title: Ubiquitin ligase TRAIP plays an essential role during the S-phase of unperturbed cell cycle in the resolution of DNA replication – transcription conflicts

city: Birmingham

first: Marco

last: Saponaro

address: Vincent Drive

department: Institute of Cancer and Genomic Sciences

institute: University of Birmingham

summary: Cell division is the basis for the propagation of life and requires accurate duplication of all genetic information. DNA damage created during replication (replication stress) is a major cause of cancer, premature aging and a spectrum of other human disorders. TRAIP E3 ubiquitin ligase has been shown over the years to play a role in a number of the cellular processes that govern genome integrity and faultless segregation. TRAIP is essential for cell viability and mutations in TRAIP ubiquitin ligase activity lead to primordial dwarfism in patients. Here, for the first time we have determined the mechanism of inhibition of cell proliferation in TRAIP-depleted cells. We have taken advantage of the auxin induced degron system to rapidly degrade TRAIP within cells to dissect the importance of various functions of TRAIP in different stages of the cell cycle. We found that upon rapid TRAIP degradation cells cease to proliferate, arrest in G2 stage of the cell cycle and undergo senescence. TRAIP degradation in specific stages of the cell cycle revealed that TRAIP plays its essential role in S-phase and that the lack of TRAIP results in the generation of DNA damage at transcription start sites due to replication-transcription collisions.

overall_design: Identification of hotspots of DNA damage following the removal of TRAIP by auxin-induced degradation

first: Agnieszka

last: Gambus


title: Insights into the regulation of the brain-placental axis (ChIP-seq)

status: Public on Sep 01 2023

city: Columbia

first: Susanta

middle: K.

last: Behura

state: Missouri

address: 920 East Campus Drive

department: Division of Animal Sciences

country: USA

institute: Univeristy of Missouri

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Fetal sex influences the accessibility of the placental chromatin to REST. REST targeted fewer sites in the female placental compared to that of male. REST bound to 7,254 common sites in both sexes but nearly 17-fold more number of sites in the male placenta compared to the female placenta.

overall_design: Pooled sample from three biological replicates of day 15 placenta of male and female fetuses of wild-type (C57BL/6) mice were subjected to chromatin-immunoprecipitation assay for transcription factor REST followed by sequencing (ChIP-seq).

first: Pramod

last: Dhakal

first: Monica

last: Strawn

first: Ananya

last: Samal

middle: K


title: RNA-seq results in the liver of female liver-specific Utx knockout mice treated with acetaminophen (APAP)

city: Wuhan

first: Yixue

last: Huang

address: Hangkong Road 13

country: China

institute: Huazhong University of Science and Technology

type: Expression profiling by high throughput sequencing

summary: To understand key pathways and regulatory genes in female liver-specific Utx knockout mice treated with APAP

overall_design: Female liver-specific Utx knockout mice and their age-, sex- matched control mice were treated with 300mg/kg APAP. For each experimental group, two biological replicates of RNA samples were sent for RNA-seq. Each sample consists of a pool of RNAs extracted from liver of 2 different mice.

first: Ling

last: Zheng

first: Kun


title: Long noncodng RNA lncPostn links TGF-b and p53 signaling pathwas to regulate cardiac fibrosis

city: ChangZhou

first: Lichan

last: Tao

address: Juqian Road 185, Changzhou, Jiangsu province, China

institute: The Third affiliated Hospital of Soochow Uniersity

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

summary: To present a potential therapeutic target for cardiac fibrotic remodeling in cardiovascular diseases

overall_design: Non-coding RNA and mRNA profiling in mouse hearts 3 weeks post-myocardial infarction versus control

first: Tao

last: Lichan

first: Hua

last: Fei


title: Functional genomics study of oral squamous cell carcinoma under PPARG overexpression by RNA-seq

city: Hefei

first: Kan

last: He

state: Anhui

address: 111 Jiulong Road

institute: Anhui University

summary: Oral squamous cell carcinoma (OSCC), one of the most common malignant tumor in head and neck, which is regulated by cellular factors. Among them, peroxisome proliferator activated receptor gamma (PPARG) has been reported to have main functions in the regulation of several human cancer cells, including OSCC. However, its regulatory mechanism remains unclear. Here, we performed a functional genomics study of PPARG overexpressing OSCC by using RNA-seq.

overall_design: SCC-15 cells transfected with PB-IP-PPARG were the experimental group, and SCC-15 cells transfected with PB-IP-2flag were used as controls. Experiments were performed in duplicate. Gene expression profiling analyses by high throughput sequencing were performed on mRNA samples isolated from the SCC-15 cells transfected with PB-IP-PPARG(P) and SCC-15 cells transfected with PB-IP-2flag (CK).

first: Jing

last: Zhang

first: Ruolan

last: Pan

first: Jinxing

last: Su


title: mRNA Profile in Kidney of NZBWF1 mice

city: beijng

first: shipeng

last: Li

address: Nan Li Shi Road No. 56,Beijing

institute: Beijing children's hospital

summary:
mRNA microarrays were performed to identify changes in mRNA expression between 8-week-old and 28-week-old NZBWF1 mice.
1796 mRNAs were identified as being significantly differentially expressed.

overall_design: 8-week-old (n=4) and 28-week-old  NZBWF1 mice (n=4)

first: Shipeng

first: Caifeng


title: miRNA Profile in Kidney of NZBWF1 mice

summary:
miRNA microarrays were performed to identify changes in miRNA expression between 8-week-old and 28-week-old NZBWF1 mice.
43 miRNAs were identified as being significantly differentially expressed.

overall_design: 8-week-old(n=4) and 28-week-old  NZBWF1 mice (n=4)


title: NAIL: an evolutionarily conserved lncRNA essential for coordinating p38 activation and NFκB mediated chromatin remodelling in inflammation_1

city: Singapore

first: Vinay

last: Tergaonkar

address: 61 Biopolis Drive,  Proteos

country: Singapore

institute: Institute of Molecular and Cell Biology

summary: We report the genome wide occupancy of p65, H3K4Me3, H3K27Ac and p300 in MCF7-NAIL-WT and MCF7-NAIL-ΔNFκB cells stimulated with TNF alpha for 0min, 45min and 90 min.

overall_design: MCF7-NAIL-WT and MCF7-NAIL-ΔNFκB cells stimulated with TNF alpha for 0min, 45min and 90 mins. After  crosslinking, ChIP was performed for the indicated molecules.

first: Semih

middle: C

last: Akincilar


title: Adrenomedullin promotes the migration of interneurons in a human forebrain assembloid model for hypoxic interneuronopathy of prematurity.

city: San Francisco

first: Arthur

middle: Jeremy

last: Willsey

state: CA

address: 675 Nelson Rising Lane, Mail Code 0518

department: Psychiatry

institute: UCSF

summary: We developed a model for hypoxic injury of migrating human cortical interneurons using forebrain organoids and forebrain assembloids derived from hiPSCs.

overall_design: Human subpallial organoids at day 46 in culture were exposed to hypoxia (<1% oxygen) for 12 and 24 hours. Some samples were exposed for 24 hours and  subsequently reoxygenated for 72 hours. Samples were immediately collected and snap frozen for processing.

first: Anca

middle: M

last: Pasca

first: Jeremy

middle: A


title: RNA-seq analysis of Caenorhabditis elegans Transcriptomes after fed with D-mannose

city: Nanchang

first: Fang

last: Xu

state: Jiangxi

address: NO.999 XUEFU ROAD, HONGGUTAN DISTRICT

department: School of life science

institute: Nanchang University

summary: we used Caenorhabditis elegans as a model organism, to investigate the effect of mannose on the lifespan. Using nematode RNAi methods, RT-PCR, RNA-seq and other experimental method, we explored the possible mechanism for how mannose change the lifespan of Caenorhabditis elegans.

overall_design: 2 groups of sample treated with or without D-mannose, and divided as 3 replications pregroup

first: Shanshan


title: Targeting RNA helicase ameliorates bortezomib resistance in glioblastoma via RNA dependent sequestration of protein phosphatase PPM1D

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

overall_design: Refer to individual Series


title: Expression data from U937 monocytes treated with LysoPPC and  FSL-1

city: Vienna

first: Markus

last: Jeitler

address: Lazarettgasse 14

country: Austria

institute: Medical University Vienna

summary: Monocytes and monocyte derived macrophages, besides natural killer (NK) cells, are crucial for elimination of senescent cells. There is evidence that TLR2/6 together with the lipid receptor CD36 may be the pattern recognition receptor that are most involved in the sensing of epitopes connected to cellular aging, senescence and severe cellular distress. Additionally, the interplay of these scavenger receptors is required for uptake of TLR2/6 agonist FSL-1. Therefore, we investigated whether lysophospholipids would induce or interfere with (TLR2/6 mediated) gene regulation in U937 monocytes. Cells were or were not pre-treated with lysophospholipids (10µM) for 1 hour and then stimulated with the TLR2/6 ligand (1µg/ml) for 2 hours.

overall_design:
The human myeloid leukemia cell line U937 was exposed to 1-palmitoyl-2-hydroxy-sn-glycero-3-phosphocoline (LysoPPC) and FSL-1
This study was performed in biological quadruplicates for human myeloid leukemia cell line U937

first: Marie-Sophie

last: Narzt

first: Vera

last: Pils

first: Ingo

last: Lämmermann

first: Johannes

last: Grillari

first: Florian

last: Gruber


title: NAIL: an evolutionarily conserved lncRNA essential for coordinating p38 activation and NFκB mediated chromatin remodelling in inflammation_3

summary: We report the differential gene expression analysis in MCF7-NAILWT and MCF7-NAILΔNFκB cells stimulated with TNF alpha for 0min, 45min and 90 min.

overall_design: MCF7-NAILWT and MCF7-NAILΔNFκB cells (WT and NAILΔNFκB cells  were generated by Crispr/Cas9 genome editing by targeting the 2 NFκB sites in the promoter of NAIL. (Loc105375914) gene. Cells were stimulated with TNFalpha (10ng/ml) for 0, 60 and 120 mins. Total RNAs were isolated using Trizol. RNA-Seq library was prepared by Illumina Truseq Total RNA sequencing kit according to manufacturer instructions. Paired-end sequencing was performed using Illumina Hiseq, 2x101bp. Raw reads were aligned to mouse genome mm10 by Tophat2 .


title: Multimodal multiscale analysis reveals flexible DNA contacts of bacterial nucleoprotein filaments

city: Madison

first: Robert

last: Landick

state: WI

address: 1550 Linden Dr.

institute: University of Wisconsin

summary: Gene silencing in bacteria is mediated by chromatin proteins, of which Escherichia coli H-NS is a paradigmatic example. H-NS forms nucleoprotein filaments with either one or two DNA duplexes. However, the overall structures, arrangements of DNA-binding domains (DBDs), positions of DBD–DNA contacts, and determinants of genomic distribution for these linear and bridged filaments are uncertain. To connect H-NS structures that silence genes in vivo with features elucidated in vitro, we developed a multimodal multiscale analysis that combines a new method for chromatin reconstitution and mapping (Nitro-seq), ChIP-seq, tethered-nuclease mapping of DBD–DNA contacts (TEN-map), ·OH footprinting, molecular dynamics, and bioinformatics. We find that DNA sequence principally governs H-NS-filament location with indistinguishable sequence specificity in bridged or linear forms with or without the H-NS modifiers StpA and Hha and that DBD–DNA contacts vary in orientation and position with ~10-bp average spacing. Our results support a hemi-sequestration model of linear-to-bridged filament switching.

