title: Distinct and convergent consequences of splice factor mutations in myelodysplastic syndromes

city: Singapore

first: SIQIN

last: ZHOU

address: 14 Medical Drive

institute: Cancer Science Institute of Singapore

summary: Myelodysplastic syndromes (MDS) are characterized by recurrent somatic alterations often affecting components of RNA splicing machinery. Mutations of splice factors SF3B1, SRSF2, ZRSR2 and U2AF1 occur in >50% of MDS. To assess the impact of spliceosome mutations on splicing and to identify common pathways/genes affected by distinct mutations, we performed RNA-sequencing of 24 MDS bone marrow samples harboring spliceosome mutations (including hotspot alterations of SF3B1, SRSF2 and U2AF1; small deletions of SRSF2 and truncating mutations of ZRSR2), and devoid of other common co-occurring mutations. We uncover the landscape of splicing alterations in each splice factor mutant MDS and demonstrate that SRSF2 deletions cause highest number of splicing alterations compared with other spliceosome mutations. Although the mis-spliced events observed in different splice factor mutations were largely non-overlapping, a subset of genes, including EZH2, were aberrantly spliced in multiple mutant groups. Pathway analysis revealed that the mis-spliced genes in different mutant groups were enriched in RNA splicing and transport as well as several signaling cascades, suggesting converging biological consequences downstream of distinct spliceosome mutations.

overall_design: RNA-sequencing of MDS bone marrow either harboring mutations or wildtype for spliceosome genes (SF3B1, ZRSR2, SRSF2 and U2AF1)

first: Vikas

last: Madan

first: Jia

last: Li

first: Siqin

last: Zhou

first: Weoi

middle: W

last: Teoh

first: Manja

last: Meggendorfer

first: Lin

last: Han

first: Torsten

last: Haferlach

first: Henry

last: Yang

first: H

last: Koeffler


title: Loss of IDH1R132H mediated D-2HG production induces genome-wide demethylation in GCIMP low loci in patient-derived glioma cells

status: Public on Nov 07 2019

city: Durham

first: Hai

last: Yan

state: NC

address: 199B-MSRB, Research Drive

department: Pathology

country: USA

institute: Duke University

type: Methylation profiling by genome tiling array

summary: Here, we describe and characterize CRISPR-Cas9 based isogenic cell line models using patient-derived IDH1R132H/WT glioma cell lines, and we use these models to explore changes in DNA methylation following genetic deletion of IDH1 alleles that ablate D2HG production.

overall_design: Comparison of CRISPR IDH1 targeted vs. parental cells or unedited clones methylation values.

first: Casey

middle: J

last: Moure

first: Lee

middle: H

last: Chen


title: In Arabidopsis hybrids and Hybrid Mimics up-regulation of cell wall biogenesis is associated with increased plant size

city: Canberra

first: Li

last: Wang

state: ACT

address: North-Science Road, Acton ACT 2601

country: Australia

institute: CSIRO

type: Expression profiling by high throughput sequencing

summary: Hybrid breeding is of economic importance in agriculture for increasing yield, yet the basis of the heterosis is not well understood. In Arabidopsis, crosses between different accessions produce hybrids with varied levels of heterosis relative to parental phenotypes in biomass. In all hybrids the advantages of the F1 hybrid is lost in the F2 for both phenotypic uniformity and yield gain. Success in generating F5/F6 Hybrid Mimic from the cross between C24 and Landsberg erecta (Ler) demonstrated that the large plant phenotype of the F1 hybrids can be stabilized. Hybrid Mimics selection was applied to Wassilewskija (Ws)/Ler and Col/Ler hybrids. The two hybrids showing different levels of heterosis. At 30 DAS, the Col/Ler hybrid generated Hybrid Mimics with rosette diameter and fresh weight equivalent to the F1 hybrid; Ws/Ler Hybrid Mimics outperformed the F1 hybrids in both the rosette size and biomass. Transcriptome analysis revealed up-regulation of cell wall biosynthesis and expansion genes could be a common pathway in increased size in Arabidopsis hybrids and Hybrid Mimics. Intercross of two independent Hybrid Mimic lines can further increase the biomass gain. Our results encourage the use of Hybrid Mimics for breeding and for investigating the molecular basis of heterosis.

overall_design: Arabidopsis hybrid seeds [Wassilewskija (Ws)/Landsberg erecta (Ler), Col/Ler and C24/Ler] were produced by hand-pollination between parental accessions. Ws/Ler and Col/Ler Hybrid Mimic lines and F7 small plant lines were produced from the recurrent selection protocol (Wang et al., 2015, Wang et al., 2017). Sterilized seeds were sown onto plates with Murashige and Skoog (MS) medium (Murashige and Skoog Basal Salts with minimal organics, Sigma-Aldrich, M6899) supplemented with 3% (wt/vol) sucrose and 0.8% wt/vol agar, pH5.7. Seeds were kept at 4 °C in the dark, then transferred into a growth room with conditions of 16h light (22°C)/8h dark (18°C) and light density at 120 -150 μmol photons m-2·s-1. Plate-grown seedlings were transferred into soil at 15 days after sowing. For the sample set of Ws/Ler system, the rosette leaves of 25 day-old parents Ws and Ler, two reciprocal hybrids Ws x Ler and Ler x Ws, seven Hybrid Mimic lines (WL_HM1-7) and two small lines (wl_sml1-2) were collected at time Zeitgeber Time (ZT)  = 6-8 (ZT = 0 refers to dawn). For the same set of Col/Ler system, the rosette leaves of 25 day-old parents Col, two reciprocal hybrids Col x Ler and Ler x Col, six Hybrid Mimic lines (CL_HM1-6) and two small lines (cl_sml1-2) were collected. The transcriptomes of Hybrid Mimics CL_HM5 and CL_HM6 were excluded from the analysis due to unsatisfactory phenotypes of plant size at sampling day -25 DAS. For the parents and hybrids, three biological replicates were collected per plant line; rosette leaves from three plants of each genotype were pooled as one biological replicate. For each Hybrid Mimic and small line, rosette leaves of three siblings were collected separately as three biological replicates.

middle: M

last: Wu

first: Ian

middle: K

last: Greaves

first: Elizabeth

middle: S

last: Dennis

first: William

last: Peacock


title: Long term cellular adaptation of protein levels to metabolic flux, coordinated by cyclic transcription

city: Oxford

first: Jack

middle: Edward

last: Feltham

state: Oxfordshire

address: South Parks Road

department: Biochemistry

country: United Kingdom

institute: University of Oxford

summary: Multiomics study of the dymanic changes in gene expression throughout the yeast metabolic cycle at the transcription, transcript, translation and protien levels.

overall_design: Timecourses of multiomics datasets across the yeast metabolic cycle

middle: E

first: Shidong

last: Xi

first: Jane

last: Mellor


title: A genome-wide long noncoding RNA CRISPRi screen identifies PRANCR as a novel regulator of epidermal homeostasis

city: Hefei

first: Kun

last: Qu

address: University of Science and Technology of China, No.96, JinZhai Road Baohe District

country: China

type: Non-coding RNA profiling by high throughput sequencing

summary: Long noncoding RNAs (lncRNAs) are a major component of the noncoding genome, but their functions in human development and disease are still incompletely understood. CRISPR interference screens allow for systematic identification of functional lncRNAs that regulate fundamental biological processes such as tissue development and homeostasis. We identified 2,263 lncRNAs transcribed in human epidermis, and performed a comprehensive CRISPR interference screen against all these elements in primary human epidermal progenitors. Our screen identified 209 lncRNAs controlling epidermal progenitor renewal, with the majority (94%) being positive regulators of proliferation. To validate the results, we performed deeper characterization of a novel lncRNA identified from this screen, PRANCR (LINC01481), using RNA interference-mediated transcript knockdown and phenotype analysis in organotypic human tissue. PRANCR depletion inhibited progenitor proliferation through a G2/M cell cycle arrest, reduced clonogenic potential, and impaired functional epidermal stratification. Transcriptome and computational analysis indicated that PRANCR governs progenitor renewal by controlling the expression of 1,136 genes in trans, in part via the p53-E2F4-CHR pathway. This pathway controls the expression of G2/M cell cycle genes and is a novel mechanism of regulating cell proliferation in epidermal progenitors.

overall_design: In this study, we identified 2,263 lncRNAs transcribed in human epidermis, and performed a comprehensive CRISPR interference screen against all these elements in primary human epidermal progenitors.

first: Pengfei

last: Cai

first: Auke

middle: C

last: Otten

first: Binbin

last: Cheng

first: Mitsuhiro

middle: A

last: Ishii

first: Wen

last: Zhang

first: Beibei

last: Huang

first: Bryan

last: Sun


title: Transcriptome profiling of liver derived from calcium channel ITPR2 KO mice

status: Public on Nov 06 2019

city: Lyon

first: jean-michel

last: flaman

address: 28 rue Laennec

department: CRCL

country: France

institute: Inserm 1052

summary: Cellular senescence is induced by multiple stresses and results in a stable proliferation arrest accompanied by a pro-inflammatory secretome. Senescent cells accumulate during aging, promoting various age-related pathologies and thus limiting lifespan. The endoplasmic reticulum ITPR2 release channel and calcium fluxes from the ER to the mitochondria have been identified as drivers of cellular senescence in human cells. Here we show that Itpr2 knockout mice display improved aging such as increased lifespan, a better response to metabolic stress, less immunosenescence, as well as less liver steatosis and fibrosis. Cellular senescence, which is known to promote these alterations, is decreased in both Itpr2 KO mice and Itpr2 KO embryo-derived cells. Interestingly, ablation of ITPR2 in vivo and in vitro decreases the number of contacts between the mitochondria and the ER and forced contacts between these two organelles induce premature senescence in normal cells. These new findings shed light on the role of contacts and facilitated exchanges between the ER and the mitochondria through ITPR2 in regulating senescence and physiological aging.

overall_design: Transcriptome analysis has been performed on liver tissue derived from 3 independent WT or Itpr2 KO mice

first: Dorian

middle: V

last: Ziegler

first: David

last: Vindrieux

last: Bernard

first: Jean-Michel

last: Flaman


title: Transcriptome of Actinosynnema pretiosum ATCC 31280 under exogenous supplement of AP-3

city: Shenzhen

first: Xinran

last: Wang

state: Guangdong

address: No.1068 Xueyuan Avenue

department: Center for Synthetic Biochemistry

institute: Shenzhen Institute of Advanced Technology, Chinese Acadamy of Science

summary: In search of AP-3 resistant genes, ATCC 31280△ansaA (inactivation of ansamitocin pksA, in avoiding of the interruption of endogenous generated AP-3) were cultured under the addition of 0, 50, 100 and 200 mg/L exogenous AP-3 for 24 h and collected, for strains under 200 mg/L AP-3, samples after 48 h and 72 h were also collected, and the RNA samples were collected and sent for sequencing.

overall_design: Exploration of the expression profile of genes under exogenous addition of AP-3 and search for ansamitocin resistant genes.

first: Xinjuan

last: Ning

first: Linquan

last: Bai


title: Effect of hypoxia and TGFβ1 on gene expression in HPF fibroblast cells

city: Stillwater

first: CHAOQUN

last: HUANG

state: OK

address: 264 McElroy Hall

department: Physiological Sciences

institute: Oklahoma State University

summary: We performed RNA sequencing to reveal genome-wide changes of genes in hypoxia and/or TGFβ1-treated human lung fibroblasts

overall_design: RNA sequencing of HPF fibroblast treated with hypoxia and/or TGFβ1

first: Chaoqun

first: Lin

last: Liu

first: Lakmini

last: Kumari Senavirathna


title: Arid1a is essential for endometrial gland development

city: Research Triangle Park

first: Ryan

last: Marquardt

address: 111 T.W. Alexander Dr, Bldg 101, Room C-416, Mail Drop C-401

department: Reproductive and Developmental Biology Laboratory

institute: National Institute of Environmental Health Sciences

summary:
Arid1a has a critical role for modulating endometrial gland develop that is required for normal uterine function and fertility after maturity.
We used microarrays to detail the mechanism underlying Arid1a loss during postnatal development.

