title: Vitamin C promotes anti-leukemia of DZNep in Acute Myeloid Leukemia

status: Public on Sep 30 2022

city: Guangzhou

first: Bing

last: Long

address: No. 600 Tianhe Road

department: Department of Hematology

country: China

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

type: Expression profiling by high throughput sequencing

summary: The epigenetic treatment by 3-Deazaneplanocin A (DZNep), a histone methyltransferase inhibitor, shows great potential against acute myeloid leukemia (AML). However, the variant sensitivity and incomplete response to DZNep are commonly observed. We reveal that vitamin C (Vc) dramatically promotes DZNep response against leukemic cells in different cell lines and primary AML samples. To examine the  molecular determinants underlying Vc enhanced anti-leukemia effect of DZNep, we conducted a genome-wide RNA sequencing and a gene ontology (GO) enrichment analysis of differentially expressed mRNAs in each group was performed.

overall_design: The experiment was divided into four groups: PBS treatment group, VC treatment group, DZNep treatment group, VC and DZNep treatment group.

first: Yongli

last: Shan

first: Tianyu

last: Wang

first: Guangjin

last: Pan


title: LIN28B alters ribosomal dynamics to promote metastasis in MYCN-driven malignancy (RNA-Seq)

city: Boston

first: Edroaldo

last: Lummertz da Rocha

state: MA

address: 1 Blackfan Circle

department: Hematology/Oncology

country: USA

institute: Boston Children's Hospital

summary: High expression of LIN28B is associated with aggressive malignancy and poor survival. Here, probing MYCN-amplified neuroblastoma as a model system, we show that LIN28B expression is associated with enhanced cell migration in vitro and invasive and metastatic behavior in murine xenografts. Sequence analysis of the polyribosome fraction of LIN28B-expressing neuroblastoma cells revealed let-7 independent enrichment of transcripts encoding components of the translational and ribosomal apparatus, particularly those with higher Adenine/Uridine (AU)-content, and depletion of GC-rich transcripts of neuronal developmental programs. We further show that LIN28B utilizes both its cold shock and zinc finger RNA binding domains to preferentially interact with MYCN-induced transcripts of the ribosomal complex, enhancing their translation. These data demonstrate that LIN28B couples the MYCN-driven transcriptional program to enhanced ribosomal translation, thereby implicating LIN28B as a post-transcriptional driver of the metastatic phenotype.

overall_design: Comparison of LIN28B WT BE2C versus LIN28B KO BE2C cells

first: Pavlos

last: Missios


title: Gene expression profile at single cell level of CD45+ from the spinal cords of WT and STAP-1 mice 15 days after EAE induction [inhibitor treatment]

city: Sapporo

first: Junichi

last: Kashiwakura

state: Hokkaido

address: 15-4-1, Maeda 7-jo, Teine-ku

country: Japan

institute: Hokkaido University of Science

summary: T cells are considered to be an important cell type for pathogenesis of multiple sclerosis. We used single cell RNA sequencing (scRNA-seq) to analyze popluation of inflitrating CD45+ cells in spinal cords of newly developed inhibitor-treated and untreated mice to figure out whehter the inhibitor can suppress severity of EAE by inhibiting  infiltration of T cells in the spinal cords.

overall_design: The cells in spinal cords were collected, CD45+ cells were stained with antbodies conjugated with hashtag and analyzed using scRNAseq.

first: Jun-ichi

first: Yuto

last: Sasaki

first: Tadashi

last: Matsuda


title: High-dose glutamine modulates amino acid transport and mediates pancreatic cancer chemosensitivity

city: Los Angeles

first: Carlos

middle: David

last: Cruz

state: California

address: 8700 Beverly Boulevard

department: SOCC

institute: Cedars Sinai

summary: We performed RNA-seq to investigate gene expression changes in pancreatic cancer cells following gemcitabine with high-dose L-Gln.

overall_design: RNA-seq was performed in MIA PaCa-2 cells with biological triplicates under various conditions (gemcitabine 0 or 0.5 uM, and L-Gln; 2 or 40 mM).

first: Neil

middle: A

last: Bhowmick

first: Hayato

last: Muranaka

first: Sungyong

last: You

middle: D

last: Cruz-Hernandez


title: RNA sequencing MOLM-13 cells treated with the UBE2N inhibitor UC-764864 or DMSO control

city: Cincinnati

first: Kwangmin

last: Choi

state: Ohio

address: 333 Burnet Avenue

department: Experimental Hematology & Cancer Biology

institute: Cincinnati Children's Hospital Medical Center

summary: Dysregulation of innate immune and inflammatory signaling pathways is implicated in various hematologic malignancies. Yet, these pathways have not been systematically examined in acute myeloid leukemia (AML). We report that AML hematopoietic stem and progenitor cells (HSPCs) exhibit a high frequency of dysregulated innate immune-related and inflammatory pathways, referred to as oncogenic immune signaling states. Through gene expression analyses and functional genetic studies, we found that the ubiquitin (Ub) conjugating enzyme UBE2N is required for leukemic cell function in vitro and in vivo by maintaining oncogenicimmune signaling states. Using newly identified small molecule inhibitors of UBE2N as chemical probes, we further revealed the therapeutic efficacy of interfering with UBE2N Ub-conjugating function by preventing ubiquitination of multiple innate immune- and inflammatory-related substrates in AML. Inhibition of UBE2N catalytic function in AML disrupted oncogenic immune signaling by promoting cell death of leukemic HSPCs while sparing healthy cells. Moreover, baseline oncogenic immune signaling states in discrete subsets of primary AML patients exhibited a selective dependency on UBE2N catalytic function. Our study reveals that interfering with UBE2N function abrogates leukemic HSPCs and underscores the dependency of AML cells on UBE2N-dependent oncogenic immune signaling states

overall_design: Three UC-744864 treated samples and three DMSO control treated samples are included in the study

first: Daniel

middle: T

last: Starczynowski

first: Laura

last: Barreyro


title: The unfolded protein response gene Ire1α is required for tissue renewal and normal differentiation in the mouse tongue and esophagus

city: University Park

first: Fiona

middle: E

last: Chalmers

state: Pennsylvania

address: 306C Life Sciences Building

institute: Penn State University

summary: The IRE1α-XBP1s signaling branch of the unfolded protein response is a well-characterized survival pathway that allows cells to adapt to and resolve endoplasmic reticulum stress. Recent data has broadened our understanding of IRE1α-XBP1s signaling beyond a stress response and revealed a physiological mechanism required for the differentiation and maturation of a wide variety of cell types. Here we provide evidence that the IRE1α-XBP1s signaling pathway is required for the proliferation and maturation of basal keratinocytes in the mouse tongue and esophageal epithelium. Mice with conditional targeted deletion of either IRE1α or XBP1 in keratin 14 expressing basal keratinocytes displayed severe thinning of the lingual and esophageal mucosa that rendered them unable to eat. In IRE1α null epithelium harvested at an earlier timepoint, genes regulating cell proliferation, cell-cell adhesion, and keratinization were significantly downregulated; indirect immunofluorescence revealed fewer proliferating basal keratinocytes, downregulation of E-Cadherin, and thinning of the loricrin-positive granular and cornified layers. The number of Tp63 positive basal keratinocytes was reduced in the absence of IRE1α, and expression of the Wnt pathway transcription factor LEF1, which is required for the proliferation of lingual transit amplifying cells, was also significantly downregulated at the transcript and protein level. Together these results reveal an essential role for IRE1α-XBP1s in the maintenance of the stratified squamous epithelial tissue of the tongue and esophagus.

overall_design: Comparison of three wildtype mice (IRE1F/F) versus three littermates with conditional knockout of IRE1a in keratin 14 expressing tissue (K14CreERT2 IRE1 F/F). Samples are total RNA extracted from the tongue epithelium of the six mice.

first: Saie

last: Mogre

first: Bipin

last: Rimal

first: Jeongin

last: Son

first: Andrew

last: Patterson

first: Douglas

middle: B

last: Stairs

first: Adam

last: Glick


title: Transcriptomic characterization of Candida albicans in response to Aureobasidin treatment in vitro.

city: Kuala Lumpur

first: Sun Tee

last: Tay

state: W.P. Kuala Lumpur

address: Jalan Profesor Diraja Ungku Aziz

department: Medical Microbiology

country: Malaysia

institute: University of Malaya

summary:
Purpose: Cellular response of Candida albicans to Aureobasidin A at transcriptomic level.
Method: The transcriptome of C. albicans SC5314 upon exposure to 1 µg/ml AbA (0.5X Minimum Inhibitory Concentration) for three hours was analyzed by RNA sequencing (RNA-Seq) on Illumina HiSeq 4000 instrument using the 2 X 150 bp chemistry.
Result: Following STAR-alignment of the quality-checked sequence reads against SC5314 reference genome and DESeq2 analysis of the read counts data,  we identified 85 differentially-expressed genes between the AbA-treated cells and DMSO-treated controls, with false discovery rate <0.001 and a log2 fold change ≥ 1. Among them, 42 were significantly up-regulated and 43 were significantly down-regulated in AbA-treated cells as compared to the controls. The analysis of biological processes and molecular functions using Gene Ontology (GO) Term Finder of the Candida Genome Database (CGD) showed down-regulation of genes associated with cellular lipid biosynthetic process, and up-regulation of genes associated with regulation of membrane lipid distribution and floppase activity. The genes associated with cell aggregation, biofilm formation and DNA packaging were also affected.
Conclusion: In summary, the analysis of transcriptomic data in this study provides beneficial and critical information contributing to our understanding of the cellular response of C. albicans to AbA and its antifungal activity.

overall_design: Transcriptomic profile of AbA-treated and DMSO-treated of C. albicans

first: Nur

middle: W

last: Hamdan

first: Sun

first: Mun

middle: F

last: Loke

first: Eng

middle: G

last: Chua


title: Functions of SARS-CoV-2 ORF3 during Virus Infection

first: Xiaolin

last: Zhang

address: No.74 Zhongshan 2nd Road

institute: Sun Yat-sen University

summary: We hope to find significantly changed genes after SARS-CoV-2 ORF3 was transfected A549 cells ,then further investigate the functions of ORF3 protein during SARS-CoV-2 infection

overall_design: We found significantly changed genes and their related pathways through RNA-Seq, and then verified the results through subsequent relevant experiments, providing a new idea of the SARS-CoV-2 researches

first: Ziwei

last: Yang


title: Single Cell RNA Sequencing of Breg-CpG cells and Breg-TLR cells

status: Public on Sep 29 2022

first: James

last: Markmann

address: 55 Fruit St., WHT 517

institute: Massachusetts General Hospital

summary: single cell RNA-sequencing (scRNA-seq) was performed to delineate the phenotype of Bregs-TLR and Bregs-CpG cells and potentially identify gene signatures characteristic of each Breg subset.

overall_design: Total of 2 Bregs-CpG samples, and 2 Bregs-TLR samples

first: Qiang

last: Fu

first: KangMi

last: Lee

first: Divyansh

last: Agarwal

first: Kevin

last: Deng


title: Single cell gene expression profile of patient-derived head and neck squamous carcinoma cells subjected to different treatments.

status: Public on Sep 28 2022

city: NIJMEGEN

first: Dyah

last: Karjosukarso

address: Geert Grooteplein Zuid 28

country: Netherlands

institute: Radboud University

summary: As other tumours, HNSCC are heterogenous, hence different cell populations within a given tumour may have different response towards treatment. Most of previous studies on HNSCC resistance towards treatment have been performed on “bulk” samples, which confound the influence of its heterogenous nature.  In the recent years, single cell sequencing technologies have been developing rapidly and successfully applied to investigate numerous cancer response towards treatment. A recent scRNA-seq study on HNSCC cell lines confirmed the heterogenous response towards cetuximab. To further investigate both intrinsic and acquired resistance in HNSCC, we employed two primary cells modelling different responses towards selection with EGFR inhibitor, radiation, as well as a combination of EGFR inhibitor and radiation. These cell populations were studied using RAID technology, in which RNA and protein level were simultaneously quantified at a single cell resolution.

