title: The loss of heterochromatin is associated with multiscale three-dimensional genome reorganization and aberrant transcription during cellular senescence

status: Public on Dec 31 2019

city: Jinan

first: Xianglin

state: Shandong

address: 247 Beiyuan Street

department: The Second Hospital of Shandong University

institute: Shandong University

summary: Heterochromatin remodeling is critical for various cell processes. In particular, the “loss of heterochromatin” phenotype in cellular senescence engages with the progress of aging and age-related disorders. Although biological processes of senescent cells including senescence-associated heterochromatin foci (SAHF) formation, chromosome compaction and entry into senescence have been closely associated with high-order chromatin structure. the relationship between the high-order chromatin organization and the loss of heterochromatin phenotype during senescence has not been fully understood. By using senescent and late senescent fibroblasts induced by DNA damage harboring the “loss of heterochromatin” phenotype, we observed progressive 3D reorganization of heterochromatin during senescence. Facultative and constitutive heterochromatin marked by H3K27me3 and H3K9me3, respectively, showed different alterations. Facultative heterochromatin tends to switch from the repressive B-compartment to the active A-compartment, whereas constitutive heterochromatin shows no significant changes at the compartment level but enhanced interactions between themselves. Interestingly, both types show increased chromatin accessibility and gene expression leakage during senescence. Furthermore, increased chromatin accessibility in potential CTCF binding sites accompanies by the establishment of novel loops in constitutive heterochromatin. Finally, we also observed aberrant expression of repetitive elements, including LTR (long terminal repeat) and satellite classes. Overall, facultative and constitutive heterochromatin show multiscale but distinct alterations in the 3D map, meanwhile they also share the same features of increased chromatin accessibility and gene expression leakage. This study provides an epigenomic map of heterochromatin reorganization during senescence.

overall_design: We build five cell states including growing, quiescence, senescence, deep senescence with human diploid BJ fibroblasts and carried out Hi-C, ATAC-seq,RNA-seq and ChIP-seq.

first: Xiaowo

last: Wang

first: Wei

last: Xie


title: The prandial status modifies the associations of BMI and fatty acids with DNA methylation in men

status: Public on Dec 02 2019

city: Irapuato

first: Gertrud

last: Lund

state: Guanajuato

address: Km 9.6 del Libramiento Norte Carretera Irapuato-León SN

department: Genetic Engineering

country: Mexico

institute: CINVESTAV Irapuato

type: Methylation profiling by genome tiling array

summary: High-density array-based DNA methylation profiling of human pheriferical blood from subjects with different BMI on a fasting day and after hypercaloric meal

overall_design: Bisulphite converted DNA was hybridised to the Infinium MethylationEPIC Beadchip

first: Silvio

last: Zaina

first: Guillermo

middle: A

last: Silva-Martinez


title: Characterization of the transcriptional response to DNA in STING KO cells

status: Public on Dec 11 2019

city: Minneapolis

first: Michael

last: Gale

state: Minnesota

address: 689 23rd Ave SE

department: Microbiology and Immunology

country: USA

institute: University of Minnesota

type: Expression profiling by high throughput sequencing

summary: Here we demonstrate that the SIDSP induces a broad and potent antiviral response that is abrogated by treatment with the DNA-PK inhibitor, Nu7441.

overall_design: We compared in triplicate the WT and STING KO response to transfected DNA relative to lipofectamine alone at 8 and 16 hours post transfection, with and without 2 uM Nu7441.

first: K

last: Burleigh

first: D

middle: B

last: Stetson


title: A comprehensive mutational scan of the TAPBPR scoop loop defines a region of the sequence-activity landscape for class I MHC interactions

status: Public on Oct 31 2019

city: Urbana

first: Erik

last: Procko

state: IL

address: 601 S Goodwin Ave

department: Biochemistry

institute: University of Illinois

summary: The loading of high affinity peptides onto nascent class I MHC (MHC-I) molecules is facilitated by chaperones, including the class I-specific chaperone TAP-binding protein-related (TAPBPR).  TAPBPR features a ‘scoop’ loop that projects towards the empty MHC-I peptide binding groove and rests above the F pocket.  The scoop loop is not found in the closely related homologue tapasin, and therefore may be partly responsible for the unique antigen editing properties of TAPBPR.  A deep mutational scan of the TAPBPR scoop loop defines the relative effects of all single amino acid mutations on binding and peptide-mediated release of the murine H2-Dd MHC-I allomorph.  Increased hydrophobic packing between the scoop loop and rim of the peptide binding groove tightens the TAPBPR-MHC-I interaction.

overall_design: The extracellular domains of human TAPBPR were fused to Aga2p for yeast surface display at the N-terminus, and a c-myc tag for expression detection at the C-terminus.  The TAPBPR scoop loop (a.a. G27-D38) was diversified by single-site saturation mutagenesis to encode all possible 240 amino acid substitutions.  The library was expressed on the yeast cell surface and sorted by fluorescence-activated cell sorting (FACS).  In a first round of selection, yeast were collected that expressed TAPBPR variants that formed tight interactions to fluorescent murine H2-Dd tetramers, either in the presence or absence of two different peptides (motif and P18) that compete for MHC-I interactions and displace TAPBPR.  In a second round of selection, the TAPBPR-expressing yeast that were first sorted for binding tightly to H2-Dd were now resorted for having weak interactions when competing peptides are present.  The choice of two rounds of selection, the first positive and the second negative, was to mimic the biological activity of TAPBPR, which must bind empty MHC-I tightly for intracellular retention, but release the MHC-I when a high affinity peptide binds.

first: Nikolaos

middle: G

last: Sgourakis


title: Transient genome-wide adaptations of nascent RNAPII transcription triggered by low temperature

city: Frederiksberg C

first: Maxim

last: Ivanov

address: Thorvaldsensvej 40

department: Dept. of Plant and Environmental Sciences

country: Denmark

institute: University of Copenhagen

summary: We determined RNA polymerase (RNAPII) transcription at single-nucleotide resolution in Arabidopsis during early stages of exposure to low temperature. Our data inform on the dynamics of RNAPII transcription and detect thousands of often short-lived uncharacterized transcripts. We demonstrate that low temperature triggers transient genome-wide effects on RNAPII activity, in particular the stalling of RNAPII at both gene ends and the distance of read-through transcription.

overall_design: Plant native elongating transcripts sequencing (plaNET-Seq) was used to determine the genomic positions of transcriptionally engaged RNAPII in Col-0 seedlings which were exposed to cold (4⁰C) for 0h, 3h or 12h.

first: Peter

last: Kindgren

first: Sebastian

last: Marquardt


title: RNA-seq time course on human CD4 memory T cells stimulated with anti-CD3/CD28 beads

status: Public on Nov 13 2019

city: Boston

first: Maria

last: Gutierrez-Arcelus

state: MA

address: 77 Avenue Louis Pasteur

department: Medicine

institute: Brigham and Women's Hospital, Harvard Medical School

summary: In this study we sought to analyze the effects of genetic variants on gene regulation in a cell-state dependent manner during CD4 memory T cell activation. To do this, we performed an RNA-seq time series experiment on CD4 memory T cells activated with anti-CD3/CD28 beads in individuals with no autoimmune disease. We measured gene expression levels, and allele-specific expression at heterozygous sites over time. We found widespread dynamic genetic regulatory effects across the genome, with an enrichment for genes found in autoimmune disease risk loci.

overall_design:
We isolated CD4 memory T cells from PBMC samples of 24 genotyped individuals of European ancestry with no autoimmune disease. We stimulated cells with anti-CD3/CD28 beads and collected cells at 0, 2, 4, 8, 12, 24, 48 and 72 hours. We performed mRNA-seq (TruSeq) for each sample. Samples from 2-4 donors were processed per week. Cells from each donor were plated typically into 8 different wells (with some exceptions), one for each time point, with 1M cells per well to ensure high library complexity. mRNA-seq library preparations happened in 3 plates, donors were randomized over the 3 plates, and samples from the same donor were kept in same plate. For two individuals we performed full time course replicates (from the sample blood draw, CD4 memory T cells were isolated and then separated into 2 independent time course experiments, so in total 16 samples).

The sequencing was carried out either with HiSeq 2000 or 2500. However, the submitter does not have the information of which specific Hiseq model each sample was sequenced in. The GEO records have been created with HiSeq 2000 as instrument model for all samples.

***RNA-Seq raw data available through dbGaP (controlled access) due to patient privacy concerns:
https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs002259.v1.p1

first: Soumya

last: Raychaudhuri


title: The SAGA complex regulates early steps in transcription via its deubiquitylase module subunit USP22

status: Public on Oct 24 2019

city: Philadelphia

first: Priyankara

middle: J

last: Wickramasinghe

state: PA

address: 3601 Spruce Street

department: Bioinformatics

institute: The Wistar Institute

type: Genome binding/occupancy profiling by high throughput sequencing

summary: SAGA is a modular cofactor complex that is essential for eukaryotic transcription. SAGA’s complement of ~20 proteins exist within four structurally and functionally distinct modules, two of which are catalytic. Within the KAT module, GCN5 acetylates histone tails, leading to increased chromatin accessibility and bromodomain protein recruitment. The DUB module contains the ubiquitin hydrolase USP22. In yeast, the USP22 ortholog deubiquitylates H2B, resulting in Pol II S2 phosphorylation and subsequent transcriptional elongation. We report here that metazoan SAGA, and USP22 specifically, are required at a more proximal stage in activator-driven transcription, i.e. pre-initiation complex (PIC) assembly. A combination of genome-wide and proteomic analyses revealed that H2B deubiquitylation is not linked to USP22-dependent transcription. Instead, USP22 controls Mediator tail subunit ubiquitylation. Mechanistically, USP22 controls loading of Mediator tail and GTFs onto promoters, with Mediator core recruitment being USP22-independent. These findings place human SAGA function at the earliest steps in activator-driven transcription.

overall_design: CHIP-seq for various factors in USP22 wild type and knockdown conditions before and after ER stress response

first: Steven

last: McMahon

first: Timothy

last: Stanek


title: Differential expression analysis of primary AML cells treated with AC220 vs DMSO in endothelial cell co-culture.

status: Public on Oct 03 2019

city: Seattle

first: Quy

middle: Ha

last: Le

state: WA

address: 1100 Fairview Ave. N., D2-367

department: Clinical Research Division

institute: Fred Hutchinson Cancer Research Center

summary: Although chemotherapy can successfully induce remission in FLT3/ITD positive acute myeloid leukemia (AML) patients, many, especially those with a high ratio of the FLT3/ITD versus wild type allele (FLT3-AR), exhibit a high relapse rate, requiring hematopoietic stem cell (HSC) transplantation to increase the chance of long-term remission. As the bone marrow tumor microenvironment (TME) has been implicated in drug resistance, we reasoned that AML-TME interactions might be critical for leukemic precursor survival and drug resistance, and that targeting AML-TME interactions might be crucial to improving survival in FLT3/ITD AML patients. In this study, we demonstrate that endothelial cells (ECs), a component of the TME, and the Notch pathway plays a critical role in the protection of FLT3/ITD positive progenitors against AC220 in AML patient samples with high FLT3-AR.  We have previously shown that high FLT3-AR disease is distinguished by the presence of the mutation in the least mature CD34+CD33- precursors, where leukemic stem cells (LSCs) reside. Here, we demonstrate that inhibiting Notch signaling overcomes the TME-mediated drug resistance of the LSC-enriched CD34+CD33- precursors, raising the possibility that Notch may serve as a therapeutic target for eradicating LSCs that are thought to be responsible for relapse in this high-risk AML subset.

