title: Gene expression analyses of three early phases of osteogenic, adipogenic, and chondrogenic differentiation of rat bone marrow mesenchymal stem cells

status: Public on Oct 23 2021

city: Jinan

first: Qingyu

last: Zhang

state: Shandong Province

institute: Shandong Provincial Hospital affiliated to Shandong First Medical University

summary: To further reveal key mRNAs deciding osteogenic, adipogenic, and chondrogenic differentiation of rat bone marrow mesenchymal stem cells (BMSCs) in early phases, we have employed next-generation high-throughput transcriptome sequencing to detect the expression of mRNA in rat BMSCs during differentiation.

overall_design: mRNAs obtained from rat BMSCs were cultured in osteogenic, adipogenic, or chondrogenic differentiation medium. For each timepoint we have generated 3 biological replicates.

first: Fanxiao

last: Liu


title: Transcriptomic dataset for early inflorescence stages of oil palm in response to defoliation stress

city: Jakarta Timur

first: Ardha

last: Apriyanto

state: DKI Jakarta

address: Puloayang Raya Blok OR I

country: Indonesia

institute: Astra Agro Lestari

type: Expression profiling by high throughput sequencing

summary: Oil palm breeding and seed development have been hindered due to the male parent's incapacity to produce male inflorescence as a source of pollen under normal conditions. On the other hand, a young oil palm plantation has a low pollination rate due to a lack of male flowers. These are the common problem of sex ratio in the oil palm industry. Nevertheless, the regulation of sex ratio in oil palm plants is a complex mechanism and remains an open question until now. Researchers have previously used complete defoliation to induce male inflorescences, but the biological and molecular mechanisms underlying this morphological change have yet to be discovered. Here, we present an RNA-seq dataset from three early stages of an oil palm inflorescence under normal conditions and complete defoliation stress. This transcriptomic dataset is a valuable resource to improve our understanding of sex determination mechanisms in oil palm inflorescence.

overall_design: Transcriptomic data were collected from three different inflorescence stages of control (untreated) and defoliation stress (treated). The tissue source is from inflorescense at leaf axil -27, -20 and +5.


title: CCDC50 suppresses NLRP3 inflammasome activity by mediating the autophagic degradation of NLRP3

status: Public on Nov 16 2021

city: Philadelphia

first: Tian

last: Tian

state: PA

address: 3615 Civic Center Blvd

department: Center of Applied Genomics

country: USA

institute: Children's Hospital of Philadelphia

summary: Autophagy and autophagy-associated genes are closely linked to NLRP3-mediated inflammation in inflammatory disorders. This study determined that the functions of CCDC50, the novel autophagy receptor, in regulating the activation of NLRP3 inflammasome and associated inflammatory diseases. We performed transcriptome profiling (RNA-seq) and quantitative reverse transcription polymerase chain reaction (qRT–PCR) in shCtrl and shCCDC50 cells to evaluate the inflammatory responses regulated by CCDC50. The deep sequencing results showed that CCDC50 defciency caused increased NLRP3 inflammasome assembly and upregulation of associated disease pathways.

overall_design: Immune signaling pathways-competent A375 cells were transduced with lentivirus carring shCtrl or shCCDC50 plasmids. The infected cells were selected with puromycin for 7 days. The deletion of CCDC50 was confirmed by qRT-PCR and immunobloting. The shCtrl and shCCDC50 cells were collected for mRNA profilling analysis.

first: Deyin

last: Guo

first: Panpan

last: Hou


title: Determine the chromatin association change of H3K27me3 and PRC2  in response to CTR9 inducible loss as well as genome-wide mapping of Flag-CTR9 binding sites in MCF7 cells

status: Public on Oct 19 2021

city: Madison

first: NGAI TING

last: CHAN

state: WI

address: 4849 Sheboygan Ave

department: Oncology

institute: University of Wisconsin -- Madison

type: Genome binding/occupancy profiling by high throughput sequencing

summary: CTR9 is the scaffold subunit in PAFc (Polymerase associated factor complex), a multifunctional complex employed in multiple steps of RNA Pol II-mediated transcription. CTR9/PAFc is well known as an evolutionarily conserved elongation factor regulating gene activation via coupling with histone modifications enzymes. However, little is known about its function to restrain repressive histone markers. Using inducible and stable CTR9 knockdown breast cancer cell lines, we discovered that the amount of H3K27me3 is strictly controlled by CTR9. Quantitative profiling on histone modifications revealed a striking increase of H3K27me3 level upon loss of CTR9. Moreover, loss of CTR9 leads to genome-wide expansion of H3K27me3, as well as increased recruitment of PRC2 on chromatin, which can be reversed by CTR9 restoration. Moreover, CTR9 depletion triggers a PRC2 subtype switch from less active PRC2.2 to PRC2.1 with higher methyltransferase activity. As a consequence, CTR9 depletion generates vulnerability that renders breast cancer cells hypersensitive to PRC2 inhibitors. Our findings that CTR9 demarcates PRC2-mediated H3K27me3 levels and genomic distribution provide a unique mechanism of transition from transcriptionally active to repressive chromatin states and shed light on the biological functions of CTR9 in development and cancer.

overall_design: 1. ChIP-Rx of H3K27me3 and PRC2 subunits (SUZ12/JARID2/MTF2) in MCF7-tet-on-shCTR9 cells (Dox inducible CTR9 KD) -- 2 replicates  2. ChIP-Rx of Flag (2 different vendors) in MCF7-3xFlag-KI-CTR(9 cells (CTR9 with 3xFlag epitope tag knock in) -- 2 replicates (PS: every ChIP reaction was incorportated with same amount of spike-in control)

first: Ngai-Ting

last: Chan


title: Single cell sequencing confirms that chemistry version sensitivity is not key factor in detection of artificial signature or identification of signature specifc genes.

status: Public on Nov 15 2021

city: Boston

first: Beth

last: Stevens

state: Massachusetts

address: 3 Blackfan Circle, 12220 Center for Life Sciences

institute: Boston Children's Hospital

summary: Single Cell Sequencing of FACS purified microglia/myeloid cells isolated with cold mechanical dounce homogenization.  Following cell dissociation, the cells from each mouse were split in half and assigned to V3.0 and V3.1 prior to FACS and cell capture.

overall_design: 3 animals,  P89

first: Samuel

middle: E

last: Marsh


title: Gene expression analysis of ccRCC cell line upon SETD2 rescue [RNAseq_JHRCC12]

city: New York

first: Christina

middle: S

last: Leslie

state: NY

address: 417 E 68th St

department: Computational Biology Program

institute: Memorial Sloan Kettering Cancer Center

summary: SETD2, a H3K36 trimethyltransferase, is frequently mutated in human cancers with the highest prevalence (13%) in clear cell renal cell carcinoma (ccRCC). Genomic profiling of primary ccRCC tumors reveals a positive correlation between SETD2 mutations and metastasis. However, whether and how SETD2-loss promotes metastasis remains unclear. Here, we detected SETD2 mutations in 24 of 51 (47%) metastatic ccRCC tumors. Using SETD2-mutant metastatic ccRCC patient-derived cell line and xenograft models, we showed that H3K36me3 restoration greatly reduced distant metastases of ccRCC in mice. An integrated ATAC-seq, ChIP-seq, and transcriptome analysis concluded a tumor suppressor model in which loss of SETD2-mediated H3K36me3 activates enhancers to drive oncogenic transcription through dysregulating histone chaperone recruitment, enhancing histone exchange, and expanding chromatin accessibility. Furthermore, we uncovered mechanism-based therapeutic strategies for SETD2-deficient cancer through inhibition of histone chaperones. Overall, SETD2-loss creates a permissive epigenetic landscape for cooperating oncogenic drivers to amplify transcriptional output, providing unique therapeutic opportunities.

overall_design: RNA-Seq assay was perfomed in SETD2-proficient and SETD2-deficient JHRCC12 cells in 3 replicates

first: Yuchen

last: Xie

first: Merve

last: Sahin

first: Emily

middle: H

last: Cheng


title: Gene expression analysis of murine renal tubular epithelial cells upon SETD2 knockout [RNAseq_RTE]

overall_design: RNA-Seq was performed in primary renal tubular epithelial (RTE) cells cultured from Setd2(F/F)Ksp-Cre+ or littermate Setd2(F/F) mice in 3 replicates.


title: Transcriptional impacts of lipids on hESC

city: Macau

first: Guokai

last: Chen

address: University of Macau Avenida da Universidade Taipa, Macau, China

country: China

institute: University of Macau

summary: Pluripotent stem cells can be maintained in a continuum of cellular states with distinct features. Exogenous lipid supplements are commonly utilized to shift the balance of global metabolism relieving the dependence on de novo lipogenesis. However, it is largely unexplored how specific lipid components regulate metabolism and pluripotency state. In this study, we investigate the impact of lipid supplements on human embryonic stem cells (hESCs), and report that signaling lipid lysophosphatidic acid (LPA) is the key component to shift the metabolic landscape in lipid supplement AlbuMAX. Although the maintenance of ERK phosphorylation and primed pluripotency is independent of exogenous lipids, LPA increases ERK phosphorylation, especially upon niche disintegration. We further demonstrate that LPA leads to distinctive transcriptome profile that is not associated with de novo lipogenesis. We also show that LPA causes unique and reversible phenotypes in cell cycle, morphology and mitochondria. This study reveals an LPA -induced primed state that allow people to drastically alter cell physiology for basic research and stem cell applications with hESCs.

overall_design: Total RNA obtained from H1 hESC cultured in E8 medium and E8 medium supplemented with 1.6% AlbuMAX, 1% Albumin, 1% CDL, 0.1x hCDL, 1 μM LPA and 1 μM LPA + 1% Albumin. Samples were collected after 2 days.


title: Analysis of microRNA expression in murine BMDCs activated by flagellin

status: Public on Nov 13 2021

city: Yangzhou

first: Xilong

last: Kang

state: Jiangsu

address: 48 East Wenhui Road

institute: Yangzhou University

summary: MicroRNAs (miRNAs) are small non-coding RNA molecules that regulate gene expression by either translational inhibition or mRNA degradation. However, the role of miRNAs in inflammation induced by flagellin (ligand of TLR5) has not been fully determined, Here, we identified differentially expressed miRNAs in murine bone marrow-derived dendritic cells (BMDCs) between flagellin (FliC) treatment and medium alone using miRNA microarray. And we further evaluated the role of miRNAs in inflammation induced by flagellin.

overall_design: Murine BMDCs were generated from C3H/HeJ murine bone marrow in vitro cultured in presence of rmGM-CSF and rmIL-4. The CD11c+ BMDCs were sorted using anti-CD11c-coated magnetic beads with the auto-MACS system. The purified BMDCs were stimulated with 100 ng/mL flagellin (FliC) or medium for 24 h. The differentially expressed miRNAs between flagellin-stimulated group and mock group were screened using miRNA microarray. Three flagellin-stimulated samples and two mock samples were included in the experiment.

first: Zhiming

last: Pan


title: NextGeneration Sequencing of Mouse Fetal Lung Tissue Following Tracheal Occlusion

status: Public on Oct 04 2021

city: Cincinnati

first: Brian

middle: Michael

last: Varisco

state: OH

address: 3333 Burnet Avenue, MLC 7006

department: Critical Care Medicine

institute: Cincinnati Children's Hospital Medical Center

summary: C57BL/6 mouse fetusus were subjected to transuterine fetal tracheal occlusion at gestational day 16.5 with collection of lung tissue at  gestational day 18.5.

overall_design: Comparison of lung tissue from four control and four tracheal occlusion lung specimens.