overall_design: The treated cells were sorted into single cells and subjected to single cell sequencing.

first: Alice

last: Dini

first: Klaas

middle: K

last: Mulder


title: Gene expression of spinal cord in neuropathic pain rats treated by paeoniflorin- liquiritin combination

city: Xi’an

first: YanYan

last: Chen

state: Jiangsu

address: Shiji Road

institute: Shaanxi University of Chinese Medicine

summary: To investigate the alleviating effect of paeoniflorin-liquiritin combination on neuropathic pain, we performed gene expression profiling analysis using data obtained from RNA-seq of spinal cord in spared nerve injury rats

overall_design: Comparative gene expression profiling analysis of RNA-seq data for spinal cord in spared nerve injury rats treated with normal saline and paeoniflorin-liquiritin combination

first: LiMei

last: Feng

first: YuPing

last: Tang


title: Single cell analysis of tumors developed from mouse dysplastic stem cells

city: Nashville

first: Eunyoung

last: Choi

state: TN

address: 2213 Garland ave, 10445 MRB4

institute: Vanderbilt University Medical Center

summary: To investigate whether the CD44v6neg/CD133+/CD166+ dysplastic stem cells are responsible for gastric adenocarcinoma development and cancer cell heterogeneity in the stomach, we used single cell RNA-seq (scRNA-seq) to examine gene expression profiles of heterogenous cancer cells in two types of gastric adenocarcinoma, cystic type and tubular type, developed from the dysplastic stem cell injection under the skin of immunodeficient nude mice.

overall_design: Cells were dissociated from fresh Cystic or tubular type of gastric adenocarcinoma tumors and encapsulated for encapsulation

first: Jimin

last: Min


title: Transcription regulation of SNCA by dystonia type 6 gene product THAP1 [Rat_ChIP-seq]

city: Tuebingen

first: Fubo

last: Cheng

address: Calwerstrasse 7

department: Institute of Medical Genetics and Applied Genomics

country: Germany

institute: University of Tuebingen

type: Genome binding/occupancy profiling by high throughput sequencing

summary: The predominantly function of THAP1 has been defined as a transcription factor, but how it regulates gene expression in human neurons is not well understood. Here, we found that THAP1 is able to regulate the expression of alpha-synuclein (SNCA), a key protein in Parkinson’s disease (PD).

overall_design: ChIP-seq of rat brain tissues

first: Olaf

last: Riess


title: Comparison of transcriptomic profiles between dysplastic stem cell subpopulations

summary: To investigate transcriptomic profiles of of two dysplastic stem cell (DSC) subpopulations, CD44v6neg/CD133+/CD166+ (DP-DSC) and CD44v6+/CD133+/CD166+ (TP-DSC), in dysplastic organoids (Meta4 organoids) established from active-Kras induced mouse stomachs

overall_design: Comparative gene expression profiling analysis of RNA-seq data for FACS-isolated DP- and TP-DSCs from mouse dysplastic organoids (Meta4 organoids)


title: Macrophage-secreted CSF1 transmits a calorie restriction self-renewing signal to mammary epithelial stem cells

city: Rehovot

first: Gilgi

last: Friedlander

address: Hertzel st

country: Israel

institute: Weizmann Institute of Science

summary: Calorie restriction (CR) enhances stem cell self-renewal in various tissues, including the mammary gland. The hypothesis propelling this study states that similarly to their intestinal counterparts, mammary epithelial stem cells are insulated from sensing changes in the energy supply and, for that matter, depend on signals from a specific niche. Combined in vivo, in vitro and in silico studies identified macrophages and secreted CSF1 as the energy sensor and paracrine transmitter, respectively, of the CR inducing effect on mammary stem cell self-renewal.

overall_design: The niche that transmits the calorie restriction (CR) self-renewing signal was identified by exposing stem cell cultures to conditioned medium collected from individual cell populations of CR and their ad libitum-fed counterparts. The signaling molecule was identified by RNA-Seq of the identified non-epithelial cell population. Conformation studies were then ensued.

first: Anna

last: Kosenko

first: Tomer-Meir

last: Salame

first: Itamar

last: Barash


title: Exosome miRNA expression in umbilical cord blood of high-parity piglets reveals the reproductive potential of sows

city: chongqing

first: Jia

last: Luo

state: chongqing

address: tiansheng road

institute: Southwest University

type: Non-coding RNA profiling by high throughput sequencing

summary: The objective of modern pig breeding is to exhaust the genetic potential in reproduction performance of sows regarding to litter size and litter weight of piglets. During gestation period, umbilical cord contributes to placenta-fetal communication and plays an indispensable role in the intrauterine embryonic development. In this study, we attempted to analyze the molecular mechanism of reproductive declined in high-parity sows from the perspective of umbilical cord blood. Firstly, we analyzed the reproductive character data of sows, and then the histological analysis of umbilical cord phenotype was performed. Next, we evaluated the effect of umbilical cord blood exosomes (UCB-EXO) on angiogenesis. Moreover, the expression characteristics of miRNA in UCB-EXO of high-parity sows with poor reproductive performance (OS) and multiparous sows with excellent reproductive performance (MS) were analyzed. Results showed that the reproductive performance performed best at 3rd-7th and gradually decreased after 8th parities. Angiogenesis was repressed in OS piglets. Moreover, the Exo-MS exhibited pro-angiogenesis properties, with those of Exo-OS were diminished. With the increase of parities, the angiogenesis and immune function of sows decreased significantly, greatly limited the reproductive potential of sows. The data demonstrated that miRNAs of UCB-EXO played a central role in intrauterine development and suggested a novel possible explanation for reproductive potential, provides reference for increasing female reproductive efficiency.

overall_design: Investigation of miRNA transcriptome of UCB between OS and MS

first: Qiang

last: Pu

first: Jie

last: Chai

first: Li

first: Changbao

last: Liu

first: Changfeng

last: Yang

first: Guojun

last: Kang

first: Yongfu

last: Huang


title: RNAseq analysis to identify differential expressed genes in glomerular cDNA of diabetic DBA/2 mice with Esm1 over-expression

city: Palo Alto

first: Xiaoyi

last: Zheng

address: 1701 Page Mill Rd

department: Med/Nephrology

institute: Stanford University

summary: We aim to study the gene expression changes in glomeruli of DBA/2 mice with diabetic nephropathy with or without Esm-1 over-expression. We extract pure mice glomeruli, prepared total cDNA with random hexamers and performed RNAseq study to quantify transcriptome and identify differential expressed genes. With a sequencing depth of 20M, we detected 12934 genes in total. We found many interferon related genes shows differences between control and DM group, suggesting DBA/2 mice with diabetic nephropathy are driven by interferon related mechanisms. We found 41 genes show biologically meaningful differences between DM and Esm-1 + DM group, suggesting these genes are downstream targets of Esm-1 in mice.

overall_design: Quantify glomerular transcriptome changes with Illumina 1.9 in 10 weeks diabetes mice with or without Esm-1 over-expression.

first: Lauren

last: Higdon

first: Alexandre

last: Gaudet

first: Manav

last: Shah

first: Angela

last: Balistieri

first: Catherine

last: Li

first: Patricia

last: Nadai

first: Latha

last: Palaniappan

first: Xiaoping

first: Briana

last: Santo

first: Brandon

last: Ginley

first: Xiaoxin

middle: X

last: Wang

first: Komuraiah

last: Myakala

first: Pratima

last: Nallagatla

first: Moshe

last: Levi

first: Pinaki

last: Sarder

first: Avi

last: Rosenberg

first: Jonathan

middle: S

last: Maltzman

first: Nathalie

last: de Freitas Caires

first: Vivek

last: Bhalla


title: Next Generation Sequencing of CRC tissue

first: Chi

last: Zhou

address: 26 Yuancun Erheng Rd

institute: The Sixth Affiliated Hospital of Sun Yat-sen University

summary: Colorectal cancer (CRC) is the third leading cause of cancer mortality worldwide. However, the underlying mechnism of cancer development remain largely unknown. The aim of this study is to analyze transcriptome expression profile to understand the molecular mechanism in  CRC development.

overall_design: RNA-depleted total RNA sequence was performed to profile transcriptome expression using 8 normal and 8 human tumor tissues

first: Ping

last: Lan

first: Xian-rui

last: Wu

first: Zhen-xing

last: Liang

first: Huan-shan

last: Liu

first: Tuo

last: Hu


title: Barley FASCIATED EAR genes determine inflorescence meristem size and yield traits

city: Shanghai

first: Jin

last: Shi

address: 800 Dongchuan Rd

department: Life Science and technology Department

institute: Shanghai Jiaotong University

summary:
Three FASCIATED EAR genes genetically determine the IM size, spike morphology and yield traits.
We performed gene expression profiling analysis using data obtained from RNA-seq of 2 genotypes (FEA mutant and wild type) at two developmental points.

overall_design: Comparative gene expression profiling analysis of RNA-seq data FEA mutant and wild type with W2.0 and W3.0 inflorescence.

first: Wang

last: Chengyu

first: Gang

last: Li


title: ChIP-seq analysis of H3K4me1 and H3K27ac in TFAM-depleted HepG2 cells

city: Kumamoto

first: Mitsuyoshi

last: Nakao

address: 2-2-1 Honjo, Chuo-ku

department: Institute of Molecular Embryology and Genetics

institute: Kumamoto University

summary: ChIP-seq analyses were used to examine the effect of TFAM inhibition on mono-methylated H3K4 (H3K4me1) and acetylated H3K27 (H3K27ac), which are histone marks characteristic of enhancer activity. Our study revealed that c-JUN-mediated enhancer activation shapes the mitochondrial stress-associated secretory phenotype.

overall_design: Examination of H3K4me1 and H3K27ac/DNA interaction in TFAM-depleted HepG2 cells.

first: Y

last: Hino

first: S

first: M


title: Trophoblast induced reprogramming of the decidualization program

city: Farmington

first: Yasir

last: Suhail

state: Connecticut

address: 263 Farmington Avenue

department: BME

institute: UCHC

summary: Transcriptional effect of trophoblast-decidual interactions.

overall_design: Sequencing of endometrial fibroblasts before and after decidualization, and before and after co-culture with HTR8 and Bewo.

first: Kshitiz

last: Gupta


title: Hnrnpk orchestrates embryonic growth plate development via regulating glycolysis

city: Guangzhou

first: Yuyu

last: Chen

state: Guangdong

address: Zhongshan II road, 74th

summary: Here we show a multifunctional protein, Hnrnpk, is essential for preventing excessive apoptosis and premature differentiation of growth plate chondrocytes. These datas were the RNA-seq of E18.5 growth plate chondrocytes with or without Hnrnpk.

