title: Single Cell Sequencing Analysis for Wolfram Syndrome (WS4) Unedited and Corrected Stem Cell-Derived Beta Cells

status: Public on Apr 22 2020

city: Saint Louis

first: Kristina

last: Maxwell

address: 660 S. Euclid Ave. Campus Box 8127

department: Medicine

institute: WASHINGTON UNIVERSITY IN ST. LOUIS

summary: We revealed transcriptome differences between corrected and unedited (diseased) Wolfram Syndrome patient stem cell-derived beta cells. We also identified several endocrine, pancreatic, and non-pancreatic cell types in the samples populations.

overall_design: Single cell RNA sequencing of human Wolfram Syndrome patient stem cell-derived beta cells and other stage 6 cells derived from differentiation protocol. The cells were differentiated from both diseased (unedited) and CRISRP/Cas9-corrected induced pluripotent stem cells.


title: Transcriptomic profile of Wildcat mycobacteriophage during lytic growth.

status: Public on Apr 23 2020

city: Pittsburgh

first: Graham

middle: F.

last: Hatfull

state: PA

address: 4249 Fifth Ave

department: Biological Sciences

country: USA

institute: University of Pittsburgh

type: Expression profiling by high throughput sequencing

summary: The goal of this sequencing project was to measure transcription levels of Wildcat mycobacteriophage during lytic growth.

overall_design: Total RNA was isolated from cultures grown in log phase, depleted of rRNA and prepared for sequencing using a strand-specific library kit after 30min and 150min of infection by phage Wildcat

middle: F

first: Ching-Chung

last: Ko

first: Rebecca

middle: A

last: Garlena


title: p53 activation induces targetable dependence on FLIPL

status: Public on Apr 25 2020

city: Belfast

first: Simon

middle: S

last: McDade

address: 97 Lisburn Road

department: CCRCB

country: United Kingdom

institute: Queen's University Belfast

summary: A better understanding of how p53 differentially activates cell cycle arrest or cell death is important to maximize benefits of therapeutic strategies dependant by wild-type p53. Here, we report that activation of pro-apoptotic p53 transcriptional targets in colorectal cancer cells imposes a critical, targetable dependence on the long splice form of the caspase-8 regulator FLIP (FLIPL) for survival. Upon Nutlin-3A induced stabilisation p53 directly upregulates FLIPL expression in a manner dependent on Class-I HDAC activity. Preventing FLIPL upregulation with the clinically relevant Class-I selective inhibitor Entinostat promotes apoptosis in response to Nutlin-3A , which predominantly induces growth arrest despite upregulating a range of pro-apoptotic target genes. Cell death in response to Nutlin-3A in FLIPL-depleted cells is mediated through two of p53's canonical transcriptional targets TRAIL-R2 and BAX and is caspase-8-dependent. This work uncovers novel, clinically relevant biology that identifies FLIPL as a key target for overcoming resistance to p53-activating agents.

overall_design: mRNA-seq analysis of treatment of HCT116 colorectal cancer cell line models isogenic for p53 treated with Nutlin-3A or Entinostat or their combination

first: Daniel

middle: B

last: Longley


title: Shifts in Ribosome Engagement Impact Key Gene Sets in Neurodevelopment and Rett Syndrome Neurons

status: Public on Apr 28 2020

city: Toronto

first: Marat

last: Mufteev

address: 686 Bay St.

department: Molecular Genetics

country: Canada

institute: University of Toronto

summary: Regulation of translationduring early human development is poorly understood anditsdysregulation is associated with disease. To discover shifts in mRNA ribosomal engagement (RE) that occur during human neurodevelopment and disease, we used parallel TRAPSeq and RNASeq on control and Rett syndrome (RTT) human induced pluripotent stem cells,neural progenitor cells and cortical neurons. We found 30% of transcribed genes were translationally regulatedincluding key gene sets (neurodevelopment, transcription and translation factors, glycolysis). Neurons more efficiently translated global mRNAs,had longer 3`UTRs and RE correlated with RNA-binding protein motif composition.In contrast, RTT neurons had reduced global translation,compromised mTOR signalingand 2100 genes were translationally dysregulated. NEDD4L E3-ubiquitin ligasewas most translationally impaired, and its protein targets accumulatedin RTT neurons. Our findings reveal a dynamic translatome in neurodevelopment, show that MECP2 regulatestranslationandubiquitin enzymes in neurons, and provide novel insight into altered proteostasis that may have therapeutic implications for RTT.

overall_design: Human WT iPSCs, iPSC-derived NPCs and Neurons were subjected to TRAP-seq and RNA-seq to characterize changes in ribosome engagement during human neurodevelopment. NPCs and Neurons derived from an isogenic iPSC line containing a deletion of the MECP2 gene were also included to study changes ribosome engagement in Rett syndrome.

first: Deivid

middle: C

last: Rodrigues

first: Benjamin

middle: J

last: Blencowe

first: James

last: Ellis


title: MYC controls Epstein Barr virus lytic switch

status: Public on Apr 20 2020

city: Boston

first: Rui

last: Guo

state: Massachusetts

address: 150 Harrison Ave.

department: School of Medicine

institute: Tufts University

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

overall_design: Refer to individual Series


title: DRB-PRO-Seq for measuring Pol II transcriptional elongation rate alterations upon inhibition of analog sensitive CDK12 and/or CDK13

status: Public on Apr 29 2020

city: Melbourne

first: Zheng

last: Fan

state: Victoria

address: 305 Grattan Street

country: Australia

institute: Peter MacCallum Cancer Centre

summary: We performed PRO-Seq to determine Pol II elongation rates  by measruing the distance of Pol II travels during 25 minutes after Pol II being relased from DRB induced pausing. We allowed Pol II to release in the presence of 1-NM-PP1 or DMSO after DRB being wahsed out in order to assess the effects of CDK12 and/or CDK13 inhibtion on transcriptional elongation rates.

overall_design: Cells were treated with 100μM DRB for 4 hours, then DRB was washed out. Washing out of DRB  allowed Pol II to elongate, at the meantime, cells were treated with 25 minutes with 1-NM-PP1 or DMSO.  Cells were harvested after 25 minutes release, and we measured the distance that Pol II travelled during 25 minutes by PRO-Seq in order to calculate elongation rates.

first: Jennifer

middle: R

last: Devlin

first: Stephin

last: Vervoort

first: Ricky

middle: W

last: Johnstone


title: Transcriptome map of nascent RNA production alterations upon CDK9 and analog senstiveCDK12 and/or CDK13 inhibition (TT-Seq)

summary: We performed TT-Seq on MV4;11  WT, CDK12AS/NULL, CDK13AS/AS, #1CDK12AS/NULL;CDK13AS/NULL and #2CDK12AS/NULL;CDK13AS/AS MV4;11 clones treated with 1-NM-PP1 or vehicle for 25 mintues to identify the effect of CDK12 and/or CDK13 on nasenct RNA production.

sample_organism:
Drosophila melanogaster
Homo sapiens

platform_organism:
Drosophila melanogaster
Homo sapiens

overall_design: Analog senstive MV4;11 cells were treated with DMSO/1-NM-PP-1 for 20 minutes and then 4sU was added to label nascent RNA for 5 minunts. Nasenct RNA were isolated and sent for sequencing


title: Genome-wide map of Pol II occupancy alteration on chromatin upon CDK12 and CDK13 inhibition (ChIP-Seq)

type: Genome binding/occupancy profiling by high throughput sequencing

summary: We performed ChIP-Seq on MV4;11 cells after 6 hours treatment of DMSO, 100nM and 200nM THZ531 to determine the location of Pol II with phosphorylated Ser2 occupancy

overall_design: MV4;11 cells,  DMSO, 100nM, 200nM THZ531 treatment for 6 hours, then Pol II bound chromatin were isolated from soniacated nuclear extracts using antibody angaist RNA polymerase II (phospho CTD Ser-2)


title: Disseminated melanoma cells transdifferentiate into endothelial cells in intravascular niches at metastatic sites (Li et al. 2020, Cell Reports)

status: Public on Apr 15 2020

city: Leuven

first: Florian

last: Rambow

address: Herestraat 49 box 912

country: Belgium

institute: VIB

summary: Here, we combined lineage tracing in a newly developed spontaneous metastatic mouse model of melanoma, advanced imaging and single-cell RNA-sequencing approaches to search for (patho) physiologically-relevant melanoma cellular states. We identified a population of reporter-positive melanoma cells located in intravascular niches of various metastatic organs. These intravascular metastatic cells were dormant, negative for characteristic melanoma markers and acquired endothelial cell markers.

overall_design: We RNA-sequenced (3' v2 10x Genomics) about 6.5k methanol fixed single cells of a melanoma infiltrated lymph node using the murine Tyr::NRASQ61K;Ink4a−/− melanoma model.


title: DRB-PRO-Seq for measuring Pol II transcriptional elongation rate alteration up on CDK12 and CDK13 inhibition by THZ531

summary: We performed PRO-Seq to measure the Pol II elongation rate  by measruing the distance of Pol II travels at viarous time points after relased from DRB induced pausing. We compared DMSO/DRB or THZ531/DRB co-treated sample to assess the effect of CDK12 and CDK13 inhibtion by THZ531 on transcriptional elongation rate.

overall_design: Cells were treated a co-treatment cosistent of 100μM DRB and DMSO/100nM THZ531/200nM THZ531 for 4 hours, then DRB was washed out to allow Pol II to elongate for 12.5 mintues, 25 minutes and 45 minutes. Before wash-out, 0 minute time point were also haversted As THZ531 covelantly binds to CDK12 and CDK13, we can assess the effect of CDK12 and CDK13 inhibtion on elongation after DRB being washed out. Control samples were treated with DMSO/THZ531 100nM and 200nM for 4 hours but no DRB.


title: Transcriptome analysis of P3HR-1 cells expressing control, smc1a, supt16h, med12, or tada2b sgRNAs and Akata EBV+ cells expressing control or myc sgRNAs

summary: To gain insights into how EBV latency is maintained, we performed a human genome-wide CRISPR screen in latently EBV-infected Burkitt lymphoma B-cells. Our analyses identified a network of host factors that repress EBV lytic reactivation, centered on the transcription factor MYC and including cohesins, FACT, STAGA and Mediator. RNAseq was used to identify host and viral transcriptome changes in P3HR-1 Burkitt lymphoma cells expressing control, smc1a, supt16h, med12, or tada2b sgRNAs. RNAseq was used to identify host and viral transcriptome changes in Akata EBV+ burkitt lymphoma cells expressing control or myc sgRNAs.

overall_design: Total RNA extracted from P3HR-1 cells expressing control, smc1a, supt16h, med12, or tada2b sgRNAs was used for RNAseq analysis.Total RNA extracted from Akata EBV+ cells expressing control, or myc sgRNAs was used for RNAseq analysis.

middle: E

last: Gewurz

first: Jiang

last: Chang


title: Small RNAs in monocots

status: Public on Apr 17 2020

city: St. Louis

first: Blake

middle: C.

last: Meyers

state: MO

address: 975 N Warson Road

institute: Donald Danforth Plant Science Center

type: Non-coding RNA profiling by high throughput sequencing

summary: In monocots other than the cereals maize and rice, the repertoire and diversity of microRNAs (miRNAs) and the populations of phased, secondary, small interfering RNAs (phasiRNAs) are poorly characterized. To remedy this, we sequenced small RNAs (sRNAs) from vegetative and dissected inflorescence tissue in 28 phylogenetically diverse monocots and from several early-diverging angiosperm lineages, as well as publicly available data from 10 additional monocot species. We annotated miRNAs, siRNAs and phasiRNAs across the monocot phylogeny, identifying miRNAs apparently lost or gained in the grasses relative to other monocot families, as well as a number of tRNA fragments misannotated as miRNAs. Using our miRNA database cleaned of these misannotations, we identified conservation at the 8th, 9th, 19th and 3’ end positions that we hypothesize are signatures of selection for processing, targeting, or Argonaute sorting. We show that 21-nt reproductive phasiRNAs are far more numerous in grass genomes than other monocots. Based on sequenced monocot genomes and transcriptomes, DICER-LIKE 5 (DCL5), important to 24-nt phasiRNA biogenesis, likely originated via gene duplication before the diversification of the grasses. This curated database of phylogenetically diverse monocot miRNAs, siRNAs, and phasiRNAs is the largest collection to date, and should facilitate continued exploration of small RNA diversification in flowering plants.

