title: Comparative Transcriptomics Analysis of Red (Wild) and Orange (Modified) Carrots Available in India

status: Public on Dec 31 2021

city: Kolkata

first: Saikat

last: Chakrabarti

state: West Bengal

address: CN-6, Sector V

country: India

institute: CSIR-IICB

type: Expression profiling by high throughput sequencing

summary: We provide a comparative transcriptomics analysis between wild (red or Delhi) and modified (orange or hybrid) carrot roots available in India.

first: P

last: Jaisankar

first: Anindyajit

last: Banerjee

first: Anushree

last: Achari


title: SHH is downstream of immediate early genes and is targeted by chemotherapy on a specific enhancer [RNA-seq]

city: xiamen

first: Qingxiang

last: Gao

address: Xiang'an south way

country: China

institute: Xiamen University

summary: Sonic Hedgehog (SHH) signaling is a key regulator of embryonic development and tissue homeostasis, and is involved in gastrointestinal (GI) cancer progression. Here we show that SHH gene expression is down-regulated by chemotherapy drugs.

overall_design: Human CRC cell line HT29 was treated with 100uM 5FU for 2h and total RNA was extracted and subject to sequencing. Untreated HT29 cells were used as control.

first: Zhicao

last: Yue


title: Global transcriptomic analysis of the Raffinose Utilization in Lactobacillus salivarius Ren

city: Beijing

first: Weizhe

last: Wang

state: Beijing

address: No. 17 Tsing Hua East Road, HaiDian District

institute: China Agricultural University

summary: This study was aimed to further illustrate the expression files of REN between glucose and raffinose in MRS broth. Transcriptomic analysis combined with mutants of the key genes based on homologous recombination technology indicated that galA1 gene cluster plays an important role in raffinose metabolism. Gene rafP and galA1 are responsible for raffinose transport and α-galactoside hydrolysis, followed by galactose hydrolysis by galKTE and sucrose hydrolysis by scrB.  Lactobacillus salivarius Ren expanded the carbon utilization spectrum to adapt the fluctuating carbohydrate sources in the environment and shifted its carbohydrate metabolism to mixed-acid fermentation and then generated extra energy to bacterial growth when exposed to raffinose.

overall_design: Sequencing libraries were generated using NEBNext® Ultra™ Directional  RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s  recommendations

first: Yanling

last: Hao

first: Zhengyuan

last: Zhai


title: Senescence induction dictates response and resistance to chemo- and immunotherapy in preclinical models of ovarian cancer

city: New York

first: Yu-Jui

last: Ho

state: New York

address: 417 E 68th St

department: Cancer Biology & Genetics Program

country: USA

institute: Memorial Sloan Kettering Cancer Center

summary: High-grade serous ovarian carcinoma (HGSOC) is associated with a dismal prognosis. While most patients initially respond to platinum-based chemotherapy, they almost always acquire resistance, and only a small subset of HGSOC patients benefit from immune checkpoint blockade (ICB). To elucidate the disease mechanisms and factors underlying sensitivity and resistance to conventional and immune-based therapies, we developed a fast and flexible pre-clinical mouse model based on somatic introduction of HGSOC-associated genetic alterations into the ovary of immune competent mice using tissue electroporation. Tumors in these mice recapitulate both the proclivity of HGSOC to metastasize to the peritoneum and omentum and display histological, molecular, and treatment response features reminiscent of the human disease. Using this model, we show that the clinically observed increase in sensitivity of homologous recombination (HR) deficient ovarian tumors to platinum-based chemotherapy is driven by the preferential induction of senescence in the tumor cells. Intriguingly, HR-deficient (but not HR-proficient) tumors are uniquely sensitive to the combination of cisplatin and ICB owing to senescence-mediated activation of the cytosolic DNA sensing. This output becomes deactivated in a therapy-resistant model. Thus, genetically defined electroporation-based mouse models can be leveraged to elucidate the biology and therapy responses of HGSOG with the goal of improving treatment options for this deadly disease.

overall_design: For RNA-seq analysis of the transcriptional profiles of MP EPO-GEMM ovarian tumors, as well as normal ovaries of wild-type (WT) C57BL/6, total RNA was extracted from bulk tissue using the RNeasy Mini Kit (Qiagen). Purified polyA mRNA was subsequently fragmented, and first and second strand cDNA synthesis performed using standard Illumina mRNA TruSeq library preparation protocols. Double stranded cDNA was subsequently processed for TruSeq dual-index Illumina library generation.

first: Stella

middle: V

last: Paffenholz

first: Camilla

last: Salvagno

first: Yu-jui

first: Matthew

last: Limjoco

first: Timour

last: Baslan

first: Sha

last: Tian

first: Amanda

last: Kulick

first: Elisa

last: de Stanchina

first: John

middle: E

last: Wilkson

first: Francisco

middle: M

last: Barriga

first: Dmitriy

last: Zamarin

first: Juan

middle: R

last: Cubillos-Ruiz

first: Josef

last: Leibold

first: Scott

middle: W

last: Lowe


title: miRNA-sequencing of human non-calcificated and calcificated aortic valves

first: Congcong

last: Zhang

address: Anzhen Road 2

institute: Beijing Institute of Heart Lung and Vascular Disease

type: Non-coding RNA profiling by high throughput sequencing

summary: Several microRNAs (miRNAs) have been identified to play crucial roles in calcificated aortic valves disease, numerous miRNAs are still waiting to be explored. In this study, we compared the miRNA expression profiles of human non-calcified (n=3) and calcified (n=5) aortic valves, and found that compared with the normal control valves, 152 miRNAs were up-regulated and 186 miRNAs were down-regulated in calcified aortic valves. Among the top hit down-regulated miRNAs, we found that the expression level of miR-139-5p was negatively correlated with the osteogenic genes RUNX2 and BMP3, and was also down-regulated during the osteogenic differentiation of primary human aortic VICs.

overall_design: miRNA sequencing of human non-calcified (n=3) and calcified (n=5) aortic valves.

first: Fan


title: Transcriptomic analysis of HDAC6-selective and broad HDAC inhibitors in human WT iPSC cardiomyocytes

city: South San Francisco

first: Farshad

last: Farshidfar

state: CA

address: 171 Oyster Point Blvd Ste 500

institute: Tenaya Therapeutics Inc.

summary: Dilated cardiomyopathy (DCM) is characterized by reduced cardiac output, as well as thinning and enlargement of left ventricular chambers. These characteristics eventually lead to heart failure. Current standards of care do not target the underlying molecular mechanisms associated with genetic forms of heart failure, driving a need to develop novel therapeutics for DCM. To identify candidate therapeutics, we developed an in vitro DCM model using induced pluripotent stem cell–derived cardiomyocytes (iPSC-CMs) deficient in BCL2-associated athanogene 3 (BAG3). With these BAG3-deficient iPSC-CMs, we identified cardioprotective drugs with a phenotypic screen and deep learning. Using a library of 5500 bioactive compounds and siRNA validation, we identified that inhibiting histone deacetylase 6 (HDAC6) was cardioprotective at the sarcomere level. We translated this finding to a BAG3 cardiac-knockout (BAG3cKO) mouse model of DCM, showing that inhibiting HDAC6 with two isoform-selective inhibitors (tubastatin A and a novel inhibitor TYA-018) protected heart function. In BAG3cKO and BAG3 E455K mice, HDAC6 inhibitors improved left ventricular ejection fraction and reduced left ventricular diameter at diastole and systole. We also found that HDAC6 inhibitors protected the microtubule network from mechanical damage, increased autophagic flux, decreased apoptosis, and reduced inflammation in the heart. Our results demonstrate the power of combining iPSC-CMs with phenotypic screening and deep learning to accelerate target and drug discovery, and they support the development of novel therapies that address underlying mechanisms associated with heart disease.

overall_design: We conducted RNA-Seq analysis on WT human iPSC-CMs treated with TYA-018, givinostat, and two HDAC6-selective inhibitors (tubastatin A and ricolinostat) in 24 hours and 4 days timeframe.

first: Jin

last: Yang

first: Francis

last: Grafton

first: Ana

last: Budan

first: Sara

last: Ranjbarvaziri

first: Marie

last: Cho

first: Emma

last: Xu

first: Jaclyn

first: Mahnaz

last: Maddah

first: Kevin

last: Loewke

first: Julio

last: Medina

first: David

last: Sperandio

first: Snahel

last: Patel

first: Tim

last: Hoey

first: Mohammad

middle: A

last: Mandegar


title: Hypomorphic ASGR1 Modulates Lipid Homeostasis via SREBPs Network

city: Guangzhou

first: Yinxiong

last: Li

address: Kaiyuan street 190

institute: Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences

summary: A population genetic study identified that the asialoglycoprotein receptor 1 (ASGR1) mutation carriers had significantly lower non-HDL-c levels and reduced risks of cardiovascular diseases. However, the mechanism behind this phenomenon remained unclear. Here, we established Asgr1 knockout mice that represented a plasma lipid profile with significantly lower non-HDL-c and triglyceride caused by decreased secretion and increased uptake of VLDL/LDL. These two phenotypes were linked with the decreased expression of microsomal triglyceride transfer protein (MTTP) and proprotein convertase subtilisin/kexin type 9 (PCSK9), two key target genes of the sterol regulatory element-binding proteins (SREBPs). Furthermore, there were less nSREBPs on account of more SREBPs being trapped in endoplasmic reticulum, which was caused by an increased expression of insulin-induced gene 1 (INSIG1), an anchor of SREBPs. Logically, two rescue experiments were conducted in ASGR1 deficient condition. Both INSIG1 knockdown and ASGR1 rescue independently reversed the ASGR1-mutated phenotypes, restoring the SREBP signaling manifested by improved APOB secretion and reduced LDL uptake. Our observation demonstrated a novel axis of ASGR1-INSIG1-SREBPs regulating lipid hemostasis, and hypomorphic manipulation of ASGR1 leads to significant reduction of lipid content via less nSREBPs. It provides multiple potential targets, including ASGR, for lipid-lowering drug development.

overall_design: Male mice of WT and Asgr1-/- were fasted overnight and collected the liver tissues. A total of 6 mice's samples were applied to the sequencing, among which 3 were WT, and the other were Asgr1-/-. WT samples were used as control when analyzed the data.

first: Yingying

first: Jiawang

last: Tao

first: Xiaorui

last: Yu

first: Yuhang

last: Wu

first: Yin-xiong


title: Effects of intermittent fasting on the cognitive impairment in Alzheimer's disease mice: the roles of the gut brain axis regulation mechanism

city: Shenzhen

first: Jin

last: Xin

state: Guangdong

address: Beishan road

institute: BGI

summary: We reported a 16-week intermittent fasting intervention alleviated cognitive impairment in Alzheimer's disease. Here we present transcriptomics data of mice hippocampus to further investigate how intermittent fasting regulates vital biological processes and pathways. After mapping clean RNA-seq reads of all mice against the Mus musculus genome, we detected 56,412 genes (including 12,527 new predicted genes) with fragments per kilobase of transcripts per million mapped reads (FPKM) value. Gene set enrichment analysis (GSEA) was used for pathway or functional analysis of RNA-seq data.

overall_design:
7 FAD mice,7 MAD mice,6 FAF mice, 7 MAF mice, 8 FWT mice, 7 MWT mice, 6 FWF mice, 7 MWF mice

