title: Transcriptome map of the human brain at the single-cell resolution

status: Public on Jan 30 2020

city: Moscow

first: Pavel

last: Mazin

address: Skolkovo Innovation Center, Building 3

department: Biomed

country: Russia

institute: Skolkovo Institute of Science and Technology

summary: The human brain is about three times larger than the brain of our closest relatives, chimpanzees and bonobos. However, increased size alone fails to explain cognitive abilities unique to humans. Functional changes acquired in the human lineage are likely mediated by divergent gene expression and cell composition in brain regions. Here we generated a map of the human brain transcriptome by assessing the gene expression levels in 33 distinct regions representing all major brain structures from four adult cognitively healthy human individuals, three chimpanzees, three bonobos, and three rhesus macaques. We further conducted single-nuclei RNA-sequencing (SN-seq) experiment in three of the 33 brain regions in four species: two regions showing excess of the human-specific differences, cingulate anterior cortex and cerebellar gray matter, as well as one region showing no such excess, caudate nucleus. We determined cell type specificity of human-specific differences observed in the bulk tissue analysis, and identified species-specific expression differences directly using SN-seq data. This data resource forms a comprehensive baseline for studies of normal and abnormal human brain function and evolution.

sample_organism:
Macaca mulatta
Pan paniscus
Pan troglodytes
Homo sapiens

overall_design: 422 polyA-selected RNA-seq samples were obtained from 33 brain regions representing all major brain structures from four adult cognitively healthy human individuals, three chimpanzees, three bonobos, and three rhesus macaques

first: Ekaterina

last: Khrameeva

first: Ilia

last: Kurochkin

first: Philipp

last: Khaitovich


title: Next Generation Sequencing facilitates Quantitative Analysis of mouse CD4+ T cells treated with butyrate

status: Public on Jul 16 2020

city: Galveston

first: Yingzi

last: Cong

state: TX

address: 301 University Boulevard

country: USA

institute: University of Texas Medical Branch at Galveston

type: Expression profiling by high throughput sequencing

summary: The goal of this study is to analyze the effect of butyrate in mouse CD4+ T cells.

overall_design: Examine the different gene profiles between CD4+ T cells treated with or without butyrate under neutral condition and Th1 condition using RNA seq


title: META-PREDICT: Dynamic responses of the global human skeletal muscle coding and noncoding transcriptome to exercise

status: Public on Jul 21 2020

city: Stirling

first: James

last: Timmons

address: Bridge of Allan

country: United Kingdom

institute: Augur Precision Medicine LTD

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

overall_design: Refer to individual Series


title: DNA methylation profiles of human buffy coat samples from Huntington's disease

status: Public on Jul 02 2020

city: Los Angeles

first: Steve

last: Horvath

state: CA

address: 695 Charles E. Young Drive South, Box 708822

department: Human Genetics

institute: University of California, Los Angeles

type: Methylation profiling by genome tiling array

summary:
Human DNA methylation Beadchip v1.2 was used to profile buffy coat samples.
The main goal of the study was to relate DNA methylation data to Huntington disease status (control, pre-manifest disease, manifest motor disease).

overall_design:
Each sample actually represents an average across 12 individuals that were located on the same Illumina chip (SENTRIX ID).

The following sample characteristics are provided for each sample:
Average chronological age at the time of the DNA sample collection. The average was formed over 12 samples with the same SENTRIX ID.
Average body mass index - The average was formed over 12 samples with the same SENTRIX ID.
DNAmAgeDNA - methylation age, i.e. the predicted age based on the epigenetic clock software (https://dnamage.genetics.ucla.edu/) described in the following reference Horvath S (2013) DNA methylation age of human tissues and cell types Genome Biology PMID: 24138928 .
HD.Status - Huntington disease status which takes 3 values: control, pre-manifest (before onset of motor symptoms) and manifest (manifests motor symptoms of the disease).

**Please note that raw data is not provided due to severe data sharing restriction and the highly sensitive nature of the disease (human Mendelian disease).**


title: Genome-Wide Profiling of DNA Methylation and Gene Expression Identifies Candidate Genes for Human Diabetic Neuropathy

status: Public on Aug 24 2020

city: Grand Forks

first: Junguk

last: Hur

state: ND

address: 1301 N. Columbia Rd. Stop 9037

department: Biomedical Sciences

institute: University of North Dakota

type: Methylation profiling by high throughput sequencing


title: Transient non-integrative nuclear reprogramming promotes multifaceted reversal of aging in human cells

status: Public on Jan 21 2020

summary: Transient reprogramming, mediated by transient expression of mRNAs, promotes a rapid reversal of both cellular aging and of epigenetic clock in human fibroblasts and endothelial cells.  Transient on-integrative reprogramming protocol optimized based on a cocktail of mRNAs expressing OCT4, SOX2, KLF4, c-MYC, LIN28 and NANOG (OSKMLN). This protocol consistently produces induced pluripotent stem cell (iPSC) colonies, regardless of age of the donors, after 12-15 daily transfections. Here we adopted a transient reprogramming protocol where OSKMLN were daily transfected for only four consecutive days. Methylation profiles were used to estimate two epigenetic clocks: the pan tissue clock from Horvath 2013 (PubMedIdentifier PMID: 24138928 or PMCID: PMC4015143) and the skin & blood clock from Horvath 2018 (PMID: 30048243 PMCID: PMC6075434).

overall_design:
Here we adopted a transient reprogramming protocol where OSKMLN were daily transfected for only four consecutive days.
Genome wide DNA methylation profiling of two cell types: human fibroblasts from skin and endothelial cells from veins. The Illumina Infinium EPIC DNA methylation Beadchip was used to obtain DNA methylation profiles

first: Tapash

middle: J

last: Sarkar

first: Vittorio

last: Sebastiano


title: Single-cell epigenomic identification of inherited risk loci in Alzheimer’s and Parkinson’s disease

status: Public on Jul 26 2020

city: Boston

first: Sundari

last: Chetty

state: MA

address: 185 Cambridge Street

department: Harvard Medical School

institute: Massachusetts General Hospital, Harvard University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Genome-wide association studies (GWAS) have identified thousands of variants associated with disease phenotypes. However, the majority of these variants do not alter coding sequences, making it difficult to assign their function. To this end, we present a multi-omic epigenetic atlas of the adult human brain through profiling of the chromatin accessibility landscapes and three-dimensional chromatin interactions of seven brain regions across a cohort of 39 cognitively healthy individuals. Single-cell chromatin accessibility profiling of 70,631 cells from six of these brain regions identifies 24 distinct cell clusters and 359,022 cell type-specific regulatory elements, capturing the regulatory diversity of the adult brain. We develop a machine learning classifier to integrate this multi-omic framework and predict dozens of functional single nucleotide polymorphisms (SNPs), nominating gene and cellular targets for previously orphaned GWAS loci. These predictions both inform well-studied disease-relevant genes, such as BIN1 in microglia for Alzheimer’s disease (AD) and reveal novel gene-disease associations, such as STAB1 in microglia and MAL in oligodendrocytes for Parkinson’s disease (PD). Moreover, we dissect the complex inverted haplotype of the MAPT (encoding tau) PD risk locus, identifying ectopic enhancer-gene contacts in neurons that increase MAPT expression and may mediate this disease association. This work greatly expands our understanding of inherited variation in AD and PD and provides a roadmap for the epigenomic dissection of noncoding regulatory variation in disease.

overall_design: Bulk ATAC-seq, single-cell ATAC-seq and HiChIP

first: Ryan

middle: M

last: Corces


title: Global skin gene expression profile of early diffuse cutaneous systemic sclerosis shows a prominent innate and adaptive immunity profile

status: Public on Nov 18 2019

city: Houston

first: Shervin

last: Assassi

address: 6431 FanninSuite 5270

institute: University of Texas Health Science Center at Houston

summary: RNA from skin biopsies from 48 patients in the Prospective Registry for Early Systemic Sclerosis (PRESS) cohort (mean disease duration 1.3 years) and 33 matched healthy controls was examined by nextGen RNA sequencing

overall_design: 3- or 4-mm diameter punch biopsies were obtained from the forearm skin and immersed in RNAlater solution (Qiagen). RNA was extracted using miRNeasy Mini kits (Qiagen).  cDNA libraries were prepared using the Illumina TruSeq stranded Total RNA Library Prep Gold kit, loaded on cBot (Illumina) at a final concentration of 10 pM to perform cluster generation, followed by 2 x 76 bp paired-end sequencing on HiSeq 2500 (Illumina), generating on average around 50 million reads per sample.

first: Brian

last: Skaug

first: Lisha

last: Zhu

first: W

last: Zheng


status: Public on Nov 01 2019

city: Giessen

first: Jochen

last: Wilhelm

state: Hessen

address: Aulweg 132

department: Institute for Lung Health

country: Germany

institute: Justus-Liebig University Giessen

summary: We observed that loss of miR142 leads to the increased  expression of  surfactant protein C and decreased Podoplanin. This indicates increased  differentiation of alveolar progenitors towards AEC II lineage. In order to understand what are the genes that are being regulated during AEC II cell differentiation in miR142 overexpressing mice we are performing this experiment.

overall_design: Two groups (wild type and mir142 overexpressing mice), n=4 mice per group

first: Amit

last: Shrestha

first: Saverio

last: Bellusci


title: AEC II cell differentiation in miR142 KO mice

summary: We observed that loss of miR142 leads to the increased  expression of  surfactant protein C and decreased Podoplanin.This indicates  increased  differentiation of alveolar progenitors towards AEC II lineage.   In order to understand 1)what are the genes that are being regulated  during AEC II cell differentiation in miR142KO mice we are performing this experiment.

overall_design: Two groups (wild type and mir142 knock-out mice), n=4 mice per group


title: Truncated stathmin-2 is a marker of TDP-43 pathology in frontotemporal dementia

status: Public on Oct 20 2020

city: New York

first: Delphine

last: Fagegaltier

state: New York

address: 101 Ave of the Americas

department: Center for Genomics of Neurodegenerative Disease

institute: New York Genome Center

summary: No treatment for frontotemporal dementia (FTD), the second most common type of early-onset dementia, is available, but therapeutics are being investigated to target the 2 main proteins associated with FTD pathological subtypes: TDP-43 (FTLD-TDP) and tau (FTLD-tau). Testing potential therapies in clinical trials is hampered by our inability to distinguish between patients with FTLD-TDP and FTLD-tau. Therefore, we evaluated truncated stathmin-2 (STMN2) as a proxy of TDP-43 pathology, given the reports that TDP-43 dysfunction causes truncated STMN2 accumulation. Truncated STMN2 accumulated in human induced pluripotent stem cell–derived neurons depleted of TDP-43, but not in those with pathogenic TARDBP mutations in the absence of TDP-43 aggregation or loss of nuclear protein. In RNA-Seq analyses of human brain samples from the NYGC ALS cohort, truncated STMN2 RNA was confined to tissues and disease subtypes marked by TDP-43 inclusions. Last, we validated that truncated STMN2 RNA was elevated in the frontal cortex of a cohort of patients with FTLD-TDP but not in controls or patients with progressive supranuclear palsy, a type of FTLD-tau. Further, in patients with FTLD-TDP, we observed significant associations of truncated STMN2 RNA with phosphorylated TDP-43 levels and an earlier age of disease onset. Overall, our data uncovered truncated STMN2 as a marker for TDP-43 dysfunction in FTD.

