title: Circulating cell-free, methylated DNA reveals tissue-specific, cellular damage from radiation treatment [Human Reference Cell-type RNA-seq]

first: Anton

summary: Radiation therapy is an effective cancer treatment although damage to healthy tissues is common. Here we establish sequencing-based, cell-type specific DNA methylation reference maps of human and mouse tissues to infer the origins of cell-free DNA fragments released from dying cells into the circulation. We find cell-type specific DNA blocks mostly hypomethylated and located within genes intrinsic to cellular identity. In a mouse model,  thoracic radiation-induced tissue damages were reflected by dose-dependent increases in lung endothelial, cardiomyocyte and hepatocyte methylated DNA in serum. The analysis of serum samples from breast cancer patients undergoing radiation treatment revealed distinct tissue-specific epithelial and endothelial responses to radiation across multiple organs. Strikingly, patients treated for right-sided breast cancers also showed increased hepatocyte and liver endothelial DNA in the circulation indicating the impact on liver tissues. Thus, cell-free methylated DNA in serum can uncover cell-type specific effects of radiation on healthy tissues and inform treatment.

overall_design: Transcriptomic profiling of gene expression reflective of cellular identity in sorted cell populations from healthy tissue donors.

first: Megan

middle: E

last: McNamara

first: Netanel

last: Loyfer

first: Amber

last: Kiliti

first: Marcel

middle: O

last: Schmidt

first: Sapir

last: Shabi-Porat

first: Sidharth

last: Jain

first: Sarah

middle: M

last: Roth

first: A

last: McDeed

first: Nesreen

last: Shahrour

first: Elizabeth

last: Ballew

first: Yun-Tien

last: Lin

first: Heng-Hong

last: Li

first: Anne

last: DMays

first: Sonali

last: Rudra

first: Anna

middle: T

last: Riegel

first: Keith

last: Unger

first: Tommy

last: Kaplan


title: Circulating cell-free, methylated DNA reveals tissue-specific, cellular damage from radiation treatment [Mouse Reference Cell-type MCC-seq]

status: Public on Jul 24 2023

city: Washington

first: Anton

last: Wellstein

state: DC

address: 3970 Reservoir Road, N.W.,

department: Oncology

country: USA

institute: Georgetown University

type: Methylation profiling by high throughput sequencing

overall_design: Identification of sequencing-based, cell-type specific DNA methylation patterns of healthy tissues and cell-types.

first: Megan

last: McNamara

middle: J

middle: P

middle: D

last: Mays


title: Circulating cell-free, methylated DNA reveals tissue-specific, cellular damage from radiation treatment [Mouse Serum MCC-seq]

overall_design: Tissue-of-origin analysis of cell-free DNA (cfDNA) using identified cell-type specific methylation patterns from reference WGBS data in healthy tissues. CfDNA from serum samples was analyzed by hybridization capture sequencing for changes in methylated cfDNA to uncover cellular damages.

first: Netanel

last: Loyfer

first: Amber

last: Kiliti

last: Schmidt


title: Circulating cell-free, methylated DNA reveals tissue-specific, cellular damage from radiation treatment [Human Reference Cell-type MCC-seq]

overall_design:
Identification of sequencing-based, cell-type specific DNA methylation patterns of healthy tissues and cell-types.
NOTE FROM SUBMITTER: Raw data are not available due to patient privacy concerns.

first: Marcel

first: Sapir

last: Shabi-Porat

last: Jain

last: Roth


title: Circulating cell-free, methylated DNA reveals tissue-specific, cellular damage from radiation treatment [Human Serum MCC-seq]

overall_design:
Tissue-of-origin analysis of cell-free DNA (cfDNA) using identified cell-type specific methylation patterns from reference WGBS data in healthy tissues. CfDNA from serum samples was analyzed by hybridization capture sequencing for changes in methylated cfDNA to uncover cellular damages.
NOTE FROM SUBMITTER: Raw data are not available due to patient privacy concerns.

first: Sidharth

first: Sarah

last: McDeed

last: Shahrour

last: Ballew


title: intact Hi-C from Right ventricle myocardium superior (ENCSR476RFQ)

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

institute: ENCODE DCC

summary:
w78-right-ventricle-myocardium-superior-intact dnase hic

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Direct Induction of Trophoblast Stem Cells from Human Fibroblasts

city: Jerusalem

first: Yosef

last: Buganim

address: Hadassah Medical School

department: Department of Developmental Biology and Cancer Research

country: Israel

institute: The Hebrew University

type: Expression profiling by high throughput sequencing

summary: Time-course transcriptomic analysis of GOKM, OSKM and GSKM reprogrmming to hiTSCs.

overall_design: Fibroblasts (KEN) were transduced with either GATA3, OCT4, KLF4, MYC (GOKM) or OCT4, SOX2,KLF4, MYC (OSKM) or GATA3, SOX2, KLF4, MYC (GSKM) were subjected to RNA-seq, along with samples of HFFs, hbdTSCs and hiPSCs

first: Moran

last: Rahamim

first: Moriyah

last: Naama

first: Dana

last: Orzech


title: Expression data from human Dendritic cells (DCs)

city: Mannheim

first: Carolina

last: Delatorre

address: Theodor-Kutzer-Ufer 1-3

country: Germany

institute: University Heidelberg

summary:
microRNAs are crucial post-transcriptional regulators which contribute to the effect of sulforaphane in cancer and are also involved in the modulation of of many aspects of DC biology, including development, maturation, surface molecule expression and released cytokines
We used microarrays to detail the regulation of miRNAs in human DCs by sulforaphane, underlying the regulation of different crucial DCs regulatory molecules and signaling pathways

overall_design: human monocyte-derived DCs (MoDCs) were produced, treated as described and used for miRNA extraction and hybridization on Affymetrix GeneChip miRNA 4.0 Arrays. We sought to increase the quality of produced MoDCs by isolation of initial Monocytes by CD14 MACS microbeads. The high quality MoDCs were proved by flow cytometry, pretreated with 30 mM sulforaphane (SF) for 30 min, treated with maturation cytokine cocktail or left untreated and collected for miRNA isolation after 48 hours incubation

first: Yangyi

last: Wang

first: Svetlana

last: Karakhanova


title: CD73-Dependent Adenosine Signaling through Adora2b Drives Immunosuppression in Ductal Pancreatic Cancer

city: Houston

first: Yulin

last: Dai

state: TX

address: 7000 fannin, suite 600

department: School of Biomedical Informatics

institute: University of Texas health science center at Houston

summary: In this experiment, we evaluted whole transcriptomic changes in ex vivo cultured ducts expressing mutant Kras compared to control ducts. The cells were cultured for 7 days before RNA was isolated for RNA-seq.

overall_design: For the ex vivo cultured ducts, Hnf1b:CreERT2; LSL-KrasG12V mice were given 10 mg tamoxifen or corn oil control and euthanized at day 4 for ex vivo culturing of ducts.

first: Jennifer

last: Bailey


title: Myc regulates the lineage commitment of transformed hepatocytes during liver tumorigenesis (RNA-Seq)

city: Vienna

first: Iros

last: Barozzi

address: Borschkegasse 8a

country: Austria

institute: Medical University Vienna

summary: The two oncogenes Myc and Kras cooperate to drive tumorigenesis and tumor suppressive pathways, to regulate the tumor microenvironment and to respond to immuno-therapies in different types of cancer. However, the interactions between Myc and Kras in cancer plasticity remain largely unknown. Primary liver cancer (PLC) comprises hepatocellular carcinoma (HCC) and intrahepatic cholangiocarcinoma (ICC), two tumor subtypes which are morphologically and clinically different, and cell intrinsic molecular mechanisms that lead to the onset of HCC or ICC remain elusive. Here using a mouse model of KrasG12D-driven ICC we show that Myc overexpression switches the tumorigenesis towards HCC. Lineage tracing experiments showed that this switch occurred in KrasG12D transformed hepatocyte fated to develop into ICC. Since cell fate decisions during lineage differentiation are coordinately regulated by transcriptional and epigenetic changes, we took advantage of transcriptomic (RNA-seq) and chromatin accessibility (ATAC-seq) profiling to analyze hepatocytes transformed either with KrasG12D only or with KrasG12D and Myc. We identified Foxa1, Foxa2 and Ets1 as the major transcription factors responsible of the lineage commitment of transformed hepatocytes towards ICC or HCC, a function that is conserved also in humans. Altogether, our study describes an unanticipated cell intrinsic mechanism of lineage determination during the development of primary liver cancer orchestrated by the oncogene Myc.

overall_design: Total RNA-seq profiling of primary hepatocytes transformed with KrasG12D alone (triplicate) or in combination with Myc (triplicate). Untransformed hepatocytes (duplicate) were also profiled.

first: L

last: D'Artista

first: I

last: Zender


title: Myc regulates the lineage commitment of transformed hepatocytes during liver tumorigenesis

type: Genome binding/occupancy profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Myc regulates the lineage commitment of transformed hepatocytes during liver tumorigenesis (ATAC-Seq)

overall_design: ATAC-seq profiling of primary hepatocytes transformed with KrasG12D alone (triplicate) or in combination with Myc (triplicate). Untransformed hepatocytes (duplicate) were also profiled.


title: Tiam1 methylation by NSD2 promotes Rac1 signaling activation and cancer metastasis

status: Public on Jul 23 2023

city: Wuhan

first: da

last: song

state: Hubei

address: Jiefang Avenue 1095

department: tongji hospital

country: China

institute: huazhong university of science and technology

summary: Metastasis is the key cause of failure of cancer therapy or mortality, but targeting metastatic seeding and colonization remains an unresolved challenge. Here, we report a novel molecular event in cancer metastasis mediated by NSD2/Rac1 signaling and provide a detailed mechanistic investigation of cancer metastasis. We found that NSD2, a histone methyltransferase responsible for di-methylating histone 3 at lysine 36, was overexpressed in metastatic tumors, and overexpressed NSD2 enhanced tumor metastasis both in vitro and in vivo. We further investigated that NSD2 promoted tumor metastasis by activating the Rac1 signaling pathway. Mechanistically, NSD2 methylated Tiam1, a guanine nucleotide exchange factor that facilitates GDP-Rac1 to GTP-Rac1 transition at K724. We demonstrated that Tiam1 K724 methylation plays a crucial role in Tiam1 activation and GDP-Rac1 to GTP-Rac1 transition. Specifically, we identified that Tiam1 K724 methylation could be a predictive factor in cancer prognosis, and we demonstrated that pharmacological blocking of Tiam1 K724 methylation by employing a transmembrane peptide inhibited tumor metastasis both in vitro and in vivo. Thus, NSD2-methylated Tiam1 promoted Rac1 signaling activation and cancer metastasis, which might provide novel insights into tumor metastasis inhibition.

overall_design: To investigate why NSD2 promotes cancer metastasis, we performed another RNA-seq analysis to identify the altered genes and signaling pathways between NSD2 wild-type (WT) cells and NSD2 KD cells

first: Da

last: Song

first: Fuqing

last: Hu

first: Junbo

first: Guihua


title: Arid1a in mouse embryonic cells

city: Shanghai

first: Ze-guang

last: Han

address: 800 Dongchuan Road

department: Shanghai Center for Systems Biomedicine

institute: Shanghai Jiao Tong University


title: miRNA profile of duck duodenum mucosa damage caused by oxidative stress

city: Wu han

first: Li

last: Zhang

state: Hu bei

address: No. 29, Nanhu Avenue, Shizishan Street, Hongshan District, Wuhan City, Hubei Pro

institute: Institute of Animal Husbandry and Veterinary Medicine, Hubei Academy of Agricultural Sciences

type: Non-coding RNA profiling by high throughput sequencing

summary: We deep sequenced and analyzed  miRNAs using deep RNA sequencing (RNA-seq) in cage rearing and traditional breeding duck's duodenum sample of Nonghu NO.2 duck.  21 differentially expressed miRNA were identified in the duodenum. 6 miRNAs were upregulated and 15 were downregulated in the cage rearing duck's duodenum of the Nonghu NO.2 duck compared to their expression in the control group. These findings provided insights into the expression profiles of miRNAs in duck duodenum, and deepened our understanding of miRNAs in oxidative injury of duck.