Treatment Definitions:
FAD: female AD mice + standard feed
MAD: male AD mice + standard feed
FAF: female AD mice + intermittent fasting treatment
MAF: male AD mice + intermittent fasting treatment
FWT: female control mice + standard feed
MWT: male control mice + standard feed
FWF: female control mice + intermittent fasting treatment
MWF: male control mice + intermittent fasting treatment

first: Mengzhen

last: Jia

first: Xin

last: Jin


title: Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and OsPEP1 Ri1 transgenic line in response to exogenous PEP1 Transcriptomes

city: Hangzhou

first: Meng

last: Funing

state: Zhejiang

address: Yuhangtang Road 866

department: College of life sciences

institute: Zhejiang University

summary: We used the NGS techonoly to compare the gene’s transcripts at rice whole genome levels of the WT (XS134) and OsPEP1 Ri1 transgenic line in response to the exogenous PEP1 signal. We found that the expgenous PEP1-mediated signal were blocked in OsPEP1 Ri1 transgenic line, but the application of exogenous PEP1 could restore this PEP1-mediated signal to the WT (XS134) level.

overall_design: Examination of two different rice samples whole gene’s transcripts in response to the exogenous PEP1 signal.

first: Xiang

last: Dan

first: Mao

last: Chuanzao


title: RNA sequencing of Chlamydia trachomatis-stimulated HIV-1-infected CD4 T cells

first: Emmanuel

last: Dzakah

address: Lujing Lu, Yuexiu District

institute: Dermatology Hospital

summary: Sexually transmitted infections (STIs) are commonly reported among HIV-1 infected patients. The increasing prevalence of the most common STI, Chlamydia trachomatis (CT), among HIV-1 infected people suggests a role in HIV-1 infectivity. However, the mechanisms modulating the enhancement of HIV-1 infectivity during HIV-1/STIs coinfection remain elusive. The stimulation of CD4 T cells during CT infection may modulate the expression of specific genes, which in turn enhance the susceptibility and infectivity of CT-specific CD4 T cells to HIV-1 infection.   After three days of CT stimulation of PBMCs followed by 3 days of HIV-1 infection, we observed a significant increase in HIV-1 p24 levels among clinically diagnosed C. trachomatis-infected patients as compared to cells from healthy donors. Similarly, ex vivo CT antigen-stimulated PBMCs from healthy donors showed enhanced susceptibility to HIV-1 as compared to unstimulated PBMCs. CT-specific CD4 T cells also harbour more HIV-1 copy numbers as compared to healthy unstimulated CD4 T cells. RNA-seq data revealed the upregulation of CCR chemokine receptors and cytokines in CD4 T cells from CT-stimulated CD4 T cells infected with HIV-1.

overall_design: PBMCs from healthy blood donors were extracted and stimulated with Chlamydia trachomatis (CT) for three days followed by infection with 50ng/ml of HIV-1 p24 for three days. CD4+ T cells were isolated using the EasySep Human CD4+ T cells isolation kit (Stemcell Technologies, Canada) according to the manufacturer’s instruction followed by RNA extraction. Total RNAs from CT-HIV-1, HIV-1 only, and negative controls were used for RNA-seq at the Beijing Genome Institute (China).

first: Jiacong

last: Zhao

first: Liuyan

last: Wang

first: Liping

last: Huang

first: Zhengwei

last: Wan

first: Farooq

last: Rashid

first: Haiying

first: Ru

last: Xue

first: Shuyi

last: Chen

first: Bing

last: Yang

first: Kai

last: Deng

first: Shixing

last: Tang


title: Methionine restriction alleviate cognitive dysfunction in Alzheimer’s disease: the mediating roles of gut microbiota-brain axis

first: Jin

last: Xin

summary: We reported that a 4-month methionine-restricted diet (MR) intervention reduced the cognitive impairment in Alzheimer’s disease. Here, we introduce the transcriptomics data of the mouse hippocampus to further study how MR regulates important biological processes and pathways. After mapping clean RNA-seq reads of all mice against the Mus musculus genome, we detected 56,412 genes (including 12,527 new predicted genes) with fragments per kilobase of transcripts per million mapped reads (FPKM) value. Gene set enrichment analysis (GSEA) was used for pathway or functional analysis of RNA-seq data.

overall_design: 11 MWT mice, 10 FWT mice, 11 MAD mice, 11 FAD mice, 10 MWTMR mice, 10 FWTMR mice, 11 MADMR mice, 11 FADMR mice

first: Yujia

last: Xi


title: Paneth cell plays critical role during the regulation of Lactobacillus salivarius and Lactobacillus agilis on the activity of intestinal stem cell in hens

first: Jian

last: Li

address: 866 Yuhangtang Rd

summary: The intestinal mucosa is the main organ that exerts nutrient absorption, which will further influence laying performance and egg nutrition in hens. Previously, we have screened out three strains of Lactobacillus (L. sa., L. ag. and L. av.) from a native chicken breed in China. However, the optimal regulation of Lactobacillus combination on poultry products needs to be verified. In this study, a total of 120 HyLine hens (n = 30) at the period of laying peak were randomly divided into four groups: (1) control, (2) L. sa. + L. ag., (3) L. sa. + L. av. and (4) L. ag. + L. av. groups, which were fed with corresponding Lactobacillus (10e8 CFUs/hen/day) for 30 consecutive days. Compared with the control group, feeding of L. sa. + L. ag. could improve the laying rate, egg weight, especially for higher amino acids level in albumen. The mechanism study showed that, in the intestine lumen, feeding of L. sa. + L.ag. could up-regulate the Lactobacillus abundance and down-regulate the Escherichia coli abundance. Meanwhile, the tryptophan metabolism pathway was up-regulated, the primary bile acid biosynthesis pathway was down-regulated. In the crypt, up-regulated genes involved the oxidative phosphorylation pathway and the ROS level were appeared in L. sa. + L.ag. feeding group. Our study further proved that the amount of Paneth cells and the mRNA abundance of Wnt3a and Dll1 in the crypt were up-regulated upon L. sa. + L. ag. feeding. Correspondingly, the mRNA abundance of Lgr5, CCND1 and CDK2 in the crypt were enhanced upon L. sa. + L. ag. feeding. In conclusion, co-feeding of L. sa. and L. ag. in hens could improve the gut microflora and altered the microflora metabolism profile in the intestine. Further, promote the crypt’s local energy metabolism and enhancing ROS level in the crypt, thereby enhance the activity of Paneth cell and regulate the activity of ISCs. Ultimately, the intestinal mucosal renewal and the laying performance were improved.

overall_design: We isolated the duodenal crypts of Hyline kens and performed RNA sequencing to determine the regulation of gene expression by Lactobacillus

first: Yi

last: Hong

first: Keyang

last: Jiang

first: Jiamiao

last: Xia


title: Methionine restriction alleviates age-associated cognitive decline via fibroblast growth factor 21

summary: We reported a 3-month MR intervention alleviated age-related cognitive impairment. Here we present transcriptomics data of mice hippocampus to further investigate how MR regulates vital biological processes and pathways. After mapping clean RNA-seq reads of all mice against the Mus musculus genome, we detected 13,218 genes (including 3,187 new predicted genes with no annotation) with fragments per kilobase of transcripts per million mapped reads (FPKM) value. Gene set enrichment analysis (GSEA) was used for pathway or functional analysis of RNA-seq data.

overall_design: 6 5M-CD mice,7 5M-MR mice,8 15M-CD mice, 8 15M-MR mice, 8 18M-CD mice, 7 18M-MR mice

first: Bo

last: Ren

first: Xin

last: Jin


title: The profile of circular RNA in lung cancer cell lines

city: Singapore

first: Azhar

middle: B

last: Ali

address: 14 Medical Drive MD6 #11-01

department: CSI Singapore

country: Singapore

institute: National University of Singapore

summary: Circular RNA is found to play a part in lung cancer progreession. The aim of our study is trying to identify a key circular RNA expression profile by using numerous lung cancer cell lines. Hopefully, the results from our study could be a relevant biomarker in the clinic.

overall_design: Circular RNA was isolated from various lung cancer cell lines and NL20 was used as a normal lung cell line control.

first: Chee

last: Fhu

first: Jun

middle: T

last: Teo


title: Next Generation Sequencing Facillitates Quantitative Analysis of Wild Type and snrk1a1/a2 mutant Transcriptomes

city: Würzburg

first: Markus

last: Henninger

address: Julius-von-Sachs Platz 2

country: Germany

institute: University of Würzburg

overall_design: mRNA profiles of 3, 4 and 5 day old wild type (WT) and snrk1a1/a2 mutant seedlings

first: Wolfgang

last: Droege-Laser


title: Non-canonical glutamine transamination sustains efferocytosis by coupling redox buffering to oxidative phosphorylation

first: Maxim

middle: N.

last: Artyomov

state: MO

address: 660 S. Euclid Avenue, Campus Box 8118

department: Immunology&Pathology

institute: Washington University in St.Louis

summary: Macrophages rely on tightly integrated metabolic rewiring to clear dying neighboring cells by efferocytosis during homeostasis and disease. Here, we reveal that glutaminase (GLS) 1-mediated glutaminolysis is critical to promote apoptotic cell clearance by macrophages during homeostasis in mice. In addition, impaired macrophage glutaminolysis exacerbates atherosclerosis, a condition during which efficient apoptotic cell debris clearance is critical to limit disease progression. Gls1 expression strongly correlates with atherosclerotic plaque necrosis in patients with cardiovascular diseases. High-throughput transcriptional and metabolic profiling revealed that macrophage efferocytic capacity relies on a non-canonical transaminase pathway, independent from the traditional requirement of glutamate dehydrogenase (GLUD1) to fuel ɑ-ketogulatrate-dependent immunometabolism. This pathway is necessary to meet the unique requirements of efferocytosis for cellular detoxification and high energy cytoskeletal rearrangements. Thus, we uncovered a novel role for non-canonical glutamine metabolism for efficient clearance of dying cells and maintenance of tissue homeostasis during health and disease in mouse and humans

overall_design: Peritoneal cavity macrophages (PCMs) were obtained from Gls1 fl/fl mice and LysM-Cre x Gls1 fl/fl mice.  Mice were i.p injected with saline or  with IL-4 complexed to anti-IL-4  mAb. Then, 36  hours later, PCMs were collected by lavage with 5ml of PBS and stained  with CD64 (Brilliant Violet 421 conjugated), ICAM-2 (Alexa Fluor 647  conjugated) and CD115 (PE conjugated) before cell sorting.

first: Johanna

last: Merlin

first: Stoyan

last: Ivanov

first: Alexey

last: Sergushichev

middle: N

first: Laurent

last: Yvan-Charvet


title: RNA-seq analysis on primary tumor and liver metastatic lesion of CRC

first: Beiping

last: Zhong

address: Erheng Road, Yuancun, Tianhe District, Guangzhou City

department: Department of Colorectal Surgery

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

summary: To compare the expression profiles of colorectal cancers and liver metastatic lesion, 4 primary tumors and 3 liver metastases from CRC patients were subject to RNA-seq analysis

overall_design: RNA of 4 primary tumors and 3 liver metastases from CRC patients were transcribed to cDNA with random primers, then the cDNA was ligated to Illumina sequencing adaptors and sequenced on the Illumina HiSeq2500.

first: Bing

last: Cheng

first: Yu-feng

last: Chen

first: Xiaoming

last: Huang

first: Wenyu

last: Wang

first: Xiao-Jian

last: Wu


title: Next Generation Sequencing Facilitates Quantitative Analysis of Solanum lycopersicum Axillary bud Transcriptomes

city: Harbin

first: Jian

address: 600 Changjiang Road

institute: Northeast Agricultural University

summary: RNA sequencing  in tomato for detect mRNA expression of Solanum lycopersicum Axillary bud.The two cultivars (monomaker, raceme) at Axillary bud for transcriptome sequencing

overall_design: This study aimed to investigates lots of different expressed genes. All tomato Axillary bud of The two cultivars (monomaker, raceme) were collected and used to RNA sequencing.

