title: Single cell RNA-sequencing on aged mouse lung mesenchymal cells.

city: Los angeles

first: Xue

last: Liu

state: CA

address: AHSP A9404, 127 S. San Vicente Blvd

department: Medicine

institute: Cedars-Sinai Medical Center

summary: QC, integration, mesenchymal fraction extraction and purity confirmation were performed as described previously. The mesenchymal cell subpopulations identified in the aged normal and fibrotic lungs were similar to those identified in adult mouse lungs and each cluster showed a distinct gene expression profile.

overall_design: As IPF is a disease of aging, to further investigate pulmonary fibroblast lineage and the subtypes in aged and disease lungs, mesenchymal cells (EPCAM/CD31/CD45-) were collected from three control aged mouse lungs and aged matched lungs 14 days after bleomycin injury.

first: X

first: S

last: Rowan

first: P

last: Noble

first: D

last: Jiang


title: Human neurodevelopmental samples

status: Public on Jun 30 2021

city: Exeter

first: Jonathan

last: Mill

address: RILD Building, RD&E Hospital

department: Medical School

country: United Kingdom

institute: University of Exeter

type: Methylation profiling by genome tiling array

summary:
This cohort is an extension of our previous dataset (Spiers et al) containing DNA methylation profiled with the EPIC array on an additional 40 human fetal brain samples.
Please note that these samples are from the same cohort as GSE58885.

overall_design: This data includes 40 human fetal brain samples age range 12-19 post conception weeks.

first: E

last: Hannon

first: J


title: Single cell ATAC-sequencing on E17.5 mouse lungs.

country: USA

type: Genome binding/occupancy profiling by high throughput sequencing

summary: After quality control, sample integration, and checking the celltype specific genes, we identified major cell types as in scRNA-seq analysis. We also identified mesenchymal cell cluster by checking markers genes identified in scRNA-seq analysis.

overall_design: To further validate the definition of the scRNA-seq on embryonic lungs, we performed another unbiased analysis, single cell ATAC-seq (scATAC-seq), on three E17.5 mouse lungs on sorted live cells from E17.5 mouse lungs.

middle: C

middle: W


title: Differential expression of genes associated with innate immunity and oncogenesis is linked to susceptibility to tropical theileriosis

city: Edinburgh

first: Stephen

last: Larcombe

state: Lothian

address: Charlotte Auerbach Road

institute: University of Edinburgh

type: Expression profiling by high throughput sequencing

summary:
Purpose: The goal of this study was to use NGS RNAseq to compare transcriptomic profiles of bovine leucocytes from different host genotypes when infected with the pathogenic apicomplexan parasite T. annulata with a view to elucidating mechanisms associated with in vivo virulence between Bos taurus and Bos indicus cattle.
Methods: infected cell lines were generated from in vivo infections of cows with T. annulata. 5 were derived from Bos taurus hosts and 6 were derived from Bos indicus hosts. We extracted RNA from each immortlaized  cell line and generated paired end reads using XXXXXX. Paired end reads were trimmed (Cudadapt 1.2.1 abd Sickle version 1.2) , and aligned to the Bos taurus genome (UMD3.1) using Bowtie 2. Differential analysis was performed useing DEseq 2. qRT PCR was used for validation on a subset of 18 genes using SYBR green.
Results: We found a total of 2022 differentially expressed genes (p < 0.05) using DEseq2, and many of these genes are involved in pathways implicated in in vivo differences in virulence observed between host genotypes, including i genes onvolved in interferon pathways, the innate immune response, or cancer-asscoiated.

sample_organism:
Bos taurus
Bos indicus

platform_organism:
Bos taurus
Bos indicus

overall_design: Conclusions: RNAseq represents a powerful tool to investiagte mechanisms underpinning observed differences in parasite-mediated morbidity and mortality between host genotypes, and our results reveal possible genes/pathways that could be exploited in breeding more resitant host animals in T. annulata endemic areas.

middle: D

first: Kirsty

last: Jensen

first: Jain

last: Kinnaird

first: Elisabeth

middle: J

last: Glass

first: Brian

middle: R

last: Shiels


title: Single cell RNA-sequencing on stimiluated mouse lung lipofibroblast-like cells and control cells.

summary: To achieve the in vitro functions of lipofibroblasts, isolated murine lung fibroblasts were cultured and biochemically stimulated. Stimulated fibroblasts in which a lipofibroblast-like phenotype had been induced using conventional methods displayed pronounced lipid inclusions. scRNA-seq analysis of lipofibroblast-like cells demonstrated that stimulated lipofibroblast-like cells displayed high transcript expression of canonical makers, like Plin2, as reported by others.

overall_design: Murine lungs were dissociated and the entire cell suspension was then plated on appropriately sized tissue culture plasticware. Fibroblasts were cultured in advanced DMEM/F12 (#12634010, Thermo Fisher Scientific), with 10 % vol/vol FBS (HyClone) or to induce a lipofibroblast like phenotype with the addition of 1 % vol/vol ITS+3 liquid media supplement (#I2771, Merck Milipore, Burlington, MA, USA) to the culture media. Media was changed every other day and the cells sub cultured when 80 % confluent. Fibroblasts cultured to passage three (P3) were considered free of contaminating cells based on previous experience in the laboratory. At P3 the cultured fibroblasts were then stimulated with one or a combination (as indicated) of 10 μM rosiglitazone (#72622, Stem Cell Technologies, Cambridge, MA, USA), 1 μM SB4315442 (#1614, R&D Systems, Minneapolis, MO, USA), 4 μM, rhBMP4 (#314-BP, R&D Systems) for 14 days. Matched control cells isolated from the same lung were stimulated in an identical media, for an identical duration, with the appropriate vehicle.


title: RNAseq for NIP and SDG708 overexpressed plant

city: Shanghai

first: Liufan

last: Yin

state: Shanghai

address: No. 2005, Songhu Road

department: School of Life Science

country: China

institute: Fudan University

summary: Chromatin modifications play important roles in plant adaptation to abiotic stresses, but the precise function of histone H3 lysine 36 (H3K36) methylation in drought tolerance remains poorly evaluated. Here, we report that SDG708, a specific H3K36 methyltransferase, functions as a positive regulator of drought tolerance in rice.

overall_design: NIP and SDG708 overexpressed plant  were grown in PEG treatment condition

first: Kai

last: Chen

first: Aiwu

last: Dong

first: Bing


title: Global patterns of enhancer activity during sea urchin embryogenesis assessed by eRNA profiling

city: Pittsburgh

first: Jian Ming

last: Khor

state: PA

address: 4400 Fifth Ave

department: Biological Sciences

institute: Carnegie Mellon University

summary: We used CAGE-seq (Capped Analysis of Gene Expression with Sequencing) to profile eRNA expression and enhancer activity during embryogenesis of the sea urchin, Strongylocentrotus purpuratus. We identified >18,000 enhancers that were active during late oogenesis and early development and documented a burst of enhancer activation during cleavage and early blastula stages. Most enhancers were located near gene bodies and eRNA expression levels were highest for elements near core promoters. Transcriptional signals from enhancers generally paralleled the expression levels of likely target genes. Furthermore, enhancers near lineage-specific genes contained signatures of inputs from developmental gene regulatory networks deployed in those lineages. A large fraction (60%) of sea urchin enhancers previously shown to be active in transgenic reporter assays were associated with eRNA expression. Moreover, a large fraction (50%) of a representative subset of enhancers identified by eRNA profiling drove tissue-specific gene expression in isolation when tested by reporter assays. Our findings provide an atlas of developmental enhancers in a model sea urchin and support the utility of eRNA profiling as a tool for enhancer discovery and regulatory biology. The data generated in this study are publicly available at Echinobase (www.echinobase.org).

overall_design: CAGE library preparation, sequencing, mapping, and eRNA identification were performed by DNAFORM (Yokohama, Kanagawa, Japan). Briefly, 30-60 mg total RNA was used for the generation of each CAGE library (9 total) and libraries were subjected to Illumina HiSeq-based sequencing. Sequence reads (>100 million reads/sample) were subjected to quality control (FastQC), filtered to remove small numbers of rRNA reads, and mapped to the S. purpuratus genome (v. 3.1) first with BWA (Li and Durbin, 2010) and then using HISAT2 (Kim et al., 2019) to align reads with BWA MAPQ<20. A total of 60-80 million uniquely mapped reads were obtained per sample and used for all subsequent analysis. De novo eRNA peak-calling was carried out as described by Hirabayashi et al., 2019. Briefly, bidirectional enhancers were identified using the FANTOM5 pipeline (FANTOM CONSRTIUM, 2014). TSSs were identified according to http://fantom.gsc.riken.jp/5/sstar/Protocols:HeliScopeCAGE_read_alignment. and clustered using the decomposition-based peak identification (DPI) software (https://github.com/hkawaji/dpi1/blob/master/identify_tss_peaks.sh). DPI was used with default parameters but without the decomposition parameter. Peaks with at least two supporting CAGE tags were retained and used as input to call bidirectional enhancers using a program available at https://github.com/anderssonrobin/enhancers/blob/master/scripts/bidir_enhancers.

first: Jian

middle: M

first: Jennifer

last: Guerrero-Santoro

first: William

last: Douglas

first: Charles

middle: A

last: Ettensohn


title: Single cell RNA-sequencing on healthy and IPF lung mesenchymal cells.

first: Xue

last: Liu

summary: Single cell lung suspensions of explanted healthy and IPF donor lung tissue were generated. scRNA-seq was performed on EPCAM negative live cells sorted by FACS. Puried mesenchymal cells were clustered to evaluate the mesenchymal cell sub-clusters

overall_design: To  investigate pulmonary fibroblast lineage and the subtypes in human healthy and IPF lungs, mesenchymal cells (EPCAM/CD31/CD45-) were collected from five lungs from healthy donors and five lungs from IPF patients, single cell RNA-sequencing was performed on the purified mesenchymal cells.

first: X

first: S

last: Rowan

first: P

first: D


title: Characterization of the epitranscriptomic landscape of HIV-infected cells IV

city: Lausanne

first: Paolo

last: Angelino

address: Quartier Sorge, Bâtiment Génopode

department: BCF

country: Switzerland

institute: SIB Swiss Institute of Bioinformatics

summary: In this study, we used a productive HIV infection model, consisting of the CD4+ SupT1 T cell line infected with a VSV-G pseudotyped HIVeGFP-based vector, to explore the transcriptomic and m6A/m5C epitranscriptomic lansdcape upon HIV infection, and compare it to mock-treated cells at 12h, 24h, and 36h post infection.

overall_design: SupT1 cells were either infected with 1 µg/10^6 cells p24 equivalent of HIV_GFP virus or left uninfected, divided into aliquots of 5*106 cells/ tube and spinoculated for 90 minutes at 1500 g and 20°C to allow nearly universal infection. Cells were then resuspended at a concentration of 10^6 cells/ml and further incubated. At 12, 24 and 36h post–infection, RNA was extracted from each cellular sample and virus-containing supernatant and further processed for RNA-Seq to investigate gene expression, MeRIP-Seq and BS-Seq to investigate m6A and m5C epitranscriptomic marks.

