title: Identification of a CD117+ CD71+  early unipotent neutrophil progenitor population in human bone marrow

status: Public on Aug 04 2020

city: La Jolla

first: Huy

middle: Q

last: Dinh

address: 9420 Athena Circle

department: Division of Inflammation Biology

institute: La Jolla Institute

summary: Neutrophils play critical roles in health and disease. Due to their very short half-life in blood and tissue, neutrophils are constantly replenished by bone marrow progenitors. Thus, a comprehensive understanding of bone marrow neutrophil development is of paramount importance to identify how neutrophil production is altered in disease. Recently, two novel human neutrophil progenitor populations were identified; ‘human neutrophil progenitor’ or ‘hNeP’ (Lin- CD66b+ CD117+ ) and ‘neutrophil precursor’ or ‘preNeu’ (Lin- CD66b+ CD15+ CD49d+ ). How these subsets fit into the neutrophil lineage is unclear. By using mass and flow cytometry, we show that hNeP are a heterogenous population containing a homogeneous progenitor subset termed ‘early neutrophil progenitor’ or ‘eNeP’ (Lin- CD66b+ CD117+ CD71+ ). Surface marker and RNA expression, together with the ability to form colonies in vitro and exclusively produce neutrophils in vivo in humanized NSG-SGM3 mouse transfer experiments indicate that eNeP are hierarchically the ‘earliest’ cells within preNeu. eNeP constitute ~0.14% of human bone marrow neutrophils, while preNeu constitute ~5% of bone marrow neutrophils. Furthermore, we have identified CD71 as a novel neutrophil surface marker associated with distinct early neutrophil developmental stages. Intriguingly, CD71+ characterizes proliferating neutrophils, which are expanded in the blood of melanoma and lung cancer patients and detectable in human lung tumors. Collectively, our findings i) identify CD117+ CD71+ eNeP as an early neutrophil progenitor population, ii) introduce a unified model of human neutrophil bone marrow development, iii) identify novel surface markers for distinct neutrophil developmental stages and iv) provide evidence for neutrophil progenitor expansion in cancer.

overall_design: Expression profiling by high throughput sequencing for sorted neutrophils cells in human bone marrow

first: Tobias

last: Eggert

first: Melissa

last: Meyer

first: Catherine

last: Hedrick


title: mRNA profiles of human Dedifferentiated Adipose Cells and Adipose-derived stem cells in young donors

status: Public on Aug 07 2020

city: Beijing

first: Fangfei

last: Nie

address: 49 North Garden Rd.,Haidian District

department: Department of Plastic Surgery

country: China

institute: Peking university third hospital

type: Expression profiling by high throughput sequencing

summary: Dedifferentiated Fat Cells (DAs) and Adipose-derived stem cells (ADSCs) are two main stem cells derived from adipose tissue. In order to explore whether there is difference in transcriptome between the two cells after multiple subcultures, and which kind of cell should be selected for different regenerative aim, high-throughput RNAseq were conducted to find differentially expressed genes. The subcutaneous adipose tissue of three young women (23-30 years old)patients with normal BMI (19-24) were obtained during liposuction operation on abdomen or thigh. Stromal Vascular Fraction (SVF) and adipocytes were obtained by collagenase digestion, ADSCs was cultured regularly, and DAs were cultured by a modified ceiling culture method. Only 186 genes with different expression between the two groups were obtained.The downregulated gene number of DAs vs. ADSCs was 112 and the upregulated number was 74. Many of the differentially expressed genes are involved in the biological functions such as transcription regulator, protein translation regulation, cytokine interaction and energy metabolism regulation. These data may provide a foundation for further clinical administration of stem cells derived from adipose tissues.

overall_design: Comparison of mRNA expression profiles between human Dedifferentiated Adipose Cells and Adipose-derived stem cells obtained from tumenecent liposuction in young donors

first: Hongsen

last: Bi


title: Transcriptome analysis of the brown rot fungus Gloeophyllum trabeum during lignocellulose degradation

status: Public on Aug 05 2020

city: Nara

first: Kiwamu

last: Umezawa

department: Applied Biological Chemistry

country: Japan

institute: Kindai University

summary: Brown rot fungi have great potential in biorefinery wood conversion systems, because they are the primary wood decomposers in coniferous forests and have an efficient lignocellulose degrading system. Their initial wood degradation mechanism is thought to consist of an oxidative radical-based system that acts sequentially with an enzymatic saccharification system, but the complete molecular mechanism of this system has not yet been elucidated. Some studies have shown that wood degradation mechanisms of brown rot fungi have diversity in their substrate selectivity. Gloeophyllum trabeum, one of the most studied brown rot species, has broad substrate selectivity and even can degrade some grasses. However, the basis for this broad substrate specificity is poorly understood. In this study, we performed RNA-seq analyses on G. trabeum grown on media containing glucose, cellulose, or Japanese cedar (Cryptomeria japonica) as the sole carbon source. Beyond the gene expression on glucose, 1129 genes were upregulated on cellulose and 1516 genes were upregulated on cedar. Carbohydrate Active enZyme (CAZyme) genes upregulated on cellulose and cedar media by G. trabeum included GH12, GH131, CE1, AA3_1, AA3_2, AA3_4 and AA9, which is a newly reported expression pattern for brown rot fungi. The upregulation of both terpene synthase and cytochrome P450 genes on cedar media suggests the potential importance of these genes in the production of secondary metabolites associated with the chelator-mediated Fenton reaction. These results provide new insights into the inherent wood degradation mechanism of G. trabeum and the diversity of brown rot mechanisms.

overall_design: Gloeophyllum trabeum was cultivated on liquid media containing glucose, microcrystalline cellulose, or Japanese cedar (Cryptomeria japonica) as the sole carbon source. The fungus was cultivated in flasks on a rotary shaker (160 rpm) at 27°C for 3 days (glucose) or 5 days (cellulose and cedar). Three biological replicates were performed for each carbon source.

first: Mai

last: Niikura

first: Yuka

last: Kojima

first: Barry

last: Goodell

first: Makoto

last: Yoshida


title: A3shNT cell transcriptomics

city: Stockholm

first: Daniel

middle: Wesley

last: Hagey

address: Nobels vag 3

country: Sweden

institute: Karolinska Institutet

summary: Altered oncogene expression in cancer cells causes loss of redox homeostasis resulting in oxidative DNA damage, e.g., 8-oxoguanine (8-oxoG), repaired by base excision repair (BER). PARP1 coordinates BER and relies on the upstream 8-oxoguanine-DNA glycosylase (OGG1) to recognise and excise 8-oxoG. Here we hypothesize that OGG1 may represent an attractive target to exploit reactive oxygen species (ROS) elevation in cancer. Although OGG1 depletion is well tolerated in non-transformed cells, we report here that OGG1 depletion obstructs A3 T-cell lymphoblastic acute leukemia growth in vitro and in vivo, validating OGG1 as a potential anti- cancer target. In line with this hypothesis, we show that OGG1 inhibitors (OGG1i) target a wide range of cancer cells, with a favourable therapeutic index compared to non-transformed cells. Mechanistically, OGG1i and shRNA depletion cause lost mitochondrial function leading to S- phase DNA damage, replication stress and proliferation arrest or cell death, representing a novel mechanistic approach to target cancer. This study adds OGG1 to the list of BER factors, e.g., PARP1, as potential targets for cancer treatment. _x000B_

overall_design: A3shNT cells were treated with OGG1 inhibitor TH5487 or DMSO and sequenced 24 hours later

first: Carlos

last: Benitez-Buelga


title: Transcriptional profiling of ileal lamina propria lymphocytes of wild type and Lyz1KO mice by single-cell RNA-seq

status: Public on Aug 19 2020

city: Newark

last: Gao

state: NJ

address: 195 University Avenue

department: Biological Sciences

country: USA

institute: Rutgers, the State University of New Jersey

summary: Paneth cells express Lyz1, a gene encoding for lysozyme. To investigate the transcriptomic profiles of wild type and Lyz1-knockout mouse ileal lamina propria cells, we performed single-cell RNA-seq.

overall_design: Lamina propria lymphocytes and stromal cells were isolated from wild type and Lyz1KO mice and analyzed by droplet-based 3' scRNA-seq (10x).

first: Shiyan

last: Yu

first: Iyshwarya

last: Balasubramanian

first: Xiang

last: Lin

first: Juan

last: Flores


title: Sex differences in nociceptor translatomes contribute to divergent prostaglandin signaling in male and female mice

city: Richardson

first: Diana

last: Tavares-Ferreira

address: 800 W. Campbell Road

department: School of Behavioral and Brain Sciences

institute: University of Texas at Dallas

summary: There are clinically relevant sex differences in acute and chronic pain mechanisms, but we are only beginning to understand their mechanistic basis.  Transcriptome analyses of rodent whole dorsal root ganglion (DRG) have revealed sex differences, mostly in immune cells. We examined the transcriptome and translatome of the mouse DRG with the goal of identifying sex differences.

overall_design: Investigation of paired unbiased total RNA profile (bulk RNA-seq) and mRNA bound to ribosome profile based on eGFP-RPL10a pulldown in Nav1.8+ DRG nociceptors (TRAP-seq) for naive mice DRG (3 mice per sex were pooled for each of 4 biological replicates)

first: Theodore

middle: J

last: Price


title: The ISW1a ATP-dependent chromatin remodeler acts specifically on dinucleosomes to regulate early transcription

status: Public on Jul 31 2020

city: Smithville

first: Blaine

last: Bartholomew

address: 1808 Park Road 1C

department: Epigenetics and Molecular Carcinogenesis

institute: MD Anderson Cancer Center

type: Genome binding/occupancy profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: The ISW1a ATP-dependent chromatin remodeler acts specifically on dinucleosomes to regulate early transcription [RNA-seq]

summary: The large family of ATP-dependent chromatin remodelers that regulate chromatin organization  and composition are thought to act only on individual mononucleosomes. We discovered  however that the yeast ISW1a remodeler has a much higher affinity for dinucleosomes and only  efficiently converts ATP hydrolysis into nucleosome movement when bound to dinucleosomes,  not mononucleosomes. The Ioc3 accessory subunit and its HLB DNA binding domain confer  dinucleosome specificity onto the Isw1 catalytic subunit. Perturbation of ISW1a dinucleosome  specificity by mutating Ioc3 interferes with its localization immediately downstream of the early  transcription complex. ISW1a and NuA4, a histone acetyl transferase, and SWR1, a histone  exchanger, are required together to slow early passage of RNA polymerase II. These findings  provide new insights into the unusual specificity of a chromatin remodeler regulating the  transition from transcription initiation to elongation and its functional interplay with other  chromatin modifiers.

overall_design: Eighteen samples - triplicate (RNA-seq). Samples were compared in presence or absence of Yaf9 background.

first: Solomon

middle: G

last: Hailu


title: RNA deep sequencing data of the whole transcriptomes of the wild-type and aa3 mutant strains of Mycobacterium smegmatis MC2 155

status: Public on Jul 29 2020

city: Busan 46241, Republic of Korea

first: Yuna

last: Oh

address: Busandaehakro63bun-gil, 2

department: Department of Integrated Biological Science

country: South Korea

institute: Pusan national university

summary: Our comparative RNA sequencing analysis of the wild-type strain of M. smegmatis and its isogenic aa3 mutant strain lacking the aa3 cytochrome c oxidase of the respiratory electron transport chain revealed that expression of the SigF regulon is strongly induced in the aa3 mutant relative to the wild-type strain

overall_design: Comparison of gene expression between the wild-type and aa3 mutant strains of mycobacterium smegmatis that are aerobically grown.

