title: Spatial localization with Spatial Transcriptomics for an atlas of healthy and injured cell states and niches in the human kidney [Visium ST]

status: Public on Oct 12 2022

city: Indianapolis

first: Michael

middle: T

last: Eadon

state: IN

address: 950 W Walnut St

institute: Indiana University

summary: To spatially localize cell types within the tissue, snCv3 subclasses were used to predict the corresponding identities in Visium transcriptomic data. This allowed for recapitulated renal corpuscle, tubular, vascular, and interstitial cell types having proportions, marker profiles, and spatial organizations consistent observed histopathology.

overall_design: Human kidney tissue was prepared and imaged according to Visium Spatial Gene Expression protocols (10x Genomics) according to the manufacturer protocol (CG000240 protocol, Visium Tissue Preparation Guide) and as previously described 89. Tissue was sectioned at 10 µm thickness from Optimal Cutting Temperature (OCT) compound embedded blocks. A Keyence BZ-X810 microscope equipped with a Nikon 10X CFI Plan Fluor objective was used to acquire hematoxylin and eosin (H&E) stained brightfield mosaics which were subsequently stitched. mRNA was isolated, libraries prepared, and sequencing was performed on an Illumina NovaSeq 6000. mRNA was isolated from stained tissue sections after permeabilization for 12 minutes. Released mRNA was bound to oligonucleotides in the fiducial capture areas. mRNA was then reverse transcribed and underwent second strand synthesis, denaturation, cDNA amplification, and SPRIselect cDNA cleanup (Visium CG000239 protocol). Space Ranger (v1.0.0) with the reference genome GRCh38 3.0.0 was used to perform expression analysis, mapping, counting, and clustering. Normalization was performed with SCTransform. Final data processing was done in Seurat (v3.2.3).  As of the design of this study, QC metrics were not established by the lab or the manufacturer. Currently, three CKD biopsies would fall below the established threshold of fraction of reads mapped to exons above 0.3. These samples were not included in the main analysis of the paper.

first: Eadon

last: Michael

first: Ricardo

last: M Ferreira

first: Ying-Hua

last: Cheng


title: Transcriptomics characterization of hepatocellular carcinoma (HCC) after incomplete radiofrequency ablation (iRFA)

status: Public on Sep 05 2022

city: Chongqing

first: Yuxin

last: Duan

state: Chongqing

address: No.1, Youyi Road, Yuanjiagang, Yuzhong District

country: China

institute: The First Affiliated Hospital of Chongqing Medical University

type: Expression profiling by high throughput sequencing

summary: So far, there is no any report about gene dysregulation from human tissues of HCC after RFA. Here, we investigated the transcriptomic  analyses in human tissues of patients with HCC following iRFA.

overall_design: Ten patients who satisfied the eligibility criteria (BCLC 0-A) were enrolled on this prospective study of iRFA treatment at 1 cm ablating range for 5 minutes. Comparative gene expression profiling of RNA-seq data was performed on HCC tissues obtained before the procedure and when the ablation tip temperature was cooled to below 37°C for 30 minutes, obtained near 1 cm from the iRFA tumor margin.

first: Rui

last: Liao


title: Concomitant Cytotoxic Effector Differentiation of CD4+ and CD8+ T Cells in Response to EBV-Infected B Cells

status: Public on Aug 26 2022

city: Berlin

first: Lars

last: Bullinger

address: Augustenburger Platz 1

department: Hematology, Oncology and Tumorimmunology

country: Germany

institute: Charité

summary: Most people infected by EBV acquire specific immunity, which then controls latent infection throughout their life. Immune surveillance of EBV-infected cells by cytotoxic CD4+ T cells has been recognized; however, the molecular mechanism of generating cytotoxic effector T cells of the CD4+ subset remains poorly understood. Here we compared phenotypic features and the transcriptome of EBV-specific effector-memory CD4+ T cells and CD8+ T cells in mice and found that both T cell types show cytotoxicity and, to our surprise, widely similar gene expression patterns relating to cytotoxicity. Similar to cytotoxic CD8+ T cells, EBV-specific cytotoxic CD4+ T cells from human peripheral blood expressed T-bet, Granzyme B, and Perforin and upregulated the degranulation marker, CD107a, immediately after restimulation. Furthermore, T-bet expression in cytotoxic CD4+ T cells was highly correlated with Granzyme B and Perforin expression at the protein level. Thus, differentiation of EBV-specific cyto  toxic CD4+ T cells is possibly controlled by mechanisms shared by cytotoxic CD8+ T cells. T-bet-mediated transcriptional regulation may explain the similarity of cytotoxic effector differentiation between CD4+ T cells and CD8+ T cells, implicating that this differentiation pathway may be directed by environmental input rather than T cell subset.

overall_design: Isogenic murine BL cell line modified by CRISPR/Cas9 genome editing

first: Sandrine

last: Sander

first: Klaus

last: Rajewsky

first: Tomoharu

last: Yasuda


status: Public on Oct 08 2022

city: Richmond

first: Janina

middle: P

last: Lewis

state: VA

address: 521 North 11th Street

department: Philips Institute of OCMB

country: USA

institute: Virginia Commonwealth University

summary: Role of RNA-binding protein, Pgr, in Porphyromonas gingivalis.

overall_design: Wild type Porphyromonas gingivalis W83 strain (V3203) was used to compare to the Pgr - deficient strain (V3139).

first: Qin

last: Gui

first: Sai

last: Yanamandra


title: Stromal reprogramming by FAK inhibition overcomes radiation resistance to allow for immune priming and response to checkpoint blockade.

status: Public on Oct 09 2022

city: St Louis

first: David

last: DeNardo

email: varintra@wustl.edu, ddenardo@wustl.edu

address: 425 S Euclid Ave

institute: Washington University in St. Louis

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

overall_design: Refer to individual Series


title: Dynamic network-guided CRISPRi screen reveals CTCF loop constrained enhancer function in cell state transitions

status: Public on Oct 01 2022

city: Baltimore

middle: A

last: Beer

state: MD

address: 733 N. Broadway

department: Biomedical Engineering and Genetic Medicine

institute: Johns Hopkins University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: We performed CRISPRi enhancer screens during differentiation of human embryonic stem cells (hESC) to definitive endoderm (DE) in genomic windows surrounding ten lineage-specifying core TFs. We also generated scRNA-seq, ATAC-seq, and TF ChIP-seq data and show that CTCF loops constrain the interactions between enhancers and their promoter targets.

overall_design:
Single-cell scRNA-seq gene expression profiling of differentiating idCas9-KRAB SOX17eGFP/+ HUES8 hESC line at 7 time points from 0hr to 72hr post-differentiation
ATAC-seq chromatin accessibility profiling of differentiating idCas9-KRAB SOX17eGFP/+ HUES8 hESC line at 7 time points from 0hr to 72hr post-differentiation
gRNA sequencing data of CRISPRi experiment at 36hr post differentiation in idCas9-KRAB SOX17eGFP/+ HUES8 hESC line
Hi-C chromatin interaction profiling in hESC and DE HUES8 hESC cell line.
TF ChIP-seq for GATA6, EOMES, SOX17, H3K27ac, and CTCF in HUES8 hESC line

first: Renhe

last: Luo

first: Danwei

last: Huangfu

first: Mike


title: Molecular heterogeneity and commonalities in pancreatic cancer precursors with gastric and intestinal phenotype

status: Public on Aug 20 2022

city: Essen

first: Laura

last: Godfrey

address: Hufelandstraße 55

institute: DKTK Partner Site Essen/Düsseldorf

summary: A comparative morpho-genetic analysis of PDAC precursors aiming at dissecting the process of carcinogenesis and tackling the heterogeneity of preinvasive lesions was performed

overall_design: RNA-sequencing of human PDAC precursor lesions (gastric and intestinal IPMN; PanIN), bulk acinus and PDAC

first: Sven-Thorsten

last: Liffers

first: Lisa

last: Frohn

first: Jens

last: Siveke

first: Irene

last: Esposito


title: Prevalence and Mechanisms of Mucus Plugging in COVID-19 Lung Disease

status: Public on Aug 03 2022

city: Chapel Hill

first: Takafumi

last: Kato

state: NC

address: 125 Mason Farm Rd, 7230-K Marsico Hall CB #7248

department: Marsico Lung Institute

institute: University of North Carolina

summary:
Purpose: To investigate molecular mechanisms of SARS-CoV-2-induced mucin expression and synthesis and test candidate countermeasures.
Methods: Bulk RNA-seq was performed on well-differentiated human bronchial epithelial (HBE) cell culture lysates with/without SARS-CoV-2 inoculation.
Results: SARS-CoV-2-infected HBE cultures exhibited peak titers 3 days post inoculation, whereas induction of MUC5B/MUC5AC peaked 7-14 days post inoculation.
Conclusions: SARS-CoV-2-infection to HBE culture causes mucus goblet cell metaplasia and increased expression of MUC5B-dominated mucin overproduction.

overall_design: HBE cells were maintained >4 weeks on air-liquid interface culture until they were well-differentiated. Then the cells were inoculated with SARS-CoV-2 (D614G strain) apically at MON=0.5 for two hours. Cell lysates for bulk RNA-seq were obtained at 1-, 3- 7- and 14-day post inoculation from mock- and virus-inoculated cultures.

first: Takanori

last: Asakura

first: Hong

last: Dang

first: Caitlin

middle: E

last: Edwards

first: Richard

middle: C

last: Boucher


title: V. cholerae transcriptome or deleted for the tgt gene in MH, supplemented or not with tobramycin or ciprofloxacin

status: Public on Oct 03 2022

city: Paris

first: Zeynep

last: Baharoglu

address: 28 Rue du Docteur Roux

department: Génomes et Génétique

country: France

institute: Institut Pasteur

summary: We study gene expression levels of V. cholerae N16961 WT and tgt mutant strains in MH medium in the presence or not of sublethal concentration on tobramycin or ciprofloxacin

sample_organism: Vibrio cholerae O1 biovar El Tor str. N16961

overall_design: Bacterial cells were grown to OD 0,3 and RNAseq was performed.

first: Louna

last: Fruchard

first: Anamaria

last: Babosan

first: André

last: Carvalho

first: Manon

last: Lang

first: Blaise

last: Li

first: Magalie

last: Duchateau

first: Quentin

last: Giai-Gianetto

first: Mariette

last: Matondo

first: Frédéric

last: Bonhomme

first: Céline

last: Fabret

first: Olivier

last: Namy

first: Valérie

last: de Crécy-Lagard

first: Didier

last: Mazel


title: Diurnal alterations in gene expression across striatal subregions in psychosis

status: Public on Aug 31 2022

city: Pittsburgh

first: WEI

last: ZONG

state: PA

address: 130 De Soto St

institute: UNIVERSITY OF PITTSBURGH

summary:
Background: Psychosis is a defining feature of schizophrenia and highly prevalent in bipolar disorder. Notably, individuals suffering with these illnesses also have major disruptions in sleep and circadian rhythms, and disturbances to sleep and circadian rhythms can precipitate or exacerbate psychotic symptoms. Psychosis is associated with the striatum, though no study to date has directly measured molecular rhythms and determined how they are altered in the striatum of subjects with psychosis.
Methods: Here, we perform RNA-sequencing and both differential expression and rhythmicity analyses to investigate diurnal alterations in gene expression in human postmortem striatal subregions (NAc, caudate, and putamen) in subjects with psychosis relative to unaffected comparison subjects.
Results: Across regions, we find differential expression of immune-related transcripts and a substantial loss of rhythmicity in core circadian clock genes in subjects with psychosis. In the nucleus accumbens (NAc), mitochondrial-related transcripts have decreased expression in psychosis subjects, but only in those who died at night. Additionally, we find a loss of rhythmicity in small nucleolar RNAs and a gain of rhythmicity in glutamatergic signaling in the NAc of psychosis subjects. Between region comparisons indicate that rhythmicity in the caudate and putamen is far more similar in subjects with psychosis than in matched comparison subjects.
Conclusions: Together, these findings reveal differential and rhythmic gene expression differences across the striatum that may contribute to striatal dysfunction and psychosis in psychotic disorders.

