title: PfAP2-G ChIP-seq in stage I gametocytes derived via next cycle conversion (NCC) and same cycle conversion (SCC)

status: Public on Jul 17 2019

city: University Park

first: Manuel

last: Llinas

address: Millennium Science Complex

department: Biochemistry and Molecular Biology

institute: Pennsylvania State University

summary: In the malaria parasite Plasmodium falciparum, the switch from asexual multiplication to sexual differentiation into gametocytes is essential for transmission to mosquitos. One of the key determinants of sexual commitment is the transcription factor PfAP2-G, which has been proposed to orchestrate this crucial cell fate decision by driving expression of gametocyte genes. Here we identify for the first time the direct targets of PfAP2-G and demonstrate that it dynamically binds hundreds of sites across the genome. We also identify major differences in PfAP2-G occupancy between gametocytes derived via next-cycle and same-cycle conversion, suggesting significant biological differences between these two pathways. By using a combination of ChIP-seq, transcriptomics, and CRISPR-Cas9, we are able to show definitively that PfAP2-G is a transcriptional activator of early gametocyte genes. Our data implicate PfAP2-G not just as a transcriptional activator of gametocyte genes, but also as a regulator of genes important for red blood cell invasion. Excitingly, we also demonstrate that PfAP2-G interacts with a second transcription factor to regulate transcription. These results shed new light on a critical part of the malaria parasite lifecycle by clarifying the role of PfAP2-G during gametocytogenesis.

overall_design: ChIP was performed using an antibody against HA on the AP2-G-DD line (+ Shld1) in stage I gametocytes produced using either next cycle conversion (NCC) or same cycle conversion (SCC). There are two biological replicates for each of the two stages, giving a total of four samples. The input material served as the control.

first: Gabrielle

last: Josling

first: Timothy

middle: J

last: Russell

first: Jarrett

last: Venezia

first: Lindsey

last: Orchard

first: Heather

last: Painter

last: Llinás


title: Gene expression profiles in hippocampus with or without neuronal PGC-1α overexpression

status: Public on Jul 16 2019

city: Tianjin

first: Bin

last: Han

address: 154 Anshan Road, Heping District

country: China

institute: Tianjin Medical University General Hospital

summary: Upregulation of neuronal PGC-1α ameliorates cognitive impairment induced by chronic cerebral hypoperfusion in mice. To investigate the underlying mechanism of PGC-1α, we have employed whole mRNA microarray expression profiling as a discovery platform to identify genes with the potential to change the hippocampal function. Indeed,  PGC-1α overexpression alters the gene expression profiles of hippocampus, this suggested that neuronal PGC-1α might play an important role after chronic cerebral hypoperfusion.

overall_design: Hippocampus was isolated from PGC-1αf/f and nPGC-1α mice after sacrificed, and immediately frozen in liquid nitrogen. Then the samples were processed to perform microarray analysis.

first: Junwei

last: Hao


title: Similarity  of therapeutic networks induced by a multi-component herbal remedy in neurovascular unit cells

status: Public on Jul 18 2019

city: Daejeon

first: Bu-Yeo

last: Kim

address: 1672 Yuseongdae-ro, Yuseong-gu

department: Herbal Medicine Research Division

country: South Korea

institute: Korea Institute of Oriental Medicine

type: Expression profiling by high throughput sequencing

summary: The neurovascular unit, which includes neurons, glial cells, and vascular cells, plays crucial roles in the onset and progression of Alzheimer’s disease (AD). Therefore, effective drugs against AD should be able to target the multi-cellular neurovascular unit and the therapeutic relationships among neurovascular cells should be defined. We aimed to examine the therapeutic effects of an herbal remedy with multi-targeting capabilities, ukgansan (UGS), using in vitro models of AD, and to assess the similarity among neurovascular cells in terms of a therapeutic network.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: UGS and its components were administered in neurovascular cells including HT22 neurons, BV-2 microglia, and HBVP pericytes stimulated with H2O2, lipopolysaccharide, and transforming growth factor, respectively. The therapeutic effects of UGS and its components were measured from the recovery patterns of gene expression.

first: Soo-Jin

last: Jeong


title: CHIP-seq analysis about Histones and Zscan4 after Zscan4 overexpression

status: Public on Jul 08 2019

city: Tainjin

first: Weiyu

last: Zhang

address: No.38 Tongyan Road, Jinnan District

institute: Nankai University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Transcription factor Zscan4 was newly discovered to be a marker of the intermediate state of 2-cell like cells . In addition, the WGCNA discovered a strong positive correlation between the expression of Zscan4 and that of MT2/MERVL .Hence, we examined the possibility for Zscan4 as an activator of MT2/MERVL.

overall_design: We overexpressed Zscan4 in J1. We performed CHIP-seq analysis in order to exam H3K27ac, H3K4me1, H3K14ac and Zscan4 after Zscan4 overexpression.

first: Ruiqing

last: Chen

first: Fuquan

first: Xinyi

last: Lu


title: Transcriptomic analysis of lignin mutants in Arabidopsis

status: Public on Aug 08 2019

city: Denton

first: Lina

last: Gallego-Giraldo

state: Texas

address: 1155 Union Circle #311428

department: Biology

country: USA

institute: University of north Texas, Biodiscovery Institute

summary: Transcriptomic analysis was performed on the main inflorescence stems of wild-type and lignin-modified lines growing under the same conditions.

overall_design: Study transcriptomic changes in arabidopsis stem manipulated in HCT and CCR. Loss of function ccr-1 mutant and HCT-RNAi lines. We used microarrays to detail the global determine changes of gene expression in loss of function ccr-1 and HCT-RNAi up and down-regulated genes were identified respect to Wildtype (WT) control.

first: Richard

middle: A

last: Dixon


title: Dynamic 3D chromosomal landscapes in acute leukemia [Hi-C]

status: Public on Aug 04 2019

city: Braunschweig

first: Andreas

last: Kloetgen

state: NI

address: Inhoffenstr 7

department: Department for Computational Biology of Infection Research

country: Germany

institute: Helmholtz Centre for Infection Research

summary:
Background: Disruptions of 3D chromatin architecture can alter the activity of topologically associated domains (TADs), rewire enhancer-promoter interactions and thus significantly impact gene regulatory programs. Recently, such disruptions have been implicated in tumorigenesis, highlighting the need for a deeper understanding of their detailed role.
Methods: T-ALL primary samples and prototypical cell lines as well as healthy T cell counterparts were profiled by in-situ Hi-C, RNA-Seq and CTCF ChIP-Seq. Data was subsequently integrated.
Results: Our studies showed that the genome of leukemia cells does not display global changes in TAD structures but presents local changes in selected TAD boundaries as well as alterations of intra-TAD activity which are associated with changes in gene expression of key oncogenes and tumor suppressors, strong correlation with CTCF-mediated insulation and enhancer activity. Finally, we showed that 3D interactions on selected loci can be partially corrected pharmacologically, potentially accounting for the anti-leukemogenic effects of these drugs.
Conclusions: Our studies underscore the need for further investigation of factors that rewire long range interactions especially during tumorigenesis, as they could be targets for pharmacological targeting.

overall_design: Primary samples and prototypical cell lines of T cell acute lymphoblastic leukemia (T-ALL) as well as healthy T cell counterparts from three different donors were collected.

first: Palaniraja

last: Thandapani

first: Panagiotis

last: Ntziachristos

first: Ioannis

last: Aifantis

first: Aristotelis

last: Tsirigos


title: Initial host response to mycobacterial infection is orchestrated through H3K4 methylation-mediated RNA polymerase II binding at key immune function genes.

status: Public on Jul 05 2019

city: Dublin

first: Thomas

last: Hall

state: Select One

address: 2, Taney Grove

department: Vet sciences

country: Ireland

institute: UCD

type: Non-coding RNA profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Initial  host  response to mycobacterial infection is orchestrated through H3K4 methylation-mediated RNA polymerase II binding at key immune function genes [miRNA-seq]

summary: Massive reprogramming of the host alveolar macrophage transcriptome occurs during the initial stages of tuberculosis. In bovine tuberculosis, Mcobacterium bovis can persist and replicate within alveolar macrophages through varied mechanisms to subvert or exploit host immune responses ( REF). To determine how these transcriptional changes are regulated we performed ChIPseq analysis of H3K4 and H3K27 methylation, established histone tail markers associated with permissive and repressive chromatin states, respectively. These analyses were carried out in parallel with RNA polymerase II ChIPseq, RNAseq and small non-coding RNAseq. This meta data file refers to the miRNA-seq datasets.

overall_design: Examination of triple methylation of histone mark H3K4 and H3K27 in bovine alveolar macrophages  infected and not infected with Mycobacterium bovis and the resulting change in expression of genes and miRNAs associated with the immune response.

first: Douglas

last: Vernimmen

first: John

last: Browne

first: Stephen

middle: V

last: Gordon

first: David

middle: E

last: MacHugh

first: Alan

middle: M

last: O’Doherty


title: Dynamic 3D chromosomal landscapes in acute leukemia [RNA-Seq]


title: Initial  host  response to mycobacterial infection is orchestrated through H3K4 methylation-mediated RNA polymerase II binding at key immune function genes [ChIP-seq]

summary: Massive reprogramming of the host alveolar macrophage transcriptome occurs during the initial stages of tuberculosis. In bovine tuberculosis, Mcobacterium bovis can persist and replicate within alveolar macrophages through varied mechanisms to subvert or exploit host immune responses ( REF). To determine how these transcriptional changes are regulated we performed ChIPseq analysis of H3K4 and H3K27 methylation, established histone tail markers associated with permissive and repressive chromatin states, respectively. These analyses were carried out in parallel with RNA polymerase II ChIPseq, RNAseq and small non-coding RNAseq. This meta data file refers to the ChIP-seq datasets.


title: Initial  host  response to mycobacterial infection is orchestrated through H3K4 methylation-mediated RNA polymerase II binding at key immune function genes [RNA-seq]

summary: Massive reprogramming of the host alveolar macrophage transcriptome occurs during the initial stages of tuberculosis. In bovine tuberculosis, Mcobacterium bovis can persist and replicate within alveolar macrophages through varied mechanisms to subvert or exploit host immune responses ( REF). To determine how these transcriptional changes are regulated we performed ChIPseq analysis of H3K4 and H3K27 methylation, established histone tail markers associated with permissive and repressive chromatin states, respectively. These analyses were carried out in parallel with RNA polymerase II ChIPseq, RNAseq and small non-coding RNAseq. This meta data file refers to the RNA-seq datasets.


title: The widely conserved microRNA, miR-1-3p, is a male-determining factor in the oriental fruit fly, Bactrocera dorsalis

status: Public on Jul 04 2019

city: Wuhan

first: Wei

last: Peng

address: Shizishan Street No. 1, Hongshan District, Wuhan,Hubei  430070, P.R. China

institute: Huazhong Agricultural University

summary: We constructed three small RNA libraries from embryos at 5, 6 and 7 post-oviposition (hpo) of Bactrocera dorsalis for deep sequencing. The data analysis revealed 147 known and 103 novel miRNAs from these libraries.

overall_design: Small RNA profiles from embryos at 5, 6 and 7 post-oviposition (hpo) of Bactrocera dorsalis were generated by Illumina deep sequencing.