first: Sara

last: Cristinelli

first: Andrew

last: Janowczyk

first: Mauro

last: Delorenzi

first: Angela

last: Ciuffi


title: RNAseq for NIP and SDG708 RNAi mutant

first: Liufan

overall_design: NIP and SDG708 RNAi mutants were grown in control or PEG treatment condition

first: Kai

first: Aiwu


title: Characterization of the epitranscriptomic landscape of HIV-infected cells

type: Methylation profiling by high throughput sequencing

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

sample_organism:
Homo sapiens
Human immunodeficiency virus

overall_design: Refer to individual Series


title: Transcriptome analysis of microglia reveals the TLR2/IRF7 signaling axis mediates neuroinflammation after subarachnoid hemorrhage

city: Hangzhou

first: Jianmin

last: Zhang

address: 88 Jiefang Road

institute: Zhejiang University

summary: Microglia-mediated neuroinflammatory response in the early brain injury after subarachnoid hemorrhage (SAH) has been reported to have an impact on progress and the mechanism is not completely understood. Here, we performed genome-wide transcriptome analysis of microglia purified from damaged hemisphere of adult mice at 3 days after SAH or sham operation. Robust transcriptional changes were observed between SAH-induced and healthy microglia, indicating rapid activation of microglia after suffering SAH. We identified 1576 differentially expressed genes (DEGs; 928 up-regulated and 648 down-regulated) in SAH-induced microglia compared with sham microglia, representing a strong alteration of the genome (6.85% of total ~23,000 genes). Functional enrichment of these DEGs indicated that cell division, inflammatory response, cytokine production and leukocyte chemotaxis were strongly activated in SAH-induced microglia. Moreover, we identified and proved the TLR2/IRF7 signaling axis was involved in regulation of this microglia-mediated inflammation in SAH mice, by performing flow cytometry, immunofluorescence. Together, these results provided a perspective of microglia-mediated neuroinflammatory response in the early stage of SAH and might give a new therapeutic target for SAH.

overall_design: transcriptome profiles of microglia purified from damaged hemisphere of adult mice at 3 days after SAH or sham operation.

first: Shenbin

last: Xu

first: Shuhao

last: Mei

first: Jia'nan

last: Lu

first: Haijian

last: Wu

first: Xiao

first: Ligen

last: Shi

first: Jingyi

last: Zhou


title: Circulating small RNAs in transplant glomerulopathy

city: Memphis

first: Canan

last: Kuscu

address: 71 S Manassas St.

institute: University of Tennessee Health Science Center

type: Non-coding RNA profiling by high throughput sequencing

summary: Transplant glomerulopathy (TG) develops through multiple mechanisms including donor-specific antibodies, T cells and innate immunity. This study investigates the role of circulating small RNAs (sRNAs) in TG

overall_design: Circulating sRNAs profiles were evaluated in serum samples of kidney transplant recipients with biopsy-proven TG and normal allograft function using RNA sequencing.

first: Manjari

last: Kiran

first: Akram

last: Mohammed

first: Valeria

last: Mas

first: Enver

last: Akalin


title: Characterization of the epitranscriptomic landscape of HIV-infected cells II

first: Paolo

last: Angelino

first: Sara

first: Andrew

first: Mauro

first: Angela


title: Characterization of the epitranscriptomic landscape of HIV-infected cells III

last: Cristinelli


title: Understanding regulation of KSHV/EBV circular RNAs

city: Baltimore

first: Myong-Hee

last: Sung

state: MD

address: 251 Bayview Boulevard, Room 06C226

department: National Institute on Aging

institute: NIH


title: Single cell RNA-sequencing on E16.5 and E17.5 mouse lungs

first: Xue

last: Liu

summary: To identify clear mesencbhymal cell clusters, sequencing libraries of embryonic lung cells were prepared using the 10x Genomics Chromium system. After quality control samples were integrated. The cells were visualized in two dimensions according to their gene expression profiles using Uniform Manifold Approximation and Projection (UMAP).

overall_design: We FACS sorted αSMA-GFP; Tbx4-Cre; Rosa26-tdTomato (Tbx4-lineage+, αSMA+) fibroblasts from one E16.5 mouse lung and live cells from three E17.5 murine lungs. Single cell RNA-seq was performed on purified single cells.

first: Simon

last: Rowan

first: Paul

last: Noble

first: Dianhua

last: Jiang


title: Expression of a surfactant protein C mutation links postnatal type 2 cell dysfunction with adult disease

city: Cincinnati

first: Yan

last: Xu

state: OH

address: 3333 Burnet Ave

institute: Cincinnati Children's Hospital Medical Center

summary: Mutations in the gene encoding surfactant protein C (SFTPC) are associated with interstitial lung disease in children and adults. To assess the natural history of disease, we knocked-in a familial disease-associated SFTPC mutation, L188Q (L184Q in mice), into the mouse Sftpc locus. Expression of L184Q (LQ) resulted in formation of an unstable, misfolded proprotein (proSP-CLQ) that was rapidly degraded by the proteasome pathway. Importantly, expression of misfolded proSP-CLQ was associated with a decrease in AT2 cells in adult mutant mice, with no effect on lung homeostasis; however, lung regeneration in response to bleomycin challenge was substantially reduced in mutant mice. Translation of proSP-CLQ exceeded that of proSP-CWT in neonatal AT2 cells and was associated with activation of oxidative stress and apoptosis leading to impaired expansion of AT2 cells during postnatal alveolarization. Collectively, these data support the hypothesis that susceptibility to disease in adult mutant mice is established during postnatal lung development and is associated with a reduction in AT2 cell numbers.

overall_design: Using the 10x Chromium platform sequencing, transcriptomes of single cells from wild-type and surfactant protein C (SP-C) mutant (L184Q) mouse lung were analyzed

first: Sneha

last: Sitaraman

first: Emily

middle: P

last: Martin

first: Cheng-Lun

first: Shuyang

last: Zhao

first: Jenna

last: Green

first: Hitesh

last: Deshmukh

first: Anna-Karina

middle: T

last: Perl

first: James

last: Bridges

first: Timothy

middle: E

last: Weaver


title: A high-fat diet exacerbates the Alzheimer's disease pathology in the hippocampus of the App[NL-F/NL-F] knock-in mouse model

city: Fukuoka

first: Yusaku

last: Nakabeppu

state: Fukuoka

address: 3-1-1 Maidashi Higashi-ku

department: Department of Immunobiology and Neuroscience

country: Japan

institute: Medical Institute of Bioregulation, Kyushu University

summary:
To investigate the effects of diabetic conditions on the development of AD pathology, we fed wild-type and Alzheimer's disease model (App[NL-F/NL-F]) mice with control or high fat diet from 6 months after birth for 12 months, then examined behavior, brain pathology and gene expression profiles.
Both groups of mice fed with high fat diet exhibited diabetic conditions, and App[NL-F/NL-F] mice exhibited aggravated cognitive impairment with enhanced Alzheimer's disease pathology.

overall_design: Six month-old male wild-type and App[NL-F/NL-F] mice harboring two pathogenic App-knock-in mutations, that promote aggressive amyloidosis by increasing total Aβ production (Swedish mutation KM670/671NL) and increasing the Aβ42/Aβ40 ratio (Iberian mutation I716F) under the control of the endogenous APP promoter, were divided into two groups (3 mice for each group), and control groups of mice were fed with control diet and HFD groups of mice were fed with high fat diet for 12 months.

first: Nona

last: Abolhassani

first: Guianfranco

last: Mazzei

first: Ryohei

last: Ikegami


title: Role of the DNR- and FNR- type regulators in regulation of the denitrification genes in Roseobacter denitrificans OCh114

city: Bunkyo-ku

first: Hiroyuki

last: Arai

state: Tokyo

address: Yayoi 1-1-1

department: Department of Biotechnology

institute: The University of Tokyo

summary: An aerobic photosynthetic bacterium Roseobacter denitrificans OCh114 has two DNR- and one FNR-type transcriptional regulators, which are predicted to sense nitric oxide and oxygen, respectively. To investigate the role of these regulators in regulation of the denitrification genes, transcriptome profiles of mutant strains of R. denitrificans OCh114 deficient in the genes for the DNR- or FNR-type regulators were determined by NimbleGen Prokaryotic Expression array (12x135K).

overall_design: The mutant strains of R. denitrificans OCh114 deficient in the genes for the DNR- (dnr1 and dnr2) or FNR-type (fnrL) regulators were unable to grow anaerobically by denitrification. Therefore, the strains were initially cultivated aerobically in glycerol medium supplemented with 20 mM NaNO3 in baffled Erlenmeyer flasks with rotary shaking at 200 rpm at 30 ºC. When optical density at 600 nm reached 0.4, the cultures were moved to vials. After the vials were sealed with butyl rubber septa, the cultures were made anaerobic by replacing the headspace gas with argon. Total RNA was extracted after the anaerobic cultivation for 3 hours. The experiment was performed in duplicate independent cultures.

first: Makoto

last: Kimura


title: Cellhesion VP enhances the therapeutic potential of human Wharton’s jelly-derived mesenchymal stem cell-derived extracellular vesicles

city: Pyeongchang-gun

first: Eun Seo

last: Kim

address: 25354 Pyeongchang-daero, Daehwa-myeon

department: Department of International Agricultural Technology

country: South Korea

institute: Seoul National University

summary: Mesenchymal stem cell (MSC) transplantation is a promising therapy for regenerative medicine. However, MSCs cultured in two-dimensional (2D) culture conditions are significantly different from the cell shape in the body, down-regulation of stemness genes and the secretion of paracrine factors. Here, we evaluated the effect of 3D culture using Cellhesion VP, a water-insoluble material composing of chitin-based polysaccharide fibers, on the characteristics of human Wharton’s jelly-derived MSCs (hWJ-MSCs). Cellhesion VP significantly increased the cell proliferation after retrieval. Transcriptome analysis revealed that genes involved in cell stemness, migration ability, and extracellular vesicle (EV) production appeared to be enhanced by 3D culture. Subsequent biochemical analyses showed that the expression levels of stemness genes including OCT4, NANOG, and SSEA4 were up-regulated, and migration capacity was elevated in 3D cultured hWJ-MSCs. In addition, the EV production was significantly increased in 3D cells, which contained a distinct protein profile from 2D cells. Gene and drug connectivity analysis revealed that the 2D and 3D EVs had similar functions as immunomodulators; however, 3D EVs had completely distinct therapeutic profiles on various infectious and metabolic diseases by activating the disease-associated signaling pathways. Therefore, EVs from Cellhesion VP-primed hWJ-MSCs appear as a new treatment for immune and metabolic diseases.

overall_design: For transcriptome analysis, RNA was prepared from 2D and 3D cultured hMSCs, DPBS-treated, 2D EV- or 3D EV-treated cells as well as Fenbendazole or Brompheniramine-treated cells.

first: Joonghoon

last: Park

first: Eun

middle: S


title: Transcriptome response to oxygen tension and light irradiation in Roseobacter denitrificans OCh114

summary: Transcriptome profiles of an aerobic photosynthetic bacterium Roseobacter denitrificans OCh114 grown under different oxygen tension and light irradiation conditions were determined by NimbleGen Prokaryotic Expression array (12x135K).

overall_design: R. denitrificans OCh114 was cultivated in glycerol medium without or with irradiation of near-infrared or blue light. For the aerobic or microaerobic conditions, the cells were grown in glass bottles with continuous bubbling of air or a gas mixture of 2% O2 and 98% N2, respectively. Total RNA was extracted when optical density at 600 nm (OD600) was 0.4-0.42. For the denitrification condition, the medium was supplemented with 20 mM NaNO3 and the cells were grown in side-armed Erlenmeyer flasks. The flasks were sealed with silicone plugs and butyl rubber septa and the headspaces of the flasks were replaced with argon. Total RNA was extracted when OD600 was 0.2-0.23. For the denitrification-shift condition, the medium was supplemented with 20 mM NaNO3 and the cells were grown in baffled Erlenmeyer flasks with rotary shaking at 200 rpm. When OD600 was 0.4, the cultures were moved to vials. After the vials were sealed with butyl rubber septa, the headspaces of the vials were replaced with argon. Total RNA was extracted after cultivation anaerobically for 3 hours. The experiment was performed in duplicate independent cultures.


