title: miRNA transcriptome and myofiber characteristics of lamb skeletal muscle during hypertrophic growth

city: Clemson

first: Susan

last: Duckett

state: South Carolina

address: 105 Collings ST, RM 112 BRC

department: Animal and Veterinary Science

institute: Clemson University

summary: Longissimus muscle samples were collected from lambs at 6 developmental time points (prenatal  gestational d 85, 110, 133, and postnatal d 42, 65, and 243). Muscle samples were examined to determine the impact of myofiber hypertrophy on the miRNA profile.

overall_design: This study is comprised of 18 samples, There are 6 developmental groups with 3 replicates each. Prenatal time gestational d 85, 110, and 133. Postnatal time d 42, 65, and 243.

first: Maslyn

last: Greene

first: Rhonda

last: Powell

first: Terri

last: Bruce

first: William

last: Bridges


title: MiniBac-seq enables bacterial RNA-seq from ultra-low input and profiling cells with arrested growth

status: Public on Jul 22 2022

city: Shanghai

first: Tianmin

last: Wang

address: Huaxia Middle Road, 393

department: School of Life Science and Technology

country: China

institute: ShanghaiTech University

type: Expression profiling by high throughput sequencing

summary: We developed miniBac-seq, a strand-specific method for high-quality bacterial RNA-seq library construction from sub-nanogram of total RNA, equivalent to a few thousand bacterial cells; we also tested its potent to be adopted as a single cell RNA-seq method. Here we provide the supporting data to the paper introducing this technology.

overall_design: We used E. coli K12 BW25113, typically cultivated in M63B1 broth and extracted total RNA at the Log phase. Fig2 Impact of customized rRNA depletion method on transcript quantification; Fig4 Overall performance of miniBac-seq; Fig 5 Detection limit of miniBac-seq, via library construction from a gradient of input RNA (5 ng, 1 ng, 100 pg, 10 pg, 1 pg, 100 fg); Fig 6 Impact of barcode introduced at RT on transcript quantification

first: Ping

last: Shen


title: RNA-sequencing of IRF5+ and IRF5- circulating monocytes from patients with Type-2 Diabetes

city: PARIS

first: Stephane

last: Le Crom

address: 46 rue Ulm

department: Genomic Core Facility

country: France

institute: IBENS

summary:
Purpose: To characterise the transcriptomic landscape in monocytes associated with IRF5 expression
Methods: RNA sequencing from FACS sorted IRF5+ and IRF5- CD14+ monocytes
Results: Differential expression based on IRF5 postiivity provides insight into its roles in monocyte function and in type-2 diabetes
Conclusions: This study represents the first analyses of IRF5-dependent transcriptome in circulating monocytes from patients with Type-2 diabetes

overall_design: mRNA-sequencing of FACS sorted cells

first: L

last: Orliaguet

first: F

last: Alzaid

first: C

last: Blugeon

first: S

last: Lemoine


title: TWAS-based translational genomics approach identifies IL10RB as the top candidate gene for COVID-19 host susceptibility and severity

city: New York

first: Shan

last: Jiang

department: Taub Institute for Research on Alzheimer’s Disease and the Aging Brain

country: USA

institute: Columbia University Irving Medical Center

summary: Recent efforts have identified genetic loci that are associated with coronavirus disease 2019 (COVID-19) infection rates and disease outcome severity. Translating these genetic findings into druggable genes that regulate COVID-19 host susceptibility is a critical next step. Using a translational genomics approach that integrates COVID-19 genetic susceptibility variants, multi-tissue genetically regulated gene expression (GReX) and perturbagen signatures, we identify IL10RB as the top key regulator of COVID-19 host susceptibility. In a series of validation steps we show that predicted GReX up-regulation of IL10RB and higher IL10RB expression in COVID-19 patient blood is associated with worse COVID-19 outcomes, and that in vitro IL10RB overexpression is associated with increased viral load and activation of disease-relevant molecular pathways.

overall_design:
3 samples each matching the following conditions/treatments (48 total):
NPCs;CoV+;CRISPRa;IL10RB-1 gRNA
NPCs;CoV+;CRISPRa;IL10RB-2 gRNA
NPCs;CoV+;CRISPRa;IL10RB-3 gRNA
NPCs;CoV+;CRISPRa;IL10RB-4 gRNA
NPCs;CoV+;CRISPRa;Scramble gRNA
NPCs;CoV+;shRNA;IFNAR2 shRNA
NPCs;CoV+;shRNA;IL10RB shRNA
NPCs;CoV+;shRNA;Scramble shRNA
NPCs;CoV-;CRISPRa;IL10RB-1 gRNA
NPCs;CoV-;CRISPRa;IL10RB-2 gRNA
NPCs;CoV-;CRISPRa;IL10RB-3 gRNA
NPCs;CoV-;CRISPRa;IL10RB-4 gRNA
NPCs;CoV-;CRISPRa;Scramble gRNA
NPCs;CoV-;shRNA;IFNAR2 shRNA
NPCs;CoV-;shRNA;IL10RB shRNA
NPCs;CoV-;shRNA;Scramble shRNA

first: Georgios

last: Voloudakis

first: Gabriel

middle: E

last: Hoffman

first: Kristina

last: Dobrindt

first: James

middle: M

last: Vicari

first: Wen

last: Zhang

first: Daisy

last: Hoagland

first: Schahram

last: Akbarian

first: Benjamin

middle: R

last: tenOever

first: Kristen

middle: J

last: Brennand

first: John

middle: F

last: Fullard

first: Panos

last: Roussos


title: Mapping the Drosophila developmental and aging atlas by single cell mRNA-seq

status: Public on Jul 23 2022

city: Hanzhou

first: Guoji

last: Guo

address: Yuhangtang street 866

department: Zhejiang University School of Medicine

institute: Center for Stem Cell and Regenerative Medicine

summary: Single-cell mRNA sequencing (scRNA-seq) technologies are reshaping current cell-type classification system. In previous studies, we constructed the Mouse Cell Atlas (MCA) and Human Cell Landscape (HCL) to catalog all cell types by collecting scRNA-seq data. Howerver, the systematic study for organism-level dynamic changes of cellular states across fruit fly (Drosophila melanogaster) life span are still lacking. Here, we constructed the Drosophila cell Landscape covering different development periods using Microwell-seq protocol. The Drosophila cell landscape provides a valuable resource for studying cross-sepciess development, maturation and aging.

overall_design: About 162,495 cells derived from Drosophila whole-body single-cell dissociation and profiling at 21 day (D21), D26, D31, D36, and D41 after laying eggs (nearly 25-30 fruit flies per timepoint).

first: Xiaoping

last: Han

first: Renying

last: Wang

first: Peijing

first: Lifeng

last: Ma


title: Expression data from tibialis anterior muscle of mice with or without treatment of dexamethasone and/or tumeric extract

city: Tokyo

first: Sihui

address: Yayoi 1-1-1

country: Japan

institute: The university of Tokyo

summary: Sarcopenia is the decline in skeletal muscle mass, strength, and functions, which decreases the quality of life in elderly people. This study investigated the suppressive effect of turmeric (Curcuma longa) extract (TE) on muscle atrophy in dexamethasone (DEX)-treated mice and C2C12 myotubes. DEX treatment significantly decreased the muscle weight and significantly increased Fbxo32 and Murf1 expression in mice, and these changes were suppressed by the supplementation of an AIN-93 based diet with 2% TE. A similar pattern was observed in FBXO32 and MuRF1 protein expression. In C2C12 myotubes, DEX treatment significantly increased FBXO32 and MuRF1 gene and protein expression, and these increases were significantly suppressed by TE supplementation at a concentration of 200 µg/ml. Furthermore, one of the five TE fractions, which were separated by high-performance liquid chromatography had a similar effect with TE supplementation. The present study proposes the suppressive effect of turmeric on sarcopenia.

overall_design: Tibialis anterior muscle of mice with or without treatment of dexamethasone and/or tumeric extract  were used for RNA extraction and hybridization on Affymetrix microarrays.

first: Kyohei

last: Furukawa

first: Malika

last: Kousaka

first: Huijuan

last: Jia

first: Hisanori

last: Kato


title: Parasitic plant sRNome analyses unveils parasite-specific signatures of miRNA retention, loss and gain

city: Uppsala

first: German

last: Martinez

state: Uppsala

address: Almas Allé 8

department: Plant Biology

country: Sweden

institute: Swedish University of Agricultural Sciences

type: Non-coding RNA profiling by high throughput sequencing

summary: Parasitism is a successful life strategy that has evolved independently in several families of Higher Plants. In parasitic plants, nutrients and water are obtained from their hosts through specifically adapted haustoria. The genera Cuscuta and Orobanche represent examples for the two profoundly different groups of parasites, one parasitizing host shoots and the other infecting host roots. In this study, we sequenced and described the overall repertoire of small RNAs (sRNome) from Cuscuta campestris and compared it to an exploratory sRNome from Orobanche aegyptiaca.  Because they regulate the genomic information by mechanisms like RNA interference, these sRNomes add important bricks to our understanding of the success of the parasitic lifestyle. We could show that Cuscuta campestris contains a number of novel microRNAs (miRNAs) in addition to a conspicuous retention of miRNAs that are typically lacking in other Solanales, while several typically conserved miRNAs seem to have become obsolete in the parasite. One new miRNA appears to be derived from a horizontal gene transfer event, a process never reported in plants for the acquisition of new miRNA sequences. The exploratory miRNome (exploratory due to the absence of a full genomic sequence for reference) from the root parasitic Orobanche aegyptiaca also revealed a loss of a number of miRNAs compared to established miRNomes of photosynthetic species from the same order. In summary, our study shows for both parasites partly similar evolutionary signatures in the RNA silencing machinery. Our data bear proof for the dynamism of this regulatory mechanism in parasitic plants.

overall_design: Sequencing of small RNAs and PARE/Degradome/5'P RNA sequencing.

first: Kirsten

last: Krause


title: Developmental and aging atlas by single cell mRNA-seq

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

sample_organism:
Drosophila melanogaster
Danio rerio
Mus musculus

overall_design: Refer to individual Series


title: Maturation and circuit integration of transplanted human cortical organoids

city: Stanford

first: Kevin

last: Kelley

state: CA

address: 318 Campus Drive

institute: Stanford University

summary: We show that human stem cell-derived cortical organoids transplanted into the somatosensory cortex of newborn athymic rats develop mature cell types that integrate into sensory and motivation-related circuits. Magnetic resonance imaging allows monitoring of post-transplantation organoid growth across multiple stem cell lines and animals, while single nucleus profiling reveals high cell diversity and progression of corticogenesis, as well as the emergence of an activity-dependent transcriptional program in neurons.

overall_design: single nucleus RNA-sequencing of transplanted human cortical organoid and age matched cortical organoid

first: Omer

last: Revah

first: Felicity

last: Gore

middle: W

first: Jimena

last: Andersen

first: Noriaki

last: Sakai

first: Xiaoyu

last: Chen

first: Min-Yin

last: Li

first: Fikri

last: Birey

first: Xiao

last: Yang

first: Nay

middle: L

last: Saw

first: Samuel

last: Baker

first: Neal

middle: D

last: Amin

first: Shravanti

last: Kulkarni

first: Rachana

last: Mudipalli

first: Bianxiao

last: Cui

first: Seiji

last: Nishino

first: Gerald

middle: A

last: Grant

first: Juliet

middle: K

last: Knowles

first: Mehrdad

last: Shamloo

last: Huguenard

first: Karl

last: Deisseroth

first: Sergiu

middle: P

last: Pașca


title: Identification and Comparative Analysis of Genes and MicroRNAs Involved in the Floral Transition of the Xinjiang Early-Flowering Walnut (Juglans regia L.)