first: Huanhuan

last: Yang


title: Small RNA sequencing Analysis of adipose in six month calf Chinese swamp buffalo

city: Xinyang

first: Yun

last: Ma

address: Shihe

institute: Xinyang Normal University

summary: Background: Intramuscular fat (IMF) content is an important index for beef quality. However, the genetics of IMF deposition is complex and still largely unclear, especially in buffalo. To identify miRNAs with potential regulatory role in lipid accumulated in muscle, we performed small RNA sequencing and identified miRNAs expressed in the longissimus dorsi muscle and back fat of Chinese buffalo, which provided vital information for further identification of miRNAs with potential regulatory role in the lipid accumulated in muscle. Results: Three small RNA libraries were constructed. A total of 32762032 raw reads were obtained from adipose groups, respectively. After filtering the adaptor and low quality reads, 32054381 clean reads were retained. In total, 623 miRNAs were identified.

overall_design: Three adipose samples from Chinese swamp buffalo were collected from Benniu abattoir, a local slaughterhouse of Xinayang, P.R. China.

first: Shuzhe


title: Comparative transcriptome analysis reveals the promoting effects of IAA on biomass production and branching of Gracilariopsis lemaneiformis

city: Ningbo

first: Xiaojiao

address: Qixing South Road

institute: Ningbo University

summary:
Purpose: Gracilariopsis lemaneiformis is one of main economical species cultivated seaweed in China. The yield of G. lemaneiformis was positive related with its rhizoid branching number and length, whereas the regulation on branching and growth of G. lemaneiformis was unclear. IAA was well known to control morphogenesis and growth in land plants. This study aimed to evaluate the roles of IAA on the growth and branch formation of G. lemaneiformis rhizoids.
Methods: Total RNA was extracted from G. lemaneiformis with branch and 2 cm of primary branch at 1 and 3 d after IAA treatment, respectively using the RNeasy Plant Mini Kit (Qiagen, Hilden, Germany). Three biological replicates are included for a treatment. RNA-seq were conducted by BGI, Shenzhen. Trinity (v2.0.6) was used to assemble the clean reads and Tgicl (v2.0.6) to perform clustering and eliminate redundant data in the assembled transcripts to obtain unique genes.
Results: IAA could activate the pathways in ABCB auxin transporters, precursor biosynthesis of growth-related hormones and plant hormone signal transduction. IAA promoted the precursors synthesis of CTKs, GAs and BR and activated the ARFs involved in IAA signal transduction, and ARR-A and ARR-B involved in CTKs signal transduction, which further regulate the genes encoding cyclin-dependent kinases, cyclins, tubulin, and cell division cycle involved in cell division process. Meanwhile, carbon fixation, carbohydrate metabolism, energy metabolism, and amino acid biosynthesis and metabolism were also responsive to IAA, revealed that IAA induced to produce more energy and metabolic intermediates for cell growth.

overall_design: Transcriptome analysis of branch rhizoids and 2 cm primary rhizoids with branch and 2 cm of primary branch at 1 and 3 d after IAA treatment, respectively.

first: YueYao

last: Tang

first: Xue

last: Sun

first: Xiaoqian

last: Zhang

first: Nianjun

last: Xu


title: Modeling oxidative injury response in human kidney organoids

city: Pittsburgh

first: Neil

last: Hukriede

state: PA

department: Developmental Biology

institute: University of Pittsburgh

summary: Analysis of human kidney organoids treated with hemin for 48 hrs, to induce reactive oxygen injury.

overall_design: Examination of control (non-treated) and hemin treated kidney organoids.

first: Aneta

last: Przepiorski


title: A STAT5B-CD9 axis determines self-renewal in hematopoietic and leukemic stem cells

city: Vienna

first: Veronika

last: Sexl

address: Veterinaerplatz 1

department: Pharmacology / Toxikology

country: Austria

institute: University of Veterinary Medicine Vienna

summary: The transcription factors STAT5A and STAT5B are critical in hematopoiesis and leukemia. They are widely believed to have redundant functions but we describe a unique role for STAT5B in driving the self-renewal of hematopoietic and leukemic stem cells (HSCs/LSCs). We find STAT5B to be specifically activated in HSCs and LSCs, where it induces many genes associated with quiescence and self-renewal, including the surface marker CD9. Levels of CD9 represent a prognostic marker for patients with STAT5-driven leukemia and our findings suggest that anti-CD9 antibodies may be useful in their treatment to target and eliminate LSCs. We show that it is vital to consider STAT5A and STAT5B as distinct entities in normal and malignant hematopoiesis.

overall_design:
Single cell RNA-Seq (10x Genomics) of FACS-sorted bone marrow LSK cells of 3 pooled mice (wt or Stat5a-/- or Stat5b-/-)

Please note that the 'data_processing_readme.txt' contains the information about how the processed data was generated from raw data.

first: Sebastian

last: Kollman

first: Barbara

last: Maurer

first: Matthias

last: Farlik

first: Reinhard

last: Grausenburger

first: Thorsten

last: Klampfl


title: Bulk RNA-seq analysis of prostate tissues treated with neoadjuvant ADT plus enzalutamide

city: Bethesda

first: Adam

middle: G.

last: Sowalsky

state: MD

address: 37 Convent Drive Building 37 Room 1062B

department: Genitourinary Malignancies Branch

institute: National Cancer Institute

summary: The purpose of this study was to identify the changes in gene expression that occur throughout the prostate in response to system therapy.

overall_design:
Biopsies were acquired prior to therapy, and prostate tissues were six months of therapy. Bulk prostate tissue was collected without microdissection, even in pathologic complete responders.
Submitter declares that the raw data will be submitted to dbGaP (https://www.ncbi.nlm.nih.gov/gap) because of patient privacy concerns.
The raw data for these samples are being submitted to dbGaP (accession ID phs001938).

first: William

middle: L

last: Dahut

middle: G


title: Next Generation Sequencing Facilitates Quantitative Analysis of control of Pseudomonas aeruginosa PAO1 and DATS-treated P. aeruginosa PAO1 Transcriptomes

first: Wenru

last: Li

address: No.100, Xianliezhong Road

institute: Institute of Microbiology, Guangdong Academy of Sciences

summary:
Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare transcriptome profiling of control of P. aeruginosa PAO1 (RNA-seq) to transcriptome profiling of DATS-treated P. aeruginosa PAO1 and to evaluate protocols for optimal high-throughput data analysis.
Methods:LB medium (50 mL) was inoculated with exponential growth phase P. aeruginosa PAO1 at a concentration of 1.0E8 CFU/mL. Diallyl trisulfide  was then added at a concentration of either 0 (control) or 0.63 μl/mL, respectively, in triplicate. All nine experiment groups were incubated in a water bath shaker at 37 ºC with a shaking rate of 180 rpm for 5 h. Cells were then sampled and centrifuged from the three control groups and three farnesol treatment groups, respectively. The cell precipitates were separately snap-frozen at -80ºC.  Total RNA was isolated from cells using Trizol (Life Technologies, USA) according to the manufacturer’s protocol.
Results: The transcriptome sequencing data of control and DATS-treated groups were compared and analyzed in the form of the following: control vs DATS. The details of the differentially expressed genes among the two groups showed that the amount of differential expressed genes between control group and DATS-treated group was high (total 5572, up-regulated 929, down-regulated 1432).
Conclusions:

overall_design: The mRNA profiles of P. aeruginosa PAO1 (control) and DATS-treated P. aeruginosa PAO1  were generated by deep sequencing, in triplicate, using Illumina Higseq 2000.

first: Wen-Ru

first: Zhi-Qing


title: Genome-wide CRISPR screen identifies synthetic lethality between DOCK1 inhibition and metformin in liver cancer

city: Hefei

first: junru

last: feng

address: huangshan road #443

institute: USTC

summary: To explore how DOCK1 deficiency enhances the anti-tumor effects of metformin, we performed RNA-seq analysis in PLC cells expressing NTC or shDOCK1 in the presence or absence of metformin.

first: Junru

last: Feng

first: Hui

last: Lu

first: Ping

last: Gao

first: Huafeng


city: Wuhan

first: Jing

last: Yang

state: Hubei

address: Shizishan street 1

institute: Huazhong Agricultural University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Toxoplasma gondii (T. gondii) is an obligate intracellular parasite that can infect almost all warm-blooded animals, causing serious public health problems. Lysine crotonylation (Kcr) is a newly discovered posttranslational modification (PTM), which has been proved that is relevant to procreation regulation, active transcription and cell signaling pathway. However, the biological functions of crotonylation have not yet been reported in macrophages infected with T. gondii. In our study, we performed a ChIP-seq analysis of porcine alveolar macrophages infected with T. gondii RH to explore the relationship of histone Kcr with T. gondii infection.

overall_design: Porcine alveolar macrophages (3D4/21 cells) were infected with tachyzoites of T. gondii type Ⅰ strain RHΔhxgprt (MOI=5) propagated in human foreskin fibroblast cells (obtained from ATCC, USA) in DMEM supplemented with 2% FBS at 37℃ with 5% CO2 or mock infected with an equal amount of phosphate-buffered saline (PBS, pH 7.4). After 24h post-infection, all samples were harvested and stored at -80 ℃ for subsequent protein and chromatin extraction. 3D4/21 cells were cross-linked with 1% formaldehyde for ran chromatin extraction. After sonication, fragmented DNA was obtained and then incubated with antibody (anti-H2BK12cr)-coated beads for 12h at 4℃. After extensive washing, 20 μL 5M Nacl was added into immunoprecipitated chromatin to de-cross-linked overnight, and the concentration and purify of de-cross-linked product was measured for subsequent sequencing.

first: Jiahui

last: Qian

first: Junlong

last: Zhao

first: Rui

last: Fang


title: Analysis transcriptome differences of 3D-cultured HUVECs upon overexpressing KANK4 or Vector.

city: shanghai

first: junhao

last: hu

address: HaiKe

institute: interdisciplinary research center on biology and chemistry

overall_design: mRNA profiles of HUVECs transducted by empty vector ctrl or KANK4 were generated by bulk sequencing.

first: Chonghe

last: Zhang

first: Hao

last: He

first: Feng

last: Han


title: Alteration in the transcriptome of lung resident fibroblast isolated from fibrotic lungs of IPF upon genetic knockdown of SOX9

city: Cincinnati

first: Anil

last: Jegga

state: OH

address: 240 Albert Sabin Way

department: Biomedical Informatics

institute: Cincinnati Children's

summary: Pulmonary fibrosis (PF) is associated with many chronic lung diseases including Systemic sclerosis (SSc), Idiopathic Pulmonary Fibrosis (IPF) and Cystic Fibrosis (CF) which are characterized by the progressive accumulation of mesenchymal cells and formation of scar tissue. Pulmonary fibrosis is a dysregulated response to alveolar injury which causes a progressive decline in lung function and refractory to current pharmacological therapies. Airway and alveolar epithelial cells and mesenchymal cells contribute to pulmonary fibrosis but the cell-specific pathways and gene networks that are responsible for the pathophysiology are unknown. Our new findings have identified the aberrant activation of Sox9 in lung resident fibroblasts and myofibroblasts in IPF lung biopsies and the mouse model of transforming growth factor-α (TGFα) and bleomycin-induced pulmonary fibrosis. In this study, we sought to determine Sox9-driven gene networks in lung resident fibroblast during pulmonary fibrosis. Our results showed that Sox9 regulates the transcriptional changes that are required for the fibroblast activation including migration, myofibroblast transformation, survival and extracellular matrix deposition during pulmonary fibrosis. In summary, this new study demonstrates that Sox9 is a critical regulator of fibroblast activation in IPF and hence serve as a target for therapeutic intervention.