overall_design: Uteri of Arid1a f/f and Arid1a d/d mice were selected at 2 weeks for RNA extraction and hybridization on Affymetrix microarrays.

first: Jae

last: Jeong

first: Tae

last: Kim


title: Transcriptome profiling of early or late passage MEFs  derived from calcium channel ITPR2 KO mice

overall_design: Transcriptome analysis has been performed on liver tissue derived from 4 independent WT or Itpr2 KO mice and from MEF derived from 3 independent WT or Itpr2 KO


title: Identification of Absidia orchidis steroid 11β-hydroxylation system and its application in engineering Saccharomyces cerevisiae for one-step biotransformation to produce hydrocortisone

city: Tianjin

first: feiyu

last: fan

state: Tianjin

address: 32 West 7th Avenue, Tianjin Airport Economic Area

department: Key Laboratory of Systems Microbial Biotechnology

institute: Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences.

summary:
Purpose: In order to identify genes for 11β-hydroxylase CYP5311B2 and associated redox partners CPR and cytochrome b5 in filamentous fungus Absidia orchidis AS3.65
Methods: Strand-specific RNA-seq libraries were constructed for two samples, including (I) Mycelia of A. orchidis treated with mock N, N-dimethylformamide (DMF); (II) Mycelia of A. orchidis treated with 170 mg/L 11-deoxycortisol 21-acetate (RSA) dissolved in N, N-dimethylformamide. For preparation of RNA samples, germinated young mycelia of A. orchidis after 22-24 pre-culture in liquid potato dextrose broth medium were harvested and transferred into a new 30 ml potassium phosphate buffer supplement with either 170 mg/L RSA dissolved in DMF, or an equal volume of DMF as mock. Additional two-hours cultivation was performed to induction of the 11β-hydroxylase gene expression. Total RNA for samples were isolated using TRIzol reagent (Invitrogen, Grand Island, USA), then used for high-throughput RNA sequencing. The two 150-nt strand-specific paired-end RNA-seq libraries were generated commercially at Novogene Biotechnology Co. Ltd (Tianjin, China) by using Illumina’s Hiseq X Ten platform (Illumina, San Diego, USA). The clean reads were used to create a  de novo transcriptome assembly using the Trinity pipeline (v2.4.0). The abundance for each of the resulted transcripts was calculated by RSEM (v1.2.0) using the Fragments Per Kilobase per Million (FPKM) method.
Results: A total of 10.4 and 10.5 million 150-bp paired-end clean reads were separately generated from the DMF mock and RSA induced samples,and 57549 unique transcripts were assembled from the pooled reads of the two samples using Trinity.  The translated sequences of these transcripts were predicted using TransDecoder, and then used as queries to search against the SWISS-PROT and the Pfam databases for functional annotation.A group of 87 translated sequences were found have a typical CYP domain (PF00067), among which,the expression levels of DN10804 and DN10492 separately increased 306- and 48-fold upon RSA induction and identifed as A. orchidis 11α- and 11β- hydroxylase genes. In addition, DN17017 and DN7580 were identifed as the transcripts for the cytochrome P450 reductase and cytochrome b5,respectively.
Conclusions: The 11β-hydroxylase system of A. orchidis was deciphered by transcriptome analysis.

overall_design: mRNA profiles of A. orchidis treat with DMF mock or steroid RSA were generated by deep sequencing, using Illumina’s Hiseq X Ten platform

first: Jing

last: Chen

first: Feiyu

last: Fan

first: Ge

last: Qu

first: Yongyan

last: Xi

first: Zhoutong

first: Changhao

last: Bi

first: Xueli

last: Zhang


title: Differential expression analysis of RNA-seq data from melanocytes driven by tumor cell-derived exosomes

city: Louisville

first: Hongying

last: Hao

state: KY

address: 505 South Hancock Street

department: Surgery

institute: University of Louisville

summary: Exosomes (40–100 nm) are organelle-like membranous structures shed into interstitial spaces and body fluids under diverse pathophysiologic conditions, including tumor development. The tumor microenvironment is abundant with exosomes secreted by the cancer cells themselves. Studies have shown that tumor-derived exosomes can transport RNA and active molecules to other cells to promote tumor growth. Exosomes are increasingly being recognized as a major contributor in the progression of malignant neoplasms.  We have found that normal melanocytes can acquire invasiveness through the internalization of melanoma cell-derived exosomes.  However, little is known about how the exosomes modulate the melanocytes in the microenvironment to optimize conditions for tumor progression and metastasis.  We hypothesize that melanoma cell-derived exosomes can drive the dysregulation of transcriptomes in normal melanocytes and facilitate melanoma progression. Our objective is to identify differentially expressed genes in melanocytes driven by tumor cell-derived exosomes through RNA sequencing and translate those genes as therapeutic targets for melanoma metastasis.

overall_design: Total RNA was extracted from three groups of human melanocytes: NHEM-c melanocytes without exosomes (control group), NHEM-c melanocytes co-cultured with A375 melanoma cell-derived exosomes, and NHEM-c melanocytes co-cultured with A549 lung cancer cellderived exosomes.

first: Deyi

last: Xiao

first: Jifu

first: Eric

last: Rouchka

first: Xiaohong

last: Li

first: Kelly

last: McMasters


title: Excluding Oct4 from Yamanaka cocktail unleashes the developmental potential of iPSCs

city: Boston

first: Sergiy

last: Velychko

state: MA

address: 77 Avenue Louis Pasteur, Room 232

department: Genetics

institute: Harvard Medical School

summary: Oct4 is widely considered the most important among the four Yamanaka reprogramming factors. Here we show that the combination of Sox2, Klf4, and cMyc (SKM) suffices for reprogramming mouse somatic cells to induced pluripotent stem cells (iPSCs). Simultaneous induction of Sox2 and cMyc in fibroblasts triggers immediate retroviral silencing, which explains the discrepancy with previous studies that attempted but failed to generate iPSCs without Oct4 using retroviral vectors. SKM induction could partially activate the pluripotency network even in Oct4-knockout fibroblasts. Importantly, reprogramming in the absence of exogenous Oct4 results in greatly improved developmental potential of iPSCs, determined by their ability to give rise to all-iPSC mice in the tetraploid complementation assay. Our data suggest that overexpression of Oct4 during reprogramming leads to off-target gene activation during reprogramming and epigenetic aberrations in resulting iPSCs, and thereby bear major implications for further development and application of iPSC technology.

overall_design:
To gain deeper insight into the mechanism of SKM reprogramming, we performed RNA-sequencing (RNA-seq) over the course of reprogramming under both SKM and OSKM conditions (Figure 4E). The pMX mCherry+ OG2 MEFs were transduced with polycistronic reprogramming vectors. Samples were collected after 2, 4, 6, 9, and 12 days of dox induction and used for total RNA isolation and sequencing. Only mCherry– cells were used for RNA isolation to reduce heterogeneity and to eliminate contamination by untransduced cells. Additionally, we sequenced subpopulations of reprogramming intermediates that underwent mesenchymal to epithelial transition (MET) on day 6 (mCherry–/GFP–/Epcam+) or activated endogenous Oct4 (mCherry–/GFP+) on days 9 and 12 (2 days after dox withdrawal) (Figure S4E).
We also compared the gene expression in all OSKM and SKM iPSC lines tested in 4N complementation assays, including those generated by episomal method, as well as ESC lines—altogether 23 lines.
To track the developmental fate of 4N-off OSKM iPSCs, we marked three high quality and four low quality lines (both tet-inducible and episomal) with constitutive mCherry expression. We used these lines to generate 4N-aggregates and examined the embryos at E9.5. At this stage all the tested lines could generate viable embryos with no obvious phenotype (Figure 7D) and the vast majority of the cells are derived from iPSCs (Figure S7E). We sorted mCherry+ iPSC-derived differentiated cells and performed RNA-seq for three embryos per iPSC line, as well 3 control embryos (altogether 24 embryos).

first: Guangming

last: Wu

first: Hans

middle: R

last: Schöler


title: Genome-wide analysis of the effects of oxygen tension on trophoblast differentiation

status: Public on Nov 05 2019

city: Vancouver

first: Alexander

middle: G

last: Beristain

state: BC

address: 950 West 28th Ave

department: Obstetrics & Gynecology

country: Canada

institute: The University of British Columbia

summary:
Analysis of gene expression in extravillous trophoblasts and column cells isolated from matrigel embedded 1st trimester placental explants cultured in 1%, 5% or 20% oxygen.
The aim of this study is to identify differentially expressed genes and pathways potentially altered by varying oxygen conditions within anchoring column trophoblasts and invasive extravillous trophoblasts.

overall_design: Total RNA was isolated from extravillous trophoblasts and column cells propagated from Matrigel-embedded placental explants. All explants were derived from placental villous tissues from 5-8 week gestation placentas. Prior to RNA isolation, placental explants were cultured in either 1%, 5% or 20% oxygen for 48 hours, after which RNA was extracted from trophoblast cells imbedded within Matrigel using Trizol LS reagent. Following RNA extraction, RNA was convereted to cDNA libraries and hybridized onto Affymetrix Clariom S Assay reagents and arrays.

first: Jenna

last: Treissman


title: CTCF confers local nucleosome resiliency after DNA replication and during mitosis

city: paris

first: Pablo

last: Navarro

address: 25 rue du Docteur Roux

institute: Institut Pasteur

type: Genome binding/occupancy profiling by high throughput sequencing

summary: The access of Transcription Factors (TFs) to their cognate DNA binding motifs requires a precise control over nucleosome positioning. This is especially important following DNA replication and during mitosis, both resulting in profound changes in nucleosome organization over TF binding regions. Using mouse Embryonic Stem (ES) cells, we show that the TF CTCF displaces nucleosomes from its binding site and locally organizes large and phased nucleosomal arrays, not only in interphase steady-state but also immediately after replication and during mitosis. While regions bound by other TFs, such as Oct4 and Sox2, display major rearrangement, the post-replication and mitotic nucleosome organization activity of CTCF is not likely to be unique: Esrrb binding regions are also characterized by persistent nucleosome positioning. Therefore, selected TFs such as CTCF and Esrrb act as resilient TFs governing the inheritance of nucleosome positioning at gene regulatory regions throughout the ES cell-cycle.

overall_design: Examination of binding of CTCF and SMC1 in mouse ES cells, fibroblasts and myoblasts in interphase and mitosis by ChIP-seq.  Examination of nucleosome positioning at CTCF sites in interphase, mitosis and immediately after replication by MNase-seq and MINCE-seq, including investigation of nucleosome positioning at CTCF sites in interphase and mitosis with auxin inducible depletion of CTCF.

first: Nick

last: Owens


title: RNA-Seq Data from fruit skin of sand pear

city: Hangzhou

first: Yuezhi

last: Wang

state: Zhejiang

address: Shiqiao Road No.139

institute: Zhejiang Academy of Agricultral Sciences

summary: Transcriptom data of pear fruit skin

overall_design: Ten russet fruits or green fruits were used for each sample.

