title: Alcohol metabolism directly fuels histone acetylation in the brain [ChIP-Seq]

overall_design: This study examines occupancy of histone H3 post-translational modification H3K9ac and H3K27ac in mouse hippocampus by chIP-seq. Mice were injected (intraperitoneal) with EtOH or left untreated and were also subjected to an ACSS2-targeting shRNA knockdown or to a control vector injected directly into the brain. Three replicates were done for each condition for H3K27ac, H3K9ac, and input, for a total of 36 samples.


title: Comparing expression in livers of 1-month vs 6-month old mice

status: Public on Aug 01 2019

city: Jerusalem

first: Jacob

last: Rachmilewitz

address: Ein -Kerem

country: Israel

institute: Hadassah Hebrew University medical center

type: Expression profiling by high throughput sequencing

summary: To look for age-related changes in the liver, we used RNAseq gene expression analysis to characterize mRNA expression profile in livers from 1-month vs. 6-month-old mice

overall_design: Liver mRNA profile of 1-month and 6-month old C57BL/6 male mice were generated by deep sequencing in triplicate (each sample is a pool of three mice) using Illumina NextSeq. The sequence reads passed quality filters. qRT–PCR validation was performed using TaqMan and SYBR Green assays

first: Anat

last: Geiger-Maor


title: Preliminary RNA-seq data obtained from H1975 and H661 cells exposed to AAT protein

status: Public on Jul 31 2019

city: Hannover

first: Stephan

last: Immenschuh

state: Deutschland

address: Carl-Neuberg-Str. 1

department: Institute for Transfusion Medicine and Transplant Engineering

country: Germany

institute: Hannover Medical School

summary: Although the classical function of AAT is to inhibit neutrophil proteases, there is evidence that the role of AAT in inflammation is multifaceted. AAT possesses anti-inflammatory activity against immune cells, affects leukotriene B4, TNF-α, IL-8, IFN-γ and IL-1β production and expresses potent anti-apoptotic properties. In addition, AAT has been shown to inhibit the activity of natural killer cells against tumor cells, which indicates that AAT may play multiple functions during cancer development. Therefore, in a situation of occurring cancer cells higher AAT levels may favor microenvironment towards malignant progression. High expression of SERPINA1 gene encoding acute phase protein, α1-antitrypsin (AAT), is associated with poor prognosis in various tumors. Here we examined the significance of SERPINA1 and AAT protein in non-small-cell lung cancer (NSCLC) patients and NSCLC cell lines.

overall_design: The H1975 and H661 cells were grown in serum free medium without or with addition of 2 mg/ml AAT for 24 hours. Afterwards, the total RNA was isolated and quality was assessed using 1 % agarose gels as well as by Agilent 2100 Bioanalyzer using Agilent RNA 6000 Nano Kit. Libraries were prepared in duplicates by using 200 ng of each cell line.

first: Evrim

last: Ercetin

first: Sarah

last: Richtmann

first: Beatriz

last: Martinez Delgado

first: Sabine

last: Wrenger

first: Elena

last: Korenbaum

first: Bin

last: Liu

first: David

middle: S

last: DeLuca

first: Mark

last: Kühnel

first: Danny

last: Jonigk

first: Kadriya

last: Yuskaeva

first: Arne

last: Warth

first: Thomas

last: Muley

first: Hauke

last: Winter

first: Michael

last: Meister

first: Tobias

last: Welte

first: Sabina

last: Janciauskiene

first: Marc

middle: A

last: Schneider


title: Transforming growth factor beta 1 induces methylation changes in lung fibroblasts [Illumina]

city: Ciudad de Mexico

first: Yalbi

middle: Itzel

last: Balderas-Martinez

state: Distrito Federal

address: Calzada de Tlalpan 4502, Sección XVI, Belisario Domínguez

country: Mexico

institute: INER

type: Methylation profiling by genome tiling array

summary: Idiopathic pulmonary fibrosis (IPF) is a complex disease of unknown etiology. Environmental factors can affect disease susceptibility via epigenetic effects. Few studies explore global DNA methylation in lung fibroblasts, but none have focused on transforming growth factor beta-1 (TGF-b1) as a potential modifier of the DNA methylome. Here we analyzed changes in methylation and gene transcription in normal and IPF fibroblasts following TGF-b1 treatment.

overall_design: Primary human lung fibroblasts were obtained from normal and IPF lungs. Control, treated for 24 hours and 5 days fibroblasts of both cell lines were selected for DNA extraction, bisulphite conversion, and further hybridization to the Illumina Infinium Human Methylation 450k array.

first: Miguel

last: Negreros

first: James

last: Hagood

first: Celia

last: Espinoza

middle: I

first: Moises

last: Selman

first: Annie

last: Pardo


title: Paxillin regulates genomic networks in prostate cancer [PC3]

city: Rochester

first: Stephen

middle: R

last: Hammes

state: NY

address: 601 Elmwood Ave, Box 693

department: Medicine

country: USA

institute: University of Rochester

summary: We report that the adaptor protein, paxillin, regulates some proliferative and apoptotic genes in the castration resistant prostate cancer cell line, PC3.

overall_design: PC3 cells were transfected with either Non-specific siRNA or Paxillin-targeted siRNA for  72 hours,  and RNA from these groups were isolated and proceeded to RNA sequecning.

first: Xiaoting

last: Ma

first: Anindita

last: Biswas


title: Transforming growth factor beta 1 induces methylation changes in lung fibroblasts

summary:
This SuperSeries is composed of the SubSeries listed below.
Idiopathic pulmonary fibrosis (IPF) is a complex disease of unknown etiology. Environmental factors can affect disease susceptibility via epigenetic effects. Few studies explore global DNA methylation in lung fibroblasts, but none have focused on transforming growth factor beta-1 (TGF-b1) as a potential modifier of the DNA methylome. Here we analyzed changes in methylation and gene transcription in normal and IPF fibroblasts following TGF-b1 treatment.

overall_design:
Refer to individual Series.
Primary human lung fibroblasts were obtained from normal and IPF lungs. Control, treated for 24 hours and 5 days fibroblasts of both cell lines were selected for analyzing the level of gene expression and DNA methylation.


title: Paxillin regulates genomic networks in prostate cancer [C4-2]

summary: We report that the adaptor protein, paxillin, regulates some androgen responsive genes in the castration resistant prostate cancer cell line,C4-2.

overall_design: C4-2 cells were transfected with either Non-specific siRNA or Paxillin-targeted siRNA for 48 hours, followed by serums starvation of 12 hours, cells are then treated with either 2.5nM dihydrotestosterone (DHT) or vehicle (ethanol), and RNA from these groups were isolated and proceeded to RNA sequecning.


title: Left atrial tissue of rats exposed to rapid atrial pacing

city: Beer-Sheva

first: Yoram

last: Etzion

state: Please Select

address: 1st Ben-Gurion Street

department: Physiology and Cell Biology

institute: Ben-Gurion University, Israel

summary:
Sustained atrial tachycardia leads to multiple molecular and cellular effects collectively defined as atrial tachycardia remodeling (ATR). ATR is thought to play a major role in the self-perpetuating nature of atrial fibrillation (AF) and has been a subject of intense research in large mammalian models of AF. Recently, rodents are increasingly used to gain insight on the pathophysiology AF. However, little is known regarding the effects of rapid pacing on the atria of rats and mice mainly due to technical challenges in electrophysiological studies of unanesthetized rodents. Using an implantable device for electrophysiological studies in unanesthetized rodents we examine, on a daily basis, the effects of continuous rapid atrial pacing (RAP) for at least 4 consecutive days on the developed AF substrate of Sprague-Dawley rats and C57BL6 mice. AF induction protocol consisted 10 aggressive bursts (20 seconds, double diastolic threshold, 10 ms cycle length [CL]). This protocol failed to induce AF at baseline in both species, but repeatedly induced AF episodes in rats following 2 days of sustained RAP. Microarray study of left atrial tissue from rats exposed for 2 days to RAP (70 ms CL) vs control pacing (140 ms CL) identified 304 differentially expressed genes (155 upregulated and 149 downregulated). Real-time qt-PCR confirmed the validity of the microarray. Enrichment analysis and comparison with a dataset of atrial tissue from AF patients revealed indications of increased carbohydrate metabolism, and changes in pathways that are thought to have critical role in human AF including TGF-beta and IL-6 signaling. Among 19 commonly affected genes in comparison with human AF, downregulation of FOXP1 and upregulation of the KCNK2 gene encoding the Kir2.1 potassium channel were conspicuous finding suggesting NFAT activation. Further results in line with NFAT activation included reduced expression of MIR-26, MIR-101, which were linked to upregulation of the KCNK2 in human AF.   Our results demonstrate electrophysiological evidence for AF promoting effects of RAP in rats and some important molecular similarities between the effects of RAP in large and small mammalian models.
The effects of atrial tachypacing are well documented in large mammals but very little is know regarding the effects of tacypacing on the rodent atria.

overall_design: Three pairs of adult male rats were subjected to either atrial tachypacing (70 ms Cycle length) or control pacing (140 ms Cycle length) for 2 days. Thereafter, left atrial tissue was extracted for the microarray analysis.

first: Wesam

last: Mulla


title: Circular RNAs in the ageing African turquoise killifish

city: Cologne

first: Franziska

last: Metge

address: Joseph-Stelzmann-Str 9b

department: Bioinformatics Corefacility

institute: Max Planck Institute for Biology of Ageing

type: Non-coding RNA profiling by high throughput sequencing

summary: In this work we took 9 samples from brain and 6 samples from muscle of the African turquoise killifish (Nothobranchius furzeri) at 3.5, 8.5 and 14 weeks. Total RNA was sequenced and circRNAs were detected.

overall_design: RNAseq of 3 timespoints, 3 replicates each for brain samples, RNAseq of 3 timepoints, 2 replicates each for muscle samples

first: Yumi

last: Kim

first: Christoph

last: Dieterich

first: Dario

last: Valenzano


title: D39 wild-type vs D39 ΔplcR in GM17 medium

city: STOCKHOLM

first: Sulman

last: Shafeeq

address: nobel vag 16

department: MTC

country: Sweden

institute: Karolinska Institutet

summary: Comparison of the Streptococcus pneumoniae D39 wild-type vsD39 ΔplcR (SPD1745) in GM17medium

overall_design: Two condition design comparison of Wild-type strain vs mutant strain including a dye swap

first: Hasan

last: Yesilkaya

first: Oscar

middle: P

last: Kuipers


title: Stress responses, M2 macrophages, and a distinct microbial signature in fatal intestinal acute graft-versus-host disease

city: Woodbury

first: Ashraf

last: Shabaneh

state: MN

address: 2768 Liberty Trail

institute: University of Minnesota

summary: Transcriptome sequencing was applied to 44 colon Graft vs Host Disease (GVHD) biopsies from 22 patients to determine differences in immunology and microbial profiles, along with general differences in somatic gene expressions by determining trends of mapped somatic alignments. Read analysis of somatic alignments were subjected to enrichment analysis of cellular pathways, expression comparisons amongst classes, and immune activity characterization based on outputs of deconvulation alogorithms.  Unmapped alignments were mapped to microbiome reference assemblies to determine non-somatic profiles. Classes were determined based on healthy vs diseased patients, steriod refractory paired with onset biopsies, and a survival cohort as well.  Distinct differences between classes have been noticed in all measures of interest.

overall_design: Characterizing the biopsies consisted of the following steps. RNA extraction was performed on FFPE rectosigmoid biopsies using FFPE biopsies using PureLink® FFPE RNA Isolation Kit (Thermo Fisher Scientific, Waltham, MA, USA). Libraries were prepared using  Illumina HiSeq 2500® platform.  nCounter® Human Immunology panel (NanoString, Seattle, WA) was used to compare immunology findings in comparison to the Cibersort cell deconvulation algorithm. Alignments were pefromed using Tophat and Cufflinks for somatic cells. Microbial reads were isolated and mapped using hisat2 and Pathseq. Gene Enrichment Analysis and Enrichr were used to analyze signal transduction pathways based on gene expressions. Limma was then used for comparison of signal gene expression. Wilcoxin rank sum was used to compare signature microbes. Signature genes and microbes were discovered indicative of survivability, along with enriched pathways discovered as well.