title: Inhaled titanium dioxyde-induced gene expression profile in rat lung

city: Vandoeuvre les Nancy

first: Carole

last: Seidel

address: Rue du Morvan

country: France

institute: INRS

summary: In this work we study the pulmonary toxicological properties of titanium dioxyde nanoparticles using molecular toxicological approach. For this, we exposed F344 rats by nose-only inhalation 6 hours/day, 5 days/week for 4 weeks.  Lung samples have been collected up to 28 days after the end of exposure and transcriptomics analysis were performed.

overall_design: 19 months old male F344 rats were exposed by nose-only inhalation  6 hours/day, 5 days/week for 4 weeks to titanium dioxyde nanoparticles (TiO2). Titanium dioxyde nanoparticles-induced gene expression profile in rat lung was performed 0 and 28 days post exposure (2 time points). Each time point is composed of 6 control, 6 exposed rats. A total of 23 samples (microarrays) was used.

first: Sarah

last: Valentino

first: Laëtitia

last: Chézeau

first: Sylvie

last: Sébillaud

first: Mylène

last: Lorcin

first: Monique

last: Chalansonnet

first: Frédéric

last: Cosnier

first: Laurent

last: Gaté


title: Molecular profiling of cumulus cells and their correlation with pregnancy outcome: away from single gene marker and toward pathways analysis [Methylation data]

city: Bonn

first: Muhammad Ahmer

last: Jamil

state: NRW

address: Sigmund-Freud Str. 25

department: Institute of experimental haematology and transfusion medicine

country: Germany

institute: University Clinic Bonn

summary: Worldwide the rate of infertility is on rise which put increasing pressure on assisted reproductive technology (ART) programs worldwide. Therefore it is important to increase the efficiency of ART. Toward this aim studies has been performed to find the best predictive biomarkers to choose the best germ cells for fertilization and the best embryo for transfer into uterus. However, across different studies no universal markers were found. In this study we addressed this issue by generating expression and CpG methylation profiles of outer cumulus cells obtained during intra-cytoplasmic sperm injection (ICSI) procedure. Our results highlight the presence of several parameters that affect the results like inter-individual differences, inter-treatment differences and above all treatment protocol specific differences. The signature of FSH hormone treatment was abundant. Therefore stratifying the samples to be compared is a prerequisite for any analysis: comparing the pregnancy outcome for only the long protocol we identified single gene markers (NME6 and ASAP1, FDR<5%), upstream regulators (like: EIF2AK3, FSH, ATF4, MKNK1, TP53) and several disease and bio-function related to cell death/apoptosis, cellular growth and proliferation. The later results were more pronounced by ranking the pairwise Z-scores between all samples: the positive samples resulting in pregnancy were classified, for example according to FSH upstream regulator, in the middle between two negative groups indicating that an overdose of FSH is equally harmful to an under dose. In conclusion, our study highlight the need to stratify the samples and the use of genomic pathway analysis as a more reliable and universal method, rather than the single gene marker in cumulus cell to predict oocyte development potential.

overall_design: Cumulus cells were collected from womed undergoing ICSI cycles. As these cells must be removed before performing the ICSI. Upon isolation, the outer cumulus cells were directly stored at -80°C in 70ul buffer RLT Plus from Qiagen (Cat. No.: 1053393, Hilden, Germany) until further used.

first: Osman

last: El-Maarri

first: Muhammad

first: Maria

last: Köster

first: Nicole

last: Nuesgen

first: Johannes

last: Oldenburg

first: Markus

last: Montag

first: Hans

last: van der Ven

first: Katrin


title: Molecular profiling of cumulus cells and their correlation with pregnancy outcome: away from single gene marker and toward pathways analysis


title: TET1 promotes adipogenesis through DNA demethylation

first: Wei

last: Qi

address: B514, L Building

department: School of Life Science and Technology

institute: ShanghaiTech University


title: TET1 promotes adipogenesis through DNA demethylation [MeDIP-seq and HmeDIP-seq]

summary: Adipose tissue is important for systemic metabolic homeostasis in response to environmental changes, and adipogenesis involves dynamic transcriptional regulation. DNA methylation on cytosine (C) of CpG (5mC) is an abundant epigenetic modification that mediates genomic imprinting and regulates gene expression. TET family enzymes (TET1, TET2 and TET3) oxidize the 5mC in DNA to 5-hydroxylmethylcytosine (5hmC), which associates with transcriptional activation. Through a phenotypic screen, we found TET inhibition decreased adipocyte differentiation from mesenchymal stem cells (MSCs). Comparing with the undifferentiated MSCs, the differentiated adipocytes exhibited much higher levels of 5hmC and slightly increased 5fC and 5caC. Higher 5hmC associated with better differentiation at single cell level. TET1 is upregulated in differentiation and depletion of it significantly impaired the gain of 5hmC. Furthermore, Tet1 depletion significantly hampered the adipocyte differentiation in vitro and adipose tissue maintenance in vivo. Using RNA-seq, 5mC and 5hmC-DNA immunoprecipitation, we found that Tet1 knockout led to decreased expression of genes associated with lipid metabolism and fat cell differentiation. Genes with loss of 5mC or gain of 5hmC in adipocytes include Lipe, Bmp4 and Rxra etc. Rxra is one of the critical TET1 modulated genes for adipose development, as RXRα agonist partially rescued the inhibitory effect of Tet1 knockout. Together, TET1-mediated active DNA demethylation plays an important role in adipose tissue.

overall_design: Examination of DNA 5mC and 5hmC in C3H10T1/2 cells after different time points of differentiation

first: Hui

last: Qian


title: Characterization of the epitranscriptomic landscape of HIV-infected cells I

first: Paolo

last: Angelino

first: Sara

last: Cristinelli

first: Andrew

last: Janowczyk

first: Mauro

last: Delorenzi

first: Angela

last: Ciuffi


title: Tip60-mediated acetylation of  H2A.Z activates Hoxa9 and Meis1 expression to promote MLL-rearranged acute myeloid leukemia

city: Tokyo

first: Kazutsune

last: Yamagata

address: 5-1-1, Tsukiji, Tyuo-ku

department: Hematological Malignancy

institute: National Cancer Center Research Institute


title: TET1 promotes adipogenesis through DNA demethylation [RNA-seq]

overall_design: Examination of polyA RNA in C3H10T1/2 cells after different time points of differentiation


title: The genome-wide maps of H3K27me3 in MLL-AF10 (Tip60 flox/flox, Cre-ERT2) cells (MATIP cells) with or without the treatment of 4-OHT

summary: Chromosome translocations involving the MLL gene are common rearrangements in leukemia. Such translocations fuse the MLL 5’-region in frame to partner genes , and the resultant fusion proteins can cause MLL-related leukemia. MLL-fusions activate transcription of target genes such as the HoxA cluster and Meis1, but the underlying mechanisms remain elusive. We found that the MLL-AF10 fusion recruits Tip60 to the Hoxa9 locus, where it acetylates H2A.Z, thereby promoting Hoxa9 expression. Following conditional deletion of Tip60, hypoacetylation of H2A.Z was accompanied by recruitment of Ezh2, the catalytic subunit of PRC2, suggesting that nucleosomes with hypoacetylated H2A.Z are the preferential targets of Ezh2. Our findings suggest that MLL-AF10 achieves active chromatin states by recruiting Tip60, which acetylates H2A.Z to prevent gene silencing by Ezh2.

overall_design: The comprisons of H3K27me3 genome-wide distribution between 4-OHT-treated and non-treated (control)  MLL-AF10 (Tip60 flox/flox, Cre-ERT2)  cells.

first: Issay

last: Kitabayashi


title: Rapid nutritional regulation of oligodendrocytes of the adult hypothalamic median eminence revealed by single-cell transcriptomic analysis

city: Cambridge

first: Brian

middle: Yee Hong

last: Lam

address: Box 289 Addenbookes Hospital, Hills Road

department: Metabolic Research Laboratories

institute: University of Cambridge

summary: The median eminence (ME) of the hypothalamus is a structure that rapidly adapts to nutrient availability. We have used single-cell RNA sequencing to characterize the transcriptional profiles of cells specifically in the median eminence in the fasted and refed states. In our study, we focus on characterizing the oligodendrocyte population of the ME, and identifying how subpopulations respond to nutrient availability.

overall_design: We sequenced 5982 cells from the median eminence of the hypothalamus of fasted and refed mice.  RNA profiles were used to characterize cells in this region and identify changes in genes and pathways between experimental conditions.

middle: N

last: Kohnke

middle: Y

first: Clemence

last: Blouet


title: RNA-seq approach to analysis of gene expression profiles between wild-type and C19orf12 knockdown A549 cell line

city: Tianjin

first: Ran

last: Liu

address: Qixiangtai

institute: Tianjin Medical University

summary: The goals of this study are to compare NGS-derived transcriptome profiling (RNA-seq) in human lung cancer cells. The mRNA profiles of wild-type and C19orf12 knockdown A549 cells were generated by deep sequencing, in triplicate, using Illumina Hiseq 4000. The sequence reads that passed quality filters were analyzed at the transcript isoform level with Burrows–Wheeler Aligner (BWA) and Bowtie2. we sequenced 6 samples of human species using RNA-Seq technology, averagely generating 24,382,600 raw sequencing reads and 24,299,184 clean reads after filtering low quality. We identified 20826 transcripts in the of WT and C19orf12 knockdown A549 samples with BWA workflow. Approximately 2% of the transcripts showed differential expression between the WT and C19orf12 knockdown A549 cells, p value <0.05. Altered expression of 21 genes was confirmed with qRT–PCR, demonstrating the high degree of sensitivity of the RNA-seq method. We conclude that RNA-seq based transcriptome characterization would providing clues for better understanding of gene function.

overall_design: mRNA profiles of sh-scramble (wild-type) and C19orf12 knockdown A549 cell line were generated by deep sequencing, in triplicate, using Illumina hiseq4000.

first: Meng

last: Zhao


title: Phytophthora infestans miRNA translocation facilitates infection in potato

city: Uppsala

first: Kristian

middle: Erik

last: Persson Hodén

address: Almas allé 5

department: Plant Biology

country: Sweden

institute: Swedish University of Agricultural Sciences

summary: Phytophthora spp. encode large sets of effector proteins and distinct populations of small RNAs (sRNAs). Reports suggest that pathogen-derived sRNAs can modulate the expression of plant defense genes. The experiments reported here were designed to shed light on impact of sRNAs in the potato-P. infestans interaction. We used the Argonaute or Ago1 from P. infestans tagged with GFP transformed into the 88069 strain to infect potato cv. Bintje plants. Collected leaf materials were used in co-immunoprecipitation experiments together with P. infestans harboring GFP (control GFP) and P. infestans mycelia grown on media (control mycelia). These three materials were sequenced at a Ion Proton platform. The reads length of 8-38 nt were adaptor-trimmed and mapped to the P. infestans genome and the Solanom tuberosum genome v4.04. Both P. infestans-associated and potato derived sRNAs were identified.

sample_organism:
Solanum tuberosum
Phytophthora infestans

overall_design: 12 small RNA samples sequenced from Co-IP.  3 replicates for each of the following: PiAgo1-GFP mycelia, Pi-GFP mycelia, PiAgo1-GFP infected Potato (cv. Bintje), Pi-GFP infected Potato (Bintje). Pi-GFP samples are controls. P. infestans strain: NL-88069

first: Xinyi

last: Hu

first: Anna

last: Åsman

first: Christina

last: Dixelius


title: Differentially gene expression analysis after 7 hours and 24 hours fermentation of curdlan in Agrobacterium  sp. CGMCC 11546

first: Deming

last: Jiang

address: No. 500, Dongchuan Road, Minhang District, Shanghai

institute: East China Normal University

summary: We report the analysis of differentially gene expression after 7 hours and 24 hours fermentation of curdlan in Agrobacterium  sp. CGMCC 11546.

