title: microRNA expression in infantile hemangioma (IH) and normal skin tissues

status: Public on Jun 06 2020

city: Jinan

first: Cong

last: Fu

state: Shandong

address: No. 324, jingwu Road, Huaiyin Dist

institute: Shandong provincial hospital

summary: To determine the microRNA expression profile in IH and non-tumor tissues, we uesed miRNA 4.0 microarray form Affymetrix to examine the expression of microRNA in IH and non-tumor tissues

overall_design: skin tissues from IH surgery were distributed into two experimental groups: tumor tissue group and normal tissue group, then perform microRNA microarray analysis by Affymetrix


title: Role of FTO in ovarian cancer (RNA-Seq)

status: Public on Jul 01 2020

city: CHICAGO

first: Manoj

last: Kandpal

state: Illinois

address: 1256 W NORTHSHORE AVE, 3R

country: USA

institute: Northwestern University

type: Expression profiling by high throughput sequencing

summary: RNA methylation plays an important role fine tuning translation and subsequently regulating cellular responses and cell fate. The fat mass- and obesity-associated protein (FTO) was recognized as an m6A demethylase and described as an oncogenic factor in leukemia and brain tumors. FTO expression levels are suppressed in ovarian tumors and ovarian cancer stem cells (CSCs). FTO induce cyclic AMP activity through targeting PDE4B and PDE1C by down-regulation of m6A levels in the mRNA transcript. In all or findings point to a tumor suppressor function of FTO in high grade serous OC. FTO induce cyclic AMP activity through targeting PDE4B and PDE1C by down-regulation of m6A levels in the mRNA transcript. In all or findings point to a tumor suppressor function of FTO in high grade serous OC

overall_design:
GFP (control) or FTO-GFP (treatment) over-expression in OVCAR-5 cells
3 biological replicates for GFP and 3 biological replicates for FTO-GFP in RNA-seq

first: Kandpal

last: Manoj

first: Hao

last: Huang

first: Daniela

last: Matei


title: The TPL-2 – ERK1/2 signalling pathway inhibits interferon beta expression in macrophages via TCF-dependent Fos transcription

status: Public on Jun 22 2020

city: London

first: Steve

last: Ley

address: Pond Street

department: Institute of Immunity & Inflammation

country: United Kingdom

institute: University College London

summary: Studies in mice have indicated that TPL2 kinase plays important roles in immune responses to pathogens and in various models of inflammatory disease. We set out to determine how TPL2 (Map3k8) regulates transcription using an in vitro system of LPS-stimulated primary macrophages. TPL2 regulated genes are involved in a number of different processes including inflammation as well as reproduction, cell cycle and signal transduction. Differentially expressed genes were used in a K means analysis, grouping based on expression profile, which identified 12 different expression profiles. There was a strong correlation between rapidly-induced genes regulated by TPL2 kinase activity and their expression in cells treated with the MKK1/2 inhibitor (PD032590)1 or from cells where phosphorylation of P105 by IKK2 is blocked. Cluster 1 genes were found to be enriched for TCF family members. TPL2 was shown to regulate ELK1 phosphorylation and known TCF targets genes such as Egr1. TPL2 is known to regulate transcription of multiple cytokines and chemokines including IFNb. Like Map3k8[D270A] macrophages, expression of Ifnb1 was increased in Elk1-/-Elk4-/- macrophages compared to WT macrophages following LPS stimulation. In fact, this increase was also seen in MKK1/2 inhibitor treated macrophages. Expression of Fos was decreased in both Map3k8[D270A] and Elk1-/-Elk4-/- macrophages. Macrophages generated from mice with myeloid-specific deletion of Fos also had elevated levels of Ifnb1 compared to controls. Similar results were obtained following activation of TLR1/2, TLR9 and TNF-R in macrophages. Furthermore, LPS or TNF stimulation of MEFs lacking Elk1, Elk3 and Elk4 had reduced FOS protein levels and increased Ifnb1 mRNA suggesting a general role for ERK1/2 > TCF pathway regulating Ifnb1 levels through Fos expression.

overall_design: Bone marrow derived macrophages (BMDMs) from WT (C57BL/6), Map3k8[D270A], Nfkb1[SS/AA], WT+PD0325901, WT+RSKi47 and Elk1-/- Elk4-/- mice were generated and stimulated with LPS to determine the genes and processes controlled by TPL2 (Map3k8) signalling. BMDMs were stimulated with LPS (100ng/ml) for various times up to 2 hours or left unstimulated. PD0325901 (MKK1/2 inhibitor) and RSKi47 (RSK inhibitor) were added prior to stimulation for 10mins at 0.1 µM and 2 µM respectively

first: Micheal

last: Pattison

first: Probir

last: Chakravarty


title: Innovations in primate interneuron repertoire

status: Public on Jun 04 2020

city: Boston

first: Fenna

middle: Marie

last: Krienen

state: MA

address: 77 Ave Louis Pasteur, NRB 260

department: Genetics

institute: Harvard Medical School

summary: We report single-nucleus transcriptomes from brain regions in 5 species: mice: Frontal Cortex, V1, Hippocampus, Striatum; common marmoset: 7 neocortical regions, Hippocampus, Striatum (Nucleus Accumbens, Caudate, Putamen); rhesus macaque: Prefrontal Cortex, V1; human: Prefrontal Cortex, V1, Striatum (Caudate); ferret:  Prefrontal Cortex, V1, Striatum

sample_organism:
Callithrix jacchus
Macaca mulatta
Homo sapiens
Mustela putorius furo
Mus musculus

overall_design: Single-nucleus suspensions were made from frozen brain tissue and sampled with Drop-seq or 10X 3' v3 chemistry.

middle: M

middle: A

last: McCarroll


title: RSK2-regulated gene signature associates with ER+ breast cancer

status: Public on Jun 01 2020

city: Nashville

first: Deborah

last: Lannigan

state: TN

address: 2220 Pierce Ave

department: Pathology, Microbiology and Immunology

institute: Vanderbilt University

summary: We used CRISPR RSK2 knock-out MCF-7 cells to identify RSK2-regulated genes.

overall_design: Wild type and RSK2-KO cells were serum starved for 12-15h and treated with EGF(10nM)/E2(1nM) for 8h before RNA purified. Library constructions were performed using TruSeq RNA Library Prep Kit (Illumina), and the sequencing was performed on an Illumina HiSeq 2500. CLC Workbench 10.0 (Qiagen) was used to align raw sequenced reads to the human reference genome hg38 (Genome Reference Consortium GRCh38) and to analyze the differential gene expression.

first: Katarzyna

last: Ludwik


title: RNAseq analysis of BRCA deficient tumors treated with saline, Nano-Talazoparib or Talazoparib

status: Public on Apr 10 2020

city: East Lansing

first: Karen

last: Liby

state: MI

address: 1355 Bogue Street

department: Pharmacology&Toxicology

institute: Michigan State University

summary: We report the gene expression profile in BRCA deficient tumors after treatment with saline, nanoparticle-formulated Talazoparib and free Talazoparib

overall_design: To study the regulation of gene expression after treatment with the PARP inhibitor Talazoparib in BRCA deficient breast cancer, Brca1Co/Co;MMTV-Cre;p53+/- mice were used in this study. Treatment was started when a tumor was 4-5 mm in diameter. Tumors from Brca1Co/Co;MMTV-Cre;p53+/- mice treated with saline, free Talazoparib (i.v.), or NanoTLZ for five doses (0.33mg/kg, three times a week) were harvested. Three samples were collected for each group. Total RNA was isolated using the RNeasy Mini Kit (Qiagen, Valencia, CA). The RNA integrity number (RIN) was detected using the Aligent Bioanalyzer at the MSU Research Technology Support Facility (RTSF) Genomics Core facility. RNAseq and the bioinformatics analysis were performed by Novogene (Sacramento, CA).

first: Di

last: Zhang


title: Single cell changes in mouse melanoma tumors treated with anti-Ang2 and radiation

status: Public on May 27 2020

city: Helsinki

first: Pauliina

last: Kallio

address: Haartmaninkatu 8

country: Finland

institute: University of Helsinki

summary: Subcutaneous B16-F0 mouse tumors were treated with anti-Ang2 injections and radiation. 5 days after radiation, tumors were collected and dissociated to obtain single cells and analyzed using the Chromium Single-cell 3'RNA-sequencing system

overall_design: We analyzed 6 samples in total, all containing 10 000 cells.

first: Kari

last: Alitalo


title: The Parkinson's disease associated mutation LRRK2-G2019S affects astrocyte specification

status: Public on May 01 2020

city: Maastricht

first: Silvia

last: Bolognin

state: -- None selected --

address: Universiteitssingel 40,

country: Netherlands

institute: Maastricht University

summary: We report the altered transcriptomic profile of astrocytes in midbrain organoids differentiated for 35 and 70 days and generated from a stem cell line carrying the LRRK2-G2019S mutation compared to the isogenic pair.

overall_design: Single-cell RNA-Sequencing experiments were performed on a total of 4 samples. These correspond to 2 time-points (Day 35 and 70 of dopaminergic differentiation). One isogenic pair was analysed for each time-point: LRRK2-WT and LRRK2-G2019S.

first: Lisa

last: Smits

first: Kamil

last: Grzyb

first: Stefano

last: Magni

first: Jens

last: Schwamborn

first: Alexander

last: Skupin


title: Single molecule nanoscopy reveals that nuclear myosin VI regulates the spatial organization of mammalian transcription initiation

status: Public on May 31 2020

city: Abu Dhabi

first: Piergiorgio

last: Percipalle

state: Abu Dhabi

address: Saadiyat Campus, Abu Dhabi

department: Biology Department, Science Division

country: United Arab Emirates

institute: New York University Abu Dhabi

summary: During transcription, RNA Polymerase II (RNAPII) is spatially organised into clusters that correlate with transcription activity. However, the assembly, organisation and stability of these transcription units remains unknown. Here, we have combined single molecule imaging with genomics approaches in order to explore the role of nuclear myosin VI in the nanoscale organisation of RNAPII. We can reveal that myosin VI acts as the molecular anchor that holds RNAPII into these transcription factories. Perturbation of myosin VI leads to the disruption of RNAPII localisation, changes in chromatin organisation and subsequently a decrease in gene expression. This role of Myosin VI is particularly important for transcription events following stimulation, where multiple genes are simultaneously activated.

overall_design: Total RNA was extracted from three replicates of WT, MVI KD and Scrambled siRNA Hela cells.

first: Tomas

last: Venit

first: Chris

last: Toseland

first: Nizar

last: Drou


title: WT and aP2-Cre Adipocyte Bmal1 KO 24hr Time Course, Liver Tissue RNA-seq

city: Philadelphia

first: Gregory

middle: Robert

last: Grant

state: PA

address: 3400 Civic Center Blvd.

institute: University of Pennsylvania

summary: Liver metabolism in mice lacking Bmal1 in adipocytes. Comparison between WT and KO revealed no differentially expressed genes at ZT12 and ZT16, and only revealed one gene at ZT8 and ZT20. In contrast many genes were differential at ZT0 and ZT4. With ZT4 having substantially more than ZT0.

overall_design: Time-series liver mRNA profiles of 4- to 6-month-old male wild type (WT) and Bmal1 knockout (KO) mice were generated by sequencing, four mice per genotype per timepoint, using Illumina HiSeq 2000.

first: Guangrui

last: Yang

first: George

middle: K

last: Paschos

middle: R

first: Garret

last: FitzGerald

first: Lihong

last: Chen


title: Molecular characterization of selectively vulnerable neurons in Alzheimer’s Disease

status: Public on Apr 05 2020

city: San Francisco

first: Kun

last: Leng

state: Calfironia

address: 675 Nelson Rising Lane, 3rd Floor

department: Institute for Neurodegenerative Diseases

institute: University of California San Francisco

summary:
Alzheimer’s disease (AD) is characterized by the selective vulnerability of specific neuronal populations, the molecular signatures of which are largely unknown. To identify and characterize selectively vulnerable neuronal populations, we used single-nucleus RNA sequencing to profile the caudal entorhinal cortex and the superior frontal gyrus – brain regions where neurofibrillary inclusions and neuronal loss occur early and late in AD, respectively – from individuals spanning the neuropathological progression of AD. We identified RORB as a marker of selectively vulnerable excitatory neurons in the entorhinal cortex, and subsequently validated their depletion and selective susceptibility to neurofibrillary inclusions during disease progression using quantitative neuropathological methods. We also discovered an astrocyte subpopulation, likely representing reactive astrocytes, characterized by decreased expression of genes involved in homeostatic functions. Our characterization of selectively vulnerable neurons in AD paves the way for future mechanistic studies of selective vulnerability and potential therapeutic strategies for enhancing neuronal resilience.