overall_design: A total of 3 primary AML samples were analyzed. Each sample was treated with either AC220 or DMSO control in endothelial cell co-culture in duplicate prior to RNA-seq analysis. Reads from technical duplicates were pooled before edgeR analysis consisting of 3 AML samples as biological replicates per treatment group.

first: Brandon

middle: K

last: Hadland

first: Soheil

last: Meshenchi

first: Irwin

middle: D

last: Bernstein


title: Vaccine-induced ICOS+CD38+ cTfh are sensitive biosensors of age-related changes in inflammatory pathways

status: Public on Oct 01 2019

city: New York City

first: Ramin

last: Herati

state: NY

address: 429 E. 29th Street, room 308

institute: NYU School of Medicine

summary: Transcriptional pathways associated with aging were studied in circulating T follicular helper CD4 cells before and 7 days after influenza vaccination

overall_design: Transcriptional signatures of aging in CD4 subsets after influenza vaccination

middle: S

first: E

last: Wherry


title: A novel target of EZH1/2 for treatment of mantle cell lymphoma

status: Public on Sep 30 2019

city: Hachioji

first: Yuki

last: Kagiyama

address: Horinouchi 1432-1

country: Japan

institute: Tokyo University of Pharmacy and Life Sciences

summary: Mantle cell lymphoma (MCL) is a rare subtype of non-Hodgkin’s lymphoma, which is characterized by the translocation of t(11:14)(q13;q32) resulting in overexpression of cyclin D1. Patients with MCL often acquire resistance to conventional chemotherapy such as R-CHOP, BR, and ibrutinib. Therefore, novel therapeutic targets for relapsed MCL are needed. EZH1/2 are catalytic components of PRC2, which trimethylates H3K27 to repress transcription of target genes and play critical roles in B-cell development. Mutation and overexpression of EZH1/2 are associated with hematopoietic malignancies. Here, we examined whether inhibition of EZH1/2 had an antitumor effect on aggressive MCL cells. In a patient-derived xenograft model of MCL, EZH1/2 dual inhibitor OR-S1 treatment by oral administration significantly inhibited MCL tumor growth. Comprehensive gene expression analysis also indicated that the expression of genes related to cell cycle and cell differentiation was changed in OR-S1-sensitive cell lines. Interestingly, CDKN1C, which contributes to cell cycle arrest, was up-regulated with decreased H3K27 trimethylation by OR-S1 treatment. Furthermore, knockout of CDKN1C by CRISPR-Cas9 decreased the sensitivity to OR-S1. These results suggest that EZH1/2 may control MCL tumor growth and be a potential target for the treatment of aggressive MCL.

overall_design: mRNA samples were isolated from the three MCL cell lines (Mino, JeKo-1 and REC-1) treated with vehicle control, 300 nM, or 1000 nM OR-S1 for 5 days and 7 days, and performed RNA-seq.

first: Issay

last: Kitabayashi


title: Critical residues within the TAPBPR scoop loop for HLA-A2 binding and peptide loading are determined by deep mutational scanning

status: Public on Sep 01 2019

first: Erik

last: Procko

summary: The loading of high affinity peptides onto nascent class I MHC (MHC-I) molecules is facilitated by chaperones, including the class I-specific chaperone TAP-binding protein-related (TAPBPR). TAPBPR features a loop (amino acids 24-35) that projects towards the empty MHC-I peptide binding groove and rests above the F pocket. The 24-35 loop is much shorter in the closely related homologue tapasin, and therefore may be partly responsible for the unique antigen editing properties of TAPBPR. Previously we reported a deep mutational scan of human TAPBPR focused on the 24-35 loop, and determined the relative effects of single amino acid mutations on binding and peptide-mediated release of the murine H2-Dd MHC-I allomorph. Here, we extend our studies to determine the mutational landscape of the 24-35 loop when TAPBPR binds a human MHC-I allomorph, HLA-A*02:01.  The data highlights how TAPBPR affinity can be increased or decreased for different MHC-I allomorphs by tuning the electrostatic complementarity of the 24-35 loop for surfaces on the rim of the peptide-binding groove.  By changing the selection pressure from HLA-A2 binding to HLA-A2 loading and processing, we find that TAPBPR is reasonably tolerant of mutations in the 24-35 loop for efficient peptide-MHC-I processing and surface trafficking.

overall_design: For investigating binding interactions, the extracellular domains of human TAPBPR were fused to Aga2p at the N-terminus for yeast surface display, and fused to a c-myc tag at the C-terminus for measuring expression. The TAPBPR 24-35 loop (a.a. G27-D38 in the deposited files based on an earlier numbering scheme) was diversified by single-site saturation mutagenesis to encode all possible 240 amino acid substitutions. The library was expressed on the yeast cell surface and sorted by fluorescence-activated cell sorting (FACS) for high binding signal to fluorescent HLA-A*02:01 tetramers, in the absence or presence of competing TAX peptide.  For investigating HLA-A2 loading and processing in human cells, TAPBPR was modified with an N-terminal FLAG tag to detect expression, and the transmembrane and cytosolic regions were replaced with the equivalent residues of tapasin.  We hypothesize that the chimeric construct may bring TAPBPR into the the peptide-loading complex for enhanced activity.  Again, a single-site saturation mutagenesis library focused on the 24-35 loop was constructed, and expressed in Expi293F cells in which the endogenous tapasin gene was knocked out using CRISPR-based genome editing.  These cells express little surface HLA-A2, yet MHC-I processing and surface trafficking can be partially rescued by transfecting in MHC-I-specific chaperones tapasin or TAPBPR.  Cells transfected with the TAPBPR library and displaying increased surface HLA-A2 were collected by FACS.  The enrichment or depletion of every TAPBPR mutation was calculated by comparing frequencies in the naive libraries with the sorted populations.

first: Christine

last: Devlin


title: Proteomic analysis of CSF from patients with leptomeningeal melanoma metastases identifies signatures associated with disease progression and therapeutic resistance

status: Public on Nov 27 2019

city: TAmpa

first: Yonghong

last: Zhang

state: FL

address: 12902 USF Magnolia Drive

department: Biomedical Informatics

institute: Moffitt Cancer Center

summary: The development of leptomeningeal melanoma metastases (LMM) is a rare and devastating complication of the late-stage disease, for which no effective treatments exist. Here, we performed a multi-omics analysis of the CSF from LMM patients to determine how the leptomeningeal microenvironment shapes the biology and therapeutic responses of melanoma cells. A total of 45 serial CSF samples were collected from 16 patients, 8 of these with confirmed LMM. Of those with LMM, 7 had poor survival (<4 months) and one was an extraordinary responder (still alive with survival >35 months). CSF samples were analyzed by mass spectrometry and incubated with melanoma cells, that were subjected to RNA-Seq analysis. Functional assays were performed to validate the pathways identified.Mass spectrometry analyses showed the CSF of most LMM patients to be enriched for pathways involved in innate immunity, protease-mediated damage, and IGF-related signaling. All of these were anti-correlated in the extraordinary responder. RNA-Seq analysis showed CSF to induce PI3K/AKT, integrin, B-cell activation, S-phase entry, TNFR2, TGF-β and oxidative stress responses in the melanoma cells. ELISA assays confirmed that TGF-β expression increased in the CSF of patients progressing with LMM. CSF from poorly responding patients conferred tolerance to BRAF inhibitor therapy in apoptosis assays. These analyses identified proteomic/transcriptional signatures in the CSF of patients who succumbed to LMM. We further showed that the CSF from LMM patients has the potential to modulate BRAF inhibitor responses and may contribute to drug resistance.

overall_design: WM164 cells were plated in a 6-well plate at 200,000 cells/well and allowed to attach overnight in normal culture media. Next day, the media was replaced to serum-free RPMI and cells were incubated overnight. Cells were treated with 3μM vemurafenib or vehicle control in 5% FBS/RPMI, or a 1:1 mixture of serum-free media:CSF from patient 1, patient 2 or patient 3 for 8 hours. RNA was extracted using Qiagen’s RNeasy Kit, with on-column DNase digestion (Hilden, Germany). RNA samples were reviewed for quality on the Agilent TapeStation followed by quantitation using the Qubit fluorometric assay.  RNAseq libraries were processed using the Ovation Human FFPE RNA-Seq Multiplex System (NuGEN Technologies, San Carlos, CA). Briefly, 100 ng of RNA was used to generate cDNA and a strand-specific library following the manufacturer’s protocol.  BioAnalyzer library size assessment and the Kapa Library Quantification Kit were used for library quantification.  The libraries were sequenced on the Illumina NextSeq 500 v2 sequencer with two 75-base paired-end runs in order to generate 25-35 million read pairs per sample. Sequencing reads were subjected to a variety of pre- and post-alignment QC measures before mapped against the hg19 reference genome using TopHat 2.0.13. Gene-level quantification was determined using HTSeq 0.6.1 by summation of raw counts of reads aligned to the region associated with each gene. Normalization and differential expression analysis was performed using R/Bioconductor package DESeq2_1.6.3. Benjamini-Hochberg correction was used to adjust p-values to account for multiple comparisons.


title: Autophagy driving ETV6-RUNX1 positive leukaemia

status: Public on Sep 16 2019

city: Utrecht

first: Judith

middle: M.

last: Boer

address: Heidelberglaan 25

country: Netherlands

institute: Prinses Maxima Centrum

summary: This file contains the gene expression data for 654 pediatric acute lymphoblastic leukemia samples

overall_design:
A population-based cohort of 654 pediatric acute lymphoblastic leukemia samples was profiled, 574 BCP-ALL and 80 T-ALL. The cohort itself was described in Van der Veer et al. Blood 2013, PMID: 23974192.
ETV6-RUNX1 positive BCP-ALL cases were compared with ETV6-RUNX1 negative BCP-ALL cases (Polak et al. 2019 PMID: 30381299), and PDGFRA high expression cases were identified and further characterized (Jerchel et al. 2018 PMID: 29170250).

first: Monique

middle: L

last: den Boer

middle: M


title: circRNA-sequencing of blood plasma exosomes from cutaneous squamous cell carcinoma patients

status: Public on Aug 22 2019

city: Shenyang‘

first: Zheng

address: 155N Nanjing Road, Heping district

department: Dermatology

country: China

institute: No.1 Hospital of China Medical University

type: Non-coding RNA profiling by high throughput sequencing

summary: circRNA sequencing for 6 samples

overall_design: Examing 2 conditions, each with 3 replicates


title: Transcriptional profiling to compare gene expression in supraorbital mesenchyme (SOM) and early migration mesenchyme (EMM) of wild type mouse embryos

status: Public on Aug 03 2019

city: New York

first: Juhee

last: Jeong

state: New York

address: 345 E 24th St

department: Basic sciences and Craniofacial development

institute: New York University College of Dentistry

summary: During embryonic development, the mesenchyme surrounding the brain (cranial mesenchyme) gives rise to several structures such as the meninges, calvaria, and the dermis of the scalp. It has been known that the two regions within the cranial mesenchyme, namely, SOM on the basolateral side and EMM on the apical side of the head, have different developmental fates. However, the molecular genetic basis underlying this difference had been unclear. To address this question, we sought to identify genes differentially expressed between EMM and SOM. Through RNAseq, we identified 1095 genes with higher expression in EMM than in SOM, and 398 genes with higher expression in SOM than in EMM (fold change>2, p<0.001, base mean count>50).

overall_design: EMM and SOM were dissected from E12.5 wild type C57BL/6 embryos. 4 EMM samples and 4 SOM samples were used for RNAseq, where each sample was a pool of tissue from 4 to 5 embryos.


