title: The transcriptome of gadE, hdeA, or hdeD null strains compared to wild-type of E. coli under minimum medium conditions

city: Koganei

first: Kaneyoshi

last: Yamamoto

address: 3-7-2 Kajinocho

department: Frontier Bioscience

institute: Hosei University

summary: To compare transcriptional profiling of a gadE-, hdeA-, or hdeD- deficient strain to wild type in E. coli under minimum medium conditions. These genes are included in the GAD cluster genes, which are involved in the glutamic acid-dependent acid resistance (GAD) in E. coli. Goal was to determine the GadE, HdeA, or HdeD regulon in E. coli. Biological replicates: 2 replicates.

platform_organism: Escherichia coli str. K-12 substr. MG1655

overall_design: To compare transcriptional profiling of a gadE-, hdeA-, or hdeD- deficient strain to wild type in E. coli under minimum medium conditions. Biological replicates: 2 replicates.

first: Yuki

last: Yamanaka


title: Monosomy X in female mice influences the regional formation and augments the severity of angiotensin II-induced aortopathies

status: Public on Jun 27 2021

city: Lexington

first: Eric

middle: M

last: Blalock

state: KY

address: 800 Rose St.

department: Molecular and Biomedical Pharmacology

country: USA

institute: University of Kentucky

type: Expression profiling by high throughput sequencing

summary: Objective: Turner Syndrome women (monosomy X) have high risk of aortopathies consistent with a role for sex chromosomes in disease development. We demonstrated that sex chromosomes influence regional development of angiotensin II (AngII)-induced aortopathies in mice. In this study, we determined if the number of X chromosomes regulates regional development of AngII-induced aortopathies.    Approach and Results:  We used females with varying numbers of X chromosomes (XXF or XOF) on an C57BL/6J (ascending aortopathies) or Ldlr-/- background (descending and abdominal aortopathies) compared to XY males (XYM). To induce aortopathies, mice were infused with AngII. XOF (C57BL/6J) exhibited larger percent increases in ascending aortic lumen diameters than AngII-infused XXF or XYM. AngII-infused XOF (Ldlr-/-) exhibited similar incidences of thoracic (XOF, 50%; XYM, 71%) and abdominal aortopathies (XOF, 83%; XYM, 71%) as XYM, which were greater than XXF (XXF, 0%). Abdominal aortic lumen diameters and maximal external diameters were similar between XOF and XYM but greater than XXF, and these effects persisted with extended AngII infusions. Larger aortic lumen diameters, abdominal aortopathy incidence (XXF, 20%; XOF, 75%), and maximal aneurysm diameters (XXF, 1.02 ± 0.17; XOF, 1.96 ± 0.32 mm; P=0.027) persisted in ovariectomized AngII-infused XOF mice. Data from RNA seq demonstrated that X chromosome genes that escape X-inactivation (histone lysine demethylases Kdm5c and Kdm6a), exhibited lower mRNA abundance in aortas of XOF than XXF (P=0.033 and 0.024 respectively). Conversely, DNA methylation was higher in aortas of XOF than XXF (P=0.038).      Conclusion: The absence of a second X chromosome promotes diffuse AngII-induced aortopathies in females.

overall_design: Female C57BL/6J Ldlr-/- mice at 14-18 wks of age (n = 5 XX genotype, n =5 X0 genotype) were fed a Western (high fat- TD88137, Envigo) diet for 1 wk, and euthanized under ketamine/xylazine anesthesia (100:10mg/Kg). RNA was extracted from the thoracic aorta (defined as the segment extending from the aortic root to the diaphragm) and abdominal aorta (defined as the segment extending from the diaphragm to the iliac bifurcation) using a Maxwell Rapid Sample Concentrator (RSC) simply RNA Tissue kit (REF#AS1340, Promega, Madison, WI). Samples were provided to UK’s Genomics Core, who prepared the samples and performed sequencing. Briefly, RNA Integrity Number [RIN]: 8.97 ± 0.04 were of sufficient quality. Poly-A enriched mRNA underwent whole transcriptome sequencing (TruSeq library kit in an Illumina HiSeq 2500 High Output, single-end 100 bp reads). Pre-alignment quality control showed an average read depth of 37.4 ± 2.2 million reads per sample at a read length of 99.5 ± 0.1/ 100 base pairs, with an average read quality of 36.21 ± 0.01 phred (between 99.9 and 99.99% base identification accuracy). Reads were aligned to Genome Reference Consortium Mouse Build 38 (mm10) using the Spliced Transcripts Alignment to a Reference [STAR] (2.6.1) sequence aligning algorithm [1]. Post-alignment assembled results (Partek Flow, v 8.0) retained 30.9 ± 1.9 million unique reads per sample with a read quality of 36.30 ± 0.01 phred. The resulting counts were normalized to abundance measures with the trimmed-mean of M values (TMM) algorithm [2] in WebMev [3]. 19,296 rows of data were filtered to retain protein encoding genes for which at least 2 samples had TMM signal ≥ 1.5, resulting in 13,270 rows of prestatistically filtered data. The filtered data set underwent statistical analysis using LIMMA [4]. The False Discovery Rate (FDR) procedure [5], as modified by Storey [6] was used to estimate the error of multiple testing. Functional categorization was determined with the prestatistically filtered gene list as a background using DAVID bioinformatic tools’ functional overrepresentation clustering algorithm output [7] on the Gene Ontology annotation set [8, 9].

first: Yasir

last: AlSiraj

first: Sean

middle: E

last: Thatcher

first: Wesley

middle: N

last: Saintilnord

first: Alan

last: Daugherty

first: Hong

middle: S

last: Lu

first: Wei

last: Luo

first: Ying

middle: H

last: Shen

first: Scott

middle: A

last: LeMaire

first: Arthur

middle: P

last: Arnold

first: Lisa

last: Cassis


title: Transcriptomic insights of a 1,3-Propanediol producer Clostridium strain  isolated from Colombian soil

city: Bogotá D.C.

first: Ximena

middle: Carolina

last: Perez-Mancilla

country: Colombia

institute: Universidad Nacional de Colombia

summary: The possibility of establishing a Clostridium-based biorefinery is an attractive and viable alternative, due to the wide metabolic versatility of these microorganisms. The Bioprocesses and Bioprospecting group of the Universidad Nacional de Colombia has obtained the genome of Clostridium sp. IBUN13A, which has shown the ability to produce solvents from various substrates and postulated the need to expand the knowledge of the physiology of the bacteria, so, this study establishes the differences in the transcriptomic profile of the strain when it is cultivated in glycerol respect to glucose after 24 hours of fermentation. For this, a RNA-seq study was carried out, and some of the genes that increased its expression on glycerol were related to the oxidative route of its consumption. The enrichment analysis of Gene Ontology terms showed that the biological phenomena with the highest representation within the differentially expressed genes correspond to oxidation-reduction processes. This first approach to the global transcriptomic study of glycerol fermentation allows the understanding of the metabolism of the microorganism with the purpose of choosing targets for genetic modification.

overall_design: Comparison of expression between glycerol and glucose consumption on a Clostridium butyricum strain

first: Diego

last: Riaño-Pachón

first: Dolly

last: Montoya-Castaño


title: Yap regulates lipid metabolism in skeletal muscle, and is perturbed by metabolic stress

city: Melbourne

first: Mark

middle: D

last: Ziemann

state: VIC

address: 85 Commercial Rd

department: Bioinformatics Working Group

country: Australia

institute: Burnet Institute

summary: The Hippo signalling pathway effector protein Yap positively regulates adult skeletal muscle mass and limits muscle atrophy in settings of neuromuscular perturbation. However, the mechanisms that lead to changes in muscle mass following alterations in Yap activity remain unclear. Here, we show in the limb musculature of adult mice, that Yap inhibition alters the expression of genes associated with metabolic capacity, with sustained inhibition of Yap resulting in incomplete metabolism of fatty acids. In the context of metabolic disease, we demonstrate that Yap levels are lower in both the glycolytic skeletal musculature of Lepr db/db mice and in the muscles of insulin-resistant humans. Restoring Yap levels in the striated muscles of Lepr db/db mice was associated with an increase in skeletal muscle oxidative potential and resulted in a reduction in adiposity and hepatic steatosis. Our findings provide the first evidence of a metabolic role for the Hippo pathway effector Yap in post-mitotic skeletal muscle cells and suggest that modulating Yap activity may be an approach to promote skeletal muscle lipid metabolism.

overall_design: We treated the contralateral tibialis anterior (TA) muscles of 8 week old male C57BL/6 mice with AAV6:Yap-shRNA or AAV6:LacZ-shRNA vectors and performed RNA-sequencing after 7 days.  Control TA muscle was paired with the treated TA muscle in n=3 animals.

first: Kevin

middle: I

last: Watt

first: Darren

last: Henstridge

first: Dorit

last: Samocha-Bonet

first: T

last: Salmi

first: Richard

last: Lee-Young

first: Rachel

last: Thomson

first: Adam

last: Hagg

first: Jonathan

middle: R

last: Davey

first: Hongwei

last: Qian

first: Assam

last: El-Osta

first: Jerry

last: Greenfield

first: Matthew

middle: J

last: Febbraio

first: Andrew

middle: G

last: Cox

first: Kieran

middle: F

last: Harvey

first: Paul

last: Gregorevic


title: mRNA gene expression profile analysis in the CD4+ T cells with miR-7 deficiency

city: Zunyi

first: Juan

middle: Juan

last: Zhao

state: Guizhou

address: 6 Xuefu west Road

department: Immunology

country: China

institute: Zunyi medical University

summary: To detect the mRNA gene expression profile in the unactivated and activated CD4+ T cells with miR-7 deficiency.

overall_design: In this study, the total RNA was extracted from naive CD4+ T cells with miR-7 deficiency, WT mice and activated CD4+ T cells with miR-7 deficiency, WT mice, all the mice are the FVB/N background. Then, the expression profile of mRNA gene in these cells was detected by microarray.

first: Juanjuan

first: Lin

last: Xu


title: Phenotypic characterization of two novel cell line models of castration resistant prostate cancer

city: Seattle

first: Michael

middle: Christoph

last: Haffner

state: WA

address: 1100 Fairview Avenue

department: Human Biology

institute: Fred Hutchinson Cancer Research Center

summary:
Purpose: Resistance to androgen deprivation therapies is a major driver of mortality in advanced prostate cancer. Therefore, there is a need to develop new pre-clinical models that allow the investigation of resistance mechanisms and the assessment of drugs for the treatment of castration resistant prostate cancer.
Methods: We generated two novel cell line models (LAPC4-CR and VCaP-CR) which were derived by passaging LAPC4 and VCaP cells in vivo and in vitro under castrate conditions. We performed detailed transcriptomic (RNA-seq) to delineate expression differences between castration-sensitive and castration-resistant cell lines. LAPC4-CR and VCaP-CR cell lines maintained AR expression, but exhibited distinct expression changes on the mRNA and protein level. Integrated analyses including data from LNCaP and the previously described castration resistant LNCaP-abl cells revealed an expression signature of castration resistance.
Results: Integrated analyses including data from LNCaP and the previously described castration resistant LNCaP-abl cells revealed an expression signature of castration resistance.

