title: HyPR-seq: Single-cell quantification of chosen RNAs via hybridization and sequencing of DNA probes (HyPR-seq dataset)

status: Public on Sep 16 2020

city: Stanford

first: Jesse

last: Engreitz

address: Biomedical Innovation Building Rm 3700

institute: Stanford University

summary: Single-cell quantification of RNAs is important for understanding cellular heterogeneity and gene regulation, yet current approaches suffer from low sensitivity for individual transcripts, limiting their utility for many applications. Here we present HyPR-seq, a method to sensitively quantify the expression of 10 to 100 chosen genes in single cells. HyPR-seq involves hybridizing DNA probes to RNA, distributing cells into nanoliter droplets, amplifying the probes with PCR, and sequencing the amplicons to quantify the expression of chosen genes. HyPR-seq achieves high sensitivity for individual transcripts, detects non-polyadenylated and low-abundance transcripts, and can profile up to 100,000 single cells. We demonstrate how HyPR-seq can profile the effects of CRISPR perturbations in pooled screens, detect time-resolved changes in gene expression via measurements of gene introns, and detect rare transcripts and quantify cell type frequencies in tissue using low-abundance marker genes. By sensitively quantifying individual transcripts and directing sequencing power to genes of interest, HyPR-seq reduces costs by up to 100-fold compared to whole-transcriptome scRNA-seq approaches for these applications. HyPR-seq will be a powerful method for targeted RNA profiling in single cells.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: We performed HyPR-seq in K562 cells (45 samples), THP1 cells (8 samples), and cells from wild-type and diabetic murine kidney (4 samples). HyPR-seq data from K562 cells includes 2 samples with probes targeting highly expressed genes and some introns, 1 sample representing a single-cell mixing experiment, and 42 samples representing a timecourse study to look at the kinetics of intron expression after promoter inhibition with CRISPR interference (3 samples each at 14 timepoints). THP1 samples include 4 replicates with LPS stimulation and 4 samples without. We also performed RNA sequencing on THP1 cells with and without LPS (3 replicates each) using the Smart-seq2 protocol in bulk. Kidney cells were obtained from 12-week old BTBR mice, 2 wt/wt and 2 ob/ob.

first: Benjamin

last: Doughty

first: Fei

last: Chen


title: Sexually dimorphic roles for the type 2 diabetes-associated C2cd4b gene in murine glucose homeostasis

city: London

first: Aida

last: Martinez-Sanchez

address: Du Cane Road

country: United Kingdom

institute: Imperial College London

type: Expression profiling by high throughput sequencing

summary: Variants close to the VPS13C/C2CD4A/C2CD4B locus are associated with altered risk of type 2 diabetes in genome-wide association studies. Here have performed RNAseq on pancreatic islets from C2CD4B-null mice and their littermate controls.

overall_design: C2cd4b-null mice (C2cd4bem2Wtsi) were generated at the International Mouse Phenotyping Consortium (IMPC), using CRISPR/Cas9. RNA from pacreatic islets was isolated and

first: Guy

middle: A

last: Rutter


title: HyPR-seq: Single-cell quantification of chosen RNAs via hybridization and sequencing of DNA probes

middle: M

state: CA

country: USA

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

overall_design: Refer to individual Series


title: HyPR-seq: Single-cell quantification of chosen RNAs via hybridization and sequencing of DNA probes (scRNA-seq dataset)

middle: R


title: Loss of the seipin gene perturbs eggshell formation in Caenorhabditis elegans

status: Public on Sep 14 2020

city: Taipei

first: Leng-Jie

last: Huang

address: 128 Sec. 2, Academia Rd, Nankang

department: Institute of Plant and Microbial Biology

country: Taiwan

institute: Academia Sinica

summary: SEIPIN, an evolutionary conserved protein, plays pivotal roles during lipid droplet (LD) biogenesis and is associated with various human diseases with unclear mechanisms. Here, we analyzed C. elegans mutants deleted of the sole SEIPIN gene, seip-1. Homozygous seip-1 mutants displayed penetrant embryonic lethality, which is caused by the disruption of the lipid-rich permeability barrier, the innermost layer of the C. elegans embryonic eggshell. In C. elegans oocytes and embryos, SEIP-1 is associated with LDs and crucial for controlling LD size and lipid homeostasis. The seip-1 deletion mutants reduced the ratio of polyunsaturated fatty acids (PUFAs) in their embryonic fatty acid pool. Interestingly, dietary supplementation of selected n-6 PUFAs rescued the embryonic lethality and defective permeability barrier. Accordingly, we propose that SEIP-1 may maternally regulate LD biogenesis and lipid homeostasis to orchestrate the formation of the permeability barrier for eggshell synthesis during embryogenesis. A lipodystrophy allele of seip-1 resulted in embryonic lethality as well and could be rescued by PUFA supplementation. These experiments support a great potential for using C. elegans to model seipin-associated human diseases.

overall_design: Analysis of embryos and young adults representing seip-1_knock_outs.

first: Sheng-Wen


title: Analysis of the DNA topology in T47D-MTVL cells by Hi-C data

status: Public on Sep 15 2020

city: Barcelona

first: Albert

last: Jordan

address: Baldiri Reixac 4

department: Molecular Genomics

country: Spain

institute: IBMB-CSIC

summary: The topology of the genome in untreated T47D-MTVL cells expressing a Dox-inducible shRNA against multiple H1 variants was analyzed by performing a Hi-C experiment. The data allowed the obtention of Hi-C chromosome interaction maps, which were used to define TADs and A/B compartments, and to study the relationship between the 3D genome in breast cancer cells and other genomic properties as well as the histone H1 variants genome-wide distribution.

overall_design: Stable breast cancer-derived cells expressing an shRNA against different histone H1 isoforms in response to doxycycline (Dox) were grown for six days in the absence of Dox. An in situ Hi-C library was subsequently prepared and high-throughput sequenced to study the 3D genome.

first: A

first: N

last: Serna

first: M

last: Salinas


title: Cellular Stress Response Links Nuclear Integrity to Type-I IFN response

status: Public on Sep 22 2020

city: New york

first: Jihye

last: Paik

state: NY

address: 1300 York Ave.

department: Pathology

institute: Weill Cornell Medical College

summary: RNA_seq analysis for neural progenitor cells (NPCs)

overall_design: mRNA profiles of NPCs treated with or without paraquat or NAC for 2 days

first: Inah

last: Hwang


title: BMP signaling cooperates with GATA factors to govern stage-specific gene expression during erythroid differentiation [RNA-Seq]

city: Boston

first: Leonard

last: Zon

state: MA

address: 1 Blackfan Circle

department: Oncology/Hematology

institute: Boston Children's Hospital

summary: Hematopoietic progenitors respond to developmental and environmental cues to differentiate. The stage-specific steps of differentiation are stereotypic for each cell lineage, and are controlled by transcription. Here we investigate how differential genomic binding of signal-responsive and lineage-restricted transcription factors can specify subsequent stages of erythropoiesis. Using a human erythroid differentiation system, we extensively characterized the co-operation of the BMP signaling transcription factor SMAD1 with the erythroid transcription factors GATA2 and GATA1 in a detailed time-course. BMP signaling enhances erythroid differentiation. SMAD1 is co-recruited with GATA factors at stage-specific genes that are required to have high expression in each stage. Additionally, we observed SMAD1-GATA co-enriched regions are within super-enhancers and span accessible chromatin. Co-bound regions harbor cell-type specific transcription factor motifs that change during commitment, in contrast to GATA-alone regions. Our studies demonstrate that signal-responsive factors together with lineage regulators mark genomic “hotspots” that function to regulate stage-specific gene expression.

overall_design: RNA-seq was performed, after a 2hr pulse of hrBMP, on progenitor and differentiating cells at 2 and 6 hours and daily from days 1 through 8 of erythroid differentiation.

first: Avik

last: Choudhuri

first: Eirini

last: Trompouki

first: Brian

middle: J

last: Abraham

first: William

last: Mallard

first: Sonja

last: Boatman

first: Song

last: Yang

first: Barbara

last: Hummel

first: Yi

last: Zhou

first: Teresa

middle: V

last: Bowman

first: John

middle: L

last: Rinn

first: Richard

last: Young

middle: I


title: BMP signaling cooperates with GATA factors to govern stage-specific gene expression during erythroid differentiation [ChIP-Seq]

type: Genome binding/occupancy profiling by high throughput sequencing

overall_design: ChIP-Seq for H3K27ac, GATA1, GATA2, and SMAD1, after a 2hr pulse of hrBMP, on progenitor and differentiating human CD34+ cells towards erythrocytes.


title: BMP signaling cooperates with GATA factors to govern stage-specific gene expression during erythroid differentiation [ATAC-Seq]

overall_design: ATAC-seq was performed, after a 2hr pulse of hrBMP, on progenitor and differentiating cells at 6 hours and daily from days 1 through 5 days of erythroid differentiation.


title: Effects of inteference with LSD1 on Spermatogenic stem cell transcriptome

status: Public on Sep 09 2020

city: yangzhou

first: Qisheng

last: Zuo

state: Jiangshu

address: wenhui road 48#

country: China

institute: Yangzhou University

summary: In order to study the effect of histone methylation modification on the formation of SSCs, this study intends to conduct interference on LSD1 in SSCs, collect treated cells for RNA-SEQ, screen differentially expressed genes, and analyze the relationship between the expression of these genes and histone methylation modification.

overall_design: The differentially expressed genes after LSD1 interference were screened

first: Zuo

last: Qisheng

first: Li

last: Bichun


title: Real-time PCR analysis during mule duck development

city: Mont de Marsan

first: Marianne

last: Houssier

address: 371 rue du ruisseau

department: GB

country: France

institute: INRA NUMEA/IUT UPPA

summary:
This study proposes to describe the basal hepatic metabolism at the level of mRNA in mule duck embryos
A kinetic study was designed to determine the level of expression of selected genes involved in liver metabolism throughout embryogenesis

overall_design: The livers of 20 mule duck embryos were collected every four days from the 12th day of embryogenesis (E12) until 4 days after hatching (D4), and gene expression analysis was performed. The expression levels of 50 mRNAs were quantified for these 7 sampling points and classified into 4 major cellular pathways

last: Massimino


title: BMP signaling cooperates with GATA factors to govern stage-specific gene expression during erythroid differentiation

last: Zon


title: HyPR-seq: Single-cell quantification of chosen RNAs via hybridization and sequencing of DNA probes (bulk RNA-seq dataset)

first: Jesse

last: Engreitz

first: Benjamin

last: Doughty

first: Fei

last: Chen


title: Expression data from wild-type and cardiac specific miR-125b-1 knockout neonatal hearts

status: Public on Sep 10 2020

first: Chen-Yun

address: 128 Sec. 2, Academia Rd.

department: Institute of Biomedical Science

institute: Acdemia Sinica

summary: MicroRNA-125b is abundant in hearts while its function is not well understood. We used microarray to investigate the global changes of transcriptome for functional evaluation.

overall_design: Total RNAs from wild-type and cardiac specific miR-125b-1 neonatal hearts were isolated from the ventricles using Trizol (Invitrogen) according to the manufacturer’s protocol and purifed with RNeasy Mini Kit (Qiagen).

first: Desy

middle: S

last: Lee


title: The RNA-binding protein SFPQ preserves long-intron splicing and regulates circRNA biogenesis

city: Aarhus C

first: Thomas

middle: B

last: Hansen

state: State...