first: Zebin

last: Shi


title: An Integrated Transcriptome and Proteome Analysis Reveals New Insights into Russeting of ‘Golden Delicious’ Apple

status: Public on Nov 04 2019

city: Zhengzhou

first: Gaopeng

last: Yuan

state: Henan

address: Weilai Road Nanduan

institute: CAAS

summary: Apple skin russeting naturally occurs in many varieties, particularly in 'Golden Delicious' and its pedigree, and is regarded as a non-invasive physiological disorder partly caused by excessive deposition of lignin. However, the understanding of its molecular mechanism is still limited. In this study, we used iTRAQ and RNA-seq to detect the changes in the expression levels of genes and proteins in three developmental stages of russeting formation, in russeted and non-russeted skin of 'Golden Delicious' apple. 2856 differentially expressed genes and 942 differentially expressed proteins in the comparison groups were detected at the transcript level and protein level, respectively. A correlation analysis of the transcriptomics and proteomics data revealed that four genes (MD03G1059200, MD08G1009200, MD17G1092400 and MD17G1225100) involved in lignin biosynthesis are significant changes during apple russeting formation. Additionally, 92 transcription factors, including 4 LIM transcription factors may be involved in apple russeting formation. Among them, one LIM transcription factor (MD15G1068200) was capable of binding to the PAL-box like (CCACTTGAGTAC) element, which indicated it was potentially involved in lignin biosynthesis. This study will provide further views on the molecular mechanisms controlling apple russeting formation.

overall_design: mRNA profiles of DAF30，DAF60 and DAF 150 of un-bagging (CK) and bagging (T), in apple, using BGISEQ-500

first: Shuxun

last: Bian

first: Xiaolei

last: Han

first: Shanshan

last: He

first: Kai

last: Liu

first: Caixia

first: Peihua

last: Cong


title: MYCi361 regulates MYC target genes

city: Chicago

first: Zachary

middle: Rockow

last: Chalmers

state: IL

address: 303 E. Superior Ave

institute: Northwestern University

summary: We report MYCi361 regulates MYC taraget genes in PC3 by deep sequencing (RNA-seq).

overall_design: We used PC3 cells with high endougenous c-MYC level to demonstrate MYCi361 regulates MYC target genes. Transcriptome profiling of PC3 with MYCi361 were generated.

first: Sarki

last: Abdulkadir

first: Huiying


title: miRNA expression profile in pediatric and adolescent and young adult rhabdomyosarcomas

city: Milan

first: Loris

last: De Cecco

address: via Venezian 1

country: Italy

institute: IRCSS Istituto Nazionale Tumori

summary: Adolescents and young adults (AYA) with rhabdomyosarcoma (RMS) form a subgroup of patients whose optimal clinical management and best possible access to care remain a challenge and survival lacks behind that of children while diagnosed with histologically similar tumors. Understanding the tumor biology that differentiate children from AYA-RMS could provide critical information and drive new initiatives to improve their final outcome. MiRNA profile was evaluated in a RMS series of 49 tumor and 13 non-neoplastic tissues. MiRNAs analysis identified miR-223 over-expression and mir-431 down-regulation in AYA, validated by Real-Time PCR and miRNA ISH.

overall_design:
A cohort of 49 RMS FFPE (formalin fixed paraffin embedded) tissues (not pre-treated primary tumors) was carefully selected and retrieved from the archive of Fondazione IRCCS Istituto Nazionale dei Tumori and were re-evaluated by expert pathologists for abundance and adequacy of material. Non-neoplastic components were identified where possible for each age groups of RMS,as controls in bioinformatic analyses. In details, RNA was successfully isolated from 27 pediatric RMS (0-14 years) and 22 AYA RMS (15-+30 years). Two samples (FF62 and FG07) were used as controls for adjacent normal tissues; the remaining 49 tumors and 13 normal conterpart was used for the analysis.  MiRNA profile using a SurePrint G3 Human miRNA r21 microarray on miRBAse 21.0 (miRNA) Agilent (~ 2.000 miRNA) was successfully performed.

When possible the normal tissue was obtained by a FFPE tissue block different from that of the tumor; otherwise, the pathologist selected a normal tissue area next to the tumor. The former was defined "normal", the latter "adjacent_normal".


title: Gene expression profiling in pediatric and adolescent and young adult rhabdomyosarcomas

summary: Adolescents and young adults (AYA) with rhabdomyosarcoma (RMS) form a subgroup of patients whose optimal clinical management and best possible access to care remain a challenge and survival lacks behind that of children while diagnosed with histologically similar tumors. Understanding the tumor biology that differentiate children from AYA-RMS could provide critical information and drive new initiatives to improve their final outcome. Gene expression profiling was evaluated in a RMS series of 48 tumor and 13 non-neoplastic tissues.  GEP analysis detected 793 age-correlated genes in tumors. NOTCH2, FGFR1 were significantly down-modulated in AYA-RMS.  GEP showed an increase in CD4 memory resting cells and a decrease in γδ T-cells in AYA-RMS. IHC analysis demonstrated an increase of infiltrated CD4, CD8 and neutrophils in AYA-RMS tumors.

overall_design:
A cohort of 48 RMS FFPE (formalin fixed paraffin embedded) tissues (not pre-treated primary tumors) was carefully selected and retrieved from the archive of Fondazione IRCCS Istituto Nazionale dei Tumori and were re-evaluated by expert pathologists for abundance and adequacy of material. Non-neoplastic components were identified where possible for each age groups of RMS, so to use as controls in bioinformatic analyses. In details, RNA was successfully isolated from 27 pediatric RMS (0-14 years) and 21 AYA RMS (15-+30 years). Two samples (FF62 and FG07) were used as controls for adjacent normal tissues; the remaining 48 tumors and 13 normal counterpart were used for the analysis.  Gene expression analysis was performed  on ClariomS (Affymetrix) chips.

When possible the normal tissue was obtained by a FFPE tissue block different from that of the tumor; otherwise, the pathologist selected a normal tissue area next to the tumor. The former was defined "normal", the latter "adjacent_normal".


title: Zebrafish liver transcriptome in response to chronic treatment with environmentally relevant concentrations of imatinib mesylate

city: Ljubljana

first: Spela

last: Baebler

address: Vecna pot 111

department: Department of Biotechnology and Systems Biology

country: Slovenia

institute: National Institute of Biology

summary: Imatinib mesylate (IM) a protein kinase inhibitor drug that selectively inhibits certain oncogenic mutant protein tyrosine kinases. After application, IM is via hospital and municipal waste water effluents released into the aquatic environment, where it can harm non-target organisms. The aim of this study was to evaluate changes in gene transcription in liver of adult F1 zebrafish (Danio rerio) continuously exposed to IM at environmentaly relevant concentrations of  0.01 µg/L and 1 µg/L.

overall_design: One color design, control and treatment in two concentrations; 6 pools of 1-3 individuals per treatment

first: Špela

first: Ana

last: Rotter


title: Gene and miRNA expression profiling in pediatric and adolescent and young adult rhabdomyosarcomas

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

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

overall_design: Refer to individual Series


title: Microglial microRNAs mediate sex-specific responses to tau pathology

city: San Francisco

first: Lay

last: Kodama

state: CA

address: 1650 Owens St

department: J David Gladstone Institutes

institute: University of California, San Francisco

summary: Sex is a key modifier of neurological disease outcomes. Microglia are implicated in neurological diseases and modulated by miRNAs, but it is unknown whether microglial miRNAs have sex-specific influences on disease. We show that microglial miRNA expression differs in males and females, and loss of miRNAs leads to sex-specific changes in the microglial transcriptome and to tau pathology. These findings suggest microglial miRNAs influence tau pathogenesis in a sex-specific manner.

overall_design: Examination of microRNA expression in microglia isolated from female and male control and P301S tauopathy mouse samples. Examination of mRNA expression in microglia isolated from female and male Dicer WT, Dicer KO, and P301S Dicer KO mouse samples.

first: Elmer

last: Guzman

first: Jon

middle: I

last: Etchegaray

first: Yaqiao

last: Li

first: Lihong

last: Zhan

first: Yungui

last: Zhou

first: Faten

last: Sayed

first: David

last: Le

first: Joe

last: Udeochu

first: Claire

middle: D

last: Clelland

first: Kenneth

last: Kosik

first: Li

last: Gan

first: Lu

first: Zuolin

last: Cheng

first: Guoqiang

last: Yu

first: Qingyun


title: Identification of novel genes involved in postnatal longitudinal muscle growth

city: Cincinnati

first: Douglas

last: Millay

state: OH

address: 240 Albert Sabin Way  MLC 7020

institute: Cincinnati Children's Hospital Medical Center

summary: Overall goal: To identify genes involved in postnatal longitudinal muscle growth through misregulation by neonatal brachial plexus injury leading to contracture formation. Purpose of analysis: To generate a transcriptional profile of mice given unilateral neonatal brachial plexus injuries. Experimental structure: The transcriptional profiles generated from the RNA-Seq analysis would be compared as neonatally-denervated biceps muscle versus the contralateral control to identify genes regulating postnatal longitudinal muscle growth.

overall_design: RNA-Seq analysis of total RNA isolated from whole biceps muscle (neonatally-denervated and contralateral control) 3 weeks following C5-T1 neonatal brachial plexus injury was carried out to generate a transcriptional profile of a model of postnatal muscle growth versus arrested growth leading to contracture formation.

first: Sia

last: Nikolaou

first: Roger

last: Cornwall

middle: P


title: Nanoparticle-coupled topical methotrexate effectively inhibits inflammation and induces re-modeling in pre-clinical psoriasis

city: Zurich

first: Ge

last: Tan

address: Winterthurerstrasse 190

department: Functional Genomics Center Zurich

country: Switzerland

institute: University of Zurich

summary: This project explores the efficacy of a novel skin-permeable MTX formulation, on murine and human xenotransplant models of psoriasis. Phenotypical and histological examinations of psoriatic tissue in these models have shown that the novel MTX can significantly suppress the inflammation. In order to understand the mechanistics of the new drug transcriptome of different treatment regimens (MTX-based, corticosteroid-based, and Vaseline control) will be compared to assess the pathological state of the skin.

overall_design: Transcriptomic changes of human skin on a xenotransplant model upon topical therapy was compared to psoriatic and normal-appearing skin from psoriasis patients

first: Alaz

last: Oezcan

first: Antonios

last: Kolios


title: MYCi975 and MYCi361 regulate MYC target genes

first: Zachary

last: Chalmers


title: Amino acid licensing of regulatory T cell function requires signaling via small G proteins Rag and Rheb

city: Memphis

first: Hongbo

last: Chi

state: TN

address: 262 Danny Thomas Place

department: Immunology

institute: St Jude Children's Research Hospital

summary:
Amino acids license Treg cell function by priming and sustaining TCR induced mTORC1 activity and Rag and Rheb GTPases as central regulators of mTORC1 activation in effector Treg (eTreg) cells
RNA was purified from CD25+ Treg cells isolated from Cd4CreRragafl/flRragabfl/fl or Cd4CreRhebfl/flRhebl1–/– mice or their littermate controls.

overall_design: In total 20 samples were analyzed: WT (3 Unsimulated and 3 Stimulated); Rheb1/2 KO (3 Unsimulated and 3 Stimulated) and additional 8 samples of Tregs (2 WT and 2 RagAB KO unstimulated) and (2 WT and 2 RagAB KO Tregs stimulated for 8 hours).

first: Hao

last: Shi

first: Nicole

last: Chapman

first: Yogesh

last: Dhungana


title: The non-coding RNome after splenectomy (cohort B)

city: Houston

first: George

last: Calin

state: TX

address: 1881 East Road

department: Experimental Therapeutics

institute: MD Anderson Cancer Center

summary: We  explored the non-coding (nc)RNome of circulating peripheral blood leukocytes by performing a ncRNA genome wide study

platform_organism:
Homo sapiens
Mus musculus

overall_design: In the study presented here, ncRNA expression levels in peripheral blood leukocytes from 5 pairs of samples obtained before and after splenectomy were analyzed (cohort B).

