title: RRBS-based quantitative methylation analysis define 100% methylation fidelity CpG sites

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

overall_design: Refer to individual Series


title: Single-cell analysis of whole hepatic non-parenchymal cells from normal and CCl4-injured mice

status: Public on Jun 06 2021

city: Xi'an

first: Bai

last: Ruan

state: Shannxi

address: No.169, Changle Road

country: China

institute: Fourth Military Medical University

type: Expression profiling by high throughput sequencing

summary: This study used 10X Genomics, single-cell RNA-sequencing to examine the heterogeneity of liver non-parenchymal cell types present in the normal and CCl4-mediated fibrotic mice.

overall_design: Two male mice of 8-week old were injected i.p with olive oil and CCl4 independently twice a week for a total 6 weeks. Then, liver non-parenchymal cells were obtained by a two-step collagenase perfusion method. Hepatocytes were elimanated by three times of low-speed centrifugation at 50g for three minutes and were not included in further analysis of this study. Single-cell suspensions were then loaded on a Chromium Single Cell Instrument (10X Genomics) to generate single-cell GEMs. After reverse transcription, libraries were prepared using version 3 Chromium Single-cell 3' Library, Gel Bead & Mutiplex Kit (10X Genomics). Sequencing was performed on illumina HiSeq 3000.

first: B

first: L

last: Wang


title: Activation of YAP/TAZ signaling reprograms the airway secretory cell fate via mTORC1-dependent amino acid metabolism

status: Public on Jun 25 2021

city: Daejeon

first: HaeYon

last: Jeon

address: 291 Daehak-ro, Eoeun-dong, Yuseong-gu

department: Biological Sciences

country: South Korea

institute: Korea Advanced Institute of Science and Technology

summary: Tissue homeostasis requires lineage fidelity of stem cells. Dysregulation of cell fate specification and differentiation leads to various diseases, yet the cellular and molecular processes remain elusive. We demonstrate that YAP/TAZ activation reprograms airway secretory cells to lose cellular identity and acquire squamous alveolar type 1 (AT1) fate in the lungs. Significantly, this cell fate conversion is mediated via distinctive transitional cell states of Damage-Associated Transient Progenitors (DATPs), recently known to emerge during injury repair, in mouse and human lungs. Further, YAP/TAZ signaling is identified to realign the amino acid metabolism by modulating mTORC1-ATF4 activity, which is integral to fate conversion of secretory cells into AT1 fate. We observed aberrant activation of the YAP/TAZ-mTORC1-ATF4 axis in the altered airway epithelium of human pulmonary fibrosis where the emergence of DATPs and A1 cells is prominent. Finally, genetic and pharmacologic inhibition of mTORC1 activity restores lineage alteration and subepithelial fibrosis driven by YAP/TAZ activation, proposing a potential therapeutic target for human fibrotic lung diseases.

overall_design:
Total 3 single-cell RNA-seq libraries (10X Chromium, v2) were sequenced. All samples are sorted CD31-CD45-EpCAM+tdTomato+ secretory cells from mouse.
Samples consist of control (Lats1fl/+;Lats2+/+;Scgb1a1-cre;tdTomato) mice at 5 days post-tamoxifen induction, and Lats1/2 knockout (Lats1fl/fl;Lats2fl/fl;Scgb1a1-creER;tdtomato) mice at 5 and 14 days post-tamoxifen induction.

first: Hae

middle: Y

first: Jinwook

last: Choi

first: Lianne

last: Kraaier

first: David

last: Eisenbarth

first: Young

middle: H

last: Kim

first: Kijong

last: Yi

first: Jin

middle: W

first: Hyosup

last: Shim

first: Joo

last: Lee

first: Dae

middle: S

last: Lim


title: Antisense-mediated repression of SAGA-dependent genes involves the HIR histone chaperone

status: Public on Jun 03 2021

city: Geneva

first: Julien

last: Soudet

address: 30 quai Ansermet

department: BICEL

country: Switzerland

institute: Université de Genève

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Eukaryotic genomes are pervasively transcribed by RNA polymerase II (RNAPII), and transcription of long non-coding RNAs often overlaps with coding gene promoters. This might lead to coding gene repression in a process named Transcription Interference (TI). In Saccharomyces cerevisiae (S. cerevisiae), TI is mainly driven by antisense non-coding transcription and occurs through re-shaping of promoter Nucleosome-Depleted Regions (NDRs). In this study, we developed a genetic screen to identify new players involved in Antisense-Mediated Transcription Interference (AMTI).  Among the candidates, we found the HIR histone chaperone complex known to be involved in de novo histone deposition. Using genome-wide approaches, we reveal that HIR-dependent histone deposition represses the promoters of SAGA-dependent genes via antisense non-coding transcription.  However, while antisense transcription is enriched at promoters of SAGA-dependent genes, this feature is not sufficient to define the mode of gene regulation. We further show that the balance between HIR-dependent nucleosome incorporation and transcription factor binding at promoters directs transcription into a SAGA- or TFIID-dependent regulation. This study sheds light on a new connection between antisense non-coding transcription and the nature of coding transcription initiation.

overall_design:
RNA-seq, MNase-seq, MNase-ChIP-seq and ChEC-seq in a Nrd1-AA and Nrd1-AA dhir2 strains treated or not with Rapamycin for 1 hour.

Please note that the processed data generated from both replicates is linked to the corresponding *rep1 sample records.

first: Nissrine

last: Beyrouthy

first: Anna

middle: M

last: Pastucha

first: Andrea

last: Maffioletti

first: Zahra

last: Bakir

first: Françoise

last: Stutz


title: Prenatal skeletal muscle transcriptome analysis reveals novel microRNA-mRNA networks associated with intrauterine growth restriction in pigs

status: Public on Jun 02 2021

city: Dummerstorf

first: Siriluck

last: Ponsuksili

address: Wilhelm-stahl-allee 2

country: Germany

institute: FBN

type:
Expression profiling by array
Non-coding RNA profiling by array


title: A molecular census of midbrain dopaminergic neurons in Parkinsons disease

status: Public on Jun 16 2021

city: Cambridge

first: Evan

last: Macosko

state: MA

address: 75 Ames St, Broad Institute

country: USA

institute: Broad Institute

summary: Midbrain dopamine (DA) neurons in the substantia nigra pars compacta (SNpc) project widely throughout the central nervous system, playing critical roles in voluntary movements, reward processing, and working memory.  Many of these neurons are highly sensitive to neurodegeneration in Parkinson’s Disease (PD), and their loss correlates strongly with the pathognomonic symptoms. To characterize these populations molecularly, we developed a protocol to enrich and transcriptionally profile DA neuron nuclei from postmortem human SNpc of both PD patients and matched controls. We identified a total of ten distinct populations, including one that was primate-specific. A single subtype, marked by the gene AGTR1, was highly susceptible to degeneration, and was enriched for expression of genes associated with PD in genetic studies, suggesting many risk loci act within this subtype to influence its neurodegeneration.  The AGTR1 subtype also showed the strongest upregulation of TP53 and its downstream targets, nominating a potential pathway of degeneration in vivo. The transcriptional characterization of differentially disease-vulnerable DA neurons in the SNpc will inform the development of laboratory models, enable the nomination of novel disease biomarkers, and guide further studies of pathogenic disease mechanisms.

sample_organism:
Macaca mulatta
Homo sapiens
Rattus norvegicus
Tupaia belangeri

overall_design:
Characterization and annotation of single nuclei transcriptomes from postmortem human, rat, macaque, and tree shrew substantia nigra and human caudate nucleus.

>>>Submitter states that raw data for human samples will be submitted to dbGaP due to patient privacy concerns<<<

first: Tushar

last: Kamath

first: Abdul

last: Abdul

first: S

middle: J

last: Burris

first: Naeem

last: Nadaf

first: Vahid

last: Gazestani

first: Charles

last: Vanderburg


title: Prenatal skeletal muscle transcriptome with intrauterine growth restriction in pigs [miRNA]

summary: Gene expression data of micro RNA from skeletal muscle samples of F2 population based DL and Pi F2 63 days post conception (dpc).

overall_design: Two groups of skeletal muscle's miRNAs with high and low weight at 63 dpc.

first: Klaus

last: Wimmers


title: Prenatal skeletal muscle transcriptome with intrauterine growth restriction in pigs [mRNA]

summary: 47,845 probe-sets were screened, in the first part of this study pig embryos at 63 days post conception (dpc).

overall_design:
Two groups of skeletal muscle's mRNAs with high and low weight at 63 dpc.
RNAs of longissimus muscle from F2 at 63 dpc were hybridized to Affymetrix Porcine Snowball Array.


title: Machine learning sequence prioritization for cell type-specific enhancer design

status: Public on Jun 01 2021

city: Pittsburgh

first: Alyssa

last: Lawler

state: PA

address: 4400 Fifth Ave

department: Computational Biology

institute: Carnegie Mellon University

summary: Recent discoveries of extreme cellular diversity in the brain warrant rapid development of technologies to access specific cell populations, enabling characterization of their roles in behavior and in disease states. Available approaches for engineering targeted technologies for new neuron subtypes are low-yield, involving intensive transgenic strain or virus screening. Here, we introduce SNAIL (Specific Nuclear-Anchored Independent Labeling), a new virus-based strategy for cell labeling and nuclear isolation from heterogeneous tissue. SNAIL works by leveraging machine learning and other computational approaches to identify DNA sequence features that confer cell type-specific gene activation and using them to make a probe that drives an affinity purification-compatible reporter gene. As a proof of concept, we designed and validated two novel SNAIL probes that target parvalbumin-expressing (PV) neurons. Furthermore, we show that nuclear isolation using SNAIL in wild type mice is sufficient to capture characteristic open chromatin features of PV neurons in the cortex, striatum, and external globus pallidus. Expansion of this technology has broad applications in cell type-specific observation, manipulation, and therapeutics across species and disease models.

overall_design: Examination of cell type-specific ATAC-seq profiles from isolated neuron populations in the adult mouse cortex, striatum, and GPe. Cell populations were isolated with affinity purification using cSNAIL or SNAIL and reflect AAV labeling from different constucts. AAVs were designed to label Parvalbumin-expressing inhibitory interneurons, to label Cre recombinase-expressing cells, or to induce non-specific expression.

first: A

first: E

last: Ramamurthy

middle: R

last: Brown

first: N

last: Shin

first: Y

last: Kim

last: Toong

first: I

last: Kaplow

first: M

last: Wirthlin

first: X

last: Zhang

first: G

last: Fox

first: P

last: Pfenning


title: Cloning and multi-omic analysis of chimpanzee cytomegalovirus: a resource for comparative functional genomics

city: Berlin

first: Emanuel

last: Wyler

address: Robert Roessle Str 10

department: Berlin Institute for Medical Systems Biology

institute: Max Delbrück Center for Molecular Medicine

summary: We assess the viral and host transcriptome during CCMV BAC virus infection

sample_organism:
Homo sapiens
Panine betaherpesvirus 2

platform_organism:
Homo sapiens
Panine betaherpesvirus 2

overall_design: PolyA RNA-sequencing was performed from CCMV BAC virus infected primary human lung fibroblasts and controls

first: Quang

middle: V

last: Phan

first: Boris

last: Bogdanow

first: Fan

last: Liu

first: Markus

last: Landthaler

first: Christian

last: Hagemeier

first: Lüder

last: Wiebusch


title: Identification of Meiotic-P26-bound RNAs in cutlured Drosophila SL2 cells by iCLIP (individual-nucleotide resolution UV crosslinking and immunoprecipitation)

city: Regensburg

first: Jan

last: Medenbach

address: Universitaetsstrasse 31

institute: University of Regensburg

summary: The TRIM-NHL protein Meiotic P26 (Mei-P26) governs gene expression and controls stem cell fate in Drosophila. Mei-P26 represses the translation of the key regulator protein Nanos and induces miRNA-dependent silencing to regulate stem cell renewal, differentiation and proliferation. The structural and mechanistic details of mRNA target recognition and RNA binding by its C-terminal NHL domain remain elusive. To identify its cellular target RNAs, we performed iCLIP2 experiments in cultured Drosophila SL2 cells that were transfected with Flag-tagged Mei-P26 full-length, or its NHL domain.