title: Identification and Characterization of Key Genes Responsible for Weedy and Cultivar Growth Types in Soybean

status: Public on Nov 12 2021

city: Chuncheon

first: Prakash

last: Basnet

state: Gangwon-do

address: Department of Agriculture and Life Industry, Kangwon National University, Bldg. Asangwan Rm.424, 1 K

department: Agriculture and Life Industries

country: South Korea

institute: Kangwon National University

summary: We report total mRNA library using Illumina Nova Seq high-throughput sequencing platform platform for analysis of transcriptome between the two relatives of the soybean ie weedy and cultivar growth types in F7 generation derived from the crossing of wild and cultivated soybean.

overall_design: Key genes responsible for weedy and cultivar growth types in the soybean plants.

first: Ik-Young

last: Choi

first: Taeyoung

last: Um

first: Neha

last: Roy

first: Kyong

middle: C

last: Park


title: Gene expression analysis to identify target genes of miR-150 in Hodgkin lymphoma cell lines

status: Public on Nov 06 2021

city: Groningen

first: Lotteke

last: Ziel-Swier

state: Groningen

address: Hanzeplein 1

department: Pathology and Medical Bi9ology

country: Netherlands

institute: UMCG

summary: In Burkitt lymphoma (BL), a network consisting of MYC, MYC-repressed miR-150, known miR-150 target MYB and two novel targets of miR-150, ZDHHC11 and ZDHHC11B, has been established. This network plays an important role on the growth of BL cells. Here, we confirmed that MYB, ZDHHC11 and ZDHHC11B are targeted by miR-150 in Hodgkin lymphoma (HL) cell lines too.

overall_design: L428 and SUPHD1 HL cell lines with low endogenous miR-150 levels were transduced with either a miR-150 overexpression vector or a control empty vector. AGO2 RNA immunoprecipitation was performed, followed by expression analysis to identify target genes of miR-150 in these HL cell lines.

middle: J

last: Swier

first: Yichen

last: Liu

first: Annika

last: Seitz

first: Jasper

last: Koerts

first: Debora

last: de Jong

first: Joost

last: Kluiver

first: Anke

last: van den Berg


title: Differentially expressed micro-RNA in head and neck squamous cell cancer (HNSCC) tissues, normal oral epithelial tissues and CAFs

status: Public on Oct 02 2021

city: Chiba city

first: Shunichi

last: Asai

address: 1-8-1 inohana,chuo-ku

country: Japan

institute: Chiba University Graduate School of Medicine

type: Non-coding RNA profiling by high throughput sequencing

summary: Next generation sequencing was perfomed to identify differentially expressed micro-RNA in HNSCC tissues, normal oral epithelial tissues and CAFs.

overall_design: All specimens and CAFs used in the study were obtained by surgical resection at Chiba University Hospital.

first: Sachi

last: Oshima

first: Naohiko

last: Seki


title: Global genomic instability caused by reduced expression of DNA polymerase ε in yeast

status: Public on Oct 07 2021

city: Hangzhou

first: Daoqiong

last: Zheng

state: Zhejiang

address: 866 Yuhangtang Road

department: Institute of Microbiology

institute: College of Life Sciences, Zhejiang University

type: Genome variation profiling by genome tiling array

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

overall_design: Refer to individual Series


title: TRACE-seq: A transgenic system for unbiased loading of mRNA into extracellular vesicles allowing non-invasive transcriptome profiling of living cells

status: Public on Nov 03 2021

first: Guoping

last: Li

state: MA

address: Cardiovascular Research Center, 185 Cambridge St, Simches 3.5000

department: CVRC

institute: Massachusetts General Hospital

summary: Changes in gene expression due to cell heterogeneity and response to stressors in specific microenvironments remains poorly understood. Current methodologies that seek to interrogate gene expression at a molecular level require sampling of cellular transcriptome and therefore lysis of the cell preventing serial analysis of cellular transcriptome. To address this area of unmet need, we have recently developed a new technology allowing transcriptomic analysis over time without cellular destruction. Our novel method, TRACE-seq (TRanscriptomic Analysis Captured in Extracellular vesicles using sequencing), is characterized by a cell-type specific transgene expression. It provides data on a representative part of the cell transcriptome inside extracellular vesicles. Thus, the transcriptome of cells expressing TRACE can be followed over time in a non-destructive manner, which is a powerful tool for many fields of fundamental and translational biology research.

overall_design: HEK cells were transfected with 4EC1 vectors (eGFP-EIF4E-C-YTHDF1/GBP1-CD9) and exposed to normoxia or hypoxia conditions. The cellular RNAs and extracellular RNAs were sequenced and analyzed.

first: François

last: Cherbonneau

first: Saumya

last: Das


title: A multi-omic single-cell atlas of human gynecological malignancies

status: Public on Nov 04 2021

city: Chapel Hill

first: Hector

middle: L

last: Franco

state: NC

address: 120 Mason Farm Rd

department: Genetics

institute: UNC Lineberger Cancer Center

summary: Tumors show substantial amounts of cellular heterogeneity by forming complex ecosystems of malignant and non-malignant cells. Herein, we present a comprehensive multi-omic cell atlas of matched single-cell transcriptome and single-cell chromatin accessibility profiles spanning over 150,000 cells from 11 human gynecologic tumors. By jointly analyzing these transcriptomic and chromatin accessibility profiles at single-cell resolution, we identify 115,734 total peak-to-gene links representing putative regulatory interactions. We find some of these regulatory interactions explain cell type-specific expression patterns of hallmark cancer pathway regulators such as the mTOR activator RHEB. We also leverage these data to infer differential transcription factor activity, such as ZEB1, across cell type-specific enhancers between two different fractions of the same patient tumor. Our work highlights the importance of precision medicine in the treatment of gynecologic cancers and we show that this resource will deepen our understanding of non-coding genomic regions in the context of tumor biology.

overall_design:
Matched single-cell RNA-seq and single-cell ATAC-seq profiling of 11 human tumors collected from the endometrium or ovary.

**The raw data were deposited in dbGaP (phs002340.v1.p1) due to patient privacy concerns**

first: Matthew

last: Regner

first: Kamila

last: Wisniewska


title: Ruminant-specific retrotransposons shape regulatory evolution of bovine immunity

city: Boulder

first: Edward

last: Chuong

state: CO

address: 3415 Colorado Ave, JSC Biotech Bldg

department: BioFrontiers/MCDB

institute: University of Colorado Boulder


title: Early brain microRNA and mRNA expression profiles after neonatal hypoxic-ischemic injury in a mouse model

status: Public on Oct 01 2021

city: Omaha

first: Eric

last: Peeples

state: NE

address: 8200 Dodge Street

department: Pediatrics

institute: University of Nebraska Medical Center


title: Early brain microRNA and mRNA expression profiles after neonatal hypoxic-ischemic injury in a mouse model [NanoString]

summary:
We report the miRNA-Seq and Nanostring mRNA data from regional brain samples after neonatal hypoxic-ischemic brain injury (induced by unilateral carotid artery ligation and 30 minutes at 8% oxygen in CD1 mice at postnatal day 9). Analyses are perfomed in the cerebellum, striatum/thalamus, and whole cortex.
Examination of regional small RNA expression between four postnatal day 9 mouse pups after hypoxic-ischemic brain injury versus four sham surgery controls

first: Namood-e

last: Sahar

first: William

last: Snyder

first: Karoly

last: Mirnics


title: Genome-wide maps of chromatin state in pre-osteoblastic and lineage-committed cells.

status: Public on Oct 30 2021

city: Turku

first: Riku

last: Kiviranta

address: Kiinamyllynkatu 10

department: Institute of Biomedicine

country: Finland

institute: University of Turku

summary: Epigenetic mechanisms regulate osteogenic lineage differentiation of mesenchymal stromal cells. Histone methylation is an important step in controlling local chromatin structure and gene expression and it is controlled by multiple lysine demethylases. Although Lsd1 knockdown did not affect global H3K4 methylation levels, genome-wide ChIP-Seq analysis revealed  high levels of Lsd1 at gene promoters and its binding was associated with di- and tri-methylation of histone 3 at lysine 4 (H3K4me2 and H3K4me3)

overall_design: Examination of 4 different histone modifications and Lsd1/Kdm1a occupancy in MC3T3-E1 at different stages of differentiation

first: K

last: Tarkkonen

first: C

last: Valensisi

first: A

last: Dudakovic


title: LATS regulates heavy metal response

city: IRVINE

first: Han

last: Han

state: CA

address: 3302A, Natural Sciences I

department: Developmental and Cell Biology

institute: University of California, Irvine

summary: Heavy metals are essential integral parts of cells and environmental toxicants, whose deregulation is associated with severe cellular dysfunction and various diseases. The Hippo pathway plays a critical role in organ size control and cancer development. In this study, we use RNA-Seq to investigate the role of the Hippo pathway in regulating heavy metal response gene transcription. Specifically, the difference of transcriptional profiles between the wild-type and the Hippo pathway kinases LATS1/2-deficient HEK293A cells was examined under control- and heavy metals zinc and cadimuim treated-conditions.

overall_design: To profile the LATS1/2-dependent transcriptome as regulated by heavy metals, we obtained the total RNAs from wild-type and the LATS1/2-double knockout HEK293A cells under the respective treatment of H2O, ZnCl2 (250 uM) and CdCl2 (50 uM) for 4 hours. Three biological replicates were performed.

first: Jeff

last: Zhou

first: Wenqi

last: Wang


title: Intrauterine hyponutrition reduces fetal testosterone production and postnatal sperm count in the C57BL/6N

status: Public on Oct 22 2021

city: Handayama, Higashiku, Hamamatsu city

first: Yasuko

last: Fujisawa

state: Shizuoka

institute: Hamamatsu University School of Medicine

summary: There has been growing interest in the relationship between maternal undernutrition and reproductive disorders in male offspring. In the present study, we determined the effects of maternal calorie restriction throughout the critical period for in utero development of the male reproductive system, termed the “masculinization programming window” on the reproductive system of mice. The intratesticular testosterone concentration of the fetuses of calorie-restricted (R) dams was lower than in control fetuses at 17.5 days post coitum. In addition, there was global down-regulation of genes encoding steroidogenic enzymes and a low sperm count in the offspring of R dams (R-offspring) at 6 weeks of age. Microarray analysis of the testes of the offspring identified dysregulation of several genes that might explain the derangement in spermatogenesis in the R-offspring. Thus, the present study provides insights into the impact of maternal undernutrition on the male reproductive system in mice. The deleterious effects probably originate in lower androgen exposure during the “masculinization programming window.”

overall_design: We used two groups of female mice with vaginal plugs. One group of mice were fed a powdered regular chow diet ad libitum throughout the pregnant course (control females) (C-females), and the other group of mice were fed 50% of the mean daily intake of the C-females from 6.5 days post coitum (dpc) (calorie-restricted females) (R-females). Pregnant C- and R-females gave birth to control offspring (C-offspring) and calorie-restricted offspring (R-offspring), respectively. After determining genetic sex, male mice only were utilized for the subsequent examinations. Male C-offspring were raised by their mothers, whereas male R-offspring were cross-fostered and raised by unrelated C-females. After weaning, male C- and R-offspring were fed a regular chow diet ad libitum. At 6 weeks (42 days) of age, they were sacrificed. Testes were immediately removed for subsequent studies including microarray analysis. RNA samples obtained from the testes of C- and R-offspring were utilized for microarray analysis using single-color SurePrint G3 mouse GE 8×60K v2 Microarrays. We extracted genes satisfying the combined criterion for true positive expression differences of a fold difference of > 1.5 or < 0.66 and a false discovery rate (q value) of < 0.05. n = 5 for C or R offspring.