city: Alar

first: Qiang

last: Jin

email: jqzky@163.com, qiangjin@taru.edu.cn

address: Alar 843300, China

institute: College of Horticulture and Forestry，Tarim University

summary: For tree crops, shortening juvenile phase is a vital strategy for early flowering that ensure to bear fruits in advance to enhance breeding efficiency. In walnut (Juglans regia L.), it usually takes 3-5 years for blooming, but the early flowering (EF) walnut can even flower in a year after planted. The juvenile phase of EF walnut is shorter than the late flowering (LF) walnut, which is more propitious to breeding efficiency. In this study, using RNA sequencing (RNA-seq) and microRNA-seq, we profiled transcriptome-wide identification of gene expression and microRNAs between EF and LF walnuts.

overall_design: RNA-seq in Xinjiang Precocious Walnut and common walnut with three replicates

first: Rongli

last: Mo

first: Wenxin

last: Chen

first: Qinglin

last: Zhang

first: Fang

last: Sheng

first: Cuiyun

last: Wu

first: Rui

first: Zhengrong

last: Luo


title: A compendium of expression profiles for Corynebacterium glutamicum ATCC13032

city: Juelich

first: Tino

last: Polen

state: NRW

address: Wilhelm-Johnen-Str 1

department: IBG-1: Biotechnology

country: Germany

institute: Forschungszentrum Jülich GmbH


title: Genome-wide transcriptome analysis of human iPSC-derived migratory cortical interneurons.

city: Greenville

first: Weihua

last: Huang

state: North Carolina

address: 600 Moye Blvd, Brody 7S-24

department: Pathology

institute: East Carolina University

summary: We report changes of gene expression in migratory cortical interneurons derived from healthy control vs schizophrenia iPSCs by genome-wide transcriptome analysis.

overall_design: RNA sequencing analysis (bulk) of healthy control interneurons and schizophrenia interneurons. Five independent iPS lines per group (totally 10 iPSC lines) for migrated interneurons and three iPSC lines per group (totally 6 iPSC lines) for those that have not migrated.

first: Sangmi

last: Chung


title: A compendium of expression profiles for Corynebacterium glutamicum ATCC13032 [no raw data]

summary: Transcriptional profiling of C. glutamicum wild-type and mutant strains grown under different conditions.

overall_design:
Wild type and mutant strains were cultivated under different conditions and the mRNA levels of the samples were compared to those of respective control strains.
Raw data are not available for samples in this series.

first: Angela

last: Kranz

first: Michael

last: Bott


title: Comparison of Corynebacterium glutamicum wild type with C. glutamicum ChrS-Ala245fs

summary: In an evolutionary experiment on high hemin concentrations, a frameshift mutation in the ChrS gene was figured out to be striking in survival at high hemin concentrations (Ala245fs). Apart from high upregulation of heme exporter hrtB, microarrays should reveal further different controlled genes compared to the WT.

platform_organism: Bacillus subtilis subsp. subtilis str. 168

platform_organism: Escherichia coli str. K-12 substr. MG1655

overall_design: The aim was to identify genes differentially expressed genes between the C. glutamicum ChrS-Ala245fs mutant and WT reference strain. Triplicate experiments inlcuding a color swap were carried out.

first: Aileen

last: Krüger

first: Julia

last: Frunzke


title: Lung gene expression profiling during acute lung injury and its modulation by IL-17A and IFN-gamma

status: Public on Jul 21 2022

city: New Haven

first: Govindarajan

last: Rajagopalan

state: CT

address: 300 Cedar Street

institute: Yale University

summary:
HLA-DR3, HLA-DR3.IL17A knockout and HLA-DR3.IFN-gamma knockout (KO) mice were challenged intraperitoneally with 10 microgram of staphylococcal enterotoxin B. 4 and 24 hours later mice were euthanized, lungs harvested, RNA extracted and processed for gene expression analysis using Clariom S arrays in comparison to respective naive mice
After transcardial perfusion of mice with 10 ml of PBS, lungs were removed, Total RNA was extracted from perfused lungs at 4- and 24- hours after SEB challenge. Gene expression profiling was determined using mouse Clariom S arrays at ThermoFisher Corporation in comparison to respective naive mice.

overall_design: Acute lung injury was induced in eight- to sixteen-week-old male and female mice by intraperitoneal injection of 10 micrograms of endotoxin-reduced staphylococcal enterotoxin B (SEB) (Toxin Technologies, Sarasota, FL) in PBS.

first: Jon

last: Koff


title: Insulin signaling in the long-lived reproductive caste of ants

status: Public on Jul 27 2022

first: Claude

last: Desplan

state: NY

address: 24 Waverly Place, Waverly Bldg 6th Floor

department: Biology

institute: New York University

summary: In most organisms, reproduction is correlated with shorter lifespan. However, the reproductive queen in eusocial insects exhibits much longer lifespan than workers. In Harpegnathos ants, when the queen dies, workers can undergo an adult caste switch to reproductive pseudo-queens (gamergates) exhibiting a 5X prolonged lifespan. To explore the relation between reproduction and longevity, we compared gene expression during caste switching. Insulin expression is increased in the gamergate brain that correlates with increased lipid synthesis and production of vitellogenin in the fat body, both transported to the egg. This results from activation of the mitogen-activated protein kinase (MAPK) branch of the insulin signaling pathway. In contrast, the production in the gamergate developing ovary of anti-insulin Imp-L2 leads to decreased signaling of the AKT/FOXO branch in the fat body, consistent with their extended longevity.

overall_design: Samples were collected from three tissues of the Harpegnathos saltator ants. Tissue-specific gene expression profiles were generated from three different ant castes (workers[W], gamergates[G] and revertants[R]). Three different tissues consist of abdominal fat body, ovary, and non-visual brain from each individuals (total of four individuals).

first: Hua

last: Yan

first: Comzit

last: Opachaloemphan

first: Francisco

last: Carmona-Aldana

first: Giacomo

last: Mancini

first: Jakub

last: Mlejnek

first: Nicolas

last: Descostes

first: Bogdan

last: Sieriebriennikov

first: Alexandra

last: Leibholz

first: Xiaofan

last: Zhou

first: Long

last: Ding

first: Maria

last: Traficante

first: Danny

last: Reinberg


title: Three distinct Atoh1 enhancers cooperate for sound receptor hair cell development [CUT&RUN]

city: Beijing

first: Du

last: Yi

state: Beijing

address: No. 1 West Beichen Road

institute: Institute of Genetics and Developmental Biology Chinese Academy of Sciences

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Cochlear hair cells (HCs) in the inner ear are responsible for sound detection. For HC fate specification, the master transcription factor Atoh1 is both necessary and sufficient. Atoh1 expression is dynamic and tightly regulated during development, but the cis-regulatory elements mediating this regulation remain unresolved. Unexpectedly, we found that deleting the only recognized Atoh1 enhancer, defined here as Eh1, failed to impair HC development. By using ATAC-seq (assay for transposase-accessible chromatin with high-throughput sequencing), we discovered two additional Atoh1 enhancers: Eh2 and Eh3. Notably, Eh2 deletion was sufficient for impairing HC development, and concurrent deletion of Eh1 and Eh2 or all three enhancers resulted in nearly complete absence of HCs. Lastly, we showed that Atoh1 binds to all three enhancers, consistent with its autoregulatory function. Our findings reveal that the cooperative action of three distinct enhancers underpins effective Atoh1 regulation during HC development, indicating potential therapeutic approaches for HC regeneration.

overall_design: Examination of genome wide chromatin accessibility in mouse P1 cochlear hair cells and P7 cerebellar granule neuron progenitors and Atoh1 binding sites in mouse P1 cochlear hair cells. For ATAC-seq, 2 replicates are involved. Each replicate contain 500 FACS purified cochlear hair cells or cerebellar granule neuron progenitors from Atoh1-3×V5-P2A-tdTomato/+ mouse strain. For CUT&RUN, Atoh1-GFP mouse strain was used and each replicate contain 2-3 fresh cochlear tissue. rabbit anti-GFP and rabbit anti-mouse IgG antibody was used for experimental and control group, respectively.

first: Zhengnan

last: Luo

first: Yi

last: Du

first: Shuting

last: Li

first: He

last: Zhang

first: Muya

last: Shu

first: Di

first: Shunji

last: He

first: Guangqin

last: Wang

first: Falong

last: Lu

first: Zhiyong

last: Liu


title: Gene expression in p62/SQSTM1-silenced A549 cells.

city: London

first: John

last: Di Guglielmo

state: ON

address: 1151 Richmond Street

department: Physiology and Pharmacology

country: Canada

institute: UWO

summary: We used microarrays to detail the programme of gene expression in control or p62/SQSTM1-silenced A549 cells.

overall_design: A549 cells were transfected with control siRNA (si CONTROL) or siRNA targetting p62/SQSTM1.  After 24 hours, total RNA was extracted and analyzed using Affymetrix microarrays.

first: C

middle: B

last: Trelford

first: E

last: Ng

first: CI

last: Campbell

first: G


title: A compendium of expression profiles for Corynebacterium glutamicum ATCC13032 [with raw data]

first: Tino

last: Polen

overall_design:
Wild type and mutant strains were cultivated under different conditions and the mRNA levels of the samples were compared to those of respective control strains.
All samples in this series include raw data files.

first: Angela

last: Kranz

first: Michael

last: Bott


title: PD-1+TCF-1+ stem-like CD8 T cells differentiate into effector T cells with enhanced anti-tumor and viral efficacy upon PD-1 cis-targeted IL-2R-agonism”

city: Atlanta

first: Haydn

last: Kissick

state: Georgia

address: 1462 Clifton Rd

institute: Emory University

summary: Here we show that IL-2Rbg-biased agonists are unable to preferentially expand better effector T cells in cancer models, and describe PD1-IL2v, a novel immunocytokine, that overcomes the need for CD25 binding by docking in cis to PD-1. In cis binding of PD1-IL2v to PD-1 and IL-2Rbg on the same cell recovers the ability to differentiate stem-like CD8 T cells into better effectors in the absence of CD25 binding in both chronic infection and cancer models, and provides superior efficacy.

overall_design: RNA-seq

first: Masao

last: Hashimoto


title: Three distinct Atoh1 enhancers cooperate for sound receptor hair cell development [ATAC-seq]

first: Du

last: Yi

first: Zhengnan

last: Luo

first: Yi

last: Du

first: Shuting

first: He


title: Human Tau Mutations in Cerebral Organoids Induce a Progressive Dyshomeostasis of Cholesterol

city: Santa Barbara

first: Stella

middle: M. K.

last: Glasauer

address: Biological Sciences II

department: Neuroscience Research Institute

institute: University of California Santa Barbara

summary: Mutations in the MAPT gene that encodes tau lead to frontotemporal dementia (FTD) with pathology evident in both cerebral neurons and glia. Human cerebral organoids (hCOs) from individuals harboring pathogenic tau mutations can reveal the earliest downstream effects on molecular pathways within a developmental context generating interacting neurons and glia. We found that in hCOs carrying the V337M and R406W tau mutations, the cholesterol biosynthesis pathway in astrocytes was the top upregulated gene set compared to isogenic controls by scRNAseq. The 15 upregulated genes included HMGCR, ACAT2, STARD4, LDLR, and SREBF2. This result was confirmed in a homozygous R406W mutant cell line, by immunostaining and sterol measurements. Cholesterol abundance in the brain is tightly regulated by efflux and cholesterol biosynthetic enzyme levels in astrocytes, and dysregulation can cause aberrant phosphorylation of tau. Our findings suggest that cholesterol dyshomeostasis is an early event in the etiology of neurodegeneration caused by tau mutations.

overall_design: Droplet-based single-cell RNA sequencing was performed on cerebral organoids carrying MAPT V337M and R406W mutations, their isogenic controls and organoids carrying homozygous R406W mutation. Organoids were sampled at ages 1-8 months.

