title: Ribosome profiling of 293T cells with or without miRNA inhibitors or non-cleaving shRNAs

city: Tokorozawa

first: Hiroaki

last: Sako

institute: Waseda University

summary: Cells treated with NC control, miRNA inhibitors (miR-361-3p, 375-3p, 769-5p, and 4521), Scr control, or non-cleaving shNBD1s were harvested for ribosome profiling

overall_design: Examination of translation status of miRNA inhibitors and non-cleaving shNBD1s

first: Tadashi

last: Yamamoto


title: Transcriptomic analysis of the abundance of snoRNAs and their host genes in 4 different cell lines, using low structure bias TGIRT-seq

status: Public on Aug 10 2022

city: Sherbrooke

first: Sherif

middle: Abou

last: Elela

state: Québec

address: 3201 Jean Mignault

department: Département de microbiologie et infectiologie

country: Canada

institute: Université de Sherbrooke

summary: Small nucleolar RNAs (snoRNAs) are highly abundant non-coding RNAs whose canonical function is to guide the 2’-O-ribose methylation or pseudouridylation of ribosomal RNAs. They are often encoded in longer genes referred to as their host genes, the expression of which is required for their own biogenesis. Due to their very stable structure, reverse transcription of snoRNAs using standard viral reverse transcriptases is very inefficient, and does not provide an adequate view of the abundance of these small RNAs. We thus employed high-throughput, low structure bias TGIRT-seq sequencing to quantified the abundance of the entire ribodepleted transcriptome, including snoRNAs and their host genes, in 4 different cell lines.

overall_design: Ribodepleted and fragmented TGIRT-Seq librairies were generated from RNA samples originating from various cell lines with two biological replicates each.

first: Danny

last: Bergeron

first: Michelle

middle: S

last: Scott


title: Lineage heterogeneity underlies the multiple origins and functions of type 1 innate lymphoid cells

status: Public on Jul 31 2022

city: Kyoto

first: Koichi

last: Ikuta

state: Kyoto

address: 53 Shogoin-Kawaharamacho, Sakyo-ku

department: Department of Virus Research

country: Japan

institute: Institute for Frontier Life and Medical Sciences, Kyoto University

type: Expression profiling by high throughput sequencing

summary: This study examines the relevance between mature type 1 innate lymphoid cell (ILC1) heterogeneity and the putative ILC1 origins.

overall_design: Transcriptional profiling of group 1 ILCs in fetal liver (FL), IL-7R(-) ILC1s, IL-7R(+) ILC1s, and NK cells in adult liver, immature ILC1s and NK cells in bone marrow (BM), ILC1s in intestinal lamina propria (LPL), and group 1 ILCs in salivary glands (SG).

first: Takuma

last: Asahi


title: Ageing transcriptomes of selected mutants on different carbon sources

status: Public on Jul 21 2022

city: Cambridge

first: Laura

last: Biggins

address: Babraham Research Campus

department: Bioinformatics

country: United Kingdom

institute: The Babraham Institute

summary: Here we show that an unrestricted galactose diet in early life minimises pathology during replicative ageing in budding yeast, irrespective of diet later in life. Lifespan and average mother cell division rate are comparable between glucose and galactose diets, but markers of senescence and the progressive dysregulation of gene expression observed on glucose are minimal on galactose, showing these to be facets of ageing pathology rather than intrinsic parts of the replicative ageing process. Respiration on galactose is critical for minimising ageing pathology, and forced respiration during ageing on glucose by over-expression of Hap4 also has the same effect though only in a fraction of cells. This fraction maintains Hap4 activity to advanced age with low senescence and a youthful gene expression profile, whereas other cells in the same population that lose Hap4 activity undergo dramatic dysregulation of gene expression and accumulate aneuploid fragments of chromosome XII aneuploidy (ChrXIIr), which are tightly associated with ageing pathology.

overall_design: Mother Enrichment Project (MEP) yeast were harvested at log phase or aged for 24 or 48 hours in YP with indicated carbon sources at 2%. Mother cells were purified, total RNA extracted and libraries processed using a NEBNext Ultra II directional RNAseq kit with poly(A)+ selection module.

first: Dorottya

last: Horkai

first: Jon

last: Houseley


title: Recruitment of ETS1 to activated accessible regions promotes cilia genes transcriptional program in ciliopathy [CUT&Tag]

status: Public on Jul 28 2022

city: Zhanjiang

first: Yun-Miao

last: Guo

address: 236 Yuanzhu Road

department: Zhanjiang Institute of Clinical Medicine

country: China

institute: Central People's Hospital of Zhanjiang

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Defects in cilia genes that is critical in cilia formation and function can cause complicated ciliopathy syndromes involving multiple organs and tissues; however, the underlying regulatory mechanisms of cilia gene networks in ciliopathy are largely unknown. Here, we define the genome-wide redistribution of chromatin accessibilities and extensive divergence of cilia genes expression programs happened in ciliopathy. Mechanistically, the distinct ciliopathy-activated accessible regions (CAAs) are characterized to positively regulate robust changes of flanking cilia genes, which are a key transcriptional feature of cilia required for the response to developmental signals. Moreover, the single transcriptional factors, ETS1, can be recruited to CAAs thus prominently reconstructing chromatin accessibility in ciliopathy. CAAs collapse driven by ETS1 suppression subsequently cause defective cilia formation and impaired developmental signal transduction, which eventually develops ciliopathy phenotypes of short fins and pericardium edema in larval fishes. Therefore, our results depicted a dynamic landscape of chromatin accessibility in ciliopathy, and uncover an insightful role of ETS1 in controlling global cilia genes transcriptional program by reprogramming widespread chromatin state.

overall_design: CutTag analysis of ETS1 and IgG

first: Dong-Hui

last: Zhang

first: Yi-Ting

last: Guan


title: LRF promotes indirectly advantageous chromatin conformation via BGLT3-lncRNA expression and switch from fetal to adult hemoglobin

status: Public on Jul 13 2022

city: Patras

first: Athanasios

middle: Nasir

last: Shaukat

state: Western Greece

address: Asklipiou 1

department: Department of Biochemistry

country: Greece

institute: University of Patras

summary: ChIP-seq for LRF/ZBTB7A in untransfected or LRF/ZBTB7A-overexpressing K562 cells, with or without hemin/EPO treatment and in K562 LRF/ZBTB7A-Knockdown cells

overall_design: ChIP-seq for LRF/ZBTB7A on the Ion torrent S5 platform

first: Vasiliki

last: Chondrou

middle: N

first: Constantinos

last: Stathopoulos

first: Argyro

last: Sgourou


title: Cardiorenal Effects of Peritoneal Dialysis in the 5/6Nx Uremic Rat Model

status: Public on Jul 08 2022

city: Milwaukee

first: Alison

middle: J.

last: Kriegel

state: WI

address: 8701 Watertown Plank Rd.

department: Physiology

country: USA

institute: Medical College of Wisconsin

summary: In this study we compare transcriptomic changes in the kidney and left ventricle in response to peritoneal dialyisis exchanges performed 3x per day for 8 days beginning 6 weeks after 5/6 nephrectomy or sham surgery in 10 week old male Sprague Dawley rats. .

overall_design: Ten week old male Sprague Dawley rats were subjected to the excision model of 5/6 nephrectomy (5/6Nx; right kidney + 2/3 of left kidney) or sham surgery (left kidney). At 5.5 weeks post surgery a dialysis port and catheter were placed in the abdominal cavity and peritoneal dialysis (3x/day for 8 days) was initiated at week 6 post-surgery.  At the end of the 7 week study left kidney and left ventricle tissue was collected for histological analysis and mRNA sequencing.

first: Victoria

middle: L

last: Nasci

first: Pengyuan

last: Liu

first: Amanda

middle: X

last: Marks

first: Adaysha

middle: C

last: Williams

middle: J


title: Development of a Novel Air-Liquid Interface Airway Tissue Equivalent Model for In Vitro Respiratory Modeling Studies

status: Public on Jul 14 2022

city: Winston-Salem

first: Sean

middle: V

last: Murphy

state: NC

address: 391 Technology Way

institute: Wake Forest Institue for Regenerative Medicine

summary: The human airways are complex structures with important interactions between cells, extracellular matrix proteins and the biomechanical microenvironment. A robust, well-differentiated in vitro culture system that accurately models these interactions would provide a useful tool for studying normal and pathological airway biology. Here, we report the analysis of a physiologically relevant air-liquid interface (ALI) 3D airway ‘organ tissue equivalent’ (OTE) model with three novel features: native pulmonary fibroblasts, solubilized lung extracellular matrix (ECM), and hydrogel substrate with tunable stiffness and porosity. We demonstrate the versatility of the OTE model by evaluating the impact of these features on HBE cell phenotype. Variations of this model were analyzed during 28 days of ALI culture by evaluating epithelial confluence, trans-epithelial resistance (TEER), and epithelial phenotype via multispectral immuno-histochemistry and next-generation sequencing (NGS). Cultures that included both solubilized lung ECM and native pulmonary fibroblasts within the hydrogel substrate formed well differentiated ALI cultures that maintained a barrier function and expressed similar levels of goblet, club and ciliated markers to native airway tissue. Modulation of hydrogel stiffness did not negatively impact HBE differentiation and could be a valuable variable to alter epithelial phenotype. This study highlights the capability and versatility of a 3D airway OTE model to model the multiple components of the human airway 3D microenvironment.

overall_design: Gene expression profiling analysis of RNA-Seq data for 3D airway OTE models with varying stiffness and 2D airway epithelial cultures. The 3D OTE cultures were fabricated with hydrogels of 3 stiffnesses (2.6kPa, 5.1kPa, 9.8kPa) each containing solubilized lung ECM and native human lung fibroblasts.

first: Timothy

last: Leach

first: Kimberly

middle: D

last: Reeves


title: Alternative splicing of a transposable element into the human long noncoding RNA CARMEN is a switch for cardiac precursor cell specification

status: Public on Aug 01 2022

city: Lausanne

first: Mohamed

last: Nemir

state: Vaud

address: Bugnon 27

department: Cœur et Vaisseau

country: Switzerland

institute: Lausanne University Hospital

summary: The major cardiac cell types composing the adult heart arise from common multipotent precursor cells. Cardiac lineage decisions are guided by extrinsic and cell-autonomous factors, including recently discovered long noncoding RNAs (lncRNAs). The CARMEN locus, which is known to dictate specification towards the cardiomyocyte (CM) and the smooth muscle cell (SMC) fates, generates a diversity of alternatively spliced lncRNAs. Here, we identify one of these isoforms, CARMEN-201, to be crucial for SMC commitment. CARMEN-201 activity is encoded within an alternatively-spliced exon containing a MIRc short interspersed nuclear element. This element binds the transcriptional repressor REST (RE1 Silencing Transcription Factor), targets it to cardiogenic loci, including ISL1, IRX1, IRX5, and SFRP1, and thereby blocks the CM gene program. In turn, genes regulating SMC differentiation are induced. These data show how a critical physiological switch is wired by alternative splicing and functional transposable elements in a long noncoding RNA.

