title: Huntington's disease brain-derived small RNAs recapitulate associated neuropathology in mice [Mouse RNA-seq]

first: Lorena

last: Pantano

address: 655 Huntington Ave

department: Biostatistics

institute: Harvard Chan School of Public Health

summary: Progressive motor alterations and selective death of striatal medium spiny neurons (MSNs) are key pathological hallmarks of Huntington's disease (HD), a neurodegenerative condition caused by a CAG trinucleotide repeat expansion in the coding region of the huntingtin (HTT) gene. Most research has focused on the pathogenic effects of the resultant protein product(s); however, growing evidence indicates that expanded CAG repeats within mutant HTT mRNA and derived small CAG repeat RNAs (sCAG) participate in HD pathophysiology. The individual contribution of protein versus RNA toxicity to HD pathophysiology remains largely uncharacterized and the role of other classes of small RNAs (sRNA) that are strongly perturbed in HD is uncertain.   Here, have injected vehicle (VEH), CTL-sRNA-PT (obtained from the putamen of non-affected individuals) or HD-sRNA-PT (obtained from the putamen of patients with HD) into the striatum of wild type (WT) mice, and demonstrate that sRNA produced in the putamen and cortex of HD patients are sufficient to induce HD pathology in vivo, including transcriptional alterations. To reveal the transcriptional changes produced by sCAG, we co-injected human sRNAs with a locked nucleic acid (LNA) modified anti-sense oligonucleotide complementary to sCAG (HD-sRNA-PT + LNA-CTG) or an analogous scrambled LNA (HD-sRNA-PT + LNA-SCB). We have performed mRNA-seq in the different experimental groups: Vehicle, CTL-sRNA-PT, HD-sRNA-PT, HD-sRNA-PT + LNA-CTG, and HD-sRNA-PT + LNA-SCB. Here we describe the procedure to obtain and sequence human sRNA dataset isolated from the different brain areas.

overall_design: Human dissected putamen of non-affected individuals and patients with Huntington's disease were placed in QIAzol solution (QIAGEN; 79306), followed by RNA extraction with the miRNeasy mini kit (QIAGEN; 217004) as indicated by the manufacturer. Determinations of RNA quality and quantity were made with a 2100 Bioanalyzer (Agilent Technologies) and an ND-1000 spectrophotometer (Thermo Fisher Scientific), respectively. All RNA samples showed an RNA integrity number (RIN) of 7 or higher). Equivalent amounts of total RNA were mixed to obtain a representative pool of CTL-RNAs-PT (n=10-14) and HD-RNAs-PT (n=11-14). Then, small RNA (sRNA) fractions were purified from total RNA with the RNA Clean & Concentrator-5 Kit (Zymo Research; R1015) according to the manufacturer's instructions.    Each sRNA pool was injected into the mouse striatum, using stainless steel bilateral cannulas (26-gauge; Bilaney Consultants Ltd) that were implanted at the following coordinates: anteroposterior (AP) +0.6 mm, mediolateral (ML) ±2 mm and dorsoventral (DV) -1 mm from bregma. Infusions were performed at 0.25 μl/min by using an infusion pump. Bilateral infusions of 2 μl of vehicle, CTL-sRNA-PT, HD-sRNA-PT, HD-sRNA-PT + LNA-SCB, HD-sRNA-PT + LNA-CTG, CTL-sRNA-PT + LNA-SCB, CTL-sRNA-PT + LNA-CTG (0.24 µg/µl) were carried out. Infusions were administered twice per week, for two weeks, and were preceded by a vehicle infusion. Infusion cannulas were left in place for 5 minutes after the injection to ensure a complete diffusion. Animals were sacrificed 48 hours after the last infusion and the cerebral hemispheres were processed for RNA extraction.

first: Georgia

last: Escaramís

first: Eulàlia

last: Martí


title: Huntington's disease brain-derived small RNAs recapitulate associated neuropathology in mice

status: Public on Feb 16 2021

city: Boston

state: MA

country: USA

type: Expression profiling by high throughput sequencing

type: Non-coding RNA profiling by high throughput sequencing

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: Huntington's disease brain-derived small RNAs recapitulate associated neuropathology in mice [human-miRNA]

summary: Progressive motor alterations and selective death of striatal medium spiny neurons (MSNs) are key pathological hallmarks of Huntington's disease (HD), a neurodegenerative condition caused by a CAG trinucleotide repeat expansion in the coding region of the huntingtin (HTT) gene. Most research has focused on the pathogenic effects of the resultant protein product(s); however, growing evidence indicates that expanded CAG repeats within mutant HTT mRNA and derived small CAG repeat RNAs (sCAG) participate in HD pathophysiology. The individual contribution of protein versus RNA toxicity to HD pathophysiology remains largely uncharacterized and the role of other classes of small RNAs (sRNA) that are strongly perturbed in HD is uncertain. Here, have injected vehicle, CTL-sRNA (obtained from non-affected individuals) or HD-sRNA (obtained from patients with HD) from different brain areas (putamen, PT; cortex, CTX and cerebellum, CB) into the striatum of wild type (WT) mice and demonstrate that sRNA produced in the putamen and cortex of HD patients are sufficient to induce HD pathology in vivo. We have performed small RNA (sRNA) sequencing of the human samples used for injection. Here we describe the procedure to obtain and sequence human sRNA isolated from the different brain areas.

overall_design: Human dissected brain areas (putamen, cortex and cerebellum) of non-affected individuals and patients with Huntington's disease were placed in QIAzol solution (QIAGEN; 79306), followed by RNA extraction with the miRNeasy mini kit (QIAGEN; 217004) as indicated by the manufacturer. Determinations of RNA quality and quantity were made with a 2100 Bioanalyzer (Agilent Technologies) and an ND-1000 spectrophotometer (Thermo Fisher Scientific), respectively. All RNA samples showed an RNA integrity number (RIN) of 7 or higher. ). Equivalent amounts of total RNA were mixed to obtain a representative pool of CTL-RNAs (n=10-14) and HD-RNAs (n=11-14) from each brain area. Then, small RNA (sRNA) fractions were purified from total RNA with the RNA Clean & Concentrator-5 Kit (Zymo Research; R1015) according to the manufacturer's instructions.


title: IL-7R signalling activates widespread VH and DH gene usage to drive antibody diversity in bone marrow B cells

status: Public on Feb 20 2021

city: Cambridge

first: Felix

last: Krueger

address: Granta Park

department: Bioinformatics

country: United Kingdom

institute: Altos Labs

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Generation of the primary antibody repertoire requires V(D)J recombination of hundreds of gene segments in the immunoglobulin heavy chain (Igh) locus. It has been proposed that interleukin-7 receptor (IL-7R) signalling is necessary for Igh recombination, but this has been challenging to partition from the receptor’s role in B cell survival and proliferation. By generating the first detailed description of the Igh repertoire of murine IL-7Ra-/- bone marrow B cells, we demonstrate that IL-7R signalling profoundly influences VH gene selection during VH-to-DJH recombination. We find skewing towards usage of 3’ VH genes during de novo VH-to-DJH recombination that is more severe than the fetal liver (FL) B cell repertoire, and we now show a role for IL-7R signalling in DH-to-JH recombination. Transcriptome and accessibility analyses suggests reduced expression of B lineage-specific transcription factors (TFs) and their targets, and loss of DH and VH antisense transcription in IL-7Rα-/- B cells.  These results refute models suggesting that IL-7R signalling is only required for survival and proliferation, and demonstrate a pivotal role in shaping the Igh repertoire by activating underpinning epigenetic mechanisms.

overall_design: Examination of WT, FL and IL-7Ra-/- Igh loci in mouse pro-B cells

first: Amanda

last: Baizan-Edge

first: Bryony

middle: A

last: Stubbs

first: Michael

middle: J

last: Stubbington

first: Daniel

last: Bolland

first: Kritina

last: Tabbada

first: Simon

last: Andrews

first: Anne

middle: E

last: Corcoran


title: The evolution of trade-offs between defense and reproduction facilitates the transition towards multicellularity

status: Public on Feb 13 2021

city: Kiel

first: Joana

middle: Pimenta

last: Bernardes

address: Am Botanischen Garten 11

department: Systems Immunology

country: Germany

institute: Institute of Clinical Molecular Biology

summary: The evolutionary transition of multicellular life initially involves growth in groups of undifferentiated cells followed by differentiation into soma and germ-like cells. This is facilitated by trade-offs between traits determining survival and reproduction, favoring the coexistence of cells with extreme trait values and a convex trade-off curve as the multicellular state dominates. However, these transitions remain poorly characterized at the ecological and genetic level. Here, we studied the evolution of cell groups in ten isogenic lines of the unicellular green algae Chlamydomonas reinhardtii with prolonged exposure to a rotifer predator. We confirmed that this trait was heritable and characterized by a convex trade-off curve between reproduction and survival. Identical mutations evolved in all cell group isolates which were linked to survival and reducing associated cell costs. Overall, we show that just 500 generations of predator selection is sufficient to lead to a convex trade-off and incorporate evolved changes into the prey genome.

overall_design: We picked one pair of cell group and single cell isolate and inoculated them to nine chemostat in COOL80 medium. After 10 days we either added rotifers (rotifer treatment), switched the resource supply to lower nitrogen concentration (low nitrogen treatment; 40μM nitrogen) or kept the algae as they were (control treatment), each treatment was replicated three times. After five additional days we harvested the algae from the chemostats. We compared the algae from the chemostats by measuring cell cluster sizes (number of cells per colony), percentage of cell clusters, and overall population sizes for the three treatments (Supplementary information Fig. S2). Simultaneously, the harvested algae were prepared for total RNA extraction with RNeasy Plant Mini Kit from Qiagen® for RNASeq analysis. We pooled the RNA extracted by treatment and RNA-sequenced it using Illumina HiSeq (2x150bp).

middle: P

first: Uwe

last: John

first: Noemi

last: Woltermann

first: Martha

last: Valiadi

first: Lutz

last: Becks


title: Titanium induces pro-inflammatory and tissue remodeling responses in human macrophages

status: Public on Feb 10 2021

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

department: ZMF

institute: University Heidelberg


title: ChIP-seq for Histone Variant H2A.W, H2A.X, H1 and H3K9me2 in WT and ddm1(-/-) to quantify loss of H2A.W in ddm1 1st generation

city: Vienna

first: Bhagyshree

middle: Babasaheb

last: Jamge

address: Dr. Bohr Gasse -3

country: Austria

institute: Gregor Mendel Institute

summary:
Silencing of transposons by the chromatin remodeler DDM1 is mediated by the deposition of heterochromatic H2A variants.
Transposon mobility and silencing participates in genome evolution but also threaten genome integrity. DECREASED DNA METHYLATION 1 (DDM1) belongs to a conserved family of chromatin remodelers that are required to silence transposons, yet the underlying molecular mechanism has remained unknown. Here we show that DDM1 binds the histone variant H2A.W through two conserved domains that are required to deposit H2A.W and maintain transposon silencing. The mechanism of transcriptional silencing described here is likely shared among chromatin remodelers of the DDM1 family and heterochromatic H2A variants that have evolved in mammals.

overall_design: ChIP-seq for Histone Variant H2A.W, H2A.X, H1 and H3K9me2 in WT and ddm1(-/-) was performed with 2 biological replicates each.

first: Akihisa

last: Osakabe


title: Gene expression data of macrophages cultured on porous titanium discs

summary:
Titanium is a common implant material. However, in some patients titanium implants fail. Macrophages are key cells involved in foreign body response. To identify macrophage response to titainum, primary human macrophages were cultured on porous titanium discs for 6 days
We used microarrays to determine the global expression pattern induced by porous titanium in macrophages and identify potential genes involved in implant failure.