overall_design: The total RNA of each sample from the Agrobacterium  sp. CGMCC 11546 after 7 and 24 hours fermentation of curdlan, samples from 7 hours fermentaion named A-7-1, A-7-2 and A-7-3; three biological repeats. samples from 24 hours fermentation named A-24-1, A-24-2 and A-24-3; three biological repeats

first: Hongliang

last: Gao


title: DNA methylation dynamics of oocyte in follicular maturation (RRBS-Seq data set)

first: Xiaolong

last: Chen

state: TN

address: 262 Danny Thomas Pl

institute: St Jude Children's Research Hospital

summary: Folliculogenesis in mammals is a cyclic and hierarchical process that the ovarian follicles undergo dramatic changes in the shape and number of granulosa cells accompanied by gradually enlarged immature oocyte. Here we show a thorough and high-resolution view of DNA methylation maps in oocyte free of somatic cells present at each distinct follicular development stages. We found that global DNA establishment occurs in Type5b follicles, the final stage of pre-antral follicles, and that the acquisition of DNA methylation at different trans-regulatory elements couples with different chromatin modifiers. Besides, we showed that Dnmt1 as well as Uhrf1 also play critical roles in requiring and retaining of de novo methylation statue, typically at LINE and LTR elements, in these immature oocytes, which successfully escape DNA replication. Our study thus refined the current knowledge on the establishment of unique DNA methylation profile in mammalian oocytes, and provide a valuable resource for further studies on female gametogenesis.

overall_design: We collected oocytes from detailed 9 stages of folliculogenesis stages and conduct RRBS-seq , each stage contains 3-6 replicates.

first: Rui

first: Chuan

first: Yuanlin

last: He

first: Xiaochen

last: Kou

first: Yanhong

first: Jing

last: Li

first: Yawei

first: Cizhong

first: Shaorong


title: Modeling cellular pliancy-dependent oncogene-induced signaling and chemotherapeutic response during breast tumorigenesis

city: Indianapolis

first: Harikrishna

last: Nakshatri

state: IN

address: 980 W. Walnut St. R3C218C

department: General Surgery

institute: Indiana University School of Medicine

overall_design: Single cell sequencing of vehicle control and HRAS V12 transformed cells


title: Genome-wide maps of chromatin state in HepG2 cells.

city: tianjin

first: yang

middle: wen

last: dong

address: tong yan road

institute: nankai

summary: Twist1 related genes detected by chipseq

overall_design: Examination of 2 different histone modifications in 2 cell types.

first: Wen-dong

last: Yang

first: Tao

last: Sun


title: Methionine biosynthetic pathway genes metH and metZ affect curdlan synthesis in Agrobacterium sp. CGMCC 11546

city: Shanghai

summary:
Purpose: The goal of this study is compare the effect of MetH and MetZ gene in curdlan synthesis in Agrobacterium  sp. CGMCC 11546.

methods: The transcriptional and metabolomics analysis the function of metH and metZ in Agrobacterium  sp. CGMCC 11546.

Results: The transcriptional and metabolomics showed that the decrease of curdlan production in the ΔmetH and ΔmetZ mutants may be caused by the insufficient supply of energy ATP

conclusion: MetH and MetZ play an important role in curdlan synthesis in Agrobacterium  sp. CGMCC 11546

overall_design: The total RNA of each sample from the wild type strain and the gene deletion mutants after 24 hours fermentation, samples from metH deletion mutant named metH-1, metH-2 and metH-3; three biological repeats. samples from metZ deletion mutant named metZ-1, metZ-2 and metZ-3; three biological repeats; samples from the wild type strain named WT-1, WT-2 and WT-3; three biological repeats


title: Control of gasdermin D oligomerization and pyroptosis by the Ragulator-Rag-mTORC1 pathway

status: Public on Jun 29 2021

city: Boston

first: Charles

middle: Lee

last: Evavold

state: MA

address: 300 Longwood Avenue

department: Immunology

institute: Harvard University

summary: The process of pyroptosis is mediated by inflammasomes and a downstream effector known as gasdermin D (GSDMD). Upon cleavage by inflammasome-associated caspases, the N-terminal domain of GSDMD forms membrane pores that promote cytolysis. Numerous proteins promote GSDMD cleavage, but none are known to be required for pore formation after GSDMD cleavage. Herein, we report a forward genetic screen that identified the Ragulator-Rag complex as being necessary for GSDMD pore formation and pyroptosis in macrophages. Mechanistic analysis revealed that Ragulator-Rag is not required for GSDMD cleavage upon inflammasome activation, but rather promotes GSDMD oligomerization in the plasma membrane. Defects in GSDMD oligomerization and pore formation can be rescued by mitochondrial poisons that stimulate reactive oxygen species (ROS) production, and ROS modulation impacts the ability of inflammasome pathways to promote pore formation downstream of GSDMD cleavage. These findings reveal an unexpected link between key regulators of immunity (inflammasome-GSDMD) and metabolism (Ragulator-Rag).

overall_design: Control input and sorted survivor cell samples are included in raw de-multiplexed FASTQ format and corresponding raw read counts to sgRNA barcodes in txt format.

middle: L

first: Iva

last: Hafner-Bratkovič

first: John

middle: G

last: Doench

first: Jonathan

last: Kagan


title: Ppara and fatty acid oxidation coordinate hepatic transcriptional architecture

first: Michael

middle: J.

last: Wolfgang

address: 855 N Wolfe Street

department: Institute for Basic Biomedical Sciences

institute: The Johns Hopkins University School of Medicine

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

overall_design: Refer to individual Series


title: Immune cells surveil aberrantly sialylated O-glycans on megakaryocytes to regulate platelet count

city: Milwaukee

first: Robert

last: Burns

state: Wisconsin

address: 8727 W Watertown Plank Rd

institute: Blood Research Institute, Versiti

summary: Immune thrombocytopenia (ITP) is a common platelet disorder in pediatric patients. Pediatric and adult ITP have been associated with sialic acid alterations, but the pathophysiology of ITP remains elusive, and ITP is often a diagnosis of exclusion. Our analysis of pediatric ITP plasma samples showed increased anti-Thomsen-Friedenreich antigen (TF-antigen) antibody representation, suggesting increased exposure of the typically sialylated and cryptic TF-antigen in these patients. The O-glycan sialyltransferase St3gal1 add sialic acid specifically on the TF-antigen. To understand if TF-antigen exposure associates with thrombocytopenia, we generated a mouse model with targeted deletion of St3gal1 in megakaryocytes (MK) (St3gal1MK-/-). TF-antigen exposure was restricted to MKs and resulted in thrombocytopenia. Deletion of Jak3 in St3gal1MK-/- mice normalized platelet counts implicating involvement of immune cells. Interferon-producing Siglec H-positive bone marrow (BM) immune cells engaged with O-glycan sialic acid moieties to regulate type I interferon (IFN-I) secretion and platelet release (thrombopoiesis), as evidenced by partially normalized platelet count following and inhibition of interferon and Siglec H receptors. Single cell RNAseq determined that TF-antigen exposure by MKs primed St3gal1MK-/- BM immune cells to release IFN-I. Single cell RNAseq further revealed a new population of immune cells with a plasmacytoid dendritic cell (pDC)-like signature and concomitant upregulation of immunoglobulin re-arrangement gene transcripts Igkc and Ighm, suggesting additional immune regulatory mechanisms. Thus, aberrant TF-antigen moieties, often found in pathological conditions, regulate immune cells and thrombopoiesis in the BM, leading to reduced platelet count.

overall_design: Bulk polyA enriched RNA was sequenced from bone marrow and splenic CD4+ cells from St3gal1 flox/flox Pf4/cre and St3gal1 flox/flox control samples (n=3 per group).  Single-cell 3’ transcriptome data was gathered from 1 control St3gal1 flox/flox mouse and 1 St3gal1 flox/flox Pf4/cremouse each.

first: Melissa

last: Lee-Sundlov


title: Ppara and fatty acid oxidation coordinate hepatic transcriptional architecture (ChIP-Seq)

summary: Mice harboring a liver-specific carnitine palmityltransferase 2 (Cpt2) knockout exhibit drastic lipid accumulation following a 24hr fast. Crossing Cpt2L-/- mice with Pparα-/- mice provides a model to drive ligand-activated Pparα signaling in liver. We use this to investigate unique patterns of Pparα target gene transcription and demonstrate the requirement for ligand-activated Pparα in maintaining transcriptionally permissive genomic architecture in liver including regulation of promoters and enhancer elements during periods of acute nutrient deprivation.

overall_design: H3K4me1, H3K9ac, and H3K27ac ChIP-seq on liver tissue from 9wk old male wild-type, Cpt2 liver knockout, Ppar⍺  knockout, and Cpt2 L-/- ;Ppar⍺ -/- double knockout mice fasted for 24 hours.

first: Kyle

last: Cavagnini

middle: J


title: Transcriptome m6A sequencing (MeRIP-seq)of human colon cancer samples

city: KunMing

first: Zhou

last: yiran

state: YunNan

address: B: No. 245 East Renmin Road

department: general surgery department

institute: Yan 'an Hospital Affiliated to Kunming Medical University

summary: We analyze Aberrant Global M6A Abundance in colon Cancer by MeRIP-seq

overall_design: Ten matched samples included colon cancer tissue and paracancerous tissue

last: Yiran

first: Li

last: Ruhong


title: MYOCD is required for cardiomyocytes induction from human urine cells and fibroblasts through remodeling chromatin [RNA-seq]

city: Hangzhou

first: Xingnan

last: Huang

address: No.18 Shilongshan Road

institute: Westlake University

summary: Despite direct reprogramming of human cardiac fibroblasts into induced cardiomyocytes (iCM) holds great potential for heart regeneration, the mechanisms are poorly understood. Whether other human somatic cells could be reprogrammed into cardiomyocytes is also unknown. Here, we report human urine cells (hUCs) could be efficiently converted into CM-like cells and the associated chromatin accessibility dynamics (CAD) by assay for transposase accessible chromatin(ATAC)-seq. hUCs transduced by MEF2C, TBX5, MESP1 and MYOCD but without GATA4 expressed multiple cardiac specific genes, exhibited Ca2+ oscillation potential and sarcomeric structures, and contracted synchronously in coculture with mouse CM. Additionally, we found that MYOCD is required for both closing and opening critical loci, mainly by hindering the opening of loci enriched with motifs for the TEAD and AP1 family and promoting the closing of loci enriched with ETS motifs. These changes differe partially from CAD observed during iCM induction from human fibroblasts. Collectively, our study offers one robust platform for iCM generation and insights into mechanisms for iCM fate determination.

overall_design: We analyzed the transcriptome expression of  human fibroblast and fibroblasts-derived cardiomyocytes and the transcriptome expression of human urine cells and urine cells-derived cardiomyocytes


title: MYOCD is required for cardiomyocytes induction from human urine cells and fibroblasts through remodeling chromatin [ATAC-seq]

overall_design: We analyzed the  associated chromatin accessibility dynamics of  human fibroblast and fibroblasts-derived cardiomyocytes and the associated chromatin accessibility dynamics of human urine cells and urine cells-derived cardiomyocytes


title: Ppara and fatty acid oxidation coordinate hepatic transcriptional architecture (ATAC-Seq)

city: Baltimore

summary: Mice harboring a liver-specific carnitine palmityltransferase 2 (Cpt2) knockout exhibit drastic lipid accumulation following a 24hr fast. Crossing Cpt2L-/- mice with Pparα-/- mice provides a model to drive ligand-activated Pparα signaling in liver. We use this to investigate unique patterns of Pparα target gene transcription and demonstrate the requirement for ligand-activated Pparα in maintaining transcriptionally permissive genomic architecture in liver, including regulation of promoters and enhancer elements during periods of nutrient deprivation.

