title: Autocrine GM-CSF signaling programs hematopoietic stem and progenitor cells during Candida albicans infection for protection against reinfection

city: Cincinnati

first: Nathan

last: Salomonis

state: OH

address: 3333 Burnet Avenue

department: Biomedical Informatics

institute: Cincinnati Children's Hospital

summary: More mechanistic studies are needed to reveal the hidden details of in vivo-induced trained immunity. Here, using a Candida albicans live vaccine mouse model we show that vaccination protects mice against a secondary infection and increases the number of bone marrow, and especially, splenic trained monocytes. Moreover, vaccination reprograms hematopoietic stem and progenitor cells (HSPCs) early during infection and mobilize them transiently to the spleen to produce trained macrophages. Trained HSPCs are not only primed for myeloid cell production but also reprogramed to produce a greater amount of proinflammatory cytokines in response to a second challenge; additionally, their adoptive transfer is sufficient to protect mice against reinfection. Mechanistically, autocrine GM-CSF activation of HSPCs is responsible for the trained phenotype and essential for the vaccine-induced protection. Our findings reveal a fundamental role for HSPCs in the trained immune protective response, opening new avenues for disease prevention and treatment.

overall_design: Transcriptomic changes in hematopoietic stem and progenitor cells were identified in the bone marrow or spleen of uninfected mice, infected with a low-virulence, nongerminative strain of C. albicans (PCA2) and reinfected with the virulent strain of C. albicans (ATCC 26555) using using the 10x Genomics Chromium 3’ v3 platform.

first: Cristina

last: Bono

first: Paula

last: Guerrero

first: Antonio

last: Jordán-Pla

first: Ana

last: Erades

first: H

last: Grimes

first: M

last: Gil

first: Alberto

last: Yáñez


title: Hobit confers tissue dependent programs to type 1 innate lymphoid cells

status: Public on Dec 06 2021

city: St. Louis

first: Marco

last: Colonna

state: Missouri

address: 425 S. Euclid

department: Pathology and Immunology

country: USA

institute: Washington University in St. Louis

type: Expression profiling by high throughput sequencing

summary: Innate responses against viral infection and other intracellular pathogens rely on immune cells that are capable of lysing infected cells and producing interferon-gamma (IFNγ). These cells encompass two major cell lineages: natural killer (NK) cells and type 1 innate lymphoid cells (ILC1s). While NK cells have been extensively characterized, identification of ILC1s and their distinction from NK cells is less clear. The transcription factor Hobit encoded by Zfp683 has been put forth as a prototypic feature of ILC1s. By analyzing Zfp683 reporter, fate-map and deficient mice, we demonstrate that the impact of Hobit on ILC1 identity, transcriptional and functional programs is tissue- and context-dependent. Thus, ILC1s functionally adapt to local stimuli and tailor their responses to the tissue niche.

overall_design: single cell transcriptional profiling of ILC1 and NK cells from various tissues was performed using the 10x Genomics platform

first: Kentaro

last: Yomogida


title: Coordinated repression of pro-differentiation genes via P-bodies and transcription maintains Drosophila intestinal stem cell identity

city: Bloomington

first: Nick

last: Sokol

state: IN

address: 1001 E 3rd Street, Biology Building

institute: Indiana University

summary: The role of Processing bodies (P-bodies), key sites of post-transcriptional control, in adult stem cells remains poorly understood. Here, we report that adult Drosophila intestinal stem cells, but not surrounding differentiated cells such as absorptive Enterocytes (ECs), harbor P-bodies that contain Drosophila orthologs of mammalian P-body components DDX6, EDC3, EDC4 and LSM14A/B. A targeted RNAi screen in intestinal progenitor cells identified 39 previously known and 64 novel P-body regulators, including Patr-1, a gene necessary for P-body assembly. Loss of Patr-1-dependent P-bodies leads to a loss of stem cells that is associated with inappropriate translation and expression of EC-fate gene nubbin. Transcriptomic analysis of progenitor cells identifies a cadre of such weakly transcribed pro-differentiation transcripts that are elevated after P-body loss. Altogether, this study identifies a coordinated P-body dependent, translational and transcriptional repression program that maintains a defined set of in vivo stem cells in a state primed for differentiation.

overall_design: Identification of RNAs regulated by P-bodies using RNA-seq.

first: Kasun

last: Buddika

first: Nicholas

middle: S


title: Transcriptomic profiling of Arabidopsis hypocotyls of brl3 mutants and tissue-specific overexpressors under elevated temperatures

city: Cerdanyola

first: Fidel

last: Lozano-Elena

state: Barcelona

address: Edifici CRAG - Campus UAB

department: Molecular Genetics

country: Spain

institute: Center for Research in Agricultural Genomics (CRAG)

summary: Climate change is having a drastic impact on global agriculture. Indeed stress factors such as elevated temperature, drought and rising atmospheric CO2 reduce arable land surface, crop cultivation and yield and overall sustainable food production on earth. However, plants possess immense innate adaptive plasticity and a more in-depth understanding of the underlying molecular mechanisms is crucial to strategize for sustaining populations under worsening climate change. Brassinosteroids (BRs) are constitutive plant growth regulators that also control plant adaptation to abiotic stress. Downstream components of the BR biosynthetic pathway, BES1/BZR1 play central role in thermomorphogenesis, but involvement of the BR receptors is not well understood. Here, we show that the BRL3 receptor is essential for plant adaptation to warmer environment. The brl3 mutants lack thermal responsiveness and the BRL3 overexpression causes hyper-thermomorphogenesis response. BRL3 activates canonical BRI1 pathway upon elevated temperature. Further, phloem-specific expression of BRL3 completely rescues the growth adaptation defects of the brl3 mutant. This ability of BRL3 represents a previously unknown thermoresponsive mechanism specifically from phloem and uncouples the roles of BR receptors in generic growth vs adaptation to changing climate conditions.

overall_design: A two factor experimental design (Genotype and temperature) with several levels in genotype factor:  The hypocotyl of 6-day-old Arabidopsis seedlings of Col-0 (WT), brl3 mutant (SALK_006024C), phloem-complemented line pSUC2:BRL3-GFP; brl3-2 and BRL3ox (35S:BRL3-GFP, Fàbregas et al., 2018) grown at 22ºC (growth optimum) and 28ºC (elevated temperature) were sampled and RNA sequenced. Two biological replicates per genotype and condition. A total of 16 samples.

first: Aditi

last: Gupta

middle: I

last: Caño-Delgado


title: What’s wrong with SwYG? Probing the limits of S. cerevisiae molecular and analytical toolbox

city: Delft

first: Marcel

last: van den Broek

address: Van der Maasweg 9

country: Netherlands

institute: Delft University of Technology

summary: The construction of powerful cell factories requires extensive remodelling of microbial genomes, entailing many rounds of transformations to perform the large number of desired gene modifications. However, increasing the number of genetic interventions inevitably increases the occurrence of unwanted mutations and effects. Using glycolysis as paradigm, a previous study developed a Saccharomyces cerevisiae strain in which the glycolytic genes, relocalized to a single locus, can be easily swapped by any new design, thereby enabling fast and easy remodelling of the entire pathway. After 27 genetic modifications performed in 43 transformation rounds, the Switchable Yeast Glycolysis (SwYG) strain grew ca. 20% slower than its ancestor with native glycolysis design. Exploring the cause of this slower growth rate, the present study reflects on the genetic and analytical challenges encountered by extensive strain construction programs and provides design guidelines for integration of large constructs in the yeast genome.

overall_design: Comparision of transcription between two strains expressing all glycolytic genes from a single locus and a strain where all major paralog genes are in their native loci. All strains were measured from biological duplicates

first: Ewout

last: Knibbe

first: Eline

middle: D

last: Postma

first: Francine

middle: J

last: Boonekamp

first: Sofiia

last: Dashko

first: Jordi

last: Geelhoed

first: Anne-Marijn

last: Maat

first: Marijke

middle: A

last: Luttik

first: Pascale

last: Daran-Lapujade


title: Generation of thyroid follicular cell organoids from adult thyroid tissue [Mouse single-cell]

city: Utrecht

first: Jelte

last: van der Vaart

address: Universiteitsweg 100

department: Center for Molecular Medicine

institute: University Medical Center Utrecht

summary: The thyroid maintains systemic homeostasis by regulating serum thyroid hormone concentrations. Here we report the establishment of adult stem cell-derived three-dimensional (3D) organoids representing murine and human thyroid follicular cells (TFCs). The TFC organoids (TFCO) harbour the complete machinery of hormone production as visualised by the presence of colloid in the lumen and by the presence of essential transporters and enzymes in the polarised epithelial cells that surround a central lumen. Both the established murine as human thyroid organoids express canonical thyroid markers PAX8 and NKX2.1, while the thyroid hormone precursor thyroglobulin is expressed at comparable levels to tissue. Single cell RNA sequencing and transmission electron microscopy confirm that TFCOs phenocopy primary thyroid tissue. Thyroid hormones are readily detectable in conditioned medium of human TFCOs.

overall_design: single cell sequencing of adult mouse thyroid tissue and thyroid follicular cell organoids from early and late passage. For each sample description, 2 biological replicates were used.

first: Lynn

last: Bosmans

first: Stijn

last: Sijbesma

first: Kèvin

last: Knoops

first: Willine

last: van de Wetering

first: Henny

last: Otten

first: Harry

last: Begthel

first: Jeroen

last: Korving

first: Carmen

last: Lopez-Iglesias

first: Peter

last: Peters

first: Hanneke

last: van Santen

first: Menno

last: Vriens

first: Hans

last: Clevers


title: The diagnostic and prognostic value of hsa_circ_0084927 in colon adenocarcinoma and its ceRNA network construction (miRNA-Seq)

city: Nanning

first: Weizhong

last: Tang

state: State...

address: Guangxi Clinical Research Center for Colorectal Cancer, Nanning, Guangxi Zhuang Autonomous Region 530021 P.R. China.

country: China

institute: Guangxi Medical University Cancer Hospital

type: Non-coding RNA profiling by high throughput sequencing

summary: Object: This study aims to analyze the differentially expressed circRNA in colon adenocarcinoma (COAD) and evaluate its diagnostic and prognostic value. Establish a new prog

overall_design: miRNA sequencing in colorectal cancer patients and colon cancer cell lines

first: Junjie

last: Liu

first: Huage

last: Zhong

first: Yi

last: Chen

first: Chunrun

last: Ling

first: Yansong

last: Xu


title: Whole transcriptome sequencing of HT22 immortalized mouse hippocampal cells treated with AA147 or veh for 16 h

city: La Jolla

first: R.

middle: Luke

last: Wiseman

address: 10550 N Torrey Pines Rd

department: Dept. of Molecular Medicine

institute: The Scripps Research Institute

summary:
Purpose: Define transcriptional remodeling associated with AA147 treatment (10uM) for 16 h in a mouse neuronal cell line.
Methods: A minimum of 27M PE100 reads were generated for triplicates of vehicle vs. AA147 treated HT22 cells.  Alignment of reads was performed using DNAstar Lasergene SeqManPro to the mouse genome GRCm39 assembly. Read counts generated by ArrayStar 12.2  QSeq package. Differential expression analysis performed using DESeq2.
Results: We mapped between 27-32 M sequence reads per sample to the mouse genome and identified 16,473 transcripts with counts greater than 10. Of these, we identified 2,742 genes with significantly different expression between vehicle and AA147 treated cells.
Conclusions: We observed substantial upregulation of prolactin and glutathione transferase genes, and upregulation of NRF2-associated pathway upregulation.

overall_design: Whole transcriptome RNA-Seq performed on HT22 mouse neuronal cells treated with vehicle or AA147 for 16 h.

first: Jessica

last: Rosarda

first: R

middle: L


title: Metabolic and transcriptional adaptations improve physical performance of zebrafish

