title: RNA-sequencing of lung tissues from Gprc5a-/- mice at baseline, end of NNK exposure,  three months and seven months post-NNK

status: Public on Mar 31 2021

city: Houston

first: Humam

last: Kadara

state: TX

address: 2130 W. Holcombe Blvd

country: USA

institute: University of Texas MD Anderson Cancer Center

type: Expression profiling by high throughput sequencing

summary: We have previously shown that Gprc5a-KO mice develop lung tumors that are accelerated by exposure to the tobacco-specific carcinogen NNK. In this study we sought to understand the temporal evolution of gene expression changes in tumors and normal-appearing tissues.

overall_design: We performed RNA-sequencing (RNA-seq) of normal-appearing lung tissues and lugn tumors (when present) along the continuum of baseline (prior to NNK exposure), at end of NNK exposure and at three and seven months post-NNK. We separately sequenced normal-appearing tissues and tumors that were needle-dissected out from the lung. Normal-appearing tissues were analyzed alone to determine temporlaly changing gene expression profiles that denote the evolution of the airway field of injury with time during lung tumor development. We also cross-compared the temporally collected lung tumors with the matching normal-appearing lung tissues.

first: H

first: K

last: Chang


title: Small RNA-seq comparing transcriptome (small RNAs) of spermatozoa from mice fed either a control-Diet or a Western-diet for One or Five successive generations

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

country: France

institute: IPMC/CNRS

type: Non-coding RNA profiling by high throughput sequencing

summary: Gene expression analysis of sperm small RNA obtained from mice fed either a control or Western diets for one or five successive generations through the paternal lineage.   The aim of the study is to identify differentially expressed  small RNA in sperm of  obese males which might be involved in the long-term epigenetic inheritance of obesity induced by the maintenance of High Fat Diet feeding for 5 successive generations.

overall_design: Small RNA profiles of spermatozoa from WT mice fed either a control (CD) or Western (WD) diet for one or five successive generations in triplicate.

first: Valérie

last: Grandjean

first: Virginie

last: Magnone

first: Pascal

last: Barbry


title: Codanin-1 Mutations Engineered in Human Erythroid Cells Demonstrate Role of CDAN1 in Terminal Erythroid Maturation

city: Rochester

first: Zachary

middle: C

last: Murphy

state: NY

address: 601 Elmwood Ave box 703

institute: University of Rochester

summary: CDAN1, and residue R1042, have a function in DNA replication and organization in terminal erythroid maturation.

overall_design: Six samples (3 controls and 3 mutants)

first: Laurie

middle: A

last: Steiner


title: E. coli K-12 MG1655 Transcriptome Quantification

city: Stanford

first: Markus

last: Covert

state: CA

address: 443 Via Ortega

department: Bioengineering

institute: Stanford University

summary: To parameterize our computational model of E. coli, we measured gene expression in key conditions.

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

overall_design: For each condition, we measured 3 biological replicates (each replicate cultured on a separate day). As a quality control step prior to sequencing, targeted fold-changes across conditions were measured using qPCR.

middle: W

first: Derek

middle: N

last: Macklin


title: P0.5 WT or Ftsj1 KO mouse brain or liver total mRNA or ribosome-contained mRNA

city: Kumamoto City

first: Takeshi

last: Chujo

state: Kumamoto prefecture

address: 1-1-1 Honjo, Chuo-ku

country: Japan

institute: Kumamoto University

summary: P0.5 WT or Ftsj1 KO mouse brain or liver ribosome-contained mRNAs or total mRNAs, and were sequenced using MiSeq and HiSeq.

overall_design: 3 wild-type male mice and 3 Ftsj1 KO male mice (C57BL/6, neonates)

first: Fan-Yan

last: Wei


title: Commensal Microbiota Regulates Skin Barrier Function And Repair Via Signaling Through The Aryl Hydrocarbon Receptor

city: Wilmington

first: Qi

last: Zheng

state: DE

address: 1701 Rockland Road

institute: Nemours Children's Health

summary: Essential to terrestrial life is the formation of a competent skin barrier that prevents desiccation and entry by harmful substances. A tightly orchestrated series of cellular changes is required for the proper formation of the epidermal permeability barrier. These changes occur in the context of the commensal skin microbiota. Using germ free mice and antibiotic depletion models, we demonstrate the microbiota is necessary for proper differentiation and repair of the barrier. These effects were mediated by keratinocyte signaling through the aryl hydrocarbon receptor (AHR), a xenobiotic receptor that also regulates epidermal differentiation. Murine skin lacking keratinocyte AHR was more susceptible to infection by S. aureus and increased pathology in a model of atopic dermatitis. Topical colonization with a defined consortium of human skin commensals restored barrier competence in germ free skin and during epicutaneous sensitization; these effects were dependent on keratinocyte AHR. We reveal a fundamental role for the commensal skin microbiota in directing skin barrier formation and repair through the AHR, with far-reaching implications for the numerous skin disorders characterized by disrupted epidermal differentiation and/or barrier competence.

overall_design: 24 total RNAseq samples were collected from 3 conditions (SPF, GF and COL) each from 4 female and 4 male replicate animals.

first: Aayushi

last: Uberoi

first: Casey

last: Bartow-McKenny

first: Laurice

last: Flowers

first: Thomas

middle: R

last: Sutter

first: Elizabeth

last: Grice


title: RNA-seq analysis of diabetes treated with FGF1 variants

city: Wenzhou

first: Dezhong

last: Wang

address: Chashan town

department: ILS

country: China

institute: Wenzhou Univsersity

summary: RNA-seq is a powerful tool to analysis differential expression of cellular pathways under different conditions. The goals of this study is to analysis the potential pathways involved in cellular defense against diabetes with or without FGF1 intervention.

overall_design: The 10-week db/db mice were treated with or without FGF1 variant (0.5mg/kg) every other day for 16 weeks. Then, the cardiac tissues were harvested for RNA-Seq analysis.

first: Zhifeng

last: Huang


title: WT or Ftsj1 KO mouse brain

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

overall_design: Refer to individual Series


title: Reprogramming of translation in yeast cells impaired for ribosome recycling favors short, efficiently translated mRNAs

city: Bethesda

first: Swati

last: Gaikwad

state: MD

address: Building 6, Room 233

department: Section on Nutrient Control Of Gene Expression

institute: National Institutes of Health

summary: Yeast strains lacking orthologs of mammalian eIF2D (Tma64), and either MCT-1 (Tma20) or DENR (Tma22) are broadly impaired for 40S recycling; however, it was unknown whether this defect leads to reduced 43S PIC levels with an impact on translation of particular mRNAs. To test this, we by combined ribosome footprint profiling with RNA-seq analysis of mRNA abundance.

overall_design: This study includes a total of 36 samples comprised of 18 RNA-seq samples (mRNA) and 18 ribosome footprint profiling samples (ribo). Experiment 1 includes 12 samples, comprised of 6 RNA-seq samples and 6 ribosome footprint profiling samples, derived from 2 biological replicates each of the BY4741 (WT1) and yeast tma64∆/tma20∆ double mutant H4520 (tma∆∆) which were grown at 30ºC in synthetic complete (SC) medium to log-phase (A600 = 0.5–0.6) and BY4741 grown in SC media lacking isoleucine and valine (SC-Ile/Val) to log-phase (A600 = 0.5–0.6) and treated with the antimetabolite Sulfometuron methyl (SM) at 1 µg/mL for 25 min to induce eIF2α phosphorylation. Experiment 2 examines the effect of the yeast homolog of eIF2D (Tma64) to promote translation initiation on the subset of mRNAs whose translation efficiencies (TEs) are reduced in the tma∆∆ mutant by complementing the function of eIF2 in delivering Met-tRNAi to the 40S subunit. This experiment includes 8 samples, 4 RNA-seq samples and 4 ribosome footprint profiling samples, derived from 2 biological replicates each of WT2 and the tma64∆ mutant 4051, cultured in SC medium at 30ºC. Experiment 3 examines effect of depleting 40S subunit protein on translation efficiencies of strong and weak mRNA and includes 8 samples, 4 RNA-seq samples and 4 ribosome footprint profiling samples, derived from 2 biological replicates each of WT3 strain H2994 and the rps26∆∆ mutant JVY09 were cultured in SC medium (SC medium with 2% galactose+2% raffinose) at 30ºC to log-phase were shifted from galactose- to glucose-containing media for 3h. Experiment 4 examines effect of the transcriptional changes evoked by Gcn4 induction responsible for the translational reprogramming produced by SM treatment of WT cells and includes 8 samples, 4 RNA-seq samples and 4 ribosome footprint profiling samples, derived from 2 biological replicates each of the gcn4∆ mutant 249, cultured in SC with or without SM treatment.

first: Fardin

last: Ghobakhlou

first: David

middle: J

last: Young

first: Jyosthna

last: Visweswariah

first: Hongen

last: Zhang

first: Alan

middle: G

last: Hinnebusch


title: Gene expression profiling of RasV12-induced brain tumors and tumor-associated macrophages

city: Minato-ku

first: Hideto

last: Koso

state: Tokyo

address: 4-6-1 Shirokanedai

institute: Institute of Medical Science, The University of Tokyo

summary: The goal of this study is to profile gene expression patterns of RasV12-induced brain tumors and tumor-associated macrophages (TAM) in the cerebellum. Ras activation in Msi1+ cells induced tumor formation in the cerebellum of Msi1-CreER;RasV12 mice (Ras). GFP+ tumor cells and CD11b+ phagocytes were isolated from the cerebellum of Ras mice at 3 weeks and used for gene expression analysis. GFP+ cells and CD11b+ phagocytes isolated from the cerebellum of Msi1-CreER;GFP mice (Cont) were used as control.

overall_design: mRNA profiles of GFP+ cells and CD11b+ cells in cont and Ras mice were generated by deep sequencing, in triplicate, using Illumina HiSeq3000.


title: Comprehensive analysis of the transcriptome-wide m6A methylome of neonatal heart regeneration via MeRIP sequencing

city: Nanjing

first: Chuanxi

last: Yang

state: China

address: 300 Guangzhou Road, 210029, Nanjing, PR China

department: Department of Cardiology

institute: School of Medicine, Southeast University

summary: Aim: To systematically classify the profile of the RNA m6A modification landscape of neonatal heart regeneration.  Materials and Methods: Cardiomyocyte proliferation markers were detected via immunostaining. The expression of m6A modification regulators was detected using quantitative real-time PCR (qPCR) and Western blotting. Genome-wide profiling of m6A-modified transcripts was conducted with m6A-modified RNA immunoprecipitation sequencing (m6A-RIP-seq) and RNA sequencing (RNA-seq). The Gene Expression Omnibus database (GEO) dataset was used to verify the hub genes.  Results: METTL3 and the level of m6A modification in total RNA were lower in P7 rat hearts than in P0 ones. In all, 1637 m6A peaks were differentially expressed using m6A-RIP-seq, with 84 upregulated and 1553 downregulated. Furthermore, conjoint analyses of m6A-RIP-seq, RNA-seq, and GEO data generated eight potential hub genes with differentially expressed hypermethylated or hypomethylated m6A levels.  Conclusion: Our data show novel information on m6A modification changes in cardiac regeneration. The modifications made possible by directly modulating m6A may attract future study of cardiac regeneration.

