title: Expression data in the human pancreatic cancer cell line RWP-1 subjected to SOX9 silencing

status: Public on Jan 11 2022

city: Donostia

first: Estefania

last: Carrasco-Garcia

state: Guipúzcoa

address: Dr. Begiritsain s/n

department: Oncology

institute: Biodonostia

summary:
The developmental transcription factor SOX9 exerts an oncogenic activity in pancreatic cancer.
We used microarrays to detail the global programme of gene expression underlying the oncogenic activity of SOX9 in pancreatic cancer.

overall_design: SOX9 expression was silenced in RWP-1 cells through short hairpin RNA and total RNA was isolated and hybridized on HuGene-2_0-st Affymetrix microarrays.

first: Ander

last: Matheu


title: Identification and characterization of novel proteins associated with CHD4

status: Public on Jan 01 2022

city: Chikusa-ku, Nagoya, Aichi

first: Kazuya

last: Ichihara

address: Furo-cho

country: Japan

institute: Nagoya University

type: Expression profiling by high throughput sequencing

summary: CHD (chromodomain helicase DNA binding protein) family is composed of nine members of chromatin remodeling factors that regulate chromatin structure in an ATP-dependent manner. Among them, CHD4 contributes to many basic cellular functions during development mainly through multiple proteins interacting with CHD4 including NuRD (nucleosome remodeling and deacetylase activities) complex, which contains histone deacetylase HDAC1/2. However, functions of CHD4 that are not mediated by NuRD complexes have also been found, implying the existence of unknown proteins that are associated with CHD4. In the present study, we generated CHD4 FLAG-tag knock-in cells in HeLa-S3 and HEK293T cells and sought proteins bound to CHD4 with the use of immunoprecipitation and liquid chromatography and tandem MS (LC-MS/MS) analysis. We found that LCORL (ligand dependent nuclear receptor corepressor like) and NOL4L (nucleolar protein 4 like) were reproducibly identified as a novel CHD4 interactors. RNA-sequencing analysis of HEK293T cells depleted of CHD4, LCORL, and NOL4L revealed consistent upregulation of genes related to the Notch pathway. Our results thus suggest that both NOL4L and LCORL may cooperate with CHD4 to suppress the Notch pathway in mammalian cells.

overall_design: Transcriprional control regulated by CHD4, NOL4L, and LCORL

first: C

last: Sakaguchi

first: K

last: Nakayama


title: In vivo M. tuberculosis transcriptome in the lung

status: Public on Jan 12 2022

city: London

first: Rachel

last: Lai

address: Du Cane Road

department: Infectious Disease

country: United Kingdom

institute: Imperial College London

summary: We compared the transcriptional signature of 7 human sputa to exponential and stationary phase culture and identified transcriptional signature to sputa

overall_design: Total RNA were extracted from sputa of 7 TB patients and from laboratory cultures and sequenced on Illumina HiSeq2500


title: Single-cell analysis of early chick hypothalamic development reveals that hypothalamic cells are induced from prethalamic-like progenitors.

status: Public on Dec 29 2021

city: Baltimore

first: Dong Won

middle: Thomas

last: Kim

state: Maryland

address: 733 N.Broadway, MRB building (Rm 332)

department: Neuroscience

country: USA

institute: Johns Hopkins University

summary: Purpose: scRNA-Seq was performed to profile chicken hypothalamus development.

overall_design: Methanol-fixed chicken embryos of dissected hypothalamus at HH8, HH8, HH13, HH15/16, HH18/19, HH20/21 were re-hydrated as previously described. Briefly, cells were washed twice (3000 x g for 5 min at 4’c) and resuspended in RNAse-free PBS with 1% BSA and 0.5 U/ul RNAse inhibitor. Cells were then used for the 10x Genomics Chromium Single Cell System (10x Genomcis, CA, USA) using V3.0 chemistry per manufacturer’s instruction loading between 8,000 and 12,000 cells per run. Libraries were sequenced on Illumina NextSeq 500 with ~ 200 million reads per library. Sequenced files were processed through the CellRanger pipeline (v.3.10, 10x Genomics) using Ensembl Gallus gallus genome (GRCg6a, release 95) compiled with CellRange mkref function.

first: Dong

middle: W

first: Elsie

last: Place

first: Kavitha

last: Chinnaiya

first: Elizabeth

last: Manning

first: Changyu

last: Sun

first: Weina

last: Dai

first: Kyoji

last: Ohyama

first: Sarah

last: Burbridge

first: Marysia

last: Placzek

first: Seth

last: Blackshaw


title: Zebrafish kidney regeneration transcriptome

status: Public on Dec 19 2021

city: chongqing

first: Xiaoliang

last: Liu

address: xinqiao street

country: China

institute: Xinqiao Hospital, Army Medical University (Third Military Medical University)

summary: We sequenced the transcriptome of gentamicin induced renal regeneration in adult zebrafish. Specifically, zebrafish kidney tissues in the first, third, fifth and seventh days of kidney injury and the control group were selected. Each sample contains three kidneys. Three samples were taken in each period, and then the total RNA of the kidney was extracted for second-generation sequencing.

overall_design: the type of zebrafish kidney cells

first: Chi


title: Pnpla2 knockout in muscle stem cells

city: West Lafayette

first: Shihuan

last: Kuang

state: IN

address: 901 W State St

institute: Purdue University

summary: Analysis of skeletal muscle satellite cells with specific knockout (KO) of Patatin-like phospholipase domain containing protein 2 (Pnpla2) gene in mouse (named Pnpla2PKO). Pnpla2 knockout disrupts lipid droplet catabolism in satellite cells and causes energy insufficiency and oxidative stress, accompanied by global lipid remodeling, which eventually impedes their expansion and fusion, leading to impairments in muscle regeneration.

overall_design: FACS (fluorescence activated cell sorting)-isolated satellite cells from the experimental Pnpla2PKO and wild type control hind limb muscles were cultured for 7 days in growth medium and switched to DMEM with 2% horse serum for 16 h. Total RNA was extracted using TRIzol reagent according to the manufacturer’s instructions. RNA quality analysis was performed by Agarose Gel Electrophoresis and Agilent 2100 Bioanalyzer. A complementary DNA library was then constructed using poly(A) selected RNA, and sequencing was performed according to the Illumina HiSeq standard protocol (high-throughput, paired-end 150bp fragment sequencing). Raw reads from RNA-seq libraries are filtered to remove reads containing adapters or with low quality. Statistics analysis of data production and quality was performed to confirm the sequencing quality. Reference genome and gene annotation files were downloaded from a genome website browser (NCBI/UCSC/Ensembl). TopHat2 was used for mapping the filtered reads to the reference genome (Mus Musculus, GRCm38/mm10). For the quantification of gene expression level, HTSeq V0.6.1 was used to analyze the read numbers mapped for each gene. The Fragments Per Kilobase of transcript per Million mapped reads (FPKM) of each gene was calculated based on the gene read counts mapped to genes or exons. A differential expression analysis was performed using the DESeq2 R/EdgeR R package with the threshold of significance set as adjusted P < 0.05.

first: Feng

last: Yue


title: adult zebrafish kidney cells

summary: To illustrate the functions of the various cell types in the zebrafish kidney, we sequenced the kidney cells by single-cell messenger RNA sequencing. Six randomly selected zebrafish kidneys were used and obtained about 7,147 cells for RNA sequencing using a modified version of the cell expression by linear amplification and sequencing (CEL-seq) method and incorporating unique molecular identifiers to count the transcripts.


title: INO80 chromatin binding profile in mouse zygotene-spermatocytes

status: Public on Dec 16 2021

city: oklahoma

first: roberto

middle: jose

last: pezza

state: OK

department: cell cycle and cancer biology

institute: oklahoma medical research foundation

type: Genome binding/occupancy profiling by high throughput sequencing

summary: INO80 ChIP-seq from synchronized early-zygotene spermatocytes (first wave)

overall_design: First generation mice from DBA/2J x C57BL/6J mix were synchronized at 2 dpp with fertilysin/retinoic acid treatment, spermatocytes were collected at early zygotene (8 days after retinoic acid treatment), purified using Percoll gradient centrifugation and INO80 ChIP-seq was performed.

first: Agustin

last: Carbajal

first: Irma

last: Gryniuk

first: Rodrigo

last: Orlandini di Castro

first: Roberto

middle: J

last: Pezza


title: Effect of chronic cold on gene expression in inguinal white adipose tissue.

status: Public on Dec 14 2021

city: Seoul

first: Kyung-Mi

last: Choi

address: 1 Gwanak-ro, Gwanak-gu

country: South Korea

institute: Seoul National University

summary: Excess weight is associated with an increased risk of insulin resistance and type 2 diabetes. Activating thermogenic mechanisms is a potentially powerful means to reduce excess weight and achieve metabolic benefits. Recent studies show that cold stimuli trigger the conversion of white fat into beige fat, which can mediate non-shivering thermogenesis. The purpose of this study is to determine effect of chronic cold exposure on gene expression in iWAT. To this end, we performed RNA-sequencing of iWAT from mice at 30 ˚C or 7 ˚C for 3 weeks and identified significantly regulated genes under chronic cold in iWAT.

overall_design: Transcriptome profiles of iWAT of 9-week-old male mice (C57BL/6J) housed at 30 ˚C or 7 ˚C for 3 weeks.

first: John

last: Yoon


title: Tumor-associated Schwann cells Expressing LncRNAs Direct Immune Resistant Metabolic Microenvironment

status: Public on Dec 08 2021

city: Shanghai

first: Youqiong

last: Ye

address: 280 Chongqing south road

institute: Shanghai Jiao Tong University School of Medicine

summary: One of the major obstacles of treating pancreatic ductal adenocarcinoma (PDAC) is the immune-resistant microenvironment, by which the mechanisms remains elusive. We demonstrated that tumor-associated Schwann cells (TAScs) play important roles in promoting an immune-resistant microenvironment. The abundance of TASc is correlated with the expression of negative immune checkpoints and infiltration of tumor-promoting immune cells. TASc-expressed Plasmacytoma Variant Translocation 1 (PVT1) is triggered by the tumor cell-produced Interleukin-6 (IL-6).  Mechanistically, PVT1 modulates the RAF proto-oncogene serine/threonine-protein kinase (RAF1)-mediated phosphorylation of Tryptophan 2,3-dioxygenase (TDO2) in TASc, facilitating the enzymatic activities of TDO2 in catalyzing Tryptophan (Trp) to Kynurenine (Kyn).  The release of Kyn in the microenvironment further modulates colony-stimulating factor 1 (CSF1) signaling, leading to the expansion of Myeloid-derived suppressor cells (MDSCs) and diminished infiltration of effector T-cells. Depletion of TASc-expressed PVT1 or TASc using small molecule inhibitor effectively sensitized PDAC to immunotherapy, signifying the important roles of TASc in PDAC immune resistance.

overall_design: 6-week-old tamoxifen-inducible KPC mice were administered a solution with- or without-tamoxifen (Sigma-Aldrich; cat#T5648) induction (20 mg/kg, i.p. injection, 5 consecutive days) (Madisen et al., 2010). At the age of 4 months, pancreases from KPC mice without tamoxifen induction or PDAC tumors from KPC mice with tamoxifen induction were suspended into single cell suspensions, described as follows: pancreases were digested as a single cell suspension using an enzyme mixture (250 U/mL Hyaluronidase Type I-S (Sigma; #H3506), 160 U/mL Collagenase Type I (Sigma; #C1639) in DMEM-F12). The tumor isolated from the KPC mice with Tamoxifen induction was digested as a single cell suspension using a mouse Tumor Dissociation kit (Miltenui Biotec Inc.; #130-096-730). After the lysis of red blood cells (RBC Lysis Buffer, BioLegend; #420302), single-cell suspensions were subjected to removal of the dead cells using a dead cell removal kit (Miltenyi Biotec; #130-090-101) and then blocked with anti-CD16/32 (BioLegend; #156604) for 20 min on ice. The cell suspensions were then stained with anti-nerve growth factor receptor Alexa Fluor488 conjugated antibody (Sigma; #MAB5592X) for 1 hrs at RT, and then subjected to cell sorting using the BD FACSMelody™ Cell Sorter. Total RNA from each sample was extracted using Trizol Reagent following standard protocols and mRNA sequencing was performed.

