 3

department: Molecular Biology and Genetics

country: Denmark

institute: Aarhus University

summary: Termination of RNA polymerase II (RNAPII) transcription in metazoans relies largely on the Cleavage and Polyadenylation (CPA) and Integrator (INT) complexes originally found to act at the ends of protein-coding and snRNA genes, respectively. Here we monitor CPA- and INT-dependent termination activities genome-wide, including at thousands of previously unannotated transcription units (TUs), producing unstable RNA. We verify the global activity of CPA, occurring at pA sites indiscriminately of their positioning relative to the TU promoter. We also identify a global activity of INT, which is, however, largely sequence-independent and restricted to a ~3 kb promoter-proximal region. Our analyses suggest two functions of genome-wide INT activity; it dampens transcriptional output from weak promoters and it provides quality-control of RNAPII complexes that are unfavorably configured for transcriptional elongation. We suggest that the function of INT in stable snRNA production is an exception from its general cellular role, the attenuation of non-productive transcription.

overall_design: Cleavage and polyadenylation complex subunit CPFS3, Integrator complex subunit IntS11, Exosome complex subunit EXOSC3 were knocked down in HeLa cells using siRNA. The corresponding controls were the non-tageting EGFP or Luc siRNA knockdown. Two biological replicates were generated for TT-seq and RNA-seq. Three biological replicates were generated for 3'-seq.

first: Kristina

last: Žumer

first: Ewa

last: Šmidová Molska

first: Jérôme

middle: O

last: Rouvière

first: Guifen

last: Wu

first: Carina

last: Demel

first: Björn

last: Schwalb

first: Manfred

last: Schmid

first: Patrick

last: Cramer

first: Torben

last: Heick Jensen


title: Che-1/AATF-induced transcriptionally active chromatin promotes cell proliferation in Multiple Myeloma

status: Public on Dec 08 2020

city: Rome

first: Maurizio

last: Fanciulli

address: via Chianesi

country: Italy

institute: IRCCS National Institute of Cancer Regina Elena

summary: We have strong evidence on the essential role of Che-1 protein in promoting the proliferation of MM cells by sustaining chromatin dynamics and cellular transcription on a global scale using numerous experimental approaches, including a generation of a specific transgenic mouse model.

overall_design: Examination of RNA-seq, BRD4, H3K27ac, ATAC-seq, HDAC in KMS27 cell lines before and upon Che interference. ATAC-seq and RNA-seq data of wild and vk-Che mice (overexpression).

first: Tiziana

last: Bruno

first: Francesca

last: De Nicola

first: Frauke

last: Goeman

first: Matteo

last: Pallocca

first: Giacomo

last: Corleone


title: Rhes, a striatal enriched protein, regulates SUMOylation of nuclear proteins and gene expression in a SUMO-dependent manner

status: Public on Nov 23 2020

city: Jupiter

first: Srinivasa

last: Subramaniam

state: FL

address: 130 Scripps Way

institute: The Scripps Research Institute

summary: Rhes, a multifunctional striatal protein, regulates nuclear proteins and gene expression via SUMO-mediated mechnisms.

overall_design: Total RNA extracted from 1 male and 1 female pooled striatum per sample using Qiagen miRNeasy kit (cat. #217004) and Dnase-treatment done on-column. Total RNA-seq libraries were prepared using the Illumina stranded total RNA-seq kit (cat. #RS-122-2201).

first: Manish

last: Sharma

first: Neelam

last: Shahani

first: Uri

middle: N

last: Ramirez-Jarquin


title: Maternal antioxidant treatment prevents behavioural and neurological changes in offspring exposed to prenatal social stress

status: Public on Dec 01 2020

city: Cardiff

first: Hannah

last: Scott

address: Hadyn Ellis Building, Maindy Road

department: UK Dementia Research Institute

country: United Kingdom

institute: Cardiff University

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

overall_design: Refer to individual Series


title: SEZ cells populations

status: Public on Nov 22 2020

city: Burjassot

first: Antonio

last: Jordan

state: Valencia

address: Doctor Moliner 50

institute: Universitat de Valencia

summary: Characterization of neural stem cells (NSC) from the adult rodent subependymal niche by flow cytometry and traceable nucleoside retention assays have indicated the co-existence of activated and quiescent NSC in this niche. Single-cell deep-sequencing has further revealed different NSC molecular states with regards to cell-cycle gene expression: quiescent, primed for activation, and fully activated. Here, we provide a multi-level procedure to classify all cells of the subependymal niche, without the need for reporter mice, into populations with coherent transcriptomes that can be functionally assayed. Our strategy reveals that primed NSC are slowly proliferating cells that contribute to NSC cultures and that neurospheres contain NSC which retain a primed-like molecular signature and exhibit slow cycling and long-term self-renewal. Our strategy provides a way to functionally assay NSC heterogeneity and to study quiescence levels in NSC populations.

overall_design: RNAseq of 8 different populations of cells freshly isolated from the adult mouse SEZ niche (between 3-4 replicates per group, 28 samples in total) and 2 populations of neurosphere forming cells showing different proliferative kinetics (4 replicates per group, 8 samples in total).

first: Germán

last: Belenguer

first: Pere

last: Duart-Abadía

last: Jordán-Pla

first: Jose

last: Morante-Redolat

first: Isabel

last: Farinas


title: Temporal profiles of gene expression in Cry1/2 KO, Bmal1 KO under night restricted feeding and ad libitum feeding regimen

status: Public on Dec 03 2020

city: Lausanne

first: Benjamin

last: Weger

state: VD

address: Station 15

department: SV

institute: EPFL

summary: The circadian clock and rhythmic food intake are both important regulators of rhythmic gene expression in the liver. It remains, however, elusive to which extent the circadian clock network and natural feeding rhythms contribute to rhythmic gene expression. To systematically address this question, we developed an algorithm to investigate differential rhythmicity between a varying number of conditions. Mouse knockout models of different parts of the circadian clock network (Bmal1, Cry1/2, and Hlf/Dbp/Tef) exposed to controlled feeding regimens (ad libitum, night restricted feeding) were generated and analyzed for their temporal hepatic transcriptome. A genetical ablation of core loop elements altered feeding patterns that were restored by night restricted feeding. Mainly genes with a high amplitude were driven by the circadian clock but natural feeding patterns equally contributed to rhythmic gene expression with lower amplitude. We observed that Bmal1 and Cry1/2 KOs differed in rhythmic gene expression and identified differences in mean expression levels as a predictor for rhythmic gene expression. In Hlf/Dbp/Tef KO, mRNA levels of Hlf/Dbp/Tef target genes were decreased, albeit rhythmicity was overall preserved potentially due to the activity of the D-Box binding repressor NFIL3. Genes that lost rhythmicity in Hlf/Dbp/Tef KOs were identified to be no direct targets of PARbZip factors and presumably lost rhythmicity due to indirect effects.   Collectively, our findings provide unprecedent insights into the diurnal transcriptome in mouse liver and defines the contribution of subloops of the circadian clock network and natural feeding cycles. The developed algorithm and a webapp to browse the outcomes of the study are publicly available to serve as a resource for the scientific community.

