title: CCN2-MAPK-Id-1 Loop Feedback Amplification is involved in Maintaining Stemness in Oxaliplatin-resistant Hepatocellular Carcinoma

status: Public on Jan 02 2019

city: Xi 'an

first: Xia

last: Liao

state: Shaanxi

address: 277# West Yanta Road

institute: Department of nutrition

summary: Hepatocellular carcinoma (HCC) is the second leading cause of cancer death worldwide. Most patients are at an advanced stage at diagnosis, and are not eligible for curative therapy. Chemotherapy is an alternative treatment for advanced HCCs, but resistance is found in many patients. Understanding the underlying mechanisms in chemo-resistance is critical to further improve the efficacy of HCC treatment. In this study, we found that increased expression of Id-1 and CCN2 were closely related to oxaliplatin resistance in HCC. Upregulation of CCN2 and Id-1 was independently associated with shorter survival and increased recurrence in HCC patients, and significantly enhanced oxaliplatin resistance and promoted lung metastasis in vivo, whereas knock-down of their expression significantly reversed the chemo-resistance and inhibited HCC cell stemness. cDNA microarrays and PCR revealed that Id-1 and MAPK pathway were the downstream signaling of CCN2, and Id-1 could upregulate CCN2 in a positive feedback manner. Moreover, CCN2 significantly enhanced oxaliplatin resistance by activating the MAPK signaling pathway and upregulating Id-1 expression. Meanwhile, MAPK/Id-1 signaling was demonstrated as one of the most important autocrine signaling pathways regulated by CCN2 in oxaliplatin-resistant models, and combination with sorafenib could improve the efficacy of oxaliplatin in HCC. Conclusions: These findings suggest that CCN2-MAPK-Id-1 loop feedback amplification is involved in oxaliplatin-resistant HCC, and the combination of oxaliplatin with inhibitor of CCN2 or MAPK signaling could provide a promising approach to ameliorating HCC progression and oxaliplatin resistance.

overall_design: In the present study, we determined that increased Id-1 and CCN2 expression were closely correlated with oxaliplatin resistance in HCC, verified that malignancy and poor prognosis were associated with Id-1 in human HCC, and explored the negative roles of Id-1 and the regulatory mechanisms of CCN2 in HCC. Finally, we demonstrated enhanced stemness and the upregulation of Id-1 in HCC after oxaliplatin treatment, which could be reversed by CCN2-MAPK-Id-1 signaling loop inhibition.

first: Shan

middle: S

last: Jiang

first: Yang

last: Bu

first: Mei

last: Zhang

first: Peng

last: Ning

first: Qing

last: Jia


title: Quantitative Analysis of PPARD RNA-Seq Transcriptomes of Mouse Gastric Corpus Epithenial Cells by Next Generation Sequencing (NGS)

status: Public on Jan 01 2019

city: Houston

first: Xiaofeng

last: Zheng

state: TX

address: 7007 Bertner Ave

department: Bioinformatics & Computational Biology

country: USA

institute: UT MD Anderson Cancer Center

type: Expression profiling by high throughput sequencing

summary:
Purpose: NGS has revolutionized systems-based analysis of cell signaling pathways. The goal of this study is to determine the effects of PPARD in gastric corpus epithenial  cell transcriptomes in relation to gastric progenitor cell transfromation and gastric tumorigenesis.
Methods: NGS-derived mRNA transcriptome profiles of gastric corpus epithelial cells from villin-PPARD and their age and sex matched WT mice at 10, 25 and 55 weeks were generated by deep sequencing (4-5 mice per group) using Illumina  HiSeq4000 .The transcriptomes of villin-PPARD and WT mice were compared to determine the differentially expressed genes. Differentially expressed genes in the top canonical pathways will be examined and validated by qRT-PCR.
Results: The raw data was aligned to the MM10 genome with Tophat2/2.0.14, and the number of reads per gene was counted with HTSeq/0.6.1.The read counts were normalized with "DESeq2". We used cutoff: FDR< 0.01 and fold change larger than 2 to identify 407 differentially expressed genes (DEGs) for 10 weeks, 717 DEGs for 25 weeks and 2694 DEGs for 55 weeks. Among those DEGs, 255 are shared by the 3 ages, in which 219 were upregulated and 36 were downregulated in villin-PPARD mice compared with the WT mice. Ingenuity Pathway Analysis for the 255 DGEs among the 3 age groups showed that IFN-g signaling was the top canonical pathway that PPAR-d activated, with an overlap ratio of 36.1% of the known genes involved in this pathway. The next two top canonical pathways, with overlap ratios of 23.7% and 15.9%, were the antigen presentation pathway and the pathway for activation of IRF by cytosolic pattern recognition receptors, respectively, both of which are related to IFN-g signaling pathway activation and immune inflammation.
Conclusions: Our study represents the detailed analysis of PPARD transcriptomes in gastric corpus epithelial cells regulated by villin-promoter, generated by mRNA-seq technology. Our results  show that NGS offers a comprehensive and  accurate quantitative and qualitative evaluations of mRNA contents in cells. We conclude that RNA-seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions.

overall_design: The RNA-seq transcriptome profile of mouse gastric corpus epithenial cells scraped from the villin-PPAR-d mice and their WT littermates at ages 10,25 and 55 weeks (4-5 mice per group) were generated by deep sequencing using Illumina HiSeq4000.

first: Imad

last: Shureiqi

first: Xiangsheng

last: Zuo

first: Jing

last: Wang


title: Genome-wide identification of putative translation regulator cis-Natural Antisense Transcripts in Arabidopsis thaliana

status: Public on Feb 16 2019

city: Illkirch-Graffenstaden

first: Jules

last: Deforges

address: Boulevard Gonthier d'Andernach

country: France

institute: Transgene SA

summary: The development of high-throughput genomic technologies has revealed that a large fraction of the genomes of eukaryotes is associated with the expression of noncoding RNAs. One class of noncoding RNA, the cis-natural antisense transcripts (cis-NATs), are particularly interesting as they are at least partially complementary to the protein-coding mRNAs. Although most studies described cis-NATs involved in the regulation of transcription, a few reports have shown recently that cis-NATs can also regulate translation of the cognate sense coding genes in plants and mammals. In order to identify novel examples of translation regulator cis-NATs in Arabidopsis thaliana, we designed a high-throughput experiment based on polysome profiling and RNA-sequencing. Expression of cis-NATs and translation efficiency of the cognate coding mRNAs were measured in roots and shoots in response to various conditions, including phosphate deficiency and treatment with phytohormones. We identified several promising candidates, and validated a few of them experimentally, in Arabidopsis thaliana transgenic lines over-expressing in trans the translation regulator candidate cis-NATs.

overall_design: total RNA and polysomal RNA was sequenced from Arabidopsis thaliana whole seedlings grown in high or low pohsphate content, or from roots or shoots from seedlings treated or not with different phytohormones (Ctrl, IAA, ABA,MeJA and ACC). 3 biological replicates were analyzed for each of the 12 experimental conditions.

first: Yves

last: Poirier


title: Antibacterial characterization of polyphosphate against Porphyromonas spp. implicated in companion animal periodontitis

city: Seoul

first: Jae-Hyung

last: Lee

address: 26 Kyungheedae-ro, Dongdaemun-gu

country: South Korea

institute: Kyung Hee University

summary: We investigated the molecular and cellular mechanism using the gene expression changes of Porphyromonas gulae upon the teatment of polyP3.

overall_design: Compare gene expression profiles between wild-type (no treatment) and polyP3 treatment Porphyromonas gulae using RNA-Seq (Illumina platform: Hi-Seq 2000)

first: Mi

middle: H

last: Noh

first: Seung-Yun

last: Shin

first: Ji-Hoi

last: Moon

first: Jin-Yong


title: A tRNA modification balances carbon and nitrogen metabolism by regulating phosphate homeostasis, to couple metabolism to cell cycle progression.

status: Public on Dec 28 2018

city: Piscataway

first: Premal

last: Shah

state: NJ

address: 145 Bevier Road, Rm 326

department: Genetics

institute: Rutgers University

summary: Cells must appropriately sense and integrate multiple metabolic resources to commit to proliferation. Here, we report that cells regulate nitrogen (amino acid) and carbon metabolic homeostasis through tRNA U34-thiolation. Despite amino acid sufficiency, tRNA-thiolation deficient cells appear amino acid starved. In these cells, carbon flux towards nucleotide synthesis decreases, and trehalose synthesis increases, resulting in metabolic a starvation-signature. Thiolation mutants have only minor translation defects. However, these cells exhibit strongly decreased expression of phosphate homeostasis genes, mimicking a phosphate-limited state. Reduced phosphate enforces a metabolic switch, where glucose-6-phosphate is routed towards storage carbohydrates. Notably, trehalose synthesis, which releases phosphate and thereby restores phosphate availability, is central to this metabolic rewiring. Thus, cells use thiolated tRNAs to perceive amino acid sufficiency, and balance amino acid and carbon metabolic flux to maintain metabolic homeostasis, by controlling phosphate availability. These results further biochemical explain how phosphate availability determines a switch to a ‘starvation-state’.

overall_design: Ribosome-footprinting and RNA-seq samples of  yeast CEN.PK, ∆uba4 and ∆ncs2 strains.

first: R

last: Gupta

first: A

last: Walvekar

first: S

last: Liang

first: Z

last: Rashida

first: P

last: Laxman


title: An AR-ERG co-mediated chromatin interactome defines the transcriptional network in prostate cancer cells

status: Public on Dec 14 2018

city: Singapore

first: Edwin

last: Cheung

state: Singapore

address: Genome Institute of Singapore 60 Biopolis Street, Genome, #02-01

department: Cancer Biology and Pharmacology

country: Singapore

institute: Genome Institute of Singapore

type: Genome binding/occupancy profiling by high throughput sequencing

summary: An aberrant androgen receptor (AR) transcriptional network underpins prostate cancer development. Even though the AR cistrome had been extensively studied in prostate cancers, information pertaining to the spatial architecture of the AR transcriptional circuitry remains limited due to the absence of an AR-associated chromatin interactome map. To resolve this, we utilized chromatin interaction analysis by paired-end tag (ChIA-PET) sequencing to profile AR-associated and ERG-associated long range chromatin interactions in an ERG fusion positive prostate cancer cell line. We identified ERG-associated long range chromatin interactions as an elemental component in the AR-associated chromatin interactome, acting in concert, to achieve coordinated regulation of AR target genes. In addition, we characterized the epigenetic signature of the AR/ERG anchor binding sites and implicated AR and ERG associated chromatin loopings for facilitating fusion gene formation in prostate cancers. Taken together, our results revealed the presence of an AR/ERG defined higher order chromatin structure exploited for driving prostate cancer progression.

overall_design: Chromatin interaction analysis coupled with Pair End Tags of AR and ERG: ChIP using anti-AR antibody and anti-ERG antibody, followed by close proximity ligations. ChIA-PET libraries were generated from VCaP cells treated with 100nM DHT. GRO-seq was performed as described previously (Core, Waterfall et al. 2008) with limited modifications. GRO-seq and RNA-PET libraries were generated from VCaP cells grown in phenol red-free RPMI medium and treated with 100 nM DHT as the timepoints indicated. The libraries of RNAs were prepared for Illumina sequencing.

first: Zhizhuo

last: Zhang

first: KernRei

last: Chng

first: MeiHui

last: Liu

first: YingYing

last: Sung

first: Charle

middle: L

last: Heng

first: Guoliang

last: Li

first: YiJun

last: Ruan

first: Wing

middle: K


title: Effects of the microRNA 137 and its connection to psychiatric disorders.

