title: Identifying heterogeneity of Schwann cell like cells via scRNA-seq.

status: Public on Nov 10 2020

city: 遵义

first: hutaotao

middle: taotao

last: hu

address: Zunyi City

institute: ZunyiMedicalUniversity

summary: Previously we have reported that Schwann cell like cells (SCLCs) induced from human amniotic mesenchymal stem cells (hAMSCs) have better peripheral nerve regeneration ability, but the heterogeneity of SCLCs is still poorly understood. Here, based on single-cell RNA sequencing, we investigated the heterogeneity of hAMSCs and SCLCs, and identified the transition from hAMSCs to SCLCs. Totally 6,008 and 5,140 cells generated from hAMSCs and SCLCs were profiled and used for deep analysis. A subpopulation of SCLCs highly expressed Schwann cell markers, JUN, JUND, and NRG1, was identified. Then, cell cycle analysis distinguished the proliferation state of each cluster, and single cells of the subpopulation in SCLCs mainly remained in G0/G1 phase. Pseudotime analysis illustrated how hAMSCs transformed into SCLCs, hAMSCs showed more possibility transformed into other cell types. Through marker gene identification, pathway enrichment, transcription factor analysis, and secreted protein validation, genes such as NRG1, PTGS2, PITX1, VEGFA, and FGF2 were highly expressed in single cells. And also, pathways associated with nerve regeneration and immune control were enriched, such as angiogenesis or TNF signaling.

overall_design: The purpose of this study was to identify the heterogeneity of SCLCs. First, SCLCs was induced from hAMSCs. Then, the total RNA of hAMSCs and SCLCs was extracted for bulk RNA-seq(n=3); and also the RNA of single cells from hAMSCs and SCLCs was profiled via 10X genomics and bioinformatic analysis.

first: Zairong

last: Wei

first: Haihong


title: Cortical single-cell RNA sequencing of the microglia specific TREM2 inducible mouse models in the early stage of amyloid deposition

status: Public on Nov 11 2020

city: jacksonville

last: Zhao

address: 4500 San Pablo Rd S

country: USA

institute: Mayo Clinic

type: Expression profiling by high throughput sequencing

summary: We induced TREM2 expression at birth in our 5xFAD/TREM2 mouse models and harvested the animals at 3.5 months of age. The single cells from the cortex were isolated and subjected to the single-cell RNA seq to investigate the effects of TREM2 on microglia transcriptomic profiles in the early stage of amyloid development. Our data showed that TREM2-WT, to a lesser extent of TREM2-R47H, restricted the disease associated microglia (DAM) signature at this stage.

overall_design: Six mice (3 males and 3 females) were analyzed for each of the four groups, including 5xFAD/TREM2-WT-Ctrl, 5xFAD/TREM2-WT-Induced, 5xFAD/TREM2-R47H-Ctrl, 5xFAD/TREM2-R47H-Induced .

first: Wenhui

last: Qiao

first: Yuka

middle: A

last: Martens

first: Yingxue

last: Ren


title: Expression of the olfactory receptors OR6X1 and OR4E2 decreases in hypothyroidism and is reversible with levothyroxine treatment in pregnancy

status: Public on Aug 31 2020

city: SAO PAULO

first: Robson

middle: José de

last: Almeida

state: SAO PAULO

address: RUA VERGUEIRO 235 249

department: Pós Graduação Stricto Sensu em Medicina

country: Brazil

institute: Universidade Nove de Julho

summary: These libraries reflect a part of a large study. We construct transcriptome libraries, using whole blood circulating RNAs, of four healthy pregnancy (CTL) and preeclamptic women (PEC). In the manuscript, we perform an edgeR three-group analysis comparing the libraries of healthy thyroid pregnancy (HTP), gestational hypothyroidism (GHT) and preeclampsia (PEC). The HTP and GHT libraries are available in GSE147527. As a result, we obtained 1276 DEG in GHT and 1185 DEG in PEC. We also found 195 olfactory receptors common between only in GHT and PEC.

overall_design: We constructed libraries of four healthy pregnancy (CTL) and four preeclamptic women (PEC). The whole blood was collected in the PAXgene Blood RNA tube (QIAGEN, NL, DE) and the RNA was extracted by PAXgene Blood RNA tube (QIAGEN, NL, DE). The sequencing was carried out using an Ion PI Chip (Thermo Fisher Scientific) in an Ion Proton Sequencer (Thermo Fisher Scientific).

first: A

last: Hirata

first: R

middle: J

first: L

last: Rocha

first: P

last: Varela

middle: S

last: Bacigalupo

first: F

last: Curi

middle: G

last: Rodrigues

first: M

middle: C

last: Albejante

middle: M

last: Silva

first: V

first: J

middle: B

last: Pesquero

first: H

last: Delle

first: C

middle: P

last: Camacho


title: Single-cell RNA sequencing of murine tumor-susceptible germ cells

status: Public on Sep 03 2020

city: Houston

first: Nicholas

last: Webster

state: TX

address: One Baylor Plaza

department: Molecular and Human Genetics

institute: Baylor College of Medicine

summary: In response to signals from the embryonic testis, germ cell intrinsic factor NANOS2 coordinates a sex-specific transcriptional program necessary for differentiation of pluripotent-like primordial germ cells toward a unipotent spermatogonial stem cell fate. Emerging evidence indicates that genetic risk factors contribute to testicular germ cell tumor initiation by disrupting sex-specific differentiation. Here, using a mouse model of spontaneous testicular teratomas, we report that a subpopulation of germ cells failing to express NANOS2 is enriched for developmental phenotypes required for tumorigenesis. We demonstrate that only in the absence of NANOS2 do germ cells have a transcriptional profile enriched for Myc signaling and primed pluripotency and transform into embryonal carcinoma cells. We conclude that NANOS2 is the nexus through which many genetic risk factors exert their influence on tumor susceptibility. We propose that NODAL signaling, which is present in the developing testis, drives germ cell transformation in the absence of sex specification.

overall_design: Single-cell RNA Sequencing of FACS-enriched germ cells pooled from four tumor-susceptible mice demarcated by NANOS2-RFP

first: Rebecca

middle: L

last: Maywald

first: Susan

last: Benton

first: Emily

last: Dawson

first: Oscar

middle: D

last: Murillo

last: LaPlante

first: Aleksander

last: Milosavljevic

first: Denise

last: Lanza

first: Jason

last: Heaney


title: ATAC-seq in mouse skeletal muscle

status: Public on Oct 01 2020

city: ILLKIRCH

first: Delphine

last: Duteil

address: 1 rue Laurent Fries

country: France

institute: IGBMC

type: Genome binding/occupancy profiling by high throughput sequencing

summary: We perfomed ATAC-seq on C57/Bl6 mouse skeletal muscle nuclear extracts

overall_design: ATAC-seq in mouse skeletal muscle

first: Daniela

last: Rovito

first: Anna-Isavella

last: Rerra

first: Daniel

last: Metzger


title: The glucocorticoid receptor coordinates myofiber-selective transcriptional networks

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

overall_design: Refer to individual Series


title: Map3k2-regulated intestinal stromal cells define a distinct intestine stem cell niche for tissue repair

status: Public on Aug 15 2020

city: Shanghai

first: Hongxiang

last: Sun

address: 280 South Chongqing Rd.

department: Shanghai Institute of Immunology

country: China

institute: Shanghai Jiaotong University

summary:
intestinal mesenchymal stromal cell subset specific accessible elements were analyzed using ATAC-seq

Bulk RNA-seq Purpose: The goals of this study are to compare WT and Map3k2 deficient mice colon tissue transcriptome upon Naive and DSS treatment for 1 day
Bulk RNA-seq Methods: Colon Tissue mRNA profiles of Naive or 2% DSS treated 16-week-old wild-type (WT) and MEKK2 knockout (Map3k2-/-) mice were generated by deep sequencing, in triplicate, using Illumina NextSeq 500. The sequence reads that passed quality filters were analyzed at the gene level with : Bowtie2 followed by HTSeq-Count and Normalized by DESeq2
Bulk RNA-seq Results: Using an optimized data analysis workflow, we mapped about 20 million sequence reads per sample to the mouse genome (build mm10) and identified 13,284 transcripts in the colon tissues of WT and Map3k2-/- mice.

Single-cell RNA-seq Purpose: The goals of this study are to characterize murine colon mesenchymal stromal cell heterogeneity upon DSS treatment for 3 days
Single-cell RNA-seq Methods: Mesenchymal Stromal Cell Single Cell Suspension Dissociated from 2% DSS treated 12-week-old wild-type (WT) mice has undergone 10x genomics single cell RNA sequencing using Illumina NextSeq 500.
Single-cell RNA-seq Results: Using CellRanger and Seurat we identified 11,284 cells after quality control and filtering

overall_design:
Examination of accessible chromatin in sorted intestinal mesenchymal stromal cell populations.
Colon Tissue mRNA profiles of 16 Week old wild type (WT) and Map3k2-/- mice upon H2O and 2% DSS Treatment
Single Cell Profiles of 12 Week old DSS treated wild type (WT) mice upon 2% DSS Treatment

first: Caixia

last: Gao

first: Ningbo

last: Wu

first: Bing

last: Su


title: Pan-cancer analysis of the developmental pathways reveals non-canonical wnt signaling as a driver of mesenchymal-type tumors

status: Public on Aug 01 2020

city: Seattle

first: Taran

last: Gujral

state: Washington

address: 1100 Fairview Avenue North

institute: Fred Hutchinson Cancer Center

summary: The processes of angiogenesis, cell proliferation, invasion, and migration, and the signaling pathways that drive these events, are activated in both cancer and during embryonic development. Here, we systematically assessed how the activity of major developmental signaling pathways, represented by the expression of genes encoding components of the pathways, correlated with patient survival in ~8000 patients across 17 cancer types. We also compared the expressed genes enriched in developmental pathways with those associated with epithelial-mesenchymal transition (EMT) both in a cancer cohort and in mice during embryonic development. We found that EMT and gene expression profiles consistent with high activity of several developmental pathways, including the TGFβ, Notch, and non-canonical Wnt pathways, significantly correlated with poor patient survival in multiple cancer types. We investigated individual components of these pathways and found that expression of the gene encoding the non-canonical Wnt receptor, frizzled 2 (FZD2), is highly correlated with both poor patient survival and gene expression indicating EMT in the tumors. Pathway analyses revealed that FZD2-regulated gene sets from the TCGA data or FZD2-regulated genes involved in mouse organogenesis or FZD2-regulated genes in cancer cells in culture converged in EMT-associated biological processes, suggesting that FZD2 is a key driver of mesenchymal-like cell state and thus a contributor to cancer progression and metastasis.

overall_design: Knockdown of Fzd2 in FOCUS samples (3 samples each) and overexpression of Fzd2 in Huh7 cells (3 samples each)

first: Gujral

last: Taran

first: Marin

last: Chan

first: Andrew

last: Xue


title: Up-regulation of JAK-STAT pathway promotes maturation of human stem cell-derived cardiomyocytes

city: Singapore

first: Boon Seng

last: SOH

address: 61 Biopolis Drive, Proteos

department: Institute of Molecular and Cell Biology (IMCB)

country: Singapore

institute: A*STAR

summary: hPSC-CM has been used to model cardiac-related disease phenotypes. However, the immaturity of hPSC-CM constrains their potential in cell-based therapy, disease modeling and drug discovery. To understand the molecular mechanism driving human PSC-CM maturation, we utilized a metabolic reporter cell line that allows for the purification of CM that reflects different physiological status (fetal-like or matured). To identify transcription factors and pathways that enhances CM maturation, bulk RNA sequencing was performed on low-GFP expressing matured CM and high-GFP expressing fetal-like CM. The results revealed up-regulated expression of pathways involved in interferon signaling and down-regulation of pathways related to cell cycle checkpoints.