overall_design: iCLIP2 assays were performed in three biological replicates using full-length Mei-P26 (samples 1-3) or the Mei-P26 NHL domain (samples 4-6) as bait. Reactions using non-transfected cells served as controls (samples 7-9)

first: Andreas

last: Horn

first: Oliver

last: Rossbach

first: Pritha

last: Ghosh

first: Janusz

last: Bujnicki

first: Sebastian

last: Glatt


title: Pecan kinome: classification and expression analysis of all protein kinases in Carya illinoinensis

status: Public on Jul 05 2021

city: Nan Jing

first: pinghua

last: Fan

state: CHINA

address: Long Pan Lu 159

institute: Nanjing Forestry University

summary: Protein kinases (PKs) are involved in plant growth and stress responses, and constitute one of the largest superfamilies due to numerous gene duplications. However, limited PKs have been functionally described in pecan, an economically important nut tree. Here, the comprehensive identification, annotation and classification of the entire pecan kinome was reported. A total of 967 PK genes were identified from pecan genome, and further classified into 20 different groups and 121 subfamilies using the kinase domain sequences, which were verified by the phylogenetic analysis. The receptor-like kinase (RLK) group contained 565 members, which constituted the largest group. Gene duplication contributed to the expansion of pecan kinome, 169 duplication events including 285 PK genes were found, and Ka/Ks ratio revealed they experienced strong negative selection. GO functional analysis indicated majority PKs involved in molecular functions and biological processes. The RNA-Seq data of PK genes in pecan were further analyzed at subfamily level, and different PK subfamilies performed various expression patterns across different conditions or treatments, suggesting PK genes in pecan involved in multiple biological functions and stress responses. Taken together, this study provided insight into the expansion, evolution and function of pecan PKs. Our findings regarding expansion, expression and co-expression analyses could lay a good foundation for future research to understand the roles of pecan PKs, and find the key candidate genes more efficiently.

overall_design: Plant leaf samples were harvested at 0, 3, 6, 9, 12, and 15 days after drought treatment.

first: Kaikai

last: Zhu

first: Pinghua

first: Hui

first: Juan

last: Zhao

first: Pengpeng

last: Tan

first: Zhenghai

last: Mo

first: Fangren

last: Peng


title: Naked1 targets Topless to up-regulate Auxin signaling and suppress immunity

city: Vienna

first: Fernando

last: Navarrete

state: Vienna

address: Dr. Bohr Gasse 3

country: Austria

institute: Gregor Mendel Institute

summary: Plants integrate endogenous and environmental signals to regulate growth and developmental programs by the use different hormonal pathways. Perception of Pathogen/Microbial Associated Molecular Patterns (PAMPs/MAMPs) from invading microorganisms triggers a series of defense reactions known as Pathogen Triggered Immunity (PTI) that inhibit growth promoting signaling pathways such as auxin signaling. On the contrary, pathogens manipulate growth signaling and metabolism to promote disease susceptibility, but how this hormone acts on immunity is not fully understood. Ustilago maydis is a fungal pathogen of maize. Infected plants show formation of galls, masses of undifferentiated tissue, and upregulation of auxin signaling. Here we show that a secreted protein from U. maydis, the effector Naked1 (Nkd1), translocates into the host nucleus where it interacts with members of the Topless/Topless related family of transcriptional co-repressors.  Nkd1 binds to TPL/TPRs through its native EAR motif and prevents recruitment of transcriptional repressors involved in hormonal signaling, leading to the de-repression of jasmonic acid and auxin responsive genes. We show that up-regulation of auxin signaling leads to inhibition of PAMP-triggered ROS burst, one of the earliest PTI responses, and increased susceptibility to pathogens. Thus, establishing a clear mechanism for auxin-induced pathogen susceptibility. Using engineered variants of Nkd1, with altered affinity/specificity to TPL/TPRs, we show that increased EAR-mediated binding triggers typical salicylic acid mediated defense reactions, leading to pathogen resistance.

overall_design: mRNA expression levels were evaluated upon transgene induction. Transgene expression was induced as described above and mRNA levels of seedlings expressing effector proteins (Nkd1, Nkd1ΔEAR and Nkd1SRDX) were compared to those of seedling expressing mCherry (control). Three biological replicates were done for each construct and time-point.

first: Martin

middle: A

last: Darino


title: DRG-CSC co-culture tissue engineered model, CSCs monoculture model and DRG monoculture model

status: Public on Jun 29 2021

city: Changsha

first: Zekai

last: Cui

state: Hunan

address: 18th floor, the New Century Building, #198, Furong Middle Road

institute: Aier Eye Institute

summary: In this study, we constructed a tissue-engineered DRG-CSC (corneal stromal cells) co-cultured model (DS model), a CSC monoculture model (S model), and a DRG monoculture model (D model). Chicken DRGs were extracted from E7-E10 chicken embryo. Human CSCs were extracted in stromal lenticules from small incision lenticule extraction (SMILE). Transcriptional profiling of DRG in the DS model (DS-D), DRG in the D model(D-D),  CSCs in the DS model (DS-S),  CSCs in the S model (S-S) was analyzed. After 7 days of culture,  RNA of each group was extracted.

sample_organism:
Gallus gallus
Homo sapiens

platform_organism:
Gallus gallus
Homo sapiens

overall_design: DS-D vs D-D, DS-S vs S-S. There are three biological replicates in each group.

first: Jiansu

last: Chen


title: Segmental chromatin states

status: Public on May 18 2021

city: New York

first: Ryan

last: Loker

state: NY

address: 3227 Broadway

institute: Columbia University

summary: We profiled the chromatin accessibility, transcription factor binding, and gene expression in the homologous wing and haltere imaginal disc of Drosophila melanogaster, which are distinguished by the expression of the Hox protein Ultrabithorax (Ubx). Through the analysis of chromatin changes, we show Ubx has widespread effects on the chromatin landscape to specify cell identity.

overall_design: Using ATAC-seq to profile chromatin accessibility and ChIP-seq to assess genome-wide TF binding patterns

first: Richard

last: Mann


title: MiRNA expression data of distal colon mucosa from young and old mice

status: Public on May 26 2021

city: Beijing

first: Tingyi

last: Sun

state: Beijing

address: No.10 Xitoutiao, You'anmenwai, Fengtai District

institute: Capital Medical University

type: Non-coding RNA profiling by high throughput sequencing

summary: The disruption of the mucosal barrier of the digestive tract is a common pathological change in the elderly, which often causes inflammatory bowel disease among old people.Given that microRNA (miRNA) molecules are dysregulated in many diseases, the miRNA expression in young and old normal distal colon mucosa in mice was determined by high-throughput analysis. Three 2-month-old mice and 3 24-month-old were enrolled in this study. We used sequencing analysis to identify miRNA expression in the distal colon mucosa.

overall_design: Male C57BL/6 mice divided into two groups according to age, i.e., 2 and 24 month old groups (n =3 per group). All mice were housed in a controlled environment under a 12 h light/dark cycle at 22 ± 2 ℃, 55 ± 5% humidity with access to food and water ad libitum and were sacrificed by appropriate anesthesia and/or cervical dislocation prior to the sample collection. The distal colon tissues were surgically and aseptically removed from the mice. After collection, the samples were stored at -80 °C.

first: Deshan

last: Zhou

first: Shu

last: Yang


title: Transcriptomic alterations in stably overexpressing (OE) clones of solute carriers SLC22A10 and SLC22A15 in PANC-1 (human pancreatic cancer cell line)

status: Public on May 31 2021

city: Columbus

first: Rajgopal

last: Govindarajan

state: Ohio

address: 496 west, 12th Ave

department: Division of Pharmaceutics and Pharmacology, College of Pharmacy

institute: The Ohio State University

summary: We conducted RNA-seq analysis of vector (control), SLC22A10_OE and SLC22A15_OE clones to identify any SLC22-specific oncogenic alterations associated with pancreatic cancer progression. Our findings demonstrate substantial activation of key regulators of epithelial-mesenchymal transition (EMT), cancer cell invasion, and drug resistance such as receptor tyrosine kinase like orphan receptor 1 (ROR1) and aldehyde dehydrogenase 1A1 (ALDH1A1) along with enrichment of interferon alpha and gamma signaling pathways in SLC22A10_ and SLC22A15_OE clones compared to the vector clone.

overall_design: mRNA profiling of vector versus SLC22A10_OE and vector versus SLC22A15_OE clones

first: Debasis

last: Nayak

first: Moray

last: Campbell


title: MiRNA expression data of distal colon mucosa from young and old human

summary: The disruption of the mucosal barrier of the digestive tract is a common pathological change in the elderly, which often causes inflammatory bowel disease among old people.Given that microRNA (miRNA) molecules are dysregulated in many diseases, the miRNA expression in young and old normal distal colon mucosa in humans was determined by high-throughput analysis. Three young people (27, 28, and 36 years of age) and 3 aged people (72, 79, and 81 years of age) were enrolled in this study. We used microarray analysis to identify miRNA expression in the distal colon mucosa.

overall_design: A total 6 normal clinical colon mucosa tissue samples from different colorectal cancer patients were collected immediately after surgical resection prior to any other therapeutic intervention. All patients fulfilled the inclusion criteria as follows: (1) Age: young adults 27-36 years old and elderly adults 72-81 years old; (2) All patients were chemotherapy and radiation therapy naïve; (3) The removed normal tissue samples located at descending colon (distal colon). After collection, the samples were stored at -80 °C.


