title: TIPARP is involved in the regulation of intraocular pressure

city: Shanghai

first: Youjia

last: Zhang

address: 83 Fenyang Road

institute: Eye & ENT Hospital

summary: Elevated intraocular pressure (IOP) is the major risk factor for glaucoma. The molecular mechanism of elevated IOP is unclear, which impedes glaucoma therapy. 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD)-inducible Poly-ADP-ribose Polymerase (TIPARP), a member of the PARP family, catalyses mono-ADP-ribosylation. Here we showed that TIPARP was widely expressed in the cornea, trabecular meshwork, iris, retina, optic nerve, sclera, and choroid of human eyes. The expression of TIPARP was significantly upregulated in the blood and trabecular meshwork of patients with primary open angle glaucoma compared with that of healthy controls. Transcriptome analysis revealed that the expression of genes related to extracellular matrix deposition and cell adhesion was decreased in TIPARP-upregulated human trabecular meshwork (HTM) cells. Moreover, western blot analysis showed that collagen types I and IV, fibronectin, and α-SMA were increased in TIPARP downregulated or TIPARP-inhibited HTM cells. In addition, cross-linked actin networks were produced, and vinculin was upregulated in these cells. Subconjunctival injection of the TIPARP inhibitor RBN-2397 increased the IOP in Sprague–Dawley rats. Therefore, we identified TIPARP as a regulator of IOP through modulation of extracellular matrix and cell cytoskeleton proteins in HTM cells. These results indicate that TIPARP is a potential therapeutic target for ocular hypertension and glaucoma.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for human trabecular meshwork cells and its TIPARP-upregulated derivatives. Human trabecular meshwork cells were transduced with lentivirus-GFP-TIPARP to upregulate the expression of TIPARP. Lentivirus-GFP was used as a control. Each group has three replacates.

first: Maomao

last: Song

first: Yingwen

last: Bi

first: Yuan

last: Lei

first: Xinghuai

last: Sun

first: Yuhong

last: Chen


title: Skin transcriptomic analysis of rainbow trout infected with infectious hematopoietic necrosis virus

status: Public on Dec 28 2022

city: Lanzhou City

first: lu

last: zhao

state: Gansu Province

address: Yintan Road Street

country: China

institute: Gansu Agricultural University

type: Expression profiling by high throughput sequencing

summary: Rainbow trout (Oncorhynchus mykiss), an economically important cold-water fish cultured worldwide, suffers from infectious hematopoietic necrosis virus (IHNV) infection, resulting in huge financial losses. In order to understand the immune response of rainbow trout during virus infection, we explored trout skin transcriptome profiles following IHNV challenge, and identified 6905 differentially expressed genes (DEGs). Transcriptome analysis revealed numerous DEGs involved in immune responses, such as NOD1, NLRC3, NLRC5, TLR3, TLR7/8, TRIM25, DHX58, IFIH1, IRF3/7, STAT1, TRAF3, MX1 and HSP90A1. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analyses showed that DEGs were significantly enriched in various immune-related terms including immune system process, innate immune response and regulation of immune effector process and pathways of cytokine-cytokine receptor interactions, NOD-like receptor signaling, RIG-I-like receptor signaling, Toll-like receptor signaling, JAK-STAT signaling, Chemokine signaling pathway, and TNF signaling pathway. In addition, protein-protein interaction network (PPI) was used to display highly interactive DEG networks involving immune-related pathways. The expression trends of 16 DEGs were further verified by quantitative real-time PCR, which confirmed the reliability of the transcriptome sequencing results. This study expands our understanding of the immune response of rainbow trout infected with IHNV, and provides valuable resources for future studies on the immune molecular mechanism and disease resistance breeding.

overall_design: In this study, rainbow trout were anesthetized with tricaine methane sulfonate (MS-222, Sigma, USA) at 48 hpi and skin tissues were collected and immediately frozen by liquid nitrogen.We explored rainbow trout skin transcriptome profiles following IHNV challenge, and identified 6905 differentially expressed genes (DEGs).

first: Jinqiang

last: Huang

first: Lu

last: Zhao


title: RNA-Seq Provides Insights into VEGF-Induced Signaling in Human Retinal Microvascular Endothelial Cells: Implications in Retinopathy of Prematurity

city: Salt Lake City

first: Mary Elizabeth

last: Hartnett

state: Utah

address: 65 Mario Capecchi Dr

department: Ophthalmology and Vision Sciences

country: USA

institute: University of Utah

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

overall_design: Refer to individual Series


title: Isogenic pairs of MPS VI gene corrected iPSC and Chondrogenic cells

city: Rotterdam

first: Mike

last: Broeders

state: Zuid-Holland

address: Dr.Molewaterplein 40

department: Department of Pediatrics, Department of Clinical Genetics, Center for Lysosomal and Metabolic Diseases

country: Netherlands

institute: Erasmus MC

summary:
To investigate the effect of MPS VI on gene expression in chondrogenic cells, we gene corrected four patient derived hiPSC using a ARSB knock-in into the AAVS1 locus.
We differentiated cells into chondrogenic cells using a 14 day protocol, we proformed gene expression profiling analysis using data obtained from RNA-seq at iPS stage in monoplo and differentiated cells in triplo.

overall_design: Comparative gene expression profiling analysis of RNA-seq data of isogenic controls after differentation to see the effect of MPS VI on gene expression

first: M

first: J

middle: G

last: van Rooij

first: E

last: Oussoren

first: T

middle: J

last: van Gestel

first: C

middle: A

last: Smith

first: S

last: Kimber

first: R

middle: M

last: Verdijk

last: Wagenmakers

last: van den Hout

first: A

middle: T

last: van der Ploeg

last: Narcisi

first: W

middle: W

last: Pijnappel


title: Expression dynamics of periodic transcripts during cancer cell cycle progression and their correlation with anticancer drug sensitivity

city: BEIJING

first: Haili

last: Qian

address: 17 South Panjiayuan Lane, Chaoyang District

institute: National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College

summary: Cell cycle is the center of cellular activities and is orchestrated by complex regulatory mechanisms, among which transcriptional regulation is one of the most important parts. Alternative splicing dramatically expands the regulatory network by producing transcript isoforms of genes to exquisitely control the cell cycle. However, the patterns of transcript isoform expression in the cell cycle are unclear. Therapies targeting cell cycle checkpoints are commonly used as anticancer therapies, but none of them were designed and have been evaluated at alternative splicing transcripts level. To explore alternative splicing patterns during cell cycle progression, we performed sequential transcriptomic assays following cell cycle synchronization in breast cancer MDA-MB-231 cell lines, used flow cytometry and reference cell cycle transcripts to confirm the cell cycle phases of samples.

overall_design: MDA-MB-231 cells were harvested at 0, 3, 4.5, 6, 7, 9, 10, 11.5, 13, and 16 hr after G1/S phase release. For M phase arrest, when MDA-MB-231 cells were released from G1/S phase, 1 µg/ml nocodazole was added, and after 10 hr, they were supplemented with 5 µg/ml actinomycin D.

first: Chunxiao

last: Li

first: Jinsong

last: Wang


title: Transcriptome analysis reveals hub genes and Ihh and KLF9 axis in the endometrial restoration in IUA mice

city: 湖北

first: Yiyi

last: Kang

address: Donghu road

institute: WuHan University

summary: To investigate the molecular mechanism during the restoration of mouse endometrium by CRCs transplantation, uterine horns were collected from the mice of CRC cells- transplanted, injury and sham operated groups at 7 days after surgery for RNAsequencing (RNA-seq). We then performed gene expression profiling analysis using data obtained from RNA-seq of three groups mice.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for sham operated group, injury group and CRCs-transplanted group.

first: Xinhao

last: Zhou

first: Yuntzu

last: Chang


title: Ketamine induces apical extracellular matrix modifications in C. elegans

city: Kayseri

first: Duygu

last: Yücel

address: Erciyes University Genome and Stem Cell Center Melikgazi

country: Turkey

institute: Erciyes University

summary: To investigate ketamine-induced modifications usign C. elegans as a model

overall_design: RNA-seq of wild-type (N2) C. elegans treated with ketamine (2.5 mM) and M9 as a vehicle. Whole animals at adult day 1 were used for RNA extraction.


title: Inflammation-associated changes in transcriptomics signature in wild-type and Selenow knock-out murine bone marrow-derived macrophages (BMDMs).

city: State College

first: Sougat

last: Misra

state: PA

address: 107 Shortlidge Road

department: Veterinary and Biomedical Sciences

institute: The Pennsylvania State University

summary: To investigate differential gene expression profile in Selenow knock-out BMDMs to elucidate the role of this small selenoprotein involving LPS-induced inflammation.

overall_design: LPS-induced changes in temporal gene expression profiling analysis using isolated BMDMs from wild-type and Selenow knock-out mice. Time points: 0 h, 4 h, 8h, 24 h.

first: Aswathy

last: Sebastian

first: Istvan

last: Albert

first: K.

middle: S

last: Prabhu


title: Transcriptome in Rat Skeletal Muscle 1 month or 3 months after Early Protein Restriction

city: Tokyo

first: Sihui

last: Ma

address: Yayoi 1-1-1

country: Japan

institute: The university of Tokyo

summary:
In the present study, we designed a 1-month protein restriction model using post-weaning rats, followed by a 2-month rebound feeding, to investigate how early life protein restriction affects overall body growth and muscle development, and whether these influences could be corrected by the following rebound feeding.
Transcriptome profiling reveal that myogenic differentiation functions are upregulated while protein catabolism are downregulated as compensatory toward protein restriction, while endo-plasmic reticulum stress are enhanced, inducing undesired apoptosis.

overall_design: Postnatal protein-restriction treated rat muscle were used for RNA extraction and hybridization on Affymetrix microarrays.

first: Emi

last: Hasegawa

first: Huijuan

last: Jia

first: Hisanori

last: Kato


title: Glucocorticoid transcriptome in S49 lymphoid cells expressing Bcl2

city: RTP

first: Xiaojiang

last: Xu

state: North Carolina

address: 111 T. W. Alexander Dr.,

institute: NIEHS

summary: S49 (Neo) cells die by apoptosis following dexamethasone (dex) treatment whereas S49 cells expressing Bcl2 are resistant to glucocorticoid-induced cell death. Provocatively, mimicking the loss of intracellular potassium using a low dose of a microbial toxin that acts as a potassium ionophore in combination with dex overcame the resistance afforded by Bcl2 and killed the cells.    The ability of the microbial toxin to trigger apoptosis of S49 (Bcl2) cells depends critically on the duration of dex treatment, as a 48-hour dex treatment sensitized the cells to die whereas a 24-hour exposure did not.  To determine how the glucocorticoid signaling profile differs at these two time points, we performed RNAseq on RNA isolated from S49 (Neo) cells and S49 (Bcl2) cells treated with and without dex for 24 and 48 hours.

overall_design: S49 (Neo) are S49.1 mouse lymphoma cells stably transfected with a recombinant amphitropic retrovirus carrying a G418 (Neomycin) antibiotic resistance gene (Cancer Res 1992; 52: 5407-5411), and S49 (Bcl2) cells were additionally transfected with the Bcl2 proto-oncogene (Cancer Res 1992; 52: 5407-5411).   S49 (Neo) cells and S49 (Bcl2) cells were treated with and without dexamethasone for 24 or 48 hours.  Total RNA was extracted and purified from cells using a QIAGEN RNeasy RNA isolation kit according to the manufacturer’s protocol.  RNA-seq libraries were generated with 1 mg of RNA as input using the TruSeq RNA Sample Prep Kit (Illumina, San Diego, CA) and poly(A)-enriched according to the TruSeq protocol.  Indexed samples were sequenced using the 75-bp paired-end protocol via the NextSeq500 (Illumina) according to the manufacturer’s protocol.