overall_design: Utilising CRISPR-Cas9 technology, we generated a HK-1-GFP knock-in reporter cell line in H7 embryonic stem cells. Flow cytometry verified that ES-derived cardiomyocytes generated reflects the metabolic shift of cardiomyocytes as they mature. Quantitative polymerase chain reaction (qPCR) and western blot was performed to further confirm the aforementioned findings. In addition, we also performed functional assays, such as glycolytic stress test on low/high GFP expressing fetal-like or matured CM. Subsequently, bulk RNA sequencing was performed to identify the molecular pathways and transcription factors that enhances maturation in hES-CM.

first: Beatrice

middle: X

last: Ho

first: Hong-Bing

last: Xu

first: Jin-Hui

last: Hor

first: Jeremy

middle: K

last: Pang

first: Christina

middle: Y

last: Lim

first: Lee

last: Liew

first: Omer

last: An

first: Henry

last: He

first: Yong

last: Fan

first: Woon-Khiong

first: Shi-Yan

last: Ng

first: Boon-Seng

last: Soh


title: Genome-wide GR occupancy and chromatin landscape in skeletal muscles

first: Delphine

last: Duteil

summary:
Purpose: The aim of this study is to identify the GR genome binding profile as well as that of Pol II, H3K27ac, H3K4me1, H3K4me3 and Ctcf in skeletal muscles.
Methods: Libraries were prepared from immunoprecipitated DNA according to standard methods. ChIP-seq libraries were sequenced using a HiSeq 4000 (Illumina) and mapped to the mm10 reference genome using bowtie 2 (Langmead et al., 2009). Data were further analysed using the peak finding algorithm MACS 2 (Zhang et al., 2008) using input as control. All peaks with FDR greater than 0.1 % were excluded from further analysis. The uniquely mapped reads were used to generate the genome-wide intensity profiles, which were visualized using the IGV genome browser (Thorvaldsdottir et al., 2012).
Results: HOMER (Heinz et al., 2010) was used to annotate peaks, to calculate overlaps between different peak files, and for motif searches. The genomic features (promoter, exon, intron, 3’ UTR, and intergenic regions) were defined and calculated using Refseq and HOMER. Genes annotated by HOMER were further used for a pathway analysis in WebGestalt (Heinz et al., 2010; Wang et al., 2013).

overall_design: Nuclei were extracted from skeletal muscles from 10-week-old mice as described in Joshi 2017.

first: Daniel

last: Metzger

first: Daniela

last: Rovito

first: Shilpy

last: Joshi

first: Anna-Isavella

last: Rerra


title: 4C-seq experiment on mouse skeletal muscle and DP thymocytes

summary:
Purpose: The aim of this study is to investigate enhancer promoter interactions in skeletal muscle
Methods: 50 ng of purified DNA were used as a template for PCR with bait-specific primers (Table S5) containing Illumina adapter termini. PCR reactions were pooled and, after primer removal with 1.8x AMPure XP beads, DNA was sequenced with the HiSeq 4000 (Illumina), as single-end 50 bp reads. Sequences were trimmed to remove primer and bait fragment sequence with the sabre tool (https://github.com/najoshi/sabre), mapped to the genome with Bowtie and converted to restriction fragment space as in van de Werken et al., 2012 (van de Werken et al., 2012). Interactions were called on single 4C experiments with peakC (Geeven et al., 2018), using a sliding window of 21 fragments.

overall_design: Nuclei were extracted from skeletal muscles from 10-week-old mice as described in Joshi 2017. Alternatively, 4 week old thymus was dissected, cells were washed and filtered in PBS, and then sorted by FACS with anti-CD4-PE and anti-CD8a-FITC antibodies (eBioScience)

first: Tom

last: Sexton

first: Nezih

last: Karasu


title: RNA-seq datasets for enhancer RNA quantification in "Enhancer RNAs predict enhancer-gene regulatory links and are critical for enhancer function in neuronal systems"

status: Public on Jul 28 2020

city: Birmingham

middle: Jason

last: Day

state: AL

address: 1825 University Blvd

department: Neurobiology

institute: UAB

summary: This dataset contains total RNA sequencing results from rat embryonic cortical, hippocampal, and striatal neuronal cultures treated with either vehicle (complete Neurobasal media) or potassium chloride (10mM) for 1hr prior to RNA extraction.

overall_design: This experiment contains 19 biological samples, each of which underwent directional, 75bp paired-end total RNA-seq on an Illumina NextSeq500 instrument. Samples were treated with neurobasal media (vehicle; samples V1C, V2C, V3C, V1H, V2H, V3H, V2S, V4S, V6S, V8S), or 10mM KCl (samples K1C, K2C, K3C, K1H, K2H, K3H, K1S, K5S, K7S) . The first letter of sample names denotes acute treatement (V = vehicle, K = KCl). The second digit denotes the unique replicate ID. The third digit denotes the region of cultured neuron (C = cortex, H = hippocampus, S = striatum). NEBnext rRNA depletion kit was used to remove ribosomal RNA to include both polyadenylated and non-polyadenylated RNA. Samples were sequenced across multiple lanes of the Illumina instrument, designated as L001, L002, L003, L004 in raw file names. Forward and reverse paired-end reads are denoted as "R1" or "R2" in raw file names.

first: Nancy

middle: V

last: Carullo

first: Robert

last: Phillips

first: Lara

last: Ianov


title: Transcriptomics analysis of the effects of electrical stimulation on rat denervated gastrocnemius muscle

status: Public on Jul 01 2020

city: Beijing

first: Gaoyan

last: La

address: Huayuan North Road NO.49

department: The Department of Rehabilitation Medicine

institute: Peking University Third Hospital

summary: We report the application of RNA sequencing technology for transcriptomics analysis of the effects of electrical stimulation on rat denervated gastrocnemius muscle. Muscle samples were selected for gene expression analyses，corresponding to the following categories: Sham operation rats, (SHAM, n = 3), sciatic nerve injury rats (DN, n = 3), and sciatic nerve injury with electrical stimulation (DN-SM, n = 3). A total of 14,334  genes (DEGs) were detected in this study.

overall_design: Rat gastrocnemius muscle mRNA profiles of SHAM, DN and DN-SM were generated by deep sequencing, using BGISEQ-500.

first: Mouwang

last: Zhou


title: Single-cell RNA-seq of pediatric ependymoma

status: Public on Jul 13 2020

city: Boston

first: Li

last: Jiang

state: MA

address: 360 Longwood Ave

department: Pediatric Oncology

institute: Dana Farber Cancer Institute

summary: Despite extensively growing knowledge on the molecular biology of ependymoma, effective treatments are still lacking for about half patients with high-risk tumors. By applying single cell RNA-sequencing, we comprehensively identify a cellular hierarchy within ependymoma spanning undifferentiated and differentiated tumor cell states across all major molecular groups. This not only refines the concept of these established molecular groups but moreover provides a biological context for the well-known capacity of aggressive ependymomas for late recurrence and treatment resistance. Our newly defined transcriptomic signatures also prove to be of prognostic relevance within established high-risk ependymoma groups. Consequently, the newly characterized cell states could serve as promising future therapeutic targets and biomarkers for clinical trials.

overall_design:
Single-cell RNA-seq: Smart-seq2 of 22 ependymoma cases and 10X data of 6 ependymoma cases

Raw Fastq files can be requested at DUOS (https://duos.broadinstitute.org/) under the dataset ID: DUOS-000120

first: Mariella

last: Filbin


title: Monocyte-derived DC Expression Data from Advanced Staged Melanoma Patients

status: Public on Sep 10 2020

city: Pittsburgh

first: Deena

middle: Marie

last: Maurer

address: 200 Lothrop Street

department: Immunology

institute: University of Pittsburgh

summary:
The metastatic form of Melanoma has a reported ten-year survival rate of approximately 15%. Clinical trials have shown modest success in a subset of patients. Particularly, combinational therapy using checkpoint blockade has shown the most success, but many patients do not respond. The patients that do respond to treatments often have a pre-existing antitumor immunity.
To generate an optimal anti-tumor immune response, we have previously created a dendritic cell (DC) based adenovirus vaccine targeted against three common melanoma associated antigens: Tyrosinase, MART-1, and MAGE-A6 (TMM2). The vaccine was used in a Phase 1 clinical trial (NCT01622933) , where 35 patients were enrolled. Immature DC (iDC) were generated from patient monocytes (GM-CSF + IL-4), matured (mDC) using IFNG + LPS, and transduced with the adenovirus vaccine (AdVTMM2 DC). Patients received three intradermal injections of the vaccine over the course of one month. Human genome RNA microarray was used to analyze the gene expression profiles of the DC vaccine for each patient.

overall_design:
34/35 patient DCs were analyzed for each DC subtype (iDC, mDC, AdVTMM2 DC) using the Affymetrix Human Gene 2.0 ST Array. We investigated  gene expression profiles that correlated with overall survival  and favorable clinical outcomes in late-stage melanoma patients.

Clinical outcome definitions:
PD: Progressive Disease
SD: Stable Disease
NED1: No Evidence of Disease at time of enrollment and remained NED for ≤ 18 months
NED2: No Evidence of Disease at time of enrollment and remained NED for ≥ 18 months
PR: Partial Responder (RECIST)

first: Lisa

middle: H

last: Butterfield


title: ATAC-seq datasets for chromatin accessibility quantification in "Enhancer RNAs predict enhancer-gene regulatory links and are critical for enhancer function in neuronal systems"

first: Jeremy

summary: This dataset contains Assay for Transposase-Accessible Chromatin (ATAC) sequencing results from rat embryonic cortical, hippocampal, and striatal neuronal cultures treated with either vehicle (complete Neurobasal media) or potassium chloride (10mM) for 1hr.

overall_design: This experiment contains 18 biological samples, each of which underwent ATAC-seq on an Illumina NextSeq500 instrument. Samples were treated with neurobasal media (vehicle; samples V1C, V2C, V3C, V1H, V2H, V4H, V1S, V2S, V4S), or 10mM KCl (samples K2C, K3C, K4C, K1H, K2H, K4H, K1S, K2S, K3S) . The first letter of sample names denotes acute treatement (V = vehicle, K = KCl). The second digit denotes the unique replicate ID for a given brain region and treatment. The third digit denotes the region of cultured neuron (C = cortex, H = hippocampus, S = striatum). Forward and reverse paired-end reads are denoted as "R1" or "R2" in raw file names.

middle: N

middle: A


title: Single Cell and Spatial Analysis of Human Squamous Cell Carcinoma

status: Public on Jun 22 2020

city: New York

first: Andrew

last: Ji

state: NY

address: 1428 Madison Ave.

institute: Icahn School of Medicine at Mount Sinai


title: Single Cell and Spatial Analysis of Human Squamous Cell Carcinoma [ST]

summary: To define the cellular composition and spatial architecture of the tumor micoenvironment, we combined single-cell RNA-sequencing, spatial transcriptomics, and multiplexed ion-beam imaging from 10 patient cutaneous squamous cell carcinoma tumors and  site-matched normal skin

overall_design: Patient tumors were fresh frozen and sectioned at 10um thickness onto spatial transcriptomics (ST) slides for mRNA capture, followed by library preparation and sequencing

first: Adam

middle: J

last: Rubin


title: mRNA sequencing of P0 primary WT and Mettl3/14nKO mouse islets

status: Public on Apr 24 2020

first: Yanqiu

last: Wang

address: 197 Rui-jin 2nd Road, Shanghai 20025, CHINA.

institute: Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.