overall_design: RNA-seq


title: Understanding the role of GLUT2 in dysglycemia associated with Fanconi-Bickel syndrome (NanoString miRNA profiling)

first: Mohammed

last: Toufiq

address: 10 Discovery Drive, Farmington, CT 06032

department: Research Department

institute: The Jackson Laboratory for Genomic Medicine

summary: Since the intronic mutation in SLC2A2 did not influence the activity of GLUT2, we undertook more investigation to understand the underlying molecular mechanisms of dysglycemia in FBS. We ran Nanostring miRNA panel v3b covering ~800 miRNAs in the patient, mother, and aged- and gender-matching healthy controls with no family history of dysglycemia. We noticed a higher degree of correlation between the patient and the gender and age-matched healthy control, rather than between the patient and the mother, suggesting that the miRNA expression profile might be more influenced by the age and gender rather than relatedness (Supplementary Fig. S5). The unsupervised hierarchical clustering revealed 123 miRs expressed specifically in the patient sample (Supplementary Table S2). The function of these miRNAs was interrogated by using Ingenuity Pathway (IPA) analysis software which returned 118 mapped miRs (Fig. 10). Here we report 30 miRNAs with the highest number of counts difference in the patient in comparison to controls (Fig. 11). We found that 14 of them were correlated with T1DM: 10 miRNAs (miR-199a, miR-25-3p, miR-93-5p, miR-19b-3p, miR-107, miR-24-3p. miR-18a-5p, miR-125b-5p, miR-324-5p, miR-331-3p, and hsa-miR-143-3p) were overexpressed in the control as compared to the patient, and 3 miRNAs (miR-144-3p , let-7e-5p, hsa-miR-29a-3p) were significantly overexpressed in the patient in comparison to the control. Molecular networks, including molecules inferred from previous studies, were generated by IPA functional analysis software (Supplementary Fig. S6). The molecular networks were given a score based on the number of molecules represented in the study dataset as compared to the literature. Network 1 (score 33) includes the genes and miRNAs implicated in organismal injury and abnormalities, skeletal and muscular system development and function, and tissue morphology. The miR-144 family integrated into the network 1. Network 2 (score 31) includes insulin and other genes and miRNAs implicated in glomerular injury, inflammatory disease, inflammatory response, and  included miR-29 and let-7 families. These results suggest that dysglycemia in the patient with intronic mutation might be associated with the deregulation of miRNAs involved in insulin production and secretion in beta cells.

overall_design: The total RNA extracted from the patient-1 (db-bl-0008), her mother, and age- and gender-matched control-1 were submitted to the Omics Core at Sidra Medicine for Nanostring miRNA profiling. The Nanostring miRNA panel v3b (including ~800 targets) was run on all samples. A total of ~150 ng of total RNA was used as input for each of the samples assessed. Sample preparation, ligation, hybridization, detection, and scanning were performed as per the manufacturer's instructions. After hybridization, samples were transferred to the nCounter Prep Station, where excess probes were removed, and samples were aligned and immobilized on the nCounter cartridge. The cartridge was placed on the nCounter Digital Analyzer for data collection. The nSolver data analysis software (version 4.0 NanoString Technologies) was used for the assessment of QC and the normalization of the raw gene expression counts. We used the recommended default parameters for quality control flagging; briefly, flags were generated if samples did not meet the following QC criteria: imaging threshold with FOV registration of at least 75%, binding density between 0.05 and 2.25, positive control, and ligation control linearity with R2>0.95, positive control limit of detection 0.5fM, positive control > or = 2 standard deviations above the mean of the negative controls. Data are presented as normalized raw counts. Data was imported on ROSALIND (https://app.rosalind.bio/) and Partek Genomic Suite (Partek, St. Louis, Missouri, US) for secondary downstream analysis. Functional gene network analysis was performed using the Ingenuity Pathway Analysis system (QIAGEN, Hilden, Germany), which transforms large data sets into a group of relevant networks containing direct and indirect relationships between genes based on known interactions in the literature.

first: Sanaa

last: Sharari

first: Basirudeen

last: Kabeer

first: Idris

last: Mohammed

first: Basma

last: Haris

first: Igor

last: Pavlovski

first: Iman

last: Hawari

first: Ajaz

last: Ahmad Bhat

first: Sara

last: Tomei

first: Rebecca

last: Mathew

first: Najeeb

last: Syed

first: Sabah

last: Nisar

first: Selma

last: Maacha

first: Jean-Charles

last: Grivel

first: Damien

last: Chaussabel

first: Johan

last: Ericsson

first: Khalid

last: Hussain


title: RNA sequencing of MOLM-13 cells transduced with  lentivirally expressed UBE2N or control short hairpin RNAs

first: Kwangmin

last: Choi

address: 333 Burnet Avenue

institute: Cincinnati Children's Hospital Medical Center

summary: Dysregulation of innate immune and inflammatory signaling pathways is implicated in various hematologic malignancies. Yet, these pathways have not been systematically examined in acute myeloid leukemia (AML). We report that AML hematopoietic stem and progenitor cells (HSPCs) exhibit a high frequency of dysregulated innate immune-related and inflammatory pathways, referred to as oncogenic immune signaling states. Through gene expression analyses and functional genetic studies, we found that the ubiquitin (Ub) conjugating enzyme UBE2N is required for leukemic cell function in vitro and in vivo by maintaining oncogenic immune signaling states. Using newly identified small molecule inhibitors of UBE2N as chemical probes, we further revealed the therapeutic efficacy of interfering with UBE2N Ub-conjugating function by preventing ubiquitination of multiple innate immune- and inflammatory-related substrates in AML. Inhibition of UBE2N catalytic function in AML disrupted oncogenic immune signaling by promoting cell death of leukemic HSPCs while sparing healthy cells. Moreover, baseline oncogenic immune signaling states in discrete subsets of primary AML patients exhibited a selective dependency on UBE2N catalytic function. Our study reveals that interfering with UBE2N function abrogates leukemic HSPCs and underscores the dependency of AML cells on UBE2N-dependent oncogenic immune signaling states

overall_design: The study includes three control shRNA and three UBE2N shRNA samples

first: Daniel

last: Starczynowski

first: Laura

last: Barreyro


title: Reconstruction and Analysis of a Long Noncoding RNA-Associated Competing Endogenous RNA Network in Hypertrophic Cardiomypathy [array]

city: Fuzhou

first: Jinyan

last: Chen

address: No.7 Wusi Road

institute: Fufian Academy of Medical Sciences

summary: Hypertrophic cardiomyopathy (HCM) is the most common heritable cardiomyopath that caused by mutations in genes encoding proteins of the cardiac sarcomere. Although multiple efforts have been made to understand the pathogenesis of HCM, the mechanisms of how long noncoding RNA (lncRNA)-associated competing endogenous RNA (ceRNA) network result in HCM still unkown. Herein, we acquired the different expression profiles of lncRNAs (DElncRNAs) and messenger RNAs (mRNA, DEGs) by using microarray, microRNAs (DEmiRNAs) by sequencing in plasma of HCM patients and healthy controls. LncRNA-miRNA pairs were predicted using miRcode and starBase, and crossed with DEmiRNAs. MiRNA-mRNA pairs were retrieved from miRanda and TargetScan, and crossed with DEGs. Combined these pairs, the ceRNA network was constructed and hub nodes were then analyzed to reconstruct subnetwork. Gene Ontology and KEGG pathways were used to analyse the mRNAs in the ceRNA. Total 520 DElncRNAs, 33 DEmiRNAs, and 371 DEGs were identified. By coexpression analysis, 682 lncRNA-mRNA pairs were identiﬁed with a coefﬁcient ≥ 0.9 and p < 0.05. The ceRNA network with 8 lncRNAs, 3 miRNAs and 22 mRNAs was constructed visualized by Cytoscape. LncRNA RP11-66N24.4 and LINC00310 are among the top 10% nodes and the associated ceRNA subnetwork may be the center of the whole ceRNA network. Furthermore, the qRT-PCR results showed that LINC00310 was signifcantly decreased in HCM patients. For LINC00310, GO analysis revealed that the biological processes was enriched in cardiovascular system development, sprouting angiogenesis, circulatory system development and so on, and Pathway analysis was mainly enriched in cGMP-PKG signaling pathway. Our study reveals the novel lncRNA-related ceRNA network in HCM and the identified lncRNA LINC00310 may be roles in the pathogenesis mechanisms of HCM, which could provide further insight into the pathogenesis of HCM.

overall_design: The experiment is divided into two groups: HCM patients and healthy controls as control group.The venous blood of HCM patients and healthy controls was collected to isolate total RNA, then perform lncRNAs chips by Arraystar Human lncRNAs chip (Arraystar).

first: Zhangxin

last: Xie

first: Jiazhen

last: Dai

first: Lirong

last: Lin

first: Kung

last: Wang

first: Junyong

last: Han

first: Lihong

last: Lu


title: Reconstruction and Analysis of a Long Noncoding RNA-Associated Competing Endogenous RNA Network in Hypertrophic Cardiomypathy

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

overall_design: Refer to individual Series


title: Reconstruction and Analysis of a Long Noncoding RNA-Associated Competing Endogenous RNA Network in Hypertrophic Cardiomypathy [miRNA-seq]

overall_design: In this study, we investigated the role of microRNA (miRNAs) in familial hypertrophic cardiomyopathy (FHCM) with MYBPC3 gene mutations. We investigated the miRNAs expression profile in three patients with FHCM with MYBPC3 gene mutations and compared the miRNA expression profiles with those of the normal control group by miRNA-seq.

first: jiazhen

first: Kun


title: Epigenome analysis of normal and ischemic stroke patients blood samples

city: Zhengzhou

first: Yang

last: Liu

state: Henan

address: No.100 science avenue

department: Medical Genetics

institute: Zhengzhou University

type: Methylation profiling by genome tiling array

summary: Genome wide DNA methylation profiling of normal and ischemic stroke patients blood samples. The Illumina Infinium 850k Human DNA methylation Beadchip  was used to obtain DNA methylation profiles across approximately 850,000 CpGs in liquid. Samples included 3 healthy people blood samples, 3 ischemic stroke patients blood samples.

overall_design: Bisulphite converted DNA from the 6 samples were hybridised to the Illumina Infinium 850k Human Methylation Beadchip

first: Hong

last: Zheng


title: RNA seq Analysis of Wild Type and CAMTA1 knockout HEK293T cell line

summary: We knocked out the CAMTA1 gene in HEK293T cells and detected differences in RNA seq in wild-type and CAMTA1 KO cells

overall_design: Examination the RNA seq of 2 different cell lines .

first: Liu

last: Yang

first: Zheng

last: Hong


title: Understanding the role of GLUT2 in dysglycemia associated with Fanconi-Bickel syndrome

first: Mohammed

last: Toufiq


title: Identification of queuosine-modified RNAs in S. pombe using metabolic labelling with preQ1-L1 (Q-RIP-Seq)

city: Berlin

first: Ann

middle: E.

last: Ehrenhofer-Murray

address: Philippstr. 13

department: Institut für Biologie

institute: Humboldt-Universität zu Berlin

summary: In most eukaryotes and bacteria, queuosine (Q) replaces the guanosine at the wobble position of tRNAs harboring a GUN anticodon. To investigate whether other RNAs are also Q-or  preQ1-modified in Schizosaccharomyces pombe, Q-RIP-Seq was established and applied to RNAs from WT (AEP1) and qtr2∆ cells (AEP288). Metabolic labeling of RNAs with azido-propyl-preQ1 (preQ1-L1), chemical clicking of a biotin-alkyne followed by immunoprecipitation on streptavidin beads and sequencing of enriched RNAs in WT compared to qtr2∆ allowed identification of Q-modified RNAs.

overall_design: S. pombe cells were metabolically labelled with azido-propyl-preQ1 (preQ1-L1) to label Q-modified RNAs. RNA was extracted, chemically clocked with biotin-alkyne; labeled RNAs were enriched on streptavidin beads and subjected to HTS. HTS reads were analyzed for RNAs enriched in wt compared to qtr2∆ cells (n = 3).

first: Navpreet

last: Kaur


title: RNA seq Analysis of Wild Type and CAMTA1 knockout SH-SY5Y cell line

summary: We knocked out the CAMTA1 gene in SH-SY5Y cells and detected differences in RNA seq in wild-type and CAMTA1 KO cells

overall_design: Examination the RNA seq of WT or CAMTA1 KO SH-SY5Y cells.