overall_design: NAc, caudate, and putamen tissue samples were collected from schizophrenia (SCZ), bipolar disorder (BD), and unaffected comparison subjects obtained through the University of Pittsburgh Brain Tissue Donation Program and the NIH NeuroBioBank. Brain tissue was obtained, following consent from the next of kin, during autopsies conducted at the Allegheny County (Pittsburgh, PA) or Davidson County (Nashville, TN) Medical Examiner’s Office. All procedures were approved by the University of Pittsburgh Institutional Review Board for Biomedical Research and Committee for Oversight of Research and Clinical Training Involving Decedents. An independent committee of experienced clinical research scientists made consensus DSM-IV diagnoses for each subject using structured interviews with family members and review of medical records and toxicology results. The absence of psychiatric diagnoses was confirmed in comparison subjects using the same approach. Subjects were included based on three criteria: 1) known time of death (TOD) within a 4-hour window and meeting the criteria of rapid death; 2) age less than 65 years; 3) postmortem interval (PMI) less than 30 hours. A total of 60 unaffected comparison, 28 SCZ, and 28 BD subjects met these criteria. One subject (ID – 960; BD with psychosis) was removed due to low correlation with the other subjects. Another subject (ID – 1180; BD with psychosis) had low expression data in the NAc and therefore was removed from NAc-specific analyses. Given the high degree of overlap between SCZ and BD with psychosis at the symptomology, genomic, and transcriptomic levels (Gandal et al., 2018; Markota et al., 2018; Enwright and Lewis, 2021), we generated a psychosis cohort (n=36 in caudate and putamen; n=35 in NAc) consisting of SCZ subjects (n=28) and BD with psychosis subjects (n=8 in caudate and putamen; n=7 in NAc). An unbiased method is used to design a matched comparison cohort (n=36) matched to the 36 psychosis subject by sex, race, age, time of death, PMI, and pH.

first: Colleen

last: McClung

first: George

last: Tseng

first: Kyle

last: Ketchesin

first: Wei

last: Zong


title: System-wide analyses reveal essential roles of N-terminal protein modification in bacterial physiology

status: Public on Jul 20 2022

city: Pasadena

first: Zikun

last: Zhu

state: CA

address: 1200 E California Blvd

institute: California Institute of Technology

summary: Removal of the N-terminal formyl group on nascent proteins by peptide deformylase (PDF) is the most prevalent protein modification in bacteria that impacts over 90% of the proteome. PDF is essential and a critical target of antibiotic development; however, its role in bacterial physiology remains a long-standing question. In this work, we used system-wide and time-resolved analyses of the E. coli translatome and proteome to investigate the consequences of PDF inhibition at different stages. We found that PDF inhibition results in the rapid activation of cellular stress responses, especially those associated with defects in protein folding and perturbations at the bacterial inner membrane, followed by a global downregulation of metabolic pathways. Functional assays reveal the rapid hyperpolarization of the plasma membrane and impaired membrane integrity upon PDF inhibition, suggesting that disruption of plasma membrane is the most immediate and primary consequence of formyl group retention on nascent proteins. Our work resolves the physiological function of a ubiquitous N-terminal protein modification and uncovers its crucial role in maintaining the proper structure and function of the bacterial membrane.

overall_design: Investigating the change in translatome upon inhibition of PDF by actinonin (ACT) treatment.

first: Chien-I

last: Yang

first: Shu-ou

last: Shan


title: Bulk RNA-Seq and single-cell RNA-Seq on GBM cells from NPCTKO and NSCHRas-shp53 mouse models

status: Public on Jul 04 2022

city: Wuhan

first: Xuan

last: Liu

address: Donghu Road, No. 115, Wuchang District, Wuhan, Hubei Province, P.R. China

institute: Wuhan university

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: Differential chromatin accessibility in peripheral blood mononuclear cells underlies COVID-19 disease severity prior to seroconversion

status: Public on Jun 19 2022

city: Durham

first: Julie

last: Steinbrink

address: 315 Trent Drive

department: Center for Applied Genomics and Precision Medicine

institute: Duke University


title: Ribosome profiling reveals multiple roles of SecA in cotranslational protein export

status: Public on May 16 2022

summary: SecA, an ATPase known to posttranslationally translocate secretory proteins across the bacterial plasma membrane, also interacts with ribosomes. Here, we used a combination of ribosome profiling methods to investigate the cotranslational actions of SecA in vivo. SecA scans translating ribosomes at the plasma membrane and cotranslationally engages large periplasmic loops on inner membrane proteins. In coordination with the proton motive force, SecA resolves the cytoplasmic accumulation of periplasmic loops during cotranslational protein translocation. SecA also associates with a subset of secretory proteins at an early stage of translation and mediates their cotranslational transport, whereas the chaperone trigger factor (TF) delays SecA engagement on other secretory proteins to impose a posttranslational mode of translocation. The hydrophobicity of signal sequence is a determinant of nascent protein triage between SecA and TF. Our results elucidate the principles of SecA-driven cotranslational protein translocation and reveal a hierarchical network of protein export pathways in bacteria.

overall_design: Investigating the SecA-nascent chain interactions in four different strain backgrounds (WT, ∆tig, secA∆ZnBD, ∆secB) and in WT strain upon CCCP treatment. Monitoring cotranslational targeting events by fractionation-coupled ribosome profiling in WT strain with and without CCCP treatment (all in replicates).

first: Shuai

last: Wang


title: Differential chromatin accessibility in peripheral blood mononuclear cells underlies COVID-19 disease severity prior to seroconversion [scRNA-Seq]

summary: SARS-CoV-2 infection triggers profound and variable immune responses in human hosts. Chromatin remodeling has been observed in individuals severely ill or convalescing with COVID-19, but chromatin remodeling early in disease prior to anti-spike protein IgG seroconversion has not been defined. We performed the Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq) and RNA-seq on peripheral blood mononuclear cells (PBMCs) from outpatients with mild or moderate symptom severity at different stages of clinical illness. Early in the disease course prior to IgG seroconversion, modifications in chromatin accessibility associated with mild or moderate symptoms were already robust and included severity-associated changes in accessibility of genes in interleukin signaling, regulation of cell differentiation and cell morphology. Furthermore, single-cell analyses revealed evolution of the chromatin accessibility landscape and transcription factor motif accessibility for individual PBMC cell types over time. The most extensive remodeling occurred in CD14+ monocytes, where sub-populations with distinct chromatin accessibility profiles were observed prior to seroconversion. Mild symptom severity was marked by upregulation classical antiviral pathways, including those regulating IRF1 and IRF7, whereas in moderate disease, these classical antiviral signals diminished, suggesting dysregulated and less effective responses. Together, these observations offer novel insight into the epigenome of early mild SARS-CoV-2 infection and suggest that detection of chromatin remodeling in early disease may offer promise for a new class of diagnostic tools for COVID-19.

overall_design: Identify transcriptomic profiles of sub-populations of CD14+ monocytes that distinguished IgG- subjects with mild from moderate symptoms.

first: Christopher

middle: W

last: Woods


title: RNA expression profile (RNA-Seq) in mouse colonic epithelium expressing endogenouse K-Ras-WT or oncogenic K-Ras-G12D

status: Public on May 13 2022

city: Boston

first: Bing

last: Shui

state: MA

address: 360 Longwood Ave

department: Cancer Biology

institute: Dana-Farber Cancer Institute

summary: K-Ras is frequently hyperactivated in human cancers through gain-of-function mutations that drive tumorigenesis. K-RasG12D, the most common oncogenic K-Ras allele, triggers massive transcriptomic and proteomic changes in the murine colon. Here, we report a comprehensive profile of physiological miRNA targets in murine colonic epithelium and tumor expressing K-RasG12D. Combining it with transcriptional, transcriptomic, and proteomic landscapes, we uncover a K-RasG12D-induced global suppression of miRNA activity that up-regulates hundreds of genes post-transcriptionally.  K-RasG12D suppresses Csnk1a1 and Csnk2a1, which can decrease Ago2 phosphorylation at Ser825/829/831/835. Hypo-phosphorylated Ago2 increases binding with mRNA, reducing its regulatory activity by locking Ago2 in a small set of target transcripts. While expanding the repertoire of miRNA targets identified, it functionally decreases active Ago2, resulting in global de-repression of miRNA targets. Our findings establish a regulatory relationship among K-Ras, Csnk1a1/Csnk2a1, and Ago2 that provides a mechanistic link between oncogenic K-Ras and the up-regulation of hundreds of miRNA targets.

overall_design: RNA-Seq of colonic epithelium from two mouse models, Fabp-Cre/+ (Control) and Fabp-Cre/+; K-Ras-G12D/+ (Experimental). Colonic epithelium from the control model expressed K-Ras-WT. Colonic epithelium from the experimental model expressed oncogenic K-Ras-G12D.

first: Kevin

last: Haigis


title: Oncogenic K-Ras suppresses global miRNA function

type: Non-coding RNA profiling by high throughput sequencing


title: Halo-enhanced Ago2 pulldown (HEAP) to identify miRNA targets in murine colonic epithelium +/- oncogenic K-Ras-G12D

overall_design: HEAP was performed on colonic epithelium from two mouse models, Halo-Ago2/+; Fabp-Cre/+ (Control) and Halo-Ago2/+; Fabp-Cre/+; K-Ras-G12D/+ (Experimental). Colonic epithelium from the control model expressed K-Ras-WT. Colonic epithelium from the experimental model expressed oncogenic K-Ras-G12D. mRNA, miRNA, and input-control (IC) libraries were generated for each sample.


title: Halo-enhanced Ago2 pulldown (HEAP) to identify miRNA targets in murine colonic tumor +/- oncogenic K-Ras-G12D

overall_design: HEAP was performed on colonic tumor from two mouse models, Halo-Ago2/+; Villin-CreER/+; Apc(fl/fl) (Control) and Halo-Ago2/+; Villin-CreER/+; Apc(fl/fl); K-Ras-G12D/+ (Experimental). Colon tumor were induced in 8-12 weeks old animal with enema of 200µl 4-hydroxytamoxifen (4-OHT, 5mg/ml in 100% ethanol). Colonic tumor from the control model expressed K-Ras-WT. Colonic tumor from the experimental model expressed oncogenic K-Ras-G12D. mRNA, miRNA, and input-control (IC) libraries were generated for each sample.


title: In Vivo Genome-wide PGR Binding in Pregnant Human Myometrium Identifies Potential Regulators of Labor

status: Public on May 05 2022

city: Chicago

first: Ariel

last: Dotts

state: IL

address: 303 E Superior Street

institute: Northwestern University


title: Single-cell analysis of human testis aging and correlation with elevated body mass index

city: Salt Lake City

first: Jingtao

last: Guo

state: UT

address: 2000 Circle of Hope

department: Department of Surgery Division of Urology

institute: University of Utah School of Medicine

summary: Aging human males display reduced reproductive health, however testis aging is poorly understood at the molecular and genomic level. Here, we utilized single-cell RNA-seq to profile over 44,000 cells from both young and older men (>60 years old) – and examined age-related changes in germline development and in the somatic niche. Interestingly, age-related changes in spermatogonial stem cells appeared modest, whereas age-related dysregulation of spermatogenesis and the somatic niche ranged from moderate to severe. Altered pathways included signaling and inflammation in multiple cell types, metabolic signaling in Sertoli cells, hedgehog signaling and testosterone production in Leydig cells, cell death and growth in testicular peritubular cells, and possible developmental regression in both Leydig and peritubular cells. Remarkably, the extent of dysregulation correlated with body mass index in older, but not younger men. Taken together, we reveal candidate molecular mechanisms underlying the complex testicular changes conferred by aging, and their exacerbation by concurrent chronic conditions such as obesity.

