title: YB-1 RIP.chip - Co-immunoprecipitation of RNAs present in YB-1 containing RNP granules in LNCaP cells in FBS, CSS and DHT culture

first: Colleen

last: Nelson

summary: The transcription factor and RNA-interacting Y-box binding protein-1 (YB-1 protein, YBX1 gene) has gained interest as a prognostic biomarker and therapeutic target in various malignancies including prostate cancer. Using a custom prostate-cancer-focussed microarray platform, we have established a transcriptome-wide profile of YB-1 target transcripts in the androgen sensitive prostate cancer cell line LNCaP.

overall_design: RNA co-immunoprecipitation (RIP) identifying RNAs bound in YB-1 containing RNP granules (YBX1-IP) compared to total cellular input RNA (TT); in LNCaP prostate cancer cells under standard proliferative conditions (FBS), androgen deprivation (CSS) and after stimulation with dihydrotestosterone (DHT).

first: Anja

last: Rockstroh

first: Morgan

last: Pokorny

first: Chelsea

last: Walker

first: Melanie

last: Lehman

first: Stephen

last: McPherson


title: smartSHAPE: a low-input method for transcriptome-wide RNA structure probing uncovers RNA structure landscape in mouse colonic macrophages

status: Public on Mar 31 2021

city: Beijing

first: Meiling

last: Piao

address: Shuangqing Road 30

department: Life Science

country: China

institute: Tsinghua University

type: Expression profiling by high throughput sequencing

summary: Here, we report the development and application of smartSHAPE, a SHAPE-like RNA structure probing method that requires low amounts of input due to the largely reduced artefact signals of premature RT stops and increased efficiency of library construction. We used smartSHAPE to profile the global RNA secondary structures of two subtypes of mouse colonic macrophages upon inflammation, and provided evidence that RNA conformational changes at protein binding sites regulate gene expression and, in turn, immune responses. We predicted functional RNA structure elements based on smartSHAPE structure data, and discovered that PD-L1 contains a YRY-motif stem-loop structural element within the 3’UTR, which triggers RNA degradation mediated by Regnase-1.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: smartSHAPE was systematically evaluated by structure probing using different amounts of RNAs from HEK293T cells and applied to RNA structure probing in two subtypes of mouse colonic macrophages. To validate structure elements predicted based on structure data, we constructed RNA-Seq libraries in Reg1 KO or WT iBMDMs and uvCLAP libraries in Raw264.7 cells overexpressing FLAG-tagged Reg1 or GFP.

first: Pan

last: Li

first: Xiaoyu

last: Hu

first: Qiangfeng

last: Zhang


title: Identification of the Global miR-130a Targetome Reveals a Novel Role for TBL1XR1 in Hematopoietic Stem Cell Self-Renewal and t(8;21) AML [miR-130a OE]

status: Public on Mar 08 2022

city: Toronto

first: Alexander

middle: James

last: Murison

state: Ontario

address: 101 College Street, TMDT room 11-706

country: Canada

institute: University Health Network

summary: Gene expression profiling and proteome analysis of normal and malignant hematopoietic stem cells (HSC) point to shared core stemness properties. However, discordance between mRNA and protein signatures underscores an important role for post-transcriptional regulation by miRNAs in governing this critical nexus. Here, we identified miR-130a as a regulator of HSC self-renewal and differentiation. Enforced expression of miR-130a impaired lymphoid differentiation and expanded long-term HSC. Integration of protein mass spectrometry and chimeric AGO2 eCLIP-seq identified TBL1XR1 as a primary miR-130a target, whose loss of function phenocopied miR-130a overexpression. Moreover, we found that miR-130a is highly expressed in t(8;21) AML where it is critical for maintaining the oncogenic molecular program mediated by AML1-ETO. Our study establishes that identification of the comprehensive miRNA targetome within primary cells enables discovery of novel genes and molecular networks underpinning stemness properties of normal and leukemic cells.

overall_design:
Characterization of gene expression changes following enforced expression of miR-130a in human HSPC

>>>Submitter states: Raw data is being submitted separately to the EGA as we require controlled access for some data.<<<

first: Gabriela

last: Krivdova

first: Alex

first: John

middle: E

last: Dick


title: Border-like cells production mediated by SgPG1 proclaims aluminum resistance in Stylosanthes guianensis

status: Public on Jul 21 2021

city: Guang Zhou

first: Yan

last: Lin

state: Guang Dong

address: 广州市石榴岗路10号

department: Institute of Nanfan ＆Seed Industry

institute: Guangdong Academy of Sciences

summary: In order to investigate molecular mechanism underlying Reyan No. 2 BLCs development, transcriptomic analysis was conducted in Reyan No. 2 root tips at 24 and 48 h after germination. For each time course, three libraries were constructed and produced around 50 and 52 million raw reads, and 40.5 and 45.5 million clean reads, respectively. A total of 2036 genes, which were involved in various biological processes, such as the cell wall modification, exhibited differential expression patterns between 48 h and 24 h after germination. Among these differential expression genes (DEGs), 467 genes were up-regulated, while 1569 genes were down-regulated. Furthermore, a total of 90 DEGs were predicted to be involved in cell wall modification, with 16 genes up-regulated and 74 genes down-regulated. The qRT-PCR assay was further conducted to investigate the expression levels of 12 randomly selected DEGs, and results were consistent with the assay of transcriptomic analysis

overall_design: transcriptomic analysis was conducted in Reyan No. 2 root tips at 24, 48 and 72h after germination

first: Cuiyue

last: Liang

first: Jiang

last: Tian

first: Pandao

last: Liu

first: Zefei

last: Cai


title: Analysis of HeLa cell transcriptome changes induced by Indole-3-pyruvate and mIL4i1

status: Public on Mar 07 2021

city: Martinsried

first: Assa

last: Yeroslaviz

state: Bavaria

address: Am Klopferspitz 18

department: computational Biology

country: Germany

institute: Max-Planck-Institute for biochemistry

summary: We analyzed the mRNA changes induced by Indole-3-pyruvate (I3P) and WT or K351A mutant mIL4i1 in HeLa cells.

overall_design: mRNA sequencing of HeLa cells treated with 200 µM Indole-3-pyruvate (I3P) and 1 µg/ml WT or K351A mutant mIL4i1.

first: Leonie

last: Zeitler

first: Alessandra

last: Fiore

first: Rinho

last: Kim

first: Peter

middle: J

last: Murray


title: Characterization of ZFP541's occupency sites on genome in pachytene and diplotene spermatocytes

status: Public on Apr 16 2021

city: Hangzhou

first: Li

state: Zhejiang

address: Shilongshan ST #18, Xihu District

institute: Westlake University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: The DSB-machinery, which induces the programmed DNA double-strand breaks (DSBs) in leptotene and zygotene stages during meiosis, needs to be kept in silence after the initiation of pachytene stage to prevent the activation of DSB checkpoint that may lead to meiotic arrest or apoptosis of germ cells. However, the mechanisms underlying this repression remain largely unknown. Here, we report that ZFP541, a germ cell-specific zinc finger protein, is responsible for the suppression of DSBs formation at late pachytene. Lack of Zfp541 in mice leads to generation of DSBs in late pachytene spermatocytes by DSB formation related-proteins and causes male infertility due to meiotic failure. Plated-based scRNA-seq of Zfp541-/- spermatocytes revealed that ZFP541 negatively regulates many meiotic prophase genes, including genes for DSB formation and their upstream transcriptional regulators, in late pachytene spermatocytes. These results were confirmed by 10x single-cell RNA-seq data on spermatogenesis of Zfp541-/- testes, which suggested that Zfp541 is required for repressing the activation of pre-pachytene gene expression programs from early to late pachytene. ZFP541 ChIP-seq on pachytene and diplotene spermatocytes demonstrated that ZFP541 occupies the promoters of meiosis initiators (e.g., Meiosin and Rxra) and a subset of their downstream genes to repress their transcription, and thus prevent the reactivation of pre-pachytene gene expression programs in pachytene spermatocytes. Thus, our results not only revealed the role of ZFP541 in maintaining the repression of pre-pachytene transcriptional programs in pachytene spermatocytes but also provide new insight into the regulation of meiotic progression by timely turning off pre-pachytene genes.

overall_design: To identify ZFP541 genomic occupency sites during male meiotic prophase, ChIP-seq was performed on enriched pachytene and diplotene spermatocytes using STA-PUT method.

first: Jianze

last: Xu

first: Jianing

last: Gao


title: Effect of DDX3 inhibitors on CD4+ T cells

status: Public on Feb 26 2021

city: Rotterdam

first: Tokameh

last: Mahmoudi

address: Dr Molewaterplein 40

country: Netherlands

institute: Erasmus Medical Center

summary: An innovative approach to eliminate HIV-1-infected cells emerging out of latency, the major hurdle to HIV-1 cure, is to pharmacologically reactivate viral expression and concomitantly trigger intracellular pro-apoptotic pathways in order to selectively induce cell death (ICD) of infected cells, without reliance on the extracellular immune system. In this work we demonstrate the effect of DEAD-box polypeptide 3, X-Linked (DDX3) inhibitors on selectively inducing cell death in latent HIV-1-infected cell lines, primary CD4+ T cells and in CD4+ T cells from cART-suppressed people living with HIV-1 (PLWHIV). RNA sequencing analysis revealed that while overall gene expression was minimally dysregulated, DDX3 inhibition in independent donor CD4+ T cells led to significant downregulation of BIRC5 and HSPB1A, genes critical to cell survival during HIV-1 infection. We used single-cell FISH-Flow technology to characterise latency reversal and the contribution of viral RNA to inducing cell death; pharmacological targeting of DDX3 induced HIV-1 RNA expression, resulting in phosphorylation of IRF3, upregulation of IFNβ and selective induction of apoptosis in viral RNA-expressing CD4+ T cells from PLWHIV but not bystander cells. DDX3 inhibitor treatment of CD4+ T cells from PLWHIV in an in vitro culture model over five days resulted in an approximately 50% reduction of the inducible latent HIV-1 reservoir as determined by quantitation of CA HIV-1 RNA, by TILDA, as well as by FISH-Flow technology. Our data support the translation of DDX3 inhibitor class compounds into HIV-1 curative strategies and provide proof of concept for pharmacological reversal of latency coupled to induction of apoptosis towards elimination of the inducible reservoir.

overall_design: Primary CD4+ T cells from two healthy donors were mock treated with DMSO, with 2uM DDX3 inhibitor RK-33 or 1uM DDX3 inhibitor FH-1321. Cells were lysed and RNA was collected 4 hours and 18 hours post treatment and subjected to RNA-seq. The goal was to check what genes were differentially expressed upon DDX3 inhibition.

first: Tokamhe

first: Robert-Jan

last: Palstra

first: Wilfred

last: van IJcken

first: Shringar

last: Rao


title: Impaired antibacterial immune signaling and changes in the lung microbiome precedes secondary bacterial pneumonia in COVID-19 (scRNA-seq)

status: Public on Mar 03 2021

city: San Francisco

first: Beth

middle: Shoshana

last: Zha

state: CA

address: 400 Parnassus Ave

department: Medicine

country: USA

institute: University of California San Francisco

summary: We preformed a systems biological assessment of lower respiratory tract host immune responses and microbiome dynamics in COVD-19 patients, using bulk RNA-sequencing, single-cell RNA sequencing, and techniques, and microbiome analysis. Are focus was on differential gene expression in severe COVID-19 patients who developed ventilator associated pneumonia (VAP) during their course versus severe COVID-19 patients who did not develop VAP. We found early impairment in antibacterial immune signaling  in patients two or more weeks prior to the development of VAP, compared to COVID-19 patients who did not develop VAP. There was no signficant difference in viral load, but an association of disruption in lung microbiome by alpha and beta diversity metrics was also found.