title: Causality of gut bacteria Klebsiella pneumoniae to hypertension development

city: Beijing

first: Jing

last: Li

state: Beijing

address: Beilishi Road 167, Xicheng District,

department: Department of Hypertension Center

institute: FuWai Hospital, National Center for Cardiovascular Diseases,  Peking Union Medical College & Chinese Academy of Medical Sciences

summary:
Purpose: we conducted this study to investigate whether gut K.pn is a causal factor for HTN pathogenesis and the potential mechanism
Methods: Renal transcriptome changes were assessed by RNA-sequencing
Results: significant upregulation of several genes related to HTN pathogenesis were observed
Conclusions:These results provide evidence that the enrichment of K.pn acts as a direct contributor for hypertension pathogenesis

overall_design: Renal transcriptome profiles of germ-free mice and antibiotic pretreated mice receiving K.pn

first: Jun

last: Cai


title: LIN28B alters ribosomal dynamics to promote metastasis in MYCN-driven malignancy (RIP-Seq)

city: Boston

first: Edroaldo

last: Lummertz da Rocha

address: 1 Blackfan Circle

institute: Boston Children's Hospital

summary: High expression of LIN28B is associated with aggressive malignancy and poor survival. Here, probing MYCN-amplified neuroblastoma as a model system, we show that LIN28B expression is associated with enhanced cell migration in vitro and invasive and metastatic behavior in murine xenografts. Sequence analysis of the polyribosome fraction of LIN28B-expressing neuroblastoma cells revealed let-7 independent enrichment of transcripts encoding components of the translational and ribosomal apparatus, particularly those with higher adenine/uridine (AU)-content, and depletion of transcripts of neuronal developmental programs. We further show that LIN28B utilizes both its cold shock and zinc finger RNA binding domains to preferentially interact with MYCN-induced transcripts of the ribosomal complex, enhancing their translation. These data demonstrate that LIN28B couples the MYCN-driven transcriptional program to enhanced ribosomal translation, thereby implicating LIN28B as a post-transcriptional driver of the metastatic phenotype.

overall_design: Comparison of LIN28B WT BE2C versus LIN28B KO BE2C cells as well as re-expression of LIN28B WT, LIN28B MUT (full mutant of cold shock domain (CSD) and zinc knuckle domain) and single Mutants LIN28B CSD MUT/ZKD MUT upon LIN28B KO BE2C.

first: George

middle: Q

last: Daley

first: Pavlos

last: Missios

first: Daniel

last: Dominguez

first: Maria

middle: M

last: Aleman


title: LIN28B alters ribosomal dynamics to promote metastasis in MYCN-driven malignancy (Polysome sequencing)

overall_design: Comparison of LIN28B WT BE2C versus LIN28B KO BE2C cells with polysome sequencing.


title: LIN28B alters ribosomal dynamics to promote metastasis in MYCN induced malignancy


title: Effect of Filip1l down-regulation on gene expression during mouse syngeneic allograft tumor growth.

city: New Brunswick

first: Mijung

last: Kwon

state: NJ

address: 195 Little Albany St

institute: Rutgers Cancer Institute of New Jersey

summary:
To investigate downstream pathways affected by Filip1l-knockdown, mTc11 (mouse lung cancer cell line) clones were generated by lentiviral shRNA of either scrambled control or Filip1l.
We then performed gene expression analysis using data obtained from RNA-seq of 2 groups of frozen subcutaneos tumors.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for control (group L; 6 tumors) and Filip1l KD derivatives (group M; 6 tumors).

first: Steven

last: Libutti


title: Effects of IL-13 on primary esophageal fibroblasts

city: San Diego

first: Ashu

last: Sethi

state: CA

address: 9420 Athena Circle

department: Health Sciences

institute: La Jolla Institute for Immunology

summary: This is part of a larger experiment in which the effects of IL-13, LIGHT and TGF-B1 on human primary esophageal fibroblasts were analyzed and compared.

overall_design: Cells were treated with vehicle or 50ng/ml IL-13 for 24 hours. The raw data for the vehicle samples can be found under GEO number:  GSE143482

first: Mario

last: Manresa

first: Mick

last: Croft

first: Seema

last: Aceves


title: Differential microRNA profiles of intramuscular and secreted extracellular vesicles in human tissue-engineered muscle

city: Durham

first: Christopher

last: Vann

state: NC

address: 300 N Duke St

department: Molecular Physiology Institute

institute: Duke University School of Medicine

summary:
Exercise affects the expression of microRNAs (miR/s) and muscle-derived extracellular vesicles (EVs). To evaluate sarcoplasmic and secreted miR expression in human skeletal muscle in response to exercise-mimetic contractile activity, we utilized a three-dimensional tissue-engineered model of human skeletal muscle (“myobundles”). Myobundles were subjected to three culture conditions: no electrical stimulation (CTL), chronic low frequency stimulation (CLFS), or intermittent high frequency stimulation (IHFS) for 7 days. RNA was isolated from myobundles and from extracellular vesicles (EVs) secreted by myobundles into culture media; miR abundance was analyzed by miRNA-sequencing. We used edgeR and a within-sample design to evaluate differential miR expression and Pearson correlation to evaluate correlations between myobundle and EV populations within treatments with statistical significance set at p<0.05. Numerous miRs were differentially expressed between myobundles and EVs; 116 miRs were differentially expressed within CTL, 3 within CLFS, and 2 within IHFS.
Additionally, 25 miRs were significantly correlated (18 in CTL, 5 in CLFS, 2 in IHFS) between myobundles and EVs. Electrical stimulation resulted in differential expression of 8 miRs in myobundles and only 1 miR in EVs. Several KEGG pathways, known to play a role in regulation of skeletal muscle, were enriched, with differentially overrepresented miRs between myobundle and EV populations identified using miEAA. Together, these results demonstrate that in vitro exercise-mimetic contractile activity of human engineered muscle affects both their expression of miRs and number of secreted EVs. These results also identify novel miRs of interest for future studies of the role of exercise in organ-organ interactions in vivo

overall_design: Differential microRNA expression analysis of miRNA-seq data for human tissue-engineered muscle and extracellular vesicles these tissues secrete

first: Virginia

last: Kraus


title: ATAC-seq Identification of Chromatin Accessibility in Both Human Host Cells and the Parasite Toxoplasma gondii

city: Tampa

first: Kami

last: Kim

state: FL

address: 3720 Spectrum BLVD IDRB 403

department: Internal Mediciine

institute: University of South Florida

summary: To identify accessible chromatin regions in the human host cells during Toxoplasma parasite infection (uninfected, RH-infected and Pru-infected human foreskin fibroblasts) and in the obligate intracellular parasite Toxoplasma gondii (Type 1 RH strain and Type 2 Pru strain), ATAC-seq was performed.

overall_design: Four biological replicates of 1) uninfected human foreskin fibroblasts (HFFs), 2) T. gondii Type 1 RH-infected, and 3) T.gondii Type 2 Pru-infected HFFs at 24-hr post-infection.

first: Li-Min

last: Ting

first: Chengqi

last: Wang

first: Thomas

last: Keller


title: Immunologic adapatations of high grade serous ovarian cancer patients to neoadjuvant carboplatin and paclitaxel therapy

city: Providence

first: Jennifer

middle: Renee

last: Ribeiro

state: RI

address: 200 Chestnut St.

department: Obstetrics and Gynecology

institute: Women and Infants Hospital of Rhode Island

summary:
770 genes as well as pathways and deconvoluted immune cell types were determined pre- and post-neoadjuvant chemotherapy in a cohort of 31 stage III-IV high grade serous ovarian cancer (HGSOC) patients, and associations were made with the duration of their platinum-free interval
n/a

overall_design: A total of 31 HGSOC patients were included in this retrospective study. Matched formalin-fixed, paraffin-embedded (FFPE) tumor tissues from treatment naive biopsies and interval debulking surgery following neoadjuvant chemotherapy were obtained from each patient, with associated clinical information, for a total of 62 samples. All patients received frontline carboplatin and paclitaxel although some patients received additional therapies. NanoString nCounter Human PanCancer IO360 panel was used to analyze isolated RNA for 770 genes associated with the tumor immune microenvironment.

middle: R

first: Nicole

last: James

first: Christoph

last: Schorl

first: Linda

middle: C

last: Hanley


title: Understanding the role of GLUT2 in dysglycemia associated with Fanconi-Bickel syndrome (RNA-Seq)

first: Mohammed

last: Toufiq

summary: Fanconi–Bickel Syndrome (FBS) is a rare disorder of carbohydrate metabolism that is characterized by the accumulation of glycogen mainly in the liver. It is inherited in an autosomal recessive manner due to mutations in the SLC2A2 gene. SLC2A2 encodes for the glucose transporter GLUT2 and is expressed in tissues that are involved in glucose homeostasis. The molecular mechanisms of dysglycemia in FBS are still not clearly understood. In this study, we report two cases of FBS with classical phenotypes of FBS associated with dysglycemia. Genomic DNA was extracted and analyzed by whole-genome and Sanger sequencing, and patient PBMCs were used for molecular analysis. One patient had an exonic SLC2A2 mutation (c.1093C > T in exon 9, R365X), while the other patient had a novel intronic SLC2A2 mutation (c.613-7T>G). Surprisingly, the exonic mutation resulted in the overexpression of dysfunctional GLUT2, resulting in the dysregulated expression of other glucose transporters. The intronic mutation did not affect the coding sequence of GLUT2, its expression, or glucose transport activity. However, it was associated with the expression of miRNAs correlated with type 1 diabetes mellitus, with a particular significant overexpression of hsa-miR-29a-3p implicated in insulin production and secretion. Our findings suggest that SLC2A2 mutations cause dysglycemia in FBS either by a direct effect on GLUT2 expression and/or activity or, indirectly, by the dysregulated expression of miRNAs implicated in glucose homeostasis.

overall_design: RNAseq analysis of PBMCs for Patients and Healthy Controls PBMCs

first: Sanaa

last: Sharari

first: Basirudeen

last: Kabeer

first: Idris

last: Mohammed

first: Basma

last: Haris

first: Igor

last: Pavlovski

first: Iman

last: Hawari

first: Ajaz

last: Ahmad Bhat

first: Sara

last: Tomei

first: Rebecca

last: Mathew

first: Najeeb

last: Syed

first: Sabah

last: Nisar

first: Selma

last: Maacha

first: Jean-Charles

last: Grivel

first: Damien

last: Chaussabel

first: Johan

last: Ericsson

first: Khalid

last: Hussain


title: Identify urinary exosome microRNAs that are unique to premature ovarian insufficiency

city: Incheon

first: meesup

last: Yoon

address: 155,Gaebeol-ro, yenosu-gu

country: South Korea

institute: Gachon university

summary: This study is to identify urinary exosome microRNAs (miRNAs) that are unique to premature ovarian insufficiency  (POI) with and without Turner syndrome and to use them as diagnostic markers for POI patients. We examined the miRNAexpression profile in urine exosomes from POI patients with and without Turner syndrome.

overall_design: We analyzed the miRNA expression profile isolated from the urinary exosomes of POI patients with or without Turner syndrome.

first: Zobia

last: Umair

first: Mi-Ock

last: Baek

first: Seona

last: An

first: Jisue

last: Song

first: SeungJoo

last: Chon

first: Mee-Sup


title: Full-length transcriptome of Glycyrrhiza uralensis Fisch. in under five treatment

city: Yinchuan

first: Xiang

last: Xiao

state: Ningxia

address: Shengli Street

institute: Ningxia Medical University

summary:
Purpose: The goal of this study are to reveal the internal mechanism of Bacillus pumilus G5 and silicon increased Glycyrrhiza uralensis Fisch. seedlings drought-tolerance by RNA-Seq.
Methods: mRNA profiles of Glycyrrhiza uralensis Fisch. Seedling in five treatment: control treatment, drought stress treatment, drought stress with G5 treatment, drought stress with Si treatment and drought stress with G5 combined Si treatment.
Results: The full-length transcriptome sequencing of 15 samples was completed, and the clean data of each sample was 6.28GB. All the consistent transcript sequences were aligned to the reference genome by minimap2 software and then de-redundant analysis was performed. Finally, 37267 genes were obtained. A total of 6934 DEGs were identified in four comparisons (D vs CK, DB vs D, DSi vs D, and DBSi vs D), among which are 967, 1559, 1278 and 3130 DEGs in four comparisons, respectively.
Conclusions: Our study help to better understand the underlying molecular mechanisms of Bacillus pumilus G5 and silicon improve the drought-tolerance of G. uralensis.