status: Public on Dec 01 2018

city: Würzburg

first: Claus

middle: Juergen

last: Scholz

address: Josef-Schneider-Str. 2

department: Core Unit SysMed

country: Germany

institute: University Hospital Würzburg

summary:
MicroRNAs have been implicated in the pathology not only of cancer, but also of psychiatric diseases, such as bipolar disorder and schizophrenia. As several psychiatric disorders share the same risk genes, we hypothesized that this microRNA could also be associated with attention-deficit/hyperactivity disorder (ADHD) and that this association to psychiatric disorders might be due to the variable number of tandem repeats (VNTR) polymorphism within the internal miR-137 (Imir137) promoter (PMID 18316599; PMID 25154622).
To further understand the role of the microRNA 137 in the brain a knock-down of miR-137 expression in SH-SY5Y neuroblastoma cells was performed followed by expression analysis using a microarray.

overall_design: Investigation of the effects of miR-137 knock-down on gene expression in a human neuronal cell line to identfy potential new miR-137 targets.

first: Stefanie

last: Berger

middle: J

first: Heike

last: Weber

first: Lena

last: Weißflog

first: Andreas

last: Reif


title: Gene expression changes in mouse fibroblasts (3T3) after sunitinib resistance and acute and chronic withdrawal

status: Public on Nov 22 2018

city: Buffalo

first: John

last: Ebos

state: NY

address: Elm & Carlton Streets

department: Department of Cancer Genetics and Genomics

institute: Roswell Park Cancer Institute

summary: Transcriptome analysis was used to identify changes in mouse fibroblasts (3T3) resistant to sunitinib (SuR) and after short and long term sunitinib withdrawal in vitro (ST-W for 48 hours and LT-W for more than 2 months, respectively).

overall_design: Mouse fibroblasts (3T3) resistant to sunitinib were derived in vitro after incremental increases of sunitinib from 250nM to 5μM. Resistant cells were maintained in vitro with 5μM sunitinib for more than 2 months.

first: Michalis

last: Mastri


title: Gene expression changes in human breast cancer cells (LM2-4) after sunitinib resistance and chronic withdrawal

summary: Transcriptome analysis was used to identify changes in human breast cancer cells (LM2-4) resistant to sunitinib (SuR) and after long term sunitinib withdrawal in vitro (LT-W for more than 6 months).

overall_design: Metastatic human breast cancer cells (LM2-4) resistant to sunitinib were derived in vivo after continuous treatment with 60mg/kg/day sunitinib from post-surgical metastatic lesions. Resistant cells were maintained in vitro with 5μM sunitinib for more than 6 months. The parental cells (MDA-MB-231) were used as a reference.


title: VD3-VDR axis regulates the homeostasis and function of alveolar macrophage

status: Public on Jan 08 2019

city: Cambridge

first: Guangan

last: Hu

state: MA

address: 500 Main Street

department: Koch Institute

institute: MIT

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

overall_design: Refer to individual Series


title: Analysis of gastrocnemius muscle from chow-fed control and skeletal muscle specific Cpt1b knockout mice

status: Public on Nov 30 2018

city: Baton Rouge

first: Jaycob

middle: D

last: Warfel

state: Louisiana

address: 6400 Perkins Road

department: RNA Homeostasis

institute: PBRC

summary: To determine the transcriptomic effects of Cpt1b loss on skeletal muscle gene expression, we assessed gastrocnemius muscle in chow-fed control and Cpt1b skeletal muscle specific knockout mice using a serial analysis of gene expression strategy. Complementary bioinformatics pathway enrichment studies were performed which indicated that differentially expressed genes between genotypes were predominantly related to various processes include carbohydrate metabolism, lipid metabolism, amino acid metabolism, cell proliferation, and apoptosis.

overall_design: Gastrocnemius muscles were dissected from 8 male wild-type and 7 male skeletal muscle-specific Cpt1b knockout mice after chow feeding for 12-14 weeks. Total RNA was prepared using Trizol, RNA concentration was determined usign a nanodrop UV spectrophotometer, and 500ng RNA per sample was given for sequencing library construction.

first: Bolormaa

last: Vandanmagsar

first: Shawna

middle: E

last: Wicks

first: Robert

middle: C

last: Noland

first: Randall

last: Mynatt

first: Sujoy

last: Ghosh

first: Susan

last: Newman

first: Richard

last: Carmouche

first: Claudia

last: Kruger

first: J

middle: M

last: Salbaum

first: Eric

last: Ravussin


title: Expression data from mouse lung alveolar epithelial type II cell with Yap/Taz deletion after bacterial pneumonia-induced lung injury

city: Philadelphia

first: Ying

last: Tian

state: PA

address: 3500 N. Broad Street

department: Pharmacology, Center for Translational Medicine

institute: Lewis Katz School of Medicine at Temple University

summary:
To define the role of Yap/Taz in alveolar epithelial regeneration, we deleted Yap/Taz in mouse lung Spc-expressing ATII cells by using Spc-CreERT2, Yap fl/fl, Taz fl/fl, R26R-mTmG mice.
This data set contains the microarrays examining gene expression in the lineage-labeled Spc-expressing ATII cells before and after Streptococcus pneumoniae infection.

overall_design: We deleted Yap and Taz in the 6-10 weeks old adult mice using the Spc-CreERT2 mouse line. We used S. pneumoniae strain T4 to infect mice by intranasal inhalation at a dose of 2x10E7 CFU. The gene expression analysis was performed on lineage labeled mouse ATII cells isolated by sorting GFP-positive cells from non-injured lung  or the lung at 8 days post-SpT4 infection.


title: Characterization of the novel spontaneously immortalized rat Müller cell line SIRMu-1

city: Adelaide

first: Daniel

middle: John

last: Peet

state: SA

address: Molecular Life Sciences Building, University of Adelaide, North Terrace

department: Molecular and Biomedical Sciences

country: Australia

institute: University of Adelaide

summary: Müller cells (MCs) play a crucial role in the retina, and cultured MC lines are an important tool with which to study MC function. Transformed MC lines have been widely used; however, the transformation process can also lead to unwanted changes compared to the primary cells from which they were derived. A monoclonal spontaneously immortalized rat Müller cell line, SIRMu-1, was derived from primary rat MCs and characterized by RNA-sequencing (in addition to immunofluorescence and western blotting) in comparison to primary MCs and the SV40-immortalized MC line, rMC-1.

overall_design: RNA-seq was performed on enriched polyA RNA from primary Müller cells (4 biological replicates of passage numbers 3-4), SIRMu-1 cells (5 biological replicates of passage numbers 6-20, two of which were cultured in the presence of the antibiotic gentamicin and the antifungal amphotericin B to match the culture conditions of the primary MCs), and rMC-1 cells (3 biological replicates of passage numbers 23-26).

first: Thaksaon

last: Kittipassorn

first: Cameron

last: Haydinger

middle: P

last: Wood

first: Teresa

last: Mammone

last: Casson


title: Gene expression changes in mouse kidney cancer cells (RENCA) after sunitinib resistance and acute and chronic withdrawal

first: John

last: Ebos

summary: Transcriptome analysis was used to identify changes in mouse kidney cancer cells (RENCA) resistant to sunitinib (SuR) and after short and long term sunitinib withdrawal in vitro (ST-W for 48 hours and LT-W for more than 2 months, respectively).

overall_design: Mouse kidney cancer cells (RENCA) resistant to sunitinib were derived in vivo after continuous treatment with 60mg/kg/day sunitinib from post-surgical metastatic lesions. Resistant cells were maintained in vitro with 5μM sunitinib for more than 2 months.

first: Michalis

last: Mastri


title: HIV Nef transfected HEK293T cell culture and HIV mock transfected HEK293T cell culture

status: Public on Nov 18 2018

city: Washington

first: Michael

last: Bukrinsky

state: District of Columbia

institute: GWU

type: Non-coding RNA profiling by high throughput sequencing


title: HIV Nef transfected HEK293T cell culture and HIV mock transfected HEK293T cell culture [mRNA]

summary:
Purpose: Comparison of RNA-sequencing datasets obtained from exosomes of Nef-transfected and Mock-transfected HEK293T cells.
Methods: Assessment of RNA content of exosomes produced by Nef-transfected HEK293T cells and and Mock-transfected HEK293T cells.
Results: Differences in a set of mRNAs.
Conclusions: Nef-transfection might induces changes in the mRNA content of exosomes.

first: Beda

last: Brichacek

first: David

last: Stern

first: Rebecca

last: Clement

first: Larisa

last: Dubrovsky

first: Anelia

last: Horvath


title: Reprogram-Seq: A platform for single-cell combinatorial reprogramming [IX]

status: Public on Nov 11 2018

city: Dallas

first: Gary

last: Hon

address: 5323 Harry Hines Blvd.

department: Department of Obstetrics and Gynecology

institute: UT Southwestern

summary: Reprogram-Seq leverages organ-specific cell atlas data with single-cell perturbation and computational analysis to predict, evaluate, and optimize TF combinations that reprogram a cell type of interest.

overall_design:
Focusing on the cardiac system, we performed Reprogram-Seq on P0 mouse heart cells to generate a reference transcriptomic map. Based on the reference map, we selected TF candidates and tests 1000s of TF cocktails for direct lineage conversion by scRNA-Seq.
This series includes reprogrammed MEFs with Myod1, day 7.

first: Nikhil

last: Munshi

first: Jialei

last: Duan


title: Reprogram-Seq: A platform for single-cell combinatorial reprogramming [V]

overall_design: Focusing on the cardiac system, we performed Reprogram-Seq on P0 mouse heart cells to generate a reference transcriptomic map. Based on the reference map, we selected TF candidates and tests 1000s of TF cocktails for direct lineage conversion by scRNA-Seq.


title: Reprogram-Seq: A platform for single-cell combinatorial reprogramming [VII]


title: Reprogram-Seq: A platform for single-cell combinatorial reprogramming [VI]


title: reproductive and vegetative leaves-Genopea 3.2

city: Orsay

first: Stéphanie

last: Pateyron

address: Rue de Noetzlin _ Batiment 630

institute: IPS2_Institute of Plant Sciences Paris-Saclay

summary: gnp10-01_genopea - reproductive and vegetative leaves - Transcriptome in leaves of Pea plants during the remobilization process . Effect of a nitrogen deficiency on this process.Note that lower leaves correspond to vegetative leaves (FV) and upper leaves correspond to leaves of the reproductive part (FR). - Analysis of expression in Pea vegetative and reproductive leaves in untreated and nitrogen deficient plants during remobilization process between beginning of flowering, pod filling and the end of pod filling.

overall_design: 24 dye-swap - time course,treated vs untreated comparison

first: Judith

last: Burstin

first: Karine

last: Gallardo

first: Sandrine

last: Balzergue

first: Marie-Laure

last: Martin-Magniette


title: Vegetative and reproductive leaves - 12plex-medicago-2012-06_GENOPEA3.2

summary: 12plex_medicago-2012-06 - vegetative and reproductive leaves - Transcriptome in leaves of Medicago truncatula plants during the remobilization process . Effect of a nitrogen deficiency on this process.Note that lower leaves correspond to vegetative leaves (FV) and upper leaves correspond to leaves of the reproductive part (FR). - Analysis of expression in Medicago truncatula reproductive leaves in untreated and nitrogen deficient plants during remobilization process between beginning of flowering, pod filling and the end of pod filling.

overall_design:
24 dye-swap - time course,treated vs untreated comparison

Veg: vegetative leaves
Rep: reproductive leaves

28: sample number

DFLO: Day of FLOwering
DFLO-14: 14 days after the Day of FLOwering
DFLO-27: 27 days after the Day of FLOwering