first: Chengcao

first: Haoqiang

last: Yin

first: Leng

last: Han

first: Chunru

last: Lin

first: Liuqing

last: Yang


title: 1α,25-Dihydroxyvitamin D3 Regulates Packaging of microRNAs within Extracellular Matrix Vesicles and Their Release in the Matrix

status: Public on Dec 06 2021

city: Richmond

first: Niels

middle: C.

last: Asmussen

state: VA

address: 601 W. Main St. Room 392

institute: Virginia Commonwealth University

type: Non-coding RNA profiling by high throughput sequencing

summary: Growth plate chondrocytes are regulated by numerous factors and hormones as they mature during endochondral bone formation. Chondrocytes in the growth plate’s growth zone (GC cells) produce and export matrix vesicles (MVs) under the regulation of 1α,25-dihydroxyvitamin D3 [1α,25(OH)2D3]. 1α,25(OH)2D3 secreted by the cells acts on the MV membrane, releasing its contents. This study examined the regulatory role 1α,25(OH)2D3 has over the production and packaging of microRNA into MVs by GC cells and the ability to release microRNA from MVs once produced. We treated GC cells with 1α,25(OH)2D3 and then sequenced the microRNA in the cells and MVs. We also treated MVs with 1α,25(OH)2D3 and determined if the microRNA was released. To assess whether MVs can act directly with chondrocytes and if this is regulated by 1α,25(OH)2D3, we stained MVs with a membrane dye and treated GC cells with them. 1α,25(OH)2D3 regulated the production and packaging of microRNA into matrix vesicles. MVs did not release microRNA when treated with 1α,25(OH)2D3, indicating a heterogeneous MV population or a protective factor. Stained MVs were endocytosed by GC cells and this was increased with 1α,25(OH)2D3 treatment. This study adds new regulatory roles for 1α,25(OH)2D3 with respect to packaging and transport of MV microRNAs.

overall_design: miRNA expression profiles of growth zone chondrocyte cells and matrix vesicles with either 24 hour vehicle (EtOH) or  1α,25-dihydroxyvitamin D3 treatment

middle: C

first: Sheikh

last: Alam

first: Zhao

first: David

last: Cohen

first: Zvi

last: Schwartz

first: Barbara

middle: D

last: Boyan


title: HuR promotes myogenesis by cooperating with YB-1 to modulate the stability of the Myogenin mRNA

status: Public on Dec 01 2021

city: Montreal

first: Brenda

middle: Janice

last: Sanchez

state: QC

address: 3655 promenade Sir-William-Osler, Room 915

department: Bichemistry

country: Canada

institute: McGill University

summary: Our study delineates a novel mechanism for HuR-mediated posttranscriptional regulation of myogenesis that requires its association to YB1 and provides new insights into the central role of posttranscriptional regulatory networks in modulating vital cellular processes such as myogenesis.

overall_design: Putative mRNA targets of HuR and YB1 in muscle cells were identified by performing RIP-seq experiments using the Illumina NextSeq 500 platform

first: Imed

middle: E

last: Gallouzi

first: Sergio

last: Di-Marco


title: RNA sequencing of wild-type and TRα (-/-) intestine with and without T3 Treatment.

status: Public on Nov 29 2021

city: Bethesda

first: Ryan

last: Dale

state: MD

address: Rm 10D39, 10 Center Drive

department: National Institute of Child Health and Human Development

institute: National Institutes of Health

summary: Conclusions: Our study represents the first detailed analysis of intestinal transcriptomes in wild-type and TRα (-/-) tadpoles, with biologic replicates, generated by RNA-seq technology. The optimized data analysis workflows reported here should provide a framework for comparative investigations of expression profiles.

overall_design: Examination of 3 technical replicate from the same RNA sample which extracted and merged from the several Xenopus tropicalis tadpoles.

first: Yuta

last: Tanizaki

first: Hongen

last: Zhang

first: Yun-Bo

last: Shi


title: Gene expression profiling of AML cell lines treated with nuclear export inhibitor, selinexor

city: Durham

first: Kris

last: Wood

state: NC

address: 450 Research Drive, LSRC C259, PO Box 3813

department: Department of Pharmacology and Cancer Biology

institute: Duke University

summary: RNA-seq analysis in OCI-AML2 and MOLM-13 cells treated with selinexor or DMSO for 36 hours.

overall_design: Gene expression profiling was conducted in triplicate and RNA was extracted OCI-AML2 and MOLM-13 cells were treated for 36 hours with vehicle or selinexor (200nM for OCI-AML2 and 75nM for MOLM-13) in biologically independent triplicate. RNA was isolated from whole cells with the RNEasy Mini kit (Qiagen) and sent for paired-end RNA-sequencing by Novogene. Mapped reads were analyzed using DEseq and assessed for differential expression in selinexor versus vehicle-treated conditions.

first: Kevin

middle: H

first: Justine

last: Rutter

first: Alex

last: Puissant


title: DNA methylation profiling of cord blood progenitor endothelial cells from overweight and GDM pregnancies

city: Parkville

first: Boris

last: Novakovic

state: Victoria

address: Murdoch Children's Research Institute, Royal Children's Hospital, Flemington Road

country: Australia

institute: Murdoch Children's Research Institute

type: Methylation profiling by genome tiling array

summary: Fetal progenitor endothelial cells (endothelial colony forming cells; ECFC) are recruited for repair, vascular growth and angiogenesis and their high abundance perinatally suggests a function in postnatal vasculogenesis and angiogenesis. In this study we profiled ECFCs from pregnancies of control, overweight and diabetic mothers to study if adverse pregnancies are associated with epigenetic variation in ECFCs.

overall_design: Endothelial progenitor cells (ECFC - Endothelial Colony Forming Cells) were isolated from cord blood from 20 control (healthy BMI), 20 overweight (high BMI) and 20 GDM (Gestational Diabetes Mellitus) pregnancies. ECFCs were cultured in vitro from total cord blood cells.

first: Elisa

last: Weiss

first: Ursula

last: Hiden

first: Richard

last: Saffery


title: Differential expression profile of liver fibrosis rats induced by CCl4

status: Public on Nov 25 2021

city: Nanning

first: xing

last: lin

address: Shuangyong Road

institute: Guangxi medical university

summary: This study aimed to investigate the protective mechanisms of helenalin on hepatic fibrosis,Rats were intragastrically administrated with 50% CCl4 for 9 weeks to induce liver fibrosis, followed by various medicines for 6 weeks. The transcriptomic analysis was performed in liver tissues by RNA-seq.

overall_design: the rats were randomly divided into several groups: the model group and helenalin-treated groups were administered with CCl4 to induce liver fibrosis, followed by various agents.

first: Yuhua

last: Xiong

first: Shujuan

last: Wen

first: Yan

last: Li

first: Yuanyuan

last: Wei


title: Comparative transcriptional analysis of the satellite glial cell injury response

status: Public on Nov 23 2021

first: Sara

middle: Elgaard

last: Jager

address: Hodgkin Building, Guy's Campus

institute: King's College London

summary: The recent advance in single cell RNAseq technologies has enabled a new approach to investigate satellite glial cells (SGCs). Here we publish a dataset from mice subjected to sciatic nerve injury as well as a dataset from dorsal root ganglia cells after 3 days in culture. We use a meta-analysis approach to compare the injury response with that in other published datasets and conclude that SGCs share a common signature following sciatic nerve crush and sciatic ligation, involving transcriptional regulation of cholesterol biosynthesis. We also observed a considerable transcriptional change when culturing SGCs, suggesting that some differentiate into a specialised in vitro state, while others start resembling Schwann cell-like precursors.

overall_design: This study is a comparison of 3 scRNAseq datasets from mouse dorsal root ganglia with focus on SGCs. The Seurat objects of all datasets can be found here under supplementary files. The first dataset contains scRNAseq data from L3 and L4 dorsal root ganglia at 7 and 14 days after sciatic nerve injury (SNI) together with data from the naive conditon. This dataset is called Cell_SNI and can be found at GSE174430. The secound dataset contains data from L3-L5 dorsal root ganglia 3 days after a crush injury and from the naive condition. This dataset is called Cell_crush and can be found at GSE139103. Finally the third dataset contains cells from all dorsal root ganglia after 3 days in culture. This dataset is called Cell_culture and can be found here. The Cell_culture dataset contains two replicates (A+B) run on the same 10X chip.

first: Paolo

last: Cesare

first: Franziska

last: Denk


title: A 2-Gene Host Signature for Improved Accuracy of COVID-19 Diagnosis Agnostic to Viral Variants

status: Public on Nov 15 2021

city: San Francisco

first: Charles

last: Langelier

state: CA

address: HSE 401, 513 Parnassus Ave

department: Medicine

institute: University of California San Francisco

summary: The continued emergence of SARS-CoV-2 variants is one of several factors that may cause false negative viral PCR test results. Such tests are also susceptible to false positive results due to trace contamination from high viral titer samples. Host immune response markers provide an orthogonal indication of infection that can mitigate these concerns when combined with direct viral detection. Here, we leverage nasopharyngeal swab RNA-seq data from patients with COVID-19, other viral acute respiratory illnesses and non-viral conditions (n=318) to develop support vector machine classifiers that rely on a parsimonious 2-gene host signature to diagnose COVID-19. We find that optimal classifiers include an interferon-stimulated gene that is strongly induced in COVID-19 compared with non-viral conditions, such as IFI6, and a second immune-response gene that is more strongly induced in other viral infections, such as GBP5. The IFI6+GBP5 classifier achieves an area under the receiver operating characteristic curve (AUC) greater than 0.9 when evaluated on an independent RNA-seq cohort (n=553). We further provide proof-of-concept demonstration that the classifier can be implemented in a clinically relevant RT-qPCR assay. Finally, we show that its performance is robust across common SARS-CoV-2 variants and is unaffected by cross-contamination, demonstrating its utility for improving accuracy of COVID-19 diagnostics.

overall_design:
Comparing host transcriptional response to SARS-CoV-2 infection versus response to other respiratory viral infection or non-viral acute respiratory infection.
>>> Submitter declares that the raw data are unavailable due to patient privacy concerns.  The raw data may be submited to dbGAP if feasible. <<<

first: Eran

last: Mick

first: Jack

last: Kamm


title: Topological screen identifies hundreds of Cp190 and CTCF dependent Drosophila chromatin insulator elements [RNA-seq]

status: Public on Jul 19 2022

city: Taipei

first: Jia-Ming

last: Chang

address: NO.64, Sec. 2, ZhiNan Rd., Wenshan District

department: Department of Computer Science

country: Taiwan

institute: National Chengchi University

summary: CTCF and Cp190 proteins are implicated at many insulator elements throughout Drosophila genome. Here we compared Hi-C maps, transcriptomes and binding of multiple insulator proteins in cultured Drosophila cells derived from CTCF-KO, Cp190-KO and control embryos.

