title: A skeletal-muscle senescence blueprint defines an aged-like inflamed niche that inhibits regeneration over lifetime [RNA-seq]

overall_design:
Muscles were mechanically disaggregated and incubated in Dulbecco's Modified Eagle's medium (DMEM) containing liberase (Roche) and dispase at 37°C with agitation for 1-2 hours. When required, SPiDER-b-gal reagent (Dojindo) was added during the second hour. The supernatant was then filtered and cells were incubated in lysis buffer (BD Pharm Lyse) for 10 min on ice, resuspended in PBS with 2.5% fetal bovine serum (FBS), and counted. BV711-conjugated anti- CD45 (BD), APC-Cy7-conjugated anti F4/80 (Biolegend), PE- conjugated anti-a7-integrin (Ablab), APC-conjugated anti-CD31 (eBioscience) and PE-Cy7-conjugated anti-Sca-1 (Biolegend) antibodies were used to isolate MCs (CD45+ and F4/80+), SCs (a7-integrin+, CD45+, F4/80+ and CD31+) and FAPs (Sca-1+, MCs CD45+, F4/80+, a7-integrin+ and CD31+). PE-Cy7-conjugated anti-CD45 antibody (Biolegend) was used to isolate CD45 positive and negative populations. SPiDER-b-gal (SPiDER) was employed to isolate senescent cells (SPiDER+) from non-senescent cells (SPiDER–) of each cell type. Isolated cells were subjected to low-input RNA sequencing. Pools of 3 animals were used for each sample.
File name legend:
We performed bulk RNA-seq analysis from young (labeled as Y) or old mice (labeled as G), senescent cells (labeled as Sen), and non-senescent cells (labeled as NSen) and NSen cells from basal (contralateral) muscles (with no further label) from three lineages: Satellite cell lineage (labeled as S), Fibroadipogenic progenitors  (labeled as F), and myeloid cells (labeled as M) at early (3 d.p.i. - 3) and late (7 d.p.i.- 7) phases of regeneration. Biological replicates are indicated with a number.

Example:

Y3SNSen_1 Young 3 d.p.i Non-senescent cells, biological replicate 1
Y3SSen_1 Young 3 d.p.i Senescent cells, biological replicate 1
Y3S_1 Young Non-senescent cells from basal (contralateral) muscles of the 3 days time point, biological replicate 1

first: Sascha

last: Jung

first: Antonio

last: del Sol


title: Exposure to the olfactory receptor 51E1 agonist nonanoic acid alters small intestinal neuroendocrine tumor phenotype

status: Public on Oct 21 2022

city: Gothenburg

first: Erik

last: Elias

address: Medicinaregatan 1G

department: Clinical Sciences

country: Sweden

institute: University of Gothenburg

type: Expression profiling by high throughput sequencing

summary: This study explores the hypothesis that stimulating the chemo-sensing olfactory receptor 51E1 (OR51E1) decreases SI-NET proliferation suggesting a mechanism that explains a difference in proliferative rate based on tumor location

overall_design: Comparative gene expression profiling analysis of RNA-seq data for GOT1 cells treated with and without the olfactory receptor 51E1 agonist nonanoic acid

first: Bilal

last: Almobarak

first: Vishal

last: Amlani

first: Linda

last: Inge

first: Tobias

last: Hofving

first: Andreas

last: Muth

first: Ola

last: Nilsson

first: Martin

last: Johansson

first: Yvonne

last: Arvidsson


title: Nucleoporins facilitate ORC loading onto chromatin

status: Public on Oct 19 2022

city: Nashville

first: Logan

last: Richards

state: Tennessee

address: 465 21st Ave S

department: Biological Sciences

country: USA

institute: Vanderbilt University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: The origin recognition complex (ORC) binds throughout the genome to initiate DNA replication. In metazoans, it is still unclear how ORC is targeted to specific loci to facilitate helicase loading and replication initiation. Here, we performed immunoprecipitations coupled with mass spectrometry for ORC2 in Drosophila embryos. Surprisingly, we found that ORC2 associates with several subunits of the Nup107-160 subcomplex of the nuclear pore. Bioinformatic analysis revealed that, relative to all modENCODE factors, nucleoporins are among the most enriched factors at ORC2 binding sites. Critically, depletion of the nucleoporin Elys, a member of the Nup107-160 complex, results in decrease ORC2 loading onto chromatin. Depleting Elys also sensitized cells to replication fork stalling, which could reflect a defect in establishing dormant replication origins. Our work reveals a new connection between ORC, replication initiation and nucleoporins, highlighting a previously unrecognized function of nucleoporins in metazoan replication initiation.

overall_design: ORC2 ChIP-seq and ATAC-seq performed on Drosophila S2 cells that are depleted for nucleoporins

first: Christopher

middle: L

last: Lord

first: Mary

last: Benton

first: John

middle: A

last: Capra

first: Jared

middle: T

last: Nordman


title: Mechanisms of iECM in infarcted rat hearts

status: Public on Oct 18 2022

city: La Jolla

last: Spang

state: CA

address: 2880 Torrey Pines Scenic Dr

institute: University of California, San Diego

summary: Hearts from 1 and 3 days post-infusion were used for gene expression analyses

overall_design: Multiple pathways were investigated regarding a potential new therapeutic infusible extracellular matrix therapy for acute myocardial infarction, including metabolic, fibrotic, and inflammatory pathways. Rat hearts were infacted, matrix was infused, hearts and corresponding RNA were isolated 1 and 3 days post-infusion.

first: Miranda

last: Diaz

first: Karen

last: Christman


title: Microglia regulate myelin growth and integrity in the central nervous system

status: Public on Oct 16 2022

city: Edinburgh

first: Nadine

last: Bestard-Cuche

address: 5 Little France Drive

country: United Kingdom

institute: University of Edinburgh

summary: Myelin is required for the function of neuronal axons in the central nervous system, yet the mechanisms supporting myelin health are unclear. Although central nervous system macrophages have been implicated, it is unknown which macrophage populations are involved and which aspects of myelin health they influence. Here, we show that resident microglia are critical for the maintenance of myelin health in adulthood in both mouse and human. We demonstrate that whereas microglia are dispensable for developmental myelin ensheathment, they are required for subsequent regulation of myelin growth and associated cognitive function, and for the preservation of myelin integrity by preventing its degeneration. We discovered that loss of myelin health in the absence of microglia is underpinned by the appearance of a myelinating oligodendrocyte subpopulation with altered lipid metabolism, regulated by a disruption of the TGFβ1-TGFβR1 axis. Our findings highlight microglia as promising therapeutic targets for conditions where myelin growth and integrity are dysregulated, such as in ageing and neurodegenerative disease.

overall_design: FIREΔ/Δ and wildtype female mice at 1 month of age. The olfactory bulbs and cerebellum were removed. Hippocampi from both hemispheres and the remainder of the left hemisphere (without the hippocampus) were used for the single cell RNA sequencing.

first: Veronique

middle: E

last: Miron

first: Niamh

middle: B

last: McNamara

first: Anna

last: Williams

first: David

last: Munro


title: Transcription factor LIM1 progresses tumor growth in endometrial cancer via CREB signaling.

city: Toon

first: Hiroaki

last: Kato

department: Obsterics and Gynecology

country: Japan

institute: Ehime university hospital

summary: The incidence of endometrial cancer (EC) is increasing worldwide, however, therapeutic options for EC are limited and novel therapeutic targets for EC are required. We reanalyzed RNA-seq data of EC registered in The Cancer Genome Atlas and found significant upregulation of transcription factor LIM homeobox1 (LIM1) in stages II-IV compared to stage I of EC patients. LIM1-knocked down (LIM1-KD) and Control sublines were established using HEC50B cell line and then RNA-sequence results were analyzed by Ingenuity pathway analysis (IPA). It revealed enrichment of CREB signaling-related genes among differentially expressed genes between Control and LIM1-KD sublines. Also, decreased levels of phosphorylated CREB were observed in LIM1-KD subline. In the Xenograft model used by HEC50B sublines, tumor growth was significantly suppressed in the LIM1-KD subline compared to Control subline. Immunofluorescent staining showed decreased phosphorylation of CREB in LIM1-KD-derived tumors. Kaplan-Meier plotter analysis indicated that the high LIM1 expression group had a significantly poorer prognosis. These results suggest that LIM1 in EC progresses tumor growth and malignancy via CREB signaling.

overall_design: mRNA profiles of HEC50B cell line that stably express  LIM1 shRNA and control shRNA  obtained by deep sequencing using illumina NextSeq 500.

first: Yuuki

last: Imai

first: Noritaka

last: Saeki


title: Expression data from Hela cells and HSF2-deficient HeLa cells subjected to heat treatment in the presence of IHSF115, an inhibitor of HSF1.

status: Public on Oct 13 2022

city: Madrid

first: Nuria

last: Vilaboa

state: Madrid

address: Edificio IdiPAZ segunda planta, Hospital Universitario La Paz, Paseo de la Castellana 261

country: Spain

institute: Fundación para la Investigación Hospital La Paz, G83727057

summary:
The majority of heat-induced genes were inhibited by IHSF115, i.e. were positively regulated by HSF1, suggesting that HSF1 plays a predominant role in the transcription of heat-induced genes
IHSF115 effectively countermanded repression in a significant fraction of heat-repressed genes, suggesting that repression of these genes is mediated by transcriptionally active HSF1.

overall_design: Transcriptomic changes in cells incubated for 2h at 37ºC with vehicle (DMSO) or IHSF115, subjected to heat treatment at 43ºC for 30min in a thermostatically controlled water bath and then incubated for an additional 1h at 37ºC. The assays were conducted by triplicate (HeLa cells) or quintuplicate (HSF2-deficient Hela cells).

first: Richard

last: Voellmy


title: Identification of Circular RNA Profiles in the Liver of Diet-induced Obese Mice and Construction of the ceRNA Network

status: Public on Oct 15 2022

city: zhangjiakou

first: xiao

middle: xiao

last: Zhang

state: hebei

address: 11 zuanshi south road

country: China

institute: Hebei North University

type: Non-coding RNA profiling by high throughput sequencing

summary: To investigate the cooperative function circRNA in the regulation of lipid metabolism, we constructed obese mouse model by high-fat diet. We then performed gene expression profiling analysis using data obtained from RNA-seq of 2 different groups.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for mouse liver (HFD, LFD).

first: Yu

last: Liu

first: Xiaoxiao

first: Rui

last: Han


title: Bidirectional changes in postmitotic H3K27me3 distributions underlie cerebellar granule neuron maturation dynamics

status: Public on Oct 11 2022

city: Durham

first: Anne

last: West

state: NC

address: 311 Research Dr

department: Neurobiology

institute: Duke University

summary: The functional and transcriptional maturation of neurons is a prolonged process that extends well beyond mitotic exit and terminal fate commitment of progenitors. The differentiation of cerebellar granule neurons (CGNs) in the postnatal mouse cerebellum provides a useful model to identify chromatin mechanisms that orchestrate temporal changes in transcription as postmitotic CGNs mature. Here we report that CGN maturation is associated with dynamic changes in the genomic distribution of histone H3 lysine 27 trimethylation (H3K27me3), a modification best known for its role in repressing alternative fates during cell specification. H3K27me3 is gained rapidly in newly postmitotic CGNs at progenitor-expressed genes that are repressed in neurons. H3K27me3 is lost more gradually at the promoters of a subset of neuronal genes that are transcriptionally induced upon CGN maturation. The loss of H3K27me3 is facilitated by the lysine demethylase KDM6B, and genes that are induced in maturing CGNs show impaired expression in the cerebellum of conditional KDM6B knockout mice. Genes that lose H3K27me3 gain H3K27 acetylation and binding of the pro-maturation ZIC1/2 transcription factors, suggesting that developmental loss of H3K27me3 may be required to permit the onset of transcriptional maturation. Interestingly, pharmacological inhibition of the H3K27 methyltransferase EZH2 in early postmitotic CGNs not only blocked the repression of progenitor genes but also impaired the induction of mature CGN genes. These data show that regulation of H3K27me3 functions in developing postmitotic neurons beyond the period of cell fate commitment to regulate the dynamics of gene expression programs that underlie functional neuronal maturation.

