title: 3D epigenome architecture orchestrates cis and trans regulation of flowering time in rice [ChIA-PET]

summary: Repressive epigenetic modification histone H3 lysine 27 tri-methylation (H3K27me3) marks many agronomically important genes in plants. However, H3K27me3-associated three-dimensional (3D) genome architecture and its regulatory functions in rice flowering time remain unclear. In this study, we map H3K27me3-associated genome topology using long-read ChIA-PET and reveal extensive chromatin loops among H3K27me3-marked regions in different rice varieties and tissues. Multiple H3K27me3-associated chromatin loops usually tether together and further form repressive chromatin interacting domains (RIDs), which provide structural bases for the regulation of the co-modification and co-expression of interacting genes. Surprisingly, we identified extensive chromatin loops between the rice florigen genes Hd3a and RFT1, and frequent chromatin interactions between the positive flowering regulator Ehd1 on the chromosome 10 and Hd3a/ RFT1 loci on the chromosome 6. These results suggest that flowering genes might form a Ehd1-Hd3a/RFT1-centered spatial gene cluster in rice. We also demonstrate the flowering regulator protein complexes comprising Ghd7, Ghd8, and Hd1 could bind to the Ehd1-Hd3a/RFT1 spatial gene cluster. In addition, liquid-liquid phase separation of Ghd7 and Hd1, as well as the essentially synchronous expression of Ehd1 and Hd3a suggest that this spatial gene cluster acts as a regulatory hub to coordinately regulates the expression of Ehd1-Hd3a. This work uncovers the frame of integrated cis and trans molecular mechanism underlying transcriptional regulation of florigen genes in rice.

platform_organism:
Oryza sativa Indica Group
Oryza sativa Japonica Group

overall_design: H3K27me3-associated genome topology in different rice varieties and tissues (MH63-seedling, MH63-root, ZS97-seedling, ZS97-root, DJ-seedling, osemf2b-seedling)

first: Yue

last: Li

first: Zhanyi

last: Zhang


title: 3D epigenome architecture orchestrates cis and trans regulation of flowering time in rice [ChIP-seq]

status: Public on Sep 28 2022

city: Wuhan

first: yue

last: li

address: Shizishan Street

country: China

institute: HUAZHONG Agriculture University

type: Genome binding/occupancy profiling by high throughput sequencing

sample_organism:
Oryza sativa Indica Group
Oryza sativa Japonica Group

overall_design: H3K27me3 modification of DJ and osemf2b; Different Ghd8 binding sites in Ghd8:GFP NILs (ZS-ghd7/Ghd8:GFP/Hd1, ZS-Ghd7/Ghd8:GFP/Hd1, ZS-Ghd7/Ghd8:GFP/hd1), ZS-ghd7/ghd8/Hd1 as control


title: RNA-seq analysis of Eriocheir sinensis muscle

status: Public on Jul 17 2022

city: Tianjin

first: Tong

last: Hao

state: China

department: College of Life Sciences

institute: College of Life Sciences, Tianjin Normal University

type: Expression profiling by high throughput sequencing

summary: the chromatin accessibility and gene expression of muscle in E. sinensis in pre-molt (D) and post-molt (A) stages were sequenced by Assay of Transposase Accessible Chromatin sequencing (ATAC-seq) and RNA-seq, respectively.The differntial peaks in ATAC-seq and differntial genes in RNA-seq were analzed. The data was used to analysis the differentially expressed genes (DEGs) in muscle before and after molting by combining ATAC-seq and RNA-seq

overall_design: Muscle of healthy crabs in pre-molt (D stages) and post molt (A stages) were collected and used for ATAC-seq and RNA-seq analysis.in each stages, three muscle samples were collected as the experimental replications. RNA-seq was performed with Illumina novaseq platform with E. sinensis genome (accession number PRJNA555707) as the reference genome.

first: Jingjing

first: Jinsheng

last: Sun


title: HSF1 activates ANXA11-mediated glutamine metabolism by super enhancer long non-coding RNA LINC00857 in colorectal cancer [ChIP-seq]

status: Public on Aug 15 2022

city: Weifang City

first: Jiaqiu

state: 省/直辖市

address: No. 2428, Yuhe Road, Kuiwen District

institute: weifang medical university

summary: We shed light on a closely cooperative machinery between HSF1 and super enhancer for the first time in CRC. HSF1 could stimulate super enhancer activity by the enrichment of acetyltransferase P300 to LINC00857 promoter region, contributing to LINC00857 transcription.

overall_design: HSF1 and H3K27ac enriched peak was analyzed by CHIP-seq with HSF1 and H3K27ac antibodies.


title: An autoregulatory feedback loop converging on H2AK119ub1 drives synovial sarcoma [CUT&RUN]

status: Public on Jun 30 2022

city: Edinburgh

first: Nezha

middle: Suzanne

last: Benabdallah

state: Midlothian

address: Crewe Road South

department: Institute of Genetics and Cancer

country: United Kingdom

institute: University of Edinburgh

summary: The SS18-SSX fusion drives oncogenic transformation in synovial sarcoma by bridging SS18, a member of mSWI/SNF complex, to polycomb repressive complex 1 (PRC1) target genes. Here we show that the SSX C-terminus, via its SSXRD domain, directs SS18-SSX chromatin binding independently of SS18. SSXRD specific targeting is mediated by interaction with H2AK119ub1 and histone MacroH2A with which the fusion overlaps genome wide. Variant Polycomb Repressive Complex 1.1 (PRC1.1) acts as the main depositor of H2AK119ub1 and consequently is required for SS18-SSX occupancy. Importantly, SSX C-terminus not only depends on H2AK119ub1 for localization but also further promotes it and consequently, high H2AK119ub1 levels are acquired during synovial sarcoma development. These results reveal an SS18-SSX/PRC1 autoregulatory feedback-loop that enforces fusion binding and could play a role in a wide-range of cancers and physiological settings where SSX proteins are overexpressed.

overall_design: Chromatin profiles of endogenous SS18-SSX1/2, H2AK119ub1 in human synovial sarcoma cells and HA occupancy in osteosarcoma or synovial sarcoma cells expressing MSCV-HA-eGFP-SS18-PGK-Puro, MSCV-HA-eGFP-SS18-SSX1-PGK-Puro and MSCV-HA-eGFP- SSX-C-PGK-Puro

middle: S

first: Ana

last: Banito


status: Public on Jul 23 2022

city: Shanghai

first: Jiajun

last: Qiu

address: West BeiJing Road

institute: Shanghai Children’s Hospital, Shanghai Institute of Medical Genetics, Shanghai Jiao Tong University School of Medicine

summary: Down syndrome (DS) is the most common genetic condition that causes intellectual disability in humans. The molecular mechanisms behind the DS phenotype remain unclear. Therefore, in the present study, induced pluripotent stem cells (iPSCs) from a patient with DS and a normal control (NC) patient were differentiated into iPSCs‐derived neural stem cells (NSCs). Single-cell RNA sequencing was performed to achieve a comprehensive single-cell level differentiation roadmap for DS-iPSCs. The results demonstrated that iPSCs can differentiate into NSCs in both DS and NC samples. Furthermore, 19,422 cells were obtained from iPSC samples (8,500 cells for DS and 10,922 cells for the NC) and 16,506 cells from NSC samples (7,182 cells for DS and 9,324 cells for the NC), which had differentiated from the iPSCs. A cluster of DS-iPSCs, named DS-iPSCs-not differentiated (DSi-PSCs-ND), which had abnormal expression patterns compared with NC-iPSCs, were demonstrated to be unable to differentiate into DS-NSCs. Further analysis of the differentially expressed genes revealed that inhibitor of differentiation family members, which exhibited abnormal expression patterns throughout the differentiation process from DS-iPSCs to DS-NSCs, may potentially have contributed to the neural differentiation of DS-iPSCs. Moreover, abnormal differentiation fate was observed in DS-NSCs, which resulted in the increased differentiation of glial cells, such as astrocytes, but decreased differentiation into neuronal cells. Furthermore, functional analysis demonstrated that DS-NSCs and DS-NPCs had disorders in axon and visual system development. Biological experiments were also performed to validate these results and the present study provided a new insight into the pathogenesis of DS.

overall_design:
Burlk and single cell RNA sequencing of neural stem cells derived from human trisomic iPSCs
This submission contains scRNA-Seq data.

first: Yanna

last: Liu

first: Hao

last: Wei

first: Fanyi

last: Zeng

first: Jingbin

last: Yan


title: HSF1 activates ANXA11-mediated glutamine metabolism by super enhancer long non-coding RNA LINC00857 in colorectal cancer.

