title: ChIA-PET from HEK293 (ENCSR410UHV)

summary:
CTCF ChIA-PET in HEK293

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


title: ChIA-PET from HepG2 (ENCSR411IVB)

status: Public on Jun 15 2021

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

country: USA

institute: ENCODE DCC

summary:
CTCF ChIA-PET with HepG2 cell

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


title: ChIA-PET from activated CD8-positive, alpha-beta memory T cell (ENCSR114KEO)

status: Public on Nov 04 2021

type: Genome binding/occupancy profiling by high throughput sequencing

summary:
RNAPII ChIA-PET in Memory_CD8_Activated_Day7

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


title: ChIA-PET from SK-N-SH (ENCSR514HBO)

summary:
CTCF ChIA-PET in SK-N-SH

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


title: ChIA-PET from AG04450 (ENCSR514BNX)

summary:
RNAPII ChIA-PET in AG04450

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


title: ChIA-PET from HEK293 (ENCSR934CYB)

summary:
RNAPII ChIA-PET in HEK293

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


title: ChIA-PET from MCF 10A (ENCSR403ZYJ)

summary:
CTCF ChIA-PET with MCF10A cell

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


title: ChIA-PET from HepG2 (ENCSR789ZIJ)

summary:
RNAPII ChIA-PET with HepG2 cell

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


title: ChIA-PET from endothelial cell of umbilical vein (ENCSR080OMN)

summary:
RNAPII ChIA-PET in HUVEC

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


title: ChIA-PET from MCF-7 (ENCSR059HDE)

summary:
RNAPII ChIA-PET in MCF7

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


title: ChIA-PET from HCT116 (ENCSR278IZK)

summary:
CTCF ChIA-PET in HCT116

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


title: ChIA-PET from RWPE1 (ENCSR030KAB)

summary:
CTCF ChIA-PET in RWPE1

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


title: Breast tissue regeneration is driven by cell-matrix interactions that coordinate multi-lineage stem cell differentiation through DDR1

status: Public on Oct 25 2021

city: Boston

first: Charlotte

last: Kuperwasser

address: 136 Harrison Ave

institute: Tufts University

type: Expression profiling by high throughput sequencing

summary: Mammary morphogenesis is an orchestrated process involving differentiation, proliferation and organization of cells to form a bi-layered epithelial network of ducts and lobules embedded in storm tissue. We have engineered a 3D biomimetic human breast that makes it possible to study how stem cell fate decisions translate to tissue-level structure and functions. Using this advancement, we describe the mechanism by which breast epithelial cells build a complex three-dimensional, multi-lineage tissue by signaling through the collagen receptor DDR1. DDR1 induces stem cells to differentiate into basal cells, which in turn stimulate luminal progenitor cells to differentiate and form lobules via Notch signaling. These findings demonstrate how human breast tissue regeneration is triggered by transmission of signals from the extracellular matrix through an epithelial bilayer to coordinate structural changes that form a complex ductal-lobular network. More broadly, these findings suggest that DDR1 may coordinate collagen and Notch signaling to regulate multi-lineage differentiation and morphogenesis across diverse tissues.

sample_organism:
Homo sapiens
Mus musculus

overall_design: Single-cell RNA sequencing experiments of mammary organoids treated with or without DDR1 inhibition

first: Dexter

middle: X

last: Jin

first: Gat

last: Rauner

first: Daniel

middle: H

last: Miller

first: Piyush

middle: B

last: Gupta


title: ChIA-PET from MCF-7 (ENCSR200VHL)

summary:
CTCF ChIA-PET in MCF7

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


title: ChIA-PET from HCT116 (ENCSR035PVZ)

summary:
RNAPII ChIA-PET in HCT116

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


title: ChIA-PET from AG04449 (ENCSR580MNR)

summary:
CTCF ChIA-PET in AG04449

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


title: ChIA-PET from HEK293T (ENCSR773XVD)

summary:
RNAPII ChIA-PET in HEK293T

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


title: ChIA-PET from K562 (ENCSR597AKG)

summary:
CTCF ChIA-PET in K562

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


title: Chromatin-directed proteomics-identified network of endogenous androgen receptor in prostate cancer cells

status: Public on Jun 03 2021

city: Kuopio

first: Ville

last: Paakinaho

address: Yliopistonranta 8

department: School of Medicine

country: Finland

institute: University of Eastern Finland

summary: Treatment of prostate cancer confronts resistance to androgen receptor (AR)-targeted therapies. AR-associated coregulators and chromatin proteins hold a great potential for novel therapy targets. Here, we employed a powerful chromatin-directed proteomics approach termed ChIP-SICAP to uncover the composition of chromatin protein network, the chromatome, around endogenous AR in castration resistant prostate cancer (CRPC) cells. In addition to several expected AR coregulators, the chromatome contained many nuclear proteins not previously associated with the AR. In the context of androgen signaling in CRPC cells, we further investigated the role of a known AR-associated protein, a chromatin remodeler SMARCA4 and that of SIM2, a transcription factor without a previous association with AR. To understand their role in chromatin accessibility and AR target gene expression, we integrated data from ChIP-seq, RNA-seq, ATAC-seq and functional experiments. Despite the wide co-occurrence of SMARCA4 and AR on chromatin, depletion of SMARCA4 influenced chromatin accessibility and expression of a restricted set of AR target genes, especially those involved in cell morphogenetic changes in epithelial-mesenchymal transition. The depletion also inhibited the CRPC cell growth, validating its functional role in CRPC cells. Although silencing of SIM2 reduced chromatin accessibility similarly, it affected the expression of a much larger group of androgen-regulated genes, including those involved in cellular responses to external stimuli and steroid hormone stimulus. The silencing also reduced proliferation of CRPC cells and tumor size in chick embryo chorioallantoic membrane assay, further emphasizing the importance of SIM2 in CRPC cells and pointing to the functional relevance of this potential prostate cancer biomarker in CRPC cells. Overall, the chromatome of AR identified in this work is an important resource for the field focusing on this important drug target.

overall_design: Examination of AR, and SMARCA4 binding by ChIP-seq from VCaP prostate cancer cells, in biological duplicates. Input sample from VCaP cells was used as control. AR binding by ChIP-seq from VCaP prostate cancer cells treated with non-targeting siRNA, SIM2 targeting siRNA, or FOXA1 targeting siRNA, in biological duplicates. Chromatin accessibility examined by ATAC-seq from VCaP cells treated with non-targeting siRNA, SMARCA4 targeting siRNA, or SIM2 targeting siRNA, in biological duplicates. Gene expression profiling by RNA-seq from VCaP cells treated with non-targeting siRNA, SMARCA4 targeting siRNA, or SIM2 targeting siRNA, in biological triplicates. All sequencing was done with Illumina NextSeq 500.

first: Kaisa-Mari

last: Launonen

first: Marjo

last: Malinen

first: Einari

middle: A

last: Niskanen

first: Jorma

middle: J

last: Palvimo


title: Simultaneous sequencing of coding and non-coding RNA from APP/PS1 transgenic mice at 15-months

status: Public on Jun 01 2021

city: Dunedin

first: Joanna

last: Williams

address: Great King St

department: Anatomy

country: New Zealand

institute: University of Otago

summary: Brain samples (left hippocampus) from APP/PS1 transgenic mice and wild-type littermate at 15-months were processed for simultaneous coding and non-coding RNA-Seq analysis using a novel RNA-Seq protocol. These data were then analyzed for differential expression.

overall_design: Total RNA was extracted from 15-month APP/PS1 mouse brain tissue (Left hippocampus; 4 transgenic, 4 wild-type littermates), and a modified RNA-Seq protocol used to simultaneously examine coding and non-coding RNA.

middle: M

first: Nikita

last: Potemkin

first: Diane

last: Guévremont

first: Sophie

last: Cawood

first: Jackson

last: Treece

first: Christy

last: Rand

first: Jo-Ann

middle: L

last: Stanton


title: Functional characteriation of histone variant H2A.B in Hodgkin lymphoma

status: Public on Jun 02 2021

city: CANBERRA

first: Jiayu

last: Wen

state: ACT

address: 133 Garran Rd

department: Department of Genome Science

country: Australia

institute: John Curtin School of Medical Research, The Australian National University

summary: The fact that the testis-specific H2A.B is ectopically expressed in Hodgkin lymphoma (HL) and its derived cell lines implicates H2A.B in having a role in oncogenesis (either as an oncogene or a tumour suppressor) similar to other epigenetic regulators of the testis. In order to understand the mechanism of H2A.B-mediated epigenetic regulation in Hodgkin lymphoa, the epigenomic profiles of pan-H2A.B and major H2A.B post-translational modificaitons were investigated using the CUT&RUN method.

overall_design: Epigenomic profiling of pan- and  post-translationally modified H2A.B in L1236 and L428 cell lines.

first: Xuanzhao

last: Jiang

first: Tanya

last: Soboleva

first: David

last: Tremethick


title: Genome-wide changes in chromatin accessibility in myoblasts lacking Hira [ATAC-seq]

status: Public on May 03 2021

city: Creteil

first: Joana

last: Esteves de Lima

address: 8 rue du general sarrail

department: IMRB INSERM U955

country: France

institute: INSERM

summary: The epigenetic mechanisms coordinating the maintenance of adult cellular lineages and the inhibition of alternative cell fates are poorly understood. Here we show that targeted ablation of the histone chaperone HIRA in myogenic cells leads to extensive transcriptional modifications consistent with a major role in maintaining skeletal muscle cellular identity. Conditional ablation of HIRA in muscle stem cells of adult mice compromised their capacity to regenerate and self-renew, leading to tissue repair failure. Epigenetic analysis of Hira-deficient cells showed a drastic reduction of histone variant H3.3 deposition and H3K27ac modification at regulatory regions of muscle genes. By contrast, genes from alternative lineages were ectopically expressed in Hira-mutant cells via MLL1/MLL2-mediated increase of H3K4me3 mark at silent promoter regions. Therefore, HIRA sustains the epigenetic landscape governing muscle cell lineage identity via incorporation of H3.3 at muscle gene regulatory regions, while preventing the expression of alternative lineage genes.