overall_design: ATAC-seq on liver tissue from 9wk old male wild-type, Cpt2 liver knockout, Ppar⍺  knockout, and Cpt2 L-/- ;Ppar⍺ -/- double knockout mice fasted for 24 hours.


title: Identification of group A Streptococcus genes directly regulated by CsrRS and novel intermediate regulators [ChIP-seq]

last: Wessels

address: 330 Longwood Ave

department: Medicine

institute: Boston Children's Hospital

summary: Adaptation of group A Streptococcus (GAS) to its human host is mediated by two component systems that transduce external stimuli to regulate bacterial physiology.  Among such systems, CsrRS (also known as CovRS) is the most extensively characterized for its role in regulating ~10% of the GAS genome including several virulence genes.  Here we show that extracellular magnesium and the human antimicrobial peptide LL-37 have opposing effects on phosphorylation of the response regulator CsrR by the receptor kinase CsrS.  Genetic inactivation of CsrS phosphatase or kinase activity, respectively, had similar, but more pronounced effects on CsrR phosphorylation compared to growth in magnesium or LL-37.  These changes in CsrR phosphorylation were correlated with repression or activation of CsrR-regulated genes as assessed by NanoString analysis.  Chromatin immunoprecipitation and DNA sequencing (ChIP-seq) revealed CsrR binding at CsrRS-regulated promoters and lower affinity binding at many other locations on the GAS chromosome.  Because ChIP-seq did not detect CsrR binding at promoters associated with some CsrR-regulated genes, we investigated whether these genes might be controlled indirectly by intermediate regulators whose expression is modulated by CsrR.  Transcriptional profiling of mutant strains deficient in expression of either of two previously uncharacterized transcriptional regulators in the CsrR regulon indicated that one or both proteins participated in regulation of 22 of the 42 CsrR-regulated promoters for which no CsrR binding was detected by ChIP-seq.  Taken together, these results illuminate CsrRS-mediated regulation of GAS gene expression through modulation of CsrR phosphorylation, CsrR binding to regulated promoters, and control of intermediate transcriptional regulators.

overall_design: Identification of DNA associated with the GAS protein CsrR

first: Meredith

middle: B

last: Finn

first: Kathryn

last: Ramsey

first: Simon

last: Dove

middle: R


title: Identification of group A Streptococcus genes directly regulated by CsrRS and novel intermediate regulators


title: Molecular profiling of cumulus cells and their correlation with pregnancy outcome: away from single gene marker and toward pathways analysis [Expression data]

first: Muhammad Ahmer

last: Jamil

summary: Worldwide the rate of infertility is on rise which put increasing pressure on assisted reproductive technology (ART) programs worldwide. Therefore it is important to increase the efficiency of ART. Toward this aim studies has been performed to find the best predictive biomarkers to choose the best germ cells for fertilization and the best embryo for transfer into uterus. However, across different studies no universal markers were found. In this study we addressed this issue by generating expression and CpG methylation profiles of outer cumulus cells obtained during intra-cytoplasmic sperm injection (ICSI) procedure. Our results highlight the presence of several parameters that affect the results like inter-individual differences, inter-treatment differences and above all treatment protocol specific differences. The signature of FSH hormone treatment was abundant. Therefore stratifying the samples to be compared is a prerequisite for any analysis: comparing the pregnancy outcome for only the long protocol we identified single gene markers (NME6 and ASAP1, FDR<5%), upstream regulators (like: EIF2AK3, FSH, ATF4, MKNK1, TP53) and several disease and bio-function related to cell death/apoptosis, cellular growth and proliferation. The later results were more pronounced by ranking the pairwise Z-scores between all samples: the positive samples resulting in pregnancy were classified, for example according to FSH upstream regulator, in the middle between two negative groups indicating that an overdose of FSH is equally harmful to an under dose. In conclusion, our study highlight the need to stratify the samples and the use of genomic pathway analysis as a more reliable and universal method, rather than the single gene marker in cumulus cell to predict oocyte development potential.

overall_design: Cumulus cells were collected from women undergoing ICSI cycles. As these cells must be removed before performing the ICSI. Upon isolation, the outer cumulus cells were directly stored at -80°C in 70ul buffer RLT Plus from Qiagen (Cat. No.: 1053393, Hilden, Germany) until further used.

first: Osman

last: El-Maarri

first: Muhammad

middle: A

first: Maria

last: Köster

first: Nicole

last: Nuesgen

first: Johannes

last: Oldenburg

first: Markus

last: Montag

first: Hans

last: van der Ven

first: Katrin


title: Identification of group A Streptococcus genes directly regulated by CsrRS and novel intermediate regulators [RNA-seq]

first: Michael

overall_design: Comparison of transcripts between wild-type GAS strain 854 and strain 854 with a deletion of csrR

middle: M


title: A double negative post-transcriptional regulatory circuit mediates the virgin behavioral state

city: New York

first: Seungjae

last: Lee

state: NY

address: 430 East 67th St.

department: Department of Developmental Biology

institute: Sloan-Kettering Institute

summary: The survival and reproductive success of animals depends on the ability to harmonize their external behaviors with their internal states. For example, females conduct numerous social programs that are distinctive to virgins compared to post-mated and/or pregnant individuals. In Drosophila, the fact that the post-mating switch is initiated by seminal factors implies the default state as virgin. Recently, we uncovered molecular and genetic control of the female virgin state. In particular, repression of the transcription factor Homothorax (Hth) by mir-iab-4/8 within the abdominal ventral nerve cord (VNC) is critical for unmated females to execute virgin behaviors. To elucidate new components of this regulatory circuit, we exploited mir-iab-4/8 deletion and hth-miRNA binding site mutants (hth[BSmut]) to elucidate doublesex (dsx) as a critical downstream factor. While Dsx has mostly been studied during sex-specific differentiation, its activities in neurons are little known. We find that accumulation of Dsx in the CNS is mutually exclusive with Hth, and downregulated in miRNA/hth[BSmut] mutants. Moreover, experimental suppression of Dsx in highly restricted sets of abdominal neurons abrogates female virgin conducts, in favor of mated behavioral programs. Thus, a double negative pathway in the VNC mediates the virgin behavioral state.

overall_design: RNA-seq from dissected Drosophila larvae VNC

first: Daniel

last: Garaulet

first: Albertomaria

last: Moro

first: Eric

middle: C

last: Lai


title: RNA sequencing of murine osteosarcoma tumors

city: Columbus

first: Timothy

middle: P

last: Cripe

address: 700 Childrens Drive

department: Center for Childhood Cancer and Blood Diseases

institute: Nationwide Children's Hospital

summary: We utilized murine osteosarcoma cell lines F420 and K7M2. F420 was originally derived from a female C57BL/6 mouse transgenic for a mutant p53 under control of a bone-selective promoter (PMID: 25579177). K7M2 was derived from a spontaneous metastatic lesion in a female Balb/C background (PMID: 16837208). F420 osteosarcoma tumors were established by subcutaneously injecting 5 x 10^6 osteosarcoma cells into the flanks of 6-week-old C57BL/6 mice (Envigo, Frederick, MD). K7M2 tumors were established by transplanting small pieces of sectioned tumor (~2mm3) into the flanks of 6-week-old Balb/C mice (Envigo). We found K7M2 to be more immunogenic than F420 as it demonstrated higher immune cell infiltrates, higher expression of immune-related genes, and slower growth in syngeneic versus nude models.

overall_design: Gene expression analysis of murine osteosarcoma tumors.

first: Katherine

middle: E

last: Miller


title: TENT4A non-canonical poly(A) polymerase regulates DNA-damage tolerance via multiple pathways which are mutated in endometrial cancer

city: Rehovot

first: Gilgi

last: Friedlander

address: Hertzel st

country: Israel

institute: Weizmann Institute of Science

summary: TENT4A (PAPD7) is a non-canonical poly(A) polymerase, of which little is known. Here we show that TENT4A is involved in the regulation of multiple biological pathways, and focus on translesion DNA synthesis (TLS), a DNA-damage tolerance process in which unrepaired lesions are bypassed by error-prone DNA polymerases. We show that TENT4A regulates mRNA stability and/or translation of DNA polymerase η, and of the RAD18 E3 ligase that monoubiquitinates PCNA, the latter being a key step in TLS which enables recruitment of error-prone DNA polymerases to damaged DNA sites. Remarkably, in addition to the effect on RAD18 mRNA stability via controlling its poly(A) tail, TENT4A indirectly regulates RAD18 via the tumor suppressor CYLD, and via the long non-coding antisense RNA PAXIP1-AS2, which had no known function. Knocking down the expression of TENT4A or CYLD, or over-expression of PAXIP1-AS2 led each to a decrease in the amount of the RAD18 protein, but the effect on PCNA ubiquitination was variable. Still, TLS was reduced under these conditions, likely due a to a parallel decrease in DNA polymerase η. Bioinformatics analysis revealed that TLS error-prone DNA polymerase genes and their TENT4A-related regulators are frequently mutated in endometrial cancer genomes, suggesting that TLS is dysregulated in endometrial cancer.

overall_design: Human osteosarcoma U2OS cell line and XP12RO (Xeroderma pigmentosum, complementation group A, SV-40 transformed) cells were selected as samples. The shRNA against TENT4A lentiviral particles was used to infect U2OS  cell line and selected stable TENT4A knockdown U2OS cells. Control shRNA infected U2OS cells were applying as control. To further knockdown, both stable TENT4A knockdown and control U2OS cells were transfected with SMARTpool siGENOME TENT4A siRNA (triplicates) and siGENOME Non-Targeting Control siRNA #5 (triplicates) using Lipofectamine RNAiMAX as recommended transfection protocols by the manufacturer. XP12RO cells were transfected with SMARTpool siGENOME TENT4A siRNA (triplicates) and siGENOME Non-Targeting Control siRNA #5 (triplicates) using Lipofectamine RNAiMAX as recommended transfection protocols by the manufacturer. After 48 h post-transfection, total RNA was extracted and expression profiles were analyzed in both U2OS and XP12RO.

first: U

last: Swain

first: G

first: Z

last: Livneh


title: Naïve and Primed MSC derived exosomes

city: Newark

first: Pranela

last: Rameshwar

state: NJ

address: 185 South Orange Avenue

institute: Rutgers NJ Medical School

summary: Here we report the change in gene expression in naïve and primed MSC exosomes

overall_design: RNA sequencing on naïve and primed (i.e. co-cultured with breast cancer cells) MSC derived exosomes to find differentially expressed genes

first: Oleta

last: Sandiford

first: Lauren

middle: S

last: Sherman


title: Microarray analysis of NS-SV-AC cells treated with TNF-a

city: Tokushima

first: Keiko

last: Aota

address: 3-18-15 Kuramoto-Cho

department: Oral Medicine

institute: Tokushima University Graduate sChool

summary:
TNF-a markedly induced the expression of IP-10 in NS-SV-AC cells.
We identified TNF-a-induced genes in NS-SV-AC cells using Affymetrix GeneAtlasTM System.

overall_design: Using Affymetrix GeneAtlas System, we determined the gene expression profiles of NS-SV-AC cells treated with TNF-a or bovine serum albumin (BSA).


title: Spindle-localized mRNA translation mediated by CPEB1 and CPEB4 controls mitotic progression

city: Barcelona

first: Oscar

last: Reina Garcia

state: Barcelona

address: C/Baldiri Reixac 10

department: Biostatistics and Bioinformatics

country: Spain

institute: IRB Barcelona

summary: Here we show sequential functions of CPEB1 and CPEB4 in the localization of repressed mRNAs to the mitotic spindle and their subsequent phase -specific activation to promote cell phase  transitions and correct chromosome segregation.

overall_design: RNA-immunoprecipitation sequencing of CPEB1 and CPEB4-associated mRNAs in Hela S3 cells.