sample_organism:
Colocasia esculenta
Acorus calamus
Lemna gibba
Oryza glaberrima
Setaria viridis
Sorghum bicolor
Zea mays
Cyperus alternifolius
Ananas comosus
Canna indica
Cocos nucifera
Zostera marina
Anomochloa marantoidea
Phyllostachys edulis
Streptochaeta angustifolia
Liriope muscari
Phoenix dactylifera
Kniphofia uvaria
Elaeis guineensis
Phalaenopsis equestris
Hemerocallis lilioasphodelus
Sagittaria montevidensis
Pharus parvifolius
Nymphaea colorata
Echinodorus uruguayensis
Musa acuminata var. zebrina
Musa ABB Group
Musa acuminata AAA Group
Freycinetia cumingiana
Tradescantia fluminensis
Raddia brasiliensis
Goudaea ospinae
Prosthechea radiata

overall_design: Small RNA (sRNA) sequencing for 28 phylogenetically diverse monocots

first: Sandra

last: Mathioni


title: Quant-seq analysis to determine the effects of CDK12 and CDK13 inhibition by THZ531 in alternative polyadenylation

summary: We performed 3' Quant-seq on MV4;11 cells after 6 hours treatment of THZ531 to determine whether CDK12 and CDK13 inhibtion cause alternative polyadenlation

overall_design: MV4;11 cells with DMSO, 100nM, 200nM THZ531 treatment for 6 hours, then RNA was extracted.


title: Ileum Transcriptomic Profiling in Inflammatory Bowel Disease

city: Atlanta

first: Angela

last: Mo

state: GA

address: 950 Atlantic Drive

department: School of Biological Sciences

institute: Georgia Institute of Technology

summary: We report ileum gene expression of 37 controls and 158 patients with either Crohn's disease (n=112), ulcerative colitis (n=44), unclassifed IBD (1), or IBS (1). We contrast gene expression in African American (n=104) versus white (n=25) CD and UC patients.

overall_design: Biopsies of the ileum were obtained from IBD patients. Transcriptome profiling was performed with RNA-Seq.

first: Dalia

last: Arafat

first: Anne

last: Dodd

first: Jarod

last: Prince

first: Subra

last: Kugathasan

first: Greg

last: Gibson


title: Expression data from human Th and Treg induced myeloid cells

status: Public on Apr 07 2020

city: Palo Alto

first: Xiangyue

last: Zhang

address: 3373 Hillview ave

department: Pathology

institute: Stanford University

summary:
Human Th, Treg and Th and Treg together can induce monocytes differentiate into different myeloid cell population. We were trying to compare the transcriptome of these populations.
We used microarrays to detail transcriptome of Th and Treg induced regulatory DCs.

overall_design:
RNA were extracted and subjeced to microarray assay.
different conditions

first: Xianyue

first: Edgar

last: Engleman


title: Transcriptional profiling of Pseudomonas aeruginosa and Candida albicans grown in mono-cultures and co-culture.

status: Public on Apr 14 2020

city: Farmington

first: Mark

last: Adams

state: CT

address: 10 Discovery Drive

institute: The Jackson Laboratory

summary: Genome-wide transcriptional profiles of Pseduomonas aerguinosa and Candida albicans after growth for 24 hours in mixed species colony biofilms.

sample_organism:
Pseudomonas aeruginosa
Candida albicans

platform_organism:
Pseudomonas aeruginosa
Candida albicans

first: Georgia

last: Doing

first: Deborah

last: Hogan


title: The landscape of RNA polymerase II-associated chromatin interactions in prostate cancer

status: Public on Apr 27 2020

city: Dallas

first: Ram

last: Mani

state: Texas

address: 5323 Harry Hines Blvd NB6.444

institute: UT Southwestern Medical Center

summary: Three dimensional genome maps of the transcriptional machinery in prostate cancer cells.

overall_design: Genome wide mapping by Chromatin Interaction Analysis with Paired- End tag sequencing (ChIA-PET).


summary: Genome wide occupany of CTCF, H3K27ac and AR

overall_design: Genome binding/occupancy profiling by high throughput sequencing


title: IRF5 promotes intestinal inflammation by guiding monocyte differentiation towards pathogenic CD11c+ macrophage phenotype [small_bulk_rnaseq]

status: Public on Apr 01 2020

city: Oxford

first: Stephen

last: Sansom

state: Oxfordshire

address: Roosevelt Drive

department: NDORMS

institute: Kennedy Institute of Rheumatology

summary: Mononuclear phagocytes (MNPs) play a key role in maintaining intestinal homeostasis but also in triggering immunopathology in response to acute microbial stimulation, which induces the recruitment of masses of Ly6Chi monocytes to the gut. The regulators that control monocyte tissue adaptation in the gut remain poorly understood. Interferon Regulatory Factor 5 (IRF5) is a transcription factor previously shown to play a key role in maintaining the inflammatory phenotype of macrophages Here we investigate the impact of IRF5 on the MNP system and physiology of the gut at homeostasis and during inflammation. We demonstrate that IRF5 deficiency has a limited impact on colon physiology at steady state, but ameliorates immunopathology during Helicobacter hepaticus induced colitis. Inhibition of IRF5 activity in MNPs phenocopies global IRF5 deficiency. Using a combination of bone marrow chimera and single cell RNA-sequencing approaches we compare the differentiation trajectories of wild type and IRF5 deficient monocytes in a shared inflammatory environment and demonstrate that IRF5 stipulates a choice in monocyte differentiation towards macrophages. Specifically, IRF5 promotes the generation of pathogenic CD11c+ macrophages and controls the production of inflammatory mediators by these cells. Thus, we identify IRF5 as a key transcriptional controller of pathogenic monocyte differentiation in the gut.

overall_design: Mixed bone marrow chimeras (mice) were constructed using wildtype (CD45.1+ve) and Irf5 knockout (CD45.2+ve) cells that were also heterozygous for knock-in of GFP to the CX3CR1 locus. These animals were subject to Helicobacter hepaticus + anti-IL10R induced colitis. Three weeks after the day of infection mononuclear phagocytes were FACs isolated from the inflamed lamina propria and subjected to small-bulk RNA-sequencing (n=100 cells per sample; Smart-seq2 protocol).

first: Alastair

middle: L

last: Corbin

first: Maria

last: Gomez-Vazquez

first: Moustafa

last: Attar

first: Irina

last: Udalova

middle: N


title: Gene expression profiles of A549 lung cancer cells with citreoviridin treatment

city: Taipei

first: Chia-Lang

last: Hsu

address: No. 7, Zhongshan S. Rd.

department: Department of Medical Research

country: Taiwan

institute: National Taiwan University Hospital

summary: Citreoviridin can suppress lung cancer cell growth by inhibiting the activity of ectopic ATP synthase, but has limited effect on normal cells. However, the mechanism of citreoviridin triggering dynamic molecular responses in cancer cells remains unclear. Here, we performed gene expression profiling to elucidate the dynamic changes after citreoviridin treatment in cells.

overall_design: The RNA of lung cancer cell lines A549 with the treatment of citreoviridin and DMSO were isolated. Three biological replicates of each condition were analyzed on Agilent microarray.

first: H

last: Juan


title: Immunological subtypes of depression: insights from monocyte gene expression III

status: Public on Mar 27 2020

city: Rotterdam

first: Hemmo

last: Drexhage

address: Dr Molewaterplein 40

department: Immunology

country: Netherlands

institute: Erasmus MC

summary:
32 genes of a previously established inflammation-related gene signature  were assessed in 197 patients with MDD and 151 controls collected during the EU-MOODINFLAME project. Monocyte gene expression data were related to age, gender, BMI, depression severity, Childhood Adversity (CA), and Suicide Risk (SR)
data studycenter 3

overall_design: qPCR gene expression profiling. Details of patient selection, recording of patient data, laboratory methods can be found in Schiweck C. et al,

first: J

middle: M

last: Wijkhuijs


title: Global gene expression of Oscar Knock-out (KO) mice with Wild Type (WT) mice.

status: Public on Mar 26 2020

city: Busan

first: Haeseung

last: Lee

address: 63 Beon-gil 2, Busandaehag-ro, Geumjeong-gu

department: College of Pharmacy

country: South Korea

institute: Pusan National University

summary:
Purpose: RNA sequencing (RNA-Seq) analyses of articular cartilage obtained after DMM surgery in Oscar-/- and WT mice.  The purpose of this experiment was to demonstrate how the deficiency of Oscar gene affects downstream signal transduction in articular cartilage.
Methods: Articular cartilage mRNA profiles of 10-weeks-old wild-type (WT) and Oscar knockout (Oscar−/−) mice were performed for the destabilization of the medial meniscus (DMM) and each cartilage tissue sample was harvested from two time-points (2- and 4-weeks after surgery). Sequencing libraries were prepared according to the manufacturer’s instructions (TruSeq Stranded mRNA Library Prep Kit; Illumina, San Diego, CA, USA). Paired-end sequencing of 101-mer read length was performed using a HISEQ 2500 sequencing system (Illumina). The sequencing quality of raw FASTQ files was assessed using FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/). Low-quality reads and adapter sequences in reads were eliminated using BBDuk (http://jgi.doe.gov/data-and-tools/bb-tools/).
Results: Usinig RNA-Seq data in articular cartilage tissues from WT and Oscar–/– mice subjected to sham or DMM surgery and each cartilage sample obtained from 2- and 4-week time points after surgery, respectively. And we found that significantly enriched pathways in the 1270 common genes.
Conclusions: Our study represents the Oscar gene deficiency analysis of articular cartilage transcriptomes, with biologic replicates, generated by RNA-seq technology. The optimized data analysis workflows reported here should provide a framework for comparative investigations of expression profiles. Our results show that NGS offers a comprehensive and more accurate quantitative and qualitative evaluation of mRNA content within a cell or tissue. We conclude that RNA-seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions.

overall_design: Articular cartilage mRNA profiles of 10-weeks old wild type (WT) and Oscar-/- mice were generated by RNA sequencing (each group, n=10) using Illumina hiseq2500.

first: Soo

middle: y


title: Transcriptome analysis of xenograft tumors treated with vehicle control or CBL0137

first: Rui

last: Guo

summary: RNAseq was used to identify host and viral transcriptome changes in xenograft tumors treated with DMSO or CBL0137. Mouse xenograft experiments were regulated by Institutional Animal Care & Use Committee (IACUC# 2017-0035) of Weill Cornell Medical Center(WCMC). Non-obese diabetic/severe combined immunodeficiency (NOD-SCID) mice were obtained from Jackson Laboratories. Six to eight-week-old male and female mice (10 male/18 female) were injected in the flank with 1 x 107 BL cells in PBS with Matrigel eleven days before the treatment. Once the mice developed tumors with the size greater than 300 mm^3, they were grouped randomly and injected with vehicle (5% dextrose), 10mg/kg, or 60mg/kg of CBL0137. One week later, mice were injected with second dose of vehicle or CBL0137. Mice were humanely sacrificed at set experimental timepoints or when tumors reached the institutional cutoff.  Tumors were harvested and snap frozen in liquid nitrogen for RNA, DNA, and sectioning for immunohistochemistry. RNAseq experiments were performed with tumor samples from 3 control and 3 60mg/kg CBL0137 treated mice.

