title: RRBS in MommeD43 NSCs

summary: Reduced Representation Bisulfite Sequencing in Smchd1MD43/MD43 and Smchd1+/+ neural stem cells.

overall_design: 3 independent female cell lines for each genotype were derived from E14.5 embryos' cortices and cultured for less than 10 passages to be used as biological replicates.


title: The transcriptional and architectural resetting of stem cell identity during G1 entry

status: Public on Mar 01 2021

city: New York

first: Effie

last: Apostolou

state: NY

address: 1161 York Avenue, Apt 8A

country: USA

institute: Weill Cornell Medicine

type: Genome binding/occupancy profiling by high throughput sequencing

type: Expression profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: H3K27ac in SARS-CoV-2 infection

status: Public on Feb 26 2021

city: Cincinnati

first: Matthew

last: Weirauch

state: Ohio

address: 3333 Burnet Avenue

department: Center for Autoimmune Genomics and Etiology (CAGE)

institute: Cincinnati Children's Hospital Medical Center

summary: The ongoing pandemic caused by Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) is currently affecting millions of lives worldwide. Large retrospective studies indicate that an elevated level of inflammatory cytokines and pro-inflammatory factors are associated with both increased disease severity and mortality. Targeting these pathways might therefore be a viable therapeutic strategy. Previously, we have reported that chromatin factors such as Topoisomerase I (Top1) play key roles in controlling the induction of inflammatory gene expression programs. Here, by using multidimensional epigenetic, transcriptional, in vitro and in vivo analyses, we show that Topoisomerase 1 (Top1) inhibition in infected cells and animals suppresses lethal inflammation induced by SARS-CoV-2.

overall_design: To study changes in the epigenome during SARS-CoV-2 infection, we performed Chip-sequencing for H3K27ac in SARS-CoV-2 infected A549-ACE2 cells at 0,8 and 24 hours post infection. Experiment was done in biological triplicate. Antibody used: ab4729.

first: Jessica

middle: S

last: Ho

first: Bobo

middle: W

last: Mok

first: Laura

last: Campisi

first: Tristan

last: Jordan

first: Soner

last: Yildiz

first: Sreeja

last: Parameswaran

first: Joseph

middle: A

last: Wayman

first: Natasha

middle: N

last: Gaudreault

first: David

last: Meekins

first: Sabarish

middle: V

last: Indran

first: Igor

last: Morozov

first: Jessie

middle: D

last: Trujillo

first: Yesai

last: Fstkchyan

first: Raveen

last: Rathnasinghe

first: Zeyu

last: Zhu

first: Simin

last: Zheng

last: Zhao

first: Kris

last: White

first: Helen

last: Ray-Jones

first: Valeriya

last: Malysheva

first: Michiel

middle: J

last: Thiecke

first: Siu-Ying

last: Lau

first: Honglian

last: Liu

first: Anna

last: Zhang

first: Andrew

middle: C

last: Lee

first: Wen-Chun

first: Teresa

last: Aydillo

first: Betsaida

last: Salom Melo

first: Ernesto

last: Guccione

first: Robert

last: Sebra

first: Elaine

last: Shum

first: Jan

last: Bakker

last: Kaufman

first: Andre

middle: L

last: Moreira

first: Mariano

last: Carossino

first: Udeni

middle: R

last: Balasuriya

first: Minji

last: Byun

first: Emily

last: Miraldi

first: Randy

last: Albrecht


title: SMCHD1 has separable roles in chromatin architecture and gene silencing that could be targeted in disease

status: Public on May 10 2021

city: Melbourne

first: Andres

last: Tapia del Fierro

state: Victoria

address: 1G Royal Parade

department: EDD

country: Australia

institute: WEHI

type: Methylation profiling by high throughput sequencing

type: Genome variation profiling by high throughput sequencing


title: Transcriptome analysis of the brain and testis of the human-derived DNMT3A transgenic rat

city: Shanghai

first: Xiaoguo

last: Zheng

address: 145 Guangyuan Road

country: China

institute: Shanghai Jiaotong University

summary: We performed global gene expression profiling of transgenic rat brain and testis tissues using mRNA sequencing (mRNA-seq) to investigate the impact of epigenetic modifier overexpression on tissue gene expression patterns.

overall_design: Examination of 2 tissues in wild-type and transgenic rats. Three replicates were setted for each tissue.

first: Zhenhua

last: Li

first: Fei

last: Sun


title: An autophagy CRISPR Screen in Jurkat cells

status: Public on Jan 13 2021

city: Ulm

first: Konstantin

middle: MJ

last: Sparrer

address: Meyerhofstr. 1

department: Institute of Molecular Virology

country: Germany

institute: Ulm University Medical Center

summary: To identify genes regulating autophagy in human T-cells (Jurkat cell line) a CRISPR screen was conducted. Populations with low autophagic flux was sorted and the contained sgRNAs analysed by next-generation sequencing. Bioinformatic analysis compared the input of the screen versus the 'autophagy low' population.

overall_design: Comparison of sgRNA reads from input vs low autophagy population

first: Lennart

last: Koepke

first: Stefan

last: Krebs

first: Helmut

last: Blum


title: Crosstalk between CAR T cell subsets and the tumor microenvironment is essential for sustained cytotoxic activity

status: Public on Mar 29 2021

city: Paris

first: Yann

last: Loe-Mie

address: 25 rue du Dr Roux

department: Computational Biology

country: France

institute: Institut Pasteur

summary: Chimeric antigen receptor (CAR) T cell therapy relies on the activity of a large pool of tumor-targeting cytotoxic effectors. Whether CAR T cells act autonomously or require interactions with the tumor microenvironment (TME) is unclear. Here, we report an essential crosstalk between CAR T cell subsets and the TME for tumor control. Using single-cell RNA sequencing, we revealed profound modification of the TME during CAR T cell therapy. IFN-gamma produced by CAR T cells and host-derived IL-12 not only enhanced endogenous T and NK cell activity but were also essential for sustaining CAR T cell cytotoxicity as revealed by intravital imaging. Compared to CD8+ CAR T cells, CD4+ CAR T cells were more efficient at host immune activation but less capable of tumor killing. In sum, CAR T cells are not acting alone in vivo but rely instead on a cytokine-mediated crosstalk with the TME for optimal activity. Invigorating CAR T cell interplay with the host represents an attractive strategy to prevent relapses.

overall_design: B cell lymphoma was established by i.v. injection of 0.5x10^6 Eμ-myc-DEVD cells in C57BL/6J mice after sublethal irradiation (4 Gy). Six days later, mice were injected i.v. with 20x10^6 CAR4 or CAR8 T cells or left untreated. Single cell RNA-seq of bone marrow cells were performed on these 3 samples.

first: Morgane

last: Boulch

first: Marine

last: Cazaux

first: Philippe

last: Bousso


title: Single cell response landscape of graded Nodal signaling  in zebrafish explants [bulk RNA-seq]

status: Public on Jan 28 2021

city: Hang Zhou

first: Tao

last: cheng

state: Zhe Jiang

address: 886 Yuhangtang Road

department: Institute of genetics

institute: Zhejiang University

summary:
Purpose: To identify nodal downsream target genes
Methods: 0pg, 2pg, 6pg or 10pg ndr2 mRNA injected explants and 10 pg ndr2 mRNA injected plus Cycloheximide (CHX) treated explants were collected at 4hpf, 5hpf and 6hpf for bulk RNA-seq
Results: We found 105 Nodal targets  (p_value <0.05, padj < 0.1, log2 fold change >= 1)
Conclusions: 105 Nodal targets were identified

overall_design: zebrafish explants injected with ndr2 mRNA

last: Cheng

first: Yan-Yi

last: Xing


title: Single cell response landscape of graded Nodal signaling  in zebrafish explants [single-cell RNA-seq]

summary:
Purpose: To construct cell landscape of graded Nodal signaling  in zebrafish explants.
Methods:  Nodal injected explants (injected with 10pg ndr2 mRNA) were harvested at 4hpf, 5hpf, 6hpf, 8hpf, 10hpf, 24hpf. Libraries were prepared using Chromium Controller and Chromium Single Cell 3’Library & Gel Bead Kit v2 (10x Genomics, PN-120237) according to the manufacturer’s protocol for 10000 cells recovery.
Results: A total of 42,317 single-cell transcriptomes were collected after stringent quality control measures.
Conclusions: 19 Cell types from 6 developmental stages were identified, Nodal explant mainly contains the axial mesoderm (prechordal plate and notochord) and anterior-posterior patterned head structures.

overall_design: zebrafish explants injected with 10pg ndr2 mRNA were harvested at 4hpf, 5hpf, 6hpf, 8hpf, 10hpf, 24hpf for scRNA-seq.


title: Mitotic bookmarking by H3K27 acetylation is critical for rapid transcriptional, but not architectural, resetting of stem cell-related genes and enhancers upon G1 entry [HiC]

first: Effie

last: Apostolou

summary: The identity of dividing cells is challenged during mitosis, as transcription is halted and chromatin architecture drastically altered. How cell type-specific gene expression and genomic organization are faithfully reset upon G1 entry in daughter cells remains elusive. To address this issue, we characterized at a genome-wide scale the dynamic transcriptional and architectural resetting of mouse pluripotent stem cells (PSCs) upon mitotic exit. This revealed distinct patterns of transcriptional reactivation with rapid induction of stem cell genes and their enhancers, a more gradual recovery of metabolic and cell cycle genes, and a weak and transient activation of lineage-specific genes only during G1. Topological reorganization at different hierarchical levels also occurred in an asynchronous manner and showed an overall weak coordination with transcriptional reactivation. Chromatin interactions around active promoters and enhancers, and particularly super enhancers, reformed at a faster rate than CTCF/Cohesin-bound structural loops. Interestingly, although regions with mitotic retention of the active histone mark H3K27ac associated both with faster transcriptional and architectural resetting, depletion of this mark specifically during mitosis perturbed transcriptional reactivation of H3K27ac-bookmarked genes without affecting chromatin topology. Our study provides an integrative map of the topological and transcriptional changes that lead to the resetting of pluripotent stem cell identity during mitotic exit, and reveals distinct patterns and features that balance the dual requirements for self-renewal and differentiation.

overall_design: Hi-C of mouse iPSCs after p300 inhibition and recovery, both in asychronous and M-to-G1 cell cycle populations. DMSO treatment was used as a control, and two replicates per condition/time point were analyzed.

first: Alexander

last: Polyzos


title: Transcriptomic Analysis Of Micropapillary High Grade T1 Urothelial Bladder Cancer

status: Public on Jan 31 2021

city: Barcelona

first: Júlia

last: Perera-Bel

address: Doctor Aiguader, 88

department: MARData-BU

country: Spain

institute: Hospital del Mar Research Institute

summary: Management of high-grade T1 (HGT1) micropapillary bladder cancer (MPBC) is controversial. An accurate genomic characterization might help predict outcome. We analyze the transcriptomic profile of MPBC in a clinically annotated HGT1 cohort establishing correlation with clinical outcome.A retrospective analysis of prospectively clinically followed series of HGT1; 23 patients with MPBC and 64 without MPBC (reference set). We identified a set of genes differentially expressed (DE). Associations between; clinical variables and gene expression (GE) levels (Wilcoxon’s rank sum); GE and time to progression (TTP) in univariate analysis (Log rank); GE levels adjusting for clinical variables (Cox regression) were evaluated.We identified a 26-gene signature that characterized MPBC in HGT1. Several genes including CD36, FAPB3 and RAETE1 were significantly associated with TTP. High expression of FABP3 and CD36 were associated with shorter TTP (P=0.045 and P=0.08 (NS)) as was low expression of RAET1E (P=0.01). Limitations include the lack of specific quantification of the percentage of MPBC tumor >10%.

