title: CTCL cell line H9:vehicle control vs.ShBCL11B

first: Wenjing

last: Fu

address: No.1 Xianmen Street, Xicheng District

department: Department of Dermatology and Venerology

institute: Peking University First Hospital

summary: Transcriptional profiling of human CTCL cell line H9 comparing cells transfected with vehicle control with ShBCL11B cells. Previous study have shown the involvements of BCL11b/BCL11B in T cell development and hematopoietic malignancies of T-cell origin. Objective was to explore the action of BCL11B in the pathogenesis of cutaneous T-cell lymphoma(CTCL).

overall_design: Two-condition experiment, BCL11B-VC H9 vs. ShBCL11B H9 cells. Biological replicates: 3 control replicates, 3 ShBCL11B replicates.

first: Yang

last: Wang


title: WDR5 regulates EMT and metastasis in breast cancer by activating TGFB pathway [ChIP-seq]

status: Public on Dec 17 2019

city: Milan

first: Chiara

last: Balestrieri

address: Via Olgettina 58

department: Center for Omics Sciences

country: Italy

institute: IRCCS San Raffaele Scientific Institute

type: Genome binding/occupancy profiling by high throughput sequencing

summary: The core subunit of the COMPASS-like complex, WD Repeat Domain 5 (WDR5) has a prominent role in reprogramming and Epithelial-to-Mesenchymal transition (EMT) in different tumor types. Our evidences support a model in which WDR5 is prominent for EMT and metastasis dissemination in breast cancer patient-derived xenografts and cell lines. Moreover, WDR5 silencing abrogates TGFB pathway activation and reverts mesenchymal into epithelial phenotype, by inhibiting transcription of main master regulators of EMT (CDH2, TWIST1, SNAI1, SNAI2 and ZEB1).  Our data suggest that WDR5 inhibition may be a successful approach to prevent progression of metastatic BC.

overall_design: Chromatin from MCF10DCIS.com breast cancer cell line was immunoprecipitated with anti-WDR5 and anti-H3K4me3 antibody and subjected to multiparallel sequencing. Experiments were carried out in shLuc (control) and WDR5 silenced cells.

first: Simona

last: Punzi

first: Luisa

last: Lanfrancone


title: Transcriptional profiling of neurons in the hypothalamus and midbrain of an Slc17a6-TRAP (JX883) mouse line

status: Public on Dec 16 2019

city: New York

first: Laura

last: Kus

state: NY

address: 1230 York Avenue # 260

department: Heintz Laboratory

country: USA

institute: The Rockefeller University

type: Expression profiling by high throughput sequencing

summary: TRAP translational profiling is a method that allows investigators to genetically characterize specific cell types in complex tissues such as mouse brain.  Using this technique we obtained RNA-Seq data from actively translating transcripts present in neurons in the hypothalamus and midbrain of adult Slc17a6-EGFP/Rpl10a (JX883) mice.

overall_design: TRAP-Seq of neurons in the hypothalamus and midbrain of adult Slc17a6-EGFP/Rpl10a (JX883) transgenic mice

first: Jie

last: Xing

first: Jim

last: Li


title: Transcriptional profiling of neurons located in the left vs right side of the medial habenula in Chat-TRAP (DW167) BAC transgenic mice

summary: TRAP translational profiling is a method that allows investigators to genetically characterize specific cell types in complex tissues such as mouse brain.  Using this technique we obtained RNA-Seq data from actively translating transcripts present in neurons in the left vs right medial habenula of adult Chat-EGFP/Rpl10a (DW167) mice

overall_design: TRAP-Seq of neurons in the right vs left medial habenula of adult Chat-EGFP/Rpl10a (DW167) mice

first: Andreas

last: Gorlich

first: Ines

last: Ibanez-Tallon


title: Transcriptional profiling of microglia in subcortical brain regions of a Cfh-TRAP (NIDA092) mouse line

summary: TRAP translational profiling is a method that allows investigators to genetically characterize specific cell types in complex tissues such as mouse brain.  Using this technique we obtained RNA-Seq data from actively translating transcripts present in microglia in subcortical brain regions of adult Cfh-EGFP/Rpl10a (NIDA092) mice.

overall_design: TRAP-Seq of microglia in subcortical brain regions of adult Cfh-EGFP/Rpl10a (NIDA092) mice


title: Transcriptional profiling of cells in the dorsal striatum and accumbens nucleus of older Drd1-TRAP (CP73) mice: immunopurified (IP) data

summary: Using translational profiling we obtained RNA-Seq data from total RNA present in the dorsal striatum and accumbens nucleus of older Drd1-EGFP/Rpl10a (CP73) mice

overall_design: RNASeq of cells in the dorsal striatum and accumbens nucleus of older Drd1-TRAP (CP73) mice, i.e. age to >20 months

first: Erika

last: Andrade

first: Johana

last: Alvarez


title: Long-access cocaine intravenous self-administration; transcriptional profiling of medium spiny neurons in the accumbens nucleus of Drd2-TRAP (CP101) mice

summary: TRAP translational profiling is a method that allows investigators to genetically characterize specific cell types in complex tissues such as mouse brain.  Using this technique we obtained RNA-Seq data from actively translating transcripts present in medium spiny neurons in the accumbens nucleus of adult Drd2-EGFP/Rpl10a (CP101) mice that were administered either saline or cocaine under long access conditions

overall_design: Long-access cocaine intravenous self-administration study; TRAP-Seq of medium spiny neurons in the accumbens nucleus of adult Drd2-EGFP/Rpl10a (CP101) mice administered either saline or cocaine


title: Long-access cocaine intravenous self-administration; transcriptional profiling of medium spiny neurons in the accumbens nucleus of Drd1-TRAP (CP73) mice

summary: TRAP translational profiling is a method that allows investigators to genetically characterize specific cell types in complex tissues such as mouse brain.  Using this technique we obtained RNA-Seq data from actively translating transcripts present in medium spiny neurons in the accumbens nucleus of adult Drd1-EGFP/Rpl10a (CP73) mice that were administered either saline or cocaine under long-access conditions

overall_design: Long-access cocaine intravenous self-administration study; TRAP-Seq of medium spiny neurons in the accumbens nucleus of adult Drd1-EGFP/Rpl10a (CP73) mice administered either saline or cocaine


title: Transcriptional profiling of interneurons in the cerebral cortex of Htr3a-Cre (NO176) mice

summary: TRAP translational profiling is a method that allows investigators to genetically characterize specific cell types in complex tissues such as mouse brain.  Using this technique we obtained RNA-Seq data from actively translating transcripts present in interneurons in the cerebral cortex of adult Htr3a-Cre (NO176) mice x Rosa26-LSL-EGFP/Rpl10a mice

overall_design: TRAP-Seq of interneurons in the cerebral cortex of adult Htr3a-Cre (NO176)::Rosa26-LSL-EGFP/Rpl10a mice

first: Cuidong


title: Long-access cocaine intravenous self-administration; transcriptional profiling of medium spiny neurons in the dorsal striatum of Drd1-TRAP (CP73) mice

summary: TRAP translational profiling is a method that allows investigators to genetically characterize specific cell types in complex tissues such as mouse brain.  Using this technique we obtained RNA-Seq data from actively translating transcripts present in medium spiny neurons in the dorsal striatum of adult Drd1-EGFP/Rpl10a (CP73) mice that were administered either saline or cocaine under long access conditions

overall_design: Long-access cocaine intravenous self-administration study; TRAP-Seq of medium spiny neurons in the dorsal striatum of adult Drd1-EGFP/Rpl10a (CP73) mice administered either saline or cocaine


title: Transcriptional profiling of neurons in the cerebral cortex of S100a10-TRAP (ES691) mice administered either saline or cocaine

summary: TRAP translational profiling is a method that allows investigators to genetically characterize specific cell types in complex tissues such as mouse brain.  Using this technique we obtained RNA-Seq data from actively translating transcripts present in pyramidal neurons in the cerebral cortex of adult S100a10-EGFP/Rpl10a (ES691) mice that were administered either saline or cocaine.

overall_design: Short access cocaine intravenous self-administration study; TRAP-Seq of neurons in the cerebral cortex of adult S100a10-EGFP/Rpl10a (ES691) mice administered either saline or cocaine


title: polyA+ RNA sequencing on FACS sorted alveolar macrophages (CD45+SiglecF+CD11c+) from air and cigarette-smoke exposed wild type and miR-155 KO mice

city: Ghent

first: Ken

middle: R

last: Bracke

address: Corneel Heymanslaan 10

department: Department of Respiratory Medicine

country: Belgium

institute: Ghent University

summary: Chronic obstructive pulmonary disease (COPD) is a highly prevalent respiratory disease characterized by airflow limitation and chronic inflammation. MiR-155 is described as an ancient regulator of the immune system. Our objective was to establish a role for miR-155 in cigarette smoke (CS)-induced inflammation and COPD. We demonstrate increased miR-155 expression by RT-qPCR in lung tissue of smokers without airflow limitation and patients with COPD compared to never smokers and in lung tissue and alveolar macrophages of CS-exposed mice compared to air-exposed mice. In addition, we exposed wild type and miR-155 deficient mice to CS and show an attenuated inflammatory profile in the latter. Alveolar macrophages were sorted by FACS from the different experimental groups and their gene expression profile was analyzed by RNA sequencing. This analysis revealed increased expression of miR-155 targets (including the NF-κB inhibitor rassf6) and an attenuation of the CS-induced increase in inflammation-related genes in miR-155 deficient mice. Finally, intranasal instillation of a specific miR-155 inhibitor significantly attenuated the CS-induced pulmonary inflammation in mice. In conclusion, we highlight a role for miR-155 in CS-induced inflammation and the pathogenesis of COPD, implicating miR-155 as a new therapeutic target in COPD.

overall_design: poly-A+ RNA sequencing was performed on 5 mice per group (4 groups: air_wild-type, air_miR-155-KO, CS_wild-type, CS_miR-155-KO)

first: Elise

middle: G

last: De Smet

first: Francisco

last: Avila Cobos


title: Transcriptional profiling of medium spiny neurons in the striatum of Drd2-TRAP (CP101) mice administered either saline or cocaine

summary: TRAP translational profiling is a method that allows investigators to genetically characterize specific cell types in complex tissues such as mouse brain.  Using this technique we obtained RNA-Seq data from actively translating transcripts present in medium spiny neurons in the whole striatum of adult Drd2-EGFP/Rpl10a (CP101) mice that were administered either saline or cocaine.

overall_design: Short access cocaine intravenous self-administration study; TRAP-Seq of medium spiny neurons in the whole striatum of adult Drd2-EGFP/Rpl10a (CP101) mice administered either saline or cocaine


title: Endogenous retroviruses direct the evolution of lineage-specific imprinting

city: Vancouver

first: Matthew

last: Lorincz

state: BC

address: 2350 Health Sciences Mall

department: Medical Genetics

country: Canada

institute: University of British Columbia

summary: Imprinted genes are expressed from a single parental allele. In mammals, this unusual mode of transcription generally depends on the epigenetic silencing of the other allele by DNA methylation (DNAme) established in the germline. While many species-specific imprinted orthologues have been documented in eutherians, the molecular mechanisms underlying the evolutionary switch from biallelic to imprinted expression are currently unknown. During mouse oogenesis, gametic differentially methylated regions (gDMRs) acquire DNAme in a process guided by transcription. Here we show that transcription initiating in proximal lineage-specific endogenous retroviruses (ERVs) is likely responsible for DNAme established in oocytes at 4/7 mouse-specific and 22/155 human-specific maternal gDMRs. The latter can be further divided into Catarrhini (old-world monkeys and apes)- or Hominoidea (ape)-specific gDMRs, which are embedded within transcription units initiating in ERVs specific to these primate lineages. Using CRISPR-Cas9 mutagenesis, we deleted the relevant murine-specific ERVs upstream of the maternally methylated genes Impact and Slc38a4. Strikingly, imprinting was lost in the offspring of dams harboring these deletions and biallelic expression was observed, revealing a novel evolutionary mechanism by which maternally silenced genes arise from biallelically expressed progenitors.