N+S+: nitrogen treatment
N-S+: nitrogen deficiency treatment
1: repetition n 1
2: repetition n 2
3: repetition n 3


title: Reprogram-Seq: A platform for single-cell combinatorial reprogramming [IV]


title: TNF response in promyelocytic and granulocytic forms of HL60/S4 cells

status: Public on Nov 15 2018

city: Auckland

first: Justin

middle: M.

last: O'Sullivan

address: 85 Park Road, Grafton

department: Liggins Institute

country: New Zealand

institute: University of Auckland

summary: The human promyelocytic cell line HL60/S4 can be differentiated into a granulocytic form with the addition of all-trans retinoic acid for 4 days. We investigated the conserved and differentiated responses to TNF in the granulocytic and promyelocytic forms of HL60/S4 cells.

overall_design: Promyeloytic and granulocytic HL60/S4 cells were treated with 16ng/ml TNF or equivalent volume of vehicle (water) in calcium supplemented growth media for two hours, then RNA was extracted with Trizol LS and the Qiagen Rneasy mini kit.

first: Elsie

last: Jacobson


title: Reprogram-Seq: A platform for single-cell combinatorial reprogramming [VIII]

overall_design: Focusing on the cardiac system, we performed Reprogram-Seq on P0 mouse heart cells to generate a reference transcriptomic map. Based on the reference map, we selected TF candidates and tests 1000s of TF cocktails for direct lineage conversion by scRNA-Seq.  This series includes uninfected, non-transformed MEFs.


title: Expression data for murine hepatocellular carcinoma in WT and Top1mt-/- mice

status: Public on Nov 14 2018

city: Bethesda

first: Yves

last: Pommier

state: MD

address: 37 Convent Drive

department: NCI/CCR

institute: NIH

summary:
Murine hepatocellular carcinoma of similar size were collected from WT and Top1mt-/- livers. Total RNA was isolated from tumors of 3 mice for each genotype.
We used RNA-seq to compare the genes differentially expressed between WT and Top1mt-/- murine HCC.

overall_design: Male mice received a diethlynitrosamine ip injection at day 14. At 8 weeks of age mice received twice weekly carbon tetrachloride for a duration of 14 weeks. Hepatocellular carcinoma were collected at 22 weeks.

first: Andrea

last: Baechler

first: Valentina

last: Factor

first: Diana

last: Becker

first: Jens

middle: U

last: Marquardt


title: Reprogram-Seq: A platform for single-cell combinatorial reprogramming [II]


title: HIV Nef transfected HEK293T cell culture and HIV mock transfected HEK293T cell culture [miRNA]

first: Michael

last: Bukrinsky

summary:
Purpose: Comparison of RNA-sequencing datasets obtained from exosomes of Nef-transfected and Mock-transfected HEK293T cells
Methods: Assessment of RNA content of exosomes produced by Nef-transfected HEK293T cells and and Mock-transfected HEK293T cells
Results: Differences in a set of microRNAs
Conclusions: Nef-transfection induces changes in the microRNA content of exosomes

first: Beda

last: Brichacek

first: David

last: Stern

first: Rebecca

last: Clement

first: Larisa

last: Dubrovsky


title: Reprogram-Seq: A platform for single-cell combinatorial reprogramming [I]

first: Gary

last: Hon

first: Nikhil

last: Munshi

first: Jialei

last: Duan


title: The alterations of gene expression in aorta from endothelial nitric oxide synthase (eNOS)-deficient mice

status: Public on Dec 15 2018

first: Bongkun

last: Choi

address: Olympic-ro 43-gil

department: Department of Biomedical Sciences

institute: Asan Medical Center, University of Ulsan College of Medicine

summary: The dysfunction of endothelial nitric oxide synthase may be involved in development of atherosclerosis; however, the underlying molecular and cellular mechanisms of atherosclerosis are poorly understood. Here, we investigated gene expressionsin relation to atherosclerosis using endothelial nitric oxide synthase (eNOS)-deficient mice.

overall_design: 3 samples of aorta from endothelial nitric oxide synthase (eNOS)-deficient mice were compared with 3 samples of aorta from age-matched normal mouse controls

first: Eun-Ju

last: Chang


title: Gene expression profiling of Huh-7 cells tranfected NC or DEPDC1 siRNA

status: Public on Nov 06 2018

city: Chongqing

first: Wubin

last: Guo

address: Friendship Road No. 1

department: Department of Gastrointestinal Surgery

country: China

institute: First Affiliated Hospital of Chongqing Medical University

summary:
Many reports shows that DEPDC1 is up-regulated in many tumor types and promotes cell proliferation and invasion, thereby functioning as an oncogene.
Hepatocellular Carcinoma has been shown to overexpress DEPDC1, and up-regulated DEPDC1 associates with poorer prognosis.In addition, we found that DEPDC1 knockdown significantly inhibited HCC cell proliferation, colony formation and migration. In order to investigate the mechanism of DEPDC1 in regulating HCC progression, we performed gene array analysis.

overall_design: Huh-7 cells were transfected with DEPDC1 siRNA or NC.  And expressed this profile by array.

first: Ziwei

last: Wang


title: Differentially expressed miRNAs and tRNA genes effect host homeostasis during highly pathogenic PRRSV infections in young pigs

status: Public on Oct 31 2018

city: Ames

first: Laura

last: Miller

state: Iowa

address: 1920 Dayton Ave

department: Virus and Prion Research Unit

institute: USDA-ARS-National Animal Disease Center

summary: Background: Porcine respiratory and reproductive syndrome virus (PRRSV) is a single stranded RNA virus member that infects pigs and causes losses to the commercial industry reaching upwards of a billion dollars annually in combined direct and indirect costs. The virus can be separated into etiologies that contain multiple heterologous low and highly pathogenic strains. Recently the United States has begun to see an increase in heterologous type 2 PRRSV strains of higher virulence (HP-PRRSV). The high pathogenicity of these strains can drastically alter host immune responses and the ability of the animal to maintain homeostasis. Because the loss of host homeostasis can denote underlying changes in gene and regulatory element expression profiles, the study aimed to examine the effect PRRSV infections has on miRNA and tRNA expression and the roles they play in host tolerance or susceptibility.   Results: Using transcriptomic analysis of whole blood taken from control and infected pigs at several timepoints (1, 3, 8 dpi), the analysis returned a total of 149 statistically significant (FDR ⫹ 0.15) miRNAs (n=89) and tRNAs (n=60) that were evaluated for possible pro and anti-viral effects. The tRNA differential expression increased in both magnitude and count as dpi increased, with no statistically significant expression at 1 dpi. The most abundant tRNA amino acid at 3 dpi was alanine , while glycine was the most abundant at 8 dpi. For the miRNAs, focus was put on upregulation that can inhibit gene expression. These results yielded candidates with potential anti and pro-viral actions such as Ssc-miR-125b, which is predicted to limit PRRSV viral levels, and Ssc-miR-145-5p shown to cause alternative macrophage priming. The results also showed that both the tRNA and miRNA displayed expression patterns  Conclusions: The results indicated that the HP-PRRSV infection effects host homeostasis at the epigenetic level through changes in miRNA and tRNA expression and their subsequent gene interactions, that target and influence the function of host immune, metabolic, and structural pathways.

overall_design: 24 9-week old pigs seperated into 2 treatment groups (HP-PRRSV and control) and 3 timepoints (1,3,8 dpi)

first: Damarius

last: Fleming


title: Stabilizing Heterochromatin by DGCR8 Alleviates Senescence and Osteoarthritis (RNA-seq)

status: Public on Oct 11 2018

city: Beijing

first: Zunpeng

last: Liu

address: Beichen West Road

department: Institute of Zoology, Chinese Academy of Sciences

institute: State Key Laboratory of Stem Cell and Reproductive Biology

summary: DiGeorge syndrome critical region 8 (DGCR8) is a critical component of the canonical microprocessor complex for microRNA biogenesis. However, the non-canonical functions of DGCR8 have not been studied. Here, we demonstrate that DGCR8 plays an important role in maintaining heterochromatin organization and preventing aging. An N-terminal-truncated version of DGCR8 (DR8dex2) accelerated senescence in human mesenchymal stem cells (hMSCs) independent of its miRNA-processing activity, which is mediated by its C-terminal domain. Further studies revealed that DGCR8 maintained heterochromatin organization by interacting with the nuclear envelope protein Lamin B1, and heterochromatin-associated proteins, KAP1 and HP1g expressing of any of these proteins, including DGCR8, reversed premature senescent phenotypes in DR8dex2 hMSCs. Finally, DGCR8 was downregulated in pathological and naturally aged hMSCs, whereas DGCR8 expressing alleviated hMSC aging and osteoarthritis in mice. Taken together, these analyses uncovered a novel, miRNA-independent role for DGCR8 in maintaining heterochromatin organization and preventing senescence. DGCR8 may therefore represent a new therapeutic target for alleviating human aging-related disorders.

overall_design: Transcriptome analysis of knee joints tissues upon the treatment of lentiviruses expressing Luc, DR8-WT, or DR8-mtDRBD in anterior cruciate ligament transection (ACLT) induced osteoarthritis (OA) mouse model.

first: Guanghui


title: The use of targeted next-generation sequencing to determine the regulatory function of TGF‐β1 in kidney fibrosis [H3K27me3 ChIP-seq]

status: Public on Oct 24 2018

city: shenzhen

first: Guanyu

last: Ji

state: GuangDong

address: 14th of middle jinxiu road

department: R&D

institute: GENEDOHEALTH

summary: Transforming growth factor‐beta (TGF‐β1) plays an important regulatory role in the progression of chronic kidney failure. Further, damage to kidney glomerular mesangial cells is central to the progression of diabetic nephropathy. The aim of this study was to explore the genetic associations between mRNA, microRNA, and epigenetics in mesangial cells in response to TGF‐β1. The regulatory effects of TGF‐β1 on mesangial cells were investigated at different molecular levels by treating mesangial cells with TGF‐β1 for 3 days followed by genome‐wide miRNA, RNA, MeDIP-seq, and H3K27Me3 expression profiling using next-generation sequencing (NGS). Each sample was designed with 3 repeat samples.

overall_design: Whole genome MeDIP-seq, miRNA, H3K27me3 and RNA-seq of mouse. This dataset includes the H3K27me3 ChIP-seq data.

first: Bo

last: Powell

first: Wenjun

first: Haroon

last: Naeem

first: Phillip

last: Kantharidis

first: Sharon

last: Ricardo


title: RNA-seq Analysis of the stem of Wild Type and HDT1 Transcriptomes II

status: Public on Oct 18 2018

city: beijing

first: zhang

middle: yong

last: zhuo

address: Beijing Forestry University

institute: Beijing Forestry University

summary: RNA-seq was performed to examine the differential expressed transcriptomes in hdt1 plants during stem development compare to wild type plants.

overall_design: To examine the differential expressed transcriptomes in hdt1 plants during stem development, the stem from hdt1 mutants and wild type plants at 35-days after flowering were collected for RNA-seq analysis. No replicates include in each samples.

first: Yongzhuo

last: Zhang


title: The use of targeted next-generation sequencing to determine the regulatory function of TGF‐β1 in kidney fibrosis [RNA-seq]

overall_design: Whole genome MeDIP-seq, miRNA, H3K27me3 and RNA-seq of mouse. This dataset includes the RNA-seq data.

first: David


title: The transcriptome comparison data between Saccharomyces cerevisiae cells in thi2p deletion strains  and the control strains BSGX001 in xylose consumption phase after glucose depleted in glucose-xylose co-fermentation.