The brain tissue used in this study were sourced from the Biobank for Aging Studies (LIM-22) in the Department of Pathology at the University of Sao Paulo, as well as from the Neurodegenerative Diseases Brain Bank in the Memory and Aging Center at the University of California, San Francisco. Detailed neuropathological, clinical and genetic data are available under request. Please contact gerolab@gmail.com and lea.grinberg@ucsf.edu.

overall_design: Single-nucleus RNA-sequencing of post-mortem brain tissue from donors spanning the range of AD progression.

first: Martin

last: Kampmann

first: Lea

last: Grinberg


title: Expression data from isorhamnetin (Iso)-treated human amnion epithelial cells (hAECs)

status: Public on Apr 17 2020

city: Tsukuba

first: Farhana

last: Ferdousi

state: Ibaraki

address: Tennodai 1-1-1

country: Japan

institute: University of Tsukuba

summary: Gene expression profiling reveals a potential role of Iso towards hepatic differentiation of hAECs.

overall_design:
hAECs were isolated from discarded term placenta and were treated with 20 μM Iso for 20 days. Microarray gene expression profiling was conducted for biological replicates of Iso-treated hAECs on day 10 and day 20 and untreated control cells on day 0, day 10 and day 20.
RNA was extracted using Isogen (Nippon Gene Co. Ltd., Toyama, Japan). The integrity of RNA was quantified using NanoDrop 2000 spectrophotometer (Thermo Scientific, Wilmington, DE, USA). RNA samples were prepared for gene expression profiling analysis with GeneChip® 3' Expression Arrays using 3' IVT PLUS Reagent Kit (Affymetrix Inc., Santa Clara, CA, USA). Two hundred and fifty ng of total RNA from each sample was used to generate amplified and biotinylated complementary RNA (cRNA) from poly (A) RNA in a total RNA sample according to the user manual. IVT Incubation time was 16 hour. GeneAtlas® Hybridization, Wash and Stain Kit was used for hybridizing 3' IVT Array Strips according to the user manual (P/N 08-0306). Human genome array strips (HG-U219) were hybridized for 16 hours in a 45oC incubator, washed and stained and finally imaging was done with the GeneAtlas Fluidics and Imaging Station.


title: Application of text mining to build AOP-based mucus hypersecretion genesets and validation with in vitro and clinical samples

status: Public on Apr 30 2020

city: Southampton

first: Emmanuel

last: Minet

address: Regents Park Road

institute: British American Tobacco

summary:
Purpose: Build genesets using text mining and validate the geneset with data from public repository and a dataset generated in house using in vitro models and RNA-seq
Methods: Mucus hypersecretion and mucociliary dysfucntion adverse outcome pathways (AOPs) genesets were build using the text mining method described by Rani et al., 2015. Validation was performed using RNA expression data from cigarette and e-cigarette aerosol treated cells, IL-13 treated airway cells, and COPD-lung biopsies. The cigarette and e-cigarette aerosol RNA-samples from airway cells were generated and sequenced in house. The other dataset were publically available.
Results: Using unsupervised clustering, the mucus hypersecretion and mucociliary dysfunction genesets were able to discriminate the cigartte treated cells from the e-cigarettes and the air control. The e-cigarette and the air control clustered together. Clustering was also observed with IL-13 treated cells. IL-13 is an induced of mucus hypersecretion. Clustering was not observed when COPD RNA-seq samples were used. PCA analysis revealed some degree of grouping based on disease status, but this was also heavily confounded by other parameters.
Conclusions: Our study described the first application of text mining to build genesets relevant to AOPs. In vitro validation confirmed the genesets could discriminates between treatment that induce mucus hypersecretion phenotypes, however this could not be confirmed with COPD biopsy samples. This could be due to a series of technical confouding factors and the heterogeneity of the COPD disease.

overall_design: RNA was extracted from in vitro primary airway cells exposed at the air liquid interface to cigarette and e-cigarette aerosol. RNA-seq data was generated using an Illumina NextSeq 500 platform at a depth of 40 million pair reads with 150 bp paired-end

first: Linsey

last: Haswell

first: Sarah

last: Corke

first: Anisha

last: Banerjee

first: Andrew

last: Baxter

first: Ivan

last: Verrastro

first: Tomasz

last: Jaunky

first: Marianna

last: Gaca


title: Expression data from HeLa cell treated with Tris(1,3-dichloro-2-propyl)phosphate

city: Seoul

first: Jun-Seok

last: Lee

address: 39-1 Hawolgok-dong Seungbuk-gu

country: South Korea

institute: Korea Institute of Science and Technology (KIST)

summary:
Tris(1,3-dichloro-2-propyl)phosphate is widely used in consumer products as a flame retardant. Humans are often exposed to this compound. However, the molecular mechanisms of the compound`s adverse effects are still unclear. We address the molecular and cellular mechanisms underlying tris(1,3-dichloro-2-propyl)phosphate effects on HeLa cells.
Here RNA-Seq analysis was performed to identify distinct classes of up- or down-regulated genes and their connections to different metabolic pathways.

overall_design: 7 samples were analyzed. We compared samples treated by tris(1,3-dichloro-2-propyl)phosphate for 2 and 24 hr with the concentration of the compound 4 µM, 20 µM, and 100 µM (1 non-treated sample, 6 samples treated by the tris(1,3-dichloro-2-propyl)phosphate).

middle: S

first: Mamunul

last: Haque

first: Taras

last: Voitsitskyi


title: The Epigenomic Landscape of Pituitary Adenomas Reveals Specific Alterations and Differentiates Among Acromegaly, Cushing's Disease and Endocrine-Inactive Subtypes

status: Public on Mar 26 2020

city: Santa Monica

first: Dave

last: Hoon

state: CA

address: 2200 Santa Monica Boulevard

department: Translational Molecular Medicine

institute: Saint John's Cancer Institute

summary: Recurrent single-nucleotide and small indel somatic mutations were infrequent among the three adenoma subtypes. However, somatic copy-number alterations (SCNA) were identified in all three pituitary adenoma subtypes. Methylation analysis revealed adenoma subtype-specific DNA methylation profiles, with GHsecreting adenomas being dominated by hypomethylated sites. Likewise, gene-expression patterns revealed adenoma subtype-specific profiles. Integrating DNA methylation and gene-expression data revealed that hypomethylation of promoter regions are related with increased expression of GH1 and SSTR5 genes in GH-secreting adenomas and POMC gene in ACTH secreting adenomas. Finally, multispectral IHC staining of immune-related proteins showed abundant expression of PD-L1 among all three adenoma subtypes.

overall_design: A multiplatform analysis was performed to identify the genomic and epigenomic underpinnings of disease among the three major subtypes of surgically resected pituitary adenomas in 48 patients: growth hormone (GH)–secreting (n= 17), adrenocorticotropic hormone (ACTH)–secreting (n= 13, including 3 silent-ACTH adenomas), and endocrine-inactive (n= 18). Whole-exome sequencing was used to profile the somatic mutational landscape, whole-transcriptome sequencing was used to identify disease-specific patterns of gene expression, and array-based DNAmethylation profiling was used to examine genome-wide patterns of DNA methylation.

first: Matthew

middle: P

last: Salomon

first: Chikako

last: Matsuba

first: Garni

last: Barkhoudarian

first: Daniel

middle: F

last: Kelly


title: TRIP assay of mismatch repair during single-strand annealing

status: Public on May 14 2020

city: Scarborough

first: Guillaume

middle: J

last: Filion

state: Ontario

address: 1265 Military Trail

department: Biological Sciences

country: Canada

institute: UTSC

summary: Biases of DNA repair can shape the nucleotide landscape of genomes at evolutionary timescales. However, such biases have not yet been measured in chromatin for lack of technologies. Here we develop a genome-wide assay whereby the same DNA lesion is repaired in different chromatin contexts. We insert thousands of barcoded transposons carrying a reporter of DNA mismatch repair in the genome of mouse embryonic stem cells. Upon inducing a double-strand break between tandem repeats, a mismatch is generated when the single strand annealing repair pathway is used. Surprisingly, the mismatch repair machinery favors the same strand 60-80% of the time. The location of the lesion in the genome and the type of mismatch have little influence on the repair bias in this context.

overall_design: Five constructs were used, each producing a different mismatch upon induction of a double-strand break (A:G, T:G, A:C, T:C and C:A, where the positions of the nucleotides are on opposite strands in A:C and C:A). Each construct was used to set two independent TRIP pools in mouse E14 ES cells. For each TRIP pool, two mapping experiments by inverse PCR (iPCR) were performed in three total batches. Then for each TRIP pool, two independent I-SceI transfections were performed and genomic DNA was collected before the transfection (no I-SceI control), or 24 hour and 48 hour after transfection. The state of the DNA after repair was assayed by either UMI-LA (linear amplification) or UMI-PCR. Each method was used twice on a given genomic DNA extraction.

first: Victoria

middle: O

last: Pokusaeva

first: Aranzazu

last: Rosado Diez

first: Lorena

last: Espinar


title: Tissue-resident memory T cell reactivation by diverse antigen-presenting cells imparts distinct functional responses

status: Public on Apr 02 2020

city: La Jolla

first: Susan

last: Kaech

address: 10010 N Torrey Pines Rd

institute: Salk Institute

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

overall_design: Refer to individual Series


title: Single-cell RNA-seq of the testis sample of ICR mice treated with busulfan and/or alginate oligosaccharides

status: Public on Mar 30 2020

city: Qingdao

first: Yong

last: Zhao

address: 700 Changcheng Road

department: College of Life Sciences

country: China

institute: Qingdao Agricultural University

summary: We profiled a single-cell RNA-seq on ICR mouse testis treated with busulfan and or Alginate Oligosaccharides (AOS) from 3 weeks of  age to 8 weeks of age (for 5 weeks) to study the rescue effect of AOS on the spermatogenesis disrupted by busulfan. We collected single cell from testis from the four groups AOS 0 (control), AOS 10 (AOS 10 mg/kg body weight (BW)), B+A 0 (busulfan alone), B+A 10 (busulfan plus AOS 10 mg/kg BW). The the cells were further captured with 10x Genomics based single-cell system. By using single-cell RNA seq, we found busulfan disrupted spermatogenesis by the dramatical decrease in germ cells. AOS significantly increased the number of germ cells and also promoted the germ cell development. Besides, we provide candidate master regulons regulated by AOS. Our data here offers the opportunity for treating  of azoospermia or oligospermia.