overall_design:
Tracheal aspirate samples were processed for either bulk or single-cell RNA sequencing: 1) Bulk RNA-sequencing from 7 patients with severe COVID-19 patients who developed VAP, 10 COVID-19 patients who did not develop VAP, and 8 patients intubated but COVID-19 negative; 2) Single cell RNA-sequencing from 7 COVID-19 patients who developed VAP and 8 COVID-19 patients who did not develop VAP. Differential gene expression was analyzed for COVID-19 patients who developed VAP versus those who did not at: a) "early" time-point (median 2 days post intubation), 2) "late" time-point (median 2 days before VAP diagnosis), and when available c) differential gene expression also analyzed in those who developed VAP comparing the "early" and "late" time-points. Lastly, differential gene expression was  done in the bulk RNA-sequencing in COVID-19 positive versus control patients at the "early" time-point.
*** Raw data is not included in this GEO submission due to patient privacy concerns ***

first: Alexandra

last: Tsitsiklis

middle: S

first: Ashley

last: Byrne

first: Catherine

last: DeVoe

first: Sara

last: Sunshine


title: Impaired antibacterial immune signaling and changes in the lung microbiome precedes secondary bacterial pneumonia in COVID-19 (bulkRNA-seq)


title: Impaired antibacterial immune signaling and changes in the lung microbiome precedes secondary bacterial pneumonia in COVID-19

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

overall_design: Refer to individual Series


title: Transcriptome analysis of Huh7 cells upon Chikungunya virus infection and capsid transfection reveals regulation of distinct cellular and metabolic pathways

status: Public on Mar 16 2021

city: Delhi

first: NITIKA

last: GAURAV

state: Delhi

address: INDIAN INSTITUTE OF TECHNOLOGY DELHI -110016, INDIA

department: Kusuma School of Biological Sciences

country: India

institute: INDIAN INSTITUTE OF TECHNOLOGY DELHI

summary: The purpose of this study is to compare the gene profiles of chikungunya virus (CHIKV) capsid transfected and CHIKV infected Huh7 cells to identify the genes differentially expressed in the presence of the capsid protein during CHIKV infection

overall_design: RNA-sequencing of Chikugunya virus capsid gene transfected, Chikungunya virus infected hepatocarcinoma cells. Transcriptome profile of mock-transfected (empty pEGFPN1 vector plasmid DNA) cells was used as a control for the study

first: Nitika

last: Gaurav

first: Ashok

last: Kumar Patel


title: Human B cell response to influenza vaccination

status: Public on Aug 13 2020

city: New Haven

first: Steven

last: Kleinstein

state: Ct

address: 300 George St.

department: Pathology

institute: Yale University

summary: We used ultrasound-guided fine needle aspiration of the draining axillary lymph nodes to interrogate influenza vaccine-induced GC responses in humans.

overall_design: Examination of 21 single-cell RNA-seq samples from PBMC and lymph node taken at multiple time points pre- and post-vaccination.

first: Jackson

last: Turner

first: Julian

middle: Q

last: Zhou

first: Julianna

last: Han

first: Aaron

last: Schmitz

first: Amena

middle: A

last: Rizk

first: Wafaa

middle: B

last: Al-Soussi

first: Tingting

last: Lei

first: Mostafa

last: Amor

first: Ketherine

middle: M

last: McIntire

first: Philip

last: Meade

first: Shirin

last: Strohmeier

first: Rafael

middle: I

last: Brent

first: Bassem

last: Mohammed

middle: T

last: Richey

first: Alem

last: Haile

first: Yuhe

middle: R

last: Yang

first: Michael

middle: K

last: Klebert

first: Teresa

last: Suessen

first: Sharlene

last: Teefey

first: Rachel

last: Presti

first: Florian

last: Krammer

middle: H

first: Andrew

last: Ward

first: Ali

last: Ellebedy


title: FGF9 Promotes Mouse Spermatogonial Stem Cell Proliferation Mediated by p38 MAPK Signaling

status: Public on Oct 26 2020

city: Philadelphia

first: Eoin

middle: Christopher

last: Whelan

state: PA

address: 3800 Spruce St

department: Biomedical Sciences

institute: University of Pennsylvania School of Veterinary Medicine


title: FGF9 Promotes Mouse Spermatogonial Stem Cell Proliferation Mediated by p38 MAPK Signaling [single-cell RNA-seq]

summary:
Objectives: Fibroblast growth factor 9 (FGF9) is expressed by somatic cells in the seminiferous tubules, yet little information exists about its role in regulating spermatogonial stem cells (SSCs).
Materials and Methods: Fgf9 overexpression lentivirus was injected into mouse testes, and PLZF immunostaining was performed to investigate the effect of FGF9 on spermatogonia in vivo. Effect of FGF9 on SSCs was detected by transplanting cultured germ cells into tubules of testes. RNA-seq of bulk RNA and single-cell was performed to explore FGF9 working mechanisms. SB203580 was used to disrupt p38 MAPK pathway. p38 MAPK protein expression was detected by western blot and qPCR was performed to determine different gene expression. Small interfering RNA (siRNA) was used to knock down Etv5 gene expression in germ cells.
Results: Overexpression of Fgf9 in vivo resulted in arrested spermatogenesis and accumulation of undifferentiated spermatogonia. Exposure of germ cell cultures to FGF9 resulted in larger numbers of SSCs over time. Inhibition of p38 MAPK phosphorylation negated the SSC growth advantage provided by FGF9. Etv5 and Bcl6b gene expression was enhanced by FGF9 treatment. Gene knockdown of Etv5 disrupted the growth effect of FGF9 in cultured SSCs along with downstream expression of Bcl6b.
Conclusions: Taken together, this data indicates that FGF9 is an important regulator of SSC proliferation, operating through p38 MAPK phosphorylation and upregulating Etv5 and Bcl6b in turn.

overall_design: single-cell RNA-seq: 1 biological replicate of cultured germ cells with one of the following treatments: control (0ng/ml FGF) and FGF9-treated (20ng/ml FGF9) for 48 hours.

first: Fan

middle: C

first: Xuebing

last: Guan

first: Bingquan

last: Deng

first: Shu

last: Wang

first: Jiachen

last: Sun

first: Mary

last: Avarbock

first: Xin

last: Wu

first: Ralph

middle: L

last: Brinster


title: Determining miR-221/222-3p targets in B cells activated with aCD40 IL4 IL21 in vitro

status: Public on Jan 01 2021

first: Eric

middle: Joseph

last: Wigton

address: 500 Parnassus Ave.

department: Immunology

institute: UCSF

summary: compared miR-221/222-3p deficient (KO) and WT (Flox) activated B cell mRNAseq and Ago2-HITSCLIP to determine mRNA targets of this miRNA cluster

overall_design:
Gene expression fo KO and Flox cells and differential Ago2-HITSCLIP
Contributor: UCSF Functional Genomics Core

first: Suparna

last: Roy

first: K

last: Ansel


title: FGF9 Promotes Mouse Spermatogonial Stem Cell Proliferation Mediated by p38 MAPK Signaling [bulk RNA-seq]

overall_design: bulk RNA seq: 4 biological replicates of cultured germ cells (labelled s6, s7, s8 and s9) of each of the following treatments: control (0ng/ml FGF), 1ng/ml FGF9, 20ng/ml FGF9 and 1ng/ml FGF2)

last: Yang


title: Establishment of induced pluripotent stem cells from common marmoset fibroblasts by RNA-based reprogramming

status: Public on Jun 12 2020

city: Shinjuku

first: Sho

last: Yoshimatsu

state: Tokyo

address: 35 Shinanomachi

department: Physiology

country: Japan

institute: Keio University School of Medicine

summary: The common marmoset (marmoset; Callithrix jacchus) shows anatomical and physiological features that are in common with humans. Establishing induced pluripotent stem cells (iPSCs) from marmosets holds promise for enhancing the utility of the animal model for biomedical and preclinical studies. However, in spite of the presence of some previous reports on marmoset iPSCs, the reprogramming technology in marmosets is still under development. In particular, the efficacy of RNA-based reprogramming has not been thoroughly investigated. In this study, we attempted RNA-based reprogramming for deriving iPSCs from marmoset fibroblasts. Although we failed to derive iPSC colonies from marmoset fibroblasts by using a conventional RNA-based reprogramming method previously validated in human fibroblasts, we succeeded in deriving colony-forming cells with a modified induction medium supplemented with a novel set of small molecules. Importantly, following one-week culture of the colony-forming cells in conventional embryonic stem cell (ESC) medium, we obtained iPSCs which express endogenous pluripotent markers and show a differentiation potential into all three germ layers. Taken together, our results indicate that RNA-based reprogramming, which is valuable for deriving transgene-free iPSCs, is applicable to marmosets.

overall_design: RNA seq of marmoset fibroblasts, ESCs and iPSCs

first: Mayutaka

last: Nakajima

first: Hideyuki

last: Okano


title: Cell profiling of acute kidney injury reveals conserved cellular responses to injury

status: Public on Jun 08 2020

city: Kyoto

first: Tetsuro

last: Kusaba

state: Kyoto

address: 465 Kajii-cho, Kamigyo-ku

department: Department of Nephrology

institute: Graduate School of Medical Science, Kyoto Prefectural University of Medicine

summary: After acute kidney injury (AKI), patients either recover or alternatively develop fibrosis and chronic kidney disease. Interactions between injured epithelia, stroma and inflammatory cells determine whether kidneys repair or undergo fibrosis, but the molecular events that drive these processes are poorly understood. Here, we use single nucleus RNA sequencing of a mouse model of AKI to characterize cell states during repair from acute injury. We identify a distinct proinflammatory and profibrotic proximal tubule cell state that fails to repair. Deconvolution of bulk RNA-seq datasets indicates that this “failed-repair proximal tubule cell” or FR-PTC, state can be detected in other models of kidney injury, increasing in the aging rat kidney and over time in human kidney allografts. We also describe dynamic intercellular communication networks and discern transcriptional pathways driving successful vs. failed repair.  Our study provides a detailed description of cellular responses after injury and suggests that the FR-PTC state may represent a therapeutic target to improve repair.

overall_design: 10X Chromium was used to profile mouse AKI kidneys

first: Benjamin

middle: D

last: Humphreys


title: Thyroid hormone enhances estrogen-mediated proliferation and cell cycle regulatory pathways in steroid receptor-positive breast Cancer

status: Public on May 14 2020

city: Cleveland

first: Hyunmin

last: Kim

state: Ohio

address: 10900 Euclid Ave.

department: Department of Genetics and Genome Sciences

institute: Case Western Reserve University

summary: Here, we treated a nove ER-positive PDX (UCD12) supplemented with estrogen (E2) with or without thyroid hormone (TH) and/or tamoxifen (Tam). Each treatment cohort (E2 alone, E2 + TH, E2 + Tam, E2+ TH+Tam) tumor growth over time was monitored. Tumors treated with TH continued to grow more that E2 alone. Tamoxifen blocked E2-mediated tumor growth, however in the presence of TH this was not seen. This analysis identified thyroid hormone as a potential driver of tumor progression in the context of estrogen receptor positive PDX tumor model.