first: Hongyu


title: Functional comparison between healthy and multiple myeloma adipose stromal cells

status: Public on Jun 27 2019

city: Toulouse

first: Nicolas

last: Espagnolle

address: Bâtiment INCERE 4 bis, avenue Hubert Curien

country: France

institute: STROMALab, Université de Toulouse, CNRS  ERL5311, EFS, INP-ENVT, Inserm U1031, UPS, Toulouse, France

summary: Multiple myeloma (MM) is a not curable B-cell neoplasia characterised by the accumulation of tumor plasma cells within the bone marrow. As a consequence, 80% of patients develop bone osteolytic lesions that remain even after complete remission. We and others had demonstrated that bone marrow derived Mesenchymal Stromal Cells (MSC) are abnormal in MM and thus could not be used for an autologous treatment to repare bone damages. Adipose Stromal Cells (ASC) represent an interesting alternative to MSC for cellular therapy. Thus, in this paper we asked if they could be a good candidate in repairing MM bone lesions. For the first time, we present a transcriptomic, phenotypic and functional comparison between ASC from MM patients and healthy donors (HD) relying on their autologous MSC counterpart. In contrast to MM MSC, MM ASC do not exhibit major abnormalities. However, the changes observed in MM ASC and the supportive property of ASC on MM cells question their putative and safety uses at autologous or allogenic level.

overall_design: Adipose tissue derived stromal cells (ASC) were compared from 12 healthy donors and 12 multiple myeloma patients (MM)

first: Jill

last: Corre


title: Angptl8 mediates food-driven resetting of hepatic circadian clock in mice

city: nanjing

first: siyu

last: chen

address: #639 longmian avenue

institute: China Pharmaceutical University

summary: Mammalian circadian clocks precisely control the rhythms of behavior and physiology, and can be reset by various environmental signals. While the light-dark (LD) cycle resets the master clock, timed food intake is a potent synchronizer of peripheral clocks. As the largest metabolic organ, the liver sensitively responds to the food signals and secrets hepatokines, leading to the robust regulation of metabolic and clock processes. However, it remains unknown which hepatokine mediates the food-driven resetting of the liver clock independent of the master clock. In our current study, we clustered high-throughput RNA sequencing results to screen out candidate genes that mediate the food-driven resetting of the liver clock

overall_design: Total RNA after subjecting to fasting/re-feeding cycles or constant darkness were isolated from mice liver and seqenced using Illumina HiSeq 3000

first: Siyu

last: Chen

first: Mengyang

last: Feng

first: Shiyao

last: Zhang

first: Zhewen

last: Dong

first: Yifan

last: Wang

first: Wenxiang


title: Identification of an eight-protein biosignature for the diagnosis of tuberculosis

status: Public on Jun 25 2019

city: Guangzhou

first: Huihua

address: 601, west Huangpu avenue, Tianhe district

department: Biomedicine Institute & Cell Biology Department

institute: Jinan University

summary: Mycobacterium tuberculosis (Mtb) antigen-specific cellular response is promising for detectionof Mtb infection, but not efficient for diagnosis of TB. We firstly identified 16 TB disease-specific protein markers measured in the culture  supernatant of Mtb-stimulated whole blood using a 640 human proteins array, the highest throughput antibody-based protein array available at the time when we did this study. Potential TB-related proteins were then analyzed across three different patient cohorts comprised of healthy controls, LTBI, non-TB pneumonia, and TB patients to evaluate how the biomarkers performed in diagnosing TB in the real clinical setting. The data finally reveal an eight-protein biosignature of TB.

overall_design: We prospectively enrolled three cohorts into for our study, including 160 subjects to screen protein biomarkers of tuberculosis, 368 subjects to establish and test the predictive model, and 102 subjects for biomarker validation. Whole blood cultures were stimulated with pooled Mtb-peptides or mitogen, and then 640 proteins within the culture supernatant were analyzed simultaneously using an antibody-based array. 16 candidate biomarkers of tuberculosis were identified and developed into a custom multiplexed antibody array for biomarker validation.

first: Ruo-Pan

last: Huang

first: Xinchun


title: Autoantibody profiles in patients with COPD and non-COPD smokers

status: Public on Jun 21 2019

city: Borstel

first: Xinhua

last: Yu

address: Parkallee 22

institute: Research Center Borstel

summary: Chronic obstructive pulmonary disease (COPD) is a highly prevalent disease leading to irreversible airflow limitation and is characterized by chronic pulmonary inflammation，obstructive bronchiolitis and emphysema. Etiologically, COPD is mediated by toxic gases and particles, e.g. cigarette smoke, while the pathogenesis of the disease is largely unknown.  Several lines of evidence indicate a link between COPD and autoimmunity but comprehensive studies are lacking.  By using a protein microarray assaying more than 19,000 human proteins we determined in this study the autoantibody profiles of COPD and non-COPD smokers.

overall_design: 10 serum samples were included, 5 from COPD patients and 5 from non-COPD smokers.  These are dual channel arrays analyzed with each channel analyzed separately.


title: Brain regions and molecular pathways responding to food reward type and value in honey bees

status: Public on Jul 02 2019

city: Princeton

first: Ian

middle: Michael

last: Traniello

state: NJ

address: Princeton University

department: Lewis-Sigler Insitute for Genomic Biology

institute: Princeton University

summary: The ability of honey bees to evaluate differences in food type and value is crucial for colony success, but these assessments are made by individuals who bring food to the hive, eating little, if any, of it themselves. We tested the hypothesis that responses to food type (pollen or nectar) and value involve different subsets of brain regions, and genes responsive to food. mRNA in situ hybridization of c‐jun revealed that brain regions responsive to differences in food type were mostly different from regions responsive to differences in food value, except those dorsal and lateral to the mushroom body calyces, which responded to all three. Transcriptomic profiles of the mushroom bodies generated by RNA sequencing gave the following results: (1) responses to differences in food type or value included a subset of molecular pathways involved in the response to food reward; (2) genes responsive to food reward, food type and food value were enriched for (the Gene Ontology categories) mitochondrial and endoplasmic reticulum activity; (3) genes responsive to only food and food type were enriched for regulation of transcription and translation; and (4) genes responsive to only food and food value were enriched for regulation of neuronal signaling. These results reveal how activities necessary for colony survival are channeled through the reward system of individual honey bees.

overall_design:
Female forager bees were collected from colonies derived from naturally mated queens maintained according to standard methods at the University of Illinois Bee Research Facility (Urbana, IL). The colonies were typical of North American populations of Apis mellifera, which are hybrids of various European‐derived subspecies, mostly A. m. ligustica. Different individual colonies were used in each of the three behavioral experiments described below. Colonies for Experiments 1–3 were located in a large outdoor, screened enclosure (6 × 20 × 3 m3) to precisely control their access to food. Additional bees were collected from one colony to detect the presence of octopaminergic and dopaminergic neuronal activation. Bees from Experiments 2–3 were used for both RNAseq and mRNA in situ hybridization (ISH); bees from Experiment 1 were only used for RNAseq.
One complication associated with this method is that the stimulus varied between dancers and non‐dancers; this absolute difference in reward may also be driving the differences in brain gene expression in addition to differences in relative reward assessment. An alternative would have been to sample bees that danced or did not dance for the same sucrose concentration (Barron et al. 2007b), but this would have led to concerns that inter‐individual differences in response may be related to a variety of factors and not just reward assessment. Of the two, we believe that the method used was preferable for capturing the transcriptomic response to differences in reward value.
The low concentration feeder was presented first on each collection day. Bees arriving at the feeder were marked on the abdomen with paint (Testors Corporation, Rockford, IL, U.S.A.) so we could easily identify them upon return to the hive. Dancing bees were those that performed ≥8 ‘round dance’ circuits, which indicates robust dancing (Barron et al. 2007a,b). Non‐dancers were those that did not perform any dance circuits within approximately 20 seconds after returning to the hive (Seeley & Tovey 1994) and then walked beyond the ‘dance floor’, an area near the hive entrance where most dances occur.
One pair of sucrose feeders was available from 1000 h to 1130 h daily for collections for RNAseq, and a second pair of feeders was available from 1330 h to 1445 h daily for collections for ISH. Bees from both colonies were used for both types of analysis, as in Experiment 2 (RNAseq, N = 20; ISH, N = 14).

first: Amy

middle: C

last: Cash Ahmed


title: Identifying the regulon of Two Component System 7 (SPD_0157 and SPD_0158) of Streptococcus pneumoniae

status: Public on Jun 15 2019

city: Odense

first: Mikkel

middle: Girke

last: Jørgensen

address: Campusvej 55

country: Denmark

institute: University of Sourthern Denmark

summary: By comparing the transcriptome of Streptococcus pneumoniae wild-type D39 (serotype 2) to an isogenic strain overexpressing the response regulator of Two-Component System 7 (SPD_0158), we identified the regulon of the two-component system. In total 20 and 24 genes were considered up- and downregulated, respectively. 11 of the upregulated genes encode for proteins involved in host-glycan metabolism, while 7 encode proteins involved in carbohydrate metabolism. Most downregulated genes encode competence genes, but later experiments proved this was likely due to an atefact of overexpression. The remaining genes encode genes with other functions.

overall_design: Comparison of the transcriptome of a wild-type and an overexpressing strain.

first: Patrick

middle: R

last: Andreassen

first: Kevin

last: Pakula

middle: G


title: Super deepSAGE sequencing of normal porcine tissues

status: Public on Jul 19 2019

city: Jingzhou

first: Tinghua

address: Jingmi Road #266

institute: Yangtze University

summary: High-density gene expression profile of 70,000+ unique genes for 224 normal porcine samples from 28 different tissues of 32 different animals using Super deepSAGE sequencing technology.

overall_design: A total of 224 tissue samples across 28 different tissues/cells were collected from a slaughtering farm located in Hubei province in china. The samples were collected from 32 animals from a Duroc × Landrace × Yorkshare (DLY) commercial crossbreed pig populations consisting of 16 males and 16 females with a median age of 21 days. The endometrium, placenta, and conceptus were collected from Landrace × Yorkshare (LY) sows of 65 days of gestation. Total RNA were extracted and the libraries were construsted using Super deepSAGE technology and submitted for deep sequencing.

first: Min

last: Yao


title: RNA decay during gammaherpesvirus infection reduces RNA polymerase II occupancy of host promoters but spares viral promoters

status: Public on Jun 12 2019

city: Berkeley

first: Britt

last: Glaunsinger

state: CA

address: 565 Li Ka Shing Center

department: Molecular and Cellular Biology

institute: University of California Berkeley

summary: We perform RNA Polymerase II ChIp sequencing on MHV68 infected MC57G B6 mouse fibroblasts alongside a MHV68 mutant (R443I) that is deficient for RNA decay. We profile the occupancy of Pol II on host and viral genes at 24h post infection.We find that host genes have less Pol II occpancy genome wide, while viral genes remain robustly transcribed irrespective of RNA decay.

