title: Expression profiling of MIR181A1HG interference in hMSC-hTERT20 cells

status: Public on May 18 2022

city: Burlington

first: Jonathan

middle: AR

last: Gordon

state: VT

address: 89 Beaumont Ave Given E209

institute: University of Vermont

summary: We identified MIR181A1HG as a lncRNA that is ubiquitously expressed in non-mineralized tissues, highly expressed in proliferating MSCs and decreases in expression during osteogenesis. We demonstrate that knockdown of MIR181A1HG in hMSC-hTERT20 cells by CRISPRi during osteogenic differentiation causes an increase in alkaline phosphatase (ALP) activity and ALPL gene expression. Increased expression of several extracellular matrix proteins was noted. We identified MIR181A1HG as a nuclear lncRNA that binds to chromatin and where it regulates gene expression, including the transcription factor SOX5. These results reveal that MIR181AHG may act as a negative regulator of osteoblast differentiation, thereby providing a novel mechanism of regulatory control of osteogenesis.

overall_design: Expression of the lncRNA MIR181AHG was knocked down by CRISPRi using pLV hU6-sgRNA hUbC-dCas9-KRAB-T2a-GFP in TERT immortalized human mesenchymal stromal cells (hMSC-hTERT20). Transcriptome changes were examined during osteogenic differentiation at three time points (Day 0, 7 and 14) after lncRNA interference.

first: Tye

last: Coralee

first: Gordon

last: Jonathan

first: Lian

last: Jane

first: Stein

last: Gary


title: Transcriptome profilng of hMSC-hTERT20 cells undergoing osteogenic differentiation

department: Biochemistry

country: USA

type: Expression profiling by high throughput sequencing

summary: Long non-coding RNAs are emerging as key regulators of development and differentiation. In this study, we profiled TERT-immortalized human mesenchymal stromal cells (hMSC-hTERT20) cells undergoing osteogenic differentiation at 3 time points. We have identified expressed mRNAs and lncRNAs at each stage of differentiation.

overall_design: Transcriptome profiling was performed on hMSC-hTERT20 cells during osteogenic differentiation at days 0, 7 and 14.

first: Coralee

last: Tye

first: Jane

last: Lian

first: Gary

last: Stein


title: Comparative transcriptomics reveals circadian and pluripotency networks as two pillars of longevity regulation

city: Rochester

first: jinlong

last: lu

state: NY

address: 213 Hutchinson Hall

institute: University of Rochester

summary: Mammals differ more than 100-fold in maximum lifespan. Here, we conducted comparative transcriptomics on 26 species with diverse lifespans. We identified thousands of genes with expression levels negatively or positively correlated with a species' maximum lifespan (Neg- or Pos-MLS genes). Neg-MLS genes are primarily involved in energy metabolism and inflammation. Pos-MLS genes show enrichment in DNA repair, microtubule organization, and RNA transport. Expression of Neg- and Pos-MLS genes is modulated by interventions, including mTOR and PI3K inhibition. Regulatory networks analysis showed that Neg-MLS genes are under circadian regulation possibly to avoid persistent high expression, whereas Pos-MLS genes are targets of master pluripotency regulators OCT4 and NANOG and are upregulated during somatic cell reprogramming. Pos-MLS genes are highly expressed during embryogenesis but significantly downregulated after birth. This work provides targets for anti-aging interventions by defining pathways correlating with longevity across mammals and uncovering circadian and pluripotency networks as central regulators of longevity.

sample_organism:
Blarina brevicauda
Marmota monax
Tamiasciurus hudsonicus
Mesocricetus auratus
Peromyscus maniculatus
Ondatra zibethicus
Mus musculus
Rattus rattus
Cavia porcellus
Hydrochoerus hydrochaeris
Myocastor coypus
Octodon degus
Heterocephalus glaber
Sciurus carolinensis
Chinchilla lanigera
Tamias striatus
Castor canadensis
Acomys russatus
Scalopus aquaticus
Neotoma cinerea
Cuniculus paca
Condylura cristata
Cricetulus barabensis
Fukomys damarensis
Bramus lutescens

overall_design: Examination of gene expression across species.

first: J

middle: Y

last: Lu

first: Vera

last: Gorbunova

first: Andrei

last: Seluanov


title: RNA sequencing of 16D LTenza cells transduced with cMyc, shRb1, shTp53, shRb1_shTp53

status: Public on May 12 2022

city: Los Angeles

first: Andrew

middle: Scott

last: Goldstein

state: CA

address: 610 Charles E Young Dr East

department: Urology

institute: University of California, Los Angeles

summary: The goal of this study was to determine how genetic alterations to AR inhibition-maintained prostate cancer cells alters transcriptional programs. We explored how MYC overexpression alters the transcriptional program of 16D cells maintained in enzalutamide for at least 2 months (LTenza) by transducing LTenza 16D cells with control (FUCRW) or MYC. To explore the effect of RB1 and TP53, we generated LTenza 16D cells with knockdown of RB1 and/or TP53 and compared these lines to control-transduced (shScr) LTenza 16D cells. Enzalutamide-naïve (DMSO-treated) cells were included to validate enzalutamide-induced inhibition of AR signaling in enzalutamide-maintained lines.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for untransduced DMSO-treated 16D cells and LTenza 16D cells transduced with shScr, FUCRW, MYC, shRB1, shTP53, or shRB1_shTP53

middle: S

first: Preston

middle: D

last: Crowell


title: RNA sequencing of LNCaP cells treated with castration and/or enzalutamide

summary: The goal of this study was to determine how androgen receptor inhibition alters transcriptional programs in prostate cancer cells. LNCaP prostate cancer cells were grown in 10% charcoal-stripped serum (CSS) supplemented with 0.5 nanomolar dihydrotestosterone (DHT), in CSS without DHT modeling castration, with CSS + DHT but in the presence of 10 micromolar enzalutamide, or in CSS without DHT (castrated) and in the presence of enzalutamide for 72 hours. Analysis shows that androgen receptor target genes are reduced with castration, enzalutamide or the combination of castration + enzalutamide.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for LNCaP cells treated for 72 hours with castration, enzalutamide or castration + enzalutamide.


title: Antiprogestins reduce epigenetic field cancerization in breast tissue of young healthy women

status: Public on May 16 2022

city: Solna

first: Nageswara Rao

last: Boggavarapu

state: stockholm

address: Visionsgatan 4

department: Women and Children health

country: Sweden

institute: Karolinska Institutet

summary: Breast cancer is a leading cause of death in premenopausal women. Progesterone drives expansion of luminal progenitor cells, leading to the development of poor-prognostic breast cancers. However, it is not known if antagonising progesterone can prevent breast cancers in humans. We suggest that targeting progesterone signalling could be a means of reducing features which are known to promote breast cancer formation.

overall_design: Core needle breast biopsies collected at baseline and after two months of 50 mg mifepristone treatment every other day from healthy women (n=16), aged 18-35 years, with regular menstrual cycles and with no hormonal treatment.  BRCA1/2 mutation status was not assessed for these subjects.

first: Nageswara

middle: R

last: Bogavarappu


title: The slit2 induces rejuveation in mid old cells.

status: Public on Apr 30 2022

city: swon

first: Tea jun

last: Park

address: 206, World cup-ro, Yeongtong-gu

department: Biochemistry and Molecular Biology

country: South Korea

institute: Ajou University School of Medicine

summary: The slit2 induces rejuveation in mid old cells such as reduces inflammation and inhibite cell cycle arrest.

overall_design: The mid old cells were treated with Slit2(100ng/ml) for 2days and cells harvested and extracted RNA and anlysis RNA sequencing.

first: Younghwa

last: Kim

first: Tae

middle: J


title: Single cell profiling of primary and paired metastatic lymph node tumors in breast cancer patients (10x Visium)

city: Beijing

first: Zhihua

last: Liu

state: Beijing

address: State Key Laboratory of Molecular Oncology, National Cancer Center, National Clinical Research Center for Cancer, Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China

country: China

summary: The microenvironment of lymph node metastasized tumors (LNMT) determines tumor progression and response to therapy, but a systematic study of LNMT is lacking. Here, we generate single-cell maps of primary tumors (PTs) and paired LNMTs in 8 breast cancer patients. We demonstrate that the activation, cytotoxicity, and proliferation of T cells are suppressed in LNMT compared with PT. CD4+CXCL13+ T cells in LNMT are more likely to differentiate into an exhausted state. Interestingly, LAMP3+ dendritic cells in LNMT display lower T cell priming and activating ability than in PT. Additionally, we identify a subtype of PLA2G2A+ cancer-associated fibroblasts enriched in HER2+ breast cancer patients that promotes immune infiltration. We also show that the antigen-presentation pathway is downregulated in malignant cells of the metastatic lymph node. Altogether, we characterize the microenvironment of LNMT and PT, which may shed light on the individualized therapeutic strategies for breast cancer patients with lymph node metastasis.

overall_design: Spatial transcriptome sequencing of primary tumor and paired lymph node metastasis in breast cancer

first: Tong

first: Cheng

first: Lei

last: Zhang

first: Jing

first: Xiaofan

last: Wei

first: Hongquan


title: The role of endogenous Smad7 in regulating macrophage phenotype following myocardial infarction

status: Public on Apr 29 2022

city: Bronx

first: Silvia

middle: C

last: Hernandez

state: New York

address: 1300 Morris Park Avenue

department: Medicine-Cardiology

institute: Albert Einstein College of Medicine

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

overall_design: Refer to individual Series


title: Single cell profiling of primary and paired metastatic lymph node tumors in breast cancer patients

department: State Key Laboratory of Molecular Oncology

institute: Chinese Academy of Medical Sciences and Peking Union Medical College

overall_design: Single cell RNA, spatial transcriptome and TCR sequencing of primary tumor and paired lymph node metastasis in breast cancer


title: Multi-task learning uncovers robust translation cis-regulatory features

status: Public on Apr 28 2022

city: Hong Kong

first: John

middle: Hoi Chun

last: Fong

address: Laboratory Block, 21 Sassoon Road, Hong Kong

department: School of Biomedical Sciences, LKS Faculty of Medicine

country: Hong Kong

institute: The University of Hong Kong

summary: To validate the sequence motifs identified by our multi-task learning model MTtrans, a new 5' UTR library with around 8,000 synthetic 5'UTRs was built to express EGFP. The reads count was used as a proxy of translation rate here to validate the estimated regulatory effect of motifs that we inferred from multiple datasets, proving the robustness of the sequence motifs.

overall_design: 5' UTR-driven-EGFP expressing HEK293T cells were sorted by isolated by Fluorescence-activated cell sorting (FACS) according to the intensity of FITC signal and analyzed using PacBio SMRT sequencing.

