title: Two novel, tightly linked, and rapidly evolving genes underlie Aedes aegypti mosquito reproductive resilience during drought

status: Public on Mar 01 2022

city: New York

first: Krithika

last: Venkataraman

state: NY

address: 1230 York Ave

institute: The Rockefeller University

summary: Female Aedes aegypti mosquitoes impose a severe global public health burden as primary vectors of multiple viral and parasitic pathogens. Under optimal environmental conditions, Aedes aegypti females have access to human hosts that provide blood proteins for egg development, conspecific males that provide sperm for fertilization, and freshwater that serves as an egg-laying substrate suitable for offspring survival. As global temperatures rise, Aedes aegypti females are faced with climate challenges, like intense droughts and intermittent precipitation, which create unpredictable and suboptimal conditions for the egg-laying step of their reproductive cycle. Aedes aegypti mosquitoes nonetheless show remarkable reproductive resilience, but how they achieve this is unknown. Here we show that under drought-like conditions simulated in the laboratory, mated, blood-fed Aedes aegypti females carrying mature eggs retain them in their ovaries for extended periods, while maintaining the viability of these eggs until they can be deposited in freshwater. Using transcriptomic and proteomic profiling of Aedes aegypti ovaries, we identify two previously uncharacterized genes – here named tweedledee and tweedledum – that show ovary-enriched, temporally-restricted expression during egg retention. These genes are mosquito-specific, linked within a syntenic locus, and rapidly evolving under positive selection, raising the possibility that they serve an adaptive function. Using loss-of-function mutagenesis to disrupt both genes, we show that, tweedledee and tweedledum, which encode secreted proteins, are specifically required for extended retention of viable eggs, such as during intermittent precipitation or drought. These results highlight an elegant example of taxon-restricted genes at the heart of an important adaptation that equips Aedes aegypti females with “insurance” to, when contextually appropriate, flexibly extend their reproductive sequence without losing reproductive capacity, thus allowing this species to exploit diverse and unpredictable habitats.

overall_design: Whole ovary tissue from Ae. aegypti female mosquitoes (wild type Liverpool strain) at 11 different reproductive time-points: non-blood-fed, 3 hours post-blood-meal (PBM), 6 hours PBM, 12 hours PBM, 1 day PBM, 2 days PBM, 3 days PBM (eggs retained), 4 days PBM (eggs retained), 6 days PBM (eggs retained), 6 days PBM (eggs laid <5 hours prior), 13 days PBM (eggs laid >1 week prior).

first: Leslie

middle: B

last: Vosshall

first: Nadav

last: Shai


title: A family of C. elegans VASA homologs control Argonaute pathway specificity and promote transgenerational silencing [IP small-RNA seq]

status: Public on Mar 10 2022

city: Worcester

first: Siyuan

last: Dai

state: MA

address: 368 Plantation St.

department: RTI

country: USA

institute: UMass Chan Medical School

summary: Germline Argonautes direct transcriptome surveillance within peri-nuclear membraneless organelles called nuage. In C. elegans, a family of Vasa-related Germ Line Helicase (GLH) proteins localize in, and promote the formation of nuage called P granules. Previous studies have implicated GLH proteins in inherited silencing but direct roles in amplification of small RNAs, or in target mRNA or Argonatue binding have not been identified. Here we show that GLH proteins compete with each other to control Argonaute pathway specificity, bind directly to Argonaute-target mRNAs and act to promote the amplification of small RNAs required for transgenerational inheritance.  We show that the ATPase cycle of GLH-1 regulates its direct binding to the Argonaute WAGO-1 which engages amplified small RNAs.  Our findings support a dynamic and direct role for GLH proteins in inherited silencing beyond their role as structural components of nuage.

overall_design: Small-RNAs for whole worms and bound to CSR-1, WAGO-1 and WAGO-9 Argonautes were cloned from WT and multiple glh mutants. CLIP-seq were carried out by pulling down protein-RNA complex pre-crosslinked by UV light and  sequencing the RNA fragments recovered from IP complex.

first: En-zhi

last: Shen

first: Craig

last: Mello


title: Peaksat: An R package for ChIP-seq peak saturation analysis

status: Public on Mar 07 2022

city: Burtlington

first: Seth

last: Frietze

state: VT

address: The University of Vermont

department: Biomedical and Health Sciences

institute: The University of Vermont

type: Genome binding/occupancy profiling by high throughput sequencing

summary: ChIP-Seq was performed on naiive cell lines from a Breast Cancer Progression model, including MCF10A, MCF10AT1, and DCIS.  Biological replicates (n=2) were performed for all factors across all cell lines described.

overall_design: ChIP-Seq from a breast cancer progression cell model (including MCF10A, MCF10AT1, and DCIS)

first: Joseph

last: Boyd

first: Cong

last: Gao

first: Kathleen

last: Quinn

first: Andrew

last: Fritz

first: Karen

last: Glass

first: Gary

last: Stein


title: mRNA transcriptome sequencing of wild type (WT) and intestinal epithelial cell specific Axin1 Knockout mice (Axin1KOΔIEC) that have udergone DSS-induced colitis and AOM/DSS-induced colorectal tumorigenesis

status: Public on Feb 09 2022

city: PARIS

first: Christine

last: Perret

address: 24, rue du faubourg Saint-Jacques

department: DRC

country: France

institute: Institut Cochin

type: Expression profiling by high throughput sequencing

summary:
Purpose : The goals of this study are to compare NGS-derived transcriptome profiling (RNA-seq) of colon samples of intestinal epithelial cell specific Axin1 Knockout mice and WT controls that were submitted to DSS-induced colitis and AOM/DSS-induced colorectal carcinogenesis.
Methods : DSS-induced colitis was performed on Axin1flfl (WT) and Vil CreERT2;Axin1fl/fl (Axin1KOΔIEC) mice by giving 3% DSS dissolved in drinking water for 7 days and subsequently placed on regular water for recovery before sacrifice at Day 7 and D13.
Methods : AOM/DSS-induced colorectal tumorigenesis was performed on Axin1flfl (WT) and Vil CreERT2;Axin1fl/fl (Axin1KOΔIEC) mice  that were sacrificed at day 100 post-AOM injection to collect colorectal tumors.
Methods : Colonic mRNA profiles of WT and Axin1KOΔIEC mice were generated by deep sequencing using Illumina NextSeq 500 instrument (150base-lengths read V2 chemistry in a paired-end mode)

overall_design: Colonic mRNA profiles of wild type (WT) and intestinal epithelial cell specific Axin1 Knockout mice that have udergone DSS-induced colitis. Three biological replicates for each group.Colorectal tumor mRNA profiles of wild type (WT) and intestinal epithelial cell specific Axin1 Knockout mice that have undergone AOM/DSS-induced colorectal tumorigenesis. Three biological replicates for each group

first: R

last: Sansom

first: B

last: Romagnolo

first: C


title: Multiomics reveals persistence of obesity-associated immune cell phenotypes in adipose tissue during weight loss and subsequent weight regain

status: Public on Mar 04 2022

city: Nashville

first: Matthew

middle: A

last: Cottam

state: TN

address: 2301 Vanderbilt Place

department: Surgical Sciences

institute: Vanderbilt University Medical Center

summary: Most individuals do not maintain weight loss, and weight regain increases cardio-metabolic risk beyond that of obesity. Adipose inflammation directly contributes to insulin resistance; however, immune-related changes that occur with weight loss and weight regain are not well understood. Single cell RNA-sequencing was completed with CITE-sequencing and biological replicates to profile changes in murine immune subpopulations following obesity, weight loss, and weight cycling. Weight loss normalized glucose tolerance, however, type 2 immune cells did not repopulate adipose following weight loss. Many inflammatory populations persisted with weight loss and increased further following weight regain. Obesity drove T cell exhaustion and broad increases in antigen presentation, lipid handing, and inflammation that persisted with weight loss and weight cycling. This work provides critical groundwork for understanding the immunological causes of weight cycling-accelerated metabolic disease.

overall_design:
Epididymal adipose tissue immune cells isolated from lean, obese, weight loss, and weight cycled mice and sorted for viable CD45+ cells.

Grant ID: 20POST35120547
Grant Title: The Influence of Trained Innate Immunity on Macrophages in Metabolic Disease
Funding Source: American Heart Association (Dallas)

first: Heather

middle: L

last: Caslin

first: Nathan

middle: C

last: Winn

first: Alyssa

middle: H

last: Hasty


title: HK-2 cell cultured with normal glucose and high glucose

status: Public on Apr 05 2022

city: Zhengzhou

first: Yi

last: Song

address: 1 Jianshe East Road

country: China

institute: The First Affiliated Hospital of Zhengzhou University

summary:
To investigate the differential expression of lncRNAs and mRNAs, and even their biological functions in human proximal tubular epithelial (HK-2) cells induced by either normal glucose or high levels of glucose.

Keywords: Expression profiling by array

overall_design: HK-2 cells were cultured in DMEM medium supplemented with 10% fetalfoetal bovine serum, and 100 U/mLU/ml penicillin, and 0.1 mg/mLl streptomycin at 37°C ℃ under humidified air with 5% CO2. Cells were incubated with 5.6 mmol/L (Ng) and 30 mmol/L (Hg) glucose for 72 h. Ng and Hg group were repeated three times.

first: Feng

last: Guo

first: Fengjuan

last: Huang


title: Reconstruction of human Somitogenesis with pluripotent stem cells

status: Public on Feb 02 2022

city: Boston

first: Yannis

last: Djeffal

state: Massachusetts

address: 60 Fenwood road

department: Pathology/Genetics

institute: Brigham and Women’s Hospital/Harvard Medical School

summary: We established two iPSC-derived 3D models recapitulating human somitogenesis, Somitoids and Segmentoids. Somitoids recapitulate the temporal sequence of somitogenesis, with all cells undergoing differentiation and morphogenesis in a synchronous manner. On the other hand, Segmentoids recapitulate the spatio-temporal features of somitogenesis, including gene expression dynamics, tissue elongation, sequential somite morphogenesis, and polarity patterning. They therefore provide an excellent proxy to study human somitogenesis.

overall_design: We collected different time points of the two models and performed single-cell RNA sequencing using the 10X Chromium v3.1 platform.

first: Miao

last: Yuchuan

first: Djeffal

last: Yannis

first: Pourquie

last: Olivier


title: The NFIB/CARM1 Axis is a Therapeutic Target for Small Cell Lung Cancer

status: Public on Feb 07 2022

city: Smithville

first: Bin

last: Liu

state: TX

address: 1808 Park Road 1C

department: Epigenetics and Molecular Carcinogenesis

institute: University of Texas MD Anderson Cancer Center

summary: We identified NFIB as a CARM1 substrate and showed that this transcription factor utilizes CARM1 as a coactivator. Importantly, NFIB harbors both oncogenic and metastatic activities, and is often overexpressed in small cell lung cancer (SCLC). Using a SCLC mouse model, we show that both CARM1 and the CARM1 methylation site on NFIB are critical for the rapid onset of SCLC. By performing the high-throughput sequecing analysis, we found that CARM1-null and NFIB-R388K mutant mouse SCLC tumors share the ability to regulate chromatin accessbility and have similar gene expression pattern.

overall_design: Gene expression and chromatin accessbility profiles in WT, CARM1-null and NFIB-R388K mutant mouse SCLC tumors.