address: C.F. Moellers Alle 3, build 1130

country: Denmark

institute: MBG, Aarhus University

type: Non-coding RNA profiling by high throughput sequencing

summary: Circular RNAs (circRNAs) represent an abundant and conserved entity of non-coding RNAs, however the principles of biogenesis are currently not fully understood. To elucidate features important for circRNA production, we performed global analyses of RNA-binding proteins associating with the flanking introns of circRNAs, and we identified two factors, SFPQ and NONO, to be highly enriched with circRNAs. We observe a subclass of circRNAs, coined DALI circRNAs, with distal inverted Alu elements and long introns to be highly deregulated upon SFPQ knockdown. Moreover, SFPQ depletion leads to increased intron retention with concomitant induction of cryptic splicing prevalent for long introns causing in some cases premature transcription termination and polyadenylation. Aberrant splicing in the upstream and downstream regions of circRNA producing exons are critical for shaping the circRNAome, and specifically, we identify a conserved impact of missplicing in the immediate upstream region to drive circRNA biogenesis. Collectively, our data show that SFPQ plays an important role in maintaining intron integrity by ensuring accurate splicing of long introns, and disclose novel features governing Alu-independent circRNA production.

overall_design: Total RNA sequencing and quantSeq on RNA from HepG2 and HEK293T subjected to SFPQ and NONO depletion

first: Lotte

last: Stagsted


title: Transcriptome analysis of Clostridium autoethanogenum under CdS autotrophic condition

city: Daejeon

first: Sangrak

last: Jin

address: 291 Daehak-ro, Yuseong-gu

department: Department of Biological Science

country: South Korea

institute: Korea Advanced Institute of Science and Technology

summary: Acetogenic bacteria utilize cellular redox energy to convert CO2 to acetate using the Wood-Ljungdahl (WL) pathway. Such redox energy can be derived from electrons generated from H2 as well as inorganic materials such as photo-responsive semiconductors. To reveal how acetogenic bacteria utilize electrons generated from external energy sources to reduce CO2, we developed a nanoparticle-microbe hybrid system and generated RNA-seq results.

overall_design: We generated RNA-seq results of Clostridium autoethanogenum under three different energy conditions in triplicates using Illumina Hiseq

first: Yale

last: Jeon

first: Min-Soo

first: Jongoh

last: Shin

first: Yoseb

last: Song

first: Seulgi

last: Kang

first: Jiyun

last: Base

first: Jung-Kul

first: Dong-Rip

last: Kim

first: Suhyung

last: Cho

first: Byung-Kwan


title: Single-cell analysis of developing and azoospermia human testicles reveals central role of Sertoli cells

status: Public on Sep 04 2020

city: Zhuhai

first: Liangyu

last: Zhao

state: Guangdong

address: 52th Meihua Road, Zhuhai, China

institute: Shanghai Jiao Tong University School of Medicinethe Fifth Affiliated Hospital of Sun Yat-sen University

summary: Non -obstructive azoospermia (NOA) affects 1% of men. However, the unknowns of NOA pathogenesis and even normal spermatogenic microenvironment establishment severely limit the clinical efficacy of NOA treatment. We profiled > 80,000 human testicular single-cell transcriptomes from 10 healthy donors spanning the range from infant to adult and 7 NOA patients. Sertoli cells, which form the scaffold in the testicular microenvironment, exhibited the most obvious damages in NOA patients. We identified roadmap of Sertoli cell maturation. Notably, Sertoli cells of patients with congenital causes (Klinefelter syndrome and Y chromosome microdeletions) are mature but with abnormal immune response, while the cells in idiopathic NOA (iNOA) are basically physiologically immature. Furthermore, inhibition of Wnt signaling promotes the maturation of Sertoli cells from iNOA patients, allowing these cells to regain their ability to support germ cell survival. We provide a novel perspective for the development of diagnostic methods and therapeutic targets for NOA.

overall_design: we profiled cells from 10 donors with normal spermatogenesis (one sample of 2, 5, 8, 11, 17 years old respectively and five normal adult samples) and 7 NOA patients (KS (3 cases), AZFa_Del (1 case), and iNOA (3 cases))

first: LiangYu

first: ChenCheng

last: Yao

first: Zhi

last: Zhou

first: Zheng

last: Li


title: Non-destructive enzymatic deamination enables single molecule long read sequencing for the determination of 5-methylcytosine and 5- hydroxymethylcytosine at single base resolution

status: Public on Sep 01 2020

city: Ipswich

first: Zhiyi

last: Sun

state: MASSACHUSETTS

address: 240 County Road

department: Research

institute: New England Biolabs

type: Methylation profiling by high throughput sequencing

summary: Bisulfite treatment damages the DNA leading to fragmentation and loss of long-range methylation information. To overcome this limitation of bisulfite treated DNA we applied a new enzymatic deamination approach, termed EM-seq (Enzymatic Methyl-seq) to long-range sequencing technologies. Our methodology, named LR-EM-seq (Long Range Enzymatic Methyl-seq) preserves the integrity of DNA allowing long-range methylation profiling of 5-mC and 5-hmC) over several kilobases of genomic DNA. Applied to known differentially methylated regions (DMR), LR-EM-seq achieves phasing of over 5 kb resulting in much broader and better defined DMRs than previously reported.

overall_design: We adapted a novel enzymatic deamination method for 5-cytosine modification detection to long read sequencing technologies (such as PacBio SMRT sequencding and Oxford Nanopore sequencing) to phase 5mC and 5hmC of long molecules. The resulting method, termed herein Long-Read-EM-seq (LR-EM-seq), utilizes the selective enzymatic protection of 5mC and/or 5hmC prior to enzymatic deamination by APOBEC3A and large fragment sequencing sample preparation to accurately profile both 5-mC and 5-hmC at base resolution. The preservation of DNA integrity allows the locus-specific amplification of several kb of genomic DNA and the long-range phasing at molecular resolution of 5-mC and 5-hmC.

first: Romualdas

last: Vaisvila

first: Laurence

last: Ettwiller


title: Transcriptomic and clonal characterization of T cells in the human central nervous system

status: Public on Sep 02 2020

city: New Haven

first: Le

last: Zhang

state: CT

address: 300 George Street

department: Neurology

institute: Yale University

summary: Tissues develop unique homeostatic immune states through specific recruitment of immune cells that are further shaped by the tissue environment. Here, we use single-cell RNA and TCR sequencing of healthy cerebrospinal fluid (CSF) and single-nucleus RNA sequencing of brain parenchyma to profile the T cell state in the human central nervous system (CNS). We observe a continuum of T cell states, reflecting a blood-CSF “axis”, that we use to reveal that T cells in the CSF largely exhibit a tissue-resident phenotype with a balance of co-inhibitory and effector function gene expression, including PD-1+ T cells retaining the ability to produce IFNg. Leveraging paired single-cell TCR sequencing to identify clonal T cell groups, we find that T cell phenotypes mirror the tissue where they reside and that clonally-expanded T cells reflect the most CSF-distinct state. To identify how this T cell state is perturbed during neuroinflammation, we profiled newly-diagnosed, treatment-naive patients with multiple sclerosis (MS) and observed that clonally expanded T cells are the most phenotypically different between patients and healthy controls. We then identify putative pathways of communication between T cells in the brain parenchyma and glia and neurons that may be involved in shaping T cell function. Our elucidation of the CNS T cell state provides context for understanding neuroinflammation and neurodegeneration as well as providing a framework for understanding tissue-driven T cell adaptation.

overall_design: This series includes only single nucleus RNA Sequencing. The TCR-seq data were submitted to dbGaP.

first: David

last: Hafler

first: Jenna

last: Pappalardo

last: van Dijk


title: Genome wide expression patterns of 19 human urinary cells as well as 6 primary urinary cells and 17 corresponding iPSCs of human, gorilla and orangutan

status: Public on Aug 31 2020

city: Planegg-Martinsried

first: Johanna

last: Geuder

address: Großhadernerstr. 2

country: Germany

institute: LMU

summary: Comparing the molecular and cellular properties among primates is crucial to better understand human evolution and biology. However, it is difficult or ethically even impossible to collect matched tissues from many primates, especially during development. An alternative is to model different cell types and their development using induced pluripotent stem cells (iPSCs). These can be generated from many tissue sources, but non-invasive sampling would decisively broaden the spectrum of non-human primates that can be investigated. Here, we report the generation of primate iPSCs from urine samples. We first validate and optimize the procedure using human urine samples and show that Sendai virus transduction of  reprogramming factors into urinary cells efficiently generates integration-free iPSCs, which maintain their pluripotency under feeder-free culture conditions. We demonstrate that this method is also applicable to gorilla and orangutan urinary cells isolated from a non-sterile zoo floor. We characterize the urinary cells, iPSCs and derived neural progenitor cells using karyotyping, immunohistochemistry, differentiation assays and RNA-sequencing. We show that the urine-derived human iPSCs are indistinguishable from well characterized PBMC-derived human iPSCs and that the gorilla and orangutan iPSCs are well comparable to the human iPSCs. In summary, this study introduces a novel and efficient approach to generate primate iPSCs non-invasively from urinary samples.

sample_organism:
Gorilla gorilla
Pongo abelii
Homo sapiens

overall_design: RNA-seq of 6 urinary cells and 17 iPSC lines of human, gorilla and orangutan and RNA-seq of 19 single urinary cell colonies from six human individuals


title: Fatty acid metabolism mediates venetoclax resistance in acute myeloid leukemia stem cells

city: Aurora

first: Brett

last: Stevens

state: CO

institute: University of Colorado

summary: The combination of venetoclax with azacitidine (ven/aza) has recently emerged as a promising  regimen for acute myeloid leukemia (AML), with approximately 70% of newly diagnosed patients  achieving complete remission (CR). However, 30% of newly diagnosed and nearly all relapsed  patients do not achieve CR with ven/aza. Mechanistically, we previously reported that ven/aza  efficacy is based on eradication of AML stem cells through a mechanism involving inhibition of  amino acid metabolism, a process which is required in primitive AML cells to drive oxidative  phosphorylation. In the present study we demonstrate that resistance to ven/aza occurs as a  consequence of up-regulated fatty acid oxidation (FAO), which occurs either as an intrinsic  property of RAS pathway mutations, or as a compensatory adaptation in relapsed  disease. Utilization of FAO obviates the need for amino acid metabolism into the TCA cycle,  thereby rendering ven/aza ineffective. Importantly, we show that pharmacological inhibition of  FAO via use of MCL-1 or CPT1 inhibitor drugs restores targeting of ven/aza resistant AML stem  cells. Based on these findings we propose that inhibition of FAO is a potential therapeutic  strategy to address ven/aza resistance.

overall_design: RNA was isolated from freshly sorted primary AML cells and subjected to RNA-seq analysis.

first: Shanshan

last: Pei

first: Craig

middle: T

last: Jordan


title: Basis of Specificity for a Conserved Promiscuous Chromatin Remodeling Protein [RNA-Seq]

city: Eugene

first: Laura

middle: Emily

last: McKnight

state: Oregon

address: 1318 Franklin Blvd Room 273 Onyx Bridge

department: Institute of Molecular Biology

institute: University of Oregon

summary: We propose an interacting barrier mechanism for cooperation between Isw2-related proteins and sequence-specific DNA binding factors.