overall_design: mRNA profiles of cultured fibrotic lung resident fibroblast isolated from IPF patients and treated with Control or SOX9-specific siRNA.

first: Prathibha

last: Gajjala

first: Rajesh

last: Kasam

first: Divyalakshmi

last: Soundararajan

first: Steven

middle: K

last: Huang

first: Satish

last: Madala


title: CCN1 forms a complex with GPC4 and heparin to fine tune signaling activities for embryonic cortical neural stem cell maintenance

city: Shanghai

first: Qin

last: Shen

address: Chifeng Street, Siping Road, Yangpu District

institute: Tongji University

summary: Radial glial cells (RGCs) are the neural stem cells (NSCs) in the developing brain, capable of self-renewing and generating neurons and glia in order. The developmental behaviors of NSCs are determined by extrinsic factors from the NSC niche, together with intrinsic factors. Here, we show that Cellular Communication Network 1 (CCN1), a secreted matricellular protein, is an autocrine factor derived from RGCs in the embryonic telencephalon. Loss of Ccn1 in RGCs leads to accelerated lineage progression of RGCs, and causes premature cell cycle exit and neuronal differentiation, resulting in a reduction in NSC pool size, disruption of the cortical projection neurons generation, and in turn, at the expense of the perinatal gliogenesis. Mechanistically, CCN1 interacts with an RGC-expressed membrane protein GPC4, one of the heparan sulfate proteoglycans (HSPGs), and is required for GPC4 to maintain NSCs through the Sonic Hedgehog (Shh) signaling pathway, depending on the binding of heparin to CCN1. Our work provides a potential mechanism for the dynamic and sophisticated interconnections of niche components that meet the needs of context-dependent maintenance, differentiation, and fate determination of NSCs.

overall_design: mRNA profiles of FACS purified GFP+ cells from dissociated wildtype (WT) or Nestin-Cre driven Ccn1 conditional knockout (CcKO) cortical cells at E17.5 that have been electroporated in utero with PiggyBac (PB)-Ctrl plasmid at E14.5, or from dissociated cortical cells at E15.5 that have been electroporated in utero with PB-Ctrl, PB-CCN1, or PB-GPC4 plasmid at E13.5, in duplicate, using NovaSeq

first: Jiangli

last: Zheng

first: Shaojun

last: Qi


title: RNA sequencing analysis of mouse cardiac endothelial cells in myocardial infarction tissues

city: Philadelphia

first: Yi

last: Fan

address: 3400 Civic Center Blvd, SCTR 8-168

department: Radiation Oncology

institute: University of Pennsylvania

summary: To investigate the transcriotome alteration in endothelial cells (ECs) under a myocardial infarction (MI) condition, we performed RNA sequcening analysis with sorted ECs derived from mouse infarcted cardiac tissues or normal left ventricle (LV).

overall_design: Myocardial infarction (MI) was induced Tie2-Cre;Rosa-LSL-tdTomato mice. 3 weeks after the surgery, infarcted tissues or normal left ventricle (LV) were harvested, and subjected to preparation of single-cell suspension. tdTomato+F4/80- cells were sorted by flow cytometry. RNA was extracted, purification, amplified, and analyzed by RNA sequencing.

first: Menggui

first: Duo


title: Cleavage of histone H2A during embryonic stem cell differentiation destabilizes nucleosomes to counteract gene activation [RNA-seq]

first: Yemin

last: Lan

address: 3400 Civic Center Blvd

summary: Histone proteolysis is a poorly understood phenomena by which the N-terminal tail of histones are irreversible cleaved by intracellular proteases. During development histone PTMs are known orchestrate gene expression and ultimately cell fate decision, therefore it will be key to decipher underlying mechanisms that lead to proteolysis during cellular differentiation. Previous reports have found that histone H2A is cleaved at the C-terminus, and here we found that the N-terminal is also proteolytically clipped and removed by the lysosomal protease Cathepsin L. Using quantitative mass spectrometry (MS), we identified L23 to be the primary site for this protease, with this clipped H2A (cH2A) form representing ~1% of the total H2A reaching a maximum after 4 days of differentiation. Using Chip-seq, we found reduced proteolysis, lead to increase acetylated H2A at promoter regions in differentiated ES cells.  We also report novel readers of acetylated H2A during in pluripotency as we identified members of the pBAF complex to recognize different forms of H2A acetylation. Moreover, our data showed that this recognition is abolished upon proteolysis. All in, our data suggest that proteolysis serve as a quick mechanism to silence genes involve in pluripotency and destabilize the nucleosome core particle as indicated by protein degradation studies.

overall_design: RNA-seq in mESCs differentiation with CTSL KD.

first: Mariel

last: Coradin

first: Benjamin

last: Garcia


title: Establishment of primitive endoderm stem cell lines in mice [coculture]

city: Yokohama

first: Takaho

middle: A.

last: Endo

state: Kanagawa

address: 1-7-22 Suehiro, Tsurumi

department: IMS

country: Japan

institute: RIKEN

summary: The mammalian blastocyst consists of three distinct cell types: epiblast, trophoblast, and primitive endoderm (PrE). Although stem cell lines that retain functional properties of epiblasts or trophoblasts have been established, establishment of stem cell lines that fully retain developmental potential of PrE has long been awaited. Here we report derivation of primitive endoderm stem (PrES) cells, which are capable to give rise functional PrE derived tissues and support fetal development of PrE-depleted blastocysts in chimeras, in mice. ES (#1M), TS cell (#1F), PrES (#6-5), and XEN (#6-5) cells were dissociated to single cells by incubation with 0.05% trypsin-EDTA at 37 °C for 3 min. The cells were resuspended in DMEM (Thermo Fisher Scientific) with 10% FBS, 1 × glutamine-penicillin-streptomycin, 0.1mM β-ME. The cells were replated alone or in combinations of each at a concentration of 20 cells per microwell (1.3×103 cells/dish) on 60mm EZSPHERE® SP dishes (Iwaki) and were placed at 37 °C and 5% CO2 for 1 day or 3 days.

overall_design: Gene expression of cultured cells were observed using RNA-seq.

first: Yasuhide

last: Ohinata

first: Haruhiko

last: Koseki

first: Hiroki

last: Sugishita


title: Establishment of primitive endoderm stem cell lines in mice [bulk]

summary: The mammalian blastocyst consists of three distinct cell types: epiblast, trophoblast, and primitive endoderm (PrE). Although stem cell lines that retain functional properties of epiblasts or trophoblasts have been established, establishment of stem cell

overall_design: C57B6N ~ 129X1 F1 (#1M, #6M) ESCs were cultured in serum-free ES medium (ESM): Neurobasal:DMEMF12(1:1), 0.5 ~ N2 supplement (Thermo Fisher Scientific), 0.5 ~ B27 supplement (Thermo Fisher Scientific), 0.15 mM 1-thioglycerol (Sigma), 0.05% bovine serum


title: Exosome from A498 cellular supernatant

first: Guoliang

last: Sun

address: 1095# Jiefang Avenue

institute: Tongji Hospital

summary: Set domain-containing 2 (SETD2) is the most frequently mutated gene among all the histone methyltransferases (HMTs) in Clear cell renal cell carcinoma (ccRCC). Loss of function of SETD2 is significantly associated with poor prognosis in patients with ccRCC. A better understanding of the roles of SETD2 played in ccRCC can greatly improve the prognosis and quality of life of patients with kidney cancer.  Clear cell renal carcinoma cell A498 were treated with si-SETD2 and si-NC, and the  exosomes were extracted.

overall_design:
Clear cell renal carcinoma cell A498 were treated with si-SETD2 and si-NC
GROUP1:si-SETD2-1,si-SETD2-2,si-SETD2-3; GROUP2:si-NC-1;si-NC-2;si-NC-3

first: Libin

last: Yan

first: Xiaoliang

last: Wu

first: Yue

last: Ge


title: The land plant-specific MIXTA-MYB lineage is implicated in the early evolution of the plant cuticle and the colonization of land

city: Cambridge

first: Bo

last: Xu

address: Downing Street

department: Plant Sciences

country: United Kingdom

institute: University of Cambridge

summary: We studied gene expression changes in MIXTA-MYB overexpression and knock-out lines compared to the wild type.

overall_design: Thalli of 10-day-old Marchantia polymorpha (Cambridge strain, male) plants grown on plates were collected for RNA-seq analysis. For each line, three biological replicates were tested. The total RNA quality was examined using the RNA 6000 nano kit (Agilent) with a Bioanalyer 2100 (Agilent). The qualified total RNA samples were sent to BGI (Hongkong, China).

first: Xu

last: Bo

first: Pucker

last: Boas

first: Brockington

last: Sam


title: Chidamide inhibits the NOTCH1-MYC signaling axis in T-cell acute lymphoblastic leukemia

first: Mengping

last: Xi

address: 197 Rui Jin Er Road

institute: Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine

summary: We report that Chidamide shows significant anti- proliferation and more specifically anti-NOTCH effects in both cell lines and primary cells of T-ALL patients. By analyzing the expression profile characterizing the response of the cell lines to Chidamide treatment, we further confirmed that the antitumor effect of Chidamide was due to the inhibition of HDAC and the anti-NOTCH1 effect.

overall_design: Examination of 2 different T-cell acute lymphoblastic leukemia cell lines without/with Chidamide treated in 2uM for 48 hours.

first: Florent

last: Chuffart

first: Ekaterina

last: Bourova-Flin

first: Sophie

last: Rousseaux


title: CircRNA expression profiles in peripheral blood mononuclear cells of patients with large-artery atherosclerotic stroke

city: Zhanjiang

first: You

last: Li

state: Guandong

address: 57# South Renmin Road

institute: Institute of Neurology, Affiliated Hospital of Guangdong Medical University, Zhanjiang 524001, China.

summary: Circular RNAs (circRNAs) are a recently discovered non-coding RNA isoform capable of regulating neurological disease incidence. The present study was designed to characterize the circRNA expression profiles present in large-artery atherosclerosis (LAA)-type acute ischemic stroke patients. Using a RNA-seq approach, we characterized circRNA expression profiles in 5 LAA-stroke patients and 4 controls.  We identified 182 and 176 circRNAs that were up- and down-regulated, respectively, in LAA-stroke patients relative to controls.  Enrichment analyses suggested these differentially expressed circRNAs to primarily be associated with chromatin modification, autophagy, platelet activation, and neural precursor cell proliferation.