overall_design: Paired-end RNA-seq for WT and Kdm6b-cKO cerebellar tissue harvested at P14. (n=2 biological replicates)

first: Vijyendra

last: Ramesh

first: Fang

first: Melyssa

last: Minto

first: Urann

last: Chan


overall_design: H3K27me3 CUT&RUN-seq for 1) cultured cerebellar granule neurons (CGN) at 1, 3, 5 and 7 days in vitro, 2) CGNs treated with DMSO or 5 uM Ezh2 inhibitor GSK-126 at DIV1 and harvested at DIV5, 3) CGNs treated with DMSO or 1 uM Kdm6b inhibitor GSK-J4 at DIV1 and harvested at DIV5. (n=3 biological replicates each)


title: GOLPH3 modulates expression and alternative splicing of transcription factors associated with endometrial decidualization in human endometrial stromal cells

status: Public on Oct 12 2022

city: fuzhou

first: yangfan

last: zhang

address: Fujian Normal University Qishan Campus, College Town, Fuzhou, Fujian Province

institute: FJNU

summary: GOLPH3 was silenced in human endometrial stromal cells (hESCs), and the transcriptome data (RNA-seq) by GOLPH3 knockdown (siGOLPH3) was obtained by high-throughput sequencing technology,

overall_design: So as to analyze the potential targets of GOLPH3 at expression and alternative splicing levels in hESCs. Through bioinformatics analysis, we found that siGOLPH3 can significantly affect the overall transcriptional level of hESCs. A total of 6025 differentially expressed genes (DEGs) and 4131 differentially alternative splicing events (DASEs) were identified. Through functional cluster analysis of these DEGs and genes where differential alternative splicing events are located,

first: Suqin

last: Zhu

first: Dianliang

last: Lin

first: Beihong

last: Zheng

first: Quan

last: Song


overall_design: H3K27me3 ChIP-seq for P7, P14 and P60 cerebellum (n=3 biological replicates); and WT and Kdm6b-cKO mouse cerebellum (WT, n=2; cKO, n=3 biological replicates)


title: Bone marrow naïve B lymphocytes improve heart function after myocardial infarction

status: Public on Oct 10 2022

city: Shanghai

first: Yaozu

last: Xiang

address: 1239 Siping Road, Yangpu District

institute: Tongji University

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

overall_design: Refer to individual Series


title: Bone marrow naïve B lymphocytes improve heart function after myocardial infarction [RNA-Seq]

summary: We provided an mRNA-seq analyses of mouse bone marrow revealing B cell development arrest in the bone marrow after MI, which was restored by treatment of empagliflozin (EMPA).

overall_design: Bone marrow RNA profiles of 12 samples including Sham, Sham-E, MI and MI-E.

first: Yue

last: Xu

first: Kai

last: Jiang

first: Feng

last: Chen

first: Dandan

last: Wang


title: Bone marrow naïve B lymphocytes improve heart function after myocardial infarction [scRNA-Seq]

summary: We provided a single cell mRNA-seq analyses of mouse bone marrow revealing B cell development arrest in the bone marrow after MI, which was restored by treatment of empagliflozin (EMPA).

overall_design: Gene profiles of mouse bone marrow cell populations derived from Sham, MI and MI-E.


title: Reassessing the abundance of miRNAs in the human pancreas and rodent cell lines and its implication

status: Public on Oct 08 2022

city: Duarte

first: Guihua

last: Sun

address: 1500 East Duarte Rd.

department: Department of Neurodegenerative Diseases

institute: City of hope

summary: The work leverages techniques we developed for bias reduction in small RNA profiling using next generation sequencing and our unique access to human pancreatic tissues. In this regard, we sequenced human islets and acinar cells as well as rodent cell lines. We identified differentially expressed miRNAs between acini and islets

sample_organism:
Homo sapiens
Mus musculus
Rattus rattus

platform_organism:
Homo sapiens
Mus musculus
Rattus rattus

overall_design: Eight pairs of human pancreas samples and four rodent cell lines

first: Meirigeng

last: Qi

first: Ismail

last: Al-Abdullah

first: Arthur

last: Riggs


title: RNA-seq of progenitors and neurons sorted from brain organoids

status: Public on Oct 06 2022

city: Vienna

first: Jaydeep

last: Sidhaye

address: Dr. Bohrgasse 3

country: Austria

institute: IMBA

summary: During development of the human cerebral cortex, multipotent neural progenitors generate excitatory neurons and glial cells. This process is faithfully recapitulated in brain organoids.  By using telencephalic brain organoids grown using a dual reporter cell line to isolate neural progenitors and neurons we generated a cell type and developmental stage-specific transcriptome dataset..

overall_design: To investigate progenitor and neuron-specific gene regulatory programs, we generated a dual reporter H9 hESC line that enables sorting of neural progenitors and neurons. To label neural progenitors, we replaced the stop codon of one allele of the pan-neural progenitor marker gene SOX2 with P2A-EGFP. On the other hand, to label neurons, we inserted dTomato driven by human Synapsin1 (hSYN1) promoter in the AAVS1 safe harbor locus. Using this reporter line, we generated telencephalon brain organoids enriched in dorsal telencephalon tissue and isolated EGFP+, dTomato+ and double positive cells across different stages of organoid development (Days 40, 60, 90 and 120) . We isolated RNA from the sorted populations and performed RNA-seq.

first: Jürgen

last: Knoblich


title: Results of RNA-seq of ribosome fractions from control and TSC2 KO Day37 organoids

summary: mTOR pathway is a major regulator of translation in eukaryotic cells. Here we investigate the impact of mTOR overactivation through TSC2 KO on the translatome of brain organoid tissue.

overall_design: Day37 organoids were dissociated and the lysate was used for polysome profiling. Monosome, low-polysome and high-polysome fractions were separately collected and the RNA associated with these fractions was isolated and used for RNA-seq


title: Alphavirus infection triggers antiviral RNAi immunity in mammals

status: Public on Oct 04 2022

city: Wuhan

first: Yang

last: Qiu

state: Hubei

address: No. 44 Xiaohongshan Central District, Wuchang District,

institute: Wuhan institue of virology, CAS

summary: RNA interference (RNAi) functions as an antiviral immune response in plants and invertebrates, whereas mammalian RNAi response has been found so far only in undifferentiated cells and in differentiated cells inactive in interferon (IFN) system or in infections with viruses disabling viral suppressors of RNAi (VSRs), thereby leading to question the physiological importance of the RNAi pathway in mammals. Here, we identified that wild-type Semliki Forest virus (SFV), a prototypic alphavirus, triggered the Dicer-dependent production of abundant viral (v)siRNAs in different mammalian somatic cells in the presence of VSR. These vsiRNAs were produced from viral dsRNA replicative intermediates, almost exclusively located at the 5’ termini of the viral genome, and loaded into AGO, and they were fully active in slicing cognate viral RNAs. Besides, Sindbis virus, another alphavirus, also induced vsiRNA generation in mammalian somatic cells. AGO2 deficiency increased SFV and SINV replication, while enoxacin, a known RNAi enhancer that functions at post steps of siRNA production, efficiently reduced viral replication. The nucleotide sequence at the 5’ termini of SFV and SINV genome is conserved among the Old World alphaviruses, and mutating the conserved sequences resulted in the recombinant SFV being deficient in vsiRNA production and irresponsive to antiviral RNAi. SFV infection also enabled the production of abundant vsiRNAs and antiviral RNAi in IFN-competent adult mice, and importantly, enhanced RNAi by enoxacin protected adult mice from lethal SFV challenge and reduced the virus-induced neuropathogenesis in the central neuron system. Overall, our findings provide evidence that mammalian antiviral RNAi is active in differentiated cells and adult mice with intact IFN response even in the presence of VSR and present a therapeutic strategy against alphaviruses that include many important emerging and reemerging human pathogens.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Small RNA profile of virus-infected cells and mice. RNA-seq of cells transfected with siRNAs.

first: Jing

last: Kong

first: Yuanyuan

last: Bie

first: Wenting

last: Ji

first: Jiuyue

first: Bao

last: Lyu

first: Xiaobei

last: Xiong

first: Xi

last: Zhou


title: Meiotic gene transcription programs are mediated by A-MYB and BRDT-dependent RNA Pol II pause release during mammalian prophase I [ATAC-Seq]

status: Public on Sep 30 2022

city: Ithaca

first: Charles

last: Danko

state: NY

address: 235 Hungerford Hill Rd

institute: Cornell University

summary: During meiotic prophase I, germ cells must balance transcriptional activation with meiotic recombination and chromosome synapsis, biological processes requiring extensive changes to chromatin state and structure. Here we explored the interplay between chromatin accessibility and transcription across a detailed time-course of murine male meiosis by measuring genome-wide patterns of chromatin accessibility, transcription, and processed mRNA. To understand the relationship between these parameters of gene regulation and recombination, we integrated these data with maps of double-strand break formation. Maps of nascent transcription showed that Pol II is loaded on chromatin and maintained in a paused state early during meiosis. In pachynema, paused Pol II is released in a coordinated transcriptional burst resulting in ~3-fold increase in transcription. Release from pause is mediated by the transcription factor A-MYB and the testis-specific bromodomain protein, BRDT. The burst of transcriptional activity is both temporally and spatially segregated from key steps of meiotic recombination: double strand breaks show evidence of chromatin accessibility earlier during prophase I and at distinct loci from those undergoing transcriptional activation, despite shared chromatin marks. Our findings uncover the mechanisms of transcriptional activation and how cells compartmentalize transcription and recombination during meiosis.

overall_design: Assay for Transposase Accessible Chromatin and Sequencing (ATAC-seq) samples for prophase I substages: Leptonema/Zygonema, Pachynema, and Diplonema.  Raw fastq files and bigWig files are provided.

first: Adriana

middle: K

last: Alexander

first: Edward

middle: J

last: Rice

first: Gilad

last: Barshad

first: Lina

last: Zhu

first: Paula

last: Cohen

middle: G


title: MHC class I and MHC class II reporter mice enable analysis of immune oligodendroglia in mouse models of multiple sclerosis

status: Public on Sep 23 2022

city: Baltimore

first: Matthew

middle: D

last: Smith

state: MD

address: 600 N Wolfe Street

department: Neurology

institute: Johns Hopkins University

summary: Oligodendrocytes and their progenitors upregulate MHC pathways in response to inflammation, but the frequency of this phenotypic change is unknown and the features of these immune oligodendroglia are poorly defined. We generated MHC class I and II transgenic reporter mice to define their dynamics in response to inflammatory demyelination, providing a means to monitor MHC activation in diverse cell types in living mice and define their roles in aging, injury and disease.

overall_design: Reporter mice for MHC I (B2m-tdTomato) or MHC II (CD74-tdTomato) were immunized with MOG35-55 to induce EAE, then at peak EAE brain was dissociated at peak disease and sorted into tdTomato+ or tdTomato- then subjected to single cell RNA sequencing analysis

first: Em

middle: P

last: Harrington

first: Riley

last: Catenacci

first: Dongeun

last: Heo

first: Cecilia

last: Miller

first: Keya

middle: R

last: Meyers

first: Jenna

last: Glatzer

first: Dwight

last: Bergles

first: Peter

last: Calabresi


title: Longitudinal single cell transcriptional and epigenetic mapping of effector, memory, and exhausted CD8 T cells reveals shared biological circuits across distinct cell fates [scATAC-Seq 1]

status: Public on Oct 31 2022

city: Philadelphia

first: E

middle: JOHN

last: WHERRY

state: PA

address: 421 Curie Blvd,354 BRB II/III

department: Systems Pharmacology       and Translational Therapeutics,Institute for Immunology

institute: University of Pennsylvania

summary: scATAC-seq  from LCMV-specific P14 CD8 T cells after LCMV-Armstrong at day 60 and day 200 post infection

overall_design: LCMV-specific P14 cells were sorted from mice infected with LCMV-Arm days 60 or 200 post infection. scATAC-seq  libraries were prepared using 10x Genomics kits.