first: Kenneth

last: Kosik


title: Repurposing E3 ubiquitin ligases as cell surface protein degraders using Proteolysis Targeting Antibodies

city: South San Francisco

first: Matthew

last: Grimmer

address: 1 DNA Way

department: Discovery Oncology

institute: Genentech

summary: The majority of current therapeutics targeting plasma membrane receptors function by antagonizing ligand binding or enzymatic activities. Typical mammalian proteins, however, consist of multiple domains executing discrete but coordinated activities, and saturating inhibition of one functional domain often incompletely suppresses the totality of the protein’s function. Recent work on targeted protein degradation technologies including Proteolysis Targeting Chimeras (PROTACs) has highlighted clinically important distinctions between target inhibition and target degradation. However, the generation of heterobifunctional compounds requiring linkage of two small molecules, each with high affinity for their targets, is highly complex, particularly with respect to achieving oral bioavailability. Here we describe the development of Proteolysis Targeting Antibodies (PROTABs) that tether cell-surface E3 ubiquitin ligases to transmembrane proteins, resulting in target ubiquitination and subsequent degradation. PROTAB-mediated degradation drives deeper pathway inhibition than inhibitory antibodies and is functional in vivo. The scope of this technology is also demonstrated through the identification  of additional cell surface E3 ubiquitin ligases that can function as “on demand” degraders of various cell surface proteins. The generality of this approach enables tissue-selective degradation, as suggested by the Wnt-responsive ligases RNF43 and ZNRF3. Furthermore, through engineering of various optimized antibody formats, we offer insights on the ground rules governing optimal target degradation. Taken together, this work describes a strategy for the rapid development of potent, bioavailable and tissue selective degradation of cell surface proteins.

overall_design: As a prototypical model of aberrant Wnt signaling, we generated mouse intestinal organoids and used CRISPR/Cas9 to introduce a frame shift truncation in the Adenomatous Polyposis Coli (APC) gene, which leads to Wnt pathway hyperactivation and colon cancer initiation. We performed RNA seq and compared expression of genes in normal and APC mutant colon murine organoids.

first: Felipe

last: de Sousa e Melo

first: Matt

first: Hadir

last: Marei

first: Fred

last: de Sauvage


title: Transcriptome analysis of nkd1 and nkd2 mutants in W22 maize endosperm

city: Ithaca

first: Hao

last: Wu

address: 236 Tower Rd, Plant Science Building Room #236

institute: Cornell University

summary: The maize NAKED ENDOSPERM (NKD) genes Nkd1 and Nkd2 encode paralogous INDETERMINATE DOMAIN (IDD) transcription factors (TFs) that have previously been shown to play critical roles in regulating endosperm gene expression and development. However, the function of each individual NKD protein is unclear. To elucidate this,  we performed a transcriptome analysis for nkd1-Ds and nkd2-Ds single mutant endosperm. We found that in nkd1-Ds single mutant, nkd2 gene expression is significantly lower than WT, and similar to the nkd2-Ds mutant.

overall_design: Transcriptomes 16 DAP endosperm from WT, nkd1-Ds and nkd2-Ds single mutant were profiled and analyzed.  All in a W22 inbred genetic background and 4 biological replicates were conducted for each genotype.

first: Junpeng

last: Zhan

first: Philip

last: Becraft

first: Ramin

last: Yadegari


title: Laser-capture microdissection and RNA sequencing of aleurone and starchy endosperm of maize R1 genotypes

summary: Three homozygous R1 genotypes, R1-g (WT), R1-sc and r1-m3 were laser microdissected and sequenced. The data showed that in aleurone (AL), expression of R1 in R1-sc and r1-m3 is higher than R1-g, and R1 is ectopically expressed in starchy endosperm (SE) in R1-sc and r1-m3. Interestingly, the ectopic expression of R1 in SE may be associated with RNA splicing process.

overall_design: Transcriptomes of AL and SE of 19 DAP endosperm from R1-g (WT), R1-sc and r1-m3 were profiled and analyzed.  All in a W22 inbred genetic background and 3 biological replicates were conducted for each tisssue type and genotype.

first: Guosheng

last: Li

first: Shanshan

last: Zhang

first: Brandon

last: Beall


title: scRNA-seq of mouse cardiac CD45+ cells with CITE-seq and cell Hashing II

city: Würzburg

first: Antoine-Emmanuel

last: Saliba

address: Josef-Schneider-Straße 2 / D15

institute: Helmholtz Institute for RNA-based Infection Research

summary: We performed scRNA-seq and CITE-seq of CD45+ cells extracted from the steady state mouse heart, and at 5 days after myocardial infarction in wildtype and Trem2 deficient mice

overall_design: Myocardial infarction (MI) was induced by permanent coronary artery ligation in Trem2+/+ (wildtype) and Trem2-/- mice. Non-infarcted wildtype mice (n=2), non-infarcted Trem2-/- mice (n=3), wildtype mice at day 5 after myocardial infarction (n=5) and Trem2-/- mice at day 5 after myocardial infarction (n=5received an i.v. injection of 2.5µg anti-CD45.2 APC (clone 104, Biolegend, cat. # 109814) under isoflurane anesthesia. The heart was perfused via intracardiac injection of PBS, excised, the right ventricle removed, and the infarct, peri-infarct area, and adjacent viable myocardium were collected, weighed and digested for 1 hour at 37°C under agitation in RPMI containing 450U/ml collagenase I (Sigma-Aldrich, #C0130), 125U/ml Collagenase XI (Sigma-Aldrich C7657), 60U/ml Hyaluronidase (Sigma-Aldrich, H3506) , 60U/ml DNAse (Roche #11284932001). Cells were washed twice in MACS buffer (PBS+0.5% BSA+2mM EDTA) and incubated for 5 minutes on ice with TruStain FcX™ (anti-mouse CD16/32, Biolegend #101320, 10µg/ml). Afterwards, cells were incubated with anti-VSIG4-PE (clone NLA-14, final concentration 2µg/ml, ThermoFisher #12-5752-82),  anti-LYVE1-Biotin (clone ALY7, 5µg/ml, ThermoFisher #13-0443-82), mouse CD45 microbeads (Miltenyi, 130-052-301, 1:10 final concentration), anti-mouse CD45.2-AlexaFluor488 (Trem2+/+ heart samples, clone 104, 2µg/ml, Biolegend) or anti-mouse CD45.2-Alexa700 (Trem2-/- heart samples, clone 104, 2µg/ml, Biolegend). After 10’ incubation at 4°C, TotalSeq-A hashtag antibodies were added as follows: Hashtag 1-2: WT no MI; Hashtag 3, 4 and 15: Trem2-/- no MI;  Hahstag 5, 6, 7, 8, 9: wildtype MI day 5; Hashtag 10, 11, 12, 13, 14: Trem2-/- MI day 5. Cells were incubated for an additional 15 minutes at 4°C, washed twice in MACS buffer, pooled, and magnetic selection was performed using LS Columns (Miltenyi (# 130-042-401) and MidiMACS separators (Miltenyi # 130-042-302). Sorted CD45+ cells were washed twice with PBS containing 0.04% BSA (Sigma-Aldrich A1595), and incubated for 25’ at 4°C in PBS/0.04% FCS containing Fixable Viability Dye eFluor™ 780 (ThermoFisher #65-0865-14, 1:1000) and anti-mouse TotalSeqA-Antibodies. Cells were washed with PBS/0.04% FCS, resuspended and sorted using a BD FACS Aria III with a 100µm nozzle. Cells from steady state hearts (~50% Trem2+/+ and ~50% Trem2-/-) and from day 5 post-MI hearts (~50% Trem2+/+ and ~50% Trem2-/-) were sorted separately and pooled post-sort so that steady state and day 5 post-MI cells represent ~30% and ~70% of the total cell pool, respectively. 20,000-25,000 cells were loaded in the 10x Genomics Chromium in duplicate lanes.

first: Panagiota

last: Arampatzi

first: Clément

last: Cochain


title: ChIP sequencing following infection with CoV-02 Orf8 or ARKSAP KO

city: Philadelphia

first: Karl

middle: Michael

last: Glastad

state: PA

address: 3400 Civic Center Blvd, Bldg 421

department: CDB

institute: University of Pennsylvania

summary: ChIP sequencing performed on A549 cells following either Mock infection, infection with WT SARS-CoV-02, or infection with SARS-CoV-02 with Orf8 or ARKSAP deletion

overall_design: Genome wide profiling of H3K9ac, sonication Input control, from two to three biological replicates of A549 cells infected with SARS-CoV-02 with or without deletion of Orf8 or ARKSAP

first: Erica

last: Korb


title: ChIP sequencing following infection with CoV-02 Orf8 KO

summary: ChIP sequencing performed on A549 cells following either Mock infection, infection with WT SARS-CoV-02, or infection with SARS-CoV-02 with Orf8 deletion

overall_design: Genome wide profiling of three histone modifications, sonication Input control, from three biological replicates of A549 cells infected with SARS-CoV-02 with or without deletion of Orf8


title: scRNA-seq of mouse cardiac CD45+ cells with CITE-seq and cell Hashing

summary: We performed scRNA-seq and CITE-seq of CD45+ cells extracted from the steady state mouse heart, and at 5 days after myocardial infarction with or without depletion of CCR2+ cells

overall_design: Mice were treated daily with a monoclonal anti-CCR2 (MC-21, i.p. 20µg/mouse/injection) or with an isotype control antibody (rat IgG2b, clone LTF-2, BioXcell # BE0090) starting 1 day before the induction of myocardial infarction (MI) to deplete circulating CCR2+ monocytes. Mi was induced by permanent coronary artery ligation. Control mice (steady state heart, n=3), day 5 post-MI isotype control treated mice (n=4), and day 5 post-MI anti-CCR2 treated mice (n=5) received an i.v. injection of 2.5µg anti-CD45.2 APC (clone 104, Biolegend, cat. # 109814) under isoflurane anesthesia. The heart was perfused via intracardiac injection of PBS, excised, the right ventricle removed, and the infarct, peri-infarct area, and adjacent viable myocardium were collected, weighed and digested for 1 hour at 37°C under agitation in RPMI containing 450U/ml collagenase I (Sigma-Aldrich, #C0130), 125U/ml Collagenase XI (Sigma-Aldrich C7657), 60U/ml Hyaluronidase (Sigma-Aldrich, H3506) , 60U/ml DNAse (Roche #11284932001). Cells were washed twice in MACS buffer (PBS+0.5% BSA+2mM EDTA) and incubated for 5 minutes on ice with TruStain FcX™ (anti-mouse CD16/32, Biolegend #101320, 10µg/ml). Afterwards, cells were incubated with anti-VSIG4-PE (clone NLA-14, final concentration 2µg/ml, ThermoFisher #12-5752-82),  anti-LYVE1-Biotin (clone ALY7, 5µg/ml, ThermoFisher #13-0443-82), mouse CD45 microbeads (Miltenyi, 130-052-301, 1:10 final concentration), anti-mouse CD45.2-eFluor506 (steady state heart samples, clone 104, 2µg/ml, ThermoFisher #69-0454-82), anti-mouse CD45.2-AlexaFluor488 (MI Day 5 isotype samples, clone 104, 2µg/ml, Biolegend #109816), anti-mouse CD45.2-BV421 (MI Day 5 isotype samples, clone 104, 2µg/ml, Biolegend #109832). After 10’ incubation at 4°C, TotalSeq-A hashtag antibodies (Biolegend, see table for CITE-seq panels) were added as follows: Hashtag 1 to 3: steady state heart; Hashag 4 to 7: MI Day 5, isotype control treated; Hashtag 8 to 12: MI Day 5, anti-CCR2 treated. Cells were incubated for an additional 15 minutes at 4°C, washed twice in MACS buffer, pooled, and magnetic selection was performed using LS Columns (Miltenyi (# 130-042-401) and MidiMACS separators (Miltenyi # 130-042-302). Sorted CD45+ cells were washed twice with PBS containing 0.04% BSA (Sigma-Aldrich A1595), and incubated for 25’ at 4°C in PBS/0.04% FCS containing Fixable Viability Dye eFluor™ 780 (ThermoFisher #65-0865-14, 1:1000) and anti-mouse TotalSeqA-Antibodies. Cells were washed with PBS/0.04% FCS, resuspended and sorted using a BD FACS Aria III with a 100µm nozzle. Number of sorted cells was adjusted so that cells from steady state hearts (CD45.2-e506+), MI Day 5 isotype-treated hearts, and MI day 5 anti-CCR2-treated hearts represent 20%, 40% and 40% of all cells, respectively. Cells were resuspended, counted (final concentration 1,200 cells/µl) and 20,000 cells were loaded in the 10x Genomics Chromium in duplicate lanes, and scRNA-seq ADT and HTO libraries were prepared.


