title: RNA-Seq analysis of the impact of a kinase NIK inhibitor (DMBP5) on the human melanoma cell line A375

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

institute: IPMC/CNRS

summary:
Introduction: there is growing evidence that the IFN-  -related cytokine signature plays a major role supporting the effect of pharmacological blockade of immune checkpoints. The expression of IFN-   in cancer cells is repressed by several factors, among them a key role is played by the oncogene EZH2, which in turns is controlled by the non-canonical NF-kB pathway and its upstream kinase, NIK.

Methodology: we developed a series of NIK inhibitors and compared the effects on cancer cells of one of them (DMBP5) to an siRNA against NIK via transcriptomic analysis (RNA-seq).

Results: mRNA modifications induced by DMBP5 on A375 melanoma cells closely resemble the ones observed with siRNA against NIK.

Conclusions: DMBP5 is a very selective and effective non-competitive NIK inhibitor (first in class).

overall_design: Refer to individual Series


title: Integrated analysis of microRNA and mRNA expression profiles of rice seedlings in response to zinc deficiency and recovery (miRNA-seq)

status: Public on Jan 08 2020

city: Hangzhou

first: Houqing

last: Zeng

address: NO.2318, Yuhangtang Rd, Yuhang District

country: China

institute: Hangzhou Normal University

type: Non-coding RNA profiling by high throughput sequencing

summary: Using Illumina’s high-throughput small RNA sequencing and RNA sequencing, miRNAs and mRNAs differentially expressed under Zn deficiency and Zn resupply conditions were identified in shoots and roots of rice seedlings. A total of 68 miRNAs were identified to be differentially expressed under Zn deficiency and/or Zn resupply, and 38 of them were novel miRNAs. The Zn-responsive miRNAs were predicted to target a total of 799 genes. The transcriptome sequencing identified a total of 360 differentially expressed genes (DEGs) under Zn deficiency in shoots and roots, and 97 of them were recovered after Zn resupply treatment. Twelve DEGs were found to be potential targets genes of several Zn-responsive miRNAs like miR171g-5p, miR397b-5p, miR398a-5p, and miR528-5p.

overall_design: Roots and shoots of rice seedlings were collected after Zn-deficient treatment for two weeks. For Zn-resupply treatment, Zn-deficient seedlings were transferred to nomal nutrient solution containing 1.5 µM ZnSO4 for three days. After Zn-resupply treatment, roots and shoots were collected for analyses at the same time point as collecting the Zn-deficient samples (four hours after illumination).


title: Identification of a multi-potent Twist2-expressing cell population in the adult heart (single cell RNA-seq data set)

city: Dallas

first: Yi-Li

last: Min

state: Texas

address: 6000 Harry Hines Blvd

department: Molecular Biology

country: USA

institute: UT Southwestern Medical Center

type: Expression profiling by high throughput sequencing

summary: Twist transcription factors function as ancestral regulators of mesodermal cell fates in organisms ranging from Drosophlia to mammals. Through lineage tracing of Twist2 (Tw2) expressing cells with tamoxifen-inducible Tw2-CreERT2 and tdTomato reporter mice, we discovered a unique cell population that progressively contributes to multiple cell types in the adult heart, including cardiomyocytes, endothelial cells and fibroblasts. Clonal analysis confirmed the ability of Tw2-derived tdTO+ (Tw2-tdTO+) cells to form CMs in vitro. Within the adult heart, Tw2-tdTO+ cardiomyocytes accounted for ~13% of total cardiomyocytes, the majority of which resulted from fusion of Tw2-tdTO+ cells with existing cardiomyocytes. Tw2-tdTO+ cells also contribute to cardiac remodeling after injury. We conclude that a Tw2-tdTO+ cells participate in lifelong maintenance of cardiac function, at least in part through de novo formation of cardiomyocytes and fusion with preexisting cardiomyocytes, as well as in the genesis of other cellular components of the adult heart.

overall_design: For RNA-seq dataset, gene expression profile was generated comparing Tw2- and Tw2+ non-CMs in the heart, by deep seqencing, with three biological replicates, using Illumina HiSeq 2500.    For single cell RNA-seq dataset, gene expression profile was generated using 10x genomics platform with four biological replicates, using illumina Nextseq 500.

first: Venkat

middle: S

last: Malladi

first: Miao

last: Cui

first: Zhaoning

last: Wang

first: Rhonda

last: Bassel-Duby

first: Eric

middle: N

last: Olspm

first: Ning

last: Liu


title: Identification of a multi-potent Twist2-expressing cell population in the adult heart

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


title: RNA-Seq analysis of the impact of a kinase NIK inhibitor (DMBP5) on the human melanoma cell line A375 (replicate 2).

country: France

summary:
Introduction: there is growing evidence that the IFN-γ-related cytokine signature plays a major role supporting the effect of pharmacological blockade of immune checkpoints. The expression of IFN-γ in cancer cells is repressed by several factors, among them a key role is played by the oncogene EZH2, which in turns is controlled by the non-canonical NF-kB pathway and its upstream kinase, NIK.
Methodology: we developed a series of NIK inhibitors and compared the effects on cancer cells of one of them (DMBP5) to an siRNA against NIK via transcriptomic analysis (RNA-seq).
Results: mRNA modifications induced by DMBP5 on A375 melanoma cells closely resemble the ones observed with siRNA against NIK.
Conclusions: DMBP5 is a very selective and effective non-competitive NIK inhibitor (first in class).

overall_design: comparisons of mRNA changes at 2 time points (48 and 96 hrs) in a melanoma cell lines (A375) between DMBP5 (NIK small molecule inhibitor) and siRNA against NIK each of them nomralized for their respective controls (DMSO or siRNA controls).

first: G

middle: M

last: De Donatis

first: T

last: Passeron

first: N

last: Nottet

first: A

last: Paquet

first: P

last: Barbry


title: Genome wide expression analysis of young and aged human endometrium

city: Cambridge

first: Laura

last: Woods

address: Babraham Hall

country: United Kingdom

institute: The Babraham Institute

summary: We use RNA-sequencing to measure global transcription in LH timed endometrial biopsies of 10 women aged ≤ 30 years and 10 women aged ≥ 40 years.

overall_design: 10 endometrial biopsies were taken from 10 women aged  ≤ 30 years, and 10 women aged ≥ 40 years. The 2 groups were matched for BMI, previous live births, and previous 1st or 2nd trimester losses. Biopsies were LH surge timed and were taken at between LH +6 to LH +10. Biospies were snap frozen before RNA extraction and subsequent RNA library preparation.

first: Paul

last: Brighton

first: Maruyama

last: Yojiro

first: Katherine

last: Fishwick

first: Pavle

last: Vrljicak

first: Shreeya

last: Tewary

first: Risa

last: Fujihara

first: Joanne

last: Muter

first: Emma

last: Lucas

first: Taihei

last: Yamada

first: Andrew

last: Sharkey

first: Raffaella

last: Lucciola

first: Saturo

last: Takeda

first: Sascha

last: Ott

first: Myriam

last: Hemberger

first: Siobhan

last: Quenby

first: Jan

middle: J

last: Brosens


title: CRISPR/Cas9 knock down line

city: South San Francisco

first: Steffen

last: Durinck

state: CA

address: 1 DNA Way

institute: Genentech


title: RNA-Seq analysis of the impact of a kinase NIK inhibitor (DMBP5) on the human melanoma cell line A375 (replicate 1)

first: Kevin

last: Lebrigand

summary:
Introduction: there is growing evidence that the IFN-γ-related cytokine signature plays a major role supporting the effect of pharmacological blockade of immune checkpoints. The expression of IFN-γ in cancer cells is repressed by several factors, among them a key role is played by the oncogene EZH2, which in turns is controlled by the non-canonical NF-kB pathway and its upstream kinase, NIK.

Methodology: we developed a series of NIK inhibitors and compared the effects on cancer cells of one of them (DMBP5) to an siRNA against NIK via transcriptomic analysis (RNA-seq).

Results: mRNA modifications induced by DMBP5 on A375 melanoma cells closely resemble the ones observed with siRNA against NIK.

Conclusions: DMBP5 is a very selective and effective non-competitive NIK inhibitor (first in class).

overall_design: comparisons of mRNA changes at 2 time points (48 and 96 hrs) in a melanoma cell lines (A375) between DMBP5 (NIK small molecule inhibitor) and siRNA against NIK each of them normalized for their respective controls (DMSO or siRNA controls).

first: G

last: De Donatis

first: T

last: Passeron

first: N

last: Nottet

first: A

last: Paquet

first: P

last: Barbry


title: Effects of a glyphosate-based herbicide on the transcriptome of Aspergillus Nidulans

city: London

first: Robin

last: Mesnage

address: Guy's Hospital, 8th Floor, Tower Wing

institute: Kings College London

summary:
In order to evaluate the molecular effects of Roundup at a concentration at which no morphological effects were identified, RNA extracted from Roundup-treated A. nidulans cultures were subjected to a global gene expression profiling using a custom agilent microarray  (8 × 15 K format), for which the reproducibility, specificity and sensitivity was described previously (Delomenie et al., Curr Genet 2016 Nov;62(4):897-910. PMID: 27038308).

This data is published in

Mesnage R, Oestreicher N, Poirier F, Nicolas V, Boursier C, Vélot C. (2020) Transcriptome profiling of the fungus Aspergillus nidulans exposed to a commercial glyphosate-based herbicide under conditions of apparent herbicide tolerance. Environmental Research. Available online 7 January 2020, 109116. https://doi.org/10.1016/j.envres.2020.109116

overall_design: Two independent series of quadruplicate cultures from A. nidulans CV125 strain were grown in liquid culture medium with 0,007% Roundup.

first: Christian

last: Velot


title: MMRN2 mutation underlies a rare form of autosomal-dominant laryngeal malformation

status: Public on Jan 07 2020

city: Shanghai

first: Luo

last: Guo

address: 83# fenyang road, 9# building, room 613

institute: Fudan University

summary: The aim of this study was to investigate the genetic basis and pathogenic mechanism of nonsyndromic laryngeal malformations, including disrupted thyroid cartilage structures and malformed vocal cords, in a four-generation family.

overall_design: Clinical characterizations, whole-exome sequencing, and co-segregation analysis were carried out on the family. Mice models were used to investigate the pathogenesis of MMRN2 mutations. RNA sequencing were used to investigate the pathogenic pathway through which the Mmrn2 leads to changes in the morphologies of the larynges.

first: X

last: Wu

first: L

first: H

last: Li

first: C

last: Wei


title: Extraction and high-throughput sequencing of oak heartwood DNA: assessing the feasibility of genome-wide DNA methylation profiling

city: Milan

first: Federico

last: Rossi

address: Via Adamello 16

country: Italy

institute: Istituto Europeo Oncologia

type: Methylation profiling by high throughput sequencing

summary: Tree ring features are affected by environmental factors and therefore are the basis for dendrochronological studies to reconstruct past environmental conditions. Oak wood often provides the data for these studies because of the durability particularly of oak heartwood and, hence the availability of samples spanning long time periods of the distant past. Wood formation is regulated in part by epigenetic mechanisms such as DNA methylation. Studies in the methylation state of DNA preserved in oak heartwood thus could identify epigenetic tree ring features informing on past environmental conditions. We investigated the feasibility of such studies using heartwood samples core-drilled from the trunks of standing oak trees spanning the AD 1776-2014. Heartwood contains little DNA, and large amounts of phenolic compounds known to hinder the preparation of high-throughput sequencing libraries. We sequenced whole-genome and DNA methylome libraries for oak heartwood up to 100 and 50 years of age, respectively. However, only 56 genomic regions with sufficient coverage for quantitative methylation analysis were identified, suggesting that the high-throughput sequencing of DNA will be in principal feasible for wood formed <100 years ago is impeded by the reduction in library complexity caused by the bisulfite treatment used to generate the oak methylome.

overall_design: Examination of whole-genome sequencing in 12 oak (Quercus robur) wood  samples (4 sapwood, 8 heartwood) from 4 trees and whole-genome bisulfite sequencing in 4 oak (Quercus robur) wood samples (2 sapwood, 2 heartwood) from 2 trees

first: Alessandro

last: Crnjar

last: Comitani

first: Rodrigo

last: Feliciano

first: Leonie

last: Jah

first: George

last: Malim

first: Laura

last: Southgate

first: Emily

last: Kay

first: Rebecca

last: Oakey

first: Richard

last: Buggs

first: Andy

last: Moir

first: Logan

last: Kistler

first: Ana

last: Rodriguez Mateos

first: Carla

last: Molteni

first: Reiner

last: Schulz


title: Identification of a multi-potent Twist2-expressing cell population in the adult heart (RNA-seq data set)

first: Yi-Li

last: Min

overall_design:
For RNA-seq dataset, gene expression profile was generated comparing Tw2- and Tw2+ non-CMs in the heart, by deep seqencing, with three biological replicates, using Illumina HiSeq 2500.