overall_design: ChIP-seq on H-NS and RNA polymerase in Escherichia coli K-12 genome with or without rifampicin treatment to inhibit active transcription. There are 12 total ChIP-seq samples including input (no-IP) control. 2 replicates were performed per IP. Nitro-seq, a new method chromatin reconsitution and mapping, on H-NS, StpA, a mixture of Hha and H-NS, and Fis binding to E. coli K-12 purified genomic DNA. The mixture of protein and DNA was applied to a nitrocellulose filter to enrich for protein::DNA complexes. The DNA bound by protein was prepared for sequencing by eluting the DNA from the nitrocellulose filter and then preparing a sequencing library. There are a total of 25 Nitro-seq samples, including 1 input DNA control. Each sample was performed in triplicate, execpt for the 5 nM Fis sample which was done in duplicate.

first: Beth

last: Shen

first: Christine

last: Hustmyer

first: Daniel

last: Roston

first: Michael

middle: B

last: Wolfe

first: Erik

middle: D

last: Jessen


title: CD28-CBCA driven PKM splicing licenses CD8 T cell glycolysis and effector function

city: Buffalo

first: Scott

last: Olejniczak

state: New York

address: Elm and Carlton, CGP Rm. L5 306

institute: Roswell Park Comprehensive Cancer Center

summary: T cells stimulated in the absence of CD28 costimulation are functionally anergic, characterized by reduced glucose metabolism and ability to produce effector cytokines. Surprisingly, previous studies have shown relatively few CD28-specific changes in gene transcription upon costimulation. Using mice expressing mutations in the CD28 cytoplasmic tail, we show a major effect of CD28 costimulation is alternative splicing of numerous genes including the glycolytic enzyme pyruvate kinase (Pkm), which is preferentially spliced from Pkm1 to Pkm2 upon stimulation. PKM2 is dispensable for T cell activation, but necessary for CD8+ T cells to utilize aerobic glycolysis, produce effector cytokines, and provide anti-tumor immunity. Mechanistically, CD28 regulates expression of the Cap-Binding Complex adaptor protein ARS2, which binds Pkm splicing factors and facilitates their interaction with the elongating transcript. Data suggest a major function of CD28 costimulation is control of RNA biogenesis in support of T cell transcriptome remodeling and acquisition of effector function.

overall_design: RNA was sequenced from murine T cells from mice of the indicated genotype was performed at 24, or 72 hours post stimulation. Total of 34 samples. Biological replicates at each time point : WT (2), ARS2 KO (3), CD28 KO (2), CD28 DKI (3), CD28 AYAA (3), CD28 Y170F (3), all samples were compared relative to unstimulated WT T cells (n=2)

first: S

middle: H

first: G

last: Holling

first: A

middle: P

last: Sharda


title: Effects of differential gut microbiota on hepatic gene expression

city: Cincinnati

first: Joo-Seop

last: Park

address: 3333 Burnet Avenue

institute: Cincinnati Children's Hospital Medical Center

summary: The goal of our study is to determine whether commensal gut microbiota modulate the expression of  DDG in the liver.

overall_design:
Method: C57BL/6 mice from two different vendors [Jackson (JAX) and Taconic (TAC)] were cohoused with either the same vendor or the other vendor creating following four groups; JAX, TAC, JAX cohoused with TAC (CoJAX) and TAC cohoused with JAX (CoTAC). After 4 weeks, mice were sacrificed and liver tissues were collected.
Examination of 4 groups; JAX, TAC, CoJAX and CoTAC

first: Sungjoon

last: Cho

first: Yukuang

last: Guo

first: Eunah

last: Chung

first: Hyunyoung

last: Jeong


title: Single-cell ATAC-seq analysis of hESCs undergoing neuronal differentiation exposed to paracetamol [scATAC-seq]

status: Public on Aug 31 2023

city: Oslo

first: Ragnhild

last: Eskeland

address: Sognsvannsveien 9

department: Institute of Basic Medical Sciences

country: Norway

institute: University of Oslo

summary: Genome-wide chromatin opening profiling of hESCs undergoing neuronal differentiation at four distinct time-points. hESCs are differentiated using a neuronal protocol, and day 20 were charachterized. Cells exposed to 100 or 200 μM paracetamol from Day 1.

overall_design:
Single-cell ATAC-seq analysis of (n=2, 1x P100 and 1x P200 Day 20) samples from neuronal differentiation Day 20. Cells were exposed to paracetamol from Day 1 and onwards.
The submitter declares **Raw data are not provided due to data sensitivity**

first: Mari

last: Spildrejorde

first: Athina

last: Samara

first: Ankush

last: Sharma

first: Magnus

last: Leithaug

first: Martin

last: Falck

first: Stefania

last: Modafferi

first: Arvind Y. M.

last: Sundaram

first: Kristina

last: Gervin

last: Lyle


title: Gene expression analysis of hESCs undergoing neuronal differentiation exposed to paracetamol [RNA-seq]

summary: Genome-wide gene expression profiling of hESCs undergoing neuronal differentiation at four distinct time-points. hESCs are differentiated using a neuronal differentiation protocol, day 7 and 20 were charachterized. Cells were exposed to 100 or 200 μM paracetamol from Day 1 were charachterised at Day 7 and Day 20.

overall_design:
Genome wide gene expression profiling of (n= 20) samples from neuronal differentiation of human embryonic stem cells (hESCs) in presence of paracetamol at day 7(n = 5 P100; n= 5 P200), and 20 (n=5 P100 and n=5 P200). Cells were exposed to paracetamol from Day 1 and onwards.
The submitter declares **Raw data are not provided due to data sensitivity**

first: Arvind Y.M.

first: Robert


title: Transcriptional profiling of Follicular B cells (FoB) in control and T follicular regulatory cell deficient mice

first: Jerod

last: Skyberg

state: MO

address: Veterinary Pathobiology, 1500 Bouchelle

institute: University of Missouri

summary: We isolated Follicular B cells from naïve and Brucella infected mice to determine how T follicular regulatory cells alter the B cell response to infection.

overall_design: Comparative gene expression profiling analysis of Follicular B cell RNA-seq data from mock and Brucella infected mice

first: Alexis

last: Dadelahi


title: Analysis of the brain metastasis-associated microenvironment in different preclinical models of brain metastasis

city: Madrid

first: Santiago

middle: García

last: Martín

state: Madrid

address: Calle de Melchor Fernández Almagro, 3

department: Bioinformatics Unit

country: Spain

institute: Spanish National Cancer Research Centre

summary: To investigate the potential similarities and differences within the brain microenvironment among three different models of orthotopic implanted brain metastatic cell lines

overall_design:
Gene expression profiling analysis using data obtained from RNA-seq of 6 brains per experimental model was performed
Comparative gene expression profiling analysis of RNA-seq data of the brain metastasis-associated microenvironment (resection of the peritumoral area) of the lung cancer brain metastasis model 482N1, the breast cancer brain metastasis model E0771-BrM and the melanoma brain metastasis model B16/F10-BrM (n=6 brains per model)

first: Mariam

last: Al-Masmudi

first: Carolina

last: Hernández-Oliver

first: Patricia

last: Baena

first: Lluís

last: Cordón

last: García-Martín

first: Neibla

last: Priego


title: Ferric citrate and apo-transferrin enable erythroblast maturation with ℬ-globin from hemogenic endothelium

city: Cheongju-si

first: JONG HEE

last: LEE

state: Chungbuk

address: 30, Yeongudanji-ro, Ochang-eup, Cheongwon-gu

department: National Primate Research Center

country: South Korea

institute: Korea Research Institute of Bioscience & Biotechnology

summary: We describe a simple and reproducible culture system that can be used to generate erythroblasts with ℬ-globin expression in culture systems. Upon treatment with Fe, erythroblasts showed advanced maturity with a high transcription of ℬ-globin.

overall_design: Single-cell RNA sequencing was performed using orthochromatic erythroblasts that maintained saturated status for hemoglobin synthesis before enucleation on day 33. single cell capture was performed using BD Rhapsody Express instrument. The samples were tagged using multiplexing kit, CTRL (PBMC_SampleTag05_hs_RSEC_MolsPerCell.csv) and IRON (PBMC_SampleTag06_hs_RSEC_MolsPerCell.csv).

first: Soo-Been

last: Jeon

first: Hyebin

last: Koh

first: A-Reum

last: Han

first: Jieun

last: Kim

first: Sunghun

last: Lee

first: Jae-Ho

first: Seung-Soon

last: Im

first: Young-Sup

last: Yoon

first: Jong-Hee

first: Ji

middle: Y


title: Cenicriviroc reduces liver fibrosis by restoring the immune cell landscape via inactivating STAT1/NF&B/ERK signaling pathways [treatment_scRNA-seq]

city: chengdu

first: chong

last: zhao

address: NO.1,4th Keyuan Road

institute: Lab of Gastroenterology and Hepatology

summary: This study depicts a novel mechanism by which CVC alleviates liver fibrosis by restoring the immune cell landscape. CVC can inhibit profibrotic gene transcription via inactivating the CCR2-STAT1/NF&B/ERK signaling pathways.

overall_design: One liver fibrosis model was induced by intraperitoneal injection of carbon tetrachloride (CCl4) with wild type for 6 weeks. For the treatment experiment, mice were injected with CCl4 for 3 weeks to establish liver fibrosis, and interventions of 2 doses of CCl4 and 4 doses of CVC per week were carried out for another 3 weeks. Control mice received the same volume of olive oil.

first: Jinhang

last: Gao


title: Single-cell transcriptomic profiling reveals immune cell heterogeneity in acute myeloid leukaemia peripheral blood mononuclear cells after chemotherapy

city: Shenzhen

first: Xuqiao

last: Hu

state: China

address: Buxin Road, Luohu District

institute: Shenzhen Center for Chronic Disease Control and Prevention

summary: Purpose Acute myeloid leukaemia (AML) is a heterogeneous disease characterised by the rapid clonal expansion of abnormally differentiated myeloid progenitor cells residing in a complex microenvironment. However, the immune cell types, status, and genome profile of the peripheral blood mononuclear cell (PBMC) microenvironment in AML patients after chemotherapy are poorly understood. In order to explore the immune microenvironment of AML patients after chemotherapy, we conducted this study for providing insights into precision medicine and immunotherapy of AML. Methods In this study, we used single-cell RNA sequencing (scRNA-seq) to analyse the PBMC microenvironment from five AML patients treated with different chemotherapy regimens and six healthy donors. We compared the cell compositions in AML patients and healthy donors, and performed gene set enrichment analysis (GSEA), CellPhoneDB, and copy number variation (CNV) analysis. Results Using scRNA-seq technology, 91,772 high quality cells of 44,950 PBMCs from AML patients and 46,822 PBMCs from healthy donors were classified as 14 major cell clusters. Our study revealed the sub-cluster diversity of T cells, natural killer (NK) cells, monocytes, dendritic cells (DCs), and haematopoietic stem cell progenitors (HSC-Prog) in AML patients under chemotherapy. NK cells and monocyte-DCs showed significant changes in transcription factor expression and chromosome copy number variation (CNV). We also observed significant heterogeneity in CNV and intercellular interaction networks in HSC-Prog cells. Conclusion Our results elucidated the PBMC single-cell landscape and provided insights into precision medicine and immunotherapy for treating AML.

overall_design:
scRNA-seq to analyse the PBMC microenvironment from five AML patients (AML1, AML2, AML3, AML3B, AML4, AML5) treated with different chemotherapy regimens and six healthy donors(H2, H3, H4, H5, H6, H7).
-----------------
Authors state:
Raw files were not submitted due to patient privacy concerns

first: Dongyan

last: Cao

first: Zhenru

last: Zhou


title: Single-cell gene expression analysis of hESCs undergoing neuronal differentiation upon exposure to paracetamol [scRNA-seq]

first: Ragnhild

last: Eskeland

summary: Single-cell RNA-seq of hESCs undergoing neuronal differentiation at four distinct time-points. hESCs are differentiated using a novel protocol, and day 0, 7, 13 and 20 were charachterized. Cells exposed to 100 or 200 μM paracetamol from Day 1 were charachterised at Day 7 and Day 20.

