title: RNA-seq at different days during the conversion of mouse fibroblasts into corneal endothelia by defined small molecules

city: Wenzhou

first: ShaoHui

last: Pan

state: Zhejiang

address: Xueyuan road #270

institute: Wenzhou Medical University

summary: we established a stepwise, small-molecule-based method to reprogram mouse fibroblasts into expandable chemically induced neural crest cells (ciNCCs) and their derivative, corneal endothelial cells (ciCECs).

overall_design: RNA expression at D0, D7, D12, ciCECs,primary CECs

first: Shao-Hui

first: Zi-Bing

last: Jin


title: Identification of ERRα target genes in human breast cancer cells

status: Public on Jun 09 2021

city: LYON

first: Jean-Marc

last: Vanacker

address: 32-34 avenue Tony Garnier

country: France

institute: IGFL, ENS de Lyon, CNRS UMR 5242

type: Genome binding/occupancy profiling by high throughput sequencing

summary: DNA-binding location of the orphan nuclear receptor ERRα was determined by ChIP-seq in MDA-MB-231 cells

overall_design: Two cell culture samples were used for two ChIP replicates against ERRα and two input samples

first: Catherine

last: Cerutti

first: Violaine

last: Tribollet


title: Transcriptomic effects of SET7 repression in human breast cancer cells

type: Expression profiling by high throughput sequencing

summary: SET7 is a histone methyltransferase suggested to influence gene expression by modifying local chromatin at H3K4me1. RNA-sequencing experiment aimed at identifying the genes regulated by SET7 in MDA-MB-231 cells after SET7 repression.   Then comparing the results with those obtained from RNA-seq data after ERRα inactivation (GSE49110) allowed to identify genes regulated by ERRα and SET7.

overall_design: MDA-MB231 cells were inactivated for SET7 using two different siRNAs. One control siRNA was used for comparison. In each condition, triplicate samples were analyzed.


title: A critical density of histone H3 lysine 9 tri-methylation is required for propagation of heterochromatin and epigenetic inheritance

city: Bethesda

first: Shiv

last: Grewal

state: MD

address: NCI bldg 37 Rm 6068 9000 Rockville Pike

department: LBMB

country: USA

institute: NCI

type: Genome binding/occupancy profiling by array

summary:
Occupancy profiling of myc-tagged Raf1 protein in fission yeast.
Occupancy profiling of lysine 9 dimethylated and trimethylated histone H3 in fission yeast.

overall_design: Agilent 60mer array was used to analyze DNA recovered by immunoprecipitation of  myc-tagged proteins or K9-di/trimethylated histones from asynchronous culture of fission yeast.

first: Amber

middle: C

last: DiPiazza

first: Nitika

last: Taneja

first: Jothy

last: Dhakshnamoorthy

first: David

last: Wheeler

first: Sahana

last: Holla

middle: S


title: Identification of competing endogenous RNA (ceRNA) and micro-RNA profiles and regulatory networks in 4-nonylphenol-induced impairment of sertoli cells

city: xiamen

first: wenjie

last: liu

address: xiangan strict xiamen university

country: China

institute: xiamen university

type: Non-coding RNA profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and RELA-/- Cornea Transcriptomes

city: shanghai

first: qian

last: yu

address: Dongchuan road 800#

institute: SJTU


title: Transcriptome analysis upon Hmg20a knockdown in astrocytes

city: Sevilla

first: Jose

middle: C.

last: Reyes

address: Av. Américo Vespucio

department: Genome biology

country: Spain

institute: CABIMER

summary: We recently demonstrated that the ‘Metabesity’ factor HMG20A is essential for beta cell functional maturity and adaptation to physiological stress. As this chromatin remodeling factor also dictates CNS development, we sought to determine whether HMG20A is expressed in astrocytes and whether it potentiates astrocyte function in response to environmental cues. To investigate the function and regulatory mechanism of HMG20A, RNA-seq was performed on astrocytes treated or not with a siHMG20A. HMG20A silencing in astrocytes resulted in repression of pro-inflammatory, cholesterol homeostasis and epithelial-to-mesenchymal transition pathways. This results indicate that HMG20A coordinates the astrocyte polarization state. Under physiological pressure such as obesity and insulin resistance that induces low grade inflammation, HMG20A expression is increased to induce astrogliosis in an attempt to preserve the neuronal network and glucose homeostasis. onetheless, a chronic metabesity state or functional mutations will result in lower levels of HMG20A, failure to promote astrogliosis and increase susceptibility of neurons to stress-mediated apoptosis.

overall_design: mRNA profiles of murine astrocytes treated with siControl or siHmg20a were generated by deep sequencing, in duplicates, using Illumina Nexseq.

first: Esther

last: de la Fuente-Martin

first: Petra

last: Lorenzo

middle: A

last: Guerrero-Martínez

first: Benoit

last: Gauthier


title: Transcriptionally regulated energy metabolism drives early erythropoiesis (mon RNA-seq)

city: Boston

first: Leonard

last: Zon

state: MA

address: 1 Blackfan Circle

department: Oncology/Hematology

institute: Boston Children's Hospital

summary: Transcription and metabolism both influence cell function yet dedicated transcriptional control of metabolic pathways that regulate cell fate has rarely been defined. Through a chemical suppressor screen, we discovered that inhibition of the pyrimidine biosynthesis enzyme DHODH rescues erythroid differentiation in bloodless moonshine mutant embryos defective for the transcription elongation factor tif1γ. This rescue depends on the functional link of DHODH to mitochondrial respiration. Low α-ketoglutarate levels caused by tif1γ loss lead to histone hypermethylation. TIFγ directly controls coenzyme Q synthesis gene expression and coenzyme Q levels are reduced in moonshine mutants. A coenzyme Q analogue rescues moonshine’s bloodless phenotype. These results demonstrate mitochondrial metabolism is a key output of a lineage transcription factor that drives cell fate decisions in the early blood lineage.

overall_design: Heterozygous mon;drl:eGFP fish were crossed with heterozygous mon fish, ensuring transmission of only one allele of drl:EGFP and embryos sorted for green fluorescence (which is markedly reduced in mon mutant embryos) beginning at ~21 hpf. 30 phenotypically mon and wild-type embryos were harvested per replicate (= clutch, each clutch from one pairwise mating) for RNA-seq by homogenizing in TRIzol.

first: Marlies

middle: P

last: Rossmann

first: Song

last: Yang

middle: I


title: Transcriptionally regulated energy metabolism drives early erythropoiesis (tif1g RNA-seq)

overall_design: tif1γ (ENSDART00000020116.9/NM_001002871.2) was knocked down (tif1γ KD) by injecting 1 ng of an ATG-blocking morpholino (Gene Tools, 5’→3’ morpholino sequence ATCTTGGCCTTTGTTGTCCGCCATC) into zebrafish wild-type (TU) embryos at the 1-2 cell stage. As a control (Ctrl KD), 1 ng of a Standard Control oligo (designed by Gene Tools, 5’→3’ morpholino sequence CCTCTTACCTCAGTTACAATTTATA) was injected into zebrafish embryos at the 1-2 cell stage. tif1γ KD and Ctrl KD embryos from each clutch were split in half and treated with either 7 μM leflunomide or the equivalent amount of DMSO from 5.3 hpf until 10 hpf, when embryos were harvested for RNA-seq by snap-freezing them.


title: Transcriptome-wide m6A profiling reveals mRNA post-transcriptional modification of boar sperm during cryopreservation

city: Chengdu

first: Ziyue

last: Qin

address: Huimin Road 211

institute: Sichuan Agricultural University

type: Methylation profiling by high throughput sequencing

summary: In present study, we first tried to reveal the transcriptome-wide m6A methylation pattern in boar fresh sperm (Fs) and frozen-thawed sperm (Fts) through MeRIP-seq, which demonstrates occurrence the diverse m6A modiﬁcation patterns during cryopreservation. Results: the expression of m6A modification enzymes were significantly dysregulated in sperm during cryopreservation. Furthermore, the m6A peaks were mainly enriched in coding regions and near stop codons with classical RRACH motifs. In Fts, a total of 1754 differentially methylated m6A genes containing 1928 differentially methylated peaks were identified as compared to Fs. Bioinformatics analysis revealed the role of these genes containing significantly altered m6A peaks (DMMGs) were significantly enriched in terms of metabolism and transcription, as well as a number of DMMGs were annotated to ubiquitin mediated proteolysis, AMPK, mTOR and MAPK signaling pathways. Furthermore, the joint analysis of DMMGs and differentially expressed genes indicated that both of these play a vital role in sperm energy metabolism and apoptosis. Conclusion: Our study is first to reveal the dynamic m6A modification in mRNAs of boar sperm during cryopreservation, and provides a new evidence regarding the potential roles of m6A in modulating sperm motility, apoptosis and metabolism. Keywords: N6-methyladenosine (m6A); Boar sperm; Cryopreservation; MeRIP-seq

overall_design: Three Duroc boars were used in this study. A total of 5 sperm-rich fractions were collected from each boar using the gloved-hand technique during the autumn-winter period (n=15). Then, the fresh ejaculates were equally divided into two parts and one was immediately exposed to liquid nitrogen and then stored for RNA extraction (Fresh sperm, Fs). While, the other part (Frozen-thawed sperm, Fts) was cryopreserved according to our previously described procedure (PMID: 24974820). Subsequently, methylated RNA immunoprecipitation sequencing (MeRIP-seq), RNA-seq and assays of m6A methylated RNA immunoprecipitation-qPCR (MeRIP-qPCR) were performed to evaluate the differences in m6A methylation and gene expression between boar fresh sperm (Fs) and frozen-thawed sperm (Fts).

first: Wencan

last: Wang

first: Malik

last: Ali

first: Yan

last: Zhang

first: Ming

first: Guangbin

last: Zhou

first: Jian-dong

first: Changjun

last: Zeng


title: Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and RELA-/- Cornea Transcriptomes [6 months]

summary: The goals of this study are to compare rela ablate cornea

overall_design: Cornea epithelium mRNA profiles of 6-m old wild type (WT) and Rela-/- mice

first: Qian

last: Yu


title: Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and RELA-/- Cornea Transcriptomes [2 months]

first: qian

overall_design: Cornea epithelium mRNA profiles of 2-m old wild type (WT) and Rela-/- mice


title: Immunotherapy Study of Evofosfamide in Combination With Ipilimumab (NCT03098160)

city: Houston

first: Michael

middle: A.

last: Curran

state: TX

address: 1515 HOLCOMBE BLVD, UNIT 901

department: Immunology

institute: The University of Texas MD Anderson Cancer Center

summary: Pre-treatment (PT) and On-Treatment (C3D8) biopsy samples from patients on the Phase I trial of Ipilimumab and Evofosfamide (NCT03098160) were analyzed by RNA sequencing.

overall_design: Tumor biopsy samples from melanoma, prostate cancer, pancreatic cancer, and HPV- head and neck cancer were collected pre-treatment and after receiving 2 doses of evofosfamide and 2 doses of ipilimumab (C3D8) and analyzed by RNA sequencing.

first: Kimal

last: Rajapakshe

first: Cristian

last: Coarfa


title: siOLFM4-Pg TIGK RNASeq Study

city: Louisville

first: Richard

last: Lamont

state: Kentucky

address: 501 S. Preston St

department: Oral Immunology and Infectious Diseases

institute: University of Louisville

summary: Investigation of epithelial cell transcripts differentially regulated by P. gingivalis which are dependent on OLFM4

overall_design: Three biological replicates of TIGK cells including non-infected cells treated with siC, cells infected with P. gingivalis ATCC 33277 strain treated with siC, non-infected cells treated with siOLFM4, and cells infected with P. gingivalis ATCC 33277 strain treated with siOLFM4.

