title: ATAC-seq from erythroid cells generated through ex vivo differentiation

summary: CD34+ Haematopoietic stem cells were differentiated under two ex vivo protocols to generate ATAC-seq data for machine learning of rules underlying open chromatin dynamics.

overall_design: CD34+ cells were isolated from peripheral blood from three healthy donors (Two males, one female) and differentiatied ex vivo using two different protocols. The first protocol (P1) uses a 2-phase differentiation and the second protcol (P2) uses a 3-phase differentiation which includes co-culture on a layer of stromal MS-5 cells. ATAC-seq was perfroemd at various days throughout differentiation.

first: Marjorie

last: Brand

first: Caroline

last: Scott


title: Transcriptomic analysis of Streptococcus suis in response to ferrous iron and cobalt toxicity

status: Public on Jul 04 2020

city: Yangzhou

first: Chengkun

last: Zheng

address: East wenhui road No.48

country: China

institute: Yangzhou University

type: Expression profiling by high throughput sequencing

summary: We explored the transcriptome change of Streptococcus suis in the presence of ferrous iron and cobalt by RNA sequencing. The data revealed that expression of a lot of genes was altered to respond to ferrous iron and cobalt toxicity. Moreover, most of the genes differentially expressed in response to cobalt are the same as those in response to ferrous iron.

overall_design: The transcription profiles of Streptococcus suis following treatment with ferrous iron and cobalt were compared with that treatment with water. Each condition contains three biological replications.

first: Mengdie

last: Jia

first: Man

last: Wei

first: Yunzeng

last: Zhang


title: DeepC: predicting 3D genome folding using megabase-scale transfer learning

status: Public on Jul 08 2020

city: Oxford

first: Ron

last: Schwessinger

address: MRC WIMM, John Radcliffe Hospital, Headington

department: MRC Weatherall Institute if Molecular Medicine

country: United Kingdom

institute: University of Oxford

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

overall_design: Refer to individual Series


title: Gene expression data for human intervertebral discs

status: Public on Jun 30 2020

city: Pok Fu Lam

first: Peikai

last: Chen

address: Sassoon Road 5

department: Faculty of Medicine

country: Hong Kong

institute: The University of Hong Kong

summary:
The human intervertebral disc (IVD) is a complex and dynamic structure that functions to provide spinal stability, mobility and flexibility. It comprises three main compartments: 1) a water-rich central compartment called the nucleus pulposus (NP), which is enveloped by 2) the annulus fibrosus (AF) and sandwiched between 3) two cartilaginous endplates (EP) from which the IVD gains its nutrition and provides a means to get rid of metabolic waste.
The IVD is constantly under extreme conditions of hypoxia, nutrition, and loading stresses. As such, it wears with ageing, and the rates of wearing may be sped up by a multitude of risk factors. Phenotypically, the AF may become weaker that a portion of it may protrude into neighboring tissues, resulting in disc bulging, or even worse, it may rupture and form a herniation
Most striking of all, magnetic nuclear imaging (MRI) of the NP may become darker, with spotted high-intensity zones (HIZs), indications of dehydration and annular disruptions (Peng, et al. 2006). In a herniated or even collapsed disc, the contents of NP may leak into the neighboring spaces and external cells (such as macrophages) may infiltrate into the NP (Nakazawa, et al. 2018), causing the disc functions to be partially or fully compromised. The underlying mechanism of these involves complex interplays of cellular and molecular changes and remains poorly understood; nevertheless, the process is suggested to be triggered and driven by both environmental and genetic factors, or their combinations.
In an effort to study the molecular dynamics of the ageing process of the human IVD, we profiled the transcriptomes of two groups of individuals: a young and non-degenerated group (N=2) and an aged and degenerated group (N=2). We profiled the transcriptomes of both AF and NP for each individual.

overall_design: We measured the transcriptome of eight samples, corresponding to 4 individuals' AF and NP structures, respectively.

first: Anita

last: Yee

first: Vivian

last: Tam

first: Danny

last: Chan


title: Transcriptome-wide high-throughput mapping of protein-RNA occupancy profiles using POP-seq

city: Pittsburgh

first: Rajneesh

last: Srivastava

state: Pennsylvania

address: 450 Technology Dr

department: Surgery, University of Pittsburgh

country: USA

institute: McGowan Institute for Regenerative Medicine

summary: Interaction between proteins and RNA is critical for post-transcriptional regulatory processes. Existing high throughput methods based on crosslinking of the protein-RNA complexes and polyA pull down are reported to contribute to biases and are not readily amenable for identifying interaction sites on non polyA RNAs. We present Protein Occupancy Profile-Sequencing (POP-seq), a phase separation based method in three versions, one of which does not require crosslinking, thus providing unbiased protein occupancy profiles on whole cell transcriptome without the requirement of polyA pulldown. Our study demonstrates that ~68% of the total POP-seq peaks exhibited an overlap with publicly available protein-RNA interaction profiles of 97 RNA binding proteins (RBPs) in K562 cells. We show that POP-seq variants consistently capture protein-RNA interaction sites across a broad range of genes including on transcripts encoding for transcription factors (TFs), RNA-Binding Proteins (RBPs) and long non-coding RNAs (lncRNAs). POP-seq identified peaks exhibited a significant enrichment (p value < 2.2e-16) for GWAS SNPs, phenotypic, clinically relevant germline as well as somatic variants reported in cancer genomes, suggesting the prevalence of uncharacterized genomic variation in protein occupied sites on RNA. We demonstrate that the abundance of POP-seq peaks increases with an increase in expression of lncRNAs, suggesting that highly expressed lncRNA are likely to act as sponges for RBPs, contributing to the rewiring of protein-RNA interaction network in cancer cells. Overall, our data supports POP-seq as a robust and cost-effective method that could be applied to primary tissues for mapping global protein occupancies.

overall_design: To investigate the transcriptome wide protein occupied sites in K562 cells, we implemented Protein Occupancy Profile-Sequencing (POP-seq) with three variants- NPOP-seq (no crosslinking), UPOP-seq (UV-crosslinking) and FPOP-seq (Formaldehyde crosslinking) that generate precise RNA fragments targeted by RBPs.

first: Mansi

first: Sarath Chandra

last: Janga


title: Gene expression changes induced by ILB in Schwann like cells

status: Public on Jun 25 2020

city: Birmingham

first: Zsuzsanna

last: Nagy

address: Medical School

institute: University of Birmingham

summary: To understand the mechanism of action of ILB  we have used gene expression analysis to document the changes induced by the drug in Schwann like cells. Human Schwann-like cells (ATCC-CRL-2884) were treated with ILB (0.01 mg/ml) for 48 hours. Control samples were cultured parallel with no drug added. The expression data was used to identify the ILB-regulated genes.

overall_design: ILB (0.01 mg/ml) induced gene expression profile was determined after 48 hours in Human Schwann-like cells.


title: Deletion of the Aspergillus niger pro-protein processing protease gene kexB results in a pH-dependent morphological transition during submerged cultivations and increases cell wall chitin content

status: Public on Jun 26 2020

city: Leiden

first: Tim

middle: Marijn

last: van Leeuwe

address: Sylviusweg 72

country: Netherlands

institute: Leiden University

summary: There is a growing interest for the use of post-fermentation mycelial waste to obtain cell wall chitin as an added-value product. In the pursuit to identify suitable production strains that can be used for post-fermentation cell wall harvesting, we turned to an Aspergillus niger strain in which the kexB (also named pclA in literature) gene was deleted. Previous work has shown that deletion of kexB causes hyper-branching and thicker cell walls, which is beneficial as these properties reduce fermentation viscosity and lysis. The deletion of kexB has been shown to exhibit a pH-dependent hyper-branching on solid agar plates at pH 6.0, but not at pH 5.0, whereas this phenotype was reported to be less pronounced during submerged growth. Here, we show a series of controlled batch cultivations performed at a pH range of 5, 5.5, and 6 to examine the pellet phenotype in liquid medium of the ΔkexB strain. Morphological analysis showed that the ΔkexB formed wild type-like pellets at pH 5.0 whereas the characteristic hyper-branching ΔkexB phenotype was found at pH 6.0. Cultivations at pH 5.5 showed that the ΔkexB strain grows as an intermediate phenotype of pH 5.0 and pH 6.0. Analyzing the cell walls of the ΔkexB strain from these controlled pH-conditions showed an increase in chitin content compared to wild type at all three pH values tested. Surprisingly, the increase in chitin content was found to be irrespective of the hyper-branching morphology. Evidence for alterations in cell wall make-up are corroborated by transcriptional analysis that showed a significant cell wall stress response in addition to upregulation of genes encoding other unrelated cell well biosynthetic genes.

overall_design: Expression profiles A. niger strains; wild type versus kexB deletion strain from bioreactor cultures, using RNA-sequencing, duplicate biological samples,  90% of maximum attained biomass per biological samples. 4 samples total

middle: M

first: Mark

last: Arentshorst

first: Gabriel

last: Forn-Cuní

first: Nicholas

last: Geoffrion

first: Adrian

last: Tsang

first: Annemarie

middle: H

last: Meijer

first: Peter

middle: J

last: Punt

first: Arthur

middle: F

last: Ram


title: Mouse Embryonic Fibroblasts (MEFs) Adipogenic Potential: A Comprehensive Transcriptome Analysis

status: Public on Jun 19 2020

city: Abu Dhabi

first: Mohamed

last: Al-Sayegh

address: Saadiyaat Island - 1st floor ERB, Room 136, P.O. Box 129188

department: Biology

country: United Arab Emirates

institute: New York University Abu Dhabi

summary: Exploration into the dynamic process of adipogenesis  in MEF cells via transcriptome analysis

overall_design: RNA isolates of MEF cells extracted at different timepoint and conditions. Timepoints included day 0,3, and 5. Conditions, for day 3 and 5, included adipocyte differentiating condition (incubation with basal growth media supplemented with 0.5 mM 3-isobutyl-1-methylxanthine , 10 μg/mL insulin, 1 μM dexamethasone, and 10 μM rosiglitazone) and non-differentiating condtion (basal growth media DMEM 10%FBS).

first: Nizar

last: Drou


title: TCF7L2 silencing results in altered gene expression patterns accompanied by local genomic reorganization

status: Public on Jun 08 2020

city: Bethesda

first: Markus

middle: Alexander

last: Brown

state: Maryland

address: 50 South Drive, Room 1408

department: Center for Cancer Research

institute: National Institutes of Health

summary: Canonical Wnt signaling is crucial for intestinal homeostasis as TCF4, the major Wnt signaling effector in the intestines, is required for stem cell maintenance. The capability of TCF4 to maintain the stem cell phenotype is contingent upon β-catenin, a potent transcriptional activator, which interacts with histone acetyltransferases and chromatin remodeling complexes. We used RNAi to explore the influence of TCF4 on chromatin structure (Hi-C) and gene expression (RNA sequencing) across a 72-hour time series in colon cancer. We found that TCF4 reduction results in a disproportionate up-regulation of gene expression, including a powerful induction of SOX2. Integration of RNA sequencing and Hi-C data revealed a TAD boundary loss, which occurred concomitantly with the over-expression of a cluster of CEACAM genes on chromosome 19. We identified EMT and E2F as the two most deregulated pathways upon TCF4 depletion and LUM, TMPO, and AURKA as highly influential genes in these networks using measures of centrality. Results from gene expression, chromatin structure, and centrality analyses were integrated to generate a list of candidate transcription factors crucial for colon cancer cell homeostasis. The top ranked factor was c-JUN, an oncoprotein known to interact with TCF4 and β-catenin, confirming the usefulness of this approach.