overall_design: RNA Pol II ChIP seq (8WG16 antibody) in WT MC57G cells infected with WT MHV68 or the R443I-ORF37 mutant MHV68

first: Ella

last: Hartenian

first: Sarah

last: Gilbertson

first: Joel

last: Federspiel

first: Ileana

last: Cristea


title: Effects of Peroxisome proliferator-γ coactivator-1α (PGC-1a) isoform over-expression +/- TNFalpha on hepatocyte gene expression

status: Public on Jun 11 2019

city: Montreal

first: Jennifer

middle: Lynn

last: Estall

state: Quebec

address: 110 avenue des Pins ouest

country: Canada

institute: IRCM

summary:
PGC-1a is a transcriptional coactivator known to regulate a broad gene program of nutrient and mitochondrial metabolism. Many splice variants of this protein have been identified, but their functions were unknown. This experiment was designed to delineate the downstream targets of two different PGC-1alpha isoforms (PGC-1a1 and PGC-1a4) in hepatocytes, and to determine whether inflammatory signaling (via TNFR activation) modulated these targets
Liver is exposed to constantly changing metabolic and inflammatory environments. It must quickly sense and adapt to metabolic need while balancing resources required to protect itself from harmful inflammatory molecules. PGC-1α is a transcriptional coactivator that mediates cellular adaptation to diverse stimuli including inflammation. PGC-1α has a protective role against inflammation in several organs, including brain, heart, kidney, muscle, and liver. However, it is not known how hepatic PGC-1α integrates extracellular signals to mitigate inflammatory outcomes. PGC-1α exists as multiple, alternatively spliced variants whose expression is differentially regulated by different gene promoters. In human liver, we found that inflammatory conditions preferentially activated the alternative versus proximal PPARGC1A promoter. Gene expression analysis performed in primary mouse hepatocytes identified many shared and isoform-specific roles for PGC-1α variants during acute inflammation. PGC-1α1 primarily impacted gene programs of nutrient and mitochondrial metabolism, while TNFα treatment revealed that PGC-1α4 uniquely influenced several pathways related to innate immunity and cell death. Gain- and loss-of-function models showed that PGC-1α4 specifically attenuated apoptosis in response to TNFα or LPS, in contrast to PGC-1α1, which reduced expression of a wide inflammatory gene network. We conclude that PGC-1α variants have distinct, yet complimentary roles in hepatic responses to inflammation, with PGC-1α4 being an important mitigator of apoptosis.

overall_design: Primary mouse hepatocytes (isolated from C57BL/6J mice) were infected with adenovirus expression PGC-1a1, PGC-1a4 or vector only control. All vectors express GFP from a separate ORF. 48 hours after infection, cells were treated with 2 ng/mL TNFalpha for 2 hours (or PBS vehicle). Cells were harvest and RNA isolated for expression analsis.

middle: L

first: Melissa

last: Leveille


title: Ribosome profiling of Cryptococcus neoformans H99

status: Public on Jun 22 2019

city: Edinburgh

first: Edward

middle: William Joseph

last: Wallace

address: Waddington Building, Max Born Crescent

department: Institute for Cell Biology, School of Biological Sciences

country: United Kingdom

institute: University of Edinburgh

summary: We measured protein translation (by ribosome profiling) and RNA levels (by polyA-enriched RNA-seq) in Cryptococcus neoformans strain H99 and Cryptococcus neoformans strain JEC21. This is the first transcriptome-wide map of translation in this species complex.

sample_organism:
Cryptococcus neoformans
Cryptococcus deneoformans

overall_design: Matched ribosome profiling and RNA-seq from 6 biological samples: 2x wild-type H99 and 2 deletion mutants (Ago1, Gwo1),  and 1x wild-type JEC21 and 1x deletion mutant (Ago1).

first: Jade

last: Sales-Lee

first: Hiten

last: Madhani


title: Real-time quantitative PCR analysis of monocytes of major depressed patients [Sertraline study]

status: Public on Jun 07 2019

city: Rotterdam

first: Hemmo

last: Drexhage

state: Zuid-Holland

address: Dr Molewaterplein 40

department: Immunology

country: Netherlands

institute: ErasmusMC

summary: Human CD14 positive monocytes were purified from major depressed patients or healthy volunteer frozen PBMC. Patients were treated with Sertralin or Sertralin + Celecoxib. Responders and non-responders to Sertralin and Sertralin + Celecoxib were recorded after 6 weeks of treatment

overall_design: qPCR gene expression profiling.  Monocytes prior to treatment were used for qPCR analysis. Details of patient selection, monocyte preparation, recording of patient data can be found in Gara Arteaga Henríquez et al, Frontiers, 2019

first: J

last: Wijkhuijs

first: H


title: Real-time quantitative PCR analysis of monocytes of major depressed patients


title: Single-cell RNA sequencing of lymphoblastoid cell lines of European and African ancestries

status: Public on Jun 09 2019

city: Austin

first: Daniel

middle: Camilo

last: Osorio

state: TX

address: 1601 Trinity St

institute: The University of Texas at Austin

summary: Here we present single-cell RNA sequencing (scRNA-seq) data of two LCLs: GM12878 and GM18502, produced from the blood of two female donors with European and African ancestry, respectively.

overall_design: Cells of three samples (the two LCLs and a 1:1 mixture of the two) were prepared separately using a 10X Genomics Chromium Controller and deeply sequenced.

first: Xue

last: Yu

first: Peng

first: Erchin

last: Serpedin

first: James

last: Cai


title: Real-time quantitative PCR analysis of monocytes of major depressed patients [Venlafaxin study]

summary: Human CD14 positive monocytes were purified from major depressed patients or healthy volunteer frozen PBMC. Patients were treated with venlafaxine. Responders and non-responders to venlafaxine were recorded after 6 weeks of treatment

overall_design: qPCR gene expression profiling.  Monocytes prior to treatment were used for qPCR analysis. Details of patient selection, monocyte preparation, recording of patient data can be found in Gara Arteaga Henríquez et al, Frontiers of Psychiatry, 2019


title: A large-scale comparative study of isoform expressions measured on four platforms

city: Orlando

first: WEI

last: ZHANG

state: FL

address: 4000 central florida blvd

department: Computer Science

institute: UNIVERSITY OF CENTRAL FLORIDA

summary:
The  NanoString  experiment  were  conducted  on  59  cell  lines  including  12  ovary cell lines, 12 lung cell lines, 11 colon cell lines, 10 breast cell lines, 4 pancreas cell lines, 2 prostate cell lines, 2 stomach cell lines, and 6 cell lines of 6 other types of tissues. A total of 404 probes were customized to estimate the isoform expressions of 155 cancer genes curated from the literature with more reliable isoform annotations, where each of the 155  gene  contains  at  least  two  isoforms.

RT-qPCR data on seven genes in twelve out of the 59 cancer cell lines are available at https://github.com/compbiolabucf/IntMTQ/tree/master/RT-qPCR

overall_design: We worked with NanoString Technologies to design an experiment for measuring the isoform expressions of 155 multi-isoform cancer genes in 59 cell lines. 79 genes contain two isoforms, 37 genes contain three isoforms, 18 genes contain four isoforms, and 21 genes contain more than four isoforms. We customized 404 capture-reporter probes to capture the 478 isoforms expressions in the genes. In addition, 14 probes for  quality  control  and  10  spike-in  probes  for  measuring  10  house  keeping  genes for normalization of the data are also introduced. Each probe is 100 bps long designed to capture a target sequence in one or multiple isoforms. For each gene, the probes were designed to best distinguish the expressions of all the isoforms in the gene, and one of the probes was always designed to measure the gene expression.

first: Rui

last: Kuang

first: Wei

last: Zhang


title: Transcriptome analysis of brainstem in gerbils with CA16-infection-induced HFMD

city: Hangzhou

first: Yisheng

last: Sun

state: Zhejiang

address: 3399# Binsheng Road, Binjiang District

department: Department of Microbiology

institute: Zhejiang Provincial Center for Disearse Control and Prevention

summary: Coxsackievirus A16 (CA16) is one of the major pathogens associated with human hand, foot, and mouth disease (HFMD) and in some countries this pathogen is the leading cause of this disease. We previously found that CA16 could induce neurological disorders in young gerbils, which could serve as a good animal model for studying the neuropathogenesis of CA16 infection. In this study, we found that 1039 genes were up-regulated and 299 genes were down-regulated in CA16-infected gerbils compared with control. Differentially expressed genes were clustered into functional pathways and the top five pathways according to the enrich factor were viral myocarditis, type 1 diabetes mellitus, toxoplasmosis, toll-like receptor signaling pathway and TNF signaling pathway. Our results provide novel insight into the neuropathogenesis of HFMD induced by CA16 infection.

overall_design: Brainstem mRNA profiles of CA16-infected gerbils were generated by deep sequencing, in triplicate, using Illumina Hiseq.

first: Yi-sheng

first: Han-ping

last: Zhu


title: Transcriptome analysis of brainstem in gerbils with EV71-infection-induced HFMD

summary: Enterovirus 71 (EV71) is one of the major pathogens associated with human hand, foot, and mouth disease (HFMD) and in some countries this pathogen is the leading cause of this disease. We previously found that CA16 could induce neurological disorders in young gerbils, which could serve as a good animal model for studying the neuropathogenesis of CA16 infection. In this study, we found that 1039 genes were up-regulated and 299 genes were down-regulated in CA16-infected gerbils compared with control. Differentially expressed genes were clustered into functional pathways and the top five pathways according to the enrich factor were viral myocarditis, type 1 diabetes mellitus, toxoplasmosis, toll-like receptor signaling pathway and TNF signaling pathway. Our results provide novel insight into the neuropathogenesis of HFMD induced by CA16 infection.

overall_design: Brainstem mRNA profiles of EV71-infected gerbils were generated by deep sequencing, in triplicate, using Illumina Hiseq.


title: miR-Seq on paired skin and oral mucosal wound healing

status: Public on May 29 2019

city: Chicago

first: Xiaofeng

last: Zhou

state: Illinois

address: 801 S Paulina Street

institute: University of Illinois at Chicago

summary: To delineate the role of microRNAs in the site-specific injury response, we compared the microRNAome of skin and oral mucosa both at baseline and throughout the time course of wound healing.

overall_design: miR-Seq based microRNA profiling was performed on tissue samples acquired from a murine wound healing model of paired skin and oral mucosal wounds throughout the wound healing process (0 hr, 6 hr, 24 hr and 5 days post-wounding).

first: Luisa

last: DiPietro


title: Transcriptional response of human synovial fibroblasts to TNF and IL-17A

status: Public on Jun 01 2019

city: Charlestown

first: Kamil

last: Slowikowski

state: Massachusetts

address: Mailstop CNY 149-8, 149 13th Street

institute: Massachusetts General Brigham

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

overall_design:
Refer to individual Series:

Microarray Data 1 (n=60)
9 time points, 2 technical replicates, 5 stimulations (Untreated; Media; IL-17A (1 ng/mL); TNF (1 ng/mL); TNF and IL-17A)

Microarray Data 2 (n=48)
1 time point (24 hours), 3 passages, 4 cell lines, 4 stimulations (Baseline; None; TNF; TNF and IL-17A)

RNA-seq Data 1 (n=175)
7 synovial fibroblast cell lines from patient tissues, 9 time points (0, 2, 4, 6, 8, 10, 12, 18, and 24 hours), 3 stimulations (TNF (1 ng/mL); TNF (1 ng/mL) and IL-17A (1 ng/mL); TNF (1 ng/mL) and IL-17A (10 ng/mL))

RNA-seq Data 2 (n=192)
4 synovial fibroblast cell lines from patient tissues, 4 time points (0, 1, 6 and 16 hours), 2 stimulations (TNF (0.1 ng/mL); TNF (0.1 ng/mL) and IL-17A (1 ng/mL)), and 5 siRNAs (CUX1, LIFR, STAT3, STAT4, ELF3)


title: Mitochondrial DNA allelic substitutions in Parkinson’s disease

status: Public on May 21 2019

city: Ancona

first: Tiziana

last: Casoli

address: Via Birarelli 8

department: Scientific Technological Area

country: Italy

institute: INRCA

type: Genome variation profiling by genome tiling array

summary: Mitochondrial DNA (mtDNA) damage is considered as a possible primary cause of Parkinson’s disease (PD). To explore the issue, mtDNA sequences from whole blood were analyzed in PD patients and controls using a resequencing chip and allelic substitutions were estimated for each nucleotide position (np) along the entire mtDNA sequence. Overall, 58 np showed a different allelic distribution in the two groups; of these, 81% showed an increase of non-reference alleles in PD patients, similar to findings reported in patients with Alzheimer’s disease, albeit in reduced proportion. These results suggest that age-related neurodegenerative diseases could share a mechanism involving mtDNA.