first: Zackary

middle: R

last: Fitzsimmonds

first: Chengcheng

last: Liu

first: Kendall

last: Stocke

first: Lan

last: Yakoumatos

first: Brian

last: Shumway

first: Daniel

last: Miller

first: Juhi

last: Bagaitkar

middle: J


title: PgSg TIGK RNASeq Study

summary: Investigation of transcripts differentially regulated in oral epithelial cells in response to P. gingivalis, but overridden or reversed by S. gordonii.

overall_design: Five biological replicates of TIGK cells including non-infected cells, cells infected with only P. gingivalis ATCC 33277 strain, cells infected with only S. gordonii DL1 strain, and cells infected with both P. gingivalis and S. gordonii.

first: Maxim

middle: N

last: Artyomov


title: Regulation of Olfactomedin 4 by Porphyromonas gingivalis in the community context


title: Transcriptomic profiling of dimorphic growth in two Ustilaginomycotina species

city: West Lafayette

first: Teeratas

last: Kijpornyongpan

state: IN

address: 915 W State St

department: Botany and Plant Pathology

institute: Purdue University

summary: In this study, we performed comparative transcriptomics to understand how mechanisms for fungal dimorphism are similar to the model species Ustilago maydis. To achieve this, we selected two non-model species from Ustilaginomycotina, Meira miltonrushii and Tilletiopsis washingtonensis, for transcriptomic profiling. Different culture conditions were used to have these two fungi display yeast growth (Holliday's minimal media with 1% glucose as a carbon source) and filamentous growth (Holliday's minimal media with 1% Tween as a carbon source). Then, we performed transcriptomic sequencing and analyses to determine which genes are differentially expressed in filamentous growth compared to yeast growth. We also incorporated public datasets from other two dimorphic species, U. maydis and Ophiostoma novo-ulmi, for comparison. We found that T. washingtonensis, despite being closely related to M. miltonrushii, is the most distant species in terms of the similarities of transcriptomic alteration, suggesting phylogenetic relatedness may not be concurrent with transcriptomic similarity under the same biological phenomenon. Functional enrichment analyses reveal that genes in cell energy production and conversion, amino acid transport and metabolism and cytoskeleton are groups of genes differentially expressed in common among the four species. Finally, although our comparative approach allows us to discover several candidate genes that may be involved in fungal dimorphism, we found very few commonly expressed genes that are know dimorphism genes characterized in U. maydis literature. This suggests the certain degree of species-specific mechanisms for dimorphic transition.

sample_organism:
Tilletiopsis washingtonensis
Meira miltonrushii

overall_design: Examination of transcriptomic profiles under two growth forms (yeast and filamentous growth) in two fungal species (Tilletiopsis washingtonensis and Meira miltonrushii).

first: M

last: Aime


title: Global transcriptomic portrait of biofilm lifestyle in the  clincial isolate of Candida glabrata

city: CHANDIGARH

first: KHEM

last: RAJ

state: Chandigarh

address: Deparment of Microbiology, BMS Block-I, PANJAB UNI, PANJAB UNIVERSITY, SECTOR -25

department: Microbiology

country: India

institute: PANJAB UNIVERSITY

summary:
Aim: of the study was to compare the transcriptomic profiling of planktonic and biofilm growth phase of clinical isolate of Candida glabrata
Methodology: RNA was extracted using Hi-PurA yeast RNA purification kit from biofilm and planktonic growth phase and sequenced by Illumina Hi-Seq 2500 platform with 250bp paired chemistry
Results: we got 959  significantly Differential Expressed Genes DEGs (logFC => 1.5) acconts for 18.11 % in which 596 (11.26 %) are getting downregulated and 363 (6.85%) upregulated in the biofilm growth mode. We validated 8 genes by qPCR
Conclusion: Comprehensive analysis of the large expression gene sets generated from experimental conditions (Planktonic vs Biofilm) by RNA Seq revealed the unique network of genes associated with this intricate and complex process. We observed that Differentially Expressed Genes (DEGs) associated with Glyoxylate and Dicarboxylate metabolism, Carbon-Carbon lyase activity

overall_design: mRNA of 24h grown biofilm growth phase from 3 biological replicates and similarly 3 biological replicates were taken from  planktonic growth phase

first: Khem

last: Raj

first: Praveen

last: Rishi


title: Innate Lymphoid Cells Activation and Transcriptomic Changes in Response to Human Dengue Infection

city: Ratchathewi

first: Ponpan

last: Matangkasombut

state: Bangkok

address: 272 Thanon Rama VI

country: Thailand

institute: Mahidol University

summary:
Background: Dengue virus (DENV) infection has a global impact on public health. The clinical outcomes (of DENV) can vary from a flu-like illness called dengue fever (DF), to a more severe form, known as dengue hemorrhagic fever (DHF). The underlying innate immune mechanisms leading to protective or detrimental outcomes have not been fully elucidated. Helper innate lymphoid cells (hILCs), an innate lymphocyte recently discovered, functionally resemble T-helper cells and are important in inflammation and homeostasis. However, the role of hILCs in DENV infection had been unexplored.

Methods: We performed flow cytometry to investigate the frequency and phenotype of hILCs in peripheral blood mononuclear cells from DENV-infected patients of different disease severities (DF and DHF), and at different phases (febrile and convalescence) of infection. Intracellular cytokine staining of hILCs from DF and DHF were also evaluated by flow cytometry after ex vivo stimulation. Further, the hILCs were sorted and subjected to transcriptome analysis using RNA sequencing. Differential gene expression analysis was performed to compare the febrile and convalescent phase samples in DF and DHF. Selected differentially expressed genes were then validated by quantitative PCR.

Results: Phenotypic analysis showed marked activation of all three hILC subsets during the febrile phase as shown by higher CD69 expression when compared to paired convalescent samples, although the frequency of hILCs remained unchanged. Upon ex vivo stimulation, hILCs from febrile phase DHF produced significantly higher IFN-g and IL-4 when compared to those of DF. Transcriptomic analysis showed unique hILCs gene expression in DF and DHF, suggesting that divergent functions of hILCs may be associated with different disease severities. Differential gene expression analysis indicated that hILCs function both in cytokine secretion and cytotoxicity during the febrile phase of DENV infection.

Conclusions: Helper ILCs are activated in the febrile phase of DENV infection and display unique transcriptomic changes as well as cytokine production that correlate with severity. Targeting hILCs during early innate response to DENV might help shape subsequent immune responses and potentially lessen the disease severity in the future.

overall_design: RNA-seq of sorted ILCs from DENV infected patients with different severities (DF or DHF) in febrile phase of infection (one day before fever subsided) and convalescent phase (two months after discharged from hospital)

first: Tiraput

last: Poonpanichakul

first: Varodom

last: Charoensawan


title: Transcriptome profiling of Wnt5A activated human coronary artery endothelial cells

city: Zürich

first: TOM

last: SKARIA

address: Rämistr. 100

department: INTERNAL MEDICINE

country: Switzerland

institute: UNIVERSITY HOSPITAL ZURICH

summary:
Wnt5A is released from macrophages during systemic inflammation and sepsis. However, the early response targets for the paracrine action of macrophage derived Wnt5A in vascular endothelial cells still remain unclear.
Here we show that Wnt5A regulates the expression of distinct molecular targets involved in inflammation, coagulation and extracellular matrix remodeling. The proteins encoded by these genes are direct targets for known drugs. Regulation of these specific targets by Wnt5A can modulate the drug response and efficiency.

overall_design: A two color competitive hybridization design was chosen.  Samples from respective treatments are labelled with Cy5  and hybridized against a Cy3 labelled non-treated reference sample from the same experiment.

first: Tom

last: Skaria

first: Gabriele

last: Schoedon


title: Proinflammatory signaling mediated by the combined action of IL-1/Wnt5A in human coronary artery endothelial cells

summary:
IL-1b and Wnt5A are released from macrophages in systemic inflammation and sepsis. However, the early response targets for the paracrine action of synergistic interaction of IL-1b with Wnt5A in vascular endothelial cells still remain unclear.
Here we show that  IL-1b synergizes with Wnt5A to stimulate vascular endothelial inflammatory pathways involved in barrier dysfunction. Molecular targets involved in actin cytoskeleton remodeling, coagulation and stress signaling which are targets for known drugs are regulated by the synergistic action.


title: Transcriptome profiling of two purebred cattle and their crossbreds

city: Roseworthy

first: Ruijie

last: Liu

state: South Australia

address: Mudla Wirra Rd

country: Australia

institute: the university of Adelaide

summary:
Purpose: The aim of this study is to determine the absolute and relative expresson levels of mRNA transcripts across two purbred (Angus and Brahman) cattle and their receipicalcross.
Methods: Total RNA was extracted and purified from five tissues using the RiboZero Gold kit.  Sequencing libraries were prepared with a KAPA Stranded RNA-Seq Library Preparation Kit following the Illumina paired-end library preparation protocol. Completed libraries were sequenced on HiSeq 2000 as 100 bp paired-end reads at the Australian Cancer Research Foundation (ACRF) Cancer Genomics Facility, Adelaide, Australia and USDA-ARS-US Meat Animal Research Center, Clay Center, USA. Approximately 60 million 100 bp single-end reads were obtained for each sample. Reads were aligned to the cattle reference genome UOA_brahman_1/UOA_angus_1 and mapped to known genomic features at the gene level using the Hisat2. Single reads were then summarized into gene-level counts using FeatureCounts.

overall_design: We used animals and semen of Angus (Bos taurus taurus) and Brahman (Bos taurus indicus) cattle, subsequently referred as Bt and Bi respectively. Pure Bt and Bi females of approximately 16-20 months of age were maintained on pasture supplemented with silage. Fetuses produced by artificial insemination with semen of pure bred Bt or Bi sires. Cows were pregnancy tested by ultrasound scanning. Cows and fetuses were humanely sacrificed by stunning and exsanguination at day 153+/- 1 of gestation. Fetuses were dissected, tissues snap-frozen in liquid nitrogen and stored at -80oC study as previously described (Xiang et al., 2013). Five of the tissues were used in this study: Brain, Liver, Lung, Muscle and Placenta. Three male and three female fetus from each of the 4 genetic types (Bt x Bt; Bi x Bt; Bt x Bi; Bi x Bi; paternal genome listed first) were used in this study for a total of 24 samples per tissue.

first: Stefan

last: Hiendleder


title: Transcriptionally regulated energy metabolism drives early erythropoiesis (RNA-Seq)

first: Leonard

last: Zon

summary: Transcription and metabolism both influence cell function but dedicated transcriptional control of metabolic pathways regulating cell fate has rarely been defined. Zebrafish moonshine mutant embryos defective for the transcription elongation factor tif1γ do not make red blood cells. Here, through a chemical suppressor screen we discovered that inhibition of the pyrimidine biosynthesis enzyme DHODH rescues erythroid differentiation in moonshine mutant embryos, which depends on the functional link of DHODH to mitochondrial coenzyme Q activity. In-vivo metabolomics analysis reveals that tif1γ loss results in mitochondrial respiration defects that are associated with reduced expression of genes that encode coenzyme Q synthesis enzymes and are directly bound and controlled by TIF1γ. Treatment of moonshine embryos with a coenzyme Q analogue rescues their bloodless defect. These results demonstrate energy metabolism is a key output of a lineage transcription factor that drives cell fate decisions in the early blood lineage.

overall_design: To analyze the effect of TIF1γ knockdown on gene expression, we generated independent human HepG2 clonal cell lines stably transduced with either one of two doxycycline-inducible control shRNAs or one of two TIF1γ shRNAs and induced them with 1 µg/ml doxycycline for 48 hours.