first: Shernan

last: Holtan

first: Jinhua

last: Wang


title: RNA-sequence of epithelial-specific Yap conditional knock out mouse lung

city: Bunkyo-ku

first: Hideaki

last: Isago

state: Tokyo

department: Department of Respiratory Medicine

country: Japan

institute: The University of Tokyo Graduate School of Medicine

summary: The purpose of this study is to identify the roles of epithelial Yap in lung bronchial morphogenesis. We conditionlly knocked out Yap in lung epithelial cells using the SPC-Cre allele, and sequenced mRNA from E14.5 total lung.

overall_design: We extracted mRNA of total lung from control and Yap conditional knock out mice embryo at E14.5.

first: Akihisa

last: Mitani


title: RNA-sequencing of multicellular human liver organoids derived from 3 different iPS cells

city: Tokyo

first: Norikazu

last: Saiki

address: 1-5-45 Yushima, Bunkyo-ku

department: Institute of Research

institute: Tokyo Medical and Dental University

summary: By taking advantage of the foregut generation method, we initially differentiated iPSCs to foregut spheroids through definitive endoderm specification as described. The foregut spheroids were embedded in Matrigel and cultured with retinoic acid (RA). Following 4-day RA treatment, we switched into hepatocyte maturation media for the induction of the hepatocyte differentiation process to establish human liver organoids, hereafter defined as HLO, as early as day 20. To characterize the lipid metabolism related genes in HLO, we conducted RNA sequencing to unbiasedly identify and visualize coordinately expressed gene signatures among groups of three different iPSC derived HLO, and various stage-derived primary-liver cells and tissues as previously described. Correlation spanning tree based on self-organizing maps analysis using 18,338 genes organized into 400 metagenes confirmed overall similarities between HLO and primary hepatocytes, yet distinct from human fetal liver samples. Highly comparable signatures to primary hepatocytes contained major hepatocyte associated genes including lipid metabolism, suggesting that the HLO continue to progress towards a hepatocyte-like fate.

overall_design: Examination of mRNA expression profile in multicellular human liver organoids derived from 3 different iPS cells

first: Takanori

last: Takebe

first: Masaki

last: Kimura

first: Rie

last: Ouchi


title: Insulin-like Growth Factor Binding Protein-7 (IGFBP7) regulation in Hepatocellular Carcinoma

city: San Antonio

first: Yidong

last: Chen

state: Texas

address: 8403 Floyd Curl Drive, MSC 7784

department: Population Health Sciences

institute: UT Health Science Center at San Antonio

summary: Insulin like growth factor binding protein-7 (IGFBP7) inhibits IGF signaling and functions as a potential tumor suppressor for hepatocellular carcinoma (HCC). We profiled genome-wide gene expression of Igfbp7 knockout (Igfbp7-/-) mouse to demonstrate the constitutive activation of IGF signaling and its relationship to the accelerated carcinogen-induced HCC.

overall_design: Three replicates of RNAs derived from WT and IGFBP7-KO adult liver tissues were prepared for RNA-seq libraries and differential expression analysis were performed.

first: Maaged

last: Akiel

first: Devanand

last: Sarkar


title: U1 snRNP complex with cleavage and polyadenylation factors controls mRNA transcription termination

city: Philadelphia

first: Gideon

last: Dreyfuss

state: PA

address: 415 curie blvd

institute: University of Pennsylvania

summary: Full-length transcription in the majority of human genes depends on U1 snRNP (U1) to co-transcriptionally suppress transcription-terminating premature 3’-end cleavage and polyadenylation (PCPA) from cryptic polyadenylation signals (PASs) in introns. However, the mechanism of this U1 activity, termed telescripting, is unknown. Here, we captured a complex, comprising U1 and CPA factors (U1–CPAFs), that binds intronic PASs and suppresses PCPA. U1–CPAFs are distinct from U1-spliceosomal complexes; they include CPA’s three main subunits, CFIm, CPSF, and CstF, lack essential splicing factors, and associate with transcription elongation and mRNA export complexes. Telescripting requires U1:pre-mRNA base-pairing, which can be disrupted by U1 antisense oligonucleotide (U1 AMO), triggering PCPA. U1 AMO remodels U1–CPAFs, revealing changes, including recruitment of CPA-stimulating factors, that explain U1–CPAFs’ switch from repressive to activated states. Our findings outline U1 telescripting mechanism and demonstrate U1’s unique role as central-regulator of pre-mRNA processing and transcription.

overall_design: Base-pairing inhibition U1 snRNP by antisense morpholino oligonucleotide followed by examining transcriptome changes by RNA-seq, mapping snRNPs and CPAFs binding sites by crosslinked IP (XLIP)-seq from HeLa cells.

first: Chao

last: Di


title: Transgenic and conventional cultivar comparison in response to salt stress

city: Jinan

first: Fengning

last: Xiang

state: Shandong

address: 27, Shandanan Road

department: School of life science

country: China

institute: Shandong University

summary: Soybean is one of the main sources of oil worldwide. Salinity severely affect its yield. GmSIN1 is a NAC transcription factor coding gene. Its overexpression (OE) transgenic lines greatly improved the yield in both common and saline fields. This study focuses on founding changes genes between GmSIN1 OE transgenic seedlings and control seedlings under salt stress or non-salt stress conditions. Illumina Solexa sequencing platform was used for the comparative analysis of transcriptome profiles in the roots and leaves of GmSIN1 OE transgenic seedlings and WEI6823 (control) seedlings under mock or 150 mM NaCl treatment for 6 hrs.

overall_design: A total of 8 samples was analyzed. Two soybean genotypes, 2 treatment and 2 biological replicates per condition were used.

first: Shuo

last: Li


title: Genome-wide maps of EGR1 binding in mouse frontal cortex

city: Bethesda

first: Mingan

last: Sun

state: Maryland

address: Building 6B, 6 Center Drive

department: Eunice Kennedy Shriver National Institute of Child Health and Human Development

institute: National Institute of Health

type: Genome binding/occupancy profiling by high throughput sequencing

summary: With anti-EGR1 immunoprecipitated chromatin from mouse prefrontal cortices, we generated  EGR1 binding maps with 12, 014 high-confidence peaks.  Approximately 81% of EGR1 peaks were within genic regions or nearby promoters, and over 45% EGR1 peaks were in the proximal promoter regions within 1 kb from transcription starting sites.

overall_design: Genome-wide profiles of EGR1 binding in prefrontal cortices of 6-week old male mice were generated in duplicate using Illumina HiSeq 2000 platform.

first: Zhixiong

first: Ming-an

first: Jianlin

last: He

first: Hehuang

last: Xie


title: Transforming growth factor beta 1 induces methylation changes in lung fibroblasts [Affymetrix]

first: Yalbi

last: Balderas-Martinez

overall_design: Primary human lung fibroblasts were obtained from normal and IPF lungs. Control, treated for 24 hours and 5 days fibroblasts of both cell lines were selected for RNA extraction and hybridization on Affymetrix microarrays.

first: Miguel

last: Negreros

first: James

last: Hagood

first: Celia

last: Espinoza

first: Moises

last: Selman

first: Annie

last: Pardo


title: AhR activation by TCDD mobilized MDSCs from bone marrow to peritoneal cavity with immunosuppressive activity

city: Columbia

first: Wurood

last: Neamah

state: SC

address: 6439 Garners Ferry Ro., Bld #1/C7

institute: School Of Medicine

summary: We used microRNA microarrays to identify dysregulated microRNAs in peritoneal exudate cells after TCDD administration

overall_design: 10 µg/kg of TCDD or VEH (corn oil) was injected i.p in mice and cells collected from peritoneal cavity after 3 days of treatment.

first: Prakash

last: Nagarkatti

first: Mitzi


title: Third-generation long-read whole-genome sequencing of Dux knockout mouse

city: Shanghai

first: Mingyue

last: Guo

state: Shanghai

address: Siping

department: School of Life science and technology

institute: Tongji University

summary: We applied Single Molecule Real-Time long-read whole-genome sequencing in Dux knockout mouse and confirmed the success of our Dux knockout mouse model.

overall_design: Genome DNA of Dux knockout mouse was deeply sequenced using PacBio Sequel II system at Zhejiang Annoroad Biotechnology Co.Ltd.

first: Yanping

last: Zhang

first: Yixuan

last: Wang


title: Role of the Exon Junction Complex in Danio rerio

status: Public on Jul 30 2019

city: Columbus

first: Pooja

last: Gangras

state: OH

address: 191 W. 9th Ave, apt A3

department: Molecular Genetics

institute: The Ohio State University

summary: The exon  junction complex (EJC) is composed of three core proteins Rbm8a, Magoh and Eif4a3 and is thought to play a role in several post-transcriptional processes. In this study we focus on understanding the role of EJC in zebrafish development. We identified transcriptome-wide binding sites of EJC in zebrafish via RNA:protein immunoprecipitation followed by deep sequencing (RIP-Seq).  We find that, as in human cells, zebrafish EJC is deposited about 24 nts upstream of exon-exon junctions. We also identify transcripts regulated by Rbm8a and Magoh in zebrafish embryos using whole embryo RNA-seq from rbm8a mutant, magoh mutant and wild-type sibling embryos.  This study shows that nonsense mediated mRNA decay is dysregulated in zebrafish EJC mutants.

overall_design: Analysis of exon junction complex (EJC) footprints in Danio rerio and analysis of gene expression in Danio rerio EJC mutants

first: Guramrit

last: Singh


title: A pliable mediator acts as a functional, rather than an architectural bridge, between promoters and enhancers

city: bethesda

first: Seolkyoung

last: Jung

state: MD

address: 10 Center Dr

department: NIAMS

institute: NIH

summary: Our mechanistic understanding of Mediator derives largely from studies of the 25-subunit yeast complex. Here we combine CRISPR-Cas9 genetic screens, degron assays, in situ Hi-C, and cryo-EM to dissect the function and structure of the 33-subunit mammalian Mediator (mMED). Deletion analyses in B, T and ES cells reveal that depletion of the entire complex blocks PolII recruitment genome-wide, while loss of non-essential subunits, including the Tail module, primarily affects promoters linked to multiple enhancers. Contrary to current models, we find that mMED is not required to tether regulatory DNA, a topological activity controlled predominantly by architectural proteins. Structurally, we show that alterations in the Tail module, particularly at the core-Tail interphase, effect crucial mMED-PolII contacts, providing a rationale for how TFs stabilize the mMED-PolII holoenzyme and promote gene expression. Our studies therefore reveal key insights into how Mediator functionally bridge promoters and enhancers to regulate transcription initiation in higher eukaryotes.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design:
ChIP-seq, ATACseq, Hi-C,PromterCaputre Hi-C, CRISPR screen and RNAseq from mouse ESC, CD4+ T cell or CH12 cell line and/or human HCT-116 cell line

The processed data files generated from multiple samples are indicated in the corresponding sample description field, and linked to the Series records or to the corresponding 'r1' sample records.