overall_design: Human fetal cardiac precursor cells (CPCs) were infected with lentivirus expressing CARMEN7 Exon2 bearing either a native WT MIRc (D1FCPCLV and D7PFCPCLV) or a scrambled (D1FCPCMV and D7FCPCMV) MIRc, with conservation of base composition. The cells were cultured in differentiation consitions and total cellular RNA was extracted 1 day (D1) or 7 days (D7) after initiation of differentaition. Uninfected fetal human CPCs maintained under proliferation conditions (PFCPC) were included as controls. Additionally, uninfected cells were also also subjected to differentiation and harvested 1 day (D1FCPC) or 7 days (D7FCPC) post initiation of differentiation. Triplicate samples were used for each biological condition. RNA samples were subjected to RNASeq analysis. For RNA immunoprescipitation, adult control CPCs (DIFFCTRL and PROCTRL) and CPCs lacking CARMEN C201 (DKOC201 and PKOC201) were grown under differentiation (DIFFCTRL and DKOC201) or proliferation (PROCTRL and PKOC201) conditions, then RIP was performed using anti-REST IgG. REST-associated transcripts were purified from differentiated adult CPCs using the RNeasy isolation kit (Qiagen). Sequencing libraries were prepared from 3 samples for each condition according to Illumina RNA Seq library kit instructions with Poly(A) selection. Libraries were sequenced with the Illumina HiSeq4000.

first: Isabelle

last: Plaisance

first: Panagiotis

last: Chouvardas

first: Yuliangzi

last: Sun

first: Parisa

last: Aghagolzadeh

first: Farhang

last: Aminfar

first: Sophie

last: Shen

first: Francesca

last: Rochais

first: Rory

last: Johnson

first: Nathan

last: Palpant

first: Thierry

last: Pedrazzini


title: Targeting meiotic recombination 11 (MRE11) nuclease for personalization of epithelial ovarian cancer therapy

status: Public on Jul 04 2022

city: Nottingham

first: Nigel

middle: P

last: Mongan

address: University Park

department: Biodiscovery Institute

institute: University of Nottingham

summary: Platinum resistance is a clinical challenge in ovarian cancer. Platinating agents induce DNA damage which activate Mre11 nuclease directed DNA damage signalling and response (DDR). Upregulation of DDR may promote chemotherapy resistance. Here we have comprehensively evaluated Mre11 in epithelial ovarian cancers. In clinical cohort that received platinum- based chemotherapy (n=331), Mre11 protein overexpression was associated with aggressive phenotype and poor progression free survival (PFS) (p=0.002). In the ovarian cancer genome atlas (TCGA) cohort (n=498), Mre11 gene amplification was observed in a subset of serous tumours (5%) which correlated highly with Mre11 mRNA levels (p<0.0001). Altered Mre11 levels was linked with genome wide alterations that can influence platinum sensitivity. At the transcriptomic level (n=1259), Mre11 overexpression was associated with poor PFS (p=0.003). ROC analysis showed an area under the curve (AUC) of 0.642 for response to platinum-based chemotherapy. Pre-clinically, Mre11 depletion by gene knock down or blockade by small molecule inhibitor (Mirin) reversed platinum resistance in ovarian cancer cells and in 3D spheroid models. Importantly, Mre11 inhibition was synthetically lethal in platinum sensitive XRCC1 deficient ovarian cancer cells and 3D-spheroids. Selective cytotoxicity was associated with DNA double strand break (DSB) accumulation, S-phase cell cycle arrest and increased apoptosis. We conclude that pharmaceutical development of Mre11 inhibitors is a viable clinical strategy for platinum sensitization and synthetic lethality in ovarian cancer.

overall_design: RNAseq was used to compare the transcriptomes of parental PE01 and mirin-resistant derivative PEO1R cell line derived mouse xenografts

first: Adel

last: Alblihy

first: Reem

last: Ali

first: Alison

last: Ritchie

first: Cinzia

last: Allegrucci

first: Paloma

last: Ordonez Moran

first: Katia

last: Mesquita

first: Mashael

last: Algethami

first: Michael

last: Toss

first: Muslim

last: Alabdullah

first: Ian

last: Hickson

first: Natalie

last: Tatum

first: Jennie

last: Jeyapalan

first: Anna

last: Grabowska

first: Emad

last: Rakha

first: Srinivasan

last: Madhusudan


title: Transcriptome profile of liver biopsy tissues from patients with non-alcoholic fatty liver disease

status: Public on Jul 01 2022

city: Dallas

first: Yujin

last: Hoshida

state: TX

address: 5323 Harry Hines Blvd

institute: University of Texas Southwestern Medical Center

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

overall_design: Refer to individual Series


title: Immune-mediated Tubule Atrophy Promotes Acute Kidney Injury to Chronic Kidney Disease Transition

status: Public on Jun 30 2022

city: New Haven

first: Leyuan

last: Xu

state: CT

address: 300 Cedar Street, Ste S255B

department: Internal Medicine/Section of Nephrology

institute: Yale University

summary: Incomplete repair after acute kidney injury (AKI) is associated with progressive loss of tubular cell function and development of chronic kidney disease (CKD). Here, we compared the kidney single-cell transcriptomes from the mice subjected to either unilateral ischemia-reperfusion kidney injury with contralateral nephrectomy (IRI/CL-NX, in which tubule repair predominates) or unilateral IRI with contralateral kidney intact (U-IRI, in which fibrosis and atrophy predominates) to investigate the mechanism(s) underlying transition to CKD following AKI.

overall_design: 10X Chromium was used to profile mouse kidneys.

first: Xu

last: Leyuan

first: Lloyd

middle: G

last: Cantley


title: Long noncoding RNA lnc-H2AFV-1 promotes cell growth by regulating aberrant N6-methyladenosine RNA modification in head and neck squamous cell carcinoma

status: Public on Jun 29 2022

city: Weifang

first: Yingying

last: Jiang

state: Shandong

address: 7166 Baotong west Road

institute: Weifang Medical University

type: Methylation profiling by high throughput sequencing

summary: Head and neck squamous cell carcinoma (HNSCC) is the most common malignant tumor in the oral and maxillofacial regions, and long noncoding RNAs (lncRNAs) play crucial roles in the occurrence and progression of HNSCC. in our study, quantified m6A RNA methylation and dot blot assays revealed that total m6A methylation in HNSCC cells was accompanied by lnc-H2AFV-1 expression. Western blotting showed that the expression of methyltransferase-like 3 (METTL3) and 14 (METTL14) was consistent with that of lnc-H2AFV-1, whereas the expression of demethylase fat mass and obesity-associated (FTO) was contrary to that of lnc-H2AFV-1. Methylated RNA immunoprecipitation sequencing (MeRIP-seq) and MeRIP-qPCR were used to determined the target genes regulated by lnc-H2AFV-1 overexpression in HNSCC cells.

overall_design: Examination of m6A modificated genes in HN6-LV-H2AFV-1 cells and HN6-LV-NC cells.

first: Xi

last: Chen


title: Transcriptional profiling of short term intestinal tissue in mice with Apc and Kras mutations

city: Glasgow

first: Kathryn

last: Gilroy

address: Garscube

institute: CRUK Scotland Institute

summary: Murine small intestinal tissue following Apc mutation, with or without Kras mutation under the control of VilCreER.

overall_design: Expression data from whole intestinal tissue of the noted genotypes.

first: Johan

last: Voorde

first: Owen

last: Sansom


title: Muscleblind-like proteins use modular domains to localize RNAs by riding kinesins and docking to membranes

status: Public on Jul 09 2022

city: Gainesville

first: Eric

middle: T

last: Wang

state: FL

address: 2033 Mowry Rd

institute: University of Florida

summary: RNA transport and local translation provide spatial control of gene expression, and RNA binding proteins (RBPs) act as critical adapters in this multi-step process. Muscleblind-like (MBNL) RNA binding proteins, implicated in Myotonic Dystrophy and cancer, localize RNAs to myoblast membranes and distal neurites, through unknown mechanisms. We found that MBNLs form motile and anchored granules in neurons and myoblasts, and selectively associate with kinesins Kif1bα and Kif1c through its zinc finger (ZnF) domains. Other RBPs with similar ZnFs also associate with these kinesins, implicating a motor-RBP specificity code. Live cell imaging and fractionation revealed that membrane anchoring is mediated through the unstructured carboxy-terminal tail of MBNL1. Both kinesin- and membrane-recruitment functions were reconstituted using MBNL-MS2 coat protein fusions; this approach, termed RBP Module Recruitment and Imaging (RBP-MRI), decouples RNA binding, kinesin recruitment, and membrane anchoring functions, while also establishing general strategies for studying multi-functional, modular domains of RBPs.

overall_design: The underside of hanging cell culture inserts with 1 µm pores (Corning, 353102) were coated with diluted Matrigel preparation (Corning, 354277) and placed into specialized, deep 6-well plates (Corning, 353502). 2 mL of 10% DMEM media was placed on top and underneath the hanging insert membrane prior to cell plating. Neuro2a cells were then densely plated onto membranes at a concentration of 1✕10^6. After 24 hours, serum-containing media was replaced with no-serum media and neurites were allowed to grow for 48 hours. Subsequently, no serum media was removed from both sides of the membrane, which was washed once with PBS, then cell bodies were collected with a cell scraper in 1 mL PBS. Membranes were separated from their housing and placed into a lysis buffer from a Quick-RNA Microprep Kit (Zymo, R1050). Cell body and neurite samples from all wells of a 6-well plate were combined separately for each condition and used for RNA isolation. Following isolation, ribosomal RNA was depleted from 300 ng of the total RNA samples using the NEBNext rRNA Depletion Kit (NEB, E6310L) used for RNA-seq library prep with the NEBNext Ultra II Directional RNA Library Prep Kit (NEB, E7530L) and sequenced using an Illumina NextSeq 500.

first: Ryan

last: Hildebrandt


title: Aberrant gene activation in synovial sarcoma relies on SSX specificity and increased PRC1.1 stability

city: Edinburgh

first: Nezha

middle: Suzanne

last: Benabdallah

state: Midlothian

address: Crewe Road South

department: Institute of Genetics and Cancer

institute: University of Edinburgh


title: Drug combination sci-Plex Data

status: Public on Jun 25 2022

city: Seattle

first: Sanjay

middle: R

last: Srivatsan

state: WA

address: 3720 15TH Ave NE Genome Sciences S Foefe Bldg

department: Genome Sciences

institute: University of Washington

summary: Recent advances in multiplexed single-cell transcriptomics experiments are facilitating the high-throughput study of drug and genetic perturbations. However, an exhaustive exploration of the combinatorial perturbation space is experimentally unfeasible, so computational methods are needed to predict, interpret, and prioritize perturbations. Here, we present the compositional perturbation autoencoder (CPA), which combines the interpretability of linear models with the flexibility of deep-learning  approaches for single-cell response modeling. CPA encodes and learns transcriptional drug responses across different cell type, dose, and drug combinations. The model produces easy-to-interpret embeddings for drugs and cell types, which enables drug similarity analysis and predictions for unseen dosage and drug combinations. We show that CPA accurately models single-cell perturbations across compounds, doses, species, and time. We further demonstrate that CPA predicts combinatorial genetic interactions of several types, implying that it captures features that distinguish different interaction programs. Finally, we demonstrate that CPA can generate in-silico 5,329 missing genetic combination perturbations ($97.6% of all possibilities) with diverse genetic interactions. We envision our model will facilitate efficient experimental design and hypothesis generation by enabling in-silico response prediction at the single-cell level, and thus accelerate therapeutic applications using single-cell technologies.

overall_design: Drug treatments were performed in triplicate including controls matching prior study (Srivatsan, 2020)

first: Riza

last: Daza


title: The differences in miRNA expression with miRNA microarrays of two-dimensional (2D)- and three-dimensional (3D)-SNP cells

status: Public on Jul 07 2022

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: 10-1 tebiro 6-chome

institute: Toray Industries,Inc.

