title: Gene expression profiles of Treg cells lacking Cdc42 GTPase

status: Public on Aug 12 2021

city: Cincinnati

first: Fukun

last: Guo

state: OH

address: 3333 Burnet Avenue

institute: Children's Hospital Medical Center

summary: Treg cells play an important role in immune tolerance and tumor immune evasion through suppression of effector T cells. Treg cell lineage instability may be harnessed to trigger anti-tumor T cell immunity. However, the mechanism underlying Treg cell stability remains poorly understand. By characterizing Treg cell-specific heterozygous and homozygous  Cdc42 knockout mice, we found that Cdc42 is essential for Treg cell stability. By RNA sequencing of heterozygous and homozygous Cdc42 knockout Treg cells, we found that Cdc42 maintains Treg cell stability through suppression of carbonic anhydrase I (CAI) expression.

overall_design: Total RNA was isolated from FACS-purified Treg cells from two wild type (WT), two heterozygous Cdc42 knockout and two homozygous  Cdc42 knockout mice

first: F

first: K

last: Kalim


title: Single-cell RNA-Seq of cisplatin-treated adult stria vascularis identifies cell type-specific regulatory networks and novel therapeutic gene targets

status: Public on Aug 17 2021

city: Bethesda

first: Robert

last: Morell

state: MD

address: 35A Convent Drive, Room 1F-103

country: USA

institute: National Institute on Deafness and Other Communication Disorders

type: Expression profiling by high throughput sequencing

summary: Single cell RNA sequencing of cisplatin-treated adult mouse stria vascularis identified cell type-specific regulatory networks and novel therapeutic gene targets.

overall_design: 1 sample, Stria vascularis dissected from adult CBA/J mice after cisplatin injection

first: Michael

last: Hoa

first: Ian

last: Taukulis

first: Rafal

last: Olszewski

first: Soumya

last: Korrapati

first: Katharine

last: Fernandez

first: Erich

last: Boger

first: Tracy

last: Fitzgerald

first: Lisa

last: Cunningham


title: Phenotypic consequences of SLC25A40-ABCB1 fusions beyond drug resistance in High Grade Serous Ovarian Cancer

status: Public on Sep 03 2021

city: Melbourne

first: Elizabeth

middle: Louise

last: Christie

state: Victoria

address: 305 Grattan St

country: Australia

institute: Peter MacCallum Cancer Centre

summary:
Purpose: Our laboratory recently identified the most common mechanism of acquired drug resistance in High Grade Serous Ovarian Cancer (HGSOC) to date, SLC25A40-ABCB1 fusions. The primary aim of this study was to examine the transcriptional profile of drug resistant fusion-positive SLC25A40-ABCB1 fusion positive cells. Single cell fusion-positive and negative clones were derived from the human HGSOC cell line AOCS-18.5
Methods: Three independent replicates of RNA was collected from five SLC25A40-ABCB1 fusion-negative AOCS 18.5 clones  (B,C, D,E,F) and five SLC25A40-ABCB1 fusion-positive AOCS 18.5 clones (8,9,13, 15B, 18B) and submitted for NextSeq 100bp paired-end, polyA RNA-sequencing. Cells were collected 48-72hrs post seeding.
20 million paired end reads per sample were generated. Reads were mapped to the human reference GRCh37.92 using the STAR two pass method (v2.6.0b).  Counts were generated on the ensemble release GRCh37.92 GTF annotation using HTSeq (v0.10.0). Counts were normalized to logged TMM values using edgeR (v3.28.1). TPM expression values were also generated. Differential gene expression analysis was performed using DESeq2 (v1.26.0) on the raw counts. In all, 3333 genes were significantly upregulated (>1.5 log2 fold change, p-adj<0.1) in fusion-positive lines, with 1751 genes significantly downregulated
Conclusions: Using a stringent cut-off of >2.0 fold change (n=2238 differentially expressed genes), Metascape pathway analysis revealed that the most significantly enriched pathways in fusion-positive clones included the NABA matrisome associated pathway (160/751 genes, 7.24%), followed by external encapsulating structure organization (102/398 genes, 4.62%) and regulation of cell adhesion (139/734 genes, 6.29%).

overall_design: mRNA profiles of five SLC25A40-ABCB1 fusion-negative AOCS 18.5  (B,C, D,E,F) and five SLC25A40-ABCB1 fusion-positive AOCS 18.5 clones (8,9,13, 15B, 18B).

first: Kathleen

middle: I

last: Pishas

first: Ahwan

last: Pandey


title: Identification of novel efficacy of Bupleuri Radix based on the transcriptome analysis

status: Public on Aug 19 2021

city: Busan

first: Haeseung

last: Lee

address: 63 Beon-gil 2, Busandaehag-ro, Geumjeong-gu

department: College of Pharmacy

country: South Korea

institute: Pusan National University

summary: Transcriptomic landscapes of A549 cell line treated with Bupleuri Radix

overall_design: A549 mRNA profiles treated with water extract of Bupleuri Radix (BR), ethanol extract of BR, or seven ingredients.

first: Seongwon

last: Cha

first: Jin-Mu

last: Yi


title: Single cell of human retina

status: Public on Aug 11 2021

city: Philadelphia

first: Dwight

middle: Edward

last: Stambolian

state: PA

address: 422 Curie Blvd.

department: Opthalmalogy

institute: University of Pennsylvania

summary: Retinal RNA profiles from macula and periphery of each eye were generated by single-cell sequencing. M11-M14 are macula retina and P11-P14 are peripheral retina from the same 78 year old donor. M21-M24 are macula retina and P21-P24 are peripheral retina from the same 90-year-old donor.

overall_design:
Single cell of human retina

Please note that the Series summary description and GSM4698512-GSM4698519 sample titles have been updated on July 14, 2022.


title: Transcriptomic analysis of HES induced [E(spl)mγ and dpn; DM] Drosophila larval primary CNS tumours vs HES allograft tumours in w1118 host flies

status: Public on Sep 01 2021

city: Heraklion

first: Christos

last: Delidakis

address: 100 N Plastira St

country: Greece

institute: FORTH-IMBB

summary:
The goal of this project was to compare NGS derived transciptional profiles of primary larval CNS tumours and allograft tumours from two stages (first-T0 and forth-T3) in Drosophila that are induced by overactivation of two HES genes [E(spl)mγ and dpn;DM]  in order to decipher if these two Hes genes control similar or different sets of genes as primary hypeplasias transition to malignant tumours.
The results of this study show that overactivation of DM continues to negatively regulate neuronal differentiation genes as the DM hyperplasias become more malignant and that genes related to stress and metabolsim are upregulated

overall_design: mRNA profiles from FACS sorted, GFP positive Drosophila larval CNS DM tumours vs the first (T0) allograft DM tumours vs the forth (T3) serial allograft DM tumours

first: E

last: Zacharioudaki

first: C

last: Voutyraki

first: V

last: Theodorou


title: Alpha-synuclein overexpression is associated with epigenomic dysregulation of glutamate signaling and locomotor pathways

status: Public on Aug 02 2021

city: Vancouver

first: Michael

last: Kobor

state: BC

address: 950 W 28th Ave

department: Medical Genetics

country: Canada

institute: University of British Columbia

type: Methylation profiling by genome tiling array

summary: Although Parkinson’s disease (PD) is one of the most rapidly growing neurological disorders, interindividual differences in PD etiology related to genetics are not fully understood. Here, we demonstrate genome-wide DNA methylation and hydroxymethylation alterations associated with overexpression of two PD-linked alpha-synuclein variants (wild type and A30P) in LUHMES cells differentiated to dopaminergic neurons. Alpha-synuclein altered DNA methylation at thousands of CpGs and DNA hydroxymethylation at hundreds of CpGs in both genotypes, and primarily at locomotor and glutamate signaling pathway genes. In some cases, epigenetic changes were associated with transcription. SMITE network analysis incorporating H3K4me1 ChIP-seq to score DNA methylation and hydroxymethylation changes across promoters, enhancers, and gene bodies confirmed epigenetic and transcriptional deregulation of glutamate signaling modules in both genotypes. Our results identify distinct and shared impacts of alpha-synuclein variants on the epigenome, and associate alpha-synuclein in the epigenetic etiology of PD.

overall_design: DNA from Lund Human Mesencephalic (LUHMES) cells was used to assess the impact of alpa-synuclein (aSyn) on cellular DNA methylation and hydroxymethylation. For this purpose, three different cell lines were generated. Briefly, proliferating LUHMES cells were infected with equimolar amounts of lentiviral particles encoding for: IRES-GFP (samples set C); full-length human wild-type (WT) aSyn (SNCA, NM_000345), WT aSyn-IRES-GFP (samples set E) or familial mutant A30P aSyn, A30P aSyn-IRES-GFP (samples set A). Positive green fluorescent cells were selected by fluorescence activated cell sorting. Seven independent replicates were generated for the GFP (control) cell line and eight independent replicates were generated for the WT and A30P aSyn lines. Total DNA from differentiated LUHMES cells, at differentiation day 8, was extracted and purified using the AllPrep DNA/RNA Mini Kit (Qiagen), according to the instructions of the manufacturer. DNA quantity and purity were assessed by spectrophotometry. 1.5 μg of DNA per sample was split into two 750 ng aliquots for sodium bisulfite (BS) conversion or oxidative bisulfite (oxBS) conversion using the NuGEN TrueMethyl oxBS Module (NuGEN Technologies Inc.). One aliquot per sample was treated with the oxidation protocol while the second aliquot underwent mock oxidation; all samples were then sodium bisulfite converted according to the manufacturer’s instructions.

first: Samantha

middle: L

last: Schaffner

first: Zinah

last: Wassouf

first: Diana

middle: F

last: Lazaro

first: Mary

last: Xylaki

first: Nicole

last: Gladish

first: David

middle: T

last: Lin

first: Julia

last: MacIsaac

first: Katia

last: Ramadori

middle: M

last: Schulze-Hentrich

first: Tiago

last: Outeiro

middle: S


title: Stress-inducible gene Atf3 dictates a dichotomous macrophage activity   in chemotherapy-enhanced lung colonization

status: Public on Aug 03 2021

city: Columbus

first: Tsonwin

last: Hai

address: 1060 Carmack Rd.

department: Biological Chemistry and Pharmacology

institute: Ohio State University

summary:
Chemotherapy can be a double-edged sword, enhancing cancer progression even while killing cancer cells. This effect is often mediated by stresses on host cells. We found that pre-treatment of mice with cyclophosphamide before cancer cell injection increases the amount of cancer cell colonization of the lung. We determined this effect is at least partially dependent on the stress-inducible gene, Atf3, in monocytes/macrophages.
We used microarrays to profile gene expression in WT/KO lung monocytes/macrophages after chemotherapy treatment and intravenous breast cancer cell injection. This was in order to find candidate genes that mediated the colonization-exacerbating role of chemotherapy.

overall_design: WT or Atf3 KO mice were injected with 150 mg/kg cyclophosphamide or vehicle four days before tail-vein injections of 10^6 MVT-1 breast cancer cells. Lungs were collected after 3 days, and monocytes/macrophages  were isolated by FACS.

first: Justin

last: Middleton

first: Jared

last: Fehlman

first: Subhakeertana

last: Sivakuma


title: Impaired Right Ventricular Calcium Cycling Is an Early Risk 2 Factor in R14del-Phospholamban Arrhythmias

status: Public on Jul 27 2021

last: Tranter

address: 2255 Kenny Road

department: Molecular Medicine and Therapeutics

institute: The Ohio State University

summary: We utilized humanized wild-type and R14 deletion (R14del) phospholamban (PLN) knock-in mice to determine the role of the inherited PLN-R14del on malignant right ventricular arrhythmias.