overall_design:
Genome wide gene expression profiling of (n= 4) samples from neuronal differentiation human embryonic stem cells (hESCs) at day  7(n = 2) and 20 (n=2) . Cells were exposed to paracetamol from Day 1 and onwards.
The submitter declares **Raw data are not provided due to data sensitivity**

first: Mari

last: Spildrejorde

first: Athina

last: Samara

first: Ankush

last: Sharma

first: Magnus

last: Leithaug

first: Martin

last: Falck

first: Stefania

last: Modafferi

first: Arvind Y. M.

last: Sundaram

first: Kristina

last: Gervin

first: Robert

last: Lyle


title: Multi-omics analysis of paracetamol exposure identifies dysregulated genes involved in neurotoxicity and neuronal differentiation of human embryonic stem cells

type: Methylation profiling by genome tiling array

summary:
This SuperSeries is composed of the SubSeries listed below.
GSE220023
GSE220024
GSE220025
GSE220026


title: Epigenome analysis of hESCs undergoing neuronal differentiation in presence or absence of paracetamol [MethylationEPIC BeadChip]

summary: Genome wide DNA methylation profiling of human embryonic stem cells (hESCs) at day 0, and day 7, 13 and 20 of neuronal differentiation. Cells were exposed to paracetamol from Day 1 and onwards. The Illumina Infinium MethylationEPIC_v-1-0_B3 was used to obtain DNA methylation profiles accross approximately 850k CpGs in differentiating cells.

overall_design:
Bisulphite converted DNA from the 43 samples were hybridised to the Illumina Infinium MethylationEPIC BeadChip
The submitter declares **.idat files are not provided due to data sensitivity**

first: Arvind Y.M.


title: Cenicriviroc reduces liver fibrosis by restoring the immune cell landscape via inactivating STAT1/NF&B/ERK signaling pathways


title: Single Cell RNA Sequencing Reveals Unique Dendritic Cell and Macrophage Subsets in the Mouse Kidney

city: Birmingham

first: James

last: George

state: Alabama

address: 725 ZRB, 1720 2nd Ave South

department: Surgery

institute: Univ. Alabama at Birmingham

summary: Mononuclear phagocytes have important functions in regulating tissue injury and regeneration after AKI. We tested the hypothesis that kidney resident macrophages (R2) and infiltrative mononuclear phagocytes (R1) exist in distinct transcriptional subsets that are resolvable by single cell RNA sequencing. A further objective was to identify transcriptional signatures for those subsets. By cell sorting R2 and R1 cells from quiescent and injured mouse kidneys, we found remarkable heterogeneity among intrarenal innate immune cells. We define four subsets of dendritic cells and six subsets of R2 cells and specify differentially expressed genes that identify these cell types. Additionally, we observed subset-specific transcriptional responses to AKI. R2 cells, which express surface phenotype homogeneity, adopt distinct transcriptional programs in the steady state and after injury. Expression of MHC class II and invariant chain genes are decreased in a predominant subset of R2 cells after AKI. In contrast, other macrophage lineage-defining genes such as C1qa, b, and c, are expressed at similar levels across R2 cell subsets and their expression does not change in response to injury. This study has allowed us to identify R2 and R1 subsets that may prove to be therapeutic targets for inhibiting damaging inflammation and fibrosis or promoting tissue regeneration.

overall_design: Mice subjected to renal ischemia reperfusion injury or left untreated: Renal leukocytes isolated and sorted by FACS to F4/80Hi/CD11bLo and F4/80Int/CD11bHi. However, how sorts were done depended on sample (see sample list)

middle: F

first: Jeremie

last: Lever

first: Anupam

last: Agarwal

first: Michal

last: Mrug

first: Bradley

last: Yoder


title: HuR-dependent NK cell expansion is required for control of solid tumors and long-term virus infection

city: Urbana

first: Sushant

last: Bangru

state: Illinois

address: 600 S Mathews Avenue

department: Biochemistry

institute: University of Illinois, Urbana-Champaign

summary: Natural Killer (NK) cells are innate lymphocytes capable of controlling tumors and virus infections through direct lysis and cytokine production. NK cells also expand and accumulate in affected tissues, but the role of NK cell expansion in tumor and viral control is not well understood. Here, we describe that post-transcriptional regulation by the RNA-binding protein HuR is essential for NK cell expansion, without overtly affecting NK cell effector functions. HuR-dependent NK cell expansion facilitated control of solid tumors, but it was dispensable for control of tumor metastases. In virus infection, HuR-dependent NK cell expansion contributed to long-term viral control in the absence of adaptive immunity without affecting acute infection. HuR-deficient NK cells displayed defects in expression of and splicing in cell cycle-associated genes, including decreased expression and alternative splicing of Ska2, a component of the spindle and kinetochore complex that is involved in chromosome separation during cell division. Furthermore, we identified an essential role for SKA2 in NK cell expansion. These results show that post-transcriptional regulation by HuR specifically affects NK cell expansion which is required for control of several solid tumors and long-term virus infection.

overall_design: gene expression and alternative splicing analysis between WT and HuR cKO NK cells

first: Sytse

last: Piersma

first: Auinash

last: Kalsotra

first: Wayne

last: Yokoyama


title: SAFB associates with nascent RNAs and can promote gene expression in mouse embryonic stem cells [RNA-seq]

city: Chapel Hill

first: Joseph

middle: Mauro

last: Calabrese

state: North Carolina

address: 120 Mason Farm Road

department: Pharmacology

institute: University of North Carolina at Chapel Hill

summary: We performed gene expression profiling analysis using data obtained from RIP-seq inputs of 7 different cell lines.

overall_design:
ESCs were grow in wells of a 6-well plate to ~80% confluency. Cells were washed twice with 1x PBS and 1 mL of TRIzol was added per well. Samples were pipetted up and down at least 10 times, transferred to a microcentrifuge tube and briefly vortexed. Samples were incubated at RT for 5 minutes then 200μl of chloroform was added, samples were vortexed and incubated for 3 minutes at RT. Samples were spun down at 12000xg for 15 min at 4°C. The upper aqueous phase was moved to a new tube and 8μL of linear acrylamide (Thermo Fisher, AM9520) was added. Then 500μL of 100% isopropanol was added, samples were vortexed and incubated at RT for 10 minutes. Tubes were spun down 12000xg for 10 minutes at 4°C. Supernatant was removed and pellets washed with 1mL of cold 75% ethanol. Samples were briefly vortexed and spun down at 7500xg for 5 min at 4°C. Supernatant was discarded and pellet was dried by repeated spin down and aspiration. Final pellets were resuspended in 100μL water by pipetting up and down.

For RIP-Seq inputs, 100ng of RNA prepared from RIP input samples was used for library preparations. For total RNA-Seq, 900ng of total RNA was used. Each library preparation included 1μL of 1:250 dilution of ERCC Spike-In RNAs (Ambion #4456653). 10μL total were prepped using the KAPA RNA HyperPrep Kit with RiboErase (Kapa Biosystems; product #KR1351). Sequencing was performed on an Illumina Next-Seq 500, using high-output, 75-cycle kits.

first: Rachel

last: Cherney

first: Zhiyue

last: Zhang

first: David

last: White

first: Quinn

middle: E

last: Eberhard

first: Laura

last: Herring

first: J


title: SAFB associates with nascent RNAs and can promote gene expression in mouse embryonic stem cells [RIP-seq]

summary: RNA-IPs in WT and SAFB1/2 DKO mESCs.

overall_design:
RIPs were performed essentially as in (Schertzer et al. 2019a), which is a protocol originally adapted from (Hendrickson et al. 2016; Raab et al. 2019). 25μL protein A/G agarose beads (Santa Cruz sc-2003) were washed three times in blocking buffer (0.5% BSA in 1xPBS) and incubated overnight at 4°C with 10μL antibody (anti-SAFB; Bethyl 812-300A; FLAG, Sigma F1804; V5, Sigma V8012) or 10μg of mouse IgG (Invitrogen). 10x10^6 cells were resuspended in 500μL RIPA Buffer (50mM Tris-HCl, pH8, 1% Triton X-100, 0.5% sodium deoxycholate, 0.1% SDS, 5mM EDTA, 150mM KCl) supplemented with 1x Protease Inhibitor Cocktail (PIC; Sigma Product #P8340), 2.5μL SuperaseIN (Thermo Fisher Scientific AM2696) and 0.5mM DTT and sonicated twice 30s on and 1 min off at 30% output using the Sonics Vibracell Sonicator (Model VCX130, Serial# 52223R). Samples were spun down at high speed and 50μL total lysate was saved for input. Beads were washed three times in 1mL fRIP buffer (25mM Tris-HCl pH 7.5, 5mM EDTA, 0.5% NP-40, 150mM KCl) and resuspended in 450μl fRIP buffer supplemented as above with PIC, SuperaseIN and DTT, then mixed with sonicated samples. Samples were rotated overnight at 4°C, then washed once with 1mL fRIP buffer and resuspended in 1mL PolII ChIP Buffer (50mM Tris-HCl pH 7.5, 140mM NaCl, 1mM EDTA, 1mM EGTA, 1% Triton X-100, 0.1% Sodium-deoxycholate, 0.1% Sodium dodecyl sulfide) before transferring to a new 1.5mL tube. Samples were rotated at 4°C for five minutes, spun down at 1200xg, and the supernatant aspirated. Samples were washed twice more with 1mL PolII ChIP Buffer, twice with 1mL High Salt ChIP Buffer (50mM Tris-HCl pH 7.5, 500mM NaCl, 1mM EDTA, 1mM EGTA, 0.1% sodium-deoxycholate, 0.1% sodium dodecyl sulfide, 1% Triton X-100), and once in 1mL LiCl buffer (20mM Tris pH 8.0, 1mM EDTA, 250mM LiCl, 0.5% NP-40, 0.5% sodium-deoxycholate); each wash included a five-minute rotation at 4°C. At the final wash, samples were transferred to a new 1.5mL tube. After the final wash, inputs were thawed and bead samples were resuspended in 56μL water, 33μL of 3x reverse-crosslinking buffer [3x PBS, 6% N-lauroyl sarcosine and 30mM EDTA], 5μL 100mM DTT, 20μL Proteinase K, and 1μL of SUPERaseIN. Samples were incubated for 1hr at 42°C, then 1hr at 55°C, then 65°C for 30 minutes, and mixed by pipetting every 15 minutes. Afterwards, 1mL Trizol was added, samples were vortexed, 200μL CHCl3 was added, samples were vortexed, and finally spun at 12000xg for 15 mins at 4°C. The aqueous phase was then extracted and one volume of 100% ethanol was added. Samples were vortexed and applied to Zymo-Spin IC Columns (from #R1013) and spun for 30 seconds at top speed on a benchtop microcentrifuge. 400μL of RNA Wash Buffer (Zymo #R1013) was added and samples were spun at top speed for 30 seconds. For each sample, 5μL DNAse I and 35μL of DNA Digestion Buffer (Zymo #R1013) was added directly to the column matrix and incubated at room temp for 20 minutes. 400μL of RNA Prep Buffer was then added (Zymo #R1013), and columns were spun at top speed for 30 seconds. 700μL RNA Wash Buffer (Zymo #R1013) was then added, and columns were spun at top speed for 30 seconds. 400μL RNA Wash Buffer was then added, and columns were spun at top speed for 30 seconds. The buffer reservoir was then emptied and columns spun again for 2 minutes to remove all traces of wash buffer. Column were transferred to a clean tube, 15μL of ddH2O was added to each, and after a five-minute incubation, samples were spun at top speed to elute.