first: Hiroyuki

last: Ono

first: Aru

last: Konno

first: Ikuko

last: Yao

first: Hiroaki

last: Itoh

first: Takashi

last: Baba

first: Kenichirou

last: Morohashi

first: Yuko

last: Katoh-Fuku

first: Mami

last: Miyado

first: Maki

last: Fukami

first: Tsutomu

last: Ogata


title: RNA-seq of backfat tissue in beef cattle

status: Public on Nov 01 2021

city: Edmonton

first: Zhi

last: Zhu

state: Alberta

address: 116 St and 85 Ave

department: AFNS

country: Canada

institute: University of Alberta

summary: RNA-seq from backfat tissues were obatained from 22 steers, including Angus (AN; n=8), Charolais (CH; n=6), and Kinsella composite (KC; n=8). In each breed, cattle were classified two groups, i.e.  high residual feed intake adjusted for off-test backfat thickness (RFIfat, RFIfat >= 0.5) and low RFIfat (RFIfat <= -0.5). For gene analysis, 46, 39 and 177 differentially expressed (DE) genes were identified in AN, CH and KC, respectively. Among them, 4, 17, 74 genes were up-regulated in high RFIfat as compared to low RFIfat in AN, CH and KC, respectively. All DE genes were used for functional and upstream analysis in Ingenuity Pathway Analysis. Some DE genes were involved in reduction of carbohydrate metabolism in AN, and reduction of lipid metabolism in KC.

overall_design: Effect of residual feed intake on fatty acid profile of subcutaneous fat in beef cattle using transcriptomic analysis

first: Le

last: Guan

first: Mi

first: Yanhong

last: Chen


title: Early brain microRNA and mRNA expression profiles after neonatal hypoxic-ischemic injury in a mouse model [miRNA-Seq]

first: Eric

last: Peeples

summary: We report the miRNA-Seq and Nanostring mRNA data from regional brain samples after neonatal hypoxic-ischemic brain injury (induced by unilateral carotid artery ligation and 30 minutes at 8% oxygen in CD1 mice at postnatal day 9). Analyses are perfomed in the cerebellum, striatum/thalamus, and whole cortex.

overall_design: Examination of regional small RNA expression between four postnatal day 9 mouse pups after hypoxic-ischemic brain injury versus four sham surgery controls

first: Namood-e

last: Sahar

first: William

last: Snyder

first: Karoly

last: Mirnics


title: Microarray data from patients samples with triple negative breast cancer

status: Public on Oct 12 2021

city: Salamanca

first: Juan Carlos

last: Montero

state: Salamanca

address: Campus Miguel de Unamuno s/n

country: Spain

institute: Institute of Biomedical Research of Salamanca (IBSAL)

summary:
The genomic studies was designed to identify genes differentially expressed in tumor versus normal breast tissue.
We aimed at identifying novel Antibody Drug Conjugate (ADC) targets that could be used to treat Triple Negative Breast Cancer (TNBC). Comparative genomic studies between normal breast and TNBC tissues, together with proteomic and bioinformatic analyses resulted in the elaboration of a catalog of potential ADC targets.

overall_design: Samples were obtained at  the University Hospital (Department of Pathology) of Salamanca from patients with triple negative breast cancer. One sample from normal breast tissue was also obtained.

first: Juan

first: Elisa

last: Calvo-Jiménez

first: Sofía

last: del Carmen  Martínez

first: Mar

last: Abad

first: Alberto

last: Ocaña

first: Atanasio

last: Pandiella


title: Spatial transcriptome analysis of gastric cancer which GAN-KP transplanted C57BL/6J mouse

status: Public on Oct 21 2021

city: Chiyoda-ku

first: Shogo

last: Okazaki

state: Tokyo

address: 1-8-13 Kanda-Surugadai

department: School of Dentistry

institute: Nihon University

summary: We have now developed an organoid-based model of gastric cancer from GAstric Neoplasia (GAN) mice, which express Wnt1 and the enzymes COX2 and microsomal prostaglandin E synthase 1 in the stomach. Both p53 knockout (GAN-p53KO) organoids and KRASG12V-expressing GAN-p53KO (GAN-KP) organoids were generated by genetic manipulation of GAN mouse–derived tumor (GAN-WT) organoids. To uncover the molecular mechanism underlying the intratumoral heterogeneity of GAN-KP tumors, we performed spatial transcriptomics analysis with the 10× Genomics Visium platform, which allows characterization of the spatial topography of gene expression.

overall_design: GAN-KP cells were transplanted into the stomach wall of mice and gene expression was analyzed two weeks later.

first: Juntaro

last: Yamasaki

first: Yuki

last: Hirata

first: Hideyuki

last: Saya

first: Osamu

last: Nagano


title: High-throughout prolifing of exosomal miRNAs from 4TO7 mouse breast tumor

status: Public on Oct 11 2021

city: Shanghai

first: Lixing

last: Zhan

state: Shanghai

address: 320 Yue-yang Road

department: Shanghai Institute of Nutrition and Health

institute: Shanghai Institutes for Biological Sciences University of Chinese Academy of Sciences

summary: Purpose: The goals of this study are to explore the main miRNA compotents in tumor exosomes in the early stage of tumor growth. Methods: miRNA profiles of mouse breast tumor exosomes

overall_design: RNA-seq of tumor exosomal miRNAs in the pre-metastatic stage of 4TO7 tumor growth.n=1

first: Meiyan

last: Qi


title: Unveiling E2F4, TEAD1 and AP-1 as regulatory transcription factors of the replicative senescence program by multi-omics analysis

city: Boston

first: Yi

last: Zhang

address: 200 Longwood Ave

department: PCMM

institute: Boston Children's Hospital

type: Methylation profiling by high throughput sequencing

summary: Senescence, a stable state of growth arrest, affects many physiological and pathophysiological processes, especially aging. Previous work has indicated that transcription factors (TFs) play a role in regulating senescence. However, a systematic study of regulatory TFs during replicative senescence (RS) using multi-omics analysis is still lacking. Here, we generated time-resolved RNA-seq, reduced representation bisulfite sequencing (RRBS) and ATAC-seq datasets during RS of mouse skin fibroblasts, which demonstrated that an enhanced inflammatory response and reduced proliferative capacity were the main characteristics of RS in both the transcriptome and epigenome. Through integrative analysis and genetic manipulation, we found that transcription factors E2F4, TEAD1 and AP-1 are key regulators of RS. Overexpression of E2f4 improved cellular proliferative capacity, attenuated SA-β-Gal activity and changed RS-associated differentially methylated sites (DMSs). Moreover, knockdown of Tead1 attenuated SA-β-Gal activity and partially altered the RS-associated transcriptome. In addition, knockdown of Atf3, one member of AP-1 superfamily TFs, reduced Cdkn2a (P16) expression in pre-senescent fibroblasts. Taken together, results of this study identified transcription factors regulating the senescence program through multi-omics analysis, providing potential therapeutic targets for anti-aging.

overall_design: mRNA, RRBS and ATAC-seq profiles of P1, P3, P5 and P7 fibroblasts.

first: Yuting

last: Wang

first: Liping

last: Liu

first: Yifan

last: Song


title: EBV-induced CXCL8 upregulation promotes vasculogenic mimicry in gastric carcinoma via NF-κB signaling

status: Public on Oct 14 2021

city: Guangzhou

first: Jingyue

address: No. 600 Tianhe Road, Guangzhou 510630, China

institute: Department of Pathology, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, China

summary: Epstein-Barr virus (EBV)-associated gastric carcinoma (EBVaGC) is a distinct entity that has conspicuously tumor microenvironment compared with EBV-negative gastric carcinoma. However, the exact role of EBV in gastric carcinogenesis remains elusive. In the present study, we found that EBV upregulated CXCL8 expression, and CXCL8 significantly promoted vasculogenic mimicry (VM) formation of gastric carcinoma cells. In accordance with these observations, CXCL8 increased cell proliferation and migration of AGS and BGC823 cells, respectively. In addition, activation of NF-κB signaling was involved in VM formation induced by CXCL8, which was blocked by NF-κB inhibitor BAY 11-7082. Furthermore, EBV encoded lncRNA RPMS1 activated the NF-κB signaling cascade, which is responsible for EBV-induced VM formation. Both xenografts and clinical samples of EBVaGC exhibit VM histologically, which are correlated with CXCL8 over-expression. Finally, CXCL8 is positively correlated with overall survival in gastric carcinoma patients. In conclusion, EBV-upregulated CXCL8 expression promotes VM formation in gastric carcinoma via NF-κB signaling and CXCL8 may serve as a novel anti-tumor target for EBVaGC.

overall_design:
EBV-infected cells (AGS-EBV ) were obtained by co-culturing AGS with Akata-EBV-GFP using the cell-to-cell infection method.
Cell culture to 80% Confluence

first: Jing-yue

first: Yu

last: Du

first: Li-ping

last: Gong

first: Yi-ting

last: Shao

first: Jing-yun

last: Wen

last: Sun

first: Dan

last: He

first: Jin-rui

last: Guo

first: Jian-ning

last: Chen

first: Chun-kui


title: lncRNA HOXC-AS3 regulates brest cancer glycolysis through binding with SIRT6 (RIP-seq)

status: Public on Oct 18 2021

city: Jinan City

first: Wenjie

last: Zhu

state: Shangdong Province

address: Wen Hua Xi Road 44

department: Department of Pathology

institute: School of Basic Medical Sciences, Shandong University

summary: Here we show that lncRNA HOXC-AS3, a key factor in controling metabolic reprogramming through binding with SIRT6, thereby promoting the metastases of brest cancer.

overall_design: RNA-immunoprecipitation sequencing of SIRT6-associated RNAs in 231 cell lines.

first: Z

last: Wenjie

first: G

last: Peng


title: Astrocyte developmental transcriptome from mouse visual cortex

status: Public on Oct 08 2021

city: San Diego

first: April

middle: Elizabeth

last: Williams

state: California

address: 10010 N Torrey Pines Rd

department: IGC

institute: Salk Institute for Biological Studies

summary: Analysis of astrocyte gene expression across postnatal development in the mouse visual cortex, spanning the time of synaptogenesis and synapse maturation.

overall_design: Profile of astrocyte-enriched mRNA from the mouse visual cortex at 4 different developmental (P7,P14,P28,P120) timepoints from GFAP-Ribotag mice (ribosomal pulldown), with 3-5 biological replicates and 1 input (non-pulldown) sample per time point

first: Matthew

middle: M

last: Boisvert

first: Isabella

last: Farhy-Tselnicker

first: Galina

middle: A

last: Erikson

first: Maxim

middle: N

last: Shokhirev

first: Nicola

last: Allen


title: Loss of TREM2 reduces hyperactivation of progranulin deficient microglia but not lysosomal pathology [14 months]

city: Munich

first: Anika

last: Reifschneider

address: Feodor-Lynen-Straße

country: Germany

institute: LMU

summary: GRN haploinsufficiency causes frontotemporal lobar degeneration and results in microglial hyperactivation, lysosomal dysfunction and TDP-43 deposition. To understand the contribution of microglial hyperactivation to pathology we evaluated genetic and pharmacological approaches suppressing TREM2 dependent transition of microglia from a homeostatic to a disease associated state.  Trem2 deficiency in Grn KO mice led to a reduction of microglia activation. To explore antibody-mediated pharmacological modulation of TREM2-dependent microglial states, we identified antagonistic TREM2 antibodies.  Treatment of macrophages from GRN-FTLD patients with these antibodies allowed a complete rescue of elevated levels of TREM2 together with increased shedding and reduction of TREM2 signaling. Furthermore, antibody-treated PGRN deficient hiMGL showed dampened microglial hyperactivation, reduced TREM2 signaling and phagocytic activity, however, lack of rescue of lysosomal dysfunction. Similarly, lysosomal dysfunction, lipid dysregulation and glucose hypometabolism of Grn KO mice were not rescued by TREM2 ablation. Furthermore, NfL, a biomarker for neurodegeneration, was elevated in the Grn/Trem2 KO. These findings suggest that microglia hyperactivation is not necessarily contributing to neurotoxicity, and instead demonstrates that TREM2 exhibits neuroprotective potential in this model.

overall_design:
In this study we analyzed gene expression in total RNA isolated from whole brain of adult mice. We compared the expression profile of Trem2 knockout mice , Grn knockout mice, and Grn/Trem2 double knockout mice (for each genotype n=3 female, n=3 male, 14 month) to wild type mice (n=3 female, n=3 female, 14 months).