title: Diet-induced changes in tuft cell dynamics couple with type 2 immune response modulation and energy metabolism

status: Public on Nov 26 2019

city: Lyngby

first: Pankaj

last: Arora

email: sbrix@dtu.dk, sbp@bio.dtu.dk, panar@dtu.dk, panar.arora@sund.ku.dk

address: Søltofts Plads - blg. 224 room 218, DK-2800 Kgs. Lyngby

department: Department of Biotechnology and Biomedicine

institute: Technical University of Denmark

summary:
Purpose: To examine the temporal changes in intestinal tuft cell number and activity in response to intake of a high fat diet and investigate the relation to whole-body energy metabolism and the immune phenotype of the small intestine and epididymal white adipose tissue (eWAT).
Methods: C57BL/6J mice were fed either a low fat reference diet (RFD, 10 % kcal fat) or a high fat diet (HFD, 60% kcal fat) for 9 or 22 weeks, followed by characterization of whole-body metabolic parameters, transcription profiles of sorted intestinal tuft cells, and immune phenotypes of tissues.
Results: HFD feeding was associated with reductions in the overall number of small intestinal epithelial cells and tuft cells and reduced expression of the intestinal type 2 tuft cell markers Il25 and Tslp. Amongst >1,700 diet-regulated genes in tuft cells identified by RNA-seq, we observed an early association between body mass expansion and increased expression of Serpini1, which encodes the serine protease inhibitor neuroserpin. By contrast, tuft cell expression of genes encoding the GABA-receptors linked to reduced body mass gain. Although we observed a HFD-induced change in the eWAT inflammatory profile, the small intestinal lamina propria displayed a consistent non-inflammatory phenotype, and small intestinal tuft cell-derived transcripts were found to correlate with whole body metabolic features independently of intestinal immune cell involvement.
Conclusion: Our These findings point to a role for small intestinal tuft cells in systems-wide metabolic regulation.

overall_design: We here aimed to characterize the functional aspects of small intestinal tuft cells in response to HFD feeding with a focus on their role in relaying immune-metabolic signals. Additionally, we explored how HFD-associated effects on small intestinal tuft cells coupled with small intestinal and eWAT immune profiles as well as whole-body metabolic parameters

first: Daniel

last: Andersen

first: Janne

last: Moll

first: Niels

last: Danneskiold-Samsøe

first: Liqin

last: Xu

first: Biaofeng

last: Zhou

first: Georgios

last: Kladis

first: Philipp

last: Rausch

first: Christopher

middle: T

last: Workman

first: Karsten

last: Kristiansen

first: Susanne

last: Brix


title: RNA Sequencing of Wild Type and CCR2-/- mouse esophageal tumor transcriptomes

status: Public on Sep 10 2019

city: Beijing

first: Hui

last: Yang

address: 7 Panjiayuan Nanli, Room314

department: Department of Toxicology

institute: China National Center for Food Safety Risk Assessment (CFSA)

summary: Wild type and CCR2-/- C57 mice were gavaged with carboxyl methyl cellulose (1%) or N-nitrosomethylbenzylamine(NMBA) 0.25 mg/kg body weight (BW) twice per week for 5 weeks. At the end of Week 25, the forestomach were harvested to carry out RNA resequencing. We found that CCR2 mediated monocyte infiltration promoted tumor evasion through activating PD-1 signaling pahtway.

overall_design: Mouse forestomach mRNA profiles of esophageal cancer mouse models were generated by sequencing, using Illumina Hiseq.

first: Yongning

last: Li


title: Transcript isoform sequencing reveals widespread promoter-proximal transcriptional termination in Arabidopsis

status: Public on Oct 29 2019

first: Quentin

middle: Angelo Pierre

last: Thomas

summary: RNA polymerase II (RNAPII) transcription converts the DNA sequence of a single gene into multiple transcript isoforms that may carry alternative functions. Gene isoforms result from variable transcription start sites (TSSs) at the beginning and polyadenylation sites (PASs) at the end of transcripts. How alternative TSSs relate to variable PASs is poorly understood. Here, we identify both ends of RNA molecules in Arabidopsis thaliana by transcription isoform sequencing (TIF-seq) and report four transcript isoforms per expressed gene. While intragenic initiation represents a large source of regulated isoform diversity, we observe that ~14% of expressed genes generate relatively unstable short promoter-proximal RNAs (sppRNAs) from nascent transcript cleavage and polyadenylation shortly after initiation. The location of sppRNAs correlates with the position of promoter-proximal RNAPII stalling, indicating that large pools of promoter-stalled RNAPII may engage in transcriptional termination. We propose that promoter-proximal RNAPII stalling-linked to premature transcriptional termination may represent a checkpoint that governs plant gene expression.

overall_design: TIF-Seq was used to simultaneously map the transcription initiation sites and termination sites on A.thaliana seedlings (Col-0,Col-0 cold treated, HEN2-deficient genotype, HEN2-deficient cold treated and FACT-deficient genotypes). We also used TSS-Seq in these genotypes to validate the TIF-Seq analaysis and quantify initiation of transcription

first: Ryan

last: Ard

first: Jinghan

last: Liu

first: Bingnan

first: Jingwen

last: Wang

first: Vicent

last: Pelechano

first: Sebastian

last: Marquardt


title: ACAA2 and OGDH bind to H2A.Z-occupied transcription start sites

city: Newark

first: Maha

last: Abdellatif

state: NJ

address: 185 S. Orange Ave.

department: Cell Biology and Molecular Medicine

institute: Rutgers-University

summary: anti-ACAA2 and anti-OGDH ChIP-high throughput sequencing (Seq) was performed on, normal and 7 day post-transverse aortic constriction, mouse heart tissue (a pool of 3 hearts for each condition)

overall_design: Methods: Hearts were extracted from from mice subjecetd to Transaortic coarctation or sham operations (n=3, pooled, each). The hearts were sent to Active Motif for ACAA2 and OGDH-ChIP-Seq.


title: Development of gene expression signatures of B7-H3 CAR-T cells for treatment of SAHA

status: Public on Aug 06 2019

first: Xinyuan

last: Lei

address: E5310 Melville library

department: Molecular and Cellular Biology

institute: Stony Brook University

summary: We have employed mRNA microarray expression profiling as a discovery platform to identify genes with the potential to explain how small dose SAHA promoted the cell toxicity of B7-H3 CAR-T cells. B7-H3 CAR-T cells were treated by 0.5μM SAHA for 5 days, and with control samples.

overall_design: Three samples for SAHA treated group and three samples for mock group.

first: Fan

last: Song


title: Gene expression profiling of the retinal microvessels and the brain microvessels

status: Public on Oct 16 2019

city: Groningen

first: Youhai

state: Groningen

address: Hanzeplein 1

department: Dept. Pathology and Medical Biology

institute: University Medical Center Groningen (UMCG)

summary:
Rat retinal microvessels (RMVs) and brain microvessels (BMVs) were mechanically isolated under ice-cold condition. Retinal and brain tissues (RT, BT) from the same animals were collected for comparisons. Total RNA were individually extracted, amplified and processed on Affymetrix rat 2.0 microarray Chips. We sought to obtain the whole gene expression profile of RMVs, RT, BMVs and BT. Differently expressed genes (DEGs) between RMVs and RT, and between RMVs and BMVs, between RT and BT were analyses.
Using these DEGs, we comprehensively analyzed gene expression of the microvessels and highlighted their involvement in critical functional structures in RMVs and BMVs, such as junctional complex, transporters and signaling pathways.

overall_design: Totally, we analyzed four groups: brain microvessels, brain tissue, retinal microvessels and retinal tissue. Each group contains 6 biological replicates. The tissues simples were used as controls.

first: Alen

last: Faiz

first: Han

last: Moshage

first: Rudolf

last: Schubert

first: Lothar

last: Schilling

first: J

last: Kamps


title: Expression data from PDGF-B and EGFRvIII induced murine gliomas

status: Public on Jun 25 2019

city: Genoa

first: Paolo

last: Malatesta

address: Largo Rosanna Benzi 10

country: Italy

institute: IRCCS Ospedale Policlinico San Martino

summary: The trascription profiles of PDGF-B and EGFRvIII induced glioma models were compared. We show that both models converge towards a phenotype that resembles proneural glioblastoma subset.

overall_design: Cells from PDGF-B or EGFRvIII induced glioma were explanted, dissociated and sorted by FACS, basing on the expression of the DsRed reporter expressed togheter with PDGF-B or EGFRvIII as a bicistronic transcript. RNA extraction, sample labeling, array hybridization and scanning were carried out by AROS - (Denmark)

first: Irene

last: Appolloni


title: Determination of 5-methyluridine in messenger RNA of mammals

status: Public on Jul 30 2019

city: Wuhan

first: cheng

last: qingyun

address: Bayi Street

department: Chemistry

institute: Wuhan Universiy

summary: The discovery of dynamic and reversible modifications in messenger RNA (mRNA) is opening new directions in RNA modification-mediated regulation of biological processes. Methylation is the most prevalent modification occurring in mRNA and the methylation group is mainly decorated in the adenine, cytosine, and guanine base, or in the 2’-hydroxyl group of ribose. However, methylation of the uracil base (5-methyluridine, m5U) hasn’t been discovered in mRNA of eukaryotes. In the current study, we established a method by N-cyclohexyl-N’-β-(4-methylmorpholinium) ethylcarbodiimide p-toluenesulfonate (CMCT) labelling coupled with liquid chromatography-electrospray ionization-mass spectrometry analysis (LC-ESI-MS/MS) for the sensitive determination of uridine modifications in RNA. Our results demonstrated that the detection sensitivities of uridine modifications in RNA increased up to 1543 folds upon CMCT labelling. Using the developed method, we identified the distinct existence of m5U in mRNA of various mammalian cells and tissues. In addition, the stable isotope tracing monitored by mass spectrometry revealed that the methylation group of m5U originated from S-Adenosyl-L-methionine (SAM). Our study expanded the list of modifications occurring in mRNA of mammals. Future work on transcriptome-wide mapping of m5U will further uncover the functional roles of m5U in mRNA of mammals.

overall_design: The isolated mRNA was processed using KAPA Stranded RNA-Seq Library Prep Kit (Illumina) for sequencing library construction following the manufacturer’s protocol. RNA-seq was carried out on Illumina HiSeq 4000 (Illumina) platform.

first: Qing-Yun

last: Cheng

first: Bi-Feng

last: Yuan


title: RNA sequencing of isogenic Phf6 wild type and  Phf6 knockout mouse T-ALL cells

status: Public on Jul 31 2019

first: Stuart

middle: Aidan

last: Quinn

address: 1130 St Nicholas Ave

department: Institute for Cancer Genetics

institute: Columbia University

summary: Loss-of-function mutations Phf6 occur frequently in both adult and pediatric T-cell Acute Lymphoblastic Leukemia (T-ALL). Although Phf6 is widely expressed, little is known about its proposed function as epigenetic regulator and tumor suppressor. To address the role of Phf6 in the leukemia development, here we analyze by RNAseq the gene expression profiles of isogenic Phf6 wild type and Phf6 knockout leukemia cells transformed by overexpression of an oncogenic mutant form of the NOTCH1 receptor.