overall_design: PBMC derived monocytes were cultured on cell culture plastic or on porous titanium discs for 6 days. Cells were stimulated either with IFNgamma or IL-4 or left unstimulated. On the 6th day RNA was isolated and whole transcriptome was analyzed using Affymetrix microarrays

first: Alexandru

last: Gudima


title: Loss of KDM4B exacerbates bone-fat imbalance and mesenchymal stromal cell exhaustion in skeletal aging

city: Los Angeles

first: Cunyu

last: Wang

state: CA

address: 10833 Le Conte Ave

department: School of Dentistry

institute: university of California, Los Angeles


title: Identification of JMJD1C target genes in  LN-229 glioblastoma cells.

status: Public on Feb 09 2021

city: Luzhou

first: hong

middle: Chuan

last: Zhong

address: Luzhou Sichuan

country: China

institute: Neurosurgery Department, Affiliated Hospital of Southwest Medical University

summary: JMJD1C shows ubiquitous expression and is often downregulated in tumor entities compared to healthy tissues.JMJD1C inhibit growth of the glioblastoma cell line LN-229.   Here, JMJD1C knockdown leads to malignant progression in the glioblastoma cell line LN-229.

overall_design: 6 Samples in total; 3 samples per condition (control-NC treated and sh-JMJD1C treated), nuclear enriched RNA was isolated and total RNA-Seq after ribosomal depletion was performed

first: Chuanhong

first: Xianglong

last: Li


title: Bisulfite amplicon sequencing can detect Glia and Neuron cell-free DNA in blood plasma.

status: Public on Feb 06 2021

city: Camperdown

first: Zac

last: Chatterton

state: Australia

address: 97 Mallet St, ME30K

department: Brain and Mind Centre

country: Australia

institute: The University of Sydney

type: Methylation profiling by high throughput sequencing

summary: Sampling the live brain is difficult and dangerous, and withdrawing cerebrospinal fluid is uncomfortable and frightening to the subject, so new sources of real-time analysis are constantly sought. Cell-free DNA (cfDNA) derived from glia and neurons offers the potential for wide-ranging neurological disease diagnosis and monitoring. However, new laboratory and bioinformatic strategies are needed. DNA methylation patterns on individual cfDNA fragments can be used to ascribe their cell-of-origin. Here we describe bisulfite sequencing assays and bioinformatic processing methods to identify cfDNA derived from glia and neurons. In proof-of-concept experiments we describe the presence of both glia- and neuron-cfDNA in the blood plasma of human subjects following mild trauma. These detection of glia- and neuron-cfDNA represents a significant step forward in the translation of liquid biopsies for neurological diseases.

overall_design: Bisulfite amplicon sequencing libraries were created from neuron (n=13) and glia gDNA (n=7) from samples used for HM450 analysis (above) and PBMC (n=11) from Breachers training day 1, and cfDNA (n=47) from Breachers training days 1, 7, 8 and 9 following the protocols in Supplementary Material I. Libraries were denatured following Illumina protocols and sequenced on either the Illumina MiSeq using 2 x 26bp sequencing or the Illumina HiSeq2500 using 2 x 50bp sequencing.


title: Genomic binding by an artificially evolved POU (ePOU)

status: Public on Feb 07 2021

city: Guangzhou

first: Chen

last: yanpu

state: guangdong

address: Kaiyuan No. 190, Luogang district

department: drug discovery pipelines

institute: Guangzhou Institute of Biomedicine and Health

summary: We generated Oct4 libraries by randomizing selected amino acids and by recombining domains of paralogous POU family genes. These libraries were subjected to iterative rounds of pooled screens to select variants that enhance pluripotency induction. We identified an artificially evolved POU factor (ePOU) that substantially outperforms wild-type Oct4 in terms of mouse embryonic fibrobast (MEF) reprogramming. To probe whether the ePOU and Oct4 differentially engage the chromatin of reprogramming cells, we performed chromatin immunoprecipitation sequencing (ChIPseq) for both factors and Sox2. Two cocktails Oct4 (O), Sox2 (S), Klf4 (K), c-Myc (M) and ePOU/S/K/M were transduced into OG2 MEF cells which is MEF cells with Oct4 promotor.

overall_design: Genome binding profiles of Oct4, Sox2 and ePOU in reprogramming intermediate cells at day 3 of retrovirus system based somatic cell reprogramming were generated by deep sequencing, using Illumina Hiseq X Ten.

first: Yanpu

last: Chen

first: Ralf

last: Jauch

first: Vikas

last: Malik

first: Daisylyn Senna

last: Tan


title: Transcriptome analysis of basal and luminal cells treatment with baicalin

status: Public on Feb 05 2021

city: Wuhan

first: Weizhen

state: Hubei

address: 115#, Donghu road

department: Medical Research Institute

institute: Wuhan University

summary: Baicalin is the main flavonoid component extracted from Scutellaria root. It has multiple potent biological activities, including estrogen-like activity. In our study, we investigated the function of baicalin on mammary stem cell proliferation and mammary development. Our results demonstrated that baicalin significantly accelerates mammary gland development at puberty and during pregnancy; In vitro, baicalin significantly promotes colony formation ability of mammary basal epithelial cells in a three-dimensional (3D) culture system; In vivo, baicalin improved mammary regeneration efficiency in mouse xenograft model. But the mechanism was unknown. Therefore, transcriptome analysis of basal and luminal cells treatment with baicalin was performed.

overall_design: Examination the different mRNA level in basal and luminal cells treatment with baicalin

first: Wei

last: Wei

first: Cheguo

last: Cai


title: G2/M DNA synthesis at transcription start sites because of RNA transcription persistence during DNA replication [G2M BrdU-Seq]

status: Public on Feb 17 2021

city: Birmingham

first: Marco

last: Saponaro

address: Vincent Drive

department: Institute of Cancer and Genomic Sciences

institute: University of Birmingham

summary: RNA transcription and DNA replication both use DNA as a substrate, that however can be engaged only by one of them at any given time. Consequently, conflicts between transcription and replication significantly affect genome stability and human health. To understand the reciprocal interplay between transcription and replication in human cells, we performed a genome-wide analysis of the two processes throughout S-phase. We found that transcription persists during replication, with direct consequences for replication progression through genes and sites of DNA damage. Importantly however, we also found that transcription start sites will not be replicated together with the surrounding regions, and remain under-replicated throughout S-phase. DNA synthesis across transcription start sites occurs specifically when cells enter mitosis, because the RNA Polymerase II is removed at that point from the majority of the genes. Intriguingly, this G2/M DNA synthesis is not associated with increased DNA damage and occurs at very high frequency.

overall_design: Genome-wide DNA replication profile of BJ-hTERT cells in G2/M phase treated with indicated siRNA and generated by NEXT-seq in two biological repeats

first: Jianming

first: Patricia

last: Rojas


title: Role of the transcriptional regulator SP140 in resistance to bacterial infection via repression of type I interferons

status: Public on Feb 04 2021

first: Daisy

last: Ji

state: Massachusetts

address: 665 Huntington Avenue, Building 1, Room 811

institute: Harvard University School of Public Health

summary: Type I interferons (IFNs) are essential for anti-viral immunity, but often impair protective immune responses during bacterial infections. An important question is how type I IFNs are strongly induced during viral infections, and yet are appropriately restrained during bacterial infections. The Super susceptibility to tuberculosis 1 (Sst1) locus in mice confers resistance to diverse bacterial infections. Here we provide evidence that Sp140 is a gene encoded within the Sst1 locus that represses type I IFN transcription during bacterial infections. We generated Sp140–/– mice and find they are susceptible to infection by Legionella pneumophila and Mycobacterium tuberculosis. Susceptibility of Sp140–/– mice to bacterial infection was rescued by crosses to mice lacking the type I IFN receptor (Ifnar–/–). Our results implicate Sp140 as an important repressor of type I IFNs that is essential for resistance to bacterial infections.

overall_design: Lung mRNA profiles of B6, B6.Sst1S, Sp140-/-, Sp110-/- mice infected with M. tuberculosis. Day 25 post-infection.

middle: X

first: Kristen

middle: C

last: Witt

first: Dmitri

middle: I

last: Kotov

first: Shally

middle: R

last: Margolis

first: Alexander

last: Louie

first: Victoria

last: Chevée

first: Katherine

first: Harmandeep

middle: S

last: Dhaliwal

first: Angus

middle: Y

last: Lee

first: Dario

last: Zamboni

first: Igor

last: Kramnik

first: Daniel

last: Portnoy

first: K

middle: H

last: Darwin

first: Russell

last: Vance


title: Effect of the expression of ELOVL5 and IGFBP6 genes on the metastatic potential of breast cancer cells

status: Public on Feb 01 2021

city: Moscow

first: Sergey

last: Nikulin

address: 7, Vavilova st.

department: Faculty of Biology and Biotechnology

country: Russia

institute: HSE University

summary: Previously, it was shown that expression of ELOVL5 and IGFBP6 genes is associated with the risk of the formation of distant metastases in breast cancer. In this work, we studied the change in phenotypical traits, as well as in the transcriptomic and proteomic profiles of breast cancer cells as a result of knockdown of ELOVL5 and IGFBP6 genes.

overall_design: Total RNA was prepared from MDA-MB-231 cells with shRNA mediated knockdown of ELOVL5 and IGFBP6 genes as well as from control MDA-MB-231(LUC) cells.

first: Galina

last: Zakharova

first: Andrey

last: Poloznikov

first: Maria

last: Raigorodskaya

last: Wicklein

first: Udo

last: Schumacher

first: Jonas

last: Bergquist

first: Georgy

last: Bakalkin

first: Lidiia

last: Astakhova

last: Tonevitsky


title: Genes expression of WT and KLF12 overexpression mouse fetues at 9.0 dpc

city: Nanjing

first: Yang

last: Liu

address: Hankou road 22

institute: Nanjing University

summary: Background: Although adequate periconceptional folic acid (FA) supplementation has reduced the occurrence of neural tube defects (NTDs)-affected pregnancies, mechanisms underlie FA resistant NTDs are poorly understood, so that NTDs still remain a global public health concern now. It has been proven that high level of Krüppel-like factor 12 (KLF12) has bad effects on heath in most cases, but there is no evidence concerning its roles during development.  Methods: We used KLF12-overexpression mice to study the effects of high level of KLF12 on neural tube development.  Findings: We showed KLF12-overexpression fetuses died in utero at around 10.5 days post coitus with 100% cranial NTDs. Neither FA or formate benefited normal neural tube closure in mutant fetuses. Further anylasis revealed high level of KLF12 caused NTDs in mice via overactivating Sonic hedgehog (Shh) signaling pathway, leading to upregulation of Ptch1, Gli1, Hhip etc. PF-5274857, an antagonist of Shh signaling pathway could significantly promote dorsolateral hinge point formation and partially rescue the phynotype.   Interpretation: The regulatory hierarchy between high level of KLF12 and FA-resistant NTDs might provide new insights for the diagnosis and treatment of unexplained NTDs in the future.

overall_design: To illustrate the mechanisms of NTDs caused by high level of KLF12, we performed RNA-seq analysis of 9.0 dpc WT (n=3) and KLF12-overexpression fetuses (n=3).