overall_design: Total RNA extracted from 100mg of xenograft tumors with DMSO or CBL0137.

first: Benjamin

last: Gewurz

first: Jiang

last: Chang


title: Disentangling pro-mitotic signaling during cell cycle progression using time-resolved single-cell imaging

status: Public on Mar 21 2020

city: Berlin

first: Manuela

last: Benary

address: Chariteplatz 1

country: Germany

institute: Charité

summary: Cells rely on input from extracellular growth factors to control their proliferation during development and adult homeostasis. Such mitogenic inputs are transmitted through multiple signaling pathways that synergize to precisely regulate cell cycle entry and progression. While the architecture of these signaling networks has been characterized in molecular detail, their relative contribution especially at later cell cycle stages remain largely unexplored. By combining quantitative time-resolved measurements of fluorescent reporters in untransformed human cells with targeted pharmacological inhibitors and statistical analysis, we quantified EGF-induced signal processing in individual cells over time and decomposed the dynamic contribution of downstream pathways. We define signaling features that encode information about extracellular ligand concentrations and critical time windows for inducing cell cycle transitions. We show that both ERK and PI3K activity is necessary for initial cell cycle entry, while only PI3K affect the duration of S-phase at later stages of mitogenic signaling.

overall_design: MCF10A cells stimulated cells with EGF and inhibited MEK and PI3K activity 15 h later. We then employed single cell RNA sequencing (scRNA-seq) to determine expression profiles of individual cells 20 h and 30 h after addition of the growth factor. The different conditions were multiplexed in one sample. Each sample resembles one biological replicate.

first: Stefan

last: Bohn

first: Nils

last: Blüthgen

first: Alexander

last: Löwer


title: Epigenetic footprint of hepatoblastoma defines a novel integrative molecular classification with clinical implications [CytoScanHD_Array]

status: Public on Mar 23 2020

city: Badalona

first: Carolina

last: Armengol

state: Barcelona

address: Crta Can Ruti; cami de les escoles, S/N

country: Spain

institute: Germans Trias i Pujol Health Research Institute

summary: Hepatoblastoma (HB) is the predominant pediatric liver cancer with limited therapeutic options for patients with aggressive tumors. Nevertheless, it is a rare disease. Here, we performed a high-throughput molecular study of 32 patients with HB and major findings were validated in additional 80 cases. We unveiled an epigenetic footprint including downregulation of RNA-editing, hyperediting of the tumor suppressor BLCAP,14q32 DLK1-DIO3 locus overexpression, DNA hypomethylation and CpG island hypermethylation. Based on these findings, we defined an integrative molecular classification of HB that improve current clinical stratification, and identified CHKA as a therapeutic target for the poor prognostic subclass.

overall_design: 34 samples from 32 patients with Hepatoblastoma

first: Juan

last: Carrillo-Reixach

first: Laura

last: Torrens

first: Marina

last: Simon-Coma

last: Royo

first: Montserrat

last: Domingo-Sàbat

first: Jordi

last: Abril-Fornaguera

first: Nicholas

last: Akers

first: Margarita

last: Sala

first: Sonia

last: Ragull

first: Magdalena

last: Arnal

first: Nuria

last: Villalmanzo

first: Stefano

last: Cairo

first: Alberto

last: Villanueva

first: Roland

last: Kappler

first: Marta

last: Garrido

last: Guerra

first: Constantino

last: Sábado

first: Gabriela

last: Guillén

first: Mar

last: Mallo

first: David

last: Piñeyro

first: María

last: Vázquez-Vitali

first: Olga

last: Kuchuk

first: María Elena

last: Mateos

first: Gema

last: Ramirez

first: Manuel

last: López-Santamaría

first: Yasmina

last: Mozo

first: Aroa

last: Soriano

first: Michael

last: Grotzer

first: Sophie

last: Branchereau

first: Nagore

last: García de Andoin

first: Blanca

last: López-Ibor

first: Ricardo

last: López-Almaraz

first: José Antonio

last: Salinas

first: Bárbara

last: Torres

first: Francisco

last: Hernández

first: José Javier

last: Uriz

first: Monique

last: Fabre

first: Julià

last: Blanco

first: Claudia

last: Paris

first: Viera

last: Bajčiová

first: Geneviève

last: Laureys

first: Helena

last: Masnou

first: Ariadna

last: Clos

first: Cristina

last: Belendez

first: Catherine

last: Guettier

first: Lauro

last: Sumoy

first: Ramón


title: Epigenetic footprint of hepatoblastoma defines a novel integrative molecular classification with clinical implications [HTA-2_0]

first: Carolina

last: Armengol

overall_design: 52 samples profiled from 32 patients with Hepatoblastoma

first: Juan

last: Carrillo-Reixach

first: Laura

last: Torrens

first: Marina

last: Simon-Coma

last: Royo

first: Montserrat

last: Domingo-Sàbat

first: Jordi

last: Abril-Fornaguera

first: Nicholas

last: Akers

first: Margarita

last: Sala

first: Sonia

last: Ragull

first: Magdalena

last: Arnal

first: Núria

last: Villalmanzo

first: Stefano

last: Cairo

first: Alberto

last: Villanueva

first: Roland

last: Kappler

first: Marta

last: Garrido

last: Guerra

first: Constantino

last: Sábado

first: Gabriela

last: Guillén

first: Mar

last: Mallo

first: David

last: Piñeyro

first: María

last: Vázquez-Vitali

first: Olga

last: Kuchuk

first: María Elena

last: Mateos

first: Gema

last: Ramírez

first: Manuel

last: López-Santamaría

first: Yasmina

last: Mozo

first: Aroa

last: Soriano

first: Michael

last: Grotzer

first: Sophie

last: Branchereau

first: Nagore

last: García de Andoin

first: Blanca


title: Immunological subtypes of depression: insights from monocyte gene expression

first: Hemmo

last: Drexhage

summary:
32 genes of a previously established inflammation-related gene signature  were assessed in 197 patients with MDD and 151 controls collected during the EU-MOODINFLAME project. Monocyte gene expression data were related to age, gender, BMI, depression severity, Childhood Adversity (CA), and Suicide Risk (SR)
data studycenter 1

first: J

last: Wijkhuijs

first: H


title: Single-cell sequencing of PDGFRα-expressing cells in the adult mouse brain.

status: Public on Mar 17 2020

city: Charlottesville

middle: Michael

last: Johanson

state: VA

address: 200 Jeanette Lancaster Way

department: Department of Neuroscience

institute: UVa School of Medicine

summary: Oligodendrocyte progenitor cells (OPCs) are a mitotically active population of glia that comprise approximately 5% of the adult brain. OPCs maintain their proliferative capacity and ability to differentiate in oligodendrocytes throughout adulthood, but relatively few mature oligodendrocytes are produced following developmental myelination. Recent work has begun to demonstrate that OPCs likely perform multiple functions in both homeostasis and disease, and can significantly impact behavioral phenotypes such as food intake and depressive symptoms. However, the exact mechanisms through which OPCs might influence brain function remains unclear. In this work, we demonstrate that OPCs are transcriptionally diverse and separate into three distinct populations in the homeostatic brain. These three groups show distinct transcriptional signatures and enrichment of biological processes unique to individual OPC populations. We have validated these OPC populations using multiple methods, including multiplex RNA in situ hybridization and RNA flow cytometry. This study provides an important resource that profiles the transcriptome of adult OPCs and will provide a significant foundation for further investigation into novel OPC functions.

overall_design:
Reporter positive cells were isolated from the brains of PDGFRα-CreER mice and sent for single-cell sequencing. Resulting cell clusters were analyzed for heterogeniety within this population of cells

Sequencing performed at UVa Genome Analysis & Technology Core,
Office of Research Core Administration.
University of Virginia Health System,
P.O. Box 800741,
Charlottesville, VA 22908-0741

first: Rebecca

last: Beiter

first: Alban

last: Gaultier

first: Christopher

last: Overall


title: Epigenetic footprint of hepatoblastoma defines a novel integrative molecular classification with clinical implications

first: Carolina

last: Armengol

type: Methylation profiling by genome tiling array

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

overall_design: Refer to individual Series


title: Single cell transcriptome profiling of the human alcohol-dependent brain samples.

city: Austin

first: Gayatri

last: Tiwari

state: TX

address: 2500 Speedway

institute: University of Texas at Austin

summary: Over 16,000 nuclei were isolated from human postmartum brain frozen prefrontal cortex  samples of alcoholic and control individuals. Libraries were prepared with 10X Genomics platform and sequenced using NovaSeq 6000.

overall_design: Single nucleus RNA sequencing (snRNA-seq) from prefrontal cortex of 3 alcoholic and 4 control individuals.

first: Eric

last: Brenner

first: Yunlong

last: Liu

first: Amy

last: Brock

first: R

middle: D

last: Mayfield


title: The role of IL-33 on red pulp macrophage (RPM) development

status: Public on Mar 11 2020

city: Cambridge

first: Davide

last: Chiarugi

address: Box 289, Addenbrooke’s Hospital

department: Metabolic Research Laboratories

institute: WT-MRC Institute of Metabolic Science

summary: This study investigated the effects of IL1RL1 deficiency on the devlopment of red pulp macrophages (RPM)

overall_design: Splenocytes were sorted from WT (male Balb/c 10 weeks old) and IL1RL1-/- (male Balb/c background, 10 weeks old) mice; monocytes (Ly6Glo CD11bhi F4/80-) and pre-RPM (Ly6Glo CD11bhi F4/80lo ) and RPM (Ly6Glo CD11blo/- F4/80hi), n=4/group.  Sorted cells were centrifuged and resuspended for RNAseq or ATACseq as described (Lu et al, Immunity 2020) Each sample originates from a single mouse.

first: Gemma

last: Basatemur

first: Ziad

last: Mallat


title: Loss of the nuclear Wnt pathway effector TCF7L2 promotes migration and invasion of human colorectal cancer cells

status: Public on Mar 20 2020

city: Freiburg

first: Elham

last: Bavafaye Haghighi

address: Breisacherstr. 153

department: Institut für Medizinische Bioinformatik und Systemmedizin

institute: University Hospital of Freiburg

summary: The transcription factor TCF7L2 is indispensable for intestinal tissue homeostasis where it transmits mitogenic Wnt/β-Catenin signals in stem and progenitor cells, from which intestinal tumors arise. Yet, TCF7L2 belongs to the most frequently mutated genes in colorectal cancer (CRC), and growth inhibitory functions of TCF7L2 were proposed. This apparent paradox calls for a clarification of the role of TCF7L2 in colorectal carcinogenesis. Here, we investigated TCF7L2 dependence/independence of CRC cells, and the cellular and molecular consequences of TCF7L2 loss-of-function. By genome editing we readily achieved complete TCF7L2 inactivation in several CRC cell lines without loss of viability, showing that CRC cells have widely lost the strict requirement for TCF7L2. Albeit phenotypic changes manifested in a cell-line-specific fashion, TCF7L2-negative cells exhibited morphological changes, enhanced migration and invasion, and augmented collagen adhesion. Additionally, TCF7L2 deficiency led to reduced proliferation, reminiscent of the physiological role of TCF7L2. To provide a molecular framework for the observed phenotypic changes, we performed global transcriptome profiling. This identified gene-regulatory networks in which TCF7L2 positively regulates the proto-oncogene MYC, while repressing the cell cycle inhibitors CDKN2C/CDKN2D. TCF7L2 also suppresses the pro-metastatic transcription factor RUNX2 and several integrin genes, which is consistent with increased motility and collagen adhesion of TCF7L2-deficient cells. Altogether, we conclude that the proliferation-stimulating activity of TCF7L2 persists in CRC cells. Additionally, TCF7L2 acts as invasion suppressor. Despite its negative impact on cell cycle progression, TCF7L2 loss-of-function may thereby increase malignancy, which could explain why TCF7L2 is mutated in a sizeable fraction of colorectal tumors.