overall_design: RNA polymerase II ChIP-seq in mouse oocytes

first: Aaron

middle: B

last: Bogutz

first: Julie

last: Brind'Amour

first: Hisato

last: Kobayashi

first: Kristoffer

middle: N

last: Jensen

first: Kazuhiko

last: Nakabayashi

first: Hiroo

last: Imai

middle: C

first: Louis

middle: L

last: Lefebvre


title: Global transcriptomic profiling of the bone marrow stromal microenvironment during postnatal development, aging, and inflammation

city: Madrid

first: Elena

last: Piñeiro-Yáñez

address: Calle de Melchor Fernández Almagro, 3

country: Spain

institute: Spanish National Cancer Research Centre (CNIO)

summary: RNA-sequencing of a longitudinal comparison of four principal mesenchymal and endothelial stromal cell types (CXCL12-abundant reticular cells, PDGFR-α+ Sca-1+, sinusoidal and arterial endothelial cells), isolated from early postnatal, adult and aged mice. Additional transcriptional profiling of the response of CXCL12-abundant reticular cells and sinusoidal endothelial cells to infection-mimicking agents.

overall_design: RNA-sequencing of four FACS-isolated mouse bone marrow stromal cells at different age stages and conditions.

first: César

last: Nombela-Arrieta

first: Markus

last: Manz


title: JBIR-140 (prethioviridamide) effect on HeLa S3 cells

city: Wako

last: Matsumoto

state: Saitama

address: 2-1 Hirosawa

department: Center for Sustainable Resource Science

country: Japan

institute: RIKEN

summary:
Analysis of HeLa S3 cells treated with 4 microM JBIR-140 (prethioviridamide) for 6 h. Results provide insight into the mode of action of JBIR-140.
We examined the change in mRNA expression upon JBIR-140 treatment by DNA microarray.

overall_design: Gene expression comparison of two groups

first: Minoru

last: Yoshida


title: Transcriptional profiling of cells in the dorsal striatum and accumbens nucleus of older Drd1-TRAP (CP73) mice

first: Laura

last: Kus

overall_design: RNASeq of cells in the dorsal striatum and accumbens nucleus of older Drd1-TRAP (CP73) mice

first: Erika

last: Andrade

first: Johana

last: Alvarez


title: 3D + LY vs. 3D culture of HUASMC

city: Mannheim

first: Carolina

last: Delatorre

address: Theodor-Kutzer-Ufer 1-3

country: Germany

institute: University Heidelberg

summary: To study the impact of TGF signaling on the transcriptome of vascular smooth muscle cells, we cultured human umbilical artery smooth muscle cells as 3D aggregates in hanging drops for 48 hours. One group was treated with TGFβRI/II inhibitor LY2109761 (10 μM, additional 10 μM after 24 h), the other group with solvent (DMSO) as control. RNA was isolated from both groups after 48h

overall_design: Comparison of RNA from 3 samples of 3D cultured HUASMCs and 3 samples of 3D cultured HUASMCs treated with LY2109761

first: Thomas

last: Korff


title: Transcriptional profiling of pyramidal neurons in the cerebral cortex of Glt25d2-TRAP (DU9) mice administered either saline or cocaine [TRAP-seq]

summary: TRAP translational profiling is a method that allows investigators to genetically characterize specific cell types in complex tissues such as mouse brain.  Using this technique we obtained RNA-Seq data from actively translating transcripts present in pyramidal neurons in the cerebral cortex of adult Glt25d2-EGFP/Rpl10a (DU9) mice that were administered either saline or cocaine.

overall_design: Short access cocaine intravenous self-administration study; TRAP-Seq of neurons in the cerebral cortex of adult Glt25d2-EGFP/Rpl10a (DU9) mice administered either saline or cocaine


title: Spatial genome re-organization between fetal and adult hematopoietic stem cells [Capture-C]

city: PHILADELPHIA

first: Kai

last: Tan

state: PA

address: 3501 CIVIC CENTER BLVD.

institute: Children's Hospital of Philadelphia

summary: Fetal hematopoietic stem cells (HSCs) undergo a developmental switch to become adult HSCs. The functional properties of the HSCs change dramatically during this switch, including their cycling behavior, hematopoietic lineage outputs and proliferation rate. The relationship between three-dimensional (3D) genome organization, epigenomic state, and transcriptome is poorly understood during this critical developmental transition. Here we conduct a comprehensive survey of the 3D genome, epigenome and transcriptome of fetal and adult HSCs in mouse. We found that chromosomal compartments and topologically associating domains (TAD) are largely conserved between fetal and adult HSCs. However, there is a global trend of increased compartmentalization and TAD boundary strength.  In contrast, dynamics of intra-TAD chromatin interactions is much higher, involving thousands? of gene promoters and distal enhancers. Such dynamic interactions target genes involved in cell cycle, metabolism, and hematopoiesis. These developmental-stage-specific enhancer-promoter interactions appear to be mediated by different sets of transcription factors in fetal and adult HSCs, such as TCF3, MAFB, TCF7L2, and NR3C1. Loss of function studies of TCF3 confirms the role of TCF3 in mediating condition-specific enhancer looping and gene regulation in fetal HSCs. In summary, our data suggest that the fetal-to-adult transition is accompanied by extensive changes in intra-TAD chromatin interactions that target genes underlying the phenotypic differences between fetal and adult HSCs.

overall_design: Examination of contact maps of selected promoters in the mouse fetal and adult HSCs

first: Changya

last: Chen


title: Transcriptional profiling of medium spiny neurons in the striatum of Drd1-TRAP (CP73) mice administered either saline or cocaine

summary: TRAP translational profiling is a method that allows investigators to genetically characterize specific cell types in complex tissues such as mouse brain.  Using this technique we obtained RNA-Seq data from actively translating transcripts present in medium spiny neurons in the whole striatum of adult Drd1-EGFP/Rpl10a (CP73) mice that were administered either saline or cocaine.

overall_design: Short access cocaine intravenous self-administration study; TRAP-Seq of medium spiny neurons in the whole striatum of adult Drd1-EGFP/Rpl10a (CP73) mice administered either saline or cocaine


title: Spatial genome re-organization between fetal and adult hematopoietic stem cells [Hi-C]

overall_design: Examination of global chromatin contact maps in the mouse fetal and adult HSCs


title: Spatial genome re-organization between fetal and adult hematopoietic stem cells [RNA-Seq]

overall_design: Examination of global gene expression in the mouse fetal and adult HSCs


title: Spatial genome re-organization between fetal and adult hematopoietic stem cells (ATAC-Seq)

overall_design: Examination of open chromatin regions in the mouse fetal and adult HSCs


title: Spatial genome re-organization between fetal and adult hematopoietic stem cells (ChIP-Seq)

overall_design: Examination of 4 histone modifications in the mouse fetal and adult HSCs


city: Singapore

first: Arsen

middle: O

last: Batagov

address: 30 Biopolis St, Matrix, 07-1

country: Singapore

institute: Bioinformatics Institute

summary: SKOV3 cells comparative genomic hybridization using Affymetrix SNP 6.0 microarray

overall_design: Four replicates of SKOV3 cell line, one control sample Affymetrix reference genomic DNA 103

first: Emilie

middle: A

last: Bard-Chapeau

first: Vladimir

last: Kuznetsov


title: Ribosome profiling study of Miwi-null testes

status: Public on Dec 15 2019

city: Beijing

first: Zonggui

state: Beijing

address: No.5 Yiheyuan Road Haidian District

department: Academy for Advanced Interdisciplinary Studies

country: China

institute: Peking University

summary: piRNAs are a novel class of small noncoding RNAs that were recently identified in animal germ cells. This class of small noncoding RNAs is specifically associated with an evolutionarily conserved PIWI family proteins, which belong to the germline-specific members of the Argonaute protein family and are indispensable to germline development in animals. The PIWI/piRNA pathway has been deemed as an innate immune system that prevents mobile genetic elements from destabilizing DNA and that protects genome integrity in animal germ cells. By ribosome profiling using Miwi-null testes, we identified a group of ~600 mRNAs as likely direct piRNA targets for translational regulation in mouse spermatids. These results suggest that the mouse PIWI (MIWI)/piRNA is responsible for activating translation of a subset of spermiogenic mRNAs to coordinate with morphological transformation into elongated spermatids.

overall_design: 8 biological samples are included in the study. These include RNA-seq and ribosome profiling in 24 dpp wild-type and Miwi-null testes.

first: Peng

last: Dai

first: Xin

last: Wang

first: Lan-Tao

last: Gou

first: Zhi-Tong

last: Li

first: Ze

last: Wen

first: Zong-Gui


title: Transcriptional profiling of neurons in the striatum of Chat-TRAP (DW167) mice administered either saline or cocaine

first: Laura

summary: TRAP translational profiling is a method that allows investigators to genetically characterize specific cell types in complex tissues such as mouse brain.  Using this technique we obtained RNA-Seq data from actively translating transcripts present in neurons in the striatum of adult Chat-EGFP/Rpl10a (DW167) mice that were administered either saline or cocaine.

overall_design: TRAP-Seq of neurons in the striatum of adult Chat-EGFP/Rpl10a (DW167) mice administered either saline or cocaine


title: miroRNA sequencing of B16 cells and exosomes derived from B16 and JB6 cells

city: Suzhou

first: Ji

last: Zhou

state: Jiangsu

address: Renai Road #199

institute: Soochow university

type: Non-coding RNA profiling by high throughput sequencing

summary: The goal of this study is to compare the miRNA profiles of  melanoma cells B16-derived exosomes with B16 cells and normal cells JB6-derived exosomes.

overall_design: miRNA profiles of B16 cells, exosomes derived from B16 cells and exosomes derived from JB6 cells were generated by deep sequencing, in one counterpart, using Illumina HiSeq 2500

first: Jinping

last: Zhang


title: Different LncRNAs in exosomes derived from skov-3 cells when exposed to normal or hypoxia condition

city: Shanghai

first: Xiaoli

last: Wu

address: 2699，West Gaoke Road

department: Department of Gynecology

institute: Shanghai First Maternity and Infant Hospital, Tongji University

summary: reports shows that EOC cell under hypoxia condition shows high malignancy. So we use the Arraystar Human LncRNA Microarray V3.0 to verify the difference expression of LncRNA in the exosomes drived from skov-3 cells which cultured in nomor/hypoxia condition

overall_design: Skov-3 cell was cultured in the 10% Exosome-Depleted FBS+RPMI1640 with 5%O2,5%CO2/2%O2,5%CO2,37°C for 72h, than collect and purify the exosomes in the supernatant.

first: Xipeng

first: Xiang

last: Ying


title: CD48-dependent protective autophagy in conventional human T cells promotes restimulation-induced cell death resistance

city: Bethesda

first: Clifton

middle: Lee

last: Dalgard

state: Maryland

address: 4301 Jones Bridge Road B2038

department: Anatomy Physiology & Genetics

institute: Uniformed Services University

summary: Transcriptome profiling and functional analyses on expanding Tcons revealed that FOXP3 enhances expression of the SLAM family receptor CD48, which in turn sustains basal autophagy and suppresses pro-apoptotic p53 signaling.  Our findings suggest that FOXP3 governs a distinct transcriptional program in early-stage effector Tcons that maintains RICD resistance via CD48-dependent protective autophagy and p53 suppression.