For RIP-Seq inputs, 100ng of RNA prepared from RIP input samples was used for library preparations. For RIP-Seq RIP samples, 9μL of RIP sample (from 15μL total) were used. Each library preparation included 1μL of 1:250 dilution of ERCC Spike-In RNAs (Ambion #4456653). 10μL total were prepped using the KAPA RNA HyperPrep Kit with RiboErase (Kapa Biosystems; product #KR1351). Sequencing was performed on an Illumina Next-Seq 500, using high-output, 75-cycle kits.


title: SAFB associates with nascent RNAs and can promote gene expression in mouse embryonic stem cells [ChIP-seq]

summary: SAFB has roles in gene repression, and we asked whether PRC2 was involved in this process

overall_design:
For H3K27me3 and total H3 ChIPs, The day before sonication, 25μL of protein A/G agarose beads (Santa Cruz sc-2003) were washed 3 times in block solution (0.5% BSA in 1xPBS) before being resuspended in 300μL blocking solution. 10μL per 10 million cells of antibody (Abcam mouse monoclonal ab6002) was added, then beads and antibody conjugated via rotation overnight at 4°C.
On the day of sonication, 10 million ESCs crosslinked with 0.6% formaldehyde were re-suspended in lysis buffer 1 (50mM HEPES pH 7.3, 140mM NaCl, 1mM EDTA, 10% glycerol, 0.5% NP-40, 0.25% Triton X-100, and 1x PIC (PIC; Sigma Product #P8340) incubated for 10 minutes at 4C, and then incubated with lysis buffer 2 (10mM Tris-HCl pH 8.0, 200mM NaCl, 1mM EDTA pH 8.0, 0.5 mM EGTA pH 8.0, and 1x PIC) for 10 minutes at room temperature. For H3K27me3 ChIPs, cells were re-suspended in lysis buffer 3 (10 mM Tris-HCl pH 8.0, 100 mM NaCl, 1 mM EDTA pH8.0, 0.5 mM EGTA pH 8.0, 0.1% Na-deoxycholate, 0.5% N-lauroyl sarcosine, and 1x PIC) and then sonicated.
ChIPs were then performed by incubating sonicated cell lysates at a concentration of 20 million cells/1ml of lysis buffer 3 containing 1% Triton X-100 with pre-conjugated with H3K27me3 antibody/agarose beads overnight at 4˙C. After overnight H3K27me3 ChIP, beads were washed 5x in RIPA buffer (50 mM HEPES pH 7.3, 500 mM LiCl, 1 mM EDTA, 1% NP-40 and 0.7% Na-Deoxycholate) for 5 minutes each and then once in TE. To elute the DNA, beads were re-suspended in Elution buffer (50mM Tris pH 8.0, 10mM EDTA, and 1% SDS) and placed on a 65°C heat block for 17 minutes with frequent vortexing. Crosslinks were reversed overnight at 65°C, eluates were incubated with Proteinase K and RNase A, and DNA was extracted with phenol/chloroform and precipitated with ethanol. DNA was prepared for sequencing on the Illumina platform using Next Reagents (NEB) and Agencourt AMPure XP beads (Beckman Coulter).

first: Mauro

middle: J


title: SAFB associates with nascent RNAs and can promote gene expression in mouse embryonic stem cells

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

overall_design: Refer to individual Series


title: Transcriptional profiling of primary human aortic smooth muscle cells (hAoSMC) isolated from non-anerysmal vs. hAoSMCs isolated from anerysmal abdominal aorta (differential expression analysis) [bulk RNA-seq]

status: Public on Aug 30 2023

city: München

first: Francesca

last: Fasolo

address: biedersteinerstr. 29

country: Germany

institute: TUM

summary: An abdominal aortic aneurysm (AAA) is a pathological widening of the aortic wall characterized by loss of AoSMCs, extracellular matrix degradation and local inflammation. This condition is often asymptomatic until rupture occurs, leading to high morbidity and mortality rates. We aimed at characterizing the transcriptional landscape AoSMCs  and to highlight aortic disease-driven changes in gene expression, in terms of contractility, synthetic, inflammation, proliferation and apoptosis markers.

overall_design: To identify AAA-driven differences in the transcriptome of AoSMCs,  we performed differential expression analysis in AAA patient-derived primary AoSMCs vs. non-AAA primary AoSMCs donors. We performed RNA sequencing of AoSMCs isolated from 5 AAA patients and 3 non-AAA donors. Sequencing reactions were perfomed in triplicate.

first: Lars

last: Maegdefessel

first: Jessica

last: Pauli

first: Greg

last: Winski


title: Skeletal muscle gene expression analysis of Shank3Δ11(-/-) and wildtype mice at postnatal day 0–1

city: Ulm

first: Medhanie

middle: Assmelash

last: Mulaw

address: Albert-Einstein-Allee 11

institute: University of Ulm

summary: We analyzed transcriptional differences by RNA-sequencing of muscle tissue of neonatal Shank3Δ11(-/-) mice and compared those to Shank3(+/+) controls. We found significant differences in gene expression of ion channels crucial for muscle contraction and for molecules involved in calcium ion regulation. In addition, calcium storage- (i.e. Calsequestrin (CSQ)), calcium secretion- and calcium- related signaling- proteins were found to be affected.

overall_design: We used RNA-seq data from five Shank3Δ11(-/-) and four wildtype mice skeletal muscle to perform gene expression profiling.

first: Berra

last: Yildiz

first: Anne-Kathrin

last: Lutz

first: Tobias

last: Böckers


title: Single cell transcriptomics of human abdominal aortic aneurysm [scRNA-seq]

summary: An abdominal aortic aneurysm (AAA) is a pathological widening of the aortic wall characterized by loss of AoSMCs, extracellular matrix degradation and local inflammation. This condition is often asymptomatic until rupture occurs, leading to high morbidity and mortality rates. We conducted single-cell RNA sequencing (scRNA-seq) from AAA patients´s specimens to profile gene expression at single cell level and to gain insight on cell types relevant to disease dynamics.

overall_design: To profile single-cell transcriptome and analyze the diversity of  cell types present in human AAA tissue specimens, we carried out  scRNA-seq from 4 AAA patients. Sequencing reactions were perfomed in duplicate.


title: Differential expression of circular RNAs (circRNAs) in Abdominal Aortic Aneurysm (AAA) patients and controls.

summary: This study aims at identifying non-coding RNA driving AAA pathogenesis and progression.To fish out AAA-relevant circRNA targets, we took advantage of array technology and  profiled differentially expressed circRNAs in AAAs vs. non-AAA human tissue specimens. We then focused on studying circRNA-exerted gene expression regulation at the locus of origin and its implication in AAA disease dynamics.

overall_design: We utilized human tissue specimens including 6 non-AAA controls (CTRL, obtained from organ transplant surgery) and 11 AAA aortas collected from elective (e) open repair (OR) surgery.Array chips (Arraystar, #AS-S-CR-H-V2.0) cover all known annotated human circRNAs (13.617 in total), with array probes targeting circRNA-specific junctions, were employed to identify deregulated targets. We discovered that a considerable amount of circRNA transcripts were significantly up- or downregulated in diseased tissue. Most deregulated targets in our dataset originated from circularization of one or multiple mRNA exons.


title: Characterization of an in vitro steatosis model for modelling the activated de novo lipogenesis

city: stockholm

first: mengzhen

last: Li

address: Drottning Kristinas Väg 36A

country: Sweden

institute: KTH Royal Institute of Technology

summary: We establish a novel in vitro steatosis model that induces steatosis based on de novo lipogenesis (DNL) using HepG2 cells without treatment of any fatty acids.To investigate the genetic features of the DNL model, we then performed gene expression profiling analysis using data obtained from RNA-seq.

overall_design: We did a comparative gene expression profiling analysis of RNA-seq data for three groups including de novo lipogenesis (DNL) steatosis model, the oleic acid-induced (OA) steatosis model, and the wild type (WT) model.  Each group contained three samples.

first: Woonghee

last: Kim

first: Mengzhen

first: Cheng

first: Adil

last: Mardinoglu


title: Breaking constraint of mammalian axial formulae

city: Melbourne

first: Gabriel

middle: Markus

last: Hauswirth

state: Victoria

address: 15 Innovation Walk, Clayton Campus

department: Australian Regenerative Medicine Institute / EMBL Australia

country: Australia

institute: Monash University


title: CD44 connects autophagy decline and aging in the vascular endothelium

city: Zhengzhou

first: Lu

state: Henan

address: Henan University of Technology, Lianhua Street, Zhengzhou

institute: Henan University of Technology

summary: The decline of endothelial autophagy is closely related to vascular senescence and disease, although the molecular mechanisms connecting these outcomes in vascular endothelial cells (VECs) remain unclear. Here, we identify a crucial role for CD44, a multifunctional adhesion molecule, in controlling autophagy and aging in VECs. The CD44 intercellular domain (CD44ICD) negatively regulates autophagy by reducing PIK3R4 and PIK3C3 levels and disrupting STAT3-dependent PtdIns3K complexes. CD44 and its homologue clec-31 are increased in aging vascular endothelium and Caenorhabditis elegans, respectively, suggesting that an age-dependent increase in CD44 induces autophagy decline and aging phenotypes. Accordingly, CD44 knockdown ameliorates age-associated phenotypes in VECs. The endothelium-specific CD44ICD knock-in mouse is shorter-lived, with VECs exhibiting obvious premature aging characteristics associated with decreased basal autophagy. Autophagy activation suppresses the premature aging of human and mouse VECs overexpressing CD44ICD, function conserved in the CD44 homologue clec-31 in C. elegans. Our work describes a mechanism coordinated by CD44 function bridging autophagy decline and aging.

overall_design: We knock-down CD44 in HUVECs by siRNA (S1, S2).  We then analyzed the differentially expressed autophagy related genes compared with control (SC) using the Affymetrix Human GeneChip® Gene1.0 ST platform.     Array data was processed by Affymetrix Exon Array Computational Tool.     No techinical replicates were performed.

first: Peichang

last: Yang


title: Transcriptome changes in the dorsal root ganglion (DRG) after spared nerve injury (SNI) in adult and infant rats.

city: Tokyo

first: Atsushi

last: Sakai

address: 1-1-5 Sendagi, Bunkyo-ku

country: Japan

institute: Nippon Medical School

summary: To investigate differences in response to nerve injury between adult and infant rats, adult and infant rats underwent SNI or sham surgery.

overall_design: Lumbar fifth DRGs of infant and adult rats 14 days after SNI or sham surgery were analyzed.

first: Ino

last: Yuka

first: Motoyo

last: Maruyama

first: Hidenori

last: Suzuki


title: Breaking constraint of mammalian axial formulae [ATAC-seq]

summary: The axial skeleton of individual mammalian species exhibits remarkable robustness in the  number and identity of vertebral elements that form(Owen 1853; Owen 1866; Narita and Kuratani 2005). Between mammalian species however, a great diversity in axial formulae has arisen due to natural selection(Narita and Kuratani 2005; Thewissen et al. 2006; Buchholtz 2007; Matsubara et al. 2017; Kingsley et al. 2017). The genetic mechanism(s) by which axial formulae in mammals is canalised, or manipulated to drive this diversity, remains a major question in biology. Here, we reveal three regulatory pathways essential in constraining total vertebral number and regional axial identity in the mouse. Specifically, the manipulation of Gdf11, Retinoic acid and microRNA-196 activity, individually and cumulatively, led to increasing total vertebral number and allowed us to understand the molecular logic constraining each major division of the vertebral column, from cervical through to tail vertebrae. All three pathways had differing control over Hox cluster expression, with heterochronic and quantitative changes in Hox expression found to parallel changes in axial identity. However, our work revealed an additional, and highly unexpected, role for Hox genes in supporting axial elongation within the tail region. This provides important support for an emerging view that mammalian Hox gene function is not limited to imparting positional identity as the mammalian body plan is laid down, and more broadly, this work provides a molecular framework with which to interrogate mechanisms of evolutionary change.