first: Reema

last: Wahdan-Alaswad

first: Ann

last: Thor

first: Aik-Choon

last: Tan


title: Natural display of nuclear-encoded RNA on the cell surface and its impact on cell interaction [Surface-FISHSeq]

status: Public on Aug 11 2020

city: San Diego

first: Sheng

last: Zhong

email: szhong@ucsd.edu, szhong.ucsd@gmail.com

address: 5556 Caminito Mundano

institute: UCSD

summary: Compared to proteins, glycans, and lipids, much less is known about RNAs on the cell surface. We developed a series of technologies to test for any nuclear-encoded RNAs that are stably attached to the cell surface and exposed to the extracellular space, hereafter called membrane-associated extracellular RNAs (maxRNAs). We visualized maxRNAs on the cell surface, sequenced selected maxRNAs, and validated two maxRNAs by RNA fluorescence in situ hybridization. To test for cell-type specificity of maxRNA, we used randomized antisense oligos to hybridize to single-stranded transcripts exposed on the surface of human peripheral blood mononuclear cells (PBMCs). Combining this strategy with imaging flow cytometry, single-cell RNA sequencing, and maxRNA sequencing, we identified monocyte as the major type of maxRNA+ PBMCs and prioritized 11 maxRNAs for functional tests. Extracellular hybridization of antisense oligos to the cell surface-exposed fragments of FNDC3B and CTSS transcripts inhibited monocyte adhesion to vascular endothelial cells. Collectively, these data highlight maxRNAs as a functional component of the cell surface, suggesting an expanded role for RNA in cell-cell interaction and communication.

overall_design: Surface RNA sequencing using Surface-FISHSeq on human PBMCs.

first: Norman

last: Huang

first: Xiaochen

last: Fan

first: Kathia

middle: Z

last: Rivera

first: Tri

last: Nguyen

first: Jiarong

last: Zhou

first: Yingjun

last: Luo

first: Ronnie

last: Fang

first: Zhen

last: Chen

first: Liangfang

last: Zhang


title: Natural display of nuclear-encoded RNA on the cell surface and its impact on cell interaction


title: Microbial single-cell RNA sequencing by split-pool barcoding

status: Public on Jul 03 2020

city: Seattle

first: Anna

last: Kuchina

state: Washington

address: 185 Stevens Way, Paul Allen Center – Room AE100R

department: Electrical and Computer Engineering

institute: University of Washington

summary: We introduce microSPLiT, a low cost and high-throughput single-cell RNA-sequencing method for gram-negative and gram-positive bacteria. We applied microSPLiT to >25,000 Bacillus subtilis cells sampled at different growth stages, creating a detailed atlas of changes in metabolism and lifestyle. We not only retrieve detailed gene expression profiles associated with known, but rare, states such as competence and PBSX prophage induction, but also identify novel and unexpected gene expression states including a heterogeneous activation of a niche metabolic pathway (myo-inositol catabolism) in a subpopulation of cells.

sample_organism:
Escherichia coli
Bacillus subtilis

platform_organism:
Escherichia coli
Bacillus subtilis

overall_design: Single-cell RNA-seq (microSPLiT) was used to sample ten optical density (OD) points along the growth curve of the laboratory strain PY79 in LB medium ranging from OD0.5  to 6.0, with one replicate of 4 OD points. For validation of the method, we grew E. coli MW1255 and B. subtilis PY79 cells to OD600=0.5 and subjected half of each culture to a brief 47°C heat-shock. We performed a microSPLiT experiment on both samples, using the first barcode as a sample identifier.

first: Leandra

last: Brettner


title: Mesenchyme Subset from IPF Cell Atlas

status: Public on Mar 16 2020

first: Tatsuya

last: Tsukui

address: 555 Mission Bay Blvd South, 282

summary: Single Cell RNAseq of lung mesenchymal cells in fibrotic and control lung

overall_design:
Anlaysis and fibrotic and control lung mesenchyme populations
Note from submitter: In light of patients' privacy, we are currently working on depositing fastq files to a platform which has controlled access mechanisms.

first: Tsukui

last: Tatsuya

first: Adams

last: Taylor

first: Sheppard

last: Dean

first: Kaminski

last: Naftali

first: Rosas

last: Ivan


title: Natural display of nuclear-encoded RNA on the cell surface and its impact on cell interaction [surfaceSeq]

first: Sheng

last: Zhong

overall_design: Targeted RNA sequencing using Surface-Seq on EL4 cell line

first: Norman

last: Huang

first: Zhangming

last: Yan


title: Deconvolution of Cell Type-Specific Drug Responses in Human Tumor Tissue with Single-Cell RNA-seq

status: Public on Apr 18 2020

city: New York

first: Peter

last: Sims

state: NY

address: 3960 Broadway, Lasker 203AC

institute: Columbia University

summary: Precision oncology requires the timely selection of effective drugs or drug combinations for individual patients. The ideal platform would enable rapid screening of cell type-specific drug sensitivities directly in patient tumor tissue and reveal strategies to overcome intratumoral heterogeneity. Here we combine multiplexed drug perturbation in acute slice culture from freshly resected tumors with single-cell RNA sequencing (scRNA-seq) to profile transcriptome-wide drug responses in individual patients. We applied this approach to glioblastoma (GBM) and demonstrated that acute slice cultures recapitulate the cellular and molecular features of the originating tumor tissue. Detailed investigation of etoposide, a topoisomerase poison, and the histone deacetylase (HDAC) inhibitor Panobinostat in acute slice cultures revealed cell type-specific responses across multiple patients, including unexpected effects on the immune microenvironment. We anticipate that this approach will facilitate rapid, personalized drug screening to identify effective therapies for solid tumors.

overall_design: Performed single-cell RNA-seq on biopsies of human glioma surgical specimens and on acute slice cultures of human glioma surgical specimens treated with various drugs

first: Wenting

last: Zhao

first: Athanassios

last: Dovas

first: Eleonora

middle: F

last: Spinazzi

last: Canoll


title: Natural display of nuclear-encoded RNA on the cell surface and its impact on cell interaction [Single Cell RNA-seq]

overall_design: Single Cell RNA seq on FACS PBMCs for maxRNAs

first: Xiaochen

last: Fan

first: Kathia

last: Rivera

first: Tri

last: Nguyen

first: Jiarong

last: Zhou

first: Yingjun

last: Luo

first: Ronnie

last: Fang

first: Zhen

last: Chen

last: Zhang


title: The response to the growth inhibitory activity of bone morphogenetic protein 4 in human glioblastoma cell lines is heterogeneous and dependent on SOX2

status: Public on Jan 21 2020

city: Uppsala

first: Bengt

last: Westermark

address: Dag Hammarskjölds väg 20

country: Sweden

institute: Uppsala University

summary: Glioblastoma multiforme (GBM) continues to have a dismal prognosis. Even though detailed information on the genetic aberrations in cell signaling and cell cycle checkpoint control is available, no effective targeted treatment has been developed. Despite the advanced molecular defects, glioblastoma cells may have remnants of normal growth inhibitory pathways, such as the bone morphogenetic protein (BMP) signaling pathway. We have evaluated the growth inhibitory effect of bone morphogenetic protein 4 (BMP4) across a broad spectrum of patient samples, using a panel of 40 human glioblastoma initiating cell (GIC) cultures. A wide range of responsiveness was observed. BMP4 response was positively correlated with a proneural mRNA expression profile, high SOX2 activity, and BMP4-dependent upregulation of genes associated with inhibition of the MAPK pathway, as demonstrated by gene set enrichment analysis (GSEA). BMP4 response in sensitive cells was mediated by the canonical BMP receptor pathway involving SMAD1/5 phosphorylation and SMAD4 expression. SOX2 was consistently down regulated in BMP4-treated cells. Forced expression of SOX2 attenuated the BMP4 response including a reduced upregulation om MAPK inhibitory genes, implying a functional relationship between SOX2 down regulation and responsiveness. The results show an extensive heterogeneity in BMP4 responsiveness among GICs, and identify a BMP4 sensitive subgroup, in which SOX2 is a mediator of the response.

overall_design: Human glioblastoma cell cultures with and without a Sox2 lentiviral vector were kept +/-BMP4 for 14 days before proceeding to RNA seq.

first: Erika

last: Dalmo

first: Patrik

last: Johansson

first: Maria

last: Niklasson

first: Ida

last: Gustavsson

first: Sven

last: Nelander


title: Human liver organoids; a patient-derived primary model for HBV Infection, Replication and Related Hepatocellular Carcinoma

status: Public on Feb 20 2020

first: Tokameh

last: Mahmoudi

summary: Here we interrogate the potential of human liver organoids as a platform for modeling HBV infection and related tumorigenesis. We show that organoids derived from HBV-infected patients display an aberrant early cancer gene signature, which clusters with the HCC cohort on the TCGA LIHC dataset and away from healthy liver tissue.

overall_design: Total RNA obtained from HBV infected patient-derived or healthy donor liver organoids

first: Elisa

last: de Crignis

first: Panagiotis

last: Moulos

first: Robert-Jan

last: Palstra

first: Pantelis

last: Hatzis


title: Single cell RNA sequencing of adult regenerating mouse digit tips

status: Public on Feb 24 2020

city: Boston

first: Jessica

last: Lehoczky

state: MA

address: 60 Fenwood Rd.

department: Orthopedic Surgery

institute: Brigham and Women's Hospital

summary: Innate regeneration following digit tip amputation is one of the few examples of epimorphic regeneration in mammals. Digit tip regeneration is mediated by the blastema, the same structure invoked during limb regeneration in some lower vertebrates. By genetic lineage analyses in mice, the digit tip blastema has been defined as a population of heterogeneous, lineage restructed progenitor cells. These previous studies, however, do not comprehensively evaluate blastema heterogeneity or address lineage restruction of closely related cell types. Here we report single cell RNA sequencing of over 38,000 cells from mouse digit tip blastemas and unamputated control digit tips and generate an atlas of the cell types participating in digit tip regeneration.

overall_design: Adult wildtype FVB/NJ mice used to generate 5 distinct datasets throughout digit tip regeneration. The five stages are: unamputated (control), 11 days post-amputation, 12 days post-amputation, 14 days post-amputation, and 17 days post-amputation.


title: Phenotypic states of leptomeningeal metastasis

city: Leuven

first: Jan

last: Remsik

address: Campus Gasthuisberg, Herestraat 49

department: Center for Cancer Biology

country: Belgium

institute: VIB

summary: Leptomeningeal metastasis (LM), or spread of cancer cells into the cerebrospinal fluid, is characterized by a rapid onset of debilitating neurological symptoms and markedly bleak prognosis. The lack of reproducible in vitro and in vivo models has prevented development of novel, LM-specific therapies. Although LM allows for longitudinal sampling of floating cancer cells with a spinal tap, attempts to culture patient-derived leptomeningeal cancer cells have not been successful. We therefore employ leptomeningeal derivatives of human breast and lung cancer cell lines that reproduce both floating and adherent phenotypes of human LM in vivo and in vitro. We introduce a trypsin/EDTA-based fractionation method to reliably separate the two cell subsets and demonstrate that in vitro cultured floating cells have decreased proliferation rate, lower ATP content, and are enriched in distinct metabolic signatures.  Long-term fractionation and transcriptomic analysis suggest a high degree plasticity between the two phenotypes in vitro. Floating cells colonize mouse leptomeninges more rapidly and associate with shortened survival. In addition, patients harboring LM diagnosed with CSF disease alone succumbed to the disease earlier than patients with adherent (MRI-positive) disease. Together, these data support mechanistic evidence of a metabolic adaptation that allows cancer cells to thrive in their natural environment but leads to death in vitro.