For single cell RNA-seq dataset, gene expression profile was generated using 10x genomics platform with four biological replicates, using illumina Nextseq 500.

first: Venkat

last: Malladi

first: Miao

last: Cui

first: Zhaoning

last: Wang

first: Ning

last: Liu

first: Rhonda

last: Bassel-Duby

first: Eric

last: Olson


title: Genome-wide profiling of Arabidopsis thaliana Col-0 and ein2/jar1 host responses to Macrophomina phaseolina infection

city: Riverside

first: Thomas

last: Eulgem

state: California

address: Genomics 3234A

department: Botany and Plant Sciences

institute: University of California, Riverside

summary: Macrophomina phaseolina (Mp) is a soil-borne pathogenic fungus known to infect more than 500 plants species including important crops.  Here we report the use of a novel agar plate-based pathosystem using the model plant Arabidopsis thaliana (Arabidopsis) to study plant defense reponses to Mp, specifically a comparison  between wild type Col-0 and double mutant ein2/jar1 roots with and without Mp infection, at two time points, by RNA-seq.

overall_design: Total mRNA expression profiling in Arabidopsis Col-0 and in ein2/jar1 roots, with and without Mp infection, at 24 hours or 48 hours post Mp contact, with two replicates respectively.

first: Mercedes

last: Schroeder

first: Tokuji

last: Tsuchiya


title: Telomerase function and binding at endogenous G-rich regions (Hi-C Seq)

city: Bonn

first: Katrin

last: Paeschke

address: Sigmund Freud Str. 25

department: Department of Oncology, Hematology and Rheumatology

country: Germany

institute: University Hospital Bonn

summary: Telomerase majorly functions at telomeres but under adverse conditions acts at endogenous regions, which is often observed in cancer calls. By mapping the global occupancy of the catalytic subunit of telomerase (Est2), we reveal that telomerase binds to multiple genomic loci, which we termed ‘non-telomere-binding sites’ (NTBS). We characterized under when and why Est2 binds to such sites and could show that telomerase is inactive but becomes activated upon global DNA damage. Indicating that those regions are of particular risk for genome stability. Using biochemical and molecular experiments we further characterized Est2 binding to NTBS. In contrast to Est2 binding to telomere neither Cdc13 nor Ku70/80 is crucial for the binding to NTBS. Strikingly, using Hi-C, we demonstrate that chromatin organization is essential and drives the interaction of Est2-NTBS binding. The here presented results provide a novel model of telomerase regulation using endogenous regions as “parking spots” awaiting its canonical function at telomeres.

overall_design: Wild type Saccharomyces cerevisiae cells were subjected to Hi-C to examine the interaction between teloemric and non-telomeric binding sites of catalytic subunit of telomerase.

first: Satyaprakash

last: Pandey

first: Stephanie

last: Schalbetter

first: Jonathan

last: Baxter

first: Stefan

middle: A

last: Juranek

first: Viktor

last: Guryev

first: Theresa

last: Schmitz

first: Andreas

last: Hofmann

first: Dieter

middle: W

last: Heermann


title: Poor Mitochondrial Reponses to Oxidative Stress in a Subset of Autism Spectral Disorder Patients

city: Clemson

first: William

last: Baldwin

state: South Carolina

address: 230 Parkway Dr

department: Biological Sciences

institute: Clemson University

summary: Over the past decade, there has been a 10X rise in the prevalence of autism spectrum disorder (ASD) from 0.2% to 2% of the U.S. population of school age children. With this rise in ASD has come an interest in identifying both the causation and biomarkers for ASDs.  Primary fibroblasts from ASD-postive and ASD-negative patients were differentiated into cortical neurons and were either left unexposed or exposed to 800 uM hydrogen peroxide for 17 hours prior to RNA extraction. RNAseq was performed to test whether poor response to H2O2 could be associated with gene expression.

overall_design: Used RNA-sequencing to explain the inability to repair mtDNA damage in ASD-positive patients on a transcriptomic level using an Illumina NextSeq 550. Undifferentiated and untreated fibroblasts from two patients were also sequenced to ensure successful differentiation to neurons.

first: Melissa

last: Heintz

first: Rooksana

middle: E

last: Noorai


title: Gene expression changes by  Foxo1 knockdown in primary human dermal lymphatic endothelial cells (HDLEC)

city: Takamatsu

first: Tatsuo

last: Furuyama

state: Kagawa

address: 281-1 Murecho-hara

country: Japan

institute: Kagawa Prefectural University of Health Sciences

summary: To identify genes regulated by FOXO1 in HDLEC, we have empolyed whole genome microarray expression profiling. We identified CXCR4 as the most reduced gene after 72h of siRNA treatment for Foxo1 and the expression change was confirmed by RT-PCR and western blot.

overall_design: Using total RNA extracted from cultured HDLEC at 72h after transfection with siRNA mix targetting for Foxo1 and control mix , we  measured gene expression changes. A mixed HDLEC derived from 3 male foreskins was used. Expression changes were confirmed by RT-PCR or WB.


title: Integrated miRNA/mRNA-Seq of the Habenulo-Interpeduncular Withdrawal Circuit

city: Worcester

first: Alper

last: Kucukural

state: MA

address: 364 Plantation Street

department: Program in Molecular Medicine

institute: UMass Medical School

summary: Nicotine dependence is responsible for perpetuating the adverse health effects due to tobacco use, the leading cause of preventable death worldwide. Nicotine is an agonist for nicotinic acetylcholine receptors, which are enriched in the habenulo-interpeduncular withdrawal circuit. Drugs of abuse, including nicotine, induce stable neuroadaptations, requiring protein synthesis through regulation of transcription factors, epigenetic mechanisms, and non-coding RNAs. It also been shown that miRNAs in brain are regulated by nicotine and that miRNA dysregulation contributes to brain dysfunction, including drug addiction. While much is known about the neurocircuitry responsible for the behaviors associated with nicotine reward or withdrawal, the underlying mechanisms of how changes in behavior are induced are less clear. Using miRNA- and mRNA-Seq, we demonstrate that there are widespread changes in both miRNA and mRNA expression in the IPN and MHb during acute nicotine withdrawal. Conserved, differentially expressed miRNAs were predicted to target inversely regulated mRNAs. This dataset represents a valuable resource, identifying a multitude of miRNAs/genes, which upon further study may reveal new mechanisms underlying the neuroadaptations of nicotine dependence and the symptoms of nicotine withdrawal.

overall_design: Male C5BL/6J mice were treated with chronic nicotine (NIC) or control tartaric acid solution (TA) orally. Additional nicotine withdrawal groups were treated with nicotine and then spontaneously withdrawn for 48 hours (NAWD) or 4 weeks (NLWD). Mice were sacrificed for tissue collection and the interpeduncular nucleus (IPN) and medial habenula (MHb) were extracted by tissue punch. Each sample contained tissue pooled from 4 animals. Total RNA was isolated and small RNAs were separated by denaturing gel electrophoresis. Separate sequencing libraries were generated for miRNAs and mRNAs from the same total RNA samples. Stranded mRNA libraries were generated using an Illumina kit by manufacturer’s instructions. miRNAs and mRNAs were sequenced and differential expression and gene ontology analyses were performed.

first: Alison

middle: P

last: Casserly

first: Junko

last: Tsuji

first: Paul

middle: D

last: Gardner


title: Telomerase function and binding at endogenous G-rich regions (ChIP)

first: Katrin

last: Paeschke

type: Genome binding/occupancy profiling by genome tiling array


title: Telomerase function and binding at endogenous G-rich regions


title: FMRP cTag CLIP from mouse CA1 pyramidal neurons

first: Kirsty

last: Sawicka

address: Robinson Way

department: University of Cambridge

institute: CRUK Cambridge Insititute

summary: Loss of the neuronal RNA binding protein FMRP causes Fragile X Syndrome (FXS), the most common cause of inherited intellectual disability, yet it is unknown which brain regions and cell types within them contribute to disease pathophysiology. We used conditional tagging of FMRP and CLIP (cTag FMRP CLIP) to examine FMRP targets specifically in CA1 hippocampal neurons, a critical cell type for learning and memory known to have altered synaptic function in FXS. Integrating this data with analysis of ribosome-bound transcripts from the same neuronal population revealed CA1-enriched binding of autism-relevant mRNAs, and unexpected CA1-specific regulation of transcripts encoding circadian proteins.

overall_design: 3 biological replicates of FMRP cTag CLIP in mouse CA1 pyramidal neurons. Each replicate includes a sample prepared from Fmr1-cTag/Camk2a-Cre hippocampal tissue and a sample prepared from animals without Cre expression as a negative control.

first: Caryn

middle: R

last: Hale

first: Robert

middle: B

last: Darnell

first: Jennifer

middle: C


title: Regulation of TFR cells by  Blimp1

city: Indianapolis

first: Alexander

last: Dent

state: IN

address: 950 W. Walnut St. R2 302, Walther Oncology Center

institute: Alexander Dent

summary: What genes does the transcription factor Blimp1 regulate in  Tfr cells?

overall_design: CD4+ T cells were isolated from the spleen from Wildtype (WT) and Blimp1-flox (Blimp1) Foxp3-cre mice 36 days after 2x oral challenge with peanut + cholera toxin. Cells were isolated via a CD4+ T isolation kit (Miltenyi Biotec). Foxp3+YFP+ CXCR5+ PD1+ cells were further isolated by  FACS (FACS Aria). Total RNA was collected from freshly sorted TFR cells using the RNeasy Plus Micro kit (QIAGEN) and subjected to RNA-seq

first: Markus

last: Xie


title: long read RNA-seq from HFFc6 (ENCSR902GAF)

status: Public on Jan 06 2020

city: Stanford

first: ENCODE

last: DCC

address: 300 Pasteur Dr

institute: ENCODE DCC

summary:
Clonal line 6 derived from hTert immortalized HFF parental line

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


title: microRNA expression profiles in myocardium of diet-induced obesity rat

city: Shenyang

last: Wu

state: Liaoning

address: 155th North of Nanjing Street

institute: The first affiliated hospital of China Medical University

summary: Diet induced obesity in rat was associated with myocardial dysfunction, hypertension and fibrosis. This study aimed to explore microRNA expression profiles in diet obesity-induced rat myocardium. Wistar rats were feed normal chow or high-fat diet for 20 weeks.  After that, cardiac function was evaluated by echocardiography.  Left ventricular myocardium was harvest to assess the extent of hypertension and fibrosis, meanwile, the left ventricular microRNA expression was analyzed using Agilent Rat miRNA microarray. Significant cardiac dysfunction, hypertension and fibrosis were found in diet-induced obesity rats as compared with normal diet rats. rno-miR-141-3p and rno-miR-144-3p were also significantly increased in myocardium of diet-induced  obesity rat. These findings suggest that specific miRNA differences may contribute to the alteration in cardiac function, hypertension and fibrosis which responses to diet-induced obesity.