first: Jeong-Il

first: Ji-A

last: Jeong


title: Control of gene expression by PdeL, a transcription regulator and c-di-GMP phosphodiesterase in Escherichia coli K12

city: Cologne

first: Karin

last: Schnetz

address: Zuelpicher Str. 47a

department: Institute for Genetics

country: Germany

institute: University of Cologne

summary: PdeL is a transcription regulator and c-di-GMP specific phosphodiesterase in Escherichia coli. To address the transcription regulator function of PdeL we analyzed the transcriptomes of four E. coli K12 strains during the exponential growth phase by RNA-sequencing. These four strains included (1) wild-type E. coli K12 strain BW30270 carrying an empty vector control plasmid, (2) an isogenic pdeL deletion mutant carrying the control plasmid, as well as the pdeL mutant that was complemented with (3) a plasmid carrying pdeL under control of the IPTG-inducible tac promoter or (4) a plasmid encoding a fusion protein of the PdeL’s DNA-binding domain and the C-terminal dimerization domain of phage Lambda cI repressor (PdeL-DBD_cI-C). Expression of plasmid-encoded pdeL and pdeL-DBD_cI-C, respectively, was induced by addition of IPTG for 15 minutes prior to RNA isolation. Analyses of the RNA-seq data revealed that plasmid-provided PdeL (and PdeL-DBD_cI-C) repress transcription of class II flagellar genes and presumably regulate the transcription of additional loci, while only little differences were observed between the transcriptomes of wild-type strain BW30270 and its isogenic pdeL mutant.

overall_design: RNA-sequencing analyses were performed of three biological replicates (rep1, rep2, and rep3) of four different E. coli K12 strains, i.e. of a total of 12 RNA samples. The strains are E.coli K12 wild-type strain BW30270 carrying empty vector control plasmid (wt+ctrl), the delta-pdeL strain complemented with plasmidic pdeL (delta-pdeL+PdeL) or with the PdeL-cI fusion (delta-pdeL+PdeLDBD_cIc). The delta-pdeL strain carrying the empty vector control served as control (delta-pdeL+ctrl).

first: Cihan

last: Yilmaz


title: Identification of Candidate COVID-19 Therapeutics using hPSC-derived Lung Organoids

status: Public on Aug 11 2020

city: New York

first: Shuibing

last: Chen

state: NY

address: A 827B, 1300 York Ave

department: Surgery

institute: Weill Cornell Medical College

summary: The SARS-CoV-2 virus has caused already over 3.5 million COVID-19 cases and 250,000 deaths globally. There is an urgent need to create novel models to study SARS-CoV-2 using human disease-relevant cells to understand key features of virus biology and facilitate drug screening. As primary SARS-CoV-2 infection is respiratory-based, we developed a lung organoid model using human pluripotent stem cells (hPSCs) that could be adapted for drug screens.

overall_design:
We performed a high throughput screen using hPSC-derived lung organoids and identified FDA-approved drug candidates, including imatinib and mycophenolic acid, as inhibitors of SARS-CoV-2 entry.

Please note that the Series/sample records have been updated on Dec 8, 2020.

first: Huanhuan


title: Bromodomain 4 inhibition leads to MYCN downregulation in Wilms’ tumor cells

status: Public on Aug 12 2020

city: Beaverton

first: Charles

last: Keller

state: Oregon

address: 12655 Sw Beaverdam Rd West

department: Pediatric Cancer Biology

institute: cc-TDI

summary: We have undertaken a functional genomics approach to uncover novel therapeutic strategies efficacious for those patients with anaplastic Wilms’ tumor. Genomic analysis, in vitro chemical screens and microfluidic experiments demonstrate that MYCN over-expression in Wilms’ tumor can be modulated via BRD4 inhibition resulting in a reduction in Wilms’ tumor cell growth.

overall_design: Transcriptome analysis, in vitro chemical screens and microfluidic experiments demonstrate that MYCN over-expression in Wilms’ tumor can be modulated via BRD4 inhibition resulting in a reduction in Wilms’ tumor cell growth.

first: Andrew

middle: D

last: Woods

first: Noah

middle: E

last: Berlow

first: Melvin

last: Lathara

first: Joel

last: Michalek

first: Hollis

last: Wright

first: Brigitte

last: Royer-Pokora

first: Renata

last: Veselska


title: Profiling expression of genes at a critical developmental timepoint in diaphragm development.

city: Salt Lake City

first: Gabrielle

last: Kardon

state: Utah

department: Human Genetics

institute: University of Utah

summary:
Purpose: The goal of this study is to determine what genes are expressed, and at what level, in the developing diaphragm at a timepoint shown to be critical in the initiation of congenital diaphragmatic hernias in mice. Methods: PPFs were dissected from staged mouse embryos
Methods: summary Purpose: The goal of this study is to determine what genes are expressed, and at what level, in the developing diaphragm at a timepoint shown to be critical in the initiation of congenital diaphragmatic hernias in mice. Methods: PPFs were dissected from staged mouse embryos

overall_design: Epression profile of  2 biological pooled E12.5 pleuroperitineal fold pairs (2 dissected pairs per biological replicate) to prioritize candidate genes implicated from human congenital diaphragmatic studies.

first: Eric

middle: L

last: Bogenschutz

first: Zachary

last: Fox


title: Transcriptomal profiling of early and late response of cells to cell penetrating peptides

city: Abu Dhabi

first: Piergiorgio

last: Percipalle

state: Abu Dhabi

address: Saadiyat Campus, Abu Dhabi

department: Biology Department, Science Division

country: United Arab Emirates

institute: New York University Abu Dhabi

summary: We performed transcriptional profiling of cells treated with different cell penetrating peptides for different timepoints to see the effect of each peptide on cell biology and pathways which are affected by it. In conclusion, CPPs evoke similar response, regardless of the CPP structure or chemistry, mostly afecting genes related to ribosome biogenesis, microtubule dynamics and expression of long non-coding RNAs

overall_design: RNA seq of HeLa cells treated with different cell penetrating peptides for different time points. 2 replicates for each group

first: Tomas

last: Venit

first: Nizar

last: Drou


title: The ISW1a ATP-dependent chromatin remodeler acts specifically on dinucleosomes to regulate early transcription [MNase-Seq]

first: Blaine

last: Bartholomew

overall_design: Nine samples (WT ISW1a, △Ioc3 and Ioc3△cHLB) are compared in triplicates (MNase-seq).

first: Solomon

last: Hailu


title: Transcriptome analysis of dissected muscle tissue from whole-animal Drosophila melanogaster tumour models across a time course.

status: Public on Jul 28 2020

city: London

first: LMS

last: Bioinformatics Core

address: Hammersmith Hospital Campus, Du Cane Road

department: Bioinformatics Core

country: United Kingdom

institute: MRC London Institute of Medical Sciences

summary: Transcriptomic profiling along a time course of muscle wasting revealed a progressive deregulation of muscle structure and organisation. An array of molecular signatures were associated with this deregulation, including a perturbed ubiquitin-proteasome system, an increase in the unfolded protein response, and an increase in MAPK pathway signalling.

overall_design: Pooled dissected body wall muscle tissue was transcriptionally profiled in quadruplicate across a time course of muscle wasting.

first: Holly

last: Newton

first: Susumu

last: Hirabayashi

first: Yi-Fang

last: Wang


title: Hispidulin attenuates cardiac hypertrophy by improving mitochondrial dysfunction

status: Public on Jul 21 2020

city: Guangzhou

first: Chen

last: Liu

state: Guangdong

address: No.58, Zhongshan Er Road

institute: The First Affiliated Hospital of Sun Yat-sen University

summary:
Purpose:RNA-Seq analysis was performed on mouse hearts with or without hispidulin treatment 4 weeks after arotic banding or sham surgery to determining the effect of hispidulin on pressure overload induced cardiac hypertrophy.
Methods:  the mRNA profiles of mouse hearts underwent sham or arotic banding surgery with treatment of hispidulin or DMSO were generated by RNA-seq analysis in triplicate. The expression level of gene was calculated by RSEM(v.1.2.12). Differential expression analysis was performed using the DESeq2(V 1.4.5).
Results: RNA isolation, library construction, and sequencing were performed on a BGISEQ-500 (Beijing Genomic Institution, www.genomics.org.cn, BGI). For the gene expression analysis, the fold changes were also estimated according to the fragments per kilobase of exon per million fragments mapped (FPKM) in each sample. The significance of different gene expression was defined by the following filter criteria: false discovery rate (FDR) ≤0.001 and log2-ratio 1. After comparing of DMSO+AB group and hispidulin+AB group, we found that 113 genes were significantly differentially expressed. Gene ontology and cluster analysis indicated that alternated genes were enriched in fatty acid oxidation, glucose metabolism, TCA cycle, oxidative phosphorylation, hypertrophic cardiomyopathy, ECM organism, oxidative stress and unfolded protein binding. This result indicated that hispidulin improved mitochondrial function.
Conclusions: Our study represents the first detailed analysis of heart transcriptomes, with biologic replicates, generated by RNA-seq technology. The optimized data analysis workflows reported here should provide a framework for comparative investigations of expression profiles. Our results show that NGS offers a comprehensive and more accurate quantitative and qualitative evaluation of mRNA content within a cell or tissue. We conclude that RNA-seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions.

overall_design: heart mRNA profiles of mouse 4 weeks after surgery with or without hispidulin treatment

first: Yan

first: Zengshuo

last: Xie


title: CTCF ChIP-seq in OCM1 cells

city: Shanghai

first: Peiwei

last: Chai

address: No.833 Zhizaoju Road

institute: Shanghai Jiao Tong University school of medcine

summary: We identified aberrant CTCF binding lead to a 3D chromosomal interactional driver in NTS locus that accelerates tumorigenesis of uveal melanoma. Both enhancer deletion and abolishing CTCF binding lead to the loss of chromosomal looping and triggered therapeutic efficacy in inhibiting tumorigenesis. Our study shed light on a functional chromosomal architecture induced enhancer hijacking, thereby provide novel concept of 3D-chromosomal conformation exploration.

overall_design: We performed CTCF ChIP-Seq in melanoma cells


title: Systemic muscle wasting drives tumourigenesis


title: CGGBP1-regulated cytosine methylation at CTCF-binding motifs resists stochasticity

status: Public on Jul 20 2020

city: Gandhinagar

first: Umashankar

last: Singh

state: Gujarat

address: Acad Block 4 Room 317 IIT Gandhinagar Palaj

department: Biological Sciences and Engineering

country: India

institute: IIT Gandhinagar

type: Methylation profiling by high throughput sequencing

summary: To study if regulation of cytosine methylation and CTCF occupancy are interdependent and governed by the levels of CGGBP1, we specifically pulled-down methylated cytosines and found that some transcription factor binding sites including that of CTCF held out against the cytosine methylation changes. The cytosine methylation at CTCF-binding repeat-free motifs show a non-stochastic depdendence on CGGBP1 and occur at sites that mark cytosine methylation transition boundaries. We also show that allelic imbalance dictates stochastic methylation changes due to CGGBP1 depletion.

overall_design: MeDIP-seq was performed on genomic DNA from CT (non-targeting RNAi) and KD (CGGBP1 knocked-down by RNAi) of both HEK293T and GM02639 cells.