title: A primed immune transcriptional program is activated in oligodendroglia in multiple sclerosis [SCATAC_10X]

status: Public on May 21 2021

city: Stockholm

first: Eneritz

last: Agirre

address: Solnavägen 9

department: MBB

country: Sweden

institute: Karolinska Institutet

summary: Multiple sclerosis (MS) is a disease characterized by a targeted immune attack on myelin in the central nervous system (CNS). We have previously shown that oligodendrocytes (OLs), myelin producing cells in the CNS, and their precursors (OPCs), acquire disease-specific transcriptional states in MS. To understand how these alternative transcriptional programs are activated in disease, we performed single-cell assay for transposase accessible chromatin using sequencing (scATAC-seq) on the OL lineage in the experimental autoimmune encephalomyelitis (EAE) mouse model of MS. We identified regulatory regions with increased accessibility in oligodendroglia (OLG) in EAE, some of which in the proximity of immune genes. A similar remodeling of chromatin accessibility was observed upon treatment of postnatal OPCs with interferon-gamma (IFNg), but not with dexamethasone. These changes in accessibility were not exclusive to distal enhancers, but also occurred at promoter regions, suggesting a role for promoters in mediating cell-state transitions. Notably, we found that a subset of immune genes already exhibited chromatin accessibility in OPCs ex vivo and in vivo, suggesting a primed chromatin state in OLG compatible with rapid transitions to an immune-competent state. Several primed genes presented bivalency of H3K4me3 and H3K27me3 at promoters in OPCs, with loss of H3K27me3 upon IFNg treatment. Inhibition of JMJD3/KDM6B, mediating removal of H3K27me3, led to the inability to activate these genes upon IFNg treatment. Importantly, OLGs from the adult human brain showed chromatin accessibility at immune gene loci, particularly at MHC-I pathway genes. A subset of single-nucleotide polymorphisms (SNPs) associated with MS susceptibility overlapped with these primed regulatory regions in OLG from both mouse and human CNS. Our data suggest that susceptibility for MS may involve activation of immune gene programs in OLG. These programs are under tight control at the chromatin level in OLG and may therefore constitute novel targets for immunological-based therapies for MS.

overall_design: We used 3 samples of EAE (MS mouse model) and 4 control samples of mouse spinal cord tissue and sequence them using 10X Genomics scATAC-seq v1 Chemistry to study the chromatin states of Oligodendroglia during disease.

first: Mandy

last: Meijer

first: Mukund

last: Kabbe

first: Cassandra

last: van Tuijn

first: Abeer

last: Heskol

first: Ana

last: Falcao

first: M

last: Corces

first: Thomas

last: Montine

first: Xingqi

first: Howard

last: Chang

first: Gonçalo

last: Castelo-Branco


title: Single cell RNA-seq analysis of normal, premalignant state and tumor  mouse models of VAV1-MYOF gene fusion in Peripheral T-Cell Lymphoma

status: Public on May 12 2021

first: Stuart

middle: Aidan

last: Quinn

address: 1130 St Nicholas Ave

department: Institute for Cancer Genetics

summary: The goal of this study is to identify transcriptomic effects of VAV1-MYOF expression in mouse CD4+ T lymphocytes and tumor progression in TET2KO and TET2WT backgrounds. To this end, mice conditionally expressing VAV1-MYOF  were crossed with the CD4CreERT2 line  or CD4-Cre,  under the control of the mouse Cd4 promoter to generate CD4 specific VAV1-MYOF models. In inducible models, mice were treated with vehicle only or Tamoxifen to induce expression of VAV1-MYOF1 in CD4+ T cells. Mice were crossed with CD4-CreERT2 Tet2f/f to obtain the experimental phenotypes. Whole spleen samples were processed and single cell suspensions were analyzed using scRNA-seq technologies.

overall_design: Single cell transcriptomic profiles of WT CD4+ lymphocytes,  pre-lymphoma CD4+ lymphocytes with VAV1-MYOF fusions and tumor samples  with TET2 KO/KO or TET2 wt backgorunds.

first: J

last: Cortes

first: I

last: Filip

last: Patino-Galindo

first: A

first: T

last: Palomero


title: Transcriptomic analysis of normal, premalignant and malignant lymphocytes from mouse models of Peripheral T-Cell Lymphoma

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

overall_design: Refer to individual Series


title: Bulk transcriptomic analysis of normal, premalignant state and tumor mouse models of VAV1-MYOF gene fusion in Peripheral T-Cell Lymphoma

summary: The goal of this study is to identify transcriptomic effects of VAV1-MYOF expression in mouse CD4+ T lymphocytes in tumor development as well as changes in the microenvironment. To this end, mice conditionally expressing VAV1-MYOF  were crossed with the CD4CreERT2 line  or CD4-Cre,  under the control of the mouse Cd4 promoter to generate CD4 specific VAV1-MYOF models. In inducible models, mice were treated with vehicle only or Tamoxifen to induce expression of VAV1-MYOF1 in CD4+ T cells. CD4CreERT2 mice were included as a negative control. Total RNA was extracted from whole spleen samples or CD4+ T cells isolated by single cell suspensions of spleen by negative selection using the mouse naive CD4+ T Cell Isolation Kit (Milteny#130-104-453) according to the manufacturer’s protocol. Standard Illumina poly-A RNA seq was performed.

overall_design: Transcriptomic profiles of CD4+ lymphocytes and whole spleen samples  from wild type (WT) , VAV1-MYOF CD4+ cells and tumor samples were generated by deep sequencing , using Illumina poly-A RNA seq.

first: R

last: Albero


title: RNA-seq data in A673 & TC71 Ewing cell lines (STAG1 and STAG2 knock-out and proficient models and silenced for EWS-FLI1)

status: Public on Apr 29 2021

city: Paris

first: Olivier

last: Delattre

address: 26 rue d'ulm

country: France

institute: Institut Curie

summary: STAG2, a member of cohesin, is one of the most recurrently mutated genes in human cancer. Here, we investigated STAG2 function in the context of Ewing sarcoma, an aggressive bone tumor driven by EWS-FLI1 oncogene chimeric transcription factor. Using a CRISPR/Cas9 approach, we generated three STAG2 knock-out isogenic clones (A673SA2m#1, TC71SA2m#1 and TC71SA2m#2) derived from A673 and TC71 STAG2 wild type (WT) Ewing sarcoma cell line. A STAG2 rescue model (A673_SA2r) generated by correcting the CRISPR mutation in the A673SA2m#1 model was also profiled using RNA-seq. Comparison of RNA-seq data allowed highlighting a broad transcriptional modulation upon STAG2 knock-out. In addition, we compared these analyses with STAG1 knock-out A673 derived model (A673SA1m#1) and with A673 (WT) and TC71 (WT) parental cells lines transfected with siCT or siEWS-FLI1.

overall_design: RNA-seq were performed in 2 different Ewing sarcoma cell lines (A673 & TC71) and their respective and derivative STAG1 and STAG2 isogenic deficient and proficient models. In A673, RNA-seq data were generated from parental A673 (WT), STAG1 KO (A673SA2m#1), STAG2 KO (A673SA2m#1) and STAG2 rescue models (A673_SA2r). In TC71, RNA-seq data were generated from parental TC71 (WT) and in 2 different STAG2 KO (TC71SA2m#1 and TC71SA2m#2) clones generated with 2 independent sgRNAs (SA2m#1 and SA2m#2). For all these models, RNA from three independent biological replicates were extracted and processed for RNA-seq. A673 and TC71 cell lines (WT) were also transfected with siRNA for 72h (non-targeting control, siCT or targeting the EWS-FLI1 fusion transcript, siEF1), RNA were extracted from both cell lines from two independent biological replicates and processed for RNA-seq.

first: Didier

last: Surdez

first: Sakina

last: Zaidi

first: Sandrine

last: Grossetête

first: Virginie

last: Raynal

first: Sylvain

last: Baulande

first: Véronique

last: Hill


title: RA-MAP: mapping molecular immunological landscapes in early rheumatoid arthritis and healthy vaccine recipients [Healthy Hepatitis B Vaccine Recipients]

city: London

first: Michael

last: Barnes

address: William Harvey Research Institute, Charterhouse Square

country: United Kingdom

institute: QMUL

summary: Rheumatoid arthritis (RA) is a chronic inflammatory disorder with poorly defined aetiology characterised by synovial inflammation with variable disease severity and drug responsiveness. To investigate the peripheral blood immune cell landscape of RA, we performed comprehensive clinical and molecular profiling of 267 RA patients and 52 vaccine recipient controls for up to 18 months to establish a high quality sample biobank including plasma, serum, peripheral blood cells, urine, genomic DNA, RNA from whole blood, lymphocyte and monocyte subsets. We have performed extensive multi-omic immune phenotyping, including genomic, metabolomic, proteomic, transcriptomic and autoantibody profiling. We anticipate that these detailed clinical and molecular data will serve as a fundamental resource offering insights into disease pathogenesis, progression and therapeutic response, ultimately contributing to the development and application of targeted therapies for RA.

overall_design: Patients were clinically profiled for 18 months with a variety of data taken every 3 months, microarray and miRNA-sequencing was performed at baseline and six-month timepoints.

first: Christopher

last: John

last: Ehrenstein

first: Dennis

last: Lendrem

first: John

last: Isaacs


title: Cytoplasmic proteotoxicity regulates HRI-dependent phosphorylation of eIF2a via the Hsp70-Bag3 module.

status: Public on Apr 14 2021

city: Ariel

first: Shivani

last: Patel

state: IL

address: 65, Ramat Hagolan

department: Molecular Biology

country: Israel

institute: Ariel University

summary: The major heat shock protein Hsp70 has been shown to form a complex with a scaffold protein Bag3, linking it to multiple signaling pathways. Via these interactions, the Hsp70-Bag3 module functions as a proteotoxicity sensor that controls cell signaling. Here, as a tool to identify signaling pathways regulated by this complex, we utilized JG-98, an allosteric inhibitor of Hsp70 that blocks its interaction with Bag3. Gene expression profiling followed by the pathway analysis indicated that a set of signaling pathways including the unfolded protein response (UPR) was activated by JG-98. Surprisingly, only the translation initiation factor eIF2a-associated branch of the UPR was activated under these conditions, while other UPR branches mediating induction of ER chaperones were not induced, suggesting that the response was not related to ER proteotoxicity and thus to ER-associated kinase PERK1. Indeed, induction of the UPR genes under these conditions was dependent on activation of a distinct cytoplasmic eIF2a kinase, HRI. We demonstrated that the Hsp70-Bag3 complex directly interacted with HRI and regulated phosphorylation of eIF2a upon induction of cytoplasmic proteotoxicity. Therefore, we uncovered a novel signaling response, which regulates cell death upon the buildup of abnormal protein species in cytoplasm via an Hsp70-Bag3-HRI-eIF2a axis.

overall_design: Comparison of sensitivity to JG-98, Hsp70 inhibitor on transformed cells.

first: Santosh

last: Kumar

first: Simone

last: Baldan

first: Arkadi

last: Hesin

first: Julia

last: Yaglom

last: Sherman


title: COV-ID: A LAMP sequencing approach for high-throughput co-detection of SARS-CoV-2 and influenza virus in human saliva

status: Public on Apr 15 2021

city: Philadelphia

first: Roberto

last: Bonasio

address: 3400 Civic Center Blvd - SCTR 9-111

department: Cell and Developmental Biology

institute: University of Pennsylvania

summary: We combined RT-LAMP with deep sequencing to detect as few as 5–10 virions of SARS-CoV-2 in unprocessed human saliva. Based on a multi-dimensional barcoding strategy, COV-ID can be used to test thousands of samples overnight in a single sequencing run with limited labor and laboratory equipment. The sequencing-based readout allows COV-ID to detect multiple amplicons simultaneously, including key controls such as host transcripts and artificial spike-ins, as well as multiple pathogens. Here we demonstrate this flexibility by simultaneous detection of 4 amplicons in contrived saliva samples: SARS-CoV-2, influenza A, human STATHERIN, and an artificial SARS spike-in. The approach was validated on clinical saliva samples, where it showed 100% agreement with RT-qPCR. COV-ID can also be performed directly on saliva adsorbed on filter paper, simplifying collection logistics and sample handling.