overall_design: Examining the changes in chromatin accessibility in proliferating myoblasts lacking Hira

first: Reem

last: Akar

first: Leo

last: Machado

first: Yuefeng

last: Li

first: Bernadette

last: Drayton-Libotte

first: F

last: Dilworth

first: Frederic

last: Relaix


title: ChIA-PET from endothelial cell of umbilical vein (ENCSR404FPI)

first: ENCODE

last: DCC

summary:
CTCF ChIA-PET in HUVEC

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


title: ChIA-PET from IMR-90 (ENCSR076TTY)

summary:
CTCF ChIA-PET with IMR90 cell

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


title: ChIA-PET from A549 (ENCSR138NSW)

summary:
RNAPII ChIA-PET in A549

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


title: ChIA-PET from SK-N-SH (ENCSR130BTG)

summary:
RNAPII ChIA-PET in SK-N-SH

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


title: Palmitic Acid Upregulates Type I Interferon-Mediated Antiviral Response and Cholesterol Biosynthesis in Human Astrocytes

status: Public on Feb 10 2021

city: Bogota

first: Cynthia

last: Martin Jiménez

state: Colombia

address: pontificia universidad javeriana

department: Computational biology

country: Colombia

institute: Pontificia Universidad Javeriana

summary: Chronic intake of a high-fat diet increases saturated fatty acids in the brain causing the progression of neurodegenerative diseases. Palmitic acid is a free fatty acid abundant in the diet that at high concentrations may penetrate the blood brain barrier and stimulate the production of pro-inflammatory cytokines, leading to inflammation in astrocytes. The use of the synthetic neurosteroid tibolone in protection against fatty acid toxicity is emerging, but its transcriptional effects on palmitic acid induced lipotoxicity remain unclear. Herein, we performed a transcriptome profiling of normal human astrocytes to investigate the molecular mechanisms by which palmitic acid causes cellular damage to astrocytes, and whether tibolone could reverse its detrimental effects. Astrocytes undergo a profound transcriptional change at 2 mM palmitic acid, affecting the expression of 739 genes, 366 upregulated and 373 downregulated. However, tibolone at 10 nM does not entirely reverse palmitic acid effects. Additionally, the protein   protein interaction reveals two novel gene clustering modules. The first module involves astrocyte defense responses by upregulation of pathways associated with antiviral innate immunity, and the second is linked to lipid metabolism. Our data suggest that activation of viral response signaling pathways might be so far, the initial molecular mechanism of astrocytes in response to a lipotoxic insult by palmitic acid, triggered particularly upon increased expression levels of *IFIT2*, *IRF1*, and *XAF1*. Therefore, this novel approach using a global gene expression analysis may shed light on the pleiotropic effects of palmitic acid on astrocytes, and provide a basis for future studies addressed to elucidate these responses in neurodegenerative conditions, which is highly valuable for the design of therapeutic strategies.

overall_design: Normal Human Astrocytes (NHA) cell cultures were treated with Palmitic Acid, Tibolone, and Palmitic Acid + Tibolone. There are two controls: 1. DMEM, for the treatment with Tibolone, and 2. Vehicle, for the treatments with Palmitic Acid and Palmitic Acid + Tibolone. The vehicle contains 1.35% BSA and 2mM carnitine. Each of these 5 treatments have 2 technical replicates (RNA coming from the same NHA donor) and 3 biological replicates (RNA coming from different NHA donors with different sex) summing up 30 samples in total. NHA1 is from a male donor, NHA2 is from a female donor, and NHA3 is from a female donor too.

first: Alexis

middle: F

last: Rojas-Cruz

last: Martin-Jiménez

first: Janneth

last: González

first: Yeimy

last: González-Giraldo

first: Andrés

last: Mauricio Pinzón

first: George

last: Barreto

last: Aristizábal-Pachón


title: R9AP is a functional receptor for Epstein-Barr virus infection in both epithelial cells and B cells

status: Public on Jan 31 2021

city: GuangZhou

first: CONG

last: Sun

state: Guangdong

address: No.651, DongFengDong road, YueXiu district

country: China

institute: Sun Yat-sen University Cancer Center

summary: Epstein-Barr virus (EBV), also known as the first human tumor virus, is linked to nearly 200,000 new cancer cases and millions of non-malignant diseases per year. EBV infects both human epithelial cells and B cells, several virally encoded glycoproteins define tropism and mediate a complicated entry process. Here, we showed that R9AP silencing, genetic knockout or antibody blocking significantly inhibits EBV infection in both epithelial and B cells, while R9AP overexpression promoted EBV infection, establishing this protein as a previously unidentified, essential entry receptor for EBV. Mechanistically, R9AP directly binds to EBV glycoprotein gH/gL to mediate membrane fusion. Importantly, the interaction of R9AP with gH/gL was inhibited by the competition of AMMO1, a highly potent anti-gH/gL neutralizing antibody blocking EBV infection of both Epithelial cells and B cells. Further, treatment with an R9AP peptide encompassing the gH/gL binding site inhibited EBV infection in vitro and reduced viral loads in EBV infected humanized mice. Altogether, we proposed R9AP as the first characterized common cellular receptor for EBV infection of the major cell types and could serve as a potential target for novel interventional strategies.

overall_design: Gene expression in NPEC1-BMI and NPEC2-BMI2 cell lines.Each cell line was harvested as MLCs, SLCs or SLCs infected EBV respectively.

first: Yan

first: Hua

last: Zhang

first: Xiao-Dong

last: Dong

first: Cong

first: Xiang-Wei

last: Kong

first: Dan-Ling

last: Dai

first: Qian-Ying

last: Zhu

first: Li

last: Yuan

first: Yu-Chun

first: Qian

last: Zhong

first: Ya-Ping

last: Tang

first: Jin-Ying

last: Yang

first: Andrew

middle: T

last: McGuire

first: Bo

last: Zhao

first: Yi-Xin

last: Zeng

first: Mu-Sheng


title: Tofacitinib modulates cardiometabolic and immunologic disease markers associated with premature atherosclerosis in SLE

status: Public on Mar 01 2021

city: Bethesda

first: Stephen

middle: R

last: Brooks

state: MD

address: 50 SOUTH DR, RM 1140

department: Biodata Mining and Discovery Section

institute: NIAMS/NIH

summary: Increased risk of premature cardiovascular disease (CVD) is well recognized in systemic lupus erythematosus (SLE) and significantly contributes to morbidity and mortality. To date, no pharmacologic intervention has shown to reduce CV risk in SLE. Dysregulation of innate immune responses, including aberrant type I-Interferon (IFN)-neutrophil interactions, has been proposed to significantly contribute to enhanced CV risk in SLE.  In lupus animal models, the Janus kinase/signal transducers and activators of transcription (JAK/STAT) inhibitor tofacitinib improves clinical features, immune dysregulation and vascular dysfunction.  We hypothesized that JAK/STAT inhibition in SLE subjects would result in amelioration of cardiometabolic and immunologic parameters previously associated with enhanced CVD risk.

overall_design: We conducted a phase 1b/2a randomized, double-blind, placebo-controlled clinical trial of oral tofacitinib, 5 mg twice daily, in 30 SLE subjects (2:1 drug to placebo ratio) with mild to moderate disease activity Patients were stratified by the presence or absence of  the STAT4 risk allele, previously shown to be associated with more severe SLE Study duration was 84 days, with 56 days of active treatment followed by 28 days off drug  We performed, non-invasive assessment of vascular function, measurements of cardiometabolic parameters, quantification of peripheral blood immune cell subsets by flow cytometry and  gene expression by whole blood RNA sequencing, quantification of circulating neutrophil extracellular trap (NET) complexes and STAT phosphorylation (pSTAT) in immune cells Adverse events (AEs) were recorded as were assessments of lupus clinical disease activity

first: Sarfaraz

last: Hasni

first: Mariana

last: Kaplan


title: Functional characterization of RebL1 highlights the evolutionary conservation of oncogenic activities of RBBP4/7 ortholog in Tetrahymena thermophila

status: Public on Apr 30 2021

city: Toronto

first: Alejandro

last: Saettone

state: Ontario

address: 686 Bay Street

department: Genetics & Genome Biology

country: Canada

institute: The Hospital for Sick Children

summary: Retinoblastoma-binding proteins 4 and 7 (RBBP4 and 7) are two highly homologous human histone chaperones. They function in epigenetic regulation as subunits of multiple chromatin-related complexes and have been implicated in numerous cancers. Due to their overlapping functions, our understanding of RBBP4 and 7, particularly outside of Opisthokonts, has remained limited. Genome-wide analyses indicated that RebL1 and Tetrahymena Lin54 (Anqa1) bind predominantly within genic regions. Anqa1 targets primarily promoter regions suggesting a role for Tetrahymena MuvB in transcription regulation.

overall_design: Examination of 2 biological replicates of RebL1-FZZ and Anqa1-FZZ during vegetative cells.

first: Hyunmin

last: Lee

first: Marcelo

last: Ponce

first: Syed

last: Nabeel-Shah

first: Jack

last: Greenblatt

first: Jeffrey

last: Fillingham


title: Single Cell Transcriptional Profile of brain endothelial cells from nine different brain regions in adult mice

status: Public on Jan 26 2021

city: La Jolla

first: Richard

last: Daneman

state: California

address: 9500 Gilman Dr

institute: UCSD

summary: tdTomato+ endothelial cells from different brain regions of healthy adult Rosa-tdTomato; VE-Cadherin-CreERT2 mice

overall_design: Brain endothelial cells from adult Rosa-tdTomato; VE-Cadherin-CreERT2 mice were dissociated into a single cell suspension, tdTomato+ cells enriched using FACS sorting and sequenced using the 10x Genomics v3.1 pipeline

first: Marie

last: Blanchette


title: Peptidylarginine deiminase IV (PADI4) has a novel tumor cell-autonomous suppressor role in regulating breast cancer stem cells [RNA-Seq_1]

status: Public on Jan 11 2021

first: Maxwell

address: Building 37, Room 5120

department: CCR

institute: National Cancer Institute, NIH

summary: Peptidylarginine deiminases (PADIs) catalyze post-translational modification of many target proteins and have been suggested to play a role in carcinogenesis. Since citrullination of histones by PADI4 was recently implicated in regulating embryonic stem and hematopoietic progenitor cells, here we investigated a possible role for PADI4 in regulating breast cancer stem cells. We showed by genetic and pharmacologic approaches that PADI4 activity limits the number of cancer stem cells (CSCs) in vitro and in vivo in multiple breast cancer models. A gene signature reflecting tumor cell-autonomous PADI4 inhibition is associated with poor outcome in human breast cancer datasets, consistent with a tumor suppressive role for PADI4. Mechanistically, PADI4 inhibition resulted in a global redistribution of histone H3 with accumulation around transcriptional start sites. Interestingly, epigenetic effects of PADI4 on the bulk tumor cell population did not explain the CSC phenotype. However, in sorted tumor cell populations, PADI4 down-regulated expression of the master transcription factors of stemness, NANOG and POU5F1, specifically in the cancer stem cell compartment, by reducing the transcriptionally activating H3R17me2a histone mark at those loci. This effect was not seen in the non-stem cells. Our findings reveal a novel role for PADI4 as a tumor suppressor in regulating breast cancer stem cells, and provide insights into context-specific effects of PADI4 in epigenetic modulation.

overall_design:
Cells were cultured in DMEM/F12 media supplemented with 5% horse serum.
Cells were treated with PADI4 inhibitor (GSK484) or control compound (GSK107) for 72 hours.

first: Nellie

last: Moshkovich

first: Humberto

last: Ochoa

first: Binwu

first: Howard

first: Yu-an

first: Jing

last: Huang

middle: P

first: Lalage

last: Wakefield


title: lncRNA sequencing of human ovarian cancer cell SKOV3 after exposure to ginsenoside 20(S)-Rg3

status: Public on Feb 16 2021

city: xian

first: zhao

last: le

address: Yanta Western Road NO.227

institute: The First Affiliated Hospital of Xi'an Jiao Tong University

type: Non-coding RNA profiling by high throughput sequencing

summary: Ginsenoside 20(S)-Rg3, an active saponin monomer extracted from red ginseng, inhibits the malignancy of ovarian cancer cells. RNA-Seq analysis was used for deep sequencing of lncRNA to detected molecular mechanisms of 20(S)-Rg3.We identified 85 differentially expressed lncRNA influenced by 20(S)-Rg3, among which 67 lncRNAs were significantly decreased (fold change<0.5, p<0.05) including 12 ncRNAs and 55 pseudo genes, and 18 lncRNAs were significantly increased (fold change>1.5, p<0.05) including 3 ncRNAs, 14 pseudo genes and 1 unknown gene. This study provide a valuable resource for the discovery of lncRNAs related to anti-tumor mechanism of 20(S)-Rg3.