first: Guozhen

last: Gao

first: Simone

last: Hausmann

first: Pawel

middle: K

last: Mazur

first: Mark

middle: T

last: Bedford


title: Comparative analysis of genome-scale, base-resolution DNA methylation profiles across 580 animal species

status: Public on Jun 18 2022

city: Vienna

first: Christoph

last: Bock

address: Lazarettgasse 14

country: Austria

institute: CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences

type: Methylation profiling by high throughput sequencing

summary: We mapped DNA methylation in 580 animal species (535 vertebrates, 45 invertebrates), resulting in 2443 genome-scale, base-resolution DNA methylation profiles of primary tissue samples from various organs. Reference-genome independent analysis of this comprehensive dataset defined a “genomic code” of DNA methylation, which allowed us to predict global and locus-specific DNA methylation from the DNA sequence within and across species. This code appears broadly conserved throughout vertebrate evolution, with two major transitions – once in the first vertebrates and again with the emergence of reptiles. Beyond the central role of species-specific DNA sequence composition, our dataset identified the tissue type and the individual as two main sources of DNA methylation variability within species. Tissue type was the dominant factor in fish, birds, and mammals, while in invertebrates, reptiles, and amphibians both factors were similarly strong. Cross-species comparisons focusing on heart and liver tissues supported a highly conserved role of DNA methylation for tissue type and identity and cross-mapping based promoter methylation analysis revealed divergence at specific genes. In summary, this study establishes a large resource of vertebrate and invertebrate DNA methylomes, it showcases the power of reference-free epigenome analysis in species for which no reference genomes are available, and it contributes an epigenetic perspective to the study of vertebrate evolution.

sample_organism:
Riftia pachyptila
Mya arenaria
Loligo vulgaris
Illex illecebrosus
Octopus vulgaris
Homarus americanus
Pisaster brevispinus
Lytechinus variegatus
Strongylocentrotus purpuratus
Strongylocentrotus droebachiensis
Holothuria
Ciona intestinalis
Branchiostoma floridae
Leucoraja erinaceus
Squalus acanthias
Mustelus canis
Galeocerdo cuvier
Negaprion brevirostris
Callorhinchus milii
Clupea harengus
Danio rerio
Cyprinus carpio
Esox lucius
Salmo salar
Salmo trutta
Salvelinus alpinus
Gadus morhua
Pollachius virens
Lophius piscatorius
Hemitripterus americanus
Cyclopterus lumpus
Zoarces americanus
Thunnus albacares
Xiphias gladius
Myzopsetta ferruginea
Ambystoma
Ambystoma mexicanum
Chelydra serpentina
Emydidae
Graptemys
Testudinidae
Iguanidae
Tiliqua rugosa
Heloderma
Varanus
Varanus exanthematicus
Gekkonidae
Boa constrictor
Natrix tessellata
Naja
Vipera ammodytes
Crotalus
Casuarius casuarius
Dromaius novaehollandiae
Rhea americana
Struthio camelus
Anas platyrhynchos
Dendrocygna viduata
Charadriidae
Ciconiidae
Ciconia ciconia
Columbidae
Columba livia
Falco peregrinus
Astur gentilis
Circus aeruginosus
Haliaeetus albicilla
Acryllium vulturinum
Gallus
Gallus gallus
Perdix perdix
Phasianus colchicus
Coturnix coturnix
Coturnix delegorguei
Serinus
Parus major
Sturnus vulgaris
Phalacrocorax carbo
Phoenicopteriformes
Ara
Ara ararauna
Aptenodytes patagonicus
Spheniscus humboldti
Sarcophilus
Macropodidae
Macropus
Petauridae
Dasypodidae
Erinaceidae
Scandentia
Tupaia
Pteropus
Lemur
Varecia
Callithrix jacchus
Saguinus
Leontocebus fuscicollis
Saguinus mystax
Saguinus oedipus
Saguinus imperator
Cercopithecus
Macaca
Macaca sylvanus
Papio
Papio hamadryas
Theropithecus gelada
Colobus polykomos
Pongo
Canis lupus
Canis lupus familiaris
Vulpes vulpes
Ursus
Ursus arctos
Ailurus fulgens
Nasua
Procyon lotor
Mustelidae
Lutra lutra
Martes foina
Meles meles
Mustela
Mustela putorius
Felis silvestris
Felis catus
Panthera leo
Panthera onca
Panthera pardus
Panthera tigris
Puma concolor
Phocidae
Equus
Equus zebra
Tapirus
Rhinocerotidae
Sus scrofa
Sus scrofa domesticus
Tayassuidae
Camelus dromedarius
Lama glama
Tragulus javanicus
Cervidae
Capreolus capreolus
Cervus elaphus
Cervus nippon
Rangifer tarandus
Muntiacus
Ammotragus
Bison bonasus
Bos
Boselaphus tragocamelus
Bubalus
Capra
Capra aegagrus
Connochaetes
Ovis aries
Kobus
Capricornis
Lepus europaeus
Oryctolagus cuniculus
Marmota
Spermophilus
Cricetinae
Cricetus
Acomys
Mus musculus
Rattus norvegicus
Rattus rattus
Apodemus sylvaticus
Hystricidae
Caviidae
Hydrochoerus hydrochaeris
Lagostomus maximus
Myocastor coypus
Heterocephalus
Saccoglossus kowalevskii
Amazona
Lynx lynx
Melopsittacus
Nymphicus hollandicus
Psittacus
Tamias
Tinca tinca
Macroscelidea
Macroscelides proboscideus
Dolichotis
Dolichotis patagonum
Castoridae
Magallana gigas
Molgula citrina
Styela montereyensis
Botryllus schlosseri
Incilius alvarius
Duttaphrynus melanostictus
Heleophrynidae
Chauna torquata
Ardea
Buteo
Buteo buteo
Rollulus
Balearica pavonina
Grus japonensis
Corvus
Corvus corone
Strigiformes
Bubo bubo
Carcharias taurus
Axis axis
Dama dama
Vicugna pacos
Vicugna
Yinpterochiroptera
Yangochiroptera
Leontopithecus
Capromyidae
Hippoglossoides elassodon
Trachemys scripta elegans
Vipera berus
Acinonyx
Colobus guereza
Scopus umbretta
Gypaetus
Pelecanus
Morone saxatilis
Hippoglossoides platessoides
Glyptocephalus cynoglossus
Capromys pilorides
Erethizon
Rupicapra rupicapra
Nyctereutes
Petaurus breviceps
Trachemys
Pythonidae
Stenotomus chrysops
Zosteropidae
Pelecanus crispus
Strix uralensis
Cucumaria frondosa
Suricata
Hemitragus
Hippotragus
Hippotragus equinus
Chloris chloris
Coccothraustes
Vidua paradisaea
Ostrea edulis
Lepas anatifera
Cebinae
Phascolarctos cinereus
Leiocephalus
Polychrus marmoratus
Cricetomyinae
Carollia perspicillata
Chamaeleonidae
Uromastyx
Lutjanus mahogoni
Cynictis
Glis glis
Cygnus melancoryphus
Circus cyaneus
Milvus milvus
Oplurus
Pithecia pithecia
Erythrura
Bothriechis schlegelii
Cynomys
Brachylophus
Patiria miniata
Phodopus campbelli
Neoniphon sammara
Psammomys obesus
Sylvia atricapilla
Passer domesticus
Jaculus
Geochelone
Cyclura
Sauromalus
Python molurus
Python regius
Eunectes
Pogona barbata
Acanthosaura
Shinisaurus crocodilurus
Aquila heliaca
Haliaeetus leucocephalus
Plegadis falcinellus
Eliomys quercinus
Apodemus flavicollis
Cariamidae
Eurypygidae
Jacanidae
Macaca silenus
Sciurus vulgaris
Lissemys punctata
Musophagidae
Centropomus robalito
Corvus corax
Garrulus glandarius
Cyclura cornuta
Leontopithecus chrysomelas
Coliiformes
Upupa epops
Ecsenius
Cornufer guentheri
Antidorcas
Antilope
Kobus leche
Agapornis
Agapornis canus
Agapornis lilianae
Agapornis personatus
Agapornis taranta
Loriculus galgulus
Mimus polyglottos
Leptailurus
Varanus gouldii
Lepus timidus
Scincidae
Astrochelys radiata
Tragelaphus angasii
Paralichthys dentatus
Nanger dama
Myoxocephalus octodecemspinosus
Canis aureus
Tragelaphus spekii
Tiliqua scincoides
Sebastes atrovirens
Sebastes caurinus
Sebastes constellatus
Sebastes hopkinsi
Sebastes miniatus
Sebastes mystinus
Sebastes ovalis
Sebastes paucispinis
Sebastolobus alascanus
Hypselecara coryphaenoides
Geoemyda spengleri
Paracanthurus hepatus
Corvus frugilegus
Ariopsis felis
Spatula querquedula
Abronia anzuetoi
Eudyptes chrysocome
Dascyllus aruanus
Pomacentrus coelestis
Coryphaenoides acrolepis
Equus asinus asinus
Terrapene
Testudo hermanni
Mullus surmuletus
Lampropeltis
Pomatomus saltator
Corucia zebrata
Elephas maximus indicus
Embiotoca jacksoni
Paracirrhites forsteri
Falco tinnunculus
Geronticus eremita
Picus viridis
Tetrao urogallus
Testudo kleinmanni
Hoplobatrachus tigerinus
Musophaga
Nothobranchius furzeri
Scyliorhinus retifer
Fromia
Fromia indica
Nardoa novaecaledoniae
Osteoglossum bicirrhosum
Chaetodon lineolatus
Chaetodon lunula
Asio otus
Strix aluco
Buteo lagopus
Ducula bicolor
Ptilinopus
Trioceros jacksonii
Batoidea
Rhinoptera bonasus
Loweina terminata
Athene noctua
Theloderma
Penaeus
Nectariniidae
Ploceus cucullatus
Caiman yacare
Cacatua alba
Probosciger aterrimus
Monacanthidae
Polypedates otilophus
Correlophus ciliatus
Paroedura picta
Halichoeres trimaculatus
Rhinogobiops nicholsii
Spinus spinus
Phyllopteryx taeniolatus
Rhacophorus reinwardtii
Otaria
Tringa totanus
Recurvirostra avosetta
Leucoraja ocellata
Pycnonotus barbatus
Chloropsis
Irena puella
Psarisomus dalhousiae
Cynoscion regalis
Acanthurus triostegus
Ctenochaetus striatus
Tockus deckeni
Bycanistes bucinator
Alectis ciliaris
Chamaeleo calyptratus
Elops affinis
Gymnothorax moringa
Lethrinus atkinsoni
Hippoglossina oblonga
Scophthalmus aquosus
Urophycis tenuis
Centropristis striata
Caloenas nicobarica
Gallicolumba
Amandava subflava
Euplectes
Furcifer pardalis
Choerodon fasciatus
Coracias garrulus
Pisaster giganteus
Pleurogrammus monopterygius
Erpeton
Glyptocephalus zachirus
Philomachus
Zamenis longissimus
Coronella austriaca
Clavelina picta
Ascidiella aspersa
Thyonella gemmata
Mungos mungo
Accipiter nisus
Laemanctus
Neurergus
Fistularia commersonii
Cygnus cygnus
Diodon hystrix
Tamiops
Canis lupus lycaon
Amblyglyphidodon leucogaster
Euplectes orix
Anoplopoma fimbria
Chromis punctipinnis
Haemulon flavolineatum
Uromastyx ocellata
Stichopus chloronotus
Trachyphonus erythrocephalus
Coris gaimard
Labroides bicolor
Semicossyphus pulcher
Cuora mccordi
Amazona agilis
Dinemellia
Histrio histrio
Aplonis panayensis
Hemisphaeriodon
Zenopsis conchifer
Rhinecanthus aculeatus
Halocynthia pyriformis
Pytilia melba
Uraeginthus bengalus
Phloeomys
Cuora mouhotii
Merops apiaster
Pseudanthias
Potamochoerus porcus
Hemilepidotus jordani
Triglops scepticus
Bathymaster signatus
Ambystoma andersoni
Oxylebius pictus
Ecteinascidia turbinata
Malacochersus
Pachyuromys
Tockus flavirostris
Pseudobalistes fuscus
Taurotragus
Holothuria atra
Cyanoliseus patagonus
Ostorhinchus aureus
Sebastes semicinctus
Zaprora silenus
Podothecus accipenserinus
Platax teira
Cephalopholis miniata
Falco cherrug
Trachemys scripta scripta
Aotidae
Saimiriinae
Pseudomonacanthus peroni
Sebastes borealis
Sebastes chrysomelas
Sebastes norvegicus
Lutjanus quinquelineatus
Pterocaesio marri
Pitta moluccensis
Notamacropus parma
Camelus ferus
Dracaena guianensis
Lepidopsetta polyxystra
Oxycheilinus digramma
Giraffa giraffa
Ptilinopus pulchellus
Pleoticus muelleri
Lamprotornis chalcurus
Aonyx cinereus
Merops bullockoides
Chiroxiphia pareola
Ovis orientalis
Geopelia placida
Ammodytes hexapterus
Sufflamen chrysopterum
Sphoeroides maculatus
Cyclopsitta diophthalma
Astrochelys yniphora
Photoblepharon palpebratum
Boltenia ovifera
Centropyge heraldi
Rhabdamia gracilis
Parupeneus spilurus
Calyptocephallela gayi
Chrysopelea
Scolopsis bilineata
Pristigenys alta
Atherinomorus vaigiensis
Boltenia echinata
Echinarachnius parma
Vermilingua
Folivora
Lethenteron camtschaticum
Leptoclinus maculatus
Alitta succinea
Callocephalon fimbriatum
Bodianus diana
Coris caudimacula
Cantherhines pardalis
Salvelinus umbla
Gadus chalcogrammus
Doryteuthis pealeii
Holothuria cinerascens
Ophiopteris papillosa
Cheilodipterus quinquelineatus
Tetrastes bonasia
Anthropoides paradiseus
Parapercis xanthozona
Lyrurus tetrix
Ophiothrix spiculata
Ammodytes dubius
Cryptacanthodes maculatus
Lumpenus lampretaeformis
Prionotus carolinus
Crocodylia
Rhyticeros narcondami
Xenagama wilmsi
Ostorhinchus rueppellii
Ostorhinchus moluccensis
Loweina rara
Coracias cyanogaster
Vanellus armatus
Oxycercichthys veliferus
Ophioderma panamensis
Onuxodon fowleri
Cirrhilabrus roseafascia
Apostichopus parvimensis
Copsychus malabaricus
Notamacropus rufogriseus
Cirrhilabrus lineatus
Hypanus americanus
Cyanoloxia brissonii
Lonchura oryzivora
Leptoptilos crumenifer
Tockus alboterminatus
Tockus nasutus
Cheilopogon californicus
Compsanthias ventralis