overall_design: Transcription profiling data (Strand-specific RNA-seq from rRNA-depleted samples) from yeast with different truncations or deletions as indicated

first: Drake

last: Donovan

first: Johnathan

last: Crandall

first: Vi

last: Truong

first: Thomas

last: Bailey

first: Devin

last: Dinwiddie

first: Abigail

last: Vaaler

first: Jeffrey


title: Chromosome localization of cohesin oligomers in mid-M arrested yeast cells

city: Berkeley, CA

first: Siheng

last: Xiang

state: California

address: 1 Barker Hall

institute: UC Berkeley

summary: We report the genomic localization of cohesin oligomers in nocodazole arrested yeast cells. Two alleles of SMC3 were expressed in yeast cells, one fused to BirA enzyme and the other tagged with AviTag. Cohesin oligomers were biotinylated and ChIP with streptavidin beads. As control experiments, cohesin localization on chromosome was determined in strains expresses freely diffusable BirA enzyme, where all Smc3 proteins were biotinylated; non-specific ChIP were determined in strains with no BirA.

overall_design: Comparing ChIP results of biotinylated Smc3p-AviTag in strains expressing Smc3p-BirA, NLS-BirA or no BirA.

first: Douglas

last: Koshland


title: Influenza virus infection induces widespread alterations of host cell splicing

city: Helsinki

first: Clara

last: Benoit-Pilven

address: Tukholmankatu 8

country: Finland

institute: Helsinki University

summary: Influenza A viruses (IAV) use diverse mechanisms to interfere with cellular gene expression and thus limit the antiviral responses and/or promote viral replication. Although many RNAseq studies have documented IAV-induced changes in host mRNA abundance, few were designed to allow an accurate quantification of changes in host mRNA splicing. Here we show that IAV infection of human lung cells induces widespread alterations of cellular splicing, with an overall increase in exon inclusion and decrease in intron retention. Over half of the mRNAs that show differential splicing undergo no significant changes in abundance or in their 3’ end termination site, suggesting that IAV can directly manipulate cellular splicing independently of other transcriptional changes. Cross-analysis of the alternative splicing profiles of IAV-infected and RED-depleted cells demonstrates a partial phenocopying of the RED-knock down phenotype in infected cells, suggesting that hijacking of the RED factor by IAVs to promote splicing of their own mRNAs could account for a minor subset of splicing changes in infected cells. All our results can be expored through a Shiny user friendly interface (http://virhostnet.prabi.fr:3838/shinyapps/flu-splicing).

overall_design: RNA-seq on polyA+ RNAs from A549 cells infected with the influenza virus A/WSN/33 or mock-infected, and either untreated, transfected with a control siRNA, or transfected with a siRNA targeting the splicing factor RED.  Four biological replicates (R2 to R5) were performed for each of the 6 experimental condition.

first: Usama

last: Ashraf

first: Vincent

last: Navratil

last: Lacroix

first: Nadia

last: Naffakh


title: Low-dose decitabine priming endows CAR T cells with enhanced and persistent anti-tumor potential by epigenetic reprogramming in vivo and in vitro

status: Public on Aug 14 2020

city: Beijing

first: Wang

last: Yao

address: No. 28, fuxing street

institute: Chinese general PLA hospital

summary: Chimeric antigen receptor T (CAR T) cells targeting CD19 have achieved breakthroughs in the treatment of haematological malignancies, but many clinical studies have also shown that a proportion of patients relapse after remission.In this study, we designed CART treatment by DNMTi（dCART) inhibitor and found that dCAR T cells retained relatively potent antitumour activity compared with CAR T cell upon target antigen recognition. It may be associated with memory and anti-exhausion. Our transcriptional analysis underscores the potential of  dCAR T cells.

overall_design: In order to assess the different phenotypic and functional patterns of CARs between dCAR T and CAR T, we compared the genome-wide transcriptional profiles of dCAR and CAR T cell before and after cocultured with Raji cells for 24 h.

first: Han

last: Weidong


title: Basis of Specificity for a Conserved Promiscuous Chromatin Remodeling Protein

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

overall_design: Refer to individual Series


title: RNAseq of nasal cells from pre-symptomatic volunteers experimentally infected with RSV

city: London

first: Christopher

last: Chiu

address: Hammersmith Campus, Du Cane Road

department: Infectious Disease

institute: Imperial College London

summary: We report the analysis of nasal curettage cells by RNAseq collected at pre-symptomatic timepoints in healthy adults experimentally challenged with respiratory syncytial virus (RSV). Following inoculation, 57% of participants developed PCR-confirmed infection. Prior to viral challenge, 80 differentially expressed genes were identified that associated with susceptibility to symptomatic infection. At day 3, 87 differentially expressed genes were associated with protection. Thus, we showed that the nasal mucosa at the time of virus exposure and during the incubation phase correlate with susceptibiltiy and protection from respiratory viral infection.

overall_design: Analysis of human nasal curettage tissue by RNA sequencing.

first: Chiu

last: Christopher


title: Real-time quantitative PCR analysis of human mesenchymal stromal (MSC)  cells extracellular vesicles (EV)

status: Public on Aug 27 2020

city: Clamart

first: Sébastien

last: Banzet

address: rue Lt Raoul Batany

institute: INSERM U1197

summary: Bone Marrow MSC were isolated from 5 donnors, EV were isolated by unltracentrifugation from the conditionned media after 48h without serum. 3 conditions are described: control, interferon priming (25 ng/ml) or hypoxia priming (O2 = 3%)

overall_design: qPCR miRNA array

first: Juliette

last: Petzer

first: Kyle

last: Lund


title: Inhibition of O-GlcNAcylation via O-GlcNAc transferase fosters megakaryopoiesis and induces thrombopoiesis

status: Public on Aug 06 2020

city: Bangkok

first: Sudjit

last: Luanpitpong

state: Bangkok

address: Bangkoknoi

department: Research Division

country: Thailand

institute: Mahidol University

summary: We report that cellular O-GlcNAcylation levels decline along the course of megakaryocyte (MK) differentiation from human-derived hematopoietic stem and progenitor cells (HSPCs) and that inhibition of O-GlcNAc transferase (OGT), of which catalyzes O-GlcNAcylation, prolongedly decreases O-GlcNAcylation and induces megakaryopoiesis and thrombopoiesis. To gain the better insight into the potential mechanisms underlying platelet regulation by O-GlcNAcylation ,we compared the genome-wide transcription profiles of megakaryblastic MEG-01 cells with decreased O-GlcNAcylation (OGTi) and its control counterpart using RNA sequencing. Gene ontology and enrichment analysis of differentially expressed genes suggest that platelet formation might be regulated through the perturbation in cell adhesion molecules, i.e. integrin-a4 and b7, downstream of O-GlcNAc/c-Myc axis.

overall_design: Genome-wide transcription profiles of CRISPR/Cas9-mediated OGT knockdown and control MEG-01 cells, using Illumina NovaSeq6000.

first: Jirarat

last: Poohadsuan

first: Xing

last: Kang


title: Fatty acid metabolism mediates venetoclax resistance in acute myeloid leukemia stem  cells

status: Public on Aug 17 2020

first: Brett

last: Stevens

first: Michael

last: Becker

first: Shanshan

last: Pei

first: Craig

last: Jordan


title: High throughput phenotypic screen and transcriptional analysis identify new compounds, targets and pathways for macrophage reprogramming

status: Public on Aug 05 2020

city: Cambridge

first: Guangan

last: Hu

address: 500 Main Street

department: Koch Institute

institute: MIT


title: High throughput phenotypic screen and transcriptional analysis identify new compounds, targets and pathways for macrophage reprogramming III

summary: Purpose: To understand the effects of signaling ligands on human macrophage polarization in the transcriptional level

overall_design: Fresh isolated human blood monocytes were  cultured with 50ng/mL M-CSF for 7 days to generate M0 status macrohages.  Macrophages were treated with serontonin, dopamine, vegfa, egf and leptin for 24 hrs. RNA was isolated and purified by Qiagen Rneasy micro kit and applied to RNAseq.

first: Jianzhu

last: Chen


title: Chromatin structure restricts origin utilization when quiescent cells re-enter the cell cycle

status: Public on Aug 07 2020

city: Albuquerque

first: Po-Hsuen

last: Lee

state: NM

address: MSC 08 4660, 1 University of New Mexico

department: Molecular Genetics & Microbiology

institute: University of New Mexico Health Science Center

summary: Quiescent cells reside in G0 phase, which is characterized by the absence of cell growth and proliferation. These cells remain viable and re-enter the cell cycle when prompted by appropriate signals.  Using a budding yeast model of cellular quiescence, we investigated the program that initiated DNA replication when these G0 cells resumed growth.  We performed BrdU IP-Seq to examine the DNA replication profile genome-wide. These data revealed that the initiation of replication was delayed and fewer origins were active when G0 cells entered the cell cycle compared to the entry of G1 cells into S phase. We found that both the transcript and protein levels of these replication factors were significantly diminished during the development of proliferating cells into quiescence. The levels of these factors, including MCM2-7 helicase, increased as G0 cells re-entered the cell cycle, suggesting that the replication program is re-established de novo. Consistent with these results, Mcm4 ChIP-seq analysis showed fewer and reduced binding at a number of origins during the re-entry of G0 cells into the cell cycle. In support of this evidence, the chromatin context surrounding inactive origins of G0 cells exhibits greater increased nucleosome occupancy and reduced periodicity of nucleosome positioning. Altogether, these observations provide insights into the important role of chromatin context that determines the ability of replication origin to accrue limiting replication factors during the the re-entry of quiescent cells into the cell cycle.

overall_design: For BrdU IP-seq, G1 or Go cells were released into YPD+0.2M HU and incubated with 800 μg/ml of BrdU for overlapping periods of 20 min prior to harvesting. G1 released cells were collected at 25, 40, 55, and 70 min and G0 released cells were collected at 85, 100, 115, 130, 145 and 165 min after BrdU pulse-labeling. For Mcm4 ChIP-seq,  G0 cells were released into YPD+0.2 M HU and collected at 90 and 105 min. G1 cells were collected after incubation with alpha-factor for 135 min. The ChIP and input DNA from collected samples were amplified separately using an Ion Xpress Plus Fragment Library kit and sequenced with the Ion S5 System (ThermoFisher).

first: Mary

last: Osley


title: High throughput phenotypic screen and transcriptional analysis identify new compounds, targets and pathways for macrophage reprogramming II

summary: Purpose: To understand compound effects on human macrophage repolarization in the transcriptional level

overall_design: Fresh isolated human blood monocytes were  cultured with 50ng/mL M-CSF for 7 days to generate M0 status macrohages. Macrophages were differentiated into M1 macrophages (M1 Mac) by 50ng/mL IFNg plus 50ng/mL TNFa or M2 macrophages (M2 Mac) by 10ng/mL IL4 plus 10ng/mL IL13.  M2 Mac were treated with different M1-type compounds or IFNg or DMSO for 24 hrs. M1 Mac were treated with different M2-type compounds or IL4 or DMSO for 24 hrs. RNA was isolated and purified by Qiagen Rneasy micro kit and applied to RNAseq.

first: Guanga

first: Jianzh


title: High throughput phenotypic screen and transcriptional analysis identify new compounds, targets and pathways for macrophage reprogramming I

summary: Purpose: To understand compound effects on human macrophage polarization in the transcriptional level

overall_design: Fresh isolated human blood monocytes were  cultured with 50ng/mL M-CSF for 7 days to generate M0 status macrohages.  Macrophages were treated with different chemicals or cytokines for 24 hrs. RNA was isolated and purified by Qiagen Rneasy micro kit and applied to RNAseq.


