title: Distinct roles for CDK-Mediator in controlling Polycomb-dependent chromosomal interactions and priming genes for induction (RNA-Seq)

city: Oxford

first: Emilia

last: Dimitrova

address: South Parks Road

department: Biochemistry

institute: University of Oxford

summary: Precise control of gene expression is essential for normal development. This is thought to rely on mechanisms that enable communication between gene promoters and other regulatory elements. In embryonic stem cells (ESCs) the CDK-Mediator (CDK-MED) complex has been reported to topologically link gene regulatory elements to enable gene expression and also prime genes for induction during differentiation. Here we discover that CDK-MED contributes little to overall genome organisation in ESCs, but interestingly has a specific and essential role in controlling interactions between inactive gene regulatory elements bound by the Polycomb repressive complexes (PRCs). These interactions are facilitated by CDK-MED but rely on canonical PRC1. However, through separation of function experiments, we reveal that the collaboration between CDK-MED and cPRC1 in creating long-range interactions does not function to prime genes for induction during differentiation. Instead, we discover that priming relies on a topology-independent mechanism whereby the CDK module supports core Mediator engagement with gene promoters to support gene activation.

sample_organism:
Drosophila melanogaster
Mus musculus

platform_organism:
Drosophila melanogaster
Mus musculus

overall_design: Gene expression profiling using spike-in calibrated nuclear RNA-seq of embryonic stem cells in which CDK-MED (Med13/13l fl/fl) or cPRC1 can be conditionally removed upon addition of tamoxifen. Cells were induced with retinoic acid.

first: Robert

last: Klose


title: Unleashing cell-intrinsic inflammation as a strategy to kill AML blasts

status: Public on May 23 2022

city: Cambridge

first: Gabriela

last: Alexe

state: MA

address: 415 Main St.

department: Computational Biology and Bioinformatics

country: USA

institute: Broad Institute

type: Expression profiling by high throughput sequencing

type: Genome binding/occupancy profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Unleashing cell-intrinsic inflammation as a strategy to kill AML blasts [RNA-seq]

summary: Leukemic blasts are immune cells gone awry. We hypothesized that dysregulation of inflammatory pathways contributes to the maintenance of their leukemic state and can be exploited as a cell-intrinsic, self-directed immunotherapy. To this end, we applied genome-wide screens to discover genetic vulnerabilities in acute myeloid leukemia (AML) cells that are also implicated in inflammatory pathways. We identified the immune modulator interferon regulatory factor 2 binding protein 2 (IRF2BP2) as a selective dependency in AML. We validated AML cell dependency on IRF2BP2 with genetic and protein degradation approaches in vitro and genetically in vivo. Chromatin and global gene expression studies demonstrated that IRF2BP2 represses IL1B/TNFA signaling via NF-KB, and IRF2BP2 perturbation results in an acute inflammatory state leading to AML cell death. These findings elucidate a hitherto unexplored AML dependency, reveal cell-intrinsic inflammatory signaling as a mechanism priming leukemic blasts for regulated cell death, and establish IRF2BP2-mediated transcriptional repression as a mechanism for blast survival.

overall_design: RNA-sequencing was performed in degradable IRF2BP2 MV4-11 and PDX 16-01 cells after 6 hours of dTAG-13 treatment,  and in MV4-11 cells after 24 hours of dTAG-13 treatment. RNA-sequencing was performed on  MV4-11 and PDX 16-01 cells after 6 hours of DMSO treatment and on MV4-11 cells after 24 hours of DMSO treatment. RNA-sequencing was performed in parental PDX cells from eight AML patients.

first: Kimberly

last: Stegmaier


title: Unleashing cell-intrinsic inflammation as a strategy to kill AML blasts [ChIP-seq]

overall_design: ChIP-sequencing was performed in parental MV4-11 cells for IRF2BP2, H3K27ac, H3K4me1, H3K4me3, and parental THP1, PDX 16-01, and PDX 17-14 cells for H3K27ac. ChIP-sequencing for HA was performed in THP1, PDX 16-01, PDX 17-14 IRF2BP2-HA cells. ChIP-sequencing for H3K27ac was performed in MV4-11 cells with degradable IRF2BP2 24 hours post degradation of IRF2BP2 with dTAG-13 or untreated control cells. All experiments were controlled with respective input samples. PDX cells from two different patients with AML (PDX 16-01 with CALM-AF10 fusion, PDX 17-14 with MLL-PTD/MLL-AF10 fusion) were used.


title: RNA-seq analysis of SCC1 and FaDu cells after FOSL1 depletion

city: Richmond

first: Jiong

last: Li

state: Virginia

address: 800 E Leigh Street, suite 212

institute: VCU

summary: In order to examine how FOSL1 affects the global gene transcriptome in HNSCC, we performed RNA-sequencing in SCC1 and FaDu cells treated with FOSL1 siRNA. Depletion of FOSL1 led to inhibition of cancer stemness genes.

overall_design: Examination of RNA-seq of HNSCC cells


title: Distinct roles for CDK-Mediator in controlling Polycomb-dependent chromosomal interactions and priming genes for induction (ChIP-Seq)

country: United Kingdom

sample_organism:
Drosophila melanogaster
Homo sapiens
Mus musculus

overall_design: Genomic distribution of Polycomb (canonical PRC1 and H3K27me3), CDK-Mediator (CDK8) and core Mediator (MED14) was profiled in Med13/13l fl/fl ESCs, in which the CDK-Mediator can be conditionally disrupted. Genomic distribution of CDK-Mediator (CDK8) was profiled in Pcgf4-/-Pcgf2 fl/fl ESCs, in which the canonical PRC1 can be conditionally depleted.

middle: J


title: The lncRNA HHIP-AS1 is required for oncogenic SHH signaling in humans

city: Homburg (Saar)

first: Marc

last: Remke

state: Saarland

address: Kirrberger Straße 100, Gebäude 9

department: Pediatric Translational Oncology Lab

country: Germany

institute: Universitätsklinikum des Saarlandes

summary: Here we show that the non-conserved lncRNA HHIP-AS1 promotes tumorigenesis in human SHH-driven brain tumors, including medulloblastoma, atypical teratoid / rhabdoid tumors (AT/RT). We reveal that GLI2 regulates a bidirectional promoter shared between the well-characterized SHH regulator HHIP and HHIP-AS1. We found a novel regulatory lncRNA mechanism, termed blocking endogenous RNA (beRNA), extending the concept of competing endogenous RNA (ceRNA), where HHIP-AS1 binds its target DYCN1I2 to avoid miRNA-425-based degradation.

overall_design: HHIP-AS1 knockdown

first: Daniel

last: Picard

first: Jasmin

last: Bartl


title: Response and resistance to first and second generation TRK inhibitors in an NTRK1-driven sarcoma

city: Worcester

first: Matthew

last: Hemming

address: 364 Plantation Street

institute: UMass Medical School

summary: We report here a patient with a TPM3-NTRK1 translocated sarcoma who developed resistance to larotrectenib arising from the p.G595R solvent-front substitution. The patient was treated with LOXO-195 with initial response followed by subsequent resistance. Molecular profiling of the resistant tumor identified a KRAS p.G12V substitution, with associated activation of KRAS signaling and immune infiltration into the tumor. Following cytoreductive surgery to remove the resistant lesion, the patient’s disease has continued to respond to LOXO-195.

overall_design: RNA-seq from NTRK-translocated sarcoma tumors, xenografts and cell line


title: RNA-sequencing-based off-target analysis of allele-specific siRNA in keratitis-ichthyosis-deafness syndrome patient-derived keratinocytes

city: London

first: Ming Yang

last: Lee

address: 30 Guilford St.

department: Immunobiology

institute: UCL Great Ormond Street Institute of Child Health

summary:
Purpose: RNA-sequencing (RNA-Seq)-based transcriptomic analysis has facilitated identification of off-target effects of drug of interest. The goals of this study are to investigate off-target effects of the therapeutic, allele-specific siRNA, S7.
Methods: mRNA profiles of KID syndrome patient-derived keratinocytes (with c.148G>A mutation in GJB2) with or without S7 treatment were generated by RNA-Seq, in triplicate, using an Illumina NextSeq 500 instrument. The sequence reads that passed quality filters were processed using RNA-STAR (v2.5b) and BioConductor SARTools package (v1.3.2). Real-time qRT–PCR validation was performed using SYBR Green.
Results: We mapped about 15 million sequence reads per sample to the human genome (build hg38) and identified expression of 19,667 genes in the samples. Only 6 genes (MMP10, MMP1, NSA2, AFAP1L1, GLB1L2, GPR137) showed differential expression between the treated and untreated cells, with |log2 fold change| ≥ 1 and adjusted p-value (padj) <0.05. Altered expression of the top 10 genes (TMEM109, MMP9, ANGPTL4, CXCL5, in addition to the 6 genes above) was confirmed using real-time qRT–PCR.
Conclusions: Our RNA-Seq findings suggest low-level off-target effects of S7, the allele-specific siRNA targeted to the most common GJB2 mutant associated with KID syndrome.

overall_design: mRNA profiles of KID syndrome patient-derived keratinocytes with or without therapeutic siRNA S7 treatment were generated by RNA sequencing, in triplicate, using Illumina NextSeq 500 System.

first: Ming

middle: Y

first: Tony

last: Brooks

first: Alan

last: Pittman

first: Veronica

middle: A

last: Kinsler

first: Wei

middle: L

last: Di


title: Anatomic and transcriptional determinants of gastrointestinal stromal tumor

summary: Malignant transformation of the interstitial cells of Cajal (ICC) or their precursors gives rise to gastrointestinal stromal tumor (GIST). This mesenchymal neoplasm is characterized by activating mutations in the receptor tyrosine kinases KIT, or other less common mutational subtypes. GIST relies on a highly conserved core transcription factor (TF) network, with expression of accessory disease-state specific TFs. In this study, we define the divergent transcriptional programs supported by accessory TFs HAND1 and BARX1, with HAND1 modulating core TF and KIT gene expression to support GIST cell proliferation. HAND1 was expressed primarily in KIT mutant tumors, including the majority of metastatic tumors or those derived from small bowel, which intrinsically portend a more aggressive clinical course. Assessing archival GIST specimens, HAND1 and BARX1 expression patterns were superior predictors of relapse free survival compared to standard risk stratification. Metastatic tumors expressing HAND1 had a shorter progression free survival on first-line imatinib than those that were HAND1-negative. In contrast, BARX1 expression was enriched in more indolent forms of GIST. Signifying developmental origins of accessory TF expression, HAND1 was expressed solely in ICCs derived from the small intestine, while BARX1 expression was restricted to ICCs of the stomach. These results define the anatomic and transcriptional determinants of GIST clinical phenotypes, and may provide important biomarkers of disease risk stratification in GIST that will inform clinical decision making.

overall_design: RNA-seq from GIST cell lines


title: Differentiation of astrocytes with characteristics of ventral midbrain from human embryonic stem cells

status: Public on May 22 2022

city: Seongbuk-gu

first: Gyu-Bum

last: Yeon

state: Seoul

address: 145, Anam-ro

department: Department of Biodtechnology

country: South Korea

institute: Korea University

summary: We hypothesized that overexpression of NFIB in the NPCs specified to VM fate can lead to generation of the astrocytes with the same regional identity. Our results presented here demonstrate that fine modulation of WNT and Sonic Hedgehog (SHH) signals during neural differentiation gave rise to NPCs with VM fate, and NFIB overexpression transformed them to astrocytes with the same regional identity.