middle: H

first: YukKei

last: Wan

first: Athena

last: Chu

first: Alan

last: Wong


title: The role of endogenous Smad7 in regulating macrophage phenotype following myocardial infarction [JunLi_MyS7KOinvivo]

summary: Induction of the inhibitory Smad, Smad7 serves as a negative feedback mechanism that restrains TGF-b-mediated actions in injured tissues. In inflammatory cells, Smad7 has been suggested to exert both pro-inflammatory actions attributed to inhibition of TGF-b-induced suppression of inflammation, and anti-inflammatory effects due to disruption of the TAK-1/NF-kB system. Myocardial infarction triggers a macrophage-driven inflammatory response that plays a central role in cardiac repair, but also contributes to adverse remodeling and fibrosis. We hypothesized that Smad7 upregulation in infarct macrophages may play a modulatory role in cardiac repair, by restraining effects of TGF-b. To test the hypothesis, we investigated the response of Myeloid cell-specific Smad7 knockout mice (MyS7KO) following myocardial infarction protocols, and we examined the in vitro effects of Smad7 in isolated macrophages. Smad7 was upregulated in a subset of infarct macrophages, peaking 7 days after infarction. Myeloid cell-specific Smad7 loss did not affect baseline macrophage gene expression and had no significant effects on homeostatic functions. Although RNA-seq analysis predicted that, in the absence of Smad7, infarct macrophages may have attenuated activation of inflammatory pathways and suppressed TREM1 signaling, myeloid cell-specific Smad7 loss had no significant effects on ventricular dysfunction, adverse remodeling, scar remodeling and collagen deposition after myocardial infarction. In isolated macrophages, TGF-b attenuated pro-inflammatory cytokine and chemokine expression, modulated synthesis of matrix remodeling genes, and had profound effects on macrophage profile, inducing genes associated with activation of sphingosine-1 phosphate and integrin signaling pathways, and inhibiting cholesterol biosynthesis genes. However, RNA-seq and PCR array experiments showed that Smad7 loss has minimal effects on TGF-b-mediated macrophage responses, restraining synthesis of only a small fraction of TGF-b-induced genes, such as Itga5, Olfml3 and Fabp7. Smad7 absence did not affect the anti-inflammatory actions of TGF-b in TNF-stimulated cells. In conclusion, our findings suggest a limited role for macrophage Smad7 in regulation of post-infarction inflammation and repair, and demonstrate that the anti-inflammatory effects of TGF-b in macrophages are not restrained by endogenous Smad7 induction.

overall_design: In order to study the role of Smad7 in myeloid cells in vivo, we generated mice with myeloid specific loss of Smad7 in lysozyme M+ cells (MyS7KO). We used a transgenic mouse line in which Cre recombinase is driven by the LyzM promoter (Jackson Laboratory, stock No: 004781). LyzM-Cre mice were bred with Smad7fl/fl mice (Jackson Laboratory, stock No: 017008) to generate LyzM-Cre;Smad7fl/fl animals (MyS7KO) and corresponding Smad7fl/fl control littermates. A model of non-reperfused myocardial infarction was induced by permanent ligation of left anterior descending coronary artery and samples were collected for baseline mice, and 3 and 7 days after coronary occlusion.

first: Jun

last: Li

first: Ruoshui

first: Izabela

last: Tuleta

first: Claudio

last: Humeres

first: Anis

last: Hanna

first: Bijun

last: Chen

first: Nikolaos

middle: G

last: Frangogiannis


title: Potent and EGFRWT Sparing HER2 Inhibitors for the Treatment of HER2 Exon 20 Insertion-Driven Tumors

status: Public on Mar 19 2022

city: Vienna

first: Daniel

last: Gerlach

address: Dr.-Boehringer-Gasse 5-11

department: Global Computational Biology and Digital Sciences

country: Austria

institute: Boehringer Ingelheim RCV GmbH & Co KG

summary: Activating mutations in ERBB receptors act as oncogenes in non-small cell lung cancer (NSCLC). Besides the more prevalent epidermal growth factor receptor (EGFR) activating mutations, oncogenic variants in human epidermal growth factor receptor 2 (HER2) occur in approximately 2% of NSCLC patients. HER2 oncogenic mutations in NSCLC predominantly affect the tyrosine kinase domain and cluster in exon 20 of the ERBB2 gene. Most clinically approved and currently tested tyrosine kinase inhibitors are limited by either insufficient potency on exon 20 altered HER2 and/or their insufficient selectivity against EGFR wild type (EGFR WT) – a major cause of dose limiting toxicity. We report herein the discovery of covalent tyrosine kinase inhibitors that potently inhibit HER2 exon 20 mutants while sparing EGFR WT. The new inhibitors presented in this study reduce tumor cell survival and proliferation in vitro, and result in regressions in in vivo preclinical xenograft models of HER2 exon 20 mutant NSCLC as well as inhibition of downstream signaling. Our results suggest that HER2 exon 20 insertion driven tumors can be effectively treated by a potent and highly selective HER2 inhibitor while sparing EGFR WT. The new inhibitors described in this study pave the way for testing potent HER2 selective inhibitors in HER2 mutant NSCLC patients and may offer an additional therapeutic option for these patients.

overall_design: In-vitro (cell lines: NCI-H2170 HER2-YVMA, NCI-H1781, OE19, and AU565) and in-vivo (patient-derived xenograft: CTG-2543) gene expression profiling under compound treatment. Groups include control (DMSO, Natrosol) and compound treated samples (Poziotinib, BI-4142, and BI-1622). CRISPR/Cas9 genome editing was used to generate NCI-H2170 HER2-YVMA cells. The HER2-YVMA variant was knocked into the endogenous HER2 locus in the HER2 amplified (HER2amp) NCI-H2170 cells to overexpress this variant. Sampling time points, compound concentrations, and biological replicates are detailed out in the respective sample descriptions. All samples were subjected to RNA isolation, followed by library preparation (QuantSeq 3' mRNA-Seq Library Prep Kit FWD for Illumina, Lexogen), and messenger RNA sequencing on an Illumina NextSeq 500 system.

first: Valeria

last: Santoro

first: Ralph

middle: A

last: Neumüller

first: Paolo

last: Chetta

first: Schlattl

last: Andreas


title: RNA-sequencing uncovers transcriptomic changes in retinal tissues after vitreous substitution with a thermogelling polymer

status: Public on Apr 09 2022

city: Singapore

first: Xinyi

last: Su

address: 61 Biopolis Drive

country: Singapore

institute: IMCB

summary: We developed a thermogelling polymer with intrinsic anti-scarring properties on retinal cells in-vitro. To study its mechanism of action in-vivo, this thermogelling polymer was injected into the rabbit eye as a vitreous substitute and the retinal tissues were harvested for RNA-sequencing to understand transcriptomic changes induced by the polymer.

overall_design: Biological triplicates of retina and retinal pigment epithelium from non-operated control rabbits, and 1-month and 2-month after vitreous replacement were harvested and sequenced.

first: Su

last: Xinyi

first: Bhav

last: Parikh

first: Paul

last: Blakeley


title: Interactions between BRD4S, LOXL2, and MED1 drive cell cycle transcription in triple-negative breast cancer

status: Public on Mar 18 2022

city: Barcelona

first: Debayan

last: Datta

address: Carrer del Rosselló, 132

country: Spain

institute: ISGlobal

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Triple-negative breast cancer (TNBC) often develops resistance to single-agent treatment, which can be circumvented using targeted combinatorial approaches. Here, we demonstrate that the simultaneous inhibition of LOXL2 and BRD4 synergistically limits TNBC proliferation in vitro and in vivo. Mechanistically, LOXL2 interacts in the nucleus with the short isoform of BRD4 (BRD4S), MED1, and the cell cycle transcriptional regulator B-MyB. These interactions sustain the formation of BRD4 and MED1 nuclear transcriptional foci and control cell cycle progression at the gene expression level. The pharmacological co-inhibition of LOXL2 and BRD4 reduces BRD4 nuclear foci, BRD4-MED1 colocalization, and the transcription of cell cycle genes, thus supressing TNBC cell proliferation. Finding novel strategies to disrupt BRD4S-LOXL2 interaction holds potential for developing successful TNBC therapies.

overall_design: mRNA (triplicates), ATAC-seq (triplicates) and ChIP-seq of BRD4L/S (AB antibody) (duplicates) and BRD4L (BB antibody) (single replicate) in control and LOXL2 downregulated conditions in MDA-MB-231 cells.

first: Laura

last: Pascual

first: Sara

last: Sdelci


title: Detecting non-canonically-targeted SpCas9 generated DSBs in human cells by LAM-HTGTS

status: Public on Feb 28 2022

city: Stanford

first: Jinglong

last: Wang

state: CA California

address: 1291 Welch Rd, CCSR Room 1240

department: Radiation Oncology

institute: Stanford University

summary: We identified robust cleavage by non-canonically-targeted SpCas9 that target protospacer with a few bases from the canonical NGG PAM in biochemistry assay. To determine whether this spaced SpCas9 cleavage exists in human cells, we employed high-throughput genome-wide translocation sequencing (LAM-HTGTS) using SpCas9 with three independent canonical sgRNAs served as bait (bait-A, bait-L and bait-D) to compared the cleavage activities of canonically-targeted and non-canonically-targeted SpCas9 in eight locus (RAG1B-D, RAG1K-O) in chromosome 11. We found that almost all 1bp-target shifted SpCas9 generated substantial DSBs as the canonical controls. While detected less frequently, 2bp-targeted shifted SpCas9 generated significant amounts of DSBs in RAG1D and RAG1L locus. These findings underscore the spaced PAM-mediated DSBs occurred in living cells.

overall_design: We measured the DNA double stranded breaks (DSBs) by canonically-targeted and non-canonically-targeted SpCas9

first: Richard

middle: L

last: Frock


title: Single cell mRNA sequencing of de novo hematopoiesis from the fetal lung

status: Public on Feb 26 2022

city: Boston

first: George

last: Murphy

state: MA

address: 670 Albany Street

institute: Center for Regenerative Medicine of Boston University and Boston Medical Center

summary: Hemogenic endothelium, which gives rise to the earliest HSCs, is thought to be isolated to very early stages of development, peaking at E10.5 in mice. However, our data suggests there may be hemogenic endothelium capable of giving rise to de-novo HSPCs in the fetal lungs of mice at E17. We've adapted a platform to recapitulate the ex-vivo development of HSPCs from E17 lung endothelium. This sequencing experiment will help us to validate whether what we are seeing in culture is indeed endothelial to hematopoietic transition (EHT) and possibly identify the subset of endothelial cells that give rise to HSPCs.

overall_design: E17 timed pregnant Wild Type C57BL6 mice are sacrificed at E17. The fetal lungs are isolated and digested with liberase into a single cell suspension. These cells are frozen down in 10% DMSO and replated on a thin later of diluted matrigel with HSPC media (containing mTPO, IL6, SCF, FGF, VEGF, Flt3). On D3, wells are washed with PBS and replaced with fresh media. On D4, D5 and D6, suspension cells are collected prepped for 10x. Adherent layers are digested with accutase, and sorted to enrich for live-VECAD+ cells, which are then prepped for 10x.

first: Anthony

last: Yeung

first: Carlos

last: Villacorta-Martin

first: Feiya


title: tRF&tiRNA sequencing of human PTC tissues and corresponding paracancer tissues

city: Jinhua

first: Pu

last: Wu

address: No. 365 Renmin East Road, Jinhua 321000

institute: Affiliated Jinhua Hospital, Zhejiang University School of Medicine, Jinhua

type: Non-coding RNA profiling by high throughput sequencing

summary:
Purpose: To study the expression and potential significance of tRF and tiRNA in PTC (Papillary thyroid carcinoma) by sequencing tRF and tiRNA in PTC tissues and corresponding paracancer tissues of thyroid cancer patients.
Methods: Four pairs of PTC tissues and paracancer tissues were collected. Small RNA sequencing was performed on Illumina NexSeq instrument.
Results: If P ≤ 0.05, fold change > 1.5 as the cutoff, there were 27 up-regulated tRFs & tiRNAs and 20 down-regulated tRFs & tiRNAs.
Conclusions: Among the differentially expressed tRFs & tiRNAs, tiRNA-1:34-Lys-CTT-2 and tRF-1:30-Gly-CCC-3 may be the potential novel regulatory factors.