overall_design:
Oct 19, 2020 release of postmortem RNASeq data from 1606 samples in the NYGC ALS Consortium; metadata is available upon request at ALSdata@nygenome.org. Differential STMN2 gene expression (processed count data) and splicing analyses of Amyotrophic Lateral Sclerosis (ALS), ALS-FTD and Control postmortem samples in Prudencio et al. 2020 were performed on samples from this release and prior NYGC ALS Consortium releases.
contributor: NYGC ALS Consortium
contributor: The Target ALS Human Postmortem Tissue Core
contributor: Jack Humphrey (processed count data)

first: Hemali

last: Phatnani

first: Jack

last: Humphrey

first: Petro

last: Fratta


title: miR-142 and alveolar epithelial lineage formation


title: Global transcriptional profile of hESC-derived macrophage (iMAC), human monocyte-derived macrophage and THP-1 macrophage

status: Public on Oct 31 2019

city: Cheongju-si

first: Kim

last: Jung-Hyun

address: 202, Osongsaengmyeong 2-ro, Osong-eup, Heungdeok-gu

department: Division of Intractable Diseases

country: South Korea

institute: Korea National Institute of Health

summary: We report here a modified protocol for generating homogenous populations of macrophage-like cells from human embryonic stem cells. The induced macrophages, referred to as iMAC, presented similar transcriptomic profiles and characteristic immunological features of classical macrophages and were permissive to viral and bacterial infection, in particular Mycobacterium tuberculosis (Mtb). Their production was amenable to scale up and the resulting cells suitable for high-throughput screening.

overall_design: We performed RNA sequencing (RNASeq) of iMAC (20-day and 60-day), hESC, hMDM and THP-1 macrophages by Illumina HiSeq 2500. For genomic characterization of iMAC, we performed RNA sequencing (RNASeq) of 20-day and 60-day iMAC and compared their profiles with that of hESC, hMDM and THP-1 macrophages. To minimize the variations induced by the culture conditions, hMDM and late-stage iMAC were cultured in the same media (RPMI1640 + M-CSF).

first: Hyo-Won

last: Han

first: Hye-Yeong

last: Jo

first: Hyang-Hee

last: Seo

first: Virgínia

middle: C

last: Falcão

first: Vincent

last: Delorme

first: Jinyeong

last: Heo

first: David

last: Shum

first: Jang-Hoon

last: Choi

first: Hye-Ryeon

first: Seok-Ho

last: Hong

first: Mi-Hyun

last: Park

first: Rajesh

middle: K

last: Thimmulappa

first: Jung-Hyun

last: Kim


title: Perinatal cardiomyocyte maturation reference isolated by large-particle fluorescence activated cell sorting

status: Public on Apr 01 2020

city: Baltimore

first: Suraj

last: Kannan

state: MD

address: 720 Rutland Avenue Ross 954

department: Cardiology

institute: Johns Hopkins University

summary: To date, there have been limited high quality libraries of cardiomyocyte maturation during the perinatal period, in part owing to the difficulty of isolating large perinatal cardiomyocytes. We previously developed a method utilizing large-particle fluorescent activated cell sorting (LP-FACS) to isolate adult cardiomyocytes for single cell RNA-seq (Kannan et al., Circ Res, 2019). We utilize this method to generate a reference of perinatal cardiomyocyte maturation.

overall_design: We isolated CMs from mice at the following timepoints using LP-FACS: e14, e18, p0, p4, p8, p11, p14, p18, p22, p28, p35, p56.

first: S

first: M

last: Farid

first: B

middle: L

last: Lin

last: Miyamoto

first: C

last: Kwon


title: Single-cell mRNA analysis of colon phagocyte heterogeneity identifies two major macrophage developmental pathways

status: Public on Sep 25 2019

city: Bethesda

first: Byunghyun

last: Kang

state: Maryland

address: 9000 Rockville Pike

institute: NIAID

summary: Tissue macrophages (MPs) develop distinctive functions due to unique transcriptional programs driven by local environmental ques. In the intestine, it is known that MPs are heterogeneous cells that differentiate from blood monocytes and embryonic precursors, and are essential for homeostasis with the vast microbiome through their ability to kill invading microbes, clear apoptotic cells, and produce regulatory cytokines. However, the full extent of MP heterogeneity, their developmental relationships, and how the intestinal microbiota affects MP generation is not known. Here, we performed single cell RNA sequencing of colonic myeloid cells from specific pathogen free (SPF) and germ free (GF) C57BL/6 mice and found extensive heterogeneity of colon MP, with at least six different identifiable populations, with less heterogeneity of dendritic cells (DCs). Unsupervised modeling of developmental pathways combined with inference of gene regulatory networks suggested two major trajectories from common CCR2+ precursors resulting in CD11c+CD9+MMRintCD121b+ and CD11c-CD9intMMRhiCD121b- MP populations with unique transcription factors activities to coordinate downstream target molecules. The generation of both mature populations of colon MPs was impaired in germ-free mice, which coincided with the appearance of a dominant unique population of MPs, whereas the generation of DC populations in GF mice were unaffected or increased. Furthermore, the two major MP populations were clearly distinct from other populations regarding their gene expression profile, localization within the lamina propria, and ability to phagocytose macromolecules from the blood. These data uncover the diversity of intestinal myeloid cell populations, highlight the importance of microbiota on the unique developmental as well as anatomical and functional fates of colon MPs. We anticipate that these findings will form the basis for future studies on how tissue myeloid cell development is influenced either directly or indirectly by signals from endogenous microbiota in the intestine, as well as other tissues.

overall_design: To understand how commensal microbiome affect the heterogeneity of colon macrophages and dendritic cells, colon macrophages and dendric cells were isolated from either SPF and GF mice and profiled using 3’-droplet-based (dropseq) single-cell RNAseq. Cell surface markers of macrophages clusters were carefully selected by downstream analysis of scRNAseq data. To confirm the selected markers are well to identify subsets of colon macrophages and get more reliable dataset with deeper sequencing depth, 8 different subsets of colon macrophages were further FACs-sorted and their transcriptomic profiles were examined by bulk RNAseq.

first: Luigi

last: Alvarado

first: Andre

last: Larochelle

first: Brian

last: Kelsall


title: The long non-coding RNA HOXB-AS3 regulates ribosomal RNA transcription in NPM1-mutated acute myeloid leukemia

status: Public on Oct 15 2019

city: Columbus

first: Ayse

middle: Selen

last: Yilmaz

state: OH

address: 1800 Cannon Drive

department: Biomedical Informatics

institute: OSU

summary: In this work we dissect the functional role of the HOXB-AS3 long non coding RNA in patients with NPM1-mutated (NPM1mut) acute myeloid leukemia (AML). We show that HOXB-AS3 regulates the proliferative capacity of NPM1mut AML blasts in vitro and in vivo. HOXB-AS3 was found to interact with the ErbB3-binding protein 1 (EBP1) and guide EBP1 to the ribosomal DNA locus. Via this mechanism HOXB-AS3 regulates ribosomal RNA transcription and de novo protein synthesis. We propose that in the context of NPM1 mutations, HOXB-AS3 overexpression acts as a compensatory mechanism, which allows adequate protein production in leukemic blasts.

overall_design: HOXB-AS3 was knocked down in AML cell lines or patient samples, then gene expression and splicing was assessed. NPM1 mutant and NPM1 wild-type cytogenetically normal (CN) AML patients were RNAsequenced to examine associations with expression of non-coding genes in the HOXB locus. OCI-AML3 cells were electroporated at 0h time-point with scramble or anti-HOXB-AS3 targeting oligonucleotides, at a final concentration of 500 nM. Cells were grown at a concentration of 0.5 million/mL in RPMI media supplemented with 10% FBS in standard cell culture conditions (37 degrees Celcius, 5% CO2). Cells were counted and samples were harvested at 12 h, 24 h and 48h.  The concentration of cells was maintained at 0.5 million/mL with addition of media.

first: Dimitrios

last: Papaioannou

first: Andreas

last: Petri

first: Oliver

last: Dovey

first: Sara

last: Terreri

first: Eric

last: Wang

first: Allison

last: Walker

first: Deedra

last: Nicolet

first: Christopher

first: Prasanthi

last: Kumchala

first: Felice

last: Pepe

first: Marius

last: Bill

first: Malith

last: Karunasiri

first: Miranda

last: Gardner

first: Frances

middle: A

last: Collins

first: Krzysztof

last: Mrózek

first: Nina

last: Zitzer

first: Virginia

last: Camilotto

first: Jonathan

last: Cooper

first: Xiongwei

last: Cai

first: Xiaoqing

last: Rong-Mullins

first: Hatice

last: Gulcin Ozer

first: Kellie

last: Archer

first: Michael

last: Freitas

first: Yi

last: Zheng

first: Robert

last: Lee

first: Iannis

last: Aifantis

first: George

last: Vassiliou

first: Guramrit

last: Singh

first: Sakari

last: Kauppinen

first: Clara

middle: D

last: Bloomfield

first: Adrienne

last: Dorrance

first: Ramiro

last: Garzon


title: Postmortem Cortex Samples Identify Distinct Molecular Subtypes of ALS: Retrotransposon Activation, Oxidative Stress, and Activated Glia

status: Public on Oct 04 2019

first: Delphine

last: Fagegaltier

summary: Amyotrophic Lateral Sclerosis (ALS) is a fatal neurodegenerative disease characterized by the progressive loss of motor neurons. While several pathogenic mutations have been identified, the vast majority of ALS cases have no family history of disease. Thus, for most ALS cases, the disease may be a product of multiple pathways contributing to varying degrees in each patient. Using machine learning algorithms, we stratified the transcriptomes of 148 ALS postmortem cortex samples into three distinct molecular subtypes. The largest cluster, identified in 61% of patient samples, displayed hallmarks of oxidative and proteotoxic stress. Another 19% of the samples showed predominant signatures of glial activation. Finally, a third group (20%) exhibited high levels of retrotransposon expression and signatures of TARDBP/TDP-43 dysfunction. We further demonstrated that TDP-43 (1) directly binds a subset of retrotransposon transcripts and contributes to their silencing in vitro, and (2) pathological TDP-43 aggregation correlates with retrotransposon de-silencing in vivo.

overall_design:
RNA-seq analysis of ALS patient samples and individuals without neurological disorders
Contributor: NYGC ALS Consortium
https://www.nygenome.org/research-areas/neurodegenerative-diseases/als-consortium/
Contributor: The Target ALS Human Postmortem Tissue Core
http://www.targetals.org/

first: Hemali

last: Phatnani

first: Oliver

middle: H

last: Tam

first: Molly

middle: G

last: Hammell


title: Accurate annotation of human protein-coding small open reading frames

status: Public on Jul 03 2019

city: La Jolla

first: Thomas

middle: Farid

last: Martinez

address: 10010 N Torrey Pines Rf

department: Peptide Biology Laboratories

institute: Salk Institute for Biological Studies

summary: Protein-coding small open reading frames (smORFs) are emerging as an important class of genes, however, the coding capacity of smORFs in the human genome is unclear. By integrating de novo transcriptome assembly and Ribo-Seq, we confidently annotate thousands of novel translated smORFs in three human cell lines. We find that smORF translation prediction is noisier than for annotated coding sequences, underscoring the importance of analyzing multiple experiments and footprinting conditions. These smORFs are located within non-coding and antisense transcripts, the UTRs of mRNAs, and unannotated transcripts. Analysis of RNA levels and translation efficiency during cellular stress identifies regulated smORFs and provides an approach for identifying smORFs for further investigation. Sequence conservation and signatures of positive selection indicate that encoded microproteins are likely functional. Additionally, proteomics data from enriched human leukocyte antigen complexes validates the translation of hundreds of smORFs and positions them as a source of novel antigens. Thus, smORFs represent a significant number of important, yet unexplored human genes.

overall_design: Annotation of protein-coding smORFs in 3 human cell lines using de novo transcriptome assembly and Ribo-Seq.

middle: F

first: Alan

last: Saghatelian

first: Maxim

middle: N

last: Shokhirev


title: Myeloablation followed by autologous stem cell transplantation normalizes systemic sclerosis molecular signatures

status: Public on Jul 10 2019

first: Shervin

last: Assassi

summary:
This is global gene expression study of whole blood samples collected in the Cyclophosphamide Or Transplantation (SCOT) randomized controlled trial, as well as unaffected controls.
Patients with diffuse cutaneous systemic sclerosis (scleroderma)  received either myeloablation followed by autologous stem cell transplantation or intravenous cyclophosphamide

overall_design: Baseline, 8 month, and 26 month samples are examined in the patients and compared to unaffected age- and gender-matched controls.