first: Josephine

last: Giles

last: Wherry


title: Transcriptome analysis of Arabidopsis Root in response to cellooligomers (cellotriose)

status: Public on Sep 20 2022

city: Jena

first: Yu-Heng

last: Tseng

state: Thuringia

address: Dornburgerstr. 159

department: Plant Physiology

country: Germany

institute: Matthias Schleiden Institute of Genetics, Bioinformatics and Molecular Botany, Friedrich-Schiller University Jena

summary: Purpose: We recently identified a mutant (cork1) which did not respond to cellooligomers (COs). To find out the signaling events following CO perception, roots from the segregated wild-type and homozygous mutants (F2 generation from cork1-2 X AeqWT) were treated with 10 µM cellotriose and water. Total RNA from root tissue was extracted after 1 hour. The raw reads were mapped to TAIR10 reference genome with STAR (v. 2.7.10a). Readcounts were generated from the mapped bam files with featureCount (v. 2.0.1). DESeq2 (v. 1.34.0) was applied to calculate the fold change and statistics for each mapped gene.

overall_design: Roots from 8 seedlings of segregated wid-type or homozygous mutant were treated with 1mL of water or 10 µM cellotriose. Root tissues were collected after 1 hour for total RNA extraction. For each sample, 16 seedlings were used.


title: Diversity of astrocytes across the mouse CNS [bulk RNA-seq]

status: Public on Sep 19 2022

city: Los Angeles

first: Riki

last: Kawaguchi

address: 760 Westwood Plaza, Room 37-420

department: Department of Psychiatry and Neurology Department of Psychiatry

institute: University of California, Los Angeles

summary: We assessed astrocyte transcriptomic signatures using RiboTag methods in 13 CNS regions.

overall_design: Tissues of 12 CNS regions were dissected from 4 adult male and female Aldh1l1-Cre/ERT2 x Ribotag mice. After homogenization, RNA was purified from cleared lysate as the input and control, and astrocyte-specific ribosome-associated RNA was precipitated via a hemagglutinin (HA) tag.

first: Fumito

last: Endo

first: Fuying

last: Gao

first: Baljit

last: Khakh


title: Meiotic gene transcription programs are mediated by A-MYB and BRDT-dependent RNA Pol II pause release during mammalian prophase I [leChRO-seq]

first: Charles

last: Danko

overall_design: length extension chromatin run-on and sequencing (leChRO-seq) samples for prophase I substages: Leptonema/Zygonema, Pachynema, and Diplonema.  Raw fastq files, bigWig, and dREG files are provided.

first: Adriana

last: Alexander

first: Edward

last: Rice

first: Gilad

last: Barshad

first: Lina

last: Zhu

first: Paula

last: Cohen


title: Meiotic gene transcription programs are mediated by A-MYB and BRDT-dependent RNA Pol II pause release during mammalian prophase I [RNA-Seq]

overall_design: RNA-seq samples for prophase I substages: Leptonema/Zygonema, Pachynema, and Diplonema.  Raw fastq files and bigWig files are provided.


title: RNA-Seq of rat cardiac fibroblasts depleted for Yap and Wwtr1

status: Public on Oct 29 2022

city: Wauwatosa

first: Michael

middle: Andrew

last: Flinn

state: WI

address: 8701 W Watertown Plank Rd

department: Physiology

institute: Medical College of Wisconsin

summary: Primary neonatal rat cardiac fibroblasts were isolated and subjected to siRNA mediated Yap and/or Wwtr1 knockdown

overall_design: Primary cardiac myocytes were isolated from two-day old rats via neonatal heart dissociation kit (Miltenyi Biotec) according to the manufacturer’s protocol followed by percoll gradient separation. Cells were transfected with siRNAs designed against  Yap, Wwtr1, a combination of Yap and Wwtr1, or universal negative control siRNAs. Transfected cells were collected 48 hours post transfection for RNAseq.

first: Micahel

first: Xiaoxu

last: Zhou

first: Pengyuan

last: Liu

first: Caitlin

middle: C

last: O'Meara


title: Endothelial Rbpj is essential for the education of tumor-associated macrophages

status: Public on Sep 15 2022

city: Heidelberg

first: Elisenda

last: Alsina Sanchis

address: Im Neuenheimer Feld 280

institute: DKFZ

summary: Epithelial ovarian cancer (EOC) is one of the most lethal gynecological cancers worldwide. EOC cells educate tumor-associated macrophages (TAMs) through CD44-mediated cholesterol depletion to generate an immunosuppressive tumor microenvironment (TME). In addition, tumor cells frequently activate Notch1 receptors on endothelial cells (ECs) to facilitate metastasis. However, little is known whether the endothelium would also influence the education of recruited monocytes. Here, we report that canonical Notch signaling through RBPJ in ECs is an important player in the education of TAMs and EOC progression. Deletion of Rbpj in the endothelium of adult mice reduced infiltration of monocyte-derived macrophages into the TME of EOC and prevented the acquisition of a typical TAM gene signature. This was associated with stronger cytotoxic activity of T cells and decreased tumor burden. Mechanistically, we identified CXCL2 as a novel Notch/RBPJ target gene. This angiocrine factor regulates the expression of CD44 on monocytes and subsequent cholesterol depletion of TAMs. Bioinformatic analysis of ovarian cancer patient data showed that increased CXCL2 expression is accompanied by higher expression of CD44 and TAM education. As such, EOC cells employ the tumor endothelium to secrete CXCL2 in order to facilitate an immunosuppressive microenvironment.

overall_design: Samples were obteined after cell sorting of tumor-associated macrophages (TAMs) CCR2+ (CD45+, CD11b+, F4/80+, CCR2+) and TAMs CCR2- (CD45+, CD11b+, F4/80+, CCR2-) in RbpjiΔEC and control mice.

first: E

last: Alsina-Sanchis

first: R

last: Mülfarth

first: I

last: Moll

first: S

last: Böhn

first: L

last: Wiedmann

last: Jordana-Urriza

first: T

last: Ziegelbauer

last: Zimmer

first: J

last: Taylor

first: F

last: De Angelis Rigotti

first: A

last: Stögbauer

first: B

last: Giaimo

last: Cerwenka

last: Borggrefe

last: Fischer

last: Rodriguez-Vita


title: Vehicle or Digoxin treatment in AC16 cells and mouse

status: Public on Sep 14 2022

city: Lille

first: Philippe

last: Lefebvre

address: Bâtiment J&K, Faculté de Médecine de Lille-Pôle Recherche, Boulevard du Professeur Leclerc

country: France

institute: INSERM UMR 1011, Université Lille-Nord de France


title: Vehicle or Digoxin treatment 1mg/kg IP dosing at ZT5 and sacrifice at ZT9 [mouse]

summary: Myocardial ischemia-reperfusion injury (MIRI) is a major threat to heart functional integrity and pharmacological means to achieve cardioprotection are sorely needed. The sequential hypoxic/normoxic status of the cardiac tissue triggers life-threatening damages through the activation of multiple intra-cellular pathways. Heart tolerance to MIRI varies according to a day-night cycle and is regulated by components of the molecular clock such as the transcriptional repressor and nuclear receptor REV-ERBα. Timed REV-ERBα antagonism alleviates sensitivity to myocardial infarction in mice.  Here we show that timed administration of digoxin is cardioprotective by triggering REV-ERBα protein degradation and involves the anti-apoptotic factor p21. Kinomics and transcriptomic assays revealed that in several cardiomyocyte cellular models, digoxin and other cardiotonic steroids induced multiple signaling pathways at subinotropic doses. Pharmacological inhibition and knockdown approaches revealed that inhibition of phosphatidylinositol 3- and of Src tyrosine-kinase partially alleviated digoxin-induced REV-ERBα degradation, which was fully prevented upon proteasome inhibition. REV44 ERBα is increasingly ubiquitinylated in digoxin-treated cells, and its degradation depends on its ability to bind its natural ligand, heme. In normal conditions, the proteasomal degradation of REV-ERBα is controlled by several known (HUWE1, FXW7, SIAH2) or novel (CBL, UBE4B) E3 ubiquitin ligases. Only SIAH2 together with the proteasome subunit PSMB5 contributed to the digoxin-induced degradation of REV-ERBα. Taken together, these results show that controlling REV-ERBα proteostasis is an appealing cardioprotective strategy, and bring further support to the rationale, timed use of CTS in prophylactic cardiac preconditioning to MIRI.

overall_design: Mice were injected intraperitoneally with 1mg/kg digoxin (Nativelle Adult)  or  Sham (a  co-solvent  consisting  of  10%  ethanol, 40%  propylene  glycol, 0.08% citric acid, 0.3% sodium phosphate) at ZT5.Mice were sacrificed by cervical dislocation at ZT9.Organs were harvested and snap-frozen RNA analysis. Gene expression from mouse hearts from Sham (4 samples) or digoxin (5 samples) treatment was analyzed with Affymetrix GeneChip Mouse Gene 2.0 ST arrays after RNA amplification, sscDNA labeling, and purification. Briefly, RNA was amplified using the GeneChip™ WT PLUS Reagent Kit (Thermo Fisher Scientific), retrotranscribed to cDNA and labeled using GeneChip™ WT Terminal Labeling Kit (Thermo Fisher Scientific), followed by hybridization on the GeneChip Mouse Gene 2.0 ST Array (Affymetrix) according to the manufacturer’s instructions. Raw data were processed further using GIANT (Galaxy-based interactive tools for Analysis of Transcriptomic data). This user-friendly tool suite was developed in-house for microarray and RNA-seq differential data analysis. It consists of modules allowing to perform quality control (QC), Robust Multi-Average method normalization, LIMMA differential analysis, volcano plot and heatmaps. Using the GSEA module, normalized data were converted to GSEA compatible format for further analysis.

first: Manjula

last: Vinod

first: Gheeraert

last: Céline


title: Transcriptomic analysis of synchonized AC16 cells treated with 0.5µM or 5µM digoxin after T0, T4, T16 and T20.

overall_design: Gene expression from AC16 cells was analyzed with Affymetrix GeneChip Hu Gene 2.0 ST arrays after RNA amplification, sscDNA labeling, and purification. Briefly, RNA was amplified using the GeneChip™ WT PLUS Reagent Kit (Thermo Fisher Scientific), retrotranscribed to cDNA and labeled using GeneChip™ WT Terminal Labeling Kit (Thermo Fisher Scientific), followed by hybridization on the GeneChip Human Gene 2.0 ST Array (Affymetrix) according to the manufacturer’s instructions. Raw data were processed further using GIANT (Galaxy-based interactive tools for Analysis of Transcriptomic data). This user-friendly tool suite was developed in-house for microarray and RNA-seq differential data analysis. It consists of modules allowing to perform quality control (QC), Robust Multi-Average method normalization, LIMMA differential analysis, volcano plot and heatmaps. Using the GSEA module, normalized data were converted to GSEA compatible format for further analysis.