first: Marlies

last: Rossmann

first: Brian

last: Abraham

first: Song

last: Yang

first: Richard

last: Young


title: Transcriptionally regulated energy metabolism drives early erythropoiesis (ChIP-Seq)

overall_design: ChIP-seq analysis of histone 3 lysine 27 acetylation (H3K27Ac), RNA polymerase II (RNA Pol II), RNA polymerase II phosphorylated at Ser2 (RNA Pol II-Ser2P), and TIF1γ in logarithmically growing human HepG2 hepatocellular carcinoma cells.


title: Transcriptionally regulated energy metabolism drives early erythropoiesis

sample_organism:
Danio rerio
Homo sapiens

platform_organism:
Danio rerio
Homo sapiens

overall_design: Refer to individual Series


title: CRL4DCAF8 Dependent Opposing Stability Control over Chromatin Remodeler LSH Governs the Epigenetic Dynamics in Ferroptosis

city: Beijing

first: Yu

last: Zhang

address: Xueyuan Road

institute: Peking University Health Science Center

summary: Despite the emerging evidence of ferroptosis implicated in diverse pathological scenarios, molecular adaptors linking its oxidative inducers and chromatin as carrier of stable epigenetic memory for its propagation remain elusive. Here, we report the identification of two WD40 proteins DCAF8 and WDR76 as substrate adaptor and molecular inhibitor respectively of the Cullin-4 RING ubiquitin ligase (CRL4) system for stability control of the chromatin remodeler LSH. Degradation analysis and CRL4-DCAF8 complex reconstitution demonstrate that CRL4DCAF8 is a bona fide E3 ligase for LSH. In contrast, WDR76 antagonizes DCAF8-targeted LSH proteolysis through competitive inhibition of the holo-CRL4DCAF8-LSH complex assembly. Importantly, this opposing regulatory strategy is utilized in lipid hydroperoxide induced ferroptosis, and we identify key redox homeostasis genes significantly regulated by the DCAF8/WDR76/LSH axis through transcriptomic epistasis analysis. Such responsiveness could be attributed to increased ratio of DCAF8 over WDR76 for antagonistic LSH association accompanying ROS overproduction invoked decrease of TET-catalyzed DNA oxidation. Evaluation of epigenetic dynamics at DCAF8/WDR76/LSH-regulated gene promoters reveals linker histone H1- and LSH-associated transcriptional repression is coordinately removed in ferroptosis. Together with phenotypes driven by WDR76 and DCAF8 manipulations, these data identify DCAF8- and WDR76-governed LSH degradation as a crucial node in ferroptosis, tumorigenesis and senescence.

overall_design: Control, DCAF8-depleted, WDR76-overexpressed or DCAF8/LSH co-depleted HT-1080 cells in treatment with erastin (10μM, 24h) or not, were all subjected to RNA-sequencing analysis.

first: Daoyuan

last: Huang

first: Qian

last: Li


title: Transcriptome analysis of senescent and reactive human fetal astrocytes

city: Erlangen

first: Beate

last: Winner

address: Glückstr. 6

country: Germany

institute: FAU Erlangen-Nürnberg

summary: Senescence was recently linked to neurodegeneration. Senescent as well as reactive astrocytes were detected in Parkinson’s disease postmortem brains. This study aimed to determine differences and similarities between senescent and reactive astrocytes. Astrocytes were treated with the stressors hydrogen peroxide or rotenone to induce senescence or with the cytokines TNFa+IL1a or with IL1b to induce reactivity in astrocytes. Comparing the transcriptome of senescent and reactive astrocytes revealed a set of genes specific to senescent astrocytes together with genes regulated in a similar way in both astrocyte states.

overall_design: Two senescence-inducing (rotenone and hydrogen peroxide) and two reactivity-inducing (TNFa+IL1a and IL1b) treatment conditions and a control condition were analyzed in triplicates.

first: Katrin

last: Simmnacher

first: Florian

last: Krach


title: RNA-Seq of rabbits treated with normal diet or high cholesterol diet

status: Public on Jun 08 2021

city: Nanjing

first: Xiaohong

last: jiang

state: Jiangsu

address: Xianlin Road

institute: Nanjing university

summary: We fed PGC1-alpha (mouse gene) transgenic rabbits and control rabits with normal diet or high cholesterol diet. Then we extract RNA from their vascular cells and performed RNA-Seq comapre the expression level of the mRNAs.

overall_design: Non-transgenic rabbits fed with chow diet were served as the ctrl group, and transgenic or non-transgenic rabbits fed with high cholesterol diet for 20 weeks were the experimental groups. For each group, RNA from 5 rabbits were included and pooled together. The total RNA was then extracted and processed with RNA-Seq.

last: Jiang

first: Chen-Yu


title: ATAC-seq profiling of Nfat5 KO and WT in Mus musculus macrophages

city: Barcelona

first: Cristina

last: Lopez-Rodriguez

address: Carrer Dr. Aiguader, 88

department: Medicine and Life Sciences

institute: Universitat Pompeu Fabra

summary: ATAC-seq profiling of Nfat5 KO and wild type macrophages derived from bone marrow (primary cells), treated or not with Lipopolysaccharide (LPS).

overall_design: A total of 8 samples are analysed; 2 biological replicates in 4 experimental groups: Nfat5 KO and Wild type non treated, Nfat5 KO and Wild Type LPS treated.

first: Maria

last: Buxade

first: Jose

last: Aramburu

first: Sarah

last: Bonnin


title: Next generation sequencing analysis in uveal melanoma cells and normal melanocytes.

city: Shanghai

first: AI

last: ZHUANG

address: 639 Zhizaoju Road

department: Ophthalmology

institute: Shanghai Ninth People's Hospital, Shanghai JiaoTong University School of Medicine

summary: Study the RNA expression differences in uveal melanoma cells and normal melanocytes, providing new insights into the tumorgenesis of uveal melanoma.

overall_design: Examination of RNA expression differences in 2 cell types.

first: A

last: Zhuang

first: P

last: Chai

first: X

last: Fan


title: FOS Guards Quiescence and Potency in Human Hematopoietic Stem Cells [CUT&Tag]

city: Guangzhou

first: Tian

state: Guangdong

address: 190 Kaiyuan Avenue,Science Park

institute: GIBH

summary: Quiescence and limited dividing are critical in preserving potency of hematopoietic stem/progenitor cell (HSPCs) during lifetime, but little is known about how this process is regulated. Here, we show that the mobilized human HSPCs in peripheral blood (PB) are predominantly in a quiescent state, but rapidly exit quiescence and reduce repopulating potency in short-term culture. Through single cell RNA-seq, we identified a panel of regulators highly associated with HSC quiescence exit and cell-cycle entry. These regulators involve different biological processes such as cell-cycle, signaling pathways, metabolisms, etc. Among them, the oncogene, FOS restrains cell-cycle entry and supports repopulating potency in human HSCs through directly binding and regulating genes both for HSC quiescence and potency. Our findings uncover the regulatory program underlying quiescence exit and highlight the critical role of FOS to guard the quiescence and potency in human HSPCs.

overall_design: We tested the possible binding sites of FOS in  FOS-3flag/eGFP+ hematopoietic stem cells by CUT&Tag

first: Ke

first: Guangjin

last: Pan


title: Unveiling complexity and multipotentiality of early heart fields

city: El Cajon

first: Daniel

last: Carlin

state: CA

address: 1250 Mountain View Rd.

institute: UC-San Diego

summary: Through high-resolution single cell and genetic lineage/clonal analyses, we show an unsuspected clonal relationship between extraembryonic mesoderm and cardiac lineages.  Single-cell transcriptomics and trajectory analyses uncovered two mesodermal progenitor sources contributing to left ventricle cardiomyocytes, one embryonic and the other with an extraembryonic gene expression signature.  Additional lineage-tracing studies revealed that the extraembryonic-related progenitors reside at the embryonic-extraembryonic interface in gastrulating embryos, and produce distinct cell types forming the pericardium, septum transversum, epicardium, dorsolateral regions of the left ventricle and atrioventricular canal myocardium, and extraembryonic mesoderm.  Clonal analyses demonstrated that these progenitors are multipotent, giving rise to not only cardiomyocytes and serosal mesothelial cell types but also, remarkably, extraembryonic mesoderm.

overall_design: To prepare single cells for scRNA-seq, Mesp1-Cre; Rosa26-tdT genetically-labeled embryos at E7.25, E7.5, E7.75 and E8.25 were dissected in cold sterile 1 X PBS without Ca2+, Mg2+ under a stereo microscope.  Embryos were staged based on their morphology.  The Reichert’s membrane and ectoplacental cone were removed, and Mesp1-Cre; Rosa26-tdT genetically-labeled embryos were selected and imaged.  The yolk sac was removed from one of the three E8.25 samples in order to enrich for cardiac cells.  Individual embryos were placed into a 1.5 ml microfuge tube and incubated in 0.25% Trypsin-EDTA (Gibco, Catalog # 25200056) at 37°C with inversion every two minutes for 30 min until no visible tissue remained.  The solution was pipetted once with a p1000 and neutralized by adding 0.75 ml DMEM containing 10% FBS (Gibco).  Cells were then passed through a 100-μm cell strainer (BD Biosciences, Catalog # 352360) and single tdT+ cells were obtained by fluorescence-activated cell sorting (FACS) on a BD Influx Cell sorter (BD Biosciences).  Living cells were gated on FSC, SSC, DAPI- and tdT+.  After sorting, cells were centrifuged at 300g for 4 minutes and pooled or kept as individual embryos.  E7.25 embryos were pooled due to the low number of Mesp1-lineage positive cells.  Libraries were prepared using the Chromium Single Cell 3′ Library and Gel Bead Kit v2 (PN-120237) and Chromium i7 Multiplex Kit (PN-120262) according to instructions from 10X Genomics (https://www.10xgenomics.com/resources/user-guides/).  Prior to sequencing cDNA, libraries were verified by the D1000 ScreenTape system (Agilent) and quantified via Qubit™ Flex Fluorometer (Thermofisher, Catalog # Q33327).  All libraries were sequenced twice on the HiSeq 4000 (Illumina) at the UCSD IGM genomics core.  An initial shallow sequencing run was done for quality control and to determine the number of cells captured.  An individual sample was excluded from further analysis due to a low number of reads per cell (60%) as analyzed by Cell Ranger (10X genomics).  A second deeper sequencing run was subsequently performed ensuring an approximate equal read depth per cell across the samples, resulting in an average of 60,450 UMIs (unique molecular identifiers) per cell and an average sequence saturation of 65.7%

first: Qingquan

last: Zhang

first: Joshua

last: Bloomekatz

first: Neil

last: Chi


title: Objective to explore the mechanism of STAT3 regulating PD-L1 expression at transcriptional level after LIFR overexpression in pancreatic cancer cells.

first: Yanhong

last: Wang

address: 5 Dong Dan San Tiao

institute: Chinese Academy of Medical Sciences

summary: The assays were performed in the standard manner to determine the influence of LIFR on the capacity of STAT3 (Cell signaling Technologyv, 124H6, cat#: 9139, 1µg) binding to DNA. Specific DNA fragments were obtained, purified, and subjected to PCR amplification using a NovoNGS® CUT&Tag 2.0 High-Sensitivity Kit (Novoprotein Scientific Inc), according to the protocol of the manufacturer. Berry Genomics Corporation (Beijing, China) was trusted to prepare the libraries and perform the sequencing.