overall_design: RNA-seq experiments in cultured Drosophila cells derived from CTCF-KO, Cp190-KO and control embryos. Two experiments started from independently grown cell cultures were performed for each genetic background

first: Tatiana

middle: G

last: Kahn

first: Mikhail

last: Savitsky

first: Caroline

last: Jacquer

first: Giacomo

last: Cavalli

first: Yuri

middle: B

last: Schwartz


title: Transcriptomic comparison between the powdery mildew resistant and susceptible progenies of distant hybridization between Brassica carinata and Brassica napus

status: Public on Nov 11 2021

city: Yangling

first: Chengyu

last: Yu

state: Shaanxi

address: 3 Taicheng Road

department: College of Agronomy

institute: Northwest A&F University

summary: Powdery mildew caused by Erysiphe cruciferarum, is an epidemic of oil rapeseed (Brassica napus) growing worldwide, but resistant germplasm is rare in this species. We obtained the hybrid seeds of distant hybridization between powdery-mildew-immune Brassica carinata cultivar ‘White flower’ and susceptible B. napus cultivar ‘Zhongshuang11’. Five lines in the BC1F3 generation (F3 after backcross to 'Zhongshuang11') were identified to be resistant or moderately resistant. In order to identify the important biological responses to powdery mildew,  the foliar transcriptomes of the resistant and susceptible plants in these progenies after powdery mildew inoculation were compared by using Illumina RNA-seq. We identified 10,454 differential expression genes  (DEGs) and 1050 genes out of them are related to disease resistance. There were 271 DEGs in Group Resistance expressed at least two fold higher than in group S, while 779 DGEs expressed two fold lower. The genes highly expressed in Group Resistance are those encoding the proteins: (1) related to wax, chloroplast and cell wall metabolism, such as KCS6, CSP41B, RWA, callose synthetase 3, pectinase 9, fructosidase 2, 9s-lipoxygenase LOX2, etc.; (2) kinases  including RKL, ERECTA, BAK1, BAM2, LysM receptor like kinase, and lipid transfer protein kinase ERl1 and ERl2; (3) broad spectrum powdery mildew resistance proteins RPW8, calmodulin MLO2, PMR5, MLP328, EDR2, RPS4 and RPS6, etc. In group susceptible, pectinesterase, cytochrome CYP81f2, LOX1, cysteine rich receptor protein kinases and serine / threonine protein kinases such as MEKK, RLK6, CRK45, APK1, BRl3, WAK1, WAK10, etc., and TIR-NB-LRR receptor like proteins R1M1, DSC1, DSC2 and pathogenesis-related protein PR-1 etc. were the most activated genes. The results provide the preliminarily knowledge about molecular mechanism in rapeseed defense response to powdery mildew.

overall_design: Comparison between the healthy and diseased leaves after powdery mildew inoculation.

first: Qiong

last: Gong


title: Genome-wide Spatial Expression Profiling in Formalin-fixed Tissues

status: Public on Oct 15 2021

city: Solna

first: Ludvig

middle: Ale

last: Larsson

state: Stockholm

address: Tomtebodavägen 23A

department: Gene Technology

country: Sweden

institute: SciLifeLab

summary: Method to perform spatial analysis of mRNA in FFPE and PFA fixed tissue sections using spatially barcoded slides and based on oligo(dT) mRNA capture.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Whole-genome transcriptomic profiling of formalin-fixed tissue sections

first: Larsson

last: Ludvig

first: Villacampa

last: Eva Gracia


title: Single-cell RNA sequencing reveals the mechanism of human breast cancer metastasis

status: Public on Oct 13 2021

city: Nanjing

first: kun

last: xu

address: 300 Guangzhou Road

institute: Department of Oncology, The First Affiliated Hospital of Nanjing Medical University

summary: To obtain more information about the lymph node metastasis of breast cancer cells, we selected the matched primary breast cancer (PC) and 2 lymph nodes (LN) of 5 patients to perform integrated analysis. The PC, LN samples were analysed with single-cell RNA sequencing.

overall_design: The matched primary breast cancer (PC) and 2 lymph nodes (LN) samples were analysed with single-cell RNA sequencing.

first: Kun

last: Xu


title: Transcriptional dynamics in HUVECs and fetal endothelial progenitor cells during establishment of innate immune memory

status: Public on Nov 06 2021

first: Boris

last: Novakovic

summary: Innate immune memory (also known as Trained immunity) is a phenomenon whereby innate immune cells such as monocytes or macrophages undergo functional reprogramming after exposure to certain microbial components, altering their responses to future exposures. Recent data show that this phenomenon occurs in endothelial cells. In this study we mapped the transcriptional changes that occur in two different types of fetal endothelial cells in response to an initial viral ligand, followed by a secondary bacterial exposure.

overall_design: HUVECs were isolated from umbilical veins, while ECFC were isolated from umbilical cord blood. Cells were incubated for 24 hours in media alone or with poly(I:C). After another 24 hours, the same cells were exposed to LPS to map the transcriptional response.

first: Richard

last: Saffery

first: Ursula

last: Hiden


title: Uncovering perturbations in human hematopoiesis associated with healthy aging and myeloid malignancies at single cell resolution

status: Public on Sep 23 2021

city: Dublin

first: Marina

last: Ainciburu

state: Dublin

address: Foster Avenue

department: Bioinformatics

country: Ireland

institute: NIBRT

summary: Early hematopoiesis is a continuous process in which hematopoietic stem and progenitor cells (HSPCs) gradually differentiate and are primed toward specific lineages. Aging and myeloid malignant transformation are characterized by changes in the composition and regulation of HSPCs. In this study, we evaluated HSPCs obtained from young and elderly healthy donors using single-cell RNA sequencing to identify the transcriptional and regulatory perturbations associated with healthy aging at single cell resolution. We then applied this knowledge to identify specific changes associated with the development of myeloid malignancies.       Based on the transcriptional profile obtained, we identified changes in the proportions of progenitor compartments during aging, and differences in their functionality, as evidenced by gene set enrichment analysis. Trajectory inference revealed that altered gene expression dynamics accompanied cell differentiation, which could explain age-associated aberrant hematopoiesis. Next, we focused on key regulators of transcription by constructing gene regulatory networks and detected regulons that were specifically active in elderly individuals. Using the previous findings as a reference, we analyzed scRNA-seq data obtained from patients with myelodysplastic syndrome and acute myeloid leukemia and detected an alteration of the expression dynamics of genes involved in erythroid differentiation and identified specific transcription factors deregulated in acute myeloid leukemia.    We demonstrate that the combination of single cell technologies and computational tools enables the study of a variety of cellular mechanisms involved in early hematopoiesis and can be used to dissect perturbed differentiation trajectories associated with aging and malignant transformation. Furthermore, the identification of abnormal regulatory mechanisms associated with myeloid malignancies could be exploited for personalized therapeutic approaches in individual patients.

overall_design: Analysis of hematopoietic stem and progenitor cells from 5 healthy young donors, 3 healthy elderly donors, 1 patient with MDS and 1 patient with AML. Cells were sorted via FACS from bone marrow aspirates. Single cell 3' RNA libraries were prepared with droplet based methods (10x chromium controller) and sequenced in a NextSeq500 (Illumina)

first: Teresa

last: Ezponda

first: Nerea

last: Berastegui

first: Ana

last: Alfonso-Pierola

first: Amaia

last: Vilas-Zornoza

first: Patxi

last: San Martin-Uriz

first: Diego

last: Alignani

first: Jose

last: Lamo de Espinosa

first: Mikel

last: San Julian

first: Tamara

last: Jimenez

first: Felix

last: Lopez

first: Sandra

last: Muntion

first: Fermin

last: Sanchez-Guijo

first: Antonieta

last: Molero

first: Julia

last: Montoro

first: Gullermo

last: Serrano

first: Aintzane

last: Diaz-Mazkiaran

first: Miren

last: Lasaga

first: David

last: Gomez-Cabrero

first: Maria

last: Diez-Campelo

last: Valcarcel

last: Hernaez

first: Juan

middle: P

last: Romero

first: Felipe

last: Prosper


title: Single nucleus transcriptomic analysis of human dorsal root ganglion neurons

status: Public on Nov 08 2021

first: Minh

middle: Q

last: Nguyen

state: MARYLAND

address: 9000, Rockville Pike

institute: NIDCR/NIH

summary: Somatosensory neurons with cell bodies in the dorsal root ganglia (DRG) project to the skin, muscles, bones, and viscera to detect touch and temperature as well as to mediate proprioception and many types of interoception. In addition, the somatosensory system conveys the clinically relevant noxious sensations of pain and itch. Here we used single nuclear transcriptomics to characterize the classes of human DRG neurons that detect these diverse types of stimuli. Notably, multiple types of human DRG neurons have transcriptomic features that resemble their mouse counterparts although expression of genes considered important for sensory function often differed between species. More unexpectedly, we demonstrated that several classes of mouse neurons have no direct equivalents in humans and human specific cell-types were also identified. This dataset should serve as a valuable resource for the community, for example as means of focusing translational efforts on molecules with conserved expression across species.

overall_design: Nuclei from dorsal root ganglia (DRG) from 5 organ donors (1 male, 4 female) were isolated.  One DRG was divided into two preparations (hDRG3 and hDRG5 are from the same donor).  Neuronal nuclei were purified with anti-NeuN antibody and single nucleus RNA-seq were performed with 10x Genomics method (v2 chemistry for hDRG1-hDRG3 and v3 chemistry for hDRG4-hDRG6).

first: Nick

last: Ryba

first: Steve

last: Davidson


title: Genome-wide levels of RNA polymerase II (RNAPII) in normally growing or heat-shocked wild-type and sumolyation-deficient ubc9-6 yeast strains

status: Public on Sep 21 2021

city: Toronto

first: Emanuel

last: Rosonina

state: ON

address: 4700 Keele Street

department: Biology

institute: York University

summary: Many transcription-related proteins are known to be modified by SUMO post-translational modification in yeast, plants, humans and other eukaryotes. We are interested in understanding how cells use sumoylation to regulate transcription of specific genes and globally. To explore this, we carried out ChIP-seq analysis to determine how genomic levels of RNA polymerase II (RNAPII) change when cellular levels of sumoylation are greatly reduced in budding yeast. Compared to wild-type yeast, RNAP occupancy in the sumoylation-deficient ubc9-6 strain was significantly altered for hundreds of genes. Among the genes with the most elevated levels of RNAPII are those involved in translation and ribosome biogenesis, including most ribosomal protein genes. On the other hand, many genes involved in small molecule and amino acid metabolism and biosynthesis showed reduced RNAPII levels in ubc9-6. Exposure of yeast to heat shock is known to cause a widespread change to RNAPII occupancy across the genome. To examine whether cellular sumoylation plays a role in this process, RNAPII ChIP-seq was performed in wild-type and ubc9-6 strains after a brief heat shock. Strikingly, the sumoylation deficient strain showed a far more dramatic redistribution of RNAPII across the genome, with significantly more genes showing a heat-shock induced increase or decrease in RNAPII occupancy. These results imply that cellular sumoylation levels have a significant impact on the regulation of transcription genome-wide, and that normal sumoylation levels are needed to restrain the vast redistribution of RNAPII that occurs in response to heat shock.

overall_design: Two independent replicates of RNAPII ChIP-seq from untreated or heat-shocked wild-type and ubc9-6 strains.