title: E6/E7 from Beta-2-HPVs 122, 38b and 107 possess transforming properties in a fibroblast model in vitro

city: Guadalajara

first: Adriana

middle: Del Carmen

last: Aguilar Lemarroy

state: Jalisco

address: Sierra Mojada 800, Independencia Oriente, 44340 Guadalajara, Jal.

department: División de Inmunología

country: Mexico

institute: Centro de Investigación Biomédica de Occidente

summary:
This analysis was performed with the aim of finding the genes differentially expressed in fibroblasts transduced with the E6/E7 genes of HPV 16, 18, 38b, 107 and 122. The name given for the samples are as follows: FB-E6E7-16, FB-E6E7-18,  FB-E6E7-38b,  FB-E6E7-107, FB-E6E7-122, and for fibroblasts transduced with the empty lentiviral vector pLVX, they were referred as FB-pLVX.
Methods: Library construction and Illumina NovaSeq 6000  sequencing was performed by Novogene Bioinformatics Technology Co., Ltd, Beijing, China, on HPV 16, 18, 38b, 107 and 122 E6E7 Transduced Fibroblasts; three independently  mRNA sequences were performed for each of the cell models. Bioinformatics analyses were performed as follows: raw reads were analyzed using the open source Galaxy platform (https://www.usegalaxy.org) and RStudio software (2021.09.0). The quality of the reads was checked using the FastQC tool, and the Trimmomatic tool was used to remove ambiguous nucleotides. Subsequently, all clean reads were mapped to the human genome reference (hg38 vs 38) using Rsubread for RStudio. Once all BAM files were obtained, reads were counted using the featureCounts tool, and gene expression analysis was performed using the DESeq2 tool. The gene expression level was normalized using the fragments per kilobase of transcript per million mapped reads (FPKM) method. Data validation was performed by real-time PCR.
Conclusions: Our study represents the first analysis of genes differentially expressed by the E6/E7 proteins of HPV genus Beta-2 (38b, 107 and 122), through RNA-seq technology. This study shows the transforming potential that genotypes of the Beta-2 genus, especially HPV122, also possess. These Beta-2 HPVs can modulate some of the genes that are well known to be regulated by Alpha-HPVs 16 and 18.

overall_design: Total RNA extraction was performed from cell models obtained from fibroblasts infected with viral particles containing the E6/E7 genes of HPV 16, 18, 38b, 107 and 122 in triplicate. Fibroblasts transduced with HPV 16 and 18 were used as positive controls, due to their known cellular transformation properties. Primary fibroblasts transduced with the empty- pLVX-vector were used as basal controls, with which all our cell models were compared. To obtain the differential expression of the genes, a comparison of the six replicates of FB-pLVX with the three replicates of each of the cell models was performed.

last: Aguilar -Lemarroy

first: Luis

last: Jave-Suarez

first: Aribert

last: Castro-Amaya


title: RNA sequencing of undifferentiated iPS cells after culturing under graded zinc concentrations

city: Yokohama

first: nobuaki

last: shiraki

address: 4259-B-25 Nagatsuta-cho, Midori-ku

institute: Tokyo Institute of Technology

summary: From our RNA-seq results, the metallothionein family members and several members of the mitochondrial ribosomal protein gene family are the top genes that are upregulated by increasing Zn concentration in human iPS cells.

overall_design: To understand the impact of zinc in undifferentiated human induced pluripotent stem cells, RNA sequencing (RNA-seq) was performed, analyzing the global expression profile of pluripotent human iPS cells after culturing for 48 h under graded concentrations of Zn (0,0.5, 3, and 10 µM).

first: Nobuaki

last: Shiraki

first: Erinn

middle: Z

last: Sim


title: Expression data from undifferentiated human iPS cell line, 201B7

summary:
In undifferentiated human ES cells, 5hr Met deprivation (delta Met) led to decreased proliferation, and promote differentiation
We used microarrays to detail the mollecular mechanism of cell-death caused by Met deprivation in undifferentiated iPS cells.

overall_design: Cells were harvested at undifferentiated stages for RNA extraction and hybridization on Affymetrix microarrays. We performed gene expression profiles of undifferentiated iPS cells cultured in complete (comple), each essential amino acid deprivation for 5 hr.

first: Tomonori

last: Tsuyama


title: RNAseq analysis of SARS-CoV-2 infection of A549ACE cells with dARKSAP virus

status: Public on Jul 20 2022

state: PENNSYLVANIA

address: 3400 Civic Center Boulevard

summary: Analysis of histone mimicry by SARS-CoV-2 Orf8 encoded protein

overall_design: SARS-CoV-2 WT virus, Orf8 deletion virus, or mock infection of A549-ACE cells was performed and RNA was collected at 24 or 48 hours after infection


title: ATACseq analysis of A549 cells infected with SARS-CoV-2 with dARKSAP virus Set 3

overall_design: A549 cells were WT SARS-CoV-2, SARS-CoV-2 with an Orf8 deletion, or mock infection and isolated 48 hours after insfection for ATAC-seq


title: NimbleGen Rat Gene Expression Microarrays for 2 samples (icariin/DMSO-treated BMSC)

city: Shanghai

first: Hongmeng

last: Yu

address: No.83, Fenyang Road

department: Department of Otolaryngology

institute: Eye & ENT Hospital, Fudan University

summary:
Total RNA from each sample was quantified by the NanoDrop ND-1000 and RNA integrity was assessed by standard denaturing agarose gel electrophoresis. Total RNA of each sample was used for labeling and array hybridization as the following steps: 1) Reverse transcription with by Invitrogen Superscript ds-cDNA synthesis kit; 2) ds-cDNA labeling with NimbleGen one-color DNA labeling kit; 3) Array hybridization using the NimbleGen Hybridization System and followed by washing with the NimbleGen wash buffer kit; 4) Array scanning using the Axon GenePix 4000B microarray scanner (Molecular Devices Corporation).
Scanned images (TIFF format) were then imported into NimbleScan software (version 2.5) for grid alignment and expression data analysis. Expression data were normalized through quantile normalization and the Robust Multichip Average (RMA) algorithm included in the NimbleScan software. The Probe level (*_norm_RMA.pair) files and Gene level (*_RMA.calls) files were generated after normalization. The 2 gene level files were imported into Agilent GeneSpring GX software (version 11.5.1). Genes that have values greater than or equal to lower cut-off: 100.0 in that at least 1 out of 2 samples (“All Targets Value”) were chosen for data analysis.

overall_design: Examing 2 conditions, each with 1 replicate

first: Yuqiong

last: Wu


title: Aging-regulated TUG1 is dispensable for endothelial cell function

city: bad nauheim

first: Stefan

last: Günther

address: ludwigtr. 43

institute: MPI for heart and lung research

summary: The evolutionary conserved Taurine Upregulated Gene 1 (TUG1) is a ubiquitously expressed gene that is one of the highest expressed genes in human and rodent endothelial cells (ECs). We here show that TUG1 expression decreases significantly in aging mouse carotid artery ECs and human ECs in vitro, indicating a potential role in the aging endothelial vasculature system. We therefore investigated if, and how, TUG1 might function in aging ECs, but despite extensive phenotyping found no alterations in basal EC proliferation, apoptosis, barrier function, migration, mitochondrial function, or monocyte adhesion upon TUG1 silencing in vitro. TUG1 knockdown did slightly and significantly decrease cumulative sprout length upon vascular endothelial growth factor A stimulation in human umbilical vein endothelial cells (HUVECs), though TUG1-silenced HUVECs displayed no transcriptome-wide mRNA expression changes explaining this effect. Further, ectopic expression of the highly conserved and recently discovered 153 amino acid protein translated from certain TUG1 transcript isoforms did not alter angiogenic sprouting in vitro. Our data show that, despite a high expression and strong evolutionary conservation of both the TUG1 locus and the protein sequence it encodes, TUG1 does not seem to play a major role in basic endothelial cell function.

overall_design: 3 control samples + 3 knockdown samples

first: Anna

middle: T

last: Gimbel

first: Günther

last: Stefan

first: Tamer

last: Ali


title: Primary Murine Macrophages as a Tool for Virulence Factor Discovery in Coxiella burnetii

city: Laramie

first: Elizabeth

middle: Di Russo

last: Case

state: WY

address: 1174 Snowy Range Rd

department: Veterinary Sciences

institute: Univeristy of Wyoming

summary: Phenotypic analysis of murine bone marrow derived macrophages upon infection with C. burnetii

overall_design: We then performed gene expression profiling analysis using data obtained from RNA-seq of murine bone marrow derived macrophages infected with C. burnetii cells at two time points.

first: Saugata

last: Mahapatra

first: Caitlyn

last: Hoffpauir

first: Kranti

last: Konganti

first: Andrew

last: Hillhouse

first: James

middle: E

last: Samuel

first: Erin

last: van Schaik


title: ATACseq analysis of A549 cells infected with SARS-CoV-2 with dARKSAP virus Set 2

first: Erica

last: Korb


title: CUT&TAG seq analysis of HEK cells transfected with SARS-CoV-2 protein Orf8

overall_design: HEK cells were transfected with GFP or Orf8 and isolated 48 hours after transfection for CUT&TAG sequencing


title: Transcriptomic Changes in Microdissected CCDs after Three Hours Lipopolysaccharide (LPS) Administration in Rats

city: Taipei

first: Chih-Chien

last: Sung

state: Taipei

address: No 325, Section 2, Cheng-Kung Road,Neihu

department: Department of Medicine

country: Taiwan

institute: Tri-Service General Hospital, National Defense Medical Center

summary: Ureteral obstruction is marked by disappearance of the vasopressin-dependent water channel aquaporin-2 (AQP2) in the renal collecting duct and polyuria upon reversal. Most studies of unilateral ureteral obstruction (UUO) models have examined late time points, obscuring the early signals that trigger loss of AQP2.  Here, we performed RNA-Seq on microdissected rat cortical collecting ducts (CCDs) to identify early signaling pathways post-UUO. To address whether the induction of inflammatory signaling is a cause of loss of AQP2 expression, we directly induced inflammatory signaling in rats with lipopolysaccharide (LPS) administration

overall_design: Cortical collecting ducts were microdissected from the kidneys 3 hours after intraperitoneal injection with lipopolysaccharide (LPS) or Vehicle (normal saline) (n=3 versus n=3, paired). Microdissected tubules were subjected to small sample RNA-Seq analysis as previously described (PMID: 31146973).

first: Brian

last: Poll

first: Shih-Hua

last: Lin

first: Adrian

middle: R

last: Murillo-de-Ozores

first: Chung-Lin

last: Chou

first: Lihe

last: Chen

first: Chin-Rang

last: Yang

first: Min-Hsiu

first: Yu-Juei

last: Hsu

first: Mark

last: Knepper


title: ATACseq analysis of HEK cells transfected with SARS-CoV-2 protein Orf8

overall_design: HEK cells were transfected with GFP or Orf8 and isolated 48 hours after transfection for ATAC-seq


title: Landscape and age dynamics of immune cells in the Egyptian Rousette Bat

first: Antoine-Emmanuel

last: Saliba

summary: Bats harbor high-impact zoonotic viruses in absence of clinical disease, which has been recently associated with unique features of their immune system. They seem to restrict inflammation and possibly limit disease manifestation to a minimum. In-depth characterization of cellular immunity in bats is yet largely missing, and imprinting of age and development on immune cell compartments remains unexplored. We employed single-cell transcriptomics and established immunostaining panels to investigate the immune cell populations peripheral blood for juvenile and adult Egyptian Rousette bats (ERB).