summary:
Canine mammary gland tumors can be used as predictive models for human breast cancer. There are several types of microRNAs common in human breast cancer and canine mammary gland tumors. The functions of microRNAs in canine mammary gland tumors are not well understood. In the present study, we compared the characterization of microRNA expression in two-dimensional and three-dimensional canine mammary gland tumor cell models.
The expression of microRNA-210 in the three-dimensional-SNP cells was 10.19 times higher than that in the two-dimensional-SNP cells.

overall_design: We evaluated the differences between 2D- and 3D-cultured canine mammary gland tumors (2D-SNP and 3D-SNP) by assessing miRNA expression levels.

first: Tomohiro

last: Osaki


title: Targeted protein degradation reveals Pol II heterogeneity and functional diversity

status: Public on Aug 09 2022

city: Beijing

first: Xiong

last: Ji

address: Haidian District, Beijing Summer Palace Road No. 5

department: School of Life Sciences

institute: Peking University


title: Molecular characterization of colorectal cancer related peritoneal metastatic disease [scRNA-seq]

city: Amsterdam

first: Leandro

last: Moreno

address: Meibergdreef 9

country: Netherlands

institute: AmsterdamUMC

summary: We present acomprehensive molecular characterization of a cohort of 5 patients with peritoneal metastasis

overall_design: Examination of single cell RNA expression profiles of primary colorectal cancers versus peritoneal metastasis

first: Kristiaan

last: Lenos

middle: F

first: Louis

last: Vermeulen


title: Multiplex GAM datasets collected with an average of three nuclear profiles each (samples failing QC)

status: Public on Jun 13 2022

city: Oxford

first: Robert

middle: A

last: Beagrie

address: Headley Way

department: Molecular Haematology Unit

institute: MRC Weatherall Institute of Molecular Medicine

summary: Technologies for measuring 3D genome topology are increasingly important for studying mechanisms of gene regulation, for genome assembly and for mapping of genome rearrangements. We developed multiplex-GAM, a faster and more affordable version of Genome Architecture Mapping (GAM), a ligation-free technique to map chromatin contacts genome-wide. We applied multiplex-GAM to Mouse ES cells.

overall_design: This series contains multiplex-GAM samples containing an average of three nuclear profiles from mouse embryonic stem (mES) cells that failed our QC checks.

first: Alexander

last: Kukalev

first: Rieke

last: Kempfer

first: Ana

last: Pombo


title: Single (1 NP) GAM datasets collected from mouse ES cells

summary: Technologies for measuring 3D genome topology are increasingly important for studying mechanisms of gene regulation, for genome assembly and for mapping of genome rearrangements. We applied  the original GAM protocol to Mouse ES cells to generate a deeper dataset for comparison to Hi-C.

overall_design: This series contains GAM samples each containing a single nuclear profiles from mouse embryonic stem (mES) cells.


title: RNA-seq in WT and ATF3 cKO  satellite cells with 3 replicates mix

status: Public on Jun 06 2022

city: Hong Kong

first: Feng

last: Yang

address: Room 503, 5/F, Li Ka Shing Medical Sciences Building, Prince of Wales Hospital

department: Chemical Pathology

institute: The Chinese University of Hong Kong

summary: Comparative gene expression profiling analysis of RNA-seq data for satellite cells and its ATF3 cKO.

overall_design: RNA-seq in WT and ATF3 cKO sample with 3 replicates mix

first: Huating

first: Suyang

last: Zhang

first: Yile

last: Huang

first: Yingzhe

last: Ding


title: Effect of S4 treatment on glioma cells

city: Dalian

first: dapeng

last: Liang

state: Liaoning

address: lvshun south road no.9

institute: Dalian Medical University

summary: S4, a sulfonamide drug, has been confirmed to induce apoptosis and autophagy in cancer cells. Immunogenic cell death is a special cell death type which is closely related to apoptosis and autophagy. We performed RNA-seq to determine the impact of S4 on global gene expression profile in LN229 cells. Our results show that S4 induces immunogenic cell death via the response to endoplasmic reticulum stress.

overall_design: LN229 cells treated with DMSO and S4 were selected for RNA extraction and transcriptomic profiling by RNA-seq.

first: Jing

last: Cui

first: Songshu

last: Meng


title: H2B CUT&RUN in WT and ATF3 iKO satellite cells

summary: H2B binding profiling analysis of ChIP-seq data for WT and ATF3-iKO satellite cells

overall_design: H2B CUT&RUN in WT and ATF3-iKO samples with 2 replicates

last: Wang


title: Targeting meiotic recombination 11 (MRE11) nuclease for personalization of epithelial ovarian cancer therapy [2]

first: Nigel

last: Mongan

overall_design: RNAseq was used to compare the transcriptomes of parental PE01 and mirin-resistant derivative PEO1R cell lines

first: Adel

last: Alblihy

first: Reem

last: Ali

first: Alison

last: Ritchie

first: Cinzia

last: Allegrucci

first: Paloma

middle: O

last: Moran

first: Katia

last: Mesquita

first: Mashael

last: Algethami

first: Michael

middle: S

last: Toss

first: Muslim

last: Alabdullah

first: Ian

last: Hickson

first: Natalie

last: Tatum

first: Jennie

last: Jeyapalan

first: Anna

last: Grabowska

first: Emad

last: Rakha

first: Srinivasan

last: Madhusudan


title: Large-scale manipulation of promoter DNA methylation reveals context-specific transcriptional responses and stability

city: Perth

first: Ryan

last: Lister

address: 35 Stirling Highway

country: Australia

institute: The University of Western Australia

summary: Cytosine DNA methylation is widely described as a transcriptional repressive mark with the capacity to silence promoters. Epigenome engineering techniques enable direct testing of the effect of induced DNA methylation on endogenous promoters, however, the downstream effects have not yet been comprehensively assessed. Here, we simultaneously induced methylation at thousands of promoters in human cells using an engineered zinc finger-DNMT3A fusion protein, enabling us to test the effect of forced DNA methylation upon transcription, chromatin accessibility, histone modifications, and DNA methylation persistence after the removal of the fusion protein. We find that DNA methylation is often not sufficient to suppress transcription which appears to be driven by the eviction of methyl-sensitive transcriptional repressors. Furthermore, we find that some regulatory networks can override DNA methylation, and that promoter methylation can cause alternative promoter usage. DNA methylation deposited at promoter and distal regulatory regions is rapidly erased after removal of the zinc finger-DNMT3A fusion protein, in a process combining active and passive demethylation. Finally, we demonstrate that induced DNA methylation can exist simultaneously on promoter nucleosomes that possess the active histone modification H3K4me3, or DNA bound by the initiated form of RNA polymerase II. These findings have important implications for epigenome engineering, and demonstrate that the response of promoters to DNA methylation are more complex than previously appreciated.

overall_design: Profiling DNA methylation, chromatin accessibility, and transcription upon conditional ZincFinger-DNMT3A expression in MCF-7 cells, plus additional ChIP-seq of the ZincFinger-DNMT3A.

first: Alex

last: de Mendoza

first: Trung

last: Nguyen

first: Ethan

last: Ford

first: Daniel

last: Poppe

first: Sam

last: Buckberry

first: Jahnvi

last: Pflueger


title: ATF3 ChIP-seq in C2C12 cells

first: Feng

last: Yang

summary: ATF3 binding profiling analysis of ChIP-seq data for C2C12 cells.

overall_design: ATF3 ChIP-seq in C2C12 cells with 1 replicate

first: Huating

last: Wang

first: Suyang

last: Zhang

first: Yile

last: Huang

first: Yingzhe

last: Ding


title: Single GAM datasets collected with one nuclear profile each (samples failing QC)

first: Robert

last: Beagrie

overall_design: This series contains GAM samples with a single nuclear profile from mouse embryonic stem (mES) cells that failed our QC checks.

first: Alexander

last: Kukalev

first: Rieke

last: Kempfer

first: Ana

last: Pombo


title: RNA-seq in WT and ATF3 iKO  satellite cells with 3 replicates mix

summary: Comparative gene expression profiling analysis of RNA-seq data for satellite cells and its ATF3-iKO.

overall_design: RNA-seq in WT and ATF3 iKO sample with 3 replicates mix


title: Next Generation RNA Sequencing - Delineation of Hepatic Transcriptome Governed by Liver Clock and Gut Microbes over Time

city: Chicago

first: Katya

last: Frazier

state: IL

address: 900 E. 57th Street

institute: The University of Chicago

summary: We report the application of bulk RNA-sequencing-based technology for high-throughput profiling to examine the individual and combinatorial effects of the liver circadian clock and gut microbes on the liver transcriptome over 24-hours. Principle Component Analysis demonstrated that functionality of the liver circadian clock is the primary driver of the hepatic transcriptome profile, and presence of microbes is the secondary driver. We identified a range of significantly oscillating transcripts within each experimental group using empirical_JTK_CYCLE, and revealed an overall increase in oscillating transcripts with both the loss of cuntional liver clock and gut microbes. Network analysis via Spearman correlation revealed that a broken liver clock results in increased connections and correlated transcripts only in the presence of gut microbes. Finally, we show by differential expression and gene set enrichment analysis that several key metabolic pathways, particularly carbohydrate and lipid metabolism, were significantly downregulated when the liver clock is broken, regardless of microbial status. This study demonstrates the complex contributions of the liver circadian clock and gut microbes in transcriptome programming, both over time and overall.

overall_design: Bulk RNA-Seq of liver tissue in WT and liver-Bmal1-KO mice at 6 timepoints over 24 hours (ZT2, ZT6, ZT10, ZT14, ZT18, ZT22), 3 samples per timepoint

first: Sumeed

last: Manzoor


title: Molecular characterization of colorectal cancer-related peritoneal metastatic disease

status: Public on Jun 01 2022

first: Leandro

last: Moreno

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

overall_design: Refer to individual Series


title: Transcriptome profile of liver biopsy tissues from patients with non-alcoholic fatty liver disease (tissue validation set 2).

first: Yujin

last: Hoshida

summary: Non-alcoholic fatty liver disease (NAFLD) is a major global health problem with its high prevalence and risk of developing lethal complications, progressive liver fibrosis and hepatocellular carcinoma (HCC), the only rising cancer mortality in the U.S. For early HCC detection to improve the dismal prognosis, there is an urgent unmet need to identify a subset of NAFLD patients with elevated risk of HCC. Herein, we derived a hepatic-transcriptome-based NAFLD-specific HCC risk biomarker, PLS-NAFLD, and validated it in two independent cohorts of HCC-naive and experienced NAFLD patients..

overall_design: Total RNA for genome-wide transcriptome profiling by RNA-Seq was extracted from formalin-fixed paraffin embedded tissues of tumor-adjacent liver tissues obtained at the time of curative surgical resection for NAFLD-related HCC.

first: Naoto

last: Fujiwara

first: Shijia

last: Zhu


title: GATA2 tumor suppressive role is displayed in an ERG driven AML mouse, unveiling a preleukemic phenotype

city: Ramat Gan

first: Avigail

last: Rein

address: Derech Sheba 2

country: Israel

institute: Sheba Medical Center

summary:
The transcription factor (TF) GATA2, is crucial for the formation, and lifelong homeostasis of hematopoietic stem cells. Mono-Allelic germline disruptions of GATA2, result in haploinsufficiency syndromes. These disorders display variable manifestations, including immune deficiency, lymphedema, pulmonary proteinosis, and bone marrow failure. The later is presented by myelodysplastic changes (MDS), that subsequently evolve to leukemia (AML). MDS/AML are the most devastating, yet most consistent outcomes, designating GATA2 deficiency as one major predisposing condition to AML development.
To date, biomolecular trajectories of GATA2 deficiency, just vaguely delineated explanatory mechanisms. Experimental models recapitulating the disease evolution are meager, and functional studies are thus hampered. Here, we created murine models, reflecting the evolution of GATA2 deficiency, from gestational stage, to malignancy. We imposed the oncogenic driving force of TF ERG, upon Gata2 heterozygote and WT mice, to create a credible model. Both ERG/Gata2WT, and ERG/Gata2het mice developed leukemia, yet ERG/Gata2het, sustained an accelerated disease, resulting in diminished survival (p<0.0001). Subsequently, we obtained expression profiles of pre-leukemic blood precursors, using high throughput genomics, followed by functional assessments of self-renewal and cycling capacities. These studies elucidated a unique proliferative phenotype held by ERG/Gata2het progenitors. Additional expression analyses, metabolic assays, and electrons-microscopy inspections, suggested ERG/Gata2het progenitors uniquely relay on oxidative phosphorylation, and harbor alterations in mitochondrial structure and function. Excitingly, similar expression signature and morphological features were observed in human GATA2+/R396W cells, and in profiles of Inv(3)/GATA2MUT AML’s. We here provide new insights into GATA2 deficiency evolutionary course, underscoring the need to deconvolute pre-malignant stages in translational studies.