sample_organism:
Homo sapiens
blank sample

platform_organism:
Homo sapiens
blank sample

overall_design: Water or human saliva was spiked with synthetic SARS-CoV-2 RNA or influenza A RNA at various concentrations. Modified set of RT-LAMP primers including sample-specific barcodes as well as landing sites for universal Illumina adapters were used to perform various RT-LAMP reactions in multiplex. Different barcoded and amplified samples were pooled and Illumina adapter sequences introduced by PCR. The resulting pools were sequenced and analyzed.

first: Robert

last: Warneford-Thomson


title: RA-MAP: mapping the molecular immunological landscape in early rheumatoid arthritis with vaccine controls [6 month RA, Whole Blood, PBMC, CD4, CD8, CD14]

middle: D


title: An NKX2-1/ERK/WNT feedback loop modulates gastric identity and response to targeted therapy in lung adenocarcinoma.

status: Public on Apr 27 2021

city: Salt Lake City

first: Eric

last: Snyder

state: UT

address: 2000 Circle of Hope Drive

department: Pathology

institute: University of Utah, Huntsman Cancer Institute

summary: Cancer cells often undergo lineage switching during their natural progression and in response to therapy.  Lung adenocarcinomas (LUADs) exhibit a variety of differentiation states accompanied by dysregulation of lineage-specific transcription factors such as NKX2-1. Loss of NKX2-1 in human and murine LUAD leads to invasive mucinous adenocarcinoma (IMA), a subtype of lung cancer that exhibits pulmonary to gastric transdifferentiation. Human IMAs harbor a distinct spectrum of mutationally activated driver oncogenes compare to LUAD overall, suggesting that the pulmonary to gastric transdifferentiation induced by NKX2-1 loss plays a context-dependent role in LUAD progression.  Using genetically engineered mouse models, we find that NKX2-1 is required for optimal BRAFV600E driven lung tumor initiation but is dispensable for growth of established lung tumors. NKX2-1-deficient, BRAFV600E driven tumors morphologically resemble human IMA, have high levels of ERK phosphorylation and exhibit a distinct response to treatment with combined BRAF/MEK inhibitors. Whereas NKX2-1-positive tumor cells enter quiescence when treated with BRAF/MEK inhibitors, residual NKX2-1-negative cells fail to exit the cell cycle in response to the same therapy. Additionally, BRAF/MEK inhibitors induce canonical WNT signaling in NKX2-1-negative lung tumor cells, which is accompanied by cell identity switching within the gastric lineage. Co-inhibition of MAPK and WNT pathways blocked elements of this lineage switch in vitro and interfered with cell cycle changes imposed by MAPK inhibition in vivo. Our data show that there is a complex and reciprocal relationship between lineage specifiers and oncogenic signaling pathways in the regulation of LUAD identity and suggest that lineage switching induced by targeted therapies may confer new therapeutic vulnerabilities.

overall_design:
For bulk RNAseq, lung tumors were isolated from BRafCA/+;Trp53f/f;Nkx2-1f/+;Rosa26tdTomato/tdTomato mice (5 control and 3 MAPK inhibitor treated BP mice- a 4th sample was an outlier/of poor quaility and was excluded from analysis) and from BRafCA/+;Trp53f/f;Nkx2-1f/f;Rosa26tdTomato/tdTomato (4 control and 5 MAPK inhibitor treated BPN mice). Transcriptome profiles were generated by Illumina HiSeq 2500 sequencing.
For single cell RNAseq, lung tumors from BRafCA/+;Trp53f/f;Nkx2-1f/f;Rosa26tdTomato/tdTomato (2 control BPN mice pooled into 1 sample and 2 MAPK inhibitor treated BPN mice pooled into 1 sample) were isolated. Transcriptome profiles were generated by NovaSeq 6000 with 2x150 PE mode sequencing.

middle: L

first: Rediet

last: Zewdu

first: Benjamin

last: Spike

first: Elnaz

last: Mehrabad


title: Gut germinal center regeneration and enhanced anti-viral immunity by mesenchymal stem/stromal (MSC) cells in SIV infection

status: Public on Apr 08 2021

city: Davis

first: Mariana

last: Guedes Weber

address: 451 Health Sciences Dr.

institute: UC Davis

summary: We performed RNAseq on whole ileum extracts to investigate the underlying gene expression changes associated with MSC administration during chronic SIV infection.

overall_design: Ileum tissue mRNA profile of SIV- controls, SIV+ and SIV+ treated  with MSC animals.

first: Chara

last: Walters

first: Bipin

last: Balan

first: Clarissa

last: Santos-Rocha


title: Epigenome-Wide Association Study of COVID-19 Severity with Respiratory Failure

city: Badalona

first: Manel

last: Esteller

state: Barcelona

address: Ctra. de Can Ruti, Cami de les Escoles s/n

department: Cancer and Leukemia Epigenetics and Biology Program (PEBCL)

country: Spain

institute: Josep Carreras Leukaemia Research Institute (IJC)

type: Methylation profiling by genome tiling array

summary: Patients infected with the severe acute respiratory syndrome coronavirus  2 (SARS-CoV-2), responsible for the coronavirus disease 2019 (COVID-19), exhibit a  wide spectrum of disease behavior. Since DNA methylation has been implicated in the  regulation of viral infections and the immune system, we performed an epigenome-  wide association study (EWAS) to identify candidate loci regulated by this epigenetic  mark that could be involved in the onset of COVID-19 in patients without comorbidities.

overall_design: 407 patients with mild or severe COVID-19 disease.  Note: The clinical outcome is protected in accordance with the study design and can only be shared upon the investigator's request and signature of the agreement.

first: Manuel

middle: C

last: de Moura

first: Verónica

last: Dávalos


title: Development of High-throughput 5Pseq and detection of ribosome stalls at termination level in Saccharomyces cerevisiae

status: Public on Apr 02 2021

city: Solna

first: Vicent

last: Pelechano

address: Nobels väg 16

department: MTC

institute: ScilifeLab - Karolinska Institutet

summary: We developed a high throughput 5’P sequencing approach (HT-5PSeq) to investigate 5'P mRNA degradome in relation with translation process.  This approach is easy and scalable; and uses an affordable rRNA depletion based on duplex-specific nuclease treatment. We use it to investigate in vivo ribosome stalls in S. cerevisiae and S. pombe at single nucleotide resolution. We investigate the 5’P degradation profiles associated to ribosome pausing, its regulation in stress conditions and the relative poly(A) length of mRNA degradation intermediates.

sample_organism:
Schizosaccharomyces pombe
Saccharomyces cerevisiae

overall_design: We performed 2 biologically independent HT-5PSeq experiments. For S.cerevisiae, we performed HT-5Pseq with DSN treatment with probes targeting ribosomal rRNA (BY-DSN) and none DSN treatment (BY-NonDSN) , DSN treatment without probes (BY-NP) as control. We also performed 5Pseq (PMID: 26046441) in S.cerevisiae as positive control. For S.pombe, we performed HT-5Pseq with DSN treatment with probes (orginally designed for S.cerevisiae ribosomal rRNA) (Pombe-DSN) and none DSN treatment (Pombe-NonDSN) as control.To inhibit translation process, we used cycloheximide (CHX) as a translation inhibitor on S.cerevisiae (BY-CHX) and S.pombe (Pombe-CHX). In addition, we performed HT-5Pseq under different growth conditions. For early exponential phase, strains were grown to a final OD600 of 0.3 (BY-lowOD). To reach stationary stage, strains were grown during 60h in YPD (BY-Stationary). We performed paired-end sequencing for read1 (61bp) and read2 (15bp) in some samples (see below). We splited libraries with polyA and non-polyA based on the length of As in read2. For other samples, we performed single end sequencing.

first: Yujie

last: Zhang


title: Expression data from Neuro2a cells treated with siRNA targeting to Cpeb1 mRNA.

status: Public on Mar 31 2021

city: Hirakata

first: Souichi

last: Oe

state: Osaka

address: 2-5-1 Shinmachi

country: Japan

institute: Kansai Medical University

summary: Cytoplasmic polyadenylation element binding protein 1 (CPEB1) regulates polyadenylation and subsequent translation of CPE-containing mRNAs, which contributes to various physiological and pathological phenomena. To clarify changes in gene expression profiles caused by dysregulation of CPEB1 expression, we performed microarray analyses and revealed that reduced CPEB1 expression altered the expression levels of numerous genes. These findings indicate that accurate post-transcriptional regulation of CPEB1 expression contributes to the maintenance of global gene expression partially through modulating lncRNA expression.

overall_design: To understand the comprehensive changes of gene expression caused by dysregulation of CPEB1 expression, we performed microarray analyses of control or CPEB1-depleted Neuro2a cells. Neuro2a cells were transfected with control siRNA or siRNA targeting Cpeb1 mRNA for RNA extraction and hybridization on Affymetrix microarrays.

first: Masaaki

last: Kitada


title: RA-MAP: mapping molecular immunological landscapes in early rheumatoid arthritis and healthy vaccine recipients [small RNA SEQUENCING]

first: Michael

last: Barnes

overall_design: Patients were clinically profiled for 18 months with a variety of data taken every 3 months, microarray and small RNA-sequencing was performed at baseline and six-month timepoints.

first: Christopher

last: John

last: Ehrenstein

first: Dennis

last: Lendrem

first: John

last: Isaacs


title: Lipoprotein Lipase Overexpression in Skeletal Muscle Attenuates Weight Regain by Potentiating Energy Expenditure

status: Public on Mar 24 2021

city: Oklahoma City

middle: C.

last: Rudolph

state: OK

address: 975 NE 10th St. BRC North rm 364

department: Biochemistry and Physiology

institute: OUHSC

summary: We investigated the effect of weight loss maintenance (WLM) and weight regain on skeletal muscle in rodents. In skeletal muscle of obesity prone rats, WLM reduced fat oxidative capacity and down-regulated genes involved in fat metabolism. After weight was regained in rats, the genes involved in fat metabolism were still reduced. Mice with skeletal muscle lipoprotein lipase overexpression (mCK-hLPL), which augments fat metabolism, were subjected to our WLM and weight regain paradigm. We found that mCK-hLPL attenuated weight regain by potentiating energy expenditure.Irrespective of genotype, weight regain suppressed dietary fat oxidation and down-regulated genes involved in fat metabolism in skeletal muscle. However, mCK-hLPL mice oxidized more fat throughout weight regain and had greater expression of genes involved in fat metabolism and lower expression of genes involved in carbohydrate metabolism during WLM and regain.

overall_design:
Rats-

Mice-

first: David

last: Presby


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

status: Public on Mar 19 2021

city: Minato-ku

first: Atsushi

last: Iwama

state: Tokyo

address: 4-6-1, Shirokanedai

department: Center for Stem Cell Biology and Regenerative Medicine

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

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

overall_design: RNA-seq in young and aged HSCs with no cytokine stimulation, 3 hours after cytokine stimulation, and 12 hours after cytokine stimulation.