overall_design: Total of 4 samples as 4 different 10x gene expression libraries prepared from ERB blood. Libraries A1  and A2 contain data about single-cell leukocytes extracted from peripheral blood of respectively three ERB adults and three ERB juveniles. Both blood collection and preparation of A1/A2 libraries were conducted on parallel on the same day. Library A5 contains data about single-cell leukocytes extracted from peripheral blood of one ERB adult and two ERB subadults. Library A6 contains data about single-cell leukocytes collected from the PBMC fraction of one ERB adult and two ERB subadults. Libraries A5 and A6 were prepared on the same day from the same 3 animals.

first: V

last: Friedrichs

first: C

last: Toussaint

first: A

last: Schäfer

first: M

last: Rissmann

first: T

middle: C

last: Mettenleiter

first: G

last: Pei

last: Balkema

last: Dorhoi


title: RNAseq analysis of SARS-CoV-2 infection of A549ACE cells

first: Erica

last: Korb


title: ChIPseq for NB4 cell line in either the absence or presence of GNE987

city: Suzhou

first: Fang

last: Fang

state: Jiangsu

address: 92 Zhongnan street

institute: Children’s Hospital of Soochow University

summary: Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to explore ChIPseq results for NB4 cell line.

overall_design: 2 NB4 sample as with no treatment and 1 NB4 sample with GNE987


title: Heat selection enables highly scalable methylome profiling in cell-free DNA for noninvasive monitoring of cancer patients [CRC]

city: Singapore

first: Lih Feng

last: Cheow

address: 4 Engineering Drive 3

department: Biomedical Engineering

country: Singapore

institute: National University of Singapore

type: Methylation profiling by high throughput sequencing

summary: Genome-wide analysis of cell-free DNA (cfDNA) methylation profile has been recognized as a promising approach for sensitive and specific detection of many cancers. However, scaling such genome-wide assays for clinical translation is impractical due to the high cost of whole genome bisulfite sequencing. We have shown that the small fraction of GC-rich genome is highly enriched in CpG sites and disproportionately harbors the majority of cancer-specific methylation signature. Here, we report on the simple but effective Heat enrichment of CpG-rich regions for Bisulfite Sequencing (Heatrich-BS) platform that allows for focused methylation profiling in these highly informative regions. Our novel method and bioinformatics algorithm enable accurate tumor burden estimation with high sensitivity and quantitative tracking of colorectal cancer patient’s response to treatment, at much reduced sequencing cost suitable for frequent monitoring. We also show, for the first time, tumor epigenetic subtyping from cfDNA using Heatrich-BS, which could enable patient stratification from non-invasive liquid biopsy. As such, Heatrich-BS holds great potential for highly scalable screening and regular monitoring of cancer using liquid biopsy.

overall_design: Analysis of GC content, CpG enrichment, methylation status and tumor burden determination in cell-free DNA of colorectal cancer patients

first: Elsie

last: Cheruba

first: Ramya

last: Viswanathan

first: Pui-Mun

last: Wong

first: Howard

middle: J

last: Womersley

first: Shuting

last: Han

first: Brenda

last: Tay

first: Yiting

last: Lau

first: Anna

last: Gan

first: Polly

middle: S

last: Poon

first: Anders

last: Skanderup

first: Sarah

last: Ng

first: Aik

middle: Y

last: Chok

first: Dawn

middle: Q

last: Chong

first: Iain

last: Tan

first: Lih

middle: F


title: RNAseq analysis of SARS-CoV-2 infection of iAT2 cells

first: Erica

last: Korb


title: RNAseq analysis of HEK293T expressing GFP, Orf8, or Orf8 with an ARKSAP deletion

overall_design: HEK293T cells were transfected with GFP, Orf8, or Orf8 with an ARKSAP deletion and RNA was collected at 48 hours after transfection


title: Analysis of histone mimicry by SARS-CoV-2 Orf8 encoded protein

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

overall_design: Refer to individual Series


title: Induced pluripotent stem cells display a unique set of MHC I-associated peptides shared by cancer cells

city: Montréal

first: Claude

last: Perreault

state: Québec

address: 2950, Chemin de Polytechnique

institute: Institute for Research in Immunology and Cancer

summary: We used a proteogenomic approach combining RNA-sequencing and mass spectrometry to study the MHC I-immunopeptidome specific to human iPSC samples. iPSCs were also analyzed after a 72h treatment with IFN-g (IFN-gamma) to boost MHC I levels and increase our chance for pluripotency-associated MHC I-associated peptide (paMAP) discovery. We identified 46 paMAPs which were absent from the RNA-seq of healthy somatic tissues and adult stem cells, but 40 of them were expressed in multiple cancer types from The Cancer Genome Atlas (TCGA). The antigens shared by iPSCs and tumors represent attractive targets for immunotherapy of poorly differentiated cancers.

overall_design: The RNA-Seq of hiPSCs was used to construct sample-specific databases for the mass spectrometry-based identification of MHC I-associated peptides. Data reported here are paired-end stranded RNA-sequencing (R1 map on reverse strand and R2 on forward strand for hiPSC22 and hiPSC22_IFN; R1 map on forward and R2 map on reverse strand for Fibro-iPSC.1 and Fibro-iPSC.2, with or without IFN-g), with a coverage > 170M reads per sample.

first: Anca

last: Apavaloaei


title: ATACseq analysis of A549 cells infected with SARS-CoV-2


title: Effects of body condition loss in lactating dairy cows on serum lipid profiles and the oocyte transcriptome

city: East Lansing

first: Peter

last: Schall

state: MI

address: 474 S. Shaw Lane

department: CMIB ANS

institute: Michigan State University

summary: The purpose of this data set was to examine the effects of excess body condition (BC) loss in dairy cattle during lactation on oocyte and cumulus cell transcriptomes. Cells were collected from dairy cattle that lost BC (L group) or maintained/gained BC (M/G group) during the first 30 days in milk (DIM).

overall_design: RNA-sequencing of oocyte and cumulus cells for two conditions: body condition loss (L), and maintain gain (MG).

first: Keith

last: Latham

first: Richard

last: Pursley

first: Meghan

middle: L

last: Ruebel

first: Lilian

last: Martins


title: Early molecular events mediating loss of aquaporin-2 in kidney collecting duct during ureteral obstruction

first: Chih-Chien

last: Sung

summary: Early stages of ureteral obstruction are marked by polyuria with impaired urinary concentrating ability, associated with loss of aquaporin-2 (AQP2) expression. Most mechanistic work in unilateral ureteral obstruction (UUO) models has been done at relatively late time points, making it difficult to discriminate the early effect on collecting ducts (CDs) in gene expression. Here, we use single-tubule RNA-Seq to identity signaling pathways at earlier time points after UUO in rat models.

overall_design: unilateral ureteral obstruction (UUO) and sham groups

first: Brian

last: Poll

first: Shih-Hua

last: Lin

first: Adrian

last: Murillo-de-Ozores

first: Chung-Lin

last: Chou

first: Lihe

last: Chen

first: Chin-Rang

last: Yang

first: Min-Hsiu

first: Yu-Juei

last: Hsu

first: Mark

middle: A

last: Knepper


title: Transcription analysis of blastocyst form oocyte exposed to the high level of NEFAs with cocultured of monolayer of GCs

city: Québec City

first: Marc-André

last: Sirard

state: Quebec

address: Offfice 2732, 2440 Hochelaga Blvd.

department: Sciences Animales

institute: Université Laval

summary: The transcriptome pattern in blastocyst that developed from oocytes exposed to the high level of NEFAs with cocultured of monolayer of GSs was investigated.  Genome-wide transcriptome analysis was performed by micro array using EDMA platform.

overall_design: Two condition experiment,  4 pools of 10 blastocysts, collected on Day 7 and Day 8

first: Meihong

last: Shi


title: Detailed analysis of dorsal-ventral gradients of gene expression in the rat hippocampus

status: Public on Jul 19 2022

city: Moscow

first: Alexander

last: Beletsky

address: Butlerova street, building 5a

country: Russia

institute: IHNA

summary: Dorsal and ventral parts of the hippocampus despite similar histological structure are known to be involved in performance of different functions. Previous studies using next generation sequencing showed that these two hippocampal parts differ in the expression of many genes, however, stability of dorsoventral gradient of gene expression remains open question. Here, we analyzed differential expression of genes between the dorsal and ventral hippocampus of rats in polyA-enriched samples and samples subjected to depletion of ribosomal RNA. We present here a detailed analysis of differentially expressed genes between the dorsal and ventral parts of the hippocampus. Intersection of our dataset with data of previous RNAseq studies revealed 544 genes are stably differentially expressed between the hippocampal parts suggesting that, despite strongly variability between the animals and sequencing approaches, there is a subset of genes whose expression stably differs between the dorsal and ventral hippocampus. Analysis of differential splicing showed that the dorsal and ventral parts of the hippocampus express 64 genes whose splice isoforms are different between the hippocampal parts. Furthermore, we show that depletion of ribosomal RNA increases representation of transposable elements in the RNAseq libraries and helps to detect a weak predominance of expression of these elements in the ventral hippocampus.

overall_design: 7 male rats were analyzed using polyA-enrichment RNAseq and 3 male rats were analyzed using RNAseq after depletion of ribosomal RNA. Dorsal and ventral parts of the hippocampus were dissected in every animal.

last: Beletskiy

first: Ekaterina

last: Positselskaya

first: Aliya

last: Vinarskaya

first: Yulia

last: Spivak

last: Dobryakova

first: Ilya

last: Tyulenev

first: Vladimir

last: Markevich

first: Alexey

last: Bolshakov


title: DNA methylation analysis of blastocyst form oocyte exposed to the high level of NEFAs when cocultured with monolayer of GCs

summary: The DNA methylation pattern in blastocyst that developed from oocytes exposed to the high level of NEFAs was investigated.  Genome-wide DNA methylation analysis was performed by micro array using EDMA platform.


title: DAXX-ATRX-H3.3 Regulation of p53 Chromatin Binding and DNA Damage Response [ATAC-Seq]

first: Priyankara

last: Wickramasinghe

address: 3601 Spruce Street

department: Bioinformatics

institute: The Wistar Institute

summary: DAXX and ATRX are tumor suppressor proteins that form a complex with histone H3.3 chaperone and are frequently mutated in cancers with the alternative lengthening of telomeres (ALT), such as pediatric glioblastoma.   Rapid loss of function of either DAXX or ATRX are not by themselves sufficient to induce the ALT phenotype.   However, cells lacking DAXX or ATRX can be readily selected for ALT-like features.  Here, we show that a key feature of ALT selected DAXX and ATRX null glioblastoma cells is the attenuation of p53 function.  RNA-seq analysis of DAXX or ATRX null U87 glioblastoma cells with ALT-like features revealed that p53 pathway is among perturbed.  ALT-selected DAXX and ATRX-null cells had aberrant response to DNA damaging agent etoposide.  Both DAXX and ATRX-null ALT cells showed a loss of p53 binding at a subset of response elements.   Complementation of DAXX null cells with wt DAXX rescued p53 binding and transcription, while the tumor associated mutation L130R, that disrupts ATRX binding, was incapable of rescuing p53 chromatin binding.  We show that histone H3.3 binding is reduced in DAXX-null cells especially at subtelomeric p53 binding sites and telomere repeats.   These findings indicate that DAXX and ATRX function to enable p53 chromatin binding through modulation of histone H3.3 binding, especially at sub-telomeric sites.