first: Carl

last: Bortner

first: John

last: Cidlowski


title: Transcriptomic profiling of canine decidualization and effects evoked by antigestagens on decidualized canine uterine stromal cells

city: Zurich

first: Genome

last: Informatics

address: Winterthurerstrasse 190

department: Functional Genomics Center Zurich (FGCZ)

country: Switzerland

institute: ETH ZURICH / University of Zurich

summary: Maternal-stroma derived decidual cells are the single population in the canine placenta expressing the nuclear progesterone (P4) receptor (PGR), rendering them crucial for the maintenance of canine pregnancy. Indeed, decreased circulating P4 levels or blockage of PGR function with antigestagens (e.g., aglepristone), culminates in the termination of canine pregnancy. As an in vitro model for canine decidualization, dog uterine stromal (DUS; Graubner et al., 2017) cells can be decidualized in vitro with cAMP. The antigestagens aglepristone and mifepristone ablate the expression of decidualization markers in DUS cells (e.g., PGR, PRLR, IGF1 or PTGES). In order to study the mechanisms involved in feto-maternal communication during pregnancy and induction of parturition, the goal of the present work was to assess transcriptional changes mediated by decidualization and antigestagens-induced effects in decidualized DUS cells. Decidualization led to the upregulation of 1841 differentially expressed genes (DEGs, P < 0.01, FDR < 0.01) involved in cellular proliferation and adhesion, mesenchymal-epithelial transition, extracellular matrix organization, and vaso- and immunomodulation. The 1475 DEGs downregulated after decidualization were mostly associated with apoptosis and cell migration. In decidualized DUS cells, aglepristone modulated 1400 DEGs and mifepristone 1558 DEGs. Interestingly, only around half of the identified DEGs were modulated uniquely by one of the antigestagens. In both situations, however, PGR-blockage was associated with an inversion of decidualization-induced effects. Comparison between antigestagens-mediated effects and transcriptional changes in the canine placenta at term allowed the identification of 191 DEGs associated with cell proliferation and adhesion, vascularization and immune activity. These findings emphasize the importance of P4/PGR signaling for decidual cells function.

overall_design: A total of 4 groups were used. Immortalized Dog Uterine Stromal (DUS) cells were cultured in vitro for 72h either in serum-free medium (non-decidualized control group, n = 3 replicates), or in the presence of 0.5mM dbcAMP (decidualized DUS/cAMP group, n = 3 replicates). Decidualized DUS cells were then treated for 6h in the presence of 1μM of aglepristone or mifepristone (n = 5 replicates for each antigestagen). At the end of each treatment, cells were washed with ice cold PBS and collected for further RNA isolation with Trizol.

first: Mariusz

middle: P

last: Kowalewski

first: Ali

last: Kazemian

first: Miguel

last: Tavares Pereira

first: Hubert

last: Rehrauer


title: Effect of deletion of PoxCxrC and overexpression of POX_f08097 in engineering strain Penicillium oxalicum TE4-10 at the transcriptional level

city: Nanning

first: Di

last: Tian

address: DaXue east road

institute: College of Life Science and Technology,GuangXi university

summary: In order to obtain genetically engineering strain of Penicillium oxalicum with high Raw Starch Digesting Glucoamylase production,we deleted PoxCxrC and overexpressed POX_f08097 in Penicillium oxalicum TE4-10 ,and we want to investigating the function of deletion of PoxCxrC and overexpression of POX_f08097 at transcriptional level.

overall_design: We then performed gene expression profiling analysis using data obtained from RNA-seq of  at 24h after tansfer to the enzyme production medium with raw starch (the only carbon source).

first: Mingzhu

last: Tan

first: Shuai

last: Zhao


title: Brucellosis Vaccine Ag85a-S2 activates cGAS-Sting Signaling Pathway in Intestinal Mucosal Cells

city: Tongliao

first: Jingbo

last: Zhai

address: 996 Xilamulun Ave, Horqin District

institute: Inner Mongolia Minzu University

summary: Brucellosis is a zoonotic disease caused by Gram-negative bacteria, resulting in an economic loss of billions of USD per year. Most of the Brucellosis vaccines in the application are the whole bacteria vaccines, which typically have high toxicity and low immunogenicity. We recently developed an S2 vaccine adjuvanted with Ag85A (Ag85A-S2), which greatly improved the immunogenic properties of S2. However, the mechanisms of Ag85A-S2 remained elusive. Here, we found that Ag85A-S2 activated cGAS-STING pathways both in intestinal mucosal cells and in a cGAS knockout cell line in vitro. We demonstrated that the cGAS knockout significantly downregulated the abundance of interferon and other cytokines induced by Ag85A-S2. In sum, Ag85-S2-mediated enhancement of immune responses was dependent on both cGAS and STING. Our results provided a new strategy for preventing Brucellosis from livestock, which might reduce the dosage and potential toxicity compared to the traditional S2 vaccine.

overall_design: We knocked out cGAS and stimulated this knockout cell line with Ag85a-S2.


title: Mesenchymal EZH2 maintains uterine adenogenic homeostasis

city: College station

first: Qinglei

last: Li

address: 400 Bizzell St

institute: Texas A&M University

summary: To determine the mesenchymal function of EZH2 in the mouse uterus, we generated Ezh2 cKO mice using anti-Mullerian hormoneÂ typeÂ 2 (Amhr2)-Cre that is expressed in the mesenchymal and not epithelial compartment of the uterus

overall_design:
We performed RNA-sequencing in the uteri of Ezh2 cKO mice and controls at the age of postnatal day 10:
Ctrl, PD10, 1 = HISAT2.on.data.18.and.data.17
Ctrl, PD10, 2 = HISAT2.on.data.22.and.data.21
Ctrl, PD10, 3 = HISAT2.on.data.26.and.data.25
Ctrl, PD10, 4 = HISAT2.on.data.30.and.data.29
cKO, PD10, 1 = HISAT2.on.data.34.and.data.33
cKO, PD10, 2 = HISAT2.on.data.38.and.data.37
cKO, PD10, 3 = HISAT2.on.data.42.and.data.41
cKO, PD10, 4 = HISAT2.on.data.46.and.data.45

last: Ni

first: Xin

last: Fang


title: Long-term functional regeneration of radiation-damaged salivary glands through delivery of a neurogenic hydrogel

city: San Francisco

first: Jianlong

state: CA

address: 513 Parnassus Avenue

department: Cell and Tissue Biology

institute: UCSF

summary:
To investigate the timing of endogenous regenerative events in response to a single 10 Gy dose of IR, we sequeced the transcriptomes of glands from adult (6-7 wks)mice and 7- and 14-days post-IR.
We then compared to the radiated glands to Non-IR (no radiation) controls, and performed differential expression analysis.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for Ct (Non-IR, no radiation control), IR7 (7 days post-radiation) and IR14 (14 days post-radiation) sublingual salivary glands.

first: Sonia

last: Sudiwala

first: Alison

last: May


title: Effect of dupilumab treatment in Netherton syndrome

city: Chongqing

first: Xiaoming

last: Bai

address: Zhongshan Road, Yuzhong district

institute: children's hospital of chongqing medical universty

summary: To investigate the effect in the patients with Netherton syndrome, four different patients was evaluated at two time points using single-cell RNA sequencing.

overall_design: Comparative citokine signaling activity profiling analysis of single-cell RNA-seq data for four different patients with Netherton syndome at two time point.

first: Xiao-ming

first: Shi

last: Yan


title: Muscle Transcriptomic Circuits Linked to Periarticular Physiology in End-Stage Osteoarthritis.

city: Birmingham

first: Kaleen

last: Lavin

state: Alabama

address: 908 20th Street South, Room 201-C

department: Medicine

institute: University of Alabama at Birmingham

summary: Long RNAseq was performed on vastus lateralis, vastus medialis, tensor fascia latae, or gluteus maximus muscle samples from patients with end-stage OA. The primary study utilized single target differential gene expression analyses coupled with network biology to determine molecular circuits in the skeletal muscle overlaying a diseased joint.

overall_design: Skeletal muscle samples from the non-surgical limb (CTRL, vastus lateralis) were compared to the surgical limb (SX, vastus medialis, tensor fascia latae, or gluteus maximus). Further, SX limb transcriptomic data were correlated with phenotypic outcomes on that same limb

first: Devin

last: Drummer

first: Zachary

last: Graham

first: Samia

last: O'Bryan

first: Jeremy

last: McAdam

first: Manoel

middle: E

last: Lixandrão

first: Regina

last: Seay

first: Inmaculada

last: Aban

first: Herrick

last: Siegel

first: Elie

last: Ghanem

first: Jasvinder

last: Singh

first: Anna

last: Bonfitto

first: Jerry

last: Antone

first: Rebecca

last: Reiman

first: Elizabeth

last: Hutchins

first: Kendall

last: Van Keuren-Jensen

first: Scott

last: Schutzler

first: C

middle: L

last: Barnes

first: Arny

last: Ferrando

first: S

last: Bridges Jr

first: Marcas

last: Bamman


title: Astrocytic yin yang 1 (YY1) is critical for murine brain development and protection against apoptosis, oxidative stress and inflammation

city: Tallahassee

first: Cynthia

last: Vied

state: Florida

address: 1115 W. Call St

department: Translational Science Laboratory

institute: Florida State University

summary: Identifying alterations in gene expression and biological pathways within three brain regions of astrocyte-specific YY1 conditional knockout mice

overall_design: mRNA of the cortex, midbrain, and cerebellum from adult males and females of YY1-floxed and astrocyte-specific conditional knockout mice were analyzed by RNA sequencing of 7 biological replicates using an Illumina NovaSeq 6000

first: Edward

last: Pajarillo

first: Eunsook

last: Lee


title: Transcriptomics and metabolomics reveal the changes of regulatory mechanisms of osteosarcoma under different culture methods in vitro

city: Taiyuan

first: Sen

last: Yang

address: 382 Wuyi Road

institute: Shanxi Medical University

summary: The purpose of this study was to reveal the differences in transcriptional and metabolic levels between osteosarcoma 2D cells, 3D cells, 3D cell printed tissue, isolated tissue, and transplanted tumor in vivo

overall_design: Comparative gene expression profiling analysis of RNA-seq data for osteosarcoma  Soas-2 2D cells, 3D cells, 3D cell printed tissue, isolated tissue, and transplanted tumor

first: Zhi

last: Lv

last: Tian

first: Yi

last: Feng


title: Gene expression profiles during the process of differentiation of HL-60 cells into neutrophils [HL60]

city: Tokushima

first: Taigo

last: Horiguchi

address: 3-18-15, Kuramoto-cho

institute: Tokushima University

summary:
To investigate the changes in gene expression during the process of differentiation into neutrophils, microarray analysis was performed.
HL-60 cells were cultured with all-trans retinoic acid (ATRA) for 4 days. The cells were collected at four different time points and total RNA was prepared for use as a sample for microarray analysis.

overall_design: HL-60 cells were cultured with 10 µM ATRA and were collected at Day 0, 1, 2, and 4. Using prepared total RNA at each time point, microarray analysis was performed.

first: Ayako

last: Tanimura

first: Keiko

last: Miyoshi

first: Hiroko

last: Hagita

first: Takafumi

last: Noma


title: Gene expression profiles during the process of differentiation of HL-60 AK2 hetero-knockout clone #5 cells into neutrophils [HL60AK2KO_clone5]

summary:
To investigate the changes in gene expression during the process of differentiation into neutrophils and to evaluate the effect of Ak2 hetero-knockout in the process, microarray analysis was performed.
HL-60 Ak2 hetero-knockout clone #5 cells were cultured with all-trans retinoic acid (ATRA) for 4 days. The cells were collected at four different time points and total RNA was prepared for use as a sample for microarray analysis.