overall_design: We totally analyzed ~27,000 single cell transcriptome profile from ICR mouse testis from the four treatment group.

first: Wei

last: Ge

first: Ruiqian

last: Zhang

first: Pengfei

last: Shen

first: Hongfu


title: Tissue-resident memory T cell reactivation by diverse antigen-presenting cells imparts distinct functional responses [II]

summary: Temporal transcriptome profiling of TCR-reactivated (P14) and bystander-reactivated (OT-I) memory T cells in the lung and mediastinal lymph node based on Nur77-GFP reporter expression and CD98 expression

overall_design: TCR-transgenic P14 and OT-I T cells were adoptively transferred to generate immune chimeras. At various timepoints post secondary influenza infection, P14 and OT-I T cells were sorted from the lung and lymph node based on their Nur77-GFP reporter or CD98 expression, in duplicate, and RNA-seq was performed.

first: Jun

last: Low


title: Next Generation Sequencing Analysis of human primary airway smooth  muscle cells treated with IL17A or DEX or  both combined.

status: Public on Apr 06 2020

city: Cleveland

first: Xiaoxia

last: Li

state: OH

address: 9500 Euclid Ave.

department: Inflammation & Immunity

institute: Cleveland Clinic

summary:
Purpose:  The goals of this study is to identify IL17A-induced transcripts differentially regulated by DEX in hASMCs.
Methods:Primary hASMCs were treated for 4 hours with IL17A or DEX or both combined. mRNA profiles were generated by deep sequencing using Illumina GAIIx. Each treatment has 3 biological replicates.
Results: Using an optimized data analysis workflow, we mapped about 40 million sequence reads per sample (>97% clean reads) to the human genome (build mm9) and identified 48,162 transcripts in hASMC samples.
Conclusions: Our study showed that DEX regulated IL17A targt genes in both synergistic and suppressive manner in hASMCs. This is the first detailed analysis of transcriptoms of hASMCs in response to IL17A and DEX.

first: Caini

last: Liu


title: Zscan4 binds nucleosomal microsatellite DNA and protects mouse two-cell embryos from DNA damage [RNA-seq]

status: Public on Mar 22 2020

city: Stanford

first: Tomek

last: Swigut

address: 265 Campus Dr

department: Chemical and Systems Biology

institute: Stanford University

summary: 2C-like cells or pluripotent cells were isolated from Zprom::GFP and Zprom::GFP-Zscan4 mouse ESC reporter lines to measure changes in gene expression.

overall_design: Stable clonal mouse ESC reporter lines were generated containing the Zscan4 promoter driving either GFP or the GFP-Zscan4 fusion and sorted on the basis of GFP fluorescence to isolate pluripotent (GFP-) or 2C-like cells (GFP+) for gene expression analysis. There are four samples analyzed.

first: Rajini

last: Srinivasan

first: Joanna

last: Wysocka


title: Differences in Gene Expression Profiles between the chorion-attached and non-chorion-attached endometrium at the mid-gestation of female rabbit

status: Public on Jun 23 2020

city: Chengdu

first: Ling

last: xu

state: Sichuan

address: No. 211 Huimin road

department: College of animal science and technology

institute: Sichuan Agricultural University

summary: The placenta, the complex of fetal membrane (the chorion is attached to the endometrium) and endometrium, is a highly specialized temporary organ responsible for the normal progression of pregnancy in mammals. Therefore, the endometrium was divided into two function regions: chorion-attached (CA) and non-chorion-attached (NCA) region. However, the difference in gene expression profiles between the CA and NCA endometrial tissue of mid-gestation still are unknown. The objective of this study was to reveal gene expressed profiles of the CA and NCA endometrium from the mid-gestational female rabbits, and to screen the differentially expressed genes (DEGs) to imply major physiological events of endometrial at mid-gestation. RNA-seq showed that a total of 12320 genes were co-expressed in the CA and NCA endometrium, and 646 DEGs were identified. Enrichment analysis of the DEGs revealed the top overrepresented gene ontology (GO) term and pathways were related to immune regulation, cellular adhesions. Furthermore, the expression levels of DEGs related to immune regulation of chemokines and their receptors, extracellular matrix (ECM) and Integrin, were compared between the CA and NCA endometrium. Overall, there was hardly difference in the expression levels of immune regulation genes (chemokines and their receptors) between the CA and NCA endometrium, while the concentration of IL-8, IL-6 and IL-1β in the CA endometrium was higher than that in the serum and the NCA endometrium, which suggested immune cytokines were accumulated in the endometrium of maternal-fetal interface. Meanwhile, the expression level of genes related to cellular adhesions (ECM-integrin) in the NCA endometrium was significantly higher than that in the CA endometrium, and high abundance of Integrin β and THBS1 were localized in the luminal epithelium of the NCA endometrium, but not in the CA endometrium. Conclusions: Our study revealed the gene expression profiles of the CA and the NCA endometrium at mid-gestation, and provides an implication of chemokine and ECM-Integrin involved in immune regulation and adhesive barrier at the endometrium.

overall_design: Three sexually mature female rabbits (2.50 ± 0.15kg) underwent synchronous estrus processing followed by mating. On the 14th day of gestation, samples from the uterine endometrial tissue and placenta, together with the junction of the allantochorial membrane and endometrium  were collected and stored in liquid nitrogen. Sampling accuracy was evaluated by hematoxylin-eosin staining. Transcriptomics analysis was performed by PTM Biolab Ltd. Co. (Hangzhou, China). Animals were housed in individual cages under a 14-h light and 10-h dark regimen at a temperature of 16°C to 25°C, and fed ad libitum on a standard diet. All experimental procedures were approved by the Animal Ethics Monitoring Committee of Sichuan Agricultural University and carried out in accordance with the Guidelines of Animal Welfare in China.

first: Xiuli

last: Mei

last: Xu

first: Minjie

last: Yu

first: Zhang

last: Ming

first: Liangde

last: Kuang

first: Congyan

first: Yan

first: Yutian

last: Zeng

first: Chuanzhi

last: Lu

last: Ren

first: Zhicheng

last: Wang

first: Zhiqiang

last: Guo

first: Xiaohong

last: Xie

first: Dengping

last: Huang


title: Zscan4 binds nucleosomal microsatellite DNA and protects mouse two-cell embryos from DNA damage

type: Genome binding/occupancy profiling by high throughput sequencing


title: Suppression of CCT3 inhibits tumor growth by downregulating CDK1 expression in melanoma

status: Public on Feb 06 2020

city: NanJing

first: Feng

last: Zhang

state: JiangSu

address: Weigang NO.1

summary:
The members of the eukaryotic chaperonin family are essential for cell survival. The dysregulation of chaperonin-containing TCP-1 subunit 3 (CCT3) is implicated in the development of several types of malignant tumors. However, its functional role in melanoma remains unknown. Herein, we elucidated the functional contribution of CCT3 to melanoma progression. The results indicated that CCT3 was frequently upregulated in melanoma tissues, and high level of CCT3 is correlated with clinical stage in melanoma patients. Knockdown of CCT3 in melanoma cells markedly inhibited cell proliferation and induced cell apoptosis in vitro and suppressed tumorigenesis in a mouse xenograft model. We also identified the cyclin-dependent kinase 1 (CDK1) as a downstream effector of CCT3 and further evaluation demonstrated that suppression of CCT3 attenuates cell proliferation via downregulating CDK1 expression and CCT3-mediated regulation of cell cycle signaling pathway in melanoma. Collectively, our results provide compelling evidence that CCT3 contributes to melanoma progression via CDK1 and is a potential therapeutic target for melanoma
A-375 cells infected with NC lentivirus and CCT3 knockdown lentivirus were prepeared and cultured for RNA extraction and hybridization on Affymetrix microarrays.

overall_design: A potential target cct3 was found in clinical samples of melanoma. In order to elucidated  its  functional contribution, we knocked down cct3 and verified it in vivo and in vitro. We also identified the CDK1  as a downstream effector of CCT3 by affymetrix microarrays.

first: Wenlou

last: Liu

first: Chunsheng

last: Yang

first: Zhengxiang

last: Han

first: Guan

last: Jiang

first: Yanqun


title: High-throughput RNA sequencing analysis of human colon cancer cell line HCT116 transfected with LINC00152 siRNA.

status: Public on Feb 18 2020

city: Changsha

first: Jian

last: Ma

state: Hunan

address: 110  Xiangya  Road

department: Cancer  Research Institute

institute: Central South University

summary:
Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are using  RNA sequencing analysis to evaluate the effects of si-LINC00152 on the mRNA of human colon cancer cell line HCT116.
Methods: Human colon cancer cell line HCT116 was transfected with a control non-targeting siRNA to cells or transfected with siRNA targeting LINC00152 for 36 hours in DMEM medium (with 10% serum). Total RNA were extracted and detected by Illumina high-throughput RNA sequencing data analysis. 2 independent biological replicates were plated, transfected in parallel for each control and siRNA.
Results: Log-fold changes of up- or down-regulated mRNAs between the control and experiment group were selected with a significance threshold of p<0.05. There are 90 mRNAs were up-regulated and 159 were down-regulated in “si-LINC00152” group comparing to “control” group.
Conclusions: Our study describes the mRNA changes of human colon cancer cell line HCT116 transfected with LINC00152 siRNA.

overall_design: Human colon cancer cell line HCT116 mRNA profiles of “control” (cells was transfected with a control non-targeting siRNA) and“si-LINC00152”(cells was transfected with LINC00152 siRNA) were generated by RNA sequecning, using Solexa high-throughput sequencing service (Oebiotech, Shanghai, China).

first: Chunlin

last: Ou


title: Assessing diagnosis value of miRNA from PBMCs and EVs in Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS)

status: Public on Feb 08 2020

city: Fort Lauderdale

first: Lubov

last: Nathanson

state: Florida

address: 3321 College Ave.

department: INIM

institute: Nova Southeastern University

summary: Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS) a debilitating multisystemic disease of unknown etiology, affecting thousands of individuals worldwide, still relies on ruling out medical problems leading to unexplained exertion for its diagnosis due to a complete lack of disease-specific biomarkers. Our group and other, have explored the potential value of microRNA profiles (miRNomes) as diagnostic tools for this disease. However, heterogeneity of participants, low numbers, the variety of samples assayed, and other pre-analytical variables, have hampered the identification disease-associated miRNomes. In this study, our team has evaluated, for the first time, ME/CFS miRNomes in PBMCs and EVs from severely ill patients recruited at the monographic UK ME biobank as a strategy to assess, using SOPs, blood fractions with optimal diagnostic power for a rapid translation of a miR-based diagnostic method into the clinic. Our results show that routine creatine kinase (CK) blood values, plasma EVs physical characteristics (including counts, size and zeta-potential), and a limited number of differentially expressed PBMC and EV miRNAs appear significantly associated with severe ME/CFS (p<0.05). Gene enrichment analysis points to epigenetic and neuroimmune dysregulated pathways, in agreement with previous reports. Population validation by a cost-effective approach limited to these few potentially discriminating variables remains.

