title: Analysis of the Clustered Protocadherin (cPcdh) Locus in Human Pluripotent Stem and Derived Cells [scRNA-seq]

status: Public on Aug 12 2019

city: La Jolla

first: Daria

last: Merkurjev

address: 9500 Gilman Drive, Mail Code 0648

department: Medicine

institute: UCSD

summary: In the mammalian genome, the clustered protocadherin (cPcdh) locus is a paradigm of stochastic gene expression with the potential to express a different cPcdh combination in every neuron. Here, we report a limited version established during the transition from the naive to the primed states of human cell pluripotency that reduces by orders of magnitude the combinatorial potential in the cPcdh locus. It is a chromatin-based mechanism that increases the frequency of stochastic selection of a subset of cPcdh promoters upon differentiation to fetal-like neurons in monolayers, organoids, or the rat spinal cord. Signs of similar preferential selections can be observed in the brain throughout fetal development, disappearing after birth, but not in a condition of delayed maturation such as Down Syndrome. We therefore propose that pluripotent cells impose a pattern of limited cPcdh diversity on neurons that increases the likelihood of cPcdh repetition until these cells acquire adult-like maturation.

overall_design: Lines/sublines: The hiPSC1-8 sublines were generated from single cells of the parent CVB hiPSC line. Six of these sublines were genetically modified (hiPSC2-7) and two were cases of failed genome editing (hiPSC1 and 8); please see Supplementary Table S1 in the associated publication for more details. Initially, these modifications should be irrelevant to the study of the cPcdh locus. The. hiPSC1 1.1-6 sublines were generated from the hiPSC1 subline and all underwent a process of genome editing, which again should be irrelevant to the study of the cPcdh locus (see Supplementary Table S1 in the associated publication for more details). The hiPSC 1.7-1.9 sublines were also generated from single cells of the parent CVB hiPSC line without undergoing any genome editing protocol. The hiPSC 1.13-15 sublines were generated from single cells of the parent CVI hiPSC line also without undergoing any genome editing protocol. The parent CVB and CVI lines were generated in the same reprogramming process and corresponded to two independent colonies. The hESC 1.7-1.9 sublines were generated from single cells of the parent HUES9 hESC line without undergoing any genome editing protocol. The HUES9 hESC 1.8 1.1-8 sublines were generated from single cells of the HUES9 1.8 subline after a process of primed-to-naive-to-reprimed conversion. All hiPSC/hESC lines/sublines were cultured in the primed state unless indicated (when indicated, some lines/sublines were cultured under naive-inducing conditions (5iLA protocol, and when returned to the primed state, the conditions were referred to as 're-primed'). For mouse cells, the 46C mESC 1.1-1.6 sublines were generated from single cells of the parent 46C mESC line. The R1 mESC 1.4/1.7 and 2.10/2.13 sublines were generated from single cells of the parent R1 mESC line. The R1 EpiSC 1.1-1.15 sublines were generated from single cells of the parent R1 mESC line after conversion to EpiSCs. The parental R1 mESC and EpiSC populations have also been included here.   ChIP-seq data: All ChIP-seq experiments were performed in pluripotent stem cells (hiPSCs/hESCs/mESCs/EpiSCs). Most profiles were based on H3K4me3, but many others also on CTCF, Rad1, H3K4me2, H3K9me3, H3K9ac, H2A.Z, REST/NRSF, SIN3A, and JMJD2A.  RNA-seq data: triplicate differentiation replicates of neurons generated from NPCs derived from hiPSC1-8 (n=24); cortical neurons generated from hiPSC1/3/5 (n=3); 10-month-old cortical organoids generated from the CVB line (n=1, pool of organoids); and primed, naive, and re-primed HUES9 1.8 subline (n=1 each).  scRNA-seq data (SMART-seq+NEXTERA; full transcript): 79 single cells of neurons generated from NPCs of the hiPSC1 line (54 to 71), hiPSC2 (1 to 51), hiPSC6 (88 to 96), and hiPSC7 (72 to 87). The libraries were sequenced twice, in one case the libraries from all cells were pooled before cleaning and measuring DNA concentration, whereas in the other case the libraries were pooled after cleaning. and measuring DNA concentration (so equal amounts were mixed).

first: D

first: A

last: Almenar-Queralt

first: I

last: Garcia-Bassets


title: Gene expression in ABHD5-KD RAW cells or RAW cell-primed CT-26 cells

status: Public on Aug 11 2019

city: Chongqing

first: Hongming

last: Miao

state: Chongqing

address: Gaotanyan Street NO.30

department: Department of Biochemistry and Molecular Biology

country: China

institute: Third Military Medical University (Army Medical University)

summary: RAW cells,ABHD5-KD RAW cells or those macrophage-primed CT-26 cells were subjected to microarray assays.Each group contain 3 samples.

overall_design: To explore the downstream pathways of macrophage ABHD5 and the effects on cancer cells, RAW cells or ABHD5-KD RAW cells and those macrophage-primed CT-26 cells were subjected to microarray assays.


title: Gene expression changes in asb2b mutant heart

city: Bad Nauheim

first: Ryuichi

last: Fukuda

state: Select...

address: Ludwigstrasse 43

country: Germany

institute: Max Planck Institute for Heart and Lung Research

summary: Tissue integrity is critical for organ formation and function1. During heart development,  cardiomyocytes have to differentiate and integrate to form a coherent tissue that contracts  synchronously2,3. However, the molecular mechanisms regulating cardiac tissue integrity are  poorly understood. Here, we show that proteolysis, via the E3 ubiquitin ligase ASB2, regulates  cardiomyocyte maturation and tissue integrity. Cardiomyocytes in asb2b mutants fail to  terminally differentiate, exhibit disorganized sarcomeres and cell-cell junctions, as well as  defects in tissue polarity, resulting in reduced cardiac contractility and output. Mosaic analyses  reveal a cell-autonomous requirement for Asb2b in cardiomyocyte integration, as asb2b mutant  cardiomyocytes are unable to meld into wild-type myocardial tissue. In vitro and in vivo data  indicate that ASB2 negatively regulates TCF3, a bHLH transcription factor. We further show  that TCF3 must be degraded for cardiomyocyte maturation, as TCF3 gain-of-function causes a  number of phenotypes associated with cardiomyocyte dedifferentiation. Overall, our results  indicate that proteolysis has an important role in cardiomyocyte maturation and the formation  of a coherent myocardial tissue.

overall_design: 50 hpf WT and asb2b mutant fish hearts were isolated and RNA expression levels were analyzed by microarray


title: Analysis of the Clustered Protocadherin (cPcdh) Locus in Human Pluripotent Stem and Derived Cells [ChIP-seq II our of II]

state: CA

country: USA

type: Genome binding/occupancy profiling by high throughput sequencing

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: Analysis of the Clustered Protocadherin (cPcdh) Locus in Human Pluripotent Stem and Derived Cells [RNA-seq II our of II]

type: Expression profiling by high throughput sequencing


title: Spop restrains inflammation-induced emergency hematopoiesis by targeting MyD88

city: New York

first: Igor

last: Dolgalev

state: New York

address: 550 1st Ave

institute: NYU Grossman School of Medicine

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

overall_design: Refer to individual Series


title: Transcriptomic and microRNAomic profiling reveals molecular mechanisms to cope with silver nanoparticle exposure in the ciliate Euplotes vannus

status: Public on Aug 10 2019

city: Xiamen

first: Jun

last: Yang

address: 1799 Jimei Road, Xiamen, 361021 PR China

institute: Chinese Academy of Sciences

type: Non-coding RNA profiling by high throughput sequencing


title: SMUG1 promotes telomere maintenance through telomerase RNA end-processing

city: Lørenskog

first: Hilde

middle: Loge

last: Nilsen

state: Lørenskog

address: Sykehusveien 25

department: Akershus University Hospital

country: Norway

institute: University of Oslo

summary: Single-strand selective uracil DNA-glycosylase (SMUG1) associates with the DKC1-H/ACA ribonucleoprotein complex, which is essential for telomerase biogenesis. We show herein, that SMUG1 interacts with the telomerase RNA component, hTERC, and is required for co-transcriptional processing of the nascent transcript towards mature hTERC. We demonstrate that SMUG1 regulates the presence of base modifications between the CR4/CR5 region and the H-box situated towards the 3´-end of hTERC. Increased levels of hTERC base modifications are accompanied by reduced DKC1 binding. Loss of SMUG1 leads to an imbalance between mature hTERC and its processing intermediates, leading to the accumulation of 3´-polyadenylated and 3´-extended intermediates that are degraded in an EXOSC10-independent RNA degradation pathway. Consequently, SMUG1-deprived cells, present telomerase deficiency leading to impaired bone marrow proliferation in SMUG1-knockout mice.

overall_design: Analysis of differential expressed genes in HAP1 SMUG1 WT and SMUG1 KO cells generated by deep sequencing (in triplicate).

first: Penelope

last: Kroustallaki

first: Lisa

last: Lirussi


title: Gene expression in migtating TAMs

status: Public on Aug 09 2019

summary: We have employed whole genome microarray expression profiling as a discovery platform to identify different gene expression in normal,tumor-primed or tumor-primed migrating macrophages.

overall_design: Peritoneal macrophages were cultured alone as control group (Ctrl) or co-cultured with CT-26 cells (Group T) in the lower chamber of Transwell. The migratory macrophages co-cultured with CT-26 cells from upper chamber of the Transwell were marked as group M. Those macrophages were then isolated and subjected to microarray assays. Each group contain 3 samples.


title: TDP-43 knockdown in primary rat astrocytes

city: Boulder

first: Thomas

last: LaRocca

state: CO

address: 1725 Pleasant St

institute: University of Colorado Boulder

summary: TDP-43 is an RNA binding protein involved in amyotrophic lateral sclerosis and other neurodegenerative diseases. The purpose of this study was to determine if loss of TDP-43 function leads to accumulation of repetitive element transcripts, double-stranded RNA (dsRNA) and innate immune activation that may be involved in disease pathology. TDP-43 was knocked down in primary rat astrocytes via siRNA, cells were treated with/without ATP (an immune modulator), and polyA RNA-seq was performed to profile gene expression. Immunoprecipitation/RNA-seq was also performed using a dsRNA-specific antibody to identify potential dsRNAs resulting from TDP-43 knockdown.

overall_design: PolyA RNA and/or immunoprecipitated total RNA from cells treated with TDP-43 siRNA, scrambled (control) siRNA and/or ATP


title: Transcriptomic and microRNAomic profiling reveals molecular mechanisms to cope with silver nanoparticle exposure in the ciliate Euplotes vannus (RNA-seq)

summary: In spite of many reports on the toxicity of silver nanoparticles (AgNPs), the mechanisms underlying the toxicity are far from clear. The present study conducted transcriptome and microRNAome sequencing for Euplotes vannus to understand the molecular mechanisms by which this protist copes with AgNPs exposure. By transcriptome profiling, 1884 and 5834 differentially expressed genes (DEGs) were identified after one hour and 12 hours exposure to 15 mg/L AgNPs, respectively. From microRNAsome profiling, totally 16 differentially expressed microRNAs were identified under AgNPs stress.In spite of many reports on the toxicity of silver nanoparticles (AgNPs), the mechanisms underlying the toxicity are far from clear. The present study conducted transcriptome and microRNAome sequencing for Euplotes vannus to understand the molecular mechanisms by which this protist copes with AgNPs exposure. By transcriptome profiling, 1884 and 5834 differentially expressed genes (DEGs) were identified after one hour and 12 hours exposure to 15 mg/L AgNPs, respectively. The DEGs were significantly enriched in macropinocytosis and phagocytic vesicles suggesting that the uptake of AgNPs may be mediated by endocytic pathways, while the differential expression of ABC transporters and copper-transporting ATPase implicates active efflux transport of Ag. Several DNA repair pathways were also significantly enriched with differentially expressed cell cycle control genes implying that exposure to AgNPs might have caused DNA damage and G2/M cell cycle arrest. The damage might have resulted from increased ROS production, as evidenced by elevated expression of several antioxidants genes to combat oxidative stress. From microRNAsome profiling, totally 16 differentially expressed microRNAs were identified under AgNPs stress. Integrated analysis of the microRNA and mRNA expression profiles found that the differentially expressed microRNAs target a series of genes involved in many important biological processes, suggesting that E. vannus exposure elicited a broad post-transcriptional regulatory mechanism through microRNAs–mRNAs–biological functions network to cope with the toxicity of AgNPs.