overall_design: To uncover the target genes directly regulated by STAT3 that is activated by LIFR overexpression  in Mia PaCa2 cells. To this end, we performed Cleavage Under Targets and Tagmentation (CUT&Tag) sequencing with anti-STAT3 antibody to probe the enhanced genomic binding sites of STAT3 upon LIFR activation


title: FOS Guards Quiescence and Potency in Human Hematopoietic Stem Cells [RNA-seq]

overall_design: We compared the transcriptome of  the eGFP+ and  FOS/eGFP- hematopoietic stem cells by RNA-Seq

last: Huang


title: Transcriptome analysis of atopic dermatitis and psoriasis lesional skin

city: Wonju

first: Seung-Phil

last: Hong

address: 20 Ilsan-ro

department: Department of Dermatology

country: South Korea

institute: Yonsei University Wonju College of Medicine

summary:
Purpose: To deeply understand the clinical as well as pathogenetic differences, we have analyzed the genes involved in the epidermal lipid synthesis, epidermal development process and immune responses in the skin of AD and PSO patients.
Materials and Methods: We have compared the transcriptomes of lesional skin (epidermis+dermis) from 2 adults AD patients and 2 PSO patients by high-throughput complementary DNA sequencing (RNA-seq). For the gene expression estimation, Cufflinks v2.1.1 was used that is the gene annotation database of Ensembl release 72.

overall_design: Full-thickness skin sample (epidermis+dermis) from lesion of 2 adult atopic dermatitis and 2 psoriasis patients.


title: FOS Guards Quiescence and Potency in Human Hematopoietic Stem Cells

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


title: Expression profile of hepatocellular carcinoma-matrix interaction

city: Taipei

first: Yung-Ming

last: Jeng

address: No.7, Zhongshan S. Rd., Zhongzheng Dist.

country: Taiwan

institute: National Taiwan University Hospital

summary: Scirrous hepatocellular carcinoma is a rare type of liver tumor that is charecterized by fibrous stroma, biliary differentiation of tumor cells, and poorer prognosis. In this study, we aim to analyze the efefcts of collagen 1 on signal tranduction pathway activation, gene expression profile, and phenotypic changes of hepatocellular carcinoma.

overall_design: HepG2 and Huh7 cells were grown on uncoated and collagen 1-coated plates for 2 days. RNA was extracted and the gene expression profiles are analyzed using RNA sequencing

first: Ray-Hwang

last: Yuan

first: Chia-Lang

last: Hsu

first: Yun-Ru

last: Liu

first: Tsung-Han

last: Hsieh

first: Yu-Ling

last: Jhuang


title: Mutual dependency between a lncRNA and NPM1 is crucial for tumor cell proliferation

first: Xuerui

last: Yang

address: Haidian District

department: School of Life Sciences

institute: Tsinghua University

summary: Silencing LETN or NPM1 in  hepatocellular carcinoma cells inhibited cell proliferation and resulted in identical phenotypes. RNA-seq further revealed that knock-down of lncRNA LETN and NPM1 resulted in similar shifts of the gene expression profiles. This lncRNA-protein axis therefore plays indispensable roles in highly proliferative cells including a multitude of cancer cells and human neuronal precursor cells. Here we provide processed raw counts files.

overall_design: siLETN, siNPM1 and control (siNC) experiments with 2 replicates respectively.

first: Xianteng

first: Xiaolin

last: Hu


title: Systematic analysis of monoallelic gene expression and chromatin accessibility across multiple tissues in hybrid mice

city: Shenzhen

first: Lei

last: Li

state: --- Select a state ---

address: China

department: Institute of Systems and Physical Biology

institute: Shenzhen Bay Laboratory

summary: In diploid eukaryotic organisms, both alleles of each autosomal gene are usually assumed to be simultaneously expressed at similar levels. However, some genes can be expressed preferentially or strictly from a single allele, a process known as monoallelic expression. Classic monoallelic expression of X-chromosome-linked genes, olfactory receptor genes and developmentally imprinted genes is the result of epigenetic modifications. Genetic-origin-dependent monoallelic expression, however, is caused by cis-regulatory differences between the alleles. There is a paucity of systematic study to investigate these phenomena across multiple tissues, and the mechanisms underlying such monoallelic expression are not yet fully understood. Here we provide a detailed portrait of monoallelic gene expression across multiple tissues/cell lines in a hybrid mouse cross between the Mus musculus strain C57BL/6J and the Mus spretus strain SPRET/EiJ. We observed pervasive tissue-dependent allele-specific gene expression: in total, 1,839 genes exhibited monoallelic expression in at least one tissue, and 410 genes in at least two tissues. Among these 88 are monoallelic genes with different active alleles between tissues, probably representing genetic-origin-dependent monoallelic expression. We also identified six autosomal monoallelic genes with the active allele being identical in all eight tissues, which are likely novel candidates of imprinted genes. To depict the underlying regulatory mechanisms at the chromatin layer, we performed ATAC-seq in two different cell lines derived from the F1 mouse. Consistent with the global expression pattern, cell-type dependent monoallelic peaks were found, and a higher proportion of C57BL/6J-active peaks were observed in both cell types, implying possible species-specific regulation. Finally, only a small part of monoallelic gene expression could be explained by allelic differences in chromatin organization in promoter regions, suggesting that other distal elements may play important roles in shaping the patterns of allelic gene expression across tissues.

overall_design: ATAC-seq data of F1-fibroblasts and F1-ES cells from Female F1 hybrid mice (female C57BL/6J x male SPRET/EiJ).

first: Wei

last: Chen


title: FOS Guards Quiescence and Potency in Human Hematopoietic Stem Cells [scRNA-seq]

first: Tian

first: Ke

first: Guangjin

last: Pan


title: Differential gene expression in iKRAS mouse tumors treated with Trametinib and 2DG

city: Houston

first: Haoqiang

last: Ying

state: Texas

address: 1515 Holcombe Blvd

institute: M. D. Anderson Cancer Center


title: POWV isolate from Long Island infects brain endothelial cells and pericytes. [hBMECs]

city: Stony Brook

first: Jonas

last: Nascimento Conde

state: NY

address: Life Sciences Building

institute: Stony Brook University

summary: POWV isolate from Long Island (POWV-LI-9) is released basolaterally from humban brain microvascular endothelial cells (hBMECs) and infects primary human brain vascular pericutes (hBVPs).

overall_design: Human brain microvascular endothelial cells (hBMECs) were infected with POWV-LI-9 1-3 dpi. Total RNA was extracted and submitted to Affymetrix microarray analysis. Mock-transduced cells were used as control for each time point.

first: J

last: Conde

first: S

last: Sanches-Vicente

first: N

last: Saladino

first: E

last: Gorbunova

first: W

last: Schutt

last: Benach

first: H

last: Kim

last: Mackow


title: POWV isolate from Long Island infects brain endothelial cells and pericytes.


title: The transcriptome differences between IFN-I-elicited subsets of arginase 1-high and -low macrophages

first: Panpan

last: Guo

state: Jiang Shu

address: High-tech District

department: medical college

institute: Nanjing University

summary:
Purpose: Using cells from the Arg1-YFP reporter mice, we discovered that only a part of macrophages from IFNβ-stimulated transitional monocytes showing Arg1-YFP expression. Therefore, we probed the overall differences between such IFN-I-elicited YFP+ and YFP- macrophages.
Method: Bone marrow mononuclear cells from Arg1-YFP mice were treated with M-CSF± IFNβ for 64 h. The macrophages (F4/80+) in the control and IFN treatment group were further sorted by flow cytometry based on YFP intensities. The dominant YFP- population from the control cells (Con), as well as the YFP- (Treated1) and YFP+ (Treated2) subsets within IFNβ-treated cells were subjected to RNAseq analyses.
Results: The most enriched biological functions for the up-regulated genes in the treated groups relate to immune activation, anti-viral responses and the IFN pathway. Most classical IFNβ downstream genes did not display differential expression between YFP- (Treated1) and YFP+ (Treated2). However, there are 84 genes displaying “Treated2 above Treated1” and 98 genes showing “Treated1 above Treated2” patterns.
Conclusions: Our result show that IFN-I-elicited YFP+ and YFP- monocyte-derived macrophages tend to be M2- and M1-skewed, respectively.

overall_design: Con, Treated1 and Treated2 groups of samples were sorted by flow cytometry. Con and Threated1 each have three biological replicates, while Treated2 have two biological replicates.

first: Jianghuai

last: Liu


title: POWV isolate from Long Island infects brain endothelial cells and pericytes. [hBVPs]

overall_design: Human brain vascular pericytes (hBVPs) were infected with POWV-LI-9 1-3 dpi. Total RNA was extracted and submitted to Affymetrix microarray analysis. Mock-transduced cells were used as control for each time point.


title: Radiation-activated secretome of Scgb1a1+ club cells increase the efficacy of immune checkpoint blockade in lung cancer (iDTR scRNA-seq)

city: New York

first: Dingcheng

last: Gao

address: 1300 York Ave

department: CT Surgery

institute: Weill Cornell Medical College

summary: We report that airway epithelial club cells affected the immune landscaping in HKP1 lungs

overall_design: Single live cells (CD45+) sorted from HKP1-bearing lungs of Scgb1a1cre /iDTR mice treated with PBS (control) or DT (Club cell depletion). Both of groups also received 4Gy-RT (4 mice/group).

first: Yi

last: Ban

first: Vivek

last: Mittal


title: Radiation-activated secretome of Scgb1a1+ club cells increase the efficacy of immune checkpoint blockade in lung cancer (Bulk048 RNA-seq)

summary: We uncovered an essential role of radiationtherapy (RT)-activated lung residential Scgb1a1+ club cells in synergizing efficacy of immuno-checkpoint inhibitors. We explored the mechanisms underlying RT by analyzing the differentially-regulated genes in tumor micro-environment.

overall_design: mRNA profiling of bulk HKP1-bearing lungs which received different does of RT with or without anti-PD-1 antibody. Each sample was pooled from 3-4 mice, 5-6 samples/RT dose.


title: Radiation-activated secretome of Scgb1a1+ club cells increase the efficacy of immune checkpoint blockade in lung cancer

overall_design: Refer to individual Series


title: MesoHET (Multi-site tumor sampling highlights molecular intra-tumor heterogeneity in malignant pleural mesothelioma)

city: Paris

first: Sandrine

last: Imbeaud

address: 15 rue de l'Ecole de Médecine

department: INSERM UMRS1138-EQUIPE 28, Sorbonne Université-Inserm-Université de Paris

institute: Centre de Recherche des Cordeliers

type: Methylation profiling by genome tiling array

summary: To analyze intra-tumor heterogeneity, DNA methylation was analysed in paired tumor samples of 16 patients from whom biopsies were taken at distinct anatomical sites. Samples were collected from 2014 to 2017 in two French hospitals. All samples obtained from surgical samples or tumor biopsy were immediately frozen in liquid nitrogen and stored at -80°C prior extraction.

overall_design: DNA methylation analysis using Infinium MethylationEPIC BeadChip (Illumina)

first: Clément

last: Meiller

first: Didier

last: Jean


title: Transcriptomic analysis (RNA-seq) of Lin- BM cells from wild type C57 BM mice and GFP+ BM cells from TBLR1-RARa mice

city: Tianjin

first: yang

last: xue

address: 288 Nanjing Road

institute: Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Science and Peking Union Medical College

summary:
Purpose: The goal of this study is to decipher the molecular basis of TBLR1-RARa-expressing APL and to explore potential treatment target based on NGS-derived transcriptome profiling (RNA-seq)
Methods: RNA-seq was performed to analyze differential gene expression between GFP+ cells from BM of TBLR1-RARa mice (TR1 and TR9) and lin- cells from BM of control mice (Control).
Results: Transcriptome profiling associates with leukemic phenotype and predicts HDACi response in TR-induced APL.
Conclusions: Our study represents the first bioinformatic analysis of DEGs from APL mice with TBLR1-RARa fusion gene, generated by RNA-seq technology. Transcriptome profiling associates with leukemic phenotype of differentiation block and predicts drug response to HDAC inhibitors.