first: Manthan

last: Patel

first: Divyesh

first: Subhamoy

last: Datta

last: singh


title: PCM1 is necessary for focal ciliary integrity and is a candidate for severe schizophrenia

status: Public on Jul 16 2020

city: Chicago

first: Tanner

middle: Oliver

last: Monroe

state: IL

address: 303 E. Superior Street

institute: Lurie Children's Hospital

summary: The neuronal primary cilium and centriolar satellites have established roles in neurogenesis. However, the role of these regions in the postnatal brain is not clear. Here we show that ablation of the pericentriolar material 1 gene (Pcm1) in the mouse leads to enlarged lateral ventricles and behavioral abnormalities in adult but not juvenile animals. Adults have concomitant reductions in cortical mass and altered hippocampal morphology. Cytoanatomical analyses revealed progressive ciliary shortening, most prominently in the CA1 hippocampus, prelimbic cortex, and amygdala, as psychomotor and cognitive function declined. RNAseq of affected regions revealed significant transcriptional changes in amine- and G-protein coupled receptor activity pathways. The physiological relevance of this phenotype was supported by decreased dopamine D2 receptor (D2R) protein levels, and the failure to rescue adult behavioral defects with antipsychotic drugs. Immunoprecipitations showed an association with Pcm1 and D2Rs. Finally, we sequenced PCM1 in two cohorts of humans with severe schizophrenia. Systematic modeling of all discovered rare alleles by in vivo complementation in zebrafish revealed a significant enrichment for pathogenic alleles. Taken together, our data highlight a role for the pericentriolar material in the postnatal brain; they suggest that a progressive degenerative ciliary/centriolar phenotype can induce behavioral defects in mice; and support a contributory role for PCM1 in individuals with severe psychosis.

overall_design: We performed RNA-seq on brain tissue from Pcm1-/- and WT littermates dissected from the frontal cortex, striatum, and hippocampus.

first: T

middle: O

first: N

last: Katsanis


title: Transcriptome analysis of dissected tumour tissue from Drosophila melanogaster larval tumour models in CD compared to HSD.

summary: Transcriptomic profiling of Ras/Src tumours from animals raised on CD versus HSD enabled the identification of (i) candidate tumour-derived factors which may impact muscle-wasting and (ii) candidate amino acid transporters which may impact tumor growth.

overall_design: Pooled dissected tumour tissue was transcriptionally profiled in quadruplicate from Ras/Src tumours in CD and HSD.


title: Deconstructing Stepwise Fate Conversion of Human Fibroblasts to Neurons by MicroRNAs: Subseries 8 [Figure 6]

status: Public on Jul 14 2020

city: Saint Louis

first: Kitra

last: Cates

state: MO

address: 4523 Clayton Ave, MCD SCI 361

department: Developmental Biology

institute: Washington University in St. Louis

summary: Cell-fate conversion generally presumes the activity of reprogramming effectors to both introduce fate programs of the target cell type and erase the identity of starting cell population. Here, we reveal novel insights into the activity of microRNAs, miR-9/9* and miR-124 (miR-9/9*-124) as reprogramming agents that orchestrate direct conversion of human fibroblasts by first eradicating fibroblast identity and promoting uniform transition to a neuronal state in sequence. Among the direct target genes of miR-9/9*-124, we identify KLF-family transcription factors whose repression is critical for erasing fibroblast fate. The subsequent upregulation of a small nuclear RNA, RN7SK induces accessibilities of chromatin regions and neuronal gene activation, pushing the reprogramming cells to a neuronal state. Our study defines deterministic components in the reprogramming cascade by microRNAs.

overall_design: De-identified healthy human adult dermal fibroblasts were transduced with lentivirus to express the brain enriched microRNAs, miR-9/9* and miR-124 to directly convert fibroblasts into neurons as previously established (Yoo et al., Nature 2011; Richner et al., Nat. Prot. 2015; Abernathy, Kim, and McCoy et al., 2017) with miR-resistant KLF4, KLF5, KLF 4 and KLF5, or luciferase (LUC). Transposed (accessible) genomic DNA was collected from all conditions, then prepared for analysis as described in the Protocols.

first: Yangjian

first: Bo

last: Zhang

first: Shaopeng

first: Woo

middle: K

last: Kim

first: Andrew

middle: S

last: Yoo


title: Deconstructing Stepwise Fate Conversion of Human Fibroblasts to Neurons by MicroRNAs: Subseries 10 [Figure 7, ATAC-seq]

overall_design: De-identified healthy human adult dermal fibroblasts were transduced with lentivirus to express the brain enriched microRNAs, miR-9/9* and miR-124 to directly convert fibroblasts into neurons as previously established (Yoo et al., Nature 2011; Richner et al., Nat. Prot. 2015; Abernathy, Kim, and McCoy et al., 2017) with shRNA to 7SK (sh7SK) or a control shRNA (shCTRL). Transposed (accessible) genomic DNA was collected from all conditions and control fibroblasts, then prepared for analysis as described in the Protocols.

first: Matthew

last: McCoy


title: Deconstructing Stepwise Fate Conversion of Human Fibroblasts to Neurons by MicroRNAs: Subseries 4 [Figure 3, RNA-seq]

overall_design: De-identified healthy human adult dermal fibroblasts were transduced with lentivirus to express the brain enriched microRNAs, miR-9/9* and miR-124  to directly convert fibroblasts into neurons as previously established (Yoo et al., Nature 2011; Richner et al., Nat. Prot. 2015; Abernathy, Kim, and McCoy et al., 2017) or motor neuron-enriched transcription factors ISL1 and LHX3 or pro-neural transcription factor MYT1L alone. Total mRNA was collected from neurons and controls, then prepared for analysis as described in the Protocols.

first: Ji-Sun

last: Kwon


title: Deconstructing Stepwise Fate Conversion of Human Fibroblasts to Neurons by MicroRNAs: Subseries 9 [Figure 7, RNA-seq]

overall_design: De-identified healthy human adult dermal fibroblasts were transduced with lentivirus to express the brain enriched microRNAs, miR-9/9* and miR-124 to directly convert fibroblasts into neurons as previously established (Yoo et al., Nature 2011; Richner et al., Nat. Prot. 2015; Abernathy, Kim, and McCoy et al., 2017) with shRNA to 7SK (sh7SK) or a control shRNA (shCTRL). Total mRNA was collected from all conditions and control fibroblasts, then prepared for analysis as described in the Protocols.


title: Deconstructing Stepwise Fate Conversion of Human Fibroblasts to Neurons by MicroRNAs: Subseries 1 [Figure 1]

overall_design: De-identified healthy human adult dermal fibroblasts were transduced with lentivirus to express the brain enriched microRNAs, miR-9/9* and miR-124 and motor neuron-enriched transcription factors ISL1 and LHX3 to directly convert fibroblasts into moto-miNs as previously established (Yoo et al., Nature 2011; Richner et al., Nat. Prot. 2015; Abernathy, Kim, and McCoy et al., 2017). Single cells were collected for RNA-seq and prepared for analysis as described in the Protocols.

first: Daniel

last: Abernathy

first: Wenjun

last: Kong

first: Samantha

middle: A

last: Morris


title: High-throughput single-cell mitochondrial DNA genotyping reveals properties of clonal variation in human contexts [MERRF-C1]

status: Public on Jul 13 2020

first: Caleb

last: Lareau

state: New York

address: 417 E 68th St, Zuckerman - ZRC 1132

institute: Memorial Sloan Kettering

summary: Natural mitochondrial DNA (mtDNA) sequence variation plays a fundamental role in human disease and enables the clonal tracing of native human cells. While various genotyping approaches revealed mutational heterogeneity in human tissues and single cells, current methodologies are limited by scale. Here, we introduce a high-throughput, droplet-based mitochondrial single-cell Assay for Transposase Accessible Chromatin with sequencing (mtscATAC-seq) protocol and computational framework that facilitate high-confidence mtDNA mutation calling in thousands of single cells. Further, the concomitant high-quality accessible chromatin readout enables the paired inference of individual cell mtDNA heteroplasmy, clonal lineage, cell state, and accessible chromatin regulatory features. Our multi-omic analyses reveals single-cell variation in heteroplasmy of a pathologic mtDNA variant (m.8344A>G), which we tie to intra-individual chromatin variability and clonal evolution. Further, using somatic mtDNA mutations, we clonally trace thousands of hematopoietic cells in vitro and in patients with chronic lymphocytic leukemia, linking epigenomic variability to subclonal evolution in vivo.

overall_design: Human GM11906 lymphoblastoid cells derived from a human donor diagnosed with myoclonic epilepsy with red ragged fibres (MERFF) carrying the pathogenic m.8344A>G mutation were processed for scATAC-seq using the C1 Fluidigm platform

first: Leif

last: Ludwig


title: Genome-wide identification and differential expression of long non-coding RNAs in hypoxic zebrafish brain

city: Safed

first: Bodhisattwa

last: Banerjee

address: 8 Henrietta Szold Street

department: Faculty of Medicine

country: Israel

institute: Bar-Ilan University

summary: Long non-coding RNAs (lncRNAs) are the master regulators of numerous biological processes. Hypoxia causes oxidative stress with severe and detrimental effects on brain function and acts as a critical initiating factor in the pathogenesis of Alzheimer's disease (AD). From the RNA-Seq in the forebrain (Fb), midbrain (Mb), and hindbrain (Hb) regions of hypoxic and normoxic zebrafish, we identified novel lncRNAs, whose potential cis targets showed involvement in neuronal development and differentiation pathways. Under hypoxia, several lncRNAs and mRNAs were differentially expressed. Co-expression studies indicated that the Fb and Hb regions' potential lncRNA target genes were involved in the AD pathogenesis. In contrast, those in Mb (cry1b, per1a, cipca) was responsible for regulating circadian rhythm. We identified specific lncRNAs present in the syntenic regions between zebrafish and humans, possibly functionally conserved. We thus identified several conserved lncRNAs as the probable regulators of AD genes (adrb3b, cav1, stat3, bace2, apoeb, psen1, s100b).

overall_design: LncRNA and mRNA profiles of hypoxic vs normoxic zebrafish brain


title: High-throughput single-cell mitochondrial DNA genotyping reveals properties of clonal variation in human contexts

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

overall_design: Refer to individual Series


title: Sex- and region-specific transcriptomic differences in brainstem and cervical spinal cord microglia in rat offspring exposed to gestational intermittent hypoxia

city: Madison

first: Andrea

middle: C

last: Ewald

state: WI

address: 2015 Linden Dr

department: Comparative Biomedical Sciences

institute: University of Wisconsin - Madison

summary: We analyzed gene expression via RNA-sequencing in medulla and C3-C6 cervical spinal cord microglia isolated from young adult rats exposed to gestational intermittent normoxia or gestational intermittent hypoxia

overall_design: G10 sprague dawley rat dams were exposed to one of the following conditions: 1) 11 days of intermittent normoxia (21%/21% O2) or 2) 11 days of intermittent hypoxia (21%/10.5% O2). Offspring were born under normoxic conditions and allowed to grow to 8 weeks. Medulla and C3-C6 cervical spinal cord from 1 male and 1 female from 5 paired litters were harvested.  Microglia were immunomagnetically isolated from each region and total RNA isolated for sequencing.

first: Jyoti

last: Watters


title: scRNA-seq TF-driven forward programmed hiPSCs to multiple fates

city: Dresden

first: Volker

last: Busskamp

state: Saxony

address: Fetscherstraße 105

department: CMCB

institute: Technische Universität Dresden

summary: This dataset consists of single-cell RNA-seq (Smart-seq2) data from 95 forward programmed cells derived from human induced pluripotent stem cells (hiPSCs). Cells conditionally expressing either ATOH1, ETV2 or NKX3-1 under the control of a tetracycline-response element (Tet-ON system) were co-cultured on Matrigel in 2 dimensions. Data was used to explore the forward-programming potential of these transcription factors (TFs) when cell lines with the capacity to differentiate in isolation are cultured together.