overall_design: Dataset comprises 2443 DNA methylation profiles (RRBS) covering 580 animal species (535 vertebrates and 45 invertebrates)  and more than 10 major tissue types with a foucs on heart and liver, analysed in a reference-free manner.

first: Johanna

last: Klughammer

first: Daria

last: Romanovskaia

first: Amelie

last: Nemc

first: Annika

last: Posautz

first: Charlotte

last: Seid

first: Linda

last: Schuster

first: Melissa

last: Keinath

first: Juan

middle: S

last: Lugo Ramos

first: Lindsay

last: Kosack

first: Annie

last: Evankow

first: Dieter

last: Prinz

first: Stefanie

last: Kirchberger

first: Bekir

last: Ergüner

first: Paul

last: Datlinger

first: Nikolaus

last: Fortelny

first: Christian

last: Schmidl

first: Matthias

last: Farlik

first: Kaja

last: Skjærven

first: Andreas

last: Bergthaler

first: Miriam

last: Liedvogel

first: Denise

last: Thaller

first: Pamela

last: Burger

first: Marcela

last: Hermann

first: Martin

last: Distel

first: Daniel

first: Anna

last: Kübber-Heiss


title: A family of C. elegans VASA homologs control Argonaute pathway specificity and promote transgenerational silencing

status: Public on Jan 30 2022

first: Siyuan

last: Dai

type: Non-coding RNA profiling by high throughput sequencing

overall_design: Small-RNAs for whole worms and bound to CSR-1, WAGO-1 and WAGO-9 Argonautes were cloned from WT and multiple glh mutants including null, K391A and DQAD worms. CLIP-seq were carried out by pulling down protein-RNA complex pre-crosslinked by UV light and  sequencing the RNA fragments recovered from IP complex.

first: En-zhi

last: Shen

first: Craig

last: Mello


title: Comprehensive 3D epigenomic maps define limbal stem/progenitor cell function and identity

status: Public on Feb 01 2022

city: Bengbu

first: Mingsen

last: Li

state: Anhui

address: No. 2600, Donghai Avenue, Bengbu City, Anhui Province

department: Interdisciplinary Eye Research Institute (EYE-X Institute)

institute: Bengbu Medical University

summary: The insights into how genome topology couples with epigenetic states to govern the function and identity of the corneal epithelium are poorly understood. Here, we generate a high-resolution Hi-C interaction map of human limbal stem/progenitor cells (LSCs) and show that chromatin multi-hierarchical organisation is coupled to gene expression. By integrating Hi-C, epigenome and transcriptome data, we characterize the comprehensive 3D epigenomic landscapes of LSCs. We found that super-silencers mediate gene repression associated with corneal development, differentiation and disease via chromatin looping and/or proximity. Super-enhancer (SE) interaction analysis identified a set of SE interactive hubs that contribute to LSC-specific gene activation. These active and inactive element-anchored loop networks occur within the cohesin-occupied CTCF-CTCF loops. We further reveal a coordinated regulatory network of core transcription factors based on SE-promoter interactions. Our results provide detailed insights into the genome organization principle for epigenetic regulation of gene expression in stratified epithelia.

overall_design: ChIP-seq for H3K9me2, CTCF, SMC1, p63 and EP300 in human limbal stem cells . Hi-C in human limbal stem cells.


title: Comparative transcriptomes of Caco-2 cells cultured under dynamic and static conditions following exposure to titanium dioxide and zinc oxide nanomaterials

status: Public on Jan 26 2022

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

country: Netherlands

institute: Wageningen University

summary: Due to the widespread application of food-relevant inorganic nanomaterials, the gastrointestinal tract is potentially exposed to these materials. Gut-on-chip in vitro model systems are proposed for the investigation of compound toxicity as they better recapitulate the in vivo human intestinal environment than static models, due to the added shear stresses associated with the flow of medium in line with what cells experience in vivo. We aimed to compare the cellular responses of intestinal epithelial Caco-2 cells at the gene expression level upon TiO2 (E171) and ZnO (NM110) nanomaterial exposure when cultured under dynamic and static conditions. For this, we applied whole genome transcriptome analyses. Differentially expressed genes and related biological processes revealed culture condition specific responses upon exposure to TiO2 and ZnO nanomaterials. The materials had more effects on cells cultured in the gut-on-chip when compared to the static model, indicating that shear stress might be a major factor in cell susceptibility. This is the first report on application of a gut-on-chip system to evaluate cellular responses upon TiO2 and ZnO nanomaterials compared to a static system and extends current knowledge on nanomaterial-cell interactions and toxicity assessment. Dynamically cultured cells appear to be more sensitive and the gut-on-chip might thus be an attractive model to be used more extensively in the toxicological hazard characterization.

overall_design: Microarray analysis was performed on Caco-2 cells that were exposed to TiO2 or ZnO for 6hrs after being cultured statically or in a gut-on-chip device for 21 days.

first: Kornphimol

last: Kulthong

middle: J

first: Meike

last: van der Zande

first: Hans

last: Bouwmeester


title: Comparative therapeutic strategies for preventing aortic rupture in a mouse model of vascular Ehlers-Danlos syndrome

status: Public on Feb 16 2022

city: Paris

first: Anne

last: Legrand

address: 56 rue Leblanc

institute: Inserm

summary: Vascular Ehlers-Danlos syndrome is a rare inherited disorder caused by genetic variants in type III collagen. Its prognosis is especially hampered by unpredictable arterial ruptures and there is no therapeutic consensus. We created a knock-in Col3a1+/G182R mouse model and performed a complete genetic, molecular and biochemical characterization. Several therapeutic strategies were also tested. Col3a1+/G182R mice showed a spontaneous mortality caused by thoracic aortic rupture that recapitulates the vascular Ehlers-Danlos syndrome with a lower survival rate in males, thin non-inflammatory arteries and an altered arterial collagen. Transcriptomic analysis of aortas showed upregulation of genes related to inflammation and cell stress response. Compared to water, survival rate of Col3a1+/G182R mice was not affected by beta-blockers (propranolol or celiprolol). Two other vasodilating anti-hypertensive agents (hydralazine, amlodipine) gave opposite results on aortic rupture and mortality rate. There was a spectacular beneficial effect of losartan, reversed by the cessation of its administration, and a marked deleterious effect of exogenous angiotensin II. These results suggest that blockade of the renin angiotensin system should be tested as a first-line medical therapy in patients with vascular Ehlers-Danlos syndrome.

overall_design: Aorta mRNA profiles of 7-week old wild type (WT) and Col3a1+/G182R mice

first: Charline

last: Guery

first: Xavier

last: Jeunemaitre


title: Effects of DNA topoisomerase inhibitor acriflavine on endothelial gene expression under hypoxic conditions

status: Public on Jan 19 2022

city: bad nauheim

first: Stefan

last: Günther

address: ludwigtr. 43

country: Germany

institute: MPI for heart and lung research

summary: RNA-Seq of human endothelial cells treated with acriflavine (ACF) with or without hypoxia revealed massive changes on gene expression. These were non-randomly and potentially due to DNA topoisomerase inhibition rather than HIF inhibition. Surprisingly, in contrast to protein-coding genes, RNA-Seq yielded that an exceeding number of lncRNAs is upregulated.

overall_design: Examination of acriflavine treatment in HUVECs under hypoxia (16h, 1% O2)

first: Sandra

last: Seredinski

first: Ralf

middle: P

last: Brandes

first: Matthias

last: Leisegang


title: RNA sequencing data of CNS-associated macrophages (CAMs) isolated from brains of Mrc1-CreERT2 mice

status: Public on Jan 27 2022

city: Freiburg

first: Gianni

last: Monaco

address: Breisacher Straße

institute: Freiburg Medical Center

summary: All tissue resident macrophages of the central nervous system (CNS), including parenchymal microglia as well as CNS-associated macrophages (CAMs) such as meningeal (mMF) and perivascular macrophages (pvMF) are part of the CNS endogenous innate immune system that acts as the first line of defense during infections or trauma. It has been suggested that microglia and all CAM subsets are derived from prenatal cellular sources in the yolk sac that were defined as early erythromyeloid progenitors. However, the precise ontogenetic relationships, the underlying transcriptional programs and the molecular signals that drive the development of distinct CAMs subsets in situ are poorly understood. Using novel fate mapping systems, single-cell profiling and cell-specific mutants, we show that only mMF and microglia share a common prenatal progenitor. In contrast, pvMF originate from perinatal mMF only after birth in an integrin-dependent manner. Furthermore, the establishment of pvMF critically requires the presence of vascular smooth muscle cells. In summary, our data reveal a novel precisely timed process in distinct anatomical niches for the establishment of CNS macrophage subsets.

overall_design: Bulk transcriptomics data of FACS sorted CAMs isolated from brain tissue of 3-4 individual mice per genotype (from wild type and Mrc1-CreERT2 lines) and RNA expression levels between genotypes were compared.

first: Marco

last: Prinz

first: Takahiro

last: Masuda

first: Lukas

last: Amann


title: Proteasome Inhibition Targets the KMT2A Transcriptional Complex

status: Public on Jan 13 2022

city: Palo Alto

first: Tanja

last: Gruber

state: CA

address: 1000 Welch Road Suite 300

department: Pediatrics

institute: Stanford University

summary: We quantitatively evaluated H2Bub and H3K79me2 epigenetic marks genome wide in a KMT2A rearranged B lineage acute lymphoblastic leukemia cell line after treatment with bortezomib over a 6 hour time course by ChIP-Rx. We identified rapid and concordant depletion of these epigenetic marks within two hours. To look at gene expression changes, RNA sequencing was performed on KMT2A rearranged B lineage acute lymphoblastic leukemia patient samples in the presence and absence of bortezomib exposure.

overall_design: Examination of 2 different histone modifications in the SEM cell line following in vitro exposure to bortezomib by ChIP with reference exogenous genome (ChIP-Rx) using Drosophila S2 cells to allow quantitation over the 6 hour time course. 5 patient samples were exposed to bortezomib or DMSO for 20 hours followed by RNA sequencing to look at changes to gene expression that correlate with these histone modifications.