first: Laila

last: Khattabi

first: Haiyan

last: Zhao

first: Jens

last: Kalchschmidt

first: Natalie

last: Young

first: Peter

last: van Blerkom

first: Philippe

last: Kieffer-Kwon

first: Kyong-Rim

first: Solji

last: Park

first: Xiang

first: Jordan

last: Krebs

first: Subhash

last: Tripathi

first: Noboru

last: Sakabe

first: Debora

last: Sobreira

first: Su-Chen

last: Huang

first: Suhas

last: Rao

first: Nathanael

last: Pruett

first: Daniel

last: Chauss

first: Erica

last: Sadler

first: Andrea

last: Lopez

first: Marcelo

last: Nobrega

first: Erez

middle: L

last: Aiden

first: Francisco

middle: J

last: Asturias

first: Rafael

last: Casellas


title: Development of a chimeric model to study and manipulate human microglia in vivo (bulk RNA-seq dataset)

city: Irvine

first: Mathew

last: Blurton-Jones

state: CA

address: 845 Health Sciences Road, Room 3200

department: Neurobiology and Behavior

institute: University of California, Irvine

summary: iPSC-derived microglia offer a powerful tool to study microglial homeostasis and disease-associated inflammatory responses. Yet, microglia are highly sensitive to their environment, exhibiting transcriptomic deficiencies when kept in isolation from the brain. Furthermore, species-specific genetic variations demonstrate that rodent microglia fail to fully recapitulate the human condition. To address this, we developed an approach to study human microglia within a surrogate brain environment. Transplantation of iPSC-derived hematopoietic-progenitors into the postnatal brain of humanized, immune-deficient mice results in context-dependent differentiation into microglia and other CNS macrophages, acquisition of an ex vivo human microglial gene signature, and responsiveness to both acute and chronic insults. Most notably, transplanted microglia exhibit robust transcriptional responses to Ab-plaques that only partially overlap with that of murine microglia, revealing new, human-specific Ab-responsive genes. We therefore have demonstrated that this chimeric model provides a powerful new system to examine the in vivo function of patient-derived and genetically-modified microglia.

overall_design: mRNA profiles were generated from in vivo iPSC-derived microglia ( 3 cell lines isolated from murine brains, n=3-6 mice/line), saline or LPS-treated iPSC-derived in vitro and in vivo microglia (n=3-5 replicates/condition), and human microglia (n=2 individuals) using an Illumina HiSeq 4000

first: Jonathan

last: Hasselmann


title: Global gene expression of human iPSC directed differentation towards smooth muscle cells using an Acta2eGFP human iPSC reporter line

city: Boston

first: Boston University

last: Microarray and Sequencing Resource

state: MA

address: 72 East Concord Street, E631

department: Microarray and Sequencing Resource

institute: Boston University

summary: Here, we generated and differentiated a human induced pluripotent stem cell line with an ACTA2eGFP reporter towards a smooth muscle-like cell that can be purified and expresses characteristic markers of smooth muscle cells. We performed microarray analysis of day 30 ACTA2eGFP+ and ACTA2eGFP- sorted populations, and the transcriptomic profile of the ACTA2eGFP+ cells is reminiscent of an immature or a synthetic smooth muscle cell phenotype.

overall_design: We prepared microarray expression profiles comparing sorted day 30 ACTA2eGFP+ and ACTA2eGFP- candidate SMCs from our iPSC-SMC directed differentiation. Biological triplicates of all samples were prepared. Global gene expression in all 15 samples was analyzed by Affymetrix GeneChip Human Gene 2.0 ST arrays.

first: George

last: Kwong

first: Darrell

last: Kotton


title: Changes in total RNA in BK deficient mice after 4h sleep deprivation [pools]

city: Zurich

first: Steven

last: Brown

address: Winterthurerstrasse 190

department: Institute of Pharmacology and Toxicology

country: Switzerland

institute: University of Zurich

summary: Animals deficient for the alpha subunit of the large conductance calcium dependent potassium channel (BK) were sleep deprived for 4 hours and compared to wildtype littermates as well as animals (wildtype littermate and BK deficient) left undisturbed for the same time.

overall_design: 4 hours sleep deprivation compared to undisturbed baseline for BK deficient and wildtype littermate control animals, all brains harvested at TZ4. Sequenced as pools.

first: Christine

middle: M

last: Muheim


title: Aging of mouse spermatogonial stem cells by Wnt7b-Jnk pathway activation

city: Kyoto

first: mito

last: shinohara

state: Kyoto

address: Sakyo-ku, Yoshida Konoe

institute: Kyoto University

type: Methylation profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: RNA-seq for AnvM

city: Hong Kong

first: Xin

last: DENG

address: 1/F, Block 1, To Yuen Building, City University of Hong Kong, 31 To Yuen Street, Kowloon Tong

department: Department of Biomedical Sciences

country: Hong Kong

institute: City University of Hong Kong

summary: Pseudomonas aeruginosa is one of the most common pathogens in hospital-acquired infection, which is tightly controlled by a multi-layered regulatory network including quorum sensing system (QS), type VI secretion system (T6SS) and resistance to host immunity. In the present study, we found that a PA3880 gene, which encodes an unknown protein, acted as a regulator of anaerobic metabolism, response to oxidative stress and virulence in P. aeruginosa. More than thirty PA3880 homologs were found in other bacterial genomes, indicating that PA3880 was widely distributed in bacterial kingdom with a conserved function. Deletion of PA3880 gene changed expression of more than seven hundred genes, including a group of virulence genes under both aerobic and anaerobic conditions. To further study the mechanisms of PA3880-mediated regulation on virulence, we utilized bacterial two-hybrid assay and found that PA3880 protein directly interacted with QS regulator MvfR and anaerobic regulator Anr. Loss of PA3880 protein significantly blunted the pathogenicity of P. aeruginosa, resulting in increased survival, decreased bacterial burdens, muffled inflammatory response, and less lung injuries in mice. Mechanistically, we identified that Cys44 was a critical site for full function of PA3880 to influence alveolar macrophage phagocytosis and bacterial clearance. We also found that AnvM directly interacted with host receptors TLR2 and TLR5, which might lead to activation of host immune response. Hence, we named PA3880 as anvM (anaerobic and virulence modulator). The present characterization of anvM will help to uncover new targets and strategies to treat P. aeruginosa infections.

overall_design: RNA-seq for AnvM

last: Deng


title: Single cell RNA-sequencing of iPS cells derived multicellular human liver organoids

first: Norikazu

last: Saiki

summary: By taking advantage of the foregut generation method, we initially differentiated iPSCs to foregut spheroids through definitive endoderm specification as described. The foregut spheroids were embedded in Matrigel and cultured with retinoic acid (RA). Following 4-day RA treatment, we switched into hepatocyte maturation media for the induction of the hepatocyte differentiation process to establish human liver organoids, hereafter defined as HLO, as early as day 20. To gain quantitative insights regarding the cellular composition in HLO, single-cell RNA sequencing was used to analyze their mRNA expression from 4,059 cells. t-distributed stochastic neighbor embedding analysis confirmed the five distinct major clusters among the cells in HLO, containing hepatocyte-, biliary cell-, hepatic stellate cell-, Kupffer cell-, biliary tree (or peribiliary gland) stem cell-like populations.

overall_design: Examination of mRNA expression profile at single cell level in multicellular human liver organoids

first: Takanori

last: Takebe

first: Masaki

last: Kimura

first: Rie

last: Ouchi


title: scRNA-Seq of iPS cells derived multicellular human liver organoids; RNA-Seq of multicellular human liver organoids derived from 3 different iPS cells


title: Aging of mouse spermatogonial stem cells by Wnt7b-Jnk pathway activation [ChIP-seq]

summary: Because spermatogonial stem cells (SSCs) are virtually immortal by serial transplantation, SSC decrease in aged testes is considered to be caused by deteriorated microenvironment. Here we report cell-intrinsic mode of SSC aging. SSCs cultured for 5 years proliferate more actively than young SSCs and showed enhanced glycolytic activity but remain euploid and exhibited stable androgenetic imprinting patterns. Moreover, the aged SSCs kept constant SSC activity despite shortened telomeres. The increased proliferative activity of aged SSCs was caused by Wnt7b expression, which likely occurred due to decreased polycomb complex2 activity. Aberrant Wnt7b expression not only decreased reactive oxygen species levels and mitochondria activity but also stimulated glycolysis via c-jun N-terminal kinase (JNK) activation. Analysis of SSCs in Klotho aging mouse model also confirmed hyperactivation of JNK pathway and increased glycolysis. Therefore, not only SSC microenvironment but also intrinsic activation of Wnt7b-mediated glycolysis plays important roles in SSC aging.

overall_design: ChIP-seq profiles of 5M- and 60M-GS cells were generated by deep sequencing using Illumina HiSeq 2500 Sequencer , in dupulicate

first: Mito

last: Kanatsu-Shinohara

first: Junichi

last: Imoto

first: Kazuho

last: Ikeo

first: Katsuhiko

last: Shirahige

first: Takashi

last: Shinohara


title: Global gene expression of mouse iPSC directed differentation towards smooth muscle cells using an Acta2hrGFP mouse iPSC reporter line

last: Microarray and Sequencing Resource

summary: Here, we generated and differentiated a mouse induced pluripotent stem cell line with an Acta2hrGFP reporter towards a smooth muscle-like cell that can be purified and expresses characteristic markers of smooth muscle cells. We performed microarray analysis of 3 timepoints in our smooth muscle directed differentiation protocol and compared it to primary adult aortic smooth muscle cells. The profiles indicated that the day 13 Acta2hrGFP+ and Acta2hrGFP- populations are fairly similar, and that the day13 Acta2hrGFP+ population's transcriptomic profile is reminiscent of an immature or a synthetic smooth muscle cell phenotype.  Using a mouse iPSC line with a transgenic GFP reporter for Acta2, we characterized the global transcriptomic proifle of cells during different developmental time points in our in vitro differentiation (undifferentiated iPSC, sorted Kdr+ mesodermal progenitors, and sorted Acta2hrGFP+ and Acta2hrGFP- candidate SMCS). We also included freshly isolated primary aortic Acta2hrGFP+ smooth muscle cells as a control.

overall_design: We prepared microarray expression profiles representing the following 3 stages of iPSC-SMC directed differentiation: undifferentiated iPSC (day 0), sorted Kdr+ mesodermal progenitors (day 5), and sorted Acta2hrGFP+ and Acta2hrGFP- candidate SMCs (day 13). For positive controls we included primary mouse aortic Acta2hrGFP+ SMCs. Biological triplicates of all samples were prepared. Global gene expression in all 15 samples was analyzed by Affymetrix GeneChip Mouse Gene 2.0 ST arrays.


title: The aryl hydrocarbon receptor regulates nucleolar activity and protein synthesis in MYC-expressing cells

city: Dallas

first: Spencer

middle: Dann

last: Barnes

address: 5323 Harry Hines Blvd

department: Bioinformatics

institute: University of Texas Southwestern

summary: MYC enhances protein synthesis by regulating genes involved in ribosome biogenesis and protein translation. Here, we show that MYC-induced protein translation is mediated by the transcription factor aryl hydrocarbon receptor (AHR), which is induced by MYC in colonic cells. AHR promotes protein synthesis by activating the transcription of genes required for ribosome biogenesis and protein translation, including OGFOD1 and NOLC1. Using surface sensing of translation (SUnSET) to measure global protein translation, we found that silencing AHR or its targets diminishes protein synthesis. Therefore, targeting AHR or its downstream pathways could provide a novel approach to limit biomass production in MYC-driven tumors.

overall_design: RNA-seq experiment to compare gene expression between 6 different conditions, including samples with and without human MYC overexpression and siRNA AHR transfection.

first: M

middle: C

last: Lafita-Navarro

first: Maralice

last: Conacci-Sorrell


title: Umbilical cord as a long-term source of activatable MSC for immunomodulation

city: Hanover

first: Anton

last: Selich

address: Carl-Neuberg-Str. 1

institute: Hannover Medical School

summary: To facilitate umbilical cord explant culture as a long-term source for mesenchymal stromal cells, we compared the transcriptome of mesenchymal stromal cell explant cultures (MSC-EM) initiated 14 days (early) post preparation,  2 months later (late) and with INF-g and TNF-a (25 ng/mL) activated samples

overall_design: We compared the early and late induced mesenchymal stromal cell explant (MSC-EM) cultures from human umbilical cord pieces from several donors versus activated samples.  MSC-EMs 1 are early.  MSC-EMs 6 and 7 are late.