first: Guijun

last: Yan

first: Haixiang

last: Sun


title: Root system responses to low temperature acclimation of Arabidopsis reil ribosome biogenesis double mutants

status: Public on Feb 03 2021

city: Docklands

first: Bo Eng

last: Cheong

state: VIC

department: School of BioSciences

institute: University of Melbourne

summary: The REIL proteins are required for late ribosomal biogenesis and accumulation of the 60S large ribosome subunit in mature leaves of Arabidopsis thaliana upon acclimation to low temperature. To validate these functions in roots, we conducted a multi-level system analysis targeted at understanding defects and compensations responses of reil mutants before acclimation to low temperature and following temperature shift. Hydroponic root tissue enabled analysis of eukaryotic ribosome complexes with negligible interference of organelle ribosomes. Hydroponic cultivation attenuated the growth defect of reil mutants at low temperature and provided new insights into the primary functions of Arabidopsis REIL proteins. Arabidopsis tightly controls the balance of non-translating 40S and 60S subunits. Reil mutants initially deplete both non-translating subunits upon shift to 10°C and subsequently replenish these pools slowly. Reil mutations compensate the 60S biosynthesis defect by increased baseline levels of non-translating 40S and 60S subunits and depletion of a likely non-translating, KCl-sensitive 80S sub-fraction in the cold. We infer that Arabidopsis buffers fluctuating translation demands following temperature cues by activating non-translating ribosome fractions before de novo synthesis meets temperature-induced demands. Reil1 reil2 double mutants accumulate 43S-preinitiation complexes and pre-60S-maturation complexes and affect the paralog composition of non-translating ribosome fractions. With few exceptions, e.g. RPL3B and RPL24C, these changes were not under transcriptional control. Our study suggests requirement of de novo synthesis of eukaryotic ribosomes for long-term cold acclimation. Double mutant analysis indicates feedback control of REIL-mediated 60S maturation on NUC2 and eIF3C2 transcription and implies functions of two so far non-described proteins in late plant ribosome biogenesis. We propose that Arabidopsis requires biosynthesis of specialized ribosomes for successful cold acclimation.

overall_design: The transcriptome data set describes the total mRNA differences between complete root systems of Arabidopsis thaliana Col-0 wild type and of the reil1-1 reil2-1 and reil1-1 reil2-2 double mutants at 20°C (day)/ 18°C (night) immediately before temperture shift and at 1 day and 7 days after shift to 10°C (day)/  8°C (night). Experiments were performed in hydroponic culture with liquid MS-media adjusted to pH 5.7 containing 2% sucrose (w/v) (Murashige and Skoog, 1962). Plants had developmental stage ~1.10 (Boyes et al. 2001) at the time of temperature shift. Three independent biological replicate experiments were harvested for microarray based transcriptome analyses. Each of the three harvested biological replicates was the pool of the complete root systems from four plants of a single hydroponic container.

first: Bo-Eng

first: Olga

last: Beine-Golovchuk

first: Federico

last: Martinez Seidel

first: Joachim

last: Kopka


title: microRNA-seq of Kynurenine stimulated mouse spleenocyte in vitro

status: Public on Jan 31 2021

city: Kunming

first: Jing

state: Yunnan

address: NO. 935,JIAO LIN ROAD

institute: Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College

summary: RNA-seq technology was conﬁrmed that miRNA expression has an important role in vaccine adjuvant in vivo and in vitro. Kynurenin, as an immunosuppressive adjuvant, but the exact mechanism of action with immune cells is still poorly understood. In the present study, RNA and miRNA sequencing was performed in mouse splenocytes stimulated by Kynurenin. These data provide an important basis for understanding the mechanisms underlying Kyn as an immunosuppressive adjuvant regulated the immune response.

overall_design: Four control samples and four Kynurenin(40μg/ml) treated samples

first: Sun

last: jing


title: Transcriptome of Subcortical White Matter and Spinal Cord After Spinal Injury and Cortical Stimulation

city: Houston

first: Haichao

last: Wei

state: TX

address: 1825 Pressler St., SRB 637.C

institute: UTHealth

summary: Spinal cord injury disrupts ascending and descending neural signals causing sensory and motor dysfunction below the injury. Neuromodulation with electrical stimulation is used in both clinical and research settings to induce neural plasticity and improve functional recovery following injury. However, the mechanisms by which electrical stimulation affects recovery remain unclear. In this study we examined the effects of cortical electrical stimulation following injury on transcription at several levels of the central nervous system. We performed a unilateral cervical spinal contusion injury in rats and delivered stimulation for one week to the contralesional motor cortex to activate a descending motor tract.RNA was purified from bilateral subcortical white matter, and 3 levels of the spinal cord. Here we provide the complete data set in the hope that it will be useful for researchers studying electrical stimulation as a therapy to improve recovery from the deficits associated with spinal cord injury.

overall_design: Four adult female Long-Evans rats weighing 275-350 grams sustained a cervical level 4 (C4) hemi-contusion injury, resulting in forelimb functional deficits. Electrodes were implanted into the caudal forelimb areas of the contralateral motor cortex. Two animals received stimulation for one week at a current 80% of that required to evoke movement in the affected forelimb. Control animals were injured and implanted without stimulation. At the end of the experiment spinal cords and brains were removed, and five subregions were snap frozen in liquid nitrogen for sequencing. Region 1 was an approximately 5 mm3 block of subcortical white matter (without cortex) directly below the implantation/stimulation site. Region 2 was the same region on the contralateral side. Region 3 was spinal cord rostral to the injury (~C2-C4). Region 4 was the lesion epicenter (C4). Region 5 was the spinal cord caudal to the injury (~C5-C7). The spinal cord regions included both gray and white matter, neuron cell bodies and processes and glia. Complete RNA was isolated and sequenced and the reads were aligned to a rat reference genome.

first: Bethany

last: Kondiles

first: Lesley

last: Chaboub

first: Philip

last: Horner

first: Jiaqian

last: Wu

first: Steve

last: Perlmutter


title: Transcriptome analysis discloses dysregulated genes in normal appearing tumor-adjacent thyroid tissues from patients with papillary thyroid carcinoma

status: Public on Jan 29 2021

city: Columbus

first: Huiling

last: He

state: OH

address: 460 W 12th Ave

institute: The Ohio State University

summary: Papillary thyroid carcinoma (PTC) is the most common type of thyroid cancer.  Histologically normal appearing tissue adjacent to the tumor (NAT) from PTC patients is commonly used as a control in thyroid cancer studies, but the molecular characteristics of NAT tissue are not well characterized. The aim of this study was to characterize the global gene expression profile of NAT and compare it with those of normal and tumor thyroid tissues. We performed RNA sequencing of three categories of thyroid tissue samples including NAT, normal thyroid (N), and PTC tumor (T). Transcriptome analysis shows that NAT presents a unique gene expression profile, which was not associated with sex and the presence of lymphocytic thyroiditis.  Among the differentially expressed genes (DEGs) of NAT vs N, 247 coding genes and 6 noncoding genes have been reported as cancer genes, being involved in cell proliferation, apoptosis, and tumorigenesis. In addition, dysregulated expression of ribosomal and small RNAs was identified in NAT. IPA analyses revealed that “Cellular Response to Therapeutics, Cardiovascular Disease, Organismal Injury and Abnormalities, Cancer, and Cellular Movement” appeared as major dysregulated pathways in the NAT tissues.  This study provides a comprehensive study of the PTC transcriptome, which provides improved insight into the complexity of gene expression changes during PTC tumorigenesis.

overall_design: Normal appearing thyroid tissue adjacent to the tumor samples (NAT, n=46) and paired PTC tumor tissue samples (T, n=16) were analyzed from 46 PTC patients. Among these PTC patients, there were 21 patients with co-existent lymphocytic thyroiditis (LT) (PTC/LT+) and 25 patients without LT (PTC/LT-).  Normal thyroid tissue samples (N, n=12) were obtained from laryngeal cancer patients without thyroid lesions.

first: Sandya

last: Liyanarachchi

first: Wei

last: Li

first: Daniel

middle: F

last: Comiskey Jr

first: Pearlly

first: Ralf

last: Bundschuh

first: Altan

middle: M

last: Turkoglu

first: Pamela

last: Brock

first: Matthew

last: Ringel

first: Albert

last: de la Chapelle


title: RNA Sequencing of unc-30(ok613) and  wild type (WT) N2 C. elegans in Pseudomonas aeruginosa (PA14) infection

first: Benson

last: Otarigho

state: Texas

address: 6767 Bertner Avenue

department: Department of Genetics

institute: The University of Texas MD Anderson Cancer Center

summary:
Purpose: To uncover immune mediated  genes and pathways by Pseudomonas aeruginosa infection that are modulated by the homeodomain PITX1/UNC-30, which plays a vital role in the GABAergic signaling  in C. elegans
Methods: RNA was extracted from synchronized Pseudomonas aeruginosa infected L4 stage unc-30(ok613) and WT using Qiagen extraction kits and following standard methods. The animals were grown on OP50 at 20 C and infected at 25 C.
Results: RNA seq analyses shows enriched and signficant Pseudomonas aeruginosa mediated upregulated immune, neuropeptide and metabolism genes and pathways that are dependent of GABAergic signaling
Conclusions: Our study uncovered GABAgergic signaling to be modulator of the innate immunity in C elegans during Pseudomonas aeruginosa infection

overall_design: RNA seq  profiles of Pseudomonas aeruginosa infected L4-stage unc-30(ok613) and wild type (WT) C. elegans animals were generated by deep sequencing, in triplicate, using Illumina NovaSeq 6000 platform.

first: Alejandro

last: Aballay


title: Transcriptome analysis of V338Y mutant mitochondrial ribosomal protein in mouse muscle tissue

city: Zurich

first: Ge

last: Tan

address: Winterthurerstrasse 190

department: Functional Genomics Center Zurich

country: Switzerland

institute: University of Zurich

summary: Analysis of muscle from C57BL/6 mice expressing V338Y mutant mitochondrial ribosomal protein.

overall_design: mRNA profiles of wild-type and V338Y mutant mouse muscle tissue samples at two time points (3 months and 19 months) generated by deep sequencing.

first: Dimitri

last: Scherbakov

first: Erik

last: Böttger


title: Role of SPARC in autoimmunity

city: Milan

first: Matteo

last: Dugo

address: via Olgettina 60

department: Department of Medical Oncology

country: Italy

institute: IRCCS Ospedale San Raffaele

summary: We performed gene expression profiling to evaluate whether macrophages from pristane-treated WT and Sparc-/- mice display a different inflammatory phenotype

overall_design: Total RNA was extracted from peritoneal macrophages of pristane-treated WT (n=5) and Sparc-/- (n=5) mice. Gene expression profiles of Sparc-/- mice were compared to WT mice.

first: Loris

last: De Cecco

first: Mario

last: Paolo Colombo


title: Genome-wide analysis of the distribution of the testis-specific double bromodomain protein BRDT reveals distinct roles in pachytene spermatocyte and round spermatids

status: Public on Jan 26 2021

city: Cincinnati

first: Iouri

last: Chepelev

address: 3200 Vine St

institute: US Department of Veterans Affairs Medical Center

summary: BRDT, a member of the BET family of double bromodomain-containing proteins, is expressed uniquely in the  testis from pachytene spermatocytes through round spermatids, and is essential for spermatogenesis in the  mouse. Although BRDT is known to bind to acetylated lysines in chromatin, it is not known where in the  genome BRDT binds or whether the sites vary during the complex stages of differentiation in which it is  expressed. Herein, we use ChIP-Seq to identify genome-wide BRDT binding sites in chromatin from mouse  male germ cells at two distinct stages of differentiation. We identified 5452 BRDT-bound genomic loci in  pachytene spermatocytes and 5618 BRDT-bound genomic loci in round spermatids. Roughly two thirds of  BRDT binding sites were located in genes and BRDT binding correlated with highly transcribed genes. BRDT  binding sites also overlapped with several histone modifications or variants that are associated with active  transcription. Motif analysis revealed that BRDT-bound regions are enriched for consensus sequences for the  MYB, RFX, ETS and ELF1 in pachytene spermatocytes, and JunD, c-Jun, CRE and RFX in round spermatids.  Taken together, our data suggest that BRDT regulates distinct downstream target genes and may have unique  functions in the meiotic and spermiogenic transcription programs.