overall_design: mRNA profiles and m6A profiles in heart tissues  of 0 day old and 7 day old rat.

first: Kun

last: Zhao

first: Jing

last: Shi


title: The SWELL1-LRRC8 complex regulates endothelial AKT-eNOS-mTOR signaling and vascular function

city: Iowa City

first: Chad

last: Grueter

state: Iowa

address: 285 Newton Rd, 4332 PBDB, 285 Newton Rd

institute: University of Iowa

summary: We used RNA-Sequencing to quantify the changes in global mRNA expression in wild-type as compared to SWELL1 (LRRC8a) knock down of human umbilical vein endothelial cells (HUVECs).

overall_design: We treated HUVECs with adenoviruses containing either Ad5-mCherry-U6-hLRRC8A-shRNA to knockdown SWELL1 or Ad5-U6-scramble-mCherry as a control. These cell lines were grown in culture and RNA was extracted for sequencing under basal culture conditions. RNA was sequenced on an Illumina Hi-Seq at the University of Iowa Core Facility.

first: Rajan

last: Sah

middle: E


title: Chronic restraint stress increases transcriptomic indicators of biological aging in mouse bone marrow leukocytes

city: Los Angeles

first: Donald

middle: M.

last: Lamkin

address: 300 UCLA Medical Plaza, Room 3160

department: Semel Institute for Neuroscience

institute: UCLA

summary: Genome-wide transcriptional profiling results were used to examine the effect of a psychological stress paradigm for rodents (chronic restraint) on indicies of biological aging in murine femoral bone marrow leukocytes and to assess the extent to which propranolol could block such effects.

overall_design: Total RNA was obtained from flow sorted bone marrow leukocytes that were gated to exclude prior-engrafted human acute lymphoblastic leukemia cells in male 6-8 week old SCID mice (CB17/Icr-Prkdcscid ) that had been randomzed to control condition, restraint stress condition, or restraint stress plus propranolol condition.  TELiS was used to bioinformatically assess differences in transcription factor activity among conditions. Composite transcriptome representation analyses were used to assess differences among conditions in the DNA repair gene transcriptome and the senescence associated secretory phenotype (SASP) transcriptome.

middle: M


title: Macrophages of embryonic origin function during early life to determine host iNKT cell levels at barrier surfaces III

city: Boston

first: Thomas

last: Gensollen

address: 77 Avenue Louis Pasteur

department: Gastroenterology

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

summary: It is increasingly recognized that immune development within mucosal tissues is under the control of environmental factors during early life. However, the cellular mechanisms that underlie such temporally and regionally restrictive governance of these processes is unclear. Here, we uncover an extrathymic pathway of immune development within the colon that is controlled by embryonic, but not bone-marrow derived, macrophages which determines the ability of these organs to receive invariant natural killer T (iNKT) cells and allow them to establish local residency. Consequently, early life perturbations of fetal-derived macrophages result in persistent decreases of mucosal iNKT cells and is associated with later life susceptibility or resistance to iNKT cell associated mucosal disorders. These studies uncover a host developmental program orchestrated by ontogenically distinct macrophages that is regulated by microbiota and reveal an important post-natal function of macrophages that emerge in fetal life.

overall_design: Pathogen free iNKT cell types

first: Xi

last: Lin

first: Ting

first: Michal

last: Pyzik

first: Peter

last: See

first: Jonathan

last: Glickman

first: Florent

last: Ginhoux

first: Matthew

last: Waldor

first: Marko

last: Salmi

first: Pia

last: Rantakari

first: Richard

middle: S

last: Blumberg


title: Gene Expression Data from Influenza A Virus-Infected and Mock-infected A549 Human Aveolar Epithelial Carcinoma Cells with Exposure to Mouse Eosinophils.

city: Memphis

first: Robert

last: Rooney

state: TN

address: 50 N. Dunlap, Room 366R, LeBonheur CFRC

department: Pediatrics

institute: University of Tennessee Health Science Center

summary:
Eosinophils are terminally differentiated granulocytes that participate in innate immunity against Influenza A Virus (IAV).  Here, we investigate transcriptional changes that occur in IAV-infected human A549 aveolar epithelial carcinoma cells with and without direct or indirect exposure to mouse bone marrow-derived eosinophils (BMdEos).
Global changes in the transcriptome of A549 cells due to Influenza A virus-infection and/or direct and indirect eosinophil exposure were assessed using ThermoFisher/Affymetrix Clariom™ S Human microarrays.

overall_design: RNA was isolated from confluent monolayers of A549 cells that were infected with 0.5 MOI of IAV strain pH1N1 or mock-infected, and co-cultured directly or indirectly with BMdEos or with no BMdEos for three days at 37ºC with 5% CO2.

first: Meenakshi

last: Tiwary

first: Amali

last: Samarasinghe


title: 8-week WT or Ftsj1 KO mouse brain total mRNAs and ribosome-contained mRNAs

first: Takeshi

last: Chujo

summary: 8-week mouse brain ribosome-contained mRNAs and total mRNAs were collected and sequenced.

overall_design: 3 wild-type male mice and 3 Ftsj1 KO male mice (C57BL/6, 8-week old)

first: Fan-Yan

last: Wei


title: Atractylenolide I enhances responsiveness to immune checkpoint blockade therapy by activating tumor antigen presentation

city: Indianapolis

first: Chi

last: Zhang

state: IN

institute: INDIANA UNIVERSITY

summary: One of the primary mechanisms of tumor cell immune evasion is the loss of antigenicity, which arises due to lack of immunogenic tumor antigens as well as dysregulation of the antigen processing machinery. In a screen for small-molecule compounds from herbal medicine thatpotetiate T cell-mediated cytotoxicity, we identified atractylenolide I (ATT-I) that significantly promotes tumor antigen presentation of both human and mouse colorectal cancer (CRC) cells and thereby enhances the cytotoxic response of CD8+ T cells. Cellular thermal shift assay (CETSA) with multiplexed quantitative mass spectrometry identified the proteasome 26S subunit non-ATPase 4 (PSMD4), an essential component of the immunoproteasome complex,as a primary target protein of ATT-I. Binding of ATT-I with PSMD4 augments the antigenprocessing activity of immunoproteasome, leading to enhanced major histocompatibility class I(MHC-I)-mediated antigen presentation on cancer cells. In syngeneic mouse CRC models and human patient-derived CRC organoid models, ATT-I treatment promotes the cytotoxicity of CD8+ T cells and thus profoundly enhances the efficacy of immune checkpoint blockade therapy. Collectively, we show here that targeting the function of immunoproteasome with ATT-I promotes tumor antigen presentation, empowers T-cell cytotoxicity, and thus elevates the tumorresponse to immunotherapy.

overall_design: Cancer microenvironment profile with different drug treatment.

first: Xiongbin

last: Lu


title: Pancreatic cancer prognosis is predicted by chromatin accessibility (RNA-Seq)

city: New York

first: Sagar

last: Chhangawala

address: 1300 York Ave.

department: PBSB

institute: Weill Cornell Medical College

summary: About 50% of resected pancreatic ductal adenocarcinoma (PDAC) recur within just one year following surgery. Prognostic molecular markers predicting rapid recurrence are currently unavailable. We hypothesized that epigenetic differences at the level of chromatin accessibility, potentially linked to distinct differentiation states, might distinguish rapidly recurrent from non-recurrent tumors.  Therefore, we interrogated genome-wide chromatin accessibility using Assay for Transposase-Accessible Chromatin sequencing (ATAC-seq) on EpCAM+ PDAC malignant cells sorted from a cohort of 54 treatment-naïve resected tumors, in hopes of defining a tumor-intrinsic chromatin signature associated with recurrence. We discovered a signature of ~1000 loci that were differentially accessible between recurrent (disease free survival (DFS) < 1 year) and non-recurrent patients (DFS > 1 year).  Through transcription factor (TF) binding motif analysis using supervised learning, we identified candidate TFs whose accessible motifs were differentially associated with recurrence. Nuclear localization of two such TFs as selected by top hits, ZKSCAN1 and HNF1b, were assessed by both immunohistochemistry and immunofluorescence on the tissue microarrays (TMA) of 40 out of 54 patients.  Nuclear staining of HNF1b was strong in the non-recurrent and weak or absent in the recurrent patients but ZKSCAN1 was not significantly associated with recurrence. In an independent TMA of PDAC cohort (n=97) preselected for 52 long (OS 6 years)- and 45 short (OS 6 months)- term survivors, the number of nuclear positive cells for HNF1b was 52-fold higher in the long-term compared to the short-term survivors and that for ZKSCAN1 was 5.3-fold higher in the short-term compared to the long-term survivors. Altogether, these results provide novel prognostic molecular markers of early recurrence in PDAC and also suggest that the global epigenetic landscape is a prognostic feature in this disease.

overall_design:
54 PDAC primary tumor samples sequenced in duplicates
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*Submitter declares that the raw data will be deposited in dbGaP due to patient privacy concerns

first: Steven

last: Leach

first: Christina

last: Leslie

first: Surajit

last: Dhara


title: Differential gene expression analysis to identify canonical Wnt signaling target genes in QR neuroblast descendants in C. elegans

city: Utrecht

first: Rik

last: Korswagen

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute

summary: Activation of canonical Wnt signaling is sufficient and necessary to inhibit the migration of the QR.pa neuroblast of C. elegans. To identify targets of canonical Wnt signaling involved in this process we isolated QR lineage descendants by FACS from control (mab-5(gk670) mutant) animals and animals expressing a constitutively active, N-terminally truncated form of BAR-1/β-catenin in the QR lineage using the egl-17 promoter (ΔN-BAR-1Q). FACS isolation was based on the expression of mCherry and GFP markers under the control of wrt-2 and egl-17 promoters, respectively. We performed differential gene expression analysis to identified genes that are differentially expressed between control and constitutive activation of canonical Wnt signaling.

overall_design: mRNA profiles of QR descendants from control (mab-5(gk670) mutant) and ΔN-BAR-1Q larvae were generated from pools of 2000 cells with CEL-seq protocol, in triplicate, using Illumina HiSeq 2500.