first: Marjan

last: Moallem

first: Benjamin

last: Bergey


title: Zebrafish pigment cells develop directly from persistent highly multipotent progenitors

status: Public on Oct 09 2021

city: Moscow

first: Leonid

last: Uroshlev

address: Gubkina, 3

country: Russia

institute: Vavilov Institute of General Genetics RAS

summary: Neural crest cells (NCCs) are highly multipotent stem cells. A long-standing  controversy exists over the mechanism of NCC fate specification, specifically regarding the  presence and potency of intermediate progenitors. The direct fate restriction (DFR) model,  based on early in vivo clonal studies, hypothesised that intermediates are absent and that  migrating cells maintain full multipotency1-6. However, most authors favour progressive fate  restriction (PFR) models, with fully multipotent early NCCs (ENCCs) transitioning to partially- restricted intermediates before committing to individual fates7-12. Here, single cell  transcriptional profiling of zebrafish pigment cell development leads to us proposing a  Cyclical Fate Restriction mechanism of NCC development that reconciles the DFR and PFR  models. Our clustering of single NCC Nanostring transcriptional profiles identifies only  broadly multipotent intermediate states between ENCCs and differentiated melanocytes and  iridophores. Leukocyte tyrosine kinase (Ltk) marks the multipotent progenitor and  iridophores, consistent with biphasic ltk expression13-15. Ltk inhibitor and constitutive  activation studies support expression at an early multipotent stage, whilst lineage-tracing of  ltk-expressing cells reveals their multipotency extends beyond pigment cell-types to neural  fates. We conclude that pigment cell development does not involve a conventional PFR  mechanism, but instead occurs directly and more dynamically from a broadly multipotent  intermediate state.

overall_design:
We investigated the transcriptional profiles of 1227 zebrafish NCCs throughout pigment cell development (18-72 hpf). To obtain sensitive quantitation of key mRNA expression, we used the NanoString platform and a set of 45 genes, focused on those known or suspected to have important roles in melanocyte or iridophore fate choice, but including multiple markers of early NCCs, plus key markers of other major NC-derived fates

Processed data are provided only for samples GSM5619061-GSM5619791.

first: T

last: Subkhankulova

first: R

middle: N

last: Kelsh


title: Sumoylation regulates general transcription factors at promoters of highly transcribed genes

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

overall_design: Refer to individual Series


title: DNA methylation and transciptomic signatures in patients with peanut- and multi-food allergy [array]

status: Public on Sep 01 2021

first: Boris

last: Novakovic

summary: This study profiled the epigenomes and transcriptomes of total B cell populations from adolescents with peanut-only (single food allergy- SA) and multi-food allergy (MA). We found distinct epigenetic and transcriptomic differences between food allergic patients and controls, in addition to SA- and MA- group specific signatures, with

overall_design: DNA methylation profiles of total B cell populations isolated using flow cytometry from single-food allergic, multi-food allergic, and non-allergic adolescents.

first: Melanie

last: Neeland

first: Samira

last: Imran

first: Richard

last: Saffery


title: Human primary alveolar epithelial cells (hAEC) exposed to cigarette smoke extract

status: Public on Oct 28 2021

city: Chapel Hill

first: Yu

last: Mikami

address: 125 Mason Farm Rd

department: Marsico lung institute

institute: The University of North Carolina at Chapel Hill

summary: hAEC cells were exposed to cigarette smoke extract (CSE) or PBS for 48h, and gene expression was evaluated by RNA-seq.In this study we explored the effect of cigarette smoke on the gene expression profile.

overall_design: Human alveolar epithelial cells stimulated with CSE for 48h were used for RNA extraction

first: Ryuji

last: Hamamoto

first: Takae

last: Tanosaki


title: DNA methylation and transciptomic signatures in patients with peanut- and multi-food allergy [RNA-Seq]

summary: This study profiled the epigenomes and transcriptomes of total B cell populations from adolescents with peanut-only (single food allergy- SA) and multi-food allergy (MA).

overall_design: mRNA sequencing of total B cell populations isolated using flow cytometry from single-food allergic, multi-food allergic, and non-allergic adolescents.

first: Kirsten

last: Perrett


title: The piRNA pathway sustains adult neurogenesis by reducing protein synthesis and cellular senescence

status: Public on Aug 30 2021

city: Genova

first: Kiril

last: Tuntevski

address: Via Morego 30

country: Italy

institute: Istituto Italiano di Tecnologia

summary: Neural progenitor cells (aNPCs) ensure lifelong neurogenesis in the mammalian hippocampus. Proper regulation of aNPC fate entails important implications for brain plasticity and healthy aging. Piwi proteins and the small noncoding RNAs interacting with them (piRNAs) are best known in gonads as repressors of transposons. Here, we show that Piwil2 (Mili) and piRNAs are abundant in aNPCs of the postnatal mouse hippocampus and demonstrate that this pathway is essential for proper neurogenesis. Particularly, depleting the piRNA pathway in aNPCs impaired neurogenesis while increasing senescence and the generation of reactive glia. Moreover, depletion of the piRNA pathway primarily elevated 5S ribosomal RNA, SINEB1 and mRNAs encoding ribosomal proteins and regulators of translation, resulting in higher polysome density and protein synthesis upon differentiation. Our results provide evidence of an essential role for the piRNA pathway in maintaining homeostasis to sustain neural stem cell fate, underpinning its possible involvement in brain plasticity and successful aging.

overall_design: mRNA sequencing was performed on proliferative (DIF0), or differentiating (DIF4, DIF7 or DIF14) primary neural stem cells from the adult hippocampus of C57BL/6 mice. Separate aNSC cultures were stably transfected with a short-hairpin scramble RNA bearing lentiviral vector, or a anti-Mili short-hairpin RNA to stably knock-down the level of MILI protein. Three samples from each differentiating timepoint (n = 4), and each transfection (n = 3), were used for mRNA sequencing in duplicate for a total of 72 quantitative samples.

first: Caterina

last: Gasperini

first: Roberta

last: Pelizzoli

first: Amanda

last: Lo Van

first: Damiano

last: Mangoni

first: Rosa

middle: M

last: Cossu

first: Giovanni

last: Pascarella

first: Paolo

last: Bianchini

first: Pascal

last: Bielefeld

first: Margherita

last: Scarpato

first: Meritxell

last: Pons-Espinal

first: Remo

last: Sanges

first: Alberto

last: Diaspro

first: Carlos

last: Fitzsimons

first: Piero

last: Carninci

first: Stefano

last: Gustincich

first: Davide

last: De Pietri Tonelli


title: A single-cell transcriptome atlas profiles early organogenesis in human embryos

city: Shanghai

first: Tengjiao

last: Zhang

state: Shanghai

address: 1239 Siping Road

department: School of life science and technology

institute: Tongji University

summary: The early window of human embryogenesis is largely a black box for developmental biologists. Here we probed the cellular diversity of 4- to 6-week human embryos when essentially all organs are just laid out. Based on over 180,000 single-cell transcriptomes, we generated a comprehensive atlas of 313 cell types that belong to 18 developmental systems, and identified hundreds of cell type specific markers. We characterized the molecule and spatial architecture of previously unappreciated cell types by integrating with spatial transcriptome. Combined with data of other vertebrates, the rich information shed light on spatial patterning of axes, systemic temporal regulation of developmental progression and potential human-specific regulation. Our study provides a compendium of early progenitor cells of human organs, which can serve as the root of lineage analysis in organogenesis.

overall_design:
185140 single-cell transcriptomes of early human embryo between Carnegie Stage 12 and 16

Please note that the 'cell_annotate.txt' file has been updated on Dec 5, 2022.

first: Yichi

last: Xu

first: Weiyang

last: Shi

first: Zhirong

last: Bao


title: DNA methylation and transciptomic signatures in patients with peanut- and multi-food allergy

status: Public on Sep 02 2021

first: Boris

last: Novakovic


title: Transcriptomic profiling of 5 dpf zebrafish livers following 24 hours of exposure to arsenic

status: Public on Aug 31 2021

city: Abu Dhabi

first: Kirsten

last: Sadler Edepli

state: Abu Dhabi

country: United Arab Emirates

institute: New York University Abu Dhabi

summary:
This study was carried out to compare potential changes in the gene expression in 5
 dpf livers between untreated, 1.0 and 1.5mM iAs exposures.

overall_design: Perform RNA-seq on 5 independent pools of 5 dpf livers collected after exposure to 1.0 and 1.5mM iAs from 4-5 dpf.

first: Anjana

middle: R

last: Nair

first: Patrice

last: Delaney

middle: S

last: Edepli


title: Single Cell Immunophenotyping of Lyme Erythema Migrans [Single-Cell BCR Repertoire Sequencing]

status: Public on Jun 07 2021

city: New Haven

first: Steven

last: Kleinstein

state: Ct

address: 300 George St.

department: Pathology

institute: Yale University

summary: Erythema migrans (EM) is a skin lesion caused by the spirochete B. burgdorferi (Bb) and is a hallmark initial sign of Lyme disease. Previous studies have demonstrated that T cells and innate immune cells mediate local inflammatory cytokine production that promote the reaction. Despite the established importance of B cells and antibodies in preventing Bb infection and resolving disease, the role of B cells in the skin immune response to Bb is incompletely defined. In this study, we characterized the immunophenotype of EM lesions and used single cell RNA-Seq to investigate B cell receptor (BCR) and T cell receptor (TCR) repertoires in the EM skin lesions and peripheral blood of patients with Lyme disease. We hypothesized that B cells from the circulation, potentially primed by exposure to Bb antigens in regional draining lymph nodes, are recruited into EM lesions and play an active role in the local response to infection. We found that B cells are more abundant in the EM lesion in comparison to autologous uninvolved skin and possess distinct characteristics, including abundant expression of MHCII genes and preferential IgM isotype usage. A subset exhibited low levels of somatic hypermutation despite a gene expression profile more consistent with memory than naïve B cell subsets. Moreover, infiltrating B cells were clonally expanded and a large fraction could be directly traced to circulating relatives. By leveraging single cell gene expression with paired BCR and TCR repertoire sequencing, we demonstrate, for the first time, that B cells are recruited to the skin infection site in early Lyme disease and express a phenotype suggesting that they could play a role in local antigen presentation and antibody production.

overall_design: Six subjects were studied, all with confirmed cases of Lyme Disease. Five of six had samples from both EM rash and unaffected skin. One subject had sample only from EM rash. One subject had an additional PBMC sample. Sequencing of BCR was performed using the 10X Genomics platform.

first: Tony

last: Melillo

first: Ruoyi

last: Jiang

first: Hailong

last: Meng

first: Linda

middle: K

last: Bockenstedt


title: Single Cell Immunophenotyping of Lyme Erythema Migrans (Seq-Well Single-Cell Gene Expression)

overall_design: Four subjects were studied, all with confirmed cases of Lyme Disease. Two of the four had samples from both EM rash and unaffected skin, the other two EM rash only. One subject had an additional PBMC sample. Single-cell GEX was performed using the SeqWell platform.


title: Multi-modal characterization of chromatin architecture from 24 hpf whole zebrafish embryos

city: Berlin-Buch

first: Scott

middle: Allen

last: Lacadie

address: Robert-Rössle-Str. 10

department: Berlin Institute for Medical Systems Biology

country: Germany

institute: Max Delbrück Center for Molecular Medicine

summary: DNA accessibility of cis regulatory elements (CREs) dictates transcriptional activity and drives cell differentiation during development. To obtain a more comprehensive view of CRE dynamics, we applied single-cell combinatorial indexing ATAC-seq (sci-ATAC-seq) to whole 24hpf stage zebrafish embryos thereby measuring DNA accessibility in ~23,000 single cells. We developed two solutions to computational challenges in analyzing single-cell accessibility maps: 1) selection of informative genome segments, and 2) genome-wide classification of both cell-type-specific and multi-cell-type accessibility dynamics. We validated the sci-ATAC-seq results with bulk measurements for histone post-translational modifications and 3D genome organization, recovering known relationships between chromatin modalities and providing additional regulatory classifications. Furthermore, we applied sci-ATAC-seq to cloche/npas4l mutant embryos which revealed known and novel cellular roles for the hemato-vascular transcriptional master regulator, and suggested an intricate network regulating its expression. These data and their extensive analysis constitute a valuable developmental, molecular, and computational resource for future studies.