overall_design: Wistar rats were randomly divided into two groups, which feed normal chow or high-fat diet for 20 weeks, respectively.  Left ventricular myocardium was harvest to detect microRNA expression using microarray. Furthermore, miRNA differences were analyzed by comparing the microRNA expression in myocardium between rats fed normal diet and rats fed high-fat diet.

first: Huimin

last: Yang


title: Transcriptional profile of gamma-delta T cells in C.difficile infection

city: Saint Louis

first: Yee-shiuan

last: Chen

state: MO

address: 660 S Euclid Ave

department: Department of Medicine

institute: Washington University School of Medicine

summary: RNAseq data of sorted IL-17A-producing and IL-17A-non-producing gamma delta T cells from C.difficile infected mice

overall_design: Mesenteric lymph node from C.difficile infected mice were isolated and simulated in vitro with PMA/Ionomycin. IL-17A-producing cells were subsequently labled by cell surface cytokine capture and sorted by FACS.

first: Yee-Shiuan

first: David

last: Haslam


title: Transcriptomic analysis of Fusobacterium nucleatum-stimulated Human gingival-derived mesenchymal stem cells

status: Public on Jan 13 2020

city: Jinan, Shandong

first: Wenyan

last: Kang

address: No. 44-1 Wenhua Road West

institute: Shandong university

summary: To better understand the global responses of GMSCs to F. nucleatum infection along the time sequence, we performed a genome-wide transcriptome analysis by RNA-sequencing technology to determine the global changes on gene expression level

overall_design: 24 samples from 3 individuals (each individual involved  4 control samples at 3d 7d, 14d and 21d with no F. nucleatum treatment, and 4 experimental samples with F. nucleatum (F. nucleatum:cell=100:1) treatment at the same time point) were sequenced to analysis the whole gene expression level

first: Qiang

last: Feng


title: Alteration of mRNA expression in breast cancer cells upon chemical inhibition of the 26S proteasome

city: RTP

first: Trevor

last: Archer

address: 111 TW Alexander

institute: NIH

summary: The 26S proteasome regulates degradation of many cellular proteins to maintain cellular homeostasis.  Disruption of proteasome activity followed by dysregulation of tumor suppressors and oncogenes is rampant in many cancers, hence chemical inhibitors of the proteasome have utility as cancer therapeutics, although the underlying mechanisms of their effects in the clinic is poorly understood. We have employed whole genome microarray expression profiling as a discovery platform to identify genes and potential signaling pathways that are affected MCF7 breast cancer cells are treated with MG132 a chemical inhibitor of the proteasome.   Total RNA was collected from MCF7 breast cancer cells treated with DMSO (vehicle control) and 1 uM MG132 for 4 or 24H . We identified time dependent changes in the expression of genes enriched in p53 and estrogen receptor pathways, two signatures relevant to breast cancer biology.

overall_design: Proteasome inhibitor induced gene expression in MCF7 breast cancer cells was measured in cells treated with DMSO (vehicle, control) or 1 uM MG132 for 4 and 24 hours.  Three independent experiments were performed at each time.

middle: K


title: long read RNA-seq from K562 (ENCSR589FUJ)

summary:
Homo sapiens K562 immortalized cell line

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


title: Chromatin state and Transcriptional regulation in MCF-7 breast cancer cells treated with proteasome inhibitor MG132

type: Genome binding/occupancy profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Enhanced and selective translation expands the lysosome size and promotes antigen presentation during phagocyte activation

city: Stockholm

first: Christian

last: Oertlin

address: Tomtebodavägen 23A

country: Sweden

institute: Karolinska Institutet

summary: The mechanisms that govern organelle remodeling remain poorly defined. Lysosomes degrade cargo from various routes including endocytosis, phagocytosis and autophagy. For phagocytes, lysosomes are a kingpin organelle since they are essential to kill pathogens and process and present antigens. During phagocyte activation, lysosomes undergo a striking reorganization, changing from dozens of globular structures to a tubular network, in a process that requires the phosphatidylinositol-3-kinase-AKT-mTOR signalling pathway. Here, we show that lysosomes undergo a remarkable expansion in volume and holding capacity during phagocyte activation within 2 h of LPS stimulation. Lysosome expansion was paralleled by an increase in lysosomal protein levels, but this was unexpectedly independent of TFEB and TFE3 transcription factors, known to scale up lysosome biogenesis. Instead, we demonstrate a hitherto unappreciated mechanism of acute organelle expansion via mTORC1-dependent increase in translation of mRNAs encoding key lysosomal proteins. Importantly, mTORC1-dependent increase in translation activity was necessary for efficient and rapid antigen presentation by dendritic cells. Collectively, we identified a previously unknown and functionally relevant mechanism for lysosome expansion that relies on mTORC1-dependent enhanced translation of mRNAs to boost protein synthesis and lysosome biogenesis in response to an infection signal.

overall_design: Polysome profiling of RAW cells treated with 2h or 6h LPS, LPS in the presence of Torin1, Torin1 or DMSO.

first: Victoria

last: Hipolito

first: Jacqueline

last: Diaz

first: Kristofferson

middle: V

last: Tandoc

first: Johannes

last: Ristau

first: Neha

last: Chauhan

first: Amra

last: Saric

first: Shannon

last: Mclaughlan

first: Ola

last: Larsson

first: Ivan

last: Topisirovic

first: Roberto

last: Botelho


title: Core components of the nuclear pore bind distinct states of chromatin and contribute to Polycomb repression II

city: Philadelphia

first: Yemin

last: Lan

state: PA

address: 3400 Civic Center Blvd

institute: University of Pennsylvania

summary: Interactions between the genome and the nuclear pore complex (NPC) have been implicated in multiple gene regulatory processes, but the underlying logic of these interactions remains poorly defined. Here, we report high-resolution chromatin binding maps of two core components of the NPC, Nup107 and Nup93, which reveal differential binding of these NPC subunits to active genes and Polycomb-covered silent regions, respectively. Comparison to Lamin-associated domains (LADs) revealed that NPC binding sites are often found within LADs, demonstrating a linear binding of the genome along the nuclear envelope. Significantly, we identified a functional role of Nup93 in silencing of Polycomb target genes and in spatial folding of Polycomb domains. Our findings lend to a model where nuclear pores bind different types of chromatin via interactions with specific core sub-complexes of the NPC, and the Nup93 sub-complex functions as a stabilizing scaffold for Polycomb domains.

overall_design: Characterization of lamin by ChIP-Seq in drosophila embryonic S2 cells and KC cells.

first: Alejandro

last: Gozalo

first: Maya

last: Capelson


title: Core components of the nuclear pore bind distinct states of chromatin and contribute to Polycomb repression


title: long read RNA-seq from heart left ventricle (ENCSR194YUY)

first: ENCODE

last: DCC

summary:
ENTEX105 Heart - Left Ventricle 3-1

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


title: RNA-Seq from CA1 pyramidal neurons

city: Cambridge

first: Kirsty

last: Sawicka

summary: RNA-Seq from CA1 pyramidal neurons purified by FACS from 4-week-old mice.

overall_design: CA1 pyramidal neurons were labeled with TdTomato by crossing Camk2a-Cre (B6.Cg-Tg(Camk2a-cre)T29-1Stl/J) and Ai14 (B6.Cg-Gt(ROSA)26Sortm14(CAG-tdTomato)Hze/J mice). The Ai14 reporter line expresses robust tdTomato fluorescence following Cre-mediated recombination. Hippocampi were dissociated from postnatal day 28-32 male Camk2a-Cre +/-, Ai14 +/- mice and TdTomato positive cells isolated by FACS. 3 biological replicates were performed each with cells from 2-4 mice. RNA was extracted from the purified CA1 pyramidal neurons and subjected to RNA-Seq.

first: Jennifer

last: Darnell

first: Robert


title: The Fragile X protein, FMRP,  has a cell-type specific role in CA1 hippocampal neurons to regulate transcripts encoding autism-spectrum proteins and circadian memory


title: A chemical genetic method for monitoring genome-wide dynamics of O-GlcNAc turnover on chromatin-associated proteins.

city: Burnaby

first: David

last: Vocadlo

state: British Columbia

address: 8888 University Drive

department: Chemistry

country: Canada

institute: Simon Fraser University

summary: O-linked N-acetylglucosamine (O-GlcNAc) is a necessary protein modification installed onto hundreds of nucleocytoplasmic proteins by O-GlcNAc transferase (OGT). Recently, we developed an antibody-free metabolic feeding approach that enables unbiased mapping of O-GlcNAcylated proteins in a genome-wide manner, providing insight into the regulation of genes by O-GlcNAcylated proteins within Drosophila. Here we apply this O-GlcNAc chemical mapping strategy to a time course (TC) feeding experiment within Drosophila larvae, generated the first ever TC ChIP-seq experiment performed on both a protein modification and within a living organism. TC metabolic labeling experiments were performed in wild-type and O-GlcNAc hydrolase (OGA) deficient Drosophila. Analysis of the resulting sequencing data revealed that a loss of OGA causes a global increase in the retention of O-GlcNAc modification on proteins bound to the genome, suggesting most nuclear proteins are sensitive to effects of O-GlcNAc cycling. Interestingly, some loci are more sensitive to the impacts of a loss of OGA compared to others. This study will present an improved understanding of the regulation of gene expression by O-GlcNAc while providing the broader community with experimental methods for time-resolved analysis of genome-wide binding by proteins.

overall_design: Time course O-GlcNAc-seq and OGA ChIP-seq in wild type (WT) and OGA knockout (OGA-null) Drosophila larvae.

first: Ta-Wei

last: Liu

first: Mike

last: Myschyshyn

first: Don

last: Sinclair


title: Ribosome profiling in transgenic and HEK293T cells treated with NAEK

city: Beijing

first: Yiming

last: Wu

state: Beijing

address: No 38 Xueyuan Road

department: Chemical Bilogy

institute: Peking University Health Science Center

summary: To investigate whether natural TAG was decoded by stably transfected Mb pyltRNA in transgenic cells, their cell lysate was subjected to ribosome profiling, examining the physical locations of ribosomes. HEK293T cells were taken as control.

overall_design: Examine the physical locations of ribosomes in both transgenic and HEK293T cells

first: Y


title: long read RNA-seq from HepG2 (ENCSR834DQL)

summary:
Homo sapiens HepG2 immortalized cell line

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


title: Core components of the nuclear pore bind distinct states of chromatin and contribute to Polycomb repression I

overall_design: Characterization of Elys, Nup93, and Nup107 by ChIP-Seq in Drosophila embryonic S2 cells.


title: TRAP from CA1 pyramidal neurons and cerebellar granule cells in Fmr1 KO and wildtype mice

summary: TRAP (translating ribosome affinity purification) from CA1 pyramidal neurons and cerebellar granule cells in wildtype and Fmr1 KO littermate pairs. These data show a global downregulation of FMRP targets in Fmr1 KO mice in these cell types.

overall_design: TRAP (translating ribosome affinity purification) from CA1 pyramidal neurons and cerebellar granule cells. For each cell type, 3 biological replicates of total mRNA (input) from WT and Fmr1 KO littermate pairs and ribosome-bound transcripts (TRAP) from the same animals were sequencing.