overall_design: We conducted transcriptome and microRNAome sequencing for Euplotes vannus, a marine benthic ciliate, grown under 15mg/L AgNPs after 0, 1 and 12 hours.

first: Yongbo

last: Pan

first: Wenjing

last: Zhang

first: Senjie

last: Lin


title: Role of diet in cardiac aging and fibrosis

city: Pittsburgh

first: Niranjana

last: Natarajan

state: PA

address: 200 Lothrop street, BST1720

institute: University of Pittsburgh

summary: Calorie restriction (CR) improved healthspan in two longitudinal studies in nonhuman primates (NHPs), yet only the University of Wisconsin (UW) study demonstrated an increase in survival in CR monkeys relative to controls; the National Institute on Aging (NIA) study did not. Here, analysis of left ventricle samples showed that CR did not reduce cardiac fibrosis relative to controls. However, there was a 5.9-fold increase of total fibrosis in UW hearts, compared to NIA. Diet composition was a prominent difference between the studies; therefore, we used the NHP diets to characterize diet-associated molecular and functional changes in the hearts of mice. Consistent with the findings from the NHP samples, mice fed UW or a modified NIA diet with increased sucrose and fat developed greater cardiac fibrosis compared to the NIA diet, and transcriptomics analysis revealed diet-induced activation of myocardial oxidative phosphorylation and cardiac muscle contraction pathways.

overall_design: 4 cohorts of mice were administered NIA, UW, chow or modified- NIA diet for a period of 6 months. Hearts were harvested and RNA was extracted from the ventricles for bulk RNA-seq on Illumina NextSeq.

first: Richard

middle: T

last: Lee


title: Transcriptomic and microRNAomic profiling reveals molecular mechanisms to cope with silver nanoparticle exposure in the ciliate Euplotes vannus (miRNA-seq)


title: Effect of 2-deoxyglucose and other unfolded protein response (UPR) stimuli on the interferon gamma-mediated response in mouse bone marrow-derived macrophages

city: Oberlin

first: Jordan

last: Price

state: OH

address: 119 Woodland St

institute: Oberlin College

summary: We report transcriptional responses of mouse macrophages to Pam3CSK4 stimulation that are additionally stimulated with interferon gamma and various stimuli that induce the unfolded protein response. We identify key transcripts associated with restrictive and permissive states of host macrophages in terms of intracellular replication of Legionella pneumophila.

overall_design: Examination of RNA isolated from mouse bone marrow-derived macrophages stimulated with Pam3CSK4 (Invivogen) ± interferon gamma (ThermoFisher) ± 2-deoxyglucose (Abcam), geldanamycin (Sigma), brefeldin A (BD), dithiothreitol (Sigma), tunicamycin (Sigma), thapsigargin (Sigma), and ISRIB (Sigma) as indicated.

middle: V

first: Russell

middle: E

last: Vance


title: Effect of unfolded protein response (UPR) stimuli on the interferon gamma-mediated response in mouse bone marrow-derived macrophages


title: Effect of 2-deoxyglucose on the interferon gamma-mediated response to intracellular bacterial infection in mouse bone marrow-derived macrophages

summary: We report transcriptional responses of mouse macrophages to Pam3CSK4 stimulation or L. pneumophila infection that are additionally stimulated with interferon gamma ± 2-deoxyglucose. We identify a strong transcriptional signature of the unfolded protein stress response in macrophages exposed to 2-deoxyglucose. Additionally we find that 2-deoxyglucose reduces the expression of several key interferon gamma-induced transcripts associated with an antimicrobial response to L. pneumophila.

overall_design: Examination of RNA isolated from mouse bone marrow-derived macrophages stimulated with Pam3CSK4 ± interferon gamma ± 2-deoxyglucose or infected with L. pneumophila ± interferon gamma ± 2-deoxyglucose


title: Mtb-induced BAL cell gene expression signature in LTBI [naive experiment]

city: cleveland

first: richard

last: silver

state: ohio

address: 2109 Adelbert Rd

institute: CWRU

summary:
In this study, we evaluated global Mtb-induced gene expression in airway immune cells obtained by bronchoalveolar lavage of individuals with latent tuberculosis infection (LTBI) and in Mtb-naïve control subjects
We used microarrays to detail the global programme of gene expression evaluating the impact of localized T cells subsets in the recall responses of individuals with LTBI

overall_design: BAL cells were collected, CD4 and CD8 T cells depleted, cells infected with H37RV and microarray performed on cells

first: Jessica

last: Jarvela

first: Michelle

last: Moyer

first: Patrick

last: Leahy

first: Tracey

last: Bonfield

first: David

last: Fletcher

first: Wambura

middle: N

last: Mkono

first: Htin

last: Aung

middle: H

last: Canaday

first: Jean-Eudes

last: Dazard

middle: F

last: Silver


title: Mtb-induced BAL cell gene expression signature in LTBI [CD8 experiment]


title: Mtb-induced BAL cell gene expression signature in LTBI [CD4 experiment]


title: Next Generation Sequencing Facilitates Quantitative Analysis of two wine yeasts: Saccharomyces cerevisiae EC1118 and Kluyveromyces marxianus IWBT Y855

city: Stellenbosch

first: Stephanie

last: Rollero

address: Victoria Street

department: DVO

country: South Africa

institute: Stellenbosch University

summary: K.marxianus and S. cerevisiae differed by their consumption of some amino acids and the production of aroma compounds (especially higher alcohols). To complete this phenotypic observation, RNA sequencing experiment was performed. Two samples were realized: at 6h of fermentation corresponding to lag phase and at the time of half of the maximal population was reached (20h for S. cerevisiae and 36h for K. marxianus). Thanks to this analyse, we can understand what regulations explain the differences between these two strains.

sample_organism:
Kluyveromyces marxianus
Saccharomyces cerevisiae

overall_design: RNA profiles of two wine strains at two different points of alcoolic femrentation were generated by RNA sequencing, in triplicate, using Illumina HiSeq2500 instrument.

first: Stéphanie

first: Audrey

last: Bloem

first: Anne

last: Ortiz-Julien

first: Florian

last: Bauer

first: Carole

last: Camarasa

first: Benoit

last: Divol


title: Mtb-induced BAL cell gene expression signature in LTBI

last: silver


title: mRNA sequencing of clinical-grade neural stem cells derived from human ES cells

status: Public on Aug 08 2019

first: Samuel

middle: L

last: Pfaff

address: 10010 N Torrey Pines Rd

institute: Salk Institute for Biological Studies

summary: We report the transcriptome profile of human neural stem cells derived from ES cells.  Cells were transplanted into rodent models, and mRNA transcripts from the chimeric graft tissue were bioinformatically split according to species of origin.

sample_organism:
Homo sapiens
Rattus norvegicus

platform_organism:
Homo sapiens
Rattus norvegicus

overall_design: Human (h)ES lines H9 and ESI-017 were differentiated into neural stem/progenitor cells (NSCs/NPCs) using a clonal morphology basis of selection, as described in Bohaciakova et al., 2019. Expression (RNA-seq) analysis of these clonal morphology (CoMo)-derived NSC suspensions demonstrate similar gene expression profiles to NSCs that were purified with FACs methods. We injected independently H9- and ESI-017-derived NSC suspensions in the central grey matter of the spinal lumbar region of n=10 adult rats (Rat 1-4, and Rat 5-10, respectively). After 1 week, 1, 2, or 8 months in H9 hESC-NSC-injected rats (Rat 1-4, respectively), and 2 or 6 months in ESI-017 hESC-NSC-injected rats (Rat 5-7 and Rat 8-10, respectively), grafted cells were processed for RNA-seq analysis. We used these samples to profile the patterns of cPcdh variations, as described in Almenar-Queralt et al., 2019. Human and rat reads were separated according to species (HG and RN) by bioinformatics methods.

first: Shawn

middle: P

last: Driscoll

first: Martin

last: Marsala


title: Dynamic Lineage Priming by ERK is Driven by Transcription Factor-Independent Enhancer Regulation [mRNA_TC]

city: Copenhagen

first: Josh

middle: M

last: Brickman

address: 3B Blegdamsvej

department: reNEW

country: Denmark

institute: Copenhagen University

summary: Extensive analysis if the means by which ERK affects transcription via enhancer regulation in mouse embryonic stem cells. This study combines analysis of mRNA, and nascent RNA dynamics and correlates this with changes in transcription factor, co-factor, and RNAPII binding and activity.

overall_design: Mouse ESCs expressing a cRAF-ERT2 construct allowing ERK activation upon the addition of 4OT to the media. Cells were left untreated (0h), or treated with 250nM 4OHT for 1-2-or 4hrs. Total RNA was collected and purified and rRNA contamination was subsequently removed using the ribogold kit from Illumina prior to library preparation.

first: Joshua

first: William

middle: B

last: Hamilton


title: MiR-29 regulates de novo lipogenesis and controls circulating triglyceride levels in a Sirt1-dependent manner

city: Ithica

first: Praveen

last: Sethupathy

state: NY

address: Cornell University College of Veterinary Medicine, Box 17

institute: Cornell University

summary: Investigation of the effect of miR-29 on de novo lipogenesis.

sample_organism:
Mus musculus
Rattus norvegicus

platform_organism:
Mus musculus
Rattus norvegicus

overall_design: Measure lipid synthesis following perturbation of miR-29 using locked nucleic acids. Further investigate the role of SIRT1 on circulating lipids using a SIRT1-knockout model.

first: Yu-Han

last: Hung

first: Matt

last: Kanke


title: Germ granules coordinate RNA-based epigenetic inheritance pathways

city: Boston

last: Dodson

address: 77 Avenue Louis Pasteur, NRB Room 266

institute: Harvard Medical School

summary: Germ granules are biomolecular condensates that promote germ cell totipotency in most, if not all, animals. In C. elegans, MEG-3 and MEG-4 are two intrinsically disordered proteins that are redundantly required for the phase separations that drive germ granule assembly in germline blastomeres. Here, we show that animals lacking MEG-3/4 exhibit defects in dsRNA-mediated gene silencing (RNAi) that are due, at least in part, to defects in systemic RNAi. Interestingly, these RNAi defects are transgenerationally disconnected from meg-3/4 genotype: RNAi defects do not arise until 5-9 generations after animals become mutant for meg-3/4, and RNAi defects persist for 9-11 generations after meg-3/4 genotype is restored to wild type. Similar non-Mendelian patterns of inheritance are associated with other mutations that disrupt germ granule formation, indicating that germ granule disruption is the likely cause of genotype/phenotype disconnects. Loss of germ granules is associated with the production of aberrant populations of endogenous siRNAs, which, remarkably, are propagated for ≅10 generations in wild-type descendants of animals that lacked germ granules. sid-1, which encodes a factor required for systemic RNAi in C. elegans, is inappropriately and heritably silenced by aberrantly expressed sid-1 endogenous siRNAs, suggesting that transgenerational silencing of sid-1 likely underlies the heritable defect in RNAi. We conclude that one function of germ granules is to organize RNA-based epigenetic inheritance pathways and that failure to assemble germ granules has consequences that persist across many generations.

overall_design: Small RNA sequencing of wild type, meg-3 meg-4 mutant animals, hrde-1; meg-3 meg-4 mutant animals, and wild-type descendants of a meg-3/4 outcross (generations F3-F7, F10, F15, F20, and F25). Two biological replicates were sequenced for each genotype and generation.