overall_design: Four Hi-C samples were generated from the SW480 colon cancer cell line. The sample set consists of 1 replicate for each time point (0, 24, 48, 72). The 24, 48, and 72 hour time points where treated with siRNA targeting TCF7L2 transcripts, while the 0 hour time point was treated with negative control siRNA.

middle: A

first: Gabrielle

last: Dotson

first: Indika

last: Rajapakse

first: Thomas

last: Ried


title: Assessment of transcriptional ERa activity following exposure to 17a-E2 and 17b-E2

status: Public on Jun 15 2020

city: BAR HARBOR

first: Niran

last: Hadad

state: Maine

address: 5 Bloomfield Rd, Unit A

institute: The Jackson Laboratory

type: Genome binding/occupancy profiling by high throughput sequencing

summary: The study shows that, regardless of dose, both estrogens elicit nearly identical ERa activity

overall_design: U2OS Cells were transfected with ERa and were exposed to vehicle, 17a-E2 (10nM & 100nM), or 17b-E2 (10nM) for 24 hours in preparation for RNA and ChIP sequencing analyses

first: Michael

last: Stout

first: John

last: Hawse

first: Willard

last: Freeman

first: Shivani

last: Mann


title: Cardiomyocytes stimulate angiogenesis after ischemic injury in a ZEB2-dependent manner

status: Public on Jun 03 2020

city: Utrecht

first: Eva

last: van Rooij

state: Utrecht

address: Uppsalalaan 8

institute: Hubrecht Institute

summary: WT or Zeb2 cKO (cardiomyocyte-specific) mice received a myocardial infarction. After 14 days, the borderzone of an infarcted region was isolated followed by RNA isolation and RNA sequencing

overall_design: Borderzone of the infarcted heart from 3 WT mice and 3 Zeb2 cKO mice were sequenced

first: Monika

last: Gladka

first: Arwa

last: Kohela

first: Bas

last: Molenaar

first: Danielle

last: Versteeg

first: Lieneke

last: Kooijman

first: Jantine

last: Monshouwer-Kloots

first: Veerle

last: Kremer

first: Harmjan

middle: R

last: Vos

first: Manon

last: Huibers

first: Jody

last: Haigh

first: Danny

last: Huylebroeck

first: Reinier

last: Boon

first: Mauro

last: Giacca


title: Comparison of mitochondrial transcription errors in wild type and mutant mitochondrial RNA polymerase overexpression flies

status: Public on Jul 14 2020

first: Mehdi

last: Pirooznia

state: MD

address: 12 SOUTH DR

summary: To determine the error rate of mitochondrial transcription, we ananlyzed 33 and 37 million reads respectively for wild type (WT) and mutant (E423P) mitochondrial RNA polymerase (POLRMT) overexpression flies and found that the error frequency of mitochondrial transcripts were over 5 fold higher in E423P flies than that of WT. To gain more insight into the molecular mechanisms that drive the error rate of transcription by POLRMT, we examined its distribution of errors along the mitochondrial genome. We also evaluated mitochondrial RNA processing by quantifying the frequency of a single read spanning two adjacent genes. There was no significant increase of unprocessed RNAs in E423P than that of WT. These observations concluded that overexpression of E423P POLRMT in adult flies leads to a statistically significant increase of mitochondrial transcripts errors.

overall_design: Examination of mitochondrial transcription errors in two overexpression files.

first: Yi

last: Liu

first: Yuesheng

last: Li


title: Multiplexed single-cell autism modeling reveals convergent mechanisms altering neuronal differentiation

status: Public on Jun 20 2020

city: New York

first: Matthew

last: Lalli

state: NY

address: 1 Gustave L. Levy Pl

department: Psychiatry

institute: Icahn School of Medicine at Mount Sinai

summary: We coupled dCas9-based transcriptional repression of autism and neurodevelopmental disease genes to single-cell RNA-sequencing in the context of human neuron differentiation to identify the unique and shared consequences of these perturbations in a pooled experimental format.

overall_design: We infected LUHMES cells with a library of sgRNAs targeting 14 ASD-relevant genes or non-targeting guides (47 unique guideRNAs total), selected cells at a low MOI to enrich for cells with only 1 perturbation, and then differentiated these cells for 8 days. After 8 days, we performed single cell RNA-sequencing using the 10X Chromium platform to identify the effects of ASD-gene knockdown on neuron differentiation. We used the CROP-seq method to recover the sgRNA sequences from polyA RNA.

first: Robi

middle: D

last: Mitra


title: Cycling stem cells regenerate the damaged intestinal epithelium upon irradiation

status: Public on Jun 07 2020

city: Bejing

first: Xiaole

last: Sheng

address: Yuanmingyuan west Rd 2, Haidian district

institute: China Agricultural University

summary: The intestinal epithelium undergoes DNA damage response, regenerative response and homeostasis after suffering irradiation. To understand the dynamic change of intestinal epithelium during the irrradiation recovery, we performed single cell RNA sequencing on irradiation-resistant +4 cells in homeostasis and its lineages at different time points after radiation.

overall_design: We generated an Msi1CreERT2 allele for lineage tracing and observe that Msi1CreERT2-marked cells are enriched at the +4 crypt position which showed resistant to DNA damage. Msi1-CreERT2; R26-mTmG mice were administrated with 12Gy γ-IR after fifteen hours tamoxifen treatment. The epithelium were collected 0, 1, 2, 3, 5 days after irradiation, GFP cells were sorted and profiled by single cells RNA sequencing.

first: Ziguang

last: Lin

first: Cong

last: Lv

first: Chunlei

last: Shao

first: Xueyun

last: Bi

first: Min

last: Deng

first: Jiuzhi

last: Xu

first: Christian

last: Guerrero-Juarez

first: Mengzhen

first: Xi

last: Wu

first: Ran

last: Zhao

first: Xu

last: Yang

first: Guilin

first: Xiaowei

first: Qingyu

last: Wang

first: Qing

last: Nie

first: Wei

last: Cui

first: Shan

last: Gao

first: Hongquan

last: Zhang

first: Zhihua

first: Yingzi

last: Cong

first: Maksim

middle: V

last: Plikus

first: Christopher

last: Lengner

first: Bogi

last: Andersen

first: Fazheng

last: Ren

first: Zhengquan

last: Yu


title: Single cell analysis of primary prostate human epithelial organoids grown in vehicle or 1,25D to day 8 and day 14

status: Public on Jun 01 2020

city: Chicago

first: Larisa

last: Nonn

state: IL

address: 840 S. Wood St, MC847

department: Pathology

institute: University of Illinois at Chicago

summary: Primary prostate epithelial cells derived from a single patient were grown as organoids in vehicle or 10nM 1,25D (vitamin D). At day 8 and day 14 of culture, organoids were dissociated to single cells, and collected & prepped for RNA-seq using the 10x Genomics Chromium Genome Reagent kit v3 Chemistry. ~5,000 cells were collected from each sample and sequenced at a depth of ~50,000 genes per cells on a 2x150nt lane in a NovaSeq 6000. CellRanger alignment was performed to produce the RAW data files.

overall_design: Four samples: organoids grown to day 8 and day 14 in vehicle or 1,25D

first: Tara

last: McCray


title: Role of phosphorylated Gonadotropin-Regulated Testicular RNA Helicase (GRTH/DDX25) in the Regulation of Germ Cell Specific mRNAs in Chromatoid Bodies during Spermatogenesis

status: Public on Jul 09 2020

city: BETHESDA

first: RAJAKUMAR

last: ANBAZHAGAN

address: 49 CONVENT DRIVE, NIH

department: NICHD, DDB

institute: NICHD, NIH

summary: In this study, we examined transcriptome profiles of Chromatoid bodies (organelle; CB) of germ cells isolated from GRTH Knock-In (Human GRTH gene with R242H mutation) and WT mice testis using RNA-Seq. We used homozygous GRTH KI mice (which show loss of phospho-GRTH) to further understand the importance of CB and phospho-GRTH and their role in spermatid development during spermiogenesis by analyzing the DEGs from RNA-Seq. The analysis of RNA-Seq data allowed us to find the relevant DEGs related to RNA Transport and Protein processing that are essential for spermatid development. This study using KI mice model demonstrated that loss of phospho-GRTH impairs CB structure and mRNA storage function (in CB) and chromatin compaction hampering initial stages of spermatid elongation process.

overall_design: Transcriptome profiles of Chromatoid bodies (organelle; CB) in germ cells of WT and GRTH-Knock-In mice by Illumina RNA-Seq for gene expression profiling.

first: Rajakumar

last: Anbazhagan

first: Raghuveer

last: Kavarthapu

first: Steven

middle: L

last: Coon

first: Maria

last: Dufau


title: Simultaneus presence of bacteriochlorophyll and xanthorhodopsin genes in freshwater bacterium Sphingomonas sp. AAP5

city: Trebon

first: Karel

middle: Vaclav

last: Kopejtka

address: Novohradska

department: Centre Algatech

country: Czech Republic

institute: Institute of Microbiology Czech Acad. Sci.


title: Failure to maternally reprogram histone methylation causes developmental delay due to germline transcription in somatic tissues

status: Public on May 29 2020

city: Atlanta

first: Brandon

middle: S.

last: Carpenter

state: Georgia

address: 615 Michael St., SOM: Cell Biology Dept.

department: Cell Biology

institute: Emory University

summary: In C. elegans, the H3K4me2 demethylase, SPR-5, and the H3K9 methyltransferase, MET-2, are maternally deposited into the oocyte where they reprogram histone methylation to prevent somatic expression of germline genes. Here, we show that the progeny of spr-5; met-2 mutants display a severe developmental delay that is associated with the ectopic expression of germline genes targeted by the H3K36me2/3 methyltransferase, MES-4. Maternally deposited MES-4 maintains H3K36me2/3 at a subset of germline genes (hereafter referred to as MES-4 germline genes) in a transcription-independent manner, and this is required for germline proliferation in the subsequent generation. By performing ChIP-seq on L1 progeny from spr-5; met-2 mutants, we find that MES-4 germline genes ectopically accumulate H3K36me3 in somatic tissues. Additionally, knocking down MES-4 suppresses the ectopic expression of MES-4 germline genes and rescues the developmental delay. These data suggest a model where SPR-5, MET-2 and MES-4 carefully balance the inheritance of histone methylation from the parental germline to ensure the proper specification of germline versus soma in the progeny. Without SPR-5; MET-2 maternal reprogramming, somatic cells struggle to specify their proper cell fate amongst the background noise of inappropriate germline gene transcription, leading to a severe developmental delay.

overall_design: RNA-seq analysis on  spr-5; met-2 L1 progeny to determine differentially expressed genes compared to wild-type ( N2)

middle: S

first: Teresa

middle: W

last: Lee

first: Caroline

last: Plott

first: Jovan

last: Brockett

first: Dexter

last: Myrick

first: David

last: Katz


title: Transcriptome response to carbon-limiting conditions.

summary: Comparison of cells grown under carbon-limited and carbon-replete conditions.

overall_design: Cells were incubated aerobically either in diluted or full liquid medium under 12-h dark/12-h light regime and harvested either 4 hours after the transition to dark or 4 hours after the transition to light.

first: Jürgen

last: Tomasch

first: Yonghui

last: Zeng

first: Vadim

last: Selyanin

first: Marko

last: Dachev

first: Kasia

last: Piwosz

first: Martin

last: Tichý

first: Boyke

last: Bunk

first: Henner

last: Brinkmann

first: Zdenko

last: Gardian

first: Robert

last: Geffers

first: Michael

last: Reck

first: Ruben

last: Sommaruga

first: Michal

last: Koblížek


title: Development of circRNA expression signatures for glioblastoma cells.