overall_design: Purified human CD4 T cells were electroporated with siRNAs against CD48 or negative-control medum GC duplex siRNA and differential gene expression analysis was performed using mRNA sequencing.

first: Andrew

last: Snow


title: Evi1 overexpression in SKOV3 cells

first: Arsen

summary: Evi1 overexpressed in SKOV3 cells

overall_design: Four samples with Evi1-Flag plasmid transiently overexpressed. Four controls with Flag-only plasmid transiently overexpressed.

first: Emilie


title: Genome-wide mapping of 5-hmC in epithelial samples from IMQ-treated skin versus control skin in mice.

city: Boston

first: Natasha

last: Frank

state: MA

address: 77 Avenue Louis Pasteur

department: Medicine

institute: Brigham and Women's Hospital

summary: Analysis of the tag densities showed lower 5-hmC levels in both CpG islands and genebodies in Imiquimod (IMQ)-treated epidermal samples. We looked further into loci-specific changes of 5-hmC and found a total of 364 differentially hydroxymethylated regions. Within these regions, 321 genes showed significantly lower 5-hmC levels and 67 genes had significantly higher 5-hmC levels in the IMQ-treated epidermis compared to control.

overall_design: We used a barcoded hydroxymethylated DNA immunoprecipitation (hMeDIP) method coupled with deep sequencing (hMeDIP-seq) for quantitative comparison of 5-hmC tag density at specific genome loci in IMQ-induced epidermal lesions compared to control non-lesional epidermis in mice.

first: Catherine

last: Lee

middle: Y


title: The analysis of copy number alterations from a lncRNA perspective reveals a regulator of lung cancer immune evasion

city: Pamplona

first: Maite

last: Huarte

state: Navarra

address: c/ Avd Pio XII, 55

institute: Centro de Investigación Médica Aplicada

summary: Cancer is characterized by genomic instability leading to deletion or amplification of oncogenes or tumor suppressors. However, most of the altered regions are devoid of known cancer drivers. Here, we identify lncRNAs frequently lost or amplified independently of protein-coding genes. Among them, we found Amplified LncRNA Associated with Lung cancer-1 (ALAL-1) as frequently amplified in lung adenocarcinomas. ALAL-1 is also overexpressed in additional tumor types, such as lung squamous carcinoma through epigenetic mechanisms. The RNA product of ALAL-1 is able to promote the proliferation and tumorigenicity of lung cancer cells. ALAL-1 is a TNF and NF-κB-induced cytoplasmic lncRNA that specifically interacts with SART3 co-regulating TNF, p53, NF-κB, TGF-β1 and IL8 pathways. Interestingly, ALAL-1 expression inversely correlates with the immune infiltration of lung squamous tumors, and tumors with ALAL-1 amplification show lower infiltration of several types of immune cells. We have thus unveiled a pro-oncogenic lncRNA that mediates cancer immune evasion, pointing to a new target for immune potentiation.

overall_design: Analysis of the transcriptomic changes following ALAL-1 or SART3 knockdown by RNAi in HCC95 cells treated or not with TNF. Each experimental condition was performed in triplicates.

first: Huarte

last: Maite

first: Athie

last: Alejandro


title: FOXP3 protects conventional human T cells from premature restimulation-induced cell death

overall_design: Purified human CD4 T cells were electroporated with siRNAs against FOXP3 or negative-control medum GC duplex siRNA and differential gene expression analysis was performed using mRNA sequencing.


title: Epigenomic variation under iron and phosphorus co-limitation in the globally important Trichodesmium

city: Los Angeles

first: Eric

middle: Alva

last: Webb

state: CA

address: 3616 Trousdale Parkway

institute: University of Southern California

type: Methylation profiling by high throughput sequencing

summary: We present population-level epigenetic variation in Trichodesmium erythraeum IMS101 associated with steady-state Fe-limitation at two different P concentrations on both short (i.e. 2 months) and long timescales (i.e. ~1 year).

overall_design: Briefly, IMS101 cell lines that were bubbled with 380 µatm CO2 air in nutrient replete media for ~7 years were then subjected to simultaneous Fe/P co-limitation for ~1 year (0.25 µM PO43- and 10 nM Fe). Following ~1 year of Fe/P co-limitation, 10 µm PO4 was supplied to Fe/P co-limited cultures generating steady-state Fe-limited cultures, which were grown for ~2 months prior to sampling. All samples for protein Walworth et al. 2016, RNA (Walworth et al. submitted), and methylation were taken simultaneously during the middle of the photoperiod until Illumina library preparation and sequencing.

first: Nathan

last: Walworth


title: Expression profiling of cricular RNA in human gastric cancer

status: Public on Dec 14 2019

city: Kyoto

first: Kenji

last: Nanishi

state: Kyoto

address: Kawaramachi-Hirokoji, Kamigyo-ku

institute: Kyoto Prefectural University of Medicine

summary: By the high sensitive cricular RNA micro array, we commpared 10211 circular RNAs abundant in the human gastric cancer tissues and adjacent normal gastric mucosa tissues, and the functional role of differentially expressed circular RNAs were analyzed by bioinformatics. The enrichment results indicated that these circular RNAs may involevd in the occurrence and progression process of gastric cancer.

overall_design: In this study, tumor tisuues and adjacent normal tissue in 3 patients with gastric cancer were used to acquire the circular RNAs expression profiling, and qPCR was performed to confirm the results of circular RNA chip.

first: Katsutoshi

last: Shoda

first: Tomohiro

last: Arita

first: Hirotaka

last: Konishi

first: Eigo

last: Otsuji


title: RNAseq of murine cancer cell lines

city: CABA

first: Soledad

last: Mac Keon

state: Buenos Aires

address: Av patricias argentinas 435

country: Argentina

institute: Fundacion Instituto Leloir

summary: Exploratory analysis of antigenic protein expression by cancer cell lines

overall_design: mRNA profiles of cancer cell lines were generated by deep sequencing using Illumina HiSeq 4000 by BGI. Sequencing reads filtering and bioinformatic analysis was also performed by BGI.

first: J

last: Mordoh

first: S

middle: M

last: Keon


title: Discovery of novel biomarkers in renal cell carcinoma

city: Cheongju

first: Yong-June

last: Kim

state: Chungbuk

address: Chungdae-ro 1, Seowon-Gu

department: College of Medicine

country: South Korea

institute: Chungbuk National University

type: Methylation profiling by genome tiling array

summary: A total of 164 ccRCC patient’s specimens were used for microarray (n=12, tumor and corresponding normal tissue) or pyrosequencing (PSQ) analyses (n=152). From The Cancer Genome Atlas (TCGA) portal, microarray methylation profiles composed of 312 subjects with ccRCC were utilized (159 for gene selection and 153 for prognostic relevance). Using the methylation profiles from our and TCGA, tumor-specific hypermethylated genes were selected, and prognostic relevance of candidate markers were examined with TCGA data set and pyrosequencing analysis data from our ccRCC patients samples.

overall_design: DNA from the 24 samples were hybridised to the Illumina Infinium HumanMethylation450 BeadChip kits


title: aCGH Detects Copy Number Variation with Similar Resolution to PacBio Sequencing Approaches

city: Portland

first: Suzy

middle: CP

last: Renn

state: Oregon

address: 3203 SE Woodstock Blvd., Biology Room B124

department: Biology

institute: Reed College

type: Genome variation profiling by genome tiling array

summary:
This study examines genomic copy-number variation between two African cichlid species through array comparative genomic hybridization. Probe level hybridization ratios were compared to copy number variation identified in Illumina and Pacific Biosciences genome assemblies from both species.
Array comparative genomic hybridization was performed with 3 samples (1 replicate array setup) of genomic DNA from Maylandia zebra vs. Orechromis niloticus XX clone genomic DNA from University of Stirling clonal lines.

sample_organism:
Oreochromis niloticus
Maylandia zebra

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

overall_design: Suzy,C,Renn

first: Joshua

middle: J

last: Faber-Hammond

first: Gabe

last: Preisling


title: ChIP-seq and RNA-seq for complex and low-abundance tree buds reveal chromatin and expression co-dynamics during sweet cherry bud dormancy

city: Villenave d'Ornon

first: Benedicte

last: Wenden

address: 71 avenue Edouard Bourlaux

country: France

institute: INRA

summary: Chromatin immunoprecipitation-sequencing (ChIP-seq) is a robust technique to study interactions between proteins, such as histones or transcription factors, and DNA. This technique in combination with RNA-sequencing (RNA-seq) is a powerful tool to better understand biological processes in eukaryotes. We developed a combined ChIP-seq and RNA-seq protocol for tree buds (Prunus avium L., Prunus persica L Batch, Malus x domestica Borkh.) that has also been successfully tested on Arabidopsis thaliana and Saccharomyces cerevisiae. Tree buds contain phenolic compounds that negatively interfere with ChIP and RNA extraction. In addition to solving this problem, our protocol is optimised to work on small amounts of material. Furthermore, one of the advantages of this protocol is that samples for ChIP-seq are cross-linked after flash freezing, making it possible to work on trees growing in the field and to perform ChIP-seq and RNA-seq on the same starting material. Focusing on dormant buds in sweet cherry, we explored the link between expression level and H3K4me3 enrichment for all genes, including a strong correlation between H3K4me3 enrichment at the DORMANCY-ASSOCIATED MADS-box 5 (PavDAM5) loci and its expression pattern. This protocol will allow analysis of chromatin and transcriptomic dynamics in tree buds, notably during its development and response to the environment.

overall_design: Branches and flower buds were collected for the RNA-seq and ChIP-seq experiments from the sweet cherry cultivar 'Burlat' at three dates (Date1: October 21st 2014, Date 2: December 5th 2014; Date 3: January 27th 2015). Dates 1 and 2 correspond to dormant flower buds and Date 3 corresponds to non-dormant buds.

first: Noémie

last: Vimont

first: Sandra

last: Cortijo

first: Bénédicte

first: Philip

last: Wigge

first: Fu

middle: X

last: Quah


title: Transcriptomic analysis of fungus Penicillium oxalicum and its mtr23B deletion and complemented strains

city: jinan

first: Zhang

last: Xiujun

state: shandong province

address: south road of shanda

institute: shandong university

summary: The goals of this study are to compare differential gene expressions for Penicillium oxalicum wild type strain (WT), mtr23B knockout strain (Δmtr23B) and complemented strain (Rmtr23B) on Vogel’s medium with 2% glucose (G) or 1% wheat bran and 1% cellulose (CW) as carbon resources. When cultivated in a repression medium for cellulolytic enzyme formation (G), the deletion of mtr23B upregulated genes involved in lyase activity, hydrolase activity, acyl carrier activity, monooxygenase activity, electron transfer activity, phosphopantetheine binding, heme binding, cell wall organization or biogenesis, oxidation-reduction process and extracellular region. The downregulated genes in Δmtr23B were mainly involved in transmembrane transporter activity, amino acid transmembrane transporter activity, membrane and integral component of membrane. When cultivated in an inducing medium for cellulolytic enzyme formation (CW), the downregulated genes in Δmtr23B were mainly involved in glucosidase activity, polygalacturonase activity, oxidoreductase activity, heme binding, oxidareductase activity, xylanase activity, cellulase activity, cellulose binding, oxidation-reduction process, cellulose catabolic process, xylan catabolic process and extracellular region. We find the expression levels of five secondary metabolism gene clusters (totally 28 clusters) were silenced in Δmtr23B. This study provides the information that mtr23B is required in conidiation and hydrolase activity of P. oxalicum.

overall_design: Examination of differential gene expressions by digital gene expression tag profiling in Penicillium oxalicum wild type strain and two mutant strains. qRT–PCR validation was performed using SYBR Green assays.