first: Rosa

last: Pascual

first: Raul

last: Mendez


title: Bulk RNA-seq of fetal and adult murine Leydig cells

status: Public on Jun 28 2021

city: Genève

first: Serge

last: Nef

address: Rue Michel-Servet 1

department: Genetic Medicine and Development

institute: University of Geneva

summary: To compare expression profiles of fetal and adult mouse Leydig cells, we performed bulk RNA sequencing.

overall_design: Mouse testis from XY Nr5a1 Tg mouse embryos at embryonic day (E) 18.5 and 100-day old mice were harvested. Tissues were enzymatically dissociated and then filtered.The single cell solution is then sorted by fluorescent-active cell sorting to obtain a solution of alive and single Nr5a1-GFP+ cells. RNA was extracted from these cells with RNeasy Mini kit (Qiagen). Sequencing libraries were prepared with the TruSeq Stranded Total RNA Library Prep Gold (Ribo-Zero) and sequenced on an Illumina HiSeq 2500 (50 bp, paired end, ~35 million reads expected). Each condition was performed in three independent replicates.

first: Pauline

last: Sararols

first: Isabelle

last: Stévant

first: Yasmine

last: Neirijnck


title: Paternal MTHFR deficiency leads to reproductive decline across generations in association with hypomethylation of young retrotransposons

city: Montreal

first: Jacquetta

last: Trasler

state: Quebec

address: 1001 Decarie Boul, Block E, ES1.4380

department: Pharmacology & Therapeutics; Human Genetics

country: Canada

institute: McGill University

summary: 5, 10-Methylenetetrahydrofolate reductase (MTHFR) is a crucial enzyme in the folate metabolic pathway with a key role in generating methyl groups. As MTHFR deficiency impacts male fertility and sperm DNA methylation, there is the potential for epimutations to be passed to the next generation. Here, we assessed whether the impact of MTHFR deficiency on testis morphology and sperm DNA methylation is exacerbated across generations. While MTHFR deficiency in F1 fathers has only minor effects on sperm counts and testis weights and histology, F2 generation sons show further deterioration in reproductive parameters. Extensive loss of DNA methylation is observed in both F1 and F2 sperm, with >80% of sites shared between generations, suggestive of regions consistently susceptible to MTHFR deficiency. These regions are generally methylated during late prenatal germ cell development and are enriched in young retrotransposons. As retrotransposons are resistant to reprogramming of DNA methylation in prenatal germ cells, their hypomethylated state in the sperm of F1 males could contribute to the worsening reproductive phenotype observed in F2 MTHFR- deficient males, findings compatible with the intergenerational passage of epimutations.

overall_design: In order to study the reproductive health of Mthfr mice across generations, Mthfr +/- mice were mated in order to obtain an F1 generation of both Mthfr +/+ and Mthfr -/- male mice.  Upon sexual maturity, male mice of the F1 generation were mated with Mthfr +/- mice to obtain the F2 generation.  An external cohort of mice (Mat_Def_colony) was also examined, where maternal- and paternal-deficient Mthfr mice were mated to obtain Mthfr -/- male mice.

first: Gurbet

last: Karahan

first: Donovan

last: Chan

first: Kenjiro

last: Shirane

first: Taylor

last: McClatchie

first: Sanna

last: Janssen

first: Jay

last: Baltz

first: Matthew

last: Lorincz


title: Chemical profiling of DNA G-quadruplex-interacting proteins in live cells

city: Cambridge

first: Sergio

last: Martínez Cuesta

address: 1 Francis Crick Avenue

department: Data Sciences and Quantitative Biology, Discovery Sciences

institute: AstraZeneca

summary: DNA-protein interactions regulate critical biological processes. Identifying proteins that bind to specific, functional genomic loci is essential for understanding the underlying regulatory mechanisms on a molecular level. Here, we describe a novel co-binding-mediated protein profiling (CMPP) strategy to investigate the interactome of DNA G-quadruplexes (G4s) in cellular chromatin. CMPP involves cell-permeable, functionalized G4-ligand probes that bind endogenous G4s and subsequently crosslink to co-binding G4-interacting proteins in situ. We show the robustness of CMPP on proximity labelling of a G4 binding protein in vitro. Employing this approach in live cells, we identify hundreds of putative G4-interacting proteins from various functional classes. Next, we observe high G4 binding affinity and selectivity for several G4 interactors in vitro and confirm direct G4 interactions for one of the top candidates in chromatin. Our studies provide a chemical approach to map protein interactions of specific nucleic acid features in living cells.

overall_design: SMARCA4 ChIP-seq experiment to detect chromatin binding sites and compare to endogenous DNA G4 structures. Three technical replicates and one input.

first: Xiaoyun

last: Zhang

first: Jochen

last: Spiegel

last: Martinez Cuesta

first: Santosh

last: Adhikari

first: Shankar

last: Balasubramanian


title: Single-cell RNA-Seq reveals a highly coordinated transcriptional program in mouse oocytes during follicular formation

city: Beijing

first: Wenjie

last: Shu

address: Taiping Road 27

institute: Beijing Institute of Radiation Medicine

summary: To delineate the developmental trajectory of oocyte during the process, we performed RNA-seq on single germ cells from newborn (P0.5) ovaries and identified a series of genes that may function between stage transitions. The significant decrease of meiosis-related genes and the dramatic increase of oocyte-specific genes marked the transition of germ cell to a functional oocyte. Our data highlighted the complexity of transcriptional control and depicted the regulatons and their regulatory networks in oocyte development. Besides that, our data first characterized patterns of alternative splicing events and linked isform usage differences to cellular stage transitions of folliculogenesis. In summary, this study reconstructed molecular cascades in oocytes and revealed the orchestration of transcription-splicing coupling regulation on follicle formation.

overall_design: Total 146 single cells from newborn mice ovary  were performed.

first: Jing

last: Li

first: Zhibin

last: Hu

first: Yuanlin

last: He

first: QiuZhen

last: Chen


title: Expression data from glioblastoma surgical specimens

first: Yi

last: An

address: Changchun Street No.45

institute: xuanwu Hospital

summary:
Surgical resection is the first choice of the standardized treatment scheme for glioblastoma and is performed under general anesthesia. Previous researches have shown that propofol and sevoflurane have different effects on the biological process of glioma cells from the molecular level. Some of them, for instance, control the glioma cell proliferation, invasion and migration In vitro or In vivo.
We used mRNA microarray to discuss the effects of propofol and sevoflurane on gene expression in patients with glioblastoma. The correlation between DEGs and patients’ prognosis was further analyzed.

overall_design: Glioblastoma specimens were obtained from neurosurgery under aseptic conditions for RNA extraction and hybridization on Affymetrix microarrays. We sought to obtain the change of glioblastoma prognostic-related genes under the treatment of propofol and sevoflurane respectively. To that end, we divided the patients into TIVA group (received propofol-remifentanil intraoperatively) and INHA group (received sevoflurane-remifentanil intraoperatively). The specimens used for gene microarray analysis were matched according to the time of anesthesia and operation, tumor location and grade, and pathological type (IDH, Ki-67, etc.).

first: Lei

last: Zhao


title: Integrated transcriptional and phenotypic analysis of peripheral blood to capture the immunomodulating properties of pazopanib in rena; cell carcinoma patients

city: Doha

first: Darawan

last: Rinchai

state: Qatar

address: Al Gharrafa St

department: Research

country: Qatar

institute: Sidra Medicine

summary:
Background: The sequential and combination treatment with immune checkpoint inhibitors (ICIs) and tyrosine kinase inhibitors (TKIs) in metastatic renal cell carcinoma (mRCC) patients has entered the clinical practice. The dissection of the molecular mechanisms governing the impact of TKIs on the immune system is critical to implement therapeutic approaches and generate biomarkers. We here investigated the immunomodulatory activity of pazopanib in peripheral blood mononuclear cells (PBMCs) of mRCC patients through an integrative genomic analysis pipeline.
Results: The transcriptional analysis indicates a modulation of leukocyte functional orientation induced by pazopanib with an increase of immune effector cell subtypes and a decrease of immune suppressive populations. At the group level transcriptome profiles revealed perturbations to peak at 3 and decrease at 6 months. These included enrichments of modules associated with cytotoxic/NK (M3.6 and M8.46), plasma cells (M4.11), T cell (M4.15) and immune responses (M8.89). At individual patient level, pazopanib administration was associated with a decrease of the immunosuppressive module M9.34 in the majority of patients. Interestingly, a rapid increase of Interferon (IFN) modules (M1.2 and M3.4) was observed exclusively in patients displaying a strong enrichment in modules associated with cytotoxic/NK cells. Multicolor flow cytometry confirmed the association of pazopanib treatment with a decrease of immune suppressive cell subsets, including CD14+HLA-DRneg myeloid derived suppressor cells (MDSCs), CD14+ and CD14+PD-L1+ monocytes, CD15+ granulocytic MDSCs and CD4+CD25highFoxp3+ regulatory T cells. Concomitantly, a boost of activated CD3+PD-1dim T lymphocytes and cytotoxic CD3-CD16+CD56dim NK cells was observed. These changes were predominantly detectable after 3 months of therapy with pazopanib.
Conclusions: As systems approach, pazopanib reshapes anti-tumor immunity by relieving immunosuppression and triggering cytotoxic mechanisms and IFN pathways. The peak of this immune modulation is observed after 3 months of therapy. Our data provides a strong rationale in support of combinatorial or sequential therapies based on TKIs and immunotherapy approaches and for implementing transcriptomic analysis of blood as biomarker of immune responses.

overall_design: Transcriptome profiles of PBMCs, collected at baseline, 3 and 6 months from 9 mRCC patients receiving first-line pazopanib, were generated by transcriptomic analysis using Illumina HT12v4BeadChip. Immune profiles were obtained in parallel by multicolor flow cytometry. An integrative approach including leukocyte subset abundance estimation using single sample gene-set enrichment, and modular repertoire analysis, was employed to identify coherent perturbations associated with treatment-induced immunomodulation

first: Elena

last: Verzoni

first: Veronica

last: Huber

first: Agata

last: Cova

first: Paola

last: Squarcina

first: Loris

last: De Cecco

first: Paolo

last: Grassi

first: Raffaele

last: Ratta

first: Matteo

last: Dugo

first: Luca

last: Lalli

first: Viviana

last: Vallacchi

first: Monica

last: Rodolfo

first: Chiara

last: Castelli

first: Damien

last: Chaussabel

first: Giuseppe

last: Procopio

first: Davide

last: Bedognetti

first: Licia

last: Rivoltini


title: ChIP-seq dataset for epigenomic landscape of MPNST

first: Ayush

middle: T

last: Raman

address: 75 Ames St

department: Epigenomics Program

institute: Broad Institute of MIT and Harvard

summary: In order to comprehensively define the epigenetic patterns specific to MPNST, we generated profiles for 6 histone modification marks, including H3K4me1 (enhancer), H3K27Ac (active enhancer), H3K9me3 (heterochromatin), H3K27me3 (polycomb repression), H3K79me2 (transcription) and H3K4me3 (promoter). Systematic epigenomic profiling of chromatin states in MPNST cells revealed epigenetic subtypes in MPNST based on Polycomb related repressive and bivalent chromatin states. We demonstrate that PRC2 loss led to de-repression and subsequent enhancer reprogramming at key neural crest specifiers aiding the acquisition of this de-differentiated aggressive tumor phenotype.

overall_design: The dataset contains 5 PRC2 mutant and 4 PRC2 WT MPNST cell lines, 1 NSC  sample for 6 histone marks (H3K4me1, H3K9me3, H3K27Ac, H3K79me2, H3K4me3, H3K27me3) and input.