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

department: ZMF

country: Germany

institute: University Heidelberg

summary:
Background: Obesity is a worldwide public health problem with increasing prevalence and affects 80% of diabetes mellitus type 2 cases. Zebrafish (Danio rerio) are an established model organism for studying obesity and diabetes including diabetic microvascular complications. We aimed to determine whether physical activity is an appropriate tool to examine training effects in zebrafish and to analyse metabolic and transcriptional processes in trained zebrafish.
Methods: A 2- and 8-weeks experimental training phase protocol with adult zebrafish in a swim tunnel system was established. We examined zebrafish basic characteristics before and after training such as body weight, body length and maximum speed and considered overfeeding as an additional parameter in the 8-weeks training protocol. Ultimately, the effects of training and overfeeding on blood glucose, muscle core metabolism and liver gene expression using RNA-Seq were investigated.
Results: Zebrafish maximum speed was correlated with body length and was significantly increased after 2 weeks of training. Maximum swim speed further increased after 8 weeks of training in both the normalfed and the overfed groups, but training was found not to be sufficient in preventing weight gain in overfed fish. Metabolome and transcriptome profiling in trained fish exhibited increased blood glucose levels in the short-term and upregulated energy supply pathways in the long-term.
Conclusion: Swim training is a valuable tool to study effects of physical activity in zebrafish, which is accompanied by metabolic and transcriptional adaptations.

overall_design: total RNA sequencing was performed with 24 zebrafish liver samples (ABTL strain), including 6 control fish, 6 overfed fish, 6 trained fish, 6 trained and overfed fish

first: Franziska

last: Heinkele

first: Bowen

last: Lou

first: Vanessa

last: Erben

first: Katrin

last: Bennewitz

first: Gernot

last: Poschet

first: Jens

last: Kroll


title: Generation of thyroid follicular cell organoids from adult thyroid tissue [mouse]

first: Jelte

last: van der Vaart

overall_design: mRNA Bulk sequencing of adult murine thyroid tissue and thyroid follicular cell organoids from early and late passage. For each sample description, 2 biological replicates were used.

first: Lynn

last: Bosmans

first: Stijn

last: Sijbesma

first: Kèvin

last: Knoops

first: Willine

last: van de Wetering

first: Henny

last: Otten

first: Harry

last: Begthel

first: Jeroen

last: Korving

first: Carmen

last: Lopez-Iglesias

first: Peter

last: Peters

first: Hanneke

last: van Santen

first: Menno

last: Vriens

first: Hans


title: Ribosome profiling analysis of zebrafish embryos injected with the codon tag reporter library

city: Saitama

first: Peixun

last: Han

address: Hirosawa Wako

country: Japan

institute: Riken

summary: We measured the effect of codons on mRNA stability in zebrafish embryos using reporter mRNAs. We showed that slow decoding of codons by the ribosome promoted mRNA degradation in zebrafish.

overall_design: Ribosome profiling of zebrafish embryos.

first: Shintaro

last: Iwasaki

first: Yuichiro

last: Mishima


title: Generation of thyroid follicular cell organoids from adult thyroid tissue

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: Integrating single-cell RNA-sequencing and transcriptomic data reveals essential genes for tooth development processes

city: Sendai

first: Yuta

last: Chiba

state: Miyagi

address: 4-1 Seiryo-cho, Aoba-ku

institute: Tohoku University

summary: The organ development is dictated by the genes preferentially expressed in tissue or cell types uniquely. The clarification of gene expression profile and identification of specific genes in organ provide detailed understanding of organogenesis. Toward this purpose, the genome-wide analysis is a growing powerful tool for understanding development processes in organogenesis. Tooth is composed from enamel, dentin and cementum and these tissues are identical from other organs. The tooth-forming cell types are therefore unique and have complexed organization. The mechanisms of signal induction during tooth development is complicated because of the function of each cell types are still unclear. Previously, we performed the CAGE (Cap Analysis of Gene Expression) using mouse tooth germ to identify the genes preferentially expressed in tooth. The CAGE has advantage in quantification because it counts short reads of 5’ end without the bias of transcript length. Single-cell RNA-sequence (scRNA-seq) is a suitable tool revealing gene expression of each cells. The fundamental question of this study is how we can identify the tooth-specific and cell-type specific genes. In this study, we approach this using combination of scRNA-seq and CAGE (Cap Analysis of Gene Expression) as bioinformatics analyses. We obtained the scRNA-seq datasets of 12,212 cells from postnatal-day (P) 1 mouse molars, and the CAGE-seq datasets from P1 molars. scRNA-seq analysis revealed the spatio-temporal expression of tooth-related genes and CAGE determined whether these genes are truly tooth-specific or are expressed in ubiquitously. Furthermore, we identified candidate genes as novel tissue- and cell type- specific markers. Our results show that the integration of scRNA-seq and CAGE-seq improves the highlight genes important for tooth development from numerous gene profiles. These findings contribute resolving the mechanism of tooth development and establish the basis of tooth regeneration in future.

overall_design: Examination of epithelial and mesenchymal cells in mouse molar.

first: Keigo

last: Yoshizaki

first: Tian

last: Tian

first: Daniel

last: Martin

first: Satoshi

last: Fukumoto


title: Generation of thyroid follicular cell organoids from adult thyroid tissue [Human]

first: Jelte

last: van der Vaart

overall_design:
mRNA Bulk sequencing of adult human thyroid tissue and thyroid follicular cell organoids from early and late passage. For each sample description, 3 biological replicates were used.
This series includes two re-analyzed samples from GSE148815: GSM4483226 (AdultLung1_tissue_lung_tissue) and GSM4483228 (AdultLung2_tissue_lung_tissue)

first: Lynn

last: Bosmans

first: Stijn

last: Sijbesma

first: Kèvin

last: Knoops

first: Willine

last: Clevers


title: Glucocorticoids and androgens suppress group 2 innate lymphoid cell activation and protect from pathogenic gastric inflammation and metaplasia

city: RTP

first: Xiaojiang

last: Xu

state: North Carolina

address: 111 T. W. Alexander Dr.,

institute: NIEHS

summary: We performed scRNAseq of leukocytes isolated from the gastric corpus of WT male mice. CD45+ leukocytes were sorted from the gastric corpus using flow cytometry and libraries were prepared using the 10x genomic chromium controller. These data provide an atlas of the inflammatory cells which reside within the gastric corpus during steady-state conditions.

overall_design: Leukocytes were isolated by flow cytometry from the gastric corpus of 3 WT male C57B6/J mice and used for scRNAseq. Cells were pooled prior to scRNAseq library preparation.

first: Jonathan

middle: T

last: Busada

first: John

last: Cidlowski


title: Expression data of exosomal miRNAs extracted from serum

city: Chengdu

first: Di

last: Cao

state: Sichuan

address: No.37 Guoxue Alley, Wuhou District

department: Department of Hematology

institute: Sichuan University

summary: Diffuse large B-cell lymphoma (DLBCL) is the most common subtype of non-Hodgkin Lymphoma with complex clinical symptoms. Currently, the diagnosis of DLBCL depends largely on pathologic analysis of biopsy tissue, which is an invasive procedure and often poses some risk to patients. Exosomal miRNAs have emerged as promising noninvasive biomarkers for detecting tumor or monitoring disease progress. We aim to investigate the potential of circulating exosomal miRNAs to assist with diagnosis of DLBCL.In the present research, we used the miRCURY LNA™ microRNA Array to investgate the profiles of differentially expressed miRNAs in the exosomes of peripheral blood serum. As a result, circulating exosomal miRNA profiling yielded a total of 332 differentially expressed miRNAs (157 with up-expression and 175 with down-expression) between the DLBCL patients and healthy controls.

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus

overall_design: Serum samples of 10 DLBCL patients and 5 healthy controls were collected for exosomal miRNAs extraction and hybridization on 7th miRCURY LNA™ microRNA Array

first: Yu

last: Jiang

first: Caixia

last: Jing


title: Transcriptional signature of BCG vaccination

city: San Diego

first: Paige

last: Dubelko

state: CA

address: 9420 Athena Circle

institute: La Jolla Institure for Immunology

summary: The century-old Mycobacterium bovis Bacillus Calmette-Guerin (BCG) remains the only licensed vaccine against tuberculosis (TB). Despite this, there is still a lot to learn about the immune response induced by BCG, both in terms of phenotype and specificity. Here, we investigated the BCG-specific gene expression changes induced in PBMCs and CD4 memory T cells by BCG in individuals pre- and 8m post vaccination. We also determined whether reactivity against a peptide pool defined in individuals with controlled latent TB infection (MTB300), and with peptides homologous to peptides found in BCG, was boosted following BCG vaccination.

overall_design: RNAseq of PBMC and sorted memory CD4 T cells from cryopreserved PBMC of 7 individuals who received BCG vaccination. Samples were taken pre- and post vaccination.

first: Akul

last: Singhania

first: Cecilia

last: Lindestam Arlehamn


title: Nup93 modulates spatiotemporal dynamics and function of the HOXA gene cluster during differentiation

city: Pune

first: Kundan

last: Sengupta

state: Maharashtra

address: Dr. Homi Bhabha Road, Pashan

department: Biology

country: India

institute: Indian Institute of Science, Education and Research, Pune

type: Genome binding/occupancy profiling by high throughput sequencing

summary: The central role of nucleoporins is to  transport RNA and proteins. In addtion, nucleoporins are also involved in gene regulation. Furthermore, nucleoporins -  Nup93, Nup153, Nup98 and Nup210, directly associate with developmental genes and regulate  developmental processes by direct association with developmental genes.  Here, we identified genome wide binding profile of Nup93 - a  core component of the nuclear pore complex in colorectal cancer cell line DLD-1 by ChIP-seq. Our ChIP-seq analysis revealed significant association of Nup93 with developmental genes and known enhancer marks such as H3K4me1 and H3K27Ac . We found that Nup93 shares binding sites with CTCF - the well known chromatin organizer, suggesting a functional overlap between Nup93 and CTCF in the organization and regulation of developmental gene expression  such as the the HOXA gene cluster.

overall_design: ChIP-seq was performed to determine the chromatin occupancy of Nup93 in DLD-1 cells in two independent biological replicates. Sonicated chromatin from Input sample was used as a control.

first: Ajay

last: Labade

first: Adwait

last: Salvi

first: Krishanpal

last: Karmodiya

first: Saswati

last: Kar


title: 10X-single cell seq of B cells during colitis (d0 and d14)

city: Stockholm

first: Eduardo

last: Villablanca

address: visiongatan 18

department: CMM

country: Sweden

institute: Karolinska Institute

summary: B cells expand during the recovery after DSS-induced colonic inflammation. To investigate if a specific subtype is expanding and to analyse the transcriptional profile of these cells a transcriptional analysis on single cell level was carried out. In detail,  B cells were isolated from the colon of mice on day 0 (no treatment) or day 14 (recovery) after 7 days of DSS treatment by flow cytometric sorting and analyzed by 10X sequencing.

overall_design: Female C57BL/6J mice were treated with 2%DSS via the drinking water followed by 7 days of recovery. Lymphocytes were isolated from the colonic lamina propria on day 0 (ctrl) and day 14 (recovery) and B cells were sorted using flow cytometry. Afterwards cells were processed according to 10x Genomics protocol for Chromium Single cell 3’ kit (version 2) and submitted for sequencing

first: Annika

last: Frede

first: Chiara

last: Sorini

first: Kumar

middle: P

last: Tripathi


title: AD-linked R47H-TREM2 mutation induces disease-enhancing microglial states via AKT hyperactivation

city: San Francisco

first: Lay

last: Kodama

address: 1650 Owens St.

