title: Multicellular human cardiac organoids transcriptomically model distinct tissue-level features of adult myocardium

status: Public on Aug 31 2021

city: Charleston

first: Charles

middle: Matthew

last: Kerr

state: SC

address: 68 President St

department: Molecular Cell Biology and Pathobiology

institute: Medical University of South Carolina

summary: Human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs) have been widely used for disease modeling and drug cardiotoxicity screening. To this end, we recently developed human cardiac organoids (hCOs) for modeling human myocardium. Here, we perform a transcriptomic analysis of various in vitro hiPSC-CM platforms (2D iPSC-CM, 3D iPSC-CM and hCOs) to deduce strengths and limitations of these in vitro models. We further compared iPSC-CM models to human myocardium samples. Our data shows that the 3D in vitro environment of 3D hiPSC-CMs and hCOs stimulates expression of genes associated with tissue formation. hCOs demonstrated diverse physiologically relevant cellular functions compared to hiPSC-CM only models. Including other cardiac cell types within hCOs led to more transcriptomic similarly to adult myocardium. hCOs lack matured cardiomyocytes and immune cells which limits a complete replication of human adult myocardium. In conclusion, 3D hCOs are transcriptomically similar to myocardium, and future developments of engineered 3D cardiac models would benefit from diversifying cell populations, especially immune cells.

relation:
Reanalysis of: GSM3122186
Reanalysis of: GSM3122187
Reanalysis of: GSM3122188
Reanalysis of: GSM1536184
Reanalysis of: GSM1536185
Reanalysis of: GSM1536186
Reanalysis of: GSM1536187
Reanalysis of: GSM1536192
Reanalysis of: GSM1536193
Reanalysis of: GSM2463767
Reanalysis of: GSM2422325
Reanalysis of: GSM2422326
Reanalysis of: GSM2422327

overall_design: Three control spheroid replicates

first: Dylan

last: Richards

first: Donald

middle: R

last: Menick

first: Kristine

last: Deleon-Pennell

first: Ying

last: Mei


title: Oncogenic c-Myc induces replication stress by increasing cohesins chromatin occupancy

status: Public on Jun 30 2021

city: London

first: Cosetta

last: Bertoli

address: Gower Street

department: MRC Laboratory Molecular Cell Biology

country: United Kingdom

institute: University College London

type: Genome binding/occupancy profiling by high throughput sequencing

summary: In this experiment we analyse SMC1 binding to DNA in RPE1 hTERT c-Myc ER cells treated with 4-hydroxytamoxifen for 48h or untreated.

overall_design: We have used RPE1 hTERT c-Myc ER cells (biological replicates) 48 hours after 4OH-TM treatment or control. For each sample we have the input and the SMC1 antibody pull down.

first: Silvia

last: Peripolli

first: Tanya

last: Singh

first: Harshil

last: Patel

first: Peter

last: Thorpe

first: Robertus

middle: A

last: de Bruin


title: Transcriptional profiling of monocytes deficient in Nuclear Orphan Receptors NR4A2 and NR4A3 reveals distinct signalling roles related to antigen presentation and viral response.

status: Public on Jun 18 2021

city: Dublin

first: Eoin

middle: P

last: Cummins

state: Dublin

address: UCD Conway Institute of Biomolecular and Biomedical Research, UCD Belfield

department: Conway Institute/School of Medicine

country: Ireland

institute: University College Dublin

type: Expression profiling by high throughput sequencing

summary: Using RNA-sequencing and strategic bioinformatic analysis we investigated the down-stream effects of NR4A2 and NR4A3 in monocytes and dissected their common and distinct signalling roles.NR4A2 selective genes were most associated with antigen presentation, NR4A3 selective genes were most associated with interferon/viral reponse and NR4A2/3 co-regulated genes were most associated with clasical innate immure response signaling e.g. TLR signaling and chemokine secretion.

overall_design: shNT, shNR4A2 and shNR4A3 THP-1 +/- LPS

first: David

middle: E

last: Phelan


title: Gene expression in roots of the proscoop12 mutant and the wild-type Ws, treated or not with SCOOP12 peptide.

status: Public on Sep 23 2021

city: BEAUCOUZE

first: Sandra

last: Pelletier

address: 42, rue Georges Morel - BP 60057

country: France

institute: INRA

summary: The SCOOP12 secreted peptide regulates root growth through the control of the O2.- / H2O2 balance and cell wall modification and has a pleiotropic effect on a bunch of hormones in Arabidopsis.

overall_design: MEZ (meristematic-elongation zone) and DZ (differentiation zone) of eleven day roots of proscoop12 mutant were compared to wild-type Ws in  control condition or 100nM SCOOP12 treated condition

first: M

middle: C

last: Guillou

first: E

last: Vergne

first: S

last: Aubourg

first: J

last: Renou


title: Transcription Factors Recruit the Cohesin Loader NIPBL to Promote Chromatin Looping and Long-range Gene Regulation

status: Public on Jun 01 2021

city: Bethesda

first: Gordon

last: Hager

state: MD

address: 41 Center Dr

department: NCI

country: USA

institute: NIH

summary: The cohesin complex is central to chromatin looping, but mechanisms by which these long-range chromatin interactions are formed and persist remain unclear. We demonstrate that interactions between a transcription factor and the cohesin loader NIPBL regulate enhancer-promoter looping and promote long-range gene regulation. Using mass-spectrometry, genome mapping, and single-molecule tracking methods, we demonstrate that NIPBL and cohesin regulate the dynamics and function of the glucocorticoid receptor (GR). Moreover, glucocorticoid treatment stabilizes NIPBL and cohesin interactions by promoting loop extrusion and chromatin looping. Patient-derived acute myeloid leukemia cells harboring cohesin mutations exhibit a reduced response to glucocorticoids (GCs), suggesting that the GR-NIPBL-cohesin interaction is defective in these patients, and they may be poor candidates for GC treatment.

overall_design: We examined the long-range interactions mediated by  GR and how NIPBL influences these structures

first: Lorenzo

last: Rinaldi

middle: L


title: Identification of Fra-1/AP-1 binding sites in macrophages

status: Public on Jun 25 2021

city: Montpellier

first: Nicole

last: Hannemann

address: 80 Avenue Augustin Fliche

department: IRMB

institute: INSERM U1183

summary: The polarization and activation of macrophages are controlled synergistically by transcription factors such as NF-κB and AP-1 transcription factor members. Surprisingly, little is known about the role of the AP-1 member, Fra-1, during macrophage responses. To determine the full spectrum of Fra-1 binding sites in macrophages, chromatin immunoprecipitation sequencing analysis was performed in macrophages pooling down for the transcription factor Fra-1.

overall_design: For ChIP analyses, peritoneal macrophages were collected by peritoneal lavage of 8-week-old C57Bl/6 (n=9). Peritoneal cells were plated over night. The next day, suspension cells were removed and adherent cells were stimulated for 1 h with 10 µg/mL LPS (n=3), apoptotic cells in a ratio of 1:5 (n=3) or left unstimulated (n=3).

first: Steffen

last: Uebe

first: Arif

last: Ekici

first: Aline

last: Bozec


title: YAP governs intratumoral heterogeneity and chemosensitivity of small cell lung cancer

city: Hangzhou

first: Li

last: Shen

state: Zhejiang Province

address: 866 Yuhangtang Road

country: China

institute: Life Sciences Institute, Zhejiang University

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

overall_design: Refer to individual Series


title: Gli1+ progenitors mediate bone anabolic function of teriparatide via Hh and Igf signaling

status: Public on Jun 06 2021

city: Chengdu

first: Yu

last: Shi

state: Sichuan

address: NO.14 South Renmin Road

institute: Sichuan University

summary: Teriparatide, a bioactive fragment of human parathyroid hormone (PTH), is the most widely prescribed bone anabolic drug in the world, but its cellular targets remain incompletely defined.  The Gli1+ metaphyseal mesenchymal progenitors (MMPs) are a main source for osteoblasts in postnatal growing mice, but their potential response to teriparatide is unknown.  Here, by lineage tracing we find that teriparatide stimulates both proliferation and osteoblast differentiation of MMPs.  Single-cell RNA sequencing reveals heterogeneity among MMPs including a chondrocyte-like osteoprogenitor (herein COP) population that expands in response to teriparatide.  COPs express the highest level of Hedgehog (Hh) target genes and the insulin-like growth factor receptor Igf1r.  Inhibition of Hh signaling, or selective deletion of Igf1r in MMPs diminishes the proliferative and osteogenic effects of teriparatide.  The study therefore identifies MMPs as teriparatide target cells wherein Hh and Igf signaling are critical for osteoblast production.

overall_design: Examination of the heterogeneity alteration of Gli1+ cells with or without teriparatide treatment.

first: Fanxin

last: Long


title: Single Cell Dissection of Transcriptional Heterogeneity in HPV Positive and Negative Cervical Cancer

status: Public on Apr 13 2021

city: Harbin

first: Fei

last: Quan

address: Baojian Road 157

institute: Harbin Medical University

summary: Here we performed single-cell RNA sequencing of more than 30,000 of cells from HPV16+ and HPV- cervical cancer patients. We comprehensively revealed the heterogeneity of both the malignant cell populations and immune lineages in HPV+ and HPV- CC, as well as the cellular crosstalks with potential relevance to tumor progression. Moreover, our results demonstrated that distinct interaction patterns in HPV+ and HPV- groups could mediate similar functions or pathways, and we further constructed a three-cell interaction resource.

overall_design:
Four fresh samples were obtained from patients with cervical cancer who underwent concurrent chemoradiotherapy
>>>  Submitter declares that the raw data have not been submitted due to patient privacy concerns.  <<<

first: Shan-Shan

last: Yang

first: Yunyan

last: Zhang

first: Lin

last: Pang

first: Min

last: Xiao

first: Xiuwei

last: Chen

first: Yunduo

last: Liu

first: Yan

last: Cui

first: Yuting

last: Du

first: Bo

first: Jinyuan

last: Xu

first: Yihan

last: Wang

first: Yue

last: Feng

first: Lina

last: Gu

first: Zhao


title: YAP governs intratumoral heterogeneity and chemosensitivity of small cell lung cancer [scRNA-seq]

first: Li

summary: Small cell lung cancer is the most aggressive type of lung cancer and has a high degree of plasticity, characterized by a remarkable response to chemotherapy followed by development  of resistance. We show that intratumoral heterogeneity of SCLC is progressively established, indicated by the appearance of YAP+ and HES1+ SCLC tumor cells. Notch signaling is required  for the generation of Non-NE SCLC cells, but not for the tumorigenesis of SCLC. Furthermore, YAP signals through Notch-dependent and independent pathway to induce REST expression to promote the conversion of NE to Non-NE SCLC tumor cells. In addition, YAP activation enhances the chemoresistance in NE SCLC tumor cells by downregulating GSDME, while inactivation of YAP in Non-NE SCLC tumor cells switches cell death from apoptosis to pyroptosis. Our study will not only provide novel insights into the molecular basis of SCLC tumorigenesis, but also the potential drug targets for SCLC therapy

overall_design: Using scRNA-seq analyzes mSCLC treated with vehicle and cisplatin

first: Qingzhe

last: Wu

first: Jingxin

last: Guo

first: Hai

last: Song


title: Single nucleus RNA-sequencing defines unexpected diversity of cholinergic neuron types in the adult mouse spinal cord

status: Public on Feb 27 2021

first: Claire

last: LE PICHON

address: 35A Convent Drive, 2D933

department: NICHD

institute: National Institutes of Health

summary: We developed a targeted single nucleus RNA sequencing approach to enrich and transcriptomically characterize cholinergic neurons of the adult mouse spinal cord. Our data expose markers for known classes of cholinergic neurons and their extremely rich diversity. Visceral/preganglionic motor neurons could be divided into more than a dozen transcriptomic classes with anatomically restricted localization along the spinal cord. The complexity of the skeletal motor neurons was also reflected in our analysis with alpha, gamma, and a third subtype clearly distinguished. We further identified previously unrecognized subtypes of cholinergic interneurons.