overall_design: Examination of miRNA expression profile in cage rearing duck's duodenum and traditional breeding duck's duodenum samples

first: Hao


title: Transcriptomic response of Arabidopsis thaliana to the two rare earth elements lanthanum and ytterbium

city: Vandoeuvre-les-Nancy

first: Nicolas

last: Grosjean

address: Faculté des Sciences et Technologies

country: France

institute: LIEC UMR 7360 CNRS-Université de Lorraine

summary: The goal of this study is to compare the transcriptome (RNA-seq) modulations in the roots and shoots of Arabidopsis thaliana, as a plant model, exposed to two toxic concentrations of rare earth elements. Lanthanum and ytterbium were used as representative of light and heavy rare earth elements, respectively.

overall_design: RNAseq data of Arabidopsis thaliana shoots (L) and roots (R) after being hydroponically grown and exposed for 3 days to the two rare earth elements lanthanum (La) and ytterbium (Yb), or not exposed (Ctrl)

first: Marie

last: Le Jean

first: Damien

last: Blaudez


title: CD44+ Lung Cancer Stem Cell-derived Vascular Pericytes Cause Brain Metastases through GPR124-mediated Trans-endothelial Migration [I]

city: Cleveland

first: Qian

last: Huang

state: OH

address: 9500 Euclid Ave

institute: Cleveland Clinic

summary: Brain metastasis of lung cancer causes high mortality, but the exact mechanisms underlying the metastasis remain unclear.  Here we report that vascular pericytes derived from CD44+ lung cancer stem cells (CSCs) in lung adenocarcinoma (ADC) potently cause brain metastases through GPR124-mediated trans-endothelial migration (TEM). CD44+ CSCs in the perivascular niche generate the majority of vascular pericytes in lung ADC. CSC-derived pericyte-like cells (Cd-pericytes) exhibit remarkable TEM capacity to effectively intravasate into vessel lumina, survive in the circulation, extravasate into the brain parenchyma, and then de-differentiate into tumorigenic CSCs to form metastases. Moreover, Cd-pericytes uniquely express GPR124, a G-protein-coupled receptor. GPR124 mediates through Wnt7-β-Catenin activation to enhance TEM capacity of Cd-pericytes for intravasation and extravasation, two critical steps during tumor metastasis. Furthermore, selective disruption of Cd-pericytes, GPR124 or Wnt7-β-Catenin signaling markedly reduced brain and liver metastases of lung ADC. Our findings uncover an unappreciated cellular and molecular paradigm driving tumor metastasis.

overall_design: Lung adenocarcinoma cell derived pericytes were transduced with non-targeting shRNA or shRNA targeting GPR124 genes. The gene expressions were analized by high throughput RNA sequencing.

first: Bao

last: Shideng

first: Huang

last: Qian


title: CD44+ Lung Cancer Stem Cell-derived Vascular Pericytes Cause Brain Metastases through GPR124-mediated Trans-endothelial Migration


title: CD44+ Lung Cancer Stem Cell-derived Vascular Pericytes Cause Brain Metastases through GPR124-mediated Trans-endothelial Migration [II]

overall_design: Surgical specimens of lung ADC were dissociated with the Papain Dissociation System. The isolated cells were cultured in neurobasal medium. CD44+ CSCs were sorted through FACS sorting according to CD44 expression. The Cd-pericytes were isolated from CD44+ CSCs cultured in pericyte-specific medium. The CSCs de-differentiated from Cd-pericyte were isolated from Cd-pericytes cultured in neurobasal medium for several generations.


title: Identification of the dedifferentiation trajectory of the cells without Arid1a using single cell RNA-seq

summary: The primary mouse hepatocytes were isolated from the liver tissue Arid1af/f mouse. To immortalize mouse primary hepatocytes, the isolated cells were first infected with lentivirus expressing simian virus 40 large-T protein (SV40LT), and then cultured until proliferated cell colonies appear. Cells were further transformed with lentivirus expressing HrasV12D to generate a cell line called AB17, which were cultured in DMEM supplemented with 10% FBS and 100 µg/ml penicillin-streptomycin in a humidified incubator at 37℃ with 5% CO2.To get insight into trajectory of dedifferentiation induced by Arid1a loss, we performed single-cell RNA sequencing (scRNA-seq) on FACS-sorted GFP+ AB17 cells using Fluidigm C1 platform, and obtained the scRNA-seq data from 76 cells with Arid1a knockout induced by Ad-Cre and 73 cells infected with Ad-GFP as control. Significantly, these AB17 cells with or without Arid1a were classified to the two distinct clusters based on their scRNA-seq data via the unsupervised clustering with SC3 software and the dimensionality reduction analysis using t-distributed stochastic neighbor embedding (tSNE) visualization, where the major Ad-Cre infected AB17 cells were assembled into cluster 1 while the majority of AB17 cells with empty Ad-GFP as a control belonged to cluster 2. These data suggest that Arid1a loss obviously dysregulated the gene expression pattern, as represented by the top ten differentially expressed genes between these two clusters.

overall_design: 48h after infection with Ad-GFP and Ad-Cre, AB17 cells were sorted to get GFP positive cells. Single cell was captured, reverse-transcribed and amplified on Fluidigm C1 platform. The next generation sequencing was performed by Nextera XT DNA library prep kit (Illumina), followed by sequencing on Illumina X Ten platform using a 150 bp paired-end sequencing strategy. An ERCC Spike-in mix (Ambion) was used as the technical control.

first: Lan

last: Wang


title: Mechanism of nonthermal plasma on melanoma cell growth suppression

city: Seoul

first: Nagendra

middle: Kumar

last: Kaushik

state: Nowon-Gu

address: 20 Kwangwoongil, Wolgye Dong 447-1

department: Biophysics

country: South Korea

institute: Kwangwoon University

summary: To investigate the miRNAs function in the regulation of nonthermal plasma induced melanoma cell suppression.

overall_design: Comparative miRNA expression profiling analysis of small-RNA-seq data for SK-MEL-2 (SK-2) cells following plasma jet treatment (control, 3 min plasma, and 5 min plasma).

middle: K

first: Neha

first: Eun

middle: H

last: Choi


first: Yulin

last: Dai

summary: Kras and Trp53 mutations promote transformation in pancreatic acinar and ductal cells. We wanted to evaluate whole transcriptomic profiles of acinar and ductal derived tumors. In addition, we studied whole transcriptomic changes in ex vivo cultured ducts expressing mutant Kras compared to control ducts.

overall_design: Mutant Kras and mutant Trp53 were genetically deleted from acinar or ductal cells using inducible CRE:ER alleles. Eight week old mice were given tamoxifen (5mg) in corn oil and mice were monitored for signs of disease progression.

first: Jennifer

last: Bailey


title: high efficiency and multiplexable Strand specificity RNA sequencing by Double Adapter Directional Capture

city: wuhan

first: zaiqiao

last: sun

institute: wuhan university

summary: The quantification of transcriptome through RNA sequencing (RNA-seq) has widely been used to characterize all patterns of genes in a certain period. However, although many experimental protocols have recently been developed, RNA-seq is still a challenging technology in application. It is necessary to develop an easy and versatile RNA-seq method available in a wide range from single cell RNA to bulk RNA. Here we introduce a novel RNA-seq method, Double Adapter Directional Capture sequencing (DADCSeq), by directly adding adaptor at both termini of library respectively in the steps of reverse transcription and second strand synthesis, which can not only produce high quality strand specificity full-length RNA-seq library but also reduces cockamamie steps of library constructions with less time consuming. The DADCSeq was also optimized for prokaryote such as Mycobacterium smegmatis, a model bacterium for Mycobacterium tuberculosis, and can detect more genes compared to traditional methods. Taken together the DADCSeq offers a greatly simplified and cost-effective protocol with high repeatable strand specificity RNA-seq results for a diversity of RNA input materials from prokaryote to eucaryote RNA-seq libraries.

sample_organism:
Mycolicibacterium smegmatis
Homo sapiens
Mus musculus

overall_design: To develop an easy and versatile RNA-seq method available in RNA library

first: Zaiqiao

last: Sun

first: Boxiao

last: He


title: BTLA NTN scRNAseq

status: Public on Jul 22 2023

city: Cologne

first: Ali

last: Abdallah

address: Joseph Stelzmann Str. 26

department: Medical Faculty

institute: University of Cologne

summary: Goal is to investigate the molecular changes in renal leukocytes during nephrotoxic nephritis in BTLA-KO mice compared to wild-type mice

overall_design: 2 vs 2 biological replicates: 2 BTLA-KO samples vs 2 wild type control samples

first: Paul

last: Diefenhardt

last: Braumann

first: Thomas

last: Schömig

first: Bastian

last: Trinsch

first: Claudio

last: Sierra-Gonzalez

first: Janine

last: Becker-Gotot

first: Linus

middle: A

last: Völker

first: Daniel

last: Hawiger

first: Bernhard

last: Schermer

first: Heike

last: Göbel

last: Brinkkötter

first: Christian

last: Kurts

last: Benzing

first: Sebastian

last: Brähler


title: Bienertia sinuspersici transcriptome on leaf tissue development of young, intermediate, and mature stages

city: Pohang

first: Sang-Yun

last: Han

state: Gyeongbuk

address: 77 Cheongam-Ro, Nam-Gu

department: Department of Life Sciences

institute: Pohang University of Science and Technology

summary: In order to understand the mechanism of single-cell C4 photosynthesis, we extracted total RNA from leaf tissues at young, intermediate, and mature stages. We then conducted gene expression profiling using RNA-seq and de novo transcriptome assembly. The gene expression data was normalized using Transcript Per Million, which was additionally adjusted by the Trimmed Mean of the M values (TPMTMM).

overall_design:
Transcriptome sequencing for understanding mechanism of single-cell C4 photosynthesis, based on leaf tissue development of young, intermediate, and mature stages.
Transcriptome assembly deposited to TSA under accession GKHT00000000

first: Woe-Yeon

last: Kim

first: Jung Sun

first: Inhwan

last: Hwang


title: Circulating MicroRNAs as Biomarkers of Metabolic Syndrome

city: Xi'an

first: Guanzhi

last: Liu

state: China

address: No.157 Xiwu road Xi'an Shanxi

institute: Bone and Joint Surgery Center, Second Affiliated Hospital of Xi’an Jiaotong University

summary: Metabolic syndrome is a common and complicated metabolic disorder and defined as a clustering of metabolic risk factors such as insulin resistance or diabetes, obesity, hypertension, and hyperlipidemia. The identification of accurate and effective biomarkers is beneficial to the early diagnosis and treatment of metabolic syndrome. Our study firstly detected the plasma miRNA expression profile of MetS patients compared with control group by high-throughput sequencing and integrated bioinformatics approaches. To our best knowledge, our study firstly perform high-throughput sequencing to obtain the circulating microRNA expression data in MetS plasma, and identified several potential plasma biomarkers for MetS.