overall_design: Transcripomic analysis of floating and adherent leptomeningeal metastatic cells

first: Adrienne

last: Boire


title: Phosphorylated Lamin A/C in the nuclear interior binds active enhancers associated with abnormal transcription in progeria

status: Public on Feb 15 2020

city: Cincinnati

first: Kohta

last: Ikegami

state: OH

address: 240 Albert Sabin Way, Cincinnati, OH 45229

department: Division of Molecular Cardiovascular Biology

institute: Cincinnati Children's Hospital Medical Center

overall_design: Refer to individual Series


title: RNA-Seq in HEK293T human cells

status: Public on Dec 03 2019

city: Moscow

first: Nickolai

last: Tchurikov

address: 32, Vavilova str.

department: Department of Epigenetic Mechanisms of Gene Expression Regulation

country: Russia

institute: Engelhardt Institute of Molecular Biology

summary: RNA-Seq procedure was used for analysis of expression in HEK293T cells. Cells were separately lysed with Trizol reagent (Invotrogen). Total RNA was extracted from cell lysed with Trizol reagent and PureLink RNA Micro Kit (Invitrogen) according to manufacture instruction. RNA quality was checked with  BioAnalyser and  RNA 6000 Nano Kit (Agilent). Poly(A)+ RNA was purified with Dynabeads® mRNA Purification Kit (Ambion). Illumina library was prepared from poly(A)+RNA with NEBNextNEBNext® Ultra™II RNA Library Prep Kit for Illumina® (NEB) according to manual. Sequencing was performed on HiSeq1500 with 50 bp read length. At least 10 millions of reads were generated for each sample.

overall_design: Analysis of HEK293T gene expression levels by RNA-Seq.

first: Yuri

middle: V

last: Kravatsky

first: Olga

last: Kretova


title: The timing mechanism for the first lineage specification in the mouse embryo

status: Public on Dec 30 2019

city: Beijing

first: Jie

state: Beijing

address: Tsinghua University

department: Basic Medical Sciences, School of Medicine

institute: Tsinghua University

summary: The transition from totipotency to pluripotency and subsequent differentiation in the mammalian embryo segregates embryonic and extra-embryonic progenitor cells. Despite its central importance, it remains entirely unknown how the timing of this major process is regulated. Here, we uncover that Tfap2c and Tead4 mediated transcriptional activity work in concert with the Rho GTPase mediated activation of actomyosin at the 8-cell stage as the upstream factors that trigger cell polarization and hence the first cell fate segregation in the mouse embryo. We show that they act together to control the establishment of cell polarisation, the activation of polarity dependent Hippo signalling, and the early expression of transcription factors required for the differentiation of the first extra-embryonic lineage. These results define the key step in the transition from totipotency to pluripotency and its relationship to the first cell fate specification event in the mouse embryo.

overall_design: Bulk cell (~80cells) RNA sequencing of embryos injected with dsRNA targeting GFP (control),Tfap2c, Tead4, or Tfap2c and Tead4.

first: Magdalena

last: Zernicka-Goetz

first: Peizhe

last: Wang

first: Meng

last: Zhu


title: Transcriptional profiling reveals differential response to heat stress in Tharparker and Crossbred Cattle

status: Public on Nov 02 2019

city: Karnal

first: Ravi Kumar

last: Gandham

state: Haryana

address: Makrampur

institute: ICAR-NBAGR

summary: We have used RNA-Seq to examine  expression profiles of PBMCs  from Crossbred and Thraparkar under heat Stress.

overall_design: Tharparkar and Crossbred were subjected to heat for a period of 7 days. RNA was  isolated from PBMCs  of both genetic groups (n=5 for each genetic group),  before ( 0 days )  and post heat stress (7 day ). The pooled RNA samples of each genetic group for both the individual time points were subjected to illumina sequencing .

first: Smita

last: Gupta

first: Pragya

last: Singh

first: Archana

last: Saxena

first: Anshul

last: Varshney

first: Waseem

last: Malla

first: Vinay

last: Verma

first: Amit

last: Sahu

first: Puneet

last: Kumar

first: Shikha

first: Aruna

last: Pandey

first: Raja

last: Khan

first: Neelima

last: Hosamani

first: Manas

last: Praharaj

first: Shakti

first: Gyanendra

first: Ravi

first: Ashok

last: Tiwari

first: Shweta

last: Sharma


title: BACH1 alters the expression of EMT-related genes to promote metastasis in pancreatic cancer

status: Public on Dec 18 2019

city: Sendai

first: Mitsuyo

last: Matsumoto

address: 2-1 Seiryo-machi Aoba-ku

department: Biochemistry

institute: Tohoku university school of medicine

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


title: ChIP-seq reported in "Phosphorylated Lamin A/C in the nuclear interior binds active enhancers associated with abnormal transcription in progeria"

first: Kohta

last: Ikegami

summary: LMNA encodes nuclear Lamin A/C that tethers lamina-associated domains (LADs) to the nuclear periphery. Mutations in LMNA cause degenerative disorders including the premature aging disorder Hutchinson-Gilford progeria, but the mechanisms are unknown. We report that Ser22-phosphorylated (pS22) Lamin A/C was localized to the nuclear interior in human fibroblasts throughout the cell cycle. pS22-Lamin A/C interacted with a subset of putative active enhancers, not LADs, at locations co-bound by the transcriptional activator c-Jun. In progeria-patient fibroblasts, a subset of pS22-Lamin A/C-binding sites were lost whereas new pS22-Lamin A/C-binding sites emerged in normally quiescent loci. New pS22-Lamin A/C binding was accompanied by increased histone acetylation, increased c-Jun binding, and upregulation of nearby genes implicated in progeria pathophysiology. These results suggest that Lamin A/C regulates gene expression by enhancer binding. Disruption of the gene regulatory rather than LAD tethering function of Lamin A/C presents a novel mechanism for disorders caused by LMNA mutations.

overall_design: The aims of this project are to 1) identify the locations of the human genome associated with Ser22-phosphorylated LMNA by ChIP-seq in normal and progeria-patient cells; 2) define the chromatin characteristics of  Ser22-phosphorylated LMNA-associated sites by histone ChIP-seq and ATAC-seq; and 3) identify genes dysregulated in progeria-patient cells by RNA-seq.


title: Exon array data from neuromuscular junction (NMJ) in mouse skeletal muscle.

status: Public on Dec 12 2019

city: nagoya

first: guiying

last: chen

address: 65 Tsurumai-cho, Showa-ku

institute: nagoya university

summary: The RNA from NMJ and non-NMJs samples were examined using microarray analysis with of identifying novel regulatory genes that are preferentially expressed in the synaptic regions of the isolated muscle fibers.

overall_design: We Isolated RNA from NMJs and non-NMJs region of mouse tibialis anterior (TA) muscle fibers by Laser capture microdissection. Then samples were examined exonarray analysis.

first: Guiying

last: Chen

first: Akio

last: Masuda

first: Jun-ichi

last: Takeda

first: Kinji

last: Ohno


title: BACH1 alters the expression of EMT-related genes to promote metastasis in pancreatic cancer [RNA-seq]

summary: BTB and CNC homology 1 (BACH1) has been implicated in RAS-driven tumor formation. We focused on the role of BACH1 in Pancreatic ductal adenocarcinoma (PDAC), more than 90% of which have KRAS mutation. BACH1  directly or indirectly repressed the expression of genes for epithelial cell adhesion in AsPC-1 cells and SW1990. Knockdown and overexpression of BACH1 in PDAC cell lines indicated that BACH1 promoted cell migration and invasion in part by reducing E-cadherin expression.

overall_design: Search of BACH1 target genes in pancreatic cancer cells

first: Masaki

last: Sato

first: Ryo

last: Funayama

first: Keiko

last: Nakayama

first: Kazuhiko

last: Igarashi


title: Transcriptomic alterations in ferroptotic murine embryonic fibroblasts

status: Public on Nov 15 2019

summary: Alterations of metabolic and biological processes occur in ferroptotic cells. We analyzed transcriptional responses of murine embryonic fibroblasts (MEFs) exposed to a ferroptosis inducer erastin. We found that  a set of genes related to protection against oxidative stress was induced upon ferroptosis and Bach1 promoted ferroptosis by repressing a set of these genes involved in synthesis of glutathione or metabolism of intracellular labile iron. Our findings suggests that ferroptosis is programmed at transcriptional level and Bach1 works as a controller in setting a threshold of ferroptosis.

overall_design: Total RNA was extracted from MEF after 24-hour treatment with DMSO or 3 µM Erastin. This experiment was triplicated, and the resulting six samples were applied to RNA-sequencing.

first: Hironari

last: Nishizawa


title: Genome-wide profile of cJun and p27 and gene expression profile in breast cancer cells

status: Public on Mar 19 2019

city: Miami

first: Joyce

middle: Marie

last: Slingerland

address: 1501 NW 10th Avenue

institute: University of Miami


title: Gene expression profile in breast cancer cells

summary: We report the gene expression patterns in MDA-MB-231 (a line selected for low metastatic ability), MDA-MB-231-1833 (its bone-tropic metastatic derivative line), MDA-MB-231p27CK-DD (a phosphomimetic cell line), MDA-MB-231-1833shp27 (p27 knockdown cell line), MDA-MB-231-1833PF1502 (PI3K inhibitor treatment). It shows that the gene expression pattern are regulated in a p27 phosphorylation-dependent manner.

overall_design: Examination in 5 cell types.

first: Hyunho

last: Yoon


title: Genome-wide profile of cJun and p27 in breast cancer cells

summary: We report the genome-wide profile of cJun and p27 in _231 (a line selected for low metastatic ability), _231-1833 (its bone-tropic metastatic derivative line), _231p27CK-DD (a phosphomimetic cell line), and _231-1833shp27 (p27 knockdown cell line). It shows that cJun and p27 broadly binds to genomic DNA and their bindings are regulated by p27 phosphorylation-dependent patterns.

overall_design: Examination of 2 different molecules, cJun and p27 in 4 cell types.


title: BACH1 alters the expression of EMT-related genes to promote metastasis in pancreatic cancer [ChIP-Seq]


title: Genome-wide contacts of rDNA units detected by 4C procedure in human genome

status: Public on Dec 05 2019

first: Nickolai

last: Tchurikov


title: An ultra high-throughput method for single-cell joint analysis of open chromatin and transcriptome

status: Public on Nov 01 2019

first: Zhu

last: Chenxu

email: cxzhu@pku.edu.cn, czhu@nygenome.org

state: New York

address: 101 Avenue of the Americas

institute: New York Genome Center

summary:
Simultaneous profiling of transcriptome and chromatin accessibility within single cells is a powerful approach to dissect gene regulatory programs in complex tissues. However, the current tools are limited by modest throughput. We now describe an ultra high-throughput method, Paired-seq, for parallel analysis of transcriptome and accessible chromatin in millions of single cells. We demonstrate the utility of Paired-seq for analyzing the dynamic and cell-type specific gene regulatory programs in complex tissues, by applying it to mouse adult cerebral cortex and fetal forebrain. The joint profiles of a large number of single cells allowed us to deconvolute the transcriptome and open chromatin landscapes in the major cell types within these brain tissues, infer putative target genes of candidate enhancers, and reconstruct the trajectory of cellular lineages within the developing forebrain.