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

overall_design: Refer to individual Series


title: Effects of knocking down RNP1A on gene expression in Dictyostelium discoideum

status: Public on Jul 01 2022

city: Baltimore

first: Yinan

state: MD

address: 725 North Wolfe Street, Physiology Builiding Rm.100

department: Cell Biology

country: USA

institute: Johns Hopkins University School of Medicine

summary: To investigate the function of RNP1A, an RNA-binding protein in Dictyostelium discoideum

overall_design: Comparative gene expression analysis of RNA-seq data from two independent rnp1A knockdowns (control + rnp1A knockdown cell lines)

first: Douglas

middle: N

last: Robinson


title: ATAC-seq analysis of Eriocheir sinensis muscle

overall_design: Muscle of healthy crabs in pre-molt (D stages) and post molt (A stages) were collected and used for ATAC-seq analysis.in each stages, three muscle samples were collected as the experimental replications. ATAC-seq was performed with Illumina Hiseq platform with E. sinensis genome (accession number PRJNA555707) as the reference genome.


title: HIV-1 Induction of Tolerogenic DCs is Mediated by Cellular Interaction with Suppressive T Cells

status: Public on Aug 05 2022

city: Linkoping

first: Cecilia

last: Svanberg

address: Molecular Virology, lab1, plan 13, Medical Faculty, Linkoping University

department: Molecular virology

country: Sweden

institute: BKV

summary: Transcriptomic analyses was performed to elucidate effects of HIV exposure on the dendritic cell phenotype after crosstalk with T cells

overall_design:
RNAseq on DCs enriched from cocultures with T cells with and without exposure to HIV
>>> Submitter declares that raw data are not available due to donor privacy concerns. <<<

first: Rada

last: Ellegard

first: Marie

last: Larsson


title: An autoregulatory feedback loop converging on H2AK119ub1 drives synovial sarcoma [ChIP-seq]

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for eGFP, SSX-C and SSX-CDeltaRD in human synovial sarcoma cells HS-SY-II using their HA tag.


title: Immune-mediated Tubule Atrophy Promotes Acute Kidney Injury to Chronic Kidney Disease Transition

city: New Haven

first: Leyuan

last: Xu

state: CT

address: 300 Cedar Street, Ste S255B

department: Internal Medicine/Section of Nephrology

institute: Yale University

summary: Incomplete repair after acute kidney injury (AKI) is associated with progressive loss of tubular cell function and development of chronic kidney disease (CKD). Here, we compared the kidney single-cell transcriptomes from the mice subjected to either unilateral ischemia-reperfusion kidney injury with contralateral nephrectomy (IRI/CL-NX, in which tubule repair predominates) or unilateral IRI with contralateral kidney intact (U-IRI, in which fibrosis and atrophy predominates) to investigate the mechanism(s) underlying transition to CKD following AKI.

overall_design: 10X Chromium was used to profile mouse kidneys.

first: Xu

last: Leyuan

first: Lloyd

middle: G

last: Cantley


title: Aberrant gene activation in synovial sarcoma relies on SSX specificity and increased PRC1.1 stability


title: ATAC-seq and RNA-seq analysis of Eriocheir sinensis muscle

status: Public on Jul 16 2022

first: Tong


title: Single-cell RNA Sequencing of Human Esophageal Epithelium in Homeostasis and Allergic Inflammation

status: Public on Jun 15 2022

city: Cincinnati

first: Hee-Woong

last: Lim

state: Ohio

address: 3333 Burnet Ave. MLC 7024

department: Division of Biomedical Informatics

institute: Cincinnati Children's Hospital Medical Center

summary: To investigate gene expression signature of the human esophageal epithelium at the homeostatic and inflammatory conditions we performed scRNAseq on the human  esophageal biopsies obtained from the healhy patients, patients with active eosinophilic esophagitis (EoE) and patients in the remission.

overall_design: Esophageal biopsies from obtained from the healhy patients, patients with active EoE and patients in the remission were collected, processed to generate single cell suspension and subjected to 10X scRNAseq

first: Mark

last: Rochman

first: Ting

last: Wen

first: Marc

last: Rothenberg


title: Prior vaccination exceeds prior infection in eliciting innate and humoral immune responses in Omicron infected outpatients

status: Public on Jun 11 2022

city: Bethesda

first: Hye Kyung

last: Lee

address: 8 CENTER DR RM 107

department: National Institute of Diabetes and Digestive and Kidney (NIDDK)

institute: National Institutes of Health (NIH)

summary: Antibody response following Omicron infection is reported to be less robust than that to other variants. Here we investigated how prior vaccination and/or prior infection modulates that response. Disease severity, antibody responses and immune transcriptomes were characterized in four groups of Omicron-infected outpatients (n=83): unvaccinated/no prior infection, vaccinated/no prior infection, unvaccinated/prior infection and vaccinated/prior infection. The percentage of patients with asymptomatic or mild disease was highest in the vaccinated/no prior infection group (87%) and lowest in the unvaccinated/no prior infection group (47%). Significant anti-Omicron spike antibody levels and neutralizing activity were detected in the vaccinated group immediately after infection but were not present in the unvaccinated/no prior infection group. Within two weeks, antibody levels against Omicron, increased. Omicron neutralizing activity in the vaccinated group exceeded that of the prior infection group. No increase in neutralizing activity in the unvaccinated/no prior infection group was seen. The unvaccinated/prior infection group showed an intermediate response. We then investigated the early transcriptomic response following Omicron infection in these outpatient populations and compared it to that found in unvaccinated hospitalized patients with Alpha infection. Omicron infected patients showed a gradient of transcriptional response dependent upon whether or not they were previously vaccinated or infected. Vaccinated patients showed a significantly blunted interferon response as compared to both unvaccinated Omicron infected outpatients and unvaccinated Alpha infected hospitalized patients typified by the response of specific gene classes such as OAS and IFIT that control anti-viral responses and IFI27, a predictor of disease outcome.

overall_design: RNA-seq were performed with peripheral blood mononuclear cells (PBMCs) of COVID-19 patients infected by SARS-CoV-2 Omicron varient.

first: Hye-Kyung

first: Ludwig

last: Knabl


title: Spatial transcriptomics stratifies psoriatic disease by emergent cellular ecosystems

status: Public on May 12 2022

city: New York

first: Shruti

last: Naik

state: NY

address: 435 East 30th Street

department: Pathology

institute: NYU Langone Health

summary: The skin is recognized as a window into the immunopathogenic mechanisms driving the vast phenotypic spectrum of psoriatic disease. To better decipher the cellular landscape of both healthy and psoriatic skin, we employed spatial transcriptomics (ST), a ground-breaking technology that precisely maps gene expression from histologically-intact tissue sections.  Findings gleaned from computationally integrating our 23 matched lesional and non-lesional psoriatic and 7 healthy control samples with publicly-available single cell RNA seq data sets provided insights into the emergent cellular ecosystems at play in psoriatic disease.

overall_design: This is a cross-sectional study involving the accrual of 3-4-mm skin punch biopsy samples from healthy controls and biologic naïve patients with psoriatic disease. The samples were then subjected to the protocols entailed by spatial transcriptomics platform.

first: Rochelle

last: Castillo

first: Ikjot

last: Sidhu


title: Single cell RNA-sequencing based characterization of cell compositions in human multiple primary lung cancer

status: Public on Apr 23 2022

city: Dalian

first: Hai-long

last: Piao

state: Liaoning

address: No.457 Zhongshan Road

institute: Dalian Institute of chemical physics

summary: Multiple primary lung cancers (MPLC) pose diagnostic and therapeutic challenges in the clinic. Here, we orchestrated the cellular atlasof MPLC by single cell RNA-sequencing and identified the heterogeneity between different lesions within the same MPLC patients.

overall_design: We collected 19 tissue samples from four MPLC patients (one squamous carcinoma and three adenocarcinomas); each patient had two separate lung tumor lesions.For the first two patients (P1 and P2), we collected one tissue specimen from each of the tumor lesions. For the third patient (P3), to understand the intra-lesion heterogeneity, two repetitive tissue specimens from each of the tumor lesions were collected. For the last patient (P4), two tissue specimens from one of the larger tumor lesions and one tissue specimen from the other small tumor lesion were collected.As comparisons, one normal tissue sample adjacent to each tumor lesion was collected. Single cell RNA-sequencing was performed on all the collected 19 samples.

first: Yawei

last: Wang

first: Di

last: Chen


title: Plants grow in lunar regolith

status: Public on May 16 2022

city: Gainesville

first: Robert

middle: J.

last: Ferl

state: Florida

address: 1301 Fifield Hall PO Box 110690

department: Horticultural Sciences

institute: University of Florida

summary: The extent to which plants can enhance human life support on other worlds depends on the ability of plants to thrive in extraterrestrial environments using in situ resources. Using samples from Apollo 11, 12 and 17, we show that the terrestrial plant Arabidopsis thaliana germinates and grows in diverse lunar regoliths. However, our results show that growth is challenging; the lunar regolith plants were slow to develop, expressed genes indicative of ionic stresses, and many showed severe stress morphologies. Therefore, although in situ lunar regolith can be useful for plant production in lunar habitats, they are not benign substrates. The interaction between plants and lunar regolith will need to be further elucidated, and likely mitigated, to enable efficient use of lunar regolith for life support.

overall_design: Arabidopsis thaliana (Col-0) was grown in lunar regolith from three different mission sites: Apollo 11, Apollo 12 and Apollo 17. The plants were grown completely within the regolith as a growth substrate and compared to plants grown in an identical fashion in a lunar simulant (JSC-1A) as the control. Comparisons between and among lunar regoliths, and the simulant controls, included morphology and development, and transcriptomic responses.