first: Scott

last: Kennedy


title: Dynamic Lineage Priming by ERK is Driven by Transcription Factor-Independent Enhancer Regulation [ERK-AS]

overall_design: Mouse embryonic stem cells, where both ERK1 and ERK2 genes have been knocked out and ERK function is replaced with a cDNA encoding for a FLAG-ERK2 Q103A mutant and also stably expressing a cRAF-ErT2 expression cassette, were treated with 4OHT for 2hrs to activate ERK signalling via cRAF-ErT2. Activation was performed in the presence of either DMSO, 1uM PD032509 to inhibit Mek acticvity, or 2uM PP1 to inhibit ERK2 Q103A. 15 minutes prior to RNA isolation, cells were treated with 5mM ethynyl uridine to label newly synthesized RNA . Subsequent to total RNA isolation, labelled RNA was purified by standard chemistry, libraries prepared, and sequenced.


title: Dynamic Lineage Priming by ERK is Driven by Transcription Factor-Independent Enhancer Regulation [ATAC-Seq]

overall_design: Mouse embryonic stem cells, stably expressing a cRAF-ErT2 expression cassette, were treated with 4OHT for 0, 1, or 2hrs to activate ERK signalling via cRAF-ErT2, and chromatin accessibility subsequently analysed .


title: Dynamic Lineage Priming by ERK is Driven by Transcription Factor-Independent Enhancer Regulation [2h_EU]

overall_design: Mouse embryonic stem cells, stably expressing a cRAF-ErT2 expression cassette, were treated with 4OHT for 2hrs to activate ERK signalling via cRAF-ErT2. 15 minutes prior to RNA isolation, cells were treated with 5mM ethynyl uridine to label newly synthesized RNA . Subsequent to total RNA isolation, labelled RNA was purified by standard chemistry, libraries prepared, and sequenced.


title: Dynamic Lineage Priming by ERK is Driven by Transcription Factor-Independent Enhancer Regulation [Med24_KO]

overall_design: Mouse embryonic stem cells, where both Med24 has been knocked out and Med24 function is replaced with a TET regulated cDNA encoding for a FLAG-Med24 and also stably expressing a cRAF-ErT2-T2A-RTTA expression cassette. Cells were maintained for several passages in then presence (WT) or absence (KO) of Doxycycline (500nM) prior to stimulation with 4OHT to activate ERK. Cells were treated with 4OHT for 2hrs or 8hrs to activate ERK signalling via cRAF-ErT2. 15 minutes prior to RNA isolation, cells were treated with 5mM ethynyl uridine to label newly synthesized RNA . Subsequent to total RNA isolation, labelled RNA was purified by standard chemistry, libraries prepared, and sequenced.


title: Dynamic Lineage Priming by ERK is Driven by Transcription Factor-Independent Enhancer Regulation [H3K27me3]

overall_design: Mouse embryonic stem cells, stably expressing a cRAF-ErT2 expression cassette, were treated with 4OHT for 2hrs to activate ERK signalling via cRAF-ErT2


title: Erk stimulation in PDK1 knockout cells

summary: expression analysis of Erk stimulation in PDK1 knockout and wildtype cells

overall_design: Rescued or KO ESCs were stimulated for 8hrs, or stimulated for 8hrs with a subesquent 2hr treatment with the Mek inbhibitor PD03


title: Dynamic Lineage Priming by ERK is Driven by Transcription Factor-Independent Enhancer Regulation [gene expression]

overall_design: WT or KO ESCs were stimulated for 8hrs, or stimulated for 8hrs with 4OHT to activate the Raf-ErT2 fusion they express and then with a subesquent 2hr treatment with the Mek inbhibitor PD03


title: Dynamic Lineage Priming by ERK is Driven by Transcription Factor-Independent Enhancer Regulation [RBP1 ChIP-seq]

overall_design: Mouse embryonic stem cells, stably expressing a cRAF-ErT2 expression cassette, were treated with 4OHT  to activate ERK signalling via cRAF-ErT2 for either 2hrs, 8hrs, or 8hrs followed by a subsequent 2hr treatement with the MEK inhibitor PD0325901.


title: Genome-wide occupancy of BDR1 and BDR3 (ChIP-seq)

city: Villenave d'Ornon

first: Pascal

middle: GP

last: Martin

address: 71 avenue Edouard Bourlaux

department: UMR1332 BFP

country: France

institute: INRAE

summary: We generated Arabidopsis lines expressing tagged (3X Myc tag) versions of BDR1 or BDR3 driven by their endogenous promoters on a bdrs triple mutant background  (bdrs: cross of bdr1/AT5G25520 mutant SALK_142108C, bdr2/AT5G11430 mutant CS852350 and bdr3/AT2G25640 mutant SALK_059905). The genome-wide distribution of BDR1 and BDR3 in 8-day old seedlings were analyzed by ChIP-seq using an anti Myc antibody. As control, we performed in parallel a ChIP in wild-type seedlings using the anti-Myc tag antibody. We found that BDR1 is enriched at the border of a large number of genes in Arabidopsis genome while BDR3 is mostly  enriched at the 3'-end of genes.

overall_design: ChIP-seq profiles in 8-day old seedlings of Myc tag-BDR1 and Myc tag-BDR3 (Myc tag-BDR proteins expressed in bdrs triple mutant background). Control is a ChIP perfomed in wild-type plants (not expressing any tagged protein) with the anti-Myc tag antibody.

middle: D

last: Michaels

middle: G

first: Xuhong

last: Yu

first: Jie

last: Huang

first: Jun

last: Liu


title: Genome-wide profiling (ChIP-seq) of RNA polymerase II in wild-type, fpa mutant and bdrs triple mutant

summary: We used 3 different antibodies targeting the YSPTSPS repeats of the C-terminal domain (CTD) of the Rpb1 subunit of RNA polymerase II (ab817: non phosphorylated repeats, ab5095: phospho Ser2 repeats and ab5131: phospho Ser5 repeats) to obtain genome-wide profiles by ChIP-seq of the localization of RNA polymerase II in wild-type (Col-0), fpa mutant (fpa/AT2G43410, line fpa-7) and a triple mutant of all three BDR proteins (bdrs: cross of bdr1/AT5G25520 mutant SALK_142108C, bdr2/AT5G11430 mutant CS852350 and bdr3/AT2G25640 mutant SALK_059905). We found that BDR proteins are involved in RNA polymerase II 3' pausing and that their deletion generates transcriptional interferences in closely spaced, tandemly organized, gene pairs.

overall_design: ChIP-seq profiles in 7 or 8-day old seedlings of RNAPII (ab817, unphosphorylated repeats), S2P (ab5095, Ser2-phosphorylated repeats) or S5P RNAPII (ab5131, Ser5-phosphorylated repeats) in wild-type, fpa single mutant (fpa-7) or bdrs triple mutant were generated by deep sequencing on an Illumina NextSeq500. Biological duplicates or triplicates (independent experiments) were obtained for ChIPs on wild-type and  bdrs triple mutant. Sequencing duplicates (same library, different sequencing runs) were obtained for a ChIP with ab817 for one wild-type and one bdrs sample. Controls include input samples and a ChIP performed with a non-specific IgG.

first: James

last: Ford


title: Genome-wide occupancy of BDR1, BDR2 and FPA (ChIP-seq)

summary: We generated Arabidopsis lines expressing tagged (3X Myc tag) versions of BDR1 or BDR2 driven by their endogenous promoters on a bdrs triple mutant background  (bdrs: cross of bdr1/AT5G25520 mutant SALK_142108C, bdr2/AT5G11430 mutant CS852350 and bdr3/AT2G25640 mutant SALK_059905). The genome-wide distribution of BDR1 and BDR2 in 8-day old seedlings were analyzed by ChIP-seq using an anti Myc antibody. We also analyzed by ChIP-seq the genome-wide distribution of FPA (AT2G43410) in wild-type seedlings using a rabbit anti-FPA polyclonal antibody raised against the C-terminal portion (position 536-901) of the FPA protein. Controls include sequencing of input DNA for each sample and a ChIP perfomed in wild-type seedlings with the anti-Myc tag antibody. We found that BDR1 and BDR2 are enriched at the border of a large number of genes in Arabidopsis genome and that FPA localizes mostly at the 3' end of genes.

overall_design: ChIP-seq profiles in 8-day old seedlings of FPA, Myc tag-BDR1 and Myc tag-BDR2 (Myc tag-BDR proteins expressed in bdrs triple mutant background). Controls include sequencing of input DNA for each sample as well as a ChIP perfomed in wild-type plants (not expressing a tagged protein) with the anti-Myc tag antibody.


title: Dynamic Lineage Priming by ERK is Driven by Transcription Factor-Independent Enhancer Regulation [H3K27ac ChIP-seq]


title: Gene expression profiling in wild-type, fpa mutant and bdrs triple mutant Arabidopsis seedlings

summary: We analyzed by RNA-seq the transcriptome of 8-day old Arabidopsis thaliana seedlings for wild-type (Col-0), single mutant for FPA (fpa/AT2G43410, line fpa-7) or a triple mutant of all three BDR proteins (bdrs: cross of bdr1/AT5G25520 mutant SALK_142108C, bdr2/AT5G11430 mutant CS852350 and bdr3/AT2G25640 mutant SALK_059905). We identified hundreds of genes differentially expressed between wild-type and bdrs triple mutant and a significant overlap in DE genes with the fpa mutant. We also analyzed the binding of BDR1 and BDR2 as well as RNA polymerase II and histone marks by ChIP-seq in wild-type, bdrs and fpa-deficient seedlings. Our data support a role of BDRs as negative elongation factors. They occupy the gene body and regulate the expression of genes involved in defense response pathways. Strikingly, by modulating 3' pausing of RNA polymerase II and possibly contributing to gene looping, they also protect a number of genes from transcriptional interferences originating from a highly expressed upstream tandem gene. Thus BDRs proteins are negative elongation factors that act as transcriptional "gatekeepers" in the Arabidopsis thaliana genome.

overall_design: mRNA profiles in 8-day old seedlings from wild-type (Col-0), fpa single mutant (fpa/AT2G43410) or bdrs triple mutant  (bdrs: cross of bdr1/AT5G25520 mutant SALK_142108C, bdr2/AT5G11430 mutant CS852350 and bdr3/AT2G25640 mutant SALK_059905) were generated by deep sequencing, in triplicates, on Illumina HiSeq2000


title: Gene expression profiling by RNA-seq of wild-type, fpa mutant, bdr1 mutant, bdr2 mutant, bdr3 mutant and bdrs triple mutant Arabidopsis seedlings

summary: We analyzed by RNA-seq the transcriptome of 8-day old Arabidopsis thaliana seedlings for wild-type (Col-0), single mutants for BDR proteins (bdr1/AT5G25520 ; bdr2/AT5G11430 or bdr3/AT2G25640), single mutant for FPA (fpa/AT2G43410, line fpa-7) or a triple mutant of all three BDR proteins (bdrs: cross of bdr1/AT5G25520 mutant SALK_142108C, bdr2/AT5G11430 mutant CS852350 and bdr3/AT2G25640 mutant SALK_059905). We identified hundreds of genes differentially expressed between wild-type and bdrs triple mutant and a significant overlap in DE genes with the fpa mutant. We also analyzed the binding of BDR1 and BDR2 as well as RNA polymerase II and histone marks by ChIP-seq in wild-type, bdrs and fpa-deficient seedlings. Our data support a role of BDRs as negative elongation factors. They bind on the gene body and regulate the expression of genes involved in defense response pathways. Strikingly, by modulating 3' pausing of RNA polymerase II and possibly contributing to gene looping, they also protect a number of genes from transcriptional interferences originating from a highly expressed upstream tandem gene. Thus BDRs proteins are negative elongation factors that act as transcriptional "gatekeepers" in the Arabidopsis thaliana genome.

overall_design: mRNA profiles in 8-day old seedlings from wild-type (Col0), bdr single mutants (bdr1/AT5G25520 ; bdr2/AT5G11430 or bdr3/AT2G25640), fpa single mutant (fpa/AT2G43410) or bdr triple mutant were generated by deep sequencing, in triplicates, on Illumina NextSeq500


title: Proteosome-Erk dependent transcriptional events

summary: Transcriptome analysis of ESCs treated with a proteosome inhibitor (MG132 1μM), with our without ERK activity to measure Erk-dependent changes in transcriptome regulation

overall_design: 3 biological replicates per experiment and control condition


title: RNA-seq, ChIP-seq and MNase-seq in WT, fpa mutant and bdr1,2,3 mutant Arabidopsis seedlings