first: Michael

last: Rothe

first: Oliver

last: Dittrich-Breiholz


title: Changes in axonal and somatic transcriptomes in response to Pum2 knockdown

city: New York

first: Ulrich

last: Hengst

address: 650 West 168th Street

department: Pathology and Cell Biology

institute: Columbia University

summary: We report that knockdown of Pum2 results in an increase of PBE containing mRNAs in axons, without changing mRNA levels in the cell bodies.

overall_design: Axonal and somatic transcriptomes of embryonic rat dorsal root ganglion neurons grown in microfluidic chambers under shControl or shPum2 conditions were generated by RNA-Seq in duplicates using Illumina HiSeq. Axons were allowed to grow for 7 days before collection.

first: U


title: Revealing the moleclar mechanisms of temperature acclimation and adaptation in marine diatoms with transcriptional responses to sub- and supra-optimal growth temperatures

city: Sackville

first: Yue

last: Liang

state: NB

address: 144 Main St

country: Canada

institute: Mount Allison University

summary:
Background: Ocean temperatures are projected to increase over the coming century, with dramatic consequences for the marine biosphere. Diatoms are important contributors to marine primary production and the ocean carbon cycle, yet the molecular mechanisms that regulate their acclimation and adaptation to temperature are poorly understood.
Method: Here we use a transcriptomic approach to identify the molecular mechanisms associated with temperature acclimation and adaptation in closely related colder- and warmer-adapted diatom species.
Results: We find contrasting patterns of differential expression at sub- and supra-optimal temperatures across the two species, which may be due to adaptive changes in baseline expression. Frontloaded and divested pathways indicate protein processing machinery, membrane structure, and the balance between temperature-independent photosynthesis and temperature-dependent metabolism are key elements of adaptation to temperature changes.
Conclusions: Our findings suggest that transcriptional frontloading and divestment may provide a framework to interpret diatom acclimation and adaptation to temperature and success under future warming.

overall_design: RNA profiles of two closely related Chaetoceros species cultured under their respective optimal temperature (Tmax), sub-optimal temperature (Tsub), and supra-optimal temperature (Tsup) were generated in triplicates with RNA-Seq using Illumina HiSeq 2000. The SRA accessions for the samples of CCMP158 are SRR8009948, SRR8009947, SRR8009955, SRR8009951, SRR8009952, SRR8009959, SRR8009958, SRR8009957, SRR8009954. The SRA accessions for the samples of CCMP160 are SRR8009953, SRR8009950, SRR8009949, SRR8009945, SRR8009960, SRR8009946, SRR8009956, SRR8009944, SRR8009943. The Bioproject accesssion is PRJNA495610.

first: Julie

last: Koester

first: Andrew

last: Irwin

first: Zoe

last: Finkel


title: Histone Recycling by FACT and Spt6 during Transcription Prevents the Scrambling of Histone Modifications

city: Montreal

first: Francois

last: Robert

state: QC

address: 110 av des Pins Ouest

institute: IRCM

type: Genome binding/occupancy profiling by genome tiling array


title: Transcriptome analysis of wt1b:eGFP positive macrophages in the regenerating zebrafish heart

city: Madrid

first: Manuel

last: Gomez

state: Madrid

address: Melchor Fernández Almagro, 3

country: Spain

institute: CNIC

summary: Little is known about zebrafish macrophage subtypes and their contribution to organ regeneration. Using the transgenic line wt1b:eGFP we identified  a subtype of macrophages in the regenerating heart  that is transcriptionally different from the rest of macrophages.

overall_design: Hearts from Tg(wt1b:eGFP; mpeg1:mCherry) zebrafish were cryoinjured and at 4 dpi mCherry and GFP/mCherry cells were FAC sorted. RNA was extracted from 4 pools of GFP/mCherry and 4 pools of mCherry single positive cells and  RNAseq was performed.

first: N

last: Mercader

first: A

last: García-Redondo


title: Comparison of the gene expression expression profile of activated and resting epicardium

summary: Zebrafish can regenerate their hearts. As a first response to injury, the epicardium reacts by upregulalion of developmental marker genes. Here we compared in an unbiased manner the expression of the epicardium from uninjured zebrafish hearts and hearts at 3 days postcryoinjury. To label epicardial cells of uninjured hearts we usd pard3:GFP (POon et al 2010) and to label epicardium of the injured heart wt1b:eGFP (Perner et al 2007)

overall_design: GFP positive cells were FAC sorted from uninjured pard3:GFP adult zebrafish hearts and wt1b:eGFP hearts 3 days postinjury (dpi). RNA was extracted from 4 pools of pard3:GFP and 4 pools of wt1b:eGFP cells. Each pool contained GFP positive cells isolated from 15 pard3:GFP hearts or 3 wt1b:eGFP hearts, respectively .

first: J

last: González-Rosa


title: Accessible chromatin profiles of intestinal epithelial cells upon HNF4 loss in embryos by ATAC-seq

status: Public on Jul 29 2019

city: Piscataway

last: Verzi

state: NJ

address: 145 Bevier Road

department: Genetics

institute: Rutgers, the State University of New Jersey

summary: HNF4 paralogs are redundantly required for proper villus elongation, differentiation and maturation in the developing gut. We find 5,391 chromatin regions become inaccessible upon HNF4 loss, and HNF4 binding sequences are most enriched in these regions. Genes nearby these 5,391 HNF4 dependent regions are associated with villus differentiation/maturation.

overall_design: ATAC-seq was employed to identify HNF4-dependent chromatin accessibility in the E16.5 mouse intestinal epithelial cells.

first: Lei

last: Chen


title: Pioneer and nonpioneer factor cooperation drives lineage specific chromatin opening [scRNA-seq]

first: Amandine

last: Bemmo

address: 110 Avenue des Pins

summary: Pioneer transcription factors are coined as having the unique property of “opening closed chromatin sites” for implementation of cell fates. We previously showed that the pioneer Pax7 specifies melanotrope cells through deployment of an enhancer repertoire: this allows binding of Tpit, a nonpioneer factor that determines the related lineages of melanotropes and corticotropes. Here, we investigated the relation between these two factors in the pioneer mechanism. Cell-specific gene expression and chromatin landscapes were defined by scRNAseq and chromatin accessibility profiling. We found that in vivo deployment of the melanotrope enhancer repertoire and chromatin opening requires both Pax7 and Tpit. In cells, binding of heterochromatin targets by Pax7 is independent of Tpit but Pax7-dependent chromatin opening requires Tpit. The present work shows that pioneer core properties are limited to the ability to recognize heterochromatin targets and facilitate nonpioneer binding. Chromatin opening per se may be provided through cooperation with nonpioneer factors.

overall_design: Single cell RNAseq of adult male mouse pituitary

first: Alexandre

last: Mayran

first: Konstantin

last: Khetchoumian

first: Jacques

last: Drouin


title: Pioneer and nonpioneer factor cooperation drives lineage specific chromatin opening [ChIP-seq]

overall_design: ChIPseq in pituitary-derived cell lines

first: Yves

last: Gauthier

first: Aurelio

last: Balsalobre


title: Bhlhe40 and Bhlhe41 transcription factors regulate alveolar macrophage self-renewal and identity

city: Solna

first: Taras

last: Kreslavsky

address: Nks Bioclinicum, J7:30, Visionsgatan 4

department: Department of Medicine, Solna (MedS)

institute: Karolinska Institutet

summary: Tissues in multicellular organisms are ‘serviced’ by resident macrophages, which perform both generic and tissue-specific functions. The latter relies on unique tissue-specific molecular programs induced by signals from the microenvironment and executed through a combinatorial action of tissue-specific and broadly expressed transcriptional regulators. Here, we identify the transcription factors Bhlhe40 and Bhlhe41 as novel regulators of alveolar macrophages (AMs) – a population that provides the first line of immune defense and executes homeostatic functions in lung alveoli. In the absence of these factors, AMs exhibited decreased proliferation that resulted in a severe disadvantage of knockout AMs in a competitive setting. Gene expression analyses revealed a broad cell-intrinsic footprint of Bhlhe40/Bhlhe41-deficiency manifested by a downregulation of AM signature genes and induction of signature genes of other macrophage lineages. Genome-wide characterization of Bhlhe40 DNA binding suggested that these transcription factors directly repress the expression of lineage-inappropriate genes in AMs. Taken together, these results identify Bhlhe40 and Bhlhe41 as key regulators of AM self-renewal and guardians of their identity.

overall_design: RNA-seq comparison of Bhlhe40–/–Bhlhe41–/– and wild-type alveolar (steady-state and from mixed bone marrow chimeras) and peritoneal (steady-state) macrophages (2 biological replicates per condition); H3K27ac ChIP-seq comparison of Bhlhe40–/–Bhlhe41–/– and wild-type alveolar macrophages (steady-state; 2 biological replicates per condition); ChIP-seq characterization of Bhlhe40 DNA binding in WT alveolar macrophages (single experiment) with ‘mock’ precipitation sample without antibody but with streptavidin sepharose magnetic beads used to generate the control library (single experiment).

first: René

last: Rauschmeier

first: Charlotte

last: Gustafsson

first: Annika

last: Reinhardt

first: Noelia

last: A-Gonzalez

first: Luigi

last: Tortola

first: Dilay

last: Cansever

first: Sethuraman

last: Subramanian

first: Reshma

last: Taneja

first: Moritz

last: Rossner

first: Michael

middle: H

last: Sieweke

first: Melanie

last: Greter

first: Robert

last: Månsson

first: Meinrad

last: Busslinger


title: RNA Sequencing of CTRL and Heat Stressed C. elegans [miRNA-seq]

city: San Deigo

first: Amy

last: Pasquinelli

address: 9500 Gilman Drive

department: Biological Sciences

institute: UCSD

summary: Two  independent replicates of wildtype C. elegans were collected at the L4 stage for RNA.

overall_design: small RNA-seq libraries were generated for L4 wildtype worms to analyze RNA expression in control vs HS worms.

first: Antti

last: Aalto

first: William

last: Schreiner


title: Histone Recycling by FACT and Spt6 during Transcription Prevents the Scrambling of Histone Modifications [ChIP-seq]

first: Francois

last: Robert

summary: The genetic information encoded in DNA is framed by additional layers of information, referred to as the epigenome. Epigenetic marks such as DNA methylation, histone modifications and histone variants are concentrated on specific genomic sites as means to instruct, but also sometimes as a consequence of, gene expression. How this information is maintained, notably in the face of transcription, is not understood. Here we show that the histone chaperones FACT and Spt6 are required for maintaining proper localization of several histone modifications including H3K4me1,2,3, H3K36me3, H3K79me3, H3K14ac, H3K18ac and H2Bub in Saccharomyces cerevisiae. In the absence of functional FACT or Spt6, transcription generates massive nucleosome loss which is partially compensated by increased histone assembly by histone chaperones such as Asf1 and HIR. Because re-incorporation of histones by these histone chaperones in not coupled to transcription, the modified histones are randomly incorporated, leading to scrambling of the epigenetic information. Hence, our work highlights the importance of local nucleosome recycling by FACT and Spt6 during transcription in the maintenance of a proper epigenetic landscape.

overall_design: Occupancy profiling by ChIP-seq of histone modifications H3K4me3 and H3K56ac as well as histones H4 and H3 in wild-type (WT) and temperature-sensitive mutants for the histone chaperones FACT and Spt6 (spt16-197 and spt6-1004 respectively) in yeast Saccharomyces cerevisiae, in duplicate, for a total of 12 Input DNA and 24 ChIP samples. For all samples, a fixed amount of crosslinked S. pombe cells (representing 10% of the S. cerevisiae cells) was added to the S. cerevisiae cells prior to cell lysis. This spike-in control was used to normalise samples.