overall_design: tRF&tiRNA sequencing of 4 pairs of human PTC tissue and paracancer tissue samples

first: Yi

last: Pan

first: Chaoyang

last: Xu


title: Diverse transcriptome response to salinity change in cod subpopulations from the Baltic Sea

status: Public on Feb 02 2022

city: Sopot

first: Magdalena

last: Malachowicz

address: Powstańców Warszawy

country: Poland

institute: Institute of Oceanology Polish Academy of Sciences

summary: The Atlantic cod (Gadus morhua L.) is one of the most important species in the Baltic Sea with high ecological and economical value. To explore the differences in adaptation to salinity between Baltic cod subpopulation: western (Kiel Bight) and eastern (Gdańsk Bay) samples were analyzed through genome-wide oligonucleotide microarray.

overall_design: Atlantic cod samples (n=81) were collected from two subdivisions: the Schleifjord, Kiel Bight (KIEL-18PSU) - SD22 and Gdańsk Bay (GDA - 8PSU) - SD 26. Gene expression changes in gills were assessed with 44 k oligonucleotide microarray

first: Aleksei

last: Krasnov

first: Roman

last: Wenne


title: RNA-sequencing uncovers transcriptomic changes induced by a multiblock thermogelling polymer on healthy and disease-modeled retinal pigment epithelial cells

status: Public on Mar 09 2022

first: Xinyi

last: Su

summary: Human embryonic stem-cell derived retinal pigment epithelial cells were co-stimulated with TNF-α and TGF-β1 to model a retinal scarring complication, proliferative vitreoretinopathy. Thermogelling polymer prevented this scarring complication. To understand the polymer-cell interaction and ultimately the mechanism underlying it's anti-scarring activity, RNA-Seq was performed.

overall_design: Triplicates of four different conditions at two time points (8 and 24 hours) were sequenced. Four conditions include, Media only control, Polymer alone, TNF-α and TGF-β1 (TNT) alone, TNT + Polymer.

first: Su

last: Xinyi

first: Bhav


title: Single-cell analyses reveal phenotypic linkage between colorectal cancer and liver metastasis

status: Public on Feb 12 2022

first: Yedan

last: Liu

address: Yiheyuan

institute: Peking University

summary: The tumor microenvironment (TME) is intrinsically associated with clinical responses of immunotherapy, but it remains opaque how cancer cells and host tissues differentially influence its immune composition. Here, we performed systematic single-cell analyses for autologous clinical samples from liver metastasized colorectal cancer patients, as well as non-metastatic primary liver and colon cancer patients to disentangle different factors shaping TME. By aligning CD45+ cells within metastatic tumors across different tissue types, we classified exhausted CD8+ T (Tex) cells and activated Tregs as M-type, whose phenotypes were associated with the malignancy, while NK and MAIT cells were defined as N-type, whose phenotypes were associated with the niche. Significant TCR sharing existed between Tex cells in primary and metastatic tumors as well as peripheral non-exhausted T cells, implicating the presence of common peripheral precursors that were independently developed into Tex. For myeloid cells, DC3s and SPP1+ tumor-associated macrophages were classified as M-type, and the latter were also predominantly present in liver metastasis, indicating its pro-metastasis roles. Our analysis bridges the immune phenotypes of primary and metastatic tumors, paving ways to better understand the tumor-specific contexture and to target key components in the metastasis process.

overall_design: We performed single-cell RNA sequencing on colorectal cancer patients with liver metastasis and obtained CD45+ cells from 101 samples including blood, mesenteric lymph nodes, matched primary and metastasis tumors and adjacent tissues.

first: Qiming

last: Zhang

first: Xianwen

last: Ren

first: Wenjun

last: Ouyang

first: Zemin


title: Molecular characterization of hypothalamus-infiltrating T cells following Pandemrix® vaccination of Orex-HA mice through bulk RNA sequencing of T cell subsets

status: Public on Jan 31 2022

city: Toulouse

first: Leila

last: Khajavi

address: TOULOUSE

country: France

institute: INSERM

summary: To identify the T cell subsets and molecular pathways potentially involved in the killing of orexinergic neurons in Pandemrix®-vaccinated Orex-HA mice, we cell-sorted activated (CD44high CD62Llow) transferred HA-specific (CD45.1+) and endogenous (CD45.1-) CD4 and CD8 T cells from dissected hypothalami, spleen and cervical lymph nodes at the peak of hypothalamic infiltration (day 14 post-vaccination). RNA sequencing on these sorted T cell populations allowed us to compare the gene expression profile of a given T cell subset across different tissue sites and of different T cell subsets in a given tissue.

overall_design: Orex-HA mice were immunized intramuscularly with Pandemrix® vaccine 1 day after the adoptive transfer of naïve (CD45.1+CD62L+CD25-) HA-specific CD4+ and CD8+ T cells. At day 14 post-vaccination, endogenous (CD45.1-) and transferred HA-specific (CD45.1+) populations of CD44highCD62LlowCD4+ and CD44highCD62LlowCD8+ T cells were isolated from spleens, cervical lymph nodes and hypothalami by FACS sorting in 4 independent experiments involving 20 to 30 mice each.   4 experiments X 3 tissues per experiment X 4 T cell populations (CD4 and CD8 both with endogenous & transferred) = 48 samples (1 samples did not sequence)…. Total of 47 samples available.

first: Raphael

last: Bernard-Valnet

first: Xuan-Hung

last: Nguyen

first: David

last: Freiser

first: Matthias

last: Zytnicki

first: Roland

last: Liblau


title: The Host Cell’s ER Proteostasis Network Shapes HIV-1 Envelope Protein Mutational Tolerance

status: Public on Jan 30 2022

city: Cambridge

first: Matthew

last: Shoulders

address: 77 Massachusetts Avenue

department: Chemistry

institute: Massachusetts Institute of Technology

summary: Buffering of deleterious mutations by molecular chaperones and degradation of aberrant proteins by quality control systems are both major factors that can impact the mutational landscape available to a client protein. The impacts of the proteostasis network on protein evolution are not limited to just endogenous clients, but can also shape the mutational landscapes accessible to rapidly evolving viral proteins. Here, we test the hypothesis that the composition of the host cell’s endoplasmic reticulum (ER) proteostasis network shapes the evolution of RNA viruses by focusing on human immunodeficiency virus-1 envelope (Env), a membrane glycoprotein that folds and matures in the host cell’s secretory pathway. We apply chemical genetic methods to activate the IRE1-XBP1s and/or the ATF6 transcriptional arms of the unfolded protein response in a stress-independent manner. We then quantitatively assess the impact of the resulting altered host cell ER proteostasis environments on the relative enrichment of all Env single amino acid substitutions using deep mutational scanning. We find that upregulation of host ER proteostasis factors globally reduces the mutational tolerance of HIV-1 Env, particularly upon induction of the IRE1-XBP1s transcriptional arm of the UPR. The effects of ATF6 activation are less global, but still significant at particular Env sites. The impact of the XBP1s-induced ER proteostasis environment is disparate for diverse structural elements of Env. Conserved, functionally important regions generally exhibit the largest decreases in mutational tolerance upon XBP1s activation. In contrast, specific regions of Env, including regions targeted by broadly neutralizing antibodies, display greatly enhanced mutational tolerance when XBP1s is activated. Altogether, these data reveal a new set of host factors that specifically shape the mutational space accessible to HIV Env and, more generally, provide compelling evidence that UPR-regulated proteostasis mechanisms play critical roles in membrane protein evolution.

overall_design: RNA-seq characterizing a clonal SupT1 cell line stably expressing both the gene encoding XBP1s under control of the tetracycline repressor (tetR) and the gene encoding E. coli dihydrofolate reductase (DHFR) destabilizing domain fused to the active form of ATF6 (amino acid residues 1-373). These cells were treated with small molecules for 24 hours in quadruplicate to modulate the proteostasis environment in a stress-independent manner. The cells were treated with: 1) 0.1% DMSO for vehicle treatment condition, 2) 2 ug/mL doxycycline (dox) to activate XBP1s, 3) 10 uM trimethoprim (TMP) to activate ATF6, and 4) 2 ug/mL dox and 10 uM TMP to induce both XBP1s and ATF6 concomitantly.

first: Emmanuel

last: Nekongo

first: Jimin

last: Yoon


title: HSF1 Activation Can Restrict HIV Replication

summary: Host protein folding stress responses can play important roles in RNA virus replication and evolution. Intriguingly, prior work revealed a complicated interplay between the cytosolic proteostasis stress response, controlled by its master regulator heat shock factor 1 (HSF1) and human immunodeficiency virus-1 (HIV-1). We sought to isolate HSF1 transcription factor activity from proteostasis stress and elucidate the function of HSF1 in HIV-1 lifecycle in absence of cellular stress. We used chemical genetic, stress-independent control of HSF1 activity to establish whether and how HSF1 influences HIV-1 replication. Stress-independent HSF1 induction decreased both the total quantity and infectivity of HIV-1 virions. Moreover, HIV-1 was unable to escape HSF1-mediated restriction over the course of several serial passages. These results promote continued consideration of the heat shock response as a potential target for antiviral drugs.

overall_design: RNA-seq characterizing a clonal human T cell line stably expressing doxycycline (dox)-inducbible constitutively active version of HSF1 (cHSF1). This cell line was treated with 1ug/mL dox or vehicle (water) for 18 hours (in biological quadruplicate) to modulate the proteostasis environment in a stress-independent manner.

first: Anna

last: Ponomarenko

middle: E

first: Mahender

middle: B

last: Dewal

first: Vincent

last: Butty

first: Edward

middle: P

last: Browne


title: Identification by RNA-seq of Prdm12 regulated genes in  trigeminal ganglia of adult mice

status: Public on Jan 26 2022

city: Goettingen

first: Gabriela

last: Salinas

state: Lower-Saxony

address: Kreuzbergring 57

department: Department of Pathology

country: Germany

institute: Universitaetsmedizin Goettingen

summary: Loss of Prdm12 induces gene deregulation in mature trigeminal ganglia  of adult mice

overall_design: RNAseq on TG of  Rosa26CreERT2; Prdm12 Fl/Fl (n=6 ) and Control (n=6) one month after tamoxifen injection.

first: Eric

last: Bellefroid

first: Sitte

last: Maren

first: Alba

last: Sabaté


title: Bulk RNA-seq and ATAC-seq of mouse uterine tissue-resident natural killer cells.

status: Public on Feb 05 2022

first: Chao

last: Zhong

address: 38 Xueyuan Rd , Haidian District

department: Institute of Systems Biomedicine

summary: Uterine natural killer(NK) cells play a crucial role in pregnancy by promoting spiral artery remodeling and secreting fetal growth factors.Uterine trNK cells before pregnancy and during pregnancy (gd6.5, gd8.5 and gd11.5) were sorted, then applied into bulk RNA-sequence to reveal the features at different timepoints. Similarily, uterine trNK cells with different treatment in vitro were also sorted for bulk RNA-sequence to identify the role of IL-21-STAT3 signaling. To interpret the differentiation trajectory of uterine trNK cells, CD45+NKp46+NK1.1+ cells in wild-type virgin mice, wild-type gd8.5 mice, Il21r-/- gd8.5 mice and Il21r-/- gd8.5 mice with Caspase3 inhibitor are sorted.Applying them to Single-Cell RNA sequence, a differentiation trait of uterine NK cells during pregancy was revealed and IL-21 significantly promoted this process at initial stage.

overall_design: We aimed to reveal the differentiation trajectory of uterine natural killer cell during pregnancy and how IL-21 promote this process. To investigate the regulated mechanism of uterine trNK differentiation, uterine trNK were treated with IL-21 in vitro. At different time cells were collected and sorted for bulk RNA-sequence and ATAC-seq.

first: Mengwei

last: Han

first: Luni

last: Hu

first: Di

last: Wu


title: MBD4 loss results in global reactivation of promoters and retroelements with low methylated CpG density.