overall_design: Full-length transcriptome analysis of Glycyrrhiza uralensis Fisch. seedling under control treatment, drought treatment and drought with Bacillus pumilus or/and silicon.

first: Xinhui

last: Zhang

first: Xin

last: Ma

first: Zhanchao

last: Xu


title: To identify novel targets of a histone acetyltransferase Gcn5, and Snf1 kinase complex in Pichia pastoris in YNBM

city: Bangalore

first: Aditi

last: Gupta

state: Karnataka

address: FE-15, Biological Sciences Building, Indian Institute of Science

department: Biochemistry

country: India

institute: Indian Institute of Science

summary: The regulation of gene expression in Pichia pastoris has so far involved study of transcription factors. However, there are factors other than transcription factors affecting mRNA synthesis such as coactivators, enhancers, and chromatin modifiers. This study is a first ever report on epigenetic regulation in Pichia pastoris where, a histone acetyltransferase is reported to regulate transcription of genes involved in utilization of alternate carbon sources. We employed RNA Seq to identify new targets of Gcn5 in methanol medium.

overall_design: Wild type and knockout cells were cultured in minimal medium with methanol as a carbon source. Cells were harvested after 14 hours followed by RNA preparation using QIAGEN RNEASY Mini Kit which was then subjected to RNA-SEQ.

first: P

middle: N

last: Rangarajan


title: Insights into the genetic influences of the microbiota on the life span of a host

city: xuzhou

first: zuobin

last: zhu

address: tongshan road 209

institute: xuzhou medical university

summary: To investigate the effect of mutant E. coli on Caenorhabditis elegans, we performed gene expression profiling of RNA-seq data from Caenorhabditis elegans fed with different E. coli mutants.

overall_design: Comparative gene expression profiling of RNA-seq data from Caenorhabditis elegans

first: Zuobin

last: Zhu


title: RNA sequencing of human esophageal myofibroblasts

city: Los Angeles

first: Anisa

last: Shaker

address: 2011 Zonal Avenue

institute: Keck School of Medicine of USC

summary: We report the effect of treatment of primary cultures of human esophageal myofibroblasts with acidic bile salts

overall_design: Primary cultures of human esophageal myofibroblasts were treated with control media (A) or acidic bile salts (B).


title: mRNA-sequencing of ILC1 cells

city: Hefei

first: Zhigang

last: Tian

state: Anhui

address: Huangshan Road，number 443

institute: Univerity of Science and Technology of China

summary:
Purpose: To understanding the effects of RORa deficiency on ILC1 cells, we conducted bulk mRNA-seqencing
Method: Firstly, we purified liver ILC1 cells (CD45.2+CD3-CD19-NKp46+NK1.1+CD49a+CD49b-) via Fluorescence Activated Cell Sorting, then frozen in -80 °C ultra-low temperature refrigerator, followed by High-throughput sequencing, in three replicates for WT (Rorafl/fl) mice and one replicate for cKO (Ncr1Cre-Rorafl/fl) , using Illumina Hiseq 1500 platform.

overall_design: Find the DEGs in cKO ILC1 cells

first: Jiaxi

first: Hao

first: Rui

last: Sun

first: Hui

last: Peng


title: Proximal tubular epithelial specific transcriptomics of diabetic mice treated with dapagliflozin

city: Kyoto

first: Tetsuro

last: Kusaba

state: Kyoto

address: 465 Kajii-cho, Kamigyo-ku

department: Department of Nephrology

institute: Graduate School of Medical Science, Kyoto Prefectural University of Medicine

summary: We show the proximal tubular specific pathway analysis demonstrating the downregulation of oxidative phosphorylation in dapagliflozin treated db/db mice, a type 2 diabetic model. After 8-week treatment of dapagliflozin for db/db mice having proximal tubule specific tdTomato reporter, tdTomato-positive cells were isolated by FACS. Pathway analysis of RNA sequence of isolated tubular epithelia revealed that oxidative phosphorylation was downregulated in dapagliflozin-treated mice. However, depletion of renal tissue ATP content in db/db mice was ameliorated by dapagliflozin administration. Pimonidazole staining demonstrated that renal cortical tissue hypoxia was noted in db/db mice, which was improved by dapagliflozin administration. These findings suggest that dapagliflozin can ameliorated the excessive oxygen and ATP consumption and subsequent tissue hypoxia in diabetic kidney, which may explain, in part, the responsible mechanisms of renoprotecitive effect by dapagliflozin.

overall_design: RNAseq was used to profile dapagliflozin treated type 2 diabetic mouse kidney


title: Transcriptomic signatures in trophectoderm and inner cell mass of human blastocysts grouped according to developmental potential

city: Yokohama

first: Azusa

last: Inoue

state: Kanagawa

address: Suehiro-cho 1-7-22, Tsurumi-ku

department: Center for Integrative Medical Sciences

institute: RIKEN

summary: Selection of high-quality embryos is important to achieve successful pregnancy in assisted reproductive technology (ART). Recently, it has been debated whether RNA-sequencing (RNA-seq) should be applied to ART to predict embryo quality. However, the information on which genes can serve as markers for pregnant expectancy is limited. Furthermore, there is no information on which transcriptome of trophectoderm (TE) or inner cell mass (ICM) is more highly correlated with pregnant expectancy. Here we performed RNA-seq analysis for TE and ICM, respectively, in human blastocysts of which the expectation of pregnancy was retrospectively determined by the clinical outcomes of 1,890 cases of frozen-thawed blastocyst transfer. We identified dozens of genes that were correlated with the expected pregnancy rate in ICM and TE, respectively, with a larger number of genes identified in TE. Importantly, downregulated genes in TE of blastocysts classified as having lower expectation of pregnancy included tight junction-related genes, such as CXADR, CLDN10, and ATP1B1, which were implicated in peri-implantation development. Additionally, we showed that aneuploidy estimation by RNA-seq datasets does not correlate with pregnancy expectation. Our study thus provide an expanded list of candidate genes for prediction of pregnancy in human blastocyst embryos.

overall_design: RNAseq were performed in trophectoderm (TE) and inner cell mass (ICM) from human blastocysts of which the expectation of pregnancy was retrospectively determined by the clinical outcomes of 1,890 cases of frozon-thawed blastocyst transfer.

first: Yoshiteru

last: Kai

first: Hailiang

last: Mei

first: Hiroomi

last: Kawano

first: Naotsuna

last: Nakajima

first: Aya

last: Takai

first: Mami

last: Kumon

first: Naoki

last: Yamashita


title: Development of a Pericyte-Based Cell-Free Strategy to Recover Aged Skeletal Muscle After Disuse

city: Urbana

first: Marni

last: Boppart

address: 405 N Matthews

department: Kinesiology

institute: University of Illinois at Champaign-Urbana

summary: Our laboratory previously demonstrated that perivascular stem/stromal cells (CD146+ pericytes) can effectively recover muscle mass after a period of immobilization in young adult mice. However, cell-based therapies are problematic in aged mouse models due to lack of viability upon transplantation. Therefore, the purpose of this study was to develop a pericyte-based, cell-free strategy to recover muscle mass after disuse in aged mice. Single-cell RNA sequencing (scRNA-Seq) was performed on adult mouse skeletal muscle after two weeks of unilateral hindlimb immobilization, which revealed that muscle-resident pericytes uniquely upregulate the long noncoding RNA Malat1, a negative regulator of Nrf2, and fail to induce antioxidant gene expression in response to reactive oxygen species (ROS; H2O2).  This information was used to guide the design of a strategy in which healthy donor pericytes were stimulated with ROS to produce small extracellular vesicles (EVs) that were subsequently transplanted into 4- and 24-26-month-old C57BL/6 mice after two weeks of unilateral hindlimb immobilization. H2O2-primed healthy muscle-derived pericytes produced EVs in culture that effectively reduced restored myofiber CSA in both adult (p=0.009) and aged (p=0.006) muscle after disuse. In contrast, unprimed pericyte-derived EVs did not influence myofiber size. Neither primed, nor unprimed EVs recovered capillary density, yet both stimulated collagen turnover. Healthy ROS-primed pericyte-derived small EVs effectively improve skeletal muscle recovery after immobilization, representing a novel cell-free approach to rebuild muscle mass in older adults after a period of disuse.

overall_design: Six mice were subjected to unilateral hindlimb immobilization for 2 weeks. The tibialis anterior (TA)  muscles from mobile (“Mobile”; control) and previously immobilized (“Immobile”) limbs were excised and pooled according to treatment.

first: Yu-Fu

last: Wu

first: Eduardo

middle: A

last: De La Toba

first: Svyatoslav

last: Dvoretskiy

first: Rebecca

last: Jung

first: Noah

last: Kim

first: Laureen

last: Daniels

first: Elena

middle: V

last: Romanova

first: Jenny

last: Drnevich

first: Jonathan

last: Sweedler

middle: D


title: Transcriptome analysis of TFAM-depleted HepG2 cells and HeLa cells

city: Kumamoto

first: Mitsuyoshi

last: Nakao

address: 2-2-1 Honjo, Chuo-ku

institute: Kumamoto University

summary: We conducted transcriptome analysis of TFAM-depleted HepG2 cells and HeLa cells as a mitochondrial stress model. We found that mitochondrial dysfunction upregulated unique secretory proteins such as amphiregulin (AREG) and thrombospondin 1 in hepatic cells.

overall_design: We depleted TFAM in HepG2 human hepatic cells or HeLa human cervix adenocarcinoma cells using two different siRNAs, and then carried out an expression microarray experiment.

first: Y

last: Hino

first: S

first: M


title: Sex- and age-dependent genetics of longevity in a heterogeneous mouse population

city: Lausanne

first: Maroun

last: Bou Sleiman

state: Vaud

address: Rue Cantonale

department: IBI

country: Switzerland

institute: EPFL

summary: DNA variants that modulate lifespan provide insight into determinants of health, disease, and aging. Through analyses in the UM-HET3 mice of the Interventions Testing Program (ITP), we detected a sex-independent quantitative trait locus (QTL) on chromosome 12 and identified sex-specific QTLs, some of which detected only in older mice. Similar relations between life history and longevity were uncovered in mice and humans, underscoring the importance of early access to nutrients and early growth. We identified common, age- and sex-specific genetic effects on gene expression that we integrated with model organism and human data to create a hypothesis-building interactive resource of prioritized longevity and body weight genes. Finally, we validated Hipk1, Ddost, Hspg2, Fgd6, and Pdk1 as conserved longevity genes using C. elegans lifespan experiments.

overall_design: RNA sequencing of livers of male and female UM-HET3 mice at two ages, 6 months and 22 months.

first: Johan

last: Auwerx

first: Richard

last: Miller


title: Analysis of predestined heterogeneity in neutrophil progenitor clones (ER-HoxB8 conditionally immortalized)

city: Boston

first: Michael

middle: K.

last: Mansour

state: MA

address: 55 Fruit Street

institute: Massachusetts General Hospital

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

overall_design: Refer to individual Series


title: Transcriptomics in olfactory cells transfected with SARS-CoV-2 structural proteins

city: Logrono

first: María

last: de Toro

state: La Rioja

address: C/Piqueras 98

department: Genomics & Bioinformatics Core Facility

country: Spain

institute: Centro de Investigación Biomédica de La Rioja

summary: One of the most common symptoms in COVID-19 is a sudden loss of smell. SARS-CoV-2 has been detected in the olfactory bulb (OB) from animal models and sporadically in COVID-19 patients. To decipher the specific role of SARS-CoV-2 proteome at olfactory level, we deeply characterized the molecular imbalance induced by the expression of GFP-tagged SARS-CoV-2 structural proteins (M, N, E, S) on mouse OB cells by RNA-seq.