overall_design: Chromatin accessablitiy profiles of NMP differentiation timecourse derived from wild type ESCs and treatment with Gdf11 on D6 for 24h

first: Victoria

last: Garside

first: Lisa

middle: S

last: Wong

first: Heidi

last: Bildsoe

first: Ildefonso

last: Diaz

first: Yi-Cheng

last: Chang

first: Jan

last: Manent

first: Christian

last: Nefzger

first: Jaber

last: Firas

first: Joseph

last: Chen

first: Fernando

last: Rosello

first: Jose-Luis

last: Gomez Skarmeta

first: Jose

last: Polo

first: Edwina

last: McGlinn


title: Fat body-specific reduction of CTPS alleviates HFD-induced obesity

city: Shanghai

first: Ji-Long

last: Liu

address: 230 Haike Road

institute: ShanghaiTech University

summary: High-fat diet (HFD)-induced obesity is a multi-factorial disease including genetic, physiological, behavioral, and environmental components. Drosophila has emerged as an effective metabolic disease model. Cytidine 5'-triphosphate synthase (CTPS) is a crucial enzyme for the de novo synthesis of CTP, governing the cellular level of CTP and phospholipid synthesis. CTPS has been found to form filaments known as cytoophidia, which are evolutionarily conserved in bacteria, archaea, and eukaryotes. Here, we show that CTPS functions in fat bodies to regulate body weight and starvation resistance in Drosophila. HFD-induced obesity enhances CTPS transcription and lengthens cytoophidia in larval adipocytes. CTPS depletion in the fat body prevented HFD-induced obesity, including body weight gain, adipocyte expansion, and lipid accumulation, by inhibiting the PI3K-Akt-SREBP axis. A dominant-negative form of CTPS also inhibits adipocyte expansion and down-regulates lipogenic genes. As a result, our findings not only establish a functional link between CTPS and lipid homeostasis but also highlight a potential role of CTPS manipulation in the treatment of HFD-induced obesity.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for fat body in CTPS knockdown and wild type larvae

first: Jingnan

first: Yuanbing

last: Zhang


title: Correlation between electrophysiological impact and the transcriptomic profile of brain metastases

first: Manuel

last: Valiente

address: Melchor Fernández Almagro, 3

institute: CNIO

summary: we obtained the individual transcriptomic profiles of the three tested models (482N1, B16F10BrM and E0771BrM) and evaluated whether their different impact on brain functional readouts (i.e., LFP, calcium activity) might have a specific correlate on gene expression.

overall_design: Comparative gene expression profile using RNA-seq data for 482N1, B16F10BrM and E0771BrM from in vitro culture

first: Mariam

last: Masmudi-Martín

first: Carolina

last: Hernández-Oliver

first: Liset

last: Menendez de la Prida


title: Dosage compensation of Z sex chromosome genes in avian fibroblast cells

first: Ruslan

last: Deviatiiarov

address: Hongo 2-1-1, Bunkyo-ku

department: Intractable Disease Research Center

institute: Juntendo University

summary: Sex in birds is genetically determined, molecular mechanism of which is not well-understood. Their Z sex chromosome (chrZ) lacks whole chromosome inactivation as known for mammalian chrX. To investigate the extent of chrZ dosage compensation and its role in somatic cell’s sex specification, we used a highly-quantitative method and analyzed transcriptional activities of male and female fibroblasts from seven birds. Our data indicate for the first time that ¾ of chrZ genes are strictly compensated, similar to that observed in chrX. We also describe non-compensated chrZ genes and identify Ribosomal Protein S6 (RPS6) as a candidate for universal, sex-dimorphic genes in birds.

sample_organism:
Dromaius novaehollandiae
Anas platyrhynchos
Gallus gallus
Pavo cristatus
Meleagris gallopavo
Taeniopygia guttata
Coturnix japonica

overall_design: Embryonic fibroblast cultures for seven bird species (chicken, quail, turkey, peacock, duck, zebra finch, and emu) obtained from males and females. At least two replicates.

first: Hiroki

last: Nagai

first: Galym

last: Ismagulov

first: Anastasia

last: Stupina

first: Kazuhiro

last: Wada

first: Woranop

last: Sukparangsi

first: Sittipon

last: Intarapat

first: Oleg

last: Gusev

first: Guojun

last: Sheng

first: Shinji

last: Ide

first: Noriyuki

last: Toji

first: Heng


title: Gene expression profile at single cell level of the lung cancer brain metastatic cell line 482N1 grew in the brain parenchyma

summary: We used single cell RNA sequencing (scRNA-seq) to analyze the heterogeneity of 482N1 brain metastatic cells intracranially injected

overall_design: GFP+ 482N1 cells from the brain of intracranially injected C57BL/6J mice were sorted and analyzed using scRNAseq

first: Neibla

last: Priego


title: Adipose transcriptome in the scalp of androgenetic alopecia

city: Tainan

first: Criselda Jean

last: Cruz

address: No. 1 University Rd.

department: Dermatology

country: Taiwan

institute: National Cheng Kung University

summary:
To identify differentially expressed genes in androgenetic alopecia specifically in the adipose, adipose tissue samples from affected male participants were collected through punch biopsy at two different sites: bald (frontal) and normal (occipital,as control) scalp.
After removal of the epidermis, dermis and hair follicle, we isolated RNA from the remaining adipose layer of the bald and normal scalp then performed gene expression analysis on the RNA-seq data to compare the profiles of the bald and normal scalp.

overall_design: Comparative gene expression analysis of RNA-seq data from the adipose layer of the bald versus normal scalp of male patients with androgenetic alopecia.

first: Criselda-Jean

middle: G

first: Yi-Kai

last: Hong

first: F

last: Wilson Jr.

first: Yen-Reu

last: Tsai

first: Pei-Lun

last: Chung

first: Yau-Sheng

first: Chao-Kai

last: Hsu

first: Chao-Chun

last: Yang


title: Breaking constraint of mammalian axial formulae [RNA-Seq]

first: Gabriel

last: Hauswirth

overall_design: RNA-seq of NMP differentiation timecourse derived from wild type ESCs and treatment with Gdf11 on D6 for 24h

first: Victoria

last: Garside

first: Lisa

last: Wong

first: Heidi

last: Bildsoe

first: Ildefonso

middle: C

last: Diaz

first: Yi-Cheng

last: Chang

first: Jan

last: Manent

first: Christian

last: Nefzger

first: Jaber

last: Firas

first: Joseph

last: Chen

first: Fernando

last: Rosello

first: Jose-Luis

last: Gomez Skarmeta

first: Jose

last: Polo

first: Edwina

last: McGlinn


title: The Atypical Antidepressant Tianeptine Confers Neuroprotection against Oxygen-Glucose Deprivation

status: Public on Aug 29 2023

city: Berlin

first: Ria

last: Göttert

address: Charitéplatz 1

department: experimental Neurology

institute: Charité

summary: Proregenerative and neuroprotective effects of antidepressants are an important topic of inquiry in neuropsychiatric research. Oxygen-glucose deprivation (OGD) mimics key aspects of ischemic injuryin vitro. Here, we studied the effects of 24-h pretreatment with serotonin (5-HT), citalopram (CIT), fluoxetine (FLU), and tianeptine (TIA) on primary mouse cortical neurons subjected to transient OGD. 5-HT (50 μM) statistically significantly enhanced neuron viability as measured by MTT assay and reduced cell death and LDH release. CIT (10 μM) and FLU (1 μM) did not increase the effects of 5-HT and neither antidepressant conferred neuroprotection in the absence of supplemental 5-HT in serum-free cell culture medium. By contrast, pre-treatment with TIA (10 μM) resulted in robust neuroprotection, even in the absence of 5-HT. Furthermore, TIA inhibited mRNA transcription of candidate genes related to cell death and hypoxia and attenuated lipid peroxidation, a hallmark of neuronal injury. Finally, deep RNA sequencing of primary neurons subjected to OGDdemonstrated that OGD induces many pathways relating to cell survival, the inflammation-immune response, synaptic dysregulation and apoptosis, andthatTIA pretreatment counteracted theseeffects of OGD. In conclusion, this study highlights the comparative strength of the 5-HT independent neuroprotective effects of TIA and identifies the molecular pathways involved.

overall_design: Primary neuronal cultures obtained from the cortex of embryonic mice at embryonic day 15 were pretreated with 10 μM TIA at 8 DIV and they were exposed to in vitro ischemic damage via 3 h-OGD at 9 DIV. Total RNA from each condition (CONTROL-VEH, CONTROL-TIA, OGD-VEH and OGD-TIA) was extracted 6 hours after OGD. 4 replicates for each condition was used for RNA-seq.

first: Burcu

last: Ersoy

first: Golo

last: Kronenberg

first: Karen

last: Gertz


title: Mimicking acute airway tissue damage using femtosecond laser nanosurgery in airway organoids

city: Hannover

first: Lara

last: Gentemann

address: Welfengarten 1

department: Institute of Quantum Optics

institute: Leibniz University Hannover

summary: Airway organoids derived from adult murine epithelial cells represent a complex 3D in vitro system mimicking the airway epithelial tissue’s native cell composition and physiological properties. In combination with a precise damage induction via femtosecond laser-based nanosurgery, this model allows for the examination of intra- and intercellular dynamics in the course of repair processes with a high spatio-temporal resolution, which can hardly be reached using in vivo approaches. For characterization of the organoids’ response to single or multiple-cell ablation, we first analyzed overall organoid survival and found that airway organoids were capable of efficiently repairing damage induced by femtosecond laser-based ablation of a single to ten cells within 24 h. An EdU staining assay further revealed a steady proliferative potential of airway organoid cells. Especially in the case of ablation of five cells, proliferation was enhanced within the first four hours upon damage induction, whereas ablation of ten cells was followed by a slight decrease in proliferation within this time frame. Analyzing individual trajectories of single cells within airway organoids, we found an increased migratory behavior in cells within close proximity to the ablation site following the ablation of ten, but not five cells. Bulk RNA sequencing and subsequent enrichment analysis revealed the differential expression of sets of genes involved in the regulation of epithelial repair, distinct signaling pathway activities such as Notch signaling, as well as cell migration after laser-based ablation. Together, our findings demonstrate that organoid repair upon ablation of ten cells involves the same key processes by which native airway epithelial wound healing is regulated. This marks the herein presented in vitro damage model suitable to study repair processes following acute airway injury, thereby posing a novel approach to gain insights into the mechanisms driving epithelial repair on a single-cell level.

overall_design: Airway epithelial organoids derived from adult murine lung cells were subjected femtosecond laser-based nanosurgery to precisely ablate 10 neighboring cells per organoid. This RNASeq study aimed to gain information about changes in transcription patterns between both ablation and control group to identify key signaling activity/protein expression up-/downregulation in the course of repair/regeneration.

first: Stefan

last: Kalies

first: Manuala

last: Büttner


title: Histone H3 K27M mediated Regulation of Cancer Cell Stemness and Differentiation in Diffuse Intrinsic Pontine Glioma (DIPG)

city: Ann Arbor

first: Brian

last: Magnuson

state: MI

address: 1500 East Medical Center Drive

institute: University of Michigan

overall_design: Refer to individual Series


title: Functional effects of DNMT3A R882 on human haematopoietic stem and progenitor cells myeloid differentiation

status: Public on Aug 28 2023

city: cambridge

first: Kendig

last: Sham

state: england

address: Jeffrey Cheah Biomedical Centre, Puddicombe Way

department: MRC Cambridge Stem Cell Institute

country: United Kingdom

institute: University of Cambridge

summary: This data presents the transcriptomes of bulk mature colonies derived from single human haematopoietic stem cells / multipotent progenitors (HSC/MPPs) and granulocyte macrophage progenitors (GMPs) purified from one indiviual with age related clonal haematopoisesis. The profiled colonies contain mature monocytes, as measured by conventional cell surface markers (CD14+, CD15-, GlyA-), but no other mature blood cell types. This  dataset is part of a larger study, the main objective of which is to understand the functional effects conferred by somatic DNMT3A R882H mutation on human haematopoietic stem cell differentiation capacity. In clonal haematopoiesis,  DNMT3A R882H and DNMT3A WT HSPCs co-exist in the same individual. We compared the transcriptional differences between mature monocytic colonies derived from DNMT3A R882H and WT HSPCs in vitro. Analysis of this dataset shows that, in this individual, DNMT3A R882H HSPCs produce less mature monocytes than their WT counterparts over the same culture time.