title: Regulatory T cells suppress the formation of super-effector CD8 T cells by limiting IL-2

status: Public on Jan 17 2022

city: Prague

first: Juraj

last: Michalik

address: Vídeňská 1083

country: Czech Republic

institute: Institute of Molecular Genetics of the Czech Academy of Sciences

summary: In this experiment, the gene expression of CD8+ T cells primed in the presence or absence of Tregs on a single cell level was analyzed. For this purpose, Ly5.1 OT-I T cells were adoptively transferred into Treg deficient (DEREG+) or Treg replete (DEREG-) mice, activated with DC-OVA, isolated after 3 days, and analyzed by scRNAseq. Invididual samples were indexed with oligo-tagged TotalSeq-C antibodies and pooled prior to the analysis. We observed that Tregs reduced the expression of IL-2 responsive genes, including key cytotoxic molecule granzyme B. Unsupervised clustering revealed 5 clusters including a cluster of cells which did not match any usual CD8+ subsets and, due to unusual co-expression of effector molecules such as GZMK and KLRK1, were dubbed super-effector cells.

overall_design: Ly5.1 OT-I T cells were adoptively transferred into double-transgenic Treg depleted DEREG+ RIP.OVA and Treg control DEREG- RIP.OVA mice (C57BL6 background, n=3 per group). The following day the mice were immunized with DC-OVA. Third day after the immunization their spleens were isolated, the OT-I cells were FACS sorted as Ly5.1+ CD8+ cells, and analyzed via scRNA-seq using 10X Genomics Single Cell Immune Profiling with Feature Barcoding.

first: Oksana

last: Tsyklauri

first: Tereza

last: Chadimova

first: Veronika

last: Niederlova

first: Sarka

last: Janusova

first: Helene

last: Rossez

first: Ales

last: Drobek

first: Hana

last: Vecerova

first: Virginie

last: Galanti

first: Marek

last: Kovar

first: Ondrej

last: Stepanek


title: Parallel analysis of transcription, integration, and sequence of single HIV-1 proviruses

status: Public on Jan 12 2022

city: Cambridge

first: Ce

last: Gao

address: 400 Technology Square

institute: Ragon Institute of MGH, MIT and Harvard

summary: HIV-1-infected cells that persist despite antiretroviral therapy (ART) are frequently considered ‘‘transcriptionally silent,’’ but active viral gene expression may occur in some cells, challenging the concept of viral latency. Applying an assay for proﬁling the transcriptional activity and the chromosomal locations of individual proviruses, we describe a global genomic and epigenetic map of transcriptionally active and silent proviral species and evaluate their longitudinal evolution in persons receiving suppressive ART. Using genome-wide epigenetic reference data, we show that proviral transcriptional activity is associated with activating epigenetic chromatin features in linear proximity of integration sites and in their inter- and intrachromosomal contact regions. Transcriptionally active proviruses were actively selected against during prolonged ART; however, this pattern was violated by large clones of virally infected cells that may outcompete negative selection forces through elevated intrinsic proliferative activity. Our results suggest that transcriptionally active proviruses are dynamically evolving under selection pressure by host factors.

overall_design: Hi-C experiments on CD4 cells from 3 ART treated patients

first: Kevin

last: Einkauf

first: Matthew

middle: R

last: Osborn

first: Weiwei

last: Sun

first: Xiaoming

first: Xiaodong

last: Lian

first: Elizabeth

middle: M

last: Parsons

first: Gregory

last: Gladkov

first: Kyra

middle: W

last: Seiger

first: Jane

middle: E

last: Blackmer

first: Chenyang

last: Jiang

first: Steven

last: Yukl

first: Eric

last: Rosenberg

first: Xu

middle: G

last: Yu

first: Mathias

last: Lichterfeld


title: RNA-seq of control and IL-33-treated WT and STAT KO ILC2s in vitro

status: Public on Jan 25 2022

city: Beijing

first: Liuhui

last: Fu

address: Zhongguancun North Street

department: Institute for Immunology

institute: Tsinghua university

summary: Group 2 innate lymphoid cell (ILC2), an innate counterpart of T helper 2 cell, plays a critical role in type 2 immune responses. However, the molecular regulation mechanism of ILC2 is still unclear. Here, we find that STAT3 signaling is essential for ILC2 effector function and could drive both acute and chronic allergic inflammation in the lung. Mechanistically, allergic alarmin IL-33 induces a non-canonical STAT3 phosphorylation at serine 727 in ILC2, which leads to its mitochondrial translocation. Mitochondrial STAT3 further promotes the methionine cycle through ATP synthesis and fuel the generation of S-adenosylmethionine (SAM), which supports the epigenetic reprogramming of type 2 cytokines in ILC2. STAT3 deficiency dampens the mitochondrial function and methionine metabolism, thus results in impairment of the ILC2 cytokines expression. Interestingly, inhibition the mitochondrial translocation of STAT3 could remarkably ameliorate the allergic lung inflammation. Together, our findings establish mitochondrial STAT3 as a key regulator shaping ILC2 effector function through metabolic and epigenetic regulation

overall_design: 8 samples: 2 control WT ILC2s, 2 control STAT3-KO ILC2s, 2 IL-33-treated WT ILC2s, 2 IL-33-treated STAT3-KO ILC2s

first: Xiaohuan

last: Guo


title: Specific genomic features underlie the co-option of SVA transposons as cis-regulatory elements in the human genome

status: Public on Jan 04 2022

city: London

first: Marco

last: Trizzino

state: UK

address: Imperial College Road

department: Life Sciences

country: United Kingdom

institute: Imperial College London

summary: Domestication of transposable elements (TEs) into functional cis-regulatory elements is a widespread phenomenon. However, why some TEs are co-opted as functional enhancers while others are not is underappreciated. SINE-Vntr-Alus (SVAs) are the youngest group of transposons in the human genome, where ~3,700 copies are annotated, nearly half of which are human-exclusive. Many studies indicated that the SVAs are among the most frequently co-opted TEs in human gene regulation, but the mechanisms underlying such process have not yet been thoroughly investigated. Here, we leveraged CRISPR-interference (CRISPRi), computational and functional genomics to elucidate the genomic features that underlie SVA domestication into human stem-cell gene regulation. We found that ~750 SVAs are co-opted as functional cis-regulatory elements in human induced Pluripotent Stem Cells. Co-opted SVAs are significantly closer to genes and harbor more transcription factor binding sites than the not co-opted ones. We show that a long DNA-motif composed of flanking YY1/2 and OCT4 binding sites is enriched in the co-opted SVAs, and that these two factors bind, as predicted, near each other on the TE sequence.  Repression of all the ~750 co-opted SVAs by CRISPRi in a line with stem-like properties (NCCIT) led to loss of YY1/OCT4 binding and alteration of neighboring gene expression. Ultimately, SVA repression resulted in ~3,000 differentially expressed genes, 131 of which were the nearest gene to an annotated SVA.  In summary, we demonstrated that SVAs contribute significantly to human gene regulation, and that both genomic location and sequence composition contribute to SVA domestication in the gene regulatory networks.

overall_design: Using stem-like NCCIT cells to compare genomic consequences and gene regulation of repressing SVA transposons using CRISPR-interference

first: Samantha

last: Barnada

first: Andrew

last: Isopi

first: Daniela

last: Tejada-Martinez

first: Clément

last: Goubert

first: Sruti

last: Patoori

first: Luca

last: Pagliaroli

first: Raquel

last: Fueyo

first: Mason

last: Tracewell


title: Transcriptional reprogramming of skeletal muscle stem cells by the niche environment

status: Public on Mar 17 2022

city: Montreal

first: Vahab

last: Soleimani

state: QC

address: 3640 rue University

department: Human Genetics

country: Canada

institute: McGill University

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

overall_design: Refer to individual Series


title: High resolution 3D chromatin maps of human primary monocytes [RNA-Seq]

status: Public on Jan 01 2022

city: Jinan

first: Yu

last: Xia

state: Shandong

address: 324 Jingwu Street

department: Department of Central Laboratory

institute: Shandong Provincial Hospital affiliated to Shandong University

summary: Although the Hi-C maps in cultured immune cell has been reported, there still lacks 3D landscape of human primary monocytes. The peripheral blood from two health people and two SLE patients was collected and CD14+ monocytes were selected to perform Hi-C, RNA-seq, ATAC-seq and ChIP-seq. The raw data of THP1 cell Hi-C library was also used in comparison. We firstly presented the 3D genome structure heterogeneity in human primary monocytes. Significantly diversity of chromatin interaction in HLA complex region might regulates many immunologic processes. The chromatin loop regulation around CD16 and its relevant expression pattern indicated the CD16 associated monocyte functions are dominated regulated by this variable TAD boundary.

first: Yuran

last: Zhao

first: Xiaowen

last: Liu


title: High resolution 3D chromatin maps of human primary monocytes [ChIP-Seq]

overall_design: The peripheral blood from two health people and two SLE patients was collected and CD14+ monocytes were selected to perform Hi-C, RNA-seq, ATAC-seq and ChIP-seq. The raw data of THP1 cell Hi-C library was also used in comparison.


title: High resolution 3D chromatin maps of human primary monocytes [Hi-C]


title: RNA-sequencing analysis of mouse epithelial NMuMG cells with Cas9 or UGCG knock out

status: Public on Jan 03 2022

city: Leiden

first: Hailiang

last: Mei

address: Einthovenweg 20

department: Sequencing Analysis Support Core

institute: Leiden University Medical Center

summary: We report the gene expression in mouse NMuMG cells with or without UGCG depletion using RNA sequencing. After data analysis, the 11218 transcripts were identified. Among these transcripts, the TGF-β signaling target genes and EMT marker genes were significantly upregulated in UGCG depleted NMuMG cells. Then we used these genes and mouse TGF-β or EMT gene signatures to do the gene set enrichment analysis and showed the negative correlation of UGCG and TGF-β signaling or EMT in NMuMG cells.

overall_design: RNA profiles of mouse NMuMG cells with Cas9 (as the control group) and UGCG knock out. Each group contains three biological replicates.

first: Jing

last: Zhang

first: Peter

last: ten Dijke

first: Cedrick

last: Agaser


title: High resolution 3D chromatin maps of human primary monocytes


title: High resolution 3D chromatin maps of human primary monocytes [ATAC-Seq]


title: High throughput gene expression data from MDA-MB-231 breast cancer cell lines with DAXX Knockdown, DAXX WT overexpression (OE), and DAXX SUMO interacting motif mutant (DSM) overexpression (DSM OW)

status: Public on Dec 24 2021

city: Gainesville

first: Daiqing

last: Liao

state: FL

address: 2033 Mowry Rd

department: Anatomy and Cell Biology

institute: University of Florida

summary: DAXX, originally discovered as a context-dependent regulator of cell death or survival. Emerging evidence suggests that DAXX has an oncogenic role in diverse cancer types. However, the molecular mechanisms underlying DAXX's oncogenic function remain to be defined. We used high throughput Illumina sequencing to analyze genes that were differentially expressed upon DAXX knockdown or DAXX OE or DSM OE.

overall_design: Stable expression of cDNA was established through lentiviral transduction of MDA-MB-231 cell line for WT OE or DSM OE and puromycin (2 µg/mL) selection. Scrambled control shRNA-transfected MDA-MB-231 cells were applying as control. Control MDA-MB-231 cells, Stable DAXX knockdown, DAXX OE and DSM OE cell lines were seeded with 2 x 10^5 cells at 10 cm culture plate. Duplicate cell cultures were conducted.

first: Iqbal

last: Mahmud


title: Characterizing Neonatal Heart Maturation, Regeneration, and Scar Resolution Using Spatial Transcriptomics [spatial]

status: Public on Dec 20 2021

city: Rochester

first: Cameron

last: Baker

address: 601 Elmwood Ave

institute: University of Rochester

summary: We use spatial transcriptomics to establish regional transcriptional profile of neonatal heart tissue obtained at indicated timpoints after apical resection surgery.

overall_design: The cardiac apex was resected at P2, within the regenerative window, and hearts were isolated at indicated timepoints for spatial transcriptomics.