overall_design: ChIP-Seq experiments for four samples: BRDT and IgG in pachytene spermatocytes and round spermatids

first: Yoon

last: Ra Her

first: Li

last: Wang

first: Marcia

last: Manterola

first: Binyamin

last: Berkovits

first: Kairong

last: Cui

first: Keji

last: Zhao

first: Debra

last: Wolgemuth


title: Male sex and age biases viral burden, viral shedding, and type 1 and 2 interferon responses during SARS-CoV-2 infection in ferrets

status: Public on Jan 27 2021

city: Cleveland

first: Mark

last: Cameron

address: 10900 Euclid Ave

department: Population and Quantitative Health Sciences

institute: Case Western Reserve University

summary: Adult female and aged male ferrets were inefcted with SARS-CoV-2. Nasal turbinates, the right cranial lung, and right caudal lung were collected on Day 2, 7, 14, and 21 after infection. Tissues were collected from uninfected animals as control. RNA was isolated and used for analysis of the transcriptome to determine any effects on gene regulation during SARS-CoV-2 infection from age or sex.

overall_design: Adult female and aged male ferrets were infected with SARS-CoV-2 and tissues collected on Day 2, 7, 14, and 21 post infection. Uninfected ferret tissues were used as control.

first: M

last: Francis

first: B

last: Richardson

last: McNeil

last: Rioux

middle: K

last: Foley

first: A

last: Ge

first: R

middle: D

last: Pechous

first: J

last: Kindrachuk

first: C

last: Lew

first: V

last: Gerdts

first: D

last: Falzarano

last: Kelvin


title: RNASeq study of migratory blackheaded buntings in two different seasonal states at different times of the day

status: Public on Jan 23 2021

city: DELHI

first: AAKANSHA

last: SHARMA

state: DELHI

address: CHATTRA MARG

department: ZOOLOGY

country: India

institute: UNIVERSITY OF DELHI

summary: We report the mRNA found in hypothalamus of a migratory bird. The aim of this study was to study how the mRNA makeup of tissue varies under different seasonal states.

overall_design:
Study of total mRNA from hypothalamus  under two different seasonal states, using Illumina Sequencing
The terms "sensitive" and "refractory" are used with respect to the sensitivity of birds to photoperiod change. Our experiment has used birds that respond to seasonal changes in photoperiod and undergo changes in their general physiology. Therefore, when the birds respond to the photoperiodic change they are called "sensitive/photosensitive" and when they are unresponsive, we call them "refractory/ photorefractory".

first: Aakansha

last: Sharma

first: Subhajit

last: Das


title: Combined single-cell and spatial transcriptomics reveal the precise cellular states of postnatal cerebellar granule cells and connection with medulloblastoma

status: Public on Jan 18 2021

city: Shanghai

first: Jia

last: Wang

state: Shanghai China

address: Huashan Rd. 1940, build 3.  Shanghai,

institute: SJTU CHINA

summary: The progenitor/differentiation states of cerebellum granule cells have been investigated for many years. Deregulation of granule cells development is associated with the pathogenesis of medulloblastoma (MB).Our study reveals the cellular and spatial organization of cerebellar granule cells and provide direct evidence showing the similarity and discrepancy between normal development and tumorigenesis.

overall_design: Single cell mRNA profiles of 2 samples from Math1-GFP mice, 2 samples from Dcx-DsRed mice, 2 samples from WT mice and 3 SHH MBs from Patched+/- mice  were generated by 10X Genomics plartform, without technical replication, and sequenced by NovaSeq 6000 (Illumina). Spatial transcriptomics (ST) profiles of 2 samples of P7 WT mice were generated by 10X Genomics plartform, without technical replication, and sequenced by NovaSeq 6000 (Illumina).

first: Wei-Qiang

last: Gao


title: Comparative transcriptome analysis of Brucella canis MucR mutant strain and its parent strain RM6/66

status: Public on Jan 24 2021

city: Beijing

first: Hao

last: Dong

address: Huatuo road NO.31

institute: National Institutes for Food and Drug Control

summary: Purpose:To uncover the related mechanisms underlie virulence attenuation of Brucella canis MucR mutant strain. Methods:Three Brucella canis RM6/66 strains and three Brucella canis  ΔmucR  strains were grown in TSB at 37℃ until the log phase was reached, total RNA was isolated using the TRIzol according to the manufacturer’s instructions.The sequencing library of each RNA sample was prepared by using NEB Next Ultra Directional RNA Library Prep Kit for Illumina as recommended by the manufacturer. An Illumina platform was used to perform the transcriptome sequencing. Results: The results revealed that expressions of 694 genes were significantly different between RM6/66 and ΔmucR. Data analysis showed that in the COG term, the different expressed genes involved in translation, ribosomal structure and biogenesis, signal transduction mechanisms, energy production and conversion, intracellular trafficking, secretion, and vesicular transport, and extracellular structures were significantly affected. Pathway enrichment analysis indicated that the genes involved in ribosome, oxidative phosphorylation, aminoacyl-tRNA biosynthesis and protein export were significantly enriched.

overall_design: mRNA profiles of Three Brucella canis RM6/66 strains and three Brucella canis ΔmucR strains were generated by deep sequencing using HiSeq 4000 platform

first: Jiabo

last: Ding


title: Integrated analysis of multimodal single-cell data

status: Public on Jan 15 2021

city: New York

first: Yuhan

last: Hao

address: 101 6th Ave

institute: New York Genome Center

summary: The simultaneous measurement of multiple modalities, known as multimodal analysis, represents an exciting frontier for single-cell genomics and necessitates new computational methods that can define cellular states based on multiple data types. Here, we introduce ‘weighted-nearest neighbor’ analysis, an unsupervised framework to learn the relative utility of each data type in each cell, enabling an integrative analysis of multiple modalities. We apply our procedure to a CITE-seq dataset of hundreds of thousands of human white blood cells alongside a panel of 228 antibodies to construct a multimodal reference atlas of the circulating immune system. We demonstrate that integrative analysis substantially improves our ability to resolve cell states and validate the presence of previously unreported lymphoid subpopulations. Moreover, we demonstrate how to leverage this reference to rapidly map new datasets, and to interpret immune responses to vaccination and COVID-19. Our approach represents a broadly applicable strategy to analyze single-cell multimodal datasets, including paired measurements of RNA and chromatin state, and to look beyond the transcriptome towards a unified and multimodal definition of cellular identity.

overall_design:
Human PBMCs were profiled using CITE-seq and cell hashing

*** Raw data will be deposited in dbGaP due to patient privacy concerns ***


title: Dissection of cMyc+ GC-B cells

status: Public on Jan 12 2021

city: London

first: Dinis

middle: Pedro

last: Calado

address: Midland Road

institute: The Francis Crick Institute

summary: Transcriptomic profiling of the cMyc+ LZ-GC-B cell subpopulations delineated by flow-cytometry

overall_design: Splenic cMyc+ GC-B cells from cMyc-GFP reporter mice 7 days after immunization with sheep red blood cells (SRBC)

first: Rinako

last: Nakagawa

first: Miriam

last: Llorian-Sopena


title: Gene expression data of macrophages cultured on polished titanium discs

status: Public on Feb 10 2021

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

institute: University Heidelberg

summary:
Titanium is a common implant material. However, in some patients titanium implants fail. Macrophages are key cells involved in foreign body response. To identify macrophage response to titainum, primary human macrophages were cultured on polished titanium discs for 6 days
We used microarrays to determine the global expression pattern induced by polished titanium in macrophages and identify potential genes involved in implant failure.

overall_design: PBMC derived monocytes were cultured on cell culture plastic or on polished titanium discs for 6 days. Cells were stimulated either with IFNgamma or IL-4 or M2Cocktail or left unstimulated. On the 6th day RNA was isolated and whole transcriptome was analyzed using Affymetrix microarrays

first: Alexandru

last: Gudima


title: mbnl mutant zebrafish RNA-Seq experiments

city: Gainesville

first: Jared

last: Richardson

state: Floirda

address: 2033 Mowry Rd

institute: University of Florida

summary: mbnl knockout Danio rerio were created using CRISPR-Cas9, including single mbnl paralog knockouts, double mbnl paralog knockouts, and a triple mbnl paralog knockout. RNA-Seq was performed using skeletal muscle of three biological replicates of four month old fish.

overall_design: RNA-Seq analysis of zebrafish mbnl paralog knockout models

first: Melissa

last: Hinman


title: Transcriptomic Analysis of the Zebrafish Prion Mutants Supports Conserved Cross-Species Function of the Cellular Prion Protein

status: Public on Jan 08 2021

city: Edmonton

first: Niall

last: Pollock

state: Alberta

address: Department of Biological Sciences, CW 405, Biological Sciences Bldg.

country: Canada

institute: University of Alberta

summary: Wild-type zebrafish larvae and our prp1ua5003/ua5003;prp2ua5001/ua5001 mutant zebrafish larvae at 3 days post fertilisation were pooled into three biological replicates each of 50 larvae. Each replicate underwent paired end 100-125 and Illumina HiSeq2500 sequencing to a depth of 40 million reads, carried out by Otogenetics (Atlanta, GA). Samples were subsequently processed using the TopHat/Cufflinks bioinformatics pipeline. Alignments were mapped to the zebrafish reference genome, GRCz10. A small amount of wild-type reads were found to contaminate two of the pooled mutant samples and were not included in subsequent analysis. In total there were 1249 genes showing at least a 50% increase (745) in transcript abundance or 50% decrease (504) decrease in transcript abundance in wild-type zebrafish larvae compared to double mutant zebrafish larvae. Subsequent gene ontology analysis shows the biological process showing genes with the biggest decrease in transcript abundance was cell adhesion, and the process with the most genes showing an increase in transcript abundance was Oxidation/Reduction. Our study finds the processes affected by prion knockdown in zebrafish is remarkably similar to other studies in early mice embryos, suggesting a conserved function of the cellular prion protein in the early development of organisms.

overall_design: RNA-Sequencing analysis of 3 days post fertlisation whole wild-type and prp1-/-;prp2-/- zebrafish larvae

first: Patricia

middle: L

last: Leighton

first: Gavin

last: Neil

first: W

middle: T

last: Allison


title: GATA6 gene regulatory network drives multi drug resistance in cutaneous melanoma

status: Public on Jan 09 2021

first: Pietro

last: Berico

state: NY

address: 550 1st Ave

department: Pathology

institute: NYU Langone Health

summary: Transcriptional co-acticvators inhibition is proving to be a powerful mean against cancer cells that shown a novel hallmarks named transcriptional addiction. This dependecy on co-activars activity lays on their presence in clusters of enhancer regulatory regions called Super-enhancers (SEs) that establish high level of expression of genes important for cancer phisiology such as oncogenes and master transcription factors of the cellular lineage of origin. Among these co-activators in SEs is the kinase CDK7 of the basal transcription factor TFIIH. Here, using a large panel of melanoma cell lines, we observed an overall dependency of melanoma cells in CDK7 activity by inhibiting its function through the drug THZ1. However, by chronically exposing melanoma cells to THZ1, they univocally become resistant, switching phenotype toward a mesenchymal-like state. By comparing the transcriptome of artificial resistant and untreated cells in culture, we observed upregulation of the transcription factor GATA6 which control indeed a small regulon that includes genes involved in multi-drug resistance (MDR).