first: Anna-Lisa

last: Paul

first: Stephen

middle: M

last: Elardo

middle: J


title: Global analysis of binding sites of U2AF1 and ZRSR2 reveals RNA elements required for mutually exclusive splicing by the U2- and U12-type spliceosome

status: Public on May 24 2022

city: Seoul

first: Young-Soo

last: Kwon

address: Nungdongro 209, Gwangjingu

department: Department of Bioscience and Biotechnology

country: South Korea

institute: Sejong University

summary: Eukaryotic nuclear introns have been dichotomously classified into common U2-type introns and rare U12-type introns. Because the highly conserved consensus sequences for the 5’ splice site and the branch point are found within all U12-type introns, weighted matrices for these motifs are used for prediction of U12-type introns. However, the U12-type consensus sequences per se are also recognized by the U2-type spliceosome. To better understand how distinct splicing systems recognize their authentic splice sites, we determined the binding sites of splicing factors, U2AF1 and ZRSR2, and found that ZRSR2 binding is mostly limited to U12-type introns. Our results reveal RNA elements contributing to selection of U2-type and U12-type splice sites in a mutually exclusive manner.

overall_design: CLIP-seq of endogenous U2AF1 by using anti-U2AF1-antibodies (Bethyl), anti-HA-antibody for HA3-tagged ZRSR2 and IgG controls.


status: Public on Mar 07 2022

city: Oxford

first: Robin

last: Choudhury

address: L6 West Wing, John Radcliffe Hospital, Headley Way

department: Cardiovascular Medicine, Radcliffe Department of Medicine

institute: University of Oxford

summary: Purpose: RNA-sequencing of peripheral blood neutrophils from STEMI and NSTEMI patients at the time of presentation versus a control sample obtained from the same patients 1 month post-AMI to determine differentially expressed genes and pathways.

overall_design: RNA-sequencing of peripheral blood neutrophils from STEMI and NSTEMI patients at presentation and 1 month post-AMI.

first: Naveed

last: Akbar

first: Adam

middle: T

last: Braithwaite

middle: P


title: Epi-genomewide study identifies epigenetic outliers in normal mucosa of colorectal cancer patients

status: Public on Mar 23 2022

city: Philadelphia

first: Carmen

last: Sapienza

state: PA

address: 3307 N Broad Street, Room 300 PAHB

department: Fels Cancer Institute for Personalized Medicine

institute: Temple University

type: Methylation profiling by genome tiling array

summary: Genome wide DNA methylation profiling of normal healthy patients and tumor and non-tumor samples of patients with colorectal cancer (CRC). The Illumina Infinium MethylationEPIC BeadChip was used to obtain DNA methylation across ~850,000 CpG sites. Samples include 78 normal sample from CRC patients, 76 tumor samples from CRC patients, and 68 samples from non-CRC patients

overall_design: Bisulphite converted DNA from 222 samples were hybridised to the Illuminia Methylation EPIC BeadChip v1.0

first: Jayashri

last: Ghosh

first: Bryant

last: Schultz

first: Joe

last: Chan


title: Temporal response of Mycobacterium tuberculosis H37Rv to vitamin C exposure in THP-1 macrophages.

status: Public on Oct 01 2021

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

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

country: India

institute: Genotypic Technology

summary: Transcriptional profiling of Mtb H37Rv infected into THP-1 macrophage cell line and treated with 100 µM vitamin C (vit C) for 96 hours and 144 hours, compared to gene expression profile of untreated bacteria post-infection.

overall_design: Agilent Mycobacterium tuberculosis 8x15 Microarray: AMADID: 026323

first: Kriti

last: Sikri

first: Kiran

last: Kumari

first: Jaya

last: Tyagi


title: Transcriptional analysis of transposon mutants disrupted in glutathione biosynthesis in Acinetobacter baumannii

status: Public on Jan 08 2022

city: Fresno

first: Mamta

last: Rawat

state: CA

address: 2555 E. San Ramon Ave. MS S/B 73

department: Biology

institute: California State University, Fresno

summary: In this study we compare logrithmically grown Acinetobacter baumannii wildtype to a transposon mutant that is disrupted in gshA, the first step in glutathione biosynthesis using RNASeq to identify novel pathways where glutathione may be involved.

overall_design: RNASeq analysis of wildtype cells and gshA:Tn grown logarithmically at 37C while shaken.

first: Rawat

last: Mamta

first: Thomas

last: Jason


title: Depletion of AUF1 from myeloid cells protects from allergic airway and tumor infiltration and alters pro-angiogenic macrophage polarization by adenosines

status: Public on Feb 09 2022

city: Vari

first: Dimitris

middle: L.

last: Kontoyiannis

state: Attiki

address: 34 Fleming

department: Institute for Fundamental Biomedical Research

country: Greece

institute: BSRC "Alexander Fleming"

summary: Our data demonstrate that in innate immune cells, AUF1 does not act as a generic anti-inflammatory factor but has a rather distinct role in selective macrophage phenotypes.

overall_design: We use a conditional allele for the myeloid deletion of the hnRNPD gene and employ a disease-oriented phenotypic screen to assess the requirement of AUF1 in contexts of innate immune reactivity.

first: Sofia

last: Gargani

first: Niki

last: Lourou

first: Christina

last: Arapatzi

last: Tzanos

first: Marania

last: Saridakι

first: Esmeralda

last: Dushku

first: Margarita

last: Chatzimike

first: Nikolaos

middle: D

last: Sidiropoulos

last: Andreadou

first: Vassilios

last: Ntafis

first: Pantelis

last: Hatzis

first: Vassiliki

last: Kostourou

middle: L


title: Type I interferon pathways in SARS-CoV-2-infected individuals from Pakistan

status: Public on Dec 01 2021

city: Karachi

first: Asghar

last: Nasir

state: Sindh

address: Stadium Road

department: Pathology and Laboratory Medicine

country: Pakistan

institute: Aga Khan University

summary: Blood transcriptomes were determined in COVID-19 cases and healthy controls using the Clariom S RNA microarray, Affymetrix assay.

overall_design: COVID-19 cases with a positive respiratory samples SARS-CoV-2 and healthy Controls cases were recruited. Blood transcriptomes were analysed using Clariom S RNA Microarray, Affymetrix Inc.

middle: I

last: Masood

first: Maliha

last: Yameen

first: Saba

last: Shahid

first: Zahra

last: Hasan


title: Gene expression profiling of filaggrin-insufficient keratinocytes exposed to inflammatory mediators and allergens

status: Public on May 20 2022

city: Gdańsk

first: Anna

last: Supernat

address: Dębinki 1

department: Division of Translational Oncology

country: Poland

institute: Medical University of Gdansk

summary: Loss-of-function mutations in the filaggrin gene are heavily associated with the incidence and severity of atopic dermatitis. Moreover, filaggrin insufficiency in epidermal keratinocytes can lead to persistent allergic inflammation and an associated immune response suggesting a role for this protein in regulation of immunity. Here, we investigate how filaggrin insufficiency affects the gene expression pattern in a filaggrin-insufficient (shFLG) keratinocyte cell line HaCaT in response to stimulation with various inflammatory mediators and allergens.

overall_design: Untreated shC and shFLG cells were used as controls for their corresponding conditions. Treatment with the following compounds was performed: histamine, amphiregulin, IFNy, IL-4/IL-13, cysteine, derp1/cysteine, derp2; concentrations for every compound were provided below in sample description. Biological triplicates of every condition were generated. A total of 48 samples were analyzed. The filaggrin gene (FLG) in the HaCaT cell line was silenced by shRNA delivered to the cells using lentiviral particles. Scrambled RNA was used for generation of control (shC) cells.

first: Eleni

last: Giannoulatou

first: Xinwen

last: Wang

first: Danuta

last: Gutowska-Owsiak

first: Graham

last: Ogg


title: HDAC5 modulates PD-L1 expression and cancer immunity via p65 deacetylation in pancreatic cancer

status: Public on Mar 15 2022

city: Wuhan

first: Haixin

last: Yu

state: Hubei Province

address: 1277, Jiefang Avenue

institute: Wuhan union hospital

summary: We performed HDAC5 knockdown in pancreatic cancer cell line (PANC-1). The expression profiling showed NF-κB signaling as a potential HDAC5 targets and the conclusions were futher validated in vivo and in vitro.

overall_design: RNA sequencing in PANC-1 cell lines with shControl or shHDAC5

first: Y

last: Zhou

first: H

last: Wu


title: Single cell RNA sequencing of peripheral retina in control and FGF signaling mutant mouse embryonic tissue

status: Public on Jan 27 2022

first: Revathi

last: Balasubramanian

address: 635 West 165th street

department: Ophthalmology

institute: Columbia University

summary: The goal of the study is to identify changes in gene expression and cell distribution in the ciliary margin upon loss of FGF signaing. Neural retinal cells from embryonic day E14 were isolated from control and mutant eyes. Dissociated cells were sorted based on GFP and TdTomato reporter expression in the control and mutant retina respectively. Flow-sorted single cells were processed by the core facility at Columbia University on a 10x platform.