first: Eric

last: Small

first: Adwiteeya

last: Misra


title: Characterizing Neonatal Heart Maturation, Regeneration, and Scar Resolution Using Spatial Transcriptomics


title: Characterization of the molecular mechanisms underlying increased mucus production of HT29-MTX-E12 cells grown on a semi-wet interface with mechanical stimulation

status: Public on Dec 06 2021

first: Guido

last: Hooiveld

summary: The multifunctional intestinal mucus layer plays a crucial role in human health. Our understanding of the human colonic mucus layer in terms of structure, function and has been largely dependent on expensive and advanced ex vivo or in vitro models, which often require high expertise. The mucus-producing intestinal cell line HT29-MTX-E12 has been commonly used in more simple in vitro models, but produces only low amounts of the intestine-specific MUC2. It has been shown previously that HT29-MTX-E12 cells cultured in Semi-Wet interface with Mechanical Stimulation (SWMS) produced higher amounts of MUC2 and had a thicker mucus layer compared to conventional culturing methods. However, it remains unknown which underlying pathways are involved. Therefore, we aimed to further explore the cellular processes underlying the increased mucus production by HT29-MTX-E12 cells grown under SWMS conditions. Cells grown on Transwell inserts for 15 days were subject to transcriptome analysis to investigate underlying molecular pathways at gene expression level. We also further characterized the model by measuring transepithelial resistance and pH and lactate production of the conditioned medium. We confirmed higher MUC2 production under SWMS conditions and demonstrated that this culturing method primarily stimulated cell growth. In addition, we also found evidence for a more aerobic cell metabolism under SWMS, as shown previously for similar models. In summary, we suggest different mechanisms in which mucus production is enhanced under SWMS and propose potential applications of this model in future studies.

overall_design: HT29-MTX-E12 and Caco-2 cells were seeded on Transwell membranes. One day after seeding, cells were further cultured for 14 days under either SWMS conditions (i.e. low apical volume and continuous shaking at 65 rpm) or static conditions (similar conditions as during seeding). After harvesting, RNA isolated from cells was subjected to microarray analysis.

first: Janneke

last: Elzinga

first: Benthe

last: van der Lugt

first: Clara

last: Belzer

first: Wilma

last: Steegenga


title: Whole genomic RNA sequencing of the Paradaux cell line after long-term culture

status: Public on Dec 03 2021

city: Pasadena

first: Yitong

last: Ma

address: 1200 E California Blvd

department: Division of Biology and Biological Engineering

institute: Caltech

summary: We analyzed the difference of gene expression between the isolates havested from long-term cultures (Ma et.al. 2020). In this study, the paradaux cell line were cultured for over 40 days under different population control conditions (uncontrolled, negative feedback and paradoxical feedback. Isolates of each culture were harvested at the end of the long-term culture and preped for whole genomic RNA sequencing.

overall_design: There are totally 19 samples are analyzed, among which, one is from parental, four from uncontrolled growth, seven from negative feedback, and seven from paradoxical feedback

first: Michael

last: Elowitz


title: Young transposable elements rewired gene regulatory networks in human and chimpanzee hippocampal intermediate progenitors

status: Public on Nov 24 2021

first: Marco

last: Trizzino

summary: The hippocampus is associated with essential brain functions such as learning and memory.  Human hippocampal volume is significantly greater than expected when compared to non-human apes, suggesting a recent expansion. Intermediate progenitors, which are able undergo multiple rounds of proliferative division before a final neurogenic division, may have played a role in the evolutionary hippocampal expansion. To investigate the evolution of gene regulatory networks underpinning hippocampal neurogenesis in apes, we leveraged the differentiation of human and chimpanzee induced Pluripotent Stem Cells into TBR2-positive hippocampal intermediate progenitors (hpIPCs). We find that the gene networks active in hpIPCs are significantly different between humans and chimpanzees, with ~2,500 genes differentially expressed. We demonstrate that species-specific transposon-derived enhancers contribute to these transcriptomic differences. Young transposons, predominantly Endogenous Retroviruses (ERV) and SINE-Vntr-Alus (SVA), were co-opted as enhancers in a species-specific manner.  Human-specific SVAs provided substrates for thousands of novel TBR2 binding sites, and CRISPR-mediated repression of these SVAs attenuates the expression of ~25% of the genes that are upregulated in human intermediate progenitors relative to the same cell population in the chimpanzee

sample_organism:
Pan troglodytes
Homo sapiens

platform_organism:
Pan troglodytes
Homo sapiens

overall_design: Using iPSCs derived from healthy humans and chimpanzees to study differences in transposon co-option and gene regulation

first: Sruti

last: Patoori

first: Samantha

last: Barnada


title: Stroke induces disease-specific myeloid cells in the brain parenchyma and pia

status: Public on Nov 26 2021

city: Muenster

last: Heming

address: Albert-Schweitzer-Campus 1, Bldg A1

department: Department of Neurology with Institute of Translational Neurology

institute: University Hospital Muenster

summary:
Inflammation triggers secondary brain damage after stroke. The meninges and other CNS border compartments serve as invasion sites for leukocyte influx into the brain thus promoting tissue damage after stroke. However, the post-ischemic immune response of border compartments compared to brain parenchyma remains poorly characterized .
Here, we deeply characterize tissue-resident leukocytes in meninges and brain parenchyma by flow cytometry, histology, and single cell transcriptomics after experimental stroke and discover that leukocytes respond differently to stroke depending on their site of residence. We thereby discover a unique phenotype of myeloid cells exclusive to the brain after stroke. These stroke-associated myeloid cells partially resemble neurodegenerative disease-associated microglia. They are mainly of resident microglial origin, partially conserved in humans and exhibit a lipid-phagocytosing phenotype. Blocking markers specific for these cells partially ameliorates stroke outcome thus providing a potential therapeutic target. The injury-response of myeloid cells in the CNS is thus compartmentalized, adjusted to the type of injury and may represent a therapeutic target.

overall_design: Single-cell RNA profiling of CD45iv-CD45+ TRL sorted from the brain parenchyma, pia and dura at 24h and 72h after transient middle cerebral artery occlusion compared to healthy control animals.

first: Carolin

last: Beuker

first: David

last: Schafflick

first: Jan-Kolja

last: Strecker

first: Gerd

last: Meyer zu Hörste

first: Jens

last: Minnerup


title: Microarray analysis of drug-tolerant cells in ALK-rearranged non-small cell lung cancer cell lines induced by ALK-TKIs

status: Public on Nov 09 2021

city: Kyoto

first: Keiko

last: Tanimura

address: 465, Kajii-cho

country: Japan

institute: Kyoto-Prefetural University of Medicine

summary: To investigate the molecular mechanisms underlying the emergence and maintenance of drug-tolerant (DT) cells in anaplastic lymphoma kinase (ALK)-rearranged lung cancer, we isolated DT cells from H2228 and A925L cells exposed to high doses of alectinib or lorlatinib for 9 days, and performed transcriptome analysis between parental and DT cells using a gene expression microarray.

overall_design: H2228 and A925L cells which were untereated or treated with alectinib or lorlatinib for 9 days were selected for RNA extraction and hybridization on Affymetrix.

first: Tadaaki

last: Yamada

first: Yuki

last: Katayama

first: Koichi

last: Takayama


title: Characterizing Neonatal Heart Maturation, Regeneration, and Scar Resolution Using Spatial Transcriptomics [RNA-seq]

first: Cameron

last: Baker

summary: We report the transcriptional changes occuring in fibroblasts obtained from mouse hearts subjected to apical resection surgery or sham surgery, compared to unmanipulated controls, at indicated timepoints.

overall_design: Cardiac fibroblasts were isoalted 3 days after apical resection surgery or sham surgery performed at postnatal (P) day 2 (regenerative) or 10 (non-regenerative) and subjected to RNA-sequencing to investigate gene changes that correlate with regeneration and fibroblast resolution.

first: Eric

last: Small

first: Adwiteeya

last: Misra


title: Involvement of flavonol synthase/flavanone 3-hydroxylase-like in expression of phytotoxic potential of potato (Solanum sp.)

status: Public on Oct 27 2021

city: Mlochow

first: Dorota

last: Sołtys-Kalina

address: Platanowa 19

department: Mlochow Research Centre

country: Poland

institute: IHAR-PIB

summary:
Glycoalkaloids are Solanum bioactive compounds and are involved in allelopathic interactions. To achieve a better understanding of plant–plant interactions, it is essential to deeply examine the trait distribution in a segregating population. In the present paper, we used transcriptomic and metabolomic approaches to recognize the phytotoxic abilities of potato plants originating from a diploid segregating F1 population with particular emphasis on glycoalkaloids in potato groups characterized by a high glycoalkaloid content.
In potato F1 individuals, six glycoalkaloids were recognized: solasonine, solamargine, α-solanine, α-chaconine, leptinine I, and leptine II. In the bulk samples characterized by a high total glycoalkaloid content and various phytotoxic potential, high - A’, low - B’ and hormesis - F’, a significant role of the glycoalkaloid composition in the expression of phytotoxic potential was revealed. In particular, leptine II, solasonine and solamargine were present.
Based on the RNA-seq analysis of the bulk samples, a flavonol synthase/flavanone 3-hydroxylase-like gene responsible for flavonoid synthesis was upregulated in comparison A’ vs. B’ and A’ vs. F’ (Log2FC=8.30 and 6.40, respectively). The population-level evaluation of phytotoxic potential confirmed a significant negative correlation between total glycoalkaloid content and phytotoxic potential (r=-0.211) but only after correction for total flavonoid content.

overall_design: Examination of potato phytotoxic potential  under high glycoalkaloids content.

first: Katarzyna

last: Szajko

first: Paulina

last: Smyda-Dajmund

first: Jarosław

last: Ciekot

first: Waldemar

last: MarczewskI


title: Co-transcriptomic analysis of intracellular Streptococcus agalactiae in human monocytes

status: Public on Nov 30 2021

city: Gold Coast

first: Glen

last: Ulett

state: QLD

address: Parklands Drive

department: School of Medical Science

country: Australia

institute: Griffith University

summary: Sa strain 874391 and human U937 monocytes at 6h post-infection

sample_organism:
Streptococcus agalactiae
Homo sapiens

platform_organism:
Streptococcus agalactiae
Homo sapiens

overall_design: In vitro infection, MOI 100-200 6h, RNA-seq. for both pathogen and host


title: Expression data from cancer stem cells derived from colorectal organoids

status: Public on Oct 01 2021

first: Masahiro

last: Inoue

state: Kyoto

address: Med-Pharm Collaboration Bldg 503, Shimoadachi-cho 46, Sakyou-ku, Kyoto, 606-8304, Japan

department: Clinical Bio-resource Research and Development

institute: Kyoto Univ Graduate School of Medicine

summary:
Colorectal cancer (CRC) is characterized by extensive intra-tumor heterogeneity. The cancer stem cell (CSC) theory may explain the mechanisms underlying the non-genetic heterogeneity and their characteristics of prominent plasticity are emerging to be elucidated. By tracking the spheroid formation and growth capacity of CRC CSCs with a single-cell resolution using an organoid culture, we revealed CSCs consisted of subpopulations with a dual (fast and slow)-growing pattern. When isolated, the slow-growing CSCs remained slow-growing and converted into dual-growing CSCs under certain conditions. The slow-growing cells showed low levels of MAP kinase activity and were resistant to a MEK1/2 inhibitor as well as chemo-drugs. The MSI1 gene was down-regulated in the slow-growing CSCs and played a key role in the transition between slow- and dual-growing CSCs. Isolation of slow-growing CSCs will provide a platform to elucidate the role of the plasticity of CSCs in drug resistance and tumor recurrence.
To disclose the molecular characteristics of the CSC subclones with the distinct growth features, we analyzed the differentially expressed genes between the subgroups.

overall_design: The single cells from C45-1, C45-4SR and C45-4D subclones were cultured for 7 days and subjected to a microarray analysis.