overall_design: RNA-seq to determine global gene expression profiles in LV and RV samples from humanized WT and R14del mutant mouse hearts

first: Litsa

last: Kranias


title: RNA-seq analysis of the gene expression profile regulated by Prdm14 in mouse ESCs

status: Public on Oct 01 2021

city: Hefei

first: shoudong

last: ye

address: No 111, Jiu Long Road

department: Cell Biology

country: China

institute: Anhui University

summary: Purpose:The goals of this study is to analyze the gene expession pattern in mouse embryonic stem cells (ESCs) ovexpressed flag or mouse flag tagged Prdm14

overall_design: 46C mouse ESCs overexpressed flag or flag tagged gadd45g and  cultured in serum-containing medium supplemented LIF were collected by using Trizol. These samples were sent to BGI (Shenzhen, China) company to do deep sequencing by using MGI2000.

first: Shoudong

last: Ye


title: Integrated molecular landscape perturbations underlie cellular responses during hyperammonemia

city: Cleveland

first: Srinivasan

last: Dasarathy

address: 9500 Euclid Ave

department: Inflammation and Immunity

institute: Cleveland Clinic Lerner Research Institute

type: Genome binding/occupancy profiling by high throughput sequencing

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: Integrated molecular landscape perturbations underlie cellular responses during hyperammonemia [mouse RNA-seq]

status: Public on Jul 28 2021

summary: Ammonia is a cytotoxic molecule generated during cellular functions and by the gut microbiome. Dysregulated ammonia metabolism initiates a hyperammonemic stress response (HASR). Hyperammonemia occurs in many chronic diseases but there is limited understanding of the overall consequences of HASR. A comprehensive array of unbiased approaches was used to identify global responses during hyperammonemia with experimental validation of critical findings. Protein/gene expression and chromatin accessibility in hyperammonemic murine myotubes and mouse skeletal muscle tissue were analyzed by quantitative proteomics, RNA sequencing (RNAseq), and Assay for Transposase Accessible Chromatin Sequencing (ATACseq). Unique clusters of expression/accessibility changes were identified in hyperammonemic myotubes. In hyperammonemic mouse muscle and myotubes, we identified enrichment of pathways involved in oxidative phosphorylation, calcium signaling, hypoxia inducible factor-1, and apoptosis and regulation of protein synthesis were altered during HASR and were experimentally validated. Enrichment of senescence signaling and glycosylation pathways during HASR were novel observations. Comparisons with RNAseq data from skeletal muscle from human patients with cirrhosis revealed similar perturbations, demonstrating the translational relevance of our observations. We identified several novel regulatory pathways during HASR that are conserved in different models and across species, and whose dysregulation could significantly impact skeletal muscle structure and function.

overall_design: Examination of the hyperammonemic stress response (HASR) in skeletal muscle from hyperammonemic and control mice

first: Dasarathy

last: Srinivasan


title: Nuclear mRNA processing domain formed by PABPN1 - mRNA phase separation is essential for the growth of oocytes and female reproduction

status: Public on Jul 06 2021

city: Hangzhou

first: Xingxing

last: Dai

address: YuHangTang 866

institute: Life Sciences Institute

summary: The growing oocytes stored a large amount of maternal mRNA to support the subsequent "maternal-zygotic transition" process, which is a key regulatory events in female reproduction. The accumulation of maternal mRNA in the growing oocyte determines the developmental potential of the oocyte. At present, it is not clear how the growing oocytes store and process the newly transcribed mRNA under physiological conditions, including the distribution and localization of mRNA in the oocyte, as well as the molecular mechanism and physiological significance of this localization. In this study, we found that poly(A) tailed mRNA has the dynamic distributions of droplet fusion and gradual disappearance in the mouse nucleus as oocyte growth and meiotic maturation. Our research found that PABPN1 modulated the dynamic compartmentalization of mRNA with poly(A) tails to form NmPD (nuclear mRNA processing domain) during the growing oocytes through phase separation. The NmPD in Pabpn1-null oocytes could not form the compartmentalized distribution, and the Pabpn1 knockout females were sterile with defects of premature ovarian failure. Combined with multi-omics sequencing analysis, we investigate that NmPD was essential for long 3'-UTR isoform formation and the stability of mRNA in growing oocytes.

overall_design: Examination of WT and Pabpn1-null  transcriptome in growing oocytes

first: Xing-Xing

first: Shuai-Bo

last: Pi

first: Yun-Wen

last: Wu


title: Transtriptome analysis of bone marrow-derived neutrophils after ferritin injection

status: Public on Jul 09 2021

city: Shanghai

first: Jinchao

last: Jia

address: No. 197 Ruijin Second Road

institute: New Markers for Adult-Onset Still's Disease

summary: How ferritin regulates neutrophil leukocyte function remains unknown. To address this question, we injected mice with ferritin. bone marrow-derived neutrophils (BMDN) were isolated by density gradient centrifugation. Then we displayed RNA-seq of isolated BMDNs.

overall_design: Transcriptomes from bone marrow-derived neutrophils of 3 mice treated with ferritin and 3 control mice.

first: Qiongyi

last: Hu

first: Mengyan

last: Wang


title: Sensory nerves enhance triple negative breast cancer migration and metastasis through PlexinB3 signaling

status: Public on Jul 22 2021

city: medford

first: Thanh

middle: Thien

last: Le

state: MASSACHUSETTS

address: 20 sawyer avenue

department: Biomedical Engineering

institute: Tufts University

summary: We identified sensory nerves as more abundant in triple-negative human breast tumors. Human triple negative breast cancer (TNBC) cells (MDA-MB-231, SUM159) were co-cultured with mice primary sensory neurons from dorsal root ganglia (DRG). Breast can-cer cells were found to attach to neurons and have higher migration speed and prolifera-tion rate. Species-specific RNA sequencing highlighted cell migration and adhesion among the most upregulated pathways for cancer cells in coculture. We identified a novel mechanism where cancer’s PlexinB3 interacted with neuron’s Sema5A to regulate attachment and migration along nerve fibers. These findings demonstrate that sensory nerves induced a drastic shift in TNBC cells gene expression, and that dirupting the nerve-cancer is a viable strategy to impede metastasis

overall_design: Bulk RNA-seq of human TNBC cells and mouse DRG neurons in coculture

first: Le

last: Thanh T

first: Payne

last: Samantha L

first: Burge

last: Christopher B

first: Oudin

last: Madeleine J


title: Hypoxia and the metabolic phenotype of Daphnia

status: Public on Jun 30 2021

city: Gainesville

first: Christopher

last: Martyniuk

state: FL

address: 8891 SW 79th Avenue

institute: University of Florida

summary: Environmental hypoxia typically induces phenotypic remodelling in animals, including bolstered oxygen transport and storage, and glycolytic enzyme activities, typically coordinated by the transcription factor hypoxia-inducible factor (HIF). The calanoid copepod Daphnia responds to hypoxia by a HIF-dependent increase in expression of extracellular hemoglobin (Hb), however little is known about the glycolytic response. We compared the Daphnia from 4 lakes in terms of transcriptome using RNASeq analysis of red versus pale animals. Cluster analysis showed that the impact of lake was much greater than the impact of colour. However, in each lake there were a series of colour dependent differences, including many of the known targets of HIF in mammals.

overall_design: Two phenotypes each for 4 lakes (eight groups)

first: Kurtis

last: Westbury

first: Ting

middle: Y

last: Lee

middle: J

first: William

middle: A

last: Nelson

middle: D

last: Moyes


title: Oct4 activates a Suv39h1-repressive antisense lncRNA to couple histone H3 lysine methylation to pluripotency

status: Public on Sep 17 2021

city: paris

first: Pablo

last: Navarro

address: 25 rue du Docteur Roux

country: France

institute: Institut Pasteur

summary: We report RNA-seq expression data of different cell lines of mouse embryonic stem cells in self-renewal conditions and upon the inactivation of Oct4 or Esrrb. ChIP-seq of H3K9me3 and ATAC-seq data of wild-type and Suv39h1as deleted cells are also provided.

overall_design:
Parallel cultures of 2 replicates with or without TF depletion (24h, for RNA-seq) or of wild-type and Suv39h1-as mutant cells for ChIP-seq and ATAC-seq

A8 and D8 are independent mutant clones.


title: H3K9 tri-methylation at Nanog times differentiation commitment and enables the acquisition of primitive endoderm fate

status: Public on Jun 25 2021

summary: We report RNA-seq expression data of wild-type (E14Tg2a) and 2 derivative mutants (∆K9.1 and ∆K9.2) lacking a region of the Nanog locus decorated by H3K9me3 and presenting severe differentiation delays particularly into primitive endoderm fate.

overall_design: Parallel culture of 2 to 3 replicates of wild-type and mutant cells at different time-points of embryoid body differentiation.


title: Bone marrow-derived human mesenchymal stem cell RNA-Seq Heat map

city: Taichung City

first: Chun-Te

last: Ho

address: 7F, No. 6, Xueshi Rd., North Dist.

department: Integrative Stem Cell Center

country: Taiwan

institute: China Medical University Hospital

summary: TET1-KD or PARP1-KD highly correlate with late MSC in RNA seq Heat map.

overall_design: RNA-Seq of bone marrow-derived mesenchymal stem cells with 2 biological replicates

first: Shih-Chieh

last: Hung


title: DOT1L complex regulates transcriptional initiation in human cells

status: Public on Jun 17 2021

first: Aiwei

last: Wu

state: Shanghai

address: 800 Dongchuan Road

department: School of Life Sciences and Biotechnology

institute: Shanghai Jiao Tong University

summary: DOT1L, the only H3K79 methyltransferase in human cells and a homolog of the yeast Dot1, normally forms a complex with AF10, AF17 and ENL/AF9, is dysregulated in most of the cases of mixed lineage leukemia (MLL) and is believed to regulate transcriptional elongation without much evidence. Here we show that the depletion of DOT1L reduced the global occupancy without affecting the traveling ratio or the elongation rate of Pol II, suggesting it not a major player in elongation. An examination of general transcription factors (GTFs) binding revealed globally reduced TBP and TFIIA occupancies near promoters after DOT1L loss, pointing to a role in transcriptional initiation. Proteomic studies uncovered that DOT1L regulates transcriptional initiation likely by facilitating the recruitment of TFIID. Moreover, we found that ENL also regulates transcriptional initiation and that DOT1L stimulates H2B monoubiquitination by limiting the recruitment of human SAGA complex. These results advanced current understanding of epigenetic regulation of transcriptional initiation and roles of DOT1L complex in MLL.