Please note that the normalized data for the GSM5617157 - GSM5617168 samples have been updated on Oct 15, 2021.

first: Anja

last: Capell


title: Whole transcriptome analysis of breast tissues prior to breast cancer diagnosis [RNA-seq]

status: Public on Sep 30 2021

city: Indianapolis

first: Natascia

last: Marino

state: IN

address: 980 W. Walnut St, R3-C238

department: Hematology/Oncology Division

institute: Indiana University School of Medicine

summary: The Susan G. Komen Tissue Bank at Indiana University Simon Cancer Center  (KTB) is the only repository of normal breast tissues donated by healthy women. As expected, a relatively small number of KTB donors (≈5%) diagnosed with breast cancer a few years post-donation. The specimens originally donated by these women (here labeled “susceptible normal tissue”) provide a window into the earliest phases of breast cancer development. Here, we investigated the transcriptomic changes in the histologically normal breast tissues donated by women 2-8 years prior to their diagnosis of breast cancer (mostly DCIS), as compared with breasts from age-matched healthy subjects.

overall_design: Fresh frozen breast tissues were obtained from the KTB and processed for DNA and RNA extraction. The DNA was then submitted to the Center for Genomics and Bioinformatics at IU Bloomington for whole transcriptome analysis. The study cohort includes 15 pre-diagnosis or suscpetible breast tissues and 15 breast tissue cores donated by age-matched healthy donors.

first: Rana

last: German

first: Ram

last: Podicheti

first: Douglas

middle: B

last: Rush

first: Jie

last: Huang

first: Anna

middle: V

last: Storniolo


title: Global genomic instability caused by reduced expression of DNA polymerase ε in yeast [DZP2-derived isolates]

city: Hangzhou

first: Daoqiong

last: Zheng

address: 866 Yuhangtang Road

institute: College of Life Sciences, Zhejiang University

summary:
Yeast Saccharomyces cerevisiae has been widely used as a model system for studying genome instability. Here, a heterozygous diploid S. cerevisiae strain DZP2 was generated to determine the genomic alterations induced by DNA polymerase ε. The expression of POL2 was regulated by the GAL1 promoter. In combination of a custom SNP microarray, the patterns of chromosomal instability induced by low Pol ε could be explored at a whole genome level in DZP2. Using this system, we found hundreds-fold higher rate of genomic alterations, including aneuploidy, loss of heterozygosity (LOH), and chromosomal rearrangement.
DNA polymerase ε (Pol ε) is one of the three replicative eukaryotic DNA polymerases. Pol ε deficiency leads to genomic instability and multiple human diseases. Here, we explored global genomic alterations in yeast strains with reduced expression of POL2, the gene that encodes the catalytic subunit of Pol ε. Using whole-genome SNP microarray and sequencing, we found that low levels of Pol ε elevated the rates of mitotic recombination and chromosomal aneuploidy by two orders of magnitude. Strikingly, low levels of Pol ε resulted in a contraction of the number of repeats in the rDNA cluster and reduced the length of telomeres. These short telomeres led to an elevated frequency of break-induced replication, resulting in terminal loss of heterozygosity. In addition, low levels of Pol ε increased the rate of single-base mutations by 13-fold by a Pol ζ-dependent pathway. Finally, the patterns of genomic alterations caused by low levels of Pol ε were different from those observed in strains with low levels of the other replicative DNA polymerases Pol α and Pol δ, providing further insights into the different roles of the B-family DNA polymerases in maintaining genomic stability.

overall_design: DZP2-derived isolates were grown on both HG (3% raffinose, 0.05% galactose) and LG (3% raffinose and 0.005% galactose) plates from a single cell to a colony (roughly 25 cell divisions) for two cycles, these independent colonies were purified on HG plates. Genomic DNA from independent DZP2-derived colonies was extracted and analyzed by the whole-genome microarrays.

first: Dao-Qiong

first: Thomas

middle: D

last: Petes


title: Global genomic instability caused by reduced expression of DNA polymerase ε in yeast [DZP2-derived sectored colonies]

overall_design: DZP2 cells were incubated in the absence of galactose (YPD medium) for 12 hours, and then the cells were plated on HGMAB6 plates to allow sectored colony formation. After incubation at 30°C for 3 days, genomic DNA from the red/white (crossover outcomes) and white/pink (BIR outcomes) sides of independent DZP2-derived sectored colonies was separately extracted and analyzed by the SNP-specific microarrays.


title: Calycosin as a novel PI3K activator reduces inflammation and fibrosis in heart failure through AKT-IKK/STAT3 axis

status: Public on Sep 27 2021

city: Beijing

first: Xiaoping

last: Wang

state: Beijing

address: No. 5, Dongdan Santiao, Dongcheng District, Beijing

institute: Peking Union Medical College

summary:
Aim: Inflammation and fibrosis have been shown to be critical factors in heart failure (HF) progression. Calycosin (Cal) is the major active component of Radix astragali and has been widely used to treat inflammation in clinical practice. However, whether Cal could ameliorate myocardial infarction (MI)-induced inflammation and fibrosis and precise mechanisms remain uncertain. The aim of this study is to explore the role of Cal in HF and to clarify the underlying mechanisms.
Methods: For in vivo experiments, rats underwent left anterior descending (LAD) artery ligation for HF model, and the cardioprotective effects of Cal were measured by echocardiographic assessment and histological examination. RNA-seq approach was applied to explore potential differential genes and pathways. For further mechanistic study, pro-inflammatory conditioned media (CM)-induced H9C2 cells injury model and TGFβ-stimulated cardiac fibroblasts model were applied to determine the regulatory mechanisms of Cal.
Results: In vivo experiment, echocardiography results showed that Cal significantly improved heart function. GO and Reactome enrichment revealed that inflammation and fibrosis pathway are involved in Cal-treated group. KEGG enrichment indicated that PI3K-AKT pathway is enriched in the Cal-treated group. Further experiments proved that Cal alleviated cardiomyocyte inflammatory responses evidenced by down-regulating the expressions of phosphorylated IκB kinase α/β (p-IKKα/β), phosphorylated nuclear factor kapa B (p-NFκB) and tumor necrosis factor α (TNFα). Besides, Cal effectively attenuated cardiac fibrosis through the inhibitions of expressions and depositions of collagen I and collagen III. In vitro experiments, the phosphatidylinositol 3 kinase (PI3K) inhibitor LY294002 could abrogate the anti-inflammation and anti-fibrosis therapeutic effects of Cal, demonstrating that the cardio-protective effects of Cal were mediated through upregulations of PI3K and serine/threonine kinase (AKT).
Conclusion: Cal improves cardiac function against HF by inhibiting cardiomyocytes inflammation and fibroblasts fibrosis via activation of the PI3K-AKT pathway.

overall_design: Cardiac mRNA profiles of  control rats, HF rats and Cal-treated rats

first: Weili

last: Li

first: Qian

last: Zhang

first: Yong


title: The circadian REV-ERB nuclear receptors are essential drivers of heart metabolism and function

status: Public on Sep 28 2021

city: Philadelphia

first: Chunjie

last: Jiang

state: PA

address: 3400 Civic Center Boulevard

department: Institute for Diabetes, Obesity, and Metabolism

institute: University of Pennsylvania

summary: The heart is a highly metabolic organ that uses multiple energy sources to meet its demand for ATP production. Diurnal feeding-fasting cycles result in substrate availability fluctuations which, together with increased energetic demand during the active period, impose a need for rhythmic cardiac metabolism. The nuclear receptors REV-ERBa and b are essential repressive components of the molecular circadian clock and major regulators of metabolism. To investigate their role in the heart, we generated mice with cardiomyocyte (CM)-specific deletion of both Rev-erbs, which died prematurely due to dilated cardiomyopathy. Loss of Rev-erbs markedly downregulated fatty acid oxidation genes prior to overt pathology, which was mediated by induction of the transcriptional repressor E4BP4, a direct target of cardiac REV-ERBs. E4BP4 directly controls circadian expression of Nampt and its biosynthetic product NAD+ via distal cis-regulatory elements. Thus, REV-ERB-mediated E4BP4 repression is required for Nampt expression and NAD+ production by the salvage pathway. Together, these results highlight the indispensable role of circadian REV-ERBs in cardiac gene expression, metabolic homeostasis and function.

overall_design: RNA-Sequencing was performed on 2-months-old control versus CM-RevDKO hearts, that were harvested at ZT10. H3K27ac Cut&Run was performed on isolated adult cardiomyocytes from control versus CM-RevDKO mice at ZT10. ChIP-Seq for HA-Rev-erba and E4BP4 was performed on biventricles of male mouse hearts (age 2 months), harvested at ZT10.

first: Pieterjan

last: Dierickx

first: Kun

last: Zhu


title: single cell RNAseq analysis of ILCs from TC-1 tumors

status: Public on Oct 03 2021

city: DIJON

first: François

last: Ghiringhelli

address: 1 rue du Professeur Marion

country: France

institute: UMR INSERM 1231

summary: study of Innate lymphoid cells from TC-1 tumors, 1,3 and 7 days after a cisplatin treatment (or PBS as control)

overall_design: study of ILCs from PBS or Cisplatin treated TC-1 tumors

first: Mélanie

last: Bruchard

first: Romain

last: Boidot

first: Caroline

last: Truntzer

first: Sandy

last: Chevrier

first: Elise

last: Ballot


title: m6A-seq analysis of Mettl3fl/fl (WT) and Mettl3fl/fl,LyzM-cre  (cKO) bone-marrow-derived macrophages(BMDMs) transcriptomes

first: Jia

last: Xiong

institute: Zhejiang University

summary: To investigate the role of RNA methyltransferase METTL3-mediated m6A modification in macrophage, we performed m6A-sequencing to map the m6A modification in bone-marrow-derived macrophages (BMDMs) from Mettl3fl/fl (WT) and Mettl3fl/fl,LyzM-cre  (cKO) mice

overall_design: m6A-seq analysis of Mettl3fl/fl (WT) and Mettl3fl/fl,LyzM-cre  (cKO) bone-marrow-derived macrophages (BMDMs) transcriptomes

first: Qingqing


title: CRISPR screens unveil signal hubs for nutrient licensing of T cell immunity

status: Public on Sep 26 2021

city: Memphis

first: Hongbo

last: Chi

state: TN

address: 262 Danny Thomas Place

department: Immunology

institute: St Jude Children's Research Hospital

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

overall_design: Refer to individual Series


title: Transcriptional adaptation to DNA replication stress induced by CCNE1 overexpression

city: Chapel Hill

first: Jeanette

last: Cook

state: North Carolina

address: 112 Founders Ridge Dr.