overall_design: Expression profiles of lineage negative bone marrow of 6-8 week old  mice and lineage negative fetal liver of 14.5E mice in 4 different genotypes -  wild type (WT) , Gata2+/-, ERG, and ERG/Gata2+/- (compouned transgenic).

first: Shai

last: Izraeli


title: Molecular characterization of colorectal cancer-related peritoneal metastatic disease [RNA-seq]

summary: We present a comprehensive molecular characterization of a cohort of 52 patients with peritoneal metastasis

overall_design: Comparasion of primary colorectal cancers versus peritoneal metastasis

first: Kristiaan

last: Lenos

first: Louis

last: Vermeulen


title: Integrated multi-omics reveals the cellular and molecular interactions governing the invasive niche in skin cancer

city: Lausanne

first: Tania

last: Wyss

address: Rue du Bugnon 25A

institute: SIB Swiss Institute of Bioinformatics

summary: To progress, tumors need to invade the surrounding tissues. However, the heterogeneity of cell types at the tumor-stroma interface and the complexity of their potential interactions hampered mechanistic insights for efficient therapeutic targeting. Here, combining single-cell and spatial transcriptomics on human basal cell carcinomas (BCCs), we define the cellular contributors of the invasive front. In the invasive niche, tumor cells harbor a collective migration phenotype, supported by the expression of cell-cell junction complexes. In physical proximity, we identify cancer-associated fibroblasts (CAFs) with extracellular matrix-remodeling features, as required to support collective migration. Moreover, while tumor cells specifically express Activin A, we find Activin A-induced gene signature enrichment in adjacent CAFs subpopulations, further supporting their biological crosstalk. Altogether, our data identify the subpopulations and their transcriptional reprogramming contributing to the spatial organization of the BCC invasive niche. They also bring the proof-of-concept for integrated spatial and single-cell multi-omics to decipher cancer-specific invasive properties and develop therapeutic targeting.

overall_design: Fresh basal cell carcinoma tumors of two patients were minced and enzymatically dissociated to single cell suspension. All single living cells were FACS-sorted and processed with the Chromium Next GEM single cell 3' reagent v3.1 kit (10x Genomics) to perform single cell RNA sequencing. Sequencing was performed on an Illumina HiSeq 4000 device. The sequence reads that passed quality filters were analyzed with Seurat R package (v.4.0.1).

first: Laura

last: Yerly

first: François

last: Kuonen


title: Vitamin B2 enables PPARa regulation of fasting glucose availability

status: Public on Jun 18 2022

city: Houston

first: Peter

last: Masschelin

address: 1 Baylor Plaza

institute: Baylor College of Medicine

summary: Flavin adenine dinucleotide (FAD) mediates oxidation-reduction reactions required for cellular energy demands. Fatty acid oxidation (FAO) disorders caused by flavoprotein mutations and FAD depletion disrupt energy balance and glucose production during fasting. These FAO disorders are difficult to manage clinically, and their biochemical pathogenesis is poorly understood. Here, we identify a mechanistic connection between FAD levels and hepatic glucose production. Depleting the FAD pool in mice with a vitamin B2 deficient diet (B2D) resulted in phenotypes associated with organic acidemia phenotypes, including reduced body weight and whole-body fat oxidation rates coupled with hypoglycemia. Integrated discovery approaches revealed that B2D broadly tempered fasting activation of target genes for the nuclear receptor PPARa, including those required for gluconeogenesis. Consistent with this, Ppara knockout depleted liver FAD levels and worsened B2D hepatic glucose production. Treatment with the PPARa agonist fenofibrate overcame B2D phenotypes and rescued glucose availability and fatty liver signatures through activation of the integrated stress response and refilling anaplerotic amino acid substrates for glucose production. We conclude that PPARa governs metabolic responses to FAD availability and suggest pharmacologic activation as a strategy for treating disorders of riboflavin and FAD deficiency.

overall_design: Comparative gene expression profiling and analysis of fasted WT mice exposed to riboflavin-deficiency with/without fenofibrate

middle: M

first: Pradip

middle: K

last: Saha

first: Scott

last: Ochsner

first: Aaron

last: Cox

first: Kang

last: Kim

first: Jessica

middle: B

last: Felix

first: Robert

last: Sharp

first: Xin

last: Li

first: Lin

last: Tan

first: Jun

last: Park

first: Liping

last: Wang

first: Vasanta

last: Putluri

first: Philip

last: Lorenzi

first: Zheng

last: Sun

first: Benny

last: Kaipparettu

first: Nagireddy

first: David

last: Moore

last: Summers

first: Neil

last: McKenna

first: Sean

last: Hartig


title: HDAC6 deacetylates IDH1 to regulate the homeostasis of hematopoietic stem/progenitor cells

status: Public on May 21 2022

city: Tianjin

first: hanxiao

last: Yin

address: Weijin road 94

institute: nankai university

summary: In order to further explore the mechanism by which increased 5hmC inhibits expansion of LSK cells from Hdac6-/- murine primary BM cells, we performed RNA sequencing (RNA-seq) analysis using LSK cells isolated from Hdac6-/- and WT mice.

overall_design: Comparative gene expression profiling analysis of RNA-seq data in bone marrow hematopoietic stem/progenitor cells (LSK) of wild-type and HDAC6-deficient mice

first: Yang

last: Liu

first: Jia

last: Yang

first: Hanxiao


title: Multiplex GAM datasets collected with an average of three nuclear profiles each

first: Robert

last: Beagrie

overall_design: This series contains multiplex-GAM samples each containing an average of three nuclear profiles from mouse embryonic stem (mES) cells.

first: Alexander

last: Kukalev

first: Rieke

last: Kempfer

first: Ana

last: Pombo


title: Treatment of IMM cells with Oscillibater valericigenes

status: Public on May 27 2022

city: Corvallis

first: Andrey

last: Morgun

state: OR

address: Pharmacy Building, 1601 SW Jefferson Way

department: Pharmaceutical Sciences

institute: Oregon State University

summary: Microbiota contributes to induction of type 2 diabetes by high-fat/high-sugar (HFHS), but which organs/pathways are impacted by microbiota remains unknown. Using multi-organ network and transkingdom analyses, we found that microbiota-dependent. impairment of OXPHOS /mitochondria in white adipose tissue (WAT) plays a primary role in regulating systemic glucose metabolism. The follow-up analysis established that Mmp12+ macrophages link microbiota-dependent inflammation and OXPHOS damage in WAT. Moreover, the molecular signature of Mmp12+ macrophages in WAT was associated with insulin resistance in obese patients. Next, we tested functional effects of MMP12 and found that Mmp12 genetic deficiency or MMP12 inhibition improved glucose metabolism in conventional, but not in germfree mice. MMP12 treatment induced insulin resistance in adipocytes. TLR2-ligands present in Oscillibacter valericigenes bacteria, which are expanded by HFHS, induce Mmp12 in WAT macrophages in a MYD88-ATF3-dependent manner. Thus, HFHS induces Mmp12+ macrophages and MMP12, representing a microbiota-dependent bridge between inflammation and mitochondrial damage in WAT and causing insulin resistance. doi: https://doi.org/10.1084/jem.20220017

overall_design: in vitro stimulation of macrophages (WT or Myd88 KO) with or without Oscillibacter valericigenes supernatant. 4 biological replicates of each group.

first: Natalia

last: Shulzhenko


title: mRNA expression profile in LGP2 and LGP2-4KR transgenic (Tg) HEK293 cells stimulated with short poly I:C

status: Public on Jun 07 2022

first: Satoshi

last: Kondo

summary: mRNA expression profiles were compared between wild-type LGP2 and four amino acid replacement LGP2 (LGP2-4KR) cells in the presence or absence of a RIG-I ligand, short poly I:C.

overall_design: LGP2 and LGP2-4KR Tg HEK293 cells were cultured in a 24-well-plate, and were then stimulated with or without 100 ng/ml of short poly I:C for 12 hours. Total RNA was extracted from stimulated and unstimulated HEK293 cells, and was subjected to the microarray analysis.

first: Takahisa

last: Kouwaki

first: Hiroyuki

last: Oshiumi


title: Treatment of RAW 264.7 cells with Oscillibater valericigenes

status: Public on May 24 2022

overall_design: in vitro stimulation of macrophages with or without Oscillibacter valericigenes supernatant and/or Myd88 siRNA. 4 biological replicates of each group


title: Identifying FOXA1-GR transcriptional targets in FOXA1-GR dependent NSCLC

status: Public on May 16 2022

city: New York

first: Madeline

middle: Anne

last: Dorso

state: New York

address: 408 East 69th Street

department: Human Oncology and Pathogenesis

institute: Memorial Sloan Kettering Cancer Center

summary: The FOXA1 pioneer factor is an essential mediator of steroid receptor function in multiple hormone dependent cancers, including breast and prostate cancers, enabling nuclear receptors such as ER and AR to activate lineage specific growth programs. . Analyzing data from loss-of-function screens, we identified a subset of NSCLC tumor lines where proliferation is FOXA1-dependent. Using rapid immunoprecipitation and mass spectrometry of endogenous protein (RIME) we identified chromatin-localized interaction between FOXA1 and glucocorticoid receptor (GR) in these tumor cells. Knockdown of GR inhibited proliferation of FOXA1-dependent, but not FOXA1-independent NSCLC cells. Here, we utilized ChIP-sequencing to identify a permissive set of genes potentially regulated by FOXA1 and GR to understand potential mechanisms underlying FOXA1-GR dependence in NSCLC.