overall_design: We profiled single cell transcriptomes of testes from eight older adults (>60 years old), and compared to four young fertile adults (17-22 years old) – resulting in a dataset consisting of over 44,000 single cell transcriptomes. We examined the transcriptional changes within each major testicular cell type during aging, which revealed a set of molecular mechanisms underlying human testis aging.

first: Xichen

last: Nie

first: Bradley

middle: R

last: Cairns


title: Single-cell and single-nucleus transcriptome analysis of pattern formation in the early embryo of the spider Parasteatoda tepidariorum

status: Public on May 04 2022

city: Takatsuki

first: Yasuko

last: Akiyama-Oda

state: Osaka

address: Murasaki-cho 1-1

country: Japan

institute: JT Biohistory Research Hall

summary: In a cellular field of the early spider embryo, Hedgehog signaling operates to specify a “fuzzy” French-flag-like pattern along the primary axis. We applied single-cell and single-nucleus RNA sequencing to the early spider embryo. We confirmed that these techniques successfully detected three cell population corresponding to germ layers and some known cell types. We showed that the data had sufficient information for reconstruction of a correct global polarity of the presumptive ectoderm.

overall_design: Cells and nuclei were isolated from whole embryos at late germ-disc stage and analyzed using single-cell and single-nucleus RNA-seq.

first: Hiroki

last: Oda


title: RNA expression profile (RNA-Seq) in mouse colonic tumor expressing endogenouse K-Ras-WT or oncogenic K-Ras-G12D

overall_design: RNA-Seq of colonic tumor from two mouse models, Villin-CreER/+; Apc(fl/fl) (Control) and Villin-CreER/+; Apc(fl/fl); K-Ras-G12D/+ (Experimental). Colon tumor were induced in 8-12 weeks old animal with enema of 200µl 4-hydroxytamoxifen (4-OHT, 5mg/ml in 100% ethanol). Colonic tumor from the control model expressed K-Ras-WT. Colonic tumor from the experimental model expressed oncogenic K-Ras-G12D.


title: Chromatin accessbility profile (ATAC-Seq) in mouse colonic epithelium and tumor expressing endogenouse K-Ras-WT or oncogenic K-Ras-G12D

overall_design: ATAC-Seq of colonic epithelium from two mouse models: Fabp-Cre/+ (Control) and Fabp-Cre/+; K-Ras-G12D/+ (Experimental), and colonic tumor from two mouse models: Villin-CreER/+; Apc(fl/fl) (Control) and Villin-CreER/+; Apc(fl/fl); K-Ras-G12D/+ (Experimental). Tissues from the control model expressed K-Ras-WT. Tissues  from the experimental model expressed oncogenic K-Ras-G12D.


title: In Vivo Genome-wide PGR Binding in Pregnant Human Myometrium Identifies Potential Regulators of Labor [RNA-seq]

summary: The alterations in myometrial biology during labor are not well understood. The myometrium is the contractile portion of the uterus and contributes to labor, a process that may be regulated by the steroid hormone progesterone. Thus, human myometrial tissues from term pregnant in-active-labor (TIL) and term pregnant not-in-labor (TNIL) subjects were used for genome-wide analyses to elucidate potential future preventive or therapeutic targets involved in the regulation of labor. Using myometrial tissues directly subjected to RNA sequencing (RNA-seq), progesterone receptor (PGR) chromatin immunoprecipitation sequencing (ChIP-seq), and histone modification ChIP-seq, we profiled genome-wide changes associated with gene expression in myometrial smooth muscle tissue in vivo. In TIL myometrium, PGR occupied predominatly promoter regions including the classical progesterone response element, whereas it bound predominantly to intergenic regions in TNIL myometrial tissue. Differential binding analysis uncovered over 1700 differential PGR-bound sites between TIL and TNIL with 1361 sites gained and 428 lost in labor. Functional analysis identified multiple pathways involved in cAMP-mediated signaling enriched in labor. A three-way integration of the data for ChIP-seq, RNA-seq and active histone marks uncovered the following genes associated with PGR binding, transcriptional activation and altered mRNA levels: ATP11A, CBX7, and TNS1. In vitro studies showed that ATP11A, CBX7, and TNS1 are progesterone responsive. We speculate that these genes may contribute to the contractile phenotype of the myometrium during various stages of labor. In conclusion, we provide novel labor associated genome-wide events and PGR-target genes that can serve as targets for future mechanistic studies.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for human myometrium from women term in labor (TIL) and term not in labor (TNIL).


title: RBAP48 modulates the oral squamous cell carcinoma process through AR-dependent and independent mechanisms

status: Public on Aug 15 2022

first: Ge

last: Sun

state: Hubei

address: Shizi Mountain Street No.1

institute: Huazhong Argriculture University

summary: Oral squamous cell carcinoma is a head and neck malignancy induced by multiple factors. The progression of OSCC involves epithelial cell proliferation from fibrosis to malignancy. However, the underlying molecular mechanisms that influence these processes remain unclear. Here, we identify RBAP48, an important AR co-activator involved in OSCC cancer progression. RBAP48 is highly expressed in OSCC tissues and has a poor prognosis. As a DHT-dependent AR coactivator, RBAP48 not only up-regulates the transcriptional activity of AR but also affects the transcription of target genes in the cell cycle and external stimulation pathways throughout the genome. RBAP48 can interact with SP1, AR, and other transcription factors in OSCC cells and co-recruit the promoter region of CCND1 and RAB31. Finally, we find that RBAP48 can promote the growth of OSCC cells, stimulate the response to drugs and external substances in vitro and in vivo, and ultimately promote cancer progression. These results suggest that RBAP48 may be an effective target for predicting the progression and treatment of OSCC cancer.

overall_design: Examination the total RNA change of RBAP48 depletion in CAL-27 cells

first: Xue


title: Transcriptomic, epigenetic and metabolic characterization of the pluripotency continuum in rabbit preimplantation embryos

status: Public on Aug 22 2022

city: BRON

first: Wilhelm

last: Bouchereau

state: Rhone-Alpes

address: 18 Avenue du Doyen Lépine

institute: INSERM

summary: Despite the growing interest in the rabbit model for developmental and stem cell biology, the characterization of embryos at the molecular level is still poorly documented. We conducted a transcriptome analysis of rabbit pre-implantation embryos from E2.7 (morula stage) to E6.6 (early primitive streak stage) using SmartSeq2 bulk RNA-sequencing, single-cell 10X Genomics RNA-seq and single-cell Biomark qPCR. In parallel, we studied oxidative phosphorylation and glycolysis and analyzed active and repressive epigenetic modifications during blastocyst formation and expansion. We generated a transcriptomic, epigenetic, and metabolic map of the pluripotency continuum in rabbit preimplantation embryos and identified novel markers of naïve pluripotency that might be instrumental for deriving naïve pluripotent stem cell lines. Although the rabbit is evolutionarily closer to mice than to primates, we found that the transcriptome of rabbit epiblast cells shares common features with that of humans and non-human primates.

overall_design: Transcriptomic profiling of rabbit embryos from day 3.0 to 6.6 post-fertilization

first: Nathalie

last: Beaujean


title: High-Throughput Profiling of Colorectal Cancer Liver Metastases Reveals Intra- and Inter-Patient Heterogeneity in the EGFR and WNT Pathways Associated with Clinical Outcome

status: Public on Apr 30 2022

city: Göttingen

first: Darius

last: Wlochowitz

address: Goldschmidtstr. 1

department: Bioinformatics

institute: Institute of Bioinformatics

summary:
Introduction: In cancer progression the development of distant metastases is the crucial adverse event. In colorectal cancer 70% of patients develop metastases in the liver. Within the BMBF-founded consortium MetastaSys, the role of the WNT and EGFR pathway in these metastases was investigated. In order to address the phenomenon of intermetastatic heterogeneity metastasis profiling was applied to several metastases of two patients.
Methods: Four and two sequential liver metastases of two pilot cases, as well as corresponding normal liver tissue were comprehensively characterized in terms of clinical annotations, standardized histopathological and molecular subtyping. In all metastases the mutational status of KRAS, NRAS, BRAF and PIK3CA was assessed, as well as alterations in DNA mismatch repair enzymes and microsatellite instability. Fresh frozen samples were characterized by an experienced pathologist (tumor cell content, amount of stroma, inflammatory infiltrate and necrosis) to assure high quality of tissue. Samples were subsequently profiled via transcriptome sequencing (RNA-Seq) and proteomic profiling with Reverse-Phase-Protein-Arrays (RPPA).
Results: A standardized data analysis pipeline for an integrated analysis of RNA-Seq and protein array data with clinical and genetic data was established. Dimensionality reduction of the transcriptome data revealed a distinct separation between normal tissue and metastases samples. Interestingly, the correlation between healthy samples of both patients was higher compared to the correlation between different metastatic samples of an individual patient. In different metastases of the same patient heterogeneous expression patterns were identified in the EGFR and the WNT pathway with relevant implication for clinical treatment approaches.
Conclusion: High-throughput profiling of gene expression allows a clear discrimination between normal and metastatic liver tissue. Identified master regulators could identify drivers of intrapatient metastasis heterogeneity. Based on our findings and the positive validation of the established methodology including innovative high-throughput profiling and comprehensive bioinformatics approaches we started analyzing a large number of metastatic patient samples within the consortium.

overall_design: Two conditions of rectal cancer patient (I+II) data separates by the event of distant metastasis:  1. good prognosis, no event (3 samples),  2. bad prognosis, event (8 samples); remaining patients are categorized as bad prognosis, event (43 samples).

first: Annalen

last: Bleckmann

first: Astrid

last: Wachter

first: Lena

last: Conradi

first: Alexander

last: Wolff

first: Kerstin

last: Menck

first: Clara

last: Hoppenau

first: Andreas

last: Scheel

last: Schlüter

first: Ulrike

last: Korf

first: Hans

middle: U

last: Schildhaus

first: Edgar

last: Wingender

first: Tobias

last: Pukrop

first: Kia

last: Homayounfar

first: Tim

last: Beißbarth


title: A multiplex platform for small RNA sequencing elucidates multifaceted tRNA stress response and translational regulation

status: Public on Mar 13 2022

first: Christopher

middle: D

last: Katanski

state: Illinois

department: Biochemistry

institute: The University of Chicago

summary: Small RNAs include tRNA, snRNA, micro-RNA, tRNA fragments and others that constitute >90% of RNA copy numbers in a human cell and perform many essential functions. Popular small RNA-seq strategies limit the insights into coordinated small RNA response to cellular stress. Small RNA-seq also lacks multiplexing capabilities. Here, we report a multiplex small RNA-seq library preparation method (MSR-seq) to investigate cellular small RNA and mRNA response to heat shock, hydrogen peroxide, and arsenite stress. Comparing stress-induced changes of total cellular RNA and polysome-associated RNA, we identify a coordinated tRNA response that involves polysome-specific tRNA abundance and synergistic N3-methylcytosine (m3C) tRNA modification. Combining tRNA and mRNA response to stress we reveal a new mechanism of stress-induced down-regulation in translational elongation. We also find that native tRNA molecules lacking several modifications are biased reservoirs for the biogenesis of tRNA fragments. Our results demonstrate the importance of simultaneous investigation of small RNAs and their modifications in response to varying biological conditions.