city: Boston

first: Kamil

last: Krawczynski

state: MA

address: 60 Fenwood Rd

department: Neurosurgery

institute: Brigham and Womens Hospital

summary: To develop circRNA expression approach, we have used Arraystar Human Circular RNA Array as a discovery platform to identify circRNA with the potential to distinguish between glioblastoma (G cells) and neural progenitor cells (N cells). Circular RNA expression patterns separate N and G cells.

overall_design: Two-conditions experiment, GSC vs. NPC. Biological replicates: GSC n=8 NPC n=3

first: Arun

middle: K

last: Rooj

first: Jakub

last: Godlewski


title: Development of gene expression signatures for glioblastoma with circ2082 knock-down (KD)

summary: To further develop gene expression approach, we have employed whole genome microarray expression profiling as a discovery platform to identify genes with the potential to identify circ2082 expression effect in different subpopulations of glioblastoma cells (G cells). Cells were transfected with either control or antisense oligos targeting circ2082.  KD of circ2082 affects gene expression patterns in cell subtype specific pattern

overall_design: Two-conditions experiment, G cells control vs. circ2082 KD. Biological replicates: 6 for each condition


title: Identification of Fam122a regulated genes in LT-HSCs.

status: Public on May 28 2020

city: Shanghai

first: Manhua

last: Liu

state: China

address: 280, Chong-Qing South Road

department: Pathophysiology

institute: Shanghai Jiao Tong University School of Medicine

summary: We report differences in gene expression between WT and Fam122a KO LT-HSCs.

overall_design: RNA profiles from WT and Fam122a KO LT-HSCs were generated in duplicate.

first: Man-Hua

first: Ying

last: Huang


title: An in vivo atlas of host-pathogen transcriptomes during Streptococcus pneumoniae colonization and disease

status: Public on Jun 05 2020

city: Baltimore

first: Suvarna

last: Nadendla

address: 670 W.Baltimore Street

department: Institute for Genome Sciences

institute: University of Maryland School of Medicine

summary: D’Mello et al. detail host-pathogen interaction gene expression profiles of Streptococcus pneumoniae (Spn) and its infected host at disease relevant anatomical sites using mice as experimental models. The authors identify the core and organ-specific transcriptomes of Spn, show that bacterial and host gene expression profiles are highly distinct during asymptomatic colonization versus disease-causing infection, and demonstrate that Spn and host genes with high levels of expression contribute to pathogenesis or host defense, respectively.

sample_organism:
Streptococcus pneumoniae
Mus musculus

platform_organism:
Streptococcus pneumoniae
Mus musculus

overall_design:
71 mRNA profiles of Streptococcus pneumoniae samples that were grown under different conditions were generated using deep sequencing: PRJNA340293 including 3 planktonic, 3 biofilm, 3 infected mouse hearts, 2 infected mouse blood and 3 uninfected mouse hearts; and PRJNA629527 including 6 mouse blood (4 infected, 2 uninfected), 8 mouse kidneys (6 infected, 2 uninfected), 8 mouse lungs (6 infected, 2 uninfected), and 8 mouse nasopharynx (6 infected, 2 uninfected).
This work was supported with funds from: i) Merck, Sharpe & Dohme, Corp. under the Merck Investigator Studies Program (MISP) award IISP ID#: 57329 – Pneumovax entitled: “Dual RNA-seq for characterization of the Streptococcus pneumoniae and host transcriptomes during bacteremia/invasive disease”, and ii) the National Institutes of Health, National Institute of Allergy and Infectious Diseases under the R01AI114800 award entitled: “Cardiac microlesion formation during invasive pneumococcal disease”.

first: Adonis

last: D’Mello

first: Ashleigh

middle: N

last: Riegler

first: Eriel

last: Martinez

first: Sarah

last: Beno

first: Tiffany

last: Ricketts

first: Ellen

last: Foxman

first: Carlos

last: Orihuela

first: Herve

last: Tettelin


title: Transcriptomic continuity and an age-dependent onset of hemoglobin expression characterize morphological PV types in the hippocampus

city: Zurich

first: Csaba

last: Földy

state: Zurich

address: Winterthurerstrasse 190

department: Brain Research Institute

country: Switzerland

institute: University of Zurich

summary: The diversity reflected by >100 different neural cell types fundamentally contributes to brain function and a central idea is that neuronal identity can be inferred from genetic information. Recent large-scale transcriptomic assays seem to confirm this hypothesis, but a lack of morphological information has limited the identification of several known cell types. For example, parvalbumin interneurons (PV-INs) comprise of a main transcriptomic cluster within all inhibitory cells. However, transcriptomics alone has not resolved the different morphological PV types that exist. To close this gap, we used single-cell RNA-seq in morphologically identified PV-INs, sampled from 10 days to 3 months-old mice and studied their transcriptomic states in the morphological, physiological, and developmental domains. Our findings reveal a small number of genes whose expression is different between morphologically different types, but overall our analysis indicates high transcriptomic similarity among PV-INs. Furthermore, morphological PV types display uniform cell adhesion molecule (CAM) profiles, despite the fact that these types have very different wiring patterns, suggesting that CAM expression in mature PV cells do not reflect wiring specificity after development. Finally, our results reveal a pronounced change of transcriptomic states between postnatal days 20 and 25, during which PV-INs display a rapid onset of hemoglobin gene expression which remains stable in later development. Together, our results suggest that while morphological PV types in the CA1 are distinguished by their anatomy and in vivo activity, their largely continuous transcriptomic and homogenous biophysical landscapes are not predictive of these distinct identities.

overall_design:
Pvalb positive cells were collected from mice between ages P10 and P77. There were 62 vertical basket cells (vBCs), 16 horizontal basket cells (hBCs), 9 vertical bistratified cells (vBICs), 14 horizontal bistratified cells (hBICs), 7 vertical axo-axonic cells (vAACs), 6 cortical cells (Corticals), and 14 unclassified cells (UCs)

Please note that the readme_Series_design.tsv list the samples included in each processed data file.

first: Lin

last: Que

first: David

last: Lukacsovich

first: Wenshu

last: Luo


title: Transcriptome profiling of quiescent muscle stem cells in vivo

status: Public on May 22 2020

city: Hong Kong

first: Tom

last: Cheung

address: Clear Water Bay, Kowloon

department: Division of Life Science

institute: Hong Kong University of Science and Technology

summary: To understand the molecular signatures of quiescent muscle stem cells in vivo, we isolated quiescent muscle stem cells by fixation using perfusion technique and profiled the transcriptome by RNA-Seq.

overall_design: The polyA+ RNA from satellite cells were sequenced using Illumina NextSeq 500 (2 x 150) and Illumina HiSeq 2000 (2 x 101).

first: Lu

last: Yue

first: Raymond

last: Wan


title: Transcriptome RNA Sequencing Data Sets of Bacillus anthracis Vollum DhtrA and Parental Isogenic Wild-Type Strains under Oxidative Stress Conditions

status: Public on May 27 2020

city: Ness Ziona

first: Inbar

last: Cohen Gihon

address: Reuven 24

department: Biochemistry

country: Israel

institute: Israel Institute For Biological Research

summary: The High Temperature Requirement (HtrA) chaperone/protease is involved in the stress-response of   the anthrax-causing pathogen Bacillus anthracis. Resilience to oxidative stress is essential for manifestation of B. anthracis pathogenicity. We submitt transcriptome data sets detailing global gene expression in B. anthracis wild-type and htrA-disrupted strains following H2O2-induced oxidative stress.

overall_design: B. anthracis parental DVollum  (acapsular and nontoxinogenic, referred as wild type, wt) and an htrA disrupted strain, were grown in Brain-Heart Infusion broth at 37°C to mid log phase and split into twin cultures in the presence  or absence of 3 mM H2O2. Cells were collected from the initial culture before treatment (WT denoted sample 1 and DhtrA denoted sample 2) and 10 minutes post treatment-without H2O2-(WT sample denoted 3 and DhtrA denoted sample 5), and with H2O2 (WT sample denoted 4 and DhtrA denoted sample 6). The project includes 14 sets of transcriptomic data: Samples 1, 2, 3 and 5, each one in biological douplicates; Samples 4 and 6, in biological triplicates. Total RNA was extracted using the RNeasy kit (Qiagen). RNA-seq was performed in-house (IIBR, Ness-Zionna, Israel).

last: Cohen-Gihon

first: Ofir

last: Israeli

first: Uri

last: Elia

first: Galia

last: Zaide

first: Ma'ayan

first: Adi

last: Beth-Din

first: Anat

last: Zvi

first: Ofer

last: Cohen

first: Theodor

last: Chitlaru


title: UAP56/DDX39b is a major co-transcriptional RNA-DNA helicase that unwinds harmful R loops genome-wide

status: Public on May 25 2020

city: Seville

first: Andrés

last: Aguilera

address: Av. Américo Vespucio 24

department: Genome BIology

country: Spain

institute: CABIMER, Universidad de Sevilla

summary: Non-scheduled R loops represent a major source of DNA damage and replication stress. Cells have different ways to prevent R loop accumulation. One mechanism relies on the conserved THO complex in association with co-transcriptional RNA processing factors including the RNA-dependent ATPase UAP56/DDX39B and histone modifiers such as the SIN3 deacetylase in humans. We investigated the function of UAP56/DDX39B in R loop removal. We show that UAP56 depletion causes R loop accumulation, R loop-mediated genome instability and replication fork stalling. We demonstrate an RNA-DNA helicase activity in UAP56 and that its overexpression suppresses R loops and genome instability induced by depleting 5 different unrelated factors. UAP56/DDX39B localizes to active chromatin and prevents the accumulation of RNA-DNA hybrids over the entire genome. We propose that, in addition to its RNA processing role, UAP56/DDX39B is a key helicase required to eliminate harmful co-transcriptional RNA structures that otherwise would block transcription and replication.

overall_design: DNA-RNA immunoprecipitation (DRIP-seq) was performed on untreated or RNase H-treated K562 control cells. DNA-RNA immunoprecipitation strand-specific (DRIPc-seq) were performed on two siC control and siUAP56 K562 cell lines. ChIP-seq and RNA-seq were performed on two K562 control cells.

first: C

last: Perez-Calero

first: A

last: Bayona-Feliu

first: X

last: Xiaoyu

first: Sonia

middle: I

last: Barroso

first: Sergio

last: Muñoz

first: V

last: Gonzalez-Basallote

first: P

last: Sung


title: Sequencing 22G small RNAs in WT and zsp-1(-) animals

status: Public on May 21 2020

first: Scott

last: Kennedy

address: 77 Avenue Louis Pasteur

department: Genetics

institute: Harvard Medical School

type: Non-coding RNA profiling by high throughput sequencing

summary: To explore how ZSP-1 (and therefore Z granules) might contribute to germline RNAi, we asked if zsp-1(-) animals were able to produce 22G siRNAs in response to dsRNA exposure. We exposed wild-type and zsp-1(-) animals to dsRNA targeting the germline-expressed gene oma-1 and sequenced the resultant oma-1 22G siRNAs. We identified similar numbers of oma-1 siRNAs anti-sense to oma-1 after oma-1 RNAi on wild-type or zsp-1(-) animals. We also used this dataset to identify genes with differential level of targeted 22G siRNAs level in zsp-1(-) versus WT animals.

overall_design: Small RNAs of ~18-35 nucleotides from WT or zsp-1(-) animals were sequenced with NextSeq500, in duplicate.