first: Célia

last: Jeronimo

first: Christian

last: Poitras

first: François


title: Development of a chimeric model to study and manipulate human microglia in vivo

first: Mathew

last: Blurton-Jones

overall_design: Refer to individual Series


title: Gene expression analysis of wt1b-positive cardiac macrophages

first: Manuel

last: Gomez


title: Aging of mouse spermatogonial stem cells by Wnt7b-Jnk pathway activation [Bisulfite-seq]

first: mito

last: shinohara

department: Medicine

overall_design: Bisulfite-seq profiles of 5M- and 60M-GS cells were generated by deep sequencing, in dupulicate

first: Mito

last: Kanatsu-Shinohara

first: Hidehiro

last: Toh

first: Hiroyuki

last: Sasaki

first: Takashi

last: Shinohara


title: G-tract RNA removes Polycomb Repressive Complex 2 from genes

city: London

first: Richard

last: Jenner

address: 72 Huntley Street

department: Cancer Biology

country: United Kingdom

institute: UCL Cancer Institute

summary: Polycomb Repressive Complex 2 (PRC2) maintains repression of genes specific for other cell types but associates with genes ectopically in cancer. How PRC2 is removed from genes is unknown but this knowledge may allow the targeted reversal of deleterious PRC2 recruitment events. We show that G-tract RNA specifically removes PRC2 from genes in human and mouse cells. PRC2 preferentially binds G-tracts within nascent pre-mRNAs, especially within predicted G-quadruplex structures. G-quadruplex RNA evicts the PRC2 catalytic core from the substrate nucleosome. PRC2 transfers from chromatin to RNA upon gene activation and chromatin-associated G-tract RNA removes PRC2 and depletes H3K27me3 from genes. Targeting G-tract RNA to CDKN2A in malignant rhabdoid tumor cells reactivates the gene and induces senescence. These data support a model in which pre-mRNA evicts PRC2 during gene activation and provides the means to selectively remove PRC2 from specific genes.

overall_design: Input iCLIP libraries matching Suz12, Fus and hnRNPC were generated from mESC Ezh2 fl/fl without tamoxifen. IP samples are in GSE66831.

last: Beltran

last: Tavares

first: Neil

last: Justin

first: Garima

last: Khandelwal

first: John

last: Ambrose

first: Benjamin

last: Foster

first: Kaylee

middle: B

last: Worlock

first: Andrey

last: Tvardovski

first: Simone

last: Kunzelmann

first: Javier

last: Herrero

first: Till

last: Bartke

first: Steven

last: Gamblin

first: Jon

last: Wilson

middle: G


title: Specialization of the Drosophila nuclear export family protein, Nxf3, for piRNA precursor export

status: Public on Jul 27 2019

city: Cambridge

first: Emma

last: Kneuss

state: Cambridgeshire

address: Li Ka Shing Centre, Robinson way

department: Cancer Research UK, Cambridge University

institute: University of Cambridge

summary: The piRNA pathway is a conserved small RNA-based immune system that protects animal germ cell genomes from the harmful effects of transposon mobilisation. In Drosophila ovaries, most piRNAs originate from dual-strand clusters, which generate piRNAs from both genomic strands. Dual-strand clusters use non-canonical transcription mechanisms. Although transcribed by RNA polymerase II, cluster transcripts lack splicing signatures and polyA tails. mRNA processing is important for general mRNA export mediated by Nuclear export factor 1. Although UAP56, a component of the transcription and export complex, has been implicated in piRNA precursor export, it remains unknown how dual-strand cluster transcripts are specifically targeted for piRNA biogenesis by export from the nucleus to cytoplasmic processing centers. Here we report that dual-strand cluster transcript export requires CG13741/Bootlegger and the Drosophila Nuclear export factor family protein, Nxf3. Bootlegger is specifically recruited to piRNA clusters and in turn brings Nxf3. We find that Nxf3 specifically binds to piRNA precursors and is essential for their export to piRNA biogenesis sites, a process that is critical for germline transposon silencing. Our data shed light on how dual-strand clusters bypass canonical mRNA features to be specifically exported via Nxf3, ensuring proper piRNA production.

overall_design: characterization of Drosophila melanogaster gene CG13741(Bootlegger) and Nuclear export factor 3 (Nxf3) involvement in piRNA precursors export

first: Marzia

last: Munafò

first: Evelyn

last: Eastwood

first: Undine-Sophie

last: Deumer

first: Jonathan

last: Preall

first: Gregory

last: Hannon

last: Czech


title: RNA sequencing of MCF-7 cells transfected with non-specific or DAXX specific siRNA

city: Maywood

first: Clodia

last: Osipo

state: Illinois

address: 2160 S. First Ave

institute: Loyola University Chicago

summary: Purpose: to determine what genes require DAXX for their regulation in ER+ breast cancer cells

overall_design: MCF-7 cells were transfected with non-specific (SCBi) or DAXX specific (DAXXi) siRNA for 2 days. Total RNA was then isolated and sequenced.

first: Jeffrey

last: Ng

first: Daniel

last: Peiffer


title: Syndecan-1 promotes lung fibrosis by regulating epithelial reprogramming through extracellular vesicles (miRNA-Seq)

city: Los Angeles

first: Tanyalak

last: Parimon

address: 127 San Vicente

institute: Cedars-Sinai Medical Center

summary: We studied transcriptomic changes of extracellular vesicles (EVs) in bronchoalveolar lavage fluid of bleomycin-injured wild-type and syndecan-1 deficient mice

overall_design: Animals received bleomycin for 21 days, PBS-treated animals served as controls. EVs were isolated from bronchoalvolar lavage fluid. miRNAs were isolated from EVs and processed for miRNAseq.

first: Peter

last: Chen


title: Copy Number Variation across 12 tribes of African cichlid species

status: Public on Jul 26 2019

city: Portland

first: Suzy

middle: CP

last: Renn

state: Oregon

address: 3203 SE Woodstock Blvd., Biology Room B124

department: Biology

institute: Reed College

type: Genome variation profiling by genome tiling array

summary: This study examines genomic copy-number variation among African cichlids spanning multiple tribes and radiations. We map CNVs and hotspots throughout the Oreochromis niloticus reference genome, categorize gene ontology enrichment within CNV regions, and compare results with sequence-based cichlid phylogenies.

sample_organism:
Oreochromis niloticus
Coptodon zillii
Sarotherodon galilaeus
Tropheus moorii
Haplochromis burtoni
Astatotilapia calliptera
Cyathopharynx furcifer
Ophthalmotilapia ventralis
Cyphotilapia frontosa
Boulengerochromis microlepis
Callochromis macrops
Lepidiolamprologus elongatus
Neolamprologus brichardi
Variabilichromis moorii
Oreochromis alcalicus
Astatoreochromis alluaudi
Sarotherodon melanotheron
Pseudocrenilabrus multicolor victoriae
Paralabidochromis sp.
Cyprichromis leptosoma
Eretmodus cyanostictus
Labeotropheus fuelleborni
Hemichromis fasciatus
Astatotilapia bloyeti
Oreochromis grahami
Oreochromis ndalalani
Oreochromis latilabris
Maylandia zebra
Stomatepia mariae
Copadichromis borleyi
Copadichromis virginalis
Diplotaxodon greenwoodi
Pallidochromis tokolosh
Astatotilapia flaviijosephi
Xenotilapia spiloptera
Haplochromis chilotes
Julidochromis ornatus
Pungu maclareni
Konia eisentrauti
Pundamilia nyererei
Neochromis omnicaeruleus
Rhamphochromis longiceps
Nyassachromis microcephalus
Benthodesmus elongatus
Tropheops sp. 'red cheek'
Haplochromis thereuterion
Coptodon deckerti
Coptodon ejagham
Coptodon fusiforme
Coptodon kottae
Sarotherodon knauerae
Sarotherodon lamprechti
Rubricatochromis bimaculatus
Lobochilotes labiata

platform_organism:
Oreochromis niloticus
Haplochromis burtoni
Neolamprologus brichardi
Maylandia zebra
Pundamilia nyererei

overall_design: Array comparative genomic hybridization was performed with 168 samples of genomic DNA from 53 African cichlid species vs. pooled Astatotilapia (Haplochromis) burtoni reference DNA.

first: Joshua

last: Faber-Hammond

first: Etienne

last: Bezault


title: Investigating the role of SMCHD1 in regulating clustered protocadherin (Pcdh) and Hox genes

city: Boston

first: Chen-Yu

last: Wang

address: 185 Cambridge Street

department: Molecular Biology

institute: Massachusetts General Hospital

summary: To investigate the effect of Smchd1 ablation on clustered Pcdh and Hox genes, we generated ChIP-seq profiles of EZH2 in clonal neural progenitor cells (NPCs) from Smchd1+/+ (wild-type, WT) and Smchd1-/- mouse embryonic stem (ES) cells. We also reanalyzed previously published Hi-C data (GSE99991) (Wang et al., 2018, Cell) in these two cell lines.

overall_design:
ChIP-seq for EZH2 in NPC clones derived from WT and Smchd1-/- female mouse ES cells.

Hi-C: The Hi-C summary files of WT and Smchd1-/- cells were downloaded from GEO (GSE99991), with two biological replicates combined:

WT: GSM2667262_WT1.HiC.rep1.comp.summary.txt.gz
WT: GSM2667264_WT1.HiC.rep2.comp.summary.txt.gz

Smchd1-/-: GSM2667263_KO1.HiC.rep1.comp.summary.txt.gz
Smchd1-/-: GSM2667265_KO1.HiC.rep2.comp.summary.txt.gz)

The combined replicates were converted to .hic files for chromosome 2, 6, 11, 15, and 18. The .hic files can be directly loaded to the Juicebox software (Durand, et al., Cell Syst, 2016).

first: Jeannie

middle: T

last: Lee


title: Peptide-conjugated oligonucleotides evoke long-lasting myotonic dystrophy correction in patient-derived cells and mice

city: Paris

first: Arnaud

middle: F

last: Klein

address: 47 bld de l'hopital - Bab Babinski

department: U974 - Centre de Recherche en Myologie

country: France

institute: Sorbonne université, Inserm, institut de Myologie

summary: Antisense oligonucleotides (ASOs) strategies for DM1 can abolish the toxic RNA gain-of-function mechanism caused by nuclear-retained mutant DMPK transcripts containing CUG expansions (CUGexp). However, systemic use of ASOs for this muscular disease remains challenging due to poor drug distribution to skeletal muscle. To overcome this limitation, we test an arginine-rich Pip6a cell-penetrating peptide and show that Pip6a-conjugated PMO dramatically enhanced ASO delivery into striated muscles of DM1 mice following systemic administration in comparison to unconjugated PMO and other ASO strategies. Thus, low dose treatment of Pip6a-PMO-CAG targeting pathologic expansions is sufficient to reverse both splicing defects and myotonia in DM1 mice and normalizes the overall disease-transcriptome.

overall_design: Examination of HSA-LR DM1 mice treated with Pip6a-CAG7-PMO compared to non-treated HSA-LR mice and WT mice.

first: Miguel

last: Varela

first: Naira

last: Naouar

first: Denis

last: Furling

first: Matthew

last: Wood


title: RNA Sequencing of CTRL and Heat Stressed C. elegans [RNA-seq]

first: Amy

last: Pasquinelli

summary: Three independent replicates of wildtype C. elegans were collected at the L4 stage for RNA. Heat Shock was performed at 35C for 4hrs.

overall_design: RNA-seq libraries were generated for L4 wildtype worms to analyze RNA expression in control vs HS worms.