first: Roberto

last: Coppo


title: MicroRNA-183-3p is a predictor of worsening heart failure in adult patients with transposition of the great arteries and a systemic right ventricle

status: Public on Sep 29 2021

city: Homburg Saar

first: Masood

last: Abu-Halima

address: Kirrberger St 60

institute: Univeristy of Saarland

summary: AIM: MicroRNAs (miRNAs) have been shown to play an important role in the progression of heart failure (HF). The aim of our study was to analyze miRNAs in the blood of patients with transposition of the great arteries and a systemic right ventricle (TGA-RV) in order to identify those that predict worsening HF.   MATERIALS AND METHODS: In 36 patients with TGA-RV, SurePrint™ 8×60K Human v21 miRNA arrays were used to determine the miRNA abundance profiles and compared to 35 age- and gender-matched healthy volunteers (HVs). MiRNAs that were most significantly abundant or best related to worsening HF were further validated by RT-qPCR.   RESULTS: Using miRNA array analysis, a total of 50 down-regulated and 56 up-regulated miRNAs were found to be differentially abundant in TGA-RV patients compared to HVs. 6 of these 106 miRNAs were significantly related to worsening HF. After validation by RT-qPCR, 4 miRNAs turned out to be significantly associated with worsening HF, namely miR-150-5p, miR-1255b-5p, miR-423-3p, and miR-183-3p. In the stepwise multivariable Cox regression analysis, ejection fraction of the systemic RV and miR-183-3p were found to be independent predictors of worsening HF (P<0.001 and P=0.008, respectively).   CONCLUSIONS: In patients with TGA-RV, miR-183-3p is an independent predictor of worsening HF and thus may be used as additional biomarker in the risk assessment of these patients.

overall_design: We profiled the miRNA repertoire of 36 TGA_RV and 35 controls samples


title: PD-1 induced proliferating T cells exhibit a distinct transcriptional signature

status: Public on Oct 20 2021

city: New York

first: Adam

last: Mor

state: New York

address: 650 West 168 Street

institute: Columbia University

summary: Analysis of primary human CD4+ T cells stained with the proliferation tracker CFSE and stimulated with anti-CD3, anti-CD28, and PDL1 or PDL2 for 5 days. Cells were sorted at the end of stimulation based on number of proliferative doublings prior to RNA isolation. Results provide insight into the PD-1 response pathway in CD4+ T cells that are proliferating or non-proliferating following stimulation.

overall_design: Comparison of proliferating and non-proliferating human CD4+ T cells following stimulation with anti-CD3, anti-CD28, and PDL1 or PDL2

first: Marianne

last: Strazza


title: Rapid evolutionary dynamics of an expanding family of Drosophila meiotic drive factors and their hpRNA suppressors

status: Public on Oct 07 2021

city: New Yor

first: Jeffrey

last: Vedanayagam

address: 1275 York Avenue

department: Department of Developmental Biology

institute: Sloan-Kettering Institute

summary: The Dox meiotic drive system distorts the sex-ratio in Drosophila simulans. Here, the authors reconstruct the step-wise emergence, and recent amplification of Dox superfamily genes in parallel with the emergence of autosomal hairpin RNA-class siRNA loci that target subsets of these putative drivers

sample_organism:
Drosophila mauritiana
Drosophila sechellia
Drosophila simulans

overall_design: The study reports small RNA and RNA-seq data from testis from 3 closely related species in the Drosophila simulans clade.

first: Ching-Jung

last: Lin

last: Lai


title: RNASeq analysis of in vitro generated myeloid-derived supressor cells (MDSCs)

status: Public on Oct 05 2021

city: Biberach (Riss)

first: Katrin

last: Fundel-Clemens

address: Birkendorferstr. 65

department: gCBDS

institute: Boehringer Ingelheim Pharma GmbH&Co KG

summary: Several mechanisms have been implicated in MDSC-mediated suppression of immune responses. To better understand the mechanism(s)/pathway(s) MDSCs utilize to suppress immune responses, we performed a transcriptome profiling of CD11b+CD11c+ (good suppressors) and CD11b+CD11c- (poor suppressors) MDSCs. Comparison of the respective transcriptomes allowed us to identify target genes associated with immunosuppression.

overall_design: Here we analyse in vitro generated myeloid-derived supressor cells (MDSCs) separated into two populations – CD11b+CD11c+ and CD11b+CD11c- with six replicates each for a total of 12 RNA-Seq samples.

first: Kerstin

last: Kitt

first: Heinrich

last: Huber

first: Jasmin

last: Scheurer

first: Stefan

last: Pflanz

first: Gudrun

last: Strauss


title: TIPE2 is a checkpoint in natural killer cell maturation and anti-tumor immunity

status: Public on Sep 22 2021

city: Shenzhen

first: Jiacheng

last: Bi

address: 1068 Xueyuan Avenue, Shenzhen University Town, Shenzhen, P.R.China

institute: Shenzhen Institute of Advanced Technology

summary: The maturation process determines NK cell functionality. We verified that tumor necrosis factor-alpha-induced protein-8 like-2 (TIPE2) works as a potent negative regulator in NK cell maturation. We found that TIPE2 expression gradually increased during NK cell ontogenesis correlating to their maturation stages in mice. NK-specific TIPE2 deficiency resulted in increased number of mature NK cells. To further confirm the role of TIPE2 in NK cell maturation, we performed single-cell RNA sequencing. Based on the key gene expression of NK cell effector molecules, transcriptional factors, maturation markers, and proliferation marker, we identified NK cell maturation program as Cluster#1->Cluster#2->Cluster#0 by which immature NK cells should go through to gain optimal effector functions at the cost of proliferation ability. According to this model, NK-specific TIPE2 deficient mice contained more NK cells belonging to the terminally mature Cluster#0 than control mice (up to 10% more), which is consistent with what we observed by flow cytometry. Therefore, these results collectively showed that NK-specific TIPE2 deficiency promotes NK cell maturation.

overall_design: Single-cell RNAseq of 6-week old NK-specific TIPE2 deficient mice and control mice


title: Unscheduled DNA replication in G1 causes genome instability and damage signatures indicative of replication collisions [ChIP-seq]

status: Public on Sep 07 2021

city: Martinsried

first: Karl-Uwe

last: Reusswig

address: Am Klopferspitz 18

institute: Max Planck Institute of Biochemistry

summary: DNA replicates once per cell cycle. Interfering with the regulation of DNA replication initiation generates genome instability through over-replication and has been linked to early stages of cancer development. Here, we engineered genetic systems in budding yeast to induce unscheduled replication in the G1-phase of the cell cycle. Unscheduled G1 replication initiated at canonical S-phase origins across the genome. We quantified differences in replisomes in G1- and S-phase and identified firing factors, polymerase α, and histone supply as factors that limit replication outside S-phase. G1 replication per se did not trigger cellular checkpoints. Subsequent replication during S-phase, however, resulted in over-replication and led to chromosome breaks via head-to-tail replication fork collisions that are marked by chromosome-wide, strand-biased occurrence of RPA-bound single-stranded DNA. Low-level, sporadic induction of G1 replication induced an identical response, indicating findings from synthetic systems are applicable to naturally occurring scenarios of unscheduled replication initiation by G1/S deregulation.

overall_design: ChIP-seq of EdU-labeled DNA synthesized in G1-arrested wild-type S. cerevisiae cells or cells undergoing unscheduled replication in G1 through bypassing CDK and DDK control of replication initiation. Strand-specific ChIP-seq of RPA-bound DNA at different timepoints in wild-type and rad52∆ cells after unscheduled replication in G1 and in cells undergoing sporadic G1 replication through BiFC-mediated stabilization of the interaction between replication initiation proteins Dpb11 and Sld2. n=2 replicates for each experiment.

first: Julia

last: Bittmann

first: Martina

last: Peritore

first: Michael

last: Wierer

first: Matthias

last: Mann

first: Boris

last: Pfander


title: Reprogramming of ovarian aging epigenome by resveratrol [methylation]

status: Public on Sep 26 2021

city: Tianjin

first: Mo

last: Gou

address: China, Tianjin, Nankai University

institute: Nankai University

summary: Depletion of oocytes and follicles and reduced oocyte quality contribute to age-associated ovarian senescence and infertility. Telomere shortening and altered methylation make two major contributions to general aging. Resveratrol acts as anti-oxidant and Sirt1 activator to alleviate aging including reproductive aging. It remains elusive whether resveratrol can reprogram the aging epigenome. We sought to examine aging ovarian epigenome and the potential effects of resveratrol by combined analysis of telomere length, transcriptome and methylome mainly in oocytes and also in granulosa cells, two major cell types in the ovary.

overall_design: for methylation analysis, 2~3 repeats of mouse MII oocytes, 10 oocytes each sample；  for RNA-Seq  analysis, ≥3 repeats of mouse MII oocytes, 1 oocyte each sample；  for RNA-Seq  analysis, 3 repeats of mouse granulosa cells(GCs) , 500 GCs each sample.

first: Jie

last: Li

first: Lizhi

last: Yi


title: A time series of the pituitary gland transcriptome during development and sexual maturation in the model fish medaka

status: Public on Sep 08 2021

city: Oslo

first: Khadeeja

last: siddique

address: Karl Staaffs vei 75, house 7

country: Norway

institute: Norwegian University of Life sciences (NMBU))

summary: Directing both organismal homeostasis and physiological adaptation, the pituitary is a key endocrine gland in all vertebrates. It communicates the needs of the organism to different organs by secreting hormones into the bloodstream. Here, we have used the model fish medaka (Oryzias latipes) to investigate the developmental dynamics in the pituitary using a comprehensive RNA-seq time series from 31 to 375 days post-fertilization.

overall_design: RNA-seq of the medaka pituitary.

first: Eirill

last: Ager-Wick

first: Gersende

last: Maugars

first: Kristine

last: von Krogh

first: Romain

last: Fontaine

last: Siddique

first: Rasoul

last: Nourizadeh-Lillabadi

first: Finn-Arne

last: Weltzien

first: Christiaan

last: Henkel


title: Reprogramming of ovarian aging epigenome by resveratrol [RNA-seq]

overall_design:
for methylation analysis, 2~3 repeats of mouse MII oocytes, 10 oocytes each sample；  for RNA-Seq  analysis, ≥3 repeats of mouse MII oocytes, 1 oocyte each sample；  for RNA-Seq  analysis, 3 repeats of mouse granulosa cells(GCs) , 500 GCs each sample.
"OKOC"for old age(10-month-old) Tet2 knockout control group
"OKOR"for old age(10-month-old) Tet2 knockout resveratrol treated group
"OWTC"for old age(10-month-old) WT control group
"OWTR"for old age(10-month-old) WT resveratrol treated group
"YKO"for young(2-month-old) Tet2 knockout control group
"YWT"for young(2-month-old) WT control group
"MWTC"for middle-age(6-month-old) WT control group
"MWTR"for middle-age(6-month-old) WT resveratrol treated group
"OKOC"for old age(10-month-old) Tet2 knockout control group
"OKOR"for old age(10-month-old) Tet2 knockout resveratrol treated group
"OWTC"for old age(10-month-old) WT control group
"OWTR"for old age(10-month-old) WT resveratrol treated group
"YKO"for young(2-month-old) Tet2 knockout control group
"MKOC"for middle age(6-month-old) Tet2 knockout control group
"MKOR"for middle age(6-month-old) Tet2 knockout resveratrol treated group
old age(10-month-old) resveratrol treated group
old age(10-month-old) control group
middle age(6-month-old) control group


title: An integrated CUT&RUN quality control workflow for histone modifications and transcription factors

city: Burlington

first: Princess

last: Rodriguez

state: Vermont

address: 89 Beaumont Avenue

department: Microbiology and Molecular Genetics

institute: University of Vermont

summary: Genome-wide analysis of H3K4me3 and Ikaros profiles in fresh or frozen mouse splenic B cells via CUT&RUN

overall_design: We created CUT&RUN profiles of H3K4me3, Ikaros, and IgG in wild-type B cells (fresh and frozen).