first: Naoki

last: Itokawa

first: Motohiko

last: Oshima

first: Wakako

last: Kuribayashi

first: Naoya

last: Takayama

first: Shuhei

last: Koide

first: Yaeko

last: Nakajima-Takagi

first: Aoyama

last: Kazumasa

first: Satoshi

last: Yamazaki

first: Koji

last: Eto


title: Transcriptome profile of tra1 mutant in S. cerevisiae

status: Public on Mar 15 2021

first: Matthew

last: Berg

state: Ontario

address: 1151 Richmond St

department: Biochemistry

country: Canada

institute: University of Western Ontario

summary: Tra1 is an essential component of the SAGA and NuA4 transcriptional co-activator complexes and is linked to multiple cellular processes associated with the yeast response to antifungal drugs. This submission contains RNA sequencing data from Saccharomyces cerevisiae strains expressing a Tra1 mutant with three arginine to glutamine mutations in the PI3K domain (tra1Q3; Berg et al., 2018). Our goal was to identify how gene expression changes due to mutation to the PI3K domain of Tra1.

overall_design: mRNA of strains expressing tra1Q3 compared to strains expressing wild type TRA1

first: Iqra

last: Razzaq

first: Yuwei

last: Jiang

first: Julie

last: Genereaux

first: Deeva

last: Uthayakumar

first: Grace

last: Kim

last: Brandl

first: Patrick

last: Lajoie

first: Rebecca

last: Shapiro


title: Transcriptome profile of tra1 mutant in C. albicans in response to the antifungal caspofungin

status: Public on Mar 17 2021

summary: The emergence of drug-resistant fungal strains is a threat to human health. Identifying targets that increase the susceptibility of fungal pathogens to current therapies will significantly improve outcomes. Tra1 is an essential component of the SAGA and NuA4 transcriptional co-activator complexes and is linked to multiple cellular processes associated with the yeast response to antifungal drugs. This submission contains RNA sequencing data from Candida albicans strain expressing a Tra1 mutant with three arginine to glutamine mutations in the PI3K domain (tra1Q3; Berg et al., 2018) treated with or without the antifungal caspofungin. Our goal was to identify genes regulated by Tra1 in C. albicans and identify genes with differential responses in the mutant tra1 strain upon capsofungin relative to the wild-type strain. We identified 68 genes that were differentially expressed when the tra1Q3 strain was treated with caspofungin, as compared to gene expression changes induced by either tra1Q3 or caspofungin alone. Included in this set were genes involved in cell wall maintenance, adhesion and filamentous growth. As a critical component of both SAGA and NuA4, Tra1 is uniquely positioned to regulate the yeast antifungal response and emerges, through targeting its PI3K domain, as a promising new therapeutic target for fungal infections.

overall_design: mRNA of strains expressing tra1Q3 compared to strains expressing wild type TRA1 with and without caspofungin treatment (10ng/ml for two hours)

first: Christopher


title: RA-MAP: mapping molecular immunological landscapes in early rheumatoid arthritis and healthy vaccine recipients [Baseline RA, Whole Blood, PBMC, CD4, CD8, CD14]

first: Michael

last: Barnes

last: John

last: Ehrenstein

first: Dennis

last: Lendrem

first: John

last: Isaacs


title: Development of gene expression signatures for ovarian cancer stem cells

status: Public on Mar 13 2021

city: Taipei

first: Hung-Cheng

last: Lai

address: No.250, Wuxing St.

department: Department of Obstetrics and Gynecology, School of Medicine, College of Medicine,

country: Taiwan

institute: Taipei Medical University

summary: To understand the differentiation of ovarian cancer stem cells (CSCs), We derived two phenotypes of CSCs and identified the gene expression profiling. The CSCs were derived from Cp70 ovarian cancer cells and cultured in suspension and examined every day for sphere formation. Spheres were then dissociated and passaged at least eight times in 2 months to generate spheres, which are henceforth referred to as SR cells. The surface of SR-I was smooth regardless of the size, whereas SR-II was morula. SR-I could differentiate into multiple-lineage cell types under specific induction conditions. SR-I spheroids could differentiate to SR-II spheroids through epithelial-mesenchymal transition.The self-renewal was slower for SR-I than for SR-II.

overall_design: The larger or equle 2x fold changes between SR-1 and SR-2.

first: Hsiang-Ju

last: Chen

first: Yi-Te

last: Yo

first: Tien-Shuo

last: Huang

first: Rui-Lan


title: Transcriptome of glioblastoma stem cells.

status: Public on Mar 09 2021

city: Clermont-Ferrand

first: franck

last: court

address: 28 Place Henri Dunant

institute: GReD CNRS

summary: In human, the 39 coding HOX genes and 18 referenced non-coding antisense transcripts are arranged in four genomic clusters named HOXA, B, C, and D. This highly conserved family belongs to the homeobox class of genes that encode transcription factors required for normal development. Therefore, HOX gene deregulation might contribute to the development of many cancer types. Here, we study HOX gene deregulation in adult glioma, a common type of primary brain tumor. We performed extensive molecular analysis of tumor samples, classified according to their isocitrate dehydrogenase (IDH1) gene mutation status, and of glioma stem cells. We found widespread expression of sense and antisense HOX transcripts only in aggressive (IDHwt) glioma samples, although the four HOX clusters displayed DNA hypermethylation. Integrative analysis of expression-, DNA methylation- and histone modification signatures along the clusters revealed that HOX gene upregulation relies on canonical and alternative bivalent CpG island promoters that escape hypermethylation. H3K27me3 loss at these promoters emerges as the main cause of widespread HOX gene upregulation in IDHwt glioma cell lines and tumors. Our study provides the first comprehensive description of the epigenetic changes at HOX clusters and their contribution to the transcriptional changes observed in adult glioma. It also identified putative "master" HOX proteins that might contribute to the tumorigenic potential of glioma stem cells.

overall_design: mRNA-seq

first: Franck

last: Court

first: Elisa

last: Le Boiteux

first: Pierre

middle: O

last: Guichet

first: Philippe

last: Arnaud


title: Chromatin states and Transcriptome in in glioblastoma stem cells

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

overall_design: Refer to individual Series


title: Stranded RNA-seq were performed on total RNA following ribosomal RNAs depletion (Ribo-zero removal kit, illumina) for glioblastoma stem cell

overall_design: RNA-seq


title: RNA-seq data of knowk-down of STAG2 or EWSR1-FLI1 in Ewing sarcoma cell lines (siCT, siEF1 & siSA2)

first: Olivier

last: Delattre

summary: STAG2, a member of cohesin, is one of the most recurrently mutated genes in human cancer. Here, we investigated STAG2 function in the context of Ewing sarcoma, an aggressive bone tumor driven by EWS-FLI1 oncogene chimeric transcription factor. Five different Ewing sarcoma cell lines were transfected with siCT or 2 different siRNAs targeting STAG2 (siSA2#6 or siSA2#8). RNA in A673 & TC71 (siSTAG2) was extracted 24, 48 and 72 hours post-transfection. RNA in EW1, CHLA-10 and CHLA-258 (siSTAG2 and siEWSR1-FLI1) was extracted 72 hours post-transfection. RNA-seq based anlayses of these experiments highligted that STAG2 knock-down alters EWSR1-FLI1 activation signature.

overall_design: RNA-seq were performed in 5 different Ewing sarcoma cell lines (A673,TC71, EW1, CHLA-10 & CHLA-258). In A673 & TC71, RNA-seq data were generated for transfection with 3 siRNA (non-targeting control-siCT, siSA2#6, siSA2#8) at 3 different time points: 24h, 48h and 72h. The 3 other cell lines (EW1, CHLA-10 & CHLA-258) were also transfected at 72h with different siRNAs: siCT, siSA2#6, siSA2#8, siRNA targeting EWSR1-FLI1 fusion transcript type 1 (CHLA-10 & CHLA-258) or type 2 (EW1). RNA were extracted from all cell lines from two independent biological replicates and processed for RNA-seq.

first: Didier

last: Surdez

first: Sakina

last: Zaidi

first: Sandrine

last: Grossetête

first: Virginie

last: Raynal

first: Sylvain

last: Baulande

first: Véronique

last: Hill


title: RA-MAP: mapping molecular immunological landscapes in early rheumatoid arthritis and healthy vaccine recipients

first: Michael

last: Barnes


title: Epigenetic regulator UHRF1 suppressively organize multiple pathogenesis in rheumatoid arthritis.

status: Public on Feb 16 2021

city: Toon

first: Noritaka

last: Saeki

state: Ehime

address: Shitsukawa

department: Advanced Research Support Center

institute: Ehime university

type: Methylation profiling by high throughput sequencing


title: Nuclear mechanosensing drives chromatin remodeling of persistently activated myofibroblasts

city: Boulder

first: Cierra

last: Walker

state: CO

address: 3415 Colorado Ave

institute: University of Colorado Boulder

summary: Fibrotic disease is caused by persistently activated fibroblasts, known as myofibroblasts, that continuously deposit extracellular matrix and fail to de-activate after injury resolution. There are currently no treatments for fibrotic disease; our study addresses the mechanisms whereby myofibroblasts persist in fibrotic tissues such as diseased cardiac valves. We exploit photo-softening hydrogels as synthetic valve tissue mimics and valve fibroblasts as a model to study how stiffness controls pathological myofibroblast activation and their persistence. We show that persistent myofibroblasts have condensed chromatin structure with genome-wide alterations and that this is associated with stabilization of the actin cytoskeleton. Disconnecting the nucleus from the cytoskeleton prevents chromatin condensation and myofibroblast persistence. Notably, myofibroblasts in patients with aortic valve stenosis display a condensed chromatin structure compared to myofibroblasts in a healthy patient, similar to the difference observed between cultured persistent myofibroblasts and transient myofibroblasts. Collectively, our results reveal that nuclear mechanosensing leads to distinct chromatin signatures in persistent myofibroblasts and that this novel cellular mechanism is likely relevant to human fibrotic disease.

overall_design: Primary porcine aortic valvular interstitial cells were isolated and seeded onto PEGdiPDA hydrogels (G' = 4 kPa (stiff) or 2 kPa (soft)). The cells were cultured in Media 199 (Life Technologies) supplemented with 1% human serum, 50 U/mL penicillin, 50 μg/mL streptomycin, and 1 μg/mL amphotericin B for 3 days or 9 days.

first: Kristi

last: Anseth

first: Leslie

last: Leinwand


title: Chromatin states in glioblastoma stem cell [ChIP-seq]

first: franck

last: court

overall_design: ChIP-seq


title: Indispensable epigenetic control of thymic epithelial cell development and function by Polycomb Repressive Complex 2

status: Public on Feb 19 2021

city: Oxford

first: Adam

last: Handel

address: John Radcliffe Hospital

department: Weatherall Institute of Molecular Medicine

institute: University of Oxford

summary: Thymic T cell development and T cell antigen receptor repertoire selection are dependent on essential molecular cues provided by thymic epithelial cells (TECs). These cells rely for their development and function on the correct placement of post-translational histone modifications. The repressive H3K27me3 mark is catalyzed by the holoenzyme Polycomb Repressive Complex 2 (PRC2). Mice with a TEC-targeted deficiency of PRC2 are differentially affected in their TEC lineage development establishing a novel differentiation path that progressively off-sets the shortage of canonical medullary TEC. The resultant hypoplastic thymus is severely compromised in its ability present antigen and to select a repertoire of T cells with normal effector and regulatory functions. A heightened peripheral activation of regulatory T cells, however, prevents the occurrence of overt autoimmunity in these mice.