overall_design: 3 control and 3 mutant embryos were pooled and sorted based on reporter expression for single cell sequencing

first: Xin

last: Zhang


title: Spt4 helps RNAPII pass the +2 nucleosome barrier in vivo

status: Public on Sep 27 2021

first: Ulku

last: Uzun

address: South Parks Rd

department: Department of Biochemistry

type: Methylation profiling by high throughput sequencing

summary:
Aim and Methods: To understand the precise role of Spt4 in budding yeast, various high throughput sequencing techniques were used. Nucleosome positions were studied using MNase-seq in WT and spt4∆ cells. The position of RNAPII was examined using NET-seq in spt4∆ cells or cells in which Spt4 has been anchored away to the cytoplasm (Spt4 AA). RNAPII was also mapped in cells in which Spt5 has been anchored away to the cytoplasm (Spt5 AA). Steady-state transcript levels were assessed using RNA-seq in samples coupled with NET-seq. The position of the Spt4 on RNAPII was mapped at single nucleotide resolution using TEF-seq. With the same technique, the position of Spt5 on RNAPII was investigated in wild type (WT) and spt4 knock-out (spt4∆) cells. The position and levels of the pre-initiation complex were assessed using ChIP-seq on Sua7(TFIIB) in WT and spt4∆ cells.
Results: The interaction between the Spt4/5 complex and RNAPII periodically changes as RNAPII transitions through nucleosomes. The dynamic interaction of Spt5 with RNAPII is dependent on Spt4. In spt4∆ and Spt4 AA cells, RNAPII distribution is altered in a similar way compared to their respective controls. After transcribing into nucleosomes, RNAPII accumulates upstream of nucleosome dyads, especially around the +2 nucleosome. In Spt5 AA cells, the distribution and amount of RNAPII on genes are severely affected. Nucleosome positions are altered in spt4∆ cells. Although the position of the +1 nucleosome remains unchanged, nucleosome spacing from this point is increased, and the level of increase in nucleosome spacing correlates with the level of RNAPII accumulation.
Conclusion: This work suggests that Spt4 regulates nucleosome positioning by a mechanism related to transcription and promotes RNAPII movement through nucleosome barriers, especially the barrier set by the +2 nucleosome.

overall_design: MNase-seq in WT and spt4∆ in triplicates; Transcription elongation factor sequncing (TEF-seq) in WT and spt4∆ for Spt4 or Spt5;  Native elongation transcript sequencing (NET-seq) in WT, spt4∆, Spt4-AA, and Spt5-AA; RNA-seq in WT, spt4∆, Spt4-AA, and Spt5-AA; ChIP-seq in WT and spt4∆ for Sua7.

first: Ülkü

first: Harry

last: Fischl

first: Jane

last: Mellor


title: Transcriptomic analsyis of Epithelial and Mesenchymal carcinoma cells using the nCounter PanCancer Immune Profiling panel (Nanostring Technologies) [human]

status: Public on Sep 15 2021

city: Cambridge

first: Anushka

last: Dongre

address: 455 Main St

institute: Whitehead Institute

summary: We undertook to determine whether carcinoma cells residing in the epithelial or quasi-mesenchymal phenotypic states differ in their expression of immunomodulatory markers.To demonstrate a direct association between activation of the EMT program and immunosuppression, we induced EMT programs in vitro in an array of cultured BrCa cell lines via the doxycycline-induced expression of various EMT-inducing transcription factors (EMT-TFs) and proceeded to determine whether activation of the EMT program also alters cell-intrinisc immuno-modulatory markers To do so, we used the nCounter PanCancer Immune Profiling Panel (Nanostring Technologies)to perform transcriptomic analyses of control E cells or those induced to undergo an EMT

overall_design: RNA was extracted from the indicated cell lines cultured in vitro or from sorted GFP+ tumor cells using the RNeasy Mini Kit (Qiagen) and transcriptomic analysis was performed using the nCounter PanCancer Immune Profiling Panel (Nanostring Technologies) Normalization of Nanostring nCounter gene expression values and differential expression were assayed by DESeq2

first: Robert

middle: A

last: Weinberg


title: Transcriptomic analsyis of Epithelial and Mesenchymal carcinoma cells using the nCounter PanCancer Immune Profiling panel (Nanostring Technologies) [mouse]

summary: We undertook to determine whether carcinoma cells residing in the epithelial or quasi-mesenchymal phenotypic states differ in their expression of immunomodulatory markers. To do so, we used the nCounter PanCancer Immune Profiling Panel (Nanostring Technologies)to perform transcriptomic analyses of the E and qM mammary carcinoma cells; these cells were either cultured in vitro or prepared by FACS sorting of GFP-labelled carcinoma cells from their corresponding tumors

overall_design: RNA was extracted from the indicated cell lines cultured in vitro or from sorted GFP+ tumor cells using the RNeasy Mini Kit (Qiagen) and transcriptomic analysis was performed using the nCounter PanCancer Immune Profiling Panel (Nanostring Technologies) Normalization of Nanostring nCounter gene expression values and differential expression were assayed by DESeq2. SnailLO cells express low levels of endogenous Snail and high levels of Epcam. SnailHI cells express high levels of Snail and low levels of Epcam.


title: Transcriptomic analsyis of Epithelial and Mesenchymal carcinoma cells using the nCounter PanCancer Immune Profiling panel

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: gene expression of aorta of ApoE KO mice after Gpnmb vaccine treatment

status: Public on Oct 22 2021

city: Los Angeles

first: Masayoshi

last: Suda

address: 8700 Beverly Blvd.

department: Medicine

institute: Cedars Sinai Medical Center

summary: Accumulation of senescent cells in various tissues has been reported to have a pathological role in age-associated diseases. Inhibition of cellular aging signals prevents the onset of age-associated pathology, but there is a risk of promoting carcinogenesis. Elimination of senescent cells (senolysis) was recently reported to reversibly improve pathological changes related to aging in aged mice without increasing the development of cancer. Here we report that glycoprotein nonmetastatic melanoma protein B (Gpnmb) could be a molecular target for senolytic therapy. Elimination of Gpnmb-positive cells by vaccination improved atherosclerosis.

overall_design: We fed the HFD to ApoE KO mice from 4 weeks of age, administered Gpnmb vaccine or control vaccine at 8 weeks of age, and analyzed these mice at 16 weeks.

first: Goro

last: Katsuumi

first: Tohru

last: Minamino


title: Metabolic adaption to extracellular pyruvate triggers biofilm formation in Clostridioides difficile

status: Public on May 04 2021

city: Paris

first: Marc

last: Monot

address: 28 rue du docteur roux

country: France

institute: Institut Pasteur

summary: We applied time-course transcriptomics and genetics to identify sigma factors, metabolic processes and adhesins that drive biofilm formation. These analyses revealed that extracellular pyruvate induces biofilm formation in the presence of DOC. In the absence of DOC, pyruvate supplementation was sufficient to induce biofilm formation in a process that was dependent on pyruvate transport by the membrane protein CstA.

overall_design: Total RNA was extracted from 3 independent biological replicates of 630 C. difficile strains at 3 conditions with 120µM, 240µM and without Deoxycholate at 9h, 14h, 24h and 48h (36 samples).

first: Yannick

last: Tremblay


title: Transcriptome analysis of wild type and sweet1 seeds upon treatments during germination

status: Public on Jun 30 2021

city: Urbana

first: Xueyi

last: Xue

state: Illinois

address: 1201 W. Gregory Dr.

department: Department of Plant Biology

institute: University of Illinois at Urbana-Champaign

summary:
Purpose: The goals of this study are to compare the transcriptome profiling between wild type and sweet1 under the treatments of either the glucose, ABA or both during germination.
Methods: After 3-day imbibition, WT and sweet1 seeds were sown on ½ MS medium and grown under constant light, 22 °C for 24 hours. Seeds were transferred to ½ MS liquid medium supplemented with either 60 mM Glc, 5 µM ABA or both for 6 hours. Four biological replicates were collected for each treatment. Total RNA was extracted by RNeasy PowerPlant Kit (13500-50, Qiagen), The libraries were prepared from 1 µg total RNA using KAPA mRNA Hyper Prep kit (KK8581, Roche) with KAPA Dual-indexed Adapter kit (KK8722, Roche). The libraries were sequenced by Hiseq 2500 (Illumina) with paired-end reads.
Results: Gene expression level was quantified using Kallisto v 0.44.0 by mapping to Arabidopsis thaliana (version 11) primary transcript sequences. Samples were evaluated based on pair-wise comparison between different conditions and outliers within each treatment were removed for the further analysis based on PCA results. There are 6230 candidates with more than 10 counts per million reads in at least 50% samples, |b| ≥ 0.2 and q-value < 0.05 were identified as differentially expressed genes (DEGs) using Sleuth program. Hierarchical clustering of DEGs uncovered several pathways that may contribute to glucose antagonizing ABA function.
Conclusions: This study represents the detailed analysis of transcriptome in germinating seeds under ABA+Glc treatment. Our study provides a new perspective on the interaction between ABA and Glc in response to external stimuli to control the seed germination.

