title: Equine fetal, adult and embryonic stem cell derived tenocytes are all immune privileged but exhibit different immune suppressive properties in vitro

status: Public on Sep 27 2019

city: Herts

first: Deborah

middle: Jane

last: Guest

address: Hawkshead Lane, North Mymms, Hatfield

department: Deptartment of Clinical Sciences and Services

institute: Royal Veterinary College

summary:
Purpose:- RNA sequencing was performed on adult, fetal and embryonic stem-cell derived equine tenocytes cultured in 2D to look at the difference in expression of  genes associated with immune suppresion.
Methods:-   mRNA profiles of three independent lines of adult, fetal and ESC derived tenocytes were generated by RNA sequencing, using Illumina NovaSeq6000. The sequence reads that passed quality filters were analyzed using the pseudoaligner Salmon and differential expression quantified using DESeq2. Gene ontology analysis was then conducted using Panther GoSlim.
Results:- 1691 genes were significantly upregulated in both fetal and adult tenocytes compared to ESC-tenocytes (logFC ± 2, padj <0.01). Response to stimulus and cell signalling were in the top 15 overrepresented pathways. The expression levels of 24 genes reportedly involved in MSC-mediated suppression of PBMCs were examined. 7 of these genes were more highly expressed in adult and/or fetal tenocytes compared to ESC-tenocytes, whereas 5 genes were expressed at lower levels in adult and/or fetal tenocytes than ESC-tenocytes.

overall_design: mRNA profiles of three independant lines of adult, fetal and ESC derived tenocytes were generated by RNA sequencing, using Illumina NovaSeq6000.

first: A

last: McClellan

first: Y

middle: Z

last: Paterson

first: R

last: Paillot

first: D


title: The genomes uncoupled dependent signaling pathway coordinates plastid biogenesis with the synthesis of anthocyanins

status: Public on Oct 18 2019

city: Rostock

first: Andreas

middle: Sven

last: Richter

address: Albert-Einstein-Strasse 3

department: Institute for Biosciences

country: Germany

institute: University of Rostock

type: Expression profiling by high throughput sequencing

summary: Transcriptome profile of Arabidopsis wild-type (Col-0) and mutants of the plastidic retrograde signalling pathway (gun1-1,gun4-1, gun5-1) germinated in the presence of  5µM Norflurazon for 5d in continious light (100µE). Analysis was performed on biological triplicates of total leaf RNA using paired-end Illumina Hi/MiSeq technology.

first: Bernhard

last: Grimm

middle: S


title: Signaling protein antibody microarray analyses for islets of control and IFT88 knockout mice [SET100]

status: Public on Oct 30 2019

city: St Louis

first: Jing

last: Hughes

state: Missouri

address: 660 S Euclid

department: Internal Medicine

country: USA

institute: Washington University

summary:
β-cell specific IFT88 knock-out mice recapitulate human diabetes with impaired insulin secretion and altered islet hormone paracrine regulation. To examine the signaling pathways regulating islet cell function, we subjected protein lysates of whole islets from control and IFT88 knockout mice to a commercial signaling-protein array analysis (Full Moon Bio, Inc).
Samples were probed against 1358 antibodies with 2 replicates per antibody on 76 x 25 x 1mm glass slides.

overall_design: IFT88 fl/fl mice and INS1-Cre mice on a C57BL/6 background were crossed to generate β-cell specific IFT88 knockout mice. Animals were weaned at age 3 weeks and maintained on a standard chow diet. Islets were isolated using modified Lacy protocol and allowed to recover in culture overnight before collection and lysis. Total protein lysates were prepared from 250 size-matched islets per sample (2 controls and 2 knockouts, each pooled from 2 mice) and used for FullMoonBio Signaling Explorer Array (SEA100) analysis.


title: Liver-derived signals sequentially reprogram myeloid enhancers to initiate and maintain Kupffer cell identity

status: Public on Oct 08 2019

city: La Jolla

first: Christopher

middle: K

last: Glass

state: CA

address: 9500 Gilman Drive

department: School of Medicine

institute: University of California, San Diego

type: Genome binding/occupancy profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Deconvolution of myeloid cell cytokine specific transcriptional profiles during tuberculosis and cancer identifies neutrophil activation as a prognostic feature [cultured cells]

status: Public on Oct 01 2019

city: New York

first: Joseph

middle: C

last: Devlin

state: NY

address: 430 East 29th Street

department: Microbiology

institute: New York University Langone Health

summary: The cytokine environment and cellular infiltrate during an inflammatory response may contain prognostic features that could guide therapy or predict disease outcome. Here we analyzed the transcriptional responses of human monocytes, macrophages, dendritic cells and neutrophils to stimulation by type 1 cytokines (IFN-g, IFN-b and IFN-l) type 2 cytokines (IL-4 and IL-13) and the immunoregulatory cytokine IL-10. This generated a myeloid cell cytokine specific response matrix to infer representation of myeloid cells and the cytokine environment they may encounter during infection and in tumors. Neutrophils were surprisingly responsive to type 1 and type 2 cytokine stimulation but did not respond to IL-10. We identified transcripts specific to IFN-b stimulation, whereas other IFN signature genes were upregulated by both IFN-g and IFN-b. When used to deconvolute blood profiles from tuberculosis patients, the IFN-b specific neutrophil signature was surprisingly reduced in TB patients with active disease whereas the shared response to IFN-g and IFN-b in neutrophils was increased. When applied to glioma patients, transcripts of neutrophils exposed to IL-4 or IL-13 and monocyte responses to IFN-g or IFN-b emerged as opposing predictors of survival in samples from patients with glioma. This approach may help delineate biological roles for myeloid cells in different cytokine environments during disease processes.

overall_design: Stimulation of 4 myeloid cell types with 6 cytokines  of 3 anonymous healthy human donors

first: Erin

middle: E

last: Zwack

first: P'ng

last: Loke

first: Victor

middle: J

last: Torres


title: circRNA expression profiles for Human metastatic renal cell carcinoma and Primary tumor tissues

status: Public on Sep 24 2019

city: SHANGHAI

first: wei

last: li

address: Yanchang RD.

country: China

institute: WFIRM

summary: We have employed circRNA microarray expression profiling as a discovery platform to identify the dysregulated circRNAs in RCC.

overall_design: Renal cell carcinoma tissues from surgery were distributed into two experimental groups: metastatic tumor tissue group and Primary tumor tissues group, then perform circRNAs chips by Arraystar Human circRNAs chip (Arraystar)

first: Wei

last: Li

first: Chen-Min

last: Sun

first: Xu-Dong

last: Yao

first: Bo

last: Peng

first: Jun-Hua

last: Zheng

first: Min

last: Liu


title: Gene analysis during the development of obliterative bronchiolitis in a murine orthotopic lung transplantation model

status: Public on Sep 11 2019

city: Chiba

first: ATSUSHI

last: HATA

state: Chiba

address: 1-8-1, Inohana, Chuo-ku

department: Department of General Thoracic Surgery and Department of Molecular Oncology

country: Japan

institute: Graduate School of Medicine, Chiba University

summary:
Background: Obliterative bronchiolitis (OB) is a known issue during minor histocompatibility antigen (mHA) disparity during lung transplantation. This study evaluated gene expression in a murine orthotropic lung transplantation model using microarray analysis.
Methods: Left lungs from C57BL/10(H-2b) donor mice were transplanted into mHA-mismatched C57BL/6(H-2b) recipient mice. Three groups (OB, non-OB, and sham controls) were confirmed pathologically and analyzed. Gene expression changes in the lung grafts were determined by microarray and immunohistochemical staining, and genes were verified by quantitative PCR in the lungs and mediastinal lymph nodes (LNs).
Results: A total of 1343 genes were differentially upregulated in the OB lungs compared to the sham group. Significant upregulation was observed for genes related to innate, e.g. Tlr2 and CCL3 and adaptive immunity, e.g. H2-ab1 and Il-21. Positive labeling for MHC class II antigen was observed in the bronchial epithelium of OB accompanied with B cells. We found increased Tlr2, Ccl3, H2-ab1, Il-21, Ighg3, Ifng, and Pdcd1 mRNA expression in the OB lung, and increased Il-21, Ighg3, and Pdcd1 expression in the OB LNs.
Conclusions: Adaptive and innate immune reactions were involved in OB after lung transplantation, and genetic examination of related genes could be used for detection of OB.

overall_design:
To detect the differentially expressed gene in obliterative bronchiolitis (OB), we conducted the microarray analysis using an Agilent SurePrint G3 Mouse Gene Expression 8X 60K array (Agilent Technologies) for allograft lungs of OB (n=3) and non-OB (n=3), and lungs of sham mice (n=3). A total of 1343 genes were differentially upregulated in the OB lungs compared to the sham group. Significant upregulation was observed for genes related to innate and adaptive immunity in OB lung.
Left lungs from C57BL/10 donor mice were transplanted into mHA-mismatched C57BL/6 recipient mice and sacrificed at 21 postoperative days. Three groups (OB, non-OB, and sham controls) were confirmed pathologically.

first: Atsushi

last: Hata

first: Hidemi

last: Suzuki

first: Ichiro

last: Yoshino


title: LGR5 marks targetable tumor-initiating cells in liver cancer

status: Public on Sep 17 2019

city: Rotterdam

first: Qiuwei

last: Pan

address: Wytemaweg 80

country: Netherlands

institute: Erasmus University Medical Center

summary: We want to investige the difference betwen untreated/5-FU treated LGR5+/LGR5- cell population, by adopting RNA-sequencing.

overall_design: Examination of the difference betwen untreated/5-FU treated LGR5+/LGR5- cell population.

first: Wanlu

last: cao


title: Differential modulation of the androgen receptor for prostate cancer therapy depends on the DNA response element

status: Public on Sep 07 2019

city: Ann Arbor

first: Steven

last: Kregel

state: MI

address: 1500 E. Medical Center Drive, Room 5320 RCC

department: MCTP

institute: University of Michigan

summary: Doxorubicin Treated LNCaP cells RNA-sequencing, and AR and TBP Chromatin immunoprecipitation sequencing

overall_design: LNCaP cells were charcoal strip serum androgen starved, then stimulated with 1nM R1881 and/or 0.1, 0.4, or 0.7 µM Doxorubicin.

first: Diane

last: Robins


title: Development of gene expression signatures for lncRNA MRPL23-AS1 up-regulation

status: Public on Aug 31 2019

city: Beijing

first: Chen

last: Chuwen

address: No.22, Zhongguancun South Avenue

institute: Peking university

summary: Lung metastasis is a major factor affecting long-term survival in adenoid cystic carcinoma patients. Here, we report the long noncoding RNA (lncRNA) MRPL23 antisense RNA 1 (MRPL23-AS1), which exhibited remarkably upregulated expression and was correlated with lung metastasis and overall survival in salivary adenoid cystic carcinoma (SACC) patients. To further  study which biological process MRPL23-AS1 may be involved in, SACC-83 cells treated with the control vector or MRPL23-AS1-overexpressing vector were subjected to an mRNA microarray.  GO analysis was used to identify the significant biological functions of differentially expressed mRNAs.

overall_design: Gene expression was measured in SACC-83 cells transiently overexpressing MRPL23-AS1 or the Vector plasmid.