first: Seth

last: Frietze

first: Joseph

last: Boyd


title: Reprogramming of ovarian aging epigenome by resveratrol

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

overall_design: Refer to individual Series


title: Next Generation Sequencing Facilitates Quantitative Analysis of Wildtype, akr1a1a-/- and Wildtype with Acrolein Treatment Zebrafish Larvae Transcriptomes

status: Public on Sep 05 2021

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

department: ZMF

institute: University Heidelberg

summary: Our previous experiments showed the function of Akr1a1a was related to insulin resistance. The knockout of Akr1a1a led to poor acrolein detoxification and accumulated acrolein inhibits insulin receptors (insra/insrb) expression. To understand how the loss of Akr1a1a and acrolein reflects at the transcriptome level, we performed full genome RNA-Seq between akr1a1a+/+, akr1a1a-/- and akr1a1a+/+ with acrolein treatment zebrafish larvae at 120 hpf. An overview of RNA-Seq, including quality control, principal component analysis (PCA), and volcano plots of regulated genes showed comparable properties between akr1a1a mutants, wild type and acrolein treated wild type zebrafish larvae. We found the insulin receptor signaling pathway was down-regulated significantly in akr1a1a mutants and acrolein treated wild type larvae as compared to wild type larvae via gene set enrichment analysis (normalized enrichment score, -1.888, p=0.028; -1.93, p=0.019). Intriguingly, downstream signaling pathways including MAPK, signal transduction by protein phosphorylation and transmembrane receptor protein tyrosine kinase signaling pathway were also significantly down-regulated in akr1a1a mutants and acrolein treated wild type larvae. Taken together, these results further suggest akr1a1a and acrolein as an important regulator in insulin receptor signaling transduction. Furthermore, we offer a comprehensive and more detailed evaluation of mRNA content within zebrafish larvae. We conclude that RNA-seq based transcriptome would clearly illustrate genetic network and clarify complex biological functions.

overall_design: mRNA expression profiles of wildtype, akr1a1a-/-  and wildtype with acrolein treatment zebrafish larvae at 120 hours after post fertilization

first: Haozhe

last: Qi

first: Sticht

last: Carsten

first: Jens

last: Kroll


title: Enhancement of leaf barriers and secondary metabolism improves Tomato endurance to Tuta absoluta

status: Public on Aug 11 2021

city: Portici

first: Daniela

last: D'Esposito

address: Via Università 100

department: Department of Agriculture

country: Italy

institute: University of Naples Federico II

summary: The leaf miner, Tuta absoluta, is a notorious destructive pest of tomato that causes important losses worldwide. Breeding of resistant/tolerant tomato cultivars could be an effective strategy for T. absoluta management but, despite the economic importance of tomato, very limited information is available about its response to this treat. To elucidate the defense mechanisms to the herbivore feeding a comparative analysis was performed between a tolerant and susceptible cultivated tomato at both morphological and at transcriptome level to highlight constitutive leaf barriers, molecular and biochemical mechanisms to counter the effect of T. absoluta attack. The tolerant genotype showed an enhanced constitutive barrier due to the higher density of trichomes and increased inducible reactions upon mild infestation thanks to the activation/repression of key transcription factors regulating a higher number of genes involved in cuticle formation and cell wall strength as well as of antinutritive enzymes, and genes involved in the production of chemical toxins and bioactive secondary metabolites. Overall, our findings provide an important foundation for further understanding the insect resistance mechanisms of resistant/tolerant varieties that can be exploited for developing T. absoluta tolerant cultivars, acting as important component of integrated pest management strategy for more sustainable production.

overall_design: Transcriptome profiles of two tomato genotypes, a tolerant/partially resistant and a susceptible (in duplicate) to Tuta absoluta, were generated by RNA sequencing and compared contrasting for each genotype infested with T. absoluta vs not infested condition

last: D’Esposito

first: Daniele

last: Manzo

first: Alessandro

last: Ricciardi

first: Antonio

last: Garonna

first: Antonino

last: De Natale

first: Luigi

last: Frusciante

first: Francesco

last: Pennacchio

first: Maria

last: Ercolano


title: Next Generation Sequencing of Wild Type and Nsd2 Treg cells conditional knock out Treg cells Transcriptomes

status: Public on Aug 03 2021

city: Nanjing

first: Yuchao

last: Jing

state: Jiangsu

address: 101 Longmian Ave Jiangning District

department: Immunology

institute: Nanjing Medical University

summary: Our study aims to characterize the different expression genes between Wild Type and Nsd2 Treg cells conditional knock out groups in Treg cells, and find the influenced pathways and functions,  moreover, we can clarify the NSD2 functions in Treg cells. It can be a clue for further Treg cells study.

overall_design: Treg cells mRNA profiles of  wild type (WT) and Nsd2 Treg conditional knock out  mice

first: Xiaoming

last: Wang

first: Le

last: Zhang

first: Yuliang


title: Executioner caspases 3 and 7 are dispensable for intestinal epithelium turnover and homeostasis at steady state

city: Zwijnaarde

first: Jordy

last: De Coninck

address: Technologiepark 71

department: Department of Biomedical Molecular Biology

country: Belgium

institute: University Gent

summary: Apoptosis is widely believed to be crucial for epithelial cell death and shedding in the intestine, thereby shaping the overall architecture of the gastrointestinal tract, but also regulating tolerance induction during homeostasis. To experimentally address this concept, we generated intestinal epithelial cell (IEC)-specific knockout mice that lack both executioner caspase-3 and caspase-7 (Casp3/7?IEC), which are the converging point of the extrinsic and intrinsic apoptotic pathway. Surprisingly, the overall architecture, cellular landscape and proliferation rate remained unchanged in these mice. However, non-apoptotic cell extrusion was increased in Casp3/7?IEC mice, compensating apoptosis deficiency, maintaining the same physiological level of IEC shedding. Microbiome richness and composition stayed unaffected, bearing no sign of dysbiosis. Transcriptome and single cell RNA sequences analyses of IECs and immune cells revealed no differences in signaling pathways of differentiation and inflammation. These findings demonstrate that during homeostasis apoptosis per se is dispensable for IEC turnover at the top of intestinal villi intestinal tissue dynamics, microbiome composition and immune regulation.

overall_design:
Single-cell RNA sequencing was performed on mesenteric lymph nodes (mLN), small intestinal intra-epithelial lymphocytes (SI-IEL), SI lamina propria lymphocytes (SI-LPL), colonic IELs and colonic LPLs isolated from Casp3/7ΔIEC mice and Casp3/7FL/FL littermates. Mesenteric lymph nodes were collected, smashed and single cells were collected by centrifugation. SI-IELs and colon IELs were were isolated from the epithelial layer by treatment with the reducing agent Dithioerythritol (DTE). Single cells were prepared from the SI and colonic lamina propria by enzymatic digestion using collagenases followed by Percoll gradient centrifugation. Finally, fluorescence activated cell sorting (FACS) of live immune cells (CD45+) and live epithelial cells (CD45-) was performed using a BD FACSAria™ cell sorter.
After preparation of single cells from the SI-IEL of both Casp3/7ΔIEC mice and Casp3/7FL/FL littermates, 50% live immune cells (expressing CD45) and 50% cells which lack expression of CD45 were sorted for RNA sequencing (samples FGH001 and FGH002). From the lamina propria fraction of both Casp3/7ΔIEC mice and Casp3/7FL/FL littermates, only CD45-expressing cells were sorted for RNA sequencing (samples FGH003 and FGH004). The same principle was applied to the colon IELs and LPLs from both Casp3/7ΔIEC mice and Casp3/7FL/FL littermates. However, for each genotype, the IELs and LPLs were combined into one sample resulting in each sample consisting of 25% CD45+ IELs, 25% CD45- IELs and 50% CD45+ LPLs (samples FGH005 and FGH006). From the mesenteric lymph nodes (mLN) of both Casp3/7ΔIEC mice and Casp3/7FL/FL littermates, only CD45+ immune cells were sorted (samples FGH007 and FGH008) .TotalSeq-A Cell Hashing Antibodies were used to include three replicates (mice) per sample.

first: Farzaneh

last: Ghazavi

first: Jelle

last: Huysentruyt

first: Stephanie

last: Kourula

first: Sofie

last: Martens

first: Behrouz

last: Hassania

first: Tim

last: Wartewig

first: Tatyana

last: Divert

first: Ria

last: Roelandt

first: Bastian

last: Popper

first: Andreas

last: Hiergeist

first: Peter

last: Tougaard

first: Tom

last: Vanden Berghe

first: Marie

last: Joossens

first: Geert

last: Berx

first: Nozomi

last: Takahashi

first: Adam

last: Wahida

last: Vandenabeele


title: Acquired resistance to PRMT5 inhibition and the consequent collateral sensitivity to paclitaxel are both Stmn2 dependent

status: Public on Aug 01 2021

city: Cambridge

first: Charles

middle: Arthur

last: Whittaker

institute: Koch Institute

summary: Drug resistance is a major hurdle for the efficacy of cancer therapies. Protein arginine methyltransferase 5 (PRMT5) is an epigenetic regulator that is upregulated in most tumor types, and PRMT5 inhibitors (PRMT5i) are now in clinical trials. Here we describe the first model of resistance to PRMT5 inhibition, using cell lines derived from murine Kras-G12D;p53-null lung adenocarcinomas (LUAD). Initially, PRMT5 inhibition induced proliferation defects and apoptosis, but eventually we were able to generate numerous independent PRMT5i resistant lines. Resistance was drug-induced, not preexisting, and reflects a novel, shared transcriptional state. This state is stable, and it creates a collateral sensitivity to the taxane, paclitaxel. Accordingly, PRMT5i and paclitaxel synergistically suppress Kras-G12D;p53-null murine LUAD cells. Remarkably, a single gene Stathmin 2 (Stmn2) is required for both PRMT5i resistance and paclitaxel sensitivity. Finally, analysis of TCGA patient data showed that high Stmn2 levels correlates with good tumor responses to taxane treatment.

overall_design: Three replicates each of Kras/P53 mouse lung adenocarcinoma cells parental (KP1) untreated (N) and treated (Y) with EPZ015666 and 3 untreated resistant lines (R3, R6 and R7).

first: Helen

last: Mueller

first: Colin

last: Fowler

first: Simona

last: Dalin

first: Enrico

last: Moiso

first: Tee

last: Udomlumleart

first: Salil

last: Garg

first: Michael

last: Hemann

first: Jacqueline

last: Lees


title: Transcriptomic analysis of mouse hepatic progenitors expressing different level of the HRasG12V oncogene (in vivo and ex vivo).

status: Public on Jul 28 2021

city: Montpellier

first: Damien

last: Grégoire

address: 1919, route de Mende

institute: CNRS

summary: Analysis was done in parrallel on tissue culture and on orthotopic tumor xenografts from primary (liver) and metastatic (peritoneum) site after separation of tumoral and stromal cells components.

overall_design: mRNA profiles of BMEL cells transduces with an empty vector or expressing eitheir low (RasLOW) or high (RasHIGH) levels of the HRasG12V oncogene were generated by deep sequencing, in triplicate, using Illumina HiSeq2500. mRNA profiles of tumor and stromal cells after dissociation and isolation from liver xenograft or peritoneal metastasis from 4 independant mice were generated using Illumina HiSeq2500

first: Urszula

last: Hibner

first: Anthony

last: Lozano


title: Network-based assessment of HDAC6 activity is highly predictive of pre-clinical and clinical responses to the HDAC6 inhibitor ricolinostat

status: Public on Jul 23 2021

city: Memphis

first: Qingfei

last: Pan

address: 262 Danny Thomas Place

department: Department of Computational Biology

institute: St. Jude Children's Research Hospital

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: Gene expression profiles of colorectal cancer organoids from 87 patients

status: Public on Jul 20 2021

city: Seoul

first: Chang Ohk

last: Sung

address: Song-Pa gu,Pung-nap dong

department: Pathology

country: South Korea

institute: Asan Medical Center

summary: Colorectal cancer organoids (CCOs) recapitulate the gene expression signatures of their respective primary tumors. These CCOs provide valuable model for studying the primary cancers.