overall_design: Cholinergic nuclei were enriched by FACS sorting of GFP+ nuclei from nuclear reporter mice and barcoded using 10X Genomics Chromium Single Cell Processor. Samples were run on an Illumina HiSeq2500.

first: Mor

last: Alkaslasi

first: Zoe

last: Piccus

first: Sangeetha

last: Hareendran

first: Hanna

last: Silberberg

first: Yajun

first: Timothy

middle: J

last: Petros

last: Le Pichon


title: FluB-RAM and FluB-RANS: Genome re-arrangement as safe and efficacious live attenuated influenza B virus vaccines

status: Public on Jul 23 2021

city: Athens

first: Daniel

middle: Roberto

last: Perez

state: GA

address: 953 College Station Road

institute: University of Georgia

summary: Influenza B virus (IBV) is considered a major respiratory pathogen responsible for seasonal respiratory disease in humans, particularly severe in children and the elderly. Seasonal influenza vaccination is considered the most efficient strategy to prevent and control IBV infections. Live attenuated influenza virus vaccines (LAIVs) are thought to induce both humoral and cellular immune responses by mimicking a natural infection, but their effectiveness have recently come into question. Thus, the opportunity exists to find alternative approaches to improve overall influenza vaccine effectiveness. Two alternative IBV backbones were developed with re-arranged genomes, re-arranged M (FluB-RAM) and a re-arranged NS (FluB-RANS). Both re-arranged viruses showed temperature sensitivity in vitro compared to the WT type B/Bris strain, were genetically stable over multiple passages in embryonated chicken eggs and were attenuated in vivo in mice. In a prime-boost regime in naïve mice, both re-arranged viruses induced antibodies against HA with hemagglutination inhibition titers considered of protective value. In addition, antibodies against NA and NP were readily detected with potential protective value. Upon lethal IBV challenge, mice previously vaccinated with either FluB-RAM or FluB-RANS were completely protected against clinical disease and mortality. In conclusion, genome re-arrangement renders efficacious LAIV candidates to protect mice against IBV.

overall_design: We developed two live attenuated vaccine candidates with re-arranged genome expressing the M2 or NS2 from the PB1 gene segment. DBAJ/2 mice were primed and boosted (3 weeks ppart) with the re-arranged viruses to test safety and protection efficacy. Body weight was recoreded for up to 12 days post vaccination and clinical signs were monitored daily throughout the length of the study. Blood samples were collected at 19 days post-boost (dpb) to assess neutralizing antibody responses through HI and virus neutralization. In addition, sera were used to performa microarrays against multiple influenza A and B protein antigens. Three weeks after boost, mice were challenged with a lethal dose of B/Brisbane/60/2008 PB2 F406Y. Body weigh was recorded for up to 12 days post-challenge (dpc) and clinical signs for up to 14 dpc. Blood and nasal wash samples were collecte at 14 dpc for serology and to determine antigen-specific IgG and IgA responses through microarray analysis.

first: Stivalis

last: Cardenas-Garcia

first: C

last: Cáceres

first: Aarti

last: Jain

first: Ginger

last: Geiger

first: Jong-Suk

last: Mo

first: Algimantas

last: Jasinskas

first: Rie

last: Nakajima

first: Daniela

middle: S

last: Rajao

first: D

middle: H

last: Davies


title: BANP opens chromatin and activates CpG-island-regulated genes

status: Public on May 17 2021

city: Basel

first: Dirk

last: Schuebeler

address: Fabrikstrasse 24

country: Switzerland

institute: Friedrich Miescher Institute for Biomedical Research

type: Methylation profiling by high throughput sequencing

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: HDAC4 controls senescence and aging by safeguarding the epigenetic identity and  ensuring the genomic integrity

status: Public on Apr 05 2021

city: Udine

first: Emiliano

last: Dalla

state: UD

address: Piazzale Kolbe 4

department: Department of Medicine

country: Italy

institute: Università degli Studi di Udine

summary:
Purpose: Define the epigenetic program of HDAC4
Outcome: HDAC4 controls the H3K27me3 of repetitive elements of retroviral origin (ERVs) and the H3K27 deacetylation of typical and super-enhancers found to be activated during senescence. The former response is due to the remodeling of the chromatin that sorrounds ERVs, while the latter is directly mediated by HDAC4 binding to the chromatin and the local deacetylation.

overall_design: The chromatin purified from SK-LMS-1 HDAC4KO cells, re-expressing HDAC4, was the control sample. The chromatin purified from SK-LMS-1 HDAC4KO cells, 36h after the removal of HDAC4, was the KO sample. 3 independent ChIP in control and KO samples were perfomed by using anti-H3K27ac,  anti-H3K27me3 and anti-HDAC4 antibodies or control IgG. 1/100 input was taken as reference. 3 biological replicates from the control and from the KO samples were independently validated in end-point PCR, pulled-down in accordance to BLUEPRINT requirements, used to prepare ChIP-seq libraries and sequenced.

first: E

last: Di Giorgio

first: H

last: Paluvai

first: A

last: Renzini

first: V

last: Moresi

first: L

last: Ranzino

last: Cutano

first: R

last: Picco

last: Brancolini


title: Type-I-interferon-responsive microglia shape cortical development and behavior

status: Public on Apr 29 2021

city: San Francisco

first: Leah

last: Dorman

state: CA

address: 499 Illinois St

department: Data Science

institute: CZBiohub

summary: This study profiles developing murine glia after induced cortical remodeling and identifies a transiently induced interferon-I responsive microglial state.

overall_design: Glial cells from the primary somatosensory (barrel) cortex were single-cell sequenced at postnatal days 5 and 7 following unilateral partial whisker cauterization at postnatal day 2.

first: Phi

middle: T

last: Nguyen

first: Ilia

middle: D

last: Vainchtein

first: Anna

middle: V

last: Molofsky

first: Caroline

last: Escoubas


title: A phylogenetic approach to the recruitment of venom proteins in a marine Polychaeta

status: Public on Jan 27 2021

city: Caparica

first: Pedro

middle: M.

last: Costa

address: Campus de Caparica

department: Department of Life Sciences

country: Portugal

institute: NOVA School of Science and Technology, NOVA University of Lisbon

summary: Transcriptome profiling of whole proboscis and body wall of the marine Polychaeta Eulalia sp. (Eulalia viridis), adults, wild population (sex undiscriminated), collected from the rocky intertidal at W Portugal (2018).

overall_design: Three individuals (independent replicates) were analysed (either organ). Total RNA from Replicate 2 (EPR2 and EBW2) was used to build the main library. The target organ is the proboscis (eversible pharynx) were toxn-secreting cells as located. Body wall (skin plus body musculature) was included as reference to allow the detection the expression of putative toxins.

first: Ana

last: Rodrigo

last: Grosso

first: Alexandra

last: Fernandes

middle: M


title: Expression profiles of human adipose tissue, adipocytes and stromal-vascular pellet cells from multiple body sites

status: Public on Jan 01 2021

city: Stanford

first: Heather

last: Clemons

address: Beckman Center

department: Dept of Biochemistry

institute: Stanford School of Medicine

summary: Adipose tissue is found throughout the human body. The diversity of physiological specialization of fat depots is reflected in the depot-specific alterations seen in lipodystrophies and links between specific patterns of fat distribution and susceptibility to diseases, including Type II Diabetes. We compared gene expression patterns in seven anatomically diverse fat depots and in adipocytes and stromal-vascular cells isolated from each sample. Adipocytes from different depots displayed distinct gene expression profiles. Characteristic patterns of expression of HOX genes distinguished adipocyte samples by site of origin. These depot-specific patterns were recapitulated when adipocyte precursors from each site were differentiated ex vivo, suggesting that these genes may have roles in specifying the depot-specific differentiation of adipocytes. Adipocyte expression of 300 genes with roles in energy metabolism showed both depot-dependent and inter-individual variation. Genes involved in glycogen metabolism and de novo fatty acid synthesis were generally most highly expressed in breast and abdominal subcutaneous adipocytes, suggesting a role for these depots in buffering glucose levels. Indeed, the role of adipocytes in primary metabolism of carbohydrate-rich foods may be considerably more important than has been appreciated. Genes involved in lipid uptake and hormone-stimulated lipolysis were on average most highly expressed in pericolonic, omental, and breast adipocytes; their expression covaried with each other and with that of the adipogenic transcription factor PPARG2. Two isoforms of PPARG, PPARG1 and PPARG2, were expressed in distinct patterns, each paralleling a discrete set of putative targets, suggesting that their differential regulation might influence important depot-specific and inter-individual differences in adipocytes. Dozens of genes encoding secreted proteins and receptors were highly expressed in adipocytes compared to adipose stromal-vascular cells and/or other tissues; many of these genes were not previously associated with adipocyte functions and are candidates for novel roles in sensing and signaling energy status to regulate global energy homeostasis.

overall_design:
An organism part comparison experiment design type compares tissues, regions, organs within or between organisms.

Samples GSM8158694-GSM8158781 processed data are available on the Series. No raw data were provided for these Samples.


title: Transcriptome sequencing of cerebrospinal fluid unravels cell landscape and neuroinflammatory signatures in the bacterial meningitis

status: Public on Dec 15 2020

city: Beijing

first: Haihan

last: Xiao

address: NO.1 Beichen West Road, Chaoyang District

institute: Institute Of Microbiology, Chinese Academy Of Sciences


summary:
Purpose: Characterizing the cell heterogeneity of CSF during the BM development in children.
Method: CSF samples were obtained via lumbar puncture from numbers of BM patients in different stages of disease progression. CSF cells were separated by direct centrifugation. A mimic assay based on QUARTZ-SEQ2 was adopted here for library preparations for scRNA-seq. Single CSF cells were sorted into two pre-prepared 384-well plates with cell lysis buffer by flow cytometry, in which each well contained a unique cell barcoding primer. An independent scRNA-seq library was constructed for 768 cells of each CSF sample, and was sequenced using a HiSeq X Ten sequencing system (Illumina). The generation of a cell-count matrix were processed in the combined workflow of UMI-tools and STAR. Secondary analysis were handled by Seurat package.
Results: The heterogeneities of CSF cells in BM progression were deciphered. Multiple immune cell clusters in CSF were identified, including two neutrophils, two monocytes, one macrophage, four myeloid dendritic cells, five T cells, one natural killer cell, one B cell, one plasmacytoid dendritic cell, and one plasma cell subtype. Their population profiles and dynamics in the initial onset, remission, and recovery stages during BM progression were also characterized.
Conclusions: This study conducted an in-depth exploration of the heterogeneities of CSF cells in BM progression, which provided novel insights into immune cell engagement in acute CNS infection.

overall_design:
Single cell mRNA profiles of CSF from children with BM.