overall_design: 39 bulk monocyte colonies derived from 33 single HSC/MPPs and 6 single GMPs were analysed from 1 individual. Single HSC/MPPs (CD19-, CD33-, CD34+, CD45dim, CD38-, CD45RA+), and GMPs  (CD19-, CD33-, CD34+, CD45dim, CD38+, CD7/CD10-, CD45RA+) were cultured in vitro for 21 days in myelo-erythroid medium (MEM), colonies containing mature monocytes but no other mature blood cell lineage were selected and harvested into RNA extraction plates and RNA extracted using the Qiagen RNeasy protocol.

first: Aditi

last: Vedi

first: Elisa

last: Laurenti

first: Daniel

last: Hayler


title: Heart transcriptome of different subtype of sepsis induced myocardium dysfunction according to ejection fraction

city: Changsha

first: Desheng

last: Qi

state: Hunan

address: Xiangya Road 87

department: Department of Emergency

institute: Xiangya Hospital, Central South University

summary: Dysregulated cardiac function after sepsis is common in intensive care unit (ICU) and known to predict poor long-term outcome and increase mortality. Effective therapeutic strategies are largely lacking. Moreover, the pathological feature and the molecular mechanism underlying cardiac dysfunction induced by sepsis remain unclear. Here, by performing echocardiograms on rodents after induction of polymicrobial sepsis with cecum ligation and puncture (CLP), we assessed the temporal dynamics of left ventricular ejection fraction (LVEF) and a serial of hemodynamics parameters on animals at different time point after CLP. Intriguingly, the mean LVEF is comparable in mice induced by CLP and sham, whereas survivors post CLP had stable LVEF and non-survivors had markedly fluctuated LVEF at early phase of CLP induction, suggesting LVEF away from normal range is highly associated with mortality. Consistent with clinical observations of depressed, preserved or hyperdynamic LVEF in septic patients from data compiled using our ICU cohort and from other studies, CLP-induced mice fall into three groups based on LVEF measured at 24 hours after surgery: high LVEF (HEF, LVEF>=90%), low LVEF (LEF, LVEF<65%), and normal LVEF (NEF, 65%=<LVEF<90%). We performed genome-wide transcriptomic and proteomic profiling on left ventricle samples collected from three CLP groups and sham mice. By implementing pathway analysis, gene set enrichment and coexpression network analysis, we identified jointly and distinctively changed genes, proteins and biologically-essential processes and pathways in three CLP groups with different LVEF. Notably, transmission electron microscopy examination shows remarkable mitochondrial and sarcomere defects in three CLP groups with different phenotypes associated with LVEF variances. Together, this study systematically characterizes the molecular, morphological, and functional alterations in CLP-induced cardiac injury, serving as a framework for future research into pathology and molecular mechanism of sepsis-induced cardiomyopathy.

overall_design: Heart tissue samples for one day after sepsis mice model, including sham group(S,n=4),high LVEF group(HEF, LVEF>=90%)(C1,n=4), low LVEF (LEF, LVEF<65%)(C2,n=3), and normal LVEF (NEF, 65%=<LVEF<90%)(C3,n=4) according to left ventricular ejection fraction

first: Milin

last: Peng

first: Zhonghua

last: Hu

first: Lina

last: Zhang


title: TKS5 mediates the formation of podosome rosettes in pulmonary fibroblasts and promotes fibrosis.

city: Vari

first: Vassilis

last: Aidinis

address: 34 Fleming Street

country: Greece

institute: BSRC 'Alexander Fleming'

summary: Here we assess the effect of Tks5 knockout on the transcriptome of activated lung fibroblasts. For this purpose we examine TGF-beta treated fibroblasts from wild type and Tks5 KO mice. We show that Tks5 deficiency affects transcriptome of lung fibroblasts leading to the suppression of biological processes relative to the extracellular matrix and cell migration.

overall_design: Comparative gene expression profiling analysis of Quant-seq data from TGF-beta treated wild type and TKS5 knock-out TGF-beta treated lung fibroblasts.

first: Iliana

last: Barbayianni

first: Vaggelis

last: Harokopos

first: Dionysios

last: Fanidis


title: Meiotic completion of the spermatocytes requires the kinase WNK1

status: Public on Aug 27 2023

city: RTP

first: Xiaojiang

last: Xu

address: 111 T. W. Alexander Dr.,

institute: NIEHS

summary: The kinase protein WNK1 is highly expressed and phosphorylated in the testis, suggesting possible functions in regulating male fertility. Indeed, conditional pachytene-spermatocyte Wnk1 knock-out mice generated using the novel Wnt7a-Cre failed to produce functional sperm which resulted from the primary spermatogenic arrest during mid-pachynema. Global transcriptomic approaches identified ‘translation’ as one of the impacted events in Wnk1-depleted spermatocytes.

overall_design: scRNA-seq profiling of Wnk1-depleted and control spermatocytes

first: Ru-pin

last: Chi

first: Francesco

last: DeMayo


title: Osteoclast differentiation and Dynamic mRNA expression during Mice embryonic palatal bone development

city: Fuzhou City , Fujian Province, China.

first: Yongzhen

last: Lai

state: Fuzhou

address: No. 28, Xinquan Road, Fuzhou City (350001), Fujian Province, China.

institute: Department of Oral and Cranio-maxillofacial Science, Fujian Medical university Union Hospital,

summary: This study is the first to investigate the process of osteoclast differentiation, its potential functions, and the associated mRNA and signaling pathway during embryonic palatal bone. Our findings suggest that osteoclasts may be involved in bone remodeling, bone marrow cavity formation, and blood vessel formation in embryonic palatal bone. We observed Trap-positive osteoclasts at E16.5, E17.5, and E18.5 at the palatal process of the palate (PPP), Posterior and anterior part of the palatal process of the maxilla (PPMXP, and PPMXA), respectively, with osteoclast differentiation starting 2 days prior to TRAP positivity. By comparing the key periods of osteoclast differentiation between PPMX and PPP (E14.5, E15.5, and E16.5) using RNA-seq data of the palates, we found that the PI3K-AKT and MAPK signaling pathways were sequentially enriched, which may play critical roles in osteoclast survival and differentiation. Csf1r, Tnfrsff11a, Ctsk, Fos, Tyrobp, Fcgr3, and Spi1 were significantly upregulated in both PPMX and PPP, while Pik3r3, Tgfbr1, and Mapk3k7 were significantly downregulated in both. Interestingly, Tnfrsff11b was upregulated in PPMX but downregulated in PPP, which may regulate the timing of osteoclast appearance. These results contribute to the limited knowledge regarding mRNA specific steps in OLCs differentiation in the embryonic palatal bone.

overall_design: E14.5-E16.5 pregnant mice were euthanized by decapitation and soaked in 100% alcohol for one minute. Afterward, embryos were obtained and transferred to ice-cold Hanks liquid. The mandibles and skulls of the embryos were removed. The ppmx and ppp of E14.5 to E16.5 embryos (n = 3 for each group) were dissected out under a stereomicroscope and then stored in RNAlater (BI, Israel) for RNA sequencing (RNA-seq) as described in our previous study.(9) Expression patterns of OLCs differentiation genes expression from E14.5 to E16.5 in PPP and PPMX were compared. The log2 (fold-change cut-off) was set at 0 or higher for analyses of differential expression, and the Q-value was set to less than 0.05. And there were E15.5 vs E14.5 pairwise, E16.5 vs E15.5 pairwise, and E16.5 vs E14.5 pairwise with the E14.5 group, E15.5 group, E14.5 were used as the control groups, respectively. We performed KEGG enrichment analysis of the total differentially expressed genes (DEGs). GSEA enrichment analysis of pathways related to osteoclast differentiation was performed, and the heat map and volcano map of differential genes were displayed, and the corresponding KEGG pathway map was depicted.

first: Yonzhen

first: Caiyu

last: Liao

first: Weihui

last: Chen


title: The tumor microenvironment shows a hierarchy of cell-cell interactions dominated by fibroblasts

city: Rehovot

first: Shimrit

last: Mayer

state: Central

address: Herzl St 234

department: Bimolecular sciences

country: Israel

institute: Weizmann Institute

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


title: The tumor microenvironment shows a hierarchy of cell-cell interactions dominated by fibroblasts [cancer CM]

summary: We preformed RNA seq on invitro fibroblasts after mono-cultured or co-cultured with macrophages in DMEM  or with 4T1-conditioned medium , In order to understand the affect of cancer on macrophages-fibroblasts interactions

overall_design: We performed RNA-sequencing of the co-cultures at the ON state. As control, we analyzed mono-cultured fibroblasts and macrophages. Fibroblasts and BMDMs were seeded at 3× 10^5 into a pre-coated 6 well plate. The co-cultures and the mono-cultures were grown in DMEM or with 4T1 conditioned medium. After 7 days of co-culture.  10^4 cells of fibroblasts were sorted using the FACSMelody instrument (BD-biosciences). Dead cells were excluded using PI, the fibroblasts were negetive stained for anti-F4/80-APC cy7 (Biolegend. cat.123117), anti-CD11b-Pacific blue antibody (Miltenyi, 130-110-802) . The cells were collected directly into lysis/binding buffer (Life Technologies) and mRNA was isolated using Dynabeads oligo (dT) (Life Technologies). RNA-seq was performed as previously described (“Massively Parallel Single-Cell RNA-Seq for Marker-Free Decomposition of Tissues into Cell Types” n.d.).

first: Tomer

last: Milo

first: Uri

last: Alon

first: Ruth

last: Shouval


title: A genetic screen identifies BEND3 as a regulator of bivalent gene expression and global DNA methylation

status: Public on Aug 26 2023

city: Paris

first: Pierre-Antoine

last: Defossez

address: 35 rue Hélène Brion

country: France

institute: Epigenetics and Cell Fate Unit

type: Methylation profiling by high throughput sequencing

summary: Epigenetic mechanisms are essential to establish and safeguard cellular identities in mammals. They dynamically regulate the expression of genes, transposable elements and higher-order chromatin structures. Consequently, these chromatin marks are indispensable for mammalian development and alterations often lead to disease, such as cancer. Bivalent promoters are especially important during differentiation and development. Here we used a genetic screen to identify new regulators of a bivalent repressed gene. We identify BEND3 as a regulator of hundreds of bivalent promoters, some of which it represses, and some of which it activates. We show that BEND3 is recruited to a CpG-containg consensus site that is present in multiple copies in many bivalent promoters. Besides having direct effect on the promoters it binds, the loss of BEND3 leads to genome-wide gains of DNA methylation, which are especially marked at regions normally protected by the TET enzymes. DNA hydroxymethylation is reduced in Bend3 mutant cells, possibly as consequence of altered gene expression leading to diminished alpha-ketoglutarate production, thus lowering TET activity. Our results clarify the direct and indirect roles of an important chromatin regulator, BEND3, and, more broadly, they shed light on the regulation of bivalent promoters.

overall_design:
Whole genome bisulfite sequencing, RNA-sequencing and ChIP-sequencing (anti-BEND3 in WT cells and anti-V5-BEND3 in Bend3 KO cells) were performed on mouse embryonic stem cells grown  in serum medium.
Amplicon-sequencing was performed on WT cells and Bend3 KO clones (GSE221710).