overall_design: NOT PROVIDED; REQUESTED

first: Byeong-Min

last: Jeon

first: Dae-Sung

last: Kim


title: Gene expression in the thyroarytenoid muscle in Pink1 knockout female rats

status: Public on May 21 2022

city: Madison

first: Cynthia

last: Kelm-Nelson

state: WI

address: 1300 University Avenue, 416 Medical Sciences Center

department: Surgery

institute: University of Wisconsin- Madiso

summary:
Parkinson’s disease (PD) is a degenerative disease with prodromal pathology hypothesized to manifest in lower brainstem regions as well as within peripheral systems. Behaviorally, vocal deficits including soft monotone speech appear early and are present in 90% of PD patients. However, the pathology mediating voice deficits is unknown. The Pink1-/- rat is a mitochondrial dysfunction model of prodromal PD. In this study, we used RNA sequencing to examine gene expression within the vocal fold muscle of female Pink1-/- rats as compared to age-matched wildtype controls.
Comparative gene expression profiling analysis using data obtained from the RNA-sequencing between the two genotypes (Pink1-/- and WT).

overall_design: Eight month old Long Evans rats; 7 female (n=3 Pink1-/-, n=4 WT).

first: Stephen

middle: C

last: Gammie


title: Silencing of KDM6A regulates TGF-β signaling pathway in MCF10A cells

city: Singapore

first: SIQIN

last: ZHOU

address: 14 Medical Drive

country: Singapore

institute: Cancer Science Institute of Singapore

summary: Massive parallel sequencing projects identified KDM6A as a tumor suppressor gene with recurrent loss-of-function mutations multiple cancers. However, in breast cancer, reports on the functional role of KDM6A is paradoxical or even puzzling, suggesting the role of KDM6A may be context dependent. We sought to investigate the functional role of KDM6A in triple negative breast cancer with using MCF10A cells.

overall_design: KDM6A (also known as UTX) was silenced in MCF10A cells using single guide RNA (sgRNA) mediated genomic editing using CRISPR/Cas9 system. Whole RNA was extracted using RNeasy mini extraction kit (74106, Qiagen). RNA-seq was performed with Illumina Hiseq4000 platform.

first: Jin-Fen

last: Xiao

first: Leyfang

last: Kua

first: Qiao-Yang

last: Sun

first: Xiu-Rong

last: Chia

first: Khine

middle: N

last: Myint

first: Xin-Yi

last: Loh

first: Xue-Bin

last: Ran

first: Nachi

last: Yappan

first: Anand

middle: M

last: Thippeswamy

first: Siqin

last: Zhou

first: Henry

last: Yang

first: Ling-Wen

last: Ding

first: H

middle: P

last: Koeffler


title: Circulating microRNA expression profiling of Graves Disease

city: zhenjiang

first: xiangmei

last: ding

address: No. 8 of Power Road

country: China

institute: The Affiliated People’s Hospital of Jiangsu University

type: Non-coding RNA profiling by high throughput sequencing

summary: NGS was performed to detect human miRNAs.  We found many upregulated and downregulated miRNAs in GD patients.  A total of 1279 dysregulated miRNAs were identified in PBMCs from GD patients and healthy volunteers, of which 487 were upregulated and 792 were  Downregulated. Among them, a total of 630 miRNAs, 188 upregulated and 442 downregulated.

overall_design: Circulating miRNA profiles of five Graves Disease patients and five healthy volunteers were generated by deep sequencing,using Illumina HiSeq 4000

first: Yingzhao

last: Liu

first: Huiyong

last: Peng

first: Si

last: Xiong

first: Xiangmei

first: Xuehua

last: Wang


title: Two Distinct Types of RNA:DNA Hybrids Revealed by Evaluating Divergent “R-loop” Profiles Detected with Different Mapping Strategies

city: Nanjing

first: Jia-Yu

last: Chen

state: CA

address: No 163 of XianlinAvenue, Qixia District

department: School of Life Sciences

institute: Nanjing University

summary: R-loop, a three-stranded nucleic acid structure, has been recognized to play pivotal roles in critical physiological and pathological processes. Multiple technologies have been developed to profile R-loops genome-wide, but the existing data suffer from major discrepancies on determining genuine R-loop localization and its biological functions. Here, we experimentally and computationally evaluate eight representative R-loop mapping technologies, and reveal inherent biases and artifacts of individual technologies as key sources of discrepancies. Analyzing signals detected with different R-loop mapping strategies, we note that genuine R-loops predominately form at gene promoter regions, whereas most signals in gene body likely result from structured RNAs as part of repeat-containing transcripts. Interestingly, our analysis also uncovers two classes of R-loops: The first class consists of typical R-loops where the single-stranded DNA binding protein RPA binds both the template and non-template strands. By contrast, the second class appears independent of Pol II-mediated transcription and is characterized by RPA binding only in the template strand. These two different classes of RNA:DNA hybrids in the genome suggest distinct biochemical activities involved in their formation and regulation. In sum, our findings will guide future use of suitable technology for specific experimental purposes and the interpretation of R-loop functions.

overall_design: To evaluate DRIP-seq, we implemented an RNase H treatment step after (rather than before, as with DRIP-seq) S9.6 IP and before sonication to deduce RNase H sentative DRIP-seq peak regions. We also sought for independent approaches to evaluate the performance of different technologies. Replication protein A (RPA) is a primary candidate that has been implicated in DNA replication/repair pathways and reported as part of R-loops. Therefore, we performed strand-specific RPA ChIP-seq and correlated its binding profile with peaks detected by R-loop mapping technologies.

first: Xiang-Dong

last: Fu


title: Viperin restricts viral replication by serving as a translational regulator

city: Seoul

first: Jaechul

last: Lim

state: CT

address: 1 Gwanak-ro, 1 Gwanak-gu

institute: Seoul National University

summary: Innate immune responses induce hundreds of interferon-stimulated genes (ISGs), many of which play an important role in antiviral immunity. Viperin, a member of the radical SAM superfamily of enzymes, is the product of one such ISG and it restricts the replication of a broad spectrum of DNA and RNA viruses. However, a general mechanism that explains all the roles proposed for viperin in the innate immune response remains to be defined. Here we report a previously unknown antiviral mechanism, in which viperin represses translation of viral RNA. We show that viperin interacts with the translation machinery and, primarily through its radical SAM enzymatic activity, inhibits global translation during the interferon response by activating the eIF2 pathway. In cell based-infection assays, viperin inhibits viral protein synthesis and viral replication of Zika virus and Kunjin virus. This study illustrates the importance of translational repression in the antiviral response and identifies viperin as a central translational regulator in innate immunity.

overall_design: mRNA profiles of mock- and viperin-transfected 293T cells were generated by deep sequencing, in duplicate, using Illumina Hiseq.

first: Jack

last: Hsu

first: Peter

last: Cresswell


title: RNA sequencing of ipsilateral cortex after transient focal ischemia in mice

first: Fangfang

last: Wu

state: Jiangsu

address: Dingjia Qiao 87#

department: Department of Pharmacology

institute: Southeast University

summary: We report the application of Illumina paired-end RNA-seq approach for transcriptome of brain tissue in mice. By removing sequence-dependent bias and amplification noise using UMI-tools. The mapped reads of each sample were assembled using StringTie. After the final transcriptome was generated, StringTie and edgeR was used to estimate the expression levels of all transcripts. By obtaining a total of million paired-end reads of sequence from cerebral cortex tissue, we generated transcriptome profiles of mouse ischemic cortex in sham, 24 h after focal ischemia, 28 d after focal ischemia, with or without neuron-specific knockdown of TIPARP, respectively. We found 2017 differentially expressed genes (DEGs) between Sham+AAV-SYN-shRNA-Con and tMCAO+AAV-SYN-shRNA-Con group, and 516 DEGs between tMCAO+AAV-SYN-shRNA-Con and tMCAO+AAV-SYN-shRNA-TIPARP group at 24 h after stroke. In addition, we found 487 DEGs between Sham+AAV-SYN-shRNA-Con and tMCAO+AAV-SYN-shRNA-Con group, and 192 DEGs between tMCAO+AAV-SYN-shRNA-Con and tMCAO+AAV-SYN-shRNA-TIPARP group at 28 d after stroke. This study provides a detailed analysis of the underlying mechanisms of neuron-specific knockdown of TIPARP in neuronal injury and long-term effect, with biologic replicates, generated by RNA-seq technology.

overall_design: Transcriptome profiles of mouse ischemic cortex in sham, 24 h after focal ischemia, 28 d after focal ischemia, with or without neuron-specific knockdown of TIPARP treatment, respectively, were generated by paired-end sequencing, in triplicate, using Illumina Hiseq 4000.

first: Honghong

last: Yao


title: Concentration-response gene expression analysis in zebrafish reveals phenotypically-anchored transcriptional responses to retene

city: Corvallis

first: Christopher

middle: Michael

last: Sullivan

state: OR

address: Sinnhuber Aquatic Research Laboratory, 28645 East HWY 34

department: Environmental & Molecular Toxicology

institute: Oregon State University

summary: Purpose: Assess transcriptomic changes in response to phenotypically-anchored retene concentrations. By combining data from all concentrations, we inferred a gene co-expression network highlighting key transcripts and modules important to toxicity response to retene.

overall_design: Transcriptomic profiles of 48 hours-post fertilization zebrafish

first: Lindsay

middle: B

last: Wilson

first: Ryan

middle: S

last: McClure

first: Michael

middle: T

last: Simonich

first: Katrina

last: Waters

first: Robyn

last: Tanguay


title: RNA-Seq of XBP1S and ATF6N cardiomyocytes

city: Jamaica Plain

first: Xiaoran

last: Zhang

address: 14 Perkins Square, Apt 11

department: Cardiology

institute: Boston Children's Hospital

summary: To characterize transcriptome changes uopn XBP1S and ATF6N overexpression in maturing cardiomyocytes

overall_design: AAV-GFP, AAV-XBP1S or AAV-ATF6N were injected into P1 wildtype mice. The cardiomyocyets were isolated at 4wk old for FACS purification and RNA-seq analysis

first: Yuxuan

last: Guo


title: Age-Related Development and Progression of Hypertension and Kidney Disease in Dahl SS/JrHsdMcwi Rats Maintained on a 0.4% NaCl Diet: Effects of Sex and Chromosome 1

city: Milwaukee

first: Alison

middle: J.

last: Kriegel

address: 8701 Watertown Plank Rd.

department: Physiology

institute: Medical College of Wisconsin

summary: We report the relative difference in medullary thick ascending limb (mTAL) transcript between SS/JrHsdMcwi and consomic SS-Chr 1BN/Mcwi (SS.BN1) rats.

overall_design: RNA-sequencing was performed on RNA extracted from isolated medullary thick ascending limb cells from 7-week old male Salt-senstive Dahl rats (SS/JrHsdMcwi) and consomic SS-Chr 1BN/Mcwi (SS.BN1) rats.  Rats were maintained on 0.4% NaCl diet

first: Jacqueline

last: Chivers

first: Shannon

last: Whiles

first: Conor

last: Miles

first: Brianna

middle: E

last: Biederman

first: Meagan

middle: F

last: Ellison

first: Connor

middle: W

last: Lovingood

first: Donald

last: Hoover

first: George

last: Youngberg

first: Nadezhda

last: Zheleznova

first: Chun

last: Yang

first: Pengyuan

last: Liu

first: Allen

last: Cowley

first: Paul

last: O’Connor

first: Maria

last: Picken

first: Aaron

last: Polichnowski


title: ChIP-Seq analysis of ATF4 in cardiomyocytes in vivo

city: Beijing

first: Yuxuan

last: Guo

address: 38 Xueyuan Road

institute: Peking University

summary: We used AAV to overexpress ATF4 in murine cardiomyocytes in vivo and perfomred bioChIP-Seq to profile the chromatin occupancy of the exogenous protein

overall_design: Two ChIP and two input samples.