department: Biochemistry and Biophysics

institute: University of North Carolina at Chapel Hill

summary: We overproduced human cyclin E from a stably-integrated  inducible CCNE1 transgene in RPE1-hTERT cells over a period of weeks. CCNE1 overproduction induced replication stress, then slow proliferation, followed by adaptation to normal growth phenotype. We analyzed mRNA transcripts at key points of the timecourse: control, 2 days, 15-18 days, 39-51 days, and at a point several weeks after induction was withdrawn

overall_design: Retinal pigmented epithelial (RPE1-hTERT) mRNA profiles of CCNE1 overexpression in adaptation experiment over period of up to 51 days

first: Juanita

last: Limas

first: Amiee

last: Littlejohn

first: Amy

last: House

first: Katarzyna

last: Kedziora

first: Maria

last: Aleman

first: Daniel

last: Dominguez

middle: G


title: 2-DG protects mouse from DSS-induced inflammatory bowel disease

city: Tokyo

first: Ikuno

last: Uehara

address: 1-1-5 Sendagi, Bunkyo

institute: Nippon medical school

summary: Anti-proinflammatory cytokine therapies against interleukin (IL)-6 and tumor necrosis factor (TNF)-a are major advances in treating inflammatory diseases. We found that 2-deoxy-D-glucose (2-DG), a simple monosaccharide, attenuated IL-6 responses by inhibiting N-linked glycosylation of the IL-6 receptor gp130. Aglyco forms of gp130 failed to bind IL-6 and to activate downstream signals. 2-DG completely inhibited dextran sodium sulfate-induced inflammatory bowel disease that was partially dependent on IL-6.

overall_design: To understand the mechanism of DSS-induced colitis with or without 2-DG, we analysed the mRNA expression profiles of mouse colons from DSS-induced colitis with or without 2-DG . The RNeasy Mini Kit (Qiagen) was used to extract total RNA from mouse colons. For microarray, total RNA was extracted from five mock colons, five colons treated with 2% DSS drinking for 7days, five colons injected 10mg 2-DG for 7days,or five colons treated with 2% DSS drinking and injected 10mg 2-DG for 7days . TAKARA BIO (the company for biological technical service) performed the microarray analysis.

first: Mitsuko

last: Kajita

first: Atsuko

last: Tanimura

first: Shigeaki

last: Hida

first: Munehiko

last: Onda

first: Zenya

last: Naito

first: Shinsuke

last: Taki

first: Nobuyuki

last: Tanaka


title: Role of  NAMPT in liver gene expression in diabetic mice

status: Public on Sep 21 2021

city: St. Louis

first: Brian

last: DeBosch

state: Missouri

address: 660 South Euclid Avenue

department: Pediatrics and Cell Biology & Physiology

institute: Washington University School of Medicine

summary: We tested they hypothesis that hepatocyte NAMPT mediates transcriptomic changes in diabetic mice

overall_design: We overexpressed NAMPT or control vector via adenovirus delivery in db/db diabetic mice for 4-5wk and subjected liver tissue to high-throughput RNA sequencing


title: Fecal filtrate transfer protects against necrotizing enterocolitis in preterm pigs

city: Frederiksberg

first: Xiaoyu

last: Pan

address: Dyrlægevej 68

department: Department of Veterinary and Animal Sciences

country: Denmark

institute: University of Copenhagen

summary: Necrotizing enterocolitis (NEC) is an acute and life-threatening gastrointestinal disorder afflicting preterm infants, which is currently unpreventable. Fecal microbiota transplantation (FMT) is a promising preventative therapy, but potential bacterial infection  raise concern. Removal of bacteria from donor feces may reduce this risk  while maintaining the NEC-preventive effects. We aimed to assess preclinical efficacy and safety of bacteria-free fecal filtrate transfer (FFT). Using fecal material from healthy suckling piglets, we administered FMT rectally, or cognate FFT either rectally or oro-gastrically  to formula-fed preterm, cesarean-delivered piglets as a model for preterm infants, We compared gut pathology and related safety parameters with saline controls, and analyzed ileal mucosal transcriptome to gauge the host e response to FMT and FFT  treatments relative to control. Results showed that oro-gastric FFT prevented NEC, whereas FMT did not perform better than control. Moreover, FFT but not FMT reduced intestinal permeability, whereas FMT animals had reduced body weight increase and intestinal growth. Global gene expression of host mucosa responded to FMT but not FFT with increased and decreased bacterial and viral defense mechanisms, respectively. In conclusion, as preterm infants are extremely vulnerable to enteric bacterial infections, rational NEC-preventive strategies need incontestable safety profiles. Here we show in a clinically relevant animal model that FFT, as opposed to FMT, efficiently prevents NEC without any recognizable side effects. If translatable to preterm infants, this could lead to a change of practice and in turn a reduction in NEC burden.

overall_design: A total of 52 samples were analyzed. This included four groups of animals receiving fecal microbiota transplantation rectally (FMT, n=16), fecal filtrate transfer rectally (FFTr, n=12),  fecal filtrate transfer oro-gastrically (FFTo, n=12) or saline oro-gastrically and rectally as control (CON, n=12).

first: Anders

last: Brunse

first: Ling

last: Deng

first: Yan

last: Hui

first: Josué

last: Castro-Mejía

first: Witold

last: Kot

first: Duc

last: Nguyen

first: Jan

last: Secher

first: Dennis

last: Nielsen

first: Thomas

last: Thymann


title: Role of SIRT1 in NAMPT-induced liver gene expression

summary: We tested they hypothesis that hepatocyte SIRT1 mediates transcriptomic changes induced by hepatocyte-specific NAMPT overexpression

overall_design: We overexpressed NAMPT in western diet-fed WT and SIRT1 liver-specific knockout mice for 12wk and subjected liver tissue to high-throughput RNA sequencing


title: Whole transcriptome and methylome analysis of breast tissues prior to breast cancer diagnosis

first: Natascia

last: Marino


title: Whole methylome analysis of breast tissues prior to breast cancer diagnosis [methyl-capture]

summary: The Susan G. Komen Tissue Bank at Indiana University Simon Cancer Center  (KTB) is the only repository of normal breast tissues donated by healthy women. As expected, a relatively small number of KTB donors (≈5%) diagnosed with breast cancer a few years post-donation. The specimens originally donated by these women (here labeled “susceptible normal tissue”) provide a window into the earliest phases of breast cancer development. Here, we investigated the DNA metylation changes in the histologically normal breast tissues donated by women 2-8 years prior to their diagnosis of breast cancer (mostly DCIS), as compared with breasts from age-matched healthy subjects.

overall_design: Fresh frozen breast tissues were obtained from the KTB and processed for DNA and RNA extraction. The DNA was then submitted to the Center for Genomics and Bioinformatics at IU Bloomington for Methyl Capture methylome analysis. The study cohort includes 15 pre-diagnosis or suscpetible breast tissues and 15 breast tissue cores donated by age-matched healthy donors.

first: Rana

last: German

first: Ram

last: Podicheti

first: Douglas

last: Rush

first: Jie

last: Huang

first: Anna

last: Storniolo


title: RNA-sequencing of livers from p40-/-IL-2Rα-/- PBC mouse model and control.

status: Public on Sep 16 2021

first: Yafei

last: XU

address: Panyu Square, High Education Mega Center

institute: South China University of Technology

summary: We performed RNA sequencing of liver transcriptome from 12-week-old p40-/-IL-2Rα-/- (a mouse model of primary biliary cholangitis) and littermate p40-/-IL-2Ra+/- (control) mice.

overall_design: Liver samples were dissected from mice, flash frozen and stored at -80℃. Total RNA was extracted using RNAiso Plus Reagent (TaKaRa). There were 2 groups: 1) p40-/-IL-2Ra+/- (control); 2) p40-/-IL-2Rα-/-. There were 3 samples per group (Total samples = 6).

first: Ya-Fei

last: Xu

first: Yuan

last: Yao

first: Min

last: Ma

first: Liang

last: Li

first: Zhe-Xiong

last: Lian


title: Operation of the atypical canonical BMP signaling pathway during human odontogenesis

city: FuZhou

first: XIAOXIAO

last: HU

address: Qishan Branch

institute: Fujian Normal University

summary: BMP (bone morphogenetic protein) signaling plays essential roles in the regulation of early tooth development. It is well acknowledged that with binding of extracellular BMP ligands to the type I and type II transmembrane serine/threonine kinase receptor complexes when triggering of the BMP canonical signaling pathway, receptor activated Smad1/5/8 in cytoplasm bind to Smad4, the central mediator of the canonical BMP signaling pathway, to form transfer complexes for entering the nucleus and regulating target gene expression. However, our recent studies reveal the functional operation of a novel BMP mediated signaling pathway named as the atypical BMP canonical signaling pathway in mouse developing tooth, which is Smad1/5/8 dependent but Smad4 independent. In the current study, we investigated whether this atypical BMP canonical signaling is conserved in human odontogenesis. We showed that pSmad1/5/8 is required for expression of MSX1, a well-defined BMP signaling target gene, in human dental mesenchyme, but the typical BMP canonical signaling is indeed not operating in the early human developing tooth, as assessed by the absence of pSMAD1/5/8-SMAD4 complexes in the dental mesenchyme and expression of MSX1 and translocation of pSMAD1/5/8 induced by BMP4 protein is SMAD4-independent in dental mesenchymal cells. Moreover, RNA-Seq data sets comparing the transcriptome profiles of human dental mesenchymal cells with and without SMAD4 knockdown by siRNA displays unchanged expression profiles of pSMAD1/5/8 downstream target genes, further affirming the functional operation of the atypical canonical BMP signaling pathway in a manner of SMAD1/5/8-dependent but SMAD4-independent in the dental mesenchyme during early odontogenesis.

overall_design: Examination of mRNA level in with and without BMP4, DMSO, Dorsomorphin, and SMAD4 siRNA TREATED human dental mesenchymal cells.

first: Xiaoxiao

last: Hu

first: Yanding

last: Zhang

first: Xuefeng


title: Single Cell RNA Sequencing of Cultured Primary Tissue Cells.

city: München

first: Stefanie

last: Doppler

address: Lazarettstraße 36

department: Department of Cardiovascular Surgery

institute: German Heart Center Munich at the Technische Universität München

summary: Using a single cell-RNA sequencing protocol from 10xGenomics, we compared so called cardiosphere-derived cells (CDCs, established protocol) to the main non-myocyte cell types of the adult heart: cardiac fibroblasts (CFs), smooth muscle cells (SMCs) and endothelial cells (ECs). Herby, CDCs were disclosed as a heterogenic cell type with clear similarities to cardiac non-myocyte cell types, particularly to CFs and SMCs. Beyond a high proliferation capacity and upregulation of immune-related genes, CDCs exhibited a strong extracellular matrix synthesizing ability and also some angiogenic potential. Subsequently, infant patient derived CDCs were compared to adult CDCs, revealing that infant-CDC upregulated developmental and angiogenic processes. This study represents the first characterization of CDCs by sc-RNAseq and unravels their age-dependent molecular differences.

overall_design:
1) Comparison of adult primary cardiac cell types to unravel the identity of CDCs. 2) Comparison of adult CDC to infant patient derived CDC.
10x Genomics protocol was used

first: Palgit-Sarit

last: Kogan

first: Archana

last: Tomar


title: RNAseq data for EndoC-βH1 treated with CM from omental stromal cells cultured either in the absence or presence of TNF-α or differentiated into adipocytes

city: PARIS

first: Blandine

last: SECCO

address: PORT ROYAL

institute: INSERM

summary: We used an in vitro model to study the paracrine effect of stromal cells isolated from omental adipose tissue at different stages of differentiation and inflammation on the beta cell lines EndoC-βH1 through the use of conditioned media. We show that the expression of beta cells markers decreased and dedifferentiation markers increased when beta cells were cultured in conditioned medium derived from omental stromal cells. We report that stromal cells with a high pro-inflammatory profile had the most severe impact. By using RNAseq, we showed the stimulation of several signaling pathways such as STAT3, SMAD2 and RELA, as well as the downregulation of genes involved in lipogenesis and cholesterol synthesis.