first: Jerry

middle: S

first: William

last: Schreiner


title: The Position Beta57 of IAg7 Controls the Early Anti-Insulin Response and Onset of Diabetes in NOD mice to Link MHC and Disease [sequencing]

status: Public on Jul 25 2019

city: La Jolla

first: Luc

last: Teyton

address: 10550 North Torrey Pines Road

institute: TSRI

summary: Abstract- The class II region of the Major Histocompatibility locus is the main contributor to the genetic susceptibility to type 1 diabetes (T1D). The loss of an aspartic acid at position 57 of diabetogenic HLA-DQ8 chains supports this association; it influences the recognition of peptides in the context of HLA-DQ8, and I-Ag7 using a mechanism termed the P9 switch. Here, we built register-specific insulin MHC tetramers, Ins12-20 and Ins13-21, to examine anti-insulin CD4 T cell responses during the early pre-diabetic phase of disease in mice. A single cell gene expression analysis and single cell T cell receptor (TCR) sequencing of anti-insulin CD4 T cells performed in 6 and 12-week-old NOD mice, revealed tissue-specific gene expression signatures. TCR signaling and clonal expansion were found only in the islets of Langerhans. and produced either classical Th1 differentiation or an unusual Treg phenotype, independent of TCR usage. The early phase of the anti-insulin response was dominated by cells specific for Ins12-20, the register that supports a P9 switch mode of recognition. The presence of the switch was demonstrated by TCR sequencing, re-expression, mutagenesis, and functional testing of alpha/beta TCR pairs in vitro. The genetic correction of the beta57 mutation resulted in the disappearance of D/E residues in the CDR3beta of anti-Ins12-20 T cells, and inability of cells normally activated by a switch to recognize the Ins9-23 peptide. These results provide the first molecular mechanistic explanation that links the unique MHC class II polymorphism of T1D with the recognition of islet antigens and disease onset.

overall_design: Murine CD4+ T cells, isolated from different tissues, were stained with IAg7 tetramers labelled with the fluorescent moiety PE. Cells stained with either tetramer were single cell sorted into single wells of 96 well plates. Single cell cDNA libraries were made according to the Fluidigm BioMark "Two Step Single Cell Gene Expression Using EvaGreen" protocol with primers for 96 genes as well as unique TCRalpha and TCRbeta chains. Next, TCR alpha and beta chains were amplified and each single well/cell was barcoded on both alpha and beta chains using the Fluidigm AccessArray. (The protocol, and the barcodes utilized, are published in detail in Holt et al; PMID 29224077). Library preparation was done by the TSRI Genomics Core and run on an Illumina MiSeq. Post-alignment, reads were run through the international ImmunoGenetics information system. Confirmed genomically encoded regions as well as CDR3 regions were analyzed via a custom R script.

first: Louis

last: Gioia

first: Marie

last: Holt

first: Anne

last: Costanzo

first: Siddhartha

last: Sharma

first: Brian

last: Abe

first: Lisa

last: Kain

first: Maki

last: Nakayama

first: Xiaoxiao

last: Wan

first: Andrew

last: Su

first: Clayton

last: Mathews

first: Yi

first: Emil

last: Unanue


title: Knockdown specificity of Mobile-CRISPRi system targeting chromosomal mRFP

city: San Francisco

first: Neha

last: Prasad

institute: UC-San Francisco

summary: The Mobile CRISPRi system with and without mRFP-targeting sgRNA was engineered into Pseudomonas aeruginosa PA14 strain with chromosomally encoded mRFP. RNA was isolated from these strains, and the corresponding cDNA library was synthesized and sequenced in 150 bp paired-end reads. Approximately 1,000,000 reads were collected for each of the two samples, with ~94% alignment to PA14 WT by Bowtie254, and transcripts were counted with HTSeq55. Only genes with a non-normalized read count greater than 1 in both samples were included in analysis, with a coverage of 1286 genes (~20% genome). This data shows that the Mobile CRISPRi system is selective for sgRNA-guided knockdown of mRFP.

overall_design: The RNA concentration for each sample was determined with a NanoDrop spectrophotometer (Thermo Fisher Scientific). 10 ng total RNA of each sample was fragmented for 6 min, cDNA libraries were prepared using “NEBNext Ultra RNA Library Prep Kit for Illumina” (NEB#E7770S). Libraries were sequenced in collaboration with the Chan Zuckerberg Biohub in San Francisco on an Illumina MiSeq in 150 bp paired-end runs. Approximately 1,000,000 reads were collected for each of the two samples, with ~94% alignment to PA14 WT by Bowtie254, and transcripts were counted with HTSeq55. Only genes with a non-normalized read count greater than 1 in both samples were included in analysis, with a coverage of 1286 genes (~20% genome).

first: Jiuxin

last: Qu

middle: K

first: Emily

last: Crawford

last: Lyden


title: Differential expression levels of mRNAs in control 4T1 versus M2 macrophages co-cultured 4T1 murine breast cancer cells

city: Wuhan

first: zhang

last: qiulei

state: hubei

address: No. 1277, Jiefang Road,

department: union hospital

institute: Huazhong university of science and technology

summary: Tumor-associated macrophages (TAMs) are closely related to poor prognosis in triple-negative breast cancer (TNBC). Thus, gaining insight into how TAMs support cancer progression could contribute to effective therapies. We utilized the 4T1 murine TNBC cell line and murine bone marrow-derived macrophages to assess TAMs mediated pro-proliferative effects in vivo and in vitro. Further, Transcriptional analysis was performed to identify pathways activated in TAMs stimulated 4T1 cells.  To simulate tumor microenvironment, M2 macrophages and 4T1 cells were plated into upper and lower chambers of Transwell co-culture systems respectively. we performed RNA-sequencing analysis of 4T1 cells incubated with vehicle control or M2 macrophages.

overall_design: A high throughput sequencing about mRNAs was perfomed  in control 4T1 versus M2 macrophages co-cultured 4T1 cells， without replicate.

first: Qiulei

last: Zhang

first: Jun

last: Zhou

first: Kehao

last: Le

first: Ming

last: Xu

first: Tao

last: Huang


title: Adverse prognosis of glioblastoma contacting the subventricular zone: biological correlates

city: Utrecht

first: Sharon

last: Berendsen

state: Utrecht

address: Heidelberglaan 100

country: Netherlands

institute: UMC Utrecht

summary:
mRNA expression analysis on human GBM samples with or without contact to the SVZ
Affymetrix Human Genome U133 Plus 2.0 Arrays

overall_design: retrospective, 71 samples.

first: Emma

last: van Bodegraven

first: Tatjana

last: Seute

first: Wim

last: Spliet

first: Marjolein

last: Geurts

first: Jeroen

last: Hendrikse

first: Laurent

last: Schoysman

first: Willemijn

last: Huiszoon

first: Meri

last: Varkila

first: Soufyan

last: Rouss

first: Erica

last: Bell

first: Jérôme

last: Kroonen

first: Arnab

last: Chakravarti

first: Vincent

last: Bours

first: Tom

last: Snijders

first: Pierre

middle: A

last: Robe


title: Pioneer and nonpioneer factor cooperation drives lineage specific chromatin opening [ATAC-seq]

first: Amandine

last: Bemmo

overall_design: ATACseq in pituitary cells and pituitary-derived cell lines

first: Alexandre

last: Mayran

first: Konstantin

last: Khetchoumian

first: Jacques

last: Drouin


title: Tau-P301S sorted neurons and astrocytes

city: South San Francisco

first: Melanie

last: Huntley

address: 1 DNA Way

institute: Genentech

summary:
Mice of indicated genotypes were perfused and their brains dissected and dissociated. Cells were fixed, immunolabeled and FACS sorted. RNA was extracted from neuron, astrocyte, and microglial cell populations. Typical RIN=4-5 for neurons, 6-8 for astrocytes, and 5-7 for microglia. Typical RNA yields 200-300ng for neurons, ~20ng for microglia, and ~5ng for astrocytes.
cDNA was generated from up to 25 ng of total RNA using Nugen’s RNA-Seq method for low-input RNA samples, Ovation RNA-Seq System V2 (NuGEN). (Per manufacturers instructions, total RNA was neither depleted of rRNA nor polyA-selected.) 1 μg of sheared cDNA was taken into further processing, starting at end repair step, using Illumina’s TruSeq RNA Sample Preparation Kit v2 (Illumina).
The SAMPLE_ID sample characteristic is a sample identifier internal to Genentech.
The ID of this project in Genentech's ExpressionPlot database is PRJ0025262

overall_design: NeuN+ neurons, Gfap+ astrocytes, and Cd11b+ myeloid cells were sorted from 6 month old Tau-P301S transgenic mice or non-transgenic littermates. Microglia from the same experiment in GSE93180.

first: Brad

last: Friedman

first: Jesse

last: Hanson

first: David

last: Hansen


title: Chemical dissection of vtamin D activity

city: Uji

first: Motonari

last: Uesugi

address: Gokasho

department: ICR

institute: Kyoto University

summary: Vitamin D3 metabolites are capable of controlling gene expression in mammalian cells through two independent pathways: vitamin D receptor (VDR) and sterol regulatory element-binding protein (SREBP) pathways. In the present study, we dissect the complex biological activity of vitamin D by designing synthetic vitamin D3 analogs specific for VDR or SREBP pathway, i.e., a VDR activator that lacks SREBP inhibitory activity, or an SREBP inhibitor devoid of VDR activity.

overall_design: Comprehensive analysis of gene expressions promoted by 25-hydroxyvitamin D3, a selective SREBP inhibitor or a selective VDR activator in Chinese hamster CHO-K1 cells.


title: RNAseq data of WT and Pparg-ablated mouse urothelium under homeostasis and during regneration

city: New York

first: Chang

last: Liu

state: NY

address: 1130 St Nicholas Ave, Room 311

institute: Columbia University

summary: Peroxisome Proliferator-Activated Receptor-gamma (PPARG) is a nuclear hormone receptor that was originally described as a master regulator of adipogenesis but could also promote cellular differentiation in a number of epithelium. PPARG also serves as an important regulator in anti-inflammatory activity after a variety of injuries, acting in part by antagonizing the NF-kB pathway. Moreover, the expression of PPARG is strongly down regulated in the basal subtype of bladder cancer, suggesting that its removal might be essential in tumorigenesis. In urothelial cells, it has been shown that PPARG promotes urothelial differentiation in vitro, but its function in vivo remains unexplored.  The urothelium is a stratified epithelium that serves as a barrier between the urinary tract and blood. It consists of terminally differentiated umbrella cells, intermediate cells which serve as umbrella cell progenitors; and unipotent basal cells. To determine the role of PPARG in vivo, we used Cre-Lox recombination to conditionally delete the Pparg gene in the mouse urothelium using the ShhCre driver, which drives recombination in basal and intermediate cells, and their respective daughters. Interestingly, ShhCre;Ppargfl/fl mutants lack umbrella and intermediate cells, but have an abnormal cell population negative for classical urothelial markers instead. Furthermore, we observed an increase of KRT14+ population in the basal compartment and squamous features in the mutant urothelium. Expression profile analysis suggested PPARG regulates metabolism, urothelial differentiation and innate immune response.  We further challenged the Pparg mutant urothelium with acute injury. In wild type animals, urinary tract infection (UTI) with uropathogenic E.coli results in a transient innate immune response, followed by a completed regernation within 2 weeks. When ShhCre;Ppargfl/fl mutants were challenged with urinary tract infection, the innate immune response was not resolved even after several weeks and the Pparg ablated urothelium exhibited squamous metaplasia. RNAseq data suggested that PPARG plays a role in regulating squmous differentiation and NFkB signial pathway.  Together these findings suggest that PPARG is essential for the normal differentiation of the urothelium and is a potent regulator of the inflammatory response after UTI. Understanding the link between the loss of PPARG, chronic inflammation and tumorigenesis in the urothelium  could shed light on the urothelial differentiation network and pave the way for the development of therapeutic approaches to various urinary diseases.