first: Mihnea

last: Dragomir


title: Comparative genome-scale analysis of Pichia pastoris variants   informs selection of an optimal base strain [protein expression]

city: Cambridge

first: Charles

middle: Arthur

last: Whittaker

institute: Koch Institute

summary: Komagataella phaffii, also known as Pichia pastoris, is a common host for the production of biologics and enzymes, due to fast growth, high productivity, and advancements in host engineering. Several K. phaffii variants are commonly used as interchangeable base strains, which confounds efforts to improve this host. In this study, genomic and transcriptomic analyses of Y-11430 (CBS7435), X-33, GS115, and eight other variants enabled a comparative assessment of the relative fitness of these hosts for recombinant protein expression. Cell wall integrity explained the majority of the variation among strains, impacting transformation efficiency, growth, methanol metabolism, and secretion of heterologous proteins. Y-11430 exhibited the highest activity of genes involved in methanol utilization, up to two-fold higher transcription of heterologous genes, and robust growth. With a more permeable cell wall, X-33 displayed a six-fold higher transformation efficiency and up to 1.2-fold higher titers than Y-11430. X-33 also shared nearly all mutations, and a defective variant of HIS4, with GS115, precluding robust growth. Transferring two beneficial mutations identified in X-33 into Y-11430 resulted in an optimized base strain that provided up to four-fold higher transformation efficiency and three-fold higher protein titers, while retaining robust growth. The approach employed here to assess unique banked variants in a species and then transfer key beneficial variants into a base strain should also facilitate rational assessment of a broad set of other recombinant hosts.

overall_design: Characterization of three clones of each of four P. pastoris strains expressing two different proteins (rhGH and rG-CSF) [=24 strains in total, all integrated using pPICZA backbone (invitrogen)] with triplicate total mRNA samples collected for each

first: Joseph

last: Brady

first: M

first: Duan

last: Ma

first: L

last: Kristensen

first: Neil

last: Dalvie

first: Kerry

last: Love

first: J


title: Tissue- and Species-Specific Patterns of RNA metabolism in Post-Mortem Mammalian Retina and Retinal Pigment Epithelium

city: Irvine

first: Les

last: Kallestad

address: 829 Health Sciences Rd

department: Ophthalmology

institute: University of California Irvine

summary: Accurate analysis of gene expression in human tissues using RNA Sequencing is often dependent on the quality of source material. One major source of variation in mRNA quality is post-mortem time. While it is known that individual transcripts show differential post-mortem stability, few studies have directly and comprehensively analyzed mRNA stability following death, and in particular, the extent to which tissue- and species-specific factors influence post-mortem mRNA stability are poorly understood. This knowledge is particularly important for ocular tissues studies, where tissues obtained post-mortem are frequently used for research or therapeutic applications. To directly investigate this question, we profiled mRNA levels in both neuroretina and retinal pigment epithelium (RPE) from mouse and baboon over a series of post-mortem intervals. We found substantial changes in gene expression as early as 15 minutes in the mouse and as early as three hours in the baboon eye tissues. Importantly, our findings demonstrate both tissue- and species- specific patterns of RNA metabolism, by identifying a set of genes that are either rapidly degraded or very stable in both species and/or tissues. Taken together, the data from this study lays the foundation for understanding RNA regulation post-mortem, and provide novel insights into RNA metabolism in the tissues of the mammalian eye.

sample_organism:
Papio anubis
Mus musculus

platform_organism:
Papio anubis
Mus musculus

overall_design: Mice at different post-mortem intervals were used to collect retina and RPE/choroid tissues.


title: The non-coding RNome after splenectomy (cohort A)

overall_design: In the study presented here, ncRNA expression levels in peripheral blood leukocytes from 5 pairs of samples obtained before and after splenectomy were analyzed (cohort A).


title: Genome-wide analysis of gene expression in MDA-MB-231 breast cancer cells in response to conditional miRNA mediated OPN knockdown

city: Heidelberg

first: Martin

last: Berger

address: INF 581

country: Germany

institute: DKFZ

summary: Our goal was to identify the genes, which are modulated following conditional OPN knockdown for 3 and 6 days. Thus, to elucidate the OPN relevance and to broaden the knowledge on the affected signalling pathways.

overall_design: Cell pellets were collected after 3 and 6 days of cultivating the cells in media with or without doxycycline. There were duplicated total RNA samples for each time interval and each condition.The mRNA expression of the in vitro miRNA treated cells was compared to the respective +dox control.

first: Marineta

last: Kovacheva


title: RNA sequencing of tissue resident macrophages, progenitors and tumor cells from murine head and neck tumors

city: La Jolla

first: Judith

middle: Anne

last: Varner

address: Center for Novel Therapeutics 9310 Athena Circle 9310 Athena Circle

institute: University of California, San Diego

summary: We report the RNA sequences of bone marrow derived and tissue resident macrophages and their progenitor cells from murine head and neck tumors We found that tissue resident macrophages express signatures of proliferation and  immune suppression. By comparison, bone marrow derived macrophages express signatures of inflammation and immune response. Sequences show that these macrophage populations are distinct from each other and  form their progenitor and tumor cells.

overall_design: Murine macrophages were sorted from implanted head and neck tumors using flow sorting for CD45+CD11b+ Gr1-F4/80hi cell populations.3 replicate samples, each pooled cells from3- 4 replicate mice were sequenced per tumor model: HPV+MEER, HPV-MEER and SSCVII. 3 replicate aliquots of tumor cell lines were also sequenced (HPV+MEER, HPV-MEER and SSCVII). Additionally, triplicate preparations of macrophage colonies derived from these sorted macrophages were also sequenced.

first: Paulina

last: Pathria

first: Hideyuki

last: Takahashi

first: Minya

last: Pu


title: Single cell profiling reveals sex, lineage and regional diversity in adult mouse kidney

city: Los Angeles

first: Andrew

last: McMahon

state: California

address: 1425 San Pablo St, BCC 312

department: Stem Cell Biol & Regen Med

institute: University of Southern California

summary: To obtain new insight into the mammalian kidney, anatomy-guided, single cell RNA sequencing was performed on the adult male and female mouse kidney. Key observations were followed up through a variety of secondary studies including genetic lineage tracing. The data document novel cell diversity, unexpected origins to key cell types, and significant sex differences centered on proximal tubules segments of the nephron and principal cells of the collecting system. A searchable database integrating these data will facilitate an understanding of gene to cell relationships in the normal and diseased mammalian kidney.

overall_design: With regard to generating the scRNASeq dataset, single cell dissociation was optimized for micro-dissected kidney zones [cortex, outer medulla and inner medulla ] of two adult male and female C57BL6/J mice.  Single cell suspensions were processed through the 10X Genomics Chromium platform with Illumina Hi-Seq sequencing of barcoded single-cell libraries.  Gene/barcode matrices were merged and further processed using the Seurat R package to perform unsupervised clustering. Profiles were annotated by matching enriched gene sets with kidney cell-type specific markers. Key observations were followed up through a variety of secondary studies including genetic lineage tracing.

last: Ransick

first: Nils

middle: O

last: Lindstrom

first: Albert

last: Kim

first: Jing

last: Liu


title: Transcriptomic changes induced by a new Src Family Kinase Inhibitor and proton radiation in glioblastoma cells

city: Cefalù

first: Valentina

last: Bravatà

address: Contrada Pietrapollastra Pisciotto

institute: IBSBC CNR

summary: Glioblastoma multiforme (GBM) is a central nervous system tumour. The current standard care for GMB is surgical resection, followed by conventional radiotherapy (RT) often combined with daily drug (temozolomide) administration. However, these treatment modalities are not currently curative and the resistance to both chemotherapy and RT plans is the main cause of GBM care failures. In this scenario, proton therapy (PT) could be used as a successful strategy for GBM treatment, being able to regulate the balance between tumour control and the normal tissue tolerance. In addition, new drugs could be used as radiosensitizing agents combined with PT in order to optimize GBM care. In this work we analyzed the GEP of the U87 MG human glioblastoma cell line, after treatment with PT alone or in combination with a new targeted compound, named Si306 (property of Lead Discovery Siena, Siena, Italy). We described GEP induced by both treatments, highlighting for the first time, the cell pathways induced by Si306. Summarizing, our results suggesting this compound as a novel possible candidate to treat GBM in combination with PT.

overall_design: We performed two-color hybridization experiments using Agilent Technologies whole human genome 4x44K microarrays after i) proton treatment and ii)new farmacological coumpound named Si306 and radiation (protons) combined treatments; in U87 MG human glioblastoma cell line. Samples were named as follow: U87_2Gy; U87_10Gy; U87 2Gy + 10µM Si306; U87 10Gy + 10µM Si306.


title: Control ChIP-seq from suprapubic skin (ENCSR531AUV)

status: Public on Nov 01 2019

city: Stanford

first: ENCODE

last: DCC

address: 300 Pasteur Dr

institute: ENCODE DCC

summary: For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Ectopic expression of the homeobox gene Cdx2 in the epiblast

city: Nantes

first: Victor

last: GOURAIN

address: 30 Bd Jean Monnet

institute: Centre de recherche en transplantation et immunologie

summary: This dataset describes the transcriptomic profiling by mRNA-seq of head tissues of E10.5 control or ectopically Cdx2-expressing embryos. Each condition was analyzed in 3 heads to address the role of Cdx2 in embryonic axis determination.

overall_design: Embryonic head samples (E10.5) from control mice and mice engineered for inducible expression of Cdx2 in the anterior epiblast at gastrulation were tested by RNASeq (3 embryos for each condition), resulting in a total of 6 samples. The pregnant females were intraperitoneally injected once with Tamoxifen at 2mg in corn oil at day 6.5 post coitum.

first: Isabelle

last: Duluc

first: Jean-Noel

last: Freund


title: Transcriptome profiles of the different expression genes in peripheral blood mononuclear cells (PBMCs) of calves infected with two different virulent Mycoplasma bovis strains

city: Wuhan

first: JIN

last: CHAO

state: Hubei

address: 1#, Shizishan Street

institute: Huazhong Agricultural University

summary: Mycoplasma bovis (M.bovis) is a critical pathogen of bovines resulting in pneumonia, mastitis, arthritis, etc. To reveal its virulence related factors, a virulent M. bovis HB0801 and its derived vaccine strain P150 were infected calve and the transcriptome profiles of PBMCs were compared by using of the microarray at 7 days after infection. The data postulated the pathogenic mechanism of wild strain and immune mechanism of the attenuated strain to provide clues for the further research of the interaction between M. bovis and its host.

overall_design: Nine calve were nasal inoculated with 109 CFU of HB0801 strain or its P150 strain respectively,or correspond volume of PPLO broth as the negative control,  with three calve in one group. After 7 days post-incubated, PBMCs were isolated from blood samples on a Ficoll gradient. Then the PBMCs were inoculated in a 12-well plate at a density of 2-4 × 106 live cells each well, and co-incubated with 2μg for each well heat-killed either HB0801 or P150 M. bovis strains. Transcriptome profiles of peripheral blood mononuclear cells (PBMC) were compared by using of the microarray.

first: Jin

last: Chao

first: Han

last: Xiaoxiao

first: Guo

last: Aizhen

first: Liu

last: Kai

first: Li

last: Qingni

first: Peng

last: Qingjie

first: Zhang

last: Hui

first: Lu

last: Siyi

first: Hu

last: Changmin

first: Chen

last: Yingyu


title: Discovery of autism/intellectual disability somatic mutations in Alzheimer's brains: mutated ADNP cytoskeletal impairments and repair as a case study

city: Rehovot

first: Dan

last: Ben-Avraham

address: Hertzel 234

department: Grand Israel National Center for Personalized Medicine

country: Israel

institute: Weizmann Institute of Science

summary: De novo mutated ADNP is a most prevalent gene driving syndromic autism with intellectual disability. Using droplet digital PCR and RNA sequencing we identified somatic mutations in ADNP and in other genes in the olfactory bulb and hipocampi of Alzheimer's disease (AD) patients.