overall_design: ChIP-seq for 5 histone post-translational modifications with two replicates each and input controls; in situ Hi-C sequenced across three lanes; two replicates of chromatin-associated RNA-seq; and single-cell combinatorial indexing ATAC-seq performed twice on wild-type embryos and once on mixed embryos wild-type, heterozygous, and homozygous npas4lbns297

middle: A

first: Uwe

last: Ohler


title: scRNA-seq of stromal vascular fraction (SVF) of lipoma and bulk RNA-seq of lipoma-derived adipocytes.

status: Public on Jul 18 2021

city: Bronx

first: Kosaku

last: Shinoda

state: NY

address: 1301 Morris Park Ave

institute: Albert Einstein College of Medicine

summary: We determined the gene signatures of adipocytes differentiated from lipoma SVF. Furthermore, single-cell RNA-sequencing was performed for SVF from inherited (familial) and sporadic lipoma.

overall_design: Patients undergoing surgical excision of lipomas were identified and the dermatologist clinically confirmed the diagnosis of lipoma. Tissues was enzymaticaly digested and SVF was obtained and diffrentiated in adipogenic media for 5-7 days before collection of the RNA.

first: Alana

last: Deutsch


title: Transcriptome analysis in sumoylation deficient (ubc9-6) budding yeast and in a strain with a sumoylation-impairing mutation in the TFIIF subunit, Tfg1

first: Emanuel

last: Rosonina

summary: Transcription related proteins are among the most frequently identified targets of SUMO post-translational modification, but the gene-specific and genome-wide effects of transcription machinery sumoylation are not well-understood. To explore this, we examined whether dramatically reducing cellular sumoylation levels affects the levels of mRNAs in budding yeast. RNA-seq was performed using polyadenylate (polyA)-enriched RNAs from the sumoylation-deficient ubc9-6 strain and its wild-type parent. Indeed, the abundance of hundreds of mRNAs were upregulated or downregulated in the mutant strain, implying that sumoylation has a widespread influence on RNA polymerase II (RNAPII) transcription or mRNA stability. Interestingly, about one third of mRNAs that were significantly upregulated in the ubc9-6 strain encode proteins that are involved in small molecule metabolic processes, suggesting that sumoylation is normally involved in restricting these pathways. As part of our analysis of transcription-related sumoylation, we determined that the large subunit of TFIIF, Tfg1, is a major target of sumoylation among the general transcription factors (GTFs) of RNAPII. To determine whether sumoylation of Tfg1 specifically is involved in regulating mRNA levels, we performed RNA-seq on polyA-enriched RNAs derived from strains expressing wild-type (Tfg1-HA) or sumoylation-deficient (Tfg1-K60,61R-HA) forms of Tfg1. However, with few exceptions, impairing Tfg1 sumoylation had no effect on the mRNA transcriptome. Together, our data demonstrate that gene expression is extensively regulated by sumoylation, but this likely involves the coordinated modification of multiple proteins at multiple levels.

overall_design: Two independent replicates of RNA-seq in ubc9-6 and Tfg1-K60,61R-HA mutant strains and their wild-type counterparts.

first: Mohammad

last: Baig

first: Marjan

last: Moallem

first: Benjamin

last: Bergey


title: Single Cell Immunophenotyping of Lyme Erythema Migrans (Bulk BCR Repertoire Sequencing)

overall_design: Bulk BCR sequencing was performed on PBMCs from six subjects, all with confirmed cases of Lyme disease.


title: Role of Endothelial and Mesenchymal cell transitions in heart failure and recovery thereafter

status: Public on Jul 01 2021

city: Houston

first: Guangyu

last: Wang

address: 6670 Bertner Ave

institute: Houston methodist research institute

overall_design: Examination of mRNA profiles level in 29 cell types

first: Ana

last: Cruz

first: Kaifu

last: Chen

first: Arvind

last: Bhimaraj


title: Vascular integrity is essential for maintaining tissue homeostasis

status: Public on Jun 01 2021

first: Junhao

last: Hu

address: No.26, Qiuyue Rd., Pudong District

department: Interdisciplinary Research Center of Biology and Chemistry

institute: Chinese Academy of Sciences


title: Vascular integrity is essential for maintaining tissue homeostasis III

summary:
Purpose: analyze the differential changed endothelial cells and pericytes interacton in normal and diseased condition
Methods: Pdgfrb-EGFP mice were given PBS or LPS treatment via trachea instillation. 24h later, dissociate lung and isolate endothelial cells and pericytes by flow cytometry, then directly processed to RNA extraction and library construction
Results: LPS induced a great transcriptomic change in pericytes than in endothelial cells and NO-sGC pathway was impaired during LPS-induced lung injury

overall_design: mRNA profiles of mice lung endothelial cells and pericytes were generated by sequencing.

first: Hao

last: He

first: Feng

last: Han

first: Jianing

last: Dai


title: Identification of neural oscillations and epileptiform changes in human brain organoids

status: Public on Jun 11 2021

city: Los Angeles

first: Bennett

last: Novitch

state: California

address: 650 Charles E Young Dr. S, CHS 66-200

department: Department of Neurobiology

institute: University of California, Los Angeles

summary: In our study, we define neural network activities in human cortex+ganglionic eminence (GE) fusion orgaonids using a combination of calcium incator imaging and electrophysiology.  We futher define abnormal network activities using fusion organoids generated from isogenic induced pluripotent stem cells containing or lacking MECP2 function derived from Rett syndrome patients.  Single cell sequencing (10X genomics) was used to characterize the compositon of the fusion organoids used in our studies, and to define differentially expressed genes associated with MECP2 mutation.

overall_design: Comparison of pools of organoids generated from isogenic control (WT) or MECP2 mutant (705delG/ E235fs; Mut) iPSC derived from a Rett syndrome patient, collected at 3 time points (Days 56, 70, and 100).  Day 56 pools each contain 3 unfused Cortex and 3 unfused Ganglionic eminence organoids.  Day 70 and 100 pools contain 3 Cortex+Gangiolnic eminence fusion organoids.

first: Ranmal

last: Samarasinghe

first: Jessie

last: Buth


title: A single cell RNA-Seq study of splenic marginal zone lymphomas (SMZL)

status: Public on Oct 31 2021

city: TOULOUSE

first: Pauline

last: Gravelle

address: 1 Avenue Irène Joliot Curie

department: Anatomy-Pathology

country: France

institute: IUCT-ONCOPOLE

summary:
Purpose: Single cell RNA-Seq was used to characterize in depth splenic samples obtained from splenic marginal zone lymphomas
Methods: 3 frozen samples of spleen from SMZL patients were selected and thawed for performing a 10X genomics single cell RNA-Sequencing 3' assay.
Results: Tumor cells formed mainly patient specific-B cell  clusters, while  T-cells from the 3 patients clustered together.
Conclusion: Single RNA-Seq unveils the cellular composition of  splenic tumors from SMZL patients.

overall_design: Frozen cell suspensions obtained from diagnosed splenic marginal zone lymphomas were selected for injection in the 10X chromium device for droplet-based RNA extraction, reverse transcription and cDNA amplification. Libraries were made with the Chromium i7 sample index plate (GENO55823). Sequencing was performed on a NextSeq 550 (Illumina).

first: Juan

last: Cerapio Arroyo

first: Camille

last: Laurent

first: Jean-Jacques

last: Fournié


title: RNA sequencing of AHNAK2 knockdown adenocarcinoma cells compared with the scramble controls

status: Public on Jul 16 2021

city: WuHan

first: Meng

last: Xu

state: Hubei

address: No.115 Donghu Road, Wuchang District

institute: Wuhan university

summary: We knockdown-expressed the AHNAK2 in Hela cells, MDA-MB-231 cells and HCT116 cells using the lentiviral construct Plko.1. Then using RNA-sequencing (Illumina) to compare AHNAK2 knockdown cells to the scramble controls.

overall_design: RNA sequencing of AHNAK2 knockdown adenocarcinoma cells including Hela, MDA-MB-231 and HCT116 to find different genes in expression from the scramble controls.

first: Anyi

last: Cheng

first: Cheguo

last: Cai


title: ALKBH7-mediated demethylation regulates mitochondrial  polycistronic RNA processing

status: Public on Jun 02 2021

city: Chicago

first: Li-Sheng

last: Zhang

state: IL

address: 929 E 57th St Rm E313

department: Department of Chemistry

institute: The University of Chicago

type: Methylation profiling by high throughput sequencing

summary: Members of the mammalian AlkB family are known to mediate nucleic acid demethylation. ALKBH7, a mammalian AlkB homologue, localizes in mitochondria (mt) and affects metabolism, but its function and mechanism of action are unknown. Here, we report an approach to site-specifically detect m1A, m3C, m1G, and m22G modifications simultaneously within all cellular RNAs, and discovered that human ALKBH7 demethylates N2, N2-dimethylguanosine (m22G) and N1-methyladenosine (m1A) within mt-Ile and mt-Leu1 pre-tRNA regions, respectively, in nascent polycistronic mt-RNA. We further show that ALKBH7 regulates the processing and structural dynamics of polycistronic mt-RNAs. Depletion of ALKBH7 leads to increased polycistronic mt-RNA processing, reduced steady-state mitochondria-encoded tRNA levels and protein translation, as well as notably decreased mitochondrial activity. Thus, we identify ALKBH7 as an RNA demethylase that controls nascent mt-RNA processing and mitochondrial activity.

overall_design:
[dataset1] 4 samples (Sample 1-4): Duplicates for DAMM-seq of cellular small RNA samples from HepG2 cells, including RNA input and Engineered-AlkB-treated.
[dataset2] 12 samples (Sample 13-24): Duplicates for DAMM-seq of mitochondrial tRNA samples to observe methylation fraction change in vivo, including siALKBH7 vs. siControl, shTRMT1 vs. shControl and o/e ALKBH7 vs. o/e Control in HepG2 and HeLa cell lines.
[dataset3] 16 samples (Sample 25-40): Duplicates for DAMM-seq of mitochondrial dsRNA samples to observe methylation fraction change in vivo, including siALKBH7 vs. siControl, ALKBH7 wild-type vs. ALKBH7 knockout, shTRMT1 vs. shControl and o/e ALKBH7 vs. o/e Control in HepG2 and HeLa cell lines.
[dataset4] 8 samples (Sample 41-48): Duplicates for icSHAPE of mitochondrial dsRNA samples to observe flexible regions within dsRNA in vivo, including input and pulldown samples for siALKBH7 vs. siControl in HepG2 cells.
[dataset5] 6 samples (Sample 49-54): Duplicates for DAMM-seq of HepG2 dsRNA samples to observe methylation fraction change in vivo, including siALKBH7+empty vector, siALKBH7+ALKBH7-WT and siALKBH7+ALKBH7-mutant.
[dataset6] 12 samples (Sample 55-66): Duplicates for DAMM-seq of HepG2 EU-labeled RNA samples to observe mt-mRNA and junction level change in vivo, including 10-min EU-labeled RNA from siALKBH7 vs. siControl, 10-min EU-labeled RNA from wild-type vs. ALKBH7 KO HepG2 cells, 20-min EU-labeled RNA from wild-type HepG2 cells and 30-min EU-labeled RNA from wild-type HepG2 cells.

first: Ru-Juan

last: Liu

first: Chuan


title: Vascular integrity is essential for maintaining tissue homeostasis II

first: Junhao

summary:
Purpose: analyze the transcriptomic difference of endothelial cells and pericytes in PBS, LPS or LPS + Riociguat treated lungs
Methods: Gucy1a1-EGFP mice were given PBS or LPS treatment via trachea instillation. Vehicle or Riociguat oral administation was performed at every 9 hours. 24h later, lungs  were dissociated and endothelial cells and pericytes were isolated by flow cytometry, then directly processed to RNA extraction and library construction
Results: Riociguat can restore LPS-induced lung injury by inhibiting pericytes activation and maintain vascular homostatsis


title: Vascular integrity is essential for maintaining tissue homeostasis I

summary:
Purpose: analyze the transcriptomic differences in PBS, LPS and LPS + Riociguat treated whole lung lysate
Methods: C57BL6 mice were given PBS, LPS or LPS + Riociguat treatment via trachea instillation. 24h later, homogenize lung and extract mRNA
Results: Riociguat can restore LPS-induced lung injury by improving immune environment

overall_design: mRNA profiles of whole lung lysate were generated by sequencing.