overall_design: Total RNA from plasma samples were extracted using TRIzol LS Reagent (Invitrogen) according to the manufacturer’s instructions. Then, sequencing libraries were generated by NEBNext Multiplex Small RNA Library Prep Set for Illumina (NEB) following the standardized protocols. Agilent Bioanalyzer 2100 system (Agilent) was used to qualified the sequencing libraries. Finally, the high-throughput next-generation sequencing was carried out using TruSeq Rapid SR Cluster Kit (Illumina) based on the Illumina NextSeq 500 sequencing platform (Illumina).

first: Chen

last: Chen

first: Pei

last: Yang

first: Xin

last: Huang


title: Genome-wide analysis of enhancers repressed by Nkx2.2 in spinal motor neuron progenitors

city: Aurora

first: Elena

last: Abarinov

state: Colorado

address: 1775 Aurora Ct

institute: University of Colorado at Denver

summary: Unambiguous consolidation of cell identity relies on transcription factors (TFs) acting to suppress alternative lineages, yet few general principles have emerged explaining how repressors manipulate chromatin landscapes to achieve stable gene silencing, especially in instances when these TFs are only temporarily activated. The TF Nkx2.2 is transiently expressed in CNS progenitors yet permanently abrogates somatic motor neuron (sMN) differentiation via interactions with Groucho (Grg) co-repressors. We show that Nkx2.2 inhibits regulatory elements of progenitor and postmitotic sMN transcripts by utilizing Grg to evict co-activators. Surprisingly, co-activator eviction was accomplished using Grg proteins already present at enhancers, rather than through the additional recruitment of Grg or other co-repressors. Nkx2.2-mediated enhancer silencing also led to the loss of H3K27ac modifications from H3K27me3+H3K27ac+ proximal promoters of key sMN genes, facilitating persistent repression of the sMN progenitor program after Nkx2.2 downregulation. These results imply that active loci are poised for suppression, and repressor binding mediates the transition through co-activator displacement.

overall_design: Examination of ChIP-seq profiles of 2 transcription factors (TFs), 3 histone modifications, 4 TF cofactors, and total RNA profiles during the differentiation of mouse ES cell-derived spinal motor neuron progenitors expressing a wildtype copy of Nkx2.2 tagged by FLAG under the control of a doxycycline (DOX) inducible promotor (iNkx2.2), a TN-domain mutant copy of Nkx2.2 tagged by FLAG under the control of a doxycycline (DOX) inducible promotor (iTNmut), or no Nkx2.2 (pMN). Replicates are provided for all ChIP-seq samples except Sox2, Med1, and H3K27me3; an input sample is also provided. RNA samples are provided in triplicates.

middle: V

first: Michael

last: Closser

first: Yuchun

last: Guo

first: Xiaoyun

first: Mary

last: Chalkey

first: David

last: Gifford

first: Esteban

last: Mazzoni

first: Lori

last: Sussel

first: Hynek

last: Wichterle


title: DNA Methyltransferase M.PaeTBCFI in a chronically adapted Pseudomonas aeruginosa strain

city: Shenzhen

first: Yang

state: Guangdong

address: Liuxian

institute: Sustech Hospital

summary: Pseudomonas aeruginosa is an opportunistic pathogen which causes acute and chronic infections that are difficult to treat. Comparative genomic analysis has showed a great genome diversity among P. aeruginosa clinical strains and revealed important regulatory traits during chronic adaptation. While current investigation of epigenetics of P. aeruginosa is still lacking, understanding the epigenetic regulation may provide biomarkers for diagnosis and reveal important regulatory mechanisms. The present study focused on characterization of DNA methyltransferases (MTases) in a chronically adapted P. aeruginosa clinical strain TBCF10839. Single-molecule real-time sequencing (SMRT-seq) was used to characterize the methylome of TBCF. RCCANNNNNNNTGAR and TRGANNNNNNTGC were identified as target motifs of DNA MTases, M.PaeTBCFI and M.PaeTBCFII, respectively.

overall_design: P. aeruginosa TBCF were grown in Luria-Bertani (LB) liquid media at 37°C with constant shaking at 220 rpm with aeration. The in-frame deletion mutagenesis of methyltransferase ap was performed through two-step allelic exchange. P. aeruginosa TBCF and mutants were cultured to mid log phase. Total RNA extraction and purification was performed for 3 biological replicates of each strain using RNeasy Mini Kit (QIAGEN) and RNase-Free DNase Set (QIAGEN) according to the manufacturer's protocol. 1ug of total RNA was used for the construction of sequencing libraries. RNA sequencing was performed on Illumina NovaSeq 6000 sequencing platform generating 150 bp paired-end reads. Raw reads of the samples were preprocessed and analyzed using RSEM v1.3.1 with unique mapping setting (--bowtie-m), using P. aeruginosa TBCF genome as reference.

first: Shuhong

first: Jihong


title: Inhibition of DNMT1 methyltransferase activity via glucose-regulated O-GlcNAcylation alters the epigenome

city: Duarte

first: Heon

last: Shin

address: 1500 E Duarte Rd, Gonda, 2132B

institute: City of Hope

summary: Profiling of DNA methylation

overall_design: Comparative DNA methylation profiling analysis of Oxford nanopore PromethION data for 5mM  or 25mM glucose treated Hep3B cells and its mutants (myc-DNMT1-WT, myc-DNMT1-S878A).

first: H

first: A

last: Leung

first: K

middle: R

last: Costello

first: P

last: Senapati

last: Kato

first: R

last: Moore

first: M

last: Lee

first: D

last: Lin

first: X

last: Tang

last: Pirrotte

first: Z

middle: B

last: Schones


title: Large scale transcriptome analysis was used to identify the genes most related to the transcription of cellulase genes and/or xylanase genes expression

city: zhengzhou

first: Li

last: Xudong

state: Henan

address: No. 1, Jianshe East Road, Erqi District

institute: The First Affiliated Hospital of Zhengzhou University

summary: Based on the transcriptome data of deletion mutants of different genes and different culture conditions of Penicillium oxalicum, the correlation of gene transcription levels in the whole genome was calculated to explore the genes most related to the transcription of cellulase gene and/or xylanase gene in Penicillium oxalicum, including transcription factors, sugar transporters and other functional genes.

overall_design: Both cellulase and xylanase are enzymes synthesized in the presence of inducers. Therefore, we believe that the transcription level of genes related to the transcription of cellulase and xylanase genes will certainly change under different culture conditions and the deletion mutants of transcription factors which have an important impact on the production of cellulase and xylanase. Consequently, it is possible to find the most relevant genes for cellulase and xylanase gene expression through correlation analysis of gene transcription levels on important transcription factor deletion mutants and a large amount of transcriptome data under different culture conditions.

first: Shuai

last: Zhao

last: Chengxi


title: FOSL1 transcriptome in cholangiocarcinoma (CCA) cells

city: Pamplona

first: Silvestre

last: Vicent

state: Outside the US or Canada

address: 55 PIO XII Ave

country: Spain

institute: Center for Applied Medical Research (CIMA)

summary: A cholangiocarcinoma cell line was used to inhibit FOSL1 and study dowsntream effectors in vitro

overall_design: EGI-1 cells expressing a TET-inducible control shRNA (GFPsh) or shRNAs against FOSL1 were treatd with doxycycline for 4 days and seeded for 24 h to harvest RNA for RNA-seq analysis.

first: Silve

first: Adrian

last: Vallejo


title: FOSL1 target genes in cholangiocarcinoma (CCA) cells

summary: We report the characterization of FOSL1-bound transcriptional targets in CCA cells. Target genes include different RNA species involving protein coding genes, lncRNA, miRNA and others

overall_design: Examination of FOSL1-bound regions in CCA cells overexpressing a Flag-tagged FOSL1 overexpressing lentivector


title: Identification of FOSL1 targets in cholangiocarcinoma

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

overall_design: Refer to individual Series


title: Single-Cell Map of Diverse Immune Phenotypes in Liver Microenvironment

city: Guangzhou

first: Yifang

last: Gao

address: NO.58 zhongshan 2nd road, YueXiu district

institute: sun yat-sen University

summary: As hepatocellular carcinoma (HCC) is the most common type of liver cancer, ranks the sixth leading cause of cancer-related death worldwide (Bray, F., et al. 2018, CA Cancer J Clin 68: 394-424), it is imminent to uncover the regulatory mechanism of immune cells in the liver microenvironment. Here, we perform deep single-cell RNA sequencing on immune cells isolated from tumors of hepatocellular carcinoma patients and healthy liver from donors.

overall_design: Liver perfusates from HCC patients and healthy donors.


title: RNA sequencing profile of cord blood endothelial progenitor cells

status: Public on Jul 21 2023

city: Parkville

first: Boris

last: Novakovic

state: Victoria

address: Murdoch Children's Research Institute, Royal Children's Hospital, Flemington Road

country: Australia

institute: Murdoch Children's Research Institute

summary: Endothelial colony forming cells (ECFC) are circulating endothelial progenitors that are recruited to sustain endothelial function, vascular growth and repair. They are particularly abundant in the perinatal period and can be isolated from umbilical cord blood, thus representing neonatal ECFC. In this study, we profiled neonatal ECFC depending on maternal metabolic derangements to investigate intrauterine epigenetic programming.

overall_design: ECFC were isolated from umbilcal cord blood after pregnancies of lean, overweight and GDM (gestational diabetes mellitus) developing mothers with male and female neonates each.

first: Elisa

last: Weiss

first: Richard

last: Saffery

first: Ursula

last: Hiden


title: Global Epigenome and Transcriptome Maps of Human Trophoblast Cell Lineage Development [Hi-C]

city: Kansas City

first: Boryana

last: Koseva

state: MO

address: 2420 Pershing Road

department: CMRI

institute: Children's Mercy Hospital

summary: The extravillous trophoblast (EVT) cell lineage is a key feature of placentation and critical for spiralartery remodeling and successful pregnancy. Our knowledge of transcriptional regulation driving EVT cell development is limited. Here, we mapped the transcriptome and epigenome landscape as well as chromatin interactions of human trophoblast stem (TS) cells and their transition into the differentiated EVT cell lineage. We identified that chromatin accessibility in intergenic regions was more extensive in EVT cells than in TS cells in the stem state, which is indicative of increased enhancer-driven gene regulation. Using reference epigenome annotation, we noted that 18% of the chromatin landscape in EVT cells was uncharted. We linked regulatory regions to their cognate target genes and characterized the three-dimensional organization of the TS cell functional genome by Hi-C. Integrational analysis of chromatin accessibility, long-range chromatin interactions, transcriptomic, and transcription factor binding motif enrichment enabled identification of transcription factors and regulatory mechanisms associated with EVT cell lineage development. Subsequent analyses elucidated functional roles forTFAP2C,EPAS1,SNAI1, andDLX6in the regulation of EVT cell lineage development.EPAS1was identified as an upstream regulator of EVT cell transcription factors, includingSNAI1andDLX6, and was found to be upregulated in idiopathic recurrent pregnancy loss. Collectively, we have revealed activation of a dynamic regulatory network that provides a framework for understanding EVT cell specification in trophoblast cell lineage development and human placentation.