first: Joaquim

last: Bellmunt

first: Josep

last: Lloreta


title: Programmable human histone phosphorylation and gene activation using a CRISPR/Cas9-based chromatin kinase

status: Public on Jan 08 2021

city: Houston

first: Isaac

middle: B

last: Hilton

state: TX

address: 6500 Main St

department: Bioengineering

institute: Rice University

summary: We report a synthetic chromatin kinase, by fusing nuclease-null CRISPR/Cas9 to a hyperactive, truncated variant of the human MSK1 histone kinase (dCas9-dMSK1). To investigate the role of MSK1 on transcriptional regulation, we explore the different transcriptome between wildtype and MSK1 knockout HEK 293T cell lines by RNA-seq. To test the efficacy of dCas9-dMSK1 at thousands of human promoters in high-throughput and to evaluate if histone phosphorylation could uncover novel mediators of pathological gene expression, we performed a CRISPRa screening assay in A375 cells using the genome wild gRNA library. The enriched gRNAs were measured by Miseq.

overall_design: Examined the transcriptional activation role of native MSK1 and synthetic dCas9-dMSK1 in different cell lines.

first: Jing

last: Li

first: Barun

last: Mahata

first: Mario

last: Escobar

first: Jacob

last: Goell

first: Kaiyuan

last: Wang

first: Pranav

last: Khemka


title: Epigenetic silencing of tumor suppressor miR-124 directly promotes STAT3 activation in Cutaneous T-cell Lymphoma

status: Public on Dec 31 2020

summary: Increasing evidences support a potential role for the Signal Transducer and Activator of Transcription-3 (STAT3) as a tumor driver in cutaneous T-cell lymphoma (CTCL). However, the mechanisms leading to STAT3 pathway activation in CTCL and how STAT3 activation contributes to lymphomagenesis remains primarily not enough explored.  Recently, we found that miR-124, a known STAT3 regulator in cancer, is robustly silenced in Mycosis Fungoides (MF) tumor-stage and CTCL cell lines and we have herein studied whether deregulation of miR-124 contributes to activate STAT3 pathway in CTCL. Material and Methods: DNA methylation status of miR-124 and its expression levels in response to the DNA-demethylating agent azacitidine were evaluated in CTCL cell lines by pyrosequencing analysis. CTCL cell lines were transient transfected with a lentiviral vector encoding miR-124 and transfected cells were analyzed for phosphorylated STAT3 (P-STAT3) levels. The impact on STAT3 signaling was evaluated using expression microarray on CTCL cell lines in both conditions, miR-124 absent (malignant condition) versus miR-124 expressed (lentiviral transduction). Results: A significant promoter methylation and silencing of miR-124 in MF tumor samples and CTCL cell lines was detected. DNA methylation levels of miR-124 in CTCL cell lines were restored (and subsequently miR-124 were overexpressed) after DNA demethylation. Ectopic lentiviral expression of miR-124 downregulated STAT3 in the different CTCL cell lines. Genes differentially expressed regarding miR-124 regulation in CTCL cell lines indicated impact on known cell survival and function pathways and, particularly, intervention on miR-124 expression modulated different STAT3 pathway components. Conclusions: Our study deciphers a novel epigenetic mechanisms regulating STAT3 pathway in CTCL. This might contribute to a better understanding the molecular basis in CTCL development. Deregulation of STAT3 seems to have a major impact on cell survival in CTCL cell lines indicating the potential interest of targeting STAT3 with specific therapies.

overall_design: 4 samples from cutaneous T-cell lymphoma cell lines

first: Fernando

last: Gallardo

first: Lidia

last: Garcia-Colmenero

first: Jessica

last: Gonzalez

first: Juan

last: Sandoval

first: Yolanda

last: Guillen

first: Angel

last: Diaz-Lagares

first: Evelyn

last: Andrade

first: Lara

last: Nonell

first: Ramon

last: Pujol

first: Anna

last: Bigas

first: Lluis

last: Espinosa


title: Gene expression profile of EGFRwt/KRASwt/ALKwt lung adenocarcinoma (“pan-driver-gene-negative” LUAD) and developing a prognostic signature for “pan-driver-gene-negative” LUAD

city: Guangzhou

first: yongmei

last: cui

address: No. 58, ZhongShan Second Road

institute: The First Affiliated Hospital, Sun Yat-sen University

summary:
For developing a accurate prognostic signature for “pan-driver-gene-negative” LUAD, we employed whole genome microarray expression profiling as a discovery platform to identify candidate genes. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis based on whole-genome microarrays indicated that the Wnt/β-catenin pathway was activated in “pan-driver-gene-negative” LUAD. Furthermore, the Wnt/β-catenin-pathway-based gene expression profiles revealed 39 transcripts differentially expressed by diagnostic status, with 30 genes being upregulated and 9 downregulated. Finally, a Wnt/β-catenin-pathway-based signature (CSDW) comprising 4 genes (β-catenin, Wnt2b, DVL3 and SOX9) was developed to classify patients into high-risk and low-risk groups in the training cohort. Patients with high-risk scores in the training cohort had shorter overall survival (hazard ratio [HR] 10·42, 6·46–16·79; p<0·001) than patients with low-risk scores. The CSDW performance was further validated in an internal cohort and two external cohorts. The protein expression levels of several hub genes, including β-catenin, SOX9, DVL3 and Wnt2b, were strongly correlated with lymphatic metastasis and distant organ metastasis. Furthermore, a nomogram comprising CSDW and other variables was generated to predict progression-free survival and overall survival in the training cohort and performed well in the three independent validation cohorts (C-index: 0·725, 0·697 and 0·693, respectively).
For developing a accurate prognostic signature for “pan-driver-gene-negative” LUAD, we employed whole genome microarray expression profiling as a discovery platform to identify candidate genes. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis based on whole-genome microarrays indicated that the Wnt/β-catenin pathway was activated in “pan-driver-gene-negative” LUAD. Furthermore, the Wnt/β-catenin-pathway-based gene expression profiles revealed 39 transcripts differentially expressed by diagnostic status, with 30 genes being upregulated and 9 downregulated. Finally, a Wnt/β-catenin-pathway-based signature (CSDW) comprising 4 genes (β-catenin, Wnt2b, DVL3 and SOX9) was developed to classify patients into high-risk and low-risk groups in the training cohort. Patients with high-risk scores in the training cohort had shorter overall survival (hazard ratio [HR] 10·42, 6·46–16·79; p<0·001) than patients with low-risk scores. The CSDW performance was further validated in an internal cohort and two external cohorts. The protein expression levels of several hub genes, including β-catenin, SOX9, DVL3 and Wnt2b, were strongly correlated with lymphatic metastasis and distant organ metastasis. Furthermore, a nomogram comprising CSDW and other variables was generated to predict progression-free survival and overall survival in the training cohort and performed well in the three independent validation cohorts (C-index: 0·725, 0·697 and 0·693, respectively).

overall_design: In this multicenter analysis, we collected 626 “pan-driver-gene-negative” LUAD samples from three independent hospitals. In the discovery phase, we profiled the mRNA expression of each candidate gene using genome-wide microarrays in 52 paired LUAD and adjacent normal tissues. In the training phase, tissue microarrays (TMAs) and LASSO Cox regression analysis were applied to further screen candidate molecules in 189 patients (SYSUFH set). In the validation phase, one internal cohort (SYSUFH set, n=182) and two external cohorts (Sun Yat-sen University Cancer Center (SYSUCC) set, n=152; WUHAN set, n=103) were used to validate our novel prognostic signature.

first: Zunfu

last: Ke

first: Yongmei

last: Cui


title: NMDA receptor positive allosteric modulator induced genome wide gene expression changes in neuronal cultures

status: Public on Jan 01 2021

city: shanghai

first: jing

last: zhao

address: Qiuyue Road

institute: IRCBC

summary: To investigate genome-wide gene expression changes induced by an NMDA receptor positive allosteric modulator in neuronal cultures using next-generation sequencing

overall_design: Neuronal mRNA profiles of 18-day-in-vitro old wild type rat hippocampal treated with either NMDA receptor positive allosteric modulator or vehicle were generated by deep sequencing, in quadruplicate, using Illumina GAIIx.

first: Qiuyan

first: Jing

last: Zhao

last: Liu

first: Yelin

last: Chen


title: c-JUN is a pioneer factor safeguarding the primed state of pluripotency (ChIP-Seq)

first: dongwei

last: Li

state: Guangdong province

address: 190 Kai Yuan Avenue, Science Park

department: South China Institute for Stem Cell Biology and Regenerative Medicine

institute: Guangzhou Institutes of Biomedicine and Health,Chinese Academy of Sciences

summary: Mouse ESCs and EpiSCs represent naive and primed states of plurioptency corresponding to two consecutive stages of embryo development. Here we map their chromatin accessibility landscapes and show that naive specific open chromatin are enriched with motifs for Oct/Sox/Klf/TCF and primed one with AP1 motifs. The AP1 founding member c-Jun is expressed in EpiSCs and occupies both open and closed chromatin. Yet, c-Jun deficiency has no impact on the self renewal nor the transcription program of EpiSCs. However, in a Klf4-driven reprogramming system, we show that c- Jun-/- EpiSCs undergo primed to naive transition more efficiently than wild type cells and Klf4 evicts c-JUN from wild type chromatin. These results suggest that c-Jun is a pioneer factor not to regulate transcription but to prevent backward reprogramming during naive-primed transition, thus providing a molecular basis for the forward principle in development.

overall_design: ChIP-Seq

first: Dongwei


title: Epstein-Barr virus nuclear antigen 2 (EBNA2) extensively rewires the human chromatin landscape at autoimmune risk loci [Bead array]

status: Public on Sep 23 2021

first: Matthew

last: Weirauch

type:
Genome variation profiling by SNP array
SNP genotyping by SNP array

summary: The interplay between environmental and genetic factors plays a key role in the development of many autoimmune diseases. In particular, the Epstein-Barr virus (EBV) is an established contributor to multiple sclerosis, lupus, and other disorders. Previously, we demonstrated that the EBV nuclear antigen 2 (EBNA2) transactivating protein occupies up to half of the risk loci for a set of seven autoimmune disorders. To further examine the mechanistic roles played by EBNA2 at these loci on a genome-wide scale, we globally examined gene expression, chromatin accessibility, chromatin looping, and EBNA2 binding, in a B cell line that was 1) uninfected, 2) infected with a strain of EBV lacking EBNA2, or 3) infected with a strain that expresses EBNA2. We identified >400 EBNA2-dependent differentially expressed human genes and >5,000 EBNA2 binding events in the human genome. ATAC-seq analysis revealed >2,000 regions in the human genome with EBNA2-dependent chromatin accessibility, and HiChIP-seq data revealed >1,700 regions where EBNA2 altered chromatin looping interactions. Importantly, autoimmune genetic risk loci were highly enriched at the sites of these EBNA2-dependent chromatin-altering events.  We present examples of autoimmune risk genotype-dependent EBNA2 events, nominating genetic risk mechanisms for autoimmune risk loci such as ZMIZ1. Taken together, our results reveal important interactions between host genetic variation and EBNA2-driven disease mechanisms. Further, our study highlights a critical role for EBNA2 in rewiring human gene regulatory programs through rearrangement of the chromatin landscape and nominates these interactions as components of genetic mechanisms that influence the risk of multiple autoimmune diseases.

overall_design: To investigate the role of genetic variants in EBNA2 binding, we genotyped 4 EBV-transformed cell lines using an Illumina Infinium Omni5-4 v1.1 BeadChip array.