first: Xuan

last: Wang

first: Guocai

last: Chen

first: Ellen

last: Goldmuntz

first: Lynette

last: Keyes-Elstein

first: Jun

last: Ying

first: Paul

last: Wallace

first: Jacob

last: Turner

first: W

first: Virginia

last: Pascual

first: John

last: Varga

first: Monique

middle: E

last: Hinchcliff

first: Chiara

last: Bellocchi

first: Peter

last: McSweeney

first: Daniel

last: Furst

first: Rechard

last: Nash

first: Leslie

last: Crofford

first: Beverly

last: Welch

first: Ashely

last: Pinckney

first: Maureen

last: Mayes

first: Keith

last: Sullivan


title: Single cell transcriptomic profiling of large intestinal enteroendocrine cells in mice

status: Public on Sep 18 2019

city: Cambridge

first: Brian

middle: Yee Hong

last: Lam

address: Box 289 Addenbookes Hospital, Hills Road

department: Metabolic Research Laboratories

institute: University of Cambridge

summary: We report the different enteroendocrine populations in the large intestine in mice based on their transcriptomics profile. Hormone, receptor and transcription factors are analysed for differential expression between the different cell clusters to give a comprehensive view of the different characterisitcs of the distal entereondocrine cells

overall_design: Large intestine epithelium from  a Neurod1-crexEYFP mouse was digested into single cells and sorted based on EYFP fluorescence to collect only the enteroendocrine cells. 3500 cells were collected and their transcriptome sequenced using the Chromium system (10x Genomics) and a Hiseq4000 sequencer. Analysis of their transcriptome was perfomed using the cellranger pipeline

first: Lawrence

last: Billing

first: Pierre

last: Larraufie

first: Fiona

last: Gribble

first: Frank

last: Reimann


title: DNA methylation profiles from a transgenic sheep model of Huntington's disease

first: Steve

last: Horvath

summary:
An Infinium microarray platform (HorvathMammalMethylChip40) was used to generate DNA methylation data from n=168 blood samples of a transgenic sheep model of Huntington's disease.
84 transgenic sheep and age matched control sheep.

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus

overall_design:
Two genotypes (transgenic) and control.  Roughly sex balanced (half females).
Each sample characteristics value represents:
characteristics: Basename = usual identifier of the methylation array comprised of the SENTRIX ID (i.e. chip identifier) and position (row and column).
characteristics: Age (Years) = Age at the time of blood draw in units of years.
characteristics: Sex = female denotes female sheep.
characteristics: Genotype = Transgenic denotes Huntington disease status,
This ovine transgenic Huntington's disease model is described in the PMID: 20154343 article:

first: Russell

last: Snell


title: Gene expression, methylome and splicing of THP-1 monocytic cells and THP-1-derived macrophage

status: Public on Apr 19 2019

city: Camperdown

first: RENHUA

last: SONG

state: NSW

address: Charles Perkins Centre - D17, Level 4 West. The University of Sydney Johns Hopkins Drive

country: Australia

institute: Centenary Institute

summary: Monocytes and macrophages are essential components of the innate immune system. Herein, we report that intron retention (IR) plays an important role in the development and function of these cells. Using mRNA sequencing, bioinformatics analyses and RT-qPCR validation, we identified differential IR and altered expression of key genes involved in macrophage development and function, both in vitro and in vivo. We demonstrate that decreased IR in nuclear-detained mRNA is coupled to increased expression of genes encoding regulators of macrophage transcription, phagocytosis and inflammatory signalling, including ID2, IRF7, ENG and LAT. We further show that this dynamic IR program persists during the polarisation of resting macrophages into activated macrophages. In the presence of proinflammatory stimuli, intron-retaining CXCL2 and NFKBIZ transcripts in macrophages are rapidly spliced, leading to timely expression of these key inflammatory regulators by macrophages. Our study provides novel insights into the molecular mechanisms controlling vital regulators of the innate immune response.

overall_design:
We determined the role of intron retention in THP-1 monocytic cells and THP-1-derived macrophage cells.

NOTE: [01-24-2024] The titles of GSM3729250-GSM3729258 and GSM6573090-GSM6573092 were revised, but the associated data did not change.

first: Justin

last: Wong

first: Immanuel

last: Green

first: Renhua

last: Song


title: DamC reveals principles of chromatin folding in vivo without crosslinking and ligation [HiC]

status: Public on May 16 2019

city: Basel

first: Luca

last: Giorgetti

address: Fabrikstrasse 24

country: Switzerland

institute: Friedrich Miescher Institute for Biomedical Research

summary: Mammalian chromosomes are folded into an intricate hierarchy of structural domains, within which topologically associating domains (TADs) and CTCF-associated loops partition the physical interactions between regulatory sequences. Current understanding of chromosome folding largely relies on chromosome conformation capture (3C)-based experiments, where chromosomal interactions are detected as ligation products after crosslinking of chromatin. To measure chromosome structure in vivo, quantitatively and without relying on crosslinking and ligation, we have implemented a new method named damC. DamC combines DNA-methylation based detection of chromosomal interactions with next-generation sequencing and a biophysical model of methylation kinetics. DamC performed in mouse embryonic stem cells provides the first in vivo validation of the existence of TADs and CTCF loops, confirms 3C-based measurements of the scaling of contact probabilities within TADs, and provides evidence that mammalian chromatin in vivo is essentially rigid below 5 kilobases. Combining damC with transposon-mediated genomic engineering shows that new loops can be formed between ectopically introduced and endogenous CTCF sites, which alters the partitioning of physical interactions within TADs. This establishes damC as a crosslinking- and ligation-free framework to measure and modify chromosome interactions combined with a solid theoretical background for rigorous data interpretation. This orthogonal approach to 3C validates the existence of key structural features of mammalian chromosomes and provides novel insights into how chromosome structure within TADs can be manipulated.

overall_design:
Mouse ESC lines #94.1_2.7 (carrying random insertions of 50x TetO arrays spanning approx. 2.7kb each) and #94.1_216_C3 (carrying different random insertions of the same 50x TetO cassette flanked by 3 CTCF sites faced outwards) were generated starting from an X0 clone of the PGKT2 line in Masui et al (Cell 145:447-458, 2011). The remaining X chromosome additionally carries the deletion of the Linx promoter within the X inactivation center (Nora et al., Nature 485:381-385, 2012). Random insertions were generated using the piggyBac transposon system. Both lines stably express rTetR-EGFP-Dam-ERT2 under the control of an ectopic Rosa26 promoter. Cells were cultured on gelatin-coated culture plates in Dulbecco Modified Eagle’s medium (Sigma) in the presence of 15% foetal calf serum (Eurobio Abcys), 100 µM β-mercaptoethanol, 20 U/ml leukemia inhibitory factor (Miltenyi Biotec, premium grade) and 250 µg/mL hygromycin in 8% CO2 at 37°C. 6x106 mESC were harvested and diluted in 1x PBS to final 1x106 cells/ml, then crosslinked with 1% formaldehyde and quenched with 0,125M glycine for 5 min at RT. After two 1x PBS washes, cells pellets were obtained by centrifugation, snap frozen and stored at -80°C. Pellets were thawed on ice and resuspended in 500 ul lysis buffer (10 nM Tris-HCl pH8.0, 10 nM NaCl, 0.2%NP40, 1x Roche protease inhibitors) and left 30 min on ice. Cells were then pelleted by centrifugation (954 x g, 5 min, 4°C ), washed once with 300 ul 1x NEB2 buffer and nuclei were extracted by 1 h incubation at 37°C in 190 ul 0.5%SDS 1xNEB2 buffer. SDS was neutralized by diluting the sample with 400 ul NEB2 buffer and adding 10% Triton X-100. After 15 min of incubation at 37°C, nuclei were pelleted, washed once in PBS and resuspended in 300 ul NEB2 buffer. 400U of MboI (NEB, 25 000 units/ml) were added and incubated at 37°C overnight. The next day, nuclei were pelleted again, resuspended in 200 ul fresh NEB2 buffer and additional 200U of MboI were added for two more hours before heat inactivation at 65°C for 15 min. 43 ul of end-repair mix (1.5 μL of 10 mM dCTP; 1.5 μL of 10mM dGTP; 1.5 μL of 10 mM dTTP; 37.5 μL of 0.4 mM Biotin-11-dATP (Invitrogen) and 1 μL of 50U/μL DNA Polymerase I Large Klenow fragment (NEB)) were added to the nuclear suspension, incubated at 37°C for 45 min and heat inactivated at 65°C for 15 min. The end repair mix was exchanged with 1.2 ml of ligation mix (120μL of 10X T4 DNA Ligase Buffer; 100 μL of 10% Triton X-100; 6 μL of 20 mg/mL BSA; 969μL of H2O) plus 5 ul of T4 ligase (NEB, 2000 units/ml) and ligation was performed at 16°C overnight. Nuclei were reconstituted in 200 ul fresh NEB2 buffer followed by RNA digestion in 0.5 mg/ml RNAse A for 10 min at 37°C. Samples were de-crosslinked with Proteinase K at 65°C overnight and DNA was purified using phenol/chloroform. 2 ug of DNA sample were sonicated using Diagenode Bioruptor Pico. MyOne Streptavidin T1 (Life Technologies # 65601) magnetic beads were used to capture biotinylated DNA followed by A-tailing. Adapter ligation was performed according to NEB Next Ultra DNA Library prep kit instructions. Two independent PCR reactions with multiplex oligos for Illumina sequencing were performed and pooled for the final PCR clean-up by magnetic AMPure bead (Beckman Coulter) purification. The final libraries were eluted in nuclease-free water, QCed by Bioanalyzer and Qubit. HiC libraries were sequenced on a Illumina Nextseq500 platform (2x42bp paired end).
Please note that processed data was generated from both replicates and is linked to the corresponding 'replicate 1' sample records.

first: Josef

last: Redolfi

first: Yinxiu

last: Zhan

first: Christian

last: Valdes

first: Mariya

last: Kryzhanovska

first: Isabel

last: Guerreiro

first: Vytausas

last: Iesmantavicius

first: Guido

last: Tiana

first: Jop

last: Kind

first: Sebastien

last: Smallwood

first: Wouter

last: de Laat


title: DamC reveals principles of chromatin folding in vivo without crosslinking and ligation [4C]

overall_design:
4C-seq was performed on a range of viewpoints in embryonic stem cells carrying TetO arrays at diverse chromosomal integrations. In order to determine the chromosome structure at the TetO arrays, a single viewpoint (VP1) was designed on top of the TetO sequence allowing the identification of chromosomal interactions from every integrated platform. The other viewpoints, CTCF and reverse CTCF (VP21 and VP22; respectively) were designed on the mouse genome.