overall_design: Mouse urothelial mRNA profile of adult WT, ShhCre;Pparg (+/-, fl/fl) and K5CreER; Pparg (+/-,fl/fl) mice under homeostasis or during regeneration were generated by RNA sequencing

first: Cathy

last: Mendelsohn


title: RNA-seq of breast cancer cell lines post ligand treatment I

first: Marc

last: Hafner

address: Building 45-1, 1 DNA Way

department: Oncology Bioinformatics

summary:
Goal: study the impact of estrogen receptor ligands on gene expression in HR+ breast cancer cells
Methods: RNA sequencing
Results: Ligand 4-OH tamoxifen, a selective ER modulator (SERM), promotes transcriptional activation of ER and mimics the transcriptional effect of natural ligand E2 for a subset of ER target genes, consistently across the seven breast cell lines (MCF-7, HCC1500, MDA-MB-330, EFM-19, T-47D, BT-474, and CAMA-1). Selective ER degraders (SERD) fulvestrant and GDC-0927 on the other hand do not induce, or induce very weakly the expression of ER target genes. The effect of GDC-0810 depends on the cellular context.

overall_design: Duplicates results of RNA-Seq of seven cell lines treated with six different estrogen receptor ligands or DMSO for 24 hours

first: Ciara

last: Metcalfe

first: Anneleen

last: Daemen

first: Wei

last: Zhou


title: ATAC-seq of MCF-7 cells post ligand treatment

summary:
Goal: study the impact of estrogen receptor ligands on chromatin accessibility in MCF-7 cells
Methods: Assay for Transposase-Accessible Chromatin using Sequencing (ATAC-Seq)
Results: Ligand 4-OH tamoxifen, a selective ER modulator (SERM), significantly alters chromatin accessibility and partially mimics the effect of natural ligand E2 on chromatin accessibility in MCF-7 breast cells. Selective ER degraders (SERD) fulvestrant and GDC-0927 on the other hand have very little impact on chromatin accessibility.

overall_design: Triplicates results of ATAC-Seq of MCF-7 cells treated with five different estrogen receptor ligands or DMSO for 45 minutes


title: ChIP-seq of ER in MCF-7 cells post ligand treatment

summary:
Goal: study the impact of estrogen receptor (ER) ligands on ER binding to chromatin in MCF-7 cells
Methods: ER Chromatin Immunoprecipitation and Sequencing (ChIP-seq)
Results: All tested ligands increase binding of ER onto DNA in MCF-7 breast cells. These ligands thus promote an association between ER and DNA, irrespective of their mode of action: selective ER modulator (SERM) 4-OH tamoxifen, and selective ER degraders (SERD) fulvestrant and GDC-0927.

overall_design: ChIP-Seq of MCF-7 cells treated with five different estrogen receptor ligands or DMSO for 45 minutes


title: RRBS (Reduced Representation Bisulfite Sequencing) of Egr1-/- and Tet1-/- mouse frontal cortex

city: NY

first: zhixiong

last: sun

address: 3908 pardes building, NYSPI

department: Psychiatry

summary: We performed methylome profiling for mouse frontal cortex tissues derived from 6~8 week old Egr1-/- and Tet1-/- mice.

overall_design: RRBS of mouse frontal cortex tissue from 6~8 week old Egr1-/- and Tet1-/- mouse brain

first: Xiguang

last: Xu

first: Hehuang

last: Xie


title: Induction of functional differentiation of induced hepatocyte-like (iHep) cells

city: Fukuoka

first: Atsushi

last: Suzuki

state: Fukuoka

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

department: Division of Organogenesis and Regeneration

institute: Medical Institute of Bioreguration, Kyushu University

summary: iHep cells maintained in two-dimensional (2D) culture can become functionally close to hepatocytes by forming cell aggregates under three-dimensional (3D) culture condition.

overall_design: We conducted comparative global gene expression analyses between 2D and 3D cultures of iHep cells. iHep cells were prepared from two independent experiments, designated iHep-1 and iHep-2.

first: Junpei

last: Yamamoto


title: Egr1 Recruits Tet1 to Shape the Brain Methylome during Early Postnatal Development

summary:
Early growth response gene-1 (Egr1) is a critical transcription factor involved in many important biological processes, including neuronal plasticity and memory formation. With a rapid increase in expression during the first few weeks after birth, Egr1 controls the selection, maturation and functional integration of newborn neurons. The regulation of Egr1-mediated gene expression has been shown to be under methylation control. However, Egr1 target sites and their epigenetic regulation in the nervous system remains largely unknown. In this study, we performed ChIP-seq for EGR1 in mouse frontal cortex and identified a large number of EGR1 binding sites with their cell-type specific methylation patterns established during postnatal frontal cortex development. More specifically, the CpG dinucleotides within these EGR1 binding sites become hypo-methylated in mature neurons but remain heavily methylated in glia. We further demonstrated that EGR1 recruits a DNA demethylase TET1 to remove DNA methylation at EGR1 binding sites and activate downstream genes. In addition, we found that the frontal cortexes from knockout mice with the loss of Egr1 or Tet1 share strikingly similar profiles in both gene expression and DNA methylation. In summary, our study reveals Egr1 as a key mediator for gene-environment interactions shaping brain methylome together with Tet1 during early postnatal development and provides an important new insight into how early life experience may shape the brain methylome.

This SuperSeries is composed of the SubSeries listed below.

overall_design: Genome-wide profiles of EGR1 binding in prefrontal cortices of 6-week old male mice were generated in duplicate using Illumina HiSeq 2000 platform. Reduced Represented Bisulfite Sequencing (RRBS) and RNA-seq of mouse frontal cortex tissue from 6~8 week old Egr1-/- and Tet1-/- mice were performed

first: Zhixiong

last: Sun

first: Jianlin

last: He

first: Ming-an


title: RNA-seq of Egr1-/- and Tet1-/- mouse frontal cortex

summary: We performed transcriptome profiling for frontal cortex tissues derived from 6~8 week old Egr1-/- and Tet1-/- mice.

overall_design: RNA-seq of mouse frontal cortex tissues from 6~8 week old Egr1-/- and Tet1-/- mice


title: ATAC-seq, ChIP-seq and RNA-seq of breast cancer cell lines post ligand treatment

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

overall_design: Refer to individual Series


title: Specific combinatorial mutations in MIR396 genes enlarge the grain size and modulate the plant architecture in rice

status: Public on Jul 24 2019

city: Nanchang

first: Dong

last: Wang

state: JiangXi

address: Hong Gu Tan New Road, No. 999

institute: Nanchang University

summary: miR396 is a key growth regulator in plants, however, the molecular mechanisms underlying its functions remained to be revealed. Here, through systematically gene-editing, we found that among the MIR396 family genes, MIR396e and -f were the main regulators of rice growth. mir396ef mutations could increase the grain yield through significantly enlarging the grain size. In addition, mir396ef mutations promoted the seedling growth and modulated the plant architecture by promoting the elongations of leaves (including leaf blades and sheaths) and panicles but suppressing the elongation of internodes, especially the uppermost internode. Our research reveals that mir396ef mutations promote the growth and organ elongation by significantly increasing the level of the gibberellin (GA) precursor, mevalonic acid (MVA), which subsequently activates the GA pathway. Our results also indicate that miR396 regulates the internode elongation through a different mechanism (probably through controlling SD37 expression) from the GA pathway. These results reveal two pathways by which miR396 regulates rice growth and provide valuable gene-editing targets to increase rice productivity.

overall_design: RNA-seq using the seedling shoots, developing uppermost internodes and young panicles (0.6–0.8 mm) of the wild type and mir396ef mutations. Two independent lines of mir396ef were used in the the transcriptome analyses of the seedling shoots. There are three biological replicates

first: Chunbo

last: Miao


title: Syndecan-1 promotes lung fibrosis by regulating epithelial reprogramming through extracellular vesicles (RNA-Seq)

first: Tanyalak

last: Parimon

summary: We evaluted the effects of extracellular vesicles of bleomycin-injured wild-type and syndecan-1 deficient mice on mouse lung epithelial cell line (MLE-12) total transcriptomic changes (bulk mRNA sequencing)

overall_design: Mouse lung epithelila cells (MLE-12) were treated with bronchoalveolar lavage fluid extracellular vesicles of bleomycin-injured wild type or syndecan-1 deficient mice or regular cell media. The mRNA of MLE-12 cells in 3 conditions were  were isolated and processed for bulk mRNA sequencing

first: Peter

last: Chen


title: Histone Recycling by FACT and Spt6 during Transcription Prevents the Scrambling of Histone Modifications [tiling]

city: Montreal

first: Francois

last: Robert

address: 110 av des Pins Ouest

institute: IRCM

summary: The genetic information encoded in DNA is framed by additional layers of information, referred to as the epigenome. Epigenetic marks such as DNA methylation, histone modifications and histone variants are concentrated on specific genomic sites as means to instruct, but also sometimes as a consequence of, gene expression. How this information is maintained, notably in the face of transcription, is not understood. Here we show that the histone chaperones FACT and Spt6 are required for maintaining proper localization of several histone modifications including H3K4me1,2,3, H3K36me3, H3K79me3, H3K14ac, H3K18ac and H2Bub in Saccharomyces cerevisiae. In the absence of functional FACT or Spt6, transcription generates massive nucleosome loss which is partially compensated by increased histone assembly by histone chaperones such as Asf1 and HIR. Because re-incorporation of histones by these histone chaperones in not coupled to transcription, the modified histones are randomly incorporated, leading to scrambling of the epigenetic information. Hence, our work highlights the importance of local nucleosome recycling by FACT and Spt6 during transcription in the maintenance of a proper epigenetic landscape.

overall_design: We profiled eight histone modifications in temperature-sensitive mutants for the histone chaperones FACT and Spt6 (spt16-197 and spt6-1004 respectively) in yeast Saccharomyces cerevisiae by ChIP-chip on tiling arrays. These histone modifications included H3K4me1, H3K4me2, H3K4me3, H3K36me3, H3K79me3, H3K14ac, H3K18ac and H2Bub. Abrogating the function of FACT or Spt6 leads to redistribution of the modified histones. The contribution of FACT and Spt6 on H3K4me3 mislocalization was also confirmed by nuclear depletion of Spt16 and Spt6 using the anchor-away system. In addition, we profiled histones (H4, H3, H2B) and RNAPII occupancy in wild type, spt16-197 and spt6-1004 cells. RNAPII occupancy was also measured in a temperature-sensitive mutant for RNAPII (rpb1-1). In order to investigate whether nucleosome loss may lead to mislocalization of histone modifications, we profiled H4, RNAPII, FACT and histone modifications in cells where H4 expression was shutdown using a system developed by the Grunstein lab (Han and Grunstein, 1988).  To test if the chromatin defects observed in the FACT and Spt6 mutants are caused by transcription, we inhibited transcription (or not) by treating cells with thiolutin, concomitantly to anchoring-away FACT or Spt6, and performed H3K4me3, H3K36me3, H4 and RNAPII ChIP-chip experiments. In addition, H3K4me3 ChIP-chip experiments were performed in htz1Δ, spt16-197/htz1Δ and spt6-1004/htz1Δ cells in order to rule out that the defects in histone modifications may occur because of the histone variant H2A.Z mislocalization in FACT and Spt6 mutants. H3K4me3 occupancy was also measured in ATP-dependent chromatin remodeler mutants including chd1Δ, spt16-197/chd1Δ, isw1Δ, spt16-197/isw1Δ, isw2Δ, spt16-197/isw2Δ. Finally, the localization of the histone chaperones Asf1 and HIR (FLAG –tagged) was determined in wild type and in spt16-197 cells. All ChIP samples were labeled with Cy5 and hybridized against appropriate samples that range from Input DNA, H2B, H3, H4 or NoTag ChIP samples (labeled with Cy3). The microarrays used were described before (Jeronimo and Robert, 2014). The data were normalized by setting the median of log2 ratios to zero. Each experiment was done in duplicate.