overall_design:
This study included a total of 15 AD patients and 15 age-matched controls from the Report-AGE Database Sample Resource, the institutional database of INRCA (Italian National Research Center on Aging). Data acquisition was performed using the Affymetrix Genechip Command Console (AGCC) software and data analysis was carried out with GSEQ 4.1. The output files used for the study were Single Nucleotide Polymorphism (SNP) View and Probe Intensity files.
Patient characteristics:
1) Locomotion mode: 0=Walk without aid  1=Walk with aid  2=Wheelchair  3=Bedridden
2) ADL Hierarchy scale: 0=Independent  1=Supervision  2=Limited  3=Extensive  4=Maximal  5=Dependent  6=Total dependence

first: Rosamaria

last: Lisa

first: Paolo

last: Fabbietti

first: Fiorenzo

last: Conti


title: Combating viral contaminants in CHO cells by engineering innate immunity

status: Public on May 31 2019

city: San Diego

first: Nathan

middle: E.

last: Lewis

address: 9500 Gilman Dr.

department: Pediatrics

institute: University of California, San Diego

summary: Viral contamination in biopharmaceutical manufacturing can lead to shortages in the supply of critical therapeutics. To facilitate the protection of bioprocesses, we explored the basis for the susceptibility of CHO cells, the most commonly used cell line in biomanufacturing, to RNA virus infection. Upon infection with certain ssRNA and dsRNA viruses, CHO cells fail to generate a significant interferon (IFN) response. Nonetheless, the downstream machinery for generating IFN responses and its antiviral activity is intact in these cells: treatment of cells with exogenously-added type I IFN or poly I:C prior to infection limited the cytopathic effect from Vesicular stomatitis virus (VSV), Encephalomyocarditis virus (EMCV), and Reovirus-3 virus (Reo) in a STAT1-dependent manner. To harness the intrinsic antiviral mechanism, we used RNA-Seq to identify two upstream repressors of STAT1: Gfi1 and Trim24. By knocking out these genes, the engineered CHO cells exhibited increased resistance to the prototype RNA viruses tested. Thus, omics-guided engineering of mammalian cell culture can be deployed to increase safety in biotherapeutic protein production.

overall_design: We infected CHO-K1 cells with a panel of RNA viruses (VSV, EMCV and Reo) from diverse pretreatment (no treatment, or exogenously-added type I IFN or poly I:C). Viral stocks were generated in susceptible Vero cells as per standard practices using DMEM (Dulbecco's Modified Eagle's medium) supplemented with 10% FBS, 2mM L-glutamine, 100 U/ml penicillin and 100 µg/ml streptomycin (DMEM-10). Library preparation was performed with Illumina’s TruSeq Stranded mRNA Library Prep Kit High Throughput (Catalog ID: RS-122-2103).


title: Low-oxygen stress responses of Brassicaceae Species

status: Public on May 15 2019

city: Seoul

first: JiHye

last: Hwang

address: 52, Ewhayeodae-gil

institute: Ewha Womans University

summary:
Expression profiling of A. thaliana, A. stelleri, R. islandica, and T. salsuginea under the low-oxygen treatment(0.1% O2/99.9% N2, various time points at 0, 1, 3, 8, 24, 72h)
Comparative analysis of transcriptional responses to low-oxygen stress with Arabidopsis and its related species to gain comprehensive insights into low-oxygen responses of the species.

sample_organism:
Arabidopsis thaliana
Arabis stelleri
Eutrema salsugineum
Rorippa islandica

overall_design: Two-condition experiment, normal vs. low-oxygen treatment. Total 10 microarrays (5 time points x dye swap) were used for understanding low-oxygen response of each species.

first: Ji-Hye

first: Dong-Hee

last: Lee


title: A survey of Fusobacterium nuceatum genes modulated by host cell infection

status: Public on May 07 2019

city: Guelph

first: Kyla

last: Cochrane

state: Ontario

address: 50 Stone Road East

department: Bioinformatics

institute: NuBiyota

summary: Here we report comprehensive transcriptomic profiles from Fusobacterium nucleatum (Fn) under conditions that mimic the first stages of bacterial infection in a highly-differentiated adenocarcinoma epithelial cell line. Our transcriptomic in vitro adenocarcinoma approach allows us to measure the expression dynamics and regulation of bacterial virulence and response factors in real time and is a novel strategy for clarifying the role of Fn infection in CRC progression. Our data shows that: (1) infection alters metabolic and functional pathways in Fn, allowing the bacterium to adapt to the host-imposed milieu; (2) infection also stimulates the expression of genes required to help induce and promote a hypoxic and inflammatory microenvironment in the host; and (3) Fn invasion occurs by a hematogenous route of infection. Our study identifies novel gene targets from Fn that are activated during invasion and which may aid in determining how this species invades and promotes disease within the human gastrointestinal tract. These invasion-specific genes may be useful as biomarkers for colorectal cancer progression in a host and could also assist in the development of new diagnostic tools and treatments (such as vaccines or small molecule drug targets), which will be able to combat infection and inflammation in the host while circumventing the potential problem of Fn tolerisation.

overall_design: Examination of changes in the Fusobacterial genome when exposed to host cells and their corresponding factors.


title: Detection of tetraploidization in chromophobe renal cell carcinoma: insights and pitfalls [Agilent CGH]

city: NICE

first: Thibault

last: FABAS

address: 28 av Valombrose

institute: CHU Nice

summary: Detection of tetraploidization in chromophobe renal cell carcinoma.

overall_design: Sample was analysed by arrayCGH method using Agilent recommendations. Sample was labeled in Cy5 and co-hybridized with control DNA cy3 labeled.

first: Ilaria

middle: D

last: MAURO

first: Damien

last: AMBROSETTI

first: Louis

last: VIGNOT

first: Jean-François

last: ROUSSEL

first: Bérengère

last: DADONE-MONTAUDIE

first: Annie-Claude

last: PEYRON

first: Hervé

last: QUINTENS

first: Matthieu

last: DURAND

first: Jean

last: AMIEL

first: Florence

last: PEDEUTOUR


title: TNF-induced Inflammatory Genes Escape Repression in Fibroblast-like Synoviocytes: Transcriptomic and Epigenomic Analysis [ATAC-seq]

status: Public on Apr 29 2019

city: New York

first: Christopher

last: Loh

state: NY

address: 515 E 71st ST

department: Research

institute: Hospital for Special Surgery

summary: Investigated genome-wide changes in gene-expression and chromatin remodeling induced by tumour necrosis factor (TNF) in fibroblast-like synovioctyes (FLS) and macrophages to understand the contribution of FLS to the pathogenesis of rheumatoid arthritis (RA).

overall_design: Analysis of transcriptional changes in human RA fibroblast-like synoviocytes (FLS) and macrophages stimulated with or without TNF and I-BET

first: Sungho

last: Park


title: TNF-induced Inflammatory Genes Escape Repression in Fibroblast-like Synoviocytes: Transcriptomic and Epigenomic Analysis

overall_design: Refer to individual Series


title: TNF-induced Inflammatory Genes Escape Repression in Fibroblast-like Synoviocytes: Transcriptomic and Epigenomic Analysis [ChIP-seq]


title: TNF-induced Inflammatory Genes Escape Repression in Fibroblast-like Synoviocytes: Transcriptomic and Epigenomic Analysis [RNA-seq]


title: Resolving the 3D landscape of transcription-linked mammalian chromatin folding

first: Xavier

last: Darzacq

address: 475D Li Ka Shing Center

department: Molecular and Cell Biology

institute: University of California, Berkeley

summary: Whereas folding of mammalian genomes at the large scale of epigenomic compartments and topologically associating domains (TADs) is now relatively well-understood, how chromatin is folded below this scale remains largely unexplored in mammals. Here, we overcome this limitation using a high-resolution 3C-based method, Micro-C, and probe the links between 3D-genome organization and transcriptional regulation in mouse stem cells. Combinatorial binding of transcription factors, cofactors, and chromatin modifiers spatially segregate TAD regions into various finer-scale structures with distinct regulatory features (i.e. stripes, dots, and domains linking promoter-promoter (P-P) or enhancer-promoter (E-P), and bundle contacts between Polycomb regions). E-P stripes extending from the edge of domains predominantly link co-expressed loci, often independently of CTCF and cohesin occupancy. Acute inhibition of transcription disrupts the gene-related folding features without altering higher-order chromatin structures. Analysis of ligation events sheds light on both the putative loop extrusion model and the “two-start” zig-zag 30-nanometer model of the chromatin fiber. Our work uncovers the finer-scale genome organization that establishes novel functional links between chromatin folding and gene regulation.

overall_design: We generated 38 replicates of Micro-C in wildtype mouse embryonic stem cells and 3 replicates with RNA polymerase II inhibition. We merged WT data into two different levels of sequencing coverage with 1.3B and 2.6B reads. The Micro-C contact information was then converted to the formats for HiGlass (.mcool) or Juicer browse (.hic). Notes that some replicates are in low read depth or low quality due to the process of optimizing protocol. We also generated ChIP-seq data of Pol II upon transcription inhibition (2 replicates for each).

first: Tsung-Han

middle: S

last: Hsieh

first: Claudia

last: Cattoglio

first: Robert

last: Tjian


title: Investigating Proteome and Transcriptome Defense Response of Pears Induced by Wickerhamomyces anomalus

status: Public on Apr 25 2019

city: Zhenjiang

first: Qiru

last: Zhang

address: Xiangshan street

institute: Jiangsu University

summary: We report the application of next-generation sequencing technology for analyzing the differentially expressed genes of pears after treated with or without W. anomalus. After analyzing the differentially expressed genes, we selected some important genes related to the resistance of pears to do RT-qPCR.

overall_design: Examination of differentially expressed genes related to the resistance of 2 types of pear tissues which treated with or without W. anomalus. RT-qPCR was performed using SYBR Green assays.

first: Hongyin


title: High-Throughput Sequencing of microRNAs and Alternative Cleavage and Polyadenylation Reveal the Mechanism of Post-Transcription Regulations in Colorectal Cancer Patients

city: Minhang district of Shanghai

first: yani

last: Kang

address: Dongchuan Road 800

institute: Shanghai Jiaotong University

summary: Few studies have reported that the mutual regulation of miRNAs and alternative cleavage and polyadenylation in CRC. Our study helps to understand the cellular regulation in CRC from the perspective of post-transcriptional level.

overall_design: In this study, we applied small RNA sequencing and 3T sequencing in cancer tissue and paired normal tissue of CRC patients.