first: Hao

first: Chuankai


title: Thyroid hormone receptor is essential for larval eptiehlial apoptosis and adult epithelial stem cell development

status: Public on Mar 31 2021

city: Bethesda

first: Ryan

last: Dale

address: Rm 10D39, 10 Center Drive

institute: National Institutes of Health

summary: Our experiment revealed that TR double knockout completely blocks intestinal length shortening, larval cell death, and adult stem cell development, demonstrating a requirement for TR in adult intestinal development.

overall_design: Compare the thyroid hormone target gene expression with or without thyroid hormone receptor in the intestine during metamorphosis climax of Xenopus tropicalis

first: Yuki

last: Shibata

first: Yun-Bo

last: Shi

first: Hongen


title: Cox10 is Required for Natural Killer Cell Expansion and Memory in Response to Viral Infection

status: Public on Apr 17 2021

city: SAINT LOUIS

first: Megan

last: Cooper

state: MISSOURI

address: MPRB, 6th floor, 4905 Childrens Place

department: Pediatrics

institute: Washington University in St Louis

summary: Single-cell RNA-sequencing revealed increased pAMPK signaling and a unique gene expression signature. Our data demonstrate that Cox10 is required by NK cells to expand in response to Ly49H stimulation during MCMV infection.

overall_design: Comparison of NK cell populations and gene expression between RosaWT and Cox10KO mice, with or without MCMV infection

first: Ana

last: Kolicheski

first: Annelise

middle: Y

last: Mah-Som


title: Antiretroviral treatment induced decrease in immune activation contributes to reduced susceptibility to tuberculosis in HIV-TB co-infected persons

status: Public on Feb 17 2021

city: London

first: Rachel

last: Lai

address: Du Cane Road

department: Infectious Disease

institute: Imperial College London

summary: Antiretroviral treatment (ART) reduces the risk of developing active tuberculosis (TB) in HIV co-infected persons. We aimed to investigate the mechanisms of ART-mediated prevention of TB in HIV and TB co-infected patients on antiretroviral therapy (ART), recruited in Khayelitsha, South Africa. RNA was extracted from whole blood collected in TempusTM Blood RNA tubes at day 0 and at 1, 3 and 6 months of ART. We first performed a pilot RNAseq experiment of 12 samples (3 patients at 4 timepoints) for 50 million reads to assess if samples with lower quality and/or quantity will still yield meaningful outputs and the minimum number of reads required for sufficient coverage. This was followed by a second RNAseq experiment of 35 samples with sufficient quality: 11 from day 0 and 24 from 6 months of ART, 8 of which are paired. However, only n=6 samples from day 0 and n=6 samples from 6 months of ART could be analyzed. Results indicated reduced immune activation at 6 months of ART compared to day 0 with significant fall in the Hallmark Interferon alpha, Interferon gamma and IL-6-JAK-STAT-signalling pathway genes. These results were supported by similar changes in soluble protein markers in the plasma. Overall, our data indicates that ART- induced decrease in immune activation may contribute to reduced susceptibility to tuberculosis in HIV-TB co-infected persons.

overall_design: We aimed to investigate the mechanisms of ART-mediated prevention of TB in HIV and TB co-infected patients on antiretroviral therapy (ART), recruited in Khayelitsha, South Africa. RNA was extracted from whole blood collected in TempusTM Blood RNA tubes at 0 and 6 months of ART.

first: Katalin

last: Wilkinson


title: The SAM domain-containing protein 1 (SAMD1) acts as a repressive chromatin regulator at unmethylated CpG islands

status: Public on May 13 2021

city: Marburg

first: Robert

last: Liefke

state: Hessen

address: Hans-Meerwein-Str. 2

department: Institute of Molecular Biology and Tumor Research (IMT)

institute: Philipps University of Marburg

summary: CpG-islands (CGIs) are key regulatory DNA elements at most promoters, but how they influence the chromatin status and transcription remains elusive. Here we identify and characterize SAMD1 (SAM domain-containing protein 1) as an unmethylated CGI-binding protein. SAMD1 possesses an atypical winged-helix domain that directly recognizes unmethylated CpG-containing DNA via simultaneous interactions with both the major and the minor groove. The SAM domain interacts with L3MBTL3, but it can also homopolymerize into a closed pentameric ring. At a genome-wide level, SAMD1 localizes to H3K4me3-decorated CGIs, where it acts as a repressor. SAMD1 tethers L3MBTL3 to chromatin and interacts with the KDM1A histone demethylase complex to modulate H3K4me2 and H3K4me3 levels at CGIs, thereby providing a mechanism for SAMD1-mediated transcriptional repression. Absence of SAMD1 impairs ES cell differentiation processes, leading to miss-regulation of key biological pathways. Together, our work establishes SAMD1 as a novel chromatin regulator acting at unmethylated CGIs.

overall_design: ChIP-Seq of SAMD1 (2x), L3MBTL3 (2x), KDM1A (2x), H3K4me2 (2x), H3K4me3 (2x), H3K27ac (1x), H3K27me3 (1x) in WT and SAMD1 knockout cells. RNA-Seq of WT and SAMD1 knockout cells (4x). RNA-Seq after 7 days of undirected differentiation (3x). RNA-Seq after KDM1A and L3MBTL3 KO (3x).

first: Bastian

last: Stielow

first: Andea

last: Nist


title: In vivo gene expression profile of human intestinal epithelial cells: from the viewpoint of drug metabolism and pharmacokinetics

status: Public on Apr 30 2021

city: Suita

first: Hiroyuki

last: Mizuguchi

state: Osaka

address: 1-6, Yamadaoka

department: Graduate School of Pharmaceutical Sciences

institute: Osaka University

summary: Orally administered drugs are absorbed and metabolized in the intestine. In order to accurately predict pharmacokinetics in the intestine, it is essential to understand the intestinal expression profiles of genes related to drug absorption, distribution, metabolism, and excretion (ADME). However, in many previous studies, gene expression analysis in the intestine has been carried out using specimens from cancer patients. In this study, in order to obtain a more accurate gene expression profile, biopsy samples were collected from 14 patients under endoscopic observation and RNA-seq analysis was performed. Gene expression analysis of drug metabolizing enzymes (CYPs), non-CYP enzymes, nuclear receptors, drug conjugating enzymes (UGTs and SULTs), and apical and basolateral drug transporters was performed in biopsy samples from the duodenum, ileum, colon, and rectum. The proportions of the CYPs expressed in the ileum were 25% (CYP3A4), 19% (CYP2C18), and 14% (CYP3A5). CYP3A4 and CYP2C19 were highly expressed in the duodenum and ileum, but not in the colon and rectum. In the ileum, apical transporters such as P-gp, PEPT1, BCRP, MRP2, and ASBT were strongly expressed, and the expression levels of P-gp and ASBT in the ileum were higher than those in other regions. In the ileum, basolateral transporters such as OSTα, OSTβ, and MRP3 were strongly expressed. Furthermore, we identified specific markers for the duodenum, ileum, colon, and rectum by conducting comprehensive gene expression analysis. We succeeded in obtaining gene expression profiles of drug ADME-related genes in vivo human intestinal epithelial cells. We expect that this information would be useful for accurate prediction of the pharmacokinetics of oral drugs.

overall_design: RNA expression profiles of Intestinal biopsy. iPS-derived enterocyte, Caco-2 cell and undifferentiated iPS-cells are used as reference control sample.

first: Kazuo

last: Takayama

first: Sayaka

last: Deguchi

first: Kohei

last: Ito

first: Akiko

last: Matsui

first: Tomoki

last: Yamashita

first: Kentaro

last: Kawakami

first: Wataru

last: Kishimoto

first: Hiroshi

last: Nakase


title: A transcriptomic taxonomy of Drosophila circadian neurons around the clock

status: Public on Jan 12 2021

city: Waltham

first: Michael

last: Rosbash

address: 415 South street

institute: Brandeis University

summary: Many different functions are regulated by circadian rhythms, including those orchestrated by discrete clock neurons within animal brains. To comprehensively characterize and assign cell identity to the 75 pairs of Drosophila circadian neurons, we optimized a single cell RNA sequencing method and assayed clock neuron gene expression at different times of day. The data identify at least 17 clock neuron categories with striking spatial regulation of gene expression. Transcription factor regulation is prominent and likely contributes to the robust circadian oscillation of many transcripts, including those that encode cell-surface proteins previously shown to be important for cell recognition and synapse formation during development. The many other clock-regulated genes also constitute an important resource for future mechanistic and functional studies between clock neurons and/or for temporal signaling to circuits elsewhere in the fly brain.

overall_design: Single cell RNA sequencing of Drosophila clock neurons around the clock in LD and DD conditions

first: Dingbang

last: Ma

first: Dariusz

last: Przybylski

first: Katharine

last: Abruzzi

first: Matthias

last: Schlichting

first: Qunlong

last: Li

first: Xi

last: Long


title: XBP1s cooperates with LEF1 to promote hepatocellular carcinoma development

city: Wuhan

first: Faming

last: Zhao

address: Hangkong road 13

department: Tongji Medical College

institute: Huazhong University of Science and Technology

summary: To gain insight into the global XBP1s target gene profile in HCC cells, we performed RNA-seq and ChIP-seq analyses in HepG2 cells.

overall_design: This dataset includes RNA-seq and ChIP-seq to understand the molecular mechanism of XBP1s in HCC cells. For RNA-seq, HepG2 cells were upon XBP1 siRNA-mediated knockdown (siXBP1). For ChIP-seq, HepG2 cells were treated with 30 nM Thapsigargin (Tg) for 3 hours.

first: Tingting

last: Zhang

first: Xia

last: Sheng


title: The corepressors GPS2 and SMRT control enhancer and silencer function linked to eRNA transcription during inflammatory activation of macrophages

status: Public on Jan 26 2021

city: Nanjing

first: Zhiqiang

last: Huang

state: Jiangsu

address: Hankou 22

department: Medical School

institute: Nanjing University

summary: Study the inflammation-associated Ccl2 functional enhancer and its related enhancer RNA in mice macrophages

overall_design: Transcriptome, DNA structure, cristome changes of GPS2 marked enhancer to the target gene expression.  Gro-seq is designed to mark the transcribed enhancer regions; ChIP-seq is designed to mark the TF bindings; RNA-seq is designed to evaluate gene expression and 4C-seq is designed to visualize the DNA structure dynamic changes.

first: Rongrong

last: Fan

first: Eckardt

last: Treuter


title: Identification of differentially expressed genes in BPA-/- and BPA+/+ mouse melanomas.

status: Public on Mar 04 2021

city: Copenhagen

first: Daniela

last: De Zio

state: Non United States Or Canada

address: Strandboulevarden 49

department: Cell Stress and Survival

country: Denmark

institute: Danish Cancer Society

summary: Aim: Identify Ambra1-dependent regulation in melanoma development by comparing bulk RNA extracted from Ambra1-depleted (BPA-/-) mouse melanomas to Ambra1-wt (BPA+/+) melanomas.

overall_design: Bulk tumour mRNA profiles of  BPA-/- and  BPA+/+ mice were generated by deep sequencing, in triplicate, using Illumina Next Seq. Each sample represents a different mouse.