title: Transcriptional and proteomic insights into phytotoxic activity of interspecific potato hybrids with low glycoalkaloid contents.

status: Public on Aug 04 2020

city: Mlochow

first: Dorota

last: Sołtys-Kalina

address: Platanowa 19

department: Mlochow Research Centre

country: Poland

institute: IHAR-PIB

summary: We examined phytotoxic potential of diploid potato hybrids from 15-1 population. Individuals were bulked in bulks C and D. Both bulks characterized low total glycoalkaloids content and differ phytotoxic potential. Water extract prepared from leaves of individuals of bulk C inhibited growth of test plant - mustard in 40%, while in bulk D no inhibition was observed. To evaluate cause  of expression of phytotoxic potential in bulk C, we examined glycoalklaoids composition in leaf water extract (mass spectrometry), compared gene (deep RNA sequencing - BGISEQ) and protein expression (nano-LC-MS-MS/MS)  profiles between the bulks. Bulks differed in glycoalkaloids composition, bulk C contained alpha-solasonine which wasn't detected  in bulk D. We concluded, alpha-solasonine may act together with alpha-solamargine and increases phytotoxic potential of leave extract of bulk C. Comparison of gene expression profiles indicating on contribution of genes, not directly involved in glycoalkaloids biosynthesis to express  phytotoxic potential of C bulk. We have found 3 proteins characteristic for C bulk and 2 proteins characteristic for D bulk. We found one protein threonine dehydratase biosynthetic, which is more abundant in D bulk and his abundance  corresponds with gene transcripts found in RNA-seq experiment.

overall_design: Examination of potato phytotoxic potential  under low glycoalkaloids content.

first: Katarzyna

last: Szajko

first: Jarosław

last: Ciekot

first: Iwona

last: Wasilewicz-Flis

first: Waldemar

last: Marczewski


title: A gene expression prognostic signature for overall survival in patients with high-grade serous ovarian cancer

status: Public on Aug 20 2020

city: Kensington

first: Susan

last: Ramus

state: NSW

address: High Street

department: School of Women's and Children's Health

country: Australia

institute: UNSW Sydney

summary: Expression of 276 genes was associated with OS at a false discovery rate (FDR) of < 0.05 in covariate-adjusted single gene analyses. The top five genes were TAP1, ZFHX4, CXCL9, FBN1, and PTGER3 (p ≪ 0.001). The best performing signature included 101 genes and for each SD difference in the gene expression score conferred a greater than two-fold increase in risk of death (HR = 2.35 [2.02, 2.71]; p ≪ 0.001). Median survival by quintile group was 9.5, 5.4, 3.8, 3.2 and 2.3 years.

overall_design:
Expression of 513 genes was measured in formalin-fixed paraffin-embedded (FFPE) tumor tissue from 3,769 women with HGSOC. Regression-based and machine learning methods were used to develop a prognostic signature for OS. Prognostic models were trained on two thirds of the data and evaluated on the remaining third.

Contributor: AOCS Group

first: Joshua

last: Millstein

first: Timothy

last: Budden

first: Ellen

last: Goode

last: Anglesio

first: Aline

last: Talhouk

first: Maria

middle: P

last: Intermaggio

first: Huei

last: Leong

first: Stephanie

first: Wafaa

last: Elatre

first: Tayyebeh

last: Nazeran

first: Mila

last: Volchek

first: Chen

last: Wang

first: Derek

last: Chiu

first: Stefan

last: Kommoss

first: Samuel

middle: C

last: Leung

first: Janine

last: Senz

first: Veronica

last: Chow

first: Hanwei

last: Sudderuddin

first: Robertson

last: Mackenzie

first: Sian

last: Fereday

first: Joy

last: Hendley

first: Helen

last: Steed

first: Jennifer

last: Koziak

first: Martin

last: Köbel

first: Iain

last: McNeish

first: Teodora

last: Goranova

first: Darren

last: Ennis

first: Geoff

last: Macintyre

first: Dilrini

last: Silva

first: Teresa

last: Ramón Y Cajal

first: Jesús

last: García-Donas

first: Susanna

middle: H

last: Polo

first: Gustavo

last: Rodriguez

first: Kara

last: Cushing-Haugen

first: Holly

last: Harris

first: Casey

last: Green

first: Rene

last: Zelaya

first: Sabine

last: Behrens

first: Renée


title: The SNARE Regulator Complexin3 is a Target of the Cone Circadian Clock in the Mouse Retina

status: Public on Aug 03 2020

city: Houston

first: Haichao

last: Wei

state: TX

address: 1825 Pressler St., SRB 637.C

institute: UTHealth

summary:
Purpose: The goals of this study are to evaluate the impact of the removal of the key circadian clock component BMAL1 on the transcriptome of cone photoreceptors
Methods: Cone mRNA profiles of adult wild-type (WT, HRGPcre;Bmal1f/+) and cone-specific BMAL1 (HRGPcre;Bmal1f/f or cone-Bmal1−/−) mice were generated by deep sequencing, in triplicate, using Illumina GAIIx. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks. qRT–PCR validation was performed using TaqMan and SYBR Green assays
Results: Comparison of the cone transcriptome between cone-Bmal1-/- and wild-type littermates at a single time point (middle of the light phase) revealed 88 genes differentially expressed (P < 0.05, fold change > 2). As expected, these 88 genes included known clock components but also genes known to be involved in a wide range of functions: gene regulation, neuron development and structure, protein binding, and transport.
Conclusions: Our study represents the first detailed analysis of cone-BMAL1 transcriptomes, with biologic replicates, generated by RNA-seq technology. These data are consistent with the view that the cone clock controls many aspects of the development, maintenance, and function of the cones through its control of the transcriptome.

overall_design: Retinal cone photoreceptor mRNA profiles of adult wild type (WT) and cone-specific BMAL1-/- mice

first: Jacob

middle: D

last: Bhoi

first: Zhijing

last: Zhang

first: Roger

last: Janz

first: Yanan

last: You

first: Jiaqian

last: Wu

first: Christophe

last: Ribelayga


title: Thipstrepton activated tumor-associated macrophage

first: Guangan

last: Hu

summary: Purpose: To understand the effects of compound thipstrepton on tumor-associated macrophage

overall_design: TAM were sorted from B16F10 tumors treated with thiostrepton by IP injection or tumor-adjacent injection (IS). RNA was isolated and purified by Qiagen Rneasy micro kit and applied to RNAseq.

first: Jianzhu

last: Chen


title: RNA-seq analysis of Scn1a +/- mouse

status: Public on Aug 01 2020

city: Huntsville

first: Gregory

last: Barsh

state: ALABAMA

address: 601 Genome Way

institute: HudsonAlpha Institute for Biotechnology

summary: In this study we recapitulated in the mouse, an SCN1A mutation found in a human Dravet syndrome (DS) patient. The targeted mutation, NC_000068.7:g.66293870C>G (GRCm38.p6) lies in a highly conserved alternate poison exon (20N) of the mouse Scn1a. We performed molecular and behavioral analysis of Scn1a +/- mice and Scn1a +/+ littermate controls. We found that the mutation causes Scn1a mRNA and protein levels to be reduced by about 50% in brain compared to control mice. In addition, the Scn1a +/- mice exhibit behavioral phenotypes seen in previous DS model mice models. We performed qPCR and RNA-seq analysis of the brains of four Scn1a +/- mice and four Scn1a +/+ littermate controls. There was a ~50% reduction in Scn1a RNA-seq counts in Scn1a +/- mice. Our data provides evidence that the mutation causes increased inclusion of the poison exon 20N in Scn1a transcripts leading to nonsense mediated decay and reduction in protein levels.

overall_design: RNA-seq analysis of four Scn1a +/- mice and four Scn1a+/+ littermate controls (brain tissue).

first: Gopal

last: Battu

first: Yuliya

last: Voskobiynyk

first: Stephanie

last: Felker

first: Nicholas

last: Cochran

first: Megan

last: Newton

first: Laura

last: Lambert

first: Robert

last: Kesterson

first: Richard

last: Myers

last: Cooper

first: Erik

last: Roberson


title: Two subsets of stem-like CD8+ memory T cell progenitors with distinct fate commitments in humans

city: Rozzano, Milan

first: Emilia Maria Cristina

last: Mazza

address: Via Alessandro Manzoni, 56

country: Italy

institute: Humanitas Clinical and Research Center

summary: T cell memory relies on the generation of antigen-specific progenitors with stem-like properties. However, the identity of these progenitors has remained unclear, precluding a full understanding of the differentiation trajectories that underpin the heterogeneity of memory and effector T cells. Here, we used a series of high-dimensional approaches guided by single-cell RNA sequencing data to map the organizational structure of the human CD8+ memory T cell pool under physiological conditions. We identified two previously unrecognized subsets of clonally, epigenetically, functionally, phenotypically, and transcriptionally distinct stem-like CD8+ memory T cells. Progenitors lacking the inhibitory receptors programmed death-1 (PD-1) and T cell immunoreceptor with Ig and ITIM domains (TIGIT) were committed to a functional lineage, whereas progenitors expressing PD-1 and TIGIT were committed to a dysfunctional, exhausted-like lineage. Collectively, these data revealed the existence of parallel differentiation programs in the human CD8+ memory T cell pool, with potentially broad implications for the development of immunotherapies and vaccines.

overall_design: Heterogeneity of the bulk CD95+ CD8+ memory T cells sorted from four human healthy donors' peripheral blood.

first: Giovanni

last: Galletti

first: Gabriele

last: De Simone

first: Emilia

first: Puccio

last: Simone

first: Clelia

last: Peano

first: Enrico

last: Lugli


overall_design: RNA-Seq profiling of TSTEM and TPEX sorted from four healthy donors' peripheral blood after in vitro stimulation.


title: Whole blood leukocytes gene expression in human subjects exposed to printing shop particles

city: Ann Arbor

first: Bioinformatics

last: Core

state: MI

address: BRCF Bioinformatics Core, 2800 Plymouth Rd

institute: University of Michigan

summary: This study investigates differential expression in human blood leukocytes, from subjects who work in print shops, exposed to particles over time. The time points range over 2 weeks: 1-Monday, 2-Friday, 3-following Monday (rested), and 4-Friday

overall_design: 40 RNA samples were extracted from human blood. Some did not pass quality control. We are left with 33 samples, from 9 individuals, most with all 4 time points (TP), and three with one TP missing.

first: Nancy

last: Guo

first: Phil

last: Demokritou


overall_design: RNA-Seq profiling of TSCM PD1-TIGIT-, TCM PD1-TIGIT-, TPEX and TEM sorted from five healthy donors' peripheral blood.


title: Global gene expression analysis of breast cancer cell line responses to Topsentinol L Trisulfate or DMSO as the vehicle control

status: Public on Jul 30 2020

city: Salt Lake City

first: Philip

last: Moos

state: UT

department: Pharmacology & Toxicology

institute: University of Utah

summary: We generated a signature for topsentinol L trisulfate in breast cancer cells to predict drug sensitivity in other available datasets. To process the mRNA sequencing data, we used the TCGA mRNA-seq Pipeline. RNA sequencing reads for the treated and control samples were aligned using MapSplice v12_07, quantified using RSEM, and gene counts were normalized using upper quantile normalization. This was the same methodology used to normalize the PANCAN12 TCGA dataset, which we obtained from TCGA fully processed for use in this analysis. To generate a TLT sensitivity signature, we used the DESeq2 package (version 1.4.5) in the Bioconductor framework (version 2.14.0, version 3.1.0 of R) to identify genes that were significantly deregulated (adjusted p < 0.05) between the treated and control samples. One hundred forty-six genes were found to be significantly deregulated, out of which only 131 were found in the TCGA dataset. To use DEseq2, the reads had to be re-mapped using the Rsubread Bioconductor package. We used this package to map the reads to version hg19 of the human genome and to summarize the data to gene-level values. We predicted TLT sensitivity for the PANCAN12 TCGA dataset using the Bayesian binary regression algorithm version 2.0 (BinReg2.0) used as a MATLAB plug-in. We used default parameters, except that our signature used 131 genes and one metagene. The probability output from the binary regression model was subtracted from one so that probabilities closer to one indicated a higher probability of sensitivity to the drug as previously described [29]. Prior to making the predictions, the data were log2 transformed and DWD normalized to reduce biases that can result from differences in batch processing and platforms.