first: Yuqi

last: Qin


title: Transcriptome analysis of lateral buds from Phyllostachys edulis rhizome during germination and early shoot stages

city: Nanjing

first: Yuting

last: Shou

address: 159 Longpan Rd

institute: Nanjing Forestry University

summary: We adopted the high-throughput sequencing technology and compared the transcriptomes of Moso bamboo rhizome buds in germination stage and late development stage. We found that the development of Moso bamboo rhizome lateral buds was coordinated by multiple pathways, including meristem development, sugar metabolism and phytohormone signaling. Phytohormones have fundamental impacts on the plant development. We found the evidence of several major hormones participating in the development of Moso bamboo rhizome lateral bud. Furthermore, we showed direct evidence that Gibberellic Acids (GA) signaling participated in the Moso bamboo stem elongation.

overall_design: Comparison of Moso bamboo lateral rhizome buds transcriptomes at two stages

first: Yihua

last: Zhu


title: Transcriptional profiling of neurons in the dentate gyrus in a Lypd1-TRAP (OI82) mouse line

status: Public on Dec 13 2019

city: New York

first: Laura

last: Kus

address: 1230 York Avenue # 260

institute: The Rockefeller University

summary: TRAP translational profiling is a method that allows investigators to genetically characterize specific cell types in complex tissues such as mouse brain.  Using this technique we obtained RNA-Seq data from actively translating transcripts present in neurons in the dentate gyrus of adult Lypd1-EGFP/Rpl10a (OI82) mice.

overall_design: TRAP-Seq of neurons in the dentate gyrus of adult Lypd1-EGFP/Rpl10a (OI82) mice

first: Cuidong

last: Wang


title: Transcription profiling by array of human gastric cancer cell line MC-4 treated with pPeOp against untreated controls

city: Hangzhou

first: Yitao

last: Chen

state: Zhejiang

address: No.548 Binwen Road, Binjiang District

institute: Zhejiang Chinese Medical University

summary: Microarray analysis was performed to find out differentially expressed genes in pPeOp-treated MC-4 gastric cancer cells.

overall_design: When MC-4 cells density reached 80%, pPeOp-treated group were added the medium containing 60 µg/mL pPeOp, while the normal group were treated with culture medium. After 24 hours’ treatment, total RNA was extracted using the TRIzol reagent. After assessed the quantification and quality of RNA (NanoDrop ND-1000, NanoDrop Technologies, Wilmington, DE, USA), RNA was hybridized to an Affymetrix 3’IVT microarray (Affymetrix, California, USA). A custom long-oligo nucleotide(60-mer) array (12×135k) was manufactured based on NimbleGen proprietary Maskless Array Synthesizer (MAS) technology. Microarrays contained 41,796 probe sets and three housekeeping genes (β-actin, Histone 3, and 18S rRNA) were used as the internal controls and their expressions signal intensity were high and consistent in the samples at different groups, confirming the reliability and accuracy of these microarrays.

first: Wenjun

last: Xu


title: Mycobacterium tuberculosis is protected from NADPH oxidase and LC3-associated phagocytosis by the LCP protein CpsA

city: St Louis

first: Jennifer

last: Philips

state: Missouri

address: 660 S. Euclid Ave

department: Dept of Medicine

institute: Washington University School of Medicine

summary: Mycobacterium tuberculosis’success as a pathogen comes from itsability to evade degradation by macrophages. Normally macro-phages clear microorganisms that activate pathogen-recognitionreceptors (PRRs) through a lysosomal-trafficking pathway called“LC3-associated phagocytosis”(LAP). AlthoughM.tuberculosisac-tivates numerous PRRs, for reasons that are poorly understoodLAP does not substantially contribute toM.tuberculosiscontrol.LAP depends upon reactive oxygen species (ROS) generated byNADPH oxidase, butM.tuberculosisfails to generate a robustoxidative response. Here, we show that CpsA, a LytR-CpsA-Psr(LCP) domain-containing protein, is required forM.tuberculosisto evade killing by NADPH oxidase and LAP. Unlike phagosomescontaining wild-type bacilli, phagosomes containing theΔcpsAmutant recruited NADPH oxidase, produced ROS, associated withLC3, and matured into antibacterial lysosomes. Moreover, CpsAwas sufficient to impair NADPH oxidase recruitment to fungal par-ticles that are normally cleared by LAP. Intracellular survival of theΔcpsAmutant was largely restored in macrophages missing LAPcomponents (Nox2,Rubicon,Beclin,Atg5,Atg7,orAtg16L1) butnot in macrophages defective in a related, canonical autophagypathway (Atg14,Ulk1,orcGAS). TheΔcpsAmutant was highlyimpaired in vivo, and its growth was partially restored in micedeficient in NADPH oxidase,Atg5,orAtg7, demonstrating thatCpsA makes a significant contribution to the resistance ofM.tu-berculosisto NADPH oxidase and LC3 trafficking in vivo. Overall,our findings reveal an essential role of CpsA in innate immuneevasion and suggest that LCP proteins have functions beyond theirpreviously known role in cell-wall metabolism.

overall_design: BMDMs were seeded at 1.6E6 cells per well in a six-well plate 1 d before infection. Cells were uninfected or infected with H37Rv or ΔcpsA using a MOI of 4 in triplicate. At 4 hpi, RNA was prepared using the Direct-Zol RNA Mini-Prep Kit

first: Stefan

last: Köster

first: Sandeep

last: Upadhyay

first: Pallavi

last: Chandra

first: Kadamba

last: Papavinasasundaram

first: Guozhe

last: Yang

first: Amir

last: Hassan

first: Steven

last: Grigsby

first: Ekansh

last: Mittal

first: Heidi

middle: S

last: Park

first: Victoria

last: Jones

first: Fong-Fu

last: Hsu

first: Mary

last: Jackson

first: Christopher

last: Sassetti


title: Transcriptional profiling of pyramidal neurons in the cerebral cortex of a Htr4-TRAP (ES1299) mouse line

first: Laura

last: Kus

state: NY

summary: TRAP translational profiling is a method that allows investigators to genetically characterize specific cell types in complex tissues such as mouse brain.  Using this technique we obtained RNA-Seq data from actively translating transcripts present in pyramidal neurons in the cerebral cortex of adult Htr4-EGFP/Rpl10a (ES1299) mice.

overall_design: TRAP-Seq of neurons in the cerebral cortex of adult Htr4-EGFP/Rpl10a (ES1299) mice

first: Cuidong

last: Wang

first: Eric

middle: F

last: Schmidt


title: eVIP2: Expression-based variant impact phenotyping to predict the function of gene variants

city: Santa Cruz

first: Alexis

middle: Marie

last: Thornton

address: 1156 High Street

department: Biomolecular Engineering

institute: UC Santa Cruz

summary: While advancements in genome sequencing have identified millions of somatic mutations in cancer, their functional impact is poorly understood. We previously developed the expression-based variant impact phenotyping (eVIP) method to use gene expression data to characterize the function of gene variants. The eVIP method uses a decision tree-based algorithm to predict the functional impact of somatic variants by comparing gene expression signatures induced by introduction of wild-type versus mutant cDNAs in cell lines. The method distinguishes between variants that are gain-of-function, loss-of-function, change-of-function, or neutral. We present eVIP2, software that allows for pathway analysis (eVIP Pathways) and usage with RNA-seq data. To demonstrate the eVIP2 software and approach, we characterized two recurrent frameshift variants in RNF43, a negative regulator of Wnt signaling, frequently mutated in colorectal, gastric and endometrial cancer. RNF43 WT, RNF43 R117fs, RNF43 G659fs, or GFP control cDNA were overexpressed in HEK293T cells. Analysis with eVIP2 predicted that the frameshift at position 117 was a loss-of-function mutation, as expected. The second frameshift at position 659, was, surprisingly, predicted to be a gain-of-function mutation. Additional eVIP Pathways analysis of RNF43 G659fs predicted 10 pathways to be significantly altered, including TNF alpha via NFKB signaling, KRAS signaling, and hypoxia. To validate these predictions, we performed reporter assays and found that all eVIP2 impactful pathways tested in the assay were activated by expression of RNF43 G659fs, but not by expression of RNF43 WT, supporting that RNF43 G659fs is a gain-of-function mutation and its effect on the identified pathways. The eVIP2 method is an important step towards overcoming the current challenge of variant interpretation in the implementation of precision medicine. eVIP2 is available at https://github.com/BrooksLabUCSC/eVIP2

overall_design: RNA-seq upon overexpression of WT RNF43, RNF43 G659fs, RNF43 R117fs, or GFP in HEK 293 cells.

first: Angela

last: Brooks

first: Marios

last: Giannakis


title: MADS78 and MADS79 are essential regulators of early seed development in rice

city: Lincoln

first: Chi

last: Zhang

state: NE

address: 1901 Vine Street

institute: University of Nebraska - Lincoln

summary: MADS-box transcription factors (TFs) are subdivided into type-I and II based on phylogenetic analysis. The type II’s regulate floral organ identity and flowering time, but type I’s are relatively less characterized. Here, we report functional characterization of two type-I MADS-box TFs in rice (Oryza sativa), MADS78 and MADS79. Transcript abundance of both these genes in developing seed peaked at 48 hours after fertilization (HAF) and was suppressed by 96 HAF, corresponding to syncytial and cellularized stages of endosperm development, respectively. Seeds overexpressing (OE) MADS78 and 79 exhibited delayed endosperm cellularization, while CRISPR-Cas9 mediated single knock-out mutants showed precocious endosperm cellularization. MADS78 and 79 were indispensable for seed development, as a double knock-out mutant failed to make viable seeds. Both MADS78 and 79 interacted with MADS89, another type-I MADS-box, which enhances nuclear localization. The expression analysis of Fie1, a rice FERTILIZATION-INDEPENDENT SEED–polycomb repressor complex 2 (FIS-PRC2) component, in MADS78 and 79 mutants and vice versa established an antithetical relation, suggesting Fie1 could be involved in negative regulation of MADS78 and 79. Mis-regulation of MADS78 and 79 perturbed auxin homeostasis and carbon metabolism, as evident by mis-regulation of genes involved in auxin transport and signaling as well as starch biosynthesis genes causing structural abnormalities in starch granules at maturity. Collectively, we show MADS78 and 79 are essential regulators of early seed developmental transition and impact both seed size and quality in rice.

overall_design: RNA deep sequencing of WT, MADS78 OE, MADS79 OE, MADS78 CRISPR and MADS79 CRISPR seeds 48 and 72 hours after fertilization (HAF).

first: Harkamal

last: Walia

first: Puneet

last: Paul


title: Transcriptional profiling of neurons in the cerebral cortex of a Kcnip2-TRAP (NIDA115) mouse line

summary: TRAP translational profiling is a method that allows investigators to genetically characterize specific cell types in complex tissues such as mouse brain.  Using this technique we obtained RNA-Seq data from actively translating transcripts present in pyramidal neurons in the cerebral cortex of adult Kcnip2-EGFP/Rpl10a (NIDA115) mice.

overall_design: TRAP-Seq of neurons in the cerebral cortex of adult Kcnip2-EGFP/Rpl10a (NIDA115) mice


title: UV-B promotes flavonoids synthesis in Ginkgo biloba leaves

city: Yangzhou

first: Li

address: Wenhui east road no. 48

institute: Yangzhou University

summary: We conducted RNA-seq from the Ginkgo leaves after UV-B treatment,and constructed the molecular regulatory network of flavonoids synthesis under UV-B radiation in G. biloba.

overall_design: Transcriptome sequencing analysis in Ginkgo leaves under UV-B treatment and UV-B free white light, in triplicate.