overall_design: RNAseq analysis of isogenic leukemia cells with two genotypes, using three samples per genotype

first: Agnieszka

last: Wendorff

first: Aidan

first: Adolfo

last: Ferrando


title: Two distinct subsets are identified from the peritoneal myeloid mononuclear cells expressing both CD11c and CD115

status: Public on Jul 01 2019

city: Seoul

first: Chae Gyu

last: Park

state: Seoul

address: 50-1 Yonsei-ro

department: Severance Biomedical Science Institute

country: South Korea

institute: Yonsei University College of Medicine

summary: The peritoneal cavity is home to various immune cells.  Previous studies have investigated the heterogenous nature of peritoneal myeloid mononuclear cells.  However, up to this date, there are no clear criteria to distinguish peritoneal macrophages and dendritic cells (DCs).  In the present study, we delineate the subsets of myeloid mononuclear cells in the mouse peritoneal cavity.  Considering phenotypical, functional, and ontogenic features, peritoneal myeloid mononuclear cells are divided into 5 subsets: large peritoneal macrophages (LPMs), small peritoneal macrophages (SPMs), DCs, and 2 MHCII+CD11c+CD115+ subpopulations (i.e., MHCII+CD11c+CD115+CD14-CD206- and MHCII+CD11c+CD115+CD14+CD206+).  Among them, 2 subsets of competent antigen presenting cells are demonstrated with distinct functional characteristics, one being DCs and the other being MHCII+CD11c+CD115+CD14-CD206- cells.  DCs are able to promote fully activated T cells and superior in expanding cytokine producing inflammatory T cells, whereas MHCII+CD11c+CD115+CD14-CD206- cells generate partially activated T cells and possess a greater ability to induce regulatory T cells under TGF-β and retinoic acid conditions.  While the development of DCs and MHCII+CD11c+CD115+CD14-CD206- cells are responsive to the treatment of FLT3L and GM-CSF, the numbers of LPMs, SPMs, and MHCII+CD11c+CD115+CD14+CD206+ cells are only influenced by the injection of GM-CSF.  In addition, the analysis of transcriptomes reveals that the gene expression profile of MHCII+CD11c+CD115+CD14+CD206+ cells share high similarity with that of SPMs.  Collectively, our study identifies 2 distinct subpopulations of MHCII+CD11c+CD115+ cells, (i) MHCII+CD11c+CD115+CD14-CD206- cells closely related to DCs and (ii) MHCII+CD11c+CD115+CD14+CD206+ cells to SPMs.

overall_design: Global mRNA sequencing of MHCII+ peritoneal myeloid mononuclear cells

first: Chae

first: Moah

last: Sohn


title: High-throughput sequencing analysis of BMMs and BMMs-derived osteoclasts

status: Public on Jul 19 2019

first: Cui

last: Ma

state: Beijing

address: No. 37 Xueyuan Road

institute: Buaa

summary: Long noncoding RNAs (lncRNAs) have emerged as integral regulators of physiology and disease, but specific roles of lncRNAs in bone resorption remain largely unknown. Here, RNA-seq analysis indicated that lncRNA Nron was a candidate funtional regulators of bone resorption. Our further experimental analysis showed that Nron regulates bone resorption in mice. We further identified a functional motif of Nron. Consequently, delivery of Nron functional motif specifically in osteoclasts reversed bone loss without obvious side-effects in vivo. Together, our study indicate that Nron is a key bone resorption suppressor and reveal Nron functional motif might be a potential therapeutic strategy to combat excessive bone absorption in osteoporosis.

overall_design: High throughput RNA-seq was performed on mouse bone marrow-derived macrophages (BMMs, OC-0_day) and BMMs-derived osteoclasts (OCs, OC-6_day).

first: Xiaogang

last: Wang

first: F

last: Jin

last: Li

first: M

last: Cai

first: R

first: C

last: Liu

last: Zhong

last: Zhang

last: Xiao

first: Z

first: X

last: Ji

first: Y

last: Sun


title: Dissecting the autonomy of the liver circadian clock

status: Public on Jun 11 2019

city: irvine

first: Siwei

last: Chen

state: CA

address: 66304 Verano Road South

department: Computer Science

institute: University of California, Irvine

summary: The mammalian circadian clock system is made up of individual cell and tissue clocks that function as a coherent network, however it remains unclear which rhythmic functions of the liver clock are autonomous or rely on clocks in other tissues. Here, using mice which only have a functioning liver clock, we investigate the autonomous vs non-autonomous reatures of the liver clock and diurnal rhythmicity in the liver

overall_design: 8-12 week-old, female WT, KO and Liver-RE BMAL1-stop-FL mice (see referenced paper for details) were fed ad libitum normal chow under 12hr light/ 12hr dark schedule. Livers were harvested every 4 hours over the circadian cycle at ZT0, 4, 8, 12, 16, 20 (n=3 per time point per group). Total RNA was extracted and used for RNA-seq.

first: Kevin

last: Koronowski

first: Kenichiro

last: Kinouchi

first: Patrick

last: Welz

first: Valentina

last: Zinna

first: Muntaha

last: Samad

first: Pierre

last: Baldi

first: Salvador

last: Benitah

first: Paolo

last: Sassone-Corsi


title: Telomere dysfunction induces Sirtuin repression that drives telomere-dependent disease

city: Houston

first: Jeffrey

last: Chang

address: 6431 Fannin St

institute: University of Texas

summary: We have characterized the p53-dependent miRNAs in murine liver in telomerase knckout mice with short telomeres

overall_design: Identification of p53-dependent miRNAs in telomerase knockout mice with and without p53

first: Ergun

last: Sahin

first: Hisayuki

last: Amano


title: Expression data from eosinophils isolated from subcutaneous fat of WT and KLF3 KO mice

status: Public on Apr 30 2019

city: UNSW Sydney

first: Kate

last: Quinlan

state: NSW

address: Room 3102, Level 3, Biosciences South Building (E26)

department: School of Biotechnology and Biomolecular Sciences

country: Australia

institute: UNSW Sydney

summary: Gene expression in eosinophils isolated by FACS from inguinal subcutaneous adipose tissue of WT and mice lacking the transcriptional repressor Kruppel-like factor 3 (KLF3). We aimed to investigate deregulation of pathways and genes in the absence of KLF3 in eosinophils that reside in the subcutaneous adipose tissue, in order to study the role of KLF3 and its target genes in adipose eosinophil function and activity.

overall_design: Inguinal subcutaneous adipose tissue was dissected from 12-wk age- and litter-matched WT and KLF3 KO mice (n=3 per genotype). Adipose was digested using type II collagenase to yield the stromal vascular fraction (SVF), which was stained with fluorescently-conjugated antibodies to isolate eosinpohils (Live CD45+ CD11b+ F4/80+ SiglecF+ SSC hi). RNA was extracted from isolated cells using a Qiagen RNeasy Micro Kit then subjected to quality control using an Agilent 2100 Bioanalyzer, following preparation with an Agilent RNA 6000 Pico Kit. An Affymetrix 3’ IVT Pico Kit was used prior to microarrays which were performed on an Affymetrix GeneChip HT MG-430PM Array Plate.

first: Merlin

last: Crossley

first: Alexander

last: Knights


title: Gene expression of zebrafish larvae upon treating with lalistat or U18666A

status: Public on Apr 07 2019

city: Baltimore

first: Wei

last: Shao

state: Maryland

address: 725 N Wolfe Street

department: Cell Biology

institute: Johns Hopkins University School of Medicine

summary: To test if HIF pathway is regulated by lipids in zebrafish larvae, we have employed whole genome microarray expression profiling as a discovery platform to identify induced genes upon lalistat or U18666A treatment. Lalistat is a specific inhibitor for lysosomal acid lipase (LAL), which is required for break down triglyceride or cholesterol ester to release free fatty acids. U18666A is a specific inhibitor for NPC, which is required for export free cholesterol oout of lysosomes.

overall_design: Zebrafish larvae (5dpf) were treated with vehicle control DMSO, lalistat (25uM) or U18666A(2uM) for 24hr. Each RNA sample were extracted from pooled 4 larvae. Three biological replicates (3 clutches from different pairs of WT zebrafish mating) were conducted.

first: Peter

last: Espenshade


title: Long-term high-grain diet altered the ruminal pH, fermentation, and epithelial transcriptomes, leading to restored oxidative phosphorylation in Japanese Black cattle

status: Public on Jun 22 2019

city: Morioka

first: Keiichiro

last: Kizaki

state: Iwate

department: Vet. Med.

institute: Iwate University

summary: We explored the effect of long-term high-concentrate diet feeding on ruminal pH and fermentation, and its effect on the rumen epithelial transcriptomes in Japanese Black beef cattle during a 20-month fattening period.

overall_design: The fattening stages included Early, Middle, and Late stages (10–14, 15–22, and 23–30 months of age, respectively), and the cattle were fed concentrate and roughage diets during the fattening stages.

first: Yo-Han

last: Kim


title: Genome-wide analysis of PDAC Pa03c cells upon lipoprotein depletion

summary: To assay differently expressed genes in PDAC cells Pa03c cultured in regular 10% FBS medium or lipoprotein depleted 10% LPDS medium

overall_design: Total RNA obtained from Pa03c cells cultured in 10% FBS or 10% LPDS for 16hr

first: Shao

last: Wei

first: Espenshade

last: Peter


title: Gene expression of zebrafish larvae upon treating with lalistat

summary: To test if HIF pathway is regulated by lipids in zebrafish larvae, we have employed whole genome microarray expression profiling as a discovery platform to identify induced genes upon lalistat treatment. Lalistat is a specific inhibitor for lysosomal acid lipase (LAL), which is required for break down triglyceride or cholesterol ester to release free fatty acids.

overall_design: Zebrafish larvae (5dpf) were treated with vehicle control DMSO or lalistat (10uM) for 2hr. Each RNA sample were extracted from pooled 4 larvae. Two biological replicates (2 clutches from different pairs of WT zebrafish mating) were conducted.


title: TNF induces Glucocorticoid Resistance by reshaping the GR Nuclear Cofactor Profile: Investigation of TNF mediated effects on the GR-DNA binding

status: Public on May 06 2019

city: Gent

first: Steven

last: Timmermans

address: Technologiepark 71

country: Belgium

institute: VIB-UGent

summary: Glucocorticoid resistance (GCR) is defined as an unresponsiveness to the anti-inflammatory properties of glucocorticoids (GCs) and their receptor, the glucocorticoid receptor (GR). It is a serious problem in the management of inflammatory diseases and occurs frequently. The strong pro-inflammatory cytokine TNF induces an acute form of GCR, not only in mice, but also in several cell lines, e.g. in the hepatoma cell line BWTG3, as evidenced by impaired Dexamethasone (Dex)-induced GR-dependent gene expression. We report that TNF has a significant and broad impact on the transcriptional performance of GR, but no impact on nuclear translocation, dimerization or DNA binding capacity of GR. Proteome-wide proximity-mapping (BioID), however, revealed that the GR interactome is strongly modulated by TNF. One GR cofactor that interacts significantly less with the receptor under GCR conditions is p300. NFκB activation and p300 knockdown both reduce transcriptional output of GR, whereas p300 overexpression and NFκB inhibition revert TNF-induced GCR, which is in support of a cofactor reshuffle model. This hypothesis is supported by FRET studies. This mechanism of GCR opens new avenues for therapeutic interventions in GCR diseases

overall_design: Examination od GR-DNA bining trough ChIP-seq in 3 conditions with 3 biological replicates (2 condictions) or two biological replicates (1 condiction) and one input control

first: Karen

last: Dendoncker

first: Jolien

last: Vandewalle

first: Melanie

last: Eggermont

first: Joanna

last: Lempiäinen

first: Evelien

last: Van Hamme

first: Sylviane

last: Dewaele

first: Sofie

last: Vandevyver

first: Marlies

last: Ballegeer

last: Souffriau

first: Lise

last: Van Wyngene

first: Kelly

last: Van Looveren

first: Tineke

last: Vanderhaeghen

first: Rudi

last: Beyaert

first: Karolien

last: De Bosscher

first: Jorma

last: Palvimo

first: Marc

last: Van Montagu

first: Claude

last: Libert


title: Mouse skeletal muscle and liver in response to physiological insulin

status: Public on Mar 19 2019

city: Boston

first: Hui

last: Pan

address: 1 Joslin Place

department: Bioinformatics and Biostatistics Core

institute: Joslin Diabetes Center

summary: Regulation of gene expression is an important aspect of insulin’s physiological action, however, most studies rely on in vitro systems or pharmacological doses of insulin. Here, we demonstrate that under euglycemic-clamp conditions, physiological levels of insulin regulate over 1500 transcripts in muscle and 1000 transcripts in liver. These include expected pathways related to glucose and lipid utilization, mitochondrial function and autophagy in muscle, and glucose production and steroidogenesis in liver, as well as unexpected pathways, such as mRNA splicing, chromatin remodeling, and regulation of hepatocyte nuclear factors. Insulin also regulates over 100 non-coding RNAs in muscle and liver. These changes in coding and non-coding RNAs, refined by alternative splicing, provide an integrated transcriptional network underlying the complexity of insulin action in vivo.