summary: Using RNA-seq, we identified 945 differentially expressed genes in P0 KO islets, compared to WT（fc>1.5）. Among them, a cluster of genes involved in insulin secretion, ion transportation were significantly changed.

overall_design: Examination of RNA modifications in P0 Mettl3/14nKO islets

first: Jiajun

last: Sun


title: Retinal Organoids derived from AIPL1-LCA Patient iPSCs Maintain Retinal Cytoarchitecture under Reduced AIPL1 Levels

status: Public on May 28 2020

city: Bethesda

first: Koray Dogan

last: Kaya

state: MD

address: 6 CENTER DR

department: NEI

institute: NIH

summary: In this study, we generated three-dimensional (3D) retinal organoids (ROs) from induced pluripotent stem cells (iPSCs) derived from an LCA4 patient carrying a Cys89Arg mutation in AIPL1. This study aimed to (i) explore whether the patient iPSC-derived ROs recapitulate LCA4 disease phenotype, and (ii) generate a clinically relevant resource to investigate the molecular mechanism of disease and safely test novel therapies for LCA4 in vitro.

overall_design: Two control iPSC lines and patient’s iPSCs  were subjected to the differentiation protocol and 15-20 organoids were pooled from 3-5 independent differentiation experiments at days (D) 25, 60, 88 and 123.

first: Dunja

last: Lukovic


title: Integrative analysis of reference epigenomes in rice [ChIP-seq]

status: Public on Apr 25 2020

city: Wuhan

first: Liang

last: Xie

state: Hubei

address: No.1,Shizishan Street

institute: Huazhong Agricultural University

summary: Approximately 73% of rice genomes were annotated with different epigenomic properties. Refinement of promoter regions using open chromatin and H3K4me3-marked regions provided insight into transcriptional regulation. Active and repressed histone modifications and the predicted enhancers varied largely across tissues, whereas inactive chromatin states were relatively stable. Further, we investigated the impact of genetic variants on epigenomic signals and gene expression. Together, these datasets constitute a resource for functional element annotation in rice and indicate the central role of epigenomic information in understanding transcriptional regulation.

overall_design: Here, we generated genome-wide profiling of five histone modifications and RNA polymerase II occupancy using an enhanced chromatin immunoprecipitation (eChIP) approach. By integrating chromatin accessibility, DNA methylation, and transcriptome datasets, we constructed comprehensive epigenome landscapes across various tissues

first: Lun

last: Zhao

first: Qing

last: Zhang


title: Single Cell and Spatial Analysis of Human Squamous Cell Carcinoma [WES]

overall_design: Genomic DNA was isolated from patient tumors and normal skin and whole-exome squencing was performed


title: Circulating RNA transcriptome of pregnant women with TSH just above the trimester-specific reference and its correlation with the hypertensive phenotype

status: Public on Mar 26 2020

first: Robson

middle: José de

last: Almeida

summary: These libraries are part of a large study to evaluate the impact of thyroid dysfunction in our patients and to compare with health subject. In this part of the study, whole blood circulating RNAs were collected from pregnant women with TSH levels just above the normal range to determine the impact of a mild elevation of TSH in pregnancy. To transcriptome, we selected healthy nonpregnant women (NPG), women with healthy thyroid pregnancy (HTP) and pregnant women with gestational hypothyroidism (GHT). As described in the paper with details, we perform an edgeR three-group analysis. Results have shown that 31.3% of the genes are downregulated and 68.7% are upregulated in HTP.

overall_design: We constructed libraries of three women in HTP, three in GHT and three in the NPG group.

first: Andrea

last: Hirata

first: Luiz

last: Jesus Rocha

first: Valdelena

last: Silva

first: Lucas

middle: S

last: Bacigalupo

first: Patrícia

last: Varela

first: Leonardo

first: João

last: Pesquero

first: Humberto

last: Delle

first: Cleber

last: Camacho


title: POL and Z1031 Gene Expression_Final

status: Public on Apr 13 2020

city: st louis

first: Cynthia

last: Ma

state: Missouri

address: 4515 Mckinley, 4515 Mckinley

department: Medical Oncology

institute: Washington University

summary:
Background: Unlike estrogen receptor (ER) negative breast cancer, ER-positive breast cancer outcomes are less influenced by lymphocyte content, indicating a need for investigation of checkpoint targets and immune tolerance mechanisms that may be specific to this disease subset.
Methods: A supervised analysis of microarray data from the Alliance/ACOSOG Z1031 trial was conducted to identify upregulated genes in Luminal B breast cancers that exhibited persistent tumor proliferation despite aromatase inhibitor therapy (33 cases Ki67 >10%) versus Luminal B breast cancers that were more sensitive (33 cases Ki67 <10%).
Results: This study identified thirty genes (Pearson’s r>0.4 with Ki67 as a continuous variable). These genes were enriched for immune tolerance processes (p<0.005) and three targetable immune checkpoint components were upregulated in resistant cases: IDO1, LAG3, and PD1. High IDO1 mRNA associated with poor prognosis in ER+ disease across two independent cohorts (METABRIC and TCGA). Furthermore, analysis indicated IDO1 was tightly associated with IFN-γ/STAT1 signaling.  As a composite immune tolerance signature, expression of these pathway components associated with higher baseline Ki67 and lower ER, PgR levels and poor disease specific survival.  In tissue microarray analysis, IDO1 was observed in stromal cells and tumor-associated macrophages, with a higher incidence in Luminal B cases.  Further mRNA and tissue microarray analyses associated IDO1 expression with the presence of macrophages (M1 by CIBERSORT) and regulatory T cells.
Conclusion: Targetable immune-checkpoint components are upregulated in majority of neoadjuvant endocrine therapy resistant Luminal B cases. Our findings suggests potential for immune checkpoint inhibitors in poor outcome ER+ breast cancer.

overall_design: 603 microarray experiments from 468 breast cancer patients were profiled using 2 channel (tumor:reference) whole human genome Agilent arrays.  Timepoints include baseline (BL), 2-4 weeks post endocrine treatment (w2, M, or 4wk), and surgery (S = ~16 weeks post endocrine therapy).

first: Jeremy

middle: W

last: Hoog


title: Single cell RNA sequencing analyses of cells from human sinonasal tissue

city: Philadelphia

first: Danielle

middle: R

last: Reed

state: PA

address: 3500 Market St

department: Not applicable

institute: Monell Chemical Senses Center

summary: Single cell RNA sequencing analyses of human sinonasal tissue samples of chronic rhinosinusitus patients clustered the sinus cell into 13 types. Two cell types (monocyte/Macrophage and dendritic cells) demonstrated over-lapping expression of MPEG1, BATF3, IRF4, CD86, and HLA-DRA.

overall_design: 4 human sinonasal tissue samples from polyps (n=2) and inferior turbinate (n=2) were analyszed to determine the clustering of sinonasal cell types

first: Cailu

last: Lin

first: Michael

last: Kolhanski

first: Noam

last: Cohen


title: Histone 1 deficiency drives lymphomagenesis through disruption of 3D chromatin architecture

status: Public on Sep 02 2020

first: Matt

last: Teater

address: 445 E 69th St

institute: Weill Cornell Medical College

summary: Linker histone H1 proteins bind to nucleosomes and cause chromatin compaction, although little is known about their biological functions. Histone H1 (HIST1H1B-E) mutations are highly recurrent in B-cell lymphomas and are present in solid tumors, but their cancer relevance and mechanism are unknown. Here we report that lymphoma-associated H1 alleles are genetic driver mutations in lymphomas.  H1 mutations disrupt their ability to bind or compact chromatin. This causes profound architectural remodeling of the genome characterized by large-scale, yet focal shifts of chromatin from a compacted, to a relaxed state.  The degree of decompaction results in distinct epigenetic states, primarily due to gain of histone H3 lysine 36 dimethylation, and/or loss of repressive H3K27 methylation. These changes unlock expression of stem cell genes that are normally silenced during early development.  Loss of H1c and H1e alleles in mice conferred enhanced fitness and self renewal properties to germinal center B-cells, ultimately leading to aggressive lymphoma with enhanced repopulating potential.  Collectively, our data indicate that H1 proteins are normally required to sequester early developmental genes into architecturally inaccessible genomic compartments. We furthermore establish H1 as a bona fide tumor suppressor, whose mutation drives malignant transformation primarily through three-dimensional genome reorganization, epigenetic reprogramming and aberrant de-repression of developmentally silenced genes.

overall_design: RNA-seq, ChIP-seq, Cut&Run, ATAC-seq, and HiC sequencing data in HIST1H1C- and HIST1H1E-deficient germinal center B cells

first: Nevin

last: Yusufova

first: Ethel

last: Cesarman

first: Ari

middle: M

last: Melnick

first: Ashley

last: Doane


title: DNMT3A and TET2 Mutations Increase Hematopoietic Stem Cell Fitness Through Distinct Mechanisms

status: Public on Apr 01 2020

city: St Louis

first: Grant

last: Challen

state: MO

address: 660 Euclid Avenue

department: Medicine

institute: Washington University School of Medicine

summary: Epigenetic modifying enzymes DNMT3A and TET2 are recurrently mutated in hematological disorders despite possessing opposing biochemical functions in the DNA methylation processes. Using conditional ablation, we show these contrasting genotypes result in different functional effects in hematopoietic stem cells (HSCs). Loss of Dnmt3a bestows enhanced self-renewal on HSCs in serial, competitive repopulation assays while Tet2 loss functionally depletes HSCs after a tertiary transplant despite an initial competitive advantage. Moreover, loss of Tet2 sensitizes HSCs to the addition of a common leukemic driver mutation Flt3-ITD. Tet2-null mice experience a 5-fold decrease in median survival time when combined with Flt3-ITD while that of Dnmt3a-null mice decreases 1.5-fold. Molecular characterization of transcriptomes and chromatin accessibility reflects the functional differences between the genotypes as Dnmt3a-null cells reside in a more stem cell-like state while Tet2 loss leads to functional attrition of down-stream progenitors. These data further prove that DNMT3A and TET2 mutations lead HSCs down different molecular and functional pathways despite similar disease destinations.

overall_design: Hematopoietic stem cells (HSCs), multipotent progenitors (MPPs), and restricted progenitors (RPs)were sorted from Vav-CRE:Control, Vav-CRE:Dnmt3a-KO, Vav-CRE:Tet2-KO mice for RNA-seq to determine gene expression and ATAC-seq  to examine chromatin accessbility

first: Elizabeth

last: Ostrander


title: Integrative analysis of reference epigenomes in rice

first: Liang

last: Xie

type: Methylation profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: RSPO1 suppresses growth of mouse intestinal adenomas

status: Public on Mar 01 2020

city: Helsinki

first: Marianne

last: Lähde

address: Haartmaninkatu 8

department: Faculty of Medicine, Translational cancer medicine program

country: Finland

institute: University of Helsinki


title: RNA-Seq profiling of ELF3 and PRR37 in Brachypodium Distachyon

status: Public on Mar 24 2020

city: Cambridge

first: Philip

last: Wigge

address: 47 Bateman street

department: Sainsbury Laboratory

country: United Kingdom

institute: Cambridge University

summary: Daylength is a key indicator of seasonal information that determines major patterns of behavior in plants and animals. Photoperiodism has been described in plants for about 100 years, but the underlying molecular mechanisms of daylength perception and signal transduction in many systems are not well understood. In trees, photoperiod perception plays a major role in growth cessation during the autumn as well as activating the resumption of shoot growth in the spring, both processes controlled by FLOWERING LOCUS T2 (FT2) expression levels and critical for the survival of perennial plants over winter.  We find that night-length information is transmitted via the expression level of a poplar clock gene, LATE ELONGATED HYPOCOTYL 2 (LHY2), which controls FT2 expression.  Repression of FT2 is a function of the night extension and LHY2 expression level. We show that LHY2 is necessary and sufficient to activate night-length repressive signaling. We propose that the photoperiodic control of shoot growth in poplar involves a balance between FT2 activating and repressing pathways.