overall_design: Eight TLT-sensitive BL-CL cell lines were treated separately with TLT (at EC75) or DMSO for 6 hours, after which total RNA was extracted using the RNeasy Mini Kit

first: Stephen

last: Piccolo

first: Andrea

last: Bild


title: MUTYH is associated with hepatocarcinogenesis in a NASH model mouse

city: sapporo

first: hiroki

last: sakamoto

address: west-16, south-1, chuo-ku

department: medical oncology

country: Japan

institute: sapporo medical university

summary:
Mice with MUTYH-null allele (Mutyh+/-, Mutyh-/-) were fed a high-fat/high-cholesterol (HFHC) diet or HFHC + high iron diet. The incidence of liver tumors and histological features of the liver were compared.
We used microarray to examine the gene expression patterns associated with hepatocarcinogenesis in our model.

overall_design: The gene expression profiles in the non-tumorous hepatic tissues were compared between wild-type mice that developed no liver tumors and MUTYH-null mice that developed liver tumors.

first: Koji

last: Miyanishi

first: Hiroki

last: Sakamoto


title: LncRNA expression data from BRCA drug-sensitive and drug-resistant cell lines

city: Shenyang

first: Ming

last: Zhang

state: China

address: Department of Pharmacology, School of Pharmacy

institute: China Medical University

summary:
Worldwide, breast cancer (BRCA) is the most common malignant tumor in women. Adriamycin (ADR) is considered one of the most effective agents for the treatment of BRCA, but its efficacy as a curative agent is compromised by intrinsic resistance and the acquisition of multidrug resistance characteristics during chemotherapy. The underlying mechanisms resulting in ADR resistance in BRCA remain poorly understood.
Long non-coding RNA (lncRNA) are abnormally expressed in many cancers and are highly involved in its pathogenesis, including drug resistance. In order to systematically study the role of lncRNA in the resistance of BRCA cells to ADR, we used lncRNA expression microarray to establish gene expression profiles of ADR resistant cell lines and ADR sensitive cell lines.

overall_design: The ADR sensitive cell line MCF-7 and the ADR resistant cell line MCF-7/ADR were used for RNA extraction and hybridization on microarrays. We are trying to study the expression profile of lncRNA in BRCA cell lines and find the key factors that mediate breast cancer drug resistance.

first: Lin

last: Zhao

first: Yan

last: Wang

first: Miao

last: He

first: Minjie

last: Wei


title: Transcriptomic profile of high and low fertile Murrah buffalo (Bubalus bubalis) bulls.

status: Public on Jul 16 2020

city: Bangalore

first: Arumugam

last: Kumaresan

state: Karnataka

address: Hosur Road

department: Veterinary Gynaecology and Obstetrics

country: India

institute: National Dairy Research Institute

summary: To identify the transcriptomic differences in spermatozoa derived from high and low fertile buffalo bulls.

overall_design: Microarray Gene expression Study : Agilent Bos Taurus 8x60k Microarray: AMADID: 29411

first: A


title: Autocrine IL6 activates the STAT3-DNMT axis to silence the TNFa-RIP1 necroptosis pathway to sustain myeloid-derived suppressor cell survival and accumulation

city: Augusta

first: Huidong

last: Shi

state: GA

department: Georgia Cancer Center

institute: Augusta University

summary: Massive accumulation of myeloid-derived suppressor cells (MDSCs) is a hallmark of cancer. It is well-known that proinflammatory mediators induce MDSC accumulation. However, the functions of cell death pathways in MDSC survival and the mechanism underlying regulation of cell death pathways in MDSCs are still elusive. Herein, we determined that DNA methylation sustains MDSC accumulation in tumor-bearing mice since pharmacological inhibition of DNMTs with Dacitabine abolished MDSC accumulation and activated antigen-specific cytotoxic T lymphocytes in tumor-bearing mice. Decreased MDSC accumulation is correlated with increased IRF8 expression in MDSCs. However, Dacitabine also abolished CD11b+Gr1+ MDSC-like cell accumulation in IRF8 KO mice, suggesting that DNA methylation regulates MDSC accumulation at the post lineage differentiation stage. Use of cell death pathway-selective inhibitors identified necroptosis as the target of DNA methylation in MDSCs. Genome-wide DNA bisulfite sequencing revealed that the promoter of Tnf is hypermethylated in tumor-induced MDSCs. Consequently, decitabine dramatically increased TNF level in MDSCs and neutralizing TNF significantly decreased Dacitabine-induced MDSC cell death. Recombinant TNF induced MDSC cell cells in a dose and RIP1-dependent manner. Inhibition of RIP1 or RIP3 did not decrease TNF expression in MDSCs. Our data determined that the TNF-RIP1 necroptosis pathway is responsible at least in part for MDSC accumulation and that the IL6-activated DNMTs hypermethylate Tnf to impair necroptosis pathway to maintain MDSC accumulation in cancer. Our data depict the IL6-STAT3-DNMT-TNFa-RIP1 necroptosis pathway as a molecular target for suppressing MDSC accumulation in cancer immunotherapy.

overall_design: CD11b+Gr1+ MDSCs were purified from spleens of AT3 tumor-bearing mice. Genomic DNA was extracted from the purified MDSCs and subjected to whole genome bisulfite sequencing analysis using the Illumina next generation sequencing.

first: Alyssa

last: Smith

first: Kebin

last: Liu


title: RCO-3 and COL-26 form an external-to-internal module that regulates the dual-affinity glucose transport system in Neurospora crassa

city: Tianjin

first: chaoguang

last: Tian

address: 32 Xi Qi Dao, Tianjin Airport Economic Area

institute: Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences

summary: To dissect the role of RCO-3 and COL-26 in glucose uptake and metabolism and to obtain a broad view of the mode of expression, we conducted high-throughput sequencing (RNA-Seq) of wild-type, Δcol-26, and Δrco-3 mycelia exposed to a gradient of glucose (0%, 0.05%, 0.5%, 2.0%) for 1 h. We found that the gene expression profiles of Δcol-26 and Δrco-3 mutants was dramatically different with that of WT strain. Transcriptional profiling analysis revealed that Δcol-26 and Δrco-3 mutants had similar transcriptional profiles, and both mutants had impaired response to a glucose gradient. The genes involved glycolytic pathway showed significantly decreased expression in both mutants. Our findings provide novel insight into the molecular basis of glucose uptake and signaling in filamentous fungi, which may aid in the rational design of fungal strains for industrial purposes.

overall_design: Conidia were inoculated into 100 mL liquid Vogel's minimal medium (VMM) supplemented with 2.0% sucrose and grown at 28˚C and 200 rpm in constant light for 16 h. Then the mycelia were transferred to 100 mL VMM with different glucose concentration (0%, 0.05%, 0.5%, 2%) for 1 h before RNA extraction. Duplicate cultures were sampled in each condition.

first: Jinyang

last: Li

first: Chaoguang


first: Emilia Maria Cristina

last: Mazza

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

overall_design: Refer to individual Series


title: Basis of Specificity for a Conserved Promiscuous Chromatin Remodeling Protein [Mnase-seq]

city: Eugene

first: Laura

last: McKnight

address: 1318 Franklin Blvd Room 273 Onyx Bridge

institute: University of Oregon

summary: We propose an interacting barrier mechanism for cooperation between Isw2-related proteins and sequence-specific DNA binding factors.

overall_design: Nucleosome Mapping by Mnase-Seq

first: Drake

last: Donovan

first: Johnathan

last: Crandall

first: Vi

last: Truong

first: Thomas

last: Bailey

first: Devin

last: Dinwiddie

first: Abigail

last: Vaaler

first: Jeffrey


title: Adipose MSC suppress breast cancer progression, metastasis and inhibit EMT pathways via exosomal-miRNAs following co-culture interaction

status: Public on Aug 18 2020

city: Cheras

first: norlaily

last: mohd ali

state: Selangor

address: Universiti Tunku Abdul Rahman, Jln Sg Long

department: Faculty of Medicine and Health Sciences

country: Malaysia

institute: Universiti Tunku Abdul Rahman

summary:
Introduction: Mesenchymal stem cells (MSCs) are commonly known to influence the progression of cancer due to their ability to migrate to the tumor microenvironment and interact with cancer cells. Exosomes have been found secreted by most cell types and have been shown to act as cargo carrying biomolecules including microRNA (miRNAs). Thus, understanding interaction between MSCs and cancer cells via exosomal miRNAs is crucial in determining the therapeutic role of MSC in treating breast cancer cells and relapse.
Methods: Exosomes were harvested from the medium of indirect co-culture of MCF7-luminal and MDA-MB-231-basal breast cancer cells (BCCs) subtypes with adipose MSCs and profiled for miRNAs using next-generation sequencing.
Results: The interaction resulted in the changes of exosomal miRNAs profiles that modulate essential signalling pathways and cell cycle arrest into dormancy via inhibition of epithelial-to-mesenchymal transition (EMT). The maintenance and induction of epithelial features in MCF7 and MDA cells have led to a positive correlation with the reduction of proliferation and metastasis as well as increased drug resistance. Overall, adipose MSCs mediated delivery of consensus miRNAs particularly miR-200 family in MCF7, miR-146a in MDA and miR-941 in both BCCs subtypes via exosomes.

overall_design: miRNA profiles of breast cancer cells subtypes co-cultured with adipose MSC were generated using next-generation sequencing.

first: Norlaily

last: Mohd Ali

first: Swee

middle: K

last: Yeap

first: Wan

middle: Y

last: Ho

first: Lily

last: Boo

first: Huynh

last: Ky

first: Dilan

last: Satharasinghe

first: Sheau

middle: W

last: Tan

first: Soon

last: Cheong

first: Hsien

last: Huang

first: Kuan

last: Lan

first: Men

last: Chiew

first: Han

last: Ong


title: Transcriptome analysis of differential gene expression of endometrium, peritoneum, and endometriosis lesions

status: Public on Jul 27 2020

city: Turku

first: Michael

last: Gabriel

address: Kiinamyllynkatu 10

institute: University of Turku

summary: Analysis of endometriosis disease associated tissues, endometrium and peritoneum at gene expression level. In this study we present, an interactive web-based user interface for browsing gene expression patterns in the normal endometrium, peritoneum and endometriotic lesions. This tool allows users to explore gene expression profiles of genes of interests in the endometrium and different lesion types without the requirement of advanced computational skills.

overall_design:
Total RNA obtained from healthy and patient endometrium, peritoneum and patient endometriosis lesions.