title: HDAC1/2 is indispensable for mouse and bovine ZGA via regulating distribution of H3K27ac and H3K4me3 [ChIP-seq]

city: Hangzhou

first: Kun

last: Zhang

address: 866 Yuhangtang Rd

institute: Zhejiang University

summary: Zygotic genome activation (ZGA) is an impressed biological event following fertilization during early embryo development. Precise reprogramming of epigenetic modifications (e.g. histone H3 lysine 27 acetylation, H3K27ac) have been found contribute to safeguard ZGA in zebrafish and Drosophila, but the dynamic of H3K27ac and the underlying regulation mechanism in mammal embryos are still enigmatic yet. As the main erasers for histone acetylation, histone deacetylase 1 and 2 (HDAC1 and HDAC2) are reported essential for mouse oogenesis and embryo lineage development, while it is unclear if they are functional for ZGA. Here, we observed significant global decrease of H3K27ac during ZGA in both mouse and bovine embryos, and accumulation of HDAC1/2 is responsible for the decline of H3K27ac. Repression of HDAC1/2 by dominant negative mutation led to arrested development at late 2-cell stage in mouse embryos, accompanied by downregulation of genes supposed to be expressed during ZGA. ChIP-seq revealed abnormal distribution of H3K27ac, and DUX participates in H3K27ac aberrant hyper-acetylation in embryos overexpressed mutant HDAC1/2. Moreover, suppression of HDAC1/2 also restrains H3K4me3 removal at gene body regions via impeding expression of KDM5s during mouse ZGA, and compensatory exogenous Kdm5b mRNA can fix the exceeding H3K4me3 and failed ZGA. Intriguingly, function of HDAC1/2 seems to be conservative between mouse and bovine embryos. Together, this study reveals that HDAC1/2 is indispensable for mouse and bovine ZGA via regulating distribution of H3K27ac and H3K4me3.

overall_design: Examination of H3K27ac and H3K4me3 genomic distribution by ULI-NChIP-seq in mouse late 2-cell embryos.

first: Yanna

last: Dang


title: The whole transcriptome expression profiling of human SKOV3  comparison between control  and CtBP1 KD, ctbp2 KD  and CTBP1/2 DKD.

city: kunming

first: shubai

state: yunnan

address: 132 lanhei road,

institute: kunming institute of botany, chinese academic of science

summary: To discover the  regulatory role of CTBP1/2 in high grade serous ovarian cancer, The full cDNA was extracted from  SKOV3 shRNA control and CtBP1/2 knockdown   and then compared the expression profiles of them to discovery the key functions and pathways regulated by CtBP1/2..

overall_design: There are  four groups  cells used for this expression profile comparison :  control and  CtBP1 KD,  CtBP2 KD  and  CtBP1/2 DKD. The RNA was extracted from well cultured cells using TRIzol reagent, and whole transcriptome gene expression profiling were performed using an Affymetrix Human Gene 1.1 ST  whole transcriptome microarray platform.

first: Yingying

last: He

first: Shubai


title: Machine Learning Identifies Signatures of Macrophage Reactivity and Tolerance

status: Public on May 20 2022

city: LA JOLLA

first: Sahar

last: Taheri

state: California

address: 9500 GILMAN DR.

institute: UCSD

summary: A continuum of macrophage polarization states is essential tissue homeostasis. We used machine learning approaches to identify universally relevant definition of macrophage polarization states and create a predictive framework for developing macrophage-targeted precision diagnostics and therapeutics. CCDC88A was identified as a key gene in the continuum state clusters that is essential for the tolerant polarization state.

overall_design: Murine peritoneal macrophage were isolated from macrophage specific CCDC88A (GIV) knockout mice and their littermate WT controls 4 days after thiglycollate injection (IP). Peritoneal macrophage were stimulated or not with 100ng/ml of LPS for 6h (n=3)

first: Debashis

last: Sahoo

first: Soumita

last: Das

first: Pradipta

last: Ghosh


title: Airway administration of flagellin regulates the inflammatory response to Pseudomonas aeruginosa

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

country: France

institute: IPMC/CNRS

summary: Here, we aim to understand the role of P38 in the airway epithelial cells response to flagellin. We report the gene expression profile of pig airway epithelial cells cultured under air-liquid conditions, pre-incubated or not with the P38 inhibitor SB203580 (20 µM, Tocris Bioscience) for 1 h and then stimulated with 100 ng/ml of a mutated flagellin (FliCΔ174-400) for 2h or 24h. Our data show that flagellin stimulation induce the expression of pro-inflammatory cytokines mainly through the NFkB pathway, with little impact of P38 inhibition in the cells response.

overall_design: RNA-seq analysis of airway epithelial cells pre-incubated (SB) or not (DMSO) with the P38 inhibitor SB203580 and stimulated with 100 ng/ml of flagellin for 2 or 24h.

first: Ignacio

last: Caballero


title: RNA-Seq of RYR2KO cardiomyocytes

summary: To characterize transcriptome changes uopn RYR2 depletion in maturing cardiomyocytes

overall_design: AAV-Cre or AAV-Ryr2gRNA were injected into P1 Rosa-Cas9GFP mice. The cardiomyocyets were isolated at 4wk old for FACS purification and RNA-seq analysis


title: Comparative omics analysis guides to further enhance the biosynthesis of erythromycin by an overproducer

city: Kongens Lyngby

first: Xiaobo

last: Li

address: Kemitorvet

country: Denmark

institute: Technical University of Denmark

summary: Omics approaches have succeeded in understanding the boosted productivity of natural products by industrial high-producing microorganisms. Here, with the updated genome sequence and transcriptomic profiles derived from next-generation high throughput sequencing, we exploited comparative omics analysis to further enhance the biosynthesis of erythromycin in an industrial overproducer, Saccharopolyspora erythraea HL3168 E3. By comparing the genome of E3 with the wild type NRRL23338, we identified large deletions of 30 kilobases in total located inside coding sequences and 255 single nucleotide polymorphisms over the whole genome of E3. A large amount of genomic variation was observed in genes responsible for pathways which supply precursors, cofactors and signals for the biosynthesis of erythromycin. Transcriptional analysis revealed 2-oxoglutarate and L-glutamine/L-glutamate as reporter metabolites to distinguish the two strains. Around the node of 2-oxoglutarate, also genomic mutations were observed. Furthermore, the transcriptomic data suggested that genes involved in the biosynthesis of erythromycin were significantly up-regulated constantly, whereas some genes in the biosynthesis clusters of other secondary metabolites contained nonsense mutations and were expressed at extremely low levels. Based on the omics analysis, readily available strategies were proposed to engineer E3 by simultaneously overexpressing sucB (coding for 2-oxoglutarate dehydrogenase E2 component) and sucA (coding for 2-oxoglutarate dehydrogenase E1 component), which increased the erythromycin titer by 45% compared to E3 in batch culture. This work provides more promising molecular targets to engineer for enhancement of erythromycin production.

overall_design: S.erythraea NRRL23338 cultivated in the minimal liquid medium was harvested both at exponential phase and stationary phase (10 h & 50 h). The total RNA were sequenced in duplicate.


title: Induced-pluripotent stem-derived vascular endothelial cells in Down syndrome

city: Sutia

first: Hidehiro

last: Suginobe

address: 2-2, Yamadaoka

department: Pediatrics

country: Japan

institute: Osaka University

summary:
To investigate the physiological characteristics of endothelial cells (EC) harboring trisomy 21 (T21), we establised isogenic pairs of T21-iPSCs and corrected disomy 21 (cDi21)-iPSCs
We then performed gene expression profiling analysis using data obtained from RNA-seq of 5 different iPSC-derived ECs.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for two independent iPSC-derived EC lines of patients with DS (T21 and T21’), two independent iPSC-derived EC lines of HC_1 and HC_2, and an isogenic iPSC-derived EC line of cDi21.

first: Yoichiro

last: Ishii

first: Hidekazu

last: Ishida


title: IL-33-activated calcitonin gene-related peptide-producing memory Th2 cells co-operate with somatosensory neurons to induce conjunctival itch

city: chiba city

first: Masahiro

last: Kiuchi

state: chiba

address: cyuoku inohana1-8-1

institute: Chiba univercity

summary: Allergic conjunctivitis is a chronic inflammatory disease that is characterized by severe itch in the conjunctiva; but how neuro-immune interactions shape the pathogenesis of severe itch remains unclear. We identified a subset of memory-type pathogenic Th2 cells that preferentially expressed Il1rl1-encoding ST2 and Calca-encoding calcitonin gene-related peptide (CGRP) in the inflammatory conjunctiva using a single-cell analysis. The IL-33-ST2 axis in memory Th2 cells controlled the axonal elongation of the peripheral sensory C-fiber and the induction of severe itch. Pharmacological blockade and genetic deletion of CGRP signaling in vivo attenuated scratching behavior. The analysis of giant papillae from patients with severe allergic conjunctivitis revealed ectopic lymphoid structure formation with the accumulation of IL-33-producing epithelial cells and CGRP-producing pathogenic CD4+ T cells accompanied by peripheral nerve elongation. Thus, the IL-33-ST2-CGRP axis directs severe itch with neuro-reconstruction in the inflammatory conjunctiva and is a potential therapeutic target for severe itch in allergic conjunctivitis.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: White blood cells of CD45+CD31- fractions that were freshly prepared from mice conjunctival tissue and sorted using a BD FACS Aria III (10,000 cells each, cell viability >98%) were encapsulated into droplets, and libraries were prepared using Chromium Single Cell 3’ Reagent Kits v3 according to manufacturer’s protocol (10X Genomics). The generated scRNA-seq libraries were sequenced using a 128 cycle (paired-end reads) with a NovaSeq 6000 (Illumina). Neuron Cells of CD45-CD31- and live cell+ fractions that were freshly prepared from trigeminal nerve tissue of mice and sorted using a BD FACS Aria III (10,000 cells each, cell viability >98%) were encapsulated into droplets, and libraries were prepared using Chromium Single Cell 3’ Reagent Kits v3 according to manufacturer’s protocol (10X Genomics). The generated scRNA-seq libraries were sequenced using a 128 cycle (paired-end reads) with a NovaSeq 6000 (Illumina). White blood cells of CD45+ and CD4+ fractions that were freshly prepared from Giant papillae from patients and sorted using a BD FACS Aria III (10,000 cells each, cell viability >98%) were encapsulated into droplets, and libraries were prepared using Chromium Single Cell 3’ Reagent Kits v3 according to manufacturer’s protocol (10X Genomics). The generated scRNA-seq libraries were sequenced using a 128 cycle (paired-end reads) with a NovaSeq 6000 (Illumina).

first: Mikiko

last: Okano

first: Kiyoshi

last: Hirahara

first: Miki

last: Onoue

first: Yuki

last: Morimoto

first: Yuzuru

last: Ikehara

first: Akira

last: Murakami

first: Nobuyuki

last: Ebihara

first: Toshinori

last: Nakayama


title: Tumor-induced double positive T cells display distinct lineage commitment mechanisms and functions (6)

city: New York

first: Bic

last: MSKCC

state: NY

address: 1275 York Ave.

institute: Memorial SLoan-Kettering Cancer Center

summary: Here we report ATAC sequencing data from sorted antigen specific Trp1 CD4+ and CD4+CD8+, and Pmel CD8+ and CD8+CD4+ T cells in steady state (naïve, no tumor) mice and also in B16-tumor bearing animals

overall_design: ATAC sequencing of antigen specific T cell subsets in triplicate

first: Sara

last: Schad

first: Andrew

last: Chow

first: Levi

last: Mangarin

first: Heng

last: Pan

first: Jiajia

last: Zhang

first: Nicholas

last: Ceglia

first: Justina

middle: X

last: Caushi

first: Roberta

last: Zappasodi

first: Mathieu

last: Gigoux

first: Daniel

last: Hirschhorn

first: Sadna

last: Budhu

first: Masataka

last: Amisaki

first: Monica

last: Arniella

first: David

last: Redmond

first: Jamie

last: Chaft

first: Patrick

last: Forde

first: Justin

last: Gainor

first: Matthew

middle: D

last: Hellmann

first: Vinod

last: Balachandran

first: Sohrab

last: Shah

first: Kellie

last: Smith

first: Drew

last: Pardoll

first: Olivier

last: Elemento

first: Jedd

last: Wolchok

first: Taha

last: Merghoub


title: Expression profile of circular RNAs in oral lichen planus: a promising study of circRNA to explore the pathogenesis of oral lichen planus

city: Shanghai

first: Zhou

last: haiwen

address: 500 Qu-xi Road, Shanghai

department: Oral Mucosal Diseases

institute: Shanghai Ninth People’s Hospital, College of Stomatology, Shanghai Jiao Tong University School of Medicine

summary: Six oral mucous biopsies from untreated patients with oral lichen planus (OLP) and six normal oral mucous tissues from healthy patients were used for circRNA sequencing. 135 circRNAs with 2-fold differential expression were identified in OLP compared with normal control, including 83 upregulated circRNAs and 52 downregulated circRNAs. Ten selected circRNAs were validated by real-time qPCR

overall_design: Examination of different circular RNA expression in 2 tissue types.  Control samples are identical to healthy oral mucosa samples in GSE131182.