first: Zhanrui

last: Mao

first: Yani


title: Single-cell RNA sequencing on breast cancer cells enriched for cancer stem cell properties using functional assays

status: Public on Apr 23 2019

city: Göteborg

first: Emma

last: Jonasson

address: Medicinaregatan 1F, floor 5

department: Sahlgrenska Center for Cancer Research

country: Sweden

institute: University of Gothenburg

summary: We used mammosphere formation assay and label-retention assay as functional cellular approaches to enrich for cells with different degree of cancer stem cell properties in the breast cancer cell line MDA-MB-231 and performed single-cell RNA sequencing

overall_design: Single cells from three different populations: 30 cells from G1 cell cycle phase cultured in adherent conditions, 46 cells with low proliferation cultured in non-adherent conditions (mammosphere assasy), 45 cells with high proliferation cultured in non-adherent conditions (mammosphere assay)

first: Anders

last: Ståhlberg


title: Association of cord blood methylation with neonatal leptin: an epigenome wide association study

status: Public on Apr 16 2019

first: Yinan

last: Zheng

address: 680 N Lake Shore Drive, Suite 1400

department: Department of Preventive Medicine

institute: Northwestern University

type: Methylation profiling by genome tiling array

summary: This is a study of 114 newborns aimed at identifying associations of cord blood methylation profiles with measures of newborn adiposity. Neonatal adiposity is a risk factor for childhood obesity. Investigating contributors to neonata adiposity is important for understanding early life obesity risk. Epigenetic changes of metabolic genes in cord blood may contribute to excessive neonatal adiposity and subsequent childhood obesity. This study aims to evaluate the association of cord blood DNA methylation patterns with markers of neonatal adiposity

overall_design:
A cross-sectional study was performed on a multiethnic cohort of 114 full
term neonates born to mothers without gestational diabetes at a university hospital. Cord blood was assayed for leptin and for epigenome-wide DNA methylation profiles via the Illumina 450K platform. Neonatal body composition was measured by air displacement plethysmography. Multivariate linear regression was used to analyze associations between individual CpG sites as well as differentially methylated regions in cord blood DNA and measures of neonatal adiposity. False discovery rate was estimated to account for multiple comparisons.

first: Rachel

last: Kadakia

first: Zhou

first: Wei

first: Lifang

last: Hou

first: Jami

last: Josefson


title: The impact of hnRNP-A2B1 on mRNA transport after DNA virus infection

status: Public on Apr 17 2019

city: Tianjin

first: Wang

last: Lei

address: Weijin Road 94

institute: Nankai University

summary: To obtain a wholistic view of hnRNP-A2B1’s role in mRNA transport in response to DNA virus infection, we profiled RNAs from nuclear and cytoplasmic fractions in both wild-type and Hnrnpa2b1–/– macrophages after Herpes simplex virus 1 (HSV-1) infection.

overall_design: Wild-type and Hnrnpa2b1–/– peritoneal macrophages were infected with HSV-1. RNAs from the nuclear fraction and the cytoplasmic fraction from both kinds of cells were isolated and subjected to array analysis.

first: Lei

last: Wang

first: Mingyue

last: Wen

first: Xuetao

last: Cao


title: Dynamic changes in chromatin accessibility and nucleosome positioning in the control of antigen receptor rearrangement

status: Public on Jun 05 2019

city: Boston

first: Mattia

last: Lion

state: MA

address: Simches Research Center 185 Cambridge Street, CPZN7250

department: Department of Molecular Biology

institute: Massachusetts General Hospital

summary:
Developing lymphocytes diversify their antigen receptor (AgR) loci by V(D)J recombination. Here, we use a low-input version of the MACC (MNase Accessibility) assay to define the chromatin accessibility landscape of primary cells during lymphoid development tracking the changes as different AgR loci become primed for recombination.
Distinct chromatin structures define unique features of IgH, Igk and TCRα loci. In particular, we find locus-specific temporal changes in accessibility both across megabase-long AgR loci and locally at the recombination signal sequences (RSSs). These changes appear to be regulated independently. We further identify local dynamic rearrangements of individual nucleosomes at RSSs during B-cell commitment.
As predicted by the original “accessibility” hypothesis, these changes correlate with AgR lymphoid lineage and developmental-stage specificity. We suggest that local and global changes in chromatin openness, in concert with nucleosome occupancy and histone modifications, represent additional regulatory layers for governing the temporal order of AgR recombination.

overall_design: MNase-seq profiles of hematopoietic stem cells (HSCs); lymphoid-primed multipotent progenitors (LMPPs); common lymphoid “A” type precursors (ALPs or CLPs); B cell–biased lymphoid progenitors (BLPs); B-cell progenitors (pro-B); large B-cell precursors (Lpre-B); and small B-cell precursors (small pre-B). Lung epithelium cells (LungEp) were used as nonlymphoid and recombinationally inactive cells. Wild-type C57BL/6N mice (4-6 weeks old) were used to isolate the above cell populations.

first: Brejnev

last: Muhire


title: Impact of Dnm3os silencing on bleomycin-induced lung fibrosis

status: Public on Apr 11 2019

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

institute: IPMC/CNRS

summary: To assess the impact of Dnm3os silencing on lung fibrogenesis, anti-Dnm3os gapmers (5mg/kg, 2 distinct designs: GP DNM3OS-1 and GP DNM3OS-3) or control gapmer (5mg/kg, GP Ctrl) formulated for in vivo delivery was instilled intratracheally 4 days and 2 days before intratracheal administration of bleomycin (1 unit/kg) or PBS as well as 4 days after bleomycin or PBS treatment.

overall_design: Experiments were performed in a one color design, corresponding to 6 conditions (GP Ctrl + PBS n = 3, GP DNM3OS-1 + PBS n = 3, GP DNM3OS-3 + PBS n = 3, GP Ctrl + Bleo n = 5, GP DNM3OS-1 + Bleo n = 5, GP DNM3OS-3 + Bleo n = 5) for a total of 24 samples.

first: G

last: Savary

first: N

last: Nottet

last: Pottier

first: B

last: Mari

first: P

last: Barbry

first: K


title: MAIT cell RNA sequencing

city: Dublin

first: Andrew

last: Hogan

address: OLCH Crumlin

institute: National Children's Research Centre

summary:
Obesity underpins the development of numerous chronic diseases such as type II diabetes mellitus. It is well established that obesity negatively alters immune cell frequencies and functions. Mucosal Associated Invariant T (MAIT) cells are a population of innate T cells, which we have previously reported are dysregulated in obesity, with altered circulating and adipose tissue frequencies and a reduction in their IFN-gamma production, which is a critical effector function of MAIT cells in host defence. Hence there is increased urgency to characterise the key molecular mechanisms that drive MAIT cell effector functions, and to identify those which are impaired in the obesity setting. In this study, we found that MAIT cells significantly upregulate their rates of glycolysis upon activation in an mTORC1 dependent manner and this is essential for MAIT cell IFN-g production. Furthermore, we show that mTORC1 activation is dependent on amino acid transport via SLC7A5. In obese patients, using RNA sequencing, Seahorse analysis and a series of in vitro experiments, we demonstrate that MAIT cells isolated from obese adults display defective glycolytic metabolism, mTORC1 signalling and SLC7A5 amino acid transport. Collectively our data details the intrinsic metabolic pathways controlling MAIT cell cytokine production and highlights mTORC1 as an important metabolic regulator that is impaired in obesity, leading to altered MAIT cell responses.
We report on MAIT cells isolated from lean and obese adults

overall_design: MAIT cells from 5 healthy bodyweight donors and 4 morbidly obese donors


title: RNA-Seq analysis of human lung fibroblasts exposed to TGF-β

summary: To assess the transcriptomic response of human lung fibroblast to TGF-β, human MRC5 pulmonary fibroblasts (CCL-171) were exposed or not to TGF-β at 10 ng/mL. RNA samples were harvested 24 hours after TGF-β exposition. Three independent experiments were carried out.

overall_design: 6 samples in triplicates: control versus TGF-β.


title: Human pluripotent stem cell-derived 2D neural tissue samples for predictive neurotoxicity screening

status: Public on May 06 2019

city: Madison

first: Finn

last: Kuusisto

state: WI

address: 1205 University Ave

institute: University of Wisconsin-Madison

summary: There is a growing need for fast and accurate methods for testing developmental neurotoxicity across industrial, pharmaceutical, and environmental chemical exposures. Current approaches, such as in vivo animal studies, and assays of animal and human primary cell cultures, suffer from challenges related to time, cost, and applicability to human physiology. Prior research demonstrated success employing machine learning to predict developmental neurotoxicity using gene expression data collected from complex human 3D tissue models exposed to various compounds, but the complexity of 3D tissue models require extensive expertise and effort to employ. While a 3D tissue model is more physiologically accurate, by focusing only on the goal of constructing an assay of developmental neurotoxicity, we propose that a simpler 2D tissue model may prove sufficient. We thus compared the accuracy of predictive models trained on data from a 2D tissue model with those trained on prior dataset from a more complex 3D tissue model, and found the accuracy of the 2D model to be substantially better than the 3D model. Furthermore, we found that the 2D tissue model is more robust and consistent under stringent gene set selection, whereas the 3D tissue model suffers substantial degradation of accuracy. While both approaches have advantages and disadvantages, we propose that our described 2D tissue model has the potential to serve as a valuable tool for decision makers when prioritizing neurotoxicity screening.

overall_design: H1-NPC cells were thawed and expanded in DF3S+N2B27+5ng/ml FGF2 for 5 days before they were harvested by Accutase treatment. Roughly 1x10e5 cells were then seeded into one well of a 48 well plate in DF3S+N2B27. Chemical treatment started on the same day (day 0). Samples are collected at indicated time points by lysing cells directly on plate with 150ul RLT buffer. Chemical information can be found a separate sheet.

first: Vitor

last: Santos Costa

first: Zhongang

first: James

last: Thomson

first: David

last: Page

first: Ron

last: Stewart


title: TGF-β signature of MRC-5 fibroblasts

summary: Human MRC5 pulmonary fibroblasts (CCL-171) were exposed or not to TGF-β at 10 ng/mL. RNA samples were harvested 24 hours after TGF-β exposition. Two independent experiments were carried out.

overall_design: 4 samples in duplicates: control versus TGF-β.


title: Small RNA-Seq analysis of human lung fibroblasts exposed to TGF-β

summary: To assess the transcriptomic response of human lung fibroblast to TGF-β, human MRC5 pulmonary fibroblasts (CCL-171) were exposed to TGF-β at 10 ng/mL. RNA samples were harvested 24 hours after TGF-β exposition. Three independent experiments were carried out.


title: Single Cell RNA Sequencing Analysis of Polystyrene Microplastic Exposed and control Zebrafish Intestine

status: Public on Oct 01 2019

city: Nanjing

first: Gu

last: Weiqing

address: Xianlin

institute: Nanjing University

summary: Microplastics (MPs) as widespread contamination pose high risk for aquatic organisms. However, current understanding of MP toxicities are based on cell population-averaged measurements. Here we used single-cell RNA sequencing to provide the transcriptome heterogeneity of 12000 intestinal cells obtained from zebrafishes exposed to 100nm, 5μm and 200μm polystyrene MPs (PS-MPs) for 21 days. Eight intestinal cell populations were identified. We found that all the three sizes of PS-MPs induced dysfunction of intestinal immune cells (including phagosome and regulation of immune system process).