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

overall_design: Refer to individual Series


title: Erk-dependent transcriptome

summary: Transcriptome analysis of ESCs harboring an 4OHT-inducible cRAF for 0h, 8h, 10h, or 8h followed by a 2h inhibition with a chemical inhibitor

overall_design: 2 biological replicates per experiment and control condition


title: Erk regulated mRNA degradation

summary: Transcriptome analysis of ESCs treated with a transcription inhibitor, with our without ERK activity to measure Erk-dependent changes in mRNA degradation


title: Gene expression profiling (RNA-seq) in wild-type and bdrs triple mutant Arabidopsis seedlings in response to light or to a heat shock

summary: We analyzed by RNA-seq the modulation of the transcriptome in response to light or a heat shock in wild-type and bdrs triple mutant Arabidopsis thaliana seedlings (bdrs: cross of bdr1/AT5G25520 mutant SALK_142108C, bdr2/AT5G11430 mutant CS852350 and bdr3/AT2G25640 mutant SALK_059905). We showed that the overall changes in the transcriptome were very similar in the two genotypes. However, when studying specifically gene pairs organized in tandem and with short intergenic distances, we showed that the rapid and strong regulations of upstream genes was associated with bdrs-dependent changes on the downstream gene expression that are consistent with bdrs-dependent transcriptional interferences.

overall_design: mRNA profiles in seedlings from wild-type (Col0), or bdr triple mutant were generated by deep sequencing, in triplicates, on Illumina NextSeq500. In the photomorphogenesis experiment, seedlings were grown for 5 days in the dark and exposed or not (DARK) to 2h (LIGHT2h) or 4h (LIGHT4h) of white light. In the heat shock experiment, seedlings were grown for 12 days in the cold (12°C) and exposed (HEAT) or not (COLD) to a heat shock of 4h at 27°C.


title: Next Generation RNA Sequencing reveals defects in nuclear mRNA maturation of Arabidopsis thaliana lefko1 mutant

city: Athens

first: Polydefkis

last: Hatzopoulos

address: Iera Odos 75

department: Biotechnology

country: Greece

institute: Agricultural University of Athens

summary:
Introduction: The Plant Organelle RNA Recognition (PORR) domain proteins are nucleus-encoded RNA-binding proteins that have acquired specific roles in organelle RNA metabolism as splicing factors of chloroplast group II introns. LEFKOTHEA (At5g62990) is a nuclear gene encoding a PORR domain protein that carries a transit peptide (TP) and monopartite or bipartite nuclear localization signals (NLS). These motifs result in dual-targeting of LEFKOTHEA to the nucleus and chloroplasts implying a role in the splicing of chloroplast group II introns and nuclear pre-mRNA introns. Therefore, we examined the splicing efficiency of plastid and nuclear genes in lefko1 mutant
Methods: The lefko1 mutant was isolated from a genetic screen of an M2 EMS-mutagenized Arabidopsis thaliana Columbia (Col-0) background seed population. The lefko1 mutant allele has a white cotyledon phenotype caused by a G to A mutation in the coding region resulting in a Glycine (G) 373 to Aspartic acid (D) conversion. Total RNA was extracted using plant RNA kit spin columns with an on-column DNase treatment from lefko1 mutant and wild-type Arabidopsis cotyledons. The quantity and integrity of the RNA was assessed using a NanoDrop 1000 spectrophotometer and agarose gel electrophoresis. RNA-seq libraries were generated using the TruSeq Low Input kit according to the manufacturer’s instructions (Illumina). Sequencing was performed on an Illumina HiSeq 2000 instrument at BGI (Beijing Genomics Institute).Raw reads were filtered into clean reads and aligned to the Arabidopsis genome (TAIR10).  RNA-seq data were analyzed using the SOAPnuke (version v.1.5.2) with parameters “-l 15 -q 0.2 -n 0.05” and the HISAT2 pipeline (version 2.0.4) with parameters “--phred64 --sensitive --no-discordant --no-mixed -I 1 -X 1000”. Differential alternative splicing events were detected for lefko1 and wild-type using rMATS and visualized using the Integrative Genomics Viewer (IGV) tool.
Results: Splicing defects were observed in numerous nuclear genes of lefko1 cotyledons compared to wild type. Among them, intron retention (IR) events were the most prominent. Further, the fidelity of 5’ splice site (5’SS) donor and 3’SS acceptor splicing was disturbed in lefko1 cotyledons. To less extend, exon skipping (ES) defects were also detected. Conclusions: Detailed nuclear splicing events were widely observed in lefko1 cotyledons demonstrating a prevalent role of LEFKOTHEA in the splicing of nuclear pre-mRNA introns. Overall design: RNA-seq libraries were generated using the TruSeq Low Input kit according to the manufacturer’s instructions (Illumina). Sequencing was performed on an Illumina HiSeq 2500 instrument at BGI (Beijing Genomics Institute).
Conclusions: Detailed nuclear splicing events were widely observed in lefko1 cotyledons demonstrating a prevalent role of LEFKOTHEA in the splicing of nuclear pre-mRNA introns.

first: Gerasimos

last: Daras


title: The immune defense of shrimp gills through Marsupenaeus japonicus gill C-type lectin (MjGCTL)

city: Minato-ku

first: ROD RUSSEL

middle: REYES

last: ALENTON

state: Tokyo

address: 4-5-7 Konan, Tokyo University of Marine Science and Technology

country: Japan

institute: TOKYO UNIVERSITY OF MARINE SCIENCE AND TECHNOLOGY

summary: To present, the only known inv*olvement of the gills in the immune response of shrimp is solely assisting the hemocytes in filtering out the harmful factors. This global expression of novel genes revealed several immune-related genes specifically expressed in high amounts only in gills. This data provide new insights on the immune defense of shrimp.

overall_design: Expression analysis were done in all apparently healthy shrimp focusing on hemocyte, gills, hepatopancreas, lymphoid organ, muscle

first: RodRussel

middle: R

last: Alenton

first: Keiichiro

last: Koiwai

first: Rika

last: Nakamura

first: Jumroensri

last: Thawonsuwan

first: Hidehiro

last: Kondo

first: Ikuo

last: Hirono


title: Population genome variations revealed by diversifying selection in chickens

city: chengdu

first: Mingzhou

last: Li

state: Sichuan

address: No.211 Huimin Road, Wenjiang District

institute: Sichuan Agricultural University

summary: We describe a total 269.15 Gb of chicken RNA-seq sequences generated from the 48 libraries

overall_design: Examination of 4 tissues of 4 chicken types raised under different altitudes

first: Diyan

first: Tiandong

last: Che


title: Transcriptomic changes induced by Gsk-3-deletion in cerebellar progenitors

status: Public on Aug 07 2019

city: Chapel Hill

first: Jennifer

middle: Karín

last: Ocasio

state: NC

address: 115 Mason Farm Rd NRB 6131

department: Neurology

institute: University of North Carolina at Chapel Hill

summary:
Cerebellar development requires regulated proliferation of cerebellar granule neuron progenitors (CGNPs). Inadequate CGNP proliferation causes cerebellar hypoplasia while excessive CGNP proliferation can cause medulloblastoma, the most common malignant pediatric brain tumor. Although Sonic Hedgehog (SHH) signaling is known to activate CGNP proliferation, the mechanisms down-regulating proliferation are less defined. We investigated CGNP regulation by GSK-3, which down-regulates proliferation in the forebrain, gut and breast by suppressing mitogenic WNT signaling. In striking contrast, we found that co-deleting Gsk-3α and Gsk-3β blocked CGNP proliferation, causing severe cerebellar hypoplasia. Transcriptomic analysis showed activated WNT signaling and up-regulated Cdkn1a in Gsk-3-deleted CGNPs.  These data show that a GSK-3/WNT axis modulates the developmental proliferation of CGNPs and the pathologic growth of SHH-driven medulloblastoma. The requirement for GSK-3 in SHH-driven proliferation suggests that GSK-3 may be targeted for SHH-driven medulloblastoma therapy.
In this experiment, we dissociated cells from whole cerebella collected from postnatal day 1 (P1) mice with the indicated genotypes.

overall_design: Whole cerebella were collected from P1 mice with both isoforms of Gsk-3 deleted, Gsk-3b deleted, or Gsk-3 intact. Cells were dissociated and CGNPs were enriched through a density gradient before isolating RNA. 5 replicates of each indicated genotype were included in the study. Gsk-3-deleted samples (Gsk-3 DKO) were compared to either Cre-containing Math1-Cre/GSKa+/- controls or controls with no Cre and Gsk-3 intact.

middle: K

first: Timothy

last: Gershon


title: Mapping Bcl11b binding in human regulatory T cells

city: Tampa

first: Dorina

last: Avram

state: Fl

address: 12902 Magnolia Drive, MRC4

department: Department of Immunology

institute: Moffitt Cancer Center

summary: T regulatory (Treg) cells have been studied in depth since their discovery for their potential use in therapies of autoimmune diseases. Treg cells have a suppression program that includes surface molecules CD25 (IL2R), cytotoxic T-lymphocyte associated protein 4 (CTLA4), and glucocorticoid-induced TNFR family (GITR) to limit aberrant and excessive inflammatory immune responses. We have shown that Bcl11b can bind to the CNS2 region in Foxp3 as well as the gene loci of those essential surface molecules for Treg suppression. Furthermore, we have identified a subset of Foxp3-independent genes in Treg cells directly regulated by Bcl11b binding. Bcl11b also directly represses expression of innate molecules such as transcription factors PU.1 and ID2 in Treg cells. Finally, we have also shown that removal of Bcl11b accelerates apoptosis in Treg cells as cleaved caspase 3 levels were significantly elevated in Bcl11b KO Treg cells when compared with WT Treg cells.

overall_design: Examination of Bcl11b binding in regulatory T cells from human peripheral blood

first: Theodore

last: Drashansky

first: Eric

last: Helm

first: Zhiguang

last: Huo


title: Mapping Bcl11b binding in regulatory T cells

overall_design: Examination of Bcl11b binding in regulatory T cells from steady state mice


title: Transcriptome analysis of Bcl11b-deficient regulatory T cells at steady state

overall_design: Examination of changes to transcriptome resulting from removal of Bcl11b in regulatory T cells


title: BRCA2 ChIP-seq hTert-HME1 cell line

city: Palo Alto

first: Michael

last: Snyder

address: 3165 Porter Dr

department: Genetics

institute: Stanford University

summary: Individuals with a single functional copy of the BRCA2 tumor suppressor have elevated risks for breast, ovarian, and other solid tumor malignancies. The exact mechanisms of carcinogenesis due to BRCA2 haploinsufficiency remain unclear, but one possibility is that at-risk cells are subject to acute periods of decreased BRCA2 availability and function ("BRCA2-crisis"), which may contribute to disease. Here, we establish an in vitro model for BRCA2-crisis that demonstrates chromatin remodeling and activation of an NF-κB survival pathway in response to transient BRCA2 depletion. Mechanistically, we identify BRCA2 chromatin binding, histone acetylation, and associated transcriptional activity as critical determinants of the epigenetic response to BRCA2-crisis. These chromatin alterations are reflected in transcriptional profiles of pre-malignant tissues from BRCA2 carriers and, therefore, may reflect natural steps in human disease. By modeling BRCA2-crisis in vitro, we have derived insights into pre-neoplastic molecular alterations that may enhance the development of preventative therapies.