overall_design: BM mRNA profiles of 6-8-week-old wild type and TBLR1-RARa mice

first: Jianxiang

last: Wang

first: Xue

last: Yang

first: Shouyun

last: Li


title: DNA methylation-mediated modulation of rapid desiccation tolerance acquisition and dehydration stress memory in the resurrection plant Boea hygrometrica

first: Run-Ze

last: Sun

address: No.20 Nanxincun, Xiangshan, Haidian District

department: Institute of Botany

institute: Chinese Academy of Sciences

summary: Pre-exposure of plants to various abiotic conditions confers improved tolerance to subsequent stress. Mild drought acclimation induces acquired rapid desiccation tolerance (RDT) in the resurrection plant Boea hygrometrica, but the mechanisms underlying the priming and memory processes remain unclear. In this study, we demonstrated that drought acclimationinduced RDT can be maintained for at least four weeks but was completely erased after 18 weeks based on a combination of the phenotypic and physiological parameters. Global transcriptome analysis identified several RDT-specific rapid dehydration-responsive genes related to cytokinin and phospholipid biosynthesis, nitrogen and carbon metabolism, and epidermal morphogenesis, most of which were pre-induced by drought acclimation. Comparison of whole-genome DNA methylation revealed dehydration stress-responsive hypomethylation in the CG, CHG, and CHH contexts and acclimation-induced hypermethylation in the CHH context of the B. hygrometrica genome, consistent with the transcriptional changes in methylation pathway genes. As expected, the global promoter and gene body methylation levels were negatively correlated with gene expression levels in both acclimated and dehydrated plants but showed no association with transcriptional divergence during the procedure. Nevertheless, the promoter methylation variations in the CG and CHG contexts were significantly associated with the differential expression of genes required for fundamental genetic processes of DNA conformation, RNA splicing, translation, and post-translational protein modification during acclimation, growth, and rapid dehydration stress response. It was also associated with the dehydration stress-induced upregulation of memory genes, including pre-mRNA-splicing factor 38A, vacuolar amino acid transporter 1-like, and UDP-sugar pyrophosphorylase, which may contribute directly or indirectly to the improvement of dehydration tolerance in B. hygrometrica plants. Altogether, our findings demonstrate the potential implications of DNA methylation in dehydration stress memory and, therefore, provide a molecular basis for enhanced dehydration tolerance in plants induced by drought acclimation.

overall_design: In this study, we explored the phenotypic and physiological changes, together with both the transcriptional and DNA methylation dynamics in leaves of B. hygrometrica plants during the progress of drought acclimation-induced RDT acquisition, maintenance and erasing. To broaden our understanding of the epigenetic control of dehydration stress memory, the effect of DNA methylation on gene expression and association of promoter methylation changes with differential gene expression were further analyzed.

first: Yuan-Yuan

first: Jie

first: Xin

last: Deng


title: Radiation-activated secretome of Scgb1a1+ club cells increase the efficacy of immune checkpoint blockade in lung cancer (0Gy4Gy scRNA-seq)

summary: We report that airway epithelial club cells harbor the genes specifically up-regulated by 4Gy-RT

overall_design: Single live cells (CD45+ and CD45-) sorted from HKP1-bearing lungs which received 0Gy-RT(mock) or 4Gy-RT (4 mice/treatment)  were sequenced.


title: Serum LncRNAs as Early Potential Biomarkers for the Prediction of Pregnancy-induced hypertension,including Preeclampisa

city: Harbin

first: Chenguang

last: Dai

address: Youzheng Street 23#,Nangang District

institute: Harbin Medical University

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

summary: To identify potential lncRNAs as early circulating biomarkers for pregnancy-induced hypertension (PIH), including both gestational hypertension (GH) and preeclampsia (PE), we sought to determine the lncRNA expression profiles in the serum of patients with PE before the 20th week of gestation and evaluated the efficacy of lncRNAs for diagnosing PIH before the onset of clinical symptoms. The screening phase assessed lncRNA expression profiles with a human lncRNA microarray in 5 pairs of serum samples (5 PE patients and 5 matched controls).

overall_design: We finally included patients with preeclampsia (PE) (n=5) and matched normotensive pregnant (NP) women (n=5). Then perform lncRNAs chips by Arraystar Human lncRNAs chip (Arraystar).

first: Yue


title: Aberrant epithelial polarity promotes precancerous airway lesions via YAP/TAZ-induced NRG1-ERBB signaling

city: Boston

first: Adam

last: Gower

address: 72 East Concord Street, E632

department: Department of Medicine

institute: Boston University School of Medicine


title: YAP/TAZ-regulated gene expression in human airway epithelial cells

summary: RNA sequencing was performed in samples isolated from primary normal airway epithelial cells, primary dysplastic airway epithelial cells (SPORE 43672) and immortalized cells (AALE), all of which were either transfected with control siRNA or with siRNA promoting the knockdown of the transcriptional regulators YAP (YAP1) and TAZ (WWTR1).

overall_design: Cells were cultured at low density, transfected with control siRNA or siRNA promoting the knockdown of the transcriptional regulators YAP (YAP1) and TAZ (WWTR1), and at 48 hours post-transfection, the cells were lysed and RNA was isolated.

first: Xaralabos

last: Varelas

first: Jennifer

last: Beane


title: RNA-Seq of SARS-Cov-2 Infection in Human Bronchial Epithelium Organoids

first: Liang

address: No. 1088 Xueyuan Avenue, Nanshan District

institute: SUStech

summary: We performed RNA-Seq of SARS-Cov-2 infection in human bronchial epithelium organoids. The organoids were infected with SARS-Cov-2 for 48hours or 72hours respectively, and compared with uninfected mock control.

overall_design: The bronchial organoids were infected with SARS-Cov-2 for 48hours or 72hours respectively, and compared with uninfected mock control.

last: LI


title: DNA methylation-based classifier to predict pathological complete response to neoadjuvant chemoradiotherapy in locally advanced rectal carcinomas.

city: Vejle

first: Luisa

last: Matos do Canto

address: Beriderbakken 4

department: Biochemistry and Immunology

country: Denmark

institute: Vejle Hospital

summary: Locally advanced rectal cancer (LARC) patients have been treated with a pre-operative multimodal regimen based on 5-fluorouracil and radiotherapy (nCRT) followed by surgery. Patients that achieve pathological complete response (pCR) present better overall survival and lower rates of recurrence. Substantial evidence indicate that these patients could be spared of surgery, while near 70% of cases present incomplete response (pIR), varying from partial response to stable-disease/progression. Markers capable of distinguishing pIR from pCR have the potential to address alternative treatment strategies. Herein, we evaluated the ability of predicting response to nCRT by DNA methylation analysis in pre-treatment biopsies of LARC.

overall_design: The methylation profiling (EPIC BeadChip platform, Illumina) of 32 LARC biopsies (11 cases with pathological complete response (pCR) to neoadjuvant chemoradiotherapy (nCRT) and 21 with incomplete response, pIR) were compared to five normal rectal tissues. The differentially methylated CpGs were assessed to develop a predictive classifier based on the response to nCRT using diagonal linear discriminant analysis.   A classifier based on the DNA methylation status of three CpGs was developed, which is easily applicable to the clinical practice and capable of identifying pCR patients prior to surgery, supporting the decision making on LARC patients management.

middle: M

last: Canto

first: Mateus

last: Barros-Filho

first: Diogo

last: Marinho

first: Bruna

middle: E

last: Kupper

first: Maria

middle: D

last: Begnami

first: Cristovam

last: Scapulatempo-Neto

first: Fabio

last: Marchi

first: Jan

last: Baumbach

first: Samuel

last: Aguiar-Jr

first: Silvia

last: Rogatto


title: A combination of circulating microRNA-375-3p, and chemokines CCL-11, CXCL12, and G-CSF differentiate Crohn’s Disease and Intestinal Tuberculosis

city: Kolkata

first: Soma

last: Banerjee

state: West Bengal

address: 244, A.J.C Bose Road

department: School of Digestive & Liver Diseases

institute: Institute of Post Graduate Medical Education & Research

summary: Differentiation of Crohn’s disease (CD) from intestinal tuberculosis (ITB) is a big challenge to the gastroenterologists because of their indistinguishable features and insensitive diagnostic tools. A non-invasive biomarker is urgently required to distinguish CD/ITB patients particularly in India, a TB endemic region, where CD frequency is increasing rapidly due to urbanization. Small RNA next generation sequencing (NGS), qRT-PCR, Bioplex pro-human cytokine screening panel-48-plex was employed to identify diagnostic marker for CD and ITB. Graphpad Prism 7 and R software were used for statistics and Receiver operative curve (ROC) analysis respectively. Among the three differentially expressed miRNAs obtained from transcriptomic profiling of ileocecal/terminal ileal tissue of ITB/CD patients (n=3), only two down-regulated miRNAs, miR-31-3p, and miR-215-5p showed comparable data in qRT-PCR.  Out of which, only miR-215-5p was detectable in the patient’s plasma, but there was no significant difference in expression between ITB and CD.  On the other hand, miR-375-3p, the pulmonary TB specific marker was found in higher amount in the plasma of ITB patients than CD while reverse expression was observed in the ileocecal/terminal tissue of the patients. Next, among 48 cytokine/chemokines,  three chemokines, Eotaxin/CCl11, SDF-1α/CXCl12 and G-CSF were noted significantly different level in the serum of ITB and CD patients.   ROC analysis has revealed that compared to a single molecule, a combination of miR-375-3p+Eotaxin/CCL11+SDF-1/CXCL12+G-CSF has better AUC of 0.83, 95%CI (0.69-0.96) with 100% specificity and positive prediction while sensitivity, negative prediction and accuracy were 56%, 69% and 78% in distinguishing ITB from CD respectively. This study suggests that the plasma markers, when assesed in combination, show high potential to distinguish ITB from CD and thus may help in the clinical management of ITB/CD patients.

overall_design: Normal non-inflammed, Crohn's Disease, Intestinal Tuberculosis Liver tissue Samples contributor: Medgenome Inc.

first: Gopal

middle: K

last: Dhali

first: Arka

first: Rajib

last: Sarkar

first: Sujoy

last: Roy


title: NRG1-induced gene expression changes in human airway epithelial cells

first: Adam

last: Gower

summary: RNA sequencing was performed using RNA obtained from AALE cells carrying an empty control construct or a construct promoting the overexpression of NRG1.

first: Xaralabos

last: Varelas

first: Jennifer

last: Beane


title: Whole gene expression profiling after overexpression of Evl or miR-342 in murine hematopoietic LSK cells

city: Heidelberg

first: Friederike

last: Herbst

address: INF 460

institute: National Center for Tumor Diseases (NCT) & German Cancer Research Center (DKFZ)

summary:
Analyzing the influence of the protein-coding gene Evl or it's intronic miR-342 on hematopoietic stem and progenitor cells on gene expression level.
Evl drives lymphopoiesis, whereas miR-342 deregulates myeloid signaling pathways.

overall_design: Total RNA obtained from murine hematopoietic primary lineage negative (lin-) Sca1+ cKit+ (LSK) cells after lentivirus-mediated overexpression of Evl or miR-342 compared to mock.