overall_design: Hi-C on stem state and extravillous trophoblast cells from cell line CT27 and CT29

first: Kaela

last: Varberg

first: Esteban

last: Dominguez

middle: S

first: Ayelen

last: Moreno-Irusta

first: Ross

last: McNally

first: Emily

last: Wesley

first: Khursheed

last: Iqbal

first: Warren

last: Cheung

first: Hiroaki

last: Okae

first: Takahiro

last: Arima

first: Courtney

last: Marsh

first: Michael

last: Soares

first: Elin

last: Grundberg


title: Human pluripotent stem cell-derived astrocyte model in fragile X syndrome

city: Helsinki

first: Juho

middle: Eemil

last: Pitkonen

address: Haartmaninkatu 8

department: Physiology

country: Finland

institute: University of Helsinki

summary: The experiment was made to compare gene expression of human control (H1) ES-derived astrocytes and isogenic astrocytes carrying a mutation causing fragile x syndrome.

overall_design: Gene expression profiling was performed using data obtained from RNA-seq of triplicate samples at 5 time points (Day 0 (D0), D12, D30, D60 and D95) during forebrain astrocyte differentation.

first: Ulla-Kaisa

last: Peteri

first: Pia

last: Laine

first: Mahmoud

last: Pouladi

first: Maija

middle: L

last: Castren


title: Macrophage-derived insulin antagonist ImpL2 induces lipoprotein mobilization upon bacterial infection

city: České Budějovice

first: Adam

last: Bajgar

state: CZ

address: Branisovska 1645/31a

department: Molecular biology and Genetics

country: Czech Republic

institute: University of South Bohemia

summary: The immune response is an energy-demanding process that must be coordinated with systemic metabolic changes redirecting nutrients from stores to the immune system. Although this interplay is fundamental for the function of the immune system, the underlying mechanisms remain elusive.   Our data show that the pro-inflammatory polarization of Drosophila macrophages is coupled to the production of the insulin antagonist ImpL2 through the activity of the transcription factor HIF1α. ImpL2 production, reflecting nutritional demands of activated macrophages, subsequently impairs insulin signaling in the fat body, thereby triggering FOXO-driven mobilization of lipoproteins. This metabolic adaptation is fundamental for the function of the immune system and an individual’s resistance to infection. We demonstrated that analogically to Drosophila, mammalian immune-activated macrophages produce ImpL2 homolog IGFBP7 in a HIF1α-dependent manner and that enhanced IGFBP7 production by these cells induces mobilization of lipoproteins from hepatocytes. Hence, the production of ImpL2/IGFBP7 by macrophages represents an evolutionarily conserved mechanism by which macrophages alleviate insulin signaling in the central metabolic organ to secure nutrients necessary for their function upon bacterial infection.

overall_design: We isolated plasmatocytes from 10days old males of Drosophila melanogaster by cell sorter, based on Crq>GFP signal. Plasmatocztes were isolated either from invdividuals infected bz injection of  thousands of Streptococcus pneumoniae or injected with 50nl of PBS.

last: Bajgarr

first: Gabriela

last: Krejcova


title: Longitudinal DNA methylation in serially passaged primary and modified human astrocytes

city: San Diego

first: Morgan

middle: E.

last: Levine

address: 5510 Morehouse Dr

institute: Altos Labs

type: Methylation profiling by genome tiling array

summary: This DNA methylation dataset describes epigenomic changes in in vitro serially passaged primary and immortalized astrocytes, in the context of studies examining cellular aging patterns that are conserved in vivo and in vitro. Primary and fetal hTERT-immortalized astrocytes were grown under normoxic conditions and serially passaged. Longitudinal DNA samples were collected throughout passaging and DNA methylation was measured using the Infinium HumanMethylation850 BeadChip.

overall_design: Primary and fetal hTERT-immortalized astrocytes were cultured and exhaustively passaged in triplicate, both derived from sinlge donors. DNA extraction of primary astrocytes (Creative Biolabs, male) ranged from passage 2 to 10 and fetal hTERT-immortalized astrocytes (Applied Biological Materials, unknown gender) from 12 to 27 (total n= 25 and 45 respectively). Bisulphite converted DNA from samples were hybridised to the Illumina Infinium HumanMethylationEPIC BeadChip.

first: Christopher

last: Minteer

first: Kyra

last: Thrush

first: Peter

last: Niimi

first: Joel

last: Rozowsky

first: Jason

last: Liu

first: Mor

last: Frank

first: Thomas

last: McCabe

first: John

last: Gonzalez

first: Erin

last: Hofstatter

first: Mariya

last: Rozenblit

first: Lajos

last: Pusztai

first: Kenneth

last: Beckman

first: Mark

last: Gerstein

first: Albert

last: Higgins-Chen

middle: E


title: Comparing transcriptional profiles of skin biopsies from healthy controls and subjects with chronic pruritus of unknown origin and atopic dermatitis

city: St. Louis

first: Aaron

last: Ver Heul

address: 660 S Euclid Ave.

department: Medicine

institute: Washington University School of Medicine

summary: Type 2 inflammation contributes to the pathology of pruritic skin diseases such as atopic dermatitis (AD). Chronic pruritus of unknown origin (CPUO) is a skin condition of unknown etiology that typically has minimal inflammation. Yet, some patients with CPUO display signs of mildly increased type 2 inflammation. This study aims to compare skin transcriptional profiles in CPUO to healthy skin and to skin from AD, a classical type 2 inflammatory condition.

overall_design: To directly compare the transcriptional profiles of healthy skin to skin from subjects with CPUO or AD, we processed skin biopsies from subjects for RNA isolation and performed RNA-sequencing.

first: Landon

last: Oetjen

first: Brian

last: Kim


title: RNA profiling of MPNST xenografts treated with anti-endoglin (ENG) therapies

city: Madrid

first: Osvaldo

last: Graña

state: Comunidad de Madrid

address: C/ Melchor Fernández Almagro, 3

department: Structural Biology

institute: CNIO

summary: In order to analyze the genes and molecular pathways modulated by ENG targeting in MPNST, we performed RNA-seq on STS26T xenografts treated with TRC105/M1043 and compared their expression profiles with those of IgG-treated control tumors.

overall_design: 1x10^6 STS26T cells were subcutaneously injected into athymic nude mice and tumors were allowed to develop for one week until they were palpable (~100 mm3 average). Then, mice were treated with either the combination of anti-human and anti-mouse monoclonal antibodies (TRC105 and M1043, respectively) or the corresponding IgG control. After three weeks of treatment, mice were sacrificed and tumors were dissected. RNA was extracted with trizol and subsequent Qiagen columns. RNA sequencing was performed afterwards.

first: Teresa

last: Graña-Castro

first: Hector

last: Peinado


title: Insulin-like growth factor receptor / mTOR signaling elevates global translation to accelerate zebrafish fin regenerative outgrowth

city: Eugene

first: Victor

last: Lewis

state: Oregon

address: 1255 Mill St

department: Institute of Molecular Biology

institute: University of Oregon

summary: We generate a single cell transcriptome dataset to characterize zebrafish fin regenerative outgrowth and explore coordinated cell behaviors.

overall_design: Regenerated fin tissue was collected from 3 and 7 days post amputation zebrafish caudal fins and analyzed using scRNA-seq

first: Heather

last: Le Bleu

first: Scott

last: Stewart

first: Kryn

last: Stankunas


title: Analysis of ENG-modulated gene expression profiles in MPNST cells

summary: In order to study the gene expression changes related to ENG silencing in MPNST cells, we performed RNA-seq gene expression profiling after knockdown of ENG in STS26T cells compared to shScramble control.

overall_design: MPNST cells were transduced with lentiviral particles encoding shRNA designed to silence human ENG (shENG) or a non-targeting control scrambled sequence (shScramble). RNA was extracted with trizol and subsequent Qiagen columns. RNA sequencing was performed afterwards.


title: Activity-dependent cholesterol biosynthesis in human-derived astrocytes regulates the functional maturation of human-derived cortical neurons

city: Cardiff

first: Jimena

last: Monzón-Sandoval

address: Maindy Road

country: United Kingdom

institute: UK Dementia Research Institute at Cardiff University

summary: Astrocytes regulate the functional maturation of neurons by providing trophic support, regulating membrane properties and coordinating synapse formation. However, it is unclear to what degree astrocytes use activity-dependent mechanisms in these intercellular signalling processes. Using an induced pluripotent stem cell system and long-term optogenetic stimulation of human astrocytes, we reveal that activity-dependent astrocytic signals enhance the functional maturation of human cortical neurons, through increases in synaptic connectivity and excitability. Transcriptomic analyses determine that this involves the activity-dependent up-regulation of cholesterol synthesis – a process ascribed to astrocytes, which regulates neuronal maturation. Up-regulated astrocyte genes encode enzymes and transcription factors that control the levels of cholesterol synthesis. Biochemical assays confirm an activity-dependent upregulation of cholesterol synthesis in astrocytes, which is required for the maturational effects upon neurons. Thus, we reveal a novel mechanism that may dynamically match astrocyte function to neuronal needs, and identify targets for modulating cholesterol synthesis in the CNS.

overall_design: 22 samples of human induced pluripotent stem cell (iPSC) derived astrocytes and neurons. Each sample corresponds to the co-culture of iPSC-astrocytes and iPSC-neurons from the same donor. A total of 3 different donors/lines were used. There were two main experimental conditions, iPSC-astrocytes were transduced with either YFP alone (the ‘YFP control’ condition) or with Channelrhodopsin-2, (ChR2-YFP condition), so that blue light could be used to selectively modulate astrocytes.

first: Anne

last: Hedegaard

first: Lori

last: Dershowitz

first: Emma

last: Whiteley

first: Sarah

last: Newey

first: Caleb

last: Webber

first: Colin

last: Akerman


title: Gene expression in pancreatic islets

city: Kobe

first: Akari

last: Inada

state: Hyogo

address: 6‑3‑7 Minatojima　Minamimachi

department: Institute of Biomedical Research and Innovation (IBRI)

country: Japan

institute: Foundation for Biomedical Research and Innovation at Kobe (FBRI)

summary: To examine gene expression in pancreatic islet in vivo exposed to E2,  we have employed whole genome microarray hene expression profiling.

overall_design: The changes in gene expression in 24-week-old mouse islets was measured. Four groups of mouse islets were compared.

first: Oogi


title: RNA Polymerase II pausing temporally coordinates cell cycle progression and erythroid differentiation [CRISPR]

city: Boston

first: Danya

last: Martell-Smart

state: MA

address: 77 Avenue Louis Pasteur

institute: Harvard Medical School

summary: The controlled release of promoter-proximal RNA polymerase II (Pol II) pausing into productive elongation is a major step in gene regulation. Yet, functionally analyzing Pol II pausing is difficult because the factors that regulate pause release are generally essential. Here, we identified  heterozygous loss-of-function mutations in SUPT5H, encoding SPT5, in individuals with β-thalassemia trait unlinked to the β-globin locus. Recapitulating the pathogenic mutations in human erythroid cells or acute treatment with transcription inhibitors replicates the patient phenotype of altered globin gene expression. Furthermore, in SUPT5H-edited cells, Pol II pause release was globally disrupted. We observed dynamic patterns of pausing at cell cycle and erythroid differentiation genes at the transition from progenitors to precursors during erythropoiesis. At this same transition, in SUPT5H-edited cells, we observed delayed differentiation and altered cell cycle kinetics, as well as a delay in the onset of gene expression programs. Therefore, hindering pause release perturbs cell cycle and delays differentiation at key stages of erythropoiesis, revealing a role for Pol II pausing in the temporal coordination between the cell cycle and differentiation.