first: Lorenzo

last: Rella

first: Euclides

last: Fernandes Póvoa

first: Annabel

last: Ebbing

first: Jonas

last: Mars

first: Luc

last: Schoppink

first: Marco

last: Betist

first: Hendrik


title: Loss of canonical splicing factor SRSF1 in hepatocytes results in acute liver injury and regeneration

city: Urbana

first: Waqar

last: Arif

state: IL

address: 506 S. Mathews Avenue

department: Biochemistry

institute: UIUC

summary: Post-transcriptional gene regulatory mechanisms (PTGRM) contribute profoundly to liver development and physiology. Alternative splicing is one of the earliest mechanisms of gene regulation acting on nascently transcribed mRNA. This process is mediated by a large class of proteins known as splicing factors. SRSF1 is a canonical splicing factor with roles in both constitutive and alternative splicing. While its biochemical activities have been studied extensively, its role in tissue physiology are not well defined. In this study we investigate the role of SRSF1 in liver physiology using hepatocyte-specific knock-out mice models. Hepatocyte-specific knock-out of SRSF1 was achieved in two ways; 1) SRSF1 floxed mice were crossed with AlbCre transgenic mice and 2) SRSF1 floxed mice were injected with AAV8-TBG-iCre viral vector. The latter model allowed for investigating acute changes in hepatocyte upon ablation of SRSF1. Both models exhibit acute liver injury with severe cellular damage, inflammation and lipid accumulation. Utilizing high-throughput transcriptome profiling on purified hepatocytes, we find acute loss of SRSF1 triggers activation of the p53 pathway and splicing dysregulation of genes involved in mRNA metabolism. Continuous hepatic injury in this model eventually triggers a regenerative response resulting in the upregulation of genes involved in proliferation and repopulation of the tissue parenchyma.

overall_design: Hepatocytes were isolated from two different mice models of hepatocyte-specific knock-out of SRSF1 referred to as SRSF1 HKO and SRSF1 acHKO. For the SRSF1 HKO model, samples were prepared at post-natal day 10 and 1 month developmental time points. For the SRSF1 acHKO model, samples were prepared two weeks after viral mediated acute knock-out. Total RNA was prepared from all samples and and sequenced on an Illumina platform after preparing polyA selected RNA-Seq libraries.

first: Auinash

last: Kalsotra


title: Integrating metabolomics and transcriptomics reveals convergent pathways driving radiation-induced salivary gland dysfunction

city: Tucson

first: Megha

last: Padi

state: Arizona

address: 1515 N Campbell

institute: University of Arizona

summary:
Purpose: The goal of this study is to integrate NGS-derived parotid salivary gland transcriptome profiling (RNA-seq) to metabolomics (UPLC-MS/MS) methods and identify mechanisms driving radiation-induced xerostomia, with potential clinical application to head and neck cancer patients.
Methods: Parotid salvary gland mRNA profiles of 28-day-old wild-type (WT) and 5 Gy radiation treated mice were generated by deep sequencing, in triplicate, using Illumina TruSeq. The sequenced reads that passed quality filters were trimmed with Trimmomatic, mapped to mm10 genome with HISAT2, and summarized at the gene level with HTSeq-count and analyzed with DESeq2.
Results: Using an optimized data analysis workflow, we mapped sequenced reads per sample to the mouse genome (build mm10) and identified 25422 genes with at least 1 read in the parotid glands of WT and radiation treated mice with HISTA2 workflow. RNA-seq data QA/QC by Principal Component Analysis showed a clear separation between conditions. 155 genes showed significant differential expression between the WT and radiation treated salivary gland, with an adjsuted p-value < 0.05. Pre ranked Gene Set Enrichment Analysis against the CPDB database led to 859 altered pathways with a p-value < 0.05. Integrative analysis pointed to 103 RNA-Seq/Metabolite joint enriched pathways with a p-value < 0.05.

overall_design: Parotid salivary gland mRNA profiles of 28-day old wild type (WT) and radiation treated mice

first: Lauren

last: Meeks

first: Diogo

last: de Oliveira Pessoa

first: Jessica

last: Martinez

first: Kirsten

middle: H

last: Limesand


title: Describing molecular coupling of the estrogen receptor and coregulators and its crosstalk with retinoic acid receptors in breast cancer

city: Montpellier

first: Gabriel

last: Jimenez-Dominguez

state: Occitanie

address: 208 Avenue des apothicaires

department: Hérault

institute: Institut de Recherche en Cancérologie de Montpellier (IRCM)

summary:
Purpose: We exploit transcriptomic data to shed light on the functional consequences of ER-RAR crosstalk mediated by RIP140 and LCoR. We compare ligand-stimulated conditions with and without knocked down of RIP140 and LCoR.
We also assess the additive  versus synergistic nature of global transcriptional changes by comparing separate 17-β estradiol (E2) and retinoic acid (RA) induced transcriptomes with the transcriptome induced by simultaneous E2 and RA stimulation.

overall_design: 16 experimental conditions available, 1 duplicate in 1 cell line (MELN)

first: Stéphan

last: Jalaguier

first: Vincent

last: Cavaillès

first: Jacques

last: Colinge

first: Patrice

last: Ravel


title: Comparison of transcriptome between E8I knock-out and wild type mouse during CD4 CTL polarization in vitro

city: Yokohama

first: kiyokazu

last: kakugawa

state: Kanagawa

address: 1-7-22 Suehiro-cho

department: IMS

institute: Riken

summary: The expression of key transcription factors drives CD4 T cells to develop into functional T helper (Th) subsets, each characterized by secretion of particular cytokines.  This process is critical for normal immune function.  CD4 T cells can also reprogram to cytotoxic T lymphocytes (CTL), but the key transcriptional mechanism that controls this process has not been defined.  Cytokine TGFb, an important regulator of CD4 Th subset differentiation induces the master transcription factor, Foxp3 in induced regulatory T cells (iTreg) or Rorc in IL-17-secreting T cells (Th17 cells).  TGFb is also important for the CD4 CTL differentiation, characterized by T-BET and RUNX3 expression whereas Foxp3 and Rorc genes are repressed in these cells. Here we identify, a long intergenic noncoding RNA transcribed from the Cd8 locus (Cd8LncRNA), as critical for the coordinated expression and function of T-BET and RUNX3 combined with Foxp3 and Rorc suppression in CD4 CTL. Since this LncRNA overlaps CD8 locus enhancer (E8I), we first analyzed the effect of LncRNA deletion for CD4 T cell polarization using E8I knock-out mouse. These findings define Cd8LincRNA as a key controller of the helper versus cytotoxic gene expression profile in differentiating CD4 effector T cells. The action of this LncRNA adds another layer of regulation of CD4 T cell functions and expands the opportunity to define new drug targets for the treatment of cancers, infections and inflammatory diseases.

overall_design: mRNA profiles of wild type (WT) and E8IKO (PMID:9806635) mice during CD4 CTL differentiation in vitro were generated by RNA sequencing.

first: Hitoshi

last: Iwaya

first: Alexandre

last: Larange

first: Kiyokazu

last: Kakugawa

first: Ryo

last: Shinnakasu

first: Gisen

last: Kim

first: Yiran

last: Wang-Zhu

first: Ichiro

last: Taniuchi

first: Mitchell

last: Kronenberg

first: Hilde

last: Cheroutre


title: DIS3 dysfunction suppresses altered alternative splicing in cells with the depletion of U2 snRNP component

city: Warsaw

first: Anna

middle: Maria

last: Hojka-Osinska

address: 4 Ks. Trojdena Street

country: Poland

institute: International Institute of Molecular and Cell Biology

summary: Precise analysis of DIS3 interactors disclosed in genome-wide siRNA screening revealed enrichment in genes responsible for transcription and processes highly connected to it like splicing and 3’ end formation. Among the strongest positive interactors were components of of SF3a complex and some of SF3b complex. SF3a complex is a substantial integral component of the pre-spliceosome and is required for complex A and B assembly and plays crucial role in initial steps of spliceosome assembly.Transcriptome analysis demonstrated that depletion of SF3A1, one of three SF3a complex components, lead to extensive alterations in multiple classes of alternative splicing events (ASE). Remarkably, the only group of ASE that was reshaped in the presence of DIS3 dysfunction was intron retention. Detailed investigations of transcripts with altered intron retention revealed high enrichment in transcripts coding ribosomal proteins (Rps).

overall_design: To investigate diffrential pre-mRNA splicing, total RNA samples were collected from model cell lines producing either WT or mut DIS3 under tetracyclin induction that were treated with SF3A1 siRNA or control scrambled siRNA. Two replicate samples were prepared for RNA-Seq.

first: Andrzej

last: Dziembowski


title: Expression data from rosette leaves of Arabidopsis thaliana wild type and rmpA/rmpB double transgenic exposed to formaldehyde

city: Kinokawa

first: Katsura

last: Izui

state: Wakayama

address: 930 Nishimitani

department: School of Biology-oriented Science and Technology

institute: Kinki University

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

overall_design: Refer to individual Series


title: Drosophila melanogaster Mutated in its GBA1b Ortholog Recapitulates Neuronopathic Gaucher Disease

city: Tel Aviv

first: Metsada

last: Pasmanik-Chor

address: Ramat Aviv

department: Biology

country: Israel

institute: Tel Aviv University

summary: Gaucher disease (GD) results from mutations in the GBA1 gene, which encodes lysosomal glucocerebrosidase (GCase). The large number of mutations known to date in the gene lead to a heterogeneous disorder, which is divided into a non-neuronopathic, type 1 GD, and two neurological, type 2 and type 3, forms. We studied the two fly GBA1 orthologs, GBA1a and GBA1b. Each contains a Minos element insertion, which truncates its coding sequence. In the GBA1am/m flies, which express a mutant protein, missing 33 C-terminal amino acids, there was no decrease in GCase activity or substrate accumulation. However, GBA1bm/m mutant flies presented a significant decrease in GCase activity with concomitant substrate accumulation, which included C14:1 glucosylceramide and C14:0  glucosylsphingosine. GBA1bm/m mutant flies showed activation of the Unfolded Protein Response (UPR) and presented inflammation and neuroinflammation that culminated in development of a neuronopathic disease. Treatment with ambroxol did not rescue GCase activity or reduce substrate accumulation; however, it ameliorated UPR, inflammation and neuroinflammation, and increased life span. Our results highlight the resemblance between the phenotype of the GBA1bm/m mutant fly and neuronopathic GD and underlie its relevance in further GD studies as well as a model to test possible therapeutic modalities.

overall_design: Known GD molecular hallmarks in the two existing GBA1 mutant lines (GBA1am/m and GBA1bm/m) in drosophila were tested.

first: Or

last: Cabasso

first: Sumit

last: Paul

first: Orly

last: Dorot

first: Gali

last: Maor

first: Olga

last: Krivoruk

first: Mina

last: Mirzaian

first: Maria

last: Ferraz

first: Johannes

last: Aerts

first: Mia

last: Horowitz


title: MicroRNA Sequencing of CD34+ Sorted Adipose Stem Cells (ASCs) Undergoing Endotheliogenesis

city: Baton Rouge

first: shahensha

last: shaik

state: LA

address: 3261 Patrick F Taylor Hall

department: Department of Mechanical Engineering

institute: Louisiana State University

summary: In this study, CD34+ ASCs sorted using magnetic bead separation were induced to differentiate along the endothelial pathway. miRNA sequencing of ASCs at day 3, 9 and 14 of endothelial differentiation was performed on Ion Proton sequencing system. The data obtained by this high-throughput method was aligned to the human genome HG38 and the differentially expressed miRNAs during endothelial differentiation at various timepoints (day 3, 9 and 14) were identified.