overall_design: HL-60 Ak2 hetero-knockout clone #5 cells were cultured with 10 µM ATRA and were collected at Day 0, 1, 2, and 4. Using prepared total RNA at each time point, microarray analysis was performed.


title: Gene expression profiles during the process of differentiation of HL-60 AK2 hetero-knockout clone #47 cells into neutrophils [HL60AK2KO_clone47]

summary:
To investigate the changes in gene expression during the process of differentiation into neutrophils and to evaluate the effect of Ak2 hetero-knockout in the process, microarray analysis was performed.
HL-60 Ak2 hetero-knockout clone #47 cells were cultured with all-trans retinoic acid (ATRA) for 4 days. The cells were collected at four different time points and total RNA was prepared for use as a sample for microarray analysis.

overall_design: HL-60 Ak2 hetero-knockout clone #47 cells were cultured with 10 µM ATRA and were collected at Day 0, 1, 2, and 4. Using prepared total RNA at each time point, microarray analysis was performed.


title: Transcriptome of sessile serrated adenoma/polyps shows a relation with MSI-high colorectal cancer and decrease of CDX2

first: Daisuke

last: Ohki

address: 7-3-1, Hongo, Bunkyo-ku

department: Department of Gastroenterology, Graduate School of Medicine

institute: The University of Tokyo

summary:
The objective of this study was to elucidate the molecular background of sessile serrated adenoma/polyp (SSA/P) endoscopically resected with comprehensive gene expression analysis. Gene expression profiling was performed for 10 tumor-normal pairs of SSA/P. Cluster analysis, gene set enrichment analysis (GSEA), and consensus molecular subtype (CMS) classification of colorectal cancer (CRC) were applied to our transcriptome analysis. Unsupervised cluster analysis showed that the gene expression profile of SSA/Ps is different from that of adjacent normal epithelial cells, even in the very early stage of tumorigenesis. According to the CMS classification, our microarray data indicated that SSA/Ps were classified as CMS1. GSEA demonstrated a strong association between SSA/P and microsatellite instability-high (MSI-H) CRC (p < 10-5). Transcriptome analysis of five MSI-related genes (MSH2, MSH6, MLH1, PMS1, and PMS2) and five CRC-related genes (BRAF, KRAS, APC, TP53, and CDX2) showed that CDX2 expression was most severely decreased in SSA/P. Immunohistochemical staining confirmed that CDX2 protein was reduced compared with the surrounding mucosa. Direct sequencing of the BRAF gene showed that the BRAF V600E mutation was detected in only nine of 36 cases. In an mouse model, BRAF, APC, or CDX2 deficiency indicated that the gene expression pattern with loss of CDX2 is more similar to our SSA/Ps compared with those induced by BRAF or APC mutation. Transcriptome analysis of SSA/Ps showed characteristic gene expression with a strong resemblance to MSI-H CRC. Downregulation of CDX2 expression is an essential molecular mechanism involved in the initial stage of SSA/P tumorigenesis.
All samples were obtained prior to treatment in order to minimize effects of cauterization, and immediately fresh-frozen.

overall_design: Specimens were obtained from the SSA/P and paired with the surrounding mucosa through endoscopic biopsy immediately before resection of the target lesions using endoscopic biopsy forceps. Specimens were homogenized and total RNA was extracted. Oligonucleotide microarray was performed using 10 SSA/P-normal pairs.

first: Nobutake

last: Yamamichi

first: Yoshiki

last: Sakaguchi

first: Yu

last: Takahashi

first: Natsuko

last: Kageyama-Yahara

first: Mitsue

first: Chihiro

last: Takeuchi

first: Yosuke

last: Tsuji

first: Yasuhiro

last: Sakai

first: Kouhei

last: Sakurai

first: Shuta

last: Tomida

first: Kazuhiko

last: Koike

first: Mitsuhiro

last: Fujishiro


title: RNA-seq and ChIP-seq in HepG2 hepatocellular carcinoma and U87 glioblastoma cells with CRISPRi knockdown of ACTR5

city: duarte

first: LU

last: YANG

address: 1500 duarte rd

institute: city of hope

type: Genome binding/occupancy profiling by high throughput sequencing

summary: This dataset examined the effect of ACTR5 knockdown in HepG2 and U87 cells. The gene expression profiling (RNA-seq) and the chromatin targeting of ACTR5 (TST-ChIP-seq) are reported.

overall_design: RNAseq:dCas9-Krab-expressing HepG2 and U87 cells were transduced with sgiNTC and sgiACTR5. The total RNA was extracted using the RNeasy Mini Kit (74104, QIAGEN) and submitted for RNA-seq at Novogene (PE150, NovoSeq6000). TST-ChIP-seq:  ACTR5-TST cautured genomic DNA was submitted for ChIP-seq at Novogene (PE150, NovaSeq6000).

first: Chun-Wei

last: Chen

first: Lu

last: Yang

first: Xiaobao

last: Xu


title: Gene expression profiles during the process of differentiation of HL-60 clone 15 cells into eosinophils [HL60cl15]

first: Taigo

last: Horiguchi

summary:
To investigate the changes in gene expression during the process of differentiation into eosinophils, microarray analysis was performed.
HL-60 clone 15 cells were cultured with apicidin for 6 days. The cells were collected at four different time points and total RNA was prepared for use as a sample for microarray analysis.

overall_design: HL-60 clone 15 cells were cultured with 100 nM apicidin and were collected at Day 0, 2, 4, and 6. Using prepared total RNA at each time point, microarray analysis was performed.

first: Ayako

last: Tanimura

first: Keiko

last: Miyoshi

first: Hiroko

last: Hagita

first: Takafumi

last: Noma


title: Gene expression profiles during the process of differentiation of HL-60 cells into neutrophils or eosinophils

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

overall_design: Refer to individual Series


title: Disturbances in microbial skin recolonization and cutaneous immune response following allogeneic stem cell transfer

city: Vienna

first: Georg

last: Stary

address: Spitalgasse 23

department: Dermatology

country: Austria

institute: Medical University of Vienna

summary: RNA seq data of pooled T cells and Dendritic cells isolated from skin  at multiple time points before and after hematopoietic stem cell transplantation

overall_design: Examination of 1 cell type at 5 time points before and after treatment

first: RV

last: Pandey

first: J

last: Strobl

first: N

last: Bayer


title: Assessing the productive and adaptive capability of two different goat breeds to heat stress based on differences in the phenotypic and genotypic traits

city: BENGALURU

first: Veerasamy

last: Sejian

address: National Institute of Animal Nutrition and Physiology

country: India

type: Methylation profiling by high throughput sequencing

summary: Assessing the adaptive capabilities of two indigenous Nandidurga and Bidri goat breeds based on skin epigenetics approach

overall_design: Goats were raised in controlled environment and samples were collected and processed to generate methylome data.

first: Sejian

last: Veerasamy


title: Genome-wide expression profiling of CUTTL1 cells upon miR-17-92 cluster overexpression with or without gamma-secretase inhibitor treatment

city: San Giovanni Rotondo (FG)

first: Fabrizio

last: Bianchi

state: Outside U.S. & Canada

address: Viale Padre Pio 7

country: Italy

institute: Fondazione IRCCS Casa Sollievo della Sofferenza

summary: T-cell acute lymphoblastic leukemia (T-ALL) is an aggressive T-cell malignancy characterized by genotypically-defined and phenotypically divergent cell populations, governed by adaptive landscapes. Clonal expansions are associated to genetic and epigenetic events, and modulation of external stimuli that affect the hierarchical structure of subclones and support the dynamics of leukemic subsets. Recently, extracellular vesicles (EVs) such exosomes were also shown to play a role in leukemia. Here, we explored the role of EVs in the realm of Notch-driven T-ALLs and found that T-ALL cells secrete Notch-dependent EVs containing microRNAs (EV-miRs), which control oncogenic pathways acting as autocrine stimuli and promote in vitro the expansion/survival of cell subsets of human T-cell leukemias.  Of interest, the highlighted Notch-dependent EV-miRs mostly comprised members of miR-17-92a cluster and paralogues, which rescued in vitro the proliferation of T-ALL cells induced by γ-secretase inhibitors (GSI). Additionally, single-cell RNA sequencing analysis of leukemia cells from primary T-ALL patients revealed cell subsets differently responsive to Notch-dependent EV-miRs. All these findings suggest that restricted EV-miRs may sustain the growth/survival of immunophenotypically defined cell populations, altering the cell heterogeneity and the dynamics of T-cell leukemias in response to conventional therapies.

overall_design: A total of 4 different experimental conditions were analyzed in this study. We performed  biological replicates for a total of 8 samples profiled.

first: Tommaso

last: Colangelo

first: Vincenzo

last: Giambra


title: Comparison of pre-leukemic and leukemic H9M AML clones from murine splenocytes

city: Hannover

first: Tobias

last: Maetzig

address: Carl-Neuberg-Str. 1

country: Germany

institute: Hannover Medical School

summary: The tracking of leukemic clones in acute myeloid leukemic promisses deeper insights into disease development and therapeutic options. We therefore established a fluorescent genetic barcoding (FGB) labeling approach that allows for flow cytomtric tracking of color-coded clones in vitro and in vivo. In Hoxa9 and Meis1 (H9M) dependent murine AML, we tracked the growth behavior of 24 clones in parallel and enriched for pre-leukemic clones as well as their de novo expanded counterparts and stably expanded clones from leukemic mice by fluorescence-activated cell sorting. These samples were subjected toRNA sequencing for the assessment of transcriptional changes underlying clonal maintenance and expansion.

overall_design: 9 samples were analyzed. 3 pre-leukemic clones were derived from a single mouse. Pairs of 3 de novo expanded clones and stably expanded clones were enriched from 3 mice at their leukemic endpoint.


title: miR-183-5p and miR-492 over-expression trigger loss of polarity and nuclear circularity and enhanced invasion and proliferation in nontumorigenic breast epithelium

city: West Lafayette

first: Nadia

middle: Marie

last: Atallah

state: IN

address: 201 S. University St

department: Center for Cancer Research

institute: Purdue University

type: Non-coding RNA profiling by high throughput sequencing

summary: microRNAs (miRNAs) are stable and abundant in body fluids and exhibit unique dysregulation signatures in cancers, making them attractive novel noninvasive cancer biomarkers. In an HMT-3522 S1 (S1) breast epithelial risk-progression 3D culture model, non-tumorigenic S1 cells form a fully polarized epithelium. Their pretumorigenic counterparts, silenced for gap junction and tumor suppressor Cx43, Cx43-KO-S1, lose epithelial polarity, multilayer, exhibit proliferative and invasion potential, and mimic tumor-initiated in vivo mammary epithelial morphology. To characterize the miRNA profile specific to Cx43 loss in the breast epithelia, miRNA-sequencing was performed and revealed 65 differentially expressed miRNAs in Cx43-KO-S1 as compared to S1 cells. A comparative analysis was conducted between the 65 differentially expressed miRNAs and 15 tumor-associated miRNAs from a young Lebanese patient validation cohort. miR-183-5p, downstream of Cx43 loss and commonly upregulated in the patient cohort and the breast epithelia and miR-492, not attributed to Cx43 loss, and only up-regulated in the young Lebanese patients were chosen for stable over-expression in the nontumorigenic S1 cells. Ectopic over-expression of miR-183 and miR-492 in S1 cells, through pLenti-III-miR-GPF tagged vectors, resulted in the formation of larger acini devoid of lumen assembly with cell multilayering, disrupted epithelial polarity and decreased nuclear circularity in 3D cultures, as well as in enhanced proliferation and invasion capacity and altered apical localization of Cx43 and apico-lateral localization of ß-catenin and Scrib. miR-183-5p and miR-492 over-expression in nontumorigenic S1 cells thus recapitulate pretumorigenic phenotypes similar to those reported upon Cx43 loss and act as oncomiRs and prognostic biomarkers.