overall_design: Examination of deregulated genes upon siRNA GATA6 in mesenchymal-like melanoma cells

first: Berico

last: Pietro

first: Max

last: Cigrang


title: Hepatic transcriptome of vehicle and bortezomib treated male C57BL/6 mice.

status: Public on Jan 11 2021

city: Kolkata

first: Abhishake

last: Lahiri

address: 4, Raja S. C. Mullick Road

institute: CSIR-Indian Institute of Chemical Biology

summary: To investigate differentially expressed genes in hepatocytes from bortezomib treated (n=3) mice and healthy control (n=3) mice, total RNA was isolated from liver tissues and analysed by RNA-seq.

overall_design: We performed RNA seq on bortezomib treated male C57BL/6 mice and control mice. Three biological replicates from each group were sequenced.

first: Partha

last: Chakrabarti


title: Gene expression during CDCP1-induced morphological changes in MDCK cysts

city: Suita

first: Daisuke

last: Okuzaki

state: Osaka

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

country: Japan

institute: Osaka univ.

summary: Analysis of MDCK (type I) cysts overexpressing CDCP1-EGFP or its mutant. After cystogenesis in collagen matrix, overexpression of exogenous CDCP1 proteins was induced by the Tet-On system.

overall_design: Four arrays (Canine Gene Expression 4x44K v2 Microarray Kit: 021193) were performed as one color experiments.

first: Kentaro

last: Kajiwara

first: Masato

last: Okada


title: Acetyltransferase Enok regulates transposon silencing by promoting transcription at piRNA clusters and genes involved in piRNA biosynthesis [Enok ChIP-seq]

status: Public on Jan 07 2021

city: Taipei

first: Fu

last: Huang

address: 128, Academia Road Sec. 2, Nankang

department: Institute of Biological Chemistry

country: Taiwan

institute: Academia Sinica

summary: The PIWI-interacting RNA (piRNA) pathway is an important mechanism to suppress transposon activation in the germline that is highly conserved between Drosophila and mammals. This pathway starts from transcribing piRNA clusters to generate long piRNA precursors. The majority of piRNA clusters lacks a conventional promoter, and therefore their transcription is considered to utilize a noncanonical mechanism. However, information regarding transcriptional regulation of piRNA clusters is limited. Here, we report that the fly KAT6 acetyltransferase, Enok, is important for transposon silencing in the germline. Further small RNA-seq analysis revealed that Enok is critical for piRNA production from a specific subset of piRNA clusters including 42AB, one of the two major sources of piRNAs. Enok is the major enzyme for establishing the H3K23ac mark, and was shown to promote gene expression by acetylating H3K23. Surprisingly, our RNA-seq and ChIP-seq/ChIP-qPCR results suggest that Enok regulates expression of genes involved in the piRNA production by H3K23ac-dependent mechanisms, and also promotes transcription at piRNA clusters through H3K23ac-independent pathways. Our co-immunoprecipitation assay further suggests that Enok interacts with RNA polymerase II to facilitate transcription of piRNA clusters. Taken together, our study provides novel insights into the regulation of noncanonical transcription at piRNA clusters and transposon silencing.

overall_design: Investigation of the genome-wide distribution of Enok in wild-type ovaries by ChIP-seq.

first: Shih-Ying

last: Tsai


title: Identification of a novel metabolic engineering target for carotenoid production in Saccharomyces cerevisiae via ethanol-induced adaptive laboratory evolution

city: Guangzhou

first: Li

middle: Bu

last: Su

address: No. 100, Xianlie Middle Road, Guangzhou, 510070, PR China

institute: Guangdong Institute of Microbiology

summary: Carotenoids are a large family of health-beneficial compounds that have been widely used in the food and nutraceutical industries. There have been extensive studies to engineer Saccharomyces cerevisiae for the production of carotenoids, which already gained high level. However, it was difficult to discover new targets that were relevant to the accumulation of carotenoids. Herein, a new, ethanol-induced adaptive laboratory evolution was applied to boost carotenoid accumulation in a carotenoid producer BL03-D-4, subsequently, an evolved strain M3 was obtained with a 5.1-fold increase in carotenoid yield. Through whole-genome resequencing and reverse engineering, loss-of-function mutation of phosphofructokinase 1 (PFK1) was revealed as the major cause of increased carotenoid yield. Transcriptome analysis was conducted to reveal the potential mechanisms for improved yield, and strengthening of gluconeogenesis and downregulation of cell wall-related genes were observed in M3. This study provided a classic case where the appropriate selective pressure could be employed to improve carotenoid yield using adaptive evolution and elucidated the causal mutation of evolved strain.

overall_design: RNA-seq of strain BL03-D-4 and M3.

first: Buli

first: Anzhang

last: Li

first: Ming-Rong

last: Deng

first: Honghui

last: Zhu


title: A yeast-optimized single-cell transcriptomics platform elucidates how mycophenolic acid and guanine alter global mRNA levels

city: Hinxton

first: Jimmy

middle: Tsz Hang

last: Lee

state: Cambridgeshire

address: Wellcome Genome Campus

department: Cellular Genetics

institute: Wellcome Sanger Institute

summary: The ability to measure the number of gene-specific mRNA molecules in individual mammalian cells has transformed the transcriptomics field. Among the key technologies enabling single-cell mRNA sequencing has been Droplet Sequencing (Drop-Seq). While this method works efficiently for mammalian cells, its direct application to yeast cells has been problematic due to cell-type specific differences such as size, doublet formation rate, and cell wall. Here we introduce YeastDropSeq, a single-cell RNA sequencing method for the study of transcriptomics in yeast. We modified and optimized the original Drop-Seq method to address the issues that emerged from smaller cell sizes and the presence of a cell wall in yeast. As proof-of-principle application of the YeastDropSeq, we investigated the transcriptomic effects of mycophenolic acid (MPA), a lifespan-extending compound that decreases de novo GMP synthesis. We compared transcript levels between cells treated with MPA and cells treated with DMSO and/or guanine, MPA’s epistatic agent. We discovered that isogenic populations of yeast cells contain transcriptionally distinct subpopulations and that the subpopulation structures were maintained despite the different treatment conditions. We found that cells treated with MPA experience an upregulation of genes coding for proteins involved in DNA replication stress-response, antioxidation, pre-RNA processing, and translation initiation. Conversely, a downregulation of mRNA expression was observed for genes encoding translation initiation and elongation factors, the 40S and 60S ribosomal subunits, and for genes involved in metal transport and mitochondrial function. YeastDropSeq will accelerate biological discovery by facilitating droplet-based transcriptomics of yeast cells.

overall_design: There are 4 samples analyzed. One sample, DMSO, is the control. The other samples: Guanine, Guanine and Mycophenolic acid, and Mycophenolic acid are treated conditions

first: Guste

last: Urbonaite

first: Ping

last: Liu

first: Guillermo

middle: P

last: Gonzalez

first: Martin

last: Hemberg

first: Murat

last: Acar


title: The DME demethylase regulates sporophyte gene expression, cell proliferation, differentiation, and meristem resurrection

status: Public on Jan 05 2021

city: Seoul

first: Yeonhee

last: Choi

state: Gwanak-gu

address: 1 Gwanak-ro

country: South Korea

institute: Seoul National University

summary: The flowering plant life cycle consists of alternating haploid (gametophyte) and diploid (sporophyte) generations, where the sporophytic generation begins with fertilization of haploid gametes. In Arabidopsis, genome-wide DNA demethylation is required for normal development, catalyzed by the DEMETER (DME) DNA demethylase in the gamete companion cells of male and female gametophytes. In the sporophyte, postembryonic growth and development are largely dependent on the activity of numerous stem cell niches, or meristems. Analyzing Arabidopsis plants homozygous for a loss-of-function dme-2 allele, we show that DME influences many aspects of sporophytic growth and development. dme-2 mutants exhibited delayed seed germination, variable root hair growth, aberrant cellular proliferation and differentiation followed by enhanced de novo shoot formation, dysregulation of root quiescence and stomatal precursor cells, and inflorescence meristem (IM) resurrection. We also show that sporophytic DME activity exerts a profound effect on the transcriptome of developing Arabidopsis plants, including discrete groups of regulatory genes that are misregulated in dme-2 mutant tissues, allowing us to potentially link phenotypes to changes in specific gene expression pathways. These results show that DME plays a key role in sporophytic development and suggest that DME-mediated active DNA demethylation may be involved in the maintenance of stem cell activities during the sporophytic life cycle in Arabidopsis.

overall_design: Transcriptomes of wild-type and dme mutant seedlings were made from whole seedlings at 7 days after germination in Arabidopsis thaliana(Ler accession)

first: Seohyun

last: Kim

first: Jin-Sup

last: Park


title: Combined analysis of ribo-seq and rna-seq reveals that Mettl3 regulates embryonic cerebral cortex development in mice by controlling the proliferation and differentiation of neural progenitor cells

status: Public on Jan 04 2021

city: xiamen

first: kunzhao

last: du

address: jimei

institute: huaqiao university

summary: N6-methyladenosine (m6A) is the most important internal messenger RNA (mRNA) modification in mammals. The role of Mettl3, the core component of methyltransferase, and Fto, the demethylase, has not been revealed in the embryonic development of the cerebral cortex in mice. We constructed the conditional knockout of Mettl3 and Fto in the cerebral cortex of mice. We found that Mettl3 deletion causes cell cycle extension of progenitors and massive proliferation of intermediate progenitors at E15.5, which lead to a fold structure of cortex, while Fto deletion hardly altered cell numbers or morphology. Meanwhile, both transcriptome sequence (RNA-Seq) and ribosome profiling (Ribo-Seq) of Mettl3-deleted cortex mRNAs in E15.5 revealed that the differential genes were enriched in cell differentiation, neurogenesis, neuron differentiation, cell proliferation, and cell cycle. Moreover, deleted Mettl3 but not Fto significantly upregulated Ythdf1 and Ythdf2, which caused a substantial change in gene translation efficiency. Our findings indicate cortex m6A represents a novel layer of complexity in gene expression regulation and provide a new mechanism of precisely programmed RNA maturation.