title: long read RNA-seq from mucosa of descending colon (ENCSR803XXZ)

summary:
ENC4_78 W80 mucosa of descending colon

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


title: long read RNA-seq from GM12878 (ENCSR706ANY)

summary:
Homo sapiens GM12878 immortalized cell line

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


title: A genome-wide view of the de-differentiation of central nervous system endothelial cells in culture

city: Baltimore

first: Mark

middle: F

last: Sabbagh

state: MD

address: 725 North Wolfe Street

department: Molecular Biology and Genetics

institute: Johns Hopkins University School of Medicine

summary: Vascular endothelial cells (ECs) derived from the central nervous system (CNS) variably lose their unique barrier properties during in vitro culture, hindering the development of robust assays for BBB function, including drug permeability and extrusion assays.  In previous work (Sabbagh et al., 2018) we characterized transcriptional and accessible chromatin landscapes of acutely isolated CNS ECs.  In this report, we compare transcriptional and accessible chromatin landscapes of acutely isolated CNS ECs versus CNS ECs in short-term in vitro culture.  We observe that standard culture conditions are associated with a rapid and selective loss of BBB transcripts and chromatin features, as well as a greatly reduced level of beta-catenin signaling.  Interestingly, forced expression of a stabilized derivative of beta-catenin, which in vivo leads to a partial conversion of non-BBB CNS ECs to a BBB-like state, has little or no effect on gene expression or chromatin accessibility in vitro.

overall_design: RNA-seq and ATAC-seq of primary brain EC culture

first: Jeremy

last: Nathans


title: Next generation sequencing allows identification of quantitave differential gene expression between four clinical strains of methicilin resistant Staphylococcus aureus

city: Brisbane

first: Imalka

middle: U P K

last: Tennakoon

state: QLD

address: 60,Musk Avenue,Kelvingrove

department: Institute of Health and Biomedical Innovation

country: Australia

institute: Queensland University of Technology

summary: Staphylococcus aureus can cause a broad spectrum of diseases that vary widely in clinical presentation and disease severity[121]. Methicillin-Resistant S. aureus (MRSA) strains first described in the 1960’s[122] were hospital acquired (HA MRSA), however in the 1990’s, community-associated MRSA strains (CA MRSA) were identified and are considered to be more virulent[16]. Therapeutics and management of MRSA focuses on novel antibacterials and vaccines targeting virulence factors. To date no clinical trials for vaccines have succeeded[123] due to the poor understanding of the pathogenic mechanisms exhibited by S.aureus.We investigated the differential gene expression of four clinical MRSA strains in vitro, belonging to HA and CA MRSA, at the stationary and exponential growth phases, using RNA-seq on the Ion torrent next generation sequencing platform. This study reveals the high diversity of virulence trait expression among MRSA strains within strains as well as between different growth phases, and also suggests potential factors other than PVL that contributes to enhanced virulence in CA MRSA

overall_design: mRNA profiles were generated for four clinical strains of methicilin resistant staphylococcus aureus at their stationary growth phase, in duplicates and in exponential phase in triplicates, using RNA-seq in ion torrent platform. Data analysis performed with CLCBio Genomic Workbench, with two reference sequences, USA300_FPR3757 (NCBI RefSeq accession numbers NC_007793.1, NC_007790.1, NC_007791.1, NC_007792.1) and N315 strains (NCBI RefSeq accession numbers NC_002745.2, NC_003140.1)

middle: U

first: Flavia

last: Hyugens


title: icSHAPE from HepG2 (ENCSR992XHC)

summary:
icSHAPE (NAi-N3) on HepG2 immortalized cell line

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


title: long read RNA-seq from left lung (ENCSR746ITG)

summary:
ENC4_79 W62 left lung

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


title: Histone ChIP-seq from Peyer's patch (ENCSR998QKF)

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


title: icSHAPE from K562 (ENCSR976RFC)

summary:
icSHAPE (NAI-N3) on K562 immortalized cell line

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


title: Histone ChIP-seq from tibial nerve (ENCSR992XOO)


title: long read RNA-seq from ovary (ENCSR587WPR)

summary:
ENC4_35 W61 ovary

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


title: Histone ChIP-seq from esophagus squamous epithelium (ENCSR960UYN)


title: long read RNA-seq from right lobe of liver (ENCSR293MOX)

summary:
W62 right lobe of liver

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


title: long read RNA-seq from left lung (ENCSR426KOP)

summary:
ENC4_81 W76 left lung

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


title: Histone ChIP-seq from testis (ENCSR956VQB)


title: Control ChIP-seq from stomach (ENCSR948DNK)


title: Histone ChIP-seq from testis (ENCSR954IGQ)


title: Histone ChIP-seq from upper lobe of left lung (ENCSR948TOS)


title: Histone ChIP-seq from thyroid gland (ENCSR942UIL)


title: Histone ChIP-seq from Peyer's patch (ENCSR927PLE)


title: Histone ChIP-seq from Peyer's patch (ENCSR912XAL)


title: Histone ChIP-seq from tibial nerve (ENCSR925FSB)


title: Histone ChIP-seq from sigmoid colon (ENCSR937EVN)


title: icSHAPE from GM12878 (ENCSR836VQU)

summary:
icSHAPE (NAi-N3) on GM12878 immortalized cell line

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


title: Control ChIP-seq from stomach (ENCSR962EJE)


title: Histone ChIP-seq from Peyer's patch (ENCSR874HIG)


title: icSHAPE from K562 (ENCSR803XFA)

summary:
icSHAPE control (DMSO) on K562 immortalized cell line

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


title: Control ChIP-seq from spleen (ENCSR803JPO)


title: TF ChIP-seq from sigmoid colon (ENCSR857RJQ)


title: Histone ChIP-seq from sigmoid colon (ENCSR860GPM)


title: TF ChIP-seq from gastroesophageal sphincter (ENCSR805YLE)


title: Control ChIP-seq from esophagus muscularis mucosa (ENCSR777AJC)


title: Histone ChIP-seq from ovary (ENCSR828CCQ)


title: TF ChIP-seq from tibial nerve (ENCSR793YAD)


title: Histone ChIP-seq from transverse colon (ENCSR792VLP)


title: Histone ChIP-seq from sigmoid colon (ENCSR792EDG)


title: Histone ChIP-seq from transverse colon (ENCSR813ZEY)


title: Histone ChIP-seq from tibial nerve (ENCSR778QHG)


title: Histone ChIP-seq from stomach (ENCSR787TQW)


title: Control ChIP-seq from Peyer's patch (ENCSR773UBR)


title: Histone ChIP-seq from spleen (ENCSR787YHR)


title: Control ChIP-seq from upper lobe of left lung (ENCSR774MLK)


title: Histone ChIP-seq from sigmoid colon (ENCSR775LGE)


title: Histone ChIP-seq from sigmoid colon (ENCSR774NRD)


title: Histone ChIP-seq from esophagus squamous epithelium (ENCSR773PIU)


title: TF ChIP-seq from esophagus squamous epithelium (ENCSR756URL)


title: Histone ChIP-seq from Peyer's patch (ENCSR758KRK)


title: TF ChIP-seq from testis (ENCSR753RME)


title: Histone ChIP-seq from stomach (ENCSR751BHO)


title: Control ChIP-seq from gastroesophageal sphincter (ENCSR728EIP)


title: Control ChIP-seq from tibial artery (ENCSR714GXC)


title: Histone ChIP-seq from tibial nerve (ENCSR726EEM)


title: Histone ChIP-seq from Peyer's patch (ENCSR735VKO)


title: Control ChIP-seq from spleen (ENCSR711URW)


title: Histone ChIP-seq from esophagus muscularis mucosa (ENCSR705BTW)


title: Histone ChIP-seq from Peyer's patch (ENCSR718LSM)


title: Histone ChIP-seq from gastrocnemius medialis (ENCSR716TNU)


title: Histone ChIP-seq from transverse colon (ENCSR749ABB)


title: Histone ChIP-seq from upper lobe of left lung (ENCSR701FGA)


title: Control ChIP-seq from body of pancreas (ENCSR700CAX)


title: Control ChIP-seq from transverse colon (ENCSR651ISB)


title: Histone ChIP-seq from spleen (ENCSR709APF)


title: TF ChIP-seq from body of pancreas (ENCSR687APM)


title: Histone ChIP-seq from tibial nerve (ENCSR677MOE)


title: Control ChIP-seq from gastroesophageal sphincter (ENCSR642QDW)


title: Histone ChIP-seq from esophagus squamous epithelium (ENCSR658EVN)


title: Histone ChIP-seq from Peyer's patch (ENCSR684EPX)


title: TF ChIP-seq from uterus (ENCSR684PGO)


title: Histone ChIP-seq from sigmoid colon (ENCSR641SDI)


title: Histone ChIP-seq from transverse colon (ENCSR643KID)


title: Histone ChIP-seq from vagina (ENCSR647HAQ)


title: Histone ChIP-seq from tibial nerve (ENCSR635DAS)


title: Histone ChIP-seq from adrenal gland (ENCSR613FYP)


title: Histone ChIP-seq from spleen (ENCSR635IRN)


title: Histone ChIP-seq from transverse colon (ENCSR640XRV)


title: Control ChIP-seq from breast epithelium (ENCSR620GYX)


title: Control ChIP-seq from vagina (ENCSR607UWA)


title: Histone ChIP-seq from gastrocnemius medialis (ENCSR601VHO)


title: Histone ChIP-seq from vagina (ENCSR612TQH)


title: Histone ChIP-seq from testis (ENCSR611DJQ)


title: TF ChIP-seq from transverse colon (ENCSR608WPS)


title: TF ChIP-seq from spleen (ENCSR601FEB)


title: TF ChIP-seq from gastrocnemius medialis (ENCSR594NSU)


title: Histone ChIP-seq from testis (ENCSR619EZG)


title: TF ChIP-seq from body of pancreas (ENCSR585KBH)


title: Histone ChIP-seq from thyroid gland (ENCSR586DVD)


title: TF ChIP-seq from spleen (ENCSR595BPR)


title: Histone ChIP-seq from tibial nerve (ENCSR590NNJ)


title: Histone ChIP-seq from adrenal gland (ENCSR581CXP)


title: Histone ChIP-seq from transverse colon (ENCSR557OWY)


title: TF ChIP-seq from Peyer's patch (ENCSR568IVD)


title: Histone ChIP-seq from thyroid gland (ENCSR558AXI)


title: Control ChIP-seq from sigmoid colon (ENCSR524NCH)


title: Histone ChIP-seq from thyroid gland (ENCSR497OVD)


title: Control ChIP-seq from transverse colon (ENCSR479HSY)


title: Histone ChIP-seq from transverse colon (ENCSR488YXS)


title: TF ChIP-seq from thyroid gland (ENCSR505ZGX)


title: Histone ChIP-seq from stomach (ENCSR492BHN)


title: Control ChIP-seq from esophagus squamous epithelium (ENCSR514EZP)


title: Control ChIP-seq from testis (ENCSR385ODY)


title: Histone ChIP-seq from stomach (ENCSR475TRZ)


title: TF ChIP-seq from Peyer's patch (ENCSR542SCB)


title: Histone ChIP-seq from heart left ventricle (ENCSR449FRQ)


title: Histone ChIP-seq from transverse colon (ENCSR516QFO)


title: Control ChIP-seq from transverse colon (ENCSR384KIB)


title: Histone ChIP-seq from uterus (ENCSR448IJB)


title: Histone ChIP-seq from thyroid gland (ENCSR500YBS)


title: Histone ChIP-seq from body of pancreas (ENCSR432DPY)


title: Histone ChIP-seq from transverse colon (ENCSR413CHO)


title: TF ChIP-seq from esophagus muscularis mucosa (ENCSR443WKD)


title: Histone ChIP-seq from vagina (ENCSR495RJG)


title: Histone ChIP-seq from coronary artery (ENCSR355GNZ)