overall_design: RNA-Seq from mRNA of mouse liver across the course of a day. Time-series include mRNA profiles of Bmal1 wild-type (WT),   Bmal1 KO and Cry1/2 WT, and Cry1/2 KO mice under an ad libitum or night restriced feeding regimen.

first: Cedric

last: Gobet

first: Eva

last: Martin

first: Frederic

last: Gachon

first: Felix

last: Naef


title: Conserved interferon signature between adult and pediatric eosinophilic esophagitis

status: Public on Aug 22 2020

city: Seattle,

first: Stephanie

last: Osmond

address: 1201 9th Ave

institute: Benaroya Research Institute

summary: Eosinophilic esophagitis (EoE) is an allergic inflammatory disease of the esophagus that occurs in both children and adults. Previous studies of affected tissue in pediatric cohorts have identified prominent signatures of eosinophilia and type 2 inflammation. However, the details of the immune response in adults with EoE are still being elucidated. To determine whether EoE in adults shares inflammatory profiles with those observed in children, we performed RNA-sequencing of paired esophageal biopsies and blood samples from adults with EoE or gastroesophageal reflux disease (GERD). Unbiased analysis of differentially expressed genes in tissue revealed a strong interferon signature that was significantly enriched in EoE patients as compared to patients with GERD. Both type I and type II interferon responsive genes were upregulated in adult biopsies, but not in blood. A similar increase in expression of interferon gene sets was observed in pediatric EoE biopsies as compared to non-EoE samples, and in public pediatric and adult RNA-sequencing data. Finally, we found that peripheral CD4+ T cells from children with EoE produce IFNG upon activation with EoE-causal allergens. Together, this work identifies a conserved interferon signature in pediatric and adult EoE, highlighting a role for non-type 2 inflammatory networks in the disease process.

overall_design: 20 samples total. 10 patients; 4 control, 5 eosinophilic esophagitis, 1 lymphocytic esophagitis. For each patient, an esophageal tissue sample and a blood sample were taken.

first: Karen

last: Cerosaletti

first: Alex

last: Hu


title: KRAS drives immune evasion in a genetic model of pancreatic cancer

status: Public on Nov 11 2020

city: Stony Brook

first: Jinyu

last: Li

address: 101 Nicolls Rd

department: Cancer Center

institute: Stony Brook University

summary: We used CRISPR/Cas9 genome editing to inactivate KRAS in pancreatic cancer cells and isolated cell populations that still produce tumors in mice. We show that the malignant phenotype of KRAS knockout cells is stable. However, KRAS deficient cancer cells fail to avoid detection and elimination by the host immune system, indicating that a key aspect of tumor maintenance by oncogenic KRAS is to promote immune evasion. Our study uncovers changes both in cancer cells and stromal immunoreactive cells attributable to KRAS expression. Complementation studies indicate that BRAF, AKT and MYC are causative drivers of KRAS-mediated immune suppression. These results show that combination treatments that both target KRAS signaling and boost antitumor immunity will be an effective strategy to treat PDAC.

overall_design: scRNAseq was performed on a total of three samples. Tumors were harvested from the pancreas of three sets of syngeneic mice. These mice were injected orthotopically with a) malignant KRASG12D p53R172H/+ b) KRASKO and c) KRAS KO BRAF/MYC cells.

first: Irene

last: Ischenko

first: Stephen

last: D'Amico

first: Manisha

last: Rao

first: Michael

last: Hayman

first: Scott

last: Powers

first: Oleksi

last: Petrenko

first: Nancy

middle: C

last: Reich


title: Gene expression in Pou5f1:EGFP-positive spermatogonia from Dazl conditional knockout and control males

status: Public on Jul 22 2020

city: Cincinnati

first: Maria

middle: M.

last: Mikedis

state: OH

address: 240 Albert Sabin Way

institute: Cincinnati Children's Hospital Medical Center

summary: RNA-seq of sorted Pou5f1:EGFP-positive spermatogonia from adult testes.

overall_design: Spermatogonia were sorted for Pou5f1:EGFP expression Dazl conditional knockout and control RNA-seq datasets were generated in triplicate.

first: Yuting

last: Fan

first: David

last: Page


title: Prevalence of alternative ATG and non-ATG translation initiators and their regulatory effects across plants

status: Public on Aug 11 2020

city: Taipei

first: Ming-Jung

last: Liu

address: 128 Sec. 2, Academia Rd, Nankang

country: Taiwan

institute: Academia sinica

summary: We report the global profile of ribosome profilig to study the relationship between alternative translation initaiton sites and gene expression in tomato.

overall_design: We examined the initiating ribosome positions to identify translation initiation sites and mRNA abundance  in tomato leaf.

first: Ya-Ru


title: Translational profiling in undifferentiated spermatogonia

summary: Germline-specific RiboTag IP-seq from postnatal testes synchronized for undifferentiated spermatogonia.

overall_design: Germline ribosomes were specifically tagged via Ddx4Cre, which activated expression of the RiboTag allele (Rpl22HA). Spermatogenesis in postnatal testes was chemically synchronized to obtain testes enriched for undifferentiated spermatogonia. For each synchronized sample collected from a single animal, RiboTag IP-seq and input RNA-seq was carried out. Synchronized samples lacking the RiboTag allele were used as negative controls for the IP-seq. RiboTag and control samples were each generated in triplicate.


title: DAZL targets in undifferentiated spermatogonia

summary: DAZL's targets were identified via iCLIP in postnatal testes synchronized for undifferentiated spermatogonia.

overall_design: Spermatogenesis in postnatal testes was chemically synchronized to obtain testes enriched for undifferentiated spermatogonia. DAZL and IgG iCLIP libraries were generated in triplicate.