overall_design: lncRNA of SKOV3 ovarian cancer cells treated with 80 μg/mL 20(S)-Rg3 for 24 h and negative control cells were generated by deep sequencing using the Ion Torrent Proton platform.

first: Xu

last: Li

first: Le

last: Zhao


title: RNA-seq of canine osteosarcoma tumor cells following angiopellosis extravasation

status: Public on Jan 05 2021

city: Raleigh

first: Hiroyuki

last: Mochizuki

state: NC

address: 1060 William Moore Dr

institute: North Carolina State University

summary: Canine osteosarcoma cells were observed to undergo extravasation through intrivital imaging. Then the extravasated cells were isolated and established as sublines and compared to control cells using RNA-seq.

overall_design: Examination of extravasating cells in comparison to control cells.

first: Tyler

last: Allen


title: Peptidylarginine deiminase IV (PADI4) has a novel tumor cell-autonomous suppressor role in regulating breast cancer stem cells

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

overall_design: Refer to individual Series


title: ATAC-seq, ChIP-seq and RNA-seq studies in myoblasts lacking Hira

first: Joana

last: Esteves de Lima


title: An Integrated Epigenomic and Transcriptomic Map of Mouse and Human ab T Cell Development (Human scATACseq)

status: Public on Nov 25 2020

first: Remy

last: Bosselut

address: 9000 Rockville Pike, Building 37

department: Laboratory of Immune Cell Biology

institute: National Cancer Institute, National Institute of Health

summary: ab lineage T cells, most of which are CD4+ or CD8+ and recognize MHC I or MHC II-presented antigens, are essential for immune responses and develop from CD4+CD8+ thymocytes. The absence of in vitro models and the heterogeneity of ab thymocytes have hampered analyses of their intrathymic differentiation. Here, combining single-cell RNA and ATAC (chromatin accessibility) sequencing, we identified mouse and human ab thymocyte developmental trajectories. We demonstrated asymmetric emergence of CD4+ and CD8+ lineages, matched differentiation programs of agonist-signaled cells to their MHC specificity, and identified correspondences between mouse and human transcriptomic and epigenomic patterns. Through computational analysis of single-cell data and binding sites for the CD4+ lineage transcription factor Thpok, we inferred transcriptional networks associated with CD4+ or CD8+ lineage differentiation, and with expression of Thpok or of the CD8+ lineage factor Runx3. Our findings provide insight into the mechanisms of CD4+ and CD8+ T cell differentiation and a foundation for mechanistic investigations of ab T cell development.

overall_design: Single cell epigenomic analysis of human thymocytes

first: Laura

last: Chopp


title: An Integrated Epigenomic and Transcriptomic Map of Mouse and Human ab T Cell Development (ThpokKO scRNAseq)

overall_design: Single cell transcriptomic profiling on CD69+ thymocytes isolated from Thpok WT and Thpok deficient mice.


title: Analysis of the transcriptomic changes of myoblasts lacking Hira [RNA-seq]

overall_design: Examining the transcriptomic changes in proliferating myoblasts lacking Hira

first: Reem

last: Akar

first: Leo

last: Machado

first: Yuefeng

first: Bernadette

last: Drayton-Libotte

first: F

last: Dilworth

first: Frederic

last: Relaix


title: An Integrated Epigenomic and Transcriptomic Map of Mouse and Human ab T Cell Development (Mouse scATACseq)

overall_design: Single cell epigenomic profiling on CD69+ thymocytes isolated from MHCI or MHCII deficient mice


title: Genome-wide chromatin state in myoblasts lacking Hira [ChIP-seq]

overall_design: Examining the changes in H3.3 incorporation and associated changes in histone modifications in the absence of Hira in myoblasts


title: An Integrated Epigenomic and Transcriptomic Map of Mouse and Human ab T Cell Development (Mouse scRNAseq)

overall_design: Single cell transcriptomic profiling on CD69+ thymocytes isolated from MHCI or MHCII deficient mice


title: An Integrated Epigenomic and Transcriptomic Map of Mouse and Human ab T Cell Development (Thpok ChIPSeq)

overall_design: Streptavidin immunoprecipitation from the chromatin of CD4+ SP cells isolated from thymi of ThpokBio/+ Rosa26BirA or Rosa26BirA animals


title: An Integrated Epigenomic and Transcriptomic Map of Mouse and Human ab T Cell Development (RNAseq Exp2)

overall_design: Population RNAseq on thymocytes sorted from Wild-type thpok-deficient thymoctes


title: An Integrated Epigenomic and Transcriptomic Map of Mouse and Human ab T Cell Development (RNAseq EXP1)

overall_design: Population RNAseq on sorted mouse thymocytes


title: An Integrated Epigenomic and Transcriptomic Map of Mouse and Human ab T Cell Development (Population ATACseq)

overall_design: Population ATAC-seq on thymocytes sorted from wlld-type and Thpok-deficient mice


title: An Integrated Epigenomic and Transcriptomic Map of Mouse and Human ab T Cell Development (Human scRNAseq)

overall_design: Single cell transcriptomic analysis of human thymocytes


title: Single-cell lineage mapping of a diverse virus-specific naïve CD4 T cell repertoire

status: Public on Nov 10 2020

city: Chicago

first: Weiguo

last: Cui

state: IL

address: 303 E Chicago Ave

department: Pathology

institute: Northwestern University

summary: The naïve polyclonal CD4 T cell repertoire can differentiate into multiple lineages during acute viral infection, with some T cell clones exhibiting a preferred lineage choice. TCR α CDR3 motifs can partially influence a clone-intrinsic lineage preference towards TFH fate.

overall_design: Activated antigen specific CD4 T cells (CD4+CD44+GP66+) were sorted from five C57BL/6J mice and used to perform Single cell gene expression (GEX) and single cell TCR sequencing (TCR) using 10x genomics kit at day 10 post acute LCMV infection

first: Achia

last: Khatun


title: Multi-omics HUVEC data of Tibetan and Han in hypoxic induction.

status: Public on Jul 15 2020

city: Beijing

first: Jingxue

last: Xin

address: 55 Zhong Guan Cun East Road

department: Academy of Mathematics and Systems Science

institute: Chinese Academy of Sciences

summary: Tibetan's adaptation to high-altitude environment at the Qinghai-Tibetan plateau represents a remarkable case of natural selection during recent human evolution. We generated time series paired RNAseq, ATACseq and Hi-C data in Tibetan and Han Chinese's umbilical endothelial cells from normoxia to hypoxia condition. Our results provide a broad resource of genome-wide hypoxia regulatory network to characterize the effect of genetic variation in high-altitude adaptation, and indicates large-scale maps of variants need proper cell types to understand its act on gene regulation.

overall_design: Time series paired RNAseq, ATACseq and Hi-C data in Tibetan and Han Chinese's umbilical endothelial cells from normoxia to hypoxia condition.

first: B

last: Su

first: Y

last: Wang

first: J

first: H

last: Zhang

last: He


title: Single cell resolution regulatory landscape of the mouse kidney highlights cellular differentiation programs and renal disease targets

status: Public on Aug 29 2020

city: Philadelphia

first: Katalin

last: Susztak

state: Pennsylvania

address: 3400 Civic Center Boulevard, 12th floor

institute: University of Pennsylvania

summary: Determining the epigenetic program that generates unique cell types in the kidney is critical for understanding cell-type heterogeneity during tissue homeostasis and injury response. Here, we profiled open chromatin and gene expression in developing and adult mouse kidneys at single cell resolution. We show critical reliance of gene expression on distal regulatory elements (enhancers). We define key cell type-specific transcription factors and major gene-regulatory circuits for kidney cells. Dynamic chromatin and expression changes during nephron progenitor differentiation demonstrated that podocyte commitment occurs early and is associated with sustained Foxl1 expression. Renal tubule cells followed a more complex differentiation, where Hfn4a was associated with proximal and Tfap2b with distal fate. Mapping single nucleotide variants associated with human kidney disease identified critical cell types, developmental stages, genes, and regulatory mechanisms. We provide a global single cell resolution view of chromatin accessibility of kidney development. The dataset is available via interactive public websites.

overall_design: 2 P0 mouse kidney snATAC-seq samples, 3 adult mouse kidney snATAC-seq samples, 1 P0 mouse kidney scRNA-seq sample, 1 adult mouse kidney scRNA-seq sample, 2 P0 mouse kidney bulk ATAC-seq samples, 2 3-week mouse kidney bulk ATAC-seq samples, and 2 8-week mouse kidney bulk ATAC-seq samples

first: Zhen

last: Miao

first: Michael

middle: S

last: Balzer

first: Ziyuan

last: Ma

first: Hongbo

last: Liu

first: Junnan

last: Wu

first: Rojesh

last: Shrestha

first: Tamas

last: Aranyi


title: Lens epithelial cell transcriptome reprogramming at 48 hours post cataract surgery (PCS) in wild type (WT) and Fibronectin Conditional Knockout (FNcKO) mice

status: Public on Jul 08 2020

city: Newark

first: Melinda

middle: K.

last: Duncan

state: DE

address: 327 Wolf Hall

department: Biological Sciences

institute: University of Delaware

summary: This trancriptome analysis reveals the first detailed analysis on how the remnant lens epithelial cells (LECs) greatly reprogram their transcriptome by 48 hours post cataract surgery (PCS) and the dependence of this phenomenom on endogenous fibronectin gene expression.

overall_design: Living mice of both WT and FNcKO were subjected to lens fiber cell removal leaving behind the lens epithelium and capsule to model human cataract surgery. llumina HiSeq 2500 (Illumina) transcriptome profiling was performed in biological triplicate on remnant LECs isolated either immediately after surgery or 48 hours later in order to ascertain the response of lens epithelial cells to cataract suregery with the goal of understanding the role of fibronectin in posterior capsular opacification (PCO) pathogenesis.

first: Mahbubul

last: Shihan

middle: K


title: Transcriptomic profiling of circadian genes in WT mouse tissues

status: Public on Jul 14 2020

city: Princeton

first: Jeff

last: Aaronson

state: New Jersey

address: 155 Village Boulevard, Suite 200

department: Discovery & Systems Biology

institute: CHDI


title: An Integrated Epigenomic and Transcriptomic Map of Mouse and Human ab T Cell Development

first: Remy

last: Bosselut

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

ab lineage T cells, most of which are CD4+ or CD8+ and recognize MHC I or MHC II-presented antigens, are essential for immune responses and develop from CD4+CD8+ thymocytes. The absence of in vitro models and the heterogeneity of ab thymocytes have hampered analyses of their intrathymic differentiation. Here, combining single-cell RNA and ATAC (chromatin accessibility) sequencing, we identified mouse and human ab thymocyte developmental trajectories. We demonstrated asymmetric emergence of CD4+ and CD8+ lineages, matched differentiation programs of agonist-signaled cells to their MHC specificity, and identified correspondences between mouse and human transcriptomic and epigenomic patterns. Through computational analysis of single-cell data and binding sites for the CD4+ lineage transcription factor Thpok, we inferred transcriptional networks associated with CD4+ or CD8+ lineage differentiation, and with expression of Thpok or of the CD8+ lineage factor Runx3. Our findings provide insight into the mechanisms of CD4+ and CD8+ T cell differentiation and a foundation for mechanistic investigations of ab T cell development.