overall_design: Three hiPSCs line were engineered using the PiggyBac transposition system. Vectors containing a cassette encoding one of three TFs (ATOH1, ETV2 or NKX3-1) and the gene for puromycin resistance, both under the control of the tetracycline response element (Tet-ON system) and flanked by sequences to be recognized by the PiggyBac transposase, were co-delivered with a vector encoding the PiggyBac transposase to hiPSCs by nucleofection. After antibiotic selection, cells from the three lines were mixed at a 1:1:1 ratio in mTeSR1 supplemented with the Y-27632 ROCK inhibitor and doxycycline and seeded on matrigel-coated 12-well plates. mTeSR1 medium supplemented with doxycycline was replaced every day until the end of the experiment. Four days (96 hours) after seeding, cells were dissociated and immunofluorescently labeled with fluorophore-conjugated antibodies against NCAM (CD56; neuronal marker), Vimentin (fibroblast marker) and VE-Cadherin (endothelial marker) in a standard buffer for flow cytometry.Individual cells were then sorted in a 96-well plate containing a lysis buffer for RNA isolation. Single cell cDNA libraries were  prepared from each cell following the Smart-seq2 workflow. 95 fastq files are provided corresponding to each individual sorted cell; a well was left empty to be used as a negative control for the presence of RNA and cDNA.

first: Alex

last: Ng

first: Parastoo

last: Khoshakhlagh

first: Jesus

last: Rojo Arias

first: Giovanni

last: Pasquini

first: Anka

last: Swiersy


title: ATAC-Seq Data of Adipose Stem Cells from Subcutaneouse Adipose Tissue of Normal-Weight Polycystic Ovary Syndrome Women Undergoing Adipogenesis in vitro

status: Public on Aug 13 2020

city: Portland

first: Brett

last: Davis

address: 3181 SW Sam Jackson Park Rd

institute: Oregon Health and Science University

summary: In previous studies, multiple animal models (rhesus monkeys, sheep) have suggested a developmental programming effect of PCOS. The goal of this study was to examine whether developmental programming may accompany epigenetic changes by examining intrinsic epigenetic differences, specifically chromatin accessibility, in adipose stem cells (ASCs) from subcutaneous (SC) adipose tissue of PCOS women vs age- and BMI-matched control samples as they mature into adipocytes in vitro.

overall_design: ASCs were isolated from SC adipose tissue following SC abdominal biopsy in 3 PCOS women and 3 age and BMI matched controls for RNA-sequencing. Second generation of stem cells were cultured until cells reached confluency and expanded for two additional generations until fourth generation. Fourth generation ASCs were then cultured in adipogenic differentiation medium for 0-12 days and processed for ATAC-seq. Libraries were prepared according to Berostro et al with minor modifications, and visualized on a TapeStation 2200 using D1000 ScreenTape. Libraries were pooled and paired-end sequenced on the Illumina HiSeq4000.

first: Karen

last: Leung

first: Mariam

last: Okhovat

first: Marco

last: Morselli

first: Lucia

last: Carbone

first: Matteo

last: Pellegrini

first: Gregorio

last: Chazenbalk


title: Inhibition of LTβR-signalling blocks epithelial apoptosis and activates endogenous Wnt-induced regeneration

status: Public on Jul 10 2020

city: Neuherberg

first: Johannes

last: Beckers

address: Ingolstaedter Landstr. 1

department: Institute of Experimental Genetics

institute: Helmholtz Zentrum Muenchen

summary: Lymphotoxin β-receptor-signalling orchestrates lymphoid neogenesis and subsequent tertiary lymphoid structures (TLS) associated with severe chronic inflammatory diseases spanning multiple organ systems. How LTβR-signalling drives chronic tissue damage particularly in the lung, which mechanism(s) regulate this process, and whether LTβR-blockade might be of therapeutic value has remained unclear. Here we demonstrate increased lymphotoxin expression of LTbR-ligands on myeloid and adaptive and innate immune-cells, enhanced non-canonical NF-κB signalling and enrichment of LTβR-target gene expression in epithelial cells of lungs from patients and mice with smoking-associated chronic obstructive pulmonary disease (COPD). Accordingly, Therapeutic inhibition of LTβR-signalling in young and aged mice with COPD disrupted TLS, reverted lung tissue destruction, airway-fibrosis and systemic muscle wasting. Mechanistically, we identified that LTβR-signalling blockade leads to diminished cell-death, concomitantly reactivated endogenous Wnt/β-catenin-signalling in alveolar epithelial cells and reduced TGFβ-signalling in airways. These findings highlight LTβR as a viable therapeutic target against TLS induced tissue damage that translates into novel anti-inflammatory, regenerative strategies to treat COPD.

overall_design: Expression data of mice exposed to either filtered air or cigarette smoke or cigarette smoke plus LTβR-Ig fusion protein

first: Thomas

middle: M

last: Conlon

first: Gerrit

last: John-Schuster

first: Danijela

last: Heide

first: Sandra

last: Prokosch

first: Jenny

last: Hetzer

first: Isis

last: Fernandez

first: Stijn

last: Verleden

first: Martin

last: Lopez

first: Hani

last: Alsafadi

first: Gizem

last: Günes

first: Mohammad

middle: Z

last: Jazi

first: Dharmesh

last: Hirani

first: Gerald

last: Burgstaller

first: Lore

last: Becker

last: Irmler

first: Darcy

last: Wagner

first: Tracy

last: O´Connor

first: Emmanuel

last: Dejardin

first: Oliver

last: Eickelberg

first: Melanie

last: Königshoff

first: Mathias

last: Heikenwalder

first: Ali

last: Yildirim


title: Plasma microRNA signatures for perioperative myocardial injury.

status: Public on Jul 26 2020

first: Shaun

last: May

address: William Harvey Research Institute

department: TMT

institute: William Harvey Research Institute

type: Non-coding RNA profiling by high throughput sequencing

summary: The pathophysiological mechanism(s) underlying PMI remain controversial. Small non-coding molecules that modulate gene expression may enhance the detection of myocardial injury and provide further mechanistic insight.  We profiled plasma exosomal microRNA in patients who sustained PMI after elective non-cardiac surgery

overall_design: Comparison of microRNA in patients who develop PMI after non-cardiac surgery

first: Ana

last: Gutierrez Del Arroyo

first: Gareth

last: Ackland


title: The landscape of H3K27me2 in mice zygotes

status: Public on Jul 07 2020

city: Beijing

first: Qingyuan

last: Sun

state: Beijing

address: Beichen West Rd., Chaoyang

department: State Key Laboratory of Stem Cell and Reproductive Biology

institute: Institute of Zoology, Chinese Academy of Sciences

summary: H3K27 di-methylation and H3K27 trimethylation are marks of facultative heterochromatin which maintains transcriptional repression established during early development in many eukaryotes. However, the mechanism underlying establishment and regulation of epigenetic asymmetry in the zygote remains obscure. Here we report the distribution pattern of H3K27me2 in Ezh2m+/p+ and Ezh2m-/p+ mice zygotes using the approach of ULI-NChIP.

overall_design: ULI-NChIP profiling of H3K27me2 in Ezh2m+/p+ and Ezh2m-/p+ mice zygotes.

first: Qing-Yuan

first: Shao-Rong

last: Gao

first: Zhen-Bo

last: Wang

first: Xiang-Hong

last: Ou

first: Tie-Gang

last: Meng

first: Xiao-Yu

last: Liu

first: Qian

last: Zhou

first: Zheng-Hui

last: Zhao


title: Splicing factor Ybx1 maintains persistent Jak2-mutated neoplasms via Mknk1-ERK-signaling persistent clones in Jak2-mutated neoplasms

status: Public on Jul 08 2020

city: Planegg

first: Sung-Huan

last: Yu

address: Am Klopferspitz 18

institute: Max Planck Institute

summary: Inactivation of Ybx1 results in RNA mis-splicing, retained intron enrichment and disruption of the transcriptional and post-translational control of extracellular signal-regulated kinase (ERK) signaling

overall_design: Examination of Ybx1 DNAbinding sites in BaF3 V617Fcells

first: Ashok

last: Jayavelu

first: Matthias

last: Mann

first: Florian

middle: H

last: Heidel


title: Deconstructing Stepwise Fate Conversion of Human Fibroblasts to Neurons by MicroRNAs

first: Kitra

last: Cates


title: Transcriptome changes in MCF-7 and T47D breast cancer cells after four day incubation in glucose deprived medium and beta-hydroxybutyrate

city: Honolulu

first: Michael

last: Weichhaus

state: Hawaii

address: 3140 Waialae Avenue

department: Natural Sciences and Mathematics

institute: Chaminade University of Honolulu

summary: We investigated gene expression changes of glucose deprived MCF-7 and T47D breast cancer cells supplemented with either 10 mM or 25 mM BHB. Glucose deprivation revealed numerous differentially expressed genes indicating an involvement of the Hippo pathway in MCF-7 cells and the NRF2-Ferroptosis axis in T47D cells. Beta-hydroxybutyrate had limited impact on breast cancer cells and differentially expressed genes were not associated with any pathways following pathway enrichment analysis.

overall_design: Two established human breast cancer cell lines were used for this analysis, MCF-7 and T47D. Cells were treated in either 225 mg/l glucose (5%) or 4.5 g/l glucose (100%). Cells treated with 225 mg/l glucose were additionally treated with no, 10 mM or 25 mM beta-hydroxybutyrate. Each condition was analyzed in duplicate except the comination glucose5%_BHB10mM in MCF-7 cells since one of the replicates failed library construction.

first: Rylee

last: Maldonado


title: FGF Signaling in the Self-Renewal of Colon Cancer Organoids

status: Public on Sep 01 2020

city: Düsseldorf

first: Wasco

last: Wruck

address: Moorenstr. 5

institute: Universitätsklinikum Düsseldorf

summary: With their ability to self-renew and simultaneously fuel the bulk tumor mass with highly proliferative tumor cells, cancer stem cells (CSC) are supposedly driving cancer progression. However, the CSC-phenotype in colorectal cancer (CRC) is unstable and dependent on environmental cues. Since FGF2 is essential for adult and embryonic stem cell culture to maintain self-renewal, we investigated its role in advanced CRC using tumor-derived organoids as experimental model. We found that FGF-Receptor (FGFR) inhibition prevents organoid formation in very early expanding cells but induces cyst formation when applied to already established organoids. Comprehensive transcriptome analyses revealed that the induction of the transcription factor activator protein-1 (AP-1) together with a MAPK stimulation was most prominent after FGFR-inhibition. These effects resemble mechanisms of an acquired resistance against other described tyrosine kinase inhibitors such as targeted therapies against the EGF-Receptor. Furthermore, we detected elevated expression levels of several self-renewal and stemness-associated genes in organoid cultures with active FGF2 signaling. The combined data assumes that CSC are a heterogeneous subpopulation while self-renewal is a common feature regulated by many different pathways. Finally, we highlight the effects of FGF2 signaling as one of numerous aspects of the complex regulation of stemness in cancer.

overall_design: The transcriptomes of colon cancer organoids with and without FGFR inhibition and human ESC lines were compared by microarray analysis (PrimeView Human Gene Expression Array, Affymetrix, Thermo Fisher Scientific).