title: Gene expression in undifferentiated spermatogonia

summary: RNA-seq of sorted undifferentiated spermatogonia from synchronized postnatal testes.

overall_design: Spermatogenesis in postnatal testes was chemically synchronized to obtain testes enriched for undifferentiated spermatogonia. Undifferentiated spermatogonia were then sorted based on tdTomato fluorescence, activated by germline-specific Ddx4Cre.  RNA-seq librares were generated in duplicate.


title: Two isoforms of the essential C. elegans Argonaute CSR-1 differentially regulate sperm and oocyte fertility through distinct small RNA classes

status: Public on Jul 19 2020

city: Toronto

first: Julie

last: Claycomb

state: Ontario

address: 661 University Ave.

department: Molecular Genetics

country: Canada

institute: University of Toronto

summary: The C. elegans genome encodes nineteen functional Argonaute proteins that utilize 22G-RNAs, 26G-RNAs, miRNAs, or piRNAs to regulate their target transcripts. Only one of these proteins is essential under normal laboratory conditions: CSR-1. While CSR-1 has been studied in various developmental and functional contexts, nearly all studies investigating CSR-1 have overlooked the fact that the csr-1 locus encodes two isoforms. These isoforms differ by an additional 163 amino acids present in the N-terminus of CSR-1a. Using CRISPR-Cas9 genome editing to introduce GFP::3xFLAG epitopes into the long (CSR-1a) and short (CSR-1b) isoforms of CSR-1, we identified differential expression patterns for the two isoforms. CSR-1a is expressed specifically during spermatogenesis and in select somatic tissues, including the intestine. In contrast, CSR-1b, is expressed constitutively in the germline. Essential functions of csr-1 described in the literature coincide with CSR-1b. In contrast,CSR-1a plays tissue specific functions during spermatogenesis, where it integrates into a spermatogenesis sRNA regulatory network including ALG-3, ALG-4, and WAGO-10 that is necessary for male fertility. CSR-1a is also required in the intestine for the silencing of repetitive transgenes. Sequencing of small RNAs associated with each CSR-1 isoform reveals that CSR-1a engages with 22G- and 26G-RNAs, while CSR-1b interacts with only 22G-RNAs to regulate distinct groups of germline genes and regulate both sperm and oocyte-mediated fertility.

overall_design: Examination of sRNAs that immunoprecipitate with C. elegans Argonautes: CSR-1(total), CSR-1a, CSR-1b, ALG-3, ALG-4, WAGO-10, WAGO-4; and mRNA profiles of wild-type and csr-1(tor159) mutant worms at 20C and 25C.

first: Amanda

middle: G

last: Charlesworth

first: Nicolas

middle: J

last: Lehrbach

first: Uri

last: Seroussi

first: Mathias

middle: S

last: Renaud

first: Ruxandra

middle: I

last: Molnar

first: Jenna

last: Woock

first: Matthew

last: Aber

first: Gary

last: Ruvkun


title: Inflammation potentiates JMML-like blood defects in Shp2 mutant Noonan syndrome

status: Public on Feb 27 2021

city: Utrecht

first: Jeroen

last: den Hertog

state: Utrecht

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute

summary: Hematopoietic stem and progenitor cells derived from a zebrafish model of Noonan syndrome, carrying a patient-associated Shp2-D61G mutation, display an expansion of monocyte/macrophage progenitors with an inflammatory gene expression signature.

overall_design: CHTs (5dpf) were dissected and dissociated, using FACS sorting HSPCs were isolated and single cell RNA seq was performed.

first: Maja

last: Solman

first: Sasja

last: Blokzijl-Franke

first: Chuan

last: Yan

first: Qiqi

last: Yang

first: Sarah

last: Kamel

last: Bakkers

last: Langenau


title: DAZL mediates a broad translational program regulating expansion and differentiation of spermatogonial progenitors

first: Maria

last: Mikedis

country: USA


title: Sequencing of commercially-available pancreatic cancer cell lines reveals selective CYP3A5 overexpression among xenobiotic-metabolizing CYPs.

status: Public on Mar 01 2020

city: Memphis

first: William

middle: C.

last: Wright

state: Tennessee

address: 262 Danny Thomas Pl

department: Computational Biology

institute: St. Jude Children's Research Hospital

summary:
Purpose: To know the expression of all cytochrome P450 (CYP) enzymes and related drug metabolizing enzymes in pancreatic cancer models
Methods: We obtained expression profiles of 8 commercially-available pancreatic cancer cell lines and one non-cancerous immortalized cell line by RNA-sequencing. The pancreatic cancer cells were compared among themselves and to the non-cancerous control cells.
Results: We confirmed reports that CYP3A5 is highly overexpressed in pancreatic cancer models, and additionally report that known xenobiotic-metabolizing CYPs are lowly expressed in comparison.

overall_design: mRNA profiles of each cell line were obtaiend in triplicate using Illumina-based RNA-Sequencing. Sequencing was conducted as paired-end 100bp reads. The HPNE (non-cancerous pancreatic cells) group is considered as the control.

first: Peter

last: Oladimeji

first: Taosheng

last: Chen


title: LncRNA NRAV promotes respiratory syncytial virus (RSV) replication by regulating vesicle transportation via targeting miR-509-3p/Rab5c axis

status: Public on Feb 24 2020

city: Shijiazhuang

first: Jian

last: Li

address: 361 Zhongshan East Road

country: China

institute: Hebei Medical University

summary: NRAV could act as a ceRNA in NRAV/miR-509-3p/Rab5c axis during RSV infection, thus promoting RSV vesicle transport and accelerating RSV entry.

overall_design:
The function of NRAV was examined in A549 cells.
**Please note that the NO9 and NO10 data columns (in the processed data file) should be disregarded.