overall_design: SUPT5H editing of hematopoietic stem and progenitor cells (HSPCs) to recapitualte los-of-function patient mutations and follow imapct on globins and erythropooesis using NET-seq, RNA-seq, Nanostring, and FACS

last: Martell

first: Hope

last: Merens

first: Claudia

last: Fiorini

first: Alexis

last: Caulier

first: Jacob

last: Ulirsch

first: Christian

last: Babbs

first: Giovanna

last: Graziadei

first: Valentina

last: Brancaleoni

first: Maria

last: Cappellini

first: Douglas

last: Higgs

first: Vijay

middle: G

last: Sankaran

first: L

last: Churchman


title: The  RNA-seq of U14 cells and U14-OEFOXP1

first: sheng

last: zhong

address: The Xinhu Road 1333

institute: The Sourthern Medical University

summary: To investigate the different gens expression  under the overexpression FOXP1 of U14 cells

overall_design: We then performed gene expression profiling analysis using data obtained from RNA-seq of 2 different cell line.

first: Xia

last: Guo

first: Xiaona

last: Chen


title: RNA Polymerase II pausing temporally coordinates cell cycle progression and erythroid differentiation [RNA-seq]


title: Zinc accumulation in Atriplex lentiformis is driven by plant genes and the soil microbiome

city: Tucson

first: Priyanka

last: Kushwaha

state: Arizona

department: Environmental Science

institute: University of Arizona

summary:
To investigate the effect of different levels of compost treatment on root gene expression of Atriplex lentiformis, we set up a greenhouse experiment with three treatments of 10% (TC10), 15 (TC15), and 20% (TC20) compost amended, metalliferrous mine tailings. Plants were harvested at ~11 weeks and root samples were flash frozen in liquid nitrogen for RNA-seq analysis.
We then performed gene expression profiling analysis using data obtained from RNA-seq of 9 root samples from 3 different treatments.

overall_design: Gene expression changes across the root samples from the three treatments were estimated using the likelihood ratio test (LRT) in the DESeq2 analysis.

first: Alexandria

last: Tran

first: Diego

last: Quintero

first: Miranda

last: Song

first: Qi

last: Yu

first: Ruth

first: Michael

last: Downes

first: Ronald

middle: M

last: Evans

first: Alicja

last: Babst- Kostecka

first: Julian

middle: I

last: Schroeder

first: Raina

last: Maier


title: RNA Polymerase II pausing temporally coordinates cell cycle progression and erythroid differentiation

first: Danya

middle: J

last: Martell-Smart


title: The two enantiomers of 2-hydroxyglutarate differentially regulate cytotoxic T cell function

city: Amsterdam

first: Monika

middle: C

last: Wolkers

address: Plesmanlaan 125

department: Hematopoiesis

country: Netherlands

institute: Sanquin Blood foundation

summary: 2-hydroxyglutarate (2HG) is a by-product of the TCA cycle, and is readily detected in the tissues of healthy individuals. 2HG is found in two enantiomeric forms: S-2HG and R-2HG. Here, we investigate the differential roles of these two enantiomers in CD8+ T cell biology, where we found they had highly divergent effects on proliferation, differentiation, and T cell function. We show here an analysis of structural determinants that likely underlie these differential effects on specific a-ketoglutarate (aKG)-dependent enzymes. Treatment of CD8+ T cells with exogenous S-2HG, but not R-2HG, increased CD8+ T cell fitness in vivo, and enhanced anti-tumour activity. These data show that S-2HG and R-2HG should be considered as two distinct and important actors in the regulation of T cell function.

overall_design: Comparative gene expression of CD8+ T cells treated with S- or R-2HG. All samples are in (biological) triplicates. Controls are H2O/vehicle.

first: Iosifina

middle: P

last: Foskolou

first: Pedro

last: Cunha

first: Eleanor

last: Minogue

first: Benoit

last: Nicolet

first: Aurelie

last: Guislain

first: Christian

last: Jorgensen

first: Nordin

middle: D

last: Zandhuis

first: Laura

last: Barbieri

first: David

last: Bargiela

first: Demitris

last: Nathanael

first: Petros

last: Tyrakis

first: Asis

last: Palazon

first: Randall

last: Johnson


title: The impact of small molecule inhibition of METTL3 on normal haematopoiesis

status: Public on Jul 20 2023

city: Cambridge

first: Bertie

last: Gottgens

address: Jeffrey Cheah Biomedical Centre

institute: University of Cambridge

summary: We performed scRNA-seq on haematoietic stem and progenitor cells of healthy wild-type mice treated with the small-molecule inhibitor of METTL3, STM2457.

overall_design: Bone marrow cells were collected from 4 vehicle-treated and 3 STM2457-treated mice and lineage-negative, cKIT positive Haematopoietic stem and progenitor cells were isolated by fluorescence activated cell sorting.  Cells were processed for scRNA-seq using Chromium Single Cell 3ʹ GEM, Library & Gel Bead Kit v3 reagents and sequenced on the Illumina Novaseq 6000 platform.

first: Katherine

last: Sturgess

first: Eliza

last: Yankova

first: MS

last: Vijayabaskar

first: Tomoya

last: Isobe

first: Justyna

last: Rak

first: Iwo

last: Kucinski

first: Melania

last: Barile

first: Natalie

last: Webster

first: Maria

last: Eleftheriou

first: Rebecca

last: Hannah

first: Malgorzata

last: Gozdecka

first: George

last: Vassiliou

first: Oliver

last: Rausch

first: Nicola

last: Wilson

first: Berthold

first: Konstantinos

last: Tzelepis


title: single-nucleus RNA-seq of healthy (sham) and heart diseased (TAC) SCGs

city: Munich

first: Karin

middle: A.

last: Ziegler

address: Biedersteiner Str. 29

institute: Technical University of Munich

summary: Disruption of the physiologic sleep-wake cycle and low melatonin levels frequently accompany cardiac disease, yet the underlying mechanism has remained enigmatic. Immunostaining of sympathetic axons in optically cleared pineal glands from humans and mice with cardiac disease revealed their substantial denervation compared to controls. Spatial, single-cell, nuclear, and bulk RNA sequencing traced this defect back to the superior cervical ganglia (SCG), which responded to cardiac disease with accumulation of inflammatory macrophages, fibrosis, and the selective loss of pineal gland-innervating neurons. Depletion of macrophages in the SCG prevented disease-associated denervation of the pineal gland and restored physiological melatonin secretion. Our data identify the mechanism underlying the disturbance of diurnal rhythmicity in cardiac disease and suggest means for therapeutic intervention.

overall_design: SCGs from heart healthy and heart diseased mice were subjected to single-nucleus RNA-seq (10x Genomics).

first: Stefan

last: Engelhardt


title: Generation of advanced cerebellar organoids for neurogenesis and neuronal network development

city: Cleveland

first: Ya

last: Chen

address: 2109 Adelbert Road, Room 747A

department: Genetics and Genome Sciences

institute: Case Western Reserve University

summary: Neurons within the cerebellum form temporal-spatial connections through the cerebellum, and the entire brain. Organoid models provide an opportunity to model the early differentiation of the developing human cerebellum, which is difficult to study in vivo, and affords the opportunity to study neurodegenerative and neurodevelopmental diseases of the cerebellum. Previous cerebellar organoid models focused on early neuron generation and single cell activity. Here, we modify previous protocols to generate more mature cerebellar organoids that allow for the establishment of several classes of mature neurons during cerebellar differentiation and development, including the establishment of neural networks during whole organoid maturation. This will provide a means to study the generation of several more mature cerebellar cell types, including Purkinje cells, granule cells, interneurons expression as well as neuronal communication for biomedical, clinical, and pharmaceutical application.

overall_design: To gain further insight into the onset of cerebellar cells differentiation and development, scRNA-seq was performed on Chap organoids and the other control line organoids using the Drop-seq method

first: Fu

first: Kimberly

middle: A

last: Aldinger

first: Anthony

last: Wynshaw-Boris


title: DNA Methylome and 3D Chromatin Landscape of Cell Types Across the Mouse Brain [9L]

city: La Jolla

first: Joseph

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

institute: HHMI-Salk-Institute

summary: Illustrating the cellular architecture of the mammalian brain is critical to understanding its diverse functions and complex animal behaviors. With support from NIMH and NINDS as part of the BRAIN Initiative Cell Census Network (BICCN), the Center for Epigenomics of the Mouse Brain Atlas (CEMBA) applied single nucleus methylation sequencing in 117 brain funtional regions across the whole adult male P56 C57BL/6J mouse brain. In each major brain regions, we identified distinct cell clusters and formed them in a hierarchical taxonomy. These clusters include known primary brain cell types and possible sub-types. We use these data to identify the epigenomic characteristics and to define specific regulatory elements for each cell cluster. We integrate the single cell methylome with single cell gene expression and chromatin accessibility profiles from the same brain region to further identify potential enhancers and their corresponding genes for several neuronal cell types. By brain region spacial comparisons, we found spatial specificity among excitatory neuronal clusters within the same cortical layer. We identify brain-region-specific transcription factors that may regulate cortical region development of excitatory neurons. These data define the landscape of cell type and spatial heterogeneity in the mouse brain and the underlining regulatory epigenomic basis.

overall_design: Apply snmC-seq2 to 117 brain functional regions to identify epigenomic landcape of the adult mouse brain, this subseries consists of one single nucleus methylation sequencing experiment of brain region (9L_200305, 9L_200520).

first: Hanqing

last: Liu

first: Anna

last: Bartlett

first: Jacinta

last: Lucero

first: Julia

middle: K

last: Osteen

first: Jordan

last: Altshul

first: Mia

last: Kenworthy

first: Rosa

last: Castanon

last: Nery

first: Peter

last: Berube

first: Huaming

first: Michael

last: Nunn

first: Jesse

last: Dixon

first: M

last: Behrens


title: Transcriptome profiling of differentially expressed genes during the development of male flowers in watermelon

city: Zhengzhou

first: Gaopeng

last: Yuan

address: Weilai Road Nanduan

institute: CAAS

summary: Watermelon (Citrullus lanatus (Thunb.) Matsum. & Nakai) is an important cucurbit crop grown worldwide. Watermelon fruit quality, fertility, and the seed setting rate are closely related to male flower development. In this study, the different developmental stages of flower buds of the watermelon variety Xinteda Zhengkang 9 were distinguished by cytological observation, and transcriptome sequencing analysis was performed subsequently. Acetocarmine staining of anthers was performed and the longitudinal and transverse diameters of the unopened male flower buds were measured. Cytological observations of anthers at different developmental stages showed that the anther grew from the tetrad to the mature stage, and the longitudinal and transverse diameters of the flower buds increased. The length of the male flower buds also changed significantly during development. Transcriptome sequencing analysis at four periods, the tetrad (A group), mononuclear (B group), dikaryophase (C group), and mature stages (D group). Total 16288 differentially expressed genes (DEGs) were detected in the four stages, with the prolongation of developmental stages the number of DEGs increased gradually in the comparison groups, such as there was 2014, 3259, 4628, 1490, 3495 and 1132 DEGs were revealed in six comparison groups (A-VS-B, A-VS-C, A-VS-D, B-VS-C, B-VS-D, and C-VS-D), respectively. Gene ontology (GO) and KEGG enrichment analysis showed that the DEGs were mainly enriched in cellular component and starch and sucrose metabolism, phenylpropanoid biosynthesis and pentose sugar, etc. Finally, we totally screened 59 DEGs were in the six comparison groups, and most of them were up-regulated, interestingly, we find one pollen-specific protein (Cla001608) was significantly up-regulated (the value of log2Fold Change up to 17.32), which indicating that it may play important role in the development of male flowers. This work provides insight into the molecular basis of the developmental stages of male flowers in watermelon and may aid in dominant cross breeding.