Please note that the processed data generated from both replicates is linked to the corresponding 'replicate 1' sample records as indicated in the REAME.txt.


title: DamC reveals principles of chromatin folding in vivo without crosslinking and ligation [capture-mapping]

overall_design: Mouse ESC lines #94.1_2.7 (carrying random insertions of 50x TetO arrays spanning approx. 2.7kb each) and #94.1_216_C3 (carrying different random insertions of the same 50x TetO cassette flanked by 3 CTCF sites faced outwards) were generated starting from an X0 clone of the PGKT2 line in Masui et al (Cell 145:447-458, 2011). The remaining X chromosome additionally carries the deletion of the Linx promoter within the X inactivation center (Nora et al., Nature 485:381-385, 2012). Random insertions were generated using the piggyBac transposon system. Both lines stably express rTetR-EGFP-Dam-ERT2 under the control of an ectopic Rosa26 promoter. Cells were cultured on gelatin-coated culture plates in Dulbecco Modified Eagle’s medium (Sigma) in the presence of 15% foetal calf serum (Eurobio Abcys), 100 µM β-mercaptoethanol, 20 U/ml leukemia inhibitory factor (Miltenyi Biotec, premium grade) and 250 µg/mL hygromycin in 8% CO2 at 37°C.  2µg of genomic DNA were fragmented to an average of 500bp by sonication (Covaris S220, duty cycle: 5%, peak power: 175W, duration: 25sec). End-repair, A-tailing and ligation of full-length barcoded Illumina adapters were performed using the TruSeq DNA PCR-free kit (Illumina) according to the manufacturer guidelines with the exception that large DNA fragments were not removed. 750ng of libraries for each sample were pooled together, and fragments of interest were captured using biotinylated probes against the the piggyBac inverted terminal repeats (ITRs) sequence and the xGen Hybridisation Capture kit (IDT) according to the manufacturer protocol (probes concentration of 2.25pmol/µl). Following the capture, libraries were amplified for 12 cycles using the Kapa Hi-fi polymerase and the following primers: 5’-AATGATACGGCGACCACCGAGAT, 5’-CAAGCAGAAGACGGCATACGAGA. Final libraries were purified using AMPure XP beads (1:1 ratio), quality controlled and sequenced on the NextSeq500 platform (paired-end 300 cycles mid-output). Capture probe sequences are as follows: ITR3-1 [Btn]ATCTATAACAAGAAAATATATATATAATAAGTTATCACGTAAGTAGAACATGAAATAACAATATAATTATCGTATGAGTTAAATCTTAAAAGTCACGTAAAAGATAATCATGCGTCATTT, ITR3-2 [Btn]TCCAAGCGGCGACTGAGATGTCCTAAATGCACAGCGACGGATTCGCGCTATTTAGAAAGAGAGAGCAATATTTCAAGAATGCATGCGTCAATTTTACGCAGACTATCTTTCTAGGGTTAA, ITR5-1 [Btn]TTAACCCTAGAAAGATAATCATATTGTGACGTACGTTAAAGATAATCATGCGTAAAATTGACGCATGTGTTTTATCGGTCTGTATATCGAGGTTTATTTATTAATTTGAA, ITR5-2 [Btn]ATTAAGTTTTATTATATTTACACTTACATACTAATAATAAATTCAACAAACAATTTATTTATGTTTATTTATTTATTAAAAAAAAACAAAA ACTCAAAATTTCTTCTATAAAGTAACAAA.


title: Epigenome-wide analyis of neurobehavioral variation in preterm infants

status: Public on Mar 26 2019

city: Atlanta

first: Carmen

last: Marsit

state: GA

address: 1518 Clifton Road

department: Environmental Health

institute: Rollins School of Public Health at Emory University

summary: Neonatal molecular biomarkers of neurobehavioral responses (measures of brain-behavior relationships), when combined with neurobehavioral performance measures, could lead to better predictions of long-term developmental outcomes. To this end, we examined whether variability in epigenomic measures from buccal cells were associated with neurobehavioral profiles in a cohort of infants born less than 30 weeks postmenstrual age (PMA) and participating in the Neonatal Neurobehavior and Outcomes in Very Preterm Infants (NOVI) Study (N=536). We tested whether epigenetic age, age acceleration, or DNA methylation (DNAm) levels at individual loci, measured via the Illumina EPIC microarray, differed between infants based on their NICU Network Neurobehavioral Scale (NNNS) profile classifications, ranging from most optimal to atypical. We adjusted for recruitment site, infant sex, PMA, and tissue heterogeneity. Infants with an optimally well-regulated NNNS profile had older epigenetic age compared to other NOVI infants (β1 = 0.201, p-value = 0.026), but no significant difference in age acceleration. In contrast, infants with an atypical NNNS profile had differential methylation at 29 CpG sites (FDR < 10%). Some of the genes annotated to these CpGs included PLA2G4E, TRIM9, GRIK3, and MACROD2, which have previously been associated with neurological structure and function, or with neurobehavioral disorders. These findings contribute to the existing evidence that neonatal epigenetic variations in buccal cells may be informative for infant neurobehavior.

overall_design:
DNA methylation was assessed for 542 samples using the Illumina MethylationEPIC Beadarray

**Additional samples (537-542) are added and the 'MatrixProcessed.txt.gz' is updated on Feb 18, 2021.

first: Todd

last: Everson


title: RNA-seq data for non-targeting siRNA and CDK11 siRNA transfection in SHhES8 cells

status: Public on Dec 07 2018

first: Jianyi

last: Ding

department: CMTB

institute: NHLBI, NIH

summary: We found that CDK11 KD in hESCs caused hESC differentiation. To get the detailed mechanism why its KD caused differentiation, we applied RNA-seq analysis, aiming to find out some clues about the mechanism. Firstly, we obtained the differentially expressed genes (DEGs) from NC and CDK11 KD hESC cells, replicated NC and 2 sets of CDK11 siRNA were transfected into SHhES8 cells for 4 days. Later, we analyzed the data and used GO analysis to enrich GO terms which might be helpful for our research.

overall_design: Examine the gene expression pattern in NC and CDK11 KD SHhES8 cells, and compare the gene expression to find out the differentially expressed genes.

first: Ying

last: Jin


title: Gene expression profiling study to identify key markers associated with disease recurrence in colorectal cancers.

status: Public on Oct 29 2019

city: Daejeon

first: Seon-Kyu

last: Kim

address: 125 Gwahak-ro, Yuseong-gu, Daejeon 305-806, Korea

department: Personalized Genomic Medicine Research Center

institute: Korea Research Institutue of Bioscience & Biotechnology

summary: The objective of this study is to identify a gene set to predict recurrence of colorectal cancer (CRC) patients. We generated RNA-seq data of 110 primary CRC samples and identified significant genes associated with recurrence of CRC. Through diverse statistical methods including generalized linear model likelihood ratio test, significant 10 genes were identified. In the validation cohorts, a risk classifier consisting of the 10 genes was an independent risk factor in colorectal cancers.

overall_design: Total RNA was isolated using an RNeasy Mini Kit (Qiagen, CA, USA) according to the manufacturer’s protocol. The quality and integrity of the RNA were confirmed by agarose gel electrophoresis and ethidium bromide staining, followed by visual examination under ultraviolet light. The sequencing library was prepared using a TruSeq RNA Sample Preparation kit v2 (Illumina, CA, USA) according to the manufacturer’s protocol. In brief, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads, fragmented and converted into cDNA. After the ligation of adapters, the fragments were amplified by PCR. Sequencing was performed on paired end reads (2×100 bp) using the HiSeq-2000 platform (Illumina).

first: Jeong-Hwan

first: Jin-Cheon

first: Seon-Young

first: Young-Sung


title: Expression data from HIF2A WT vs KD Madin-Darby canine kidney epithelial cells (MDCK strain II cells (ATCC:CCL-34))  under normoxic and hypoxic conditions

status: Public on Oct 17 2018

city: Oulu

first: Irina

last: Raykhel

address: Aapistie 5

department: FBMM

country: Finland

institute: University of Oulu

summary:
No one pathway was identified in up- and downregulated genes profile in HIF2A KD Madin-Darby canine kidney epithelial cells (MDCKII) in normoxic condition.
We used microarray to study the differential expression of genes in HIF2A knockdown versus WT Madin-Darby canine kidney epithelial cells (MDCKII)

overall_design: Madin-Darby canine kidney epithelial cells (MDCKII) were incubated 24h in normoxic condition then additionaly were incubated 24h in normoxic or hypoxic conditions and total RNA was extracted for microarray analysis.

first: Johanna

last: Myllyharju


title: The effect of genetic background on cognitive and pathological traits: AD-BXD [dataset 2]

status: Public on Jan 29 2019

city: Bar Harbor

first: Catherine

last: Kaczorowski

state: ME

address: 600 Main Street

institute: The Jackson Laboratory

summary: Cg.5XFAD females (MMRRC Stock No #34848-JAX) were bred to males from BXD strains. The resulting F1 progeny were monitored throughout their lifepan to evaluate the effect of genetic background on cognitive and pathological traits. Samples here come from various AD-BXD lines at either 6 or 14 months of age. An earlier dataset of similar design (plus Non-transgenic littermates) was deposited as GSE101144. Ntg littermates of mice sampled here will be deposited as a separate GEO series.

overall_design: 88 AD samples. For final by-strain analysis, samples were averaged into strain/age/genotype/sex groups (For example, all D2 6mo 5XFAD males were averaged for final by-strain analysis)

first: Sarah

last: Neuner

first: Matthew

last: Huentelman


title: The effect of genetic background on cognitive and pathological traits: AD-BXD

status: Public on Dec 14 2018

summary: Female C57BL/6J mice hemizygous for the 5XFAD transgene  (MMRRC Stock No #34848-JAX) were bred to males from BXD strains, which do not carry the 5XFAD transgene. The resulting F1 progeny were monitored throughout their lifespan to evaluate the effect of genetic background on cognitive and pathological traits. All of the mice were fear conditioned and sacrificed within 30 minutes of testing. On the sample records, the characteristics: age field provides the age at which fear conditioning, sacrifice, and tissue collection occurred. Samples here come from various AD-BXD lines and their non-transgenic (Ntg) littermate counterparts at either 6 or 14 months of age.

overall_design: 133 samples, 64 Ntg and 69 AD. For final by-strain analysis, samples were averaged into strain/age/genotype/sex groups (For example, all D2 6mo 5XFAD males were averaged for final by-strain analysis)

first: Ryan

last: Richholt


title: Single cell RNA-seq profiling of two bladder cancer specimen

status: Public on Sep 01 2019

first: Li

last: Wang

address: 1 Gustave L. Levy Pl

institute: Icahn school of medicine at Mount Sinai

summary: To explore the heterogeneity of stromal compartment of bladder cancer, we performed scRNAseq on two muscle-invasive bladder cancer specimens

overall_design:
After sorting into CD45-negative and CD45-positive cells, we collected CD45-negative cells for subsequent scRNAseq sequencing.
---------------------------------------------
Authors state "the raw data (fastq) is deposited to dbGAP".