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) to map overlapping binding regions of Glucocorticoid receptor (GR) and FOXA1, as well as the histone modification H3K27ac, with and without GR ligand stimulation in NCI-H441 cells.

first: Aleksandr

last: Pankov

first: Jacob

last: Boyer


title: Transcriptional Profile Of Human Pancreatic Acinar Ductal Metaplasia

city: Los Angeles

first: Hesamedin

last: Hakimjavadi

state: California

address: 4650 Sunset Blvd

department: Pathology and Laboratory Medicine

institute: Childrens Hospital Los Angeles

summary: Aberrant acinar to ductal metaplasia (ADM), one of the earliest events involved in exocrine pancreatic cancer development, is typically studied using pancreata from transgenic mouse models. We used primary, human pancreatic acinar cells to evaluate the transcriptional profile during the course of ADM.

overall_design: Following 6 days of three-dimensional (3-D) culture on Matrigel, acinar cells underwent morphological and molecular changes indicative of ADM. mRNA from 14 donors’ paired cells (day 0 and 6 of culture) was subjected to whole transcriptome sequencing.

first: Jinmai

last: Jiang

first: Julie

last: Bray

first: Alyssa

last: Gosling

first: Lais

last: daSilva

first: Gamze

last: Bulut

first: Corey

last: Perkins

first: Jamel

last: Ali

first: V

middle: W

last: Setiawan

first: Martha

last: Campbell-Thompson

first: Srikar

last: Chamala

first: Thomas

last: Schmittgen


title: Single and Multiplex GAM datasets from mouse ES cells

first: Robert

last: Beagrie

overall_design:
Refer to individual Series

Processed data files included at the foot of this record:
gam_contact_matrices_40kb.tar.gz - "GAM normalised linkage (Dprime) matrices at 40kb resolution."
slice_interaction_matrices_40kb.tar.gz - "SLICE prominent interaction matrices (thresholded at p<=0.05) at 40kb resolution."


title: Nano-TRAP Input and IP sequencing of WT and Rpl3l-/- mouse hearts

city: Barcelona

first: Eva Maria

last: Novoa

address: Dr. Aiguader 88

country: Spain

institute: Center for Genomic Regulation

summary: RPL3L is a ribosomal protein expressed exclusively in adult straited muscle tissues, and a paralogue of the ubiquitously expressed RPL3. Here, we are looking into the effects of Rpl3l knockout on translation in adult mice hearts.

overall_design: Nano-TRAP (Input and IP) done on WT and Rpl3l-/- mouse hearts in biological triplicates.

first: Eva

first: Ivan

last: Milenkovic


title: Ribo-Seq and RNA-seq sequencing of WT and Rpl3l-/- mouse hearts

overall_design: Ribo-SEQ and RNA-seq done on WT and Rpl3l-/- mouse hearts in biological triplicates.


title: Increased intra-tumoral glucose level is associated with enhanced chemotherapeutic response in pancreatic cancer

city: Cleveland

first: Ata

last: Abbas

state: OH

address: 10900 Euclid Ave

department: Division of Hematology & Oncology

institute: Case Western Reserve University

summary: Pancreatic tumors are refractory to current chemotherapies, and there are no effective alternative therapies available for patients with pancreatic cancer (PC). We present an innovative approach to improve chemotherapy efficacy in preclinical models of pancreatic cancer. The effectiveness of various chemotherapies, including standard of care FOLFIRINOX, was remarkably enhanced by inducing a state of hyperglycemia. This was achieved by either providing animals with a high glucose diet or by a pharmacologic method involving streptozotocin coupled with long-acting insulin. Comprehensive integrative analyses revealed a key metabolic pathway, glutathione biosynthesis, mitigated by the high glucose diet. Combining chemotherapies with either the high glucose diet or an inhibitor of glutathione biosynthesis as a feasible approach caused a significant survival benefit in mice bearing orthotopic pancreatic tumors.

overall_design: Orthotopic tumors under hyperglycemic (D30) compared to normoglycemic condition. Five independent biological replicates were used.

first: Ali

last: Vaziri-Gohar

first: Jordan

last: Winter


title: Spatial transcriptomics stratifies psoriatic disease by emergent cellular ecosystems

status: Public on May 12 2022

first: Shruti

last: Naik

state: NY

address: 435 East 30th Street

department: Pathology

institute: NYU Langone Health

summary: The skin is recognized as a window into the immunopathogenic mechanisms driving the vast phenotypic spectrum of psoriatic disease. To better decipher the cellular landscape of both healthy and psoriatic skin, we employed spatial transcriptomics (ST), a ground-breaking technology that precisely maps gene expression from histologically-intact tissue sections.  Findings gleaned from computationally integrating our 23 matched lesional and non-lesional psoriatic and 7 healthy control samples with publicly-available single cell RNA seq data sets provided insights into the emergent cellular ecosystems at play in psoriatic disease.

overall_design: This is a cross-sectional study involving the accrual of 3-4-mm skin punch biopsy samples from healthy controls and biologic naïve patients with psoriatic disease. The samples were then subjected to the protocols entailed by spatial transcriptomics platform.

first: Rochelle

last: Castillo

first: Ikjot

last: Sidhu


title: Phenotype screens of genetically engineered mouse models of pancreatic cancer identify a Tgfa-Ccl2-paxillin axis driving human-like perineural invasion

status: Public on May 05 2022

city: Munich

first: Rouzanna

last: Istvánffy

address: Ismaningerstr. 22

department: Department of Surgery

country: Germany

institute: Klinikum rechts der Isar

summary:
Solid cancers such as pancreatic cancer (PDAC) often exploit nerves for rapid spread. This neural invasion (NI) is an independent prognostic factor in PDAC and the main trigger for local recurrence and severe pain. However, genetically engineered mouse models (GEMM) of PDAC do not adequately represent the morphology of human NI.
Therefore, we performed a systematic morphological screening of mutant mice with combinations of mutant alleles of oncogenes and tumour suppressors from our mouse repository.
In a newly generated TPAC and TPC mouse mutant with pancreas-specific overexpression of transforming growth factor alpha (TGFa) and conditional deletion of p53, we identified human-like NI. To dissect the molecular mechanisms behind, we compared the transcriptome of TPAC and TPC mouse mutants with known KPC and KC mice lacking NI pathology.
Our results revealed strong enrichment of genes encoding the extracellular matrix, including ECM glycoproteins, collagens and proteoglycans involved in biological oxidation, nuclear receptors, and proteins encoding drug metabolism via cytochrome P450 and retinoic acid signaling in TPAC cancer cells.

overall_design: We analysed global RNA expression in pancreatic tumours from mouse PDAC cell lines with high neuroinvasive potential and compared them to non-invasive tumour cells.

first: Ekin

middle: I

last: Demir

last: Istvanffy


title: Apolipoprotein A1-Manipulated Cholesterol Efflux Subverts the Phagocytic Fragility of TAMs and Improves Oncolytic Viro-Immunotherapy in Glioblastoma

status: Public on May 04 2022

city: Nanjing

first: Shiqun

last: Wang

state: Jiangsu

address: 22 Hankou Road

institute: Nanjing university

overall_design: Refer to individual Series


title: iBAT histone modification ChIP seq of wild type C57BL/6N mice exposed to cold and high fat diet.

city: Odense

first: Jan

middle: Wilhelm

last: Kornfeld

address: Campusbej 50

department: Biochemistry and Molecular Biology

country: Denmark

institute: University of Southern Denmark

summary: Cold and nutrient activated brown adipose tissue (BAT) is capable of increasing systemic energy expenditure via uncoupled respiration and secretion of endocrine factors thereby protecting mice against diet-induced obesity and improving insulin response and glucose tolerance in men. Long non-coding RNAs (lncRNAs) have recently been identified as fine tuning regulators of cellular function. While certain lncRNAs have been functionally characterised in adipose tissue, their overall contribution in the activation of BAT remains elusive. We identified lncRNAs correlating to inter- scapular brown adipose tissue (iBAT) function in high fat diet (HFD) and cold stressed mice. We focused on Gm15551 which has an adipose tissue specific expression profile, is highly upregulated during adipogenesis and downregulated by β-adrenergic activation in mature adipocytes. Albeit we performed comprehensive transcriptional and adipocyte physiology profiling in vitro and in vivo, we could not detect an effect of gain or loss of function of Gm15551.

overall_design: Genome wide examination of 4 different histone marks of inguinal brown adipose tissue of 20-week old  C57BL/6N mice on high fat diet for 12 weeks and cold treated for 24 h at 4°C in duplicate.

first: Christoph

last: Engelhard

first: Chien

last: Huang

first: Sajjad

last: Khani

first: Petr

last: Kasparek

last: Procházka

last: Rozman

first: David

last: Reguera

first: Radislav

last: Sedláček

first: Jan-Wilhelm


title: ACVR1-mutant posterior fossa ependymoma

status: Public on May 01 2022

city: Bethesda

first: Drew

last: Pratt

state: Maryland

address: 10 Center Drive, Building 10, Room 2S235

department: Laboratory of Pathology

institute: National Institutes of Health

type: Methylation profiling by genome tiling array

summary: Genomewide DNA methylation array profiling of nine posterior fossa ependymomas harboring activating mutations in ACVR1. Two samples clustered with the PFA subtype and demonstrated H3K27me3 loss by immunohistochemistry, while the remaining 7 showed retained H3K27me3 and formed a methylation cluster distinct from other ependymal tumors. For these previsouly unpublished cases, the Illumina Infinium EPIC 850k Human DNA Methylation Beadchip was used to obtain DNA methylation profiles across approximately 850,000 CpG sites of genomic DNA extracted from formalin-fixed, paraffin-embedded tumor tissue.

overall_design: Bisulfite converted genomic DNA extracted from 7 tumor samples was hybridized to Illumina Infinium EPIC Human DNA Methylation Beadchips

first: D


title: Spatial transcriptome profiling of pancreatic cancer identifies multicellular dynamics associated with neoadjuvant treatment

city: Cambridge

first: Karthik

last: Jagadeesh

state: MA

address: 415 Main St

department: Human Cell Atlas

institute: Broad Institute

summary: Pancreatic ductal adenocarcinoma (PDAC) is a highly lethal and treatment-refractory cancer. Molecular stratification in pancreatic cancer remains rudimentary and does not yet inform clinical management or therapeutic development. Here we construct a high-resolution molecular landscape of the multicellular subtypes and spatial communities that compose PAC using single-nucleus RNA-seq and whole-transcriptome digital spatial profiling (SP) of 43 primary PDAC tumor specimens that either received neoadjuvant therapy or were treatment-naïve. We uncovered expression programs across malignant cells and fibroblasts, including a newly-identified neural-like progenitor malignant cell program that was enriched after chemotherapy and radiotherapy and associated with poor prognosis in independent cohorts. Integrating spatial and cellular profiles revealed three multicellular communities: classical, squamoid-basaloid, and treatment-enriched. Our refined molecular and cellular taxonomy can advance precision oncology in PAC through stratification in clinical trials and as roadmap for therapeutic targeting of specific cellular phenotypes and multicellular interactions.

overall_design: 14 specimens received no treatment prior to resection; 7 specimens received neoadjuvant chemotherapy, radiotherapy, losartan, and/or nivolumab prior to resection

first: William

middle: L

last: Hwang

first: Jimmy

last: Guo

first: Hannah

last: Hoffman

first: Jennifer

last: Su

first: Carina

last: Shiau

first: Tyler

last: Jacks

first: Aviv

last: Regev


title: Histone H1 facilitates restoration of H3K27me3 during DNA replication by chromatin compaction

city: Beijing

first: Yu

last: Juan

address: 15 Datun Road, Chaoyang District

institute: Chinese Academy of Sciences

summary: Here we adopt ChOR-seq (Chromatin Occupancy after Replication) to monitor the dynamic re-establishment of H3K27me3 on nascent DNA during DNA replication. We found that the linker histone H1 facilitates the rapid post-replication restoration of H3K27me3 on repressive genes, which is essential for maintaining gene silencing and cell identity during cell division. Interestingly, the restoration rate of H3K27me3 on nascent DNA is greatly compromised after depletion of H1c/d/e. Finally, our in vitro biochemical experiments demonstrate that H1 facilitates the propagation of H3K27me3 by PRC2 through compacting chromatin. Collectively, our results indicate that H1-mediated chromatin compaction facilitates the propagation and restoration of H3K27me3 after DNA replication, which is key to cell fate determination.