overall_design: Identifying miRNAs during endotheliogenesis of CD34+ ASCs at different time points

first: Shahensha

last: Shaik

first: Elizabeth

last: Martin

first: Daniel

last: Hayes

first: Jeffrey

last: Gimble

first: Ram

last: Devireddy


title: The Intrinsic Activity of Thyroxine is Critical for Survival and Growth and Regulates Gene expression in Neonatal Liver

city: Lebanon

first: Valerie

middle: Anne

last: Galton

state: New Hampshire

address: 1 Medical Center Drive

department: Physiology and Neurobiology

institute: Dartmouth Geisel School of Medicine

summary: Background: Thyroxine (T4) is generally considered to be a pro-hormone that requires conversion to 3,5,3’-triiodothyronine (T3) to exert biological activity. Although evidence suggests that T4 has intrinsic activity, it is questionable if this activity has any physiological relevance. Methods: To answer this question, triple KO mice (Triples) that cannot express the types 1 (D1) and 2 (D2) deiodinase and the Pax8 genes were generated. Thus they lack a thyroid and cannot convert T4 to T3.  Triples were injected on alternate days with either vehicle or physiological doses of T4, T3 or T3+T4 from postnatal days 2 to 14.  They were euthanized at P15 and RNA-seq was employed to profile gene expression in liver. In another experiment, Pax8KO mice were injected with T3, T4 or T4 +T3, and growth rate and survival to P84 were determined. Results: The growth retardation of Triples was not improved by either T3 or T4 alone but was significantly improved by T4+T3.  In liver, T4 significantly regulated the expression of genes that were also regulated by T3, but the proportion of genes that were negatively regulated was higher in mice treated with T4 than with T3. Treatment with T4+T3 identified genes that were regulated synergistically by T3 and T4, and genes that were regulated only by T4+T3.  Analysis of these genes revealed enrichment in mechanisms related to cell proliferation and cholesterol physiology, suggesting a unique contribution of T4 to these biological functions. Pax8KO mice all survived to P84 when injected with T4 or T4+T3 but survival rate with T3 was 50% and 10% at 3.5 and 12 weeks of life, respectively. Conclusion: T4 has intrinsic activity in vivo and is critical for survival and growth. At a physiological level, T4 per se can up- or down-regulate many T3 target genes in the neonatal liver. While most of these genes are also regulated by T3, subsets respond exclusively to T4 or demonstrate enhanced or normalized expression only in the presence of both hormones. These studies demonstrate for the first time a complex dependency on both T4 and T3 for normal mammalian growth and development.

overall_design: newborn mice lacking a thyroid and type 1 and type 2 deiodinases as well as littermate controls with a thyroid were injected with vehicle, T3, T4 or T3+T4 for two weeks

last: Martinez

first: Julie

last: Dragon

first: Donald

middle: L

last: St Germain

first: Arturo

last: Hernandez


title: 8-week WT or Ftsj1 KO mouse brain tRNA and tRF MiSeq

city: Kumamoto City

first: Takeshi

last: Chujo

address: 1-1-1 Honjo, Chuo-ku

institute: Kumamoto University

summary: 8-week brain total tRNA, total tRNA fragments (tRFs), and ribosome-contained tRNAs were sequenced using MiSeq.

first: Fan-Yan

last: Wei


title: Extensive Sub-RPE Complement Deposition in a Nonhuman Primate Model of Early Stage Diabetic Retinopathy

city: Stockholm

first: Jiawei

last: Zhong

address: Blickagången 16, Flemingsberg

department: Department of Medicine, Huddinge

country: Sweden

institute: Karolinska Institutet

summary:
Purpose: This study aims to reveal retinal abnormities in a spontaneous diabetic nonhuman primate (NHP) model and explore the mechanism of featured injuries.
Methods: Twenty-eight cynomolgus monkeys were identified to suffer from spontaneous Type 2 diabetes from a colony of more than eight hundred aged monkeys and twenty-six age-matched ones were used as controls. Their blood biochemistry profiles were determined and the retinal changes were examined by multimodal imaging, hematoxylin-eosin (H&E) staining and immunofluorescence. Retinal pigment epithelium (RPE) cells were isolated and determined by RNA-sequencing  and computational analyses.
Results: Diabetic monkeys were characterized by early vascular and neural damage in the retina and dyslipidemia. The typical acellular capillaries and pericyte ghost were found in the diabetic retina, which also exhibited reduced retinal nerve fiber layer (RNFL) thickness compared to the controls. Of note, distinct sub-RPE drusenoid lesions were extensively observed in these diabetic monkeys and complements deposition including C3 and C5b-9 were accumulated in these lesions. The RNA-seq data of RPE cells showed complement activation, AGE/RAGE activation and 18 inflammatory response at the setting of diabetes. Consistently, the plasma levels of C3 and C4 were also increased in the diabetic monkeys.
Conclusions: The spontaneous Type 2 diabetic cynomolgus monkeys featured with early-stage retinopathy including not only typical vascular and neural damage, but also a distinct sub-RPE deposition. The complement activation and metabolic stress of RPE cells in response to hyperglycemia might contribute to the deposition, revealing an unrecognized role of RPE cells in the early-stage pathological process of diabetic  retinopathy (DR).

overall_design: RPE cells were collected from 3 diabetic and 3 control subjects using an ophthalmic spatula. Total RNA was purified using a TRIzol (Thermo Fisher Scientific) in accordance with the manufacturer’s protocol. The RNA sample quality was confirmed by the Agilent 2100 Bioanalyzer (Agilent Technologies). Libraries were constructed using the TruSeq RNA-Seq kit (Illumina) following the manufacturer’s instructions. After evaluating the quality by Agilent 2100 Bioanalyzer, libraries were pooled and sequenced on Illumina Hiseq X10.


title: Expression data from rosette leaves of Arabidopsis thaliana which has formaldehyde tolerance (rmpA/rmpB double transgenic) upon formaldehyde exposure

first: Katsura

last: Izui

summary: Formaldehyde is a toxic volatile organic compound and its mechanism of toxicity to plant has not yet been revealed. This experiment was designed to identify formaldehyde-responsible genes under exposure to low or high concentration of airborne formaldehyde for a short period of time. 7 weeks old Arabidopsis thaliana transformant (ecotype: Columbia) plants were exposed to gaseous formaldehyde at 1-2 ppm (low), 14-16 ppm (high), or less than 0.04 ppm (air control) at 24oC under light-condition for 150 minutes inside a chamber for formaldehyde exposure. Total RNA was isolated from rosette leaves of exposed plants and was applied to microarray analysis. We investigated into formaldehyde dose response on gene expression of Arabidopsis and tried to understand the toxic mechanisms of formaldehyde using an Affymetrix Arabidopsis genome array ATH-1.

overall_design: In this study, we used Arabidopsis thaliana Columbia double transgenic plants that expressed 3-hexulose-6-phosphate synthase gene (rmpA) and 6-phospho-3-hexuloisomerase gene (rmpB) from Mycobacterium gastri MB19 in chloroplasts (Chen et al. 2010). The transgenic plants (Arabidposis AB plants) can assimilate and tolerant to formaldehyde. 7 weeks old Arabidopsis thaliana (Col) AB plants were exposed to gaseous formaldehyde at 1-2 ppm (low), 14-16 ppm (high), or less than 0.04 ppm (air control) at 24oC under light condition for 150 minutes inside of exposure chamber. When exposed under each condition, 3 plants were placed inside the exposure chamber, and these plants were treated as replications. In addition to treatment samples, non-treatment plants that were placed outside the chamber at 24oC under light-condition for 150 minutes until exposure were also prepared. Total RNA was isolated from rosette leaves of plants. In total, 12 samples were used in this experiment.

first: Shigeru

last: Kubo

first: Emi

last: Sudo

first: Hitoshi

last: Sakakibara


title: Expression data from rosette leaves of Arabidopsis thaliana wild type upon formaldehyde exposure

summary: Formaldehyde is a toxic volatile organic compound and its mechanism of toxicity to plant has not yet been revealed. This experiment was designed to identify formaldehyde-responsible genes under exposure to low or high concentration of airborne formaldehyde for a short period of time. 7-weeks old Arabidopsis thaliana wild type (ecotype: Columbia) plants were exposed to gaseous formaldehyde at 1-2 ppm (low), 14-16 ppm (high), or less than 0.04 ppm (air control) at 24oC under light-condition for 150 minutes inside a chamber for formaldehyde exposure. Total RNA was isolated from rosette leaves of exposed plants and was applied to microarray analysis. We investigated into formaldehyde dose response on gene expression of Arabidopsis and tried to understand the toxic mechanisms of formaldehyde using an Affymetrix Arabidopsis genome array ATH-1.

overall_design: 7-week old Arabidopsis thaliana wild type (ecotype: Columbia) plants were exposed to gaseous formaldehyde at 1-2 ppm (low), 14-16 ppm (high), or less than 0.04 ppm (air control) at 24oC under light condition for 150 minutes inside of exposure chamber. When exposed under each condition, 3 plants were placed inside the exposure chamber, and these plants were treated as replications. In addition to treatment samples, non-treatment plants that were placed outside the chamber at 24oC under light-condition for 150 minutes until exposure were also prepared. Total RNA was isolated from rosette leaves of plants. In total, 12 samples were used in this experiment.


title: Effects of androgen receptor degradation by PROTAC ARCC-32 on gene expression in LN95 prostate cancer cells

status: Public on Mar 30 2021

first: Steven

last: Balk

state: MA

address: 330 Brookline Avenue

institute: Beth Israel Deaconess Medical Center

summary: RNA-seq was performed in duplicate on LN95 prostate cancer cells at 16, 24, and 48 hours after degrdation of full length androgen recpetor by ARCC-32

overall_design: LN95 prostate cancer cells, which express both full length androgen receptor (AR-FL) and the V7 splice variant (AR-V7) were cultured in steroid depelted medium. They were then treated with a PROTAC (ARCC-32) that selectively degrades AR-FL, and assessed for gene expression in duplicate after 16, 24, or 48 hours versus vehicle control treated cells.

first: Jiaqian

last: Liang

first: Liyang

last: Wang

first: Mannan

last: Nouri

first: Larysa

last: Poluben

first: Seiji

last: Arai

first: Lisha

last: Xie

first: Olga

last: Voznesensky

first: Xin

last: Yuan

first: Joshua

last: Russo

first: Shaoyong

last: Chen

middle: P


title: RNA-seq analysis of control and MCUR1-depleted HSCs - BioProject

city: Beijing

first: Yiming

last: Lu

address: Taiping Road

institute: State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine

summary: We sought to explore the underlying mechanisms by which MCUR1 promotes erythropoiesis. Total RNAs were extracted from cultured human CD34+ HPCs stably expressing sh-MCUR1 or sh-Ctrl under hypoxia (1% O2) following 2 days of EPO stimulation, using TRIZOL Reagent (Invitrogen, CA, USA). RNA sequencing (RNA-seq) was performed using Illumina NovaSeq6000 at Berry Genomics Co. Ltd. (Beijing, China), and a mean of 40 million paired-end reads per sample was obtained.

overall_design: mRNA profiles of NC and sh-MCUR1 CD34+ HPCs

first: Jie

last: Ping


title: RNA sequencing of cells transfected with SSE mimetics

city: San Francisco

first: Hani

last: Goodarzi

state: CA

department: Biochemistry and Biophysics

institute: UCSF

summary: We used RNA sequencing to measure the transcriptomic consequences of transfecting cells with SSE mimetics (compared to scrambled controls).