first: Chuwen

last: Chen


title: Development of gene expression signatures for lncRNA MRPL23-AS1 down regulation

summary: Lung metastasis is a major factor affecting long-term survival in adenoid cystic carcinoma patients. Here, we report the long noncoding RNA (lncRNA) MRPL23 antisense RNA 1 (MRPL23-AS1), which exhibited remarkably upregulated expression and was correlated with lung metastasis and overall survival in salivary adenoid cystic carcinoma (SACC) patients. To further  study which biological process MRPL23-AS1 may be involved in, SACC-LM cells treated with si-control or si-MRPL23-AS1 were subjected to an mRNA microarray.  GO analysis was used to identify the significant biological functions of differentially expressed mRNAs.

overall_design: Gene expression was measured in SACC-LM cells transfected with si-control or si-MRPL23-AS1.


title: Development of gene expression signatures for lncRNA MRPL23-AS1


title: Dissecting cell composition and cell-cell interaction network of human disease heart tissue by single-cell sequencing

status: Public on Oct 21 2019

city: Durham

first: Li

last: Wang

address: 111 T.W. Alexander Dr

institute: NIH

summary: We studied the cell compositon of two types of human heart disease (coronary atherosclerotic heart disease and dilated cardiomyopathy) by single-cell sequencing. Distinct subgroups of cardiac muscle, fibroblast cell and endothelial cell were detected. We generated a cell-cell interaction network using specific expressed ligands and receptors of cells. And we also observed the change of interaction and cell transformation with age.

overall_design: Extract cells from left ateria and ventricle of human heart tissue and conduct single-cell sequencing

first: Peng

last: Yu

first: Zheng

first: Zongna

last: Ren


title: Profiling circular RNAs in HeLa cell

status: Public on Sep 13 2019

city: SAINT LOUIS

first: Xiaoxin

state: MO

address: ONE BROOKINGS DRIVE

department: Computer Science & Engineering

institute: WASHINGTON UNIVERSITY IN ST LOUIS

type: Non-coding RNA profiling by high throughput sequencing

summary: We used RNA-seq to examine circular RNAs from RNase R treated ribo-zero RNAs in HeLa cells.

overall_design: HeLa total RNA was supplied in the Ion Total RNA-Seq Kit v2, 12-Reaction Kit (Life technologies, Cat. no. 4475936) for preparing cDNA library. cDNA library preparation and sequencing were performed on Ion Torrent, and preliminary data acquisition and preprocessing was performed in house.

first: Weixiong

last: Zhang

first: Junfei

last: Zhou


title: N-Myc-mediated epigenetic reprogramming drives lineage plasticity in advanced prostate cancer [ChIP-seq]

status: Public on Aug 26 2019

first: Nicholas

last: Brady

address: 1188 York Ave

department: Pathology and Laboratory Medicine

institute: Weill Cornell Medicine

summary: Despite recent advances in highly effective androgen receptor (AR)-directed therapies for the treatment of prostate cancer, a significant subset of patients with resistant disease develop AR-null, androgen signaling-indifferent neuroendocrine prostate cancer (NEPC). A majority of these NEPC cases that arise following anti-androgen therapy are driven by the aberrant expression of the transcription factor N-Myc. To define the cell lineage states associated with the development of prostate cancer resistance phenotypes, we analyzed whole transcriptome data from a cohort of primary and metastatic tumors compared to benign tissues. NEPC tumors are significantly enriched for stem cell genes associated with embryonic and neural crest lineages, as well as for neural lineage-defining genes. Analysis of the N-Myc transcriptome, cistrome and chromatin-bound interactome using in vivo (GEMM and human xenografts), in vitro (human prostate cancer cell lines) and ex vivo models (NEPC-patient-derived organoids) revealed that the N-Myc cistrome is androgen-dependent and drives a transcriptional program that leads to epithelial plasticity and the acquisition of clinically-relevant neural lineage markers. Moreover, we show that histone marks specifically associated with lineage-defining genes are epigenetically reprogrammed by N-Myc. Finally, we demonstrate how N-Myc-induced gene expression and epigenetic changes can accurately classify patients with advanced prostate cancer which may provide a molecular signature to inform future therapeutic strategies.

overall_design: ChIP-seq in LNCaP cells, 22Rv1 xenografts and PM154 organoids for N-Myc, H3K4me3 and H3K27me3

first: Adeline

last: Berger

first: David

last: Rickman


title: N-Myc-mediated epigenetic reprogramming drives lineage plasticity in advanced prostate cancer

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: N-Myc-mediated epigenetic reprogramming drives lineage plasticity in advanced prostate cancer [RNA-seq]

overall_design: RNA-seq in LNCaP cells, 22Rv1 xenografts and genetically-engineered mouse models (GEMM)


title: A novel lymphoid-primed progenitor marked by Dach1 downregulation identified with single cell multi-omics

status: Public on Aug 23 2019

city: Cambridge

first: Luyi

last: Tian

state: MA

address: 415 main st Cambridge

institute: Broad institute

summary: A classical view of blood cell development is that multipotent haematopoietic stem and progenitor cells (HSPCs) become lineage-restricted at defined stages. The Lin–c-kit+Sca1+Flt3+ stage, termed lymphoid-primed multipotent progenitors (LMPPs), have lost megakaryocyte and erythroid potential but are heterogeneous in their fate. Through single cell RNA-sequencing, we identify heterogeneous expression of Dach1 and associated genes in this fraction where it co-expressed with myeloid/stem genes but inversely correlated with lymphoid genes. Through generation of Dach1-GFP reporter mice, we identify a transcriptionally and functionally unique Dach1– subpopulation within LMPPs with lymphoid potential but devoid of myeloid potential. We term these ‘lymphoid-primed progenitors’, or LPPs. These findings define the earliest branch point of lymphoid development in haematopoiesis and a means for their prospective isolation.

overall_design: Mouse HSPCs were isolated from bone marrow and sorted into 384 PCR plate, with library generated using the CEL-seq2 protocol.

first: Daniela

last: Amann-Zalcenstein

first: Jaring

last: Schreuder

first: Shalin

middle: H

last: Naik


title: RNA-seq analyses of wild-type and PML KO mESCs

status: Public on Aug 14 2019

city: Okazaki

first: Misuzu

last: Kurihara

state: Aichi

address: 5-1 Higashiyama, Myodaiji

institute: National Institute for Basic Biology

summary: Promyelocytic leukemia (PML) body is a phase-separated nuclear structure composed of various proteins including several chromatin regulators, and physically associates with chromatin. To address roles of PML bodies in transcriptional regulation, we performed RNA-seq analyses with wild-type and PMK knockout mESCs

overall_design: Wild-type and PML KO mESCs were analyzed by RNA-seq to profile polyA tail mRNAs. Sequence reads were processed with Cutadapt and aligned to mm10 using Tophat. Differential expression analysis was performed using edgeR. TDF file was generated by using IGV. An XLSX file includes FC and false discovery rate (FDR) computed by using edgeR.

first: Kagayaki

last: Kato

first: Chiaki

last: Sanbo

first: Shuji

last: Shigenobu

first: Yasuyuki

last: Ohkawa

first: Takeshi

last: Fuchigami

first: Yusuke

last: Miyanari


title: Gene expression changes in adult mammary fibroblasts followin in utero BPA exposure

status: Public on Aug 21 2019

city: Columbus

first: Craig

middle: Joseph

last: Burd

state: OH

address: 460 W. 12th Ave. Rm 920 BRT

department: Molecular Genetics

institute: The Ohio State University

summary: Mammary fibroblasts (CD1 strain of mouse) that were exposed to BPA or oil control in utero were isolated from 12 week old mice.  RNA was harvested and sequenced from the fibroblasts.

overall_design: Fibroblast RNA from BPA exposed mice is compared against oil treated controls

first: Clarissa

last: Wormsbaecher

first: Andrea

middle: R

last: Hindman


title: ATAC-seq analyses with wild-type and PML KO mESCs

summary: Promyelocytic leukemia (PML) body is a phase-separated nuclear structure composed of various proteins including several chromatin regulators, and physically associates with chromatin, implying its crucial roles for particular genome functions. To investigate functional roles of PML bodies in chromatin organization, we conducted ATAC-seq with wild-type and PML KO mESCs.

overall_design: ATAC-seq profile of wild-type and PML-/- mouse embryonic stem cells. Sequence reads were trimmed by using Trimmomatic, then mapped to mm10 using bowtie2 with parameters --maxins 2000 --very-sensitive. Multiple mapped reads were filtered out using a MAPQ threshold of 30. PCR duplicates and ENCODE blacklisted regions were removed using Picard Tools and bedtools. bigWig files were generated by using bamCoverage with option --normalizeUsing RPKM and --ignoreForNormalization chrX chrY


title: ChIP-seq analysis of wild-type and PML KO mESCs

summary: Promyelocytic leukemia (PML) body is a phase-separated nuclear structure composed of various proteins including several chromatin regulators, and physically associates with chromatin, implying its crucial roles for particular genome functions. To investigate roles of PML bodies in transcriptional regulation, we conducted ChIP-seq analysis for histone modifications, including H3K4me3, H3K27ac, H3K27me3, and H3K9ac with wild-type and PML knockout mESCs.

overall_design: Sequence reads were trimmed by using Trimmomatic, then mapped to mm10 using bowtie2 with parameters --maxins 2000 --very-sensitive. Multiple mapped reads were filtered out using XS tag. PCR duplicates and ENCODE blacklisted regions were removed using Picard Tools and bedtools. BigWig files were generated by using bamCoverage with option --normalizeUsing RPKM and --ignoreForNormalization chrX chrY.


title: Genome-wide analysis of SHORTROOT targets in the Arabidopsis root stele

status: Public on Aug 01 2019

city: Seoul

first: Ji-Young

last: Lee

address: 1 Gwanak-ro, Gwanak-gu

department: Biological Sciences

country: South Korea

institute: Seoul National University

summary: Asymmetric cell division (ACD) and positional signals play critical roles in the tissue patterning during multicellular organ development. In the Arabidopsis root meristem, two major phloem cell types arise via ACDs of distinct origins: one for companion cells and the other for proto- and metaphloem sieve elements.  The molecular mechanisms underlying each of these processes have been reported, however, how these two are coordinated has remained elusive. Here, we report that SHORTROOT (SHR) is the key coordinator of two ACD processes for phloem development. SHR moving into the endodermis regulates ACD for companion cells by turning on microRNA165/6.  ACD that generates phloem sieve elements is mediated by SHR moving into phloem precursors. To find the downstream targets of SHR in the stele, pCRE1::erGFP was introduced into wild type and shr-2 backgrounds to express GFP in the stele cells in the root meristem.  We then collected GFP-expressing stele cells from the wild type, shr-2 and pCRE1::SHRΔNLELDV:nlsGFP; shr-2 through Fluorescence Activated Cell Sorter (FACS).  RNAs were extracted from the sorted cells of each line and processed for generating labeled probes to be hybridized onto GeneChip Arabidopsis Tiling 1.0R Array (Affymetrix). We then examined the influence of SHR on  phloem enriched genes in the tiling array data. In this analysis, we found 224 genes that are down-regulated in shr-2 in comparison to the wild type and then restore expression in pCRE1::SHRΔNLELDV:nlsGFP; shr-2.

overall_design: A total of 7 data (2 replicates of pCRE1::erGFP;shr-2 mutant, 2 replicates of pCRE1::SHRΔNLELDV:nlsGFP; shr-2, 3 replicates of pCRE1::erGFP in the wild type Col-0) are submitted. Three genotypes were germinated and grown for 6 days on MS agar media with 1% of Sucrose. Protoplasts from these roots  were isolated and sorted through FACS, and then RNA transcripts collected from GFP expressing protoplasts were profiled on the Arabidopsis Tiling 1.0R Array.