overall_design: Study the roles of DOT1L complex in transcriptional regulation

first: Ming

last: Yu

first: Junhong

last: Zhi

first: Tian

last: Tian

first: Ziling

last: Liu


title: Integrated spatial multi-omics reveals fibroblast fate during tissue repair

status: Public on Jun 24 2021

city: Stanford

first: Michael

last: Januszyk

state: CA

address: 257 Campus Dr

department: Surgery

institute: Stanford University

summary: In the skin, tissue injury results in fibrosis in the form of scars composed of dense extracellular matrix deposited by fibroblasts. The therapeutic goal of regenerative wound healing has remained elusive in part because principles of fibroblast programming and adaptive response to injury remain incompletely understood. Here, we present a multimodal -omics platform for the comprehensive study of cell populations in complex tissue, which has allowed us to characterize the cells involved in wound healing across both time and space. We employ a stented wound model that recapitulates human tissue repair kinetics and multiple Rainbow transgenic lines to precisely track fibroblast fate during the physiologic response to injury. Through integrated analysis of single cell chromatin landscapes and gene expression states, coupled with spatial transcriptomic profiling, we are able to impute fibroblast epigenomes with temporospatial resolution. This has allowed us to define the mechanisms controlling cell fate during migration, proliferation, and differentiation following tissue injury and thereby reexamine the canonical phases of wound healing. We show that wounding triggers a polyclonal proliferation of tissue-resident, mechano-responsive fibroblasts, the subpopulations of which inhabit spatially-distinct regions within the wound and harbor distinct activities. These findings have broad implications for the study of tissue repair in complex organ systems.

overall_design: Mouse wound tissue transcriptomes were profiles using RNA bulk and single cell RNA sequencing, single cell ATAC sequencing, and Visium spatial transcriptomics. For bulk RNA sequencing, RNA was obtained from mouse inner wound region and outer wound region, as well as uninjured control fibroblasts at post-operative day (POD) #7 and #14, as well as inner wound region and outer wound region fibroblasts from POD #14 treated with a small molecule FAK inhibitor. For single-cell RNA sequencing, FACS-isolated Rainbow mouse inner wound region and outer wound region fibroblasts harvested at 3 timepoints over the course of wound healing (POD #2, #7, and #14) and single cell sorted for plate-seq. For single-cell ATAC sequencing, Rainbow mouse wound fibroblasts were FACS-isolated from inner and outer wound regions at the same 3 timepoints as single-cell RNA sequencing. For Visium spatial transcriptomics, mouse wound tissue sections were mounted and sequenced from POD #2, #7, and #14 as well as uninjured skin.

first: Deshka

last: Foster


title: Stool small RNA-Seq profile of healthy subjects with different dietary habits

status: Public on Jul 30 2021

city: Orbassano

first: Giulio

last: Ferrero

state: TO

address: Regione Gonzole, 10

department: Dept. Clinical and Biological Sciences

country: Italy

institute: University of Turin

type: Non-coding RNA profiling by high throughput sequencing

summary: Small RNA-Seq analysis of on stool samples from an Italian  cohort of 120 healthy individuals with three dietary habits. The cohort includes 72 women and 48 men included an equal proportion of vegetarians, vegans and omnivores.

overall_design: Stool small RNA-Seq profile 120 healthy subjects with three dietary habits: omnivorous, vegetarian, and vegan

first: Sonia

last: Tarallo

first: Alessio

last: Naccarati

first: Barbara

last: Pardini

first: Antonio

last: Francavilla

first: Francesca

last: Cordero

first: Danilo

last: Ercolini

last: De Filippis

first: Edoardo

last: Pasolli

first: Valentina

last: Panero

first: Ruggero

last: Pensa

first: Sara

last: Grioni


title: Skeletal Stem Cell Diversity in Mouse Long Bones

status: Public on Jun 11 2021

city: Sacramento

first: Thomas

middle: H

last: Ambrosi

state: California

address: 2700 Stockton Blvd

institute: UC Davis

summary: We have used SmartSeq2 to sequence single phenotypic skeletal stem cell (SSCs) populations purified via FACS from adult mouse long bones. Two putative SSC populations were isolated based on their previously reported surface marker profiles. An osteochondrogenic SSC (ocSSC, CD45-CD31-Tie2-Ter119-CD51+6C3-Thy1-CD105-) and a perivascular SSC (pvSSC, CD45-CD31-Pdgfra+Sca1+CD24+) were investigated.

overall_design: SmartSeq2 single cell RNA sequencing of flow cytometrically purified single mouse osteochondral and perivascular skeletal stem cells from adult mouse long bones.

first: Charles

middle: K

last: Chan

first: Rahul

last: Sinha


title: Integrated molecular landscape perturbations underlie cellular responses during hyperammonemia [ATAC-seq]

first: Srinivasan

last: Dasarathy

overall_design: Examination of the hyperammonemic stress response (HASR) in differentiated C212 murine myotubes

first: Dasarathy

last: Srinivasan

first: Shah

last: Yatrik


title: identifying mRNA expression regulated by FLT3/ITD and Cxcl12

status: Public on Jun 09 2021

city: Izumo

first: Seiji

last: Fukuda

state: Shimane

address: 89-1 Enya

department: Pediatrics

country: Japan

institute: Shimane University

summary: mRNA expression regulated by FLT3/ITD and Cxcl12 were compared in the Ba/F3 cells expressing wild type FLT3 or FLT3/ITD and incubated with or without Cxcl12.

overall_design: mRNA expression was compared between cells expressing wild type FLT3 incubated with or without 100ng/ml of Cxcl12 and those expressing FLT3/ITD incubated with or without 100ng/ml Cxcl12.


title: Multiple de novo copy number variant (MdnCNV) driven mirror traits and blended phenotype

status: Public on Jun 10 2021

city: Houston

first: Christopher

last: Grochowski

state: Texas

address: 1 Baylor Plaza

department: Molecular and Human Genetics

institute: Baylor College of Medicine

type: Genome variation profiling by genome tiling array

summary: Purpose: To determine the genetic variation underlying phenotypic trait manifestation in a Multiple de novo copy number variant (MdnCNV) case. Method: Clinical microarray identified a previously unreported MdnCNV proband. Short and long-read genomic sequencing, SV analyses, and visualization tools for merged datasets were implemented to characterize MdnCNV mutagenesis. Human phenotype ontology based quantitative analyses identified gene(s) driving proband phenotype.Results: Eight dnCNVs of average length ~1 Mb were mapped in the MdnCNV proband. Sequence microhomology/microhomeology was present at 6/8 breakpoint junctions. dnSNVs (6/79) and de novo indels (1/12) are enriched within 4 Mb of the dnCNV regions. Of the duplication encompassed genes, NSD1 and SMARCC2 had the highest phenotypic match to the proband. Conclusion:  Biparental origin of constitutive dnCNVs (4:4) supports an early perizygotic mutagenesis event as the cause of genome-wide hypermutation. Microhomology/microhomeology and regional hypermutation supports microhomology-mediated break-induced replication as the process underlying MdnCNV formation. The family reported here, together with published NSD1 variation associated cases further define NSD1 as a triplosensitivity locus that exhibits mirror quantitative traits from those associated with its haploinsufficiency. Quantitative phenotype analysis identified NSD1 and SMARCC2 as contributors to a blended phenotype.

overall_design: The goal of this experiment was to determine the size, genomic extent and gene content of a family with a proband carrying the multiple de novo CNV phenotype.

first: Haowei

last: Du

first: Angad

last: Jolly

first: Claudia

last: Carvalho

first: Pengfei

last: Liu


title: Transcriptome of differentiated  AST and NAS iPS cell lines to human-like dopamine neurons

status: Public on Jun 15 2021

last: Martyniuk

overall_design: AST- and NAS-derived dopamine neurons were compared for their gene expression profiles after differentiation. Functional data was also collected in terms of neurophysiology. iPSCs were generated from a member of the Iowa kindred carrying a triplication of the SNCA locus (AST) and an unaffected member of the family without this mutation (NAS). Dopamine neurons were differentiated from iPSCs. Transcriptome profiling was done on n=3 AST and n=3 NAS (replicate and independent cell cultures).

first: Habibeh

last: Khoshbouei

first: Chris

first: Landon

last: Min


title: Integrated molecular landscape perturbations underlie cellular responses during hyperammonemia [human RNA-seq]

overall_design: Examination of the hyperammonemic stress response (HASR) in skeletal muscle from humans with and without cirrhosis


title: miRNA sequence analysis of drug-resistant small cell lung cancer

status: Public on Jun 05 2021

city: Kagoshima

first: Kengo

last: Tanigawa

address: 8-35-1 Sakuragaoka

department: Pulmonary Medicine

institute: Kagoshima university

summary: We obtained small cell lung cancer specimens and normal lung specimens from patients who died of drug-resistant SCLC.  The small lung cancer specimens include primary lesions and metastatic lesions. Next generation sequencing was performed to assess the expression of miRNA in drug-resistant small cell lung cancer.

overall_design: Twelve samples (4 normal lung tissues, 2 primary tumors, 4 lymph node metastases, 1 liver metastasis, 1 lung metastasis) were collected from autopsy specimens of three treatment-resistant small cell lung cancer patients.

first: Shunsuke

last: Misono

first: Naohiko

last: Seki


title: Modeling pancreatic beta cell senescence by induction of DNA double-strand breaks

status: Public on Jun 08 2021

city: Winnipeg

first: Peter

last: Thompson

state: MB

address: 715 McDermot ave

department: Physiology & Pathophysiology

institute: University of Manitoba

summary: Pancreatic beta cell senescence occurs during the development of Type 1  Diabetes. To model the transcriptional responses of islet cells to DNA damage, we previously developed a human islet culture model in which the DNA damage response and senescence can be induced via double strand-breaks with the agent bleomycin. Here, we report the transcriptome-wide changes in human pancreatic islet cells following bleomycin exposure.

overall_design: Human donor islets isolated from a 44 year old normoglycemic female by Scharp-Lacy and distributed by the Integrated Islet Distribution Program (RRID:SAMN13186657) and from a 50 year old normoglycemic female by Alberta Diabetes Institute (RRID:SAMN26419385) were rested 24 h and then treated with vehicle (DMSO) or 50 uM bleomycin for 48 h. Islets from each donor were treated with Veh or Bleo in n=3 biological replicates (wells of islets). Following this, the islets were transferred to fresh drug free media and cultured an additional 4 days before harvest and RNA extraction. Approximately 1 ug of total RNA was submitted to LC Sciences for total RNA-seq on Illumina NovaSeq 6000 platform.

first: Gabriel

last: Brawerman


title: The SNF2 ATPase-independent function of the INO80 chromatin remodeler [ChIP-seq]

status: Public on May 25 2021

city: Beijing

first: xinjian

last: He

address: No. 7, zhongguancun life science park road, changping district

institute: National Institute of Biological Sciences

summary: In the multi-subunit INO80 chromatin-remodeling complex, all the auxiliary subunits assemble on three distinct domains of the catalytic chromatin remodeler INO80, which are N-terminal domain, HSA domain, and ATPase domain. While the ATPase and HSA domains and the auxiliary subunits assembling on the domains are known to be responsible for ATP hydrolysis and chromatin remodeling, it is largely unknown how the auxiliary subunits assembling on the INO80 N-terminal domain regulate the chromatin status. We identify both conserved and non-conserved auxiliary subunits of the INO80 complex in Arabidopsis thaliana. All the auxiliary subunits assemble on the conserved N-terminal domain, HSA domain, and ATPase domain of INO80 in Arabidopsis. While the auxiliary subunits assembling on the INO80 ATPase domain are required for the ATPase-dependent function, the INO80 N-terminal domain and the auxiliary subunits assembling on the domain can regulate gene expression and development even when the ATPase domain is absent, suggesting that INO80 has an ATPase-independent role. Furthermore, we find that a subclass of the COMPASS histone H3K4 methyltransferase complexes assemble on the INO80 N-terminal domain in the INO80 complex and function together with the other auxiliary subunits assembling on the INO80 N-terminal domain, thereby facilitating the ATPase-independent function. This study suggests that the conserved chromatin remodeler INO80 has an ATPase-independent role and demonstrates that the auxiliary subunits assembling on the INO80 N-terminal domain are required for the ATPase-independent role.