platform_organism:
Homo sapiens
Mus musculus


title: Molecular Quantitative Trait Locus Mapping In Human Endothelial Cells Identifies Regulatory SNPs Underlying Gene Expression and Complex Disease Traits

status: Public on Jun 02 2020

city: Tucson

first: Lindsey

middle: Kathleen

last: Stolze

state: AZ

address: 1333 N Martin Ave

institute: The University of Arizona

summary: Identification of causal variants and mechanisms underlying complex disease traits in humans requires strategies to locate and fine-map functional regulatory variants in disease-relevant cell types. To discover functional regulatory variants in primary aortic endothelial cells (ECs) from humans, we collected genetic, transcriptomic, and four epigenomic phenotypes in a population of up to 150 human donors representing individuals of both sexes and three major ancestries. We found thousands of EC eQTLs that were not present in GTEx at all ranges of effect sizes, indicating novel functional variants not observable from tissue data. We performed several epigenetic assays across 53 donors’ EC to enable molecular QTL mapping, which included chromatin accessibility, histone modification, and transcription factor binding of proteins ERG and NF-kB/p65 in two activation states. We discovered over 3000 regulatory elements where cis-regulatory variants associated to significant differences in epigenetic marks. Co-localization with our eQTLs, TF motif mutations, and 3D confirmation capture data in ECs enabled our discovery of hundreds of high-confidence functional regulatory elements that perturb endothelial molecular phenotypes. Furthermore, this set of variants is enriched at GWAS loci for Coronary Artery disease and other disease traits, with some SNPs demonstrating pleiotropic effects. Together, our dataset and analytical approach provide the genetics and vascular biology communities with specific variants affecting EC biology and serves as a proof-of-principle for how to detect functional regulatory variants in human cells with relevance to complex traits.

overall_design: Examination of molecular traits of 157 Human Aortic Endothelial Cell Samples as follows: RNA-seq in 53 samples in two treatments (control, IL-1B treated), Microarray expression from 156 (control) and 157 samples (OxPAPC treated), H3K27ac ChIP-seq in 42 samples in two treatments (control, IL-1B treated), ATAC-seq in 44 (control) and 43 (IL-1B treated) samples, ERG ChIP-seq in 22 samples (untreated), p65 ChIP-seq in 36 samples (IL-1B treated).

first: Casey

middle: E

last: Romanoski


title: Genome-wide chromatin structure alteration during Epstein-Barr virus infection (Hi-C)

status: Public on May 23 2020

city: Chiba

first: Masaki

last: Fukuyo

address: 1-8-1 Inohana, Chuo-ku

department: Department of Molecular Oncology

country: Japan

institute: Chiba University

summary: We analysed chromatin structure alterations by EBV infection to elucidate their contribution to tumorigenesis. We performed Hi-C using gastric epithelial cells with or without EBV infection.

overall_design: Hi-C experiments in 14 Gastric cancer cell lines, 2 normal gastric epithelial cells, a primary EBV(+) gastric cancer tissue, and EBV infected or uninfected gastric cancer cells.

first: Atsushi

last: Okabe

last: Kaneda


title: Transcriptome analyses of PROKR1-activated HEK293T cells

status: Public on Apr 14 2020

city: Gangwon-do

first: MOK

last: JONGSOO

state: Pyeongchang-gun

address: 25354 Pyeongchang-daero, Daehwa-myeon

department: Department of International Agricultural Technology

country: South Korea

institute: Seoul National University

summary: In order to gain insight into the molecular mechanism of PROKR1, we investigated transcriptomic response in PROKR1 overexpressed HEK293 T cells following Pk2 stimulation We identified 578 differentially expressed genes (DEGs) fold change cutoff = 2 in activated HEK293 T overexpressed HEK293 T cells by Pk2, including 269 up-regulated and 309 down-regulated genes.

overall_design: These results indicate that MAPK / Erk and PI3K / Akt signaling pathways are putative signaling pathways that are dominantly affected by Prokr1 activation.

first: Joonghoon

last: Park

first: Jongsoo

last: Mok


title: Transcriptomic profiling of circadian genes in WT mouse tissues (mRNA-Seq)

summary: A goal of a collaboration between the CHDI Foundation and Prof. Jenny Morton at Cambridge University was to identify genes in mice with diurnal/circadian expression patterns. Tissues from wild type mice were harvested every 3 hrs over a 36 hour time period, for a total of 13 time points. Striatal, cortical, hypothalamic and liver samples were harvested, flash frozen, and transferred to Expression Analysis for RNA extraction and mRNA-seq sequencing. Samples passing QC were analyzed to produce high quality, 50-base paired-end RNA-seq results.

overall_design: Striatal, cortical, hypothalamic and liver samples were collected from 26-week-old wild type C57BL/6J male mice every 3 hours for 36 hours, number of replicates 2 to 12 for each ZT group. mRNA-Seq was performed.

first: Jenny

last: Morton

first: Jim

last: Rosinski


title: Characterizing the temporal dynamics of gene expression in single cells with sci-fate

status: Public on Apr 12 2020

city: Seattle

first: Junyue

last: Cao

state: WA

address: Foege Building S-210, 3720 15th Ave NE

department: Department of Genome Sciences

institute: University of Washington

summary: Gene expression is a dynamic process on multiple scales, e.g. the cell cycle, response to stimuli, normal differentiation and development, etc. However, nearly all techniques for profiling gene expression in single cells fail to directly capture these temporal dynamics, which limits the scope of biology that can be effectively investigated. Towards addressing this, we developed sci-fate, a new technique that combines S4U labeling of newly synthesized mRNA with single cell combinatorial indexing (sci-), in order to concurrently profile the whole and newly synthesized transcriptome in each of many single cells. As a proof-of-concept, we applied sci-fate to a model system of cortisol response, and characterized expression dynamics in over 6,000 single cells. From these data, we quantify the dynamics of the cell cycle and of glucocorticoid receptor activation, while also exploring their intersection. We furthermore use these data to develop a framework for estimating cell state transition probabilities, and to identify factors whose dynamic expression potentially regulates these transitions. The experimental and computational methods described here may be broadly applicable to quantitatively characterize cell state dynamics in in vitro systems.

overall_design:
sci-fate profiling for HEK293T cells, NIH/3T3 cells, A549 cells across different treatment conditions (DEX 0 hour, 2 hour, 4 hour, 6 hour, 8 hour and 10 hour treatment).

Please note that [1] the fastq files are generated from combined samples of different treatment samples [2] the processed cell information and transcriptome barcode are listed in the cell annotation file of processed data [3] the *gene_annotate.txt and *gene_annotate_newly_synthesised.txt files are identical, yet provided in duplicate as they are reference data for two different data sets.

first: Wei

last: Zhou

first: Stanley

last: Fields

first: Frank

last: Steemers

first: Cole

last: Trapnell

first: Jay

last: Shendure


title: The eukaryotic translation initiation factor eIF4E elevates steady-state m7G capping of coding and noncoding transcripts

status: Public on Sep 30 2020

city: New York

first: Maria

middle: Victoria

last: Revuelta

state: New York

address: 1300 York Avenue

department: Medicine

institute: Weill Cornell Medicine

summary: Methyl-7-guanosine (m7G) “capping” of coding and some noncoding RNAs is critical for their maturation and subsequent activity. Here, we discovered that eukaryotic translation initiation factor 4E(eIF4E), itself a cap-binding protein, drives the expression of the capping machinery and the increased capping efficiency of ∼100 coding and noncoding RNAs. This dataset collects transcriptomic data for quantitative cap immunoprecipitation (CapIP) assay in eIF4E-Flag or vector stable U2Os cells.

overall_design: RNA-seq of eIF4E-Flag or vector stable U2Os cells was generated by Illumina sequencing

first: Biljana

last: Culjkovic-Kraljacic

first: Lucy

last: Skrabanek

first: Jadwiga

last: Gasiorek

first: Victoria

last: Cowling

first: Leandro

last: Cerchietti

first: Katherine

last: Borden


title: Genome-wide analysis of histone modification alteration in EBV(+) GC cell lines

first: Masaki

last: Fukuyo

overall_design: Refer to individual Series


title: Single-cell transcriptomes of the aging human skin reveal loss of fibroblast priming

status: Public on Mar 31 2020

city: Heidelberg

first: Guenter

last: Raddatz

address: Im Neuenheimer Feld 580

country: Germany

institute: German Center for Cancer Research

summary: Fibroblasts are the main dermal cell type and are essential for the architecture and function of human skin. Important differences have been described between fibroblasts localized in distinct dermal layers, and these cells are also known to perform varied functions. However, this phenomenon has not been analyzed comprehensively yet. Here we have used single-cell RNA sequencing to analyze >15,000 cells from a sun-protected area in young and old donors. Our results define four main fibroblast subpopulations that can be spatially localized and functionally distinguished. Importantly, intrinsic aging reduces this fibroblast ‘priming’, generates distinct expression patterns of skin aging-associated genes, and substantially reduces the interactions of dermal fibroblasts with other skin cell types. Our work thus provides comprehensive evidence for a functional specialization of human dermal fibroblasts and suggests that the age-related loss of fibroblast priming contributes to human skin aging.

overall_design:
Overall 5 samples were analyzed. Two of them are from young subjects (y1=25y, y2=27y) and serve as replicates, three of them are from old subjects (o1=53y, o2=70y, o3=69y) and serve as replicates.