overall_design: RNA-Seq of the olfactory bulb of 19 AD patients and 20 age-matched controls were generated by deep sequencing postmortem tissue, using Illumina Hi-seq 2500. Mutation frequencies of different genes was compared between the groups.

first: Yanina*

last: Ivashko-Pachima

first: Adva*

last: Hadar

first: Iris

last: Grigg

first: Vlasta

last: Korenkova

first: Oxana

last: Kapitansky

first: Gidon

last: Karmon

first: Michael

last: Gershovits

first: Laura

last: Sayas

first: Frank

last: Kooy

first: Johannes

last: Attems

first: David

last: Gurwitz

first: Illana

last: Gozes


title: Impact of biotic and abiotic factors on the expression of fungal effector-encoding genes in axenic growth conditions

city: Thiverval Grignon

first: Julie

last: Gervais

address: Avenue Lucien Brétignières

department: BIOGER

institute: INRA

summary: In phytopathogenic fungi, the expression of hundreds of small secreted protein (SSP)-encoding genes is induced upon primary infection of plants while no or a low level of expression is observed during vegetative growth. In some species such as Leptosphaeria maculans, this coordinated in-planta upregulation of SSP-encoding genes expression relies on an epigenetic control but the signals triggering gene expression in-planta are unknown. In the present study, biotic and abiotic factors that may relieve suppression of SSP-encoding gene expression during axenic growth of L. maculans were investigated. Some abiotic factors (temperature, pH) could have a limited effect on SSP gene expression. In contrast, two types of cellular stresses induced by antibiotics (cycloheximide, phleomycin) activated strongly the transcription of SSP genes. A transcriptomic analysis to cycloheximide exposure revealed that biological processes such as ribosome biosynthesis and rRNA processing were induced whereas important metabolic pathways such as glycogen and nitrogen metabolism, glycolysis and tricarboxylic acid cycle activity were down-regulated. A quantitatively different expression of SSP-encoding genes compared to plant infection was also detected. Interestingly, the same physico-chemical parameters as those identified here for L. maculans effectors were identified to regulate positively or negatively the expression of bacterial effectors. This suggests that apoplastic phytopathogens may react to similar physiological parameters for regulation of their effector genes.

overall_design: Leptosphaeria maculans expression profiles in vitro with and without cyclohemide were generated by deep sequencing, in duplicate using Illumina HiSeq.

first: Michel

last: Meyer

first: Salim

last: Bourras

first: Karine

last: Labadie

first: Corinne

last: Cruaud

first: Marie-Hélène

last: Balesdent

first: Thierry

last: Rouxel


title: Chip-chip from MDA-MB-231 cells with SMYD2 and EZH2

status: Public on Nov 03 2019

city: Tianjin

first: Yan

last: Wang

address: #22 Qixiangtai Road

department: Department of Biochemistry and Molecular Biology

institute: Tianjin Medical University

type: Genome binding/occupancy profiling by genome tiling array

summary: The histone methyl transferase EZH2 and SMYD2 are master epigenetic regulators involved in histone methylation and gene transcription repression. Here, we report that SMYD2 and EZH2 may act as a complex in transcriptional regulation and are involved in the progression of breast cancer. ChIP-on-chip assays were performed to find unique promoters co-targeted by EZH2 and SMYD2 in MDA-MB-231 cells.

overall_design: comparison of SMYD2 and EZH2 target genes in MDA-MB-231 cell line.


title: Comparative genome-scale analysis of Pichia pastoris variants informs selection of an optimal base strain

first: Charles

last: Whittaker

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

overall_design: Refer to individual Series


title: Condensin II is recruited to promoters by pRb and regulates expression of divergently paired genes

city: London

first: Fred

last: Dick

state: ON

address: Cancer Research Labs 790 Commissioners Road East

institute: Western University


title: Histone ChIP-seq from tibial nerve (ENCSR981CTV)

first: ENCODE

last: DCC


title: Histone ChIP-seq from esophagus muscularis mucosa (ENCSR522MTS)


title: Histone ChIP-seq from stomach (ENCSR552ICY)


title: Histone ChIP-seq from tibial nerve (ENCSR516LQO)


title: Replication-fork arrest at tRNA genes in S. cerevisiae does not require tRNA transcription and is facilitated by topoisomerases and Rad18-dependent repair pathways

status: Public on Nov 02 2019

city: New York

first: Duncan

last: Smith

state: NY

address: 1009 Silver Center, 100 Washington Sq E

department: Dept. of Biology/Center for Genomics and Systems Biology

institute: New York University

summary: tRNA genes (tDNAs) are widely studied sites of replication-fork arrest and genome instability in the budding yeast Saccharomyces cerevisiae. tDNAs are extremely highly transcribed, and serve as constitutive condensin binding sites. Although tRNA transcription by RNA polymerase III (RNAPIII) has previously been identified as stimulating replication-fork arrest at these loci, the nature of the block to replication has not been incontrovertibly demonstrated. Here, we describe a systematic, genome-wide analysis of the contributions of transcription factor binding,  transcription, topoisomerase activity, and condensin-mediated clustering to replication-fork arrest at tDNAs in yeast. We show that a polar block to replication is maintained at tDNAs even when tRNA transcription is abolished by depletion of one or more subunits of RNAPIII. By contrast, analogous depletion of the essential transcription factor TFIIIB removes the obstacle to replication in the same background. Therefore, our data suggest that the RNA polymerase III transcription complex itself represents an asymmetric obstacle to replication even in the absence of RNA synthesis. We additionally demonstrate that replication-fork mobility past tDNAs is unaffected by the global depletion of condensin from the nucleus, but can be stimulated by the removal of topoisomerases or Rad18-dependent DNA repair pathways.

overall_design: Factors with the potential to block replication forks at tDNAs were depleted. The resultant changes in fork progression were quantified as the ratio of Watson:Crick-mapping Okazaki fragments from high-throughput sequencing data.

first: Rani

last: Yeung

middle: J


title: Control ChIP-seq from stomach (ENCSR538MSN)


title: BCG stimulated C57BL/6-derived BMDM

city: Fort Collins

first: Angelo

last: Izzo

state: Colorado

address: 1682 Campus Delivery

department: MIcrobiology, Immunology, and Pathology

institute: Colorado State University

summary: BCG stimulated C57BL/6-derived BMDM, using PAMM-150Z RT2 Profiler™ PCR Array for Mouse Cytokines and Chemokines

overall_design:
Bone marrow derived macrophages (BMDM) from C57BL/6 mice were stimulated with either BCG or gamma-irradiated BCG for 24 hours
The aim of the study was to determine whether live BCG was required to produce inflammatory cytokines from macrophages

first: Linda

first: Antonio


title: Histone ChIP-seq from esophagus muscularis mucosa (ENCSR525JJM)


title: Control ChIP-seq from breast epithelium (ENCSR980TBV)


title: Histone ChIP-seq from tibial artery (ENCSR960VRR)


title: Histone ChIP-seq from sigmoid colon (ENCSR960AAL)


title: Histone ChIP-seq from gastroesophageal sphincter (ENCSR965BLU)


title: AlkB-facilitated RNA methylation sequencing (ARM-seq) and Demethylase-thermostable group II intron RT tRNA sequencing (DM-tRNA-seq) [spleen]

status: Public on Nov 08 2019

city: Santa Cruz

first: Todd

last: Lowe

address: 1156 High Street

department: Biomolecular Engineering and Bioinformatics

institute: University of California Santa Cruz

summary: The goal of this study was to determine the state of the tRNA transcriptome in Spleen tissue of Mus Musculus (Mouse).  This includes expression data of mature tRNAs and tRNA fragments (tRFs), as well as associated modification  states of these RNAs assessed using mismatching percentages from sequencing data.

overall_design: Included are ARM-seq and DM-tRNA-seq libraries derived from isolated total small RNA from C57BL/6J male Spleens.  These experiments were performed in triplicate (biological) and subjected to NGS.

first: Jonathan

middle: M

last: Howard

first: Andrew

last: Holmes

first: Patricia

last: Chan

first: Aidan

last: Manning


title: Histone ChIP-seq from upper lobe of left lung (ENCSR505YFA)


title: Histone ChIP-seq from stomach (ENCSR503XFW)


title: Histone ChIP-seq from spleen (ENCSR506DCR)


title: Histone ChIP-seq from esophagus squamous epithelium (ENCSR952BJX)


title: TF ChIP-seq from prostate gland (ENCSR946MNG)


title: Histone ChIP-seq from stomach (ENCSR944KAZ)


title: Histone ChIP-seq from stomach (ENCSR493MQY)


title: TF ChIP-seq from suprapubic skin (ENCSR485VQV)


title: Histone ChIP-seq from gastroesophageal sphincter (ENCSR939CJE)


title: Histone ChIP-seq from upper lobe of left lung (ENCSR469YCE)


title: Histone ChIP-seq from Peyer's patch (ENCSR440PMP)


title: Histone ChIP-seq from right atrium auricular region (ENCSR459CKR)


title: Histone ChIP-seq from spleen (ENCSR928BGP)


title: Histone ChIP-seq from spleen (ENCSR426VHO)


title: Histone ChIP-seq from breast epithelium (ENCSR936LAH)


title: Histone ChIP-seq from tibial artery (ENCSR923DBA)


title: Histone ChIP-seq from Peyer's patch (ENCSR416ZMW)


title: Control ChIP-seq from spleen (ENCSR889RIF)


title: Histone ChIP-seq from suprapubic skin (ENCSR410BWN)


title: Histone ChIP-seq from esophagus squamous epithelium (ENCSR463NAD)


title: Histone ChIP-seq from stomach (ENCSR843UEZ)


title: Histone ChIP-seq from tibial artery (ENCSR891BTJ)


title: Histone ChIP-seq from suprapubic skin (ENCSR836VZX)


title: Histone ChIP-seq from right atrium auricular region (ENCSR392WQN)


title: Histone ChIP-seq from tibial nerve (ENCSR860ZCZ)


title: Histone ChIP-seq from suprapubic skin (ENCSR413QLR)


title: Histone ChIP-seq from tibial nerve (ENCSR384MUF)


title: Histone ChIP-seq from spleen (ENCSR407UEE)


title: Control ChIP-seq from right atrium auricular region (ENCSR368NLE)


title: Histone ChIP-seq from right atrium auricular region (ENCSR817FGU)


title: Histone ChIP-seq from suprapubic skin (ENCSR362QYU)


title: Histone ChIP-seq from prostate gland (ENCSR841AJO)


title: Histone ChIP-seq from suprapubic skin (ENCSR374XIN)


title: Histone ChIP-seq from esophagus muscularis mucosa (ENCSR821VGC)


title: Control ChIP-seq from tibial artery (ENCSR807FIZ)


title: Histone ChIP-seq from right atrium auricular region (ENCSR361XMB)


title: Histone ChIP-seq from sigmoid colon (ENCSR807XUB)


title: Histone ChIP-seq from breast epithelium (ENCSR793QCL)


title: Histone ChIP-seq from gastroesophageal sphincter (ENCSR353MNV)


title: Histone ChIP-seq from Peyer's patch (ENCSR349GPJ)


title: Histone ChIP-seq from tibial artery (ENCSR780CNW)


title: Control ChIP-seq from gastroesophageal sphincter (ENCSR343GIV)


title: Control ChIP-seq from tibial nerve (ENCSR329HFV)


title: Histone ChIP-seq from prostate gland (ENCSR768PFZ)


title: Histone ChIP-seq from tibial artery (ENCSR764OHK)


title: Histone ChIP-seq from breast epithelium (ENCSR263XKR)


title: Control ChIP-seq from upper lobe of left lung (ENCSR746QZL)


title: Histone ChIP-seq from tibial nerve (ENCSR245VRR)