first: Jörg

last: Otte

first: James

last: Adjaye


title: Age-induced methylmalonic acid accumulation promotes tumor progression

status: Public on Jul 03 2020

city: NEW YORK

first: John

last: Blenis

address: 413 E 69TH ST FL 13

institute: Weill Cornell Medicine

summary: From age 65 onwards, the risk of cancer incidence and associated mortality is substantially higher. Nonetheless, our understanding of the complex relationship between age and cancer is still in its infancy. For decades, the link has largely been attributed to increased exposure time to mutagens in older individuals. However, this view does not account for the well-established role of diet, exercise and small molecules that target the pace of metabolic aging. Here, we show that metabolic alterations that occur with age can render a systemic environment favorable to progression and aggressiveness of tumors. Specifically, we show that methylmalonic acid (MMA), a by-product of propionate metabolism, is significantly up-regulated in the serum of older people, and functions as a mediator of tumor progression. We traced this to the induction of SOX4 and a consequent transcriptional reprogramming that can endow cancer cells with aggressive properties. Thus, accumulation of MMA represents a novel link between aging and cancer progression, implicating MMA as a novel therapeutic target for advanced carcinomas.

overall_design: Global analysis of RNA levels to determine transcriptional reprogramming in A549 cells treated with MMA for 3 days or 10 days, in triplicate

first: Ana

middle: P

last: Gomes

first: Didem

last: Ilter


title: Deconstructing Stepwise Fate Conversion of Human Fibroblasts to Neurons by MicroRNAs: Subseries 3 [Figure 2]

overall_design: De-identified healthy human adult dermal fibroblasts were transduced with lentivirus to express the brain enriched microRNAs, miR-9/9* and miR-124 to directly convert fibroblasts into neurons as previously established (Yoo et al., Nature 2011; Richner et al., Nat. Prot. 2015; Abernathy, Kim, and McCoy et al., 2017). Single cells were collected for RNA-seq and prepared for analysis as described in the Protocols.

first: Ji-Sun

last: Kwon

first: Andrew

last: Yoo


title: High-throughput single-cell mitochondrial DNA genotyping reveals properties of clonal variation in human contexts [HumanMix]

city: New York

first: Caleb

last: Lareau

overall_design: Mix of two human cell lines, TF1 and GM11906, were processed together using a modified 10x scATAC-seq protocol as detailed in the manuscript related to this work.

first: Leif

last: Ludwig


title: Osteomodulin and proline/arginine-rich end leucine rich repeat protein contribute to bladder cancer initiation and progression by controling transition between epithelial and mesenchymal cells through regulation of TGF-b and EGF pathways

status: Public on Jul 01 2020

city: London

first: Alex

last: Leung

state: London

address: 11-43 Bath Street

institute: UCL Institute Of Ophthalmology

summary: Two secreted proteins, osteomodulin (OMD) and proline/arginine-rich end leucine repeat protein (PRELP), are specifically expressed in bladder epithelial umbrella cells. At the initiation of human bladder cancer, their expression levels are dramatically down-regulated. To reveal the functional role of both proteins in bladder cancer, we constructed OMD or PRELP knockout mice and found that, in bladder epithelia, tight junctions between umbrella cells are strongly reduced while adherens junctions are remained as observed as a typical partial epithelial-mesenchymal transition (EMT). In addition, OMD or PRELP knockout mouse bladder showed many spontaneous breakdown sites in the umbrella cell layer. Furthermore, a third of the PRELP-/- mice developed non-muscle invasive papillary bladder cancer (NMIBC).  mRNA expression profiling and in vitro functional analysis revealed that OMD and PRELP strongly regulate cell-cell adhesion and EMT via tight junction regulation through inhibition of TGF-b and EGF pathways. Interestingly, we found that activation of OMD or PRELP in bladder cancer cells strongly inhibits anchorage independent growth in vitro and tumorigenicity in in vivo mouse xenograft studies associating with the transition from mesenchymal cancer cells to epithelial-like cells as well as with tight junctions. Our data indicate that OMD and PRELP are involved in NMIBC initiation through regulation of the transition between epithelial and mesenchymal cells. Thus, it suggests that OMD and/or PRELP mediated EMT may have a potential target for bladder cancer therapy.

overall_design: 4 wild type bladder tissue samples controls were compared against 3 PRELP gene knockout mice bladder samples and 3 OMD gene knockout mice bladder samples.

first: Vasiliki

last: Papadaki

first: Ryuji

last: Hamamoto

first: Toshiya

last: Tamura

first: Ken

last: Asada

first: Julie

last: Watson

first: Jack

last: Hopkins

first: Margaret

last: Dellett

first: Noriaki

last: Sasai

first: Hongorzul

last: Davaapil

first: Serena

last: Nik-Zainal

first: Rebecca

last: Longbottom

first: Makoto

last: Nakakido

first: Vassiliki

last: Saloura

first: Ryo

last: Torii

first: Abhi

last: Veerakumarasivam

first: David

last: Neal

first: Gill

last: Murphy

first: Bruce

last: Ponder

first: Kohei

last: Tsumoto

last: Kelly

first: Shin-ichi

last: Ohnuma


title: Effect of ADGRF4 knockdown on gene expression pattern in A549 cells

city: Jeungpyoung

first: Sung-Gook

last: Cho

address: 61 University RD

institute: KNUT

summary: A549 human lung cancer cells were knocked down with either siControl or siADGRF4. Gene expression levels were analyzed by RNA sequencing. ADGRF4 globally altered expression patterns of genes in A549 cells.

overall_design: A549 cells were knocked down with either siControl or siADGFR4, and QuantSeq 3’-mRNA-Seq was conducted to analyzed gene expression patterns.

first: Ji-Hye

last: Yoon


title: RNA-seq data of human T cells treated with decidual cell conditioned medium

city: West Haven

first: Arun

middle: Rajendra

last: Chavan

state: CT

address: 850 West Campus Drive

department: Ecology and Evolutionary Biology

institute: Yale University

summary: RNA-seq data of Naïve T cells treated with decidual cell conditioned medium. Naïve T cells were differentiated into Th17 cells by IL6, TGFB1, and IL23 stimulation, in the presence of either unconditioned (control) or conditioned medium from uterine decidual stromal cells

overall_design: Examination of gene expression differences induced by decidual cell conditioned medium on naïve T cells differentiating into Th17 cells

middle: R

first: Gunter

last: Wagner


title: Gene expression analysis reveals close resemblance between Glioblastoma (GBM) patient tumors and corresponding patient-derived orthotopic xenografts (PDOXs)

city: Luxembourg

first: Anna

last: Golebiewska

state: Strassen

address: 84 Val Fleuri

department: Department of Oncology

country: Luxembourg

institute: Luxembourg Institute of Health

summary: Glioblastoma (GBM) patient-derived orthotopic xenografts (PDOXs) were derived from organotypic spheroids obtained from patient tumor samples.  To detect whether gene expression profiles of GBM patient tumors are retained in PDOXs, we performed genome-wide transcript analysis by human-specific microarrays . In parallel, we analyzed GBM cell cultures and corresponding intracranial xenografts from stem-like (NCH421k, NCH644) and adherent GBM cell lines (U87, U251). PDOXs show a better transcriptomic resemblance with patient tumors than other preclinical models. The major difference is largely explained by the depletion of human-derived non-malignant cells.

overall_design: 58 samples from human GBM patient tumor samples (n=6), GBM PDOXs (6 PDOX models, n=1-3), GBM cell lines (5 cell lines, n= 3-6 per line), GBM cell line-derived xenografts (5 cell lines, n= 2-4 per line) and human normal brain RNA (n=2) were analysed using GeneChip® Human Gene 1.0ST affymetrix array.

first: Yahaya

last: Yabo

first: Daniel

last: Stieber

first: Tony

last: Kaoma

first: Simone

last: Niclou


title: Deconstructing Stepwise Fate Conversion of Human Fibroblasts to Neurons by MicroRNAs: Subseries 5 [Figure 3, ATAC-seq]

first: Kitra

last: Cates

address: 4523 Clayton Ave, MCD SCI 361

institute: Washington University in St. Louis

summary: Cell-fate conversion generally presumes the activity of reprogramming effectors to both introduce fate programs of the target cell type and erase the identity of starting cell population. Here, we reveal novel insights into the activity of microRNAs, miR-9/9* and miR-124 (miR-9/9*-124) as reprogramming agents that orchestrate direct conversion of human fibroblasts by first eradicating fibroblast identity and promoting uniform transition to a neuronal state in sequence. Among the direct target genes of miR-9/9*-124, we identify KLF-family transcription factors whose repression is critical for erasing fibroblast fate. The subsequent upregulation of a small nuclear RNA, RN7SK induces accessibilities of chromatin regions and neuronal gene activation, pushing the reprogramming cells to a neuronal state. Our study defines deterministic components in the reprogramming cascade by microRNAs.

overall_design: De-identified healthy human adult dermal fibroblasts were transduced with lentivirus to express the brain enriched microRNAs, miR-9/9* and miR-124  to directly convert fibroblasts into neurons as previously established (Yoo et al., Nature 2011; Richner et al., Nat. Prot. 2015; Abernathy, Kim, and McCoy et al., 2017) or motor neuron-enriched transcription factors ISL1 and LHX3 or pro-neural transcription factor MYT1L alone. Transposed (accessible) genomic DNA was collected from neurons and controls, then prepared for analysis as described in the Protocols.

first: Ji-Sun

last: Kwon

first: Bo

last: Zhang

first: Shaopeng

last: Liu

first: Andrew

last: Yoo


title: Multiplexed functional assessment of dominant genetic variants in CARD11

city: Seattle

first: Richard

last: James

state: WA

address: 1900 9th ave

institute: Seattle Children's Research Institute

type: Genome variation profiling by high throughput sequencing

summary: We describe the use of saturation genome editing to measure the effects of CARD11 variants on protein function, splicing and lymphoma cell survival. We find the results to predict the clinical effects of the variants.

overall_design: Saturation genome editing of the N-terminal 145 amino acids in CARD11.

first: Eric

middle: J

last: Allenspach

first: Iana

last: Meitlis

first: Bradly

last: Bauman

first: Isabelle

last: Phan

first: Gina

last: Dabbah

first: Erica

last: Schmitt

first: Troy

last: Torgerson

first: Deborah

last: Nickerson

first: Michael

last: Bamshad

first: David

last: Hagin

first: Christopher

last: Luthers

first: Jeffrey

last: Stinson

first: Ingrid

last: Lundgren

first: Joseph

last: Church

first: Manish

last: Butte

first: Mike

middle: B

last: Jordan

first: Seema

last: Aceves

first: Daniella

last: Schwartz

first: Josh

last: Milner

first: Suzanne

last: Skoda-Smith

first: Megan

last: Cooper

first: Lea

last: Starita

last: Snow

last: Rawlings


title: Deconstructing Stepwise Fate Conversion of Human Fibroblasts to Neurons by MicroRNAs: Subseries 2 [Figure S1]

city: Saint Louis

first: Kitra

last: Cates

overall_design: De-identified healthy human adult dermal fibroblasts were transduced with lentivirus to express the brain enriched microRNAs, miR-9/9* and miR-124 and motor neuron-enriched transcription factors ISL1 and LHX3 to directly convert fibroblasts into moto-miNs as previously established (Yoo et al., Nature 2011; Richner et al., Nat. Prot. 2015; Abernathy, Kim, and McCoy et al., 2017). Single cells were collected for RNA-seq and prepared for analysis as described in the Protocols.