last: Haiwen

first: Song

last: Yuhan

first: Xu

last: Siming


title: PGC-1α isoform heterodimerization restricts transcription factor docking and limits metabolic adaptations in skeletal muscle

city: Solna

first: Igor

last: Cervenka

address: Solnavägen 9

department: Physiology and Pharmacology

country: Sweden

institute: Karolinska Institutet

summary: The PGC-1a gene is expressed as several transcriptional coactivator variants that regulate numerous adaptive processes. These include thermogenesis, hepatic metabolism, neuroprotection, and skeletal muscle adaptation to exercise training. To support such diverse functions, PGC-1 isoform expression and activation are under tight tissue- and context-specific control. Notably, PGC-1 isoforms generated by alternative gene promoter usage, and splicing are highly induced in skeletal muscle upon exercise. Here we show that PGC-12 and 3 are PGC-11 dimerization partners that limit its activity. Skeletal muscle PGC-12 and PGC-13 transgenics have reduced exercise performance and strength, which partially overlaps with PGC-1 loss-of-function. Mechanistically, PGC-11/3 dimerization precludes ERR recruitment and coactivation, so their co-expression in skeletal muscle impairs the innate bioenergetic adaptations characteristic of PGC-11 transgenics and reduces oxidative metabolism gene expression and exercise capacity. Removing this break to PGC-1a1 activity may have therapeutic applications in metabolic diseases and increase responsiveness to training.

overall_design: Gastrocnemius muscle from either wild-type or HSA-PGC-1a3 transgenic mouse was used for RNASeq analysis to determine the overall changes of transcriptome of PGC-1a3 mice.

first: Vicente

last: Martinez-Redondo

first: Serge

last: Ducommun

first: Manizheh

last: Izadi

first: Tomoyoshi

last: Nakadai

first: Mark

last: Jedrychowski

first: Paulo

middle: R

last: Jannig

first: William

middle: O

last: Jonsson

first: Maarten

last: Steinz

first: Jorge

last: Correia

first: Margareta

last: Porsmyr-Palmertz

first: Duarte

last: Ferreira

first: Paula

last: Valente-Silva

first: Arthur

middle: J

last: Cheng

first: Patricia

last: Brum

first: Donny

last: Camera

first: John

last: Hawley

first: Johanna

last: Lanner

first: Robert

middle: G

last: Roeder

last: Ruas


title: RNA-Seq of ATF4 and DDIT3 OE cardiomyocytes

first: Yuxuan

last: Guo

summary: To characterize transcriptome changes uopn ATF4 or DDIT3 in maturing cardiomyocytes

overall_design: AAV-GFP or AAV-ATF4 or AAV-DDIT3 were injected into P1 Rosa-Cas9GFP mice. The cardiomyocyets were isolated at 4wk old for FACS purification and RNA-seq analysis


title: ATAC-seq of SLTM knockdown in HIV infected Jurkats

city: New Haven

first: Jack

middle: Anthony

last: Collora

address: 295 Congress Ave

department: Microbial Pathogenesis

institute: Yale University

summary: In order to identify novel factors associated with regulation of HIV-1 transcription, we completed a genome-wide CRISPRi screen in a monogenic model of HIV-1. We identified SLTM mediated suppression of HIV-1 transcription. We hypothesized that SLTM would alter the chromatin acessibility at the site of HIV-1 integration. We conducted ATAC-seq of CRISPR ready cells encoding a single HIV-1 provirus in the SPECC1 gene transduced with a gRNA targetting SLTM and a Non-Targeting gRNA. We found that SLTM knockdown increased HIV-1 proviral acessibility across the provirus and host acessibility downstream of the site of HIV-1 integration.

overall_design: We conducted ATAC-seq of a monogenic Jurkat line with HIV-1 integrated into SPECC1. This line stably expresses dCas9-KRAB and nontargetting and SLTM guide RNAs.

first: Ya-Chi

last: Ho


title: Tumor-induced double positive T cells display distinct lineage commitment mechanisms and functions (4)

first: Bic

last: MSKCC

summary: Here we report RNA sequencing data from sorted antigen specific Trp1 CD4+ and CD4+CD8+, and Pmel CD8+ and CD8+CD4+ T cells in steady state (naïve, no tumor) mice and also in B16-tumor bearing animals

overall_design: Single cell RNA sequencing of antigen specific T cell subsets in triplicate

first: Sara

last: Schad

first: Andrew

last: Chow

first: Levi

last: Mangarin

first: Heng

last: Pan

first: Jiajia

last: Zhang

first: Nicholas

last: Ceglia

first: Justina

last: Caushi

first: Roberta

last: Zappasodi

first: Mathieu

last: Gigoux

first: Daniel

last: Hirschhorn

first: Sadna

last: Budhu

first: Masataka

last: Amisaki

first: Monica

last: Arniella

first: David

last: Redmond

first: Jamie

last: Chaft

first: Patrick

middle: M

last: Forde

first: Justin

last: Gainor

first: Matthew

last: Hellmann

first: Vinod

last: Balachandran

first: Sohrab

last: Shah

first: Kellie

middle: N

last: Smith

first: Drew

last: Pardoll

first: Olivier

last: Elemento

first: Jedd

last: Wolchok

first: Taha

last: Merghoub


title: Tumor-induced double positive T cells display distinct lineage commitment mechanisms and functions

first: Bic

last: MSKCC

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

overall_design: Refer to individual Series


title: Tumor-induced double positive T cells display distinct lineage commitment mechanisms and functions (3)

summary: Here we report transcriptional and TCR specificities associated with murine open repertoire CD45.1+ CD4+ and CD4+CD8+, and CD45.2+ CD8+ and CD8+CD4+ T cells isolated from murine B16 tumors

overall_design: Single cell TCR/RNA sequencing was performed on sorted open repertoire CD45.1+ CD4+ and CD4+CD8+, and CD45.2+ CD8+ and CD8+CD4+ T cells isolated from murine B16 tumors.

first: Sara

last: Schad

first: Andrew

last: Chow

first: Levi

last: Mangarin

first: Heng

last: Pan

first: Jiajia

last: Zhang

first: Nicholas

last: Ceglia

first: Justina

last: Caushi

first: Roberta

last: Zappasodi

first: Mathieu

last: Gigoux

first: Daniel

last: Hirschhorn

middle: P


title: Tumor-induced double positive T cells display distinct lineage commitment mechanisms and functions (2)

summary: Here we report transcriptional and TCR specificities associated with melanoma patient TIL populations.

overall_design: Single cell TCR/RNA sequencing was performed on sorted CD4+, CD8+, and CD4+CD8+ T cells isolated from melanoma patient tumor resections.

first: Sadna

last: Budhu

first: Masataka

last: Amisaki

first: Monica

last: Arniella

first: David

last: Redmond

first: Jamie

last: Chaft

first: Patrick

last: Forde

first: Justin

last: Gainor

first: Matthew

last: Hellmann

first: Vinod

last: Balachandran

first: Sohrab

last: Shah


title: Tumor-induced double positive T cells display distinct lineage commitment mechanisms and functions (5)

first: Bic

last: MSKCC

summary: Here we report bulk TCR sequencing data associated with open repertoire murine CD4+, CD4+CD8+, and CD8+ T cells isolated from B16 melanoma tumor resections

overall_design: Bulk TCR sequencing was performed on sorted open repertoire murine CD4+, CD4+CD8+, and CD8+ T cells isolated from B16 melanoma tumor resections.

first: Sara

last: Schad

first: Andrew

last: Chow

first: Levi

last: Mangarin

first: Heng

last: Pan

first: Kellie

last: Smith

first: Drew

last: Pardoll

first: Olivier

last: Elemento

first: Jedd

last: Wolchok

first: Taha

last: Merghoub


title: Tumor-induced double positive T cells display distinct lineage commitment mechanisms and functions (1)

summary: Here we report transcriptional specificities associated with murine Trp1 CD4+ and Trp1 CD4+CD8+ T cells isolated from B16 melanoma tumor resections.

overall_design: Single cell TCR/RNA sequencing was performed on sorted antigen specific Trp1 CD4+ and CD4+CD8+ T cells isolated from murine B16 tumors.

first: Jiajia

last: Zhang

first: Nicholas

last: Ceglia

first: Justina

last: Caushi

first: Roberta

last: Zappasodi

first: Mathieu

last: Gigoux

first: Daniel

last: Hirschhorn

first: Sadna

last: Budhu

first: Masataka

last: Amisaki

first: Monica

last: Arniella

first: David

last: Redmond


title: Cooperative assembly confers regulatory specificity and long-term genetic circuit stability [ChIP-Seq]

city: Boston

first: Ahmad

last: Khalil

address: 610 Commonwealth Avenue, Rm 405C

department: Biomedical Engineering

institute: Boston University

summary: In eukaryotes, links in gene regulatory networks are often maintained through cooperative self-assembly between transcriptional regulators (TR) and DNA cis-regulatory motifs, a strategy widely thought to enable highly specific regulatory connections to be formed between otherwise weakly-interacting, low-specificity molecular components. Here, we directly test whether this regulatory strategy can be used to engineer regulatory specificity in synthetic gene circuits constructed in yeast. We show that circuits composed of artificial zinc-finger TRs can be effectively insulated from aberrant misregulation of the host cell genome by using cooperative multivalent TR assemblies to program circuit connections. As we demonstrate in experiments and mathematical models, assembly-mediated regulatory connections enable mitigation of circuit-driven fitness defects, resulting in genetic and functional stability of circuits in long-term continuous culture. Our naturally-inspired approach offers a simple, generalizable means for building evolutionarily robust gene circuits that can be scaled to a wide range of host organisms and applications.

overall_design: ChIP-seq of yeast strains expressing a low-affinity synthetic transcription factor, high-affinity synthetic transcription factor, or low-affinity synthetic transcription factor with cooperative binding module, each with or without the transcription factor activation domain.

first: Meghan

last: Bragdon

first: Nikit

last: Patel

first: James

last: Chuang

first: Ethan

last: Levien

first: Caleb

last: Bashor


title: Cooperative assembly confers regulatory specificity and long-term genetic circuit stability [RNA-seq]

overall_design: RNA-seq of yeast strains expressing a low-affinity synthetic transcription factor, high-affinity synthetic transcription factor, or low-affinity synthetic transcription factor with cooperative binding module, each with or without the transcription factor activation domain.


title: RNA deep sequencing data of the whole transcriptomes of the wild-type and crp2 (MSMEG_0539) mutant strains of Mycobacterium smegmatis MC2 155

city: Pusan

first: Eon-Min

last: Ko

address: pusandaehak-ro

institute: Pusan national university

summary: Our comparative RNA sequencing analysis of the wild-type strain of M. smegmatis and its isogenic crp2 (MSMEG_0539) mutant strain lacking the cAMP receptor protein 2 revealed Crp2 regulon in the M. smegmatis

overall_design: Comparison of gene expression between the wild-type and crp2 (MSMEG_0539) mutant strains of Mycobacterium smegmatis that are aerobically grown.