*** For consistency with the publication (PMID 36119025), new data  have been added (GSM8118500-GSM8118537, February 2024).  The original data (GSM4974392-GSM4974410, December 2020) are not discussed in the above publication and have been removed. ***


title: Bulk transcriptome sequencing (bulkRNA-seq) of peripheral blood leukocytes (PBLs) in the bacterial meningitis (BM) of children

summary:
Purpose: Profiling the bulk transcriptomes of PBLs in sepsis-developed BM progression.
Methods: The total RNA of PBLs from BM patients were extracted, and constructed into cDNA library. Raw data of mRNA profiles were sequenced by paired-end strategy. Gene-counts were generated through handling sequencing data with the combined workflow of UMI-tools, STAR, Subread package and Samtools.
Results: Successfully acquirng multiple bulk-transcriptomic profiles of PBLs from BM patients in different sepsis conditions.

overall_design:
mRNA profiles of PBLs in onset (named SB1) or recovered (named SB2) conditions of sepsis during BM progression.

*** For consistency with the publication (PMID 36119025), new data have been added (GSM8118572-GSM8118583, February 2024).  The original data (GSM4974422-GSM4974434, December 2020) are not discussed in the above publication but they remain.  Reason: GSM4974422-GSM4974434 are discussed in a third-party publication (https://link.springer.com/article/10.1007/s10528-023-10530-6 Fig.2B). For clarity, GSE163196's original Title/Summary/Overall design are in supplementary file December2020_README.***


title: A single-cell survey of cellular hierarchy in acute myeloid leukemia

status: Public on Oct 06 2020

first: Junqing

last: Wu

address: Yuhangtang Road 866

institute: Zhejiang University

summary: We applied Micro-well seq, a high-throughput and low-costing single-cell RNA platform, to 40 patients with 3 healthy donors. We identified a key subgroup and characterized its gene expression pattern from diagnosis to relapse, revealing its features in refractory patients. In addition, we combined next generation and SMRT sequencing to track the clonal evolution.

sample_organism:
Homo
Homo sapiens

platform_organism:
Homo
Homo sapiens

overall_design: Expression profiling of de novo AML by Microwell-seq

first: Yanyu

first: Huiyu

last: Sun


title: YAP governs intratumoral heterogeneity and chemosensitivity of small cell lung cancer [bulk RNA-seq]

first: Li

last: Shen

summary: Small cell lung cancer is the most aggressive type of lung cancer and has a high degree of plasticity, characterized by a remarkable response to chemotherapy followed by development of resistance. We show that intratumoral heterogeneity of SCLC is progressively established, indicated by the appearance of YAP+ and HES1+ SCLC tumor cells. Notch signaling is required for the generation of Non-NE SCLC cells, but not for the tumorigenesis of SCLC. Furthermore, YAP signals through Notch-dependent and independent pathway to induce REST expression to promote the conversion of NE to Non-NE SCLC tumor cells. In addition, YAP activation enhances the chemoresistance in NE SCLC tumor cells by downregulating GSDME, while inactivation of YAP in Non-NE SCLC tumor cells switches cell death from apoptosis to pyroptosis. Our study will not only provide novel insights into the molecular basis of SCLC tumorigenesis, but also the potential drug targets for SCLC therapy

overall_design: RNA-seq comparing NE, Non-NE and OE-YAP5SA NE mSCLC cell lines

first: Qingzhe

first: Jingxin

last: Guo

first: Hai

last: Song


title: Pervasive promoter-proximal regulation in archaea: RNA-seq of cells during exponential growth (Cappable _sRNA-seq)

status: Public on Sep 14 2020

first: Finn

last: Werner

address: Gower Street

department: Institute of Structural and Molecular Biology

institute: University College London

summary: Recruitment of RNA polymerase and initiation factors to the promoter is the only known mechanisms for transcription activation and repression in archaea. Whether any of the subsequent steps towards productive transcription elongation is involved in regulation is not known. We characterised how the basal transcription machinery is distributed along genes in the archaeon Sulfolobus solfataricus. We discovered a distinct early elongation phase where RNA polymerases sequentially recruit the elongation factors Spt4/5 and Elf1 to form the transcription elongation complex (TEC) before the TEC escapes into productive transcription. TEC escape is rate-limiting for transcription output during exponential growth. Oxidative stress causes changes in TEC escape that correlate with changes in the transcriptome.  Our results thus establish that TEC escape contributes to the basal promoter strength and facilitates transcription regulation. Impaired TEC escape coincides with the accumulation of initiation factors at the promoter and recruitment of termination factor aCPSF1 to the early TEC. This suggests two possible mechanisms for how TEC escape limits transcription, physically blocking upstream RNA polymerases during transcription initiation and premature termination of early TECs.

overall_design: RNA-seq

first: Fabian

last: Blombach


title: In-depth analysis of proteomic and genomic fluctuations during the time course of human embryonic stem cells directed differentiation into beta cells

status: Public on Sep 28 2020

city: Wakefield

first: Dmitry

last: Shvartsman

state: MA

address: 11 Audbubon Rd

department: Research Development

institute: Cellaria Inc

summary: We describe fluctuations in the correlation between gene expression, its protein abundance, and phosphorylation, which follow beta-cell differentiation protocol perturbations of stem cell fates

overall_design: RNA extracts were collected in four replicates of every stage of the differentiation protocol including undifferentiated embryonic stem cells. Deep sequencing was done with Illumina deep sequencing protocol for transcript abundance, variant detection of mammalian samples with  25M reads of polyA modified transcripts

first: Juerg

last: Straubhaar


title: Pervasive promoter-proximal regulation in archaea: RNA-seq of cells during stationary phase

summary: Recruitment of RNA polymerase and initiation factors to the promoter is the only known mechanisms for transcription activation and repression in archaea. Whether any of the subsequent steps towards productive transcription elongation is involved in regulation is not known. We characterized how the basal transcription machinery is distributed along genes in the archaeon Sulfolobus solfataricus. We discovered a distinct early elongation phase where RNA polymerases sequentially recruit the elongation factors Spt4/5 and Elf1 to form the transcription elongation complex (TEC) before the TEC escapes into productive transcription. TEC escape is rate-limiting for transcription output during exponential growth. Oxidative stress causes changes in TEC escape that correlate with changes in the transcriptome.  Our results thus establish that TEC escape contributes to the basal promoter strength and facilitates transcription regulation. Impaired TEC escape coincides with the accumulation of initiation factors at the promoter and recruitment of termination factor aCPSF1 to the early TEC. This suggests two possible mechanisms for how TEC escape limits transcription, physically blocking upstream RNA polymerases during transcription initiation and premature termination of early TECs.


title: Bulk transcriptome sequencing (bulkRNA-seq) of human cerebrospinal fluid (CSF) cells in the bacterial meningitis (BM) of children

summary:
Purpose: Profiling the bulk transcriptomes of CSF cells in sepsis-developed BM progression.
Methods: The total RNA of CSF cells from BM patients were extracted, and constructed into cDNA library. Raw data of mRNA profiles were sequenced by paired-end strategy. Gene-counts were generated through handling sequencing data with the combined workflow of UMI-tools, STAR, Subread package and Samtools.
Results: Successfully acquirng multiple bulk-transcriptomic profiles of CSF cells from BM patients in different sepsis conditions.

overall_design:
mRNA profiles of CSF cells in different onset conditions during BM progression.

*** For consistency with the publication (PMID 36119025), new data have been added (GSM8118556-GSM8118567, February 2024).  The original data (GSM4974411-GSM4974421, December 2020) are not discussed in the above publication and have been removed. ***


title: Effect of maternal iron deficiency on placental transcriptome in mouse

status: Public on Sep 23 2020

city: BOSTON

first: CHANG

last: CAO

address: 185 CAMBRIDGE ST.

department: CENTER FOR GENOMIC MEDICINE

institute: Mass General Brigham

summary: the goal of this study is to use high-throughput RNA-Sequencing technology to identify genes that are differentially expressed in iron deficient (ID) placentas compared to iron adequate (IA) placentas. A secondary aim is to explore whether iron deficiency has differential impact on male compared with female placental transcriptome.

overall_design: Examination of placental transcriptome expression in iron deficient (ID) and iron adequate (IA) mouse placenta

first: Chang

last: Cao

first: Mark

last: Fleming


title: Changes to energy metabolism, and signal transduction (i.e. Notch and Wnt signalling) define the brain transcriptomic differences between mutations causative for early-onset familial Alzheimer’s disease or familial acne inversa in PRESENILIN 1

status: Public on Feb 01 2021

city: Adelaide

first: Karissa

last: Barthelson

state: South Australia

address: North Terrace Campus

country: Australia

institute: The University of Adelaide

summary: Background: Mutations in PRESENILIN 1 (PSEN1) which still produce a transcript encoding a full-length, but mutant protein are the most common cause of early-onset familial Alzheimer’s disease (EOfAD). The only frameshift mutations found in PSEN1 causes familial acne inversa (fAI) without EOfAD. The molecular consequences of heterozygosity for these mutations, and how they lead to completely different diseases, remains largely unexplored. Objective: To identify the similarities and differences of the effects of heterozygosity for mutations in psen1 causing EOfAD (T428del) or fAI (W233fs) on the brain transcriptome of young adult zebrafish. Methods: RNA sequencing was performed with high read depth on mRNA isolated from the brains of young adult (6 month old) zebrafish arising from a single family which contained either a single, heterozygous EOfAD-like or fAI-like mutation in the endogenous psen1 gene, and their wild type siblings. Results: Both mutations appeared to downregulate genes encoding the ribosomal subunits, and upregulated genes involved in inflammation. Genes involved in energy metabolism appeared to only be affected in EOfAD-like mutants, while genes involved in Notch, Wnt and neutrophin signalling pathways were only significantly altered by the fAI-like mutation. Further investigation of direct transcriptional targets of Notch revealed an apparent increase in Notch signalling.  Conclusion: We observed both common, and distinct effects on transcriptomes of the heterozygous mutants compared to their wild type siblings. The distinct effects observed may shed light to how these mutations give rise to completely different diseases.

overall_design: mRNA-seq of 6 month old zebrafish whole brains from fish either heterozygous for a EOfAD-like mutation, or heterozygous for an fAI-like mutation and their wild type siblings.

first: Yang

last: Dong

first: Morgan

last: Newman

first: Michael

last: Lardelli


title: Pervasive promoter-proximal regulation in archaea: ChIP-seq stationary phase

city: London

overall_design: ChIP-seq with polyclonal antibodies


title: Pervasive promoter-proximal regulation in archaea: RNA-seq of cells during exponential growth


title: Pervasive promoter-proximal regulation in archaea: RNA-seq of hydrogen peroxide-treated cells and mock-treated control

overall_design: Saccharolobus solfataricus str. P2 cells were grown in modified Brock medium with 0.2% tryptone to mid-exponential growth phase and treated with 30 µM hydrogen peroxide for 105 min


title: Pervasive promoter-proximal regulation in archaea: Permanganate ChIP-seq exponential growth

overall_design: Permananganete ChIP-seq with polyclonal antibodies


title: Follicular T Cells are Clonally and Transcriptionally Distinct in B Cell-Driven Autoimmune Disease

status: Public on Sep 20 2021

city: Boston

first: Elliot

last: Akama-Garren

address: 200 Longwood Ave

institute: Harvard Medical School

summary: To better understand the role of follicular T cells in autoantibody-mediated disease, we performed single cell RNA and T cell receptor (TCR) sequencing of follicular T cells in a mouse model of autoantibody-mediated disease.  This repository provides paired transcriptomes and unbiased TCRab repertoires from sorted CD4+CXCR5+PD1+ follicular T cells at single cell resolution.  Our analysis revealed that a minority of clonotypes are preferentially shared amongst autoimmune follicular T cells, and clonotypic expansion is associated with differential gene signatures in autoimmune disease. These data provide insight into the phenotypic differences of follicular T cells in B cell-driven autoimmune disease versus foreign immunization.