first: Leah

last: Kottyan

middle: T


title: Alpha-tocopherol exerts protective function against the mucotoxicity of particulate matter in amphibian and human goblet cells

status: Public on Dec 27 2020

city: Ulsan

first: Taejoon

last: Kwon

address: 50 Unist-gil

department: Department of Biomedical Engineering

country: South Korea

institute: Ulsan National Institute of Science and Technology

summary: Exposure to particulate matter (PM) in ambient air is known to increase the risk of cardiovascular disorders and mortality. The cytotoxicity of PM is mainly due to the abnormal increase of reactive oxygen species (ROS), which damage cellular components such as DNA, RNA, and proteins. The correlation between PM exposure and human disorders, including mortality, is based on long-term exposure. In this study we have investigated acute responses of mucus-secreting goblet cells upon exposure to PM derived from a heavy diesel engine. To this end, we employed the mucociliary epithelium of amphibian embryos and human Calu-3 cells to examine PM mucotoxicity. Our data suggest that acute exposure to PM significantly impairs mucus secretion and results in the accumulation of mucus vesicles in the cytoplasm of goblet cells. RNA-seq analysis revealed that acute responses to PM exposure significantly altered gene expression patterns; however, known regulators of mucus production and the secretory pathway were not significantly altered. Interestingly, pretreatment with α-tocopherol nearly recovered the hyposecretion of mucus from both amphibian and human goblet cells. We believe this study demonstrates the mucotoxicity of PM and the protective function of α-tocopherol on mucotoxicity caused by acute PM exposure from heavy diesel engines.

sample_organism:
Bombina orientalis
Xenopus laevis

platform_organism:
Bombina orientalis
Xenopus laevis

overall_design: For each species (X. laevis and B. orientalis), we treated 100 ug/mL of the particulate matters (PM) to whole embryo. For each condition, we used duplicated biological replicates. To evaluate the transcriptonal response among time, we sampled at two time points: 3 hours after PM treatment, and 9 hours after the treatment.

first: Hee-Sun

last: Yang

first: Hyo

last: Sim

first: Hanna

last: Cho

first: Woo

middle: Y

last: Bang

first: Ha

middle: E

last: Kim

first: Taeg

middle: K

first: Tae

last: Park


title: c-JUN is a pioneer factor safeguarding the primed state of pluripotency (ATAC-Seq)

overall_design: ATAC-Seq


title: Affymetrix HTA-2_0 arrays profiling of monocytes-derived dendritic cells transfected with miR-142-3p and control mimic

status: Public on Dec 07 2020

city: Chicago

first: Afsar

middle: Raza

last: Naqvi

state: Illinois

address: 801 S Pauline

department: Periodontics

institute: University of Illinois

summary: To examine the trascriptome profiling in monocytes-derived dendritic cells transfected with miR-142-3p by Affymetrix HTA-2_0 arrays

overall_design: Monocytes-derived dendritic cells transfected with miR-142-3p and control negative mimic for 36h and the cells were harvested after washing twice with PBS. Total RNA was isolated using miRNeasy kit (Qiagen). Samples were then processed for Affymetrix HTA-2_0.

first: Araceli

last: Valverde

first: Salvador

last: Nares


title: Transcriptomic analysis of mRNA of inguinal white adipose tissues from  ZSF1 lean and obese rats, ZSF1 obese rats under calorie restriction, as well as ZSF1 obese rats  dosed with Cmpd1.

status: Public on Dec 03 2020

city: Cambridge

first: Ju

last: Wang

state: MA

address: 610 Main Street

department: Inflammation & Immunology

institute: Pfizer Inc

summary: The analysis is performed to understand the role of Cmpd1 in modulating transcritomic profiles in the inguinal white adipose tissues of ZSF1 rats.

overall_design: Five animals from each of the four groups (ZSF1 lean, ZSF1 obese, ZSF1 obese calorie restrction, ZSF1 obese cmpd1) were selected at random for this analysis. RNA from the inguinal white adipose tissues of these animals was extracted with RNeasy Plus Universal Kits (Qiagen 73404) following the manufacturer’s protocol.

first: Shanrong

first: Li

last: Xi

first: Baohong

last: Zhang

first: Wen

last: He

first: Bryce

last: Johnson

first: Ken

last: Dower


title: Understanding tumor evolution and its clonality by single-cell transcriptomic analysis in liver cancer

status: Public on Feb 07 2021

city: Bethesda

first: Xin

middle: Wei

state: MARYLAND

address: 37 Convent Drive

department: Laboratory of Human Carcinogenesis

institute: National Cancer Institute

summary: Single-cell transcriptomic profiling of liver cancer biospecimens from hepatocellular carcinoma and intrahepatic cholangiocarcinoma patients.

overall_design: A total of 46 tumor samples were profiled


title: Trancriptome profiling of human THP-1 knockdown for HOXA9 vs treated with DB1055

status: Public on Nov 13 2020

city: lille

first: frédéric

last: leprêtre

address: Boulevard du Pr Leclercq

department: CHU of Lille, CBP

institute: Lille University

summary: Effect of HOXA9 shRNA versus DB1055 treatment of human THP-1 AML cell line

overall_design: Comparisons of genes regulated by HOXA9 or DB1055 treatment in human THP-1 AML cell line

first: M

middle: H

last: DAVID-CORDONNIER


title: RNAseq analysis of small cell lung cancer (SCLC) cell lines

status: Public on Nov 24 2020

first: Yuanxin

address: 1400 Pressler St

department: Bioinformatics and Computational Biology

institute: The University of Texas MD Anderson Cancer Center

summary: Small cell lungcancer (SCLC) is an aggressive malignancy with dismal clinical outcomes, due inpart to the scarcity of post-relapse tissue samples. To understand more of transcriptional changes associated with treatment resistance, we performed RNAseq analysis of 61 SCLC cell lines.

overall_design: Small Cell Cancer Cell Line RNAseq

first: C

middle: A

last: Stewart


title: Stromal upregulation of SOX2 promotes tumorigenesis through the generation of a SFRP1/2-expressing cancer-associated fibroblast population [scRNA-seq]

status: Public on Nov 17 2020

first: Jorge

last: Moscat

address: 1188 York Avenue

department: Pathology and Laboratory Medicine

institute: WEILL CORNELL MEDICINE

summary: Although how CAFs impact the tumor epithelium is being progressively unveiled,  transcriptional processes of lineage plasticity in fibroblasts govern the acquisition of the CAF phenotype are much less understood. Here we show that the upregulation of SOX2 is a critical step in this process, which is negatively regulated by the atypical protein kinase (aPKC) PKCz. We demonstrate that the loss of PKCz is essential for the acquisition of the CAF phenotype and for the induction of the desmoplastic and more aggressive phenotype of intestinal tumors in a SOX2-dependent manner. Furthermore, we show here that the loss of PKCz drives the reprogramming of colon stromal fibroblasts into two different subpopulations that express either the Wnt regulators Sfrp1/2 or osteopontin, both ligands positively impinging into the mesenchymal and stem cell activation programs.

overall_design: WT sgScr, Prkcz-/- sgScr and Prkcz-/- sgSox2 colon fibroblasts were profiled in four biological replicates under normal conditions.

first: Hiroaki

last: Kasashima

first: Angeles

last: Duran

first: Yuki

last: Nakanishi

first: Anxo

last: Martinez-Ordoñez

first: Hiroto

last: Kinoshita

first: Juan

middle: F

last: Linares

first: Miguel

last: Reina-Campos

first: Yotaro

last: Kudo

first: Antoine

last: L'Hermitte

first: Masakazu

last: Yahiro

first: Masaichi

last: Ohira

first: Daniele

last: Tauriello

first: Eduard

last: Batlle

first: Maria

last: Diaz-Meco


title: Effects of spheroid and adherent growth conditions in ovarian cancer

status: Public on Oct 03 2020

city: BETHESDA

first: Christina

last: Annunziata

state: Maryland (MD)

address: 10 center drive, Building 10, room 12N226

summary:
Purpose: To understand the changes in RNA expression in tumor-initiating cell (TIC) (spheroid) and non-TIC populations (adherent) in ovarian cancer.
Methods: OV90 cells were grown in adherent (non-TIC) or spheroid (TIC) conditions. Total RNA was extracted from each condition and RNAseq was performed and analysed for differential gene expression between the conditions.

overall_design: Comparison of OV90 cells grown in adherent or spheroid conditions.

first: Carrie

last: House

middle: M

first: Nathan

middle: W

last: Wong


title: Stromal upregulation of SOX2 promotes tumorigenesis through the generation of a SFRP1/2-expressing cancer-associated fibroblast population

city: New York

first: Jorge

last: Moscat

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

overall_design: Refer to individual Series


title: Transcriptome of cassava seedling under different treatments

status: Public on Aug 22 2020

city: Haikou

first: Pingjuan

last: Zhao

address: XueYuan Road 4

department: Institute of Tropical Bioscience and Biotechnology

institute: Chinese Academy of Tropical Agricultural Sciences

summary: Transcriptome of cassava seedling were analysised  in 7% PEG and  50 μmol of ABA by RNA-seq.The goal of this study was to compare the phenotypic and transcriptome differences between treatment and WT plants, and to analyze how treatment changed the expression patterns.

overall_design: mRNA profiles of 2-month-old wild type (WT) under different treatments

first: Xin

last: Guo

first: Bin

last: Wang


title: Symmetry breaking of tissue mechanics in wound induced hair follicle regeneration

status: Public on Feb 19 2021

city: Los Angeles

first: Hans I-Chen

last: Harn

state: CA

address: 2011 Zonal Ave. HMR304

institute: University of Southern California

sample_organism:
Acomys cahirinus
Mus musculus

platform_organism:
Acomys cahirinus
Mus musculus


title: Phenotype and function of ex vivo expanded liver progenitor-like cells through liver parenchymal and non-parenchymal reversion

status: Public on Jul 30 2020

first: yan

last: hexin

address: No. 1630 East Road

institute: Renji Hospital Affiliated to Shanghai Jiaotong University School of Medicine

summary: The cellular source for hepatocyte transplantation and liver regeneration in chronically hepatic diseases is a fundamental topic in liver biology. A successful therapeutic approach based on a benificial stem/progenitor cells would involve replacing damaged cells or restoring homeostasis to the areas that underlie the fibrotic response. This study aims to isolate and culture hepatocyte and non-parenchymal cells derived liver progenitor-like cells (HepLPCs and NPC-LPCs) to identify a beneficial cell sources for cell-based therapy against chronic liver injury. Two types of lineage tracing models including tdTomato mice with AAV8-TBG-Cre and AlbCreERT/R26GFP were purified for hepatocytes and non-parenchymal cells respectively, and cultured for transition to progenitor-like cells (LPCs) in TEM. The differences between them were clarified by RNA sequencing, suggesting that HepLPCs retaining basal levels of hepatic function and transcription factors (TFs), including Foxa3. Organoids and 3D hepatic spheroids culturing systems were used for further analysis of bile duct and hepatic functioning diversity. When transplanting in mice with CCL4 treatment, HepLPCs displayed the characteristics of TFs regulatory reactivation and physiological balance restoration, resulting in a significant improvement in liver fibrosis compared with NPC-LPCs, which are crucial for liver regeneration in the treatment of patients with a broad range of hepatic fibrosis.

overall_design: global expression analysis of RNA sequencing data to compare expression levels of liver progenitor-like cells derived from hepatocytes and non-parenchymal cells.

first: Weijian

last: Huang

first: Hexin

last: Yan


title: Epigenomic Atlas of Embryonic Human Heart Development

status: Public on Jul 29 2020

city: New Haven

first: Jennifer

last: VanOudenhove

state: CT

address: 300 George St RM 786

department: Internal Medicine - Section of Hematology

institute: Yale University

summary: Chromatin State Profilining using multiple histone modifications in human embryonic heart tissue spanning 4 post conception weeks (pcw) to 8 pcw

overall_design:
Parallel profiling of seven distinct histone modifications via ChIP-Seq in human embryonic heart tissue samples from individual human embryos
All Raw FASTQ files are being deposited in dbGAP.

first: Justin

last: Cotney


title: Transcriptome analyses in glioma

status: Public on Jul 31 2020

city: hefei

first: Xiaolin

address: anhui,hefei,huangshan road 443

institute: USTC

type: Non-coding RNA profiling by high throughput sequencing

summary: To identify glioma-related RNAs, we used four glioma patients' fresh tumor tissues and normal tissues for RNA sequencing. Differential expression of mRNAs and lncRNAs were then analyzed.

overall_design: lncRNA, mRNA and circRNA profiles of 3 paired tumor and paratumor tissues of glioma patients.