overall_design: miRNA-seq on control and Cx43 knock-down cells

first: Nataly

middle: N

last: Deen

last: Lanman

first: Shirisha

last: Chittiboyina

first: Sabreen

last: Fostok

first: Rihab

last: Nasr

first: Sophie

last: Lelièvre

first: Rabih

last: Talhouk


title: Integrated analysis of ovarian juvenile granulosa cell tumors reveals distinct epigenetic signatures and recurrent TERT rearrangements

city: New York

first: Varshini

last: Vasudevaraja

state: NY

address: 240 E 38th street

department: Pathology

institute: NYU Langone Health

summary:
Genome wide DNA methylation profiling of ovarian granulosa cell tumors. The Illumina Infinium  EPIC Human DNA methylation Beadchips were used to obtain DNA methylation profiles across 32 samples.
JGCTs show a distinct methylation signature compared to AGCTs

overall_design: Bisulphite converted DNA from the 32 samples were hybridised with Illumina Infinium  EPIC Human Methylation Beadchip.

first: George

last: Jour

first: Matija

last: Snuderl

first: Theodore

last: Vougiouklakis


title: Comparative assessment of the resilience capacity of different indigenous goat breeds to summer heat stress based on selective thermo-tolerant gene expression pattern

first: Veerasamy

last: Sejian

institute: National Institute of Animal Nutrition and Physiology

summary: Assessing the adaptive capabilities of two indigenous Kanni Aadu and Kodi Aadu goat breeds based on skin epigenetics approach

overall_design: Skin tissue was chopped into fine pieces and lysed by adding Buffer ATL, ProteinaseK and Buffer AL. The lysate was bound to Dneasy Mini Spin Column and the DNA was eluted in Buffer AE after subsequent washes. (Dneasy® Blood& Tissue Kit Cat.No.69506)

last: Veerasamy


title: Aberrant Nrf2 activation delays erythroid maturation during chemotherapeutic drug-induced erythropoiesis

city: Yangzhou

first: Lei

last: Yang

state: Jiangsu

address: 136 Jiangyang Road

institute: Yangzhou University Medical College

summary: Nuclear factor (erythroid-derived 2)-like2 (Nrf2) and miR-144/451 regulate two well-established systems that have been identified to maintain redox homeostasis in erythroid cells by removing excess reactive oxygen species (ROS). Whether Nrf2 plays a role in the differentiation process during erythropoiesis has not been reported. In this study, we demonstrate that miR-144/451 gene knockout (KO) in mice dampens erythroid differentiation when 5-Fluorouridine is used to induce acute anemia. Surprisingly, inactivation of Nrf2 by crossing Nrf2 KO mice completely alleviates the delayed erythropoiesis in miR-144/451 KO mice. Nrf2 is a miR-144/451 target and depletion of miR-144/451 leads to the derepression of Nrf2, and thus an overexpression of Nrf2. Therefore, our findings indicate that persistent Nrf2 activation blocks erythroid maturation. We further reveal that even physiological levels of Nrf2 impair the erythroid differentiation. The underlying mechanism is that hyperactivity of Nrf2 leads to the sustained proliferation of erythroblasts partially by activation of Myc signaling. We also find that Nrf2 and miR-144/451 coordinate to scavenge ROS but do not phenotypically copy each other, indicating that they control two distinct anti-oxidant systems in erythroid cells. Furthermore, we find that miR-144/451 deficiency produces a more profound defect of erythropoiesis than dysfunctional Nrf2. Given that Nrf2 is ubiquitously expressed in tumor tissues, which facilitates cancer malignancy and chemoresistance; and that cancer is often accompanied by anemia that markedly inhibits antineoplastic treatment efficacy and anticancer immunity, our findings suggest that targeting Nrf2 holds great promise that not only harms cancer cells, but also reverses cancer-related anemia.

overall_design: mRNAs from four groups of mouse erythroblasts derived from spleens 11 days after 5-FU treatment

first: Duonan

last: Yu


title: Transcriptome analysis of total RNA from the Rhodobacter sphaeroides 2.4.1 UdsC (sRNA) deletion mutant strain and UdsC (sRNA) overexpression strain under microaerobic growth conditions

city: Gießen

first: Gabriele

last: Klug

address: Heinrich-Buff-Ring 26-32

department: Molecular- and Microbiology

institute: Justus-Liebig University Gießen

summary: The sRNA UdsC ist derived from the 3´ UTR of RSP_7527. To analyse the effect of the sRNA on the transcriptome of R. sphaeroides we performed the RNAseq analysis with a chromosomal knockout and an inducible overexpression of this sRNA.

overall_design: Comparative gene expression profiling analysis of RNAseq data of independent biological triplicates of the Rhodobacter sphaeroides UdsC deletion mutant strain and inducible UdsC overexpression strain under microaerobic growth conditions.

first: Daniel-Timon

last: Spanka

first: Julian

last: Grützner


title: Profiling chromatin accessibility during stomatal development

city: Austin

first: Keiko

middle: U

last: Torii

address: 2506 SPEEDWAY

institute: University of Texas at Austin

summary: Plant cells are totipotent and hence can dedifferentiate and re-differentiate, making it possible to clone entire plant parts from a single cell. It is hence critical for plant cells to maintain specific cell-states during and after differentiation. Stomata, microscopic valves on the plant epidermis required for efficient gas exchange and water management, have emerged as a powerful model system for understanding how de novo lineage-specific stem cell initiate, proliferate and differentiate into specialized cell types during their development of the plant epidermis. The stomatal lineage emerged from a subpopulation of protodermal cells as meristemoid mother cells (MMCs) that undergoes an asymmetric entry division to give a rise meristemoid and its sister cell called the stomatal-lineage ground cell (SLGC). After several rounds of asymmetric cell division, meristemoids differentiate into round guard mother cells (GMC), which divide symmetrically and terminally differentiate into paired guard cells (GCs). We have adapted the INTACT (Isolation of Nuclei TAgged in Specific Cell Types) system to isolate each stomatal lineage-specific nuclei followed by ATACseq (Assay for Transposase-Accessible Chromatin). We showed that chromatin accessibility is dynamic throughout the stomatal lineage progression. Further, the analysis of TF binding sites in differentially accessible regions led to discover that combinatorial cis-regulatory elements and transcription factor circuits controls lineage specific cell state transition during stomatal development.

overall_design: Biotinylated nuclei were isolated from transgenic Arabidopsis thaliana Col-0 seedlings. Seedlings were harvested from 3day old seedlings containing the INTACT system under the cell type-specific promoter. To generate the ATACseq library,  isolated nuclei were transposed with Tn5 from the Illumina Nextera Kit, followed by DNA purification.  Purified transposed DNA was used for ATACseq library construction.

first: Eun-Deok

last: Kim

first: Miachel

last: Dorrity

first: Christine

last: Queitsch


title: RNA-seq of oligodendroglia progenitor cells(OPCs) isolated from WT and DISC1-Δ3 mice

city: SHENZHEN

first: Yixun

last: Su

state: GUANGDONG

address: 628 Zhenyuan Road

department: Research center

institute: The Seventh Affiliated Hospital, Sun Yat-sen University

summary: Disrupted-in-schizophrenia-1 (DISC1), as one of the schizophrenia susceptibility genes highly expressed in oligodendrocyte precursor cells (OPCs), impacts oligodendroglial differentiation and myelination. Several DISC1 splicing variants, including DISC1-Δ3 (a DISC1 transcript with deleted exon 3 in a single allele), are abnormally upregulated in human schizophrenia patients, however, how they trigger the onset of the disease has not been explored yet. Here, we generate a mouse line that mimics human DISC1-Δ3 in oligodendrocyte lineage cells, and demonstrate that hypertrophic OPCs rather than myelin, are responsible for the neuronal deficits and schizophrenia-like symptoms. RNAseq was performed to analyze the transcriptome change in DISC1-Δ3 OPC, revealing that DISC1-Δ3 elevates the Wnt pathway activity in OPCs, which promotes Wif1 expression, thereby leading to disrupted synapse formation in neighboring neurons. Interfering or knockout of Wif1 in DISC1-Δ3 OPCs could rescue neuronal synaptic and functional deficits in our mouse model. Our findings shed light on the myelination-independent role of OPCs on the onset of schizophrenia, and may pave the way for new rational lines of inquiry in developing therapeutic strategies for schizophrenia.

overall_design:
RNA-seq was performed to understand the transcriptome change in DISC1-Δ3 forced expressed OPC in vivo
Mice were divided in 2 groups: wt: control group. ko: NG2-CreERTM: DISC1 exon3 fl/+ (DISC1 ∆3) mice. Tamoxifen was given at the gavage for 4 consecutive days (p4-p7).On postnatal day 7, mice were sacrificed to isolate OPCs from the brain by pdgfrα immunopanning.

first: Jianqin

last: Niu

first: Guangdan


title: Active enhancers strengthen TAD insulation by bRNA mediated CTCF enrichment at the TAD boundaries

city: Bangalore

first: Bharath

last: Saravanan

state: Karnataka

address: Bellary Road

department: Genetics and Development

institute: National centre for Biological Sciences

summary: The genome is partitioned into Topologically Associating Domains (TADs). About half of the boundaries of these TADs exhibit transcriptional activity and are correlated with better TAD insulation. However, the association between these transcripts and TAD insulation, enhancer:promoter interactions and transcription of genes remains unknown. Here we investigate the functional roles of these bRNAs (boundary-RNA) in boundary insulation and consequent effects on enhancer-promoter interactions and TAD transcription genome-wide and more specifically on the disease relevant INK4a/ARF TAD. Using a series of CTCF site deletions and bRNA knockdown experiments at this TAD boundary, we show a direct association of CTCF with the bidirectional bRNAs where the loss of bRNA triggers the concomitant loss of: CTCF at the TAD boundary, its insulation, enhancer:promoter interactions and gene transcription within the targeted TAD. We used another series of enhancer deletions and CRISPRi on promoters within INK4a/ARF TAD to better understand the regulation and origins of bRNA itself. We observe that the enhancers interact with boundaries and positively regulate the bRNA transcription at TAD boundaries. In return, the bRNAs recruit/stabilize the CTCF even on weak motifs within these boundaries and supports CTCF binding in clusters, therefore enhancing TAD insulation. This favors the intra-TAD enhancer:promoter interactions and leads to robust gene transcription. Functionally, bRNAs are more stable than eRNAs and their knockdown exactly mimics the CTCF site deletion. Furthermore, transcribing boundaries exhibit high TAD transcription in TCGA tumour datasets. Together, these results show that active enhancers directly mediate better insulation of TADs by activating the transcription at TAD boundaries triggering CTCF clustering at the boundary which results in better insulation and favours robust intra-TAD enhancer:promoter interactions to activate the gene transcription.

overall_design:
The occupancy of CTCF was tested by cut and run with and without RNase in HeLa cells.