overall_design: TCF7L2 knockout (KO) clones were generated using the CRISPR/Cas9 system targeting exon 6 in HCT116 and HT29 cells. RNA from one wild-type (WT) and one knockout clone was processed and submitted for sequencing for HCT116 cells. For HT29 cells, RNA from one wild-type, one heterozygous (Het), and three knockout clones was processed and submitted for sequencing. In all cases, RNA-seq data from two independent biological replicates were collected.

first: Janna

last: Wenzel

first: Katja

last: Rose

last: Haghighi

first: Constanze

last: Lamprecht

first: Gilles

last: Rouen

first: Vivien

last: Freihen

last: Kesselring

first: Melanie

last: Börries

first: Andreas

last: Hecht


title: T cell transcriptomes in the course of allogeneic hematopoietic stem cell transplantation

status: Public on Mar 07 2020

city: Vienna

first: Georg

last: Stary

address: Spitalgasse 23

department: Dermatology

country: Austria

institute: Medical University of Vienna

summary: RNA seq data of pooled T cells isolated from skin and blood at multiple time points before and after hematopoietic stem cell transplantation

overall_design: Examination of 1 cell type at 4 time points before and after treatment

middle: V

last: Pandey

first: J

last: Strobl


title: IRF5 promotes intestinal inflammation by guiding monocyte differentiation towards pathogenic CD11c+ macrophage phenotype [single_cell_rnaseq]

first: Stephen

last: Sansom

overall_design: Mixed bone marrow chimeras (mice) were constructed using wildtype (CD45.1+ve) and Irf5 knockout (CD45.2+ve) cells that were also heterozygous for knock-in of GFP to the CX3CR1 locus. These animals were subject to Helicobacter hepaticus + anti-IL10R induced colitis. Three weeks after the day of infection mononuclear phagocytes were FACs isolated from the inflamed lamina propria and subjected to single-cell RNA-sequencing analysis with the 10x Genomics platform.

first: Alastair

last: Corbin

first: Maria

last: Gomez-Vazquez

first: Moustafa

last: Attar

first: Irina

last: Udalova


title: Distinct immune microenvironments between primary and paired metastatic tumors in gastric cancer patients

status: Public on Mar 16 2020

city: Cheongju

first: Seung-Myoung

last: Son

state: Chungbuk

address: 1, Chungdae-ro, Seowon-gu

institute: Chungbuk National University College of Medicin

summary: We performed RNA-seq to investigate the differences in the gene expression profiles between primary gastric cancer (PGC) and paired metastatic gastric cancer (MGC).  RNA-sequencing was performed on 7 paired PGC and MGC FFPE tissues. The transcriptome profiling of the two groups (MGC vs PGC) including immune response gene signature was analyzed. Total RNA was isolated using Trizol reagent. Extracted RNA samples were processed using the QuantSeq 3’mRNA-Seq Library Prep Kit and sequenced on an Illumina NextSeq 500. QuantSeq 3’mRNA-Seq reads were aligned using Bowtie2. The alignment file was used to assemble transcripts and the Read Count data was processed based on quantile normalization method using EdgeR within R.  We identified 519 differentially regulated genes between the two sets, 76 of which were significantly up-regulated and 443 significantly down-regulated in MGCs. Among DEGs, 33 immune response genes were selected using QuickGO database (https://www.ebi.ac.uk/QuickGO/), with majority (27/33) of them exhibiting downregulation in the MGC samples.   In summary, RNA sequencing data revealed that immune-related gene expression were down-regulated in MGC compared to PGC.  We performed RNA-seq to investigate the differences in the gene expression profiles between primary gastric cancer (PGC) and paired metastatic gastric cancer (MGC).  RNA-sequencing was performed on 7 paired PGC and MGC FFPE tissues. The transcriptome profiling of the two groups (MGC vs PGC) including immune response gene signature was analyzed. Total RNA was isolated using Trizol reagent. Extracted RNA samples were processed using the QuantSeq 3’mRNA-Seq Library Prep Kit and sequenced on an Illumina NextSeq 500. QuantSeq 3’mRNA-Seq reads were aligned using Bowtie2. The alignment file was used to assemble transcripts and the Read Count data was processed based on quantile normalization method using EdgeR within R.  We identified 519 differentially regulated genes between the two sets, 76 of which were significantly up-regulated and 443 significantly down-regulated in MGCs. Among DEGs, 33 immune response genes were selected using QuickGO database (https://www.ebi.ac.uk/QuickGO/), with majority (27/33) of them exhibiting downregulation in the MGC samples.   In summary, RNA sequencing data revealed that immune-related gene expression were down-regulated in MGC compared to PGC.

first: Hye Sook

last: Han


title: Transcriptional analysis of mouse CD4 T cells with high and low tonic signaling-naive and D7 in vivo activated.

status: Public on Feb 28 2020

city: St. Louis

first: Paul

last: Allen

address: 660 S. Euclid, Box 8118

department: Pathology and Immunology

institute: Washington University

summary: These studies utilized two TCR transgenic mouse lines, LLO118 and LLO56, that our laboratory has developed and characterized, which recognize the same Listeria monocytogenes LLO/IO-Ab epitope with equal affinities. When 104 naive CD4+ LLO T cells are transferred into a B6 mouse and one day later infected with wild type Listeria monocytogenes, the LLO118 T cells have a more robust primary expansion than LLO56. In contrast, after a secondary challenge, LLO56 T cells have a much greater expansion than LLO118 T cells. One striking phenotypic difference between the LLO118 and LLO56 T cells lies in their CD5 expression. CD5 expression has been shown to correlate directly with TCR affinity for self-pMHC and tonic signaling. LLO56 cells have a higher basal phosphorylation of the TCR chain, and they have significantly increased expression of Nur77 mRNA.  These transcriptional profiling experiments examined if there were transcriptional differences between LLO118 and LLO56 T cells, either naive or after D7 of infection, that would account for their disparate in vivo behaviors.

overall_design: T cells were isolated from the spleens from individual mice for each TCRtg line as naive T cells or D7 in vivo activated. There were 4 to 5 biological replicates for the 2 conditions.  All data were normalized using RMA in Arraystar.  The data table includes normalized probe intensities for every probe.

first: Ashley

last: Milam


title: Human Transcriptome Array 2.0 (HTA) from SW480 colon adenocarcinoma cells transfected with LINC00152 Stealth siRNAs or Stealth Negative Control Medium GC siRNAs

status: Public on Mar 04 2020

city: Budapest

first: Wichmann

last: Barna

address: Szentkirály

country: Hungary

institute: SOTE

summary: Whole transcriptome expression levels of SW480 colon adenocarcinoma cells transfected with LINC00152 Stealth siRNAs or Stealth Negative Control Medium GC siRNAs, analyzed by HTA 2.0 microarrays

overall_design: SW480 colon adenocarcinoma cells transfected with LINC00152 Stealth siRNAs (n=3) or Stealth Negative Control Medium GC siRNAs (n=3). HTA 2.0 microarray experiments were performed according to the manufacturer’s instructions. 100 ng input total RNA samples were applied as staring material. For sscDNA synthesis 15 µg cRNA was used and 5.5 µg fragmented and labeled sscDNA sample was hybridized to HTA 2.0 microarrays (Affymetrix) for 16 hours at 45°C with 60 rpm rotation in the Hybridization Oven (Affymetrix). Microarrays were washed and stained with GeneChip® Hybridization, Wash, and Stain Kit reagents according to FS450_0001 protocol using the Fluidics Station 450 instrument (Affymetrix). Scanning was performed with GeneChip Scanner 3000 (Affymetrix).

first: Orsolya

last: Galamb

first: Alexandra

last: Kalmár

first: Anna

last: Sebestyén

first: Titanilla

last: Dankó

first: Csilla

last: Kriston

first: Péter

last: Hollósi

first: István

last: Csabai

first: Barnabás

last: Wichmann

first: Barbara

middle: K

last: Barták

first: Zsófia

last: Nagy

first: Gábor

first: Zsolt

last: Tulassay

last: Igaz

first: Bela

last: Molnar


title: Caloric restriction reprograms the single-cell transcriptional landscape of Rattus norvegicus aging

status: Public on Feb 21 2020

city: Beijing

first: Shuai

last: Ma

address: No.15, Da Tun road

country: China

institute: Chinese Academy of Sciences

summary: Aging causes a functional decline in tissues throughout the body that may be delayed by caloric restriction (CR). However, the cellular profiles and signatures of aging, as well as those ameliorated by CR, remain unclear. Here, we built comprehensive single-cell and single-nucleus transcriptomic atlases across various rat tissues undergoing aging and CR. CR attenuated aging-related changes in cell type composition, gene expression, and core transcriptional regulatory networks. Immune cells were increased during aging, and CR favorably reversed the aging-disturbed immune ecosystem. Computational prediction revealed that the abnormal cell-cell communication patterns observed during aging, including the excessive proinflammatory ligand-receptor interplay, were reversed by CR. Our work provides  multi-tissue single-cell transcriptional landscapes associated with aging and CR in a mammal, enhances our understanding of the robustness of CR as a geroprotective intervention, and uncovers how metabolic intervention can act upon the immune system to modify the process of aging.

sample_organism:
Homo sapiens
Rattus norvegicus

platform_organism:
Homo sapiens
Rattus norvegicus

overall_design: Single-cell and single-nucleus RNA sequencing for 210K cells/nuclei from 9 kinds of tissues of rats

first: Guang-Hui

last: Liu


title: Expression data from mouse with vasectomy or sham surgery

city: Baltimore

first: TAKASHI

last: KAWAHARA

state: MD

address: 600 N. Wolfe Street, Marburg 148

institute: The Johns Hopkins Hospital

summary: Vasectomy was thought to be a risk factor for prostate cancer. We investigated the mechanism on vasectomy using Affymetrix microarray.

overall_design: Vasectomy or sham surgery (control) were performed at the age of 16 weeks.

first: Hiroshi

last: Ishiguro

first: Takashi

last: Kawahara


title: Fractionated ionizing radiation evokes diverse patterns of long-term changes in gene expression and tumor-propagating capacity in human glioma stem cells.

status: Public on Mar 01 2020

city: Moscow

first: Daniil

last: Nikitin

address: Miklucho-Maklaya

country: Russia

institute: Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry

summary: This study addresses long-term effects of clinically relevant regimens of radiation in human glioma stem cells. Our investigations reveal a strikingly diverse spectrum of changes in cell behavior, gene expression patterns and tumor-propagating capacities evoked by radiation in different types of glioma stem cells. Evidence is provided that degree of cellular plasticity but not the propensity to self-renew is an important factor influencing radiation-induced changes in the tumor-propagating capacity of glioma stem cells. Gene expression analyses indicate that paralell transcriptomic responses to radiation underlie similarity of clinically relevant cellular outcomes such as the ability to promote tumor growth after radiation. Our findings underscore the importance of longitudinal characterizations of molecular and cellular responses evoked by cytotoxic treatrments in glioma stem cells.

overall_design: Affymetrix gene expression profiling of human glioma stem cells treated by radiation in order to detect long-term gene expression changes.