overall_design: Expression profiles of castration sensitive and castration resistant prostate cancer cell lines

first: Srinivasan

last: Yegnasubramanian


title: Next Generation Sequencing Facilitates Quantitative Analysis of Wild and spinal cord injury mice

status: Public on Jun 26 2021

city: shenzhen

first: feng

last: duan

address: Dongmen North Road, Luohu District

institute: Clinical Medical Research Center, Shenzhen People's Hospital

summary: Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare NGS-derived intervertebral disc transcriptome profiling (RNA-seq) to microarray and quantitative reverse transcription polymerase chain reaction (qRT–PCR) methods and to evaluate protocols for optimal high-throughput data analysis

overall_design: Methods: Retinal mRNA profiles of 21-day-old Wild and spinal cord injury mice were generated by deep sequencing, in triplicate, using Illumina GAIIx. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks. qRT–PCR validation was performed using TaqMan and SYBR Green assays

first: Sun

last: jia


title: Effect of electroacupuncture on the skeletal muscle atrophy induced by hindlimb suspension in mice

city: Mikajima, Tokorozawa

first: akiko

last: onda

state: Saitama

department: graduate school of sport sciences

country: Japan

institute: waseda university

summary:
The effect of electroacupuncture on the transcriptional profile of the skeletal muscle atrophy induced by hindlimb suspension were examined.
We used microarrays to detail the global programme of gene expression underlying cellularisation and identified distinct classes of up-regulated and down-regulated genes during this process.

overall_design: Total RNA samples were isolated from soleus muscle obtained from mice. The RNA was converted to biotin-labeled cRNA, which was hybridized to Affymetrix 1.0 ST array. The hybridization experiments were performed in duplicate.

first: A

last: Onda

first: Q

last: Jiao

first: S

last: Minamisawa

first: T

last: Fukubayashi


title: Transcriptomic analysis of ovarian tumor pairs from primary and metastatic lesions

city: Hong Kong

first: Mingo Ming Ho

last: YUNG

address: 21 Sassoon

department: O&G

country: Hong Kong

institute: HKU

summary: Ovarian cancer is one of the most lethal gynaecological malignancies among female population. The high mortality rate of this disease is due to its poor prognosis and most patients present at an advanced stage accompanied with metastasis. The frequent tumor recurrence rate associated with metastasis and chemoresistance are the major obstacles in clinical management of the disease. Different from other solid tumors, ovarian cancer perfers transcoelomic metastasis amd mounting evidence has suggested ovarian cancer patients who have peritoneal metastasis are usually poor prognosis and highly chemoresistant recurrence. In this study, we examined the differential gene expression profile between the primary tumors and their paired metastastic lesions with a view to discover novel target therapies in combating ovarian cancer.

overall_design: mRNA profile of 5 pairs of ovarian tumors from primary and omental metastasis were analysed.

first: M

last: Yung

first: D

middle: W

last: Chan

first: H

last: Ngan

first: K

middle: L


title: Single-Cell RNA-Seq Datasets of residual AML cells purifed from Patient Derived Xenograft bone marrow treated or not with venetoclax plus cytarabine

city: Toulouse

first: Jean-Emmanuel

last: Sarry

state: Occitanie

address: 2 Avenue Hubert Curien

country: France

institute: INSERM -CRCT

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

overall_design: Refer to individual Series


title: Single-Cell RNA-Seq Datasets of residual AML cells purifed from Patient Derived Xenograft bone marrow treated or not with venetoclax plus cytarabine [Patient TUH69]

summary:
The goal of this study is to compare single cell transcriptome of in vivo AML cells profiling before treatment and after venetoclax and cytarabine in single agent or after the duplet.
This study uncovered transcriptionally different cell subpopulations that specifically emerge in VEN+AraC residual disease.

overall_design:
Residual AML cells purifed from bone marrow of patient samples xenografted in 8 weeks NOD/LtSz-SCID/IL-2Rγchain null (NSG) mice and treated for 5 days with AraC treatment by intra-peritoneal injection alone or in association with 7 days of venetoclax treatment by oral gavage.
Viable primary human AML cells from mice bone marrow of PDX before treatment or following AraC, venetoclax treatment or venetoclax plus AraC doublet therapy were isolated using cell sorter cytometer.
To generate single-cell libraries the Chromium Single Cell 3' Reagent Kits (v3 Chemistry, 10x Genomics) was used and the sequencing-ready library was cleaned up prior to sequencing on a NextSeq550 instrument (Illumina).
The single-cell RNA data was processed using cellranger v.3.0.2. and analyzed with the R package Seurat v.3.0.

first: Claudie

last: Bosc

first: Aurélie

last: Bousard

first: Nathaniel

last: Polley

first: Marie

last: Tolosini

first: Céline

last: Mazzotti

first: Hervé

last: Avet-Loiseau

first: Jean-Christophe

last: Marine


title: Single-Cell RNA-Seq Datasets of residual AML cells purifed from Patient Derived Xenograft bone marrow treated or not with venetoclax plus cytarabine [Patient TUH07]


title: Metabolic switch explains the sublethal effects induced by glyphosate-based herbicide in tadpoles of a farmland frog Microhyla fissipes

city: Chengdu

first: Liming

last: Chang

address: No.9 Section 4,Renmin Nan Road,Chengdu, Sichuan, P.R. China

department: Chengdu Institute of Biology

institute: Chinese Academy of Sciences

summary: The sublethal effects of a practically nontoxic GBH (KISSUN®) were investigated in tadpoles of M. fissipes, a farmland inhabiting amphibian. GBH exposure caused higher temperature preference, growth suppression, shorter and weaker tails in these tadpoles. These sublethal effects would likely affect the environmental adaptation ability, locomotor activity, competitive capacity and survival rate of tadpoles and thus might have profound influence on their population dynamics. Higher temperature preference might be an adaptive strategy for improving the efficiency of damage repair system activated by GBH exposure, as well as compensating for the reduced locomotor activity and sustaining energy metabolism. Growth suppression and tail morphological change were associated with reduced intensity of overall protein synthesis and structural protein synthesis, especially muscle specific genes. Transcriptional analysis suggested that GBH-treated tadpoles had suppressed carbohydrate and lipid catabolism, while encouraged amino acid catabolism. We speculated that metabolic switch to amino acid might be an adaptive strategy for compensating the reduced contribution of carbohydrate and lipid in energy production, and it provide a metabolic explanation for the downregulation of protein synthesis, growth synthesis and morphological change. Our results systemically revealed the molecular processes underlying the sublethal effects in an amphibian caused by GBH. It suggested that metabolic switch might be a consensus toxicologic mechanism of growth suppression across fish and amphibians.

overall_design: GBH exposure were carried out in plastic containers (29 cm×19.5 cm×7 cm) with 1000 mL water at 24 ± 0.5°C (L : D = 12 : 12). Tadpoles were randomly assigned to 0 mg/L (control), 60 mg/L, 90 mg/L, and 120 mg/L GBH exposure groups (5 replicates/containers for each treatment group; 20 tadpoles in each replicate). GBH exposure lasted for 10 days, and survival rates were recorded daily. Firstly, observe the distribution of tadpoles in plastic containers and measure the morphological traits of tadpoles. Next, Paraffin section and H&E staining were performed to explore the histopathological response of tadpoles. Thirdly, Comparative transcriptomics was conducted to analyze the underlying mechanisms between control, 60 mg/L and 90mg/L GBH exposure group.

first: Wang

last: Xungang

first: Chang

last: Liming

first: Zhao

last: Tian

first: Liu

last: Lusha

first: Zhang

last: Mengjie

first: Li

last: cheng

first: Xie

last: Feng

first: Jiang

last: Jiangping

first: Zhu

last: Wei


title: METTL1 promotes hepatocarcinogenesis via m7G tRNA modification dependent translation control

city: Guangzhou

first: Wanjie

last: Zhu

state: Guangdong

address: Zhongshan er road

institute: Sun Yat-sen University

type: Non-coding RNA profiling by high throughput sequencing

summary: N7-methylguanosine (m7G) modification is one of the most prevalent tRNA modifications in human. The precise function and molecular mechanism of m7G tRNA modification in regulation of cancer remain poorly understood. Here we showed that m7G tRNA modification, METTL1 and WDR4 are elevated in hepatocellular carcinoma (HCC) tissues and associated with HCC patient prognosis. Functionally, silencing METTL1 or WDR4 inhibits HCC cell proliferation, migration and invasion, while forced expression of wild type METTL1 but not its catalytic dead mutant promotes HCC progression. Knockdown of METTL1 reduces m7G tRNA modification and decreases m7G modified tRNA expression. Mechanistically, METTL1 depletion selectively decreases the mRNA translation of a subset of oncogenic genes, especially cell cycle and EGFR pathway genes, in m7G-related codon dependent manner. Moreover, in vivo studies using Mettl1 knock-in and knockout mice reveal a critical function of Mettl1 mediated m7G tRNA modifications in promoting hepatocarcinogenesis in the hydrodynamics transfection HCC model. Our work uncovers the critical functions of tRNA m7G modification in regulating cancer mRNA translation and promoting hepatocarcinogenesis, thus provides new insights into role of the mis-regulated tRNA modifications in cancers.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: TRAC-Seq were developed to identify the tRNA m7G methylome in hepatocellular carcinoma cell line and c57 mouse liver tumor tissue. Polyribosome associated mRNA sequencing was used to study the differential translated genes in the Mettl1 knockdown and control cells.

first: Zhihang

last: Chen

first: Shuibin

last: Lin


title: Dynamics of parental genomic imprinting during human male germ cell development

city: Amsterdam

first: Robin

last: Struijk

address: Meibergdreef 9

department: Center for Reproductive Medicine

country: Netherlands

institute: Amsterdam UMC location AMC

type: Methylation profiling by high throughput sequencing

summary: It is generally assumed that parental DNA imprinting is complete before the onset of meiosis in human spermatogenesis. Conversely, we here demonstrate dynamic DNA methylation in multiple imprinted regions during meiosis and subsequent maturation of spermatids. This suggests a role for these genes in spermatogenesis and has implications for the effectiveness and safety of assisted conception using testicular sperm.

overall_design: A total of 25 pooled testicular cell samples were analyzed (n=5 patients per sample pool). Testicular tissue fragments were obtained from 50 healthy adult men with obstructive azoospermia, including vasectomy reversal, in the age range of 28 – 60 that visited the Center for Reproductive Medicine in Amsterdam, The Netherlands for TESE/IVF. Testicular morphology was visualized by hematoxylin/eosin staining and intact spermatogenesis was confirmed across most seminiferous tubules in the full cohort of patients, concurrent with a high yield of sperm cells obtained after TESE. Seminal fluid samples were obtained from an additional 25 adult fertile men that came to the clinic for semen collection for IVF based on a female subfertility indication.

first: Robert

middle: B

first: Callista

last: Mulder

first: Saskia

middle: K

last: van Daalen

first: Cindy

middle: M

last: de Winter-Korver

first: Aldo

last: Jongejan

first: Sjoerd

last: Repping


title: Analysis of circulating microRNAs during early gestation in Japanese-Black cattle

city: Morioka

first: Keiichiro

last: Kizaki

state: Iwate

department: Vet. Med.

institute: Iwate University

summary: We found four circulating miRNAs showing high levels in plasma of pregnant Japanese Black cows. Since these miRNAs are less affected by the measurement system due to hemolysis, it was suggested that they may be used as markers for early pregnancy diagnosis in cattle.

overall_design: The Japanese-Black (JB) cattle were subjected to controlled estrus, and artificially inseminated (AI) according to the AM–PM rule following detected estrus twice daily. Peripheral blood from a total of seven AI cows was collected on day 21 (day 0 being the date of AI) to compare circulating miRNA levels in four pregnant and three non-pregnant statuses.