title: Impact of circadian time, feeding-fasting rhythm and the autonomous clock on the transcriptome

status: Public on Sep 13 2022

city: irvine

first: Siwei

last: Chen

address: 66304 Verano Road South

department: Computer Science

institute: University of California, Irvine

summary: Using an "omics"-based approach, we investigated the interaction between the autonomous liver clock and feeding-fasting rhythm. Transcriptomic analysis and subsequent quantification of exonic and intronic reads revealed that transcriptional mechanisms mediate, at least in part, the integration of feeding signals by the liver clock to drive mRNA oscillations. Therefore, we performed ATAC-seq to probe the state of chromatin accessibility genome-wide. While most open chromatin regions are unchanged across genotype, time and feeding status, transcription factor (TFs) footprints showed altered activity of certain TFs in Liver-RE AL vs NF. For example, CEBPB activity is altered in Liver-RE AL and restored in NF, an observation accompanied by restored CEBPB and BMAL1 common target gene oscillations. Finally, metabolomics analysis illustrated the partial rescue of hepatic metabolism in Liver-RE NF compared to AL (extensive carbohydrate pathway oscillations), and made clear that extra-hepatic clocks contribute significantly to metabolic oscillations in the liver, particularly for pathways involving lipids. Please see the associated reference for full results.

overall_design: 8-12 week old male wild type (WT), Bmal1-KO (Bmal1 stop-Fl; KO) and Bmal1 Liver-reconstituted (Bmal1 stop-Fl, AlfP cre +/-; Liver-RE) mice were subjected to ad libitum feeding (AL) or feeding restricted to the nighttime (NF, ZT12-24) of normal chow for 2 weeks under a standard 12 hr light - 12 hr dark cycle. Livers were collected at ZT0, 4, 8, 12, 16 and 20 and prepared for RNA-sequencing.

first: Kevin

last: Koronowski

first: Carolina

middle: M

last: Greco

first: Jacob

last: Smith

first: Muntaha

last: Samad

first: Pierre

last: Baldi

first: Paolo

last: Sassone-Corsi


title: Microgravity on the International Space Station promotes survival and proliferation of human stem cell cardiomyocytes

status: Public on Sep 08 2022

city: Atlanta

first: Gregory

last: Tharp

state: GA

address: 954 Gatewood Dr

department: Developmental and Cognitive Neuroscience

institute: Yerkes National Primate Research Center

summary: Efficient generation of functional cardiomyocytes from human induced pluripotent stem cells (hiPSC-CMs) is critical for their use in regenerative medicine and other applications. In this study, we evaluated the effect of space microgravity (µg) on the differentiation of hiPSC-derived cardiac progenitors compared with parallel 1g condition on the International Space Station. Cryopreserved 3D cardiac progenitors derived from hiPSCs were cultured for 3 weeks. Compared with 1g culture, the µg culture had larger sphere sizes, increased expression of proliferation markers, higher counts of nuclei, and higher cell viability. Highly enriched cardiomyocytes generated in µg had appropriate gene expression and cardiac structure as well as improved function including contractility and Ca2+ handling. RNA-seq analysis of 3-day cultures revealed that short-term exposure of cardiac progenitor spheres to space microgravity upregulated genes involved in cell proliferation, cardiac differentiation, and contraction. These results indicate that space microgravity increased survival and proliferation of hiPSC-CMs and improved their structures and functions.

overall_design: Three replicates of cardiac progenitor cells were cultured in space microgravity (µg), space 1g. Aliquots harvested after 3 days of culture were examined for mRNA expression differences.

first: Antonio

last: Rampoldi

first: Parvin

last: Forghani

first: Dong

last: Li

first: Hyun

last: Hwang

first: Lawrence

last: Armand

first: Jordan

last: Fite

first: Gene

last: Boland

first: Joshua

last: Maxwell

last: Maher

first: Chunhui

last: Xu


title: Inflammation and senescence-related microRNAs from circulating small extracellular vesicles are altered in women undergoing preterm birth.

city: Bauru

first: Bruna

last: Ribeiro de Andrade Ramos

state: São Paulo

address: R. Prof Gérson Rodrigues

department: Pathology

country: Brazil

institute: São Paulo State University

summary: Preterm labor (PTL) and preterm premature rupture of membranes (PPROM) lead to severe perinatal morbidity/mortality worldwide. Small extracellular vesicles (sEV) act in cell communication and contain microRNAs that are potential biomarkers for these complications. We aimed to compare the expression, in sEV from peripheral blood, of miRNAs between term and preterm pregnancies.

overall_design: Case-control study with women with PTL, PPROM, term pregnancy with and without labor, seen at the Botucatu Medical School Hospital, SP, Brazil. sEV were isolated from plasma. Western blot for detection of exosomal protein CD63 and Nanoparticle Tracking Analysis were performed. The expression of 800 miRNAs was assessed by nCounter Humanv3 miRNA Assay (NanoString). Comparison of miRNAs expression and relative risk was performed.

first: Júlia

last: Tronco

first: Márcio

last: Carvalho

first: Tainara

middle: F

last: Felix

first: Patrícia

last: Reis

first: Juliano

last: Silveira

first: Márcia

last: Silva


title: Dissecting the genetic and microenvironmental factors of gastric tumorigenesis in mice

status: Public on Sep 05 2022

city: Chengdu, China

first: Ailing

last: Zhong

state: Sichuan

address: No.17 Renmin road section3

department: State Key Laboratory of Biotherapy, West China Hospital, Sichuan University.

institute: Sichuan University

summary: Gastric cancer (GC) is one of the most frequent and lethal malignancies in the world. However, our understanding of the mechanisms underlying its initiation and progression is limited. Here, we applied genome-edited gastric organoids to establish a series of primary GC models in mice, which elucidated the genetic drivers for sequential transformation from dysplasia to well-differentiated and poorly differentiated GC. Further, we found that the orthotopic GC, but not the subcutaneous GC even with the same genetic drivers, displayed remote metastasis, suggesting critical roles of the microenvironment in GC metastasis. Through single-cell RNA-seq analyses and functional studies, we revealed that the molecular interaction between fibronectin 1 on stomach-specific macrophages and integrin α6β4 on GC cells promoted liver metastasis. Taken together, our studies proposed a new strategy to model GC and dissected the genetic and microenvironmental factors driving the full-range gastric tumorigenesis.

overall_design: Gastric tumorigenesis in mice

first: Zhenghao

last: Lu

first: Hongyu

last: Liu

first: Chong

last: Chen


title: Glucocorticoid Activation of Anti-Inflammatory Macrophages in Coordination with STAT6 Protects Against Insulin Resistance

status: Public on Sep 01 2022

city: Odense

first: Alexander

last: Rauch

address: Campusvej 55

department: Department of Clinical Research

country: Denmark

institute: University of Southern Denmark and Odense University Hospital

summary: Deletion of the GC receptor (GR) in macrophages in mice, aggravates obesity-related insulin resistance, by reducing anti-inflammatory macrophages, and enhancing adipose tissue inflammation. Consequently, the reduction of anti-inflammatory macrophages leads to exaggerated adipose tissue lipolysis and severe hepatic steatosis. Mechanistically, macrophages deficient for GR show a diminished response to IL-4 driven anti-inflammatory polarization, due to disruption of an epigenetic crosstalk between GC and IL-4 signaling involving synergistic loading of GR and STAT6. Our results demonstrate that GR plays an important role in macrophage polarization during obesity by limiting adipose tissue inflammation and lipolysis to promote insulin sensitivity

overall_design: RNA-seq of F4/80 purified ATMs isolated from eWAT of obese WT and GRLysMCre mice. RNA-seq from cultured fetal liver derived macrophages from WT and GRnull mice treated with dexamethasone, interleukin 4 or a combination of both. ChIP-seq of anti-H3K27ac precipitated chromatin from cultured bone marrow liver derived macrophages from WT and GRLysMCre mice treated with dexamethasone and interleukin 4.

first: Giorgio

last: Caratti

first: Ulrich

last: Stifel

first: Bozhena

first: Ali

last: Jamil

first: Kyoung-Jin

last: Chung

first: Michael

last: Kiehntopf

first: Matthias

last: Blüher

first: Jan

last: Tuckermann


title: Tumor cell efferocytosis in monocyte derived macrophages

city: New York

first: Miriam

last: Merad

address: 1470 Madison Ave, 5th Floor

department: Department of Oncological Sciences

institute: cahn School of Medicine at Mount Sinai

summary: Using GFP as a surrogate tumor antigen, we isolated monocyte derived macrophages (MoMac) from KP-GFP tumor lungs based on high and low tumor antigen burden and compared their transcriptome using high-throughtput bulk RNA sequencing

overall_design: Samples belong to two independent experiments. From each one, we FACS sorted MoMacs (CD45+ Ly6G- CD64+ MERTK+ CD2- MHCII+) with either high or low GFP signal (2 samples per condition and per experiment).

first: Ivan

last: Reyes-Torres


title: scRNAseq profiling of lung myeloid cells in Trem2+/+ : Trem2-/- mixed bone marrow chimeric mice

summary: scRNAseq profiling of FACS-sorted Trem2 +/+ (CD45.2+) and Trem2 -/- (CD45.1+) myeloid enriched (DAPI-CD45+Ly6G- CD3e-CD11b+ and/or CD11c+) fractions purified from KP-GFP bearing lungs (21 days after tumor delivery intravenously) isolated from mixed bone marrow chimeric mice.

overall_design: Two samples

first: Travis

last: Dowson


title: scRNAseq profiling of myeloid and lymphoid cells in total Trem2+/+ and Trem2-/- lungs

summary: scRNAseq profiling of FACS-sorted myeloid enriched (DAPI-CD45+Ly6G- CD3e-CD11b+ and/or CD11c+) and lymphoid enriched (DAPI-CD45+Ly6G- CD3e+) fractions purified from murine lungs bearing KP-GFP tumor lesions (28 days after tumor delivery intravenously) isolated from Trem2+/+ and Trem2-/- animals

overall_design: 2 samples


title: Treadmill physical exercise on prearthritic phase of collagen induced arthritis in DBA1 mice_transcriptome responses on tarsal joint

status: Public on Aug 30 2022

city: Chihuahua

first: Susana

middle: Aideé

last: González-Chávez

state: Chihuahua

address: Circuito Universitario Campus II

department: Facultad de Medicina

country: Mexico

institute: Universidad Autónoma de Chihuahua

summary: Gene expression profiles in the tarsal joints of DBA/1 mice whit collagen-induced arthritis that performed treadmill exercise in the pre-arthritic phase vs. those who were not exercised were compared. Exercise induced the downregulation of inflammatroy genes and signaling pathways.

overall_design: Pools of total RNA were made per study group (eight mouse per group): CIA exercised mice (test group) and CIA non-exercised mice (reference). The reverse transcription polymerase chain reaction (RT-PCR) was performed and the resulting complementary DNAs were labeled with Cy5 (CIA exercised mice) or Cy3 (CIA non-exercised mice). Hybridation analysis used the mouse 65-mer oligo library from Sigma-Genosys to compare the expression of 23,232 gene-specific oligonucleotide probes for mouse.

first: César

last: Pacheco-Tena


title: Gene expression data of serially sorted primary AML patient blasts prior and after treatment with the DNMT inhibitor decitabine (DAC)

status: Public on Aug 31 2022

city: Freiburg

first: Gabriele

last: Greve

address: Hugstetter Str 55

department: Department of Internal Medicine 1

institute: University of Freiburg Medical Center

summary: The therapeutic effect of DNA-hypomethylating agents (HMAs) in AML/MDS is discussed to be via its effects on aberrant gene silencing by reactivation (e.g. through promoter demethylation). While this has been broadly studied in cell line models, only very few studies have addressed the global effects of HMAs in primary blasts serially isolated from AML patients (pts) undergoing HMA treatment (Claus et al., Leuk. Res. 2013, Klco et al., Blood 2013, Welch et al., N. Engl. J. Med. 2016). We therefore conducted prospective serial methylome and transcriptome analyses on AML blasts from pts of the DECIDER trial (NCT00867672), hypothesizing that both random and non-random effects of the HMA may be observed in vivo.