overall_design: mouse OBC1 cells total RNA profile of 5 group of samples: M, E, N, S and control GFP group. Three replicates per sample. Deep sequencing in Illumina HiSeq1500.

first: Enrique

last: Santamaría

first: Mercedes

last: Lachén-Montes

first: Naroa

last: Mendizuri

first: Grazyna

last: Kochan

first: Joaquín

last: Fernandez-Irigoyen

first: David

last: Escors


title: Lnc-Pim1 promotes neuron-like cell differentiation and neurite regeneration following ACR-induced neuronal injury

city: Shanghai

first: Li

last: He

address: Xiangyin road of Yangpu district

institute: Second military medical university

summary:
Gm-26885 (ENSMUSG0000097125) is encoded by chromosome17:29 (446,919-29,491,925) on Chromosome17 of C57 mice and is located in the 3 sub-band 3 of the region of Chromosome17 long arm (17qa3.3).  Gm-26885 and PIM-1 genes overlap each other, and have certain sequence similarity with PIM-1 gene, which is the antisense RNA of PIM-1.  Therefore, we refer to GM-26885 as Lnc-pim1.  In order to investigate the molecular mechanism of Lnc-pim1 in neuron regeneration .The N-2a-N cell injury model was constructed, and the experimental subjects were divided into normal N-2a-N cell group, N-2a-N cell group with Lnc-pim1overexpression and N-2a-N cell group with Lnc-pim1 knockdown.
We then performed gene expression profiling analysis using data obtained from RNA-seq of 3 different cells at the same points.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for three different groups of cells.

first: He

last: Li

first: Ruo

middle: y

last: Jiang

first: Ya

middle: j

last: Tang

first: Cong

last: Ling

first: Fang

last: Liu


title: Effects of coronary artery disease-associated variants on vascular smooth muscle cells

city: Leicester

first: Shu

last: Ye

state: Leicestershire

address: British Heart Foundation Cardiovascular Research Centre, Department of Cardiovascular Sciences, University of Leicester, Glenfield General Hospital

country: United Kingdom

institute: University of Leicester

summary: We undertook RNA-sequencing analysis on a large bank (n = 1,499) of vascular smooth muscle cells (VSMCs).

overall_design:
Total transcriptome was obtained from passage-3 vascular smooth muscle cells isolated from artery of umblical cords.

**Submitters declare that they do not have ethics approval to share the raw data files**

first: Charles

middle: U

last: Solomon

middle: G

last: McVey


title: Fasting Induces a Highly Resilient Deep Quiescent State in Muscle Stem Cells via Ketone Body Signaling

city: Stanford

first: Pieter

last: Both

state: California

address: 300 Pasteur Drive

institute: Stanford University

summary: Short-term fasting is beneficial for the regeneration of multiple tissue types. However, the effects of fasting on muscle regeneration are largely unknown. Here we report that fasting slows muscle repair both immediately after the conclusion of fasting as well as after multiple days of refeeding. We show that ketosis, either endogenously produced during fasting or a ketogenic diet, or exogenously administered, promotes a deep quiescent state in MuSCs. Although deep quiescent MuSCs are less poised to activate, slowing muscle regeneration, they have markedly improved survival when facing sources of cellular stress. Further, we show that ketone bodies, specifically b- hydroxybutyrate, directly promote MuSC deep quiescence via a non‐metabolic mechanism. We show that b-hydroxybutyrate functions as an HDAC inhibitor within MuSCs leading to acetylation and activation of an HDAC1 target protein p53. Finally, we demonstrate that p53 activation contributes to the deep quiescence and enhanced resilience observed during fasting.

overall_design: Skeletal muscle stem cells (MuSCs) were isolated by FACS from wild type mice that were treated with either ketone bodies or PBS processed for RNA-seq.

first: Thomas

last: Rando


title: Methylated RNA immunoprecipitation sequencing in the Kasumi-1 cell line transfected with WTAP shRNA or scramble control shRNA

city: Beijing

first: Xiao-ning

last: Gao

address: 28 Fuxing Road

department: Department of Hematology

institute: Chinese PLA General Hospital

summary: To evaluate the role of WTAP in modulating the m6A abundance, we conducted m6A sequencing in the Kasumi-1 cell line transfected with a lentivirus-mediated short hairpin RNA (shRNA) targeting WTAP gene or a scramble control shRNA.

overall_design: Stable silencing of the WTAP gene in leukemia cells was achieved through a lentiviral vector-based system for RNAi (GV112/hU6-MCS-CMV-Puromycin) constructed by GeneChem Technologies (China). Transfection of lentivirus was conducted according to the manufacturer's instruction. Kasumi-1 cells were seeded into 6-well plates overnight before transfection and the medium was changed approximately 12 to 16 hours after transfection. Forty-eight hours after shRNA transfection, cells were selected with puromycin (2 microgram per milliliter) for at least 24 hours before further investigations. A total of 3 biological replicates were performed.


title: Zrsr2 is essential for hematopoiesis and splicing of minor introns in RNA and protein processing genes in zebrafish

city: Bethesda

first: Kai

last: Yu

state: Maryland

address: 50 South Drive, Bldg 50, Room 5151

institute: NHGRI

summary: ZRSR2 is an essential splicing factor involved in 3’-splice site recognition as a component of both the major and minor spliceosomes that mediate splicing of U2- and U12-type introns, respectively.   Transcriptome analysis of ZRSR2-mutated bone marrow samples and ZRSR2-knockdown cell lines has revealed its essential role in the minor spliceosome. We established a zrsr2-knockout zebrafish line, termed zrsr2hg129/hg129 (p.Trp167Argfs*9) using CRISPR/Cas9 technology.   Global transcriptome analysis of 3 dpf zrsr2hg129/hg129 embryos revealed that loss of Zrsr2 leads to aberrant retention of minor introns in about one third of all minor intron-containing genes in zebrafish. Interestingly, these genes showed an enrichment for the RNA and protein processing pathways. Overall, our study has demonstrated that the role of Zrsr2 as a component of the minor spliceosome is conserved in zebrafish.

overall_design: mRNA from decapitated 3dpf wild-type and zrsr2hg129/hg129 zebrafish embryos

first: Rachel

last: Weinstein

first: Kevin

last: Bishop

first: Elizabeth

last: Broadbridge

first: Blake

last: Carrington

first: Abdel

last: Elkahloun

first: Wuhong

last: Pei

first: Shawn

last: Burgess

first: Paul

first: Erica

last: Bresciani

first: Raman

last: Sood


title: The impact of the carbon-regulation protein SbtB on CO2-dependent gene expression in Synechocystis sp. PCC 6803 [sbtB]

city: Freiburg

first: Wolfgang

middle: R.

last: Hess

state: Baden-Würtemberg

address: Schänzlestrasse 1

department: Institute of Biology III

institute: University of Freiburg

summary: Gene expression changes were followed in cultures of the cyanobacterium Synechocystis sp. PCC 6803 three and 24 hours after shift from high carbon (HC) to low carbon (LC) concentrations. The acclimation to fluctuating inorganic carbon (Ci) concentrations is crucial for photoautotrophic organisms living in aquatic environments such as cyanobacteria. The PII-like regulator protein SbtB binds the second messengers cAMP or c-diAMP and is involved in the acclimation to LC. Here, we investigated the impact of SbtB and of second messengers on gene expression changes during this acclimation response. We analyzed cultures of the wild type (WT), the ΔsbtB mutant lacking the PII-like regulator protein SbtB, the ΔcyaI mutant, lacking the main soluble adenylate cyclase for cAMP production and ΔdacA, lacking the diadenylate cyclase for c-diAMP production. The majority of LC-induced genes behaved in these mutants like in wild type. However, a defined subset of LC-regulated genes in WT was found to be changed in mutant ΔsbtB already under high CO2. Collectively, the results indicate that SbtB regulates a particular subset of genes during the LC acclimation response.

overall_design: Total RNA was prepared from cells of Synechocystis sp. PCC 6803 wild type and the ΔsbtB mutant lacking the PII-like regulator protein SbtB. Samples were taken in biological replicates.

first: Oliver

last: Mantovani

first: Viktoria

last: Reimann

first: Felix

middle: P

last: Herrmann

first: Khaled

last: Selim

first: Karl

last: Forchhammer

first: Martin

last: Hagemann


title: Expression analysis of C2C12 cells treated with scramble siRNA or siRNA directed against Brd4

city: Singapore

first: Pierre-alexis

last: Goy

state: Singapore

address: 60 Biopolis Street

country: Singapore

institute: Genome Institute of Singapore (GIS-ASTAR)

summary: We transfected C2C12 cells with 100nM of scrambled siRNA scramble and an siRNA directed against Brd4. Cells were harvested at 48h post-transfection and RNAseq was performed with polyA selection

overall_design: For RNA-Seq library preparation we followed the Illumina TruSeq RNA Sample Preparation Kit v2 manual. At least 40 million, 75bp long paired end reads were mapped to the mm9 version of the mouse genome per replicate using STAR 2.4.2a (doi: 10.1093/bioinformatics/bts635) using the default parameters.

first: Naidi

last: Yang

first: Pierre-Alexis

first: Heike

last: Wollmann


title: Transcription regulation of SNCA by dystonia type 6 gene product THAP1

city: Tuebingen

first: Fubo

last: Cheng

address: Calwerstrasse 7

department: Institute of Medical Genetics and Applied Genomics

institute: University of Tuebingen

sample_organism:
Homo sapiens
Rattus norvegicus

platform_organism:
Homo sapiens
Rattus norvegicus


title: Promoter repression and 3D-restructuring resolves divergent developmental gene expression in TADs [DamID]

city: Berlin

first: Michael

middle: I

last: Robson

address: Max Planck Institut für molekulare Genet, Ihnestrasse 63-73

institute: Max Planck Institute for Molecular Genetics

summary: Cohesin loop extrusion facilitates precise gene expression by continuously driving promoters to sample all enhancers located within the same topologically-associated domain (TAD). However, many TADs contain multiple genes with divergent expression patterns, thereby indicating additional forces further refine how enhancer activities are utilised. Here, we unravel the mechanisms enabling a new gene, Rex1, to emerge with divergent expression within the ancient Fat1 TAD in placental mammals. We show that such divergent expression is not determined by a strict enhancer-promoter compatibility code, intra-TAD position or nuclear envelope-attachment. Instead, TAD-restructuring in embryonic stem cells (ESCs) separates Rex1 and Fat1 with distinct proximal enhancers that independently drive their expression. By contrast, in later embryonic tissues, DNA methylation renders the inactive Rex1 promoter profoundly unresponsive to Fat1 enhancers within the intact TAD. Combined, these features adapted an ancient regulatory landscape during evolution to support two entirely independent Rex1 and Fat1 expression programs. Thus, rather than operating only as rigid blocks of co-regulated genes, TAD-regulatory landscapes can orchestrate complex divergent expression patterns in evolution.

overall_design: We mapped LADs in mouse ESCs and E11.5 cultured limb buds using DamID-seq as described in Vogel et al, 2007.