overall_design: The samples included in the study consisted on PBMCs (>106 cells) and plasma from 15 severely ill female ME/CFS patients and 15 female, age-population matched healthy subjects, obtained in EDTA blood-collection tubes, by the monographic UK ME Biobank professionals.

first: Eloy

last: Almenar-Perez

first: Leonor

last: Sarria

first: Elisa

last: Oltra


title: Difference of DNA methylation and Chromatin accessibility of J82 SP cell and J82 NSP cell

status: Public on Jan 30 2020

city: Los Angeles

first: Gangning

last: Liang

address: 1441 Biggy street

department: Urology

institute: USC Keck school of medicine

type: Methylation profiling by genome tiling array

summary: Subpopulations of highly tumorigenic, drug resistant cancer stem-like cells play a key role in cancer recurrence and progression. Surprisingly, these aggressive cells can arise repeatedly de novo from bulk tumor cells independently of mutational events. We investigated whether transition to and from a cancer stem-like state is associated with epigenetic alterations, such as DNA methylation and chromatin accessibility. By Hoechst dye staining and FACS analysis, side population (SP) and non-side population cells were sorted from J82 cells. AcceSssIble assay by Infinium EPIC BeadArray platform was used to identify potential epigenetic driver genes in the process of SP /NSP phenotype plasticity. Genes with differential accessible promoter regions were overlapped with genes differentially expressed by HuEx array analysis. Oncomine and Basespace were adopted to explore the clinical relevance of the target genes.

overall_design: Intact nuclei are harvested from J82 SP and NSP cells and treated with M.SssI at 37 ˚C for 15 minutes supplied with S-Adenosyl methionine (SAM). The no-enzyme (NE) controls are also included for each cell. DNA is then extracted, bisulfite converted and run on an Infinium methylationEPIC array. The Beta values of the no-enzyme controls show the original DNA methylation level. The subtracted beta values (M.SssI treated - NE) are used to determine regions that have gained by the in vitro M.SssI treatment, and these are used to infer chromatin state.

first: Hongtao

last: Li

first: Tong

last: xu

first: Meng


title: Difference of DNA methylation and Chromatin accessibility of T24 SP cell and T24 NSP cell

overall_design: T24 SP and NSP nuclei were purified and incubated with/without M.SssI enzyme with SAM supplied for 15 min at 37 degrees and analyzed on Illumina Infinium Human MethylationEPIC Beadchip.

last: Xu


title: Meta-analysis of honey bee neurogenomic response to deformed wing virus

status: Public on Feb 04 2020

city: Princeton

first: Ian

middle: Michael

last: Traniello

state: NJ

address: Princeton University

department: Lewis-Sigler Insitute for Genomic Biology

institute: Princeton University

summary: Plant pollination by the western honey bee Apis mellifera is an irreplaceable agroecological and economic cornerstone currently under threat. Recent colony loss has been consistently linked to the increased prevalence of deformed wing virus (DWV), an Iflavirus transmitted from the ecoparasitic mite Varros destructor. While DWV has been detected in the honey bee brain and causally linked to behavioral impairment, the molecular impact of infection on brain gene expression is largely unknown. Recently, we discovered that two published and two new brain transcriptomic studies conducted in our lab contained DWV contamination in over 99% of sequenced honey bee samples. This unanticipated finding sharply contrasted with the experimental paradigms of these four studies, as no physical or behavioral signs of DWV were detected in any of the 335 individual honey bees sampled. We took this opportunity to perform a meta-analysis and test the hypothesis that DWV influences brain gene expression, a relationship which could be linked to the massive depopulation events observed around the world. Results from our study support commonalities in the molecular consequences of DWV in the honey bee brain and implicate specific genes and biological processes associated with infection. Next, we used single-cell RNA-Sequencing to implicate glia as active responders to viral infection. Finally, we performed viral gene expression analysis on a subset of samples and found DWV type A as well as a previously unreported A-B recombinant in the brain. We present this meta-analysis as a first step toward addressing a potential missing link between viral infection and behavior in honey bees.

overall_design: Two seven-day-old bees from a single colony headed by a queen inseminated with semen from a single drone (male).


title: Promoter-proximal CTCF binding promotes distal enhancer-dependent gene activation II

status: Public on Mar 06 2020

first: Bing

last: Ren

address: 9500 Gilman Dr., CMM-East, Admin Area/Rm 2071

institute: University of California, San Diego School of Medicine

summary: The CCCTC-binding factor (CTCF) is widely regarded as a key player in chromosome organization in mammalian cells, yet direct assessment of its role in genome architecture and gene regulation has been difficult. Here, we use auxin-inducible degron techniques to acutely deplete CTCF to determine how loss of CTCF affect chromatin organization and gene expression. In mouse embryonic stem cells, depletion of CTCF results in rapid loss of chromatin loops anchored at CTCF-binding sites without major disruption to chromatin compartments and topological domains. In the absence of CTCF, many lineage-specific genes fail to express properly during differentiation to neural precursor cells, but transcriptional regulation of most genes is unaffected. Genes dependent on CTCF for induction are generally bound by the factor at promoters, which are connected to distal enhancers via CTCF-dependent chromatin loops. By contrast, CTCF-independent genes generally lack CTCF binding at the promoter and are generally closer to enhancers. These results refine our understanding of CTCF function in chromatin organization and gene regulation.

overall_design: PLAC-seq. Hi-C, mRNA-seq and ChIP-seq experiments in CTCF depleted mouse embryonic stem cells and during neural progenitor cell differentiation.

first: Naoki

last: Kubo


title: Bladder cancer cell lines side population and non-side population cells


title: Expression data from Cyanidine (Cyanidine 3-glucoside)-treated human amnion epithelial cells (hAECs)

first: Farhana

last: Ferdousi

summary: Gene expression profiling of the effect of Cyanidine 3 glucoside treatment in hAECs.

overall_design:
hAECs were isolated from discarded term placenta and were treated with 20 μM Cyanidine 3-glucoside for seven days. Microarray gene expression profiling was conducted for biological replicates of Cyanidine-treated and untreated control cells on day 7.
RNA was extracted using Isogen (Nippon Gene Co. Ltd., Toyama, Japan). The integrity of RNA was quantified using NanoDrop 2000 spectrophotometer (Thermo Scientific, Wilmington, DE, USA). RNA samples were prepared for gene expression profiling analysis with GeneChip® 3' Expression Arrays using 3' IVT PLUS Reagent Kit (Affymetrix Inc., Santa Clara, CA, USA). Two hundred and fifty ng of total RNA from each sample was used to generate amplified and biotinylated complementary RNA (cRNA) from poly (A) RNA in a total RNA sample according to the user manual. IVT Incubation time was 16 hour. GeneAtlas® Hybridization, Wash and Stain Kit was used for hybridizing 3' IVT Array Strips according to the user manual (P/N 08-0306). Human genome array strips (HG-U219) were hybridized for 16 hours in a 45oC incubator, washed and stained and finally imaging was done with the GeneAtlas Fluidics and Imaging Station.


title: Genome-wide maps of gene expression in liver of alkaline sphingomyelinase knockout mice

status: Public on Jan 01 2020

city: Daqing

first: Jiang

last: Zhu

state: Hei Longjiang

address: Xinyang Road 39, Gaoxin District

institute: Daqing Branch of Harbin Medical University

summary: Intestinal alkaline sphingomyelinase (alk-SMase) generates ceramide and inactivates platelet-activating factor and associated with digestion and inhibition of cancer. There is few study to analyze the correlated function and characterize the genes related to alk-SMase comprehensively. In this work, deep RNA sequencing was performed to investigate the function of alk-SMase. Our RNA-seq data found 239 differentially expressed mRNAs between the wild type (WT) mice and alk-SMase (gene NPP7) knockout (KO) mice, in which 73 were significantly up-regulated and 166 were down-regulated, including protein coding genes, non-coding RNAs. Notably, the results of gene ontology functional enrichment analysis indicated that differentially expressed genes were functionally associated with the immune response, regulation of cell proliferation and development related terms using DAVID. Additionally, an integrated PPI and KEGG network was chose to study the relationship of differentially expressed genes, it was shown that some modules was significantly related to alk-SMase and with accordance of previously results. We chose 6 of these genes randomly were validated the accuracy of RNA-seq technology using quantitative real-time polymerase chain reaction (qPCR) and 2 genes showed difference significantly (P<0.05).

overall_design: Mouse intestinal tissues were harvested from three pairs of wildtype and alk-SMase knockout mice. Total RNA was extracrted with TRizol method according to manufacturer’s instructions. RNA samples were deeply sequenced using Illumina HiSeq 2500 platform after further cleaning-up using Qiagen RNeasy mini columns, and 50bp single end reads were genetated.

first: Ping

last: Zhang


title: Tubulointerstitial transcriptome data in the Neptune Cohort

city: Ann Arbor

first: Sean

last: Eddy

address: 1150 West Medical Center Drive

institute: University of Michigan

summary: summary : Tubular Transcriptome in the Neptune Cohort

overall_design: Expression profiling of kidney tubulointerstitium from healthy donors and patients with kidney diseases: Membranous Nephropathy, Focal and Segmental Glomerulosclerosis, Minimal Change Disease, Glomerular Disease (other).

first: Viji

last: Nair

first: Sebastian

last: Martini

first: Laura

last: Mariani

first: Matt

last: Sampson

first: Felix

last: Eichinger

first: Brad

last: Godfrey

first: Matthias

last: Kretzler


title: Expression profiling of D. melanogaster guts with suppression of Imd in progenitors

status: Public on Dec 13 2019

city: Edmonton

first: Edan

last: Foley

state: Alberta

address: 116 st and 85 ave

department: Medical Microbiology and Immunology

institute: University of Alberta


title: The transcriptomic analysis of four tissues in growth and reproductive axes of Starry Flounder (Platichthys stellatus)

status: Public on Dec 31 2019

last: Wang

state: Shandong

address: 106 Nanjing Road

institute: Yellow Sea Fisheries Research Institute, Chinese Academy Fishery Science

summary: In the present study, four important somatotropic and reproductive tissues including brain, liver, gonad and muscle from 3 females and 3 males were used for transcriptomic analysis. A mean of 47,102,115 high quality clean reads were obtained from each library and 156, 67, 3434, and 378 differentially expressed genes in female and male were identified from brain, liver, gonad, and muscle, respectively (q < 0.05). These genes were further enriched in to ion channel activity, protein binding, lipid transporter activity, and glycolytic process GO terms. The KEGG enrichment analysis revealed that insulin secretion, Calcium signaling pathway, Signaling pathways regulating pluripotency of stem cells, Glycolysis / Gluconeogenesis were significantly enriched.

overall_design: Examination of four important somatotropic and reporductive tissues including brain, pituitary, liver and gonad from 3 females and 3 males Starry Flounder

first: Yongsheng

last: Tian


title: Essential functions of the Glucocorticoid Receptor require direct DNA binding

city: Freising

first: Franziska

last: Greulich

address: Gregor-Mendel-Str. 2

department: Metabolic Programming

country: Germany

institute: TU München


title: Gene expression profiling (RNA-seq) in wild-type Arabidopsis seedlings in response to heat acclimation and heat shock

status: Public on Dec 24 2019

city: Thuwal

first: Magdalena

last: Julkowska

state: Makkah

address: KAUST

department: BESE

country: Saudi Arabia

institute: King Abdullah University of Science and Technology

summary: Changes in Arabidopsis thaliana transcriptome throughout the acclimation and the subsequent heat shock treatment.