first: Ella

last: Kim

first: Darius

last: Kalasauskas

first: Maxim

last: Sorokin

first: Bettina

last: Sprang

first: Alhassan

last: Elmasri

first: Sina

last: Viehweg


title: Multiple myeloma tumors from Vk*MYC mice

status: Public on Feb 20 2020

city: Scottsdale

first: Marta

last: Chesi

state: AZ

address: 13400 E Shea Blvd

institute: Mayo Clinic

type:
Genome variation profiling by array
Expression profiling by array


title: IGF2BP1 is a druggable, post-transcriptional super-enhancer of E2F-driven gene expression hallmark in cancer

status: Public on Mar 12 2020

city: Halle

first: Markus

last: Glaß

address: Kurt-Mothes-Str. 3a

department: Institute of Molecular Medicine

institute: Martin Luther University Halle-Wittenberg


title: Expression profiling of garlic genes

status: Public on Feb 19 2020

city: Changsha

first: Touming

address: NO.348, western road of xianjia lake

department: Institute of Bast Fiber Crops

institute: Chinese Academy of Agricultural Sciences

summary: To characterize the expression of 58219 genes annotated from garlic genome, the transcriptomes of seven tissues (including garlic sprouts, shoots, bulbs, flowers, roots, pesudostems, and leaves) were sequenced, and finally identified 45,750 genes expressed in various tissues investigated. In addition, the bulbs-transcriptomes in the eight stages of bulbs-development were sequenced, resulting in 6,234 genes isentified to show dynamic expression changes in the bulbs-developmental process.

overall_design: The garlic Ershuizao cultivated in the experimental farm of the Shandong Agricultural University, Taian, China, in Oct. 2018 was used for the transcriptome analysis. When the garlic buds, the shoots were collected. In May 2019, the leaves, bulbs, pesudostems, garlic sprouts, roots and flowers were individually sampled. In addition, to characterize the expression of expanding bulbs dynamically, bulbs samples from eight stages of growth were collected, by sample each five day from April 11 to May 16 in 2019 when the bulbs have not start the expanding growth and have finished the expansion, respectively, and correspondingly, the sample names were designated orderly from S1 to S8. Three replicates were performed for each sample.   Total RNAs for all 42 samples were separately extracted and used to construct the cDNA library with fragment lengths of ~250 bp. Thereafter, paired-end sequencing was performed for these 48 samples using the Illumina HiSeq 2500 sequencing platform.


title: Next Generation Sequencing Facilitates Quantitative Analysis of Runx2fl/fl  and Gli1-CreERT2;Runx2fl/fl Incisor Transcriptomes

status: Public on Mar 05 2020

city: Los Angeles

first: Shuo

last: Chen

state: California

address: 2250 Alcazar Street, Clinical Science Annex, Room 103, CLINICAL SCIENCE ANNEX ROOM 103

institute: Center for Craniofacial Molecular Biology, University of Southern California

summary:
Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare NGS-derived incisor transcriptome profiling (RNA-seq)  between Runx2fl/fl  and Gli1-CreERT2;Runx2fl/fl mice to identify the potential target of Runx2.
Methods: Incisor mRNA profiles from one week after induction of one-month-old  Runx2fl/fl and Gli1-CreERT2;Runx2fl/fl mice were generated by deep sequencing, in triplicate, using Illumina NextSeq500.
Results: Using an optimized data analysis workflow, we mapped about 68 million sequence reads per sample to the mouse genome ( mm10) and identified  80,214 transcripts in th incisors of Runx2fl/fl  and Gli1-CreERT2;Runx2fl/fl  mice with Partek E/M workflow. Five hundred and eleven differentially regulated genes were identified (＞2-fold, p＜0.05), of which 299 were upregulated and 212 were downregulated.

first: Yang

last: Chai


title: Evaluation of CNAs in multiple myeloma tumors from Vk*MYC mice

summary: Myeloma tumors arose in Vk*MYC mice share copy number abnormalities with multiple myeloma tumors from human patients

overall_design:
Genomic DNA from CD138+ magnetically selected myeloma cells harvested from aged Vk*MYC mice (original tumors) or from C57BL/6 WT mice engrafted with original Vk*MYC myeloma tumors (recipients) was hybridized to Agilent mouse whole genome 244K CGH array

CL= cell line
OT=original tumor
R=recipient
BN= bortezomib naïve
BR=bortezomib resistant
MM=multiple myeloma
EMM= extramedullary MM
NPC=normal plasma cell

first: Esteban

last: Braggio

first: P

last: Bergsagel


title: Control or KZFP KD hESC-derived organoids RNA-seqs

status: Public on Feb 18 2020

city: Lausanne

first: Delphine

last: Grun

address: route Cantonale

country: Switzerland

institute: EPFL

summary: Control or KD hESC were differentiated into organoids as decribed in Methods. RNA was extracted from individual organoids at day 20 after commencing the STEMdiff™ Cerebral Organoid Kit protocol. Day 0 was designated as the day of transfer of hESC to a 96-well plate for differentiation into embryoid bodies .

overall_design: hESC were transduced with a control lentivector or a lentivector expressing a sh targeting the KZFPs, selected with puromycin and differentiated into cerebral organoids post-selection.

first: Priscilla

last: Turelli

first: Playfoot

last: Christopher


title: RNA-seq of untreated- or STING inhibitor treated control and ZNFKD iN.

summary: hiPSC were treated or not with STING inhibitor, transduced with KD or control lentivectors and differentiated in induced neurons.

overall_design: hIPSC treated or not for 45 min with STING inhibitor, were transduced with lentivectors coding for a sh either targeting the KZFPs genes (KD) or the Luciferease gene  as control (Ctrl). Transduced cells were puromycin selected for 3 days and pushed to differentiate in neurons with the doxycyclin-induction of neurogenins (1µg/µl).


title: Therapeutically reversible zonation-dependent endothelial cell transcriptomic changes with neurodegenerative disease associations in the aged brain

status: Public on Mar 30 2020

city: Hong Kong

first: Ho

last: Ko

address: 30-32 Ngan Shing Street, Shatin

department: Medicine and Therapeutics

institute: The Chinese University of Hong Kong

summary: With advances in single-cell genomics, molecular signatures of cells comprising the brain vasculature are revealed in unprecedented detail, yet the ageing-associated cell subtype transcriptomic changes which may contribute to neurovascular dysfunction in neurodegenerative diseases remain elusive. Here, we performed single-cell transcriptomic profiling of brain endothelial cells (EC) in young adult and aged mice to characterize their ageing-associated genome-wide expression changes. We identified zonation-dependent transcriptomic changes in aged brain EC subtypes, with capillary ECs exhibiting the most transcriptomic alterations. Pathway enrichment analysis revealed altered immune/cytokine signaling in ECs of all vascular segments, while functional changes impacting the blood-brain barrier (BBB) and glucose/energy metabolism were most prominently implicated in ECs of the capillary bed – the primary site where ECs and other neurovascular unit (NVU) cell types closely interact and coordinate to regulate BBB and cerebral blood flow in health and diseased conditions. Furthermore, an overrepresentation of Alzheimer’s disease (AD)-associated genes identified from GWAS studies was evident among the human orthologs of differentially expressed genes of aged capillary ECs but not other EC subtypes. Importantly, for numerous EC-enriched differentially expressed genes with important functional roles at the BBB and/or association with AD, we found concordant expression changes in human aged or AD brains. Finally, we demonstrated that treatment with exenatide, a glucagon-like peptide-1 receptor (GLP-1R) agonist, strongly reverses transcriptomic changes in ECs and largely reduces BBB leakage in the aged brain. Thus, our study revealed novel vascular ageing-associations of AD in the brain capillary endothelium, and provides insights into detailed transcriptomic alterations underlying brain EC ageing that are complex with subtype specificity yet amenable to pharmacological interventions.

overall_design: Perform single cell transcriptome sequencing of young, aged and drug treatment groups with each 3 replications.


title: Identification of distinct immune subtypes in colorectal cancer based on stroma compartment

status: Public on Feb 03 2020

first: Rongfang

last: Shen

address: No. 17 South Panjiayuan, Chaoyang District

department: National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital

institute: Chinese Academy of Medical Sciences and Peking Union Medical College

summary: Tumor environment is of vital importance for the incidence and development of colorectal cancer. In order to decipher tumor environment feature of colorectal cancer and explore the role of its immune context composition in cancer classification, we performed gene expression microarray on microdissection processed stroma compartments of colorectal cancer and adjacent normal tissues. Integrated analysis of our data with public gene expression microarray data of microdissection processed stromal and epithelial tissues of colorectal, we identified three immune subtypes — active immune, active stroma and mixed type. These immune subtypes differed by immune cell infiltration pattern, expression of immune checkpoint inhibitors mutation landscape, extent of mutation burden, extent of copy number burden and prognosis. Together, these results suggested that dividing colorectal cancer characterized by tumor environment is of vital important in predicting patients clinical outcome and help to guide precision and personalized management.

overall_design: Tissues from 6 cases of colorectal cancer and 6 adjacent normal tissues(located more than 5cm away from the tumor edge) were performed mRNA expression profiles using Agilent  8x60K human whole genome gene expression microarray. All patients underwent resection of the primary tumor at Department of Colorectal Surgery, Beijing Shijitan Hospital,Capital Medical University (Beijing,China) between February 2016 and December 2016.No chemotherapy or radiotherapy was administered to the patients prior to therapeutic resection.

first: Ping

last: Li

first: Bing

first: Botao

last: Zhang

first: Lin

last: Feng

first: Shujun

last: Cheng


title: Genome-wide identification of differentially methylated promoters and enhancers associated with response to anti-PD-1 therapy in non-small cell lung cancer

city: Boston

first: JAE WON

last: CHO

state: MA

address: 60 Fenwood Road

department: Neurology

institute: Brigham and Women's Hospital

summary: The purpose of this study is to compare transcriptional profiles of non-small-cell lung cancer between responder patients and non-responder patients during anti-PD-1 treatment.

overall_design: 16 patients sample were obtained as 11 fresh samples and 5 formalin-fixed paraffin-embedded (FFPE) samples. Each sample was subsequently prepared by TruSeq RNA Access Library Prep Guide Part # 15049525 Rev. B with TruSeq RNA Access Library Prep Kit. RNA-sequencing was performed by HiSeq 2500 with HiSeq 2500 System User Guide Document # 15035786 v01 HCS 2.2.70.

first: Jae-Won

last: Cho

first: Min

middle: H

last: Hong

first: Sang-Jun

last: Ha

first: Young-Joon

last: Kim

first: Byoung

first: Insuk

last: Lee

first: Hye


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

overall_design: Refer to individual Series


title: Photoperiodic time-series mRNASeq assays of the sheep pars tuberalis

status: Public on Feb 04 2020

city: Edinburgh

first: Matthew

last: Hindle

state: Midlothian

address: Easter Bush

department: Functional Genetics and Development

institute: The Roslin Institute

summary: Accurate timing and anticipation of seasonal changes are required to initiate physiological adaptations over the course of the year such as hibernation, changes in metabolism, fattening and reproductive activity. To achieve this, organisms have evolved complex seasonal timekeeping systems that rely on day length sensing (photoperiodism). The aim of this project is to investigate the role of the circadian clock in photoperiodism within the crucial photoperiod sensing tissue the pars tuberalis.

overall_design: BioProject: PRJNA391103 SRA Study: SRP110487

first: Shona

last: Wood

first: Yasutaka

last: Mizoro

first: Yuanyuan

first: Dave

last: Burt

first: Simone

last: Meddle

first: Andrew

last: Loudon


title: Transcriptomic analysis of the porcine anterior pituitary gland during the peri-implantation period

status: Public on Feb 09 2020

city: Olsztyn

first: Agata

last: Zmijewska

address: Oczapowski 1a

department: Demartment of Animal Anatomy and Physiology

country: Poland

institute: Univeristy of Warmia and Mazury

summary: In pigs, the peri-implantation period is recognized as determinant of successful reproduction, and it is controlled by neuroendocrinal interactions among signals originating from the female hypothalamic-pituitary-ovarian axis, uterus, and developing embryo. The transcriptomic activity of the pituitary gland may influence reproductive processes occurring in pigs during the peri-implantation period. The aim of this study was to determine alternations in gene expression in the porcine pituitary gland during the peri-implantation period (days 15-16 of pregnancy) in comparison with that during the respective days of the estrous cycle using a microarray approach.