overall_design: Examination of H3K4me3 levels in wild type and two mutants grown under long day or short day conditions.

first: Xin


title: A TNFR2-hnRNPK axis promotes primary liver cancer development via activation of YAP signaling in hepatic progenitor cells

first: qiudong

last: zhao

address: 225 Changhai Road

department: Tumor Immunology and Gene Therapy Center

institute: Shanghai Eastern Hepatobiliary Surgery Hospital

summary: Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type,  Tnfrsf1α-/- and Tnfrsf1β-/- (with or without TNFα treat) HPCs Transcriptomes.The mRNA profiles of  Wild Type,  Tnfrsf1α-/- and Tnfrsf1β-/- (with or without TNFα treat) HPCs were generated by deep sequencing, in triplicate, using Illumina GAIIx. The sequence reads that passed quality filters were analyzed at the transcript isoform level . qRT–PCR validation was performed using TaqMan and SYBR Green assays.We performed RNA-seq analysis to assess the global impacts of TNFR2 on HPCs' response to TNFα. Upon TNFα treatment, 519 genes were significantly upregulated in wild type HPCs .  39% of these genes (203 out of 519) were further upregulated in Tnfrsf1a-/- HPCs treated with TNFα. However, these 203 genes were dramatically downregulated in TNFα-treated Tnfrsf1b-/- HPCs relative to their expression in either TNFα-treated Tnfrsf1a-/- HPCs or wild type HPCs,  indicating an inhibitory role for deletion of TNFR2 in the regulation of these genes.

first: Lixin

last: Wei

first: Yan

last: Meng

first: Zhaocai

last: Zhou

last: Sang


title: Lineage transcription factors ASCL1, NKX2-1, and PROX1 are enriched at super enhancers and co-regulate subtype-specific genes in small cell lung cancer [ChIP-seq]

status: Public on May 01 2021

city: Dallas

first: Jane

middle: E

last: Johnson

state: TX

address: 5323 Harry Hines Blvd

department: Neuroscience

institute: UT Southwestern Medical Center

summary: Heterogeneity between tumors is a major barrier to the treatment of small cell lung cancer (SCLC). Identification of molecular markers to characterize and classify tumors can facilitate the diagnosis and development of targeted therapies. Here, we analyzed genomic regions, called super enhancers (SE), across multiple SCLC cell lines and patient-derived xenograft models, and find SE enrichment is sufficient to classify SCLC models into recently defined SCLC molecular subtypes SCLC-A, SCLC-N, and SCLC-P defined by the transcription factors ASCL1, NEUROD1, and POU2F3, respectively. 3D chromatin structure analysis identified genes associated with the SE that assemble into subtype-specific tumor-signatures with genes functioning in diverse processes. Focusing on the SCLC-A subtype, transcription factors NKX2-1 and PROX1 were identified as ASCL1-interacting proteins. All three factors bind overlapping genomic regions within SEs in SCLC-A cell line models. Nevertheless, combined loss of all three factors suppresses growth of SCLC-A similar to that seen with ASCL1 loss alone, continuing to place ASCL1 as a key dependency factor in a subset of SCLC. Focusing on genes co-regulated by the three transcription factors, two SCLC-A subtype-specific cell surface proteins, SCN3A and KCNB2, were identified. Loss of either channel alone did not disrupt SCLC-A growth in vitro, but they may serve as diagnostic tools in subtyping SCLC.

overall_design:
Mapping of superenhancers and transcription factor binding sites in a panel of small cell lung cancer preclinical models based on chromatin-immunoprecipitation of an histone modification and 3 transcription factors.

Please note that each processed data was generated from both ChIP and input samples, and is linked to the corresponding ChIP sample records.

first: Karine

last: Pozo

first: Rahul

last: Kollipara


title: Microarray and qPCR Analysis of Mitochondrial Metabolism Activation during Prenatal and Early Postnatal Development in Rats and Humans   with Emphasis on CoQ10 Biosynthesis

status: Public on May 10 2021

city: Prague 2

first: Jana

last: Krizova

state: Non United States Or Canada

address: Ke Karlovu 2

department: Department of Pediatrics and Inherited Metabolic Disorders

country: Czech Republic

institute: Charles University in Prague, First Faculty of Medicine, and General University Hospital in Prague

summary:
During the mammalian ontogenesis, a rapid switch from glycolytic metabolism to oxidative phosphorylation must proceed during postnatal adaptation to extra-uterine conditions. It was proposed that in the course of intra-uterine fetal development, expression changes proceed to cover all metabolic demands all along this critical and extremely fast period. Using microarray techniques, quantitative PCR, enzyme activities’ and coenzyme Q content measurements, we describe perinatal mitochondrial metabolism acceleration in rat liver and skeletal muscle between the 16th day of gestation and the first days of life and possible correlation with results in human. Out of 1546 mitochondrial genes, 72% and 53% were significantly changed in liver and skeletal muscle, respectively. The most important expression shift occurred in the liver at least two days before parturition.
We used microarrays to detail the orchestration of gene expression underlying perinatal metabolic shift and identified up- and down-regulated genes during this process.

overall_design: Rattus norvegicus perinatal liver and skeletal muscle tissues were selected as a model of mammalian adaptation to extra-uterine conditions. To study gene expression, we used Affymetrix microarrays. Analysis wasperformed by The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Canada. For analysis we used tissues at five time-points: fetal day 16 (F16), fetal day 20 (F20), last day before parturition - fetal day 22 (F22), first postnatal day (P1) and 4th postnatal day (P4). We obtained also data from fetal day 18 (in skeletal muscle) and 90th day of life (liver, “adult” control), which were not used in analysis, but are part of this data submission. For liver tissue analysis, we used four biological replicates per time-point. For skeletal muscle analysis, five biological replicates were used.

first: Martina

last: Hulkova

first: Vaclav

last: Capek

first: Petr

last: Mlejnek

first: Jan

last: Silhavy

first: Jiri

last: Zeman

first: Hana

last: Hansikova


title: Decoction mediates spinal cord repair in vitro and in vivo through the PI3K-AKT signaling pathway

status: Public on May 17 2021

city: xi'an

first: Erliang

last: Li

address: xin si street

institute: tangdu hospital

summary:
Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to find the potential molecular mechanism of traditional Chinese medicine in the treatment of spinal cord injury
Methods: Total RNA was isolated and purified using TRIzol reagent following the manufacturer's procedure. The RNA amount and purity of each sample was quantified using NanoDrop ND-1000 . The RNA integrity was assessed by Bioanalyzer 2100 with RIN number >7.0, and confirmed by electrophoresis with denaturing agarose gel. Poly (A) RNA is purified from 1μg total RNA using Dynabeads Oligo (dT)25-61005  using two rounds of purification. Then the poly(A) RNA was fragmented into small pieces using Magnesium RNA Fragmentation Module under 94℃ 5-7min. Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase , which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I, RNase H and dUTP Solution . An A-base is then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contains a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Single- or dual-index adapters are ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products are amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA library was 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina Novaseq™ 6000 following the vendor's recommended protocol.
Results:In this study, we obtained: chromosome: 23, Genes (G): 32623, Transcripts (T): 40808, GO Annoated: 20795, KEGG Annoated: 8299; in further pathway analysis, it was shown that PI3K-AKT signaling pathway may be the underlying molecular mechanism.
Conclusions: Our study represents the first detailed analysis of the spinal cord transcriptome generated by RNA-seq technology with biological replicates. Our results suggest that Modified Erxian decoction may mediate spinal cord repair through the PI3K-AKT pathway.

overall_design: Spinal Cord Injury in Wistar Rats and Intervention Treatment with Modified Erxian Decoction, RNA-Seq Analysis of Spinal Cord Tissue, The experiment was divided into treatment group (T_Spinal group, MED treatment after injuring the spinal cord), control group (C_Spinal group, distilled water  after injuring the spinal cord) and sham group (sham group, only the lamina was opened without injuring the spinal cord), and all experiments were repeated three times.

first: Bo

last: Liao

first: Qiong

last: Ma

first: Rongbao

last: Yan


title: Transcriptome-wide maps of subcutaneous adipose tissues in cancer-associated cachexia and noncachexia patients

first: Diya

last: Sun

address: Dongan Street

institute: Zhongshan Hospital Fudan University

summary: Cancer-associated cachexia (CAC) is a metabolic syndrome characterized by progressive depletion of adipose and muscle tissue which cannot be corrected by conventional nutritional therapy. Adipose tissue, as an important energy storage, could appear obvious loss in early stage of CAC, which becomes a negative factor affecting the quality of life, efficacy of chemotherapy and so on. In order to identify differentially expressed RNAs in adipose tissue of CAC patients with noncachexia patients, we chose three gastric cancer patients with remarkable weight loss as CAC group and three gastric cancer patients without significant weight change within half a year as the control group. We resected a small subcutaneous adipose tissue from the abdomen of these six patients at time of surgery and completed transcriptome sequencing using  Illumina platform. Compared with NCBI genome detabase, etc, we finally identified 386 differentially expressed mRNAs, 410 differentially expressed lncRNAs, 66 differentially expressed cirRNAs and 98 differentially expressed miRNAs. We hoped to provide more bases for follow-up study of adipose metabolism in cachexia.

overall_design: Adipose tissues of 3 cancer-associated cachexia patients and 3 noncachexia cancer patients

first: Jun

last: Han


title: Multiomics analysis couples mRNA turnover and translational control of glutamine metabolism to the differentiation of the activated CD4+ T cell

status: Public on Apr 28 2021

city: Cambridge

first: Louise

last: Matheson

address: Babraham Research Campus

department: Laboratory of Lymphocyte Signalling and Development

country: United Kingdom

institute: The Babraham Institute

summary: The ZFP36 family of RNA-binding proteins acts post-transcriptionally to repress translation and promote RNA decay. Studies of genes and pathways regulated by the ZFP36 family in CD4+ T cells have focussed largely on cytokines, but their impact on metabolic reprogramming and differentiation is unclear. Using CD4+ T cells lacking Zfp36 and Zfp36l1, we combined the quantification of mRNA transcription, stability, abundance and translation with crosslinking immunoprecipitation and metabolic profiling to determine how they regulate T cell metabolism and differentiation. Our results suggest that ZFP36 and ZFP36L1 act directly to limit the expression of genes driving anabolic processes by two distinct routes: by targeting transcription factors and by targeting transcripts encoding rate-limiting enzymes. These enzymes span numerous metabolic pathways including glycolysis, one-carbon metabolism and glutaminolysis. Direct binding and repression of transcripts encoding glutamine transporter SLC38A2 correlated with increased cellular glutamine content in ZFP36/ZFP36L1-deficient T cells. Increased conversion of glutamine to α-ketoglutarate in these cells was consistent with direct binding of ZFP36/ZFP36L1 to Gls (encoding glutaminase) and Glud1 (encoding glutamate dehydrogenase). We propose that ZFP36 and ZFP36L1 as well as glutamine and α-ketoglutarate are limiting factors for the acquisition of the cytotoxic CD4+ T cell fate. Our data implicate ZFP36 and ZFP36L1 in limiting glutamine anaplerosis and differentiation of activated CD4+ T cells, likely mediated by direct binding to transcripts of critical genes that drive these processes.