overall_design: ChOR-seq, ChIP-seq and RNA-seq for WT and H1TKO cells

first: Guohong

last: Li


title: Apolipoprotein A1-Manipulated Cholesterol Efflux Subverts the Phagocytic Fragility of TAMs and Improves Oncolytic Viro-Immunotherapy in Glioblastoma [Tumor RNA-seq]

first: Shiqun

last: Wang

summary: We found that overexpression of APOA1 in glioblastoma (GBM) promotes cholesterol efflux from TAMs and restores phagocytosis and antigen presentation. Therefore, we constructed a recombinant oncolytic adenovirus expressing APOA1 to carry the cholesterol regulatory elements of TAMs. AdV-APOA1 exhibited better antitumor effects than AdV-Ctrl in several orthotopic GBM tumor models. Further, we collected virus-treated GL261-CAR tumors for RNA-seq to reveal differences in biological processes between them. Specifically, intracranial 14-day GL261-CAR-bearing C57BL/6J mice were i.t. injected with 1 × 108 PFU AdV-Ctrl or 1 × 108 PFU AdV-APOA1. The tumor bulks were then collected to perform transcriptome RNA-seq analysis 3 days after virus injection.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for tumors from AdV-APOA1 (n=3) or AdV-Ctrl (n=3) treated intracranial GL261-CAR-bearing C57 mice.

first: Wang

last: Shiqun

first: Zuo

last: Shuguang

first: Wu

last: Jingyi

first: Kong

last: Lingkai


title: Rad21 is the core subunit of cohesin complex in directing genome organization

first: Wenxue

last: Zhao

address: Yiheyuan Road

institute: Peking University

summary: In eukaryotes, the nuclear chromatin in the interphase is a hierarchical organization. Previous studies have suggested that cohesin-DNA interactions play important architectural functions for chromatin structure in the interphase. In this study, we applied super-resolution imaging, single-molecule imaging to measure the distribution of cohesin subunits. Hi-C and RNA-seq were used to reveal the 3D genome structures alterations and the relationship with breast cancer upon Rad21 up-regulation. Hi-C experiment showed that the contact frequency of short distance was increased while that of long distance was decreased in the absence of Rad21 up-regulation. Chromatin interactions between A and B compartments increased and compartmentalization strength was reduced significantly upon Rad21 up-regulation. Correspondingly, accumulated contacts were shown at TAD corners and inter-TAD interactions increased. These observations support cohesin loop extrusion model and lead us to propose the unique role of Rad21-loader interaction in cohesin loading and further cohesin extrusion. Moreover, we combined transcriptome changes and chromatin structure alterations upon Rad21 up-regulation and revealed the correlation between Rad21 and breast cancer by affecting chromatin architecture.

overall_design: Analysis of 3D genome architecture and gene expression data in control and Rad21 overexpression HeLa cell lines.

first: Yuao

last: Sun

last: Zhang

first: Xin

last: Xu


title: Pyramidal neuron subtype diversity governs microglia states in the neocortex [MERFISH]

status: Public on Apr 26 2022

first: Paola

last: Arlotta

address: 7 Divinity Ave

department: Stem Cell and Regenerative Biology

institute: Harvard University

summary: Microglia are the resident immune cells of the brain, and have critical roles in circuit development and plasticity. During embryonic and postnatal development, microglia exist in multiple transcriptional states. However, it is still poorly understood how these states are established, and whether they are influenced by their cellular environment. Here we show that in the juvenile neocortex, microglia exist in multiple states whose identity and laminar distribution is instructed by the neuronal class identity of local pyramidal neurons. Using single-cell RNA sequencing, we unveil molecular signatures of distinct microglia sub-states, and show that they can be divided into layer-restricted or broadly-distributed states. Strikingly, conversion of deep-layer pyramidal neurons to an alternate class identity reconfigures both the density and molecular state of local layer-restricted microglia to correspond to the new neuronal niche, thus identifying specific populations of microglia that are sensitive to pyramidal neuron subtypes. Ligand-receptor interactomes for individual neuronal subtype-microglia pairings uncovers two categories of neuron-to-microglia communication: one associated with neuronal class identity and one associated with microglial state. Our findings highlight the fundamental role that neuronal identity and neuronal niches play in locally controlling the transcriptional status of postnatal microglia.

overall_design: Examination of Mg states from different neuronal niches of the cerebral cortex.

first: Jeffrey

last: Stogsdill

first: Kwanho

last: Kim

first: Loic

last: Binan

first: Samouil

last: Farhi

first: Joshua

middle: Z

last: Levin


title: Stochastic models of nucleosome dynamics reveal regulatory rules of stimulus-induced epigenome remodeling

status: Public on Apr 24 2022

first: Katherine

last: Sheu

state: CA

address: 611 Charles E Young Dr E

institute: UCLA

summary: The genomic positions of nucleosomes are a defining feature of the epigenomic state and hence of cell identity.  Signal-dependent transcription factors (SDTFs), upon activation, modify the positioning of nucleosomes and cause epigenome remodeling. Here, we developed Markov models of nucleosome wrapping and unwrapping, and fit them to high resolution deep sequencing data of DNA accessibility to reveal biophysical principles of nucleosome dynamics.  We found that 1) the dynamics of DNA unwrapping are significantly slower in vivo than reported from in vitro experimental data, 2) there is clear evidence for cooperativity in wrapping and unwrapping, 3) SDTF activity produced highest eviction probability when its binding site is close to but not on top of the nucleosome dyad, and 4) oscillatory SDTFs produce more variability than constant SDTF activities.  Our work uncovers the regulatory rules governing nucleosome dynamics in vivo, which can predict epigenomic alterations during inflammation at single nucleosome resolution.

overall_design: Paired-end ATAC-sequencing of mutant macrophage cells at 0hrs and treated with TNF and LPS at 4hrs.

first: Alexander

last: Hoffmann

first: Jinsu

first: German

last: Enciso


title: Bap1 shapes the bone marrow niche for lymphopoiesis by fine-tuning epigenetic profiles in endosteal mesenchymal stromal cells [RNA-Seq]

status: Public on Apr 25 2022

city: Seoul

first: Do Young

last: Hyeon

state: Select State

address: 1 Gwanak-ro, Gwanak-gu

department: School of Biological Sciences

country: South Korea

institute: Seoul National University

summary: Hematopoiesis occurs within a unique bone marrow (BM) microenvironment which consists of various niche cells, cytokines, growth factors and extracellular matrix components. These multiple components directly or indirectly regulate the maintenance and differentiation of hematopoietic stem cells (HSCs). Here we report that Bap1 in BM mesenchymal stromal cells (MSCs) is critical for the maintenance of HSCs and B lymphopoiesis. Mice lacking Bap1 in MSCs show aberrant differentiation of hematopoietic stem and progenitor cells, impaired B lymphoid differentiation, and expansion of myeloid lineages. Mechanistically, Bap1 loss in distinct endosteal MSCs, expressing Prx1 but not Lepr, leads to aberrant expression of genes affiliated with BM niche functions. Bap1 deficiency leads to a reduced expression of pro-hematopoietic factors such as Scf, caused by increased H2AK119-ub1 and H3K27-me3 levels on the promoter region of these genes. On the other hand, the expression of myelopoiesis stimulating factors including Csf3 was increased by enriched H3K4-me3 and H3K27-ac levels on their promoter, causing myeloid skewing. Notably, loss of Bap1 substantially blocks B lymphopoiesis and skews the differentiation of hematopoietic precursors toward myeloid lineages in vitro, which is reversed by G-CSF neutralization. Thus, our study uncovers a key role for Bap1 expressed in endosteal MSCs in controlling normal hematopoiesis in mice by modulating expression of various niche factors governing lymphopoiesis and myelopoiesis via histone modifications.

overall_design: RNA sequencing of endosteal mesenchymal stromal cells (MSCs) isolated from control mice (Bap1 WT) and Bap1 cKO mice.

first: Rho

middle: H

last: Seong

first: Daehee

last: Hwang


title: Integrated single-cell transcriptomics and functional genomics reveal RAD51B as an essential gene in near-haploid leukemia

status: Public on Apr 21 2022

first: Michael

last: Hemann

address: 500 Main St

department: Koch Institute

institute: Massachusetts Institute of Technology

summary: Whole chromosome losses resulting in near-haploid karyotypes are found in a rare subgroup of treatment-refractory acute lymphoblastic leukemia. To systematically dissect the unique physiology and uncover susceptibilities that can be exploited in near-haploid leukemia, we leveraged single-cell transcriptomics and computational inference of cell cycle stages to pinpoint key differences between near-haploid and diploid leukemia cells. Combining cell cycle stage-specific differential expression with gene essentiality metrics obtained from a genome-wide CRISPR-Cas9-mediated knockout screen, we identified the homologous recombination pathway component RAD51B as an essential gene in near-haploid leukemia. DNA damage analyses revealed significantly increased sensitivity of RAD51-mediated repair to RAD51B loss in the G2/M stage of near-haploid cells, suggesting a unique role of RAD51B in the homologous recombination pathway. We observed elevated G2/M checkpoint signaling as well as a RAD51B signature expression program in response to chemotherapy in a xenograft model of human near-haploid B-ALL, as well as overexpression of RAD51B and its associated programs in a large panel of near-haploid B-ALL patients. These data highlight a unique genetic dependency on DNA repair machinery in near-haploid leukemia and demarcate RAD51B as a promising candidate for targeted therapy  in this treatment-resistant disease.

overall_design:
KBM7 cell lines (haploid, diploidized), PDX model of near-haploid B-ALL, bone marrow and spleen cells from one mouse each in 6 groups: untreated diploidized B-ALL (WT dip), untreated near-haploid B-ALL (WT hap), vehicle treated diploidized B-ALL (WTVeh dip), vehicle treated near-haploid B-ALL (WTVeh hap), combination chemotherapy treated diploidized B-ALL (WTTX dip), combination chemotherapy treated near-haploid B-ALL (WTTX hap)

Please note that the raw data was withrawn on Nov 21, 2022 as it is protected human data that is not consented for public display in an unrestricted database.

first: Yunpeng

last: Liu

first: James

middle: D

last: Ham

first: Swarna

last: Jeewaji

first: Lan

last: Nguyen

first: Toni

last: Delorey

first: Azucena

last: Ramos

first: David

last: Weinstock

first: Aviv

last: Regev

middle: T


title: Single-cell RNA-Seq of kidneys of Brg1-deficiency and wild type mice

status: Public on Apr 08 2022

first: XIANXIAO

last: ZHOU

address: 1470 Madison AVE

department: Department of Genetics and Genomic Sciences

institute: Ichan School of Medicine at Mount Sinai

summary: We deleted the chromatin regulator Brg1 in Wnt4-expressing cells and FACS-purified Wnt4-lineage cells of wild-type and Brg1-deficient mouse kidneys. We then carried out single-cell RNA sequencing (scRNA-seq) to investigate the cell subpopulations and the effects of Brg1-deficiency in the differentiation of Wnt4-lineage cells. scRNA-seq analyses identify 35 clusters of Wnt4-descendant cells and uncover novel cell types and genes that have so far not been linked to Wnt4-lineage cells. Brg1-deficiency leads to increased endothelial, stromal, and smooth-muscle cells and decreased nephron tubular cells. In Brg1-deficient kidneys, the expression of Pttg1 and proliferation are increased in Wnt4-expressing precursors, which cannot transition to a characteristic tubular state and appear to undergo fibrosis.

overall_design: One Brg1-deficiency and one wild type samples

first: Xianxiao

last: Zhou

first: Pin-Xian

last: Xu


title: Large intestine lamina propria CD45 positive cells

status: Public on Apr 15 2022

city: Baltimore

first: Immunometabolism

last: Department

address: 1650 Orleans Street

department: Immunometabolism

institute: Johns Hopkins University

summary: Obesity was induced by ad libitum feeding of C57/BL6 mice for 12 week with irradiated high fat diet (Rodent Diet 60% kcal from fat, Research Diets, Inc., Cat #D12492). Control diet (chow) containing 24% protein, 47.5% carbohydrate, and 4.9% fat, was given to age and sex matched animals as a control group.