status: Public on Oct 01 2018

city: Qingdao

first: Yu

last: Shen

state: Shandong

address: binhai road 72

department: Microbiology and Biotechnology Institute

institute: Shandong University

summary: The xylose fermentation rate of thi2p deletion strains was higher than the control strains BSGX001 during xylose consumption phase after glucose depleted in glucose-xylose co-fermentation (defined as GX stage).  BSGX001 was derived from the haploid strain CEN.PK113-5D, which is a  engineered strains that have the xylose-utilizing capacity. Here,we investigate the transcriptional differences between  BSGX001 (thi2Δ) and BSGX001 in GX stage.

overall_design: Samples were taken from the cells in GX stage. Each strain had triplicates. Then RNAseq-technology was employed to generate the transcriptome data.

first: Shan

last: Wei


title: Reprogram-Seq: A platform for single-cell combinatorial reprogramming [III]

first: Gary

last: Hon

first: Nikhil

last: Munshi

first: Jialei

last: Duan


title: Reprogram-Seq: A platform for single-cell combinatorial reprogramming

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

overall_design: Refer to individual Series


title: Array-based genome-wide transcriptome analysis of IL-4-treated RAW264 macrohage cell line

city: Sakai

first: OSAMU

last: ISHIBASHI

address: 1-1 Gakuen-cho, Naka-ku

department: Grad Sch Life & Environmental Sciences

country: Japan

institute: Osaka Prefecture University

summary: The role of G-protein-coupled receptors (GPCRs) in the macrophage polarization remains not well understood. In this study, we illuminate the role of Gpr137b, a GPCR expressed strongly in macrophages, in macrophage polarization. We used RAW264 as a mouse macrophage-like cell line and generated Gpr137b-knockout (KO) cell clones using the CRISPR/Cas9 genome editing system. The Gpr137b-KO and wildtype cells were the treated with interleukin-4 (IL-4) to induce M2 polarization, and their gene expression was analyzed using microarrays.

overall_design: Gpr137b-knockout and wildtype Raw264 cells treated with or without IL-4.

first: Zohir

last: Islam

first: Osamu

last: Ishibashi

first: Aya

last: Horikawa

first: Takashi

last: Inui


title: Whole head tissue of mated female w1118 Drosophila melanogaster exposed to 20% w/v coconut oil in solid medium high fat diet

status: Public on Jul 30 2018

city: Monroe

first: Matthew

middle: Edward

last: Talbert

state: LA

address: 700 University Avenue

department: Biology

institute: University of Louisiana at Monroe

summary: Obesity predisposes humans and other mammals to a range of life-threatening comorbidities, including type 2 diabetes and cardiovascular disease. Obesity and its associated dietary habits also aggravate neural pathologies, such as Alzheimer’s disease, but this class of comorbidity is less understood. When Drosophila melanogaster (flies) are exposed to high fat diet (HFD) by supplementing a standard cornmeal-sucrose-yeast medium with coconut oil, they adopt an obese phenotype of decreased lifespan, increased triglyceride storage, and hindered climbing ability. The latter development is an indicator of neurological decline in flies. Our objective was to establish the obesity-like phenotype in Drosophila and identify a correlation, if any, between obesity and neurological decline in flies through behavioral and expression microarray. We found that mated female w1118 flies exposed to HFD maintained an obese phenotype throughout adult life with onset at seven days, evidenced by increased triglyceride stores, diminished life span, and impeded climbing ability. Analysis of gene expression of the fly head via microarray and qRT-PCR validation revealed functionally relevant genes with significant fold changes. These genes had functions including in memory, metabolism, olfaction, mitosis, cell signaling, and motor function. An Aversive Phototaxis Suppression assay indicated short term memory impairment as a result of HFD. Meanwhile, there was a decline but no significant difference in odor-seeking ability with HFD. Overall, our results point to the suitability of Drosophila melanogaster to investigate connections between diet-induced obesity and nervous or neurobehavioral pathology, and to the existence of such a dynamic in an evolutionarily broad range of organisms.

overall_design: 3 biological replicates of mated females of genotype w1118 exposed to a high fat diet vs. 3 biological replicates of mated females of genotype w1118 exposed to a normal diet (which lacks the source of dietary fat). Mated females were synchronously mated with isogenic males of the same background across diet group. Mated females were exposed to their respective diets for 7 days. Heads were removed by snap freezing and vibration. Total RNA was extracted. Gene expression levels in the high fat diet relative to the normal diet were obtained by Affymetrix 2.0 Genome Arrays and compared.

first: Osvaldo

last: Rivera


title: Enhancers contribute to Hdac3-regulated RNA polymerase recruitment to the promoter-proximal region [PRO-seq]

status: Public on Jul 31 2018

city: Nashville

first: Jing

last: Wang

state: TN

address: 2220 Pierce Avenue

institute: Vanderbilt University Medical Center

summary: HDAC3 is known to repress gene transcription, however, whether it directly regulates transcription initiation or elongation is still under debate. We generated a PRO-seq dataset derived from WT and Hdac3 KO mouse livers and used NRSA to explore the functional role of Hdac3 in transcriptional regulation. We reported that the deletion of Hdac3 caused a global accumulation of transcription in promoter-proximal regions and enhancer regions.

overall_design: WT and Hdac3-KO mice liver were extracted on day 14. PRO-seq was performed to study transcriptional changes. Two biological replicates were included for each conditon.

first: Scott

last: Hiebert

first: Yue

last: Zhao

first: Qi

last: Liu


title: Expression data for T24 bladder cancer cell line - scrambled, SOX4-KD and SOX4 overexpression

status: Public on Aug 16 2018

city: Atlanta

first: Josue

last: Moran

state: GA

address: 615 Michael Street

institute: Emory University

summary:
We knocked down SOX4 in T24 cell and created 3 cell lines: T24-scrambled, T24-SOX4-knockdown and T24-SOX4-rescue and compared gene expression changes
SOX4 is a developmental transcription factor that is overexpressed in as many as 23% of bladder cancer patients, but the role of SOX4 in bladder cancer tumorigenesis is not well understood. Given SOX4’s many roles in embryonic development and context-dependent regulation of gene expression, we sought to understand SOX4’s contribution to bladder cancer and to elucidate SOX4 regulated genes that might contribute to tumorigenesis. We employed a CRISPR interference (CRISPRi) method to transcriptionally repress SOX4 expression in T24 bladder cancer cell lines, rescued these cell lines with lentivirally expressed SOX4, and performed whole genome expression profiling. SOX4 knockdown cells exhibited decreased invasive capabilities but no changes in migration or proliferation, while rescue with SOX4 lentiviral vector restored the invasive phenotype. Gene expression profiling revealed 173 high confidence SOX4 regulated genes

overall_design: We created scrambled sgRNAk SOX4-sgRNA and transduced T24 bladder cell lines stably expressing Krab-dCas9-mCherry. We then stably re-expressed SOX4 into the T24-SOX4-sgRNA cells using a YFP-HA-SOX4 lentiviral vector

first: Carlos

last: Moreno


title: Expression analysis of genes modulated after knock-down of lncRNA CHROME.

status: Public on Sep 20 2018

city: New York City

first: Coen

last: van Solingen

state: New York

address: 435 E30th street, Science Building 723T, Science Building 723T

department: Cardiology/Medicine

institute: NYU School of Medicine

summary: Thousands of long non-coding RNAs (lncRNAs) have been identified in the human genome, many of which are not conserved in lower mammals. The majority of these lncRNAs remain functionally uncharacterized and may have important implications in human physiology and disease. Here, we identify a primate-specific lncRNA, CHROME, which is increased in the plasma and atherosclerotic plaques of individuals with coronary artery disease compared to healthy controls. Using a loss-of-function approach, we show that CHROME functions as a competing endogenous RNA of microRNAs  and regulates the concentration and biological functions of target genes.

overall_design: We used three replicate samples of HEPG2 cells that were treated with shRNA for CHROME compated to three replicate control samples.

first: Elizabeth

last: Hennessy

first: Kathryn

last: Moore


title: Targeted, long-read RNA sequencing of non-coding genomic regions associated with neuropsychiatric functions.

status: Public on Aug 07 2018

city: Darlinghurst

first: Simon

middle: Andrew

last: Hardwick

state: NSW

address: 384 Victoria Street

institute: Garvan Institute of Medical Research

summary: The human brain is one of the last frontiers of biomedical research. Genome-wide association studies (GWAS) have succeeded in identifying thousands of haplotype blocks associated with a range of neuropsychiatric traits, including disorders such as schizophrenia, Alzheimer’s and Parkinson’s disease. However, the majority of single nucleotide polymorphisms (SNPs) that mark these haplotype blocks fall within non-coding regions of the genome, hindering their functional validation. While some of these GWAS loci may contain cis-acting regulatory DNA elements such as enhancers, we hypothesized that many are also transcribed into non-coding RNAs that are missing from publicly available transcriptome annotations. Here, we use targeted RNA capture (‘RNA CaptureSeq’) in combination with nanopore long-read cDNA sequencing to transcriptionally profile 1,023 haplotype blocks across the genome containing non-coding GWAS SNPs associated with neuropsychiatric traits, using post-mortem human brain tissue from three neurologically healthy donors. We find that the majority (62%) of targeted haplotype blocks, including 13% of intergenic blocks, are transcribed into novel, multi-exonic RNAs, most of which are not yet recorded in GENCODE annotations. We validated our findings with short-read RNA-seq, providing orthogonal confirmation of novel splice junctions and enabling a quantitative assessment of the long-read assemblies. Many novel transcripts are supported by independent evidence of transcription including cap analysis of gene expression (CAGE) data and epigenetic marks, and some show signs of potential functional roles. We present these transcriptomes as a preliminary atlas of non-coding transcription in human brain that can be used to connect neurological phenotypes with gene expression.

overall_design: Targeted RNA capture of GWAS haplotype blocks associated with neuropsychiatric traits from four human brain regions (caudate, prefrontal cortex, primary visual cortex, superior colliculus). Following capture, samples were transcriptionally profiled using both long-read (Oxford Nanopore Technologies' PromethION) and short-read (Illumina's HiSeq 2500) RNA sequencing.

middle: A

first: John

last: Mattick


title: Methyl-CpG-binding domain 9 (MBD9) is required for H2A.Z incorporation into chromatin at a subset of H2A.Z-enriched regions in the Arabidopsis genome

status: Public on Aug 31 2018

first: Roger

middle: B

last: Deal

address: 1510 Clifton Rd NE

summary: The SWR1 chromatin remodeling complex, which deposits the histone variant H2A.Z into nucleosomes, has been characterized in yeast and animals but had not been purified from plants. We used the conserved SWR1 subunit ACTIN RELATED PROTEIN 6 (ARP6) as bait in tandem affinity purification experiments to isolate associated proteins from Arabidopsis thaliana. We identified all 11 subunits found in yeast SWR1 and the homologous mammalian SRCAP complexes, demonstrating that this complex is conserved in plants. We also identified several additional proteins not previously associated with SWR1, including Methyl-CpG-BINDING DOMAIN 9 (MBD9). Since mbd9 mutant plants were phenotypically similar to arp6 mutants, we further explored a potential role for MBD9 in H2A.Z deposition. We found that MBD9 is required for proper H2A.Z incorporation at thousands of discrete sites, which represent a subset of the regions normally enriched with H2A.Z. Genetic analyses showed that arp6;mbd9 double mutants have far more severe phenotypes than either single mutant. In conjunction with the finding that MBD9 does not appear to be a core subunit of the Arabidopsis SWR1 complex, this suggests that MBD9 also has important roles beyond H2A.Z deposition. Our data establish the SWR1 complex as being conserved across eukaryotes and also provide new insights into the mechanisms that target H2A.Z to chromatin.