title: Histone ChIP-seq from sigmoid colon (ENCSR734ZTQ)


title: Histone ChIP-seq from esophagus squamous epithelium (ENCSR731QXN)


title: Control ChIP-seq from Peyer's patch (ENCSR708OCZ)


title: Histone ChIP-seq from upper lobe of left lung (ENCSR276OPI)


title: TF ChIP-seq from spleen (ENCSR343RJH)


title: Histone ChIP-seq from esophagus squamous epithelium (ENCSR706KWR)


title: Histone ChIP-seq from esophagus muscularis mucosa (ENCSR188HXK)


title: Histone ChIP-seq from upper lobe of left lung (ENCSR714FDJ)


title: TF ChIP-seq from right atrium auricular region (ENCSR232OFD)


title: Histone ChIP-seq from suprapubic skin (ENCSR702JHA)


title: Histone ChIP-seq from stomach (ENCSR227DGG)


title: Histone ChIP-seq from sigmoid colon (ENCSR181HTE)


title: Control ChIP-seq from esophagus squamous epithelium (ENCSR644XSS)


title: Histone ChIP-seq from sigmoid colon (ENCSR654KVJ)


title: Histone ChIP-seq from prostate gland (ENCSR690CSD)


title: Histone ChIP-seq from prostate gland (ENCSR155XVP)


title: Histone ChIP-seq from tibial artery (ENCSR626BAM)


title: Histone ChIP-seq from tibial nerve (ENCSR639JPM)


title: Histone ChIP-seq from Peyer's patch (ENCSR632SLJ)


title: Histone ChIP-seq from esophagus muscularis mucosa (ENCSR621MTP)


title: Histone ChIP-seq from esophagus squamous epithelium (ENCSR153AXQ)


title: Histone ChIP-seq from breast epithelium (ENCSR134LLK)


title: Histone ChIP-seq from gastroesophageal sphincter (ENCSR600TOW)


title: Histone ChIP-seq from upper lobe of left lung (ENCSR595MTV)


title: Control ChIP-seq from sigmoid colon (ENCSR099RQB)


title: Histone ChIP-seq from prostate gland (ENCSR153NDQ)


title: Control ChIP-seq from prostate gland (ENCSR559IPI)


title: Histone ChIP-seq from gastroesophageal sphincter (ENCSR134KZX)


title: Histone ChIP-seq from Peyer's patch (ENCSR667SCY)


title: Histone ChIP-seq from breast epithelium (ENCSR568QQU)


title: Histone ChIP-seq from breast epithelium (ENCSR081OTO)


title: TF ChIP-seq from tibial artery (ENCSR079YAP)


title: Histone ChIP-seq from esophagus squamous epithelium (ENCSR079NLY)


title: Histone ChIP-seq from Peyer's patch (ENCSR063BPD)


title: Histone ChIP-seq from sigmoid colon (ENCSR043RXI)


title: Histone ChIP-seq from spleen (ENCSR556QXD)


title: Histone ChIP-seq from upper lobe of left lung (ENCSR074WIB)


title: Histone ChIP-seq from esophagus squamous epithelium (ENCSR012KZW)


title: Characterisation of HIF-dependent alternative isoforms in pancreatic cancer

city: Zurich

first: Gunnar

last: Rätsch

state: -None-

address: Universitatstrasse 6

department: Institute for Machine Learning

institute: ETH Zürich

summary: Intra-tumor hypoxia is a common feature in many solid cancers. Although transcriptional targets of hypoxia-inducible factors (HIFs) have been well characterized, alternative splicing or processing of pre-mRNA transcripts which occurs during hypoxia and subsequent HIF stabilization is much less understood. Here, we identify HIF-dependent alternative splicing events after whole transcriptome sequencing in pancreatic cancer cells exposed to hypoxia with and without downregulation of the aryl hydrocarbon receptor nuclear translocator (ARNT), a protein required for HIFs to form a transcriptionally active dimer.

overall_design: We set out to perform whole transcriptome sequencing in pancreatic cancer cells with and without perturbation of HIF transcriptional activity (via siARNT) in normoxic (21% O2) and hypoxic (1% O2) settings. This results in 4 conditions, 3 replicates each.

first: Philipp

last: Markolin

first: Wilhelm

last: Krek

first: Natalie

last: Davidson


title: Histone ChIP-seq from spleen (ENCSR091IRL)


title: Transcription profiling of rice (cv. Nipponbare) coleoptiles treated with low-fluence UV-B

city: Katano shi

first: Moritoshi

last: Iino

state: Osaka Prefecture

address: Kisaichi

department: Graduate School of Science

country: Japan

institute: Osaka City University

summary: The elongation growth of japonica rice (cv. Nipponbare) coleoptiles was found  to be inhibited specifically by a short UV-B irradiation (e.g., 10 min) that provides a fluence as low as 1.0 μmol m-2. Here we analyzed if there is a similar response at transcriptional level using rice microarray.

overall_design: The gene expression profile of the red-light-grown rice coleoptiles treated with low-fluence UV-B (0.065 μmol m-2 s-1, 10 min) was compared with that of non-treated controls using the Rice Expression 4x44K Microarray (two-color system). Comparisons were made at two time points: 20 and 60 min after the onset of UV-B irradiation and using three sample sets obtained on different occasions.

first: Muhammad

last: Idris

first: Lei

last: Jiang

first: Seiichiro

last: Kiyota

first: Jun

last: Hidema


title: Mycobacterium tuberculosis m4C DNA methyltransferase Rv3204 promotes mycobacteria survival under oxidative stress

city: chongqing

first: jingjing

last: niu

institute: Southwest University

summary: ROS can damage cellular components and is a key player in many cellular signaling. Tuberculosis remains a major global public health concern largely due to the ability of its causative agent-Mycobacterium tuberculosis (Mtb) to subvert ROS toxicity. DNA methylation deficiency was previously shown to attenuate the Mtb virulence. But the role of DNA methyltransferase in Mycobacteria survival and the link with ROS are unknown. Mycobacterial protein Rv3204 is a DNA methyltransferase specific for N4-methylcytosine instead of N6-methyladenine (m6A) or 5-methylocytosine (m5C). The survival rate of m4C methyltransferase deletion mutants was lowered, accompanied by higher accumulation of ROS and failure of upregulating the transcription of gene engaged in ROS clearance upon rifampin(Rif) exposure.

overall_design: mRNA profiles of M.smegmatis overexpression strains WT and  Ms_1939 by deep sequencing, using Illumina GAIIx

first: Jianping

last: Xie

first: Jingjing

last: Niu


title: Histone ChIP-seq from gastroesophageal sphincter (ENCSR037GFN)

first: ENCODE

last: DCC


title: The retrograde signals responsible for photoacclimation in the marine diatom Phaeodactylum tricornutum

city: New Brunswick

first: Ananya

last: Agarwal

state: New Jersey

address: 71 Dudley Road

department: Microbial Biology

institute: Rutgers, The State University of New Jersey

summary: Photoacclimation of unicellular algae allows for reversible changes in the number and/or effective absorption cross section of photosynthetic units on time scales of hours to days in response to changes in irradiance. The process involves an enigmatic signaling pathway from the plastid to the nucleus.Our results reveal, for the first time, a fundamental pathway of retrograde signal transduction in a eukaryotic photosynthetic alga.

overall_design: Phaeodactylum tricornutum mRNA profiles of low light (20 umol photons/m2/s) and high light (940 umol photons/m2/s) acclimated wild-type (WT) were generated by deep sequencing, in triplicate, using Illumina TruSeq. The most differentially expressed genes were targeted by RNA interference to identify genes of interest. Phenotypic characterization of resultant transformants along with RT-qPCR verification was conducted on applicable strains.

first: Orly

last: Levitan

first: Maria

middle: H

last: Cruz de Carvalho

first: Paul

last: Falkowski


title: Single-cell transcriptomics uncovers zonation of function in the mesenchyme during liver fibrosis

city: Edinburgh

first: John

middle: Roger

last: Wilson-Kanamori

address: 47 Little France Crescent

department: Centre for Inflammation Research

institute: University of Edinburgh

summary: We profile the transcriptomes of ~30,000 mouse single cells to deconvolve the hepatic mesenchyme in healthy and fibrotic liver at high resolution. We reveal spatial zonation of hepatic stellate cells across the liver lobule, designated portal vein-associated HSC and central vein-associated HSC, and uncover an equivalent functional zonation in a mouse model of centrilobular fibrosis. Our work illustrates the power of single-cell transcriptomics to resolve key collagen-producing cells driving liver fibrosis with high precision.

overall_design: Single-cell transcriptomic data (10x and SS2) are presented from both healthy mice and following carbon tetrachloride administration (acute (72h) and chronic (6wk) injury models). SS2 data also contains cells harvested from mice 14d post bile duct ligation.

first: Ross

last: Dobie

first: Neil

last: Henderson


title: Dual recognition of H3K4me3 and DNA by the ISWI component ARID5 regulates floral phase transition in Arabidopsis [ChIP-Seq]

city: Beijing

first: Xin-Jian

last: He

address: No. 7, zhongguancun life science park road, changping district

institute: National Institute of Biological Sciences

summary: Chromatin remodeling and histone modifications are important for development and floral phase transition in plants. However, it is largely unknown whether and how these two epigenetic regulators coordinately regulate the important biological processes. Here, we identified three types of ISWI chromatin remodeling complexes in Arabidopsis thaliana. We found that ARID5, a subunit of a plant-specific ISWI complex, can regulate development and floral phase transition. The ARID-PHD dual domain cassette of ARID5 recognizes both the H3K4me3 histone mark and AT-rich DNA. We determined the ternary complex structure of the ARID5 ARID-PHD cassette with an H3K4me3 peptide and an AT-containing DNA. The H3K4me3 peptide is combinatorially recognized by the PHD and ARID domains, while the DNA is specifically recognized by the ARID domain. Both PHD and ARID domains are necessary for the association of ARID5 with chromatin. The results suggest that the dual recognition of AT-rich DNA and H3K4me3 by the ARID5 ARID-PHD cassette may facilitate the association of the ISWI complex with specific chromatin regions to regulate development and floral phase transition

overall_design: Extract the whole genomic DNA for analysis

first: Lian-mei

last: Tan

first: Yin-na

last: Su


title: Transcriptomic analysis of Zinc treatment in Acinetobacter baumannii

city: North Ryde

first: Varsha

last: Naidu

state: NSW

address: 14 Eastern Rd

department: Molecular Sciences

institute: Macquarie University

summary: In A. baumannii, adequate zinc acquisition is required for the bacterium to express its full virulence potential. In excess, zinc can also induce significant cellular toxicity. The impact of zinc toxicity on biological systems has primarily been linked to its ability to bind non-zinc metalloproteins. The consequences of zinc intoxication include enhanced oxidative stress susceptibility and alteration of carbon source utilisation.