first: H

first: L

last: Fish

last: Nguyen


title: Monocytes as endogenous immunologic biosensors: identification of inflammatory, adhesion, and mTOR-related signatures in psoriasis

city: Cleveland

first: Mark

last: Cameron

state: OH

address: 10900 Euclid Ave

department: Population and Quantitative Health Sciences

institute: Case Western Reserve University

summary: Psoriatic monocyte singlets and doublets (MonD) have a distinct gene expression profile compared to singlet control monocytes. Furthermore, there is dysregulation of adhesion markers, tetraspanins, adipocytokines, and mTOR-related genes in singlets and doublets from both psoriatic and control individuals.

overall_design: 12 individuals (8 healthy controls and 4 psorasis patients); 24 total samples (classical monocytes and monocyte doublets for each individual)

first: J

last: Golden

first: B

last: Richardson

first: D

last: Seth

first: S

last: Goldberg

first: T

last: McCormick

first: K

last: Cooper

first: M


title: Role of Top1 and Genome structure in SARS-CoV-2 infection [RNA-Seq human]

first: Sook Yuin Jessica

last: Ho

state: New York

address: 1468 Madison Avenue

department: Microbiology

institute: Icahn School of Medicine at Mount Sinai

summary: The ongoing pandemic caused by Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) is currently affecting millions of lives worldwide. Large retrospective studies indicate that an elevated level of inflammatory cytokines and pro-inflammatory factors are associated with both increased disease severity and mortality. Targeting these pathways might therefore be a viable therapeutic strategy. Previously, we have reported that chromatin factors such as Topoisomerase I (Top1) play key roles in controlling the induction of inflammatory gene expression programs. Here, by using multidimensional epigenetic, transcriptional, in vitro and in vivo analyses, we show that Topoisomerase 1 (Top1) inhibition in infected cells and animals suppresses lethal inflammation induced by SARS-CoV-2.

overall_design: To study alterations in genome structure after SARS-CoV-2 infection, we performed Hi-C on SARS-CoV-2 infected A549-ACE2 cells at 0,8 and 24 hours post infection. Experiment was done in biological duplicate. Each biological replicate was sequenced with 4 technical replicates. To study the impact of Top1 on the inflammatory response to SARS-CoV-2, we knocked-down TOP1 expression using siRNA in A549-ACE2 cells. Cells were then left uninfected or infected with SARS-CoV-2. Cells that were not treated with siRNA (no siRNA) or scrambled siRNA (siSCR) were used as controls. The experiment was done in triplicate.

first: Jessica

first: Bobo

last: Mok

first: Laura

last: Campisi

first: Tristan

last: Jordan

first: Soner

last: Yildiz

first: Sreeja

last: Parameswaran

first: Joseph

last: Wayman

first: Natasha

last: Gaudreault

first: David

last: Meekins

first: Sabarish

middle: V

last: Indran

first: Igor

last: Morozov

first: Jessie

middle: D

last: Trujillo

first: Yesai

last: Fstkchyan

first: Raveen

last: Rathnasinghe

first: Zeyu

last: Zhu

first: Simin

last: Zheng

last: Zhao

first: Kris

last: White

first: Helen

last: Ray-Jones

first: Valeriya

last: Malysheva

first: Michiel

last: Thiecke

first: Siu-Ying

last: Lau

first: Honglian

last: Liu

first: Anna

last: Zhang

first: Andrew

last: Lee

first: Wen-Chun

first: Teresa

last: Aydillo

first: Betsaida

last: Melo

first: Ernesto

last: Guccione

first: Robert

last: Sebra

first: Elaine

last: Shum

first: Jan

last: Bakker

last: Kaufman

first: Andre

last: Moreira

first: Mariano

last: Carossino

first: Udeni

middle: B

last: Balasuriya

first: Minji

last: Byun

first: Emily

last: Miraldi


title: Transcriptome profiling reveals the regulatory role of CSA-mediated photoperiod-dependent male fertility

city: Shanghai

first: Jingbin

last: Li

address: 800 Dongchuan Road

institute: Shanghai Jiao Tong University

summary: The discovery of photoperiod-sensitive male genic sterile (PGMS) lines started the development of two-line hybrid rice, which is critical to sustain production of high-yielding hybrid rice varieties. Previous reports about the PGMS lines are mainly focused on the gene cloning and their function description. The mechanisms by which PGMS lines perceive changes in photoperiod and transmit those signals to elicit downstream effects is rarely mentioned. In this work, we described the effects of photoperiod on gene expression in wild type (WT) and csa, a PGMS line, flag leaves and anthers to identify putative central factors that transduce photoperiod signals via CSA in both leaves and anthers. We also dissect the potential mechanisms that: cause csa-induced sterility under SD conditions; partially restore fertility in csa anthers under LD conditions; and finally, are responsible to restore full WT fertility under LD and SD conditions. These results provide an overview how the PGMS rice perceives and transmits photoperiod changes, and how the CSA and its homologs response to the environmental cues by regulating down-stream gene expression. That will be helpful to understand the photoperiod-sensitive mechanism and identify new photoperiod-sensitive genes.

overall_design: At Stage12 of the anther development, flag leaves were collected at 08:00,12:00,16:00,20:00,00:00, 04:00 for a whole period under short-day(12 hours light) and long-day(14.5 hours light) condition. Anther was collected at 16:00 and 4:00 from the same tillers with the flag leaves. Each sample have two biological replicates.

first: Duoxiang

last: Wang

first: Shiyu

last: Sun

first: Linlin

first: Jie

last: Zong

first: Yaqi

last: Lei

first: Jing

last: Yu

first: Wanqi

last: Liang

first: Dabing


title: Role of Top1 and Genome structure in SARS-CoV-2 infection [RNA-Seq hamster]

city: New York

first: Sook Yuin Jessica

last: Ho

overall_design: To study the role of Top1 in modulating inflammation during SARS-CoV-2 in vivo, we infected golden syrian hamsters with SARS-CoV-2. Animals were dosed with either 10mg/kg TPT or vehicle control alone (DMSO) at Days 1 and 2 post infection. Thereafter, lungs of animals were collected at either day4 or day 6 post infection. All conditions were done with 3 animals (3 biological replicates).

first: Jessica

first: Bobo

middle: W

last: Mok

first: Laura

last: Campisi

first: Tristan

last: Jordan

first: Soner

last: Yildiz

first: Sreeja

last: Parameswaran

first: Joseph

middle: A

last: Wayman

first: Natasha

last: Gaudreault

first: David

last: Meekins

first: Sabarish

last: Indran

first: Igor

last: Morozov

first: Jessie

last: Trujillo

first: Yesai

last: Fstkchyan

first: Raveen

last: Rathnasinghe

first: Zeyu

last: Zhu

first: Simin

last: Zheng

last: Zhao

first: Kris

last: White

first: Helen

last: Ray-Jones

first: Valeriya

last: Malysheva

first: Michiel

last: Thiecke

first: Siu-Ying

last: Lau

first: Honglian

last: Liu

first: Anna

last: Zhang

first: Andrew

middle: C

last: Lee

first: Wen-Chun

first: Teresa

last: Aydillo

first: Betsaida

last: Melo

first: Ernesto

last: Guccione

first: Robert


title: RNA-seq of 14 days old arabidopsis in Col jmj28 andJMJ28np5-OE

city: Taipei

first: Fu-Yu

last: Hung

address: Institute of Plant Biology, National Taiwan University

country: Taiwan

institute: NTU, IPB

summary: We report the application of high-throughput profiling of total transcript in Col jmj28 andJMJ28np5-OE. The total RNA were extracted and analysed by NGS to identify the differential expressed genes between WT with jmj28 and JMJ28np5-OE.

overall_design: Total RNA were extracted from Col jmj28 andJMJ28np5-OE Arabidopsis and than analyzed by illumina novaseq 6000, pairend 150bp length.

first: Keqiang

last: Wu


title: Identifying SF3B1 binding sites across the transcriptome

first: Hani

last: Goodarzi

summary: Revealing the binding sites of endogenous SF3B1 using HITS-CLIP (high-throughput sequencing coupled with cross-linking immunoprecipitation).

overall_design: SF3B1 HITS-CLIP was performed in biological duplicate in MDA-231-LM2 cells.

first: H

first: L

last: Fish


title: RNA-seq of Col jmj28 andJMJ28np5-OE and genome-wide maps of JMJ28 binding in 14 day old arabidopsis

type: Genome binding/occupancy profiling by high throughput sequencing


title: Temporal gene regulation by p53 is associated with the rotational setting of its binding motifs in nucleosomes

city: Rochester

first: Julia

last: Freewoman

state: NY

address: 1 Lomb Memorial Dr

department: Thomas H. Gosnell School of Life Sciences

institute: Rochester Institute of Technology

summary: HCT116  cells treated with 5-FU along with DMSO and non-treatment controls using time-course RNA-seq were used to investigate target genes regulated by p53 at the different timepoints.

overall_design: Fourteen samples of HCT116 derived mRNA.   These samples include 2 replicates of non-treatment, 2 replicates each of DMSO treatments for 6, 12 and 24 and 2 replicates each of 5-FU treatment for 6, 12 and 24 hours.   Both CuffDiff2 and DESeq2 were used to determine the differentially expressed genes.

first: Feng

last: Cui


title: Genome-wide maps of JMJ28pro::JMJ28:3xFLAG in 14 days old arabidopsis

summary: We report the application of single-molecule-based sequencing technology for high-throughput profiling of JMJ28 in 14 days old arabidopsis. By obtaining sequence from chromatin immunoprecipitated DNA, we generated genome-wide JMJ28-binding maps of 14 days old arabidopsis. To reveal bound genes by JMJ28, chimeric protein JMJ28-3xFLAG was expressed under JMJ28 promoter in jmj28 (JMJ28pro:JMJ28:3xFLAG/ jmj28). ChIP was performed using anti-FLAG antibody (FLAG-M2, F1804; SIGMA), and ChIP DNA were analyzed by Illumina Novaseq 6000.

overall_design: Chromatin immunoprecipitation was performed forJMJ28pro::JMJ28:3xFLAG-expressing Arabidopsis. ChIP DNA was analyzed by  Illumina Novaseq 6000.


title: Identifying SNRPA1 binding sites across the transcriptome

summary: Revealing the binding sites of endogenous SNRPA1 using irCLIP (cross-linking immunoprecipitation).

overall_design: SNRPA1 irCLIP was performed in biological duplicate in MDA-231-LM2 cells.


title: Genome-wide maps of H3K4me2 in 14 days old WT, hda6, ldl1/2 and hda6/ldl1/2 arabidopsis

summary: We report the application of single-molecule-based sequencing technology for high-throughput profiling of H3K4me2 in 14 days old WT, hda6, ldl1/2 and hda6/ldl1/2 arabidopsis. By obtaining sequence from chromatin immunoprecipitated DNA, we mapped genome-wide H3K4me2 levels of 14 days old WT, hda6, ldl1/2 and hda6/ldl1/2 arabidopsis. ChIP was performed using anti-H3K4me2 antibody (diagenode; C15410035), and ChIP DNA were analyzed by Illumina HiSeq 2500.