overall_design:
Antibodies to BRCA2 (Bethyl A300-005A) were used to immunoprecipitate BRCA2 from formaldehyde-crosslinked human hTert-HME1 cell line.
2 replicates of BRCA2 ChIP were compared to 2 replicates of input chromatin compared by Diffbind

first: Joshua

last: Gruber


title: Genome wide mapping of chromatin accessibility in Treg cells at steady state

overall_design: Examination of changes to chromatin accessibility in Treg cells caused by the removal of Bcl11b


title: ChIP-seq analysis of H4K12Ac antibody binding in hTert-HME1 cells treated with either control or BRCA2 siRNAs

summary: Individuals with a single functional copy of the BRCA2 tumor suppressor have elevated risks for breast, ovarian and other solid tumor malignancies.  The exact mechanisms of carcinogenesis due to BRCA2 haploinsufficiency remain unclear, but one possibility is that at-risk cells are subject to acute periods of decreased BRCA2 availability and function (“BRCA2-crisis”), which may contribute to disease.  Here we establish an in vitro model for BRCA2-crisis that demonstrates novel epigenetic remodeling and activation of an NF-κB survival pathway in response to transient BRCA2-depletion.  Mechanistically, we identify BRCA2 chromatin binding, histone acetylation and associated transcriptional activity as critical determinants of the epigenetic response to BRCA2-crisis.  These epigenetic alterations are reflected in transcriptional profiles of pre-malignant tissues from BRCA2-carriers and therefore may reflect natural steps in human disease.  By modeling BRCA2-crisis in vitro we have derived insights into pre-neoplastic molecular alterations that may enhance the development of preventative therapies.

overall_design: 2 replicates of siControl, 2 replicates of siBRCA2, 1 siControl input, 1 siBRCA2 input.  hTert-HME1 cell line was transfected with siRNA, passaged for 12 days to undergo BRCA2 crisis and recovery then cells were cross linked with 1% formaldehyde and processed for ChIP-seq.  Diffbind was used to identify differentially increased peaks in siBRCA2 condition versus siControl condition.


title: Gene expression profiling by RNA-seq in hTert-HME1 cell line treated with control or BRCA2 siRNAs and grown with or without EGF (epithelial growth factor) II

overall_design:
hTert-HME1 cells were treated with control or BRCA2 siRNAs and then allowed to recover, then grown in mammary epithelial growth media supplemented with or without EGF (epithelial growth factor).
Control siRNA transfection grown in media +EGF (3 replicates), control siRNA transfection grown in media -EGF (2 replicates), BRCA2 siRNA transfection grown in media +EGF (3 replicates), BRCA2 siRNA transfection grown in media -EGF (3 replicates)

middle: J


title: Genome wide mapping in regulatory T cells at steady state


title: Neocortical layer 4 in adult mouse differs in major cell types and circuit organization between primary sensory areas

status: Public on Aug 06 2019

city: Solna

first: Leonard

last: Hartmanis

address: Solnavägen 9

department: Cell & Molecular Biology

country: Sweden

institute: Karolinska Institutet

summary: Layer 4 (L4) of mammalian neocortex plays a crucial role in cortical information processing, yet a complete census of its cell types and connectivity remains elusive. Using whole-cell recordings with morphological recovery, we identified one major excitatory and seven inhibitory types of neurons in L4 of adult mouse visual cortex (V1). Nearly all excitatory neurons were pyramidal and all somatostatin-positive (SOM+) non-fast-spiking interneurons were Martinotti cells. In contrast, in somatosensory cortex (S1), excitatory neurons were mostly stellate and SOM+ interneurons were non-Martinotti. These morphologically distinct SOM+ interneurons corresponded to different transcriptomic cell types and were differentially integrated into the local circuit with only S1 neurons receiving local excitatory input. We propose that cell type specific circuit motifs, such as the Martinotti/pyramidal and non-Martinotti/stellate pairs, are used across the cortex as building blocks to assemble cortical circuits.

overall_design: Electrophysiological measurements were performed on neurons from the L4 region in mouse neocortex and the mRNA from the cells was isolated and made into sequenceable libraries using the Patch-seq/Smart-Seq2 library preparation method

first: Rickard

last: Sandberg


title: Hierarchy of mono- and bi-allelic TP53 alterations in Multiple Myeloma cell fitness

city: Würzburg

first: Tom

last: Gräfenhan

address: Josef-Schneider-Str. 2, Bau D15

department: Core Unit SysMed

institute: University of Wuerzburg

summary: Comparison of the TP53 wild-type myeloma cell line AMO1 with the CRISPR/Cas9 engineered AMO1 cell line named UMC901. UMC901 harbors bi-allelic alterations to TP53:  TP53 del/mut. Analysis of impact of TP53 alterations on gene transcription and identification of affected pathways by transcriptome-wide differential gene expression analysis.

overall_design: Triplicates for each cell line, comparison of UMC901 against AMO1 as reference. Circa 50 million single-end 75 nt reads per sample

first: Umair

last: Munawar

first: Cornelia

last: Vogt

first: Tobias

last: Heckel

first: Panagiota

last: Arampatzi

first: Sascha

last: Dietrich

first: Martin

last: Kortüm


title: LSD1 regulates splenic B cell chromatin accessibility

city: Atlanta

first: Jeremy

middle: Matthew

last: Boss

state: Georgia

address: 1510 Clifton Rd NE, Room 3120

department: Microbiology and Immunology

institute: Emory University

summary: To understand the role of LSD1 in splenic B cell development, spleens from mice with B cell conditional deletion of LSD1 were harvested, B220+CD93–GL7–CD23–CD21hiCD1d+ marginal zone B cells and B220+CD93–GL7–CD23+CD21midCD1d– follicular B cells were FACS-sorted, and ATAC-seq was performed to identify LSD1-target regulated chromatin.

overall_design: ATAC-seq on control or LSD1-deficient murine splenic marginal zone B cells and follicular B cells

first: R

last: Haines

first: C

last: Scharer

first: J


title: LSD1 regulates the plasmablast transcriptome

summary: To understand the role of LSD1 in marginal zone B cell development, CD93+ transitional B cells were enriched from the spleens of mice with B cell conditional deletion of LSD1, the cells were cultured for 3 days in the presence of OP9-DL1 cells and BAFF, and day 0 B220+CD93+ transitional B cells and day 3 B220+CD21+CD1d+ ex vivo-derived marginal zone B cells were FACS-sorted and RNA-seq was performed to identify LSD1-target regulated genes.

overall_design: RNA-seq on control or LSD1-deficient murine splenic transitional B cells and ex vivo-derived marginal zone B cells


title: LSD1 cooperates with non-canonical NF-êB signaling to regulate marginal zone B cell development

overall_design: Refer to individual Series


title: Epigenetic analysis of DU-4475 human breast cell line

city: Badalona

first: Manel

last: Esteller

state: Barcelona

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

department: Cancer and Leukemia Epigenetics and Biology Program (PEBCL)

country: Spain

institute: Josep Carreras Leukaemia Research Institute (IJC)

summary: Illumina Infinium MethylationEPIC Beadchip of DU-4475 human breast cancer cell line

overall_design: Bisulphite converted DNA from DU-4475 breast cell line was hybridised to the Illumina Infinium MethylationEPIC Beadchip.

first: David

last: Piñeyro


title: Zika Virus Noncoding sfRNA Sequesters Multiple RNA Binding Proteins and Impacts mRNA Decay and Splicing

city: Fort Collins

first: Jeffrey

last: Wilusz

address: 1682 Campus Delivery

institute: Colorado State University

summary: Previous reports studying similar flavivirus infections (DENV, WNV, etc.) revealed an increase in both the abundance and stability of normally short-lived cellular mRNAs. This resulted from the stalling/repression of the major 5’-3’ host exoribonuclease XRN-1 on three-helix junction structures present in the 3’-UTR of insect-borne flaviviruses.   Therefore we sought to identify the endogenous mRNA abundance and stability changes induced during early and late times following Zika virus infection (PRBRAC59) in human choriocarcinoma (JAR) cells.

overall_design: To investigate the impact of Zika virus infection on relative transcript abundances in human choriocarcinoma (JAR) cells, we analyzed total RNA of sample cells infected with Zika virus for 12 hours or 72 hours and compared their transcriptional profiles. Three replicates of 12 hour ZIKV-infected cellular RNA and three replicates of 72 hour ZIKV-infected cells were evaluated for a total of six samples.

first: Daniel

last: Michalski

last: Ontiveros

first: Joseph

last: Russo

first: Phillida

middle: A

last: Charley

first: John

last: Anderson

first: Adam

last: Heck

first: Brian

last: Geiss


title: Epigenetic analysis of four human breast cell lines

summary: Illumina Human Methylation 450k Beadchip of 4 human breast cancer cell lines

overall_design: Bisulphite converted DNA from MDA-MB-231, MCF7, MDA-MB-436 and MDA-MB-453 breast cell lines were hybridised to the Illumina Infinium 450k Human Methylation Beadchip.


title: LSD1 regulates the marginal zone B cell transcriptome

summary: To understand the role of LSD1 in splenic B cell development, spleens from mice with B cell conditional deletion of LSD1 were harvested, B220+CD93–GL7–CD23–CD21hiCD1d+ marginal zone B cells and B220+CD93–GL7–CD23+CD21midCD1d– follicular B cells were FACS-sorted, and RNA-seq was performed to identify LSD1-target regulated genes.

overall_design: RNA-seq on control or LSD1-deficient murine splenic marginal zone B cells and follicular B cells


title: Epigenetic analysis of twelve human normal breast tissue samples

summary: Illumina Human Methylation 450k Beadchip of 12 human normal breast tissue samples

overall_design: Bisulphite converted DNA from 12 normal breast tissue samples were hybridised to the Illumina Infinium 450k Human Methylation Beadchip


title: Expression data of mesenchymal stromal cells derived from human bone marrow (BM-MSC) or autologous adipose tissues (ASC)

city: RENNES

first: vonick

last: sibut

address: avenue du Prof Leon BERNARD

summary: GEP on Affymetrix HuGene-1.0-ST arrays was performed on 14 BM-MSCs and 14 autologus paired ASCs in order to explore the biological significance of tissue source (bone marrow vs adipose tissue) in MSC production.

overall_design: GEP was performed on MSC fractions of 14 BM and 14 autologous paired  ASCs at the end of culture (passage 1) (see above growth protocol)

first: Vonick

last: Sibut

first: Philippe

last: Bourin

first: Cédric

last: Ménard

first: Karin

last: Tarte


title: Transcriptome profiling of CD8+ T cells exposed to vehicle or IL-1b treatment in vivo

city: Bethesda

first: Devikala

last: Gurusamy

state: Maryland

address: Building 10, 3W-5816

department: Surgery Branch

institute: NCI - NIH

summary: RNA sequencing analysis is capable of quantitatively analyzing transcriptome of a cell population at a genome-wide level.  To determine the impact of systemic IL-1b administration on T cell differentiation in vivo, we adoptively transferred OT-I CD8+ T cells to a host, followed by OVA/LPS immunization and 3 daily injections of PBS or IL-1b. On day 4, OT-I cells from draining lymph nodes were sorted and the RNA was extracted for sequencing.

overall_design: Compare the transcriptome profile of OT-I cells isolated from vehicle- or IL-1b-treated mice.

first: Ping-Hsien

last: Lee

first: Nicholas

last: Restifo


title: RNA-sequencing of human retinal pigment epithelum

city: Kyoto

first: Akira

last: Watanabe

state: Kyoto

address: Rm504, Miyako Bldg, 233, Isa-cho, kamigyo-ku

institute: CyberomiX Inc

summary: We assessed the feasibility of transplanting a sheet of retinal pigment epithelial (RPE) cells differentiated from induced pluripotent stem cells (iPSCs) in a patient with neovascular age-related macular degeneration. The iPSCs were generated from skin fibroblasts obtained from two patients with advanced neovascular age-related macular degeneration and were differentiated into RPE cells. The RPE cells and the iPSCs from which they were derived were subject to extensive testing. A surgery that included the removal of the neovascular membrane and transplantation of the autologous iPSC-derived RPE cell sheet under the retina was performed in one of the patients. At 1 year after surgery, the transplanted sheet remained intact, best corrected visual acuity had not improved or worsened, and cystoid macular edema was present.

overall_design: We conducted a series of genome and epigenome analysis, including RNA-sequencing, for assessment of the RPE. In addition, we compared gene expression profile of iPSC-derived RPE with that of cultured RPE and RPE tissues.