status: Public on Jan 10 2022

city: ILLKIRCH-GRAFFENSTADEN

first: Christophe

last: Papin

address: 1 rue Laurent Fries

institute: IGBMC - CNRS UMR 7104 - Inserm U 964

type: Methylation profiling by high throughput sequencing

summary: Inherited defects in the base-excision repair gene MBD4 predispose individuals to adenomatous polyposis and colorectal cancer, which is characterized by an accumulation of C>T transitions resulting from spontaneous deamination of 5’-methylcytosine. Despite its significance, this DNA repair pathway is still poorly understood. Here we show that the protein MBD4 is required for DNA methylation maintenance and G/T mismatch repair. Transcriptome and methylome analyses reveal a genome-wide hypomethylation of promoters, gene bodies and repetitive elements in the absence of MBD4 in vivo. Methylation mark loss is accompanied by a broad transcriptional derepression phenotype affecting promoters and retroelements with low methylated CpG density. MBD4 in vivo forms a complex with the mismatch repair proteins (MMR), which exhibits high bi-functional glycosylase/AP-lyase endonuclease specific activity towards methylated DNA substrates containing a G/T mismatch. Experiments using recombinant proteins reveal that the association of MBD4 with the MMR protein MLH1 is required for this activity. The described data identify MBD4 as an enzyme specifically designed to repair deaminated 5-methylcytosines and illustrates how MBD4 functions in normal and pathological conditions.

overall_design: Immunoprecipitation of 5mC- and 5hmC-modified DNA isolated from WT (Mbd4+/+) and KO (Mbd4-/-) mouse embryonic fibroblasts. 10 µg of DNA was used as input, and 2 µl of 5mC antibody (Active Motif, 39649) or 4 µl of 5hmC antibody (Active Motif, 39791) was used to immunoprecipitate modified DNA. Four independent DNA immunoprecipitations were pooled for each condition before sequencing analysis.

first: Ali

last: Hamiche


title: Transcripts identified by microarray analysis that were deregulated in E14.5 Tbx18(cre/+);Gata6(fl/fl) (Gata6cKO) ureters

status: Public on Jan 04 2022

city: Hannover

first: Andreas

last: Kispert

address: Carl-Neuberg-Str. 1

department: Molekularbiologie

institute: Medizinische Hochschule Hannover

summary: Evaluation of the transcriptional changes in E14.5 ureters upon loss of Gata6 in the ureteric mesenchyme.

overall_design: Total RNA from dissected ureters of E14.5 Gata6cKO and control embryos was analyzed by microarray analysis.


title: Identification by RNAsequencing of deregulated genes due to the loss of Prdm12 in dorsal root ganglia of mice in inflammatory condition

summary: Loss of Prdm12 deregulates a similar set of gene in dorsal root ganglia of adult mice in naive and inflammatory condition

overall_design: RNA-seq analysis on lumber dorsal root ganglia (L3-L4-L5) of Rosa26CreERT2; Prdm12 Fl/Fl inducible conditional knock-out formalin injected (n=4) and non injected (n=5) versus controls formalin injected (n=5) and non injected (n=5) one month after tamoxyfen injection


title: Identification by RNA-seq of Prdm12 regulated genes

status: Public on Jan 25 2022

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

overall_design: Refer to individual Series


overall_design: Methylome (RRBS) analysis of mouse embryonic fibroblasts isolated from Mbd4+/+ (WT) and Mbd4-/- (KO) mice.


overall_design: Transcriptome (RNA-seq) analysis of mouse embryonic fibroblasts isolated from Mbd4+/+ (WT) and Mbd4-/- (KO) mice.


title: Single-cell characterization of neovascularization using hiPSC-derived endothelial cells in a 3D microenvironment

status: Public on Mar 08 2022

city: Neuherberg

first: Simon

middle: Thomas

last: Rosowski

state: bayern

address: Ingolstädter Landstr 1

department: HPC

institute: Helmholtz Zentrum München

summary: The formation of vascular structures is fundamental for in vitro tissue engineering. Vascularization can enable the nutrient supply within larger structures and increase transplantation efficiency, which are currently limiting factors in organoid research. We differentiated human induced pluripotent stem cells toward endothelial cells in 3D suspension culture. To investigate in vitro neovascularization and various 3D microenvironmental approaches, we designed a comprehensive single-cell transcriptomic study. Time-resolved single-cell transcriptomics of the endothelial and co-evolving mural cells gave insights into cell type development, stability, and plasticity. Transfer to a 3D hydrogel microenvironment induced neovascularization and facilitated tracing of sprouting, coalescing, and tubulogenic endothelial cells states. During maturation, we monitored two pericyte subtypes evolving of mural cells. Profiling cell-cell interactions between pericytes and endothelial cells confirmed in vivo angiogenic signaling and emphasized new cytokine signals during tubulogenesis. Our data, analyses, and results provide an in vitro roadmap to guide vascularization in future tissue engineering.

overall_design: single-cell RNA sequencing of hiPSC-derived endothelial cells in different 3D microenvironments to study differentiation efficiency and impacts on sprouting, tubulogenesis, and cell type maturation

first: Caroline

last: Braehler

first: Maren

last: Marder

first: Misao

last: Akishiba

first: Alina

last: Platen

first: Siegfried

last: Ussar

first: Fabian

last: Theis

first: Sandra

last: Wiedenmann

first: Matthias

last: Meier


title: The gene expression difference of African swine Fever virus (ASF) outer membrane protein CD2v in iPAM cell line analyzed by RNA-SEQ

status: Public on Dec 01 2021

city: Minhang District

first: Min

last: Zhang

state: Shanghai

address: 518 Ziyue RD

department: The viruses and Swine diseases of reproductive failures

institute: Shanghai Veterinary Research Institute, CAAS

summary: We constructed a stable iPAM cell line expressing ASFV-CD2 protein using lentivirus system, which has the function of CD2v protein agglutinating red blood cells. In order to study the changes of intracellular gene expression caused by CD2v protein expression, we constructed iPAM control cell lines expressing GFP protein, and then we performed library construction and RNA-SEQ analysis for the total RNA of the two cell lines.

first: Changlong

last: Liu

first: Lilei

last: Lv

first: Hongming

last: Cai


title: Circadian regulation of lung repair and regeneration

status: Public on Nov 30 2021

city: Philadelphia

first: Amruta

last: Naik

state: PA

address: 3400 CIVIC CENTER BLVD

institute: Children's Hospital of Philadelphia

summary: To elucidate the mechanistic basis of the regenerative deficiency seen with clock disruption we undertook an unbiased approach with single-cell RNA sequencing (scRNA-seq) of epithelial and mesenchymal cells from Bmal1-/-, Bmal1creERT2/+, and their respective WT littermates

overall_design: Lungs from embryonic Bmal1-/-, Bmal1+/+ controls, Bmal1creERT2/+, and Bmal1creERT2neg littermates were dissected, and single-cell preparation was obtained as described above. Single cell suspension was sorted as DARQ7-CD31-CD45- lung cells

first: Shaon

last: Sengupta


title: RNA-Seq timecourse of Chlamydomonas reinhardtii strain CC-849 hydrogen production

status: Public on Dec 31 2021

city: Beijing

first: Zhenzhen

last: Yang

address: Building 104,Beichen West Road No.1,Chaoyang District

institute: Beijing Institute of Genomics,CAS


title: Rapid and robust directed differentiation of mouse epiblast stem cells into definitive endoderm and forebrain organoids II

city: New York

first: Daniel

last: Medina Cano

email: medinacd@mskcc.org, dmcdmc156@gmail.com

address: 411E 67th St

department: Developmental Biology

institute: MSKCC

summary: Mouse is the pre-eminent model system for studying genetic regulation of embryonic development. Directed differentiation of pluripotent stem cells (PSCs) has emerged as a powerful complement to in vivo studies of development, allowing for examination of developmental mechanisms at the molecular and cellular level. However, the limited availability of high-quality protocols for directed differentiation of mouse PSCs into defined lineages and organoids has prevented the widespread application of mouse PSC directed differentiation models. Here, we examine the potential of mouse epiblast stem cells (EpiSCs) cultured in media containing Wnt pathway inhibitors (primed ground state conditions) as a starting point for directed differentiation. First, we systematically optimized conditions to generate definitive endoderm that are significantly faster and more efficient than current state-of-the-art protocols for mouse PSCs. Second, we developed a robust protocol for generation of forebrain-patterned organoids. These new models can complement and empower in vivo studies in the mouse and can inform human PSC-based studies of development, which cannot readily be compared to analogous stages in vivo.

overall_design: Day 12 mouse forebrain organoids were dissociated into single cells with accutase, washed with PBS and used for scRNA-seq (10x Genomics, Single Cell 3' Kit v3.1, dual index)

last: Medina-Cano

first: Thomas

last: Vierbuchen

first: Mohammed

last: Islam


title: Time-Series Single Cell RNA Sequencing of Inner Ear Organoid Development

status: Public on Nov 23 2021

first: Karl

last: Koehler

address: 3 Blackfan Cir

institute: Boston Children's Hospital

summary: We report the application of single cell RNA sequencing for determining cell type and quantity in developing inner ear organoids derived from human pluripotent stem cells. By obtaining samples from multiple time points throughout differentiation, we developed a roadmap at single cell resolution of the multiple cell lineages which give rise to in vitro inner ear tissue as well as 'off-target' tissue types. We find that the cells in the day 0 sample contained primarily a homogenous population of pluripotent stem cells. On day 3, after treatment with BMP4, we find that the cells have differentiated into a split between surface ectoderm, the progenitor of the inner ear tissue, and neuroectoderm. On day 6 and 8, we observed the emergence of cranial placode tissue, both anterior and posterior. Then, after treatment starting on day 8 with a WNT agonist, CHIR, we observed the maturation of inner ear tissue into hair cells and neurons, starting on day 18 and increasing through the last time point collected, day 36. This study provides an atlas of inner ear organoid differentiation from human pluripotent stem cells.

overall_design: We examined 10 time points during the differentiation of inner ear organoids by single cell RNA-sequencing. We also collected samples for comparison at days 10 and 13 which did not receive CHIR treatment.

first: Matthew

last: Steinhart


title: The role of ATXR6 expression in modulating genome stability and transposable element repression in Arabidopsis [RNA-seq_med]

city: Los Angeles

first: magdalena

middle: ewelina

last: potok

address: 4045 Terasaki Life Sciences Building

department: MCDB

institute: UCLA

summary: ARABIDOPSIS THRITHORAX-RELATED PROTEINS 5 (ATXR5) AND ATXR6 are required for the deposition of H3K27me1 and for maintaining genomic stability in Arabidopsis. Reduction of ATXR5/6 activity results in activation of DNA damage response genes, along with tissue-specific derepression of transposable elements, chromocenter decompaction, and genomic instability characterized by accumulation of excess DNA from heterochromatin. How loss of ATXR5/6 and H3K27me1 leads to these phenotypes remains unclear. Here we provide extensive characterization of the atxr5/6 hypomorphic mutant by comprehensively examining gene expression and epigenetic changes in the mutant. We found that the tissue-specific phenotypes of TE derepression and excessive DNA in this atxr5/6 mutant correlated with residual ATXR6 expression from the hypomorphic ATXR6 allele. However, upregulation of DNA damage genes occurred regardless of ATXR6 levels and thus appears to be a separable process. We also isolated an atxr6 null allele which showed that ATXR5 and ATXR6 are required for female germline development. Finally, we characterize three previously reported suppressors of the hypomorphic atxr5/6 mutant and show that these rescue atxr5/6 via distinct mechanisms, two of which involve increasing H3K27me1 levels.