title: Histone ChIP-seq from upper lobe of left lung (ENCSR348FGT)


title: Histone ChIP-seq from uterus (ENCSR354ZUG)


title: TF ChIP-seq from upper lobe of left lung (ENCSR463XCZ)


title: Histone ChIP-seq from testis (ENCSR376JOC)


title: Histone ChIP-seq from transverse colon (ENCSR500QVK)


title: Histone ChIP-seq from adrenal gland (ENCSR379BVL)


title: Control ChIP-seq from thyroid gland (ENCSR347VUG)


title: Histone ChIP-seq from tibial nerve (ENCSR338PGG)


title: Histone ChIP-seq from sigmoid colon (ENCSR343NWC)


title: Histone ChIP-seq from stomach (ENCSR330MAM)


title: Control ChIP-seq from sigmoid colon (ENCSR316ZPQ)


title: TF ChIP-seq from thyroid gland (ENCSR331OGX)


title: Histone ChIP-seq from tibial artery (ENCSR303BUB)


title: icSHAPE from HepG2 (ENCSR286LXS)

summary:
icSHAPE control (DMSO) on HepG2 immortalized cell line

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


title: Histone ChIP-seq from sigmoid colon (ENCSR333HMT)


title: Histone ChIP-seq from transverse colon (ENCSR315EZG)


title: Histone ChIP-seq from vagina (ENCSR278TQE)


title: Histone ChIP-seq from sigmoid colon (ENCSR277SUG)


title: TF ChIP-seq from gastroesophageal sphincter (ENCSR298ZPF)


title: TF ChIP-seq from esophagus squamous epithelium (ENCSR266UTR)


title: Histone ChIP-seq from right atrium auricular region (ENCSR250AAV)


title: Histone ChIP-seq from uterus (ENCSR244ZKA)


title: Histone ChIP-seq from upper lobe of left lung (ENCSR263OXW)


title: Histone ChIP-seq from spleen (ENCSR272CIV)


title: Control ChIP-seq from adrenal gland (ENCSR234FYG)


title: Histone ChIP-seq from breast epithelium (ENCSR224STY)


title: Control ChIP-seq from testis (ENCSR215WNN)


title: TF ChIP-seq from transverse colon (ENCSR236YGF)


title: Histone ChIP-seq from gastroesophageal sphincter (ENCSR195JWZ)


title: Histone ChIP-seq from stomach (ENCSR204OJS)


title: Histone ChIP-seq from gastroesophageal sphincter (ENCSR219QSM)


title: Histone ChIP-seq from esophagus squamous epithelium (ENCSR204TAU)


title: Histone ChIP-seq from uterus (ENCSR189JIH)


title: TF ChIP-seq from stomach (ENCSR185CCV)


title: Control ChIP-seq from coronary artery (ENCSR163XFK)


title: Histone ChIP-seq from esophagus muscularis mucosa (ENCSR200AFX)


title: TF ChIP-seq from spleen (ENCSR225YGX)


title: Histone ChIP-seq from tibial nerve (ENCSR176ZMW)


title: Histone ChIP-seq from stomach (ENCSR158WBG)


title: Control ChIP-seq from tibial nerve (ENCSR152HLZ)


title: Histone ChIP-seq from sigmoid colon (ENCSR172LVU)


title: Control ChIP-seq from gastrocnemius medialis (ENCSR138WRC)


title: Control ChIP-seq from Peyer's patch (ENCSR118FQN)


title: Control ChIP-seq from prostate gland (ENCSR113QDZ)


title: Histone ChIP-seq from uterus (ENCSR111DTF)


title: Histone ChIP-seq from testis (ENCSR136ZQZ)


title: Histone ChIP-seq from ovary (ENCSR440UCR)


title: Histone ChIP-seq from sigmoid colon (ENCSR104CCB)


title: Histone ChIP-seq from esophagus squamous epithelium (ENCSR101KMF)


title: Histone ChIP-seq from tibial nerve (ENCSR091KXI)


title: Control ChIP-seq from tibial nerve (ENCSR059VTG)


title: Histone ChIP-seq from testis (ENCSR091MNT)


title: Histone ChIP-seq from adrenal gland (ENCSR086QZY)


title: Histone ChIP-seq from thyroid gland (ENCSR064LHU)


title: Histone ChIP-seq from vagina (ENCSR046OON)


title: Histone ChIP-seq from upper lobe of left lung (ENCSR050LBS)


title: Histone ChIP-seq from transverse colon (ENCSR083DXD)


title: Histone ChIP-seq from uterus (ENCSR035ONO)


title: Histone ChIP-seq from ovary (ENCSR029TTW)


title: TF ChIP-seq from stomach (ENCSR037GKL)


title: Histone ChIP-seq from transverse colon (ENCSR047JMV)


title: TF ChIP-seq from esophagus muscularis mucosa (ENCSR073TPC)


title: Histone ChIP-seq from stomach (ENCSR009RJD)


title: Histone ChIP-seq from adrenal gland (ENCSR006TUH)


title: Genome-wide transcriptome profiling of human duodenal organoids, Duodenum Intestine-Chip and adult duodenal tissue using RNA-seq.

city: Boston

first: Magdalena

last: Kasendra

address: 27 Drydock avenue

institute: Emulate Inc.

summary: The goal of this study was to compare global RNA expression data obtained from: i) duodenal organoids cultured in conventional plastic-adherent Matrigel drop overlaid with growth medium; ii) Duodenum Intestine-Chips derived from organoids in the presence of constant flow and stretch; iii) human adult duodenum tissue and to verify whether Duodenum Intestine-Chip faithfully recapitulates human adult duodenum tissue and to better understand how much it differs from the organoids from which it’s derived.

overall_design: Global RNA expression profiles of duodenal organoids (Organoids; n=3) and Duodenum Intestine-Chips derived from organoids (Duodenum Intestine-Chip; n=3) were generated by deep sequencing using Illumina HiSeq.

first: Raymond

last: Luc

first: Dimitris

last: Manatakis


title: Histone ChIP-seq from stomach (ENCSR007GED)

first: ENCODE


title: Transcriptome Dynamics of Long Non-Coding RNAs and Transcription Factors Demarcate Human Neonatal, Adult, and MSC-derived Engineered Cartilage

city: Cleveland

first: Daniel

middle: Joseph

last: Vail

state: OH

address: BRB 647C 2109 Adelbert Road

department: Genetics

institute: Case Western Reserve University

summary: Characterization of the transcriptional differences between human bone marrow MSC-derived cartilage, human neonatal, and adult cartilage

overall_design: RNA-seq and analysis from three samples each of human neonatal articular cartilage (AC), human adult AC, and MSC-derived cartilage from 3D pellet cultures (6 time points)

first: Ahmad

last: Khalil

first: Arnold

middle: I

last: Caplan

first: Rodrigo

last: Somoza


title: Gene expression (RNA-Seq) in pediatric high-grade glioma cell lines treated with selinexor and vehicle

city: Aurora

first: John

last: DeSisto

state: CO

department: Pediatrics

institute: University of Colorado

summary: Cultured pediatric high-grade glioma cell lines (SU-DIPG-IV, HSJD-DIPG-007, HSJD-GBM-001,BT 245 (RRID:CVCL_IP13)) were treated with selinexor (Karyopharm Therapeutics) at 5xIC50 for 16 hours or vehicle (0.1% DMSO) followed by bulk RNA-Seq

overall_design: Examination of the effects on gene expression of selinexor treatment of cultured pediatric brain tumor cell lines

first: Adam

last: Green


title: The transcriptional repressor SNAI2 impairs neuroblastoma differentiation and inhibits response to retinoic acid therapy

city: Utrecht

first: Kirsten

last: Vrenken

address: Heidelberglaan 25

country: Netherlands

institute: Princess Máxima Center for Pediatric Oncology

summary: Analyses of the effect of CRISPR/CAS9 mediated knock out of the EMT-transcription factor SNAI2 on the mRNA expression profile of human neuroblastoma SH-SY5Y cells to identify genes that are differentially expressed upon loss of SNAI2. Results provide insight into genes that are repressed by SNAI2 in neuroblastoma cells under normal culture conditions, where loss of SNAI2 enhances the expression of genes involved in biological processes such as neuron development and neuron differentiation.

overall_design: RNAseq of mRNA of pools of SH-SY5Y cells expressing CRISPR/CAS9 + control or SNAI2 targeting gRNA#1 or SNAI2 targeting gRNA#2 in triplicate

middle: S

first: Britt

last: Vervoort

first: Dorette

last: van Ingen Schenau

first: Yvonne

last: Derks

first: Liesbeth

last: van Emst

first: Pavlo

last: Gritsenko

first: Jeroen

middle: M

last: Middelbeek

first: Frank

middle: N

last: van Leeuwen


title: Histone ChIP-seq from tibial artery (ENCSR000SNM)

last: DCC


title: Enhanced interferon response genes in bronchial epithelial cells after in vivo rhinovirus challenge of asthma patients

city: Amsterdam

first: Richard

last: Volckmann

state: Noord-Holland

address: van der Boechorststraat 6a

department: Laboratory of Experimental Oncology and Radiobiology

institute: msterdam UMC and University of Amsterdam

summary: In asthma there are exaggerated rather than impaired innate and adaptive interferon responses in vivo after RV16 infection, which strongly correlate with inflammation and loss of asthma control.

overall_design: Mild asthma patients (n=15) and healthy controls (n=4) were challenged with RV16. PBECs were obtained by bronchial brushes before and 6 days after RV16. The transcriptome was determined by RNAseq and also correlated with clinical outcomes.

first: Abilash

last: Ravi

first: René

last: Lutter

first: Jan

last: Koster


title: The structural basis for cohesin/CTCF anchored loops

first: Angela

last: Sedeno Cacciatore

address: Plesmanlaan 121

department: Gene regulation

institute: Netherlands Cancer Institute

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


title: MMP14-wild type (WT) vs. MMP14-deficient (KO) liver mesenchymal cells derived from embryonic day (E) 16.5 mouse livers

status: Public on Jan 05 2020

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: 10-1 tebiro 6-chome

institute: Toray Industries,Inc.

summary: Transcriptional profiling of systemic MMP14-KO and littermate WT mesenchymal cells in E16.5 livers. CD45-Ter119-p75NTR (NFGR)-positive liver mesenchymal cells were purified using fluorescence-activated cell sorter (FACS).

overall_design: Liver samples were collected from E16.5 MMP14-WT and -KO mice with a C57B/6J background and dissociated by collagenase treatment. CD45-Ter119-p75NTR (nerve growth factor receptor, NGFR)+ liver mesenchymal cells were purified by FACS. Total RNA samples were extracted from the sorted cells derived from 21 MMP14-WT fetuses or 18 MMP14-KO fetuses, obtained from several independent experiments.

first: Ayako

last: Sato

first: Sei

last: Kakinuma


title: Transcriptional regulation in denervated murine GA muscle

first: Doaa

middle: AS

last: Megahed

address: 200 Longwood Avenue, Harvard Medical schooL, WaB 536D

department: Systems Biology

institute: Harvard Medical School

summary: Samples of denervated GA muscle were compared to contralateral controls to determine transcriptional changes associated with skeletal muscle denervation.

overall_design: Denervation was performed as described (Moresi et al., 2010). In brief, adult mice were anesthetized with isoflurane. The sciatic nerve of the left leg was exposed and a 2 mm piece was removed. The right leg remained innervated and was used as a control. Mice were sacrificed and the gastrocnemius muscles was then prepared and snap frozen in liquid nitrogen 14 days after denervation.

first: Douaa

last: Mugahid


title: Cholangiocytic cysts (CCs) treated with or without vasoactive intestinal peptide (VIP)

summary: Transcriptional profiling of CCs derived from embryonic day (E) 13.5 wild type (WT) mouse hepatoblasts treated with or without VIP.