** The submitter states that there may be issues in the Cut and Run treatment. **

first: Dimple

last: Notani


title: Single-cell transcriptomics reveal cell type-specific molecular changes and altered intercellular communications in chronic obstructive pulmonary disease

city: Nan Jing

first: js

last: wang

address: tian yuan

institute: Nanjing Medical University

summary: Chronic obstructive pulmonary disease (COPD) is a common and heterogeneous respiratory disease, the molecular complexity of which remains poorly understood, as well as the mechanisms by which aging and smoking facilitate COPD development. Here, using single-cell RNA sequencing of more than 65,000 cells from COPD and age-stratified control lung tissues of donors with different smoking histories, we identified monocytes, club cells, and macrophages as the most disease-, aging-, and smoking-relevant cell types, respectively. Notably, we found these highly cell-type specific changes under different conditions converged on cellular dysfunction of the alveolar epithelium. Deeper investigations revealed that the alveolar epithelium damage could be attributed to the abnormally activated monocytes in COPD lungs, which could be amplified via exhaustion of club cell stemness as ages. Moreover, the enhanced intercellular communications in COPD lungs as well as the pro-inflammatory interaction between macrophages and endothelial cells indued by smoking could facilitate signaling between monocyte and the alveolar epithelium. Our findings complement the existing model of COPD pathogenesis by emphasizing the contributions of the previously less appreciated cell types, highlighting their candidacy as potential therapeutic targets for COPD.

overall_design: Here we performed single-cell RNA-seq analysis for lung of COPD and age-stratified control lung tissues of donors with different smoking histories

first: Qiqing

last: Huang

first: Jingshen

last: Wang

first: Shaoran

last: Shen

first: Yuanyuan

first: Yan

last: Chen

first: Shuangshuang

last: Wu

first: Wei

last: Xu

first: Bo

first: Mingyan

last: Lin

first: Jianqing


title: Multi-omics profiling reveals the interactions of host defense and hyper-keratinization in psoriasis

city: Utrecht

first: Aridaman

last: Pandit

address: Heidelberglaan 100

institute: University Medical Center Utrecht

summary:
Objectives: To understand the crosstalk between the immune system and keratinization in psoriatic skin, using a systems biology approach based on transcriptomics, proteomics and microbiome profiling.
Methods: We collected the skin tissue biopsies and swabs in both lesion and non-lesion skin of 13 patients with psoriasis (PsO), 15 patients with psoriatic arthritis (PsA), and healthy skin from 12 patients with ankylosing spondylitis (AS). We performed transcriptome sequencing and metagenomics profiling on the local skin sites to study the similarities and differences in the molecular profiles between the three conditions. To assess the systemic nature of the disease, we performed a high-throughput proteome profiling to study the profiles of proteins circulating in the serum of the same donors.
Results: We found that lesion and non-lesional samples were remarkably different in terms of their transcriptome profiles. Functional annotation of differentially expressed genes (DEGs) showed a major enrichment in neutrophil activation. By using co-expression gene networks, we identified a gene module that was associated with local psoriasis severity at the site of biopsy. From this module, we extracted a “core” set of genes that were functionally involved in neutrophil activation, epidermal cell differentiation and response to bacteria. Skin microbiome analysis revealed that the abundance of Enhydrobacter, Micrococcus and Leptotrichia were significantly correlated with the “core network” of genes. We further identified 39 circulating proteins from the serum that were significantly correlated with the corresponding local skin gene expression, highlighting systemic aberrations due to skin disease. Integration of “core” genes identified from skin with circulating protein profiles revealed PI3 as a key biomarker for psoriasis.
Conclusions: We identified a core network that regulates inflammation and hyper-keratinization in psoriatic skin, and is associated with local disease severity and microbiome composition. Multi-omics analysis identified PI3 as a psoriasis-specific biomarker for disease severity and potential target for treatment strategies.

overall_design: Skin transcriptome profiles of both lesion and non-lesion of 13 patients with psoriasis (PsO), 15 patients with psoriatic arthritis (PsA), and healthy skin from 12 patients with ankylosing spondylitis (AS)

first: Jingwen

last: Deng


title: EZH2-mediated epigenetic suppression of IFNa/b-STAT2 signaling enhances anti-tumor immunity in breast cancer [ChIP-Seq]

city: San Antonio

first: Kexin

state: Texas

address: 7703 Floyd Curl, MC 8257

department: Molecular Medicine

institute: UT Health Science Center at San Antonio

summary: Knockdown of catalytic inhibiton of EZH2 stimulates STAT2 recruitment in ISG promoter regions in luminal breast cancer cells

overall_design: MCF7 cells treated with EZH2 inhibitor or transduced shEZH2  were cross-linked unsing formaldehyde, and sonciation was performed to fragment chromtain between 100-300 bp in size ragne using sonciatior. Chromatin was immunoprecipitated with antibodies conjugated protein G dynabeads, followed by washing and elution. ChIP DNA was reverse crosslinked overnight and purifed by phenol precipitation. 2ng ChIP DNA was used for library construction and sequenced with Illumina HiSeq 3000.

first: Zhang

last: Zhao

first: Hong

last: Juyeong

first: Lee

last: Jihoon

first: Xu

last: Kexin


title: EZH2-mediated epigenetic suppression of IFNa/b-STAT2 signaling enhances anti-tumor immunity in breast cancer [RNA-Seq]

summary: EZH2 knockdown or catylytic inhibition induces interferon signaling pathway

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: MCF7 cells were transduced by shEZH2 and selected with puromycin. RNA was extracted by TRIzol and 1-2 ug RNA was used for library construction.


title: Next generation sequencing of monkey ICSI, SCNT and TR placentas

status: Public on Dec 27 2022

city: Shanghai

first: Liao

last: Zhaodi

address: 500, Qiangye Road

department: Institute of Neuroscience

institute: Chinese Academy of Sciences

summary: Somatic cell nuclear transfer (SCNT) has been used to clone cynomolgus monkeys (Macaca fascicularis), but the cloning of other non-human primate species remains to be achieved. On the other hand, our histological examination indicated severe calcification of the placenta of SCNT fetuses. Additionally, we found that some of the maternal-biased imprinting genes were aberrantly lost in the cloned embryos by multi-omics analysis. We thus developed a trophoblast replacement (TR) method, providing an ICSI-derived placenta for the SCNT fetus, to support the full-term development of the cloned embryos after implantation. By combining this TR method with treatment with epigenetic modification factors, we obtained a healthy somatic cell cloned rhesus monkey. Thus, TR represents a useful approach for rhesus monkey cloning.

first: Zhaodi

last: Liao


title: Knockdowns of total NFYA and a NFYA long 3’ UTR isoform followed by RNA-seq to determine isoform-specific effects on gene expression

city: Houston

first: Angela

middle: H

last: Ting

state: Tx

address: 1881 East Road

department: Epigenetics and Molecular Carcinogenesis

institute: The University of Texas MD Anderson Cancer Center

summary: Alternative cleavage and polyadenylation (APA) produces multiple isoforms of the Nuclear Transcription Factor Y Subunit Alpha (NFYA) gene with variable length 3? untranslated regions (UTRs). These isoforms have been detected in HCT116 colon cancer cells via polyA-seq and northern blots, as well as colon cancer tissue RNA-seq data. NFYA is a transcription factor that may regulate cell growth and proliferation in cancer and development. To determine if there may be transcriptional regulation unique to the long 3’ UTR isoform, we conducted an siRNA knockdown in HCT116 cells specific to either the long isoform (by targeting sequence uniquely present in the longer transcript) or total NFYA mRNA (by targeting sequence shared by all long and short NFYA mRNA isoforms) followed by next generation sequencing of RNA (RNA-seq) to analyze the transcriptome.

overall_design: RNA-seq was performed for mock transfected cells (no siRNA present), control siRNA cells (non-targeting siRNA), siRNA targeting total NFYA (siTotal), and siRNA targeting long-isoform NFYA specifically (siLong). Two distinct siRNA sequences were used for both the siTotal and siLong experiments. Experiments and RNA-seq were performed in biological duplicate for each of the 5 distinct siRNA sequences and mock transfection.

first: Thomas

last: Sweet

first: Jeffrey

last: Bhasin


title: Single cell RNA sequencing of normal thyroid

city: Daejeon

first: Yea Eun

last: Kang

address: 282Munhwa-ro, Jung-gu Daejeon

department: Department of Endocrinology and Metabolism

country: South Korea

institute: Chungnam National

summary: We performed single-cell RNA-sequencing of 54,762 cells derived from normal thyroid tissue from 7 patients, revealing distinct cell types including epithelial cells, fibroblasts, endothelial cells, smooth muscle cells/pericytes, and various immune cells.

overall_design:
Single-cell RNA-seq data were mapped, and counts of molecules per barcode were quantified using the 10x software package cellranger (version 3.0.2) and GRCh38 reference genome supplied by 10x Genomics. To exclude low quality or doublets, we performed Scrublet and filtered cells with fewer than 200 genes or cells with 25% or higher mitochondrial proportion and obtained 54,726 cells from 7 normal thyroid samples.

**To ensure preservation of patient confidentiality, raw data are available on request.**

first: Yea

first: Bon

last: Koo

first: Minho

last: Shong


title: The effects of various levels of drought and heat on the rice shoot transcriptome

city: Winnipeg

first: Olivia

last: Wilkins

state: Manitoba

address: 66 Chancellors Cir

department: Biological Sciences

country: Canada

institute: University of Manitoba

summary: To investigate the relative effects of drought and heat on the rice (Oryza sativa) transcriptome, we subjected rice seedlings to 3 levels of long-term drought or 2 levels of short-term heat stock

overall_design: Rice was grown for 10 days in 3 water levels: wet/control (3g/g SWC), mild drought (1.5g/g SWC) or severe drought (1.25g/g SWC). At 10 days, additional wet-condition plants were subjected to 30min or 60min heat shock. 3 reps of each condition above were collected at midday (6hr after dawn) for RNA-sequencing.

first: Sean

last: Robertson

first: Solihu

middle: K

last: Sakariyahu


title: Extracellular vesicles confer disease phenotype in Y402H-retinal pigment epithelium cell model of age-related macular degeneration.

city: NEWCASTLE

first: Megan

middle: Saphana Rose

last: Hasoon

address: Newcastle University

country: United Kingdom

institute: Newcastle University

summary: Age related macular degeneration (AMD) is a leading cause of legal blindness. Vision loss is caused by the retinal pigment epithelium (RPE) and photoreceptors loss and/or retinal and choroidal angiogenesis. Here we report enhanced polarised secretion of extracellular vesicles (EVs) in complement factor H (CFH) Y402H AMD patient specific RPE. As indicated by multi ‘omics analyses, AMD RPE EVs carry a repertoire of RNA, proteins and lipids that reflect disease changes in the RPE cells of origin and mediate pathological processes such as oxidative stress, cytoskeletal dysfunction and angiogenesis. We demonstrate that exposure of control RPE to AMD RPE EVs leads to the formation of numerous cytoplasmic stress vacuoles, cytoskeletal destabilization, and abnormalities in the morphology of the nucleus in the recipient cells. Treatment of laminated retinal organoids containing photoreceptor cells with apical AMD RPE EVs leads to disrupted neuroepithelium and appearance of enlarged cells immunopositive for cytoprotective alpha B crystallin. The presence of cells expressing alpha B crystallin and progenitor cells markers Pax6 or Vsx2 are consistent with the activation of regenerative pathways upon injury. These findings suggest that AMD RPE EVs act as signalling messengers in the outer retina and may be involved in disease progression.

overall_design: 4 AMD patient CFH Y402H carriers-derived samples (F180_A, F180_B, F181_A and F181_B) and 4 control individuals-derived samples (F018_A, F018_B, AD3_A and AD3_B). All samples in duplicates. A- apical, B-basal - RPE cell conditioned media fractions-derived extracellular vesicles.