first: Jing

last: Zhou

first: Jose

last: Sabastian


title: A retained transcriptomic profile characterizes the CD138+ cells in the progression from smoldering to active multiple myeloma

status: Public on Jul 17 2019

city: MILAN

first: Luca

last: Agnelli

address: Venezian 1

department: Department of Advanced Diagnostics

country: Italy

institute: IRCCS Istituto Nazionale dei Tumori

summary: Smoldering myeloma (SMM) is a pre-malignant monoclonal gammopathy with a 10% annual risk to progress to active multiple myeloma (MM). SMM diagnostic criteria, as well of those of others monoclonal gammopathies, have been updated by the International Myeloma Working Group (IMWG) in 2014. In particular, the previously defined “ultra high-risk” SMM (characterized by the presence of specific biomarkers associated with a ≥ 80% risk of progression to symptomatic MM within 2 years) has been included among patients with active MM.   SMM is biologically heterogeneous, including a subset of patients with biological pre-malignancy and a subset with biological malignancy who have not yet developed organ damage, defined as onset of the classical CRAB criteria or Myeloma Defining Events (MDE). Thus, SMM encompassed patients with a very low rate of progression to symptomatic MM, similar to patients with monoclonal gammopathy of uncertain significance (MGUS), as well as patients who acquired organ damage and progress to active MM within the first year from diagnosis.  The molecular mechanisms involved in the SMM to MM progression are still far to be fully understood.  Genomic studies indicate that the genetic alterations that characterize MM patients are already present in SMM ones, who present similar mutational and copy number alteration load. However, few data are available on the transcriptional profiles of SMM patients in relationship to the progression to active MM, overall indicating minimal differential expression either in coding or non-coding RNA fraction. To date, robust data are still lacking which describe the transcriptional profiles of plasma cells (PCs) from paired samples obtained at the time of SMM and at MM onset.    Herein,  we compared the transcriptome of purified CD138+ PCs from paired samples of SMM patients progressed to active MM (P-SMM), aimed at describing any possible common transcriptional discrepancy that may help to understand the intra-patient disease evolution; at the same time, we investigated the transcriptional differences between P-SMM and a subset of non-progressed SMM (NP-SMM) at a minimum of 36 months.

overall_design: A total number of 20 SMM patients, admitted to the Hematological Unit of our Institution over the last 11 years, were considered: 12 non-progressed(NP)-SMM and 8 progressed(P)-SMM for whom paired active MM samples were available

first: Paola

last: Storti

first: Benedetta

last: Della Palma

first: Katia

last: Todoerti

first: Valentina

last: Marchica

first: Fabrizio

last: Accardi

first: Federica

last: Deluca

first: Marina

last: Bolzoni

first: Luisa

last: Craviotto

first: Franco

last: Aversa

first: Antonino

last: Neri

first: Nicola

last: Giuliani


title: Time-Dependent Transcriptome Profiling Reveals the Importance of Multiple Transcription Factors in Brachypodium Root Development

status: Public on Jul 27 2019

city: pasco

first: aaron

last: ogden

state: wa

address: 902 battelle boulevard

department: integrative omics

institute: Pacific Northwest National Lab

summary: The goal of this study was to examine the transcriptional events occuring during stress-free Brachypodium distachyon root development via illumina paired-end RNA-seq. 4 time-points were chosen that capture the transition from rapid vegetative growth into slower reproductive growth. Abstract - Root systems are dynamic, adaptable organs that play critical roles in plant development. Roots, however, remain understudied and therefore present opportunities for trait improvement in food and bioenergy crops. A comprehensive growth stage-based root phenotyping integrated with molecular signatures is required to advance our understanding of root growth and development. Here we studied Brachypodium distachyon rooting process by monitoring root biomass, length, branching, root-to-shoot ratio and Carbon-to-Nitrogen ratio during time. To provide insight into gene regulation that accompanies root development and biomass accumulation, we generated comprehensive transcript profiles of Brachypodium whole-root system at four initial developmental stages that capture the transition from vegetative to reproductive growth. Our stringent data analysis revealed that multiple biological processes and various families of transcription factors (TFs) were differentially expressed during root development. In particular, the AUX/IAA, ERFs, WRKY, NAC, and MADS TF family members were upregulated, while ARFs and GRFs were downregulated in a time-dependent manner. Our results suggested particular TF families and biological processes including trehalose metabolism as important factors possibly involved in root biomass accumulation. We introduced several Brachypodium root biomass-promoting genes which can be employed by the genome editing approaches for improving biomass productivity in grasses.

overall_design: Brachypodium distachyon whole-root RNA-seq via illumina. 4 timepoints with 3 biological replicates each. Timepoints were collected 18, 25, 32, and 36 days post sowing.

first: Aaron

last: Ogden

first: Amirhoussein

last: Ahkami


title: Discovery of genes and proteins regulating wool diameter

city: Qingdao

first: Hegang

last: Li

state: Shandong

address: 149 Xiazhuang Road, Licang District

department: Animal Reproduction and Breeding

institute: Qingdao Institute of Animal Science and Veterinary Medicine

summary: Sheep provide considerable materials for the animal fibre industry. Identifying genes of major effect for wool growth would offer strategies for improving the quality of fine wool. In this study, we employed Agilent Sheep Gene Expression Microarray and proteomic technology to investigate the gene expression patterns of body side skin between Aohan fine wool sheep and small tail Han sheep (two Chinese indigenous breed) at the anagen stage of wool follicle. Several potential gene families might participate in hair growth regulation, including fibroblast growth factors, transforming growth factor-β, WNTs, insulin-like growth factor, vascular endothelial growth factors and so on. Furthermore, according to the results at both mRNA and protein levels, similar regulation mechanism of gene activity might be engaged during skin development and embryo development.

overall_design: All animals were treated in accordance with the animal protocols deﬁned by national and local animal welfare bodies, and all animal work was approved by the Shandong Province Biological Studies Animal Care and Use Committee.One ram and two ewes of 12-month-old Aohan fine wool sheep and small tail Han sheep were used in the microarray study. These animals were half sibs (sharing the same father) for each breed. In August 2010, full-thickness skin from body side were sampled from each animal under local anaesthesia for microarray and proteomic experiments. The area of each sample was about 1 cm2. All samples were immediately put into collection tubes and stored in liquid nitrogen for RNA and protein extraction. A total of 15, 208 probes were spotted on this Agilent Sheep Gene Expression Microarray (Santa Clara, CA, USA).

last: Liu

first: Kaidong

first: Feng

last: Yang

first: Ming

last: Cheng

first: Wei

last: De

first: Jinshan

last: Zhao


title: RNA seq analysis of human macrophages after treatment of glimepiride versus empagliflozin.

first: Yong-ho

last: Lee

address: Yonsei-ro 50-1, SeoDaeMunGu

institute: Yonsei University College of Medicine

summary:
Purpose: The goal of this study is to compare NGS-derived macrophage transcriptome profiling (RNA-seq) between diabetic patients treated with glimepiride versus empagliflozin.
Methods: Macrophage mRNA profiles of 7 patients treated with either glimepiride or empagliflozin were generated by deep sequencing using Illumina HiSeq 4000 system. The sequence reads that passed quality filters were analyzed at the transcript isoform level using CLC Genomics Workbench v.9.0.1 software (CLC Bio, Cambridge, USA).
Conclusion: A total of 64 genes were differentially expressed in the glimepiride treated patients compared to those of the empagliflozin treated patients, with 47 genes increased and 17 genes decreased in the glimepiride group. Most of these genes were related to immune-related receptor signaling pathway.


title: Gene expression profiling from whole VNOs after tfap2eCre-mediated Smad4 ablation in immature basal vomeronasal neurons  and OMPCre-mediated Smad4 ablation in all mature vomeronasal neurons

status: Public on Jul 19 2019

city: Albany

first: Paolo

last: Forni

state: New York

address: 1400 Washington Avenue

institute: University at Albany

summary: The vomeronasal organ (VNO) of mice contains two main types of vomeronasal sensory neurons (VSNs)- Apical and Basal. Apical VSNs express vomeronasal receptors (VRs) of the V1R family and project to the anterior accessory olfactory bulb (AOB) and VSNs in the basal portions of the epithelium express receptors of the V2R family and project to the posterior portion of the AOB. In the vomeronasal epithelium of mice we found active BMP signaling. By generating Smad4 conditional mutants we disrupted canonical TGF-b/BMP signaling in either maturing basal VSNs or in mature apical and basal VSNs.

overall_design: We compared transcriptome of controls- Smad4flox/flox and AP-2eCre+/- to conditional knockout AP-2eCre+/-/Smad4flox/flox in order to analyze the changes in gene expression when Smad4 is ablated in immature Basal VSNs. We also compared transcriptome of controls- Smad4flox/flox and OMPCre+/- to conditional knockout OMPCre+/-/Smad4flox/flox to investigate role of Smad4 mediated transcription in mature Apical and Basal VSNs.

first: Ankana

last: Naik

first: Morgan

last: Sammons


title: Dissecting roles of PML bodies by genome-wide profiling of PML body-associated regions

first: Misuzu

last: Kurihara

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

overall_design: Refer to individual Series


title: Altered fecal small RNA profiles in colorectal cancer reflect gut microbiome composition in stool samples

status: Public on Aug 30 2019

city: Orbassano

first: Giulio

last: Ferrero

state: TO

address: Regione Gonzole, 10

department: Dept. Clinical and Biological Sciences

institute: University of Turin

summary: Dysbiotic configurations of the human gut microbiota have been linked with colorectal cancer (CRC). Human small non-coding RNAs are also implicated in CRC and recent findings suggest that their release in the gut lumen contributes to shape the gut microbiota. Bacterial small RNAs (bsRNAs) may also play a role in carcinogenesis but their role is less explored. Here, we performed small RNA and shotgun sequencing on 80 stool specimens of patients with CRC, or adenomas, and healthy subjects collected in a cross-sectional study to evaluate their combined use as a predictive tool for disease detection. We reported a considerable overlap and correlation between metagenomic and bsRNA quantitative taxonomic profiles obtained from the two approaches. Furthermore, we identified a combined predictive signature composed by 32 features from human and microbial small RNAs and DNA-based microbiome able to accurately classify CRC from healthy and adenoma samples (AUC= 0.87). In summary we reported evidence that host-microbiome dysbiosis in CRC can be observed also by altered small RNA stool profiles. Integrated analyses of the microbiome and small RNAs in the human stool may provide insights for designing more accurate tools for diagnostic purposes.

overall_design: Small RNA-Seq was performed on small RNA extracted from stool samples from a cohort of 80 subjects (29 CRC patients, 27 adenomas and 24 controls). CRC patients were recruited at the first CRC diagnosis and had not received any treatment prior to fecal sample collection. Naturally evacuated fecal samples were obtained from all patients previously instructed to self-collect the specimen at home before any bowel preparation for the colonoscopy. The stool was collected in Stool Nucleic Acid Collection and Transport Tubes with RNA stabilizing solution (Norgen Biotek Corp) and returned at the time of performing a colonoscopy in the endoscopy unit or at the time of blood sampling. RNA was extracted using the Stool Total RNA Purification Kit (Norgen Biotek Corp). Small RNA (sRNA) transcripts were converted into barcoded cDNA libraries. Library preparation was performed with the NEBNext Multiplex Small RNA Library Prep Set for Illumina (Protocol E7330, New England BioLabs Inc., USA). The obtained libraries were subjected to the Illumina sequencing pipeline, passing through clonal cluster generation on a single-read flow cell (Illumina Inc., USA) by bridge amplification on the cBot (TruSeq SR Cluster Kit v3-cBOT-HS, Illumina Inc., USA) and 50 cycles sequencing-by-synthesis on the HiSeq 2000 (Illumina Inc., USA).