first: Robert

middle: P

last: Sebra


title: DamC reveals principles of chromatin folding in vivo without crosslinking and ligation [damC]

first: Luca

last: Giorgetti

overall_design:
Mouse ESC lines #94.1_2.7 (carrying random insertions of 50x TetO arrays spanning approx. 2.7kb each) and #94.1_216_C3 (carrying different random insertions of the same 50x TetO cassette flanked by 3 CTCF sites faced outwards) were generated starting from an X0 clone of the PGKT2 line in Masui et al (Cell 145:447-458, 2011). The remaining X chromosome additionally carries the deletion of the Linx promoter within the X inactivation center (Nora et al., Nature 485:381-385, 2012). Random insertions were generated using the piggyBac transposon system. Both lines stably express rTetR-EGFP-Dam-ERT2 under the control of an ectopic Rosa26 promoter. Cells were cultured on gelatin-coated culture plates in Dulbecco Modified Eagle’s medium (Sigma) in the presence of 15% foetal calf serum (Eurobio Abcys), 100 µM β-mercaptoethanol, 20 U/ml leukemia inhibitory factor (Miltenyi Biotec, premium grade) and 250 µg/mL hygromycin in 8% CO2 at 37°C.To induce nuclear translocation of the rTetR-Dam fusion protein to the nuclei, mESC were trypsinized and directly seeded in culture medium containing 4-hydroxy-tamoxifen (4-OHT) at various concentration as indicated in the sample titles. Binding of the Dam fusion protein to the TetO arrays was induced by simultaneously adding 2.5 μg/ml doxycycline (Dox). After 18 hours, 3x106 cells were harvested using trypsin. Genomic DNA was extracted using the Qiagen blood and tissue kit adding RNaseA in step 1. Genomic DNA was eluted in 80ul ddH2O. DNA concentration was measured using the Qbit DNA Broad Range kit. Genomic DNA (100ng input) was treated with Shrimp Alkaline Phosphatase treatment (NEB, 1U), followed by DpnI digestion (ThermoFisher Scientific, 10U), A-tailing (0.6mM final dATP, 5U Klenow exo-, ThermoFisher Scientific), and UMI adapters ligation (30U T4 DNA ligase, PEG4000, ThermoFisher Scientific) performed within the same tube and buffer (Tango 1X, ThermoFisher Scientific) by heat inactivating each enzymatic step followed by adjustment with the reagents required for the next step. UMI adapters were made by annealing the following oligos: 5’-AATGATACGGCGACCACCGAGATCTACACNNNNNNNNACACTCTTTCCCTACACGACGCTCTTCCGATC*T  and 5’-pGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT. Ligation reactions were treated with Exonuclease I (20U, ThermoFisher Scientific ) then purified using AMPureXP beads (1:0.8 ratio, Agencourt) and the second sequencing adapter   (5’ TGACTGGAGTTCAGACGTGTGCTCTTCCGATCTNNNNN*N 3’, IDT) was tagged using heat denaturation and second strand synthesis (5U T4 DNA Polymerase, ThermoFisher Scientific). The tagging reaction was purified using AMPure XP beads (1:1 ratio) followed by a final library amplification (10 cycles) using 1U of Phusion polymerase, 2μl 10 μM DAM_UMIindex_PCR (5’ AATGATACGGCGACCACCGAGATCTACA*C  3’), and 2μl 10μM NEBnext indexed primer (NEB). Final libraries were purified AMPure XP beads (1:1 ratio) and QCed using Bioanalyser and Qbit. DamC libraries were sequenced on a NextSeq500 (75 cycles single-end) with a custom sequencing protocol (dark cycles at the start of read1 to "skip" the remaining DpnI site TC sequence). Samples index were determined using index1 read, and UMI sequence using index2 read. UMIs are contained in the readname of each read in each fastq file

Please note that processed data was generated from multiple samples (as indicated in the corresponding sample description field and in the README.txt) and is linked as Series supplementary file.

first: Josef

last: Redolfi

first: Yinxiu

last: Zhan

first: Christian

last: Valdes

first: Mariya

last: Kryzhanovska

first: Isabel

last: Guerreiro

first: Vytausas

last: Iesmantavicius

first: Guido

last: Tiana

first: Jop

first: Sebastien

first: Wouter


title: Human skeletal muscle transcriptome

status: Public on Jul 31 2018

city: Stirling

first: James

last: Timmons

address: Bridge of Allan

institute: Augur Precision Medicine LTD

summary: The annotation of the Affymetrix HTA 2.0 array was updated to optimise the detection of both coding and non-coding RNA in human skeletal muscle biopsy samples by removing invalid and low signal-high-variance probes. A transcript level CDF specific to skeletal muscle is provided to use within the standard aroma.affymetrix pipeline.

overall_design: 527 human muscle profiles from men and women aged 18 to 95yrs. There are three age groupings: young adult (18-39), middle-aged adult (40-60), older adult (61+).


title: Transcriptome changes during inducible gametocytogenesis in Plasmodium berghei parasites

status: Public on Jun 30 2018

city: Glasgow

first: Katarzyna

middle: Kinga

last: Modrzynska

state: Glasgow (City of)

address: B627 Sir Graeme Davies Building, 120 University Place

institute: Wellcome Trust Centre for Molecular Parasitology

summary: During the malaria infection, Plasmodium parasites invade the host’s red blood cells where they can differentiate into two different life forms. The majority will replicate asexually and infect new erythrocytes. A small percentage, however, will transform into gametocytes – a specialized sexual stage able to survive and develop when taken up by Anopheles mosquito. As the gametocytes ensure the parasite’s transmission to a new host, their generation is an attractive target for new antimalarial interventions. The molecular mechanisms controlling gametocytogenesis, however, remain largely unknown due to the technical challenges: the early gametocytes are morphologically indistinguishable from asexual parasites and present in very low numbers during the infection.     Recently, AP2-G  - a transcription factor from an apicomplexa-specific apiAP2 family – was described as indispensable for gametocyte commitment in both human malaria parasite Plasmodium falciparum and rodent malaria model Plasmodium berghei. Therefore, we have decided to test whether the overexpression of this factor alone could increase gametocyte production and enable the investigation of uncharacterised, earliest stages of gametocyte development. To this end, we have engineered PBGAMi  - a Plasmodium berghei line, in which all parasites were ap2-g deficient by default but able to overexpress it when induced with rapamycin. While the control parasites (PBGAMi R-), as expected, differentiated into asexual forms (schizonts) only, almost all rapamycin-treated parasites (PBGAMi R+) transformed into gametocytes. We used the generated line to perform RNA-seq analysis of the R- and R+ populations at different time points of their development and identify the changes arising between them, mapping the sequence of events leading to the formation of gametocytes.

overall_design: A synchronised population of Plasmodium berghei PBGAMi parasites was either induced with rapamycin (which caused the ap2-g overexpression and gametocyte conversion) or allowed to develop asexually. Parasites from both groups were harvested at different time points post induction and RNA-seq was used to analyse their transcriptome

first: Andrew

last: Waters

first: Oliver

last: Billker


title: mRNA-seq analysis of hypertrophic zone of wild type (WT) and Adamts17-/- growth plates

status: Public on Mar 01 2019

city: Tokyo

first: Takeshi

last: Oichi

address: 7-3-1, Bunkyo-ku, Hongo

country: Japan

institute: The University of Tokyo

summary: We compared gene expression profiles of hypertrophic zone of WT and Adamts17-/- growth plates through laser microdissection (LMD) using adhesive tape, linear amplification of mRNA, and mRNA-seq analysis.

overall_design: gene expression profiles of hypertrohic zone obtained from proximal tibia growth plates of 3 WT and Adamts17-/- littermates

first: Taku

last: Saito


title: MicroRNA expression profile in human hepatocellular carcinoma

status: Public on Jun 23 2018

city: Shantou

first: Jincheng

last: Guo

address: Xinling Road

department: Medical collage

country: China

institute: Shantou University

type: Non-coding RNA profiling by high throughput sequencing

summary: We used Affymetrix microarray profiling to analyze microRNA expression patterns in HCC patients.

overall_design: For microRNAs expression profiling,  64 tumor patients were carried out on GeneChip™ miRNA 2.0 Array (Affymetrix, CA) according to the manufacturer's protocol.

first: JIncheng

first: Yingnan

last: Ye

first: Yi

last: Zhao

first: Jinpu

last: Yu


title: Comparison of RNA expression between Drosophila Lactate Dehydrogenase mutants and controls

city: Bloomington

first: Jason

last: Tennessen

state: IN

address: 1001 E. Third St

department: Department of Biology

institute: Indiana University

summary: We analyzed RNA levels in Drosophila Lactate Dehydrogenase mutants and precise excision controls during mid-L2 development.

overall_design: Examination of RNA levels in two genotypes with each sample containing 25 mid-L2 larvae

first: Hongde

last: Li


title: Expression data from B6-sst1S and B6(WT) mouse bone-marrow derived macrophages

status: Public on May 30 2018

city: Boston

first: Boston University

last: Microarray and Sequencing Resource

address: 72 East Concord Street, E631

department: Microarray and Sequencing Resource

institute: Boston University

summary:
Using forward genetics in mice, we have identified a novel host resistance gene Ipr1, which mediates resistance to tuberculosis. We have shown that Ipr1-mediated pathway is regulated by IFNg in macrophages and plays an important role in resistance to several intracellular bacterial pathogens: Listeria, Francisella and Chlamydia. Functional studies of sst1 locus revealed that it plays a novel role in integrating signals generated by intracellular pathogens or viruses with mechanisms regulating activation, gene expression and cell death of host cell. Thus performing RNA-seq from sst1R and sst1S macrophages (BMDM) will help to uncover the global repertoire of events regulated by the sst1 locus and lead to the discovery of novel regulatory pathways necessary for host defense, thus providing a platform for developing novel therapeutics to improve host recovery after infections.
We used microarrays to detail the global programme of gene expression mediated by the cytokine TNFα and identified upregulation of several important regulatory genes important for the susceptible phenotype.

overall_design: Bone marrow derived macrophages from B6-sst1S and B6(WT)  treated with 10ng/ml TNFα for 18hrs were selected for RNA extraction and hybridization on Affymetrix microarrays.

first: Bidisha

last: Bhattacharya

first: Igor

last: Kramnik


title: Unexpected similarities between C9ORF72 and sporadic forms of ALS/FTD suggest a common disease mechanism

status: Public on Jul 13 2018

city: New York

first: Delphine

last: Fagegaltier

address: 101 Ave of the Americas

institute: New York Genome Center

summary: Amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD) represent two ends of a disease spectrum with shared clinical, genetic and pathological features. These include near ubiquitous pathological inclusions of the RNA binding protein (RBP) TDP-43, and often the presence of a GGGGCC expansion in the C9ORF72 (C9) gene. Here we show unexpectedly that the signature of hnRNP H sequestration and altered splicing of target transcripts we identified in C9ALS patients (Conlon et al. 2016) also occurs in fully half of 50 post-mortem sporadic, non-C9 ALS/FTD post-mortem brains. Furthermore, and equally surprisingly, these “like-C9” brains also contained correspondingly high amounts of insoluble TDP-43, as well as several other disease-related RBPs, and this correlates with widespread global splicing defects. Finally, we show that the like-C9 sporadic patients, like actual C9ALS patients, were much more likely to have developed FTD. We propose that these unexpected links between C9 and sporadic ALS/FTD define a common mechanism in this disease spectrum.

overall_design:
Differential splicing analysis of Amyotrophic Lateral Sclerosis  (ALS) and Control samples
contributor: NYGC ALS Consortium
contributor:  The Target ALS Human Postmortem Tissue Core

first: Hemali

last: Phatnani

first: Phaedra

last: Agius


title: Comprehensive Epigenetic Landscape of Rheumatoid Arthritis Fibroblast-like Synoviocytes

status: Public on Apr 30 2018

first: Gary

middle: S

last: Firestein

state: California

address: 9500 Gilman Dr

institute: UCSD

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

overall_design: Refer to individual Series


title: Comprehensive Epigenetic Landscape of Rheumatoid Arthritis Fibroblast-like Synoviocytes [ATAC-seq]

summary: Epigenetics is important in the pathogenesis of immune-mediated diseases like rheumatoid arthritis (RA). Here we show the first complete epigenomic characterization of RA fibroblast-like synoviocytes (FLS) by profiling histone modifications (H3K27ac, H3K4me1, H3K4me3, H3K36me3, H3K27me3, H3K9me3), open chromatin, RNA expression and whole genome DNA methylation. To address the complex multidimensional relationship and reveal the epigenetic regulation of RA, we perform integrative analyses using a novel unbiased method to identify genomic regions with similar profiles. Epigenomically similar regions exist in RA cells are particularly associated with active enhancers and promoters as well as specific transcription factor binding motifs. Differentially marked genes are enriched for immunological and unexpected pathways, with “Huntington's Disease Signaling” identified as particularly prominent. We validate the relevance of this pathway to RA by showing that Huntingtin-interacting protein-1 regulates FLS invasion into matrix. This work establishes a high-resolution epigenomic landscape of RA and demonstrates the potential for integrative analyses to identify unanticipated therapeutic targets.

overall_design:
Establishing a high-resolution epigenomic landscape of RA FLS by integrating diverse epigenomic data. This series contains ATAC-seq data for Fibroblast-like synoviocytes from RA and OA patients.