*** Processed files of brain cells can be downloaded from: https://github.com/cxzhu/Paired-seq/tree/master/matrices/

 - Compressed files for cell-gene/bin-counts matrices of Adult Cerebral Cortex cells only.
 - Compressed files for cell-gene/bin-counts matrices of merged Fetal and Adult brain cells.
 - Metadata files of sequenced cells are inside the compressed files.
 - Cluster/Ident to Annotation information available from the GitHub page.

overall_design: Combined analysis of RNA and accessible chromatin in single-cells.

first: Chenxu

last: Zhu

first: Miao

last: Yu

first: Bing

last: Ren


title: Dynamic molecular monitoring reveals that SWI/SNF mutations mediate resistance to ibrutinib plus venetoclax in mantle cell lymphoma [RNA-Seq]

status: Public on Nov 21 2018

city: Melbourne

first: Mark

last: Dawson

address: 305 Grattan Street

department: Cancer Research

country: Australia

institute: Peter MacCallum Cancer Centre

summary: Ibrutinib plus venetoclax is a highly effective combination in mantle cell lymphoma. However, strategies to enable the evaluation of therapeutic response are required. Our prospective analyses of patients within the AIM study revealed genomic profiles that clearly dichotomized responders and non-responders. Mutations in ATM were present in most patients who achieved a complete response, while chromosome 9p21.1-p24.3 loss and/or mutations in components of the SWI/SNF chromatin remodeling complex were present in all patients with primary resistance and 2/3 patients with relapsed disease. Circulating tumor DNA analysis revealed that these alterations could be dynamically monitored providing concurrent information on treatment response and tumour evolution. Functional modeling demonstrated that compromise of the SWI/SNF complex facilitated transcriptional upregulation of BCL2L1 (Bcl-xL) providing a selective advantage against ibrutinib plus venetoclax. Together these data highlight important insights into the molecular basis of therapeutic response and provide a paradigm for real-time assessment of innovative targeted therapies.

overall_design: Examining the effect of SMARCA4 knockdown and the response to ibrutinib plus venetoclax in mantle cell lymphoma cell lines Z-138

first: Sarah-Jane


title: RNAseq analysis of total skin from control or JunBdep mice

status: Public on Oct 16 2019

city: Madrid

first: Kevin

last: Troulé

state: Madrid

address: Melchor Fernandez Almagro, 3

country: Spain

institute: SPANISH NATIONAL CANCER CENTER

summary: RNA was isolated from total skin of control or JunBdep mice at 6-7 months of age when the skin of mutant mice resemble Atopic Dermatitis.

overall_design: 3 control and 3 mutant mice were included in the experiment. Mice were littermates.

first: Ozge

last: Uluckan

first: Osvaldo

last: Graña


title: TALEN Editing of APP Gene in WiCell WA09 (H9) Cells to directly express amyloid beta proteins

status: Public on Dec 31 2018

city: Duarte

first: Paul

middle: M.

last: Salvaterra

address: 1500 E. Duarte Rd.

department: Stem Cell and Developmental Biology

institute: Beckman Research Institute of the City of Hope

summary: We used TALEN editing to insert a direct expression cassette of either Abeta42 or Abeta 40 eliminating any requirement for amyloidogenic processing of APP to produce Abeta.

overall_design: WiCell WA09 human embryonic stem cells were edited to directly express Abeta42 or Abeta40 under control of the normal APP transcriptional regulatory DNA. Two independently isolated clones were screened, verified by qRT-PCR for insertions and used to assess Alzheimer's like phenotypes in differentiated neurons.


title: RNA-seq analyses of kdm5[A512P] and enzymatically inactive kdm5[JmjC*] in adult heads

city: Bronx

first: Julie

last: Secombe

address: 1300 Morris park ave

department: Genetics

institute: Albert Einstein College of Medicine

summary: The goal of this study was to generate a Drosophila model of intellectual disability caused by mutations in kdm5. RNA-seq was used to define the transcriptional defects of a mutation in Drosophila that is analogous to a human intellectual disability-associated allele, kdm5[A512p]. These data revealed a total of 1609 dysregulated genes, 778 of which were upregulated and 831 were downregulated. To determine whether these transcriptional defects were due to the loss of KDM5-induced histone demethylation, we also carried out RNA-seq from a enzymatic inactive strain, kdm5[Jmjc*]. These data revealed a striking similarity between the two datasets and suggest that the primary defect of KDM5[A512P] is loss of histone demethylase activity.

overall_design: 3-5 day old adult heads from wildtype, kdm5[A512P] and kdm5[JmjC*] were used to generate RNA that was subsequently subjected to deep sequencing.


title: Double knockout of Bach1 and Bach2 reveals shared compensatory mechanisms in regulating alveolar macrophage function and lung surfactant homeostasis

status: Public on Nov 05 2018

address: Seiryo 2-1

institute: Tohoku University


title: Bach2 keeps homeostasis in lung by regulating inflammatory response and maintaining function of alveolar macrophage [array]

summary: Tissue resident macrophages show their specific function to maintain homeostasis in our body. Dysfunction of alveolar macrophages (AMs), which regulate the proper amount of surfactant protein, leads to the development of pulmonary alveolar proteinosis (PAP). Here we found that inflammation ruins the function of AMs and is one of the causes of secondary PAP. Inflammation leads to the loss of specific gene expression pattern of AMs and furthermore, it leads to gain the specific gene expression pattern of other tissue resident macrophages and DC lineage. We also found the critical roles for Bach2 expressed in AMs and T cells, whose expression is induced by IFNg released from T cells. Bach2 bounds to super-enhancer regions of the inflammatory genes of the myeloid lineage and represses excess inflammation in lungs. Our results suggest that Bach2 function among several cell lineages to modify the inflammation, maintaining homeostasis in lungs.

overall_design: Gene expression in alveolar macrophage from WT, Bach1 KO, Bach2 KO and Bach1/Bach2 DKO mouse was measured. 3 independent mice were used for each genotype.

first: Risa

middle: E

last: Shibuya


title: Gene Networks Underlying the Early Regulation of Paraburkholderia Phytofirmans Psjn-induced Systemic Resistance in Arabidopsis

status: Public on Jul 31 2019

city: Santiago

first: Andrea

last: Vega

address: Vicuña Mackenna 4860

department: Ciencias Vegetales

country: Chile

institute: Pontificia Universidad Catolica de Chile

summary: Plant defense responses to biotic stresses are complex biological processes, all governed by sophisticated molecular regulations. Induced systemic resistance (ISR) is one of these defense mechanisms where beneficial bacteria or fungi prime plants to resist pathogen or pest attacks. In ISR the defense arsenal in plants remains dormant and it is only triggered by the infection, allowing a rapid response and a better allocation of plant resources. We recently described that the well-known beneficial bacterium Paraburkholderia phytofirmans PsJN is able to reduce Arabidopsis thaliana susceptibility to Pseudomonas syringae Pst DC3000 through ISR. Nevertheless, the molecular networks governing this beneficial interaction remain unknown. To tackle this issue we analyzed the temporal changes in the transcriptome of PsJN-inoculated plants before and after the infection with Pst DC3000 strain. These data were used to perform a gene network analysis to identify highly connected transcription factors that may be acting as hubs in controlling this ISR response. Before the pathogen challenge, strain PsJN regulated 405 genes (corresponding to 1.5% of the analyzed genome). PsJN-inoculated plants presented a faster and stronger transcriptional response 1-hour post infection (hpi) compared with the non-inoculated plants, which presented the highest transcriptional changes 24 hpi. A principal component analysis showed that PsJN-induced plant responses to the pathogen could be differentiated from those induced by the sole pathogen. Forty-eight transcription factors were regulated by PsJN 1 hpi, and a system biology analysis revealed a network with 4 modules where LHY, WRKY28, MYB31 and RRTF1 are highly connected transcription factors, that can be acting as hub regulators in this interaction. These modules are related to Jasmonate, Ethylene, Salicylic acid and ROS pathways. Additionally, the down- and up-regulation of ANAC32 and ORA59, respectively, support an important role of PDF1.2. These results indicate that a rapid and specific response of PsJN-inoculated plants to this virulent pathogen could be the pivotal element in the protection mechanism. A role for specific transcriptional regulators in the orchestration of this complex molecular response is also proposed

overall_design: Transcriptome-profiling assay using non-inoculated plants and strain PsJN-inoculated (0 hpi) plants was performed. Additionally, the analyses included samples 1 and 24 h after a challenge with P. syringae Pst DC3000 (1 and 24 hpi)

first: Tania

last: Timmermann

first: María

middle: J

last: Poupin

first: Cristóbal

last: Urrutia

first: Gonzalo

middle: A

last: Ruz

first: Bernardo

last: González


title: RNA sequencing of lung tissue from Fra-2 transgenic mouse (Fra-2tg) and wild-type littermates

status: Public on Jan 01 2019

first: Álvaro

last: Ucero

address: Calle de Melchor Fernández Almagro, 3

department: Grupo de Genes, Desarrollo y Enfermedad

institute: Spanish National Cancer Research Centre (CNIO)

summary: Fra-2tg mice develop spontaneous lung fibrosis. We carried out this sequencing with tissue from young animals before they develop the tissue fibrosis, to explore the early gene expression changes that might contribute to the phenotype.

overall_design: Lung tissue from 3 Fra-2tg mice and 3 wild-type littermates (C57BL/6 genetic background) was homogenized and RNA was isolated. After analysis of the RNA quality (RIN>8) in a Bioanalyzer, 1ug of RNA material was provided for the cDNA synthesis and sequencing. The initial objective was to look for differentially expressed genes after comparing Fra-2tg and wild-type groups.

first: Latifa

last: Bakiri

first: Coral

last: Fustero-Torre

first: Erwin

last: Wagner


title: Comprehensive molecular classification of bladder cancer reveals distinct prognostic subgroups with different sensitivities to immunotherapy

status: Public on Oct 03 2018

city: Daejeon

first: Bic-Na

last: Song

address: 125 Gwahak-ro, Yuseong-gu, Daejeon 34141, Korea

department: Korean Bioinformation Center

country: South Korea

institute: Korea Research Institutue of Bioscience & Biotechnology

summary: Previous studies successfully revealed molecular characteristics of bladder cancers, dealing with non-muscle invasive bladder cancer and muscle invasive bladder cancer, separately. At the molecular level, however, there is a great need to aggregate these subtypes, which may share biological characteristics. This study aimed to identify distinct molecular subtypes of BC and the clinical and/or biological characteristics of each subtype. We used seven gene expression data sets for bladder cancer, which included data from 118 primary bladder cancer samples and 27 recurrent bladder tumor tissues from the Yonsei University Severance Hospital. Hierarchical clustering revealed four molecular subtypes of BC with different clinical outcomes: class 1 with low-grade NMIBC and the best prognosis; class 2 characterized by active FGFR3 and inhibited immune response pathways; class 3 with high-grade NMIBC and the worst progression-free survival; and class 4 mainly comprised of MIBC along with EMT activation. By applying the classifier based on these characteristics, we stratified all BC samples into newly identified molecular subtypes. When comparing previously reported subtypes, our subtypes well agreed with their molecular characteristics regardless of breast cancer-based biology, and showed a strong prognostic relevance in class 3. Integrative analysis of mutation and gene expression suggested that class 3 may have the potential benefit from anti-PD-L1 immunotherapy. Our classifier, constructed by NMIBC and MIBC integration, successfully stratified BC patients into distinct subtypes with different clinical outcomes and a possible treatment option.

overall_design: 118 primary bladder cancer samples and 27 recurrent bladder tumor tissues from 25 patients were taken in the Yonsei University Severance Hospital.

first: Seon-Kyu

last: Kim

first: Sun-Hee

last: Leem

first: In-Sun

last: Chu


title: Genome-wide contacts of rDNA units detected by 4C procedure in human genome [old]

first: Nickolai

last: Tchurikov

summary: 4C-rDNA procedure was used for analysis of genomic contacts of rDNA units in HEK 293T cells. The primers for 4C were selected downstream from EcoRI site at coordinate  30487 in rDNA sequence with Accession number U13369.1.