first: Sonia

last: Tarallo

first: Gaetano

last: Gallo

first: Antonio

last: Francavilla

first: Giuseppe

last: Clerico

first: Alberto

last: Luc

last: Manghi

first: Andrew

middle: M

last: Thomas

last: Vineis

last: Segata

first: Barbara

last: Pardini

first: Alessio

last: Naccarati

first: Francesca

last: Cordero


title: RNAseq of Rhesus macaque adipose tissue and skeletal muscle in response to FGF21 treatment

status: Public on Jul 13 2019

city: Seattle

first: Sara

middle: A

last: Murray

state: WA

address: 530 Fairview Ave N

department: Obesity Research Group

institute: Novo Nordisk Research Center Seattle, Inc.

summary: Ten diet-induced obese Rhesus macaques were treated with fibroblast growth factor 21 (FGF21) for 12 weeks, which resulted in an average of 18% weight loss.  Tissue punch biopsies were taken from abdominal subcutaneous adipose tissue and gastrocnemius skeletal muscle pre-treatment, at the end of treatment, and after a 16 week washout period.  Numerous genes were found to be differentially expressed between pre-treatment, post-treatment, and washout time points in adipose tissue; however, high amounts of inter-sample variation in muscle tissue gene expression levels obscured any differences between pre- and post-treatment in skeletal muscle.

overall_design: From adipose tissue, 10 samples each from pre-treatment, post-treatment, and washout time points.  From skeletal muscle, only 6-7 samples per time point met RNA integrity or RNA sequencing quality requirements.  As the same animals were used for all three time points, the pre-treatment time point served as an untreated control in a paired design.

first: Paul

last: Kievit

first: Kevin

middle: L

last: Grove

first: Burak

last: Kutlu


title: Assigning a role for chemosensory signal transduction in Campylobacter jejuni biofilms using a combined omics approach

status: Public on Jul 04 2019

city: Southport

first: Greg

last: Tram

state: Queensland

address: Parklands Drive

department: Institute for Glycomics

country: Australia

institute: Griffith University

summary: Biofilms serve as a protective mechanism for bacteria to cope with environmental stress. Whilst ordinarily a fastidious organism, it has been long suggested that C. jejuni is able to utilise this mode of growth as a way to transmit infection from the avian host to humans. Herein, we undertook a combinatorial approach to examine differential expression of C. jejuni genes and protein abundance during biofilm formation. RNA sequencing and proteomics via quantitative liquid chromatography – tandem mass spectrometry (LC-MS/MS) revealed biofilm growth induced a substantial rearrangement of the C. jejuni transcriptome and proteome, with ~600 genes differentially expressed in biofilms compared to planktonic cells. Biofilm-induced genes / proteins were those involved in iron metabolism and acquisition, cell division, glycan production and attachment, while those repressed were associated with metabolism, amino acid uptake and utilisation, and large tracts of the chemotaxis pathway.

overall_design: Examination of differentially expressed transcripts from planktonic cells and those in a biofilm in Campylobacter jejuni

first: William

middle: P

last: Klare

first: Joel

last: Cain

first: Basem

last: Mourad

first: Stuart

last: Cordwell

first: Christopher

last: Day

first: Victoria

last: Korolik


title: Transcriptomic and gene ontology profiling of the human corneal cell types

status: Public on Jun 13 2019

city: Los Angeles

first: Anthony

middle: J.

last: Aldave

address: 200 Stein Plaza DSERC 3-143

department: Ophthalmology

institute: Stein Eye Institute, UCLA

summary: Purpose: To identify distinct gene expression and functional profiles for the three main cell types (epithelial, keratocyte and endothelial) of the human cornea. Methods: RNA-sequencing was performed using total RNA isolated from ex vivo corneal epithelial cells (evCEpC), keratocytes (evK) and endothelial cells (evCEnC) obtained from 3 donor corneas obtained from a commercial eye bank. Transcriptomic analysis was performed using Kallisto (alignment (hg38) and quantification) and Sleuth (differential gene expression(DGE)), with transcript abundances calculated as transcripts per kilobase million (TPM). Expression was defined as TPM≥7.5 and significant DGE as a fold-change ≥4 and a false-discovery rate adjusted p-value≤0.05. Cell type specificity was defined as genes adhering to the above expression and DGE criteria and not expressed (i.e., TPM<7.5) in the other two cell types. Gene ontology enrichment analysis was performed on the cell type-specific gene lists using the gene group functional profiling (g:GOSt) tool within the web-based g:Profiler suite. Results: We identified 205 genes specific in evCEpC, and enrichment of epithelial-associated GO terms (e.g., cornified envelope, epidermis development, cell-cell adhesion). We identified 76 genes specific in evK, and fibroblast-associated GO terms (e.g., collagen metabolic process, metallopeptidase activity, extracellular matrix organization). We identified 96 genes specific in evCEnC, and at least one CEnC-associated GO term (e.g., cellular cation homeostasis) but several synapse-associated GO terms (e.g., synapse organization, synapse part). Conclusions: The human cornea is comprised of three main cell types that play important roles in maintaining corneal clarity and vision. Our results demonstrate that a small subset (0.4-1%) of the protein-coding genes confers distinct and classic functional properties associated with each cell type. In addition, we identified a novel association and significant functional overlap between CEnC and synapses. This may lead to insights into the molecular mechanisms of transendothelial transport and secretion, which are integral metabolic features of the corneal endothelium.

overall_design: Corneal epithelium, corneal endothelium and corneal stroma were isolated from three donor corneas (i.e., 3 biological replicates). Keratocyte RNA was isolated from corneal stroma tissue.

first: Ricardo

middle: F

last: Frausto

first: Vinay

last: Swamy


title: Developmentally regulated Shh expression is robust to TAD perturbations

status: Public on Aug 15 2019

city: Edinburgh

first: Iain

last: Williamson

address: Crewe Road

department: Chromosomes and Gene Expression

country: United Kingdom

institute: IGMM MRC Human Genetics Unit

summary: Topologically Associating Domains (TADs) have been proposed to both guide and constrain enhancer activity. Shh is located within a TAD known to contain all its enhancers. To investigate the importance of chromatin conformation and TAD integrity on developmental gene regulation, we have manipulated the Shh TAD – creating internal deletions, deleting CTCF sites, and  deleting and inverting sequences at TAD boundaries. Chromosome conformation capture and fluorescence in situ hybridisation assays were used to investigate the changes in chromatin conformation that result from these manipulations. Our data suggest that these substantial alterations in TAD structure has no readily detectable effect on Shh expression patterns during development – except where enhancers are deleted - and results in no detectable phenotypes. Only in the case of a larger deletion of one TAD boundary could ectopic influence of the Shh limb enhancer be detected on a gene (Mnx1) in the neighbouring TAD. Our data suggests that, contrary to expectations, the developmental regulation of Shh expression is remarkably robust to TAD perturbations.

overall_design: 5C oligonucleotides were designed around HindIII restriction sites following an alternative scheme

first: Lauren

last: Kane

last: Devenney

first: Eve

last: Anderson

first: Fiona

last: Kilanowski

first: Ilia

last: Fliamer

first: Robert

last: Hill

first: Wendy

last: Bickmore

first: Laura

last: Lettice


title: ZEITLUPE regulates auxin signaling and the temporal gating of auxin responses that allow flowers to move

status: Public on Jun 30 2019

city: Jena

first: Klaus

last: Gase

address: Hans-Knoell-Strasse 8

department: Molecular Ecology

institute: Max-Planck-Institute for Chemical Ecology

summary: Wild tobacco flowers wave rhythmically to facilitate specific pollinator interactions. This movement behavior is controlled by a regulatory network that involves the circadian clock- and auxin-signaling pathways. The plant hormone auxin, similarly to its function in tropic movements, acts as growth regulator in the circadian regulation of floral movement. Dorsoventral asymmetry in auxin levels and auxin transcriptional responses mediate the growth responses in the floral peduncle that make flowers move. Multiple components of the auxin-signaling pathway and auxin responses are under the control of circadian clock. However, it is unclear where these two pathways intersect and how  collectively contribute to regulate specific rhythmic outputs. Here we found that the blue light photoreceptor and circadian clock component ZEITLUPE (ZTL) controls auxin responses through the regulation of the auxin-signaling pathway in a time-of-day and blue light specific manner. Abrogation of ZTL expression abolishes flower movement and the temporal gating of auxin-induced growth responses in the floral peduncle. ZTL regulates transcription and directly interacts with indole-3-acetic acid inducible 19 (IAA19), a circadian controlled gene that regulates development of curvature in moving organs. Indicating that ZTL modulates auxin sensitivity in part through the regulation of AUX/IAA transcriptional repressors. At night, growth responses in the peduncle to the synthetic auxin 2,4-D revealed that ZTL additionally controls auxin responses regulating auxin homeostasis. These results indicate that ZTL conveys temporal and environmental information, at multiple levels, into the auxin signaling-pathway and in this way sculpts the temporal gating of auxin responses that allow flowers to move. To gain further insight into the molecular basis of temporal regulation of the movement of flowers we used a whole genome microarray  as a discovery platform to identify genes differentially expressed in a RNAi knockdown line silenced in the expression of the circadian clock component ZEITLUPE (irZTL-314).

overall_design: Peduncles of empty vector (EV) and the RNAi knockdown irZTL were plants collected at ZT0. Each replicate is a pool of peduncles collected at same timepoint. Three replicate samples per genotype were used for the analysis. Total RNA was extracted from floral peduncles using the Plant RNeasy kit (Qiagen) and quality checked by spectrophotometry (NanoDrop). Genomic DNA was removed by DNAse treatment (Ambion) following manufacturer instructions. RNA was cleaned up with RNeasy MinElute columns (Qiagen) and the RNA quality was checked with the RNA 6000 Nano kit (Agilent) in the Agilent 2100 Bioanalyzer (Agilent). RNA was labeled with Cyanine-3 (Cy3) with the Quick Amp labeling kit (Agilent) according to manufacturer instructions and followed by RNAeasy column purification (Qiagen). Dye incorporation and cRNA yield were checked with a NanoDrop ND-1000 Spectrophotometer. Samples were hybridized in a N. attenuata whole genome single color array (Agilent 8×60K; GPL19764). Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565BA) using one color scan setting. Probe feature extraction was performed with the feature extraction software (Agilent). Quality control, data filtering and normalization were performed in Genespring GX (Agilent). Probe filtering was performed in Genespring GX using the platform flag (gIswellAboveBG). Probes that did not pass the condition in all replicates for one of the conditions were filtered out. Probe signals were log2 transformed and normalized to the 75th percentile. Differential expression analysis between peduncles of EV and irZTL-314 plants at ZT0 was performed with a t-test (fold change>2, padj<0.05) in Genespring GX (Agilent). Probe to gene association and gene annotations were based in the N. attenuata genome assembly v2.5.

first: Lucas

last: Cortes-Llorca

first: Sang-Gyu

last: Kim

first: Ian

middle: T

last: Baldwin


title: circNFIB suppresses lymphatic metastasis of pancreatic cancer

status: Public on Aug 29 2019

city: Guangzhou

first: Yuming

last: Luo

state: Guangdong

address: 107 Yanjiang West Avenue,Yuexiu district

department: General Surgery

institute: Sun yat-sen Memorial Hospital

summary: Pancreatic ductal adenocarcinoma (PDAC) is one of the most lethal malignany and currently the fourth leading cause of cancer related death worldwide. Circular RNAs (circRNAs) are a kind of novel noncoding RNA with a covalently circular structure arise from the non-canonical splicing of precursor-mRNA(pre-mRNA). To identify circRNAs involved in the progression of PDAC, next-generation sequencing (NGS) was performed in five paired PDAC and normal adjacent tissues. Our results suggest that the differential expressed circRNAs in PDAC tissues and normal adjacent tissues associated with the metastasis of PDAC.