title: Expanding highly homogenous population of human primordial germ cell like cells in long-term and feeder-free culture condition [scRNA-seq]

status: Public on Jun 25 2021

city: Charlestown

first: Mutsumi

last: Kobayashi

state: Massachusetts

address: Building 147, 13th street, Rm# 7103

institute: MGH, center for cancer reserch

summary: The culture methods for human primordial germ cell like cells (hPGCLCs) has not been established. Here we report the culture method to expand long-term culture hPGCLCs (LTC-hPGCLCs) representing migrating morphology and early hPGC transcriptome and methylome. Key components of the culture media are stem cell factor, STO-conditioned media and absence of fetal calf serum. In this condition, these LTC-hPGCLCs were highly homogenous population without feeder cells and expanded at least 150 days. They did not express senescent phenotype such as β-galactosidase activity and shortening of telomere length at the 150-day culture, indicating that the cell might be a perpetual cell line. LTC-hPGCLCs still have potent pluripotency indicating the phenotype that the cells become human embryonic germ cells which were distinguishable from human iPS cells in strong DLK1 expression and H19 biallelic expression. In summary this simple culture method and highly homogenous LTC-hPGCLCs would be a useful resource that supports investigations on human germline cells.

overall_design: Single-cell transcriptomal profiles of human iPS cells and long-term culture (LTC) hPGCLCs.

first: Toshi

last: Shioda


title: DNA methylation profiling across six histological states of prostate cancer

city: Dublin 4

first: Antoinette

last: Perry

address: Belfield

country: Ireland

institute: University College Dublin

type: Methylation profiling by genome tiling array

summary: In spite of its prevalence as one of the world’s leading malignancies, prostate cancer (PCa) continues to evade molecular taxonomic sub-classification. However, gross clinical differences are observed within the umbrella term ‘prostate adenocarcinoma’; the majority of tumors appear indolent in nature, whilst a subset manifest aggressively. Contributing factors towards this resistance to molecular classification are an atypically low mutation frequency and a poorly delineated pathobiology. Conversely, epigenetic changes are evidenced to be amongst the earliest and most-widespread aberrations in PCa . We thus hypothesized that delineating epigenomic alterations during the stepwise progression of PCa would improve our understanding of the disease pathobiology and the molecular underpinning of indolent and aggressive tumors. Herein, we report the first epigenomic roadmap of prostate tumorigenesis, in which we dissected DNA methylation and microRNA expression in enriched epithelial cells across the entire trajectory of PCa, through tumor initiation, primary disease and metastatic dissemination.  We provide evidence in support of proliferative inflammatory atrophy (PIA) as a precursor lesion, distinct from high-grade prostatic intraepithelial neoplasia (HGPIN) and show that indolent and aggressive tumors display unique sets of epigenetically dysregulated loci, which we further investigated as potential discriminatory markers. This study also establishes the importance of DNA methylation beyond the gene promoter in human cancer, with pronounced intra- and inter-genic CpG methylation observed.

overall_design:
45 human formalin fixed paraffin embedded prostate samples were analysed. Samples were enriched for epithelial cell population by laser capture microdissection. The chort consisted of 10 benign prostate samples (B), 7 proliferative inflammatory atrophy (PIA), 6 high-grade prostatic intraepithelial neoplasia (HGPIN), 7 indolent primary cancers (PCI), 8 aggressive primary prostate cancers (PCA), and 6 metastatic prostate cancers (PCM). Benign samples were procured from radical cystoprostatecomy from patients with no evidence of prostate cancer. PIA, HGPIN and primary tumours were all obtained from radical prostatectomy cases. PCI was defined as Gleason 6, pT2 disease, with a pre-operative PSA <10 ng/ml and no evidence of biochemical or clinical recurrence (5-year follow-up). PCA was defined as primary Gleason ≥4, pT3 disease, with evidence of biochemical or clinical recurrence. Metastatic lesions were obtained from visceral metastases (liver, adrenal, lymph node and per-aortic), obtained during rapid autopsy.
Five samples excluded from the final analysis: PCI06-1, PCI06-2, PBL-1, PBL-2, PBL-3

middle: S


title: Gene expression profiling upon Knockdown of KDM5A and 5C in Gliobastoma stem-like cells

city: Heidelberg

first: Violaine

last: GOIDTS

address: IM NEUENHEIMER FELD, 580

country: Germany

institute: DKFZ

summary: Investigating the changes of gene expression upon knockdown of KDM5A/5C and the mechanisms underlying the observed apoptotic phenotype.

overall_design: NCH644 GSC-cells were transduced with two inducible shRNAs respectively against KDM5A and 5C.  Induction was achieved by incubation with 2 μg/ml doxycycline for 5 days

first: Paul

last: Windisch

first: Murat

last: Iskar

first: Martje

last: Tönjes

last: Rosenstiel-Goidts


title: The Unfolded Protein Response Regulator, ATF6, is Essential for Cone Photoreceptor Development

city: La Jolla

first: R. Luke

last: Wiseman

state: CA

address: 10550 North Torrey Pines Road

department: Molecular Medicine

institute: The Scripps Research Institute

summary: The Unfolded Protein Response is a conserved intracellular signal transduction mechanism that maintains endoplasmic reticulum homeostasis and may contribute to the pathogenesis and progression of human diseases associated with ER stress.  Genetic mutations in the UPR regulator, ATF6, lead to vision loss in heritable retinal diseases.  Our prior studies found that disease mutations disrupt ATF6 function, but the pathomechanism by which loss of ATF6 activity causes vision loss in people is unknown.  To investigate this, we developed retinal organoids from patient iPSCs carrying ATF6 disease mutations and from hESCs bearing CRISPR-edited ATF6 null alleles.  Unexpectedly, we found that retinal organoids lacking functional ATF6 failed to form cone photoreceptors while rod photoreceptors were unaffected.  We used adaptive optics imaging of the retinas in patients with ATF6 mutations and saw pronounced loss of cones and preservation of rods that closely mirrored our in vitro organoid phenotypes.  Last, we found that a small molecule proteostasis agonist partially restored cone photoreceptor outer segment formation and gene expression in ATF6 mutant retinal organoids.  Our results reveal a surprising and novel function for ATF6 in human cone photoreceptor development.  Our findings identify a potential therapeutic strategy for patients based on small molecule reprogramming of the proteostasis network in the retina.  Our study suggests that the UPR guides intrinsic developmental processes in specialized metazoan cell types in addition to its role in responding to extrinsic pathologic events.

overall_design: Comparisons of the transcriptomes of retinal organoids harboring either the homozygous or heterozygous ATF6 Y567N mutation and treatment with ATF6 activator 147.

first: Heike

last: Kroeger

first: Julia

last: Grandjean

first: Evan

middle: T

last: Powers

first: R

first: Jonathan

middle: H


title: Venn diagram of PARP1-ChIP, TET1-ChIP and MeDIP in bone marrow-derived human mesenchymal stem cell

city: Taichung City

first: Chun-Te

last: Ho

address: 7F, No. 6, Xueshi Rd., North Dist.

department: Integrative Stem Cell Center

country: Taiwan

institute: China Medical University Hospital

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Venn diagram showing overlap in binding sites. Genomic regions from MeDIP analysis (Late > Early) were compared for PARP1 ChIP-seq analysis (Early > Late) and TET1 ChIP-seq analysis (Early > Late). Numbers indicate the number of overlapping genes or regions.

overall_design: PARP1-ChIP-Seq, TET1-ChIP-Seq and MeDIP-Seq of bone marrow-derived mesenchymal stem cells with 2 biological replicates

first: Shih-Chieh

last: Hung


title: Molecular response mechanisms of encapsulated Tamoxifen (N-TAM) on DNA damage regulatory pathways

city: Boston

first: Jean-Bosco

last: Tagne

state: MA

address: 72 East Concord

department: Medicine/Pulmonary

institute: Boston University

summary:
Background: We have applied an integrative approach, including classical genomic, microarray, and refined computational systems biology to study the regulatory pathways that involve DNA damage associated with typical drug preparations of Tamoxifen (TAM). We compared the effects of newly formulated Nano-emulsions of TAM (NanoTAM or N-TAM) on cultured HTB-20 cells to those of liquid preparations of TAM. Phenotypic screening was used to identify changes induced. Implicated regulatory pathways were systematically investigated by chromatin immunoprecipitation (ChIP) and DNA microarray analyses to identify alterations in protein-DNA interactions as well as genome-wide expression patterns.
While liquid solutions of clinically used TAM can have a Z-score average of thousands of nm, after encapsulation and application of high pressure particle size was ~41 nm. ChIP-chip technology was used to classify promoter regions for target genes bound by E2F4 in human primary HTB-20 cells upon treatment with TAM or N-TAM.  Specific drug effects were defined by comparing results obtained for Control/Control (CC) Control/Nano (CN), TAM (Drug)/Control (TC), and N-TAM (Drug)/Nano (TN). Functional effects noted included changes in apoptosis, cell proliferation, RNA processing, DNA damage, repair and replication, lipid and protein metabolism, transport, and transcriptional regulators. Cells treated with clinical TAM only expressed the ataxia telangiectasia mutated protein ATM as well as several histone proteins important for DNA damage sensing and activation of repair proteins, while N-TAM did not illicit this response.. In contrast N-TAM could not only enter the cells it could cross the inner mitochondrial membrane, induced more apoptosis and affecting mitochondrial DNA.

overall_design: 15 samples in triplicates. 3 Nano controls and 3 treatments N-Tam, 3 treatments Tam for each of the 3 non treated cancer cells

first: Srikanth

last: Kakumanu

first: Christopher

last: Workman

first: Sumeet

last: Gupta

first: Jennifer

last: Love

first: Thomas

last: Shea

last: Volkert

first: Robert

last: Nicolosi


title: The impact of cold priming on the alerting phase of light and cold regulation of gene expression in Arabidopsis thaliana

city: Berlin

first: Margarete

last: Baier

address: Königin-Luise-Straße 12-16

department: Institute of Biology

institute: Freie Universität Berlin

summary: We analysed the effect of a short 24 hours cold exposure (priming-stimulus) on gene regulation upon the first two hours of a second cold (4°C) stimulus (cold-triggering) and upon the first two hours of excess light exposure (800 µmol photons m-2 s-1, light triggering). The first and the second stress treatment was seperated by 5 days long lag-phase, which is long enough to reset most of the primary stress response. Several early light and early cold responsive genes showed however a altered transcript abundance in plants, which received five days befor the cold priming stimulus. Espicially JA responsive genes showed a common priming regulation within the cold and light exposure.

overall_design: Transcript levels were assessed in a transcriptome wide scale by peired end next generation sequencing (BGI-Seq-500). Half of the 4-week old Arabidopsis thaliana Col-0 plants were primed for 24 hours at 4 °C (cold-priming) and than retransferred to control conditions for addiotinal 5 days. Than rosette tissue of 20 % of the cold-primed and control non-primed plants were harvested two hours after the onset of the light period. The remaining 80% were split into two groups were either treated with second cold stimulus (4 °C) or were exposed to a 8-fold higher light intensity applied by heat-filtered halogen lamps. The cold treated and light treated plants were harvested after 30-, 60-, and 120 min of stress exposure. For each sample leave tissue of at least 5 plants were pooled and combined for cDNA library construction.