The submitter declares that the raw data will be made available in dbGaP (phs001615.v1.p1) due to patient privacy concerns.

first: Rizi

last: Ai

first: Teresina

last: Laragione

first: Deepa

last: Hammaker

first: David

last: Boyle

first: Andre

last: Wildberg

first: Keisuke

last: Maeshima

first: Emanuele

last: Palescandolo

first: Vinod

last: Krishna

last: Pocalyko

first: John

middle: W

last: Whitaker

first: Yuchen

last: Bai

first: Sunil

last: Nagpal

first: Kurtis

last: Bachman

first: Richard

middle: I

last: Ainsworth

first: Mengchi

last: Wang

first: Bo

last: Ding

first: Percio

last: Gulko

first: Wei


title: Comprehensive Epigenetic Landscape of Rheumatoid Arthritis Fibroblast-like Synoviocytes [RNA-seq]

first: Gary

last: Firestein

overall_design:
Establishing a high-resolution epigenomic landscape of RA FLS by integrating diverse epigenomic data. This series contains RNA-seq of Fibroblast-like synoviocytes from RA or OA patients.

The submitter declares that the raw data will be made available in dbGaP (phs001615.v1.p1) due to patient privacy concerns.

first: Rizi

last: Ai


title: Comprehensive Epigenetic Landscape of Rheumatoid Arthritis Fibroblast-like Synoviocytes [WGBS]

overall_design:
Establishing a high-resolution epigenomic landscape of RA FLS by integrating diverse epigenomic data. This series includes WGBS data on Fibroblast-like synoviocytes from RA or OA patients.

The submitter declares that the raw data will be made available in dbGaP (phs001615.v1.p1) due to patient privacy concerns.

first: Teresina

last: Laragione

first: Deepa

last: Hammaker


title: Comprehensive Epigenetic Landscape of Rheumatoid Arthritis Fibroblast-like Synoviocytes [ChIP-seq]

overall_design:
Establishing a high-resolution epigenomic landscape of RA FLS by integrating diverse epigenomic data. This series contains ChIP-seq data for H3K27ac, H3K4me1, H3K4me3, H3K36me3, H3K27me3, H3K9me3 on  fibroblast-like synoviocytes from RA or OA patients.

The submitter declares that the raw data will be made available in dbGaP (phs001615.v1.p1) due to patient privacy concerns.

first: David

last: Boyle

first: Andre

last: Wildberg


title: DamC reveals principles of chromatin folding in vivo without crosslinking and ligation

status: Public on May 15 2019

first: Luca

last: Giorgetti


title: Deep Transcriptomic Profiling Of M1 Macrophages Lacking Trpc3

status: Public on Dec 30 2017

city: Toledo

first: Guillermo

last: Vazquez

address: 3000 Arlington Ave

department: Physiology and Pharmacology

institute: University of Toledo College of Medicine and Life Sciences

summary: Previous studies from our laboratory using mice with macrophage-specific loss of Trpc3 function revealed a significant, selective effect of Trpc3 in the biology of M1, or inflammatory macrophages. Whereas the activation of some components of the unfolded protein response and the pro-apoptotic mediators CAMKII and STAT1 was found impaired in the Trpc3-deficient M1 cells, gathering insight on all of the molecular signatures within macrophages that might be affected by Trpc3 requires more than a simple query for known candidate molecules. In the present study we conducted RNA-seq analysis to interrogate the transcriptome of M1 macrophages derived from mice with macrophage-specific loss of TRPC3 function and their littermate controls. Gene ontology analysis revealed enrichment in a majority of processes associated to cellular movement and lipid signaling, whereas the enriched KEGG pathways included networks for calcium signaling, cell adhesion molecules, cell cycle and focal adhesion, and salivary secretion, among others. This is the first deep transcriptomic analysis of macrophages in the context of TRPC3 deficiency and the data presented thus constitutes a unique resource for further exploring novel functions of TRPC3 in macrophage biology.

overall_design: RNA sequencing of bone marrow derived M1 macrophages from control and Trpc3-deficient mice RNA samples in triplicate, using Illumina.

first: Kumarasamy

last: Sivarajan

first: Bina

last: Joe

first: Lutz

last: Birnbaumer


title: Differential Methylation during MERS-CoV and H5N1 infection

status: Public on Jan 16 2018

city: Chapel Hill

first: Alexandra

last: Schaefer

state: NC

address: 3109 MHRC

institute: University of North Carolina at Chapel Hill

summary: MERS-CoV and H5N1 infection

overall_design: Examination of  differential methylation status in 1 cell type under 2 infection conditions.

first: Ralph

last: Baric


title: Lung cell transcriptome response to a wild type Mers-CoV

status: Public on Dec 29 2017

city: Richland

first: Natalie

last: Heller

address: 902 Battelle Blvd.

institute: PNNL

summary: The purpose is to obtain samples for mRNA analysis in mouse lung cells infected with wild type Mers-CoV.

overall_design: Mouse lung cells were infected with a multiplicity of infection of 3 PFU per cell.  Infected samples were collected in triplet time-matched mocks were collected in triplicate in parallel with infected samples. Time points: 2, 4, and 7 day post-infection. MERSCOV004.0P references the write up of the experimental procedure.

first: Amy

last: Sims

first: Katrina

middle: M

last: Waters

first: Amie

middle: J

last: Eisfeld

first: Yoshihiro

last: Kawaoka


title: Gene expression profile in human hepatocellular carcinoma

first: Jincheng

last: Guo

summary: We used Affymetrix microarray profiling to analyze gene expression patterns in HCC patients.

overall_design: For gene expression profiling, tumors tissues were profiled separately using a single channel array platform. 64 tumor patients were carried out on Affymetrix GeneChip HG-U133A 2.0 arrays (Affymetrix, Santa Clara, CA) according to the manufacturer's protocol. The fluorescent intensities were determined with an Affymetrix GeneChip Scanner 3000, controlled by GCOS Affymetrix software.

first: JIncheng

first: Yingnan

last: Ye

first: Yi

last: Zhao

first: Jinpu

last: Yu


title: Differential expression profile of mRNAs and lncRNAs regulated by HNF1α in hepatocellular carcinoma cells HuH7

status: Public on Aug 26 2017

city: Shanghai

first: xin

last: zhang

address: 415 Fengyang Road

institute: Changzheng hospital

type:
Non-coding RNA profiling by array
Expression profiling by array

summary: To determine the role of HNF1α on long noncoding RNAs (lncRNAs) and the overall mechanisms in hepatocellular carcinoma, we analyzed the expression profiles of lncRNAs and mRNAs in huh7 cells with overexpression or knockdown of HNF1α. Expression profile showed that there were 339 mRNAs and 22 intergenic lncRNAs positively regulated by HNF1α for more than 2 times. The up-regulated genes separated samples by comparing lenti-HNF1α group with lenti-ctrl group, with overlap the down-regulated genes separated in HNF1α knockdown groups were identified as the genes positived regulated by HNF1α. Expression of seven genes from these 22 intergenic lncRNAs was quantified in the same RNA samples by real-time PCR, confirming the regulatory effect of HNF1α on lncRNAs as well as the microarray analysis pattern.

overall_design: HuH7 cells were infected with lentivirus which carrying HNF1α or shHNF1α with their control group, respectively. The total RNA of four groups (lenti-ctrl, lenti-HNF1α, lenti-shNC, lenti-shHNF1α) was measured by microarray at 6 days after HuH7 cells infected with lentivirus. And then we analyzed the mRNAs expression profile and lncRNAs expression profile, respectively.

first: Chenhong

last: Ding

first: Xin

last: Zhang

first: Weifen

last: Xie


title: Histone Modification during MERS-CoV and H5N1 infection

summary: MERS-CoV and H5N1 infection

overall_design: Examination of 2 different histone modifications in 1 cell type under 2 infection conditions.


title: Whole blood DNA methylation profiles in participants of the Environmental Risk (E-Risk) Longitudinal Twin Study at age 18.

status: Public on Jan 15 2018

city: Exeter

first: Jonathan

last: Mill

address: RILD Building, RD&E Hospital

department: Medical School

institute: University of Exeter

summary: Genome-wide patterns of DNA methylation were quantified using the Illumina Infinium HumanMethylation450 BeadChip (“450K array”) in DNA samples isolated from whole blood collected at age 18 from members of the Environmental Risk (E-Risk) Longitudinal Twin Study.

overall_design: This data include 1658 samples that passed our QC pipeline, including 1468 participants who were members of complete twin pairs (430 MZ pairs and 304 DZ pairs) and 190 participants whose co-twin did not have complete data (e.g., did not provide blood, did not pass QC).

first: E

last: Hannon

first: J

first: K

last: Sugden

first: A

last: Caspi

first: L

last: Arsenault


title: Primary human lung microvascular endothelial cells treated with universal interferon alpha beta or interferon gamma

status: Public on Dec 27 2017

first: Natalie

last: Heller

summary: The purpose is to obtain samples for mRNA analysis in primary human lung microvascular endothelial cells treated with universal interferon alpha beta or interferon gamma.

overall_design: Human lung microvascular endothelial cells were treated with a multiplicity of 4 PFU per cell.  Treated samples were collected in triplet; time-matched mocks were collected in triplet in parallel with treated samples.  Time points: 3, 6, and 24hr post-treatment.  MERSCOV002.0P references the write up of the experimental procedure.

first: Ralph

last: Baric

first: Amy

last: Sims

first: Katrina

first: Amie


title: Primary human microvascular endothelial cell transcriptome response to wild type MERS-CoV (icMERS-CoV EMC2012), MMVE003

status: Public on Jun 27 2017

summary: The purpose is to obtain samples for mRNA analysis in primary human microvascular endothelial cells infected with wild type MERS-coronavirus (MERS-CoV) (icMERS).

overall_design: Human microvascular endothelial cells were infected with a multiplicity of infection of 5 PFU per cell. Infected samples were collected in quintuplet; time-matched mocks were collected in quintuplet in parallel with infected samples. Time points: 0, 12, 24, 36, and 48 h post-infection. MERSCOV002.0P references the write up of the experimental procedure.

last: Waters

last: Eisfeld

first: Yoshihiro

last: Kawaoka


title: HUH VP30 cells with and without interferon α and β treatment

status: Public on Nov 13 2017

summary: The purpose is to obtain HUH VP30 samples for mRNA analysis with and with out interferon α and β treatment.   Huh VP30 cells have been stably transfected with the Ebola VP30 gene, enabling replication of VP30-deficient Ebola virus. PubMed ID 18212124  and 19211761.

overall_design: Treatments were initiated by replacing culture medium (containing 10% FBS) with fresh medium containing 250 U/ml of human interferon α and 250 U/ml of human interferon β(PBL Biosciences) with a multiplicity of 5 PFU per cell.  Mock-treated cells were given normal culture medium only.  Mock and treated cells were incubated at 37°C until sample collection time points of 6, 12, and 18 hours.  MERSCOV003.0P references the write up of the experimental procedure.


title: Role of FGFR1 in neuronal devlopment

status: Public on Nov 17 2017

city: Buffalo

first: Michal

last: Stachowiak

state: NY

address: 3435 Main Street

department: Pathology and Anathomical Sciences

institute: State University of New York at Buffalo

summary: Purpose: The goal was to study the effects of nFGFR1 on neuronal progenitor cells, by analyzing different effects of FGFR1 mutants through RNA-seq.

overall_design: NPCs were transfected with either Beta-Gal, FGFR1(SP-/NLS+) or FGFR1(SP-/NLS+)(TK-)

middle: K


title: Genome-wide Mapping and Analysis of Aryl Hydrocarbon Receptor (AHR) and Aryl Hydrocarbon Receptor Repressor (AHRR) by ChIP-Seq

status: Public on Jul 08 2017

city: Oslo

first: Jason

last: Matthews

address: Sognsvannsveien 9

department: Nutrition

country: Norway

institute: University of Oslo

summary: In this study, we compared the genome-wide binding profiles of AHR and AHRR in MCF-7 human breast cancer cells treated for 24 h with TCDD using chromatin immunoprecipitation followed by next generation sequencing (ChIP-Seq). Overall, this study reveals that AHR and AHRR exhibit similar but also distinct genome-wide binding profiles, supporting the notion that AHRR is a context- and gene-specific repressor of AHR activity.