first: Veena

last: Kochat

first: Keila

last: Torres

first: Kunal

last: Rai


title: SREBF1 coordinates with master transcription factors in regulating lipid metabolism and cancer-promoting pathways in squamous cell carcinoma [4C]

status: Public on Jun 26 2021

city: Los Angeles

first: Qian

last: Yang

state: CA

address: 8700 Beverly Blvd

department: Department of Surgery

institute: CEDARS SINAI MEDICAL CENTER

summary: To determine whether a TP63/KLF5-regulated super-enhancer region can impact SREBF1 transcription, circularized chromosome conformation capture (4C) assays were performed. 4C assays identified complex, extensive interactions between the SREBF1 promoter and the super-enhancer region Moreover, these DNA-DNA contacts were strictly confined within the super-enhancer region, highlighting the specificity of chromatin interactions

overall_design: We performed Circularized chromosome conformation capture (4C) assays in TE5 cells using the SREBF1 promoter as bait to measure the direct contact between the super-enhancer and SREBF1 promoter. The viewpoint of SREBF1 promoter region was chr17:17738740-17740085 (hg19) with 4C primers: NEST-Forward-GCAACCAGCTGGGCTCAT, OUTER-Forward-GAAGCAACGGGCCTCCTAAT, NEST-Reverse-CTGCTGACCGACATCGAAGG and OUTER-Reverse-TTGCGAGGTTACTCACGGTC

first: Li-Yan

last: Li

first: Yan-Yi

last: Jiang

first: Wei

first: Yuan

first: Masaharu

last: Hazawa

first: Bo

last: Zhou

first: Guowei

last: Huang

first: Xiu-E

last: Xu

first: Sigal

last: Gery

first: Ying

last: Zhang

first: Ling-Wen

last: Ding

first: Allen

last: Ho

first: Zachary

last: Zumsteg

first: Mingrong

last: Wang

first: Melissa

last: Fullwood

first: Stephen

last: Freedland

last: Meltzer

first: En-Min

first: H

last: Koeffler

first: De-Chen

last: Lin


title: Integrated analysis of the transcriptome wide m6A methylome in Peripheral nerve injury

status: Public on Jun 27 2021

city: Tian Jin

first: Xianhu

address: NO.154,Anshan Road,Heping District

department: Department of Orthopedics

institute: Tianjin Medical University General Hospital

summary: N6-methyladenosine(m6A) is the most plentiful internal RNA modification, especially in eukaryotic messenger RNA (mRNA), which plays pivotal roles in mRNA life cycle and nerve development processes. In this study, samples were collected from Sciatic Nerve Injury (SNI) after 7 days and control rats. Altered peaks of m6A-modified transcripts were mainly related to immune system process, cell activation and nervous system development. KEGG pathway analyses highlighted the Axon guidance pathway, Calcium signaling pathway and B cell receptor signaling pathway. These data further enrich the contents of epigenetics in Peripheral Nerve Injury and provide a new opinion to promote the function recovery

overall_design: Transcriptome profile of m6A methylation in Peripheral Nerve Injury

first: Lei


title: Analysis on Replication and Transcription of SARS-CoV-2 and inhition effect of Remdesivir

city: Shenzhen

first: Yan

last: Zhao

address: No. 1088,Xueyuandadao

department: BIology

institute: Southern University of Science and Technology

summary: SARS-CoV-2, a betacoronavirus with a positive-sense, single-stranded RNA genome, caused the COVID-19 pandemic with unprecedent health and socio-economic crisis. Although its general sense mRNA architecture was reported, that of its negative strand was unexplored. We combined poly(A)-mRNA and ribosomal RNA-depleted sequencing to delineate several fine features of both RNA strands. Together with the transcriptome data under the perturbation of anti-viral drug Remdesivir, this project opens new sights into SARS-CoV-2 replication mechanism and may facilitate the anti-viral drug design.

sample_organism: Severe acute respiratory syndrome coronavirus 2

overall_design: Overall 10 samples are analyzed, six of which are Poly(A) RNA-seq and four are Ribozero RNA-seq samples.  Poly(A) RNA-seq samples contain two treatment conditions with triplicates. Ribozero RNA-seq samples contain two treatment conditions with duplicates.

first: YuHui

last: Hu

first: JinCun

first: Jing

last: Sun


title: Genome-wide maps of chromatin state in kidney of  wild type (WT) and pod-SAHH-/- mice and ADA-treated mice

first: Yunjun

last: Xiao

address: Zhenyuan Road 628

institute: Sun Yat-sen University

summary: We report the application of single-molecule-based sequencing technology for high-throughput profiling of histone modifications in kidney. By obtaining over four billion bases of sequence from chromatin immunoprecipitated DNA, we generated genome-wide chromatin-state maps of mouse kidney. This study provides a framework for the application of comprehensive chromatin profiling towards characterization of  kidney of  wild type (WT) and pod-SAHH-/- mice and ADA-treated mice.

overall_design: Examination of 1 histone modifications in  kidney.


title: RNA-seq dataset for MPNST patient tissue samples

first: Ayush

last: Raman

summary: Comprehensive transcriptomic profiling of PRC2 mutant MPNST patient tissues with adjacent normal tissues and neurofibroma patient tissues was performed to investigate gain of specific transcriptional signature associated with PRC2 loss during transformation to MPNST.

overall_design: There are 17 samples with 7 tumor samples, 7 adjacent normal samples and 3 neurofibroma samples.

first: Veena

last: Kochat

first: Sharon

last: Landers

first: Angela

last: Bhalla

first: Keila

last: Torres

first: Kunal

last: Rai


title: Genetic and pharmacological evidence for kinetic competition between alternative poly(A) sites in yeast - 3'end cleavage factor mPAT

status: Public on Jun 25 2021

city: Clayton

first: Rachael

last: Turner

state: Victoria

address: Wellington Road

department: Biochemistry and Molecular Biology

country: Australia

institute: Monash University

summary: mPAT approach was used to determine changes to 3'UTR length in yeast upon mutation of cleavage and polyadenylation factor subunits compared to wild type cells

overall_design: Yeast cells were grown at 25ºC until an OD600 of 0.6 was reached then transferred to 37ºC for 1 hour before harvesting. Replicates were pooled and samples were analysed via mPAT using the Illumina MiSeq platform.

first: Traude

middle: H

last: Beilharz

first: Bernhard

last: Dichtl


title: Epigenomic reprogramming due to PRC2 functional loss induces an aggressive de-differentiated neural crest-like phenotype in MPNST

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

overall_design: Refer to individual Series


title: mRNA-seq data for DDX3 knockdown in murine hepatocytes in vivo and in vitro

city: Moscow

first: Evgeniya

last: Shcherbinina

address: Bolshoy Boulevard 30, bld. 1

country: Russia

institute: Skolkovo Institute of Science and Technology

summary: A transcriptome analysis was performed to estimate a primary response of the hepatocytes to depletion of DDX3 RNA helicase both in vitro and in vivo. We used two siRNAs with different efficacy and demonstrated protein level-dependent effects on DDX3 RNA helicase depletion in the murine liver. We found that strong reduction of DDX3 protein (>85%) leads to similar changes in vitro and in vivo – we observed deregulation of cell cycle, Wnt and cadherin pathways. However, more modest downregulation of DDX3 protein (60-65%) resulted in discordant results between gene expression in vitro and in vivo – in vitro data were close to those under strong reduction, while in vivo phenotype was weak. These results demonstrate that the level of active DDX3 protein can dramatically influence on the phenotype in vivo, which should be taken into account during drug development.

overall_design: Analysis of differential expression after DDX3 knockdown with two different siRNAs in murine hepatocytes in vivo and in vitro

first: O

middle: V

last: Sergeeva


title: RNA-seq dataset for MPNST cell lines

summary: Comprehensive transcriptomic profiling of PRC2 mutant and WT  MPNST cell lines were performed to investigate PRC2-dependent transcriptional programs that are activated due to PRC2 loss

overall_design: There are 6 PRC2 mutant and 6 PRC2 WT MPNST cell lines each with 3 biological replicates. 1 NSC  sample with 3 biological replicates is included as control.


title: Genetic and pharmacological evidence for kinetic competition between alternative poly(A) sites in yeast - NNS complex

summary: PAT-seq approach was used to determine changes to 3'UTR length in yeast upon mutation of NNS subunits Nrd1 (nrd1-5), Nab3 (nab3-11) and Sen1 (sen1-1) compared to wild type cells

overall_design: Yeast cells were grown at 25ºC until an OD600 of 0.6 was reached then transferred to 37ºC for 1 hour before harvesting. Samples were analysed via PAT-seq 3'UTR focused deep-sequencing in replicate using the Illumina Hiseq1500 platform.


title: Cell-to-cell variability in PAX3:FOXO1 expression determines tumorigenic potential in rhabdomyosarcoma

city: Freiburg

first: Manching

last: Ku

address: Mathildenstrasse 1

department: Hematology and Oncology

institute: Medical Center - University of Freiburg

summary: The rhabdomyosarcoma (RMS) cell pool is phenotypically and functionally heterogeneous. Low passage cell lines established from Myf6Cre,Pax3:Fkhr,p53 mouse RMS and primary human RMS cultures were used to demonstrate marked heterogeneity in PAX3:FOXO1 (P3F) expression at the single-cell level. In mouse Myf6Cre,Pax3:Fkhr,p53 RMS cells, expression of P3F is directed by the Pax3 promoter and coupled to an eYFP fluorescent marker. YFPlow/ P3Flow mouse RMS cells included 87±0.2% G0/ G1 cells, differentially expressed transcripts involved in extracellular matrix interaction and reorganized their actin cytoskeleton to produce a cellular phenotype characterized by more efficient adhesion and migration compared to YFPhigh/ P3Fhigh cells. By contrast, 49±3.2% of YFPhigh/ P3Fhigh cells were in the G2/ M phase of the cell cycle, and higher P3F expression correlated with higher proliferation rates. These differences translated into higher tumor-propagating cell frequencies in limiting dilution analyses and higher clonal activity of YFPlow/ P3Flow compared to YFPhigh/ P3Fhigh cells. Both YFPlow/ P3Flow and YFPhigh/P3Fhigh cells gave rise to mixed clones, consistent with fluctuations in P3F expression at the cellular level over time. Finally, exposure to the anti-tropomyosin compound TR100 disrupted the actin cytoskeleton and reversed more efficient migration and adhesion in YFPlow/ P3Flow RMS cells. We speculate that conversion from one phenotype to another may result in adaptive plasticity and may provide a critical advantage during tumor progression

overall_design: We performed ATAC-Seq on YFP high / P3F high and YFP low / P3F low cells isolated from mouse rhabdomyosarcoma cells U23674.

first: Eugene

last: Ke

first: Carla

last: Regina

first: Simone

last: Hettmer


title: Negative correlation of Pax3:Foxo1 expression at the single-cell-level with tumorigenic potential in rhabdomyosarcoma

first: Geoffroy

last: Andrieux

address: Breisacherstr 153

institute: University clinics Freiburg

summary:
In mouse Myf6Cre,Pax3:Foxo1,p53 rhabdomyosarcoma (RMS) cells, expression of Pax3:Foxo1 (P3F) is directed by the Pax3 promoter and coupled to an eYFP fluorescent marker.
YFPlow/P3Flow mouse RMS cells differentially expressed transcripts involved in extracellular matrix interaction, reorganized their actin cytoskeleton to promote adhesion/ migration and exhibited higher tumor-propagating capacity in limiting dilution analyses.

overall_design: Total RNA was isolated from YFPlow/P3Flow, YFPhigh/P3Fhigh and unfractionated low-passage mouse RMS cells (U23674) and analyzed by Clariom S Assays, mouse arrays (Affymetrix 902931).