first: Ji-Sun

last: Kwon

first: Andrew

last: Yoo


title: Bone marrow stromal cells induce an ALDH+ stem cell-like phenotype and enhance  chemotherapy resistance in AML cells through a TGF-β-p38-ALDH2 pathway

status: Public on Jun 23 2020

city: Houston

first: Venkata

middle: Lokesh

last: Battula

state: Texas

address: 1515 holcombe blvd

department: Leukemia

institute: MD Anderson Cancer Center

summary: Our study aims to examine the interaction between AML cells and other cells in the tumor microenvironment, specifically bone marrow derived mesenchymal stromal cells. To delineate the specific genes/pathways involved in this interaction, we have co-cultured AML cell lines alone or with bone marrow derived mesenchymal stromal cells for 3 days, extracted total RNA from AML cells and analyzed the samples by RNA-seq. We identified the genes that are differentially expressed in co-cultured AML cells compared to AML cells alone. We found that TGF-β1 associated gene signature is activated in AML cells in the presence of BM-MSCs compared to AML cells alone.

overall_design: We examined differential gene expression in AML cell lines cultured alone versus AML cell lines co-cultured with BM-MSCs for 3 days

first: Bin

last: Yuan

first: Fouad

last: El-Dana

first: Stanley

last: Ly

first: Yuanqing

last: Yan

first: Vivian

last: Ruvolo

first: Elizabeth

last: Shpall

first: Marina

last: Konopleva

first: Michael

last: Andreeff


title: Mutations primarily alter the inclusion of alternatively spliced exons

status: Public on Jun 29 2020

city: Barcelona

first: Pablo

last: Baeza

address: Dr. Aiguader, 88

department: Systems Biology

country: Spain

institute: Centre for Genomic Regulation

summary: Systematic mutagenesis has revealed that synonymous, non-synonymous and intronic mutations frequently alter the inclusion levels of alternatively spliced exons, suggesting that altered splicing might be a common mechanism by which mutations cause disease. However, most exons expressed in any cell are highly-included in mature mRNAs. Here, by performing deep mutagenesis of highly-included exons and by analysing the association between sequence variation and exon inclusion across the genome, we report that mutations only very rarely alter the inclusion of highly-included exons. This is true for both exonic and intronic mutations as well as for perturbations in trans. Therefore, mutations that affect splicing are not evenly distributed across the genome but are focussed in and around alternatively spliced exons with intermediate inclusion levels. These results provide a resource for prioritising synonymous and other variants as disease-causing mutations.

overall_design: Deep mutational scan of two exons: (1) the primate ancestor of FAS exon 6 and (2) PSMD14 exon 11

last: Baeza-Centurion

first: Belén

last: Miñana

first: Juan

last: Valcárcel

first: Ben

last: Lehner


title: Chronic Folate Deficiency in the Mouse Hippocampus

city: Lynchburg

first: Abigail

last: Lawton

state: Virginai

address: 1971 University Blvd

department: Biology and Chemistry

institute: Liberty University

type:
Expression profiling by array
Non-coding RNA profiling by array

summary: Short-term folate deficiency has been linked to cognitive defects. Given folate’s role in regulating nucleotide synthesis and DNA and histone methylation, these changes are often linked to altered gene expression. We hypothesize that chronic folate deficiency will induce memory deficits that can be linked to tissue-specific changes in gene expression. This study placed mice on folic acid deficient or replete diets, containing either no source of folate or AIN-93G normal folic acid intake, beginning post-weaning and persisting through the end of adult life at 18 months. Cognitive outcomes were assessed using the novel object test for memory. Changes in hippocampal gene expression were examined by RNA microarray analysis and confirmed by qPCR. qPCR was also use to compare a subset of significant hippocampal genes to potential changes in liver and heart expression. Ontological categories were determined using GeneCodis for genes whose expression significantly changed in the deficient condition. Significantly enriched motifs in the deficient genes were examined using the HOMER bioinformatics analysis tool to identify transcription factors associated with changing genes. Folic acid deficient mice showed significant memory impairment (P<0.05) compared to replete counterparts beginning at 5 mo and persisting through 17 mo. These deficits were associated with 363 significantly downregulated and 101 significantly upregulated genes (P<0.05, fold change > 2) in the deficient condition. Of the 16 genes whose differential hippocampal expression was confirmed by qPCR, none were also differentially regulated in the heart, and only one was differentially regulated in the liver (P<0.05). Significant ontological categories for differential genes included nucleotide regulation, ion channel activity, and MAPK signaling. Two enriched motifs were identified and determined to be associated with MafB and Zfp410 binding sites. These genes and enriched motifs may represent targets for treatment or investigation of memory-related diseases.

overall_design: Samples from 12 different mice were analyzed in the study, including 3 mice from each of the following categories: 6 months of folic acid deficiency, 6 months of folic acid supplementation, 18 months of folic acid deficiency, and 18 months of folic acid supplementation. The 6 month dietary groups were compared to one another for analysis, as were the 18 month dietary groups. Each of the 3 mice within a dietary group was used as a biological replicated for the given time/condition. The mice used were outbred CD1 mice. Folic acid (FA) replete mice were used as controls, which FA deficient mcie were considered the experimental group.

first: Caroline

last: Morgan

first: Caleb

last: Schreiner

first: Chris

middle: G

first: Jacqueline

last: Baumann

first: Britton

last: Upchurch

first: Feifan

last: Xu

last: Price

first: Gary

middle: D

last: Isaacs


title: RNA-seq data of nine-banded armadillo uterus

first: Arun

last: Chavan

summary: RNA-seq data of non-pregnant and peri-implantation stage nine-banded armadillo (Dasypus novemcinctus) uterus

overall_design: Examination of gene expression differences between non-pregnant and peri-implantation stage uterus

first: Gunter

last: Wagner


title: Molecular Elucidation of in vitro spermatogenesis in the testis organ culture

status: Public on Jun 30 2020

city: Yokohama

first: Takahiro

last: Suzuki

state: Kanagawa

address: 1-7-22 Suehiro-cho, Tsurumi-ku

department: Center for Integrative Medical Sciences

institute: RIKEN

summary: Cultivation of neonatal mouse testis tissue can induce spermatogenesis and produce fertile sperms. However, this in vitro spermatogenesis by the current organ culture method comes short in fully mimicking the in vivo counterpart, partly due to a lack of knowledge about the underlying molecular phenotypes. In this study, we investigated transcriptome of cultured testis tissues using microarray method. Principle component analysis of the transcriptome data revealed delay and/or arrest of spermatogenesis and immediate radical immune reactions in the cultured testis tissues. The delay/arrest of spermatogenesis occurred before and during early meiotic phase, resulting in inefficient progression of meiosis. The immune reaction, on the other hand, was drastic and overwhelming, in which TLR4-NF-kB signaling was speculated to be involved. Notably, treatment with TAK242, an inhibitor of TLR4-NF-kB signaling pathway, ameliorated the macrophage activation which otherwise would exacerbate the inflammation. The present study revealed for the first time the immense immune reaction in the cultured tissue by transcriptomic analysis, which could be a cause of the inefficiency of in vitro spermatogenesis.

overall_design: Total RNA obtained from in vitro testes and corresponding in vitro cultured testes.

first: Takeru

last: Abe

first: Takehiko

last: Ogawa


title: Gene regulation gravitates towards either addition or multiplication when combining the effects of two signals

status: Public on Jun 19 2020

city: Philadelphia

first: Eric

last: Sanford

state: PA

address: 2135 Clymer St

institute: University of Pennsylvania

summary: Signals often ultimately affect the transcription of genes, and often, two different signals can affect the transcription of the same gene. In such cases, it is natural to ask how the combined transcriptional response compares to the individual responses. Mechanistic models can predict a range of combined responses, with the most commonly applied models predicting additive or multiplicative responses, but systematic genome-wide evaluation of these predictions are not available. Here, we performed a comprehensive analysis of the transcriptional response of human MCF-7 cells to two different signals (retinoic acid and TGF-β), applied individually and in combination. We found that the combined responses exhibited a range of behaviors, but clearly favored both additive and multiplicative combined transcriptional responses. We also performed paired chromatin accessibility measurements to measure putative transcription factor occupancy at regulatory elements near these genes. We found that increases in chromatin accessibility were largely additive, meaning that the combined binding response was the sum of the binding responses to each signal individually. We found some association between super-additivity of accessibility and multiplicative or super-multiplicative combined transcriptional responses, while sub-additivity of accessibility associated with additive transcriptional responses. Our findings suggest that mechanistic models of combined transcriptional regulation must be able to reproduce a range of behaviors.

overall_design: We treated MCF-7 cells with retinoic acid, TGF-beta, or both signals simultaneously over a period of 72 hours, after which we performed paired bulk RNA-seq and ATAC-seq. We performed three biological replicates (with one biological unit consisting of one 10 cm dish of cells) and within each experimental replicate we tested three different doses of retinoic acid (50, 200, and 400 nM), TGF-beta (1.25, 5, and 10 ng/ml), and both signals (50 nM + 1.25 ng/ul, 200 nM + 5 ng/ul, 400 nM + 10 ng/ul), as well as three different ethanol controls with varied starting cell densities.

first: Benjamin

middle: L

last: Emert

first: Allison

last: Cote

first: Arjun

last: Raj


title: Profiling of miRNAs involved in liver carcinogenesis by age

status: Public on Jun 20 2020

city: Shinjyuku

first: Tomohiro

last: Umezu

state: Tokyo

address: 6-1-1 Shinjyuku

department: Department of Molecular Pathology

institute: Tokyo Medical University

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

overall_design: Refer to individual Series


title: Cigarette Smoke Activates NOTCH3 to Promote Goblet Cell Differentiation in Human Airway Epithelial Cells

status: Public on Jun 16 2020

city: Oklahoma City

first: Jonathan

last: Wren

state: OK

address: 825 N.E. 13th Street

department: Genes & Human Disease Research Program

institute: OMRF

summary: Chronic obstructive pulmonary disease (COPD) is the 3rd leading cause of death in the United States and is caused primarily by cigarette smoking. Increased numbers of mucus-producing secretory (“goblet”) cells defined as goblet cell metaplasia or hyperplasia (GCMH), contributes significantly to COPD pathophysiology. The objective of this study was to determine whether NOTCH signaling regulates goblet cell differentiation in response to cigarette smoke. To this end, primary human bronchial epithelial cells (HBECs) from nonsmokers and COPD smokers were differentiated in vitro on air-liquid interface and exposed to cigarette smoke extract (CSE) for 7 days. NOTCH signaling activity was modulated using (1) the NOTCH/γ-secretase inhibitor Dibenzazepine (DBZ), (2) lentiviral over-expression of the NOTCH3-intracellular domain (NICD3) or (3) NOTCH3-specific siRNA. Cell differentiation and response to CSE were evaluated by qPCR, Western blotting, immunostaining and RNA-Seq. Our data demonstrate that CSE exposure of nonsmoker airway epithelium induced goblet cell differentiation characteristic of GCMH. Treatment with DBZ suppressed CSE-dependent induction of goblet cell differentiation. Furthermore, CSE induced NOTCH3 activation, as revealed by increased NOTCH3 nuclear localization and elevated NICD3 protein levels. Over-expression of NICD3 increased expression of the goblet cell associated genes SPDEF and MUC5AC, whereas NOTCH3 knockdown suppressed CSE-mediated induction of SPDEF and MUC5AC. Finally, CSE exposure of COPD airway epithelium induced goblet cell differentiation in a NOTCH3-dependent manner. These results identify NOTCH3 activation as one of the important mechanisms by which cigarette smoke induces goblet cell differentiation, thus providing a potential strategy to control GCMH-related pathologies in smokers and patients with COPD.

overall_design: mRNA profiling of primary human bronchial epithelial cells (HBECs) from nonsmokers and COPD smokers cultured on air-liquid interface (ALI) for 28 days and then exposed to 2.5% cigarette smoke extract (CSE) for 7 days.