overall_design: MCF7 treated with DMSO (vehicle) or TCDD for 24h; ChIP-seq in triplicates using AHR- and AHRR-specific antibodies with Illumina HiSeq 2500

first: Sunny

middle: Y

last: Yang

first: Shaimaa

last: Ahmed


title: RNA sequencing analysis of  gene expression in rat hippocampus exposed to chronic stress and albiforin treatment

status: Public on Jan 20 2018

city: San Diego

first: Kefeng

last: Li

institute: University of California, San Diego

summary: We performed high-throughput profiling of gene expression in rat hippocampus in response to chronic unpredictable mild stress (CUMS) and albiflorin treatment.  Total 415 differentially expressed genes (DEGs) were identified in rat hippocampus in response to albiflorin treatment compared with CUMS rats treated with saline (CUMS-Sal). We conducted the integrated metabolomics and transcriptomics analysis and found the correction of 16 biochemical pathways by albiflorin such as sphingolipids, phospholipids, tryptophan metabolism, fatty acid oxidation, and purine and pyrimidine metabolism. Our study provided deep insights into the understanding of the molecular mechanisms underlying the rapid antidepressant actions of albiflorin.

overall_design: Rats were exposed to chronic unpredictable mild stress (CUMS) for 5-weeks. At the last week of the exposure, rats were treated with saline, fluoxetine (7 mg/kg/d) or albiflorin (7 mg/kg/d) for 7 days.  Total 4 groups were set up:  rats without CUMS exposure and with saline treatment (Control-Sal), rats received CUMS and saline (CUMS-Sal), rats received CUMS and fluoxetine (CUMS-Flx) and rats received CUMS and albiflorin (CUMS-Alb). Three replicates were used for each group.

first: Yuan-Lu

last: Cui

first: Kuo

last: Yan


title: Primary human lung fibroblast cells transcriptome response to interferon αβ or interferon γ

summary: To obtain samples for RNA analysis following treatment of primary human lung fibroblasts (FB)) with universal interferon alpha beta or interferon gamma.

overall_design: Human lung fibroblasts cells were infected with a multiplicity of 4 PFU per cell.  Infected samples were collected in triplet; time-matched mocks were collected in triplet in parallel with infected samples.  Time points: 3, 6, and 24 hrs, post-infection.  MERSCOV003.0P references the write up of the experimental procedure.


title: Mouse lung tissue transcriptome response to H1N1 and mutants

status: Public on Apr 13 2017

summary: The purpose is to obtain samples for virus titration, transcriptome, bioplex and histopathology analysis of mouse lungs after etoposide treatment and infection with a pandemic H1N1 influenza strain.

overall_design: Groups of 7-8 week-old C57BL/6J mice were treated with etoposide or vehicle by oral gavage one day before virus, wild-type A/Oklahoma/Vir09-1170038L3/2009(H1N1; 'OK/09'), infection, on day of infection, and all subsequent days post-infection.  Infections were done at 100,000 PFU/mouse for H1N1 strain.  Time points were 0, 3, and 6 days post infection.  There were 5 mice for all infection groups.  Lung samples were collected for virus load and transcriptional analysis.  Weight loss and animal survival were also monitored.

first: Allison

last: Thompson


title: Gene expression in HPAECs with ERG and FLI1 knockdown

status: Public on Jun 22 2017

first: Boston University

last: Microarray and Sequencing Resource

summary: ERG and FLI1 were silenced in HPAECs using siRNA for 48h.

overall_design: The goal of the study was to identify groups of genes regulated by ERG and FLI1 transcription factors.

first: Agnieszka

last: Grzegorzewska

first: Rong

last: Han

first: Maria

last: Trojanowska


title: Genome-wide transcriptome profiles in Control and Schizophrenia hiPSC-dervied NPC [RNA-seq]

status: Public on Jun 01 2017

summary: We Report the genome-wide RNA expression levels in control and schizophrenia hiPSC dervied NPC treated with neuronal media for 2 days.  In total about 15,000 gene expression were detected in all samples, of which 1349 were dysregualted.

overall_design: Examination, identification and comparision of mRNA expression profliles in control and schizophrenia npc


title: Next-generation sequencing of control and schizophrenia hiPSC derived NPC

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

overall_design: Refer to individual Series


title: Primary human airway epithelial cell transcriptome response to a wild type Mers-CoV (icMERS-CoV EMC2012), MHAE003

first: Natalie

last: Heller

summary: The purpose is to obtain samples for mRNA analysis in primary human airway epithelial cells infected with wild type Mers-CoV (icMERS).

overall_design: Human airway epithelial cells were infected with a multiplicity of infection of 5 PFU per cell. Infected samples were collected in quintuplet; time-matched mocks were collected in quintuplet in parallel with infected samples. Time points: 0, 12, 24, 36, and 48 h post-infection. MERSCOV004.0P references the write up of the experimental procedure.

first: Ralph

last: Baric


title: Gene expression of mouse brain and mouse microglia in NRROS WT and NRROS KO animals

status: Public on Apr 07 2017

city: South San Francisco

first: Mark

last: McCreary

address: 1 DNA Way, MS 93

department: Bioinformatics

institute: Genentech

summary:
Mice deficient in NRROS exhibit neurological phenotype similar to ALS. Our previous work showed that in phagocytes, NRROS regulates the degradation of Nox2, the enzymatic component of the NADPH oxidase that generates reactive oxygen species. NRROS is expressed in phagocytes, including macrophages, neutrophils and microglia but not neurons.

Keywords: Expression profiling by high throughput sequencing

overall_design: To help understand the mechanism of the neurological phenotype caused by loss of NRROS, we looked at NRROS WT (n=5) vs. NRROS KO (n=5) in brains, and NRROS WT (n=5) vs. NRROS KO (n=5) in microglia tissue. Samples were sequenced by the Illumina HiSeq 2500 Sequencing System.

first: Kit

last: Wong

middle: A

last: Hackney

first: Zora

last: Modrusan

first: Connie

last: Ha

first: Jeremy

last: Stinson

first: Joseph

last: Guillory

first: Wenjun

last: Ouyang


title: Primary human fibroblasts transcriptome response to a wild type Mers-CoV (icMERS-CoV), MFB003

summary: The purpose is to obtain samples for mRNA analysis in primary human fibroblasts infected with wild type Mers-CoV (icMERS).

overall_design: Human fibroblasts were infected with a multiplicity of infection of 5 PFU per cell. Infected samples were collected in quintuplet; time-matched mocks were collected in quintuplet in parallel with infected samples. Time points: 0, 12, 24, 36, and 48 h post-infection. MERSCOV003.0P references the write up of the experimental procedure.

first: Amy

last: Sims

first: Katrina

last: Waters

first: Amie

last: Eisfeld

first: Yoshihiro

last: Kawaoka


title: Gene expression of mouse brain, mouse microglia, and mouse perivascular macrophages (pvm) in NRROS WT and NRROS KO animals

status: Public on Apr 06 2017

first: Jason


title: Role of NRROS in microglia and perivascular macrophages in the brain

summary: Mice deficient in NRROS exhibit neurological phenotype similar to ALS. Our previous work showed that in phagocytes, NRROS regulates the degradation of Nox2, the enzymatic component of the NADPH oxidase that generates reactive oxygen species. NRROS is expressed in phagocytes, including macrophages, neutrophils and microglia but not neurons. Previous results on RNA-sequencing from WT and NRRO KO CD11b+ population (NGS601) identified perivascular macrophage (pvm)-like expression profile in NRROS KO cells. FACS data revealed a loss of microglia and concomitant gain of pvm-like cells in the brains of NRROS KO mice.

overall_design: To further these findings, we would like to directly compare gene expression between WT microglia (n = 3), WT pvm (n = 3) and NRROS KO pvm (n = 3).

last: Guilory


title: Primary human Huh (human hepatocyte) cells transcriptome response to wild type Ebola Zaire (delta-VP30), EHUH003 [miRNA]

status: Public on Feb 17 2017

summary: The purpose is to obtain samples for microRNA analysis in Huh (human hepatocyte) cells infected with wild type Ebola Zaire (delta-VP30).

overall_design: Huh (human hepatocyte) cells were infected with a multiplicity of infection of 3 PFU per cell.  Infected samples were collected in triplet; time-matched mocks were collected in triplet in parallel with infected samples. Time points: 8h, 24h, and 48h post-infection. references the write up of the experimental procedure.

first: Allison

last: Thompson


title: Human liver Huh cell transcriptome response to a Wild-type ΔVP30 Ebola virus, EHUH003 [mRNA]

status: Public on Feb 13 2017

summary: The purpose is to obtain samples for mRNA analysis in human liver Huh cells using the following viruses obtained by reverse genetics: Zaire Ebola virus wild-type (WT) in the ΔVP30 background (wild).

overall_design: Human liver Huh cells were infected with  a Wild-type ΔVP30 Ebola virus. The Huh7.0 VP30 cells were on split 5 for this experiment. Infected samples were collected in quintuplet; time-matched mocks were collected in quintuplet in parallel with infected samples. Two time courses were performed to generate samples for this experiment (the second set was started within 24 h of the first set). The time courses were 0h, 8h, 24h, 48h, and 72h.

first: Pete

last: Halfmann


title: Palbociclib, PD0325901 and combination treatment induced gene expression in DLD1

status: Public on Nov 02 2016

city: singapore

first: Qiang

last: Yu

address: 60 Biopolis Street

country: Singapore

institute: Genome Institute of Singapore

summary: Analysis of transcriptional changes after treatment with Palbociclib, PD0325901 or combined treatment in DLD1 (colorectal cancer cell line). The aim of the study was to identify differentially regulated genes after the various treatment, particularly on the downregulated genes as these drugs are inhibitors of the CDK4/6 and MEK pathways and upon inhibition, should lead to the downregulation of pro-tumorigenic genes. Results provide important information on which transcription factors or genes that will be targeted by the inhibition of these 2 pathways

overall_design: Total RNA obtained from untreated, Palbociclib-, PD0325901- or combination- treated DLD1 at 24hour, 48hour and 72hour time points.

first: Michelle

last: Pek


title: 30 paired normal and tumor colorectal samples

summary: Analysis of differentially regulated genes in patients normal and colorectal tumor samples. The aim of this study was to identify genes that were differentially up- or down-regulated in the tumor samples as compared to the normal colon tissue

overall_design: Total RNA obtained from patients' normal and tumor tissue. Please note that the patient tumor samples as these were obtained from the Singapore tissue bank and no further information were provided.


title: Primary human microvascular endothelial cell transcriptome response to wild type Mers-CoV (icMERS-CoV EMC2012), MHAE002

status: Public on Oct 04 2016

first: Natalie

last: Heller

overall_design: Human airway epithelial cells were infected with a multiplicity of infection of 5 PFU per cell.  Infected samples were collected in quintuplet; time-matched mocks were collected in quintuplet in parallel with infected samples. Time points: 0, 12, 24, 36, and 48 h post-infection. MERSCOV004.0P references the write up of the experimental procedure.

first: Ralph

last: Baric


title: Primary human airway epithelial cell transcriptome response to wild type MERS-CoV (icMERS) [mRNA]

status: Public on Jun 21 2016

summary: The purpose is to obtain samples for mRNA analysis in primary human airway epithelial cells infected with wild type MERS-coronavirus (MERS-CoV) (icMERS).

first: Kelly

last: Stratton


title: Primary human fibroblasts transcriptome response to wild type Mers-CoV (icMERS-CoV EMC2012), MFB002

overall_design: Human fibroblasts were infected with a multiplicity of infection of 5 PFU per cell.  Infected samples were collected in quintuplet; time-matched mocks were collected in quintuplet in parallel with infected samples. Time points: 0, 12, 24, 36, and 48 h post-infection.  references the write up of the experimental procedure.


title: Primary human fibroblasts transcriptome response to wild type MERS-CoV  (icMERS-CoV EMC2012), MMVE002

summary: The purpose is to obtain samples for mRNA analysis in primary human fibroblasts infected with wild type  MERS-coronavirus (MERS-CoV) (icMERS).

overall_design: Human fibroblasts were infected with a multiplicity of infection of 5 PFU per cell.  Infected samples were collected in quintuplet; time-matched mocks were collected in quintuplet in parallel with infected samples. Time points: 0, 12, 24, 36, and 48 h post-infection.  MERSCOV002.0P references the write up of the experimental procedure.


title: Transcriptomic changes in the crown (stem base) of barley (Hordeum vulgare L. cv. Golden Promise) during crown-root initiation and development

status: Public on Nov 01 2016

city: Olomouc

first: Veronique

last: Bergougnoux

address: Slechtitelu 27

department: Molecular Biology

country: Czech Republic

institute: CRH/UPOL

summary:
Purpose: The goal of this study was to investigate the mechanisms involved in the initiation and development of crown-roots (CRs) in barley and to estimate the role of cytokinins (CKs) in this process.