first: Luca

last: Di Leo

first: Valérie

last: Bodemeyer


title: Pharmacological modulation of H3K9me2 deposition in human intestinal models and transformed ES cells

status: Public on Dec 14 2020

city: Ottawa

first: Yannick

middle: D.

last: Benoit

state: Ontario

address: 451 Smyth road

institute: University of Ottawa

summary: Transformed variant of H9 human ES cells (t-hESC) represent a surrogate model for cancer stem cells in adherent cultures, which faithfully recapitulate the main functional, transcriptional, and epigenetic characteristics of CSCs in culture and in vivo. The use of G9a inhibitor BIX-01294 reduced the levels of H3K9me2 and global DNA methylation in t-hESCs. Thus, we performed transcriptome-profiling experiments on control and BIX-treated t-hESC to study the impact of G9a inhibition on gene networks associated with neoplastic stemness. Moreover, using a phenotypic chemical screening assay, we identified vanoxerine (YB-1471) as a new small molecule decreasing H3K9me2 deposition in t-hESCs. In addition to t-hESCs, transcriptome profiling was performed normal human intestinal epithelial crypt (HIEC) cells and colorectal cancer cell line HT29 upon treatment with vanoxerine.

overall_design: Whole transcriptome profiling.

first: Christopher

middle: J

last: Bergin

middle: D


title: Secondhand smoke alters arachidonic acid metabolism in infants and children with cystic fibrosis

status: Public on Dec 01 2020

city: Dallas

first: Nicole

last: Baldwin

address: 3434 Live Oak St

institute: Baylor Research Institute

summary: Children ages 0-10 years old with CF were recruited from 2012-2015 at the outpatient CF clinic, and classified according to age (infants <1 year old, vs. children 1-10 years old). The diagnosis of CF was defined as two disease-causing mutations or a sweat chloride test ≥ 60 mmol/L. Hair and blood samples were collected from each subject. Hair nicotine concentrations were determined and considered as the primary objective measure of SHSe.  Hair nicotine provides a long-term measure of SHSe as nicotine is integrated into the growing hair shaft over multiple months. (15)  For each subject, 30-40 shafts of hair of approximately 2-3 cm in length were cut at the hair root from the occipital skull.  Hair samples were refrigerated at 4° for storage, washed before analyses to remove ambient nicotine (15) and batch-tested at a contract research facility (Environmental Health Sciences, Johns Hopkins School of Public Health). Samples were processed by reverse-phase high-performance liquid chromatography with electrochemical detection as described. (15) Hair nicotine concentrations were expressed as ng/mg of hair and the assay limit of detection was 0.087 ng/mg.

overall_design: 40 total samples: 12 healthy, 28 cycstic fibrosis (CF); Of the CF samples, 10 were negative for nicotine as tested by hair sample and 18 were positive

first: Benjamin

middle: T

last: Kopp

first: Jeeho

last: Kim

first: Robert

last: Konstan

first: Bennett

last: Smith

first: Alejandro

last: Diaz

first: Rohan

last: Thompson

first: Chandra

last: Shrestha

first: Lynette

last: Rogers

first: D

last: Sanders

first: Don

last: Hayes Jr

first: Dmitry

last: Tumin

first: Frederick

middle: W

last: Woodley

first: Octavio

last: Ramilo

first: Judith

last: Groner

first: Asuncion

last: Mejias


title: Modulation of post-ischemic remodeling by an acellular hydrogel injection

status: Public on Jan 05 2021

city: Galway

first: Oliver

last: Carroll

address: Newcastle Rd

institute: National University of Galway, Ireland

summary: RNA seq analysis on cardiac tissue samples 21 days after the intramyocardial injection of an acellular hydrogel in infarcted sheep hearts.

overall_design: In the experimental design, the in vivo study was powered for statistical significance (power = 0.8), and this required a minimum of four animals per group. The alpha value (Type 1 error) was set at the level of 5% (P = 0.05). Endpoint was set at 28 days post-MI as extensively performed in the field to assess the efficacy of the proposed treatment on the post-ischemic remodeling.

first: Paolo

last: Contessotto

first: Abhay

last: Pandit


title: Single cell RNA sequencing of HSC and MPP in DNA damage tolerant deficient mutants

status: Public on Jan 20 2021

city: Amsterdam

first: Heinz

last: Jacobs

address: Postbus 90203

department: Tumor Biology & Immunology

country: Netherlands

institute: The Netherlands Cancer Institute

summary: We performed scRNA-seq according to the CEL-seq2 protocol in order to define transcriptome changes in mouse hematopoietic stem cell containing LSKs in different mutants with defects in DNA damage tolerances.

overall_design: Using FACS, we sorted 2-4 96 well plates for WT, Rev1-/-, PcnaK164R/K164R, and PcnaK164R/K164R;Rev1-/- LSK cells.

first: Olimpia

last: Buoninfante

first: Bas

last: Pilzecker

first: Ji

last: Song

first: Colin

last: Pritchard

first: Ivo

last: Huijbers

last: Vivie

first: Sjaak

last: Philipsen

first: Paul

middle: C

last: van den Berk


title: Data set from hematopoietic stem cell transcriptome elucidating specific targets of Class 1A PI3K

status: Public on Nov 27 2020

city: Bronx

first: Kristina

last: Ames

address: 1300 Morris Park Avenue, Chanin 410

department: Cell Biology

institute: Albert Einstein College of Medicine

summary: Purpose: To detect the global effects of Class1A PI3K TKO deletion on the HSC transcriptome. Method: Whole BM cells from donor mice TKO: Pik3calox-lox; Pik3cblox-lox; Pik3cd-/-;Mx1-Cre, δ KO: Pik3calox-lox; Pik3cblox-lox;Pik3cd-/- (littermate control) and WT: WT, Mx1-Cre (control) were transplanted into lethally irradiated 6-8 week old B6.SJL mice (N=7 per group). Recipient mice were injected 4 weeks post transplant interperitoneally with pIpC 250μg x2, 48 hours apart to ensure Pik3ca and Pik3cb excision. At 4 weeks post PIPC, BM cells were harvested from femurs, tibiae, ilia and vertebrae by gentle crushing. Donor-derived HSCs (Lin-cKit+Sca1+Flk2-CD48-CD150+) cell populations were sorted into RNA extraction buffer (ARCTURUS PicoPure). cDNA was amplified from total RNA using the Ovation® RNA‑Seq System V2. Sequencing was performed using the NGS platform llumina-HiSeq2500/4000.

overall_design: Examination of transcriptome differences in hematopoietic stem cells between non-competitively transplanted Pik3ca lox/lox;Pik3cblox/lox;Pik3cd-/-;Mx1-Cre (TKO) vs Pik3calox/lox;Pik3cblox/lox;Pik3cd-/- (δKO) littermate controls vs WT;Mx1-Cre (WT) controls all samples are in three biological replicates. Each of the biological replicates was done in 2 technical replicates.

first: Kira

last: Gritsman


title: Transcriptomic profiling of whole larvae and the liver from dnmt1 mutant zebrafish larvae compared to their phenotypically normal siblings at 120 hpf

city: Abu Dhabi

first: Kirsten

last: Sadler Edepli

department: Biology

institute: New York University Abu Dhabi

summary: This SuperSeries is composed of the SubSeries listed below which has both RNAseq (from whole larvae and pools of dissected livers) and methylome profiling using reduced representation bisulfite sequencing (from whole larvae) at 120 hours post-fertilization (hpf).

overall_design: Refer to individual Series.


title: p38α activation is essential for germinal center B cell to plasma cell differentiation

status: Public on Feb 27 2021

city: xiamen

first: cai

last: shaowei

address: fujian province xiamen city Xiang 'an area Xiang 'an south road 4221

institute: university

summary: We report the RNA-seq data of B cell derived from p38αfl/fl and p38αfl/flVavcre mouse in our In vitro plasma cell (iPC) differentiation system.Significantly differential expression analyses show that p38α deficient mainly affects the gene expression at the plasma cell stage.

overall_design: B cell mRNA expression profile of  p38αfl/fl and p38αfl/flVavcre in our In vitro plasma cell (iPC) differentiation system

first: Jiahuai

last: Han

first: Changchun

last: Xiao

first: Wen-Hsien

last: Liu

first: Jianfeng

last: Wu

first: Kang

last: Yang

first: Shaowei

last: Cai

first: Xiaohan

last: Zhang


title: Transcriptome analysis of alternative splicing under heat stress condition in atcyp18-1 mutant compared to wild type of Arabidopsis

status: Public on Oct 22 2020

city: Daejeon

first: Seung Hee

last: Jo

address: 125, Gwahakro

institute: KRIBB

summary: To investigate whether the observed changes in pre-mRNA splicing led to AtCYP18-1 depletion, we conducted RNA-sequencing to analyse the quantitative profiling of alternative splicing

overall_design: RNA was immediately extracted from atcyp18-1 and WT seeds and treated with or without heat stress for 2 h at 1 day after imbibition.

first: Hye

last: Cho

first: Seung

middle: H


title: Omics multi-layers networks and identification of the key genes and miRNAs involved in fat storage and metabolism: systems biology approach

status: Public on Oct 26 2020

city: Karaj

first: Abolfazl

last: Bahrami

address: Daneshgah

country: Iran

institute: University of Tehran

summary: In spite of the importance of fat metabolism in different species, there has been little success dissecting the inreactome basis of fat storage. To better understand the molecular basis of fat metabolism, we study transcriptome profiling of abdominal fat  between chicken with either good or poor genetic merit for meat quality.

overall_design: 6 samples total; 3 samples for Fat-H (high fat) vs 3 samples for Fat-L (low fat) differential non-coding RNA expression analysis.

first: Maryam

last: Bakherad


title: Liver and fat transcriptomic changes related to fat content in pigs

status: Public on Oct 30 2020

city: Balice

first: Kacper

last: Zukowski

address: Krakowska 1 Street

country: Poland

summary: The present work emplyed pigs as an animal model for recognition of molecular processes associated with fat deposition. The transcriptomic changes dependent on fat content were showed at the fat and liver levels. In the experiment Złotnicka White pigs were used that were not under selection pressure, because they are included in to National Preservation Program.

overall_design: The fat and liver transcriptomic changes related to fat deposition in pigs experiment was supported by the statutory activity of National Research Institute of Animal Production no. 01-18-05-21 and BIOSTRATEG2/297267/14/NCBR/2016

first: Piórkowska

last: Katarzyna

first: Żukowski

last: Kacper

first: Szulc

last: Karolina

first: Katarzyna

last: Ropka-Molik

first: Mirosław

last: Tyra


title: Single Cell Transcriptomic Characterization of CAR T-Cell Products Reveals Subpopulations, Stimulation and Exhaustion Signatures

status: Public on Jan 22 2021

city: Shanghai

first: Xiaonan

last: Wang

address: 227 Chongqing South Road

department: School of Public Health

institute: Shanghai Jiao Tong University School of Medicine

summary: Chimeric antigen receptor (CAR) T-cell adoptive therapy is set to transform the treatment of a rapidly expanding range of malignancies. Although the activation process of normal T cells is well characterized, comparatively little is known about the activation of cells via the CAR. Here we have used flow cytometry together with single cell transcriptome profiling to characterize the starting material (peripheral blood mononuclear cells –PBMCs-) and CAR therapeutic products of 3 healthy donors in the presence and absence of antigen specific stimulation. Bioinformatic analysis of the 57,676 single cell transcriptomes showed the CAR products to contain several subpopulations of cells, with the cellular composition reproducible from donor to donor, and all major cellular subsets compatible with CAR expression. Only 50% of CAR-expressing cells displayed transcriptional changes upon CAR-specific antigen exposure. The resulting molecular signature for CAR T-cell activation provides a rich resource for future dissection of the underlying mechanisms. Targeted data interrogation also revealed that a small proportion of antigen-responding CAR-expressing cells displayed an exhaustion signature, with both known markers and genes not previously associated with T-cell exhaustion. Comprehensive single cell transcriptomic analysis thus represents a powerful way to guide the assessment and optimization of clinical-grade CAR-T-cells, and inform future research into the underlying molecular processes.