first: Melanie

last: Boerries

first: Charles

last: Keller


title: Genetic and pharmacological evidence for kinetic competition between alternative poly(A) sites in yeast


title: Genetic and pharmacological evidence for kinetic competition between alternative poly(A) sites in yeast - 4tU cordycepin treatment

summary: mPAT approach using an anchored oligo-dT (TV12VN) primer to determine changes to 3'UTR length in yeast upon cordycepin treatment and new transcription using 4-thiouracil (4tU) labelling of RNA. This appears as a T to C conversion in sequencing reads.

overall_design: BY4741 yeast cells were grown at 30ºC until an OD600 of 0.6 was reached then 20µg/ml cordycepin and 500µM 4tU or equivalent volumes of DMSO added for 0, 20 or 40 minutes before harvesting. Samples were analysed via mPAT with an anchored oligo-dT primer using the Illumina MiSeq platform.


title: Genetic and pharmacological evidence for kinetic competition between alternative poly(A) sites in yeast - cordycepin treatment

summary: PAT-seq approach was used to determine changes to 3'UTR length in yeast upon addition of 20µg/ml cordycepin (3'deoxyadenosine) for 0, 5, 10, 20 or 40 minutes

overall_design: BY4741 yeast cells were grown at 30ºC until an OD600 of 0.6 was reached then 20µg/ml cordycepin was added for 0, 5, 10, 20 or 40 minutes before harvesting. Samples were analysed via PAT-seq 3'UTR focused deep-sequencing in replicate using the Illumina Hiseq1500 platform.


title: Genetic and pharmacological evidence for kinetic competition between alternative poly(A) sites in yeast - 4tU cordycepin treatment with rpb1 slow mutant

summary: mPAT approach using an anchored oligo-dT (TV12VN) primer to determine changes to 3'UTR length in yeast with a slow RNA polymerase II mutant rpb1-1, complemented with wild-type RPB1 or a slow rpb1 mutant plasmid, upon cordycepin treatment and new transcription using 4-thiouracil (4tU) labelling of RNA. This appears as a T to C conversion in sequencing reads.

overall_design: rpb1-1 yeast cells carrying plasmids with either RPB1 wild-type (pCK859) or the rpb1-H1085Y slow mutation (pCK870) were grown at 25ºC until an OD600 of 0.6 was reached then 20µg/ml cordycepin and 500µM 4tU or equivalent volumes of DMSO added for 0, 20 or 40 minutes before harvesting. Samples were analysed via mPAT with an anchored oligo-dT primer using the Illumina MiSeq platform.


title: Genetic and pharmacological evidence for kinetic competition between alternative poly(A) sites in yeast - 3'end cleavage factors

summary: PAT-seq approach was used to determine changes to 3'UTR length in yeast upon mutation of the core cleavage and polyadenylation subunits Rna14 (rna14-1), Pcf11 (pcf11-2), Clp1 (clp1-K136A-T137A), Hrp1/Nab4 (Nab4-1), Ysh1 (ysh1-13), Fip1 (fip1-1) and Pap1 (pap1-1) compared to wild type cells


title: Mouse HFD Liver Skeletal Muscle SLC16A13 Knock-Out

status: Public on Jun 24 2021

city: Biberach a.d. Riss

first: Eric

last: Simon

address: Birkendorfer Str. 65

institute: Boehringer Ingelheim Pharma GmbH & Co KG

summary: Genome-wide association identified SLC16A13 as novel type 2 diabetes gene locus. The  SLC16A13 gene encodes for SLC16A13/MCT13, member of the solute carrier 16 family of  monocarboxylate transporters. This transporter family recently raised interest in metabolic  research with the identification of SLC16A11 polymorphisms associated with type 2 diabetes;  and human as well as mouse data suggest causal relationship between SLC16A11/MCT11  transporter dysfunction and type 2 diabetes development. In contrast, SLC16A13 biology and  physiological function is not characterized at all. Here, we validate SLC16A13 as  monocarboxylate transporter expressed at the plasma membrane and report the first  Slc16a13 knockout mouse line. Deletion of Slc16a13 ameliorates metabolic disease in the  context of diet-induced obesity. The improved metabolic phenotype is characterized by  increased mitochondrial respiration in the liver, leading to reduced hepatic lipid accumulation  and increased insulin sensitivity of Slc16a13 knockout mice. Mechanistically, we propose  reduced intracellular lactate availability in Slc16a13 knockout hepatocytes, affecting hepatic  energy metabolism by AMPK activation and increased oxidative phosphorylation, reducing  hepatic lipid content and insulin resistance in obese mice. Together, these data suggest  SLC16A13/MCT13 as potential novel target to treat fatty liver, insulin resistance and related  metabolic disorders.

overall_design: We profiled liver and skeletal muscle bulk tissue from 11 SCL16A13 knock-out vs. 11 wild type mice

first: T

last: Schumann

first: B

last: Hamilton

first: E


title: The type 3 deiodinase contributes to the reduced sensitivity of the fetal brain to thyroid hormone

city: Scarborough

first: Arturo

last: Hernandez

state: ME

address: 81 Research Drive

department: Center for Molecular Medicine

institute: Maine Medical Center Research Institute

summary: We examined the impact of thyroid hormone on the mouse fetal brain utilizing a model of deficiency in DIO3, the enzyme that is responsible for clearing thyroid hormones

overall_design: RNA sequencing profile of male fetal brain at E13.5 and E18.5 of gestation

first: M

last: Martinez


title: MeCP2 is a microsatellite binding protein that protects CA repeats from nucleosome invasion

city: ILLKIRCH-GRAFFENSTADEN

first: Christophe

last: Papin

address: 1 rue Laurent Fries

institute: IGBMC - CNRS UMR 7104 - Inserm U 964

summary: The Rett syndrome protein MeCP2 was described as a methyl-CpG-binding protein, but its exact function remains unknown. Here we show that MeCP2 is a microsatellite binding protein that specifically recognizes hydroxymethylated CA repeats. Depletion of MeCP2 alters chromatin organization of CA repeats and lamina-associated domains and results in nucleosome accumulation on CA repeats and genome-wide transcriptional dysregulation. The structure of MeCP2 in complex with a hydroxymethylated CA repeat reveals a characteristic DNA shape, with significantly modified geometry at the 5-hydroxymethylcytosine, which is recognized specifically by Arg133, a key residue whose mutation causes Rett syndrome. Our work identifies MeCP2 as a microsatellite DNA binding protein that targets the 5hmC-modified CA-rich strand and maintains genome regions nucleosome-free, suggesting a role for MeCP2 dysfunction in Rett syndrome.

overall_design: In this work we have carried out an in-depth study on the role of MeCP2 in mouse embryonic fibroblasts. The use of cell lines WT and KO for MeCP2 combined with biochemical, genomic and structural approaches, has allowed to demonstrate that MeCP2 is a (CA)n microsatellite DNA binding protein. We show that within the MBD family, MeCP2 is the only protein that specifically recognizes and binds to CA repeats, with much stronger affinity as compared to mCG and mCA. While MeCP2 can bind in vitro to modified and non-modified CA repeats, it exhibits impressive selectivity towards hydromethylated CA repeats, which are modified by the enzyme DNMT3A. The modified cytosine, only when located within a CA repeat, serves as a nucleation point for both MeCP2 accumulation and spreading around the repeat, which correlates in turn with nucleosome exclusion. In addition, loss of MeCP2 results in widespread increase in nucleosome density within lamina-associated domains (LADs) and transcriptional dysregulation of CA repeat–enriched genes located outside LADs.


title: Gene expression Analysis in Renal Allograft Biopsies from Deceased and Living Donors

status: Public on Jun 23 2021

city: Leicester

first: Bin

last: Yang

state: Leicestershire

address: University Road

department: Cardiovascular Sciences

institute: University of Leicester

summary: The survival of transplant kidneys using deceased donors (DD) is inferior to living donors (LD). In this study, we conducted a whole-transcriptome expression analysis of 24 human kidney biopsies paired 30 minutes and 3 months post-transplantation using DD and LD. The transcriptome profile was found significantly different between two time points regardless of donor types. There were 446 differentially expressed genes (DEGs) between DD and LD at 30 minutes and 146 DEGs at 3 months, with 25 genes common to both time points. These DEGs reflected donor injury and acute immune responses associated with inflammation and cell death as early as at 30 minutes, which could be a precious window of potential intervention. DEGs at 3 months mainly represented the changes of adaptive immunity, immunosuppressive treatment, remodeling or fibrosis via different networks and signaling pathways. The expression level of 20 DEGs involved in kidney diseases, and 10 genes found dysregulated at 30 minutes were validated by quantitative PCR (qPCR) in the 24 samples analyzed by microarray as well as in a validation cohort of 33 unpaired allograft biopsies. Their expression levels were found correlated with renal function and histology at 12 months, suggesting they could be potential biomarkers to predict kidney function. This analysis revealed that SERPINA3, SLPI and CBF is upregulated at 30 minutes in DD compared to LD, whereas FTCD and TASPN7 are up-regulated at both time points; at 3 months VCAN and TIMP1 are up-regulated, whereas FOS is decreased in both donors. Taken together, divergent transcriptomic signatures between DD and LD, and changed by the time post-transplantation, might contribute to different allograft survival of two type kidney donors. Some DEGs such as FTCD and TASPN7 could be novel biomarkers not only for timely diagnosis, but also early for precise genetic intervention at donor preservation, implantation and post-transplantation, in particular to effectively improve the quality and survival of DD.

overall_design: A total of 24 biopsies were taken from allograft kidneys 30 minutes (n=12) and then 3 months (n=12) post-transplantation. Biopsies come 12 deceased donors and 12 living donors.

first: Nicolas

last: Sylvius


title: Sex-based differences in cardiac gene expression and function in BDNF Val66Met mice

city: Pittsburgh

first: Cristi

middle: Lara

last: Galindo

state: Pennsylvania

address: 200 Lothrop Avenue

institute: University of Pittsburgh

summary:
Purpose: The goal of this study was to compare whole heart transcriptomes of hBDNF trasngenic mice to ascertain underlying molecular mechanisms for differences in cardiac function among genotypes
Methods: Total RNA extracted from whole hearts of 8-week-old mice, and RNA libraries were constructed using the Illumina TruSeq Stranded Total RNA kit. Libraries were sequenced using Illumina HiSeq 3000 on paired-end-150 flow cell runs at ~32M PF reads per sample. Raw reads (fastq files) were uploaded to the Partek Flow server and pre-alignment quality assessment was performed. Mean base-call quality scores were above Phred-like values of 36 in all positions of all samples, and no hard trimming of the reads was necessary. Sequences were aligned to the mm10 assembly of the mouse genome using STAR 2.5.3a and resulting summary of reads filtered (<80) and quantified at the gene level to Ensemble transcripts 83 using Partek’s expectation maximization (E/M) annotation model. Gene counts were normalized to total read count per sample and then log-transformed (with an offset of 0.0001). To identify differentially expressed genes, statistical analysis was performed using Partek’s Gene Specific Analysis (GSA) multimodal estimation algorithm, followed by SYBR Green qPCR validation.
Results: We found female-specific cardiac alterations in both heterozygous and homozygous carriers, including reduction in the gene encoding SERCA2 (Atp2a2) in homozygous Met/Met mice but more profoundly in females compared to males. Enriched functions in females with the Met allele included cardiac hypertrophy in response to stress, with down-regulation of the gene encoding titin (Tcap) and upregulation of BNP (Nppb), in line with altered cardiac functional parameters. Homozygous male mice on the other hand exhibited an inflammatory profile characterized by interferon-γ (IFN-γ)-mediated Th1 immune responses.
Conclusions: . These results provide evidence for sex-based differences in how the BDNF polymorphism modifies cardiac physiology, including female-specific alterations of cardiac-specific transcripts and male-specific activation of inflammatory targets.

overall_design: Whole heart mRNA profiles of 8 week old wild type (Val), hterozygous (Val/Met) and homozygous (Met) mice