overall_design: mRNA profiles of  anther of different developmental stages(A,B,C and D), in watermelon, using IlluminaHiSeq.

first: Yingchun

last: Zhu

first: Shengfeng

last: Jia

first: Yun

last: Deng

first: Guolin

last: An

first: Weihua

last: Li

first: Dexi

last: Sun

first: Junpu


title: RNA Polymerase II pausing temporally coordinates cell cycle progression and erythroid differentiation [NET-seq]

first: Danya

last: Martell-Smart

last: Martell

first: Hope

last: Merens

first: Claudia

last: Fiorini

first: Alexis

last: Caulier

first: Jacob

last: Ulirsch

first: Christian

last: Babbs

first: Giovanna

last: Graziadei

first: Valentina

last: Brancaleoni

first: Maria

last: Cappellini

first: Douglas

middle: R

last: Higgs

first: Vijay

last: Sankaran

first: L

last: Churchman


title: Protein phosphatase 2A activation promotes heart transplant acceptance in mice

city: Atlanta

first: Qian

last: Xu

state: GA

address: 101 Woodruff Circle

institute: Emory University

summary: Background: While heart transplantation is the standard treatment for heart failure, both acute and chronic transplant rejection frequently occur. Since the modulation of protein phosphatase PP2A activity is critical for tissue and organ homeostasis under physiological and pathophysiological conditions, PP2A may also affect the ability to tolerate transplanted organs. Here we demonstrate that administration of a novel class of small molecule activators of PP2A (SMAPs) prolonged cardiac allograft survival in a mouse heterotopic heart transplantation model. Mechanistically, SMAPs effectively suppressed the inflammatory immune response while increasing Treg population in the allografts, findings corroborated by functional analysis of RNAseq data derived from Tregs of treated splenic tissue. Importantly, SMAPs further prolonged CTLA4-Ig (an immunosuppressive agent utilized in organ transplantation)-induced cardiac rejection tolerance and extended allograft survival. SMAPs also strongly mitigated cardiac allograft vasculopathy as evidenced by a marked reduction of neointimal hyperplasia and smooth muscle cell proliferation. Mechanistic studies implicate SMAPs elicited suppression of MEK/ERK pathways as a unifying mechanism for the aforementioned effects in Tregs and SMCs. These findings highlight the potential of PP2A activation in improving alloengraftment in heart transplantation and add knowledge to the phosphatase driven regulation of the immune system in the context of organ transplantation.

overall_design: Male C57BL/6 (B6, H-2b) and BALB/c (B/c, H-2d) mice aged 12–16 weeks were used in this study. Donor hearts from BALB/c male mice were transplanted onto the inferior vena cava and aorta in the peritoneal cavity of male C57BL/6J mice. Syngeneic heart graft is defined as a donor heart from C57BL/6J male mice transplanted into C57BL/6J male mice. A 5 mg/kg dose of DT-061 was given intragastrically twice a day beginning on the day of transplantation and continued until the completion of experiments. After 7 days, CD3+CD4+CD25+CD127low cells (Tregs) were sorted by flow cytometry from the spleens of vehicle group and the DT-061 treated group and sent for RNA-seq study.

first: Xianming

last: Zhou

first: Nianguo

last: Dong

first: Goutham

last: Narla

first: Zhiyong

last: Lin


title: Switching mechanism from AR to EGFR signaling via 3-O-sulfated heparan sulfate in castration-resistant prostate cancer

city: Hachioji

first: Shoko

last: Nishihara

state: Tokyo

address: 1-236 Tangi-machi

department: Graduate School of Engineering

institute: Soka University

summary: Expression of HS3ST1 is markedly upregulated in castration-resistant prostate cancer, which proliferates hormone-independently. In a novel mechanism, EGFR–ERK1/2 signaling is activated via 3-O-sulfated HS and EGF/HB-EGF binding in castration-resistant prostate cancer.

overall_design: RNA-seq to compare the expression of  genes between C4-2 cells cultured  in FBS- and CSS- containing meium

first: Hayato

last: Ota

first: Hirokazu

last: Sato

first: Shuji

last: Mizumoto

first: Ken

last: Wakai

first: Kei

last: Yoneda

first: Kazuo

last: Yamamoto

first: Hayao

last: Nakanishi

first: Jun-Ichiro

last: Ikeda

first: Shinichi

last: Sakamoto

first: Tomohiko

last: Ichikawa

first: Shuhei

last: Yamada

first: Satoru

last: Takahashi

first: Yuzuru

last: Ikehara

last: Nshihara


title: Characterization of EndoC-BH5 a novel human pancreatic beta cell line. Comparative expression profile with EndoC-BH1 and effect of stimulation with Interferon gamma and interleukin 1b.

city: Paris

first: Philippe

last: Ravassard

address: ICM 47 bd de l'hopital

institute: Paris Brain Institute

summary: We have developped a novel human pancreatic beta cell line: EndoC-βH5. EndoC-βH5 cells are ready-to-use and storable cells with physiological insulin secretion. EndoC-βH5 cells were generated by integrative gene transfer of immortalizing transgenes hTERT and SV40 large T along with Herpes Simplex Virus-1 thymidine kinase into human fetal pancreas. Immortalizing transgenes were removed after amplification using CRE activation and remaining non-excized cells eliminated using ganciclovir. Resulting cells were distributed as ready to use EndoC-βH5 cells. We performed comparative transcriptome analysis with  EndoC-βH1 cells , extensive functional and immunological assays. RNA-seq confirmed abundant expression of beta cell transcription factors and functional markers, including incretin receptors.

overall_design: 5 independent batches of EndoC-BH1 and EndoC-BH5 were used to compare the RNA expression profile in both cell lines


title: Characterization of EndoC-BH5 a novel human pancreatic beta cell line. Comparative expression profile after stimulation stimulation with Interferon gamma and interleukin 1b.

summary: Responsiveness of EndoC-BH5 cells to cytokines was examined by RNA-seq of cells treated with IFNγ and IL1β for 24 h. The treatment resulted in profound changes in their transcriptome and upregulation of genes involved in the inflammatory pathwayand antigen processing and presentation, similar to previous studies on EndoC-BH1 cells and adult human islets. EndoC-BH5 cells hence represent a powerful tool to investigate the dialogue between beta cells and the immune system.

overall_design: 3 batches of EndoC-BH5 were treated with interferon gamma and interleukin 1b and compared to 3 batches of EndoC-BH5 treated with vehicle as control and were compared.

first: Arnaud

last: Zaldumbide


title: Characterization of EndoC-BH5 a novel human pancreatic beta cell line

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

overall_design: Refer to individual Series


title: Establishment of bovine trophoblast stem cells [ATAC-seq]

city: Gainesville

first: Zongliang

last: Jiang

state: Florida

address: 2033 Mowry Rd, Cancer & Genetics Research Bldg, Room 303

department: Dept. of Animal Sciences

institute: University of Florida

summary: Here we report that a chemical cocktail (LCDM: hLIF, CHIR99021, DiM and MiH) previously reported for extended potential pluripotent stem cells enables the de novo derivation and long-term culture of bovine trophoblast stem cells (TSCs). Bovine TSCs exhibit transcriptomic and epigenetic features characteristic of trophectoderm cells from bovine embryos and retain developmental potency to differentiate into functional trophoblasts in vitro and in vivo

overall_design: bTSC, D7_TE, D14_TE and differentiated TSC (4 days) were pooled for ATAC sequencing analysis

first: Yinjuan

last: Wang

first: Jie

last: Li


title: Establishment of bovine trophoblast stem cells [WGBS]

overall_design: Whole genome bisulfite sequencing analysis was used to determined genome-scale DNA methylation patterns of bTSC, D7_TE, and D14_TE.

first: Linkai

last: Zhu


title: Culture expansion of CAR T cells evokes aberrant DNA methylation that is associated with adverse clinical outcome (RNA-Seq)

city: Aachen

first: Wolfgang

last: Wagner

address: Pauwelsstrasse 20

department: Helmholtz Institute for Biomedical Engineering

institute: RWTH Aachen University

summary: Cellular immunotherapy using autologous, genetically modified T cells has delivered remarkable initial response rates in various hematological malignancies, including acute lymphoblastic leukemia (ALL) or lymphoma. Upon treatment with these chimeric antigen receptor (CAR) T cells, approximately 30–40% of patients show long-term remission. There is a growing perception that not only CAR constructs, but also in vitro manufacturing processes may determine therapeutic efficacy. However, little is known about how duration of culture expansion affects molecular and functional features of CAR T cells. A better understanding of molecular signatures, reflecting therapeutic activity of CAR T cells, may help to further optimize the manufacturing process. In this study, we therefore investigated DNAm changes during culture expansion of T cells and CAR T cells during a period of up to three weeks. The results of our current study indicate that culture expansion of CAR T cells leads to DNAm changes that are continuously acquired during culture expansion, which is also reflected on gene expression level. Further analysis of culture-associated methylation profiles in CAR T cells from clinical trials support the notion that these chnages are disadvantageous with regards to therapeutic outcome. A shortened cultivation period to avoid dysfunctional methylation programs might be a promising manufacturing strategy to improve therapeutic efficacy of adoptive cell therapies. Our epigenetic signature for culture-associated DNAm may provide a biomarker for quality control of CAR T cell productions and to identify patients at risk for adverse events.

overall_design: Total RNA was isolated from freshly isolated T cells (day 0) of four healthy donors, as well as from CD2/CD3/CD28-microbead activated T cells of the same donors upon three weeks of culture (day 22) in IL-2 supplemented medium, with the NucleoSpin RNA Plus kit (Macherey-Nagel). Library preparation with the QuantSeq 3’ mRNA-Seq Library Prep Kit FWD (Lexogen, Vienna, Austria) and sequencing on the HiSeq 2500v4 platform (Illumina; 10 M 50 bp single-end reads) was performed at Life and Brain GmbH. RNA sequencing (RNA-seq) reads were aligned with the R package QuasR and Rhisat2 as aligner to the human genome (hg19) with default parameters. Reads that aligned with less than 10 reads per gene were excluded from further analysis and counts per million (CPM) were calculated and TMMwsp normalized with standard parameters using the R package edgeR. Count data was voom-transformed by applying the R package limma. For differential expression analysis the limma model was then fitted and t-statistics were computed using the Empirical Bayes method with the adjusted p-value threshold of 0.05.

first: Salz

last: Lucia


title: Culture expansion of CAR T cells evokes aberrant DNA methylation that is associated with adverse clinical outcome (Methylation)

summary: Cellular immunotherapy using autologous, genetically modified T cells has delivered remarkable initial response rates in various hematological malignancies, including acute lymphoblastic leukemia (ALL) or lymphoma. Upon treatment with these chimeric antigen receptor (CAR) T cells, approximately 30–40% of patients show long-term remission. There is a growing perception that not only CAR constructs, but also in vitro manufacturing processes may determine therapeutic efficacy. However, little is known about how duration of culture expansion affects molecular and functional features of CAR T cells. A better understanding of molecular signatures, reflecting therapeutic activity of CAR T cells, may help to further optimize the manufacturing process. In this study, we therefore investigated DNAm changes during culture expansion of T cells and CAR T cells during a period of up to three weeks. The results of our current study indicate that culture expansion of CAR T cells leads to DNAm changes that are continuously acquired during culture expansion. Further analysis of culture-associated methylation profiles in CAR T cells from clinical trials support the notion that these chnages are disadvantageous with regards to therapeutic outcome. A shortened cultivation period to avoid dysfunctional methylation programs might be a promising manufacturing strategy to improve therapeutic efficacy of adoptive cell therapies. Our epigenetic signature for culture-associated DNAm may provide a biomarker for quality control of CAR T cell productions and to identify patients at risk for adverse events.