overall_design: Two batches of samples contaning 11 time-points during the heat stress regime

first: Ge

last: Gao

first: Yong

last: Woo

first: Christoph

last: Gehring

first: Mark

last: Tester


title: Single cell expression data from D. melanogaster guts with suppression of Imd in progenitors

summary: We used Single-cell RNA-seq to examine transcriptional proflies of midguts with suppression of Imd in progenitors.

overall_design: Genotype control flies and flies with Imd inhibition were riased on regular food (Bloomington standard food) for 10 days at 29ºC after eclosion. Guts were dissected and dissociated by elastase. Sorting live single cells used by OptiprepTM Density Gradient medium and generated library and sent to Novogene for sequencing.

first: Minjeong

last: Shin


title: Heteroplasmy between wild type mitochondrial DNA variants is detrimental and shorten life span

city: Madrid

first: Fatima

last: Sanchez-Cabo

address: Melchor Fernandez Almagro

country: Spain

institute: CNIC

summary: We evaluated here the physiological consequences of the generation of heteroplasmic embryos by mix of two wild type mtDNAs in the same zygote. In this animal model, mtDNA heteroplasmy is actively combated during germ-line transmission, embryonic development and somatic life of most differentiated cells. mtDNA heteroplasmy alone, even when both mtDNA types are individually non-pathogenic, causes a disease affecting mainly those tissues that are not able to reduce their heteroplasmy: heart, lung and skeletal muscle.

overall_design:
Transcriptome analysis of 12-weeks-old conplastic mice (BL/6^C57 and BL/6^NZB) versus heteroplasmic mice (BL/6^C57-NZB) in heart tissue.
We generated heteroplasmic mice by electro-fusion of an embryo and an enucleated embryo, using two conplastic mouse strains: nuclear genome from C57BL/6JOlaHsd strain and mtDNA either of NZB/OlaHsd (BL/6^NZB) or C57BL/6JOlaHsd mtDNA (BL/6^C57).

first: Ana

middle: V

last: Lechuga

last: Latorre

first: Jose

last: Enriquez

first: Fátima

last: Sánchez-Cabo


title: Transcriptome of Pseudomonas aeruginosa PAO1 genes induced by exposure to extracellular DNA

status: Public on Jan 29 2020

city: Calgary

first: Shawn

last: Lewenza

state: AB

address: 3330 Hospital Drive NW

department: Microbiology, Immunology & Infectious Diseases

institute: University of Calgary

summary: We identify a group of bacterial genes that are induced and repressed by the addition of eDNA, due to cation chelation, acidification or nutrient utilization.

overall_design: Triplicate cultures were grown to mid-log with and without 0.75% eDNA for isolation of RNA.


title: Essential functions of the Glucocorticoid Receptor require direct DNA binding [RNA-seq]

summary: We performed RNA sequencing in Mouse Embryonic Fibroblasts (MEFs) of GR wild-type and GR Zn. Cells were treated with: vehicle (EtOH), Dexamethasone (Dex), Lipopolysaccharide (LPS) or Dex+LPS. We show that GR Zn does not regulate any GR target gene

overall_design: mRNA profile of GR wild-type and GR Zn MEFs treated with vehicle, Dex, LPS or DexLPS

first: Laura

last: Escoter-Torres

first: Nina

middle: H

last: Uhlenhaut


title: Gene expressions of IBMX-induced neuron differentiation from placenta-derived multipotent stem cells

status: Public on Nov 01 2019

city: New Taipei

first: Chih-Cheng

last: Chien

address: No 2, Ln 59, Jian-Cheng Rd, Sijhih Dist

country: Taiwan

institute: Sijhih Cathay General Hospital

summary: Little is known about factors that induce stem cells differentiated into astrocyte. Using double cross strategy, we effective narrow down the candidate molecules crucial for astroglial differentiation. By cross comparison the data from transcriptomic and proteomic experiments, we selected 24 candidate genes which might be involved in the neuron differentiation. The 24 genes were further cross compared with Alzheimer disease (AD) database, which regarded as a neuron degenerative database. There were 18 out of 24 candidates showed opposite expression level in our data and AD database. Among them, the combination of Heat Shock Protein 27 (HSP27) and S100 calcium-binding protein A16 (S100A16) showed predominant crucial in neuronal differentiation than other gene combination. We previously showed that the expression level of HSP27 directly related to the glutamatergic neuron differentiation under IBMX induction. In this paper, we found co-silence of HSP27 and S100A16 directly induced PDMCs differentiate into functional glutamatergic neurons and astrocytes while IBMX is no longer required in this process. The resulting astrocyte not only exhibit the classic morphology but also with astrocyte function.

overall_design: We used our existing neuron differentiation model derived from placenta-multipotent stem cells (PDMCs) as a cell model. The neuron differentiation was induced by adding 0.4 mM IBMX. The differentiated neurons were harvested 12h and 24h after induction , and the mRNAs were collected by RNeasy Mini Kit (Qiagen, Hilden, Germany), and mRNAs were used for probing of a human oligonucleotide microarray (Agilent SurePrint G3 Human GE 8x60K oligonucleotide microarrays; Agilent Technologies, USA).

first: Yu-Che

last: Cheng

first: Chi-Jung

last: Huang

first: Wei-Chi

last: Ku

first: Lu-Tai

last: Tien

first: Chia-Te

first: Yih-Jing

last: Lee


title: Identification and definition of a Bro1 domain proteins associated with sophorolipids synthesis in Starmerella bombicola

status: Public on Sep 27 2019

city: Qingdao

first: Liu

last: Jun

address: Binhai Road 72

institute: Shandong University

summary: The goals of this study are to compare different gene expressions for starmerella bombicola Bro1,gme3597 and gme3787 knockout strain, the reference strain wild-type was considered as a control. The deletion of Bro1 significantly downregulated genes involved in the sophorolipids synthesis-related pathwaw and resulted in the inability of the mutant to synthesize sophorolipids. The deletion of gme3696 also down-regulated the expression of sophorolipid synthesis-related genes. The knockout of gme3787 up-regulated the expression of UDP-glucose pyrophosphorylase.This study provides the information that Bro1 function are required in sophorolipids synthesis of starmerella bombicola.

overall_design: A total of 12 samples were analzyed, which include biological triplicates. The reference strain wild-type was considered as a control.

first: Jun

last: Liu

first: Xin

last: Song


title: Genome-wide transcriptional profiles of intestinal macrophages from WT and Csf1r-EP4-/-  mice during dextran sodium sulfate induced colitis.

status: Public on Nov 28 2019

city: Seongnam-si

first: Daun

last: Jung

state: Gyeonggi-do

address: Bundang-gu, 삼평동 689

department: Department of Pathology

institute: CHA Bundang Medical Center

summary: To define the mechanisms that underlie regeneration driven by EP4+ macrophages, we transcriptionally compared the WT and Csf1r-EP4-/- mature macrophages isolated from colon by 39 days post DSS treatment.

overall_design: mRNA profiles of intestinal macrophages from WT and Csf1r-EP4-/- mice during dextran sodium sulfate induced colitis were generated by sequencing, in triplicate, using NextSeq 500 (Illumina, Inc., USA)

first: Yirang


title: Expression data from Verbenalin-treated human amnion epithelial cells (hAECs)

status: Public on Sep 09 2019

city: Tsukuba

first: Farhana

last: Ferdousi

address: Tennodai 1-1-1

institute: University of Tsukuba

summary:
Gene expression profiling reveals a potential role of Verbenalin in neural induction and neuronal differentiation of hAECs.
hAECs were isolated from discarded term placenta and were treated with 20 μM verbenalin for seven days. Microarray gene expression profiling was conducted for biological replicates of RA-treated (T7) and untreated control cells on day 0 (D0) and day 7 (D7).

overall_design: RNA was extracted using Isogen (Nippon Gene Co. Ltd., Toyama, Japan). The integrity of RNA was quantified using NanoDrop 2000 spectrophotometer (Thermo Scientific, Wilmington, DE, USA). RNA samples were prepared for gene expression profiling analysis with GeneChip® 3' Expression Arrays using 3' IVT PLUS Reagent Kit (Affymetrix Inc., Santa Clara, CA, USA). Two hundred and fifty ng of total RNA from each sample was used to generate amplified and biotinylated complementary RNA (cRNA) from poly (A) RNA in a total RNA sample according to the user manual. IVT Incubation time was 16 hour. GeneAtlas® Hybridization, Wash and Stain Kit was used for hybridizing 3' IVT Array Strips according to the user manual (P/N 08-0306). Human genome array strips (HG-U219) were hybridized for 16 hours in a 45oC incubator, washed and stained and finally imaging was done with the GeneAtlas Fluidics and Imaging Station.


title: Lineage specification and pluripotency revealed by transcriptome analysis from oocyte to blastocyst in pig

status: Public on Oct 29 2019

city: harbin

first: xu

last: yangx

address: mucai 59

institute: neau

summary: The inner cell mass in blastocyst is the origin of all the somatic and germ cells in mammals, and of pluripotent stem cells in vitro. As the conserved principles between pig and human, here we performed comprehensive single-cell RNA-seq for porcine early embryos from oocyte to early blastocyst. We show the specification of inner cell mass and trophectoderm in morula, and the molecular signature of the precursors. We demonstrate the existence of naïve pluripotency signature in morula and inner cell mass of early blastocyst, and the specific pluripotent genes and the activity of signalling pathways highlight the characteristics of the naïve pluripotency. We observe absence of dosage compensation with respect to X-chromosome in morula, and incomplete dosage compensation in early blastocyst. However, the dynamics of dosage compensation may be independent on the expression of XIST induced X-chromosome inactivation. Our study describes molecular landmarks of embryogenesis in pig that will provide a better strategy for derivation of porcine pluripotent stem cells and improve the research in regenerative medicine.

overall_design: scRNA-seq of pig preimplantation embryos

first: Qingran

last: Kong

first: Xu

last: Yang

first: Heng

last: Zhang

first: Shichao

first: Jianchao

last: Zhao

first: Jiaming

first: Xiaogang

last: Weng

first: Junxue

last: Jin

first: Zhonghua


title: High-Throughput Translational Profiling with riboPLATE-seq

status: Public on Oct 23 2019

city: New York

first: Jordan

middle: Benjamin

last: Metz

state: NY

address: 3960 Broadway Room 203A

department: Systems Biology

institute: Columbia University

summary: Protein synthesis is dysregulated in many diseases, but we lack a systems-level picture of how signaling molecules and RNA binding proteins interact with the translational machinery, largely due to technological limitations. Here we present riboPLATE-seq, a scalable method for generating paired libraries of ribosome-associated and total mRNA. As an extension of the PLATE-seq protocol, riboPLATE-seq utilizes barcoded primers for pooled library preparation, but additionally leverages rRNA immunoprecipitation on whole polysomes to measure ribosome association (RA). We demonstrate the performance of riboPLATE-seq and its utility in detecting translational alterations induced by inhibition of protein kinases.