overall_design: This study contains 64 samples divided between the following experimentes: CMC treatment, demethylase treatment, input titrations, stressed tRNA, stressed tRNA from polysomes, stressed mRNA, and stressed mRNA from polysomes. 4 samples are associated with CMC project, two replicates of RNA with and without N-cyclohexyl-N′-β-(4-methylmorpholinium) ethylcarbodiimide (CMC) treatment. 6 samples are associated with demethylase treatment, three replicates of RNA with and without AlkB demethylase treatment. 6 samples are assoicated with input titrations, two replicates for each of 10ng 100ng and 1000ng input amounts. 12 samples are associated with stressed tRNA, three replicates for each of no stress, heat stress, H2O2 stress, and AsO2. 12 samples are assoicated with stressed tRNA from polysomes, three replicates from four conditions as before. 12 samples are assoicated with stressed mRNA, three replicates from four treatments as before. 12 samples are assoicated with stress mRNA from polysomes, three replicates from four treatments as before.

last: Watkins

first: Wen

last: Zhang

first: Adam

last: Wylder

first: Tao

last: Pan


title: Effects of stressful life-events on DNA methylation in panic disorder and major depressive disorder

status: Public on Apr 22 2022

city: Munich

first: Binder

last: Elisabeth

address: Kraepelinstr. 2+10

institute: Max-Planck-Institute Psychiatry

type: Methylation profiling by genome tiling array

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

overall_design: Refer to individual Series


title: Male and female flow sorted adipose tissue macrophages and hematopoietic stem cells

status: Public on Mar 07 2022

city: Ann Arbor

first: Bioinformatics

last: Core

state: MI

address: BRCF Bioinformatics Core, 2800 Plymouth Rd

institute: University of Michigan

summary: Comparison of hematopoetic stem cells (HSC) and adipose tissue macrophages (ATM) in mouse adipose tissue. HSCs are progenitors for circulating leukocytes and recruited tissue macrophages. Males have increased numbers of ATMs and HSCs in response to high fat diet. In addition there are qualitative differencs with male ATMs releasing pro-inflamatory cytokines and factors impairing adipocyte function.  M: male, F: female, ND: normal diet, HF: high fat diet.

overall_design: The sample design includes two cell types (ATM and HSC), two feeding regimes (ND and HF), and both sexes (M and F), giving 8 groups: ATM.M.ND, ATM.M.HF, ATM.F.ND, ATM.F.HF, HSC.M.ND, HSC.M.HF, HSC.F.ND, and HSC.F.HF. There are 4 replicates per group, giving 32 samples.

first: Kanakadurga

middle: V

last: Singer


title: Mouse DNA methylation atlas using Infinium Mouse Methylation Beadchips

status: Public on Apr 11 2022

city: Philadelphia

first: Wanding

last: Zhou

address: 3501 Civic Center Blvd

department: Pathology and Lab Medicine

institute: Children's Hospital of Philadelphia

summary: Design, annotation, and technical and biological validation of the MouseMethylation Beadchips (MM285) platform. Application of the mouse array for tissue and tumor epigenetics, comparative epigenomics, genomic imprinting, epigenetic inhibitors, PDX assessment, backcross tracing, and epigenetic clocks.

sample_organism:
Homo sapiens
Cricetulus griseus
Mus musculus
Rattus norvegicus

overall_design:
1239 DNA samples encompassing distinct tissues, strains, age, sex, and pathologies.

We have developed a mouse DNA methylation array that contains 296,070 probes representing the diversity of mouse DNA methylation biology. We present a mouse methylation atlas as a rich reference resource of 1,239 DNA samples encompassing distinct tissues, strains, ages, sexes, and pathologies. We describe applications for comparative epigenomics, genomic imprinting, epigenetic inhibitors, patient-derived xenograft assessment, backcross tracing, and epigenetic clocks. We dissect DNA methylation processes associated with differentiation, aging, and tumorigenesis. We find that tissue-specific methylation signatures localize to binding sites for transcription factors controlling the corresponding tissue development. Age-associated hypermethylation is enriched at regions of Polycomb repression, while hypomethylation is enhanced at regions bound by cohesin complex members. ApcMin/+ polyp-associated hypermethylation affects enhancers regulating intestinal differentiation, while hypomethylation targets AP-1 binding sites. This Infinium Mouse Methylation BeadChip (version MM285) is widely accessible to the research community and will accelerate high-sample-throughput studies in this important model organism.

More probe annotations can be found at
http://zwdzwd.github.io/InfiniumAnnotation#mouse
More sample information can be found at
https://github.com/zhou-lab/2022MM285CellGenomics

first: Hui

last: Shen

first: Peter

last: Laird


title: Transcriptome of hBMSCs

status: Public on Apr 09 2022

city: 大连

first: 张

last: 疆雨

address: 甘井子区凌工路2号

institute: 大连理工大学

summary:
We selected three neonicotinoids and nicotine to expose the hBMSCs
We obtained the gene expression which can help us identify the potential toxic effects of NEOs on human body

overall_design: Detection of gene expression in hBMSCs.

first: Liu

last: Wei

first: Luo

last: Fang


title: Epigenome-wide association analysis on weighted life events in PD patients - replication cohort

summary:
Background: Panic disorder (PD) is characterized by recurrent panic attacks and higher affection of women as compare to men. The lifetime prevalence of PD is about 2-3 % in the general population leading to tremendous distress and disability. Etiologically, genetic and environmental factors, such as stress, contribute to the onset and relapse of PD. In the present study, we investigated epigenome-wide DNA methylation (DNAm) in respond to a cumulative, stress-weighted life events score (wLE) in patients with PD and its boundary to major depressive disorder (MDD), frequently co-occurring with symptoms of PD.
Methods: DNAm was assessed by the Illumina HumanMethylation450 BeadChip. In a meta-analytic approach, epigenome-wide DNAm changes in association with wLE were first analyzed in two PD cohorts (with a total sample size of 183 PD patients and 85 healthy controls) and lastly in 102 patients with MDD to identify possible overlapping and opposing effects of wLE on DNAm. Additionally, analysis of differentially methylated regions (DMRs) was conducted to identify regional clusters of association.
Results: Two CpG-sites presented with p-values below 1x10-05 in PD: cg09738429 (p=6.40x10-06, located in an intergenic shore region in next proximity of PYROXD1) and cg03341655 (p=8.14x10-06, located in the exonic region of GFOD2). The association of DNAm at cg03341655 and wLE could be replicated in the independent MDD case sample indicating a diagnosis independent effect. Genes mapping to the top hits were significantly upregulated in brain and top hits have been implicated in the metabolic system. Additionally, two significant DMRs were identified for PD only on chromosome 10 and 18, including CpG-sites which have been reported to be associated with anxiety and other psychiatric phenotypes.
Conclusion: This first DNAm analysis in PD reveals first evidence of small but significant DNAm changes in PD in association with cumulative stress-weighted life events. Most of the top associated CpG-sites are located in genes implicated in metabolic processes supporting the hypothesis that environmental stress contributes to health damaging changes by affecting a broad spectrum of systems in the body.

overall_design:
DNAm was assessed by the Illumina HumanMethylation450 BeadChip. In a meta-analytic approach, epigenome-wide DNAm changes in association with weighted life events were analyzed in two PD cohorts (with a total sample size of 183 PD patients and 85 healthy controls). This is the data from the replication cohort.
Bisulphite converted DNA from the 159 samples were hybridized to the Illumina Infinium 450k Human Methylation Beadchip

first: Darina

last: Czamara

first: Stella

last: Iurato

first: Angelika

last: Erhardt


title: Integrative analysis of DNA methylation and gene expression identified follicular thyroid cancer-specific diagnostic biomarkers

status: Public on Mar 05 2022

city: Hangzhou

first: Lisong

last: Teng

address: Yuhangtang Road

institute: Zhejiang University


title: Integrative analysis of DNA methylation and gene expression identified follicular thyroid cancer-specific diagnostic biomarkers [Methylation]

summary: The diagnosis of follicular thyroid carcinoma (FTC) prior surgical resection remains a challenge, as routine screening methods, such as ultrasound or even FNAB, could not diagnose FTC preoperatively. Here, we performed an integrative analysis of DNA methylation and RNA assays data from our own cohort (14 Follicular thyroid carcinoma vs 16 Benign thyroid lesion) to identify thyroid cancer-specific DNA methylation markers. We first identified differentially methylated and expressed genes and examined their correlations. Candidate DNA methylation sites were selected and further verified in validation set. Among all candidate methylation sites, cg06928209 was the most promising site as a molecular marker for early diagnosis, with a sensitivity of 90%, a specificity of 80% and an AUC of 0.77. Overall, our study demonstrates the potential use of methylation markers in FTC diagnosis and may boost the development of new epigenetic therapies.

overall_design: Here, we performed an integrative analysis of DNA methylation and RNA expressing data from our own cohort (14 Follicular thyroid carcinoma vs 16 Benign thyroid lesion) to identify thyroid cancer-specific DNA methylation markers.

first: Li

middle: S

first: Wang

last: Weibin

first: Lou

last: Xiaoming


title: Transcriptome profile of LX-2 cells

status: Public on Feb 28 2022

city: Pozzuoli

first: Rossella

last: De Cegli

address: Via Campi Flegrei 34

country: Italy

institute: Tigem

summary: To analyse gene expression differences between treated and untreated cells with human recombinant TGF beta in presence and in absence of mimic miR34b/c.

overall_design: Total RNA was extracted from n=5  or n=4 samples for group

first: R


title: Epigenome-wide association analysis on weighted life events in PD patients - discovery cohort

first: Binder

overall_design:
DNAm was assessed by the Illumina HumanMethylation450 BeadChip. In a meta-analytic approach, epigenome-wide DNAm changes in association with weighted life events were analyzed in two PD cohorts (with a total sample size of 183 PD patients and 85 healthy controls). This is the data from the discovery cohort.
Bisulphite converted DNA from the 109 samples were hybridized to the Illumina Infinium 450k Human Methylation Beadchip


title: The gastrin-releasing peptide regulates stress-enhanced fear and dopamine signaling

status: Public on Dec 01 2021

city: Piscataway

first: Premal

last: Shah

state: NJ

address: 145 Bevier Rd

department: Genetics

institute: Rutgers University

summary: Fear extinction is an adaptive behavioral process critical for organism’s survival, but deficiency in extinction may lead to PTSD. While the amygdala and its neural circuits are critical for fear extinction, the molecular identity and organizational logic of cell types that lie at the core of these circuits remain unclear. Here we report that mice deficient for amygdala-enriched gastrin-releasing peptide gene (Grp-/-) exhibit enhanced neuronal activity in the basolateral amygdala (BLA) and stronger fear conditioning, as well as deficient extinction in stress-enhanced fear learning (SEFL). rAAV2-retro-based tracing combined with visualization of the GFP knocked in the Grp gene showed that BLA receives several GRPergic conditioned stimulus projections: from the indirect auditory thalamus-to-auditory cortex pathway, medial prefrontal cortex, ventral hippocampus and ventral tegmental area. Transcription of dopamine-related genes was decreased in BLA of Grp-/- mice following SEFL extinction recall, suggesting that the GRP may mediate fear extinction regulation by dopamine.

overall_design: RNA-seq from mouse brain tissue. Gene expression from 4 replicates each from 4 separate conditions were compared. The sample names are WT or KO (for wild type or Grp -/- mice), an S indicates the mouse had undergone stress treatment (a lack of S indicates no stress treatment), and the mouse number.