overall_design: Seed transcript profiles in WT and sweet1 under glucose, ABA and ABA+glucose treatments in 30 hours after imbibition.

first: Li-Qing

last: Chen


title: Multiple physiological roles of both specific and non-specific DNA binding modes of HU protein in Escherichia coli

status: Public on Aug 01 2021

city: Bethesda

first: Subhash

middle: (Optional)

last: Verma

address: 37 Convent Drive, BLDG 37 Room 5138

institute: National Institutes of Health

summary: The histone-like protein HU is crucial for genome organization and the expression of many genes in Escherichia coli. HU binds DNA independent of any specific nucleotide sequence but exhibits two binding affinities; low-affinity to any B-DNA (non-specific) and high affinity to DNA with distortions like kinks and cruciforms (structure-specific). We validated and defined the three conserved lysine residues, K3, K18, and K83, in HU as critical amino acid residues for the non-specific binding and the conserved P63 together with the lysine residues critical for the structure-specific binding both in vitro and in vivo. By determining the effects of disrupting the two DNA binding modes on various HU-dependent physiological processes, we demonstrate that the DNA structure-specific binding regulates expression of many genes including those involved in DNA metabolic processes that control chromosome maintenance and partition. On the other hand, HU associates with the chromosome at numerous sites primarily through the lysines-mediated non-specific binding and control chromosome dynamics and structural maintenance. Thus, we demonstrate that two different DNA binding mode of HU plays separate roles: (i) The high-affinity DNA structure-specific binding regulates many distinct DNA metabolic processes, primarily through transcription regulation. (ii) Its low-affinity, non-specific binding directly helps general organization of the genome.

overall_design: Three biological replicates were analyzed for each strain

middle: C

first: Sankar

last: Adhya


title: A reservoir of stem-like CD8+ T cells in the tumor-draining lymph node preserves the ongoing anti-tumor immune response

status: Public on Aug 27 2021

city: New Haven

first: Kelli

last: Connolly

address: 300 Cedar St.

department: Immunobiology

institute: Yale University

summary:
“Stem-like” TCF1+ CD8+ T cells (TSL) are necessary for long-term maintenance of T cell responses and the efficacy of immunotherapy but, as tumors contain signals that should drive T-cell terminal-differentiation, how these cells are maintained in tumors remains unclear. In this study, we found that a small number of TCF1+ tumor-specific CD8+ T cells were present in lung tumors throughout their development. Yet, most intratumoral T cells differentiated as tumors progressed, corresponding with an immunologic shift in the tumor microenvironment (TME) from “hot” (T cell-inflamed) to “cold” (non-T cell-inflamed). By contrast, most tumor-specific CD8+ T cells in tumor-draining lymph nodes (dLNs) had functions and gene expression signatures similar to TSL from chronic LCMV infection, and this population was stable over time, despite the changes in the TME. dLN T cells were the developmental precursors of, and were clonally related to, their more-differentiated intratumoral counterparts. Our data support the hypothesis that dLN T cells are the developmental precursors of the TCF1+ T cells in tumors which are maintained by continuous migration. Finally, CD8+ T cells similar to TSL were also present in LNs from lung adenocarcinoma patients, suggesting a similar model may be relevant in human disease. Thus, we propose that the dLN TSL reservoir has a critical function in sustaining antitumor T cells during tumor development and protecting them from the terminal differentiation that occurs in the TME.
Methods:  We analyzed single-cell RNA-sequencing to assess the differentiation state and trajectory of the cell subsets present after FACs sorting on endogenous GP33-specific CD8+ T cells from tumors and draining lymph nodes of tumor-bearing KP-NINJA mice, comparing them to GP33-specific CD8+ T cells from spleens of mice infected with acute or chronic LCMV. In order to determine the clonal relationship of these cells from tumors and draining lymph nodes, we analyzed paired single-cell TCR sequencing.

overall_design: GP33-loaded MHC I tetramer+ CD8+ T cells were FACS sorted from tumor-draining lymph nodes and tumors of n=3 KP-NINJA mice and pooled for RNA- and TCR- sequencing at two different time points (8 weeks and 17 weeks after tumor induction). GP33-loaded MHC I tetramer+ CD8+ T cells were FACS sorted from the spleens of C57BL/6 mice 28 days after infection with either LCMV Armstrong (acute) or LCMV Clone 13 (chronic) and used as a reference for T cell differentiation states.

first: Manik

last: Kuchroo

first: Aarthi

last: Venkat

first: Achia

last: Khatun

first: Jiawei

last: Wang

first: Ivana

last: William

first: Noah

last: Hornick

first: Brittany

last: Fitzgerald

first: Martina

last: Damo

first: Moujtaba

middle: Y

last: Kasmani

first: Can

last: Cui

first: Eric

last: Fagerberg

first: Isabel

last: Monroy

first: Amanda

last: Hutchins

first: Julie

middle: F

last: Cheung

first: Gena

last: Foster

first: Dylan

last: Mariuzza

first: Mursal

last: Nader

first: Hongyu

last: Zhao

first: Weiguo

first: Smita

last: Krishnaswamy

first: Nikhil

last: Joshi


title: Clostridium difficile Biofilm with and without deoxycholate at 48H

first: Marc

last: Monot

summary: To understand the molecular mechanisms induced by deoxycholate (DCA) during biofilm formation and to identify factors implicated in the strong density of biofilms in this condition, we performed a transcriptomic analysis using microarrays. The microarrays were used to compare C. difficile transcription profiles of a 48 h biofilm (in BHISG medium) treated with DCA with an untreated biofilm.

overall_design: Two-conditions experiments, 630E strain WT with and without Deoxycholate Biofilm 48h, 4 biological replicates for each condition

first: Thomas

last: Dubois

first: Monot

last: Marc


title: Rapid redistribution and extensive co-binding of NANOG and GATA6 at shared regulatory elements underlie specification of divergent cell fates [CUT&TAG, CUT&RUN]

status: Public on Jul 30 2021

first: Pedro

last: Rocha

state: Maryland

address: 6 Center Drive Building 6B 2B220

department: NICHD

summary: Establishment of divergent cell types from a common progenitor requires transcription factors (TFs) to promote lineage-restricted transcriptional programs while suppressing alternative fates. In the mouse blastocyst, cells of the inner cell mass (ICM) coexpress NANOG and GATA6, two TFs that drive the bifurcation of these progenitors into either the epiblast (Epi) or the primitive endoderm (PrE), respectively. Here, using in vitro differentiation, we describe the molecular mechanisms of how GATA6 quickly induces the PrE fate while repressing the Epi lineage. GATA6 functions as a pioneer TF by inducing nucleosome repositioning at regulatory elements controlling PrE genes, making them accessible for deposition of active histone marks and leading to rewiring of chromatin interactions and ultimately transcriptional activation. GATA6 also binds most regulatory elements of Epi genes followed by eviction of the Epi-specific TFs NANOG and SOX2, loss of active histone marks, and reduction in chromatin accessibility that culminates in transcriptional repression. Unexpectedly, evicted NANOG and SOX2 transiently bind PrE regulatory elements occupied by GATA6. Our study shows that GATA6 binds and modulate the same regulatory elements as Epi TFs, a phenomenon we also validated in blastocysts. We propose that the ability of PrE and Epi-specific TFs to extensively bind and regulate the same gene networks contributes to ICM plasticity and allows rapid cell lineage specification by coordinating both activation and repression of divergent transcriptional programs.

overall_design:
Mapping transcription factor binding and histone distribution changes during primitive endoderm differentiation.

Please note that the records have been updated with additional processed data *peaks.narrowPeak files on June 16th, 2022.

first: Joyce

last: Thompson


title: CUT&Tag on H3K4me3, H3K27ac, H3K4me1, H3K9me3, H3K27me3, H3K36me3 and H2AK119ub in TX1072 XXΔXic and XO mESCs during differentiation

status: Public on Mar 04 2021

city: Berlin

first: Till

last: Schwämmle

state: Berlin

address: Ihnestrasse 63

department: Otto-Warburg-Laboratory

country: Germany

institute: Max Planck Institute for Molecular Genetics

summary: Developmental genes are controlled by complex cis-regulatory landscapes that integrate multiple signals to ensure the correct spatio-temporal expression pattern. To investigate the underlying regulatory principles, we use the Xist locus as a model, which encodes the master regulator of X-chromosome inactivation. Xist is upregulated at the primed pluripotent state in a female-specific manner, thus integrating developmental cues and X-dosage information. It remains poorly understood how these signals are decoded by the ~800kb genomic region that controls Xist. While a series of repressive cis-regulatory elements have been identified, the distal enhancers that activate Xist transcription remain largely unknown. Here we use CUT&Tag on several histone modifications to profile the chromatin landscape of the X inactivation center at the onset of random X-chromosome inactivation using an endogenous cell model of the inactive (TX 1072 XXΔXic) and active (TX 1072 XO) X chromosome.