overall_design: scRNA-seq and scTCR-seq was performed on 10 bone marrow chimeras (5 controls and 5 autoimmune mice)

last: Carroll


title: Pervasive promoter-proximal regulation in archaea: ChIP-seq mock-treated cells


title: Pervasive promoter-proximal regulation in archaea: ChIP-exo exponential growth

overall_design: ChIP-exo with polyclonal antibodies


title: Pervasive promoter-proximal regulation in archaea: ChIP-seq exponential growth


title: Pervasive promoter-proximal regulation in archaea: ChIP-exo hydrogen peroxide-treated cells


title: Pervasive promoter-proximal regulation in archaea: Permanganate ChIP-seq hydrogen-peroxide treated cells

overall_design: Permanganate ChIP-seq with polyclonal antibodies


title: Expression data from kidney cortex of control and transgenic sgk1 mice under DOCA/NaCl treatment

status: Public on Aug 31 2020

city: La Laguna

first: Diego

last: Alvarez de la Rosa

state: Tenerife

address: Campus de Ciencias de la Salud

department: Basic Medical Sciences

country: Spain

institute: Universidad de La Laguna

summary:
Serum and glucocorticoid-induced kinase 1 (SGK1) regulates blood pressure and has been implicated in inflammation and fibrosis. We have tested whether increased SGK1 activity potentiates mineralocorticoid/NaCl-induced hypertension and kidney injury. To that end we have used a transgenic mouse model with increased SGK1 activity (Tg.sgk1).
This data set consists on transcriptomic analysis of kidney cortex samples to obtain differential gene expression due to excess SGK1 activity between wild type or Tg.sgk1 animals that were uninephrectomized and then treated with DOCA/NaCl

overall_design: 8 total RNA samples. Four replicates from wild type (C57BL/6) mice and four replicates from Tg.sgk1 mice.

first: Ozlen

last: Konu

first: Ayşe

middle: G

last: KEŞKÜŞ


title: Intraarticular injection of liposomal adenosine reduces cartilage damage  in established murine and rat models of osteoarthritis

status: Public on Sep 01 2020

city: New York

first: Zhi

last: Li

state: NY

address: 435 East 30th St, 9th Floor  New York, NY 10016

institute: NYU School of Medicine

summary: Osteoarthritis (OA) affects nearly 10% of the population of the United States and other industrialized countries and, at present, short of surgical joint replacement, there is no therapy available that can reverse the progression of the disease OA. Adenosine, acting at its A2A receptor (A2AR), is a critical autocrine factor for maintenance of cartilage homeostasis. Here we report that injection of liposomal suspensions of a selective A2AR agonist, CGS21680, significantly reduced OA cartilage damage in  a rat model of established post-traumatic OA (PTOA). Differential expression analysis of mRNA from chondrocytes harvested from knees of rats with PTOA treated with liposomal A2AR agonist revealed downregulation of genes associated with matrix degradation and upregulation of genes associated with cell proliferation as compared to liposomes alone.

overall_design: Articular chondorcytes were isolated and submitted for RNA sequencing with subsequent KEGG pathway analysis to characterize drivers of OA. oPOSSUM and the flatiron database were used for transcription factor binding enrichment and tissue specific network analyses.

first: Carmen

last: Corciulo

first: Cristina

last: Castro

first: Thomas

last: Coughlin

first: Samson

last: Jacob

first: David

last: Fenyo

first: Daniel

middle: B

last: Rifkin

first: Oran

last: Kennedy

first: Bruce

middle: N

last: Cronstein


title: Transcriptional dynamics of hepatic sinusoid-associated cells after liver injury [scRNA-seq]

status: Public on Aug 25 2020

city: Odense M

first: Kim

last: Ravnskjaer

address: Campusvej 55

department: Department of Biochemistry and Molecular Biology

country: Denmark

institute: University of Southern Denmark

summary: Here we profile the transcripts of app. 35.000 single cells isolated from livers of healthy and diseased mice. We show the transcriptomic change associated with fibrosis induction in the non-parenchymal cell types (hepatic stellate cells, liver endothelial cells and macrophages). We reveal a hitherto unknown feature of the HSCs otherwise functionally attributed to the LECs.

overall_design: 10x Genomics single-cell transcriptomic data of isolated non-parenchymal liver cells from healthy and diseased (2w and 4w CCl4 treated) mice.

first: Mike

middle: K

last: Terkelsen


title: Pervasive promoter-proximal regulation in archaea

first: Finn

last: Werner

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

sample_organism:
Saccharolobus solfataricus
Saccharolobus solfataricus P2

overall_design: Refer to individual Series


title: Methylomic analysis of ovarian cancers identifies tumor-specific alterations readily detectable in early precursor lesions

status: Public on Aug 06 2020

city: Baltimore

last: Pisanic

address: Shaffer Hall 200D, 3400 N Charles St

department: Institute for NanoBioTechnology

institute: Johns Hopkins University

type: Methylation profiling by genome tiling array

summary: High-grade serous ovarian carcinoma (HGSOC) typically remains undiagnosed until advanced stages when peritoneal dissemination has already occurred. Here, we sought to identify HGSOC-specific alterations in DNA methylation and assess their potential to provide sensitive and specific detection HGSOC at its earliest stages.

overall_design:
MethylationEPIC genome-wide methylation analysis was performed on a  cohort comprising 23 HGSOC, 37 non-HGSOC malignant and 36 cancer-free fresh-frozen gynecologic tissue samples.

Please note that the records have been updated with the raw data IDAT files on Mar 01, 2024.

middle: R

last: Pisanic II

first: Leslie

last: Cope

first: Shiou-Fu

last: Lin

first: Ting-Tai

last: Yen

first: Pornpat

last: Athamanolap

first: Ryoichi

last: Asaka

first: Kentaro

last: Nakayama

first: Amanda

last: Fader

first: Tza-Huei

last: Wang

first: Ie-Ming

last: Shih

first: Tian-Li


title: Microarray expression data following the treatment of mouse ESC with Panobinostat/LBH589

status: Public on Aug 01 2020

city: LEICESTER

first: RICHARD

middle: DAVID WILLIAM

last: KELLY

address: LANCASTER ROAD

department: BIOCHEMISTRY

institute: UNIVERSITY OF LEICESTER

summary:
Histone acetylation is a dynamic modification regulated by the opposing actions of histone acetyltransferases and histone deacetylases (HDACs). Deacetylation of histone tails results in chromatin tightening and therefore HDACs are generally regarded as transcriptional repressors. Counterintuitively, simultaneous deletion of HDAC1 and HDAC2 in embryonic stem cells (ESC) reduced expression of pluripotent transcription factors, Oct4, Sox2 and Nanog (OSN). By shaping global histone acetylation HDACs indirectly regulate the activity of acetyl-lysine readers, such as BRD4. To examine the direct effects of HDAC (LBH589) and BRD4 (JQ1) inhibition on the ESC transcriptome, we performed precision nuclear run-on and sequencing (PRO-seq) analysis. Both LBH589 and JQ1 caused a marked reduction in the pluripotent network. However, while JQ1 treatment induced widespread transcriptional pausing of genes, HDAC inhibition caused a reduction in both paused and elongating polymerase, suggesting an overall reduction in recruitment of RNAPII. Using enhancer RNA (eRNA) expression to measure enhancer activity, we found that while HDAC activity regulates fewer enhancers than JQ1, LBH589 sensitive eRNAs were preferentially associated with super-enhancers and OSN binding sites. These findings suggest that HDAC activity is required for maintenance of pluripotency by regulating the OSN enhancer network via optimal recruitment of RNA polymerase II.
Comparative gene expression using the Illumina mouseWG-6 v2 expression BeadChip platform. The effects of Panobinostat/LBH589 (50nM)

overall_design: wild type (Ctrl/0hr) E14 ESC were compared to ESC treated with Panobinostat/LBH589 for 2hr, 6hr and 18hr.  Each time points were analyzed in triplicate.

first: R

last: Kelly

first: S

last: Cowley


title: Histone Deacetylases (HDACs) are essential for transcription of the pluripotent network in embryonic stem cells


title: A conserved odor detection pathway via modulation of chromatin and cellular gene expression

status: Public on Jul 28 2020

city: Riverside

first: Christi Ann

last: Scott

address: 3401 Watkins Drive

department: Molecular, Cell, and Systems Biology

institute: University of California, Riverside

summary: Odorants in the environment that can cross the cell membrane are likely important detection targets for a conserved pathway and using one such odorant, diacetyl, we show that the ancient family of histone deacetylase enzymes (HDACs) can act as an atypical odorant detection pathway. Based on our testing we demonstrate that this response meets 6 characteristics of an odor-sensing pathway to odorant exposure: (1) a highly specific response to volatile compounds by altering gene expression, (2) differential modulation of different HDACs, (3) dose-dependent response in vitro, (4) dose-dependent response in vivo, (5) reversible to some degree, and (6) highly conserved across eukaryotes such as invertebrates, vertebrates and plants. We observe that exposure to diacetyl vapors modulates gene expression over a period of days in the Drosophila antenna. The up-regulated genes significantly overlap with genes altered by known histone deacetylase inhibitors administered in the food. In vitro assays with purified human proteins showed that different members of  class I HDACs are differentially inhibited. Moreover exposure to diacetyl increased histone H3K4 acetylation in a human cell line. Organisms spanning multiple taxa can respond to diacetyl volatiles by altering gene expression, presumably in part via inhibition of histone deacetylase proteins causing epigenetic changes. Our finding reveals a highly conserved and slow-acting pathway for responding to odorants beyond the fast-acting neuronal activation via transmembrane receptors, and raises questions about the effects of this odorant detection pathway on physiology and health of organisms.

sample_organism:
Arabidopsis thaliana
Drosophila melanogaster
Mus musculus

overall_design:
Drosophila diacetyl-exposed antenna: RNA-Seq profiles were generated with the Illumina HiSeq2000 platform with biological replicates. Diacetyl-treated antennal samples were compared to control antennal samples from flies exposed to the solvent (paraffin oil, PO) alone.
Drosophila diacetyl-recovery antenna: RNA-Seq profiles were generated with the Illumina HiSeq2000 platform with biological replicates. Diacetyl flies were put into recovery for 5days. These antennal samples were compared to control antennal samples exposed to the solvent (paraffin oil, PO) alone throughout the experiment.
Drosophila HDACi antenna: RNA-Seq profiles were generated with the Illumina HiSeq2000 platform with biological replicates. HDACi-treated antennal samples were compared to control, untreated antennal samples.
Mus musculus lung: RNA-Seq profiles were generated with the Illumina NextSeq200 platform with biological replicates. Diacetyl-treated lung samples were compared to control lung samples from mice exposed to the solvent (PO) alone.
Arabidopsis thaliana leaflet: RNA-Seq profiles were generated with the Illumina NextSeq200 platform with biological replicates. Diacetyl-treated leaflet samples were compared to control leaflet samples from plants exposed to the solvent (PO) alone.
Mus musculus brain: RNA-Seq profiles were generated with the Illumina NextSeq200 platform with biological replicates. Diacetyl-treated brain samples were compared to control brain samples from mice exposed to the solvent (PO) alone.