overall_design: mRNA-seq (3 biological replicates), nascent, 4sU-labelled mRNA-seq (2 biological replcates, separated into labelled [nascent RNA], unlabelled [pre-existing RNA] and total fractions) and Ribo-seq (5 biological replicates) were performed in activated CD4+ T cells from control and Zfp36/Zfp36l1 double conditional knockout mice. To identify direct targets of ZFP36-family proteins, iCLIP was performed on activated CD4+ T cells from WT C57BL/6 mice (3 biological replicates), using two independent antibodies that bind to ZFP36L1.

first: Sebastian

last: Łukasiak

first: Manuel

last: Díaz-Muñoz

first: Martin

last: Turner


title: Lineage transcription factors ASCL1, NKX2-1, and PROX1 are enriched at super enhancers and co-regulate subtype-specific genes in small cell lung cancer [HiCHIP]

first: Jane

last: Johnson

overall_design: HiChIP of H3K27ac to map enhancer-promoter loops in small cell lung cancer cell lines

first: Karine

last: Pozo

first: Rahul

last: Kollipara

first: Xiaoyang

last: Zhang


title: The SNF2 ATPase-independent function of the INO80 chromatin remodeler

first: xinjian

last: He

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

overall_design: Refer to individual Series


title: Mapping genotype-expression associations in Heterogeneous Stock rat brains to advance behavioral genetics research [Lateral habenula]

status: Public on Apr 23 2021

city: La Jolla

first: Daniel

last: Munro

address: 9500 Gilman Drive

department: Psychiatry

institute: UC San Diego

summary: Research into the genetic influences of impulsivity and reward motivated behavior relies heavily on outbred animal populations, including Heterogeneous Stock (HS) rats, for the genetic diversity necessary to identify genotype-trait associations. Many such associations have been detected, but it is not always clear which gene or other feature near the identified genomic location is functionally responsible for the association. Since these traits are in part mediated by gene expression, mapping the associations between genotype and gene expression in these animals will enable the discovery and deeper understanding of these trait associations. We therefore obtained genotypes and RNA-Seq gene expression for five brain regions from 88 HS rats and mapped expression quantitative trait loci (eQTLs) for each region. We identified cis-eQTLs in over 3,000 genes per brain region and validated their effect sizes using allele specific expression. This resource will enable new discoveries of the genetic influences of complex behavioral traits.

overall_design: mRNA profiles from 4-5 brain regions from each of 88 naïve HS rats

first: Tengfei

last: Wang

first: Apurva

last: Chitre

first: Oksana

last: Polesskaya

first: Laura

last: Saba

first: Hao

last: Chen

first: Pejman

last: Mohammadi

first: Abraham

last: Palmer


title: Mapping genotype-expression associations in Heterogeneous Stock rat brains to advance behavioral genetics research [Prelimbic cortex]


title: Mapping genotype-expression associations in Heterogeneous Stock rat brains to advance behavioral genetics research [Infralimbic cortex]


title: Mapping genotype-expression associations in Heterogeneous Stock rat brains to advance behavioral genetics research


title: Mapping genotype-expression associations in Heterogeneous Stock rat brains to advance behavioral genetics research [Orbitofrontal cortex]


title: Bisulfte sequnencing and DNA-seq of miP1aOX in Arabidopsis thaliana

status: Public on Apr 24 2021

city: Frederiksberg C

first: Bin

last: Sun

address: Thorvaldsensvej 40

department: Department of Plant and Environmental Sciences

country: Denmark

institute: Copenhagen Plant Science Centre – University of Copenhagen

type: Methylation profiling by high throughput sequencing


title: Mapping genotype-expression associations in Heterogeneous Stock rat brains to advance behavioral genetics research [Nucleus accumbens core]


title: Transcriptome  analysis of G6PD overexpression(OE) and wildtype(WT) cells in Multiple Myeloma

status: Public on Apr 20 2021

city: 中国江苏

first: rui

last: li

address: 138 Xianlin Road, Nanjing 210023, China

institute: Nanjing University of Chinese Medicine

summary: RNA-seq experiments was conducted to analyze changes in related signaling pathways and gene expression in multiple myeloma  cells when G6PD was overexpression.

overall_design: Examination of  two cell types

first: Rui

last: Li


title: Metabolic capacities of Novosphingobium sp. HR1a in the rhizosphere

status: Public on Apr 19 2021

city: Little Rock

first: Zulema

last: Udaondo

state: AR

address: 501 Jack Stephens Drive

department: Biomedical Informatics

institute: UAMS

summary: Rhizoremediation, the biotechnology of the utilization of rhizospheric microorganisms associated with plant roots for the elimination of soil contaminants, is based on the ability of microorganisms to metabolize nutrients from plant root exudates, in order to survive the stressful conditions of the rhizosphere, and thereby, to co-metabolize or even mineralize toxic environmental contaminants. Novosphingobium sp. HR1a is a bacterial strain able to degrade a wide variety of polycyclic aromatic hydrocarbons (PAHs). We have demonstrated that this bacterium is able to grow in vegetated microcosms and to eliminate phenanthrene in the presence of clover faster than in non-vegetated systems, establishing a positive interaction with clover. We have studied the molecular basis of this interaction by phenomic, metabolomic and transcriptomic analyses, demonstrating that the positive interaction between clover and Novosphingobium sp. HR1a is a result of the bacterial utilization of different carbon and nitrogen sources (such as sugars, amino acids and organic acids) released during seedling development, and the capacity of exudates to induce the PAH degradation pathway. These results are pointing out to Novosphingobium sp. HR1a as a promising strain for the bioremediation of PAH-contaminated soils.

overall_design: To investigate the metabolic abilities of Novosphingobium sp. HR1a in the clover rhizosphere, we carried out a transcriptomic analysis to identify the genes that were expressed in the presence of clover roots and their respective exudates.

first: Lázaro

last: Molina

first: María

last: Montero-Curiel

first: Regina-Michaela

last: Wittich

first: Alicia

last: García-Puente

first: Ana

last: Segura


title: Transcriptomic analysis of breast cancer patients sensitive and resistant to chemotherapy: Looking for overall survival and drug resistance biomarkers

status: Public on Apr 30 2021

city: Guadalajara

first: Carlos

middle: Alfredo

last: Barrón Gallardo

state: Jalisco

address: Sierra Mojada 950

country: Mexico

institute: Universidad de Guadalajara

summary:
Purpose: Neoadjuvant chemotherapy is one important therapeutic strategy for breast cancer with the drawback of resistance development. Chemotherapy has adverse effects that combined with resistance could contribute to lower overall survival. This work aimed to evaluate the molecular profile of patients who received neoadjuvant chemotherapy trying to discover differentially expressed genes (DEGs) that could be used as biomarkers of chemotherapy response and overall survival.
Methods: Breast cancer patients who received neoadjuvant chemotherapy were enrolled in this study and according to their pathological response were assigned as sensitive or resistant. To evaluate DEGs, GO, KEGG and protein-protein interactions, RNAseq information from all patients was obtained by next generation sequencing.
Results: A total of 1985 DEGs were found and KEGG analysis indicated a great number of DEGs in metabolic pathways, pathways in cancer, cytokine-cytokine receptor interactions, and neuroactive ligand-receptor interactions. A selection of 73 DEGs were used further for an analysis of overall survival using the METABRIC study. Seven of those DEGs were found to correlated with overall survival, of them the sub-expression of C1QTNF3, CTF1, OLFML3, PLA2R1, PODN and the over expression of TUBB and TCP1 were found in resistant patients and related to patients with lower overall survival.
Conclusions: This work highlights differences at the level of gene expression in patients resistant and sensitive to neoadjuvant chemotherapy. Cellular components related to extracellular region and plasma membrane were mainly involved. Furthermore, 73 DEGs were able to discriminate patients resistant and sensitive to neoadjuvant chemotherapy, and 7 of them were able to predict overall survival.

overall_design: A total of 22 mRNA profile of breast cancer patients prior treatment who were then treated with neoadjuvant chemotherapy

last: Barrón-Gallardo

first: Mariel

last: García-Chagoyan

first: Andrés

last: de Jesús Morán-Mendoza

first: Raúl

last: Delgadillo-Cristerna

middle: G

last: Martínez-Silva

first: Adriana

last: Aguilar-Lemarroy

first: Luis

last: Jave-Suárez


title: Invariant Natural Killer T Cell Subsets Have Diverse Graft-Versus-Host-Disease-Preventing and Anti-Tumor Effects

city: Stanford

first: Juliane

last: Lohmeyer

address: 269 W. Campus Drive

institute: Stanford University

summary: Invariant Natural Killer T (iNKT) cells are a T cell subset with potent immunomodulatory properties. Experimental evidence in mice and observational studies in humans indicate that iNKT cells have antitumor potential as well as the ability to suppress acute and chronic Graft-versus-Host-Disease (GvHD). Murine iNKT cells differentiate during thymic development into iNKT1, iNKT2 and iNKT17 sublineages, which differ transcriptomically and epigenomically, and have subset-specific developmental requirements. Whether distinct iNKT sublineages also differ in their antitumor effect and their ability to suppress GvHD is currently unknown. In this work, we generated highly purified murine iNKTsublineages, characterized their transcriptomic and epigenomic landscape, and assessed specific functions. We demonstrate that iNKT2 and iNKT17, but not iNKT1 cells, efficiently suppress T cell activation in vitro and mitigate murine acute GvHD in vivo. Conversely, we show that iNKT1 cells display the highest antitumor activity against murine B-cell lymphoma cells both in vitro and in vivo. Thus, we demonstrate for the first time that iNKT sublineages have distinct and different functions, with iNKT1 cells having the highest antitumor activity and iNKT2 and iNKT17 cells having immune-regulatory properties. These results have important implications for the translation of i

overall_design: Highly purified murine iNKT-sublineages derived from thymi of FVB mice were characterized by bulkRNA and ATAC-sequencing. Total thymic iNKT from single thymi from 2 8 week old FVB/N mice were analyzed by single cell RNAseq. Donor CD4 and CD8 Tcon from FVB mice on day 7 after transplantation in a major mismatch GvHD model (FVB -> Balb/C) and treatment with iNKT1, iNKT2 or iNKT17 cells or no treatment were sorted and analyzed by bulk RNAseq.

first: Kristina

last: Maas-Bauer

first: Toshihito

last: Hirai

first: Teresa

last: Ramos

first: Furqan

last: Fazal

first: Ulrike

last: Litzenburger

first: Kathryn

last: Yost

first: Jessica

middle: V

last: Ribado

first: Neeraja

last: Kambham

first: Arielle

last: Wenokur

first: Po-Yu

last: Lin

first: Maite

last: Alvarez

first: Melissa

last: Mavers

first: Jeanette

last: Baker

first: Ami

last: Bhatt

first: Howard

last: Chang

first: Federico

last: Simonetta

first: Robert

last: Negrin


title: Condensin DC spreads linearly and bidirectionally from recruitment sites to create loop-anchored TADs in C. elegans (Hi-C)

status: Public on Mar 24 2021

city: New York

first: Jun

last: Kim

state: NY

address: 100 Washington Square East 1009 Silver Center

department: Biology

institute: NYU

summary: Condensins are molecular motors that compact DNA for chromosome segregation and gene regulation. In vitro experiments have begun to elucidate the mechanics of condensin function but how condensin loading and translocation along DNA controls eukaryotic chromosome structure in vivo remains poorly understood. To address this question, we took advantage of a specialized condensin, which organizes the 3D conformation of X chromosomes to mediate dosage compensation (DC) in C. elegans. Condensin DC is recruited and spreads from a small number of recruitment elements on the X chromosome (rex). We found that ectopic insertion of rex sites on an autosome leads to bidirectional spreading of the complex over hundreds of kilobases. On the X chromosome, strong rex sites contain multiple copies of a 12-bp sequence motif and act as TAD borders. Inserting a strong rex and ectopically recruiting the complex on the X chromosome or an autosome creates a loop-anchored TAD. Unlike the CTCF system, which controls TAD formation by cohesin, direction of the 12-bp motif does not control the specificity of loops. In an X;V fusion chromosome, condensin DC linearly spreads into V and increases 3D DNA contacts, but fails to form TADs in the absence of rex sites. Finally, we provide in vivo evidence for the loop extrusion hypothesis by targeting multiple dCas9-Suntag complexes to an X chromosome repeat region. Consistent with linear translocation along DNA, condensin DC accumulates at the block site. Together, our results support a model whereby strong rex sites act as insulation elements through recruitment and bidirectional spreading of condensin DC molecules and form loop-anchored TADs.