Please note that the 'seurat_analysis_lyko.RData' file was replaced with the seurat_analysis_lyko.rds on Aug 6th, 2020.

last: Lyko

first: Manuel

last: Rodriguez-Paredes


title: MiR-1253 exerts tumor-suppressive effects in medulloblastoma via inhibition of CDK6 and CD276 (B7-H3) (RNA-seq dataset)

status: Public on Apr 10 2020

city: Omaha

first: Pranita

last: Atri

state: NE

address: S 42nd and Emile St

department: Biochemistry

institute: UNIVERSITY OF NEBRASKA MEDICAL CENTER

summary: Of the four primary subgroups of medulloblastoma, the most frequent cytogenetic abnormality, i17q, distinguishes Groups 3 and 4 which carry the highest mortality; haploinsufficiency of 17p13.3 is a marker for particularly poor prognosis. At the terminal end of this locus lies miR-1253, a brain-enriched microRNA that regulates bone morphogenic proteins during cerebellar development. We hypothesized miR-1253 confers novel tumor-suppressive properties in medulloblastoma. Using two different cohorts of medulloblastoma samples, we first studied the expression and methylation profiles of miR-1253. We then explored the anti-tumorigenic properties of miR-1253, in parallel with a biochemical analysis of apoptosis and proliferation, and isolated oncogenic targets using high-throughput screening. Deregulation of miR-1253 expression was noted, both in medulloblastoma clinical samples and cell lines, by epigenetic silencing via hypermethylation; specific de-methylation of miR-1253 not only resulted in rapid recovery of expression but also a sharp decline in tumor cell proliferation and target gene expression. Expression restoration also led to a reduction in tumor cell virulence, concomitant with activation of apoptotic pathways, cell cycle arrest and reduction of markers of proliferation. We identified two oncogenic targets of miR-1253, CDK6 and CD276, whose silencing replicated the negative trophic effects of miR-1253. These data reveal novel tumor-suppressive properties for miR-1253, i.e., (i) loss of expression via epigenetic silencing; (ii) negative trophic effects on tumor aggressiveness; and (iii) downregulation of oncogenic targets.

overall_design: RNA-seq analysis of 14 normal and 26 tumor tissues with subgroup classfication. Each sample was sequenced on 4 Illumina lanes.

first: Mahapatra

last: Sidharth


title: Profiling of the reprogramome and quantification of fibroblast reprogramming to pluripotency

status: Public on Jun 07 2020

city: Fort Worth

first: Kejin

last: Hu

state: TX

address: 3400 Camp Bowie Boulevard

department: Microbiology, Immunology and Genetics

institute: UNT Health Science Center

summary:
Recognized as being intensive and extensive, the degree of pluripotency reprogramming, however, has not been quantitatively determined before. Here we report a novel concept, reprogramome. Fine mapping of reprogramome indicates that the amount of reprogramming genes is equivalent to 57% of the fibroblast transcriptome, with a large erasome and activatome.
We further developed a simple mathematical model to quantitate reprogramming. The total reprogramming is 26,032 LFC units (log2-transformed fold changes). Such quantification indicates that reprogramming in WNT pathways represents 2% of the total reprogramming; and reprogramming in genes involved in cellular morphogenesis represents 7.7% of the total reprogramming.
In summary, we have developed a novel concept, reprogramome, for fine profiling of the reprogramming, as well as a mathematical model for accurate quantification of the reprogramming.

overall_design: Human embryonic stem cell (n=3) expression were compared to human fibroblasts (n=4).

first: Lara

last: Ianov

first: David

last: Crossman

first: Michael

last: Crowley


title: LncRNA profiling of skeletal muscles related to muscle metabolism at QingYu pig growth inflection point

status: Public on Dec 18 2019

city: chongqing

first: Jia

last: Luo

state: chongqing

address: tiansheng road

institute: Southwest University

summary: Muscle growth at different developmental stages are a potentially good model for studying the mechanism underlying muscle development and phenotypes differences. However, no studies focused on the lncRNAs at extreme growth rate based on growth curve.The aim of this study was to identify differentially expressed genes that are linked to phenotypic differentiation (eg. grow rate, meat quality) between the inflection point and plateau phase.

overall_design: lncRNA profiles of porcine  skeletal muscles were generated by deep sequencing, in triplicate, using Illumina Hi-Seq 4000.

first: Linyuan

last: Shen

first: Mailin

last: Gan

first: Anan

last: Jiang

first: Jideng

last: Ma

first: Long

last: Jin

first: Yihui

last: Liu

first: Guoqing

last: Tang

first: Yanzhi

first: Mingzhou

last: Li

first: Xuewei

first: Shunhua

last: Zhang

first: Li

last: Zhu


title: SIP Identifies a Network of Dosage Compensation Condensin I Loops

status: Public on Feb 04 2020

first: M

middle: Jordan

last: Rowley

address: 601 S Saddle Creek Rd

department: GCBA

institute: Univ of Nebraska Medical Center

summary: Chromatin loops are a major componant of 3D nuclear organization that appear as intense point-to-point interactions in Hi-C maps. Identification of these loops is an important part of Hi-C analysis. We present SIP, Significant Interaction Peak caller, a platform independent program to identify these loops in a time and memory efficient manner and which is resistant to noise and sequencing depth. We also present a companion tool, SIPMeta, to create more visually accurate average plots of Hi-C and HiChIP data. We then demonstrate that use of SIP and SIPMeta can lead to biological insight through characterizing the contribution of several transcription factors to CTCF loops in human cells. We then use SIP and SIPMeta to discover loops associated with condensin IDCC in C. elegans and confirm these loops by HiChIP.  These loops form a network of interactions and likely explain the partial condensation of dosage compensated X chromosomes in hermaphrodites.

overall_design: Hi-C, HiChIP

first: Jordan

first: Axel

last: Poulet

first: Brianna

last: Bixler

last: Nichols

first: Elizabeth

last: Brouhard

first: Karen

last: Hermetz

first: Hannah

last: Linsenbaum

first: Erez

last: Lieberman Aiden

first: Gryorgyi

last: Csankovszki

first: Victor

middle: G

last: Corces


title: Sex Differences in the Effects of Prenatal Bisphenol A Exposure on Genes Associated with Autism Spectrum Disorder in the Hippocampus

status: Public on Nov 14 2019

city: Pathumwan

first: Surangrat

last: Thongkorn

state: Bangkok

address: Rama I

country: Thailand

institute: Chulalongkorn University

summary: In this study, we investigated the prenatal effects of bisphenol-A (BPA) exposure on transcriptome profiles in the hippocampus of the rat offspring. Transcriptome profiling by RNA-seq analysis of hippocampi isolated from neonatal pups prenatally exposed to BPA was conducted and revealed a list of differentially expressed genes (DEGs) associated with ASD. Among the DEGs, several ASD candidate genes, including Auts2 and Foxp2, were dysregulated and showed sex differences in response to BPA exposure. The interactome and pathway analyses of DEGs revealed significant associations between the DEGs in males and neurological functions/disorders associated with ASD. The findings from this study indicate that prenatal BPA exposure alters the expression of ASD-linked genes in the hippocampus and suggest that maternal BPA exposure may increase ASD susceptibility by dysregulating genes associated with neurological functions known to be negatively impacted in ASD.

overall_design: We conducted experiments using the neonatal rat hippocampus maternally exposed to BPA or vehicle control (BPA treament; pooled 3 hippocampi, vehicle control; pooled 3 hippocampi). 10-week-old female rats were daily treated with BPA at the concentration of 5,000 µg/kg·BW or vehicle control from gestation day 1 (GD1) until parturition. RNA was isolated and cDNA was synthesized. The transcriptome profiles was performed using a high-throughtput RNA-seq.

first: Songphon

last: Kanlayaprasit

first: Depicha

last: Jindatip

first: Tewin

last: Tencomnao

first: Valerie

middle: W

last: Hu

first: Tewarit

last: Sarachana


title: Paired-end RNA Sequencing on Madin-Darby Canine Kidney (G-MDCK) epithelial cells infected or not with Listeria monocytogenes

status: Public on Nov 19 2019

first: Effie

middle: Efthimia

last: Bastounis

address: UW Biology Life Sciences Bldg, Room 565, 4000 15th Ave NE

department: Biology

summary:
Purpose: When we infect MDCK epithelial cells we low dosage of Listeria monocytogenes we observe that at late times (24 h) post infection that infected cells pertaining in infection foci get collectively extruded out of the epithelial monolayer forming a 3D mound. The formation of the infection mound results from the competition between two populations: the uninfected cells ("surrounders") that eventually squeeze and extrude the infected cells ("mounders"). Using RNA-Sequencing, we performed gene expression profiling for uninfected MDCK cells, cells infected for 24 h with Listeria monocytogenes at an MOI of 200 (both "mounders" and "surrounders") and cells sorted to infected ("mounders") or uninfected ("surrounders") populations after being infected for 24 h with Listeria monocytogenes. Our goal was to understand how transcriptional regulation leads to the collective extrusion of infected epithelial cells triggered by surrounding uninfected cells.
Methods and Results: By analyzing the differentially expressed genes between all conditions we find a significant number of up- or down-regulated genes between all groups. Through pathway enrichemnet analysis we find that compared to cells not exposed to infection "mounders" showed significant downregulation in 31 genes related to tight junctions and ZO-1 was one of the key genes downregulated and to a lesser degree to pathways related to adherens junctions, focal adhesions and regulation of the actin cytoskeleton. "Surrounders" showed significant downregulation to genes related to actin cytoskeleton, to endocytosis to ahderens junctions and to a lesser degree focal adhesions and tight junctions. Especially "surrounders" and to a lesser degree "mounders" showed upregulation on IL-17 and NF-kB and TNF related signaling pathways, which underlines the fact that although "surrounders" are uninfected their distinct mechanical behavior might arise from cytokines released from "mounders" which impact crucially their phenotype. Interestingly "mounders" only showed additionally upregulation on DNA replication, cell cycle related pathways and ferroptosis suggesting that these cells might be undergoing some kind of stress response.
Conclusions: Infection of MDCK epithelial cells with Listeria monocytogenes significantly alters the transcriptome of the infected host cells when those are examined 24 h post infection. Both infected and uninfected cells in an infected well show significant transcriptomic changes compared to uninfected cells but also compared to each other. Most importnantly innate immunity related pathways are singificanlty upregulated for un infected cells in an infected well and to a lesser degree for infected cells as compared to cells not exposed to infection.

overall_design: Epithelial cell mRNA profiles of cells previously residing in confluency on glass substrates coated with 0.25 mg/mL collagen I and being (1) uninfected; or (2) infected with low dosage of Listeria monocytogenes; or (3-4) infected with low dosage of Listeria monocytogenes and flow sorted into (3) infected or (4) uninfected populations were generated in quadruplicate, using Illumina NovaSeq 6000 using the TruSeq SR Cluster Kit v3-cBot-HS with 2x150 read length and 40 million reads per sample.

first: Julie

middle: A

last: Theriot


title: RACS: Rapid Analysis of ChIP-Seq data for contig based genomes

status: Public on Sep 03 2019

city: Toronto

first: Alejandro

last: Saettone

address: 686 Bay Street

institute: The Hospital for Sick Children

summary: The biological samples are from untagged Tetrahymena thermophila to be used as a control for unspecific binding. Whole cells extracts were crosslinked and immunoprecipitated using M2 affinity gel (Sigma). The obtained DNA was sequenced by HiSeq2500 (Illumina). The processed fastq files were analyzed by RACS that segregates the found read accumulations between genic and intergenic regions being highly efficient for rapid downstream analyses.

overall_design: Examination of 2 sets of 2 biological replicates of  untagged cells during vegetative growth

first: Marcelo

last: Ponce

first: Syed

last: Nabeel-Shah

first: Jeffrey

last: Fillingham


title: Early embryogenesis involves a switch from parentally repressive chromosomal domains to de novo TADs

status: Public on Mar 28 2020

city: Paris

first: samuel

last: Collombet

address: 46 rue d'Ulm

institute: Ecole Normale Superieure

summary: Paternal and maternal epigenomes undergo dramatic changes after fertilization. How this relates to the 3D reorganisation of the parental genomes and their transcription patterns during early development remains unclear. Here we track structural dynamics during early mouse development using allele-specific single cell HiC integrated with transcriptome and chromatin changes, to combine parental features with early gene expression including during imprinted X-chromosome inactivation. We uncover a marked structural asymmetry following fertilization, with mostly maternal-specific domains of interaction that coincide with polycomb H3K27me3 domains. They form local repressive compartments and result in parentally-biased gene expression, including transient imprinting loci such as the X-inactivation center. These asymmetric domains later resolve into classical active and inactive compartments. Topologically associated domains are also established progressively, in a non parental specific manner and are associated with active chromatin. They are lost when gene expression is not maintained on the paternal X. Our study reveals unprecedented dynamics in parental specific 3D genome organization and gene expression during early development.