overall_design: Human PBMCs circRNA profiles in 5 patients with large-artery atherosclerotic stroke and 4 matched controls

first: Shengnan

first: Weidong

last: Hu

first: Fu

last: Deng

first: Shaofeng

last: Chen

first: Peiyi

last: Zhu

first: Mengxu

last: Wang

first: Xinglan

first: Ying

first: Xingjuan

first: Bin

last: Zhao

first: Wangtao

last: Zhong

first: Guoda

last: Ma


title: RNA sequence of gestational diabetes mellitus (GDM) and healthy control placentas

city: Jinan

first: Jin

state: China

address: No.2,  Jianguo xiaojing road, Jinan City, Shandong Province, PR China

institute: Jinan Maternal and Child Health Care Hospital

summary: GDM is a multi-system disorder that is primarily characterised by new-onset hypertension accompanied by proteinuria during gestation. This disease is one of the leading causes of maternal and perinatal morbidity and mortality. In this work, placental samples were collected from GDM and control patients. RNA-seq was performed to identify differences in gene expression. Significantly differentially expressed genes between the GDM and control samples included 64 up-regulated and 296 down-regulated genes. This study may provide further insight in the mechanisms of GDM and function as preventive, predictive and therapeutic measures.

overall_design: mRNA profile of placental samples of GDM (n=4) and control patients (n=4), and each group were generated by Illumina Hiseq 4000.

first: Hua

last: Jin


title: Establishment of primitive endoderm stem cell lines in mice [scRNA-Seq]

first: Takaho

last: Endo

summary: The mammalian blastocyst consists of three distinct cell types: epiblast, trophoblast, and primitive endoderm (PrE). Although stem cell lines that retain functional properties of epiblasts or trophoblasts have been established, establishment of stem cell lines that fully retain developmental potential of PrE has long been awaited. Here we report derivation of primitive endoderm stem (PrES) cells, which are capable to give rise functional PrE derived tissues and support fetal development of PrE-depleted blastocysts in chimeras, in mice.

overall_design: Single-cell RNA-seq experiments were performed to see whether cells were heterogeneous or not.

first: Yasuhide

last: Ohinata

first: Haruhiko

last: Koseki

first: Takashi

last: Watanabe

first: Osamu

last: Ohara


title: RIP-Seq analysis of non-PPR editing factors OZ1, ORRM1, RIP9/MORF9

city: Los Angeles

first: Michael

middle: Lloyd

last: Hayes

address: 5151 State University Dr

department: Chemistry and Biochemistry

institute: California State University Los Angeles

summary: We provide sequences of maize chlroplast RNAs associated with non-PPR editing factors through immunoprecipitation. The accumulated sequences indicate expansive role in RNA processing and potential associations of OZ1-ORRM1 complexes with the ribosome and less efficiently translated mRNAs.

overall_design: Three specific purified polyclonal antibodies were bound to magnetic protein A/G beads. Beads were then suspended in maize chloroplast extracts and RNAs isolated and sequenced after washing.

first: Paola

middle: I

last: Santibanez

first: Vihn

last: Ngo


title: Effects of EZH2 ablation on promoter accessibility in mouse PDAC lines derived from KrasG12D/PEC/IkkαΔPEC tumors

city: La Jolla

first: Michal

last: Krawczyk

address: 9500 Gilman Dr

department: Ophthalmology

institute: UCSD

summary: We analyzed chromatin accessibility genome wide in EZH2KO and control cells derived from PDAC tumors of KrasG12D/PEC-IkkαΔPEC PDAC model mice to gain insight how the ablation of EZH2 affects the accessibility of genes involved in PDAC tumorigenesis.

overall_design: ATAC-seq was performed in two established cell lines, EZH2KO-UN-KC-6141, and control-UN-KC-6141. UN-KC-6141 is a line derived from PDAC tumors from KrasG12D/PEC-IkkαΔPEC mice.

first: Laura

last: Antonucci

first: Qianlan

last: Xu

last: Karin


title: LncRNA SNHG8d impedes chromatin condensation and epithelial differentiation by phase separating histone H1.

first: Ping

last: He

address: No. 280, South Chongqing Road.

institute: Shanghai Jiao Tong University, School of Medicine

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

sample_organism:
Homo
Homo sapiens

platform_organism:
Homo
Homo sapiens

overall_design: Refer to individual Series


title: LncRNA SNHG8d impedes chromatin condensation and epithelial differentiation by phase separating histone H1 [RNA-seq]

summary: Linker histone H1, the key chromatin structural protein facilitating higher order chromatin folding, isan important epigenetic mark and regulator for gene expression and cellular differentiation. However, mechanisms thatregulate H1 binding affinity to chromatin remain elusive. In an attempt to screen functionallong non-coding RNAs(lncRNAs), we designed a cell-type specific score (CTSS) algorithm on the basis of RNA-seq data derived fromcell lines of different origins, which leads to the identification of an epithelium-specific lncRNA designated assmall nucleolar RNA host gene 8 (SNHG8). In epithelial cells, loss of SNHG8d, a major transcriptof SNHG8, remodels the genomic expression profiletowards differentiation. Mechanistically, SNHG8d is localized in the nucleus and manifests stronginteraction withallthe histone H1 variants detected.Loss of SNHG8dleads to increasedH1 binding affinity to chromatinand subsequentchromatin condensationwhichdictates the epithelial differentiation-orientedgenomic expression remodeling.Further analysis proposes that SNHG8d regulates H1-chromatin affinityby competing with linker DNA forhistone H1 binding througha phase-separation mechanism. Thus, our study revealed a lncRNA-conducted mechanismthat sequesters histone H1 from chromatin through phase separation to sequentially regulatechromatin structure, gene expressionandepithelialdifferentiation.

overall_design: Examination of the gene expression pattern and chromatin accessibility in MCF10A cells by knockdown SNHG8.

first: Cheng

last: Zhang

first: Shaoming

last: Shen

first: Guoqiang

last: Chen


title: RNA-Seq analysis of porcine islets and pancreas to characterize the differentially expressed genes between higher and lower islet density

city: Minneapolis

first: Christopher

last: Burlak

state: Minnesota

address: 420 Delaware Street SE

institute: University of Minnesota

summary: Gene expression patterns that form the basis for the observed variation in islet density among porcine pancreata were examined. RNA-Seq analysis was performed to investigate differential gene expression of intact porcine pancreas samples and pure cultured islet samples according to a density of islets. Most prominently upregulated genes in the islet-rich pancreas samples included GP2 and GCG. The mRNA expression of pure islet cell samples from both groups were statistically identical. This transcriptome RNA-Seq analysis showed that pancreatic islet density is associated with GP2 expression.

overall_design: RNA-Seq analysis of 20 porcine islets and pancreas

first: Juan

last: Abrahante

first: Yoshihide

last: Nanno


title: LncRNA SNHG8d impedes chromatin condensation and epithelial differentiation by phase separating histone H1 [ATAC-seq]

summary: Linker histone H1, the key chromatin structural protein facilitating higher order chromatin folding, is an important epigenetic mark and regulator for gene expression and cellular differentiation. However, mechanisms thatregulate H1 binding affinity to chromatin remain elusive. In an attempt to screen functionallong non-coding RNAs(lncRNAs), we designed a cell-type specific score (CTSS) algorithm on the basis of RNA-seq data derived fromcell lines of different origins, which leads to the identification of an epithelium-specific lncRNA designated assmall nucleolar RNA host gene 8 (SNHG8). In epithelial cells, loss of SNHG8d, a major transcriptof SNHG8, remodels the genomic expression profiletowards differentiation. Mechanistically, SNHG8d is localized in the nucleus and manifests stronginteraction withallthe histone H1 variants detected.Loss of SNHG8dleads to increasedH1 binding affinity to chromatinand subsequentchromatin condensationwhichdictates the epithelial differentiation-orientedgenomic expression remodeling.Further analysis proposes that SNHG8d regulates H1-chromatin affinityby competing with linker DNA forhistone H1 binding througha phase-separation mechanism. Thus, our study revealed a lncRNA-conducted mechanismthat sequesters histone H1 from chromatin through phase separation to sequentially regulatechromatin structure, gene expressionandepithelialdifferentiation.


title: Bulk RNA seq of NGP cells

city: Ghent

first: Kaat

last: Durinck

address: Corneel Heymanslaan 10

department: Biomolecular Medicine

country: Belgium

institute: Center for Medical Genetics

summary: Technological advances in transcriptome sequencing of single cells provided an unprecedented view on tissue composition and cellular heterogeneity. While several studies have compared different single cell RNA-seq methods with respect to data quality and their ability to distinguish cellular  subpopulations, none of these comparative studies investigated the heterogeneity of the cellular transcriptional response upon a chemical perturbation. In this study, we evaluated the transcriptional response of NGP neuroblastoma cells upon nutlin-3 treatment using the C1, ddSeq and Chromium single cell systems. These systems and library preparation methods are representative for the wide variety of platforms, ranging from microfluids chips to droplet-based systems and from full transcript sequencing to 3’ end sequencing. In parallel, we used bulk RNA-seq for molecular characterization of the transcriptional response. Two complementary metrics to evaluate performance were applied: the first is the number and identification of differentially expressed genes as robustly assessed by two statistical models, and the second is enrichment analysis of biological signals, which is independent of sample size or number of cells evaluated. Where relevant, we downsampled sequencing library size, selected cell subpopulations based on specific RNA abundance features, or created pseudobulk samples to make the data more comparable. While the C1 detects the highest number of genes per cell and better resembles bulk RNA-seq, the Chromium identifies most differentially expressed genes, albeit still substantially fewer than bulk RNA-seq. Gene set enrichment analyses reveals that detection of the most abundant genes in single cell RNA-seq experiments is sufficient for molecular phenotyping. Finally, single cell RNA-seq reveals a heterogeneous response of NGP cells upon nutlin-3 treatment, pinpointing putative late-responders or resistant cells, hidden in bulk RNA-seq experiments.

overall_design:
Bulk RNA sequencing of Nutlin-3 and vehicle treated cells on Illumina Nextseq 500 (Illumina)

**Please note that one merged normalized count table (count_data.xlsx) was generated from both scRNA-seq and bulk-RNA seq dataset and is linked to the scRNA-seq records.

first: Verboom

last: Karen

first: Alemu

last: Assefa

first: Nurten

last: Yigit

first: Jasper

last: Anckaert

first: Niels

last: Vandamme

first: Dries

last: Rombaut

first: Yvan

last: Saeys

first: Olivier

last: Thas

first: Frank

last: Speleman

first: Jo

last: Vandesompele


title: Single cell RNA sequencing of Chromium isolated NGP cells

overall_design:
Single cell RNA sequencing of Nutlin-3 and vehicle treated cells on Chromium (10X Genomics)
Please note that one merged normalized count table (count_data.xlsx) was generated from both scRNA-seq and bulk-RNA seq dataset and is linked to the scRNA-seq records.


title: Engineered methanotrophic platform for biomanufacturing of non-oxidative ribulose monophosphate pathway-derived products from methane and xylose

city: Yongin

first: Anh

middle: Duc

last: Nguyen

address: Kyung Hee University

country: South Korea

institute: Kyung Hee University

summary: Comparative transcriptomic analysis between methane- and methane plus xylose- grown cultures revealed different transcriptional responses of pXyl M. alcaliphilum 20Z strain on diffirent growth modes.

overall_design: Examination differental expression genes when pXyl strain grown on two growth modes: methane as sole carbon source and methane plus xylose as co-substrates

middle: D

first: Tin

middle: H

last: Chau

first: Eun-Yeol

last: Lee


title: The H3K27M mutation alters stem cell growth, epigenetic regulation, and differentiation potential [MeDIP-Seq]

city: Saint Louis

first: Kristen

last: Kroll

address: 320 McDonnell Sciences/660 S. Euclid Ave.