overall_design: ChIP-seq was performed in biological triplicate on 6-day-old WT, arp6-1, and mbd9-1 seedlings using antibodies against histone H2A.Z (Deal et al. [2007] Plant Cell 19) or Acetylated histone H4 (Millipore cat no. 06-866)


title: Gene expression evaluation of urinary bladder in a mouse model for two-week treatment of 50 ppm arsenic contained in the drinking water

city: Chiayi

first: Shou-Tsung

address: No. 300, Syuefu Rd.

country: Taiwan

institute: National Chiayi University

summary: The aim of this cDNA array study is to search for advanced markers related to the pathogenesis of arsenic-induced urinary bladder tumor. The result revealed a number of gene expressions involved in carcinogenic progression of mice urinary bladder.

overall_design: Each two female C57BL/6 mice were distributed into the control (fed with RO water) and arsenic-treated (fed with 50 ppm arsenic-contained RO water) groups for two weeks. Subsequently, their urinary bladders were used to acquire expression profiles of 26,423 unique genes, leading to successful determination of the differentially expressed genes and pathways involved in arsenic-induced carcinogenesis.

first: Cheng-Huang

last: Shen

first: Shou-Chieh

first: Yi-Wen


title: Activation of Wnt signaling promotes olaparib resistant ovarian cancer.

status: Public on Jul 28 2018

city: Cleveland

first: Hyunmin

last: Kim

state: Ohio

address: 10900 Euclid Ave.

department: Department of Genetics and Genome Sciences

institute: Case Western Reserve University

summary: Sequencing of olaparib-resistant PEO1 derivatives (C4, C5, C10 and C18) and parental PEO1 (P1 and P2) cells was performed in order to determine mechanisms of acquired resistance in the resistant cell lines. PEO1 parental cell lines were authenticated prior to sequencing. PEO1 parental were confirmed to be BRCA2-mutated (5139C>G). Olaparib PEO1 resistant cells were generated through a step-wise escalation of olaparib (10nM to 8uM olaparib). In olaparib resistant lines an increase canonical Wnt signaling and loss of of non-canonical Wnt signaling was observed.

overall_design: Sequencing of olaparib-resistant PEO1 derivatives (C4, C5, C10, and C18) and parental PEO1 cells was performed in order to determine mecahnisms of acquired resistance.

first: Benjamin

middle: G

last: Bitler

first: Aik-Choon

last: Tan


title: Rad9/53BP1 controls the initiation and the elongation of DNA replication in budding yeast

status: Public on Aug 27 2018

city: Montpellier

first: romain

last: forey

address: 142 avenue de la Cardonille

institute: IGH

type: Genome binding/occupancy profiling by genome tiling array

summary: In budding yeast, DNA lesions and stalled replication forks are sensed by the apical checkpoint kinase Mec1/ATR, which leads to the downstream activation of the effector kinase Rad53/CHK1. This activation depends on Rad9 and Mrc1, two checkpoint mediators that integrate the nature of the challenge in different phases of the cell cycle. Rad9 mediates the activation of the DNA damage checkpoint throughout the cell cycle, while the function of Mrc1 is restricted to the S phase of the cell cycle, when it travels with the replication fork and activates the DNA replication checkpoint in response to a variety of replication impediments. In this scenario, the role of Rad9 in S phase has been largely disregarded since the discovery of Mrc1, because Rad9 is dispensable for the timely activation of Rad53 in response to the drug hydroxyurea, which halts forks, and is only recruited to those stalled forks when Mrc1 is absent. Thus, Rad9 is simply believed to act as a backup pathway for Mrc1 during replication. We have re-evaluated the role of Rad9 when DNA damage arises during replication and characterized its functional interplay with Mrc1. To this end, we have used genome-wide approaches, single-molecule analysis, pulsed-field and 2D gel electrophoresis, as well as a careful combination of different replication-challenging drugs. We have found that both Mrc1 and Rad9 play distinct but complementary functions in the replication stress response during S phase, for they coordinate the early and late functions of Rad53, respectively. While Mrc1 is responsible for the fast activation of Rad53 in response to fork-halting drugs in order to repress late origins, Rad9 maintains Rad53 in an active state during prolonged fork arrest and is necessary to sustain this response for long periods. Remarkably, we also have found that Rad9 possesses the unprecedented activity of slowing down replication fork progression in response to DNA damage. This work thus restores the legitimate role of Rad9 as a central actor in the maintenance of genome integrity during replication. This has important implications for our understanding of the management of the checkpoint during perturbed replication in human cells, for Rad9 has three orthologues, 53BP1, BRCA1 and MDC1, whose contribution to this aspect of genome integrity remains largely unexplored.

overall_design: microarray-based analysis of origin activity in S. cerevisiae cells exposed to MMS

first: Julien

last: Bacal

first: María

last: Moriel-Carretero

first: Armelle

last: Lengronne

first: Philippe

last: Pasero


title: Differential  gene expression in the stellate ganglia of 16 week wistar and spontaneously hypertensive rat samples

status: Public on Jun 21 2018

city: Oxford

first: David

last: Paterson

address: Parks Road

department: Department of Physiology, Anatomy and Genetics

country: United Kingdom

institute: University of Oxford

summary: Hypertension remains a poorly understood condition, and the understanding of the sympathetic nervous systems role in this disease remains even more limited. In this study, RNA-sequencing is used to identify transcriptomal differences in the sympathetic stellate ganglia between the 16-week-old normotensive wistar strain and the spontaneously hypertensive rat strain.This dataset should allow for further molecular characterisation of hypertensive changes in a cardiac-innervating sympathetic ganglion.

overall_design: Comparison of normotensive and hypertensive rat stellate ganglia. 4 biological replicates for both 16 week wistar and SHR stellate ganglia samples were contrasted

first: Harvey

last: Davis

first: Emma

last: Bardsley


title: The use of targeted next-generation sequencing to determine the regulatory function of TGF‐β1 in kidney fibrosis [miRNA-seq]

first: Guanyu

last: Ji

overall_design: Whole genome MeDIP-seq, miRNA, H3K27me3 and RNA-seq of mouse. This dataset includes the miRNA-seq data.

first: Bo

last: Wang

last: Powell

first: Wenjun

first: Haroon

last: Naeem

first: Phillip

last: Kantharidis

first: Sharon

last: Ricardo


title: Acinetobacter baumannii transcriptome-level alterations upon omega76 exposure

status: Public on Jun 26 2018

city: Bangalore

first: Deepesh

last: Nagarajan

state: Karnataka

address: FB-04, B-wing, Department of Biochemistry, New Biology Building, IISc

department: Department of Biochemistry

country: India

institute: Indian Institute of Science

summary: A. baumannii was incubated with differing concentrations of omega76 (MBC=4ug/ml).

overall_design: A. baumannii was incubated with differing concentrations of omega76 (MBC=4ug/ml): 0.1X, 0.25X, and 0.5X MBC. 3 treated samples (2 technical replicates each) and 1 untreated samples (2 technical replicates) were used in this study. All cultures were grown in 10 ml LB broth at 37C/180rpm for 12 hours before flash-freezing and RNA extraction.

first: Sathyabaarathi

last: Ravichandran

first: Nagasuma

last: Chandra


title: The endoribonuclease YbeY is linked to proper cellular morphology and virulence in Brucella abortus

status: Public on Apr 18 2018

city: Rochester

first: Paul

last: Dunman

state: NY

address: 601 Elmwood Avenue

department: Microbiology and Immunology

institute: University of Rochester

summary:
The ybeY locus is hypothesized to produce an endoribonuclease, that is expressed during late exponential phase growth and regulate transcript titers.
We used custom-made Affymetrix B. abortus strain 2308 derived GeneChips to compare the gene expression properties of wild type and isogenic ybeY mutant cells.

overall_design: B. abortus strain 2308 or ybeY mutant cells were grown to late exponential phase growth, total bacterial RNA was isolated and subjected to GeneChip hybridization and analysis.  We sought to determine the regulatory effects of the ybeY RNA specie(s).

first: Clayton

last: Caswell


title: Effect of H3.3 depletion on NuRD subunit binding and GE

status: Public on Sep 03 2018

city: Bethesda

first: Keji

last: Zhao

address: 9000 Rockville Pike

department: Systems Biology Center

institute: NHLBI,NIH

summary: Genome-wide mapping of NuRD subunits, H3.3, and histone modifications in WT and H3.3 KD 3T3 MEFs. RNAseq data from WT and H3.3 KD cells.

overall_design: ChIP, Sequential ChIP and RNA-seq experiments

first: Zuozhou

last: Chen

first: Jungfang

last: Zhang

first: Daniel

last: Kraushaar


title: Parental high dietary arachidonic acid levels modulated the hepatic transcriptome of adult zebrafish (Danio rerio) progeny

status: Public on Oct 06 2018

city: Bergen

first: Kai

middle: Kristoffer

last: Lie

state: Hordaland

address: Pobox 2029 Nordnes

department: Feed Safety

country: Norway

institute: Institute of Marine research

summary: Disproportionate high intake of n-6 polyunsaturated fatty acids (PUFAs) in the diet is considered as a major human health concern. The present study examines changes in the hepatic gene expression pattern of adult male zebrafish progeny associated with high levels of the n-6 PUFA arachidonic acid (ARA) in the parental diet. The parental generation (F0) was fed a diet which was either low (control) or high in ARA (high ARA). Progenies of both groups (F1) were given the control diet. No differences in body weight were found between the diet groups within adult stages of either F0 or F1 generation. Few differentially expressed genes were observed between the two dietary groups in the F0 in contrast to the F1 generation. Nonetheless, several links were found between the previous metabolic analysis of the parental fish and the gene expression analysis in their adult progeny. Main gene expression differences in the progeny were observed related to lipid and retinoid metabolism by PPAR/RXR playing a central role in mediating changes to lipid and long-chain fatty acid metabolism. The enrichment of genes involved in β-oxidation observed in the progeny, corresponded to the increase in peroxisomal β-oxidative degradation of long-chain fatty acids in the parental fish metabolomics data. Similar links between the F0 and F1 generation were identified for the methionine cycle and transsulfuration pathway in the high ARA group. In addition, estrogen signalling was found to be affected by parental high dietary ARA levels, where gene expression was opposite directed in F1 compared to F0. This study shows that the dietary n-3/n-6 PUFA ratio can alter gene expression patterns in the adult progeny. Whether the effect is mediated by permanent epigenetic mechanisms regulating gene expression in developing gametes needs to be further investigated.

overall_design: In the present study, we fed parental zebrafish either a diet low in arachidonic acid (ARA) (control diet) or a diet high in ARA, whereas offspring from both dietary groups were fed the control diet until adulthood. We demonstrate that parental high dietary ARA levels can impact transcriptomic patterns in mature offspring. 6 fish from each group and each generation were sampled and sequenced, in total 24 fish was analyzed

first: Anne-Catrin

last: Adam

first: Kaja

middle: H

last: Skjærven

last: Whatmore

first: Mari

last: Moren

middle: K


title: Identification of intermediate transcriptome states and synergistic effects of Isl1 in Atoh1-mediated cochlear hair cell conversion

status: Public on Jul 23 2018

city: Memphis

first: David

last: Finkelstein

address: 332 N. Lauderdale St.

department: Computational Biology

institute: St Jude Children's Research Hospital

summary: Ectopic expression of Atoh1 in non-sensory supporting cells (SCs) in mouse cochleae induces their conversion to hair cells (HCs) in vivo. cHCs in multiple intermediate states of the conversion process that most closely resembled neonatal differentiating HCs, but differed from the progenitors. We further identified 52 transcription factors that are differentially expressed in cHCs, SCs, and mature HCs and confirmed that Isl1 synergistically enhanced the efficiency of Atoh1-mediated HC conversion in cochlear explants. Our results demonstrate that direct HC conversion from SCs in vivo follows a different path from normal development and requires multiple factors for maximum efficiency and completion.