overall_design: Single samples were taken at each condition.

first: Mingjun

last: Gao

first: Katja

last: Jaeger

first: Feng

last: Geng


title: ChIP-Seq profiling of ELF3,PRR37 and PHYC in response to photoperiod change at different ZTime in Brachypodium distachyon

status: Public on Feb 29 2020

summary: Daylength is an important seasonal cue, and genetic variation in the regulation of photoperiodism has been selected for in adapting wheat and barley to northern latitudes. Despite the importance of this trait, the mechanism by which monocot plants sense photoperiod is not known. We find in Brachypodium distachyon that photoperiodism is mediated by phytochromeC (phyC), a chromophore that acts as a molecular timer and measures the length of the night. The phyC signal is directly communicated to the circadian clock via the activity of EARLY FLOWERING3 (ELF3). ELF3 is a central regulator of photoperiodism, and elf3 mutants display a constitutive long day transcriptome. By coordinating an endogenous timer for night length perception with rhythmical circadian clock controlled gene expression, this mechanism resolves how Brachypodium, and likely other monocots, perceive photoperiod. Using ChIP-Seq, we detected that occupancy of ELF3 at various genomic regions varies in response to photoperiod and ZTime.

overall_design: Single samples were taken at each time point. ELF3,PHYC,PRR37 ChIP-Seqs were sampled at different photoperiod and ZTime.


title: RNA Profiling of FAC-Sorted Neurons From the Developing Zebrafish Spinal Cord.

status: Public on Feb 26 2020

city: Syracuse

first: Samantha

middle: Jane

last: England

address: 107 College Place

department: Biology

institute: Syracuse University

summary: In this report, we describe a successful protocol for isolating and expression-profiling live fluorescent- protein-labelled neurons from zebrafish embryos. As a proof-of-principle for this method, we FAC-sorted and RNA-profiled GFP-labelled spinal CiA interneurons and compared the expression profile of these cells to those of post-mitotic spinal neurons in general and to all trunk cells. We show that RNA of sufficient quality and quantity to uncover both expected and novel transcription profiles via Affymetrix microarray analysis can be extracted from 5,700 to 20,000 FAC-sorted cells. As part of this study, we also further confirm the genetic homology of mammalian and zebrafish V1 interneurons, by demonstrating that zebrafish V1 cells (CiAs) express genes that encode for the transcription factors Lhx1a and Lhx5. This protocol for dissociating, sorting and RNA-profiling neurons from organogenesis-stage zebrafish embryos should also be applicable to other developing organs and tissues and potentially other model organisms.

overall_design: Fifteen samples were analysed in total, all at 27 hours post fertilization (hpf).  Five biological replicates were performed for all spinal neurons (isolated from Tg(elavl3:EGFP)), six biological replicates were performed for V1 (CiA) spinal interneurons (isolated from Tg(pax2a:GFP)), and four biological replicates were performed for all trunk cells (FAC-sorted trunk cells).

first: Gustavo

last: Cerda

first: Murray

last: Hargrave

first: Katharine

middle: E

last: Lewis


title: Capybara: A tool to measure cell identity and fate transitions

status: Public on Feb 14 2020

last: Morris

address: Department of Developmental Biology, Washington University School of

institute: Washington University in St Louis

summary: Using our Capybara tool to measure cell identity, we profiled induced endoderm progenitors, reprogrammed from fibroblasts (via overexpression of Hnf4a and Foxa1), and cultured long-term, for 12 months.

overall_design: Single-cell RNA sequencing was performed on long-term cultured, expanded iEPs.


title: Lewis Lung Carcinoma UROD

status: Public on Feb 01 2020

city: Dallas

first: Shruthy

last: Suresh

state: Texas

address: 6000 Harry Hines Blvd NA6.300

department: Molecular Biology

institute: UT Southwestern Medical Center

summary: We studied the effects of loss of UROD in lung cancer progression

overall_design: Lewis Lung Carcinoma cells expressing a Scrambled shRNA lentivirus or UROD shRNA were treated with 2ug/ml doxycycline for 4 days to induce shRNA expression. Cells were then processed for RNA Isolation and RNA Sequencing.

first: Kathryn

last: O'Donnell


title: Single cell changes in AAV-Ctrl or AAV-RSPO1-Fc treated intestinal adenoma cells from ApcMin/+ mice

summary: We constructed AAV-vectors for systemic expression of a soluble RSPO1 protein in ApcMin/+ mice. We found that the RSPO1-Fc fusion protein suppresses the Wnt/ß-catenin signaling activity in intestinal adenomas and in adenoma-derived intestinal organoids ex vivo, but not in normal intestinal epithelial cells. In the Apc mutant cells, the RSPO1-Fc fusion protein activated the TGFß/SMAD signaling pathway to suppress several Wnt target genes and adenoma growth, which effect was rescued suppressed by the TGFß receptor kinase inhibitor SB-431542. Simultaneously, RSPO1-Fc induced proliferation of the normal intestinal stem cells, giving them a growth advantage over the mutant cells, which enabled the intestinal epithelium to eventually outgrow the adenoma cells. Prolonged systemic expression of AAV-RSPO1-Fc decreased significantly the number of the intestinal adenomas and improved the overall survival of ApcMin/+ mice. Thus RSPO1-Fc provides the normal intestinal epithelial cells a growth advantage when compared to the adenoma cells, which eventually leads to the extrusion of the adenomatous tissue. An attractive idea now is to exploit such differential response of normal vs. cancer cells in cancer therapy.

overall_design: We analyzed 5 total samples (2 AAV-Ctrl and 3 AAV-RSPO1-Fc), all containing 5000 cells. Single cell RNA-seq.

first: Kari

last: Alitalo


title: EIF5B drives integrated stress response-dependent translation of PD-L1 in lung cancer

summary: Cancer cells express high levels of PD-L1, a ligand of the PD-1 receptor on T  cells, allowing tumors to suppress T cell activity 1-3. Clinical trials utilizing  monoclonal antibodies that disrupt the PD-1/PD-L1 immune checkpoint have  yielded remarkable results, with PD-1 immunotherapy approved as a first-line  therapy for human lung cancer patients 4-6. Despite significant progress in  targeting this pathway, the mechanisms through which PD-L1 is upregulated in  non-small cell lung cancer (NSCLC) and other tumor types remain incompletely  understood. Here we used CRISPR-based screening to identify regulators of PDL1  in human lung cancer cells, revealing potent induction of PD-L1 levels upon  disruption of the heme biosynthesis pathway. Impairment of heme production  activates the integrated stress response (ISR), allowing bypass of inhibitory  upstream open reading frames in the PD-L1 5¢ UTR, resulting in enhanced PD-L1  translation and suppression of anti-tumor immunity. We further demonstrated  that ISR-dependent translation of PD-L1 requires the translation initiation factor  EIF5B. EIF5B overexpression, which is frequent in human lung cancers and is  associated with poor prognosis, is sufficient to induce PD-L1. These findings  uncover a new mechanism of immune checkpoint activation and suggest novel  targets for therapeutic intervention.

overall_design: H358 cells were transuced with lentiCRISPR V2 library virus, selected and sorted by PD-L1-APC. Genomic DNA was isolated and deep sequencing was performed to identify sgRNA enriched in sorted vs unsorted cells


title: Single cell changes in RSPO1-Fc treated intestinal adenoma organoids from ApcMin/+ mice

overall_design: We analyzed 2 samples in total, both containing 5000 cells. Single cell RNA-seq.


title: Meta-analysis of Blood Genome-Wide Expression Profiling Studies in Pulmonary Arterial Hypertension

status: Public on Oct 08 2019

first: Gabriela

last: Ferreyra

address: 9000 Rockville Pike - Building 10 room 4D03

department: CCMD

institute: Clinical Center

summary: Aberrantly remodeled vasculature in pulmonary arterial hypertension (PAH) features a prominent inflammatory cell infiltrate suggesting that immune effector cells may contribute to disease progression. Global expression studies of peripheral blood mononuclear cells (PBMCs) and whole blood have attempted to better define this inflammatory component of PAH pathobiology.

overall_design: PBMCs from patients with pulmonary arterial hypertension (PAH) and gender/age matching controls were isolated from whole blood. Total RNA was extracted from PBMCs and gene expression was assessed using the Affymetrix GeneChip Human Gene 1.0 ST Array

first: J

last: Elinoff

first: A

last: Mazer

first: R

last: Cai

last: Sun

first: G

last: Graninger

first: B

last: Harper

first: M

last: Solomon

middle: L

last: Danner


title: Transcriptome analysis between primary and iPS-derived monocytes and macrophages and comparison of iPS-derived macrophages between CCR5 patients and healthy controls

status: Public on Dec 04 2019

first: Manfred

last: Boehm

address: 9000 Rockbille Pike

institute: NHLBI

summary: iPS-derived monocytes and macrophages are similar with primary monocytes and macrophages compared to iPS cells from the genome-wide overview and have similar gene expression patterns.

overall_design:
Primary monocytes were isolated from peripheral blood collected from 8 healthy volunteers and differentiated to macrophages; iPS cells are reprogrammed from skin fibroblast obtained from 3 healthy controls and then differentiated to patient specific iPS-derived monocytes(imono) and macrophages(iMac)cells,  and mRNA expression profiles were analyzed by RNA-Seq.
*** Submitter declares that the raw data will be deposited in dbGaP due to patient privacy concerns.

first: Xianfeng

last: Ping


title: Single cell transcriptomic comparison of human fetal retina, hPSC-derived retinal organoids, and long-term retinal cultures.

status: Public on Jan 10 2020

city: SEATTLE

first: THOMAS

last: REH

state: WA

address: 1959 NE PACIFIC STREET

department: BIOLOGICAL STRUCTURE

institute: UNIVERSITY OF WASHINGTON

summary: To study the development of human retina, we used single cell RNAseq at key fetal stages and followed the development of the major cell types, as well as populations of transitional cells. We also analyzed stem cell (hPSC)-derived retinal organoids; although organoids have a very similar cellular composition at equivalent ages to the fetal retina, there are some differences in gene expression of particular cell types. Moreover, the inner retinal lamination is disrupted in more advanced stages of organoids when compared with fetal retina. To determine whether the disorganization in the inner retina was due to the culture conditions, we analyzed retinal development in fetal retina maintained under similar conditions. These retinospheres develop for at least 6 months, displaying better inner retinal lamination than retinal organoids. Our scRNAseq comparisons between fetal retina, retinal organoids and retinospheres provide a new resource for developing better in vitro models for retinal disease.

overall_design: Single cell Analysis of fetal retina versus human retinal organoids

first: Akshayalakshmi

last: Sridhar

first: Akina

last: Hoshino

first: Connor

last: Finkbeiner

first: Thomas

last: Reh


title: Mitochondrial 3243A > G mutation confers pro-atherogenic and pro-inflammatory properties in MELAS iPS derived endothelial cells

status: Public on Oct 29 2019

first: Boon Seng

last: SOH

address: 61 Biopolis Drive, Proteos

institute: A*STAR

summary: We obtained three independent sets of endothelial cells differentiated from iPSCs derived from a Mitochondrial encephalomyopathy, lactic acidosis, and stroke-like episodes (MELAS) patient as well as iPSCs that has been corrected for the mitochondrial mutation.

overall_design:
To determine transcriptomic differences between diseased endothelial cells when compared to normal controls.
Please note that the processed data contains 9 sample data columns. The H9.EC.B* sample data was included in the initial analysis but removed from further analysis, and their raw data is unavailable. The H9 data was included in the processed data file to enable other users to reproduce the normalized data (e.g. Normalized Read Counts).