overall_design: The association between zinc stress and oxidative stress has been studied in significant detail, where the oxidative stress catalyses the ability of zinc to bind non-cognate metalloproteins, and particular, iron-sulphur cluster proteins

first: Karl

last: Hassan

first: Ian

last: Paulsen


title: Dual recognition of H3K4me3 and DNA by the ISWI component ARID5 regulates floral phase transition in Arabidopsis [RNA-Seq]

overall_design: Extract the whole RNA for analysis

first: lian-mei


title: Dual recognition of H3K4me3 and DNA by the ISWI component ARID5 regulates floral phase transition in Arabidopsis


title: MTAP loss promotes stemness and epigenetic reprogramming in Glioblastoma

city: Durham

first: Landon

last: Hansen

state: NC

address: 203 Research Drive, MSRB1 Rm 171

institute: Duke University School of Medicine

summary: Methylthioadenosine Phosphorylase (MTAP) loss is one of the most frequent genetic alterations in Glioblastoma and has been associated with poor clinical outcomes in several cancer types. Here we used patient derived glioblastoma cell lines and manipulated MTAP status to create isogenic pairs with which to study the effects of this alteration on epigenetics, gene expression, and cell identity

overall_design: Comparison of GBM cells with or without functional MTAP protein

first: Ran

last: Sun

first: Rui

last: Yang

first: Simranjit

middle: X

last: Singh

first: Lee

last: Chen

first: Christopher

last: Pirozzi

first: Casey

last: Moure

first: Carlee

last: Hemphill

first: Chin-Pu

first: Ryan

last: Ruger

first: Paula

middle: K

last: Greer

first: Fangping

last: Zhao

first: Carole

last: Grenier

first: Zhiqing

last: Huang

first: Susan

last: Murphy

first: Allan

last: Friedman

first: Roger

middle: E

last: McLendon

first: Darell

last: Bigner

first: Hai

last: Yan

first: Yiping


title: Tyr1 phosphorylation promotes the phosphorylation of Ser2 on the C-terminal domain of RNA polymerase II by P-TEFb

city: San Antonio

first: Zhijie

middle: Jason

last: Liu

state: TEXAS

address: 7703 Floyd Curl Drive

department: Department of Molecular Medicine

institute: Universality of Texas Health Science Center at San Antonio

summary: The Positive Transcription Elongation Factor b (P-TEFb) phosphorylates Ser2 residues of RNA polymerase II’s C-terminal domain (CTD) and is essential for the transition from transcription initiation to elongation in vivo. Surprisingly, P-TEFb exhibits Ser5 phosphorylation activity in vitro. The mechanism garnering Ser2 specificity to P-TEFb remains elusive and hinders understanding the transition from transcription initiation to elongation. Through in vitro reconstruction of CTD phosphorylation, mass spectrometry analysis, and chromatin immunoprecipitation-seq analysis we uncover a mechanism by which Tyr1 phosphorylation directs the kinase activity of P-TEFb and alters its specificity from Ser5 to Ser2. The loss of Tyr1 phosphorylation causes the reduction of Ser2 and accumulation of RNA polymerase II in the promoter region as detected by ChIP-seq. We demonstrate the ability of Tyr1 phosphorylation to generate a heterogeneous CTD modification landscape that expands the CTD’s coding potential. These findings provide direct experimental evidence for a combinatorial CTD phosphorylation code wherein previously installed modifications direct the identity and abundance of subsequent coding events by influencing the behavior of downstream enzymes.

overall_design: Chromatin immunoprecipitation followed by Next-gen sequencing (ChIP-seq)

first: Zhao

last: Zhang

first: Seema

last: Irani

first: Jessie


title: Chemical Inhibition of Salt-Inducible Kinase as Therapeutic Strategy in Acute Myeloid Leukemia [ChIP-Seq]

city: Cold Spring Harbor

first: Yusuke

last: Tarumoto

address: 1 Bungtown Road

institute: Cold Spring Harbor Laboratory

summary: Genome-wide binding/occupancy profiling by high throughput sequencing

overall_design: Genome-wide analysis of H3K27ac modification in AML with SIK inhibitor treatment

first: Christopher

last: Vakoc


title: pNET-seq (Pol II Ser5) in Arabidopsis

first: Jincong

last: Zhou

address: Tsinghua Yuan

institute: Tsinghua University

summary: Intronic transposon elements (TEs) comprise a large proportion in eukaryotic genomes, but how they regulate the host genes remains to be explored. Our forward genetic screen disclosed the plant specific RNA polymerases IV and V in suppressing intronic TE-mediated cryptic transcription initiation of a chimeric transcripts at FLC (FLCTE). Initiation of FLCTE transcription is blocked by the locally formed intronic heterochromatin, and RNA Pol V direct associates and establishes intronic heterochromatin, thus inhibits the entry of RNA Pol II Ser5p and the occupancy of H3K4 methylation for promoting initiation. Genome-wide Pol II Ser5p native elongation transcription sequencing revealed that this is a common mechanism among intronic heterochromatin-containing genes. This study sheds light on deeply understanding the function of intronic heterochromatin on host genes expression in eukaryotic genome.

overall_design: We conducted pNET-seq with Arabidopsis wild-type (Col-0) and nrpe1-11 mutant seedlings to proflie the Pol II (Ser5) associated RNA.

first: Liangyu

first: Qianwen

last: Sun


title: Unique Transcription Factor Functions Regulate Epigenetic and Transcriptional Dynamics During Cardiac Reprogramming

city: San Francisco

first: Nicole

last: Stone

address: 1650 Owens St.

institute: Gladstone Institutes - UCSF

type: Methylation profiling by high throughput sequencing

summary: To determine the molecular mechanisms by which expression of Gata4, Mef2c, and Tbx5 (GMT) induces direct reprogramming from a cardiac fibroblast toward an induced cardiomyocyte, we performed a comprehensive transcriptomic and epigenomic interrogation of the reprogramming process. Single cell RNA sequencing (GEO Series GSE133452) indicated that a reprogramming trajectory was acquired within 48 hours of GMT introduction, did not require cell division, and was limited mainly by successful expression of GMT. Evaluation of chromatin accessibility by ATAC-seq supported the expression dynamics and revealed widespread chromatin remodeling at early stages of the reprogramming process. Chromatin immunoprecipitation followed by sequencing of each factor alone or in combinations revealed that GMT bind DNA individually and in combination, and that ectopic expression of either Mef2c or Tbx5 is sufficient in some contexts to increase accessibility. We also find evidence for cooperative facilitation and refinement of each factor’s binding in a combinatorial setting. A random-forest classifier that integrated the observed gene expression dynamics with regions of dynamic chromatin accessibility suggested Tbx5 binding is a primary driver of gene expression changes and revealed additional transcription factor motifs co-segregating with reprogramming factor motifs, suggesting new factors that may be involved in the reprogramming process.

overall_design: Examination of methylome of induced cardiomyocytes. Whole genome bisulfite sequencing (WGBS) was performed with three biological replicates on our starting population of neonatal cardiac fibroblasts, and cardiac reporter-positive cells from day 3 and day 7 after reprogramming induction.

middle: R

first: Casey

middle: A

last: Gifford

first: Deepak

last: Srivastava


title: Chemical Inhibition of Salt-Inducible Kinase as Therapeutic Strategy in Acute Myeloid Leukemia

sample_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: Regulation of the Integrated Stress Response through ATF4 and FAM129A in Prostate Cancer

city: Oslo

first: Fahri

last: Saatcioglu

address: Blindernveien 31

department: Department of Biosciences

country: Norway

institute: University of Oslo

summary:
Cancer cells exploit many of the cellular adaptive responses to support their survival needs. One such  critical pathway in eukaryotic cells is the integrated stress response (ISR) that is important in normal  physiology as well as disease states, including cancer. Since ISR can serve as a lever between survival  and death, regulated control of its activity is critical for tumor formation and growth although the  underlying mechanisms are poorly understood. Here we show that the main transcriptional effector  of ISR, activating transcription factor 4 (ATF4), is essential for prostate cancer (PCa) growth and  survival.
LNCaP cells were transfected with control siRNA or an ATF4-specific siRNA, and 4 days later treated  with 300nM Tg for 5h. Total RNA was isolated and Illumina Human HT-12  expression Bead-Chips (Illumina) were used for global transcriptome analysis according to the  manufacturer’s protocol. The experiment was performed in triplicates.

overall_design: LNCaP cells were induced with Thapsigargin treated with either scrambled siRNA as control or ATF4-  specific siRNA. 3 replicates per group.

first: Nora

last: Pällmann

first: Marte

last: Livgårda

first: Martina

last: Tesikova

first: Hatice

middle: Z

last: Nenseth

first: Yixin

last: Jin

first: Dogukan

last: Koc

first: Nermin

last: Kahraman

first: Hamada

last: Mokhlis

first: Bulent

last: Ozpolat

first: Ladan

last: Fazli

first: Paul

middle: S

last: Rennie

first: Yang


title: Tumor region-specific microarray analysis according to trastuzumab distribution in breast cancer patient derived xenograft

city: Fukuoka

first: Ryosuke

last: Matsukane

address: 3-1-1, Maidashi, Higashi-ku

department: Department of Pharmacy

institute: Kysuhu University Hospital

summary: Our novel drug imaging technique revealed that trastuzumab, which is representative antibody drug for breast and gastric cancer in clinical, distributed heterogeneously inside tumor even though its target receptor, HER2 (Human epidermal growth factor receptor 2) expressed homogeneously. For identifying a predominant regulator of trastuzumab tumor delivery in the tumor site, we tried tumor region-specific microarray analysis according to trastuzumab distribution in patient derived xenograft model.

overall_design: First, we found that trastuzumab was less distributed in stroma high density area in NCC-BCP69 PDX tumor. Then, trastuzumab poor and rich distributed area were selected respectively (each n=3 from several tumor) according to PID-drug imaging analysis and each area was cut off by laser microdissection and a small amount of mRNA was extracted for microarray. We also conducted tumor region specific microarray for the area of stroma-rich and stroma-poor in NCC-BCP69 PDX without trastuzumab treatment as a vehicle (control) experiment (each n=3 from several tumor).

first: Mitsuhiro

last: Hayashi


title: Identification of distinct murine brown adipocyte lineages

city: Neuherberg

first: Dominik

last: Lutter

address: Ingolstädter Landstraße 1

department: Institute for Diabetes and Obesity

institute: Helmholtz Zentrum München

summary: We identify distinct murine brown adipocytes lineages using bioinformatics analysis of gene expression profiles generated by RNAseq. Further comparison with established-database for human and mouse brown fat genes enables us to sort and determine three genes to distinguish different lineages.

overall_design: Analyzing 20 different cell lines isolated from murine brown adipose tissue in 2 developmental stages.

first: Ruth

last: Karlina


title: Genetic signatures of retinal ganglion cells revealed through single cell profiling [non-dissociated RGC]

city: Ames

first: Jeff

last: Trimarchi

state: IA

address: 2437 Pammel Drive

department: Genetics, Development and Cell Biology

institute: Iowa State University

summary: This study aimed to characterize the transcriptomes of adult retinal ganglion cells (RGCs). The physiological properties of these cells were characterized first in non-dissociated retinal tissue. With that information recorded, the cells were isolated for transcriptome profiling.

overall_design: We isolated 29 cells based on their physiological properties and attempted to distinguish them by array profiling.

first: Lauren

last: Laboissonniere

first: Jillian

last: Goetz

first: Adam

last: Mani

first: Gregory

middle: W

last: Schwartz

first: Jeffrey


title: Genetic signatures of retinal ganglion cells revealed through single cell profiling

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


title: PDGFR-alpha signaling in cardiac stems

city: Westmead

first: Ashley

last: Waardenberg

address: 214 Hawkesbury Road

institute: Children's Medical Research Institute


title: Genome-wide transcriptome analysis of NIPBL hematopoeitic progenitors and megakaryocytes

city: Philadelphia

first: Jason

middle: Adam

last: Mills

state: PA

address: 422 Curie Blvd

department: Ophthalmology

institute: The University of Pennsylvania

summary:
The purpose of this study was to compare the transcriptome of NIPBL patient derived Hematopoietic progenitors and patient-derived megakaryocytes to healthy unaffected individuals
Methods: HPC transcriptome profiles of three CdLS patient iPSCs harboring mutations in the NIPBL gene  and megakaryocytes generated from patient-iPSCS were generated by deep sequencing, in triplicate, using Illumina HiSeq 2500. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks.
Results: Using an optimized data analysis workflow, we mapped about 15 million sequence reads per sample to the  human genome and identified transcripts in CdLS-HPCs and transcripts in CdLS-MEGs.
Conclusion: Our data supports dysregulation of megakaroyctye maturation and growth arrest in response to multiple conserved developmental pathways.