overall_design: We analized anterior pituitary glands obtained from 8 indyviduals (n=8). Pituitaries were collected from mature gilts  on days 15-16 of early pregnancy (n = 4) and the estrous cycle (n = 4).

first: Wioleta

last: Czelejewska

first: Ewa

last: Waszkiewicz

first: Alina

last: Gajewska

first: Stanislaw

last: Okrasa

first: Anita

last: Franczak


title: Transcriptomic and anatomic profiling reveal germination process of different wheat varieties in response to waterlogging stress

status: Public on Jan 31 2020

city: xinxiang

first: changwei

last: shen

state: henan

address: East Section of Hualan Avenue

institute: Henan Institute of Science and Technology

summary:
Background: Waterlogging was one of the most serious abiotic stresses in wheat-growing regions of China. There were great differences in waterlogging tolerance among different wheat varieties, and the mechanism of waterlogging tolerance of wheat seeds during germination was unclear.
Methods: In order to reveal the adaptability of wheat to waterlogging stress during germination, we analyzed the germination rate and anatomical structure of three wheat seeds, ‘Zhoumai 22’, ‘Bainong 207’ and ‘Bainong 607’. At the same time, Illumina sequencing technology was used to determine the transcriptome of these three wheat varieties during germination.
Results: The results showed that there was no significant difference between the germination rate of ‘Bainong 207’ after 3 days of waterlogging treatment and that of the control seeds. However, under waterlogging stress, the degree of emulsification and degradation of endosperm cells was higher than that of the control treatment, and starch granules in endosperm were significantly reduced. Transcriptome data were obtained from seed samples (a total of 18 samples) of three wheat varieties under waterlogging and control treatment. A total of 2,775 differentially expressed genes (DEGs) were identified by comprehensive analysis. In addition, by analyzing the correlation between the expression levels of DEGs and seed germination rates in three wheat varieties under waterlogging stress, it was found that the relative expression levels of 563 and 398 genes were positively and negatively correlated with the germination rate of wheat seeds, respectively. The GO and KEGG analysis found that the difference in waterlogging tolerance of the three wheat varieties was related to the abundance of key genes involved in the glycolysis pathway, the starch and sucrose metabolism pathway, and the lactose metabolism pathway. The ethanol dehydrogenase (ADH) gene in the endosperm of ‘Bainong 607’ was immediately induced after a short period of waterlogging, and the energy provided by glycolysis pathway enabled the seeds of ‘Bainong 607’ to germinate as early as possible, while the expression level of AP2/ERF transcription factor was up-regulated to further enhance its waterlogging tolerance.
Conclusions: In general, this study provided a deeper understanding of the mechanisms by which different wheat varieties respond to waterlogging stress during germination.

first: Changwei

last: Shen

first: Jingping

last: Yuan

first: Hong

last: Qiao

first: Zijuan

last: Wang

first: Yuanhai

last: Liu

first: Xiujuan

last: Ren

first: Xingqi

last: Ou

first: Fei

first: Xing

first: Ying

last: Zhang

first: Xiling

last: Chen


title: Circadian Rhythms in Bmal1-/- Mouse Fibroblast Cells and Liver Tissue

status: Public on Feb 14 2020

city: Philadelphia

first: Utham Kashyap

last: Valekunja

state: PA

address: 3400 Civic Center Boulevard,

department: Department of Systems Pharmacology & Therapeutics, Perelman School of Medicine,

institute: University of Pennsylvania

summary: Circadian clocks exist in almost all levels of living organisms and play elementary roles in the persistence of regular physiological and behavioural processes. Canonical transcription/translation feedback loop models portray BMAL1 (ARNTL) as one of the principal drivers of circadian periodicity in mammalian systems. In this integrated multi-omics study, we demonstrate, for the first time, 24 hr circadian oscillations in the expression levels of several transcripts and proteins in dexamethasone-synchronized Bmal1-/- mouse fibroblast cells and liver tissue slices. Intriguingly, daily oscillations were also observed in phosphoproteome profiles in the absence of this core clock gene. Our findings reveal that Bmal1 knockout radically alters the expression and phosphorylation patterns of mice hepatic proteome, which possibly attributes to considerably different sets of rhythmic candidates compared to wild-type. It is, therefore, reasonable to accentuate that circadian rhythms are not obliterated in mammalian systems due to deletion of the core clock genes.

overall_design: Wild-type and Bmal1-/- MSF cells were grown in Dulbecco’s Modified Eagle Medium (DMEM) containing 10% (v/v) HyClone III Serum (Analab; Cat # SH30109.03), 1/100  Glutamax-I (Invitrogen; Cat # 35050-038), 1/100 Penicillin-Streptomycin (SIGMA; Cat # P4333) and 1/500 MycoZap™ (Lonza; Cat # VZA-2022) in multiple six-well plates until complete confluency (n=3, per time-point, per genotype). Wild-type and Bmal1-/-  mice liver tissues were sliced in small pieces (~500 micron) and were placed on membrane discs in multiple 24 well plates (n=3, per time-point, per genotype). The confluent MSF cells and mice liver tissue slices were treated with 100nM (final concentration) of dexamethasone (DEX) for 15 min to synchronize the cells/tissues [Balsalobre et al. Science 2000]29. MSF cells/liver tissue slices were then washed three times with PBS (37°C) and were incubated in HEPES-buffered Medium; 1X DMEM powder (SIGMA; Cat # D5030), 0.35mg/mL sodium bicarbonate, 5mg/mL glucose, 0.01M HEPES, 10% (v/v) HyClone III Serum, 1/100 Glutamax-I, and 1/500 MycoZap™, pH 7.3 (adjusted with HCl) and osmolality 320 mOsm (adjusted with NaCl) at 37°C under DD cycle. 48 hrs after DEX treatment, MSF cells/liver tissue slices were harvested at every three hrs interval for three days for transcriptomics analyses.

first: Utham

first: Akhilesh

last: Reddy


title: Gene expression profile in multiple myeloma tumors from Vk*MYC mice

first: Marta

last: Chesi

summary: Myeloma tumors arose in Vk*MYC mice share gene expression profile with multiple myeloma tumors from human patients

overall_design:
Total RNA from CD138+ magnetically selected myeloma cells harvested from aged Vk*MYC mice (original tumors) or from C57BL/6 WT mice engrafted with original Vk*MYC myeloma tumors (recipients), or from normal plasma cells was hybridized to Affymetrix Mouse genome 430 2.0. Controls include B cell lymphoma cell lines originated from Vk*MYC mice and two balb/c plasmacytoma cell lines.

ASC = ascite
BL = B cell lymphoma
BM = bone marrow
BN = bortezomib naïve
BR = bortezomib resistant
CL = cell line
EMM = extra-medullary multiple myeloma
LV = liver
MIR = mir15a/16-1
MDR = DLeu2/miR15a/16-1
MM = intra-medullary multiple myeloma
NPC = normal plasma cells
OT = original tumor
PCT = plasmacytoma
R = recipient
SPL = spleen
TM = Tumor
WT = wild type

first: Esteban

last: Braggio

first: P

last: Bergsagel

first: Caleb

last: Stein


title: RNA-seq of ZNF417/ZNF587 KD or control H1 cells

status: Public on Jan 24 2020

first: Delphine

last: Grun

summary: RNAseq of human embryonic stem cells depleted for ZNF417 and ZNF587 or control cells

overall_design: H1 human embryonic stem cells have been transduced with lentivectors coding for an sh targeting both ZNF417/ ZNF587 (sh587) or no sh (shE) as control and selected with puromycin.

first: Priscilla

last: Turelli


title: Single cell RNA-sequencing of gonadal and inguinal adipose tissue Pdgfrβ+ cells

status: Public on Jan 27 2020

city: Durham

first: Rana

last: Gupta

state: North Carolina

address: Carmichael Building, 300 North Duke St.

department: Duke Molecular Physiology Institute

institute: Duke University

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

The processed data files at the foot of this SuperSeries record are an aggregate of data in both series.


title: RNAseq of hIPS cells at day 0 and hiPS-differentiated induced neuron at day 4 post neuronal induction

summary: RNA-seq of hiPS or induced neurons depleted for ZNF417 and ZNF587 or control cells.

overall_design: hiPS cells have been transduced  with lentivectors coding for an sh targeting both ZNF417/ ZNF587 (sh587) or no sh (shE) as control in cells. Transduced cells have been selected with puromycin and then induced to differentiate in neurons with doxycyclin (1µg/µl)-dependent expression of Neurogenins.


title: RNA-seq of HERVK-CRIPRi IPS and iN cells

summary: dCas9KRAB and gRNA targeting HERVK TEs were used to repress the TEs in stem cells (hiPS) and in differentiated induced neurons (iN). As control, dCas9KRAB alone without gRNA was used.

overall_design: hiPS cells have been transduced at an MOI15 with lentivectors coding for dCas9KRAB and gRNA targeting LTR5hs, or no gRNA as control. Transduced cells have been selected with puromycin and then induced to differentiate in neurons with doxycyclin (1µg/µl)-dependent expression of Neurogenins.


title: Genome-wide maps of chromatin state in sheep pars tuberalis

first: Matthew

last: Hindle

summary: Photoperiodism represents the biological response to annual day-length changes, driving seasonal changes in physiology. We aimed to determine if there was an epigenetic component to photoperiodism. We identify photoperiod-dependent epigenetic regulation of transcription, which facilitates the circadian transcription factor drive on long day physiology.

overall_design:
SRA: SRP110487 BioProject: PRJNA391103
Seasonally breeding sheep are a well-established photoperiodic model for the study of neuroendocrine mechanisms underpinning seasonal physiology. Castrate 6-month old males were housed on artificial SP conditions (8hLight:16hDark) for 84 days from 15th October 2014 to 8th January 2015, and then moved to LP (16hLight:8h Dark). Individual cohorts were collected on Days 1, 7, 28, 112 of LP exposure, and remaining animals switched back to SP conditions on Day 112 of LP-exposure (8th May 2015), and sampled on Day 1, 7 and 28. Therefore, both the LP and SP cohorts were similarly pre-conditioned by prior exposure to alternative photoperiods. PT tissue was collected at Zeitgeber times (ZT), where ZT0 marks the onset of light in each photoperiod. ZT4 was chosen as an early light phase time-point. We quantified gene expression by RNA-Seq and H3K4me3 abundance by ChIP-seq against the most recent complete sheep reference genome (Oar_rambouillet_v1.0; 5th published sheep genome) at all time-points. 2 animals pertime-point were selected for ChIP-seq.

first: Shona

last: Wood

first: Yasutaka

last: Mizoro

first: Andrew

last: Loudon


title: Histones ChIP-seq in control and ZNFKD H1 cells

summary: Active and repressive histones ChIPseqs in controls and ZNF417/587 depleted hESC.

overall_design: Active and repressive histones ChIPseqs in H1 hESC puro-selected cells transduced with lentivectors delivering control sh or sh targeting ZNF417 and ZNF587


title: Primate-restricted KRAB zinc finger proteins control gene expression in human brain


title: ZNF417 and ZNF587 ChIP-seq in H1 cells

summary: KZFP ChIP-seqs in H1 cells overexpressing the proteins

overall_design: H1 cells were transduced with lentivectors to stably overexpress the tHA-agged versions of the proteins immunoprecipated with an anti-HA antibody.