overall_design: 96 paired riboPLATE- and PLATE-seq libraries, corresponding to independent TS543 glioma neurosphere samples seeded on a 96-well plate, plus 13 RNA-seq and 10 ribosome profiling libraries. 6 replicates per drug treatment (PP242, MNK-i1, BKM120, PP242+BKM120, PP242+MNK-i1, BKM120+MNK-i1, AZD8055, 4EGi-1) and 48 DMSO-treated controls, plus three replicates each of ribosome profiling and RNA sequencing for PP242 or DMSO treatment at 30 minutes, two further replicates at 6 hours PP242 or DMSO treatment, and one additional unpaired 6-hour DMSO-treated RNA-seq library.

first: Nicholas

last: Hornstein

first: Sohani

middle: D

last: Sharma

first: Christian

last: Gonzalez

first: Jeremy

last: Worley

first: Peter

last: Sims


title: AGO4 participates in germination during salinity

status: Public on Sep 30 2019

city: Cuernavaca

first: Veronica

last: Jimenez-Jacinto

state: Morelos

address: Av. Universidad 2001. Col. chamilpa

department: Unidad Universitaria de Secuenciación Masiva y Bioinformática

country: Mexico

institute: Universidad Nacional Autonoma de Mexico

summary: In this work we studied the participation of RdDM pathway in response to salinity during germination, we found that the RdDM promotes germination whule AGO4 has an additional RdDM-independent activity that negatively regulates the germination process.

overall_design: Col-0, ago4-2 and ago4-3 Arabidopsis germinating seeds under control and salinity conditions, each run was performed with a biological replicate

first: V

last: Palomar

first: Verónica

last: Jimenez

first: Alejandra

last: Covarrubias


title: Genetic influences on DNA methylation (mQTL) in pediatric Crohn's disease patients

status: Public on Aug 17 2019

city: Atlanta

first: Suresh

last: Venkateswaran

state: Georgia

address: 1760 Haygood Drive, HSRB, Room No: E-250

department: Pediatrics

institute: Emory University

summary: Previously, we conducted an epigenome-wide study of DNA methylation (~850K sites) in peripheral blood at diagnosis and during follow-up from the RISK pediatric Crohn’s disease inception cohort and data are deposited in GEO with an access number GSE112611. We further followed up this study and identified here the genetic influence on ~850K DNAm sites (mQTL) in peripheral blood as well as newly added 41 ileal biopsies. All the ileal biopsies DNAm data are collected from the subset of primary 238 pediatric CD cohort that contains the peripheral blood DNAm data in GSE112611. Comparing the mQTL effect sizes among 164 CD cases at baseline, 164 CD cases at 3 years follow-up, 74 healthy controls and 41 ileal biopsies confirms that genetic influence on DNAm sites are strongly consistent among these groups. This study further concludes that the mQTLs are largely not disease-specific or inflammation-specific or tissue-specific.

overall_design: DNA methylation was assessed in Ileal biopsies from pediatric non-IBD controls and patients with Crohn's disease at diagnosis. Ileal biopsy DNA was extracted, bisulfite converted and genome-wide DNA methylation was interrogated using the HumanMethylationEPIC BeadChip (Illumina).

first: Hari

last: Somineni

first: Varun

last: Kilaru

first: Seyma

last: Katrinli

first: David

middle: T

last: Okou

first: Jeffrey

last: Hyams

first: Lee

last: Denson

last: Cutler

first: Alicia

last: Smith

first: Subra

last: Kugathasan

first: Karen

middle: N

last: Conneely


title: Engineering a Niche Supporting Hematopoietic Stem Cell Development Using Integrated Single Cell Transcriptomics

status: Public on Mar 01 2020

city: Seattle

first: Brandon

last: Hadland

state: WA

address: 1100 Fairview Avenue N., D2-115, P.O. Box 19024

institute: Fred Hutchinson Cancer Research Center

summary: Hematopoietic stem cells (HSC) develop from hemogenic endothelium (HE) within embryonic arterial vessels such as the aorta of the aorta-gonad-mesonephros region (AGM).  To identify the signals responsible for HSC formation, we used single cell RNA-sequencing to simultaneously analyze the transcriptional profiles of AGM-derived cells transitioning from HE to HSC, and AGM-derived endothelial cells which provide signals sufficient to support HSC maturation and self-renewal. Pseudotemporal ordering revealed dynamics of gene expression during the HE to HSC transition, identifying surface receptors specifically expressed on developing HSC. Transcriptional profiles of niche endothelial cells enabled identification of corresponding ligands, including those signaling to Notch receptors, VLA-4 integrin, and CXCR4, which, when integrated in an engineered platform, were sufficient to support the generation of engrafting HSC.  These studies provide a transcriptional map of the signaling interactions necessary for the development of HSC and advance the goal of engineering HSC for therapeutic applications

overall_design: single cell RNA-sequencing (10X Genomics platform) of murine E10-E11 AGM-derived cultured endothelial cells expressing mAkt (AGM-EC) used as stroma to support HSC development ex vivo; and murine E10-E11 AGM-derived FACS-isolated VE-Cadherin+CD61+EPCR+ cells enriched for HSC precursors (primary cells and progeny following co-culture with AGM-EC)


title: Expression data from J82 side population and non-side population cells

status: Public on Jan 30 2020

city: Los Angeles

first: Gangning

last: Liang

state: CA

address: 1441 Biggy street

institute: USC Keck school of medicine

summary: Subpopulations of highly tumorigenic, drug resistant cancer stem-like cells play a key role in cancer recurrence and progression. Surprisingly, these aggressive cells can arise repeatedly de novo from bulk tumor cells independently of mutational events. We investigated whether transition to and from a cancer stem-like state is associated with epigenetic alterations, such as DNA methylation and chromatin accessibility. By Hoechst dye staining and FACS analysis, side population (SP) and non-side population cells were sorted from J82 cells. AcceSssIble assay by Infinium EPIC BeadArray platform was used to identify potential epigenetic driver genes in the process of SP /NSP phenotype plasticity. Genes with differential accessible promoter regions were overlapped with genes differentially expressed by HuEx array analysis. Oncomine and Basespace were adopted to explore the clinical relevance of the target genes.

overall_design: By Hoechst dye staining and FACS analysis, side population (SP) and non-side population cells were sorted from J82 cells. RNA were isolated and HuEx array was run for gene expression analysis.

first: Tong

last: Xu

first: Hongtao

last: Li

first: Meng

first: Amir

last: Goldkorn


title: Slit2 protects hearts against ischemia-reperfusion injury by inhibiting inflammatory responses and maintaining myofilament contractile properties

status: Public on Jul 04 2019

city: Guangzhou

first: Xiang

state: Guangdong

address: 11 fengxin road, guangzhou science city

institute: Guangdong Laboratory Animals Monitoring Institute

summary:
Background The axon guidance cue Slit2 recently has been found to regulate calcium homeostasis and molecular signaling in various stress events in different organs. However, whether Slit2 plays a role in cardiac ischemia-reperfusion (IR) injury has not been reported. Here, we aimed to investigate the role of Slit2 and the underlying mechanisms in cardiac IR injury.
Methods Langendorff-perfused isolated hearts from Slit2-overexpressing (Slit2-Tg) mice and their background strain C57BL/6J mice were subjected to 20 min of global ischemia followed by 40 min of reperfusion. Left ventricular function of isolated hearts was monitored. Infarct size of post-IR hearts was determined by staining with 2,3,5-triphenyltetrazolium chloride (TTC) and histological changes of cardiac tissues and cells were determined with hematoxylin-eosin (HE) staining and transmission electron microscopy. Transcriptomic analysis was used to predict the biological processes and signaling pathways affected by Slit2 overexpression in the post-IR myocardium. Pro-Q staining and Western blotting was used to assess the phosphorylation levels of cardiac myofilaments and expression levels of myofilament-associated protein kinase and phosphatases.
Results Slit2 overexpression increased post-IR left ventricular developed pressure (LVDP) by 35% and reduced infarct size by 53%, along with decreased myofibrillar disruption, mitochondrial swelling, and mitochondrial cristae dissolution. Slit2 overexpression significantly changed post-IR gene expression profiles. Functional products of these genes include regulation of cation transmembrane transport, cation homeostasis, collagen fibril organization, and regulation of heart rate. And post-IR myocardial
KEGG pathways upregulated by Slit2 overexpression include ECM-receptor interaction, PI3K-Akt signaling pathway, and adrenergic signaling. Slit2 overexpression impacted myofilament phosphorylation together with myofilament-associated protein kinase C (PKC) isoforms and protein phosphatases (PPs). IR in C57BL/6J hearts upregulated phosphorylation of cardiac troponin-I (cTnI), which was suppressed by Slit2 overexpression. Myofilament‐associated PKCε, PKCδ, and PP2A were significantly increased post‐IR in C57BL/6J hearts, but in Slit2‐Tg hearts, myofilament‐associated PKCε and PP2A were increased and PKCδ was suppressed.
Conclusions Our results demonstrate that Slit2 overexpression protects cardiac function and reduces IR injury, which is associated with Slit2‐induced gene profile shifts. The suppression of MyBP‐C and troponin‐I phosphorylation, and myofilament‐associated PKCδ levels induced by Slit2 overexpression could contribute to the cardioprotection of Slit2 in post-IR myocardium.

overall_design: Total RNAs from C57BL/6J and Slit2-overexpressing (Slit2-Tg) hearts after IR or non-IR were isolated using TRIzol® Reagent. Each group contains three independent samples.Subsequently, a total amount of 3 µg RNA per sample were used for transcriptome sequencing.

first: Feng hua

last: Yang


title: Expression data from rosmarinic acid-treated human amnion epithelial cells (hAECs)

status: Public on Jun 26 2019

first: Farhana

last: Ferdousi

state: Ibaraki

summary:
Gene expression profiling reveals a potential role of rosmarinic acid in neural induction and neuronal differentiation of hAECs.
hAECs were isolated from discarded term placenta and were treated with 20 μM RA for seven days. Microarray gene expression profiling was conducted for biological replicates of RA-treated (T7) and untreated control cells on day 0 (D0) and day 7 (D7).


title: Genome-wide mapping of DNA-methylation in hTert-HME1 cell line treated with control or BRCA2 siRNAs and grown with or without EGF (epithelial growth factor)

status: Public on Aug 07 2019

city: Palo Alto

first: Michael

last: Snyder

address: 3165 Porter Dr

department: Genetics

institute: Stanford University

type: Methylation profiling by high throughput sequencing

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

overall_design: Control siRNA transfection grown in media +EGF (7 replicates), BRCA2 siRNA grown in media +EGF (4 replicates), BRCA2 siRNA grown in media -EGF (4 replicates)

first: Joshua

last: Gruber


title: Muscle transcriptome response to stress in bovine

status: Public on Sep 01 2019

city: Saint Genes Champanelle

first: Celine

last: BOBY

address: Centre INRA Auvergne-Rhône-Alpes

country: France

institute: INRA

summary: The conditions to which cattle are subjected before slaughter (social isolation, transportation, deprivation of food and water) are sources of emotional and physical stress that may affect the nutritional and organoleptic qualities of meat from these animals. We have examined the muscle transcriptomes (m. Longissimus thoracis and the m. Semitendinosus) in cows exposed to stress vs cows with limited stress. Stress was a combination of emotional and physical stress.