first: Matthew

last: Walters


title: Immunogenetic and tolerance strategies against a novel parasitoid of wild field crickets

status: Public on Jun 02 2020

city: Saint Paul

first: Kristin

last: Sikkink

state: MN

address: 1987 Upper Buford Circle

department: Ecology, Evolution, and Behavior

institute: University of Minnesota

summary: Among the parasites of insects, endoparasitoids impose a costly challenge to host defenses because they use their host’s body for the development and maturation of their eggs or larvae, and ultimately kill the host. Tachinid flies are highly specialized acoustically-orienting parasitoids that release first instar mobile larvae which burrow into the host’s body to feed. We investigated the possibility that Teleogryllus oceanicus field crickets employ post-infestation strategies to maximize survival when infested with the larvae of the parasitoid fly Ormia ochracea. Using crickets from the Hawaiian island of Kauai, where the parasitoid is present, and crickets from the Cook Islands (Mangaia), where the parasitoid is absent, we evaluated fitness consequences of infestation by comparing feeding behavior, reproductive capacity, and survival of males experimentally infested with O. ochracea larvae. We also evaluated genetic mechanisms underlying host responses by comparing gene expression in crickets infested with fly larvae for different lengths of time with that of uninfested control crickets. We observe some differences in fitness (spermatophore production) and survival (total survival time post-infestation) between populations. However, for both traits significant population effects 1) were not associated with the slope of the response to different numbers of larvae and 2) only emerged from models containing body condition at one but not both time points evaluated. Gene expression patterns also revealed population differences in response to infestation. We did not find evidence for consistent differences in genes associated with immunity or stress response. Taken together, these results suggest that coevolution with the fly does not strongly select for either post-infestation resistance or tolerance of parasitoid larvae in male crickets.

overall_design: Unstranded mRNA profiles from two populations of Teleogryllus oceanicus. Abdominal tissue was collected from control crickets and from crickets 4 or 7 days after artifical infestation with larvae of the parasitoid fly Ormia ochracea. 6 individuals from each treatment group (control, 4 days, or 7 days post-infestation) from each population (Mangaia or Kauai) were included in this study.

first: Nathan

middle: W

last: Bailey

first: Marlene

last: Zuk

first: Susan

last: Balenger


title: Evaluating the Efficacy of Small Molecules for Neural Differentiation of Common Marmoset ESCs and iPSCs

status: Public on Jun 12 2020

city: Shinjuku

first: Sho

last: Yoshimatsu

address: 35 Shinanomachi

department: Physiology

institute: Keio University School of Medicine

summary: The common marmoset (marmoset; Callithrix jacchus) harbors various desired features as a non-human primate (NHP) model for neuroscience research. Recently, efforts have been made to induce neural cells in vitro from marmoset pluripotent stem cells (PSCs), including embryonic stem cells (ESCs) and induced pluripotent stem cells (iPSCs), which are characterized by their capacity to differentiate into all cell types from the three germ layers. Successful generation of marmoset neural cells is not only invaluable for understanding neural development and for modeling neurodegenerative and psychiatric disorders, but is also necessary for the phenotypic screening of genetically-modified marmosets. However, differences in the differentiation propensity among PSC lines hamper the applicability and the reproducibility of differentiation methods. To overcome this limitation, we evaluated the efficacy of small molecules for neural differentiation of marmoset ESCs (cjESCs) and iPSCs using multiple differentiation methods. By immunochemical and transcriptomic analyses, we confirmed that our methods using the small molecules are efficient for various differentiation protocols by either enhancing the yield of a mixture of neural cells including both neurons and glial cells, or a pure population of neurons. Collectively, our findings optimized in vitro neural differentiation methods for marmoset PSCs, which would ultimately help enhance the utility of the animal model in neuroscience.

overall_design: RNA seq of marmoset ESCs, ESC-derived neural differentiated cells and cortex

first: Mayutaka

last: Nakajima

first: Hideyuki

last: Okano


title: Differential expression of genes associated with inflammation in KC (Kupffer cells) and MNCs (blood monocytes):

status: Public on May 20 2020

city: Moscow

first: Polina

last: Vishnyakova

address: Oparina 4

country: Russia

institute: National Medical Research Center for Obstetrics, Gynecology and Perinatology

summary: As a rule, mammalian organs contain a mixed population of macrophages from different sources of origin. It is assumed that the self-sustaining resident macrophages and the monocyte-derived transient macrophages differ by their functional properties and their roles in repair processes . The analysis of the functional features of different populations of macrophages is of significant practical importance, since macrophages are considered as therapeutic targets in various pathological conditions and as prospective basis for cell therapy products. The aim of this study was to compare gene expression profiles of the two alternative macrophage species exemplified, respectively, by Kupffer cells of the liver and monocytes of the blood.

overall_design: In the study presented here, six samples of KC and six samples of MNC  was used to acquire expression profiles of a total of 248 unique genes associated with inflammation. For each sample, sorted cells from 5 mice were pooled.

first: Maria

last: Nikitina

first: Andrey

last: Elchaninov


title: Single cell analysis of osteosarcoma tissues

status: Public on Jun 09 2020

city: Shanghai

first: Peizhan

last: Chen

institute: Ruijin Hospital North

summary: We performed the scRNA-seq anakysis of 11 osteosarcoma tissues based on the 10X Genomics platform. The heterogneity of maglignant cells and the tumor microenvironment were analyzed.

overall_design: sc-RNA-seq of the single cells from the osteosarcoma tissues

first: Haiyan

last: Hu

first: Xinghua

last: Pan

first: Yang

last: Yao


title: miRNA expression data from CITED4 knockout and control mouse hearts after transverse aortic constriction

status: Public on May 12 2020

city: Charlestown

first: Robert

last: Kitchen

state: MA

institute: MGH / HMS

summary: To investigate the role of CITED4 in a murine model of cardiac pressure overload

overall_design: Ten samples were analyzed overall, five samples from CITED4 knockout hearts and five samples from floxed control hearts

first: Carolin

last: Lerchenmuller


title: Transcriptome  data of mouse distal lung epithelial cells with different Wnt/β-catenin activity

city: Columbus

first: Yan

state: OH

address: 575 Children’s Crossroad, RB3 6th Floor WB6271

department: Pediatrics

institute: Nationwide Children's Hospital

summary:
Wnt/β-catenin signaling regulates progenitor cell fate decisions during lung development and in various adult tissues. Ectopic activation of Wnt/β-catenin signaling promotes tissue repair in emphysema, a devastating lung disease with progressive loss of parenchymal lung tissue. The identity of Wnt/β-catenin responsive progenitor cells and the potential impact of Wnt/β-catenin signaling on adult distal lung epithelial progenitor cell function in emphysema, are poorly understood. Here, we used a TCF/Lef:H2B/GFP reporter mice to investigate the role of Wnt/β-catenin signaling in lung organoid formation.
We identified an organoid-forming adult distal lung epithelial progenitor cell population characterized by a low Wnt/β-catenin activity, which was enriched in club and alveolar epithelial type (AT)II cells. To further characterize the lung epithelial populations with different Wnt activities, we perform microarray analysis using freshly isolated Wnthigh/low/negative lung epithelial cells to study their transcriptome, specially the enriched genes and signaling pathways in the Wnt low population related epithelial stem cell functions.

overall_design: Fresh lung epithelial cells with different Wnt activities labeld by GFP expression were isolated and FACS sorted to perform transcriptome analysis using microarray. Totally 18 samples with 6 experimental replicates of 3 epithelial populations with high, low and negative Wnt activity were generated.

first: Melanie

last: Koenigshoff


title: Circular RNA circRIMS1 acts as a sponge of miR-433-3p to promote bladder cancer progression by regulating CCAR1 expression (mRNA)

status: Public on May 09 2020

city: Hangzhou

first: xiaodong

last: jin

address: The First Affiliated Hospital

department: Department of Urology

institute: The First Affiliated Hospital, Zhejiang University School of Medicine

summary: Background: Circular RNAs (circRNAs), a subclass of noncoding RNAs, have been reported to be involved in the progression of various diseases. However, the exact role of circRIMS1, also termed hsa_circ_0132246, in human bladder cancer remains to be discovered.  Methods: By performing RNA-seq comparing bladder cell lines and normal uroepithelial cells, circRIMS1 was selected as the research object. We further verified by qRT-PCR that circRIMS1 was upregulated in bladder cancer tissue and cell lines. Proliferation, colony formation, Transwell migration, Matrigel invasion, apoptosis, western blotting and in vivo tumorigenesis and metastasis assays were utilized to evaluate the roles of circRIMS1, miR-433-3p and CCAR1. For mechanistic investigation, RNA pull-down, fluorescence in situ hybridization (FISH) and luciferase reporter assay confirmed the binding of circRIMS1 with miR-433-3p.    Results: CircRIMS1 was significantly upregulated in bladder cancer and circRIMS1 expression was associated with the pathological stage and histological grade of bladder cancer. Inhibition of circRIMS1 suppressed the proliferation, migration and invasion of bladder cancer cells in vitro and in vivo, while overexpression of circRIMS1 exerted the opposite effects. Moreover, the circRIMS1/miR-433-3p/CCAR1 regulatory axis was confirmed to be responsible for the biological functions of circRIMS1.  Conclusions: CircRIMS1 acts as a tumor promoter in bladder cancer to enhance tumor growth, migration and invasion via the miR-433-3p/CCAR1 regulatory axis, which provides a new therapeutic target and a novel biomarker in bladder cancer.  Keywords: CircRIMS1, Bladder cancer, miR-433-3p, CCAR1, Progression, Metastasis

overall_design: Examination of differential mRNAs expression  in NC and sh-circRIMS1 T24 cells.

first: Feifan

last: Wang

first: Mengjing

last: Fan

first: Yueshu

last: Cai

first: Xuejian

last: Zhou

first: Hongshen

last: Wu

last: Zhang

first: Jiaxin

last: Liu

first: Shihan

last: Huang

first: Shengcheng

last: Tai

first: Ning

last: He

first: Zhenghui

first: Xiaodong

last: Jin


title: LncRNA and mRNA in human  embryonic stem cell-derived motor neurons during  differentiation

status: Public on Jun 04 2020

city: Wuhan

first: Xuejiao

last: Sun

state: Hebei

address: Jiefang Avenue 1095

institute: Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology

summary: We performed RNA-sequencing to detect the whole transcriptome of ESCs at different stages during motor neuron differentiation.

overall_design: ESCs were differentiated into motor neuron. Total RNA from cells at D0, D6, D12, and D18 were extracted, and submitted to RNA-sequencing.

first: X

first: H

last: Chen


title: Circular RNA circRIMS1 acts as a sponge of miR-433-3p to promote bladder cancer progression by regulating CCAR1 expression (circRNA)

overall_design: Examination of circular RNAs expression  in 3 cell types.

first: Yanlan

last: Yu

first: Yan

last: Hu


title: Circular RNA circRIMS1 acts as a sponge of miR-433-3p to promote bladder cancer progression by regulating CCAR1 expression

first: xiaodong


title: Transcriptome analysis of synovial osteoprogenitor populations in mice with antigen-induced arthritis and non-immunized mice

status: Public on May 05 2020

city: Zagreb

first: Nina

last: Lukač

address: Šalata 11

department: Department of Anatomy

country: Croatia

institute: University of Zagreb School of Medicine

summary: The aim of this experiment was to analyze differences in gene expression between potential osteoprogenitor populations in synovial compartment of non-immunized mice and mice with antigen-induced arthritis (AIA). We analyzed transcriptome of TER119–CD31–CD45–CD51+CD200+CD105– cells from nonimmunized mice, TER119–CD31–CD45–CD51+CD200+CD105– cells from mice with arthritis, and TER119–CD31–CD45–CD51+CD200–CD105+ from mice with arthritis. Comparison between nonimmunized and arthritic mice served to determine changes in TER119–CD31–CD45–CD51+CD200+CD105–population induced by arthritis. Comparison of TER119–CD31–CD45–CD51+CD200+CD105– and TER119–CD31–CD45–CD51+CD200–CD105+ from mice with arthritis aimed to define transcriptomic differences between those two populations.