first: Sachiko

last: Haga-Yamanaka

first: Christi

middle: A

first: Sarah

last: Perry

first: Crystal

last: Pontrello

first: Meera

last: Goh

first: Anandasankar

last: Ray


title: Differences in directionality of RNA polymerase initiation underlie epigenome differences between plants and animals

status: Public on Jun 11 2020

city: Atlanta

first: Roger

last: Deal

address: 1510 Clifton Rd NE

department: Biology

institute: Emory University

summary: Transcriptional regulation is a universal mechanism for a wide array of biological processes, and is driven in large part by genetic enhancer elements. These regulatory elements have been well-studied in animal species, yet their plant counterparts remain poorly characterized.  While high-throughput profiling of animal genomes has yielded great success in identifying genetic enhancers through secondary characteristics – flanking histone posttranslational modifications (PTMs), chromatin accessibility, and the production of enhancer RNAs (eRNAs) – it is an active line of investigation as to whether these secondary characteristics can be used in a similar way to locate regulatory regions of plant genomes.  Here, we compare the enrichment of the four histone PTMs most commonly associated with animal enhancers – H3K27ac, H3K27me3, H3K4me1, and H3K4me3 – between Drosophila melanogaster, Homo sapiens, and Arabidopsis thaliana genomes. Regions of accessible chromatin were identified through ATAC-seq or DNase-seq, and were analyzed as putative enhancer regions.  Additionally, as it has been shown that enhancer activity varies widely from cell type to cell type, matched, single-cell type datasets were used for each species whenever available.  Through the intersection of these data it becomes clear that there are distinct differences between the epigenetic makeup of plant and animal genomes.  While these four histone PTMs are present at transcription start sites (TSSs) in all three of the species investigated, A. thaliana showed a marked depletion of these modifications upstream of the TSS, while the animal species showed bimodal enrichment.  The plant histone PTM pattern is consistent with the pattern observed at unidirectional promoters, which was further supported by GRO-seq data.  When intergenic regions of accessible chromatin were examined – putative enhancer regions – the plant epigenomes showed a one-sided, rather than bimodal, enrichment of all four of the histone PTMs.  However, these sites retain the ability to produce eRNAs, suggesting that they are likely functionally active enhancer elements.  While it is known that animal promoters and enhancers have bidirectional transcription, this analysis revealed that plant promoters and enhancers have a distinct pattern, and only exhibit histone PTM deposition and transcription in the sense direction.  While further investigation is merited, this may speak to a fundamental difference between the transcriptional machinery of plant and animal kingdoms.

overall_design: Examination of enhancer histone modification enrichment across the Arabidopsis epigenome using single cell-type data

first: Kelsey

last: Maher

first: Dongxue


title: Transcriptomic analysis of Wild-type and Mfsd7c-/-knockout brain embryos

status: Public on May 18 2020

city: SINGAPORE

first: LONG

middle: NAM

last: NGUYEN

address: 28 Medical Drive

country: Singapore

institute: NUS YONG LOO LIN SCHOOL OF MEDICINE

summary: Mfsd7c is expressed in CNS blood vessels. Deletion of Mfsd7c results in embryonic lethality with signs of hypoxia. We performed transcriptomic analysis of genes in brains of E14.5 wild-type (WT) and Mfsd7c-knockout (KO) embryos.

overall_design: The total mRNA from whole brain of E14.5 WT and KO embryos was isolated for RNA sequencing using Novaseq6000 (the newest IIIumina platform).

first: Toan

middle: Q

last: Nguyen

first: Long


title: Histone Deacetylases (HDACs) are essential for transcription of the pluripotent network in embryonic stem cells [Pro-Seq]

summary: Histone acetylation is a dynamic modification regulated by the opposing actions of histone acetyltransferases and histone deacetylases (HDACs). Deacetylation of histone tails results in chromatin tightening and therefore HDACs are generally regarded as transcriptional repressors. Counterintuitively, simultaneous deletion of HDAC1 and HDAC2 in embryonic stem cells (ESC) reduced expression of pluripotent transcription factors, Oct4, Sox2 and Nanog (OSN). By shaping global histone acetylation HDACs indirectly regulate the activity of acetyl-lysine readers, such as BRD4. To examine the direct effects of HDAC (LBH589) and BRD4 (JQ1) inhibition on the ESC transcriptome, we performed precision nuclear run-on and sequencing (PRO-seq) analysis. Both LBH589 and JQ1 caused a marked reduction in the pluripotent network. However, while JQ1 treatment induced widespread transcriptional pausing of genes, HDAC inhibition caused a reduction in both paused and elongating polymerase, suggesting an overall reduction in recruitment of RNAPII. Using enhancer RNA (eRNA) expression to measure enhancer activity, we found that while HDAC activity regulates fewer enhancers than JQ1, LBH589 sensitive eRNAs were preferentially associated with super-enhancers and OSN binding sites. These findings suggest that HDAC activity is required for maintenance of pluripotency by regulating the OSN enhancer network via optimal recruitment of RNA polymerase II.


title: Identification of herpes simplex virus 1 and host targets of miR-138 by combined RNAseq/PARCLIP

status: Public on Apr 27 2020

city: Hangzhou

first: Dongli

last: Pan

state: Zhejiang

address: 866 Yuhangtang Road

sample_organism:
Homo sapiens
Mus musculus
Human alphaherpesvirus 1


title: Self-reporting transposons enable simultaneous readout of gene expression and transcription factor binding in single cells

status: Public on Jul 23 2020

city: St. Louis

first: Robi

last: Mitra

state: Missouri

address: 4515 McKinley Ave

department: Genetics

institute: Washington University in St. Louis

summary: In situ assays of transcription factor (TF) binding are confounded by cellular heterogeneity and represent averaged profiles in complex tissues. Single cell RNA-seq (scRNA-seq) is capable of resolving different cell types based on gene expression profiles, but no technology exists to directly link specific cell types to the binding pattern of TFs in those cell types. Here, we present self-reporting transposons (SRTs) and their use in single cell calling cards (scCC), a novel assay for simultaneously capturing gene expression profiles and mapping TF binding sites in single cells. First, we show how the genomic locations of SRTs can be recovered from mRNA. Next, we demonstrate that SRTs deposited by the piggyBac transposase can be used to map the genome-wide localization of the TFs SP1, through a direct fusion of the two proteins, and BRD4, through its native affinity for piggyBac. We then present the scCC method, which maps SRTs from scRNA-seq libraries, thus enabling concomitant identification of cell types and TF binding sites in those same cells. As a proof-of-concept, we use scCC to map the binding of BRD4 and three additional TFs in cultured cells. We then apply this technique to discover bromodomain-dependent cell state dynamics in K562 cells. Finally, we map BRD4 binding sites in the mouse cortex at single cell resolution, thus establishing a new technique for studying TF biology in situ.

overall_design: 1 bulk DNA calling card library, 8 bulk RNA calling card libraries, 9 single cell RNA-seq libraries, 9 single cell calling card libraries

first: Arnav

last: Moudgil


title: Identification of herpes simplex virus 1 and host targets of miR-138 by comparative PAR-CLIP in Neuro-2a and 293T cells

summary: This is a part of the study that shows that a host microRNA, miR-138, represses herpes simplex virus 1 (HSV-1) gene expression through both viral and host targets. These PAR-CLIP analyses identified viral and host targets of miR-138 in Neuro-2a (mouse neuroblastoma) and 293T (human embryonic kidney) cells. We constructed two cell lines derived from Neuro-2a cells, one overexpressing miR-138 (N2A138) and one antagonizing miR-138 (N2Aanti138). We also constructed two cell lines derived from 293T cells, one overexpressing miR-138 (293T138) and one control cells (293Tcontrol). Uninfected N2A138 and N2Aanti138 were compared by PAR-CLIP for host targets in Neuro-2A cells. 293T138 and 293Tcontrol cells infected for 4 and 8 hours were compared by PAR-CLIP for HSV-1 targets in 293T cells. 293T138 and 293Tcontrol cells infected for 4 hours were also compared for host targets in 293T cells.

platform_organism:
Homo sapiens
Mus musculus
Human alphaherpesvirus 1

overall_design: Comparison of cells overexpressing miR-138 with control cells. Infect the cells for viral target identification

first: Donald

last: Coen


title: The sequence of human ACE2 is suboptimal for binding the S spike protein of SARS coronavirus 2

status: Public on Mar 19 2020

city: Urbana

first: Erik

last: Procko

state: IL

address: 601 S Goodwin Ave

department: Biochemistry

institute: University of Illinois

summary: The rapid and escalating spread of SARS coronavirus 2 (SARS-CoV-2) poses an immediate public health emergency, and no approved therapeutics or vaccines are currently available. The viral spike protein S binds membrane-tethered ACE2 on host cells in the lungs to initiate molecular events that ultimately release the viral genome intracellularly. The extracellular protease domain of ACE2 inhibits cell entry of both SARS and SARS-2 coronaviruses by acting as a soluble decoy for receptor binding sites on S, and is a promising candidate for therapeutic and prophylactic development. Using deep mutagenesis, variants of ACE2 are identified with increased binding to the receptor binding domain of S at a cell surface. Mutations are found across the protein-protein interface and also at buried sites where they are predicted to enhance folding and presentation of the interaction epitope. The mutational landscape offers a preliminary blueprint for engineering high affinity ACE2 receptors to meet this unprecedented challenge.

overall_design: The cDNA encoding full-length human ACE2 (GenBank NM_021804.1) with an N-terminal c-myc tag was diversified by site-saturation mutagenesis at 117 positions. This was accomplished by introducing degenerate NNK codons at the respective sites, which fully spanned the known binding epitope for SARS-CoV as well as additional sites in the ACE2 substrate-binding cleft. The ACE2 library was expressed in human Expi293F cells under conditions where most cells express no more than a single coding variant. The cell culture was then incubated with the receptor binding domain (RBD; a.a. 333-529) of the S1 subunit (GenBank YP_009724390.1) from SARS-CoV-2. The RBD was fused at its C-terminus to sfGFP for fluorescence detection in an oxidizing extracellular environment. The cell culture was simultaneously stained with Alexa 647-conjugated anti-myc to measure surface ACE2 expression. After washing, bound RBD-sfGFP was found to be proportional to ACE2 levels. There were unambiguous populations of cells expressing ACE2 variants with high and low RBD-sfGFP binding; these cell populations were collected by FACS and are called nCoV-S-High and nCoV-S-Low, respectively. Transcripts in the collected cell populations were Illumina sequenced and their frequencies compared to the naive plasmid library. The enrichment or depletion of all 2,340 single amino acid variants in the library was calculated, which acts as a proxy for relative “binding” to the RBD of SARS-CoV-2. This “binding” signal is a product both of S/ACE2 affinity and surface display of properly folded ACE2.


title: In vivo structure analysis of SINEUP RNA

status: Public on Mar 06 2020

city: Yokohama

first: Harshita

last: Sharma

state: Kanagawa

address: 1-7-22 Suehiro-cho, Tsurumi-ku

department: Division of Genomic Medicine

country: Japan

institute: RIKEN Center for Integrative Medical Sciences

summary: To analyze SINEUP RNA secondary structure in living cells, multiple SINEUP RNA and target EGFP mRNA plasmids were transfected in HEK293T/17 cells and icSHAPE libraries were prepared.