first: Marzena

last: Kurzawa-Akanbi

first: Phillip

last: Whitfield

first: Florence

last: Burte

first: Birthe

last: Hilgen

first: Andrew

last: Porter

first: Mary

last: Doherty

first: Mark

last: Platt

first: Jonathan

last: Coxhead

first: Rachel

last: Queen

first: Maria

last: Oberg

first: Daniel

last: Fabrikova

first: Chia

last: Beh

last: Georgiou

first: Joseph

last: Collin

first: Anetta

last: Hartlova

first: Jumana

last: Al-Aama

first: Viktor

last: Korolczuk

first: David

last: Steel

first: Lyle

last: Armstrong

first: Majlinda

last: Lako


title: EZH2-mediated epigenetic suppression of IFNa/b-STAT2 signaling enhances anti-tumor immunity in breast cancer

first: Kexin

last: Xu

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

overall_design: Refer to individual Series


title: RNA-seq analysis of human colorectal cancer cells with NAT10 deficiency.

city: Nanjing

first: Chi

last: Jin

address: Han Zhong Road

institute: Nanjing university school

summary: Transcriptional analysis of DLD-1 and SW480 cells with NAT10 knockdown.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for DLD-1 and SW480 cells and its KD derivatives (shNAT10).

first: Tuo

last: Wang

first: Peng

last: Yang

first: Chuan

last: Zhang

first: Wen

last: Peng

first: Dongsheng

first: Kangpeng

first: Lu

first: Jiahui

last: Zhou

first: Chaofan

first: Yuqian

last: Tan

first: Jiangzhou

last: Ji

first: Zhihao

last: Chen

first: Qingyang

last: Sun

first: Sheng

first: Junwei

last: Tang

first: Yifei

last: Feng

first: Yueming


title: NOX1 is essential for TNFα-induced intestinal epithelial ROS secretion and inhibits M cell differentiation [RNA-seq organoid]

first: Judy

last: Cho

address: 1470 Madison Avenue, 8th Fl., Box 1498;

department: Pathology, Molecular and Cell-Based Medicine

institute: Icahn School of Medicine at Mount Sinai

summary: Loss-of-function mutations of NOX1 is associated with inflammatory bowel disease (IBD). In what epitheial cell types in human colon Nox1 is expressed is unclear. Here we performed RNA seq analysis of 50% WRN or 5% WRN treated human colonoid lines from IBD, UC and heathy donors. We showed Nox1 is mainly expressed in stem cell (50% WRN treated condition ) when comparing to coloncyte (5% WRN treated contion).

overall_design: Transcriptome analysis of 50%WRN or 5% WRN treated human colonoid lines . 8 biological replicates colonoids lines per group were used in the studies.

first: Kyle

last: Gettler


title: NOX1 is essential for TNFα-induced intestinal epithelial ROS secretion and inhibits M cell differentiation [scRNA-seq]

summary: Loss-of-function mutations of NOX1 is associated with inflammatory bowel disease (IBD). Mechanisms whereby loss of Nox1 drives IBD are incompletely defined. Here we used TNF⍺ treated colonoids to model IBD inflammation followed by single cell sequencing to get transcriptome profile of IBD relevant cells.

overall_design: Single cell seq analysis of mice intestinal colonoid from untreated and TNF⍺-treated samples

first: Christopher

last: Tastad


title: Whole-transcriptome analysis of dermal fibroblasts from patients with hypermobile Ehlers-Danlos syndrome and hypermobility spectrum disorders supports their categorization as a single clinical entity with a contribution of inflammatory pathways

city: Brescia

first: Nicola

last: Chiarelli

state: Lombardy

address: Viale Europa 11

department: Molecular and Translational Medicine

institute: University of Brescia

summary: Hypermobile Ehlers-Danlos syndrome (hEDS) and hypermobility spectrum disorders (HSD) are clinically overlapping connective tissue disorders of unknown etiology and without any validated diagnostic biomarker and specific therapies. Herein, we in-depth characterized the cellular phenotype and gene expression profile of hEDS and HSD dermal fibroblasts by immunofluorescence, amplicon-based RNA-seq, and qPCR. We demonstrated that both cell types show a common cellular trait, i.e., generalized extracellular matrix (ECM) disarray, myofibroblast differentiation, and dysregulated gene expression. Functional enrichment and pathway analyses clustered gene expression changes in different biological networks that are likely relevant for the disease pathophysiology. Specifically, the complex gene expression dysregulation (mainly involving growth factors, structural ECM components, ECM-modifying enzymes, cytoskeletal proteins, and different signal transducers), is expected to perturb many ECM-related processes including cell adhesion, migration, proliferation, and differentiation. Based on these findings, we propose a disease model in which an unbalanced ECM remodeling triggers a vicious cycle with a synergistic contribution of ECM degradation products and proinflammatory mediators leading to a functional impairment of different connective tissues reflecting the multisystemic presentation of hEDS/HSD patients. Our results offer many promising clues for translational research aimed to define molecular bases, diagnostic biomarkers, and specific therapies for these challenging connective tissue disorders.

overall_design: Comparative gene expression profiling analysis of RNA-seq data of fibroblast cell strains derived from 20 hEDS and 20 HSD patients, and 40 healthy donors


title: NOX1 is essential for TNFα-induced intestinal epithelial ROS secretion and inhibits M cell differentiation


title: NanoString analysis of mouse granulomas induced by H. polygyrus infection

city: Calgary

first: Constance

last: Finney

state: Alberta

address: 2500 University Drive NW

institute: University of Calgary

summary: Heligmosomoides polygyrus larvae induce a strong intestinal granuloma response within their murine host, which has been associated with resistance. Immune cells, mostly alternatively activated macrophages and eosinophils, accumulate around the tissue encysted parasites to immobilize and damage/kill developing worms. In a one dose (bolus) experimental infection, infected C57Bl/6 mice are unable to clear parasites which results in chronic infection with high worm burdens. However, using a frequent dose trickle model of infection, we, like others, have found that C57Bl/6 mice can clear infection. The nanoString data included here measure the expression of key myeloid genes within the granuloma tissue from bolus and trickle infections. Our results highlight the importance of the granuloma in the host’s ability to clear H. polygyrus and emphasise the need to study this key tissue in more depth, rather than using correlates such as general intestinal or systemic responses.

overall_design: A total of 15 samples are included, for five separate infection conditions with replicates. One of the conditions is uninfected control mice (intestinal tissue from the same area of intestine the worms infect), 2 replicates. The experimental conditions include 2 time points (7 days post infection and 21 days post infection) for bolus- and trickle-style infections, each done with 3 or 4 replicates.

first: Anupama

last: Ariyaratne

first: Sang

middle: Y

last: Kim

first: Stephen

last: Pollo

first: Mayara

last: de Cassia Luzzi

first: Joel

last: Bowron

first: Edina

last: Szabo

first: James

middle: D

last: Wasmuth

first: Meera

last: Nair


title: Cell autonomous expression of Bcl6 is required to maintain lineage identity of mouse CCR6+ ILC3s

city: Beijing

first: Yuling

last: Li

address: 30 ShuangQing Street

department: Institute for Immunology and School of Medicine,

institute: Tsinghua University

summary: Innate lymphoid cells (ILC) are similar to T helper (Th) cells in expression of cytokines and transcription factors. For example, RORγt is the lineage-specific transcription factor for both ILC3 and Th17 cells. However, the ILC counterpart for BCL6-expressing T follicular helper (Tfh) cells has not been defined. Here, we report that in the ILC compartment, BCL6 is selectively co-expressed with not only CXCR5, but also RORγt and CCR6 in ILC3 from multiple tissues. BCL6-deficient ILC3 produce enhanced levels of IL-17A and IL-22. More importantly, phenotypic and single-cell ATAC-seq analysis show that absence of BCL6 in mature ILC3 increases the numbers of ILC1 and transitional cells co-expressing ILC3 and ILC1 marker genes. A lineage-tracing experiment further reveals BCL6+ ILC3 to ILC1 trans-differentiation under steady state. Lastly, microbiota promote BCL6 expression in colonic CCR6+ ILC3, and thus reinforce their stability. Collectively, our data have demonstrated that CCR6+ ILC3 have both Th17 and Tfh programs and that BCL6 expression in these cells functions to maintain their lineage identity.

overall_design: Single cell ATAC-seq of total intestinal ILC from WT (Bcl6^fl/fl) and KO (Vav1^cre Bcl6^fl/fl) mice


title: Arhgdia regulates disease tolerance in IAV-infected epithelial cells

city: Tel-Aviv

first: Gal

last: Yankovitz

address: Haim Levanon

department: The Shmunis School of Biomedicine and Cancer Research

country: Israel

institute: Tel-Aviv University

summary: When challenged with an invading pathogen, host defense mechanisms are engaged to eliminate the pathogen (resistance) and limit tissue damage that results from host-pathogen interactions (disease tolerance). We identified Arhgdia as a driver of the molecular disease-tolerance response in epithelial cells. The effect of Arhgdia on disease tolerance and resistance was evaluated at early stages of influenza A virus (IAV) infection. Our observations indicates that Arhgdia has an effect on disease tolerance during IAV infection.

overall_design: To test the role of Arhgdia in the regulation of disease-tolerance state, we deleted Arhgdia in mouse epithelial cells (LET1 and MLE cells) by CRISPR-Cas9 editing, and then tested the effect of this deletion on the host response to infection. Control (non-targeting sgRNA) and Arhgdia-deleted (Arhgdia-targeted sgRNA) cells, with and without IAV infection, were analyzed.

first: Ofir

last: Cohn

first: Naama

last: Peshez-Yaloz

first: Yael

last: Steuerman

first: Amit

last: Frishberg

first: Michal

last: Mandelboim

first: Eran

last: Bacharach

first: Irit

last: Gat-Viks


title: Inactivation of p21-Activated Kinase 2 (Pak2) Inhibits the Development of Nf2-Deficient Tumors by Restricting Downstream Hedgehog and Wnt Signaling

city: Philadelphia

first: Michael

last: Slifker

address: 333 Cottman Ave.

institute: Fox Chase Cancer Center

summary: RNAseq analysis revealled that the expression of Hedgehog and Wnt pathway members were altered by Pak2 gene knockout during mesotheliomagenesis.

overall_design: RNA SEQUENCING ON PERITONEAL PRIMARY TUMORS was performed to compare the transcriptome changes during the formation of mesothelioma in different genotypes of mice

first: Eleonora

last: Sementino

first: Joseph

middle: R

last: Testa


title: HNF1B induced three-dimensional genome analysis of patient-derived pancreas neoplasm organoids [HiC]

city: Tokyo

first: Keisuke

last: Tateishi

address: 7-3-1 Hongo, Bunkyo-ku

department: Department of Gastroenterology

institute: Graduate School of Medicine, The University of Tokyo

summary: Three-dimensional (3D) genome structures are organized in a hierarchy of various module layers, including chromosome compartment, topologically associating domain, and enhancer-promoter loop. These modules are important in regulating cell type specific gene expression. Here, we aimed to elucidate how 3D genome organization is related to regulating subtype specific genes in pancreatic neoplasms.