department: Gladstone Institute of Neurological Disease

institute: University of California San Francisco

summary: The hemizygous R47H variant of TREM2, a microglia-specific gene in the brain, increases risk for late-onset Alzheimer’s disease (AD). Using transcriptomic analysis at the single-nuclei level from brain tissue of AD patients with the R47H mutation or the common variant (CV)-TREM2, we found that R47H-associated microglial subpopulations had enhanced inflammatory signatures reminiscent of previously-identified disease-associated microglia (DAM) and hyperactivation of AKT, one of the signaling pathways downstream of TREM2. We established a tauopathy mouse model with heterozygous knock-in of the human TREM2 with R47H mutation or CV, and found that R47H induced and exacerbated tau-mediated spatial memory deficits in female mice. Single-cell transcriptomic analysis of microglia from these mice also revealed transcriptomic changes induced by R47H that had significant overlaps with R47H microglia in human AD brains, including robust increases in proinflammatory cytokines, activation of Akt signaling, and elevation of a subset of disease-associated microglial signatures. Pharmacological Akt inhibition with MK-2206 largely reversed the enhanced inflammatory signatures in primary R47H microglia treated with tau fibrils. Strikingly, in R47H heterozygous tauopathy mice, MK-2206 treatment abolished a tauopathy-dependent microglial subcluster, and rescued tauopathy-induced synapse loss. By uncovering disease-enhancing mechanisms of the R47H mutation conserved in human and mouse, our study supports inhibitors of AKT signaling as a novel microglial modulating strategy to treat AD.

overall_design: Bulk RNA sequencing of hippocampal tissue from female and male Trem2+/+;PS19, R47H-TREM2/+;PS19, and WT-TREM2/+;PS19 mice.

first: Faten

last: Sayed

first: Li

last: Fan

first: Gillian

middle: K

last: Carling

first: Joe

middle: C

last: Udeochu

first: David

last: Le

first: Qingyun

last: Li

first: Lu

last: Zhou

first: Man Ying

last: Wong

first: Rose

last: Horowitz

first: Pearly

last: Ye

first: Hansruedi

last: Mathys

first: Minghui

last: Wang

first: Xiang

last: Niu

first: Linas

last: Mazutis

first: Xueqiao

first: Xueting

first: Fuying

last: Gao

first: Matthew

last: Brendel

first: Maria

last: Telpoukhovskaia

first: Tara

middle: E

last: Tracy

first: Georgia

last: Frost

first: Yungui

first: Yaqiao

first: Yue

last: Qiu

first: Zuolin

last: Cheng

first: Guoqiang

last: Yu

last: Hardy

first: Giovanni

last: Coppola

first: Fei

first: Michael

last: DeTure

first: Bin

last: Zhang

first: Lei

last: Xie

middle: Q

last: Trajnowski

first: Virginia

middle: M

last: Lee

first: Shiaoching

last: Gong

first: Subhash

last: Sinha

first: Dennis

middle: W

last: Dickson

first: Wenjie

last: Luo

last: Gan


title: RNA-Seq of Vibrio alginolyticus: Vibrio alginolyticus 18672

city: Shanghai

first: Jun

state: Shanghai

address: NO.130 meilong road

department: School of biological engineering

institute: East China University Of Science and Technology

summary: RNA-seq analysis demonstrated that VqsA (18672) controls ~275 genes' expression in V. alginolyticus. Collectively, our data established that VqsA plays essential roles in QS regulation and may facilitate the illumination of the mechanisms bacterial cells sense environmental signals and integrate them into coordinated QS responses.

overall_design: Bacteria were incubated overnight and then total RNA was isolated using TRIzol (Thermo Fisher Science). rRNA was removed from sample using Ribo-Zero (Illumina, San Diego, CA, USA) and library construction refered to TruSeq RNA sample Prep kit (Illumina, San Diego, CA, USA). The final libraries were sequenced on a HiSeq X-Ten platform (GENEWIZ, Su Zhou, China).

first: Qiyao

last: Wang

first: Yuan

last: Hao


title: Transcriptome profiling of HepG2 cells in Cdc20 overexpressed and downregulated condition

city: Kolkata

first: Susanta

last: Roychoudhury

state: West Bengal

address: 4, Raja S. C. Mullick Road

department: Cancer Biology and Inflammatory Disorder Division

institute: CSIR-Indian Institute of Chemical Biology

summary: Cdc20 acts as a regulatory protein interacting with many other proteins at multiple points in the cell cycle. Here we tried to explore the novel transcription regulatory function of Cdc20 by means of altering Cdc20 level in HepG2 cells. We transiently over expressed Flag tagged Cdc20 (F) and siRNA mediated knocked down Cdc20(S) in HepG2 cell line and performed whole genome microarray analysis using illumina BeadChip Array. Significantly altered genes were subjected to the analysed by Ingenuity pathway analysis software (Build version: 302937) and crucial cellcycle and apoptotic pathways were found to be altered. These pathways could further be explored as anticancer therapy in liver carcinoma.

overall_design: Identification of potential  signature genes in Cdc20 altered condition in hepatocellular carcinoma cells


title: Transcriptome analysis of cattle experimentally infected with foot-and-mouth disease virus

city: Bengaluru

first: Suresh

middle: H

last: Basagoudanavar

state: Karnataka

address: IVRI, Hebbal

department: FMD Research Laboratory

institute: Indian Veterinary Research Institute

summary: We present  the RNA-seq based transcriptome profile of ventral soft palate tissue from two Indian indigenous breeds (Malnad Gidda and Hallikar; Bos indicus) of cattle and Holstein Friesian (HF) crossbred calves. Differentially expressed gene pattern showed stronger innate immune response in the indigenous calves. We find that induction of innate and cell mediated immune response is associated with early viral clearance and mild form of foot-and-mouth disease.

sample_organism:
Bos taurus
Bos indicus

platform_organism:
Bos taurus
Bos indicus

overall_design: RNA-sequencing was performed at Sandor Life Sciences Pvt. Ltd., Hyderabad (India) on Illumina HiSeq (151 nt, paired-end) platform, using RNA isolated from ventral soft palate tissue of three breeds of cattle. Number of of samples of each breed included three (n=3) infected with FMDV and two mock controls (n=2). In total there were nine cattle calves infected with FMDV and six mock control calves.

first: B

last: Sreenivasa

first: Aniket

last: Sanyal

first: V

last: Umapathi

first: Madhusudan

last: Hosamani

first: S

last: Saravanan

first: Neha

last: Guleria


title: γH2A.X Modulates Self-renewal and Differentiation of Human Pluripotent Stem Cells.

city: Hamilton

first: Mickie

last: Bhatia

state: Ontario

address: 1200 Main Street West

department: Stem Cell and Cancer Research Institute (SCC-RI)

country: Canada

institute: McMaster University


title: γH2A.X Modulates Self-renewal and Differentiation of Human Pluripotent Stem Cells. [HuGene-1_0-st]

summary: Histone variants are important epigenetic regulators known to play a role in governing the processes of self-renewal and lineage specific differentiation . Phosphorylation of the histone variant H2A.X (γH2A.X) has historically been associated with DNA damage response, but more recent investigations have further demonstrated it’s role in cell cycle, aging and early development.  Through both genetic and chemical targeting approaches, we now reveal a direct involvement of γH2A.X in hPSC self-renewal and differentiation decisions in vitro and in vivo. Namely, reduction of γH2A.X levels enhance hPSC differentiation toward mesodermal  derivatives with concomitant inhibition of ectodermal derivatives. In contrast, ectopic expression of a constitutively phosphorylated mimic of γH2A.X enhanced hPSCs differentiation toward ectodermal fate while mesodermal differentiation was hindered. These phenotypic observations were associated with γH2A.X occupancy in the promoter regions of key regulatory genes associated with pluripotency and lineage choice. Our study suggests γH2A.X is a functional epigenetic pluripotency marker and novel target for guiding cell-fate commitment during differentiation.

overall_design: 1 replicate for each sample has been analyzed. tPSC sample has been analyzed in triplicate.

first: Orlando

last: Luca

first: Tanasijevic

last: Borko

first: Reid

last: Jennifer

first: Shapovalova

last: Zoya

first: Mitchell

middle: R

last: Ryan


title: RNA-Seq analysis of hearts in foxc1anju18 mutants and WT zebrafish embryos

status: Public on Dec 05 2021

city: Nanjing

first: Luqingqing

last: He

address: 12 Xuefu Road, Pukou High-tech Development Zone

institute: Model Animal Research Center

summary: The goal of this study is to compare the relative expression genes in hearts of foxc1a-null mutants and WT siblings. 96hpf  hearts of foxc1anju18 and WT siblings were dissected for total RNA extraction. RNA profiles were generated using Illumina deep sequencing. Our study represents the reduced expression of several trabeculation related signaling pathways and cell processes.

overall_design: Cardiac mRNA profiles of 96hpf wild-type and foxc1anju18 zebrafish embryos.

first: Qingshun

last: Zhao


title: ATOH8 inhibits cell proliferation through transcriptional regulating cell cycle related genes, and ATOH8 and SMAD3 form a transcriptional complex to induce an anti-cell cycle signature and prevent cell cycle progression

city: Guangzhou

first: Ximeng

last: Liu

address: Zhongshan Road No.2 Yuexiu district

institute: SUN YAT-SEN UNIVERSITY


title: ATOH8 inhibits cell proliferation through transcriptional regulating cell cycle related genes [RNA-seq]

summary: This experiment is designed to evaluate differential expression genes through comparing transcriptome profiling of ATOH8 overexpressing A549 with vector control.

overall_design: Total RNA were extracted from A549 cells stably transduced with ATOH8 or vector control and subjected to transcriptome sequencing analysis. Differential expression genes is provided.

first: Xiaonan

last: Xu


title: Gene expression in secondary lymphoid organ stromal cell populations of Cxcr4WHIM/+ mice [SLO]

status: Public on Dec 04 2021

city: Seoul

first: Jungmin

last: Choi

state: Seoul

address: 73, Goryeodae-ro, Seongbuk-gu

department: Department of Biomedical Sciences

country: South Korea

institute: Korea University College of Medicine

summary: This study provides gene expression profiles of spleen and peripheral lymph node stromal cell subsets from a CXCR4 gain-of- function mouse model of WHIM syndrome at the population level.

overall_design: Single cell RNA sequencing data of stromal cell populations from spleen and peripheral lymph nodes of Cxcr4WHIM/+ (1 sample) and Cxcr4+/+ mice (1 sample). Cells from 2 mice (for lymph nodes) and 3 mice (for spleens) per genotype were pooled.

first: João

last: Pereira

first: Sandra

last: Zehentmeier

first: Lee

last: Ho-Joon

first: Guilin

last: Wang


title: γH2A.X Modulates Self-renewal and Differentiation of Human Pluripotent Stem Cells. [HuGene-2_0-st]

overall_design: 2 replicates for each sample have been included in the analysis.


title: Electrospun scaffold micro-architecture induces an activated transcriptional phenotype within tendon fibroblasts. Bulk RNA-seq data.

city: Oxford

first: Adam

last: Cribbs

address: Windmill Road

department: NDORMS

country: United Kingdom

institute: University of Oxford

summary: Biomaterial augmentation of surgically repaired rotator cuff tendon tears aims to improve the high failure rates (~40%) of traditional repairs. Biomaterials that can alter cellular phenotypes through the provision of microscale topographical cues are now under development.  We aimed to systematically evaluate the effect of topographic architecture on the cellular phenotype of fibroblasts from healthy and diseased tendons.    Electrospun polydioxanone scaffolds with fiber diameters ranging from 300 to 4000 nm, in either a highly aligned or random configuration, were produced. Healthy tendon fibroblasts cultured for 7 days on scaffolds with highly aligned fibers demonstrated a distinctive elongated morphology, whilst those cultured on randomly configured fibers demonstrated a flattened and spread morphology.  The effect of scaffold micro-architecture on the transcriptome of both healthy and diseased tendon fibroblasts was assessed with bulk RNA-seq. Both healthy (n=3) and diseased tendon cells (n=3) demonstrated a similar transcriptional response to architectural variants. Gene set enrichment analysis revealed that large diameter (≥ 2000 nm) aligned scaffolds induced an upregulation of genes involved in cellular replication and a downregulation of genes defining inflammatory responses and cell adhesion. Similarly, PDPN and CD248, markers of inflammatory or ‘activated’ fibroblasts, were downregulated during culture of both healthy and diseased fibroblasts on aligned scaffolds with large (≥ 2000 nm) fiber diameters.     In conclusion scaffold architectures resembling that of disordered type III collagen, typically present during the earlier phases of wound healing, resulted in tendon fibroblast activation. Conversely, scaffolds mimicking aligned diameter collagen I fibrils, present during tissue remodelling, did not activate tendon derived fibroblasts. This has implications for the design of scaffolds used during rotator cuff repair augmentation.