first: Andras

last: Bittner


title: Evaluation of the effects of microgravity and hypergravity on hepatic stellate cells

city: Ube

first: Koichi

last: Fujisawa

state: Yamaguchi

address: Minamikogushi 1-1-1

institute: Yamaguchi University

summary: In this study, we evaluated cell proliferation and gene expression of hepatic stellate cells (HSCs) in simulated microgravity (SMG) and hypergravity (5 G).

overall_design: HHSteC was purchased from ScienCell Research Laboratories, Inc. (catalog number 5300) and cells from passages 3-5 were used. HHSteCs were cultured in Dulbecco's Modified Eagle's Medium (DMEM) (GIBCO, NY, USA) supplemented with 10 % fetal bovine serum (FBS) (GIBCO) and penicillin/streptomycin (GIBCO) in a 12.5 cm2 culture flask (Falcon 353107) with an oxygen permeable cap. Cells were seeded at a density of 500-1000 cells/cm2. The cells were cultured in a 3D-clinostat (Zeromo CL5000, Kitagawa, Hiroshima, Japan) (F1 SMG) and kept in the same incubator as 1G control (F1 1G). The cells were cultured in Zeromo at 5G (F2 5G)and kept in the same inculbator as 1G control (F2 1G).

first: Taro

last: Takami

first: Akino

last: Sakuragi

first: Jolien

last: Duponselle

first: Yuto

last: Nishimura

first: Toshihiko

last: Matsumoto

first: Naoki

last: Yamamoto

first: Tomoaki

last: Murata

first: Isao

last: Sakaida


title: RNA-seq analysis of peripheral nerve with conditional knockout of H3K27 demethylases.

city: Madison

first: John

last: Svaren

state: WI

address: 1500 Highland Ave.

department: Comparative Biosciences

institute: University of Wisconsin

summary: The goal of the experiment was to determine the role of H3 emethylases in the nerve injury response in peripheral nerve. A Schwann cell specific knockout of the H3K27 demethylases (Jmjd3 and Utx) was generated to compare with wild type mice in sham and injured mice at 1d and 7d timepoints after nerve injury.

overall_design: For each condition, three independent biological replicates were prepared.

first: Phu

last: Duong


title: RNA-sequencing of Vg4+Vd4+gdT cells isolated from skin-draining lymph nodes of WT and NF-kB1 deficient mice after imiquiod treatment

city: Chiba City

first: Kazumasa

last: Suzuki

state: Chiba

address: 1-8-1 Inohana

department: Department of Allergy and Clinical Immmunology

institute: Chiba University

summary:
Purpose: The numbers of Vg4+Vd4+gdT17 cells in skin-draining lymph nodes were significantly reduced in imiqimod-treated NF-kB1-/- mice compared to those in IMQ-treated WT mice. To address the mechanism of NF-kB1-mediated proliferation of Vg4+Vd4+gdT17 cells, we performed RNA-sequencing of Vg4+Vd4+gdT cells isolated from the draining lymph nodes.
Method: Mice were treated daily with 50 mg of 5% imiquimod cream or sham cream on both ears for 4 days. Single cell suspensions were separated from cervical lymph nodes. Vg4+Vd4+gdT cells were isolated by a cell sorter. N=3 each.
Results: Using an optimized data analysis workflow, 552 of the transcripts showed differential expression between the WT and NF-kB1 deficient mice after imiquiod treatment, with a fold change ≥2 and p value <0.05.

overall_design: mRNA profiles of Vg4+Vd4+gdT cells isolated from skin-draining lymph nodes of WT and NF-kB1 deficient mice after imiquiod treatment


title: Screening for differentially expressed circRNAs in ischemic stroke by RNA sequencing

status: Public on Jun 24 2021

city: Shantou

first: wenzhen

last: he

address: 57 Changping Road

institute: First Affiliated Hospital of Shantou University Medical College

summary: Background: Ischemic stroke is a disease with high rate of death and disability worldwide. This study investigated key circRNAs related to ischemic stroke.  Methods: Three ischemic stroke patients and three healthy individuals were included in the current study to obtain the circRNA expression profiles by RNA sequencing. Through bioinformatic analysis, differentially expressed circRNAs (DEcircRNAs) were identified, and GO and pathway analyses for the host genes of DEcircRNAs were conducted. To further explore the functions of key circRNAs, a DEcircRNA-miRNA interaction network was constructed. Finally, the expression levels of selected circRNAs were validated with qRT-PCR.  Results: A total of 736 DEcircRNAs were detected in ischemic stroke. Functional annotation of host genes of DEcircRNAs revealed several significantly enriched pathways, including Fc epsilon RI signaling pathway, B cell receptor signaling pathway, and T cell receptor signaling pathway. A circRNA-miRNA network, including 1544 circRNA-miRNA pairs, 456 circRNAs and 4 miRNAs, was obtained. The qRT-PCR results were largely in keeping with our RNA-seq data.  Conclusion: The results of our study may help to elucidate the specific mechanism underlying ischemic stroke.

overall_design: The cohort subjected to RNA-Seq consisted 3 ischemic stroke patients and 3 healthy individuals.

first: Wenzhen

last: He


title: Assessing the identity and relative fold changes of mRNA species associating with polyribosomes in the mouse hippocampus after novel context exposure

city: Cambridge

first: Weifeng

last: Xu

address: The Picower Institute of Learning and Memory

institute: MIT

summary: The objectives of this experiment were to identify and quantify the relative levels of mRNA species that exhibited relative fold changes in a hippocampal fraction of isolated polyribosomes in reponse to novel context exposure.

overall_design: NGS RNA-Seq profiling of mouse hippocampus after fear condition

first: Sebastian

last: Templet

first: Kendrick

last: Jones

first: Fan

last: Gao


title: Transcriptomics analysis of aged asthmatic lung and treated with dexamethasone during HDM induced airway inflammaton

city: Auburn

first: Amarjit

last: Mishra

state: AL

address: 1130 Wire Road, 264 Greene Hall

department: Pathobiology

institute: Auburn University

summary: This study was designed to evaluate the lung transcriptome analysis against dexamethasone treatment throughout HDM challenge period in the aged (80-82 Weeks) mice. The lung samples from aged inflammed mice with or without dexamethasone treatmrnt were isolated followed by RNA isolation and RNA sequence analysis.

overall_design: First, we sensitized aged (80-82 Weeks) mice with 50 μg of HDM in a volume of 40 μL through intranasal (i. n) route on days 1, 3, and 5. The challenge phase consisted of 3 consecutive phases of 3 doses (i.n) of HDM (50 μg) on days 11-13, 18-20, and 25-27 respectively. Dexamethasone (4 mg/Kg body weight, intraperitoneal, route) treatment was given throughout the challenge period after every 72 h interval. Post 24 h, last challenge all the lung samples were collected for futher processing. Further, RNA was isolated, checked for RNA quality and processed for RNA sequence analysis.

first: A

last: Jaiswal

last: Mitra

first: S

last: Mazumder


title: TNFα-producing Macrophages Determine Subtype Identity and Prognosis via AP1 Enhancer Reprogramming in Pancreatic Cancer

city: Bochum

first: Stephan

middle: A

last: Hahn

address: Universitaetsstrasse 150

department: MGO

institute: Ruhr-University Bochum

summary: Global mRNA expression profiling of patient derived pancreatic carcinoma xenograft models (N=4) were collected using Agilent human whole genome array (G4845A AMADID  026652, cRNA 4x44k V2) . Mice were treated daily with JQ1 (50 mg/kg, MedChem express/ Hycultec) to establish response characteristics.

overall_design: Two conditions (untreated control (K) vs 5 days JQ1 treatment (5dJQ1). Untreated control and JQ1 treated tumors are represented by two biological replicates.

first: Shiv

last: Singh


title: Transcriptomic Profiling of Vagal and Sacral Level Neural Crest Cell from Mouse Embryos Using Next Generation Sequencing

city: Hongkong

first: Taida

last: Huang

address: 39 Area

department: School of Biomedical Sciences

institute: The Chinese University of Hong Kong

summary: The ENS of vertebrates develops from neural crest cell (NCC) deriving from mainly the vagal neural crest, while NCCs from the sacral level to a less extent. In mouse embryos, the vagal NCCs emigrate from the neural tube adjacent to the somite level from 1-7 at Embryonic day (E)9.0, and sacral NCCs emigrate from the neural tube adjacent to the level of somites caudal to somite 24 in the mouse (in the chick, caudal to somite 28) at E9.5. The spatial difference in cell colonization between vagal and sacral NCCs is that vagal NCCs completely colonize the whole gut, while the distribution of sacral NCCs is only restricted to the hindgut segment. To determine the differences between these two groups of cells, we isolated vagal and sacral NCCs by neural tube explant culture and then performed high-throughput RNA-seq to examine the transcriptional variation. We analyzed that differentially expressed genes (DEGs) by gene ontology (GO) analysis in which the DEGs were enriched in cell adherin, proliferation, transcriptional regulation, et al. This study might help to explore the underlying basis for the different cell behaviors between vagal and sacral NCCs during mouse embryonic development.

overall_design: Transcriptomic profiles were compared between vagal and sacral level neural crest cell isolated from E9.0 and E9.5 mouse embryonic neural tube explant culture respectively.

last: HUANG

first: Wood

middle: Y

last: CHAN


title: Hsa_circ_0001021 regulates intestinal epithelial barrier function via sponging miR-224-5p in ulcerative colitis

city: jinan

first: Bing

last: Li

address: Wenhua Xi Road 107

institute: Qilu Hospital

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

summary: In this study, we aim to investigate the role of circRNAs in UC pathogenesis.

overall_design: Microarrays were used to detect dysregulated circRNAs and mRNAs of inflamed mucosa and non-inflamed mucosa from 5 UC patients as well as mucosa from 5 healthy controls.

first: Xiuli

last: Zuo


title: Mouse lung DC RNA-Seq after allergic sensitization

city: Research Triangle Park

first: Sara

last: Grimm

state: NC

address: 111 TW Alexander Dr

institute: NIEHS

summary: Transcriptome analysis of mouse lung Ly-6C+ and other DC populations with or without allergic sensitization

overall_design: Lung APCs and BM preDCs were purified before or after instillation of house dust extract and ovalbumin

first: Gentaro

last: Izumi

first: Hideki

last: Nakano

first: Keiko

first: Donald

middle: N

last: Cook


title: Osteoblast-derived intraflagellar transport 140 suppresses insulin sensitivity

city: Shanghai

first: Chenyang

last: Zhang

address: Middle Fuxing Rd

institute: Fudan University

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

overall_design: Refer to individual Series


title: RECK isoforms are differentially expressed in patients with stable and unstable coronary artery disease: A pilot study.

city: Paris

first: Noémie

last: Robil

address: 29, rue du Faubourg Saint-Jacques

department: Paris Biotech Santé

institute: GenoSplice technology

summary: Four male patients were enrolled for this study in collaboration with the Cardiology Unit of Policlinico Tor Vergata-Fondazione PTV (Rome). We have performed RNA-Sequencing using NextSeq 500 ILLUMINA platform on PBMCs of patients with clinically proven healthy coronary arteries (CTR) and patients with chronic coronary artery disease (CAD) confirmed by coronary angiography. RNA sequencing results showed differentially Altenative Splicing (AS) events and filtering for a statistically significant Splicing-Index Fold-Change≥ ±1.5 (p≤0.05) we observed 113 differentially regulated AS events (24 up and 89 down-regulated) from 86 genes. We validated AS results using Real-time PCR method and then we extended the expression analysis to a large case study including 24 CTR subjects, 72 CAD patients and 32 patients with unstable coronary artery disease, arrived at the attention of the clinicians during a myocardial infarction event (AMI group).