overall_design: Total RNA of serially sorted blasts from 23 patients (at day 0 and 8) was isolated by TRIZOL (Thermo Fisher Scientific, Waltham, MA, USA) extraction and RNA phase was purified with the Qiagen RNeasy MinElute Cleanup Kit. Total RNA concentration was measured with the Qubit Fluorometer (Thermo Fisher Scientific) and integrity was determined by fragment analysis. RNA samples with RQN > 8.5 were further processed with the Affymetrix WT Plus kit and hybridized to GeneChip Human Gene 2.0 ST expression arrays (Affymetrix, Santa Clara, CA, USA) as described by the manufacturer. To avoid a possible batch effect, samples were pipetted in triplicates and randomized across and within plates.

first: Geoffroy

last: Andrieux

first: Nadja

last: Blagitko-Dorfs

first: Pascal

last: Schlosser

first: Melanie

last: Börries

last: Lübbert


title: Macrophage-specific Act1 Knockdown Promoted Adenoma-Adenocarcinoma Transition in Apcmin+/- Mice via Activation of the CXCL9/10-CXCR3 axis

city: Guangzhou

first: Lingyun

last: Zheng

state: Guangdong

address: No. 280, Waihuan East Road, Guangzhou Higher Education Mega Center,Panyu district,

department: School of Life Sciences and Biopharmaceutics

institute: Guangdong Pharmaceutical University

summary: macrophages involve in colorectal adenocarcinoma transition. Mouse MC38 colorectal cancer cells were co-cultured with BMDM from both anti-Act1 and Wildtype mice. MC38 cells have higher migration speed and express higher EMT markers including Snail, E-cadherins, and Twist after co-culture with anti-Act1 macrophage.  Expression profiling by high throughput sequencing highlighted that by co-culturing with MC38 cells, anti-Act1 macrophage increase proinflammatory cytokines secretion and consequently activates cytokines receptor signaling pathway. Specifically, we identified the mechanism where CXCL9/10 from anti-Act1 macrophage interacted with CXCR3 receptor in MC38 cell to promote MC38 migration as well as EMT. Besides, coculturing with MC38 cells enhanced expressions of PD-L1 and MDSCs markers such as Arg1, iNOS, IDO1 in anti-Act1 macrophages. Among activating pathways,  we reveal that anti-Act1 macrophage orchestrates NF-kB and STAT3 signaling pathways to upregulate CXCL9/10 secretion and PD-L1 expression. These findings demonstrate that anti-Act1 in macrophage induced a significant shift in MC38 cells gene expression, and modulating the macrophage-cancer is a viable strategy to assist PD-L1 immunotherapy.

overall_design: Bulk RNA-seq of  mouse BMDM  coculturing with mouse MC38 cells for 48h

first: Shunyi

last: Wang

first: Yihe

last: Hui

first: Lijing


title: Synaptic Scaling of Corticostriatal Circuits Underlies Hyperactivity in GABA Transporter-1 Deficient Mice

status: Public on Aug 20 2022

city: Shanghai

first: Yanjiao

last: WU

state: Shanghai

address: 280 South Chongqing Road

department: Discipline of Neuroscience and Department of Anatomy and Physiology

institute: Shanghai Jiao Tong University School of Medicine

summary: To explore the potential mediators of corticostriatal synaptic scaling in GAT1–/– mice, whole-tissue mRNA sequencing was carried out for the dorsal striatum of GAT1+/+ and GAT1–/– mice.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for striatum of GAT1 wild type and its knockout mice (GAT1+/+ and GAT1–/– mice).

first: Yan-Jiao

last: Wu


title: HALTING THE NAD+-DEPENDENT DEACETYLASE SIRT6 UNVEILS SPLICEOSOME DEREGULATION AS EXPLOITABLE VULNERABILITY FOR AGGRESSIVE MYELOMA

status: Public on Aug 19 2022

city: Genoa

first: Michele

last: Cea

state: Genoa

address: viale Benedetto XV, 6

department: Department of Internal Medicine (DiMI)

country: Italy

institute: University of Genoa

summary: Epigenetic defects play a major role in tumors, by promoting aggressiveness, drug resistance and disease progression. Targeting enzymes responsible for these changes holds promise but the knowledge-gap and lack of selective inhibitors severely hampers their clinical use. Recently, we found that Multiple Myeloma (MM) cells exhibit high level of NAD+-dependent deacetylase SIRT6 as an adaptive response to their intrinsic genomic instability. Here we focus on splicing-related events resulting as the most enriched pathways among MM patients with high SIRT6 levels. CoMMpass dataset analysis confirmed the prognostic role of SIRT6 in MM, with its presence correlating with poor outcome and aggressiveness. Transcriptome analysis of SIRT6-depleted MM cells indicated spliceosome perturbation as critical: chemical and genetic approaches resulted in enhanced anti-MM activity of spliceosome modulator Sudamycin D6 (SD6) thus supporting RNA splicing deregulation as vulnerability for these cells. Spliceosome is a therapeutic weakness for MYC-driven cancer, as such we found that while c-MYC oncogene loss shows resistance, its re-expression enhances efficacy of tested strategy. A direct role for SIRT6 on splicing factors genes was also demonstrated using ChIP-seq analyses. Overall, the dysregulated spliceosome activity triggered by epigenetic machinery blocking represents a novel therapeutic strategy for poor-prognosis subset of MM patients overexpressing c-MYC

overall_design: The HMCL were purchased from ATCC or DSMZ. All cell lines were Mycoplasma-free and routinely tested for it. Cells were cultured in RPMI-1640 medium containing 10% fetal bovine serum (FBS; GIBCO), 4mM glutamine, 100 U ml−1 penicillin, and 100 μg ml−1 streptomycin (GIBCO). 293T were cultured in DMEM high glucose containing 10% FBS (GIBCO), 4 mM glutamine, 100 U ml−1 penicillin, and 100 μg ml−1 streptomycin (GIBCO). RNA samples from NCI-H929 and MM1.S cells scramble (SCR) and silenced for SIRT6 (shSIRT6) were obtained in duplicate for each condition and processed using WT PLUS Reagent Kit, according to manifacturer’s protocol (Thermo Fisher). mRNA-transcriptome profiling was assessed using GeneChip™ Human Gene 2.0 ST Array (Thermo Fisher).

first: Elisa

last: Gelli

first: Debora

last: Soncini

first: Pamela

last: Becherini

first: Claudia

last: Martinuzzi

first: Katia

last: Todoerti

first: Antonia

last: Cagnetta

first: Sara

last: Aquino

first: Fabio

last: Guolo

first: Maurizio

last: Miglino

first: Santina

last: Bruzzone

first: Alessio

last: Nencioni

first: Antonino

last: Neri

first: Roberto

last: Lemoli


title: Effect of progesterone and PSAT1 treatment on endometrial epithelial transcript expression

city: Leeds

first: LeedsOmics

last: UoLeeds

state: West Yorkshire

address: Clarendon Way

department: Cross-faculty

institute: University of Leeds

summary: We tested the hypothesis that a panel of placental mammal-specific miRNAs and their targets play important to establish receptivity to implantation and their dysregulated expression may be a feature in women with early pregnancy loss. Relative expression levels of miR-340-5p, -542-3p, and -671-5p all increased following treatment of Ishikawa cells with progesterone (10 mg/ml) for 24 hrs (p < 0.05). RNA sequencing of these P4-treated cells identified co-ordinate changes to 6,367 transcripts of which 1713 were predicted targets of miR-340-5p, 670 of miR-542-3p, and 618 of miR-671-5p. Quantitative proteomic analysis of Ishikawa cells transfected with mimic or inhibitor (48 hrs: n=3 biological replicates) for each of the P4-regulated miRNAs was carried out to identify targets of these miRNAs. Excluding off target effects, mir-340-5p mimic altered 1,369 proteins while inhibition changed expression of 376 proteins (p < 0.05) of which, 72 were common to both treatments. A total of 280 proteins were identified between predicted (mirDB) and confirmed (in vitro) targets. In total, 171 proteins predicted to be targets by mirDB were altered in vitro by treatment with miR-340-5p mimic or inhibitor and were also altered by treatment of endometrial epithelial cells with P4. In vitro targets of miR-542-3p identified 1,378 proteins altered by mimic while inhibition altered 975 a core of 200 proteins were changed by both. 100 protein targets were predicted and only 46 proteins were P4 regulated. miR-671-mimic altered 1,252 proteins with inhibition changing 492 proteins of which 97 were common to both, 95 were miDB predicted targets and 46 were also P4-regulated. All miRNAs were detected in endometrial biopsies taken from patients during the luteal phase of their cycle, irrespective of prior or future pregnancy outcomes Expression of mir-340-5p showed an overall increase in patients who had previously suffered a miscarriage and had a subsequent miscarriage, as compared to those who had infertility or previous miscarriage and subsequently went on to have a life birth outcome. The regulation of these miRNAs and their protein targets regulate the function of transport and secretion, and adhesion of the endometrial epithelia required for successful implantation in humans. Dysfunction of these miRNAs (and therefore the targets they regulate) may contribute to endometrial-derived recurrent pregnancy loss in women.

overall_design: N=3 biological replicates of Ishikawa cells were analysed via RNA sequencing following treatment of cells with prgoesterone or recombinant human PSAT1 for 24 hours.

first: Laura

last: Hume

first: Haidee

last: Tinning

first: Dapeng

last: Wang

first: Niamh

last: Forde


title: Heterozygous variants in POLR1A cause diverse human phenotypes

status: Public on Aug 15 2022

city: Cincinnati

first: Kelly

last: Smallwood

state: OH

address: 3333 Burnet Ave, S4.200BC

department: Human Genetics

institute: Cincinnati Childrens Hospital Medical Center

summary: Heterozygous pathogenic variants in POLR1A were identified as the cause of Acrofacial Dysostosis, Cincinnati-type in 2015. Craniofacial anomalies reminiscent of Treacher Collins syndrome were the predominant phenotype observed in the first 3 affected individuals. We have subsequently identified 17 additional individuals with 12 unique (11 novel) heterozygous variants in POLR1A and observed numerous additional phenotypes including developmental delay, infantile spasms, and structural cardiac defects. To understand the pathogenesis of this pleiotropy, we created an allelic series of POLR1A using a combination of in vivo (mouse) and in vitro models.   We describe distinct spatiotemporal requirements for Polr1a during mouse embryogenesis and identify a requirement for Polr1a for survival of pre migratory and migratory neural crest cells, forebrain precursors, and the second heart field. We used CRISPR/Cas9 to recapitulate two human alleles in mouse, demonstrating pathogenicity of one and likely benign nature of the other. Our work greatly expands the phenotype of human POLR1A-related disorders, provides new evidence of reduced penetrance and variable expression of POLR1A heterozygous variants, and demonstrates a multi-faceted approach to characterize and define pathogenicity of variants.

overall_design: Comparing differentially expressed genes in two Polr1a mutants; a null allele and a p.C1559F missense allele.

middle: A

first: Kathryn

middle: N

last: Weaver


title: High-resolution spatial transcriptomics of myocarditic heart from reovirus-infected neonatal mice

status: Public on Aug 14 2022

city: Ithaca

first: Iwijn

last: De Vlaminck

state: New York

address: Weill Hall, 237 Tower Road

department: Meinig School of Biomedical Engineering

institute: Cornell University

summary: A significant fraction of sudden death in young adults is due to myocarditis, an inflammatory disease of the heart, most often caused by viral infection. Here we used high resolution spatially RNA sequencing using Slide-seq platform to study  cellular phenotypes in a myocarditic heart from reovirus-infected neonatal mice at day 7 post infection. Our measurements give insight into the cardiac cell-type specific spatially-restricted inflammatory and stress responses in the myocarditic heart. Overall, our data identify spatially restricted cellular interactions and cell-type specific host responses during reovirus-induced myocarditis.