overall_design: To identify circRNAs involved in the progression of PDAC, NGS was performed in five paired PDAC and normal adjacent tissues. The RNA of tissue was extracted and hybridized on illumina Hiseq Xten.

first: Changhao

last: Chen

first: Rufu


title: Inositol pyrophosphate dynamics impact phosphate homeostasis via modulation of RNA 3' processing and transcription termination

status: Public on Jun 16 2019

city: New York

first: Angad

last: Garg

department: Molecular Biology

institute: Memorial Sloan Kettering Cancer Center

summary: Fission yeast phosphate acquisition genes pho1, pho84, and tgp1 are repressed in phosphate-rich medium by transcription of upstream lncRNAs. Here we show phosphate homeostasis is subject to metabolite control by inositol pyrophosphates (IPPs), exerted through the 3'-processing/termination machinery and the Pol2 CTD code. Increasing IP8 (via Asp1 IPP pyrophosphatase mutation) de-represses the PHO regulon and leads to precocious termination of prt lncRNA synthesis. pho1 de-repression by IP8 depends on cleavage-polyadenylation factor (CPF) subunits, termination factor Rhn1, and the Thr4 letter of the CTD code. pho1 de-repression by mutation of the Ser7 CTD letter depends on IP8. Simultaneous inactivation of Asp1 and Aps1 pyrophosphatases (i.e., too much IP8) is lethal, but this lethality is suppressed by mutations of CPF subunits Ppn1, Swd22, Ssu72, and Ctf1 and CTD mutation T4A. Failure to synthesize IP8 (via Asp1 IPP kinase mutation) results in pho1 hyper-repression. Synthetic lethality of asp1∆ with Ppn1, Swd22, and Ssu72 mutations argues that IP8 plays an important role in essential 3'-processing/termination events, albeit in a manner genetically redundant to CPF. Transcriptional profiling delineates an IPP-responsive regulon composed of genes overexpressed when IP8 levels are increased. Our results establish a novel role for IPPs in cell physiology.

overall_design: 3 test samples (mutants) were analyzed; 1 WT control sample was processed (each sample has 3 replicate experiments).

first: Beate

last: Schwer

first: Stewart

last: Shuman


title: FBP1 loss disrupts liver metabolism and results in distinct transcriptome

status: Public on Aug 10 2019

city: Philadelphia

first: Fuming

last: Li

state: PA

address: 421 Curie Blvd

department: Cancer Biology

institute: University of Pennsylvania

summary: This study set out to globally compare the liver transcriptomes from 24-week old wild type (WT) and FBP1-deficient mice. Total RNA was isolated from 10 snap frozen liver tissue samples using RNeasy Mini Kit (Qiagen). 250~300 bp insert eukaryotic mRNA derived cDNA non-directional libraryRNA libraries were prepared using standard Illumina protocols. The sequencing were performed on  Illumina Platform PE150, with 20M raw reads/sample.

overall_design: mRNA profiles of 24-week old wild type (WT) and FBP1-deficient mouse livers were generated by RNA sequencing, 5 biological replicates in each group, using Illumina Platform PE150. Data was analyzed at the Molecular Profiling Facility at the University of Pennsylvania. Briefly, Fastq files were checked for quality using FastQC and qualimap. Alignment was performed using the STAR aligner under default settings with the mm10 reference genome. Raw counts of gene transcripts were obtained from the resulting bam files using feature Counts. The raw count matrix was subsequently imported into R-studio (R version 3.3.3) and used as input for DESeq2 following the vignette of the package for normalization and differential gene expression analysis. Salmon/Sailfish was used in parallel to normalize and quantitate gene expression in transcripts per million (TPM) through quasi-alignment. Differentially expressed genes from the DESeq2 analysis were used as input for GSEA MSigDB geneset enrichment analysis68 (http://software.broadinstitute.org/gsea/msigdb).

first: M

last: Simon


title: Decoupling behavioral and transcriptional responses to color in an eyeless cnidarian

status: Public on Jun 12 2019

city: Charlotte

first: Whitney

middle: at

last: Leach

address: 9201 University City Blvd.

institute: University of North Carolina at Charlotte

summary: We utilized the eyeless sea anemone, Nematostella vectensis, to quantify gene expression differences between different colors of light (red, green, blue) and in constant darkness through comparisons of 96 transcriptomes

overall_design: ntotal = 96. 6 time points (4 replicates at each) for 4 conditions. (6*4*4 = 96)

middle: B

first: Adam

last: Reitzel


title: Cysteine-rich peptides promote interspecific genetic isolation in Arabidopsis

city: Bei Jing

first: huang

last: jiaying

address: Yiheyuan Road

department: School of life science

institute: Peking University

summary: RNA was extracted from mature ovules of two samples (i.e., WT and myb98) and sequenced with an Illumina Hi-seq 2000 sequencer in the Biodynamic Optical Imaging Center (BIOPIC) of Peking University followed by the analysis on the High Performance Computing Platform of the Center for Life Science.

overall_design: Calculate the RNA expression level of 2 types of mature ovules, wild-type and myb98

first: Qingpei

last: Hunag


title: RNA-seq expression data from Human iPSC-derived Brain Microvascular Endothelial-like Cells (iBMECs)

status: Public on Jun 05 2019

first: Michael

last: Workman

address: 8700 Beverly Blvd., AHSP Suite 8405

institute: Cedars-Sinai Medical Center

summary: Comparison of Human iPSC-derived Brain Microvascular Endothelial-like Cells (iBMECs) grown in poly(dimethylsiloxane) tissue chips.  Data contains RNA-seq profiles of iBMECs exposed to various levels of shear stress ranging from 0, 0.01, 0.5, and 2.4 dyn/cm2; as well as RNA-seq profiles of FACS sorted iBMECs cultured alone or with primary human astrocytes and pericytes or with iPSC-derived neural progenitor cells.

overall_design: RNA-seq profiles of iBMECs under increasing levels of laminar flow to generate shear stress or co-cultured with neural cells in PDMS-based tissue chips

first: Clive

middle: N

last: Svendsen


title: Oligogenic inheritance of congenital heart disease involving a NKX2-5 modifier [human]

status: Public on May 31 2019

city: San Francisco

first: Deepak

last: Srivastava

address: 1650 Owens St, 4A

institute: Gladstone Institutes

summary: Complex genetic inheritance is thought to underlie many human diseases, yet experimental proof of this model has been elusive. Here, we show that a human congenital heart defect, left ventricular non-compaction (LVNC), can be caused by a combination of rare, inherited heterozygous missense single nucleotide variants. Whole exome sequencing of a nuclear family revealed novel single nucleotide variants of MYH7 and MKL2 in an asymptomatic father while the offspring with severe childhood-onset LVNC harbored an additional missense variant in the cardiac transcription factor, NKX2-5, inherited from an unaffected mother. Mice bred to compound heterozygosity for the orthologous missense variants in Myh7 and Mkl2 had mild cardiac pathology; the additional inheritance of the Nkx2-5 variant yielded a more severe LVNC-like phenotype in triple compound heterozygotes. RNA sequencing identified genes associated with endothelial and myocardial development that were dysregulated in hearts from triple heterozygote mice and human induced pluripotent stem cell–derived cardiomyocytes harboring the three variants, with evidence for NKX2-5’s contribution as a modifier on the molecular level. These studies demonstrate that the deployment of efficient gene editing tools can provide experimental evidence for complex inheritance of human disease.

overall_design: Patient-specific induced pluripotent stem cells were differentiated towards cardiomyocytes for 8 days and then collected for RNA sequencing.

first: Casey

last: Gifford


title: ChIP-Seq of CBFA2T3 (ETO2) in CD34+ HSPC and AML cells

status: Public on May 29 2019

city: St. Louis

first: Jinsong

last: Zhang

address: 1402 South Grand Blvd.

department: Department of Pharmacology & Physiology

institute: Saint Louis University School of Medicine

summary: ETO2 (CBFA2T3) functions as a transcriptional corepressor, which can directly bind to E-protein family of transcriptional factors. Translocation of ETO2 has been implicated in multiple leukemogenic pathways. ETO2 also plays an important role in self-renewal, proliferation, and expansion of hematopoietic stem/progenitor cells (HSPCs). Here we report the genomic binding sites of ETO2 in human cord-blood derived CD34+ HSPCs, Kasumi-1 t(8;21) AML cells, and U937 AML cells. All ChIP-Seq assays were performed with an ETO2 specific antibody that does not recognize other ETO/MTG family proteins (ETO or MTGR1).

overall_design: Chromatin immunoprecipitation using anti-ETO2 antibody followed by deep sequencing in three cell lines (normal CD34+ HSPCs and two different AML cells).


title: Comparison of expressed pdxJ variants on global gene expression in E. coli

status: Public on May 13 2019

city: Juelich

first: Tino

last: Polen

state: NRW

address: Wilhelm-Johnen-Str 1

department: IBG-1: Biotechnology

institute: Forschungszentrum Jülich GmbH

summary: DNA microarray analyses was carried out to identify genes which are differentially expressed in E. coli when mutant variants of pdxJ are expressed that rescue growth of auxotrophic E. coli delta serB and delta serC mutants.

platform_organism: Bacillus subtilis subsp. subtilis str. 168

overall_design: Cells were grown in minimal M9-glucose medium. When a culture reached an optical density of 0.5 cells were harvested by centrifugation for RNA preparation. For each comparison pdxJ(11+) / pdxJ(11-) and pdxJ(X3+)/ pdxJ(WT) two independent biological samples grown from separate cultures were used.

first: Bettina

last: Rohweder

first: Christina

last: Mack

last: Bott

first: Reinhard

last: Sterner


title: Oligogenic inheritance of congenital heart disease involving a NKX2-5 modifier [mouse]

state: CA

overall_design: Wt hearts were compared to triple mutant hearts to identify genes differentially regulated in the diseased state. Double mutant hearts were also compared to triple mutant hearts to identify genes dysregulated in the presence of the Nkx2-5 modifier.


title: Genes associated with the progression of neurofibrillary tangles in Alzheimer's disease

status: Public on May 24 2019

city: Niigata

first: Akinori

last: Miyashita

address: 1-757 Asahimachi, Chuo-ku

department: Department of Molecular Genetics

institute: Brain Research Institute, Niigata University

summary: Transcriptome analysis of post-mortem brain tissue specimens from three brain regions (BRs), entorinal, temporal and frontal cortices, of 71 Japanese brain-donor subjects to identify genes relevant to the expansion of neurofibrillary tangles. In total, 213 brain tissue specimens (= 71 subjects × 3 BRs) were involved in this study. The spreading of neurofibrillary tangles (NFTs), intraneuronal aggregates of highly phosphorylated microtubule-associated protein tau, across the human brain is correlated with the cognitive severity of Alzheimer’s disease (AD). To identify genes relevant to NFT expansion defined by the Braak stage, we conducted exon array analysis with an exploratory sample set consisting of 213 human post-mortem brain tissue specimens from the entorinal, temporal and frontal cortices of 71 brain-donor subjects: Braak NFT stages 0 (N = 13), I–II (N = 20), III–IV (N = 19) and V–VI (N = 19). We identified eight genes, RELN, PTGS2, MYO5C, TRIL, DCHS2, GRB14, NPAS4 and PHYHD1, associated with the Braak stage. The expression levels of three genes, PHYHD1, MYO5C and GRB14, exhibited reproducible association on real-time quantitative PCR analysis. In another sample set, including control subjects (N = 30) and patients with late-onset AD (N = 37), dementia with Lewy bodies (N = 17) and Parkinson disease (N = 36), the expression levels of two genes, PHYHD1 and MYO5C, were obviously associated with late-onset AD. Protein–protein interaction network analysis with a public database revealed that PHYHD1 interacts with MYO5C via POT1, and PHYHD1 directly interacts with amyloid beta-peptide 42. It is thus likely that functional failure of PHYHD1 and MYO5C could lead to AD development.