overall_design: 8 unique conditions (scaffold architectural variants), in biological triplicate (n= 3 donors).  2 cell types (Healthy tendon fibroblasts [Hamstring derived] and diseased tendon fibroblasts [massive (>5cm in AP diameter, rotator cuff tears]). Single time point (7 days). 48 samples total.

first: Mathew

last: Baldwin

first: Sarah

last: Snelling

first: Jolet

last: Mimpen


title: Gene expression profiles in ML medium for the phytopathogenic fungus Botrytis cinerea

city: Palaiseau

first: Adeline

last: SIMON

address: 22 place de l'agronomie

country: France

institute: INRAE

summary: Full transcriptome of the Botrytis cinerea wild-type strain B0510, grown in ML medium, was studied.

overall_design: Botrytis cinerea B0510 was grown in ML solid medium. 3 replicates were performed. The 3 total-RNA samples were used for RNA-SEQ sequencing.

first: Colin

last: Clairet

first: Nicolas

last: Lapalu

last: Simon

first: Jessica

last: Soyer

first: Muriel

last: Viaud

first: Enric

last: Zehraoui

first: Berengere

last: Dalmais

first: Isabelle

last: Fudal

first: Nadia

last: Ponts


title: Gene expression profile in MS medium for the phytopathogenic fungus Fusarium graminearum

summary: Full transcriptome of the Fusarium graminearum wild-type strain CBS185.32, grown in MS medium, was studied.

overall_design: Fusarium graminearum CBS185.32 was grown in modified liquid MS (glucose was substituted with sucrose). 3 replicates were performed. The 3 total-RNA samples were used for RNA-SEQ sequencing.


title: Gene expression in bone marrow mesenchymal lineage cell and endothelial cell populations of Cxcr4WHIM/+ mice [BM]

first: Jungmin

last: Choi

summary: This study provides gene expression profiles of bone marrow mesenchymal lineage cell and endothelial cell subsets from a CXCR4 gain-of- function mouse model of WHIM syndrome at the population level.

overall_design: Single cell RNA sequencing data of mesenchymal lineage cells (MSC) and endothelial cells isolated from bone marrow (BM) of Cxcr4WHIM/+ (1 sample) and Cxcr4+/+ mice (1 sample). Cells from two mice per genotype were pooled.

first: João

last: Pereira

last: Zehentmeier


title: Activation of the interferon signaling pathway is associated with resistance to CDK4/6 inhibitors and immune checkpoint activation in ER-positive breast cancer [RNA-seq]

city: Boston

first: Rinath

last: Jeselsohn

state: MD

address: 450 Brookline Ave, D728

department: Medical Oncology

institute: DFCI

summary: CDK4/6 inhibitors are highly effective against ER+/HER2- breast cancer (BC); however, intrinsic and acquired resistance is common. Elucidating the molecular features of sensitivity and resistance to CDK4/6 inhibitors may lead to the identification of predictive biomarkers and novel therapeutic targets, paving the way toward improving patient outcomes. Parental BC cells and their endocrine-resistant derivatives (EndoR) were used in this study. Derivatives with acquired resistance to palbociclib (PalboR) were generated from parental and estrogen deprivation-resistant MCF7 and T47D cells. Transcriptomic and proteomic analyses were performed in palbociclib-sensitive and PalboR lines. We found that parental and EndoR BC lines showed varying degrees of sensitivity to palbociclib. Transcriptomic analysis of these cell lines identified an association between high Interferon (IFN) signaling and reduced sensitivity to CDK4/6 inhibitors, thus an ‘IFN-Related Palbociclib-Resistance Signature’ (IRPS) was derived. In two neoadjuvant trials of a CDK4/6 inhibitor plus endocrine therapy, IRPS and other IFN-related signatures were highly enriched in patients with tumors exhibiting intrinsic resistance to CDK4/6 inhibition. PalboR derivatives displayed a dramatic activation of IFN/STAT1-signaling compared to their short-term treated or untreated counterparts. In primary ER+/HER2- tumors, the IRPS score was significantly higher in lumB than lumA subtype and correlated with increased gene expression of immune checkpoints, endocrine resistance, and poor prognosis. Our study demonstrates that aberrant IFN-signaling is associated with intrinsic resistance to CDK4/6 inhibitors. Experimentally, acquired resistance to palbociclib is associated with activation of the IFN-pathway, which warrants additional studies to clarify its involvement in resistance to CDK4/6 inhibitors.

overall_design: RNA-seq of ER+ breast cancer cell models and derivatives with resistance to endocrine therapy or dual resistance to estrogen deprivation and palbociclib, in duplicates, using Illumina NextSeq500.

first: Myles

last: Brown

first: Rachel

last: Schiff

first: Xiaoyong

last: Fu

first: Carmine

last: De Angelis

first: Agostina

last: Nardone


title: Transcriptomic profiling of Angiotensin II induced fibrotic myocardial tissue in response to EHP-101 or Losartan

city: Córdoba

first: Eduardo

last: Muñoz

address: Avda Menéndez Pidal s/n

institute: Instituto Maimónides de Investigación Biomédica de Córdoba (IMIBIC), University of Córdoba

summary: In order to obtain a global perspective of the effect of EHP-101 and Losartan on cardiac fibrosis, we performed a mRNA-Seq analysis of the myocardial tissue changes in response to Ang II, Ang II + EHP-101 and Ang II + Losartan.

overall_design: Eight-week old male C57/BL6 mice were housed under controlled conditions with free access to standard food and water. First, mice were anesthesized and exposed to a subcutaneous infusion of Ang II (or saline) using osmotic pumps during 28 days. In the last two weeks, mice were treated with oral EHP-101 (20 mg/kg), dilued Losartan in the drinking water (0,6 gr/L) or vehicle. Finally, mice were sacrified by cervical dislocation and skin, heart, aorta, lung and kidney were removed and processed for further analysis.

first: Adela

last: García-Martín

first: Carmen

last: Navarrete

first: Martín

last: Garrido-Rodríguez


title: Genome-wide regulations of the preinitiation complex formation and elongating RNA polymerase II by an E3 ubiquitin ligase, San1.

city: Carbondale

first: Sukesh

middle: R.

last: Bhaumik

state: IL

address: 1245 Lincoln Drive, Neckers Building, Rm 229

department: Biochemistry and Molecular Biology

institute: Southern Illinois University School of Medicine

summary: San1 is an E3 ubiquitin ligase involved in nuclear protein quality control via its interaction with intrinsically disordered proteins for ubiquitylation and 26S proteasomal degradation. Since a number of transcription/chromatin regulatory factors contain intrinsically disordered domains and can be inhibitory to transcription when in excess, San1 might be involved in regulation of transcription. To address this, we carried out ChIP-seq (Chromatin immunoprecipitation sequencing) here to analyze the role of San1 in genome-wide association of TBP (TATA-box binding protein that nucleates the preinitiation complex formation at the promoter for transcription initiation) and RNA polymerase II (that is recruited to the promoter by TBP and subsequently engaged in transcription elongation at the coding sequence for mRNA biosynthesis). Our results reveal the genome-wide role of San1 in facilitating the recruitment of TBP to the promoter, thus indicating its involvement in promoting the preinitiation complex formation for transcription initiation. Further, we find the global role of San1 in regulating RNA polymerase II at the coding sequence.

overall_design: Yeast cells were subjected to Formaldehyde cross-linking and sonicated; the sonicated lysates were immunoprecipitated with Pol II or TBP antibody; Following reverse cross-linking ChIP DNA and corresponding Input DNA were purified and sent to Genome Technology Access Center at the McDonnell Genome Institute of Washington University, St. Louis, USA, for sequencing

first: Chhabi

last: Govind

first: Priyanka

last: Barman

first: Rwik

last: Sen


title: Gene expression datasets

last: Choi

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

overall_design: Refer to individual Series


title: Gene expression of leptin receptor (LEPR)+ bone marrow (BM)  mesenchymal stem cells after lymphotoxin 𝛽 receptor (LT𝛽R) inhibition [LTbR]

summary: This study provides gene expression profiles of LEPR+ BM mesenchymal stem cells from wildtype mice treated with soluble LT𝛽R-Ig decoy for 3 weeks and from control mice.

overall_design: Bulk RNA sequencing of LEPR+ BM mesenchymal stem cells sorted from LT𝛽R-Ig decoy or control C57BL/6 mice (4 pairs).

first: Joao

last: Pereira

first: Vivian

last: Lim


title: Exome Genotyping Study of Scripps Venous Thrombosis Registry using Axiom® Exome Genotyping Array

city: La Jolla

first: Hiroshi

last: Deguchi

state: Ca

address: 10550 N Torrey pines Rd

institute: The Scripps Research Institute

type: Genome variation profiling by genome tiling array

summary:
Younger age and VTE recurrence are more likely to be caused by genetic risk factors than secondary VTE in older patients who more likely have comorbidities.  When the exome rare variant genotyping database of the Scripps VTE Registry for adults < 55 yrs old was generated and analyzed for single nucleotide polymorphisms (SNPs).
Two  F5 related SNPs (rs6025, factor V Leiden and rs6687813) exceeded significance (FDR (false discovery rate) p < 0.05).  No other variants met genome-wide significance.  When the data for the subgroup of cases with recurrent VTE that are more likely to have genetic risk factors than cases with a single VTE episode were compared to controls (N=211 controls and N=32 recurrent VTE cases), 28 SNPs, including the F5 rs6025 SNP, achieved significance (FDR p < 0.05).

overall_design: The study population consisted of 104 VTE cases and 211 controls from the Scripps Venous Thrombosis Registry. The quality of each DNA stored in the freezer was re-evaluated according to the manufacture’s protocol for performing Axiom® Exome Genotyping Array analysis. Subjects were genotyped using the Axiom® Exome Genotyping Array” (Affymetrix)

first: Darlene

last: Elias

first: John

last: Griffin


title: Physiological and molecular mechanisms of maize adapting to drought conditions with negative pressure continuous water supply

status: Public on Dec 03 2021

city: Daqing

first: jili

last: zhang

address: 5 Xinfeng Road

institute: heilongjiang bayi agricultural university

summary: The test result showed that ribosome, photosynthesis, cysteine and methionine metabolism, photosynthesis antenna proteins pathway enriched more genes in LW treatment. It was found that 5 genes  included PsbE, PsbA, atpH, psaB, Zm00001d045620. it was found that four genes were highly downregulated in the photosynthesis antenna proteins pathway included Zm00001d044396, Zm00001d044399, Zm00001d044401, Zm00001d044402, these high-fold down-regulation genes related to inhibit maize growth. There was four highly upregulated in the ribosome pathway included Zm00001d006924, Zm00001d023293, Zm00001d036464, Zm00001d051662, these genes are closely related to maize adaptation to the drought conditions with negative pressure continuous water supply environment.