overall_design: one-color experiment ; two groups of cows : finished and slaughtered under conditions of limited stress (n = 16) or physical and psychological stress (n = 16) ; 2 muscles studied : m. Longissimus thoracis (LT) and m. Semitendinosus (ST)

first: Isabelle

last: Cassar-Malek

first: Jean-François

last: Hocquette


title: On-Treatment Biomarkers Improve Prediction of Response to Neoadjuvant Chemotherapy in Breast Cancer

status: Public on Jul 02 2019

city: Carrington Crescent

first: Andrew

last: Sims

state: Edinburgh

address: Systems Medicine Building

department: Institute of Genetics and Molecular Medicine

institute: University of Edinburgh

summary:
Background: Neoadjuvant chemotherapy is increasingly being used to preoperatively shrink breast tumours prior to surgery. This approach also provides the opportunity to study the molecular changes associated with treatment and evaluate whether on-treatment sequential samples can improve response and outcome predictions over diagnostic or excision samples alone.
Methods: A total of 95 samples from a cohort of 50 neoadjuvant chemotherapy-treated primary breast cancer patients (aged 29-76, 48% ER+, 20% HER2+) enrolled in the NEO trial taken before, at 2 weeks on-treatment, mid-therapy and at resection were sequenced with Ion Ampliseq transcriptome yielding expression values for 12,635 genes. Differential expression analysis was performed across 16 responders and 34 non-responders defined by pathological complete response and over treatment time to identify significantly differentially expressed genes, pathways and markers indicative of response status. Prediction accuracy was compared with estimations of established gene signatures, for this dataset and validated using data from the I-SPY1 trial.
Results: AAGAB was identified as a novel on-treatment biomarker for pathological complete response, with an accuracy of 100% in the NEO training dataset and 78% accuracy in the I-SPY1 Trial. AAGAB levels on treatment were also significantly predictive of term survival (p = 0.048, p = 0.031) in the two cohorts. This single gene on-treatment biomarker, had greater predictive accuracy than established prognostic tests, Mammaprint and Pam50 risk of recurrence score, although interesting both of these tests performed better in the on-treatment rather than the accepted pre-treatment setting (accuracy improving consistently by 2-8%).
Conclusion: Changes in gene expression measured in sequential samples from breast cancer patients receiving neoadjuvant chemotherapy resulted in the identification of a novel on-treatment biomarker and suggest that established prognostic tests may have greater prediction accuracy on- than before treatment. These results support the potential use and further evaluation of on- treatment testing in breast cancer to improve the accuracy of tumour response prediction.

overall_design: A cohort of 95 paired sequentially sampled breast cancer patients with known treatment response were pooled. Samples were taken via needle aspiration at T1 (Pre-treatment), T2 (2 weeks on treatment), T3 (mid chemo, usually 6 weeks), and T4 at surgical resection. Samples were fresh frozen after collection. Samples were sequenced on the Ampliseq platform and differential analysis and processing were performed in R.

first: Richard

last: Bownes

first: Arran

last: Turnbull

first: Carlos

last: Matínez-Pérez

first: David

last: Cameron

first: Olga

last: Oikonomidou


title: RNA-seq of human normal lung and lung cancer tissue

status: Public on Jun 25 2019

city: Shinjuku-ku

first: Shin-ichiro

last: Ohno

state: Tokyo

address: 6-1-1 Shinjuku

department: Molecular Pathology

institute: Tokyo Medical University

summary: In order to identify divergent transcripts involved in cancer development, next-generation sequencing analysis of RNA extracted from cancer and normal lung tissue was performed.

overall_design: RNA profiles of human normal lung and lung cancer were generated by deep sequencing, using Illumina HiSeq 4000.

first: Masahiko

last: Kuroda


title: CD97 is a Critical Regulator of Acute Myeloid Leukemia Stem Cell Function

status: Public on Jul 30 2019

first: Christopher

middle: Y.

last: Park

state: New York

address: 550 First Avenue

department: Pathology

institute: New York University

summary: Despite significant efforts to improve therapies for acute myeloid leukemia (AML), clinical outcomes remain poor. Understanding the mechanisms that regulate the development and maintenance of leukemic stem cells (LSC) is important to reveal new therapeutic opportunities. We have identified CD97, a member of the adhesion class of G-protein coupled receptors (GPCRs), as a frequently upregulated antigen of AML blasts that is a critical regulator of blast function. High levels of CD97 correlate with poor prognosis, and silencing of CD97 reduces disease aggressiveness in vivo. In order to analyze the functional pathways associated with CD97 expression, we generated RNA-sequence data from scrambled shRNA transfected (s-shRNA) and CD97 KD human AML cell line HL60, as well as from MLL-AF9 (MA9) transduced GMPs isolated from CD97-/- and WT mice. These phenotypes are due to CD97’s function to promote proliferation, survival, and the maintenance of the undifferentiated state in leukemic blasts. Collectively, our data credential CD97 as a promising therapeutic target on LSCs in AML.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: CD97 knock down (CD97-KD) was performed in the human AML cell line HL60 using lentiviral vectors expressing scramble control sequences (scramble shRNA, s-shRNA) or two shRNAs targeting CD97 (shCD97.1 and shCD97.3). Both shRNAs induced a significant decrease in CD97 mRNA expression. For the MA9 RNA-seq data, we purified HSPCs from wild-type (WT) and CD97 deficient (CD97-/-) mice and transduced them with the leukemogenic oncogene, MLL-AF9 (MA9). We analyzed the transcriptomes of i) scrambled shRNA transduced (s-shRNA) HL60 and CD97 KD HL60, and ii) WT-MA9 and CD97-/--MA9 mouse LSCs (L-GMPs).

first: Gaëlle

last: Martin

middle: Y


title: Phenotyping spermatogenic defects by single-cell expression profiling

status: Public on Jun 30 2019

city: Beaverton

first: Donald

middle: F.

last: Conrad

state: OR

address: 505 NW 185th Ave

department: Division of Genetics; Oregon National Primate Research Center

institute: Oregon Health & Science University

summary: Using Drop-seq, we generated high-throughput single-cell expression data from wild-type and four mutant models with male infertility phenotype. Our study demonstrates the applicability of single-cell RNA-sequencing in study of male gonadal dysfunction and provides cell atlas resource for testis.

overall_design: Drop-seq was performed on FACS sorted germ cell populations, wild-type whole testes and mutant whole testes. Different experimental batches for wild-type and mutant strains were generated.

first: Min

last: Jung

first: Don


title: Mouse models of Alzheimer’s disease with natural genetic variation

status: Public on May 22 2019

city: Farmington

first: Asli

last: Uyar

state: CT

address: 10 Discovery Dr

department: Computational Sciences

institute: The Jackson Laboratory

summary: Classical laboratory strains show limited genetic diversity and do not harness natural genetic variation. Mouse models relevant to Alzheimer’s disease (AD) have largely been developed using these classical laboratory strains, such as C57BL/6J (B6), and this has likely contributed to the failure of translation of findings from mice to the clinic. Therefore, here we test the potential for natural genetic variation to enhance the translatability of AD mouse models. Two widely used AD-relevant transgenes, APPswe and PS1de9 (APP/PS1), were backcrossed from B6 to three wild-derived strains CAST/EiJ, WSB/EiJ, PWK/PhJ, representative of three Mus musculus subspecies. These new AD strains were characterized using metabolic, functional, neuropathological and transcriptional assays. Strain-, sex- and genotype-specific differences were observed in cognitive ability, neurodegeneration, plaque load, cerebrovascular health and cerebral amyloid angiopathy. Analyses of brain transcriptional data showed strain was the greatest driver of variation. We identified significant variation in myeloid cell numbers in wild type mice of different strains as well as significant differences in plaque-associated myeloid responses in APP/PS1 mice between the strains. Collectively, these data support the use of wild-derived strains to better model the complexity of human AD.

overall_design: Brain transcriptomes of 8-month-old wild type (WT) and APP/PS1 mice from C57BL/6J (B6) and three wild derived strains (CAST/EiJ, WSB/EiJ, PWK/PhJ) were generated.

first: Kristen

last: Onos

first: Kelly

last: Keezer

first: Harriet

middle: M

last: Jackson

first: Christoph

last: Preuss

first: Casey

last: Acklin

first: Rita

last: O'Rourke

first: Rebecca

middle: A

last: Buchanan

first: Travis

middle: L

last: Cossette

first: Stacey

last: Sukoff Rizzo

first: Ileana

last: Soto

first: Gregory

middle: W

last: Carter

first: Gareth

last: Howell


title: Genome wide analysis of AR-associated factors and histone modifications in castration-resistant prostate cancer

status: Public on Apr 01 2019

city: Itabashi-ku

first: Ken-ichi

last: Takayama

address: Sakaecho

institute: Tokyo Metropolitan Institute of Gerontology

summary: Prostate cancer is the most common cancer in men and androgen receptor (AR) downstream signalings promote prostate cancer progression. Although androgen deprivation therapy is effective for treating prostate cancer, most of tumors relapsed as castration-resistant prostate cancer (CRPC). We performed ChIP-seq analysis to investigate the role of AR-associated factors and histone modifications using CRPC model cells, 22Rv1.

overall_design: ChIP-sequence analysis of AR-associated factors (FOXA1 and OCT1) and histone modifications in CRPC cells.


title: A Human Liver Cell Atlas reveals Heterogeneity and Epithelial Progenitors

status: Public on Jun 18 2019

city: Freiburg

first: Nadim

last: Aizarani

address: Stübeweg 51

department: Independent group leaders

institute: MPI-IE

summary: We perfomed single-cell RNA-sequnecing of around 10,000 cells from normal human liver tissue to construct a human liver cell atlas. We reveal previously unknown subtypes in different cell type compartments. We also use our normal liver cell atlas to infer perturbed phenoytpes of cells from HCC samples, human cells engrafted into a mouse liver and liver organoids.

overall_design:
Single cells were isolated from human liver resection specimens and then sorted by FACS into 384 well plates in a unbiased way and on the basis of cell surface markers for distinct cell types. ScRNA-seq was done using the mCelSeq2 protocol
cellbarcodes_cellid.csv Supplemetary file contains cellds and one of the 192  unique cellbarcode associated with the cellid.

first: Dominic

last: Grün


title: Expression data from hepatoblastoma tissues

status: Public on May 17 2019

city: Hiroshima

first: Eiso

last: Hiyama

state: Hiroshima

address: 1-2-3, Kasumi, Minami-ku

department: Natural Science Center for Basic Research and Deve

institute: Hiroshima University

summary: We elucidated the genetic profile of HBLs to identify biological markers for diagnosis and to determine the grade of malignancy.

overall_design: 53 hepatoblastoma tissues and 14 noncancerous liver tissue samples were extracted RNA and hybridization on Affymetrix microarrays.