overall_design: Dlk-positive hepatoblasts derived from E13.5 livers of WT mice with a C57B/6J background were cultured and induced into CCs in a three dimensional (3D)-culture system, preceeded by 7-day two dimensional (2D) pre-culture. VIP or vehicle was added in the culture media during the 3D culture and the cells were harvested on the 12th day of 3D culture. The samples were a mixture of  triplicated wells for each group.


title: The chromatin accessibility and transcriptome landscapes of Monomorium pharaonis brain

status: Public on Jan 04 2020

city: shenzhen

first: CNSA

last: CNGB

address: BGI

institute: BGI

summary: The emergence of eusociality is one of the major transitions in evolution. There have been several investigations into the reasons for shaping caste differentiation and social behavior of eusocial insects, such as ants and honeybees. However, the molecular mechanisms governing the sociality of these insects remain obscure. In this study, we profiled the transcriptome and chromatin accessibility of brain tissues in all castes: queens, males, gynes and workers in Monomorium pharaonis which is a typical caste-dependent eusocial insect. We created a comprehensive dataset including 16 RNA-seq and 16 ATAC-seq profiles from 4 biological replicates. We also demonstrated strong reproducibility of the datasets and identified specific genes and open chromatin regions in the genome that may be associated with caste differentiation. Overall, our data will be a valuable resource for further study of the mechanisms underlying eusocial insect behavior, particularly the role of the brain in the control of eusociality.

overall_design: We have profiled caste-dependent transcriptomes in the brain of Monomorium pharaonis, which is a typical eusocial insect, and the colony consists of four adult castes: queens, males, gynes and workers. We analyzed the gene expression by producing RNA-seq and ATAC-seq profiles of four castes brain. 16 samples from 4 biological replicates were processed and sequenced.

first: Mingyue

last: Wang

first: Yang

last: Liu


title: Dataset of banana transcriptome in response to endophyte bacteria inoculation prior to Fusarium oxysporum f.sp. cubense tropical race 4 (Foc TR4) infection

city: Bandung

first: Fenny

last: Dwivany

address: Jl. Ganesha No. 10

country: Indonesia

institute: Institut Teknologi Bandung

summary: We report the first data of RNA sequencing of banana Musa acuminata cv. Pisang ambon kuning (AAA group) inoculated by two different endophyte bacteria named Stenothropomonas nitritireducens (BR-49) and Kocuria rhizophila (SL-08), respectively, prior to Fusarium oxysprorum f.sp. cubense tropical race 4 (Foc TR4).

overall_design: mRNA isolated from root of Foc TR4 infected banana plantlet grown in split root assay. Endophyte bacteria are inoculated into endophyte compartment prior to Foc TR4 infection in Fusarium compartment of split root assay. We have one treatment (endophyte inoculation and Foc TR4 infection) and three different control groups (positive control: endophyte inoculation, no Foc TR4 infection; negative control: no endophyte inoculation, Foc TR4 infection; and neutral control: no endophyte inoculation and no Foc TR4 infection) for each endophyte bacteria species (BR-49 and SL-08). We also have 4 time points: 72 hours after endophyte inoculation (72E) and 6 (6EF), 24 (24EF), and 72 hours (72EF) after Foc TR4 infection of endophyte bacteria preinoculated banana plantlet. Composite of mRNA samples from three biological replicates ere examined.

first: L

last: Karmawan

first: F

first: R

last: Esyanti

first: I

last: Aryantha


title: Gradual evolution of cell cycle regulation by cyclin-dependant kinases during the transition to animal multicellularity

city: Barcelona

first: Alberto

last: Perez-Posada

address: Passeig Marítim de la Barceloneta, 37-49

country: Spain

institute: Institut de Biologia Evolutiva

summary: We assessed temporal gene expression in synchronous cultures of Capsaspora owczarzaki in order to better understand cell cycle regulation in another opisthokont more closely related to animals retaining the ancestral toolkit of cell cycle regulators. Our data suggests that cell cycle regulation in the ancestor of Capsaspora and animals involved one single CDK binding to multiple cyclins of subfamilies in the same temporal order as in animals, and that expansion of CDKs occured later in the lineage that gave rise to animals.

overall_design: RNASeq from Capsaspora synchronous cells upon release from hydroxyurea; two independent replicates of sixteen time points. This comprises a window of time where cells progress through DNA replication and mitosis. One additional, non-synchronous sample.

first: Iñaki

last: Ruiz-Trillo

first: Andrej

last: Ondracka


title: Gene expression in PBMCs of patients with hepatocarcinoma: effect of ablative treatment - genes

city: Bari

first: Vincenzo

middle: Ostilio

last: Palmieri

address: P.za Giulio Cesare

department: Biomedical Sciences and Human Oncology

institute: University of Bari

summary: Gene expression profiles of PBMCs in patients with hepatocarcinoma after ablative treatment. Results provide the information of changes in PBMPs transcriptome following ablative treatment of hepatocarcinoma.

overall_design:
RNA obtained from PBMCs of the same patients before and after ablative treatment (paired samples). Comparisons: T0 vs. T1 (paired samples)
PR= partial response to treatment
CR= complete response to treatment

first: Andria

last: D'Orazio

first: Simona

last: D'Amore

first: Marica

last: Cariello


title: Global gene expression profile in epithelium of control and haze predisposed subjects

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

address: 259, Apoorva 4th cross,80 feet Road,RMV 2ND STAGE

country: India

institute: Genotypic Technology

summary: The gene expression profile of various cell signaling pathway associated genes were compared between the controls and haze predisposed groups

overall_design: Corneal epithelium were collected from control and haze predisposed subjects after the surgical procedures of photorefractive keratectomy (PRK)

first: Nimisha

last: Rajivkumar

first: Rohit

last: Shetty

first: Arkasubhra

last: Ghosh


title: Genome-wide DNA methylation in cultured human Schelmm's Canal endothelial cells and trabecular meshwork cells with or without glaucoma

status: Public on Jan 03 2020

city: Augusta

first: Jingwen

last: Cai

state: GA

address: 1460 Laney Walker Blvd

department: Cellular biology and Anatomy

institute: Augusta University

type: Methylation profiling by genome tiling array

summary: Genome-wide DNA methylation profiling in cultured human Schelmm's Canal endothelial cells (SC) and trabecular meshwork (TM) cells derived from post-mortem eyes with or without glaucoma. Our study aimed to identify glaucoma-associated genes that were affected by DNA methylation.

overall_design: DNA were extracted from cultured human SC (n=9, 2 glaucoma, 7 non-glaucoma) and TM (n=5, 1 glaucoma, 4 non-glaucoma) cells using Allprep DNA Mini spin column kit. DNA samples were hybridized to the Illumina Infinium HumanMethylation450 Beadchips. Probe and intensity data were normalized and analyzed by RnBeads package in the R program.FDb.InfiniumMethylaion.hg19 package was used to annotate probes. The selected genes were validated using Zymo qMethyl kit.HumanMethylation450 Beadchips.

first: Yutao


title: The single cell RNA seq of pulmonary alveolar type II (AT2) cells

first: huanwei

last: huang

address: 7 Science Park Rd., ZGC life science park

institute: NIBS

summary: The pulmonary alveolar epithelium mainly composed of two types of epithelial cells: alveolar type I (AT1) and type II (AT2) cells. AT2 cells are the alveolar stem cells, and can differentiate into AT1 cells post-pneumonectomy (PNX). Here, we found that, compared with control mice (Sftpc-CreER; Cdc42flox/+; Rosa26-mTmG) at post-PNX day 21, Cdc42 AT2 null mice (Sftpc-CreER; Cdc42flox/-; Rosa26-mTmG) at post-PNX day 21 undergone fibrotic change. By using 10X genomics “Chromium Single Cell” technology, we performed single-cell RNA-seq analyses of AT2 cells of sham treated control mice (C0), AT2 cells of control mice at post PNX day 21 (C21) , AT2 cells of sham treated Cdc42 AT2 null mice (N0), and AT2 cells of Cdc42 AT2 null mice at post PNX day 21 (N21). The study identified a specific gene signature in AT2 cells of Cdc42 AT2 null mice at post PNX day 21 which is related to the fibrosis phenotype of Cdc42 AT2 null mice.

overall_design: We performed 10X genomics single-cell RNA-seq of AT2 cells of sham treated control mice (C0), AT2 cells of control mice at post PNX day 21 (C21) , AT2 cells of sham treated Cdc42 AT2 null mice ( N0) and AT2 cells of Cdc42 AT2 null mice at post PNX day 21 (N21).

first: Huijuan

last: Wu

last: Tang

first: Huanwei

last: Huang


title: Synapse alterations precede neuronal damage and storage pathology in a human cerebral organoid  model of CLN3-Juvenile Neuronal Ceroid Lipofuscinosis

city: Belvaux

first: Jens

middle: Christian

last: Schwamborn

state: Luxembourg

address: Avenue du Swing, 6

country: Luxembourg

institute: Luxembourg Center for Systems Biomedicine (University of Luxembourg)

summary: We developed an invitro model for Juvenile Neuronal Ceroid Lipofuscinosis (JNCL) using isogenic CLN3 mutated human iPS cell lines and performed transcriptomic profiling of brain organoids derived from these lines to identify transcriptomic changes in the early developing brain model.

overall_design: The study consists of mRNA-Seq (6 Control and 6 CLN3 mutant samples) performed in organoids differentiated for 55 days in vitro.

first: Gemma

last: Gomez-Giro

first: Jonathan

last: Arias-Fuenzalida

first: Javier

last: Jarazo

first: Dagmar

last: Zeuschner

first: Muhammad

last: Ali

first: Nina

last: Possemis

first: Silvia

last: Bolognin

first: Rashi

last: Halder

first: Christian

last: Jäger

first: Willemijn

middle: E

last: Kuper

first: Holm

last: Zaehres

first: Antonio

last: del Sol

first: Herman

last: van der Putten

first: Hans

last: Schöler


title: Genome-wide blood transcriptional profiling in human endotoxemia given human adipose-derived mesenchymal stem cells

city: Msida

first: Brendon

last: Scicluna

address: Msida campus

country: Malta

institute: University of Malta

summary: Mesenchymal stem cells (MSCs) can modulate various immune responses implicated in the pathogenesis of sepsis. Intravenous injection of lipopolysaccharide (LPS) into healthy subjects represents a model with relevance for the host response to sepsis.

overall_design: To determine the effect of MSCs on the early inflammatory response to intravenous LPS we conducted a randomized study in 32 healthy subjects with 4 treatment arms: placebo or adipocyte-derived MSCs intravenously at either  250.000, 1 million or 4 million cells/kg; all subjects received LPS intravenously  (2 ng/kg)  one hour after the end of MSC infusion. PAXgene blood RNA was isolated before and at 2, 4, 6 and 24 hours after LPS injection. Through the use of genome-wide transcriptional profiling we aimed to identify features of the systemic host transcriptional response to E.coli LPS endotoxemia that were altered due to mesenchymal stem cell administration. Moreover, biological pathway analysis was used to tease out the most relevant biological units.

middle: P

first: Tom

last: van der Poll


title: circRNA expression data from human colorectal cancer tissues and the correponding non-cancerous tissues

city: Nanjing

first: Keith

last: Ma

address: No.44 Baiziting Road

institute: Nanjing Medical University

summary:
To identifythe the functional roles of circRNAs in human colorectal cancer, we analysed the differenial expression of circRNAs in 5 colorectal cancer tissues and the corresponding non-cancerous tissues.
We used microarrays to detail the global programme of circRNA expression in human colorectal cancer tissues and correponding non-cancerous tissues.

overall_design: Total RNA from 5 pairs human colorectal cancer tissues and correponding non-cancerous tissues were isolated and digested with Rnase R. The enriched circular RNAs were amplified and transcribed into fluorescent cRNA. The labeled cRNAs were hybridized onto the Arraystar Human circRNA Array (8x15K, Arraystar)

first: Liu

last: Yang

first: Zhifei


title: Differentiation of PSC into lung organoids with endogenous functional alveolar macrophages and blood vessels

city: Gwangju

first: Seongmin

last: Cheon

state: N/A = Not Applicable

address: Yongbong street 77

department: School of Biological Sciences and Technology

country: South Korea

institute: CHONNAM NATIONAL UNIVERSITY.

summary:
The goals of this study are to determine tissue composition of human lung organoids (hLOs) when maintained long-term (day 230). hLOs consist of alveolar epithelial cells, mesenchymal/endothelial cells, smooth muscle cells and immune cells. After dissociated hLOs, a target capture of 1x 104 cells was performed using the 10X Genomics Chromium Single Cell RNA sequencing.