overall_design:
We analyzed total RNA of the post-mortem brain tissues from the 71 subjects (36 females, 35 males) using the Affymetrix GeneChip Human Exon 1.0 ST Arrays. All reactions were carried out according to the manufacturer’s instruction manual (P/N 701880, Rev. 4). Although no techinical replicates for the GeneChip analysis were performed, we attempted to replicate the association of the genes identified in the study by means of a real-time quantitative PCR method with a TaqMan Gene Expression Assay.
[contributor]  Japanese Alzheimer’s Disease Neuroimaging Initiative (J-ADNI)

first: Hiroyuki

last: Hatsuta

first: Masataka

last: Kikuchi

first: Akihiro

last: Nakaya

first: Yuko

last: Saito

first: Tamao

last: Tsukie

first: Norikazu

last: Hara

first: Soichi

last: Ogishima

first: Nobutaka

last: Kitamura

first: Kohei

last: Akazawa

first: Akiyoshi

last: Kakita

first: Hitoshi

last: Takahashi

first: Shigeo

last: Murayama

first: Yasuo

last: Ihara

first: Takeshi

last: Ikeuchi

first: Ryozo

last: Kuwano


title: Genome-wide profiling of gamma-ray-responsive transcriptomes from Arabidopsis thaliana ecotype Col-0

city: Jeongeup-si

first: Jin-Hong

last: Kim

state: Jeonbuk-do

address: 29 Geumgu-gil

institute: Korea Atomic Energy Research Institute

summary: To analyze the genes of which their expressions are modulated by gamma irradiation, we performed the whole genome expression microarray profiling by comparing normal whole seedlings of Arabidopsis thaliana as control with those of gamma irradiated as test sample.

overall_design: Gamma-ray-responsive gene expression in the whole seedlings of 14-day-old Arabidopsis thaliana was measured 24 hours after gamma irradiation with a dose rate of 50 Gy/hour for 4 hours.  This experiment was repeated five times  using independent biological samples at different days.

first: TaeHo

last: Ryu


title: Global gene expression profile of human peripheral blood-derived endothelial colony-forming cells is similar to coronary artery and umbilical vein endothelial cells

city: Novosibirsk

first: Marsel

last: Kabilov

address: Lavrentyev av. 8

country: Russia

institute: ICBFM SB RAS

summary: We performed a transcriptome-wide study to compare gene expression profiles of ECFC, human coronary artery endothelial cells (HCAEC) and human umbilical vein endothelial cells (HUVEC) utilising subcutaneous adipose tissue-derived stromal vascular fraction (SAT-SVF) as a negative control population. Baseline gene expression in ECFC fully corresponds to their endothelial specification and may contribute to the basement membrane organisation, fulfilling the requirements for the suitable cell population for in vitro pre-endothelialisation of tubular scaffolds.

overall_design: Comparison of gene expression in 4 cell types by Hiseq sequencing.

first: Anton

middle: G

last: Kutikhin

first: Alexey

last: Tupikin

first: Vera

last: Matveeva

first: Larisa

middle: V

last: Antonova

first: Elena

last: Velikanova


title: RNA-seq of laser captured oculomotor, cervical and lumbar spinal motor, and Onufs nucleus motor neurons in post mortem material of control human subjects

status: Public on May 09 2019

city: Stockholm

first: Eva

last: Hedlund

address: Svante Arrhenius v. 16C

department: Department of Biochemistry and Biophysics

country: Sweden

institute: Stockholm University

summary: Oculomotor neurons, which regulate eye movement, are resilient to degeneration in the lethal motor neuron disease amyotrophic lateral sclerosis (ALS). It would be highly advantageous if motor neuron resilience could be modeled in vitro. Towards this goal, we generated a high proportion of oculomotor neurons from mouse embryonic stem cells through temporal overexpression of Phox2a in neuronal progenitors. We demonstrate, using electrophysiology, immunocytochemistry and RNA sequencing, that in vitro generated neurons are bona fide oculomotor neurons based on their similarity to their in vivo counterpart in rodent and man. We also show that in vitro generated oculomotor neurons display a robust activation of survival-promoting Akt signaling and are more resilient to the ALS-like toxicity of kainic acid than spinal motor neurons. Thus, we can generate bona fide oculomotor neurons in vitro which display a resilience similar to that seen in vivo.

overall_design: A total of 39 samples were analyzed. Each sample is consists of between 30-120 laser-captured motor neurons from post-mortem human tissue. Samples are divided over 3 groups: lumbar/cervical spinal cord motor neurons (n=12), oculomotor neurons (n=20) and motor neurons of Onuf's nucleus in the sacral spinal cord (n=7).

first: Julio

last: Aguila Benitez

first: Jik

last: Nijssen

first: Christoph

last: Schweingruber


title: Exploring the in vivo role of the mitochondrial calcium uniporter in brown fat bioenergetics

status: Public on Apr 30 2019

city: Boston

first: Daniel

last: Flicker

address: Department of Molecular Biology, 185 Cambridge Street, 6th floor

institute: Massachusetts General Hospital

summary: The mitochondrial calcium uniporter has been proposed to coordinate the organelle’s energetics with cytosolic calcium signaling. Previous studies have shown that the uniporter current is extremely high in mitochondria from brown adipose tissue (BAT), yet the contribution of the uniporter to BAT physiology in vivo is not known. Here, we report the generation and characterization of a mouse model lacking Mcu, the pore forming subunit of the uniporter, specifically in BAT (BAT-Mcu-KO). BAT-Mcu-KO mice are born in Mendelian ratios on a C57BL6/J genetic background, without any overt phenotypes. Although uniporter based calcium uptake is selectively ablated in BAT mitochondria, these mice are able to defend their body temperature in response to cold challenge and exhibit a normal body weight trajectory on a high fat diet. BAT transcriptional profiles at baseline and following cold-challenge are intact and not impacted by loss of Mcu. Unexpectedly, we found that cold powerfully activates the ATF4-dependent integrated stress response in BAT, and increases both circulating FGF21 and GDF15 levels, raising the hypothesis that the integrated stress response partly underlies the pleiotropic effects of BAT on systemic metabolism.  Our study demonstrates that the uniporter is largely dispensable for BAT thermogenesis, and unexpectedly, uncovers a striking activation of the integrated stress response of BAT to cold challenge.

overall_design: RNA-seq was performed on BAT RNA isolated from BAT-Mcu-KO and control animals housed for 6 hours at 4C or room temp (RT). Samples include 6 control animals at RT; 5 control animals at 4C; 6 BAT-Mcu-KO animals at RT; and 6 BAT-Mcu-KO animals at 4C.

first: Yasemin

last: Sancak

first: Eran

last: Mick

first: Olga

last: Goldberger

first: Vamsi

middle: K

last: Mootha


title: Single-cell skeletal muscle satellite cells and endothelial cells during homeostasis and regeneration

status: Public on Mar 30 2019

city: Minneapolis

first: Mayank

last: Verma

state: MN

address: 2001 6th st se

department: Stem Cell Institute

institute: University of Minnesota

summary: We performed single cell RNA sequencing on muscle satellite cells (MuSCs) and endothelial cells (ECs) isolated from mouse hind limb muscle from both basal condition and 3-days post CTX injury to look at both quiescent and activated SCs from mice expressing genetic reporters (Pax7CreERT2:R26RtdT:Flk1GFP) by FACS. We could reliably find injury and activated SC as judged by side and forward scatter. We FACS isolated cells from both days separately and spiked in 20% of the ECs into the SCs, and performed single cell RNA-seq for each time point. We performed extensive sequencing averaging more than 300K read/cell. We were able to align the data and overlap the basal and injured cells and able to deconvolve the quiescent SCs from the activated and more differentiated MuSCs, ECs  and contaminating cell types from gene signatures.

overall_design: Cells for single cell sequencing were obtained from Pax7tdT:Flk1GFP mice hind limb muscles following enzymatic digestion as previously described (Liu et al., 2015). Dead cells were excluded from the analysis using ZombieNIR (Biolegends, 423105). TdTomato+ and GFP+ cells were sorted individually and then 20% of GFP+ cells were spiked into 80% TdTomato+. We loaded ~5,000 cells into 1 channel of the Chromium system for each of these samples and prepared libraries according to the manufacturer’s protocol using version 2.0 chemistry (10x Genomics). Following capture and lysis, we synthesized cDNA and amplified for 12 cycles as per the manufacturer’s protocol (10X Genomics). The amplified cDNA was used to construct Illumina sequencing libraries that were each sequenced on one lane of an Illumina HiSeq 2500 machine. We used Cell Ranger 2.0 (10X Genomics) to process raw sequencing data. This pipeline converted Illumina basecall files to fastq format, aligned sequencing reads to the mm10 transcriptome using the STAR aligner, quantified the expression of transcripts in each cell using Chromium barcodes.

first: Atsushi

last: Asakura


title: Induction and maintenance of specific multipotent progenitor stem cells synergistically mediated by Activin A and BMP4 signaling

status: Public on Apr 19 2019

city: Hohhot

first: Chen

last: Yanglin

address: Xilin road

institute: Inner Mongolia University

summary:
We recently reported that epiblast stem cells (EpiSCs)-like cells could be derived from preimplantation embryos (named as AFSCs). Here, we established AFSCs from pre‐implantation embryos of multiple mouse strains and showed that unlike EpiSCs, the derivation efficiency of AFSCs was affected by the genetic background. We then used AFSCs lines to dissect the roles of Activin A (Act A) and basic fibroblast growth factor and reported that Act A alone was capable of maintaining self renewal but not developmental potential in vivo. Finally, we established a novel experimental system, in which AFSCs were efficiently converted to multipotent progenitor stem cells using Act A and BMP4 (named as ABSCs). Importantly, these ABSCs contributed to neural mesodermal progenitors and lateral plate mesoderm in postimplantation chimeras. Taken together, our study established a robust experimental system for
the generation of specific multipotent progenitor stem cells that was self-renewable and capable of contributing to embryonic and extra-embryonic tissues.