first: Alessa

last: Ringel


title: Inhibition of macrophage migration inhibitory factor (MIF) suppresses apoptosis signal-regulating kinase 1 to protect against liver ischemia/reperfusion injury

city: Zhengzhou

first: Sanyang

last: Chen

address: No. 1, Jianshe Road, Erqi District

institute: The First Affiliated Hospital of Zhengzhou University

summary:
Background: Hepatic ischemia–reperfusion (I/R) injury is a major complication leading to surgical failures in liver resection, transplantation, and hemorrhagic shock. The role of cytokine macrophage migration inhibitory factor (MIF) in hepatic I/R injury is unclear. Methods: We examined changes of MIF expression in mice after hepatic I/R surgery and hepatocytes challenged with hypoxia–reoxygenation (H/R) insult. Subsequently, MIF global knock-out mice and mice with adeno-associated-virus (AAV)-delivered MIF overexpression were subjected to hepatic I/R injury. Hepatic histology, the inflammatory response, apoptosis and oxidative stress were monitored to assess liver damage. The molecular mechanisms of MIF function were explored in vivo and in vitro.  Results: MIF was significantly upregulated in the serum whereas decreased in liver tissues of mice after hepatic I/R injury. MIF knock-out effectively attenuated I/R -induced liver inflammation, apoptosis and oxidative stress in vivo and in vitro, whereas MIF overexpression significantly aggravated liver injury. Via RNA-seq analysis, we found a significant decreased trend of MAPK pathway in MIF knock-out mice subjected hepatic I/R surgery. Using the apoptosis signal-regulating kinase 1 (ASK1) inhibitor NQDI-1 we determined that, mechanistically, the protective effect of MIF deficiency on hepatic I/R injury was dependent on the suppressing of the ASK1-JNK/P38 signaling pathway. Moreover, we found MIF inhibitor ISO-1 alleviate hepatic I/R injury in mice. Conclusion: Our results confirm that MIF deficiency suppresses the ASK1-JNK/P38 pathway and protects the liver from I/R -induced injury. Our findings suggest MIF as a novel biomarker and therapeutic target for the diagnosis and treatment of hepatic I/R injury..
We then performed gene expression profiling analysis using data obtained from RNA-seq of 6 different liver tissues of mice subjected to hepatic I/R injury.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for liver tissues of WT mice and MIF-KO mice subjected to hepatic I/R injury

first: Changju

last: Zhu


title: RNA sequencing results using Solanum tuberosum cv. Desiree at NT and HT at 3 and 8 weeks

city: Daejeon

first: Ji-Sun

last: Park

address: 125, Gwahak-ro

institute: Korea Research Institute of Bioscience and Biotechnology

summary: Leaves of the potatoes grown for 3 and 8 weeks at NT and HT were harvested for total RNA extraction. Total RNA was extracted from 100 mg of ground leaves using the Trizol reagent (MRC) following the manufacturer’s instructions. Five micro gram of each RNA sample were generated for a strand-specific library as previously described. The library was containing inserts of 150-200 bp. For RNA sequencing, paired-end 150 nt sequencing was performed using a HiSeq 4000 platform (Illumina, USA) at Microgen (Korea).

overall_design: Examination of differential expression of genes at NT and HT at 3 and 8 weeks

first: Ah-Young

last: Shin

first: Suk-Yoon

last: Kwon

first: Hyo-Jun

last: Lee


title: Transcription regulation of SNCA by dystonia type 6 gene product THAP1 [RNA-Seq]

summary: The predominantly function of THAP1 has been defined as a transcription factor, but how it regulates gene expression in human neurons is not well understood. Here, we found that THAP1 is able to regulate the expression of alpha-synuclein (SNCA), a key protein in Parkinson’s disease (PD).

overall_design: RNA-seq analysis of THAP1 iPSC differentiated into mDA neurons

first: Olaf

last: Riess


title: Transcription regulation of SNCA by dystonia type 6 gene product THAP1 [4C-Seq]

overall_design: 4C-seq analysis of SNCA promoter interact regions


title: Transcription regulation of SNCA by dystonia type 6 gene product THAP1 [ChIP-seq]

overall_design: ]analysis of SNCA promoter interact regions


title: Expression profiling of Solanum chacoense diploid potato lines to identify candidate Colorado potato beetle (Leptinotarsa decemlineata) resistance genes

city: East Lansing

first: Natalie

last: Kaiser

state: MI

address: 1066 Bogue Street

department: PSM

institute: Michigan State University

summary: Analysis of the mapped reads showed that 496 transcripts are differentially expressed between resistant and susceptible plants at 16-wks post-transplant. Of these, 188 transcripts are down-regulated in resistant plants, as well as significantly enriched on chromosome 2, while up-regulated genes are distributed across the genome. Previously uncharacterized uridine diphosphate-glycosyltransferases and ethylene response transcription factors within the QTL region identified by bulk-segregant analysis are candidate genes for further analysis.

overall_design: The Colorado potato beetle resistant line S. chacoense USDA8380-1 (80-1) was crossed to the inbred, beetle susceptible S. chacoense line M6 and a F2 population segregating for beetle resistance was developed. Ten individuals exhibiting extreme beetle resistance and ten individuals with extreme susceptiblilty in a replicated field trial  were selected for bulk segregant analysis. Three individuals in each bulk pool were also examined for differences in gene expression. Three biological replicates of the parental lines and the three susceptible and three resistant F2 lines (N=24)  were grown in a growth chamber. RNA was extracted from the lines at 16-wks post-transplant.

first: David

last: Douches


title: Gene expression changes during EpiLC differentiation in embryonic stem cells that are unable to express Tcf15

city: Edinburgh

first: Sally

last: Lowell

state: Denmark

address: 5 Little France Drive

department: MRC Centre for Regenerative Medicine

institute: University of Edinburgh

summary: We analyzed the gene expression changes occuring at the first 24h of EpiLC differentiation in embryonic stem cells in which a regulatory region driving expression of Tcf15 has been deleted. These changes has been compared with wild-type embryonic stem cells.

overall_design: E14Tg2a (Wild type) and delta 0.7 (cells with the homozygous deletion of Tcf15 regulatory region;chr2:152,177,049-152,177,722) cells were cultured in serum-free 2iL medium. For the induction of differentiation, cells were plated onto fibronectin coated plates with N2B27 medium containing Activin, bFGF and KOSR. Samples were collected from 0h (2iL), 12h and 24h of differentiation in duplicates.

first: Tulin

last: Tatar


title: CINS: Cell Interaction Network Inference from Single cell expression data in lungs of yound and aged mice

city: New Haven

first: Jonas

last: Schupp

state: CT

address: 300 Cedar Street

department: PCCSM

institute: YALE UNIVERSITY

summary: We report the development of a new computational method to assess differences in cell-cell interactions between conditions through utilizing single-cell RNA sequencing data. The pipeline, known as Cell Interaction Network Inference from Single-cell Expression data (CINS), combines Bayesian network analysis with regression-based modeling to identify differential cell type interactions and the proteins that underlie these interactions.

overall_design: The CINS pipeline was constructed and tested on a human single-cell dataset from Adams et al., 2020 on idiopathic pulmonary fibrosis (IPF). Additionally, the pipeline was applied to a pilot single-cell RNA sequencing dataset focused on studying lung aging in FENDRR-floxxed mice.

first: Naftali

last: Kaminski

first: Koji

last: Sakamoto

first: Nikos

last: Xylourgidis

first: Taylor

middle: S

last: Adams

first: Carlos

last: Cosme


title: The impact of the carbon-regulation protein SbtB on CO2-dependent gene expression in Synechocystis sp. PCC 6803 [dacA]

first: Wolfgang

last: Hess

overall_design: Total RNA was prepared from cells of Synechocystis sp. PCC 6803 wild type and the ΔdacA mutant, lacking the diadenylate cyclase for c-diAMP production. Samples were taken in biological replicates. For data analysis, the same raw data from wild type were taken as in the experiment with the ΔsbtB mutant but normalized here together with the data obtained for the ΔdacA mutant.

first: Oliver

last: Mantovani

first: Viktoria

last: Reimann

first: Felix

last: Herrmann

first: Khaled

last: Selim

first: Karl

last: Forchhammer

first: Martin

last: Hagemann


title: Mice inflammatory responses to inhaled aerosolized LPS: effects of various forms of human alpha1-antitrypsin

city: Hannover

first: Stephan

last: Immenschuh

state: Deutschland

address: Carl-Neuberg-Str. 1

department: Institute for Transfusion Medicine and Transplant Engineering

institute: Hannover Medical School

summary: Characterize how Balb/c mice responses to aerosolized LPS (lipopolysaccharide) alone or with intraperitoneal (i.p.) delivery of alpha1-antitrypsin (AAT)

overall_design: We aimed to characterize Balb/c mice responses to aerosolized LPS alone or with intraperitoneal (i.p.) delivery of alpha1-antitrypsin (AAT). On days one, two, and three mice were exposed for 10 min to clean air or aerosol LPS (0.21 mg/ml). One hour after each challenge, animals were treated i.p. with saline or with (4 mg/kg body weight) one of the AAT preparations: native (nAAT), oxidized (oxAAT), recombinant (recAAT) or peptide of AAT (C-36). Experiments were terminated 6 h after the last dose of AATs.

first: Kokilavani

last: Sivaraman

first: Sabine

last: Wrenger

first: Bin

last: Liu

first: Dirk

last: Schaudien

first: Christina

last: Hesse

first: Gema

last: Gomez-Mariano

first: Sara

last: Perez-Luz

first: Katherina

last: Sewald

last: DeLuca

first: Maria

last: Wurm

first: Paco

last: Pino

first: Tobias

last: Welte

first: Beatriz

last: Martinez-Delgado

first: Sabina

last: Janciauskiene


title: Chromatin status under knock-down of SNHG1 in neuroblastoma

status: Public on Sep 27 2022

city: Taipei

first: Chia-Lang

last: Hsu

address: No. 7, Zhongshan S. Rd.

department: Department of Medical Research

country: Taiwan

institute: National Taiwan University Hospital

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

overall_design: Refer to individual Series


title: RNA-seq of 2D-culture balding and non-balding dermal papilla cells

city: London

last: Philipott

address: 4 Newark St

department: Center for Molecular Medicine Cologne

institute: Blizard Institute Barts and The London School of Medicine and Dentistry

summary: Androgenetic alopecia (AGA, male patterned baldness) is a prevalent hair loss condition in males that develops due to the influence of androgens and genetic predisposition. With the aim of elucidating genes involved in AGA pathogenesis, we cultured immortalised balding human dermal papilla cells (BAB) and immortalised non-balding human dermal papilla cells (BAN) in 2-dimensional culture format, and compared gene expression using RNA-seq between BAB and BAN cells.

overall_design: Examination of transcriptome difference between immortalised balding human dermal papilla cells (BAB) and immortalised non-balding human dermal papilla cells (BAN) under 10nM DHT treatment, technical triplicate.

first: A

middle: M

last: Hillmer


title: Chromatin status under knock-down of SNHG1  in neuroblastoma [ChIP-seq]

summary: The small nucleolar RNA host gene 1 (SNHG1) is a novel oncogenic long non-coding RNA (lncRNA) aberrantly expressed in different tumor types. We previously found highly expressed SNHG1 was associated with poor prognosis and MYCN status in neuroblastoma (NB). However, the molecular mechanisms of SNHG1 in NB are still unclear. Here, we disrupted endogenous SNHG1 in the MYCN-amplified NB cell line SK-N-BE(2)C using the CRISPR/Cas9 system, and demonstrated the proliferation and colony formation ability of SNHG1-knowndown cells were suppressed. The transcriptome analysis and function assays of SNHG1-knockdown cells revealed SNHG1 was involved in various biological processes including cell growth, migration, apoptosis, cell cycle, and reactive oxygen species (ROS). Interestingly, the expression of core regulatory circuitry (CRC) transcription factors in MYCN-amplified NB, including PHOX2B, HAND2, GATA3, ISL1, TBX1, and MYCN, were decreased in SNHG1-knockdown cells. The chromatin-immunoprecipitation sequencing (ChIP-seq) and transposase-accessible chromatin using sequencing (ATAC-seq) analyses show that chromatin status of these CRC members is altered, which may stem from interactions between SNHG1 and HDAC1/2. These findings demonstrate that SNHG1 plays a crucial role in maintaining NB identity via chromatin regulation and reveal the function of the lncRNA SNHG1 in NB.