overall_design: Study on gene expression under different soil water content

first: zhang

last: Jili

first: Wang

last: Peng


title: A transcriptional rheostat couples past activity to future sensory responses

first: David

last: Brann

state: MA

address: 220 Longwood Ave

department: Neurobiology

institute: Harvard Medical School

summary: Animals traversing different environments encounter both stable background stimuli and novel cues, which are thought to be detected by primary sensory neurons and then distinguished by downstream brain circuits. Here we show that each of the ~1000 olfactory sensory neuron (OSN) subtypes in the mouse harbors a distinct transcriptome whose content is precisely determined by interactions between its odorant receptor and the environment. This transcriptional variation is systematically organized to support sensory adaptation: expression levels of more than 70 genes relevant to transforming odors into spikes continuously vary across OSN subtypes, dynamically adjust to new environments over hours, and accurately predict acute OSN-specific odor responses. The sensory periphery therefore separates salient signals from predictable background via a transcriptional rheostat whose moment-to-moment state reflects the past and constrains the future; these findings suggest a general model in which structured transcriptional variation within a cell type reflects individual experience.

overall_design: 152 replicates of single cell RNA-seq libraries using 10x genomics chromium single cell 3' library reagents from various experiments (home-cage, OR swap, unilateral naris occlusion, odor exposure, optogenetic stimulation, environment switch).

first: Tatsuya

last: Tsukahara

first: Sandeep

last: Datta


title: Disruption of the IL-33-ST2-AKT signaling axis impairs neurodevelopment by inhibiting microglial metabolic adaptation and phagocytic function

city: Hangzhou

first: DANYANG

last: HE

state: Zhejiang

address: 600 Dunyu Road Sandun Town

department: School of Life Sciences

institute: Westlake Univeristy

summary: Using single-cell RNA-Seq coupled with pharmacological and genetic perturbation to indentify a range of microglial states and uncover novel pathways that regulate microglial function and activation during postnatal development.

overall_design: 1, To define the transcriptional landscape of developing microglia in postnatal cortex, we profiled 9,391 CD45int CD11bint cells from postnatal (postnatal day 9, P9) and young adult (postnatal day 28, P28) cortices by massively parallel droplet-based 3’ scRNA-seq. 2. To explore the role of IL33-ST2 signaling in regulating the microglial activation gene program and the microglia heterogeneity, we performed scRNA-seq of cortical microglia from ST2−/− mice and littermate controls at P9. 3, To analyze the molecular signature induced by IL-33 in primary microglia, we profiled low-input bulk RNA Sequencing of primary mouse microglia stimulated with IL-33 and unstimulated control cells. 4, To analyze transcriptional features of pro-phagocytic microglia from developing brain, Tau-GFP positive and negative microglia were sorted from postnatal day 9 cortex for low-input bulk RNA Seq by SmartSeq2. 5, To analyze transcriptional signature of metabolically active microglia in developing brain, TMRM staining high and low microglia subsets were sorted from postnatal day 9 cortex for low-input bulk RNA Seq by SmartSeq2

first: Danyang

last: He

first: Heping

last: Xu

first: Elena

last: Christian

first: Aviv

last: Regev

first: Vijay

last: Kuchroo

first: Yu

last: Hou


title: LncRNA expression profile and target gene prediction of calcification in human aortic smooth muscle cells induced by DPP4

city: Luzhou

first: tongjie

last: xu

state: sichuan

address: No. 25, Taiping street, Luzhou city

department: Department of Vascular Surgery

institute: The Affiliated Hospital of Southwest Medical University

summary: Arterial media calcification caused by diabetes is an important cause of vascular calcification. Dipeptidyl peptidase-4 (DPP4) is associated with diabetic arterial media calcification. At the same time, long non-coding RNA(lncRNA) is closely related to the evolution of a variety of cardiovascular diseases, but the involvement of lncRNA in vascular calcification induced by DPP4 has not been reported in details. In this study, we established a model of human aortic smooth muscle cells (HASMCs) calcification induced by DPP4. There was a significant difference in the expression of lncRNAs and mRNAs between normal and calcified vascular smooth muscle cells detected by gene chip technology. Based on the results of microarray detection, we found that lncRNA may be involved in vascular calcification induced by DPP4 through regulating target genes.

overall_design: Human aortic vascular smooth muscle cells were induced by DPP4 after four days, and the expression of lncRNA and mRNA genes in the intervention group and the blank control group were detected. The independent experiment was repeated for 3 times.

first: yong

last: liu


title: Establishment and characterization of BAP1 knockout gene in human mesothelial cell line generated by using CRISPR/Cas9 technology

city: Nagoya

first: Akinobu

last: Ota

state: Aichi

address: 1-1 Yazakokarimata

department: Food and Nutritional Environment

institute: Kinjo Gakuin University

summary: To investigate the effect of BAP1 on gene expression, we have emoloyed whole genomic microarray expression profiling using MeT-5A and HOMC-D4 cells

overall_design: The MeT-5A  and HOMC-D4 cells were plated at 80% confluence and cultured for 24 hours in vitro.

first: Sivasundaram

last: Karnan


title: Response to1 µM dexamethasone in MEF cells expressing GR dimer deficient mutant receptors

city: Gent

first: Steven

last: Timmermans

address: Technologiepark 71

country: Belgium

institute: VIB-UGent

summary: The glucocorticoid (GC) receptor (GR) is essential in development and inflammation. Healthy GRdim/dim mice with reduced dimerization propensity due to a point mutation (A465T) at the dimer interface of the GR DNA binding domain (DBD) (here GRD/D) have helped to define GR monomer and dimer functions of GR. Since GRD/D retains residual dimerization capacity, we generated the dimer-nullifying double mutant GRD+L/D+L mice, featuring an additional mutation (I634A) in the ligand binding domain (LBD) of GR. These mice are perinatally lethal, as are GRL/L mice, displaying improper lung and skin formation. We used embryonic fibroblasts, high and low doses of dexamethasone (Dex), nuclear translocation, RNAseq, dimerization assays and ligand binding assays (and Kd values), we suggest that the lethal phenotype is due to insufficient ligand binding. The data suggest cross talk between GR dimerization potential and ligand affinity. We conclude that a mutation as subtle as this I634A, at a position not directly involved in ligand interactions senso stricto, can thus still influence ligand binding and have a lethal outcome.

overall_design: RNA-seq on MEF cells: 5 GR genotypes (GRwt/wt (run 1, run 2), GRD/D (run 1), GRL/L (run 2) and GRD+L/D+L (run 1) and GRko/ko (run 1)) after stimulation with vehicle or 1 µM dexamethasone for a total of 12 sample groups .3 primary MEF cultures per genotype were used, each derived from a different mouse to obtain 3 biological replicates

first: Nicolette

last: Verhoog

first: Kelly

last: Van Looveren

first: Sylviane

last: Dewaele

first: Tino

last: Hochepied

first: Melanie

last: Eggermont

first: Barbara

last: Gilbert

first: Anne

last: Boerema-de Munck

first: Tineke

last: Vanderhaeghen

first: Joke

middle: V

last: Berghe

first: Natalia

middle: G

last: Gonzalez

first: Yehudi

last: Bloch

first: Mathias

last: Provost

first: Savvas

middle: N

last: Savvides

first: Karolien

last: De Bosscher

first: im

last: Declercq

first: Robbert

last: Rottier

first: Ann

last: Louw

first: Claude

last: Libert


title: Single-cell transcriptional profiles in the visceral adipose tissue from obese and lean C57BL6 mice

city: Farmington

first: William

middle: F

last: Flynn

state: CT

address: 10 Discovery Drive

institute: The Jackson Laboratory

summary: Cellular senescence has been reported to play an important role in insulin resistance. While the molecular mechanism remains unclear. Here we applied  the scRNA-seq analysis for the visceral fat from the obese mice with 2 month of high-fat diet. Visceral fat was digested by type II collagenase. Stromal Vascular  Fraction was collected, incubated with hashing antibody and then subjected to the 10X Chromium. 8180 cells were found from the obese mice and 14,502 cells were from the lean mice. 14 clusters and 9 cell types were identified. The key senescence marker  P21 were found  highly expressed in the obese group, when compared to the lean group. However, the other senescence marker P16 were unchanged. P21+ cells are mainly preadipocytes, macrophage and endothelial cells.  More than 300 different expressed genes were found among the P21+ cells. The NF-kB pathway was activate according to the GO analysis, which is strongly associated with insulin resistance and diabetes

overall_design: Examnination of the senescence in the insulin resistance condition

first: Ming

last: Xu

first: Binsheng

last: Wang

first: Lichao

first: Wulin

last: Zuo

first: Paul

last: Robson


title: DDX5 in colonic tumors

city: San Diego

first: Wendy

last: Huang

address: 9500 Gilman Drive #0651

department: Cellular and Molecular Medicine

institute: University of California San Diego

summary: The Asp-Glu-Ala-Asp (DEAD)-box RNA binding protein, DDX5, is ubiquitously expressed in many cell types, yet its role in RNA metabolism and its downstream function in vivo has not been fully elucidated. In the intestine, DDX5 is highly expressed in the intestinal epithelial cell (IECs) and contributes to tumorigenesis. Here, we used a conditional mouse lines where DDX5 is knocked out in IECs upon Tamoxifen administration to uncover mechanisms underlying DDX5 functions in colon tumors.

overall_design: For tumor collection, 8 week old littermates were treated with Tamoxifen on day 1, 2, 3 and tumor tissues were harvested betwee day 30-37 post first Tamoxifen (TAM) administration.


title: Vitamin D treatment timing is critical for transcriptome modulation of immune challenged primary human cells

city: Kuopio

first: Andrea

last: Hanel

address: Yliopistonranta 1E, POB 1627

department: Institute of Biomedicine

country: Finland

institute: University of Eastern Finland

summary: In this study, the transcriptome of peripheral blood mononuclear cells (PBMCs) of a healthy adult was investigated in response to in vitro treatment with LPS, beta-glucan and 1,25(OH)2D3.

overall_design: RNA-seq of PBMCs of one individual treated immediately after isolation in 3 biologial repeats with 10 ng/ml lipopolysaccharide (L), 5 µg/ml beta-glucan (B), their solvent (0.1% DMSO (D)), the biologically active form of vitamin D, 10 nM 1,25(OH)2D3 (V) or its solvent (0.1% ethanol (E))

first: Carsten

last: Carlberg


title: Spatial transcriptomic studies of the small intestine from WT and DDX5△IEC (KO) mice

summary: DDX5, a DEAD box containing RNA binding protein, is involved in multiple aspects of RNA metabolism and is abundantly expressed in all subsets of the intestinal epithelial cells (IEC). Here, we characterized the DDX5-dependent transcriptome in the small intestine. In the DDX5△IEC tissue, we found that secretory IEC lineage progenitor containing spots (Atoh1hi and Sox4hi) had reduced expression of Pou2f3, a master regulator of a subset of IECs called tuft cells. As a result of the loss of Pou2f3 expression in the progenitors, DDX5△IEC tissue harbored lower number of tuft cell containing spots (Dclk1hi) compare to WT tissues.

overall_design: One intestine tissue from each genotype were obtained from 8wk old cohoused mice. Results of ileum epithelium from DDX5△IEC mutant mice were compared to those from WT mice.

first: Tianyun

last: Long

first: Attilio

last: Lemolo

first: Francesca

last: Telese


title: A novel whole blood gene expression signature for asthma, dermatitis and rhinitis multimorbidity in BAMSE and INMA cohort

city: La Tronche

first: Nathanaël

last: Lemonnier

address: Allée des Alpes

department: Institute for Advanced Biosciences

institute: University Grenoble Alpes


title: RNA-seq of macrophages and microglia from injured spinal cord after IL-13, IL-4 or PBS treatment

city: Bellaterra

first: Jesus

last: Amo-Aparicio

state: Barcelona

address: Av Can Domenech s/n, Facultad de Medicina M4-129

institute: Universitat Autonoma de Barcelona

summary: Spinal cord injured mice were treated with IL-13, IL-4 or PBS. Populations of macrophages and microglia were sorted and analyzed separately.