first: Lounis

last: Yakhou

first: Anaelle

last: Azogui

first: Nikhil

last: Gupta

first: Julien

last: Richard Albert

first: Fumihito

last: Miura

first: Laure

last: Ferry

first: Kosuke

last: Yamaguchi

first: Sarah

last: Battault

first: Pierre

last: Therizols

first: Frédéric

last: Bonhomme

first: Elouan

last: Bethuel

first: Arpita

last: Sarkar

first: Maxim

middle: V

last: Greenberg

first: Paola

last: Arimondo

first: Gael

last: Cristofari

first: Olivier

last: Kirsh

first: Takashi

last: Ito


title: Standard and targeted single-cell transcriptomics of CD8+ T cell samples and targeted single-cell transcriptomics of B cell samples for systematic analysis

city: Leuven

first: Lies

last: Van Horebeek

address: Herestraat 49

department: Neurosciences

country: Belgium

institute: KU Leuven

summary: We developed a straightforward targeted sequencing approach as extension to high-throughput droplet-based scRNA-seq. By overlaying standard gene expression data with genotype information at the transcript level, we created a powerful method for evaluating the impact of genetic variants. We systematically analysed the effect of technical parameters on the targeted sequencing method and demonstrated how the targeted sequencing method can be used.

overall_design:
T, CD8+ T or B lymphocytes were isolated from PBMCs using EasySep Human T, CD8+ T or B Cell Isolation Kits (STEMCELL Technologies). Single cell suspensions were used for single cell transcriptomics with the Chromium Next GEM Single Cell 3’ Reagent Kits v3.1 (10x Genomics; CD8+ T and B cells) or the Chromium Single Cell V(D)J Reagent Kits v.1.1 (10x Genomics; T cells). Left-over amplified cDNA was used as input for our targeted sequencing extension.
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Authors state "Raw data files cannot be shared because of GDPR."

first: An

last: Goris


title: Molecular signature of human muscle reserve cells (Pax7High and Pax7Low subpopulations)

status: Public on Aug 25 2023

city: Geneva

first: Thomas

last: Laumonier

address: Rue Michel-Servet 1

country: Switzerland

institute: University of Geneva

summary: We compared the transciptome of human myoblasts, of human muscle reserve cells expressing high level of Pax7 (MuRCPax7High) and of human MuRCPax7Low

overall_design: Transcriptomic analysis of human myogenic cells (myoblasts and MuRC) that were fixed and permeabilized and sorted by flow cytometry after Pax7 staining (before RNA-seq).

first: Axelle

last: Bouche

first: Benoit

last: Borner

first: Chloé

last: Richard

first: Ysaline

last: Grand

first: Didier

last: Hannouche


title: A comparative analysis of gene and protein expression in chronic and acute models of photoreceptor degeneration in adult zebrafish

city: Detroit

first: Ashley

middle: Catherine

last: Kramer

state: Michigan

address: 540 E. Canfield St

department: Ophthalmology, Visual and Anatomical Sciences

country: USA

institute: Wayne State University School of Medicine

summary: Adult zebrafish are capable of photoreceptor (PR) regeneration following acute phototoxic lesion (AL). We developed a chronic low light (CLL) exposure model that more accurately reflects chronic photoreceptor degeneration observed in many human retinal diseases. Here, we characterize the morphological and transcriptomic changes associated with acute and chronic models of PR degeneration at 8 time points over a 28-day window using immunohistochemistry and 3’mRNA-seq. We first observed a differential sensitivity of rod and cone PRs to CLL. Next, we found no evidence for Müller glia (MG) gliosis or regenerative cell-cycle reentry in the CLL model, which is in contrast to the robust gliosis and proliferative response from resident MG in the AL model. Differential responses of microglia between the models was also observed. Transcriptomic comparisons between the models revealed gene-specific networks of PR regeneration and degeneration, including genes that are activated under conditions of chronic PR stress. Finally, we showed that CLL is at least partially reversible, allowing for rod and cone outer segment outgrowth and replacement of rod cell nuclei via an apparent upregulation of the existing rod neurogenesis mechanism. Collectively, these data provide a direct comparison of the morphological and transcriptomic photoreceptor degeneration and regeneration models in zebrafish.

overall_design: 3'mRNA sequencing of single adult zebrafish retinas harvested at 7 different time-points post chronic exposure to ~5,000 lux "low light" lesion, along with dark adapted 0hr controls (n=6).

first: Justin

last: Carthage

first: Yasmeen

last: Berry

first: Katherine

last: Gurdziel

first: Tiffany

middle: A

last: Cook

first: Ryan

last: Thummel


title: RNA-seq to perform gene expression profiling analysis regarding to ac4C regulation

city: Beijing

first: Yuan

last: Zhou

address: 38 college road

country: China

institute: Peking University

summary:
NAT10-catalyzed N4-acetylcytidine (ac4C) has emerged as a vital post-transcriptional modulator on the coding transcriptome by promoting mRNA stability.
To investigate the effect of NAT10-mediated ac4C acetylation modification on gene expression level, we performed high throughput RNA sequencing experiments of control and NAT10 KD hESCs each with 4 replicates.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for control and NAT10 KD hESCs.

first: Rucong

last: Liu

first: Zibaguli

last: Wubulikasimu

first: Runze

last: Cai

first: Fanyi

last: Meng

first: Qinghua

last: Cui

first: Yang

last: Li


title: Intra- and interchromosomal contact mapping reveals the Igh locus has extensive conformational heterogeneity and interacts with B-lineage genes [RNA-seq]

city: Cambridge

first: Louise

last: Matheson

address: Babraham Research Campus

department: Laboratory of Lymphocyte Signalling and Development

institute: The Babraham Institute

summary: To produce a diverse antibody repertoire, immunoglobulin heavy-chain (Igh) loci undergo large-scale alterations in structure to facilitate juxtaposition and recombination of spatially separated variable (VH), diversity (DH), and joining (JH) genes. These chromosomal alterations are poorly understood. Uncovering their patterns shows how chromosome dynamics underpins antibody diversity. Using tiled Capture Hi-C, we produce a comprehensive map of chromatin interactions throughout the 2.8-Mb Igh locus in progenitor B cells. We find that the Igh locus folds into semi-rigid subdomains and undergoes flexible looping of the VH genes to its 3′ end, reconciling two views of locus organization. Deconvolution of single Igh locus conformations using polymer simulations identifies thousands of different structures. This heterogeneity may underpin the diversity of V(D)J recombination events. All three immunoglobulin loci also participate in a highly specific, developmentally regulated network of interchromosomal interactions with genes encoding B cell-lineage factors. This suggests a model of interchromosomal coordination of B cell development.

overall_design: Nuclear RNA-seq libraries from Rag1-/- pro-B cells and Rag1-/-VH81X pre-B cells, with two biological replicates each

first: Olga

last: Mielczarek

first: Carolyn

last: Rogers

first: Anne

last: Corcoran


title: Identification of a c-type heme oxygenase and its function during acclimation of cyanobacteria to nitrogen fluctuations

status: Public on Aug 24 2023

city: Shanghai

first: Weimin

last: Ma

address: No.100 Guilin Rd

department: College of Life Sciences

institute: Shanghai Normal University

summary: The mechanisms of acclimating to a nitrogen-fluctuating environment are necessary for the survival of aquatic cyanobacteria in their natural habitats, but our understanding is still far from complete. Here, the synthesis of phycobiliprotein is confirmed to be much earlier than that of photosystem components during recovery from nitrogen chlorosis and an unknown protein Ssr1698 is discovered to be involved in this synthetic process. The unknown protein is further identified as a c-type heme oxygenase (cHO) in tetrapyrrole biosynthetic pathway and catalyzes the opening of heme ring to form biliverdin IXα, which is required for phycobilin production and ensuing phycobiliprotein synthesis. In addition, the cHO-dependent phycobiliprotein is found to be vital for the growth of cyanobacterial cells during chlorosis and regreening through its nitrogen-storage and light-harvesting functions, respectively. Collectively, the cHO expressed preferentially during recovery from nitrogen chlorosis is identified in photosynthetic organisms and the dual function of this enzyme-dependent phycobiliprotein is proposed to be an important mechanism for acclimation of aquatic cyanobacteria to a nitrogen-fluctuating environment.

overall_design: A comparative transcriptomic analysis was conducted after the nitrate was added to chlorotic cells for 4 h or not

first: Dezhi

first: Lanzhen

last: Wei

first: Zhaoxing

last: Ran

first: Zhenyu

last: Du

first: Gengkai

last: Miao

first: Mei

last: Zheng

first: Ligang

last: Luo

first: Xiaoqin

last: Pang


title: Regulation of brain endothelial cell physiology by the TAM receptor tyrosine kinase Mer

city: San Diego

first: April

middle: Elizabeth

last: Williams

state: California

address: 10010 N Torrey Pines Rd

department: IGC

institute: Salk Institute for Biological Studies

summary: The receptor tyrosine kinase Mer (gene name Mertk) acts in vascular endothelial cells (ECs) to tighten the blood-brain barrier (BBB) subsequent to viral infection. Correspondingly, we found that Mer regulates the expression and activity of a large cohort of cytoskeletal and BBB proteins, together with endothelial nitric oxide synthase, in brain ECs. We further found that Mer controls the expression of multiple angiogenic genes, and that EC-specific Mertk gene inactivation results in perturbed vascular sprouting and a compromised BBB after induced photothrombotic stroke. Unexpectedly, stroke lesions in the brain were also markedly reduced in the absence of EC Mer, which was linked to reduced plasma expression of fibrinogen, prothrombin, and other effectors of blood coagulation. Together, these results demonstrate that Mer is a central regulator of angiogenesis, BBB integrity, and blood coagulation in the mature vasculature. They may also account for disease severity following infection with the coronavirus SARS-CoV-2.

overall_design: Primary brain endothelial cells from WT and Mertk-/- mice were treated with the Mer inhibitor UNC2025 or vehicle alone (PBS) for 20h, after which RNA was harvested and used for bulk RNAseq

first: Kaisa

last: Happonen

first: Patrick

last: Burrola

first: Greg

last: Lemke


title: Essential role of the Pax5 C-terminal domain in controlling B cell commitment and development

city: Vienna

first: Moritz

middle: M

last: Gaidt

address: Campus-Vienna-Biocenter 1

country: Austria

institute: IMP

summary: The B-cell regulator Pax5 consists of multiple domains, whose function we analyzed in vivo by deletion in Pax5. While B-lymphopoiesis was minimally affected in mice with homozygous deletion of the octapeptide or partial homeodomain, both sequences were required for optimal B-cell development. Deletion of the C-terminal regulatory domain 1 (CRD1) interfered with B-cell development, while elimination of CRD2 modestly affected B-lymphopoiesis. Deletion of CRD1 and CRD2 arrested B-cell development at an uncommitted pro-B cell stage. Most Pax5-regulated genes required CRD1 or both CRD1 and CRD2 for their activation or repression, as these domains induced or eliminated open chromatin at Pax5-activated or Pax5-repressed genes, respectively. Co-immunoprecipitation experiments demonstrated that the activating function of CRD1 is mediated through interaction with the chromatin-remodeling BAF, H3K4-methylating Set1A-COMPASS and H4K16-acetylating NSL complexes, while its repressing function depends on recruitment of the Sin3-HDAC and MiDAC complexes. These data provide novel molecular insight into how different Pax5 domains regulate gene expression to promote B-cell commitment and development.