first: Miao

first: Xiuli

last: Wang

first: Mengfei

last: Sun

first: Cuiqing

last: Ma

first: Wenzhang

last: Liang

first: Xue

last: Gao

first: Lin

last: Wei


title: TLR-dependent transcriptional reprogramming of LXRα cistrome in bone marrow-derived macrophages

status: Public on May 01 2020

city: Madrid

first: ANTONIO

last: CASTRILLO

address: Arturo Duperier 4

department: metabolism and cellular signaling

institute: Instituto Investigaciones Biomedicas Alberto Sols CSIC

summary: The Liver X receptors (LXRα and LXRβ) are members of the nuclear receptor superfamily of transcription factors, and play key roles in the coordination of both metabolic and immune responses in macrophages. Both LXRs are expressed in macrophages and they share a high degree of sequence homology but their individual roles in different models of macrophage cultures, particularly in response to inflammation, have not been characterized. Previous studies have shown that ligand pre-treated LXRs repress the induction of pro-inflammatory cytokines in macrophages. Here, we show evidence that the expression of LXRα (but not LXRβ) is transcriptionally regulated at late phases of an LPS-induced inflammatory response in bone marrow-derived macrophages (BMDMs). Regulation of LXRα expression is controlled at the transcriptional levels by inflammatory signaling networks. Transcriptional profiling studies and ChIP-seq data identified a number of innate immune pathways whose expression is substantially controlled by LXRα in BMDMs. In summary, our data shows that LXRα plays a previously unrecognized role in innate immunity by transcriptional regulation of a battery of inflammatory genes through TLR and Type-I IFN-dependent signaling in macrophages.

overall_design: For bone marrow-derived macrophage (BMDM) cell differentiation, bone marrow from femurs and tibias of 8-10 week-old WT or LXRα-/- mice were isolated and cultured for 7 days in DMEM supplemented with 10% conditioned media from L-929 cells expressing M-CSF and 1% antibiotics (penicillin and streptomycin).

first: Antonio

last: Castrillo


title: Transcriptional signatures that define Ulcerative Colitis in remission

status: Public on Jan 18 2020

city: Tromso

first: Christopher

last: Fenton

state: Norge

address: MH bygget

department: GSCT

institute: Universiry of Tromso

summary:
Background: This study addresses whether existing specific transcriptional profiles can improve and support the current status of the definition of ulcerative colitis (UC) remission apart from the existing endoscopic, histologic, and laboratory scoring systems. For that purpose, a well-stratified UC patient population in remission was compared to active UC and control patients and was investigated by applying the next-generation technology RNA-Seq.

Methods: Mucosal biopsies from patients in remission (n = 14), patients with active UC (n = 14), and healthy control patients (n = 16) underwent whole-transcriptome RNA-Seq. Principal component analysis, cell deconvolution methods, gene profile enrichment, and pathway enrichment methods were applied to define a specific transcriptional signature of UC in remission.

Results: Analyses revealed specific transcriptional signatures for UC in remission with increased expression of genes involved in O-glycosylation (MUC17, MUC3A, MUC5AC, MUC12, SPON1, B3GNT3), ephrin-mediated repulsion of cells (EFNB2E, EFNA3, EPHA10, EPHA1), GAP junction trafficking (TUBA1C, TUBA4A, TUBB4B, GJB3, CLTB), and decreased expression of several toll-like receptors (TLR1, TLR3, TLR5, TLR6).

Conclusions: This study reveals specific transcriptional signatures for remission. Partial restoration and improvement of homeostasis in the epithelial mucus layer and revival of immunological functions were observed. A clear role for bacterial gut flora composition can be implied. The results can be useful for the development of treatment strategies for UC in remission and may be useful targets for further investigations aiming to predict the outcome of UC in the future.

overall_design:
Mucosal biopsies from UC patients in remission (n=14), UC patients (n=14), and healthy controls (n=16) underwent RNA-Seq. Principal component analyse (PCA), cell deconvolution methods and diverse statistical methods were applied to obtain and characterize a dataset of significantly differentially expressed gens (DEGs) during UC remission.

** Raw data not provided due to patient privacy concerns. **

first: Ruth

middle: H

last: Paulssen


title: DAZL targets during male meiotic prophase I

status: Public on Nov 22 2019

summary: DAZL's targets were identified via iCLIP in leptotene-synchronized postnatal testes.

overall_design: Spermatogenesis in postnatal testes was chemically synchronized to obtain testes enriched for leptotene spermatocytes. DAZL and IgG iCLIP libraries were generated in triplicate.

first: David

last: Page


title: Spatially discrete signalling niches regulate fibroblast heterogeneity in human lung cancer

status: Public on Jun 24 2020

city: Southampton

first: Sara

last: Waise

state: Hampshire

address: Somers Building MP284, Southampton General Hospital, Tremona Road

department: Cancer Sciences

institute: University of Southampton

summary: Fibroblasts are functionally heterogeneous cells, capable of promoting and suppressing tumour progression. Across cancer types, the extent and cause of this phenotypic diversity remains unknown. We used single-cell RNA sequencing and multiplexed immunohistochemistry to examine fibroblast heterogeneity in human lung and non-small cell lung cancer (NSCLC) samples. This identified seven fibroblast subpopulations: including inflammatory fibroblasts and myofibroblasts (representing terminal differentiation states), quiescent fibroblasts, proto-myofibroblasts (x2) and proto-inflammatory fibroblasts (x2). Fibroblast subpopulations were variably distributed throughout tissues but accumulated at discrete niches associated with differentiation status. Bioinformatics analyses suggested TGF-β1 and IL-1 as key regulators of myofibroblastic and inflammatory differentiation respectively. However, in vitro analyses showed that whilst TGF-β1 stimulation in combination with increased tissue tension could induce myofibroblast marker expression, it failed to fully re-capitulate ex-vivo phenotypes. Similarly, IL-1β treatment only induced upregulation of a subset of inflammatory fibroblast marker genes. In silico modelling of ligand-receptor signalling identified additional pathways and cell interactions likely to be involved in fibroblast activation, This highlighted a potential role for IL-11 and IL-6 (among other ligands) in myofibroblast and inflammatory fibroblast activation respectively. This analysis provides valuable insight into fibroblast subtypes and differentiation mechanisms in NSCLC.

overall_design: mRNA profiles of cultured primary human lung fibroblasts

last: Hanley


title: Spatially discrete signalling niches regulate fibroblast heterogeneity in human lung cancer [single-cell RNA-seq]

status: Public on Jul 08 2020

overall_design: mRNA profiles of primary human lung samples (D1-12; “TLDS_All Cells.txt”).  Third-party stromal cell data (included in "Merged_Stromal Cells.txt") were downloaded as the "all cells" file from https://gbiomed.kuleuven.be/scRNAseq-NSCLC. Stromal cells were identified in these data using a random forest classifier trained on the TLDS dataset variable genes.