overall_design: Three month-old male C57BL/6J mice (n = 6 per condition) were anestethized and had an indwelling catheter placed in the right internal jugular vein. After recovery (4-5 days), conscious mice were continuously perfused with either 4 or 12 mU/kg/min insulin or saline as control. Blood glucose was verified every 5-30 min and adjusted with infusion of a 20% glucose solution. At 20 min or 3 h of clamp, mice were euthanized by cervical dislocation, and tissues were harvested, snap frozen in liquid nitrogen and kept at -80 oC. Total RNA was isolated from quadriceps muscle and liver fragments. Stranded cDNA libraries with unique index tags for each sample (48 multiplexed) were made using a directional RNA-seq kit (Wafergen). Sequencing was performed on an Illumina HiSeq 2500 run on rapid mode (2x50).

first: T

last: Batista

first: C

middle: R

last: Kahn


title: Three-dimensional genomic structure and cohesin occupancy correlates with transcriptional activity during spermatogenesis

status: Public on Jun 03 2019

city: Cerdanyola del Vallès (Bellaterra)

first: Covadonga

last: Vara

state: Barcelona

address: Campus UAB

department: Biologia cel·lular, Fisiologia i Immunologia

country: Spain

institute: Universitat Autònoma de Barcelona

summary: Here we generated a high-resolution structural and functional atlas of mouse spermatogenesis by combining in situ Hi-C, RNA-seq and ChIP-seq of CTCF and meiotic cohesins RAD21L and REC8.

overall_design: Spermatogenesis cell populations were isolated by Fluorescence-Activated Cell sorting. Hi-C of isolated populations (spermatogonia, primary spermatocytes at leptonema/zygonema and pachynema/diplonema stage, round spermatids and sperm) and C57BL6 fibroblasts as control. RNA-seq of the same populations except for leptonema/zygonema. ChIP-seq of CTCF, RAD21L and REC8 in pachynema/diplonema cells and round spermatids.

first: Andreu

last: Paytuví-Gallart

first: Aurora

last: Ruiz-Herrera


title: RNAseq of murine models of high-grade gliomas induced by overexpression of PDGF-B or EGFRvIII

status: Public on Mar 13 2019

first: Paolo

last: Malatesta

summary: High grade glioma cells obtained by overexpression of PDGF-B in neural progenitors of Balb/c mice or by overexpression of EGFRvIII in neural progenitors of Ink/Arf -/- Balb/c mice and orthotopically transplanted in adult Balb/c mice.

overall_design: mRNA profiles of 3 indipendent high grade gliomas for PDGF-B driven model and 3 indipendent high grade gliomas for EGFRvIII driven model.

first: Francesco

last: Alessandrini


title: Transcriptomic features of trophoblast lineage cells derived from BMP4-treated human induced pluripotent stem cells

status: Public on Jan 31 2019

city: Shinjuku-ku

first: Nanae

last: Tsuchida

state: Tokyo

address: 6-7-1 Nishishinjuku

department: Obstetrics and Gynecology

institute: Tokyo Medical University

summary: We explored the trophoblast differentiation model using human induced pluripotent stem cells (hiPSCs) to gain new insights into the early development of human placenta. In our previous study, we have optimized culture conditions for hiPSC-derived trophoblasts. To identify the characteristics of trophoblast lineage cells derived from BMP4-treated hiPSCs, we collected cells using a pan-trophoblast marker, KRT7, with flow cytometry and performed comprehensive gene expression analysis.

overall_design: For characterization of BMP4-treated hiPSCs, four types of hiPSCs were treated with 50ng/ml BMP4 for 10 days. Subsequently, KRT7-positive cells were purified from differentiated cells using flow cytometry and analyzed using DNA microarray.

first: N

first: J

last: Kojima

first: A

last: Fukuda

last: Kawasaki

first: H

last: Ito

last: Kuji

first: K

last: Isaka

last: Nishi

last: Umezawa

last: Akutsu


title: Transcriptome changes across Col-0, klu and 35S:KLU

status: Public on Apr 01 2019

city: Potsdam

first: Alisdair

last: Fernie

address: Am Mühlenberg 1

department: Department Willmitzer

country: Germany

institute: Max Planck Institute of Molecular Plant Physiology

summary: The Arabidopsis cytochrome P450 gene KLU (also known as CYP78A5) is predicted to produce a mobile molecule that has tremendous effects on the plant growth. To gain insight the mechanism of KLU affects plant growth, we use the RNA-seq to profile the transcriptome changes across wild-type,klu mutant, and overexpression of KLU.

overall_design: We use the RNA-seq to profile the transcriptom changes in the leaves across wild-type, klu mutant and overexpression of KLU.

first: Liang

last: Jiang


title: Exosomal lncRNA sequencing in Atorvastatin treated and non-treated MSC-derived exosomes

status: Public on Feb 28 2019

first: Peisen

last: Huang

address: No.167 Bei Li Shi Road, Xicheng District

institute: Fuwai Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College

summary: In order to investigate the molecular mechanisms underlying the further enhancement of Atorvastatin pretreated MSC-derived exosomes (MSCATV-Exo) in cardiac protection, we performed lncRNA sequencing on exosomes secreted from ATV pretreated MSCs and non treated MSCs to identify differentially expressed lncRNA. We found that 450 lncRNAs were identified to be upregulated and 1332 lncRNAs downregulated (over 1.5 fold change) in MSCATV-Exo compared to MSC-Exo.

overall_design: Two samples were processed for each kind of exosomes that derived from normal MSCs and ATV pretreating MSCs (MSC-Exo and MSCATV-Exo). MSCATV-Exo was isolated from conditioned medium of MSCs pretreated by 1μmol/L  of ATV for 24 hours. RNA isolated from exosomes were analyzed using Illumina HiSeq 2500.

first: Yuejin

last: Yang


title: Choice of alternative polyadenylation sites, mediated by the RNA-binding protein Elavl3, plays a role in differentiation of inhibitory neuronal progenitors

status: Public on Jan 10 2019

city: Torino

first: Elena

last: Grassi

address: Via Nizza 52

department: Dept. of Molecular Biotechnology and Health Sciences

institute: Molecular Biotechnology Center

summary: Alternative polyadenylation is a widespread mechanism involving about half of the expressed genes, resulting in varying lengths of the 3' UTR and changes of the post-transcriptional processing, localization, miRNA targeting and stability of mRNAs. During neuronal differentiation a variety of mRNAs change the length of their 3' UTR, promoting the longer version of the transcripts. Little is known about polyA+ site usage during differentiation of mammalian neural progenitors. Here we exploit a model of adherent neural stem (ANS) cells, which homogeneously and efficiently differentiate into GABAergic neurons. RNAseq data shows a global trend towards lengthening of the 3’ UTRs during differentiation. Enriched expression of the long 3’ UTR variants of Pes1 and Gng2 was detected in areas of cortical and subcortical neuronal differentiation, respectively, in the mouse brain by two-probes FISH analyses. In Drosophila the choice of polyA+ site has been shown to be regulated by the RNA-binding protein Elav, which inhibits polyadenylation at proximal sites while interacting with paused Pol-II promoters. Among the coding genes upregulated during differentiation of ANS cells we found Elavl3, a neural-specific RNA-binding protein homologous to Drosophila Elav. The silencing of Elavl3 in ANS cells resulted in impaired elongation of the 3’UTR length and delayed neuronal differentiation. These results indicate that choice of the polyA+ site and lengthening of 3’ UTRs is a possible additional mechanism of posttranscriptional RNA modification involved in neuronal differentiation.

overall_design: We studied the transcriptome in four time points during in vitro neuronal differentiation of murine neural stem cells. We had different numbers of biological replicates for each time point, specifically: T0-3 replicates, T1-3 replicates, T2-4 replicates, T3 2 replicates.

first: Roberto

last: Santoro

first: Alessandro

last: Umbach

first: Anna

last: Grosso

first: Salvatore

last: Oliviero

last: Neri

first: Luciano

last: Conti

last: Provero

first: Ferdinando

last: Di Cunto

first: Giorgio

last: Merlo


title: Genome-wide regulatory adaptation shapes population-level genomic landscapes in Heliconius [ATAC-seq]

status: Public on Feb 05 2019

city: Ithaca

first: James

middle: Joseph

last: Lewis

address: 215 TOWER ROAD

department: Ecology & Evolutionary Biology

institute: Cornell University

summary: We test the hypothesis that intraspecific genomic divergence is linked to regulatory variation between Heliconius butterfly populations. We show that population-level divergence in chromatin accessibility and regulatory activity during wing development is abundant, and that differences in regulatory activity between populations are strongly associated with developmental stage. Genomic regions with high Fst are highly enriched for regulatory variants, and enrichment patterns vary significantly across development. Regulatory variants are associated with most differential gene expression between populations, and our data point to two roles for histone modifications in the evolution of gene expression.

sample_organism:
Heliconius himera
Heliconius erato petiverana
Heliconius erato lativitta

overall_design: Examination of chromatin accessibility in wing tissue over 2 developmental stages.

first: Robert

last: Reed


title: High-resolution clonal mapping of multi-organ metastasis in triple negative breast cancer

status: Public on Dec 11 2018

first: Jeffrey

last: Chang

summary: Most triple negative breast cancers (TNBCs) are aggressively metastatic with a high degree of intratumoral heterogeneity. We employed patient-derived xenograft models established from the breast tumors of patients with treatment-naïve metastatic TNBC to study clonal dynamics during metastasis. Genomic sequencing coupled with high-complexity barcode-mediated clonal tracking revealed robust alterations in clonal architecture between primary tumors and corresponding metastases that were deterministic rather than stochastic. The presence of numerous rare subclones in each metastatic lesion demonstrated that polyclonal seeding occurred and that heterogeneous populations of low-abundance clones were maintained in metastases. An identical population of subclones was enriched in lung, liver, and brain metastases, demonstrating that primary tumor clones harbor properties enabling them to seed and thrive in multiple organ sites. Further, clones that dominated multi-organ metastases shared a genomic lineage. Thus, intrinsic properties of rare primary tumor subclones enable the seeding and colonization of metastases in multiple organ sites.

overall_design:
A tumor from a breast cancer patient was engrafted into the mammary fat pad of NOD-SCID/gamma mice as a PDX model.  At passage 3, the tumors were allowed to grow and metastasize to the lung.  Samples were collected from the primary mammary gland as well as the lung metastases.  The transcription profiles were generated, and the changes in the profiles from primary to metastatic tumors were compared.