first: Jeong-Il

last: Oh


title: Profiling and Bioinformatics Analysis of Differentially Expressed circRNAs in Osteogenically Differentiated MSCs of Patients with Ankylosing Spondylitis

city: Shenzhen

first: Fenglei

last: Chen

state: Guangdong Province

address: Futian District

department: orthopedics department

institute: The Eighth affilited Hospital of Sun-Yat-Sen University

summary:
Recent studies have reported that circular RNAs (circRNAs) play a crucial regulatory role in a variety of human diseases. However, the roles of circRNAs  in MSC osteogenesis in ankylosing spondylitis (AS) remain unclear.
these results revealed the expression profiles of miRNAs and the potential functions of the DE miRNAs in the MSC of patients with AS, which may provide new clues for understanding the mechanisms of ossify associated with AS, and proceed to identify novel potential molecular targets for the diagnoses and treatment of AS.

overall_design: We conducted circRNA and miRNA expression profiling of osteogenically differentiated MSC of patients with AS compared with healthy donors (HD) by RNA sequencing (RNA-seq) and analyzed the potential functions of differentially expressed (DE) circRNA by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses. The circRNA-miRNA interaction networks were also established.

first: Shan

last: Wang


title: Nov2016_CircadianRhythmPlasmaRNA

first: Ionita

middle: Calin

last: Ghiran

address: 3 Blackfan Circle

department: Medicine

institute: Beth Israel Deaconess Medical Center

summary: Impact of circadian rhythm in obtaining reference profiles of exRNAs in healthy individuals

overall_design: 23 samples from 8 subjects, 3 time points (8:30am, 2:30pm, 6:30pm) from each subject

first: Shulin

last: Lu


title: Cooperative assembly confers regulatory specificity and long-term genetic circuit stability

middle: S


title: Differential expression of genes in Geobacter sulfurreducens PCA under different electron acceptor and donor conditions

city: Tempe

first: César

middle: Ivan

last: Torres

state: AZ

address: 797 E. Tyler St.

institute: Arizona State University

summary: Geobacter sulfurreducens has a complex metabolism that adapts to use electron acceptors at a wide range of redox potentials. In this study, we used RNA-seq to identify genes associated with electron transfer pathways at different redox potentials. By correlating the RNA-seq data with cyclic voltammetry, we associated several multiheme cytochromes with specific electron transfer pathways.

overall_design: We sequenced RNA from Geobacter sulfurreducens PCA grown at 7 different conditions in triplicate.

middle: T

last: Howley

first: Cesar

middle: I

first: Rosa

last: Krajmalnik-Brown


title: Sox9 directs divergent epigenomic states in brain tumor subtypes

city: Houston

first: Debosmita

last: Sardar

address: 1 Baylor Plaza

institute: Baylor College of Medicine


title: Transcriptomic analysis of porcine PSCs  (pLCDM and pPSC(KOFL)) and  pLCDM_TSC induced from pLCDM

city: wenzhou

first: Lijun

state: zhejiang

address: chashan

institute: wenzhou medical university

summary: To further understand the biological characteristics of porcine pluripotent stem cells (pLCDM) established under LCDM system, transcriptome analyses were performed. The data showed that the biological events related to placental development were found in pLCDMs, while pLCDMs expressed more biological events related to embryo development and organ development of each layer than TE.  Transcriptomic analysis demonstrated that pLCDMs expressed higher levels of trophoblast lineage genes than pPSCs (KOFL). Furthermore, we successfully induced trophoblastic-like cells and pLCDM_TSCs with high expression of trophoblast lineage marker genes in vitro using a pure chemical medium. To comprehensively analyze the difference between pLCDM_TSCs and pLCDMs, low input RNA-seq was performed on the cell lines. A total of 3,594 DEGs were found, and 1,606 genes were significantly upregulated in pLCDM_TSCs, including BMP signaling pathway related genes BMPR1A, ID1, and trophoblast lineage marker genes ITGA1, ITGA6, FZD5, etc. It was worth noting that we found 509 highly expressed genes in hTSCs among the genes that were highly expressed in pLCDM_TSCs. Together, these results demonstrated the unique cellular potency of pLCDMs for trophoblast lineage.

overall_design:
mRNA profiles of porcine PSCs (pLCDM and pPSC(KOFL)) and  pLCDM_TSC induced from pLCDM
pLCDM: The porcine pluripotent stem cells which established from LCDM [1] (consists of human LIF, GSK3   inhibitor CHIR99021, G protein coupled receptors (GPCRs) inhibitor  (S) - (+) -dimethindene maleate  and PARP1 inhibitor minocycline hydrochloride)  condition using blastocysts.
pLCDM-TSC: The pLCDMs were cultured in human TSC conditions.These pLCDM-derived TSC-like cells were referred to as pLCDM-TSCs in this study.
pPSC(KOFL): The porcine pluripotent stem cells which established from KOFL [2] (A novel chemically defined serum    and feeder   free medium) condition using blastocysts.
The icm and te samples have been re-analyzed from samples  included in GSE139512. These samples have also been included here for completeness.
REFERENCES
[1] Yang Y, Liu B, Xu J et al. Derivation of Pluripotent Stem Cells with In Vivo Embryonic and Extraembryonic Potency. Cell. 2017;169(2):243-257 e225.
[2] Zhang X, Xue B, Li Y et al. A novel chemically defined serum- and feeder-free medium for undifferentiated growth of porcine pluripotent stem cells. J Cell Physiol. 2019.

first: Zhuoran

last: Yu

first: Sihan

last: Zhou

first: Minli

last: Liu

first: Xue

last: Zhang

first: Xu

last: Yang

first: Hongdi

last: Cui

first: Chaoqian

last: Jiang

first: Yanjiao

last: lv

first: Tingsheng

last: Yan

first: Qingran

last: Kong

first: Zhonghua


title: mRNA-Seq identifies the differentially expressed mRNA in negative control and METTL3 knockdown HULEC-5a

first: Yi

last: Chen

address: No.160 Pujian Road

department: Department of Anesthesiology

institute: Renji Hospital, Jiaotong University School of Medicine

summary: To identify the molecular mechanism by which METTL3 regulates endothelial barrier function, we performed RNA-seq and MeRIP-seq in HULEC-5a cells with stable METTL3 knockdown and control cells. The RNA-seq results revealed that 437 transcripts were significantly downregulated (fold change <0.5) after METTL3 knockdown. The MeRIP-seq results revealed that the m6A peaks in 1011 transcripts were decreased in abundance (fold change >1.2). Intriguingly, 55 transcripts overlapped in the RNA-seq and MeRIP-seq data

overall_design: Examination of differentially expressed mRNA in HULEC-5a , each with 2 replicates


title: Taurocholate acid signals a specific gene expression reprogramming affecting amino-acids and nucleotides metabolisms

city: Jouy-en-Josas

first: Cyprien

last: Guérin

address: INRAE - Domaine de Vilvert

institute: INRAE

summary: Enterococcus faecalis is a natural inhabitant of the human gastrointestinal tract. In a healthy physiological state of the gut (eubiosis), E. faecalis is a subdominant species in the intestinal microbiota. When the intestinal homeostasis is disrupted (dysbiosis), it becomes dominant species and can cause infections. The taurocholate bile acid (TCA) becomes prominent during dysbiosis. This experiment aimed to better understand how E. faecalis adapts to TCA. We showed that TCA reprograms genes involved in the pool management of amino acids and nucleotides.

overall_design: Impact of TCA on E. faecalis gene expression. Samples were sequenced at different time points after addition of 2 mM TCA (0.1% final).

first: Francis

last: Repoila

first: Françoise

last: Le-Bohec

first: Pierre

last: Nicolas


title: Sox9 directs divergent epigenomic states in brain tumor subtypes (ChIP-Seq)

first: Debosmita

summary: The goal of this study was to profile active H3K27ac marks between autochthonous mouse models of high-grade glioma (HGG) and ependymoma (EPN). Furthermore, with the objective of how transcription factor Sox9 affect H3K27ac states in these two models, we also profiled H3K27ac status between HGG and EPN after Sox9 overexpression (Sox9-GOF) or deletion (Sox9-LOF) in each of these models. In addition, we extended our studies to evaluate both H3K27ac and Sox9 states in human HGG and mouse EPN derived tumor cells.

overall_design: Chromatin immunoprecipitation (ChIP-seq) for H3K27ac in tumors from mouse models HGG, EPN and human HGG; ChIP-Seq for Sox9 in human HGG; ChIP-Seq for Sox9 from mouse EPN derived tumor cells. All experiments performed in independent biological replicates except for human HGG and mouse EPN derived cells.

first: Hsiao-Chi

first: Brittney

last: Lozzi

first: Srinidhi

last: Varadharajan

first: Stephen

last: Mack

first: Benjamin

last: Deneen


title: MeRIP-Seq (m6A-Seq) identifies the mRNA m6A modification target in negative control and METTL3 knockdwon HULEC-5a

overall_design: Examination of mRNA m6A modificaitons in HULEC-5a , each with 2 replicates


title: Gene expression in response to deoxycholate acid constraints growth of Enterococcus faecalis

summary: Enterococcus faecalis is a natural inhabitant of the human gastrointestinal tract. In a healthy physiological state of the gut (eubiosis), E. faecalis is a subdominant species in the intestinal microbiota. When the intestinal homeostasis is disrupted (dysbiosis), it becomes dominant species and can cause infections. The prominence of bile acids deoxycholate (DCA) hallmarks eubiosis. This experiment aimed to better understand how E. faecalis adapts to DCA. We showed that DCA impairs E. faecalis growth and imposes permanent adjustments to the expression of many crucial genes, including a majority of factors enabling translation. Thus, the drastic decrease of DCA amounts during dysbiosis may account for the rise of E. faecalis population.

overall_design: Impact of DCA on E. faecalis gene expression. Samples were sequenced at different time points after addition of 25 µM DCA (0.01% final). Some of the samples were treated with RppH (New England Biolabs; 1 unit / µg of RNA; 37°C for 30 min).


title: miR-378-3p Knockdown Mimics of MDS

city: Nashville

first: Yan

last: Guo

state: TN

address: 639 Preston Research Bld

institute: Vanderbilt Cancer Center

summary: The files represent mRNAseq data of the HL60 cell line (untransduced), and duplicate samples of HL60s transduced with empty (scrambled) control vector (System Biosciences, Cat. #MZIP000-VA-1) and duplicate samples of HL60s transduced with miRZip anti-miRNA Expression lentivector for miR-378-3p (System Biosciences, Cat# CS970A-1).

overall_design: miRZip-378a-3p (ZIP) and scramble (SCR) pGreenPurTM lentivectors (Cat# CS970A-1, System Biosciences, Palo Alto, CA) encode either a miRZip hairpin interfering RNA designed to generate the full-length antisense miR-378a-3p or an empty vector, respectively. HL60 were seeded in 24-well plates and infected with a multiplicity of infection of 20 with ZIP or SCR using polybrene transduction reagent (8ug/mL) (Cat# TR-1003-G, Millipore, Burlington, MA) by spin transduction (1500g, 2 hours). Initial transduction efficiency was measured by flow cytometry on day 3. After puromycin (Cat# P8833; Sigma Aldrich; Burlington, MA) (2ug/mL) treatment on day 3 through day 8, selection efficiency was measured by flow cytometry.  Expression of the ZIP construct normalized to U6 was confirmed by real time polymerase chain reaction (qPCR) using QuantiMirTM (Cat#RA420A-hU6, System Biosciences), using the ABI 7300 Real Time PCR System (Applied Biosystem, Foster City, CA).  Expression of miR-378-3p normalized to U6 was assessed by qPCR using TaqManTM MicroRNA Assays (Cat# 4427975, Applied Biosystems). Presence of green fluorescent protein (GFP) in both ZIP and SCR vectors was confirmed by polymerase chain reaction (PCR) and fluorescent microscopy (Nikon Eclipse TE2000-S Inverted microscope, Melville, NY). Library construction was conducted on total RNA using the TruSeq Small RNA sample preparation kit (Illumina, San Diego, CA) and sequenced on an Illumina HiSeq 2500. The raw sequencing reads in BCL format were processed through CASAVA-1.8.2 for FASTQ conversion and demultiplexing.  The RTA chastity filter was used, and only the pass filter reads were retained for further analysis. RNA-seq data went through multi-perspective quality control procedures following established guidelines. Alignment was performed by TopHat 2. Gene quantification using both Cufflinks and HTSeq was converted to differential expression analysis using Cuffdiff from the Cufflinks package and MultiRankSeq, respectively, which is a combination of DEGseq, edgeR, and baySeq.  A list of the most differentially expressed genes was generated from all four methods based on a weighted flexible compound covariate method (WFCCM).