overall_design: ATAC-seq in DAXX/ATRX WT and DAXX KO or ATRX KO conditions in control or etoposide treated cells

first: Paul

last: Lieberman

first: Nitish

last: Gulve


title: Analysis of blastocyst form oocyte exposed to the high level of NEFAs with cocultured of monolayer of GCs


title: ChIP-seq to reveal the genomic binding landscape of Smad3 in renal tubular cells TCMK1

city: Luzhou

first: Honglian

last: Wang

state: Sichuan

address: No. 182, Chunhui Road, Longmatan District

department: Research Center for Integrative Medicine

institute: the Affiliated Traditional Medicine Hospital of Southwest Medical University

summary: Smad3 is an important downstream transcriptional factor of TGF-β signaling in the pathogenesis of renal fibrosis. Understanding the target genes is essential to decode the mechanism underlying Smad3-regulated renal fibrosis. To uncover the potential target genes of Smad3 in renal tubular cells, we applied the ChIP-seq technology to analyze the genomic chromatin binding landscape of Smad3 in TCMK-1 cells. The TCMK-1 cells of 90% confluence were starved in low-serum (0.5% FBS) medium for 6 h followed by stimulation with 5 ng/ml TGF-β1 for 30 min. The cells were harvested for ChIP assay. The precipitated chromatin was used for DNA isolation and deep-sequencing.

overall_design: ChIP-seq for Smad3 in TGF-β1-stimulated renal tubular cell TCMK-1.

first: Hong-Lian

first: Li

first: Ze

last: Peng

first: Yu-Qing

last: Li


title: Targeting the EIF2AK1 signaling pathway rescues red blood cell production in SF3B1-mutant myelodysplastic syndromes with ringed sideroblasts

city: Houston

first: Simona

last: Colla

state: TX

address: 1515 Holcombe Blvd

institute: University of Texas MD Anderson Cancer Center

summary:
SF3B1 mutations, which occur in 20% of patients with myelodysplastic syndromes (MDS), are the hallmarks of a specific MDS subtype, MDS with ringed sideroblasts (MDS-RS), which is characterized by the accumulation of erythroid precursors in the bone marrow and affects the elderly population. Here, using single-cell technologies and functional validation studies of primary SF3B1-mutant MDS-RS samples (MDS-RS-3-bis, MDS-RS-13, and MDS-RS-14), we show that SF3B1 mutations lead to the activation of the EIF2AK1 pathway in response to heme deficiency and that targeting this pathway rescues aberrant erythroid differentiation and enables the red blood cell maturation of MDS-RS erythroblasts. These data support the development of EIF2AK1 inhibitors to overcome transfusion dependency in patients with SF3B1-mutant MDS-RS with impaired red blood cell production.
MACS-purified CD34+ cells were subjected to a 3-phase in vitro culture as described previously (Huang et al., 2020a). Cells were maintained in phase 1 from the day of collection until day 8, at which time the cells underwent ribonucleoprotein-based gene editing and were transitioned to phase 2 medium. On day 13 of culture, the cells were transitioned to phase 3 medium. Samples for Western blot and cytospin analyses, and sample for flow cytometry were harvested on day 13 or 15 of culture, respectively.

overall_design: RNA sequencing of NT vs. EIF2AK1 [KO] samples on day 13 was used to determine the VAF % of SF3B1 and to perform comparative gene expression profiling analysis of  NT vs. EIF2AK1 [KO] samples. Three primary SF3B1-mutant MDS-RS samples were used (MDS-RS-3-bis, MDS-RS-13, and MDS-RS-14). The number 3, 13 and 14 in each sample name is a consecutive number of the sample in the study.

first: Vera

last: Adema

first: Feiyang

last: Ma


title: Regulation of metabolic and transcriptional responses by the Thyroid Hormone in cellular models of murine macrophages

city: Madrid

first: ANTONIO

last: CASTRILLO

address: Arturo Duperier 4

department: metabolism and cellular signaling

country: Spain

institute: Instituto Investigaciones Biomedicas Alberto Sols CSIC

summary: Although there is increasing evidence that the thyroid hormones could modulate macrophage functions, their global metabolic and transcriptional effects in cellular models of murine macrophages have not yet been examined. In this study we found that immortal macrophages, obtained by infection of mouse bone marrow cells with the J2 oncogene, are totally dependent on the thyroid hormone T3 for proliferation and survival. The hormone induces the activation of the main signaling pathways regulating cell growth and anabolic processes, altering the levels of key metabolites known to affect macrophage functions and modulating the expression of genes involved in stimulation of protein synthesis and cell proliferation, while reducing interferon-mediated signaling. The metabolic and transcriptomic effects of T3 in primary cultures of bone-marrow derived macrophages are much weaker than in the immortal cells, but the response to interferon is similarly reduced by the hormone. These results provide essential data on the pathways, metabolites and genes involved in the maintenance of immortal macrophages, as well as on the crosstalk between the cellular thyroid hormone status and the macrophage responses.

overall_design: mRNA profiles of mouse primary bone marrow derived macrophages differentiated with L929 conditioned media (source M-CSF) treated or not with thyroid hormone T3, and compared with mouse bone marrow derived immortalized macrophages under the same treatment conditions

first: Ana

last: Aranda

first: Antonio

last: Castrillo


title: A regulatory network of Sox and Six transcription factors initiate a cell fate transformation during hearing regeneration in adult zebrafish

city: Bethesda

first: Erin

last: Jimenez

state: MD

address: 50 South Drive

department: NHGRI

institute: NIH

summary: Using adult zebrafish inner ears as a model for sensorineural regeneration, we performed a targeted ablation of the mechanosensory receptors in the saccule and utricle and characterized the single-cell epigenome and transcriptome at consecutive time-points following hair cell death.

overall_design: To elucidate the transcriptional regulatory network that controls tissue regeneration, we characterized the gene expression profiles (scRNA-seq) and the map of accessible regions (scATAC-seq) associated with the response to hair cell ablation in adult zebrafish sensory epithelia. We dissected out saccules and utricles at three time points: Days 4, 5 and 7 post-DT, and each were processed separately in both scRNA-seq and scATAC-seq experiments. Untreated Tg(myo6b:DTR) transgenic zebrafish and wild-type DT injected (and untreated) zebrafish lacking the Tg(myo6b:DTR) transgene were used as non-regenerating controls. Cell suspensions of isolated sensory epithelia were subjected to single cell sequencing for both their transcriptome and open chromatin regions using 10X Genomics Chromium Single Cell Gene Expression and Single Cell ATAC Sequencing. We also include biological triplicates of untreated wild-type saccules and utricles for bulk ATAC-seq.

first: Shawn

middle: M

last: Burgess

first: Claire

last: Slevin

first: Weiwei

last: Wu

first: Abdel

middle: G

last: Elkahloun


title: DAXX-ATRX-H3.3 Regulation of p53 Chromatin Binding and DNA Damage Response [ChIP-Seq]

city: Philadelphia

first: Priyankara

last: Wickramasinghe

overall_design: CHIP-seq of p53 in DAXX WT and KO conditions in etoposide treated cells

first: Paul

first: Nitish


title: DAXX-ATRX-H3.3 Regulation of p53 Chromatin Binding and DNA Damage Response


title: Oncogene addiction to GNAS in GNASR201 mutant tumors

city: HOUSTON

first: John Paul

last: Shen

department: Gastrointestinal Medical Oncology

institute: The University of Texas MD Anderson Cancer Center

summary: The GNASR201 gain-of-function mutation is the single most frequent cancer-causing mutation across all heterotrimeric G proteins, driving oncogenesis in various low-grade/benign gastrointestinal and pancreatic tumors.  In this study, we investigated the role of GNAS and its product Gαs in tumor progression using peritoneal models of colorectal cancer (CRC). GNAS was knocked out in multiple CRC cell lines harboring GNASR201C/H mutations (KM12, SNU175, SKCO1), leading to decreased cell-growth in 2D and 3D organoid models. Nude mice were peritoneally injected with GNAS-knockout KM12 cells, leading to a decrease in tumor growth and drastically improved survival at 7 weeks. Supporting these findings, GNAS overexpression in LS174T cells led to increased cell-growth in 2D and 3D organoid models, and increased tumor growth in PDX mouse models. GNAS knockout decreased levels of cyclic AMP in KM12 cells, and molecular profiling identified phosphorylation of β-catenin and activation of its targets as critical downstream effects of mutant GNAS signaling. Supporting these findings, chemical inhibition of both PKA and β-catenin reduced growth of GNAS mutant organoids. Our findings demonstrate oncogene addiction to GNAS in peritoneal models of GNASR201C/H tumors, which signal through the cAMP/PKA and Wnt/β-catenin pathways. Thus, GNAS and its downstream mediators are promising therapeutic targets for GNAS mutant tumors.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Comprehensive analyses of RNA-seq profiles of GNAS mutant cell lines and cell lines derived xenograft (CDX) models

first: John

middle: P

first: Aditya

last: More

first: Ichiaki

last: Ito

first: Valsala

last: Haridas

first: Saikat

last: Chowdhury


title: Hippocampal cells multiplex positive and negative engrams

city: New York

first: Xiaonan

last: Guan

address: 1150 St Nicholas Ave, 403

institute: Russ Berrie Medical Science Pavillion

summary: The hippocampus contains neurons that correspond to positive and negative engrams, which are segregated by their molecular, cellular, and projection-specific features.

overall_design: We performed reduced representation bisulfite sequencing (RRBS) to characterize the DNA methylation landscapes in aversive and appetitive vCA1 cells.

first: Monika

last: Shpokayte

first: X

last: Liu

first: Steve

last: Ramirez


title: Subtype-Specific and Structure Variation-Induced Chromatin Spatial Reorganization in Acute Myeloid Leukemia [Hi-C]

city: Chicago

first: Feng

last: Yue

state: IL

address: 303 E Chicago Ave. Simpson Querrey 7-518

department: Biochemistry and Molecular Genetics

institute: Northwestern University

summary: Acute myeloid leukemia (AML) is a set of heterogeneous myeloid malignancies hallmarked by mutations in epigenetic modifiers, transcription factors and kinases that can cause epigenetic reshaping. It is unclear whether those mutations drive chromatin 3D structure alteration and contribute to oncogenic dysregulation in AML. By performing Hi-C and whole genome sequencing in 21 primary AML and healthy donors’ samples, we identified recurrent AML- or subtype-specific alteration of compartments, TADs, and chromatin loops. To study the impact on gene regulation, we performed RNA-Seq, ATAC-Seq and CUT&TAG for CTCF, H3K27ac, and H3K27me3 in the same samples. We observed dysregulation of many AML-related genes, represented by MYCN, MEIS1, WT1, ERG, MYC GATA3, BCL11B and IKZF2, intimately linked to the recurrent gain of loops and switch of compartment or TAD, alongside acquisition of AML-specific enhancer or repressor. Further, we profiled structure variations using WGS and Hi-C data to reconstruct the cancer 3D genome, by which we identified structure variation-induced neo-loops and enhancer-hijacking events. Furthermore, through conducting whole genome bisulfite sequencing in patient samples, we found altered methylation correlated with A/B compartment switch, and loss of CTCF insulation due to hypermethylation, leading to extensive gain of loops in AML. By treating the AML cells with DNA hypomethylation agent 5-azacytidine, the altered chromatin structure and gene expression can be restored, with switched compartment reverted and gained loops dissociated, alongside compromised AML cell proliferation, overall providing insights into AML treatment through therapeutic restoration of chromatin structure.

overall_design:
We performed Hi-C and RNA-seq in 18 primary luekmiea samples and purified PBMC from 3 healthy controls. We also performed Hi-C in the following 5 conditions: Kasumi-1 treated wih DMSO for 48 hours, Kasumi-1 treated with 2uM 5-azacytidine for 48 hours and 0.5uM 5-azacytidine for 12 days, HL-60 treated with DMSO for 48 hours and HL-60 treated with 1uM 5-azacytidien for 48 hours . We also performed RNA-seq with two biological replicates each in Kasumi-1 cells treated with DMSO (48h) and Kasumi-1 cells treated with 2uM 5-azacytidine (48h). We performed whole genome sequencing on 18 leukemia samples, whole geome bisulfite sequencing in 10 AML samples and 2 controls, ATAC-seq in 3 controls and 15 leukemia samples, and CUT&TAG for H3K27ac and H3K27me3 in 2 controls  and 11 leukemia samples, and CUT&TAG for CTCF in 2 controls and 8 leukemia samples.
The raw data files have not been included due to privacy concerns.

first: Xu

last: Jie

first: Song

last: Fan

first: Zhang

last: Baozhen

first: Yue

last: Feng


title: Subtype-Specific and Structure Variation-Induced Chromatin Spatial Reorganization in Acute Myeloid Leukemia [WGBS]


title: Subtype-Specific and Structure Variation-Induced Chromatin Spatial Reorganization in Acute Myeloid Leukemia [ATAC-Seq]

overall_design:
We performed Hi-C and RNA-seq in 18 primary luekmiea samples and purified PBMC from 3 healthy controls. We also performed Hi-C in the following 5 conditions: Kasumi-1 treated wih DMSO for 48 hours, Kasumi-1 treated with 2uM 5-azacytidine for 48 hours and 0.5uM 5-azacytidine for 12 days, HL-60 treated with DMSO for 48 hours and HL-60 treated with 1uM 5-azacytidien for 48 hours . We also performed RNA-seq with two biological replicates each in Kasumi-1 cells treated with DMSO (48h) and Kasumi-1 cells treated with 2uM 5-azacytidine (48h). We performed whole genome sequencing on 18 leukemia samples, whole geome bisulfite sequencing in 10 AML samples and 2 controls, ATAC-seq in 3 controls and 15 leukemia samples, and CUT&TAG for H3K27ac and H3K27me3 in 2 controls  and 11 leukemia samples, and CUT&TAG for CTCF in 2 controls and 8 leukemia samples.