first: Gang

last: Wan

first: Yuhan

last: Fei


title: Transcriptomes of H1650 cells with and without SETD2 depletion

status: Public on May 19 2020

city: Changzhou

first: You

last: Zhou

state: Jiangsu

address: Juqian Rd No.185

institute: The Third Affiliated Hospital of Soochow University

summary: RNA sequencing of H1650 cells with and without SETD2 depletion to identify SETD2-regulated genes

overall_design: Total RNA from H1650 cells with and without SETD2 depletion was generated by deep sequencing, in triplicate, using Illumina HiSeq 4000.

first: Jingting

last: Jiang


title: Gene expression profile of OT-I CD8+ T cell subtypes

status: Public on May 10 2020

first: Thomas

last: Kupper

address: 77 Avenue Louis Pasteur - HIM671

department: Dermatology

institute: Brigham and Women's Hospital

summary: Modified Vaccinia Ankara (MVA) was recently approved as a Smallpox vaccine. Transmission of Variola is by respiratory droplets, and MVA delivered by skin scarification (ss) protected mice far more effectively against lethal respiratory challenge with VACV than any other route of delivery, and at much lower doses. Comparisons of ss with intradermal, subcutaneous or intramuscular routes showed that MVAOVA ss-generated T cells were both more abundant and transcriptionally distinct. MVAOVA ss produced greater numbers of lung Ova-specific CD8+ TRM and was superior in protecting mice against lethal VACVOVA respiratory challenge. Nearly as many lung TRM were generated with MVAOVA ss compared to direct pulmonary immunization with MVAOVA, and both routes vaccination protected mice against lethal pulmonary challenge with VACVOVA. Strikingly, MVAOVA ss-generated effector T cells exhibited overlapping gene transcriptional profiles to those generated via direct pulmonary immunization. Overall, our data suggest that heterologous MVA vectors delivered via ss are uniquely well-suited as vaccine vectors for respiratory pathogens like COVID-19. In addition, MVA delivered via ss could represent a more effective dose-sparing smallpox vaccine.

overall_design:
OT-I naïve T cells, activated OT-I cells, central meory T cells, effector memory T cells were sorted out from mice at different timepoints post 1.8X10-6 MVA infection via indicated infection routes
OT-I cells from 15-20 mice were pooled together for each microarray dataset
By comparing the gene expression profile among different T cell subtypes, we aimed to identify core regulatory genes differentially expressed in T cell subtypes activated via distinct infection routes (skin scarification, intradermal, subcutaneous, intramuscular, intratracheal,intraperitoneal)

first: Youdong

last: Pan


title: Transcriptome profiling of Brassica rapa subsp. pekinensis treated with immunity elicitors

city: Seoul

first: Cecile

last: Segonzac

address: 1 Gwanak-ro, Gwanak-gu

department: Department of Plant Science

country: South Korea

institute: Seoul National University

summary: Plant leaf discs were treated with plant immunity elicitors (chitin or flg22) or water for 30 or 180 minutes

overall_design: Leaf discs from 17-day-old B. rapa plants grown on soil in short day conditions were treated with water or water solution of chitin (100µg/mL) or flg22 (100nM) for 30 or 180 minutes. mRNA expression profiles were generated in three biological replicates. Sequencing was performed with Illumina NovaSeq 6000 sequencing platform.

first: Wanhui

last: Kim

first: Maxim

last: Prokchorchik


title: RNA sequencing data of aging zebrafish brain progenitor cells

city: ANKARA

first: Ayca

last: Arslan Ergul

state: ÇANKAYA

address: Bilkent Üniversitesi UNAM

department: UNAM

country: Turkey

institute: Bilkent University

summary: Our aim in this study was to investigate the gene expression changes through pre-adult to adult, and adult to old age, in zebrafish brains. We isolated the neuronal cells and performed RNA sequencing in 3 months old, 6-8.5 months old, and 26-31 months old zebrafish brains. The cells were enriched in progenitor cell markers, which diminished throughout the aging process.

overall_design: Transcriptome profiling of brain progenitor cells from 3, 8, and 30 mo-old zebrafish

last: Arslan-Ergul

first: Ozge

middle: P

last: Burhan

first: Aydan

last: Sarac


title: Multiple freeze-thaw cycles lead to a loss of consistency in poly(A)-enriched RNA sequencing

status: Public on May 09 2020

city: La Jolla

first: Nathan

last: Lewis

state: CA

address: 9500 Gilman Dr. MC 0760 BRF2 4a16

department: Pediatrics

institute: UC San Diego

summary: RNA-Seq is ubiquitous, but depending on the study, sub-optimal sample handling may be required, resulting in repeated freeze-thaw cycles. However, little is known about how each cycle impacts downstream analyses, due to a lack of study and known limitations in common RNA quality metrics, e.g., RIN, at quantifying RNA degradation following repeated freeze-thaws. Here we quantify the impact of repeated freeze-thaw on the reliability of downstream RNA-Seq analysis. To do so, we developed a method to estimate the relative noise between technical replicates independently of RIN. Using this approach we inferred the effect of both RIN and the number of freeze-thaw cycles on sample noise. We find that RIN is unable to fully account for the change in sample noise due to freeze-thaw cycles. Additionally, freeze-thaw is detrimental to sample quality and differential expression (DE) reproducibility, approaching zero after three cycles for poly(A)-enriched samples, wherein the inherent 3’ bias in read coverage is more exacerbated by freeze-thaw cycles, while ribosome-depleted samples are less affected by freeze-thaws. The use of poly(A)-enrichment for RNA sequencing is pervasive in library preparation of frozen tissue, and thus, it is important during experimental design and data analysis to consider the impact of repeated freeze-thaw cycles on reproducibility.

overall_design: For 47 samples (from 16 individuals)--and an additional 9 industry standards--, mRNA was extracted using polyA selection with the TruSeq Stranded mRNA library preparation kit (Illumina). Ribosomal depletion was used to prepare an additional 52 samples. Ribosome depletion prepared samples used the TruSeq Stranded Total RNA with RiboZero Gold library preparation kit (Illumina). RNA Integrity Numbers (RIN) were measured using a NanoDrop ND-1000 (ThermoFisher). Poly-A selected samples were sequenced using 50-base pair single end sequencing on a HiSeq4000 (Illumina) to a depth of 25M reads. The ribo-depletion prepared libraries were sequenced using 100-base pair paired end sequencing on a HiSeq4000 (Illumina) to a depth of 50M reads.  Fastq files for each sample underwent quality control using FastQC (v0.33). PolyA and adaptor-trimming were conducted using Trimmomatic. Reads were aligned to the gencode annotated (v25) human reference genome (GRCh38) using STAR (v2.4.0). Alignments were processed to sorted SAM files using SAMtools (v1.7). Finally, HTSeq using default settings (v0.6.1) was used to quantify reads.

middle: E


title: Loss of furin in β cells induces an mTORC1-ATF4 anabolic pathway that leads to β cell dysfunction

status: Public on May 12 2020

city: Leuven

first: John

last: Creemers

address: ON I Herestraat 49 - box 607

department: Department of Human Genetics

country: Belgium

institute: KU Leuven

summary:
ABSTRACT: Furin is a proprotein convertase (PC) responsible for proteolytic activation of a wide array of precursor proteins within the secretory pathway. It maps to the PRC1 locus, a type 2 diabetes susceptibility locus, yet its specific role in pancreatic β cells is largely unknown. The aim of this study was to determine the role of furin in glucose homeostasis. We show that furin is highly expressed in human islets, while PCs that potentially could provide redundancy are expressed at considerably lower levels. β cell-specific furin knockout (βfurKO) mice are glucose intolerant, due to smaller islets with lower insulin content and abnormal dense core secretory granule morphology. RNA expression analysis and differential proteomics on βfurKO islets revealed activation of Activating Transcription Factor 4 (ATF4), which was mediated by mammalian target of rapamycin C1 (mTORC1). βfurKO cells show impaired cleavage of the accessory V-ATPase subunit Ac45, and by blocking this pump in β cells the mTORC1 pathway is activated. Furthermore, βfurKO cells show lack of insulin receptor cleavage and impaired response to insulin. Taken together, these results suggest a model of mTORC1-ATF4 hyperactivation in β cells lacking furin, which causes β cell dysfunction.
METHOD: Data obtained for the β cell specific knockout (RIP-Cre+/- furin flox/flox) and control (furin flox/flox) samples were compared to investigate the effect of furin loss on the mRNA profile of islets. Although this method does not directly provide furin targets, the notion of differential gene expression might elucidate affected cellular processes, potentially leading to upstream furin substrates.

overall_design: Islets were isolated from male RIP-Cre+/- furin flox/flox and furin flox/flox mice for RNA extraction and hybridization on Affymetrix microarrays. Four biological replicates were used per genotype.

first: Bas

last: Brouwers

first: Leentje

last: Van Lommel

first: Frans

last: Schuit


title: Statins affect gene expression in pancreatic cancer

status: Public on Apr 30 2020

city: Kunming

first: Hongjin

last: Wu

state: China / Yunnan

address: Xichang Road#295

institute: The NHC Key Laboratory of Drug Addiction Medicine

summary: The statin family of cholesterol-lowering drugs was shown to influence the risk of multiple types of cancers. However, the anti-tumor effects of statins in pancreatic cancer and their efficacy differs among the individual statins, are not currently well-defined. Thus, the aim of the present study was to identify the biological pathways affected by individual statins in human pancreatic cancer. The study was performed on human pancreatic cancer cell linesMiaPaCa-2 and PANC-1, exposed to three statins (Lovastatin, Fluvastatin and Simvastatin). mRNA-seq were performed (Sequenced with PE150, and 20M reads were generated.)

overall_design: RNA-seq analysis was performed to determine alterations in the gene expression of low (2μM) and high concentration statins (20μM) treated cancer cells.

first: Juehua

last: Yu


title: Unilateral ureteral obstruction in IL-33-deficient and wild type C57/BL6 mice

status: Public on May 06 2020

city: Oslo

first: Guttorm

last: Haraldsen

address: Sognsvannsveien 20

department: Pathology

country: Norway

institute: Oslo University Hospital

summary: Interleukin (IL)-33 is a cytokine that appears to mediate fibrosis by signaling via its receptor ST2 (IL-33R/IL1RL1). It is also, however, a protein that after synthesis is sorted to the cell nucleus, where it appears to affect chromatin folding. Here we describe a novel role for nuclear IL-33 in regulating the fibroblast phenotype in murine kidney fibrosis driven by unilateral ureteral obstruction. Transcriptional profiling of IL-33-deficient kidneys 24h after ligation revealed enhanced expression of fibrogenic genes and enrichment of gene sets involved in extracellular matrix formation and remodeling. These changes relied on intracellular effects of IL-33, because they were not reproduced by treatment with a neutralizing antibody to IL-33 that prevents IL-33R/ST2L receptor signaling nor were they observed in IL33R/ST2-deficient kidneys. To further explore the intracellular function of IL-33, we established transcription profiles of human fibroblasts, observing that knockdown of IL-33 skewed the transcription profile from an inflammatory towards a myofibroblast phenotype, reflected in higher levels of COL3A1, COL5A1 and transgelin protein, as well as lower expression levels of IL6, CXCL8, CLL7 and CCL8. In conclusion, our findings suggest that nuclear IL-33 in fibroblasts dampens the initial profibrotic response until persistent stimuli, as enforced by UUO, can override this protective mechanism.

overall_design: Expression profiling of WT and IL-33 KO deficient kidney from animals treated with UUO or without treatment.