title: Study of sarcopenia in human muscle biopsies of elderly individuals

status: Public on Nov 14 2019

first: Jerome

last: Feige

address: EPFL Innovation Park, Building H

department: Musculo-Skeletal Health

country: Switzerland

institute: Nestle Institute Of Health Sciences

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

overall_design:
Refer to individual Series
The RNA-sequencing experiments for the 3 individual series were run at different time.


title: Identification and characterization of centromeric sequences in Xenopus laevis

city: Stanford

first: Owen

middle: Kabnick

last: Smith

address: 279 Campus Drive

department: Biochemistry

institute: Stanford University School of Medicine

summary: Centromeres play an essential role in cell division by specifying the site of kinetochore formation on each chromosome so that chromosomes can attach to the mitotic spindle for segregation. Centromeres are defined epigenetically by the histone  H3 variant CEntromere Protein A (CENP-A). Dividing cells maintain the centromere  by depositing new CENP-A each cell cycle to replenish CENP-A diluted by replication. The CENP-A nucleosome serves as the primary signal to the machinery responsible for its replenishment. Vertebrate centromeres are frequently built on repetitive sequences organized in tandem arrays. Repetitive centromeric DNA has been suggested to play a role in centromere maintenance and in de novo centromere formation, but this has been difficult to dissect because of the difficulty in manipulating centromere in cells. Extracts from Xenopus laevis eggs are able to assemble centromeres and kinetochores in vitro and thus provide a useful system for studying the role of centromeric DNA in centromere formation. However centromeric sequences in X. laevis have not been extensively characterized.. In this study we characterize repeat sequences found at  X. laevis centromeres. We utilize a k-mer based approach in order to uncover the previously unknown diversity of X. laevis centromeric sequences. We validate centromere localization of repeat sequences by in situ hybridization and identify the location of the centromeric repetitive array on each chromosome by mapping the distribution of centromere enriched k-mers on the Xenopus genome. Our identification of X. laevis centromere sequences enables previously unapproachable genomic studies of centromeres. The k-mer based approach that we used to investigate centromeric repetitive DNA is suitable for the analysis of other repetitive sequences found across the genome or the study of repeats in other organisms.

overall_design: four replicates each of native Mnase ChIP-seq from CENP-A and H4 Ips, along with input seqeuncing libraries were sequenced on Illumina MiSeq. One replicate of each was further sequenced on Illumina HiSeq

middle: K

first: Charles

last: Limouse

first: Kelsey

middle: A

last: Fryer

first: Nikki

last: Teran

first: Kousik

last: Sundararajan

first: Rebecca

last: Heals

first: Aaron

last: Straight


title: Next Generation Sequencing on HMEC-1 or HUVEC residing on SOFT or STIFF matrices

status: Public on Jul 31 2019

city: Seattle

first: Effie

middle: Efthimia

last: Bastounis

state: WA

address: UW Biology Life Sciences Bldg, Room 565, 4000 15th Ave NE

institute: University of Washington

summary:
Purpose: Endothelial cells respond to changes in subendothelial stiffness altering their proliferation, migration and barrier integrity but whether that is due to transcriptional reprogramming was largely unknown. Using RNA-Sequencing, we performed gene expression profiling for two endothelial cell types grown on soft or stiff matrices: primary human umbilical vein endothelial cells (HUVEC) and immortalized human microvascular endothelial cells (HMEC-1), to understand whether subendothelial stiffness-dependent changes in endothelial cell mechanics are due to transcriptional regulation.
Methods and Results: By analyzing the differentially expressed genes between all samples we found that endothelial cell type rather that subendothelial stiffness is the primary determinant of the endothelial cell transcriptome. Both cell types respond to changes in their subendothelial stiffness by increasing the traction stresses they exert on stiffer as opposed to softer matrices, however it is apparently not the endothelial cell transcriptome that regulates this universal biomechanical response to subendothelial stiffness. Only a handful of genes were differentially expressed in each cell type in a stiffness-dependent manner, and none were shared between the two cell types examined. In contrast, thousands of genes were differentially regulated in HUVEC as compared to HMEC-1. HUVEC (but not HMEC-1) upregulate expression of TGF-2 on stiffer matrices, and also enhance their endogenous TGF-2 expression and their cell-matrix traction stresses in response to application of exogenous TGF-2.
Conclusions: Altogether, these findings provide insights into the relationship between subendothelial stiffness, endothelial mechanics and variation of the transcriptome between distinct endothelial cell types, and reveal that subendothelial stiffness while critically impacting endothelial cell mechanics is minimally altering their transcriptome.

overall_design: Confluent endothelial cell mRNA profiles for cells residing for 24 h on soft 3 kPa or stiff 70 kPa polyacrylamide hydrogels coated with 0.25 mg/mL collagen I  were generated in sextuplicate, using Illumina NextSeq 500 System using the High-Output Kit with 2x75 read length and 30 million reads per sample.

middle: E

first: Julie

last: Theriot


title: Role for citron kinase in prostate cancer growth

status: Public on Oct 01 2019

city: BUFFALO

first: Eduardo

last: Cortes

state: NY

address: ELM AND CARLTON STREETS

department: Biostatistics and Bioinformatics

institute: ROSWELL PARK CANCER INSTITUTE

summary: To study the effect of siRNA-mediated CIT silencing on androgen-responsive genes in LNCaP cells.

overall_design: Human LNCaP prostate cancer cells were transfected with siRNA SmartPools targeting CIT or a non-targeting siRNA SmartPool.  Forty-two hours after transfection, cells were treated with synthetic androgen R1881 (0.1nM) or vehicle.  Three biological replicates were generated per treatment group.  Forty-eight hours later, total RNA was isolated and processed for RNA-Seq analysis.

first: Salma

last: Ben-Salem

first: Qiang

last: Hu

first: Song

last: Liu

first: Hannelore

last: Heemers


title: Study of sarcopenia in human muscle biopsies of elderly individuals, Singapore Sarcopenia Study

summary:
Purpose: The main goal of this study is to compare skeletal muscle transcriptome profilings derived from sarcopenic versus healthy subjects.
Methods: We use high coverage RNA sequencing of human skeletal muscle biopsies to analyze genome-wide transcriptional changes in human sarcopenia benchmarked to healthy elderly controls.
Results: Muscle transcriptomic profiles demonstrate a prominent signature of mitochondrial dysfunction in sarcopenic patients.
Conclusions: Our study supports the fundamental role of mitochondrial dysfunction in driving pathological muscle and mobility decline in the elderly.