overall_design: To characterize CAR-T cell products

first: Carlotta

last: Peticone

first: Ekaterini

last: Kotsopoulou

first: Berthold

last: Göttgens

first: Fernando

last: Calero-Nieto


title: Identification of ESX-1-dependent transcriptional response of human macrophages to Mycobacterium tuberculosis infection

status: Public on Nov 16 2020

city: London

first: Rachel

last: Lai

address: Du Cane Road

country: United Kingdom

institute: Imperial College London

summary: Human macrophage transcriptional response to Mtb infection diverges at late timepoints post-infection with wild-type Mtb, eliciting a more sustained immune response than RD1-deleted mutant

overall_design: A total of 18 human macrophage samples (infected vs. uninfected; wild-type vs. RD1 mutant Mtb) were collected at 2 timepoints (2h and 48h) and total RNA extracted for sequencing.

first: Elliott

last: Bernard

first: Maximiliano

last: Gutierrez


title: Single-cell RNA sequencing of basophils from mouse bone marrow

status: Public on Oct 20 2020

city: Solna

first: Joakim

last: Dahlin

address: CMM, Visionsgatan 18

department: Department of Medicine, Solna

institute: Karolinska Institutet

summary: We performed single-cell RNA-sequencing of Lin- Sca1- FcεRI+ bone marrow cells from mice

overall_design: 47 Lin- Sca1- FcεRI+ CD34+ basophils and 47 Lin- Sca1- FcεRI+ CD34- basophils were isolated from bone marrow of three female C57BL/6 mice.

first: Fiona

last: Hamey

first: Winnie

last: Lau

first: Evangelia

last: Diamanti

first: Bertie


title: Effects of Pten knockout in dystrophic skeletal muscles of mdx mouse

status: Public on Oct 06 2020

city: West Lafayette

first: Shihuan

last: Kuang

state: IN

address: 901 W State St

country: USA

institute: Purdue University

summary: Analysis of skeletal muscles with specific knockout (KO) of Phosphatase and tensin homolog (Pten) gene in an animal model of DMD (mdx mice). Pten knockout alleviates myofiber degeneration and restores muscle function in mdx mice.

overall_design: Total RNA was isolated from ~30 mg diaphragm muscles from experimental Pten knockout and control D2.B10-mdx mice (10-week old) using TRIzol reagent according to the manufacturer’s instructions. RNA was quantitated at the Qubit fluorometer and quality-controlled at an Agilent 2100 Bioanalyzer. A complementary DNA library was constructed using polyA selected RNA, and sequencing was performed according to the Illumina HiSeq standard protocol (high-throughput, paired-end 150bp fragment sequencing). Raw reads from RNA-seq libraries are filtered to remove reads containing adapters or reads of low quality. After filtering, statistics analysis of data production and quality was performed to confirm the sequencing quality. Reference genome and gene annotation files were downloaded from a genome website browser (NCBI/UCSC/Ensembl). TopHat2 was used for mapping the filtered reads to the reference (Mus Musculus, GRCm38/mm10) genome. For the quantification of gene expression level, HTSeq V0.6.1 was used to analyze the read numbers mapped for each gene. The Fragments Per Kilobase of transcript per Million mapped reads (FPKM) of each gene was calculated based on the gene read counts mapped to genes or exons. A differential expression analysis was performed using the DESeq2 R/EdgeR R package with the threshold of significance set as adjusted p < 0.05.

first: Feng

last: Yue


title: Activin A promotes the development of acquired heterotopic ossification and is an effective target for disease attenuation in mice

status: Public on Jan 01 2021

city: Philadelphia

first: Maurizio

last: Pacifici

state: PA

address: 3600 civic center blvd

department: Orthopaedic

institute: Children Hospital of Philadelphia

summary: Heterotopic ossification (HO) is a common, potentially debilitating, acquired pathology that is instigated by tissue damage or other insults and involves inflammation followed by  chondrogenesis, osteogenesis and extraskeletal bone accumulation. Current standard of care are not very effective and have side effects, making the search for new treatments urgent. Activin A is a member of the transforming growth factor-b (TGF-b) superfamily, is produced by activated macrophages and other inflammatory cells and signals through activation of canonical SMAD2 and SMAD3 (SMAD2/3) intracellular effectors. Because HO starts with inflammation and because pSMAD2/3 activation is chondrogenic, here we tested whether activin A stimulates HO development. Using standard mouse models of acquired intramuscular and subdermal HO, we found that systemic administration of a neutralizing activin A antibody markedly reduced HO development and bone accumulation. Single-cell RNAseq and developmental trajectories showed that the antibody treatment had sharply reduced the number of Sox9+ skeletal progenitors, many of which also expressed the gene encoding activin A (Inhba), that were recruited to the HO site. In line with the latter finding, gain-of-function assays showed that treatment of progenitors with recombinant activin A enhanced their chondrogenic differentiation and did so through SMAD2/3 signaling, and inclusion of activin A to HO-inducing in vivo implants enhanced HO development. Together, our data reveal that activin A is a critical upstream signaling stimulator of HO in mice and could represent an effective therapeutic target against acquired forms of this pathology in patients.

overall_design: Single cell RNA seq of cells from Ectopic masses were harvested on day 5  from mice implanted with Matrigel alone or Matrigel/rhBMP2 mixture, with the latter mice treated systemically with pre-immune control IgG or activin A neutralizing antibody

first: Christina

last: Mundy

first: Lutian

last: Yao


title: Single-cell transcriptional profiling of late mast cell differentiation in mouse

summary: Single-cell RNA sequencing of Lin- c-Kit+ FcεRI+ cells from mouse peritoneum captured the late mast cell differentiation

overall_design: We performed single-cell RNA-sequencing of 95 basophil-mast cell progenitors (BMCPs) and 94 mature mast cells (MCs) isolated from the peritoneal cavity of four female C57BL/6 mice.


title: Human neutrophils before and after in vivo exposure to Bacillus Calmette-Guérin vaccine

status: Public on Sep 30 2020

city: Parkville

first: Boris

last: Novakovic

state: Victoria

address: Murdoch Children's Research Institute, Royal Children's Hospital, Flemington Road

institute: Murdoch Children's Research Institute

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

overall_design: Refer to individual Series


title: H3K4me3 ChIP-seq of human neutrophils before and after in vivo exposure to Bacillus Calmette-Guérin vaccine

summary: Innate immune memory is the phenomenon whereby innate immune cells undergo functional reprogramming after exposure to microbial components.  In this study we apply epigenomic and transcriptomic analysis to circulating neutrophils from a clinical trial of BCG vaccination in healthy adults.

overall_design: Healthy volunteers were injected with the BCG vaccine, and neutrophils were collected before vaccination, and 3 month after vaccination.

first: Simone

last: Moorlag

first: Mihai

last: Netea


title: Transcriptomes of human neutrophils before and after in vivo exposure to Bacillus Calmette-Guérin vaccine


title: Converting Escherichia coli to a synthetic methylotroph growing solely on methanol

status: Public on Sep 01 2020

city: Taipei

first: James

middle: C.

last: Liao

address: 128 Academia Road, Section 2, Nankang, Taipei 11529, Taiwan

institute: Academia Sinica

summary: Methanol, being electron-rich and derivable from methane or CO2, is a potentially renewable one-carbon (C1) feedstock for microorganisms. Although the ribulose monophosphate (RuMP) cycle used by methylotrophs to assimilate methanol differs from the typical sugar metabolism by only three enzymes, turning a non-methylotrophic organism to a synthetic methylotroph that grows to a high cell density has been challenging. Here, we reprogrammed E. coli using metabolic robustness criteria followed by laboratory evolution to establish a strain that can utilize methanol as the sole carbon source efficiently. This synthetic methylotroph alleviated a heretofore uncharacterized hurdle, DNA-protein crosslinking (DPC), by insertion sequence (IS) mediated copy number variations (CNV) and balanced the metabolic flux by mutations. Being capable of growing at a rate comparable to natural methylotrophs in a wide-range of methanol concentrations, this synthetic methylotrophic strain illustrates genome editing and evolution for microbial tropism changes, and expands the scope of biological C1 conversion.

overall_design: SM1 strain RNA expression profile in 400 mM methanol MOPS medium at OD600=1.1 and OD600=0.7

first: Frederic

last: Chen

first: Hsin-Wei

last: Jung

first: Chao-Yin

last: Tsuei


title: Isthmin-1 is a novel mediator of experimental glomerulonephritis through a pro-apoptotic action in podocytes

status: Public on Aug 31 2020

first: JONATHAN

last: CARON

state: Greater London

address: New Hunt's House, Newcomen St

department: Cancer Studies

institute: KING'S COLLEGE LONDON

summary: Focal segmental glomerulosclerosis (FSGS) is a leading cause of end stage renal disease and remains without specific treatment. To identify novel actors involved in the progression of FSGS, we used an experimental model of nephroangiosclerosis with FSGS in rats and performed a differential transcriptomic analysis. Among the genes that were several-fold upregulated in glomeruli, was Isthmin-1 (ISM), an ‘unknown’ to the kidney gene. The objective of the present study was to find if and what role plays ISM to renal pathophysiology.

overall_design: Group W0 sacrificed at the peak of renal damage (UPER> 1 g/mmol) (n = 3).  - Group W1, in which all animals developed UPER> 1g/mmol and were sacrificed after 1 week interruption of L-NAME and renal repair (n = 3).  - Group W5, in which all animals developed UPER> 1 g/mmol and were sacrificed after 5 weeks of interruption of L-NAME and renal repair (n = 3).  - CTL group, which did not receive L-NAME and was sacrificed alongside other groups to obtain animals of the same age (n = 3).

first: J

last: Caron

last: Boffa


title: ChIP-seq of H3K9ac and H3K14ac in U87 glioma cells treated with differentiation agents(0.5mM 8-cpt-cAMP combined with 1nM MS275) for 48h

status: Public on Sep 22 2020

city: GuangZhou

first: liu

last: xincheng

address: zhongshan Road 74

country: China

institute: sysu

summary: We report the diverse histone acetylation pattern on histone 3 lysine 9 and lysine14 under the cell differentiation. The genes controlled by this two histone acetylation modification can transformed the cell identity of the glioma by downregualted the promoter of oncogenes' H3K9 acetyltion and improve the promoter of neuron-differentiation related genes' H3K14 acetylation

overall_design: Examination of 2 different histone modifications in glioma cells treated with differentiation agent.The ChIP-seq data were generated using 50 bp single-end sequencing reads by BGI (Beijing, China)

first: Xincheng

last: Liu


title: Transcriptomes of human monocytes exposed to oxLDL ex vivo

status: Public on Oct 03 2021

summary: Innate immune memory is the phenomenon whereby innate immune cells such as monocytes or macrophages undergo functional reprogramming after exposure to microbial components such as Beta glucan or the BCG vaccine. Here we characterize the transcriptional events following oxidized low-density lipoprotein (oxLDL) duced trained innate immunity using RNA-seq data.

overall_design: Primary human monocytes were exposed to oxLDL or media alone for 24 hours in culture. oxLDL was then removed and cells were allowed to differentiate to macrophages for an additional 5 days. RNA was collected at baseline, day 1, day 6 and upon 4 hour re-exposure to LPS at day 6. .

first: Laszlo

last: Groh

first: Werner

last: Koopman

first: Niels

last: Riksen