title: MiR-378a-3p is critical for Burkitt lymphoma cell growth

status: Public on Jun 30 2020

city: Groningen

first: Fubiao

last: Niu

address: Hanzeplein 1

department: Pathology and Medical Biology

institute: University Medical Center of Groningen

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

summary: To gain further knowledge on the role of microRNAs (miRNAs) in the pathogenesis of Burkitt lymphoma (BL), we performed small RNA sequencing in BL cell lines and normal germinal center B (GC-B) cells. This revealed 26 miRNAs with significantly different expression levels. Altered levels were validated by qRT-PCR for six of eight selected miRNAs. For five miRNAs, the differential expression pattern was confirmed in BL primary tissues compared to GC-B cells. Inhibition of miR-378a-3p reduced the growth of multiple BL cell lines. RNA immunoprecipitation of Argonaute 2 followed by microarray analysis (Ago2-RIP-Chip) upon inhibition and ectopic overexpression of miR-378a-3p revealed 63 and 20 putative miR-378a-3p targets, respectively. These included 28 genes with a putative miR-378a-3p binding site. Effective targeting by miR-378a-3p was confirmed by luciferase reporter assays for four out of eight selected genes: MNT, FOXP1, IRAK4, and lncRNA JPX, all of which have been implicated in proliferation and cancer. In summary, our study identified several differentially expressed miRNAs in BL. We identified miR-378a-3p as a miRNA with an oncogenic role in BL and revealed 4 novel miR-378a-3p target genes, i.e. MNT, FOXP1, IRAK4, and JPX.

overall_design: Identification of miRNA targets (mRNAs and lncRNAs) in Burkitt lymphoma cell lines

first: Agnieszka

last: Dzikiewicz-Krawczyk

first: Jasper

last: Koerts

first: Debora

last: de Jong

first: Laura

last: Wijenberg

first: Margot

last: Fernandez Hernandez

first: Izabella

last: Slezak-Prochazka

first: Melanie

last: Winkle

first: Wierd

last: Kooistra

first: Tineke

last: van der Sluis

first: Bea

last: Rutgers

first: Miente

last: Martijn Terpstra

first: Klaas

last: Kok

first: Joos

last: t Kluiver

first: Anke

last: van den Berg


title: RNA-seq of GAP43 overexpressed and control SW620 cancer cells

status: Public on May 01 2020

first: Hongjin

last: Wu

summary: We found GAP43 was significantly downregulated in colorectal cancer. So we reintroduced GAP43 to colorectal cancer cell line, and investigated the influence to cancer cells. In order to get the transcriptome-wide impact of GAP43 overexpression in colorectal cancer, we made stable transfected GAP43 in SW620 cancer cells, and mRNA-seq were performed (Sequenced with PE150, and 20M reads were generated.) This study provides the DEGs of GAP43 overexpressed and control colorectal cancer cells.

overall_design: Changes in mRNA expression caused by GAP43 overexpression in colorectal cancer cell lines were examined.

first: Ming

last: Shi


title: Interleukin-33 in experimental kidney fibrosis

first: Guttorm

last: Haraldsen

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: Neuroinflammation and EIF2 signaling persist despite antiretroviral treatment in an HiPSC tri-culture model of HIV infection

status: Public on Apr 27 2020

city: Philadelphia

first: James

last: Garifallou

address: 3615 Civic Center Boulevard, ARC1014

department: Neonatology

institute: Children's Hospital of Philadelphia


title: Neuroinflammation and EIF2 signaling persist despite antiretroviral treatment in an HiPSC tri-culture model of HIV infection [bulk RNA-seq]

summary: HIV-Associated Neurocognitive Disorders (HAND) affect over half of HIV-infected  individuals, despite antiretroviral therapy (ART). Therapeutically targetable  mechanisms underlying HAND remain elusive, partly due to a lack of a proper model.  We developed a human-induced pluripotent stem cell (HiPSC) based model,  independently differentiating HiPSCs into neurons, astrocytes, and microglia, and  systematically combining to generate a tri-culture with or without HIV-infection and  ART. Single cell RNAseq analysis on tri-cultures with HIV-infected microglia revealed  inflammatory signatures in the microglia and EIF2 signaling in all three cell types.  Treatment with the antiretroviral compound EFZ mostly resolved these signatures.  However, EFZ increased RhoGDI and CD40 signaling in the HIV-infected microglia.  This activation was associated with a persistent increase in TNFa production by  microglia. This work establishes a tri-culture that recapitulates key features of HIV  infection in the CNS and provides a new model to examine the effects of infection, its  treatment, and other co-morbid conditions.

overall_design: 16 Bulk RNAseq samples were analyzed across 5 treatment groups for differential expression analysis where "WT" samples made up the untrt group, "WT_HIV" samples made up the trt1 group, "MDM" samples made up the trt2 group, "HA" samples made up the trt3 group, and "SC/iAST" samples made up the trt4 group.

first: Sean

last: Ryan

first: Michael

last: Gonzalez

first: Frederick

middle: C

last: Bennett

first: Kimberly

last: Williams

first: Hakon

last: Hakonarson

first: Stewart

last: Anderson

first: Kelly

last: Jordan-Sciutto


title: Transcription of photosynthetic genes in AAP5 during growth on solid and liquid media

status: Public on Jun 01 2020

city: Trebon

first: Karel

last: Kopejtka

address: Novohradska

department: Centre Algatech

institute: Institute of Microbiology Czech Acad. Sci.

summary: Comparison of cells grown for 4 and 8 days on agar plates with cells from liquid cultures after reaching their maximum optical density.

overall_design: Cells were incubated aerobically either in liquid medium or on agar plates under 12-h dark/12-h light regime and harvested 4 hours after the transition to dark.

first: Jürgen

last: Tomasch

first: Yonghui

last: Zeng

first: Vadim

last: Selyanin

first: Marko

last: Dachev

first: Kasia

last: Piwosz

first: Martin

last: Tichý

first: Boyke

last: Bunk

first: Henner

last: Brinkmann

first: Zdenko

last: Gardian

first: Robert

last: Geffers

last: Reck

first: Ruben

last: Sommaruga

first: Michal

last: Koblížek


title: Expression data from adult transgenic zebrafish

status: Public on Apr 12 2020

city: Zhunan Town

first: Chiou-Hwa

last: Yuh

state: Miaoli County

address: #35 Keyan Road

country: Taiwan

institute: National Health Research Institutes

summary:
Hepatocellular carcinoma is the fourth leading cause of cancer-related deaths worldwide. Many carcinogens induce inflammation and cirrhosis, and eventually develop into liver cancer. Fucoidan is sulfated polysaccharide that is mainly found in brown seaweeds. In this study, we investigated the effects and mechanisms of low molecular weight fucoidan (i.e. oligo-fucoidan) preventing hepatocarcinogenesis using HBx,Src, and HBx,Src,p53-/+ transgenic zebrafish liver cancer model.
Using an oligo-fucoidan oral gavage in adult transgenic zebrafish, we then used microarrays to detail the global programme of gene expression after fucoidan treatment and identified distinct classes of up- and down-regulated genes during this process.

overall_design: Three-month-old female HBx,Src and HBx,Src,p53–/+ transgenic zebrafish were allocated to 2 different diets: normal diet (NOR) and diet-induced obesity (DIO). The amount of Artemia fed to the NOR and DIO groups was approximately 6.9 mg and 83 mg cysts/fish/day respectively. OF (300 mg/kg) was administrated by oral gavage for one month starting at 4 months of age, totally 2 months dietary induction. The fish were sacrificed and the hepatic tissue was immediately frozen in liquid nitrogen and stored at −80 °C for later RNA extraction and hybridization on Affymetrix microarrays.

first: Szu-Yuan

last: Wu

first: Wan-Yu

last: Yang

first: Chun-Chia

last: Cheng

first: Ming-Chen

last: Hsiao

first: Kuan-Hao

last: Lin


title: Neuroinflammation and EIF2 signaling persist despite antiretroviral treatment in an HiPSC tri-culture model of HIV infection [scRNA-seq]

first: James

last: Garifallou

overall_design: Five samples each consisting of a Tri-culture of differentiated HiPSC into neurons, astrocytes, and microglia were analyzed for this scRNAseq analysis using the 10x Genomics Single Cell platform. Each tri-culture sample was either infected with HIV or uninfected in addition to either being treated with anti-retroviral or untreated.

first: Sean

last: Ryan

first: Michael

last: Gonzalez

first: Frederick

last: Bennett

first: Kimberly

last: Williams

first: Hakon

last: Hakonarson

first: Stewart

last: Anderson

first: Kelly

last: Jordan-Sciutto


title: Single cell transcriptomic analysis of endoderm derived cell lineages contribution in pituitary

status: Public on Apr 14 2020

city: Los Angeles

first: Gage

last: Crump

address: 1425 San Pablo St.

department: Stem Cell

institute: USC

summary: Single cell transcriptomic analysis of pituitary gland from adult zebrafish that had specifically cells labeled with endoderm lineage by different strategies. The goal of this study is to examine the contribution of endoderm derived cell in the pituitary of vertebrate animals.

overall_design: We applied two strategies for labeling the endoderm derived cell in the pituitaries of zebrafish. The contribution of endoderm derived cells and the cell heterogeneity was later analyzed and resolved through constructing the single cell transcriptome through 10X Genomic pipeline.   The first strategy is through endodermal lineage tracing techniques by Sox17 driven Cre recombinase conjuncted with an estrogen receptor (Sox17:CreERT2), which allows us to induce the conversion by addition of tamoxifen. We are able to identify the endoderm derived cell by microscopic observation with expression of mCherry gene from EGFP background. We made two single cell transcriptomic libraries by this strategy: the males library (file names started with M_Pituitary_Sox17creERUbiGtR) was derived by pooling 6 adult zebrafish pituitaries with moderate Sox17:CreERT2 conversion rate. The male1 library (file names started with M1_Pituitary_Sox17creERUbiGtR) was derived from the pituitary from a male zebrafish with high conversion rate.  The second strategy is through transplant of taram-a mRNA injected GFP+ embryo to limit the cell into endoderm lineage. The treated embryonic cells were then injected into a BFP+ wild type embryo for tracing. The endoderm derived cells can be identify by expression of GFP. We made one single cell transcriptomic library by this strategy: the ubeGFP_transplanted (file names started with ubieGFP_Pit-Endo-transp) library was derived from pooling of pituitaries from adult transplanted fish.

first: Peter

last: Fabian

first: Kuo-Chang

last: Tseng


title: Gene Expression Analysis of the response to ACC inhibition

status: Public on Apr 24 2020

city: Foster City

first: Ricardo

last: Ramirez

address: 333 Lakeside Drive

institute: Gilead Sciences, Inc.

summary: BACKGROUND & AIMS: Nonalcoholic steatohepatitis (NASH) is a chronic liver disease characterized by hepatic lipid accumulation, inflammation, and progressive fibrosis. Acetyl-CoA carboxylase (ACC) catalyzes the rate-limiting step of de novo lipogenesis and regulates fatty-acid beta-oxidation in hepatocytes. ACC inhibition reduces hepatic fat content and markers of liver injury in NASH patients; however, the effect of ACC inhibition on liver fibrosis has not been reported. METHODS: A direct role for ACC in fibrosis was evaluated by measuring de novo lipogenesis, procollagen production, gene expression, glycolysis, and mitochondrial respiration in hepatic stellate cells (HSCs) in the absence or presence of small-molecule inhibitors of ACC. ACC inhibitors were evaluated in rodent models of liver fibrosis induced by diet or the hepatotoxin, DEN. Fibrosis and hepatic steatosis were evaluated by histological and biochemical assessments. RESULTS: In TGF-beta-stimulated HSCs, ACC inhibition reduced activation and collagen production independent of mitochondrial beta-oxidation by blocking de novo lipogenesis. ACC inhibition prevented a metabolic switch necessary for induction of glycolysis and oxidative phosphorylation during HSC activation. Consistent with this direct anti-fibrotic mechanism in HSCs, ACC inhibition reduced liver fibrosis in a rat CDHFD model and in response to chronic DEN-induced liver injury that lacked hepatic lipid accumulation. CONCLUSIONS: In addition to reducing lipid accumulation in hepatocytes, ACC inhibition also directly impairs the pro-fibrogenic activity of HSCs. Small molecule inhibitors of ACC may reduce liver fibrosis by both reducing lipotoxicity in hepatocytes and directly reducing HSC activation, providing a mechanistic rationale for the treatment of patients with advanced liver fibrosis due to NASH.