overall_design: Population Hi-C contact matrices of mixed embryo worms harboring rex site insertions and a dCas9-SunTag block strain

first: David

last: Jimenez

first: Bhavana

last: Ragipani

first: Bo

last: Zhang

first: Sarah

last: Albritton

first: Lena

last: Street

first: Maxwell

last: Kramer

first: Lara

last: Winterkorn

first: Sevinc

last: Ercan


title: Effect of rapamycin on murine subcutaneous MC38 tumor cell populations

status: Public on Feb 26 2021

city: Nashville

first: Jeffrey

middle: C

last: Rathmell

state: Tennessee

address: 1161 21st Ave S

department: PMI

institute: Vanderbilt University Medical Center

summary: To determine differential metabolic gene expression in distinct cell populations from subcutaneous MC38 tumors at baseline and in response to rapamycin, tumors from mice treated with vehicle or rapamycin were harvested, reconstituted to single cell suspensions, and flow sorted into cancer cell (CD45-), tumor-associated macrophage (TAM, CD45+ CD11b+ Ly6G- Ly6C lo F4/80 hi), monocytic myeloid-derived suppressor cell (M-MDSC, CD45+ CD11b+ Ly6G- Ly6C hi),  CD8 T cell (CD45+ CD3+ CD8a+), and CD4 T cell (CD45+ CD3+ CD8a-) populations. RNA was extracted and transcripts were quantified by the NanoString nCounter Metabolic Pathways Panel.

overall_design: There are 3 biological replicates for all cell populations including whole tumor single cell suspension (6 cell populations) and vehicle (control) and rapamycin treatment (2 treatments) except for M-MDSC +rapamycin and CD4 +rapamycin, which have 2 biological replicates due to QC concerns in discarded samples. Therefore, in total there are 6 cell populations x 2 treatments x 3 replicates -2 samples = 34 samples

first: W


title: Cytosine base editors induce prevalent unwanted out-of-protospacer editing and target-strand editing

status: Public on Apr 08 2021

last: MENG

state: Beijing

address: No.5 Yiheyuan Road Haidian District

department: School of Life Sciences

institute: Peking University

summary: The Detect-seq provides an unbiased method for genome-wide identification of CBE induced off-targets inside of cells.     Purpose: Cytosine base editors (CBEs) have the potential to correct human pathogenic point mutations. However, its genome-wide specificity remains poorly understood, precluding its therapeutic applications. Unbiased tools are urgently needed to comprehensively evaluate CBE off-targets at the genome-wide level.     Methods: The genomic DNA from CBE transfected cells are processed with fragmentation, endogenous d5fC protection, damage repair, biotin-dUTP and 5fdCTP labeling, and pull-down steps. After the sequencing library preparation, the  FASTQ files are produced by the Illumina HiSeq XTen platform. To guarantee the reproducibility, each case of the experiment is present with two biological replicates.     Results: Through Detect-seq, we comprehensively profiled the genome-wide off-targets of CBE for several representative sgRNAs, and observed both weak, “random-like” off-targets as well as strong Cas9-dependent off-targets in different human cell lines. Cas9-dependent off-targets can be prevalent for several sgRNAs, and demonstrate a divergent degrees of sequence similarity to the sgRNA. These CBE-induced off-target sites differ greatly from those caused by Cas9 nuclease alone, suggesting inherently different properties among these genome editing tools. Targeted amplicon sequencing further corroborated the novel off-target sites by Detect-seq; quite a few sites showed editing ratio that is on the same order of magnitude or even comparable to the on-target sites. Detect-seq also revealed two unexpected types of Cas9-dependent off-targets, which are out-of-protospacer editing and target-strand editing. These novel off-targets were likely caused by an unstable structure at the PAM-distal side of the Cas9-sgRNA-DNA complex. Based upon such understanding to the off-target editing, we engineered several CBE variants bearing mutations in APOBEC1 and obtained improved CBEs with significantly reduced off-target editing activities.    Detect-seq utilized a dU-mapping strategy to profile on-target and off-target editing events by CBE at the whole-genome level. We applied Detect-seq to off-target evaluation in HEK293T and MCF7 cells for BE4max with several frequently used sgRNAs: “VEGFA site 2”, “HEK293 site 4”, “EMX1”, and “RNF2”.

overall_design: 26 samples.

first: Lei

last: Zhixin

first: Meng

last: Haowei

first: Lv

last: Zhicong

first: Yi

last: Chengqi


title: SARS-CoV-2 spike protein interacts with and activates TLR4

status: Public on Feb 25 2021

first: Xuefei

last: Guo

state: Bejing

address: Xueyuan road, haidian district

department: Institute of Systems Biomedicine

institute: Peking university health science center

summary: We here identified that the trimeric spike protein of SARS-CoV-2 could bind to TLR4 directly and robustly activate downstream signaling in monocytes and neutrophils. Moreover, specific TLR4 or NFKB inhibitor, or knockout of MyD88 could significantly block IL-1B induction by spike protein. We thus reveal that spike protein of SARS-CoV-2 functions as a potent stimulus causing TLR4 activation and sepsis related abnormal responses.

overall_design: RNAseq analysis of THP-1 cells with SARS-CoV-2 Spike protein or LPS stimuli.

first: Yingchi

last: Zhao

first: Ming

last: Kuang


title: Condensin DC spreads linearly and bidirectionally from recruitment sites to create loop-anchored TADs in C. elegans (ChIP-seq)

first: Jun

last: Kim

overall_design: Population ChIP-seq profiles of mixed embryo worms harboring rex site insertions and a dCas9-SunTag block strain

first: David

last: Jimenez


title: Lack of human papilloma virus transcriptional activity in cutaneous squamous cell carcinoma stratified by histological grade and host immune status

status: Public on Mar 02 2021

city: Los Angeles

first: Peter

last: Tontonoz

address: 675 Charles E Young

department: Pathology

institute: UCLA

summary: Human Papilloma Virus (HPV) infection is known to contribute to mucosal (m)SCC, but its role in cutaneous (c)SCC progression remains unclear, especially in lesions determined to be at high-risk for metastasis. We hypothesized that histologically high grade cSCCs in immunosuppressed patients would display increased transcriptional activity of HPV when compared to low histologic grade lesions in otherwise healthy patients. To assess the role of viruses in cSCC pathogenesis we utilized high throughput RNA sequencing across risk-stratified lesions. Skin excisions classified as high grade in immunocompromised patients, low grade in otherwise healthy patients, and normal skin were used for detection of any non-human RNA. Reads were aligned to known viral transcriptomes using our recently developed Microbiome Coverage Profiler. While approximately two-thirds of all samples tested positive for HPV gDNA, no skin sample had detectable expression of HPV RNA.

overall_design:
To assess the role of HPV and other viral gene expression in cSCC disease pathogenesis we have utilized high throughput sequencing of cSCC across risk-stratified lesions. A collection of histologically high-risk, low-risk, and normal skin biopsies were used for detection of non-human RNA. High-quality, non-human reads were used for viral analysis using Microbiome Coverage Profiler and differential human gene expression analysis were conducted comparing risk groups to normal skin using edgeR. The processed data for these records includes only the differential human gene expression analysis.

The HPV DNA Detection status of these samples was not available at the time of submission but submitter states that the records will be updated with this information when it becomes available.

first: Brandon

last: Thomas

first: Philip

middle: O

last: Scumpia


title: Condensin DC spreads linearly and bidirectionally from recruitment sites to create loop-anchored TADs in C. elegans (RNA-seq)

overall_design: Population mRNA profiles of mixed embryo worms harboring autosomal rex insertions

first: Bhavana

last: Ragipani

first: Bo

last: Zhang

first: Sarah

last: Albritton

first: Lena

last: Street

first: Maxwell

last: Kramer

first: Ercan

last: Sevinc


title: Functional characterization of RNF219

status: Public on Mar 05 2021

city: Nanjing

first: Xiaoxu

last: Liu

state: Jiangsu

address: 2 Sipailou

department: Institute of Life Sciences

institute: Southeast University

summary: In this study, we analyzed the function of RNF219 in gene expression control by RNA-Seq analyses in mouse embryonic stem cells after RNF219 knockdown.

overall_design: ES cells were infected with lentivirus carrying either non-targeting shRNA or Cnot10 shRNA. 2 replicates each.

first: Chengqi

last: Lin


title: Tramtrack safeguards tissue identity of Drosophila intestinal stem cells by preventing neuroblast-like program activation and neuroendocrine tumors

status: Public on Feb 23 2021

first: huanwei

last: huang

address: 7 Science Park Rd., ZGC life science park

institute: NIBS


title: Transcriptome profiling of Drosophila wild type and ttk-RNAi, dpn overexpressed, Nicd overexpressed and seq&Nicd overexpressed intestinal progenitor cells

summary:
Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study  are to compare transcriptome profiling (RNA-seq) of intestinal progenitor cells in Drosophila wild type and ttk-RNAi, dpn overexpressed, Nicd overexpressed and seq&Nicd overexpressed midguts
Methods: mRNA profiles of intestinal progenitor cells isolated from 7-day-old wild-type (Ctrl) and ttk-RNAi, dpn overexpressed(dpn OE), Nicd overexpressed(Nicd OE) and seq&Nicd overexpressed(seq&Nicd OE) Drosophila midgut were generated by deep sequencing using Illumina HiSeq 2500.
Results: ttk-RNAi in intestinal progenitor cells induces the expression of  many neural-specific genes, including dpn and seq. Dpn ectopic expresion explains most of the ttk-RNAi expression profile change. Seq ectopic expression explains the expression of neural-specific Notch targets in the ttk-RNAi intestinal progenitor cells.

first: Zhaohui

last: Li

first: Rongwen

last: Xi


title: Genome-wide DNA-binding analysis for Ttk in intestinal progenitor cells and Su(H) in wildtype, seq overexpressed and ttk-RNAi intestinal progenitor cells by DamID

summary:
Purpose:  Genome-wide DNA-binding analysis for Ttk in intestinal progenitor cells and comparing Su(H) binding sites  between seq overexpressed and ttk-RNAi intestinal progenitor cells in Drosophila midgut by DNA adenine methyltransferase identification(DamID)
Methods: Dam(Ctrl) , Ttk-Dam transgenes, Su(H)-Dam, Su(H)-Dam&seq and Su(H)-Dam&ttk-RNAi were expressed in intestinal progenitor cells by esg-Gal4.The guts within 2 days was used for  DNA adenine methyltransferase identification (DamID), followed by deep sequencing analysis
Results: Ttk suppresses neural specific Notch targets through suppressing Seq in intestinal progenitor cells

overall_design: Dam(Ctrl) , Ttk-Dam transgenes, Su(H)-Dam, Su(H)-Dam&seq and Su(H)-Dam&ttk-RNAi were expressed in intestinal progenitor cells by esg-Gal4.The guts within 2 days was used for DamID-seq, followed by deep sequencing analysis.