first: Hu

last: Shanshan


title: Genome-wide CRISPRi/a screens in human neurons link lipid imbalance to ferroptosis

status: Public on Jun 23 2020

city: San Francisco

first: Ruilin

last: Tian

address: 675 Nelson Rising Lane, 3rd Floor

department: Institute for Neurodegenerative Diseases

institute: University of California, San Francisco

summary: Neurons are unique among all human cell types in their high energy demand, long lifespans and rich lipid contents. As such, neurons exhibit unique vulnerability to oxidative stress caused by redox imbalance in aging and neurodegenerative diseases (NDDs). To systematically identify regulators of neuronal survival under oxidative stress and regulators of neuronal redox homeostasis, we conducted multiple survival- and FACS-based genome-wide screens in human iPSC-derived neurons, using our functional genomics toolkit including a previously established CRISPRi approach and a newly developed CRISPRa approach. So far, these are the first genome-wide screens in human neurons. Our results revealed that inhibiting glycosphingolipids (GSLs) degradation by depletion of prosaposin (PSAP) drives the formation of lipofuscins in neurons which leads to iron accumulation and strongly induces ROS production that oxidizing lipids and leads to neuronal ferroptosis under oxidative stress. We also conducted single cell CROP-seq screens that revealed transcriptomic signatures of NDD-associated genes. These datasets are freely available through our open-access database CRISPRbrain.

overall_design: For the CROP-seq experiments, we included 184 genes for CRISPRi and 100 genes for CRISPRa, which were hits in at least one of our genome-wide pooled screens and were also associated with human neurodegenerative diseases (NDDs). We curated a list of NDD-associated genes based on the literature and the DisGeNET database (https://www.disgenet.org/). The CROP-seq libraries included 2 sgRNAs per gene plus 6 non-targeting control sgRNAs, for a total of 374 sgRNAs for CRISPRi and 206 sgRNAs for CRISPRa. Top and bottom strands of sgRNA oligos were synthesized (Integrated DNA Technologies) and annealed in an arrayed format. The annealed sgRNAs were then pooled in equal amounts and ligated into our optimized CROP-seq vector (Gilbert et al., 2014).The CROP-seq experiments were carried out similarly as previously described (Tian et al., 2019). Briefly, Day 0 CRISPRi and CRISPRa neurons were infected by the corresponding CROP-seq sgRNA library at a MOI of 0.1-0.2, followed by puromycin selection at 4 µg/ml for 3 days and recovery. On Day 10, neurons were dissociated with Papain and approximately 98,000 CRISPRi neurons and 50,000 CRISPRa neurons were loaded into 10X chips with about 25,000 input cells per lane. Sample preparations were performed using the ChromiumNext GEM Single Cell 3ʹ Reagent Kits v3.1 (10X Genomics; Cat. No.PN-1000121) according to the manufacturer’s protocol. To facilitate sgRNA assignment, sgRNA-containing transcripts were additionally amplified by hemi-nested PCR reactions as described (Tian et al., 2019). The sgRNA-enrichment libraries were separately indexed and sequenced as spike-ins alongside the whole- transcriptome scRNA-seq libraries using a NovaSeq 6000 using the following configuration: Read 1: 28, i7 index: 8, i5 index: 0, Read 2: 91.  3′-tag RNA-seq was performed to obtain gene expression profiles of WT and PSAP KO neurons cultured in the medium lack of antioxidants. Each genotype has 3 replicates. Raw sequencing reads from 3′-tag RNA-seq were mapped to the human reference transcriptome (GRCh38, Ensembl Release 97) using Salmon (v.0.14.139) with the ‘–noLengthCorrection’ option to obtain transcript abundance counts. Gene-level count estimates were obtained using tximport (v.1.8.040) with default settings. Subsequently, genes with more than 10 counts were retained for differential gene-expression analysis, and adjusted P values (Padj) were calculated using DESeq2 (v.1.20.041).

first: Martin

last: Kampmann


title: A Transcriptome Fingerprinting Assay for Clinical Immune Monitoring (TB Datasets)

status: Public on Jun 16 2020

city: Dallas

first: Nicole

last: Baldwin

address: 3434 Live Oak St

institute: Baylor Research Institute

summary: Development of a cost-effective and practical targeted transcriptional fingerprinting assay (TFA) for monitoring a diverse repertoire of immune responses identified in the human blood transcriptome relying on a modular transcriptional repertoire built on the basis of variations in transcript abundance measured on a genome wide scale in the blood of nearly 1000 subjects across 16 immunologic conditions.

overall_design: TB (23 condition, 11 control, 34 total)

first: Matthew

last: Altman

first: Prasong

last: Khaenam

first: Vivian

last: Gersuk

first: Laurent

last: Chiche

first: Noemie

last: Jourde-Chiche

first: J

last: Phillips

first: Goran

last: Klintmalm

first: Anne

last: O’Garra

last: Berry

first: Chloe

last: Bloom

first: Marc

last: Lipman

first: Robert

last: Wilkinson

first: Christine

last: Graham

first: Ganjana

last: Lertmemongkolchai

first: Mary

last: Conley

first: Jason

last: Skinner

first: Farrah

last: Kheradmand

first: Peter

middle: S

last: Linsley

first: Karolina

last: Palucka

first: Roman

last: Lukaszewski

first: Asuncion

last: Mejias

first: Octavio

last: Ramilo

first: Virginia

last: Pascual

first: Jacques

last: Banchereau

first: Charlie

last: Quinn

first: Scott

last: Presnell

first: Elizabeth

last: Whalen

first: Damien

last: Chaussabel


title: A Transcriptome Fingerprinting Assay for Clinical Immune Monitoring (Staph Datasets)

first: Nicole

last: Baldwin

overall_design: Staph aureus (99 condition, 44 control, 143 total)

first: Matthew

middle: C

last: Altman

first: Prasong

last: Khaenam

first: Vivian

last: Gersuk

first: Laurent

last: Chiche

first: Noemie

last: Jourde-Chiche

first: J

last: Phillips

first: Goran

last: Klintmalm

first: Anne

last: O’Garra

last: Berry

first: Chloe

last: Bloom

first: Marc

last: Lipman

first: Robert

last: Wilkinson


title: A Transcriptome Fingerprinting Assay for Clinical Immune Monitoring (SoJIA Datasets)

overall_design: SoJIA (62 condition, 23 control, 85 total)

first: Christine

last: Graham

first: Ganjana

last: Lertmemongkolchai

first: Mary

last: Conley

first: Jason

last: Skinner

first: Farrah

last: Kheradmand

first: Peter

last: Linsley

first: Karolina

last: Palucka

first: Roman

last: Lukaszewski

first: Asuncion

last: Mejias

first: Octavio

last: Ramilo

first: Virginia

last: Pascual

first: Jacques

last: Banchereau

last: Quinn


title: Epigenomic analysis of Parkinson’s disease neurons identifies TET2 loss as neuroprotective [TET2_LPS_RNA_Seq]

status: Public on Jun 19 2020

city: Grand Rapids

first: Lee

last: Marshall

state: MI

address: 333 Bostwick Ave NE

department: Center for Neurodegenerative Science

institute: Van Andel Research Institute

summary: Epigenetic control of enhancers is centrally involved in modifying neuronal functions and may contribute to Parkinson's disease (PD) pathogenesis. Here, we comprehensively profile DNA methylation at enhancers genome-wide in neurons of 57 PD patients and 48 healthy individuals. There is a widespread increase in cytosine modifications at enhancers in PD neurons, which is partly due to elevated hydroxymethylation levels. Epigenetic dysregulation of enhancers in PD converge on transcriptional abnormalities affecting neuronal signaling and immune activation pathways. In particular, PD patients exhibit an epigenetic and transcriptional upregulation of TET2, a master-regulator of cytosine modification status. TET2 inactivation in a neuronal cell line enriches for cytosine modification changes that are reciprocal to those observed in PD neurons. Furthermore, Tet2 inactivation in mice fully prevents dopaminergic neuronal loss in the substantia nigra induced by prior inflammation. Tet2 loss in mice also attenuates transcriptional immune responses to an inflammatory trigger. Thus, widespread epigenetic dysregulation of enhancers in PD neurons may, in part, be mediated by increased TET2 expression. Decreased Tet2 activity is neuroprotective, in vivo, and may be a novel therapeutic target for PD.

overall_design: To determine effects of inflammation on the the brain of mice with Tet2 inactivation, we performed RNA-sequencing of midbrain tissue of Tet2 knock-out and wild-type mice treated with lipopolysaccharide (LPS) or saline. LPS or saline was administered to mice 2 months of age and midbrain tissue was harvested 24 h later (n=14 mice: 3 Tet2 knock-out LPS, 4 Tet2 wild-type LPS, 3 Tet2 knock-out saline, 4 Tet2 wild-type saline).

first: Bryan

last: Killinger

first: Peipei

last: Li

first: Elizabeth

last: Ensink

first: Wei

last: Cui

first: Katie

first: Juozas

last: Gordevicius

first: Matthew

last: Weiland

first: Stefan

last: Jovinge

first: Viviane

last: Labrie


title: Single-cell temporal transcriptomics of the human cell cycle

status: Public on Dec 11 2020

city: Solna

first: Emma

last: Lundberg

address: Science for Life Laboratory, Tomtebodavägen 23A

country: Sweden

institute: KTH Royal Institute of Technology

summary: We present the first comprehensive map of spatiotemporal heterogeneity of the human proteome by integrating proteomics at subcellular resolution, single-cell transcriptomics, and pseudotime measurements of each cell within the cell cycle. The cell cycle transcriptomic data in this series provide context for single-cell proteomic measurements of the cell cycle, and this subsequent single-cell proteogenomic analysis that can be found in this code repository: https://github.com/CellProfiling/SingleCellProteogenomics .

overall_design: A total of 1,152 single U2OS FUCCI cells were sorted by FACS, and RNA-Seq was collected for each cell using SMART-seq2 chemistry.

first: Diana

last: Mahdessian

first: Anthony

middle: J

last: Cesnik

first: Christian

last: Gnann

first: Frida

last: Danielsson

first: Lovisa

last: Stenström

first: Muhammad

last: Arif

first: Cheng

last: Zhang

first: Trang

last: Le

first: Fredric

last: Johansson

first: Rutger

last: Shutten

first: Anna

last: Bäckström

first: Ulrika

last: Axelsson

first: Peter

last: Thul

first: Nathan

last: Cho

first: Oana

last: Carja

first: Mathias

last: Uhlén

first: Adil

last: Mardinoglu

first: Charlotte

last: Stadler

first: Cecilia

last: Lindskog

first: Burcu

last: Ayoglu

first: Manuel

middle: D

last: Leonetti

first: Fredrik

last: Pontén

first: Devin

middle: P

last: Sullivan


title: A Transcriptome Fingerprinting Assay for Clinical Immune Monitoring (MS Datasets)

first: Nicole

last: Baldwin

overall_design: MS - untreated (34 condition, 22 control, 56 total)

first: Matthew

last: Altman

first: Prasong

last: Khaenam

first: Vivian

last: Gersuk

first: Laurent

last: Chiche

first: Noemie

last: Jourde-Chiche

first: J

last: Phillips

first: Goran

last: Klintmalm

first: Anne

last: O’Garra

last: Berry

first: Chloe

last: Bloom

first: Marc

last: Lipman

first: Robert

last: Wilkinson

first: Christine

last: Graham

first: Ganjana

last: Lertmemongkolchai

first: Mary

last: Conley

first: Jason

last: Skinner

first: Farrah

last: Kheradmand

last: Linsley

first: Karolina

last: Palucka

first: Roman

last: Lukaszewski

first: Asuncion

last: Mejias

first: Octavio

last: Ramilo

first: Virginia

last: Pascual

first: Jacques

last: Banchereau

first: Charlie

last: Quinn

first: Scott

last: Presnell

first: Elizabeth

last: Whalen

first: Damien

last: Chaussabel


title: c-JUN is a pioneer factor safeguarding the primed state of pluripotency (RNA-Seq)

status: Public on Dec 31 2020

city: Guangzhou

first: dongwei

last: Li

address: 190 Kai Yuan Avenue, Science Park

institute: Guangzhou Institutes of Biomedicine and Health,Chinese Academy of Sciences

summary: Mouse ESCs and EpiSCs represent naive and primed states of plurioptency corresponding to two consecutive stages of embryo development. Here we map their chromatin accessibility landscapes and show that naive specific open chromatin are enriched with motifs for Oct/Sox/Klf/TCF and primed one with AP1 motifs.  The AP1 founding member c-Jun is expressed in EpiSCs and occupies both open and closed chromatin. Yet, c-Jun deficiency has no impact on the self renewal nor the transcription program of EpiSCs. However, in a Klf4-driven reprogramming system, we show that c-Jun-/- EpiSCs undergo primed to naive transition more efficiently than wild type cells and Klf4 evicts c-JUN from wild type chromatin.  These results suggest that c-Jun is a pioneer factor not to regulate transcription but to prevent backward reprogramming during naive-primed transition, thus providing a molecular basis for the forward principle in development.