overall_design:
3D genome structure analysis together with epigenomic and expression profiling using patient-derived organoids. HNF1B was overexpressed to identify its role in subtype specific genome modulation.
**Please note that raw data are submitted to JGA (Japanese Genotype-phenotype Archive) with JGAS000514 accession number***

first: Hiroyuki

last: Kato


title: HNF1B induced three-dimensional genome analysis of patient-derived pancreas neoplasm organoids


title: RELMβ Sets the Threshold for Microbiome-Dependent Oral Tolerance

city: Boston

first: KLaus

last: Schmitz-Abe

state: MA

address: 300 Longwood Avenue

department: Asthma, Allergy and Immunology

institute: Children's Hospital Boston

summary: Tolerance to dietary antigens is critical to avoid deleterious type 2 immune responses resulting in food allergy (FA) and anaphylaxis. However, the mechanisms resulting in both the maintenance and failure of tolerance to food antigens is poorly understood. Here we demonstrate that the goblet cell-derived resistin-like molecule beta (RELMb) is a critical regulator of oral tolerance. We find that RELMb is abundant in serum in both food allergic patients and mouse models of FA. Deletion of RELMβ protects mice from FA, development of food antigen specific IgE and anaphylaxis. RELMb disrupts food tolerance through modulation of the gut microbiome by suppressing gut Lactobacilli. Tolerance is maintained via local production of indole derivatives driving FA protective RORgt+ regulatory T (Treg) cells via activation of the aryl hydrocarbon receptor (AhR). RELMb antagonism in the peri-weaning period restored oral tolerance and protected genetically prone offspring from developing FA later in life. Together, our data identify RELMb as mediating both a novel gut immune-epithelial circuit regulating tolerance to food antigens, a new mode of innate control of antigen specific adaptive immunity via microbiome editing and targetable candidates in this circuit for prevention and treatment of FA.

overall_design: Small intestinal epithelial cells from WT, Il4raF709 or Retnlb–/–Il4raF709 were cell sorted using BD FACS Aria and Snap Freeze before RNA preparation.

first: Emmanuel

last: Victor

first: Klaus

first: Talal

middle: A

last: Chatila


title: HNF1B induced three-dimensional genome analysis of patient-derived pancreas neoplasm organoids [RNA-seq]


title: Identification of NAT10 targets in CRC by RNA immunoprecipitation and acethyl-RNA immunoprecipitation

first: Chi

last: Jin

summary: To identify potential mRNAs that are acetylated by NAT10, RIP with a NAT10 antibody and acRIP with a ac4C antibody were conducted in DLD-1 and SW480 cells

overall_design: Total RNA isolated from DLD-1 or SW480 cells was framented and subjected to immunoprecipitation using anti-ac4C antibody. After incuation and washing, samples were eluted using elution buffer containing ac4C nucleoside. The resultant final product was used for RNA-seq. Besides, RNA immunoprecipitation was performed in DLD-1 and SW480 cells according to manufacturer's protocol. RNA isolated from RIP was also used for RNA-seq.

first: Tuo

last: Wang

first: Peng

last: Yang

first: Chuan

last: Zhang

first: Wen

last: Peng

first: Dongsheng

first: Kangpeng

first: Lu

first: Jiahui

last: Zhou

first: Chaofan

first: Yuqian

last: Tan

first: Jiangzhou

last: Ji

first: Zhihao

last: Chen

first: Qingyang

last: Sun

first: Sheng

first: Junwei

last: Tang

first: Yifei

last: Feng

first: Yueming


title: HNF1B induced three-dimensional genome analysis of patient-derived pancreas neoplasm organoids [ChIP-seq]

first: Keisuke

last: Tateishi

first: Hiroyuki


title: The molecular programs underpinning ‘tolerance’ and ‘resistance’ in health and viral infection

first: Gal

last: Yankovitz

summary: We collected lung transcriptomes 96 hours after influenza A virus (IAV) infection across 12 genetically-distinct mouse strains (2 individuals per strain).

overall_design: Lungs gene expression of Collaborative Cross mice taken 96 hours after the infection with influenza A virus.

first: Ofir

last: Cohn

first: Naama

last: Peshez-Yaloz

first: Yael

last: Steuerman

first: Amit

last: Frishberg

first: Michal

last: Mandelboim

first: Fuad

last: Iraqi

first: Eran

last: Bacharach

first: Irit

last: Gat-Viks


title: Studying heterogeneity in embryonic stem cells using the approach of search-engine

city: Singapore

first: Vibhor

last: Kumar

address: 60 Biopolis Street, Genome, #02-01

country: Singapore

institute: Genome Institute of Singapore

summary: Here we designed a search-engine for single-cell epigenome profiles. We tested different application of search-engine using different data-sets including mESC scATAC-seq profile.

overall_design: scATAC-Seq of E14

first: Kedar

last: Natrajan


title: The molecular programs underpinning 'tolerance' and 'resistance' in health and viral infection

summary: The immune protection against invading pathogens is governed by pathogen elimination (‘resistance’) and by limitation of tissue damage that results from host-pathogen interactions (‘tolerance’). However, distinct molecular states of resistance and tolerance remain obscure. Here, we collected longitudinal lung transcriptomes and clinical phenotypes of disease severity during influenza A virus (IAV) infection across 39 genetically-distinct mouse strains (32 strains of time series data and additional 7 strains with selected time points). Using transcriptional diversity in this data, we uncovered two key programs that together describe the cellular states for resistance and tolerance. The identified programs offer an unprecedented comprehensive view on shared and distinct roles of resistance and tolerance for the regulation of immune defense – for instance, we identified an antagonistic regulation of resistance and tolerance on protein production. Importantly, the framework reveals that both inflammatory states and the healthy steady state are remarkably diverse in resistance and tolerance levels, with implications on disease severity: a baseline state (before infection) of high tolerance and low resistance results in increased severity of IAV infection. Overall, our work provides a framework for the study of resistance and tolerance that could aid in clinical diagnosis and disease management.

sample_organism: Influenza A virus (A/Puerto Rico/8/1934(H1N1))

overall_design: To characterize the host defense, we investigated longitudinal data during IAV infection across genetically distinct mouse strains. We recorded lung transcriptomes of mouse strains of the collaborative cross (CC) cohort, both in steady state (before infection) and at five time points during the course of IAV infection (3h to 96h p.i.).


title: RNA-seq analysis of mouse hearts over-expressing PTBP1 using an AAV9 vector

city: Cold Spring Harbor

first: Carlos

last: Martí-Gómez

email: carlos199m1@gmail.com, martigo@cshl.edu

state: New York

address: 1 Bungtown Rd

department: Quantitative Biology

institute: Cold Spring Harbor Laboratory

summary: The goal of this study is to study alternative splicing changes driven by PTBP1 in the mouse heart

overall_design: Left ventricle samples from mice over-expressing PTBP1 using an AAV9 vector were are compared to those injected with a control virus carrying luciferase 28 days after injection

first: Javier

last: Larrasa

last: Martí

first: Enrique

last: Lara-Pezzi


title: RANKL-RANK activation in mmtv-Pymt primary tumor cultures

city: Hospitalet de Llobregat

first: Eva

last: González-Suárez

state: Barcelona

address: Hospital Duran i Reynals - 3a planta -Gran Via de l'Hospitalet, 199

department: Epigenetics and Cancer Biology

country: Spain

institute: Institut d'Investigació Biomèdica de Bellvitge

summary: MMTV-PyMT late carcinomas, orthotopically injected in syngeneic RANK+/+ mice were digested until single cells and cultured over Matrigel in the prescence or abscence of RANKL for 24 hours.

overall_design: RNA was isolated from tumors derived from three different mmtv_PyMT tumor-bearing mice growing in vitro in the prescence (or absence) of RANKL for 24 hours. DNAse treated RNA from each sample was hybridized to the Agilent-028005 SurePrint G3 Mouse GE 8x60K Microarray (GPL13912).

first: Guillermo

last: Salinas

first: Clara

middle: G

last: Aleza


title: Effect of nitrogen compounds on imbibed mutant seeds impaired in glucosinolate biosynthesis

status: Public on Dec 26 2022

city: Angers

first: Jerome

last: Verdier

address: Rue Georges Morel

country: France

institute: INRAE / IRHS

summary: These RNAseq data are from germinating cyp79B2, cyp79B3, myb28, myb29 (qko), cyp79B2, cyp79B3 (cyp) and myb28 myb29 (myb) mutant seeds. Col-0 genotype was used as the Arabidopsis' WT reference ecotype and all mutant seeds are from the Col-0 genetic background. Samples were sown on agarose 0,8%, supplemented or not by nitrate KNO3 10Mm or potassium thiocyanate KSCN 8µM. RNA isolation was performed using NucleoSpin® RNA Plant and Fungi kit. RNA quantification was obtained with a NanoDrop ND-100 (NanoDrop Technologies, DE, USA) and the RNA Integrity was measured with a 4100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). cDNA library construction and sequencing were performed with DNBseq™ technology at Beijing Genomics Institute BGI. FastQC was used to check read quality, mapping analysis and transcript quantiifcation were performed using a quasi-mapping alignment from Salmon.

overall_design: The workflow started with the seed surface sterilization, dry seeds and 6h imbibed seeds either  in water, either in KNO3 10Mm or in KSCN 8µM were compared. Total RNAs were obtained and sequenced via cDNA library construction.

first: Philippe

last: Grappin

first: Mailen

middle: O

last: Cuadros

first: Sophie

last: Aligon


title: miRNA-sequencing of human non-calcificated and calcificated aortic valve interstitial cells

first: liu

last: cuiying

address: no.87 Dingjiaqiao

department: Cardiology

country: China

institute: The Medical School of Southeast University

summary: To explore the miR expression profile of calcified valve interstitial cells (VICs) induced by high calcium/phosphate, identify the key miRNA in the calcification process of VICs, and probe effect of miRs in regulating valve calcification.

overall_design:
We then performed gene expression profiling analysis using data obtained from miRNA-seq of 2 different treat cells.
Comparative gene expression profiling of miRNA-seq data from calcified and non-calcified human aortic valve interstitial cells (Calcification and Normal).

first: Jing

last: Liu

first: Cuiying

first: Xiangqing

last: Kong


title: RNA-Seq data of ruminal epithelial tissue and 16S rRNA sequencing data of rumen digesta in goats infusion of three short-chain fatty acids

city: Yangzhou

first: Yongkang

last: Zhen

state: — Please Select —

address: Yangzhou University

institute: Yangzhou University

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

overall_design: Refer to individual Series


title: RNA-Seq data of ruminal epithelial tissue and 16S rRNA sequencing data of rumen digesta in goats infusion of three short-chain fatty acids [16s rRNA-seq]

summary: Emerging data has highlighted the importance of short-chain fatty acids (SCFAs), particularly butyrate, in regulating ruminal homeostasis in vivo isolated epithelial cells. However, little is known about other SCFAs like acetate or propionate, and the interaction between rumen microbes and epithelial immunity are rarely reported. Here, we firstly combined infusion of three SCFAs, to study their different roles in ruminal development, antioxidant capacity, barrier functions, and immunity, as well as cross-talk with ruminal microbiome (16S rRNA sequencing data of rumen digesta) and derived transcriptome (RNA-Seq) and metabolism using an in vivo goat model.

overall_design: A total of twenty-four healthy multiparous Guanzhong goats with an average body weight of 47.44 ± 3.38 kg at 1.5 years old in latter half of gestation period were selected in this study. All dairy goats were then randomly divided into four groups (n = 6 for each group) after adaption with the diet and light conditions to receive different SCFAs infusion treatments. They were assigned to a normal control group infusion with normal saline (NC), an infusion with sodium acetate solution (SA), an infusion with sodium propionate solution (SP), and an infusion with sodium butyrate solution (SB) according to previous studies in ruminants. The same volume of SCFAs and normal saline solutions at 1 L were slowly perfused into the rumen with a rumen tube daily before morning feeding. All solutions were calibrated to be consistent with a pH meter before infusion. The experiment lasted for 13 days, which combined with a 12-days of infusion period and a 1-day of sampling period. All goats were fasted for 12 hours before the sampling day. The animals were then weighed, and slaughtered and dressed by professional butchers. Firstly, the rumen digesta was immediately collected and stored directly in liquid nitrogen for the analysis of rumen microbiome using 16S rRNA sequencing. Then, another part of 5 g rumen epithelial tissue was rapidly frozen in liquid nitrogen for rumen epithelial RNA-Seq.