overall_design:
Colorectal cancer organoids and matched primary colorectal cancers from 87 patients were compared using gene expression profile.
>>> Submitter declares that the raw data will be deposited in the European Genome-phenome Archive (EGA) due to patient privacy concerns. <<<

first: Se

last: Jang

first: Minsuh

last: Kim

first: Daum

last: Jo

first: Sun-hye

last: Lee

first: Tea

first: Chang

last: Yu

middle: O


title: Immuno-genomic classification of colorectal cancer organoids reveals cancer cells with intrinsic immunogenic properties associated with patient survival


title: Expression data from tumour celllines and non-tumour cells.

status: Public on Jun 30 2021

city: Ulm

first: Johannes

last: Bloehdorn

address: Albert-Einstein-Allee 23

institute: University of Ulm

summary:
Chronic lymphocytic leukemia shows a variable clinical course which is associated with distinct alterations such as chromosomal aberrations, gene mutations or IGHV mutation status. Refining biologic categories may help to improve clinical management with available and future treatment, lymphoma/leukemia celllines and non-tumour cells of the microenvironment can be used for models to better categorize biologic CLL entities.
We used Affymetrix Exon 1.0 ST microarrays to investigate differences in CLL biology.

overall_design: Gene expression profiling on samples from celllines and non-tumour cells.


title: Metabolically controlled histone H4K5 acylation/acetylation ratio drives BRD4 genomic distribution VII

status: Public on Jun 25 2021

city: La Tronche

first: Sophie

last: Rousseaux

address: Bd de la Chantourne

department: IAB

institute: INSERM-UGA

summary: In addition to acetylation, histones are modified by a series of competing longer chain acylations. Most of these acylation marks are enriched and co-exist with acetylation on active gene regulatory elements. Their seemingly redundant functions have hindered the understanding of histone acylations’ specific roles. Here, by using an acute lymphoblastic leukaemia (ALL) cell model and blasts from B-ALL patients, we demonstrate a role for mitochondrial activity in controlling histone acylation/acetylation ratio, especially at H4K5. An increase of the crotonylation and butyrylation over acetylation on H4K5 weakens BRD4-chromatin interaction and increases BRD4 nuclear mobility and availability for binding transcription start site associated nucleosome free regions of active genes. Our data suggest that, with regard to BRD4 dynamics, histone acylations including acetylation, should be considered collectively. A metabolism dependant control of the histone acetylation/longer chain acylation(s) ratio could constitute a common mechanism regulating bromodomain factors’ “reservoir” pool, availability and functional genomic distribution.

overall_design: Chromatin immunoprecipitation assays and sequencing (ChIPseq) of REH cells (WT and FASTKD1 ko) with anti-H4K5 butyrylation and anti-BRD4

first: Florent

last: Chuffart

first: Mengqing

last: Gao

last: Barral

first: Lisa

last: Bargier

first: Denis

last: Puthier

first: Ekaterina

last: Bourova-Flin

first: Yingming

last: Zhao

first: Jian-Qing

last: Mi

first: Saadi

last: Khochbin


title: Expression data from CLL patient samples investigated to define biologic heterogeneity.

summary:
Chronic lymphocytic leukemia shows a variable clinical course which is associated with distinct alterations such as chromosomal aberrations, gene mutations or IGHV mutation status. Refining biologic categories may help to improve clinical management with available and future treatment approaches.
We used Affymetrix Exon 1.0 ST microarrays to investigate differences in CLL biology.

overall_design: Gene expression profiling on samples from CLL patients was conducted by using CD19 sorted and unsorted peripheral blood mononuclear cells from patients treated on randomized international CLL trials using chemo or chemoimmunotherapy.


title: Gene expression profile of colorectal cancer tissues from 87 patients

first: Chang Ohk

last: Sung


title: Metabolically controlled histone H4K5 acylation/acetylation ratio drives BRD4 genomic distribution III

overall_design: RNAseq analysis of REH cells WT versus FASTKD1 KO1 and KO2


title: Metabolically controlled histone H4K5 acylation/acetylation ratio drives BRD4 genomic distribution V

overall_design: RNAseq analysis of malignant blasts from B-ALL patients with high or low acylation levels


title: An optimized protocol for single cell transcriptional profiling by combinatorial indexing

status: Public on Nov 05 2021

city: Seattle

first: Chengxiang

last: Qiu

state: WA

address: William H. Foege Hall, 3720 15th Ave NE

department: Genome Sciences

institute: University of Washington

summary: Single cell combinatorial indexing RNA sequencing (sci-RNA-seq) is a powerful method for recovering gene expression data from an exponentially scalable number of individual cells or nuclei. However, sci-RNA-seq is a complex protocol that has historically exhibited variable performance on different tissues, as well as lower sensitivity than alternative methods. Here we report a simplified, optimized version of the three-level sci-RNA-seq protocol that is faster, higher yield, more robust, and more sensitive, than the original sci-RNA-seq3 protocol, with reagent costs on the order of 1 cent per cell or less. We showcase the optimized protocol via whole organism analysis of an E16.5 mouse embryo, profiling ~380,000 nuclei in a single experiment. Finally, we introduce a “tiny sci-*” protocol for experiments where input is extremely limited.

overall_design: Nuclei were isolated from one E16.5 mouse embryo to perform the optimized sci-RNA-seq3 protocol.

first: Beth

last: Martin

first: Eva

last: Nichols

first: Melissa

last: Phung

first: Rula

last: Green-Gladden

first: Sanjay

last: Srivatsan

first: Ronnie

last: Blecher-Gonen

first: Brian

last: Beliveau

first: Cole

last: Trapnell

first: Junyue

last: Cao

first: Jay

last: Shendure


title: Metabolically controlled histone H4K5 acylation/acetylation ratio drives BRD4 genomic distribution II

first: Sophie

last: Rousseaux

overall_design: Chromatin immunoprecipitation assays and sequencing (ChIPseq) of REH cells (WT and FASTKD1 ko) with anti-BRD4

first: Florent

last: Chuffart

first: Mengqing

last: Gao

last: Barral

first: Lisa

last: Bargier

first: Denis

last: Puthier


title: Metabolically controlled histone H4K5 acylation/acetylation ratio drives BRD4 genomic distribution


title: Metabolically controlled histone H4K5 acylation/acetylation ratio drives BRD4 genomic distribution VI

overall_design: RNAseq analysis of REH cells control versus FASTKD1 sh

first: Ekaterina

last: Bourova-Flin

first: Yingming

last: Zhao

first: Jian-Qing

last: Mi

first: Saadi

last: Khochbin


title: Metabolically controlled histone H4K5 acylation/acetylation ratio drives BRD4 genomic distribution I

overall_design: Chromatin immunoprecipitation assays and sequencing (ChIPseq) of REH cells (WT and FASTKD1 ko) with anti-H4K5 acetylation and anti-H4K5 crotonylation


title: The E2F4/p130 repressor complex cooperates with oncogenic ΔNp73α to promote cell survival in human papillomavirus 38 E6/E7-transformed keratinocytes and in cancer cells

status: Public on Jun 08 2021

city: Lyon

first: Eugénie

last: Lohmann

state: Auvergne-Rhône-Alpes

address: Cours Albert Thomas

department: infectiology

institute: IARC

summary: Tumor suppressor p53 and its related proteins, p63 and p73, can be synthesized as multiple isoforms lacking part of the N- or C-terminal regions. Specifically, high expression of the ΔNp73α isoform is notoriously associated with various human malignancies characterized by poor prognosis. This isoform is also accumulated by oncogenic viruses such as Epstein–Barr virus (EBV), as well as genus beta human papillomaviruses (HPV) that appear to be involved in carcinogenesis. To gain additional insight into ΔNp73α mechanisms, we have performed proteomics analyses using human keratinocytes transformed by the E6 and E7 proteins of the beta-HPV type 38 virus as an experimental model (38HK). We find that ΔNp73α associates with the E2F4/p130 repressor complex through a direct interaction with E2F4. This interaction is favored by the N-terminal truncation of p73 characteristic of ΔNp73 isoforms. Moreover, it is independent of the C-terminal splicing status, suggesting that it could represent a general feature of ΔNp73α isoforms (α, β, γ, δ, ε, ζ, θ, η, and η1). We show that the ΔNp73α-E2F4/p130 complex inhibits the expression of specific genes, including genes encoding for negative regulators of proliferation, both in 38HK and in HPV-negative cancer-derived cell lines. Such genes are not inhibited by E2F4/p130 in primary keratinocytes lacking ΔNp73α, indicating that the interaction with ΔNp73α rewires the E2F4 transcriptional program. In conclusion, we have identified and characterized a novel transcriptional regulatory complex with potential implications in oncogenesis.

overall_design:
Gene expression analysis in presence or absence of the E2F4/E2F5 transcription factors in 38HK cell line.
38HK cells are transiently transfected with Scramble siRNA (3 control samples) or E2F4+E2F5 siRNAs (3 knockdown samples) using Lipofectamine 2000 reagent. Cells are collected 48 hours post-transfection and the level of proteins evaluated by Western-blot. Total RNA samples are extracted from 38HK cells (around 10e6 cells per sample) using the RNeasy Mini kit form QIAGEN. Samples are quantified by Qubit.

first: Valerio

last: Taverniti

first: Katia

last: Zanier


title: Metabolically controlled histone H4K5 acylation/acetylation ratio drives BRD4 genomic distribution IV

overall_design: RNAseq analysis of REH cells WT untreated or treated with the BET bromodomain small inhibitor JQ1 at the respective concentrations of 100nM or 500nM


title: miRNA expression data from sedentary and exercised rats

status: Public on May 24 2021

city: Mexico City

first: Gibrán

last: Pedraza-Vázquez

address: Av. San Rafael Atlixco #186, Colonia Vicentina, Iztapalapa

department: Ciencias de la Salud

country: Mexico

institute: Universidad Autónoma Metropolitana

summary:
Loss of skeletal muscle mass during aging, also known as sarcopenia, is a worldwide health problem. The etiology of sarcopenia remains unknown; however, recent studies revealed that sedentarism, fat gain, and epigenetic regulators such as miRNAs are critical regulators in its developing. One effective intervention to prevent and treat sarcopenia is aerobic exercise.
We used miRNA microarrays to determine the changes in miRNA expression through time and the differences between sedentary and lifelong exercised rats.

overall_design: 4 month-old rats were caged and randomly selected for sedentary conditions (no exercise) and exercised (25 cm/s, 30 min, 5 days/week on a Panlab rat treadmill). Gastrocnemius muscles were obtained at 8, 12, 18 and 24 months old for RNA extraction and hybridization on Affymetrix microarrays.

first: Gibran

first: Armando

last: Luna-López


title: Multimodal profiling of 500,000 memory T cells from a tuberculosis cohort

city: Boston

first: Aparna

last: Nathan

state: MA

address: 77 Avenue Louis Pasteur

country: USA

institute: Harvard Medical School, Brigham and Women's Hospital

summary: We profiled peripheral memory T cells from donors with prior TB disease or latent infection to identify cell states associated with disease or other demographic and environmental variables. For higher-resolution definition of T cell states, we performed CITE-seq to measure single-cell mRNA and surface expression of 31 key memory T cell proteins, integrated these modalities, and quantified asssociations with variables of interest.

overall_design: PBMCs were collected from 259 donors, including former progressors (cases) and non-progressors (controls). Technical replicates were included across separate batches for 12. We isolated memory T cells and profiled 500,089 high-quality cells with CITE-seq (using a surface marker panel of 31 antibodies). Raw sequencing data for human samples will be available on dbGAP.

first: Soumya

last: Raychaudhuri


title: RNA-sequencing data of lung tissue of pigs infected with parasites and adminstered proanthocyanidins (PAC)

status: Public on Jun 01 2021

city: Frederiksberg C

first: Andrew

last: Williams

state: --- Select One ---

address: Dyrlægevej 100

country: Denmark

institute: University of Copenhagen

summary: We show here the transcriptional response in the lung of pigs infected or not with Ascaris suum, fed either a control pr a PAC-enriched diet

overall_design: RNA was obtained from the lungs of 12 pigs infected with A. suum and 12 uninfected pigs. Within each infection group, pigs were fed either a control diet or the control diet supplemented with 1 % PAC derived from grape seed