first: Tonio

last: Lang

first: Elias

last: Eckert

first: Peer

last: Wünsche

first: Alexander

last: Wurm

first: Tim

last: Kindinger

first: Karin

last: Laaber

first: Shayda

last: Hemmati

first: Agnes

last: Hotz-Wagenblatt

first: Oksana

last: Zavidij

first: Anna

last: Paruzynski

first: Junyan

last: Lu

first: Christof

last: von Kalle

first: Thorsten

last: Zenz

first: Christoph

last: Klein

first: Manfred

last: Schmidt

first: Claudia

last: Ball

first: Hanno

last: Glimm


title: GATA6 defines endoderm fate by controlling chromatin accessibility during differentiation of human induced pluripotent stem cells [TF_ChIP-seq]

status: Public on Jun 07 2021

city: Charleston

first: Stephen

last: Duncan

state: SC

address: 173 Ashley Avenue, BSB 6th Floor, Room 657A

department: Regenerative Medicine and Cell Biology

institute: Medical University South Carolina

summary: Investigation of the role played by GATA6 in establishing the definitive endoderm chromatin accessbility profile. We used pluripotent stem cells as a model of early development. We derived GATA6-/- pluripotent cells with an inducible GATA6 or FOXA2 construct that permits exongenous GATA6 or FOXA2 cDNA expression upon supplementation of doxycycline. We differentiated GATA6+/+ and GATA6-/- (with and without doxycyline) cells to definitive endoderm and analyzed transcription factor binding profiles using CHIP-seq.

overall_design: Examination of GATA6, EOMES and FOXA2 binding profiles during definitive endoderm formation in the absence and presence of GATA6.

first: James

last: Heslop


title: Urinary exosome microRNA signatures as a non-invasive prognostic biomarker for prostate cancer

city: Seoul

first: Sun

last: Shin

address: Banpodaero 222

department: Dept. of Microbiology

institute: The Catholic University of Korea

summary: We aimed to identify urinary exosomal miRNAs associated with PCa metastasis and develop a non-invasive risk-scoring model for PCa metastasis in this study. MiRNA profiles were examined using the Taqman low-density miRNA array (TLDA). Megaplex reverse transcription reactions and pre-amplification reactions were performed to increase the quantity of cDNA for miRNA expression analysis using the Megaplex PreAmp Primers Human Pool A and TaqMan PreAmp Master Mix (Thermo Fisher Scientific). MiRNA expression was evaluated via the TLDA panel A v2.0 (Thermo Fisher Scientific). Raw data were processed using the QuantStudio Real-Time PCR Software (Thermo Fisher Scientific) to determine a cycle threshold (Ct) value for each miRNA.

overall_design: We analyzed miRNA expression profiles of 42 patients (19 localized and 23 metastatic) using the Taqman low-density miRNA array (TLDA) containing 381 miRNAs. Exosomes were isolated from 5 mL of urine, and Total RNA was isolated from the pellets using TRIzol.

first: Yeun-Jun

last: Chung

first: Yong Hyun

last: Park


title: The human β-globin enhancer LCR HS2 plays a role in forming a TAD by activating chromatin structure at neighboring CTCF sites

city: Busan

first: AeRi

last: Kim

address: 2, Busandaehak-ro 63beon-gil, Geumjeong-gu

institute: Pusan national university

summary: We propose that the HS2 has a role in forming a β-globin TAD by activating neighboring CTCF sites and the role is beyond typical enhancer activity.

overall_design: H3K27ac, H3K27me3 ChIP-seq was performed in control and LCR HS2 deletion cells.


title: Differentially expressed genes in iKRAS cell treated with Trametinib, 2DG and Combo

first: Haoqiang

last: Ying

summary: To identify the differentially expressed gene in ikras cells treated with Trametinib, 2DG and Trametinib/2DG combination. Two ikras cells were used for transcriptomics analysis by RNAseq.

overall_design: Two iKras cell lines were treated as indicated and samples were prepared in duplicate.

first: Liang

last: Yan

first: Jun

last: Yao

first: Bo

last: Tu

first: Jing

last: Gong

first: Qiuyun

last: Wang

first: Christopher

last: Bristow

first: Wantong


title: Differentially expressed genes in iKRAS tumor treated with Trametinib or Kras extinction

summary: To identify the differentially expressed gene in ikras tumors treated with Trametinib or Kras extinction.

overall_design: Despite the essential role of MAPK pathway in PDAC maintenance, blocking MAPK signaling with MEK inhibitors has been shown to exert marginal impact on tumor growth or overall survival in both preclinical models and PDAC patients. In an effort to further explore potential MAPK co-inhibition targets, we leveraged the unique ability of the iKras model to genetically extinct oncogenic Kras in advanced tumors and conducted global transcriptomic analysis to identify KRAS downstream effector pathways/activities that are not affected by MAPK inhibition. Specifically, RNAseq analysis was performed in orthotopic xenograft tumors established with primary tumor lines from the iKras/p53 model to compare the transcriptomic profiles following KRAS extinction or Trametinib treatment for 1 or 3 days.


title: GATA6 defines endoderm fate by controlling chromatin accessibility during differentiation of human induced pluripotent stem cells [ATAC-seq]

summary: Investigation of the role played by GATA6 in establishing the definitive endoderm chromatin accessbility profile. We used pluripotent stem cells as a model of early development. We derived GATA6-/- pluripotent cells with an inducible GATA6 construct that permits exongenous GATA6 cDNA expression upon supplmentation of doxycycline. We differentiated GATA6 +/+ and GATA6-/- (with and without doxycyline) cells to definitive endoderm and analyzed the chromatin profile using ATAC-seq.

overall_design: Examination of chromatin accessibility during definitive endoderm formation in the absence and presence of GATA6.


title: T cell maturation, selection, and function differentially depend on the chaperonin CCT

city: Oxford

first: Adam

last: Handel

address: John Radcliffe Hospital

department: Weatherall Institute of Molecular Medicine

country: United Kingdom

institute: University of Oxford

summary: T cell homeostasis rely on de-novo transcription of proteins to ensure antigen-specific immunity. Central in this process and to ensure efficient and correct protein folding and turn-over is the Eukaryotic Type II chaperons, which primary targets are actin and tubulin. So far its role in T cell development and function remain unclear. Using a conditional deletion of a subunit within the type II chaperon complex we show this complex to be indispensable for correct maturation of thymocytes, with a reduced thymic output of mature effector and regulatory T cells. Accordingly, we found the formation of nuclear actin filaments to be reduced resulting in an array of functional effects with the most prominent being the failure to commit to the Th2 cell linage with a further insufficiency in recruiting cellular and humoral effector mechanisms to command an effective anti-parasitic response. Hence, our results highlight the importance of the Eukaryotic Type II chaperons in shaping the fate and function of CD4 T cells.

overall_design: RNA-seq in wild-type and Cct8 KO in lymphocytes

first: Bergithe

last: Oftedal

first: Georg

last: Hollander


title: Mapping of m6A and Its Regulatory Targets in Prostate Cancer Reveals a METTL3-low Induction of Therapy Resistance

city: Bern

first: Kellie

last: Cotter

state: Bern

address: Murtenstrasse 35

department: Dept for BioMedical Research

institute: University of Bern

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

overall_design: Refer to individual Series


title: GATA6 defines endoderm fate by controlling chromatin accessibility during differentiation of human induced pluripotent stem cells [RNA-seq]

first: Stephen

last: Duncan

summary: Investigation of the role played by GATA6 in establishing the definitive endoderm chromatin accessbility profile. We used pluripotent stem cells as a model of early development. We derived GATA6-/- pluripotent cells with an inducible GATA6 construct that permits exongenous GATA6 cDNA expression upon supplmentation of doxycycline. We differentiated GATA6 +/+ and GATA6-/- (with and without doxycyline) cells to definitive endoderm and analyzed the gene expression profile by RNA-seq.

overall_design: Examination of gene expression during definitive endoderm formation in the absence and presence of GATA6.

first: James


title: The Enrichment and Regulation of High-methylated CpG sites in CGI Border in ARPE-19 [RNA-seq]

city: Shanghai

first: Jianing

address: Dongchuan Road

institute: Shanghai JiaoTong University

summary: Stable maintenance of cytosine methylation is essential for mammalian biological processes such as gene transcription. To investigate the relationship of stably high methylation sites with gene expression, we cultured the ARPE-19 for lasting 10 generations and performed reduced representation bisulfite sequencing (RRBS) to obtain the highly methylated sites. Then we analyzed the characters of highly methylated sites and detected the transcription level of the cells. After filtered the low methylated CpG island (CGI), we found that highly methylated CpG sites had a preference for CGI boundary. In the promoter CGI, only in the condition as the gene expression is inhibited and the promoter CGI is at a high methylation level, a significant enrichment of the highly methylated sites is observed in the promoter CGI boundary. Our results showed that the enrichment of high methylation sites at the boundary of the CGI in the promoter region would have a significant inhibitory effect on the gene expression. In summary, we provide new insights into the regulatory mechanisms of DNA methylation.

overall_design: Using RNA-seq to evaluate the transcription level.

first: Yulan

last: Qin

first: Yani

last: Kang

first: Daniel

last: Czajkowsky

first: Hua

last: Li

first: Zhifeng

last: Shao


title: Che-1/AATF sustains cell growth and global transcription in Multiple Myeloma through the maintenance of open chromatin structure. [ATAC-Seq, mouse]

city: Rome

first: Matteo

last: Pallocca

address: Via Fermo Ognibene

country: Italy

institute: Italian National Cancer Institute "Regina Elena"

summary: This series contains the ATAC-seq data for control and Che-1 silencing in the Multiple Myeloma mice model.

first: Tiziana

last: Bruno

first: Francesca

last: De Nicola

first: Frauke

last: Goeman

first: Simona

last: Iezzi

first: Maurizio

last: Fanciulli


title: GATA6 defines endoderm fate by controlling chromatin accessibility during differentiation of human induced pluripotent stem cells [ChIP-seq]

summary: Investigation of the role played by GATA6 in establishing the definitive endoderm chromatin accessbility profile. We used pluripotent stem cells as a model of early development. We derived GATA6-/- pluripotent cells with an inducible GATA6 construct that permits exongenous GATA6 cDNA expression upon supplmentation of doxycycline. We differentiated GATA6 +/+ and GATA6-/- (with and without doxycyline) cells to definitive endoderm and analyzed histone tail modification profiles using CHIP-seq.

overall_design: Examination of 3 different histone modifications during definitive endoderm formation in the absence and presence of GATA6.

last: Heslop


title: Peripheral Insulin Regulates A Broad Network of Gene Expression in Brain

first: Hui

last: Pan

address: 1 Joslin Place

department: Bioinformatics and Biostatistics Core

institute: Joslin Diabetes Center

summary: The brain is now recognized as an insulin sensitive tissue, however, the role of insulin on gene expression in the brain is largely unknown. Here, we show that increases in peripheral insulin within the physiological range regulate expression of a broad network of gene expression, with the most robust effect in the hypothalamus followed by the hippocampus then nucleus accumbens. In hypothalamus, insulin regulates many genes involved in neurotransmission, including up-regulating expression of GABA-A receptor components, differentially modulating glutamate receptors, and suppressing multiple neuropeptides. Insulin also strongly modulates brain metabolism by suppressing genes involved in the glycolysis and pentose phosphate pathways while increasing expression of genes regulating pyruvate dehydrogenase complex, long-chain fatty acyl-CoA and cholesterol biosynthesis, rerouting carbon substrates to the biogenesis of plasma membrane for neuronal and glial function and synaptic remodeling. Thus, peripheral insulin acutely and potently regulates expression of genes involved in neurotransmission, neuromodulation and brain metabolism.

overall_design: Three month-old male C57BL/6J mice were anestethized and had an indwelling catheter placed in the right internal jugular vein. After recovery (4-5 days), conscious mice were continuously perfused with either 4 or 12 mU/kg/min insulin or saline as control. Blood glucose was verified every 5-30 min and adjusted with infusion of a 20% glucose solution. After 3 h of clamp, mice were euthanized by cervical dislocation, and brain tissues were harvested, snap frozen in liquid nitrogen and kept at -80C. Total RNA was isolated from hypothalamus, hippocampus and nucleus accumbens. Stranded cDNA libraries with unique index tags for each sample (48 multiplexed) were made using a directional RNA-seq kit (Wafergen). Sequencing was performed on an Illumina HiSeq 2500 run on rapid mode (2x50).