first: Célia

last: Jeronimo

first: Christian

last: Poitras

first: François


title: meg-3 meg-4 mutants are defective in exogenous RNAi signal amplification

status: Public on Jul 23 2019

city: Baltimore

first: Geraldine

last: Seydoux

address: 725 North Wolfe Street, PCTB 706

department: Molecular Biology and Genetics

institute: JHU School of Medicine

summary: Worms were fed a dsRNA trigger against the pos-1 gene and subjected to sRNAseq to see if they could amplify the exogenous RNAi trigger. meg-3 meg-4 were not able to amplify the signal as robustly as wild-type.

overall_design: Worms were starvation synchronized and plated on bacteria expressing dsRNA corresponding to the pos-1 gene. Samples were collected at the young mother stage, and subject to sRNAseq.

first: John

last: Ouyang


title: P granules protect RNA interference genes from silencing by piRNAs


title: Transcriptome analysis of auxin-regulated genes in Ceratopteris richardii sporophytes

city: Shanghai

first: Lin

last: XU

address: 300 Fenglin Road

department: Chinese Academy of Sciences

institute: Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences

summary: To explore the role of auxin in Ceratopteris richardii root initiation,  we carried out RNA-seq to analyze gene expression levels upon 2,4-D treatment.

overall_design: Ceratopteris richardii (wild type RNWT1) spores were cultured on 1/2MS medium at 26 °C under a 16-h-light/8-h-dark photoperiod in a growth chamber. After 30 days (mock group), sporophyte seedlings were transferred to medium with 2 μM 2,4-D  for 24 or 48 h. The whole seedlings were harvested and frozen in liquid nitrogen for RNA extration. Library construction and deep sequencing were carried out using the Illumina HiSeq 3000 platform following the manufacturer's instructions by Genergy Biotechnology (Shanghai, China).

first: Yuyun

last: Zhang

first: Jie

last: Yu


title: The Position Beta57 of IAg7 Controls the Early Anti-Insulin Response and Onset of Diabetes in NOD mice to Link MHC and Disease

first: Luc

last: Teyton


title: meg-3 meg-4 upregulate endogenous sRNAs targeting RNAi genes and downregulate their mRNAs

summary: sRNAseq was conducted on four independently generated meg-3 meg-4 lines, and upregulation of sRNAs targeting several RNAi genes was found. mRNAseq found that the transcript levels for several of these genes was also down. meg-3 meg-4 mutants also showed a similar pattern of sRNA misregulation as the rde-11 mutant.

overall_design: Mixed-staged populations of independently generated meg-3 meg-4 lines (meg-3 meg-4 #1, #2, #3, #4) and N2 worms (grown on NA22) were collected and subject to sRNAseq. mRNAseq was additionally conducted on young mother-staged populations of meg-3 meg-4 #1 and N2 grown on HT115 with the L4440 plasmid. sRNAseq was also conducted on young mother-staged N2 and rde-11 mutants.


title: The hrde-1 mutation suppresses the rde-11 and sid-1 sRNA upregulation phenotype of meg-3 meg-4 mutants

summary: sRNAseq was conducted on the hrde-1; meg-3 meg-4 triple mutant, revealing that the hrde-1 mutation suppresses the rde-11 and sid-1 sRNA upregulation phenotype of meg-3 meg-4 mutants  .

overall_design: Worms were starvation synchronized and plated on HT115-L4440. Samples were collected at the young mother stage, and subject to sRNAseq.


title: Characterisation of the EZH2 regulated transcriptome in de novo transformed cells (RNA-Seq)

city: London

first: Paola

last: Scaffidi

state: Choose a state

address: 1 Midland Road

institute: Francis Crick Institute

summary: Epigenetic regulators are often hijacked by cancer cells to sustain and enhance their malignant phenotypes. Co-opted proteins are typically not mutated and their intrinsic properties remain unaltered. How cancer cells repurpose key regulators of cell identity as tumour-promoting factors is unclear. The antithetic role of the Polycomb component EZH2 in normal brain and glioma provides a paradigm to dissect how wild-type chromatin modifiers gain a pathological function in cancer. In this study, we show that oncogenic signalling induces redistribution of EZH2 across the genome, which in turn misregulates key homeotic genes and corrupts the identity of neural cells. Characterisation of EZH2 direct targets in de novo transformed cells reveals that acquisition of tumorigenic potential is accompanied by a transcriptional switch involving de-repression of spinal cord-specifying HOX genes and concomitant silencing of the empty spiracles homologue EMX2, a key regulator of neurogenesis in the forebrain and negative regulator of neural stem cell proliferation. Our results suggest that by redistributing EZH2 across the genome, cancer cells subvert developmental transcriptional programs that specify normal cell identity and remove physiological breaks that normally restrain cell proliferation.

overall_design: The transcriptome of cells at different stages of de novo neoplastic transformation treated with an EZH2 inhibitor or DMSO control was characterised by total RNA-seq, in triplicate, using an Illumina Hiseq 4000.

first: Thomas

last: Mortimer


title: Genome-wide maps of TET1 binding in mouse frontal cortex

first: zhixiong

last: sun

summary: With anti-TET1 immunoprecipitated chromatin from mouse frontal cortices, we generated TET1 binding maps with 4496 high-confidence peaks and approximately 90% of TET1 peaks were within intergenic regions.

overall_design: Genome-wide profiles of TET1 binding in frontal cortices of 6-week old male mice were generated in duplicate using Illumina HiSeq 4000 platform.

first: Zhixiong

last: Sun

first: Hehuang

last: Xie


title: Characterisation of EZH2 and H3K27me3 genome-wide distribution in de novo transformed cells (ChIP-Seq)

overall_design: The genome-wide distribution of EZH2 and H3K27me3 in cells at different stages of de novo neoplastic transformation was characterised by ChIP-seq, in duplicate, using an Illumina HiSeq 2500.


title: Regulation of human epidermal progenitor cell function by HNRNPK through transcriptional and post-transcriptional mechanisms

city: San Diego

first: George

last: Sen

address: 9500 Gilman Drive

institute: UCSD

summary: Maintenance of high-turnover tissues such as the epidermis requires a tight balance between stem and progenitor cell proliferation and differentiation. The molecular mechanisms governing this process are an area of active investigation. Here we show that HNRNPK, a multifunctional protein, is necessary to prevent premature differentiation and sustains the proliferative capacity of epidermal stem and progenitor cells. To prevent premature differentiation of progenitor cells, HNRNPK recruits DDX6 to a subset of mRNAs that code for transcription factors that induce differentiation. Upon binding, these mRNAs such as GRHL3, KLF4, and ZNF750 are degraded which prevents premature differentiation. To sustain the proliferative capacity of the epidermis, HNRNPK recruits RNA polymerase II to genomic sites of proliferation genes such as MYC, FGFBP1, PTHLH, ITGB4 to promote their expressions. Our study establishes a prominent role for HNRNPK in maintaining adult tissue homeostasis through both transcriptional and post-transcriptional mechanisms.

overall_design: HNRNPK RNA-seq in primary keratinocytes. HNRNPK RNA IP-seq in primary keratinocytes. ChIP-seq with HNRNPK and RNA POL II antibodies in primary keratinocytes.

first: Jingting

last: Li


title: Effects of agricultural pesticides in aquafeeds on wild fish feeding on leftover pellets near fish farms

city: Bergen

first: Fekadu

last: Yadetie

address: Thormøhlensgt. 53A/B

country: Norway

institute: University of Bergen

summary: Screening has revealed that modern-day feeds used in Atlantic salmon aquaculture might contain trace amounts of agricultural pesticides. To reach slaughter size, salmon are produced in open net pens in the sea. Unconsumed feed pellets and undigested feces deposited beneath the net pens represent a source of contamination for marine organisms. To examine the impacts of long-term and continuous dietary exposure to an organophosphorus pesticide (OP) found in Atlantic salmon feed, we fed juvenile Atlantic cod (Gadus morhua), an abundant species around North Atlantic fish farms, three concentrations (0.5, 4.2 and 23.2 mg/kg) of chlorpyrifos-methyl (CPM) for 30 days. Endpoints included liver and bile bioaccumulation, liver transcriptomics and metabolomics, as well as plasma cholinesterase activity, cortisol, liver 7-ethoxyresor-ufin-O-deethylase (EROD) activity and hypoxia tolerance. The results show that Atlantic cod can accumulate relatively high levels of CPM in the liver after continuous exposure, which is then metabolized and excreted via the bile. All three exposure concentrations led to significant inhibition of plasma cholinesterase activity, the primary target of CPM. Transcriptomics profiling pointed to effects on cholesterol and steroid biosynthesis. Metabolite profiling revealed that CPM induced responses reflecting detoxification by glutathione-S-transferase, inhibition of monoacylglycerol lipase, potential inhibition of carboxylesterase, and increased demand for ATP, followed by secondary inflammatory responses. A gradual hypoxia challenge test showed that all groups of exposed fish were less tolerant to low oxygen saturation than the controls. In conclusion, this study suggests that wild fish continuously feeding on leftover pellets near fish farms over time may be vulnerable to OPs.

overall_design: The four treatment groups were Control (0 mg CPM/kg, with DMSO), 0.5 mg CPM/kg, 4.2 mg CPM/kg and 23.2 mg CPM/kg.  Each treatment group consisted of 9 fish. These fish were sampled from 3 different tanks per treatment, with n=9 per treatment. A total of 36 samples were sequenced. For each sample, about 50 million 150 bp paired-end reads were generated.

first: Pål

last: Olsvik

first: Anett

last: Larsen

first: Marc

last: Berntssen

first: Anders

last: Goksøyr

first: Odd

last: Karlsen

first: Monica

last: Sanden

first: Torstein

last: Kristensen


title: PS2APP sorted cell types

first: Melanie

last: Huntley

summary:
Mice of indicated genotypes were perfused and their brains dissected and dissociated. Cells were fixed, immunolabeled and FACS sorted. RNA was extracted from neuron, astrocyte, and microglial cell populations. Typical RIN=4-5 for neurons, 6-8 for astrocytes, and 5-7 for microglia. Typical RNA yields 200-300ng for neurons, ~20ng for microglia, and ~5ng for astrocytes.
cDNA was generated from up to 25 ng of total RNA using Nugen’s RNA-Seq method for low-input RNA samples, Ovation RNA-Seq System V2 (NuGEN). (Per manufacturers instructions, total RNA was neither depleted of rRNA nor polyA-selected.) 1 μg of sheared cDNA was taken into further processing, starting at end repair step, using Illumina’s TruSeq RNA Sample Preparation Kit v2 (Illumina).
The SAMPLE_ID sample characteristic is a sample identifier internal to Genentech.
The ID of this project in Genentech's ExpressionPlot database is PRJ0006717

overall_design: NeuN+ neurons, Gfap+ astrocytes, and Cd11b+ myeloid cells were sorted from 11.5 month old PS2APP transgenic mice or non-transgenic littermates.

first: Brad

last: Friedman

first: Jesse

last: Hanson

first: David

last: Hansen


title: RNA-seq of breast cancer cell lines post ligand treatment II

last: Hafner

summary:
Goal: study the impact of estrogen receptor ligands on gene expression in HR+ breast cancer cells
Methods: RNA sequencing
Results: Ligand 4-OH tamoxifen, a selective ER modulator (SERM), promotes transcriptional activation of ER and mimics the transcriptional effect of natural ligand E2 for a subset of ER target genes, consistently across the seven breast cell lines (MDA-MB-134 VI, MDA-MB-330, EFM-19, T-47D, and BT-474). Selective ER degraders (SERD) fulvestrant and GDC-0927 on the other hand do not induce, or induce very weakly the expression of ER target genes. The effect of GDC-0810 depends on the cellular context.

overall_design: Duplicates results of RNA-Seq of seven cell lines treated with six different estrogen receptor ligands or DMSO for 24 hours

first: Ciara

last: Metcalfe

first: Anneleen

last: Daemen

first: Wei

last: Zhou