institute: Washington University School of Medicine

type: Methylation profiling by high throughput sequencing

summary: Lysine 27 to methionine mutation (H3K27M) of the H3F3A gene, which encodes the variant histone H3.3, is found in the majority of Diffuse Intrinsic Pontine Gliomas (DIPGs). DIPGs are the most aggressive form of pediatric gliomas and have a median survival of <1 year from diagnosis. As H3K27M mutation is necessary but not sufficient to cause DIPGs, it is accompanied by several other mutations in tumors. However, the mechanisms by which H3K27M increases vulnerability to DIPG tumorigenesis, while expected to involve altered epigenetic regulation is unclear. Thus, in this work we built pairs of isogenic human embryonic stem cell lines with versus without this mutation, in the absence of other DIPG contributory mutations, to investigate mechanisms by which H3K27M mutation could affect cellular proliferation and differentiation and how these were related to alterations in the transcriptome, H3K27me3, and the DNA methylome. We found that H3K27M increased stem cell proliferation and interfered with differentiation, resulting in loss of most H3K27me3 and resulting in anomalous onset of expression of developmental genes during multilineage or directed differentiation. This work suggests mechanisms by which H3K27M mutation influences stem cell properties, contributing to DIPG tumorigenesis.

overall_design: The H3F3a-K28M-Puro clonal cell lines (mutant clone 1 and clone 9)  were generated from H1 embryonic stem cell (H1ESC) line (obtained from WiCell) by the Genome Engineering and iPSC Center (GEiC), Washington University in St. Louis. These lines were used for derivation of neural progenitor cells, as described below, and comparisons of gene expression in the wild type versus mutant hESCs and neural progenitor cells were performed. MeDIP was performed on four biological replicates of WT and H3K27M mutant undifferentiated H1 hESCs and their 5-day differentiated neural EB derivatives cultured in parallel to those used for RNA-sequencing.

first: Santhi

last: Pondugula

first: Najla

last: Kfoury

first: Ramachandran

last: Prakasam

first: Scot

middle: J

last: Matkovich

first: Hiroko

last: Yano

first: Albert

last: Kim

first: Josh

last: Rubin


title: RNA-seq analysis of primary dermal fibroblasts of Hutchinson-Gilford progeria syndrome.

city: Beijing

first: Xiangyang

last: Wang

address: No.5 Yiheyuan Road, Haidian District

department: College of Life Sciences

institute: Peking University

summary: We identified two HGPS patients with the classical mutation site c.1824C>T. We seperated primary dermal fibroblasts from these  patients and one normal child, and performed RNA-seq. By analyzing gene expression level, we identified 5567 common differential exprssion genes of two HGPS patients compared to norml child. We classified these genes into three groups, including common up genes (2243), common down genes (2644) and differential genes (680). We focused on common up and common down genes, and performed GO analysis and KEGG analysis. Our study provides a sight for better understanding HGPS and normal aging.

overall_design: RNA-seq analysis of primary dermal fibroblasts from two HGPS patients and one normal child.

first: Chuanmao

last: Zhang


title: DUX4 promotes mitochondrial impairment in skeletal muscle

city: Melbourne

first: Mark

last: Ziemann

state: VIC

address: 85 Commercial Rd

department: Bioinformatics Working Group

country: Australia

institute: Burnet Institute

summary: Facioscapulohumeral muscular dystrophy (FSHD) is characterised by a progressive degeneration and weakness of skeletal muscle fibers attributed to inappropriate expression of the transcription factor double homeobox 4 (DUX4). However, the cellular events that precede pathology in DUX4 expressing muscle fibers remain incompletely understood. Using recombinant AAV vectors to activate species-specific DUX transcription factors in murine and human skeletal muscle fibers, we developed models for examining DUX4-induced pathology. RNA-sequencing prior to the onset of muscle pathology reveals that perturbation of metabolic and mitochondrial function is an early event following activation of DUX transcription factors across species. A reduction in mitochondrial membrane potential was confirmed following DUX4 activation in human muscle fibers prior to reductions in force generating capacity. These studies present new models that can be used to delineate the changes in biological processes following acute DUX4 activation in mouse and human skeletal muscle fibers, for greater insight into the pathogenesis of FSHD, and support further investigation of mitochondrial function as a therapeutic target in FSHD.

overall_design: RNA-seq was performed to understand gene expression changes of engineered human micromuscles (organoids) expressing DUX4.

first: Kevin

last: Watt

first: Richard

last: Mills

first: Man-Kit-Sam

first: Adam

last: Hagg

first: Hongwei

last: Qian

first: Fergus

last: Sully

first: Assam

last: El-Osta

first: Andrew

last: Murphy

first: Stephen

last: Tapscott

first: James

middle: E

last: Hudson

first: Paul

last: Gregorevic


title: Transcriptional Profliing of small molecules induced endothelial cells of stem cells from apical papilla (SCAP-ECs), stem cells from apical papilla (SCAP) and human vein endothelial cells (HUVECs)

city: Hong Kong

first: Baicheng

last: Yi

address: 34 Hospital Road, Sai Ying Pun, Hong Kong

department: Faculty of Dentistry

institute: The University of Hong Kong

summary: Recently, a new strategy has been developed to directly reprogram one cell type towards targeted cell type by using different combinations of small molecule compounds. Here we attempted to induce stem cells from apical papilla (SCAP) into endothelial cells (ECs) by the same strategy. We developed a set of small molecules and growth factors that facilitates the conversion of SCAP into stable endothelial lineage. The SCAP-derived endothelial cells (SCAP-ECs) expressed some up-regulated endothelial specific genes and proteins, exhibited the ability to form functional tubular-like structures in vitro, and contributed to generate blood vessels in vivo. The aim of this study is to compare the ECs-related gene profile of SCAP, SCAP-derived ECs and HUVECs (primary ECs) and to explore whether SCAP-derived ECs showed enriched ECs gene expression.

overall_design: Examination of the endothelial cells-related genes profile of SCAP, SCAP-derived-ECs and HUVECs ere generated by deep sequencing, in triplicate, using Illumina Hiseq 4000.


title: Deletion of TNF in Winnie-ApcMin/+ mice reveals its protective role in the progression of colorectal cancer

city: Castellana Grotte (BA)

first: Grazia

last: Serino

address: Via Turi, 27

country: Italy

institute: National Institute of Gastroenterology “S. de Bellis”, Research Hospital

summary: To examine the effects of chronic, low-grade inflammation on the pathogenesis of colorectal cancer (CRC), we developed a novel murine model of colitis-associated cancer by crossing Winnie mice with ApcMin/+ mice thus combining the inflammatory background with a genetic predisposition to develop small intestinal polyposis, respectively. Winnie-ApcMin/+ mice showed early, spontaneous occurrence of colonic dysplastic lesions with a distinct molecular signature. Since TNF is a major clinical target for suppression of chronic intestinal inflammation, we investigated its impact on Winnie-ApcMin/+ model. Surprisingly, deletion of Tnf in Winnie-ApcMin/+ mice resulted in an initial reduction of dysplastic lesions at disease onset, but facilitated disease progression with a unique molecular footprint. Our results confirm that even a mild, but chronic, inflammation represents a crucial risk factor in individuals genetically-predisposed to CRC, and support a dual role for TNF in the onset vs. progression towards CRC.

overall_design: Gene expression profiling of aberrant crypt foci (ACF) macrodissected from 8-wk-old Winnie-ApcMin/+-5540 mice and Winnie-ApcMin/+ mice were performed by RNA Exome sequencing

first: Stefania

last: De Santis

first: Marcello

last: Chieppa


title: P75 neurotrophin receptor regulates BMP-induced SVZ neural stem cell migration.

city: Freising

first: Franziska

last: Greulich

address: Gregor-Mendel-Str. 2

department: Metabolic Programming

institute: TU München

summary: RNA sequencing of neuronal stem/progenitor cells from wildtype and p75NTR-/- mice isolated at E12.5

overall_design: Polyadenylated RNA from 2 wildtype and 3 p75NTR-/- E12.5 neuronal stem/progenitor cells were sequenced.

first: Sachin

middle: S

last: Deshpande

first: Christian

last: Schachtrup


title: Glioblastoma cell fate is differentially regulated by the microenvironments of the tumour bulk and infiltrative margin.

city: Badalona

first: Elisabetta

last: Mereu

address: Ctra de Can Ruti, Camí de les Escoles, s/n

country: Spain

institute: Josep Carreras Leukemia Research Institute

summary: Glioblastoma recurrence originates from invasive cells that escape surgical resection, but their biology remains poorly understood. Here we generated three somatic mouse models recapitulating the main driver mutations of the human disease to characterise the infiltrative tumour margin. We find that, regardless of genetics, tumours are fuelled by highly proliferative glioma stem-like cells (GSCs) resembling active neural stem cells (NSCs), which recapitulate normal and injury-induced neurogenesis in both bulk and margin. Surprisingly, GSCs are evenly distributed across both regions, suggesting that invasive potential is uncoupled from stemness. However, tumour region influences fate choice, with margin cells progressing towards astrocyte-like, and bulk cells towards injured NSC-like (iNSCs) fates. iNSCs account for a significant proportion of dormant glioblastoma cells and are induced by interferon signalling within T-cell-rich niches that form selectively in the bulk. These findings identify key differences between bulk and margin and indicate that glioblastoma cell fate is under cell-extrinsic control.

overall_design: Full-length single cell RNA sequencing libraries were prepared using the Smart-seq2 protocol with minor modifications.

first: Simona

last: Parrinello

first: Claudia

last: Garcia-Diaz

first: Holger

last: Heyn


title: Isolation of heart field specific cardiomyocytes provides a platform for safe cardiac regenerative therapy

first: Reza

last: Ardehali

address: 675 Charles E Young Dr S

institute: UCLA

summary: Single-cell analysis of first and second heart field-like cardiomyocytes from differentiating hESCs.

overall_design: Cells from cardiac differentiation protocols to generate first and second heart field-like cardiomyocytes were isolated at day 20 for transcriptomic analysis.

first: Arash

last: Pezhouman

last: Engel

first: Ngoc

middle: B

last: Nguyen

first: Rhys

middle: P

last: Skelton

first: W

last: Gilmore

first: Debashis

last: Sahoo

first: David

middle: A

last: Elliott

first: Peng

last: Zhao


title: scRNA-seq and bulk RNA-seq of NGP cells

first: Kaat

last: Durinck


title: Post-transcriptional mechanisms distinguish human and chimpanzee forebrain progenitors

city: Lund

first: Johan

last: Jakobsson

address: Sölvegatan 17, building A11

country: Sweden

institute: Lund University

summary: The forebrain has expanded in size and complexity during hominoid evolution. The contribution of post-transcriptional control of gene expression to this process is unclear. Using in-depth proteomics in combination with bulk and single-cell RNA sequencing, we analyzed protein and RNA levels of almost 5,000 genes in human and chimpanzee forebrain neural progenitor cells. We found that species differences in protein expression level was often independent of RNA levels, and more frequent than transcriptomic differences. Low-abundant proteins were more likely to show species-specific expression levels, while proteins expressed at a high level appeared to have evolved under stricter constraints. Our study implicates a previously unappreciated broad and important role for post-transcriptional regulatory mechanisms in the evolution of the human forebrain.

sample_organism:
Pan troglodytes
Homo sapiens

platform_organism:
Pan troglodytes
Homo sapiens

overall_design: Bulk RNA-seq was performed on iPSC-derived forebrain neural progenitors at day 14 of differentiation from two human and two chimpanzee individuals, two differentiation replicates per line. For one human and one chimpanzee, bulk RNA-seq was also performed at day 13, 15, and 16 of differentiation, two differentiation replicates per line. Single cell RNA-seq was done for one human and one chimpanzee individual, with one differentiation replicate.