overall_design: 20 muscle biopsies from healthy subjects and 20 muscle biopsies from sarcopenic subjects.

first: Eugenia

last: Migliavacca

first: Aline

last: Charpagne

first: Stacy

last: Tay

first: Frédéric

last: Raymond

first: Neerja

last: Karnani

first: Descombes

last: Patrick


title: Differential gene expression analysis between pre-metamorphic WT control X. laevis tadpoles and tadpoles with thioridazine-induced craniofacial abnormalities.

status: Public on Jun 30 2019

city: Medford

first: Kelly

last: McLaughlin

state: MA

address: 200 Boston Avenue

institute: Tufts University

summary: We found 101 differentially expressed genes between control and thioridazine samples at NF stage 45 and 135 at NF stage 47.

overall_design: We utilized whole-head tissue samples from thioridazine tadpoles with malformed craniofacial features and compared them to wild-type controls, at NF stage 45 and 47.

first: Kaylinnette

last: Pinet


title: Human trophoblast differentiation is associated with profound genetic and epigenetic changes

city: Dallas

first: Youn

last: Kwak

state: TX

address: 5323 Harry Hines Blvd

department: Microbiology

institute: UT-Southwestern Medical Center

summary: Increased RNA polymerase II binding to promoters of a subset of genes during trophoblast differentiation was closely correlated with active histone marks.

overall_design: ChIP-seq of mid-gestation human trophoblasts before (CytT) and after SynT differentiation in primary culture to analyze changes in binding of RNA polymerase II and of active (H3K4me3, H3K9Ac, H3K27Ac) and repressive (H3K27me3) histone marks during SynT differentiation.

first: Youn-Tae

first: Sribalasubashini

last: Muralimanoharan

first: Aishwarya

last: Gogate

first: Carole

middle: R

last: Mendelson


title: Sex-specific gene regulation in malaria parasites by an AP2 Family Transcription Factor

status: Public on May 05 2019

city: tsu

first: masao

last: yuda

state: mie

address: edobashi 2-174

country: Japan

institute: mie university

overall_design: Refer to individual Series


title: Sex-specific gene regulation in malaria parasites by an AP2 Family Transcription Factor [Agilent]

summary: Malaria gametocytes, the precursors of gametes, is the stage essential for malaria transmission to the mosquito vector. In the circulation they arise from asexual erythrocytic stages and then develop into mature females and males. Identification of sex-specific transcription factors is a key to understand biology of this stage. However, despite of intensive studies, none of them have been identified yet. In this paper we report an AP2 family transcription factor AP2-FG is responsible for female-specific gene expression.

overall_design: To establish synchronous infection in Wistar rats, whole blood was harvested from rats infected with AP2-FG(-) or wild-type parasites and cultured for 16 h. Mature schizonts were purified from the culture with Nicodenz  and inoculated into rats. Whole blood was harvested from these rats at 26 h after the innoculation. Four and five biologically independent experiments were performed in AP2-FG(−) and wild-type parasites, respectively.

first: Masao

last: Yuda

first: Izumi

last: Kaneko

first: Shiroh

last: Iwanaga

first: Tomomi

last: Kato

first: Yuho

last: Murata


title: Bioinformatics Analyses Determined the Distinct CNS and Peripheral Surrogate Biomarker Candidates between Two Mouse Models for Progressive Multiple Sclerosis

status: Public on Apr 09 2019

city: Osakasayama

first: Seiichi

last: Omura

state: Osaka

address: 377-2 Ohnohigashi

department: Department of Microbiology

institute: Kindai University Faculty of Medicine

summary:
Previously, we have established two distinct progressive multiple sclerosis (MS) models by induction of experimental autoimmune encephalomyelitis (EAE) with myelin oligodendrocyte glycoprotein (MOG) in two mouse strains.  A.SW mice develop ataxia with antibody deposition, but no T cell infiltration, in the central nervous system (CNS), while SJL/J mice develop paralysis with CNS T cell infiltration.  In this study, we determined biomarkers contributing to the heterogeneities of the two models.
Using the CNS and spleen microarray transcriptome and cytokine data, we conducted computational supervised analyses (volcano plot, heat map, and pathway analysis) and unsupervised principal component analysis (PCA) with pattern matching analysis (PMA).

overall_design: Mice with primary progressive experimental autoimmune encephalomyelitis (PP-EAE) were induced by sensitization with myelin oligodendrocyte glycoprotein (MOG) alone or MOG and cardlan.  Microarray analysis was conducted using brain and spleen samples collected from PP-EAE mice at the disease peak.  Microarray data were analyzed by bioinformatics methods, e.g. principal component analysis (PCA).

first: Fumitaka

last: Sato

first: Nicholas

last: Martinez

first: Ah-Mee

last: Park

first: Mitsugu

last: Fujita

first: Nikki

last: Kennett

first: Urska

last: Cvek

first: Alireza

last: Minagar

first: J

last: Alexander

first: Ikuo

last: Tsunoda


title: Sex-specific gene regulation in malaria parasites by an AP2 Family Transcription Factor [ChIP-Seq]

overall_design:
Mice were infected with P. berghei expressing GFP-fused AP2-FG. Sulfadiazine was added to their drinking water in order to deplete asexual blood-stage parasites. Chromatins associated with GFP-tagged AP2-FG was IPed with anti-GFP antibody, and.target genes of this transcription factor were predicted.