first: Annette

last: Kim


title: Transcriptome data of Alcaligenes sp. HO-1 in response to ammonium stimulation at several time points.

city: Beijing

first: Meng-Ru

last: Wu

address: Beichen West Road

department: State Key Laboratory of Microbial Resources

institute: Institute of Microbiology, Chinese Academy of Sciences

summary:
A heterotrophic ammonia-oxidizing bacterium Alcaligenes sp. HO-1 was isolated from the activated sludge of a bioreactor treating ammonia-rich piggery wastewater. The goal and objectives of this experiment are to analyze the transcriptome profiles of nitrogen-metabolism-related genes of Alcaligenes sp. HO-1 in response to ammonium stimulation over time and to find out potential genes involved in ammonia oxidation process. So the RNA-seq anaylsis was performed by setting up each time points (0, 3.5, 10, 22 hours) when strain HO-1 were exposed to ammonia.
HO-1 was cultured with 83 mM succinate and 14 mM ammonium sulfate until ammonia was completely consumed and then another 14 mM of ammonium sulfate was added to the culture. Cells were harvested at 0 h, 3.5 h, 10 h and 22 h after the addition of ammonium sulfate. The sequencing data of RNAs obtained from strain HO-1 cells at each time was analyzed.

overall_design: 4 conditions were analzyed with 3 biological replicates : total 12 samples

first: Zhi-Pei

last: Liu

first: Shuang-Jiang


title: Contrasted effects of deoxycholate and taurocholate bile acids on the gut pathobiont Enterococcus faecalis

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

overall_design: Refer to individual Series


title: RNA-seq analyzes the effect of ptsI on transcriptome in Escherichia coli during ciprofloxacin treatment.

city: Newark

first: Yuzhi

last: Hong

state: NJ

address: 225 Warren St

department: PHRI, New Jersey Medical School

institute: Rutgers, the University of New Jersey

summary: A deficiency in ptsI, encoding a cytoplasmic protein that serves as the gateway for the phosphoenolpyruvate:sugar phosphotransferase system, was found to confer tolerance to diverse types of disinfectants and antimicrobials.  To understand the molecular basis of the increased tolerance, we performed RNA-seq analysis to compare the transcriptional profiles of the wild-type and the ΔptsI mutant strains before and after ciprofloxacin treatment. The data showed that cirpofloxacin treatment drastically increased the exprerssion of genes encoding enzymes in the TCA cycle and that the ptsI mutation suppressed the expression of most TCA genes and all ATP synthase genes, but elevated some of the genes involved in glycolysis and the pentose phosphate pathway (PPP) genes. Such transcriptomic alteration reduced stress-induced surge in respiration and accumutaion of toxic reaactive oxygen species, thereby conferring bacterial tolerance to diverse lethal stressors.

overall_design: Mid-log-phase cultures of E. coli K-12 were treated with ciprofloxacin (5 MIC) for 0 min and 90 min. Cells were collected for total RNA extraction and subsequent RNA-seq. Differential expression of various conditions was analyzed.

first: Weiwei

first: Xilin

last: Zhao


title: Effects of thyroid hormone on human preimplantation embryos

city: Paris

last: de la Grange

address: 29, rue du Faubourg Saint-Jacques

department: Paris Biotech Santé

institute: GenoSplice technology

summary: We found that the exposure of human preimplantation embryos to triiodothyronine (T3) has a profound impact on gene transcription only in the cells of inner cell mass (ICM) and no effect on cells of trophectoderm (TE).

overall_design: A total of 30 embryos at the two pronuclear (2PN) stage were used for the experiment; fifteen embryos were exposed to 10-7 M T3 till blastocyst stage and the remaining 15 embryos acted as controls.

first: Dusko

last: ILIC

first: Laila

last: NOLI


title: Sox9 directs divergent epigenomic states in brain tumor subtypes (RNA-Seq)

last: Sardar

summary: The goal of this study was to profile gene expression differences between autochthonous mouse models of high-grade glioma (HGG) and ependymoma (EPN). Furthermore, with the objective of how transcription factor Sox9 affect gene expression in these two models, we also profiled gene expression differences between HGG and EPN after Sox9 overexpression (Sox9-GOF) or deletion (Sox9-LOF) in each of these models.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for mouse tumor tissue from HGG and EPN models.

last: Chen


title: Persistent epigenetics changes due to elevated temperature during early development in mature zebrafish gonads

city: BARCELONA

first: Alejandro

last: Valdivieso

state: BARCELONA

address: PASSEIG MARÍTIM DE LA BARCELONETA, 37-49

country: Spain

institute: Insituto de Ciencias del Mar

type: Methylation profiling by high throughput sequencing

summary: Sexual development is a process regulated by complex interactions of molecular events that define the final sexual phenotype. Although the genetic and transcriptomic mechanisms involved in the formation of an ovary or a testis are largely studied, the epigenetic mechanisms regulating the fate of an undifferentiated gonad remain poorly understood. Using the zebrafish model (Danio rerio), we exposed larvae of two independent families to high temperature during sex differentiation (18-32 days post fertilization), and by a targeted sequencing approach, we analyzed the methylation profiles of 18 genes related to sexual development in mature gonads two months after the exposure. Gene expression patterns were measured by qPCR in order to correlate them with the DNA methylation. Methylation profiles were family-dependent. However, general patterns of sexual dimorphism were observed in the DNA methylation levels of steroidogenic enzymes (e.g. cyp19a1a, hsd17b1 and hsd11b2), transcription factors (e.g. dmrt1 and amh) and epigenetic-related (dnmt1) genes. In testes, temperature was able to alter the methylation levels of some genes by hypermethylation (cyp19a1a, cyp11a1, amh) or hypomethylation (dmrt1), whereas in ovaries, no changes in the methylation levels were observed. Our results indicate that high temperature during sex differentiation altered methylation in the adult fish gonads and as a novelty, methylation patterns of some genes (e.g., cyp11c1, hsd11b2, dmrt3a and ar) were described here for the fish time in fish.

overall_design: We analyzed DNA methylation level in the promoter regions of 18 genes in mature testis and ovaries (90 dpf) of laboratory zebrafish strains exposed to 28ºC and 36ºC during its gonadal development. Methylation patterns were analyzed by Multiplex Bisulfite Sequencing (MBS, Anastasiadi et al. 2018)

first: Dafni

last: Anastasiadi

first: Laia

last: Ribas

first: Francesc

last: Piferrer


title: Identification of a novel enhancer of CEBPE essential for granulocytic differentiation

city: Singapore

first: Pushkar

last: Dakle

address: 14 Medical Drive, #12-01,

institute: Cancer Science Institute of Singapore

summary: RNA-Seq of Control, dCas9-KRAB-EV, dCas9-KRAB-sg2 and dCas9-KRAB-sg5

overall_design: Differential expression between cell types (EV and sg2/sg5 knock down)


title: Synchronous cell cycle progression in the diatom Thalassiosira pseudonana

status: Public on May 19 2022

city: La Jolla

first: Raffaela

last: Abbriano

address: 9500 Gilman Dr

department: Scripps Institution of Oceanography

institute: University of California San Diego

summary: To identify the molecular components involved in diatom cell division, global transcript level changes were monitored over the silicon-synchronized cell cycle the model diatom Thalassiosira pseudonana.

overall_design: Silicon resupplementation T. psuedonana culture after 24 hour silicon starvation-induced cell cycle arrest. 9 timepoints taken every hour monitoring synchronous cell cycle progression in biological duplicate

first: Roshan

last: Shrestha

first: Jing

last: Li

first: Matteo

last: Pellegrini

first: Mark

last: Hildebrand


title: NIMA Related Kinase 7 reduction mediates acetaminophen-induced acute liver injury: role of impaired cell cycle regulation

city: Nanjing

first: Zhenzhen

last: Sun

address: Guangzhou Road#72

institute: Children’s Hospital of Nanjing Medical University

summary: Explored and demonstrated a new function of NEK7 in the liver against APAP-induced acute liver injury probably by dysregulating cyclins and disturbing cell cycle progression.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for liver tissue from NEK7 whole body knockout mice with tamoxifen inducibility (iKO_1, iKO_2, iKO_3) and wild type mice (Ctrl1, Ctrl2, Ctrl3).

first: Zhanjun

last: Jia


title: RiboReport - Benchmarking ribosome profiling based identification of open reading frames in bacteria.

city: Freiburg

first: Florian

last: Eggenhofer

address: Georges Köhler Allee 106

department: Institute for Informatics

institute: University of Freiburg

summary: Generation of a Ribo-seq dataset for E. coli MG1655 for benchmarking Ribo-seq analysis tools

sample_organism: Escherichia coli str. K-12 substr. MG1655

overall_design:
Ribosome profiling analysis of the E. coli translatome paired with transcriptome sequencing during log phase growth in LB.

RBP1 - Ribosome profiling, ribosomes purified with sucrose density gradient
S400-RBP1 - Ribosome profiling, ribosomes with size exclusion chromatography
TR1 - RNA-sequencing

first: Sarah

middle: L

last: Svensson

first: Cynthia

last: Sharma


title: In-depth transcriptomic analyses investigating molecular mechanisms underlying the osteogenic differentiation of human renal interstitial fibroblasts.

city: CHANGSHA

first: Hequn

state: HUNAN

address: 87 Xiangya Road, Kaifu DIstrict

department: Department of Urology

institute: Xiangya Hospital, Central South University

summary: Randall’s plaques (RP) are well established as precursor lesions of idiopathic calcium oxalate (CaOx) stones, and the process of biomineralization driven by osteogenic-like cells has been highlighted in RP formation, but the mechanism is poorly understood. Given the potential role of osteogenic-like renal interstitial fibroblasts in biomineralization, the isolated primary human renal interstitial fibroblasts (hRIFs) were either induced with a widely used osteogenic medium or cultured in normal medium for 7 days, and a transcriptomic analysis of LncRNA and mRNA was performed to study molecular mechanisms underlying the osteogenic differentiation of human renal interstitial fibroblasts.

overall_design: After obtaining approval from the Xiangya Hospital Ethics Committee and written informed consent from patients, human renal interstitial fibroblasts (hRIFs) were isolated from normal renal tissues without tumor invasion obtained from patients undergoing nephrectomy due to renal tumor. For renal fibroblast identification, immunofluorescence staining was used to detect the expression of vimentin and E-cadherin. Passages 4 of hRIFs were either induced with a widely used osteogenic medium (n=3) or cultured in normal medium (3) for 7 days. Total RNA was extracted using TRIzol reagent (Takara, Japan), and transcriptomic analysis of LncRNA and mRNA was performed to study molecular mechanisms underlying the osteogenic differentiation of human renal interstitial fibroblasts.

first: Zewu

last: Zhu

first: Fang

last: Huang


title: Transcription factor fluctuations underlie cell-to-cell variability in the Hedgehog response

city: St. Louis

first: Barak

last: Cohen

state: Missouri

address: 4515 McKinley Ave

department: Genetics

institute: Washington University in St. Louis School of Medicine

summary: Stochastic differences among clonal cells can initiate cell fate decisions in development or cause cell-to-cell differences in the responses to drugs or extracellular ligands. We hypothesize that some of this phenotypic variability is caused by stochastic fluctuations in the activities of transcription factors. We tested this hypothesis in NIH3T3-CG cells using the response to Hedgehog signaling as a model cellular response. Here we present evidence for the existence of distinct fast and slow responding substates of NIH3T3-CG cells. These two substates have distinct expression profiles, and fluctuations in the activity of the Prrx1 transcription factor (TF) underlie some of the differences in expression and responsiveness between fast and slow cells. We speculate that similar variability in other TFs may underlie other phenotypic differences among genetically identical cells.