first: Nicole

last: Pek

first: Qian

last: Phua

first: Beatrice

middle: X

last: Ho

first: Jeremy

middle: P

last: Sheng

first: Omer

last: An

first: Henry

last: He

first: Yang

last: Yu

first: Yong

last: Fan

first: Ng

last: Yan

first: Boon

last: Soh


title: Distinct mesenchymal cell populations generate the essential intestinal BMP signaling gradient

status: Public on Jan 17 2020

first: Ramesh

last: Shivdasani

address: 450 Brookline Ave. Dana 720D

institute: Dana Farber Cancer Institute

summary: The intestinal epithelium requires trophic factors and signaling gradients to maintain proper positioning of Intestinal Stem Cells (ISC) and proper differentiation of ISCs. Because the underlying mesenchyme is composed of numerous cell types, we utilized both transgenic and antibody methods to isolate specific mesenchymal populations including GFP-hi and GFP-lo cells from the murine transgenic PDGFRAH2BEGFP mouse (Jackson, #007669), endothelial and lymphatic endothelial cells via antibody for CD31+LYVE1- and CD31+LYVE1+, respectively. We found distinct molecular signatures of these cell types and focused our analyses on known trophic factors of the overlaying intestinal epithelium.

overall_design: Examination of mRNA profiles of distinct mesenchymal cell types.

first: Neil

last: McCarthy

first: Elisa

last: Manieri

first: Elaine

last: Storm

first: Assieh

last: Saadatpour

first: Adrienne

last: Luoma

first: Varun

last: Kapoor

first: Shariq

last: Madha

first: Liam

last: Gaynor

first: Christian

last: Cox

first: Shilpa

last: Keerthivasan

first: Kai

last: Wucherpfennig

first: Guo-Cheng

last: Yuan

first: Frederic

last: de Sauvage

first: Shannon

last: Turley


title: Transcriptomic profile of cystic fibrosis airway epithelial cells undergoing repair

city: Geneva

first: Sylvain

last: LEMEILLE

address: 1 rue Michel-Servet

department: Department of Pathology and Immunology

country: Switzerland

institute: University of Geneva Medical School

summary: The purpose of the study is to compare the transcriptomic profile of the airway epithelium generated from bronchial airway epithelial cells isolated from healthy donors (NCF) and patients with cystic fibrosis (CF). Cells were grown at the air-liquid interface for at least 2-months. CF is caused by mutations of the cystic fibrosis transmembrane conductance regulator (CFTR) gene. Only patients homozygous for the F508del mutation of the CFTR gene were considered. The reconstituted airway epithelium was mechanically wounded and allowed to repair with time. We considered four steps: 1) intact, non-wounded (NW) epithelium; 2) 24h hours post-wounding (pW); 3) time at which the wound is closed (WC); 4) two days post-wound closure (pWC). We also mimicked infection by exposing the cells to Pseudominas aeruginosa flagelin for NW and WC conditions.

overall_design: mRNA profiles between NCF and CF cultures at different steps of the repair process (NW, pW, WC, pWC) were generated by deep sequencing using Illumina.

first: Alice

last: Zoso

first: Aderonke

last: Sofoluwe

first: Marc

last: Bacchetta

last: Lemeille

last: Chanson


title: A methylation analysis of human normotrophic scar dermal fibroblasts

status: Public on Sep 10 2019

city: Crawley

first: Andrew

middle: William

last: Stevenson

state: Western Australia

address: Room 112b, Curnow Building, Hackett Drive Carpark Entrance 2, UWA

department: School of Biomedical Sciences

country: Australia

institute: University of Western Australia

type: Methylation profiling by genome tiling array

summary:
3mm punch biopsies were taken from a healed normotrophic scar and a contralateral matched control site in burn patients with a scar at least 1 year old. Fibroblasts were cultured from explants to passage 2 and DNA was extracted and run on methylation arrays to examine differences in scar and control fibroblast gene expression
Normotrophic scar maintains its abnormal scar phenotype for the rest of the patients life, long after the injury has healed. Differences in gene expression may reaveal target genes that can be modulated to improve scar appearance

overall_design: 6 patients had normotrophic scar and matched control fibroblasts extracted and compared


title: A transcriptional analysis of normotrophic scar and control fibroblasts

status: Public on Sep 06 2019

summary:
3mm punch biopsies were taken from a healed normotrophic scar and a contralateral matched control site in burn patients with a scar at least 1 year old. Fibroblasts were cultured from explants to passage 2 and RNA was extracted and run on expression arrays to examine differences in scar and control fibroblast gene expression
Normotrophic scar maintains its abnormal scar phenotype for the rest of the patients life, long after the injury has healed. Differences in gene expression may reaveal target genes that can be modulated to improve scar appearance


title: STAT pathway activation limits the Ascl1-mediated chromatin remodeling required for neural regeneration from Müller glia in adult mouse retina

status: Public on Nov 01 2019

city: Seattle

first: Thomas

last: Reh

address: 1959 NE Pacific St

department: Biological Structures

institute: University of Washington

summary: Müller glia can serve as a source for retinal regeneration in some non-mammalian vertebrates. Recently we found that this process can be induced in mouse Müller glia after injury, by combining transgenic expression of the proneural transcription factor Ascl1 and the HDAC inhibitor TSA. However, new neurons are only generated from a subset of Müller glia in this model, and identifying factors that limit Ascl1-mediated MG reprogramming could potentially make this process more efficient, and potentially useful clinically. One factor that limits neurogenesis in some non-mammalian vertebrates is the STAT pathway activation that occurs in Müller glia in response to injury. In this report, we tested whether injury induced STAT activation hampers the ability of Ascl1 to reprogram Müller glia into retinal neurons. Using a STAT inhibitor, in combination with our previously described reprogramming paradigm, we found a large increase in the ability of Müller glia to generate neurons, similar to those we described previously. Single-cell RNA-seq showed that the progenitor-like cells derived from Ascl1-expressing Müller glia have a higher level of STAT signaling than those that become neurons. Using Ascl1 ChIP-seq and DNase-seq, we found that developmentally inappropriate Ascl1 binding sites (that were unique to the overexpression context) had enrichment for the STAT binding motif. This study provides evidence that STAT pathway activation reduces the efficiency of Ascl1-mediated reprogramming in Müller glia, potentially by directing Ascl1 to developmentally inappropriate targets.

overall_design: Characterizing epigenetic and transcriptomic differences between Müller glia and Ascl1-mediated  reprogrammed Müller glial-derived neurons. Ascl1 ChIP-seq datasets from developmental P0 whole retina to determine where Ascl1 binds normally in development. Ascl1 ChIP-seq datasets from P12 cultured Müller glia to determine where Ascl1 binds in a transgenic overexpression model. Ascl1 ChIP-seq datasets from P12 cultured with/without a STAT pathway inhibitor to determine STAT’s effect on Ascl1 binding. Single-cell RNA-seq dataset from FACS-purified MG-derived neurons that received improved reprogramming paradigm, including an intravitreal injection of a STAT pathway inhibitor.

first: Nikolas

last: Jorstad

first: Matthew

last: Wilken

first: Levi

last: Todd

first: Connor

last: Finkbeiner

first: Paul

last: Nakamura

first: Nick

last: Radulovich

first: Marcus

last: Hooper

first: Alex

last: Chitsazan

first: Brent

last: Wilkerson

first: Fred

last: Rieke


title: Distinct chromatin signitures of promoters, enhancers and transposons in allohexaploid wheat

status: Public on Jun 21 2019

city: shanghai

first: yijing

last: zhang

address: 2005 Songhu Road

department: Biochemistry

institute: Fudan University

type: Non-coding RNA profiling by high throughput sequencing

summary: Bread wheat is allohexaploid with 16 Gb genome, which has large intergenic region with abundant TEs and regulatory sequences . Our results give insight into the connections between chromatin modifications and transcriptional regulatory activity and provide the first systematic epigenomic map for functional annotation of the allohexaploid wheat genome.

overall_design: We integrated seven major chromatin marks, DNA methylome and open chromatin, along with transcriptomic data in allohexaploid wheat to systematically characterize distinct chromatin archetectures surrounding regulatory elements including promoters, enhancers and transposons.

first: Yijing

last: Zhang


title: A cellular taxonomy of the bone marrow stroma in homeostasis and leukemia demonstrates cancer-crosstalk with stroma to impair normal tissue function

status: Public on May 23 2019

first: Aviv

last: Regev

address: 415 Main Street

institute: Broad Institute

summary: Here, we use single-cell RNA-seq to define a cellular taxonomy of the mouse bone marrow stroma and its perturbation by malignancy. We identified stromal subsets expressing distinct hematopoietic regulatory genes, spanning new fibroblastic, and osteoblastic subpopulations. Emerging acute myeloid leukemia resulted in impaired osteogenic differentiation and reduced production of hematopoietic regulatory molecules necessary for normal hematopoiesis. Thus, cancer can affect tissue stroma in which they reside to disadvantage normal parenchymal cells. Our taxonomy of the regulatory stromal compartment provides experimental support for a model where malignant cells are more an architect than a destroyer of normal tissue, remodeling tissue stroma to enable emergent cancer.

overall_design: We profiled non-hematopoietic bone and bone marrow cells from Mouse by scRNA-seq. We enriched stroma cells from eight mice C57Bl/6 mice at the age of 8-10 weeks by FACS through selective depletion of hematopoietic cells and immune lineage cells as labeled by CD45, lineage and Ter119, profiled them by droplet-based scRNA-seq. To study changes under leukemia, we profiled by scRNA-seq 12,456 bone marrow stromal cells from MLL-AF9 (MLL) mice (n=4) and 10,548 cells from matched control transplanted mice (n=5). Finally, we profiled additional separate samples of bone and flushed bone marrow cells (~21,000 cells) to establish contribution of each component in the original cluster map of bone marrow stroma.

first: David

last: Scadden


title: Oncogenic Antisense LncRNA P14AS Regulates Expression of ANRIL through AUF1 Binding

status: Public on Mar 07 2019

city: beijing

first: wanru

last: ma

address: 52 Fucheng Road,Haidian District,Beijing

institute: beijing cancer hospital

summary: The CDKN2A/B locus at 9p21.3 contains crucial tumor suppressor (P16, P14, and P15) and oncogenic lncRNA ANRIL genes. This locus is most frequently inactivated in cancer genomes by deletion and DNA methylation. However, the mechanisms coordinately regulating their expression level are far from clear. In the present study, a novel lncRNA, P14AS, was characterized in the antisense strand of the fragment near CDKN2A exon1 in human cell lines using CDKN2A-specific probe captured RNA-sequencing (RNACap-Seq).

overall_design: Different gene expression in HCT116 cells with P14AS stable over-expression and/or transient AUF1 knockdown at 72 post-transfection hrs.