Please note that the AP2-FG_ChIP_*.bw files have been added to the records on Oct 26, 2023.

first: izumi

last: kaneko

first: shiroh

last: iwanaga

first: tomomi

last: kato


title: TGFβ-induced fibroblast activation requires persistent and targeted HDAC-mediated gene repression

status: Public on Aug 29 2019

city: Rochester

first: Daniel

middle: Rothschild

last: OBrien

state: MN

address: 200 First St. SW

institute: The Mayo Clinic

summary: Tissue fibrosis is a chronic disease driven by persistent fibroblast activation that has recently been linked to epigenetic modifications.  Here, we screened a small library of epigenetic small-molecule modulators to identify compounds capable of inhibiting or reversing TGFβ-mediated fibroblast activation. We identified pracinostat, an HDAC inhibitor, as a potent attenuator of lung fibroblast activation and confirmed its efficacy in patient-derived fibroblasts isolated from fibrotic lung tissue. Mechanistically, we found that HDAC-dependent transcriptional repression was an early and essential event in TGFβ-mediated fibroblast activation. Treatment of lung fibroblasts with pracinostat broadly attenuated TGFβ-mediated epigenetic repression and promoted fibroblast quiescence. We confirmed a specific role for HDAC-dependent histone deacetylation in the promoter region of the anti-fibrotic gene PPARGC1A (PGC1α) in response to TGFβ stimulation. Finally, we identified HDAC7 as a key factor whose RNAi-mediated knockdown attenuates fibroblast activation without altering global histone acetylation. Together these results provide novel mechanistic insight into the essential role HDACs play in TGFβ-mediated fibroblast activation via targeted gene repression.

overall_design: Examination of genes which are regulated by TGFbeta and HDACs in cultured human lung fibroblasts.

first: Dakota

middle: L

last: Jones

first: Andrew

last: Haak

first: Nunzia

last: Caporarello

first: Kyoung

middle: M

last: Choi

first: Zhenqing

last: Ye

first: Huihuang

last: Yan

first: Xaralabos

last: Varelas

first: Tamas

last: Ordog

first: Giovanni

last: Ligresti

last: Tschumperlin


title: Bone marrow microenvironment mediated drug resistance in Acute promyelocytic leukemia

status: Public on Jan 10 2020

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

address: 259, Apoorva 4th cross,80 feet Road,RMV 2ND STAGE

country: India

institute: Genotypic Technology

summary: About 5-10% newly diagnosed and about 20-30% of relapsed acute promyelocytic leukemia (APL) patients will have disease recurrence after receiving currently accepted standards of care. While there are reports of micro-environment mediated drug resistance (EM-DR) in AML, there is no data on the effect of malignant promyelocyte and stromal interaction on Arsenic trioxide (ATO) induced apoptosis. There are limited study available on the effect of leukemic cell interaction on stromal cells. We undertook a preliminary study to evaluate the changes induced by leukemic cells on stromal cells. In a gene expression profiling comparing HS-5 cells in co-culture with NB4 cells alone, 8456 genes were differentially regulated. On a preliminary analysis, we observed an up-regulation of various pathways such as adhesion, Cytokines, Wnt signalling  in the stromal cells.

overall_design: The HS-5 cells were co-cultured with NB4 cells for 48 hours and the stromal cells were taken out after washing with PBS, characterized by flow cytometry to obstain a purity of more than 95% and subjected to RNA isolation. Similarly HS-5 cells alone were alone used as controls

first: Vikram

last: Mathews

first: Saravanan

last: Ganesan

first: Hamenth

last: Kumar Palani


title: Genome-wide map of ETS2 binding in gastrula stage Xenopus.laevis embryos

status: Public on Mar 22 2019

city: Berkeley

first: Richard

last: Harland

state: CA

address: Life Sciences Addition #3200

institute: University of California, Berkeley

summary: We examined the location of ETS2 biding in gastrula stage Xenopus embryos to identify direct transcriptional targets of the FGF signaling pathway.

overall_design: Examination of tripple-FLAG tagged ETS2 binding in whole Xenopus embryos

first: Rachel

last: Kjolby


title: Single-Cell Transcriptomes of the Regenerating Intestine Reveal a Revival Stem Cell [part 2]

status: Public on Feb 28 2019

city: Toronto

first: Bibaswan

last: Ghoshal

address: 600 University Avenue

institute: Lunenfeld Tanenbaum Research Institute

summary: The weekly turnover of the intestinal epithelium is driven by multipotent, Lgr5+, crypt base columnar cells (CBCs). In response to injury, however, Lgr5+ cells are lost but then re-emerge and are required for successful recovery. How these resurgent Lgr5+ stem cells arise is unclear. We transcriptionally profiled single cells from regenerating intestinal epithelia and identified a unique cell type we term the revival stem cell (rSC). rSCs are mutually exclusive to CBCs and are distinguished by elevated expression of cell survival and DNA repair genes. In homeostasis, rSCs are extremely rare, but nevertheless give rise to all the major cell types of the intestine including crypt-villus axes. After damage rSCs display a 20-fold, Yap-dependent, transient expansion, reconstitute the Lgr5+ CBC compartment and are required to regenerate a functional intestine. These studies define a unique stem cell phenotype that is mobilized by damage to reconstitute the intestinal epithelium.

overall_design: Examination of regenerating mouse intestinal epithelium.

first: Arshad

last: Ayyaz

first: Sandeep

last: Kumar

first: Bruno

last: Sangiorgi

first: Jessica

last: Gosio

first: Shaida

last: Ouladan

first: Mardi

last: Fink

first: Seda

last: Barutcu

last: Trcka

first: Jess

last: Shen

first: Kin

last: Chan

first: Jeffrey

last: Wrana

first: Alex

last: Gregorieff


title: Single-Cell Transcriptomes of the Regenerating Intestine Reveal a Revival Stem Cell


title: CDK9 knock-out Xenopus tropicalis

status: Public on Feb 02 2019

city: Nijmegen

first: Saartje

last: Hontelez

address: Geert Grooteplein 28

department: Molecular developmental biology

institute: Radboud University

summary: To study the role of CDK9 in RNAPII pausing

overall_design: Knock-down of CDK9 by injection of CDK9.S morpholino

first: GertJan

middle: C

last: Veenstra

first: Marta

last: Marin-Barba

first: Grant

middle: N

last: Wheeler

first: Ines

last: Desanlis


title: Preparing for the first breath at single cell level [whole lung time course]

status: Public on Jan 06 2019

city: Cincinnati

first: Yan

last: Xu

address: 3333 Burnet Ave

institute: Cincinnati Children's Hospital Medical Center

summary: The respiratory system undergoes remarkable structural, biochemical, and functional changes necessary for adaptation to air breathing at birth. To identify dynamic changes in gene expression in the diverse pulmonary cells at birth, we performed Drop-seq based massive parallel single-cell RNA sequencing. An iterative cell type identification strategy was used to unbiasedly identify the heterogeneity of murine pulmonary cell types on postnatal day 1. Distinct populations of epithelial, endothelial, mesenchymal, and immune cells were identified, each containing distinct subpopulations. Cell type predictions and signature genes identified using Drop-seq were cross-validated using an independent single cell isolation platform. Temporal changes in RNA expression patterns were compared before and after birth to identify signaling pathways selectively activated in specific pulmonary cell types, demonstrating activation of UPR signaling during perinatal adaptation of the lung. Present data provide the first single cell view of the adaptation to air breathing after birth. All data from the present study are freely accessed at https://research.cchmc.org/pbge/lunggens/SCLAB.html.