overall_design: Single cell RNA-seq, bulk RNA-seq and ChIP-seq on thymic epithelial cell subsets (cTEC and mTEChi) from wild-type and Eedfl/fl::ZsGreen::beta5tCre mice

middle: E

first: HongYing

last: Teh

first: Georg

last: Holländer


title: Epigenetic regulator UHRF1 suppressively organize multiple pathogenesis in rheumatoid arthritis [RNA-seq]

summary: Rheumatoid arthritis (RA) is characterized by chronic synovial inflammation with aberrant epigenetic alterations, leading joint destruction. However, epigenetic regulatory mechanisms underlying RA pathogenesis remain largely unknown. Here we showed that Ubiquitin-like containing PHD and RING finger domains 1 (known as UHRF1) is a central epigenetic regulator to suppressively orchestrate the expression of multiple exacerbation factors in RA. We found remarkable up-regulation of Uhrf1, which is known as a key molecular for maintenance of DNA methylation during cell division 1-3, in murine arthritis tissue, especially synovial fibroblasts (SF). SF-specific Uhrf1 conditional knockout mice indicated more severe arthritic phenotypes with apoptosis resistant SF. Integrative analysis between transcriptome and methylome showed that expression of several cytokines including Ccl20 were up-regulated in Uhrf1-deficient SF. In RA patients, disease activity scores, CCL20 expression, Th17 accumulation, apoptosis resistance were negatively correlated with UHRF1 expression in synovium. Finally, stabilization of UHRF1 by administration of Ryuvidine improved pathogenesis of arthritis model mice. Our results demonstrated that UHRF1 expressed in SF contributes to suppressively orchestrate expression of genes of multiple exacerbating factors under RA progression. Targeting UHRF1 could provide a novel therapeutic strategy for RA.

overall_design: mRNA profiles of primary synovial fibroblasts obtained from ankle tissue of K/BxN serum transfer arthritis were generated by deep sequencing, in triplicate, using Illumina Miseq.

first: Yuuki

last: Imai


title: Single Cell Sequencing Reveals Early PGC-like Intermediates During Mouse Primed to Naïve Transition

city: GuangZhou

first: Jiangping

last: He

address: Kai yuan avenue 190

institute: Guangzhou Institutes of Biomedicine and Health (GIBH), CAS

summary: Single cell analysis provides clarity unattainable with bulk approaches. Here we apply single cell RNA-seq to a newly established BMP4 induced mouse primed to naive transition (Bi-PNT) system and show that the reset is not a direct reversal of cell fate but through developmental intermediates. We first show that mEpiSCs bifurcate into c-Kit+ naïve and c-Kit- placenta-like cells, among which, the naive branch undergoes further transition through a primordial germ cell-like cells (PGCLCs) intermediate capable of spermatogenesis in vivo. Indeed, deficiency of Prdm1/Blimp1, the key regulator for PGC specification, blocks the induction of PGCLCs and naïve cells. Instead, Gata2 knockout arrests placenta-like  fate, but facilitates the generation of PGCLCs. Our results not only reveal a newly cell fate dynamics between primed and naive states at single-cell resolution, but also provide a model system to explore mechanisms involved in regaining germline competence from primed pluripotency.

overall_design:
We analyzed the single-cell transcriptome expression profiles (scRNA-seq) during mouse primed naïve transition (PNT).
We analyzed the transcriptome expression of BV+SC+ cells generated during mouse primed to naïve transition.
We analyzed the transcriptome expression and chromatin remodelling of cKit positive and negative cells during mouse primed naïve transition (PNT).


title: Identification of TFAP2A and MITF binding sites in the melanoma cell line SK-MEL-28

status: Public on Feb 08 2021

city: Iowa City

first: Colin

last: Kenny

state: Iowa

address: 51 Newton Road 100 Bowen Science Building Iowa

department: Anatomy and Cell Biology

institute: University of Iowa

summary: TFAP2A and MITF binding sites were identified in SK-MEL-28 cell lines using Cleavage Under Targets and Release Using Nuclease (CUT&RUN).

overall_design: We targeted TFAP2A and MITF by CUT&RUN sequencing in wild-type SK-MEL-28 cell lines. All experiments were conducted in duplicate. IgG was used as a background control.

first: Robert

last: Cornell


title: Human pluripotent stem cell-derived myogenic progenitor cells engraft to become quiescent functional satellite cells in vivo

status: Public on Jan 20 2021

city: Baltimore

first: Suraj

last: Kannan

state: MD

address: 720 Rutland Avenue Ross 954

department: Cardiology

institute: Johns Hopkins University

summary: In this study, we generated human pluripotent stem cell-derived myogenic progenitor cells and transplanted into injured skeletal muscle. We performed two single cell RNA-seq experiments. In the first experiment, we compared transplanted satellite cells with in vitro controls. In the second study, we did a time-series analysis of transplanted cells.

overall_design: In the first experiment, we sequenced 1) human embryonic stem cells, 2) hESC-derived myogenic cells in vitro, 3) hESC-derived myogenic cells, cultured for a further month in vitro, 4) hESC-derived myogenic cells, transplanted in vivo and harvested one month later. In the second experiment, we sequenced hESC-derived myogenic cells, transplanted in vivo, at 1, 2, 3, and 4 weeks post-transplantation.

first: C

last: Sun

first: S

first: G

last: Lee


title: Discovery and functional assessment of a novel adipocyte population driven by intracellular Wnt/β-catenin signaling in mammals

status: Public on May 01 2021

city: NEW ORLEANS

first: Zhi

last: Liu

state: United States

address: 2734 CALHOUN

institute: Tulane

summary: Wnt/β-catenin signaling has been well established as a potent inhibitor of adipogenesis. Here, we identified a population of adipocytes that exhibit persistent activity of Wnt/β-catenin signaling, as revealed by the Tcf/Lef-Gfp reporter allele, in embryonic and adult mouse fat depots, named as Wnt+ adipocytes. We showed that this β-catenin-mediated signaling activation in these cells is Wnt ligand- and receptor-independent but relies on AKT/mTOR pathway and is essential for cell survival. Such adipocytes are distinct from classical ones in transcriptomic and genomic signatures and can be induced from various sources of mesenchymal stromal cells including human cells. Genetic lineage-tracing and targeted cell ablation studies revealed that these adipocytes convert into beige adipocytes directly and are also required for beige fat recruitment under thermal challenge, demonstrating both cell autonomous and non-cell autonomous roles in adaptive thermogenesis. Furthermore, mice bearing targeted ablation of these adipocytes exhibited glucose intolerance, while mice receiving exogenously supplied such cells manifested enhanced glucose utilization. Our studies uncover a unique adipocyte population in regulating beiging in adipose tissues and systemic glucose homeostasis.

overall_design:
We took advantage of the Wnt/β-catenin signaling specific reporter mouse line TCF/Lef:H2B-GFP that allows real-time monitoring of Wnt/β-catenin activity at single-cell resolution. We cultured Wnt+ and Wnt- adipocytes in vitro and enriched them based on FACS separation, using GFP as a readout. To distinguish Wnt+ adipocytes from Wnt- fat cells and explore the global diversity at molecular and genomic levels, we profiled cultured Wnt+ and Wnt- adipocytes derived from adult mice adipose tissues by scRNA-seq and scATAC-seq.

Wnt+ adipocytes from immortalized GFPpos-1 precursor cells, after 3-day pro-adipogenic induction, were subject to LF3 treatment for one day to suppress the intracellular /β-catenin-mediated signaling. Wnt+ adipocytes without LF3-treated were included as control groups. Total RNAs were extracted from control and treatment groups (n = 3 each)  and prepared using a NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEW ENGLAND BioLabs) according to the manufacturer?s instruction. The normalized dsDNA libraries were pooled and sequenced on Illumina NextSeq 1000 and NextSeq 2000 with P2 (100 cycles) kit at the Center for Translation Research in Infection and Inflammation in Tulane School of Medicine. HISAT2, featureCounts, and DESeq2 softwares were used for reads alignment to mouse reference genome (version mm10), quantification of transcript abundances, and differential gene expression analysis.

first: Tian

last: Chen

first: Weidong

last: Tian

first: YiPing


title: Hnf4a regulated transcriptome

status: Public on Jan 14 2021

first: Eric

last: Snyder

address: 2000 Circle of Hope Drive

institute: University of Utah, Huntsman Cancer Institute


title: Sequencing of proximal tubular carnitine-acetyl transferase Heterozygous knockout kidney cortex from mouse

status: Public on Apr 01 2021

city: Baton Rouge

first: Krisztian

last: Stadler

state: LA

address: 6400 Perkins Rd

institute: Pennington Biomedical Research Center

summary: We report the comparison of normal vs proximal tubular cell specific CrAT heterozygous knockout kidney cortex by sequencing analysis

overall_design:
CrAT was deleted in proximal tubular cells of mice using Cre/Lox technology (Ggt -CRE). First generation of Heterozygous mice were used. Mice were aged out to 12-15 months.
RNA was isolated by the TRIzol method, libraries and sequencing were done using a Lexogen/Illumina platform.

first: Claudia

last: Kruger


title: The phosphatase PTEN links platelets with immune regulatory functions of mouse T follicular helper cells

status: Public on Jan 01 2021

city: shanghai

first: chen

last: xue

address: Nanchen Road381 room305

department: College of Life Science

institute: shanghai university

summary: Beyond a function in hemostasis and thrombosis, platelets can regulate innate and adaptive immune responses. Hyperactive platelets are frequently associated with multiple human autoimmune diseases, yet their pathogenic functions in these diseases have not been fully established. Emerging studies show an essential function of the phosphatase and tensin homolog (PTEN) in maintenance of immune homeostasis. Here, we show that mice with platelet-specific deletion of Pten, develop age-related lymphoproliferative diseases and humoral autoimmunity not seen in wildtype animals. Platelet-specific Pten-deficient mice have aberrant T cell activation, excessive T follicular helper (Tfh) cell responses and accumulation of platelet aggregates in lymph nodes. Transferred Pten-deficient platelets are able to infiltrate into the peripheral lymphoid tissues and form more aggregates. Moreover, Pten-deficient platelets are hyperactive and overproduce multiple Tfh-promoting cytokines via activation of the PDK1/mTORC2-AKT-SNAP23 pathway. Pten-deficient platelets show enhanced interaction with CD4+ T cells and promote conversion of CD4+ T cells into Tfh cells. Our results implicate PTEN in platelet-mediated immune homeostasis, and provide evidence that hyperactive platelets function as an important mediator in autoimmune diseases using mouse models.

overall_design: 6 samples are analyzed; Lymphoid CD4 positive T cells from Pten fl/fl Pf4-Cre mice and littermate control Pten fl/fl mice

first: Xue

first: ChuanXin

last: Huang

first: Junling


title: Improving the efficacy of EGFR inhibitors by topical treatment of cutaneous squamous cell carcinoma with miR-634 ointment

status: Public on Dec 15 2020

city: Tokyo

first: Jun

last: Inoue

address: Yushima 1-5-45, Bunkyo-ku

department: Molecular Cytogenetics

institute: Tokyo Medical & dental univ.