overall_design: Atoh1-HA was ectopically expressed in mouse supporting cells to convert into hair cells. The converted hair cells were labeled with tdTomato as well as α9 AChR-EGFP. Mouse supporting cells were labeled with tdTomato. Mouse outer hair cells were labeled with prestin-YFP using knockin strategy. Mouse inner hair cells were labeled with tdTomato.

first: Tetsuji

last: Yamashita

first: Fei

last: Zheng

first: Zoe

last: Kellard

first: Ken

last: Sugino

first: Charles

last: Gawad

first: Jian

last: Zuo


title: Single Cell RNA sequencing of Adult Human Breast Epithelial Cells [C1_Individual_3]

status: Public on Apr 17 2018

city: Irvine

last: Kessenbrock

state: CA

address: 839 Health Sciences Road

department: Biological Chemistry

institute: UC Irvine

summary: Breast cancer arises from breast epithelial cells that acquire genetic alterations leading to subsequent loss of tissue homeostasis. Several distinct epithelial subpopulations have been proposed, but complete understanding of the spectrum of heterogeneity and differentiation hierarchy in the human breast remains elusive. Here, we used single-cell mRNA sequencing (scRNAseq) to profile the transcriptomes of 25,790 primary human breast epithelial cells isolated from reduction mammoplasties of seven individuals. Unbiased clustering analysis reveals the existence of three distinct epithelial cell populations, one basal and two luminal cell types, which we identify as secretory L1- and hormone-responsive L2-type cells. Pseudotemporal reconstruction of differentiation trajectories produc one continuous lineage hierarchy that closely connects the basal lineage to the two differentiated luminal branches. Our comprehensive cell atlas provides novel insights into cellular blueprint of the human breast epithelium and will form the foundation to understand how the system goes awry during breast cancer.

overall_design: Microfluidics-enabled Single Cell RNA sequencing libraries were generated for 3 adult human women using the Fluidigm C1 and sequenced on the Illumina HighSeq 2500

first: Quy

last: Nguyen

first: Nicholas

last: Pervolarakis


title: Expression data from mouse Malignant Mesothelioma  (MM) tumors and normal tissues

status: Public on Nov 01 2018

city: Honolulu

first: Pietro

last: Bertino

state: HI

address: 651 Ilalo St., BSB222

department: Cell and Molecular Biology

institute: University of Hawaii

summary:
With the goal of designing a universal vaccine that can be used to target MM in mice, we analyzed expression of all the mRNA produced by different MM tumors and normal tissues.
Our hypothesis was that antigens highly expressed in MM tumors can be used as target for vaccination, as long the expression of those antigens is extremely low in all normal mouse tissues.

overall_design: mRNA was analyzed in two tumors originated from two different MM cell lines injected in BALB/c mice, CRH5 and EOH6. These cells were previously generated by injecting asbestos or erionite in the same strain of mice. For the normal tissues, we have analyzed antigen expression in lungs and kidneys isolated from naïve BALB/c mice.

first: Mark

last: Menor

first: Vedbar

middle: S

last: Khadka

first: Youping

last: Deng


title: Single Cell RNA sequencing of Adult Human Breast Epithelial Cells [Individual 4..7]

first: Kai

overall_design: Droplet Based Single Cell RNA sequencing libraries were generated for 4 adult human women using the 10x Genomics Chromium Platform and sequenced on the Illumina HighSeq 4000


title: Single Cell RNA sequencing of Adult Human Breast Epithelial Cells

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

overall_design: Refer to individual Series


title: Stabilizing Heterochromatin by DGCR8 Alleviates Senescence and Osteoarthritis (ChIP-Seq)

city: Beijing

first: Zunpeng

last: Liu

address: Beichen West Road

institute: State Key Laboratory of Stem Cell and Reproductive Biology

summary: DiGeorge syndrome critical region 8 (DGCR8) is a critical component of the canonical microprocessor complex for microRNA biogenesis. However, the non-canonical functions of DGCR8 have not been studied. Here, we demonstrate that DGCR8 plays an important role in maintaining heterochromatin organization and preventing aging. An N-terminal-truncated version of DGCR8 (DR8dex2) accelerated senescence in human mesenchymal stem cells (hMSCs) independent of its miRNA-processing activity, which is mediated by its C-terminal domain. Further studies revealed that DGCR8 maintained heterochromatin organization by interacting with the nuclear envelope protein Lamin B1, and heterochromatin-associated proteins, KAP1 and HP1gamma Overexpression of any of these proteins, including DGCR8, reversed premature senescent phenotypes in DR8dex2 hMSCs. Finally, DGCR8 was downregulated in pathological and naturally aged hMSCs, whereas DGCR8 overexpression alleviated hMSC aging and osteoarthritis in mice. Taken together, these analyses uncovered a novel, miRNA-independent role for DGCR8 in maintaining heterochromatin organization and preventing senescence. DGCR8 may therefore represent a new therapeutic target for alleviating human aging-related disorders.

overall_design: H3K9me3 ChIP-seq profiles of DR8dex2 and WT hMSCs

first: Guanghui


title: Single Cell RNA sequencing of Adult Human Breast Epithelial Cells [C1_Individual_2]


title: Molecular Signatures of retrotransposon Ty3 insertion into the RNA Polymerase III transcription initiation site (Rpc34)

status: Public on Apr 15 2018

city: IRVINE

first: James

last: Yu

state: ca

address: Med Sci D262

institute: University of California Irvine

summary: The Gypsy-like element Ty3 inserts proximal to the transcription start sites of genes transcribed by RNA polymerase 3 (RNAP3).  In this study, a random-barcode Ty3 was used to count Ty3 insertions at specific sites.  Surprisingly, saturation transposition of the yeast genome showed that tDNAs even within isoacceptor families are targeted at widely different frequencies.   Ectopic expression of Ty3 integrase showed that it localizes to integration targets independent of other Ty3 proteins.  Binding of integrase, RNAP3 and factor Brf1 at individual targets did not differ to the same extent as integration.  Metadata analysis showed that histone modification H3K4Ac correlated positively with insertion frequency. Targeting frequency could be reconstituted on high copy plasmids containing only 75 bp of 5’ flanking sequence plus the tDNA target.  Weighting of insertions according to frequency identified an A/T-rich sequence followed by C as the site of gene-proximal strand transfer.  This site lies immediately adjacent to the adenines of the RNAP3 transcription start site motif (CAA).   Recent structures of DNA in RNAP3 initiation complexes show that in the initiation complex the transcription start site is sharply bent at the position adjacent to the gene-proximal Ty3 strand transfer. We propose that Ty3 integration occurs in two steps: in the first, host Brf1 engages integrase; in the second, integrase exploits YR flexibility, and that together, these steps determine the wide range of Ty3 targeting frequencies.

overall_design: In the S. cerevisiae strain BY4741, the genomic RPC34 gene was modified to express a N-terminal 3X FLAG tagged protein for ChIP-seq. The native RPC34 gene protmoter was retained to maintain wild type gene expression after modification.

first: Kurt

last: Patterson

first: Suzanne

last: Sandmeyer


title: Single Cell RNA sequencing of Adult Human Breast Epithelial Cells [C1_Individual_1]


title: Molecular Signatures of retrotransposon Ty3 insertion into the RNA Polymerase III transcription initiation site (Integrase)

overall_design: The Ty3 Integrase was cloned into Estradiol-inducible plasmid pKP3915 with a N-terminal 3X FLAG sequence to make plasmid pKP4010. For ChIP-seq, pKP4010 or pKP3915 (empty vector control) were transformed into the S. cerevisiae strain BY4741 and selected for on synthetic media lacking Uracil. Prior to harvesting cells for immuoprecipitation, 10 µM β-estradiol was added to cultures to induce integrase expression for approximately six hours.


title: Molecular Signatures of retrotransposon Ty3 insertion into the RNA Polymerase III transcription initiation site


title: Molecular Signatures of retrotransposon Ty3 insertion into the RNA Polymerase III transcription initiation site (Brf1)

overall_design: In the S. cerevisiae strain BY4741, the genomic BRF1 gene was modified to express a N-terminal 3X FLAG tagged protein for ChIP-seq. The native BRF1 gene protmoter was retained to maintain wild type gene expression after modification.  As a negetive control, untagged wild type BY4741 culture was grown and treated identically to Brf1 and Rpc34 ChIP protocols.


title: SCML2 establishes germline-specific bivalent domains.

status: Public on Apr 12 2018

city: Cincinnati

first: Satoshi

last: Namekawa

address: 3333 Burnet Ave

institute: Cincinnati Children's Hospital Medical Center

summary: Bivalent domains marked with repressive H3K27me3 and activating H3K4me2/3 are a molecular signature of totipotency in stem cells and development. While bivalent domains are retained throughout the germline to recover totipotency in the next generation, the mechanisms establishing bivalent domains remains unknown. Here we demonstrate that a germline-specific Polycomb protein, SCML2, binds to chromatin containing hypomethylated DNA to induce H3K27me3, thereby initiating the establishment of germline-specific bivalent domains in mice. SCML2 regulates two distinct classes of autosomal bivalent domains, the first are maintained constitutively through spermatogenesis (Class I), and the second are specifically established during meiosis (Class II). In postmeiotic spermatids, the loss of H3K27me3 leads to an increase of H3K4me2/3 on bivalent domains and disorganization of pericentromic heterochromatin. We propose that SCML2 regulates dynamic bivalent domains in the germline as a molecular imprint to recover totipotency after fertilization.

overall_design: ChIP-seq, ATAC-seq and RNA-seq analyses using wild-type and Scml2-KO spermatogenic cells

first: So

last: Maezawa

first: Kazuteru

last: Hasegawa

first: Andrey

last: Kartashov

first: Artem

last: Barski


title: Transcriptomic study of couch grass rhizomes exposed to dehydration

city: Praha 6 - Ruzyně

first: Pavel

last: Svoboda

state: Česká republika

address: Drnovská 507/73

department: Molecular Genetics

country: Czech Republic

institute: Crop Research Institute in Prague

summary: This study explored the transcriptomic response of couch grass rhizome meristhematic region exposed to mild, medium and severe drought. The couch grass stress response was compared with the response of two contrasting barley cultivars and the specificities and commonalities in transcriptomic stress response of both species were identified.

overall_design: RNA was isolated from both non-treated couch grass rhizomes and rhizomes exposed to 2 h, 4.5 h and 8 h at 28°C, chosen to simulate an episode of, mild, medium and severe dehydration. RNA was extracted from three rhizome segments per treatment and each sample was represented by three independent replicates. The RNA samples were hybridized to an Affymetrix 22K Barley1 GeneChip Genome Array.

first: Anna

last: Janská

first: Vojtěch

last: Spiwok

first: Vladislav

last: Kučera

first: Jaroslava

last: Ovesná


title: Stabilizing Heterochromatin by DGCR8 Alleviates Senescence and Osteoarthritis

status: Public on Apr 14 2018

summary: DiGeorge syndrome critical region 8 (DGCR8) is a critical component of the canonical microprocessor complex for microRNA biogenesis. However, the non-canonical functions of DGCR8 have not been studied. Here, we demonstrate that DGCR8 plays an important role in maintaining heterochromatin organization and preventing aging. An N-terminal-truncated version of DGCR8 (DR8dex2) accelerated senescence in human mesenchymal stem cells (hMSCs) independent of its miRNA-processing activity, which is mediated by its C-terminal domain. Further studies revealed that DGCR8 maintained heterochromatin organization by interacting with the nuclear envelope protein Lamin B1, and heterochromatin-associated proteins, KAP1 and HP1gamma.  Overexpression of any of these proteins, including DGCR8, reversed premature senescent phenotypes in DR8dex2 hMSCs. Finally, DGCR8 was downregulated in pathological and naturally aged hMSCs, whereas DGCR8 overexpression alleviated hMSC aging and osteoarthritis in mice. Taken together, these analyses uncovered a novel, miRNA-independent role for DGCR8 in maintaining heterochromatin organization and preventing senescence. DGCR8 may therefore represent a new therapeutic target for alleviating human aging-related disorders.