overall_design: Bisulphite converted DNA from the 32 CAR T and T cell samples from distinct culture conditions that were harvested during distinct time points of in vitro expansion were hybridised to the Illumina Infinium Methylation850 BeadChips.

first: Lucia

last: Salz

first: Alexander

last: Seitz

first: Daniel

last: Schäfer


title: Culture expansion of CAR T cells evokes aberrant DNA methylation that is associated with adverse clinical outcome


title: Epigenome analysis of placenta/cord blood/saliva samples

city: Brussels

first: Laura

last: Saucedo

address: Laarbeeklaan 103

country: Belgium

institute: Follicle Biology Lab - VUB

summary: Genome wide DNA methylation profiling of placenta/cord blood/saliva samples obtained from babies born by oocyte in vitro maturation (IVM) or in vitro fertilization (IVF). The Illumina Infinium EPIC Human DNA methylation Beadchip v1.2 was used to obtain DNA methylation profiles across approximately 850,000 CpGs. The main goal of this project was to find specific methylation profiles associated to use of IVM.

overall_design: Bisulphite converted DNA from the157 samples were hybridised to the Illumina Infinium EPIC Human Methylation Beadchip

last: Saucedo-Cuevas

first: Johan

last: Smitz

first: Ellen

last: Anckaert

first: Vuong

middle: N

last: Lan


title: Spatially resolved multi-omics single-cell analyses inform mechanisms of immune-dysfunction in pancreatic cancer

city: Tübingen

first: MENGJIE

last: QIU

address: Otfried-Müller-Str. 37

institute: M3 Forschungszentrum für Malignom, Metabolom und Mikrobiom

summary: As pancreatic ductal adenocarcinoma (PDAC) continues to be recalcitrant to therapeutic interventions including poor response to immunotherapy, albeit effective in other solid malignancies, a more nuanced understanding of the immune microenvironment in PDAC is urgently needed. Using a spatially-resolved multimodal single cell approach we unveil a detailed view of the immune micromilieu in PDAC with specific emphasis on the correlation of immune subtypes with patient survival. We substantiate the exhausted phenotype of CD8 T cells and immunosuppressive features of myeloid cells, and highlight immune subpopulations with potentially underappreciated roles in PDAC, particularly CD4 T cell subsets presenting immunosuppressive phenotypes with varying modes of exhaustion. We also demonstrate the dynamic changes associated with transcriptional reprogramming of immune subtypes within adjacent normal tissue and tumor surrounding stroma, and further reveal striking differences between immune phenotypes in PDAC and lung adenocarcinoma, which at least partially explain their differential responsiveness to current immunotherapies and might have implications for the development of novel treatment strategies.

overall_design: Eight tissue sections were subjected to spatial transcriptomic analysis by using the Visium technology(30) (10x Genomics) according to the protocol of the manufacturer. Briefly, tissue slices approximately 10um in size were cut from fresh frozen OCT embedded tissue sections and placed on the Visium slide. The tissue sections were lysed in situ on the slide, mRNA was released which was captured by the oligonucleotides attached to the slide. Double stranded cDNA was prepared and finally eluted out from the slide into a tube. cDNA was amplified, cleaned and a dual indexed library was prepared. The library was sequenced at the DKFZ sequencing core facility using a NextSeq platform. Cell types in different regions of the tissue sections were annotated by pathologists and the annotation was transferred to the spatial transcriptomic experiments in the array of spots.

first: Suhail

last: Yousuf

first: Lena

middle: V

last: von Voithenberg

first: Charles

last: Imbusch

first: Susanne

last: Roth

first: Mengjie

last: Qiu


title: Spatially Resolved Multi-Omics Single-Cell Analyses Inform Mechanisms of Immune Dysfunction in Pancreatic Cancer

summary: As pancreatic ductal adenocarcinoma (PDAC) continues to be recalcitrant to therapeutic interventions including poor response to immunotherapy, albeit effective in other solid malignancies, a more nuanced understanding of the immune microenvironment in PDAC is urgently needed. Using a spatially-resolved multimodal single cell approach we unveil a detailed view of the immune micromilieu in PDAC with specific emphasis on the correlation of immune subtypes with patient prognosis. We substantiate the exhausted phenotype of CD8 T cells and immunosuppressive features of myeloid cells, and highlight immune subpopulations with potentially underappreciated roles in PDAC that diverge from immune populations within adjacent normal areas, particularly CD4 T cell subsets presenting immunosuppressive phenotypes with varying modes of exhaustion. We reveal striking differences between immune phenotypes in PDAC and lung adenocarcinoma, which explain their differential responsiveness to current immunotherapies, providing a comprehensive resource for functional studies and the exploration of therapeutically actionable targets in PDAC.

overall_design: mRNA profiles of 9 PDAC and paired adjacent tissues


title: Effect of gene POX09752 deletion on gene expression of Penicillium oxalicum

city: zhengzhou

first: Li

last: Xudong

address: No. 1, Jianshe East Road, Erqi District

institute: The First Affiliated Hospital of Zhengzhou University

summary: To explore the effect of transcription factor POX09752 on the transcription levels of cellulase-encoding genes and xylanase-encoding genes

first: Shuai

last: Zhao

first: Ma

last: Bo


title: Transcriptome analysis among young and senescent fibroblasts

city: Minato ku

first: Satotaka

last: Omori

state: tokyo

address: shirokanedai, 4-6-1

institute: the university of Tokyo

summary: We carried out the analysis using human skin fibrobllast HCA2 (MJ90) cells. Cells were indcued to be senescent cells by treatment with RO3306 and Nutlin3a. The transcriptome analysis between young cells (uniduced cells) nd senescent cells revealed lonrf2, a ubiqutin E3 ligase, is one of the genes highly expressed in senescnet cells.

overall_design: Examination of young (uninduced) and senescent HCA2 cells

first: Yoshikazu

last: Johmura

first: Makoto

last: Nakanishi


title: Effect of gene POX07071 deletion on gene expression of Penicillium oxalicum

summary: To explore the effect of G-protein POX07071 on the transcription levels of cellulase-encoding genes and xylanase-encoding genes

first: Pang

last: Xiaoming


title: Effect of gene POX00158 deletion on gene expression of Penicillium oxalicum

summary: To explore the effect of phosphokinase POX00158 on the transcription levels of cellulase-encoding genes and xylanase-encoding genes


title: ARID1A, a SWI/SNF subunit, is critical to acinar cell homeostasis and regeneration and is a barrier to transformation and epithelial-mesenchymal transition in the pancreas.

status: Public on Jul 19 2023

city: Rochester

first: Aram

middle: F.

last: Hezel

state: New York

address: 601 Elmwood Ave, Box 704

institute: Wilmot Cancer Institute

summary: RNA-sequencing of cancer cell lines derived from genetically engineered mouse models KPC (Ptf1a-Cre; LSL-KrasG12D; p53f/+) vs KPCAf/f (Ptf1a-Cre; LSL-KrasG12D; p53f/+; Arid1af/f) followed by GSEA revealed that gene signatures for EMT and stem cells were enriched in KPCAf/f, consistent with phenotypic observations of increased migration, invasion and anchorage-independent growth.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for KPC vs KPCAf/f cancer cell lines

first: Wenjia

last: Wang

first: Scott

last: Friedland


title: Effect of gene POX05503 deletion on gene expression of Penicillium oxalicum

summary: Explore the functions of protein kinase that regulate the expression of cellulase gene and xylanase gene


title: Effect of gene POX06509 deletion on gene expression of Penicillium oxalicum

summary: Explore the functions of important transcription factors that regulate the expression of cellulase gene and xylanase gene


title: Effect of gene POX01907 deletion on gene expression of Penicillium oxalicum

summary: Explore the functions of important transcription factors that regulate the expression of amylase genes

first: Ning

last: Yuanni


title: Gene expression signatures for auricular cartilages of microtia patients and controls

city: Shanghai

first: Xin

state: None Selected

address: No. 83 Fenyang Road, Xuhui District, Shanghai, China.

institute: Eye & ENT Hospital of Fudan University

summary: To explore the coding and non-coding gene expression in the auricular cartilage of microtia patients, we have employed RNA microarray expression profiling as a discovery platform to identify the coding and non-coding genes differentially expressed in microtia patients and controls. The discarded auricular cartilage tissue from 10 unilateral Grade III isolated microtia patients during auricular reconstruction surgery and 5 volunteers without ear malformation or other physical abnormalities during tympanoplasty surgery were collected. All fresh tissues were harvested from the tragus and cavum conchae of the auricle.

overall_design: The RNA expression in auricular cartilage tissue was measured by microarray. One independent experiment was performed on each clinical sample.

first: Jing

last: Ma


title: Krill oil treatment ameliorates lipid metabolism imbalance in chronic unpredicted mild stress-induced depression-like behavior in mice.

city: Qingdao

first: Hao

last: Zhang

address: 38 Dengzhou, Qingdao Shandong China

institute: Qingdao University School of Pharmacy

summary: The deficiency of n-3 PUFAs in the brain and depressive symptoms are closely related. Krill oil contains abundant amounts of n-3 PUFAs incorporated in phosphatidylcholine.However, the effect of krill oil treatment on depression-like behaviors induced by chronic stress and its molecular mechanism in the brain remain poorly understood. Here, we used a chronic unpredictable mild stress (CUMS) model to evaluate the effect of krill oil on depression-like behaviors and explored its molecular mechanism through lipid metabolomics and mRNA profiles in the whole brain.

overall_design: Brains of four differently treated C57/BL6J mice, control group, krill oil group, CUMS group and CUMS+krill oil group

first: Zhenhua

last: Song


title: B cell-derived IL-10 promotes the resolution of lipopolysaccharide-induced acute lung injury

city: Guang zhou

first: zhun

last: sun

address: Xinzao , Panyu District, Guangzhou

institute: Guang zhou medical university

summary: Inflammation resolution is critical for acute lung injury (ALI) recovery. Interleukin (IL)-10 is a potent anti-inflammatory factor. However, its role in ALI resolution remains unclear. We investigated the effects of IL-10 during the ALI resolution process in a murine lipopolysaccharide (LPS)-induced ALI model. Blockade of IL-10 signaling aggravates LPS-induced lung injury, as manifested by elevated pro-inflammatory factors production and increased neutrophils recruitment to the lung .Thereafter, we used IL-10 GFP reporter mice to discern the source cell of IL-10 during ALI. We found that IL-10 is predominantly generated by B cells during the ALI recovery process. Furthermore, we used IL-10-specific loss in B-cell mice to elucidate the effect of B-cell-derived IL-10 on the ALI resolution process. IL-10-specific loss in B cells leads to increased pro-inflammatory cytokine expression, persistent leukocyte infiltration, and prolonged alveolar barrier damage. Mechanistically, B cell-derived IL-10 inhibits the activation and recruitment of macrophages and downregulates the production of chemokine KC that recruits neutrophils to the lung. Moreover, we found that IL-10 deletion in B cells leads to alterations in the cGMP–PKG signaling pathway. In addition, an exogenous supply of IL-10 promotes recovery from LPS-induced ALI, and IL-10-secreting B cells are present in sepsis-related ARDS. This study highlights that B cell-derived IL-10 is critical for the resolution of LPS-induced ALI and may serve as a potential therapeutic target.