first: Weixing

last: Li

first: Beibei

last: Zhao


title: Long-access cocaine intravenous self-administration; transcriptional profiling of medium spiny neurons in the dorsal striatum of Drd2-TRAP (CP101) mice

summary: TRAP translational profiling is a method that allows investigators to genetically characterize specific cell types in complex tissues such as mouse brain.  Using this technique we obtained RNA-Seq data from actively translating transcripts present in medium spiny neurons in the dorsal striatum of adult Drd2-EGFP/Rpl10a (CP101) mice that were administered either saline or cocaine under long access conditions

overall_design: Long-access cocaine intravenous self-administration study; TRAP-Seq of medium spiny neurons in the dorsal striatum of adult Drd2-EGFP/Rpl10a (CP101) mice administered either saline or cocaine

first: Erika

last: Andrade

first: Johana

last: Alvarez


title: RNAseq of cecum content of gnotobiotic mice

city: Munich

first: Bärbel

last: Stecher

address: Pettenkoferstr. 9a

department: Max von Pettenkofer Institute

institute: Ludwig Maximilian University of Munich

summary: We analyze differential gene expression of Salmonella Tm M2702 and E. coli Mt1B1 in mice colonized with two different gnotobiotic consortia

overall_design: RNAseq data was generated from cecal content of gnotobiotic mice by extracting total RNA, cDNA transcription and Illumina Nextseq500 sequencing.

first: Claudia

last: Eberl

first: Simone

last: Herp

first: Lara

last: Jochum


title: Transcriptional profiling of neurons in the deep nuclei of the cerebellum of an Htr6-TRAP (NIDA113) mouse line

first: Laura

last: Kus

summary: TRAP translational profiling is a method that allows investigators to genetically characterize specific cell types in complex tissues such as mouse brain.  Using this technique we obtained RNA-Seq data from actively translating transcripts present in neurons in the deep nuclei of the cerebellum of adult Htr6-EGFP/Rpl10a (NIDA113) mice.

overall_design: TRAP-Seq of neurons in the deep nuclei of the cerebellum of adult Htr6-EGFP/Rpl10a (NIDA113) transgenic mice

first: Cuidong


title: RNA sequencing of Acinetobacter baylyi and E. coli while co-incubating on LB agar plates

status: Public on Dec 20 2019

city: Basel

first: Marek

last: Basler

address: Klingelbergstr. 50/70

country: Switzerland

institute: Biozentrum, University of Basel

summary: The bacterial type VI secretion system is a widespread secretion mechanism important for competition in many Gram-negative bacteria. Killing and lysing of competing bacteria can provide advantages such as nutrients or acquisition of new genes by DNA uptake. Here, we show that T6SS-dependent lysis of prey cells by the naturally competent Acinetobacter baylyi results in extensive filamentation of a significant subpopulation of A. baylyi cells. This is dependent on the release of genomic DNA from the lysed prey cells and its uptake by the competence system of A. baylyi. Single-cell level analysis using live-cell imaging shows that filamentous A. baylyi cells appear at the interface between the species. The analysis of A. baylyi transcriptome and the response of transcriptional reporters suggest that the uptake of genomic DNA results in a highly upregulated SOS response, which often leads to the cell division arrest. Using competition experiments, we show that the parental strain is outcompeted by a strain lacking the DNA uptake machinery because such mutant shows no SOS response-dependent cell division arrest. Our data suggest that the cost of SOS-response may drive selection of decreased DNA uptake in T6SS positive bacteria.

sample_organism:
Escherichia coli
Acinetobacter baylyi

platform_organism:
Escherichia coli
Acinetobacter baylyi

overall_design:
We analyzed expression profiles of A. baylyi in competition with E. coli.
We deep-sequenced cDNA prepared from a mixture of E. coli with tae1-expressing (no other effectors present) and T6SS-deficient A. baylyi upon 10-30min of incubation.

first: Peter

last: Ringel

first: Lin

last: Lin


title: Reduced cellular levels of DNA polymerase delta alter replication-fork dynamics and  enzymology, and globally impair lagging-strand processing

first: Duncan

last: Smith

address: 1009 Silver Center, 100 Washington Sq E

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

institute: New York University

summary: DNA polymerase delta (Pol ∂) plays several essential roles in eukaryotic DNA replication and repair.  At the replication fork, Pol ∂ is responsible for the synthesis and processing of the lagging strand; this  role requires Pol ∂ to extend Okazaki fragment primers synthesized by Pol ⍺-primase, and to carry out  strand-displacement synthesis coupled to nuclease cleavage during Okazaki fragment termination.  Destabilizing mutations in human Pol ∂ subunits cause replication stress and syndromic  immunodeficiency. Analogously, reduced levels of Pol ∂ in Saccharomyces cerevisiae lead to  pervasive genome instability. Here, we analyze the how the depletion of Pol ∂ impacts replication  initiation and elongation in vivo in S. cerevisiae. We determine that Pol ∂ depletion leads to a  dependence on checkpoint signaling and recombination-mediated repair for cellular viability. By  analyzing nascent lagging-strand products, we observe both a genome-wide change in the  establishment and progression of replication forks and a global defect in Pol ∂-mediated Okazaki  fragment processing. Additionally, we detect significant lagging-strand synthesis by the leading-strand  polymerase (Pol ɛ) in late regions of the genome when Pol ∂ is depleted.

overall_design: Pol3 levels were altered by treatment with IAA in a strain containing an auxin-inducible degron on Pol3 and the resulting Okazaki fragments were sequenced from asynchronous and synchronous cultures. Addtionally, changes in ribonucleotide incorporation by ribonucleotide-hyperincorporating strains was assesed by HydEN-seq in order to determine the changes in polymerase usage during Pol3 depletion.

first: Natasha

last: Koussa


title: Identification of potential tobramycin-resistant mutagenesis of Escherichia coli strains after spaceflight

city: Beijing

first: Yi

last: Yu

address: No. 28, Fuxing Road, Haidian District,

department: Nanlou Respiratory Diseases Department

institute: Chinese PLA General Hospital

summary: Background: This study aimed to explore potential tobramycin-resistant mutagenesis of Escherichia coli (E. coli) strains after spaceflight. Methods: A spaceflight-induced mutagenesis of multi-drug resistant E.coli strain (T1_13) on the outer space for 64 days (ST5), and a ground laboratory with the same conditions (GT5) were conducted. Both whole-genome sequencing and RNA-sequencing were performed. Results: A total of 75 SNPs and 20 InDels were found to be associated with the resistance mechanism. Compared to T1_13, 1242 genes were differentially expressed in more than 20 of 38 tobramycin-resistant E. coli isolates while not in GT5. Function annotation of these SNPs/InDels related genes and differentially expressed genes was performed. Conclusion: This study provided clues for potential tobramycin-resistant spaceflight-induced mutagenesis of E. coli.

overall_design: RNA-sequencing of one GT5 isolate, and 39 ST5 isolates were performed on IlluminaHiSeq PE150.

first: Xian

first: Yinghua

last: Guo

first: Diangeng

first: Po

last: Bai

first: Bin

last: Zhang

first: Xuelin

first: Junfeng

last: Wang

first: Changting

last: Liu


title: Next generation RNA-sequencing of Kdm6a/b double knckout mice

status: Public on Dec 12 2019

city: Boston

first: Tatsuya

last: Kobayashi

address: 50 Blossom St

department: Endocrine Unit

institute: Massachusetts General Hospital

summary: The goal of this study is to compare the transcriptome of wild type and Kdm6a/b conditional knockout mice.

overall_design: Chondrocyte mRNA profiles of 10-day old wild type (WT) and Col2Cre(Tg):Kdm6a(fl/fl):Kdm6b(fl/fl) mice were generated by deep sequencing, in triplicate, using Illumina GAIIx.

first: Matthew

last: McKeon


title: Cortical transcriptome reveals widespread inflammation in brain of Gaa-/- mice

city: Hershey

first: Nuno

last: Raimundo

address: 500 University Dr, College Of Medicine, Room C4769

department: Cellular and Molecular Physiology

institute: Penn State College of Medicine

summary: Glycogen storage disease type II (Pompe's disease) is a lysosomal storage disorder which is associated with intralysosomal accumulation of glycogen impais muscle and nerve function. Mice that lack the lysosomal enzyme, acid alpha glucosidase model the human Pompe's disease. To understand signaling mechanisms that could potentially drive the progression of the disease, we employed RNA-Seq to unbiasedly characterize transcriptional changes in the cortex of Gaa-/- mice. We studied Gaa-/- mice and their wild type littermates at 12 months of age and found a robust induction of inflammatory genes in the cortex of Gaa-/- mice.

overall_design: WT and Gaa KO mice at 12 months of age

first: King

last: Yambire


title: Transcriptomic analysis of CLL4-induced liver injury in WT and DPT KO mice

status: Public on Dec 11 2019

city: Lille

first: Jérôme

last: Eeckhoute

address: Bâtiment J&K, Faculté de Médecine de Lille-Pôle Recherche, Boulevard du Professeur Leclerc

institute: CNRS

summary: C57Bl6J mice were injected CCL4 for 8 weeks to induce liver injury and livers were used to prepare RNA.

overall_design: Dpt-null mice and their WT littermates were treated with CCL4 or olive oil (control) for 8 weeks. RNA from livers were processed for analysis using MoGene-2_0-st Affymetrix microarrays according to standard procedures.

first: Fanny

last: Lalloyer

first: Eric

last: Bauge

first: Michal

last: Pawlak

first: Philippe

last: Lefebvre


title: Transcriptome Sequencing of  Rhodotorula mucilaginosa

city: Zhenjiang

first: Qian

last: xin

address: 301 Xuefu Road

institute: Jiangsu University

summary: Changes of induced expression level of related genes in the degradation of patulin by Rhodotorula mucilaginosm

overall_design: The culture of Rhodotorula mucilaginosm  was induced by patulin, and the culture of Rhodotorula mucilaginosm  was common.

first: Qiyang

last: Yang


title: Bulk RNA sequencing of various morphological locations and colony differentiation stages of Cristatella mucedo

city: Hinxton

first: Alexander

last: Predeus

address: Wellcome Trust Genome Campus

country: United Kingdom

institute: Wellcome Sanger Institute

summary: RNA-sequencing of Cristatella mucedo: two dissections of mature colonies, and characterization of different developmental stages starting from frozen statoblasts.

overall_design: The dataset compises of three groups of samples: two dissections of mature colonies, and one characterizing different developmental stages starting from frozen statoblasts. In the first case, the colony was divided into central (cent) and peripheral (edge) zones. In the second case, elongated colonies were divided into middle (mid) and terminal (ends) parts. In case of statoblast differentiation, differentiating statoblasts were sequenced immediately after being defrosted (freezer), or on day 2, 4, or 6 after the beginning of differentiation.

first: Viktor

last: Starunov

middle: V

first: Yury

last: Barbitoff

first: Vladimir

last: Kutiumov

first: Arina

last: Maltseva

first: Leonid

last: Moroz

first: Andrew

last: Ostrovsky


title: Gene expression changes in IDH mutant or IDH wildtype gliomas treated with All-trans Retinoic Acid

city: Pittsburgh

first: Nduka

last: Amankulor

address: 5117 Center Avenue

institute: University of Pittsburgh

summary:
IDH mutant cells are deficient in retinoic acid production, which impacts downstream gene expression and pathways. We looked at the effect of supplementing IDH mutant glioma cells with ATRA
on gene expression and downstream pathways. We compared gene expression changes with IDH WT cells that were also treated with ATRA

overall_design: Primary IDH mutant/ wildtype glioma cells were cultured in vitro and treated with 1uM ATRA for 48 hours. DMSO treated cells were used as controls. After treatment, RNA was extracted from cells and sent for microarray analysis at the Genomics core at the University of Pittsburgh

first: Aparna

last: Rao


title: A Molecular Profile of the Endothelial Cell Response to Ionizing Radiation

city: Milwaukee

first: Heather

last: Himburg

state: Wisconsin

address: 8701 W Watertown Plank Rd

institute: Medical College of Wisconsin

summary: Sorted VE-Cadherin+ endothelial cells from C57/Bl6 mice at different time points following total body irradiation.