overall_design: We performed single cell HiC in mouse embryos from hybrid crosses at different stages

first: Samuel

first: Noemie

last: Ranisavljevic

first: Katia

last: Ancelin

first: Takashi

last: Nagano

first: Csilla

last: Varnai

first: Leung

last: Wing

first: Peter

last: Fraser

first: Edith

last: Heard


title: Next Generation Sequencing of Wild Type and Gata2+/- HSCs

status: Public on Jun 25 2019

city: CARDIFF

last: Giles

address: Heath Park

country: United Kingdom

institute: Cardiff University

summary: Gata2, a zinc finger TF, is essential for the generation and survival of HSCs in the embryo and has been implicated in the pathogenesis of AML, yet the requirement for Gata2 in adult HSCs and LSCs remains unclear. Using a conditional mouse model where Gata2 was deleted specifically in hematopoietic cells, we show that knockout of Gata2 leads to a rapid and complete cell-autonomous loss of adult HSCs. We then performed RNA-seq in sorted HSCs (LSK CD48- CD150+) from control and Gata2+/fl;Vav-iCre+ 8-to-10-week old mice.

overall_design: Wild Type and Gata2+/- HSCs were harvested from 8-to-10-week old mice

first: Ali

last: Abdelfatah

first: Neil

last: Rodrigues


title: Profiling cellular diversity in sponges informs animal cell type and nervous system evolution

status: Public on Jul 01 2020

first: Jacob

last: Musser

address: Meyerhofstrasse 1

institute: European Molecular Biology Laboratory

summary: We collected 10x single-cell RNAseq and bulk RNAseq data from 8-day old juvenile Spongilla lacustris

overall_design: 4, 10x 3' single-cell RNAseq samples and 1 bulk RNA experiment were collected. 10x samples 1-3 were sequenced in two separate sequencing runs. 10x sample 4 was sequenced only once. Bulk RNA was extracted from juvenile S. lacustris collected from the same population as those of the 10x single-cell samples. Bulk RNAseq was sequenced in two sequencing runs.

middle: M


title: TOPORS, a tumor suppressor protein, maintains higher-order chromatin organization in mouse hepatocytes [HiC]

status: Public on Jun 24 2020

city: Shanghai

first: Luzhang

last: Ji

address: 1239 Siping Rd.

institute: Tongji University

summary: Within mammalian nuclear space, chromosomes are hierarchically folded into active (A) and inactive (B) compartments composed of topologically associating domains (TADs). Genomic regions interact with nuclear lamina, termed lamina-associated domains (LADs), associated with transcriptional repression. However, the molecular mechanisms underlying these 3D chromatin architectures remain undeciphered. Here, we demonstrate the role of a potential tumor suppressor, TOP1 Binding Arginine/Serine Rich Protein (TOPORS), in genome organization. Topors knockdown in mouse hepatocytes results in cell proliferation and migration promotion, as well as arrest in the S phase of the cell cycle. RNA-seq analysis shows that 373 genes are up-regulated, some of which are associated with nuclear structure, and 316 genes exhibit down-regulated, many related to metabolic process. Chromatin accessibility is inclined to alter in the intergenic regions, including enhancers. Chromatin-lamina interactions decrease globally, and the coverage of LADs reduces from 53.31% to 46.52%. Furthermore, Topors knockdown leads to significantly increasing interactions between A and B compartments in cis and in trans. Correspondingly, strength of TAD boundaries located at A/B borders is weakened. Collectively, our data reveal that TOPORS functions as a regulator in chromosome folding, providing novel insights into the architectural role of tumor suppressors in higher-order genome organization.

overall_design: Hi-C data in Control and Topors KD AML12 cells.


title: Timeseries analysis of gene expression in Adrb2+/+ and Adrb2-/- Clone4-transgenic CD8+ T cells responding to Vesicular Stomatitis Virus expressing hemagglutinin from influenza A PR/8.

status: Public on Aug 01 2019

city: Dallas

first: J.

middle: David

last: Farrar

address: 5323 Harry Hines Blvd.

department: Immunology

institute: University of Texas Southwestern Medical Center

summary: RNA sequencing was performed to elucidate the role of beta2-adrenergic receptor (Adrb2) signaling on CD8+ T cell function and memory development after a viral infection. This was done by transferring 2,000 Clone4-transgenic CD8+ T cells from Adrb2+/+ and Adrb2-/- mice were (co-transferred at a 1:1 mix) into naïve Balb/cJ mice and the mice were then infected with 10^6 PFU of vesicular stomatitis virus expressing hemaglutinin peptide from Influenza A PR/8 (VSV-HA). Cells were then FACS-purified on days 4, 5, 7, and 12 post-infection for RNA isolation. RNA from purified naïve CD8+ T cells from each genotype, before transfer, was used for day 0 samples.

overall_design: There are a total of 30 samples, including a total of 5 timepoints with 2 genotypes at each timepoint and triplicates for each genotype at each timepoint.

first: Leonardo

middle: D

last: Estrada

first: J


title: Biomarkers of Cavernous Angioma with Symptomatic Hemorrhage (CASH) [small RNA-seq]

status: Public on May 13 2019

city: Chicago

first: Yan

last: Li

address: 900 East 57th St.

department: Center for Research Informatics

institute: The University of Chicago

summary:
Background: Cerebral cavernous angiomas with a symptomatic hemorrhage (CASH) have a high-risk of recurrent hemorrhage and serious morbidity.
Methods: Eighteen plasma molecules with postulated mechanistic roles in cavernous angioma (CA) pathobiology were investigated in 114 patients and 12 healthy subjects. The diagnostic biomarker of a CASH in the prior year was derived as minimizing the Akaike Information Criterion (AIC) and validated using machine-learning, and then compared to the prognostic CASH biomarker predicting bleeding in the subsequent year. Both biomarkers were longitudinally followed in a subset of cases. The biomarkers were queried in the transcriptome of human lesional micro-dissected neurovascular units (NVUs) and in relation to plasma miRNAs from CASH and non-CASH patients.
Results: The diagnostic CASH biomarker included a weighted combination of four molecules (sCD14, VEGF, CRP, and IL-10) distinguishing CASH patients with 76% sensitivity and 80% specificity (p=0.0003). The prognostic CASH biomarker included two of these molecules (sCD14 and VEGF) and two others (IL-1β and sROBO-4) was confirmed to predict a bleed in the subsequent year, with 83% sensitivity and 93% specificity (p=0.001). Genes associated with the diagnostic and prognostic CASH biomarkers were differentially expressed in CASH lesional NVUs. Thirteen miRNAs were also differentially expressed in the plasma of CASH patients compared to non-CASH.
Conclusion: There are shared and unique biomarkers of recent symptomatic hemorrhage and of future bleeding in CA, and are mechanistically linked to the lesional transcriptome and miRNA regulation. The biomarkers may be applied for risk stratification in clinical trials and developed as a tool in clinical practice.

overall_design: 12 micro RNA samples from plasma from 9 subjects with human cerebral cavernous malformations and 3 healthy controls

first: Seán

last: Lyne

first: Romuald

last: Girard

first: Janne

last: Koskimäki

first: Hussein

last: Zeineddine

first: Dongdong

last: Zhang

first: Ying

last: Cao

first: Agnieszka

last: Stadnik

first: Thomas

last: Moore

first: Rhonda

last: Lightle

first: Changbin

last: Shi

first: Robert

last: Shenkar

first: Julián

last: Carrión-Penagos

first: Sean

last: Polster

first: Sharbel

last: Romanos

first: Amy

last: Akers

first: Miguel

last: Lopez-Ramirez

first: Kevin

middle: J

last: Whitehead

first: Mark

middle: L

last: Kahn

last: Ginsberg

first: Douglas

last: Marchuk

first: Issam

last: Awad


title: Mitochondrial hetereogeneity in hematopoietic stem cells (HSC)

status: Public on Mar 05 2020

first: Saghi

last: Ghaffari

state: NY

address: One Gustave L. Levy Place, Box 1496

institute: Icahn School of Medicine at Mount Sinai

summary: Quiescence is a fundamental property that maintains hematopoietic stem cells (HSCs)’ potency throughout life. Quiescent HSCs are thought to rely on glycolysis for their energy but the overall metabolic properties of HSCs remain incompletely understood. Using combined approaches including single cell RNA-Seq we show that mitochondrial membrane potential (MMP) distinguishes the quiescent from cycling-primed HSCs. We found that primed but not quiescent HSCs relied readily on glycolysis. Notably, in vivo inhibition of glycolysis robustly enhanced the competitive repopulation ability of primed HSCs. We further show that HSC quiescence is maintained by an abundance of large lysosomes. Repression of lysosomal activation led to further enlargement of lysosomes, while repressing mTOR activation and glucose uptake. This also induced increased lysosomal sequestration of mitochondria and enhanced the competitive repopulation ability of primed HSCs by over 90-fold in vivo. These findings show that restraining lysosomal activity is key in preserving HSC quiescence and potency, and may be therapeutically relevant.

overall_design: To elucidate the potential diversity of cellular identity at the single cell level in quiescent mitochondrial membrane potential (MMP)-low versus primed MMP-high HSCs we used single-cell RNA-Seq (scRNA-Seq). Using the Fluidigm C1 platform, a total of 122 MMP-low HSCs and 126 MMP-high HSCs were deemed healthy after FACS purification and subsequently sequenced. A total of 224 cells were included for further analysis after the reads were mapped, processed, and filtered (>600,000 reads, >5,500 genes detected).

first: Raymond

last: Liang


title: ChIP-Seq Analysis of Med31-FZZ

status: Public on Jul 09 2019

first: Alejandro

last: Saettone

department: Genetics & Genome Biology

summary: The biological samples are from Med31-FZZ tagged Tetrahymena thermophila. Whole cells extracts were crosslinked and immunoprecipitated using M2 affinity gel (Sigma). The obtained DNA was sequenced by HiSeq2500 (Illumina). The processed fastq files were analyzed by RACS that segregates the found read accumulations between genic and intergenic regions being highly efficient for rapid downstream analyses.