overall_design: ChIP-Seq for H3K27ac in neuroblastoma cell SK-N-BE(2)C

first: H

middle: F

last: Juan

first: C

middle: L


title: Epigenetic priming using low-dose 5-azazcytidine in diffuse large B-cell lymphoma (MBD-Seq)

city: Seoul

first: Junshik

last: Hong

state: Seoul

address: 101 Daehak-ro, Jongno-gu

department: Department of Internal Medicine

institute: Seoul National University

type: Methylation profiling by high throughput sequencing

summary: MBD sequencing of low-dose 5-azacytidine treated and PBS treated DLBCL cell lines to measure DNA methylation changes

overall_design: MBD sequencing using gDNA obtained from low-dose 5-azacytidine treated DLBCL cell lines and PBS treated controls

first: Jun


title: Epigenetic priming using low-dose 5-azazcytidine in diffuse large B-cell lymphoma


title: Comprehensive Molecular Characterizations of Gastric Tissue and Gastric Cancer Revealed by Single-cell RNA-seq

first: Ji

last: Dong

address: Yiheyuan 5#

institute: Peking University

summary:
Molecular knowledge of normal gastric tissues and gastric cancers remains incomplete. Here, we used single-cell RNA-seq to study the cell diversity of gastric tissues and gastric cancers. The expression landscape of normal gastric cell types and several candidate stem cell markers were obtained. Surprisingly, nearly all cell types in the antrum could transdifferentiate to intestinal metaplasia (IM). We also explored intra-tumoral heterogeneity and identified four common features of gastric cancer. In addition, we classified tumor cells into three major subtypes, which are associated with their prognosis. Finally, the proportions of mesenchymal and endothelial cells in the tumor microenvironment (TME) were negatively correlated with the prognosis of gastric cancer. Therefore, our work provides comprehensive molecular characterizations of both gastric development and gastric cancer at single-cell resolution and has significant potential to inspire better treatment strategies for gastric cancer.

Keywords: Expression profiling by high throughput sequencing

overall_design: Here, we performed single-cell RNA sequencing (RNA-Seq) analysis of gastric tissue and gastric cancer.

first: Xinglong

last: Wu

first: Wendong

last: Wang

first: Xin

last: Zhou

first: Jingyun

last: Li

first: Wei

last: Fu

first: Fuchou

last: Tang


title: The effect of crizotinib in A549 lung cancer cell

first: Ju-Hong

last: Jeon

address: 28 Yongon-Dong, Chongno-Gu

department: Department of Physiology and Biomedical Sciences

institute: Seoul National University College of Medicine

summary: TGFb and/or crizotinib were treated on A549 cell line to understand molecular mechanisms of action of crizotinib in TGF signaling pathway in lung cancer through gene expression profile data.

overall_design: TGFb or Crizotinib were dissolved in 4mM HCl or DMSO as a vehicle and treated TGFb (1 ng/ml) and/or Crizotinib (10 microM) for 24 h in A549 cells in triplicate. Vehicle-treated A549 cells in triplicate were used as control.

first: Jung

last: Chun

first: Sanghoon

last: Lee


title: Epigenetic analysis of predestined heterogeneity in neutrophil progenitor clones (ER-HoxB8 conditionally immortalized)

city: Boston

first: Michael

last: Mansour

address: 55 Fruit Street

institute: Massachusetts General Hospital

summary: Examination of open chromatin regions between clonal neutrophil progenitor populations. Conditionally immortalized CD45.1 naive paired granulocyte-monocyte progenitors (GMPs) and their mature neutrophil counterpart were profiled in an in vitro cell system. We identified 29,966 differentially accessible regions (DARs) between GMPs and neutrophils, from a total of 74,009 consensus peaks of chromatin accessibility. There is some correlation of open chromatin between GMP and mature neutrophil clones.

overall_design: We utilized a technique of retroviral ER-Hoxb8 expression (Wang et al. Nature Methods 2006) to examine clonal granulocyte-monocyte progenitors (GMPs) and the corresponding mature neutrophil from a C57Bl/6-CD45.1-STEM mouse. The GMPs are will grow indefinitely in the presence of stem cell factor and beta-estradiol. Eight paired naïve granulocyte monocyte progenitors (GMPs) and neutrophil clones were processed for ATAC-seq using the method previously described by Buenrostro et al (2015).

first: Allison

middle: K

last: Scherer

first: Murat

last: Cetinbas

first: Ruslan

last: Sadreyev


title: Low red to far-red light environments alter nitrogen assimilation in corn (Zea mays)

city: Guelph

first: Clarence

last: Swanton

state: Ontario

address: 50 Stone Road East

department: Plant Agriculture

country: Canada

institute: University of Guelph

summary:
The goal of this work was to investigate the influence of low red to far-red  (R:FR) signals generated by a biological weedy and an artificial source of far-red light on the nitrate assimilation pathway in maize.
In the absence of direct resource competition, far-red light reflected from neighboring weeds compromises light quality (red to far-red ratio; R/FR) and causes a wide range of morphological and physiological responses at early growth stages of crop plants. This study has investigated the effects of low R/FR light signals on nitrate assimilation in maize seedlings. The transcript levels of genes, metabolites, and activities of enzyme in the nitrate assimilation pathway under a biological and a simulated low R:FR light environment were compared with a high R:FR control environment. Low R:FR signals stimulated nitrate accumulation in maize leaves, which  did not appear to result from the upregulation of nitrate transporter genes. A significant reduction in ferredoxin-dependent glutamine:2-oxoglutarate aminotransferase activity appears to play a major role in nitrate accumulation under low R:FR light environments, while activities of other enzymes of the nitrate assimilation pathway remain unchanged.

overall_design: In total, 9 samples were analyzed. Samples consisted of 3 treatments. A weed-free control (WF), a biological (weedy) low R:FR (W), and an artificial low R:FR (FR) with 3 replicates. Each replicate consisted of a pool of second leaves from 3 individual plants (9-day-old).

first: William

last: Kramer

first: Sasan

last: Amirsadeghi


title: Real-time quantitative PCR analysis of white spruce (Picea glauca) families with different growth rates

city: Starkville

first: Esteban

last: Galeano

state: Mississippi

address: 775 Stone Blvd, 351 Thompson Hall, Mississippi State

institute: Mississippi State University

summary: Tree improvement programs select genotypes for faster growth, at both early and late stages, to increase yields over unimproved material, and the improvement is frequently attributed to genetic control in growth parameters among genotypes. Underutilized genetic variability among genotypes also has the potential to ensure future gains are possible. However, the genetic variation in growth, physiology and hormone control among genotypes generated from different breeding strategies has not been well characterized in conifers. We assessed growth, biomass, gas exchange, gene expression and hormone levels in white spruce seedlings obtained from three different breeding strategies (controlled crosses, polymix pollination, open pollination) using parents grafted into a clonal seed orchard in Alberta, Canada. A pedigree-based best linear unbiased prediction (ABLUP) mixed model was implemented to quantify variability and narrow-sense heritability for target traits and the levels of several hormones and expression of gibberellin-related genes in apical internodes were also determined. Over the first 2-years of development, the estimated heritabilities for height, volume, total dry biomass, above ground dry biomass, root:shoot ratio and root length, varied between 0.10 and 0.21, with height having the highest value. The ABLUP values showed large genetic variability in growth and physiology traits both between families from different breeding strategies, and within families. The principal component analysis showed that developmental and hormonal traits explained 44.2% and 29.4% of the total phenotypic variation between the three different breeding strategies and two growth groups. In general, controlled crosses from the fast growth group showed the best apical growth, with more accumulation of indole-3-acetic acid, abscisic acid, phaseic acid, and a 4-fold greater gene expression of PgGA3ox1 in genotypes from controlled crosses versus those from open pollination, but in some cases, open-pollination from the fast and slow growth groups showed the best root development, higher water use efficiency (iWUE and δ13C) and more accumulation of zeatin and isopentenyladenosine. In conclusion, tree domestication can lead to trade-offs between growth, carbon allocation, photosynthesis, hormone levels and gene expression, and we encourage the use of this phenotypic variation identified in improved and unimproved trees to advance white spruce tree improvement programs.

overall_design:
The experiment was a randomized complete block design with a total of 23 families, from three different breeding strategies (CC,PM, OP), each families with three repetitions (total samples=69). CC= controlled crosses, PM= polymix pollination, OP=open pollination. OP is the control.
For the qPCR gene expression profiling, an equal amount of total RNA from each sample was pooled e gene expression analysis. To set up the plates, three technical replicates were used for the PgGA2ox, PgGA3ox and PgGA20ox genes, and two technical replicates were used for PgDELLA and PgGID genes.

first: Barb

middle: R

last: Thomas


title: The impact of the carbon-regulation protein SbtB on CO2-dependent gene expression in Synechocystis sp. PCC 6803

first: Wolfgang

last: Hess

address: Schänzlestrasse 1

institute: University of Freiburg


title: Sox13 is a novel flow-sensitive transcription factor that prevents inflammation by repressing chemokine expression in endothelial cells

city: ATLANTA

first: Catherine

last: Demos

state: GA

address: 5310 Sloan Square NE

institute: Emory University

summary: SOX13 was identified as a novel flow-sensitive transceiption factor. We found that siRNA-mediated knockdown of SOX13 increased endothelial inflammatory responses even under the unidirectional laminar shear stress (ULS, mimicking s-flow) condition. To understand the underlying mechanisms, we conducted an RNAseq study in HAECs treated with SOX13 siRNA under shear conditions (ULS vs. oscillatory shear mimicking d-flow). We found 94 downregulated and 40 upregulated genes that changed in a shear- and SOX13-dependent manner. Several cytokines, including CXCL10 and CCL5, were the most strongly upregulated genes in HAECs treated with SOX13 siRNA.

overall_design: HAECs treated with siRNA against SOX13 or control siRNA for 24h were subjected to unidirectional laminar shear stress (LS) or oscillatory shear stress (OS) for the following 24h (n=4 biological replicates in each group). Total RNAs were collected and submitted for RNAsequencing

first: Sandeep

last: Kumar

first: Hanjoong

last: Jo


title: Systemic lipolysis promotes healthspan in Drosophila melanogaster

city: Minneapolis

first: Douglas

middle: Gene

last: Mashek

state: Minnesota

address: Suite 6-155, 321 Church St. SE

department: Biochemistry, Molecular Biology and Biophysics

institute: University of Minnesota

summary: Since healthspan-extending interventions such as caloric restriction or fasting robustly promote lipid catabolism, we investigated how lifespan and healthspan were affected by increased lipid catabolism via bmm (brummer, FBgn0036449), the major triglyceride hydrolase in Drosophila. Global overexpression of bmm strongly promoted lifespan extension as well as numerous markers of healthspan, including increased female fecundity, fertility maintenance, preserved locomotion activity, increased mitochondrial biogenesis and oxidative metabolism. Increased Bmm robustly upregulated the heat shock protein 70 (Hsp70) family of proteins, which equipped the flies with higher resistance to heat, cold, and ER stress via improved proteostasis. Overexpression of bmm recapitulated major physiological changes associated with dietary restriction (DR) and conveyed its effects through dSir2. Taken together, these data show that bmm overexpression has broad beneficial effects on healthspan, and implicate lipolysis as a key node underlying the beneficial effects of dietary interventions known to improve healthspan.

overall_design: RNA-seq analysis was performed to identify differentially expressed genes between control flies and bmm overexpression flies in female and male groups.

first: Marissa

last: Macchietto

first: Juan

middle: E

last: Abrahante

first: Linshan

last: Shang