first: Yoshikazu

last: Morishita

first: Ileana

last: Fuentes

first: John

last: Favate

first: Ko

last: Zushida

first: Akinori

last: Nishi

first: Charles

last: Hevi

first: Noriko

last: Goldsmith

first: Steve

last: Buyske

first: Stephanie

last: Silivan

first: Courtney

last: Miller

first: Eric

last: Kandel

first: Shusaku

last: Uchida

first: Gleb

last: Shumyatsky


title: 25-Hydroxycholesterol Inhibits KSHV and EBV Infections and Activates Inflammatory Cytokines

status: Public on Nov 24 2021

city: Bethesda

first: Joseph

middle: M

last: Ziegelbauer

address: 10 Center Dr. 6N110

institute: NIH / National Cancer Institute

summary: We previously demonstrated that 25HC (25-hydroxycholesterol, a derivative of cholesterol) blocks KSHV (Kaposi Sarcoma-associated Herpesvirus/ Human Herpesvirus-8) de novo infection of primary endothelial cells at a post-entry step and decreases viral gene expression. Herein we sought to determine transcriptomic changes associated with 25HC treatment of primary endothelial cells and primary B cells using RNA sequencing. To understand how 25HC inhibits KSHV infection, we examined global gene expression changes induced by 25HC in HUVECs, with or without KSHV infection. We pre-treated HUVEC with 25HC or vehicle control, then infected with KSHV (four conditions: -/+ 25HC, -/+ infection). At 2 days post-infection (dpi), we harvested RNA and performed RNA-seq to determine differentially expressed genes. We found that 25HC treatment inhibited KSHV gene expression globally and induced several inflammatory cytokines (CXCL8, IL1?), AP-1 components, and innate immunity receptors (RIG-I, TLR2) . Likewise, we also observed 25HC to block EBV de novo infection by inducing apoptosis and blocking transformation into lymphoblastoid cell lines. To determine transcriptomic changes that contributes to this, we purified B cells from healthy donors and infected them with EBV after 25HC pre-treatment with 4 similar conditions mentioned above. Samples were sent for RNA-Seq at 10-12 dpi. In contrast to KSHV infection, we found that only a subset of EBV viral transcripts are downregulated in the 25HC-treated samples. LMP1, which is the primary oncogenic factor, was suppressed and several downstream host targets that would prevent apoptosis during infection were likewise dysregulated. Additionally, several viral noncoding RNAs were also highly downregulated. Further analyses revealed that some 25HC-induced genes in our KSHV data set overlap with antiviral genes that were previously identified in various published screens involving other viruses, demonstrating the broad activity of 25HC. Together, these results answer some important questions about a widely acting antiviral (25HC), with implications for multiple viral and bacterial infections.

overall_design: Four biological replicates of KSHV de novo infected HUVEC were submitted for total RNA sequencing. Sixteen RNA samples were depleted for ribosomal RNA and pooled for sequencing on four lanes on HiSeq4000 with Illumina Hiseq3000-4000 chemistry. All the samples have excellent yield with yield above 146 million reads. Alignment was performed with reference human hg19 genome with KSHV [hg19v24 with KSHV(NC_009333.1)] and gencode v24 transcripts using STAR software. Quantification was carried out with RSEM using transcriptome bam file created by STAR and gencode v24 transcriptome as index for RSEM. Four biological replicates of EBV de novo infections and 3 biological replicates of uninfected (mock) control of B cells (purified using MACSExpress from Buffy coats) were submitted for total RNA sequencing. Fourteen RNA samples were depleted for ribosomal RNA using Illumina Ribo-Zero rRNA removal kit and submitted for sequencing using HiSeq 4000 or equivalent machine. All the samples have excellent yield with yield above 270 million reads. Alignment was performed with reference human hg38 genome with EBV [hg38v30 with EBV (NC_007605.1)] and gencode v30 transcripts using STAR software. Quantification was carried out with RSEM using transcriptome bam file created by STAR and gencode v30 transcriptome as index for RSEM.

first: Anna

last: Serquiña

first: Guruswamy

last: Mahesh


title: Extended data for pancreas single-cell patch-seq dataset in nondiabetic and T2D

status: Public on Jan 27 2022

city: Gothenburg

first: Joan

last: Camunas-Soler

address: Medicinaregatan 9C

country: Sweden

institute: University of Gothenburg

summary: Combined single-cell RNAseq and electrophysiological profiling of human pancreatic islet cells (pancreas patch-seq).

overall_design: The dataset contains 640 pancreas patch-seq cells from human donors (nondiabetic and with T2D). Single-cell RNA libraries are done using SmartSeq2.

first: Xiaoqing

last: Dai

first: Seung

middle: K

last: Kim

first: Patrick

last: MacDonald

first: Stephen

last: Quake


title: A Convergent Mechanism of High Risk Factors ADNP and POGZ in Neurodevelopmental Disorders

status: Public on Nov 17 2021

city: Buffalo

first: Zhen

last: Yan

state: NY

address: 955 Main St

institute: SUNY Buffalo

summary: We performed RNAseq experiments to examine genome-wide transcriptional changes in PFC of shRNA-Adnp and shRNA-Pogz KD mice compared to GFP injected controls mice.

overall_design: mRNA via RNAseq analysis of three 6-8 week old  shRNA-Adnp-injected and shRNA-Pogz-injected KD mice  (C57BL6/J) , and two 6-8 week old GFP-injected control mice (C57BL6/J) PFC tissue were compared.

first: Jamal

last: Williams


title: Kidney RNA expression levels in the Hybrid Rat Diversity Panel for the PhenoGen website (https://phenogen.org)

status: Public on Apr 01 2022

city: Aurora

first: Laura

last: Saba

state: CO

address: 12850 E. Montview Blvd

department: Skaggs School of Pharmacy and Pharmaceutical Sciences

institute: University of Colorado Anschutz Medical Campus

summary: As part of the PhenoGen Project (https://phenogen.org), kidney RNA-Seq data has been collected from the HXB/BXH recombinant inbred rat panel, which is part of the Hybrid Rat Diversity Panel (HRDP). RNA expression levels were estimated using high throughput RNA sequencing (RNA-Seq) on long (>200 nucleotides) RNAs, i.e., total RNA where ribosomal RNA was depleted. These data can be used to examine predisposition phenotypes in the HRDP. Processed data and interactive graphics are also available through the PhenoGen website.

overall_design:
RNA expression data has been gathered over several tissues (e.g., brain, liver, heart, kidney) on rats from the Hybrid Rat Diversity Panel (HRDP) as part of the RGAP: The heritable transcriptome and alcoholism project funded by NIAAA R24 AA013162. For each strain, RNA from 3 naive male biological replicates is extracted and a separate RNA-Seq library is generated from each replicate. rRNA-depleted total RNA is used to generate libraries and libraries are sequenced using Illumina sequencing technology. All rats used in this study were alcohol and drug naive and were NOT subjected to any behavioral testing. Therefore, these data represent a predisposition database that can be used for integrative systems genetics studies.
This dataset includes data from kidney.

Please note that the records have been updated with the additional PhenoGen.HRDP.v6* processed data (generated with a new genome version (rn7.2)) on Sep 14, 2023.

first: Boris

last: Tabakoff

first: Paula

last: Hoffman


title: In vitro expansion of human sperm through nuclear transfer

status: Public on Dec 30 2021

city: Shanghai

first: Yuxuan

last: Zheng

address: 825 Zhangheng Rd.

institute: Fudan University

type: Methylation profiling by high throughput sequencing

summary:
We reported a kind of new haploid embryonic stem cell, human haploid androgenetic embryonic stem cell, which kept the sperm characteristic epigenetic modification patterns for imprinting genes. In this study, two human haploid androgenetic embryonic stem cell lines (ha-AGHESC) and two human haploid parthenogenetic embryonic stem cell lines (ha-PGHESC) with somatic control and diploid HESC control, were processed with RNA-sequencing (RNA-seq) and whole genome bisulfite sequencing (WGBS). We showed that the reconstructed semi-clone HESCs were similar to the diploid HESC in transcriptome and the methylome especially related to the known human imprinting genes.

The raw data of WGBS and bulk RNA-seq are deposited at Genome Sequence Archive (GSA) of Human with accession number HRA004100.

overall_design:
In this study, ha-AGHESC lines and ha-PGHESC lines each with two biological replications in early passages and elder passages were processed with RNA-seq and WGBS. One somatic sample, blood, and one HESC sample HUES42 were set as diploid controls. ICA1 and ICA2 were reconstructed diploid semi-clone HESC derived from semi-clone blastocysts that constructed by fusing ha-AGHESC with in vitro maturation (IVM) oocytes. Each sample had two technical replications.

Please note that the processed data *1X_sort_CpG.bed files have been added for the GSM3737096-GSM3737117 samples on Jun 3, 2025.

first: Xiaoyu

last: Zhang

first: Keliang

last: Wu

first: Han

last: Zhao

first: Junpeng

last: Gao

first: Zhenzhen

last: Hou

first: Meiling

first: Jiaoyang

last: Liao

first: Jingye

first: Yuan

first: Yuanyuan

last: Li

first: Lin

first: Fuchou

last: Tang

first: Zi-Jiang

last: Chen

first: Jinsong


title: Single-cell profiling of T lymphocytes in deficiency of adenosine deaminase 2

status: Public on Nov 22 2021

first: Shouguo

address: 9000 Rockville Pike

department: NHLBI

institute: National Institutes of Health

summary:
Background and methods: Deficiency of adenosine deaminase 2 (DADA2) is the first molecularly described monogenic vasculitis syndrome. DADA2 is caused by autosomal-recessive loss-of-function mutations in the ADA2 gene (previously known as CECR1). Vasculitis, vasculopathy and inflammation are dominant clinical features of this disease; however wide spectrum of clinical manifestations includes immunodeficiency, lymphoproliferation, as well as hematologic manifestations. ADA2 is primarily secreted by stimulated monocytes and macrophages. It has been shown that monocytes differentiation to macrophages, and neutrophils play a pathogenic role in DADA2, but little is known about T lymphocytes in this disease.
Results: We performed combined single cell RNA sequencing and TCR sequencing to profile T cell repertoire in ten patients with DADA2. Although there are no significant alterations of T cell subsets, we observed activation of both CD8+ and CD4+ T cells, and inflammatory status in these patients. We did not observe clonal expansion of T cells: majority TCRs are expressed at basal level in patients and healthy donors. TCR usage is individual-specific in patients and not disease-specific, indicating unlikely a common pathogenic background or predisposition to a common pathogen in this cohort of patients. We recognized activation of interferon pathways as signature of T cells, and STAT1 as a hub gene in the gene network of T cell activation and cytotoxicity. Overall, T cells in DADA2 patients have altered cell-cell interactions with monocytes, as compared to that in healthy donors, many of these ligand-receptor interactions likely drive upregulation of STAT1 in both T cells and lymphocytes in patients.
Conclusion: In conclusion, our single cell analysis of T cells discloses subsets, clonality and transcriptome of a previously undercharacterized cell type in DADA2. Activation of immune response especially IFN pathways remain the core signature of T cells and monocytes. Modulation of IFN pathway, as well as ligand-receptor pairs between immune cells may contribute a novel and directed therapeutic approach in the treatment of DADA2.