overall_design: mRNA profiles of 3 cell types, generated by RNA sequencing in 3 duplicates, using HiSeq x10. Paired-end 150-bp sequencing was applied

first: Y

last: Chen

first: S

last: Bao


title: Oligogenic inheritance of congenital heart disease involving a NKX2-5 modifier

first: Deepak

last: Srivastava

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

overall_design: Refer to individual Series


title: The prominent transcriptional and metabolites changes of Mycobacterium bovis BCG str. Tokyo 172 induced by vitamin B1

status: Public on May 08 2019

city: harbin

first: Ningning

last: Song

address: No.678. Haping Road

institute: Harbin Veterinary Research Institute

summary: Vitamin B1 (VB1) is a key dietary nutrient and crucial cofactor, which exhibits a series of regulatory functions on cellular processes and the activation of the immune system. To date, the precise effect of VB1 on Mycobacterium tuberculosis has not been fully described. In the present study, the direct influence of VB1 treatment on M. bovis BCG was determined using RNA-sequencing and LC/MS. The selection of this strain was used due to its common physiological features with M.tuberculosis. The investigation of the M. bovis BCG transcription demonstrated significant changes in certain metabolic and cellular process such as the decrease in fatty acid, cholesterol and glycolipid catabolism, the decrease in DNA replication and protein translation, the reduction in cell division and cell wall formation. LC/MS indicated that most of amino acids and ADP decreased in VB1 processed culture. In addition, growth assays indicated that VB1 inhibited the BCG growth rate in vitro. This study will be benefit for our deeply understanding for impact of VB1 to M.tuberculosis.

sample_organism: Mycobacterium tuberculosis variant bovis

overall_design: 2 groups (control and treated group), each group contain triplicates

first: Zhaoli

last: Li

first: Ziyin

last: Cui

first: Liping

first: Yingying

first: Guanghui

last: Dang

first: Zhe

first: He

first: Siguo

last: Liu


title: Gene expression profiling of human  CD19+ B cells and EBV transformed lymphoblastoid cell lines (LCLs)

status: Public on Apr 01 2019

city: Kingswood

first: Grant

last: Parnell

state: NSW

address: Nepean Hospital

department: Nepean Clinical School

institute: University of Sydney

summary: Genome wide association studies have identified >200 susceptibility loci accounting for much of the heritability of Multiple Sclerosis (MS). Epstein-Barr virus (EBV), a memory B cell tropic virus, has been identified as necessary but not sufficient for development of MS. The molecular and immunological basis for this has not been established. Infected B cell proliferation is driven by signalling through the EBV produced cell surface protein LMP1, a homologue of the MS risk gene CD40.  Methods: We have investigated transcriptomes of B cells and EBV infected B cells at Latency III (LCLs) and identified MS risk genes with altered expression on infection

overall_design: 5 individuals with paired CD19+ B cells and LCLs

first: David

last: Booth


title: Ultra-High Throughput Single Cell Analysis of Proteins and RNAs by Split-pool Synthesis

status: Public on May 07 2019

city: Pleasanton

first: Maeve

last: Ohuallachain

state: CALIFORNIA

address: 4300 Hacienda Drive

institute: ROCHE SEQUENCING SOLUTIONS INC

summary: We report a method enabling simultaneous, ultra-high throughput single-cell-barcoding, of millions of cells for targeted single cell analysis of proteins and RNAs.  This method termed Quantum Barcoding (QBC) circumvents the need to isolate single cells by building cell-specific oligo barcodes dynamically within each cell.  With minimal instrumentation (four 96-well plates and a multichannel pipette) cell-specific codes are added to each tagged molecule within cells.  This is accomplished through sequential rounds of the well-established process of classic “split-pool synthesis”. We demonstrate the utility of this currently research use only technology in multiple model systems.

overall_design: Analysis of various cell types by the QBC single-cell analysis technology

last: O’Huallachain

first: Sri

last: Paladugu


title: Epigenetic evolution and lineage histories of chronic lymphocytic leukemia

status: Public on May 02 2019

city: New York

first: Federico

last: Gaiti

state: NY

address: 413 East 69th St.

institute: Weill Cornell Medicine

type: Methylation profiling by high throughput sequencing

summary: Genetic and epigenetic intra-tumoral heterogeneity cooperate to shape the evolutionary course of cancer. In addition to genetic mutations, chronic lymphocytic leukemia (CLL) undergoes diversification through stochastic DNA methylation changes – epimutations. To measure the epimutation rate at single-cell resolution, we applied multiplexed reduced representation bisulfite sequencing (MscRRBS) to healthy donors B cells and CLL patient samples. We observed that the common clonal CLL origin results in consistently elevated epimutation rate (i.e., low cell-to-cell epimutation rate variability). In contrast, variable epimutation rates across normal B cells reflect diverse evolutionary ages across the B cell differentiation trajectory, consistent with epimutations serving as a molecular clock. Heritable epimutation information allowed high-resolution lineage reconstruction with single-cell data, applicable directly to patient sample. CLL lineage tree shape revealed earlier branching and longer branch lengths than normal B cells, reflecting rapid drift after the initial malignant transformation and a greater proliferative history. To validate the inferred tree topology, we integrated MscRRBS with single-cell transcriptomes and genotyping, which confirmed that genetic subclones map to distinct clades inferred solely based on epimutation information. Lastly, to examine potential lineage biases during therapy, we profiled serial CLL samples prior to and during ibrutinib-associated lymphocytosis. Lineage trees revealed divergent clades of cells preferentially expelled from the lymph node with ibrutinib therapy, marked by distinct transcriptional profiles. These data offer direct single-cell integration of genetic, epigenetic and transcriptional information in the study of leukemia evolution, providing deeper insight into its lineage topology and enabling the charting of its evolution with therapy.

overall_design: We profiled the single-cell DNA methylomes of 831 normal B cells from six healthy donor samples and 1,821 cells from 12 primary IGHV mutated and unmutated CLLs. Single-cell methylome profiling was performed with multiplexed single-cell reduced representation bisulfite sequencing (MscRRBS), an adaption of a previous scRRBS protocol that allows to increase throughput through the addition of cell barcodes early in the scRRBS protocol. We also integrated single-cell DNAme and whole transcriptome sequencing with targeted sequencing of known somatic mutations in the cDNA.

first: Ronan

last: Chaligne

first: Hongcang

last: Gu

first: Catherine

middle: J

last: Wu

first: Alexander

last: Meissner

first: Dan

last: Landau


title: Dram1 deficiency enhances mycobacterial disease progression due to pyroptotic cell death of infected macrophages

city: Leiden

first: Gabriel

last: Forn-Cuní

state: Zuid-Holland

address: Einsteinweg 55

department: IBL-ASH-CO

institute: Universiteit Leiden

summary: DNA Damage Regulated Autophagy Modulator 1 (DRAM1) is a stress-inducible regulator of autophagy and cell death. DRAM1 has been implicated in cancer, myocardial infarction, and infectious diseases, but the molecular and cellular functions of this transmembrane protein remain poorly understood. Previously, we have proposed DRAM1 as a host resistance factor for tuberculosis (TB) and a potential target for host-directed anti-infective therapies. In this study, we generated a zebrafish dram1 mutant and investigated its loss-of-function effects during Mycobacterium marinum (Mm) infection, a widely used model in TB research. In agreement with previous knockdown analysis, dram1 mutation increased the susceptibility of zebrafish larvae to Mm infection. RNA sequencing revealed major effects of Dram1 deficiency on metabolic, immune response, and cell death pathways during Mm infection, whereas only minor effects on proteinase and metabolic pathways were found under uninfected conditions. Furthermore, unchallenged dram1 mutants did not display overt autophagic defects, while autophagic targeting of Mm was reduced in absence of Dram1, despite overall increased Lc3-II accumulation. The phagocytic ability of dram1 mutants was unaffected, but acidification of Mm-containing vesicles was strongly reduced, indicating that Dram1 is required for phagosome maturation. By in vivo imaging we observed that Dram1-deficient macrophages fail to restrict Mm during early stages of infection. The resulting enhanced bacterial burden phenotype could be rescued by knockdown of inflammatory caspase (caspa) and gasdermin (gsdmeb), demonstrating pyroptosis as the mechanism underlying premature cell death of Mm-infected macrophages in dram1 mutants. Collectively, these data demonstrate that dissemination of mycobacterial infection in zebrafish larvae is promoted in absence of Dram1 due to reduced maturation of mycobacteria-containing vesicles, failed intracellular containment, and consequent pyroptotic cell death of infected macrophages. These results provide new evidence that Dram1 plays a central role in host resistance to intracellular infection, acting at the crossroad of autophagy and cell death.

overall_design: Mutant embryos and their controls were manually dechorionated at 24 hours post fertilization (hpf) and at 28 hpf they were infected by injecting 150 or 300 colony forming units of M. marinum strain M into the blood island, or mock-injected with PBS/2%PVP. After injections embryos were transferred into fresh egg water containing 0.003% 1-phenyl-2-thiourea (Sigma-Aldrich) to prevent melanisation and incubated for 4 days at 28,5°C. After the incubation period, infected and uninfected mutants and their controls were imaged and groups of 20 embryos were snap-frozen in liquid nitrogen and RNA was isolated for Illumina RNAseq analysis.

first: Rui

last: Zhang

first: Monica

last: Varela

last: Forn-Cuni

first: Vincenzo

last: Torraca

first: Michiel

last: van der Vaart

first: Annemarie

middle: H

last: Meijer


title: rnadapt- Non-coding RNAs in the adaptation of root growth to phosphate starvation [miRNA-Seq]

status: Public on Mar 14 2019

city: Gif-sur-Yvette

first: Thomas

last: Blein

address: Avenue des Sciences

country: France

institute: CNRS

summary: Identification of new elements (non-coding-RNA) controlling root growth in response to phosphate.-Plants (Columbia er 105, or Landsberg erecta) were grown one week on media with Phosphate (+P) and then transfered on media without (-P = P starvation) for 1h or 2h. Root apices were harvested and total RNA extracted for RNA sequencing.

overall_design: 18 samples with 3 biological replicats. dose response,ecotype comparison,time course

first: Coline

last: Balzergue

first: Marc

last: Gabriel

first: Ludivine

last: Taconnat

first: Sandrine


title: scRNA-seq of pediatric glioblastoma patient-derived xenografts

status: Public on Mar 15 2019

city: Houston

first: Marco

last: Gallo

state: TX

address: 1102 Bates Avenue

department: Pediatrics

institute: Baylor College of Medicine

summary: scRNA-seq of patient-derived xenografts.

overall_design: scRNA-seq of 2 patient-derived xenografts using 10xGenomics technology.

first: Mary

last: Hoffman


title: RNAseq profiling of miR-132/212-deficient CD4+ T cells activated in vitro and in vivo.

status: Public on Mar 22 2019

city: York

first: Katherine

last: Newling

address: Wentworth Way

department: Biology

institute: University of York

summary: Transcriptomic profiling of miR-132/212-deficient and WT CD4 T cells isolated from spleens of L donovani infected mice (d28) to determine the effects of miR-132/212 on CD4 T cell activation in vivo. This was combined by transcriptomic analysis of early stage in vitro activated WT and miR-132/212-deficient CD4 T cells to identify direct miR-132/212 targets in CD4 T cells.

overall_design: Examination of expression profiles of splenic CD4+ T cells from L. donovani-infected WT (samples 1-4) and miR-132/212-/- mice (samples 5-9) using RNASeq. This was followed by similar RNASeq in naïve CD4+ T-cells in WT and miR-132/212 -/- mice prior to and following 18h of in vitro TCR stimulation under Th1 conditions (samples 10-25).

first: Dimitris

last: Lagos

first: James

last: Hewitson

first: Kunal

last: Shah

first: Najmeeyah

last: Brown

first: Paul

last: Grevitt

first: Sofia

last: Hain

first: Tyson

last: Sharp

last: Kaye


title: rnadapt-Non-coding RNAs in the adaptation of root growth to phosphate starvation

summary: ngs2013_14_rnadapt-rnadapt-Identification of new elements (non-coding-RNA) controlling root growth in response to phosphate.-Plants (Columbia er 105, or Landsberg erecta) were grown one week on media with Phosphate (+P) and then transfered on media with (+P) or without (-P = P starvation) for 1h or 2h. Root apices were harvested and total RNA extracted for RNA sequencing.