overall_design: Two biological replicates of each NAI-N3 and DMSO (mock) treated samples


title: Pervasive promoter-proximal regulation in archaea: ChIP-seq hydrogen peroxide-treated cells

status: Public on Sep 14 2020

first: Finn

last: Werner

address: Gower Street

summary:
Genome-wide occupancy of the basal transcription machinery in Saccharolobus solfataricus strain P2 (Sulfolobus solfataricus) after hydrogen peroxide treatment
Recruitment of RNA polymerase and initiation factors to the promoter is the only known mechanisms for transcription activation and repression in archaea. Whether any of the subsequent steps towards productive transcription elongation is involved in regulation is not known. We characterised how the basal transcription machinery is distributed along genes in the archaeon Sulfolobus solfataricus. We discovered a distinct early elongation phase where RNA polymerases sequentially recruit the elongation factors Spt4/5 and Elf1 to form the transcription elongation complex (TEC) before the TEC escapes into productive transcription. TEC escape is rate-limiting for transcription output during exponential growth. Oxidative stress causes changes in TEC escape that correlate with changes in the transcriptome.  Our results thus establish that TEC escape contributes to the basal promoter strength and facilitates transcription regulation. Impaired TEC escape coincides with the accumulation of initiation factors at the promoter and recruitment of termination factor aCPSF1 to the early TEC. This suggests two possible mechanisms for how TEC escape limits transcription, physically blocking upstream RNA polymerases during transcription initiation and premature termination of early TECs.

overall_design: ChIP-seq with polyclonal antibodies (custom-made, not commercially available).

first: Fabian

last: Blombach


title: Cardiac organoid model of human myocardial infarction

status: Public on Apr 14 2020

city: Charleston

first: Gary

last: Hardiman

address: 135 Cannon Street

department: Medicine

institute: Medical University of South Carolina

summary: While human organoid systems have provided a powerful platform in modeling diseases caused by genetic disorders, non-genetic factors, such as lifestyle and environment, are the largest attributable factors to devastating diseases like cardiovascular disease (CVD), the leading cause of death worldwide. Specifically, myocardial infarction (MI) (i.e., heart attack) makes up ~8.5% of CVD and is a common cause of heart failure with a 40% five-year mortality after the first MI. This highlights an urgent need to develop relevant human heart failure models for drug development. This is further evidenced by the disappointing performance of heart failure drugs in clinical trials during the last decade, which has been partially attributed to the distinct differences between human patient hearts and animal heart failure models. Here, we combined major non-genetic causal factors of MI with our previously established cardiac organoids to create the first human organoid model of cardiac infarction. In particular, we leveraged the diffusion limitation in 3D microtissues to recreate the nutrient diffusion gradient across infarcted hearts (i.e., infarct-border-remote zones) in human cardiac organoids to induce cardiac organotypic response to infarction. This enabled the recapitulation of major MI hallmarks in human cardiac organoids at the transcriptomic, structural and functional level.

overall_design: Three Control Organoid replicates versus Three Infarct Organoid replicates

first: Dylan

middle: J

last: Richards

first: Yang

last: Li

first: Jenny

last: Yao

first: Robert

middle: C

last: Coyle

first: Jia

last: Jia

first: Brooke

last: Damon

first: E

last: Hazard

last: Menick

first: Hai

first: Tong

last: Ye

first: Ying

last: Mei


title: The methylomic landscape of fallopian tube lesions associated with ovarian high-grade serous carcinoma

first: Thomas

last: Pisanic


title: Combinatorial single-cell CRISPR screens by direct guide RNA capture and targeted sequencing

status: Public on Mar 03 2020

city: Cambridge

first: Joseph

last: Replogle

state: Massachussetts

address: 455 Main St

institute: UCSF / Whitehead Institute / MIT

summary: Single-cell CRISPR screens allow for the exploration of mammalian gene function and genetic regulatory networks, but their utility has been limited in part by their reliance on indirect sgRNA indexing. Here, we present direct capture Perturb-seq, a versatile screening approach in which expressed sgRNAs are sequenced alongside single-cell transcriptomes. Direct capture Perturb-seq enables the detection of multiple distinct sgRNAs expressed from a single vector within individual cells and thus allows pooled single-cell CRISPR screens to be easily paired with combinatorial perturbation libraries. We demonstrate that this approach allows high-throughput investigations of genetic interactions, and we leverage this ability to dissect epistatic interactions between cholesterol biogenesis and DNA repair. We also show that targeting individual genes with multiple sgRNAs per cell improves the efficacy of CRISPR interference and activation, facilitating the use of compact, highly active CRISPR libraries for single-cell screens. Lastly, we show that hybridization-based target enrichment permits sensitive, specific sequencing of informative transcripts from single-cell RNA-seq experiments.

overall_design: Single-cell, pooled CRISPR screening experiments comparing the transcriptional effects of knockdown or overexpression of genes. This repository includes five discrete experiments. (1) CRISPRi knockdown of genes known to induce the UPR across 5 different Perturb-seq platforms to compare data quality. (2) Paired CRISPRi knockdown of genes involved in cholesterol biosynthesis and DNA repair, to assess the utility of direct capture Perturb-seq for epistasis analysis. (3) CRISPRi knockdown of genes with either a single sgRNA or two sgRNAs, to assess compact library design. (4) CRISPRa overexpression of genes with either a single sgRNA or two sgRNAs, to assess compact library design. (5) Hybrid-capture based target enrichment applied to the above scRNA-seq libraries. experiments.

first: J

middle: S

last: Weissman

first: B

last: Adamson


title: NLRP3-inflammasome suppression improves longevity and prevents cardiac aging in mice

status: Public on Oct 01 2019

city: La Línea de la Concepción

first: Alejandro

last: Peralta-Garcia

state: Cádiz

address: Gabriel Miró 52 A

institute: Pablo de Olavide University

summary:
Aging is the major risk factor for cardiovascular and many other chronic diseases. During this natural process, many alterations occur in the organism which are associated with progressive impairment of several metabolic pathways related to body composition, insulin resistance, mitochondrial and autophagy dysfunction and inflammation. Recently, the role of NLRP3 inflammasome has been studied in cardiovascular diseases showing its implication in the pathological progression of atherosclerosis, heart failure, and hypertension. However, the role of the NLRP3 inflammasome in cardiac aging has been less well studied. Herein, we investigate the molecular mechanisms by which NLRP3 inhibition may attenuate cardiac aging.
Ablation of NLRP3 inflammasome increased lifespan and protected mice from age-related increased insulin sensitivity, reduced IGF-1 and leptin/adiponectin ratio levels, and reduced cardiac damage with protection of the prolongation of age–dependent PR interval, which is associated with atrial fibrillation by cardiovascular aging. Furthermore, old NLRP3 KO mice showed an inhibition of PI3K/AKT/mTOR pathway and autophagy improvement compared with old wild type mice and preserved Nampt-mediated NAD+ levels with increased SIRT1 protein expression. These findings suggest that suppression of NLRP3 prevented many age-associated changes in the heart and preserved cardiac function of aged mice.

overall_design: Microarrays were made on cardiac tissue from 22-month-old mice. Four groups were compared: WT young mouse, WT old mouse, NLRP3 -/- young mouse and NLRP3 -/- old mouse. Old mice were 22 months old and young mice were 3 months old. Each condition had three replicates. Thus, we had a total of 12 microarrays.

first: Fabiola

last: Marín-Aguilar

first: Ana

last: Lechuga-Vieco

first: Diego

last: Cañadas-Lozano

first: Elísabet

last: Alcocer-Gómez

first: Beatriz

last: Castejón-Vega

first: Antonio

last: Pérez-Pulido

first: Alfonso

last: Varela-López

first: José

middle: L

last: Quiles

first: Avril

last: Robertson

first: Matthew

last: Cooper

first: Bernhard

last: Ryffel

first: Pedro

last: Bullón

last: Enriquez

first: Jesús

last: Ruiz-Cabello

first: Mario

last: Cordero


title: Microarray expression data from HDAC1-/-; HDAC2-/wt conditional knock-out mouse embryonic stem cells

first: RICHARD

last: KELLY

summary:
Histone acetylation is a dynamic modification regulated by the opposing actions of histone acetyltransferases and histone deacetylases (HDACs). Deacetylation of histone tails results in chromatin tightening and therefore HDACs are generally regarded as transcriptional repressors. Counterintuitively, simultaneous deletion of HDAC1 and HDAC2 in embryonic stem cells (ESC) reduced expression of pluripotent transcription factors, Oct4, Sox2 and Nanog (OSN). By shaping global histone acetylation HDACs indirectly regulate the activity of acetyl-lysine readers, such as BRD4. To examine the direct effects of HDAC (LBH589) and BRD4 (JQ1) inhibition on the ESC transcriptome, we performed precision nuclear run-on and sequencing (PRO-seq) analysis. Both LBH589 and JQ1 caused a marked reduction in the pluripotent network. However, while JQ1 treatment induced widespread transcriptional pausing of genes, HDAC inhibition caused a reduction in both paused and elongating polymerase, suggesting an overall reduction in recruitment of RNAPII. Using enhancer RNA (eRNA) expression to measure enhancer activity, we found that while HDAC activity regulates fewer enhancers than JQ1, LBH589 sensitive eRNAs were preferentially associated with super-enhancers and OSN binding sites. These findings suggest that HDAC activity is required for maintenance of pluripotency by regulating the OSN enhancer network via optimal recruitment of RNA polymerase II.
Comparative gene expression using the Illumina mouseWG-6 v2 expression BeadChip platform. Wild type (Day 0) ESC compared to HDAC1-/-; HDAC2-/wt; CreER ESCs on day 4 following for OHT treatment in presence (+LIF) or absence (-LIF) of Leukemia inhibitory factor (LIF).

overall_design: wild type (Day 0) were compared to HDAC1-/-; HDAC2-/wt; CreER ES cells on day 4 following OHT treatment. Each time points were analyzed in triplicate.

first: R

middle: D

last: Kelly

first: S

last: Cowley


title: The emergence of transcriptional identity in somatosensory neurons

status: Public on Oct 19 2019

first: Nikhil

last: Sharma

address: 200 Longwood Avenue, Armenise 435

institute: Harvard University

summary: Primary somatosensory neurons are diverse neurons that report salient features of our internal and external environments. How specialized gene expression programs emerge during development to endow each somatosensory neuron subtype with unique properties is unclear. To analyze the developmental progression of transcriptional maturation of each principal somatosensory neuron subtype, we generated a transcriptomic atlas of cells traversing the somatosensory lineage. We find that somatosensory neurogenesis leads to neurons in a transcriptionally unspecialized state, characterized by trace expression of subtype-specific genes yet co-expression of transcription factors (TFs) that become restricted to select subtypes as development proceeds. Single cell transcriptomic analysis using sensory neurons from mutant mice lacking representative broad-to-restricted TFs revealed that they are essential for establishing subtype specific gene programs in subtypes where their expression is maintained, while leaving other subtypes unaffected. We also identify a role for neuronal targets by demonstrating that nerve growth factor influences subtype-restricted patterns of TFs. Our findings support a model in which extrinsic cues orchestrate somatosensory neuron diversification by influencing the expression pattern of TFs that promote transcriptional specialization of somatosensory neuron subtypes.

overall_design: Single-cell RNA-seq from dorsal root ganglia

first: Kali

last: Flaherty

first: Karina

last: Lezgiyeva

first: Daniel

middle: E

last: Wagner

first: Allon

last: Klein

first: David

last: Ginty


title: Runx1 and Runx3 cooperatively repress Pmp22 to drive neurofibromagenesis [ChIP-seq]

status: Public on May 01 2019

city: Cincinnati

first: Kwangmin

last: Choi

state: Ohio

address: 333 Burnet Avenue

department: Experimental Hematology & Cancer Biology

institute: Cincinnati Children's Hospital Medical Center

summary: Neurofibromatosis type 1 (NF1) patients are predisposed to develop neurofibromas but the underlying molecular mechanism(s) of neurofibromagenesis are not fully understood. We showed that dual genetic deletion of Runx1 (Rx1) and Runx3 (Rx3) in Schwann cells (SCs) and Schwann cell precursors (SCPs) significantly delayed neurofibromagenesis and prolonged mouse survival. We identified peripheral myelin protein 22 (Pmp22/Gas3) related to tumor initiation. Knockdown of Pmp22 with shRNAs increased Rx1fl/fl;Rx3fl/fl;Nf1fl/fl;DhhCre sphere numbers and enabled significantly more neurofibroma like micro-lesions on transplantation. Conversely, overexpression of Pmp22 in mouse neurofibroma SCs decreased proliferation. Mechanistically, Rx1/3 regulated alterative Pmp22 promoter usage and reduced post transcriptional expression of Pmp22. Finally, pharmacological inhibition of Runx/core binding factor beta (Cbf-β) activity significantly reduced neurofibroma volume in vivo. Thus, we identified a novel signaling pathway involving Rx1/3 suppression of Pmp22 in neurofibroma initiation and/or maintenance. Targeting disruption of Runx/Cbf-β interaction might provide a novel therapy for neurofibroma patients.