overall_design: NIH3T3-CG cells were stimulated with the hedgehog pathway agonist SAG. We harvested cells at different time-points after SAG treatment to perform single-cell RNA sequencing.

first: Ramu

last: Avinash

first: Cohen

last: Barak


title: Endogenous tRNA fragments suppress hypoxia-driven bone cancer progression

city: Norwich

first: Darrell

last: Green

address: Earlham Road

department: Norwich Medical School

institute: University of East Anglia

summary: We report a modulated expression of tRNA fragments and microRNAs linked to chondrosarcoma progression and demonstrate a method for re-modulating this pathway

overall_design: normal tissue was recovered from trauma surgery and used as a control tissue to identify differential expression of small RNAs in malignant chondrosarcoma

first: Irina

last: Mohorianu

first: Nicole

last: Ward

first: Vaiyapuri

last: Sumathi

first: Simon

last: Carter

first: Iain

last: McNamara

first: Tamas

last: Dalmay

first: William

last: Fraser


title: Transcriptome Sequencing to Identify Important Genes and lncRNAs Regulating Abdominal Fat Deposition in Ducks

first: Zhixiu

last: Wang

address: No. 2 Yuanmingyuan West Road

institute: China Agricultural University

summary: Abdominal fat deposition is an important trait in meat-producing ducks. F2 generations of 304 Cherry Valley and Runzhou Crested White ducks were studied to identify genes and lncRNAs affecting abdominal fat deposition. RNA sequencing was used to study abdominal fat tissue of four ducks each with high or low abdominal fat rates. In all, 336 upregulated and 297 downregu-lated mRNAs, and 95 upregulated and 119 downregulated lncRNAs were identified. Target gene prediction of differentially expressed lncRNAs identified 602 genes that were further subjected to Gene Ontology and KEGG pathway analysis. The target genes were enriched in pathways associ-ated with fat synthesis and metabolism and participated in biological processes, including Linoleic acid metabolism, lipid storage, and fat cell differentiation, indicating that these lncRNAs play an important role in abdominal fat deposition. This study lays foundations for exploring molecu-lar mechanisms underlying the regulation of abdominal fat deposition in ducks and provides a theoretical basis for breeding high-quality meat-producing ducks.

overall_design: Abdominal fat deposition affects the quality of duck meat and the feed conversion ratio. Here, we performed transcriptome sequencing of the abdominal adipose tissue of ducks with high and low abdominal fat rate by RNA sequencing, exploring the key regulatory genes and lncRNAs related to abdominal fat deposition. As a result, several candidate genes, lncRNAs, and pathways related to abdominal fat deposition in ducks were retrieved. This study lays the foundations for exploring molecular mechanisms underlying the regulation of abdominal fat deposition in ducks, providing a theoretical reference for breeding high-quality meat-producing ducks.

first: Chunyan

last: Yang

first: Guobin

last: Chang

first: Guohong

last: Chen


title: Genome-wide identification of codanin-1 binding sites in human K562 erythroleukemia cells with chromatin immunoprecipitation coupled with next-generation sequencing

city: New Haven

first: Gary

last: Kupfer

address: 333 Cedar St

institute: Yale

summary: Congenital dyserythropoietic anemia type I (CDA-I) is an autosomal recessive disorder marked by ineffective erythropoiesis, abnormal morphology of bone marrow erythroblasts, and iron overload. Most cases of CDA-I are caused by mutations in the CDAN1 gene, which encodes for a ubiquitous protein of unknown function, codanin-1. To study the function of codanin-1 in CDA-I erythroid pathophysiology several erythroid models were developed. Here we show that codanin-1 expression is required for erythroid progenitor development and normal erythroid cell differentiation. Erythroid cells lacking codanin-1 demonstrated morphologic changes similar to that observed in CDA-I. Global gene expression changes after codanin-1 knockdown revealed alterations in a set of key erythroid genes. In particular, the AHSP gene, which showed decreased mRNA expression after codanin-1 knockdown in CD34+ cells, also demonstrated increased codanin-1 occupancy at its gene regulatory region by chromatin immunoprecipitation coupled to high-throughput sequencing. Using cell models recapitulating many features of CDA-I, we have confirmed the importance of codanin-1 during erythroid differentiation and provide mechanistic insight into how loss of codanin-1 expression results in CDA-I.

overall_design: ChIP-Seq analysis of codanin-1 binding sites in human K562 erythroleukemia cells. ChIP assays were performed using anti-codanin-1 antibodies (Cod1, Cod2). Cod1 corresponds to homemade antibody raised against N-terminal fragment of codanin-1 (amino acids 123-142, ProteinTech). Cod2 corresponds to commercial antibody raised against C-terminal fragment of codanin-1 from Santa Cruz (sc-68404, Santa Cruz). As controls, anti-GATA1 antibody (N6) (sc-265X, Santa Cruz) and rabbit IgG (sc-2027, Santa Cruz) were used.

first: Linette

last: Bosques

first: Shilpa

last: Hattangadi

first: Caroline

last: Tang

first: Sameet

last: Mehta


title: Robust colonic epithelial regeneration and amelioration of colitis via FZD-specific activation of Wnt signaling

city: South San Francisco

first: Russell

last: Fletcher

address: 171 Oyster Point Blvd, Suite 400

department: Discovery Biology

institute: Surrozen, Inc.

summary: Background and aims: Current management of inflammatory bowel disease (IBD) leaves a clear unmet need to treat the severe epithelial damage. Modulation of Wnt signaling might present an opportunity to achieve histological remission and mucosal healing when treating IBD. Exogenous R-spondin (RSPO), which amplifies Wnt signals by maintaining cell surface expression of Frizzled (FZD) and low-density lipoprotein receptor-related protein (LRP) receptors, helps repair intestine epithelial damage, but it also induces hyperplasia of normal epithelium. Wnt signaling may also be modulated with the recently developed Wnt mimetics, recombinant antibody-based molecules mimicking endogenous Wnts. Methods: We first compared the epithelial healing effects of RSPO2 and a Wnt mimetic with broad Fzd-specificity in an acute Dextran Sodium Sulfate (DSS) mouse colitis model. Guided by Fzd expression patterns in the colon epithelium, we also examined the effects of Wnt mimetics with sub-family Fzd-specificities. Results: In the DSS model, Wnt mimetics repaired damaged colon epithelium and reduced disease activity and inflammation and had no apparent effect on uninjured tissue. We further identified that the FZD5/8 and LRP6 receptor-specific Wnt mimetic, SZN-1326-p, was associated with the robust repair effect. Through a range of approaches including single-cell transcriptome analyses, we demonstrated that SZN-1326-p directly impacted epithelial cells, driving transient expansion of stem and progenitor cells, promoting differentiation of epithelial cells, histologically restoring the damaged epithelium and, secondarily to epithelial repair, reducing inflammation. Conclusion: It is feasible for treating epithelial damage in IBD to design Wnt mimetics such as SZN-1326-p that affect damaged intestine epithelium specifically and restore its physiological functions.

overall_design: Mouse total colon cells from uninjured and the DSS colitis model  were isolated by tissue dissociation and FACS purification prior to scRNA-seq using 10x Genomics reagents (v3). There were four uninjured replicates and three anti-GFP control treatments and three Surrozen protein (SZN-1326-p) treated samples per timepoints (24-hours and 48-hours after dosing).

middle: B

first: Liqin

last: Xie

first: Diksha

last: Bhatia

first: Darshini

last: Shah

first: Jaqueline

last: Phipps

first: Shalaka

last: Deshmukh

first: Haili

last: Zhang

first: Jingping

last: Ye

first: Sungjin

last: Lee

first: Lucas

last: Le

first: Maureen

last: Newman

first: Hui

first: Asmiti

last: Sura

first: Suhani

last: Gupta

first: Laura

middle: E

last: Sanman

first: Fan

first: Weixu

last: Meng

first: Hélène

last: Baribault

first: Geertrui

middle: F

last: Vanhove

first: Wen-Chen

last: Yeh

first: Yang

last: Li

first: Chenggang

last: Lu


title: Codanin-1 binding sites in human K562 erythroleukemia cells; Global Gene expression changes in response codanin-1 knockdown in erythroid-committed cells

first: Gary

last: Kupfer


title: RNA sequencing reveals global gene expression changes in response to codanin-1 knockdown in erythroid-committed cells

overall_design: RNA-Seq was used to analyze the effects of CDAN1 (codanin-1) knockdown in erythroid-induced human primary cells transduced with non-targeting shRNA (shControl) or shRNAs targeting different regions of CDAN1, the 3’UTR or the coding sequence.

first: Linette

last: Bosques

first: Caroline

last: Tang

first: Sameet

last: Mehta


title: A single local delivery of paclitaxel and nucleic acids via an immunoactive polymer eliminates solid tumors and induces systemic antitumor immunity

city: West Lafayette

first: Nadia

middle: Marie

last: Atallah

state: IN

address: 201 S. University St

department: Center for Cancer Research

institute: Purdue University

summary: Despite recent advances in cancer therapy, hard-to-reach, unidentified tumors remain a significant clinical challenge. A promising approach is to treat locatable and accessible tumors locally and stimulate antitumor immunity in situ to exert systemic effects against distant tumors. We hypothesize that a local carrier of immunotherapeutics is critical to the effective activation of in-situ antitumor immunity. Here, we develop a polyethyleneimine derivative (2E’), which activates immune cells and co-delivers hydrophobic immunogenic cell death inducers and immunomodulatory nucleic acids/nucleotides. A single local administration of 2E’ or its combination with paclitaxel and PD-L1 siRNA or cyclic dinucleotide induces strong antitumor immunity, resulting in immediate regression of large established tumors, tumor-free survival, and the resistance to rechallenge and metastasis in different models. This study supports that effective in-situ induction of antitumor immunity can lead to systemic protection from distant and recurrent diseases, where 2E’ plays multiple roles as a simple and versatile carrier of immunotherapeutics.

overall_design: RNA-seq in control (untreated day 0) and day 7 treated mice

first: Fanfei

first: Jianping

last: Wang

first: Gregory

last: Creswell

middle: A

last: Lanman

first: Timothy

last: Ratliff

first: Yoon

last: Yeo


title: CAPTURE of the human U2 snRNA genes expands the repertoire of associated factors.

status: Public on May 18 2022

city: Leicester

first: Michael

last: Tellier

state: Select State

address: Lancaster Road

department: Department of Molecular and Cell Biology

institute: University of Leicester

summary: In order to identify factors involved in transcription of human snRNA genes and 3’ end processing of the transcripts, we have carried out CRISPR affinity purification in situ of regulatory elements (CAPTURE), which is deadCas9-mediated pull-down, of the tandemly-repeated U2 snRNA genes in human cells. CAPTURE enriched many factors expected to be associated with human snRNA genes including pol II, NELF, CDK9, SPT5 and several subunits of the Integrator Complex. SPT6, Mediator subunits 16, 20 and 23, TAF15, CDK7, CDK9, Cyclin K, and the SPT16 subunit of FACT were also enriched. Several polyadenylation factors, including CPSF1, CPSF6 and CstF1-3 were also enriched by U2 gene CAPTURE. These add to the polyadenylation factors CstF2, Pcf11 and Ssu72 which we previously showed are associated with the human U1 and U2 genes. Analysis of genome-wide studies and ChIP-qPCR confirms the association of SPT6 with the U2 genes. In addition, SPT6 knockdown causes loss of subunit 3 of the Integrator complex from the U2 genes and transcriptional readthrough, indicating a functional role in snRNA gene expression. CAPTURE has therefore expanded the repertoire of transcription and RNA processing factors associated with these genes.