first: Wanru

last: Ma

first: Juanli

last: Qiao


title: Vasculature-associated fat macrophages readily adapt to inflammatory and metabolic challenges

status: Public on Feb 20 2019

city: NEW YORK

first: Hernandez

last: Moura Silva

address: 430 E 29th street. 4th floor, Lab 460A

department: Kimmel Center for Biology and Medicine at the Skirball Institute

institute: New York University Langone Medical Center

summary: We show that the epididymal white adipose tissue harbors 4 subpopulations of macrophages (VAM1, VAM2, PreVAM and DPs), 2 subpopulations of Dendritic Cells (CD11B+CD103- and CD11B-CD103+) and monocytes. VAMs display a gene signature enriched in pathways related to anti-inflammatory/ detoxifying and repair processes. Our gene expression work shows no evidence of an M2 to a Classically Activated/M1 shift during diet-induced obesity (DIO). Gene expression of VAMs or DP macrophages cannot be defined as M1 or M1-like. Our data are more compatible with the category of “Metabolically-activated” macrophages (MMe)

overall_design: Examination of RNA expression changes in different epididymal adipose tissue myeloid subpopulations in lean versus obese animals harboring metabolic syndrome

first: Juan

last: Lafaille

last: Silva


title: RNA-seq of MLLT3-overexpressing cultued HSPC, compared to non-overexpressing and uncutured FL-HSPC [RNAseq_MLLT3_OE]

status: Public on Mar 06 2019

city: Los Angeles

first: Vincenzo

last: Calvanese

address: 615 Charles E Young Dr S

institute: UCLA

summary: MLLT3 preserves the FL-HSPC gene expression signature in culture

overall_design: FL-HSPC were infected with Control or MLLT3-OE lentivirus and cultured for 4 weeks on OP9M2. sorted HSPC were profiled before (n=3) or after (n=6) culture

first: Andrew

middle: T

last: Nguyen

first: Timothy

last: Bolan

first: Yanling

last: Wang

first: Fides

middle: D

last: Lay

first: Mattias

last: Magnusson

first: Siavash

middle: K

last: Kurdistani

first: Hanna

last: Mikkola


title: Mllt3 Governs Self-Renewal And Engraftment Of Human Hematopoietic Stem Cells

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

overall_design: Refer to individual Series


title: CALGB 40601: Randomized Phase III Trial of Paclitaxel Combined With Trastuzumab, Lapatinib, or Both As Neoadjuvant Treatment of HER2-Positive Primary Breast Cancer

status: Public on Oct 16 2018

city: Chapel Hill

first: Charles

middle: M.

last: Perou

state: NC

address: 12-044 Lineberger Comprehensive Cancer Center CB# 7295

department: Professor of Genetics, and Pathology & Laboratory Medicine; Lineberger Comprehensive Cancer Center

institute: University of North Carolina at Chapel Hill

summary: CALGB 40601 was activated as a 3-arm study (paclitaxel + trastuzumab + lapatinib [THL], paclitaxel + trastuzumab [TH] and paclitaxel + lapatinib [TL]). In December 2010, twoneoadjuvant studies were presented at the Cancer Therapy and Research Center-American Association for Cancer Research (CTRC-AACR) San Antonio Breast Cancer Symposium that affected the scientific and practical enthusiasm for the TL arm. For this reason the CALGB 40601 has been amended to omit the TL treatment arm (arm 3). In the Geparquinto trial, patients with HER2-positive breast cancer received epirubicin/cyclophosphamide followed by docetaxel combined either with trastuzumab (EC-DOC-H) or lapatinib (EC-DOC-L) neoadjuvantly, then trastuzumab for a total of 12 months adjuvantly [34]. Pathologic complete response (pCR) in breast and axilla was the primary endpoint. Among 620 patients randomized, there was a higher pCR rate (31% vs 22%) and lower toxicity with fewer discontinuations (10% vs 16%) among patients on the trastuzumab arm than the lapatinib arm. The first results of the NeoALTTO trial were similar [35]. Approximately 450 women with HER2-positive breast cancer received a lead-in phase of 6 weeks of biologic therapy withlapatinib (L), trastuzumab (H), or both, then paclitaxel was added for an additional 12 weeks prior to surgery. All drugs were given at doses similar to CALGB 40601. Postoperative  adjuvant therapy included additional chemotherapy and biologic therapy, however, the presentation focused solely on the primary endpoint of pCR in the breast at surgery; no longterm outcomes were presented. There were more grade > 3 adverse events in the lapatinib arm compared with the trastuzumab arm, including diarrhea (23% vs 2%), hepatic abnormalities (13% vs 1%), and neutropenia (16% vs 3%). The only death occurred in the combined biologic (LH) arm. Failure to complete treatment as planned was higher in the L (34%) and LH arms (39%) that in the H arm (u%). PCR was highest with LH-paclitaxel (51%), followed by H-paclitaxel (30%), and L-paclitaxel (25%). Based on the inferior results and higher toxicity of the investigational lapatinib arms of these studies and in discussion with CTEP, in January 2011 it was decided to amend CALGB 40601 to omit Arm 3 (TL). Those patients on this arm will complete protocol therapy as perthe original study design. In CALGB 40601, it is recommended that all patients receive trastuzumab adjuvantly for 1 year, hence all of the patients including those previously randomized to the TL neoadjuvant arm, will be able to receive the known benefit of trastuzumab. After local IRB approval of Update #5, the remainder of the patients will be enrolled and randomized to Arm 1 (THL) and Arm 2 (TH) in a 2:1 fashion. Given that TH isthe standard regimen, and is also clearly the best tolerated, we will continue that arm of thestudy as the comparator, with THL as the only investigational arm.

overall_design:
This randomized phase III trial studies paclitaxel and trastuzumab with or without lapatinib to see how well they work in treating patients with stage II or stage III breast cancer that can be removed by surgery. Drugs used in chemotherapy, such as paclitaxel, work in different ways to stop the growth of tumor cells, either by killing the cells, by stopping them from dividing, or by stopping them from spreading. Monoclonal antibodies, such as trastuzumab, can block tumor growth in different ways. Some block the ability of tumor cells to grow and spread. Others find tumor cells and help kill them or carry tumor-killing substances to them. Lapatinib may stop the growth of tumor cells by blocking some of the enzymes needed for cell growth. Giving paclitaxel with trastuzumab and/or lapatinib before surgery may make the tumor smaller and reduce the amount of normal tissue that needs to be removed. It is not yet known which regimen is more effective in treating patients with breast cancer.
Raw data are not publicly available for this series due to patient privacy concerns. The raw data have been deposited at dbGaP for controlled access under accession ID: phs001570

first: Lisa

last: Carey

first: Ian

last: Krop

first: Deanna

last: Kroetz

last: Ollila

first: Baljit

last: Singh

first: Jennifer

last: Bellon

first: Patricia

last: Spears

first: Matthew

middle: G

last: Soloway


title: Molecular specification of cell types underlying central and peripheral vision in primates

status: Public on Feb 06 2019

first: Wenjun

last: Yan

address: 52 Oxford Street

department: Department of Molecular  and Cellular Biology

institute: Harvard University

first: Yi-Rong

last: Peng

first: Karthik

last: Shekhar

first: M

last: Do

first: Aviv

last: Regev

first: Joshua

last: Sanes


title: Nascent RNA variation reveals architecture and interactions of transcribed regulatory elements

city: Ithaca

first: Hojoong

last: Kwak

address: 317 Biotechnology Building

department: Molecular Biology and Genetics

institute: Cornell University

summary: Active transcriptional regulatory elements are bidirectionally transcribed, the level of transcription correlating with regulatory activity. Using capped nascent RNA sequencing (PRO-cap) in 69 human lymphoblastoid cell lines, we identify 87,826 transcribed transcriptional regulatory elements (tTREs) and thousands of genetic variants that associate with tTRE transcription. Many of these variants associate with gene expression and are enriched at specific positions – central transcription factor (TF) binding sites or surrounding transcription start sites – consistent with a dual-hub tTRE architecture. Additionally, co-expression analyses reveal interactions between tTREs. We find evidence of TFs influencing mid- to long-range interactions and of strand-dependent cooperativity at closely-spaced tTREs.

overall_design: Identification and quantification of transcriptional activity at transcriptional regulatory elements (using PRO-cap) across YRI population.

first: Hyun

last: Kang


title: Gene expression profiling from high-fat diet (HFD)-treated and regular diet (RD)-treated lung cancer

status: Public on Sep 08 2018

city: Taipei

first: Yun-Ting

last: Hsieh

address: Rm. 521-1, 5F., No.1, Changde St., Zhongzheng Dist.

department: Department of Clinical Laboratory Sciences and Medical Biotechnology

country: Taiwan

institute: National Taiwan University

summary: We utilized inducible transgenic mouse with spontaneous lung cancer formation driven by mutant EGFR (by Doxycycline induction) for experiments. Mice fed with regular diet (RD) or high-fat diet (HFD) were induced lung cancer followed by tumor burden evaluation. Lung tissues were harvested for whole-genome transcriptomic, gene enrichment analysis, and cytokine array for potential signatures identification.Gene set enrichment analysis showed the whole-genome transcriptome in HFD vs. RD treated lung cancer was enriched in immune responses and cytokine stimulus.

overall_design: To evaluate the gene expression profiles after high-fat-treated lung environment, total RNAs from the following 2 groups were extracted for whole trancriptomic analysis : (1)HFD+Dox (2) RD+Dox

first: YUN-TING

first: KANG-YI

last: Su


title: ER proteostasis and temperature differentially impact the mutational tolerance of influenza hemagglutinin

status: Public on Sep 10 2018

last: Shoulders

address: 77 Massachusetts Avenue

department: Chemistry

institute: Massachusetts Institute of Technology

summary: Here, we present a systematic and quantitative test of the hypothesis that the composition and activities of the endoplasmic reticulum (ER) proteostasis network impact mutational tolerance of secretory pathway client proteins. We focus on influenza hemagluttinin (HA), a viral coat protein that folds in the host’s ER via a complex but well-characterized pathway. By integrating chemical methods to modulate the unfolded protein response with deep mutational scanning to assess mutational tolerance, we discover that upregulation of ER chaperones broadly enhances HA mutational tolerance across numerous sites and secondary/tertiary structure elements, including sites targeted by host antibodies. Remarkably, this host chaperone-enhanced mutational tolerance is observed at the same HA sites where mutational tolerance is most reduced by propagation at a fever-like temperature. Thus, host ER proteostasis mechanisms and temperature modulate HA mutational tolerance in opposite directions. This finding has important implications for influenza evolution, because influenza immune escape is contingent on HA possessing sufficient mutational tolerance to acquire antibody resistance while still maintaining the capacity to fold and function. More broadly, this work provides the first experimental evidence that the composition and activities of the ER proteostasis network critically define the mutational tolerance and, therefore, the evolution of secretory pathway client proteins.

overall_design: RNA-seq characterizing a clonal HEK293T-Rex cell line, expressing DHFR ATF6f, Tet XBP1s, and the tetracycline repressor. These cell lines were treated with small molecules for 24 hours (in triplicate) to modulate the proteostasis environment in a stress-independent manner, at either 37C or 39C. XBP1s was activated by treatment with 0.1 ug/mL Doxycycline; ATF6f/XBP1s were activated by treatment with 0.1 ug/mL Doxycycline and 1 uM TMP; basal cells were vehicle-treated (0.01% DMSO). These cells were previously characterized in Shoulders et al. Cell Reports, 2013.

first: Angela

last: Phillips

first: Vincent

last: Butty


title: Bcl11b defines pro-T identity by site-specific cofactor recruitment and by repressing Id2 and Zbtb16.

status: Public on Sep 21 2018

city: Isehara

first: Hiroyuki

last: Hosokawa

state: Kanagawa

address: 143 Shimokasuya

department: Department of Immunology

country: Japan

institute: Tokai University School of Medicine

summary: Multipotent progenitors confirm their T-lineage identity at the DN2a to DN2b pro-T cell transition, when expression of the essential transcription factor Bcl11b begins. This study defines the molecular basis of direct and indirect actions of Bcl11b in acquisition of T cell identity. In vivo and in vitro stage-specific deletions identify functional regulation targets genome-wide for mechanistic analysis. Bcl11b can associate with multiple co-factors and its direct action is needed to recruit these to selective target sites. Sites of Bcl11b-dependent cofactor recruitment are enriched at functionally regulated targets, and deletion of individual cofactors can relieve repression of many Bcl11b-repressed genes. In parallel, Bcl11b indirectly regulates a subset of its target genes by a gene network circuit via Id2 and Zbtb16, which are directly repressed by Bcl11b and control distinct alternative programs.