title: RNA-seq in 73 B-lineage ALL patients

status: Public on Jan 23 2020

city: Memphis

first: Robert

middle: Joseph

last: Autry

state: TN

address: 262 Danny Thomas Pl, MS 313

department: Pharmaceutical Sciences

institute: St. Jude Children's Research Hospital

summary: RNA-seq from RNA isolated from bone marrow or peripheral blood of newly diagnosed acute lymphoblastic leukemia patients on TotalXVI protocol

overall_design: LC50 determination performed with concordant RNA-seq expression analysis

first: Wenjian

last: Yang

first: William

last: Evans


title: Elucidating photorespiration pathways in a chemolithoautotroph

city: Wageningen

first: Nico

last: Claassens

address: Stippeneng 4

department: Laboratory of Microbiology

institute: Wageningen University

summary: We investigate photorespiration pathways in the chemoautotroph Cupriavidus necator H16 when growing autotropically on hydrogen and carbon dioxide via the Calvin Cycle. We demonstrate an upregulation of the glycerate pathway under photorespiration (ambient carbon dioxide) conditions

overall_design: Transcriptomes are compared for growth under photorespiration conditions (H2, ambient CO2) versus growth at H2 and 10% CO2, as versus heterotrophic growth on pyruvate, biological triplicates are used (9 samples total)

first: Giovanni

last: Scarinci

first: Axel

last: Fischer

first: Arren

last: Bar-Even


title: RNA-seq CELSR2 knockdown vs NTC

summary: RNA-seq experiments in two B-lineage leukemia cell lines (NALM6 and 697) either 0hr prednisilone treated or 24hr prednisolone treated in either NTC or CELSR2 knockdown (240-1)

overall_design: Treated for 0 or 24 hours 10uM prednisolone (Solu-Medrol) in either NTC or CELSR2 knockdown (240-1)


title: Molecular causes of an evolutionary shift along the parasitism-mutualism continuum in a bacterial symbiont

status: Public on Jan 20 2020

city: Vienna

first: Matthias

last: Horn

address: Althanstrasse 14

department: Division of Microbial Ecology

institute: University of Vienna

summary: Symbiosis is a ubiquitous phenomenon in nature, and these inter-species interactions have a massive impact on organisms, shaping the world around us today. The relationship between the partners in microbial symbioses have been described as existing along a parasitism-mutualism continuum, and the dynamics of this continuum are dependent upon numerous genotypic and environmental factors. Theoretical and experimental studies show that vertical transmission (VT) leads to the evolution of mutualistic traits, whereas horizontal transmission (HT) facilitates the emergence of parasitic features. However, these studies focused on phenotypic data, and we know little about underlying molecular changes at the genomic level. Here we show that a dramatic shift in the frequency of genetic variants, coupled with major changes in gene expression, allow an obligate intracellular bacterial symbiont to alter its position in the mutualism-parasitism continuum depending on the mode of between-host transmission. We found that increased virulence in horizontally transmitted chlamydiae residing in amoebae was a result of processes occurring at the infectious stage of the chlamydia’s developmental cycle. Specifically, genes involved in energy production required for extracellular survival as well as the type III secretion system (T3SS) - the symbiont’s primary virulence mechanism - were significantly upregulated. Our results identify the genomic and transcriptomic dynamics sufficient to favor parasitic or mutualistic strategies.

overall_design: RNA-seq of Parachlamydia acanthamoebae UV-7 in Acanthamoeba sp. at 3 different time points during infection (2 hpi, 24 hpi, released elementary bodies [EBs] accumulated at 7 days post infection) for 2 experimental set-ups in triplicates; the 18 samples were sequenced on two lanes using a 50bp single read Illumina HiSeq 2500 system.

first: Paul

last: Herrera

first: Lisa

last: Schuster

first: Cecilia

last: Wentrup

first: Lena

last: König

first: Thomas

last: Kempinger

first: Hyunsoo

first: Jasmin

last: Schwarz

first: Stephan

last: Köstlbacher

first: Florian

last: Wascher

first: Markus

last: Zojer

last: Rattei


title: Omipalisib Inhibits Esophageal Cancer Growth through PI3K/AKT/mTOR Signalling Pathway Disruption

status: Public on Jan 11 2020

city: Changchun Jilin

first: Dongshan

last: Zhu

address: 71 Xinmin Street

department: thracic department

institute: Jilin University First Hospital

summary: Esophageal squamous cell carcinoma (OSCC) is a lethal digestive tract malignancy with limited effective interventions. This study aims to explore a new potential inhibitor on OSCC and investigate the underlying mechanisms. Based on a drug screen of an FDA-proven library consisting of 1404 compounds, we demonstrated that Omipalisib, a dual PI3K/mTOR inhibitor, markedly inhibited cell proliferation and colony formation in a panel of OSCC cell lines. Mechanistically, Omipalisib induced G0/G1 phase cell cycle arrest and apoptosis. Moreover, RNA-seq, KEGG and GSEA confirmed that the PI3K/mTOR signalling pathway is the primary target of Omipalisib in OSCC cells. Omipalisib treatment suppressed the PI3K/mTOR signalling pathway. Furthermore, Omipalisib exerted a significant antineoplastic effect on OSCC tumour xenografts in BALB/c nude mice without obvious side effects. The present study supports the rationale for using Omipalisib as a therapeutic approach for OSCC cases and suggests the potential clinical evaluation of this strategy.

overall_design: In this study, we investigated the therapeutic effects and underlying mechanisms of Omipalisib in OSCC cells based on a screen of compound library.

first: Dong-shan

first: Jing-yao

last: Dong

first: Yao-yao

last: Xu

first: Xin-tong

last: Zhang

first: Shi-bo

last: Fu

first: Wei

last: Liu


title: p53 activates the long noncoding RNA Pvt1b to inhibit Myc and suppress tumorigenesis

city: LOS ANGELES

first: Jesse

last: Zamudio

state: CA

address: 610 CHARLES E. YOUNG DRIVE EAST BOX 957239

department: MCDB

institute: University of California, Los Angeles

summary: P53 activation in response to cellular stress has long been known to result in downregulation of c-myc, a gene that is frequently overexpressed in cancer due to its role in promoting cellular proliferation. However, the mechanism underlying this p53 dependent myc repression is poorly understood. Here we report p53 regulation of the lncRNA PVT1, a neighboring myc gene which is upregulated following p53 activation via p53 binding to a canonical p53 response element (p53RE) in the first intron of PVT1. Specifically, we find that p53 activation results in induction of an isoform of PVT1 initiated from an alternative first exon, which we have termed PVT1alt. When the PVT1 p53RE is mutated and PVT1alt induction is inhibited, we observe increased levels of myc mRNA in cells undergoing DNA damage or oncogenic stress and corresponding increases in cellular proliferation. The PVT1alt RNA is required for this p53-dependent myc repression, suggesting a important growth suppressive role for this lncRNA in the p53 response. Our study reveals a novel mode of myc regulation in cis by an alternative lncRNA isoform, providing insight into an important mechanism of crosstalk between the p53 and myc transcriptional networks.

overall_design: RNA seq from WT MEFs infected with a sgRNA targeting the PVT1 p53 response element or a control sgRNA, untreated or treated with doxorubicin for 24 hours. Three biological replicates are included.


title: RNA-seq in 247 B-lineage ALL

first: Robert

last: Autry

summary: RNA-seq from RNA isolated from bone marrow or peripheral blood of newly diagnosed acute lymphoblastic leukemia patients

overall_design: RNA-seq expression analysis in primary leukemia cells

first: Wenjian

last: Yang

first: William

last: Evans


title: KAP1 ChIP-seq in hESC

first: Delphine

last: Grun

summary: endogenous KAP1 ChIPseq remapping (previously published in GSE57989)

overall_design: endogenous KAP1 ChIPseq in H1 WT hESC

first: Priscilla

last: Turelli


title: Caco2 response to methotrexate, lactoferrin, and methotrexate-lactoferrin co-exposure

status: Public on Jan 10 2020

city: San Francisco

first: Thomas

last: Wallach

address: 550 16th St. 5th floor

department: Pediatrics

institute: UCSF

summary:
bulk sequencing outputs of Caco2 cells after exposure to permeability modifying and permeability rescuing agents.
To identify the molecular drivers for methotrexate-induced barrier dysfunction, we conducted RNA sequencing on Caco2 spheroids treated with methotrexate and lactoferrin. Given our observation that barrier function was compromised as early as 4-6 hours after exposure to methotrexate, we isolated RNA from spheroids 4-hour post-treatment to capture the transcriptional events responsible for initiating the processes.

overall_design: Caco-2 spheroids were exposed to methotrexate, lactoferrin, and lactoferrin with methotrexate. RNA was extracted using RNeasy Plus Micro kit (Qiagen, Hilden, Germany) after 4 hour exposure as per protocol. The cDNA library preparation and paired-end sequencing was performed by Novogene Corporation Inc. (Sacramento, CA). Analysis was performed using the DEseq2 package in R-Suite (Warsaw, Poland). Differentially expressed genes were identified as genes that had >2-fold change in expression with adjusted p-value less than 0.01. Gene ontology analysis on the top 500 upregulated genes was performed using the PGSEA package in R.

first: Vasudha

last: Srivastava

first: Zev

last: Gartner


title: Alignment and quantification of ChIP-exo crosslinking patterns reveal the spatial organization of protein-DNA complexes

status: Public on Dec 08 2019

city: University Park

first: Shaun

last: Mahony

address: 404 South Frear Bldg

department: Biochemistry & Molecular Biology

institute: Penn State University

summary: Each protein within a regulatory complex associates with the genome by either binding DNA directly or by forming protein-protein interactions with DNA-bound proteins. In the chromatin immunoprecipitation (ChIP) assay, each protein’s unique mode of genomic association may be reflected by their patterns of formaldehyde-induced crosslinks to the DNA sequences that are in very close proximity. The ChIP-exo protocol precisely delineates protein-DNA crosslinking patterns by combining ChIP with 5' to 3' exonuclease digestion. Within a regulatory complex, the physical distance of a regulatory protein to the DNA affects crosslinking efficiencies. Therefore, the spatial organization of a protein-DNA complex could potentially be inferred by analyzing how crosslinking signatures vary between the subunits of a regulatory complex, and how they remain consistent over a set of coordinately regulated regions. Here, we present a computational framework that aligns ChIP-exo crosslinking patterns from multiple proteins across a set of regulatory regions, and which detects and quantifies protein-DNA crosslinking events within the aligned profiles. Our gapped multiple profile alignment approach does not rely on sequence motif features, but rather operates directly on the multi-protein, strand separated ChIP-exo tag patterns. The output of the alignment approach is a set of composite profiles that represent the crosslinking signatures of the complex across analyzed regulatory regions. We then use a probabilistic mixture model to deconvolve individual crosslinking events within the aligned ChIP-exo profiles, enabling consistent measurements of protein-DNA crosslinking strengths across multiple proteins. Lastly, we apply dimensionality reduction to visualize the relative organization of proteins within the regulatory complex. We demonstrate our approach by applying it to characterize regulatory complex organization in three biological settings. Firstly, we demonstrate that our alignment approach can recover the known organization of regulatory proteins at yeast ribosomal protein genes, without relying on any DNA sequence features. Secondly, we apply our gapped alignment and crosslinking quantification approaches to a novel set of ChIP-exo data to characterize the spatial organization of Pol III transcriptional machinery assembly at yeast tRNA genes. Finally, we demonstrate that our approach can be used to quantify changes in protein-DNA complex organization when applied to ChIP-nexus data from Drosophila Pol II transcriptional components in two experimental conditions. Our results suggest that principled analyses of ChIP-exo crosslinking patterns enable inference of spatial organization within protein-DNA complexes.