overall_design: Chromatin immunoprecipitation was performed fo rWT, hda6, ldl1/2 and hda6/ldl1/2 arabidopsis. ChIP DNA was analyzed by Illumina HiSeq 2500.


title: RNA sequencing of SNRPA1 and SNRPB knockdown in MDA-LM2 cells

summary: We used RNA sequencing to compare SNRPA1 and SNRBP knockdown cells to mock-transfected controls respectively.

overall_design: We used three independent siRNAs to silence SNRPA1 and two siRNAs to silence SNRPB in MDA-LM2 cells. We then used RNA sequencing (smarter-seq pico v2) to compare SNRPB2 knockdown cells to mock-transfected controls (siControl; IDT).


title: RNA sequencing of SNRPA1 knockdown in MDA-LM2 cells

summary: We used RNA sequencing to compare SNRPA1 knockdown cells to mock-transfected controls respectively.

overall_design: We used two independent siRNAs to silence SNRPA1 in MDA-LM2 cells. We then used RNA sequencing (Scriptseq v2) to compare SNRPA1 knockdown cells to mock-transfected controls (siControl; IDT).


title: RNA sequencing of SNRPB2 knockdown in MDA-LM2 cells

summary: We used RNA sequencing to compare SNRPB2 knockdown cells to mock-transfected controls.

overall_design: We used two independent siRNAs to silence SNRPB2 in MDA-LM2 cells. We then used RNA sequencing (smarter-seq pico v2) to compare SNRPB2 knockdown cells to mock-transfected controls (siControl; IDT).


title: RNA sequencing of MDA-LM2 and MDA-Parental cells

summary: We used RNA sequencing to compare MDA-MB-231 cells to their higly metastatic MDA-LM2 derivatvies.

overall_design: We used RNA sequencing (Scriptseq v2) to compare MDA-MB-231 to their highly lung metastatic MDA-LM2 derivatvies.

last: Nguyen


title: IFNAR1 Signaling in NK Cells Promotes Persistent Virus Infection

city: San Diego

first: John

middle: R

last: Teijaro

address: 10550 North Torrey Pines Rd

department: Immunology and Microbial Science

institute: The Scripps Research Institute

summary: Inhibition of IFN-I signaling promotes the control of persistent virus infection, but the underlying  mechanisms remain poorly understood. Here we report that genetic ablation of IFNAR1  specifically in NK cells led to elevated numbers of T follicular helper cells, germinal center B  cells, and plasma cells, resulting in hastened virus clearance comparable to IFNAR1 blockade  by an IFNAR1 neutralizing antibody. Antigen-specific B cells and antiviral antibodies were  essential for the accelerated control of LCMV Cl13 infection following IFNAR1 blockade.  IFNAR1 signaling in NK cells promoted NK cell maturation, function, and killing of antigenspecific  CD4 and CD8 T cells. Therefore, Inhibition of IFN I signaling in NK cells enhances CD4  and CD8 T cell responses, elevates humoral immune response, and thereby facilitates the  control of persistent virus infection.

overall_design: NK cells from individual mice treated with anti-IFNAR1 or isotype control antibody were isolated for RNA-seq, four biological replicates per group were used for a total of eight samples sequenced.

first: Jaroslav

last: Zak

first: Zhe

last: Huang

first: Changchun

last: Xiao


title: Effect of a SNRPA1-interacting RNA structural element on alternative splicing

summary: Assessing the influence of RNA structural and sequence variations on SNRPA1-mediated regulation of alternative splicing

overall_design: A SNRPA1-interacting RNA structural element (WT sequence hg38: chr8:143925142-143925188), along with sequence and structure mutants of this element, was transfected into human breast cancer cells and then RNA-seq was used to assess the resulting changes in alternative splicing. Mock-transfected cells were used as a control. The sequence of the WT and variant structural RNA are available in the file "structural_RNA_sequence_with_variants.txt" at the foot of this record.


title: Genome-wide maps of H3Ac in 14 days old WT, hda6, ldl1/2 and hda6/ldl1/2 arabidopsis

summary: We report the application of single-molecule-based sequencing technology for high-throughput profiling of H3Ac in 14 days old WT, hda6, ldl1/2 and hda6/ldl1/2 arabidopsis. By obtaining sequence from chromatin immunoprecipitated DNA, we mapped genome-wide H3AC levels of 14 days old WT, hda6, ldl1/2 and hda6/ldl1/2 arabidopsis. ChIP was performed using anti-H3K9K14Ac antibody (Millipore; 06-599), and ChIP DNA were analyzed by Illumina HiSeq 2500.


title: RNA-seq of 14 days old arabidopsis in Col hda6 ldl1/2 and hda6/ldl1/2

summary: We report the application ofr high-throughput profiling of total transcript in WT, hda6, ldl1/2 and hda6/ldl1/2. The total RNA were extracted and analysed by NGS to identify the differential expressed genes between WT with hda6, ldl1/2 and hda6/ldl1/2.

overall_design: Total RNA were extracted from WT, hda6, ldl1/2 and hda6/ldl1/2 Arabidopsis and than analyzed by Illumina HiSeq 2500, pairend 150bp length.


title: Genome-wide maps of HDA6pro::HDA6:GFP in 14 days old arabidopsis

summary: We report the application of single-molecule-based sequencing technology for high-throughput profiling of HDA6 in 14 days old arabidopsis. By obtaining sequence from chromatin immunoprecipitated DNA, we generated genome-wide HDA6-binding maps of 14 days old arabidopsis. To reveal bound genes by HDA6, chimeric protein HDA6-GFP was expressed under HDA6 promoter in hda6 (HDA6pro:HDA6:GFP/ hda6). ChIP was performed using anti-GFP antibody (ab290; ABCAM), and ChIP DNA were analyzed by Illumina HiSeq 2500.

overall_design: Chromatin immunoprecipitation was performed for HDA6pro::HDA6:GFP-expressing Arabidopsis. ChIP DNA was analyzed by Illumina HiSeq 2500.


title: Control ChIP-seq from K562 (ENCSR281WXF)

status: Public on Mar 29 2021

city: Stanford

first: ENCODE

last: DCC

address: 300 Pasteur Dr

institute: ENCODE DCC

summary:
Input control ChIP-seq on human eGFP-ZNF193 tagged K562 cell line.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: ATAC-seq from heart left ventricle (ENCSR286STX)

summary:
ATAC-seq on human heart left ventricle

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Control ChIP-seq from A549 (ENCSR279OHT)

summary:
ChIP-seq on human A549

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Control ChIP-seq from GM12878 (ENCSR279VWA)

summary: For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Control ChIP-seq from K562 (ENCSR814UCX)

summary:
Control ChIP-seq in K562

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Control ChIP-seq from SK-N-SH (ENCSR086KKZ)

summary:
ChIP-Seq on SK-N-SH

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: ATAC-seq from pancreas (ENCSR808ZMK)

summary:
ATAC-seq on human pancreas

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Control ChIP-seq from progenitor cell of endocrine pancreas (ENCSR077RBB)

summary:
Control ChIP-seq on progenitor cell of endocrine pancreas originated from progenitor cell of endocrine pancreas

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Control ChIP-seq from K562 (ENCSR080NUS)

summary:
ChIP-Seq on K562

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Control ChIP-seq from HepG2 (ENCSR079WWH)

summary:
Control ChIP-seq on HepG2

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Control ChIP-seq from K562 (ENCSR275WKO)

summary:
ChIP-seq on human K562

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Control ChIP-seq from brain (ENCSR076IYM)

summary:
Control ChIP-seq on brain male adult (53 years)

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Control ChIP-seq from HepG2 (ENCSR479INP)

summary:
ChIP-Seq on HepG2

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Control ChIP-seq from endodermal cell (ENCSR273FER)

summary:
Control ChIP-seq on endodermal cell originated from endodermal cell

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: ATAC-seq from sciatic nerve (ENCSR072UYN)

summary:
ATAC-seq on human sciatic nerve

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Control ChIP-seq from pancreas (ENCSR067CHO)

summary:
Control ChIP-seq on pancreas female child (16 years)

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Control ChIP-seq from A549 (ENCSR267NPO)


title: Control ChIP-seq from K562 (ENCSR785AHP)


title: Control ChIP-seq from HepG2 (ENCSR792MRQ)


title: Control ChIP-seq from nephron progenitor cell (ENCSR795YGE)

summary:
Control ChIP-seq on nephron progenitor cell

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Control ChIP-seq from K562 (ENCSR793RRM)


title: ATAC-seq from heart right ventricle (ENCSR053SGP)

summary:
ATAC-seq on human heart right ventricle

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Control ChIP-seq from endothelial cell of umbilical vein (ENCSR049NDZ)


title: TF ChIP-seq from heart left ventricle (ENCSR778ZPK)

summary:
CTCF ChIP-seq on heart left ventricle female adult (59 years)

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Control ChIP-seq from HepG2 (ENCSR257XAX)


title: Control ChIP-seq from HepG2 (ENCSR775ETD)


title: Control ChIP-seq from K562 (ENCSR257URH)


title: Control ChIP-seq from breast epithelium (ENCSR776ZDB)


title: Control ChIP-seq from HepG2 (ENCSR776XHE)


title: TF ChIP-seq from transverse colon (ENCSR449SEF)


title: Control ChIP-seq from HepG2 (ENCSR770PLF)


title: Control ChIP-seq from MCF 10A (ENCSR775RVY)


title: ATAC-seq from uterus (ENCSR775SYU)

summary:
ATAC-seq on human uterus

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: ATAC-seq from pancreas (ENCSR251POP)


title: Control ChIP-seq from K562 (ENCSR251EHJ)


title: ATAC-seq from psoas muscle (ENCSR774NXA)

summary:
ATAC-seq on human psoas muscle

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Control ChIP-seq from K562 (ENCSR257RVS)


title: Control ChIP-seq from HepG2 (ENCSR042HRU)


title: Control ChIP-seq from endothelial cell (ENCSR233WMP)

summary:
Control ChIP-seq on endothelial cell

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Control ChIP-seq from K562 (ENCSR440JAU)

summary:
Control ChIP-seq in K562

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Control ChIP-seq from skin epidermis (ENCSR436NLU)

summary:
Control ChIP-seq of keratinocyte basal cell carcinoma female adult (66 years). Note that tissue excised from donor is cancerous.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: ATAC-seq from heart right ventricle (ENCSR437OOJ)


title: Control ChIP-seq from HepG2 (ENCSR743HNM)


title: Control ChIP-seq from K562 (ENCSR426BBS)


title: Control ChIP-seq from K562 (ENCSR248LOQ)


title: Control ChIP-seq from MCF-7 (ENCSR734XLI)

summary:
ChIP-seq on human MCF-7

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Control ChIP-seq from GM12878 (ENCSR422KXZ)

summary:
GM12878 immortalized cell line stably expressing C-terminal eGFP-ZBTB17 fusion protein.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Control ChIP-seq from K562 (ENCSR733QVR)