*** Raw data are not available due to patient privacy concerns. ***

first: Gloria

middle: V

last: Echeverria

first: Emily

last: Powell

first: Sahil

last: Seth

first: Zhongqi

last: Ge

last: Carugo

first: Christopher

last: Bristow

first: Michael

last: Peoples

first: Frederick

last: Robinson

first: Huan

last: Qiu

first: Jiansu

last: Shao

first: Sabrina

last: Jeter-Jones

first: Xiaomei

last: Zhang

first: Vandhana

last: Ramamoorthy

first: Shirong

last: Cai

first: Wenhui

last: Wu

first: Giulio

last: Draetta

first: Stacy

last: Moulder

first: William

middle: F

last: Symmans

first: Timothy

middle: P

last: Heffernan

first: Helen

last: Piwnica-Worms


title: TGFβ1-mediated functional inhibition of mesenchymal stromal cells in MDS and AML

status: Public on Nov 29 2018

city: Duesseldorf

first: Thomas

last: Schroeder

address: Moorenstr. 5

department: Department of Hematology, Oncology and Clinical Immunology

institute: University of Duesseldorf, Medical Faculty

summary: Mesenchymal stromal cells (MSC) are involved in the pathogenesis of myelodysplastic syndromes (MDS) and acute myeloid leukemia (AML), but how they contribute to the expansion of malignant cells and hematopoietic failure is poorly understood. To further characterize the pathological phenotype we performed RNA sequencing of MSC from patients with MDS and AML. Data analysis revealed a specific molecular signature with a significant overlap of genes commonly deregulated in all MDS subtypes and in AML. Pathway analysis revealed a strong enrichment of genes related to osteogenesis, senescence, inflammatory processes and inhibitory cytokines thereby reflecting the structural and functional deficits of MDS- and AML-derived MSC on a molecular level. Further analysis identified TGFß1 as the most probable extrinsic trigger factor for this altered gene expression. Following exposure to TGFß1 healthy MSC adopted a phenotype reminiscent of that observed in primary patient-derived MSC which was characterized by impaired growth potential, osteogenic differentiation capacities, a specific gene expression profile and diminished stromal hematopoietic support. These suppressive effects of TGFß1 on MSC functionality were abrogated by SD-208, an established inhibitor of TGFß receptor signalling. Blockade of TGFß signalling by SD-208 also restored the osteogenic differentiation capacity of patient-derived MSC, thus confirming the role of TGFß1 in the bone marrow microenvironment of patients with MDS and AML. Our findings establish TGFß1 as a relevant trigger causing functional inhibition of MSC in MDS and AML and identify SD-208 as a candidate for the reversal of these effects

overall_design: RNA sequencing of MSCs from 3 Healthy, 3 RCMD, 3 RAEB and 3 AML patients

first: Stefanie

last: Gey

first: Manuel

last: Rodríguez-Paredes

first: Paul

last: Jäger

first: Annemarie

last: Koch

first: Felix

last: Bormann

first: Julian

last: Gutekunst

first: Christoph

last: Zilkens

first: Ulrich

last: Germing

first: Guido

last: Kobbe

first: Frank

last: Lyko

first: Rainer

last: Haas


title: Gene expression profiling of cutaneous T cell lymphoma cell lines and primary tumor samples treated with mechlorethamine and romidepsin.

status: Public on Dec 10 2018

city: New York

first: Stuart

last: Quinn

institute: Columbia University

summary: In this study, we demonstrated the synergistic effect of the mechlorethamine-romidepsin combination in cutaneous T cell lymphoma cell lines and CD4+ T cells derived from patients with Sezary Syndrome. We identify the signaling pathways specifically perturbed under treatment with mechlorethamine-romidepsin combination.

overall_design: Gene expression profiling by RNA sequencing of cutanieous T cell lymphoma cell lines SeAX, HH, and Hut78 as well as cells isolated from 6 primary tumor samples upon treatment with vehicle control or mechlorethamine and romidepsin individually and in combination.

first: Christina

last: Patrone

first: S

middle: A

first: Teresa

last: Palomero


title: Quantitative multiplexed ChIP-Seq comparing mouse embryonic stem cells grown in Serum or 2i condition.

status: Public on Mar 06 2019

city: Solna

first: Simon

middle: J

last: Elsässer

address: Tomtebodavägen 23A

department: Medical Biochemistry and Biophysics

country: Sweden

institute: Karolinska Institutet

summary: Quantitative multiplexed ChIP-Seq reveals high levels of H3K27me3 broadly covering the genome and low levels of H3K4me3 in 2i condition (ground state). Bivalent promoters, a defining feature of pluripotent cells, are also present in the ground state. H3K27me3 is maintained at high levels at bivalent promoters, similar to those in Serum, while H3K4me3 is reduced more than twofold.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Rw4 mouse embryonic stem cells were grown in either serum-free medium with PD0325901 and CHIR99021 (“2i”), regular serum-based medium (“Serum”), or serum-based medium with 2i (“2i/Serum”) for at least three passages. mTORi cells were treated with 200nM INK128 (VWR, CAYM11811) for 48h. 1e6 cells of each condition/replicate were collected. This dataset contains MINUTE-ChIP data from three pools (P1-3). Biological replicates, where applicable, are stored in distinct raw files under the same entry and combined in the processed data file

last: Elsasser

first: Banushree

last: Kumar


title: Identification of functional enteroendocrine regulators by real-time single-cell differentiation mapping

city: Utrecht

first: Helmuth

last: Gehart

address: Uppsalalaan 8

institute: Hubrecht Institute

summary: Homeostatic regulation of the intestinal enteroendocrine lineage hierarchy is a poorly understood process. We resolved transcriptional changes during enteroendocrine differentiation in real-time at single-cell level using a novel knock-in allele of Neurog3, the master regulator gene briefly expressed at the onset of enteroendocrine specification. A bi-fluorescent reporter, Neurog3Chrono, measures time from the onset of enteroendocrine differentiation and enables precise positioning of single-cell transcriptomes along an absolute time axis. This approach yielded a definitive description of the enteroendocrine hierarchy and its sub-lineages, uncovered differential kinetics between sub-lineages, and revealed time-dependent hormonal plasticity in enterochromaffin and L-cells. The time-resolved map of transcriptional changes predicted multiple novel molecular regulators. Nine of these were validated by conditional knockout in mice or CRISPR-modification in intestinal organoids.  Six novel candidate regulators (Sox4, Rfx6, Tox3, Myt1, Runx1t1 and Zcchc12) yielded specific enteroendocrine phenotypes. Our time-resolved single cell transcriptional map presents a rich resource to unravel enteroendocrine differentiation.

overall_design: We generated transcriptomic bulk and single cell data from Neurog3Chrono reporter mice.

first: Johan

middle: H

last: van Es

first: Karien

last: Hamer

first: Joep

last: Beumer

first: Kai

last: Kretzschmar

first: Johanna

last: Dekkers

first: Anne

last: Rios

first: Hans

last: Clevers


title: Genome-wide mRNA Transcriptional Profiling Reveals Regulatory Network for Coordinated Early Wheat Spike Development

status: Public on Oct 25 2018

city: Shanghai

first: Xing

last: Fu

address: 3888 Chenhua Road

institute: Shanghai Center for Plant Stress Biology, Chinese Academy of Sciences

summary: Wheat panicle development is a coordinated process of proliferation and differentiation with distinctive phase and architecture changes. However, the multiple genes involved networks controlling this process remain enigmatic. Here, we characterized and dissected common wheat panicles in the stages of vegetative stage before elongation, elongation, single ridge, double ridge, glume primodium differentiation and floret differentiation, respectively, followed by RNA-seq and bioinformatics analysis to study genome-wide mRNA transcriptome profiling in wheat early spike development. High gene expression correlations between any two stages (R2>0.97) and only 4000 Differentially Expressed Genes (DEGs) out of 49624 expressed transcripts in all stages indicated that wheat early panicle development is just controlled by an small proportion of important genes. Three subgenomes (A, B and D) contribute equally to this process. K-means clustering analysis revealed the dynamic expression patterns of DEGs and Hierarchical Clustering analysis demonstrated that single bridge stage and double bridge stage are most important for wheat panicle development. Interestingly, 306 transcription factors (TFs) with various functions from different families were identified and the spatial-temporal expression patterns of some were verified by quantitative PCR or in situ hybridization. At early stages, repressing flowering TFs combined with AP2/ERF TFs and cytokinin promote inflorescence meristem development and repress meristem differentiation. At single ridge and double ridge stages, highly expressed stress-response TFs balance the interaction between stress response and development. During reproductive stages, crosstalk between auxin and cytokinin coordinate the meristem proliferation and differentiation, and promoting flowering TFs with polarity establishment TFs and MADS-box TFs promote floral meristem generation and floral organ identity and development. This dataset provided an ideal resource for wheat panicle developmental research. Our study uncovered the regulatory network for coordinated wheat early spike development and would eventually contribute to the improvement of grain number and crop yield.

overall_design: mRNA profiles of early wheat spike in six stages

first: Xigang

last: Liu

first: Reny

last: i Liu


title: Deciphering the role of importin alpha in mammalian central neurons - Hippocampal gene expression profiling in importin alpha5-deleted mice

status: Public on Nov 22 2018

city: Rehovot

first: Mike

last: Fainzilber

address: 234 Herzl Street

department: Department of Biomolecular Sciences

country: Israel

institute: Weizmann Institute of Science

summary:
Introduction: The mechanisms governing synaptonuclear transport, and the transcriptional pathways that are at the core of neuronal disorders are poorly understood. The importin family of nuclear import factors has pivotal roles in such pathways, due to their involvement in intracellular transport from both synapse to soma and cytoplasm to nucleus. Mammals express six different isoforms of importin α, which bind an Importin β to form transport complexes for specific cargoes.
Methods: We addressed the roles of importin α isoforms in mammalian CNS by evaluation of a systematic series of importin α knockout mice. A comprehensive battery of behavioral tests was used to investigate spontaneous and novelty-induced locomotion, basal ganglia function, motor coordination, neuromuscular integration, anxiety-related behaviors and memory. Subsequent analyses using acute-brain slice electrophysiology, RNA-seq, bioinformatics, imaging and pharmacology was used in order to delineate the contribution of genes and signaling pathways involved in the identified phenotype and screen for new therapeutic approaches.
Results and Discussion: During the course of comprehensive behavioral profiling of importin α mouse mutants, we identified an importin α knockout (KO) mouse with significantly reduced anxiety levels. Electrophysiological recordings in acute hippocampal slices showed a reduced short-term and presynaptic plasticity (paired-pulse facilitation deficit, lower PTP), while LTP was not affected in these mutants. We then performed transcriptional profiling (RNA-seq) from hippocampal extracts of wild type versus mutant animals after exposure to an anxiogenic drug. Computational analysis revealed differences in the expression of genes and the involvement of transcription factors. Drugs that activate LXR or the Sphingosine 1 phosphate receptor have robust anxiolytic effects, while a Sphk1 blocker reverses anxiolysis in the importin α5 knockout mouse. Thus, importin α5 influences anxiety by regulating nuclear import in neurons.

overall_design: RNA-seq performed on: 4 experimental groups, 3 animals per each vehicle group and replicate, 3 replicates of the entire set - Exception in the FG7142-treated Importin α5-/- group (n=2) where 1 animal was identified outlier and discarded from the analysis

first: Nicolas

last: Panayotis


title: Deciphering clonal evolution and dissemination of Multiple Myeloma cells in vivo

status: Public on Oct 10 2018

first: Jiantao

last: Shi

address: 3 Blackfan Circle

institute: dana farber cancer institute

summary: Clonal evolution drives tumor progression, dissemination and relapse in cancer, and dissemination or metastasis of the tumor cells from primary site to other organs is the leading cause of death for cancer patients. This multi-stage process requires tumor cells to survive in the circulation, extravasate at distant sites, then colonization. The whole process involves contributions from both the tumor cells and microenvironment. Here we developed and applied a clonal tracking ‘rainbow’ system into a tumor dissemination xenograft mouse model (SCID-mu) to study the clonal behaviors with the presence of a bone marrow environment showing that only a few subclones successfully remodeled by BM environment can exit the primary site and further colonize in distant tissues. RNA-sequencing results of primary and disseminated MM tumor cells revealed a metastatic signature, which is sequentially activated during human MM progression and significantly associated with overall survival when evaluated against a public patient dataset suggesting SCID-mu model characterizes MM dissemination phenotypically and mechanistically.