overall_design: AIA was induced in C57BL6 mice by immunization with methylated bovine serum albumin (mBSA) and subsequent intra-articular injection of mBSA. Non-immunized mice (NI) were injected with phosphate buffered saline (PBS) at all timepoints. Ten days after intra-articular injection knee joints were harvested and synovial cells were released by injection of collagenase into joint cavities. Released cells were labeled with anti-mouse CD90.2-FITC, CD200-PE, CD105-PECy7, CD31-APC, CD45-APC, TER119-APC, CD51-biotin, streptavidin-APCeF780 and DAPI. 4 samples of TER119–CD31–CD45-CD51+CD200+CD105- cells from nonimmunized mice, 5 samples of TER119–CD31–CD45-CD51+CD200+CD105- cells from mice with arthritis, and 5 samples of TER119–CD31–CD45-CD51+CD200-CD105+ from mice with arthritis were sorted using BD FASCAria IIu. In each sample, 200-500 live (DAPI-) cells of described phenotypes were sorted directly into cell lysis buffer (Smartseq v4 Ultra® Low Input RNA Kit for Sequencing, TakaRa) according to the manufacturer’s instructions. ERCC RNA Spike-In Mix (Invitrogen) was added to lysed cell samples. cDNA amplicons were created using SmartSeq v4 Ultra® Low Input RNA Kit for Sequencing (TakaRa) and libraries for sequencing were prepared using Nextera XT DNA Library Preparation Kit (Illumina) and sequenced on NextSeq 500 (Illumina) instrument.

first: Nataša

last: Kovačić


title: A PIANO (Proper, Insufficient, Aberrant, and NO reprogramming) response to the Yamanaka factors in the initial stages of human iPSC reprogramming

status: Public on Jun 07 2020

city: Fort Worth

first: Kejin

state: TX

address: 3400 Camp Bowie Boulevard

department: Microbiology, Immunology and Genetics

institute: UNT Health Science Center

summary: Yamanaka reprogramming is revolutionary but inefficient, slow and stochastic. The underlying molecular events for these mixed outcomes of iPSC reprogramming is still unclear. Previous studies about transcriptional responses to reprogramming overlooked human reprogramming, and are compromised by the fact that only a rare population proceeds towards pluripotency and a significant amount of the collected transcriptional data may not represent the positive reprogramming. We recently developed a concept of reprogramome, which allows one to study the early transcriptional responses to the Yamanaka factors in the perspective of reprogramming legitimacy of a gene response to reprogramming. Using RNA-seq, this study scored 579 genes successfully reprogrammed within 48 hours, indicating the potency of the reprogramming factors. This report also tallied 438 genes reprogrammed significantly but insufficiently up to 72 hours, indicating a positive drive with some inadequacy of the Yamanaka factors. In addition, 953 member genes within the reprogramome were transcriptionally irresponsive to reprogramming, showing the inability of the reprogramming factors to directly act on these genes. Furthermore, there were 305 genes undergoing six types of aberrant reprogramming: over, wrong, and unwanted up- or down- reprogramming, revealing significant negative impacts of the Yamanaka factors. The mixed findings about the initial transcriptional responses to the reprogramming factors shed new insights into the robustness as well as limitations of the Yamanaka factors.

overall_design: Human embryonic stem cell (n=3) expression were compared to human fibroblasts (n=4) to define the reprogramome. Human fibroblasts BJ cells with and without transduction with lentiviral GFP were RNA-sequenced, the their transcriptomes were compared with the human fibroblasts transduced with the Yamanaka factors, OCT4, SOX2, KLF4 and c-MYC. Different patterns of transcirptional responses to reprogramming were identified with the perspective of reprogramming legitimacy.


title: RNA-Seq Quantitative Analysis of the regulation of exosomes on metastasis related gene transcriptome in NPC cells

status: Public on May 02 2020

city: Guangzhou

first: Fei

last: Li

address: Xingang West Road

department: School of Life Science

institute: Sun Yat-sen university

summary: In our study, We found that exosomal transfer occurred from highly metastatic nasopharyngeal carcinoma (NPC) cells to poorly metastatic NPC cells mediates cell-cell communication and therefore enhanced metastasis potential and decreased intracellular ROS levels of low metastatic NPC cells. To investigate the detailed mechanism of exosomes derived from highly metastatic NPC cells (H-exo) mediated low metastatic NPC cells metastasis and ROS reduction, low metastatic NPC cells 6-10B and S26 were treated with or without H-exo for RNA-SEQ analysis to exame the expression of metastasis- and ROS-related genes. Our results indicate that the levels  of  the "leading edge" genes that the majority of these genes correlated with ROS suppressing genes were significantly increased in H-exo treated 6-10B and S26 cells. In contrast, the expression levels of ROS production promoting gene were significantly lower in H-exo treated 6-10B and S26 cells than untreated 6-10B and S26 cells. Meanwhile, the majority of the genes correlated with anti-apoptotic responses and pro-metastasis could be potentially up-regulated by treated 6-10B and S26 cells with H-exo.

overall_design: Examination of H-exo treated 6-10B and S26 cells and untreated 6-10B and S26 control group

first: Qing


title: GLUD1 blockade triggers glutamine production by macrophages, nourishing satellite cells and promoting muscle regeneration

status: Public on Jul 01 2020

city: Leuven

first: Massimiliano

last: Mazzone

address: Herestraat 49

country: Belgium

institute: VIB

summary: RNAseq was performed on Glud1-deficient macrophages vs. WT macrophages sorted at baseline and at the peak of muscle damage (1day after intramuscular injection of cardiotoxin). By analysing the clustered for M1 and M2 genes as well as for wound healing genes of Glud1-deficient macrophages vs. WT macrophages recovered from muscle damage model, our understanding of key macrophage-dependent events in the damaged muscles will be improved.

overall_design: Study of M1 and M2 genes as well as wound healing genes of Glud1-deficient macrophages vs. WT macrophages sorted at baseline and at the peak of muscle damage.

first: Min

last: Shang

first: Federica

last: Cappellesso

first: Ricardo

last: Amorim

first: Jens

last: Serneels

first: Mario

last: Di Matteo

first: Guy

last: Eele

first: Stefania

last: Carobbi

first: Pierre

last: Maechler

first: Bart

last: Ghesquière

first: Peter

last: Carmeliet

first: Emanuele

last: Berard


title: Spectrum of Viral Load and Host Response Seen in Autopsies of SARS-CoV-2 Infected Lungs

city: Boston

first: David

middle: T

last: Ting

address: 149 E 13th street

department: Cancer Center

institute: Massachusetts General Hospital

summary: The relationship of SARS-CoV-2 lung infection and severity of pulmonary disease is not fully understood. We visualized viral RNA by in situ hybridization and assessed the immune infiltrate using immunohistochemistry and total RNA sequencing on five COVID-19 positive patients.  Patients with high levels of viral RNA showed hyaline membranes on histology, extensive pneumocyte loss, low T-cell numbers and were enriched for the interferon gene signature, while patients with lower levels of viral RNA showed lower numbers of T-cells and CD8 cells and were enriched for fibrosis-associated genes. The study highlights the need to assess both pulmonary viral load and immune response in patients with severe COVID-19 infection.

overall_design: Autopsy samples from patients deceased due to SARS-Cov2 infection were collected for total RNA-seq analysis to assess viral load and immune response.

first: Niyati

last: Desai

first: Azfar

last: Neyaz

first: Annamaria

last: Szabolcs

first: Angela

last: Shih

first: Linda

last: Nieman

first: Vishal

last: Thapar

first: Alexander

last: Solovyov

first: Arnav

last: Mehta

last: Lieb

first: Anupriya

last: Kulkarni

first: Christopher

last: Jaicks

first: Jonathan

last: Chen

last: Pinto

first: Robert

last: Monroe

first: Dejan

last: Juric

first: Ivan

last: Chebib

first: Nir

last: Hacohen

first: Benjamin

last: Greenbaum

first: Miguel

middle: N

last: Rivera

first: James

last: Stone

first: Ikram

last: Deshpande


title: Profiling of miRNAs involved in liver carcinogenesis by age [CH]

first: Tomohiro

last: Umezu

summary:
Previous studies have identified several microRNAs (miRNAs) that may coordinate multiple pathways associated with age-related carcinogenesis. We compared hepatic miRNA expression patterns in chronic hepatitis (CH) and hepatocellular carcinoma (HCC) to elucidate age-related differences potentially underlying hepatocarcinogenesis.
2565 miRNAs in 360 liver tissues specimens were analyzed.

overall_design: Three hundred and sixty samples from CH patients were collected by fine needle biopsy.

first: Y

last: Murakami


title: MicroRNA expression profiles in livers during pigeon (Columba livia) development

status: Public on Apr 29 2020

city: Chengdu

first: Xun

last: Wang

state: China

address: Huimin road 211#, Wenjiang district

institute: Sichuan agricultural university

summary: A comparative profile of miRNAs in livers during pigeon development was performed by using high-throughput sequencing. We identified known pigeon miRNAs, novel miRNAs, and miRNAs that are conserved in other birds and mammals.Our results expanded the repertoire of pigeon miRNAs and may be of help in better understanding the mechanism of squab’s rapid development from the perspective of liver development.

overall_design: we investigated miRNA expression profiles from pigeon liver during differentiation by using high-throughput sequencing technology.

first: Siyuan

last: Feng


title: Argonaute 2 is a key regulator for maternal mRNA degradation in mouse early embryos

city: Harbin

first: Hou

middle: wei

last: bo

state: Heilongjiang

address: Xiangfang District

institute: College of Life Science,Northeast Agricultural University

summary: Growing oocyte possesses high transcriptional activity, and accumulates massive maternal mRNAs and proteins, which control the initial stages of development. Maternal mRNA degradation (MRD) is required to remove repressive factors and enable zygotic genome activation (ZGA). To explore the function of Ago2 in MRD, we knocked Ago2 down by injection of small interfering RNA (siRNA) targeting Ago2 and AGO2 antibody into mouse zygote, and demonstrate that the deletion of Ago2 impairs normal early embryonic development, accompanied by abnormal MRD and ZGA. AGO2 guided by endosiRNAs could target maternal mRNAs and cooperate with P-bodies to promote MRD. We also indicate that AGO2 may associate with saRNA to regulate ZGA-dependent MRD. Our findings provide insights into the function of AGO2 on MRD and suggest its role in ZGA.

overall_design: As the control, 2 replicates were performed at MII oocyte stage of wild type samples. The Ago2-kd embryo as well as control embryo at the 2- and 4-cell stage were collected and peformed for RNA-seq.

first: Jiaming

last: Zhang

first: Weibo

last: Hou

first: Zhonghua

last: Liu

first: Qingran

last: Kong


title: Time course Total RNA-Seq and XBP1s ChIP-Seq in Xbp1 flx/flx (WT, wild-type) mice and AlbCre;Xbp1 flx/flx (XBP1 LKO, liver-specific knockout) mice

status: Public on May 24 2020

city: Houston

first: Huan

last: Meng

address: One Baylor Plaza BCM 130

department: Department of Molecular & Cellular Biology

institute: Baylor College of Medicine

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

overall_design: Refer to individual Series