overall_design: CUT&Tag targeting H3K4me3, H3K27ac, H3K4me1, H3K9me3, H3K27me3, H3K36me3 and H2AK119ub was performed in the TX1072 XXΔXic (XX line carrying a heterozygous deletion of the Xic: chrX:103182701-103955531 on the B6 allele) and TX1072 XO (X chromosome from Cast background) cell lines. The data was collected in replicates from cells in 2i+LIF medium (day 0), as well at day 2 and day 4 of differentiation (via 2i+LIF-withdrawal).

first: Rutger

last: Gjaltema

first: Pauline

last: Kautz

first: Michael

last: Robson

first: Robert

last: Schöpflin

first: Liat

last: Ravid

first: Lennart

last: Brandenburg

first: Ilona

last: Dunkel

first: Carolina

last: Vechiatto

first: Evgenia

last: Ntini

first: Verena

last: Mutzel

first: Vera

last: Schmiedel

first: Annalisa

last: Marsico

first: Stefan

last: Mundlos

first: Edda

last: Schulz


title: Transcriptome characterization of organoids derived from healthy and irreversibly damaged NASH patient liver

status: Public on Jul 28 2021

first: Tobias

last: Raabe

address: 3400 Civic Center Blvd

institute: University of Pennsylvania

summary: Background and Aims: Nonalcoholic steatohepatitis (NASH) will soon become the leading cause of liver transplantation in the US and is  also associated with increased COVID-19 mortality. Currently, there are no FDA approved drugs available that slow NASH progression or address NASH liver involvement in COVID-19. Since animal models cannot fully recapitulate human NASH, we hypothesized that stem cells isolated directly from end-stage NASH patient liver may address current knowledge gaps in human NASH pathology.  Approach and Results: We devised methods allowing derivation, proliferation, hepatic differentiation and extensive characterization of bipotent ductal organoids from irreversibly damaged NASH patient liver. The transcriptomes of organoids derived from NASH liver, but not healthy liver show significant upregulation of pro-inflammatory and cytochrome p450-related pathways, as well as of known liver fibrosis and tumor markers, with the degree of upregulation being NASH patient-specific.

overall_design: Hepatically differentiated organoids from 3 healthy livers (FDD,FLD,MLD) and 8 diseased livers (NASH1-6, AC and CF) were subjected to RNA seq. In addition liver samples correponding to NASH5 and NASH6 organoids were also squenced


title: Gene regulatory networks controlling temporal patterning, neurogenesis, and cell fate specification in the mammalian retina.

status: Public on Aug 03 2021

city: Baltimore

first: Seth

last: Blackshaw

address: 733 N. Broadway Avenue

institute: Johns Hopkins University

summary: Gene regulatory networks (GRNs), consisting of transcription factors and their target cis-regulatory sequences, control neurogenesis and cell fate specification in the developing central nervous system, but their organization is poorly characterized.  In this study, we performed integrated scRNA-seq and scATAC-seq analysis from both mouse and human retina to profile dynamic changes in gene expression, chromatin accessibility and transcription factor footprinting during retinal neurogenesis and gliogenesis.  We identified multiple interconnected, evolutionarily-conserved GRNs consisting of cell type-specific transcription factors that both activate expression of genes within their own network and often inhibit expression of genes in other networks.  These GRNs control state transitions within primary retinal progenitors that underlie temporal patterning, regulate the transition from primary to neurogenic progenitors, and drive specification of each major retinal cell type.  We confirmed the prediction of this analysis that the NFI transcription factors Nfia, Nfib, and Nfix selectively activate expression of genes that promote late-stage temporal identity in primary retinal progenitors.  We also used GRNs to identify additional transcription factors that selectively promote (Insm1/2) and inhibit (Tbx3, Tcf7l1/2) rod photoreceptor specification in postnatal retina.  This study provides an inventory of cis- and trans-acting factors that control retinal development, identifies transcription factors that control the temporal identity of retinal progenitors and cell fate specification, and will potentially help guide cell-based therapies aimed at replacing retinal neurons lost due to disease.

overall_design:
[scATAC-seq_whole retina]  To comprehensively profile dynamic changes in chromatin accessibility across the full course of retinogenesis, we conducted scATAC-seq analysis using the 10x Genomics Chromium platform on dissociated cell nuclei from whole mouse retina at 11 timepoints: embryonic (E) day 11, 12, 14, 16, and 18, as well as postnatal (P) day 0, 2, 5, 8, 11 and 14.
[scATACseq_electroporation]  We used ex vivo electroporation to overexpress human homologues of NFIA/B/X in E14 retina, and then profiled changes in gene expression and chromatin accessibility in primary RPCs at E16 using scATAC-seq. In parallel, we performed similar analysis in P2 and P14 Nfia/b/x cKO retina
[ChIPseq]  We used ex vivo electroporation to overexpress human homologues of NFIA/B/X in E14 retina, and then profiled changes in gene expression and chromatin accessibility in primary RPCs at E16 and P0 using scRNA-seq. In parallel, we performed similar analysis in P2 and P14 Nfia/b/x cKO retina
[scRNAseq]  We used ex vivo electroporation to overexpress human homologues of NFIA/B/X in E14 retina, and then profiled changes in gene expression and chromatin accessibility in primary RPCs at E16 and P0 using scRNA-seq. In parallel, we performed similar analysis in P2 and P14 Nfia/b/x cKO retina

first: Pin

last: Lyu

first: Thanh

last: Hoang

first: Clayton

last: Santiago

first: Eric

last: Thomas

first: Andrew

middle: E

last: Timms

first: Haley

last: Appel

first: Megan

last: Gimmen

first: Nguyet

last: Le

first: Lizhi

last: Jiang

first: Dong

middle: W

last: Kim

first: Siqi

last: Chen

first: David

last: Espinoza

first: Ariel

last: Telger

first: Kurt

last: Weir

first: Brian

middle: S

last: Clark

first: Timothy

last: Cherry

first: Jiang

last: Qian


title: MicroRNA array analysis of mature microRNAs of adipogenic differentiated human bone marrow stromal cells

city: Ancona

first: Jacopo

last: Sabbatinelli

state: AN

address: Via Tronto 10/A

department: Department of Clinical and Molecular Sciences

country: Italy

institute: Università Politecnica delle Marche

summary: In bone marrow, mesenchymal stromal cells (BMSCs), the precursors of adipocytes and osteoblasts, are exposed to a plethora of stimuli that determine the balance between adipogenesis and osteogenesis which in turn are competing and reciprocal. The differentiation of BMSCs, in fact, is a two-step process, lineage commitment (from MSCs to lineage-specific pro-genitors) and maturation (from progenitors to specific cell types).  Adipogenesis is a finely tuned multi-step process requiring the sequential activation of numerous transcription factors driving the typical physiological and morphological changes observed in the progenitor cells, i.e., cell cycle arrest, metabolic reprogramming, and lipid accumulation. Among the small non-coding RNAs, microRNAs represent an additional mechanism for controlling adipogenic gene expression. Given their unique ability to simultaneously regulate multiple protein targets and processes, it has been suggested that microRNAs may play a leading role in BMSC differentiation.  Here, we evaluated miRNAs differentially regulated during human BMSC adipogenic differentiation in vitro.

overall_design: MicroRNA expression profile obtained from qRT-PCR of hBMSCs treated under adipogenic conditions for 14 days compared to untreated hBMSCs.

first: Angelica

last: Giuliani

first: Maria Rita

last: Rippo


title: TT-seq and RNA-seq in TX1072 XXΔXic and XO mESCs during differentiation

first: Till

last: Schwämmle

summary: Developmental genes are controlled by complex cis-regulatory landscapes that integrate multiple signals to ensure the correct spatio-temporal expression pattern. To investigate the underlying regulatory principles, we use the Xist locus as a model, which encodes the master regulator of X-chromosome inactivation. Xist is upregulated at the primed pluripotent state in a female-specific manner, thus integrating developmental cues and X-dosage information. It remains poorly understood how these signals are decoded by the ~800kb genomic region that controls Xist. While a series of repressive cis-regulatory elements have been identified, the distal enhancers that activate Xist transcription remain largely unknown. Here we use TT-seq and RNA-seq to profile nascent and processed RNA transcription within the X inactivation center at the onset of random X-chromosome inactivation using an endogenous cell model of the inactive (TX 1072 XXΔXic) and active (TX 1072 XO) X chromosome.

overall_design: TT-seq was performed in the TX1072 XXΔXic (XX line carrying a heterozygous deletion of the Xic: chrX:103182701-103955531 on the B6 allele) and TX1072 XO (X chromosome from Cast background) cell lines. The data was collected in replicates from cells in 2i+LIF medium (day 0), as well at day 2 and day 4 of differentiation (via 2i+LIF-withdrawal).