overall_design: To explore the underlying molecular mechanisms that contribute to tumor metastasis, we performed RNA sequencing on three human cell lines MM.1S, IM9 and OPM2 that were harvested from primary bone chips and metastatic BM using SCID-mu xenograft model.

first: Yujia

last: Chen

first: Yuji

last: Mishima


title: Title: Transcriptional profiles (mRNA-seq) of Drosophila G9aDD1 mutants and control during 0, 6 and 12 hours of paraquat oxidative stress exposure.

status: Public on Feb 01 2019

city: Nijmegen

first: Human

last: Riahi Asl

state: Gelderland

address: Geert Grooteplein Zuid 10

department: Human Genetics

institute: Radboud UMC

summary:
Purpose: Investigating the role of Drosophila G9a in oxidative stress responses.
Methods: Flies were collected after eclosion and allowed to recover from CO2 exposure for 5 days prior to paraquat  exposure. Paraquat (Methyl viologen dichloride hydrate 98 %; Sigma 856177) was mixed into the flyfood at 40 °C to a final concentration of 50 mM. For OS induction, 5-9 day old flies were transferred to paraquat containing food and incubated at 25 °C and 70 % humidity. At each time point, flies were flash frozen in liquid nitrogen followed by vortexing and filtering through a series of sieves to isolate heads from other body parts. 200 fly heads per sample were used for RNA extraction using QIAGEN lipid mini tissue kit. The TruSeq RNA Sample Preparation Kit v2 (Illumina) was used to prepare adapter ligated PCR fragments for sequencing. PCR was used to selectively enrich the fragments containing the adapters. The PCR fragments were validated using Agilent 2200 TapeStation. Single indexed samples were multiplexed and sequenced on an Illumina HiSeq 2000 sequencing system (Illumina) in single-end mode with a read length of 35 bp. Quality of sequenced reads was assessed with FastQC. The RNAseq experiments were conducted on two biological duplicates for each condition. Sequenced reads were aligned with Burrows-Wheeler algorithm (BWA) (Li & Durbin, 2010) to the Drosophila reference genome (BDGP.5, http://www.fruitfly.org/) and per gene read counts were generated with HTSeq count (Anders et al, 2015). 25–30 million reads with high quality alignment were obtained for each sample and used for differential expression analysis. DESeq (Anders & Huber, 2010) was used to obtain library size-normalized read counts and to calculate differential expression of genes in 4 pairwise comparisons: 0 h versus 6 h and 0 h versus 12 h after OS in both G9a mutants and controls (fold change ≥1.5, adjusted p-value≤ 0.05, Benjamini-Hochberg).
Results: We found 2731 genes to be differential expressed in at least one of the four pairwise comparisons. The largest group of differentially expressed (DE) genes are highly augmented upon OS induction in the G9a mutant (41.7 % of all DE genes). The second largest group of DE genes (23.9 % of all DE genes) were more downregulated in G9a mutant in response to OS. Genes that are over-activated in G9a mutants are predominantly involved in OS response and OS mediated damage, whereas genes that are downregulated in G9a mutants are involved in energy metabolism.
Conclusions: Our data suggest that G9a provides an epigenetic mechanism that safeguards an appropriate transcriptional response to OS and preserves immediately available energy, thereby acting as a critical regulatory hub between the transcriptional and physiological responses to oxidative stress.

overall_design: fly-head mRNA libraries of 5-9 days old male G9aDD1 mutant and control during 0, 6 and 12 hours of paraquat oxidative stress exposure were sequenced in duplicate on Hi-seq 2000.

last: Riahi

first: Jamie

last: Kramer

first: Annette

last: Schenck


title: Identification of target genes regulated by NANOG-HDAC1 axis

status: Public on Oct 18 2018

city: Seoul

first: Kwon-Ho

last: Song

address: 73 Inchon-ro, Sungbuk-gu

institute: Korea University College of Medicine

summary: To gain insight into the role of HDAC1 in NANOG-mediated transcriptional regulation, we performed genome-wide RNA-sequencing analysis (RNA-seq) in CaSki-no insert-siGFP, CaSki-NANOG-siGFP and CaSki-NANOG-siHDAC1 cells.

overall_design: Total RNAs from CaSki-no insert and CaSki-NANOG cells transfected with the indicated siRNA were subjected to genome-wide total RNA-sequencing analysis

first: Tae

middle: W

last: Kim


title: Expression data of lncRNAs and mRNAs extracted from PBMCs of tuberculosis patients and healthy individuals[HTA2.0]

status: Public on Aug 29 2018

city: Chengdu

first: Bai

last: Hao

state: Sichuan

address: Wuhou District Guoxue Lane 37

department: Laboratory Medicine

institute: West China Hospital of Sichuan University

summary:
Tuberculosis (TB) is the ninth leading cause of death worldwide and the leading cause from a single infectious agent, ranking above HIV/AIDS.Although considerable advances have been achieved in recent years, the genetic and molecular mechanisms underlying this disease remain largely unclear.
In the present research, we used the Affymetrix GeneChip Human Transcriptome Array 2.0 to investgate the profiles of differentially expressed lncRNAs and mRNAs from the peripheral blood mononuclear cells (PBMCs) of 7 TB patients and 5 healthy controls (HC).

overall_design: Peripheral blood samples of 7 TB patients and 5 healthy individuals were collected for the PBMCs total RNAs extraction and hybridization on Affymetrix microarrays. In TB group, 7 newly diagnosed pulmnary TB patients were selected: TB-1, TB-2, TB-3, TB-4, TB-5, TB-6 and TB-7. Meanwhile, 5 healthy individuals were selected as controls: HC-1, HC-2, HC-3, HC-4 and HC-5.

first: Xuejiao

last: Hu

first: Hao

last: Bai

first: Qian

last: Wu

first: Tangyuheng

first: Jiajia

first: Zhenzhen

last: Zhao

first: Wu

last: Peng

first: Binwu

last: Ying


title: Pre-invasive versus microinvasive carcinoma of the cervix

status: Public on Dec 22 2018

first: Alexander

last: Poltorak

state: Massachusetts

address: 150 Harrison avenue

institute: Tufts University

summary: Comparative analysis of gene expression prodfiles of cervical biopsy from two (2) patients with pre-invasive neoplastic lesions (carcinonma in citu, or high-grade cervical intraepithelial neoplasia) and 2 patients with earliest stage of invasive cancer

overall_design: By comparing two earliest stages that are adjacent in the course of cervical cancer development but have completely different growth strategies, we aimed to identify genes and molecular pathways that may underlie acquisition of invasive phenotype and metastatic properties  (including lymphangiogenesis and epithelial-to mesenchymal transition) by cervical cancer cells.

first: Olga

last: Kurmyshkina


title: The nucleolar SAHY1 is involved in pre-rRNA processing and normal plant growth in Arabidopsis

status: Public on Aug 13 2018

city: Taipei

first: Wan-Hsing

last: Cheng

address: 128 Academia Road, Section 2, Nankang

department: Institute of Plant and Microbial Biology

country: Taiwan

institute: Academia Sinica, Taiwan

summary:
Although the nucleolus is known to be involved in the plant stress response, the underlying mechanisms remain unclear. In the present study, we genetically isolated and characterized the Arabidopsis thaliana salt hypersensitive mutant 1 (sahy1), which exhibits slow growth, short roots, and sterility. SAHY1 encodes an unknown protein that is predominantly expressed in root tips and mature pollens. Subcellular localization further demonstrated that SAHY1 is a nucleolar protein. Ploidy analysis and detection of S-phase cell cycle progression indicated that mitosis is reduced in the root tips of sahy1 plants. Furthermore, levels of reactive oxygen species (ROS) are reduced in the mutant. In addition to exhibiting changes in venation pattern, palisade mesophyll cells, the auxin response, and fertility, the sahy1 mutant is resistant to the protein translation inhibitors, streptomycin and cycloheximide, and has altered expression profiles of ribosome-related genes, reflecting the involvement of SAHY1 in ribosome assembly. Using a combination of transcriptome and gene coexpression clustering analyses, we identified a striking functional module in which SPIRAL 1-LIKE 4 (SPL4), which encodes a microtubule-localized protein, mediates the salt response that acts by modulating dynamic microtubule instability. Supporting evidence indicates that sahy1 is resistant to a microtubule-destabilizing drug (oryzalin), that the cortical microtubule array in sahy1 exhibits changes in dynamic instability, and that the spr1/spl2/spl3/spl4 quadruple mutant is oversensitive to salt. Collectively, these data demonstrate that a novel nucleolar protein, SAHY1, plays critical roles in salt sensitivity, plant growth, and development by integrating the diverse functions of its downstream genes.
As the sahy1 mutant plants showed slow growth, short roots, and sterility, the aim of this experiment is to examine gene expression profile in root tissues mediated by SAHY1. The data obtained from this study was compared with chip database derived from root tissues and performed an analysis of gene coexpression clustering.

overall_design: included, are there control and/or reference Samples, etc...Arabidopsis seeds were grown on basal medium for five days, transferred to fresh medium and grown vertically for another seven days. After the 12-day culture, the roots were removed and used for RNA extraction. Ten micrograms of total RNA was used for cDNA synthesis and labeled by in vitro transcription. Eleven micrograms of labeled sample was hybridized to Affymetrix ATH1 GeneChips at 45oC for 16.5 h. Samples were washed and stained using a Fluidic Station-450, and the ATH1 chips were scanned with an Affymetrix GeneChip Scanner 7G. Data analysis was performed using GeneSpring GX 10.0.1 software (Agilent). Statistical analysis included a cut-off value of P<0.05, T-test unpaired, asymptotic p-value computation, and multiple testing correction by Benjamini-Hochberg FDR (1995). The microarray analysis was performed in biological triplicate.

first: Pei-Jung

last: Hsu

first: Mai

middle: C

last: Tan

first: Ya

last: Chen

first: Hwei

last: Shen

middle: Y

last: Wang

first: San

middle: G

last: Hwang

first: Ming

last: Chiang

first: Q

last: Le

first: Wen

last: Kuo

first: Y

last: Chou

first: S

last: Lin

first: G

last: Jauh

first: Wan


title: Morphological, physiological, transcriptomic and metabolomic responses of Arabidopsis leaves to prolonged warming and heat shock

status: Public on Aug 08 2018

city: Yangzhou

first: Biao

last: Jin

state: Jiangsu

address: Wenhui east road no. 48

department: College of Horticulture and Plant Protection

institute: Yangzhou University

summary: We sequenced mRNA from leaves of  Arabidopsis under the control (CK), warming (W) and heat (H) treatments using the Illumina HiSeq4000 platform to generate the transcriptome dynamics that may serve as a gene expression profile blueprint for different response patterns under prolonged warming versus rapid-onset heat stress in Arabidopsis.

overall_design: Transcriptome sequencing in control, warming and heat treatments leaves of Arabidopsis

first: Kaibiao

last: Ma

first: Li


title: Establishment and characterization of CRISPR/Cas9-mediated insertion of FLT3 ITD K562 cell line: Molecular insight of CD52 in leukemia

status: Public on Jul 07 2018

city: Nagoya

first: Akinobu

last: Ota

state: Aichi

address: 1-1 Yazakokarimata

department: Food and Nutritional Environment

institute: Kinjo Gakuin University

summary: To investigate the effect of FLT3-ITD on gene expression, we have employed whole genomic microarray expression profiling using K562 cells

overall_design: The K562cells were plated at 80% confluence and cultured for 24 hours in vitro.