first: Madhav

last: Mantri

first: David

last: McKellar

first: John

middle: S

last: Parker


title: Placental gene expression-based cell type deconvolution: Cell proportions drive preeclampsia gene expression differences

status: Public on Aug 22 2022

city: Ann Arbor

last: Bakulski

state: MI

address: 1415 Washington Heights

department: Epidemiology

institute: University of Michigan

summary: The placenta mediates adverse pregnancy outcomes, including preeclampsia, characterized by gestational hypertension and proteinuria. Placental cell type heterogeneity in preeclampsia is not well-understood and limits mechanistic interpretation of bulk gene expression measures. We generated single-cell RNA-sequencing samples for integration with existing data to create the largest deconvolution reference of 19 fetal and 8 maternal cell types from placental villous tissue at term. We deconvoluted eight published microarray case-control studies of preeclampsia. Our findings indicate substantial placental cellular heterogeneity in preeclampsia that predict previously observed bulk gene expression differences. Our deconvolution reference lays the groundwork for cellular heterogeneity-aware investigation into placental dysfunction and adverse birth outcomes.

overall_design: Five placentas were collected for study. Four placentas were dissociated for cell type sorting and bulk RNA-sequencing. Two placentas were dissociated for single-cell RNA-sequencing; each included a technical replicate. One placenta contributed data for both experiments.

first: Kyle

last: Campbell

first: Justin

last: Colacino

first: Muraly

last: Puttabyatappa

last: Dou

first: Elana

last: Elkin

first: Saher

last: Hammoud

first: Steven

middle: E

last: Domino

first: Dana

last: Dolinoy

first: Jaclyn

last: Goodrich

first: Rita

last: Loch-Caruso

first: Vasantha

last: Padmanabhan


title: Cut&Run Analysis of ATF4 genomic occupancy in HCT116 colon carcinoma cell lines after treatment with DMSO, etoposide, tunicamycin, or histidinol

city: Albany

first: Morgan

last: Sammons

address: 1400 Washington Ave, Life Sciences 2075

department: Biological Sciences

institute: University at Albany - SUNY

summary: We examined ATF4 genomic occupancy resulting from treatment of HCT116 colon carcinoma human cell lines with DMSO, etoposide, histidinol, or, tunicamycin, using Cut&Run.

overall_design: Genomic Occupancy of a DNA binding transcription factor (ATF4) or IgG control using Cut&Run.


title: Targeting the RNA m6A reader YTHDF2 in tumor-associated macrophages shapes tumor immunity and immunotherapy [scRNA-seq]

status: Public on Aug 01 2022

city: duarte

first: Shoubao

last: Ma

state: California

address: 1500 East Duarte Road

institute: City of Hope

summary: The presence of tumor-associated macrophages (TAMs) in the tumor microenvironment (TME) affects cancer progression and immunotherapy response. The RNA m6A methylation, an epigenetic modification, has recently been found to play a pivotal role in shaping the TME. However, the role and underlying mechanisms by which RNA m6A methylation regulates TAMs function and anti-tumor immunity remain elusive. Here we show that depletion of YTHDF2, a well-known m6A reader, in TAMs suppresses tumor growth and metastasis. Myeloid YTHDF2 deficiency reprograms TAMs to anti-tumorigenic type and increases their cross-presentation ability, thereby enhancing CD8+T cell-mediated anti-tumor immunity. Transcriptome-wide screening identifies YTHDF2 deficiency facilitates anti-tumorigenic TAMs reprogramming through targeting IFN-γ-STAT1 signaling. Selectively targeting YTHDF2 in TAMs using toll-like receptor 9 agonist - conjugated small interfering RNA against YTHDF2 effectively promotes anti-tumor immunity, restrains tumor growth, and enhances the efficacy of anti-PD-L1 therapy. Together, our findings suggest that YTHDF2 in TAMs might be a promising therapeutic target for cancer immunotherapy.

overall_design: Tumors from WT or cKO mice were extracted and digested with collagenase type IV (1 mg/ml) and DNase type I (30 U/ml) for 30 min at 37 °C. The cells were filtered through the 70 μm cell strainers, washed with phosphate-buffered saline (PBS), lysed in red blood cell buffer, and resuspended in PBS. Tumor-infiltrating immune cells (CD45+ cells) were sorted by FACSAria Fusion Flow Cytometer (BD Biosciences). The cell suspension (300-600 living cells per microliter) was loaded onto the Chromium single cell controller (10 x Genomics) to generate single-cell gel beads in the emulsion according to the manufacturer’s protocol. Libraries were subsequently prepared sing Single Cell 5’Library and Gel Bead Kit and sequenced on an Illumina NovaSeq 6000 instrument with pair-end 100 bp (PE100) reading strategy.

first: Jianhua

last: Yu


title: Targeting the RNA m6A reader YTHDF2 in tumor-associated macrophages shapes tumor immunity and immunotherapy

summary: The presence of tumor-associated macrophages (TAMs) in the tumor microenvironment (TME) affects cancer progression and immunotherapy response. The RNA m6A methylation, an epigenetic modification, has recently been found to play a pivotal role in shaping the TME. However, the role and underlying mechanisms by which RNA m6A methylation regulates TAMs function and anti-tumor immunity remain elusive. Here we show that depletion of YTHDF2, a well-known m6A reader, in TAMs suppresses tumor growth and metastasis. Myeloid YTHDF2 deficiency reprograms TAMs to anti-tumorigenic type and increases their cross-presentation ability, thereby enhancing CD8+T cell-mediated anti-tumor immunity. Transcriptome-wide screening identifies YTHDF2 deficiency facilitates anti-tumorigenic TAMs reprogramming through targeting IFN-γSTAT1 signaling. Selectively targeting YTHDF2 in TAMs using toll-like receptor 9 agonist - conjugated small interfering RNA against YTHDF2 effectively promotes anti-tumor immunity, restrains tumor growth, and enhances the efficacy of anti-PD-L1 therapy. Together, our findings suggest that YTHDF2 in TAMs might be a promising therapeutic target for cancer immunotherapy.

overall_design: Total RNA was isolated by TRIzol reagent from fifty million M1-type BMDMs of WT and Ythdf2 cKO mice. m6A MeRIP sequencing was performed to detect the m6A modification alterations in two groups. YTHDF2 RNA immunoprecipitation sequencing was performed to map the target transcripts bound by YTHDF2 in M1-type BMDM.


title: Tonic-signaling chimeric antigen receptors drive human regulatory T cell exhaustion

status: Public on Jul 28 2022

city: Memphis

first: Tian

last: Mi

state: TN

address: 262 Danny Thomas Pl MS351

department: Immunology

institute: St. Jude Children's Research Hospital

type: Methylation profiling by high throughput sequencing

summary: Whether or not human Tregs are susceptible to exhaustion, and if so, if this would limit their therapeutic effect, was unknown. We studied how a tonic-signaling CAR, which induces Tconv exhaustion, affects human Tregs. We thus sorted naïve Tregs and naïve conventional CD4s and transduced them with a non-TS CAR (CD19) or a TS-CAR (HA).

overall_design: 3 TCONV CD19 CAR samples, 4 TCONV HA CAR samples, 5 TREG CD19 CAR samples, 5 TREG HA CAR samples

first: Caroline

last: Lamarche

first: Kirsten

last: Ward-Harstonge

first: Megan

last: Levings


title: Theoretical and practical refinements of sans spike-in quantitative ChIP-seq with application to p300/CBP inhibition

status: Public on Jul 11 2022

city: Grand Rapids

first: Scott

last: Rothbart

address: 333 Bostwick Avenue NE

institute: Van Andel Research Institute

summary: Previously, we introduced an absolute and physical quantitative scale for chromatin immunoprecipitation followed by sequencing. The scale itself was detemined directly from measurements routinely made on sequencing samples without additional reagents or spike-ins. We called this approach sans spike-in quantitative ChIP, or siQ-ChIP. In this paper we extend those results in several ways. First, we simplified the calculations defining the quantitative scale. Second, we highlight the normalization constraint implied by the quantitative scale and introduce a new scheme for generating 'tracks' for siQ-ChIP. We next introduce some whole-genome analyses that are unique to siQ-ChIP which allow us, for example, to project the IP mass onto the genome to evaluate how much of any genomic interval was captured in the IP. We apply these analyses to p300/CBP inhibition and demonstrate that response to inhibition is a function of genomic architecture. In particular, active transcription start sites are only weakly perturbed by p300/CBP inhibition while enhancers are strongly perturbed. Similar observations have been reported in the literature, but without a quantitative scale, those observations have been misinterpreted. We discuss how the siQ-ChIP approach precludes such misinterpretations, which stem from the wide spread community practice of treating unquantified and unnormalized ChIP-seq tracks as though they are quantitative.

overall_design: quantitative ChIP-seq (using siQ-ChIP) of H3K18ac and H3K27ac in p300/CBP inhibited cells. DMSO control and two inhibitors A485, CBP30 were used.

first: Bradley

last: Dickson

first: Ariana

last: Kupai

first: Robert

last: Vaughan

middle: B


title: Meiotic gene transcription programs are mediated by A-MYB and BRDT-dependent RNA Pol II pause release during mammalian prophase I

status: Public on Sep 30 2022

first: Charles

last: Danko

state: NY

address: 235 Hungerford Hill Rd

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

overall_design: Refer to individual Series


title: microRNA accumulation from Cuscuta campestris in vitro haustoria

status: Public on Jul 06 2022

city: University Park

first: Michael

last: Axtell

state: PA

address: 280 Mueller Lab

department: Biology

institute: Pennsylvania State University

summary: The parasitic plant Cuscuta campestris produces specialized microRNAs that are specifically expressed at the haustorial interface. Some of these "Interface-Induced MicroRNAs" function to target host mRNAs. C. campestris haustoria can be induced in the absence of any host tissues using a combination of light and physical pressure. This experiment tested with such in vitro, host-free haustoria produced interface-induced microRNAs. Small RNA-seq was performed from three different treatments: Shoot tips of C. campestris without any haustoria formation, in vitro haustoria formed in the presence of host tissue (detached leaves of Arabidopsis thaliana) and in vitro haustoria formed in the absence of any host tissue.

overall_design: Three biological replicate libraries for each specimen type (shoot tips, in vitro haustoria with host, and in vitro haustoria without host) were prepared, for a total of nine sRNA-seq libraries.

first: Collin

last: Hudzik


title: Dynamic mitochondrial transcription and translation in B cells control germinal centre entry and lymphomagenesis

status: Public on Jul 19 2022

city: Oxford

first: Alexander

last: Clarke

address: Roosevelt Drive

department: Kennedy Institute of Rheumatology

institute: University of Oxford

summary: Study of the effects of Tfam deletion on germinal centre B cells

overall_design: Mice with conditional deletion of Tfam upon Aicda expression, marked by tdTomato expression (Aicda-Cre x Tfam flox x Rosa26-Stop-tdTomato) or Aicda-Cre x Rosa26-Stop-tdTomato) wild type mice were immunised with NP-CGG, and tdTomato+ cells were sorted at D14.