overall_design: One mouse from each condition was taken, cells isolated and sequenced using 10X Chromium Controller.

first: Angela

last: Catoldi

middle: E

last: Sanin

first: Edward

middle: J

last: Pearce


title: Bap1 shapes the bone marrow niche for lymphopoiesis by fine-tuning epigenetic profiles in endosteal mesenchymal stromal cells

first: Do Young

last: Hyeon

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


title: Genome-wide methylation analysis of an Acute Myeloid Leukemia (AML) case with complex mutational DNMT3A profile.

status: Public on May 10 2022

city: Bari

first: Francesco

last: Albano

state: Bari

address: P.zza G. Cesare, 11

department: Department of Emergency and Organ Transplantation (D.E.T.O.) - Hematology and Stem Cell Transplantation Unit

country: Italy

institute: University of Bari "Aldo Moro", School of Medicine Policlinico Hospital

summary: Genome-wide DNA methylation profiling of diagnosis, complete remission and disease relapse samples of an AML case with complex and unusual DNMT3A mutational profile. The Illumina Infinium MethylationEPIC BeadChip was used to obtain DNA methylation profiles across approximately 850,000 CpGs from bone marrow samples at the three different conditions of disease.

overall_design: Bisulphite converted DNA from the diagnosis, complete remission and disease relapse samples were hybridised to the Illumina Infinium MethylationEPIC BeadChip arrays.

first: Cosimo

last: Cumbo


title: Apolipoprotein A1-Manipulated Cholesterol Efflux Subverts the Phagocytic Fragility of TAMs and Improves Oncolytic Viro-Immunotherapy in Glioblastoma [TAMs RNA-seq]

first: Shiqun

last: Wang

summary: We found that TAMs in the glioblatoma (GBM) tumor microenvironment are enriched for cholesterol and highly express ABCA1/G1. To investigate the biological effects of enhancing cholesterol efflux of TAMs in GBM, we constructed APOA1-overexpressing GL261 cell line. We harvested tumor tissue and sorted these TAMs by anti-mouse F4/80 magnetic beads 17 days after intracranial transplantation of GL261-APOA1 cell line and control cells in immunocompetent C57 mice. Samples were subjected to transcriptome sequencing.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for TAMs sorted from GL261-APOA1 (n=4) or GL261-Puro (n=4) tumors

first: Wang

last: Shiqun

first: Zuo

last: Shuguang

first: Wu

last: Jingyi

first: Kong

last: Lingkai


title: Comprehensive transcriptional profiling and mouse phenotyping reveals dispensable role for adipose tissue selective long noncoding RNA Gm15551.

first: Jan

last: Kornfeld


title: Spatial organization of H3K9me2/3-marked heterochromatin is redundantly maintained by either the H3K9 or H3K27 methylation pathway [RNA-Seq]

status: Public on Apr 05 2022

city: Saitama

first: Kei

last: Fukuda

state: Japan

address: 2-1 Hrosawa, Wakoshi

institute: RIKEN

summary: Heterochromatin is a key architectural feature of eukaryotic chromosomes, which is critical for cell type specific gene expression and genome stability. In the mammalian nucleus, heterochromatin is segregated from transcriptionally active genomic regions, and exists as large condensed and inactive nuclear compartment. However, the underlying mechanism of spatial organization of heterochromatin is still poorly understood. Histone H3 lysine 9 di- and tri-methylation (H3K9me2/3) and lysine 27 trimethylation (H3K27me3) are two major epigenetic modifications that define constitutive and facultative heterochromatin, respectively. In mammals, there are at least five H3K9 methyltransferases (SUV39H1, SUV39H2, SETDB1, G9a and GLP) and two H3K27 methyltransferases (EZH1 and EZH2). In this study, we addressed the role of H3K9 and H3K27 methylation in heterochromatin organization by using a combination of compound mutant cells for the five H3K9 methyltransferases and an EZH1/2 dual inhibitor, DS3201. We show that H3K27me3, which is normally segregated from H3K9me2/3, was redistributed to regions targeted by H3K9me2/3 after the loss of H3K9 methylation, and loss of both H3K9 and H3K27 methylation resulted in impaired both condensation and spatial organization of heterochromatin. Our data demonstrate that the two major repressive epigenome pathways exclusively but also coordinately maintain H3K9me2/3-marked heterochromatin organization in mammalian cells.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for WT and 5KO iMEFs treated with/without DS3201

first: Yoichi

last: Shinkai


title: Spatial organization of H3K9me2/3-marked heterochromatin is redundantly maintained by either the H3K9 or H3K27 methylation pathway [Hi-C]

overall_design: Hi-C analysis for WT and 5KO iMEFs treated with/without DS3201


title: Analysis of the effects of unilateral LMAN lesioning on gene expression in birdsong neural circuitry

city: San Francisco

first: Michael

last: Brainard

address: 675 Nelson Rising Ln

institute: University of California, San Francisco

overall_design: Five birds received unilateral LMAN lesions, three with left-hemisphere lesions and two with right-hemisphere lesions. LMAN was electrolytically lesioned using a 100 kOhm platinum/iridium electrode. LMAN was stereotactically located at 4.7 mm AP, 1.7 mm ML, and 2.1 mm DV using a beak angle of 50 degrees. In one hemisphere, five penetrations were made, one at the given coordinates and four more +/- 300 microns from this center position. At each penetration, 100 μA of current at the anode was passed for 60 seconds. At experiment end, birds were euthanized as described in Euthanasia and brain preparation. To assess lesion completeness, 20 um coronal cryosections were collected at 100 um intervals across the anterior-posterior extent of LMAN onto SuperFrost Plus slides (FisherBrand), then Nissl stained as described in Standard Nissl stain, fresh-frozen cryosections. The volume of LMAN was estimated in ImageJ/FIJI by calculating the area of LMAN on the unlesioned side in each section that it was visible, interpolating a smooth curve in R across these measured areas and the known distance between cryosections, then calculating the area under the curve. This procedure was repeated for any residual LMAN visible on the lesioned side, and lesion percentage was calculated as 100 * (1 - [volume LMAN lesioned] / [volume LMAN unlesioned]). LMAN was considered lesioned if more than 25% of volume was spanned by the lesion.

first: Bradley

last: Colquitt


title: Transcriptomic profiling of  mouse PDAC cells flow sorted from an orthotopic murine tumor model, cultured in standard celll culture nutrients or in physiological nutrients

city: Chicago

first: Juan

middle: Jose

last: Apiz Saab

state: Illinois

address: 5515 S. Cornell Ave Apt 102

department: Ben May

institute: University of Chicago

summary: Next-generation sequencing and transcriptomic profiling was performed for mouse PDAC cells grown under different nutrient formulations with the ultimate goal of studying differentially expressed genes

overall_design: mRNA Normalized Counts of PDAC cells grown in an orthotopic murine tumor model  in RPMI, in a chemically defined physiological nutrient formulation, or in the latter without citrulline and ornithine

last: Saab

first: Alexander

last: Muir


title: Spatial organization of H3K9me2/3-marked heterochromatin is redundantly maintained by either the H3K9 or H3K27 methylation pathway [ChIP-Seq]

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for histone modifications in iMEFs


title: Decoding the m6A expression profiling of spinal cord after spared nerve injury at three time points with RIP-Seq

status: Public on May 06 2022

city: guangzhou

first: Fanning

last: Zeng

state: Guangdong

address: Jingxi Street, Baiyun District

department: Department of Anesthesiology

institute: Nanfang hospital, Southern Medical University

summary:
We  performed gene expression profiling analysis using data obtained from RNA-seq and m6A peaks profiling analysis using data obtained from RIP-Seq of spared nerve injury model at 3rd, 7th, 14th postoperative day and sham group.
To investigate the differential m6A expression profiling, we established spared nerve injury model at 3rd, 7th, 14th postoperative day and sham group.

overall_design: The spinal cord of mice at 3rd, 7th, 14th day after spared nerve injury and sham group was isolated for MeRIP-Seq and RNA-Seq.

first: Jun

last: Cao

first: Zexuan

last: Hong

first: Yitian

last: Lu

first: Tao

last: Tao

first: Zaisheng

last: Qin


title: Single-cell RNA-seq of goat early embyos and GFFs cells

status: Public on Apr 04 2022

city: xian

first: Miaomiao

last: Jin

address: yangling

institute: northwest A&F university

type: Non-coding RNA profiling by high throughput sequencing

summary: We use high-throughput single cell RNA-seq to determine expression profile of IVF-2cell 、 IVF-8cell and SCNT-8cell embryos,and C1 and over3720. At present, the strand-specific library could not be generated for the analysis of goat embryo lncRNA because of the lack of available specific rRNA removal kits for goats. In this study, single-cell RNA-seq technology was used to analyze early embryonic transcripts, enrich the involving transcripts, and construct an common transcript library. For identifying transcripts expressed during the early goat embryonic stage, three cDNA libraries were established from early goat embryos at the three developmental stages, namely, two-cell (IVF-2c)、 eight-cell embryos (IVF-8c) and somatic cell nuclear transfer（SCNT-8c). The  GFFs cells transfected with control (no-load) and recombinant vectors were collected, total RNA was extracted, and the quality of the RNA was determined.

overall_design: Examination of expression differences between goat IVF 2-cell 、IVF 8-cell emryos and SCNT 8-cell

last: Liu

first: Lu

last: Zhao


title: Dynamic interplay between structural variation and 3D chromosome organization in pancreatic cancer

first: hebing

last: chen

address: taiping road 27

institute: Institute of Health Service  and Transfusion Medicine

summary: We investigate the spectrum of SVs and three-dimensional (3D) chromatin architecture in human pancreatic ductal epithelial cell carcinogenesis by using the state of art long-read single molecular real time (SMRT) and high-throughput chromosome conformation capture (Hi-C) sequencing techniques. Systematic integration of matched SMRT, in situ Hi-C, and RNA-seq datasets revealed the complicated dynamic interplay of SVs and 3D chromosome organization and their impacts on gene expression. Our studies identify and focus remodeling of chromatin folding domains associated with cross boundary SVs enabling aberrant interactions between regulatory elements. Moreover, our data also demonstrate the existence of complex genomic rearrangements associated with two key driver genes CDKN2A and SMAD4, and characterize their influence on cancer related gene expression from linear view to 3D perspective.

overall_design: Long read sequencing, Hi-C and RNA-seq of human pancreatic ductal epithelial cells (HPDE6-C7) and human pancreatic cancer cell lines PANC1 and BxPC3.

first: Yongxing

last: Du

first: Hebing

last: Chen

first: Chengfeng

last: Wang


title: Differences in fetal liver gene expression between low and high maternal nutrition

status: Public on Mar 30 2022

city: Tsukuba

first: Susumu

last: Muroya

state: Ibaraki

address: Ikenodai 2

department: Animal Products Research Division

institute: NARO Institute of Livestock and Grassland Science

summary: To investigate the impact of maternal nutrient restriction on gene expression in the fetal liver, we profiled gene expression in the liver of Japanese Black fetal calves in high and low nutrient condition of pregnant maternal cows .

overall_design: Japanese Black cows were fed with 60% (low-nutrition (LN) group, n=4) or 120% (high-nutrition (HN) group, n=4) of overall nutritional requirement during gestation. The fetal liver was obtained at 8.5-mo post-conception of the maternal cows. The microarray-based gene expression was analyzed using the pooled total RNA samples for each of the nutritional treatment group.