overall_design: RNA-Seq

first: Dongwei


title: Neuronal diversity and convergence in a visual system developmental atlas (bulk RNA-seq)

status: Public on Jul 16 2020

city: Kansas City

first: Mehmet Neset

last: Ozel

state: MO

institute: Stowers Institute for Medical Research

summary: Deciphering how neuronal diversity is established and maintained requires a detailed knowledge of neuronal gene expression throughout development. In contrast to mammalian brains, the large neuronal diversity of the Drosophila optic lobes and its connectome are almost completely characterized. However, a molecular characterization of this diversity, particularly during development, has been lacking. We present novel insights into brain development through a nearly exhaustive description of the transcriptomic diversity of the optic lobes. We acquired the transcriptome of 275,000 single-cells at adult and five pupal stages, and developed a machine learning framework to assign them to almost 200 cell-types at all timepoints. We discovered two large neuronal populations that wrap neuropils during development but die just before adulthood, as well as neuronal subtypes that partition dorsal and ventral visual circuits by differential Wnt signaling throughout development. Moreover, we showed that neurons of the same type but produced days apart synchronize their transcriptomes shortly after being produced. We also resolved during synaptogenesis neuronal subtypes that converge to indistinguishable transcriptomic profiles in adults while greatly differing in morphology and connectivity. Our datasets almost completely account for the known neuronal diversity of the optic lobes and serve as a paradigm to understand brain development across species.

overall_design: We sequenced 2 FACS-sorted single cell types from the Drosophila optic lobe, as well as FACS-sorted neurons and glia as a control.

first: Katarina

last: Kapuralin

first: Mehmet-Neset

first: Felix

last: Simon


title: Single cell response landscape of graded Nodal signaling  in zebrafish explants

status: Public on Jan 28 2021

city: Hang Zhou

first: Tao

last: cheng

address: 886 Yuhangtang Road

institute: Zhejiang University


title: A Transcriptome Fingerprinting Assay for Clinical Immune Monitoring (SLE Datasets)

first: Nicole

last: Baldwin

overall_design: Pediatric SLE (55 condition, 14 control, 69 total)

first: Matthew

last: Altman

first: Prasong

last: Khaenam

first: Vivian

last: Gersuk

first: Laurent

last: Chiche

first: Noemie

last: Jourde-Chiche

first: J

last: Phillips

first: Goran

last: Klintmalm

first: Anne

last: O’Garra

last: Berry

first: Chloe

last: Bloom

first: Marc

last: Lipman

first: Robert

last: Wilkinson

first: Christine

last: Graham

first: Ganjana

last: Lertmemongkolchai

first: Mary

last: Conley

first: Jason

last: Skinner

first: Farrah

last: Kheradmand

first: Peter

first: Karolina


title: A Transcriptome Fingerprinting Assay for Clinical Immune Monitoring (Flu Datasets)

first: Nicole

last: Baldwin

overall_design: Flu (25 condition, 14 control, 39 total)

first: Matthew

last: Altman

first: Prasong

last: Linsley

last: Palucka

first: Roman

last: Lukaszewski

first: Asuncion

last: Mejias

first: Octavio

last: Ramilo

first: Virginia

last: Pascual

first: Jacques

last: Banchereau

first: Charlie

last: Quinn

first: Scott

last: Presnell

first: Elizabeth

last: Whalen

first: Damien

last: Chaussabel


title: A Transcriptome Fingerprinting Assay for Clinical Immune Monitoring (Sepsis Datasets)

overall_design: Sepsis (35 condition, 12 control, 47 total)

last: Khaenam

first: Vivian

last: Gersuk

first: Laurent

last: Chiche

first: Noemie

last: Jourde-Chiche

first: J

last: Phillips

first: Goran

last: Klintmalm

first: Anne

last: O’Garra

last: Berry

first: Chloe

last: Bloom

first: Marc

last: Lipman

first: Robert

last: Wilkinson

first: Christine

last: Graham

first: Ganjana

last: Lertmemongkolchai

first: Mary


title: A Transcriptome Fingerprinting Assay for Clinical Immune Monitoring (Pregnancy Datasets)

first: Nicole

last: Baldwin

overall_design: Pregnancy (25 condition, 20 control, 45 total)

first: Matthew

last: Altman

first: Prasong

last: Conley

first: Jason

last: Skinner

first: Farrah

last: Kheradmand

first: Peter

last: Linsley

first: Karolina

last: Palucka

first: Roman

last: Lukaszewski

first: Asuncion

last: Mejias

first: Octavio

last: Ramilo

first: Virginia

last: Pascual

first: Jacques

last: Banchereau

last: Quinn


title: A Transcriptome Fingerprinting Assay for Clinical Immune Monitoring (B-cell deficiency Datasets)

overall_design: B-cell deficiency (20 condition, 13 control, 33 total)

last: Khaenam

first: Vivian

last: Gersuk

first: Laurent

last: Chiche

first: Noemie

last: Jourde-Chiche

first: J

last: Phillips

first: Goran

last: Klintmalm

first: Anne

last: O’Garra

last: Berry

first: Chloe

last: Bloom

first: Marc

last: Lipman

first: Charlie

first: Scott

last: Presnell

first: Elizabeth

last: Whalen

first: Damien

last: Chaussabel


title: A Transcriptome Fingerprinting Assay for Clinical Immune Monitoring (RSV Datasets)

first: Nicole

last: Baldwin

overall_design: RSV (70 condition, 14 control, 84 total)

first: Matthew

last: Altman

first: Prasong

first: Robert

last: Wilkinson

first: Christine

last: Graham

first: Ganjana

last: Lertmemongkolchai

first: Mary

last: Conley

first: Jason

last: Skinner

first: Farrah

last: Kheradmand

first: Peter

last: Linsley

first: Karolina

last: Palucka

first: Roman

last: Lukaszewski

last: Mejias

last: Ramilo


title: A Transcriptome Fingerprinting Assay for Clinical Immune Monitoring (Kawasaki Datasets)

overall_design: Kawasaki (21 condition, 23 control, 44 total)

last: Khaenam

first: Vivian

last: Gersuk

first: Laurent

last: Chiche

first: Noemie

last: Jourde-Chiche

first: J

last: Phillips

first: Goran

last: Klintmalm

first: Anne

last: O’Garra

last: Berry

first: Chloe

last: Bloom

first: Marc

last: Lipman

first: Asuncion

first: Octavio

first: Virginia

last: Pascual

first: Jacques

last: Banchereau

last: Quinn


title: A Transcriptome Fingerprinting Assay for Clinical Immune Monitoring (COPD Datasets)

first: Nicole

last: Baldwin

overall_design: COPD (19 condition, 24 control, 43 total)

first: Matthew

last: Altman

first: Prasong

first: Robert

last: Wilkinson

first: Christine

last: Graham

first: Ganjana

last: Lertmemongkolchai

first: Mary

last: Conley

first: Jason

last: Skinner

last: Kheradmand

last: Linsley

last: Palucka

first: Charlie

first: Scott

last: Presnell

first: Elizabeth

last: Whalen

first: Damien

last: Chaussabel


title: Identification of differentially expressed genes in actinic keratosis samples treated with ingenol mebutate gel

status: Public on May 18 2020

city: Barcelona

first: Júlia

last: Perera-Bel

address: Doctor Aiguader, 88

institute: Hospital del Mar Research Institute

summary: Actinic keratosis is a common skin disease that may progress to invasive squamous cell carcinoma. Ingenol mebutate has demonstrated efficacy in field treatment of actinic keratosis.  However, molecular mechanisms on ingenol mebutate response are not yet fully understood.

overall_design: Single-center, single-arm, prospective observational study conducted in Hospital del Mar in Barcelona from April 2016 to April 2018, to evaluate mRNA expression profile of actinic keratoses before and after treatment with ingenol mebutate gel.

first: Sonia

last: Segura

first: Agustí

last: Toll

first: Alejandra

last: Gadea

first: Lara

last: Nonell

first: Evelyn

last: Andrades

first: Silvia

last: Sánchez

first: Ramon

last: Pujol

first: Inmaculada

last: Hernández-Muñoz


title: A Transcriptome Fingerprinting Assay for Clinical Immune Monitoring (Liver Transplant Datasets)

first: Nicole

last: Baldwin

overall_design: Liver Transplant (94 condition, 30 control, 124 total)

first: Matthew

last: Altman

first: Prasong

last: Khaenam

first: Vivian

last: Gersuk

first: Laurent

last: Chiche

first: Noemie

last: Jourde-Chiche

first: J

last: Phillips

first: Goran

last: Klintmalm

first: Anne

last: O’Garra

last: Berry

first: Chloe

last: Bloom

first: Marc

last: Lipman

first: Robert

last: Wilkinson

first: Christine

last: Graham

last: Lertmemongkolchai

last: Conley

first: Farrah

first: Peter

first: Karolina

first: Roman

last: Lukaszewski

first: Asuncion

last: Mejias

first: Octavio

last: Ramilo

first: Virginia

last: Pascual

first: Jacques

last: Banchereau

last: Quinn


title: A Transcriptome Fingerprinting Assay for Clinical Immune Monitoring (Melanoma Datasets)

first: Nicole

last: Baldwin

overall_design: Melanoma Stage IV (22 condition, 5 control, 27 total)

first: Matthew

last: Altman

first: Prasong

last: Khaenam

first: Vivian

last: Gersuk

first: Laurent

last: Chiche

last: Jourde-Chiche

first: Ganjana

first: Mary

first: Jason

last: Skinner

last: Kheradmand

last: Linsley

last: Palucka

first: Charlie

first: Scott

last: Presnell

first: Elizabeth

last: Whalen

first: Damien

last: Chaussabel


title: Mutational scans of the chemokine receptors CXCR4 and CCR5 based on bimolecular fluorescence complementation reveal multiple mechanisms for receptor association

status: Public on May 01 2020

city: Urbana

first: Erik

last: Procko

state: IL

address: 601 S Goodwin Ave

department: Biochemistry

institute: University of Illinois

summary: Many G protein-coupled receptors (GPCRs) are found to homo- or hetero-oligomerize, but how and why GPCRs associate remains controversial.  The class A chemokine receptors CCR5 and CXCR4 both homo- and heterodimerize with each other, and crystal structures of CXCR4 in inactive conformations have captured dimeric organization.  By selecting libraries of CCR5 and CXCR4 variants based on bimolecular fluorescence complementation, we determine how nearly every single amino acid substitution effects homo-associations.  We find three mechanisms for chemokine receptor association: (i) non-specific aggregation in the membrane phase enhanced by destabilizing structural mutations, (ii) specific protein-protein dimerization interfaces, and (iii) motifs in the cytoplasmic tails that are hypothesized to promote lipid raft localization, thereby bringing receptors close together at high density.  We identify mutations that tease apart the effects of these respective mechanisms, and show that specific dimer organization, despite reducing agonist binding, is necessary for active signaling within the cell.

overall_design:
Single-site saturation mutagenesis libraries were constructed of myc-tagged CXCR4 and CCR5 fused at their cytosolic C-termini with VC (Venus I152L a.a. D155-K238).  The libraries were transfected into human Expi293F lines over-expressing wildtype FLAG-tagged CXCR4 or CCR5 fused to VN (Venus I152L a.a. V1-A154) at the receptors' cytosolic C-termini. Cells were evolved by FACS for surface expression based on the extracellular myc tag, and for receptor oligomerization based on complementation of split Venus. Frequencies of variants in the sorted population (measured from RNA transcripts) were compared to frequencies in the DNA libraries to calculate log(base2) enrichment ratios for all amino acid substitutions.  All evolution experiments were in duplicate.