overall_design: RNAseq on EndoC-βH1 cultured for 48h in CM prepared from stromal cells from 3 patients. CM was from omental stromal cells cultured in the absence (D0) or presence of TNF-α (D0TNFa) or differentiated into adipocytes (Ad). For the control medium (Ctr), EndoC-βH1 were used for the 48h incubation

first: Raphael

last: SCHARFMANN


title: RNA sequencing of genes expressed by  macrophages isolated from hearts control (cts), with compensated concentric hypertrophy (HCC) or with heart failure (IC)

status: Public on Sep 15 2021

first: Catherine

last: PAVOINE

address: 91 boulevard de l'hôpital

department: UMR ICAN 1166

institute: INSERM Sorbonne Université

summary: purpose: to use a transcriptomic approach (RNAseq) to compare control, HCC and IC macrophage gene expression.

overall_design: cardiac macrophages (CD14+/CD64+) sorted by FACS from mice implanted with saline (cts) or isoproterenol pumps (30mg/kg/day) for 14 days (HCC) or 28 days (IC).

last: Pavoine

first: Mathilde

last: Flamant


title: Multiple in vivo roles for the C-terminal domain of the RNA chaperone Hfq

status: Public on Sep 17 2021

city: Bethesda

first: Kumaran

last: Ramamurthi

state: MD

address: 37 Convent Drive

institute: National Cancer Institute

summary: Hfq, a bacterial RNA chaperone, stabilizes small regulatory RNAs (sRNAs) and facilitates sRNA base-pairing with target mRNAs. Hfq has a conserved N-terminal domain and a poorly conserved disordered C-terminal domain (CTD). In a transcriptome-wide examination of the effects of a chromosomal CTD deletion (Hfq1-65), the Escherichia coli mutant was most defective for the accumulation of sRNAs that bind the proximal and distal faces of Hfq (Class II sRNAs), but other sRNAs also were affected. There were only modest effects on the levels of mRNAs, suggesting little disruption of sRNA-dependent regulation. However, cells expressing Hfq lacking the CTD deletion in combination with a weak distal face mutation were defective for the function of the Class II sRNA ChiX and repression of mutS, both dependent upon distal face RNA binding. Loss of the region between amino acids 66-72 was critical for this defect. The CTD region beyond amino acid 72 was not necessary for distal face-dependent regulation, but was needed for functions associated with the Hfq rim, seen most clearly in combination with a rim mutant. Our results suggest that the C-terminus collaborates in various ways with different binding faces of Hfq, leading to distinct outcomes for individual sRNAs.

overall_design: Wild Type (WT) and Hfq65 (CTD deleted mutant) E.coli total RNA and RNA immunoprecipitated with Hfq were collected and sequenced with Illumina.  The experiments were duplicated.

first: Kumari

last: Kavita

first: Aixia

first: Chin-Hsien

last: Tai

first: Nadim

last: Majdalani

first: Gisela

last: Storz

first: Susan

last: Gottesman


title: Laser microdissection transcriptome data derived gene regulatory networks of developing rice endosperm revealed tissue- and stage-specific regulators modulating starch metabolism

status: Public on Sep 07 2021

city: Jeddah

first: Sabiha

last: Parween

address: Thuwal

department: Hirt lab

country: Saudi Arabia

institute: KAUST

summary: Gene expression of fine tissues of developing rice endosperm

overall_design: The single channels Agilent microarray expression data of 12 microdissected samples of AL, DSE, CSE and LSE at 7DAF and 12 DAF of three replicates were used for the study

first: Tsutomu

last: Ishimaru

first: Yuhi

last: Saito

first: Takehiro

last: Masumura

first: Motohiko

last: Kondo

first: Nese

last: Sreenivasulu


title: The protective role of hydrogen sulfide and its impact on gene expression profiling in rat model of COPD

status: Public on Sep 24 2021

first: Yahong

last: Chen

address: Haidian District, Huanyuan North Road, No49

institute: Peking University Third Hospital

summary: To investigate the role of H2S in Chronic obstructive pulmonary disease (COPD), a rat model of COPD was established by cigarette smoking (CS) and intratracheal instillation of lipopolysaccharide (LPS). Rats were randomly divided into 4 groups: Control, CS+LPS, CS+LPS+NaHS and CS+LPS+propargylglycine (PPG). Transcription profiling of lung tissue comparing Control with CS+LPS, CS+LPS with CS+LPS+NaHS, and CS+LPS with CS+LPS+PPG. The goal was to determine the impact of H2S on gene expression profiling in rat model of COPD.

overall_design: 4 groups, Control vs. CS+LPS; CS+LPS vs. CS+LPS+NaHS; CS+LPS vs. CS+LPS+PPG; each group has 3 replicates.

first: Yanjing

last: He

first: Yun

last: Sun

first: Chengcheng

last: Liao

first: Fan

last: Lin

first: Zhengyuan

last: Xia

first: Yongfen

last: Qi


title: The schizophrenia-associated variant in SLC39A8 alters N-glycosylation in the mouse brain

status: Public on Sep 23 2021

first: Robert

last: Mealer

state: NC

address: 120 Mason Farm Road, 5023F

summary: In this experiment we performed RNAseq from two different bran regions of wild-type and mice containing the A391T missense mutation in SLC39A8.

overall_design: RNAseq was performed on 4 wild-type cortex, 4 wild-type cerebellum, 4 A391T cortex, and 4 A391T cerebellum

first: Murat

last: Cetinbas

first: Ruslan

last: Sadreyev

first: Richard

last: Cummings


title: Transcriptomic study of heart tissue from diabetic cardiomyopathy mice

first: Xin

last: Huang

state: Zhejiang

address: 88 Jiefang Road

summary: To explore the key genes involved in spontaneous diabetic cardiomyopathy, db/db and BKS mice were used to examine the differently expressed genes in the related progresses. Briely, the heart transcriptome of db/db and BKS mice was correlated with the heart function, cardiomyocyte ultrastructure and histopathology characters.

overall_design: Two murine strains with C57BL/6 background were used in this study. Db/db group was used as the spontaneous diabetic cardiomyopathy group, and the BKS group was used as the healthy control group. Both groups of mice were housed under standard conditions with food and water provided without limitation and maintained on a 12 hour light/12 hour dark cycle. Body weight and food consumption were recorded every other day.

first: Kunkai

last: Su


title: Follicular helper-like T cells in the lung highlight a novel role of B cells in sarcoidosis

city: Berlin

first: Pawel

last: Durek

address: Charitéplatz 1

institute: Deutsches Rheuma-Forschungszentrum

summary: Effector/memory T cells were sorted from sarcoidosis patient's bronchoalveolar lavage (BAL) and peripheral blood (PBMC) as well as healthy donor peripheral blood and tonsil. RNA-sequencing was performed to assess their global phenotype. Total number of samples: 15.

overall_design: T cells from BAL (4 samples), tonsil (2 samples) and PBMC (3 patients and 3 healthy donor controls) were sorted on an ARIA II flow sorter (Becton Dickinson) as DAPI- CD14- CD16- CD19- CD3+ CD4+ CD45RA- CD45RO+. Tonsillar T cell were further sorted for CXCR5/PD-1 double-positive or -negative to discriminate Tfh and non-Tfh cells. RNA was isolated using a Qiagen (Hilden, Germany) RNeasy Micro Kit.

first: Laura

last: Bauer

first: Lisa

last: Müller

first: Sarah

last: Volkers

first: Frederik

last: Heinrich

first: Mir-Farzin

last: Mashreghi

first: Clemens

last: Ruppert

first: Leif

last: Sander

first: Andreas

last: Hutloff


title: Prolonged blue light exposure mimics age-dependent gene expression changes in   white eyed Drosophila photoreceptors

status: Public on Sep 22 2021

city: West Lafayette

first: Vikki

last: Weake

state: Indiana

address: 175 S University St

department: Biochemistry

institute: Purdue University

summary: Purpose: The goal of this study was to identify the differential expressed genes in Drosophila photoreceptors with age or upon blue lgiht exposure.

overall_design: Method: RNA extracted from immunoenriched Drosophila photoreceptor nuclei from aged D5, D15 or D30 and D5 3h, D5 5h, or D5 8h blue light exposed flies was used to generate cDNA libraries using Universal Plus™ Total RNA-Seq (Tecan) . Samples were sequenced using the Ilumina HiSeq4000 platform (three biological replicates per age or conditon: D5, D15, D30, D5 3h, D5 5h, D5 8h)

first: Spencer

last: Escobedo


title: Smarca4 inactivation promotes lineage-specific transformation and early metastatic features in the lung [scATAC-seq]

city: Cambridge

first: Carla

last: Concepcion

state: MA

address: 500 Main Street, 76-431

department: Koch Institute

institute: MIT

summary: SMARCA4 (BRG1) encodes for one of two mutually-exclusive ATPases present in SWI/SNF chromatin remodeling complexes, and is among the most frequently mutated genes in human lung adenocarcinoma. Despite its prevalence, the functional consequences of SMARCA4 alterations on lung cancer initiation and progression remain poorly understood. Using genetically engineered mouse models, patient-derived xenografts, and single-cell epigenomic profiling, we demonstrate that loss of Smarca4 sensitizes CCSP+ cells within the lung to malignant transformation and tumor progression, resulting in highly advanced dedifferentiated tumors and increased metastatic incidence. Consistent with these phenotypes, Smarca4-deficient tumors lack lung lineage transcription factor activities and instead show activation of embryonic stem cell-like programs, resembling a metastatic cell state. Thus, the SWI/SNF complex – via Smarca4 – acts as a gatekeeper for lineage-specific cellular transformation and metastasis during lung cancer evolution.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Single-cell ATAC-seq on isolated cancer cells from murine lung adenocarcinoma models of Smarca4 loss

first: Tyler

last: Jacks


title: High throughput sequencing data of ovarian hyperstimulation syndrome (OHSS) mouse model

status: Public on Sep 05 2021

city: Shanghai

first: Wenzhi

last: LI

address: No. 639, Zhizaoju Road, Huangpu District, Shanghai, China

department: Department of Assisted Reproduction

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

summary: We found that in the mouse OHSS model, certain drug treatment can improve the symptoms of OHSS. The results of high-throughput sequencing showed that the cell connection between ovarian vessels was strengthened.

overall_design: The ovarian gene expression of OHSS mice treated with different drugs was detected

first: Shutian

last: JIANG


title: Gene expression analysis in canine pemphigus

status: Public on Sep 20 2021

city: North Grafton

first: Jillian

last: Richmond

state: Massachusetts

address: 200 Westboro Road

department: Comparative Pathobiology

institute: Tufts Cummings School of Veterinary Medicine

summary: We performed a comparative immunology case study of client-owned dogs to determine if immune and skin gene expression profiles in spontaneous canine pemphigus mirror those observed in human pemphigus

overall_design: Gene expression was analyzed using 160 custom Nanostring probes to analyze 4 canines with Pemphigus compared to 5 healthy controls (leg margin excisions).

first: Nicholas

last: Robinson


title: Calibration data EPIC array: Mouse and Rat

status: Public on Aug 27 2021

city: Los Angeles

first: Steve

last: Horvath

state: CA

address: 695 Charles E. Young Drive South, Box 708822

department: Human Genetics

institute: University of California, Los Angeles

summary:
Illumina Infinium HumanMethylation850 BeadChip  (also known as Illumina EPIC array, GPL23976)   was used to generate DNA methylation data from synthetic DNA from 3 species.
The DNA samples from each species were enzymatically manipulated so that they would exhibit 0%, 25%, 50%, 75% and 100% percent methylation at each CpG location, respectively. The variable “ProportionMethylated” (with ordinal values 0, 0.25, 0.5, 0.75, 1) can be interpreted as a benchmark for each CpG that maps to the respective genome. Thus, the DNA methylation levels of each CpG are expected to have a high positive correlation with ProportionMethylated across the arrays measurement for the human species. The human EPIC array was applied to calibration data from mouse (n=15 EPIC arrays, 3 per methylation level) and rat (n=10, 2 per methylation level). The EPIC array data were normalized using the noob method (R function preprocessNoob in minfi).