overall_design:
Liver samples from mice fed a normal diet or fed an FFD and treated with vehicle or an ACC inhibitor.
Primary hepatic stellate cells from three donors treated with an ACC inhibitor, TGF beta, and/or a TGF inhibitor.

first: Jamie

last: Bates

first: Archana

last: Vijayakumar

first: Kathy

last: Liu

first: Li

last: Li

first: David

last: Lopez


title: Knockdown of interleukin-33 in human fibroblasts

first: Guttorm

last: Haraldsen

overall_design: Human IL-33 (#4392422) and Silencer Select Negative Control No. 2 siRNA (#4390846) were purchased from Thermo Fisher Scientific (Oslo, Norway). Fibroblasts were transfected with 30 nM siRNA using Lipofectamine RNAimax (Invitrogen, Oslo) in Opti-MEM for 12 hours followed by a change to serum free fibroblast growth medium, containing IFN-γ (100 ng/ml) and TGF-β (2ng/ml) for another 12 hours before harvest and RNA extraction.


title: Next-Generation Sequencing Revealed L-Carnitine Rescues Congenital Myopathy in Transgenic Zebrafish with Tropomyosin 3 Novel Mutation

first: Chiou-Hwa

last: Yuh

summary:
Purpose: Congenital myopathies (CM) are a group of clinically and genetically heterogeneous muscle disorders, characterized by muscle weakness and hypotonia from birth. Currently, no definite treatment exists for CM. A novel and de novo mutation in tropomyosin 3 [TPM3(E151G)] was identified from a 7-year-old boy with clinically diagnosed CM. TPM3(E151A) mutation was previously reported as causing CM. In this study, we created transgenic zebrafish to investigate the pathogenicity and find potential treatment. The goals of this study are to describe the RNA contents in muscle specimens derived from TPM3(WT), TPM3(E151A), TPM3(E152G) at embryos and adult stages and to compare the differences TPM3(E151A), TPM3(E151G) mutants and TPM3(WT). The biological function of L-carnitine treatment TPM3(E151G) versus without treatment are also predicted and evaluated.
Methods: Muscle mRNA profiles of 6 months adult zebrafish from TPM3(WT), TPM3(E151A) and TPM3(E151G) were extracted and performed deep sequencing, in duplicate, using Illumina Novaseq6000. We also obtained the muscle mRNA profiles of 2 day's zebrafish embryos from TPM3(WT), TPM3(E151A), TPM3(E151G) and TPM3(E151G) treated with L-carnitine. RNA profiles of adult and embryos were generated by deep sequencing, using Illumina NovaSeq 6000.
Results: After acquiring of clean reads, we mapped about 40 million sequence reads per sample to the zebrafish genome (GRCz11). Saturation rate analysis was then performed evaluating the gene coverage rate along with read depth increase. The transcripts mapping to difference functional region of the genome was then analyzed. Circos software was used to map the consistency of samples with zebrafish genome on a chromosomal level. The quantification of transcript intensity was analyzed using Fragments Per Kilobase of exon modelper Million mapped fragments (FPKM).
Conclusions: Our study represents the first detailed analysis of zebrafish muscle transcriptomes, with biologic replicates, generated by RNA-seq technology. The optimized data analysis workflows reported here should provide a framework for comparative investigations of expression profiles between TPM3(WT), TPM3(E151A) and TPM3(E151G) and L-carnitine treatment. Our results show that NGS offers a comprehensive and more accurate quantitative and qualitative evaluation of mRNA content within a cell or tissue. We conclude that RNA-seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions.

overall_design: Next-generation sequencing experiment was performed by NHRI Genomics Core Facility. Sequencing libraries 1 µg total RNA were generated using RNA HyperPrep kit with RiboErase (KAPA Biosystems, Pleasanton, CA, USA), and sequenced on NovaSeq 6000 instrument (Illumina, San Diego, CA, USA). All RNA sample preparation procedures were carried out according to the Illumina's official protocol.


title: Multiplexed characterization of rationally designed promoter architectures deconstructs combinatorial logic for IPTG-inducible systems

status: Public on Apr 01 2020

first: Guillaume

last: Urtecho

address: 607 Charles E. Young Drive

department: Molecular Biology

institute: University of California, Los Angeles

summary: We report the synthesis and expression measurement of ~9000 inducible promoter variants. By tagging individual variants with barcodes, we can measure the expression levels of all variants under both induced and uninduced conditions in a single pooled experiment. Sequencing data here is used for 1) paired-end sequencing to map barcodes to their promoters or 2) Quantifying the counts of barcodes at the DNA and RNA levels

overall_design: Expression measurement of ~9000 inducible promoter variants under 2 IPTG conditions in E. coli

first: Timothy

last: Yu


title: Laser wounded vs unwounded syncytium Drosophila embryos

status: Public on Apr 06 2020

city: Seattle

first: Susan

middle: M

last: Parkhurst

state: WA

address: 1100 Fairview Ave N; A1-162

department: Division of Basic Sciences

institute: Fred Hutchinson Cancer Research Center

summary: Transcriptional profiling of laser wounded syncytial Drosophila embryos compared with control unwounded embryos. Early Drosophila embryos (Nuclear cycle 4-6) were collected, either laser wounded or not wounded, and then collected and processed immediately. Wounded and unwounded embryos express sGMCA (actin reporter)

overall_design: Two-condition experiment, laser wounded vs unwounded. Each experiment was done independently, with four samples. One replicate per array. One experiment correspond to the dye swap.

first: Maria

middle: T

last: Abreu-Blanco

first: Raymond

first: Jeffrey

middle: J

last: Delrow


title: Laser wounded vs unwounded syncytium Drosophila embryos study


title: 30 minutes post-laser wounded vs unwounded syncytium Drosophila embryos

summary: Transcriptional profiling of laser wounded syncytial Drosophila embryos compared with control unwounded embryos. Early Drosophila embryos (Nuclear cycle 4-6) were either laser wounded or not wounded, and then collected and processed after 30 minutes. Wounded and unwounded embryos express sGMCA (actin reporter).

overall_design: Two-condition experiment, laser wounded vs unwounded. Each experiment was done independently, with three samples. One replicate per array.


title: Type II lung cells in young mice exposed to differing levels of oxygen

status: Public on Mar 31 2020

city: Rochester

first: Andrew

last: McDavid

address: 265 Crittenden Boulevard, CU 420630

institute: University of Rochester

summary: Alveolar epithelial type 2 (AT2) cells are an adult lung stem cell. Oxidative stress, mitogens, and cytokines affect their proliferation through poorly understood mechanisms. We previously showed in mice how neonatal hyperoxia between postnatal days (PND) 0-4 accelerates AT2 proliferation that normally takes place on PND7. Here, RNA-seq analysis of revealed neonatal hyperoxia stimulates expression of the mitochondrial-specific methylenetetrahydrofolate dehydrogenase (Mthfd) 2 and other genes involved in serine synthesis and one carbon-coupled folate metabolism. While MTHFD2 is important for embryonic development and proliferation of cancer cells, it is non-essential after birth. However, Mthf2 mRNA and other enzymes in serine and folate metabolism were highly expressed when AT2 cells proliferate on PND7. They were nearly undetectable in adult AT2 cells, but re-expressed when AT2 cells proliferated in response to fibroblast growth factor (FGF) 7 or during alveolar regeneration. Suppressing Mthfd2 or phosphoglycerate dehydrogenase (Phgdh) used to generate serine blocked FGF7-dependent proliferation of AT2 cells.

overall_design: Examination of type II cells in mice exposed to 100% oxygen or room air at E18.5 and PND4 ages. PND4 replicates represent individual mice, while E18.5 samples are derived from pools of mice.

first: Michael

last: O'Reilly


title: Single cell Chromatin Accessibility profiling of forelimb bud at stage E11.5 in WT and Hox13 mutant (10x Chromium)

status: Public on Mar 26 2020

city: Montreal

first: Marie

last: Kmita

state: QC

address: 9730 Avenue de Lorimier

country: Canada

institute: IRCM (institut de Recherche Clinique de Montreal)

overall_design: Exploring the effect of HOX13's on chromatin landscape in the developping limb

first: Ines

last: Desanlis

first: Yacine

last: Kherdjemil

first: Alexandre

last: Mayran

first: Yasser

last: Bouklouch

first: Claudia

last: Gentile

first: Rushikesh

last: Sheth

first: Rolf

last: Zeller

first: Jacques

last: Drouin


title: Global transcriptome of Helianthus annuus, Beta vulgaris, Ricinus communis and Phaseolus vulgaris healthy plants and plant infected by the fungal pathogen Sclerotinia sclerotiorum (strain 1980)

status: Public on Apr 15 2020

city: Castanet tolosan

first: Sylvain

last: Raffaele

address: 28 chemin de borde rouge

country: France

institute: INRAE

summary: Quantitative disease resistance (QDR) is a form of plant immunity conserved across species able to limit infections caused by a broad range of pathogens. QDR has a complex genetic determinism, the bases of which are not fully understood. The number of genes contributing to the QDR response and the extent to which molecular components of the QDR response vary across plant species remain elusive. The fungal pathogen Sclerotinia sclerotiorum, causal agent of white mold disease on hundreds of plant species, triggers QDR responses in host populations. To document the diversity of plant responses to S. sclerotiorum at the molecular level, we analyzed the complete transcriptome of six plant species spanning the Pentapetalae group inoculated by the same strain of S. sclerotiorum.  We identified 48,910 genes differentially expressed (DEGs) upon infection across six species, enriched in 286 gene ontologies and 148 PFAM domains. DEGs represented ~32% of the plant genome, with an excess of down-regulated over up-regulated genes in all species. DEGs were enriched among orthologous gene groups conserved in all six species (core) compared to other orthologous groups and lineage-specific groups. Although 86.9% of core orthogroups included DEGs, only 5.5% included DEGs from all six species, revealing a high degree of regulatory divergence at the interspecific level. Focusing on a group of ABCG/PDR transporters with up-regulated members in all species, we propose that an ancestral function of AtPDR12 in acclimation to abiotic stress was exapted into QDR against S. sclerotiorum through reinforcement of pathogen responsiveness at the transcriptional level. Our results suggest that exaptation by cis-regulatory divergence contributed to the evolution of QDR and support an infinitesimal model of QDR determinism. It provides resources for functional studies on gene regulation and QDR molecular bases across the Pentapetalae clade.

sample_organism:
Beta vulgaris subsp. vulgaris
Phaseolus vulgaris
Ricinus communis
Helianthus annuus

overall_design: Periphery of S. sclerotiorum disease lesions (Ss) and uninfected plants grown together (control), Ss and control samples collected simultaneously in three independent replicates

first: Malick

last: Mbengue


title: Genome-wide study of ONAC127 and ONAC129 regulatory network in rice caryopsis

city: Wuhan

first: Ye

last: Ren

state: Hubei

address: NO.1, Shizishan

department: College of Life Science and Technology

country: China

institute: Huazhong Agriculture University

summary: ONAC127 and ONAC129 are NAC transcription factors that involved in abiotic stress response and play key regulatory roles in apoplasmic transportation during rice caryopsis filling. To reveal the transcription regulatory network of ONAC127 and ONAC129 in rice caryopsis, we performed genome-wide identification of ONAC127 and ONAC129 targets by immunoprecipitation sequencing (ChIP-seq) analyses in the overexpression lines of ONAC127 and ONAC129 under natural heat stress(H) and normal cultivation condition(N) with three technical replicates.