first: Michiko

last: Mandai

first: Chihiro

last: Okada

first: Shinya

last: Yamanaka

first: Masayo

last: Takahashi


title: Metabolic reprogramming of macrophage polarization by creatine [RNA-seq]

city: Beijing

first: Liangliang

last: Ji

address: Tsinghua University

department: School of Medicine

institute: Institute for Immunology

summary: We found that the creatine metabolic pathway was differentially regulated under M1 versus M2 polarizing conditions. In return, creatine could suppress M1 by blocking STAT1 tyrosine phosphorylation while promote M2 by sustaining chromatin accessibility of specific gene loci.

overall_design: Analyze the changes of transcriptomes in macrophages lack of creatine during macrophage polarization

first: Xinbin

last: Zhao


title: Metabolic reprogramming of macrophage polarization by creatine [ATAC-seq]

overall_design: Analyze the changes of chromatin accessibility in macrophages lack of creatine during macrophage polarization

first: Bin

last: Zhang


title: Transcriptional Blood Signatures for Active and Amphotericin B Treated Visceral Leishmaniasis in India [exp2]

status: Public on Aug 05 2019

city: Milan

first: Michaela

last: Fakiola

address: Via Francesco Sforza 35

country: Italy

institute: INGM

summary: In this study we set out to determine whole blood transcriptional profiles that might distinguish asymptomatic infection with Leishmania donovani from active disease, as well as to monitor the changes in transcriptional profiles that accompanied drug treatment. Amphotericin B provides improved therapy for visceral leishmaniasis (VL) caused by Leishmania donovani, with single dose liposomal-encapsulated Ambisome providing the best cure rates.  The VL elimination program aims to reduce the incidence rate in the Indian subcontinent to <1/10,000 population/year.  Ability to predict which asymptomatic individuals (e.g. anti-leishmanial IgG and/or Leishmania-specific modified Quantiferon positive) will progress to clinical VL would help in monitoring disease outbreaks.  Here we examined whole blood transcriptional profiles associated with asymptomatic infection, active disease, and in treated cases.  Two independent microarray experiments were performed, with analysis focussed primarily on differentially expressed genes (DEGs) concordant across both experiments.  No DEGs were identified for IgG or Quantiferon positive asymptomatic groups compared to negative healthy endemic controls.  We therefore concentrated on comparing concordant DEGs from active cases with all healthy controls, and in examining differences in the transcriptome following different regimens of drug treatment.  In these comparisons 6 major themes emerged: (i) expression of genes and enrichment of gene sets associated with erythrocyte function in active cases; (ii) strong evidence for enrichment of gene sets involved in cell cycle in comparing active cases with healthy controls; (iii) identification of IFNG encoding interferon- as the major hub gene in concordant gene expression patterns across experiments comparing active cases with healthy controls or with treated cases; (iv) enrichment for interleukin signalling (IL-1/3/4/6/7/8) and a prominent role for CXCL10/9/11 and chemokine signalling pathways in comparing active cases with treated cases; (v) the novel identification of Aryl Hydrocarbon Receptor signalling as a significant canonical pathway when comparing active cases with healthy controls, and to a lesser extent with treated cases; and (vi) global expression profiling support for more effective cure at day 30 post-treatment with a single dose of liposomal encapsulated amphotericin B compared to multi-dose non-liposomal amphotericin B treatment over 30 days.

overall_design: Two independent microarray experiments were performed. Blood samples were collected pre- (N=10 experiment 1; N=11 experiment 2) and post- (day 30; N=10 experiment 1; N=12 experiment 2) treatment. There were 9 paired pre-/post-treatment samples for experiment 1; 10 for experiment 2. VL patients were treated with either (a) experiment 1: 0.75 mg/kg non-liposomal Amphotericin B on alternate days by infusion for 15 doses (total dose 11.25 mg/kg over 30 days); or (b) experiment 2: 10 mg/kg of Ambisome (liposome-encapsulated Amphotericin B) as a single dose by infusion. Healthy control subjects included (i) asymptomatic individuals (N=2 experiment 1; N=6 experiment 2) who had high anti-leishmanial antibody levels by direct agglutination test (DAT titer >1:25,600); (ii) asymptomatic individuals who were positive by Leishmania-specific modified quantiferon assays (N=8 experiment 1; N=9 experiment 2); and (iii) Serology (DAT titer ≤1:1600) and quantiferon negative healthy endemic controls (N=6 experiment 1; N=10 experiment 2). Samples from different control or clinical groups were distributed evenly across 3 (experiment 1) or 4 (experiment 2) Illumina HT12v4 expression beadchips. Background correction, quantile normalisation and log2 transformation of the data was carried out using the Bioconductor package Limma [21]. Removal of non-expressed (detection P-value > 0.05 in all arrays) and poor quality probes previously shown to have unreliable annotation provided 21,959 and 23,466 probe sets which passed QC in experiments 1 and 2, respectively.

first: Om-Prakash

last: Singh

first: Genevieve

last: Syn

first: Toolika

first: Bhawana

first: Jaya

last: Chakravarty

first: Shyam

last: Sundar

first: Jenefer

last: Blackwell


title: Transcriptional Blood Signatures for Active and Amphotericin B Treated Visceral Leishmaniasis in India

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


title: Characterization of an E2f1 acetylation-deficient knock-in mouse model by RNA-Seq profiling

city: Smithville

last: Liu

state: TX

address: 1808 Park Road 1C

department: Epigenetics and Molecular Carcinogenesis

institute: University of Texas MD Anderson Cancer Center

summary: Objective: The E2F1 transcription factor regulates the expression of genes involved in cell proliferation, apoptosis and other cellular processes. In addition to regulating transcription, a number of studies have revealed novel, transcription-independent functions for E2F1 in regulating DNA repair. E2F1 localizes to sites of DNA damage dependent on its phosphorylation at serine 31 (serine 29 in mice) by the ATM or ATR kinases. In addition to phosphorylation, E2F1 is also acetylated in response to DNA damage on three lysine residues (K117, K120, and K125 in human E2F1), however how acetylation regulates the DNA repair function of E2F1 is unknown. To study the functional significance of E2F1 acetylation in DNA repair in vivo, we generated a targeted mutant mouse line in which the three sites of E2F1 acetylation were mutated from lysine to arginine and named this allele E2f1 3KR.  RNA-seq analysis was performed on wild type and E2f1 3KR mouse embryonic fibroblasts (MEFs), before and after treatment with the radiomimetic drug neocarzinostatin (NCS), to examine the impact of the 3KR mutation on global gene expression patterns.

overall_design: mRNA-Seq profiles of primary wild type (WT) and E2F1 acetylation mutant (3KR) knock-in MEFs before (C) and after treatment (T) with radiomimetic drug neocarzinostatin (NCS)

first: Swarnalatha

last: Manickavinayaham

first: Jianjun

last: Shen

first: David

last: Johnson


title: Engineering orthogonal signaling pathways reveals the sparse distribtion of protein protein interactions in sequence space

city: Cambridge

first: Conor

middle: James

last: McClune

state: MA

address: 31 Ames St

department: Biology

institute: Massachusetts Institute of Technology

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


title: Metabolic reprogramming of macrophage polarization by creatine


title: Transcriptional Blood Signatures for Active and Amphotericin B Treated Visceral Leishmaniasis in India [exp1]


title: Transcriptome analysis in the medial prefrontal cortex of mice exposed to multi-hit early adversity

status: Public on Aug 04 2019

city: Bordeaux

first: Muriel

last: DARNAUDERY

address: rue leo saignat

department: INRA

institute: bordeaux university

summary: We have employed whole genome microarray expression profiling to identify long-term gene expression changes associated with early adversity in male and female C3H/HeN mice

overall_design: Multi-hit early adversity consisted in lipopolysaccharide injection at embryonic day 17 combined with maternal separation from post natal day 2 to 14. At adulthood (5.5 months) mice were euthanized and  brains were collected for micropunch sampling within the medial prefrontal cortex

first: Marion

last: Rincel

last: Darnaudéry

first: Claire

last: Naylies

first: Yannick

last: Lippi


title: Single-cell RNA-seq in monozygotic twins discordant for multiple sclerosis

status: Public on Aug 02 2019

city: Planegg-Martinsried

first: Eduardo

last: Beltrán

state: Bayern

address: Großhaderner Str. 9

department: Institute of Clinical Neuroimmunology

institute: University Hospital, LMU Munich

summary: Here we investigated the earliest possible evidence of subclinical neuro-inflammation (SCNI) using a small cohort of monozygotic twins where one sibling had clinically definite MS and the other been clinically "healthy" but has a maximal genetic for developing MS. In contrast to subjects with radiologically isolated syndrome (RIS), our group of very early SCNI does not even fulfill the (arbitrary) MRI criteria for RIS but have more subtle MRI changes and/or evidence of neuro-inflammation in the CSF, e.g. oligoclonal bands (OCBs). For analyzing CSF samples from Twin pairs and controls in greater detail we applied single-cell whole transcriptome sequencing (scRNAseq). Our findings demonstrate that even the earliest experimentally approachable stage of MS is characterized by synergistic activation of CD8+ T cells, CD4+ T cells and B cells.

overall_design: scRNA-seq. Library preparation: Smart-seq2; alignement: to UCSC hg38 using HISAT2; gene counts: featureCounts (Liao et al.); single-cell analysis: Seurat // PRJNA513835 - SRP180896


title: Tamoxifen induction of Cre recombinase does not cause long lasting or sexually divergent responses in the CNS epigenome or transcriptome: implications for the design of aging studies.

status: Public on Aug 01 2019

city: Oklahoma City

first: Michael

last: Stout

state: OK

address: 825 N.E. 13th Street

department: Aging and Metabolism

institute: Oklahoma Medical Research Foundation

type: Methylation profiling by high throughput sequencing

summary: The systemic delivery of tamoxifen (Tam) to activate inducible CreERT2-loxP transgenic mouse systems is now widely used in neuroscience studies. This critical technological advancement allows temporal control of DNA-cre recombination, avoidance of embryonically lethal phenotypes, and minimization of residual cell labeling encountered in constitutively active drivers. Despite its advantages, the use of Tam has the potential to cause long-lasting, uncharacterized side effects on the transcriptome and epigenome in the CNS, given its mixed estrogen receptor (ER) agonist/antagonist actions. With the welcome focus on including both sexes in biomedical studies and efforts to understand sex differences, Tam administration could also cause sexually divergent responses that would confound studies. To examine these issues, epigenetic and transcriptomic profiles were compared in C57BL/6J female and male hippocampus, cortex, and retina 1 month after a five- day Tam treatment typical for cre induction, or vehicle control (sunflower seed oil). Cytosine methylation and hydroxymethylation levels, in both CG and non-CG contexts, were unchanged as determined by oxidative bisulfite sequencing. Long-lasting Tam transcriptomic effects were also not evident/minimal. Furthermore, there is no evidence of sexually divergent responses with Tam administration and Tam did not alter sex differences evident in controls. Combined with recently reported data that Tam alone does not cause long-lasting changes in behavior and neurogenesis, our findings provide confidence that Tam can be used as a cre-recombinase inducer without introducing significant confounds in transcriptomic and epigenomic neuroscience studies, particularly those focused on genomic and transcriptomic aspects of the aging brain.

overall_design: Examination of the effect of tamoxifen administration on DNA methylation and hydroxymethylation in the retina, cortex, and hippocampus of mouse by Whole Genome Oxidative Bisulfite-Seq.