type:
Expression profiling by array
Other

summary: For cutaneous squamous cell carcinoma (cSCC), topical treatment is an essential option for patients who are not candidates for or refuse surgery. Epidermal growth factor receptor (EGFR) plays a key role in the development of cSCC, but EGFR tyrosine kinase inhibitors (TKIs), such as gefitinib, have shown only partial clinical benefit in this disease. Thus, there is an unmet need to develop novel strategies for improving the efficacy of TKIs in cSCC. We previously demonstrated that the tumor-suppressive microRNA (miRNA) miR-634 functions as a negative modulator of cytoprotective cancer cell survival processes and is a useful anticancer therapeutic agent. Here, we found that topical application of an ointment containing miR-634 inhibited in vivo tumor growth without toxicity in a cSCC xenograft mouse model and a DMBA/TPA-induced papilloma mouse model. Functional validation revealed that miR-634 overexpression reduced glutaminolysis by directly targeting ASCT2, a glutamine transporter. Furthermore, overexpression of miR-634 synergistically enhanced TKI-induced cytotoxicity by triggering severe energetic stress in vitro and in vivo. Thus, we propose that topical treatment with miR-634 ointment is a useful strategy for improving for EGFR TKI-based therapy for cSCC.

overall_design: We identified transcripts enriched in RNP immunoprecipitation (RIP) assays using an antibody against AGO2 in cells overexpressing miR-634 in A431 cells by microarray analysis (RIP-chip analysis). Cells were transfected with 10 nM miR-NC or miR-634 and then lysed after 24 h. The lysates were precleared and incubated with AGO2 antibody-immobilized beads or normal rabbit IgG antibody-immobilized beads for RIP. Each bead complex was washed, and RNA was isolated. RNA from AGO2-RIP (RIP) and total RNA (input) were labelled and hybridized on the Agilent 8 × 60K array. Each experiment was performed in duplicate. In both miR-NC-overexpressing cells and miR-634-overexpressing cells, the enrichment (RIP/Input) was calculated. Then, the fold change of enrichment (miR-634/miR-NC) was calculated.

first: Kyoko

last: Fujiwara

first: Hidetoshi

last: Hamamoto

first: Katsunori

last: Kobayashi

first: Johji

last: Inazawa


title: Gene expression profiling using RNA-Seq data of MMTV-Wnt1 tumor tissue from mice treated with E7386

status: Public on Dec 21 2020

city: Tsukuba-shi

first: Kazuhiko

last: Yamada

address: 5-1-3 Tokodai

institute: Eisai Co., Ltd.

summary: We conducted an RNA-Seq analysis using total RNA extracted from MMTV-Wnt1 tumor tissues resected from mice orally administered E7386 at 25 or 50 mg/kg twice daily, or vehicle, for 3 days (Day 4) or 7 days (Day 8) and examined the differentially expressed gene levels compared with vehicle at days 4 and 8.

overall_design: MMTV-Wnt1 transgenic mice (B6SJL-Tg(Wnt1)1Hev/J) were obtained from the Jackson Laboratory (Bar Harbor, ME). Spontaneously developed breast tumors were resected from the MMTV-Wnt1 transgenic mice, diced, and inoculated into C57BL/6J mice (Charles River Laboratories Japan). Tumors were allowed to grow to approximately 200 mm3 in size (designated Day 1); tumor-bearing mice were then randomly allocated to treatment groups and orally administered E7386 (25.0, or 50.0 mg/kg twice daily) for 3 days (Day 4) or 7 days (Day 8).

first: Yusaku

last: Hori

first: Takayuki

last: Kimura

first: Yasuhiro

last: Funahashi

first: Yoichi

last: Ozawa


title: CUT&Tag for analysis of Nrf2-regulated genes in liver of heat-stressed chicken (Gallus gallus)

status: Public on Dec 05 2020

city: Shanghai

first: Ding

last: Yu

address: Number 953 Jianchuan Road

institute: Newcore biotechnology

summary: The CUT&Tag and high-throughput sequencing technologies were used in this experiment. Results showed that 54857512-63235094 clean reads were obtained in this study.

overall_design: CUT&Tag for analysis of Nrf2-regulated genes in liver of heat-stressed chickens

first: Hong

last: Hu

first: Xi

last: Bai


title: EPIC-based DNA methylation analysis of glioblastoma stem cells.

first: franck

last: court

overall_design: DNA methylation from glioblastoma stem cell GSC11

first: Franck

last: Court

first: Elisa

last: Le Boiteux

first: Pierre

middle: o

last: Guichet

first: Philippe

last: Arnaud


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

first: Atsushi

last: Iwama

address: 4-6-1, Shirokanedai

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

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

overall_design: Chromatin Accessibility

first: Naoki

last: Itokawa

first: Motohiko

last: Oshima

first: Wakako

last: Kuribayashi

first: Naoya

last: Takayama

first: Shuhei

last: Koide

first: Yaeko

last: Nakajima-Takagi

first: Aoyama

last: Kazumasa

first: Satoshi

last: Yamazaki

first: Koji

last: Eto


title: Single-cell lineages reveal the rates, routes, and drivers of metastasis in cancer xenografts

status: Public on Dec 13 2020

city: San Francisco

first: Matthew

middle: Gregory

last: Jones

state: CA

institute: UCSF

overall_design: 9 scRNA-seq libraries of metastatic A549 cell lines. 4 of the libraries correspond to "TargetSite" libraries in which we extract lineage information for each cell. 5 of the libraries correspond to 3'-capture transcriptional libraries. In total, this repository includes: (1) Fastq files for each library; (2) processed "alleleTable" describing the lineage information for each TargetSite library; (3) "Character matrices" for lineage reconstruction; (4) reconstructed trees for each clone, in newick format; (5) scRNA-seq raw count matrices for the RNA-seq samples; and (5) meta data for each cell.

first: Jeffrey

last: Quinn

middle: G

last: ones

first: Ross

last: Okimoto

first: Shigeki

last: Nanjo

first: Michell

last: Chan

first: Nir

last: Yosef

first: Trever

last: Bivona

first: Jonathan

last: Weissman


title: Epigenetic traits inscribed in chromatin accessibility in aged hematopoietic stem cells (ChIP-seq H3K27me3 H3K4me3)

first: Atsushi

last: Iwama

overall_design: H3K4me3, H3K27me3, and H2AK119ub profiling by ChIP-seq

first: Naoki

last: Itokawa

last: Oshima


title: Epigenetic traits inscribed in chromatin accessibility in aged hematopoietic stem cells

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

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

overall_design: Refer to individual Series


title: RNA sequencing analysis of CD4 and CD8 LN T cells from B6 and FlipFlop mice

status: Public on Feb 07 2021

city: Frederick

first: Jack

last: Chen

address: SAIC-Frederick Miller Dr

institute: NIH

summary: We performed genome-wide RNA sequencing to analyze gene expression in CD4 and CD8 LN T cells from B6 and FlipFlop mice.   We first identified 335 genes in B6 mice that were differentially expressed in CD4 helper and CD8 cytotoxic T cells.   Assessment of these genes in FlipFlop mice further revealed that FlipFlop CD4 T cells resembled B6 CD8 T cells, while FlipFlop CD8 T cells resembled B6 CD4 T cells.

overall_design: Comparison of mRNA profiles of LN CD4 and CD8 T cells from B6 and FlipFlop mice.

first: Alfred

last: Singer

first: Miho

last: Shinzawa


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

city: Minato-ku

overall_design: RNA-seq of Young and Aged hematopoietic cells

first: Motohiko

first: Wakako

last: Kuribayashi

first: Naoya

last: Takayama

first: Shuhei

last: Koide

first: Yaeko

last: Nakajima-Takagi

last: Kazumasa

last: Yamazaki


title: Hnf4a regulated transcriptome in 2D cell lines derived from murine pancreatic tumors [2D cell lines]

city: Salt Lake City

first: Eric

last: Snyder

summary: Pancreatic ductal adenocarcinoma is an aggressive disease with a dismal five-year survival of 5%. Gene expression profiling has been instrumental for subtype classification in cancer, highlighting fundamental differences in tumors at the molecular level. Over the last years, multiple genomics studies have led to the classification of PDAC into two major subtypes: classical and basal-type. The classical subtype expresses higher levels of endodermal lineage specifiers, including HNF4A, GATA6, FOXA2, FOXA3 than the basal-type. The basal-type confers a worse prognosis, raising the possibility that loss of these lineage specifiers might enhance the malignant potential of PDAC. We found that the lineage specifier HNF4a plays a key role in maintaining a transcriptional network that characterizes the classical subtype, restraining growth in different PDAC models. Additionally, we demonstrated that HNF4a controls PDAC cell identity and proliferation, and represses the expression of SIX family members, two mesodermal lineage specifiers highly expressed in basal-type.

overall_design: The study was designed to compare transcriptome profiles between isogenic Hnf4a-negative and Hnf4a-expressing murine pancreatic cancer cell lines. Hnf4a expression was restored by treating cell cultures with doxycycline.

first: Soledad

last: Camolotto

first: Veronika

middle: K

last: Belova

first: Luke

last: Torre-Healy

first: Hannah

last: Conway

first: Chris

last: Stubben

first: Richard

last: Moffit


title: Epigenetic regulator UHRF1 suppressively organize multiple pathogenesis in rheumatoid arthritis [MBD-seq]

first: Noritaka

last: Saeki

overall_design: DNA methylation profiles of primary synovial fibroblasts obtained from Control and cKO mice were analyzed using MBD2 mediated methylated DNA enrichment followed by next generation sequencing (MBD-seq) with Illumina MiSeq.

first: Yuuki

last: Imai

first: Katsuhide

last: Igarashi

first: Maky

last: Ideta-Otsuka


title: The INO80 complex regulates epigenetic inheritance of heterochromatin (ChIP-seq, Mnase-seq)

status: Public on Nov 18 2020

city: New York

first: Songtao

last: Jia

state: New York

address: 116th & Broadway

department: Biological Sciences

institute: Columbia University

summary: One key aspect of epigenetic inheritance is that chromatin structure can be stably inherited through generations even after removal of the signal that establishes such structure. In fission yeast, the RNA interference (RNAi) machinery is critical for initial targeting of histone methyltransferase Clr4 to pericentric repeats to establish heterochromatin. However, pericentric heterochromatin cannot be properly inherited in the absence of RNAi, suggesting the existence of mechanisms that counteract chromatin structure inheritance. Here we show that in the absence of certain components of the INO80 chromatin-remodeling complex, pericentric heterochromatin can be properly inherited in RNAi mutants. The ability of INO80 to counter heterochromatin inheritance is attributed to one accessory subunit Iec5, which promotes histone turnover at heterochromatin regions, but has little effects on nucleosome positioning at heterochromatin, gene expression, or the DNA damage response. Slow histone turnover preserves parental histones at repeat regions to enhance epigenetic inheritance of heterochromatin not only in RNAi mutants but also in wild type cells. Our analyses demonstrate the importance of INO80 in controlling heterochromatin inheritance and maintaining the proper heterochromatin landscape of the genome.