first: Daniela

last: Grassi

first: Per

last: Brattås

first: Jeovanis

last: Valdés

first: Melinda

last: Rezeli

first: Marie

last: Jönsson

first: Sara

last: Nolbrant

first: Malin

last: Parmar

first: György

last: Marko-Varga


title: RNA-seq analysis of the first mandibular molars from K14-Cre; Wnt10aflox/flox mice and littermate control

first: Miao

last: Yu

address: 22 Zhongguancun South Avenue

summary: Wnt ligands are continuously expressed during tooth development and are essential for cell proliferation; therefore, we hypothesized that other Wnt ligands may be up-regulated to compensate the loss of Wnt10a. To test this hypothesis, we investigated mRNA expression levels in the first mandibular molars at PN4 by RNA-seq analysis. A list of 26 Wnt pathway associated genes were identified to be expressed differently in K14-Cre;Wnt10aflox/flox mice. Among them, 7 genes were up-regulated and 19 genes were down-regulated. And the up-regulation of Wnt4 appeared to be the most significant. Moreover, heat map displayed that among the Wnt ligands with relatively high endogenous expression level, Wnt4 was up-regulated in K14-Cre;Wnt10aflox/flox mice than in control.

overall_design: mRNA profiles of 4-day old wild type (Wnt10aflox/flox) and K14-Cre; Wnt10aflox/flox mice were generated by RNA sequencing, in triplicate, using BGISEQ-500.

first: Yang

last: Liu


title: HO1 activates autophagy to protect intervertebral disc degeneration

city: Shanghai

first: Chen

last: Xu

address: No, 800, Rd. Xiangyin

institute: The Second Military Medical University

summary: Intervertebral disc degeneration (IDD) is majorly resulted from disordered extracellular matrix (ECM) metabolism, including decreased anabolism and increased catabolism activities in the nucleus pulposus (NP) cells of discs. Pro-inflammatory cytokines such as interleukin-1β (IL-1β) are considered to be potent mediators of ECM loss. We reported previously that hemeoxygenase-1 (HO-1) inducer cobalt protoporphyrin IX (CoPP) could attenuate the ECM breakdown which induced by IL-1β, however, the underlying mechanism remains elusive. Here we found that autophagy family genes were involved in the HO-1 mediated anti-inflammatory processes in human NP cells by using high throughput RNA-Seq technique. These findings suggest that autophagy might play a role in inflammation related ECM metabolism disorder, thus offering a direction of our in-depth study and providing a framework for the searching of potential therapeutic targets in the treatment of IDD

overall_design: Examination of the gene expression profile of human nucleus pulposus cells treated with CoPP or/and Interlukin-1β

first: Hu

last: Bo


title: Raw RNA-seq data of HSV-1-infected human cells (HFF and MRC5)

city: Canberra

first: Yeu-Yang

last: Tseng

state: ACT

address: 131 Garran Rd

institute: ANU

summary:
We report transcriptomic data from HSV-1-infected human cells (HFF and MRC5)
Herpes simplex virus type I (HSV-1) is a common human pathogen causing cold sores, and in rare cases, severe keratitis and encephalitis. Mouse models are commonly used to study pathogenesis of HSV-1 infection due to the neurotropic properties of HSV make it hard to reach information from infected humans, but mice are not a natural host for this virus. Therefore, it is important to have insights into transcriptional regulation in human cell cultures, which gave us more information before we interpret experimental results from humans and mouse models.  Herein, we provide overall transcriptomic data from two HSV-1infected cells, HFF and MRC5. We found that these two human cells downregulated many genes in an antiviral pathway characterized by interferon-stimulated genes.

overall_design: Investigate human-mouse differences in HSV-1 infection

first: Zhi-Ping

last: Feng

first: Si

middle: M

last: Man

last: Tscharke


title: Raw RNAseq data of HSV-1-infected mouse skin fibroblasts

summary: Herpes simplex viruses (HSV) are responsible for a broad variety of human diseases, including cold sores, ocular herpes and herpetic encephalitis, leading to a great burden worldwide. However, the role for sex in herpes infection is controversial and unclear due to the complexity of factors involving in the formation of HSV diseases. Herein, we ask whether there is a sexual dimorphism based on the chromosomal rather than hormonal differences in the primary skin cells during low exposure of HSV. Profiling of male and female transcriptional programs reveals that cytosolic sensing pathway is induced to a greater degree in female cells, correlated with higher yields of infectious virions in male counterparts. Female skin cells distinctively reactivate Xist, a critical component of X inactivation, to silence the expression of the transcriptional repressor on X chromosome, which thereby maintains higher viperin level and further explains the different growth phenotypes between two sexes. Collectively, we propose a model that HSV-1 triggers a sex-specific regulation of antiviral response in the cytosolic sensing signaling via the control of Xist.

overall_design: We report transcriptomic data from both male and female HSV-1-infected mouse skin fibroblasts to nvestigate sex differences in HSV-1 infection

first: David


title: Proinflammatory TIFA-NF-κB axis drives intrinsic survival signaling and acquires macrophage niches via DAMPs to promote HCC resistance to sorafenib

city: Taipei City

first: Pei-Yu

last: Wu

address: 128 Academia Road, Section 2, Nankang Dist.

department: Institute of Biological Chemistry

country: Taiwan

institute: Academia Sinica

summary: Sorafenib is the first-line treatment for advanced stage hepatocellular carcinoma (HCC), but rapid disease re-progression occurs in most treated cases, with molecular mechanism remaining elusive. The resistance to sorafenib has been correlated with inflammation, and here we investigated how the pro-inflammatory TIFA signaling modulates the inflammatory tumor microenvironment to negate sorafenib cytotoxicity and prime for HCC dissemination. We found that the TIFA-NF-κB axis in HCC cells compromised sorafenib cytotoxicity in alliance with pro-tumor M2 macrophages, suggesting an intensive crosstalk between HCCs and M2 macrophages. To identify the key mediators of such crosstalk between HCC cells and macrophages underlying sorafenib resistance, primary macrophages were cocultured with HCC cells and then subjected to targeted RNA-panels for transcriptome analysis of innate immune and inflammatory factors.

overall_design: 6 samples. Mahlavu cells were transfected with control siRNA or TIFA siRNA and then treated with sorafenib. Treated cells were respectively cocultured with M0, M1, and M2 macrophages. Total RNAs of these macrophages were thus subjected to targeted RNA-seq transcriptome analysis using QIAGEN Human Inflammation and Immunity Transcriptome RNA targeted panel (Cat#333002 RHS-005Z).

first: Tong-You

middle: W

last: Wei

first: Ming-Daw

last: Tsai


title: The DNA polymerase subunit Pol32 and RNase H1 are required for stress granule formation through R-loop regulation

city: Gothenburg

first: Per

last: Sunnerhagen

address: Box 462

department: Chemistry and Molecular Biology

institute: University of Gothenburg

summary: Strong cellular stress causes wide-spread perturbations in the transcriptome and in several types of DNA/RNA interactions, and through incompletely understood pathways to formation of cytoplasmic stress granules (SGs).   We have investigated the relationships between strong transcriptional induction, RNA:DNA hybrid stretches (R-loops), and SG formation under severe hyperosmotic and glucose stress. Several mutations affecting DNA processing proteins, including the DNA polymerase subunit Pol32, confer SG formation defects. Severe stress increased R loop levels globally. We found that facilitating removal of R-loops by RNase H overexpression, with activity towards RNA:DNA hybrids, accelerated and enhanced transcriptional induction of stress-activated genes. Thus, overexpression of RNase H1, but not RNase H2, reduced R-loops globally around the 1 h mark. Remarkably, it also reduced SG formation. We performed a genome-wide analysis of the induction or repression kinetics of gene expression under severe stress conditions. RNase H1 overexpression reduced R-loops locally in highly transcribed stress-affected genes, as expected. Notably, it also increased expression of several stress-induced genes. Conversely, in cells where R-loops are not efficiently resolved, transcriptional induction of the same genes under stress was muted and occurred with a delay. Thus, in pol32∆ mutants, where SG accumulation is delayed, R-loop levels are elevated, and induction of stress genes suppressed. The pol32∆ mutants are also refractory to the effects of RNase H1 overexpression on stress gene induction, R-loop resolution, and SG formation, indicating that Pol32 may act downstream of Rnh1 in the regulation of these three processes. These findings demonstrate an unexpected link between R-loops and formation of SGs.  Together, these observations indicate that under stress, strong transcriptional induction of specific genes or genomic regions causes R-loop accumulation, which then requires RNase H1 activity for resolution. If unresolved, the accumulated R-loops impede continued stress-induced transcription, and delay or prevent SG formation.

overall_design: Samples were collected every 30 min after onset of 1.5 M KCl stress, up to 2 h. Samples were collected from two independent replicate experiment time series Total number of samples = 10.  Control samples were collected at the 0 h time point.

first: Heejung

last: Kim


title: Analysis of gene expression in co-culture of PBMCs with breast cancer cell lines by High-Throughput Sequencing

city: Bangkok

first: Nakarin

last: Kitkumthorn

address: Yothee road

department: Oral Biology

country: Thailand

institute: Mahidol University

summary:
The goal of this study is to investigate paracrine effect of peripheral blood mononuclear cells (PBMCs) on breast cancer cell lines.
Transcription profiles of PBMCs (control) and PBMCs co-cultured with breast cancer cell lines (treatment) were generated by deep sequencing, in triplicate for MCF7 and duplicate for T47D, using Illumina HiSeq 4000.
Transcriptome analysis of PBMCs has shown the gene expression changed when co-cultured with breast cancer cell lines. The result revealed significantly up- and down-regulated genes.

overall_design: Transcription profiles of PBMC (control) and PBMC co-cultured with breast cancer cell lines (treatment) were generated by deep sequencing, in triplicate for MCF7 and duplicate for T47D, using Illumina HiSeq 4000.

first: Sutasinee

last: Asayut

first: Apiwat

last: Mutirangura


title: Chronologic age and morbidities could converge on gene-specific traits through length-dependent failure of transcript polymerization

city: Chicago

first: Alexander

last: Misharin

state: IL

address: SQBRC 303 E Superior St 5-404

department: Medicine (Pulmonary Division)

institute: Northwestern University

summary: We provide evidence for the decrease of long transcripts during aging using a unique reference transcriptomic survey of 17 mouse organs sampled at 5 timepoints over the lifespan.

overall_design: Transcriptomic profiles of 17 mouse organs, sampled at 4, 9, 12, 18, 24 months of age, were generated by standard illumina RNA-Seq protocols.

first: Thomas

last: Stoeger

first: Rogan

last: Grant

first: Alexandra

middle: C

last: McQuattie-Pimentel

first: Kishore

last: Anekalla

first: Sophia

first: Heliodoro

last: Tejedor-Navarro

first: Benjamin

last: Singer

first: Hiam

last: Abdala-Valencia

first: Michael

last: Schwake

first: Marie-Pier

last: Tetreault

first: Harris

last: Perlman

first: William

last: Balch

first: Navdeep

last: Chandel

first: Karen

last: Ridge

first: Jacob

last: Sznajder

first: Richard

last: Morimoto

middle: V

first: G

last: Budinger

first: Luis

last: Nunes Amaral


title: The Neuronal CCAAT/enhancer binding protein α mediates HIF-1α-induced inflammatory brain damage after ischemia

city: Xuzhou

first: Wu

last: Dongmei

state: Jiangsu

address: 101 Shanghai Road

institute: Jiangsu Normal University

summary: Through transcriptome analysis, we uncovered 3 modules correlated with specific stages/time frames after photothrombotic ischemia. Then, 3 modules were identified by hub gene network analysis in combination with biological function analysis and KEGG pathway analysis. Among these 3 modules, the E-module hubs, the G-module hubs, and the I-module hubs contained genes correlated with the chemotaxis, the cell cycle and mitosis or the immune response/inflammation, respectively. Evidence shows that CCAAT/enhancer binding protein α (C/EBP-α)-induced inflammation has been linked to ischemic stroke. More interestingly, CEBPA, which encodes C/EBP-α, was shown to be one of the hub genes associated with the immune response/inflammation, which prompted us to carry out a more detailed investigation in this study. Here, we investigate the potential mechanism underlying the action of C/EBP-α in the etiology of ischemic brain injury.