title: ATAC-seq from psoas muscle (ENCSR040DJK)


title: Control ChIP-seq from MCF-7 (ENCSR730RCJ)


title: Control ChIP-seq from K562 (ENCSR025GHD)

summary:
K562 immortalized cell line stably expressing C-terminal eGFP-JunB fusion protein.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Control ChIP-seq from astrocyte (ENCSR730VRY)

summary:
Control ChIP-seq on astrocyte originated from astrocyte

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: ATAC-seq from adrenal gland (ENCSR241OBO)

summary:
ATAC-seq on human adrenal gland

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Control ChIP-seq from K562 (ENCSR233HNT)

summary:
ChIP-seq on human K562

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Control ChIP-seq from MCF-7 (ENCSR744FDJ)

summary:
Input control ChIP-seq on human eGFP-ZNF148 tagged MCF7 cell line.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Control ChIP-seq from HepG2 (ENCSR020QUJ)

summary:
ChIP-Seq on HepG2

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Control ChIP-seq from K562 (ENCSR721XZK)


title: Control ChIP-seq from K562 (ENCSR032KPU)


title: Control ChIP-seq from HepG2 (ENCSR019ZGX)


title: Control ChIP-seq from K562 (ENCSR028NPT)


title: Control ChIP-seq from K562 (ENCSR018OYI)

summary:
Input control ChIP-seq on human eGFP-ELK1 tagged K562 cell line.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: ATAC-seq from heart right ventricle (ENCSR439TZT)


title: Control ChIP-seq from HepG2 (ENCSR730QNM)


title: Control ChIP-seq from A549 (ENCSR414IDX)

summary: For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Control ChIP-seq from K562 (ENCSR418YQO)

summary:
Input control ChIP-seq on human eGFP-E2F4 tagged K562 cell line.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Control ChIP-seq from K562 (ENCSR412OEE)


title: ATAC-seq from ovary (ENCSR227FVE)

summary:
ATAC-seq on human ovary

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Control ChIP-seq from MCF-7 (ENCSR712GVO)


title: Control ChIP-seq from K562 (ENCSR415ETK)


title: Control ChIP-seq from MCF-7 (ENCSR716YEJ)


title: Control ChIP-seq from K562 (ENCSR012KTG)


title: Control ChIP-seq from nephron (ENCSR008HBN)

summary:
Control ChIP-seq on nephron female embryo (5 days) originated from H9

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: ATAC-seq from heart right ventricle (ENCSR710SMN)

summary:
ATAC-seq on human heart right ventricle

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Control ChIP-seq from K562 (ENCSR006OWT)


title: ATAC-seq from pancreas (ENCSR705KEB)

summary:
ATAC-seq on human pancreas

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Control ChIP-seq from lower leg skin (ENCSR010HMS)


title: ATAC-seq from fallopian tube (ENCSR212LAZ)

summary:
ATAC-seq on human fallopian tube

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Control ChIP-seq from A549 (ENCSR002ABL)

summary:
A549 immortalized cell line stably expressing C-terminal eGFP-FOSL2 fusion protein.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Control ChIP-seq from excitatory neuron (ENCSR408LXD)

summary:
Control ChIP-seq on excitatory neuron

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Control ChIP-seq from K562 (ENCSR712UUA)


title: Control ChIP-seq from chondrocyte (ENCSR004UBJ)

summary:
Control ChIP-seq on chondrocyte originated from chondrocyte

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: ATAC-seq from right cardiac atrium (ENCSR213YPO)

summary:
ATAC-seq on human right cardiac atrium

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Control ChIP-seq from osteocyte (ENCSR702WFF)

summary:
Control ChIP-seq on osteocyte originated from osteocyte

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Atoh7-independent specification of retinal ganglion cell identity

city: St. Louis

first: Brian

middle: Stewart

last: Clark

state: Missouri

address: 660 S Euclid Ave; Campus Box #8096

department: Ophthalmology and Visual Sciences

institute: Washington University

summary: Atoh7 Cut&Run on the developing mouse retina

overall_design: Identification of Genomic Sites of Atoh7 transcription factor interation

first: Michel

last: Cayouette

last: Fries

first: Awais

last: Javed


title: Transcriptional profiling of the mid-secretory phase eutopic endometrial samples from women with endometriosis

status: Public on Mar 28 2021

city: MUMBAI

first: Geetanjali

last: Sachdeva

state: Opp KEM Hospital, Jehangir Merwanji Street, Parel,

address: Jehangir Merwanji Street, Parel

department: Primate Biology

country: India

institute: ICMR-National Institute for Research in Reproductive Health

summary:
Purpose- To identify the pathways and processes that are dysregulated in the eutopic endometrium of women with endometriosis
Methods-RNA sequencing was used to detect and quantify the transcripts encoded by the whole genome in the eutopic endometrium.  Mid-secretory phase eutopic endometrial samples from women with (n=4) and without endometriosis (n=4) were processed for RNA sequencing and the data were compared to identify the transcripts displaying differential abundance in women with endometriosis, compared to those without endometriosis (controls)

overall_design: Total RNA isolated from mid-secretory phase eutopic endometrial samples from women with (n=4) and without endometriosis (n=4) were enriched for messenger RNA (mRNA) using poly (A) selection. Strand-specific libraries were synthesised, adapter ligated, amplified and sequenced to obtain paired-end reads using Illumina Next Seq 500 platform. The data were analysed using the Tuxedo pipeline to  detect differentially abundant transcripts in the endometrial samples from women with endometriosis, compared to those without endometriosis. This was followed by annotation for the pathways and processes enriched by the differentially expressed transcripts in endometrial samples from women with endometriosis.

first: Kashmira

last: Bane

first: Junita

last: Desouza

first: Diksha

last: Shetty

first: Prakash

last: Choudhary

first: Shalaka

last: Kadam

first: Rajendra

last: Katkam

first: Gwendolyn

last: Fernandez

first: Raj

last: Sawant

first: Uddhavraj

last: Dudhedia

first: Neeta

last: Warty

first: Anahita

last: Chauhan

first: Uddhav

last: Chaudhari

first: Rahul

last: Gajbhiye


title: Identification of factors involved in somatic stem cells in the Drosophila testis

first: Erika

last: Bach

department: Biochemistry and Molecular Pharmacology

institute: NYU Grossman School of Medicine

summary: We report the transcriptional profiles obtained by next-generation sequencing (NGS) of FACS-purified somatic cyst stem cells (CySCs) from adult testes of Drosophila melanogaster. The goals of this study are to compare NGS-derived transcriptome profiling (RNA-seq) of wild type CySCs to those that have decreased Chinmo, increased Chinmo, elevated JAK/STAT signaling or elevated Hh signaling.

overall_design: Examination of differentially-regulated genes in four types of CySCs, those with decreased Chinmo, increased Chinmo, increased JAK/STAT signaling or increased Hh signaling, compared to controls.

first: Lydia

last: Grmai


title: Prefrontal cortical transcriptome analysis of Cyfip2 mutant mice (adult mouse)

city: Seoul

first: Kihoon

last: Han

address: 73, Inchon-ro, Seongbuk-gu

department: Neuroscience

country: South Korea

institute: Korea University College of Medicine

summary: CYFIP2 is a component of the WAVE regulatory complex which regulates actin polymerization and branching in diverse cellular compartments. Recent molecular genetic studies identified mutations of CYFIP2 in patients with intellectual disability and seizures, suggesting that CYFIP2 may have some roles in brain development and function. To understand its functions in vivo at the molecular level, we performed RNA-seq analysis in adult Cyfip2 mutant mice.

overall_design: Prefrontal cortical transcriptome of postnatal day 56 wild-type and Cyfip2 mutant mice.

first: Yinhua

last: Zhang

first: Hyojin

last: Kang


title: Network effects of the 15q13.3 microdeletion on the transcriptome and epigenome in human induced neurons

city: Palo Alto

first: Siming

address: 3165 Porter Drive

institute: Stanford University

type: Methylation profiling by high throughput sequencing

summary: Background: Deletions in the 15q13.3 region are associated with several neuropsychiatric disorders, including autism and schizophrenia. Association studies in humans and functional studies in mice have suggested that several genes within the 15q13.3 microdeletion may play a role in neuronal dysfunction, but the intermediate molecular mechanisms remain unknown.  Methods: Induced pluripotent stem cells from 3 patients with the 15q13.3 microdeletion and 3 sex-matched controls were generated and converted into induced neurons. We analyzed the genome-wide effects of the 15q13.3 microdeletion on gene expression, DNA methylation, chromatin accessibility, and sensitivity to cisplatin-induced DNA damage. We also evaluated gene expression changes in  induced neurons containing CRISPR knockouts of single 15q13.3 microdeletion genes.  Results: In both cell types, gene copy number change within the 15q13.3 microdeletion was accompanied by significantly decreased gene expression and no compensatory changes in DNA methylation or chromatin accessibility, supporting the model that haploinsufficiency of genes within the deleted region drives the disorder. Further, we observed global effects of the microdeletion on the transcriptome and epigenome, with disruptions in several neuropsychiatric disorder-associated pathways, such as Wnt signaling, ribosome biogenesis, DNA binding, and cell adhesion. Conclusions: Our multi-omics analyses of the 15q13.3 microdeletion revealed downstream effects in pathways previously associated with neuropsychiatric disorders. This molecular systems analysis can also be applied to other brain relevant chromosomal aberrations to further our etiological understanding of neuropsychiatric disorders.

overall_design: 15q13.3 microdeletion and control iPSCs and iNs were analyzed with RNA-seq, Methyl-seq, and ATAC-seq. CRISPR knockout iNs were analyzed with RNA-seq.

first: Xianglong

first: Carolin

last: Purmann

first: Shining

last: Ma

first: Anima

last: Shrestha

first: Kasey

last: Davis

first: Marcus

last: Ho

first: Yiling

last: Huang

first: Reenal

last: Pattni

first: Wing

last: Wong

first: Jonathan

last: Bernstein

first: Joachim

last: Hallmayer

first: Alexander

last: Urban


title: Hyaluronan-CD44 signaling promotes pro-tumor inflammation in breast cancer

city: Minneapolis

first: Sarah

last: Munro

state: MN

address: 117 Pleasant Street SE

institute: University of Minnesota

summary:
We report the application of next-generation sequencing (NGS) technology for high-throughput profiling of RNA expression in human breast cancer cells. The goal of this study was to compare NGS-derived transcriptome profiling (RNA-seq) from cells expressing either wildtype or knockout CD44 to identify key downstream signaling events of HA-CD44 interactions.
Methods: This experiment was repeated for a total of three times and replicate RNA samples were extracted and submitted for Illumina Sequencing. Twelve dual-indexed Illumina TruSeq stranded mRNA libraries were pooled for sequencing on 1 lane of a HiSeq 2500 using v4 chemistry to generate 2x50 bp paired-end reads. After applying the Benjamini-Hochberg multiple hypothesis adjustment to raw p-values, differentially expressed genes were identified requiring that they had a log2 fold change > 0 and an adjusted p-value ≤ 0.01.
Results: A total of 1,530 and 320 genes were impacted by CD44 KO in the Hs578T cells and MDA-MB-231 cells, respectively. When comparing each of these data sets, 40 genes were differentially expressed in both Hs578T and MDA-MB-231 cells upon deletion of CD44.
Conclusions: Gene ontology (GO) analysis revealed that CD44 KO in breast cancer cells altered expression of genes involved in both cell adhesion and cytokine activity. This study provides a framework for the application of NGS to compare differential gene expression between genetically edited mammalian cell populations.