overall_design: Analysis of RNA-seq expression profile of two different groups of patients (CTR, CAD). In total we have analyzed 4 samples for RNAseq analysis.

first: Chiara

last: Vancheri

first: Elena

last: Morini

first: Francesco

last: Romeo

first: Giuseppe

last: Novelli

first: Francesca

last: Amati


title: Bag3-P209L RNA Seq Project

city: Indianapolis

first: Monte

last: Willis

address: 635 Barnhill Street Drive

institute: University of Indiana School of Medicine

summary: Cardiac-specific Bag3-P209L transgenic (Tg+) mice develop dilated cardiomyopathy by 12 months of age. The goals of this project are to utilize RNA-sequencing to compare both cardiomyocyte and cardiac fibroblast transcriptomes between aged Bag3-P209L Tg+ and Bag3-WT mice to identify cardiomyocyte and fibroblast specific gene sets that contribute to the functional and morphological changes previously identified in Bag3-P209L Tg+ hearts.

overall_design: Both cardiomyocytes and fibroblasts were isolated from three 16-month old Bag3-P209L Tg+ and three age matched Bag3-WT mice. RNA from cardiomyocytes and fibroblasts were then extracted and submitted to Novogene for cDNA library creation and subsequent RNA sequencing.

first: Samuel

middle: C

last: Eaton


title: IL-6 promotes drug resistance through formation of polyploid giant cancer cells and stromal fibroblast reprogramming

city: Houston

first: Haoqiang

last: Ying

state: Texas

address: 1515 Holcombe Blvd

institute: M. D. Anderson Cancer Center

summary: To understand the role of polyploid giant cancer cells (PGCCs) in drug resistance and disease relapse, we examined the mRNA expression profile of PGCCs in ovarian cancer cells. An acute activation of IL-6 dominated senescence associated secretory phenotype lasted 2-3 weeks and declined during the termination phase of polyploidy. IL-6 activates embryonic stemness during the initiation of PGCCs and can reprogram normal fibroblasts into cancer-associated fibroblasts (CAFs) via increased collagen synthesis, activation of VEGF expression, and enrichment of CAFs and the GPR77+/CD10+ fibroblast subpopulation. Blocking the IL-6 feedback loop with tocilizumab or apigenin prevented PGCC formation, attenuated embryonic stemness and the CAF phenotype, and inhibited tumor growth in a patient-derived xenograft high-grade serous ovarian carcinoma model. Thus, IL-6 derived by PGCCs is capable of reprogramming both cancer and stromal cells and contributes to the evolution and remodeling of cancer. Targeting IL-6 in PGCCs may represent a novel approach to combating drug resistance

overall_design: Two ovarian cell lines were treated with  paclitaxel (500 nM) for 16-18h and recovered in regular medium. mRNA from parental, PGCCs, and daughter cells were analyzed

last: Niu

first: Jun

last: Yao

first: Robert

last: Bast

first: Anil

last: Sood

first: Jinsong

last: Liu


title: The m6A reader IMP2 directs autoimmune  inflammation through an IL-17– and TNFa-dependent  C/EBP transcription factor axis

city: Pittsburgh

first: Sarah

last: Gaffen

state: PA

address: 200 lothrop street

institute: University of Pittsburgh

summary:
Posttranscriptional regulation of C/EBPs through m6A/IMP2 represents a new paradigm of cytokine-driven autoimmune inflammation
Using an optimized data analysis workflow, we mapped about 40 million sequence reads per sample to the mouse genome (build mm10) and identified potential differentially regulated transcripts in the MEFs of siImp2 vs siControl with an absolute fold change ≥2 and p value <0.05. Altered expression of potential genes was confirmed with qRT–PCR, demonstrating the high degree of sensitivity of the RNA-seq method.
Conclusions: Our study represents the first detailed analysis of retinal transcriptomes, with biologic replicates, generated by RNA-seq technology. The optimized data analysis workflows reported here should provide a framework for comparative investigations of expression profiles. Our results show that NGS offers a comprehensive and more accurate quantitative and qualitative evaluation of mRNA content within a cell or tissue. We conclude that RNA-seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions.

overall_design: Mouse embryonic fibroblasts mRNA profiles transfected with siRNA control or siRNA against IMP2 and treated or not with IL-17 for 8 hours

first: Bechara

last: Rami

first: Gaffen

last: Sarah


title: Diverse Heterochromatin-Associated Proteins Repress Distinct Classes of Genes and Repetitive Elements (srHC-seq)

city: Seattle

first: Ryan

middle: Lehman

last: McCarthy

address: 1900 9th Ave

department: Pediatrics

institute: University of Washington

summary: Heterochromatin, typically marked by H3K9me3 or H3K27me3, is key to the repression of genes and repetitive elements. The mechanisms responsible for establishing and maintaining heterochromatin in a locus specific manner are unclear. Heterochromatin restricts cell identity by preventing activation of alternative lineage genes. This barrier can be partially overcome by inducing ectopic transcription factors (TFs) to activate an alternative transcriptional program. However, TFs are impeded by highly restrictive heterochromatin leading to low reprogramming rates and incomplete activation of the target transcriptome. Previously we utilized the heterochromatin property of sonication resistance to identify 172 proteins associated with sonication resistant heterochromatin (srHC) by mass spectrometry (Becker, et al., 2017). We hypothesized that by functionally assessing the srHC proteins and identifying the genes they repress during reprogramming we could improve our understanding of heterochromatin maintenance and learn how to disrupt heterochromatin to enhance reprogramming. Focusing on reprogramming from fibroblasts to induced human hepatocytes (hiHeps) we conducted an siRNA screen of 97 srHC proteins without reprogramming factors (noTF) and with hiHep reprogramming and assessed the impact on the expression of genes located in srHC domains by RNA-seq. We identified enhancer of rudimentary homolog (ERH) as a key regulator of H3K9me3 heterochromatin maintenance. ERH was found to associate broadly with H3K9me3 domains and when depleted caused global changes in H3K9me3 and srHC. Collectively our screen of srHC protein repressive function demonstrates specific functionality of groups of srHC proteins and increases our understanding of H3K9me3 gene repression.

overall_design: This study was designed to assess changes to sonication resistant heterochromatin (srHC) following knockdown of sonication resistant heterochromatin depleted proteins in human BJ fibroblasts. This study focused on knockdown of ERH.

first: Kelsey

middle: E

last: Kaeding

last: Keller

first: Yu

last: Zhong

first: Liqin

last: Xu

first: Anthony

last: Hsieh

first: Yong

last: Hou

first: Greg

last: Donahue

first: Oscar

last: Alberto

first: Bomyi

last: Lim

first: Kenneth

last: Zaret


title: Diverse Heterochromatin-Associated Proteins Repress Distinct Classes of Genes and Repetitive Elements (ChIP-seq)

overall_design: This study was designed to assess changes to H3K9me3 and H3K27me3 following knockdown of sonication resistant heterochromatin depleted proteins in human BJ fibroblasts. This study focused on knockdown of ERH. This study controlled for global changes to these epigenetic marks with the use of Drosophila Spike-In chromatin, and spike-in Drosophila H2Av antibody.

first: Samuel


title: Revisiting the characteristics of testicular germ cell lines GC-1(spg) and GC-2(spd)ts

city: MUMBAI

first: PRIYANKA

last: PARTE

state: MAHARASTRA

address: J M STREET

department: GAMETE IMMUNOBIOLOGY

country: India

institute: ICMR-NIRRH

summary: The study aims to explore gene expression changes associated with commerically available germ cell lines, GC-1 (spg) and GC-2 (spd)ts

overall_design: Agilent Mouse Whole Genome 8x60k Microarray: AMADID: 74809

first: Pratibha

last: Verma

first: Priyanka

last: Parte


title: Osteoblast-derived intraflagellar transport 140 suppresses insulin sensitivity I

first: Chenyang

last: Zhang

summary: Hyperglycemia-induced damage to bone formations and function has been recognized.However, as the largest connective tissue organ, whether bone and osteocytes in turn regulate blood sugar and insulin sensitivity has not been addressed. Here we identified a novel protein termed intraflagellar transport 140 with functional importance in regulating osteogenesis, which is also related to the osteoblastic insulin sensitivity. We established Ift140 osteoblastic conditional knockout mice model, and found that blood glucose metabolism could be regulated through osteoblastic IFT140 interacting with O-GlcNAc transferase to regulate insulin signaling. The discovery provides new insight for two-way regulation between bone and glucose metabolism, and also exploring potential new target for blood glucose interventions.

overall_design: MRNA profiles of 2-week old wild type (ctrl) and Ift140-/-(cko) mouse bone marrow deriived progenitor cells.The experimental group and the control group each had three biological replicates.

first: Yao

last: Sun


title: Osteoblast-derived intraflagellar transport 140 suppresses insulin sensitivity II

overall_design: The mRNA expression profiles in femur of diabetic mice, diabetic insulin-treated mice and non-diabetic mice were compared.


title: Diverse Heterochromatin-Associated Proteins Repress Distinct Classes of Genes and Repetitive Elements


title: Diverse Heterochromatin-Associated Proteins Repress Distinct Classes of Genes and Repetitive Elements (RNA-seq)

overall_design: This study was designed to assess the role of 97 sonication resistant heterochromatin associated proteins in impeding the activation of sonication resistant heterochromatin embedded genes. RNA seq was performed on Human BJ Fibroblasts that were treated with two rounds of siRNAs.  This was assessed both in cells expressing the hepatic transcription factors (FOXA3/HNF1A/HNF4A) for 7 days ("hepatic TF" protocol) , and cells expressing no ectopic transcription factors ("noTF" protocol). There were a total of ___ samples analyzed, including controls with three independent non-targetting siRNAs, labelled as NT siRNAs. There were a total of ___ siRNAs used, with two biological replicates for each samples in each of the two experimental conditions.


title: Altered expression of genes in WDR5 inhibited (by OICR-9429) bladder cancer cells

city: Guangzhou

first: Xu

last: Chen

address: 107. W. Yanjiang Road

department: Department of Urology

institute: Sun Yat-sen Memorial Hospital

summary: To explore the molecular mechanism underlying OICR-9429-induced WDR5 inhibition in BCa cells, a genome-wide RNA-sequencing was conducted to compare gene expression profiles between OICR-9429 treated T24, UM-UC-3 cells and their control cells

overall_design: Bladder cancer cell line T24 and UM-UC-3 was treated with OICR-9429 or DMSO for 48h, respectively. The RNA of the treated cells was extracted and sequenced on Illumina NovaSeq 6000 (S4) platform and 150-bp paired-end reads were generated.

first: Jingtong

first: Tianxin

last: Lin

first: Jian

last: Huang


title: Multiplex genome editing uncovers a class of non-CG methylation specific for GC-rich regions in rice

city: shenzhen

first: yiming

last: yu

state: --- Select a state ---

address: 1088 Xueyuan Avenue

institute: Southern University of Science and Technology

summary: We report the BS-Seq, mRNA-Seq and sRNA-Seq of the homozygous mutants and wide type in rice T1 plants, including single and multiple knock-out mutants. We found the major DNA methyltransfereases in regulating DNA methylation of rice.

overall_design: Examination of DNA methyltransfereases in rice.