overall_design: ChIP-seq on Runx-antibody treated sample and input DNA control sample

first: Jianqiang

last: Wu


title: Runx1 and Runx3 cooperatively repress Pmp22 to drive neurofibromagenesis

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

overall_design: Refer to individual Series


title: RNA sequencing of the left ventricle from non-failing donors and heart failure samples from the MAGNet consortium

status: Public on Dec 13 2019

city: Philadelphia

first: Michael

middle: Patrick

last: Morley

state: PA

address: 3400 Civic Center Blvd, Bldg 421

department: Penn Cardiovascular Institute

institute: Perelman School of Medicine at the University of Pennsylvania

summary: The Myocardial Applied Genomics Network (MAGNet; www.med.upenn.edu/magnet), collects and banks human cardiac tissue for genomic research.  All subjects or next of kin provided written informed consent for tissue donation and analyses and all study protocols were approved by relevant institutional review boards. Left ventricular free-wall tissue was harvested at the time of cardiac surgery from subjects with heart failure undergoing transplantation and from unused donor hearts with apparently normal function. The heart was perfused with cold cardioplegia prior to cardiectomy to arrest contraction and prevent ischemic damage, and tissue specimens were frozen in liquid nitrogen.

overall_design:
Resource of  left ventricular transcriptomes of non-failing healthy donors, Peripartum cardiomyopathy (PPCM), Hypertrophic cardiomyopathy (HCM) and Dilated cardiomyopathy (DCM) samples
----------------------------
MAGnet Consortium

Additional processing information can be found at:
https://github.com/mpmorley/MAGNet
https://github.com/mpmorley/MAGNet/wiki

first: Kenneth

last: Margulies

first: Thomas

middle: P

last: Cappola


title: Epigenetic reprogramming at estrogen-receptor binding sites alters 3D chromatin landscape in endocrine resistant breast cancer

status: Public on Dec 11 2019

city: Adelaide

first: Joanna

last: Achinger-Kawecka

state: SA

address: AHMS Building, North Terrace

institute: South Australian Immunogenomics Cancer Institute


title: Runx1 and Runx3 cooperatively repress Pmp22 to drive neurofibromagenesis [RNA-seq]

overall_design: Two group comparison between Nf1-/- mouse nerve tissues and Runx1/Runx3 double kockout neurofibroma tumors


title: The gene expression profiles of antigen-primed wildtype and Ddit3-/- CD8 Pmel T cells

status: Public on Apr 02 2019

city: Tampa

first: Paulo

middle: Cesar

last: Rodriguez

address: 12902 Magnolia Drive, MRC2067E

institute: Moffitt Cancer Center

summary: T cell undergoes ER stress during regular priming which may lead to T cell dysfunction in cancer. ER stress downstream sensor Chop (encoded by Ddit3 gene) negatively regulates CD8 T cell function and cytotoxicity. Because Chop is a C/EBP homologous transcription factor, we sorted antigen-primed wildtype or ddit3-/- Pmel CD8 T cells perform RNA-seq and gene expression profile analysis.

overall_design: CD8 T cells from wildtype or Ddit3-/- Pmel mice were stimulated by specific antigen gp10025-33 and the gene expression profiles were tested by RNA-seq

first: Yu

last: Cao

first: Ling

last: Cen


title: Single-cell transcriptional diversity is a hallmark of developmental potential

status: Public on Jan 28 2020

city: Stanford

first: Gunsagar

middle: Singh

last: Gulati

address: 265 Campus Drive

department: Institute for Stem Cell Biology and Regenerative Medicine, Department of Biomedical Data Science

institute: Stanford University

summary: Single-cell RNA sequencing (scRNA-seq) is a powerful approach for reconstructing cellular differentiation trajectories. However, inferring both the state and direction of differentiation is challenging. Here, we demonstrate a simple, yet robust, determinant of developmental potential—the number of expressed genes per cell—and leverage this measure of transcriptional diversity to develop a computational framework (CytoTRACE) for predicting differentiation states from scRNA-seq data. When applied to diverse tissue types and organisms, CytoTRACE outperformed previous methods and nearly 19,000 annotated gene sets for resolving 52 experimentally determined developmental trajectories. Additionally, it facilitated the identification of quiescent stem cells and revealed genes that contribute to breast tumorigenesis. This study thus establishes a key RNA-based feature of developmental potential and a platform for delineation of cellular hierarchies (https://cytotrace.stanford.edu).

overall_design:
Single-cell RNA-sequencing (Smart-seq2) profiles (n = 1,902 cells) of human basal (tumor: n = 294, adjacent normal: n = 366), luminal progenitor (tumor: n = 213, adjacent normal: n = 319), and mature luminal cells (tumor: n = 354, adjacent normal: n = 356) from 8 human breast cancer patients (luminal-like: n = 6; basal-like: n = 2)
-----------------------------------------
The authors state that they will "upload the remaining raw data to dbGap".

first: Shaheen

last: Sikandar

first: Angera

middle: H

last: Kuo

first: Robert

middle: W

last: Hsieh

first: Shang

last: Cai

first: Maider

last: Zabala

first: Ferenc

last: Scheeren

first: Neethan

last: Lobo

first: Dalong

last: Qian

first: Feiqiao

middle: B

last: Yu

first: Frederick

middle: M

last: Dirbas

middle: F

last: Clarke

first: Aaron

last: Newman


title: B lymphocyte alterations accompany abatacept resistance in new-onset type 1 diabetes

status: Public on Feb 28 2019

city: Seattle,

first: Stephanie

last: Osmond

state: WA

address: 1201 9th Ave

institute: Benaroya Research Institute

summary: Peripheral blood samples were collected from subjects enrolled in the TrialNet study TN-09. This was a phase II study of the effects of the T cell costimulation inhibitor CTLA4-Ig (abatacept) in new-onset T1D. Total RNA was isolated from whole blood samples and then globin-reduced. RNAseq libraries were prepared from the globin-reduced RNA.

overall_design: The abatacept trial was a randomized, double-blind study of patients (N = 112) with newly diagnosed T1D assigned to receive infusions of CTLA4-Ig (abatacept) or placebo on on days 1, 14, and 28, and then every 28 days with the last dose on day 700. The primary outcome was the baseline-adjusted geometric mean of the 2-h area-under-the-curve (AUC) serum C-peptide concentration after a mixed-meal tolerance test at 2 years’ follow-up. We obtained RNA-seq data from a subset of subjects in the original trial (N = 105 subjects originally), sampled at different visits (0, 84, and 728 days) for a total of 286 samples (mean 2.7 samples per patient). Of 286 initial samples, 272 yielded high-quality RNA-seq data consistent with subject annotation, and were used in downstream analyses.

first: Peter

last: Linsley

first: Carla

last: Greenbaum

first: Cate

last: Speake

first: S

middle: A

last: Long

first: Matthew

last: Dufort


title: Runx1 and Runx3 cooperatively repress Pmp22 to drive neurofibromagenesis [ATAC-seq]

first: Kwangmin

last: Choi

overall_design: Chromatic structure comparison between FACS-sorted EGFP+ Nf1fl/fl;DhhCre DRG and Rx1fl/fl;Rx3fl/fl;Nf1fl/fl;DhhCre mouse tumors cells.

first: Jianqiang

last: Wu


title: RNA sequencing of nasal lavage samples from mock- and Streptococcus pneumoniae-infected infant and adult mice

status: Public on Oct 16 2018

city: New York

first: Varshini

last: Vasudevaraja

address: 550 1st Avenue

department: Pathology

institute: NYU Langone Health

summary: Acute respiratory infections (ARI), which generally begin with colonization of the mucosal surfaces of the upper respiratory tract (URT), are a leading cause of morbidity and mortality with the highest rate in infants. As a common colonizer of the URT, and one of the most prevalent causes of life-threatening infections in the pediatric population, Streptococcus pneumoniae (Spn) was used as a model pathogen to investigate the effect of age during URT infection. We used RNA-sequencing to transcriptionally profile and compare the mucosal epithelia of infant and adult mice at baseline (mock-infected) and during Spn infection. Analysis of the screen revealed an age-dependent alteration of genes involved in mucosal defense mechanisms that included dampened expression of ubiquitous antimicrobial molecules and tight junction proteins in infant mice compared to adults. These results demonstrate a window of vulnerability during postnatal development when altered mucosal barrier function may facilitate bacterial colonization and invasion.

overall_design: We performed gene expression profiling of the nasal epithelium and associated tissue from mock- and Streptococcus pneumoniae-infected infant and adult mice, with a n=5 per group.

first: Kirsten

last: Kuipers

first: Kristen

last: Lokken

first: Jeffrey

middle: N

last: Weiser


title: The dose- and time-dependent effects of perfluorooctanoic acid on rat liver

status: Public on Jan 31 2020

city: Bloomington

first: Xilin

last: Li

state: Indiana

address: 2719 E 10th street Rm230

institute: Indiana University

summary: We reported the hepatic gene expression profiling in male Sprague-Dawley rats treated by different concentrations of perfluorooctanoic acid (PFOA) for 7, 14, and 28 days. We confirmed that PFOA induced liver tumor formation was mainly through the activation of peroxisome proliferator-activated receptor α (PPARα). We identified a panel of 7 genes (Cyp4a1, Nr1d1, Acot2, Vnn, Ehhadh, and Acot1) that might serve as the biomarkers for PPARα activation. We also meausred the apical endpoints of PPARα activation and found a good correlation with the expression level of these biomarker genes. Consitituitive androstane receptor mediated Cyp2b enzymatic activity and gene expression was also upregulated by PFOA in a dose-response manner. On the other hand, acyl hydrocarbon receptor (AhR) target gene Cyp1a2 were significantly downregulated at all time points studied. To our surprise, results of KEGG and Reactome pathway analyses suggested that PFOA did not drive the cell cycles and proliferations in the liver. While some of the DNA replication genes such as Pold2 and Mcm8 were upregulated by PFOA treatment, several key cyclin-dependent cell growth genes, including Ccnd1, Ccne2, Ccnb1, and Ccna2 were all significantly downregulated by PFOA in a dose-dependent manner, especailly at 28 days. Ingenuity Pathway Analysis also indicated that PFOA led to a suppression of liver cancer related pathways at later time points studied.  These results suggest that while PFOA clearly induced PPARα activation, the increased cell growth (the second key event in the tumor mode of action), was transient and tightly regulated by feedback mechanisms. Whether such changes will eventually cause the formation of preneoplastic foci and liver tumors in rats remains unclear.

overall_design: A total 60 (5-6 weeks old) male Sprague-Dawley rats were used. Rats were singly housed upon arrival and treated with vehicle control (water) or PFOA at the doses of 1, 5, 15mg/kg/d (volume 10ml/kg) via oral gavage for 7, 14 and 28 days (n = 5/dose/time point). The doses selected approximated the ones that were tested in the chronic dietary studies. Each animal was considered a biological replicate.