overall_design: Determining the effects of CD44 KO in 2 different human breast cancer cell lines. Three replicates were prepared for each of the four experimental conditions.

first: Kaylee

last: Schwertfeger

first: Patrice

last: Witschen


title: Control ChIP-seq from K562 (ENCSR200QDR)

first: ENCODE

last: DCC

summary:
ChIP-seq on human K562

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: ATAC-seq from heart right ventricle (ENCSR204SMO)


title: Expression Data from Ets1/2 WT, Ets1KO, Ets2KO and Ets1/2 DKO endothelial cells

status: Public on Mar 27 2021

city: Charleston

first: Michael

last: Ostrowski

state: SC

address: 86 Jonathan Lucas street

department: Biochemistry and Molecular Biology

institute: Medical University of South Carolina

summary: Angiogenesis is a highly orchestrated process involving complex crosstalk between several endothelial cell (EC) processes including cell cycle, cell survival and migration. Transcription factors ETS1 and ETS2 are required for EC functions necessary for embryonic angiogenesis. However owing to the lethal nature of the double mutant embryo, the specific gene targets of these factors are yet to be identified. In the current study, we try to elucidate the effect of endothelial cell specific deletion of Ets1 and Ets2 on post natal angiogenesis and characterize the downstream regulatory pathways. Deletion of Ets1 and Ets2, restricted to endothelial cells in new born mice (P1-P3), reduced retinal angiogenesis. Similarly, EC infiltration and invasion into matrigel plugs subsided when matrigel admixed with mouse mammary tumor cells was injected into adult mice with inactivated Ets1 and Ets2 specifically in ECs. Expression of key cell cycle and cell survival regulators were diminished in double mutant cells as compared to controls. In addition, both these factors were found to occupy the enhancer regions of the target genes. Deletion of Ets1 and Ets2 in cultured aortic EC resulted in altered cell cycle phases with a G2/M phase arrest and increased sensitivity to apoptosis in vitro. These results demonstrate that deletion of Ets1 and Ets2 in endothelial cells inhibits angiogenesis by altering cell cycle progression and decreasing cell survival.

overall_design: Endothelial cells were infected either with lentiviral-egfp or lentiviral-egfp-Cre to generate Ets1/2 WT, Ets1KO, Ets2KO and Ets1/2 DKO endothelial cells, cultured, RNA was extracted and Affymetrix gene expression arrays were performed.

first: Sankha

last: Ghosh

first: Sudarshana

last: Sharma


title: Comparative High-Resolution Transcriptome Sequencing of Lymphoma Cell Lines and de novo Lymphomas Reveals Cell-Line-Specific Pathway Dysregulation

city: Graz

first: Leila

last: Taher

address: Stremayrgasse 16/I

country: Austria

institute: Graz University of Technology

summary: In dogs as well as humans, lymphoma is the most common hematopoietic malignancy. Furthermore, due to its characteristics, canine lymphoma is recognized as a clinically relevant in vivo model to study the corresponding human disease. Immortalized cell lines are widely used as in vitro models to evaluate novel therapeutic agents and characterize their molecular mechanisms. However, it is known that long-term cultivation leads to clonal selection, genetic instability, and loss of the initial heterogenic character, limiting the usefulness of cell lines as preclinical models.  Herein, we present a systematic characterization and comparison of the transcriptomic landscape of canine primary B- and T-cell lymphomas, five lymphoid cell lines (CLBL-1, CLBL-1M, GL-1, CL-1, and OSW) and four non-neoplastic control samples. We found that lymphomas and cell lines exhibit a common "differentiation and proliferation signature". However, our analysis also showed that, independently of the cell of origin, the transcriptional signatures of lymphomas are more similar to each other than they are to those of cell lines. In particular, we observed that not all common therapeutic targets are similarly expressed between lymphomas and lymphoid cell lines, and provide evidence that different lymphoid cell-lines should be used to model distinct aspects of lymphoma dysregulation.

overall_design: mRNA profiles of primary canine lymphomas and lymphoid cell lines were generated by RNA-sequencing, using Illumina Hiseq.

first: Julia

last: Beck

first: Wen

last: Liu

first: Catrin

last: Roolf

first: Jan

middle: T

last: Soller

first: Barbara

last: Rütgen

first: Sabine

middle: E

last: Hammer

first: Murali

last: Chodisetti

first: Sina

last: Sender

first: Katharina

last: Sterenczak

first: Georg

last: Fuellen

first: Christian

last: Junghanss

first: Bertram

last: Brenig

first: Ingo

last: Nolte

first: Ekkehard

last: Schütz

first: Hugo

last: Escobar


title: Calcineurin inhibitor-induced renal side effects – Identification of underlying molecular mechanism via transcriptional analysis on large-scale isolated renal tubules

city: Zürich

first: Peter

last: Leary

address: Winterthurerstrasse 190

department: Functional Genomics Center Zürich

country: Switzerland

institute: ETH Zürich

summary: Comparing the transcriptional profiles of the CnB1-KO and control animals in order to to identify molecular pathways that are involved in the signal transduction of calcineurin in the DCT and explore the exact molecular pathogenesis of the CNI-induced renal side-effects.

overall_design: Examination of the transcriptional profile of control and DCT-specific calcineurin knockout mice

first: Johannes

last: Loffing

first: Eszter

last: Banki


title: Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and Zfyve19-/- hepatic Transcriptomes

first: Jing

last: Yang

state: Shanghai

address: No. 1508 Longhang Road  Jinshan District

department: Pediatrics

institute: Jinshan Hospital of Fudan University

summary: Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare NGS-derived hepatic transcriptome profiling (RNA-seq) to microarray and quantitative reverse transcription polymerase chain reaction (qRT–PCR) methods and to evaluate protocols for optimal high-throughput data analysis

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: hepatic mRNA profiles of 6-8 weeks wild type (WT) and Zfyve19-/- mice

first: Jianshe

last: Wang

first: Yiling

last: Qiu


title: Systemic inflammation drives rapid conversion of conventional CD4+ T cells to Treg in vivo.

city: La Jolla

first: Joseph

middle: S.

last: Dolina

state: California

address: 9420 Athena Circle

department: Division of Developmental Immunology

institute: La Jolla Institute for Immunology

summary: The immune system faces a task that approximates cognition in its complexity as it processes a multitude of intrinsic and extrinsic signals and integrates these into responses of the appropriate class, specificity, magnitude, and duration for a given threat, with the host’s life often depending on the outcome. CD4+ T lymphocytes occupy a unique role in the generation and regulation of immunity within this context and influence multiple innate and adaptive cell types. With respect to CD8+ cytotoxic T lymphocytes (CTL), CD4+ T cells function early in the response as ‘helpers’ (TH) to increase its magnitude and functionality, and later as regulatory cells (Treg) to restore homeostasis and avoid immune pathology. Using a Listeria monocytogenes (Lm) infection model, we probed whether the conditions of initial pathogen encounter could influence the generation of TH versus Treg. Infection induces rapid polyclonal conversion to functional FoxP3+CD25+ Treg within 24 hours. These findings resolve long-standing questions regarding the requirement for TH and reveal a remarkable degree of plasticity in the function of CD4+ T cells, which can be quickly converted to Treg in vivo in response to acute inflammation.

overall_design: Differential gene expression analysis of total RNA isolated from splenic CD4+eGFP+ (Treg) from Foxp3eGFP mice

first: Joey

last: Lee

first: Lara

last: Labarta-Bajo

first: Sumetha

last: Kannan

first: Jason

last: Greenbaum

first: Zbigniew

last: Mikulski

first: Nawal

last: El Idrissi

first: Margot

middle: J

last: Pont

first: Sandy

last: Rosales

first: Gregory

last: Seumois

first: Pandurangan

last: Vijayanand

first: Michael

last: Croft

first: Stephen

last: Schoenberger


title: Genome wide DNA binding of ETS1 and ETS2 in aortic endothelial cells

last: Ostrowski

summary: Genome wide DNA binding of ETS1 and ETS2 in murine aortic endothelial cells

overall_design: To evaluate the ETS1 and ETS2 regulome WT aortic endothelial cells were subjected to chromatin immunoprecipitation using standard protocol and genome wide binding sites were determined by next generation single end sequencing using Illumina Hiseq 2000

first: Sankha

last: Ghosh

first: Sudarshana

middle: M

last: Sharma


title: Transcriptome analyses of bicolor leaf development in ornamental kale

city: Shenyang City

first: jie

last: ren

address: Dongling Road NO.120

institute: Shenyang Agricultural University

summary:
Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of leaf color at different development stages. The goals of this study are to compare anthocyanin biosynthesis, chlorophyll metabolism and chloroplast organization transcriptome profiling (RNA-seq) to microarray and quantitative reverse transcription polymerase chain reaction (qRT–PCR) methods and to evaluate protocols for optimal high-throughput data analysis
Methods: Leaf mRNA profiles of 12 RNA sequencing libraries (S1, S2, S3_S, and S3_C) were generated by deep sequencing, in triplicate, using an Illumina HiSeq 4000 system. After removing reads of low quality, those that remained were mapped to the reference genome (ftp://ftp.ensemblgenomes.org/pub/release-38/plants/genbank/brassica_oleracea/) using the HISAT package, allowing for a maximum of two mismatches and multiple alignments per read (up to 20 by default). qRT–PCR validation was performed using SYBR Green assays
Results: Using an optimized data analysis workflow, we mapped about 571.74 million sequence reads per sample to the the reference genome (ftp://ftp.ensemblgenomes.org/pub/release-38/plants/genbank/brassica_oleracea/) and identified 99, 391, 74, and 543 DEGs were detected in pairwise comparison (S2 vs. S1, S3_S vs. S2, S3_C vs. S2, and S3_S vs. S3_C, respectively). The DEGs were associated with ‘photosynthesis’and other pathways in the Kyoto Encyclopedia of Genes and Genomes database; DEGs related to chloroplast organization were identified in the Gene Ontology analysis. The DEGs identified by RNA sequencing were confirmed by qRT-PCR analysis, indicating that the data were reliable. These findings provide information that can be useful for investigating the molecular basis for leaf variegation in ornamental kale and other plants.
Conclusions: The results presented here reveal changes in the transcriptome profile of a bicolor leaf kale. DEGs related to anthocyanin biosynthesis, chlorophyll metabolism and chloroplast organization were detected. These results demonstrate that leaf color at different stages of development is influenced by anthocyanin biosynthesis, chloroplast and pigment metabolism, providing a foundation for investigating the molecular basis for bicolor leaf in ornamental kale and other plants.

first: Hui

last: Feng

first: Jie

last: Ren