overall_design: Examination of 2 sets of Med31-FZZ tagged cells during vegetative growth

first: Jyoti

last: Garg

first: Marcelo

last: Ponce

first: Ronald

last: Pearlman

first: Jeffrey

last: Fillingham


title: Biomarkers of Cavernous Angioma with Symptomatic Hemorrhage (CASH)

first: Yan

last: Li

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

overall_design: Refer to individual Series


title: Biomarkers of Cavernous Angioma with Symptomatic Hemorrhage (CASH) [RNA-seq]

overall_design: 13 total RNA samples, including 10 laser microdissected  neurovascular units (NVUs) from 10 human cerebral cavernous malformations and from 3 human brain autopsy controls

first: Seán

last: Lyne

first: Romuald

last: Girard

first: Janne

last: Koskimäki

first: Hussein

last: Zeineddine

first: Dongdong

last: Zhang

first: Ying

last: Cao

first: Agnieszka

last: Stadnik

first: Thomas

last: Moore

first: Rhonda

last: Lightle

first: Changbin

last: Shi

first: Robert

last: Shenkar

first: Julián

last: Carrión-Penagos

middle: P

last: Polster


title: TOPORS, a tumor suppressor protein, maintains higher-order chromatin organization in mouse hepatocytes

first: Luzhang

last: Ji


title: Arabidopsis DXO1 links RNA turnover and chloroplast function independently of its enzymatic activity

status: Public on Feb 08 2019

city: Warsaw

first: Michal

last: Krzyszton

address: Pawinskiego 5a

country: Poland

institute: Institute of Biochemistry and Biophysics, Polish Academy of Sciences

summary:
The DXO family of proteins participates in eukaryotic mRNA 5'-end quality control, removal of non-canonical NAD+ cap and maturation of fungal rRNA precursors. In this work, we characterize DXO1, the Arabidopsis thaliana DXO homolog. We demonstrate that the plant-specific modification within the active site negatively affects 5'-end capping surveillance properties of DXO1, but has only a minor impact on its strong deNADding activity. Unexpectedly, catalytic activity does not contribute to striking morphological and molecular aberrations observed upon DXO1 knockout in plants, which include growth and pigmentation deficiency, global transcriptomic changes and accumulation of RNA quality control siRNAs. Conversely, these phenotypes depend on the plant-specific N-terminal extension of DXO1. Pale-green coloration of DXO1-deficient plants and our RNA-seq data reveal that DXO1 affects chloroplast-localized processes. We propose that DXO1 mediates the connection between RNA turnover and retrograde chloroplast-to-nucleus signaling independently of its deNADding properties.

Founded by National Science Centre Grant, Poland (UMO-2013/08/M/NZ1/00931, UMO-2018/29/B/NZ3/01980, UMO‐2021/40/Q/NZ1/00014, UMO‐2014/13/B/NZ3/00405, MINIATURA 2017/01/X/NZ1/00332, UMO‐2021/41/B/NZ3/02605).

overall_design: Transcriptome profiles of Col-0 and dxo1-2 mutant plants using RNA-seq (three biological replicates) and small RNA-seq (three biological replicates). RNA-seq data for Col-0 plants are part of the previous submission: GSE95473. Samples for RNA-seq in GSE95473 submission and dxo1-2 RNA-seq in this experiment were prepared in parallel from plants grown at the same time.

first: Aleksandra

last: Kwasnik

first: Vivien

middle: Y

last: Wang

last: Gozdek

first: Monika

last: Zakrzewska-Placzek

first: Karolina

last: Stepniak

first: Jaroslaw

last: Poznanski

first: Liang

last: Tong

first: Joanna

last: Kufel


title: RNA-Seq analysis of Sleep deprivation in wildtype and Shank3 mutant mice

status: Public on Dec 31 2018

city: Spokane

first: Lucia

last: Peixoto

address: PO Box 1495

department: College of Medicine

institute: Washington State University, Spokane

summary: This dataset constitutes the first RNA-Seq study of gene expression following sleep deprivation in wildtype and Shank3 exon 21 mutant mice

overall_design: 20 total samples were analyzed, including wildtype and mutant (Shank3e21-/-) mice. Pre-frontal cortex tissue was collected at 5 hours of sleep deprivation (SD5). Animals that were left to sleep in their homecage were dissected at the same time of day to control for variations due to circadian rhythms (HC5). The protocol was repeated over the course of 5 days to obtain 5 animals per group, so that 5 independent SD experiments were represented in each time point and all animals for each group were dissected at exactly the same time of day.

first: Leandro

last: Roser

first: Hannah

last: Schoch

first: Taylor

last: Wintler


title: Gene expression profiling of treated and untreated primary prostate cancer

status: Public on May 31 2018

city: Bethesda

first: Adam

middle: G.

last: Sowalsky

state: MD

address: 37 Convent Drive Building 37 Room 1062B

department: Genitourinary Malignancies Branch

institute: National Cancer Institute

summary: In clinical trials assessing neoadjuvant androgen deprivation therapy plus next-generation androgen receptor axis inhibitors, a subset of patients fail to demonstrate a complete pathologic response following treatment and radical prostatectomy. We performed transcriptome analyses on laser capture microdissected foci of residual tumor from these patients.

overall_design: This study consists of 3 control (untreated) samples of primary prostate cancer and 19 samples of prostate cancer treated with neoadjuvant androgen deprivation therapy.

first: Huihui

last: Ye

first: Manoj

last: Bhasin

first: Mary

last: Ellen-Taplin

first: Steven

last: Balk


title: Lens epithelial cell transcriptome reprogramming at 24 hours post cataract surgery

status: Public on Oct 18 2018

city: Newark

first: Melinda

middle: K.

last: Duncan

address: 327 Wolf Hall

institute: University of Delaware

summary: This trancriptome analysis reveals the first detailed analysis on how the remnant lens epithelial cells (LECs) greatly reprogram their transcriptome towards inflammation/fibrosis by 24 hours post cataract surgery (PCS).

overall_design: Living mice were subjected to lens fiber cell removal leaving behind the lens epithelium and capsule to model human cataract surgery. llumina HiSeq 2000 (Illumina) transcriptome profiling was performed in biological triplicate on  remnant LECs isolated either immediately after surgery or 24 hours later in order to ascertain the response of lens epithelial cells to cataract suregery with the goal of understanding the molecular basis of posterior capsular opacification.

first: Mahbubul

middle: H

last: Shihan

middle: K


title: Hemogenic endothelial fate mapping reveals dual developmental origin of mast cells.

status: Public on Jun 01 2018

city: Singapore

first: jinmiao

last: chen

address: 8A Biomedical Grove, #04-06 Immunos

country: Singapore

institute: Singapore Immunology Network

summary: Hematopoiesis occurs in distinct waves. ‘Definitive’ hematopoietic stem cells (HSC) with the potential for all blood lineages emerge in the aorta-gonado-mesonephros (AGM), while ‘primitive’ progenitors, whose potential is thought to be limited to erythrocytes, megakaryocytes and macrophages (MΦ), arise earlier in the yolk sac (YS). Here, we questioned whether other YS lineages exist that have not been identified, partially owing to limitations of current lineage tracing models. We established the use of Cdh5CreERT2 for hematopoietic fate mapping, which revealed the YS origin of mast cells (MC). YS derived MC are replaced by definitive MC, which maintain themselves independently from the BM in the adult. Replacement occurs with tissue specific kinetics. MC in the skin, but not other organs, remain largely YS derived prenatally and are phenotypically and transcriptomically distinct from definite adult MC. We conclude that dual hematopoietic origin is not MΦ specific, but shared between these two myeloid lineages.

overall_design: RNAsequencing of YS HE derived embryonic (E16.5) and definitive adult skin MC. 3 replicates for each population.

first: Rebecca

last: Gentek

first: Marc

last: Bajénoff


title: Bcl11b- and GATA3-mediated gene regulation in Th2 cells

status: Public on Mar 05 2018

first: Andrew

last: Oler

address: 31 Center Drive, Room 3B62E

department: Bioinformatics and Computational Biosciences Branch (BCBB)

institute: NIAID/NIH

summary: GATA-binding protein 3 (GATA3) acts as the master transcription factor for type 2 T helper (Th2) cell differentiation and function. However, it is still elusive how GATA3 function is precisely regulated in Th2 cells. Here, we report that the transcription factor B cell lymphoma 11b (Bcl11b), a previously unknown component of GATA3 transcriptional complex, is involved in GATA3-mediated gene regulation. Bcl11b binds to GATA3 through protein-protein interaction, and they co-localize at many important cis-regulatory elements in Th2 cells. The expression of type 2 cytokines, including IL-4, IL-5 and IL-13, is up-regulated in Bcl11b-deficient Th2 cells both in vitro and in vivo; such up-regulation is completely GATA3-dependent. Genome-wide analyses of Bcl11b- and GATA3-regulated gene (from RNA-Seq), co-binding pattern (from ChIP-Seq), and Bcl11b-mediated epigenetic changes (in H3K27ac and DHSs) suggest that GATA3/Bcl11b complex is involved in limiting Th2 gene expression, as well as in inhibiting non-Th2 gene expression. Thus, Bcl11b controls both GATA3-mediated gene activation and repression in Th2 cells.

overall_design: Naïve CD4 T cells were isolated from Bcl11bfl/fl-CreERT2 mice and cultured under Th2 conditions with or without 4-OHT for 4 days (early Th2 cells). Naïve CD4 T cells were isolated from Bcl11bfl/fl-CreERT2 mice and cultured under Th2 conditions for 4 days. Then, after resting in IL-2-containing medium for one day, the primed cells were further cultured under Th2 conditions with or without 4-OHT for 4 days (late Th2 cells). ChIP-Seq of Bcl11b and GATA3 analysis in early and late WT or KO Th2 cells. RNA-seq for early and late WT or KO Th2 cells, with 2 replicates. Raw data is in SRP104190.

first: Difeng

last: Fang

first: Kairong

last: Cui

first: Gangqing

last: Hu

first: Rama

last: Gurram

first: Chao

last: Zhong

first: Ryoji

last: Yagi

first: Ming

last: Zhao

first: Suveena

last: Sharma

first: Pentao

last: Liu

first: Bing

last: Sun

first: Keji

first: Jinfang

last: Zhu


title: MBD1 activates neuronal developmental genes through modulating chromatin structure during neuronal maturation

status: Public on May 15 2018

city: Madison

first: Xinyu

state: WI

address: 1500 HIGHLAND AVE, T513 Waisman Center

department: Department of Neuroscience

institute: University of Wisconsin-Madison


title: Bcl11b, a Novel GATA3-Interacting Protein, Suppresses Th1 while Limiting Th2 Cell Differentiation (H3K27ac and DNase-Seq)

overall_design: Naïve CD4 T cells were isolated from Bcl11bfl/fl-CreERT2 mice and cultured under Th2 conditions with or without 4-OHT for 4 days (early Th2 cells). Naïve CD4 T cells were isolated from Bcl11bfl/fl-CreERT2 mice and cultured under Th2 conditions for 4 days. Then, after resting in IL-2-containing medium for one day, the primed cells were further cultured under Th2 conditions with or without 4-OHT for 4 days (late Th2 cells). ChIP-Seq of histone modification H3K27ac and scDNase-Seq analysis in early and late WT or KO Th2 cells.


title: Developmental analysis of bone marrow neutrophil reveals populations specialised in expansion, trafficking and effector functions

status: Public on Feb 23 2018

first: jinmiao

summary: RNAseq was performed on bone marrow GMP and neutrophil subsets to understand the difference in their transcriptome profile. The data here presents the distinct molecular signatures present in each stage of neutrophil development and the factors required for each stage of development.

overall_design: Bone marrow cells were depleted of B and T cells before fluroscence activated cell sorting with phenotypic markers presented in our paper. Bone marrow GMPs and Neutrophil subsets were sorted for sequencing. DEGs were obtained to observe if any signicant genes were affected. Pathway analysis was performed with the set of DEGs.