first: Weikang

last: Cai

first: C

last: Kahn


title: GATA6 defines endoderm fate by controlling chromatin accessibility during differentiation of human induced pluripotent stem cells.

first: Stephen


title: Che-1/AATF sustains cell growth and global transcription in Multiple Myeloma through the maintenance of open chromatin structure. [RNA-Seq, mouse]

summary: This series contains the transcriptomic profiling for control and Che-1 silencing in the Multiple Myeloma mice model’s.


title: Genetic, clinical, and biomarker correlates of EGFR inhibitor-related rash

city: Baltimore

first: Theresa

last: Hodges

state: MD

address: 801 W. Baltimore Street

department: Institute for Genome Sciences

institute: University of Maryland Baltimore

summary: Dermal fibroblasts that were cultured from skin biopsy samples were treated for three days with either 1µM of erlotinib, 1µM of DMSO (vehicle), or no treatment. The cells were harvested on the fourth day for total RNA extraction and hybridization on Affymetrix Human GeneChip 133 Plus 2.0 microarrays.

overall_design: Differential gene expression in fibroblasts of individuals who developed an EGFR inhibitor-related rash, versus those who did not, were compared.

first: K

last: Wickersham

first: T

first: A

last: Shetty

last: Griffith

first: M

first: S

last: Zhu

first: Y

last: Song

last: Edelman

last: Fraser

middle: G

last: Dorsey


title: Che-1/AATF sustains cell growth and global transcription in Multiple Myeloma through the maintenance of open chromatin structure [RNA-Seq]

first: Matteo

last: Pallocca

summary: Tumor transformation is the result of genetic modifications that alter gene transcription, thus producing a specific oncogenic program. However, in recent years, several exciting discoveries have shown that also aberrant epigenetic modifications play a major role in the genesis and progression of cancer. Multiple myeloma (MM) is a cancerous pathology resulting from the clonal expansion of plasma cells, and characterized by abnormal production and secretion of antibody proteins. This disease shows a great heterogeneity, caused by both genetic and epigenetic abnormalities, and despite the numerous therapeutic advances remains an incurable pathology. Here we show that the RNA Polymerase II binding protein, Che-1/AATF is required for MM cells growth by sustaining genome wide transcription and the recruitment of Pol II to the DNA. Notably, we found that Che-1 localizes on active chromatin and its depletion leads to accumulation of heterochromatin by a global decrease of histone acetylation. Moreover, we show that Che-1 directly interacts with histones and competes with HDAC class I members for histones binding. Strikingly, Che-1 downregulation decreases BRD4 chromatin accumulation and further sensitize MM cells to bromodomain and extra-terminal (BET) inhibitors. Overall, our findings identify an essential role of Che-1 in maintaining open chromatin required for sustaining MM growth, and support Che-1 as a possible target for MM therapy, alone or in combination with BET inhibitors.

overall_design: This series contains the transcriptomic profiling for control and Che-1 silencing in the Multiple Myeloma KMS-27 cell line.

last: Bruno

last: De Nicola


title: Prognostic factors of atypical meningiomas treated with gross total resection and early radiotherapy: microRNA-221/222 co-modulated radiosensitivity regulatory mechanism and malignent progression

status: Public on Jun 06 2021

city: Beijing

first: Qing

last: Zhang

address: Tiantan Xili 6, Dongcheng Distract

institute: Beijing Tian Tan Hospital, Capital Medical University

summary:
Background. The impact of adjuvant radiation therapy (XRT) after gross-total resection (GTR) of atypical meningiomas (AMs) has always been controversial. Considering that intrinsic differences among these AMs may exist, our study aim to seek which kind of these patients is more likely to recur and to explore its underlying causes.
Methods. The case database and the pathological records of our hospital between Jan 2008 and Jul 2016 were reviewed, 46 AMs received early XRT after GTR (confirmed by the 2016 revision of WHO diagnostic criteria). Microarray analysis and quantitative real-time polymerase chain reaction (qRT-PCR) were performed to detect aberrant expression of microRNAs (miRs). Immunohistochemical staining for the biomarker was performed, and its expression was semi-quantitative analyzed by using Image Pro Plus (IPP) 6.0. Univariate and multivariate Cox proportional hazards regression analysis were used to assess the correlation between various factors and recurrence.
Results. Microarray analysis and qRT-PCR demonstrated that miR-221/222 were upregulated in radiotherapy resistance (RTR) AM tissues compared with radiotherapy sensitive (RTS) AM tissues. Multivariable analysis showed that malignant progression (MP) (P=0.011), low expression level of PTEN (P=0.026) and skull-base AMs (P=0.028) were associated with higher recurrence.
Conclusion. We first demonstrated that upregulated miR-221/222 could decrease the radiosensitivity of the combination-therapy-treated AMs. Meanwhile, AMs with low expression level of PTEN, skull-base located were more likely to recur. MP-AMs were associated with increased possibility of recurrence by comparing to primary AMs. Treatment and consideration of MP-meningiomas were advocated to refer to the therapeutic strategy for higher grade meningiomas rather than restricted to its present grade.

overall_design: Among these 46 AMs, 6 patients (13.0%) presented with recurrent tumours at the last follow-up. The median time of recurrence was 33.5 months. Patients with recurrence time shorter than 33.5 months were classified into Radiotherapy resistance group (RTR), while those with PFS longer than 33.5 months, regardless of recurrence, were classified into Radiotherapy sensitive group (RTS). 3 AMs from each group were selected. Their FFPE samples (from the surgery right before XRT) were applied. Microarray analysis and qRT-PCR were performed to detect aberrant expression of microRNAs.

first: Guo-Bin

first: Lai-Rong

first: Liang

last: Wang

first: Zhen

last: Wu

first: Wang

last: Jia

first: Yun-Sheng

first: Da

last: Li

first: Ke

first: Ming

last: Ni

first: Li-Wei

first: Jun-Ting

first: Gui-Jun


title: Global transcriptomic response to chilling temperature in Col-0 wild type and sig5-3 (SALK_141383C) mutant Arabidopsis plants.

city: Bristol

first: Antony

last: Dodd

address: 24 Tyndall Avenue

department: Life Sciences Building

institute: University of Bristol

summary: Purpose: Investigate whether a nuclear-encoded sigma factor (SIGMA FACTOR5, SIG5; controls chloroplast transcription) regulates the transcriptome (RNA-seq) in response to chilling.

overall_design: Col-0 wild type and sig5-3 seedlings were grown under light/dark cycles for 11 days and exposed to continuous light for 24 h before start of experiment.  After 24 h under continuous light, one set of seedlings was exposed to 5 h chilling (4 °C), commencing at ZT27, and the other set was exposed to 3 h of chilling, commencing at ZT45. Both sets of chilled samples had parallel controls that were not chilled (19 °C). Each treatment had 3 independent replicates. Total RNA was extracted and RNA sequencing libraries were prepared using the Illumina TruSeq Stranded mRNA kit. Sequencing was performed using an Illumina NextSeq 500 using NSQ 500 Hi-Output kit v2 (150 cycle). Sequence data were imported into Partek Genomics Suite version 6.6 (Partek, St. Louis, 385 MO, USA), further trimmed and aligned to the Arabidopsis thaliana genome (TAIR11) using STAR (version 2.4.1d). Genes with a fold change of |log2| > 1.5 and a false detection rate of < 0.05 were considered as differentially-expressed.

first: Dora

last: Cano-Ramirez


title: The study of the effects of dauricine(dau) on human pancreatic carcinoma cells  [miRNA]

status: Public on Jun 05 2021

first: Yun

last: Bai

state: Hei Long Jiang

address: No.24 heping Street, XiangFang district

institute: Hei Long Jiang University of Chinese medicine

summary: Pancreatic  cancer is one of the most malignant digestive tract tumors with the worst prognosis. Few treatments are available; thus, the discovery of potential new anti-cancer agents has always been a hot issue. Dauricine (Dau) can inhibit the proliferation of the pancreatic cancer cell line BxPC3, and has the potential to be used as an adjuvant drug against pancreatic cancer; however, how Dau inhibits tumor cell proliferation has not been elucidated. To unravel the effects of Dau on proteins and metabolic pathways of pancreatic cancer cells, and to elucidate its anticancer mechanisms, we evaluated mRNA and microRNA expression in BxPC3 cells treated with Dau.

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus

overall_design: The samples included 3 groups of untreated BxPC3 cells and 3 groups of BxPC3 cells treated with 24 μmol Dau for 72h. Extract total RNA,then sequece mRNA.

first: Ling

last: Jiang


title: Gene age predicts the transcriptional landscape of sexual morphogenesis in multicellular fungi [Ptegra1]

city: Szeged

first: Laszlo

middle: G.

last: Nagy

state: Csongrad

address: Temesvari krt 62

department: Institute of Biochemistry, Synthetic and Systems Biology Unit

country: Hungary

institute: Biological Research Centre, Hungarian Academy of Sciences

summary: Pterula gracilis developmental stages

overall_design: Developmental stages and tissue samples from dikariotic Pleurotus ostreatus (N001; CECT-20600) species during fruiting body formation were collected and profiled. Each group has 2-3 replicates.

first: Zsolt

last: Merenyi

first: Máté

last: Virágh

first: Emile

last: Gluck-Thaler

first: Jason

last: Slot

first: Brigitta

last: Kiss

first: Torda

last: Varga

first: András

last: Geösel

first: Botond

last: Hegedüs

first: Balázs

last: Bálint

first: László


title: Effect of planting density on leaf yield and active compound accumulation in Ginkgo biloba

city: Yangzhou

first: Li

last: Wang

address: Wenhui east road no. 48

institute: Yangzhou University

summary: We sequenced mRNA of G. biloba leaves from different planting densities using the Illumina HiSeq4000 platform. We identified the transcriptome changes in leaves , which provided valuable information for uncovering the molecular mechanisms of flavonoid accumulation in G. biloba under different densities.

overall_design: Transcriptome sequencing in different planting denties leaves of G. biloba

first: Jinkai

last: Lu


title: Bevacizumab treatment for ovarian cancer alter the expression of micro RNAs (miRNAs), leading to activate VEGF-independent angiogenesis pathway.