first: Ana

last: Chucair-Elliott

first: Sarah

last: Ocanas

last: Stanford

first: Niran

last: Hadad

first: Benjamin

last: Wronowski

first: Laura

last: Otalora

first: Willard

last: Freeman


title: Convergent evolution of a vertebrate-like methylome in a marine sponge

city: London

first: Alex

last: de Mendoza

address: Mile End Road. Fogg Building 5.14

department: School of Biological and Behavioural Sciences

country: United Kingdom

institute: Queen Mary University of London

summary: Vertebrates have highly methylated genomes at CpG positions while most invertebrates have sparsely methylated genomes. Therefore, hypermethylation is considered a major innovation that shaped the genome and the regulatory roles of DNA methylation in vertebrates. However, here we report that the marine sponge Amphimedon queenslandica, belonging to one of the earliest branching animal lineages, has evolved a hypermethylated genome with remarkable similarities to that of a vertebrate. Despite major differences in genome size and architecture, independent acquisition of hypermethylation reveal common distribution patterns and repercussions for genome regulation between both lineages. Genome wide depletion of CpGs is counterbalanced by CpG enrichment at unmethylated promoters, mirroring CpG islands. Furthermore, a subset of CpG-bearing transcription factor motifs are enriched at Amphimedon unmethylated promoters. We find that the animal-specific transcription factor NRF has conserved methyl-sensitivity over 700 million years, indicating an ancient cross-talk between transcription factors and DNA methylation. Finally, the sponge shows vertebrate-like levels of 5-hydroxymethylcytosine, the oxidative derivative of cytosine methylation involved in active demethylation. Hydroxymethylation is concentrated in regions that are enriched for transcription factor motifs and show developmentally dynamic demethylation. Together, these findings push back the links between DNA methylation and its regulatory roles to the early steps of animal evolution. Thus, the Amphimedon methylome challenges the prior hypotheses about the origins of vertebrate genome hypermethylation and its implications for regulatory complexity.

sample_organism:
Mnemiopsis leidyi
Sycon ciliatum
Nematostella vectensis
Amphimedon queenslandica

overall_design: Profiling of cytosine methylation for Amphimedon queenslandica, Sycon ciliatum, Mnemiopsis leidyi and Nematostella vectensis. Profiling hydroxymethylation with TAB-seq for Amphimedon queenslandica and Nematostella vectensis. DAP-seq and ampDAP-seq for Amphimedon transcription factors on Amphimedon queenslandica genomic DNA.

first: Ryan

last: Lister


title: Differential impact of co-expressed SP-A1/SP-A2 protein on AM miRNome; sex differences

city: hershey

first: Nithyananda

last: Thorenoor

address: 500 University Drive

department: Pediatrics

institute: Penn State University College of Medicine

summary: In humans there are two surfactant protein A (SP-A) functional genes SFTPA1 and SFTPA2 encoding innate immune molecules, SP-A1 and SP-A2, respectively, with numerous genetic variants each.  SP-A interacts and regulates many of the functions of alveolar macrophages (AM).  It is shown that SP-A variants differ in their ability to regulate the AM miRNome in response to oxidative stress (OxS).  Because humans have both SP-A gene products, we were interested to determine the combined effect of co-expressed SP-A1/SP-A2 (co-ex) in response to ozone (O3) induced OxS on AM miRNome.  Human transgenic (hTG) mice, carrying both SP-A1/SP-A2 (6A2/1A0, co-ex) and SP-A- KO were utilized.  The hTG and KO mice were exposed to filtered air (FA) or O3 and miRNA levels were measured after AM isolation with or without normalization to KO.  We found: (i)  The AM miRNome of co-ex males and females in response to OxS to be largely downregulated after normalization to KO,  but after Bonferroni multiple comparison analysis only in females the AM miRNome remained significantly different compared to control (FA); (ii) The targets of the significantly changed miRNAs were downregulated in females and upregulated in males; (iii) Several of the validated mRNA targets  were involved in pro-inflammatory response, anti-apoptosis, cell cycle, cellular growth and proliferation; (iv) The AM of SP-A2 male, shown, previously to have major effect on the male AM miRNome in response to OxS, shared similarities with the co-ex, namely in pathways involved in the pro-inflammatory response and anti-apoptosis but also exhibited differences with the cell-cycle, growth, and proliferation pathway being involved in co-ex and ROS homeostasis in SP-A2 male.  We speculate that the presence of both gene products versus single gene products differentially impact the AM responses in males and females in response to OxS.

overall_design: Humanized transgenic (hTG) mice carrying both gene variants, SP-A1/SP-A2 (6A2/1A0, co-ex), as well as SP-A knockout (KO) mice were used in this study.  They were 12 weeks old.  hTG mice were generated on the C57BL/6J SP-A (KO) background. The animals were exposed to FA or O3 in parallel as described previously.  A group of 4 animals (males, females) were exposed to FA or O3 for 3 h, and alveolar macrophages (AM) were isolated after 4 h of recovery. Total RNA was extracted, Small RNA-seq libraries were generated followed by deep sequencing  to identiy desired microRNA population. The differentially expressed miRNAs (DEG) between FA to O3, males and females were identified by using the edgeR and the TCC v1.14.0 R package  with false discovery rate (FDR) adjusted p value of 0.1 as a significance cutoff.

first: Joanna

last: Floros


title: Analysis of the Clustered Protocadherin (cPcdh) Locus in Human Pluripotent Stem and Derived Cells (ChIP-seq I out of II)

city: La Jolla

first: Daria

last: Merkurjev

state: CA

address: 9500 Gilman Drive, Mail Code 0648

department: Medicine

institute: UCSD

summary: In the mammalian genome, the clustered protocadherin (cPcdh) locus is a paradigm of stochastic gene expression with the potential to express a different cPcdh combination in every neuron. Here, we report a limited version established during the transition from the naive to the primed states of human cell pluripotency that reduces by orders of magnitude the combinatorial potential in the cPcdh locus. It is a chromatin-based mechanism that increases the frequency of stochastic selection of a subset of cPcdh promoters upon differentiation to fetal-like neurons in monolayers, organoids, or the rat spinal cord. Signs of similar preferential selections can be observed in the brain throughout fetal development, disappearing after birth, but not in a condition of delayed maturation such as Down Syndrome. We therefore propose that pluripotent cells impose a pattern of limited cPcdh diversity on neurons that increases the likelihood of cPcdh repetition until these cells acquire adult-like maturation.

overall_design:
Lines/sublines: The hiPSC1-8 sublines were generated from single cells of the parent CVB hiPSC line. Six of these sublines were genetically modified (hiPSC2-7) and two were cases of failed genome editing (hiPSC1 and 8); please see Supplementary Table S1 in the associated publication for more details. Initially, these modifications should be irrelevant to the study of the cPcdh locus. The. hiPSC1 1.1-6 sublines were generated from the hiPSC1 subline and all underwent a process of genome editing, which again should be irrelevant to the study of the cPcdh locus (see Supplementary Table S1 in the associated publication for more details). The hiPSC 1.7-1.9 sublines were also generated from single cells of the parent CVB hiPSC line without undergoing any genome editing protocol. The hiPSC 1.13-15 sublines were generated from single cells of the parent CVI hiPSC line also without undergoing any genome editing protocol. The parent CVB and CVI lines were generated in the same reprogramming process and corresponded to two independent colonies. The hESC 1.7-1.9 sublines were generated from single cells of the parent HUES9 hESC line without undergoing any genome editing protocol. The HUES9 hESC 1.8 1.1-8 sublines were generated from single cells of the HUES9 1.8 subline after a process of primed-to-naive-to-reprimed conversion. All hiPSC/hESC lines/sublines were cultured in the primed state unless indicated (when indicated, some lines/sublines were cultured under naive-inducing conditions (5iLA protocol, and when returned to the primed state, the conditions were referred to as 're-primed'). For mouse cells, the 46C mESC 1.1-1.6 sublines were generated from single cells of the parent 46C mESC line. The R1 mESC 1.4/1.7 and 2.10/2.13 sublines were generated from single cells of the parent R1 mESC line. The R1 EpiSC 1.1-1.15 sublines were generated from single cells of the parent R1 mESC line after conversion to EpiSCs. The parental R1 mESC and EpiSC populations have also been included here.
ChIP-seq data: All ChIP-seq experiments were performed in pluripotent stem cells (hiPSCs/hESCs/mESCs/EpiSCs). Most profiles were based on H3K4me3, but many others also on CTCF, Rad1, H3K4me2, H3K9me3, H3K9ac, H2A.Z, REST/NRSF, SIN3A, and JMJD2A.

first: Angels

last: Almenar-Queralt

first: Ivan

last: Garcia-Bassets


title: Oligodendrocyte intrinsic miR-27a controls myelination and remyelination

status: Public on Aug 03 2019

city: Portland

first: Selva

last: Baltan

state: OR

address: 3181 S.W. Sam Jackson Park Rd.

department: Anesthesia and Perioperative Medicine (APOM)

institute: Oregon Health and Science University

summary: The goal of this study was to understand miR-27a gene regulation in mouse OPCs

overall_design: Method- RNA isolated from biotin-tagged miRNA mimic (control and miR-27a)-transfected OPCs, as well as pulldown assays, were subjected to mRNA deep sequencing. RNA-seq libraries were prepared with Illumina’s TruSeq Stranded Total RNA with Ribo-Zero Globin kit and sequenced on HiSeq-2500 sequencer using Rapid Run v2, 100bp, Paired-end run. Post-sequencing, raw demultiplexed fastq paired end read files were trimmed of adapters and filtered using the program skewer to throw out any with an average phred quality score of less than 30 or a length of less than 36. Trimmed reads were then aligned using the HISAT2 aligner to the Mus musculus NCBI reference genome assembly (v GRCm38) and sorted using SAMtools. Aligned reads were counted and assigned to gene meta-features using the program featureCounts part of the Subread package. These count files were imported into the R programming language and were assessed for quality control, normalized, and analyzed using an in-house pipeline utilizing the edgeR Bioconductor library for differential gene expression testing.

first: Ajai

last: Tripathi

first: Brian

last: Richardson

first: Mark

last: Cameron

first: Ranjan

last: Dutta


title: Analysis of the Clustered Protocadherin (cPcdh) Locus in Human Pluripotent Stem and Derived Cells (RNA-seq I out of II)

overall_design:
Lines/sublines: The hiPSC1-8 sublines were generated from single cells of the parent CVB hiPSC line. Six of these sublines were genetically modified (hiPSC2-7) and two were cases of failed genome editing (hiPSC1 and 8); please see Supplementary Table S1 in the associated publication for more details. Initially, these modifications should be irrelevant to the study of the cPcdh locus. The hESC 1.8 subline was generated from a single cell of the parent HUES9 hESC line and it was profiled in the primed state,  naive state (conversion from the primed state,  5iLA protocol), and re-primed state (which are cells converted into the naive state and returned to the primed state).
RNA-seq data: triplicate differentiation replicates of neurons generated from NPCs derived from hiPSC1-8 (n=24); cortical neurons generated from hiPSC1/3/5 (n=3); 10-month-old cortical organoids generated from the CVB line (n=1, pool of organoids); and primed, naive, and re-primed HUES9 1.8 subline (n=1 each).