first: Bing

last: Wu

first: Weiqing

last: Gu


title: Real-time quantitative PCR analysis of monocytes of major depressed patients [Imipramine study]

status: Public on Jun 07 2019

city: Rotterdam

first: Hemmo

last: Drexhage

address: Dr Molewaterplein 40

institute: ErasmusMC

summary: Human CD14 positive monocytes were purified from major depressed patients or healthy volunteer frozen PBMC. Patients were treated with imipramin. Responders and non-responders to imipramin were recorded after 6 weeks of treatment

overall_design: qPCR gene expression profiling.  Monocytes prior to treatment were used for qPCR analysis. Details of patient selection, monocyte preparation, recording of patient data can be found in Gara Arteaga Henríquez et al, Frontiers of Psychiatry, 2019

first: J

last: Wijkhuijs

first: H


title: Impact of miR-199-5p, miR-199a-3p and miR-214-3p overexpression on human lung fibroblasts

first: Kevin

last: Lebrigand

summary: To identify putative novel specific targets of miR-199-5p, miR-199a-3p and miR-214-3p, we overexpressed these miRNAs in human MRC5 pulmonary fibroblasts (CCL-171) using synthetic pre-miRNAs or a synthetic “negative” pre-miRNA control (miR-Neg). RNA samples were harvested 48 hours post-transfection and 3 independent experiments were carried out.

overall_design: 3 independent experiments performed in a one color design, corresponding to 4 conditions (miR-Neg, miR-199-5p, miR-199a-3p, and miR-214-3p) for a total of 12 samples.

first: G

first: N


title: Impact of DNM3OS silencing on human lung fibroblast response to TGF-β

summary: To assess the role of the lncRNA DNM3OS in TGF-β-induced lung fibroblast activation, we transfected in human MRC5 pulmonary fibroblasts (CCL-171) a gapmer designed against DNM3OS for 48h and then exposed these cells to TGF- β (10 ng/mL). RNA samples were harvested 24 hours after TGF-β exposition. Two independent experiments were carried out.

overall_design: 2 independent experiments performed in a one color design, corresponding to 4 conditions (gapmer control, gapmer anti-DNM3OS, gapmer control + TGF-β, gapmer anti-DNM3OS + TGF-β) for a total of 8 samples.

last: Savary

first: B

first: P

first: K


title: Impact of CAV1 target site blocker (CAV1 TSB) on bleomycin-induced lung fibrosis

summary: To assess whether CAV1 represents the main target associated with miR-199a-5p profibrotic activity, we designed a CAV1 target site blocker (TBS) to specifically disrupt miR-199a-5p interaction with mCAV1 3’UTR. CAV1 TSB (5mg/kg) or control formulated for in vivo delivery (Control TSB) was instilled intratracheally 4 days and 2 days before intratracheal administration of bleomycin (1 unit/kg) or PBS as well as 4 days after bleomycin or PBS treatment.

overall_design: Experiments were performed in a one color design, corresponding to 4 conditions (Control TSB + PBS n = 2, CAV1 TSB + PBS n = 2, Control TSB + bleomycin n = 6, CAV1 TSB + bleomycin n = 6) for a total of 16 samples.

last: Nottet


title: Impact of miR-199a-5p silencing on bleomycin-induced lung fibrosis

summary: To assess the impact of miR-199a-5p silencing on lung fibrogenesis, LNA-miR-199a-5p (5mg/kg) or control formulated for in vivo delivery was instilled intratracheally 4 days and 2 days before intratracheal administration of bleomycin (1 unit/kg) or PBS as well as 4 days after bleomycin or PBS treatment.

overall_design: Experiments were performed in a one color design, corresponding to 4 conditions (LNA-control + PBS n = 3, LNA-miR-199a-5p + PBS n = 3, LNA-control + Bleomycin n = 5, LNA-miR-199a-5p + bleomycin n = 5) for a total of 16 samples.

last: Pottier


title: The emergent landscape of the mouse gut endoderm at single-cell resolution

status: Public on Apr 10 2019

city: Seattle

first: Manu

last: Setty

state: WA

address: 1100 Fairview Ave N

department: Basic Sciences Division

institute: Fred Hutchinson Cancer Center

summary: To comprehensively delineate the ontogeny of an organ system, we generated 112,217 single- cell transcriptomes representing all endoderm populations within the mouse embryo until midgestation. We employed graph-based approaches to model differentiating cells for spatio- temporal characterization of developmental trajectories. Our analysis reveals the detailed architecture of the emergence of the first (primitive or extra-embryonic) endodermal population and pluripotent epiblast. We uncover an unappreciated relationship between descendants of these lineages, before the onset of gastrulation, suggesting that mixing of extra-embryonic and embryonic endoderm cells occurs more than once during mammalian development. We map the trajectories of endoderm cells as they acquire embryonic versus extra-embryonic fates, and their spatial convergence within the gut endoderm; revealing them to be globally similar but retaining aspects of their lineage history. We observe the regionalized localization of cells along the forming gut tube, reflecting their extra-embryonic or embryonic origin, and their coordinate patterning into organ-specific territories along the anterior-posterior axis.

overall_design: Cells were isolated from sequentially-staged wild-type mouse embryos between E3.5 and E8.75. Whole embryos were used for single-cell isolations for stages E3.5-E5.5. Endodermal tissue layers were isolated from E6.5-E8.75 stages. Gut tube of E8.75 were sorted based on GFP expression and another dataset was generated using anterior - posterior positioning. Each sample was measured in replicate with E5.5 and E7.5 measured in triplicates.

first: Sonja

last: Nowotschin

first: Ying-Yi

last: Kuo

first: Vincent

last: Lui

first: Vidur

last: Garg

first: Roshan

last: Sharma

first: Claire

last: Simon

first: Nestor

last: Saiz

first: Rui

last: Gardner

first: Stephane

last: Boutet

first: Deanna

last: Church

first: Pamela

last: Hoodless

first: Anna-Katerina

last: Hadjantonakis

first: Dana

last: Pe'er


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

overall_design: Refer to individual Series


title: Comprehensive genomic profiling of matched glioblastoma tumors, cell-lines and xenografts reveals genomic stability and adaptation to disparate growth environments

status: Public on Mar 22 2019

city: Vancouver

first: Michael

middle: S.

last: Kobor

state: BC

address: 950 West 28th Avenue

department: Medical Genetics

institute: Centre for Molecular Medicine and Therapeutics / University of British Columbia

summary: Glioblastoma Multiforme (GBM) is the most deadly brain tumor, and currently lacks effective treatment options. Brain tumor initiating cells (BTICs) and orthotopic xenografts are widely used in investigating GBM biology and new therapies for this aggressive disease. However, the genomic characteristics and molecular resemblance of these models to GBM tumors remain undetermined. We used massively parallel sequencing technology to decode the genomes and transcriptomes of BTICs and xenografts and their matched tumors in order to delineate the potential impacts of the distinct growth environments. Using data generated from whole‐genome sequencing of 201 samples and RNA sequencing of 118 samples, we showed that typical GBM genomic driver alterations found in the tumors were retained in BTICs and xenografts. In contrast, gene expression and methylation profiles indicated higher levels of divergence, likely due to the different growth environment for each sample type. These findings suggest that a comprehensive genomic understanding of in vitro and in vivo GBM model systems is crucial for interpreting data from  drug‐screens, and can help control for biases introduced by cell culture conditions and the microenvironment in mouse models.

overall_design: The Illumina Infinium HumanMethylation450 Beadchip was used to obtain genome-wide DNA methylation from 31 matched parent tumor‐BTIC pairs and 4 matched trios of tumor-BTIC-‐xenograft.

first: Yaoqing

last: Shen

first: Cameron

middle: J

last: Grisdale

first: Sumaiya

last: Islam

first: Pinaki

last: Bose

first: Jake

last: Lever

first: Eric

middle: Y

last: Zhao

first: Natalie

last: Grinshtein

first: Yussanne

last: Ma

first: Andrew

last: Mungall

first: Richard

last: Moore

first: Xueqing

last: Lun

first: Donna

last: Senger

first: Stephen

last: Robbins

first: Alice

last: Wang

first: Julia

last: MacIsaac

first: H

last: Luchman

first: Samuel

last: Weiss

first: Jennifer

last: Chan

last: Blough

first: David

last: Kaplan

first: J

last: Cairncross

first: Marco

last: Marra

first: Steven

last: Jones


title: The DNM3OS lncRNA is a reservoir of fibromiRs with major functions in fibroblast response to TGF-beta and fibrogenesis

first: Kevin

last: Lebrigand

summary:
RATIONALE:
Given the paucity of effective treatments for Idiopathic Pulmonary Fibrosis (IPF), new insights into the deleterious mechanisms controlling lung fibroblast activation, the key cell type driving the fibrogenic process, are essential to develop new therapeutic strategies. Transforming growth factor β (TGF-β) is the main pro-fibrotic factor, but its inhibition is associated with severe side effects due to its pleiotropic role.
OBJECTIVES:
We hypothesized that downstream non-coding effectors of TGF-β in fibroblasts may represent new effective therapeutic targets whose modulation may be well-tolerated.
METHODS:
We investigated the whole non-coding fraction of TGF-β-stimulated lung fibroblast transcriptome to identify new genomic determinants of lung fibroblast differentiation into myofibroblast. Differential expression of the long non-coding RNA DNM3OS and its associated miRNAs was validated in a murine model of pulmonary fibrosis and in IPF tissue samples. Distinct and complementary antisense oligonucleotide-based strategies aiming at interfering with DNM3OS were used to elucidate the role of DNM3OS and its associated miRNAs in IPF pathogenesis.
MEASUREMENTS AND MAIN RESULTS:
We identified DNM3OS as a fibroblast-specific critical downstream effector of TGF-β-induced lung myofibroblast activation. Mechanistically, DNM3OS regulates this process in trans by giving rise to three distinct profibrotic mature miRNAs (i.e. miR-199a-5p/3p and miR-214-3p), which influence both SMAD and non-SMAD components of TGF-β signaling in a multifaceted way. In vivo, we showed that interfering with DNM3OS function not only prevents lung fibrosis but also improves established pulmonary fibrosis.
CONCLUSION:
Pharmacological approaches aiming at interfering with DNM3OS may represent new effective therapeutic strategies in IPF.

This SuperSeries is composed of the SubSeries listed below.

first: G

last: Savary

first: N

last: Nottet

last: Pottier

first: B

last: Mari

first: P

last: Barbry

first: K


title: Tristetraprolin specifically regulates the expression and alternative splicing of immune response genes in Hela cells

status: Public on Mar 24 2019

city: Wuhan

first: Dong

last: Chen

state: Hubei

address: 388 GaoXin 2nd Road, East Lake Hi-Tech Development Zone

department: Center for Genome Analysis

institute: ABLife, Inc.

summary: we cloned and overexpressed human TTP-encoding gene ZFP36 in HeLa cell in the absence of inflammatory stimuli. The transcriptomes of the control and ZFP36-overexpression cells were sequenced and subjected to analysis and validation. Upon ZFP36 overexpression, expression of genes in innate immunity, including those in type I interferon signaling pathway and viral response, were specifically up-regulated, implying a transcriptional regulatory mechanism associated with the predicted DNA binding activity of TTP. TTP preferentially regulates the alternative splicing of genes involved in positive regulation of I-B/NF-B cascade and TRIF-dependent toll-like receptor signaling pathway, MAPK signaling pathway, TNF signaling pathway and T cell receptor signaling pathways.Our study indicates that TTP may regulates immune response via alternative splicing regulation and possibly by transcriptional regulation as well, which greatly expands the current understanding of the central role of TTP in regulating immune response and tumorigenesis.

overall_design: Tristetraprolin TTP plays a fundamental role in tumorigenesis and immunity by destabilizing target mRNAs via binding to their 3’-UTR AREs. A recent CLIP-seq study reveals that TTP binding to intronic RNA regions is enriched. TTP is also a nuclear located protein and convey putative DNA binding activity. However, it is unclear yet whether the nuclear-located TTP in the absence of stimulation regulates any gene transcription or alternative splicing of pre-mRNAs.To address these two related questions, we cloned and overexpressed human TTP-encoding gene ZFP36 in HeLa cell in the absence of inflammatory stimuli.