first: Nagisa

last: Morihara

first: Kyoko

last: Ikeda


title: Neocortical projection neurons instruct inhibitory interneuron circuit development in a lineage dependent manner

status: Public on Mar 06 2019

city: Bethesda

first: Chris

last: McBain

state: Maryland

address: 35 Convent Drive

department: National Institute of Child Health and Human Development

institute: National Institutes of Health

summary: Neocortical circuits consist of stereotypical motifs that must self-assemble during development. Recent evidence suggests the subtype identity of both excitatory projection neurons (PNs) and inhibitory interneurons (INs) is important for this process. We knocked out the transcription factor Satb2 in PNs to induce those of the intratelencephalic (IT)-type to adopt a pyramidal tract (PT)-type identity. Loss of IT-type PNs selectively disrupted the lamination and circuit integration of INs derived from the caudal ganglionic eminence (CGE). Strikingly, reprogrammed PNs demonstrated reduced synaptic targeting of CGE-derived INs relative to controls. In control mice, IT-type PNs targeted neighboring CGE INs while PT-type PNs did not in deep layers, confirming this lineage-dependent motif. Finally, single cell RNA-sequencing revealed that major CGE IN subtypes were conserved after loss of IT PNs, but with differential transcription of synaptic proteins and signaling molecules. Thus, IT-type PNs influence CGE-derived INs in a non-cell autonomous manner during cortical development.

overall_design: Single-cell RNA-seq (10X Genomics Chromium) of FAC sorted GFP+ interneurons derived from the caudal ganglionic eminence (5HT3A-GFP mouse line), from primary visual cortex of juvenile (p21) mice

first: Jason

middle: C

last: Wester

first: Vivek

last: Mahadevan

first: Christopher

last: Rhodes


title: A murine systemic bleomycin model of scleroderma

city: Pennington

first: Ron

last: Ammar

state: New Jersey

address: 311 Pennington Rocky Hill Road

institute: Bristol-Myers Squibb

summary: A well-characterized mouse model of SSc involves daily subcutaneous injections of the antitumor antibiotic bleomycin (BLM), which leads to localized dermal fibrosis as well as pulmonary fibrosis. We have termed this the “Systemic Bleomycin Model” to distinguish it from the already-established Intratracheal (IT) model. We utilize this model, which mimics several key features of human SSc, to examine the pathological mechanisms underlying the development and progression of fibrosis in SSc.

overall_design: Female C57BL/6 mice (~12 weeks old) were used for this study. An electric shaver was used to shave the interscapular region on the back of each mouse, and a non-toxic permanent marker was used to draw two small circles on the skin within the shaved area on each mouse. Fibrosis was induced by daily subcutaneous injections of either bleomycin (10mg/kg/day; 100μl per injection site of 1mg/ml solution for these ~20gm mice) or PBS (vehicle control) within the marked interscapular regions. Injections began on Day 0 and were done five times per week for two weeks, using a 27-gauge needle. (Bhattacharyya S. et al., Sci Transl Med 2014 Apr 16;6(232):232ra50; Huang J. et al., Ann Rheum Dis 2015 Apr 9. pii: annrheumdis-2014-207109). Beginning on Day 12, the ALK5 inhibitor SB525334 (30mpk) or vehicle was delivered (PO, BID dosing). Note that Groups 1-2 and Groups 3-4 were sacrificed on Day 7 and Day 14, respectively, and thus did not receive oral dosing. Groups 5-7 were sacrificed on Day 21. The last oral doses were administered on Day 27. Groups 8-10 were sacrificed on Day 28. Groups 11-12 (which specifically serve to assess resolution in this model, and do not examine the effect of Alk5 inhibition) were sacrificed on Day 42.

first: Lauren

last: Reinke-Breen


title: JMJ17, a H3K4 demethylase, regulates chlorophyll biosynthesis during the transition from dark to light in Arabidopsis seedlings

status: Public on Oct 31 2019

city: Taipei

first: Wan-Sheng

last: Lo

state: Taiwan

address: 128 Academia Road, Section 2, Nankang

department: IPMB

institute: Academia Sinica

summary: We have reported that, JMJ17 regulates photosynthesis, tetrapyrrole biosynthesis, light responsive and stress related genes in Arabidopsis. JMJ17 directly associates and modulates H3K4me3 level at chromatin region of PORC, HEMA1, CHLI1, CHLM and LHCA4 genes and repress their expression in the dark.

overall_design: Global gene regulation by JMJ17 were analysed in 7-day old wild type (WT) and jmj17-1 seedling  by deep sequencing, Illumina HiSeq 2500

first: Torikul

last: Islam

first: Long-Chi

last: Wang

first: I-Ju

last: Chen


title: Polarized B -cell functions

city: Brest

first: Sophie

last: Hillion

address: Felix le Dantec

institute: INSERM U1227

summary: In this study, we designed an in vitro approach to help us understand how extracellular components participate in human B cell functional plasticity and how this network might be involved in auto-immune diseases. Two activated T cell subsets were used to expose a common pool of B cells to distinct, controlled microenvironments. We showed that the same B cell population could experience two possible opposite evolutions, to either helper or suppressor functions, in a flexible manner. These cells were thus referred to as effector B cells (Eff B) or suppressor B cells (Supp B). We thus analyzed their different transcriptional programs by RNA sequencing.

overall_design: B cells cultured with memory or naive T cells  were analyzed by RNA sequencing

first: Quentin

last: Simon

first: Alexis

last: Grasseau


title: The induction of core pluripotency master regulators in cancers defines poor clinical outcomes and treatment resistance

status: Public on Feb 25 2019

city: Belfast

first: Rebecca

middle: Elizabeth

last: Steele

address: 97 Lisburn Road

department: CCRCB

institute: Queen's University Belfast

summary: Clinical expression of core pluripotent stem cell master regulators OCT4, SOX2 and NANOG is associated with treatment resistance and lethal cancers. We have described a novel model to induce the expression of these factors in vitro. We term this culture environment ‘Acquired Pluripotent Stem Cell Environment (APSCE)’ and RNA-seq comparisons were made to culture in conventional serum supplemented ‘Full Media’ (FM) in human prostate (LNCaP, CWR22Rv1) and bladder (RT112) cancer cell lines. Depletion of the androgen receptor (AR) with siRNA targeting exon1(siEX1) was additionally performed in the CWR22Rv1 cell line alongside a scrambled control (siCTRL).

overall_design: mRNA profiles of LNCaP, CWR22Rv1 and RT112 cell lines cultured in APSCE and FM were generated in triplicate via RNA-Seq. CWR22Rv1 mRNA profiles of Scrambled and AR Exon1 siRNA knockdown cultured in the APSCE and FM were additionally generated in triplicate.

first: Anastasia

last: Hepburn

middle: E

first: Rajan

last: Veeratterapillay

first: Laura

last: Wilson

first: Amy

last: Barnard

first: Philip

last: Berry

first: James

last: Cassidy

first: Mohammad

last: Moad

first: Amira

last: El-Sherif

first: Luke

last: Gaughan

first: Ian

middle: G

last: Mills

first: Craig

last: Robson

first: Rakesh

last: Heer


title: The analysis of gene expression profiles of splenocytes from wild type and UBL4A/GdX-/Y mice upon LPS stimulation

status: Public on Mar 20 2019

city: Beijing

first: Yifan

last: Zhou

address: No. 30 Shuangqing Road

department: School of Medicine

institute: Tsinghua University

summary:
Purpose: To compared the gene expression profiles of splenocytes from wild type and UBLA4/GdX (Ubiquitin-like protein 4A, also named GdX) knockout mice upon LPS stimulation.
Methods: GdX+/Y and GdX-/Y mice were injected with LPS. Their splenocytes were collected at different time (90min or 6 hrs), and then performed RNA-sequencing analysis. We sequence the samples used BGISEQ-500 platform.
Results: The average mapping ratio with reference genome is 93.42%, the average mapping ratio with gene is 83.40%; A total of 17,920 genes were detected.A number of NF-κB targeting genes, such as IL-6, IL-1a and IL-12, have dramatic higher expressions in the splenocytes of GdX+/Y mice than that of GdX-/Y mice. Gene ontology (GO) analysis of GdX function in LPS-treated mice showed one of the most significantly enriched biological processes is related to inflammatory response.
Conclusions: Our study revealed the gene expression profiles of the splenocytes from LPS-treated wild type and GdX-/Y mice.

overall_design: mRNA profiles of splenocytes from four wild type and three GdX-/- mice were generated by RNA-sequencing analysis

first: Chunxiao

last: Liu

first: Liu

last: Yang


title: Genome-scale screens identify JNK/JUN signaling as a barrier for pluripotency exit and endoderm differentiation

status: Public on Mar 18 2019

city: NEW YORK

first: QINGL

last: LI

address: 1275 YORK AVE

institute: MEMORIAL SLOAN KETTERING CANCER CENTER

summary: Human embryonic and induced pluripotent stem cells (hESCs/hiPSCs) hold great promise for cell-based therapies and drug discovery. However, homogeneous differentiation remains a major challenge, highlighting the need for understanding developmental mechanisms. We performed genome-scale CRISPR screens to uncover regulators of definitive endoderm (DE) differentiation, which unexpectedly uncovered five JNK/JUN family genes as key barriers of DE differentiation. The JNK/JUN pathway does not act through directly inhibiting the DE enhancers. Instead JUN co-occupies ESC enhancers with OCT4, NANOG and SMAD2/3, and specifically inhibits the exit from the pluripotent state by impeding the decommissioning of ESC enhancers and inhibiting the reconfiguration of SMAD2/3 chromatin binding from ESC to DE enhancers. Therefore, the JNK/JUN pathway safeguards pluripotency from precocious DE differentiation. Direct pharmacological inhibition of JNK significantly improves the efficiencies of generating DE and DE-derived pancreatic and lung progenitor cells, highlighting the potential of harnessing the knowledge from developmental studies for regenerative medicine.

overall_design: We performed genome-wide CRISPR screen using GeCKO and Brunello libraries in hESC to identify regulators of definitive endoderm differentiation. We identified JNK signaling as an inhibitory pathway for definitive endoderm differentiation. We performed RNA-seq, scRNA-seq, ATAC-seq and ChIP-seq to study the role of JNK pathway in DE differentiation.

first: Qing

last: Li


title: DNA methylation data comparing Wilms tumor primary samples to patient-derived xenografts

status: Public on Feb 14 2019

city: Memphis

first: Tong

last: Lin

state: TN

address: 262 Danny Thomas Place

department: Biostatistics

institute: St. Jude Children's Research Hospital

summary: The lack of model systems limits the preclinical testing of novel therapies to address Wilms tumor patient groups with poor outcomes. Therefore, we established 45 heterotopic Wilms tumor patient-derived xenografts (WTPDX) in CB17 scid-/- mice that capture the biological heterogeneity of Wilms tumor (WT). These WTPDX include six showing diffuse anaplasia, nine from patients who went on to experience disease relapse, and thirteen from patients with bilateral disease. WTPDX retained the genetic alterations and the global transcriptomic and methylation profile of corresponding primary WT. In addition, favorable histology WTPDX were chemosensitive, while unfavorable histology WTPDX were resistant to conventional chemotherapy with vincristine, actinomycin-D, and doxorubicin. This WTPDX library is a unique scientific resource that retains the spectrum of biological heterogeneity present in WT and provides an essential tool for the testing of novel targeted therapies in the era of precision medicine.

overall_design: Genomic DNA (1 µg) from 39 Wilms tumor patient derived xenografts and corresponding primary tumors was bisulfite converted using the EZ DNA Methylation kit (Zymo Research Corp, Irvine, CA) according to the manufacturer’s instructions. Converted samples were processed and hybridized to the Infinium MethylationEPIC BeadChip (850K) system (Illumina, San Diego, CA).

first: Andrew

last: Jackson Murphy