title: Spatial organization of H3K9me2/3-marked heterochromatin is redundantly maintained by either the H3K9 or H3K27 methylation pathway [MethylC-seq]

first: Kei

last: Fukuda

overall_design: MethylC-seq analyisis in WT, TKO and 5KO iMEFs

first: Yoichi

last: Shinkai


title: Spatial organization of H3K9me2/3-marked heterochromatin is redundantly maintained by either the H3K9 or H3K27 methylation pathway

overall_design: Refer to individual Series


title: Genetic Loci and Metabolic States Associated With Murine Epigenetic Aging

city: Memphis

first: Khyobeni

last: Mozhui

state: TN

address: 66 N. Pauline Street, #631

department: Preventive Medicine

institute: University of Tennessee Health Science Center

summary: DNA methylation measured in mice belonging to the BXD Family using the HorvathMammalMethylChip40

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus

overall_design: Liver DNAm data is from 321 female and 18 male belonging to 45 members of the BXD Family, including both parental strains and F1 hybrids. Age ranged from 5.6 to 33.4 months. Mice were all weaned onto a normal chow (control diet; CD) and a balanced subset of cases were then randomly assigned to high fat diet (HFD)

first: Steve

last: Horvath


title: Circulating miRNAome of dry cows transitioned from forage to 65% grain diet

status: Public on Mar 20 2022

city: Vienna

first: Cátia

last: Pacífico

state: Vienna

address: Veterinaerplatz 1

country: Austria

institute: University of Veterinary Medicine Vienna

summary: This study aimed to explore the changes in miRNAome in plasma and blood leucocytes during diet transition from forage to high-grain.

overall_design: Blood was collected from 4 ruminally-canulated non-lactating Holstein cows fed a 100% baseline forage diet (FD) and then transitioned to high-grain (HG; 65% concentrate) feeding.

first: Catia

last: Pacifico

first: Susanne

last: Kreuzer-Redmer


title: Bronchoalveolar lavage fluid reveals factors contributing to the efficacy of PD-1 blockade in lung cancer

status: Public on Apr 07 2022

city: Suita

first: Daisuke

last: Okuzaki

state: Osaka

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

institute: Osaka univ.

summary: Bronchoalveolar lavage is commonly performed to examine inflammation and responsible pathogens in lung diseases, and its findings may be used to assess the immune profile of the lung tumor microenvironment (TME). To investigate whether analyses of bronchoalveolar lavage fluid (BALF) can help identify non-small cell lung cancer (NSCLC) patients who respond to immune checkpoint inhibitors (ICIs), BALF and blood were prospectively collected before initiating nivolumab. The secreted molecules, microbiome, and cellular profiles based on BALF and blood analysis were compared regarding therapeutic effect in 12 patients. Compared to non-responders, responders showed significantly higher CXCL9 levels and greater diversity in the lung microbiome profile in BALF, and greater frequency of CD56+ subset in blood T cells, whereas no significant difference was found in PD-L1 expression of tumor cells. Antibiotic treatment in a preclinical lung cancer model significantly decreased CXCL9 in the lung TME, resulting in reduced sensitivity to nivolumab, which was reversed by CXCL9 induction in tumor cells. Thus, CXCL9 and the microbiome in the lung TME might be associated with each other, and their balance could contribute to nivolumab sensitivity in NSCLC patients. BALF analysis can help predict the efficacy of ICIs when performed along with currently approved examinations.

overall_design: The transcriptome profiles of bulk cells collected from BALF were compared between four responders and three non-responders.

first: Kentaro

last: Masuhiro

first: Shohei

last: Koyama


title: 3D vascularized proximal tubule model improves cell phenotype

city: Mölndal

first: Julie

last: Williams

address: Pepparedsleden 1

country: Sweden

institute: AstraZeneca

summary: Cultured proximal tubule epithelial cells (PTECs) under physiological flow in a 3D channel embedded within an engineered extracellular matrix (ECM) that is colocalized with an adjacent channel lined with human glomerular endothelial cells (HGECs) to mimic a peritubular capillary. After a period of maturation under continuous flow, both cell types were harvested for RNAseq analyses. Our results revealed that PTECs’ transcriptional profile is highly dependent on both the matrix on which these cells are cultured and the flow conditions. By contrast, endothelial cells exhibit greater phenotypic plasticity and are affected by matrix, flow, and co-culture conditions.

overall_design: PTECs and HGECs were grown alone or in co-culture in three different condition: plastic, embedded within an engineered extracellular matrix, or embedded within an engineered extracellular matrix under flow. RNA was extracted and RNA-seq performed.

first: Miguel

last: Carracedo

first: Babak

last: Alaei


title: Transcriptional profile analysis of Caco-2 cell line upon inflammatory signals and ER stress induction

status: Public on Apr 16 2022

city: MADRID

first: Eduardo

last: Martínez-Naves

state: MADRID

address: AVDA COMPLUTENSE S/N

department: Dpt. Immunología, Ophthalmology and ORL

institute: Universidad Complutense de Madrid, Facultad de Medicina

summary:
We stimulated Caco-2 cells, with the TLR5 agonist flagellin (Fl), with the chemical ER stress inducer thapsigargin (TG), or a combination of both (TGFl).
This strategy mimics a pro-inflammatory response in the presence of ER stress.

overall_design: Different treatments are represented as C (non-treated cells), Fl (treated with flagellin 1 μg / mL for 2 hours), TG (treated with TG at 1 μM for 5 hours), or X (treated with 1 μM TG for 5 hours, and with 1 μg / mL Fl for additional 2 hours).

last: Naves


title: Human tRF & tiRNA sequencing in serum of sarcoidosis

status: Public on Mar 15 2022

city: Changchun

first: Min

last: Zhao

address: Changchun

institute: Jilin University

summary: Transfer-RNA-Derived Small RNA (tsRNA) is a novel class of short non-coding RNA including stress-induced tRNA fragments (tiRNA) and tRNA-derived fragments (tRF). Using RNA sequencing, we evaluated the tsRNA expression profiles in the serum of sarcoidosis (n = 3) compared with healthy control group (n = 3). Bioinformatics analyses indicated that tsRNAs were the important regulators and potential new biomarkers of sarcoidosis.

overall_design: tiRNA and tRF profiles in serum of sarcoidosis  compared with healthy control group, in triplicate, using Illumina NextSeq 500 system.

first: Ke

last: Wang


title: Transcriptomic response of ginsenoside Rc (gRc) in C2C12 myotube under H2O2-induced oxidative stress

status: Public on Mar 18 2022

city: Busan

first: Haeseung

last: Lee

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

department: College of Pharmacy

institute: Pusan National University

summary: Effect of gRc on C2C12 myotube under resting state and H2O2 treatment

overall_design: mRNA profiles of C2C12 myotube treated with vehicle, gRc alone, H2O2 alone, or gRc with H2O2, in triplicate

first: Aeyung

last: Kim


title: Anti-hyperuricemic Potential of Abietic Acid: Identified from Helianthus annuus L. and Modulate Uric Acid in Human Embryonic Kidney Cells

status: Public on Mar 11 2022

first: ning

middle: Hui

last: Dai

state: Jilin

address: Qianjin Street

department: Life Sciences

institute: Jilin university

summary: Sunflower (Helianthus annuus L.) calathide is becoming more well-known as a result of its anti-hyperuricemia bioactivity. Aiming at developing anti-hyperuricemic ingredients in sunflower calathide extract (SCE), we were fortunate to discover abietic acid (AA), identified from SCE, has the capacity to inhibit xanthine oxidase activity at low concentrations (IC50 = 10.60 µM and inhibition constant was 193.5 nM) that examined by inhibitor screening experiment in vitro and computer-simulated molecular docking. To further explore the anti-hyperuricemia effects, the UA-stimulated human embryonic kidney (HEK) 293T cells were evaluated as a conceivable model in the current study. The huge amounts of high-throughput sequencing data, which mapping to reference genome, were analyzed by bioinformatics approaches: Weighted Gene Co-Expression Network Analysis (WGCNA) along with Kyoto Encyclopedia of Genes and Genomes (KEGG). Interestingly, the purine metabolism-related genes expressed in the AA treatment were nearly opposite to that of the UA group, indicating negative feedback regulations that AA perhaps contributes to maintain urate homeostasis in the high UA-exposed kidney cellular environment. Here, we consider that HEK293T cells ought to be an achievable in vitro model for UA metabolism research because the PNPase, PRPS1, PRPS2, and RPIA, which participate in UA generation, widely expressed in the untreated 293T cells as well. And AA markedly suppressed the PNPase, PRPS2, and RPIA expressed in UA-stimulated 293T cells, implying inhibitions for UA biosynthesis. As a result, AA not only inhibited xanthine oxidase activity efficiently but also regulated genes PNPase, PRPS2, and RPIA. It is promising to be developed as an inhibitor against hyperuricemia. Therefore, abietic acid, which could be isolated from plants, has the potential for anti-hyperuricemia, and the current study provided a precedent for pharmacology  analysis of natural ingredients.

overall_design: three biological repeats for control, abietic acid, sunflower calathide extract, and UA treatment in HEK293T cells

first: Huining

first: Xueqi

last: Fu

first: Wannan

last: Li


title: Spatial organization of H3K9me2/3-marked heterochromatin is redundantly maintained by either the H3K9 or H3K27 methylation pathway [HistoneLamin]

first: Kei

last: Fukuda

overall_design: Cross linked Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for Lamin A/C in iMEFs

first: Yoichi

last: Shinkai


title: Identification and characterization of human CD34+ and CD34dim/- neutrophil-committed progenitors (NCPs) [scRNA-seq]

city: Verona

first: Francisco

middle: Miguel Angel

last: Bianchetto-Aguilera

state: VR

address: Strade le Grazie, 8

department: Department of Medicine

institute: University of Verona

summary: In this study we report the identification of a unipotent human neutrophil-committed progenitors (NCPs) within bone marrow (BM) CD34+ and CD34dim/- cells. We show that NCPs can be either CD45RA+ or CD45RA-. By scRNA-seq experiments, we could uncover that NCPs actually consist of four cell clusters (c1-c4), substantially matching with the phenotypic identification of NCPs based on CD34, but not CD45RA, expression. c1-c4 cells were found to be at different maturation levels, aligned along two developmental neutrophil trajectories, as well as characterized by specific gene profiles.

overall_design: Examination by single cell RNA-seq of four BM neutrophil progenitors (CD34+CD45RA- NCP1, CD34+CD45RA+ NCP2, CD34dim/-CD45RA+ NCP3 and CD34dim/-CD45RA- NCP4) and the common monocyte progenitor (cMoP)

last: Bianchetto

first: Nicola

last: Tamassia

first: Marco

middle: A

last: Cassatella

first: Federica

last: Calzetti

first: Giulia

last: Finotti


title: Gut microbiota: uterine fibroids patients vs. healthy control

status: Public on Mar 05 2022

city: Changsha City of Hunan Province

first: xuan

last: peng

state: Hunan

address: 88 Xiangya Road

institute: Kaifu District, Changsha City, Hunan Province

summary: Gut microbial profiling of uterine fibroids (UFs) patients comparing control subjects. The gut microbiota was examined by 16S rRNA quantitative arrays and bioinformatics analysis. The goal was to reveal alterations in the gut microbiome of uterine fibroids patients.

sample_organism:
synthetic construct
human feces metagenome

overall_design: Two-condition experiment, uterine fibroids(UFs) patients vs. control subjects gut microbiota. Biological replicates: 42 uterine fibroids fecal replicates, 43 control replicates.

first: Xuetao

last: Mao

first: Xuan

last: Peng