first: Rutger

last: Gjaltema

first: Pauline

last: Kautz

first: Michael

last: Robson

first: Robert

last: Schöpflin

first: Liat

last: Ravid

first: Lennart

last: Brandenburg

first: Ilona

last: Dunkel

first: Carolina

last: Vechiatto

first: Evgenia

last: Ntini

first: Verena

last: Mutzel

first: Vera

last: Schmiedel

first: Annalisa

last: Marsico

first: Stefan

last: Mundlos

first: Edda

middle: G

last: Schulz


title: Lineage transcription factors ASCL1, NKX2-1, and PROX1 are enriched at super enhancers and co-regulate subtype-specific genes in small cell lung cancer

status: Public on May 01 2021

city: Dallas

first: Jane

last: Johnson

state: TX

address: 5323 Harry Hines Blvd

department: Neuroscience

institute: UT Southwestern Medical Center


title: HIF1α/HIF2α-miR210-3p network promotes glioblastoma proliferation and tumorigenesis through EGFR-PI3K/AKT signaling pathway with a positive feedback

status: Public on Nov 24 2020

city: Chongqing

first: liao

last: bin

address: 118 Xingguang Avenue

institute: Chongqing General Hospital, Chongqing University

type: Non-coding RNA profiling by high throughput sequencing

summary: HIF1α promotes glioblastoma cell proliferation and tumorigenesis under hypoxia conditions, leading to poor prognosis; however, none of the targeted therapies of HIF1α for glioblastoma is success nowadays. Therefore, we focused to look for the reason and wondered whether HIF2α contributed GBM growth. We did gene-chip and found that HIF2α contributed to the malignant progression of glioblastoma while blocking of HIF1α. Furthermore, our results revealed knock-out of HIF1α and HIF2α simultaneously improved the chemo-sensitization significantly. Moreover, miR-210-3p induced HIF1α expression but inhibited HIF2α, which meant the existence of regulation of cycle between HIF1α/HIF2α and miR-210-3p. Traditional studies have proved EGF as an upstream gene regulator of HIF1α in hypoxia conditions through EGFR-PI3K/AKT-mTOR signaling pathway. However, in this study, besides the signaling pathways mentioned above, we found the upstream regulators HIF1α and HIF2α also promoted EGF with the binding regions AGGCGTGG and GGGCGTGG. Briefly, in hypoxia microenvironment HIF1α/HIF2α-miR210-3p network promotes malignant progression of glioblastoma through EGFR-PI3K/AKT-mTOR signaling pathway with a positive feedback.

overall_design: The control cells without HIF1α and HIF2α interference, HIF1α-ko, HIF2α-ko and HIF1α/HIF2α knock-out simultaneously cells were cultured under hypoxia conditions for 24h and then the cells were collected. The cells were then sent to undergo miRNA-Seq.

first: Pan

last: Wang

first: Sheng

last: Gong

first: Lu

last: Zhao

last: WU

first: Bin

last: Liao


title: ATAC-seq in TX1072 XXΔXic and XO mESCs during differentiation

first: Till

last: Schwämmle

summary: Developmental genes are controlled by complex cis-regulatory landscapes that integrate multiple signals to ensure the correct spatio-temporal expression pattern. To investigate the underlying regulatory principles, we use the Xist locus as a model, which encodes the master regulator of X-chromosome inactivation. Xist is upregulated at the primed pluripotent state in a female-specific manner, thus integrating developmental cues and X-dosage information. It remains poorly understood how these signals are decoded by the ~800kb genomic region that controls Xist. While a series of repressive cis-regulatory elements have been identified, the distal enhancers that activate Xist transcription remain largely unknown. Here we use ATAC-seq to profile DNA accessibility within the X inactivation center at the onset of random X-chromosome inactivation using an endogenous cell model of the inactive (TX 1072 XXΔXic) and active (TX 1072 XO) X chromosome.

overall_design: ATAC-seq was performed in the TX1072 XXΔXic (XX line carrying a heterozygous deletion of the Xic: chrX:103182701-103955531 on the B6 allele) and TX1072 XO (X chromosome from Cast background) cell lines. The data was collected in replicates from cells in 2i+LIF medium (day 0), as well at day 2 and day 4 of differentiation (via 2i+LIF-withdrawal).

first: Rutger

last: Gjaltema

first: Pauline

last: Kautz

first: Michael

last: Robson

first: Robert

last: Schöpflin

last: Ravid


title: Lineage transcription factors ASCL1, NKX2-1, and PROX1 are enriched at super enhancers and co-regulate subtype-specific genes in small cell lung cancer [ChIP-seq]

summary: Heterogeneity between tumors is a major barrier to the treatment of small cell lung cancer (SCLC). Identification of molecular markers to characterize and classify tumors can facilitate the diagnosis and development of targeted therapies. Here, we analyzed genomic regions, called super enhancers (SE), across multiple SCLC cell lines and patient-derived xenograft models, and find SE enrichment is sufficient to classify SCLC models into recently defined SCLC molecular subtypes SCLC-A, SCLC-N, and SCLC-P defined by the transcription factors ASCL1, NEUROD1, and POU2F3, respectively. 3D chromatin structure analysis identified genes associated with the SE that assemble into subtype-specific tumor-signatures with genes functioning in diverse processes. Focusing on the SCLC-A subtype, transcription factors NKX2-1 and PROX1 were identified as ASCL1-interacting proteins. All three factors bind overlapping genomic regions within SEs in SCLC-A cell line models. Nevertheless, combined loss of all three factors suppresses growth of SCLC-A similar to that seen with ASCL1 loss alone, continuing to place ASCL1 as a key dependency factor in a subset of SCLC. Focusing on genes co-regulated by the three transcription factors, two SCLC-A subtype-specific cell surface proteins, SCN3A and KCNB2, were identified. Loss of either channel alone did not disrupt SCLC-A growth in vitro, but they may serve as diagnostic tools in subtyping SCLC.

overall_design:
Mapping of superenhancers and transcription factor binding sites in a panel of small cell lung cancer preclinical models based on chromatin-immunoprecipitation of an histone modification and 3 transcription factors.

Please note that each processed data was generated from both ChIP and input samples, and is linked to the corresponding ChIP sample records.

UPDATE: [Mar-20-2026] The antibody was corrected for Samples GSM4563928, GSM4563930, GSM4563932, GSM4563934, GSM4563935, GSM4563937, and GSM4563939.

first: Karine

last: Pozo

first: Rahul

middle: K

last: Kollipara


title: Rapid redistribution and extensive co-binding of NANOG and GATA6 at shared regulatory elements underlie specification of divergent cell fates

status: Public on Jul 29 2021

first: Pedro

last: Rocha


title: Distal and proximal cis-regulatory elements sense X-dosage and developmental state at the Xist locus

summary: Developmental genes such as Xist, the master regulator of X-chromosome inactivation (XCI), are controlled by complex cis-regulatory landscapes, which decode multiple signals to establish specific spatio-temporal expression patterns. Xist integrates information on X-chromosomal dosage and developmental stage to trigger XCI at the primed pluripotent state in females only. Through a pooled CRISPR interference screen in differentiating mouse embryonic stem cells, we identify functional enhancer elements of Xist during the onset of random XCI. By quantifying how enhancer activity is modulated by X-dosage and differentiation, we find that X-dosage controls the promoter-proximal region in a binary switch-like manner. By contrast, differentiation cues activate a series of distal elements and bring them into closer spatial proximity of the Xist promoter. The strongest distal element is part of an enhancer cluster ~200 kb upstream of the Xist gene which is associated with a previously unannotated Xist-enhancing regulatory transcript, we named Xert. Developmental cues and X-dosage are thus decoded by distinct regulatory regions, which cooperate to ensure female-specific Xist upregulation at the correct developmental time. Our study is the first step to disentangle how multiple, functionally distinct regulatory regions interact to generate complex expression patterns in mammals.

sample_organism:
Mus musculus
synthetic construct

platform_organism:
Mus musculus
synthetic construct


title: Epigenetic modification of the COX-2/PGE2 pathway modulates macrophage phenotype and cell-targeted manipulation improves diabetic tissue repair

status: Public on Oct 07 2020

city: Ann Arbor

first: Lam

last: Tsoi

state: MI

address: Medical Sciences 1 Bldg. 1301 E. Catherine

institute: University of Michigan

summary: RNA-sequencing techniques to profile the transcriptomes of lesional skin of diabetic patients

overall_design: Comparison between lesional skin from diabetic patients to normal skin

first: Frank

middle: M

last: Davis

first: Katherine

last: Gallagher


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

status: Public on Nov 11 2020

city: Jacksonville

state: FL

address: 4500 San Pablo Rd S

institute: Mayo Clinic

summary: We induced TREM2 expression at 2 months of age in our 5xFAD/TREM2 mouse models and harvested the animals at 5 months of age. The single cells from the cortex were isolated and subjected to the single-cell RNA seq to investigate the effects of TREM2 on microglia transcriptomic profiles in the middle stage of amyloid development. Our data showed that TREM2-WT induced the mTOR/EIF2 signaling pathways and restricted the disease associated microglia (DAM) signature. In contrast TREM2-R47H variant significantly upregulated the MHC class II molecules, enriched the antigen presentation pathway, and exacerbated a signature of antigen presentation contributing to enhanced amyloid pathology.