first: Zemin

last: Wang

first: Qiangen

first: Ram

last: Podicheti

first: James

last: Klaunig


title: Quantitative analysis of  transcriptomes in control and mTORC2-suppressed glioblastoma cells

status: Public on Nov 07 2019

city: Shinjuku

first: Kenta

last: Masui

state: Tokyo

address: 8-1 Kawada-cho

department: Department of Pathology

institute: Tokyo Women's Medical University

summary: We herein demonstrate that mammalian target of rapamycin complex 2 (mTORC2), a critical core component of the growth factor signaling system, globally alters histone modification as well as transcriptome through metabolic reprogramming in the highly malignant brain tumor glioblastoma (GBM). Integrated analyses unravel that mTORC2 regulates mineral metabolism including iron trafficking via histone H3K9 acetylation of the ferritin promoter, facilitating GBM growth and survival.

overall_design: mRNA profiles of glioblastoma cell lines with Scramble or Rictor (a core component of mTORC2) knockdown were generated by deep sequencing.

first: Masui

last: Kenta


title: Nuclear actin is required for transcription during Drosophila oogenesis

status: Public on Aug 01 2018

city: Helsinki

first: Maria

last: Sokolova

address: Viikinkaari 5

department: Institute of Biotechnology

country: Finland

institute: University of Helsinki


title: Sleep-wake driven and circadian contributions to daily rhythms in gene expression and chromatin accessibility in the murine cortex

status: Public on Nov 13 2019

city: Lausanne

first: Maxime

last: Jan

state: Suisse

address: University of Lausanne

department: CIG

institute: University of Lausanne

summary: We monitored gene expression and chromatin accessibility in the cerebral cortex of 10-12 week-old male C57BL/6J mice for 24 hours before and until 48 hours after the end of a single total sleep deprivation (SD) episode. The aim was to characterise the response to SD and recovery thereafter.

overall_design: Mice were sleep deprived for 6 hours starting at light onset (ZT0-ZT6; Time 24-30) of the light-dark cycle. Control mice (NSD, Non Sleep Deprived) were sacrificed at ZT0, ZT3, ZT6, ZT12, ZT18 of the first day of experimentation (named samples T0-T24 and corresponding to the 24 hours before SD), serving as a baseline day (Day 0). On Day 1, SD mice were sacrificed at the same time of day as on Day 0 (samples T27-42, with T27 and T30 samples being taken after 3h and 6h SD, respectively), on Day 2 at ZT0, ZT6, ZT12, ZT18 (samples T48-66), as well as ZT0 and ZT6 on Day 3 (samples T72-78). Two groups of mice were allowed to recover for 7 days after SD, before being sacrificed at ZT0 and ZT6 (Day 8, samples T192-198). We collected 3-4 replicates per time point and condition, and 8 replicates of ZT0 controls from two different animal batches. RNAseq and ATAC-seq libraries originate each time from the same animal, i.e. the data sets are paired. Sequencing failed for 2 ATAC-seq libraries at T66, resulting in only one biological replicate at this time point (corresponding RNAseq was not affected and thus comprises 3 biological replicates)..

first: Charlotte

last: Hor

first: Jake

last: Yeung

first: Yann

last: Emmenegger

last: Hubbard

first: Ioannis

last: Xenarios

first: Felix

last: Naef

first: Paul

last: Franken


title: The influence of PPFIA1 silencing to gene expression in breast carcinoma cell line and head and neck squamous cell carcinoma cell lines by RNA-sequencing in three dimensional collagen I

status: Public on Jul 19 2018

first: Outi

last: Monni

address: Haartmaninkatu 8

department: Department of Biomedicine

summary: PPFIA1 (encodes for liprin-α1) locates at the commonly amplified 11q13 region in cancer, but the precise mechanism of liprin-α1 function has remained unclear. In this study we show how genes are differentially expressed after liprin-α1 knockdown in different cell lines, grown in three dimensional matrix. The overall goal was to gain insight into the mechanism by which liprin-α1 has an effect on the progression of head and neck carcinomas and breast carcinomas in three dimensional environment.

overall_design: RNA-seq analysis was carried out to identify differentially expressed genes between the two conditions, control (shScr) and PPFIA1 silenced (shPPFIA1), in breast and head and neck squamous cell carcinoma cell lines cultivated in three dimensional collagen I. Cells were transduced with shPPFIA1 using three different shRNA constructs (shPPFIA1_14, shPPFIA1_44 and shPPFIA1_69) and selected with puromycin. shScramble (shScr) with three replicates were done with separate transductions and used as controls. Cells were grown inside three dimensional collagen I culture for five days, after which RNA was extracted and further prosessed for RNA sequencing analysis. Illumina NextSeq High Output 1 x 75 bp was used.

first: Henna

last: Pehkonen

first: Mira

last: Lento

first: Mikko

last: Kivento

first: Artemis

last: Filippou


title: Runx1 and Runx3 cooperatively repress Pmp22 to drive neurofibromagenesis [microarray]

first: Kwangmin

last: Choi

overall_design: EGFR- and + Schwann cell stem cell were selected for RNA extraction and hybridization on Affymetrix microarray.

first: Jianqiang

last: Wu


title: Cisplatin-DNA Adduct Repair of Transcribed Genes is Controlled by Two Circadian Programs in Mouse Tissues

status: Public on Jun 21 2018

city: Chapel Hill

first: Yanyan

last: Yang

state: NC

address: 120 Mason Farm Road

department: Biochemistry & Biophysics

institute: University of North Carolina  at Chapel Hill

summary: We tested the impact of clock time on excision repair of cisplatin-induced DNA damage at single nucleotide resolution across the genome in mouse liver and kidney. We found that genome repair is controlled by two circadian programs.

overall_design: we perform XR-seq in mouse kidney and liver at different  Zeitgeber time. After we injected the mouse with cisplatin 10mg / kg 2 hours, we sacrificed the mouse at indicated time and took the kidneys and liver. then lysed tissue and did TFIIH IP and cisplatin IP for construct the XR-seq library and sequence.

first: Ogun

last: Adebal

first: Gang

first: Christopher

last: Selby

first: Yi-Ying

last: Chiou

first: Naim

last: Rashid

first: Jinchuan

last: Hu

first: John

last: Hogenesch

first: Aziz

last: Sancar


title: Functional Screening in Human Cardiac Organoids Reveals a Metabolic Mechanism for Cardiomyocyte Maturation

status: Public on Aug 30 2017

city: Brisbane

first: James

last: Hudson

state: QLD

address: 300 Herston Rd

institute: QIMR Berghofer Medical Research Institute

summary: The mammalian heart undergoes maturation during postnatal life to meet the increased functional requirements of the adult. However, the key drivers of this process remain poorly defined. We developed as 96-well screening platform, using human pluripotent stem cell derived cardiac organoids, to determine the molecular requirements for in vitro cardiomyocyte maturation. Here, we describe gene expression changes resulting from culturing human cardiac organoids in standard cell culture conditions and under optimized maturation conditions. We assessed our maturation conditions by comparing transcriptional changes of human cardiac organoids to RNA isolated from human heart. Interesting, analysis of these data revealed that a switch to fatty acid oxidative metabolism is a key governor of cardiomyocyte maturation and mature cardiac organoids were refractory to mitogenic stimuli.

overall_design: 3D cardiac organoids were cultured in CTRL or MM for 11 days before collecting for RNA-seq.

first: Richard

middle: J

last: Mills

first: Gregory

last: Quaife-Ryan

first: Enzo

middle: R

last: Porrello


title: Hif2a-cardiomyocyte deficient mice response to myocardial ischemia and reperfusion

status: Public on Dec 31 2016

city: Munich

first: Michael

last: Koeppen

address: Marchioninistr. 15

country: Germany

institute: Ludwig-Maximilians-University

summary: Analysis of heart of Hypoxia-inducible 2 alpha-deficient mice, specific in cardiomyocytes (Hif2aloxP/loxP Myosin Cre+)  subjected to myocardial ishcemia reperfusion. Hif2a belongs to the family of transcription factors, that regulate a transcriptional response to tissue hypoxia.

overall_design: Untreated Myosin Cre+ and Hif2aloxP/loxP Myosin Cre+ mice were compared to wMyosin Cre+ and Hif2aloxP/loxP Myosin Cre+ mice  with 45 min ischemia followed by 2 hours reperfusion.

first: M

first: I

middle: V

first: H

middle: K

last: Eltzschig


title: Transcriptome profiling of human keratoconus corneas through RNA sequencing identifies collagen synthesis disruption and downregulation of core elements of TGF-β, Hippo, and Wnt pathways

status: Public on Feb 02 2017

city: Poznań

first: Michal

last: Kabza

address: ul. Fredry 10

country: Poland

institute: Poznan University of Medical Sciences

summary: To understand better the factors contributing to keratoconus (KTCN), we used RNA sequencing to perform a transcriptome profile of human KTCN corneas. Over 82% of the genes and almost 75% of the transcripts detected as differentially expressed in KTCN and non-KTCN corneas were confirmed in the replication study using another set of samples. We used these differentially expressed genes to generate a network of KTCN-deregulated genes. We found an extensive disruption of collagen synthesis and maturation pathways, as well as downregulation of the core elements of the TGF-β, Hippo, and Wnt signaling pathways influencing corneal organization. We identified long noncoding RNAs (lncRNAs) and conducted a computational analysis of their potential functions, and found that lncRNAs regulated the processing and expression of the aforementioned genes. This first comprehensive transcriptome profiling of human KTCN corneas points further to a complex etiology of KTCN.

overall_design: Transcription profiling of 25 KTCN and 25 non-KTCN corneas using RNA-Seq

first: Justyna

last: Karolak

first: Malgorzata

last: Rydzanicz

first: Michał

last: Szcześniak

first: Dorota

last: Nowak

first: Barbara

last: Ginter-Matuszewska

first: Piotr

last: Polakowski

first: Rafal

last: Ploski

first: Jacek

last: Szaflik

first: Marzena

last: Gajecka


title: Cell type-specific immune phenotypes predict loss of insulin secretion in new-onset type 1 diabetes

first: Stephanie

last: Osmond

summary: Peripheral blood samples were collected from control-arm subjects enrolled in 6 clinical trials conducted by the Immune Tolerance Network and Type 1 Diabetes TrialNet. The included trials evaluated immune-modifying therapy in new-onset T1D, with similar trial timecourses, primary outcomes, and data and sample collection. Total RNA was isolated from whole blood samples and then globin-reduced. RNAseq libraries were prepared from the globin-reduced RNA.

overall_design: Subjects from the control arms of 6 clinical trials in new-onset T1D were aggregated to evaluate variation in disease course in the immediate post-diagnostic period.  All trials used serum C-peptide concentration after a mixed-meal tolerance test as the primary outcome, with an initial trial duration of approximately two years, with longer-term follow-up in some cases. We obtained RNA-seq data from all available subject visits (N = 138 subjects), ranging from the time of study entry to three years, for a total of 496 samples (mean 3.6 samples per subject). Three samples were removed due to SNP-based kinship values indicating sample contamination or mis-identification; these samples are excluded from the submitted dataset. Of the remaining 493 samples, 471 yielded high-quality RNA-seq data from unique visits consistent with subject annotation, and were used in downstream analyses.

first: Matthew

last: Dufort

first: Carla

last: Greenbaum

first: Cate

last: Speake

first: Peter

middle: S

last: Linsley