overall_design: RNA-SEQ and Ribo-SEQ of the cerebral cortex of Emx1-Cre: Mettl3flox/flox and Emx1-Cre: Ftoflox/flox mice at E15.5

first: Kunzhao

last: Du

first: Tao

last: Sun


title: Acetyltransferase Enok regulates transposon silencing by promoting transcription at piRNA clusters and genes involved in piRNA biosynthesis

first: Fu

last: Huang

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

overall_design: Refer to individual Series


title: Male mice lacking Teshl lncRNA exhibit inactivation of Y chromosomal multicopy genes and female distortion-biased sex ratio change in offspring

status: Public on Jan 01 2021

city: Gwangju

first: Seonghyeon

last: Hong

address: 123 Cheomdangwagi-ro, Buk-gu, Gwangju, 61005, Korea

department: School of Life Science

institute: GIST

summary: Deletion of multicopy genes located in the male-specific region of the mouse Y chromosome long arm (MSYq) is associated with sperm head abnormalities and male infertility. Heat shock factor 2 (HSF2) regulates the transcription of multicopy genes in MSYq. Little is known how HSF2-dependent regulation of the MSYq genes occurs only in testis. Testis harbors the largest number of tissue-specific long noncoding RNAs (lncRNAs). Here, we report that the novel mouse testis-specific lncRNA NR_038002 is conserved in humans and displayed a spatiotemporal expression pattern in the nucleus of elongating spermatids. NR_038002-deficient male mice produced sperm with abnormal head morphology and exhibited reduced fertility accompanied by female-biased sex ratio change in offspring. Molecular analyses revealed that NR_038002 interacts with HSF2, and thereby activates the expression of the MSYq genes, such as Sycp3 like Y-linked (Sly) and spermiogenesis-specific transcript on the Y (Ssty). We designate NR_038002 as Teshl (testis-specific HSF2-interacting lncRNA). Taken together, our study establishes a molecular relationship of Teshl-HSF2-MSYq, and provides evidence for the critical role of the Teshl-HSF2 complex in acquiring the normal quality of Y-bearing sperm, leading to balanced offspring sex ratio

overall_design: Transcriptomic profiles of 8-weeks old wild type (WT) and NR_038002-deficient (KO) mice were generated by deep sequencing, in triplicate, using Illumina HiSeq2500

first: S

first: C

last: Cho


title: Gastrodin alleviates cardiac hypertrophy by inhibition of insulin-like growth factor type 2/insulin-like growth factor type 2 receptor

city: Kunming

first: Hong-Yi

last: Zheng

address: No. 32 jiaochang East Road, Wuhua District

institute: Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming

summary:
Background: Pathological cardiac hypertrophy is commonly associated with upregulation of fetal genes, fibrosis, cardiac dysfunction and leads to heart failure. Previous studies demonstrated that gastrodin (GAS) inhibited cardiac hypertrophy and thus improved cardiac function. However, the theraputic targets by which GAS regulates in the regression of cardiac hypertrophy has not been well elucidated yet.
Methods: A mouse model of myocardial hypertrophy was estavlished by angiotensin II (Ang II) induction, then treated with GAS (0, 5 or 50 mg/kg/d) combined with the sham-operated controls. Heart samples from each dose group were collected for the next RNA sequencing.Through bioinformatics analysis, the key differentially expressed genes (DEG) involved in the recovery of cardiac function were identidied. They were further confirmed by quantitative real-time PCR (qRT-PCR) and western blotting in neonatal rat cardiomyocytes (NRCMs).
Results: We identified 620 up-regulated and 87 down-regulated DEGs induced by Ang II, of which the expression patterns of 58 and 146 genes were reversed by low-dose and high-dose GAS, respectively. These reversed DEGs are mainly enriched in biological processs of regulation of Ras protein signal transduction, heart contraction, covalent chromatin modification, glucose metabolism and positive regulation of cell cycle. Among them, insulin-like growth factor type 2 (Igf2) gene, which was highly reversed and down-regulated by GAS, served as the core gene linking energy metabolism, immune regulation and system development. Subsequent functional verification demonstrated that the system of Igf2 and its receptor Igf2r is one of the targets of GAS in the treatment of cardiac hypertrophy, and knocking out Igf2r can protect NRCM from cardiac hypertrophy.
Conclusions: Taken together, we, for the first time, identified Igf2/Igf2r as a therapeutic target influenced by GAS in the pharmacological intervention of cardiac hypertrophy

overall_design: Heart mRNA profiles of Ang-II-induced cardiac hypertrophy mouse model and sham-operated controls after gastric treatment of gastrodin for 7days

first: Chang-Bo


title: Resolving the function of FoxO6 during Somatic Cell Reprogramming by RNA-seq

status: Public on Dec 31 2020

city: guangzhou

first: huan

last: chen

address: Huangpu District

institute: Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory)

summary:
Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to explore the function of FoxO6 in reprogramming system
Methods: The mRNA profiles of OKS induced reprogramming systems with and without FoxO6 were generated by deep sequencing.

overall_design: In order to explore the function of FoxO6 in reprogramming, we using high efficient OKS induced reprogramming systems. We collected cells at Day0, Day1, Day3, Day5, Day7 in two reprogramming system: OKS and OKS plus FoxO6. OKS induced reprogramming systems as the control. And the data has no replications.

last: Cao

first: M

last: Fu


title: Using RNAseq for identifying hepatic genes involved in  multi- (F1 generation) and transgenerational (F2 generation) responses to chronic benzo[a]pyrene exposure (F0 generation) in Xenopus tropicalis

city: Saint Martin d'Hères

first: Stéphane

last: REYNAUD

address: 2233 rue de la piscine

country: France

institute: Grenoble-Alpes University

summary: We investigated the multi- and transgenerational impact of BaP on Xenopus females following F0 generation exposure from the tadpole to the mature adult stage at a concentration (50 ng.L-1).  5 females from F1 and F2 generations by parentale xposure conditions (control vs BaP) were used for studying liver transcriptome by RNAseq. RNA-seq libraries were sequenced on an illumina GAIIx sequencer as 75bp single reads

overall_design: mRNAseq from liver of mature F1 and F2 females.

last: Reynaud


title: Transcriptional profiling of intestinal changes in Apc Kras tumours with MYC activation and/or drug combination treatment

city: Glasgow

first: Andrew

last: Campbell

address: Switchback Road

institute: CRUK Beatson Institute

overall_design: Apc Kras or Apc Kras MYC mice were treated with or without a eFT508/rapamycin drug combination, then whole intestines were extracted and transcriptomic analysis performed to investigate changes occuring with MYC and/or drug treatment.

first: John

last: Knight

first: Kathryn

last: Gilroy

first: Owen

last: Sansom


title: Control of the anterior pituitary cell lineage regulator POU1F1 by the stem cell determinant Musashi

city: Little Rock

first: Allen

last: Gies

state: AR

address: 4301 W. Markham

department: Biochemistry and Molecular Biology

institute: University of Arkansas for Medical Sciences

summary: The high energetic cost of reproduction requires that female fertility be closely linked to metabolic status. However, the mechanisms by which the metabolic and reproductive systems communicate is still largely undefined.  We have previously reported that signaling through the major metabolic cytokine leptin controls levels of the pituitary maturation determinant POU1F1 (also referred to as Pit1) that is required for optimal reproductive function. These studies further indicated that leptin increases POU1F1levels in females by promoting Pou1f1 mRNA translation, although the mechanism ofPou1f1 mRNA translation control is unknown.  In this study, we report that the stem cell marker and mRNA translational control protein, Musashi, represses translation of the Pou1f1 mRNA. In FACS-sorted purified female somatotropes, Msi1 mRNA and Musashi protein levels are increased in the mouse model that lacks leptin signaling (Gh-CRE leprLepr-null), coincident with the observed attenuation of Pou1f1 mRNA translation. Single-cell RNA sequencing of pituitary cells from control female animals indicates that Msi1 and Pou1f1 mRNAs are co-expressed in Gh-expressing cells and immunocytochemistry analyses of these cells confirms that Musashi protein is present in the GH-containing somatotrope population. We demonstrate that Musashi interacts directly with the Pou1f1 mRNA 3’ UTR and exerts translational repression of a Pou1f1 mRNA translation reporter in vitro, and interacts with the Pou1f1 mRNA in vivo.  These findings indicate a critical role for Musashi-mediated mRNA translational regulation in the coordination between metabolic status and the maturation of pituitary somatotropes that is required for optimized reproductive function .

overall_design: single cell RNA sequencing (scRNA-seq) on pooled pituitary samples from 8-week old, virgin, diestrous female mice. Three animals were pooled to generate two scRNA-seq control samples for sequencing.  After sequencing and bioinformatics clustering using the 10x Genomics cellular barcodes and unique molecular identified (UMI) counts (see Methods), the predominant pituitary cell types (somatotropes, lactotropes, thyrotropes, gonadotropes, corticotropes and melanotropes) were identified primarily based on established pituitary endocrine expression markers (Pou1f1, Gh, Prl, Tshb, Lhb, Fshb, Pomc, Pax7),

first: Melody

last: Allensworth-James

first: Angela

last: Odle

first: Jewel

last: Banik

first: Linda

last: Hardy

first: Alex

last: Lagassse

first: Jordan

last: Bird

first: Christian

last: Thomas

first: Nathan

last: Avaritt

first: Stephanie

last: Byrum

first: Melanie

last: MacNicol

first: Gwen

middle: V

last: Childs

first: Angus


title: MTA1 interacts with primary RNAs to regulate expression and AS by protein dependent manner [CLIP]

city: wuhan

first: dong

last: chen

address: GaoXin 2nd Road

institute: ablife

summary: MTA1 is known as its metastatic and invasive function in cancers and the core member of NuRD complex. But the mechanism of regulating gene expression by MTA1 is limited. Besides the interaction with chromosome, MTA1 may play important role at the transcriptional level. We performed co- immunoprecipitation (co-IP) on HCT116 cells and found numerous RNA binding proteins (RBPs), which functions as spliceosome and RNA transport. We then validated that MTA1 interacts with RBPs by RNA dependent manner. By performing the CLIP-seq of MTA1, ten thousands of peaks and thousands of genes were emerged. More detailed analysis and high level of intronic peaks reveal MTA1 prefers to bind pre-mRNAs and regulate the alternative splicing progression by binding the splice site. High overlapping between MTA1 binding and MTA1 regulated genes highlights the direct regulation of RNAs by MTA1 coupling with RBPs. LTK is one of the obvious examples regulated by MTA1. Together, these findings uncover a novel mechanism of MTA1 regulation in transcriptional level as RBPs, and suggest MTA1 regulates pre-mRNA splicing with other RBPs.

overall_design: CLIP-seq experiments performed on MTA1 protein. IgG was performed with the same steps as control.

first: Yi

last: Zhang

first: Haili

last: Qian


title: The chromatin and regulatory properties of pluripotency-associated poised enhancers are conserved in vivo [ChIP-seq]

city: Cologne

first: Giuliano

last: Crispatzu

address: Joseph-Stelzmann-Straße 26

department: CECAD

institute: University of Cologne (UoC), Germany

summary: Transcriptional and phenotypic robustness during development is believed to require complex regulatory landscapes whereby multiple enhancers redundantly control the expression of major cell identity genes. In contrast, we previously described a limited and genetically distinct set of distal regulatory elements, known as poised enhancers (PEs), that control the induction of genes involved in early brain development in a hierarchical and non-redundant manner. Before becoming activated in neural progenitors, PEs are already bookmarked in pluripotent cells with unique chromatin and topological features that could contribute to their privileged regulatory properties. However, since PEs were originally identified and subsequently characterized using embryonic stem cells (ESC) as in an in vitro differentiation system, it is currently unknown whether PEs are functionally conserved in vivo. Here, we generate and mine various types of genomic data to conclusively show that the epigenetic and 3D structural features of PEs are conserved among pluripotent cells both in vitro and in vivo. Furthermore, by genetically disrupting evolutionary conserved PEs in mouse and chicken embryos, we demonstrate that these regulatory elements play essential and non-redundant roles during the induction of major anterior neural genes in vivo.

sample_organism:
Gallus gallus
Mus musculus

platform_organism:
Gallus gallus
Mus musculus

overall_design: Genome-wide binding profiles for various histone modifications were investigated in mESC (undifferentiated and differentiated), as well as early murine and avian embryonic stages using ChIP-seq.