title: Sinorhizobium meliloti as a model system to study Ca. Liberibacter asiaticus regulators. [phrR]

city: Stanford

first: Melanie

last: Barnett

address: 371 Jane Stanford Way

institute: Stanford University

summary: We characterized the transcriptome of a Sinorhizobium meliloti phrR deletion mutant (MB1142) expressing Ca. Liberibacter asiaticus phrR

platform_organism:
Sinorhizobium meliloti
Medicago truncatula

overall_design: Gene expression profiling of Sinorhizobium meliloti strains was performed using custom Affymetrix GeneChips. Strain MB1142 (phrR1phrR2 deletion), carrying Ca. Liberibacter asiaticus phrR (locus tag = CLIBASIA_01545, codon optimized for expression in Sinorhizobium meliloti) was compared to strain MB1142, carrying the empty vector, pSRKGm (Khan et al. 2008, Appl Environ Microbiol 74:5053-5062)

first: Sharon

last: Long


title: Sinorhizobium meliloti as a model system to study Ca. Liberibacter asiaticus regulators. [VisNR]

summary: We characterized the transcriptome of a Sinorhizobium meliloti visNR deletion mutant (MB1102) expressing Ca. Liberibacter asiaticus visNR

overall_design: Gene expression profiling of Sinorhizobium meliloti strains was performed using custom Affymetrix GeneChips. Strain MB1102 (visNR deletion), carrying Ca. Liberibacter asiaticus visNR (locus tags = CLIBASIA_02905 & CLIBASIA_2900, codon optimized for expression in Sinorhizobium meliloti) was compared to strain MB1102, carrying the empty vector, pSRKGm (Khan et al. 2008, Appl Environ Microbiol 74:5053-5062)


title: Cell intrinsic Wnt4 influences cDC fate determination to suppress Type 2 immunity

city: Philadelphia

first: Herbert

last: De'Broski

state: PA

address: 3800 Spruce St

institute: University of Pennsylvania

summary: We demonstrate that Wnt4, a beta-catenin independent Wnt ligand, is produced by both hematopoietic and non-hematopoietic cells and is both necessary and sufficient for pre-cDC1/cDC1 maintenance. Whereas BM cDC precursors undergo phosphoJNK/c-Jun activation upon Wnt4 treatment, loss of cDC Wnt4 in CD11cCreWnt4flox/flox mice impaired differentiation of CD24+, Clec9A+, CD103+ cDC1 compared to CD11cCre controls. Conversely, sc-RNAseq analysis of BM revealed a 2-fold increase in cDC2 gene signature genes and flow cytometry demonstrated increased numbers of SIRP-α + cDC2 amid lack of Wnt4. Increased cDC2 numbers due to CD11c-restricted Wnt4 deficiency increased interleukin 5 production, group 2 innate lymphoid cell (ILC2) expansion, and host resistance to the hookworm parasite Nippostrongylus brasiliensis. Collectively, these data uncover a novel and unexpected role for Wnt4 in cDC subset differentiation and Type 2 immunity.

overall_design: Single-cell RNA-seq in CD11c+ cells isolated from bone marrow in WT and CD11cCre-Wnt4flox/flox KO mice

first: Li-yin

last: Hung


title: Sinorhizobium meliloti as a model system to study Ca. Liberibacter asiaticus regulators. [RpoH]

summary: We characterized transcriptomes of a Sinorhizobium meliloti rpoH1rpoH2 deletion mutant (RFF231; Lang et al. 2018, mSphere 3:e00454-18) expressing either Ca. Liberibacter asiaticus rpoH or Sinorhizobium meliloti rpoH1

overall_design: Gene expression profiling of Sinorhizobium meliloti strains was performed using custom Affymetrix GeneChips. Strain RFF231 (rpoH1rpoH2 deletion), carrying either Ca. Liberibacter asiaticus rpoH (locus tag = CLIBASIA_02490, codon optimized for expression in Sinorhizobium meliloti) or Sinorhizobium meliloti rpoH1 (locus tag = SMc00646) was compared to strain RFF231, carrying the empty vector, pSRKGm (Khan et al. 2008, Appl Environ Microbiol 74:5053-5062)


title: Sinorhizobium meliloti as a model system to study Ca. Liberibacter asiaticus regulators. [LsrB]

summary: We characterized the transcriptome of a Sinorhizobium meliloti lsrB deletion mutant (MB1105) expressing Ca. Liberibacter asiaticus lsrB

overall_design: Gene expression profiling of Sinorhizobium meliloti strains was performed using custom Affymetrix GeneChips. Strain MB1105 (lsrB deletion), carrying Ca. Liberibacter asiaticus lsrB (locus tag = CLIBASIA_00835, codon optimized for expression in Sinorhizobium meliloti) was compared to strain MB1105, carrying the empty vector, pSRKGm (Khan et al. 2008, Appl Environ Microbiol 74:5053-5062)


title: Sinorhizobium meliloti as a model system to study Ca. Liberibacter asiaticus regulators. [LdtR]

summary: We characterized the transcriptome of a Sinorhizobium meliloti ldtR deletion mutant (MB1101) expressing Ca. Liberibacter asiaticus ldtR

overall_design: Gene expression profiling of Sinorhizobium meliloti strains was performed using custom Affymetrix GeneChips. Strain MB1101 (ldtR deletion), carrying Ca. Liberibacter asiaticus ldtR (locus tag = CLIBASIA_01180, codon optimized for expression in Sinorhizobium meliloti) was compared to strain MB1101, carrying the empty vector, pSRKGm (Khan et al. 2008, Appl Environ Microbiol 74:5053-5062)


title: Sinorhizobium meliloti as a model system to study Ca. Liberibacter asiaticus regulators. [CtrA]

summary: We characterized transcriptomes of a Sinorhizobium meliloti wild type strain (CL150) expressing either Ca. Liberibacter asiaticus ctrA or Sinorhizobium meliloti ctrA

overall_design: Gene expression profiling of Sinorhizobium meliloti strains was performed using custom Affymetrix GeneChips. Strain CL150, carrying either Ca. Liberibacter asiaticus ctrA (locus tag = CLIBASIA_03950, codon optimized for expression in Sinorhizobium meliloti) or Sinorhizobium meliloti ctrA (locus tag = SMc00654) was compared to strain CL150, carrying the empty vector, pSRKGm (Khan et al. 2008, Appl Environ Microbiol 74:5053-5062)


title: Sinorhizobium meliloti as a model system to study Ca. Liberibacter asiaticus regulators.

overall_design: Refer to individual Series


title: Hyperglycemia Alters the Fetal Islet Transcriptome and Leads to Progeny Islet Dysfunction

city: Indianapolis

first: Kok

middle: Lim

last: Kua

state: IN

address: RR208  PNEO  IN

department: PED-NEONATAL MEDICINE

institute: Indiana University

summary: The overall goal of this project is to identify transcriptome alteration in fetal islets exposed to transient maternal hyperglycemia from GD20 to GD22.

overall_design: Left uterine horn fetus rats were subjected hyperglycemic infusion, while right uterine horn normoglycemic fetuses were used as paired internal controls. Upon completing glucose infusion from GD20 to 22, 2 fetal pancreata were pooled and islets were extracted via collagenase digestion and hand picked. After 24 hour of recovery in RPMI containing 5mM glucose, RNA was collected from the islets and sequenced using HiSeq4000.


title: Expression data from Aracidopsis roots

city: Fuchu-shi

first: Ohtsu

last: Naoko

address: 3-5-8 Saiwai-cho

department: Biological Production

institute: Tokyo University of Agriculture and Technology

summary:
Sulfate is recognized as a primary sulfur source for plant growth and effects of thiosulfate as a sulfur source on plant growth and metabolism, gene expression have not been studied.
We used microarrays to detail the global programme of gene expression in response to thiosulfate as a sulfur source.

overall_design: Arabidopsis Col-0 WT plants were hydroponically grown for 8 wks under short day condition, and roots were sampled for RNA extraction and hybridization on Affymetrix microarrays.

first: Takatsugu

last: Nakajima

first: Naoko

last: Ohtsu


title: Identification of C2CD4A as a human diabetes susceptibility gene with a role in β-cell insulin secretion

status: Public on Jul 31 2019

city: New York

first: Taiyi

middle: Diana

last: Kuo

state: NY

address: 1150 St Nicholas Ave., Ste. 237

institute: Columbia University

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


title: Identification of C2CD4A as a human diabetes susceptibility gene with a role in β-cell insulin secretion [ChIP-Seq]

summary: To identify effector genes of pancreatic beta cell failure, we integrated analyses of FoxO1 regulated genes with ChIPseq and RNAseq, super-enhancers, and human type 2 diabetes GWAS loci.

overall_design: We performed FoxO1 ChIPseq in our FoxO1-Venus knock-in mice, and H3K27ac ChIPseq in FAC-sorted beta cells from WT and db/db mice.

first: Domenico

last: Accili

first: Mitchell

last: Lazar


title: Identification of C2CD4A as a human diabetes susceptibility gene with a role in β-cell insulin secretion [RNA-Seq]

summary: To investigate the function of C2CD4A, we analyzed RNA profiles in MIN6 cells expressing C2cd4a-GFP or control-GFP.

overall_design: We performed RNAseq in mouse insulinoma MIN6 cells expressing C2cd4a-GFP or control-GFP.


title: CHO_library_B_GCN Screen

status: Public on Jul 26 2019

first: Heather

last: Harding

state: Cambridge

address: Hills Road

department: CIMR Clinical Biochemistry

institute: University of Cambridge

summary: CRISPR screen targeting 3022 CHO (Chinese hamster) genes to identify those contributing to induction of the Integrated Stress Response by histidinol treatment.

sample_organism:
Cricetulus griseus
synthetic construct

platform_organism:
Cricetulus griseus
synthetic construct

overall_design: FACS sorting was used to select CHO cells that failed to induce a CHOP::GFP Integrated Stress Response (ISR) reporter following targeting with a focused CRISPR mutagenesis library.

first: Adrianna

last: Ordonez

first: Felicity

last: Allen

first: Leopold

last: Parts

first: Alison

last: Ingles

first: Roger

middle: L

last: Williams

first: David

last: Ron


title: Targets of CDK12 on ZR-75-30 breast cancer cells (RNA-seq)

status: Public on Jul 21 2019

city: Seoul

first: Gu

last: Kong

address: 17 Haengdang-dong, Seongdong-gu

department: Department of Pathology

country: South Korea

institute: College of Medicine, Hanyang University

summary: RNA-sequencing analysis of CDK12 overexpressiong ZR-75-30 cell lines. Cyclin dependent kinase 12 (CDK12) is amplified in approximately 70-90% of HER2 amplified breast cancer. Results provide insight into the targets of CDK12 in HER2 positive breast cancer.

overall_design: Total RNA was isolated from ZR-75-30 cell infected with control (pLVX) or CDK12 (pLVX-CDK12) lentiviruses using Trizol reagent. For each of the 2 conditions, 3 biological replicates were included. In total, 6 RNA-sequencin samples were analyzed; 3 controls and 3 CDK12 overexpressing cells.

first: Hee-Joo

last: Choi


title: Differential gene expression of static and intermittent compressive force treated human periodontal ligament cells

status: Public on Jul 23 2019

city: Pathumwan

first: Thanaphum

last: Osathanon

state: Bangkok

address: 34 Henri-dunant Rd. Wongmai

country: Thailand

institute: Chulalongkorn University

summary: Mechanical force has been shown to regulate periodontal ligament cells (PDLs) behaviors. However, different force types lead to distinct PDLs’ responses. Here, the differential gene expression profiling of PDLs subjected to static and intermittent compressive forces was examined using RNA sequencing technique. Results demonstrated that the static and intermittent compressive force treated PDLs exhibited the differential regulation genes. KEGG pathway enrichment analysis revealed that focal adhesion and transforming growth factor beta signaling pathway were commonly upregulated while calcium signaling pathway was downregulated in both static and intermittent compressive force-treated PDLs. Interestingly, Wnt signaling pathway was upregulated only in the PDLs that subjected to the intermittent compressive force.

overall_design: Human periodontal ligament cells were treated with the computerized controlled compressive force application apparatus. For static compressive force stimuli, cells were loaded with 1.5 g/cm2 of force continuously while cells were loaded with 1.5 g/cm2 with the loading frequency of 0.23 Hz. All loading was performed in serum free condition and the total RNA was collected at 24 h after loading. Differential gene expression was determined using RNA sequencing technique.

first: Jeeranan

last: Manokawinchoke

first: Chalida

middle: N

last: Limjeerajarus

first: Prasit

last: Pavasant

first: Hiroshi

last: Egusa


title: Gene Expression Analysis of Essential Tremor via RNA-sequencing

first: Phyllis

last: Faust

address: 630 W 168th Street

department: Pathology and Cell Biology

institute: Columbia Unversity

summary: RNA-seq evaluation of post-mortem human cerebelllum from 33 patients with diagnosed Essential tremor, compared to 22 age-matched control patients. Two samples were under-sequenced and therefore removed from the final analysis. The raw data has been included in this submission.

overall_design: Compare post-mortem cerebellar cortex between patients diagnosed with Essential tremor and patients who are neurologically clear.

first: Regina

middle: T

last: Martuscello

first: Chloe

last: Kerridge

first: Debotri

last: Chatterjee

first: Whitney

last: Hartstone

first: Sheng-han

last: Kuo

first: Peter

last: Sims

first: Elan

last: Louis