overall_design: Genome-wide analysis of tRNA PIC in yeast using ChIP-exo

first: Naomi

last: Yamada

first: Matthew

last: Rossi

first: Nina

last: Farrell

first: B

middle: F

last: Pugh


title: PAX5 CHIP-seq in NALM6 cell line

summary: CHIP-seq performed with no drug treatment in NALM6 cells

overall_design: PAX5 binding in NALM6 cell line


title: Canonical Wnt pathway controls mESCs self-renewal through inhibition of spontaneous differentiation via β-catenin/TCF/LEF functions

city: Barcelona

first: Maria Pia

last: Cosma

address: Dr. Aiguader

department: Gene regulation, stem cells and cancer

institute: CRG

summary: The Wnt/β-catenin signalling pathway is a key regulator of embryonic stem cell self-renewal and differentiation. Constitutive activation of this pathway has been shown to significantly increase mouse embryonic stem cell (mESC) self-renewal and pluripotency marker expression. In this study, we generated a novel β-catenin knock-out model in mESCs by using CRISPR/Cas9 technology to delete putatively functional N-terminally truncated isoforms observed in previous knock-out models. While we showed that aberrant N-terminally truncated isoforms are not functional in mESCS, we observed that canonical Wnt signalling is not active in mESCs, as β-catenin ablation does not alter mESC transcriptional profile in LIF-enriched culture conditions; on the other hand, Wnt signalling activation represses mESC spontaneous differentiation. We also showed that transcriptionally silent β-catenin (ΔC) isoforms can rescue β-catenin knock-out self-renewal defects in mESCs, cooperating with TCF1 and LEF1 in the inhibition of mESC spontaneous differentiation in a Gsk3 dependent manner.

overall_design: Gene expression analysis of β-catenin knock-out mouse embryonic stem cells treated with the Gsk3 inhibitor CHIR 99021 for 72 hours in serum and their parental cell line. A total of 8 samples is analysed: two cell lines (parental and β-catenin knock-out) in presence of CHIR 99021 or vechicle (DMSO) in duplicate.

first: Francesco

last: Aulicino

first: Elisa

last: Pedone

last: Sottile

first: Frederic

last: Lluis

first: Lucia

last: Marucci

first: Maria

middle: P


title: Inter-embryo gene expression variability recapitulates the hourglass pattern of evo-devo

status: Public on Dec 31 2019

city: Basel

first: Jialin

last: Liu

address: biozentrum, Spitalstrasse 41

institute: University of Basel

summary:
Background: The evolution of embryological development has long been characterized by deep conservation. In animal development, the phylotypic stage in mid-embryogenesis is more conserved than either early or late stages among species within the same phylum. Hypotheses to explain this hourglass pattern have focused on purifying the selection of gene regulation. Here, we propose an alternative-genes are regulated in different ways at different stages and have different intrinsic capacities to respond to perturbations on gene expression.

Results: To eliminate the influence of natural selection, we quantified the expression variability of isogenetic single embryo transcriptomes throughout fly Drosophila melanogaster embryogenesis. We found that the expression variability is lower at the phylotypic stage, supporting that the underlying regulatory architecture in this stage is more robust to stochastic variation on gene expression. We present evidence that the phylotypic stage is also robust to genetic variations on gene expression. Moreover, chromatin regulation appears to play a key role in the variation and evolution of gene expression.

Conclusions: We suggest that a phylum-level pattern of embryonic conservation can be explained by the intrinsic difference of gene regulatory mechanisms in different stages.

overall_design: 288 fly single embryo transcriptomes at eight developmental stages covering the whole embryo development with 3 h intervals

first: Michael

last: Frochaux

first: Vincent

last: Gardeux

first: Bart

last: Deplancke

first: Marc

last: Robinson-Rechavi


title: Chromatin Remodeler Ino80C acts independently of H2A.Z to evict promoter nucleosomes and stimulate transcription of highly expressed genes in yeast

status: Public on Dec 24 2019

city: Bethesda

first: Alan

middle: G.

last: Hinnubusch

address: 6 Center Dr. Bldg 6, Rm 230

institute: NICHD

summary: The chromatin remodelers (CRs) SWI/SNF and RSC function in evicting promoter nucleosomes at highly expressed yeast genes, particularly those activated by transcription factor Gcn4. Ino80 remodeling complex (Ino80C) can establish nucleosome-depleted regions (NDRs) in reconstituted chromatin, and was implicated in removing histone variant H2A.Z from the -1 and +1 nucleosomes flanking NDRs; however, Ino80C’s function in transcriptional activation in vivo is not well understood. Analyzing the cohort of Gcn4-induced genes in ino80Δ mutants has uncovered a role for Ino80C on par with SWI/SNF in evicting promoter nucleosomes and transcriptional activation. Compared to SWI/SNF, Ino80C generally functions over a wider region, spanning the -1 and +1 nucleosomes, NDR, and proximal genic nucleosomes, at genes highly dependent on its function. Defects in nucleosome eviction in ino80Δ cells are frequently accompanied by reduced promoter occupancies of TBP, and diminished transcription; and Ino80 is enriched at genes requiring its remodeler activity. Importantly, nuclear depletion of Ino80 impairs promoter nucleosome eviction even in a mutant lacking H2A.Z. Thus, Ino80C acts widely in the yeast genome together with RSC and SWI/SNF in evicting promoter nucleosomes and enhancing transcription, all in a manner at least partly independent of H2A.Z editing.

overall_design: Immunoprecipitated chromatin DNA from WT and mutant ino80∆ (induced(+SM) and uninduced(no SM)) using antibodies anti-H3, anti-H2B, anti-Rpb3, anti-TBP and anti-myc followed by paired-end sequencing.

first: Hongfang

last: Qiu

first: Emily

last: Biernat

first: Chhabi

first: Yashpal

last: Rawal

first: Razvan

last: Chereji

first: David

middle: J

last: Clark

middle: G

last: Hinnebusch


title: The effect of TRIP13 on glioma cell function and signaling pathways

status: Public on Dec 06 2019

city: Dalian

first: dapeng

last: Liang

state: Liaoning

address: lvshun south road no.9

institute: Dalian Medical University

summary: To gain insight into the molecular mechanisms underlying TRIP13-mediated oncogenic activity in GBM, we performed RNA-seq on spheres derived from U87MG-shTRIP13 and control cells .This analysis identified 1094 genes whose expression was markedly reduced by TRIP13 knockdown in U87MG-derived spheres (fold change >2, p < 0.05; Supplementary ). These downregulated genes were highly overrepresented in gene ontologies (GO) that are associated with growth factor activity, angiogenesis and chemotaxis. Gene set enrichment analysis (GSEA) showed that genes related to phosphatidylinositol 3-kinase (PI3K/AKT) pathway and genes involved in pluripotency of stem cells were significantly altered in TRIP13 knockdown GBM cells . KEGG pathway analysis revealed that the altered genes were enriched to PI3K–AKT signaling, JAK-STAT signaling and cytokine-cytokine receptor interaction. We conclude that RNA-seq based transcriptome characterization would expedite cancer signaling pathway analyses.

overall_design: Differential mRNA expression analysis of two groups

first: Lulu

last: Hu

first: Songshu

last: Meng

first: Dapeng


title: LncRNA/mRNAs expression profiling in a mouse model of age-related hearing loss

status: Public on Dec 05 2019

city: Guangzhou

first: Zhongwu

last: Su

address: 107 West Yan Jiang Road

institute: Sun Yat-sen Memorial Hospital

summary: The goals of this study are to identify transcripts that participate in the development of age-related hearing loss.

overall_design: Cochlear lncRNA and mRNA  profiles of 1-month old and 12-month old C57BL/6 mice were generated by deep sequencing, in triplicate, using Illumina  Hiseq 4000 platform.

first: Hao

last: Xiong

first: Jiaqi

last: Pang

first: Hanqing

last: Lin

first: Lan

last: Lai

first: Huasong

last: Zhang

first: Weijian

first: Yiqing

last: Zheng


title: RNA-seq identifies expressions changes upon loss of BCoR-AF9 binding

status: Public on Dec 01 2019

city: Charlottesville

first: John

last: Bushweller

state: Virginia

address: 1340 Jefferson Park Avenue

department: Molecular Physiology and Biological Physics

institute: University of Virginia

summary:
Purpose: To identify the expression changes responsible for loss of leukemogenesis upon abrogation of BCoR binding to AF9
Methods: Cells were transfected with LentiViral particles containing either WT AF9 or E531R mutants. Cells were allowed to grow for 24 hours and then harvested into TriZol for RNA isolation and sequencing.
Results: Loss of BCoR-AF9 results in change in expression of a number of genes involved in the hematopoietic lineage, cell motility and migration, and cell adhesion

overall_design: C-Kit positive bone marrow cells were examined after transfection with WT AF9 or E531R mutant AF9.

first: Charles

last: Schmidt

first: Nicholas

last: Achilles

first: Adam

last: Boulton

first: Nancy

last: Zeleznik-Li


title: Deletion of the Tug1 locus leads to male sterility and affects gene expression in multiple tissues

status: Public on Nov 22 2019

city: Cambridge

first: Abbie

last: Groff

address: 7 Divinity Ave

department: Stem Cell and Regenerative Biology;

institute: Harvard University

summary: We have sequenced wild type and mutant testes, prostate, liver, heart, spleen, and eye from adult males, as well as embryonic fibroblasts from the mutant lncRNA strain Tug1_tm1.1Vlcg (Tug1).

overall_design: Comparison between wild type and mutant organs and primary cell transcriptomes from the Tug1_tm1.1Vlcg mutant strain.

first: M

last: Sauvageau

first: E

last: Jacobs-Palmer

first: S

middle: C

last: Liapis

first: A

first: N

last: Rubinstein

first: C

last: Gerhardinger

first: J

last: Lewandowski

last: Engreitz

last: Lander

last: Dulac

first: H

middle: E

last: Hoekstra

last: Rinn


title: RNA-sequencing analysis of colon tissue in a murine EAE model after dietary tryptophan deprivation.

status: Public on Nov 01 2019

city: Kiel

first: Neha

last: Mishra

address: Rosalind-Franklin-Str. 12

institute: Institute of Clinical Molecular Biology

summary: In the experimental autoimmune encephalomyelitis (EAE) model we found that omission of the essential amino acid tryptophan (trp) abrogates central nervous system (CNS) autoimmunity. Impaired encephalitogenic T responses were accompanied by an inflammatory response in the colonic mucosa, as well as a profound shift in the gut microbiota. Here, we performed transcriptional profiling of colon tissue by RNA-sequencing 14 days after disease induction in mice that received a trp-free diet or a matched control group to identify key networks that drive this immunosuppressive effect.

overall_design: Two groups of female C57BL/6J wildtype mice were immunized with myelin oligodendrocyte glycoprotein (MOG)35-55 in Complete Freund’s Adjuvant (CFA) at the age of 7-8 weeks. One group received a trp-free diet from day 0 on until the end of the experiment. Distal colon tissue for RNA-sequencing analysis was collected 14 days post-immunization.

first: Jana

last: Sonner

first: Maren

last: Falk-Paulsen

first: Magdalena

last: Kramer

first: Katrin

last: Deumelandt

first: Lara

last: Wolf

first: Philip

last: Rosenstiel

first: Michael

last: Platten


title: Modular transcriptional programs separately define axon and dendrite connectivity

status: Public on Nov 05 2019

city: Los Angeles

first: Yerbol

middle: Z.

last: Kurmangaliyev

address: 675 Charles E. Young Drive South

summary: Patterns of synaptic connectivity are remarkably precise and complex. Single-cell RNA sequencing has revealed a vast transcriptional diversity of neurons. Nevertheless, a clear logic underlying the transcriptional control of neuronal connectivity has yet to emerge. Here, we focused on Drosophila T4/T5 neurons, a class of closely related neuronal subtypes with different wiring patterns. Eight subtypes of T4/T5 neurons are defined by combinations of two patterns of dendritic inputs and four patterns of axonal outputs. Single-cell profiling during development revealed distinct transcriptional programs defining each dendrite and axon wiring pattern. These programs were defined by the expression of a few transcription factors and different combinations of cell surface proteins. Gain and loss of function studies provide evidence for independent control of different wiring features. We propose that modular transcriptional programs for distinct wiring features are assembled in different combinations to generate diverse patterns of neuronal connectivity.

overall_design: Single-cell profiling of FACS purified populations of Drosophila melanogaster T4/T5 neurons during pupal development (24h and 48h APF).

middle: Z

first: Lawrence

middle: S

last: Zipursky