overall_design: Non irradiated or 5 Gy TBI.

first: John

last: Chute


title: CRISPR screening reveals targets to reprogram long-lived effector CD8+ T cells for cancer therapy [scRNA-seq]

city: Memphis

first: Hongbo

last: Chi

state: TN

address: 262 Danny Thomas Place

department: Immunology

institute: St Jude Children's Research Hospital

summary: CD8+ T cells can be reprogrammed for better persistence and robust effector function in TME. By performing an in vivo pooled CRISPR-Cas9 mutagenesis screening of metabolism-associated factors, we identify Regnase-1 as a major negative regulator of antitumor responses, whose deficiency results in drastically increased CD8+ T cell accumulation in tumors

overall_design: We used scRNA seq to compare transcriptional profiles of Regnase1-null and WT CD8+ T cells population from tumors.

first: Jun

last: Wei

first: Lingyun

last: Long

first: Yogesh

last: Dhungana


title: RNA-sequencing

city: Changchun

first: ren

last: shengnan

state: State...

address: NO.126 Xiantai street

institute: China-Japan union hospital of Jilin university

summary: RNA sequencing for 10 samples

overall_design: Examing 2 conditions, each with 5 replicates

first: Ren

last: Shengnan

first: Fang

last: Xuedong

first: Chen

last: Fangfang


title: Regulated local synthesis of ribosomal proteins maintains ribosome function in axons

city: Cambridge

first: Christine

middle: E

last: Holt

address: Anatomy Bldg., Downing St.

department: Department of PDN

institute: University of Cambridge

summary: Ribosome assembly occurs mainly in the nucleolus yet recent studies have revealed robust enrichment and translation of mRNAs encoding many ribosomal proteins (RPs) in axons, far away from neuronal cell bodies. Here, we report a physical and functional interaction between locally synthesized RPs and ribosomes in the axon. We show that axonal RP translation is regulated through a novel sequence motif, CUIC, that forms an RNA-loop structure in the region immediately upstream of the initiation codon. Using imaging and subcellular proteomics techniques, we show that RPs synthesized in axons join axonal ribosomes in a nucleolus-independent fashion. Inhibition of axonal CUIC-regulated RP translation causes a significant decline in local translation activity and markedly reduces axon branching in the brain, revealing the physiological relevance of axonal RP synthesis in vivo. These results suggest that axonal translation supplies cytoplasmic RPs to maintain/modify local ribosomal function far from the nucleolus in neurons.

overall_design: The profiling of mRNAs in Xenopus laevis retinal ganglion cell axons

first: Toshiaki

last: Shigeoka

first: Max

last: Koppers

first: Hovy

middle: H

last: Wong

first: Julie

middle: Q

last: Lin

first: Roberta

last: Cagnetta

first: Asha

last: Dwivedy

first: Janaina

last: de Freitas Nascimento

first: Francesca

last: van Tartwijk

first: Florian

last: Ströhl

first: Jean-Michel

last: Cioni

first: Julia

last: Schaeffer

first: Mark

last: Carrington

first: Clemens

last: Kaminski

first: Hosung

last: Jung

first: William

last: Harris


title: Abundances of transcripts, proteins, metabolites, and lipids in the cell cycle of budding yeast

city: Colleg Station

first: Michael

last: Polymenis

state: TX

address: 300 Olsen Blvd

department: Biochemistry and Biophysics

institute: Texas A&M University

summary: For the first time in any system, we generated experiment-matched datasets of the levels of RNAs, proteins, metabolites, and lipids from un-arrested, growing, and synchronously dividing yeast cells.

overall_design:
We used centrifugal elutriation to obtain our synchronous cell cultures. From ~100 different elutriated cultures, we generated a cell size-series, spanning a range from 40 to 75 fL, sampled approximately every 5 fL intervals, in three biological replicates in each case. The same 24 distinct pools were aliquoted as needed to generate the input samples for measurements of RNA (with RNAseq), proteins (with LC MS/MS), and metabolites (GC-TOF MS for primary metabolites; HILIC-QTOF MS/MS for biogenic amines; and CSH-QTOF MS/MS for lipids).
Here, we deposit the RNA datasets.


title: Chemical reprogramming of fibroblasts to photoreceptor like cells

city: Bethesda

first: Koray Dogan

last: Kaya

state: MD

address: 6 CENTER DR

department: NEI

institute: NIH

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

overall_design: Refer to individual Series


title: Comparison of Drosophila melanogaster ovarian transcriptome after germline specific knock down of  lid or sin3A genes

city: Lyon

first: Gerard

last: BENOIT

address: 46 allée d'Italie

institute: CNRS/ENS Lyon/UMR5239

summary: Transcriptomic analysis and identification of differentially expressed genes in wt vs KD Drosophila melanogaster ovaries. We compared gene expression profiles in Drosophila melanogaster ovaries in which the lid or the sin3A gene have been selectively knocked down by tissues specific shRNA expression.

overall_design: Drosophila melanogaster ovaries mRNA profiles of 3-day old wild type (WT), germline specific lid knock-down (lidKD) germline specific sin3A knock-down female were generated by deep sequencing, in duplicate, using Illumina Hiseq 4000.

first: Benjamin

last: Loppin

last: Benoit


title: Phosphorylation of the transcriptional coregulator aNAC by DNA-PKcs regulates osteoblastogenesis

status: Public on Dec 10 2019

city: Rochester

last: Nair

address: 200 1ST ST SW

institute: Mayo Clinic

summary: The αNAC (alpha chain of the Nascent polypeptide-Associated Complex) transcriptional coregulator is developmentally expressed in osteoblasts and regulates osteoblast differentiation in vitro and in vivo. αNAC can activate or repress gene transcription, a function that is dynamically regulated by post-translational modification. Phosphorylation of residue Ser132 stimulates the sumoylation of αNAC on Lys127 to repress gene expression. Using in vitro kinase assays, we show that Ser132 phosphorylation is mediated by the DNA-dependent protein kinase catalytic subunit (DNA-PKcs). Pharmacological inhibition of DNA-PKcs kinase activity or gene silencing of Prkdc (encoding DNA-PKcs) in murine osteoblastic MC3T3-E1 cells and human adipose-derived mesenchymal stromal cells markedly enhanced osteogenesis and the expression of osteoblast differentiation marker genes. ChIP-seq identified Ezh2 as a target of the αNAC/DNA-PKcs signaling pathway. Mechanistically, inhibition of DNA-PKcs repressed Ezh2 expression, induced cell cycle block, and increased osteogenesis by significantly enhancing the bone morphogenetic protein 2 (BMP-2) response in osteoblasts and other mesenchymal cells. Importantly, in vivo inhibition of the kinase enhanced bone biomechanical properties, and bones from osteoblast-specific conditional Prkdc-knockout mice exhibited increased stiffness. In conclusion, DNA-PKcs is a negative regulator of osteoblast differentiation, and therefore DNA-PKcs inhibitors may have therapeutic potential for bone regeneration and metabolic bone diseases.

overall_design: MC3T3-E1 cells were grown in αMEM (Gibco) supplemented with 10% FBS (Gibco) to confluency, followed by a treatment with either NU7441 (1 μM) (Selleckchem) or DMSO (Sigma) for 16h. Cells were harvested, and total RNA was isolated using mRNeasy Mini Kit (Qiagen) according to the manufacturer's protocol. Triplicates from each of the three independent experiments were pooled together, quantified, and assessed by RNA-Seq

first: Amel

last: Dudakovic

first: Andre

last: van Wijnen


title: Transcriptional profiling of neurons in the prefrontal cortex of an Slc17a6-TRAP (JX883) mouse line

city: New York

first: Laura

last: Kus

address: 1230 York Avenue # 260

department: Heintz Laboratory

institute: The Rockefeller University

summary: TRAP translational profiling is a method that allows investigators to genetically characterize specific cell types in complex tissues such as mouse brain.  Using this technique we obtained RNA-Seq data from actively translating transcripts present in neurons in the prefrontal cortex of adult Slc17a6-EGFP/Rpl10a (JX883) mice.

overall_design: TRAP-Seq of neurons in the prefrontal cortex of adult Slc17a6-EGFP/Rpl10a (JX883) transgenic mice

first: Jie

last: Xing

first: Cuidong

last: Wang


title: Gene expression in PC3 cells(human prostate cancer cell line) upon HIC1 knockout

city: Shanghai

first: Tianqi

last: Wu

address: No.270 Dong'an Road

department: Cancer institute

institute: Fudan University Shanghai Cancer Center

summary: To explore the role of HIC1 deletion in regulating prostate cancer(PCa) microenvironment development, Human Gene Expression Microarrays were searched for altered genes upon HIC1 knockout expression in PC3 cells. According to fold-change screening between HIC1-knockout and its respective control cells, both up-regulated and down-regulated genes were shown.

overall_design: Human PCa cell line PC3 was transfected with Lenticas9-blast and the sgRNA expression plasmid Lentiguid-puro (sgRNA targeting HIC1 and respective control). HIC1-knockout cells were respectively noted as PC3 sgHIC1. Their respective control cells were respectively noted as PC3 Ctrl.

first: Jianhua


title: Comparison of white adipose tissue and bone marrow adipose tissue from New Zealand White rabbits

city: Edinburgh

middle: P

last: Cawthorn

address: 47 Little France Crescent

department: Centre for Cardiovascular Science, The Queen's Medical Research Institute

institute: The University of Edinburgh

summary:
Microarray analysis of white adipose tissue (WAT) and bone marrow adipose tissue (BMAT) from 22-week-old or 13-week-old male New Zealand White rabbits.
From both cohorts, BMAT was sampled from the distal tibia (dBMAT) and the radius and ulna (ruBMAT), while WAT was sampled from the inguinal (iWAT) and gonadal (gWAT) depots. From the 13-week-old cohort, BMAT was also sampled from the proximal tibia (pBMAT). Sufficient RNA could not be isolated from all tissues for all rabbits, so for some rabbits only a subset of tissues is included.

overall_design: The goal of this study was to determine global differences in gene expression between WAT and BMAT and whether these differ by WAT and/or BMAT depot. Five rabbits were included in the 22-week-old cohort and six rabbits in the 13-week-old cohort.

first: Erica

middle: L

last: Scheller

first: Ormond

last: MacDougald


title: CRISPR screening reveals targets to reprogram long-lived effector CD8+ T cells for cancer therapy [microarray]

first: Hongbo

last: Chi

summary:
CD8+ T cells can be reprogrammed for better persistence and robust effector function in TME. By performing an in vivo pooled CRISPR-Cas9 mutagenesis screening of metabolism-associated factors, we identify Regnase-1 as a major negative regulator of antitumor responses, whose deficiency results in drastically increased CD8+ T cell accumulation in tumors
We used microarrays to compare the global transcription profiles of Regnase1-null,  Ptpn2/Regnase1-null and Socs1/Regnase1-null tumor infiltrating CD8+ T cell populations

overall_design: In total 24 samples were analyzed: TIL CD8+ cells (Regnase1-null, n = 12; Ptpn2/Regnase1-null, n=4;Socs1/Regnase1-null, n = 4).