overall_design: RNA profiles of single peripheral blood T cells of 10 DADA2 patients and 5 healthy donors were generated by deep sequencing using Illumina HiSeq 3000

first: Zhijie


title: Liver RNA expression levels in the Hybrid Rat Diversity Panel for the PhenoGen website (https://phenogen.org)

first: Laura

summary: As part of the PhenoGen Project (https://phenogen.org), liver RNA-Seq data has been collected from strains of the Hybrid Rat Diversity Panel (HRDP). RNA expression levels were estimated using high throughput RNA sequencing (RNA-Seq) on long (>200 nucleotides) RNAs, i.e., total RNA where ribosomal RNA was depleted. These data can be used to examine predisposition phenotypes in the HRDP. Processed data and interactive graphics are also available through the PhenoGen website. Additional data from additional strains will be added as they become available.

overall_design:
RNA expression data has been gathered over several tissues (e.g., brain, liver, heart, kidney) on rats from the Hybrid Rat Diversity Panel (HRDP) as part of the RGAP: The heritable transcriptome and alcoholism project funded by NIAAA R24 AA013162. For each strain, RNA from 3 naive male biological replicates is extracted and a separate RNA-Seq library is generated from each replicate. rRNA-depleted total RNA is used to generate libraries and libraries are sequenced using Illumina sequencing technology. All rats used in this study were alcohol and drug naive and were NOT subjected to any behavioral testing. Therefore, these data represent a predisposition database that can be used for integrative systems genetics studies.
This dataset includes data from liver.

first: Boris

first: Paula


title: Exceptional response of high-risk neuroblastoma to RBM39 degrader Indisulam (ATAC-Seq)

city: Memphis

first: Hongjian

last: Jin

state: TN

address: 262 Danny Thomas Place

department: Center for Applied Bioinformatics

institute: St Jude Children's Research Hospital

summary: Indisulam selectively bridges splicing factor RBM39 to DCAF15 for proteasomal degradation. However, clinical trials indicate that patient stratification based upon the mechanism of action of indisulam may be required to achieve the best response. Here we show that neuroblastoma, a MYC-driven cancer characterized by splicing dysregulation, requires RBM39 for survival, expresses high levels of DCAF15 among different solid tumor lineages, and is the most sensitive cancer lineage to indisulam that achieves therapeutic effect by specifically targeting RBM39 in neuroblastoma. Genetic depletion or proteasomal degradation of RBM39 by indisulam induces drastic splicing event changes in neuroblastoma cells. Through specifically targeting RBM39, indisulam induces exceptional tumor response in multiple high-risk neuroblastoma models. Collectively we demonstrate that high RBM39 dependency and high-level expression of DCAF15 provide indisulam a more efficacious therapeutic window to treating high-risk neuroblastoma.

overall_design: Examination of chromatin accessibility, histone modification in these indisulam resistant tumor derived cell lines.

first: J

last: Fang

first: S

last: Singh

first: H

last: Yang


title: Exceptional response of high-risk neuroblastoma to RBM39 degrader Indisulam

overall_design: Refer to individual Series


title: Deep sequencing of yeast and mouse tRNAs and tRNA fragments using OTTR

status: Public on Mar 06 2022

city: Worcester

first: Oliver

last: Rando

state: Massachusetts

address: 364 Plantation St

department: BMP

institute: University of Massachusetts

summary: Deep sequencing of tRNAs have historically been nutoriously difficult. Here, we benchmark a newly developed library prep protocol termed OTTR agains intact tRNAs as well as tRNA fragments and show that OTTR outperforms any other commercial cloning protocol.

sample_organism:
Saccharomyces cerevisiae
Mus musculus

platform_organism:
Saccharomyces cerevisiae
Mus musculus

overall_design: Intact tRNA from mouse testisand S. cerevisiae, as well as tRNA fragments (tRFs) from mouse cauda epididymis and S. cerevisiae were cloned using three different protocols. Results were then compared to published data generated using different clonign protocols.

last: Gustafsson

first: Carolina

last: Galan

first: Tianxiong

last: Yu

first: Heather

last: Upton

first: Lucas

last: Ferguson

first: Ebru

last: Kaymak

first: Zhiping

last: Weng

first: Kathleen

last: Collins

middle: J

last: Rndo


title: Shear stress switches the association of endothelial enhancers from ETV/ETS to KLF transcription factor binding sites

status: Public on Mar 14 2022

city: PHILADELPHIA

first: Arndt

last: Siekmann

state: Pennsylvania

address: 421 Curie Boulevard, 1114 Biomedical Research Building II/III

department: Perelman School of Medicine

institute: UNIVERSITY OF PENNSYLVANIA

summary: The study shows transcriptional and chromatin changes in human umbilical cord endothelial cells (HUVEC) exposed to shear stress. In addition transcriptional changes in zebrafish endothelial cells in response to blood flow block are shown

sample_organism:
Danio rerio
Homo sapiens

platform_organism:
Danio rerio
Homo sapiens

overall_design: HUVEC were exposed to shear stress of 18 dyn/cm2 for 6 h and used for RNA-Seq, ATAC-Seq and H3K27ac ChIP-Seq. Blood flow was stopped in zebrafish embryos 48 hours post fertilization (hpf) for 4 h and endothelial cells were used for RNA-Seq

first: Roman

last: Tsaryk

first: Nora

last: Yucel

first: Elvin

last: Leonard

first: Noelia

last: Diaz

first: Olga

last: Bondareva

first: Maria

last: Odenthal-Schnittler

first: Zoltan

last: Arany

first: Juan

last: Vaquerizas

first: Hans

last: Schnittler

middle: F


title: A single-cell massively parallel reporter assay detects cell type specific cis-regulatory activity

status: Public on Nov 11 2021

city: St. Louis

first: SIQI

last: ZHAO

state: MO

address: Campus Box 8232 4515 McKinley Ave.

institute: Washington University in St. Louis

summary: We developed a single-cell massively parallel reporter assay (scMPRA) to measure the activity of libraries of cis-regulatory sequences (CRSs) across multiple cell-types simultaneously. As a proof of concept, we assayed a library of core promoters in a mixture of HEK293 and K562 cells and showed that scMPRA is a reproducible, highly parallel, single-cell reporter gene assay. Our results show that housekeeping promoters and CpG island promoters have lower activity in K562 cells relative to HEK293, which likely reflects developmental differences between the cell lines. Within K562 cells, scMPRA identified a subset of developmental promoters that are upregulated in the CD34+/CD38- sub-state, confirming this state as more “stem-like.” Finally, we deconvolved the intrinsic and extrinsic components of cell-to-cell variability and found that developmental promoters have a higher proportion of extrinsic noise compared to housekeeping promoters. We anticipate scMPRA will be widely applicable for studying the role of CRSs across diverse cell types.

sample_organism:
Escherichia coli
Homo sapiens
Mus musculus

overall_design: single-cell massively parallel reporter assay of a core promoter library with 676 members and each sequence is barcoded 3 times with a 16 bp DNA barcode. A second 25 bp random barcodes was added during cloning. The library was sequencd using bulk RNA-seq and single-cell RNA-seq in K562 and HEK293 cells. Each experiment contains 2 replicates.

first: Siqi

last: Zhao

first: Clarice

last: Hong

first: Connie

last: Myers

first: David

last: Granas

first: Micahel

last: White

first: Joseph

last: Corbo

first: Barak

last: Cohen


title: RNA expression levels in the Hybrid Rat Diversity Panel for the PhenoGen website (https://phenogen.org)

first: Laura

last: Saba

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


title: Transcriptome profiling of the mouse suprachiasmatic nucleus at single cell resolution

status: Public on Sep 06 2021

city: Cambridge

first: Emma

last: Morris

address: Francis Crick Avenue

department: Neurobiology

country: United Kingdom

institute: MRC Laboratory of Molecular Biology

summary: Circadian rhythms are governed by the hypothalamic suprachiasmatic nucleus (SCN) which consists of ca. 20,000 cellular oscillators bound together in a powerful time-keeping network. The goal of this study was to characterise its component cells and network structure by conducting single-cell sequencing of SCN organotypic slices. scRNASeq libraries were prepared using 10x Genomics Chromium Single Cell 3’ Library and Gel Bead v2 kit. SCN cells, diluted in 0.04% BSA-nuclease-free water, reverse transcription master mix and partitioning oil, were loaded on a ChromiumTM Single Cell A Chip and run on the Chromium Controller to obtain at target cell recovery rate of 8,000 cells. Final libraries were sequenced on one flow cell of an Illumina HiSeq 4000 with a read length of 26bp for read 1 (cell barcode and unique molecule identifier and sample barcode) and 98bp for read 2 (RNA read) to yield approximately 340 million reads per sample. We sequenced 13,324 cells from 52 SCN slices at circadian time 7.5 (mid-day) over three independent sequencing runs, and 16,996 cells from 36 SCN slices at circadian time 15.5 (mid-night) over two independent sequencing runs.

overall_design: 10X Genomics Single Cell Transcriptome Sequencing of the mouse SCN

first: E

middle: L

first: A

last: Patton

first: J

last: Chesham

first: M

middle: H

last: Hastings


title: Transcriptome profiling of nonlactating goat mammary glands.

status: Public on Oct 22 2021

city: Tai an

first: Rong

last: Xuan

state: Shan Dong

address: 61 Daizong Street

department: College of Animal Science and Veterinary Medicine

institute: Shandong Agricultural University

summary: The mammary gland redeveloped to the pre-pregnancy state during involution, which shows that the mammary cells have the characteristics of remodeling. The rapidity and degree of mammary gland involution are different between mice and dairy livestock (dairy cows and dairy goats). However, the molecular genetic mechanism of involution and remodeling of goat mammary gland has not yet been clarified. Therefore, this study carried out the RNA-sequencing of nonlactating mammary gland tissue of dairy goats in order to reveal the transcriptome characteristics of nonlactating mammary tissues and clarify the molecular genetic mechanism of mammary cell involution and remodeling.

overall_design: This research used nine healthy, disease-free Laoshan dairy goats raised at the Qingdao Aote goat breeding farm (Qingdao, Shandong, China). The goats were provided with the farm’s standard feeding and management environment. All goats were of third parity, and their average age was four years. Mammary gland tissues were collected during late lactation (LL) (n = 3, 240 d postpartum), the dry period (DP) (n = 3, 300 d postpartum), and late gestation (LG) (n = 3, 140 d after mating). And high-throughput transcriptome sequencing was conducted on these samples.

first: Tianle

last: Chao

first: Xiaodong

first: Aili

last: Wang

first: Yunpeng

last: Chu

first: Qing

last: Li

first: Yilin

first: Zhibin

last: Ji

first: Jianmin


title: DNA Methylation Signatures in Blood DNA of Hutchinson Gilford Progeria Syndrome

status: Public on Feb 15 2022

city: Doha

first: Georges

last: Nemer

address: Education City

country: Qatar

institute: Hamad Bin Khalifa university

summary: Genome wide DNA methylation profiling of 12 control and  15 progeroid laminopahties samples. The Infinium MethylationEPIC Kit was used to measure DNA methylation across approximately 868,564 CpG sites.

overall_design: Bisulphite converted DNA of 15 progeroid laminopahties samples and 12 controls were hybridized to the Illumina Infinium EPIC Human Methylation Beadchip.

first: Nady

last: El Hajj


title: Whole brain RNA expression levels in the Hybrid Rat Diversity Panel for the PhenoGen website (https://phenogen.org)

first: Laura

summary: As part of the PhenoGen Project (https://phenogen.org), whole brain RNA-Seq data has been collected from strains of the Hybrid Rat Diversity Panel (HRDP). RNA expression levels were estimated using high throughput RNA sequencing (RNA-Seq) on long (>200 nucleotides) RNAs, i.e., total RNA where ribosomal RNA was depleted. These data can be used to examine predisposition phenotypes in the HRDP. Processed data and interactive graphics are also available through the PhenoGen website. Additional data from additional strains will be added as they become available.