overall_design:
ChIP-seq; Ten million of BM-derived DN3 cells or Schd.adh.2c2 cells were fixed with 1 mg/ml DSG (Thermo Scientific) in PBS for 30 min at RT followed by additional 10 min with addition of formaldehyde up to 1%.  The reaction was quenched by addition of 1/10 volume of 0.125M glycine and the cells were washed with HBSS (Gibco).  Pelleted nucleus were dissolved in lysis buffer (0.5% SDS, 10 mM EDTA, 0.5 mM EGTA, 50 mM Tris-HCl (pH 8) and PIC) and sonicated on a Bioruptor (Diagenode) for 18 cycles of 30sec sonication followed by 30sec rest, with max power.  Six μg per 107 cells of anti-Bcl11b Abs (a mixture of A300-383A (Bethyl), A300-385A (Bethyl), ab18465 (Abcam) and 12120 (CST)), anti-Chd4 (A301-081A), anti-Mta2 (sc-9447), anti-Hdac2 (ab12169), anti-Rest (12C11-1B11), anti-Ring1b (A302-869A), anti-LSD1 (ab17721) or anti-Runx1 (ab23980) were hybridized to Dynabeads anti-Rabbit, Dynabeads anti-Mouse or Dynabeads Protein A/G (Invitrogen) and added to the diluted chromatin complex.  They were incubated over night at 4°C, then washed and eluted for 6hr at 65°C in ChIP elution buffer (20 mM Tris-HCl, pH 7.5, 5 mM EDTA 50 mM NaCl, 1% SDS, and 50 μg/ml proteinase K).  Precipitated chromatin fragments were cleaned up using Zymo ChIP DNA Clean & Concentrator.  ChIP-seq libraries were constructed using NEBNext ChIP-Seq Library Preparation Kit (E6240, NEB) and sequenced on Illumina HiSeq2500 in single read mode with the read length of 50 nt.
RNA-seq; Total RNA was isolated from 300,000 cells using an RNAeasy MicroKit (Qiagen).  Libraries were constructed using NEBNext Ultra RNA Library Prep Kit for Illumina (E7530, NEB) from ~1 μg of total RNA following manufacturer’s instructions.  Libraries were sequenced on Illumina HiSeq2500 in single read mode with the read length of 50 nt.
Please note that each *peaks.csv file was generated from both rep1 & rep2 and is linked to the corresponding rep1 sample records.

first: Maile

last: Romero-Wolf

first: Mary

middle: A

last: Yui

first: Jonas

last: Ungerbäck

first: Masaki

last: Matsumoto

first: Keiichi

middle: I

last: Nakayama

first: Tomoaki

last: Tanaka

first: Ellen

middle: V

last: Rothenberg


title: Next-generation sequencing of microRNAs in different locations of hair follicles (bulb, bugle)in androgenetic alopecia

status: Public on Dec 24 2018

city: GuangZhou

first: Qian

last: Qu

address: 1838 North Guangzhou AV

institute: Nanfang Hospital of Southern Medical University

summary: To fully interrogate location-specific variations of microRNAs of the hair follicle in AGA and normal persons, we sought to perform a thorough and comprehensive microRNA profiling of different locations of hair follicles (bulb  portions, bugle  portions)

overall_design: Hair follicles harvested by follicular unit extraction came respectively from vertex (balding) and occipital (nonbalding) areas from 12 patients and occipital areas from 12 control subjects. Using microdissection, hair follicle was separated into two part

first: Zhi-Qi

last: Hu

first: Yong

last: Miao


title: Gene expression profiling of subclinical acute kidney rejection I

status: Public on Jul 24 2018

city: La Jolla

first: Sunil

last: Kurian

state: CA

address: 10550 N Torrey Pines Road

department: Molecular and Experimental Medicine

institute: The Scripps Research Institute

summary: Sub-clinical acute rejection (subAR) in kidney transplant recipients (KTR) leads to chronic rejection and graft loss. Non-invasive biomarkers are needed to detect subAR. 307 KTR were enrolled into a multi-center observational study. Precise clinical phenotypes (CP) were used to define subAR. Differential gene expression (DGE) data from peripheral blood samples paired with surveillance biopsies were used to train a Random Forests (RF) model to develop a gene expression profile (GEP) for subAR. A separate cohort of paired samples was used to validate the GEP. Clinical endpoints and gene pathway mapping were used to assess clinical validity and biologic relevance. DGE data from 530 samples (130 subAR) collected from 250 KTR yielded a RF model: AUC 0.85; 0.84 after internal validation with bootstrap resampling. We selected a predicted probability threshold favoring specificity and NPV (87% and 88%) over sensitivity and PPV (64% and 61%, respectively). We tested the locked model/threshold on a separate cohort of 138 KTR undergoing surveillance biopsies at our institution (rejection 42; no rejection 96): NPV 78%; PPV 51%; AUC 0.66. Both the CP and GEP of subAR within the first 12 months following transplantation were independently associated with worse graft outcomes at 24 months, including de novo donor-specific antibody (DSA). Serial GEP tracked with response to treatment of subAR.  DGE data from both cohorts mapped to gene pathways indicative of allograft rejection.


title: A global map of RNA binding protein occupancy guides functional dissection of post-transcriptional regulation of the T cell transcriptome [Hs]

status: Public on Jul 01 2018

city: San Francisco

first: Adam

middle: Jacob

last: Litterman

address: 513 Parnassus Avenue, UCSF Box 0414, HSE-201

department: Microbiology and Immunology

institute: UCSF

summary: RBP binding sites were globally mapped by a biochemical technique in human T cells

overall_design: Protein bound segments of mammalian mRNAs were sequenced by capture of crosslinked, biotinylated RBPs and compared to RNAseq

middle: J

first: K

last: Ansel


title: Gene expression profiling of subclinical acute kidney rejection


title: Arabidopsis SE coordinates histone methyltransferases ATXR5/6 and RNA processing factor RDR6 to regulate transposon expression [sRNA-Seq]

status: Public on Jun 26 2018

city: college station

first: Xiuren

last: Zhang

address: 2123 tamu

department: biochemistry & biophysics

institute: texas a&m university

summary: We performed Illumina sequencing of sRNA libraries prepared from 10-day-old seedlings in Arabidopsis.  SE is a key component in miRNA processing and pre-mRNA splicing, whereas ATXR5/6 is engaged in epigenetic silencing. Genome-wide sRNA sequencing revealed that ATXR5/6 did not participate in SE-mediated miRNA biogenesis.

overall_design: Non-coding RNA profiling by high throughput sequencing.

first: Zeyang

last: Ma

first: Claudia

last: Castillo-González

first: Zhiye

last: Wang

first: Di

last: Sun


title: Arabidopsis SE coordinates histone methyltransferases ATXR5/6 and RNA processing factor RDR6 to regulate transposon expression [RNA-Seq]

summary: We performed Illumina sequencing of ribosome depletion RNA libraries prepared from 10-day-old seedlings in Arabidopsis. SE is required for transposon reactivation in atxr5 atxr6 mutant.

overall_design: Ribosome depletion RNA profiling by high throughput sequencing.


title: Arabidopsis SE coordinates histone methyltransferases ATXR5/6 and RNA processing factor RDR6 to regulate transposon expression [ChIP-Seq]

summary: We performed ChIP-seq of SE and selected histone modifications. ATXR5/6 deposit histone3 lysine27 monomethylation (H3K27me1) to promote heterochromatin formation and repress transposable elements (TEs) in Arabidopsis. SE binds to ATXR5/6-regulated TE loci and promotes H3K27me1 accumulation in these regions.

overall_design: Examination of chromatin enrichment of SE and selected histone modifications in four genetic backgrounds of Arabidopsis thaliana.


title: Buparlisib-treated Patient Derived Xenograft (PDX) Reversed Phase Protein Array (RPPA) Data

status: Public on May 29 2018

city: st louis

first: Cynthia

address: 4515 Mckinley, 4515 Mckinley

department: Medical Oncology

institute: Washington University

summary: Phosphoinositide 3-kinase (PI3K) signaling activation is frequently observed in triple negative breast cancer, however, PI3K inhibitors have shown limited clinical activity. To investigate resistance mechanisms, we performed global transcriptome, proteome, phosphoproteome and kinome analysis of a panel of triple negative breast cancer patient derived xenograft models with varying responsiveness to buparlisib, a pan-PI3K inhibitor, for differentially expressed baseline and post-treatment biomarkers. Resistance was associated with incomplete inhibition of PI3K and upregulated MAPK/MEK signaling in response to buparlisib. Outlier phosphoproteome and kinome analyses identified additional candidates in association with buparlisib resistance, including NEK9 and MAP2K4. Knockdown of NEK9 or MAPK2K4 reduced both baseline and feedback MAPK/MEK signaling and enhanced buparlisib efficacy in vitro. Interestingly, we show that a complex ins/del in PIK3CA led to a change in buparlisib response in a NEK9/MAP2K4 dependent manner. In summary, our study indicates a role for NEK9 and MAP2K4 in mediating buparlisib resistance and demonstrates the value of unbiased global analyses in uncovering resistance mechanisms to targeted therapy.

overall_design: 6 PDX models were analyzed under 5 treatment conditions: 1) 2hr control, 2) 2hr Buparlisib, 3) 50hr Buparlisib, 4) 50hr control, 5) 50hr washout.  3 bioreplicates and 3 technical replicates were analyzed when possible.

first: Jeremy

middle: W

last: Hoog


title: Yki- and Ras-induced intestinal stem cells (ISCs) overproliferation affects  gene expression in the midgut of adult flies

status: Public on Apr 27 2018

city: Boston

first: Wei

last: Song

email: rocwsong@gmail.com, songw@whu.edu.cn

state: Massachusetts

address: 77 Ave Louis Pasteur, NRB 336

department: Department of Genetics

institute: Harvard Medical School

summary: Purpose: Activation of yki or Ras signaling pathways in ISCs causes overproliferation and ISC reprogramming. To gain insight into yki- and Ras-induced ISC reprogramming and gene expression, we performed a transcriptomic analysis of adult midgut with overexpression of yki-3SA or Ras1A in the ISCs.

overall_design: Methods: To extract total RNAs for RNA-Seq experiment, we used 10 midguts dissected from both esg-Gal4, tub-Gal80ts, UAS-GFP/+ (Con) and esg-Gal4, tub-Gal80ts, UAS-GFP/UAS-Yki-3SA (Yki) and esg-Gal4, tub-Gal80ts, UAS-GFP/UAS-Ras1A (Ras) flies incubated for 8 days at 29°C. After assessing RNA quality with Agilent Bioanalyzer, mRNAs were enriched by poly-A pull-down from total RNA samples (200ng - 1ug per sample, RIN > 7 required). Then, sequencing libraries constructed with Illumina TruSeq RNA prep kit were sequenced using Illumina HiSeq2000 at the Columbia Genome Center (http://systemsbiology.columbia.edu/genome-center). We multiplexed samples in each lane, which yields targeted number of single-end 100 bp reads for each sample, as a fraction of 180 million reads for the whole lane. We use RTA (Illumina) for base calling and bcl2fastq (version 1.8.4) for converting BCL to fastq format, coupled with adaptor trimming. We map the reads to a reference Drosophila genome (flybase genome annotation version r5.51) using Tophat (version 2.1.0) with 4 mismatches (--read-mismatches = 4) and 10 maximum multiple hits (--max-multihits = 10). To tackle the mapping issue of reads that are from exon-exon junctions, Tophat infers novel exon-exon junctions ab initio, and combine them with junctions from known mRNA sequences (refgenes) as the reference annotation.  We estimate the relative abundance (aka expression level) of genes and splice isoforms using cufflinks (version 2.0.2) with default settings. We test for differentially expressed genes under various conditions using DEseq. It is an R package based on a negative binomial distribution that models the number reads from RNA-seq experiments and test for differential expression.