title: RNA-Seq data of ruminal epithelial tissue and 16S rRNA sequencing data of rumen digesta in goats infusion of three short-chain fatty acids [RNA-seq]


title: Genome-Wide Analysis of TCP Transcription FactorFamily in Sunflower and Identification of HaTCP1 Involved in the Regulation of Shoot Branching

city: Hefei

first: yu

middle: wuyu

last: wu

state: Anhui

address: changjiang  road

department: College of Horticulture

institute: Anhui Agricultural University

summary: These findings could lay a critical foundation for further exploring the functions of HaTCPs.

overall_design: Differential gene expression in different tissues of sunflower

first: Lili

last: Dong

first: Yu

last: Wu

first: Jianbin

last: Zhang

first: Chaoqun

last: Li

first: Xinyi

last: Deng

first: Tian

last: Wang


title: High-throughput sequencing analysis of mRNA and lncRNA in macrophages of wild-type and GM1082-/- mice

city: tianjin

first: Yunhuan

last: Gao

address: Wei Jin Road No. 94

department: School of Medicine

institute: Nankai University

summary: At the epigenetic level, lncRNAs play important roles in cell differentiation and function. We identified novel long-stranded non-coding RNA (GM1082) in macrophage.We used high-throughput sequencing to detail the global programme of gene expression and identified distinct classes of up or down regulated genes in macrophage of wild-type and GM1082-/- mice.

overall_design: wild-type and GM1082-/- bone marrow cells were exposed to M-CSF for 5 days, and mRNA and lncRNA expression was evaluated using High-throughput sequencin

first: Ya

first: Yazheng

last: Yang

first: Rongcun


title: STAT3 regulates CD8+ T cell differentiation and functions in cancer [RNA-seq]

status: Public on Dec 25 2022

first: Chen

address: Haidian District

department: Institute for Immunology and School of Medicine

summary: In cancer, persistent antigens drive CD8+ T cell differentiation into exhausted progenitor (Texprog) and terminally exhausted (Texterm) cells. However, how the extrinsic and intrinsic regulatory mechanisms cooperate during this process still remain not well understood. Here, we found STAT3 signaling plays essential roles in promoting intra-tumor Texterm cell development, by enhancing their effector functions and survival, which results in better tumor control. In tumor microenvironments, STAT3 is predominantly activated by IL-10 and IL-21, but not IL-6. Besides, STAT3 also plays critical roles in the development and function of terminally differentiated effector CD8+ T cells in acute infection. Mechanistically, STAT3 transcriptionally promotes the expression of effector function-related genes, while suppresses those expressed by progenitor Tex subset. Moreover, STAT3 functions in collaboration with BATF and IRF4 to mediate chromatin activation at effector gene loci. Thus, we have elucidated the roles of STAT3 signaling in terminally differentiated CD8+ T cell development, especially in cancer, which benefits developing more effective immunotherapies against tumor.

overall_design: RNA-seq of WT and Stat3-/- OT-I cells from B16-OVA tumors at about day 16 post inoculation

first: Qinli

last: Sun


title: STAT3 regulates CD8+ T cell differentiation and functions in cancer [ChIP-seq]

overall_design: FACS sorted naïve CD8+ T cells were activated with the plate-bound anti-CD3 and anti-CD28 for three days. For pSTAT3 ChIP-seq, the activated WT CD8+ T cells were cultured at 37 ℃ for 30 minutes in fresh medium with 10ng/ml IL-6, 10ng/ml IL-10 or 10ng/ml IL-21. For H3K27ac ChIP-seq, the activated WT and Stat3-/- CD8+ T cells were stimulated by 10ng/ml IL-10 for another three days. Chromatin from 1x10^7 live cells was used for each ChIP experiment. 7.5µg anti-pSTAT3(Y705) antibody or 1µg anti-H3K27ac antibody were used.


title: STAT3 regulates CD8+ T cell differentiation and functions in cancer [ATAC-seq]

overall_design: ATAC-seq of WT and Stat3-/- OT-I cells from B16-OVA tumors at about day 16 post inoculation


title: STAT3 regulates CD8+ T cell differentiation and functions in cancer


title: Whole brain RNA-seq from maternal Astatotilapia burtoni

city: Portland

first: Suzy

middle: CP

last: Renn

state: Oregon

address: 3203 SE Woodstock Blvd., Biology Room B124

department: Biology

country: USA

institute: Reed College

summary: Brains from female Astatotilapia burtoni were sampled at four timepoints throughout the reproductive cycle with the primary goal of comparing transcriptome profiles at the different stages and identifying genes and networks involved in parental and fasting behaviors.

overall_design: Females were maintained in 30 gallon mixed sex stock tanks with 2-4 males and 8-12 females. Tanks were checked daily, and when brooding females were captured and fry development stage was confirmed. Females were systematically assigned to one of four treatment groups: 2 days mouthbrooding (B02), 14 days mouthbrooding (B14), 2 days post-release of fry (R02), and 14 days post release (R14) (Fig 1). Only females confirmed to be holding stage 0 fry were assigned to the B02 group.

first: Joshua

middle: J

last: Faber-Hammond

first: Susan

middle: C


title: Gene expression profile at single cell level of podocyte-specific I-PpoI expressing mice kidney cortex

city: tokyo

first: akihito

last: hishikawa

address: Shinanomachi35, shinjyukuku

institute: keio university

summary: To investigate the alterations in cell populations in the kidney after podocyte DNA DSBs, we performed single-cell RNA sequencing (scRNA-seq)  on the renal cortex of 12-week-old podocyte-specific I-PpoI expressing mice that had not yet developed glomerulosclerosis or fibrosis.

overall_design: Kidneys were harvested, minced into 1 mm3 cubes, digested using digestion buffer and analyzed using scRNA-seq.

first: Ran

last: Nakamichi

first: Akihito

last: Hishikawa

first: Kaori

last: Hayashi


title: Transcriptome analysis of MCF-7 breast cancer cells in which VASP gene was knocked down

city: Wuhan

first: Kai

address: 185 Donghu Road, Wuchang District

institute: Wuhan University

summary: Previous studies have shown that the main function of VASP is to regulate the cytoskeleton and play an important role in promoting tumor cell metastasis. In this study, we first reveal that VASP is located in the nucleus of breast cancer cells and elucidate a Wnt/β-catenin/VASP positive feedback loop. We identify that VASP is a target gene of Wnt/β-catenin signaling pathway, and activation of Wnt/β-catenin signaling pathway can significantly upregulate VASP protein expression, while upregulated VASP protein can in turn promote translocation of β-catenin and DVL3 proteins into the nucleus. In the nucleus, VASP, DVL3, β-catenin and TCF4 can form VASP/DVL3/β-catenin/TCF4 protein complex, activating Wnt/β-catenin signaling pathway, and promoting the expression of target genes VASP, c-myc and cyclin D1. Thus, our study reveals that there is a Wnt/β-catenin/VASP malignant positive feedback loop in breast cancer, which promotes the proliferation and migration of breast cancer cells, and breaking this positive feedback loop may provide new strategy for breast cancer treatment.

overall_design: Examination of the effect of VASP knockdown on the human breast cancer cells MCF-7

first: Lei

last: Wei


title: Macrophage DCLK1 promotes atherosclerosis via binding to IKKβ and inducing inflammatory responses

status: Public on Dec 24 2022

city: Wenzhou

first: Guang

last: Liang

address: Chashan

institute: Wenzhou Medical University

summary: Atherosclerosis is a chronic inflammatory disease with high morbidity and mortality rates worldwide. Doublecortin-like kinase 1 (DCLK1), a microtubule-associated protein kinase, is involved in neurogenesis and human cancers. However, the role of DCLK1 in atherosclerosis remains undefined. In this study, we identified up-regulated DCLK1 in macrophages in atherosclerotic lesions of ApoE-/- mice fed an HFD and determined that macrophage-specific DCLK1 deletion attenuates atherosclerosis by reducing inflammation in mice. Mechanistically, RNA sequencing analysis indicated that DCLK1 mediates oxLDL-induced inflammation via NF-κB signaling pathway in primary macrophages. Co-immunoprecipitation followed by LC-MS/MS analysis identified IKKβ as a binding protein of DCLK1. We confirmed that DCLK1 directly interacts with IKKβ and phosphorylates IKKβ at S177/181, thereby facilitating subsequent NF-κB activation and inflammatory gene expression in macrophages. Finally, a pharmacological inhibitor of DCLK1 prevents atherosclerotic progression and inflammation both in vitro and in vivo. Our findings demonstrated that macrophage DCLK1 promotes inflammatory atherosclerosis by binding to IKKβ and activating IKKβ/NF-κB. This study reports DCLK1 as a new IKKβ regulator in inflammation and a potential therapeutic target for inflammatory atherosclerosis.

overall_design: we performed RNA sequencing analysis on  three WT+oxLDL groups and three KO+oxLDL groups

first: Zhuqi

last: Huang


title: Transcriptome analysis of breast cancer cells in which VASP gene was knocked down


title: Tracking chromatin state changes using nanoscale protoproximity labeling (ATAC-Seq)

city: Jupiter

first: Ciaran

last: Seath

state: Florida

address: 120 Scripps Way

institute: UF-Scripps

summary: Effect of histone mutation H2A E92K on open reading frames in HEK293T cells

overall_design:
Comparative gene expression profiling analysis of ATAC-seq data for HEK293T cells transfected with H2A or H2A(E92K).

*reads are next aligned to reference genome hg38*

middle: P


title: Transcriptome analysis of MDA-MB-231 breast cancer cells in which VASP gene was knocked down

overall_design: Examination of the effect of VASP knockdown on the human breast cancer cells MDA-MB-231


title: Tracking chromatin state changes using nanoscale protoproximity labeling


title: An Interactome Map of Maize (Zea mays L.)

city: wuhan

first: qian

middle: lin

last: han

state: hubei

address: Huazhong Agricultural University, No.1 Shizishan Street, Hongshan District

institute: Huazhong Agricultural University

summary: These data include RNA-seq, circRNA-seq, and small RNA-seq of transcriptome, Ribo-seq of translatome and protein protein binary interactions by recombination-based library vs. library yeast-2-hybrid throughout the lifecycle of the maize inbred line B73.

overall_design: We constructed an interactome involving genome, transcriptome, translatome and proteome.

first: Linqian

last: Han

first: Jia

last: Qian

first: Wanshun

last: Zhong


title: Stroke-induced transcriptomic alterations in mouse cerebral microvessels

city: New York

first: Teresa

last: Sanchez

state: NY

address: 1300 York Ave

institute: Weill Cornell Medicine

summary:
To investigate the stroke-induced changes in gene expression in cerebral microvessels, we subjected mice to transient middle cerebral artery occlusion (tMCAO) or sham surgeries. 24h hours later, cerebral microvessels were harvested and RNA was isolated.
We then performed gene expression profiling analysis using data obtained from RNA-seq of cerebral microvessels isolated from 8 mice (4 shams and 4 tMCAO)

overall_design: Comparative gene expression profiling analysis of RNA-seq data for sham and tMCAO mice

first: Keri

last: Callegari

first: Sabyasachi

last: Dash

first: Tuo

last: Zhang

first: Yun

last: Lee

first: Hiroki

last: Uchida

first: Akira

last: Ito

first: Yuto

last: Shingai

first: Jenny

middle: Z

last: Xiang