first: Yafang

last: Tu


title: Expression profiles of long non-coding RNAs and messenger RNAs in laser-induced choroidal neovascularization in mice.

status: Public on Apr 13 2019

city: Changsha

first: Yedi

last: Zhou

state: Hunan

address: No. 139, Middle Renmin Road

department: Department of Ophthalmology

institute: The Second Xiangya Hospital, Central South University

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

summary: Choroidal neovascularization (CNV) is a severe complication of the late-stage form of wet age-related macular degeneration. In order to identify lncRNAs and coding genes involved in the pathogenesis of CNV, we performed microarray analysis to identify expression profiles of lncRNAs and mRNAs in laser-induced CNV samples and controls in mice.

overall_design: Arraystar Mouse LncRNA Microarray V3.0 was used to identify differentially expressed lncRNAs and mRNAs in 3 RPE-choroid-sclera complexes samples of CNV (day 7) mice and 3 RPE-choroid-sclera complexes samples of control mice.

first: Liwei

last: Zhang


title: Xenotransplantation of Human PSC-derived Microglia Creates a Chimeric Mouse Brain Model that Recapitulates Features of Adult Human Microglia

status: Public on Apr 02 2019

city: Piscataway

first: Ronald

middle: P.

last: Hart

state: NJ

address: 604 Allison Rd Rm B430

department: Cell Biology & Neuroscience

institute: Rutgers University

summary: Microglia, the brain-resident macrophages, exhibit highly dynamic functions in neurodevelopment and neurodegeneration. Human microglia possess unique features as compared to mouse microglia, but our understanding of human microglial functions is largely limited by an inability to obtain human microglia under resting, homeostatic states. We developed a human pluripotent stem cell (hPSC)-based microglial chimeric mouse brain model by transplanting hPSC-derived primitive macrophage precursors into neonatal mouse brains. The engrafted human microglia widely disperse in the brain and replace mouse microglia in corpus callosum at 6 months post-transplantation. Single-cell RNA-sequencing of the hPSC microglial chimeric mouse brains reveals that xenografted hPSC-derived microglia largely retain human microglial identity, as they exhibit signature gene expression patterns consistent with physiological human microglia and recapitulate heterogeneity of adult human microglia. Importantly, the chimeric mouse brain also models species-specific transcriptomic differences in the expression of neurological disease-risk genes in microglia. This model will serve as a novel tool to study the role of human microglia in brain development and degeneration.

overall_design: Single-cell RNA sequencing was performed using 10X Genomics Chromium equipment and kits to assess human iPSC-derived microglia transplanted into postnatal day 0 immunocompromised mice.  Forebrain samples were collected from four different transplanted animals at 6 months after transplant.  Cells were dissociated and processed for sequencing.

first: Ranjie

last: Xu

first: Andrew

last: Boreland

first: Anthony

last: Posyton

first: Kelvin

last: Kwan

middle: P

first: Peng

last: Jiang


title: CDKN2A-specific probe captured RNA-sequencing (RNACap-Seq) (HEK293T MCF7)

status: Public on Mar 13 2019

city: beijing

first: wanru

last: ma

address: 52 Fucheng Road,Haidian District,Beijing

institute: beijing cancer hospital

summary: The CDKN2A/B locus at 9p21.3 contains crucial tumor suppressors (P16, P14, and P15) and oncogenic lncRNA ANRIL genes. This locus is most frequently inactivated in cancer genomes by deletion and DNA methylation. However, the mechanisms coordinately regulating their expression level are far from clear. In the present study, a novel lncRNA, P14AS, was characterized in the antisense strand of the fragment near CDKN2A in human cell lines using CDKN2A-specific probe captured RNA-sequencing (RNACap-Seq).

overall_design: RNAs were characterized in the antisense strand of the fragment near CDKN2A in human cell lines using CDKN2A-specific probe captured RNA-sequencing (RNACap-Seq).

first: Wanru

last: Ma

first: Juanli

last: Qiao


title: Tissue specific innate lymphoid cells promote checkpoint blockade PD-1 immunotherapy in pancreatic cancer

status: Public on Apr 06 2019

city: New York

first: John Alec

middle: Gaite

last: Moral

address: 408 East 69th Street, Room Z-445G

department: Hepatopancreatobiliary Surgery

institute: Memorial Sloan Kettering Cancer Center

summary: Transcriptomic profiling of the tumor microenvironment was performed by RNA Seq of bulk tumor and tumor-infiltrating lymphocytes isolated by magnetically-activated cell sorting.

overall_design: Sorted tumor infiltrating leukoctyes and bulk tumor. Wild type and IL33-/-.

first: John

middle: A

first: Vinod

last: Balachandran


title: Comparative RNA-seq analysis of the transcriptome of the Pseudomonas aeruginosa PAO1 wild-type strain with that of the ΔvreR mutant

city: Granada

first: Maria

middle: A.

last: Llamas

state: Andalusia/Granada

address: Profesor Albareda, 1. E-18008.

department: Environmental Protection. Environmental Microbiology and Biodegradation

country: Spain

institute: Estación Experimental del Zaidín (CSIC)

summary: Bacterial gene expression is controlled by modifying the promoter affinity of the RNA polymerase (RNAP). This control occurs through the substitution of the RNAP σ subunit and by the interaction with transcription factors. The pathogen Pseudomonas aeruginosa contains several σ factors, including σVreI. This protein belongs to the extracytoplasmic function group of the σ70 family. Expression and activity of σECFs are tightly regulated and only occur in response to specific signals. σVreI is encoded within the vreAIR gene cluster. The expression of this cluster occurs in response to inorganic phosphate (Pi) limitation. σVreI activity is modulated by VreR anti-sigma factor, which keeps σVreI inactive. In response to a still unidentified host signal, VreR is proteolytically degraded and σVreI released and activated. σVreI interacts then with the RNAP and targets expression of the σVreI regulon, which includes virulence genes that increase P. aeruginosa pathogenicity. In this work, we compared the transcriptome of the P. aeruginosa PAO1 wild-type strain with that of the ΔvreR mutant upon bacterial growth in Pi starvation. Forty-six transcripts were more abundant in the ΔvreR mutant than in the PAO1 wild-type strain, and nine were less abundant, including the vreR transcript.

overall_design: P. aeruginosa PAO1 and ΔvreR mutant were grown until late exponential phase in low Pi medium and total RNA was isolated. A mixture of the three isolations was used for RNA-seq analyses.

first: Jose

middle: M

last: Quesada

first: María


title: Genomewide Localization of Yeast CENP-A (Cse4) in Wild-type, met30-6, and cdc4-1 Strains

status: Public on Apr 03 2019

city: Worcester

first: Richard

middle: E

last: Baker

address: 55 Lake Avenue North

department: Microbiology & Physiological Systems

institute: University of Massachusetts Medical School

summary: The evolutionarily conserved F-box proteins Met30 and Cdc4 interact with Cse4 in vivo and cooperatively regulate cellular levels of Cse4 by ubiquitin-mediated proteolysis. To survey genomewide localization of Cse4 in met30-6 and cdc4-1 mutants, chromatin immunoprecipitation (ChIP) was carried out in strains expressing HA-tagged Cse4 from its endogenous promoter. Prominent Cse4 peaks were observed only at centromeres (CENs) in all three strains, and a statistically significant increase of Cse4 enrichment at CENs was observed in the mutants. Though extracentromeric peaks of Cse4 accumulation are detected in both wild-type and mutant strains, peak enrichment (vs. the 10-kb local background) in these regions is much lower than that observed for any of the 16 centromeres, and there is no statistically significant difference in Cse4 enrichment at non-CEN peaks between wild-type and mutants. This analysis reveals that the increased mislocalization of Cse4 in met30-6 and cdc4-1 strains detected by Cse4 staining on chromosome spreads is not the result of high levels of enrichment at discrete extracentromeric loci; rather, endogenously expressed Cse4 in met30-6 and cdc4-1 strains accumulates at low levels across the genome.

overall_design: Cse4 ChIP-seq was carried out in wild-type, met30-6, and cdc4-1 yeast strains. Replicate samples of input and immunoprecipitated DNA were analyzed. Untagged control strains were included as additional controls.

first: Wei-Chun

last: Au

first: Tianyi

first: Prashant

middle: K

last: Mishra

first: Robert

last: Walker

first: Paul

last: Meltzer

first: Munira

last: Basrai


title: Gene expression changes in HT-22 cells with or without PGC-1α overexpression upon OGD stimulation

status: Public on Mar 05 2019

first: Bin

last: Han

address: 154 Anshan Road, Heping District

institute: Tianjin Medical University General Hospital

summary: PGC-1α overexpression in neurons protects against chronic cerebral hypoperfusion-induced cognitive impairment in mice. To investigate the neuroprotective mechanism of PGC-1α, we employed RNA-Seq analysis on PGC-1α-overexpressed HT-22 cells, a hippocampal neuron cell line. We performed OGD experiment to mimick chronic cerebral hypoperfusion. Indeed, PGC-1α overexpression alters the gene expression profiles of HT-22 cells, suggesting that neuronal PGC-1α might play an important role after chronic cerebral hypoperfusion.

overall_design: PGC-1α-overexpressed HT-22 cells and control were subjected to the hypoxia incubator chamber (5% CO2 and 95% N2) and exposed to oxygen and glucose deprivation (OGD) treatment for 2 h in EMEM medium without serum/glucose. After that, HT-22 cells were cultured in normal medium at 37°C for 24 h. Then the samples were processed to perform RNA-Seq analysis.

first: Junwei

last: Hao


title: Identification of putative biomarkers for Infantile Hemangiomas and Propanolol treatment via data integration

status: Public on Mar 01 2019

city: Little Rock

first: Horacio

last: Gomez-Acevedo

state: Arkansas

address: 4301 W. Markham St

department: Biomedical Informatics

institute: University of Arkansas for Medical Sciences

summary:
Infantile hemangiomas are the most common type of benigh tumors in early childhood, and propanolol is a standard treatment with yet unknown mechanism of action.
In this study, we identify putative biomarkers for infantile hemangioma stages (proliferative and involution) in the context of propanolol treatment.

overall_design: Tissue was collected from children with hemangiomas. Patient's normal skin from demographically matched children were used as controls.

first: Annjanette

last: Stone

first: Gresham

middle: T

last: Richter


title: Impact of EWS knockdown on LTBR mediated Gene Activation in human fibroblasts

city: La Jolla

last: Virgen-Slane

state: CA

address: 10901 North Torrey Pines Rd

department: Infectious and Inflammatory Diseases Center

institute: Sanford Burnham Prebys Medical Discovery Institute

summary: LTβR signaling is crucial for immune development, homeostasis, and inflammation. To identify protein determinants that control the quality of LTβR function, we use a novel proteomics approach to identify EWS as a novel signaling component of this pathway. LTβR signaling protein, TRAF3, controls the protein binding activity of EWS via formation of mutually exclusive protein-protein interactions. With transcriptomics and knockdown experiments we identify several pro-inflammatory genes with induction kinetics that are controlled by EWS during LTβR signaling. Given the link between gene induction responsiveness and mRNA decay, we show EWS controls the decay of these transcripts.