overall_design: Transcriptional profiles of DR8dex2 and WT hMSCs


title: Tumor immune evasion arises through loss of TNF sensitivity [MC38]

status: Public on Apr 01 2018

city: Melbourne

first: Stephin

middle: J

last: Vervoort

address: 305 Grattan Street

institute: Peter MacCallum Cancer Centre

summary: Investigation of the transcriptional response to TNF and Interferon gamma or T cells

overall_design: MC38 cell line treated with TNF, IFNG, TNF + IFNG OR OTI T CELLS FOR 6 HOURS. OT1 cells were either treated with IgG or PD1.

first: Conor

last: Kearney


title: Muscle-specific gene Zmynd17/Mss51 controls mitochondrial quality and whole body metabolism

status: Public on Mar 01 2018

city: Tsukuba

first: Ryo

last: Fujita

state: Ibaraki

department: Transborder Medical Research Center

institute: University of Tsukuba

summary: Transcriptional profiling of mouse plantaris muscles comparing wild type mouse with Zmynd17/Mss51 knockout mouse

overall_design: Wild type vs Zmynd17/Mss51 KO (plantris muscles)

first: Yusuke

last: Ono


title: Multiwalled carbon nanotube-induced pulmonary inflammatory and fibrotic responses and genomic changes following aspiration exposure in mice: A 1-year postexposure study.

status: Public on Apr 06 2018

city: Morgatown

first: Nancy

middle: Lan

last: Guo

state: WV

address: 2816 Health Sciences Center

department: Occupational and Environmental Health Sciences

institute: West Virginia University

summary: Pulmonary exposure to multiwalled carbon nanotubes (MWCNT) induces an inflammatory and rapid fibrotic response, although the long-term signaling mechanisms are unknown. The aim of this study was to examine the effects of 1, 10, 40, or 80 µg MWCNT administered by pharyngeal aspiration on bronchoalveolar lavage (BAL) fluid for polymorphonuclear cell (PMN) infiltration, lactate dehydrogenase (LDH) activity, and lung histopathology for inflammatory and fibrotic responses in mouse lungs 1 mo, 6 mo, and 1 yr postexposure. Further, a 120-µg crocidolite asbestos group was incorporated as a positive control for comparative purposes. Results showed that MWCNT increased BAL fluid LDH activity and PMN infiltration in a dose-dependent manner at all three postexposure times. Asbestos exposure elevated LDH activity at all 3 postexposure times and PMN infiltration at 1 mo and 6 mo postexposure. Pathological changes in the lung, the presence of MWCNT or asbestos, and fibrosis were noted at 40 and 80 µg MWCNT and in asbestos-exposed mice at 1 yr postexposure. To determine potential signaling pathways involved with MWCNT-associated pathological changes in comparison to asbestos, up- and down-regulated gene expression was determined in lung tissue at 1 yr postexposure. Exposure to MWCNT tended to favor those pathways involved in immune responses, specifically T-cell responses, whereas exposure to asbestos tended to favor pathways involved in oxygen species production, electron transport, and cancer. Data indicate that MWCNT are biopersistent in the lung and induce inflammatory and fibrotic pathological alterations similar to those of crocidolite asbestos, but may reach these endpoints by different mechanisms.

overall_design: We evaluated bronchoalveolar lavage (BAL) fluid for polymorphonuclear cell (PMN) infiltration and lactate dehydrogenase (LDH) activity, and lung histopathology for inflammatory and fibrotic responses in mouse lungs after 1 year post-exposure to a dispersion media (DM) control (Porter et al., 2008); 1, 10, 40, or 80 g MWCNT; or 120 g crocidolite asbestos by pharyngeal aspiration. Additionally, we determined gene expression changes in mouse lung tissue with increasing doses of MWCNT at 1 year post-exposure to determine potential underlying mechanisms of fibrotic signaling after exposure to MWCNT.

middle: L


title: TAF-ChIP: An ultra low input approach for genome wide chromatin immunoprecipitation assay

status: Public on Apr 11 2018

city: Mainz

first: Junaid

last: Akhtar

state: Rheinland-Pflaz

address: Johannes-Joachim-Becherweg, 32

department: Institute of Neurobiology and Developmental Biology

institute: University of Mainz

summary: The transcriptional regulation is often controlled by the epigenetic modifications or by chromatin associated proteins. To understand this regulation, chromatin immunoprecipitation (ChIP) followed by next generation sequencing is an invaluable and powerful technique. However, the major limitation of this approach is often the requirement of large amount of starting material for generating high-quality datasets, and often the workflow is laborious. This limitation also results in application of this approach to study of rare cell populations even more challenging, if not impossible. Here, we present a tagmentation-assisted fragmentation ChIP (TAF-ChIP) and sequencing method to generate high quality dataset from as few as 100 human and 1000 Drosophila cells. The method itself is straightforward and is by far less labor-intensive than conventional library preparation, and other contemporary low amount ChIP-Seq methods. Furthermore, this approach can be applied directly on 100 cells rather than relying on de-multiplexing strategies to generate the profile from limited number of cells. This can be extremely useful when the access to the starting material is very restricted, for example clinically isolated cells from patients. Using this approach we generated the H3K4Me3 and H3K9Me3 profiles from 100 K562 cells and 1000 sorted neural stem cells (NSC) from Drosophila. We benchmarked our TAF-ChIP datasets from K562 cells against the Encode datasets. For validating the TAF-ChIP datasets obtained from Drosophila NSCs we took advantage of Notch induced over proliferation specifically in type II NSCs. The epigenetic profile obtained from conventional ChIP-Seq approach and TAF-ChIP approach shows high degree of agreement, thereby underlining the utility of this approach for generating ChIP-Seq profiles from very low cell numbers.

sample_organism:
Drosophila melanogaster
Homo sapiens

platform_organism:
Drosophila melanogaster
Homo sapiens

overall_design: ChIP Seq datasets from sorted Neural stem cells (NSCs) from Drosophila larval brain and sorted K562 cells. To benchmark the TAF-ChIP dataset, previously published datasets from ENCODE consortium and CUT&RUN (Nature Protocols volume 13, pages 1006?1019 (2018)) was donwloaded and processed identically as the TAF-ChIP datasets.


title: Tumor immune evasion arises through loss of TNF sensitivity [Ado]

summary: Investigation of the transcriptional response of wild type or Ado knockout MC38 cells to TNF

overall_design: MC38 cells targeted with Control guide 1 and 2 or Ado targeting guide 1 and 2 were left untreated or treated with TNF-alpha for either 1 hour or 6 hours


title: Tumor immune evasion arises through loss of TNF sensitivity


title: Genome-wide identification of ParB binding sites in Pseudomonas aeruginosa

status: Public on Mar 27 2018

city: Warszawa

first: Adam

last: Kawałek

address: Pawinskiego 5A

department: Department of Microbial Biochemistry

country: Poland

institute: Institute of Biochemistry and Biophysics, PAS

summary: ParA and ParB homologs are involved in accurate chromosome segregation in bacteria. ParBs participate in proper folding and initial separation of ori domains by binding to specific parS sites (palindromic centromere-like sequences), mainly localized close to oriC. Bioinformatic analyses identified 10 parS sequences in the Pseudomonas aeruginosa PAO1 genome. One parS from the parS1-parS4 cluster is required for ParB mediated chromosome segregation. To verify the binding of ParB to all known parSs in vivo as well as to identify additional ParB binding sites we performed chromation immunoprecipitation (ChIP) using polyclonal anti-ParB antibodies followed by high throughput sequencing. ChIP was performed with P. aeruginosa PAO1161 (WT) cells, PAO1161 pKB9 (ParB+++) cells with a slight, non-toxic ParB overproduction as well as with 3 strains containing parS modifications impairing ParB binding to these sites. The data confirmed ParB binding to all known parS sequences with the exception of parS5. Moreover, we identified more than a 1000 of new ParB-bound regions, majority of which contained a DNA motif corresponding to inner 7 nt from one arm of the parS palindrome. ParB interactions with these numerous sites could affect chromosome topology, compaction and gene expression classifying P. aeruginosa ParB as a Nucleoid Associated Protein (NAP).

overall_design: ChIP was performed with P. aeruginosa PAO1161 (WT) cells, PAO1161 pKB9 (araBADp-parB) cells with a 5-fold ParB overproduction. Additionally, three parS mutants were included: parSnull with all ten parS sites mutated, parS1-4 mutant with the four high affinity ParB sites inactivated, and parS2+ strain with nine parS sequences modified and only parS2 left intact (Jecz et al., 2015). PAO1161 parBnull mutant, with parB gene disrupted was used as a negative control. Each strain was analysed in duplicate. Additionally, input DNA (DNA before incubation with antibodies) was sequenced for WT strain.

first: Aneta

last: Bartosik

last: Kawalek

first: Krzysztof

last: Glabski

first: Grazyna

last: Jagura-Burdzy


title: Single-cell RNA-seq reveals the transcriptional landscape and heterogeneity of aortic macrophages in murine atherosclerosis

status: Public on Mar 29 2018

city: Würzburg

first: Antoine-Emmanuel

last: Saliba

address: Josef-Schneider-Straße 2 / D15

institute: Helmholtz Institute for RNA-based Infection Research

summary: We have applied single-cell RNA sequencing as an unbiased profiling strategy to interrogate and classify aortic macrophage heterogeneity at the single-cell level in atherosclerosis.

overall_design: We performed single-cell RNA sequencing of total aortic CD45+ cells extracted from the non-diseased (chow fed) and atherosclerotic (11 or 20 weeks of high-fat diet) aorta of low-density lipoprotein receptor-deficient (Ldlr-/-) mice.

first: Clément

last: Cochain

first: Ehsan

last: Vafadarnejad

first: Panagiota

last: Arampatzi

first: Jaroslav

last: Pelisek

first: Holger

last: Winkels

first: Klaus

last: Ley

first: Dennis

last: Wolf

first: Antoine

middle: E

first: Alma

last: Zernecke


title: ChIP Seq with NKX2-5 antibody in human embryonic stem cells in cardiomyogenesis

status: Public on Mar 21 2018

first: Katrina

middle: M

last: Bell

state: Victoria

address: RCH, Flemington Rd, Parkville

institute: MCRI

summary: ChIP Seq with NKX2-5 antibody in hESC's

overall_design: Experiment involved the analysis of 3 ChIP Seq NKX2-5 replicates using 2 different antibodies (Abcam ab35842, Santa Cruz sc-14033) with IgG as a control (Sigma)

first: David

last: Elliot

last: Anderson


title: HtrA-Mediated Selective Degradation of DNA Uptake Apparatus Accelerates Termination of Pneumococcal Transformation

status: Public on Mar 22 2018

first: Yanni

last: Liu

address: Qinghuayuan, Haidian district

department: Medicine of School

institute: Tsinghua University

summary: As a sextual behavior, competence or natural transformation mediates lateral gene transfer, and thereby promotes exchange of antibiotic resistance and virulence traits among bacteria. Competence is assoicated with activation of many genes, rapid build-up of membrane-bound DNA uptake apparatus, and transient growth arrest. It is completely unknown how transformable bacteria recover from the competence-associated status. This work reveals that the membrane-associated HtrA protease enables the pneumococcus (an important human pathogen) to recover from the competence-associated status by breaking down the DNA uptake apparatus. This is achieved by selective degradation of ComEA and ComEC, the major components of the DNA uptake apparatus. Deleting htrA and/or over-expressing comEA-EC led to dramatic delay in competence termination. Based on high conservation of HtrA and DNA uptake proteins among transformable bacterial, the HtrA protease may serve as a general regulator of bacteria recovery from the competence-associated status.