Briefly, single cell gel bead-in-emulsions(GEMs) are generated by passing cells with enzyme mix, partitioning oil, and barcoded gel beads by 10X Chromium chip. After GEM formation, the gel bead is dissolved and co-partitioned cell is lysed. Subsequently, reverse transcription (RT) occurs inside GEMs and barcoded full-length cDNA is generated. After RT, amplified cDNAs with barcode sequences (cell index and UMI) are pooled and single cell library is constructed using the Single Cell 3` Reagent Kit (v3 chemistry). The resulting library was sequenced on illumina HiseqX platform with 150bp paired end. Raw base calling files generated by illumine sequencing were demultiplexed based on the sample index read to generate FASTQ files using the 10X Genomics Cell Ranger (v3.0.2) pipeline. The raw reads were trimmed from the 3’ end to get the recommended number of cycle for read pairs (read1: 28bp; read2 : 91bp). The trimmed reads were mapped to the hg38 reference human genome with subsequent analysis, including filtering, barcode counting, and UMI counting. The resulting data were used to generate the multidimensional feature-barcode matrix using the CellRanger count with default parameters.

overall_design: Examination of various cell types of differentiated human ES cell-derived lung organoids

first: Eun-Mi

last: Kim


title: Regulation of the gamma delta T cell functional programming by the Slam/SAP signaling pathway

status: Public on Jan 02 2020

city: Burlington

first: Julie

last: Dragon

state: VT

address: 95 Carrigan Dr

department: MMG

institute: UNIVERSITY OF VERMONT & ST AGRIC COLLEGE

summary: Slam receptors regulate the development and function of several lymphocyte subsets. Nevertheless, their role on gamma delta T cells is largely unknown. We discovered the presence of distinct Vgamma4+ T cell subsets expressing either SLAMf1 or SLAMf6, but not both. We used microarray gene expression analysis of SLAMf1+ and SLAMf6+ single positive Vgamma4+ T cells to investigate the functional significance of those SLAM receptors in gamma delta T cell biology.

overall_design: Single cell suspensions of mouse lungs were prepared, stained with specific antibodies for SLAMf1, SLAMf6 and Vγ4 T cell receptors and flow sorted.

first: Oliver

last: Dienz

first: Victoria

middle: L

last: DeVault

first: Somen

last: Mistri

first: Linda

last: Mei

first: Shawn

last: Musial

first: Camarie

last: Spear

middle: A

first: Jonathan

last: Boyson


title: The human CCHC-type Zinc Finger nucleic acid binding protein binds G-rich elements in target mRNA coding sequences initiation promotes translation.

city: Wuerzburg

first: Sanjay

middle: Kumar

last: Gupta

state: Bavaria

address: Biozentrum, Am Hubland

department: Dept of Biochemistry

institute: University of Wuerzburg

overall_design: Refer to individual Series


title: The human CCHC-type Zinc Finger nucleic acid binding protein binds G-rich elements in target mRNA coding sequences initiation promotes translation (Ribosome profiling).

summary: CNBP is a eukaryote-conserved nucleic-acid binding protein required in mammals for embryonic development. It contains seven CCHC-type zinc-finger domains and was suggested to act as a nucleic acid chaperone, as well as a transcription factor. Here, we identify all CNBP isoforms as cytoplasmic messenger RNA (mRNA)-binding proteins. Using Photoactivatable Ribonucleoside Enhanced Cross-linking and Immunoprecipitation, we mapped its binding sites on RNA at nucleotide-level resolution on a genome-wide scale and find that CNBP interacted with 3961 mRNAs in human cell lines, preferentially at a G-rich motif close to the AUG start codon on mature mRNAs. Loss- and gain-of-function analyses coupled with system-wide RNA and protein quantification revealed that CNBP did not affect RNA abundance, but rather promoted translation of its targets. This is consistent with an RNA chaperone function of CNBP helping to resolve secondary structures, thus promoting translation.

overall_design: CNBP protein knockout and Ribosome profiling

first: S

middle: K

first: D

last: Benhalevy

first: C

middle: H

last: Danan

first: M

last: Hafner

last: Juranek


title: The human CCHC-type Zinc Finger nucleic acid binding protein binds G-rich elements in target mRNA coding sequences initiation promotes translation (RNA-Seq).

overall_design: CNBP protein knockout and RNA-seq


title: Genetic variation in four highland populations in the context of broader genetic diversity in Daghestan.

city: Tucson

first: Tatiana

middle: M.

last: Karafet

state: AZ

address: BSW #246, 1041 E Lowell Str.

department: ARL

institute: University of Arizona

type:
Genome variation profiling by SNP array
SNP genotyping by SNP array

summary: Daghestan, with its exceptional combination of linguistic, geographic, and cultural diversity, presents an excellent natural laboratory for tracking the influence of demographic processes on patterns of genetic variation. This study was designed to investigate the co-evolution of genes and languages, comparing and contrasting patterns of linguistic, genetic and geographic variation among Daghestani populations.

overall_design: 62 samples from 4 populations have been genotyped using the Illumina platform GPL19699

first: Kazima

last: Bulayeva

first: J

last: Lansing

first: Olga

middle: V

last: Savina


title: Reprogramming Hutchinson-Gilford Progeria Syndrome fibroblasts resets epigenomic landscape in patient-derived induced pluripotent stem cells Jan 01, 2018   pending   None

city: Ottawa

first: Theodore

last: Perkins

state: ON

address: 501 Smyth Rd.

department: Cellular and Molecular Medicine

institute: Ottawa Hospital Research Institute

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


title: isolation and identification of bovine preadipocytes and screening of microRNAs associated with adipogenesis

status: Public on Jan 01 2020

city: Changchun

first: xiang

last: yu

state: Jilin Provine

address: Xinzhu Road

country: China

institute: Jilin University

summary: Bovine preadipocytes were isolated from subcutaneous fatty tissue and induced differentiation into adipocytes and RNAs were extracted from preadipocytes and adipocytes respectively. Small RNA-seq was performed by Beijing Genomics Institute biotechnology. A total of 250 differential expression miRNAs were screened, while 131 miRNAs were highly expressed in bovine adipocytes and 119 miRNAs were highly expressed in bovine preadipocytes. KEGG pathway analysis presented that 4.76% (p-value<0.001) differently expression genes enriched in lipid metabolism. GO analysis showed the target genes were mainly associated with cell process, cell and binding. Together these results provided important insights into the research of miRNAs for bovine preadipocytes differentiation.

overall_design: Examination of different expression patterns between preadipocytes and adipocytes.

first: Yu

last: Xiang

first: Yang

last: Yunjun


title: Analysis of the role of Mcu in the regenerating mouse liver after partial hepatectomy

city: Philadelphia

first: Egle

last: Juskeviciute

state: PA

address: 1020 Locust st. JAH 527

department: Pathology

country: USA

institute: Thomas Jefferson University

summary: In this study, we analyzed global liver gene expression in MCU knock-down (KD) mice.  MCUloxp/loxp male mice were treated with an AAV8-Cre under the control of a hepatocyte specific promoter (TBG) to generate liver-specific MCU KD mice. AAV8-TBG-Null treated littermates were used as controls. Knockdown was verified 3 weeks after injection by protein and mRNA (80%). 5 weeks after injection mice were subjected to 70% partial hepatectomy and liver semples were collected 30h after the sugery.  Mouse Clariom S (Affymetrix, Santa Clara, CA) arrays were used to obtain global gene expression data from pooled liver samples (pools of 4 biological replicates per array).

overall_design: Gene expression was profiled in the regenerating livers of  wild type and in liver-specific MCU knockdown mice at t=0 and 30h after 70% partial hepatectomy; pools of 4 biological replicates per genotype.

first: Anil

last: Noronha Antony

first: Máté

last: Katona

first: Kai-Ting

last: Huang

first: David

middle: G

last: Smith

first: Zuzana

last: Nichtova

first: Manan

last: Damani

first: György

last: Csordás

first: John

last: Elrod

first: Gyorgy

last: Hajnoczky

first: Jan

middle: B

last: Hoek


title: Identification of genome-wide binding sites of Plasmodium falciparum GCN5-acetyltransferase

city: New Delhi

first: Sunita

last: Verma

state: Delhi

address: JNU Campus

department: School of Computational and Integrative Sciences

institute: Jawaharlal Nehru Univesity

summary: Genome-wide ChIP-sequencing analysis of PfGCN5 was carried out in asynchronous stage (trophozoite and schizont stage enriched) parasites using PfGCN5 antibodies. We have observed that PfGCN5 is majorly associated with promoter regions of genes. Moreover, a uniform distribution was found in exons, transcription termination site, and intergenic regions. This study shed some light on PfGCN5 binding sites on Plasmodium falciparum genome.

overall_design: Examination of PfGCN5 binding sites in asexual stage of Plasmodium falciparum.

first: Suman

last: Dhar

first: Annangarachari

last: Krishnamachari

first: Krishanu

last: Bhowmick


title: Reprogramming Hutchinson-Gilford Progeria Syndrome fibroblasts resets epigenomic landscape in patient-derived induced pluripotent stem cells [Affymetrix]

first: Theodore

last: Perkins

summary: Hutchinson-Gilford Progeria Syndrome (HGPS) is a segmental premature aging disorder caused by the accumulation of the truncated form of Lamin A known as Progerin within the nuclear lamina.  Cellular hallmarks of HGPS include nuclear blebbing, loss of peripheral heterochromatin, defective epigenetic inheritance, altered gene expression, and senescence. To model HGPS using iPSCs, detailed genome-wide and structural analysis of the epigenetic landscape is required to assess the initiation and progression of the disease. We generated a library of iPSC lines from fibroblasts of HGPS patients and controls, including one family trio. Our microarray results suggest that despite the presence of defects associated with Progerin in the nuclear lamina including structural defects, senescence and abnormal epigenetic marks, HGPS fibroblasts can be reprogrammed into iPSCs with transcriptomes that are essentially identical to control iPSCs and hESCs.

first: William

last: Stanford

first: Zhaoyi

last: Chen


title: Defining Murine Monocyte Differentiation into Colonic and Ileal Macrophages

city: Rehovot

first: Steffen

last: Jung

address: 234 Herzl Street

department: Department of Immunology

country: Israel

institute: Weizmann Institute of Science

summary: Monocytes are circulating short-lived macrophage precursors that are recruited on demand from the blood to sites of inflammation and challenge. In steady state, classical monocytes give rise to vasculature-resident cells that patrol the luminal side of the endothelium. In addition, classical monocytes feed macrophage compartments of selected organs, including barrier tissues, such as the skin and intestine, as well as the heart. Monocyte differentiation under conditions of inflammation has been studied in considerable detail. In contrast, monocyte differentiation under non-inflammatory conditions remains less well understood. Here we took advantage of a combination of cell ablation and precursor engraftment to investigate the generation of gut macrophages from monocytes. Collectively, we identify factors associated with the gradual adaptation of monocytes to tissue residency. Moreover, comparison of monocyte differentiation into the colon and ileum-resident macrophages revealed the graduated acquisition of gut segment-specific gene expression signatures.