overall_design: Embryos and mice for this study were collected from timed pregnant mice. Whole lungs were surgically dissected at embryonic (E) days 16.5, 18.5 and postnatal days (PND) 1, 3, 7, 14, and 28

first: Y

first: J

last: Whitsett

first: S

last: Potter

first: M

last: Guo

last: Du


title: Preparing for the first breath at single cell level [single cell Drop-seq]

overall_design: Left and right lobes of PND1 mouse lungs were rapidly dissected in ice-cold PBS. Cell concentration was examined with a hemocytometer and adjusted to around 100 cells per microliter for Drop-seq.


title: Preparing for the first breath at single cell level [single cell Fluidigm C1]

overall_design: Left and right lobes of PND1 mouse lungs were rapidly dissected in ice-cold PBS. Cell concentration was examined with a hemocytometer and adjusted to around 300 cells per microliter for Fluidigm C1.


title: Preparing for the first breath at single cell level


title: Single-Cell Transcriptomes of the Regenerating Intestine Reveal a Revival Stem Cell [part 1]

first: Bibaswan

last: Ghoshal

summary: The weekly turnover of the intestinal epithelium is driven by multipotent, Lgr5+, crypt base columnar cells (CBCs). In response to injury, however, Lgr5+ cells are lost but then re-emerge and are required for successful recovery. How these resurgent Lgr5+ stem cells arise is unclear. We transcriptionally profiled single cells from regenerating intestinal epithelia and identified a unique cell type we term the revival stem cell (rSC). rSCs are mutually exclusive to CBCs and are distinguished by elevated expression of cell survival and DNA repair genes.  In homeostasis, rSCs are extremely rare, but nevertheless give rise to all the major cell types of the intestine including crypt-villus axes. After damage rSCs display a 20-fold, Yap-dependent, transient expansion, reconstitute the Lgr5+ CBC compartment and are required to regenerate a functional intestine. These studies define a unique stem cell phenotype that is mobilized by damage to reconstitute the intestinal epithelium.

overall_design: Examination of regenerating mouse intestinal epithelium

first: Arshad

last: Ayyaz

first: Sandeep

last: Kumar

first: Bruno

last: Sangiorgi

first: Daniel


title: Impact of shRNA-mediated KLF4 down-modulation on the transcriptome profile of human keratinocyte precursor cells

status: Public on Jan 01 2019

city: EVRY

first: Nicolas

last: Fortunel

address: 2 rue Gaston Cremieux

department: IRCM/SCSR

country: France

institute: CEA

summary: Characterization at the global transcriptome level of the gene networks ensuring the regulation of the immature status of cutaneous stem- and precursor-cells is a necessary step to further understand the concept of ‘stemness’ in this tissue. Moreover, considering possible clinical applications, the search for molecular targets to control stem cell characteristics and regenerative capacity is a necessary step to improve therapeutic approaches. Cutaneous cell therapy is concerned by this objective, as skin graft bioengineering requires a phase of ex vivo expansion of keratinocytes from donors, during which the preservation of a sufficient stem cell pool is critical for graft take and long-term skin regeneration. We have investigated the role of transcription factor KLF4 in native keratinocyte precursors from adult human skin. A stable lentiviral-based shRNA-mediated KLF4 knock‑down (KD) approach was developed and used to study the properties of KLF4-deficient [KLF4KD] versus control [KLF4WT] native keratinocyte precursors. Using long-term cultures and clonal assays, we found that decreased KLF4 expression increased keratinocyte precursor immaturity and clonogenic potential, thus promoting self-renewal. Importantly, [KLF4KD] keratinocyte precursors exhibited an improved grafting capacity in an in vivo skin xenograft model and in serial grafting.  To analyze the biological impact of KLF4 knock‑down at the molecular level, comparative transcriptome profiling of [KLF4WT] and [KLF4KD] cells was performed using next-generation RNA sequencing (RNA-seq). This set of data provides a material that permits the dissection of genetic networks modulated by KLF4 in human keratinocyte precursor cells, and controlling their immature status and epidermis regeneration capacity.

overall_design: The study is based on the comparative RNA-seq analysis of human keratinocyte precursor cells corresponding to 3 cellular contexts: 1) non-transduced wild-type (WT) cells, [KLF4WT]; 2) cells transduced with a control lentiviral vector driving the expression of the reporter gene GFP, [KLF4WT]; 3) cells transduced with a lentiviral vector driving the expression of GFP and an anti-KLF4 shRNA, [KLF4KD]. For each cellular context 3 biological replicates were conducted (Bio rep), each including 3 technical replicates (Tech rep).

middle: O

first: Loubna

last: Chadli

first: Jean-François

last: Deleuze

first: Michèle

middle: T

last: Martin


title: Coupling of microRNA-directed phasiRNA generation with alternative splicing in small RNA-mediated gene silencing

status: Public on Dec 20 2018

city: GUANGZHOU

first: Wuqiang

last: Ma

state: GUANGDONG

address: 483 WUSHAN ROAD , TIANHE DISTRICT

department: College of Horticulture

institute: South China Agricultural University

type: Non-coding RNA profiling by high throughput sequencing

summary:
Purpose:We aimed to characterize genome-widely the miRNA population  and phasiRNA-generating genes/loci in litchi (Litchi chinensis).
Multiple high throughput sequencing strategies, including sRNA sequencing, parallel analysis of RNA ends (PARE) sequencing, and strand-specific RNA-seq, were applied in combination with thorough bioinformatics analyses using a variety of computational methods.

overall_design: 6 tissues sRNA libraries were builtin lithi, including: fruit pedicel, fruitlet, leaf, root, stem shoot and flower; 4 parallel analysis of RNA ends (PARE) libraries were built, including mixed (equal amounts of RNA from all tissues), pedicel, flower and fruitlet;Two strand-specific RNA-seq (ssRNA-seq) libraries were generated for the flower tissues

first: Rui

last: Xia

first: Jianguo

last: Li

first: Blake

last: Meyers

first: Chenjie

last: Chen

first: Yuanlong

last: Liu