The library construction protocol and data processing details are also provided in the readme.txt file.

first: Kevin

last: Gill


title: A Transcriptome Fingerprinting Assay for Clinical Immune Monitoring (Juvenile Dermatomyositis Datasets)

overall_design: Juvenile Dermatomyositis (40 condition, 9 control, 49 total)

first: Noemie

first: J

last: Phillips

first: Goran

last: Klintmalm

first: Anne

last: O’Garra

last: Berry

first: Chloe

last: Bloom

first: Marc

last: Lipman

first: Robert

last: Wilkinson

first: Christine

last: Graham

last: Lertmemongkolchai

last: Conley

first: Farrah

first: Peter

first: Karolina

first: Roman

last: Lukaszewski

first: Asuncion

last: Mejias

first: Octavio

last: Ramilo

last: Pascual

last: Banchereau


title: Exploring the role of potato Pti5 in hypersensitive response-conferred resistance to Potato virus Y using short hairpin RNA-mediated gene silencing

status: Public on Apr 11 2020

city: Ljubljana

first: Marko

last: Petek

address: Večna pot 111

department: Department of Biotechnology and Systems Biology

country: Slovenia

institute: National Institute of Biology

summary:
Pti5 is an ERF transcription factor that was differentially expressed in PVY-infected potato plants. The purpose of generating this dataset was to identify genes with perturbed expression due to silencing the Pti5 gene.

Grant ID: P4-0165  Slovenian Research Agency ARRS  Biotechnology and Plant Systems Biology

Grant ID: J4-7636  Slovenian Research Agency ARRS  Spatiotemporal analysis of hypersensitive response to Potato virus Y in potato

Grant ID: J4-1777  Slovenian Research Agency ARRS  Unraveling mechanisms of effectiveness and specificity in potato immune signaling through innovative data acquisition and modeling

overall_design: NahG and NahG_shPti5 plants; PVY-inoculated vs mock samples; 3 biological replicates per treatment

first: Anna

last: Coll

first: Tjaša

last: Lukan

first: Kristina

last: Gruden


title: Chromatin accessibility dynamics and single cell RNA-Seq reveal new regulators of regeneration in neural progenitors

status: Public on Mar 12 2020

city: Seattle

first: Anneke

middle: Dixie

last: Kakebeen

state: WA

address: 5611 9th Ave NW

institute: University of Washington

overall_design: Refer to individual Series


summary: Vertebrate appendage regeneration requires precisely coordinated remodeling of the transcriptional landscape to enable the growth and differentiation of new tissue, a process executed over multiple days and across dozens of cell types. The heterogeneity of tissues and temporally-sensitive fate decisions involved has made it difficult to articulate the gene regulatory programs enabling regeneration of individual cell types. To better understand how a regenerative program is fulfilled by neural progenitor cells (NPCs) of the spinal cord, we analyzed pax6-expressing NPCs isolated from regenerating Xenopus tropicalis tails. By intersecting chromatin accessibility data with single-cell transcriptomics, we find that NPCs place an early priority on neuronal differentiation. Late in regeneration, the priority returns to proliferation. Our analyses identify Pbx3 and Meis1 as critical regulators of tail regeneration and axon organization. Overall, we use transcriptional regulatory dynamics to present a new model for cell fate decisions and their regulators in NPCs during regeneration.

overall_design: Single-cell RNA-seq experiments were performed on the 10X Genom+D:Dics platform from FAC sorted, pax6:GFP positive cells from uninjured stage 41 Xenopus tropicalis tadpoles and 24 hours post amputation regenerated tail tissue.

first: A

last: Wills


title: A Transcriptome Fingerprinting Assay for Clinical Immune Monitoring (HIV Datasets)

first: Nicole

last: Baldwin

overall_design: HIV (28 condition, 35 control, 63 total)

first: Matthew

last: Altman

first: Prasong

last: Khaenam

first: Vivian

last: Gersuk

first: Laurent

last: Chiche

first: Noemie

last: Jourde-Chiche

first: J

middle: T

last: Phillips

first: Goran

last: Klintmalm

first: Anne

last: O’Garra

last: Berry

last: Bloom

first: Ganjana

first: Mary

first: Jason

last: Skinner

last: Kheradmand

last: Linsley

last: Palucka

first: Virginia

first: Jacques

first: Charlie

last: Quinn

first: Scott

last: Presnell

first: Elizabeth

last: Whalen

first: Damien

last: Chaussabel


title: Epigenomic analysis of Parkinson's disease neurons identifies TET2 loss as neuroprotective

first: Lee

last: Marshall

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: BONE MARROW MONOCYTES AND DERIVED DENDRITIC CELLS FROM MYELODYSPLASTIC PATIENTS HAVE FUNCTIONAL ABNORMALITIES ASSOCIATED WITH DEFECTIVE RESPONSE TO BACTERIAL INFECTION

status: Public on Feb 10 2020

city: Sao Paulo

first: Patricia

last: Severino

state: Sao Paulo

address: Rua Comendador Elias Jafet, 755

department: Albert Einstein Research and Education Institute

country: Brazil

institute: Hospital Israelita Albert Einstein

summary: Myelodysplastic syndromes (MDS) are a heterogeneous group of hematopoietic stem cell diseases characterized by dysplasia of one or more hematologic lineages and a high-risk of developing acute myeloid leukemia (AML). MDS patients have recurrent bacterial infections and abnormal expression of CD56 by monocytes. We investigated MDS patients’ bone marrow CD56+/CD56- monocytes and their in vitro derived dendritic cell (DCs) populations in comparison to cells obtained from disease-free subjects. We found that monocytes from MDS patients, irrespective of CD56 expression, have reduced phagocytosis activity and low expression of genes involved in triggering immune responses, regulation of immune and inflammatory response signaling pathways, and in the response to lipopolysaccharide. Dendritic cells (DCs) derived in vitro from MDS monocytes failed to develop dendritic projections and had reduced expression of HLA-DR and CD86 suggesting that antigen processing and T cell activation capabilities are impaired. In conclusion, we identified in both CD56+ and CD56- monocytes from MDS-patients several abnormalities that may be related to the increased susceptibility to infections observed in these patients.

overall_design: The aim of the present study was to study CD56+ and CD56- bone marrow monocytes and derived DCs obtained from MDS patients and free-disease individuals. We analyzed the monocyte populations by flow cytometry, their morphological aspects and phagocytic activity, as well as gene expression patterns and cell surface markers. Taken together, alterations in the expression of MHC-class II and co-stimulatory molecules, toll-like receptors and cytokine gene expression, suggest functional abnormalities within the monocyte population that may contribute to deficient response to bacterial infection, a common feature in MDS patients.

first: Laiz

last: Cameirão Bento

first: Nydia

last: Strachman Bacal

first: Fernanda

last: Agostini Rocha

first: Luciana

last: Cavalheiro Marti


title: Single cell profiling reveals an endothelium-mediated immunomodulatory pathway in the eye choroid

status: Public on Feb 28 2020

city: Madrid

first: Ignacio

last: Benedicto

state: Madrid

address: Melchor Fernández Almagro, 3

institute: Centro Nacional de Investigaciones Cardiovasculares (CNIC)

summary: The activity and survival of retinal photoreceptors depend on support functions performed by the retinal pigment epithelium (RPE) and on oxygen and nutrients delivered by blood vessels in the underlying choroid. By combining single cell and bulk RNA sequencing, we categorized mouse RPE/choroid cell types and characterized the tissue-specific transcriptomic features of choroidal endothelial cells. We found that choroidal endothelium adjacent to the RPE expresses high levels of Indian Hedgehog, and identified its downstream target as stromal GLI1+ mesenchymal stem cell-like cells. Genetic impairment of Hedgehog signaling in vivo induced significant loss of choroidal mast cells, as well as an altered inflammatory response and exacerbated visual function defects after retinal damage. Our studies reveal the cellular and molecular landscape of adult RPE/choroid and uncover a Hedgehog-regulated choroidal immunomodulatory signaling circuit. These results open new avenues for the study and treatment of retinal vascular diseases and choroid-related inflammatory blinding disorders.

overall_design: Single cell RNAseq experiments (10x Genomics Chromium platform) were performed using RPE/choroid tissue from 90 day-old mice of two different strains, C57BL/6J and B6129PF1/J. For each strain, experiments were carried out with pooled RPE/choroid tissue from one eye from a male and another from a female. Bulk RNAseq: a) tissue-specific endothelial cells isolated from 30 day-old B6129PF1/J mice (3 independent isolations, 7 animals per isolation for neural retina, 1 animal per isolation for lung, liver and heart); b) RPE/choroid tissue from 6 month-old, tamoxifen-treated Ihh+/+ and IhhiΔEC/ΔiEC mice (3 mice per genotype); c) cultured choroidal GLI1+ cells isolated from Gli1GFP/+ mice and treated with DMSO or 100nM SAG for 24h (3 replicates per treatment).

first: Guillermo

middle: L

last: Lehmann

first: Yang

last: Hu

first: Rohan

last: Bareja

first: Olivier

last: Elemento

first: Enrique

last: Rodriguez-Boulan


title: Metabolic flexibility of SUP05 under low DO growth conditions

status: Public on Jun 01 2020

city: Iowa City

first: Timothy

middle: E

last: Mattes

address: 4105 Seamans Center

institute: University of Iowa

summary:
Chemoautotrophic bacteria from the SUP05 clade often dominate anoxic waters in marine oxygen minimum zones (OMZs) where reduced sulfur can fuel carbon fixation and denitrification. Some members of the SUP05 clade are facultative aerobes that thrive at the boundaries of OMZs where they experience fluctuations in dissolved oxygen (DO).
The degree to which SUP05 contribute to nitrate reduction in these regions depends on their sensitivity to oxygen. We evaluated growth and quantified differences in gene expression in Ca. T. autotrophicus strain EF1 from the SUP05 clade under high DO (22 μM), anoxic, and low DO  (3.8 μM) concentrations.
We show that strain EF1 cells respire oxygen and nitrate and that cells have higher growth rates, express more genes, and fix more carbon when oxygen becomes  available for aerobic respiration.
Evidence that facultatively aerobic SUP05 are more active and respire nitrate when oxygen becomes available at low concentrations suggests that they are an important source of nitrite across marine OMZ boundary layers.