overall_design: Analysis of rDNA genome-wide contacts in HEK 293T cells using 4C approach.

first: Yuri

last: Kravatsky

first: Olga

last: Kretova


title: Genome-wide maps of transcriptomic and epigenomic state in melanoma cell lines

status: Public on Sep 23 2019

city: Los Angeles

first: Xiang

last: Lu

address: 10833 Le Conte Ave

department: Department of Molecular and Medical Pharmaacology

institute: University of California, Los Angeles

summary: A mechanistic relationship between tumor epigenetic plasticity and nongenetic adaptive resistance to therapy is described, with MAPK inhibition of BRAF-mutant melanoma cells providing the model system. Upon inhibition, these largely melanocytic cells undergo reversible cell-state changes, ultimately yielding a drug-resistant mesenchymal-like phenotype. Epigenomic and transcriptomic kinetic studies, coupled with information theory and dynamic system modeling, revealed that, after just 3-days of treatment, RelA drives chromatin remodeling to establish an epigenetic program encoding long-term phenotype changes. Specifically, RelA transcriptionally inhibits SOX10 and NFKBIE through recruiting KDM5B and HDAC1 to down-regulate histone marks H3K4me3 and H3K27ac at their promoter regions. Suppression of SOX10 mediates melanoma regression towards drug-refractory phenotypes. These findings were confirmed in melanoma patients under MAPK inhibitor treatment, providing mechanistic insights into resistance-leading epigenetic reprogramming triggered following drug exposure.

overall_design: Examination of 2 different histone modifications and chromatin accessibility and transcriptome in melanoma cell lines

first: Yapeng

last: Su

first: Chunmei

last: Liu


title: Genomic distribution of H3K9me2 in wild-type vs. arle-14 mutant C. elegans embryos

status: Public on Aug 22 2018

city: Cambridge

first: Susan

middle: E.

last: Mango

address: 16 Divinity Ave

department: Molecular and Cellular Biology

institute: Harvard University

summary: We discovered arle-14/B0336.5 as a critical gene for H3K9 di-methylation. To test the hypothesis that ARLE-14 targets the H3K9 methyltransferase MET-2 to specific loci, we compared the distribution of H3K9me2 in wild-type and arle-14 mutants by ChIP-Seq. Our results reveal that H3K9me2 genomic distribution is similar in wild-type vs. mutants and ARLE-14 is not required for targeting MET-2.

overall_design: We used two biological replicates for each genotype (wild-type and arle-14 mutant).  Input DNA was used as a control for each sample.  arle-14 mutants have overall lower levels of H3K9me2. In this experiment, we collected 3 times more material from arle-14 mutants compared to wild-type to get enough material for sequencing. We note that the results are not quantitative in terms of H3K9me2 levels.

first: John

middle: M

last: Gaspar

first: Beste

last: Mutlu


title: Double knockout of Bach1 and Bach2 reveals shared compensatory mechanisms in regulating alveolar macrophage function and lung surfactant homeostasis [ChIP-Seq]

first: Kazuhiko

last: Igarashi

summary:
Background: Pulmonary alveolar proteinosis (PAP) is a rare disease showing excess accumulation of surfactant protein in the alveolar spaces. It chiefly results from a dysfunction of alveolar macrophages (AMs) due to a lack of granulocyte macrophage colony-stimulating factor (GM-CSF) signaling including the expression of PU.1. We previously reported that mice deficient for Bach2 developed PAP-like disease due to a defect of lipid handling by AMs. Recently, Bach1 and Bach2 have been reported to function redundantly in early B cell development. The aim of this study was to investigate the function of Bach1 and Bach2 in alveolar macrophage and lung homeostasis.
Methods: We generated mice lacking both Bach1 and Bach2 (Bach1/2 DKO mice) and investigated their body weight and survival rate. Whole lungs of mice were observed with Hematoxylin and eosin (HE) stain when they were 8 or 12-13 weeks old. The expression of surface markers and the numbers of alveolar macrophages and eosinophils in BAL were analyzed by flow cytometry (FACS). We also analyzed tissue macrophages in bone marrow and spleen by FACS. We administered N-acetyl cysteine to mice from prenatal stage and observed lung pathology at 12 weeks.
Result: Bach1/2 DKO mice showed a more rapid and severe PAP phenotype than Bach2-deficient mice (Bach2 KO mice), whereas Bach1-deficient mice (Bach1 KO mice) did not develop any pulmonary disease. AMs in Bach1/2 DKO mice showed a foamy appearance, suggesting a defect in lipid handling. In contrast, the numbers of bone marrow macrophages and red pulp macrophages were not affected in Bach1/2 DKO mice. The PAP-like disease in Bach1/2 DKO and Bach2 KO mice was not ameliorated by N-acetyl cysteine.
Conclusion: We suggest that Bach1 and Bach2 work in a complementary manner for the normal function of AMs and the maintenance of surfactant homeostasis in the lungs. Oxidative stress may be involved in the process of PAP by inactivating Bach1 and Bach2.

overall_design: Examination of target regions of Bach1 and Bach2 in murine myeloid leukemia cell line (M1)

first: Risa

last: Shibuya

first: Mitsuyo

last: Matsumoto

first: Hiroki

last: Kato

first: Ryo

last: Funayama

first: Keiko

last: Nakayama


title: A folic acid-enriched diet attenuates prostate involution in response to androgen deprivation

city: Madison

first: Chad

middle: Michael

last: Vezina

state: WI

address: 1656 Linden Drive

department: Comparative Biosciences

institute: University of Wisconsin-Madison

summary: Folic acid is present in pre-natal vitamins, fortified cereal grains and multi-vitamin supplements. High intake of folic acid through these sources has resulted in populations with increased levels of serum folate and unmetabolized folic acid. Although the benefits of folic acid in the prevention of neural tube defects are undeniable, the impact of long-term consumption of folic acid on the prostate is not fully understood. In this study, we used a rodent model to test whether dietary folic acid (FA) supplementation changes prostate homeostasis and response to androgen deprivation. Although intact prostate weights do not differ between diet groups, we made the surprising observation that dietary folic acid supplementation confers partial resistance to castration-mediated prostate involution.  More specifically, male mice that were fed a folic acid supplemented diet and then castrated had greater prostate wet weights, greater prostatic luminal epithelial cell heights, and more abundant RNAs encoding prostate secretory proteins compared to mice that were fed a control diet and castrated. We used RNA-seq to identify signaling pathways enriched in the castrated prostates from folic acid supplemented diet fed mice compared to control mice.  We observed differential expression of genes involved in several metabolic pathways in the FA supplemented mice. Together, our results show that dietary FA supplementation can impact metabolism in the prostate and attenuate the prostate’s response to androgen deprivation. This has important implications for androgen deprivation therapies used in the treatment of prostate disease, as consumption of high levels of folic acid could reduce the efficacy of these treatments.

overall_design: Ventral prostate lobes were collected from intact or castrated mice on one of two diet groups: control diet and folic acid enriched diet. A total of 23 samples from 6 treatment groups were profiled by RNA-Seq.

first: Diya

middle: B

last: Joseph

first: Li-Fang


title: The C. elegans ortholog of TDP-43 regulates the chromatin localization of the heterochromatin protein 1 homolog, HPL-2

status: Public on May 17 2018

city: Boulder

first: Christopher

last: Link

state: Colorado

address: 1725 Pleasant st

department: Integrative Physiology

institute: University of Colorado Boulder

summary: TDP-1 is the C. elegans ortholog of mammalian TDP-43, which is strongly implicated in the etiology of Frontotemporal Dementia (FTD) and Amyotrophic Lateral Sclerosis (ALS). We discovered that deletion of the tdp-1 gene results in enhanced transcriptional gene silencing leading to increased sensitivity to heritable RNA interference (RNAi). As heritable RNAi in C. elegans depends on chromatin changes moderated by HPL-2, a homolog of heterochromatin protein 1 (HP1), we investigated the interaction of TDP-1 and HPL-2. We find that TDP-1 and HPL-2 interact directly, and loss of TDP-1 dramatically alters the chromatin association of HPL-2.   We have shown previously that deletion of the tdp-1 gene results in transcriptional alterations and the accumulation of double-stranded (ds) RNA. These molecular changes are replicated in an hpl-2 deletion strain, consistent with HPL-2 acting downstream of TDP-1 to modulate these aspects of RNA metabolism. Our observations identify novel mechanisms by which HP1 homologs can be recruited to chromatin, and by which nuclear depletion of human TDP-43 could lead to disease-relevant changes in RNA metabolism.

overall_design: A total of 22 samples were used for this study. Three replicate hpl-2(tm1489) polyA RNAseq samples that were compared with 3 replicate polyA N2 controls.. Four hpl-2 ChIP samples in the N2 (2) and tdp-1(ok803) (2) strains along with 2 respective genomic controls. Six total RNA samples in the hpl-2(tm1489) background which consist of 3 replicate J2 immunoprecipitated samples and 3 corresponding input RNA samples. N2 control data for the J2 immunoprecipitation comparison were pulled from GSE61581.

first: Tassa

middle: K

last: Saldi

first: Patrick

last: Gonzales

first: Alfonso

last: Garrido-Lecca

first: Vishantie

last: Dostal

first: Christine

last: Roberts

first: Lenoard

last: Petrucelli


title: Memory CD4+ T cell subsets show differential responses to HIV latency reversing agents

status: Public on Jan 26 2018

city: Cleveland

first: AARTHI

last: TALLA

address: 2103 Cornell Rd

department: Pathology

institute: Case Western Reserve University School of Medicine

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

overall_design: Refer to individual Series


title: Crenolanib in combination with azacitidine abrogates stromal protection and survival of leukemia-initiating cells in FLT3-ITD+ AML

status: Public on Apr 03 2017

city: Martinsried

first: Christoph

last: Ziegenhain

state: Bavaria

address: Großhaderner Str. 2

department: Department Biology II

institute: Ludwig-Maximilians University Munich

summary: Effectively targeting leukemia-initiating cells (LIC) in FLT3-internal-tandem-duplication (ITD)-mutated acute myeloid leukemia (AML) remains a crucial goal for achievement of cure. FLT3 tyrosine kinase inhibitors (TKI) have limited impact as single agents and have thus far been unable to eradicate LIC enriched in the CD34+CD38- bone marrow compartment and protected by contact with niche cells.Using primary AML samples in vitro as well as in an in vivo xenograft model, we investigated whether combining the novel FLT3-selective TKI crenolanib with the hypomethylating agent azacitidine (AZA) can eliminate LIC in FLT3-ITD+ AML and determined whether efficacy of this combination is dependent on coexisting genetic mutations in DNMT3A, NPM1 and TET2. Our data show that crenolanib as a single agent was unable to target FLT3-ITD+ LIC in contact with niche cells while the addition of AZA overcame stromal protection and resulted in dramatically reduced clonogenic capacity of FLT3-ITD+ LIC in vitro as well as severely impaired engraftment capacity of FLT3-ITD+ LIC in NSG mice. Strikingly, FLT3-mutated AML samples harboring concurrent TET2 mutations were completely resistant to crenolanib as a single agent. Mutations in DNMT3A or NPM1 had no influence on response to crenolanib while DNMT3A mutations conferred increased sensitivity of FLT3-ITD+ LIC to AZA. Our data suggest that response to crenolanib or AZA as single agents in FLT3-ITD+ AML is highly dependent on coexisting mutations in epigenetic regulators. However, the combination of AZA + crenolanib effectively eliminated FLT3-ITD+ LIC irrespective of additional mutations in NPM1, DNMT3A or TET2.