overall_design: On the fourth day of LPS exposure, total RNA was extracted from the lungs of 12 mice which were infected with LPS. Six of the mice knockout IL-10 in B cells  while the other six were wild type mice. Subsequently, RNA-seq analysis was performed to examine gene expression in the mouse lungs.

first: Zhun

last: Sun

first: Anning

last: Chen

first: Hongwei

last: Fang

first: Donglin


title: Salivary miRNA profiles in COVID-19 patients with different disease severity

city: Milan

first: Irma

last: Saulle

address: G.B. Grassi 74

country: Italy

institute: University of Milan

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


title: Salivary miRNA profiles in COVID-19 patients with different disease severity [Saliva]

summary: The oral mucosa is the first site of SARS-CoV-2 entry and replication, and it plays a central role in the early defense against infection. Thus, SARS-CoV-2 viral load, miRNAs, cytokines, and neutralizing activity (NA) were assessed in saliva and plasma from mild (MD) and severe (SD) COVID-19 patients.  Here we show that of the 84 miRNAs analysed, 8 are differently express in plasma and saliva of SD. In particular: 1) miRNAs let-7a-5p, let-7b-5p, let-7c-5p are significantly downregulated; and 2) miR-23a and b, miR-29c, as well as three immunomodulatory miRNAs (miR-34a-5p, miR-181d-5p, miR-146) are significantly upregulated. The production of pro-inflammatory cytokines (IL-1β, IL-2, IL-6, IL-8, IL-9 and TNFα) and chemokines (CCL2 and RANTES) increase in both saliva and plasma of SD and MD. Notably, disease severity correlates with NA and immune activation.  Monitoring these parameters could help to predict disease outcome and identify new markers of disease progression.

overall_design: This study included a total of 20 COVID-19-positive patients (as determined by SARS-CoV-2 molecular test of nasopharyngeal swabs) enrolled from a larger cohort hospitalized at the Infectious Diseases Unit, Policlinic “Riuniti” of Foggia (Italy), between March 1st and May 31st,2020. Patients were divided into Mild Patients (MD; n=10) and Severe Patients (SD; n=10) according to COVID-19 disease severity and following the National Institute of Health (NIH) guidelines for COVID-19 treatment. Age and sex matched Uninfected Subjects (HC) (n= 10) were included

first: Claudia

last: Vanetti

first: Micaela

last: Garziano


title: changes in olfactory receptor gene expression in Colorado potato beetles

city: Beijing

last: Li

address: 11 Ronghuanan Road, Yizhuang

institute: Chinese Academy of Inspection and Quarantine

summary: Compared with the non-treatment group, 1728 significantly differentially expressed genes in the three antibiotic treatment groups were identified, of which 822  were upregulated and 906 were downregulated. According to the mean TPM value ≥ 5, |log2fold change| > 1, and a P-value < 0.05, only one upregulated OR gene, LdecOR9, and one downregulated OR gene, LdecO17, were identified

overall_design: To investigate the changes in OR gene expression induced by gut microbiota, we screened the expression differences of all genes through transcriptome analysis with a reference genome. According to the results of all samples and splicing, the transcript per million (TPM) value was used to screen differentially expressed genes.


title: A Shared Pathogenic Mechanism for Valproic Acid and SHROOM3 Knockout in a Brain Organoid Model of Neural Tube Defects

city: Ann Arbor

first: Bioinformatics

last: Core

state: MI

address: BRCF Bioinformatics Core, 2800 Plymouth Rd

institute: University of Michigan

summary: Neural tube defects (NTDs) including anencephaly and spina bifida are common major malformations of fetal development resulting from incomplete closure of the neural tube. These conditions lead to either universal death (anencephaly) or life-long severe complications (spina bifida). Despite hundreds of genetic mouse models having neural tube defect phenotypes, the genetics of human NTDs are poorly understood. Furthermore, pharmaceuticals such as antiseizure medications have been found clinically to increase the risk of NTDs when administered during pregnancy. Therefore, a model that recapitulates human neurodevelopment would be of immense benefit to understand the genetics underlying NTDs and identify teratogenic mechanisms. Using our self-organizing single rosette spheroid (SOSRS) brain organoid system, we have developed a high-throughput image analysis pipeline for evaluating SOSRS structure for NTD-like phenotypes. Similar to small molecule inhibition of apical constriction, the antiseizure medication valproic acid (VPA), a known cause of NTDs, increases the apical lumen size and apical cell surface area in a dose-responsive manner. This expansion was mimicked by GSK3b and HDAC inhibitors; however, RNA sequencing suggests VPA does not inhibit GSK3b at these concentrations. Knockout of SHROOM3, a well-known NTD-related gene, also caused expansion of the lumen as well as reduced f-actin polarization. The increased lumen sizes were caused by reduced cell apical constriction suggesting that impingement of this process is a shared mechanism for VPA treatment and SHROOM3-KO, two well-known causes of NTDs. Our system allows the rapid identification of NTD-like phenotypes for both compounds and genetic variants and should prove useful for understanding specific NTD mechanisms and predicting drug teratogenicity.

overall_design: Day 6 single rosette brain organoids after 48 hours of treatment with valproic acid (VPA; 200 or 400 µM), CHIR99021 (10 µM), or vehicle control. Each sample is replicated 4 times except CHIR99021 (N=3). Each sample comes from 6 wells of a 96-well plate containing ~30-50 organoids in each well.

first: Andrew

last: Tidball

first: Taylor

last: Takla


title: Controlling Genetic Heterogeneity in Gene-edited Hematopoietic Stem Cells by Single Cell Expansion

city: Tokyo

first: Hans

middle: Jiro

last: Becker

address: Shirokanedai 4-6-1, Minato-ku

department: Institute of Medical Science

institute: The University of Tokyo

summary: Gene editing using engineered nucleases frequently produces unintended genetic lesions in hematopoietic stem cells (HSCs). Gene-edited HSC cultures thus contain heterogenous populations, the majority of which either do not carry the desired edit or harbor unwanted mutations. In consequence, transplanting edited HSCs carries the risks of suboptimal efficiency and of unwanted mutations in the graft. Here, we present an approach for expanding gene-edited HSCs at clonal density, allowing for genetic profiling of individual clones before transplantation. We achieved this by developing a defined, polymer-based expansion system and identifying long-term expanding clones within the CD201+CD150+CD48-c-Kit+Sca-1+Lin-(KSL) population of pre-cultured HSCs. This dataset compares the gene expression in three different populations: (1) CD201+CD150+CD48-KSL (2) CD201+CD150+CD48+KSL and (3) CD201-KSL cells.

overall_design: We performed gene expression profiling analysis using data obtained from RNA-seq of 3 populations phenotypically isolated by FACS from 10-day PVA-based HSC expansion cultures (Wilkinson, Ishida et al., Nature 2018). The populations were: (1) CD201+CD150+CD48-KSL (2) CD201+CD150+CD48+KSL and (3) CD201-KSL

first: Becker

last: Hans Jiro

first: Kimura

last: Takaharu

first: Yamazaki

last: Satoshi


title: DNA Methylome and 3D Chromatin Landscape of Cell Types Across the Mouse Brain [9G, 9Ka & 9Kb]

city: La Jolla

first: Joseph

last: Ecker

address: 10010 North Torrey Pines Road

institute: HHMI-Salk-Institute

summary: Illustrating the cellular architecture of the mammalian brain is critical to understanding its diverse functions and complex animal behaviors. With support from NIMH and NINDS as part of the BRAIN Initiative Cell Census Network (BICCN), the Center for Epigenomics of the Mouse Brain Atlas (CEMBA) applied single nucleus methylation sequencing in 117 brain funtional regions across the whole adult male P56 C57BL/6J mouse brain. In each major brain regions, we identified distinct cell clusters and formed them in a hierarchical taxonomy. These clusters include known primary brain cell types and possible sub-types. We use these data to identify the epigenomic characteristics and to define specific regulatory elements for each cell cluster. We integrate the single cell methylome with single cell gene expression and chromatin accessibility profiles from the same brain region to further identify potential enhancers and their corresponding genes for several neuronal cell types. By brain region spacial comparisons, we found spatial specificity among excitatory neuronal clusters within the same cortical layer. We identify brain-region-specific transcription factors that may regulate cortical region development of excitatory neurons. These data define the landscape of cell type and spatial heterogeneity in the mouse brain and the underlining regulatory epigenomic basis.

overall_design: Apply snmC-seq2 to 117 brain functional regions to identify epigenomic landcape of the adult mouse brain, this subseries consists of one single nucleus methylation sequencing experiment of brain region (9G_200903, 9G_200910, 9Ka_201112, 9Ka_201119, 9Kb_201112, 9Kb_201119).

first: Hanqing

last: Liu

first: Anna

last: Bartlett

first: Jacinta

last: Lucero

first: Julia

last: Osteen

first: Jordan

last: Altshul

first: Mia

last: Kenworthy

first: Rosa

last: Castanon

last: Nery

first: Peter

last: Berube

first: Huaming

first: Michael

last: Nunn

first: Jesse

last: Dixon

first: M

last: Behrens


title: Gene expression data from human adipose-derived stem cells (hASCs) treated with 20 uM oleacein

city: Tsukuba

first: Farhana

last: Ferdousi

state: Ibaraki

address: Tennodai 1-1-1

institute: University of Tsukuba

summary:
Gene expression profiling reveals multiple biological functions of oleacein.
We evaluated the effects of oleacein on human adipose-derived stem cells. We performed an untargeted whole-genome transcriptome analysis to explore functionality of oleacein in a adipose stem cell-based tool.

overall_design: According to the manufacturer's guide, the RNA was extracted using Isogen kit (Nip-pon Gene Co. Ltd., Japan). Then, RNA quantity and quality were determined using the NanoDrop 2000 spectrophotometer (ThermoScientific, USA). DNA microarray analysis was conducted on control and oleacein treated hASCs samples using the GeneChip WT PLUS Reagent Kit (ThermoFisher Scientific) and GeneChip™ Hybridization, Wash and Stain Kit (ThermoFisher Scientific) following the manufacturer's instructions. In brief, complementary DNA (cDNA) was synthesized from 100 ng of RNA solutions. cRNA was synthesized from in vitro transcription of cDNA and then purified and reverse transcribed. Finally, single-stranded cDNA (ss-cDNA) was synthesized, purified, fragmented, and labeled following the manufacturer's instructions. Cartridge Array Hybridization was performed using the Clariom S array (Human; ThermoFisher Scientific) on the GeneChip™ Fluidics Station (ThermoFisher Scientific). Scanning was performed using GeneChip Scanner (ThermoFisher Scientific). The raw image data obtained after scanning were analyzed using the Transcriptome Analysis Console (TAC) software (ver. 4.0.2, ThermoFisher Scientific). The raw data were normalized following the signal space transformation robust multi-chip analysis (SST-RMA) algorithm. Further, gene-level analysis was performed using the Limma Bioconductor package. For differential expression analysis, a One-Way ANOVA followed by an empirical Bayes correction was performed.ar space) were considered as differentially expressed genes (DEGs). A threshold value of FC >2 (in linear space) and p-value <0.05 (one-way between-subject analysis of variance ANOVA) were set to identify as differentially expressed genes (DEGs) in analysing the comparasions to normal hASCs (undiff). After adipocyte differentiation, DEGs were filtered using a linear fold change (FC) of greater than 1.1 and a p-value less than 0.05 for comparing the OLE+diff and diff groups in h-ASCs.

first: Wang

last: Rui