title: Time course of trans-species miRNAs from Cuscuta campestris grown on Arabidopsis thaliana

summary: Cuscuta campestris is an obligate stem parasite which uses an organ called the haustoria to divert water and photosynthates from the host.  Previously, we have identified that at the haustorial interface between Cuscuta campestris and Arabidopsis thaliana, miRNAs generated by the parasite are able to move into the host and regulate host gene expression.  This study identifies how long after attachment does trans-species miRNA transcription begin in Arabidopsis thaliana and Solanum lycopersicum, as well as identifying which stage of haustoria development they become detectable.  A time course was performed by harvesting interfaces every 24 hours post attachment, and samples were subjected to RNA extraction and sRNA sequencing. We have identified that in Arabidopsis thaliana, trans-species miRNAs become detectable two days post attachment. In S. lycopersicum, some trans-species miRNAs are detectable one day post attachment, but all become detectable by day 2.  Secondary siRNA accumulation was detected four days post attachment in both hosts.  In order to determine which stage of haustoria development trans-species miRNAs become detectable, vibratome sectioning was performed on the haustorial interfaces of both hosts.  By looking at the morphology of the developing haustoria, it was determined that trans-species miRNAs become detectable during the adhesive phase.  This suggests that trans-species miRNA production is one of the first steps of haustoria development, as the parasite tissue has not started to invade host tissue before they become detectable.

overall_design: Samples were taken every 24 hours for 15 days (days 0 through 14) after coiling of the parasite around the host stem. There were between 1 and 3 replicate samples per time point.


title: Gene expression profiling of tumor-infiltrating CD45+CD8+ cells and CD45- tumor cells of tumor bearing mice treated with metformin or anti-PD-1 Ab or both

status: Public on Jul 01 2022

city: Suita

first: TAISAKU

last: OGAWA

state: Osaka

address: 6-2-3 Furuedai

institute: RIKEN

summary: B16 Mouse melanoma cells (MO5) grow in syngeneic C57BL/6 mice. Anti-PD-1 Ab as an Immunecheck point inhibitor and/or metformin were administered on day 7 after tumor inoculation to mice. The tumor growth was decreased by either anti-PD-1 Ab or metformin treatment. Anti- tumor effect was more pronounced by the combination therapy of anti-PD-1 Ab and metformin. The mechanism underlying the superior effect of the combination therapy to mono-therapies were investigated by RNA sequencing of tumor infiltrating CD8+ cells (CD8TILs) and tumor cells. As a result, CD8TILs with the combination therapy was found to express IFNg and GzmB and to activate IRF1/8, STAT1/2, NFkB, TBX21. Moreover, tumor cells were found to activate IRF1/8, STAT1/2, NFkB, indicating that tumor cells sharply responded to IFNg produced from CD8TILs. The IFNg was also found to downregulate metabolism both glycolysis and oxidative phosphorylation (OxPhos) of tumor cells, while it upregulates metabolism of CD8T cells. Collectively, the metabolic competition between CD8TILs and tumor cells was found to shift to the advantage of CD8TILs over tumor cells, resulting in the strong inhibition of tumor growth by the combination therapy of anti-PD-1 Ab and metformin.

overall_design:
Examination of CD8TILs and tumor cells of mice treated with either anti-PD-1 Ab or metformin or both.

Note: The GSE134191 and Sample metadata were updated on April 05, 2023.

first: Mikako

last: Nishida

first: Heiichiro

last: Udono

first: Taisaku

last: Ogawa

first: Katsuyuki

last: Shiroguchi


title: Transcriptome analysis for miR-10b-5p transfected leiomyosarcoma cells

status: Public on Jun 30 2022

city: Nagoya

first: Kosuke

last: Yoshida

state: Aichi

address: 65 Tsuruma-cho

institute: Nagoya University

summary: To investigate the functions of miR-10b-5p in uterine leiomyosarcoma, transcriptome analysis was performed.

overall_design: SK-LMS-1 and SK-UT-1 cells were transfected with either miR-10b-5p or Negative Control #1, and total RNA was extracted.

first: Akira

last: Yokoi

first: Jun

last: Nakayama

first: Yusuke

last: Yamamoto


title: Time course of trans-species miRNAs from Cuscuta campestris grown on Solanum lycopersicum


title: Transcriptome and microRNA profiles of uterine leiomyosarcoma and myoma


title: The microRNA profiles of uterine leiomyosarcoma

summary:
To investigate molecular biological features of uterine leiomyosarcoma, microRNA and mRNA sequencing were performed.
Here, we provide the microRNA sequencing data, and the mRNA data is GSE185543.

overall_design: Comprehensive microRNA sequencing was performed using archival-fresh frozen samples of six uterine leiomyosarcoma and three myoma samples.


title: Transcriptome analysis for uterine leiomyosarcoma and myoma

summary: Uterine leiomyosarcoma is a most aggressive gynecological malignancy, and uterine leiomyoma is a benign tumor. Here, we performed bulk RNA-seq using archival fresh-frozen tumor samples stored at the National Cancer Center Biobank.

overall_design: RNA sequencing for fresh-frozen samples of six uterine leiomyosarcoma and three myoma


title: Single-cell TCR sequencing of in vitro peripheral blood cell stimulation in ankylosing spondylitis

status: Public on Jun 29 2022

first: Liang

last: Chen

address: 99 ShangDa Road

institute: Shanghai University

summary: Single-cell TCR sequencing of in vitro DCs (DC-C96car) stimulated CD4+ T cell single cell TCR sequencing in ankylosing spondylitis

overall_design: T cells obtained from PBMCs stimulated by DCs (DC-C96car) for 30 days were sorted by FACS. CD3+CD4+ T cells and CD3+CD8+ T cells were collected, and T cells were used in further 10x Genomics Chromium™ Single Cell V(D)J immune repertoire profiling.

first: Yue

last: Zhai

first: Ping

last: Zhu


title: Multi-omic analysis of cell-of-origin and epigenomic state in pediatric H3K27M gliomas

status: Public on Jun 27 2022

city: Montréal

first: Claudia

middle: L

last: Kleinman

state: Québec

address: 3999 Côte Ste-Catherine Road

country: Canada

institute: Lady Davis Institute for Medical Research

summary: It is not known whether midline pediatric gliomas driven by Histone 3 K27M mutations (oncohistones) or EZHIP expression (oncohistone-mimics) share a common cell-of-origin, or arise from distinct cell types with unique vulnerabilities to PRC2 inhibition and partner alterations. Here, we define the etiological and oncogenic relationship between pediatric midline gliomas characterized by inhibition of K27M and K27M-like oncohistones. We assemble an extensive reference for gliogenesis from the developing mouse and human fetal brain. With bulk and single-cell transcriptomics and epigenomics, we profiled a large cohort of primary tumors comprising H3.1K27M and H3.3K27M pontine gliomas, H3.3K27M thalamic gliomas, and EZHIP+ posterior fossa ependymomas. We focus on differences across axes of location (thalamus vs. pons vs. posterior fossa), tumor type (diffuse midline gliomas vs. ependymomas), and oncohistone (H3.1/2K27M vs. H3.3K27M vs. EZHIP). We use tumor molecular features to delineate transcriptional states and cell-of-origin in each entity. Finally, we use culture models in isogenic contexts to interrogate the effect of each oncohistone or mimic.

overall_design: 8 single-cell RNA-seq samples from healthy mouse forebrains, hindbrain and pons were sequenced at E10.5, E13.5, E16.5 and E18.5. H3K27ac, H3K27me2 and H3K27me3 ChIP-seq experiments on multiple human cell lines were also performed (102 samples)

first: Selin

last: Jessa

first: Abdulshakour

last: Mohammadnia

first: Ashot

last: Harutyunyan

first: Maud

last: Hulswit

first: Srinidhi

last: Varadharajan

first: Hussein

last: Lakkis

first: Nisha

last: Kabir

first: Zahedeh

last: Bashardanesh

first: Steven

last: Hébert

first: Damien

last: Faury

first: Maria

last: Vladoiu

first: Samantha

last: Worme

first: Marie

last: Coutelier

first: Brian

last: Krug

first: Augusto

last: Andrade

first: Manav

last: Pathania

first: Andrea

last: Bajic

first: Alexandre

last: Weil

first: Benjamin

last: Ellezam

first: Jeffrey

last: Atkinson

first: Roy

last: Dudley

first: Jean-Pierre

last: Farmer

first: Sebastien

last: Perrault

last: Garcia

first: Valerie

last: Larouche

first: Mathieu

last: Blanchette

first: Livia

last: Garzia

first: Aparna

last: Bhaduri

first: Keith

last: Ligon

first: Pratiti

last: Bandopadhayay

last: Taylor

first: Stephen

last: Mack

first: Nada

last: Jabado


title: Analysis of exosomal cargo provides accurate clinical, histologic and mutational information in non-small cell lung cancer.

city: Madrid

first: Cristian

last: Suarez Cabrera

state: Madrid

address: Av. Complutense 40

institute: CIEMAT

summary: Despite advances in the understanding of lung cancer biology and the development of new drugs, most cases of lung cancer are diagnosed at an advanced stages. The present study is a proof of concept with the main aim of implementing the use of exosomes as a minimal invasive platform to search new biomarkers and determine tumor features in NSCLC.

overall_design: Gene expression was analysed in tumor-derived exosomes secreted by cell lines and primary cultures grown under different conditions, comparing between LUAD and LUSC; and adherent cells (2D) vs spheroids (3D). Two replicates were analyzed per each group.

first: Elena

last: Duréndez-Sáez

first: Silvia

last: Calabuig-Fariñas

first: Susana

last: Torres-Martínez

last: Moreno-Manuel

first: Alejandro

last: Herreros-Pomares

first: Eva

last: Escorihuela

first: Marais

last: Mosqueda

first: Sandra

last: Gallach

first: Ricardo

last: Guijarro

last: Serna

last: Suárez-Cabrera

first: Jesús

last: Paramio

first: Ana

last: Blasco

first: Carlos

last: Camps

first: Eloisa

last: Jantus-Lewintre


title: An optimized RNA-seq workflow for isolating single nuclei from clinical biopsies

status: Public on Jun 22 2022

city: Baltimore

first: Amol

middle: Carl

last: Shetty

state: Maryland

address: 670 W. Baltimore Street, Floor 3

department: Institute for Genome Sciences

institute: University of Maryland Baltimore

summary: We developed an optimized protocol for nuclei isolation from small core needle biosies taken from both healthy and diseased human kidney samples

overall_design: Profiled the single nuclei transcriptome of 5 kidney allograft biopsies histologically characterized as normal/nonspecific (N=1), acute tubular necrosis (N=2), and chronic antibody mediated rejection (N=2)

first: Valeria

last: Mas

first: Thomas

last: Rousselle

first: Jennifer

last: McDaniels

first: Daniel

last: Maluf

first: Elissa

last: Bardhi


title: Generation of mesenchymal stem/stromal cells (MSCs) from human iPSCs via neural crest cells (NCCs)

status: Public on Jun 19 2022

city: Fujisawa

first: Daisuke

last: Kamiya

state: Kanagawa

address: 26-1 Muraoka-Higashi 2-chome

department: CiRA

institute: Kyoto University

summary: To clarify the changes in cell properties during the differentiation process from iPSCs into MSC through NCCs, we sampled each cell during the differentiation process and compared gene expression patterns.

overall_design: During MSC differentiation process from iPSC, we sampled NCCs and MSCs induced from differential passage number (PN) of NCC expansion culture.

first: Teppei

last: Akaboshi

first: Makoto

last: Ikeya


title: Characterization of human erythropoiesis using ex vivo differentiation of CD34 HSC (RNA-seq)

city: Headington

first: Damien

last: Downes

state: Oxfordshire

address: John Radcliffe Hospital

department: MRC Weatherall Institute of Medicine

institute: The University of Oxford

summary: Genome Wides Association Studies (GWAS) have identified tens of thousands of associations between human genetic variation and common disease. Despite the abundance of GWAS associations, functional identification and characterization of causative variants and effector genes remains a challenging prospect. Human erythropoiesis provides a highly tractable model system for the development of tools for GWAS analysis. We have developed a three-phase protocol for differentiation of peripheral CD34+ Haematopoietic Stem Cells (HSC) into mature enucleating erythrocytes. This protocol has been characterized for it’s the changes observed morphologically, immunologically (by FACS) and epigenetically (by ATAC-seq, ChIP-seq, and RNA-seq). We have used this protocol to study the effects of common GWAS variants affecting red blood cell traits, and more severe mutations causing  Type-1 Congenital Dyserythropoietic Anemia (CDA-I).