sample_organism:
Homo sapiens
Mus musculus
Rattus norvegicus

overall_design: N=28 tissue samples from artifical/synthetic DNA from species. Genome annotations of the array can be downloaded from https://github.com/shorvath/MammalianMethylationConsortium


title: Cohesin core complex gene dosage contributes to germinal center derived lymphoma phenotypes and outcomes [HiC]

status: Public on Sep 01 2021

city: Braunschweig

last: Kloetgen

state: NI

address: Inhoffenstr 7

department: Department for Computational Biology of Infection Research

institute: Helmholtz Centre for Infection Research

summary: The cohesin complex plays critical roles in genomic stability and gene expression through effects on 3D architecture. Cohesin core subunit genes are mutated across a wide cross-section of cancers, but not in germinal center (GC) derived lymphomas. In spite of this, haploinsufficiency of cohesin ATPase subunit Smc3 was shown to contribute to malignant transformation of GC B-cells in mice. Herein we explored potential mechanisms and clinical relevance of Smc3 deficiency in GC lymphomagenesis. Transcriptional profiling of Smc3 deficient murine lymphomas revealed downregulation of genes repressed by loss of epigenetic tumor suppressors Tet2 and Kmt2d. Profiling 3D chromosomal interactions in lymphomas revealed impaired enhancer-promoter interactions affecting genes like Tet2, which was aberrantly downregulated in Smc3 deficient lymphomas. Tet2 plays important roles in B-cell exit from the GC reaction, and single cell RNA-seq profiles and phenotypic trajectory analysis in Smc3 mutant mice revealed a specific defect in commitment to the final steps of plasma cell differentiation. Although Smc3 deficiency resulted in structural abnormalities in GC B-cells, there was no increase of somatic mutations or structural variants in Smc3 haploinsufficient lymphomas, suggesting that cohesin deficiency largely induces lymphomas through disruption of enhancer-promoter interactions of terminal differentiation and tumor suppressor genes. Strikingly, the presence of the Smc3 deficient GC B-cell transcriptional signature in human patients with GC-derived diffuse large B-cell lymphoma (DLBCL) was linked to inferior clinical outcome and low expression of cohesin core subunits. Reciprocally, reduced expression of cohesin subunits was an independent risk factor for worse survival int DLBCL patient cohorts. Collectively, the data suggest that Smc3 functions as a bona fide tumor suppressor for lymphomas through non-genetic mechanisms, and drives disease by disrupting the commitment of GC B-cells to the plasma cell fate.

overall_design: HiC was performed using the in situ Hi-C protocol as per Rao et al., Cell 2017.

first: Martin

last: Rivas

first: Ari

last: Melnick


title: Vitamin B6 metabolism determines T cell anti-tumor responses

status: Public on Aug 31 2021

first: David

last: Bargiela

address: 4, 7 Downing Pl

country: United Kingdom

institute: University of Cambridge

summary: Targeting T cell metabolism is an established method of immunomodulation. Following activation, T cells engage distinct metabolic programs leading to the uptake and processing of nutrients that determine cell proliferation and differentiation. Redirection of T cell fate by modulation of these metabolic programs has been shown to boost or suppress immune responses in vitro and in vivo.   Using publicly available T cell transcriptomic and proteomic datasets we identified vitamin B6-dependent transaminases as key metabolic enzymes driving T cell activation and differentiation. Inhibition of vitamin B6 metabolism using the pyridoxal 5’-phosphate (PLP) inhibitor, aminoxyacetic acid (AOA), suppresses CD8+ T cell proliferation and effector differentiation in a dose-dependent manner. We show that pyridoxal phosphate phosphatase (PDXP), a negative regulator of intracellular vitamin B6 levels, is under the control of the hypoxia-inducible transcription factor (HIF1), a central driver of T cell metabolism. Furthermore, by adoptive transfer of CD8 T cells into a C57BL/6 mouse melanoma model, we demonstrate the requirement for vitamin B6-dependent enzyme activity in mediating effective anti-tumor responses.  Our findings show that vitamin B6 metabolism is required for CD8+ T cell proliferation and effector differentiation in vitro and in vivo. Targeting vitamin B6 metabolism may therefore serve as an immunodulatory strategy to improve anti-tumor immunotherapy.

overall_design: RNA expression was measured by RNA-Seq at day 7 following activation of MACS-sorted mouse CD8+ T cells using anti-CD3/anti-CD28 Dynabeads in the presence of 100 units/ml recombinant human IL-2 and either vehicle or 0.25mM aminoxyacetic acid (AOA).

first: Pedro

middle: P

last: Cunha

last: Velica

first: Iosifina

last: Foskolou

first: Laura

last: Barbieri

first: Helene

last: Rundqvist

first: Randall

last: Johnson


title: Cohesin core complex gene dosage contributes to germinal center derived lymphoma phenotypes and outcomes

city: New York City

first: Christopher

middle: Russell

last: Chin

state: NY

address: 413 E 69th Street, Belfer Building, BB-1462

institute: Weill Cornell

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

overall_design: Refer to individual Series


title: Calibration data mammalian array: Human, Mouse, Rat

summary:
An Infinium microarray platform (GPL28271, HorvathMammalMethylChip40) was used to generate DNA methylation data from synthetic DNA from 3 species.
The DNA samples from each species were enzymatically manipulated so that they would exhibit 0%, 25%, 50%, 75% and 100% percent methylation at each CpG location, respectively. The variable “ProportionMethylated” (with ordinal values 0, 0.25, 0.5, 0.75, 1) can be interpreted as a benchmark for each CpG that maps to the respective genome. Thus, the DNA methylation levels of each CpG are expected to have a high positive correlation with ProportionMethylated across the arrays measurement from a given species. The mammalian array was applied to synthetic DNA data from 3 species: human (n=10 mammalian arrays, 2 per methylation level), mouse (n=20, 4 per methylation level), and rat (n=15, 3 per methylation level).

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus

overall_design: N=45 tissue samples from artifical/synthetic DNA from species. Genome annotations of the array can be downloaded from https://github.com/shorvath/MammalianMethylationConsortium


title: Role of hepatocyte NAMPT in fasting-induced liver gene expression

first: Brian

last: DeBosch

address: 660 South Euclid Avenue

institute: Washington University School of Medicine

summary: We tested they hypothesis that hepatocyte NAMPT mediates transcriptomic changes induced by fasting

overall_design: We subjected wild-type and mice lacking liver-specific  NAMPT to fasting 24h or 22hr fast-refeed 2hrs


title: Transcriptome analysis of polymorphic p53 codon 72 under genotoxic stress

status: Public on Sep 10 2021

city: Daejeon

first: Sang-Min

last: Park

address: Youseong-Daero

department: College of Pharmacy

institute: Chungnam National University

summary: We report the transcriptome data produced from isogenic polymorphic p53 codon 72 iPSCs under doxorubicin treatment. By inserting BAC DNA into one allele of the heterozygous polymorphic p53 codon 72, each clone expressed a p53 protein encoding P72 or R72 from another allele in which it was not inserted. The transcriptional regulation of p53 target genes was compared between the isogenic lines under doxorubicin treatment.

overall_design: One set of RNA seq data was prepared from P72, R72 or p53 null human iPSCs under 0.2 μM doxorubicin treatement for 2 or 4 hrs.

first: Bu-Yeo

last: Kim

first: Seo-Young

last: Lee

first: Sun-Ku

last: Chung


title: Inhibition of Bromodomain and Extra Terminal (BET) domain activity modulates the IL-23R/IL17 axis and suppresses acute Graft-Versus-Host Disease [ChIP-seq]

status: Public on Sep 12 2021

city: Columbus

first: Parvathi

last: Ranganathan

state: Ohio

address: 460 W 12th Ave, BRT 420

department: Hematology

institute: The Ohio State Univeristy

summary: Acute graft-versus-host disease (GVHD) is the major cause of non-relapse mortality post-allogeneic stem cell transplantation. The majority of patients non-responsive to front line treatment with steroids have an estimated overall 2-year survival rate of only 10%. Treatment options for steroid-refractory acute GVHD are limited. Bromodomain and Extraterminal Domain (BET) inhibitors PLX51107 and PLX2853, deemed safe in human clinical trials in high risk malignancies, significantly downregulate pro-inflammatory Th1 and Th17 responses without impacting T regulatory cells, improving survival in murine models of acute GVHD while retaining beneficial graft-versus-leukemia effects.  Modulation of the IL23/STAT3 axis via BET inhibition resulted in a reduction of pathogenic Th1/Th17 cells in the spleen and acute GVHD target organs such as the gastrointestinal tract.  Based on our preclinical data presented here, PLX51107 will enter clinical trial for refractory acute GVHD in a Phase 1 safety, biological efficacy trial.

overall_design: 6 samples; 3 control (DMSO) vs. 3 treated (PLX2)

first: Katiri

last: Snyder

first: Lotus

last: Neidemire-Colley

first: Hannah

middle: K

last: Choe


title: Ulcerative Colitis is characterized by an intense and plasmablast skewed humoral response that associates with treatment resistance and disease complications

status: Public on Aug 24 2021

city: New York

first: Darwin

last: D'Souza

address: 1470 Madison Avenue

department: ImmunoBio

institute: Human Immune Monitoring Center

summary: B cells, critical for intestinal homeostasis, remain under-studied in ulcerative colitis (UC). Using single-cell RNA sequencing, single cell IgH gene sequencing, and protein-level validation across three large UC cohorts, we mapped the cellular and clonotypic landscape of mucosal and circulating B cells in UC. We found major perturbations within the mucosal B cell compartment, including an expansion of naïve B cells and IgG+ plasma cells (PC) with curtailed diversity and maturation. Furthermore, we isolated an autoreactive plasma cell clone from inflamed UC intestines. We also identified a subset of intestinal CXCL13-expressing T follicular helper cells that were associated with the pathogenic B cell response. Finally, across three distinct cohorts, we confirmed that changes in intestinal humoral immunity are reflected in circulation by the expansion of gut-homing plasmablasts that associate with disease activity and predict disease complications. Our data demonstrate a highly dysregulated B cell response in UC and revisit the role of B cells in disease pathogenesis.

overall_design:
Single cell RNA sequencing was performed on cells extracted from colonic biopsies of inflamed mucosa (ulcerative colitis patients, n=5) and normal colonic mucosa (healthy controls, n=4)

Please note that sample titles have been updated on Sep 21, 2021.

first: Effi

last: Kenigsberg

first: Jerome

last: Martin

first: Saurabh

last: Mehandru

first: Mathieu

last: Uzzan


title: Resident stroma recruits myeloid-derived suppressor cells via CCL2/CCR2 axis in oral squamous cell carcinoma

status: Public on Aug 18 2021

city: Okayama

first: Hotaka

last: Kawai

state: Okayama

address: Shikata

department: Oral pathology and medicine

institute: Okayama University

summary: In the tumour microenvironment (TME), stroma components play a vital role in tumour development. Myeloid-derived suppressor cells (MDSC) recruited by tumour cells in TME support tumour development. However, the influence of stroma on MDSC is unclear. Here we aimed to unveil the roles of stroma in the recruitment of MDSC in oral squamous cell carcinoma (OSCC). We created xenograft OSCC models on GFP+ bone marrow transplanted nude mice. We co-xenografted human OSCC cells line (HSC-2) with three different types of stromal cells, including human dermal fibroblasts (HDF) or patient-derived stromal cells (PDS1 and PDS2) isolated from two OSCC patients, or without stromal cells. Tumour/stroma co-xenograft models recruited significantly higher numbers of GFP+ bone marrow (BM) cells than the tumour cells alone xenografted group. However, only patient-derived stroma xenograft (PDSX) models promoted GR1/CD11b/Arg1 triple-positive MDSC, which was the main population influenced by stromal character and depended on the stroma secreted CCL2. In vitro inhibition of CCL2 synthesis in PDS cocultures also resulted in significantly decreased migration of BM cells than in HDF coculture and HSC-2 alone culture. Moreover, CCR2+ MDSC infiltrated considerably higher in PDSX models. Taken together, we demonstrated that stromal cells are responsible for MDSC recruitment and stroma secreted CCL2 play an essential role in MDSC recruitment in OSCC.