first: Maximilien

last: Evrard

first: Immanuel

last: Kwok

first: Ng

last: Lai Guan


title: Expression profile of 22Rv1 cells upon DHT treatment

status: Public on Nov 01 2017

city: New York

first: Shipra

last: Shukla

address: 417 East 68th Street

institute: MSKCC

summary: To determine genes regulated by Androgen Receptor in response to DHT treatment in 22Rv1, we cultured 22Rv1 cells in full serum containing media and then added DHT for 24 hrs. RNA was harvested after 24 hrs of treatment and gene expression profiling was performed by RNA-Seq

overall_design: RNA profiles were generated by deep sequencing using Illumina HiSeq 2000.

first: Yu

last: Chen


title: Bcl11b, a Novel GATA3-Interacting Protein, Suppresses Th1 while Limiting Th2 Cell Differentiation

first: Andrew

last: Oler


title: Defective XRN3-mediated transcription termination in Arabidopsis affects the expression of protein-coding genes [seq]

status: Public on Jan 24 2018

first: Michal

last: Krzyszton

summary:
Arabidopsis thaliana contains two nuclear XRN2/3 5'-3' exonucleases that are homologs of yeast and human Rat1/Xrn2 proteins involved in the processing and degradation of several classes of nuclear RNAs and in transcription termination of RNA polymerase II. Using strand-specific short read sequencing we show that knockdown of XRN3 leads to an altered expression of hundreds of genes and the accumulation of uncapped and polyadenylated read-through transcripts generated by inefficiently terminated Pol II. Our data support the notion that XRN3-mediated changes in the expression of a subset of genes are caused by upstream read-through transcription and these effects are enhanced by RNA-mRNA chimeras generated in xrn3 plants. In turn, read-through transcripts that are antisense to downstream genes may trigger production of siRNA. Our results highlight the importance of XRN3 exoribonuclease in Pol II transcription termination in plants and show that disturbance in this process may significantly alter gene expression.

Founded by National Science Centre Grant, Poland (UMO-2018/29/B/NZ3/01980, UMO‐2021/40/Q/NZ1/00014, UMO‐2014/13/B/NZ3/00405, MINIATURA 2017/01/X/NZ1/00332, UMO‐2021/41/B/NZ3/02605).

overall_design: Transcriptome profiles of Col-0 and xrn3-8 mutant plants using RNA-seq (three biological replicates) and small RNA-seq (three biological replicates).

first: Monika

last: Zakrzewska-Placzek

first: Aleksandra

last: Kwasnik

first: Norbert

last: Dojer

first: Wojciech

last: Karlowski

first: Joanna

last: Kufel


title: The bromodomain-containing protein Ibd1 links multiple chromatin-related protein complexes to highly expressed genes in Tetrahymena thermophila

status: Public on Feb 28 2018

first: Alejandro

last: Saettone

state: Ontario

summary: We hypothesize that Ibd1 coordinates the recruitment of several chromatin remodeling complexes to promote transcription of highly expressed genes in T.thermophila. We developed a ChIP-seq protocol including a heuristic method (in preparation paper, Ponce & Saettone, et al., 2017) to call peaks present in genic and intergenic regions specifically. We used the obtained data from the 2 NGS biological replicas, each of which had an INPUT and an Immunoprecipitated (IP) sample.

overall_design: Examination of 2 biological replicates of Ibd1 (BRD-containing protein) during vegetative growth.

first: Jeffrey

last: Fillingham

first: Marcelo

last: Ponce


title: TET-mediated epimutagenesis of the Arabidopsis thaliana methylome

status: Public on Mar 02 2018

city: Athens

first: Robert

last: Schmitz

state: GA

address: B416 Davison Life Sciences

department: Genetics

institute: University of Georgia

type: Methylation profiling by high throughput sequencing

summary: DNA methylation in the promoters of plant genes sometimes leads to transcriptional repression, and the wholesale removal of DNA methylation as seen in methyltransferase mutants results in drastic changes in gene expression and severe developmental defects. However, many cases of naturally-occurring DNA methylation variations have been reported, whereby the altered expression of differentially methylated genes is responsible for agronomically important traits. The ability to manipulate plant methylomes to generate populations of epigenetically distinct individuals could provide invaluable resources for breeding and research purposes. Here we describe “epimutagenesis”, a novel method to rapidly generate variation of DNA methylation through random demethylation of the Arabidopsis thaliana genome. This method involves the expression of a human Ten-eleven translocation (TET) enzyme, and results in widespread hypomethylation that can be inherited to subsequent generations, mimicking mutants in the maintenance DNA methyltransferase met1. Application of TET-mediated epimutagenesis to agriculturally significant plants may result in differential expression of alleles normally silenced by DNA methylation, uncovering previously hidden phenotypic variations.

overall_design: 19 MethylC-seq, three TAB-seq, one ChIP-seq and nine RNA-seq of Arabidopsis thaliana


title: Simultaneous profiling of 3D genome structure and DNA methylation in single human cells

status: Public on Sep 09 2019

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

institute: HHMI-Salk-Institute

summary:
Dynamic 3D chromatin conformation is a critical mechanism for gene regulation during development and disease. Despite this, profiling of 3D genome structure from complex tissues with cell-type specific resolution remains challenging. Recent efforts have demonstrated that cell-type specific epigenomic features can be resolved in complex tissues using single-cell assays. However, it remains unclear whether single-cell
Chromatin Conformation Capture (3C) or Hi-C profiles can effectively identify cell types and reconstruct cell-type specific chromatin conformation maps. To address these challenges, we have developed single-nucleus methyl-3C sequencing (sn-m3C-seq) to capture chromatin organization and DNA methylation information and robustly
separate heterogeneous cell types. Applying this method to >4,200 single human brain prefrontal cortex cells, we reconstruct cell-type specific chromatin conformation maps from 14 cortical cell types. These datasets reveal the genome-wide association between cell-type specific chromatin conformation and differential DNA methylation, suggesting
pervasive interactions between epigenetic processes regulating gene expression.

overall_design: Multi-omic method single-nucleus methyl-3C sequencing (sn-m3C) to profile chromatin conformation and DNA methylation from the same cell.

first: Chongyuan

last: Luo

first: Dong-Sung

last: Lee

first: Jingtian

last: Zhou

first: Sahaana

last: Chandran

first: Angeline

last: Rivkin

first: Anna

last: Bartlett

last: Nery

first: Conor

last: Fitzpatrick

first: Carolyn

last: O’Connor

first: Jesse

last: Dixon


title: HNF4G, AR, FOXA1, H3K4me1, H3K27acetyl binding sites upon knockdown and overexpression of HNF4G in 22Rv1 and LNCaP prostate cancer cells respectively

first: Shipra

last: Shukla

summary: HNF4G is a gastrointestinal tissue enriched master transcriptional regulator seen overexpressed in a subset of prostate cancer. Here we have mapped binding sites of HNF4G, AR, Foxa1, H3K4me1, H3K27acetyl upon knockdown and overexpression of HNF4G in in 22Rv1 and LNCaP cells respectively

overall_design: ChIPSeq mapping of HNF4G, AR, Foxa1, H3K4me1, H3K27acetyl upon knockdown and overexpression of HNF4G in in 22Rv1 and LNCaP cells respectively

first: Yu

last: Chen


title: Expression profiling and occupancy after knockdown or over-expression of HFN1A or HNF4G in prostate cancer cells


title: Expression profile of HNF1A knockdown and overexpression in 22RV1 and LNCaP cells respectively

summary: To determine genes regulated by HNF1A in 22Rv1, we performed siRNA  mediated knockdown of HNF1A using pooled siHNF1A (L-008215-00-0005 5 nmol) and pooled siSCR purchased from Dharmacon.  RNA was harvested 3 days after transfection and gene expression profiling was performed. Similarly to determine genes regulated by HNF1A in LNCaP, we performed retroviral transduction of  LNCaP cells in duplicate for HNF1A  and empty vector control expression. cDNA for HNF1A in RC211201 vector (origene) was subcloned  into a murine stem cell virus (MSCV)-based retroviral vector with hygromycin selection marker (Addgene). After 3 days of transduction, cells were selected for four days in hygromycin and later on RNA was harvested for gene expression profiling.

overall_design: RNA profiles were generated by deep sequencing using Illumina HiSeq.


title: Expression profile of LNCaP/AR cells with or without HNF4G expression grown for long term in charcoal stripped-serum (CSS) media

summary: To study the underlying mechanism of androgen independent growth we performed transcriptome analysis of LNCaP/AR-Vec and LNCaP/AR-HNF4G at day 9 of growth in CSS and LNCaP/AR-HNF4G at 32 days of growth in CSS to identify the HNF4G transcriptome, as well as determinants of castration-resistant growth

overall_design: RNA-seq


title: A comparative analysis of 5-azacytidine and zebularine induced DNA demethylation using whole-genome bisulfite sequencing

status: Public on Jun 24 2016

summary: The non-methylable cytosine analogs, 5-azacytidine and zebularine, are widely used to disrupt DNA methyltransferase activity and reduce genomic DNA methylation. In this study, whole-genome bisulfite sequencing is used to construct maps of DNA methylation with single base pair resolution in Arabidopsis thaliana seedlings treated with each demethylating agent. We find that 5-azacytidine and zebularine-treated seedlings have nearly indistinguishable patterns of DNA methylation genome-wide and that 5-azacytidine, despite being more unstable in aqueous solution, has a slightly greater demethylating effect at higher concentrations across the genome. Transcriptome analyses revealed a substantial number of up-regulated genes and transposable element genes, particularly CACTA-like elements, demonstrating that chemical demethylating agents have a disproportionately large effect on loci that are silenced by DNA methylation.

overall_design: Bisulfite-Seq and RNA-Seq


title: Expression data from euploid and trisomic 13, 18 and 21 human fetal cells

status: Public on Oct 09 2015

city: 91400 Orsay

first: Florent

last: Dumont

state: Ile de France

address: 17 avenue des sciences

institute: Université Paris-Saclay

summary:
The organization and dynamics of chromatin within the in vivo interphase nucleus and the latter's relationship with transcriptional regulation are still not fully understood. To better understand these relationships, we studied a natural example of chromosomal disorganization: aneuploidy due to trisomies 13, 18 and 21. We hypothesized that the presence of an extra copy of one chromosome alters the CT distribution in the nucleus, which in turn perturbs transcriptional activity.
We used microarrays to highlight the overall genome expression changes occurring in amniocytes and fibroblasts carrying a trisomy 13, 18 or 21.

overall_design: Cultured amniocytes and fibroblasts cells were used for RNA extraction and hybridization on Affymetrix microarrays. We used two trisomy 13, two trisomy 18 and nine controls from amniocytes cells; and five trisomy 21 and five controls from chorionic villi (fibroblasts).


title: Massively multiplex single-cell Hi-C

status: Public on Jan 28 2017

city: San Francisco

first: Vijay

last: Ramani

state: California

department: Biochemistry & Biophysics

institute: UCSF

summary: Proof-of-concept for a massively parallel single-cell version of the Hi-C protocol

overall_design:
Single-cell Hi-C

Raw data for GSM2254215, GSM2254216, GSM2254218, GSM2254219 and GSM2438426 were submitted to dbGaP due to patient privacy concerns. The raw data are available at dbGaP accession ID phs001269.v1.p1.