overall_design: Fibroblasts expressing control or EWS targeting shRNAs were stimulated with agonistic goat anti-human LTBR antibody for 0, 2, or 6 hours. Total RNA harvested and assayed using nCounter Human Inflammation panel V2

first: Carl

middle: F

last: Ware


title: Polyketide synthase function is a determinant of bacterial persistence and antibiotic tolerance in Burkholderia thailandensis

status: Public on Mar 06 2019

city: Los Alamos

first: Migun

last: Shakya

state: NM

address: Bikini atoll road

institute: Los Alamos National Lab

summary: Persister cells are genetically identical variants in a bacterial population that have phenotypically modified their physiology to survive environmental stress. .  To better define general persistence mechanisms that can be targeted to develop anti-persistence therapeutics, we performed transcriptomics analyses of Burkholderia thailandensis enriched for persisters using three methods: flow sorting by low proton motive force, meropenem treatment, and culture aging. Although the three persister populations generally expressed divergent gene expression profiles that underscores the multi-mechanistic nature of persistence, there were several common gene pathways expressed in two or more persister populations, including polyketide and non-ribosomal peptide synthesis,  Clp proteases, mobile elements, enzymes involved in the lipid metabolism, and ATP-binding cassette (ABC) transporter systems. In particular, identification of genes that encode for polyketide synthases (PKS) and fatty acid catabolism indicate that generation of secondary metabolites, natural products, and complex lipids are needed for the maintenance of the persistence state.  Persisters are markedly reduced in transposon mutants of the PKS gene BTH_I2366. Furthermore, treatment of multiple bacterial pathogens with the fatty acid synthesis inhibitor, CP-640186, potentiated antibiotic efficacy against the persisters. All together, our results suggest that bacterial persisters may exhibit an outward dormant physiology, but maintain active metabolic processes that are required to maintain persistence.

overall_design: Comparative analysis of the transcriptome profile of B.thailandensis persister populations isolated from three independent phenotypic screens: low proton motif force, exposure to beta-lactam antibiotic, and 3-week old cultures on solid media

first: Patrick

last: Chain

first: Sofiya

middle: N

last: Micheva-Viteva

first: Elizabeth

last: Hong-Geller


title: ISL1 predicts poor outcomes for patients with gastric cancer and drives tumor progression through binding to the ZEB1 promoter together with SETD7

first: guo

last: ting

address: 52 Fucheng Road, Haidian District

institute: Peking University Cancer Hospital & Institute, Beijing

summary: The goals of this study are to analyze the transcriptome profiling (RNA-seq) after ISL1 overexpression in SGC7901.

overall_design: SGC7901cells were transfected by ISL1 expression lentivirus and blank lentivirus as control.Total RNA was extraced by Qiagen kit and the RNA profiles were generated by deep sequencing, in duplicate, using Illumina Hiseq 2500.

first: Jiafu

last: Ji

first: Ting

last: Guo


title: Immune impact of neoadjuvant chemo/radio-therapy in the pancreatic cancer microenvironment

status: Public on Apr 09 2019

city: Atlanta

first: Gregory

middle: Brian

last: Lesinski

state: GA

address: 1365 Clifton Rd., NE

department: Hematology and Medical Oncology

institute: Emory University

summary: Pancreatic ductal adenocarcinoma (PDAC) has dismal five-year survival (<9%). We examined the impact of neoadjuvant FOLFIRINOX alone or in combination with radiation therapy (conventional radiotherapy, XRT, or stereotactic body radiotherapy, SBRT) on immunologically relevant genes in the PDAC tumor microenvironment (TME). We hypothesize conventional therapies may induce immune alterations in the TME that can be leveraged to enhance the efficacy of immunotherapy in PDAC. PDAC patients who underwent upfront surgical resection or who received neoadjuvant FOLFIRINOX with or without neoadjuvant radiotherapy followed by surgical resection were selected for study. The expression of 730 immunologically relevant transcripts was quantitated using the Nanostring PanCancer immune profiling panel (Platform GPL19965). This analysis identified189 genes that were differentially expressed at the RNA level on the basis of neoadjuvant therapy. On average specimens were obtained 6.6-17.0 weeks after the conclusion of neoadjuvant therapy, depending on treatment group. These data provide insight into the immunological effects of standard of care neoadjuvant therapy for resectable/borderline-resectable PDAC. This work provides data to guide strategic new combination therapies for pancreatic cancer.

overall_design: Gene expression profiles were generated on a total of 24 individuals who underwent surgical resection for PDAC at Emory University using the Nanostring PanCancer Immune Profiling Panel (XT-CSO-HIP1-12; Platform GPL19965). Patients who received upfront surgical resection (no neoadjuvant therapy) served as an overall control group for comparison purposes (n=6). Patients who received neoadjuvant FOLFIRINOX served as a secondary comparator-control (n=6). These two groups were compared to each other, and to patients who received neoadjuvant FOLFIRINOX and neoadjuvant radiation therapy (steriotactic body radiotherapy or conventional external beam radiotherapy, n=6 each). Following image acquisition mRNA counts were extracted from raw RCC files using nSolver analysis software v3.0 (Nanostring). Data was then normalized using nSolver.

first: Matthew

middle: R

last: Farren

first: Layal

last: Sayegh

first: Hsiao-Rong

last: Chen

first: Alyssa

last: Krasinskas

first: Shishir

last: Maithel

first: Mohammad

last: Zaidi

first: Juan

last: Sarmiento

first: David

last: Kooby

first: Pretesh

last: Patel

first: Bassel

last: El-Rayes

first: Walid

last: Shaib

middle: B


title: Cell cycle dynamics of human pluripotent stem cells primed for differentiation

status: Public on Feb 20 2019

city: Boston

first: Sundari

last: Chetty

address: 185 Cambridge Street

department: Harvard Medical School

institute: Massachusetts General Hospital, Harvard University

summary: Understanding the molecular properties of the cell cycle of human pluripotent stem cells (hPSCs) is critical for effectively promoting differentiation. Here, we use the Fluorescence Ubiquitin Cell Cycle Indicator (FUCCI) system adapted into hPSCs and perform RNA-sequencing on cell cycle sorted hPSCs primed and unprimed for differentiation. Gene expression patterns of signaling factors and developmental regulators change in a cell cycle-specific manner in cells primed for differentiation without altering genes associated with pluripotency. Furthermore, we identify an important role for PI3K signaling in regulating the early transitory states of hPSCs towards differentiation.

overall_design: H9 FUCCI hPSCs were cell-cycle sorted into the early G1, late G1, and SG2M phases. For each phase, cells were treated with 2% DMSO for a 24 hour time course. RNA-seq was performed on the DMSO-treated samples and corresponding controls (2 technical replicates for each cell-cycle phase x DMSO status combination).


title: Transcriptomic Profiling of Circulating Tumor Cells in Multiple Myeloma: A New Model to Understand Disease Dissemination III

status: Public on Feb 26 2019

first: Juan-Jose

last: Garces

state: New York

address: 321 E 61st St

summary: The number of peripheral blood (PB) circulating tumor cells (CTCs) predicts risk of transformation in smoldering multiple myeloma (MM) and survival in active MM. Growing evidence suggests that as the tumor progresses and the microenvironment becomes hypoxic, clonal plasma cells (PCs) constantly invade new regions of the bone marrow (BM) through induced systemic recirculation. Of note, the frequency of CTCs is typically low and thus, it could be hypothesized that the dissemination of MM is made by few tumor cells with unique features that induce them to egress the BM and spread the disease through PB. This hypothesis has not been demonstrated because the molecular profile of CTCs in MM has not been investigated.

overall_design: We used index sorting single-cell RNA sequencing (Precise Assay, Becton Dickinson) to identify genes and cell clusters related to disease dissemination by comparing the molecular profile of CTCs with patient-matched BM clonal PCs.

first: Michal

last: Šimíček

first: Marco

last: Vicari

first: Lucie

last: Brozova

first: Leire

last: Burgos

first: Renata

last: Bezdekova

first: Diego

last: Alignani

first: Maria-Jose

last: Calasanz

first: Kateřina

last: Growková

first: Ludek

last: Pour

first: Rafel

last: Rios

first: Joaquin

last: Martinez-Lopez

first: Pamela

last: Millacoy

first: Luis

last: Palomera

last: del Orbe

first: Sonia

last: Garate

first: Laura

last: Blanco

first: Maria

last: Collantes

first: Patricia

last: Maiso

first: Zuzana

last: Chyra

first: Alexander

last: Vdovin

first: Tomas

last: Jelinek

first: Cirino

last: Botta

first: Halima

last: El Omri

first: Jonathan

last: Keats

first: Xabier

last: Agirre

first: Felipe

last: Prosper

first: Roman

last: Hajek

first: Jesús

last: San Miguel

first: Bruno

last: Paiva


title: Transcriptomic Profiling of Circulating Tumor Cells in Multiple Myeloma: A New Model to Understand Disease Dissemination

first: Juan-Jose

last: Garces

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

overall_design: Refer to individual Series


title: Oligonucleotide Microarrays Identified Potential Regulatory Genes Related To Early Outward Arterial Remodeling Induced By Tissue Plasminogen Activator

status: Public on Feb 16 2019

city: Moscow

first: Olga

last: Plekhanova

address: Lomonosovsky prospect, 27-1

country: Russia

institute: Lomonosov Moscow State University

summary: Constrictive vascular remodeling limiting blood flow, as well as compensatory outward remodeling, have been observed in many cardiovascular diseases; however, the underlying mechanisms regulating the remodeling response of the vessels remain unclear. Plasminogen activators (PA) are involved in many of the processes of vascular remodeling. We have shown previously that increased tissue-type PA (tPA) contributes to outward vascular remodeling. To elucidate the mechanisms involved in the induction of outward remodeling we characterized changes in the expression profiles of 8799 genes in injured rat carotid arteries one and four days after recombinant tPA treatment compared to vehicle. Periadventitial tPA significantly increased lumen size and vessel area, encompassed by the external elastic lamina, at both one and four days after treatment. Among 41 differentially expressed known genes one day after tPA application, 5 genes were involved in gene transcription, 5 genes were related to the regulation of vascular tone (for example, thromboxane A2 receptor (D32080) or nonselective-type endothelin receptor (S65355)), and 8 genes were identified as participating in vascular innervation (for example, calpain (D14478) or neural cell adhesion molecule L1 (X59149)). Four days after injury in tPA-treated arteries, 4 genes, regulating vascular tone, were differentially expressed. Thus, tPA promotes outward arterial remodeling after injury, at least in part, by regulating expression of genes in the vessel wall related to function of the nervous system and vascular tone.

overall_design: Male Wistar-Kyoto rats (3 months old) were obtained from a colony maintained at standard colony conditions including 12 h-12 h light-dark cycle, 22 ± 2 °C temperature and free access to food and water. Their left common carotid artery was subjected to balloon catheter injury using surgical procedures approved by the Cardiology Research Center's Animal Experimentation Committee. Following balloon catheter injury, 20 nmol/kg of recombinant tissue-type plasminogen activator dissolved in pluronic gel or 500 μl of plain Pluronic gel, F-127 (BASF) was applied to the adventitial side of the left common carotid arteries. Either 1 or 4 days after the experimental balloon angioplasty or sham-operated animals or intact animals were narcotized and total RNA was isolated from left carotids or right carotids of ballooned and sham-operated as well as non-operated animals (not less than 9 rats per group, 3 vessels were pooled for 1 sample). Changes in gene expression profiles were analyzed using U34A microarray hybridization (Affymetrix, Santa Clara, CA) and Quantitative Real-Time PCR (Applied Biosystems).

first: Yelena

last: Parfyonova

first: Bradford

middle: C

last: Berk

first: Vsevolod

last: Tkachuk