first: Jun

last: Wei

first: Lingyun

last: Long

first: Yogesh

last: Dhungana


title: Entrectinib Resistance in a Neuroblastoma Xenograft Model

city: Philadelphia

first: Kai

last: Tan

state: PA

address: 3501 Civic Center Blvd

institute: CHOP

summary: TrkB with its ligand, brain-derived neurotrophic factor (BDNF), are overexpressed in the majority of high-risk neuroblastomas (NBs). Entrectinib is a novel pan-TRK, ALK, and ROS1 inhibitor that has shown excellent preclinical efficacy in NB xenograft models, and recently it has entered phase 1 trials in pediatric relapsed/refractory solid tumors. We examined entrectinib-resistant NB cell lines to identify mechanisms of resistance. Entrectinib-resistant cell lines were established from five NB xenografts initially sensitive to entrectinib therapy. Clonal cell lines were established in increasing concentrations of entrectinib and had >10X increase in IC50. Cell lines underwent genomic and proteomic analysis using whole-exome sequencing, RNA-Seq, and proteomic expression profiling with confirmatory RT-PCR and Western blot analysis. There was no evidence of NTRK2 (TrkB) gene mutation in any resistant cell lines. Inhibition of TrkB was maintained in all cell lines at increasing concentrations of entrectinib (target independent). PTEN pathway downregulation and ERK/MAPK pathway upregulation were demonstrated in all resistant cell lines. One of these clones also had increased IGF1R signaling, and two additional clones had increased P75 expression, which likely increased TrkB sensitivity to ligand. In conclusion, NB lines overexpressing TrkB developed resistance to entrectinib by multiple mechanisms, including activation of ERK/MAPK and downregulation of PTEN signaling. Individual cell lines also had IGF1R activation and increased P75 expression, allowing preservation of downstream TrkB signaling in the presence of entrectinib. An understanding of changes in patterns of expression can be used to inform multimodal therapy planning in using entrectinib in phase II/III trial planning.

overall_design: RNA-Seq was conducted in triplicate on parental cell line and five entrectinib resistant cell lines

first: Suzanne

last: MacFarland

first: Yuxuan

last: Hu

first: Garrett

last: Brodeur


title: Breast Cancer - immune clusters - RNA-seq

city: Oslo

first: Xavier

last: Tekpli

address: Ullernchauséen 70

department: Cancer Genetics

country: Norway

institute: Oslo University Hospital Radiumhospitalet

summary: We use expression data from breast cancer tumors to define immune clusters in breast cancer. Immune clusters have gradual levels of immune infiltration. In the intermediate immune infiltration cluster, we found a worse prognosis which is independent of known clinicopathological features. We also found the immune clusters associated with treatment response. Further we use gene expression data and deconvolution algorithms to dissect the immune contexture of the clusters.

overall_design:
RNA-seq gene expression profiling of breast tumors

******************************************************************
Raw data are not publicly available due to patient privacy concerns. Raw data have been submitted for controlled access at EGA: EGAS00001003631.
******************************************************************

first: Kristine

middle: K

last: Sahlberg

first: Vessela

last: Kristensen


title: H3K4me3 profiling in Drosophila melanogaster ovaries

first: Gerard

last: BENOIT

summary: Compare the distribution of H3K4me3 between two experimental conditions (WT and Germ cell specific Lid KD) in Drosophila ovaries

overall_design: Profiling of H3K4me3 in ovaries of  WT and Lid germ cell specific knock-down  Drosophila melanogaster.

first: Benjamin

last: Loppin

last: Benoit


title: CRISPR screening reveals targets to reprogram long-lived effector CD8+ T cells for cancer therapy [ATAC-seq]

overall_design: We used single transfer system to perform ATAC seq to compare chromatin accessibility profiles of Regnase1-null, Batf single KO, Batf/Reg1 double KO and WT CD8+ T cells population from tumors.


title: Genome-wide mapping of ligand-dependent ERα binding sites in the ERα AF-2 mutant mouse uterus

city: Durham

first: Yukitomo

last: Arao

state: NC

address: 111 TW Alexandr Dr.

institute: NIEHS

summary: Estrogen receptor alpha (ERα) is a ligand dependent transcription regulator, which contains two transactivation functional domains, AF-1 and AF-2. These activities are regulated differently by the ligands. Specifically, the selective estrogen receptor modulators (SERMs) regulate AF-1 rather than AF-2. It is important to know whether AF-1/AF-2 predominantly regulated genes exist in the tissues for a better understanding of the SERMs functionality. We sought out AF-1 dependent estrogenic genes by using the AF-2 mutated knock-in (KI) mouse model, AF2ERKI. AF2ER is an estrogen-insensitive AF-2 disrupted ERα mutant mouse but unique to this model, AF-1 can be activated by the estrogen-antagonists, such as fulvestrant (ICI) and 4-hydroxytamoxifen (Tam) in vitro and in vivo. The information of genome-wide ICI or Tam dependent AF-2 mutated ERα binding sites could explain the mechanism of the selective estrogenic action of SERMs through AF-1 dependent gene regulation.

overall_design: Ovariectomized (OVX) mice were treated with ICI, Tam or vehicle for 1h. Uterus was collected from the six mice in each treatment then put together for a sample.Each dataset was obtained from a single pool of uterine tissue (n = 6 mice)

first: Katherine

last: Hamilton

first: Sara

middle: A

last: Grimm

first: Kenneth

last: Korach


title: CRISPR screening reveals targets to reprogram long-lived effector CD8+ T cells for cancer therapy. [RNA-Seq]

first: Hongbo

last: Chi

overall_design: We used RNA seq to compare gene expression profiles of Regnase1-null and WT CD8+ T cells population from tumors and peripheral lymph nodes.

last: Wei


title: Molecular profiling of the mature Organiser (Hensen's node) as a stem zone.

first: Octavian

last: Voiculescu

address: Downing Street

department: Physiology, Development and Neuroscience

summary: We report that four genes are upregulated when the chick Hensen's node becomes a stem zone (contributing cells to make the entire notochord and medial somitic mesoderm, without recruitment of cells from the surrounding epiblast), and that they remain expressed in the mature node throughout axial elongation.

overall_design: Methods:The Organiser was labelled at the end of gastrulation and the embryos let to develop 8-10 somites. Fluorescent cells remaining in the Organiser were separated from their neighbours (adjacent neural plate, emerging presomitic mesoderm) either manually, from live embryos (M series), or by laser-capture microdissection from paraffin sections of embryos fixed with modified methacarn.

first: Timothy

last: Wood


title: Gene expression analysis of neuropathic pain-induced depression in the anterior cingulate cortex of mice

city: Freiburg

first: Ralf

last: Gilsbach

address: Albertstr. 25

institute: Institute of Pharmacology

summary:
We used the sciatic nerve cuffing model to induce neuropathic pain and depression in mice. Gene expression was studied in the anterior cingulate cortex, a brain region crucial for mood disorders.
We studied gene expression after 2 and 8 weeks in cuff or sham operated mice. The 8 week time point corresponded to the presence of both nociceptive and anxiodepressive-like phenotype. The 2 week time point correspond to the animals displaying no anxiodepressive phenotype.

overall_design: This study includes 24 samples. For each treatment group we analyzed 6 biological replicates. The groups include control (sham) and operated (cuff) samples after 2 and 8 weeks after cuff surgery.

first: R

first: I

last: Yalcin

first: F

last: Barthas


title: Transcriptional profiling of neurons in an Slc17a6-TRAP (JX883) mouse line

first: Laura

last: Kus


title: Expression data from coculture of retinoblastoma (RB) and bone marrow stromal cells (BMSC)

city: Chennai

first: Krishnakumar

last: Subramanian

address: Sankara Nethralaya, College road, Nungambakkam

department: Department of Ocular Pathology

country: India

institute: Vision Research Foundation

summary: The study hypothesizes that tumor microenvironment is responsible for progression of RB tumors. We performed whole genome microarray on direct cocultures of RB cells and BMSC. RB cells (NCC-RbC-51 and Weri-Rb-1) were cocultured with BMSC for 24 hrs. Total RNA was isolated and whole genome microarray was performed.

overall_design: Whole genome microarrays were used to analyze the pattern of differentially expressed genes in coculture samples of RB and BMSC cells.


title: CRISPR screening reveals targets to reprogram long-lived effector CD8+ T cells for cancer therapy. [ATAC-Seq]

summary: CD8+ T cells can be reprogrammed for better persistence and robust effector function in TME. By performing an in vivo pooled CRISPR-Cas9 mutagenesis screening of metabolism-associated factors, we identify Regnase-1 as a major negative regulator of antitumor responses, whose deficiency results in drastically increased CD8+ T cell accumulation in tumors

overall_design: We used Co-Transfer system ATAC seq to compare chromatin accessibility profiles of Regnase1-null and WT CD8+ T cells population from tumors.

first: Jun

first: Lingyun

last: Long

first: Yogesh

last: Dhungana


title: Expression data from mouse liver at the early phase of treatment with permethrin or clofibrate

city: Osaka

first: Takako

last: Fukuda

address: 1-98, Kasugadenaka 3-chome, Konohana-ku

institute: Sumitomo Chimical Co., Ltd

summary:
Crlj:CD1(ICR) female mice were fed diets containing 0 ppm (control), 5000 ppm permethrin, and 5000 ppm clofibrate for periods of 2 weeks.
We used microarrays to evaluate gene expression profiling in mouse liver at the early phase of treatment with permethrin or clofibrate.

overall_design: After treatment periods, livers of 9 mice (3 mice in each group) were excised for RNA extraction and hybridization on Affymetrix microarrays.


title: BRCA1 mutation influences progesterone response in human  benign mammary organoids.

city: Chicago

first: Julie

last: Kim

state: IL

address: 303 E. Superior St

department: Obstetrics and Gynecology

institute: Northwestern University

summary: Mammary organoids treated with a 28 day menstrual cycle profile of estradiol and progesterone with or without TPA:  Comparison of normal versus BRCA1 mut cells. Purpose: The goals of this study are to determine  1) the effects of a 28 day menstrual cycle profile of estradiol and progesterone, 2) the effects of TPA, and 3) the responses in normal versus BRCA1 carriers, in benign breast organoids using RNA-seq

overall_design: Breast organoids from patients without (normal) or with BRCA1 mutations were cultured in vitro.  Organoids from each patient were divided into 2 groups. One group was treated with estradiol and progesterone and the second group was treated with estradiol, progesterone and TPA.  Hormone treatment over the course of 28 days was as follows:  0.1nM estradiol on days 1-7, 1nM estradiol on days 7-14, 1nM estradiol + 10nM progesterone (with or without 1uM TPA) on days 14-21 and 0.1nM estradiol + 50nM progesterone (with or without 1uM TPA)  on days 21-28.  Media was changed every 2 days.

first: J

first: Batzaya

last: Davaadelger


title: CRISPR screening reveals targets to reprogram long-lived effector CD8+ T cells for cancer therapy.

city: Memphis

address: 262 Danny Thomas Place

institute: St Jude Children's Research Hospital

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

overall_design: Refer to individual Series


title: Re-education of tumor-associated macrophages by CXCR2 blockade drives senescence and tumor inhibition in advanced prostate cancer

city: Biella

first: Paola

last: Ostano

address: via Malta 3

institute: Fondazione Edo ed Elvo Tempia

summary: Tumor-associated macrophages (TAMs) represent a major component of the tumor microenvironment that supports tumorigenesis. Here we found that prostate tumors are strongly infiltrated by TAMs expressing the C-X-C chemokine receptor type 2 (CXCR2). Pharmacological blockade of the CXCR2 receptor by a selective antagonist promoted the re-education of TAMs towards a pro-inflammatory phenotype. Strikingly, CXCR2 knockout monocytes infused in Ptenpc-/-; Trp53pc-/- mice preferentially differentiatied in TNFα-releasing pro-inflammatory macrophages leading to senescence induction and tumor inhibition. Moreover, tumor cells harboring PTEN deletion were more sensitive to TNFα-induced senescence, when compared to PTEN WT tumors, due to increased levels of TNFR1. Our results identify TAMs as a target in prostate cancer therapy and describe a novel therapeutic strategy based on CXCR2 blockade to harness the anti-tumorigenic potential of macrophages against this disease.