overall_design: Examination of macrophages and microglia signature from spinal cord injured mice after cytokine treatment.

first: Isaac

last: Francos-Quijorna

first: Anna

last: Esteve-Codina

first: Marta

last: Gut

first: Ruben

last: Lopez-Vales


title: A novel whole blood gene expression signature for asthma, dermatitis and rhinitis multimorbidity in INMA cohort

summary: Allergic diseases correspond to a broad range of hypersensitivity reactions, often occurring as co-morbidities. Investigation of the molecular basis of allergy is a challenge because of its highly heterogeneous nature. We combined large-scale and high-throughput gene expression technology and systems biology approaches to retrieve relevant biomarkers and signalling pathways.

overall_design:
Gene expression data was generated and analysed from whole blood of a total of 201 subjects provided by the spanish INMA cohort of children in relation to allergy status (presence of one or multiple diseases among asthma, eczema and/or rhinitis). The data production and analysis pipeline includes Affymetrix HTA 2.0 Genechips from quality-controlled RNA and transformed and biotin-labelled cRNA using restricted randomization and replicate reference sample to control and minimize batch effect, and pre-processing with RMA normalization.
characteristics: gender -> 1: male ; 0: female
characteristics: age -> in months
characteristics: allergy/asthma/dermatitis/rhinitis -> 1: yes, 0: no

first: Camille

last: Ménard

first: Stéphane

last: Joly

first: Josep

last: Anto

first: Jean

last: Bousquet

first: Loreto

last: Santa Marina Rodríguez

first: Mariona

last: Bustamante

first: Jesús

last: Ibarluzea Maurolagoitia

first: Jordi

last: Sunyer


title: ChIP-seq of KLF2 Binding Site 1-targeting CRISPRi in MDA-MB-231 cells

city: Singapore

first: Muhammad Sufyan

last: Bin Masroni

address: Special Histopathology Laboratory, Level 3, Main Building, 5 Lower Kent Ridge Road, National University Hospital

department: Pathology

country: Singapore

institute: National University Singapore

summary: This experiment is designed to verify that the targeted CRISPRi indeed bind specifically at the intended site (KLF2 binding site 1 on the miR-125b-1 promoter) in MDA-MB-231 cells. At the same time, off-target binding can be explored.

overall_design: Comparison between MDA-MB-231 cells treated with control CRISPRi (targeting copGFP sequences) and targeted CRISPRi (KLF2 binding site 1 on the miR-125b-1 promoter)

first: Muhammad

middle: S

last: Masroni

first: Leong

last: Sai Mun


title: The proteasome inhibitor MG132 adjusts the transcriptome in Brassica napus roots

city: Nottingham

first: Marios

last: Georgiou

address: Queen's Medical Centre

institute: University of Nottingham

summary:
The goal of this study was to determine how proteasome inhibition alters the transcriptome in Brassica napus roots.
Specifically, we wished to see if proteasome inhibition resulted in transcriptome signatures of oxidative stress, protein catabolism, or nitrogen assimilation

overall_design: Three control samples (0.1% DMSO) and three experimental (50 uM MG132 dissolved in DMSO)

first: Doug

last: Van Hoewyk

first: Sean

last: May

first: Marcos

last: Castellanos-Uribe


title: A unique adipocyte progenitor population that promotes age-related adiposity

status: Public on Dec 02 2021

city: Los angeles

first: Gaoyan

last: Li

address: 1929 beloit ave, apt315

institute: UCLA

summary: The average fat (adipose tissue) mass in adults increases dramatically with age, and older people often suffer from visceral obesity and related adverse metabolic disorders. Unfortunately, how aging leads to adipose accumulation is poorly understood. It is known that fat cell (adipocyte) turnover is very low in young mice, similar to that in young humans. Single-cell RNA sequencing analyses reveal that aging globally remodels APCs. Herein, we identify a novel, age-specific committed APC population as CP-A cells, existing both in mice and humans, with a global activation of proliferation and adipogenesis pathways. CP-A cells display high proliferation and adipogenesis activity, both in vivo and in vitro. M1 macrophages may regulate the remodeling of APCs and the generation of CP-A cells during aging.

overall_design: single cell RNA sequencing profiles of Lin- stromal vascular fraction (SVF) cells and CD45+ immune cells from 2.5-month-old or 12-month-old C57BL/6J male mice epididymal white adipose tissue or Lin- SVFs from human peri-pancreatic adipose tissue.

first: Guan

last: Wang

first: Qiong

middle: A

first: Xia

last: Yang


title: Identification of ASCL1 as a determinant for human iPSC-derived dopaminergic neurons

city: Chicago

first: Rajeshwar

last: Awatramani

address: 320 E. Superior Ave.

institute: Northwestern University

summary: To better understand how human pluripotent stem cells (hPSCs) differentiate from progenitor cells into distinct neuronal states, we performed 10x single cell RNA sequencing on in vitro directed differentiation cultures. We established differentiation platforms that model neural induction from human induced pluripotent stem cells (iPSCs) and single cell profiled two systems: 1) co-culture of progenitors and neurons and 2) purified neurons.

overall_design: A human iPSC line, 2131, generated by reprogramming dermal fibroblasts were stimulated with small molecules and recombinant proteins to promote neural differentiation. Both neural co-cultures and purified neuronal cells were extracted for 10x single cell RNA sequencing with 3 replicates for each system.

first: Dimitri

last: Krainc

first: Aaron

last: Earley


title: MitomiR profiling of mitochondria extracted from monocytic cell line

city: Montpellier

first: Isabelle

middle: Duroux

last: Richard

address: Hôpital Saint Eloi  80 avenue Augustin Fliche

institute: INSERM

summary:
MiRNAs play pivotal roles in regulating macrophage functions, including differentiation, polarization, recruitment, and activation of inflammation. in this review, to provide novel insight into macrophage differentiation-specific mitomiR signatures and associated mitochondrial pathways, we performed a global miRNA profiling on extracted mitochondria and total cell content of human macrophages. The THP-1 monocytic cell line was treated with phorbol-12-myristate-13-acetate (PMA) to induce differentiation into macrophages
The human monocytic cell line THP-1 cells were differentiated into THP-1 derived macrophages with 40 ng/mL phorbol 12-myristate 13-acetate (PMA),The mitochondrial fraction of the cells were enriched and purified using anti-TOM22 microbeads (Miltenyi Biotec). After total RNA extraction, and using Taqman low-density arrays (TLDA), we performed the global miRNA profiling on extracted mitochondria and compared with total cell content

overall_design: qPCR miRNA expression profiling of 4 samples.

last: Duroux-Richard

first: Florence

last: Apparailly


title: SOX2 Genomic Localization in Small Cell Lung Cancer Cell Lines

city: Sioux Falls

first: Michael

last: Kareta

state: SD

address: 2301 East 60th Street North

department: Genetics & Genomics

institute: Sanford Research

summary: We utilized CUT&RUN to assess the genome-wide binding of SOX2 in human small cell lung cancer cell lines.

overall_design: 3 samples, 2 technical replicates each

first: Madeline

last: Van de Kamp

first: Ethan

last: Thompson


title: Cell-Type-Specific Impact of Glucocorticoid Receptor Activation on the Developing Brain: A Cerebral Organoid Study [Wafergen iCell8]

city: Munich

first: Elisabeth B

last: Binder

address: Kraepelinstr. 2-10

institute: Max Planck Institute of Psychiatry

summary: These data describe single-cell RNA sequencing in cerebral organoids treated with the glucocorticoid Dexamethasone or with a vehicle control (DMSO) at different culture time-points (Day-30, Day-60 and Day-90).

overall_design: Single-cell RNA sequencing was performed in cerebral organoids grown in vitro for 30, 60, or 90 days days. Both treated (Dexamethasone 100nM) and untreated (DMSO) organoids were collected immediately after a 12-hour exposure and four biological replicates were employed at each timepoint. Randomization was performed in advance of library preparations.

first: Cristiana

last: Cruceanu

first: Elisabeth

last: Bider

first: Leander

last: Dony

first: Simone

last: Roeh


title: Cell-Type-Specific Impact of Glucocorticoid Receptor Activation on the Developing Brain: A Cerebral Organoid Study

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

overall_design: Refer to individual Series


title: Investigation of gene expression in murine Shh-Medulloblastoma, ocular lesions of Rax-creERT2::Ctnnb1(ex3)Fl/+SmoM2 Fl/+ (RBS) mice and healthy murine eyes.

city: Hamburg

first: Julia

middle: Elisabeth

last: Neumann

state: Hamburg

address: Martinistr. 52

department: Institute of Neuropathology

institute: University Medical Center Hamburg-Eppendorf

summary: The objective of this study was to compare gene expression of RBS ocular lesions with human intraocular medulloepithelioma (IO-MEPL), using murine and human Shh-Medulloblastomas as a reference.

overall_design: Gene expression data was obtained from FF tissue samples of three 14 day old hGFAP-cre::SmoM2Fl/+ mice, as well as eyes of five E18.5 Rax-creERT2::Ctnnb1(ex3)Fl/+SmoM2Fl/+  and four E18.5 Ctnnb1(ex3)Fl/+SmoM2Fl/+ mice as controls.

first: Matthias

last: Dottermusch

first: Piotr

last: Sumislawski

last: Krevet

first: Hannah

last: Voß

first: Maximilian

last: Middelkamp

first: Harald

last: Bartsch

first: Karl

last: Sotlar

first: Andrey

last: Korshunov

first: Markus

last: Glatzel

first: Ulrich

last: Schüller


title: A novel whole blood gene expression signature for asthma, dermatitis and rhinitis multimorbidity in BAMSE cohort

first: Nathanaël

last: Lemonnier

overall_design:
Gene expression data was generated and analysed from whole blood of a total of 256 subjects provided by the swedish BAMSE cohort of teenagers in relation to allergy status (presence of one or multiple diseases among asthma, eczema and/or rhinitis). The data production and analysis pipeline includes Affymetrix HTA 2.0 Genechips from quality-controlled RNA and transformed and biotin-labelled cRNA using restricted randomization and replicate reference sample to control and minimize batch effect, and pre-processing with RMA normalization.
characteristics: gender -> 1: male ; 0: female
characteristics: age -> in months
characteristics: allergy/asthma/dermatitis/rhinitis -> 1: yes, 0: no

first: Camille

last: Ménard

first: Stéphane

last: Joly

first: Josep

last: Anto

first: Jean

last: Bousquet

first: Kebede

last: Simon

first: Olena

last: Gruzieva

first: Magnus

last: Wickman

first: Erik

last: Melén


title: AD-linked R47H-TREM2 mutation induces disease-enhancing microglial states via AKT hyperactivation

city: San Francisco

first: Lay

last: Kodama

state: CA

address: 1650 Owens St.

department: Gladstone Institute of Neurological Disease

institute: University of California San Francisco

summary: The hemizygous R47H variant of TREM2, a microglia-specific gene in the brain, increases risk for late-onset Alzheimer’s disease (AD). Using transcriptomic analysis at the single-nuclei level from brain tissue of AD patients with the R47H mutation or the common variant (CV)-TREM2, we found that R47H-associated microglial subpopulations had enhanced inflammatory signatures reminiscent of previously-identified disease-associated microglia (DAM) and hyperactivation of AKT, one of the signaling pathways downstream of TREM2. We established a tauopathy mouse model with heterozygous knock-in of the human TREM2 with R47H mutation or CV, and found that R47H induced and exacerbated tau-mediated spatial memory deficits in female mice. Single-cell transcriptomic analysis of microglia from these mice also revealed transcriptomic changes induced by R47H that had significant overlaps with R47H microglia in human AD brains, including robust increases in proinflammatory cytokines, activation of Akt signaling, and elevation of a subset of disease-associated microglial signatures. Pharmacological Akt inhibition with MK-2206 largely reversed the enhanced inflammatory signatures in primary R47H microglia treated with tau fibrils. Strikingly, in R47H heterozygous tauopathy mice, MK-2206 treatment abolished a tauopathy-dependent microglial subcluster, and rescued tauopathy-induced synapse loss. By uncovering disease-enhancing mechanisms of the R47H mutation conserved in human and mouse, our study supports inhibitors of AKT signaling as a novel microglial modulating strategy to treat AD.