>>>Submitter states that raw data are unavailable due to patient privacy concerns<<<


title: Subtype-Specific and Structure Variation-Induced Chromatin Spatial Reorganization in Acute Myeloid Leukemia [RNA-Seq]


title: Gene expression of keratinocytes with miR-885-5p inhibited vs control

city: Barcelona

first: Cristina

last: Sole Marce

address: Pg Vall Hebron 119-129

institute: Vall Hebron Institute Research

summary:
As miR-885-5p is a microRNA downregulated in Cutaneous Lupus Erythematosus (CLE) and it is localted in the epidemis and its function is focused in keratinocytes, human Arrays to study the role of miR-885-5p in Cutaneous Lupus Erythematosius will be conducted.Gene expression in keratinocytes transfected with anti-miR-885-5p will be studied.
We have included 24 Samples: Non-stimulated control (4), Non-stimulated anti-miR-885-5p (4), UVB-stimulated control (4), UVB-stimulated antimiR-885-5p (4), IFN alpha-stimulated control (4) and IFN alpha-stimulated anti-miR-885-5p

overall_design: Microarray gene expression profiling. We will compare the gene expression of keratinocytes with miR-885-5p inhibited vs control. Keraitnocytes were cultured in 24 well plated and transfected with anti-miR-885-5p or anti-miRNA control according to standard protocols. 24h post-transfection, they will be stimulated with different inflammatory treatments: UVB 25 mJ/cm2, IFN alpha 10 ng/mL or PBS (control, non-stimualted). UVB and IFN alpha are known CLE triggers and revelant in the pathogenesis of CLE. Three comparisons will be analysed in order to understand the role of miR-885-5p: 1) Non-stimulated control vs Non-stimulated anti-miR 885-5p 2) UVB control vs UVB anti-miR-885-5p.  3) IFN alpha control vs IFN alpha anti-miR-885-5p.

first: Josefina

last: Cortés-Hernández

last: Sole

first: Sandra

last: Domingo


title: Single-cell multi-omics profiling links dynamic DNA methylation to cell fate decisions during early mammalian organogenesis [10X_Dnmt]

city: Cambridge

first: Felix

last: Krueger

address: Granta Park

country: United Kingdom

institute: Altos Labs

summary: Perturbation of DNA methyltransferases and of the active demethylation pathway via TET enzymes results in severe developmental defects and embryonic lethality. Dynamic control of DNA methylation is therefore vital for embryogenesis, yet the underlying mechanisms remain poorly understood. Here we report a single-cell transcriptomic atlas from a variety of DNA methylation mutant mouse embryos during mouse early organogenesis. We show that both the maintenance and de novo methyltransferase enzymes are dispensable for the formation of all major cell types at E8.5. However, DNA methyltransferases are required for silencing of prior or alternative cell fates such as pluripotency and extraembryonic programmes. Deletion of all three TET enzymes produces substantial lineage biases, in particular, a failure to generate primitive erythrocytes. Single-cell multi-omics profiling moreover reveals that this is linked to a failure to demethylate distal regulatory elements in Tet triple-knockout embryos. This study therefore provides a detailed analysis of the effects of perturbing DNA methylation on mouse organogenesis at whole organism scale, and affords new insights into the regulatory mechanisms of cell fate decisions.

overall_design: 18  mouse embryos collected at E8.5 from Dnmt1, Dnmt3a, Dnmt3b homozygous mutants and matching wildtype controls processed using 10x genomics scRNA-seq

first: Tim

last: Lohoff

first: Stephen

last: Clark

first: Ricard

last: Argelaguet

first: Deborah

last: Drage

first: Brthold

last: Gottgens

first: John

last: Marioni

first: Jennifer

last: Nichols

first: Wolf

last: Reik


title: Single-cell multi-omics profiling links dynamic DNA methylation to cell fate decisions during early mammalian organogenesis.

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

overall_design: Refer to individual Series


title: Single-cell multi-omics profiling links dynamic DNA methylation to cell fate decisions during early mammalian organogenesis [10X_Tet]

overall_design: 8 Samples from E7.5 and E8.5 chimeric mouse embryos. Cells were flow sorted for td-Tomato which labelled the Tet-TKO ESCs used to generate chimeras. TdTomato negative were collected as wildtype host cells. processed using 10x genomics scRNA-seq


title: Subtype-Specific and Structure Variation-Induced Chromatin Spatial Reorganization in Acute Myeloid Leukemia [CUT&TAG]

first: Feng

last: Yue

last: Jie


title: Single-cell multi-omics profiling links dynamic DNA methylation to cell fate decisions during early mammalian organogenesis [scNMT_RNA-seq]

overall_design: 1824 single cells isolated from TET triple knockout chimeric mouse embryos at E7.5 and E8.5 and processed using either scNMT-seq (Clark et al 2018) or scM&T-seq (Angermueller et al 2016). These are the RNA-seq data.


title: mRNA expression profile from retinoblastoma tumors and pediatric controls

status: Public on Jul 18 2022

city: Bangalore

first: Vishnu

last: Suresh Babu

state: Karnataka

address: NH Health city, Bommasandra

department: Narayana Nethralaya Foundation

country: India

institute: GROW Research Laboratory

summary: To discover differentially expressed mRNA's in Rb tumors compared to pediatric retina

overall_design: Nine enucleated human retinoblastoma tumors and two pediatric retina controls used for the study. Total RNA was isolated from 9 Rb tumors and 2 control pediatric retina samples using Agilent Absolutely RNA miRNA kit. Twenty-five nanograms of RNA from Rb tumors and control pediatric retina samples were labeled with Cy3 dye using an Agilent Low Input Quick Amp Labeling Kit

first: Arkasubhra

last: Ghosh

first: Nilanjan

last: Guha


title: Lymphangiocrine signals are required for proper intestinal repair after cytotoxic injury

city: San Francisco

first: Ophir

last: klein

address: 505 Parnassus Ave

institute: UCSF


title: Lymphangiocrine signals are required for proper intestinal repair after cytotoxic injury [endothelial cells]

summary: We find that lymphatic Rspo3 is essential for intestinal regeneration after cytotoxic injury.

overall_design: Endothelial cells (blood and lymphatic) were FACS isolated from 8-12 week old male and female wild type (Bl6) mice

first: Brisa

last: Palikuqi

first: Jeremie

last: Rispal


title: Single-cell multi-omics profiling links dynamic DNA methylation to cell fate decisions during early mammalian organogenesis [scNMT BS-seq]

last: Krueger

overall_design: 768 single cells isolated from TET triple knockout chimeric mouse embryos at E8.5 and processed using either scNMT-seq (640 cells, Clark et al 2018) or scM&T-seq (128 cells, Angermueller et al 2016)


title: SARS-CoV-2 infection in BMMs

city: Shanghai

first: Junjie

last: Gao

address: 600 Yishan Road

institute: Shanghai Sixth People’s Hospital Affiliated to Shanghai Jiao Tong University School of Medicine

summary: SARS-CoV-2 infection in human can cause medical complications across various tissues and organs. Despite of the advances to understanding the pathogenesis of SARS-CoV-2, its tissue tropism and interactions with host cells have not been fully understood. Existing clinical data have suggested possible SARS-CoV-2 infection in human skeleton system. In the present study, we exmined the effects of authentic SARS-CoV-2 on bone marrow-derived macrophages (BMMs).

overall_design: RNA-seq of SARS-CoV-2 infection in cultured BMMs


title: Lymphangiocrine signals are required for proper intestinal repair after cytotoxic injury [Rspo3 KO]

overall_design: Control and Prox1-cre ert2 Rspo3 knock-out mice underwent 3 doses of 5FU injury. Intestines were collected for single cell analysis at day 3 after the last 5FU injection.


title: DAXX-ATRX-H3.3 Regulation of p53 Chromatin Binding and DNA Damage Response [RNA-Seq]

first: Priyankara

last: Wickramasinghe

overall_design: RNA-seq of DAXX and ATRX WT and KO conditions in control and etoposide treated cells

first: Paul

last: Lieberman

first: Nitish

last: Gulve


title: Knockdown of ASD risk genes leads to a shared transcriptional signature

first: Erica

last: Korb

address: 3400 Civic Center Boulevard

institute: University of Pennsylvania

summary: RNAseq analysis of shRNA-mediated knockdown of chromatin modifiers associated with Autism Spectrum Disorder

overall_design: E16.5 primary cortical neurons were cultured for 5 days before infection by shRNAs targeting one of Ash1L, Chd8, Crebbp, Ehmt1, Nsd1, Gtf2i, or Luciferase. Neurons were cultured for 5 additional days before RNA was collected.

first: Samuel

last: Thudium

first: Katherine

last: Palozola

first: Éloïse

last: L'Her


title: Subtype-Specific and Structure Variation-Induced Chromatin Spatial Reorganization in Acute Myeloid Leukemia

last: Yue


title: Longitudinal analysis reveals that probiotics are a significant driver of gut microbiome development in very preterm infants

city: Newcastle Upon Tyne

first: Christopher

last: Stewart

address: Medical School, Framlington Place

department: Translational and Clinical research institute

institute: Newcastle University

summary: Impact of small molecules from different microbial gut community types on gene expression from preterm intestinal derived organoids

overall_design:
17 samples prepared for bulk RNA Sequencing (total 92 samples) on the Illumina Novaseq
CT = community type and CTRL = control.

first: Lauren

last: Beck


title: Comprehensive gene expression analysis of calvarial cells stimulated with a locomomimetic drug Locamidazole (LAMZ)

city: Tokyo

first: Takehito

last: Ono

address: Yushima, 1-5-45

department: Department of Cell Signaling

institute: Tokyo Medical and Dental University

summary: LAMZ was found to enhance osteoblastogenesis.  This analysis was conducted so that we would find how it works.