overall_design: Genome-wide identification binding sites of ONAC127 and ONAC129 in the caryopsis of overexpression lines under natural heat stress and normal cultivation condition. Examination of 7 days after pollination (DAP) rice caryopsis of ONAC127-FLAG (OX127) and ONAC129-FLAG (OX129)  with FLAG antibody.

first: Hao

last: Jiang

first: Jialing

last: Yao


title: HOX13-dependent chromatin accessibility underlies the transition towards the digit development program

status: Public on Mar 25 2020

city: LAUSANNE

first: ALEXANDRE

last: MAYRAN

state: Waadt

address: Station 19

institute: EPFL


title: HOX13-dependent chromatin accessibility underlies the transition towards the digit development program[ChIP-seq]

summary: Pioneer factors are transcription factors able to recognize their target site even concealed in “closed” chromatin, eventually eliciting the switch to accessible targets for other transcription factors and the transcriptional machinery. As such, pioneer factors play a key role in switching cell fate. Here, we provide evidence that HOXA13 and HOXD13 (HOX13 hereafter), two transcription factors of the Hox family of developmental genes, act as pioneer factors in the developing limb. We show that Hox13 function is mandatory for switching a series of target loci to an accessible chromatin state, allowing the binding of other transcription factors. These target loci include an enhancer previously identified as essential for the pentadactyl state, providing evidence that the pioneer activity of HOX13 is key for digit patterning. Based on the data reported here and previous studies, we propose that, during the fin-to-limb transition, the implementation of digit-specific enhancer elements had required an ancestral pioneer function of the HOX13 TFs.

overall_design: ChIP-seq:  e11.5 mouse forelimb WT HOXA11, e11.5 mouse forelimb RA11KI HOXA11.


title: Skeletal Muscle Transcriptomics

status: Public on Apr 07 2020

city: Baltimore

first: Supriyo

last: De

state: Maryland

address: 251 Bayview Blvd

department: Laboratory of Genetics and Genomics

institute: NIA-IRP, NIH

summary: Healthy human skeletal muscle samples were processed and analyzed to infer age associated skeletal muscle changes.

overall_design: Total RNA-seq of human skeletal muscle biopsies across different ages

first: Ceereena

last: Ubaida-Mohien

first: William

middle: H

last: Wood

first: Yulan

last: Piao

first: Myriam

last: Gorospe

first: Luigi

last: Ferrucci


title: ONAC127 and ONAC129 regulatory network

overall_design: Refer to individual Series


title: Single-cell RNA sequencing reveals compromised immune microenvironment in precursor stages of multiple myeloma

status: Public on Apr 28 2020

city: Boston

first: Irene

last: Ghobrial

address: 4 Blackfan Circle, 2nd Floor, Suite 240

department: Medical Oncology

institute: Dana-Farber Cancer Institute

summary: Precursor states of Multiple Myeloma (MM) and its native tumor microenvironment need in-depth molecular characterization to better stratify and treat patients at risk. Using single-cell RNA sequencing of bone marrow cells from precursor stages, MGUS and smoldering myeloma (SMM), to full-blown MM alongside healthy donors, we demonstrate early immune changes during patient progression. We find NK cell abundance is frequently increased in early stages, and associated with altered chemokine receptor expression. As early as SMM, we show loss of GrK+ memory cytotoxic T-cells, and show their critical role in MM immunosurveillance in mouse models. Finally, we report MHC class II dysregulation in CD14+ monocytes, which results in T cell suppression in vitro. These results provide a comprehensive map of immune changes at play over the evolution of pre-malignant MM, which will help develop strategies for immune-based patient stratification.

overall_design:
We employed single-cell RNA sequencing on 40.8K immune microenvironmental cells using 32 bone marrow samples from a cohort of 22 patients with varying stages of Multiple Myeloma progression and 9 healthy donors.

>>>Submitter states that raw data will be submitted to dbGaP due to patient privacy concerns<<<

first: Gad

last: Getz


title: RNA-seq of Chlorella sp. HS2: Comparison between freshwater and marine conditions at exponential and stationary growth phases

status: Public on Mar 12 2020

city: Marseille Cedex 9

first: Michaël

last: Pierrelée

address: Case 907 - Parc Scientifique de Luminy

institute: Aix-Marseille University, CNRS, IBDM

summary: Chlorella sp. HS2 is a halotolerant microalga exhibiting relatively high biomass productivity and substantially high lipid accumulation in marine growth media, which suggests this alga as an important crop for industrial algal cultivation systems. To determine pathways leading to HS2's acclimation responses to salt stress, we performed RNA-seq analysis with triplicated cultures grown in freshwater and marine media at both exponential and stationary growth phases. We then run de novo assembly to obtain HS2 transcriptome, which in turn was annotated and processed to extract dysregulated pathways. Results showed a large proportion of down-regulated genes, for instance photosynthesis and TCA pathways. Photosynthesis appeared, however, to recover at the stationary phase, while the general down-regulation pattern was maintained.

overall_design: Algal cultures grown in marine medium (3% (w/v) of supplemental sea salt) was compared to the cultures grown in freshwater medium, at the exponential growth phase (4 days after the beginning of the cultivation) and then at the stationary growth phase (6 days). Each condition had 3 biological replicates, resulting in the total of 12 samples. Samples were sequenced by 100 bp paired-end Illumina HiSeq 2000 platform. We processed raw reads using Trinity for de novo assembly and RSEM for count quantification, to perform differential expression analysis of genes with SVCD for the count normalization and DESeq2 for the statistical test. Gene isoforms were annotated by the Trinotate pipeline (BlastX, TransDecoder and BlastP)

first: Jin-Ho

last: Yun

first: Dae-Hyun

last: Cho

first: Urim

last: Kim

first: J

last: Heo

first: Dong-Yun

last: Choi

first: Yong

last: Lee

first: Bongsoo

first: HyeRan

first: Bianca

last: Habermann

last: Chang

first: Hee-Sik


title: ZFAS1 promotes rRNA 2’O-methylationin by recruiting NOP58 contributes to colorectal cancer progression

status: Public on Mar 11 2020

city: shenyang

first: wu

last: huizhe

address: No.77, puhe avenue, shenbei new area

institute: Department of pharmacology, college of pharmacy, China medical university

summary: Increasing evidence suggested that small nucleolar RNAs (snoRNAs) and long non-coding RNAs (LncRNAs) were master regulators of gene regulation at epigenetic modification level, however, the underlying mechanism in colorectal cancer (CRC) have not been investigated. To demonstrate the involvement of LncRNA and snoRNAs in 2’-O-methylation (Me) in tumorigenesis, we develop the LncRNAs-snoRNAs microarray of paired CRC tissues, and found an unrecognized ZFAS1-NOP58- SNORD12C/78 signaling axis in CRC tumorigenesis through recognizing the consensus AAGA motif of ZFAS1 which directly binds to NOP58 protein, and accelerating the snoRNPs assemble for further guiding 2’-O-Me of 28S rRNA. Strikingly, overexpression SNORD12C/78 induces 2’-O-Me modification upon ZFAS1, and affects RNA stability and translation activity of their downstream targets (e.g., EIF4A3,LMAC2, etc.), thereby promoted CRC cell proliferation, invasion and inhibited apoptosis in vitro and in vivo. Thus, these results sheds new light on our understanding of lncRNAs-snoRNPs mediated rRNA 2'-O-methylations in CRC tumorigenesis.

overall_design: RNA expression profiles of 4 colorectal cancer tissues and 4 paracancer tissues

first: Huizhe

last: Wu

first: Wenyan

last: Qin

first: Senxu

last: Lu

first: Xiufang

last: Wang

first: Jing

last: Zhang

first: Qiuchen

last: Chen

first: Tong

last: Sun

first: Zhikun

first: Yalun

last: Li

first: Yuanhe

first: Xiaoyun

last: Hu

first: Haishan

last: Zhao

first: Jian

last: Ding

first: Minjie

last: Wei


title: Serum microRNA profiles and functional enrichment analysis in comorbidity between Arnold-Chiari and Tourette syndromes: insights into their related pathological pathways

status: Public on Mar 09 2020

city: Catania

first: Marco

last: Ragusa

address: Via Santa sofia 87

department: Biomedical and Biotechnological Sciences

country: Italy

institute: University of Catania

summary:
To identify the differential expression of serum microRNA as molecular fingerprints for Arnold-Chiari (AC) and Tourette syndromes (TS), also in comorbid status between both disorders (ACTS).
To investigate on differentially expressed miRNA associations with the neuropsychological and neuroimaging parameters for each participant and their potential involvement in AC and TS pathological pathways.

overall_design: This study profiled the miRNA expression in sera of 10 AC patients, 11 ACTS patients, 6 TS patients and 8 unaffected controls (NC)

first: Federica

last: Mirabella

first: Mariangela

last: Gulisano

first: Mara

last: Capelli

first: Giovanni

last: Lauretta

first: Matilde

last: Cirnigliaro

first: Stefano

last: Palmucci

first: Michele

last: Stella

first: Davide

last: Barbagallo

first: Cinzia

last: Di Pietro

last: Purrello

first: Renata

last: Rizzo


title: Next Generation Sequencing Facilitates Quantitative Analysis of ZH11 and ONAC127/ONAC129 transgenic plants Transcriptomes

first: Ye

last: Ren

summary: ONAC127 and ONAC129 are NAC transcription factors that involved in abiotic stress response and play key regulatory roles in apoplasmic transportation during rice caryopsis filling. To reveal the transcription regulatory network of ONAC127 and ONAC129 in rice caryopsis, we identified significantly differentially expressed genes by RNA-Seq analysis using the caryopses of the CRISPR-mutants(CR) and overexpression lines(OX) of ONAC127 and ONAC129 under natural heat stress(H) and normal cultivation condition(N).

overall_design: Total RNA was extracted from unripe caryopses at 7 DAP by TRIzol Regnant (Invitrogen). For each library, three independent replicated RNA samples were prepared. The RNA samples were then sequenced on the HiSeq 2000 platform

first: Hao

last: Jiang

first: Jialing

last: Yao


title: Synchrony and asynchrony between an epigenetic clock and developmental timing

first: Steve

last: Horvath

address: 695 Charles E. Young Drive South, Box 708822

department: Human Genetics

type: Methylation profiling by genome tiling array

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


title: Changes of Gene expression in Tartary Buckwheat (Fagopyrum tataricum) under Frozen stress [BS-Seq]

status: Public on Mar 08 2020

city: Lanzhou

first: Yuan

last: Song

address: the south of Tianshui road

institute: Lanzhou university

type: Methylation profiling by high throughput sequencing

summary: We performed a genome methylation analysis in Tartary Buckwheat (Fagopyrum tataricum) in different freezing treatments

overall_design: whole-genome bisulphite sequencing, WGBS linked bisulfite conversion and second generation sequencing technology.The DNA methylation status of the whole genome can be detected efficiently at the level of single base resolution.