overall_design: Monocyte-derived macrophages were sorted from ileum and colon. Sorted cells were subjected to RNAseq in triplicates. In total, 3 time points were investigated per organ. Further, naïve monocytes and tissue-resident macrophages were sorted for RNAseq (triplicates).

first: Mor

last: Gross-Vered

first: Sébastien

last: Trzebanski

first: Anat

last: Shemer

first: Biana

last: Bernshtein

first: Caterina

last: Curato

first: Gil

last: Stelzer

first: Tomer-Meir

last: Salame

first: Eyal

last: David

first: Sigalit

last: Boura-Halfon

first: Louise

last: Chappell-Maor

first: Dena

last: Leshkovitz


title: Histone ChIP-seq from transverse colon (ENCSR101EEJ)

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

institute: ENCODE DCC

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


title: Prevention of Mycobacterium tuberculosis infection and disease in nonhuman primates following intravenous BCG vaccination

city: Cambridge

first: Alex

last: Shalek

state: MA

address: 45 Carleton Street

department: Chemistry

institute: MIT

summary: Mycobacterium tuberculosis (Mtb) is the leading cause of death from infection worldwide. Intradermal (ID) vaccination with BCG has variable efficacy against pulmonary tuberculosis, the major cause of mortality and disease transmission. Here we show that the route and dose of BCG vaccination alters circulating and lung resident T cells and subsequent protection against Mtb challenge in nonhuman primates (NHP). NHP immunized with BCG by the intravenous (IV) route induced substantially higher antigen-specific CD4 (Th1 or Th17) and CD8 responses in blood, spleen, bronchoalveolar lavage (BAL), and lung lymph nodes compared to the same BCG dose administered by ID or aerosol (AE) routes. Moreover, IV immunization was the only route that induced a high frequency of antigen-specific tissue resident T cells in lung parenchyma. Six months after BCG vaccination, NHP were challenged with virulent Mtb. Strikingly, 9 of 10 NHP that received BCG IV were highly protected, with 6 NHP showing no detectable infection as determined by PET CT imaging, mycobacterial growth, pathology, granuloma formation, or de novo immune responses to Mtb-specific antigens. The finding that BCG IV prevents or significantly limits Mtb infection in NHP has important implications for vaccine development and provides a model for determining immune correlates and mechanisms of protection against TB.

overall_design: Single-cell RNA-Sequencing of Bronchoalveolar Lavages from animals vaccinated using different routes and doses of BCG

first: Patricia

last: Darrah

first: Joseph

middle: J

last: Zeppa

first: Joshua

last: Hackney

first: Marc

last: Wadsworth II

first: Travis

last: Hughes

first: Supriya

last: Pokkali

first: Phillip

last: Swanson

first: Nicole

last: Grant

first: Mark

last: Rodgers

first: Charles

last: Scanga

first: Chelsea

last: Causgrove

first: Dominick

last: Laddy

first: Aurelio

last: Bonavia

first: Danilo

last: Casimiro

first: Philana

last: Lin

first: Edwin

last: Klein

first: Pauline

last: Maiello

first: Mario

last: Roederer

first: JoAnne

last: Flynn

first: Robert

last: Seder


title: A precisely positioned MED12 activation helix stimulates CDK8 kinase activity

city: Bayreuth

first: Claus

last: Kuhn

address: Universitätsstr. 30

department: BIOmac Research Center, NW I

institute: University of Bayreuth

summary: The Mediator kinase module regulates eukaryotic transcription by phosphorylating transcription-related targets and by modulating the association of Mediator and RNA Polymerase II. The activity of its catalytic core, cyclin-dependent kinase 8 (CDK8), is controlled by Cyclin C and MED12, with its deregulation contributing to numerous malignancies. Here, we combine in vitro biochemistry, crosslinking coupled to mass spectrometry and in vivo studies to describe the binding location of the N-terminal segment of MED12 on the CDK8/Cyclin C complex and to gain mechanistic insights into the activation of CDK8 by MED12. Our data demonstrate that the N-terminal portion of MED12 wraps around CDK8, whereby it positions an "activation helix" close to the T-loop of CDK8 for its activation. Intriguingly, mutations in the activation helix that are frequently found in cancers do not diminish the affinity of MED12 for CDK8, yet likely alter the exact positioning of the activation helix. Furthermore, we find the transcriptome-wide gene expression changes in human cells that result from a mutation in the MED12 activation helix to correlate with deregulated genes in breast and colon cancer. Last, functional assays in presence of kinase inhibitors reveal that binding of MED12 remodels the active site of CDK8 and thereby precludes the inhibition of ternary CDK8 complexes by type-II kinase inhibitors. Taken together, our results not only allow us to propose a revised model of how CDK8 activity is regulated by MED12, but they also offer a path forward in developing small molecules that target CDK8 in its MED12-bound form.

overall_design: RNA-Seq of HCT116 wild-type and HCT116 knock-in cell line (E33Q MED12) upon 24 hours of interferon-γ (IFN-γ)  treatment. For each tested condition two biological replicates were prepared and sequenced. As a reference non-treated with IFN-γ cell samples were used.

first: Felix

last: Klatt

first: Alexander

last: Leitner

first: Iana

last: Kim

first: Xuan-Hung

last: Ho

first: Franziska

last: Langhammer

first: Robin

last: Weinmann

first: Melanie

last: Müller

first: Elisabeth

last: Schneider

first: Gunter

last: Meister

last: Huber

first: Claus-D


title: Temporal transcriptional profiling of in vivo cellular reprogramming and transorganogenesis in C. elegans

city: Santa Barbara

first: Erik

last: Spickard

address: UCSB

department: MCDB

institute: University of California Santa Barbara

summary: Cellular reprogramming of differentiated tissues within a living animal is a rare and poorly understood phenomenon. In the nematode C. elegans a single transcription factor, the endoderm-specific GATA factor ELT-7, is capable of reprogramming cells of the fully differentiated muscular feeding organ, the pharynx, into intestine-like cells. It can also convert the spermatheca and entire uterus into a secondary intestine-like organ, a phenomenon we have called “transorganogenesis.” To reveal transcriptional changes occurring during these cellular transformations, we performed mRNAseq in animals undergoing this forced reprogramming. This analysis revealed that gene expression characteristic of the post-embryonic pharynx and somatic gonad is dramatically altered within the first few hours following forced expression of ELT-7. Unexpectedly, we found that transcripts associated with a diverse assortment of cell types precipitously decrease in abundance ~6 hours after ELT-7 expression but later recover, implying substantial cell fate elasticity. Further, we observed that ELT-7 expression results in a rapid activation of the innate immune response that is specifically activated following intracellular infection by microsporidia and viruses. These findings raise the possibility that activation of an intracellular innate immunity mechanism may be associated with certain cell fate conversions and can serve as a roadmap for further investigation into the control and maintenance of fully differentiated cell fates.

overall_design: Whole worm RNA-Seq profiling of control and ectopic elt-7 transcription factor expressing strains at 5 time points.

first: Joel

last: Rothman


title: tsRNA microarray of parental normal-like and breast cancer cell lines and with inhibited or induced RUNX1 expression

first: Nicholas

last: Farina

address: 89 Beaumont Avenue

department: Biochemistry

institute: University of Vermont Cancer Center

summary: The expression levels of tRNA-derived small RNA, known as tsRNA, were interrogated in the following parental cell lines: MCF10A normal-like mammary epithelial cell, MCF7, MCF10AT1, MCF10CA1a, and MDA-MB-231 breast cancer cells.  In addition, tsRNA expression was determined after shRNA-inhibition of RUNX1 in MCF10A cells or RUNX1 induction in MCF10CA1a cells.

overall_design: Total RNA isolated from three biological replicates (subsequent passages) per cell line.

first: Stephanie

last: Scalia

first: Caroline

last: Adams

first: Deli

last: Hong

first: Andrew

last: Fritz

first: Terri

last: Messier

first: Veronica

last: Balatti

first: Dario

last: Veneziano

first: Jane

last: Lian

first: Carlo

middle: M

last: Croce

first: Gary

middle: S

last: Stein

first: Janet


title: Metabolic drivers of human keratinocyte differentiation revealed by integrated metabolome and transcriptome analysis

city: Zurich

first: Nicola

last: Zamboni

state: Zurich

address: Institute of Molecular Systems Biology, Otto-Stern-Weg 3

country: Switzerland

institute: ETH Zurich

summary: Epidermal function is maintained through a continuous process called epidermal homeostasis, in which keratinocytes gradually differentiate from proliferating stem cells to dead corneocytes that shed off the skin. We investigated the metabolic rewiring that occur during keratinocyte differentiation. We analyzed endometabolome, exometabolome and transcriptome during differentiating in vitro under high calcium conditions. Using network-based computational approaches, we found that proliferating keratinocytes gain energy through branched-chain amino acid-fueled TCA cycle that is shut down during differentiation. Upon differentiation, metabolism is repurposed to serve two main purposes. First, to form the epidermal barrier. Specifically, glucose and nucleotides are utilized for the formation of the lipid-enriched hydrophobic extracellular matrix, the transformation from keratinocytes to corneocytes and their cross-linking. Second, we found active regulation of metabolites with signaling functions during differentiation including hydrocortisone, sphingosines, and exonucleotides. Functional relevance of these findings was tested experimentally by 14 metabolic perturbations that were inferred by our analysis, and effectively affected keratinocytes differentiation and proliferation. Overall, this work provides an integrated and mechanistic analysis of the metabolic underpinnings that sustain epidermal function.

overall_design: Gene Expression of normal human epidermal keratinocytes of four individual donors were determined during high calcium induced differentiation (0 h, 72 h, 168 h treatment)

first: Andreas

last: Kuehne

first: Michael

last: Zimmermann

first: Marc

last: Winnefeld

first: Frank

last: Fischer

first: Stefan

last: Gallinat

first: Horst

last: Wenck

first: Janosch

last: Hildebrand


title: m6A mRNA methylation is essential for oligodendrocyte maturation and CNS myelination

city: Chicago

first: Qili

last: Fei

state: Illinois

address: 929 E 57th Ave

institute: University of Chicago

summary: Oligodendrocytes are responsible for myelin formation and axonal trophic support in the vertebrate CNS. While a number of factors have been discovered that regulate oligodendrocyte lineage progression, the exact molecular mechanisms involved in this process remain unclear. Emerging studies have shown that N6-methyladenosine (m6A), the most common internal RNA modification of mammalian mRNA, plays a critical role in various developmental processes. In this study, we demonstrate that oligodendrocyte lineage progression is accompanied by changes in m6A modification on numerous transcripts. In vivo conditional inactivation in oligodendrocyte lineage cells of an essential m6A writer component, METTL14, results in decreased oligodendrocyte numbers and CNS hypomyelination, although oligodendrocyte precursor cell (OPC) numbers are normal. In vitro Mettl14 ablation disrupts post-mitotic oligodendrocyte maturation. In addition, Mettl14 ablation has distinct effects on OPC and oligodendrocyte transcriptomes. Together, our findings indicate that dynamic RNA methylation plays a critical regulatory role in oligodendrocyte development and CNS myelination.

overall_design:
Illumina TruSeq stranded mRNA libraries prepared for m6A-seq in three replicates by Illumina HiSseq 4000 platform.

Each processed data file was generated from both IP and input samples and is linked to the corresponding IP sample records.

first: Chuan

last: He