overall_design: Total RNA was extracted from four-week-old rosette leaves grown on soil under long day conditions.  Two to three replicates from seperate plants were collected for each genotype.  RNA was extracted using Direct-zol RNA Miniprep kit (Zymo).

first: Magdalena

last: Potok

first: Steven

last: Jacobsen


title: The role of ATXR6 expression in modulating genome stability and transposable element repression in Arabidopsis [SMARTSeq2]

sample_organism:
Arabidopsis thaliana
blank sample

platform_organism:
Arabidopsis thaliana
blank sample

overall_design: Fresh nuclei  isolated from two-week-old cotyledons  grown on 1%MS under long day conditions were isolated as follows.  Roughly 50 cotyledons were finely chopped with razor into 50 ul Partec nuclei extraction buffer (Sysmex America, 05-5002), and stained with 400 ul Partec nuclei staining buffer. Samples were filtered once through a 35um nylon mesh (Falcon, 352235) and subjected to fluorescent activated nuclei sorting. Nuclei were sorted from 2C, 4C, 8C and 16C peaks based on DAPI fluorescence. 50 nuclei from each peak were sorted into individual wells of a 96 well plate. Three to four replicates per ploidy/genotype were collected. Negative controls, with no nuclei sorted into a well, were included in every plate and carried through library preparation and sequencing.


title: Rapid and robust directed differentiation of mouse epiblast stem cells into definitive endoderm and forebrain organoids I

overall_design: Examination of chromatin accessibility profile and bulk transcriptome in mouse epiblast stem cells (mEpiSCs) in culture and mouse definitive endoderm samples (DE) obtained after differentiation of mEpiSCs during 46h and MACS-based sorting of the CXCR4 positive cells. Additionally, we compare the transcriptome and chromatin accesbility profile of the EpiSCs across different genetic backgrounds

first: Emily

last: Corrigan

first: Rachel

last: Glenn


title: The role of ATXR6 expression in modulating genome stability and transposable element repression in Arabidopsis [RNA-seq_22]

overall_design: Total RNA was extracted from two-week-old cotyledons grown on 1%MS under long day conditions. Four replicates, grown on separate plates were collected for each genotype.Each replicate conisted of ~ 20 cotyledons. RNA was extracted using Direct-zol RNA Miniprep kit (Zymo)


title: The role of ATXR6 expression in modulating genome stability and transposable element repression in Arabidopsis [RNA-seq_20]

overall_design: Total RNA was extracted from four-week-old floral buds grown on soil under long day conditions.  Three replicates from seperate plants were collected for each genotype. Each replicate conisted of 4 floral bud. RNA was extracted using Direct-zol RNA Miniprep kit (Zymo).


title: The role of ATXR6 expression in modulating genome stability and transposable element repression in Arabidopsis [RNA-seq_16]

overall_design: Total RNA was extracted from two-week-old cotyledons grown on 1%MS under long day conditions. Four replicates, grown on separate plates were collected for each genotype. Each replicate conisted of ~ 20 cotyledons. RNA was extracted using Direct-zol RNA Miniprep kit (Zymo)


title: The role of ATXR6 expression in modulating genome stability and transposable element repression in Arabidopsis [RNA-seq_15]

overall_design: Total RNA was extracted from two-week-old cotyledons grown on 1%MS under long day conditions. A single replicate was collected for each genotype. Each replicate conisted of ~ 20 cotyledons. RNA was extracted using Direct-zol RNA Miniprep kit (Zymo)


title: Identification by RNA-seq of Prdm12 regulated genes in dorsal root ganglia of adult mice

first: Gabriela

last: Salinas

summary: Loss of Prdm12 induces gene deregulation in mature dorsal root ganglia neurons of adult mice

overall_design: RNAseq on DRG of Rosa26CreERT2; Prdm12 Fl/Fl (n=6 ) and Control (n=6) one month after tamoxifen injection.

first: Eric

last: Bellefroid

first: Orr

last: Shomroni

first: Alba

last: Sabaté


title: The role of ATXR6 expression in modulating genome stability and transposable element repression in Arabidopsis [RNA-seq_17-18]

overall_design: Total RNA was extracted from two-week-old cotyledons grown on 1%MS under long day conditions. Four replicates, grown on separate plates were collected for each genotype. Each replicate conisted of ~ 20 cotyledons. RNA was extracted using Direct-zol RNA Miniprep kit (Zymo). RNA for stubl2-3 atxr5/6 (W) genotype was successfully extracted for only two out of four replicates.


title: The role of ATXR6 expression in modulating genome stability and transposable element repression in Arabidopsis [RNA-seq-12_13]

overall_design: Total RNA was extracted from two-week-old roots grown on 1%MS under long day conditions. Four replicates, grown on separate plates were collected for each genotype.Each replicate conisted of ~ 10 roots from individual plants. RNA was extracted using Direct-zol RNA Miniprep kit (Zymo)


title: The role of ATXR6 expression in modulating genome stability and transposable element repression in Arabidopsis [RNA-seq_9_12]


title: The role of ATXR6 expression in modulating genome stability and transposable element repression in Arabidopsis [RNA-seq_5_6]

overall_design: Total RNA was extracted from two-week-old cotyledons grown on 1%MS under long day conditions. A single replicate was collected for each genotype.Each replicate conisted of ~ 20 cotyledons. RNA was extracted using Direct-zol RNA Miniprep kit (Zymo)


title: The role of ATXR6 expression in modulating genome stability and transposable element repression in Arabidopsis [RNA-seq_11]


title: The role of ATXR6 expression in modulating genome stability and transposable element repression in Arabidopsis [DNA-seq]

overall_design: DNA-seq in rosette leaves in atxr5/6 (W) mutants.


title: The role of ATXR6 expression in modulating genome stability and transposable element repression in Arabidopsis [ChIP-seq_27]

overall_design: Examination of H3K27me1 profiles in 4-week-old leaves in atxr5/6 (W) mutants.


title: The role of ATXR6 expression in modulating genome stability and transposable element repression in Arabidopsis [ChIP-seq_25]

overall_design: Examination of H3K27me1 profiles in 4-week-old rosette leaves in atxr5/6 (W) mutants.


title: The role of ATXR6 expression in modulating genome stability and transposable element repression in Arabidopsis

overall_design: Refer to individual Series


title: Genome-wide maps of Transcriptionalregulation of EGR1 transcription factor in iPAM cells.

status: Public on Nov 20 2021

first: Min

last: Zhang

summary: We applied single-molecule sequencing and high-throughput analysis to analyze the regulation of EGR1 transcription in iPAM cells. By obtaining more than 4 billion base sequences from chromatin immunoprecipitation DNA, we generated a genome-wide chromatin state map of transcriptional regulation of EGR1 transcription factors in iPAM cells. Then, we analyzed the influence of EGR1 transcription regulation on macrophages by analyzing the binding position of EGR1 transcription factor to the genome.

overall_design: Examination of EGR1 ranscriptional regulation in iPAM cells.

first: Changlong

last: Liu

first: Lilei

last: Lv

first: Hongming

last: Cai


title: EP300 selectively controls the enhancer landscape of MYCN-amplified neuroblastoma [CUT&RUN]

status: Public on Nov 09 2021

city: Memphis

first: Brian

last: Abraham

state: TN

address: 262 Danny Thomas Blvd

department: Computational Biology

institute: St. Jude Children's Research Hospital

summary: Gene expression is regulated by promoters and enhancers marked by histone H3-lysine-27 acetylation (H3K27ac), which is established by the paralogous histone acetyltransferases (HATs), EP300 and CBP. These enzymes display overlapping regulatory roles in untransformed cells, but less characterized roles in cancer cells. We demonstrate that the majority of high-risk pediatric neuroblastomas (NB) depend on EP300, whereas CBP has a limited role. EP300 controls enhancer acetylation by interacting with TFAP2β, a transcription factor member of the lineage-defining transcriptional core regulatory circuitry (CRC) in NB. To disrupt EP300, we developed a proteolysis-targeted-chimaera (PROTAC) compound termed “JQAD1” that selectively targets EP300 for degradation. JQAD1 treatment causes loss of H3K27ac at CRC enhancers and neuroblastoma apoptosis, with limited toxicity to untransformed cells where CBP compensates. Comparing HAT inhibition and EP300-specific degradation, we identified a non-catalytic role for EP300 in promoting MYCN expression and repression of apoptosis.

overall_design: CUT&RUN-sequencing targeting H3K27ac-marked nucleosomes in Kelly neuroblastoma cells

first: Adam

last: Durbin

first: Tingjian

last: Wang

first: Virangika

middle: K

last: Wimalasena

first: Mark

middle: W

last: Zimmerman

first: Deyao

last: Li

first: Neekesh

middle: V

last: Dharia

first: Luca

last: Mariani

first: Noha

last: Shendy

first: Stephanie

last: Nance

first: Anand

last: Patel

first: Ying

last: Shao

first: Maya

last: Mundada

first: Lily

last: Maxham

first: Paul

last: Park

first: Logan

last: Sigua

first: Ken

last: Morita

first: Amy

last: Conway

first: Amanda

last: Robichaud

first: Antonio

last: Perez-Atayde

first: Melissa

last: Bikowitz

first: Taylor

last: Quinn

first: Olaf

last: Wiest

first: John

last: Easton

first: Ernst

last: Schönbrunn

first: Martha

last: Bulyk

first: Kimberly

last: Stegmaier

first: A

middle: T

last: Look

first: Jun

last: Qi


title: EP300 selectively controls the enhancer landscape of MYCN-amplified neuroblastoma [RNA-seq]

first: Brian

last: Abraham

summary: Gene expression is regulated by promoters and enhancers marked by histone H3-lysine-27 acetylation (H3K27ac), which is established by the paralogous histone acetyltransferases (HATs), EP300 and CBP. These enzymes display overlapping regulatory roles in untransformed cells, but less characterized roles in cancer cells. We demonstrate that the majority of high-risk pediatric neuroblastomas (NB) depend on EP300, whereas CBP has a limited role. EP300 controls enhancer acetylation by interacting with TFAP2?, a transcription factor member of the lineage-defining transcriptional core regulatory circuitry (CRC) in NB. To disrupt EP300, we developed a proteolysis-targeted-chimaera (PROTAC) compound termed ?JQAD1? that selectively targets EP300 for degradation. JQAD1 treatment causes loss of H3K27ac at CRC enhancers and neuroblastoma apoptosis, with limited toxicity to untransformed cells where CBP compensates. Comparing HAT inhibition and EP300-specific degradation, we identified a non-catalytic role for EP300 in promoting MYCN expression and repression of apoptosis.