overall_design: To analyse the gene expression of patient-derived stromal cells (PDS)  in OSCC, we collected the PDS from two OSCC patients and named as PDS1 and PDS2. Gene expression of PDS1 and PDS2 were analysed by comparing with HDF.

first: Kiyofumi

last: Takabatake

first: Keisuke

last: Nakano

first: Hitoshi

last: Nagatsuka


title: Smarca4 inactivation promotes lineage-specific transformation and early metastatic features in the lung [RNA-seq]

first: Carla

last: Concepcion

summary: SMARCA4 (BRG1) encodes for one of two mutually-exclusive ATPases present in mammalian SWI/SNF chromatin remodeling complexes, and is among the most frequently mutated genes in human lung adenocarcinoma. Despite its prevalence, the functional consequences of SMARCA4 mutation on tumor initiation, progression and chromatin regulation in lung cancer remains poorly understood. Using genetically engineered mouse models, patient-derived xenografts, and single-cell epigenomic profiling, we demonstrate that loss of Smarca4 sensitizes CCSP+ cells within the lung in a cell-type dependent fashion to malignant transformation and tumor progression, resulting in highly advanced dedifferentiated tumors and increased metastatic incidence. Consistent with these phenotypes, Smarca4-deficient primary tumors lack lung lineage transcription factor activities and instead show hyper-activation of embryonic stem cell-like programs, resembling a metastatic cell state. Mechanistically, we show that all three classes of SWI/SNF complexes are unable to bind and open chromatin at distinct regulatory regions in the absence of SMARCA4, thereby preventing lineage factors from binding to their targets and maintaining cell identity – ultimately accelerating tumor progression. Thus, the SWI/SNF complex – via Smarca4 – acts as a gatekeeper for lineage-specific cellular transformation and metastasis during lung cancer evolution.

overall_design: Isogenic pairs of murine KrasG12D/+;Trp53-/- lung adenocarcinoma cell lines harboring intact Smarca4 or loss-of-function Smarca4 mutations generated by CRISPR in vitro. Biological replicates were generated from two independent tumor-derived parental cell lines

first: Sai

last: Ma

first: Lindsay

last: LaFave

first: Arjun

last: Bhutkar

first: Manyuan

last: Liu

first: Lydia

last: DeAngelo

first: Jonathan

middle: Y

first: Isabella

last: Del Priore

first: Adam

last: Schoenfeld

first: Vinay

last: Kartha

first: Peter

last: Westcott

first: Francisco

last: Sánchez-Rivera

first: Kevin

last: Meli

first: Manav

last: Gupta

first: Gregory

last: Riely

first: Natasha

last: Rekhtman

first: Charles

last: Rudin

middle: F

first: Aviv

last: Regev

first: Jason

last: Buenrostro

first: Tyler

last: Jacks


title: Evaluation of comprehensive gene expression and NK cell-mediated killing in glioblastoma cell line-derived spheroids

status: Public on Aug 19 2021

city: Kashihara

first: Takayuki

last: Morimoto

state: Nara prefecture

address: 840 Shijo-Cho

department: Department of Neurosurgery

institute: Nara Medical University


title: Smarca4 inactivation promotes lineage-specific transformation and early metastatic features in the lung [ATAC-seq]

first: Carla

last: Concepcion

first: Sai

last: Ma

first: Lindsay

last: LaFave

first: Arjun

last: Bhutkar

first: Manyuan

last: Kim


title: Transcriptome datasets of neural progenitors and neurons differentiated from induced pluripotent stem cells of healthy donors and Parkinson's disease patients with mutations in PARK2 gene

city: Boston

first: Ksenia

middle: S

last: Anufrieva

address: 60 Fenwood Rd

institute: Brigham and Women's Hospital

summary: Parkinson's disease (PD) is a complex systemic disease caused by neurodegenerative processes in the brain, in which the death of dopaminergic neurons (DN) of the substantia nigra is primarily noted. 50% of cases of familial PD are associated with mutations in the PARK2 gene. Induced pluripotent stem cells (iPSCs) and their neuronal derivatives are powerful tool for disease modeling. Here, we presented the transcriptome profiles for neural progenitors (NP) and neurons, presumably DN, differentiated from iPSC lines of healthy donors and PARK2 mutations-associated PD patients generated on an NextSeq 500 System (Illumina). A comparative transcriptome analysis of neuronal derivatives of healthy donors and patients with PD will allow determining the contribution of mutations of the PARK2 gene to PD pathogenesis upon neuronal differentiation.

overall_design: iPSCs from three healthy donors and from three PD patients, carrying the different mutations in PARK2 gene, were differentiated into uncommitted neural progenitors and then into dopaminergic neurons. Transcriptome profiles for the obtained samples were generated using NextSeq 500 System

first: Valentina

last: Nenasheva

first: Ekaterina

last: Novosadova


title: Single-cell sequencing unveils the heterogeneity of nonimmune cells in chronic apical periodontitis

city: Guangzhou

first: XInwei

last: Lin

address: No. 135, Xingang Xi Road, Guangzhou, 510275, P. R. China

department: Stomatology

institute: Sun Yat-sen University

summary: Chronic apical periodontitis (CAP) is a unique dynamic interaction between microbial invasions and host defense mechanisms, resulting in bone absorption, infiltration of immune cells and sporadic periapical granuloma. In this study, we constituted a single-cell atlas for 26,737 high-quality cells from hyperplastic periapical tissue using single-cell RNA sequencing. Identifying cell types and signatures at the single-cell level might generate novel insights into the clinical pathogenesis of CAP. A histological analysis to verify the gene signatures of nonimmune cells was combined with immunohistochemistry staining. We then discovered the diversity and heterogeneity of nonimmune cells in regional CAP lesions. The temporal profiling of genomic alterations from common CAP to typical periapical granuloma provided predictions for key transcription factors and biological processes. Our study also inferred that the marked shift of inflammatory cytokines, chemokines, proteases and growth factors enables the initiation of polymorphic cell differentiation, lymphangiogenesis and angiogenesis during CAP.

overall_design: Three samples from extracted residual molars with chronic apical periodontitis

first: Zhongchun

last: Tong

first: Xinwei

first: Qimei

last: Gong

first: Danlu

last: Chi

first: Qingzhen

last: Meng


title: Development  depression-associated ncRNA biomarkers research

status: Public on Aug 17 2021

first: Ting

last: Zhou

address: No.6600, Nanfeng highway, Fengxian District

institute: Fengxian Hospital, Southern Medical University

summary: we profiled whole transcriptome in depression patients’ and healthy volunteers blood samples via microarray analysis.Differentially expressed circRNAs, lncRNAs and mRNAs were selected for deep analysis. Especially the Differentially expressed genes that associated with cancer

overall_design: Peripheral venous blood sample was collected from six depression patients’ and healthy volunteers respectively, SBC Human (4*180K) ceRNA gene chip was used for CircRNA, lncRNA, Mrna microarray analysis

first: Feng

last: Xu


title: Integrative Proteome, Transcriptome and DNA Methylome Analysis of Regulatory Networks During U937-derived Macrophage Polarization from an M2 to M1 Phenotype

city: Nanning

first: Lequn

last: Li

state: Guangxi

address: Department of Hepatobiliary Surgery, Affiliated Tumor Hospital of Guangxi Medical University, He Di Rd #71

institute: Guangxi Medical University


title: A nitrogen source-regulated microprotein confers an alternative mechanism of G1/S transcriptional activation in budding yeast

status: Public on Aug 25 2021

city: Toronto

first: Micheal

last: Tyers

state: Ontario

address: 555 University Avenue

institute: The Hospital for Sick Children

summary: Commitment to cell division at the end of G1 phase, termed Start in the budding yeast Saccharomyces cerevisiae, is strongly influenced by nutrient availability. To identify new dominant activators of Start that might operate under different nutrient conditions, we screened a genome-wide ORF overexpression library for genes that bypass a Start arrest caused by absence of the G1 cyclin Cln3 and the transcriptional activator Bck2. We recovered a hypothetical gene YLR053c, renamed NRS1 for Nitrogen-Responsive Start regulator 1, which encodes a poorly characterized 108 amino acid microprotein. Endogenous Nrs1 was nuclear-localized, restricted to poor nitrogen conditions, induced upon mTORC1 inhibition, and cell cycle-regulated with a peak at Start. NRS1 interacted genetically with SWI4 and SWI6, which encode subunits of the main G1/S transcription factor complex SBF. Correspondingly, Nrs1 physically interacted with Swi4 and Swi6 and was localized to G1/S promoter DNA. Nrs1 exhibited inherent transactivation activity and fusion of Nrs1 to the SBF inhibitor Whi5 was sufficient to suppress other Start defects. Nrs1 appears to be a recently evolved microprotein that rewires the G1/S transcriptional machinery under poor nutrient conditions.

overall_design: RNA-seq analysis of galactose-induced NRS1/YLR053C overexpression in S. cerevisiae.

first: Sylvain

last: Tollis

first: Jaspal

last: Singh

first: Yogitha

last: Thattikota

first: Roger

last: Palou

first: Xiaojing

last: Tang

first: Ghada

last: Ghazal

first: Deborah

last: Blake

first: Susan

last: Moore

first: Jasmin

last: Coulombe-Huntington

first: Éric

last: Bonneil

first: Catherine

last: Royer

first: Pierre

last: Thibault

first: Mike


title: Regulation of translation by site-specific ribosomal RNA methylation [RNA-Seq]

status: Public on Aug 16 2021

city: Copenhagen

first: Anders

middle: Henrik

last: Lund

address: Ole Maaløes Vej 5

institute: University of Copenhagen,BRIC

summary: We report that 2’-O-methylation levels at subset of positions in human ribosomal RNA are variable between cell types and conditions, and that the degree of methylation at distinct sites is responsive to key cellular pathways. MYC overexpression results in increased methylation at a particular rRNA site (18S:C174). We find that this methylation is important for modulating translation of distinct mRNAs, leading to phenotypic changes including modulation of cell proliferation rate.

overall_design:
Ribosome profiling of HelaS3 and HelaS3-SNORD45C knockout cells. HelaS3 cells have rRNA 18S:Cm174 methylation whereas HelaS3-SNORD45C knockout cells cells do not have 18S:Cm174 methylation.

Please note that each processed data was generated from all replicates and is linked to the corresponding *_1 sample records.

first: Martin

last: Jansson

first: Kübra

last: Altinel

middle: H


title: Development  depression-associated miRNA biomarkers research

first: Ting

last: Zhou

summary: we profiled whole transcriptome in depression patients’ and healthy volunteers blood samples via microarray analysis.Differentially expressed miRNAs were selected for deep analysis. Especially the Differentially expressed genes that associated with cancer

overall_design: Peripheral venous blood sample was collected from six depression patients’ and healthy volunteers respectively, Agilent human miRNA, Release 21.0 (8*60K, Design ID:070156) microRNA Array was used for miRNA microarray analysis.

first: Feng

last: Xu