overall_design: FACS and plate-based single cell RNA Smart-seq2 sequencing of microglia from tauopathy P301S and non transgenic control female mouse hippocampus with TREM2-R47H mutation and their age-matched mouse controls

first: Faten

last: Sayed

first: Li

last: Fan

first: Gillian

middle: K

last: Carling

first: Joe

last: Udeochu

first: David

last: Le

first: Qingyun

last: Li

first: Lu

last: Zhou

first: Man Ying

last: Wong

first: Rose

last: Horowitz

first: Pearly

last: Ye

first: Hansruedi

last: Mathys

first: Minghui

last: Wang

first: Xiang

last: Niu

first: Linas

last: Mazutis

first: Xueqiao

last: Jiang

first: Xueting

first: Fuying

last: Gao

first: Matthew

last: Brendel

first: Maria

last: Telpoukhovskaia

first: Tara

last: Tracy

first: Georgia

last: Frost

first: Yungui

first: Yaqiao

first: Yue

last: Qiu

first: Zuolin

last: Cheng

first: Guoqiang

last: Yu

first: John

last: Hardy

first: Giovanni

last: Coppola

first: Fei

first: Michael

last: DeTure

first: Bin

last: Zhang

first: Lei

last: Xie

last: Trajnowski

first: Virgina

last: Lee

first: Shiaoching

last: Gong

first: Subhash

last: Sinha

first: Dennis

last: Dickson

first: Wenjie

last: Luo

last: Gan


title: The impacts of miRNA-125b expression on transcriptome of cancer cells

city: Kent Ridge

first: Sai Mun

last: Leong

address: Lvl 3, NUH Main Building, 5 Lower Kent Ridge Road

institute: National University of Singapore

summary:
We report the use of single-cell RNA sequencing (scRNA-seq) technique to compare the transcriptomic profiles of human breast cancer cells with high and low expression of miR-125b.
Methods: MDA-MB-231(miR-125b-promo-EGFP) cells were flow sorted at maximum and minimum 5% of miR-125b expression level, and deep sequenced using Illumina HiSeq 2000. The sequencing reads that passed quality filters were mapped to the reference genome using TopHat, followed by counting of reads numbers using HTSeq
Results: Using an optimized data analysis workflow, we mapped about 30 million sequence reads per sample to the human DNA reference genome (build hg19) and identified 48162 transcripts in MDA-MB-231(miR-125b-promo-EGFP) cells with low and high miR-125b expression. A total of 303 transcripts showed differential expression between low and high miR-125b expression cells, with |log2 (Fold change)| ≥ 2 and adjusted p value ≤ 0.05

first: Leong

last: Mun

first: Lee

last: Wah


title: Transcriptional alteration by alpha-glucosyl-rutin in human fibroblasts, iPSCs, and keratinocytes.

city: Minato-ku

first: Tomoko

last: Miyake

state: Tokyo

address: 7-1-19 Akasaka

department: Cosmetic R&D

institute: Takara Belmont Corp.

summary: Three genetically identical cells, NB1RGB human fibroblasts, C2 iPSCs generated from NB1RGB, and P1 keratinocytes differentiated from C2 iPSCs were treated with 50 mM alpha-glucosyl-rutin (AGR) for 4 hours. Total RNA was extracted and RNA sequencing was performed to investigate the effects of AGR on transcriptional change in stem cells and differentiated cells.

overall_design: Examined 3 types of cells (fibroblasts, iPSCs, and keratinocytes) and 2 types of treatments (non treatment or AGR), total 6 samples were analyzed.

first: Munekazu

last: Kuge

first: Yoshihisa

last: Matsumoto

first: Mikio

last: Shimada


title: Cell-Type-Specific Impact of Glucocorticoid Receptor Activation on the Developing Brain: A Cerebral Organoid Study [10x Genomics]

first: Elisabeth B

last: Binder

summary: These data describe single-cell RNA sequencing in cerebral organoids treated with the glucocorticoid Dexamethasone or with a vehicle control (DMSO) at 90 days in culture.

overall_design: Single-cell RNA sequencing was performed in cerebral organoids derived for iPSCs from two different donors were grown in vitro for 90 days. Both treated (Dexamethasone 100nM) and untreated (DMSO) organoids were collected immediately after a 12-hour exposure and four biological replicates were employed at each timepoint.

first: Cristiana

last: Cruceanu

first: Elisabeth

last: Bider

first: Leander

last: Dony

first: Simone

last: Roeh


title: Post-natal meningeal macrophages protect against viral neuroinfection

city: Marseille

first: Rejane

last: Rua

state: PACA

address: Centre d'Immunologie de Marseille Luminy Parc Scientifique et technologique de Luminy 163 Avenue de Luminy Case 906

institute: CIML

summary: Due to the vital importance of the Central Nervous System (CNS), its potential infection and inflammation have to be tightly controlled. The surface of the CNS is connected to the periphery by a rich and complex tissue, the meninges. They contain a vast network of macrophages subdivided in at least two subpopulations endowed with elusive functions: a neonatal, MHC-II negative macrophage population, and an post-natal population expressing MHC-II. Using in situ-histocytometry, flow cytometry, and single-cell RNA sequencing approaches, we showed that those populations have opposite dynamic behaviors in response to in vivo peripheral challenges such as LPS, SARS-CoV2 and lymphocytic choriomeningitis virus (LCMV), with an apparent contraction of the MHC-II+ population. Focusing on LCMV infection in experimental mouse models and using innovative pharmacological and genetic depletion strategies, we show that meningeal macrophages (MM) represent an early line of protection against this neuroinvasive pathogen. In their absence, specific areas in the meninges became highly infected, leading to fatal brain disease. While their intrinsic sensing of viral replication through the Mitochondrial antiviral-signaling protein (MAVS) was dispensable, sensing of IFNs through the STAT1 pathway played an important role in controlling viral spread. Unexpectedly, the post-natal MHC-II+ macrophage population had an important role in controlling neuroinfection, by shutting down biosynthesis pathways and efficiently blocking viral replication. This work helps understanding the spatial organization of the brain defense system and the cellular and molecular mechanisms involved in CNS protection.

overall_design: Meningeal cells were extracted as described in the Mononuclear cell isolation and Flow cytometry sections above (apart from sacrifice, which was performed using an overdose of Ketamine/Xylasine) and stained with Hoescht 33342 (10µg/ml, Sigma) and Draq7 (0.3µM, ThermoFischer). The 4 samples were differentially labelled using 4 Hashtags (TotalSeq-A, clone M1/42; 30-F11, Biolegend) at 0.1mg/ml for 15min at 4°C. After a wash, nucleated cells were isolated from 2 PBS or 2 LPS-injected mice (7 weeks-old males) at day 1 post-injection using a FACS Aria III SORP (BD) using a 100 µm nozzle. 52 000 cells of each sample were pooled, centrifuged at 350g for 3 minutes, and 35 000 cells of the pool were loaded on a Chromium Single Cell Instrument (10x Genomics) to generate single-cell gel beads-in-emulsion (GEM). GEM and scRNA-libraries were prepared using the Single Cell 3’v3 Gel Bead and Library Kit (10X Genomics, No. 1000092) and the Chromium i7 Multiplex kit (10x Genomics, No 120262) according to the manufacturer’s instructions.

first: Julie

last: Rebejac

first: Elisa

last: Eme-Scolan

first: Matei

last: Teleman

first: Lionel

last: Spinelli

first: Emeline

last: Gallo

first: Annie

last: Roussel-Queval

first: Ana

last: Zarubica

first: Amandine

last: Sansoni

first: Quentin

last: Bardin

first: Philippe

last: Hoest

first: Bernard

last: Malissen

first: Marie-Cécile

last: Michallet

first: Toby

last: Lawrence

first: Monica

last: Manglani

first: Dorian

middle: B

last: McGavern


title: Expression data from prostate tissues from mouse models of prostate cancer fed a high-fat diet or a control diet.

city: Osaka

first: Makoto

last: Matsushita

address: 2-2 Yamadaoka, Suita

department: Urology

institute: Osaka University Graduate School of Medicine

summary: To examine the effects of high-fat diet on gene expression in the prostate of a mouse model of prostate cancer, we extracted RNA from the prostates,  and evaluated their gene expressions using microarrays.

overall_design: Prostate tissues from 5 high-fat diet fed prostate cancer model mice and 5 control diet fed prostate cancer model mice at 22 weeks of age were analyzed for microarray

first: Kentaro

last: Jingushi


title: Transcriptomic and Epigenomic Profiles of CIC-knockout and IDH1 mutant cells [WGBS]

status: Public on Dec 01 2021

city: Vancouver

first: Marco

last: Marra

state: BC

address: 675 W 10th Ave, 7th Floor

institute: Canada's Michael Smith Genome Sciences Centre

type: Methylation profiling by high throughput sequencing

summary: Capicua (CIC)’s transcriptional repressor function is implicated in neurodevelopment and in oligodendroglioma (ODG) aetiology. However, CIC’s role in these contexts remains obscure, primarily from our currently limited knowledge regarding its biological functions. Moreover, CIC mutations in ODG invariably co-occur with a neomorphic IDH1/2 mutation, yet the functional relationship between these two genetic events is unknown. Here, we analysed models derived from an E6/E7/hTERT-immortalized (i.e. p53- and RB-deficient) normal human astrocyte cell line. To examine the consequences of CIC loss, we compared transcriptomic and epigenomic profiles between CIC wildtype and knockout cell lines, with and without mutant IDH1 expression. Our analyses revealed dysregulation of neurodevelopmental genes in association with CIC loss. CIC ChIP-seq was also performed to expand upon the currently limited ensemble of known CIC target genes. Among the newly identified direct CIC target genes were EPHA2 and ID1, whose functions are linked to neurodevelopment and the tumourigenicity of in vivo glioma tumour models. NFIA, a known mediator of gliogenesis, was discovered to be uniquely overexpressed in double mutant cells (CIC-knockout + IDH1-mutant). These results identify neurodevelopment and specific genes within this context as candidate targets through which CIC alterations may contribute to the progression of IDH-mutant gliomas.

overall_design: Whole-genome bisulfite sequencing performed in immortalized normal human astrocytes stably expressing IDH1-WT or IDH1-R132H, and in matched CIC knockout lines (two independent replicates each).

first: Stephen

middle: D

last: Lee

first: Jungeun

last: Song

first: Veronique

last: LeBlanc


title: UBR7 Acts as a Chaperone for Post-Nucleosomal Histone H3

first: Daniel

last: Foltz

address: 303 E Superior St

summary: Histone chaperones modulate the stability of histones beginning from histone synthesis, through incorporation into DNA, and during recycling during transcription and replication. Following histone removal from DNA, chaperones regulate histone storage and degradation. Here we characterize UBR7 as a histone H3.1 chaperone that modulates the supply of pre-existing post-nucleosomal histone complexes. UBR7 is a largely nuclear soluble protein. We demonstrate that UBR7 binds to post-nucleosomal H3K4me3 and H3K9me3 histones via its UBR box and PHD. UBR7 binds to the non-nucleosomal histone chaperone NASP. The pool of NASP-bound post-nucleosomal histones accumulate and chromatin is depleted of H3K4me3 nucleosomes in the absence of UBR7. We propose that the interaction of UBR7, NASP, and histones opposes the histone storage functions of NASP as UBR7 promotes reincorporation of post-nucleosomal H3 complexes.