overall_design: RNA-seq in neuroblastoma model systems treated with JQAD1 or A485

first: Adam

middle: D

last: Durbin

first: Tingjian

last: Wang

first: Virangika

last: Wimalasena

first: Mark

last: Zimmerman

first: Deyao

last: Li

first: Neekesh

last: Dharia

first: Luca

last: Mariani

first: Noha

last: Shendy

first: Stephanie

last: Nance

first: Anand

last: Patel

first: Ying

last: Shao

first: Maya

last: Mundada

middle: S


title: EP300 selectively controls the enhancer landscape of MYCN-amplified neuroblastoma [RNA-seq xenograft]

middle: J

overall_design: RNA-seq in neuroblastoma xenograft system treated with JQAD1 or vehicle

first: Lily

last: Maxham

first: Paul

last: Park

first: Logan

last: Sigua

first: Ken

last: Morita

first: Amy

last: Conway

first: Amanda

last: Robichaud

first: Antonio

last: Perez-Atayde

first: Melissa

last: Bikowitz

first: Taylor

last: Quinn

first: Olaf

last: Wiest

first: John

last: Easton

first: Ernst

last: Schönbrunn

first: Martha

last: Bulyk


title: Ultrafine Mapping of Chromosome Conformation at hundred basepair resolution reveals regulatory genome architecture

status: Public on Nov 02 2021

city: Bronx

first: Yizhou

last: Zhu

address: Price469 1301 Morris Park Ave

department: Genetics

institute: Albert Einstein College of Medicine

summary: The resolution limit of chromatin conformation capture methodologies (3Cs) has restrained their application in detection of fine-level chromatin structure mediated by cis-regulatory elements (CREs). Here we report two 3C-derived methods, Tri-4C and Tri-HiC, utilizing mult-restriction enzyme digestions capable of achieveing ultrafine genome digestion for targeted and global chromatin interaction mapping, respectively, at a one hundred basepair resolution. Tri-4C identified loops associated with CREs including those involving regulatory elements devoid of typical epigenomic marks, quantifatively revealing alterations in interaction networks underlying dynamic gene control. Tri-HiC successfully uncovers fine-gage enhancer:promoter (E:P) loops at genome-wide level, identifying > 20-fold more CRE loops than in situ HiC. In addition to refined loop detection, Tri-HiC also reveals interaction stripes and contact domain insulation from promoters and enhancers, revealing their loop extrusion behaviors resembling the topologically-associated domain (TAD) boundaries. Tri-4C and Tri-HiC provide robust approaches to achieve the high resolution interactome maps required for characterizing fine-gage regulatory chromatin interactions in analysis of development, homeostasis and disease.

overall_design: High resolution mapping of global long range chromatin interaction in IMR90 cells

first: Yousin

last: Suh


title: Avian ceca are required for hindgut enteric nervous system development by promoting enteric neural crest cell proliferation and inhibiting neuronal differentiation via non-canonical Wnt signaling

status: Public on Nov 01 2021

first: Rhian

last: Stavely

address: 185 Cambridge Street, CPZN, 6100

department: Pediatric Surgery

institute: Massachusetts General Hospital

summary: The enteric nervous system (ENS), which is derived from enteric neural crest cells (ENCCs) during gut development, represents the neuronal innervation of the gastrointestinal tract and is critical for regulating normal intestinal function. Compromised ENCC migration can lead to Hirschsprung Disease, which is characterized by an aganglionic distal bowel. We find that removal of the ceca, a paired structure present at the midgut-hindgut junction in avian intestine, leads to severe hindgut aganglionosis, suggesting that the ceca are required for ENS development. To test this, we replaced the ceca of embryonic day 6 (E6) wild-type chicks with ceca from transgenic GFP chicks. Interestingly, the entire hindgut ENS arises from the GFP+ ceca-derived ENCC population. Comparative transcriptome profiling of the cecal buds compared to the interceca region shows that the non-canonical Wnt signaling pathway is preferentially expressed within the ceca. Specifically, Wnt11 is highly expressed in the ceca, as confirmed by RNA in situ hybridization, leading us to hypothesize that cecal expression of Wnt11 is important for ENCC colonization of the hindgut. Organ cultures were prepared using E6 avian intestine, when ENCCs are migrating through the ceca, and showed that Wnt11 inhibits enteric neuronal differentiation. These results reveal an essential role for the ceca during hindgut ENS formation and highlight an important function for non-canonical Wnt signaling in regulating ENCC differentiation and thereby promoting their migration into the colon.

overall_design: Examination of mRNA profiles in the ceca and interceca of E5/HH26 chick embryos

first: Nandor

last: Nagy

first: Tamas

last: Kovacs

first: Viktoria

last: Halasy

first: Adam

last: Soos

first: Emoke

last: Szocs

first: Ryo

last: Hotta

first: Hannah

last: Graham

first: Allan

middle: M

last: Goldstein


title: Lineage tracing and single-cell analysis reveal proliferative Prom1+ tumor-propagating cells and their dynamic cellular transition during liver cancer progression

status: Public on Oct 04 2021

city: Hong Kong

first: Ken Hung-On

last: Yu

address: 21 Sassoon Road, Pokfulam

department: School of Biomedical Sciences

institute: The University of Hong Kong

summary: Hepatocellular carcinoma (HCC) is highly heterogeneous, and this heterogeneity contributes to therapeutic resistance and tumor recurrence. The aim of this study was to investigate the role, heterogeneity, and properties of Prom1+ cells in HCC in intact mouse models. We used Prom1C-L/+;Rosa26tdTomato/+ mice to establish two HCC mouse models representing chronic fibrotic HCC and rapid steatosis-related HCC. We performed lineage tracing at different time points post-HCC induction. We ablated the Prom1+ cell population in Prom1C-L/+;Rosa26DTA/+ mice. Single cell RNA-seq (scRNA-seq) was carried out to analyse the lineage properties, heterogeneity, and dynamics of the traced Prom1+ cells in the chronic fibrotic HCC model. Bulk RNAseq was carried out to analyse the change in transcriptome in Prom1 depleted tumor.

overall_design: scRNA-seq: Prom1-CreERT2-LacZ mice crossed with Rosa26-LSL-Tomato reporter mice were used (Prom1C-L/+;Rosa26tdTomato/+). HCC was induced by DEN+CCL4 treatment: mice were treated with N-nitrosodiethylamine (DEN, i.p., 1 mg/kg) at the age of 14 days; when the mice were 8 weeks of age, carbon tetrachloride (CCL4, i.p., 0.2 ml/kg) was administered twice weekly for 12-16 weeks. After tumor nodules formed (12 weeks after CCL4 treatment initiated), a single dose of 4mg tamoxifen were administrated to the mice. 3, 10 and 30 days thereafter, all viable tdTomato+ and tdTomato- tumor resident cells were sorted and sequenced by 10X Genomics to reconstruct a single-cell landscape of HCC tumors.   Bulk RNA-seq: Prom1C-L/+;Rosa26DTA/+ mice and their control littermates (Prom1+/+;Rosa26DTA/+) were used. DEN+CCL4 model was established as above mentioned. N-Ras+AKT model was established by hydrodynamic tail vein injection of 20 μg of pT3-EF1a-NRasV12, 20 μg of pT3-EF1a-myr-AKT and 1.6 μg sleeping beauty transposase to the mice. Multiple doses of 4mg tamoxifen or vehicle (olive oil) were administered every other day after tumor formed. Tumor tissues were collected 16 or 6 days after the last dose of tamoxifen treatment in DEN+CCL4 or N-Ras+AKT model, respectively.

first: Lei

last: Zhou

first: Ken

middle: H

first: Tin-Lok

last: Wong

first: Zhao

last: Zhang

first: Chun-Ho

last: Chan

first: Jane

last: Loong

first: Noélia

last: Che

first: Hua-Jian

first: Kel

last: Tan

first: Man

last: Tong

first: Elly

last: Ngan

first: Joshua

last: Ho

first: Stephanie

last: Ma


title: Efficient stimulation of retinal regeneration from Muller glia in adult mice using combinations of proneural bHLH transcription factors.

status: Public on Oct 19 2021

city: SEATTLE

first: THOMAS

last: REH

state: WA

address: 1959 NE PACIFIC STREET

department: BIOLOGICAL STRUCTURE

institute: UNIVERSITY OF WASHINGTON

summary: Regenerative neuroscience aims to stimulate endogenous repair mechanisms in the nervous system to replace neurons that have been lost from degenerative diseases or trauma.  In the retina, many non-mammalian vertebrate species spontaneously regenerate retinal neurons from glial cells, through an injury-induced reprogramming of the cells to a retinal progenitor state. Recently, we have reported that engineering mouse Muller glia to express a retinal progenitor gene, the proneural transcription factor, Ascl1, is sufficient to stimulate neurogenesis in the glia to generate functional neurons. However, this process is inefficient and only a third of the Ascl1-expressing glia generate new neurons. Here we test whether proneural transcription factors of the Atoh1/7 class can further promote the neurogenic capacity of MG. We report that the combination of Ascl1:Atoh1 is remarkably efficient at stimulating neurogenesis (>80% expressing cells), even in the absence of retinal injury or TSA. We use electrophysiology and scRNA-seq to demonstrate that Ascl1:Atoh1 generates a diversity of retinal neuron types with the majority expressing characteristics of retinal ganglion cells. Overall, our results provide a proof-of-principle that transcription factors that are normally sequentially active in cell fate specification, can when combined, substantially improve glial reprogramming to neurons and expand the repertoire of cell fates that can be regenerated in the adult mouse retina.  The ability to stimulate the neurogenic potential of glia in adult mice with high efficiency is a key step towards translation of this approach to repair the central nervous system.

overall_design: This submission includes 4 scRNA-seq samples. The Control cultured glia sample contains cultured mouse glia treated infected with a lentivirus containing RFP. The Atoh7 5day in vitro sample contains cultured mouse glia infected with pLOC-hATOH7-IRES-copGFP virus. The Ascl1 5day in vitro sample contains cultured glia  infected with pLOC-hAscl1-IRES-turboGFP virus. Lastly there is a sample of retinal cells from Glast-CreER:LNL-tTA:tetO-mAscl1-tetO-Atoh1-ires-GFP mice. All samples were FACS sorted to identify affected cells.

first: Levi

last: Todd

first: Marcus

last: Hooper

first: Alexandra

last: Haugan

first: Connor

last: Finkbeiner

first: Nikolas

last: Jorstad

first: Nicholas

last: Radulovich

first: Claire

first: Phoebe

middle: C

last: Donaldson

first: Wesley

last: Jenkins

first: Qiang

last: Chen

first: Fred

last: Rieke

first: Thomas

last: Reh


title: Mapping the global chromatin connectivity network in colorectal cancer cell HCT116 and Oxaliplatin-resistant cell HCT116OxR

status: Public on Oct 01 2021

city: Ji'nan

first: lian

middle: qing

last: jiao

state: Shandong Province

address: 247 Beiyuan Road

institute: the Second Hospital of Shandong University


title: The role of ATXR6 expression in modulating genome stability and transposable element repression in Arabidopsis [RNA-seq_2_3]

first: magdalena

last: potok

overall_design: Total RNA was extracted from four-week-old rosette leaves grown on soil under long day conditions.  Three replicates from seperate plants were collected for each genotype. Each replicate conisted of 1 rosette leaf. RNA was extracted using Direct-zol RNA Miniprep kit (Zymo)

first: Magdalena

last: Potok

first: Steven

last: Jacobsen


title: c-MAF defines the phenotype of a family of perivascular macrophages

status: Public on Sep 30 2021

city: NEW YORK

first: Hernandez

last: Moura Silva

address: 430 E 29th street. 4th floor, Lab 460A

department: Kimmel Center for Biology and Medicine at the Skirball Institute

institute: New York University Langone Medical Center

summary: Tissue-resident Macrophages have long been appreciated as playing a fundamental role in the ontogeny and function of several organs.  For example, osteoclasts are crucial for proper bone remodeling, microglia for synaptic pruning, and lung alveolar macrophages for clearance of surfactant.  Perivascular macrophages have been described in many organs.  Our analysis of murine perivascular macrophages in several tissues and organs led us to define a macrophage family, whose members share the expression of a number of surface molecules that are not typically considered macrophage markers, such as Lyve1, Folate Receptor 2 (Folr2), Enpep/CD249, and CD38, as well as other more typical macrophage markers such as CD206 and Tim4.  This family of perivascular macrophages also occurs in humans.  Importantly, this family of perivascular macrophages relies on the transcription factor c-MAF, encoded by the gene Maf, for its full function. Conditional deletion of the Maf gene in the Lyve1+Folr2+CD38+ macrophage family caused their ablation in the brain, without impact on the microglia, while in the adipose tissue the conditional deletion of the Maf gene in perivascular macrophages resulted in a profoundly altered macrophage gene expression, and brought about an increased vascular branching in this tissue. Mice with conditional Maf deletion were protected from metabolic syndrome when submitted to high fat diet (HFD). Our results show that c-MAF is the master regulator of a family of perivascular macrophages.