title: Cellular proteo-transcriptomic changes in the immediate early-phase of HIV-1 and 2 transduction

status: Public on Feb 20 2021

city: Nyíregyháza

first: Judit

last: Dobránszki

state: Szabolcs-Szatmár-Bereg

address: Westsik Vilmos út 4-6.

department: Centre for Agricultural Genomics and Biotechnology

country: Hungary

institute: University of Debrecen

summary: Human immunodeficiency viruses type 1 and 2 (HIV-1 and 2) are known to depend on the cellular machinery for their replication and survival. While most of the studies on cellular proteomic and transcriptomic changes focused on the late-phase of the infection, studies of those changes in early time-points; especially in the case of HIV-2, are widely lacking. Using 2nd generation HIV-1 and 2 VSV-G pseudotyped lentiviral vectors, we transduced HEK-293T cells, and carried out transcriptomic profiling and proteomic analysis at 0 and 2h time points. Significant variations were observed in gene expression profile between HIV-1 and HIV-2 transduced samples. Thrombospondin 1 (THBS1), collagens (COL1A2, COL3A1) and eukaryotic translation factors (EIF3CL), in addition to various genes coding for long-non-coding RNA (lncRNA) were significantly upregulated at 2h time-point after HIV-2 transduction, compared to HIV-1. Label-free quantification mass spectrometry indicated that 7 proteins involved in RNA binding, mRNA transport, and chaperoning were significantly downregulated. Identification of cellular protein targets of HIV, and their effect on the cellular transcriptome will undoubtedly shed more light on their complex life cycle, and may be utilized against the infection, furthermore, characterizing the early-phase of HIV-2 infection may aid in the understanding of its pathomechanism, and long incubation period.

overall_design: Transcriptomic analysis of HIV-1,HIV-2 and VSV.G-MOCK transduced HEK 293T cells at 0 and 2h timepoints

first: Tamás

middle: R

last: Linkner

first: Viktor

last: Ambrus

first: Balázs

last: Kunkli

first: Zsófia

middle: I

last: Szojka

first: Gergő

last: Kalló

first: Éva

last: Csősz

first: Miklós

last: Emri

first: József

last: Tőzsér

first: Mohamed

last: Mahdi


title: Condensin DC spreads linearly and bidirectionally from recruitment sites to create loop-anchored TADs in C. elegans

status: Public on Mar 23 2021

first: Jun

last: Kim


title: Mouse peritoneal macrophages treated with LPS for 6 hours

status: Public on Jan 30 2021

city: Changsha

first: Songqing

last: Tang

state: Hunan

address: Tianma Road

department: Department of pharmacy

institute: Hunan University

summary: MicroRNA Let-7 has abundant expression in macrophages and can repress the expression of IL-6 via binding the 3'UTR of IL-6 mRNA. Here, the IL-6 ceRNAs, which compete let-7 with IL-6, was investigated by cDNA Microarray. We reveal that RasGRP1 specifically derepress the expression of IL-6 by competing Let-7a in inflammatory response. Our data elucidated a previously uncharacterized coding-independent role of RasGRP1 in innate immunity, providing an insight into the ceRNAs modulation of innate immune response, and found that RasGRP1 have a dual-function in promoting inflammation and inhibiting tumor by a protein-independent or dependent manner respectively, which may well explain why acute inflammation rarely leads to tumorigenesis.

overall_design: Comparison the expression level of Let7 target-genes in LPS or PBS treated macrophages.

first: Cong

last: Wang

first: Xue

first: Changping

last: Yu

first: Haizhen

last: Zhu

first: Jianli


title: Hsa_circ_0001583 a novel biomarker for breast cancer related to immune response

status: Public on Feb 02 2021

city: Fuzhou City

first: Yong-Jin

last: Cao

address: Chazhong Road

department: Department of Thyroid and Breast Surgery

institute: The First Affliated Hospital of Fujian Medical University

summary: The differently expressed circRNAs were analysis by microarray. There were 256 differentially upregulated circRNAs and 277 differentially downregulated circRNAs based on fold change ≥2.0 and p<0.05. We found hsa_circ_0001583 expression was up-regulated in BC groups (p<0.05) by RT-qPCR. Therefore, we though hsa_circ_0001583 may serve as a novel kind of biomarker for BC.

overall_design: A total of 4 pairs of breast cancer tissue samples and adjacent nontumor tissue samples were obtained from five BC patients. The circRNA expression profiles were detected with microarray, and validated by RT-qPCR.

first: Min

last: Zheng

first: Wei-Hua

last: Cai

first: Mou-Feng

first: Yu-Jie

last: Deng

first: Ling-Ling

last: Huang


title: The chemically-defined induction of a primitive endoderm and epiblast-like niche supports post-implantation progression from blastoids.

status: Public on Apr 01 2021

city: Utrecht

first: Isabel

last: Guerreiro

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute

summary: The early mammalian conceptus (blastocyst) contains two supporting extraembryonic tissues - the trophectoderm and the primitive endoderm (PrE) - that encase and guide the epiblast (Epi) to eventually form the all body. Modifications of the conceptus exposed key genes regulating these tissues co-development. However, the combination of signalling pathways at play remains elusive. Stem cell-based models including embryoid bodies and blastoids can be generated in large numbers and subjected to high-content screens. Here, we use combinatorial screens of proteins, GPCR ligands and small molecules to rapidly (<96 hours) and efficiently (80%) guide embryoid bodies to form a three dimensional PrE-/Epiblast-like niche in chemically-defined conditions (gel-free, serum-free). This bipotent niche spontaneously progresses, without growth factors, to form a pro-amniotic cavity surrounded by a polarized Epi covered by parietal and visceral endoderm-like cells. In blastoids, these molecules enhance the ratio and number of Gata6+/Nanog+ cells and promote the survival, expansion and morphogenesis of a post-implantation-like Epi in vitro. Altogether, modelling early development in chemically-defined conditions delineates the pathways sufficient to form a functional PrE/Epiblast niche that fuels post-implantation development.

overall_design: Single cell RNA-seq from Embryoid bodies sorted based on Pdgfra staining (421 single cells)

first: Erik

last: Vrij

first: Javier

middle: F

last: Aldeguer

first: Jop

last: Kind

first: Nicolas

last: Rivron


title: Single Cell Transcriptional and Chromatin Accessibility Profiling on the human adult kidneys

status: Public on Feb 21 2021

city: St. Louis

first: Yoshiharu

last: Muto

state: MO

address: 660. S Euclid Ave., CB 8118

department: Medicine / Nephrology

institute: Washington University in St. Louis

summary: We performed single nucleus ATAC (snATAC-seq) and RNA (snRNA-seq) sequencing to generate paired, cell-type-specific chromatin accessibility and transcriptional profiles of the adult human kidney.  snRNA-seq on 3 samples (Healthy1/2/3) were already done and deposited on GSE131882 as control1/2/3 (GSM3823939/GSM3823940/3823941, respectively)

overall_design: n=5 human adult kidney cortex samples were analyzed with snRNA-seq and snATAC-seq (10xGenomics platform). snRNA-seq sequencing of 3 samples (Healthy1/2/3) were already done and deposited on GSE131882 as control1/2/3

first: Y

first: P

last: Wilson

first: B

last: Humphreys


title: Association of common genetic variation with Parkinson’s disease is driven by microglial modulation of Leucine-rich repeat kinase 2 expression

status: Public on Jan 29 2021

city: Bethesda

first: Mark

last: Cookson

state: MD

address: 35 Convent Drive

department: National Institute on Aging

institute: National Institutes of Health

summary: Previous studies have shown that non-coding genetic variation in the 5’ region of the leucine-rich repeat kinase 2 (LRRK2) gene contributes to Parkinson's disease risk and influences LRRK2 expression, with the risk allele associated with increased expression of LRRK2. To interrogate the biological basis of this expression quantitative trait locus (eQTL), we used single nuclei RNA sequencing of human frontal cortex from donors with known LRRK2 risk genotypes to show that the eQTL propagates via microglia, despite robust expression of LRRK2 in other cell types. Second, we found that chromatin in the 5’ region of LRRK2 is differentially accessible in microglia compared to other brain cell types using single nuclei ATAC sequencing. We confirmed these effects in a microglia cell model derived from human induced pluripotent stem cells (iPSCs) by generating single cell RNA sequencing and bulk ATAC sequencing datasets. Our results demonstrate that gene expression as a quantitative trait may influence specific cell populations, and that non-coding genetic variants that are associated with other diseases may propagate through restricted cell types.

overall_design: Single nuclei RNA sequencing datasets were generated from frontal cortex samples from 15 donors (snRNAseq). Single nuclei ATAC sequencing datasets were generated from frontal cortex samples from 12 of the same group of 15 donors (snATACseq). Single cell RNA sequencing datasets were generated from iPSC-derived microglia from two cell lines (scRNAseq). Bulk ATAC sequencing datasets were generated from iPSC-derived microglia differentiated from four cell lines and also from iPSC-derived forebrain neurons differentiated from one cell line with three technical replicates (bulkATACseq). Single nuclei Multiome sequencing (snMulti-seq) was used to generate both ATAC and gene expression (GEX) datasets from the same nuclei extracted from 3 human substantia nigra samples. A large-scale scRNAseq CRISPRi screen was completed using iPSC-derived microglia differentiated from iPSC constitutively expressing dCas9-KRAB transduced with a pooled lentiviral sgRNA library.

first: Rebekah

last: Langston

first: Xylena

last: Reed

first: Raphael

last: Gibbs


title: Endometrial Tissue RNA expression in recurrent pregnancy losses and unexplained infertility vs. conrol

status: Public on Jan 18 2021

city: Istanbul

first: Tuba

last: Günel

address: İstanbul Üniversitesi Fen Fakültesi Moleküler Biyoloji ve Genetik Bölümü Vezneciler

department: Department of Molecular Biology and Genetics

country: Turkey

institute: Istanbul University

summary:
Recent studies are directed to decode the genetic signature of endometrial receptivity for better outcomes in assisted reproductive technologies. In this study, we aimed to understand the transcriptomic profile of midsecretory phase endometria of patients with recurrent pregnancy losses (RPL) and unexplained infertility (UI) by comparing with the endometria of healthy fertile women (Controls).
In this prospective cohort study, we took endometrial samples from 24 patients with RPL, 24 patients with UI and 24 Controls at day 19-21 of the menstrual cycle. By performing genomic analysis, we assessed for differentially expressed genes (DEGs) and pathway analysis.