first: Daoheng

last: Hu

first: Yiming

last: Yu

first: Chun

last: Wang

first: Kejian

first: Jixian

last: Zhai


title: An integrated analysis of small RNAs, degradome and transcriptome in rice seedling exposure to cadmium stress [degradome]

city: Fu Yang

first: Min

last: Zhong

state: Hang Zhou

address: Rice research road NO.28

institute: China National Rice Research Institute

summary: Cadmium (Cd) influence in rice is a growing global environmental concern. Although many miRNAs and target genes have been identified in rice exposure to Cd stress, no comprehensive study has been done comprising integrative analysis of small RNAs, degradome and trascriptome sequencing to identify Cd-regulated miRNAs and their targets under Cd stress. In this study, 40 miRNAs including 38 known miRNAs representing 22 miRNA families and 2 novel miRNAs were substantially altered in response to Cd exposure. 18 differentially altered target genes were inversely correlated with 18 Cd responsive miRNAs. Majority of these targeted genes are transcript factors such as Auxin response factor 13 (ARF13), Scarecrow-like protein 6 (SCL6), Squamosa promoter-binding-like proteins (SPLs), Nuclear transcription factor Y subunit A-6 (NFYA6), Gibberellin-dependent avian myeloblastosis virus oncogene (GAMYB) and No apical meristem protein domain containing proteins (NACs), most of which were involved in signal transduction such as abscisic acid (ABA), Auxin, Gibberellin acid (GA) and MAPK (Mitogen-activated protein kinase). Functional analysis revealed that genes involved in photosynthesis pathway (osa00196, osa00195 and osa00710) and protein degradation pathway (osa04612) were identified to be participated in response to Cd in rice, including osa-miR156I-5p_R-1/SPLs, osa-miR171a_1ss12CT/DEGP10 and osa-miR169r-5p_R/NFYA6 circuits, respectively. We conclude that a combination of transcriptome, sRNAs and the degradome would confer a useful approach to investigate miRNA-mediated molecular mechanisms underlying plant response to Cd stress.

overall_design: The cultivar used in these experiments was ‘Zhong Jiazao-17’ (Hangzhou, Zhejiang Province, China), a fast maturing indica type known to accumulate low Cd in the grain. Germinating seedlings were removed to a hydroponics solution consisting of Hoagland’s solution (pH 5.5) in a climate chamber (relative humidity 80%, 30/28℃ day/night temperature). Once the first leaf was fully expanded, seedlings were subjected to CdCl2•2.5H2O in different concentrations, including 0 µM (the control, MC) and 100 µM (MS), in triplicate. After 12 days  cadmium treatment, total RNA profiles of rice shoot for three replicates of every treatment were generated for degradome sequencing, using Illumina Hiseq2500.


title: An integrated analysis of small RNAs, degradome and transcriptome in rice seedling exposure to cadmium stress [miRNA-seq]

summary: Cadmium (Cd) influence in rice is a growing global environmental concern. Although many miRNAs and target genes have been identified in rice exposure to Cd stress, no comprehensive study has been done comprising integrative analysis of small RNAs, degradome and transcriptome sequencing to identify Cd-regulated miRNAs and their targets under Cd stress. In this study, 40 miRNAs including 38 known miRNAs representing 22 miRNA families and 2 novel miRNAs were substantially altered in response to Cd exposure. 18 differentially altered target genes were inversely correlated with 18 Cd responsive miRNAs. Majority of these targeted genes are transcript factors such as Auxin response factor 13 (ARF13), Scarecrow-like protein 6 (SCL6), Squamosa promoter-binding-like proteins (SPLs), Nuclear transcription factor Y subunit A-6 (NFYA6), Gibberellin-dependent avian myeloblastosis virus oncogene (GAMYB) and No apical meristem protein domain containing proteins (NACs), most of which were involved in signal transduction such as abscisic acid (ABA), Auxin, Gibberellin acid (GA) and MAPK (Mitogen-activated protein kinase). Functional analysis revealed that genes involved in photosynthesis pathway (osa00196, osa00195 and osa00710) and protein degradation pathway (osa04612) were identified to be participated in response to Cd in rice, including osa-miR156I-5p_R-1/SPLs, osa-miR171a_1ss12CT/DEGP10 and osa-miR169r-5p_R/NFYA6 circuits, respectively. We conclude that a combination of transcriptome, sRNAs and the degradome would confer a useful approach to investigate miRNA-mediated molecular mechanisms underlying plant response to Cd stress.

overall_design: The cultivar used in these experiments was ‘Zhong Jiazao-17’ (Hangzhou, Zhejiang Province, China), a fast maturing indica type known to accumulate low Cd in the grain. Germinating seedlings were removed to a hydroponics solution consisting of Hoagland’s solution (pH 5.5) in a climate chamber (relative humidity 80%, 30/28℃ day/night temperature). Once the first leaf was fully expanded, seedlings were subjected to CdCl2•2.5H2O in different concentrations, including 0 µM (the control, MC) and 100 µM (MS), in triplicate. After 12 days  cadmium treatment, miRNA profiles of rice shoot for every replicate were generated by ssRNA sequencing, using Illumina Hiseq2500.


title: Histone methyltransferases SDG25/ATX1 regulate heat stress memory by antagonizing DNA remethylation

city: Hangzhou

first: Ze-Ting

last: Song

state: Zhejiang

address: No.866 Yuhangtang Road

department: College of Life Science

institute: Zhejiang University

summary: Heat stress is a great threat to plant growth because of their sessile lifestyle. Here, we show that histone methyltransferases SDG25 and ATX1 regulate gene expression and antagonize DNA remethylation under recovery stage after long-term high temperature treatment by catalyzing the methylation of histone H3K4 loci.

overall_design:
RNA-Seq: 16 samples, wild type (WT) and sdg25-1/atx1-2 (DM) treated by long-term heat stress (R0) or living in suitable temperature (C0), WT and DM recovery from stress for 24 hours (R24) or living in suitable temperature (C24), both of which are in two biological replicates.
Bisulfite-Seq: 12 samples, WT and DM recovery from long-term heat stress for 24 hours (R24) or living in suitable temperature (C24), both of which are in three biological replicates.

first: Jian-Xiang

last: Liu


title: Evaluation of bovine milk extracellular vesicles on mouse  intestinal gene expression

status: Public on Jun 23 2021

city: Seoul

first: Sangdon

last: Ryu

address: 1, Gwanak-ro, Gwanak-gu

country: South Korea

institute: Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Science

summary: Intestinal tissue samples from dextran sodium sulfate-induced colitis mice were analyzed on their transcriptomic changes using RNA-seq to elucidate the effects of extracellular vesicles pretreatment on the colitis-associated gene expressions.

first: Minhye

last: Shin


title: Discovery of pre-mRNA structural scaffold as a contributor to mammalian splicing code [In Vivo]

city: La Jolla

first: Kaushik

last: Saha

address: 9500 Gilman Drive

department: Chemistry and Biochemistry

institute: University of California San Diego

summary: The specific recognition of splice signals at or near the exon-intron junctions is not explained by their weak conservation across the mammalian transcriptome and postulated to require a multitude of features embedded in the pre-mRNA strand. We explored the possibility of three-dimensional structural scaffold of a pre-mRNA guiding early spliceosomal components to the splice signal sequences. We find that mutation in non-cognate splice signal sequences of a model pre-mRNA substrate could impede recruitment of early spliceosomal components due to disruption of global structure of the pre-mRNA. We also find distribution of pre-mRNA segments potentially interacting with early spliceosomal component U1 snRNP across the intron, spatial proximity of 5′ and 3′ splice sites within the pre-mRNA scaffold, and an interplay between the structural scaffold and splicing regulatory elements in recruiting early spliceosomal components. These results suggest that early spliceosomal components could recognize a three-dimensional structural scaffold beyond the short splice signal sequences and that in our model pre-mRNA, this scaffold is formed across the intron involving the major splice signals. This work provides a conceptual base to extend our understanding of prevalence, distribution, and splicing regulatory potential of recognizable three-dimensional structural scaffolds across the mammalian transcriptome.

overall_design: Estimation of in vivo SHAPE reactivity by SHAPE-MaP of Adenovirus 2 major late transcript IVS1 and its mutants

first: Gourisankar

last: Ghosh


title: Discovery of pre-mRNA structural scaffold as a contributor to mammalian splicing code

overall_design: Refer to individual Series


title: An integrated analysis of small RNAs, degradome and transcriptome in rice seedling exposure to cadmium stress [transcriptome]

overall_design: The cultivar used in these experiments was ‘Zhong Jiazao-17’ (Hangzhou, Zhejiang Province, China), a fast maturing indica type known to accumulate low Cd in the grain. Germinating seedlings were removed to a hydroponics solution consisting of Hoagland’s solution (pH 5.5) in a climate chamber (relative humidity 80%, 30/28℃ day/night temperature). Once the first leaf was fully expanded, seedlings were subjected to CdCl2•2.5H2O in different concentrations, including 0 µM (the control, MC) and 100 µM (MS), in triplicate. After 12 days  cadmium treatment, total RNA profiles of rice shoot for every replicate were generated by ssRNA sequencing, using Illumina Hiseq4000.


title: Analysis of the mp clv3 transcriptome profile in Arabidopsis

city: Hefei

first: Zhong

last: Zhao

state: Anhui

address: Huangshan Road 443

department: School of Life Sciences

institute: University of Science and Technology of China

summary: Due to the major limitation of small set of stem cells located in the Shoot Apical Meristem (SAM), it is difficult to perform the whole genome analysis specific for those stem cells. Here, we generated the mp clv3 double mutant with a larger Shoot Apical Meristem,in which shoot stem cells were drastically enriched while the differentiation of stem cells was blocked. Then we performed the mRNA profiling on wild type and mp clv3 double mutant. And this could offer an ideal genetic material to highly increase the resolution of plant shoot stem cell profiling, also to further explore the mechanism of plant stem-cell regulation.

overall_design: Examination of transcriptome profile in 2 genotypes with 2 biological replicates each.

last: Zeng


title: An integrated analysis of small RNAs, degradome and transcriptome in rice seedling exposure to cadmium stress


title: Next generation sequencing for lncRNA profile of bone marrow mesenchymal stem cells through establishing exercise rat model by treadmill running experiment

city: 广州

first: Runguang

last: LI

address: 广州大道北沙太南路

institute: 南方医科大学

summary: In this study, we proved the exercise-induced promotion of osteogenic differentiation and inhibition of adipogenic differentiation of bone marrow mesenchymal stem cells (BMSCs) through establishing exercise animal model by treadmill running experiment. lncRNA sequencing analysis identified  44 upregulated lncRNAs and 39 downregulated lncRNAs in exercise group.

overall_design: Examination of and lncRNA profile in bone marrow mesenchymal stem cells (BMSCs) of  two model.

last: Li

first: Guozheng

last: Zhu


title: RNA sequencing of blood monocyte subsets in COVID patients

city: SAINT LOUIS

last: Zhang

state: MO

address: 425 S Euclid Ave

department: Pathology and Immunology

institute: Washington University in St. Louis

summary: We report mRNA expression profiles of blood monocyte subsets in COVID patients with comparison to non-COVD samples. COVID patients were grouped into mild without hospitalization and ICU without ventilation. Monocytes were FACS sorted based on CD14 and CD16 expression, generating classical CD14+CD16- monocytes and CD16+CD14+/++ nonclassical monocytes. The mRNA expression comparison demonstrates a strong response to viral infection and suggests a defect in nonclassical monocytes maturation. It also provides several biomarkers for prognosis purposes, including CD55 and CD81.