overall_design: Pairwise comparison of different competence-ON samples to competence-OFF sample of Streptococcus pneumoniae Rx1 (RNA-seq), analyzing the transcriptome dynamics during comeptence development. It was performed with deep sequencing, using an Illumina Hiseq_X-TEN machine with 150 nt paired-end reads.

first: Yuna

last: Zeng

first: Yijia

last: Huang

first: Lixiao

last: Gu

first: Shaolin

last: Wang

first: Chunhao

last: Li

first: Donald

last: Morrison

first: Haiteng

last: Deng

first: Jing-Ren

last: Zhang


title: Population snapshots predict early haematopoietic and erythroid hierarchies

status: Public on Feb 21 2018

city: Worcester

first: Merav

last: Socolovsky

state: MA

address: 364 Plantation St

department: Molecular, Cell and Cancer Biology

institute: University of Massachusetts Medical School

summary: The formation of red blood cells begins with the differentiation of multipotent haematopoietic progenitors. Reconstructing the steps of this differentiation represents a general challenge in stem-cell biology. Here we used single-cell transcriptomics, fate assays and a theory that allows the prediction of cell fates from population snapshots, to demonstrate that mouse hematopoietic progenitors differentiate through a continuous, hierarchical structure into seven blood lineages. We uncovered coupling between the erythroid and the basophil or mast cell fates, a global haematopoietic response to erythroid stress and novel growth factor receptors that regulate erythropoiesis. We defined a flow cytometry sorting strategy to purify early stages of erythroid differentiation, completely isolating classically defined burst-forming and colony-forming progenitors. We also found that the cell cycle is progressively remodelled during erythroid development and during a sharp transcriptional switch that ends the colony-forming progenitor stage and activates terminal differentiation. Our work showcases the utility of linking transcriptomic data to predictive fate models, and provides insights into lineage development in vivo.

overall_design:
Single-cell mRNA sequencing of hematopoietic progenitors from mouse bone marrow and fetal liver.
Sample Bone marrow, basal: 5432 single cells.
Sample Bone marrow, Epo-stimulated: 2954 single cells.
Sample Fetal liver: 9482 single cells.
Sample P1: 3104 single cells.
Sample P1-CD71hi: 752 single cells.
Sample P2: 2435 single cells.
Sample P3: 2032 single cells.
Sample P4: 1210 single cells.
Sample P5: 2460 single cells.

first: Betsabeh

last: Khoramian Tusi

first: Samuel

last: Wolock

first: Caleb

last: Weinreb

first: Yung

last: Hwang

first: Daniel

last: Hidalgo

first: Rapolas

last: Zilionis

first: Ari

last: Waisman

first: Jun

middle: R

last: Huh

first: Allon

last: Klein


title: BMS_IM125001_WB_study

status: Public on Feb 06 2018

city: Atlanta

first: Hanjoong

last: Jo

address: 1760 Haygood Drive, Health Sciences Research Bldg E170

department: Coulter Department of Biomedical Engineering

institute: Georgia Tech and Emory Univ

summary: The goal of this study is to define the molecular signatures of prednisolone and BMS-791826 in normal healthy volunteers. IM125001 (NCT03198013) is a phase I, placebo-controlled, double-blind, ascending single and multiple oral dose study to evaluate the safety, pharmacokinetics and pharmacodynamics of bms-791826 and to assess its marker specific pharmacodynamics in relation to prednisolone in healthy males, sponsored by Bristol-Myers Squibb.

overall_design: Total RNA from normal healthy volunteers taking prednisolone, BMS-791826 or placebo over time were collected.

first: Yanhua

last: Hu

first: Julie

last: Carman


title: RNA Seq analysis of NKX2-5 Null and Het human embryonic stem cells in cardiomyogenesis

first: Katrina

last: Bell

summary: Differentiation of human pluripotent stem cells (hPSCs) can be used to model human heart development and, in turn, to analyze the developmental consequences of genetic abnormalities. Here, we deleted NKX2-5, a critical component of the cardiac gene regulatory network, in human embryonic stem cells (hESCs) and identified a novel genetic interaction between NKX2-5 and HEY2 that is required for heart development

overall_design: Comparision of Null and Het NKX2-5 hESCs

first: David

last: Elliot

last: Anderson


title: Genome-wide identification of natural RNA aptamers in prokaryotes and eukaryotes

status: Public on Mar 06 2018

city: Singapore

first: YANG

last: SHEN

address: Genome Institute of Singapore (A*STAR) 60 Biopolis Street, #02-01 Genome

institute: Genome Institute of Singapore

summary: RNAs are well-suited to act as cellular sensors that detect and respond to metabolite changes in the environment due to their ability to fold into complex structures. Here, we introduce a genome-wide strategy called PARCEL that experimentally identifies RNA aptamers in vitro, in a high-throughput manner. By applying PARCEL to a collection of prokaryotic and eukaryotic organisms, we have revealed 58 new RNA aptamers to three key metabolites, greatly expanding the list of natural RNA aptamers. The newly identified RNA aptamers exhibit significant sequence conservation, are highly structured and show an unexpected prevalence in coding regions.  We identified a prokaryotic precursor tmRNA that acts as a vitamin B2 (FMN) binder to facilitate its maturation, as well as new coding-region eukaryotic riboswitches that bind and respond to FMN, highlighting FMN as a second class of eukaryotic riboswitches.  PARCEL results show that RNA-based sensing and gene regulation is more widespread than previously appreciated in different organisms.

sample_organism:
Pseudomonas aeruginosa
Bacillus subtilis
Candida albicans

overall_design: PARCEL analysis of C.albicans, B.subtilis and P.aeruginosa using various metabolites (e.g. SAM,TPP)

first: Yue

last: Wan

first: Yang

last: Shen


title: BMS_Prednisolone_hPBMC_InVitro_study2

summary: The goal of these studies is to identify genes that are regulated by glucocorticoids in human peripheral blood mononuclear cells in vitro.

overall_design: hPBMCs were cultured for 6 hours with either dimethyl sulfoxide (DMSO) vehicle or 1 μM prednisolone.


title: Massively Parallel Single Nucleus Transcriptional Profiling Defines Spinal Cord Cell Types and Their Activity During Behavior

status: Public on Feb 02 2018

city: Bethesda

first: Kory

last: Johnson

state: MD

address: 10/3B01, 9000 Rockville Pike

department: DIR IT & Bioinformatics

institute: NINDS/NIH

summary: To understand the cellular basis of behavior, it is necessary to know the types of cells that exist in the nervous system and their contributions to function. Spinal cord networks are essential for sensory processing and motor behavior; however, the cellular correlates of these functions are not well understood. Here, we developed a massively parallel single nucleus RNA sequencing technique to first create a cell type atlas of the adult mouse spinal cord and then to use the transcriptional signatures of neuronal activity to map the cell types associated with specific behaviors. This approach, which we term Activity-SEQ, provided a broad and unbiased definition of the set of neuronal populations that were active in response to a painful stimulus and during locomotion. In the future, Activity-SEQ could provide a powerful strategy to reveal the molecular and cellular basis for a wide range of behaviors.

overall_design: Single-cell RNA profiles for nuclei collected from 24 different mouse brains via Drop-Seq protocol. Included among the nuclei profiled were those from 9 control mice (f1, m1, M4, M5, F3, F4, facx, fbcx, Macx), 10 formalin-exposed mice, and 5 rotarod-challenged mice.

first: Anupama

last: Sathyamurthy

first: Li

last: Li

first: Kaya

last: Matson

first: Anna

last: Ryba

first: Tzippora

last: Bergman

first: Courtney

middle: I

last: Dobrott

first: Michael

middle: C

last: Kelly

first: Matthew

middle: W

last: Kelley

first: Ariel

last: Levine


title: Human intrahepatic cholangiocarcinoma (IHCC) cells cultured with expansion medium (EM) or differentiation medium (DM)

status: Public on Feb 01 2018

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

institute: Toray Industries,Inc.

summary: Human IHCC cells were cultured with EM or DM and gene expression profiling was analyzed by microarray.

overall_design: Two-condition experiment, IHCC cells cultured with EM vs. IHCC cells cultured with DM

first: Yoshimasa

last: Saito

first: Toshiaki

last: Nakaoka


title: BMS_TRD_SLE_RA_WB_study

first: Hanjoong

last: Jo

state: GA

summary: The goal of this study is to define the molecular signatures of SLE and RA patients.

overall_design: Total RNA from patients with SLE or RA were collected, and profiled together with samples from normal healthy controls.

first: Yanhua

last: Hu

first: Julie

last: Carman


title: CRISPR/Cas9-mediated ASXL1 mutation in U937 cells perturbs myeloid differentiation

status: Public on Mar 14 2018

first: Zhijie

last: Wu

address: 10 Center Drive

department: NHLBI

institute: NIH

summary:
Purpose: Recurrent ASXL1 mutations are frequently observed in all spectrums of myeloid malignancies and published data suggests that ASXL1 mutations may be involved in leukemic transformation as a tumor suppressor. Yet the molecular mechanisms of cell desitiny regulated by ASXL1 are  to be further delineated.
Methods: mRNA profiles of wild-type (WT) and CRISPR/Cas9 induced ASXL1 mutated U937 cell lines were generated by next generation sequencing, using Illumina HiSeq2500. Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality at the ends. Remaining sequence reads were then aligned to the human reference genome (hg19) using Tophat2. Gene read counts were measured using FeatureCounts and FPKM values were calculated with cufflinks. edgeR was used to identify differentially expressed genes between conditions, and topGO was used for annotation (Alexa, Rahnenfuhrer, and Lengauer, 2006). Sample comparison for differential gene expression was as follows: WTblk and WT1 versus MT2, MT3, MT4, and MT5. Gene enrichment set analysis (GSEA) was conducted with KEGG, Biocarta, and Reactome pathway datasets (Subramanian et al., 2005).
Results: ASXL1-mutated cells displayed impaired differentiation capacity. RNA-seq was used to compare transcriptomes of ASXL1-mutated and WT U937 cells. Transcriptom analysis revealed that ASXL1 mutations decreased the expression of genes essential to myeloid differentiation, including CYBB and CLEC5A genes, which manifested in ASXL1-MT U937 cells as perturbed potential of differentiation compared with WT cells. Also, gene set enrichment analysis revealed that ASXL1 mutations masively affected gene sets relating to cell death and survival.
Conclusion: By introduction of mutations into genome using the CRISPR/Cas9 system, we established ASXL1-mutated U937 cell lines. Our results indicated that ASXL1 mutations perturbed monocytic/phagocyte differentiation, which is a hallmark of myeloid malignancies, by down regulating genes essential to myeloid differentiation, including CYBB and CLEC5A, also massively affected multiple gene sets involving in cell survival.

overall_design: mRNA profiles of wild type (WT) and ASXL1 mutated U937 cell lines were generated by deep sequencing using Illumina HiSeq2500


title: BMS_IM124001_WB_study

summary: The goal of this study is to define the molecular signatures of prednisolone in vivo. IM124001 (NCT03196557) is an experimental medicine study to assess the pharmacodynamics following administration of multiple doses of prednisolone to healthy male subjects, sponsored by Bristol-Myers Squibb.

overall_design: Total RNA from normal healthy volunteers taking prednisolone or placebo over time were collected.