overall_design: Examination of RNA expression changes in Perivascular macrophages from epididymal adipose tissue. Macrophages conditionallly ablated of CMAF expression were compared to WT counterparts

first: Juan

last: Lafaille

last: Silva


title: Mapping the global chromatin connectivity network in colorectal cancer cell HCT116 and Oxaliplatin-resistant cell HCT116OxR [RNA-seq]

summary: Numerous studies have highlighted the critical role of genetic and epigenetic modifications in the regulation of oxaliplatin resistance, but whether changes involving chromatin structure have not been fully investigated. We have integrated a variety of techniques to explore a comprehensive overview of chromatin changes in oxaliplatin-resistant processes.

overall_design: HCT116 cells and oxaliplatin-resistant HCT116 cells, HCT116OxR

first: Yunshan

last: Wang

first: Qinlian

last: Jiao


title: Whole gene transcriptomic analysis of testosterone/17 beta-estradiol degrading in Comamonas testosteroni JLU460ET

status: Public on Sep 17 2021

city: Changchun city

first: Tingdi

last: Zhang

state: Jilin Province

address: 2519 Jiefang Road

department: college of new energy and environment

institute: Jilin University

summary: Purpose: find testosterone/17 beta-estradiol degrading genes in strain  Comamonas testosteroni JLU460ET

overall_design: Strain  Comamonas testosteroni JLU460ET was incabated with testosterone or 17 beta-estradiol. Samples were collected at different incubation time points for RNA sequencing.

first: Zhang

last: tingdi

first: Zhao

last: yongkang

first: Chen

last: mingming

first: Ru

last: jintao


title: Transposon-triggered innate immune response confers cancer resistance to the blind mole rat

status: Public on Sep 09 2021

city: Rochester

first: Yang

last: Zhao

address: 60 Crittenden Blvd, Apt1240

department: Biology

institute: University of Rochester

type: Methylation profiling by genome tiling array

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

sample_organism:
Mus musculus
Nannospalax ehrenbergi

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus
Nannospalax ehrenbergi


title: Transposon-triggered innate immune response confers cancer resistance to the blind mole rat [seq]

summary: Blind mole rats (BMRs) are small rodents, characterized by exceptionally long lifespan (> 21 years) and resistance to both spontaneous and induced tumorigenesis. Here we report that cancer resistance in the BMR is mediated by retrotransposable elements (RTEs). BMR cells and tissues express very low levels of DNA methyltransferase 1 (DNMT1). Upon cell hyperplasia, the BMR genome DNA loses methylation, resulting in activation of RTEs. Up-regulated RTEs form cytoplasmic RNA/DNA hybrids, which activate cGAS-STING pathway to induce cell death. Although this mechanism is enhanced in the BMR, we show that it functions in mice and human. We propose that RTEs were coopted to serve as tumor suppressors that monitor cell proliferation and are activated in premalignant cells to trigger cell death via activation of innate immune response. RTEs activation is a double-edged sword, serving as a tumor suppressor but in late life contributing to aging via induction of sterile inflammation.

platform_organism:
Mus musculus
Nannospalax ehrenbergi

overall_design: RNA sequencing comparing genes and transposons expression between young and old fibroblasts of blind mole rat, as well as different tissues between blind mole rats and mice; MeDIP comparing methylation between young and old fibroblasts of blind mole rat.

first: Vera

last: Gorbunova

first: Andrei

last: Seluanov


title: single-cell RNA-sequencing on human naïve and memory CD4+ T cells during Plasmodium falciparum infection

status: Public on Aug 28 2021

first: Gregoire

last: Lauvau

address: 1301 Morris park

department: M&I

summary: Plasmodium falciparum (Pf) malaria causes high rates of morbidity and mortality and lacks an effective vaccine. Clinical immunity develops in residents of malaria endemic regions which confers reduced clinical symptoms during infection and protects against severe disease. We hypothesized that understanding the immune mechanisms of clinical immunity could inform vaccine design to improve efficacy. We compared the peripheral blood cellular and humoral immune responses during Pf malaria infection between clinically susceptible and protected participants from a malaria endemic region in Malawi during a prospective 18-month longitudinal study. Participant classifications were defined by the number of recurrent clinical malaria episodes with susceptible participants having more than three while protected less than one episode during the study period. Protected participants exhibited higher immunoglobulin G (IgG) breadth and titers against Pf antigens, and greater antibody (Ab)-dependent Pf opsonization compared to susceptible participants, consistent with our classifications. Using high dimensional mass cytometry (CyTOF) and spectral flow cytometry, and single-cell transcriptomic analyses, we identified expanded memory CD4+ T cell clonotypes in the blood of protected participants undergoing malaria infection. These cells express a strong cytolytic T helper 1 effector program with transcripts encoding granzymes (A, B, H, M), granulysin, NKG7 and the ZEB2 master transcriptional regulator of terminally differentiated effector T cells. ZEB2+ memory CD4+ T cells were CD39hiTIGIThi and expressed multiple chemotactic and inhibitory receptors. Yet, their levels of several chemokine and checkpoint inhibitory receptors were reduced in protected compared to susceptible individuals. We propose that clonally expanded ZEB2+ cytolytic memory CD4+ Th1 cells could represent essential contributors to clinical immunity against Pf malaria infection.

overall_design: We sorted naïve and memory CD4+ T cells from frozen PBMC of 3 patients undergoing an episode of Plasmodium falciparum infection by flow cytometry. Sorted cells were applied to the 10x genomics platform to conduct single-cell RNA-sequencing including whole gene expression and V(D)J expression profiles. Single-cell transcriptome profile and TCR alpha and beta sequences of naïve and memory CD4+ T cells were obtained.

first: Raquel

last: Furtado

first: Fabien

last: Delahaye

first: Johanna

last: Daily


title: RNAseq analysis comparing siRNA knocked down FOXF2 in and MKX in human normotrophic scar dermal fibroblasts

status: Public on Aug 27 2021

city: Crawley

first: Andrew

middle: William

last: Stevenson

state: Western Australia

address: Room 112b, Curnow Building, Hackett Drive Carpark Entrance 2, UWA

country: Australia

institute: University of Western Australia

summary: 3mm punch biopsies were taken from a healed normotrophic scar in burn patients with a scar at least 1 year old and fibroblasts were cultured from explants. Previous transcriptomic and epigenomic work found MKX and FOXF2 genes were overexpressed and these were knocked down using siRNA. RNA was then extracted and analysed using RNAseq to determine genes and pathways affected by this knockdown

overall_design: 3 patients fibroblasts were transfected with either scrambled siRNA, MKX siRNA or FOXF2 siRNA

first: Zhenjun

last: Deng


title: The role of ATXR6 expression in modulating genome stability and transposable element repression in Arabidopsis [ChIP-seq_10_12_14]

first: magdalena

last: potok

overall_design: Examination of H3K27me1 profiles in 2-week-old cotyledons in wild type and atxr5/6 (W) mutants.

first: Magdalena

middle: E

last: Potok

first: Steven

last: Jacobsen


title: Genome-wide analysis of enhancer landscape in colorectal cancer subgroups

status: Public on Aug 26 2021

city: Wuhan City

first: Qinglan

last: Li

state: Hubei Province

address: Room 5005, Life Science College, Wuhan University

institute: Wuhan University

overall_design: Refer to individual Series


title: RNA-Seq based analysis of chondroblasts subjected to general caspase inhibition revealed modulation of a spectrum of osteoarthritis related genes

status: Public on Aug 24 2021

city: Brno

first: Martina

last: Zapletalová

address: Kamenice 5

department: Department of Biochemistry

country: Czech Republic

institute: Masaryk University

summary: Objective: The knowledge about functions of caspases, traditionally associated with cell death and inflammation, keeps expanding also regarding cartilage. Active caspases are expressed by chondrocytes within the growth plate and caspase inhibition in limb-derived chondroblasts altered osteogenesis-related genes. Caspase inhibitors were reported to reduce the severity of cartilage lesions in osteoarthritis (OA) and caspase-3 might be a promising biomarker for OA prognosis. Design: To provide an overview about impact of caspase inhibition on expression profile in chondroblasts, the whole transcriptome RNA sequencing was performed. Limb-derived chondroblasts were cultured with two different inhibitors, Z-VAD-FMK (FMK) and Q-VD-OPH (OPH). Results: The analysis revealed a statistically significant increase in the expression of 252 genes in the FMK samples and 163 genes in the OPH samples compared to controls. Conversely, there was a significant decrease in the expression of 290 genes in the FMK group and 188 in the OPH group. Among the top up- and down-regulated genes (more than 10 times changed), almost half of them have been associated with OA. Both inhibitors displayed the highest up-regulation of the inflammatory chemokine Ccl5. In the presence of one or the other inhibitor, the most down-regulated gene was the one for mannose receptors Mrc1.  Conclusion: The results of this investigation yielded not only a list of genes associated with OA as being up- or down-regulated, but also a comprehensive expression profile in primary chondroblasts after general caspase inhibition. Additionally, comparison of the inhibitory impact in the case of FMK inhibitor vs. OPH inhibitor was provided.

overall_design: Examination of 2 different inhibitors, Z-VAD-FMK (FMK) and Q-VD-OPH (OPH), and control group (DMSO). Each condition was done in triplicates.

first: Barbora

last: Vesela

last: Zapletalova

first: Eva

last: Svandova

first: Alice

last: Ramesova

first: Jaroslav

last: Doubek

first: Herve

last: Lesot

last: Matalova


title: CTCF knockout in zebrafish induces alterations in regulatory landscapes and developmental gene expression

status: Public on Aug 02 2021

city: Seville

first: José

middle: M.

last: Santos-Pereira

address: Avda. Manuel Siurot s/n

institute: IBiS, Universidad de Sevilla-CSIC


title: CTCF knockout in zebrafish induces alterations in regulatory landscapes and developmental gene expression [Hi-C]

summary: CTCF is an 11-zinc-finger DNA-binding protein that acts as a transcriptional repressor and insulator, as well as an architectural protein required for 3D genome folding. CTCF mediates long-range chromatin looping and is enriched at the boundaries of topologically associating domains (TADs), which are sub-megabase chromatin structures composed of genomic regions with high contact frequency. Although CTCF is essential for cycling cells and developing embryos, its in vitro removal has only modest effects over gene expression, challenging the generally accepted idea that TADs facilitate enhancer-promoter interactions within gene regulatory landscapes. However, the effects of an altered CTCF-mediated chromatin structure on gene regulation in vivo are poorly understood. Here, we have generated a ctcf knockout mutant in zebrafish that allows us to monitor the effect of CTCF loss of function during embryo patterning and organogenesis. CTCF absence leads to a loss of chromatin structure in zebrafish embryos and affects the expression of thousands of genes, among them many developmental genes. In addition, we show that chromatin accessibility, both at CTCF sites and at developmental cis-regulatory elements (CREs), is severely compromised in ctcf mutants. Probing chromatin interactions from developmental genes at high resolution, we further demonstrate that promoters fail to fully establish long-range contacts with their associated regulatory landscapes, leading to altered gene expression patterns during development. Therefore, our results demonstrate that CTCF and TADs are essential to finetune gene expression during embryonic development, providing the structural basis for the establishment of developmental gene regulatory landscapes.