first: Rizwan

last: Rehimi

first: Alvaro

last: Rada-Iglesias


title: Genome-wide expression analysis of high-growth and low-growth capacity human mesenchymal stem cells

city: Singapore

first: Padmapriya

last: Sathiyanathan

address: 8A Biomedical Grove

department: Glycotherapeutics Group

country: Singapore

institute: Institute of Medical Biology

summary: Human mesenchymal stem cells (hMSCs) were stratified into high- and low-growth capacity groups according to their growth potential in vitro which correlated with potency as assessed by standard MSC characterization assays. Gene expression profiling was then performed to undertand transcriptome level differences between them.

overall_design: Total RNA obtained from the high- and low-growth capacity hMSCs at early passage was studied by microarray


title: Roles of membrane-Anchoring ARHGAP fusions in peritoneal metastasis of gastric and pancreatic cancer.

city: Tokyo

first: Masayuki

last: Komatsu

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

institute: National Cancer Center Research Institute

summary:
Diffuse-type gastric cancer (DGC) frequently metastasizes to the peritoneal cavity and causes malignant ascites. Although recent studies revealed that RHOA mutation and CLDN18-ARHGAP6/26 fusions are a hallmark of DGC, their roles are largely unknown. Here, we report the roles of two novel ARHGAP fusions (RP2-ARHGAP6 and OCLN-ARHGAP26) and the above CLDN18-ARHGAP26 fusion in ascites-derived DGC cell lines. A series of experiments revealed that X-ARHGAP6 /26 fusion acts as an inhibitor of RhoA and further suggested that the ARHGAP6 fusion induces cell-adhesion loss and maintains a putative ALDH-high cancer stem cell population, whereas the ARHGAP26 fusion evades apoptosis. Notably, these ARHGAP6/26 fusions were frequently found not only in the ascites of DGC but also in that of pancreatic cancer (12% and 38%, respectively). Together, these data demonstrate that ARHGAP6/26 fusions are useful for developing therapeutics and diagnostics for peritoneal metastasis control of DGC and pancreatic cancer.
We used microarrays to identify gene sets regulated by RP2-ARHGAP6-centered signaling in DGC cells.

overall_design: We established two ARHGAP6 shRNA-expressing clones from RP2-ARHGAP6 harbored DGC cell line (NSC-10X1aF).  In addition to these clones, control shRNA-expressing NSC-10X1aF cells were also established as control. Total 6 samples (2 independent biological experiments for each cell line) were analyzed by microarray.

first: Fumiko

last: Chiwaki

first: Rie

last: Komatsuzaki

first: Hiroki

last: Sasaki


title: The chromatin and regulatory properties of pluripotency-associated poised enhancers are conserved in vivo


title: Dcaf11 facilitates telomere elongation in early embryos and embryonic stem cells (ESCs) through activating the Zscan4-mediated alternative lengthening telomere (ALT) mechanism

city: Shanghai

first: Yixin

last: Huang

address: Siping Road

institute: Tongji University


title: CD96+ and CD96- NK cells from human livers

city: Hefei

first: Cheng

last: Sun

state: Anhui

address: 17, Lujiang Road

department: the First Affiliated Hospital of USTC

institute: University of Science and Technology of China

summary:
To better define primary CD96+ NK cells and CD96- NK cells from human liver, we isolated primary hepatic lymphocytes from healthy liver and purified CD96+ and CD96- NK cells through negative selection and flow cytometry sorting.
Purified NK cells from human liver tissues were first enriched by MACS using NK Cell Isolation Kit (Miltenyi Biotec, German) and CD96+/- hepatic NK cells were isolated by FACS Aria cell sorter (BD Biosciences, United States) to attain a purity greater than 95%.

overall_design: Expression profiling of CD96+ hepatic NK and CD96- hepatic NK cell types.  Three healthy donors were pooled for each cell type.


title: The chromatin and regulatory properties of pluripotency-associated poised enhancers are conserved in vivo [ATAC-seq]

overall_design: Chromatin accessibility in early murine and avian embryonic stages using ATAC-seq.


title: The chromatin and regulatory properties of pluripotency-associated poised enhancers are conserved in vivo [HiChIP]

overall_design: Chromosome confirmation capture for various histone modifications were investigated in mESC (undifferentiated and differentiated), as well as early murine and avian embryonic stages using HiChIP.


title: Gene expression altered by Chrebp deficiency and fructose treatment

status: Public on Jan 06 2021

city: Ann Arbor

first: Deqiang

state: MI

address: 1137 Catherine Street

department: Molecular & Integrative Physiology

institute: University of Michigan

summary:
To identify hepatic genes specifically regulated by fructose-activated ChREBPα.
Fgf21 is one of the genes activated by fructose dependent on ChREBP.

overall_design: Micro-array assay was performed with RNA samples from wildtype and Chrebp-KO primary hepatocytes treated with or without fructose.

first: Xin

last: Tong


title: H3K4methylation in Setd1a loss-of-function Raw264.7 cells upon LPS or Dex+LPS stimulation

city: Freising

first: Franziska

last: Greulich

address: Gregor-Mendel-Str. 2

department: Metabolic Programming

institute: TU München

summary: Nuclear interaction studies by ChIP coupled with mass spectrometry identified the COMPASS/SETD1A complex as interaction partner of the glucocorticoid receptor (GR) in murine bone marrow-derived macrophages (BMDMs). Here, we profiled H3K4me1, H3K4me2 and H3K4me3 in wild-type and Setd1a hypermorphic (Setd1aDel/+) Raw264.7 cells after LPS and Dex+LPS stimulation by spike-in ChIP-Seq.

overall_design: We profiled changes in H3K4me1, H3K4me2 and H3K4me3 in wild-type and Setd1aDel/+ (loss-of-function) Raw264.7 cells after challenge with LPS or Dex+LPS. All ChIP-Seq experiments were done in duplicates or more. We used Drosophila melanogaster chromatin as spike-in control.

first: Nina

last: Uhlenhaut


title: Allele-specific genome editing using the CRISPR/Cas9 system phenocopies alopecia areata symptomatic patched hair loss in mice

city: isehara

first: Akira

last: Oka

state: Kanagawa

address: 143 Shimokasuya

institute: Tokai university

summary: Using CRISPR/Cas9 for allele-specific genome editing we phenocopied AA symptomatic patched hair loss in mice engineered to carry the Cchcr1 risk allele.

overall_design: Fluorescent cRNA synthesis derived from eight skin RNAs was performed using Agilent’s Low RNA Input Linear Amplification kit (Agilent Technology) and subjected to DNA microarray analysis using single-color microarray-based gene-expression analysis (SurePrint G3 Mouse GE Ver 2.0, 8 x 60K, Agilent Technology). All procedures were performed according to the manufacturer’s instructions.

first: Shigaku

last: Ikeda


title: Assessment of DNA methylation patterns related to osteoarthritis in baboon bone and cartilage using the 850K array

status: Public on Dec 28 2020

city: Chicago

first: Genevieve

last: Housman

state: IL

address: 920 East 58th Street, CLSC 317

department: Genetic Medicine

institute: University of Chicago

summary: The aim of this study was to identify DNA methylation patterns in femur trabecular bone and cartilage of adult baboons (n=28 with knee OA, n=28 without knee OA). The Illumina Infinium MethylationEPIC Array was used to assess these genome-wide methylation patterns.

overall_design: Bisulphite converted DNA from the 56 baboons (n=56 bone samples, n=56 cartilage samples) were hybridized to the Illumina Infinium MethylationEPIC array.


title: MTA1 interacts with primary RNAs to regulate expression and AS by protein dependent manner

first: dong

last: chen

state: Hubei

overall_design: Refer to individual Series


title: DNA methylation dynamics of oocyte in follicular maturation

status: Public on Dec 25 2020

city: Memphis

first: Xiaolong

last: Chen

state: TN

address: 262 Danny Thomas Pl

institute: St Jude Children's Research Hospital


title: Differential expression of genes on the Enterococcus faecalis plasmid pCF10 in the presence and absence of prgU

status: Public on Dec 24 2020

city: Minneapolis

first: Julia

last: Willett

state: MN

address: 689 23rd Avenue SE, 4-149 Micro Research Facility

institute: University of Minnesota

summary: Efficient horizontal gene transfer of the conjugative plasmid pCF10 from Enterococcus faecalis depends on the expression of its Type 4 Secretion System (T4SS) genes, controlled by the PQ promoter. The PQ promoter is strictly regulated, partially to limit cell toxicity caused by overproduction of PrgB, a T4SS adhesin. PrgU plays an important role in regulating this toxicity by decreasing PrgB levels. PrgU has an RNA-binding fold, prompting us to test whether PrgU exerts its regulatory control through binding of prgQ transcripts. We used a combination of in vivo methods to quantify PrgU effects on prgQ transcripts at both single cell and population levels.

overall_design: Comparison of transcript levels in parental and prgU deletion strains using RNAseq

first: Gary

last: Dunny

middle: E


title: Single cell RNA seq analysis of postnatal mouse utricle

status: Public on Dec 27 2020

city: Nashville

first: Taha

last: Jan

address: 2220 Pierce Ave, PRB 752

department: Otolaryngology

institute: VUMC

summary: Undamaged utricular sensory epithelia from P2, P4, and P6 mice were isolated using FACS and underwent Smartseq-2 protocol for single cell RNA seq. Data was generated using Illumina NextSeq 500, paired end, 75-150bp reads with median depth of ~0.5 million reads per cell.

overall_design: FACS sorted mouse utricle cells, Smart-seq2 protocol

first: Alan

middle: G

last: Cheng

first: Stefan

last: Heller


title: Evaluation of chromosomal abnormalities and copy number variations in fetuses with ultrasonic soft markers

city: Fuzhou

first: Hailong

state: Fujian

address: No.18 Daoshan Road, Gulou District

institute: Fujian Maternity and Child Health Hospital

summary: This study aimed to evaluate the clinical value of copy number variations (CNVs) in fetuses with ultrasonic soft markers. Among 1131 fetuses, 729 had single ultrasonic soft marker, 322 had two ultrasonic soft markers, and 80 had three or more ultrasonic soft markers. All fetuses underwent single nucleotide polymorphism (SNP) array analysis. Among 1131 fetuses with ultrasonic soft markers, 46 had chromosomal abnormalities. In addition to the 46 fetuses with chromosomal abnormalities consistent with the results of the karyotyping analysis, the SNP array identified additional 6.1% (69/1131) abnormal CNVs. No significant difference was found in the rate of abnormal CNVs among the groups. The SNP array can fully complement conventional karyotyping in fetuses with ultrasonic soft markers, improve detection rate of chromosomal abnormalities, and affect pregnancy outcomes.

overall_design: 1131 fetuses  underwent single nucleotide polymorphism (SNP) array analysis, and the SNP array identified 6.1% (69/1131) abnormal CNVs.

first: Meiying

last: Cai


title: Genome-wide maps of AF10( MLLT10) PZP binding in MOLM13 human AML cells

status: Public on Dec 15 2020

city: San Diego

first: Aniruddha

last: Deshpande

state: California

address: 10901 N Torrey Pines Road

institute: Sanford Burnham Prebys Medical Discovery Institute

summary: We report genomic occupancy of the AF10 PZP domain in MOLM13 cells

overall_design: Examination of AF10-PZP binding using a custom AF10 -terminal antibody

first: Anagha


title: Patient-Derived Orthotopic Xenografts and Cell Lines from Pediatric High-Grade Glioma Recapitulate Heterogeneity of Histopathology, Molecular Signatures and Drug Response

status: Public on Dec 09 2020

city: MEMPHIS

first: Suzanne

middle: J.