first: Sivasundaram

last: Karnan


title: Comparison of irradiation-induced genes from freshly isolated bone-adherent mesenchymal cells of p53-WT and p53-null mice

status: Public on Jul 25 2018

city: Buffalo

first: Amanda

last: Perez

state: NY

address: Elm and Carlton Streets

institute: Roswell Park Cancer Institute

summary:
Gene expression profiling was determined in BAMC isolated from non-irradiated and irradiated p53-null and p53-WT mice. We selected strongly expressed genes in p53-WT compared to p53-null BAMC. They belonged
to different pathways.Also, a number of genes coded secreting proteins that , probably, were responsible for the improved hematopoiesis in p53-null mice.

overall_design: Total RNA was isolated from BAMC isolated from bone marrow of irradiated (13 Gy, 24h) or control p53-WT and p53-null mice.

first: Natalia

last: Fedtsova

first: Andrei

last: Gudkov


title: RNA-seq data from human SGBS adipocytes differentiated with marine oxohexadecenoic acids

status: Public on Jun 26 2018

city: Oslo

first: Thomas

last: Sæther

state: Oslo

address: Sognsvannsveien 9

department: Dept. of Molecular Medicine

country: Norway

institute: University of Oslo

summary: We recently isolated and identified (7E)-9-oxohexadec-7-enoic acid (1) and (10E)-9-oxohexadec-10-enoic acid (2) from the marine algae Chaetoceros karianus. Synthesis and biological characterization show that these are PPARα/γ dual agonists. Herein we report the gene expression data from human SGBS pre-adipocytes, stimulated to differentiate with 1, 2 or the classical PPARγ agonist rosiglitazone. The transcriptome analysis shows that both compounds induce anti-diabetic gene programs in adipocytes by upregulating insulin-sensitizing adipokines and repressing pro-inflammatory cytokines.

overall_design: Human SGBS pre-adipocytes were stimulated with adipogenic media supplemented with either (7E)-9-oxohexadec-7-enoic acid, (10E)-9-oxohexadec-10-enoic acid, or rosiglitazone from day 0 to day 4. On day 4, agonists were withdrawn, and the cells were allowed to differentiate following standard protocol. On day 8, RNA was isolated and sent to sequencing.

first: Steinar

last: Paulsen

first: Jørn

middle: E

last: Tungen

first: Anders

last: Vik

first: Marius

last: Aursnes

first: Torgeir

last: Holen

first: Trond

last: Hansen

first: Hilde

middle: I

last: Nebb


title: Profiling of pluripotency factors in single cells and early embryos

status: Public on Jul 20 2018

city: Pittsburgh

first: Sarah

last: Hainer

state: PA

address: 4249 Fifth Ave

department: Department of Biological Sciecnes

institute: University of Pittsburgh

summary: Cell fate decisions are governed by sequence-specific transcription factors (TFs) that act in small populations of cells within developing embryos. To understand their functions in vivo, it is important to identify TF binding sites in these cells. However, current methods cannot profile TFs genome-wide at or near the single cell level. Here we adapt the CUT&RUN method to profile TFs in low cell numbers, including single cells and individual pre-implantation embryos. Single-cell experiments demonstrate that only a fraction of TF binding sites appear to be occupied in most cells, in a manner broadly consistent with measurements of peak intensity from multi-cell studies. We further show that chromatin binding by the pluripotency TF NANOG is highly dependent on the SWI/SNF chromatin remodeling complex in individual blastocysts but not in cultured cells. Ultra-low input CUT&RUN (uliCUT&RUN) therefore enables interrogation of TF binding from rare cell populations of particular importance in development or disease.

overall_design: ultra-low input CUT&RUN. Antibody enriched DNA was fragmented using proteinA-Mnase, and libraries were generated.

first: Ana

last: Boskovic

first: Kurtis

middle: N

last: McCannell

first: Oliver

last: Rando

last: Fazzio


title: Transcriptome of Gossypium hirsutum floral and extrafloral nectaries

status: Public on Apr 19 2018

city: Duluth

first: Marshall

last: Hampton

state: MN

address: 1117 University Drive

institute: University of Minnesota Duluth

summary: Comparative RNA-Seq study of expression in Gossypium hirsutum nectaries

overall_design: Seeds for Gossipium hirsutum cv. TM1 were chipped and germinated in 8cm x 8cm x 10 cm pots filled with a soil mixture of 3-parts LC8 soil to 1-part sand. Plants were grown in Environmental Growth Chambers kept at 12h light 26 °C /12h dark 22 °C cycle. Seedlings were transplanted into two-gallon (2A) pots after reaching approximately 30 cm in height. Upon transplanting, 10 g of Osmocote Pro 19-5-8 was mixed into the previously described soil mixture per pot. Plants were water each day and once per week with a 10% fertilizer solution of Scotts Excel 21-5-20 all purpose water soluble fertilizer and Scotts Excel 15-5-15 Cal-Mag water soluble fertilizer. All tissues were collected from plants after the first flower bloomed, approximately ten weeks after sowing, between the times of 1000 and 1500.    RNA isolation: For a single biological replicate, approximately five nectaries were transferred with a clean forcep to a 2 ml Lysing matrix A tube (MP Biomedicals, Ref # 6910-500) containing a ceramic bead, resting in a liquid nitrogen bath. The tubes were quickly transferred to a QuickPrep adaptor (containing dry ice) and attached to the FastPrep 24™-5G  (MP Biomedicals) benchtop homogenizer. The tissue were subjected to 5 to 6 homogenizing runs of 40 seconds each at 6 m/sec, with each run interjected with a period of immersing the tubes in liquid nitrogen and refilling the adaptor with dry ice. Post-pulverization, 600µl of the RNA lysis buffer of the Quick-RNA™ MiniPrep kit (Zymo Research, Cat# R1054) was quickly added to the Lysing matrix tube and the tubes were vortexed. This was followed by addition of 50µl of the Plant RNA Isolation Aid (Thermo Fisher Scientific Cat#AM9690; erstwhile Ambion) and a quick vortex to aid removal of common plant contaminants such as polyphenolics and polysaccharides. Quick-RNA™ MiniPrep kit directions were followed for RNA isolation. Agarose gel electrophoresis and UV spectrophotometry were used to assess RNA quality for all samples prior to submission to the University of Minnesota Genomics Center for barcoded library creation and Illumina HiSeq 2500 sequencing. All libraries were pooled and sequenced across two and a half lanes, then sequencing was repeated for quality concerns. This generated ≥24 M reads for each sample and the average quality scores were above Q30.    Tissue types and stages: RNA was isolated from four types of nectaries (foliar, bracteal, circumbracteal, floral) at two or three different stages for each (pre-secretory, secretory and/or post-secretory). In parallel, RNA was also isolated from control samples from tissues adjacent to each nectary type. A total of 51 RNA samples were isolated as described below.    Foliar nectary stages included: pre-secretory (‘FO_pre_x’; lack of visible nectar and midvein length of 5 to 6 cm on main stem leaf; 2 replicates), secretory [‘FO_S_x’; fully mature main stem leaf (midvein length 12 to 15 cm) with visible nectar, 1 replicate], and post-secretory (‘FO_P_x’; lack of visible nectar on fully mature main stem leaf; 3 replicates). In parallel, RNA was also isolated from control samples from tissues adjacent to the foliar nectaries (labeled ‘FO_pre_xC’, ‘FO_S_xC’ and ‘FO_P_xC’ where ‘x’ refers to a sample number).   Bracteal nectary stages included: pre-secretory (‘B_pre_x’; matchhead square, 2 replicates) and post-secretory (‘B_post_x’; 19 to 24 days after anthesis; 3 replicates). In parallel, RNA was also isolated from control samples from tissues adjacent to the bracteal nectaries (labeled ‘B_pre_xC’ and ‘FO_post_xC’ where ‘x’ refers to a sample number).  Circumbracteal nectary stages included: pre-secretory (‘C_pre_x’; matchhead square; 3 replicates) and post-secretory (‘C_post_x’; 19 to 24 days after anthesis; 3 replicates). In parallel, RNA was also isolated from control samples from tissues adjacent to the circumbracteal nectaries (labeled ‘B_pre_xC’ and ‘FO_post_xC’ where ‘x’ refers to a sample number).  Floral nectary stages included: pre-secretory (‘FL_pre_x’; Candle, 24 hours pre-anthesis), secretory (‘FL_sec_x’; anthesis), and post-secretory (‘FL_post_x’; 24 hours post-anthesis). In parallel, RNA was also isolated from control samples from tissues adjacent to the floral nectaries (labeled ‘FL_pre_xC’, ‘FL_S_xC’ and ‘FL_P_xC’ where ‘x’ refers to a sample number.

first: Clay

last: Carter

first: Elizabeth

last: Chatt


title: Epigenomic conservation of transposable element silencing [RNA-seq]

status: Public on Apr 26 2018

city: Chicago

first: Michelle

last: Ward

state: IL

address: 920 E. 58th Street, CLSC 317

institute: University of Chicago

summary: Transposable elements (TEs) comprise a substantial proportion of primate genomes. Because of the potential deleterious effects of TEs during development, TEs are targeted for silencing by sequence-specific KRAB-ZNF proteins, which recruit the TRIM28-SETDB1 complex, to deposit the repressive histone modification H3K9me3. TEs, in turn, acquire mutations to evade detection by the host, and hence KRAB-ZNF proteins need to rapidly evolve to counteract them. To investigate the short-term evolution of TE silencing, we profiled the genome-wide distribution of H3K9me3 in both human and chimpanzee induced pluripotent stem cells. We performed chromatin immunoprecipitation followed by high-throughput sequencing for H3K9me3, as well as total RNA sequencing in ten human and seven chimpanzee individuals. H3K9me3 enrichment was quantified in 141,642 regions determined to be orthologous between the two species. These H3K9me3-enriched regions were overlaid on a compiled set of 4 million orthologous TEs that can be mapped in both species.

sample_organism:
Pan troglodytes
Homo sapiens

platform_organism:
Pan troglodytes
Homo sapiens

overall_design: We collected RNA-seq data from 10 human and 7 chimpanzee iPSC lines.


title: Reprogramming of heterologous cells by defined factors to generate lineage-restricted biomolecules

status: Public on Jan 11 2018

city: UNSW Sydney

first: Kate

last: Quinlan

address: Room 3102, Level 3, Biosciences South Building (E26)

department: School of Biotechnology and Biomolecular Sciences

institute: UNSW Sydney

summary: The ability of transcriptional regulators to drive lineage conversion of somatic cells offers great potential for the treatment of human disease. While current research in this field is focused on the generation of induced pluripotent stem cells or direct lineage transdifferentiation, less attention has been paid to the possibility of reprogramming cells to produce cytokines, growth factors and hormones. To explore the concept of switching on specific target genes in heterologous cells, we developed a model system to screen candidate factors for their ability to activate the archetypal megakaryocyte-specific chemokine platelet factor 4 (PF4) in fibroblasts.   We found that co-expression of the transcriptional regulators GATA1 and FLI1 resulted in a significant increase in levels of PF4, which became magnified over time.  We also determined that inclusion of a third factor, TAL1, further enhanced upregulation of PF4 expression. Our study therefore identified of TAL1 as an important component in the combination of transcriptional regulators that contribute to megakaryocyte programming, and demonstrated that such combinations can be used to produce potentially beneficial chemokines in readily available heterologous cell types.

overall_design: 8 total samples were run on an affymetrix genechip mouse gene 1.0 ST array

first: Crisbel

middle: M

last: Artuz

first: Alexander

last: Knights

first: Alister

last: Funnell

last: Gonda

first: Katya

last: Ravid

first: Richard

last: Pearson

first: Merlin

last: Crossley


title: Epigenomic conservation of transposable element silencing

status: Public on Apr 25 2018

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

overall_design: Refer to individual Series