overall_design:
Total RNA of LAMZ-stimulated calvarial cells was harvested on days 7 and 14
*** Submitter statement: "As this analysis is conducted many years ago, fastq files would no longer exist." ***

first: Ryosuke

last: Denda

first: Yuta

last: Tsukahara

first: Takashi

last: Nakamura

first: Kazuo

last: Okamoto

first: Hiroshi

last: Takayanagi

first: Tomoki

last: Nakashima


title: Lacripep promotes corneal regeneration in autoimmune mediated dry eye disease

first: Sarah

last: Knox

state: California

address: 513 Parnassus Ave

department: Cell Tissue Biology

institute: University of California San Francisco

summary: Corneal architecture is essential for vision and is greatly perturbed by the absence of tears due to the highly prevalent disorder dry eye. With no regenerative therapies available, pathological alterations of the ocular surface in response to dryness, including persistent epithelial defects and poor wound healing, result in lifelong morbidity. Here, using a mouse model of aqueous-deficient dry eye, we reveal that topical application of the synthetic tear protein lacripep reverses the pathological outcomes of dry eye through restoring the extensive network of corneal nerves that are essential for tear secretion, barrier function, epithelial homeostasis and wound healing. Intriguingly, the restorative effects of lacripep occur despite extensive immune cell infiltration, suggesting tissue reinnervation and regeneration can be achieved under chronic inflammatory conditions. In summary, our data highlight lacripep as a first-in-class regenerative therapy for returning the cornea to a near homeostatic state in individuals who suffer from dry eye.

overall_design: Comparative analysis of gene expression between wild type, untreated Aire KO (dry eye disease) , Aire KO treated with PBS, and Aire KO treated with 4uM lacripep whole corneas at day 7 of treatment (6 wk of age).

first: Yael

last: Efraim

first: Feeling

last: Chen

first: Ka

middle: N

last: Cheong

first: Eliza

last: Gaylord

first: Nancy

last: McNamara


title: Gene expression profile at single cell level of E12.5 mouse heart with transcription factor Gata4 knockout by inducible Cre in endocardium

status: Public on Jul 16 2022

city: Boston

first: Yan

last: Zhang

state: MASSACHUSETTS

address: 300 Longwood Ave.

institute: Boston Children's Hospital

summary: Gata4 is required for mouse endocardium development. To identify genes regulated by Gata4 in endocardium, we deleted Gata4 in endocardium with Cdh5(Pac)-CreERT2 and performed single cell RNA sequencing (scRNA-seq) to analyze all cells from the ventricles.

overall_design: Cdh5-CreERT2 was induced by tamoxifen at E9.5 and Gata4 flox/+ or Gata4flox/flox hearts were collected at E12.5 for scRNAseq.

first: Pingzhu

last: Zhou

first: William

last: Pu


title: Identification of antimalarial compounds that inhibit Apicomplexan AP2 transcription factor proteins in the human malaria parasite Plasmodium falciparum [ChIP-seq]

status: Public on Jul 15 2022

city: STATE COLLEGE

first: Timothy

last: Russell

address: W122 Millennium Science Complex

institute: Pennsylvania State University

summary: Plasmodium parasites are reliant on the Apicomplexan AP2 (ApiAP2) transcription factor family to regulate gene expression programs. AP2 DNA binding domains have no homologs in the human or mosquito host genomes, making them potential antimalarial drug targets. Using an in-silico screen to dock thousands of small molecules into the crystal structure of the AP2-EXP (Pf3D7_1466400) AP2 domain (PDB:3IGM), we identified compounds that interact with this domain. Four compounds were found to compete for DNA binding with AP2-EXP and at least one additional ApiAP2 protein. Our top ApiAP2 competitor compound perturbs the transcriptome of P. falciparum trophozoites and results in a decrease in abundance of log2 fold change > 2 for 50% (46/93) of AP2-EXP target genes.  Additionally, two ApiAP2 competitor compounds have multi-stage anti-Plasmodium activity against blood and mosquito stage parasites. In summary, we describe a novel set of antimalarial compounds that are targeted against the ApiAP2 family of proteins. These compounds may be used for future chemical genetic interrogation of ApiAP2 proteins or serve as starting points for a new class of antimalarial therapeutics.

overall_design: ChIP-seq based mapping of the genomic occupancy of the Plasmodium falciparum transcription factor AP2-EXP (PF3D7_1466400) in the asexual blood stage

first: Erandi

middle: K

last: De Silva

first: Valerie

last: Crowley

first: Kathryn

last: Shaw-Saliba

first: Namita

last: Dube

first: Gabrielle

last: Josling

first: Charisse

last: Pasaje

first: Irene

last: Kouskoumvekaki

first: Gianni

last: Panagiotou

first: Jacquin

last: Niles

first: Marcelo

last: Jacobs-Lorena

first: C

middle: D

last: Okafor

first: Francisco-Javier

last: Gamo

first: Manuel

last: Llinás


title: Impaired proteolysis of non-canonical RAS proteins drives clonal hematopoietic transformation

city: South San Francisco

first: Simon

last: Hogg

address: 1000 Gateway Boulevard

department: Oncology Discovery Research

institute: AbbVie


title: RNA-seq analysis on human primary breast cancer tumor and distant metastasis tumor

city: Singapore

first: Gokce

last: OGUZ

address: 60 Biopolis St, GENOME, #02-01

department: Bioinformatics Consulting and Training Platform

institute: Genome Institute of Singapore

summary: To further understand the molecule changes between primary and distant metastasis of HER2+ breast tumor, we have profiled RNA expression in those two groups.

overall_design: 13 primary breast tumor and 7  distant metastasis tumors were conducted with RNA-seq

first: Li-Teng

last: Ong

first: Henrik

last: Ditzel

first: Qiang

last: Yu


title: Transcriptomic analysis of injured and uninjured knee joints from Trem2 KO mice [bulk RNA-seq]

city: Livermore

first: Stephen

middle: Patrick

last: Wilson

state: CA

address: 7000 East Ave

department: BBTD

institute: LLNL

summary: Trem2 is a single-pass transmembrane receptor of the immunoglobulin superfamily and is primarily expressed in myeloid cells. Cells from injured and uninjured knee joints of wildtype C57BL/6 mice and Trem2 KO mice were sequenced to determine if Trem2 plays a role in macrophage differentiation or function after joint injury.

overall_design: Right knee joints of 10-week-old C57BL/6 and Trem2 KO mice were injured using a tibial compression injury model. Uninjured and 7-day post-injury joints were collected and cells were analyzed using bulk RNA-seq.

first: Gabriela

last: Loots

first: Aimy

last: Sebastian


title: Diverse maturity-dependent and complementary anti-apoptotic brakes safeguard human iPSC-derived neurons from cell death.

city: Mannheim

first: Philipp

last: Koch

state: Deutschland

institute: Hector Institute for Translational Brain Research

overall_design: Refer to individual Series


title: Diverse maturity-dependent and complementary anti-apoptotic brakes safeguard human iPSC-derived neurons from cell death [scRNA-seq]

summary: In humans, most neurons are born during embryonic development and have to persist throughout the entire lifespan of an individual. Thus, human neurons have to develop elaborate survival strategies to protect against accidental cell death. We set out to decipher the developmental adaptations resulting in neuronal resilience. We demonstrate that, during the time course of maturation, human neurons install a complex and complementary anti-apoptotic signaling network. This includes i.) a downregulation of central proteins of the intrinsic apoptosis pathway including several caspases, ii.) a shift in the ratio of pro- and anti-apoptotic BCL-2 family proteins, and iii.) an elaborate regulatory network resulting in upregulation of the inhibitor of apoptosis protein (IAP) XIAP. Together, these adaptations strongly increase the threshold for apoptosis initiation when confronted with a wide range of cellular stressors. Our results highlight how human neurons are endowed with complex and redundant preemptive strategies to protect against stress and cell death.

overall_design: iPSCs were differentiated into forebrain neurons and samples were harvested at day 6,10, 17, 24,31,38,45 and 52. Samples were pooled before sequencing

first: Ruven

last: Wilkens

first: Anne

last: Hoffrichter

first: Bettina

last: Bohl


title: Molecular characterization of kidney compartments from serial biopsies to differentiate treatment responders from non-responders in lupus nephritis

city: Columbus

first: Samir

last: Parikh

state: OH

address: 395 W 12th Avenu, -Address 2-

department: Nephrology

institute: Ohio State University

summary: The immune pathways that define treatment response and non-response in lupus nephritis (LN) are unknown. To characterize these intra-renal pathways, transcriptomic analysis of protocol kidney biopsies was done.  Kidney biopsies were done at flare (Bx1) and after treatment (Bx2) in 58 LN patients and healthy controls (HC). Glomeruli and tubulointerstitium (TI) were isolated using laser microdissection. RNA was extracted and analyzed by nanostring.  Transcript expression from clinical complete (CR), partial (PR) and non-responders (NR) were compared at Bx1 and Bx2 and to HC. Top transcripts that differentiate CR from NR were identified. Confocal microscopy and urine ELISA was done to evaluate the protein expression of top transcripts.   At Bx1 cluster analysis determined that glomerular integrin, neutrophil, and chemokine/cytokine, and TI chemokine, T cell and leukocyte adhesion genes differentiated NR from CR. At Bx2, glomerular monocyte, extracellular matrix, and interferon, and TI interferon, complement, and T cell transcripts differentiated NR from CR.  Protein analysis recapitulated top transcript findings. Urine C5a and FN1 differentiated NR from CR after treatment.    Transcript analysis of serial kidney biopsies taken during the treatment of LN demonstrated how gene expression in the kidney changes with clinically successful and unsuccessful therapy. These insights into the molecular landscape of response and non-response may help better align LN management with the pathogenesis of kidney injury.

overall_design:
58 paired kidney biopsies from patients with proliferative lupus nephritis (class III, class IV or class III/IV+V)  were initially evaluated. This is a well defined, well curated dataset with clinical and histologic data available for all patients. Glomeruli and tubulointerstitium (TI) was isolated separately and samples with adequate RNA were submitted for nanostring analysis. Overall, 70 glomerular samples and 92 TI samples were submitted for nanostring analysis (35 glomerular and 46 TI pairs). Pre-implantation donor kidney biopsies (n=10) served as healthy controls. All kidney biopsy tissue used for this study were from FFPE blocks. 574 immune transcripts were analyzed by nanostring.  Technical replicates with control samples are included
Please note that the 'Nanostring_RAW_1-21.xlsx' contains raw data in 21 spreadsheets for all samples as indicated in the corresponding sample description field.

middle: V

first: Ana

last: Malvar

first: Huijuan

last: Song

first: John

last: Shapiro

first: Juan

last: Mejia-Vilet

first: Isabelle

last: Ayoub

first: Salem

last: Almaani

first: Sethu

last: Madhavan

first: Valeria

last: Alberton

first: Celeste

last: Besso

first: Bruno

last: Lococco

first: Anjali

last: Satoskar

first: Jianying

last: Zhang

first: Lianbo

first: Paolo

last: Fadda

first: Michael

last: Eadon

first: Dan

last: Birmingham

first: Latha

last: Ganesan

first: Wael

last: Jarjour

first: Brad

last: Rovin


title: Profiling RNA at chromatin targets in situ by antibody-targeted tagmentation.

city: Seattle

first: Jorja

last: Henikoff

state: WA

address: 1100 Fairview AV N, A1-162

department: Basic Sciences

institute: Fred Hutchinson Cancer Research Center

summary: Whereas techniques to map chromatin-bound proteins are well-developed, mapping chromatin-associated RNAs remains a challenge. Here we describe Reverse Transcribe & Tagment (RT&Tag), in which RNAs associated with a chromatin epitope are targeted by an antibody followed by a protein A-Tn5 transposome. Localized reverse transcription generates and the Tn5 transposase tagments RNA/cDNA hybrids. We demonstrate the utility of RT&Tag in Drosophila cells for capturing the noncoding RNA roX2 with the dosage compensation complex and maturing transcripts associated with silencing histone modifications. We also show that RT&Tag can detect N6-methyladenosine (m6A)-modified mRNAs, and show that genes producing methylated transcripts are characterized by extensive promoter pausing of RNA polymerase II. The high efficiency of in situ antibody tethering and tagmentation makes RT&Tag especially suitable for rapid low-cost profiling chromatin-associated RNAs from small samples.

overall_design: We used an antibody-tethering based approach to perform localized reverse transcription and tagmentation to profile RNA associated with chromatin targets.

first: Nadiya

last: Khyzha

first: Kami

last: Ahmad

first: Steven