overall_design: mRNA time course profiles of photothrombotic ischemia focal region (caudate nucleus) from male C57BL/6J mice by deep sequencing, mixed samples (>6) for each time point, using Illumina HiSeq2500.

first: Jun

last: Lu

first: Sheng

last: Zhao

first: Juehua

last: Yu


title: The FSHD effector protein Dux promotes myopathy via Myostatin-Smad signaling

first: Mark

last: Ziemann

summary: Facioscapulohumeral muscular dystrophy (FSHD) is an autosomal-dominant condition that is characterised by a progressive degeneration and weakness of skeletal muscle fibers. The underlying cause of FSHD has been attributed to inappropriate expression of the transcription factor double homeobox (Dux); however, the mechanisms leading to myopathy in response to Dux expression remain incompletely understood. To study the acute effects of Dux activation in mammalian skeletal muscle fibers, we generated a recombinant adeno-associated viral vector allowing tunable Dux expression. Consistent with previous findings, we confirmed that the ectopic expression of Dux in mouse skeletal muscle results in a degenerative myopathy. Building on these findings, we observed that the acute expression of Dux in muscle fibers causes profound transcriptome changes prior to the onset of pathology. Furthermore, muscles expressing Dux display elevated levels of the TGF-beta superfamily member, Myostatin and increased Smad2/3 activity. Notably, inhibition of Myostatin is sufficient to prevent Dux-induced myopathy. Collectively, these findings support further investigation of interventions targeting the Myostatin-Smad2/3 pathway as prospective approaches to treating myopathy associated with Dux mis-expression.

overall_design: RNA-seq was performed to understand gene expression changes in skeletal muscle caused by overexpression of Dux from a doxycycline inducible transgene.

first: Kevin

last: Watt

first: Chao-Jen

last: Wong

first: Man-Kit-Sam

last: Lee

first: Fergus

middle: L

last: Sully

first: Adam

last: Hagg

first: Rachel

last: Thomson

first: Hongwei

last: Qian

first: Assam

last: El-Osta

first: Andrew

last: Murphy

first: Stephen

last: Tapscott

first: Paul

last: Gregorevic


title: Methylome of of HepG2 cells uninfected ("Cont") or infected with the pathogen Listeria monocytogenes ("Inf") by Methyl-binding domain-sequencing (MBD-Seq/MethylCap-Seq)

city: Jouy-en-Josas

first: Helene

last: Bierne

address: Domaine de Vilvert, bat 442, INRA Micalis

department: Micalis Institute

country: France

institute: INRAE - University PARIS SACLAY

summary: We report the partial methylome (CG-rich regions) of human hepatocytes (HepG2) infected or not by the bacterium Listeria monocytogenes

overall_design: We used MBD-seq (MethylCap-Seq) to identify genomic regions differentially methylated after 3 days of infection with GFP-expressing Listeria. Infected and uninfected cells were purified by FACS prior to DNA extraction.

first: Anupam

last: Paliwal

first: Emanuele

last: Libertini

first: Jean-Yves

last: Coppee


title: In Vivo Organ Regeneration via Stroma-Dependent Adult Lineage Reprogramming

city: Carrington Crescent

last: Sims

state: Edinburgh

address: Systems Medicine Building

department: Institute of Genetics and Molecular Medicine

institute: University of Edinburgh

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

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

platform_organism:
Caenorhabditis elegans
Drosophila melanogaster
Danio rerio
Gallus gallus
Homo sapiens
Mus musculus
Rattus norvegicus

overall_design: Refer to individual Series


title: Analysis of gene expression in co-culture of PBMCs with lung cancer cell lines by High-Throughput Sequencing

first: Nakarin

last: Kitkumthorn

summary:
Objective: The goal of this study is to investigate paracrine effect of Peripheral Blood Mononuclear Cells (PBMCs) on lung cancer cell lines.
Method: Transcription profiles of PBMCs (control) and PBMCs co-cultured with lung cancer cell lines (treatment) were generated by deep sequencing,in triplicate, using Illumina HiSeq 4000.
Results and Conclusions: With demonstrating of RNA sequencing approach, PBMCs has been shown the gene expression changed when co-cultured with lung cancer cell lines. The result revealed that up-regulated genes were 8,073 and 8,070 genes co-cultured with A549 and H292, respectively. In the other hand, down-regulated genes were 8,341 and 8,342 genes co-cultured with A549 and H292, respectively. Comparing the data to expression array databases from lung cancer patients, up-regulated genes were shown 29 genes co-cultured with A549 and 37 genes with H292 which, among them, there were 2 genes, ANKRD37 and BUB3, found in both treatments. Down-regulated genes were found 24 and 35 genes in the co-culture of A549 an d H292, respectively, that no similar genes found in both treatments.

overall_design: Transcription profiles of PBMC (control) and PBMC co-cultured with lung cancer cell lines (treatment) were generated by deep sequencing, in triplicate, using Illumina HiSeq 4000.

first: Ratakorn

last: Srisuttee

first: Apiwat

last: Mutirangura


title: In Vivo Organ Regeneration via Stroma-Dependent Adult Lineage Reprogramming (mRNA)

summary: Remarkable progress has been made in cell fate reprogramming by forced expression of a small number of transcription factors. Major challenges remain, however, in regenerative medicine regarding how to target multiple cell types and direct them to form a functional organ in vivo. Here, we demonstrate that, by changing their stromal microenvironment, adult differentiated cells of endodermal origin can be reprogrammed to generate a functional ectodermal organ. The process of organ regeneration is highly efficient and complete, and depends on epithelial-stromal interactions that lead to successful remodeling of the extracellular matrix and stromal cells that are essential for organ function. Furthermore, it is a multistep process consisting of changes in cell fate, where dedifferentiation occurs more rapidly than redifferentiation, and subsequent morphogenetic reprogramming. Remarkably, neither direct transdifferentiation nor a complete reversion to the pluripotency state is involved in the reprogramming process; instead it features dynamic activities of essential genes that regulate pluripotency and lineage development. Our data have important implications for stem cell biology, cancer biology, and regenerative medicine.

overall_design: Three replicates of adult and reprogrammed mouse lung and mammary cells were profiled for mRNAs


title: Transcriptome (Affymetrix arrays) and Methylome of HepG2 cells uninfected (Cont) or infected with the pathogen Listeria monocytogenes (Inf)

summary:
This SuperSeries is composed of the SubSeries listed below.
Note that transcriptomes are performed with Affymetrix arrays and samples noted "S72h" have been sorted by FACS.

overall_design: Refer to individual Series.


title: Transcriptome (Affymetrix arrays) of HepG2 cells uninfected (Cont) or infected with the pathogen Listeria monocytogenes (Inf) for 24 or 72 hours.

summary: Comparisons of gene expression profiles of human hepatocytes (HepG2) infected or not by the bacterium Listeria monocytogenes (strain EGD-e expressing GFP) for 24 or 72 hours and use of Affymetrix microarrays. Samples noted S72h have been sorted by FACS.

overall_design: We used Affymetrix arrays to identify the repertoire of genes differentially expressed after 1 or 3 days of infection with GFP-expressing Listeria. Infected and uninfected cells were directly used (a) or purified by FACS (S) prior to RNA extraction.

first: Guillaume

last: Soubigou


title: Analysis of the transcriptomes of salt tolerant and susceptible cultivars of indica rice by microarray

city: New Delhi

first: Jitendra

middle: Paul

last: Khurana

address: Benito Juarez Road

department: Department of Plant Molecular Biology

country: India

institute: University of Delhi South Campus

summary: Over the years, many traditional rice varietites of India were sourced and studied owing to their ability to withstand abiotic pressures like excessive salinity in the soil and water. These cultivars growing in specific areas of the country represent a rich gene pool from where a deeper understanding of the processes underlying tolerance to abiotic stress can be gained. Indigenous varieties like Nonabokra and Pokkali are known salt tolerant varieties and are being studied in great detail. In the present study, we have analyzed the transcriptomes of the contrasting cultivars; Nonabokra (tolerant), Pokkali (tolerant) and IR29 (susceptible) in order to decipher the differences in their responses to salinity stress by utilizing microarray.

overall_design: Seedlings of Nonabokra, Pokkali and IR29 were grown hydropnically for seven days and then subjected to salinity stress by placing them in 200 mM NaCl solution under light for 3 h and 6 h at 28±1oC. For control samples, seedlings were kept in RGM (root growth medium) for 6 h at 28±1oC. RNA extracted from each sample was hybridized on rice Affymetrix microarrays. Three biological replicates of each sample were used for microarray analysis. Overall, twenty seven samples were analyzed representing control, 3 h and 6 h of salinity stress for each cultivar (Nonabokra, Pokkali and IR29).

first: Pratikshya

last: Borah

first: Sanjay

last: Kapoor


title: Gene expression-based imatinib response prediction in chronic phase CML

city: Innsbruck

first: Stefan

last: Schmidt

address: Anichstr. 35

institute: Medical University Innsbruck

summary: Tyrosine kinase inhibitor (TKI) treatment of chronic myeloid leukemia (CML) is guided by the pre-defined European Leukemia Net (ELN) or other response criteria. This allows patient stratification only during but not prior to treatment initiation. Gene expression profiling (GEP)-based response prediction might become a valuable tool for patient stratification in CML, but so far published data for response prediction are conflicting. We generated an imatinib response predicting gene signature by GEP from peripheral blood samples of pre-treated CML patients in late chronic phase.

overall_design: We generated an imatinib response predicting gene signature by GEP from peripheral blood samples of pre-treated CML patients in late chronic phase withdrawn prior to (n=135) and 6 weeks after starting imatinib therapy (n=63). According to the study protocol, patients received either standard (400 mg) or high dose (800 mg) imatinib for six months followed by standard dose maintenance therapy. GEP were generated by using the Affymetrix hgu133plus2 GeneChip. Prediction was based on linear discriminatory analysis applied in a nested cross-validation

first: Thomas

last: Lion

first: Andreas

last: Petzer

first: Günther

last: Gastl

first: Dominik

last: Wolf


title: Identification of genomic associations of transcription factors BCL11B, Ikaros, and Mi2beta in primary mouse thymocytes

city: Corvallis

first: Walter

middle: K

last: Vogel

state: OR

address: 1601 SW Jefferson Street

department: College of Pharmacy

institute: Oregon State University

summary: BCL11B and Ikaros, transcription factors essential to normal development and maturation of T cells are associated with the Mi2-beta NuRD complex in CD4+ CD8+ double-positive thymocytes.

overall_design: Examination of genone-wide association of NuRD Complex associated transcription factors BCL11B, Ikaros (IKZF1), and Mi2beta (CHD4)

first: Attila

last: Oravecz

first: Philippe

last: Kastner

first: Mark

last: Leid