overall_design: Examination of mRNA expression profiles in blood monocyte subsets in COVID patients.

first: Emma

last: Erlich

first: John

middle: R

last: Edwards

first: Gwendalyn

middle: J

last: Randolph


title: Downregulated Luteolytic Pathways in Early Pregnant Bovine CL: Mimicry by Interferon-tau in vitro

city: Rehovot

first: Rina

last: Meidan

address: Herzl Street POB 12

country: Israel

institute: The Hebrew University of Jerusalem

summary: The downregulated pathways in early pregnant CL unraveled in this study span a wide range of luteal functions: angiogenesis, apoptosis and survival, steroidogenesis, and ECM remodeling. Notably, selective DEGs in luteinized granulosa cells (LGCs) were modulated by IFNT in vitro in a similar manner to their regulation in the CL of P cows, suggesting that IFNT may contribute to the characteristics of early pregnant CL.

overall_design: Unravel the differences in molecular profiles of pregnant and non-pregnant cows on day 18.

first: Raghavendra

last: Basavaraja

first: Gilgi

last: Friedlander


title: 1,25(OH)2D3 up-regulated lncRNA

city: Iwaki

first: Yoshiaki

last: Kanemoto

state: Fukushima

address: kaminodai 57, jyobankamiyunagaya-town

institute: Jyoban Hospital

summary: The purpose of this study are to identify new target for vitaminD.

overall_design: RNA Seq in HaCaT WT and VDR KO treated with 1,25(OH)2D3 or not.

first: Rei

last: Amano

first: Takahiro

last: Sawada

first: Kouichi

last: Nishimura

first: Jinichi

last: Mori

first: Shigeaki

last: Kato


title: Next Generation Sequencing Facilitates Quantitative Analysis of Control siRNA, RAB11A siRNA1 and RAB11A siRNA2 suppressed EBC-1 cell's Transcriptomes

city: Maebashi, Gunma

first: Navchaa

last: Gombodorj

state: Gunma ken

address: Showa machi 3-39-22

department: Division of Integrated Oncology Research

institute: Gunma University Graduate School of Medicine

summary: This study aims to find cellular pathway changes in RAB11A suppressed in lung squamous cell carcinoma cell line EBC-1 compared to control and to evaluate downregulating genes by RAB11A suppression by siRNA. Total RNA was extracted from EBC-1 transfected with control siRNA and RAB11A specific siRNAs using the RNeasy mini kit (Qiagen, Hilden, Germany). CAGE library preparation, sequencing, mapping, and gene expression and motif discovery analysis were performed by DNAFORM (Yokohama, Japan). In brief, RNA quality was assessed by Bioanalyzer (Agilent) to ensure that RIN (RNA integrity number) is over 7.0 and A260/280 and 260/230 ratios are over 1.7. First-strand cDNAs were transcribed to the 5’end of capped RNAs, attached to CAGE “bar code” tags, and the sequenced CAGE tags were mapped to human hg19 genomes using BWA software (v0.5.9) after discarding ribosomal or non-A/C/G/T base-containing RNAs. For tag clustering, CAGE-tag 5’ coordinates were input for CAGEr clustering using Paraclu algorithm with default parameters. Using CAGE analysis, we could validate the downregulation of FGF/FGFR signal-related genes in RAB11A-suppressed EBC-1 cells compared to the control cells. Finally, this study showed that RAB11 was related to tumor aggressiveness and growth in vitro and in vivo via activation of FGFR signals.

overall_design: Comparison of gene expression of lung squamous cell carcinoma cell line EBC-1 with Control siRNA, RAB11A siRNA1 and RAB11A siRNA2

first: Yoko

last: Azuma

first: Takehiko

last: Yokobori

first: Toshihide

first: Takayuki

last: Kosaka

first: Yoichi

last: Ohtaki

first: Seshiru

last: Nakazawa

first: Bilguun

last: Erkhem-Ochir

first: Akira

last: Mogi

first: Toshiki

last: Yajima

first: Hiroyuki

last: Kuwano

first: Hiroshi

last: Saeki

first: Ken

last: Shirabe


title: Discovery of a pre-mRNA structural scaffold as a contributor to the mammalian splicing code [in vitro]

first: Kaushik

last: Saha

state: CA

summary: The specific recognition of splice signals at or near exon-intron junctions is not explained by their weak conservation and instead is postulated to require a multitude of features embedded in the pre-mRNA strand. We explored the possibility of three-dimensional structural scaffold of AdML – a model pre-mRNA substrate – guiding early spliceosomal components to the splice signal sequences. We find that mutations in the non-cognate splice signal sequences impede recruitment of early spliceosomal components due to disruption of the global structure of the pre-mRNA. We further find that the pre-mRNA segments potentially interacting with the early spliceosomal component U1 snRNP are distributed across the intron, that there is a spatial proximity of 5′ and 3′ splice sites within the pre-mRNA scaffold, and that an interplay exists between the structural scaffold and splicing regulatory elements in recruiting early spliceosomal components. These results suggest that early spliceosomal components can recognize a three-dimensional structural scaffold beyond the short splice signal sequences, and that in our model pre-mRNA, this scaffold is formed across the intron involving the major splice signals. This provides a conceptual basis to analyze the contribution of recognizable three-dimensional structural scaffolds to the splicing code across the mammalian transcriptome.

overall_design: Estimation of SHAPE reactivity by SHAPE-MaP of Adenovirus 2 major late transcript IVS1 and its mutants

first: Gourisankar

last: Ghosh


title: The RyfA small RNA serves as a master regulator of stress responses and virulence in uropathogenic Escherichia coli

city: Laval

first: Charles

middle: Martin

last: Dozois

state: Québec

address: 531 Boul des Prairies

department: centre Amrand-Frappier Santé Biotechnologie

country: Canada

institute: Institut National de la Recherche scientifique

summary: Urinary tract infections (UTIs) are a very common bacterial infectious disease  in humans, and uropathogenic Escherichia coli (UPEC) are the most frequent cause of UTIs. During infection, UPEC must cope with a variety of stressful conditions in the urinary tract. Here, we demonstrated that the small RNA (sRNA) RyfA of UPEC strains was required for resistance to oxidative and osmotic stresses.  Inactivation of ryfA in UPEC strain CFT073 decreased urinary tract colonization in CBA/J mice and the ryfA mutant also had reduced production of type 1 and P fimbriae, which are known to be important for UTI. Transcriptomic analysis of the ryfA mutant showed changes in expression of genes associated with general stress responses, metabolism, biofilm formation and genes coding for cell surface proteins. Furthermore, loss of ryfA also reduced UPEC survival in human macrophages. Thus, ryfA plays a key regulatory role in UPEC adaptation to stress, that contributes to UTI and survival in macrophages.

overall_design: Examination of transcriptome of CFT073 vs ΔryfA  in LB at O.D 0.6

first: Hicham

last: Bessaiah


title: Loss of Phf6 enhances HSC self-renewal and leukemia stem cell activity

city: New York

first: Stuart

middle: Aidan

last: Quinn

state: NY

address: 1130 St Nicholas Ave

department: Institute for Cancer Genetics

institute: Columbia University

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


title: Next generation sequencing for miRNA  profile of bone marrow mesenchymal stem cells through establishing exercise rat model by treadmill running experiment

first: Runguang

last: LI

summary: In this study, we proved the exercise-induced promotion of osteogenic differentiation and inhibition of adipogenic differentiation of bone marrow mesenchymal stem cells (BMSCs) through establishing exercise animal model by treadmill running experiment. miRNA sequencing analysis identified 16 upregulated and 2 downregulated miRNAs in exercise group.

overall_design: Examination of miRNA profile in bone marrow mesenchymal stem cells (BMSCs) of  two model.

last: Li

first: Guozheng

last: Zhu


title: Genome-wide chromatin accessibility profiling of LT-HSCs isolated from WT and Phf6-deficient mice

summary: The plant homeodomain 6 gene (PHF6) is frequently mutated in human T-cell acute lymphoblastic leukemia (T-ALL); however, its specific functional role in leukemia development remains to be established. Here, we show that loss of PHF6 is an early mutational event in leukemia transformation. Mechanistically, genetic inactivation of Phf6 in the hematopoietic system enhances hematopoietic stem cell (HSC) long-term self-renewal and hematopoietic recovery after chemotherapy by rendering Phf6 knockout HSCs more quiescent and less prone to stress-induced activation. Consistent with a leukemia-initiating tumor suppressor role, inactivation of Phf6 in hematopoietic progenitors lowers the threshold for the development of NOTCH1-induced T-ALL. Moreover, loss of Phf6 in leukemia lymphoblasts activates a leukemia stem cell transcriptional program and drives enhanced T-ALL leukemia-initiating cell activity. These results implicate Phf6 in the control of HSC homeostasis and long-term self-renewal and support a role for PHF6 loss as a driver of leukemia-initiating cell activity in T-ALL.

overall_design: ATAC-seq profiling of LT-HSCs isolated from 3xWT and 3xPhf6-null mice

first: Agnieszka

last: Wendorff

first: Aidan

first: Adolfo

last: Ferrando


title: Single-cell RNA-seq analysis of the brainstem of mutant SOD1 mice reveals perturbed cell types and pathways of amyotrophic lateral sclerosis

city: Los Angeles

first: Xia

last: Yang

state: California

address: 610 Charles E. Young Drive East

department: Integrative Biology and Physiology

institute: University of California, Los Angeles

summary: Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disease in which motor neurons throughout the brain and spinal cord progressively degenerate resulting in muscle atrophy, paralysis and death. Recent studies using animal models of ALS implicate multiple cell-types (e.g., astrocytes and microglia) in ALS pathogenesis in the spinal motor systems. To ascertain cellular vulnerability and cell-type specific mechanisms of ALS in the brainstem that orchestrates oral-motor functions, we conducted parallel single cell RNA sequencing (scRNA-seq) analysis using the high-throughput Drop-seq method. We isolated 1894 and 3199 cells from the brainstem of wildtype and mutant SOD1 symptomatic mice respectively, at postnatal day 100. We recovered major known cell types and neuronal subpopulations, such as interneurons and motor neurons, and trigeminal ganglion (TG) peripheral sensory neurons, as well as, previously uncharacterized interneuron subtypes. We found that the majority of the cell types displayed transcriptomic alterations in ALS mice. Differentially expressed genes (DEGs) of individual cell populations revealed cell-type specific alterations in numerous pathways, including previously known ALS pathways such as inflammation (in microglia), stress response (ependymal and an uncharacterized cell population), neurogenesis (astrocytes, oligodendrocytes, neurons), synapse organization and transmission (microglia, oligodendrocyte precursor cells, and neuronal subtypes), and mitochondrial function (uncharacterized cell populations). Other cell-type specific processes altered in SOD1 mutant brainstem include those from motor neurons (axon regeneration, voltage-gated sodium and potassium channels underlying excitability, potassium ion transport), trigeminal sensory neurons (detection of temperature stimulus involved in sensory perception), and cellular response to toxic substances (uncharacterized cell populations). DEGs consistently altered across cell types (e.g., Malat1), as well as cell-type specific DEGs, were identified. Importantly, DEGs from various cell types overlapped with known ALS genes from the literature and with top hits from an existing human ALS genome-wide association study (GWAS), implicating the potential cell types in which the ALS genes function with ALS pathogenesis. Our molecular investigation at single cell resolution provides comprehensive insights into the cell types, genes and pathways altered in the brainstem in a widely used ALS mouse model.