overall_design: ChIP-seq of H3K9me2 of iec5Δ. MNase-seq of three Ino80 mutants and dcr1Δ. MNase-seq for wild-type and iec5Δ in strains with tetO-ura4-GFP reporter

first: Chun-min

last: Shan

first: Kehan

last: Bao

first: Jolene

last: Diedrich

first: Xiao

last: Chen

first: Chao

last: Lu

first: John

last: Yates


title: Osteocyte necrosis triggers osteoclast-mediated bone loss through macrophage-inducible C-type lectin

city: Erlangen

first: Darja

last: Andreev

address: Glückstraße 6

department: Medicine 3

institute: Friedrich-Alexander-University Erlangen-Nürnberg and Universitätsklinikum Erlangen

summary: It is generally believed that bone micro-fractures, associated with osteocyte death, lead to osteoclast recruitment and thereupon to removal and replacement of damaged bone. However, the underlying mechanism is still incompletely defined. In this study we hypothesized that the pattern recognition receptor macrophage-inducible C-type lectin (Mincle) is expressed in osteoclasts and is responsible for the recognition of osteocyte death. To understand the mechanistic role of Mincle in osteoclasts, we performed in-depth analysis of the effect of Mincle deficiency on the genomic transcriptional network of osteoclasts. Whole transcriptome RNA sequencing (RNAseq) was performed on osteoclasts stimulated with necrotic osteocyte supernatant compared to control osteoclasts (stimulated with viable osteocyte supernatant), derived from either wildtype or Mincle knockout mice.

overall_design: In vitro differentiated osteoclasts from wildtype (WT, C57BL/6 mice) or Mincle knockout (KO, C57BL/6 background) mice were stimulated on day 1 of culture with either supernatant from viable osteocytes (control condition) or supernatant from necrotic osteocytes (generated by serum starvation) for 24h. The osteoclast RNA was extracted on day 3 of differentiation for RNA-seq.

first: Aline

last: Bozec


title: Hnf4a regulated transcriptome in murine PDAC autochthonous tumors [FFPE tumors]

first: Eric

last: Snyder

overall_design: The study was designed to compare the expression profiles of Hnf4a-positive pancreatic ductal adenocarcinomas with tumors in which Hnf4a was deleted at the time of initiation. RNA was isolated from aniline blue-stained FFPE sections of micro-dissected autochthonous tumors.

first: Soledad

last: Camolotto

first: Veronika

last: Belova

first: Luke

last: Torre-Healy


title: Hnf4a regulated transcriptome in organoid cultures derived from murine pancreas where HNnf4a is deleted after tumor initiation. [organoid]

overall_design: The study was designed to compare transcriptome profiles between isogenic Hnf4a-positive and Hnf4a-negative murine pancreatic cancer organoid lines. Hnf4a was deleted by treating the 3D cultures with 4OH-Tamoxifen

first: Chris

last: Stubben

first: Richard

last: Moffit


title: miRNA landscape of corticotroph pituitary neuroendocrine tumor from bilateral petrosal sinus sampling

status: Public on Dec 29 2020

city: Riga

first: Raitis

last: Peculis

address: Ratsupites str 1 k-1

country: Latvia

institute: Latvian Biomedical Research and Study Centre

summary:
Background
Micro RNAs (miRNAs) are a class of small non-coding RNAs that are involved in post transcriptional gene expression regulation. miRNAS can be found in various bodily fluids including plasma. Recently circulating plasma miRNAs have been studied as biomarkers in various tumors including pituitary neuroendocrine tumors (PitNETs). However the identification of PitNET derived miRNAs in plasma remains a challenging task due to tumor volume, mass and miRNA dilution within blood. To our knowledge this is the first study that has used the NGS approach to characterize circulating miRNAs in plasma acquired from Bilateral petrosal sinus sampling (BIPSS) - a gold standard in diagnosis of ACTH secreting PitNETs.
Results
We sequenced plasma samples that were acquired from sinistral and dextral sides of sinus petrosus inferior and complementary plasma from peripheral venous blood (PVB). BIPSS samples were collected in three separate time periods: before administration of corticotropin releasing hormone (CRH), 5 minutes after stimulation and 15 minutes after stimulation with CRH. The highest amount of differentially expressed miRNAs was observed 5 minutes after CRH stimulation (20 upregulated, 14 downregulated). During the BIPSS procedure the highest amount of ACTH was released in the sinistral side during the 5th minute after the stimulation by CRH. In the plasma of sinistral side at the 5th minute we identified two miRNAs: hsa-miR-7-5p and hsa-miR-375-3p that were highly upregulated compared to other BIPSS samples and samples from PVB. Using clustering analysis we were able to distinguish plasma samples acquired from BIPSS from PVB plasma, indicating that the miRNA fraction characterized in this study has potentially PitNET borne origin.
Conclusions
In this study we provided the first insight into the landscape of circulating miRNAs in close proximity to the ACTH secreting PitNET. The data indicates that ACTH secreting PitNET releases two circulating miRNAs upon stimulation with CRH (hsa-mir-7-5p, hsa-mir-375-3p) alongside with ACTH implying the further studies of these miRNA as diagnostic markers.

overall_design: Case report, comparison of PitNET and normal tissue secreting miRNA, additional background of peripheral blood miRNA profile

first: Helvijs

last: Niedra

last: Pečulis

first: Ilze

last: Konrāde

first: Inga

last: Balcere

first: Mihails

last: Romanovs

first: Līva

last: Šteina

first: Jānis

last: Stuķēns

last: Kloviņš

first: Vita

last: Rovīte


title: Single cell RNA-seq for PBMC from rheumatoid arthritis patient

status: Public on Nov 10 2020

city: Beijing

first: Bin

last: Zhang

address: Zheng Yutong Building room D311

institute: Tsinghua University

summary: The transcriptome of PBMC from rheumatoid arthritis patient hasn't been compenhensively profiled, and heterogeneous characteristics of blood monocytes in RA patients are much unknown. We performed the single cell transcriptomic analysis of PBMC from rheumatoid arthritis (RA) patient, and monocyte populations were extracted during the analysis.  CD127 expression associated expression pattern of inflammatory genes was identified in RA patient's blood monocytes.

overall_design: PBMC were isolated from peripheral blood of RA patient by Ficoll gradients, and isolated PBMC were frozen for preservation and sent out for scRNA-seq library construction by using 10x genomics platform.


title: Decoding myofibroblast origins in human kidney fibrosis [ATAC-seq]

status: Public on Oct 07 2020

city: Aachen

first: Mahmoud

last: Ibrahim

address: Pauwelsstraße 30

department: Faculty of Medicine

institute: RWTH Aachen University

summary: Kidney fibrosis is the hallmark of chronic kidney disease progression, however currently no antifibrotic therapies exist. This is largely because the origin, functional heterogeneity and regulation of scar-forming cells during human kidney fibrosis remains poorly understood. Here, using single cell RNA-seq, we profiled the transcriptomes of proximal tubule and non-proximal tubule cells in healthy and fibrotic human kidneys to map the entire human kidney in an unbiased approach. This enabled mapping of all matrix-producing cells at high resolution, revealing distinct subpopulations of pericytes and fibroblasts as the major cellular sources of scar forming myofibroblasts during human kidney fibrosis. We used genetic fate-tracing, time-course single cell RNA-seq and ATAC-seq experiments in mice, and spatial transcriptomics in human kidney fibrosis to functionally interrogate these findings, shedding new light on the origin, heterogeneity and differentiation of human kidney myofibroblasts and their fibroblast and pericyte precursors at unprecedented resolution. Finally, we used this strategy to facilitate target discovery, identifying Nkd2 as a myofibroblast-specific target in human kidney fibrosis.

overall_design: ATAC-Seq from PDGFRa+/PDGFRb+ cells from mice that underwent UUO surgery was generated

first: Christoph

last: Kuppe

first: Rafael

last: Kramann


title: Single cell transcriptomes of hepatic immune cells from mice with and without colorectal cancer liver metastasis

status: Public on Oct 02 2020

city: ANN ARBOR

first: Shasha

last: Li

state: MI

address: 1109 Maiden Ln, ct apt 104

institute: University of Michigan

summary: Metastasis is the primary cause of cancer mortality. Cancer frequently metastasizes to the liver. We report that liver metastases diminish immunotherapy efficacy systemically in patients and preclinical models. Mechanistically, liver metastases siphon activated CD8+ T cells from systemic circulation. Within the liver, activated antigen-specific Fas+CD8+ T cells undergo apoptosis following their interaction with FasL+CD11b+F4/80+ monocyte-derived macrophages. Consequently, liver metastases create a systemic immune desert in both preclinical models and patients. Liver-directed radiotherapy eliminates immunosuppressive hepatic macrophages, increases hepatic T-cell survival, and reduces hepatic siphoning. Thus, liver metastases co-opt host peripheral tolerance mechanisms to cause acquired immunotherapy resistance through CD8+ T-cell deletion and the combination of liver-directed radiotherapy and immunotherapy is a novel therapeutic strategy to promote systemic anti-tumour immunity.

overall_design: Single cell RNA sequencing of hepatic immune cells isolated from mouse livers with and without colorectal cancer metastasis

first: Jiali

last: Yu

first: Michael

last: Green

first: Arul

last: Chinnaiyan

first: Marcin

last: Cieslik

first: Weiping

last: Zou


title: Decoding myofibroblast origins in human kidney fibrosis [RNA-seq]

overall_design: single cell profiles of PDGFRab cells from mouse sham (healthy) and fibrotic (UUO model) kidneys were generated


title: Decoding myofibroblast origins in human kidney fibrosis

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


title: Effect of E7386 on gene expression chenges in whisler follicle tissues of ApcMin/+ mice

first: Kazuhiko

last: Yamada

summary: Gene expression profiling of whisker follicle tissues of ApcMin/+ mice treated with E7386

overall_design: ApcMin/+ mice were administered with E7386 (30 mg/kg orally, twice daily) for 4 cycles (each cycle, 5 days on/2 days off) from 8 weeks of age. Whisker follicles were collected at 6 h after the final administration.

first: Yusaku

last: Hori

first: Mai

last: Uesugi

first: Yasuhiro

last: Funahashi

first: Yoichi

last: Ozawa


title: Next Generation Sequencing Facilitates Quantitative Analysis of WT and Il2ra mut/mut memory OT-I cell transcriptomes

status: Public on Sep 30 2020

city: Bronx

first: Shu Shien

last: Chin

state: NY

address: 1301 Morris Park Ave

institute: Albert Einstein College of Medicine

summary: Cognate antigen signals control CD8+ T cell priming, expansion size and effector versus memory cell fates, however, it is not clear whether they can also modulate the functional features of memory CD8+ T cells.  We observed that OT-I cells that were primed with weak cognate antigen signals incorporate more cytokine signals, leading to a hypothesis that CD8+ T cells that receive weak TCR signals require cytokine signals to form functional memory. Using a previously described mouse model in which IL-2 signaling via its high affinity receptor CD25 is selectively impaired, the “Il2ramut/mut” mouse, we conducted a comparative analysis of gene expression and epigenetic landscape of Il2ramut/mut and WT OT-I memory cells that were primed with strong (Lm-Ova N4) versus weak (Lm-Ova T4). RNA seq data showed that both TCR and IL-2 priming signals have minimal effect on gene expression in resting memory CD8 T cells, but they significantly modify the epigenetic landscape of the memory CD8 T cells. These findings have important contributions to the current understanding of how priming signals program memory CD8 T cells in vivo.

overall_design: We adoptively transferred Il2ramut/mut and WT OT-I cells to sets of hosts and immunized them with Lm-Ova N4 (4 replicates)  or Lm-Ova T4 (4 replicates). Spleens of the hosts were harvested 3-4 weeks later and memory OT-I cells were enriched by negative selection (dynabeads) and flow-sorted (Aria III) before proceeding to first strand cDNA synthesis and library preparation for sequencing (RNA-seq).

first: Shu

middle: S

first: Fabien

last: Delahaye

first: Gregoire

last: Lauvau