overall_design: mRNA profiles of a pure culture of Ca. T. autotrophicus strain EF1 growing under three different dissolved oxygen concentrations, anoxic, low DO and high DO, were generated in duplicate by Illumina Miseq high-throughput sequencing

first: Anitra

last: Ingalls

first: Susan

last: Burke

first: Robert

last: Morris


title: A Transcriptome Fingerprinting Assay for Clinical Immune Monitoring

first: Nicole

last: Baldwin

overall_design: Total of 985 samples across 16 datasets. Each dataset contains it's own biological controls, there are no replicates. Samples are distributed as follows: TB (23 condition, 11 control, 34 total); Staph aureus (99 condition, 44 control, 143 total); Sepsis (35 condition, 12 control, 47 total); HIV (28 condition, 35 control, 63 total); Flu (25 condition, 14 control, 39 total); RSV (70 condition, 14 control, 84 total); B-cell deficiency (20 condition, 13 control, 33 total); Liver Transplant (94 condition, 30 control, 124 total); Pregnancy (25 condition, 20 control, 45 total); Melanoma Stage IV (22 condition, 5 control, 27 total); Kawasaki (21 condition, 23 control, 44 total); Juvenile Dermatomyositis (40 condition, 9 control, 49 total); COPD (19 condition, 24 control, 43 total); MS - untreated (34 condition, 22 control, 56 total); Pediatric SLE (55 condition, 14 control, 69 total); SoJIA (62 condition, 23 control, 85 total)

first: Matthew

last: Altman

first: Prasong

last: Khaenam

first: Vivian

last: Gersuk

first: Laurent

last: Chiche

first: Noemie

last: Jourde-Chiche

first: J

last: Phillips

first: Goran

last: Klintmalm

first: Anne

last: O’Garra

last: Berry

first: Chloe

last: Bloom

first: Marc

last: Lipman

last: Wilkinson

first: Christine

last: Graham

first: Ganjana

last: Lertmemongkolchai

first: Mary

last: Conley

first: Jason

last: Skinner

first: Farrah

last: Kheradmand

first: Peter

last: Linsley

first: Karolina

last: Palucka

first: Roman

last: Lukaszewski

first: Asuncion

last: Mejias

first: Octavio

last: Ramilo

first: Virginia

last: Pascual

first: Jacques

last: Banchereau

first: Charlie

last: Quinn

first: Scott

last: Presnell

first: Elizabeth

last: Whalen

first: Damien

last: Chaussabel


title: Time-driven molding of the epidermal stem cell transcriptome

status: Public on Jan 23 2020

city: Salamanca

first: L. Francisco

last: Lorenzo-Martín

state: Castilla y León

address: Campus Miguel de Unamuno

institute: University of Salamanca (USAL) – Centro de Investigación del Cáncer (CIC)

summary:
Epidermal stem cells ensure proper faring of skin homeostatic processes under both physiological and challenging conditions. Currently, the molecular events underpinning ageing within the epidermal stem cell niche are poorly understood.
Here, we report that epidermal stem cells are endowed with a collection of time-sensitive genes which constitute specific functional programs that become deregulated in an age-dependent manner.

overall_design: Epidermal stem cells (CD34+;Itga6+) from dorsal skin of 0.6-, 1-, 2.5-, 4-, 6- and 12-month-old mice (n = 3 per time point)

first: L

first: Xosé

middle: R

last: Bustelo


title: Sphingosine kinase 2 in stromal fibroblasts creates a hospitable tumor microenvironment in breast cancer

status: Public on Jan 01 2020

city: Richmond

first: Mikhail

last: Dozmorov

state: VA

address: 830 E Main St

department: Biostatistics

institute: Virginia Commonwealth University

summary: Reciprocal interactions between breast cancer cells and the tumor microenvironment are important for cancer progression and metastasis. We report here that the deletion or inhibition of sphingosine kinase 2 (SphK2), which produces sphingosine-1-phosphate (S1P), markedly suppresses syngeneic breast tumor growth and lung metastasis in mice by creating a hostile microenvironment for tumor growth and invasion. SphK2 deficiency decreased S1P and concomitantly increased ceramides, including C16-ceramide, in stromal fibroblasts. Ceramide accumulation suppressed activation of cancer-associated fibroblasts (CAFs) by upregulating stromal p53, which restrained production of tumor-promoting factors to reprogram the tumor microenvironment and restrict breast cancer establishment. Ablation of p53 in SphK2-deficient fibroblasts reversed these effects, enabled CAF activation and promoted tumor growth and invasion. These data uncovered a novel role of SphK2 in regulating non-cell autonomous functions of p53 in stromal fibroblasts and their transition to tumor-promoting CAFs, paving the way for the development of a strategy to target the tumor microenvironment and enhance therapeutic efficacy.

overall_design: mRNA expression profiles of wild type and SphK2 null mouse embryonic fibroblasts were determined in triplicate using Illumina.

first: Cynthia

last: Weigel

first: Melissa

last: Maczis

first: Elisa

last: Paladino

first: Christopher

last: Green

first: Michael

last: Maceyka

first: Chunqing

last: Guo

first: Xiang-Yang

last: Wang

middle: G

first: Sheldon

last: Milstien

first: Sarah

last: Spiegel


title: RNAseq for the identification of genes induced upon TGR5 stimulation in intestinal stem cells

status: Public on Nov 19 2019

city: Lausanne

first: Gaby

last: El Alam

state: Vaud

address: Station 15

department: SV LISP

country: Switzerland

institute: École polytechnique fédérale de Lausanne

summary:
Purpose: Transcriptomic exploration for the identification of genes induced upon TGR5 stimulation in intestinal stem cells
Methods: For each biological replicate, GFPhi cells were isolated by FACS from intestines from 4 pooled Lgr5-eGFP-IRES-CreERT2 mice. About 200.000 GFPhi cells were then embedded in Matrigel (20.000 per well in 10µL Matrigel drop) and after 4 hours were treated with INT-777 (30µM) or DMSO as control. After 16 hours RNA was extracted (RNAqueous Kit, Thermofisher) for RNAseq analysis. This experiment was repeated 3 times in 3 different days (n=3 biological replicates).
Results: INT-777 treatment results in the activation of a panel of genes showing high enrichment of TEADs family of TF in associated motifs.

overall_design: Design: For each biological replicate, GFPhi cells were isolated by FACS from intestines from 4 pooled Lgr5-eGFP-IRES-CreERT2 mice. About 200.000 GFPhi cells were then embedded in Matrigel (20.000 per well in 10µL Matrigel drop) and after 4 hours were treated with INT-777 (30µM) or DMSO as control. After 16 hours RNA was extracted (RNAqueous Kit, Thermofisher) for RNAseq analysis. This experiment was repeated 3 times in 3 different days (n=3 biological replicates).

first: Giovanni

last: Sorrentino


title: Extensive changes in transcriptomic “fingerprints” and immunological cells in the large organs of patients dying of acute septic shock and multiple organ failure caused by Neisseria meningitidis

status: Public on Jan 14 2020

city: Oslo

first: Berit

middle: Sletbakk

last: Brusletto

address: Kirkeveien 166

department: Oslo University Hospital

country: Norway

institute: Medical Biochemisty

summary:
Background: Patients developing meningococcal septic shock reveal very high levels of Neisseira meningitidis and endotoxin in the circulation and organs, leading to acute cardiovascular, pulmonary and renal failure, coagulopathy and a high case fatality rate within 24 hours.
Objective: To investigate transcriptional profiles in heart, lungs, kidneys, liver and spleen and immunostain key inflammatory cells and proteins in post mortem formalin-fixed, paraffin-embedded (FFPE) tissue samples from meningococcal septic shock patients.
Patients and methods: Total RNA was isolated from FFPE and fresh frozen (FF) tissue samples from five patients and two controls (non-inflammatory disease). Differential expression of genes was detected using Affymetrix GeneChip Human Transcriptome 2.0 Arrays. Lung and heart tissue samples were immunostained for T-and B cells, macrophages, neutrophils and the inflammatory markers Plasminogen activator inhibitor-1 (PAI-1) and Monocyte chemoattractant protein 1 (MCP-1). Inflammatory mediators were quantified in lysates from FF tissues.
Results: The transcriptional profiles showed significant regulation of pathways associated with organismal death, cell death and survival, leukocyte migration, cellular movement, proliferation of cells, cell-to-cell signaling, immune cell trafficking and inflammatory responses in an organ-specific clustering manner. The canonical pathways including acute phase response-, EIF2-, TREM1-, IL-6-, HMBG1-, PPAR signaling and LXR/RXR activation were associated with acute heart, pulmonary and renal failure and with inflammatory changes in liver and spleen were identified. The main upstream regulators were TNF, IL-1β, IL-6, RICTOR, miR-6739-3p and CD3. Increased numbers of inflammatory cells (CD68+, MPO+, CD3+ and CD20+) were found in lungs and heart. PAI-1 inhibiting fibrinolysis and MCP-1 attracting leukocyte were found significantly present in the septic tissue samples compared to the controls.
Conclusions: Hundreds of transcripts were altered in lungs, heart and kidneys, all organs with an acute dysfunction. Relatively fewer transcripts were changed in the spleen. Certain transcripts were associated with the number of. N. meningitidis in the tissues. We identified specific biomarker panels which differed from organ to organ. Our results highlight the complexity of gene regulation in the different tissues. Future treatment strategies blocking or stimulating only one molecule or pathway appear unlikely to succeed.

overall_design: Reference : Meningococcal septic shock (MSS) patients (N=5 patients with FFPE tissue and from 3 of the same patients FF tissue (n=3)), from each patient tissue samples from lungs, heart, kidneys, liver, spleen. Control patients (N=2) with acute non-infectious death. FFPE tissue samples from lungs, heart, kidneys, liver, spleen.

first: Else

last: Løberg

first: Bernt

last: Hellerud

first: Ingeborg

last: Goverud

first: Jens

last: Berg

first: Ole

middle: K

last: Olstad

first: Unni

last: Gopinathan

first: Petter

last: Brandtzaeg

first: Reidun

last: Øvstebø


title: RNA-RNA interactomes of Hfq and ProQ reveal overlapping and competing roles for RNA chaperones

status: Public on Dec 08 2019

city: Bethesda

first: Ryan

last: Dale

state: MD

address: Rm 10D39, 10 Center Drive

department: National Institute of Child Health and Human Development

institute: National Institutes of Health

summary: In many bacteria, the base pairing between most small regulatory RNAs (sRNAs) and their targets is facilitated by the Hfq RNA chaperone. However, recent studies have shown FinO-domain proteins also bind sRNAs. To compare the contributions of Hfq and the FinO-domain ProQ protein in Escherichia coli, we carried out RIL-seq, which allows global identification of two RNAs bound to the same protein. We detected hundreds of RNA pairs on ProQ. Intriguingly, 33% of the ProQ-bound RNA pairs are also found associated with Hfq, suggesting overlapping, complementary or competing roles for the two proteins.

overall_design: Applying RIL-seq to strains carrying chromosomly Hfq-FLAG or ProQ-3XFLAG in the presence or in the absence of the other RNA chaperon.

first: Sahar

last: Melamed

first: Philip

last: Adams

first: Aixia

last: Zhang

first: Hongen

first: Gisela

last: Storz


title: Microarray analysis of mouse bone marrow-derived macrophages (BMDM)

status: Public on Nov 13 2019

first: Júlia

last: Perera-Bel

department: MARData-BU

summary: Microarray analysis of differentially expressed genes in wild-type and NFAT5-deficient BMDM.

overall_design: BMDM were generated by culturing bone marrow cell suspensions from wild-type and NFAT5-deficient mice in 25% (vol/vol) conditioned medium from M-CSF-producing L929 cells for 7 days. BMDM were left unstimulated or stimulated with poly(I:C) for 6h. 2 concentrations of poly(I:C) were used: 0.2 micrograms/ml and 1 microgram/ml. 18 samples were analyzed: KO (n=9) and WT (n=9).

first: Hector

last: Huerga Encabo

first: Cristina

last: Lopez-Rodriguez


title: Changes in calcium homeostasis and gene expression implicated in epilepsy in hippocampi of mice overexpressing ORAI1

status: Public on Dec 17 2019

city: Warsaw

first: Bartosz

last: Wojtas

address: Pasteura 3

country: Poland

institute: Nencki Institute of Experimental Biology

summary: We showed that the overexpression of ORAI1 in the neurons of murine brain leads to spontaneous occurrence of seizure-like events in aged animals. We aimed to identify the mechanism responsible for this phenomenon. Using modified Ca2+-addback assay in the slices of CA1 hippocampal region and FURA-2AM calcium indicator we found that overexpression of ORAI1 in neurons leads to altered Ca2+ response. Next, by RNASeq we identified set of genes, whose expression was changed in FVB/NJ-Tg(ORAI1)Ibd mice.