overall_design: CD45+CD11b+F480+ cells isolated from the whole prostate of a Pten KO; Trp53 KO mouse; treated with aCXCR2 or untreated

first: Diletta

last: Di Mitri

first: Jelena

last: Vasilevska

first: Michela

last: Mirenda

first: Arianna

last: Calcinotto

first: Nicolas

last: Delaleu

first: Ajinkya

last: Revandkar

first: Veronica

last: Gil

first: Gunther

last: Boysen

first: Marco

last: Losa

first: Simone

last: Mosole

first: Emiliano

last: Pasquini

first: Rocco

last: D'antuono

first: Elena

last: Zagato

first: Giovanna

last: Chiorino

first: Andrea

last: Rinaldi

first: Letizia

last: Gnetti

first: Mariona

last: Graupera

first: Ana

last: Fonseca

first: David

last: Waugh

first: Simon

last: Barry

first: Johann

last: De Bono

last: Alimonti


title: Transcriptional profiling of neurons in the deep nuclei of the cerebellum of an Slc17a6-TRAP (JX883) mouse line

first: Laura

last: Kus

summary: TRAP translational profiling is a method that allows investigators to genetically characterize specific cell types in complex tissues such as mouse brain.  Using this technique we obtained RNA-Seq data from actively translating transcripts present in neurons in the deep nuclei of the cerebellum of adult Slc17a6-EGFP/Rpl10a (JX883) mice.

overall_design: TRAP-Seq of neurons in the deep nuclei of the cerebellum of adult Slc17a6-EGFP/Rpl10a (JX883) transgenic mice

first: Jie

last: Xing

first: Cuidong

last: Wang


title: Transcriptomic analysis of Bptf wild-type and Bptf heterozygous lymphomas arising from Em-Myc tumors

city: Paris

first: Laia

last: Richart

address: 13 Rue Pierre et Marie Curie

department: Developmental Biology

institute: Institut Curie

summary:
Purpose: Evaluation of the impact of a reduction in Bptf levels on the nature of lymphomas arising from Em-Myc mice.
Results: Bptf heterozygous tumors show reduced activity of the E2F and c-MYC pathways, together with increased activity of the NF-kB pathway.

overall_design: Tumor samples were harvested when mice showed clinical signs of tumor development (palpable lymph nodes, hunched posture, tachypnoea, swollen abdomen, or ruffled fur). A collection of samples from both genotypes and multiple onsets was gathered and submitted for RNA-Sequencing.

first: Irene

last: Felipe

first: Pilar

last: Delgado

first: Monica

last: Perez de Andres

first: Jaime

last: Prieto

first: Natalia

last: del Pozo

first: Juan

last: Garcia

first: Miguel

last: Piris

first: Almudena

last: Ramiro

first: Francisco

last: Real


title: Gene expression analysis of BeWo  cells  stimulated  by tumor necrosis factor-alpha and  insulin-like growth factor-I

city: Mitaka

first: Kei

last: Tanaka

state: Tokyo

department: Medicine

institute: Kyorin University

summary: Cellular functions of trophoblasts are regulated by various cytokines and growth factors. We previously reported the synergistic effects of tumor necrosis factor-α (TNF-α) and insulin-like growth factor-I (IGF-I) on BeWo cells proliferation. We performed gene expression array to elucidate the genes involved in the cross-talk of TNF-α and IGF-I in BeWo cells. We identified 553 differentially expressed genes (DEGs) under the co-stimulation of TNF-α and IGF-I. Gene ontology analysis identified “NF-kappa B signaling pathway”, “Calcium signaling pathway”, and “Arachidonic acid metabolism”. Among DEGs, PTGS2 was up-regulated and PTGER2 was down-regulated.

overall_design: Total RNA from 12 samples of BeWo cells were hybridiesed to Agilent Sure Print  G3 Human 8x60K ver.3

first: Tomoko

last: Kawai

first: Kazuhiro

last: Nakabayashi

first: Kenichiro

last: Hata


title: RNA sequencing analysis of hepatic transcriptome profiles in experimental nonalcoholic steatohepatitis

city: kansas city

first: Yuxia

last: Zhang

state: KS

address: 3901 Rainbow Blvd, Hemenway 4001

department: Pharmacology, Toxicology, and Therapeutics

institute: University of Kansas Medical Center

summary: Two-month-old C57BL/6J male mice were placed on either chow diet or a diet enriched in high fat, cholesterol, and fructose (Research diet D09100301: 40 kcal% fat, 2% cholesterol, 20 kcal% fructose, HFCF diet) for 1 or 3 months. RNA-seq was used to analyze hepatic gene expression from mice on 1-month chow diet, 1-month HFCF diet, 3-month chow diet, and 3-month HFCF.

overall_design: Total RNA for Illumina sequencing was extracted from mouse liver tissues using a Direct-zol RNA kit. During RNA isolation, DNA was removed by treating the samples with RNase-free DNase to avoid DNA contamination. Three biological replicates in each group for a total of 12 samples were submitted for RNA sequencing.

first: Nancy

last: Magee


title: An atlas of transcription factors expressed in the Drosophila melanogaster pupal terminalia

city: Kansas City

first: Madelaine

last: Gogol

state: MO

address: 1000 E. 50th Street

department: Computational Biology Core

institute: Stowers Institute

summary: The male terminalia of Drosophila melanogaster has undergone rapid morphological change between it and its closely related species, making it a useful model for studying evolution and development. In order to identify the network components that pattern the male terminalia, we isolated and sequenced whole RNA from two timepoints during pupal development, and next performed in situ hybridization for 100 highly expressed transcription factors during pupal development.

overall_design: RNA from 4 samples each from 24 hour APF and 28 hour APF D. melanogaster male pupal terminalia were isolated and sequenced using Illumina sequencing.

first: Ben

last: Vincent

first: Gavin

middle: R

last: Rice

first: Gabriella

last: Wong

first: William

last: Glassford

first: Kayla

middle: I

last: Downs

first: Jessica

last: Shastay

first: Kenechukwu

last: Charles-Obi

first: Malini

last: Natarajan

first: Julia

last: Zeitlinger

first: Mark

last: Rebeiz


title: Gene expression profiling of fetal liver-derived hematopoietic stem cells in conditional ESAM-knockout mice.

city: Suita

first: Daisuke

last: Okuzaki

state: Osaka

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

institute: Osaka univ.

summary: Endothelial cell-selective adhesion molecule (ESAM) is a life-long maker for hematopoietic stem cells (HSCs). Although we previously elucidated the functional importance of ESAM on HSCs in stress-induced hematopoiesis in adults, it remained unknown how ESAM affects hematopoietic development during fetal life. To address this issue, we analyzed fetuses of conditional ESAM-knockout mice.

overall_design: LSK CD48- cells of E14 healthy FLs, on which high amount of ESAM is uniformly expressed, were incubated with or without a rat mAb against mouse ESAM. Then, the cells were incubated with goat anti-rat IgG Abs-conjugated microbeads for 4 hrs and were subsequently applied to RNA-sequencing analyses.

first: Tomoaki

last: Ueda

first: Takafumi

last: Yokota


title: Polysome profiling RNAseq of cells transfected with an oligonucleotide targeting the ES6S region of the 40S subunit

city: Madrid

first: Irene

last: Diaz-Lopez

address: C/Nicolas Cabrera 1

institute: Centro de biologia molecular Severo Ochoa

summary: Polysome profiling experiments were carried out to identify the mRNAs that have altered the translation efficiency (counts in polysomal fraction/counts in monosomal fractions) in the presence of an oligonucleotide targeting a specific region of the ribosomal RNA, to study the implication of this region in the translation of specific mRNAs

overall_design: Polysome profiling experiments of cuture cells transfected with the oligonucleotide of study and a control oligonucleotide with duplicates. Sequencing of the polysomal and monosomal fraction and the total RNA of each sample. There were 4 biological samples ( duplicates of cells transfected with the targeted oligonucleotide and cells tranfected with the control oligonucleotide), and 12 sequencing samples (monosomal fraction, polysomal fraction and TOTAL RNA of each biological sample)


title: Gene expression profiling of fetal liver-derived hematopoietic stem cells in conventional ESAM-knockout mice.

summary: Endothelial cell-selective adhesion molecule (ESAM) is a life-long maker for hematopoietic stem cells (HSCs). Although we previously elucidated the functional importance of ESAM on HSCs in stress-induced hematopoiesis in adults, it remained unknown how ESAM affects hematopoietic development during fetal life. To address this issue, we analyzed fetuses of conventional ESAM-knockout mice.

overall_design: We conducted RNA-Seq comparing gene expression patterns of WT and ESAM-null HSCs to learn more about molecular mechanisms involved in the developmental failure of hematopoiesis in the ESAM-null fetal liver.


title: Global gene expression profiling of lung-resident CD8+ T cells from uninfected, Mtb-infected and BCG-infected mice

city: Durban

first: Adrie

last: Steyn

address: 519 Umbilo Road

country: South Africa

institute: Africa Health Research Institute

summary: Transcriptomics on lung-resident CD8+ T cells reveals how global gene expression patterns diverge over the course of infection with virulent Mtb and non-pathogenic BCG strains. CD8+ T cells from Mtb-infected animals respond with a stronger activation profile than cells from BCG-infected animals, promoting a more inflammatory gene expression profile that contributes to increased indicators of T cell exhaustion, apoptosis and metabolic reprogramming. These data provide new insights into the differential regulation of T cell immunity in virulent and non-virulent Mycobacterial infections.

overall_design: CD8+ T cell transcriptomics were compared among mice infected with virulent Mtb, or the vaccine strain, BCG alongside uninfected controls at two time points over the course of chronic infection (Day 21 and Week 12 post-infection)

first: Shannon

last: Russell


title: Myc/Max dependent long antisense noncoding RNA, EVA1A-AS, participates in survival of hepatocellular carcinoma (HCC) by suppressing anti proliferating gene Eva1A.

city: Hannover

first: Doan Duy Hai

last: Tran

state: Niedersachsen

address: Carl-Neubergsstr. 1

department: Institut of physiological Chemistry

institute: Hannover Medical School

summary: Cancer cells associated with multiple survival strategies, and how cancer cells escape cell death under different conditions are still largely unknown. The Myc gene has been implicated in the pathogenesis of most types of human tumors. We show here that Eva1 (eva-1homolog A)/TMEM166 (transmembrane protein 166)/family with sequence similarity 176 (FAM176A) is upregulated by Myc/Max, however, overexpression of Eva1A induced mitotic catastrophe in hepatocellular carcinoma (HCC).  Here, expression of Eva1A in HCC is suppressed by antisense long noncoding RNA, Eva1A-AS, that is induced also by Myc/Max, suggesting that Eva1A-AS expression supports HCC survival.  Eva1A-AS is located within intron of Eva1A gene suppressed Eva1 expression by forming double stranded RNA with DiGeorge syndrome chromosomal region 8 (DGCR8). Depletion of Eva1A-AS in HepG2 cells upregulates Eva1A expression, and induced accumulation of lipid droplets and stopped cell proliferation. Furthermore, suppressed Eva1A expression levels are negatively correlated with differentiation grade in 371 primary HCCs. These data also suggest that EVA1A-AS may be useful target for a subset of HCCs.

overall_design: mRNA profile of shRNA control infected HepG2 and shTHOC5 infected were generated by deep sequencing.

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last: Tamura