overall_design: 4 Samples, 2 age-matched non-carrier wild-types and 2 human SOD1(G93A) (mutant)

first: Wenting

last: Liu

first: Sharmila

last: Venugopal

first: Sana

last: Majid

first: In

last: Ahn

first: Graciel

last: Diamante

first: Jason

last: Hong

first: Scott

last: Chandler


title: Gene expression profiling of Acute Myeloid Leukemia

city: Meldola

first: Giorgia

last: Simonetti

state: FC

address: Via Piero Maroncelli, 40

country: Italy

institute: IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori"

summary:
The transcriptional profile of acute myeloid leukemia (AML) cells changes according to the disease molecular and genomic properties and to the microenvironmental features. Moreover, it shapes the interaction with the tissue and immune microenvironment. We analyzed the gene expression profile of 61 AML cases (Affymetrix Human Transcriptome Array 2.0, Thermo Fisher Scientific) in order to identify investigate the potential involvement of adrenomedullin in AML and the alterations having a putative causal and/or tolerogenic role towards aneuploidy.
The gene expression profile of 61 AML cases was determined using Affymetrix Human Transcriptome Array 2.0, in order to identify alterations with a putative causal and/or tolerogenic role towards aneuploidy.

overall_design: Bone marow cells from AML patients (more than or equal to 80% blast cells) were used for RNA extraction and hybridization on microarrays.

first: Antonella

last: Padella

first: Cristina

last: Papayannidis

first: Annalisa

last: Astolfi

first: Giovanni

last: Martinelli


title: Next generation sequencing for lncRNA and miRNA profile of bone marrow mesenchymal stem cells through establishing exercise rat model by treadmill running experiment

first: Runguang

last: LI


title: lncRNA Mitochondrial oxygen responsive transcript 1 (MTORT1) downstream gene microarray

city: Taipei

first: Liang-Chuan

last: Lai

state: Taiwan

address: 1 Jen-Ai Road, Sec 1

department: Physiology

institute: National Taiwan University

summary: Long non-coding RNAs (lncRNAs) have been regarded to participate in multiple genetic pathways in cancer. Also, mitochondria-associated lncRNAs have been discovered to module mitochondrial function and metabolism. Previously, our lab identified oxygen responsive lncRNAs in breast cancer MCF-7 cells under normoxic, hypoxic and re-oxygenated conditions by using next generation sequencing technology. Among them, a novel mitochondrial lncRNA Mitochondrial Oxygen Responsive Transcript 1 (MTORT1) was chosen for further investigation. Therefore, the purpose of this study was to investigate the characterizations, function roles, and mechanisms of MTORT1 in breast cancer cells.

overall_design: Total RNA obtained from MCF-7 cells transfected with siRNA against MTORT1 for 48 hours compared to MCF-7 cells transfected with control siRNA

first: Yi-Chun

last: Cheng


title: Profiling of CD14+ monocytes from humans with Type diabetes and without diabetes

city: Duarte

first: Xiwei

last: Wu

address: 1500 E. Duarte Rd.

department: Computational and Quantitative Medicine

institute: City of Hope National Medical Center


title: Transcriptome analysis of young human oocytes identifies a potential antioxidant to rescue unusable immature oocytes

city: Hong Kong

first: Wing Tung

last: Lee

address: Room Y934, 9/F, Lee Shau Kee Building, The Hong Kong Polytechnic University, Hung Hom, Kowloon

department: Department of Health Technology and Informatics

institute: The Hong Kong Polytechnic University (PolyU)

summary: We highlighted the effects of age and ovarian responses on rescue IVM oocyte quality.

overall_design: SMART-seq2 on in vitro matured human oocytes from different age groups and in vivo-matured human oocytes, for which age was not considered.

first: Annie

middle: W

first: Tin-Lap


title: Affymetric SNP Array Data of 45 liver metastasis samples from colorectal cancer patients

city: Montreal

first: Gerald

last: Batist

address: 3755 Cote Ste-Catherine

institute: Jewish General Hospital

type:
SNP genotyping by SNP array
Genome variation profiling by SNP array

summary: To investigate genomic plasticity over time associated with response to standard chemotherapy, we collected longitudinal liver metastasis (LM) samples from 155 patients and characterized the copy number aberration (CNA) landscape and its effect on the transcriptome. CNA profiles of lesions exhibiting different treatment response were compared and focal genomic divergences reported. By investigating genomic-phenotype associations of the largest reported LM cohort to date, we identified novel molecular features associated with drug response supporting the relevance of collecting clinical metastatic samples.

overall_design:
Affymetrix SNP arrays were performed according to the manufacturer's directions on DNA extracted from fresh frozen liver metastasis samples at baseline (pre-treatment) and at the time of clinical progression (post-treatment)
In this study,  45 liver metastasis samples (35 pre-treatment and 10 post treatment) were analyzed using Affimetrix CytoScan HD platform and 149 liver metastasis samples (97 pre-treatment and 52 post-treatment) were analyzed by whole exome sequencing (WES) for copy number abberation assessment. 45 samples were analyzed using both platforms. We evaluated and compared the performance of WES and the  CytoScan HD platforms for CNA inference

first: Karen

last: Gambaro

first: Maud

last: Marques

first: Suzan

last: McNamara

first: Mathilde

last: Couetoux du Tertre

first: Zuanel

last: Diaz

first: Cyrla

last: Hoffert

first: Archana

last: Srivastava

first: Steven

last: Hébert

first: Benoit

last: Samson

first: Bernard

last: Lespérance

first: Yoo-Joung

last: Ko

first: Richard

last: Dalfen

first: Eve

last: St-Hilaire

first: Lucas

last: Sideris

first: Felix

last: Couture

first: Ronald

last: Burkes

first: Mohammed

last: Harb

first: Errol

last: Camlioglu

first: Adrian

last: Gologan

first: Vincent

last: Pelsser

first: André

last: Constantin

first: Celia

last: Greenwood

first: Sabine

last: Tejpar

first: Petr

last: Kavan

first: Claudia

middle: L

last: Kleinman


title: A novel combination of serum microRNAs for the detection of early gastric cancer

city: Kanagawa

first: Satoko

last: Takizawa

address: kamakurashi

institute: Toray industries inc

summary: A serum miRNA combination could be a powerful classifier for the detection of patients with early stage gastric cancer.

overall_design: Serum microRNA profiles of 2940 samples, which consist of 1423 gastric cancers, 1417 non-cancer controls, 50 esophageal cancers, and 50 colorectal cancers.

first: Seiichiro

last: Abe

first: Juntaro

last: Matsuzaki

first: Kazuki

last: Sudo

first: Ichiro

last: Oda

first: Hitoshi

last: Katai

first: Ken

last: Kato

first: Hiromi

last: Sakamoto

first: Fumitaka

last: Takeshita

first: Shumpei

last: Niida

first: Yutaka

last: Saito

first: Takahiro

last: Ochiya


title: Profiling of CD14+ monocytes from humans with Type diabetes and without diabetes [CHIRP-seq]

first: Xiwei

last: Wu

summary: We identified a novel lncRNA DRAIR that is downregulated in CD14+ monocytes from type 2 diabetes relative to controls. Functional studies showed that DRAIR regulates anti-inflammatory genes and its knockdown enhances proinflammatoory phentype of monocytes. To examine mechanisms of DRAIR actions, we performed Chromatin isolation by RNA purification (ChIRP) assays using DRAIR biotinylated tiling oligonucleotides to identify chromatin inding sites in THP-1 monocytes.

overall_design: ChIRP-seq analysis of lncRNA DRAIR was performed in THP-1 monocytes to identify chromatin binding sites using published protocols (Chu et al, Molecular cell. 2011;44(4):667-78).

first: Marpadga

last: Reddy

first: Rama

last: Natarajan


title: Expression data from freshly isolated murine muscle satellite cells

status: Public on Jun 22 2021

city: suita

first: so-ichiro

last: fukada

address: 1-6 yamadaoka

institute: osaka University

summary:
Calcitonin receptor (CalcR) signaling is essential pathway for maintaining quiescence in muscle stem cells (Stem Cells. 2007 Oct;25(10):2448-59, Cell Rep. 2015 Oct 13;13(2):302-14). Collagen V functions as a surrogate ligand for CalcR, and Protein kinase A (PKA)-mediated Yap1 suppression serve as the downstream of CalcR in quiescent muscle stem cells (Nature. 2018 May;557(7707):714-718, Cell Rep. 2019 Nov 19;29(8):2154-2163.e5.). The aim of this study is to further characterize CalcR-cKO MuSCs.
The aim of this study is to characterize CalcR-cKO MuSCs.

overall_design: Two weeks after tamoxifen treatment, YFP+ muscle satellite cells were purified using Aria II cell sorter.

first: So-ichiro

last: Fukada


title: Profiling of CD14+ monocytes from humans with Type diabetes and without diabetes [RNA-Seq]

summary: Monocyte activation by high glucose and free fatty acids promotes inflammation implicated in vascular complications associated with Type 2 diabetes (T2D). Emerging evidence shows that long non coding RNA (lncRNA)s regulate inflammation, but their  role in  T2D induced monocyte dysfunction is unclear. To examine this, we profiled the transcriptome of CD14+ monocytes from volunteers with T2D and without diabetes (n=5 each) using strand-specific RNA-seq on Illumina HiSeq 2500. Our study identified several differentially regulated lncRNAs along with coding genes involved in monocyte functions related to inflammation and monocytosis.

overall_design: Following approved IRB protocols (at City of Hope and Baylor College of Medicine) informed consent was obtained from volunteers and fasting blood (15 ml) was collected from Control volunteers and volunteers with T2D at the Baylor College of Medicine. PBMC were isolated using Ficoll-Hypaque gradient (Sigma) and CD14+ monocytes were isolated by cell depletion with magnetic beads (Miltenyi Biotech, San Diego, CA). Total RNA was isolated from CD14+ monocytes using RNeasy mini kit and on-column DNase I digestion to eliminate genomic DNA (Qiagen). Total RNA from CD14+ human monocytes was subjected to strand-specific RNA-seq on Hi-Seq 2500 platform (Illumina, San Diego, CA).


title: Transgenerational inheritance of increased mtDNA triggers mitochondrial UPR and modulates aging [WT vs. TGQ]

city: Beijing

first: qian

last: zhang

address: No. 1 West Beichen Road, Chaoyang District

department: State Key Laboratory of Molecular Developmental Biology

institute: Institute of Genetics and Developmental Biology

summary: It would be evolutionarily beneficial if the information of transient stresses experienced by parents could be passed on to descendants as a forecast of the challenges to come. Here, we discovered that neuronal mitochondrial perturbations can transmit the mitochondrial unfolded protein response (UPRmt) to offspring for multiple generations in Caenorhabditis elegans. The transgenerational induction of UPRmt was caused by a higher level of maternally inherited mitochondrial DNA (mtDNA), which disturbed the balance of oxidative phosphorylation subunits encoded by mtDNA and nuclear DNA. Furthermore, an increase in mtDNA levels requires Wnt/b-catenin signaling to propagate across generations, thereby inducing the UPRmt and conferring increased lifespan and stress tolerance. Thus, transgenerational increase in mtDNA levels and the UPRmt enable offspring to live longer and confer stress tolerance.

overall_design: Comparison of gene expression changes of WT and TGQ C. elegans L4 animals

first: Qian

last: Zhang

first: Ye

last: Tian