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: 10-1 tebiro 6-chome

country: Japan

institute: Toray Industries,Inc.

summary: We could successfully detected the miRNAs which down-regulated in Bevacizumab group compared with those in Control group through expression profiling of a total of 1,899 miRNAs in two C57BL/6 mice. And also, we could extracted the miRNA which might regulate the expression of SERPINE1 gene.

overall_design: In the study presented here, C57BL/6 mice (aged 5 weeks) were purchased from CLEA Japan Inc. (Tokyo, Japan). A total of 2 × 10^6 ID-8 LUC2 cells were suspended as single cells in a volume of 0.2 mL PBS and injected intraperitoneally into the mice. Mice were assessed daily for general health. 14 days after the inoculation, the mice were intraperitoneally administered either control IgG 5 mg/kg (control group) or bevacizumab 5 mg/kg (bevacizumab group) twice a week. And finally the mice were sacrificed at day 42. The tumor’s RNA was extracted using RNeasy Mini Kit (74104, QIAGEN).

first: Taro

last: Yagi

first: Mayuko

last: Miyamoto

first: Kenjiro

last: Sawada


title: Gene age predicts the transcriptional landscape of sexual morphogenesis in multicellular fungi

first: Laszlo

sample_organism:
Pleurotus ostreatus
Pterulicium gracile

platform_organism:
Pleurotus ostreatus
Pterulicium gracile


title: The study of the effects of dauricine(dau) on human pancreatic carcinoma cells  [mRNA array]

city: Harbin

first: Yun

last: Bai

first: Ling

last: Jiang


title: Gene age predicts the transcriptional landscape of sexual morphogenesis in multicellular fungi [Pleos]

last: Nagy

summary: Pleurotus ostreatus tissue types and developmental stages

first: Zsolt

last: Merenyi

first: Máté

first: Emile


title: PLEKHG5 stabilized by HDAC2-related deacetylation is the master regulator of sorafenib resistance in HCC

city: Chongqing

first: yu

last: sha

address: No.1 Yi Xue Yuan Road, Yuzhong District, Chongqing

institute: Chongqing Medical University

summary: Objective: Advanced HCC patients have few choices for life-prolonging therapy due to the high incidence of drug resistance. This study aimed to clarify the mechanism of sorafenib resistance and seek more effective treatments.Design:Two sorafenib-resistant (SR) cell lines were established to study the mechanism of drug resistance. RNA sequencing was used to characterize the global transcriptional consequences of sorafenib resistance, and immunoprecipitation-mass spectrometry (IP-MS) was performed to identify specific acetylation sites.Results： We found that Rho-GTPases were upregulated in SR cells and that PLEKHG5 was most abundantly expressed among all Rho GEFs (activators of Rho-GTPases). PLEKHG5 knockdown increased HCC cell sensitivity to sorafenib and inhibited the activation of Rac1 and downstream AKT/NF-κB signaling, while overexpression of PLEKHG5 reduced sorafenib sensitivity, which suggested that PLEKHG5 activation could be targeted to limit sorafenib resistance. IP-MS confirmed that three lysine sites in PH domain of PLEKHG5 could be acetylated, and their acetylation levels were correlated with PLEKHG5 stability. Further study demonstrated that HDAC2 interacted with PLEKHG5 to deacetylate lysine sites within the PH domain and maintain its stability. Finally, both knockout of HDAC2 and treatment with the selective HDAC2 inhibitor CAY10683 reduced PLEKHG5 protein levels and thereby enhanced the sensitivity of HCC to sorafenib in vivo and in vitro.Conclusion.:PLEKHG5 plays a key role in the occurrence of sorafenib resistance by activating Rac1/AKT/NF-κB signaling. HDAC2 regulates PLEKHG5 protein stability by regulating the acetylation level of its PH domain, and thus HDAC2 may be a potential therapeutic target for overcoming PLEKHG5-mediated sorafenib resistance in HCC.

overall_design: mRNA profiles of MHCC97H control and sorafenib-resistant cells

first: Yu

last: Sha

first: Jie

last: Xia


title: DRUGseq U2OS cells treated with small molecules

city: Cambridge

first: Daniel

last: Ho

address: 250 Massachusetts Avenue

institute: Novartis Institutes for Biomedical Research

summary: We report the transcriptional changes associated with treatment of U2OS osteosarcoma cell line with DMSO, ND-09-QY33, CA-90-VK59, JC-68-AL90, MB-03-IE36, JC-43-ZO95, PA-33-CK45, KA-73-NB69, QC-05-UB63, SE-15-AV21, NV-67-DX31, DB-85-YA47, NA-37-JQ34, VA-76-OV33, & LD-22-SA99

overall_design:
U2OS cells were treated with  3.18nM, 10.04nM, 31.74nM, 100.29nM, 316.91nM, 1001.44nM, 3164.56nM, and 10000nM of DMSO, ND-09-QY33, CA-90-VK59, JC-68-AL90, MB-03-IE36, JC-43-ZO95, PA-33-CK45, KA-73-NB69, QC-05-UB63, SE-15-AV21, NV-67-DX31, DB-85-YA47, NA-37-JQ34, VA-76-OV33, & LD-22-SA99 for 24 hrs and subjected to DRUGseq

Please note that a github repository has been created to assist in all downstream analysis:
https://github.com/Novartis/DRUG-seq

first: Martin

last: Henault

first: Chian

last: Yang

first: Carsten

last: Russ

first: Alicia

last: Lindemann


title: Identification of altered cell signaling pathways in stable and progressive chronic lymphocytic leukemia

city: Brest

first: Cristina

last: Bagacean

address: 2 Avenue Foch

institute: UBO

summary: Chronic lymphocytic leukemia (CLL) is characterized by significant biological and clinical heterogeneity. This study was designed to explore CLL B-cells’ proteomic profile in order to identify biological processes affected at an early stage and during disease evolution as stable or progressive. Purified B cells from 11 untreated CLL patients were tested at two time points by liquid chromatography-tandem mass spectrometry. Patients included in the study evolved to either progressive (n=6) or stable disease (n=5). First, at an early stage of the disease (Binet stage A), based on the relative abundance levels of 389 differentially expressed proteins (DEP), samples were separated into stable and progressive clusters with the main differentiating factor being RNA splicing pathway. Next, in order to test how the DEPs affect RNA splicing, a RNA-Seq study was conducted for 4 Stable and 4 Progressive CLL patients, showing 4217 differentially spliced genes between the two clusters. Distinct longitudinal evolutions were observed with predominantly proteomic modifications in the stable CLL group and spliced genes in the progressive CLL group. Splicing events were shown to be 6 times more frequent in the progressive CLL group. The main aberrant biological processes controlled by DEP and spliced genes in the progressive group were cytoskeletal organization, Wnt/β-catenin signaling, mitochondrial and inositol phosphate metabolism with a downstream impact on CLL B-cell survival and migration. This study suggests that proteomic profiles at the early stage of CLL can discriminate progressive from stable disease and that RNA splicing dysregulation underlies CLL evolution, which opens new perspectives in terms of biomarkers and therapy.

overall_design:
Purified B cells from 8 untreated CLL patients were tested at two time points by RNA-Seq. Patients included in the study evolved to either progressive (n=4, samples tested at diagnosis in Binet A disease and at the time of progressive disease to Binet B/C) or stable disease for more than 5 years (n=4, samples tested at diagnosis and 3 years after diagnosis).
Longitudinal study of stable and progressive CLL.

first: Yves

last: Renaudineau


title: Maternal Circulating Exosomal miRNAs as Non-Invasive Biomarkers for Prediction of Fetal Ventricular Septal Defect

city: jiaxing

first: yuxia

last: jin

address: East Zhong huan Road, 2468#

institute: Jiaxing University Affiliated Women and Children Hospital

summary:
Objective:This study aims to discover circulating exosomal miRNAs as potential noninvasive biomarkers early detection of fetus with ventricular septal defect (VSD).
Method:A total of 182 pregnant women including 91 VSD cases and 91 matched controls were included in this study. Exosomes were isolated and  next-generation sequencing was used to obtain a profile of dysregulated exosomal miRNA. The differential abundance was verified by quantitative real-time PCR (q RT-PCR). . Receiver operating characteristic (ROC) curves were conducted  to evaluate the diagnostic accucary
Results: 77 serum exosomal miRNA were uncovered to be differentially expressed in the VSD group as compared to the control group. Among these, five down-regulated exosomal miRNA were validated by qRT-PCR. hsa-miR-146a-5p was identified to be capable of distinguishing VSDs from controls (area under the ROC (AUC): 0.997; p < 2.2e-16).
Conclusion: circulating exosomal miRNA, in particular, hsa-miR-146a-5pmay be a predictive biomarker for non-invasive prenatal diagnosis of fetal VSDs.

overall_design: Maternal circulating exosomal miRNAs profiles of ventricular Septal Defect and control.

first: Yuxia

last: Jin

first: Suping

last: Li


title: A systematic dissection reveals the key genes and mechanisms underlying the natural variation of silique length in rapeseed (Brassica napus L.)

status: Public on Jun 04 2021

city: Wuhan

first: Quaid

last: Hussain

address: Oil Crops Research Institute of CAAS,  No.2 Xudong Second Road, Wuchang, Wuhan, 430062, Hubei China

department: Crop Breeding and Genetics

institute: Student

summary: Transcriptomic analysis of two pools of silique walls with extreme length identified a total of 3248 differentially expressed genes (DEGs), which were enriched in several pathways (such as cell wall, cell division, and hormone metabolism etc.) that are associated with cell proliferation/expansion and silique development.

overall_design: The silique walls at 15-days after flowering were sampled from the 12 long- and 11 short-silique accessions and then equally mixed to form two pools, respectively. The RNA extraction, purification, and quantification were performed according to the Plant Mini RNeasy Kit (Qiagen, Shanghai, China). The RNA-seq libraries were prepared using the Illumina TrueSeq RNA Sample Preparation Kit (Illunima Inc., San Diego, USA). The final cDNA libraries were sequenced using the Illumina Hiseq platform, which generated the raw reads. Then, the low-quality, low-complexity, and repetitive raw reads were filtered, and the clean reads that passed quality control were used for subsequent analysis. All reads of each library were mapped to the reference genome of Darmor, and the uniquely mapped reads were selected for transcript quantification. In this study, the false discovery rate (FDR) ≤0.05 and the p-value ≤0.005 were used as a threshold to characterize the differentially expressed genes (DEGs).

first: Jiaqin

last: Shi

first: Hanzhong

last: Wang


title: RNA-seq of S63845 sensitive and resistant myeloma cell lines.

city: Vienna

first: Arnold

last: Bolomsky

address: Montleartstraße 37

country: Austria

institute: Wilhelminen Cancer Research Institute

summary: We performed RNA-seq analysis of in-house generated S63845 sensitive and resistant myeloma cell lines OPM-2 and KMS-12-BM in order to define common events in the acquisition of MCL-1 inhibitor resistance. Our results, however, point to the occurrence of cell line specific, heterogeneous paths to resistance as no common differences were observed. Subsequent experiments rather revealed that the binding kinetics of BH3 family members are a major driver of MCL-1 inhibitor resistance and that individual shifts during the establishment of resistance dependent on the baseline BH3 family profile.

overall_design: Comparison of myeloma cell line models with acquired S63845 resistance and their sensitive (long-term culture) control. RNA-seq was performed in untreated cells.

first: Alina

last: Malyutina

first: Juho

last: Miettinen


title: Early life inflammation promotes depressive symptoms in adolescents via microglial engulfment of dendritic spines

city: Hefei

first: zhi

last: zhang

state: Anhui

address: 443 Huangshan Road

department: School of Life Science

institute: University of Science and Technology of China

summary: Early life inflammation is known to promote the risk of depression in later life. Here, we demonstrate how early life inflammation causes adolescent depressive-like symptoms: by altering the long-term neuronal spine engulfment capacity of microglia. For mice exposed to lipopolysaccharide (LPS)-induced inflammation via the Toll-like receptor 4/NF-κB signaling pathway at postnatal day 14 (P14), ongoing longitudinal imaging of the living brain revealed that later stress (delivered during adolescence on P45) increases the extent of microglial engulfment around anterior cingulate cortex (ACC) glutamatergic neuronal (ACCGlu) spines. Through bluk RNA-seq of ACC tissue, we find that the fractalkine receptor CX3CR1 mediates stress-induced engulfment of ACCGlu neuronal spines.

overall_design: mRNA profiles of ACC in P45 mice that were treated with saline or LPS on P14

first: Peng

last: Cao

first: Changmao

last: Chen

first: An

last: Liu

first: Zhi

last: Zhang


title: RNA sequencing in AGS cells with SFA and SFE treatment

city: beijing

first: sichong

last: han

address: No. 15 North Third Ring East Road, Chaoyang District

institute: beijing university of chemical technology

summary: SFA and SFE have received more and more attention for their antioxidant, antiinflammatory and anticarcinogenic properties.Gastric cancer is the fourth most common malignant tumor with limited strategies and poor prognosis.To identify whether and how SFA and SFE can inhibit gastric cancer progression, we carry out RNA-seq analysis in AGS cells treated with SFA and SFE

overall_design: Treated AGS cells with SFA and SFE respectively to detect the change of gene expression. DMSO is used as negative control

first: SiChong

last: Han

first: Zhe

first: JiNing

first: QiPeng

last: Yuan