overall_design:
RNA expression data has been gathered over several tissues (e.g., brain, liver, heart, kidney) on rats from the Hybrid Rat Diversity Panel (HRDP) as part of the RGAP: The heritable transcriptome and alcoholism project funded by NIAAA R24 AA013162. For each strain, RNA from 3 naive male biological replicates is extracted and a separate RNA-Seq library is generated from each replicate. rRNA-depleted total RNA is used to generate libraries and libraries are sequenced using Illumina sequencing technology. All rats used in this study were alcohol and drug naive and were NOT subjected to any behavioral testing. Therefore, these data represent a predisposition database that can be used for integrative systems genetics studies.
This dataset includes data from whole brain.

first: Boris

last: Tabakoff

first: Paula

last: Hoffman


title: A multi-omics approach incorporating single-cell RNASequencing reveals murine Leishmania major infection drives a proinflammatory signature alongside a signature of decreased ribosomal biogenesis.

status: Public on Aug 12 2021

city: Milwaukee

first: Yu-Chieh

state: WI

address: 8701 Watertown Plank Rd.,

department: Dermatology and Cancer

institute: Medical College of Wisconsin

summary: RNA-seq analysis was performed in ear samples from naïve control and L. major infected mice. Using scRNASeq, we investigated the transcriptomic changes within individual cell types present in leishmanial lesion. Transcriptomic analysis through scRNASeq revealed 35 distinct cell populations which include both resident and recruited cell types following L. major infection. In addition, our scRNASeq analysis confirms a significant recruitment of various immune cell types such as macrophages, inflammtory monocytes, neutrophils, dendritic cells, CD4 and CD8 T cells in the infected ears that are seen at higher frequencies compared to naive controls. In overall, our scRNASeq data revealed that DEGs within each immune cell type driving a proinflammtory state during L. major infection, alongside a signature of decreased ribosomal biogenesis.

overall_design: Single-cell RNASeq of naïve control ears compared to ear samples from 4 week post infection with L. major promastigote parasites.

first: Gopinath

last: Venugopal

first: Jordan

last: Bird

first: Hayden

last: Roys

first: Anne

last: Bowlin

first: Tiffany

last: Weinkopff


title: Comprehensive RNA-seq transcriptomic profiling in adult T lymphoblastic leukemia

city: Marseille

first: Salvatore

last: Spicuglia

state: France

address: Luminy

institute: Aix-Marseille University, INSERM, TAGC, UMR 1090

summary: RNA-seq data to study expression profiles in different adult T lymphoblastic leukemia

overall_design: RNA-Seq of 41 adult T lymphoblastic leukemia

first: Agata

last: Cieslak

first: Guillaume

last: Charbonnier

first: Yasmine

last: Kermezli

first: Melania

last: Tesio

first: Eve-Lyne

last: Mathieu

first: Mohamed

last: Belhocine

first: Aurore

last: Touzart

last: Hypolite

last: Andrieu

first: Nicolas

last: Boissel

first: Arnaud

last: Petit

first: Denis

last: Puthier

first: Elizabeth

last: Macintyre

first: Beatrice

last: Loriod

first: Aurélie

last: Bergon

first: Vahid

last: Asnafi


title: Age-associated cryptic transcription in mammalian stem cells is linked to permissive chromatin at cryptic promoters [CMS-Seq]

status: Public on Jul 15 2021

city: Houston

first: Weiwei

last: Dang

state: Texas

address: 1 Baylor Plaza

institute: Baylor College of Medicine

summary: Suppressing spurious cryptic transcription by a repressive intragenic chromatin state featuring trimethylated lysine 36 on histone H3 (H3K36me3) and DNA methylation is critical for maintaining self-renewal capacity in mouse embryonic stem cells. In yeast and nematodes, such cryptic transcription is elevated with age, and reducing the levels of age-associated cryptic transcription extends yeast lifespan. Whether cryptic transcription is also increased during mammalian aging is unknown. We show for the first time an age-associated elevation in cryptic transcription in several stem cell populations, including murine hematopoietic stem cells (mHSCs) and neuronal stem cells (NSCs) and human mesenchymal stem cells (hMSCs). Using DECAP-seq, we mapped and quantified age-associated cryptic transcription in hMSCs aged in vitro. Regions with significant age-associated cryptic transcription have a unique chromatin signature: decreased H3K36me3 and increased H3K4me1, H3K4me3, and H3K27ac with age. Furthermore, genomic regions undergoing such age-dependent chromatin changes resemble known promoter sequences and are bound by the promoter-associated protein TBP even in young cells. Hence, the more permissive chromatin state at intragenic cryptic promoters likely underlies the increase of cryptic transcription in aged mammalian stem cells.

overall_design: CMS-seq of young and old MSC

first: Brenna

last: McCauley

first: Luyang

last: Sun

first: Dena

last: Leeman

first: Yun

last: Huang

first: Ashley

last: Webb


title: Age-associated cryptic transcription in mammalian stem cells is linked to permissive chromatin at cryptic promoters [WGBS]

overall_design: WGBS of young and old MSC


title: C/EBPδ drives key endocrine signals in human fetal membranes at parturition [RNA-seq]

first: Wangsheng

last: Wang

state: Please Select

address: 845 Lingshan Rd.

institute: Shanghai Jiao Tong University

summary: Amnion-derived prostaglandin E2 (PGE2) and cortisol are key to labor onset. Identification of the common transcription factor driving the expression of both cyclooxygenase-2 (COX-2) and 11β-hydroxysteroid dehydrogenase 1 (11β-HSD1), the key enzymes in their production, may hold the key to the treatment of pre- and post-term labor. Here, we have found that the CCAAT enhancer binding protein δ (C/EBPδ) is such a transcription factor which underlies the feed-forward induction of COX-2 and 11β-HSD1 expression by their own products PGE2 and cortisol in human amnion fibroblasts so that their production would be ensured in the amnion for the onset of labor. Moreover, the abundance of C/EBPδ in amnion increases along with COX-2 and 11β-HSD1 at term and further increases at parturition. Knockout of C/EBPδ in mice delays the onset of labor further supporting the concept. In conclusion, C/EBPδ may serve as a novel pharmaceutical target in the amnion for treatment of pre- and post-term labor.

overall_design: RNA sequencing of  human amnion tissue obtained from TL and TNL patients

first: Wang-sheng


title: Exceptional response of high-risk neuroblastoma to RBM39 degrader Indisulam  (RNA-Seq)

first: Hongjian

last: Jin

overall_design: Examination of mRNA and splicing profiles post indisulan treatment or RBM39 shRNA knockdown in neuroblasoma cell line and xenograft.

first: Waise

last: Quarni

first: Shivendra

last: Singh

first: Jie

last: Fang

first: Shibiao

last: Wan

first: Jun

last: Yang


title: Functional multi-omics reveals genetic and pharmacologic regulation of surface CD38 in multiple myeloma

status: Public on Aug 02 2021

city: San Francisco

first: Arun

last: Wiita

state: CALIFORNIA

address: 185 Berry St, Ste 290/Rm 2410

institute: University of California San Francisco

summary: The goals of this study are to use multi-omics to design strategies to enhance efficacy of CD38-targeting immunotherapies in myeloma. We compared RNA-seq to cell surface proteomics after genetic and chemical manipulation of CD38 levels in myeloma cell lines.

overall_design: Examination of cell surface proteins, phosphoproteins, and RNA levels in myeloma cell lines with different levels of CD38 expression

first: Priya

last: Choudhry

first: Olivia

last: Gugliemini

first: Huimin

last: Geng

first: Vishesh

last: Sarin

first: Letitia

last: Sarah

first: Yu-Hsiu

middle: T

last: Lin

first: Poornima

last: Ramkumar

first: Neha

last: Paranjape

first: Makeba

last: Marcoulis

first: Donghui

first: Paul

last: Phojanokong

first: Veronica

last: Steri

first: Byron

last: Hann

first: Martin

last: Kampmann


title: Age-associated cryptic transcription in mammalian stem cells is linked to permissive chromatin at cryptic promoters (TL-Seq)

first: Weiwei

last: Dang

overall_design: Gene expression profiles of young and old MSC

first: Brenna

last: McCauley

first: Luyang

last: Sun

first: Dena

last: Leeman

first: Yun

last: Huang

first: Ashley

last: Webb


title: Age-associated cryptic transcription in mammalian stem cells is linked to permissive chromatin at cryptic promoters (RNA-Seq)


title: The healing myocardium mobilizes a distinct B-cell subset through a CXCL13-CXCR5-dependent mechanism

status: Public on May 29 2021

city: Würzburg

first: Alexander

middle: M.

last: Leipold

address: Josef-Schneider-Str. 2

institute: Helmholtz Institute for RNA-based Infection Research

summary: Recent studies have revealed that B-cells can influence post-myocardial infarction (MI) inflammation and repair, but the mechanisms controlling their mobilization and in situ activity remain poorly understood. Herein, we sought to dissect the mechanisms underlying B-cell cardiotropism and assess the B-cell antigen specificity profile in an experimental model of MI. Our study reveals that B-cells that are not antigen-specifically expanded readily infiltrate the infarcted myocardium via the CXCL13-CXCR5 axis. The restricted distribution of CXCR5 among hB cells could offer a suitable opportunity to selectively target this leukocyte subset therapeutically while minimally interfering with other local or systemic immunological processes.

overall_design: Histological, flow cytometry and single-cell RNA-sequencing (scRNAseq) analyses revealed the rapid accumulation of diverse B-cell subsets in the murine infarcted myocardium, including a distinct B-cell cluster exclusively found in the heart  (hB). The hB-cells exhibited upregulated expression of activation markers (e.g., Cd69) and expressed high levels of C-C-chemokine receptor type 7 (CCR7) and CXC-chemokine receptor type 5 (CXCR5). This distinct chemokine receptor signature was not shared with any other cell population in the healing myocardium. Moreover, we detected a myocardial gradient of CXC-motif chemokine ligand 13 (CXCL13, the ligand of CXCR5) in the early post-MI inflammatory (d1) and healing (d5) phases. Notably, mice treated with a neutralizing CXCL13-specific antibody showed reduced infiltration of myocardial B-cells after MI compared to control animals. Finally, global B-cell receptor (BCR) repertoire analyses revealed that the vast majority of B-cells infiltrating the infarcted myocardium were not clonally expanded and showed no sign of antigen specificity. In addition to the in situ B-cell responses, slight clonal expansion of a few germinal centre B-cells (GCs) was detected in the mediastinal lymph nodes (med-LNs).

first: Margarete

last: Heinrichs

first: Diyaa

last: Ashour

first: Lotte

last: Büchner

first: Georg

last: Wedekind

first: Katrin

last: Heinze

first: Panagiota

last: Arampatzi

first: Antoine-Emmanuel

last: Saliba

first: Clement

last: Cochain

first: Ulrich

last: Hofmann

first: Stefan

last: Frantz

first: Gustavo

last: Ramos


title: Genome-wide binding of  Bmal1 and Clock in adult mouse skeletal muscle.

city: Gainesville

first: Karyn

middle: A

last: Esser

state: Florida

address: 1345 Center Drive

department: PHYSIOLOGY & FUNCTIONAL GENOMICS

institute: University of Florida

summary: The goal of this study was to define the binding sites of the core circadian factors, BMAL1 and CLOCK across the genome in adult mouse skeletal muscle. We found  that mitochondrial inner-membrane genes were among the most enriched rhythmic genes via gene ontology analysis, and ChIP-Seq analysis corroborated the role of Clock and Bmal1 in targeting promoters of mitochondrial inner-membrane genes.

overall_design:
We collected mouse gastrocnemius muscles from 10 adult C57BL/6J male at 2hrs after lights on (ZT2). Nuclei were extracted and proteins fixed and we used antibodies to Bmal1 and Clock for Chromatin IP.   There are two biological replicates for Bmal1, two biological replicates for Clock, one input sample for Bmal1, and one input sample for Clock. Libraries were prepared using NEBNext Ultra DNA library kit and the libraries were sequenced on HiSeq3000 Illumina system.