overall_design: ChIP-seq of CDK12 in human HEK293 cells

first: Joana

last: Guiro

first: Mathias

last: Fagbemi

first: Justyna

last: Zaborowska

first: Stephanie

last: Barker

first: Marjorie

last: Fournier

first: Shona

last: Murphy


title: Ovarian Stroma RNA-seq of Progesterone receptor null vs WT mice at 8hrs post hCG

city: ADELAIDE

first: Kirsten

last: Smith

address: Lvl 5, AHMS, North Terrace

country: Australia

institute: University of Adelaide

summary: Progesterone receptor-dependent expression of the ovairan stroma is investigated to determie PGR control of stromal functions at ovulation.

overall_design: Ovaries were collected from 21-25day old PGR(-/-) and PGR(+/+) littermates at 8hrs post-hCG. N=3-4 per genotype with each experimental replicate consisting of tissue pooled from 3 mice. The Stromal tissue of the ovary (GC-depleted ovary) was used for mRNA-seq Illumina Truuseg Strandard mRNA kit, Illumina Novaseq 600 SP. Paired end, 100bp, depth of 54-72M reads. Qualisty control checked using FastQC. Salmon lignment to GRCm39 M26  mouse transcriptome. DESeq2 used to asses differentially expressed genes.

first: Doan

last: Dinh

first: Darryl

last: Russell

first: Rebecca

last: Robker


title: H3K4 demethylase KDM5B regulates epigenetic plasticity and cancer cell identity

city: Detroit

first: Benjamin

last: Kidder

state: MI

address: 4100 John R St

department: Oncology

institute: Wayne State University

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

overall_design: Refer to individual Series


title: long non-coding RNA GDAR regulate ovine granulosa cells apoptosis by affecting the expression of apoptosis-related genes

city: Baoding

first: Yong

last: Wang

address: lekai street

institute: Hebei Agricultural University

summary: Short-term dietary supplementation of female sheep during the luteal phase can increase fertility and most probably by stimulating glucose uptake by the follicles. However, the molecular mechanism of glucose regulates follicular development has not yet been clarified, especially the further study of long non-coding RNA (lncRNA) in determining fertility during follicular development. We generated GCs models of different doses of glucose (0, 2.1, 4.2, 8.4, 16.8 and 33.6 mM), and observed that the highest cell viability was recorded in the 8.4 mM group and the highest apoptosis rates were recorded in the 33.6 mM groups. Therefore, the control (n = 3, 0 mM glucose group), low glucose (n = 3, add 8.4 mM glucose concentration group), and high glucose (n = 3, add 33.6 mM glucose concentration group) of GCs were created for the next whole genomic RNA sequencing (RNA-seq). In total, 11,221 novel lncRNAs and 510 annotated lncRNAs were identified in the GCs samples. Gene ontology term enrichment indicates the obvious enrichment in apoptosis and its related pathways, which suggests that cell apoptosis could play a critical role in the process of glucose-induced GCs differentiation. Furthermore, we focused on the function of a lncGDAR and verified that lncGDAR could involve cell apoptosis by effecting the expression of Bcl-2, BAX, Caspase-3, and Caspase-7 genes. These results provide the basis for further study of LncRNA regulation mechanism in nutrition on female fertility.

overall_design: Fresh ewe ovaries from Thin-tailed Han sheep aged one year were collected from the local abattoir and transported to the laboratory within 3 h in a buffered saline solution supplemented with a streptomycin/penicillin mixture (1%) and maintained at 37 ℃. Ovaries were washed three times with prewarmed normal saline before isolation of follicles. The follicles (the diameter of 3-5 mm) were isolated and punctured with a disposable syringe to collect follicular fluid. The follicle suspensions were pooled, and GCs were harvested immediately after centrifuging at 1000×g for 10 min. GCs were counted with a hemocytometer and their viability was confirmed by trypan blue exclusion. Then, the GCs were seeded in cell culture plates (Thermo Fisher Scientific, USA) at a density of 1×105/well and cultured in Dulbecco’s Modified Eagle Medium (DMEM/F12, Gibco, USA) supplemented with 10% fetal bovine serum (FBS) (Gibco, Grand Island, NY, USA) and 1% streptomycin/penicillin mixture in a humidiﬁed atmosphere at 37 ℃ and 5% CO2 for 48 h with the medium changed every 24 h.   The GCs were allocated to six treatments and cultured in 6-well plates at a density of 1×106/well using DMEM/F12 medium supplemented with 10% FBS. All treatments were cultured without glucose and serum but containing streptomycin/penicillin mixture (1%) for 8 h; then, the treatments received various solutions of glucose and were cultured for an additional 24 h as follows: 0 mM (i.e., zero glucose), 2.1 mM (378.3 μg/ml), 4.2 mM (756.6 μg/ml), 8.4 mM (1513.2 μg/ml), 16.8 mM (3026.4 μg/ml), 33.6 mM (6052.8 μg/ml). These doses were designed to span the normal physiological ranges of follicles (1.1- 2.1 mM) [27-31]. The 16.7 mM glucose concentration that represented the normal rate of glucose supplementation in commercial preparations of these media, and the maximum glucose concentration of 33.6 mM represents 30 times the super-physiological concentration, which is used to detect the changes in cell apoptosis and proliferation at the super-physiological concentration of glucose. This culture system has been developed so that GC retain hormonally responsive aromatase activity and do not luteinize with time in culture [32-35]. The media and GCs were collected for subsequent measurements after the 24 h treatment period.     Sequencing data were deposited with the NCBI. The procedures regarding sequencing, data processing, and further bioinformatics analyses can be found in detail in the Supplemental Materials and Methods. Total RNAs from ovine granulosa cells subjected to control (n = 3, 0 mM glucose groups), low glucose (n = 3, add 8.4 mM glucose concentration groups), and high glucose (n = 3, add 33.6 mM glucose concentration groups) were isolated and quality controlled. The preparation of whole-transcriptome libraries and next-generation sequencing were conducted by Novogene Bioinformatics Technology (Beijing, China). RNA-seq was performed on an Illumina Hiseq  platform, and 150-bp-paired single-end reads were generated according to Illumina’s protocol. All the downstream bioinformatics analyses were based on clean data of high quality.

first: Ying-jie

last: Zhang


title: Transcriptomics biomarkers in prostate cancer

city: Créteil

first: Virginie

last: Firlej

address: Ur Trepca

institute: UPEC TrePca

summary:
Prostate cancer (PCa) is the number one cancer in men. It represents a challenge for its management due to its very high incidence but low risk of lethal cancer. Over-diagnosis and over-treatment are therefore two pitfalls. The PSA (Prostate Specific Antigen) assay used for early diagnosis and clinical or molecular prognostic factors are not sufficiently reliable to predict the evolution of the cancer and its lethal or non-lethal character. Although PCa is most often detected at a localised stage, there are almost 30% of metastatic or locally advanced forms for which treatments can slow down the evolution but cannot be curative.
With the use of high-throughput technological tools such as transcriptomics , it is becoming possible to define molecular signatures and identify predictive biomarkers of tumour aggressiveness . Here, we have analyzed 137 samples.

overall_design: array with total RNA were extracted from frozen primary prostatectomie tissue

first: Pierre

last: De la Grange

first: Arturo

last: Londono-Vallejo

first: Yves

last: Allory


title: Transcriptome sequencing for exploring the mechanism of islet cell protection by anthocyanin.

city: Guangzhou

first: Yunan

last: Chen

state: Guangdong

address: Guangzhou, Guangdong Province, P.R. China.

institute: SUN YAT-SEN UNIVERSITY

summary: We applied GSIS, immunofluorescence staining, WB, and flow cytometry to observe the protective effects of C3G on palmitate-induced beta cell apoptosis and insulin deficiency, after which we explored the mechanism using RNA sequencing (RNA-seq) and quantitative real-time PCR (qPCR), and finally validated the mechanism using Western Blot (WB) and small interfering RNA (siRNA).The results of GSIS on both INS-1E cells and mouse primary islets plus a series of experiments related to cell apoptosis showed that C3G could restore the damage caused by lipotoxicity through promoting insulin secretion and alleviating cell apoptosis. RNA-seq and qPCR results indicated that the protective effect of C3G was most likely mediated by repressing ER stress pathways, especially the PERK pathway, while partly due to elevated expression of insulin secretion-related genes. Finally, the results of knockdown of the pro-apoptotic marker CHOP in PERK pathway further confirmed the above findings.Conclusion: C3G may act though reducing ER stress to exert its protective impact on pancreatic beta cells under lipotoxicity. This research provides favorable evidence for the therapeutic application of C3G in T2DM.

overall_design: Examination of the transcriptome of INS-1E cell lines in the presence of palmitic acid, palmitic acid and anthocyanin mixtures, and controls, with three replicates of each of the three groups.


title: Sustainedcorrection of hippocampal neurogenic and cognitive deficits after a brief treatment by Nutlin-3 in a mousemodel of Fragile X Syndrome.

city: Madison

first: Xinyu

last: Zhao

state: Wisconsin

address: 1500 HIghland Ave, Wiasman Center North Tower T513

institute: University of Wisconsin Madison

summary: We found that transient treatment with Nutlin-3 of 2-month-old young adult FMR1-deficient mice prevents the emergence of neurogenic and cognitive deficits in mature adult FXS mice at 6-month of age. We further found that the long-lasting restoration of neurogenesis and cognitive function might not be mediated by changing intrinsic properties of adult neural stem cells. Transcriptomic analysis of the hippocampal tissue demonstrated that transient Nultin-3 treatment leads to significant expression changes in genes related to extracellular matrix, secreted factors, and cell membrane proteins in FMR1-deficient hippocampus

overall_design: We dissected the hippocampal tissue of 6-month-old mice and performed RNA-seq analysis

first: Sahar

last: Javadi

first: Jie

last: Sheng

first: Daifeng


title: Transcriptome in NSCLC cell lines

city: Sevilla

first: Amancio

last: Carnero

state: Sevilla

address: Maura Montaner sn

department: Oncohematology and Genetics

institute: IBIS/CSIC

summary: Analysis of the whole transcriptome in 15 NSCLC cell lines of different origin

first: Javier

last: Peinado


title: Multimodal measurement of the transcriptome and proteome in single cells using nanoSPLITS

city: Richland

first: James

middle: Michael

last: Fulcher

state: Washington

address: 902 Battelle Blvd

department: Environmental Molecular Sciences Laboratory

institute: Pacific Northwest National Laboratory

summary: We report the development of a method (nanoSPLITS) capable of performing global proteome and transcriptome measurements from the same single-cell.

overall_design: RNAseq and scRNAseq data of mouse C10 and SVEC cell lines that were processed with nanoSPLITS

first: Meng

last: Markillie

first: Hugh

middle: D

last: Mitchell

first: Kristin

last: Engbrecht

first: Ying

last: Zhu


title: Transcriptome-wide N6-Methyladenosine (m6A) modifications in Anopheles sinensis

city: Shanghai

first: Congshan

last: Liu

address: 207 Rui Jin Er Road

institute: National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention

summary: We profile transcriptome-wide m6A in female and male Anopheles sinensis and reveal that m6A is also a highly conserved modification of mRNA in mosquitoes were generated by deep sequencing, in triplicate, using illumina Novaseq™ 6000. Distinct from mammals and yeast, but similar to Arabidopsis thaliana, m6A in An. sinensis is enriched not only around the stop codon and within 3’-untranslated regions, but also around the start codon and 5’-UTR. Gene ontology analysis indicates that the unique distribution pattern of m6A in An. sinensis is associated with mosquito sex-specific pathways. In addition, the positive correlation between m6A deposition and mRNA abundance indicates that m6A can play roles in regulating gene expression in mosquitoes. Our study proposed a transcriptional regulatory network of m6A in An. sinensis, which may provide a new clue for the control of this disease-transmitting vector.

overall_design: Examination of the m6A modification on mRNA of female and male Anopheles sinensis.

first: Jianhai

last: Yin