overall_design:
ChIP-Seq: Peak calling and read signal comparison between Pax5(+/+), Pax5(DCRD1/DCRD1), Pax5(DCRD1,2/DCRD1,2) and Pax5(Prd/floxed) conditions (Pax5 antibody); SB(+/+), Pax5(DCRD1/-) conditions (Brg1 antibody).
ATAC-Seq: Peak calling and read signal comparison between Pax5(+/+), Pax5(DCRD1/DCRD1), Pax5(DCRD1,2/DCRD1,2) and KO (vav-cre Pax5(fl/fl)) conditions. Two replicates each.
RNA-Seq: Comparative gene expression profiling analysis of RNA-seq data for wild type Pro-B cells (Pax5(+/+) and various central (Pax5(DOP/DOP), Pax5(DHD/DHD), Pax5(DOP,HD/DOP,HD)) ,C-terminal (Pax5(DCRD1/-),Pax5(DCRD2/-),Pax5(DCRD1,2/-),Pax5(DCRD1/DCRD1),Pax5(DCRD2/DCRD2),Pax5(DCRD1,2/DCRD1,2) mutants and KO (vav-cre Pax5(fl/fl)). Furthermore comparisons between vav-cre Pax5(floxed/+), vav-cre Pax5(Prd/floxed) and vav-cre Pax5(floxed/floxed). At least two replicates per condition. Various other tracks are reported only for expression analysis (TPMs) (LMPP-,ALP-,BLP-,Pre-B-,Immature B-,DN1-,DN2a-,DN2b-,DN3a-,DN3b-cells).

first: Sarah

last: Gruenbacher

first: Markus

last: Jaritz

first: Louisa

last: Hill

last: Schäfer

first: Meinrad

last: Busslinger


title: NAT10-mediated N4-acetylcytidine mRNA Modification Regulates Self-Renewal in Human Embryonic Stem Cells

first: Yuan

last: Zhou


title: RNA-seq to profile the alterations in transcript half-lives regarding to ac4C regulation

summary:
NAT10-catalyzed N4-acetylcytidine (ac4C) has emerged as a vital post-transcriptional modulator on the coding transcriptome by promoting mRNA stability.
To investigate the effect of NAT10-mediated ac4C acetylation modification on RNA stability at the transcriptome scale, we performed high throughput RNA sequencing experiments of control and NAT10 KD hESCs at three time points each with 3 replicates.

overall_design: Comparative RNA stability analysis of RNA-seq data for control and NAT10 KD hESCs.

first: Rucong

last: Liu

first: Zibaguli

last: Wubulikasimu

first: Runze

last: Cai

first: Fanyi

last: Meng

first: Qinghua

last: Cui

first: Yang

last: Li


title: Intra- and interchromosomal contact mapping reveals the Igh locus has extensive conformational heterogeneity and interacts with B-lineage genes

first: Louise

last: Matheson

overall_design: Refer to individual Series


title: Intra- and interchromosomal contact mapping reveals the Igh locus has extensive conformational heterogeneity and interacts with B-lineage genes [Hi-C]

overall_design: Hi-C libraries from Rag1-/- pro-B cells (including two different Rag1-/- models), Rag1-/-VH81X pre-B cells and thymus, with two biological replicates each, and corresponding capture Hi-C (CHi-C) libraries in which the immunoglobulin loci and other genes of interest were captured

first: Olga

last: Mielczarek

first: Carolyn

middle: H

last: Rogers

first: Anne

last: Corcoran


title: Expansion of human bone marrow-derived mesenchymal stromal cells with enhanced immunomodulatory properties

city: Singapore

first: Shu Hui

last: Neo

address: 61 Biopolis Dr, Proteos, Singapore 138673

department: IMCB

country: Singapore

institute: A*STAR

summary: Cell culture confluency affects gene expression profiles of human bone marrow-derived mesenchymal stromal cells (MSCs). High-confluency MSCs are enriched in pathways that confer them a more immunosuppressive phenotype as compared to low-confluency MSCs.

overall_design: To investigate whether cell culture confluency affects the transcriptome of human bone marrow-derived MSCs, we expanded the cells by seeding at low and high density, and harvested these cells within a same time frame, leading to two conditions: low-confluency (LC) and high-confluency (HC). We then harvested total RNA from cells of these two conditions. Comparative gene expression profiling analysis of RNA-seq data for LC and HC was performed.


title: Activation of AKT induces EZH2-mediated β-catenin trimethylation in colorectal cancer. [Cut & Run]

status: Public on Aug 23 2023

city: Bloomington

first: Ahmed

last: Ghobashi

state: IN

institute: Indiana University

summary: The lysine methyltransferase EZH2 is overexpressed in colorectal cancer (CRC) and has been found to be positively and negatively correlated with CRC patient survival depending on the study suggesting that EZH2 has a complex role in CRC. Here, we demonstrate that AKT-mediated EZH2 S21 phosphorylation induced EZH2 to trimethylate β-catenin at K49, which increased β-catenin’s binding to the chromatin. Additionally, EZH2-mediated β-catenin trimethylation induced β-catenin’s interaction with TCF1 and RNA polymerase II and resulted in a dramatic gain in genomic regions with β-catenin occupancy. Interestingly, EZH2 catalytic inhibition decreased stemness but increased migratory phenotypes of CRC cells with active AKT. Overall, we demonstrated that EZH2 modulates AKT-induced changes in gene expression through the AKT/EZH2/β-catenin axis in CRC. Our results suggest that EZH2 inhibitors have tumor-inhibiting and promoting effects in CRC as they inhibit EZH2-mediated methylation of histone and non-histone targets like β-catenin.

overall_design: Testing if EZH2 binding to the chromatin is regulated by EZH2 phosphorylation at Serine 21. CUT&RUN was performed using HA antibody to determine EZH2's enrichment over the chromatin in EV and PTEN knockdown SW480 cells expressing equal levels of HA-EZH2 wild type and HA-EZH2 S21A (phospho-null). SW480 cells not transfected with HA-expressing plasmid were used as a negative control

first: Heahter

last: O'Hagan


title: RNA sequencing of chicken limb distal mesenchyme to compare gene expression over time and in heterochronic grafted cells.

city: Sheffield

first: Sofia

last: Sedas Perez

address: Western Bank

institute: The University of Sheffield

summary:
Distal limb mesenchyme cells were collected from embryonic chickens at Hamburger Hamilton (HH) stages HH24 and HH27, and from samples that had been grafted from HH20 to HH24 and left to develop for 24 hours.
Bioinformatics and clustering analyses were then performed to determine whether grafted cells are more similar to HH24 (graft stage) or HH27 (host stage).

overall_design: Comparative gene expression profiling analysisand clustering analyses of RNA-seq data for distal limb bud mesemchyme at different stages.

first: Joe

last: Pickering

first: Matthew

last: Towers


title: Unique activities of two overlapping PAX6 retinal enhancers

city: Edinburgh

first: Hannah

last: Long

address: Crewe Rd South

department: MRC Human Genetics Unit

institute: University of Edinburgh

summary: Enhancers play a critical role in development by precisely modulating spatial, temporal, and cell type-specific gene expression. Sequence variants in enhancers have been implicated in disease, however establishing the functional consequences of these variants is challenging due to a lack of understanding of precise cell types and developmental stages where the enhancers are normally active. PAX6 is the master regulator of eye development, with a regulatory landscape containing multiple enhancers driving expression in the eye. Whether these enhancers perform additive, redundant, or distinct functions is unknown. Here we describe the precise cell types and regulatory activity of two PAX6 retinal enhancers, HS5 and NRE. Using a unique combination of live imaging and single-cell RNA sequencing in dual enhancer-reporter zebrafish embryos, we uncover differences in the spatiotemporal activity of these enhancers. Our results show that although overlapping, these enhancers have distinct activities in different cell types and therefore likely non-redundant functions. This work demonstrates that unique cell type-specific activities can be uncovered for apparently similar enhancers when investigated at high resolution in vivo.

overall_design: In order to define the precise cell types within the retina where the PAX6 enhancers HS5 and NRE are active, we carried out scRNA-seq on eyes from NRE-eGFP/HS5-mCherry zebrafish reporter embryos. With this technique, we aimed to uncover cell type or transcriptional differences between the two enhancer-active populations. We dissected eyes from 48 hpf NRE-eGFP/HS5-mCherry embryos and used FACS to enrich for either mCherry-positive/HS5-active cells or eGFP-positive/NRE-active cells. Three samples for each population were processed for scRNA-seq using the 10x Genomics Chromium single cell 3’ gene expression technology.

first: Kirsty

last: Uttley

first: Andrew

last: Papanastasiou

first: Wendy

last: Bickmore

first: Shipra

last: Bhatia


title: Single-cell analysis of colonic organoids deficient for tumor necrosis factor receptor 2

status: Public on Aug 22 2023

city: Chicago

first: Cambrian

middle: Yangshao

last: Liu

state: IL

address: 5841 S Maryland Ave

department: Department of Medicine

institute: The University of Chicago

summary: Colonic epithelial repair is a key determinant of health. After injury, repair initiates through phenotypic reprogramming of wounded epithelium to a regenerative state permissive for the activation of alternative stem cell populations and healing. Although cytokine signals such as interferon help induce regenerative reprogramming, the signals that modify this state as the wound resolves remain largely unknown. Here we show that, during healing, the late upregulation of a cytokine receptor, tumor necrosis factor (TNF) receptor 2 (R2, TNFR2, Tnfrsf1b), clears the phenotype of regenerative signaling and restores homeostatic patterns of epithelial differentiation. Mice lacking epithelial-specific expression of TNFR2 also failed to complete colon ulcer healing, suggesting that full repair requires coordination of both regenerative and homeostatic epithelial phenotypes. In single-cell RNA-seq experiments, we find that colonic epithelial organoids grown from Tnfr2-/- mice retain a highly enriched census of progenitor cells and reduced representation of differentiated cells, consistent with TNFR2's role in promoting differentiation. These results demonstrate how epithelial cells adapt to inflammatory cues to choreograph repair.

overall_design: Colonic organoids from wildtype or Tnfr2-/- mice were grown in the presence or absence of tumor necrosis factor (TNF), n=1 culture per condition.

first: Zohreh

last: Sharifkhodaei

first: D

middle: B

last: Polk


title: Influenza virus decreases albumin uptake and megalin expression in alveolar epithelial cells

city: bad nauheim

first: Stefan

last: Günther

address: ludwigtr. 43

institute: MPI for heart and lung research

summary: To investigate whether influenza A virus (IV) infection impairs alveolar protein clearance we analyzed AEC and BAL cells of IV-infected mice.  We performed gene expression profiling analysis using data obtained from RNA-seq of AEC and BAL cells after 5 days of IV infection.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for mouse lung alveolar epithelial cells and bronchoalveolar lavage cells under influenza A infection conditions.

first: Andrés

last: Alberro Brage

first: Christin

last: Peteranderl

first: Janine

last: Koepke

first: Larissa

last: Hamann


title: Effect of FGF singaling inhibition on gene expression on limb bud mesenchyme explants.

summary:
To investigate the role FGF signaling in limb bud development we inhibited FGF signaling in limb bud explants by treatment with 5µM SU5402, an FGFR inhibitor, or DMSO as control.
We then performed mRNA sequencing on RNA collected after 48h of treatment to analyse the effect on gene expression.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for limb bud mesemchyme explants treated with an FGF signaling inhibitor (SU5402) or DMSO.


title: ac4C-RIP-seq to identify mRNA ac4C peaks

first: Yuan

last: Zhou

summary:
NAT10-catalyzed N4-acetylcytidine (ac4C) has emerged as a vital post-transcriptional modulator on the coding transcriptome by promoting mRNA stability.
To explore the transcriptome-wide profile of ac4C modification, we mapped the locations of ac4C modification on wild-type (WT) hESCs and NAT10 KD hESCs by high-throughput ac4C RNA immunoprecipitation sequencing (ac4C-RIP-seq).

overall_design: Both NAT10 KD hESCs and wild-type (WT) hESCs were analyzed with 2 duplications for ac4C-RIP-seq.

first: Rucong

first: Zibaguli

last: Wubulikasimu

first: Runze

last: Cai

first: Fanyi

last: Meng

first: Qinghua

last: Cui

first: Yang

last: Li