overall_design: To characterise the changes in gene expression during erythropoiesis, PolyA+ RNA-seq was carried out at days 7, 10, and 13 of HSC differentiation. CD34+ HSC were differentiated from three separate donors on multiple occasions with single replicates (rep1 and rep2) performed for each differentiation.

middle: J

first: Caroline

last: Scott

first: Lea

last: Nussbaum

first: Stephanie

last: Hill

first: Jim

last: Hughes


title: RNA sequencing revealed the multi-stage transcriptome transformations during the development of gallbladder cancer associated with chronic inflammation

status: Public on May 31 2022

city: Zhengzhou

first: Sen

last: Yang

state: Henan

address: Weiwu Road 7

department: Department of Hepatobiliary and Pancreatic Surgery

institute: People's Hospital of Zhengzhou University, Henan Provincial People’s Hospital

summary: Purpose Gallbladder cancer (GBC) is a highly malignant tumor with extremely poor prognosis. Previous studies have suggested that the carcinogenesis and progression of GBC is a multi-stage and multi-step process, but most of them focused on the genome changes. And a few studies just compared the transcriptome differences between tumor tissues and adjacent noncancerous tissues. The transcriptome changes, relating to every stage of GBC evolution, have rarely been studied. Methods We selected three cases of normal gallbladder, four cases of gallbladder with chronic inflammation induced by gallstones, five cases of early GBC, and five cases of advanced GBC, using next-generation RNA sequencing to reveal the changes in mRNAs and lncRNAs expression during the evolution of GBC. Results In-depth analysis of the sequencing data indicated that transcriptome changes from normal gallbladder to gallbladder with chronic inflammation were distinctly related to inflammation, lipid metabolism, and sex hormone metabolism; transcriptome changes from gallbladder with chronic inflammation to early GBC were distinctly related to immune activities and connection between cells; and the transcriptome changes from early GBC to advanced GBC were distinctly related to transmembrane transport of substances and migration of cells. Conclusion Expression profiles of mRNAs and lncRNAs change significantly during the evolution of GBC, in which lipid-based metabolic abnormalities play an important promotive role, inflammation and immune activities play a key role, and changes in membrane proteins are the most highlighted molecular changes.

overall_design: We selected three cases of normal gallbladder, four cases of gallbladder with chronic inflammation induced by gallstones, three cases of gallbladder adenoma，five cases of early GBC, and five cases of advanced GBC, using next-generation RNA sequencing to reveal the changes in mRNAs and lncRNAs expression during the evolution of GBC.

first: Litao

last: Qin

first: Pan

last: Wu


title: Characterization of human erythropoiesis using ex vivo differentiation of CD34 HSC

status: Public on Jun 23 2022


title: Mouse SINE B2 elements function as IFN-inducible enhancer elements

status: Public on May 30 2022

city: Boulder

first: Edward

last: Chuong

state: Colorado

address: 3415 Colorado Ave. JSC Biotech Bldg

department: Molecular, Cellular and Developmental Biology

institute: BioFrontiers Institute at University of Colorado Boulder


title: Longitudinal DNA methylation in exhaustively passaged astrocytes

status: Public on May 23 2022

city: New Haven

first: Albert

middle: T

last: Higgins-Chen

state: CT

address: 60 Temple St

institute: Yale University

type: Methylation profiling by genome tiling array

summary: This DNA methylation dataset describes epigenomic changes in astrocytes culture in vitro with passaging, in the context of studies examining cellular aging patterns that are conserved in vivo and in vitro. Fetal astrocytes were derived from cerebral cortex. Cells were grown under normoxic conditions and exhaustively passaged until cellular senescence. Longitudinal DNA samples were collected throughout passaging and DNA methylation was measured using the Infinium HumanMethylationEPIC BeadChip. In addition, some samples were sorted by FACS using senescence markers prior to DNA extraction for additional DNA methylation measurements.

overall_design: Astrocytes were cultured and exhaustively passaged for 3 cell lines derived from one male fetal donor. Samples taken at passages 2 through 10 (total n = 27 samples) and DNA extracted. DNA was also extracted again from samples at passages 2, 6 and 10 after sorting by FACS. This included bulk, low beta-galactosidase expression, high beta-galactosidase expression, and senescent cell samples (total n = 23 samples). These experiments were also performed using a fourth cell line isolated from a female fetal donor (n = 13 samples). Bisulphite converted DNA from samples were hybridized to the Illumina Infinium HumanMethylationEPIC BeadChip.

first: Morgan

last: Levine

first: Christopher

last: Minteer


title: Mouse SINE B2 elements function as IFN-inducible enhancer elements [RNA-Seq]

summary: B2_Mm2 acts as a STAT1 binding site and interferon inducible enhancer of the nearbby interferon-stimulated gene Dicer1 during an innate immune response (IFNG stimulated). J774 knockouts deficient of B2_Mm2 were also found to have downregulated expression of Serpina3f and Serpina3g, indicating that B2_Mm2 acts as an enhancer on these nearby genes likely due to its capability as a CTCF-binding site.

overall_design: Transcriptional profiling (RNA-seq) of wildtype mouse cell lines (J774) that were either untreated or stimulated with 100 ng/mL interferon gamma (IFNG) for 4h. RNA-seq is also provided from clonal B2 knockout J774 lines that were modified using CRISPR Cas9 and a pair of gRNAs targetting the B2_Mma2 element in the first intron of Dicer1 on chr12.

first: Adam

last: Dziulko

first: Horton

last: Isabella

first: Kelly

last: Conor

first: Simpson

last: David


title: CD36 deficiency inhibits proliferation by cell cycle control in skeletal muscle cells

status: Public on May 27 2022

city: SHANGHAI

first: sun

last: jingyu

address: SIPINGLU

institute: Tongji university

summary: Obesity-related muscular dysfunction and relative muscle atrophy affect an increasing number of people. Elucidating the molecular mechanisms of skeletal muscle cell development and growth may contribute to the maintenance of skeletal muscle mass in obesity. Fatty acid translocase (FAT/CD36), as a long-chain fatty acid transport protein, is crucial for lipid metabolism and signaling. CD36 is known to function in myogenic differentiation, and whether it affects the proliferation of skeletal muscle cells and the underlying mechanisms remain unclear. In this study, the effect of CD36 deficiency on skeletal muscle cell viability and proliferation was examined using C2C12 myoblasts. Results showed that the deletion of CD36 enhanced the inhibitory effect of PA on the proliferation and the promotion of apoptosis in skeletal muscle cells. Intriguingly, the silencing of CD36 suppressed cell proliferation by preventing the cell cycle from the G0/G1 phase to the S phase in a cyclin D1/CDK4-dependent manner. Overall, we demonstrated that CD36 was involved in skeletal muscle cell proliferation by cell cycle control, and these findings might facilitate the treatment of obesity-related muscle wasting.

overall_design: In this study, the effect of CD36 deficiency on skeletal muscle cell viability and proliferation was examined using C2C12 myoblasts.Skeletal myogenesis is regulated by the transcriptional control of various genes, including encoding myogenic regulatory factors

first: Yajuan

last: Su

first: Duran


title: Next Generation Sequencing Identifies the Heterogeneity of Human Pluripotent Stem Cell-Derived AGM-like Cells

status: Public on May 13 2022

city: West Lafayette

first: Shihuan

last: Kuang

state: IN

address: 270 S. Russell Street

institute: Purdue University

summary: Next-generation sequencing (NGS) has significantly advanced the elucidation of developmental signaling mechanisms that are important for different cell lineage formation from human pluripotent stem cells (hPSCs). We report here the application of single cell RNA-sequencing (scRNA-seq) technology for transcriptome profile of hPSC-derived aorta-gonad-mesonephros (AGM)-like endothelial and hematopoietic cells, and compare to those of primary AGM cells. Day 8 and day 18 samples were collected and performed in IIIumina NovaSeq6000. The resulting sequence reads (day 8: 90,000 reads/cells and day 18: 75,000 reads/cell) were mapped to human genome (hg19) using Cell Ranger, and the RefSeq transcript levels (RPKMs) were quantified using the Seurat R package version 3.2. Our scRNA-seq data confirmed the stable expression of key definitive hematopoietic cell markers including SOX17, RUNX1, LMO4 and CD44, and no detectable expression of primitive hematopoietic cell markers, such as GYPA (CD235a), were observed. This study represents the first detailed analysis of AGM-like cell transcriptomes generated by scRNA-seq technology, providing insight into the mechanisms underlying the differentiation of hPSCs into AGM-like cells.

overall_design: Endothelial and hematopoietic transcriptome profiles of hPSC-derived AGM-like cells were generated by scRNA-seq technology using IIIumina NovaSeq6000

last: Oprescu

first: Yun

last: Chang

first: Xiaoping

last: Bao


title: Next Generation Sequencing Facilitates Quantitative Analysis of Human Pluripotent Stem Cell-Derived Hematopoietic Cell Transcriptomes

state: Indiana

address: 480 Stadium Mall Drive

department: Chemical Engineering

summary: Next-generation sequencing (NGS) has significantly advanced the elucidation of developmental signaling mechanisms that are important for different cell lineage formation from human pluripotent stem cells (hPSCs). We report here the application of RNA-sequencing technology for transcriptome profile of hPSC-derived hematopoietic cells, and compare to those of other cell lineages including hPSCs, mesoderm, primary aorta-gonad-mesonephros (AGM) cells and cord blood hematopoietic stem cells (HSCs). IIIumina HiSeq 2X150 bp sequencing was performed on three hematopoietic cell samples from three hPSC lines by GENEWIZ. The resulting sequence reads (about 34 million reads per sample) were mapped to human genome (hg19) using HISAT, and the RefSeq transcript levels (RPKMs) were quantified using the python script rpkmforgenes.py. Our RNA-seq data confirmed the stable expression of key hematopoietic cell markers including CD45, RUNX1, CD34 and HOXA clusters, and the gene set enrichment analysis (GSEA) showed enrichment in “aorta development”, “cell migration”, “hematopoietic stem cell proliferation”, “Notch signaling regulation”, et al. Hierarchical clustering of differentially expressed genes uncovered several as yet uncharacterized genes that may contribute to hematopoietic function. This study presented a detailed analysis of hematopoietic transcriptomes generated by RNA-seq technology, providing insight into the mechanisms underlying the differentiation of hPSCs into hematopoietic cells.

overall_design: Hematopoietic transcriptome profiles of 3 different samples from 3 hPSC lines were generated by RNA-seq technology using IIIumina HiSeq


title: RNA profiling of wild-type and hnRNPF-knockout splenic B cells

status: Public on May 11 2022

city: Shenzhen

first: Hengjun

last: Huang

address: 1088 Xueyuan Avenue

department: Department of Biology

institute: Southern University of Science and Technology

summary: Alternative splicing (AS) plays an important role in the development and activation of B cells. RNA-binding proteins (RBPs) have emerged as critical players in AS regulation. RNA-binding protein hnRNPF regulates AS of several important genes, such as c-Src, Bcl-xl, Mcl-1 and Tcf3 in tumor cells, but its function in  B cell biology is not known.Here we constructed CD19-Cre mediated hnRNPF conditional knockou mice and performed RNA-sequencing to profile mRNA expression and AS regulated by hnRNPF in splenic B cells.

overall_design: RNA sequencing of splenic follicular B cells in wild-type (WT) and hnRNPF knockout (HFKO) mice

first: Gaopu

last: Zhang

first: Gui-xin

last: Ruan

first: Jia

last: Zou

first: Xijun

last: Ou