overall_design: EL08 and PDX cells were co-cultured ind the presence of Crenolanib and AZA or a combination of both. RNA-seq was performed on EL08 and PDX cells after separation. Controls includes EL08 cells before co-culture as well as co-cultured EL08 and PDX treated with DMSO.

first: Anne

last: Garz

first: Katharina

last: Götze


title: Mechanism of early light signaling by the carboxy-terminal output module of Arabidopsis phytochrome B

status: Public on Dec 31 2017

city: Riverside

first: Meng

last: Chen

state: CA

address: 2150 Batchelor Hall, 900 University Ave.

institute: University of California, Riverside

summary: Phytochromes are evolutionarily conserved photoreceptors in bacteria, fungi, and plants. The prototypical phytochrome comprises an N-terminal photosensory module and a C-terminal histidine kinase signaling-output module. However, the plant phytochrome has been postulated to transduce light signals by interacting with a group of nodal Phytochrome-Interacting transcription Factors (PIFs) and triggering their degradation via the N-terminal photosensory module, while its C-terminal output module, including a Histidine Kinase-Related Domain (HKRD), is thought not to participate directly in signaling. Here, we show that the C-terminal module of Arabidopsis phytochrome B (PHYB) is unexpectedly sufficient to mediate the degradation of PIF3 and to induce a distinct set of PIF-regulated photosynthetic genes. These signaling functions require the HKRD and particularly its dimerization. A D1040V mutation, which disrupts the dimerization of HKRD and the interaction between the C-terminal module and PIF3, abrogates the early light signaling functions of PHYB in nuclear accumulation, photobody biogenesis, and PIF3 degradation. In contrast, disruption of the interaction between PIF3 and PHYB’s N-terminal photosensory module has little effect on PIF3 degradation. Together, this study provides novel insight into the central mechanism of early phytochrome signaling that the C-terminal signaling-output module of PHYB interacts with PIF3 in the nucleus to mediate PIF3 degradation by light.

overall_design: Whole seedling mRNA profiles of 100h dark-grown phyB-9 mutant and BCY overexpression line were generated by deep sequencing, in triplicate, using Illumina NextSeq 500

first: Yongjian

last: Qiu

first: Elise

last: Pasoreck

first: Lingyun

last: Long

first: Amit

last: Reddy

first: Akira

last: Nagatani

first: Wenxiu

last: Ma

first: Joanne

last: Chory


title: Microarray analysis of derived doxorubicin resistant neuroblastoma SK-N-Be(2)C and SK-N-SH cell lines

status: Public on May 31 2016

city: Des Moines

first: Chunfa

last: Jie

state: IA

address: 3200 Grand Ave

institute: Des Moines University

first: Jessica

last: Naiditch


title: MethMotif: An integrative cell specific database of transcription factor binding motifs coupled with DNA methylation profiles

status: Public on Aug 10 2018

city: St. John's

first: Touati

last: Benoukraf

state: NL

address: Craig L. Dobbin Genetics Research Centre,

department: Faculty of Medicine, Division of BioMedical Sciences

institute: Memorial University of Newfoundland

type: Methylation profiling by high throughput sequencing

summary: Integration of whole-genome bisulfite sequencing with ChIPseq datasets.

overall_design: DNA methylation profiles of transcription factor binding sites.

first: Quy Xiao Xuan

last: Lin

first: Matthew

last: Dyer

first: Stephanie

last: Sian

first: Omer

last: An

first: Denis

last: Thieffry

first: Sudhakar

last: Jha


title: Human 5′ UTR design and variant effect prediction from a massively parallel translation assay

status: Public on May 03 2018

city: Seattle

first: Paul

last: Sample

address: West Stevens Way NE

department: Electrical Engineering

institute: University of Washington

summary: Predicting the impact of cis-regulatory sequence on gene expression is a foundational challenge for biology. We combine polysome profiling of hundreds of thousands of randomized 5′ UTRs with deep learning to build a predictive model that relates human 5′ UTR sequence to translation. Together with a genetic algorithm, we use the model to engineer new 5 UTRs that accurately target specified levels of ribosome loading, providing the ability to tune sequences for optimal protein expression. We show that the same approach can be extended to chemically modified RNA, an important feature for applications in mRNA therapeutics and synthetic biology. We test 35,000 truncated human 5′ UTRs and 3,577 naturally-occurring variants and show that the model accurately predicts ribosome loading of these sequences. Finally, we provide evidence of 47 SNVs associated with human diseases that cause a significant change in ribosome loading and thus a plausible molecular basis for disease.

overall_design: Polysom profiling and sequencing was performed using a library of 300,000 randomized 5' UTR 50-mers with eGFP used as the CDS. Three RNA chemistries were tested: unmodified, pseudouridine, and 1-methylpseudouridine. These were performed in duplicate (6 samples total). A designed library that includes human 5' UTRs, SNVs, and sequences engineered with a genetic algorithm was used with the eGFP CDS (no duplicate). A second randomized library used mCherry as the CDS, also performed in duplicate.

first: Ban

last: Wang

first: Georg

last: Seelig


title: Memory CD4+ T cell subsets show differential responses to HIV latency reversing agents [LRA stimulated]

first: AARTHI

last: TALLA

summary: HIV-1 persists in individuals on ART in infected central (CM), transitional (TM) and effector memory (EM) CD4+ T cells. We developed LARA (latency and reversion assay), which facilitates the examination of HIV latency reversal in CM, TM and EM subsets in a single assay. Studies with latency reversing agents (LRAs) revealed responses specific to each subset, including compounds that significantly reversed latency in all subsets but with a range of efficiency (bryostatin) to those that demonstrated subset specificity (IL-15). Significantly, LARA has allowed the demonstration that EM cells display a more activated profile compared to CM, which translated to enhanced efficiency in responsiveness to multiple LRAs and allowed the identification of mechanisms associated with the compounds that reactivate latent HIV in all subsets. Understanding the responsiveness of memory CD4+ T cells subsets to LRAs will accelerate the development of anti-latency therapy to interfering with viral persistence in vivo.

overall_design: CD4 T cells were isolated from a cohort of Florida HIV-infected subjects that have been on successful ART for >36 months with a viral load ≤50 copies/mL. Three subjects in this cohort have previously been characterized according to their reservoir size (pDNA copies/million CD4) and relative distribution of the reservoir in memory CD4 T cell subsets namely central memory (TCM), transitional memory (TTM) and effector memory (TEM) CD4 T cells (R. Fromentin & N. Chomont unpublished data). We compared different classes of agents including PKC activators (Bryostatin), gamma-c cytokines (IL-15) and PMA+Ionomycin in their ability to induce viral transcription in the sorted memory CD4 T cell subsets. RNA from the sorted and 24h-stimulated subsets were purified. Unstimulated sorted cells from the same donors were included as pre-reactivation baseline controls.

first: Deanna

last: Kulpa

first: Aarthi

last: Talla

first: Susan

last: Pereira Ribeiro

first: Nicolas

last: Chomont

first: Rafick-Pierre

last: Sékaly


title: Memory CD4+ T cell subsets show differential responses to HIV latency reversing agents [LARA]

overall_design: RNA-Seq was performed on samples generated in LARA from ex vivo (day 0) and in vitro culture (day 14) cells sorted on memory CD4+ T cell CM, EM and TM subsets.


title: Expression data from human bronchial epithelial cells (treatment with IL-4)

status: Public on Nov 09 2016

city: Pozzuoli

first: Diego

last: Carrella

state: NAPOLI

address: Via Campi Flegrei 34

country: Italy

institute: TIGEM

summary:
Goblet cell hyperplasia (GCH) is a feature of respiratory diseases characterized by mucus hypersecretion. GCH is driven by Th2 cytokines such as IL-4.
To investigate the gene expression changes associated with GCH, we treated human bronchial epithelial cells with IL-4. By microarray analysis and functional studies, we found that IL-4 promotes a profound change that results in enhanced bicarbonate secretion.  This change may be required to support mucus release.

overall_design: Human bronchial epithelial cells were differentiated as epithelial monolayers on porous membranes (Snapwell inserts).  After treatment with IL-4, gene expression changes were determined with microarrays.  In parallel, ion transport, mucus release, intracellular pH, and apical fluid composition were measured.

first: Luis

last: Galietta


title: DNA methylation changes in fetal germ cells exposed to endocrine disruptors and in the next generation [methylation set 1]

status: Public on Feb 18 2015

city: Grand Rapids

first: Piroska

last: Szabo

state: MI

address: 333 Bostwick Ave. NE

department: Center for Epigenetics

institute: Van Andel Research Institute

type: Methylation profiling by genome tiling array

summary: According to recent reports, exposure to environmental endocrine disrupting chemicals (EDs) during pregnancy may harm multiple subsequent generations. We hypothesized that EDs must directly alter DNA methylation and/or transcription in the exposed fetal germ cells to affect the grandchild. In addition, the aberrant pattern must be retained in the germ cells of the grandchild -- withstanding global epigenome remodeling -- to affect the great-grandchild. To test this hypothesis, we extensively searched for immediate and persistent epigenetic effects in purified germ cells of the exposed fetus and those of the next generation. We treated gestating female mice with previously validated doses of vinclozolin (VZ), bisphenol A (BPA), di-(2-ethylhexyl) phthalate (DEHP), or control oil, during the time when the prospermatogonia of the exposed fetus undergo global de novo DNA methylation. Using genome-wide assays, we detected changes in transcription and DNA methylation in the exposed prospermatogonia but these did not persist into the prospermatogonia of the next generation. There was no evidence for transgenerational inheritance of these epigenetic aberrations. Our results suggest that EDs exert direct epigenetic effects in the exposed fetal germ cells, but the germline corrects against deleterious effects in the next generation.

overall_design: Pregnant mice were gavaged daily with endocrine distruptors (VZ at 100 mg/kg/day, DEHP at 750 mg/kg/day, BPA at 0.2 mg/kg/day or control oil) starting at 12.5 days post coitum (dpc) and the G1R germ cells were purified from the exposed fetuses at 17.5 dpc. The G2R germ cells were purified from fetuses that were sired by males that had been treated in utero in a G0 mother. G1R spermatozoa were collected from adult males that had been treated in utero at the fetal stages. G2R spermatozoa were collected from adult males who were sired by in-uteo-treated males.

first: Arthur

middle: X

last: Li


title: Intrinsic histone acetyltransferase activity of BRD4 is responsible for nucleosome eviction and transcriptional activation

status: Public on May 08 2016

city: Bethesda

first: Dinah

middle: S.

last: Singer

state: MD

address: Building 10, Room 4B-17

department: Division of Cancer Biology

institute: National Cancer Institute

summary: Purpose: BRD4 is a chromatin reader and transcriptional activator of M/G1 genes.We discovered that BRD4 is a novel histone acetyltransferase that acetylates histones and evicts nucleosomes. Here, investigated genome-wide changes in nucleosome occupancy and transcription caused by BRD4 HAT activity . Method: Human U2OS cells were transfected with either wild type BRD4 (WT), a BRD4 HAT mutant (MT) or a empty vector (NT) in biological duplicates, harvested 18 hrs post transfection and subjected to global MNase-seq and RNA-seq analysis. Results: The results show that while wild type BRD4 reduces nucleosome occupancy and increases transcription genome-wide, the BRD4 HAT mutant does not. Conclusion: BRD4 HAT activity is responsible for evicting nucleosomes and activating transcription.

overall_design:
Examination of genome-wide nucleosome occupancy and transcript abundance (mRNA) in three (WT,MT, NT) transfected U2OS cell samples in biological duplicates.