first: Norbert

last: Perrimon


title: Arabidopsis SE coordinates histone methyltransferases ATXR5/6 and RNA processing factor RDR6 to regulate transposon expression


title: BKM120 Treated PDX's

summary: The objective of this study was to analyze gene expression changes with  BKM120 treatment across PDX models.

overall_design: Phosphoinositide 3-kinase (PI3K) signaling activation is frequently observed in triple negative breast cancer, however, PI3K inhibitors have shown limited clinical activity. To investigate resistance mechanisms, we performed global transcriptome, proteome, phosphoproteome and kinome analysis of a panel of triple negative breast cancer patient derived xenograft models with varying responsiveness to buparlisib, a pan-PI3K inhibitor, for differentially expressed baseline and post-treatment biomarkers. Resistance was associated with incomplete inhibition of PI3K and upregulated MAPK/MEK signaling in response to buparlisib. Outlier phosphoproteome and kinome analyses identified additional candidates in association with buparlisib resistance, including NEK9 and MAP2K4. Knockdown of NEK9 or MAPK2K4 reduced both baseline and feedback MAPK/MEK signaling and enhanced buparlisib efficacy in vitro. Interestingly, we show that a complex ins/del in PIK3CA led to a change in buparlisib response in a NEK9/MAP2K4 dependent manner. In summary, our study indicates a role for NEK9 and MAP2K4 in mediating buparlisib resistance and demonstrates the value of unbiased global analyses in uncovering resistance mechanisms to targeted therapy.


title: Arabidopsis SE coordinates histone methyltransferases ATXR5/6 and RNA processing factor RDR6 to regulate transposon expression [Bisulfite-Seq]

summary: We performed whole genome bisulfite sequencing in se-2 and the related triple mutants. se-2 mutant did not display obvious changes in genome wide methylation in CG, CHG and CHH contexts. Thus, the H3K27me1 hypomethylation and suppression of atxr5/6-reactivated loci in se-2 mutant was not through DNA methylation defect.

overall_design: Examination of DNA methylation using bisulfite conversion of unmethylated cytosines in six genetic backgrounds of Arabidopsis thaliana.


title: NEUROG1 regulates CKD2 expression to promote proliferation

status: Public on Mar 07 2018

city: Piscataway

first: Kelvin

middle: Y.

last: Kwan

state: NJ

address: 604 Allison Rd.

department: Cell Biology & Neuroscience

institute: Rutgers University

summary: An immortalized multipotent otic progenitor (iMOP) cell was used to determine H3K4me3 and H3K27me3 histone marks.  Promoters containing enriched with both histone marks were considered bivalent promoters. Neurog1 dependent transription was determined in genes with bivalently marked promoters.

overall_design: ChIP-Seq was accomplished by immunoprecipitating endogenous H3K4me3 and H3K27me3

first: Zhichao

first: Azadeh

last: Jadali

first: Bernd

last: Fritzsch


title: Determination of Nir (Noc2l) function in epidermis during mouse development by global transcriptome analysis

status: Public on Mar 05 2018

city: ILLKIRCH

first: Delphine

last: Duteil

address: 1 rue Laurent Fries

institute: IGBMC

summary: To investigate the role of Nir in epidermis during embryogenesis, we crossed mice harboring conditional Nir alleles with the Krt14-Cre deleter strain, which results in Cre-mediated loss of Nir selectively in epidermis. Transciptome analysis of keratinocytes obtained from control and knock-out mice at E15.5 revealed 4393 genes differentially expressed between Nir knock-out and control mice (p-value<10-2). At E17.5, we found 5673 differentially expressed genes.

overall_design: We selectively knocked-out Nir in epidermis by crossing Nir floxed mice to Krt14-Cre mice. At E15.5 and E17.5, epidermis was separated from the dermnis and RNA from control Nir floxed mice) and knock-out mice was extracted with trizol according to the manufacturer protocol. RNA samples were sequenced by the standard Illumina protocol to create raw sequence files (.fastq files). We annotated these reads to the mm10 build of the mouse genome using TopHat version 2. The aligned reads were counted with the homer software (analyze RNA) and DEG’s were identified using EdgeR.

first: Dominica

last: Willmann

first: Roland

last: Schüle


title: Modified cross-linking, ligation, and sequencing of hybrids (qCLASH) identifies KSHV microRNA targets in endothelial cells

status: Public on Jan 25 2018

city: Gainesville

first: Rolf

last: Renne

address: 2033 Mowry Road

institute: University of Florida

summary: KS lesions consist of endothelial cells latently infected with KSHV which express the KSHV miRNAs.  Identifying the targets of the KSHV miRNAs will help us understand their role in viral oncogenesis.  Cross-Linking and Sequencing of Hybrids (CLASH) is a method for unambiguously identifying miRNA targetomes.  We developed a streamlined version of CLASH, called quick CLASH (qCLASH).  qCLASH requires a lower initial input of cells than its parent protocol.  Additionally, a new fast-growing KSHV-negative endothelial cell line, named TIVE-EX-LTC cells, was established.  qCLASH was performed on TIVE-EX-LTC cells latently infected with WT KSHV or a mutant virus lacking miR-K12-11/11*.  A number of novel targets of the KSHV miRNAs were identified, including targets of miR-K12-11, the ortholog of cellular oncomiR miR-155.  Many of the miRNA targets were involved in processes related to oncogenesis, such as glycolysis, angiogenesis, and cell cycle control.

overall_design: Cells were infected with WT KSHV or KSHV ΔmiR-K12-11.  Argonaute was crosslinked to bound RNAs in living cells with UV irradiation.  Argonaute was immunoprecipitated and bound RNAs were ligated to one another and then isolated.

first: Lauren

last: Gay

first: Sunantha

last: Sethuraman

first: Vaibhav

last: Jain

first: Merin

last: Thomas

first: Alberto

last: Riva

first: Peter

middle: C

last: Turner


title: Molecular specification of cell types underlying central and peripheral vision in primates (macaque fovea single cell RNA-seq)

city: Cambridge

first: Wenjun

last: Yan

summary: Among mammals, only primates including human possess a small central retinal region called the fovea, which mediates high acuity vision. As other mammals lack a fovea, molecular bases of its specialized function and dysfunction in retinal diseases remain poorly understood. By analyzing >165,000 single-cell transcriptomes from macaque fovea and peripheral retina, we identified and molecularly characterized >60 major cell types in each region. A few cell types are unique to each region, and there are also substantial differences in proportions and gene expression between corresponding types in the two areas, some of which can be related to functional differences. Comparison of macaque and mouse retinal taxonomies reveals both similarities and differences between species. Many molecular features of macaque retinal cell types are conserved in two other primates, marmosets and humans, and key human retinal disease-associated genes are expressed in specific macaque cell types

overall_design: Fovea samples from four crab-eating macaque are included. For fovea1 and fovea2, each have 8 replicates; there are 3 replicates of fovea3

first: Yi-Rong

last: Peng

first: Karthik

last: Shekhar

first: M

last: Do

first: Aviv

last: Regev

first: Joshua

middle: R

last: Sanes


title: Response of HEK293 Freestyle cells to 36 h of culture in Zn(II)-depleted Freestyle medium

status: Public on Jan 18 2018

first: Matthew

last: Shoulders

summary: We describe the preparation, evaluation, and application of an S100A12 protein-conjugated solid support, hereafter the “A12-resin,” that can remove 99% of Zn(II) from complex biological solutions without significantly perturbing the concentrations of other metal ions. The A12-resin can be applied to selectively deplete Zn(II) from diverse tissue culture media and from other biological fluids including human sera. To further demonstrate the utility of this approach, we investigated metabolic, transcriptomic, and metallomic responses of HEK293T cells cultured in medium depleted of Zn(II) using S100A12. Our data indicate that dividing cells can maintain a constant pool of free Zn(II), even under conditions of severe Zn(II) deprivation. We expect that the A12-resin will facilitate interrogation of disrupted Zn(II) homeostasis in biological settings, uncovering novel roles for Zn(II) in biology.

overall_design: Defining the response of a cell line to Zn(II) starvation

first: Christopher

middle: E

last: Richardson


title: Single cell RNA-seq of mouse mammary gland epithelium cells

status: Public on Nov 20 2017

city: Parkville

first: Gordon

last: Smyth

state: Vic

address: 1G Royal Pde

department: Bioinformatics

institute: Walter and Eliza Hall Institute of Medical Research

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

overall_design: Refer to individual Series


title: Single cell RNA-seq of ten-thousand epithelium cells from the mammary glands of mice in puberty, estrus and diestrus phases

summary: Epithelial cells were isolated by FACS from the mammary glands of pubescent (5 week old), estrus adult (10 week old) and diestrus adult (10 week old) female mice. Freshly sorted cells were submitted to a 10X Genomics Chromium System for single cell capture. cDNA synthesis and library preparation was done according to the protocol supplied by the manufacturer. Sequencing was carried out on an Illumina NextSeq500 sequencer using parameters recommended by 10X Genomics.

overall_design: Transcriptional profiling was completed for 5387 total epithelial cells from pubescent (5 week old) mice, 2729 total epithelial cells from adult (10 week old) mice in the estrus phase, and 2439 total epithelial cells from adult (10 week old) mice in the diestrus phase.

first: Yunshun

last: Chen

first: Bhupinder

last: Pal

first: Jane

last: Visvader


title: Single cell RNA-seq of eight thousand epithelium cells from the mammary glands of adult mice

summary: Epithelial cells were isolated by FACS from the mammary glands of adult (10 week old) female mice. A basal subpopulation of the epithelial cells was also isolated. Freshly sorted cells were submitted to a 10X Genomics Chromium System for single cell capture. cDNA synthesis and library preparation was done according to the protocol supplied by the manufacturer. Sequencing was carried out on an Illumina NextSeq500 sequencer to achieve 75 bp paired-end reads.

overall_design: Transcriptional profiling was completed for 4771 basal cells and 3302 total epithelial cells from 8 mice.


title: Host Proteostasis Modulates Influenza Evolution

status: Public on Nov 15 2017

summary: Predicting and constraining RNA virus evolution require understanding the molecular factors that define the mutational landscape accessible to these pathogens. RNA viruses typically have high mutation rates, resulting in frequent production of protein variants with compromised biophysical properties. Their evolution is necessarily constrained by the consequent challenge to protein folding and function. We hypothesize that host proteostasis mechanisms, may be significant determinants of the fitness of viral protein variants, serving as a critical force shaping viral evolution. Here, we test this hypothesis by propagating influenza in host cells displaying chemically-controlled, divergent proteostasis environments. We find that both the nature of selection on the influenza genome and the accessibility of specific mutational trajectories are significantly impacted by host proteostasis. These findings provide new insights into features of host–pathogen interactions that shape viral evolution, and into the potential design of host proteostasis-targeted antiviral therapeutics that are refractory to resistance.

overall_design: RNA-seq characterizing two clonal MDCK cell lines, one stably expressing DHFR HSF1, and another stably expressing DHFR YFP. These cell lines were treated with small molecules for 24 hours (in triplicate) to modulate the proteostasis environment in a stress-independent manner. The DHFR HSF1 MDCK cells were treated with: 0.1% DMSO, 10 µM TMP, or 10 nM STA-9090. The DHFR YFP MDCK cells were treated with either 0.1% DMSO or 10 µM TMP.

first: Angela

middle: M

last: Phillips

first: Vincent

middle: L

last: Butty

middle: S