first: Zhifeng

last: Jia


title: Changes of Gene expression in Tartary Buckwheat (Fagopyrum tataricum) under Frozen stress [RNA-Seq]

summary: We performed a transcriptomics analysis in Tartary Buckwheat (Fagopyrum tataricum) in different freezing treatments

overall_design: RNA-sequencing analysis was performed on an Illumina Hiseq2000/2500 (LC Sciences, USA) following the vendor's recommended protocol


title: Changes of Gene expression in Tartary Buckwheat (Fagopyrum tataricum) under Frozen stress


title: Expression data from microglial cell line BV-2

status: Public on Feb 12 2020

city: Tsukuba

first: Fuminori

last: Tsuruta

address: 1-1-1 Tennodai

country: Japan

institute: University of Tsukuba

summary:
Microglial morphology is tightly associated with aspects of their functions during the postnatal stage. It is affected by not only intrinsic cues but also external factors.
To pursue the novel factor that controls microglial morphology, we conducted microarray analysis using microglial cell line BV-2. We identified distinct candidates of both up-regulated and down-regulated genes from this experiment.

overall_design: Mice microglia cell lines, BV-2, were collected incubated with either DMEM or DMEM/F12 for RNA extraction and hybridization on Affymetrix microarray.

first: Tomomi

last: Okajima


title: Construction of Human Primary Epidermal Organoids and Modeling of Dermatophyte Infection

status: Public on Mar 01 2020

city: YiWu

first: wang

middle: chuan

last: wen

address: No. 288, Yang Cun road, Chou Jiang Street, Yiwu, Zhejiang

institute: AnnoGene

summary: Despite the strong need for the large-scale generation of human epidermal cells for cell therapy of extensive and severe skin injury, tissue-engineered skin construction and dermatological investigation, the effectiveness of current culture methods is limited and have yet to meet the huge demands sufficiently. Here, we report the establishment of a simple and robust 3D culture system using chemical defined, serum-free medium supplemented with small molecules and growth factors, tailored for human epidermal organoids generation and expansion. The conditions allowed 10,000-fold expansion of the primary epidermal cells within 6 weeks, with the cell architecture and gene expression preserved. We further noticed that only Integrin α6-positive basal stem cells freshly isolated from human epidermis could form expandable epidermal organoids. The epidermal cells inside of the organoids also have the potential to reconstruct multi-layered human epidermis equivalents under classical air-liquid interface condition. Remarkably, the epidermal organoids enable to model the anthropophilic and epidermis-restricted Trichophyton Rubrum infection. This model faithfully mimics and reflects the clinical pathological reactions of reinforced physical barrier by promoting keratinocytes differentiation and accelerated formation of the stratum corneum for adaptation and resistance to infection. Furthermore, the infection model also suggested that constraining host IL-1 signaling may underline the high degree of adaptation of Trichophyton Rubrum to human skin, and the tendency to be chronic and recurrent infection. Thus, human epidermal organoids present a powerful platform for modeling human dermatology, skin tissue engineering and cell therapy.

overall_design: Evaluation of whole transcriptome of cells in 2 groups, each of them include 2 replication

first: Yunfang

last: Wang

first: Shuyong


title: Expression data from normal LNCAP cells and LNCAP cells treated with PC-3 exosomes

status: Public on Feb 25 2020

city: Guangzhou

first: Yiming

last: Zhang

address: No.253 Gongyedadao middle Road, Haizhu district

institute: Zhujiang Hospital

summary: We used microarrays to detail the global gene expression in normal LNCAP cells and LNCAP cells treated with PC-3 exosomes.

overall_design: Normal LNCAP cells and PC-3 exosomes treated LNCAP cells were for RNA extraction and hybridization on Affymetrix microarrays.


title: JunB-dependent expression in colonic and Peyer's patch regulatory T cells

status: Public on Feb 26 2020

city: Durham

first: Maria

last: Ciofani

state: NC

address: 207 Research Drive, 128 Jones Building

department: Integrative Immunobiology

country: USA

institute: Duke University School of Medicine

summary: Foxp3-expressing regulatory T (Treg) cells are critical mediators of immunological tolerance to both self and microbial antigens. Tregs activate context-dependent transcriptional programs to adapt effector function to specific tissues; however, the factors controlling tissue-specific gene expression in Tregs remain unclear. Here, we find that the AP-1 transcription factor JunB regulates the intestinal adaptation of Tregs by controlling select gene expression programs in multiple Treg subsets. Treg-specific ablation of JunB results in immune dysregulation characterized by enhanced colonic T helper cell accumulation and cytokine production. However, in contrast to its classical binding-partner BATF, JunB is dispensable for maintenance of effector Tregs as well as most specialized Treg subsets. In the Peyer’s patches, JunB activates a transcriptional program facilitating the maintenance of CD25- Tregs, leading to the complete loss of T follicular regulatory cells in the absence of JunB. This defect is compounded by loss of a separate effector program found in both major colonic Treg subsets that includes the cytolytic effector molecule granzyme B. Therefore, JunB is an essential regulator of intestinal Treg effector function through pleiotropic effects on gene expression.

overall_design: RNA-seq transcriptomes of 3 regulatory T cell populations from 2 organs and 4 genotypes of mice in duplicate or triplicate.

first: Joshua

middle: D

last: Wheaton


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

status: Public on Mar 06 2020

city: La Jolla

first: Bing

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

institute: University of California, San Diego School of Medicine

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

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

first: Naoki

last: Kubo


title: Single-cell RNA-sequencing of CD45+ splenocytes from aged WT, miR146a knockout, and miR146a-miR155 T cell conditional double knockout mice

status: Public on Jan 31 2020

city: Salt Lake City

first: Ryan

middle: M.

last: O'Connell

state: UT

address: 15 N Medical Drive East, Emma Eccles Jones Medical Research Bldg, Rm 2100, Salt Lake City, UT 84112-5650

institute: University of Utah

summary: Chronic age-dependent inflammation, or inflammaging, is a risk-factor for many disorders that emerge in aging human populations. Mechanisms underlying these aberrant immune responses are complex and remain to be elucidated. Among recently appreciated regulators of inflammaging are microRNAs; one example of which is the anti-inflammatory miR-146a, where deficient mice succumb to life-shortening chronic inflammation. In this study, we found that deletion of miR-155 in T cells significantly extends the lifespan of miR-146a-/- mice. Using single-cell RNA sequencing and flow cytometry we found that miR-155 promotes the activation of effector T cell populations, including Tfh cells, in mice aged over 15 months. This correlated with miR-155 dependent increases in germinal center B cells, autoantibody responses and serum IgG targeting tissue antigens throughout the body. Mechanistically, we found that the aerobic glycolysis genes are elevated in T cells during aging, and to even greater levels in the absence of miR-146a, and this was reduced upon deleting miR-155 in T cells. Finally, through deletion of the mitochondrial pyruvate carrier (MPC) complex in T cells, which skews metabolism towards aerobic glycolysis, we demonstrate that several of the age-dependent, activation phenotypes of miR-146a-/- T cells were recapitulated, thus revealing the sufficiency of metabolic reprogramming to influence immune cell functions during aging. Altogether, these data indicate that miRNAs play pivotal roles in regulating lifespan through T cell mediated inflammaging.

overall_design: WT (miR155 fl/fl), miR146a whole body knockout (146ko), and miR146-miR155 T cell conditional double knockout (tcko) (miR146ko-miR155tcko) mice were aged for 15 months. Single cell suspensions were prepared from spleens at the endpoint, pooled per each group (n=3-6 mice), followed by flow cytometric sorting of live (DAPI-) CD45+ lymphocytes (FSC-low, SSC-low). Sorted cells were processed for 10X Genomics 3' single cell sequencing.

first: H

middle: A

last: Ekiz

first: Andrew

middle: G

last: Ramstead


title: Non-linear relationship between chromatin accessibility and estradiol-regulated gene expression

city: Indianapolis

first: Duojiao

last: Chen

state: INDIANA

address: 410 W. 10th Street

department: Departments of Medical and Molecular Genetics

institute: Indiana University

summary: Chromatin accessibility is central to basal and inducible gene expression. Through ATAC-seq experiments in Estrogen Receptor-positive (ER+) breast cancer cell line MCF-7 and integrationvwith multi-omics data, we found that estradiol (E2) induced chromatin accessibility changes in the widely studied E2-regulated genes. As expected, open chromatin regions associated with E2-inducible gene expression showed enrichment of estrogen response element and those associated with E2-repressible gene expression were enriched for PBX1, PBX3, and ERE. Surprisingly, a significant number of E2-inducible genes displayed closed promoters/enhancers and these were enriched for binding for transcription factors such as NF-Y, FOXA1, GRHL2, and BATF, which are known to interact with nucleosomes. While a significant number of open chromatin regions showed FOXA1 occupancy in the absence of E2, E2-treatment further enhanced FOXA1 occupancy suggesting that ER-E2 enhances chromatin occupancy of FOXA1 to a subset of E2-regulated genes. In summation, our results reveal complex mechanisms of ER-E2 interaction with nucleosomes.

overall_design: We conducted both ATAC-seq and RNA-seq for MCF7 cells. Total RNA from MCF-7 cells treated with vehicle ethanol or E2 for three hours in biologic triplicates was used for sequencing. MCF-7 cells treated with vehicle (ethanol) control, E2 (10-10 M) for one or three hours were were done in biologic triplicates with ~50,000 cells.

first: Taylor

last: Parker

first: Poornima

last: Bhat-Nakshatri

first: Yue

first: Xiaona

last: Chu


title: Regulation of the circadian clock by the metabolic enzyme AHCY

status: Public on Feb 01 2020

city: Irvine

first: Jiejun

last: Shi

address: 5270 California Ave

department: School of Medicine

institute: University of California Irvine

summary: Mammalian circadian rhythms are based on coupled transcriptional-translational feedback loops driven by the transcription factors CLOCK and BMAL1. Chromatin remodeling mechanisms are essential for the proper timing and extent of circadian gene expression. We report that the S-adenosylhomocysteine (SAH) hydrolysing enzyme AHCY binds to CLOCK-BMAL1 at chromatin and drives circadian transcription by promoting  cyclic H3K4 trimethylation and recruitment of BMAL1 to chromatin.

overall_design: H3K4me3 and BMAL1 ChIP-seq in mouse embryonic fibroblasts (MEF)  synchronized with dexamethasone and treated with a specific inhibitor for AHCY (DZnep). ChIP was performed at circadian time (CT) 12 and CT24.

first: Carolina

last: Greco

first: Paolo

last: Sassone-Corsi


title: Deep sequencing identified serum extracellular vesicle delivered miR-181a-5p as an indicator for bone-metastatic prostate cancer (microarray)

city: Shanghai

first: Yanqing

address: NO. 160 Pujian Road

department: Urology

institute: Shanghai Renji Hospital

summary:
Purpose: The goals of this study are to compare the serum extracellular vesicle (EV) delivered miRNA levels of patients with bone-metastatic prostate cancer (PCa),  non-bone -metastatic PCa and benign prostatic hyperplasia (BPH), and to identify EV-delivered microRNAs in patient’s serum as indicators for bone-metastatic PCa.
Methods:Serum extracellular vesicle delivered miRNA profiles of patients with bone-metastatic PCa or non-bone -metastatic PCa or BPH were generated by miRNA chip array,  using Agilent-070156 Human_miRNA_V21.0_Microarray plateform.
Results:  Differential analysis showed the expressions of 27 EV delivered miRNAs were significantly different between serum of patients with bone-metastatic PCa and non-bone-metastatic PCa with a p value <0.05. the expressions of  5 EV delivered miRNAs were confirmed with qRT–PCR.
Conclusions: Serum EV-delivered miR-181a-5p is a promising diagnostic biomarker for bone-metastatic PCa.

overall_design: Serum extracellular vesicle delivered miRNA profiles of patients with bone-metastatic PCa or non-bone -metastatic PCa or benign prostatic hyperplasia were generated by miRNA chip array, and  contrastive analysis.

first: Yuxiang

last: Fang