last: Baker

state: TENNESSEE

address: 262 Danny Thomas Place

institute: ST. JUDE CHILDREN'S RESEARCH HOSPITAL

type: Methylation profiling by genome tiling array

summary: We established 21 patient-derived pHGG orthotopic xenograft (PDOX) models and 8 matched cell lines from diverse pHGG subgroups. Models recapitulated histopathology, DNA methylation signatures, mutations and gene expression patterns of the patient tumors from which they were derived, and included rare subgroups not well-represented by existing models. We also included 6 DIPG cell lines generously shared by Dr. Michelle Monje (Stanford University).  An online interactive data portal is available to explore associated detailed molecular characterization and HTS chemical sensitivity data.

overall_design: Bisulphite converted DNA from these samples were hybridised to the Illumina Infinium MethylationEPIC or HumanMethylation450 BeadChip

first: Brian

last: Gudenas

first: Ke

last: Xu

middle: J


title: Common and private vitamin D target genes of human primary immune cells: a personalized approach

status: Public on Dec 08 2020

city: Olsztyn

first: Carsten

last: Carlberg

address: ul. Trylińskiego 18

department: Food Research

country: Poland

institute: Polish Academy of Sciences

summary: In this study, the transcriptome of peripheral blood mononuclear cells (PBMCs) of healthy adults was investigated in response to in vitro treatment with 1,25(OH)2D3.

overall_design: RNA-seq of PBMCs of 5 individuals (#5, 9,12,13,14) treated in 3 biologial repeats with the biologically active form of vitamin D, 1,25(OH)2D3 (1,25D) or solvent (0.1% Ethanol (EtOH))

first: Antonio

last: Neme

first: Andrea

last: Hanel


title: Cardiac Nestin+ mesenchymal stromal cells enhance healing of ischemic heart through Periostin-mediated M2 macrophage polarization

city: Guangzhou

first: Yan

last: Liao

state: Guangdong

address: the NO.2nd Zhongshan Road

department: Zhongshan School of Medicine

institute: Sun Yat-sen University

summary:
Background—Mesenchymal stem cells (MSCs) have shown therapeutic potency for treating cardiovascular diseases, but their therapeutic efficacy shows significant heterogeneity depending on their tissue of origin. We herein sought to identify the optimal source of MSCs for cardiovascular disease therapy.
Methods—Heart- and bone marrow (BM)-derived GFP+ cells positive for the MSCs marker, Nestin, were flow cytometrically sorted from 7-day-postnatal Nestin-GFP transgenic mice. To study their biological characteristics in vitro, we characterized their self-renewal capacity, multi-lineage differentiation ability, and surface markers. To investigate their therapeutic potential in vivo, we intramyocardially injected Nestin+ cells (3×105) into the infarct border zone of mice subjected to acute myocardial infarction (MI), and performed echocardiography and Masson’s-Trichrome staining at 1 and 3 weeks post-MI. We characterized gene profiles with RNA-sequencing analysis, and analyzed the putative reparative mechanism, that of Periostin-mediated M2 macrophages polarization, by immunofluorescence staining, qPCR, ELISA, and flow cytometry in vivo and in vitro.
Results—In vitro, the heart- and BM-derived Nestin+ cells (Nes+cMSCs and Nes+bmMSCs, respectively) were found to possess self-renewal ability, show similar tri-lineage differentiation potentials, and express some MSCs-related surface markers. Importantly, Nes+cMSCs significantly improved cardiac function, attenuated left ventricular (LV) remodeling, and decreased infarct size in the mouse MI model, compared with Nes+bmMSCs- or saline-treated MI controls. Nes+cMSC treatment notably reduced the total number of CD68+ pan-macrophages while inducing the polarization of macrophages toward an anti-inflammatory M2 phenotype in ischemic myocardium, compared with the saline-treated MI control. Periostin, which was highly expressed in Nes+cMSCs, could promote the polarization of M2-subtype macrophages in vitro and in vivo. Finally, Periostin knockdown remarkably reduced the therapeutic effects of Nes+cMSCs, inhibiting the survival and LV remodeling of MI model mice and significantly decreasing the number of M2 macrophages at lesion sites.
Conclusions—Nestin+ cMSCs have greater efficacy than Nestin+ bmMSCs for cardiac repair following acute MI, using a reparative mechanism that acts at least partly through Periostin-mediated M2 macrophage polarization.

overall_design: Examination of 2 different Nestin+ cells from Bone marrow and heart of 7-day old Nestin-GFP transgenic mice.

first: Weijun

last: Huang

first: Andy

last: Xiang


title: Characterizing cerebrospinal fluid immunity in neurological manifestations of COVID-19

status: Public on Dec 11 2020

city: Muenster

first: I-Na

last: Lu

state: NRW

address: Domagkstraße 20

department: Department of Pediatric Hematology and Oncology

institute: University Children's Hospital Münster

summary: Patients suffering from Coronavirus disease 2019 (COVID-19) can develop neurological sequelae, such as headache, neuroinflammatory or cerebrovascular disease. These conditions - here termed Neuro-COVID - are more frequent in patients with severe COVID-19. To understand the etiology of these neurological sequelae, we utilized single-cell sequencing and examined the immune cell profiles from the cerebrospinal fluid (CSF) of Neuro-COVID patients compared to patients with non-inflammatory and autoimmune neurological diseases or with viral encephalitis. The CSF of Neuro-COVID patients exhibited an expansion of dedifferentiated monocytes and of exhausted CD4+ T cells. Neuro-COVID CSF leukocytes featured an enriched interferon signature; however, this was less pronounced than in viral encephalitis. Repertoire analysis revealed broad clonal T cell expansion and curtailed interferon response in severe compared to mild Neuro-COVID patients. Collectively, our findings document the CSF immune compartment in Neuro-COVID patients and suggest compromised antiviral responses in this setting.

overall_design: Single-cell RNA sequencing of cerebrospinal fluid-derived leukocytes from patients with Neuro-COVID (n=8), non-inflammatory (n = 9) and autoimmune (n=9) neurological diseases and viral encephalitis (n=5).

first: Michael

last: Heming

first: Xiaolin

last: Li

first: Gerd

last: Meyer zu Hörste


title: Translatomic analysis of regenerating and degenerating spinal motor neurons in injury and ALS

city: Stanford

first: Jennifer

last: Shadrach

state: CA

address: 290 Jane Stanford Way, Room E365

department: Neurosurgery

country: USA

institute: Stanford University

summary: The neuromuscular junction (NMJ) is a specialized synapse that allows for the communication between spinal motor neurons and muscle fibers. Maintenance of motor-muscle connectivity at the NMJ is critical for the preservation of muscle strength and coordinated motor function. Unlike injuries that damage the central nervous system, motor neurons can mount a robust regenerative response after peripheral nerve injuries. In contrast, motor neurons selectively degenerate in diseases such as amyotrophic lateral sclerosis (ALS), which leads to progressive muscle wasting and paralysis. To assess how different insults affect motor neurons in vivo, we adapted the RiboTag methodology developed by Sanz et al. to perform ribosomal profiling of mouse motor neurons. Using this strategy we isolated and sequenced motor neuron-specific transcripts from spinal cord tissue following sciatic nerve crush, a model of acute injury and regeneration, and in the SOD1-G93A mouse model of ALS.

overall_design: 50 total samples are included, in replicates of 3 (except 3-month RiboWT group, n=4). An RPL22-HA immunopreciptiation (IP) and input lysate controls is included for each sample. Injury samples contain injured (INJ) and uninjured (UNJ) controls and ALS samples are from RiboALS and RiboWT littermate mice at 1-mo, 3-mo, and 4-mo ages.

first: Rachel

last: Ives

first: Elizabeth

middle: A

last: Fogarty

first: Anthony

last: Antonellis

first: Wesley

last: Stansberry

last: Pierchala


title: AI-guided Discovery of a Paradoxical Immune Response in Fatal COVID-19 (Hamster)

status: Public on Dec 07 2020

city: La Jolla

first: Debashis

last: Sahoo

address: 9500 Gillman Drive

department: Pediatrics

institute: UCSD

summary: We sought to define the host immune response, a.k.a, the “cytokine storm” that has been implicated in fatal COVID-19 using an AI-based approach. Over 45,000 publicly available transcriptomic datasets of viral pandemics were analyzed to extract a 166-gene signature using ACE2 as a ‘seed’ gene; ACE2 was rationalized because the receptor it encodes enables the virus that causes Covid-19, SARS-CoV-2, to enter host cells. The signature was surprisingly conserved in all viral pandemics, including COVID-19, inspiring the nomenclature ViP-signature. A subset of 20-genes classified disease severity in respiratory pandemics. The ViP signatures pinpointed airway epithelial and myeloid cells as the major contributors of an IL-15 cytokine storm, and epithelial and NK cell destruction as determinants of severity/fatality. They also helped formulate precise therapeutic goals to reduce disease symptoms and severity. Thus, the ViP signatures provide a quantitative and qualitative framework for titrating the immune response in viral pandemics and may serve as a powerful unbiased tool in our armamentarium to rapidly assess disease severity and vet candidate drugs.

overall_design: Lung samples from 8-week old Syrian hamsters were used from a previously published study (PMID:32540903). We chose three different groups of samples: uninfected control, SARS-CoV-2 challenge after Den3 (antibody to dengue virus), and SARS-CoV-2 challenge after Anti-CoV2 (CC12.2; a potent SARS-CoV-2 neutralizing antibodies) (PMID:32540903).

first: Soumita

last: Das

first: Pradipta

last: Ghosh


title: Spatio-temporal mRNA tracking in the early zebrafish embryo

city: Berlin

first: Jan Philipp

last: Junker

address: Hannoversche Str. 28

department: BIMSB

institute: MDC

summary: We performed spatially resolved transcriptomics with sub-single-cell resolution in zebrafish embryos at the one-cell stage, which allowed us to identify a class of mRNAs that is specifically localized at an extraembryonic position in the yolk sac, the vegetal pole. The 3’ UTRs of these localized genes are enriched in specific sequence motifs. Comparison to two frog species revealed relatively low conservation of localized genes, but high conservation of sequence motifs. In vivo RNA labeling followed by scRNA-seq revealed that a large number of the localized transcripts are specifically transported to the primordial germ cells.

sample_organism:
Danio rerio
Xenopus laevis
Xenopus tropicalis

overall_design: Spatial transcriptomic data (tomo-seq) from zebrafish one-cell stage embroys, mature X. laevis and X. tropicalis oocytes. Single-cell metabolic labeling (scSLAM-seq) of zebrafish embryos at 6 hpf.

first: Karoline

last: Holler

first: Anika

last: Neuschulz

first: Philipp

last: Boß

first: Janita

last: Mintcheva

first: Roberto

last: Arsiè

first: Uwe

last: Ohler

first: Markus

last: Landthaler

first: Jan


title: Hypo-methylated Igf2r gene locus marks phthalate-mediated trans-generational inheritance of murine allergic phenotypes

city: Chiayi County

first: Mita

last: Tran

address: 168 University Road

department: Biomedical Sciences

institute: National Chung Cheng University

summary: Global DNA methylation analysis on DEHP treated dendritic cells vs control using MethylCap-Seq

overall_design: Female mice were preexposed to DEHP and splenic CD11c high DCs from OVA-immunized F1 female offspring were subjected to Methyl-Cap Seq analysis for global methylation changes

first: Michael

middle: W

last: Chan

first: Jau-Ling

last: Suen

first: Pearlly

middle: S

last: Yan

first: Jora

last: Lin