Each processed data was generated from both replicates and is linked to the corresponding rep1 sample records.

first: Xiping

last: Zhang

first: Zhiguang

last: Huo

first: Juleen

last: Zierath

first: Brendan

last: Gabriel


title: RNA-Seq in Jurkat treated with either PBIT or DMSO

status: Public on Apr 16 2021

first: Salvatore

last: Spicuglia

summary: To assess whether genes associated with BH4Ds are more or less sensitive than genes associated with sharp H3K4me3 peaks to perturbation of H3K4me3 levels, we performed RNA-Seq experiment from Jurkat cells treated with DMSO or with 2-(4-methylphenyl)-1,2-benzisothiazol-3(2H)-one (PBIT), a specific inhibitor of JARID1 family of H3K4me3 demethylases, also known as KDM5 (Blair et al. 2011; Sayegh et al. 2013).

overall_design: 3 samples in singlicate.

first: Mohamed

last: Belhocine

first: Mathieu

last: Simonin

first: Agata

last: Cieslak

first: Lydie

last: Pradel

first: Charlotte

last: Smith

first: Eve-Lyne

last: Mathieu

first: Guillaume

last: Charbonnier

first: José-David

last: Flores

first: Iris

last: Manosalva

first: Joost

last: Martens

first: Hendrik

middle: G

last: Stunnenberg

first: Denis

last: Puthier

first: Pierre

last: Ferrier

first: Vahid

last: Asnafi


title: Age-associated cryptic transcription in mammalian stem cells is linked to permissive chromatin at cryptic promoters (ChIP-Seq)

first: Weiwei

last: Dang

first: Brenna

last: McCauley

first: Luyang

last: Sun

first: Dena

last: Leeman

first: Yun

last: Huang

first: Ashley

middle: E

last: Webb


title: LINC01133 inhibits invasion and promotes proliferation in an endometriosis epithelial cell line

status: Public on Aug 23 2021

city: Klosterneuburg

first: Florian

last: Pauler

address: Am Campus 1

country: Austria

institute: Institute of Science and Technology Austria (IST Austria)

summary: Endometriosis is a common gynecological disorder characterized by ectopic growth of endometrium outside the uterus and associated with chronic pain and infertility. We investigated the role of LINC01133 in endometriosis, an lncRNA that has been implicated in several types of cancer. We found that LINC01133 is upregulated in ectopic endometriosis lesions. As expression appeared higher in the epithelial endometrial layer, we performed an siRNA knockdown of LINC01133 in an endometriosis epithelial cell line. Phenotypic assays indicated that LINC01133 may promote proliferation and suppress cellular migration, and affect the cytoskeleton and morphology of the cells. Gene ontology analysis of differentially expressed genes detected by RNA sequencing indicated that cell proliferation and migration pathways were affected in line with the observed phenotype. We validated upregulation of p21 and downregulation of cyclin at the protein level, which together with DNA FACS analysis indicated that the observed effects on cellular proliferation may be due to changes in cell cycle progression. Further, we validated upregulation of the protein kinase TESK1 at the protein level, and found a corresponding increased phosphorylation and therefore inactivation of the actin severing protein Cofilin, which may explain changes in the cytoskeleton and cellular migration. These results indicate that LINC01133 upregulation is associated with endometriosis, which may be due to its effects on genes involved in the cellular proliferation and migration pathways.

overall_design: We compared gene expression in the 12Z endometrial endometriosis cell line between 3 control samples (non-targeting siRNA oligo, Cat. 4390846, Ambion, USA)  and 3 LINC01133 knockdown samples (Cat. S444575)

first: Quanah

last: Hudson

first: Iveta

last: Yotova

first: Rene

last: Wenzl


title: Age-associated cryptic transcription in mammalian stem cells is linked to permissive chromatin at cryptic promoters

overall_design: Refer to individual Series


title: Evidence for additive and synergistic action of mammalian enhancers during cell fate determination [BRD4-ChIP-seq, H3K4me1-ChIP-seq, TT-seq, RNA-seq]

status: Public on Apr 07 2021

city: Göttingen

first: Jinmi

last: Choi

address: Am Fassberg 11

department: Molecular Biology

institute: Max Planck Institute for Biophysical Chemistry

summary: Enhancer activity is known to drive cell differentiation and cell type determination, but it remains unclear how enhancers cooperate during these processes. Here we investigate enhancer cooperation during transdifferentiation of human B-cells to macrophages using enhancer RNA synthesis from accessible, H3K4-monomethylated chromatin regions as a proxy for enhancer activity. Most enhancers cooperate in an additive way to induce transcription of target genes. However, at ~130 loci, enhancers cooperate synergistically, changing activity of target genes exponentially over time. The latter genes are cell type-specific, indicating that enhancer synergy can drive differentiation and cell type determination. Pioneering factor occupancy, DNA accessibility profiling and eRNA synthesis reveal the temporal order of events that lead to enhancer synergy. Our results are consistent with a condensation model for transcription activation of cell type-specific genes that involves simultaneous contacts of multiple enhancers with their target promoter.

overall_design: TT-seq, Total RNA-seq, and ChIP-seq of H3K4me1, BRD4 during transdifferentiation (time course)


title: ChIP-Seq targeting TLX3 in DN-TL3

status: Public on Apr 27 2021

first: Salvatore

last: Spicuglia

summary: ChIP-Seq to study the binding of TLX3 in the mouse cell line DN-TLX3

overall_design: 1 ChIP and its input

first: Mohamed

last: Belhocine

first: Mathieu

last: Simonin

first: Agata

last: Cieslak

first: Lydie

last: Pradel

first: Charlotte

last: Smith

first: Eve-Lyne

last: Mathieu

first: Guillaume

last: Charbonnier

first: José-David

last: Flores

first: Iris

last: Manosalva


title: Discovery of target genes and pathways of blood trait loci using pooled CRISPR screens and single cell RNA sequencing

status: Public on Apr 08 2021

city: New York

first: John

last: Morris

state: New York

address: 101 Avenue of the Americas, 4th Floor

institute: New York Genome Center

summary: The majority of variants associated with complex traits and common diseases identified by genome-wide association studies (GWAS) map to noncoding regions of the genome with unknown regulatory effects. By leveraging ancestrally diverse biobank-scale GWAS data, massively parallel CRISPR screens and single cell transcriptomic and proteomic sequencing, we discovered target genes of noncoding variants for blood trait loci. For 91 GWAS loci, we identified 124 target genes in cis, which were often — but not always — the closest genes to the fine-mapped variant. Using precise variant insertion via base editing, we connect specific variants with gene expression changes. We also identified trans-effect networks of noncoding loci when cis target genes encoded transcription factors or microRNAs, such as GFI1B and miR-142. Trans-regulatory networks were themselves enriched for fine-mapped GWAS variants, demonstrating polygenic contributions to complex traits. Co-expression clustering of GFI1B trans-target genes identifies gene networks specific to different blood cell fates and differentiation stages. This platform will enable massively parallel assays to characterize the target genes and mechanisms of human noncoding variants in both cis and trans.

overall_design:
Multimodal single-cell sequencing of human erythroid progenitor cells (K562) to quantify per cell, the whole transcriptome, CRISPR guide RNAs, cell surface proteins, and cell hashing markers, allowing for the identification of GWAS target genes.

UPDATE: [Jun-17-2025] The GSM7108118 matrix.mtx.gz file was corrected.


title: Dynamic of broad H3K4me3 domains uncover an epigenetic switch between cell identity and cancer-related genes

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


title: Ethnicity-specific transcriptomic variation in immune cells and correlation with disease activity in systemic lupus erythematosus

status: Public on Mar 04 2021

city: Toronto

first: Gaia

last: Andreoletti

state: ON

address: 686 Bay St

country: Canada

institute: Sick Kids

summary: Participants were recruited from the California Lupus Epidemiology Study (CLUES). CLUES was approved by the Institutional Review Board of the University of California, San Francisco. Peripheral blood mononuclear cells were isolated from patient donors. Cells were isolated from peripheral blood utilizing magnetic beads (CD14+monocytes, B cells, CD4+T cells and NK cells) using EasySep protocol from STEM cell technologies on 120 patients. RNA and DNA were extracted using Qiagen column and quality was assessed on Agilent bioanalyzer. 1ng - 5ng of RNA was used with SmartSeqv2 protocol to get cDNA, followed by Illumina Nextera XT DNA library prep with input of 0.8ng cDNA and 15 cycles of PCR amplification. Both cDNA and DNA libraries qualities were controlled on Agilent bioanalyzer. Libraries were sequenced on HiSeq4000 PE150.

overall_design:
Bulk RNAseq of 120 patients with SLE.

**The raw data and processed data will be made available in dbGaP (https://www.ncbi.nlm.nih.gov/gap/) through controlled access due to patient privacy concerns**

first: Marina

last: Sirota

first: Cristina

last: Lanata


title: Dynamic of H3K4me3-broad domains uncover an epigenetic switch between cell identity and cancer-related genes

summary: Broad domains of H3K4 methylation have been associated with tissue specific, cell identity and tumor suppressor genes. Here, we identified broad H3K4me3 domains (BH4D)-associated genes in human thymic T cell populations and a collection of T-Acute Lymphoblastic Leukemia (T-ALL) primary samples and cell lines. We found that BH4D are highly dynamic throughout T cell differentiation, flag key leukemia associated oncogenes and distinguish between normal and neoplastic cells. Leukemic cells loss broad domains at T cell identity genes and gain broad domains at cancer-related genes. Moreover, the expression of genes, both coding and non-coding, associated with BH4D is frequently deregulated in T-ALL. Using an ex-vivo model we demonstrated that the ectopic expression of TLX3 oncogenic factor preferentially impact on the expression of BH4D-associated genes in T cell leukemia. Finally, an H3K4me3 demethylase inhibitor differentially targets T-ALL cell lines depending on the extend of the broad domains. Our results show that regulation of BH4D-associated genes is critical for leukemogenesis and suggest that association with BH4D might be used as epigenetic prioritization of cancer-relevant genes, including long non-coding RNAs

overall_design: ChIP-seq of H3K4me3  from human T acute lymphoblastic blasts and cell lines

first: Vahid

last: Asnafi


title: A cohesin cancer mutation reveals a role for the hinge domain in genome organization and gene expression [RNA-seq]

status: Public on Feb 23 2021

city: Chapel Hill

first: Zachary

last: Carico

state: NC

address: 250 Bell Tower Dr, CB7100

department: Integrative Biological and Genome Sciences program

institute: University of North Carolina

summary:
Purpose: Chromatin loop formation and maintenance is regulated by the cohesin complex. Here, we investigate whether a cancer mutation to a cohesin complex subunit, SMC1A-R586W, alters genome architecture and gene expression.
Method: Global gene expression was assessed using RNA-seq in wildtype and CRISPR-Cas9 genome edited SMC1A-R586W mouse embryonic stem cells (mESCs).

overall_design: Three replicates of RNA-seq were obtained in wild type and SMC1A-R586W mESCs growing under standard conditions.

first: Jill

last: Dowen

first: Megan

middle: N

last: Justice

first: Holden

middle: C

last: Stefan