overall_design: All patients involved in this prospective cohort study were recruited from Istanbul University School of Medicine between August 2014 and August 2015. Three cohorts (fertile controls, patients with RPL and UI) were studied and 24 patients were included in each cohort. None of the patients has received a prior infertility treatment and were not under a current treatment. The first cohort comprised fertile control patients who presented to our gynecology department for well woman examinations. The inclusion criteria were regularly cycling women aged under 35 years with at least one live birth, no history of infertility/treatment, no previous miscarriages and no associated gynecologic (endometriosis, fibroids, active or history of pelvic inflammatory disease) or other medical comorbidities (hyperprolactinemia, thyroid disease etc). The remaining cohorts constituted patients who presented to our in vitro fertilization (IVF) unit. The second cohort included patients with RPL with no history of successful pregnancies. The inclusion criteria for this group were regularly cycling women aged under 35 years with at least two consecutive pregnancy losses of 20 weeks or less, normal follicle-stimulating hormone (FSH), luteinizing hormone (LH), estradiol (E2), prolactin (PRL), and thyroid-stimulating hormone (TSH) levels at day 2-3, normal uterine cavity shape and size, and bilateral tubal patency observed on hysterosalpingogram, no mutations detected in Factor V (Leiden) and prothrombin gene analysis, normal antithrombin III, protein C and S activity, negative results for lupus anticoagulant evaluation, cardiolipin antibody (IgM and IgG), and beta2-glycoprotein antibody (IgM and IgG) and normal karyotype. Their partners have normal spermiogram results and normal karyotype. The third cohort was formed by women with UI at least of 18 months of duration. The inclusion criteria for this group were regularly cycling women aged under 35 years with normal FSH, LH, E2, PRL, and TSH levels at day 2-3, normal uterine cavity shape and size, and bilateral tubal patency observed on a hysterosalpingogram. Their partners have normal spermiogram results.

first: Ercan

last: Baştu

first: Uğur

last: Sezerman

first: Ege

last: Ülgen

first: Irem

last: Demiral Keleş


title: Landscape of transcriptional and translational changes over 22 years of bacterial adaptation

status: Public on Jan 12 2021

city: Piscataway

first: Premal

last: Shah

state: NJ

address: 145 Bevier Rd

department: Genetics

country: USA

institute: Rutgers University

summary: We use RNA-seq and Ribo-seq to analyze expression changes in the Long Term Evolution Experiment. By comparing expression levels between the ancestral strains and each of the evolved lines, we find that expression changes are largely parallel after 22 years of evolution, that these changes occur in specific pathways, and that known mutations may be responsible for some of the observed expression changes.

overall_design: 2 biological replicates each of RNA-seq and Ribo-seq of 13 E. coli cell lines. AraM and AraP refer to the 6 evolved lines of the ancestral REL606 and REL607 strains, respectively. Each file contains the data for the indicated biological replicate (rep1 or rep2), the indicated sequencing method (RNA-seq or ribo-seq), and the indicated cell lines (Ara-1-6 or Ara+1-6 and the corresponding ancestor). Code for processing the data can be found at https://github.com/shahlab/LTEE-gene-expression.

first: John

last: Favate

first: Shun

last: Liang

first: Sam

last: Yadavali


title: Colorectal cancer stem cell states uncovered by simultaneous single-cell analysis of transcriptome and telomeres

status: Public on Dec 30 2020

city: Tianjin

first: Jie

last: Li

address: Wei Jin Road Nankai District No. 94

department: Department of Cell Biology and Genetics

institute: Nankai University

summary: Here, simultaneous measurement of telomere length and transcriptome in the same cells enable systematic assessment of CSCs in primary colorectal cancer (CRC). The in-depth transcriptome profiled by SMART-seq2 is independently validated by high-throughput scRNA-seq using 10x Genomics. We find that rare CSCs exist in dormant state and display plasticity towards cancer epithelial cells (EPCs) that essentially are presumptive tumor-initiating cells (TICs), while both retaining the prominent signaling pathways including WNT, TGF-b and HIPPO/YAP. Moreover, CSCs exhibit chromosome copy number variation (CNV) pattern resembling cancer EPCs but distinct from normal stem cells, suggesting the phylogenetic relationship between CSCs and cancer EPCs. Notably, CSCs maintain shorter telomeres and possess minimal telomerase activity consistent with their non-proliferative nature, unlike cancer EPCs.

overall_design: 10x RNA-seq of three human colorectal cancer with their paired normal tissue

first: Hua

last: Wang


title: Specific ablation of PD-1 on regulatory T cells promotes antitumor immunity

status: Public on Dec 31 2020

city: Seoul

first: Kyungsoo

last: Kim

address: 50 Yonsei-ro, Seodaemun-gu

department: Biotechnoloty

institute: Yonsei University

summary: Regulatory T cells (Tregs) have an immunosuppressive function and highly express PD-1 in tumor microenvironment, but the function of PD-1 in Tregs is still controversial. Using murine tumor model, we demonstrated that Tregs-specific PD-1 conditional Knock-Out mice are resistant to tumor progression. Using PD-1 hetero conditional Knock-Out mice in which both PD-1 expressing Tregs and deficient Tregs co-exist, we found that specific ablation of PD-1 on Tregs results in impaired proliferative capacity and functionality of Tumor-infiltrating Tregs. Single cell RNA and VDJ sequencing revealed that PD-1 signaling in TI Tregs induces global transcriptome crucial for Tregs homeostasis and functionality. Taken together, we suggest that specific ablation of PD-1 on Tregs promotes antitumor immunity by exacerbating Tregs stability and functionality.

overall_design:
mRNA profile of Tumor infiltrating CD4+ T cells from Isotype control or αPD-1 treated TC-1 tumor bearing PD-1 hetero conditional KO mice (PD-1fl/fl X Foxp3eGFP-Cre-ERT2(+/-)) at day 14 after tumor injection

Please note that the *Whole_Processed_*.tsv.gz files contain the GSM4995463-GSM4995466 processed data, the *Integrated-2 and *Integrated-3 files contain processed data for seq 2 and sep3 samples, respectively.

first: Myeong

first: Sang-Jun

last: Ha

first: Insuk

last: Lee


title: Nitric oxide prevents aortic valve calcification by S-nitrosylation of USP9X to activate NOTCH signaling

status: Public on Dec 22 2020

city: Columbus

first: Vidu

last: Garg

state: OH

address: 700 Children's Drive WB4239

department: Cardiovascular Research

institute: Research Institute at Nationwide Children's Hospital

summary: Calcific aortic valve disease (CAVD) is an increasingly prevalent condition and endothelial dysfunction is implicated in its etiology. We previously identified nitric oxide (NO) as a calcification inhibitor by its activation of NOTCH1, which is genetically linked to human CAVD. Here, we show that NO rescues calcification by a S-nitrosylation-mediated mechanism in porcine aortic valve interstitial cells (pAVICs) and single cell RNA-seq demonstrated regulation of NOTCH pathway by NO. A unbiased proteomic approach to identify S-nitrosylated proteins in valve cells found enrichment of the ubiquitin proteasome pathway and implicated S-nitrosylation of USP9X in NOTCH regulation during calcification. Furthermore, S-nitrosylated USP9X was shown to deubiquitinate and stabilize MIB1 for NOTCH1 activation. Consistent with this, genetic deletion of Usp9x in mice demonstrated aortic valve disease and human calcified aortic valves displayed reduced S-nitrosylation of USP9X. These results demonstrate a novel mechanism by which S-nitrosylation dependent regulation of ubiquitin-associated pathway prevents CAVD.

overall_design: Comparison of porcine primary aortic valve interstitial cells with varying treatments

first: Uddalak

last: Majumdar

first: Sathiyanarayanan

last: Manivannan

first: Madhumita

last: Basu


title: DHT (androgen) effect on the gene expression of LNCaP cell line

first: Xuanrong

last: Chen

state: New York

address: 1300 York Ave

institute: Weill Cornell Medicine

summary: Androgen receptor (AR) is essential for the development and progression of prostate cancer (PCa), but the exact role of AR in these processes remains unclear. To examine the direct effect of AR signaling on gene transcription, the cells were perfused with charcoal-dextran stripped fetal bovine serum (CD-FBS) for 3 days, and then treated with 10 nM dihydrotestosterone (DHT) for 24 hours. Deep sequencing of rRNA-depleted total RNAs was performed in biological duplicates on LNCaP cells.

overall_design: Quantification of RNA expression in LNCaP cells treated with androgen (DHT) to manipulate endogenous AR signaling.

first: Zhiqun

last: Shang


title: Characterization of metabolic patterns in mouse oocytes during meiotic maturation

status: Public on Dec 21 2020

city: Beijing

first: Wenjie

last: Shu

address: Taiping Road 27

institute: Beijing Institute of Radiation Medicine

summary: Well balanced and timed energy metabolism is essential for making a high quality egg. However, the metabolic framework that supports oocyte development remains poorly understood. Here we obtained the temporal metabolome profiles of mouse oocytes during in vivo maturation by isolating large number of cells at key stages. In parallel, quantitative proteomic analyses were conducted to bolster the metabolomic data, synergistically depicting the global metabolic patterns in oocytes. In particular, we discovered novel metabolic features during oocyte maturation, such as the fall in polyunsaturated fatty acids (PUFAs) level and the active serine-glycine-one-carbon (SGOC) pathway. Using functional approaches, we further identified two key targets (NKAP and BTG4) through which arachidonic acid (ARA) inhibits meiotic maturation, and demonstrated the control of epigenetic marks in maturing oocytes by SGOC network. Our data serves as a broad resource on the dynamics occurring in metabolome and proteome during oocyte maturation, and provides opportunities for predicting and improving oocyte quality.

overall_design: three replicates for control oocytes; three replicates for siShmt2 oocytes.

first: Qiang

first: Chao

last: Ren


title: A harmonized atlas of spinal cord cell types and their computational classification

first: Ryan

middle: Barlow

last: Patterson-Cross

address: 9000 Rockville Pike

department: NINDS

institute: NIH

summary: Single cell sequencing is transforming many fields of science but the vast amount of data it creates has the potential to both illuminate and obscure underlying biology. To harness the exciting potential of single cell data for the study of the mouse spinal cord, we have created a harmonized atlas of spinal cord transcriptomic cell types that unifies six independent and disparate studies into one common analysis. With the power of this large and diverse dataset, we reveal spinal cord cell type organization, validate a combinatorial set of markers for in-tissue spatial gene expression analysis, and optimize the computational classification of spinal cord cell types based on transcriptomic data. This work provides a comprehensive resource with unprecedented resolution of spinal cord cell types and charts a path forward for how to utilize transcriptomic data to expand our knowledge of spinal cord biology.

overall_design: Integration and classification of 6 publicly available sc-RNAseq datasets

first: Daniel

last: Russ

middle: B

first: Li

first: Stephanie

last: Koch

first: Kaya

last: Matson

first: Ariel

last: Levine


title: Effect of fibulin-3 knockdown on malignant mesothelioma cells

status: Public on Dec 15 2020

city: Syracuse

first: Mariano

middle: S

last: Viapiano

address: 505 Irving Ave Rm 4604

department: Neuroscience and Physiology

institute: SUNY Upstate Medical University

summary: Whole transcriptome comparison of mesothelioma cells transfected with control vs Fibulin-3 (EFEMP1) siRNAs. Mesothelioma cells H-226 (ATCC) and H-2595 (Harvey Pass, New York University) were transfected with two fibulin-3 or control siRNAs and collected 48h after transfection. Gene expression was quantified by RNAseq using standard procedures. The results suggest that downregulation of fibulin-3 negatively affects a PI3K/AKT-dependent gene signature involved in cell growth, adhesion, and association with the extracellular matrix.

overall_design: Three independent cultures from each cell line were transfected with two previously validated fibulin-3 siRNAs or control siRNA (Hu et al., Cancer Res (2012) 72: 3873-3885). Total RNA was extracted using column purification and analyzed by RNAseq using the Illumina NSQ 500/550 Hi Output KT v2.5 (75 CYS, #20024906). Analysis of gene expression was used to determine a gene signature correlated with fibulin-3 downregulation. Design: 2 cell lines x 2 conditions per cell line x 3 independent replicates

first: Arivazhagan

last: Roshini

first: Harvey

last: Pass

first: Frank

last: Middleton