Method: stranded libraries were obtained from RNA extracted from the stem base of 1 day-after-germination (DAG) and 10DAG-seedlings of wild-type (WT) and AtCKX-overexpressing barley lines (OE-CKX). OE-CKX lines have a reduced content of endogenous CKs and are characterized by a higher number of CRs. Libraries were deep sequenced on Illumina HighSeq platform. Each sample was investigated in three independent biological replicates.

Results: Using a data analysis workflow optimized for barley, we identified more than 4000 transcripts differentially expressed in the stem base of 1DAG and 10DAG-seedlings. Expression as determined by RNA-seq was validated by real-time PCR. Our data were compared to the transcriptomic profiling obtained from rice and we were able to identify genes potentially involved in the initiation/development of CRs in barley. Also the use of the transgenic line with altered endogenous CK content allowed us to conclude about the role of CKs in the process.

Conclusions: Our study represents the first analysis aiming to understand the initiation and development of CRs in barley.

overall_design:
mRNA profiles of stem base of 1 day-after-germination (DAG) and 10DAG seedling were generated by deep sequencing, in triplicate, using Illumina HighSeq
the analysis was performed on wild-type (WT) as well as on AtCKX1-overexpressing lines, accumulating lower amount of cytokinins

first: Thu

last: Nguyen

first: Filip

last: Zavadil Kokáš

first: Jérémy

last: Lavarenne

first: Pascal

last: Gantet

first: Véronique


title: Human U937 cell transcriptome response to Zaire Ebola virus wild-type in the ΔVP30 background and Δmucin virus [mRNA]

status: Public on May 19 2016

summary: The purpose is to obtain samples for mRNA analysis in human U937 cells infected with Zaire Ebola virus wild-type in the ΔVP30 background and Δmucin virus.

overall_design: Human U937 cells (monocyte-like) expressing the Ebola VP30 protein were infected with Zaire Ebola virus wild-type (wild) in the ΔVP30 background and Δmucin virus (encodes a GP lacking the mucin domain) (mucin) in the Ebola ΔVP30 background. Infected samples were collected in quintuplet; time-matched mocks were collected in quintuplet in parallel with infected samples. Time points: 0, 8, 18, and 30 h post-infection.

first: Katrina


title: Primary human airway epithelial cell transcriptome response to wild type MERS-CoV (icMERS) [miRNA]

status: Public on Jun 09 2016

summary: The purpose is to obtain samples for microRNA analysis in primary human airway epithelial cells infected with wild type MERS-coronavirus (MERS-CoV) (icMERS).

overall_design: Human airway epithelial cells were infected with a multiplicity of infection of 5 PFU per cell. Infected samples were collected in quintuplet; time-matched mocks were collected in quintuplet in parallel with infected samples. Time points: 12, 24, and 36 h post-infection. MERSCOV004.0P references the write up of the experimental procedure.

first: Amy

last: Sims

first: Amie


title: Colon cancer


title: Human Calu-3 cell transcriptome response to wild-type pandemic H1N1 (A/California/04/2009), natural isolate

status: Public on May 07 2016

summary: The purpose is to obtain samples for mRNA, miRNA, proteomics, lipidomics, metabolomics, and histopathology analysis in human Calu-3 cells infected with wild-type pandemic H1N1 (A/California/04/2009), natural isolate.

overall_design: Human Calu-3 cells were seeded at  1 x 10^6 cells per well on 6 well plates 2 days before infection. Cells were infected with an MOI of 3. After infection, wash and replace with 2 ml of DMEM-F12 + .3% BSA and 1 ug/ml TPCK-trypsin. Infected samples were collected in quintuplet; time-matched mocks were collected in quintuplet in parallel with infected samples. Time points: 12,  24, and 36 hr post-infection.

first: Kevin

last: Walters

last: Waters

first: Yoshihiro


title: Primary human fibroblast transcriptome (miRNA) response to wild type MERS-CoV (icMERS)

status: Public on Apr 28 2016

summary: The purpose is to obtain samples for microRNA analysis in primary human fibroblasts infected with wild type MERS-CoV (icMERS).

overall_design: Human primary fibroblasts were infected with a multiplicity of infection of 5 PFU per cell.  Infected samples were collected in quintuplet; time-matched mocks were collected in quintuplet in parallel with infected samples. Time points: 12, 24, and 36 h post-infection. MERSCOV003.0P references the write up of the experimental procedure.

first: Allison

last: Eisfeld

last: Kawaoka


title: Human liver Huh cell transcriptome (mRNA) response to a Wild-type ΔVP30 Ebola virus, Δmucin, and ssGP mutants

summary: The purpose is to obtain samples for mRNA analysis in human liver Huh cells using the following viruses obtained by reverse genetics: Zaire Ebola virus wild-type (WT) in the ΔVP30 background (wild), ΔsGP virus (eliminates expression of soluble glycoprotein [GP]) (ssGP), and Δmucin virus (encodes a GP lacking the mucin domain) (mucin).

overall_design: Human liver Huh cells were infected with  a Wild-type ΔVP30 Ebola virus, Δmucin, and ssGP mutants. The Huh7.0 VP30 cells were on split 5 for this experiment. Infected samples were collected in quintuplet; time-matched mocks were collected in quintuplet in parallel with infected samples. Two time courses were performed to generate samples for this experiment (the second set was started within 24 h of the first set). The time courses were 00, 8, and 18 hours, and 0, 24, and 48 hours.

first: Pete

last: Thompson


title: Human liver Huh cell transcriptome (miRNA) response to a Wild-type ΔVP30 Ebola virus, Δmucin, and ssGP mutants

summary: The purpose is to obtain samples for microRNA analysis in human liver Huh cells using the following viruses obtained by reverse genetics: Zaire Ebola virus wild-type (WT) in the ΔVP30 background (wild), ΔsGP virus (eliminates expression of soluble glycoprotein [GP]) (ssGP), and Δmucin virus (encodes a GP lacking the mucin domain) (mucin).

overall_design: Human liver Huh cells were infected with a Wild-type ΔVP30 Ebola virus, Δmucin, and ssGP mutants. The Huh7.0 VP30 cells were on split 5 for this experiment. Infected samples were collected in quintuplet; time-matched mocks were collected in quintuplet in parallel with infected samples. Two time courses were performed to generate samples for this experiment (the second set was started within 24 h of the first set). The time courses were 8 and 18 hours, and 24 and 48 hours.

last: Halfmann


title: Helminth-induced arginase-1 exacerbates lung inflammation and disease severity in tuberculosis.

status: Public on Apr 22 2016

first: Shabaana

last: Khader

state: MO

address: 660 South Euclid Avenue

department: Department of Molecular Microbiology

institute: Washington University in St.Louis

summary: We analyzed gene expression in CD4+ cells sorted from naïve or D30 Mycobacterium tuberculosis-infected mice and incubated  in vitro in the presence or absence of Schistosoma egg antigen. We found genes associated with Th1 function, T cell signaling, T cell costimulation and T cell activation were downregulated in SEA-treated cells, while expression of Th2 cytokines was below the threshold for detection.

overall_design: RNAseq results for 3 replicates for naïve or CD4+ T cells from M.tuberculosis-infected mice treated with or without Schistosoma egg antigen in vitro.

first: Leticia

last: Monin

first: Kristin

middle: L

last: Griffiths

first: Wing

last: Lam

first: Radha

last: Gopal

first: Dongwan

middle: D

last: Kang

first: Anuradha

last: Rajamanickam

first: Alfredo

last: Cruz-Lagunas

first: Joaquín

last: Zúñiga

first: Subash

last: Babu

first: Jay

last: Kolls

first: Makedonka

last: Mitreva

first: Bruce

last: Rosa

first: Rosalio

last: Ramos-Payan

first: Peter

last: Murray

first: Javier

last: Rangel-Moreno

first: Edward

last: Pearce


title: Primary human fibroblast transcriptome (mRNA) response to wild type MERS-CoV (icMERS)

status: Public on Apr 17 2016

first: Natalie

last: Heller

summary: The purpose is to obtain samples for mRNA analysis in primary human fibroblasts infected with wild type MERS-CoV (icMERS).

overall_design: Human primary fibroblasts were infected with a multiplicity of infection of 5 PFU per cell.  Infected samples were collected in quintuplet; time-matched mocks were collected in quintuplet in parallel with infected samples. Time points: 0, 12, 24, 36, and 48 h post-infection. MERSCOV003.0P references the write up of the experimental procedure.

first: Ralph

last: Baric

first: Amy

last: Sims

first: Allison

last: Thompson

first: Katrina

last: Waters

first: Amie

last: Eisfeld

first: Yoshihiro

last: Kawaoka


title: Primary human microvascular endothelial cell transcriptome (mRNA) response to a wild type MERS-CoV (icMERS-CoV EMC2012)

status: Public on Mar 25 2016

summary: The purpose is to obtain samples for mRNA analysis in primary human microvascular endothelial cells infected with wild type MERS-CoV (icMERS).

overall_design: Human microvascular endothelial cells were infected with a multiplicity of infection of 5 PFU per cell.  Infected samples were collected in quintuplet; time-matched mocks were collected in quintuplet in parallel with infected samples. Time points: 0, 12, 24, 36, and 48 h post-infection. MERSCOV002.0P references the write up of the experimental procedure.


title: Mouse popliteal lymph node transcriptome response to a wild type West Nile virus (WNV), New York 99 Strain, and mutant WNV-E218A viruses [mRNA]

status: Public on Mar 15 2016

summary: The purpose is to obtain samples for mRNA, miRNA, proteomics, lipidomics, metabolomics, and histopathology analysis in mouse cortex infected with wild-type West Nile virus (WNV; WNV-NY99 382), and mutant WNV-E218A (WNV-NY99 382 E218A 2 nt).

overall_design: Mice are inoculated with WNV in both hind footpads at a dose of 100 FFU. Infected samples were collected in quintuplet; time-matched mocks were collected in triplets in parallel with infected samples. Time points: 1, 2, 4, and 6 days post-infection.

first: Larissa

last: Thackray

first: Michael

last: Diamond


title: Primary human dendritic cell transcriptome response to a wild type MERS-CoV (icMERS)

summary: The purpose is to obtain samples for mRNA analysis in primary human dendritic cells infected with wild type MERS-CoV (icMERS).

overall_design: Human primary dendritic cells were infected with a multiplicity of infection of 5 PFU per cell.  Infected samples were collected in triplet; time-matched mocks were collected in triplet in parallel with infected samples. Time points: 0, 3, 7, 12, and 24 h post-infection. MERSCOV001.0P references the write up of the experimental procedure used to infect the human DC.

first: Vineet

last: Menachery