overall_design: Examine transcriptome of Control and NIPBL HPCs and MEGs.

first: Ian

middle: D

last: Krantz


title: Proteinase-Activated Receptor 4 (PAR4) mediates cell membrane blebbing in a Gaq/11, Gai independent, RhoA and ß-arrestin-dependent manner.

city: London

first: Jamie

last: Kramer

state: Ontario

address: 1151 Richmond St.

department: Physiology and Pharmacology

institute: University of Western Ontario

summary: To gain a comprehensive understanding of *-arrestin mediated signaling downstream of PAR4 and to guide future studies, we undertook RNAseq analysis of PAR4 activated genes in control cells and in cells lacking *-arrestin-1/-2. The results of this analysis revealed PAR4 regulation of genes involved in processes including blood coagulation and circulation, cell-cell adhesion, sensory perception and neuron-neuron synaptic transmission, terms that relates back to known function of PAR4.

overall_design: RNA profiles of beta-arrestin 1/2 double knockout cells treated with and without PAR4 agonist with respective controls. 2 replicates each.

first: Christina

last: Vanderboor

first: Pierre

last: Thibeault

first: Kevin

middle: C

last: Nixon

first: Rithwik

last: Ramachandran


title: Transcriptome analysis to uncover potential roles of a barley ASR gene in stress tolerance

city: Guelph

first: JOSE

last: CASARETTO

address: 50 Stone Road E

department: MCB

institute: University of Guelph

summary: Whole genome microarray expression profiling was used to identify potential downstream targets and understand cellular processes regulated by a plant ASR protein, particularly HvASR5 from barley, involved in abiotic stress tolerance in cereals. When expressed ectopically, HvASR5 is able to improve growth performance of rice plants under stress conditions. For this experiment, leaf samples from transgenic rice lines overexpressing HvASR5 were compared to wild-type plants. HvASR5 can up-regulate the expression of a distinct set of genes associated with stress responses, metabolic processes, as well as reproduction and development.

overall_design: Two transgenic rice lines showing different transgene expression levels and wild-type rice (Oryza sativa L., cv. Tainung 67) grown under control conditions were chosen for the trancriptome analysis.   Total RNA was extracted from leaves and three biological replicates for each transgenic line and WT were considered for the experiment.

first: Jorge

last: Pérez-Díaz

first: Ellen

last: Zuther

first: Dirk

last: Hincha

first: José

last: Casaretto


title: Genetic signatures of retinal ganglion cells revealed through single cell profiling [dissociated RGC]

first: Jeff

last: Trimarchi

summary:
This study aimed to characterize the transcriptomes of adult retinal ganglion cells (RGCs).
These cells were isolated through their expression of a TdTomato molecule that would only turn on when Cre was present. Cre was controlled by the Parvalbumin promoter.

overall_design: We isolated 14 retinal ganglion cells based on Tomato expression.

first: Lauren

last: Laboissonniere

first: Jillian

last: Martin


title: PDGFR-alpha signaling in P5-P15 small and large cCFU-fibroblasts

summary:
The interstitial and perivascular spaces of the heart contain stem-like cells including cardiac colony forming units - fibroblast (cCFU-F), a sub-fraction of SCA1+PDGFR-alpha +CD31- (S+P+) immature stromal cells with the qualities of mesenchymal stem cells, that we have characterized previously.
Here we explore the role of platelet-derived growth factor receptor (PDGFR-alpha in cCFU-F and S+P+ cell niche regulation in homeostasis and repair. PDGFR-alpha signaling modulated quiescence, metabolic state, mitogenic propensity and colony formation, as well as the rate and stability of self-renewal. Exogenously administered PDGF-AB ligand had anti-aging effects on cCFU-F, akin to those seen in heterochronic parabiotic mice. Post-myocardial infarction (MI), PDGF-AB stimulated S+P+ cell proliferation and conversion to myofibroblasts through a metabolic priming effect, yet significantly enhanced anatomical and functional repair via multiple cellular processes.
Our study provides a rationale for a novel therapeutic approach to cardiac injury involving stimulating endogenous repair mechanisms via activation of cardiac stem and stromal cells.

overall_design: Transcriptome of cardiac derived cultured cCFU-F at P5 or P15 (small and large treated with PDGF-AB (3 replicates) or untreated)


title: Chemical Inhibition of Salt-Inducible Kinase as Therapeutic Strategy in Acute Myeloid Leukemia [RNA-Seq]

first: Yusuke

last: Tarumoto

summary: Transcriptome analysis by high throughput sequencing

overall_design: Gene expression profiles in AML with gene knockout or SIK inhibitor treatment

first: Christopher

last: Vakoc


title: Study of Gene expression under no salt condition from total leaf RNA and  Gene expression after five days of salt stress in 150mM NaCl from total leaf RNA

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

address: 259, Apoorva 4th cross,80 feet Road,RMV 2ND STAGE

country: India

institute: Genotypic Technology

summary: Study of gene expression under no salt condition from total leaf RNA and gene expression after five days of salt stress in 150mM NaCl from total leaf RNA of PcINO1 and OsINO1 introgressed IR-64 transgenic rice lines.

overall_design: Organism : Oryza sativa, Agilent  Rice Gene Expression  8x60k Array (AMADID: 031380) designed by Genotypic Technology Private Limited, Bangalore

first: Sonali

last: Sengupta

first: Sritama

last: Mukherjee

first: Rajeswari

first: A

middle: N

last: Lahiri Majumder


title: Expression data from shRFP, shATF1 in human embryonic stem cells (hESCs)

city: Taipei

first: Shang-Chih

last: Yang

address: 128 Academia Road, Section 2, Nankang, Taipei, 115, Taiwan

department: Genomics Research Center

country: Taiwan

institute: Academia Sinica

summary: Human embryonic stem cells (hESCs) are infected by shRFP and shATF1 lentivirus for 6 days. The global gene profiles are analyzed by Affymatrix expression array.

overall_design: We generated shRFP and shATF1 lentivirus and tested the titer of each virus.  10MOI of each virus were used as infection condition to infect hESCs. 6 Days infected hESCs were collected and performed microarray analysis.


title: PDGFR-alpha signaling in P0 cCFU-fibroblasts

first: Ashley

last: Waardenberg

overall_design: Transcriptome of cardiac derived cultured cCFU-F at P0 bulk cultures, treated with PDGF-AB (3 replicates), AG1296 inhibitor or untreated

middle: J


title: Expression data for E17 mouse placentas harvested 7h after intrauterine injection of LPS in WT and Nrf2-/- mice on a CD-1 background.

city: Baltimore

first: Thomas

last: Sussan

state: MD

address: 615 N. Wolfe Street

department: Environmental Health & Engineering

institute: Johns Hopkins Bloomberg School of Public Health

summary:
Preterm birth (PTB) is the leading cause of neonatal mortality, and surviving infants are at increased risk for lifelong disabilities. Intrauterine inflammation is an etiological factor that drives PTB, and oxidative stress is associated with it. Nuclear erythroid 2-related factor 2 (Nrf2) is a redox-sensitive transcription factor that is the key regulator of the response to oxidative and inflammatory stress. Here, we used the established mouse model of intrauterine inflammation-induced PTB to determine whether Nrf2 is a modifier of susceptibility to PTB and prematurity-related morbidity and mortality in the offspring. We determined that Nrf2-/- mice exhibited a greater sensitivity to exposure to intrauterine inflammation, as indicated by decreased time to delivery, reduced birthweight, and 100% mortality. Placentas from preterm Nrf2-/- mice showed elevated markers of inflammation, oxidative stress, and cell death, and transcriptomic analysis identified numerous key signaling pathways that were differentially expressed between WT and Nrf2-/- mice in both preterm and control samples. Thus, Nrf2 could be a critical factor for gene-environment interactions that may determine susceptibility to PTB. Further studies are needed to determine if Nrf2 is a viable therapeutic target for women who are at risk for PTB and associated complications in the affected offspring.
Pregnant dams on a WT CD-1 and Nrf2-/- background were given intrauterine injections of 25ug LPS on embryonic day 17, according to an established model of preterm birth. Placentas near the injection site were harvested 7h later, prior to onset of delivery.

overall_design: 16 total samples were analyzed, with N=4 samples per group x 4 groups (WT PBS, Nrf2-/- PBS, WT LPS, and Nrf2-/- LPS). Each sample represents multiple placentas from a single litter.

first: Irina

last: Bird

first: Shyam

last: Biswal

first: C

last: Talbot

first: Yuriy

last: Alekseyev


title: Gene expression changes caused by the IRAK1/IRAK4 inhibitor R191 in cell lines of Waldenström’s macroglobulinemia

city: Houston

first: Zhiqiang

last: Wang

state: Texas

address: 7455 Fannin St.

department: Lymphoma and Myeloma

institute: University of Texas MD Anderson Cancer Center

summary:
The L265P mutation in MYD88 is very frequent in tumor cells of Waldenström’s macroglobulinemia (WM), and activates NF-kappaB through IRAK1 and IRAK4. We examined the effect of the IRAK1/4 inhibitor R191 on two cell lines of WM.
Gene expression profiling suggested that R191 reduced activity of AKT and mTOR signaling, consistent with other assays and functional studies. Other changes suggested reduced proliferation and MYC activity, and an ER stress response.

overall_design: Cell lines BCWM.1 and MWCL-1 were treated with R191 at 1.25 uM for 24 hr, and compared to untreated cells.

first: Haiwen

last: Ni

first: Isere

last: Kuiatse

first: Fazal

last: Shirazi

first: Hua

first: Richard

last: Jones

first: R

last: Davis

first: Robert

last: Orlowski


title: Genome-wide disclosure of the Nkx2.2 targets in oligodendrocytes and their progenitor cells suggests several novel target genes

city: odense

first: mads

last: thomassen

address: soender boulevard 29

country: Denmark

institute: odense university hospital

summary: The Nkx2.2 transcription factor contributes to regulate the timing of myelination in the CNS. Still, information about the regulon of Nkx2.2 in oligodendrocytes (Ols) and their progenitor cells (OPCs) is restricted to a few genes. Therefore we aimed to identify the entire regulon of Nkx2.2. We performed transcript profiling of postnatal Nkx2.2-/- mice, investigated the expression of selected transcripts in Ol lineage cells after siRNA induced Nkx2.2 knock-down, and identified the genome-wide active Nkx2.2 binding sites in murine OPCs and Ols by use of ChIP-sequencing technique. Thereby we have found 521 genes with active Nkx2.2 binding sites within 10,000 bp of their gene loci that furthermore are differently expressed in absence or lower expression of Nkx2.2. Functionally, the target genes are associated with mitosis, migration stop, protein transport, lipid metabolism, mitochondrial biogenesis, formation of Ca2+ waves, and WNT signalling. Furthermore, motif discovery techniques and tests for overlaps between sequencing reads suggest that MYRF, OLIG2, SOX10, and TCF3 interact or compete with Nkx2.2 in OPCs/Ols. However, the activator versus repressor activity of Nkx2.2 does not seem to depend on the potential interaction with either of the transcription factors. Test for overlaps with sites of specific histone 3 modifications show that the Nkx2.2 binding sites are more frequently associated H3K4me3 and H3K27ac in genes to which Nkx2.2 may act as an activator. This supports previous studies showing that Nkx2.2 acts in a HDAC1 dependent way. Together this provides new insight into how Nkx2.2 contributes to the timing of OPC differentiation and myelination in CNS.

overall_design: Genome-wide Nkx2.2 targets in mouse oligodendrocyte progenitor cells and in ex vivo differentiated oligodendrocytes examined by ChIP-sequencing technique.

first: Christina

last: Fenger

first: Ben

last: Emery