"cycle phase: medication" refers to the inability of determining cycle phase for patients on hormonal medication.

first: Matti

last: Poutanen


title: Evolutionary transcriptomics implicates HAND2 in the origins of implantation and regulation of gestation length

status: Public on Jul 28 2020

city: Chicago

first: Katelyn

last: Mika

email: kmmika12@gmail.com, kmmika@uchicago.edu

state: IL

address: 1025 E. 57th Street

department: Organismal Biology; Genetic Medicine

institute: University of Chicago

summary: The developmental origins and evolutionary histories of cell types, tissues and organ systems contribute to the ways in which their dysfunction leads to disease. In mammals for example, the nature and extent of maternal-fetal interactions, how those interactions develop, and their evolutionary history likely influence diseases of pregnancy such as infertility and preterm birth. Here we show genes that evolved to be expressed at the maternal-fetal interface in Eutherian (‘Placental') mammals play essential roles in the evolution of pregnancy and are associated with immune system disorders and preterm birth. Among these genes is the transcription factor HAND2, which suppresses estrogen signaling, an innovation of Eutherians, thereby allowing blastocyst implantation. We found that HAND2 is dynamically expressed in the decidua throughout the menstrual cycle and pregnancy, gradually decreasing to reach a low at term. HAND2 regulates a small but distinct set of target genes in endometrial stromal fibroblasts including the cytokine IL15, which was also dynamically expressed throughout the menstrual cycle and gestation, and promoted the migration of natural killer cells and extravillous cytotrophoblasts. Remarkably, we found that the HAND2 promoter loops to a distal enhancer containing SNPs implicated in the regulation of gestation length and birth weight. Collectively, these data connect HAND2 expression at the maternal-fetal interface with the evolution of implantation and gestation length regulation, and preterm birth.

sample_organism:
Papio anubis
Mesocricetus auratus
Mus musculus
Carollia perspicillata
Ictidomys tridecemlineatus

overall_design: Multi-species RNA-Seq to identify genes expressed in the pregnant uterus

first: K

middle: M

first: V

last: Lynch


title: Transcriptome-wide gene expression analysis of prostate cancer (PCa) tissue specimen on a custom expression microarray

status: Public on Jul 21 2020

city: Leipzig

first: Kristin

last: Reiche

address: Perlickstr. 1

institute: Fraunhofer Institute for Cell Therapy and Immunology

summary:
We assessed transcriptome-wide gene expression in tissue specimens of PCa patients who underwent radical prostatectomy by a custom expression microarray. We applied Cox proportional hazard models to the cohorts from different platforms and specimen types and combined the evidence from these by fixed effect meta-analysis to identify genes predictive for time to DoD (death of disease). Genes were combined by a weighted median approach into a prognostic score.
We stratified PCa patients according to seven clinical risk groups based on Gleason Score (GS), the presence of regional lymph node metastases (pN) and the occurrence of death of disease (DoD): (i) very low  risk (group V: GS<7, pN0), (ii) low risk (group L: GS=7, pN0), (iii) medium risk (group M: GS<=7, pN1), (iv) high risk survivors without lymph node infiltration (group H-s: GS>7, pN0), (v) high risk non-survivors without lymph node infiltration (group H-d: GS>7, pN0, DoD), (vi) high risk survivors with lymph node infiltration (group H+s: GS>7, pN1), (vii) high risk non-survivors with lymph node infiltration (group H+d: GS>7, pN1, DoD). For high risk groups adjacent tumor-free prostate tissue samples were obtained (groups H+sf, H-sf, H+df, H+df).
Information on the course of the disease, survival of the patients and the cause of death were obtained from the general practitioners or treating urologists or from records of the regional tumor registry. Clinicopathological parameters were obtained by routine histopathological examination of the surgical specimens. Serum levels of the prostate-specific antigen (PSA) were determined preoperatively (Abbott, Wiesbaden, Germany).
Frozen tissue samples were embedded in Tissue-Tek OCT-compound (Sakura Finetek GmbH, Staufen im Breisgau, Germany) and fixed on metal indenters by freezing. Cryo-sections were prepared using a cryo-microtome (Leica Biosystems, Nußloch, Germany) equipped with a microtome blade C35 cooled to   -28 °C. For every tissue three stacks of consecutive cryo-sections (10 µm) were generated, each bordered/flanked by HE-stained cryo-sections (4 µm), which were evaluated by a pathologist with regard to tumor and stroma cell content. PCa tissue stacks had to be flanked on either side by sections containing at least 50 % tumor cells to be used for further analyses. Sections of the tissue stacks were immediately transferred to 1 ml Qiazol (Qiagen, Hilden, Germany) and stored at -80 °C until RNA isolation.

overall_design: Total RNA of RPE-derived freshly frozen tissue of 164 PCa patients was assessed for gene expression profiling by custom microarrays.

first: Gustavo

last: Baretton

first: Sophie

last: Bartsch

first: Catharina

last: Bertram

first: Conny

last: Blumert

first: Tilo

last: Buschmann

first: Sabina

last: Christ

first: Kati

last: Erdmann

first: Maik

last: Friedrich

last: Froehner

first: Susanne

last: Fuessel

first: Joerg

last: Hackermueller

first: Friedemann

last: Horn

first: Markus

last: Kreuz

first: Dennis

last: Loeffler

last: Muders

first: Dominik

last: Otto

first: Sven-Holger

last: Puppel

last: Rade

last: Specht

first: Marieta

last: Toma

first: Karolin

last: Wiedemann

first: Manfred

last: Wirth


title: Basis of Specificity for a Conserved Promiscuous Chromatin Remodeling Protein [ChIP-Seq]

status: Public on Aug 31 2020

first: Laura

last: McKnight

overall_design: Chromatin Immunoprecipitation Data for FLAG-tagged Chromatin Binding Factors

first: Drake

last: Donovan

first: Johnathan

last: Crandall

first: Vi

last: Truong

first: Thomas

last: Bailey

first: Devin

last: Dinwiddie

first: Abigail

last: Vaaler

first: Jeffrey


title: TRACE-Seq Reveals Clonal Reconstitution Dynamics of Gene Targeted Human Hematopoietic Stem Cells

status: Public on Aug 09 2020

city: Stanford

first: Ravindra

last: Majeti

state: CA

address: 875 Blake Wilbur Dr Clinic F

institute: Stanford University

summary: We present Tracking Recombination Alleles in Clonal Engraftment using sequencing (TRACE-Seq), a novel methodology that utilizes barcoded rAAV6 donor template libraries, carrying either in-frame silent mutations or semi-randomized nucleotide sequences outside the coding region, to track the in vivo lineage contribution of gene targeted HSPC clones.  By targeting the HBB gene with a rAAV6 donor template library consisting of ~20,000 possible unique exon 1 in-frame silent mutations, we track the hematopoietic reconstitution of HBB targeted myeloid-only, lymphoid-only, and multi-lineage repopulating human HSPC clones in immunodeficient mice.

sample_organism:
Homo sapiens
synthetic construct

platform_organism:
Homo sapiens
synthetic construct

overall_design: Trace-seq barcode fractions of CD34+ cord blood cells before and after engraftment in mice.

first: Rajiv

last: Sharma

first: Daniel

last: Dever

first: Cirian

last: Lee

first: Armon

last: Azizi

first: Yidan

last: Pan

first: Joab

last: Camanera

last: Koehnke

first: Gang

last: Bao

first: Matthew

last: Porteus


title: Effects of Gongronella sp. w5 on Medicago truncatula transcriptome

status: Public on Aug 11 2020

city: Hefei

first: Wang

last: Xiaojie

address: No. 111 Road, Kowloon

institute: Anhui University

summary: To investigate the gene expression levels of Medicago truncatula roots after beneficial fungi Gongronella sp. w5 inoculated.Gongronella sp. w5 promoted M. truncatula growth and caused the accumulation of sucrose in M. truncatula root tissue at 16 day-post-inoculation (dpi) without invading into the root cells. The transport of photosynthetic product sucrose to the rhizosphere by M. truncatula root cells was accelerated by upregulating the SWEET gene.

overall_design: Three biological replicates of M. truncatula root with or without w5 inoculation were used for the transcriptome analysis.

first: Fang

last: Zemin


title: Ongoing classical IL-6 signaling is required to maintain a pathogenic Th17 response in vivo

status: Public on Jul 17 2020

city: Birmingham

first: Min

last: Gao

state: AL

address: 1900 University Blvd, THT Building Suite #130G

institute: University of Alabama at Birmingham

summary:
Th17 precursors from WT and IL6ra-/- mice were co-transferred into Rag1-/- mice to induce colitis. RNA was isolated from CD4+ T cells pre-transfer and from colonic CD4+ T cells 4 weeks post- transfer

Another aim is to compare gene expression of WT (IL-6) v WT (HDS) v IL6RaKO (HDS) in vitro polarized Thy1.1+ Th17p cells

overall_design:
WT (CD45.1) and Il6ra-/- (CD45.2) IL-17F/Thy1.1 CD4 T cells were cultured under Th17 conditions in vitro (2.5 ug/ml anti-CD3, 10 ug/ml anti-IFN-g, 10 ug/ml anti-IL-4, 2.5 ng/ml TGF-b, 20 ng/ml hyper-IL-6, with irradiated splenic APCs) then Th17p (Thy1.1+) were harvested (pre_WT and pre_KO) and co-transferred into Rag-/- mice to induce colitis. Four weeks after transfer, live CD4+ TCRb+ cells from the colon of recipient mice were sorted into CD45.1+ WT (post_WT) and CD45.2+ IL-6Ra KO (post_KO) groups for RNA-Seq analysis.

3 samples (WT IL-6, WT HDS63, KO HDS63) of T cells from spleen and lymph nodes with 2 replicates each (6 samples), plus two controls (WT Tn and KO Tn) also with two replicates (4 samples).

first: Stacey

last: Harbour

first: Steve

last: Witte

first: Robin

last: Hatton

first: Casey

last: Weaver


title: The impact of H2O2 exposure on the transcriptome of Streptococcus mutans wild type and perR mutant strains

status: Public on Sep 17 2020

city: Gainesville

first: Jessica

last: Kajfasz

state: FL

address: 1395 Center Drive

department: Oral Biology

institute: University of Florida

summary: H2O2 is an oxidative stress agent known to trigger an upregulation in expression of detoxification genes in Streptococcus mutans.  Following discovery of a spontaneously-occurring perR mutation, we wanted to compare the transcriptomic responses of H2O2 exposure in S. mutans strains bearing an intact perR or a perR deletion.

overall_design: Streptococcus mutans UA159 was grown in BHI medium to mid-exponential phase (OD600 = 0.4).  At this point, the samples were split into two equal volumes.  One volume was reserved as the control; H2O2 was added to the stressed volume to 0.5mM.  The cultures were incubated at 37C, 5% CO2 for an additional 5 minutes.  Cells were then harvested by centrifugation (4000 RPM, 10 minutes).  RNA was isolated using the Qiagen RNeasy Mini Kit, and RNA from control and H2O2-stressed samples was prepared for RNA-Seq analysis.

first: Tridib

last: Ganguly

first: Jacqueline

last: Abranches

first: Jose

last: Lemos


title: Isolation of Foxg1Cre;Gli3TFlag/+ Foreguts

city: Cincinnati

first: Aaron

last: Zorn

state: OH

address: 240 Albert Sabin Way, Bld S

department: Developmental Biology

institute: Cincinnati Children's Hospital and Medical Center

summary: E10.5 and E11.5 Foxg1Cre;Gli3TFlag/+ mouse mutant and control foreguts and tracheas, respectively, were sequenced to examine the role of overexpression of Gli3 repressor on tracheal development.