title: WDR5, BRCA1 and BARD1 co-regulate the DNA damage response and modulate the mesenchymal-to-epithelial transition during early reprogramming

city: Nijmegen

first: Georgina

last: Peñalosa Ruiz

address: Geert Grooteplein 30

institute: Radboud University


title: CELSeq2-profiles for siRNA screening and daily timecourse for early reprogramming to pluripotency.

summary:
AIM: To find molecular signatures associated to the siRNA-mediated knockdowns in order to be able to identify similarities among different knockdowns.
DESCRIPTION: Each sample includes biological triplicates for 35 siRNA-mediated knockdowns targeting 30 chromatin-associated proteins during in early reprogramming to iPS at day 6. A daily timecourse from reprogramming cells, without treatment from MEFs until day 6 is also included in triplicate.

overall_design: RNA was harvested for all samples in bulk and the CELSeq2 method was used to prepare the RNAseq libraries

first: Jan

last: Gerlach

first: Gert

last: Veenstra

first: Klaas

last: Mulder


title: CENPA-Bound Genes and Transcriptional Profiling of CENPA-Depleted Prostate Cancer Cells

status: Public on Mar 06 2019

city: Ann Arbor

first: Anjan

middle: Kumar

last: Saha

state: MI

address: 1150 West Medical Center Drive

institute: University of Michigan


title: Transcriptional Profiling of CENPA-Depleted Prostate Cancer Cell Lines

summary: Overexpression of centromeric proteins has been identified in a number of human malignancies, though their functional and mechanistic contributions to disease progression have not been characterized. CENPA, the centromeric histone H3 variant, is the epigenetic mark that determines centromere identity. Here, we demonstrate that CENPA is highly overexpressed in prostate cancer in both tissue and cell lines, and the level of CENPA expression correlates with the stage of disease. Gain-of- and loss-of-function experimentation confirms that CENPA promotes prostate cancer cell line growth. Integrated sequencing studies further reveal a previously unidentified function of CENPA as a transcriptional regulator that modulates expression of critical proliferation, cell-cycle, and centromere/kinetochore genes. Our findings, therefore, suggest a previously undescribed biological function for CENPA, a protein normally thought to be solely and importantly involved in centromere identity.

overall_design: Examination of transcriptional profile of prostate cancer cells under CENPA-depleted condtions

first: Tingting

last: Qin

first: Maureen

last: Sartor

first: David

last: Markovitz


title: RNA-seq profiles of reprogramming cells at Day 3 and Day 6 from MEFs to iPS cells

summary:
AIM: To detect differences in transcriptional profiles after knocking down Brca1, Bard1 or Wdr5, compared to a negative control in early reprogramming to pluripotency.
DESCRIPTION: RNA-seq profiles of early reprogramming mouse embryonic fibroblasts (MEFs) transduced with lentivirus containing doxycycline-inducible OSKM factors to induce pluripotency . Before starting reprogramming, OSKM-MEFs were transfected with different siRNAs and then they were reprogrammed for 3 or 6 days.

overall_design: The control sample consists of cells transfected with non-targeting siRNA. The other samples were transfected with either siBrca1, siWdr5 or siBard1. For every knockdown there is a biological replicate.

last: Peñalosa-Ruiz

first: GertJan

middle: C

middle: W


title: RNA-seq expression profiling of cardiac macrophages and splenic monocytes from naïve and CAWS challenged mice

status: Public on Mar 29 2019

city: Parkville

first: Gordon

last: Smyth

state: Vic

address: 1G Royal Pde

department: Bioinformatics

institute: Walter and Eliza Hall Institute of Medical Research

summary: The adult heart contains macrophages derived from both embryonic and adult bone-marrow derived precursors. Such population diversity raises the possibility that macrophages of distinct origins occupy differing biological roles or anatomical niches within the heart. Here, we provide evidence for the latter, showing that bone-marrow derived macrophages express the chemokine receptor Ccr2 and preferentially localise to the aortic root of the heart. This targeted migration occurs via a Ccr2-Ccl7 axis, whereby Ccl7-producing cardiac fibroblasts populating the aortic root, recruit Ccr2pos macrophages. Notably, the selective recruitment of Ccr2pos macrophages renders the aortic root sensitive to inflammatory disease. In a mouse model of Kawasaki Disease, acute inflammation drives a numerical increase in bone-marrow derived Ccr2pos macrophages, which accumulate at the aorta and trigger local inflammation at this site. We propose that cardiac fibroblasts recruit Ccr2pos macrophages to the aortic root, and that this process targets inflammatory disease to the heart’s major vessels.

overall_design: Mice were either naïve or challenged with a Candida albicans water-soluble complex (CAWS) to induce a mouse model of Kawasaki Disease. Cardiac macrophages were extracted from three independent pools of naive mice and three independent pools of CAWS challenged mice. Splenic monocytes were extracted from three independent pools of naive mice. In each case, cardiac macrophages were divided into three subpopulations (R1, R2 and R3) based on Ccr2 and MHC-II expression.


title: A dataset of microRNAs during embryonic development of common carp, Cyprinus carpio

status: Public on Mar 26 2019

city: Wuxi

first: Lanmei

last: Wang

address: East Shanshui Road 9

institute: Freshwater Fisheries Research Centre of Chinese Academy of Fishery Sciences

summary: The Cyprinus carpio is one of the most important food fish with over hundred varieties in the world. It shows many morphological and genetic variations after selection breeding. It is also considered an alternative vertebrate fish model to zebrafish.  MicroRNAs (miRNAs) and long non-coding RNAs (lncRNAs) have been suggested to have a crucial role in embryonic development. However, systemic research on the lncRNAs and miRNAs during embryonic development of C. carpio has not been reported yet. In this study, we investigated the miRNA, lncRNA and mRNA expression profiles during six main embryonic development stages (cleavage (2 hours post-fertilization hpf)), blastocyst (6 hpf), gastrulation (12 hpf), organ formation (20 hpf), hatching (64 hpf) and 1 day post-hatching). A total of 9,888,123 clean reads were obtained frommiRNA library. After filtering,  2886 miRNAs were identified. The results would open the way for future genetic, genomic, and evolutionary studies and enable better understanding of gene regulation during embryonic development of C. carpio.

overall_design: miRNAs in embryonic development stages of common carp were detected by deep sequencing using Illumina HiSeq 2500.

first: Feibiao

last: Song

first: Wenbin

last: Zhu

first: Jianjun

last: Fu

first: Zaijie

last: Dong


title: Mating enhances expression of hormonal and trophic factors in the midbrain of female rats

status: Public on Feb 28 2019

city: Rensselaer

first: Sridar

last: Chittur

address: One Discovery Drive, CRC 342G

department: Center for Functional Genomics

institute: SUNY-University at Albany

summary:
Among female Long-Evans rats, mating enhances neurosteroid formation in the midbrain ventral tegmental area (independent of peripheral steroid-secreting glands, the ovaries and adrenals). The sources/targets for these actions are not well-understood. In Experiment 1, proestrous rats engaged in a mating paradigm, or did not, and had midbrains assessed via Affymetrix rat genome microarrays. In Experiment 2, the influence of gonadal and adrenal glands on the expression of these genes was assessed in rats that were proestrous, ovariectomized (OVX), or OVX and adrenalectomized (ADX).
Microarrays revealed 53 target genes that were significantly up-regulated (> 2.0-fold change) in response to mating. Mating significantly enhanced midbrain mRNA expression of genes involved in hormonal and trophic actions: Gh1, S100g, and Klk1b3 in proestrous, but not OVX and/or ADX, rats; Fshb in all but OVX/ADX rats; and Lhb and Tshb in all rats. Thus, mating enhances midbrain gene expression, independent and dependent of, peripheral glands.

overall_design: Experiment 1: proestrous rats engaged in a mating paradigm, or did not, and had midbrains assessed via Affymetrix rat genome 2.0 microarrays. In Experiment 2, the influence of gonadal and adrenal glands on the expression of these genes was assessed in rats that were proestrous, ovariectomized (OVX), or OVX and adrenalectomized (ADX).

first: Cheryl

middle: A

last: Frye

first: John

last: Tine


title: Functional Taxonomy of CENPA-Bound Genes in Prostate Cancer

overall_design: Identification of extracentromeric CENPA binding in prostate cancer using ChIP-seq


title: Induction of human regulatory innate lymphoid cells from group 2 innate lymphoid cells by retinoic acid

status: Public on Jan 26 2019

city: Zurich

first: Ge

last: Tan

address: Winterthurerstrasse 190

department: Functional Genomics Center Zurich

country: Switzerland

institute: University of Zurich

summary: We aimed to determine the characteristic of IL-10-producing ILCs induced from ILC2s by RA. We found that IL-10-producing ILCs has distinct characteristic compared to IL-10 negative ILCs.

overall_design: mRNA profile of IL-10 positive ILCs and IL-10 negative ILCs genarated from ILC2s

first: Hideaki

last: Morita

first: Cezmi

last: Akdis


title: STX4 Over-Expression in Human islets

status: Public on Mar 01 2019

city: Indianapolis

first: Debbie

middle: Carolyn

last: Thurmond

state: IN

address: 635 Barnhill Drive, MS 2031

institute: Indiana University

summary: We have used RNA-seq to identify transcripts expressed in human islets harboring beta cells transduced  to overexpress STX4 and induce chemokine ligand by adenoviral transduction

overall_design: 3 human islets preparations examed under 2 conditions, beta cell specific expressed STX4 and control GFP. A human islets preparation tested under no tranduction and ctrol GFP transduction by adenovirus.

first: Miwon

last: Ahn

first: Eunjin

last: Oh

first: Charles

last: Warden


title: The effect of very-high-molecular-mass hyaluronan (vHMM-HA) on IMR90 transcriptome

status: Public on Jan 01 2019

city: Osaka-shi

first: Masaki

last: Takasugi

state: Osaka

address: 1-4-3 Asahimachi, Abeno-ku

department: Graduate School of Medicine

institute: Osaka Metropolitan University

summary: Naked mole-rat skin fibroblasts (NSF) produces vHMM-HA. Although NSF-HA has been shown to suppress NSF transformation, it is still unclear if exceptional polymer length of vHMM-HA is important for its functions. Here, we compared the effect of intact control NSF-HA (cNSF-HA) and partially fragmented NSF-HA (fNSF-HA) on the transcriptome of IMR90 cells. Related RNA-Seq datasets are deposited in ArrayExpress (E-MTAB-8943).

overall_design: Transcriptome of IMR90 cells treated with PBS, cNSF, fNSF were analyzed before and after exposing cells to oxidative stress.


title: Multi-modal analysis of the aging mouse lung at cellular resolution

status: Public on Jan 10 2019

first: Lukas

last: Simon

address: 1 Baylor Plaza

department: THINC

summary: A) Whole lung tissue from 24 months (n=7) and 3 months old (n=8) mice was dissociated and single-cell mRNAseq libraries generated with Drop-Seq. B) Bulk RNA-seq data was generated from whole mouse lung tissue of old (n=3) and young (n=3) samples. C) Bulk RNA-seq data was generated from flow-sorted macrophages from old (n=7) and young (n=5) mice and flow-sorted epithelial cells from old (n=4) and young (n=4) mice.

overall_design: Integration of bulk RNA-seq from whole mouse lung tissue and bulk RNA-seq from flow-sorted lung macrophages and epithelial cells was used to validate results obtained from single cell RNA-seq of whole lung tissue.

middle: M

first: Herbert

last: Schiller