overall_design: We isolated total RNA from hippocampi of wild-type (n=3) and of FVB/NJ-Tg(Orai1)Ibd (n=3) females and performed RNAseq experiments.

first: Lukasz

last: Majewski


title: IgG is differentially and selectively transferred across the placenta in HIV-infected women

status: Public on Sep 11 2019

city: Raleigh

first: Xinxia

last: Peng

address: 1060 William Moore Drive

institute: North Carolina State University

summary: The transplacental transfer of maternal IgG to the developing fetus is critical for infant protection against infectious pathogens in the first year of life. However, factors that modulate the transplacental transfer efficiency of maternal IgG that could be harnessed for maternal vaccine design remain largely undefined. HIV-infected women have impaired placental IgG transfer, yet the mechanism underlying this impaired transfer is unknown, presenting an opportunity to explore factors that contribute to the efficiency of placental IgG transfer. We measured the transplacental transfer efficiency of maternal HIV and other pathogen-specific IgG in historical U.S. (n=120) and Malawian (n=47) cohorts of HIV-infected mothers and their HIV58 exposed uninfected and HIV-infected infants. We then examined the role of maternal HIV disease progression, infant factors, placental Fc receptor expression, and IgG Fc region subclass and glycan signatures and their association with transplacental transfer efficiency of maternal antigen-specific IgG. We established 3 distinct phenotypes of placental IgG transfer efficiency in HIV-infected women, including: 1) efficient transfer of the majority of antigen-specific IgG populations; 2) generally poor IgG transfer phenotype that was strongly associated with maternal CD4+ T cell counts, hypergammaglobulinemia, and frequently yielded non-protective levels of vaccine-specific IgG; and 3) variable transfer of IgG across distinct antigen specificities. Interestingly, maternal IgG characteristics, such as binding to placentally expressed Fc receptors FcgRIIa and FcgRIIIa, IgG subclass frequency, and Fc region glycan profiles were associated with placental IgG transfer efficiency. These maternal IgG transplacental transfer determinants were distinct among different antigen-specific IgG populations. Our findings suggest that in HIV-infected women, both maternal disease progression and Fc region characteristics modulate the selective placental transfer of distinct IgG subpopulations, with implications for both the health of HIV-exposed uninfected infants and maternal vaccine design.

overall_design: Placental biopsy samples from HIV-infected Malawian women were sequenced on a Nextseq500 sequencer (Illumina) using 75bp paired-end reads.

first: David

last: Martinez

first: Youyi

last: Fong

first: Shuk

middle: H

last: Li

first: Fang

last: Yang

first: Madeleine

last: Jennewein

first: Joshua

middle: A

last: Weiner

first: Erin

last: Harrell

first: Jesse

last: Mangold

first: Ria

last: Goswami

first: George

last: Seage

first: Galit

last: Alter

first: Margaret

last: Ackerman

first: Genevieve

last: Fouda

first: Sallie

last: Permar


title: IκBα deficiency imposes a fetal phenotype to intestinal stem cells

status: Public on Feb 04 2020

first: Júlia

last: Perera-Bel

summary: The intestinal epithelium is a paradigm of adult tissue in constant regeneration that is supported by intestinal stem cells (ISCs). The mechanisms regulating ISC homeostasis after injury are poorly understood.  We previously demonstrated that IκBa, not only controls NF-κB activation, but also exerts nuclear functions as cytokine sensor in a subset of PRC2-regulated genes. We now uncover nuclear phosphorylated IκBa (P-IκBa) in the ISC compartment where it binds highly histone methylated genomic regions. Mice deficient for IκBa show aberrant distribution of H3K27me3 mark, and altered intestinal differentiation with persistence of a fetal-like ISC signature. In vitro, IκBa deficient intestinal cells produced morphologically aberrant organoids carrying a PRC2, Notch and IFN-dependent fetal-like transcriptional signature. Induction of the fetal-like phenotype by DSS treatment is associated with loss of nuclear P-IκBa in the damaged colonic epithelium and it subsequent accumulation in early CD44 positive regenerating areas. Importantly, IκBa deficient animals showed higher resistance to damage, likely due to persistent fetal-like phenotype. These results point out intestinal IκBa as chromatin sensor of inflammation in the ISC compartment.

overall_design: 10 samples were analyzed: WT (n=5); KO (n=5);

first: Lluis

last: Blay

first: Laura

middle: M

last: Aylagas


title: KLF4 binding during reprogramming is linked to enhancer rewiring and is critical for the architecture and regulation of enhancer hubs [4C-Seq]

status: Public on Sep 06 2019

city: New York

first: Effie

last: Apostolou

state: NY

address: 1161 York Avenue, Apt 8A

institute: Weill Cornell Medicine

summary:
Purpose: We captured on a genome-wide scale the binding of KLF4 during iPSC formation and its effects on chromatin state, transcriptional activity and chromatin topology around its targets.
Methods: We used a well-characterized reprogramming system to apply genome-wide assays that map KLF4 binding (ChIP-seq), chromatin accessibility (ATAC-seq), enhancer and gene activity (H3K27ac ChIP-seq and RNA-seq), enhancer connectivity (H3K27ac Hi-ChIP) as well as KLF4-centric chromatin looping (KLF4 Hi-ChIP) at different stages during acquisition of pluripotency.
Results: Integrative analysis of our results generated a reference map of stage-specific chromatin changes around KLF4 bound loci and established strong links with enhancer. rewiring and concordant transcriptional changes. Genetic manipulation of KLF4 binding from a PSC enhancer further supported the ability of KLF4 to function both as a transcriptional regulator and a chromatin organizer.
Conclusions: Our study offers novel insights into the intricate roles of a master regulator during cell fate transition.

overall_design: Mouse embryonic fibroblasts (MEFs) (Rosa26-M2rtTA/Col1a1-OKSM) induced with doxycycline (dox) in the presence of ascorbic acid. We collected bulk populations on day 3 after dox treatment, whereas at later stages, on day 6 and day 9, we sorted SSEA1 positive cells to enrich for cells on the trajectory towards induced pluripotency. Finally, we used pluripotent stem cells (PSCs) as a reference point for established pluripotency. Biological replicates were collected to assay for chromatin accessibility (paired-end ATAC-seq), gene activity (single-end RNA-seq), H3K27ac ChIP-seq (single-end) in MEFs, day3, 6, 9 and PSCs. KLF4 binding (single-end ChIP-seq) was assessed in day3, 6, 9 and PSCs. KLF4/H3K27ac centric looping (paired-end Hi-ChIP) was studied in either day3, day6 and PSCs for KLF4 or MEFs and PSCs for H3K27ac. 4C-Seq was conducted for individual viewpoints (Mycn, Ets1, Tbx3) to validate findings from HiChIP/Hi-C assays.

first: Aristotelis

last: Tsirigos


title: KLF4 binding is involved in the organization and regulation of 3D enhancer networks during acquisition and maintenance of pluripotency [ChIP-seq]

summary: Cell fate transitions are accompanied by global transcriptional, epigenetic and topological changes driven by transcription factors (TFs), as is strikingly exemplified in somatic cell reprogramming to pluripotent stem cells (PSCs) by OCT4, KLF4, SOX2 and cMYC. How TFs orchestrate the complex molecular changes around their targets in a temporal manner remains largely elusive. Here, using KLF4 as a paradigm, we provide the first TF-centric view of chromatin reorganization and the association to 3D enhancer rewiring and the transcriptional changes of linked genes during reprogramming of mouse embryonic fibroblasts to (MEFs) to PSCs. Inducible depletion of KLF factors in PSC caused a genome-wide decrease in connectivity of enhancers and disruption of KLF4 binding site from PSC-specific enhancers was sufficient to reduce expression of genes within the enhancer hub partly by impairing long-range contacts. Our study provides an integrative view of the intricate activities of a master regulator during a controlled cell fate transition and offers novel insights into the order and nature of molecular events that follow TF binding.

overall_design:
Integrative analysis of ChIP-seq, HiChIP, HiC, ATAC-seq, RNA-seq and 4C-seq techniques.
ChIP-seq TKO samples: For ESC TKO samples in WT and 24 hours after KLF KO we also generated 2 biological replicates for H3K27ac ChIPseq and 2 input for both.
ChIP-seq iPSCs: 2 ChIPseq biological replicates for KLF4 and H3K27ac were generated from iPSC cells with one corresponding input for KLF4 and H3K27ac.

first: E


title: KLF4 binding is involved in the organization and regulation of 3D enhancer networks during acquisition and maintenance of pluripotency [RNA-seq]

summary:
Summary: Cell fate transitions are accompanied by global transcriptional, epigenetic and topological changes driven by transcription factors (TFs), as is strikingly exemplified in somatic cell reprogramming to pluripotent stem cells (PSCs) by OCT4, KLF4, SOX2 and cMYC. How TFs orchestrate the complex molecular changes around their targets in a temporal manner remains largely elusive. Here, using KLF4 as a paradigm, we provide the first TF-centric view of chromatin reorganization and the association to 3D enhancer rewiring and the transcriptional changes of linked genes during reprogramming of mouse embryonic fibroblasts to (MEFs) to PSCs. Inducible depletion of KLF factors in PSC caused a genome-wide decrease in connectivity of enhancers and disruption of KLF4 binding site from PSC-specific enhancers was sufficient to reduce expression of genes within the enhancer hub partly by impairing long-range contacts. Our study provides an integrative view of the intricate activities of a master regulator during a controlled cell fate transition and offers novel insights into the order and nature of molecular events that follow TF binding.

Purpose: We captured on a genome-wide scale the binding of KLF4 during iPSC formation and its effects on chromatin state, transcriptional activity and chromatin topology around its targets.

Methods: We used a well-characterized reprogramming system to apply genome-wide assays that map KLF4 binding (ChIP-seq), chromatin accessibility (ATAC-seq), enhancer and gene activity (H3K27ac ChIP-seq and RNA-seq), enhancer connectivity (H3K27ac Hi-ChIP) as well as KLF4-centric chromatin looping (KLF4 Hi-ChIP) at different stages during acquisition of pluripotency.

Results: Integrative analysis of our results generated a reference map of stage-specific chromatin changes around KLF4 bound loci and established strong links with enhancer. rewiring and concordant transcriptional changes. Genetic manipulation of KLF4 binding from a PSC enhancer further supported the ability of KLF4 to function both as a transcriptional regulator and a chromatin organizer.

Conclusions: Our study offers novel insights into the intricate roles of a master regulator during cell fate transition.

overall_design: Mouse embryonic fibroblasts (MEFs) (Rosa26-M2rtTA/Col1a1-OKSM) induced with doxycycline (dox) in the presence of ascorbic acid. We collected bulk populations on day 3 after dox treatment, whereas at later stages, on day 6 and day 9, we sorted SSEA1 positive cells to enrich for cells on the trajectory towards induced pluripotency. Finally, we used pluripotent stem cells (PSCs) inclusive of embryonic stem cells (ESCs) as a reference point for established pluripotency. Biological replicates were collected to assay for chromatin accessibility (paired-end ATAC-seq), gene activity (single-end RNA-seq), H3K27ac ChIP-seq (single-end) in MEFs, day3, 6, 9 and PSCs. KLF4 binding (single-end ChIP-seq) was assessed in day3, 6, 9 and PSCs. KLF4/H3K27ac centric looping (paired-end Hi-ChIP) was studied in either day3, day6 and PSCs for KLF4 or MEFs and PSCs for H3K27ac.


title: Circadian transcriptome of soybean unifoliolate leaves

status: Public on Oct 15 2019

city: Ames

first: Wei

last: Wang

state: IA

address: 415 Bessey Hall

department: Department of Plant Pathology and Microbiology

institute: Iowa State University

summary: The goal of this study is to obtain the circadian transcriptome of soybean leaf and derive the time-indicating genes for the molecular timetable analysis.

overall_design: Soybean unifoliolate mRNA profiles of 11-day-old Williams82 seedlings under the circadian condition were generated by HiSeq in triplicates

first: Meina

last: Li

first: Ling