overall_design: Foreguts were dissected from E10.5 control and mutant embryos, and tracheas were dissected from E11.5 control and mutant embryos. Samples then underwent bulk RNA sequencing.

first: Talia

last: Nasr

first: Praneet

last: Chaturvedi


title: Single-Cell Transcriptome Profiling of the Kidney Glomerulus Identifies Key Cell Types and Reactions to Injury

status: Public on Jul 13 2020

city: South San Francisco

first: Jun-Jae

last: Chung

address: 1 DNA Way

institute: Genentech

summary:
Background: The kidney glomerulus is a specialized capillary bed that is involved in urine production and blood pressure control. Glomerular injury is a major cause of chronic kidney disease, a widespread epidemic without therapeutic options. Single-cell transcriptomics have radically improved our ability to characterize complex organs, such as the kidney. Cells of the glomerulus, however, have been largely underrepresented in previous single cell kidney studies due to their paucity and intractability.
Methods: We used single-cell RNA sequencing to comprehensively characterize the different types of cells in the glomerulus from healthy mice and from four different disease models (nephrotoxic serum nephritis, diabetes, doxorubicin toxicity, CD2AP deficiency).
Results: All cell types in the glomerulus were identified using unsupervised clustering analysis. We identified novel marker genes and gene signatures of mesangial cells, vascular smooth muscle cells of the afferent and efferent arteriole, parietal epithelial cells, and three different types of endothelial cells. Analysis of the disease models revealed cell type-specific and injury type-specific responses in the glomerulus, including acute activation of the Hippo pathway in podocytes after nephrotoxic immune injury.
Conclusions: We have generated a comprehensive high-resolution single-cell transcriptomic profile of the kidney glomerulus from healthy and injured mice. The dataset provides a useful resource for identifying novel disease-related genes and pathways.

overall_design: Single cell RNA sequencing of glomerular cells from control mice and four different glomerular injury models

first: Leonard

last: Goldstein

first: Ying-Jiun

last: Chen

first: Zora

last: Modrusan

first: Andrey

last: Shaw


title: Role of HRP2 in mixed lineage leukemia compared to its paralog LEDGF/p75

status: Public on Jul 11 2020

city: Leuven

first: Siska

last: Van Belle

state: Vlaams Brabant

address: Herestraat 49, bus 1023

country: Belgium

institute: KU Leuven

summary: Mixed lineage leukemia-rearranged (MLLr) leukemia is a genetically distinct subtype of leukemia driven by a reciprocal chromosomal translocation or partial tandem duplications of internal coding regions of the MLL gene KMT2A. These rearrangements result in in-frame genes, translated to oncogenic fusion proteins deregulating the MLL target genes (e.g. HoxA family, Meis1, Cdk6), promoting leukemogenesis and tumor progression. To regulate gene expression, unstructured N-terminal motifs found in MLL form a ternary complex with menin and the integrase binding domain (IBD) of the p75 splice variant of Lens Epithelium Derived Growth Factor (LEDGF/p75). Formation of the ternary complex is crucial for MLL-r leukemogenesis. Hepatoma derived growth factor related protein 2 (HRP2) is the only human paralog of LEDGF/p75 with identical functional domains. We investigated its role in normal hematopoiesis and leukemia. We demonstrate that adult Hrp2 knockout mice can be distinguished from their wild type littermates by increased neutrophils in the hematopoietic system. Colony formation experiments and Gene Set Enrichment Analysis on lin- HSC hinted towards a stem-like state supported by HRP2. In context of leukemia, we observe a more general role for HRP2 in the survival of leukemic cells independently of MLL.

overall_design: mRNA profiling of lineage depleted cells from bone marrow of Hrp2 wildtype and knockout mice (strain C57BL/6N-Hdgfrp2<tm1b (KOMP)Wtsi>/Tcp (Hrp2tm1b)).

first: Filip

last: Matthijssens

first: Courtney

last: Hodges

first: Zeger

last: Debyser


title: Genome scale epigenomic analysis of response to acute stress in the European sea bass

status: Public on Jul 07 2020

city: MONTPELLIER

first: Bruno

last: GUINAND

address: Place E. Bataillon - Campus Triolet

institute: Université de Montpellier

summary: Understanding the molecular basis of stress is crucial in biology and of long standing interest in fish science. We tackled this question by modifying the epiGBS (epiGenotyping By sequencing) technique to screen for cytosine methylation and explore the genome-wide epigenomic response to a three months repeated acute stress challenge in the European sea bass (Dicentrarchus labrax). Following a minimally invasive sampling using nucleated red blood cells (RBCs), our modified epiGBS protocol retrieved 501,108,033 sequencing reads after trimming, with a mean mapping efficiency of 73.0% for unique best hits. Sequencing reads were shown to map across all linkage groups (LGs) of sea bass. A total of 47,983 CpG coordinates with a minimum 30X read depth was retained for differential methylation analysis between pre- and post-stress fish. A strong family effect was demonstrated, and fifty-seven distinct differentially methylated cytosines (DMCs) distributed on 17 of 24 LGs were found between RBCs of pre- and post-stress individuals. Twelve of them were located in intergenic regions, one in a repeated element; and forty four in gene bodies. Overall, DMCs were found inside or in the vicinity of 51 distinct genes shown previously to be related to stress. Thirty-eight of these genes were previously reported as differentially expressed in the brain of zebrafish, most of them involved in stress coping differences.

overall_design: 74 samples of sea bass (paired-end sequencing) analyzed with epiGBS

first: Madoka

last: Krick

first: Erick

last: Desmarais

first: Athanasios

last: Samaras

first: Elise

last: Gueret

first: Arkadios

last: Dimitroglou

first: Michalis

last: Pavlidis

first: Costas

last: Tsigenopoulos

last: Guinand


title: Runx-mediated gene regulation during thymic T cell development and stage specific genomic interactions of Runx3

status: Public on Jul 14 2020

city: Pasadena

first: Boyoung

last: Shin

state: California

address: 1200 E. California Blvd

country: USA

institute: Californial Institute of Technology

summary:
Runx transcription factors play pivotal roles in the development of hematopoietic cells, including T cells.  However, the Runx-target genes in early stages of thymic T cell development have been only partially elucidated.  Moreover, the relationships of different Runx paralogs, whether they compete or collaborate with each other, are unknown.
We have performed CRISPR-Cas9 mediated acute deletion of Runx1 and Runx3, alone and in combination, to define the functions of Runx factors and their target genes.  We focused on two distinct stages of early T cell development; before lineage commitment (Phase1) and after commitment (Phase2).  Our data suggest that Runx1 and Runx3 are functionally redundant in Phase1, hence the absence of one factor was compensated by the other factor.  In Phase2, Runx1 becomes a major contributor, while low levels of Runx3 still strengthened the Runx1-mediated target gene regulation and showed an additive effect.
Of importance, we found that Runx1 and Runx3 upregulate T cell programs and inhibit alternative lineage genes.  In order to capture the developmental status of Runx-perturbed cells, we performed supervised principal component analysis (PCA) using a fixed frame of PC loadings from single cell RNA-seq analysis of normal in vivo-derived thymocytes.  Unlike the reference in vitro and in vivo pro-T cell population or sgControl introduced cells, Runx knockout cells either failed to progress fully (Phase1) or deflected from the normal developmental trajectory (Phase2), suggesting essential roles of Runx factors in early stages of T development.
In addition, we analyzed the correlation between stage-specific genomic occupancy of Runx1 and Runx3 (using previously published data for Runx1, GSE103953) and Runx-mediated gene regulation responses at each stage.  Interestingly, genes with dynamic, stage-sensitive expression showed a very significant association with phase-specific genomic interactions of Runx factors, and an especially strong correlation with Runx activated target genes.
In summary, our data suggest a pivotal role for Runx transcription factors in thymic T cell development by imposing T lineage specification in Phase1 and instructing the lineage-committed progenitor cells to progress through a normal T developmental trajectory.

overall_design:
ChIP-seq:
Bone-marrow progenitor cells from C57BL/6J wild-type animals were cultured on OP9-DLL1 stromal cells with IL-7 and Flt3-ligand to promote T-lineage development.  The following populations were FACS sorted for ChIP-seq:
Phase1 cells: Lineage marker (Lin)- CD45+ cKithigh CD25- cells on day5
Phase2 cells: Lin- CD45+ cKitlowCD25+ cells on day10.
Approximately 5-10 million cells were fixed at RT in 1 mg/ml DSG followed by addition of 1% formaldehyde and subjected to ChIP-seq.
RNA-seq after Phase1 and Phase2 Runx-perturbation:
Bone-marrow progenitor cells from B6.CRISPR-Cas9/Bcl2 transgene expressing mice were cultured on OP9-DLL1 stromal cells with IL-7 and Flt3-ligand for 2 days (for Phase1 perturbation) or 10 days (for Phase2 perturbation).  Three sgRNAs against Runx1 and/or three sgRNAs against Runx3 were retrovirally introduced either to target a single gene or to target both in combination.  After 3 days post infection, Lineage marker (Lin)- infection marker+ cKit high (for Phase1 perturbation) or Lin - infection marker+ CD25+ (for Phase2 perturbation) cells were FACS sorted and subjected to bulk RNA-seq.
RNA-seq for in vitro ETP, Bcl11b- DN2a, and Bcl11b+ DN2b pro-T cells:
Bone-marrow progenitor cells from B6.Bcl11b-YFP reporter animals were cultured on OP9-DLL1 stromal cells with IL-7 and Flt3-ligand for 4 or 6 days.  The following gating strategy was applied for FACS sorting of the indicated populations:
ETP: Lin- cKit high CD44 high CD25- Bcl11b(YFP)-
Bcl11b- DN2a: Lin- cKit high CD44 high CD25+ Bcl11b(YFP)-
Bcl11b+ DN2a: Lin- cKit high CD44 high CD25+ Bcl11b(YFP)+
Sorted cells were subjected to bulk RNA-seq analysis.

first: Hiroyuki

last: Hosokawa

first: Wen

last: Zhou

first: Maile

last: Romero-wolf

first: Kaori

last: Masuhara

first: Victoria

middle: R

last: Tobin

first: Ditsa

last: Levanon

first: Yoram

last: Groner

first: Ellen

last: Rothenberg


title: Ets1 confers context-dependent activation of Notch signaling in T-cell leukemia [ChIP-Seq]

city: Ann Arbor

first: Mark

middle: Yat-fung

last: Chiang

address: 109 Zina Pitcher Place

department: Internal Medicine/Heme-onc

institute: University of Michigan

summary: Notch activation is highly prevalent in several cancers, including more than 60% of cases of T-cell acute lymphoblastic leukemia (T-ALL). However, the use of pan-Notch inhibitors to treat cancers has been hampered by excessive toxicities, particularly affecting intestinal health. In order to combat Notch-driven oncogenic signals with less toxicity, one strategy is to target the transcriptional cofactors that promote tissue-specific Notch activation.  We previously showed that Zmiz1 is a direct Notch1 cofactor that selectively promotes T-cell development and leukemogenic functions of Notch1. Ets1 is an excellent candidate as a transcription factor (TF) that promotes Notch functions selectively in T-ALL since the scope of Ets1 expression is far more limited than Notch expression and since Ets1 co-occupies Notch-bound enhancers with  high frequency. Here, we used  comparative ChIP-Seq and gene expression methods to show that Ets1 withdrawal impaired Notch complex recruitment and H3K27 acetylation at co-bound enhancers and disabled shared oncogenic pathways. ChIP-Seq showed that Ets1 peaks overlapped with 73-76% of Zmiz1 peaks and 71-75% of Notch1 peaks. Ets1 knockdown reduced Notch1, Rbpj, and Zmiz1 occupancy at enhancers that regulate  genes that drive T-cell differentiation and/or T-ALL proliferation. RNA-Seq showed that Ets1 coregulated ~22% of Notch target genes with induction of Myc as a dominant and functional contribution. Our data support an emerging model in which transcription factors like Ets1 assist Notch in activating a subset of enhancers with important functions for T-cell leukemogenesis and development. Strategies that exploit the context dependence of Notch might combat the Notch pathway in cancer cells with less toxicity than pan-Notch inhibitors.