overall_design: ChIP-Seq for GFP in GFPUBR7-293T cells (n=1), ATAC-Seq (n=2), CUT&RUN for H3K4me3 (n=1 of 2 antibodies), and RNA-Seq (n=3) in UBR7KO and parental 293T cells.

first: Ann

last: Hogan

first: Kizhakke

last: Sathyan

first: Sakshi

last: Khurana

first: Kyle

last: Eagen

first: Celeste

last: Rosencrance


title: Transcriptomic and Epigenomic Profiles of CIC-knockout and IDH1 mutant cells [cic_chip]

overall_design: ChIP-seq against CIC performed in immortalized normal human astrocytes stably expressing IDH1-WT. Input was used as a negative control.


title: Investigation of gene expression in IO-MEPL, ETMR and SHH-, Group 4-, as well as WNT-Medulloblastoma

first: Julia

last: Neumann

summary: The objective of this study was to investigate human IO-MEPL for SHH and WNT pathway activation.

overall_design: Gene expression data was obtained from FFPE tumor samples of 8 human IO-MEPL, as well as 16 intracranial embryonal tumors comprising the entities ETMR and SHH-medulloblastoma (MB), WNT-MB and Group 4-MB for comparison.

first: Matthias

last: Dottermusch

first: Piotr

last: Sumislawski

last: Krevet

first: Hannah

last: Voß

first: Maximilian

last: Middelkamp

first: Harald

last: Bartsch

first: Karl

last: Sotlar

first: Andrey

last: Korshunov

first: Markus

last: Glatzel

first: Ulrich

last: Schüller

middle: E


title: Genome wide maps of binding patterns of atypical kinase RIOK2

city: Boston

first: Shrestha

last: Ghosh

state: Massachusetts

address: SM 752, Smith building, 1 Jimmy Fund Way

institute: Dana Farber Cancer Institute, Boston

summary: We report that the atypical Kinase RIOK2 binds to transcription start sites, 5'UTR regions and promoters of a variety of genes, and the genome binding patterns of RIOK2 are analogous to that of bona-fide transcription factors.

overall_design: CHIP-sequencing analysis was performed after immunoprecpitating DNA from TF-1 cells using monoclonal antibodies against RIOK2.

first: Laurie

last: Glimcher


title: Hemoglobin induced changes in the transcriptome of lupus patients.

city: New Delhi

first: Rahul

last: Pal

state: Delhi

address: Aruna Asaf Ali Marg

institute: National Institute of Immunology

summary: The expression of genes like IL-6, IL-10, TNF, OSM, CXCL1 and CXCL5 were found out to be heightened in patient's peripheral blood mononuclear cells compared to unstimulated cells.

overall_design: Differential expression of inflammatory genes in lupus patients upon hemoglobin stimulation.

first: Hritika

last: Sharma


title: Transcriptomic analysis of the rpoN mutant in Erwinia amylovora

city: Urbana

first: Frank

last: Zhao

address: 1201 W. Gregory Dr.

department: Crop Sciences

institute: University of Illinois

summary: This RNA-seq analysis examined the global effect of RpoN in E. amylovora under the T3SS-inducing condition. The rpoN mutant showed differential expression of 8% genes in the genome, which include significant down-regulation of T3SS genes.

overall_design: Differential gene expression of the rpoN mutant versus wild type grown in the T3SS-inducing condition for 6 hours

first: Ho-wen

last: Yang

first: Youfu


title: Transcriptomic and Epigenomic Profiles of CIC-knockout and IDH1 mutant cells [RNA-seq]

first: Marco

last: Marra

overall_design: RNA-seq profiles of parental immortalized normal human astrocytes stably expressing IDH1-WT or IDH1-R132H, and of matched CIC knockout cell lines (three independent replicates each).

first: Stephen

last: Lee

first: Jungeun

last: Song

first: Veronique

last: LeBlanc


title: Single-cell atlas of head and neck squamous cell carcinoma

city: Stanford

first: Zinaida

last: Good

state: California

address: 265 Campus Drive, Room G2105

department: Stanford Cancer Institute, Department of Biomedical Data Science

institute: Stanford University School of Medicine

summary: Purpose: To build an atlas of head and neck squamous cell carcinoma (HNSCC) using single-cell RNA-sequencing (scRNA-seq) data with surface protein expression using AbSeq oligo-tagged antibodies.

overall_design: 9 samples from 7 HNSCC patients were analyzed. These include 2 matched pairs of primary tumor and lymph node metastasis, 2 unmatched pairs, and 1 unmatched primary tumor. Fractions from mechanical digestion and enzymatic digestion were processed separately for each sample.

first: Sylvia

last: Plevritis


title: GFI1 maintains a chromatin state that is essential in human endothelial-to-hematopoietic transition [RNA-seq]

city: Guangzhou

first: qianyu

last: chen

address: 190 Kai Yuan Avenue, Science Park

institute: Guangzhou Institutes of Biomedicine and Health,Chinese Academy of Sciences

summary: During early embryonic hematopoiesis, hematopoietic stem/progenitor cells (HSPCs) are considered to develop from hemogenic endothelial cells (HECs) though endothelial to hematopoietic transition (EHT). However, little is known about how EHT is regulated in human. Here, we report that GFI1 plays an essential role in ensuring EHT during hematopoietic differentiation of human embryonic stem cells (hESCs). GFI1 deletion in hESCs showed a complete EHT defect due to a closed chromatin state of hematopoietic genes in HECs. Further analysis revealed that GFI1 directly binds and maintains the open chromatin state of genes important for EHT, such as PI3K signaling. Together, our findings reveal an essential role of GFI1 mediated epigenetic mechanism underlying human EHT during hematopoiesis.

overall_design: We compared the transcriptome of  the GATA2/eGFP+ endothelial cells of WT and GFI1-KO by RNA-Seq

first: Baoqiang

last: Kang

first: Guangjin

last: Pan


title: Transcriptomic and Epigenomic Profiles of CIC-knockout and IDH1 mutant cells [histone_chip]

overall_design: ChIP-seq against six histone marks performed in immortalized normal human astrocytes stably expressing IDH1-WT or IDH1-R132H, and in matched CIC knockout lines. Inputs were used as negative controls. Two independent replicates were obtained for each experiment.


title: GFI1 maintains a chromatin state that is essential in human endothelial-to-hematopoietic transition [CUT&TAG]

overall_design: We analyzed the transcriptome of  the GATA2/eGFP+ endothelial cells of GFI1-KO by CUT&Tag


title: GFI1 maintains a chromatin state that is essential in human endothelial-to-hematopoietic transition

overall_design: Refer to individual Series


title: Transcriptional data from overexpression of OsBIERF3 rice

city: Hangzhou

first: Yongbo

last: Hong

address: No.28 Shuidaosuo Rd. Fuyang distract

institute: China National Rice Research Institute

summary: We used microarrays to understand the downstream target genes regulated by OsBIERF3 transcription factor.

overall_design: Leaf samples were collected from 3-week-old OsBIERF3-OE and WT plants and total RNA were used for microarray.

first: Fengming


title: Maternal DDB1 regulates apoptosis and lineage differentiation in porcine preimplantation embryos

city: Bengbu

first: Biao

last: Ding

state: Anhui

address: No.287 Changhuai Road

department: Reproductive Medicine Center

institute: The First Affiliated Hospital of Bengbu Medical College

summary: we reported the potential molecular mechanisms of DDB1 in preimplantation embryos in porcine using siRNA microinjection and single cell transcriptome sequencing.

overall_design: Examination of 10 different samples about non-specific-siRNA injected  (Negative control, NC) and DDB1-siRNA injected (DDB1-knockdown, DDB1-kD) morulae

first: Di

last: Gao

first: Xuegu

last: Wang

first: Meng

last: Liang

first: Lei

last: Liu

first: Junpei

last: Sun

first: Fengrui

last: Wu

first: Yunhai

last: Zhang

first: Xiang

last: Li

first: Wenyong


title: MicroRNA array analysis of mature microRNAs of adipogenic differentiated human bone marrow stromal cells

city: Ancona

first: Jacopo

last: Sabbatinelli

state: AN

address: Via Tronto 10/A

department: Department of Clinical and Molecular Sciences

country: Italy

institute: Università Politecnica delle Marche

summary: In bone marrow, mesenchymal stromal cells (BMSCs), the precursors of adipocytes and osteoblasts, are exposed to a plethora of stimuli that determine the balance between adipogenesis and osteogenesis which in turn are competing and reciprocal. The differentiation of BMSCs, in fact, is a two-step process, lineage commitment (from MSCs to lineage-specific pro-genitors) and maturation (from progenitors to specific cell types).  Adipogenesis is a finely tuned multi-step process requiring the sequential activation of numerous transcription factors driving the typical physiological and morphological changes observed in the progenitor cells, i.e., cell cycle arrest, metabolic reprogramming, and lipid accumulation. Among the small non-coding RNAs, microRNAs represent an additional mechanism for controlling adipogenic gene expression. Given their unique ability to simultaneously regulate multiple protein targets and processes, it has been suggested that microRNAs may play a leading role in BMSC differentiation.  Here, we evaluated miRNAs differentially regulated during human BMSC adipogenic differentiation in vitro.

overall_design: MicroRNA expression profile obtained from qRT-PCR of hBMSCs treated under adipogenic conditions for 14 days compared to untreated hBMSCs.

first: Angelica

last: Giuliani

first: Maria

last: Rippo


title: Rif1 and Hmgn3 Regulate Conversion of Murine Trophoblast Stem Cells

city: Tianjin

first: Ling

last: Shuai

address: 38 Tong Yan Road, Jinnan district

department: State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy

institute: Nankai University

summary: The arising of trophectoderm (TE) is a hallmark event in preimplantation development during embryogenesis. However, little is known about the mechanisms underlying TE specification. Our findings demonstrate that depletion of Rif1 breaks down the barriers to conversion of trophoblast stem cells (TSCs). Rif1-null induced TSCs show typical TE properties, and differentiation potentials to terminal trophoblast lineages. Global transcriptome analysis reveals that Rif1-null activates 2-cell embryo (2C) related genes and induces a totipotent-like state, which is probably the main reason for the conversion of TSCs from Rif1-null embryonic stem cells (ESCs). Chimeric assays further confirm that Rif1-null ESCs can contribute to TE, further yielding TSCs in vitro. Over-expression of a downstream gene of Rif1, Hmgn3, can also activate 2C related genes and facilitate induction of TSCs. Here, we report two pioneer genes regulating conversion of TSCs and provide insights for investigating the mechanisms of TE specification.

overall_design: Comparation of the transcriptomes between and WT-ESCs, WT-TSCs, Rif1-KO ESCs and Rif1-KO iTSCs by RNA-seq analysis

first: Wenhao

first: Yanrui

last: Luo


title: Effect of combination treatment with BRAF and MEK inhibitors (BRAFi/MEKi) in BRAFV600E mutant cell lines using RNAseq

city: Debrecen

first: Viktoria

last: Koroknai

address: 26/B Kassai str.

department: Department of Public Health and Epidemiology

country: Hungary

institute: University of Debrecen

summary: We defined the molecular alterations associated with acquired resistance using combined treatment with BRAFi/MEKi in melanoma cell lines. After the successful establishment of six resistant cell lines, we determined the invasion properties and gene/protein expression differences between sensitive and resistant cells. We observed that the in-vasive potential of three of six resistant cell lines increased significantly compared to sensitive cell lines. We also observed that resistant cells were not drug addicted and did not exhibit significantly increased lethality following the “drug holiday”. RNA sequencing (RNA-Seq) analysis showed that the differentially expressed genes were associated with epithelial-mesenchymal tran-sition (EMT), the reactive oxygen species (ROS) pathway, and KRAS signalling

overall_design: Examination of molecular alterations using RNAseq to study the effect of combination treatment with encorafenib and binimetinib.

first: Margit

last: Balázs