UPDATE: [07-23-2024] Originally, the MNase-seq Samples were associated with the RNA-seq raw data, and the RNA-seq Samples were associated with the MNase-seq raw data. To correct these misassociations, the titles of the MNase-seq Samples were swapped with the titles of the RNA-seq Samples, and the processed data files were re-associated with the GSMxxx records accordingly. The association of the raw data with the GSMxxx records did not change.

middle: S

first: Daoud

last: Meerzaman


title: Transgenerational Gene Expression Changes Caused by Exposing Fetal Germ Cells to Endocrine Disruptors

summary: We treated gestating female mice with vinclozolin (VZ), bisphenol A (BPA), di-(2-ethylhexyl) phthalate (DEHP), or control oil, during the time when the prospermatogonia of the exposed fetus undergo global de novo DNA methylation. Using genome-wide assays we detected changes in transcription and DNA methylation, respectively, in fetal prospermatogonia. Our results suggest that EDs exert direct epigenetic effects in the exposed fetal germ cells, but the germline corrects against deleterious effects in the subsequent generation.

overall_design: Pregnant mice were administered endocrine distruptors (VZ at 100 mg/kg/day, DEHP at 750 mg/kg/day, and BPA at 0.2 mg/kg/day) startin g at 12.5 days post coitum (dpc) and tissue samples were collected at 17.5 dpc.

first: Szabo

last: Piroska


title: Identification of CRTC1-MAML2/MAML2-regulated transcriptional program in H3118 cells

status: Public on Apr 21 2014

city: Gainesville

first: Lizi

last: Wu

state: FL

address: 2033 Mowry Road

institute: University of Florida

summary: Mucoepidermoid carcinomas (MEC) is the most common salivary gland malignancy. To date, advanced and nonresectable MEC have poor prognosis and no effective treatment.  The CRTC1-MAML2 fusion oncogene, which is associated with more than 50% of MEC, consists of the N-terminal CREB-binding domain of the CREB transcriptional co-activator CRTC1 and the C-terminal transcriptional activation domain of the Notch transcriptional co-activator MAML2.  CRTC1-MAML2 fusion was found to interact with CREB and constitutively activate their transcriptional targets.  To investigate the genes and pathways regulated by CRTC1-MAML2 fusion oncogene, gene expression profiling analysis were performed in human fusion-positive MEC cells before and after knockdown of both CRTC1-MAML2 and MAML2 as well as in human fusion-negative salivary gland cancer cells before and after MAML2 knockdown only.  This study revealed specific transcriptional program induced by the CRTC1-MAML2 fusion oncogene, which potentially mediates CRC1-MAML2 functions in MEC initiation and maintenance.  The information will be useful for developing new approaches to block CRTC1-MAML2 fusion-expressing MEC.

overall_design: The fusion-positive H3118 MEC cells were used in this study.  The fusion knockdown was performed with two biological replicates for each group.  We utilized pSuperRetro-based retroviruses that express shRNA targeting the MAML2 TAD as well as GFP for fusion and MAML2 knock down, and the retroviruses express shRNA targeting luciferase gene (shLuc) and GFP for the control.  Cells were infected with retroviruses and cultured for 72 hours.  FACS sorting was performed to obtain GFP-positive cells and thus enrich shRNA-expressing cells. RNA was subsequently harvested for microarray analysis.  The shMAML2 retroviruses caused the knockdown of MAML2 and CRTC1-MAML2 fusion in fusion-positive H3118 cells.

first: Jie

last: Chen

first: Jian

middle: L

first: James

middle: D

last: Griffin


title: CRTC1-MAML2 fusion oncogene-induced transcriptional program is regulated by CREB-dependent and -independent mechanisms

status: Public on Jul 25 2014


title: Global analysis of mRNA isoform half-lives: identification of stabilizing and destabilizing elements in yeast

status: Public on Apr 02 2014

city: Boston

first: Zarmik

last: Moqtaderi

address: 240 Longwood Avenue C2-355

department: BCMP

institute: Harvard Medical School

summary: We measured half-lives of 21,248 mRNA 3’ isoforms in yeast by rapidly depleting RNA polymerase II from the nucleus and performing direct RNA sequencing throughout the decay process. Interestingly, the half-lives of mRNA isoforms from the same gene, including nearly identical isoforms, often vary widely.  Based on clusters of isoforms with different half-lives, we identify hundreds of sequences conferring stabilization or destabilization upon mRNAs terminating downstream.  One class of stabilizing element is a polyU sequence that can interact with poly(A) tails, inhibit the association of poly(A) binding protein, and confer increased stability upon introduction into ectopic transcripts.  More generally, destabilization and stabilization elements are linked to the degree to which the poly(A) tail can engage in double-stranded structures.  Isoforms engineered to fold into 3’ stem-loop structures not involving the poly(A) tail exhibit even longer half-lives.  We suggest that double-stranded structures at the 3’ ends are a major determinant of mRNA stability.

overall_design: Half-lives of 21,248 mRNA 3’ isoforms in yeast were measured by rapidly depleting RNA polymerase II from the nucleus and performing direct RNA sequencing throughout the decay process.

first: Joseph

last: Geisberg

first: Xiaochun

last: Fan

first: Fatih

last: Ozsolak

first: Kevin

last: Struhl


title: miR-124, -128 and -137 orchestrate neural differentiation by acting on overlapping gene sets containing a highly connected transcription factor network

status: Public on Mar 20 2016

city: Blacksburg

first: Allison

middle: N

last: Tegge

address: 250 Drillfield Drive

institute: Virginia Tech

summary: We report the application of RNA-seq profiling on neural stem cells after antagomiR transfection.

overall_design: Examination of three antagomirs

first: Luiz

middle: O

last: Penalva


title: Genome-wide analysis of parental wild-type and derived doxorubicin resistant SK-N-SH neuroblastoma cell lines as well as those co-treated with the histone deacetylase inhibitor SAHA

first: Chunfa

last: Jie

summary: Analysis of varied biologic pathways in neuroblastoma SK-N-SH cells grown in doxorubicin and/or SAHA. The hypothesis was that SK-N-SH cells undergo a mesenchymal change through mesenchymal change resulting in a more invasive as well as drug resistant phenotype, and that the mechanism of SAHAs effect on drug resistance may be revealed through this analysis.

overall_design: Total RNA was isolated from wild type, SAHA treated wild type cells, doxorubicin resistant, and SAHA treated doxorubicin resistant SK-N-SH cell lines in triplicate.

first: Jessica

last: Naiditch


title: Hepatitis C virus-induced expression profiling of Hepatic and non-hepatic cancer cell lines

status: Public on Jul 10 2015

city: Suita

first: Daisuke

last: Okuzaki

state: Osaka

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

institute: Osaka univ.


title: Identification of MAML2 regulated transcriptional program in HSY cells

status: Public on Oct 30 2015

summary: Mucoepidermoid carcinomas (MEC) is the most common salivary gland malignancy. To date, advanced and nonresectable MEC have poor prognosis and no effective treatment. The CRTC1-MAML2 fusion oncogene, which is associated with more than 50% of MEC, consists of the N-terminal CREB-binding domain of the CREB transcriptional co-activator CRTC1 and the C-terminal transcriptional activation domain of the Notch transcriptional co-activator MAML2. CRTC1-MAML2 fusion was found to interact with CREB and constitutively activate their transcriptional targets. To investigate the genes and pathways regulated by CRTC1-MAML2 fusion oncogene, gene expression profiling analysis were performed in human fusion-positive MEC cells before and after knockdown of both CRTC1-MAML2 and MAML2 as well as in human fusion-negative salivary gland cancer cells before and after MAML2 knockdown only. This study revealed specific transcriptional program induced by the CRTC1-MAML2 fusion oncogene, which potentially mediates CRC1-MAML2 functions in MEC initiation and maintenance. The information will be useful for developing new approaches to block CRTC1-MAML2 fusion-expressing MEC.

overall_design: The fusion-negative HSY parotid adenocarcinoma cells were used in this study. The MAML2 knockdown was performed with two biological replicates for each group. We utilized pSuperRetro-based retroviruses that express shRNA targeting the MAML2 TAD as well as GFP, and the retroviruses express shRNA targeting luciferase gene (shLuc) and GFP for the control. Cells were infected with retroviruses and cultured for 72 hours. FACS sorting was performed to obtain GFP-positive cells and thus enrich shRNA-expressing cells. RNA was subsequently harvested for microarray analysis. The shMAML2 retroviruses caused MAML2 knockdown in fusion-negative HSY cells.

last: Li


title: Genome-wide analysis of parental and wild-type SK-N-Be(2)C neuroblastoma cell lines as well as those co-treated with the histone deacetylase inhibitor SAHA

summary: Analysis of varied biologic pathways in neuroblastoma SK-N-Be(2)C cells grown in doxorubicin and/or SAHA. We hypothesized that SK-N-Be(2)C cells undergo a mesenchymal change through mesenchymal change resulting in a more invasive as well as drug resistant phenotype, and that the mechanism of SAHAs effect on drug resistance may be revealed through this analysis.

overall_design: Total RNA was isolated from wild type, SAHA treated wild type cells, doxorubicin resistant, and SAHA treated doxorubicin resistant SK-N-Be(2)C cell lines in triplicate.


title: DNA methylation changes in fetal germ cells exposed to endocrine disruptors and in the next generation [methylation set 2]

first: Piroska

last: Szabo

first: Arthur


title: Gene expression in hemera mutants in red light condition

status: Public on Jun 01 2014

first: Meng

summary: The hemera (hmr) mutant was identified as the first photomorphogenetic mutant with the combination of long hypocotyl and albino phenotypes in the light. Phytochrome-Interacting bHLH transcription Factors (PIFs), which are repressors of photomorphogenesis accumulate in darkness and are degraded in the light in a phytochrome-dependent manner. Two PIFs, PIF1 and PIF3 accumulated in the light in hmr mutants. In order to determine the gene expression of PIF-dependent genes in hmr mutants in the light, we have performed whole-genome expression analysis on two hmr mutants: a null allele, hmr-5; and a weak allele, hmr-22.

overall_design: Wild-type (Col-0) and hmr mutant seeds were surface-sterilized and plated on half-strength Murashige and Skoog (MS) growth medium without sucrose. The seeds were stratified in the dark at 4ºC for 4d. Seedlings were grown in constant red light (Rc, 10μmol/m2/s) at 21°C for 4d.

first: Meina


title: seq-ab8895_H3K4me1_733246_N2_Eemb

status: Public on Aug 28 2013

city: Toronto

first: DCC

last: modENCODE

state: Ontario

address: MaRS Centre, South Tower, 101 College Street, Suite 800

institute: Ontario Institute for Cancer Research

summary:
modENCODE_submission_5158
This submission comes from a modENCODE project of Jason Lieb. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. Our 126 strategically selected targets include key histone modifications and histone variants. We will integrate information generated with existing knowledge on the biology of the targets and perform ChIP-seq analysis on mutant and RNAi extracts lacking selected target proteins.
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

overall_design: EXPERIMENT TYPE: CHIP-seq. BIOLOGICAL SOURCE: Strain: N2; Developmental Stage: Early Embryo; Genotype: wild type; Sex: mixed Male and Hermaphrodite population;  EXPERIMENTAL FACTORS: Developmental Stage Early Embryo; temp (temperature) 20 degree celsius; Strain N2; Antibody ab8895 H3K4me1:733246 (target is H3K4me1)

first: Susan

last: Strome

first: Thea

last: Egelhofer

first: Andreas

last: Rechtsteiner