overall_design: ChIP-Seq analysis of THP-6 cells, a human T-ALL cell line, that was transduced with shControl and two independent shEts1. ChIP-quality antibodies target Ets1 (sc, cleaved Notch1 (ICN1),  Rbpj, Zmiz1, and H3K27ac.

first: Anna

last: McCarter

first: Travis

last: Saari

first: Ryan

last: Russell


title: ChEC-Seq: a robust method to identify protein-DNA interactions genome-wide

status: Public on Jul 01 2020

city: Geneva

first: Maria

middle: Jessica

last: Bruzzone

address: 30, quai Ernest-Ansermet

department: Molecular Biology Department

country: Switzerland

institute: Univeristy of Geneva

summary: Here we show that the ChEC-Seq technique is able to differentiate the binding specificities of Esa1 and Gcn5 two chromatin-binding factors displaying widespread genome-wide associations. We also show that the ChEC-Seq technique reveals strong binding of the transcription factor Sfp1 at Ribi gene promoters. Furthermore, our data provide the first evidence that a specific DNA motif previously identified by ChEC-Seq (Albert 2019 PMID: 30804227) is in fact an in vivo binding site for Sfp1.

overall_design: ChEC-Seq of Esa1 and Gcn5 in S.cerevisiae cells. ChEC-Seq of Sfp1 in wild type and pYPL245-mutant S.cerevisiae cells.

middle: J

first: David

last: Shore


title: RNA-seq of brain and sperm and Bisulfite-seq of embryos from normal and stress-induced depressed mice

status: Public on Jun 28 2020

city: Nanjing

first: Zhen

state: Jiangsu

address: 22th,Hankou Road

department: School of Lifesciences

institute: Nanjing University

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

overall_design: Refer to individual Series


title: HCV infection of adult hepatocytes results in temporally structured transcriptional responses which partially overlap with the IRF1 regulon

status: Public on Jul 02 2020

city: Hannover

first: Birthe

middle: Maren

last: Tegtmeyer

address: Feodor-Lynen-Str. 7

institute: TWINCORE - Centre for Experimental and Clinical Infection Research

summary: We describe the adult hepatocyte response to initial HCV infection and detect temporal perturbations in the transcriptional landscape which correlate with known shifts in replication site location. We also describe an expanded IRF1 regulon and quantify the intrinsic and inducible component in PHHs.

overall_design: Primary human hepatocytes were isolated from livers of multiple donors undergoing partial hepatectomy. Plated PHHs were infected with HCV, or left uninfected, and incubated (6 or 72 hours) prior to RNA extraction and RNA-seq.

first: Gabrielle

last: Vieyres

first: Richard

last: Brown


title: Low KLF11 Determines the CSC–like Identity in Sarcoma via restraining YAP transactivity [ATAC-seq]

status: Public on Jun 25 2020

first: Le

last: Qu

address: 305 East Zhongshan Road

institute: Jinling Hospital, Clinical School of Medical College, Nanjing University

summary: We conducted Transposase-accessible chromatin using sequencing (ATAC-seq) experiments to compare chromatin open regions between control and KLF11-knockdown cells.

overall_design: ATAC-Seq profiles in MG63 cells transfected with KLF11 or control siRNA.


title: Low KLF11 Determines the CSC–like Identity in Sarcoma via restraining YAP transactivity [RNA-seq]

summary: We conducted transcriptome comparison of control and KLF11-knockdown MG63 cells.

overall_design: Transcriptional profiling by RNA-seq of control and KLF11-knockdown MG63 cells (two replicates for each).


title: Low KLF11 Determines the CSC–like Identity in Sarcoma via restraining YAP transactivity [ChIP-seq]

summary: We conducted ChIP-seq experiments to investigate the role of KLF11 in YAP/TEAD transcriptional activity.

overall_design: ChIP-Seq profiles for KLF11, YAP, TEAD1, SIN3A, and HDAC2 in MG63 cells. ChIP-Seq profiles for H3K27ac in MG63 cells transfected with KLF11 or control siRNA. ChIP-Seq profiles for KLF11 in MG63 cells transfected with YAP or control siRNA.  BioProject accession is PRJNA549158


title: Genome-wide bisulfite sequencing of embryos at E4.5 stage injected with sRNAs from normal and stress-induced depressed mice

last: Zhou

summary: We demonstrated that DNMT3a was decreased at E3.5 to E6.5 stage in embryos developing from zygotes injected with sperm sRNAs from depressed mice.To uncover the consequence caused by DNMT3a transient reduction in developing embryos, we injected sperm sRNAs from normal or depressed mice into zygotes and systematically profiled the DNA methylome of embryos at E4.5 stage (sRNA-Dep-E4.5 vs sRNA-Ctl-E4.5) by single-cell level whole genome bisulphite sequencing (SC-WGBS).

overall_design: sRNAs isolated from normal or depressed mice sperm  were microinjected in to fertilized eggs of C57BL/6 background. Embryos at E4.5 stage were collected after microinjection, respectively. Single E4.5-stage embryo was subjected to extraction of the genomic DNA.

first: Yanbo

last: Wang


title: FcγRIIB engagement drives agonistic activity of Fc-engineered αOX40 antibody to stimulate human tumor-infiltrating T cells

status: Public on Jun 22 2020

city: Rotterdam

first: Lucia

last: Campos Carrascosa

address: Doctor Molewaterplein 40

country: Netherlands

institute: Erasmus Medical Center

summary:
Background: OX40 (CD134) is a co-stimulatory molecule of the tumor necrosis factor receptor (TNFR) superfamily, that is currently investigated as a target for cancer immunotherapy. However, despite promising results in murine tumor models, the clinical efficacy of agonistic αOX40 antibodies in treatment of cancer patients has fallen short of the high expectation in earlier stage trials.
Methods: Using lymphocytes from resected tumor, tumor-free tissue and PBMC of 4 hepatocellular and colorectal cancer patients, we performed RNA-Seq to evaluate OX40-mediated transcriptional changes in CD4+ and CD8+ human tumor-infiltrating lymphocytes (TILs).
Results: The transcriptional landscape of CD4+ and CD8+ TILs shifted towards a pro-survival, inflammatory and chemotactic profile upon treatment with αOX40_v12.

overall_design: RNA-Seq of HCC or CRC-derived TILs after 3-5 days in vitro in the presence of CD3/28 activation beads (ctrl) or additionally αOX40_v12 antibody (v12)

first: Jaap

last: Kwekkeboom

first: Wenjing

last: Yang

first: Keith

last: Ching

first: Tim

last: Fisher


title: Small RNA sequencing of sperm sample from normal or stress induced depressive male mice

country: China

summary: We demonstrated that sperm sRNAs are sufficient to reproduce the effect of sperm RNAs on inducing depressive symptoms in offspring.To identify the specific subtypes of sperm sRNAs that cause abnormalities in offspring, we examined the sRNA profiles of sperm derived from normal or depressed male mice by RNA deep sequencing.

overall_design: Mature sperm were extracted from the cauda epididymis of male mice of the C57BL/6J backgrounds and processed for RNA extraction by Trizol. All sRNA library construction and deep sequencing were performed by BGI (Shenzhen, China).


title: RNA sequencing of hippocampal sample from normal male mice, stress induced depressive male mice and  male offspring born to stress-induced depressed male mice

summary: We demonstrated that the offspring of depressed fathers display reduced resilience to stress and enhanced susceptibility to depression. To explain the observed behavioural phenotypes of depression in offspring produced by depressed fathers, molecular profiling was performed in key brain regions.We examined the hippocampal sample from normal male mice, stress induced depressive male mice and  male offspring born to stress-induced depressed male mice by RNA sequencing.

overall_design: Hippocampal samples collected from 3 independent male mice of normal (F0-Ctl), stress induced depressive (F0-Dep) and offspring born to normale male mice (F1-Ctl) or stress-induced depressed male mice (F1-Dep) groups were processed for RNA extraction.


title: Transcriptome Analysis of Caenorhabditis elegans Lacking Heme Peroxidase SKPO-1 Reveals an Altered Response to Enterococcus faecalis

status: Public on Jun 24 2020

city: London

first: Daniel

middle: Martinez

last: Martinez

state: London

address: Hammersmith Hospital, Du Cane Road

country: United Kingdom

institute: Medical Research Council

summary: The nematode Caenorhabditis elegans is commonly used as a model organism in studies of development and the host immune response. The worm encodes twelve peroxidase-cyclooxygenase superfamily members. SKPO-1 was localized to the hypodermis of the animals where it also affected cuticle development. In this work, a better understanding of how loss of skpo-1 impacts both sensitivity to pathogen as well as cuticle development was sought by subjecting a deletion mutant of skpo-1 to transcriptome analysis using RNA sequencing following exposure to control (Escherichia coli) and pathogenic (E. faecalis) feeding conditions.

overall_design: C.elegans transcriptome from two different bacterial backgrounds (E. coli and E. faecalis) and two different genetic backgrounds (N2 wild type, and skpo-1 mutant).

first: Danielle

middle: A

last: Garsin


title: A novel model of chronic limb ischemia with translational significance enables proper evaluation of therapeutic angiogenesis

status: Public on Jun 10 2020

city: Tsukuba

first: Kenichiro

last: Shimatani

state: Ibaraki

address: 21, Miyukigaoka

institute: Astellas Pharma Inc

summary:
We aimed to develop a novel chronic and severe hindlimb ischemia mice model to properly evaluate the therapeutic effects of drug candidates in translational research for critical limb ischemia treatments.
We used microarray to compare the gene expression patterns of gastrocnemius muscles at 1st week and 9th week after hindlimb ischemia model operation.

overall_design: Gastrocnemius muscles of NOG mice at 1st and 9th week after ischemia operation were selected for RNA extraction and hybridization on Affimetrix microarrays.

first: Hiromu

last: Sato


title: The transcriptomic and phenotypic response of the melanized yeast Exophiala dermatitidis to ionizing particle exposure

city: Washington

first: Zachary

last: Schultzhaus

state: DC

address: 4555 Overlook Avenue SW

institute: Naval Research Laboratory

summary: The yeast E. dermatitidis is highly resistant to ionizing particle irradiation, and exposure to this stress elicits a transcriptomic response that is distinct from that induced by photonic irradiation. Melanin, in this organism, does not exhibit substantial control over this transcriptomic response, nor does it protect the cells from radiation-induced death under the conditions we tested. However, the strong response we observed here at the gene expression level inprovides insights into the unique types of damage that particle irradiation causes to fungal cells, allowing for future dissection of radiation source-specific resistance mechanisms.

overall_design: Examine transcriptomic profiles of E. dermatitidis wild type and pks1 mutant and their exposues to ionizing particle radiation

first: Zheng