overall_design:
Hi-C assays in wild-type and ctcf zebrafish mutants, at developmental stage 48 hpf
Please note that each processed dat file was generated from both rep1 and rep2 samples, and is linked to the corresponding rep1 sample records.

first: Martin

last: Franke

first: Elisa

last: De la Calle-Mustienes

first: Ana

last: Neto

first: María

last: Almuedo-Castillo

first: Ibai

last: Irastorza-Azcárate

first: Rafael

last: Acemel

first: Juan

last: Tena

middle: L

last: Gómez-Skarmeta


title: Mapping the global chromatin connectivity network in colorectal cancer cell HCT116 and Oxaliplatin-resistant cell HCT116OxR [ChIP-seq]

first: lian

last: jiao

first: Yunshan

last: Wang

first: Qinlian

last: Jiao


title: RNAseq of wild type and GDF11-/- Neuro-2a cells

status: Public on Oct 06 2021

city: Hangzhou

first: Dixian

state: Zhejiang

address: Yuhangtang Road No.866

department: School of Basic Medical Sciences

institute: Zhejiang University

summary: Growth differentiation factor 11 (GDF11), is one of the members of transforming growth factor β (TGFβ) superfamily. We set out to unequivocally reveal the effect of endogenous GDF11 on biological process by adopting CRISPR/Cas9 gene knockout strategy to specifically delete GDF11 gene in Neuro-2a cells. We analyze mRNA profiles of differentially genes in wild type (WT) and GDF11 knockout (GDF11-/-) Neuro-2a cells by using RNA-seq technology. The RNA-seq data reported here provide a fundamental materials and evidence for investigations of biological function of GDF11.

overall_design: Examination of mRNA profiles in wild type (WT) and GDF11-/- Neuro-2a cells.

first: Jingwei

last: Zhao


title: Mapping the global chromatin connectivity network in colorectal cancer cell HCT116 and Oxaliplatin-resistant cell HCT116OxR [Hi-C]


title: A single-cell atlas of the microenvironment of implanted biomaterials and computational analysis of the transcriptional signalling networks [single-cell RNA-seq]

status: Public on Aug 01 2021

city: Baltimore

first: Christopher

last: Cherry

state: MD

address: 1800 Orleans St

institute: Johns Hopkins University

summary: The understanding of the foreign-body responses to implanted biomaterials would benefit from the reconstruction of intracellular and intercellular signalling networks in the microenvironment surrounding the implant. Here, by leveraging single-cell RNA-sequencing data from 42,156 cells harvested from the site of implantation of either polycaprolactone or an extracellular-matrix-derived scaffold in a mouse model of volumetric muscle loss, we report a computational analysis of intercellular-signalling networks reconstructed from data of transcription-factor activation. We found that intercellular signalling networks can be clustered into modules associated with specific cell subsets, and that biomaterial-specific responses can be characterized by interactions between signalling modules for immune, fibroblast and tissue-specific cells. In a Il17ra–/¬– knockout mouse model, we validated that predicted IL-17-linked transcriptional targets led to concomitant changes in gene expression. Moreover, we identified cell subsets that had not been implicated in the responses to implanted biomaterials. Single-cell atlases of the cellular responses to implanted biomaterials will facilitate the design of implantable biomaterials and the understanding of the ensuing cellular responses.

overall_design: To generate the scRNAseq data sets we created single cell suspensions from the muscle tissue with and without biomaterials for application to 10X and Drop-seq. Single cell suspensions from whole tissue preparations were enriched for CD45+ cells to enable capture of less frequent cell populations and processed with Drop-seq. Fluorescence activated cell sorting (FACS) was used to apply mesenchymal/fibroblasts (CD45-CD19-CD31-CD29+) to Drop-seq. Finally, a previously published data set of sorted macrophages (CD45+F4/80hi+Ly6c+CD64+) was included. Most samples collected were from young mice (6 week old at time of surgery) during the acute phase of injury one week after surgery. A detailed description of age, time of harvest, treatment, and sorting methodology for each of the samples in the atlas is provided in Supplementary Table 2. The resulting dataset includes 42,156 cells with an average of 198,000 reads and 1,167 genes per cell after filtering low-quality cells and genes across multiple time points and ages.

first: Jennifer

last: Elisseeff


title: A single-cell atlas of the microenvironment of implanted biomaterials and computational analysis of the transcriptional signalling networks [bulk RNA-seq]

overall_design: Triplicate of animals given volumetric muscle loss in wild type C57BL/6 or IL17ra knockout animals.


title: A single-cell atlas of the microenvironment of implanted biomaterials and computational analysis of the transcriptional signalling networks


title: Distinct transcriptional programs characterize neoantigen-specific T cells in   lung cancers treated with neoadjuvant PD-1 blockade [bulk TCR-seq]

status: Public on Jul 21 2021

first: Kellie

middle: Nicole

last: Smith

address: 1650 Orleans Street, CRB1, 4M

summary: Immune checkpoint blockade (ICB) has revolutionized cancer treatment, but most patients do not respond. PD-1 blockade “unleashes” CD8 T cells, including those specific for mutation-associated neoantigens (MANA), but factors in the tumor microenvironment can inhibit responses by dampening MANA-specific T cell function. Recent advances in single cell transcriptomics are revealing global T cell dysfunction programs in tumor-infiltrating lymphocytes (TIL). However, the vast majority of TIL do not recognize tumor antigens and little is known about transcriptional programs of true MANA-specific TIL. Here, we use an integrated approach to identify MANA-specific T cell clones using the MANA functional expansion of specific T cells (MANAFEST) assay in neoadjuvant anti-PD-1-treated lung cancers and use their TCR CDR3 as barcodes to track them and analyze their transcriptional programs and function in the tumor microenvironment using single cell RNA sequencing. We find both MANA-and virus-specific clones in TIL and adjacent normal lung, regardless of response status. MANA-specific, influenza (flu)-specific and EBV-specific TIL each have unique transcriptional programs. Most MANA-specific clones are tissue resident memory (TRM) cells, an incompletely activated cytolytic program, including EOMES deficiency, and higher levels of genes encoding T cell inhibitory molecules and Tox2. Notably, MANA-specific T cells express low levels of IL-7R and are functionally less responsive to IL-7 compared with tissue-resident flu-specific clones. MANA-specific clones from anti-PD-1 non-responding tumors express TCR with markedly lower ligand-dependent signaling capability, are largely confined to HOBIThi TRM subsets and coordinately up-regulate genes encoding specific checkpoints, killer inhibitory receptors, and intracellular inhibitors of T cell activation and cytotoxicity. These findings provide mechanistic and potential therapeutic insights into overcoming resistance to PD-1 blockade.

overall_design: We utilized peripheral blood and surgical resection specimens obtained from the first-in-human clinical trial of neoadjuvant anti-PD-1 (nivolumab) in resectable non-small cell lung cancer (NCT02259621). MANAFEST (Mutation Associated NeoAntigen Functional Expansion of Specific T cells) was used to detect in vivo antigen-experienced T cell responses and identifies the clonal identity of the T cell receptor (TCR) corresponding to these cells in 6 patients.

middle: N

first: Justina

last: Caushi

first: Jiajia

last: Zhang


title: Epigenetic abnormality due to maternal Zika virus infection [snRNA-seq]

status: Public on Jun 30 2021

city: los angeles

first: Guoping

last: Fan

state: ca

address: 695 Charles E Young Drive South

department: Human Genetics

institute: university of california, los angeles

summary: We report the application of single nucleus RNA-seq and Enzymatic Methyl-seq in the prefrontal cortex from the mice treated with maternal zika virus infection

overall_design: Examination the epigeneitc changes and gene expression changes due to maternal zika virus infection

first: jing

last: wang

first: li

last: ma


title: Epigenetic abnormality due to maternal Zika virus infection [Methyl-seq]


title: 10X Genomics scRNA-seq profiling of mammary gland cells from mice at different life stages

status: Public on Jul 02 2021

city: Parkville

first: Gordon

middle: K

last: Smyth

state: Vic

address: 1G Royal Pde

department: Bioinformatics

institute: Walter and Eliza Hall Institute of Medical Research

summary:
Background: Heterogeneity within the mouse mammary epithelium has been recently explored by single-cell RNA profiling. To further understand how cellular diversity changes during mammary development, we profiled single cells from different developmental stages including late embryogenesis, early postnatal, prepuberty, resting adult, mid-pregnancy, late-pregnancy, lactation and post-involution. We also compared the transcriptomes and chromatin accessibility of micro-dissected ducts versus terminal endbuds (TEBs) to help decipher the molecular properties of these specialized units that drive morphogenesis.
Results: The single cell transcriptomes of 110,726 cells isolated from different stages were determined on the 10x Chromium platform and integrative analyses were performed to compare specific time-points. The mammary rudiment at E18.5 aligned more closely with the basal than the luminal lineage, while prepubertal epithelial cells at 2 weeks exhibited lineage segregation but to a less differentiated state than their adult counterparts. Integrated analysis of five stages spanning the pregnancy cycle revealed a novel alveolar progenitor that arises in late-pregnancy and stage-specific expression profiles. A continuum of states was uncovered along the basal-luminal progenitor cell axis following interrogation with >3,200 lineage-specific signature genes. Finally, exploration of micro-dissected TEBs and ducts showed that luminal cells within TEBs harbored intermediate expression profiles, and that ductal basal cells exhibited a higher level of accessible chromatin than their counterparts in TEBs.

overall_design: The data provides 18 biologically independent scRNA-seq profiles comprising a total of 149,371 cells supported by at least 500 sequence reads assigned to genes.

first: Yunshun

last: Chen

first: Bhupinder

last: Pal

first: Jane

last: Visvader


title: Mouse models of acute and chronic liver damage

city: Heidelberg

first: Christian

middle: H.

last: Holland

address: Im Neuenheimer Feld 267

department: Institute for Computational Biomedicine

institute: Heidelberg University


title: Acute, chronic, normobaric and hypobaric hypoxia elicit differential responses in the mouse retina on the genomic level

status: Public on Aug 10 2021

city: Schlieren

first: Lynn

middle: Jenny Alix

last: Ebner

state: Zürich

address: Wagistrasse 14

department: Department of Ophthalmology

country: Switzerland

institute: Universität Zürich

summary:
Purpose: Bulk RNA-Seq of wild-type mice retina after different hypoxic exposures, to evaluate the influence on retinal pathologies.
Methods: Retinal mRNA profiles of C57BL/6J mice after 6 different hypoxic exposures were generated by deep sequencing (n=6) using paired-end high output sequencing (Illumina Novaseq 6000).
Results: Longitudinal studies over 11 weeks in normobaric hypoxia revealed four classes of genes that adapted differentially to the long-term hypoxic condition. Many differentially expressed genes were involved in the regulation of gene expression. Seventeen genes were specifically regulated in hypobaric hypoxia. Some of these genes may affect the structural integrity of the retina or individual cells, resulting in the slight shortening of photoreceptor segment length detected in various hypoxic groups.

overall_design:
Besides the normoxic control group (Normoxia), hypoxic goups are defined as such: "Oxygen saturationt- time spend in hypoxia- location of experiment (ZH: Zürich (400masl); JFJ: Jungfraujoch (3450masl).

Please note that the raw data has been updated on Dec 14, 2023, as the initially-submitted files do not represent the full dataset and were not used for the publication.
The analysis was carried out on the original, fastq files, which are included in the 12-14-2023 update.

first: Cristian

last: Grimm

first: Marijana

last: Samardzija

first: Federica

last: Storti

first: Vyara

last: Todorova

first: Duygu

last: Karademir

first: Julian

last: Behr

first: Fraser

last: Simpson

first: Markus

last: Thiersch