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

first: Wenhui

last: Qiao

first: Yuka

last: Martens

first: Yingxue

last: Ren


title: Vascular Damage, Thromboinflammation, Plasmablast Activation, T-Cell Dysregulation and Pathological Histiocytic Response in Pulmonary Draining Lymph Nodes of COVID-19

status: Public on Nov 23 2021

city: Basel

first: Jasmin

last: Haslbauer

address: Schönbeinstrasse 40

country: Switzerland

institute: Pathology, Institute of Medical Genetics and Pathology, University Hospital Basel, University of Basel, Switzerland

summary: This study aims to characterize pathophysiological changes in lethal COVID-19 lymph nodes. 22 lethal COVID-19 cases and 28 controls were enrolled in this study. Pulmonary draining lymph nodes (mediastinal, tracheal, peribronchial) were collected at autopsy. Control lymph nodes were selected from a range of histomorphological sequelae [unremarkable histology, infectious mononucleosis, follicular hyperplasia, non-SARS related HLH, extrafollicular plasmablast activation, non-SARS related diffuse alveolar damage (DAD), pneumonia]. Gene expression profiling was performed using the HTG EdgeSeq Immune Response Panel. Characteristic patterns of a dysregulated immune response were detected: 1. An accumulation of extrafollicular plasmablasts with a relative paucity or depletion of germinal centers. 2. Evidence of T-cell dysregulation demonstrated by immunohistochemical paucity of FOXP3+, T-Bet+ and LEF1+ positive T-cells and a downregulation of key genes responsible for T-cell crosstalk, maturation and migration as well as a reactivation of herpes viruses in 6/21 COVID-19 lymph nodes (EBV, HSV). 3. Macrophage activation by a proinflammatory, CD163+ phenotype and increased incidence of hemophagocytic activity. 4. Microvascular dysfunction, evidenced by an upregulation of hemostatic (CD36, PROCR, VWF) and proangiogenic (FLT1, TEK) genes and an increase of fibrin microthrombi and CD105+ microvessels. Taken together, these findings imply widespread dysregulation of both innate and adoptive pathways with concordant microvascular dysfunction in severe COVID-19.

overall_design:
Examination of autopsy lymph node tissue of lethal COVID-19 cases versus controls by gene expression profiling
Please note that the  'VLP00581_AI_Plate1_09JAN2021_Parsed-forReveal_QualityControlled.xlsx' processed data file contains 78 data columns, while 50 samples (used for the final manuscript of the study) are included in the records. The extra data columns refer to either universal RNA samples used for correlations tests by HTG Molecular, which are labelled uRNA on the second sheet ‘QC_Raw' of the count matrix excel file, -or- samples which failed the internal quality controls of HTG Molecular, such as poor quality of sample (Q0), insufficient read depth (Q1) or expression variability (Q2),  marked on the third sheet ‘QC_summary’.  Further samples were excluded as described in the forthcoming manuscript, such as inadequate patient data.

first: Carl

last: Zinner

first: Anna

last: Stalder

first: Jan

last: Schneeberger

first: Thomas

last: Menter

first: Stefano

last: Bassetti

first: Kirsten

last: Mertz

first: Philip

last: Went

first: Matthias

last: Matter

first: Alexandar

last: Tzankov


title: RNAi Screening Identifies that TEX10 Promotes the Proliferation of Colorectal Cancer Cells by Increasing NF-κB Activation

status: Public on Oct 05 2020

city: Guangzhou

first: Ziyang

last: Wang

state: --- Select One ---

address: 58 Zhongshan 2nd Road

institute: Ziyang Wang, Doctor, The First Affiliated Hospital, Sun Yat-sen University

summary: Colorectal cancer (CRC) has become a predominant cancer worldwide. In order to understand the process of carcinogenesis, an shRNA library screening is employed for searching candidate genes that promote proliferation in the CRC cell line HT29. The candidate genes overlapped with differentially expressed genes in 32 CRC tumor tissues in the GEO dataset GSE8671. The seventh-ranked TEX10 is upregulated in CRC and its knockdown decreased cell proliferation. The TEX10 high-expression group exhibits worse overall survival (P = 0.003) and progression-free survival (P < 0.001) than the TEX10 low-expression group. TEX10 depletion decreases the growth of CRC cells in vitro and in vivo. GSEA indicates that the NF-κB pathway is significantly enriched in the genes downregulated by TEX10 knockdown. Mechanistically, TEX10 interacts with p65 and increases its nuclear localization. TEX10 promotes p65 occupancy at gene promoters and regulates the expression of a subset of p65-targeted genes including TNFAIP8, SAT1 and IL6ST. Taken together, this study identifies that TEX10 promotes the proliferation of CRC cells in a p65-dependent manner. In addition, high TEX10 expression is associated with poor prognosis in CRC patients.

overall_design: TEX10 or p65 were knocked down in HCT116 cells, and the differences in gene expression were compared with shNC, respectively, using RNAseq.

first: Shuai

last: Chen


title: The DISARM study: effects of inhaled corticosteroids on bronchial epithelial cell gene expression in COPD

status: Public on Mar 22 2021

city: Vancouver

first: Don

last: Sin

state: BC

address: Room 166, 1081 Burrard Street

country: Canada

institute: Centre for Heart Lung Innovation, St. Paul’s Hospital, University of British Columbia

summary: The Differential Effects of Inhaled Symbicort and AdvaiR on Lung Microbiota (DISARM) study aimed to determine the effects of inhaled corticosteroids (ICS) on the lung microbiome. The full trial protocol is registered at clinicaltrials.gov (NCT02833480) and the study was approved by the Human Research Ethics Committee of the University of British Columbia and Providence Health Care (H14-02277). Participants were randomized to receive inhaled long-acting beta agonist (LABA) treatment with formoterol, or LABA/ICS combination treatment with formoterol/budesonide or salmeterol/fluticasone propionate, for 12 weeks. Bronchoscopy was performed before and after treatment, and bronchoalveolar lavage fluid and bronchial brushes (6th-8th generation) were collected. This dataset contains RNA-seq data from the bronchial brushes. RNA was extracted from cytological brush specimens stored in QIAzol RNA lysis buffer (QIAGEN, Stockach, Germany) using the RNeasy Plus kit (QIAGEN) according to the manufacturer’s instructions, and specimens were submitted for sequencing at the University of British Columbia Biomedical Research Centre. Sample quality control was performed using the Agilent 2100 Bioanalyzer (Agilent, Santa Clara, CA, USA). Qualifying samples were then prepared following the standard protocol for the NEBnext Ultra ii Stranded mRNA (New England Biolabs, Ipswich, MA, USA). Sequencing was performed on the Illumina NextSeq 500 (Illumina, San Diego, CA, USA) with paired end 42bp × 42bp reads. Samples were sequenced in batches of 24, with batches formed by random selection of samples.

overall_design: Randomized controlled trial. No placebo group was included in the DISARM trial due to the risk of acute exacerbation of COPD during the treatment period. FOR monotherapy is considered the control group. 63 participants with mild to very severe COPD were randomised into 3 groups: FOR (n=21), FOR/BUD (20), or SAL/FLU (n=22). 61 participants have pre-treatment sequencing data available, and 54 participants have both pre- and post-treatment sequencing data available.

first: Xuan

last: Li

first: Stephen

last: Milne


title: Single cell RNA-seq analysis reveals the crucial role of Collagen triple helix repeat containing 1 (Cthrc1) cardiac fibroblasts for ventricular remodeling after myocardial infarction [scRNA-seq]

status: Public on Sep 29 2020

city: New York

first: Silvia

last: Hernandez

state: New York

address: 1300 Morris park avenue

department: Medicine- Cardiology

institute: Albert Einstein College of Medicine

summary: Cardiac fibroblasts have a central role during the ventricular remodeling process associated to different types of cardiac injury. Recent studies have shown that fibroblasts do not respond homogeneously to heart damage, suggesting that the adult myocardium may contain specialized fibroblast subgroups with specific functions. Due to the limited set of bona fide fibroblast markers, a proper characterization of fibroblast population dynamics in response to cardiac damage is still missing. Using single cell RNA-seq we have identified and characterized a fibroblast subpopulation that emerges in response to myocardial infarction (MI) in a murine model. These activated fibroblasts exhibit a clear pro-fibrotic signature, express high levels of the hormone CTHRC1 and of the immunomodulatory co-receptor CD200, and localize to the wounded myocardium. Combining epigenomic profiling with functional assays, we unveil important candidate regulators mediating their response to cardiac damage. We show that the absence of CTHRC1, a top marker of this activated fibroblast subpopulation, results in pronounced lethality due to ventricular rupture within the first week post-myocardial infarction. Finally, we find evidence for the existence of similar mechanisms in a pig pre-clinical model of MI and establish a positive correlation between Cthrc1 levels and cardiac function after MI.

overall_design: Time-course study of cardiac fibroblasts after myocardial infarction. Samples include Healthy Myocardium (Control) and 7, 14 and 30 days post-infarction. Cardiac fibroblasts were also selected (mEFSK4) from Cthrc1-KO mice 7 days post-infarction.

first: Adrian

last: Ruiz-Villalba

first: Juan

last: Romero

first: Amaia

last: Vilas-Zornoza

first: Nikolaus

last: Fortelny

first: Laura

last: Castro

first: Patxi

last: San Martin-Uriz

first: Erika

last: Lorenzo-Vivas

first: Paula

last: Garcia-Olloqui

first: Marcel

last: Palacios

middle: J

last: Gavira

first: Gorka

last: Bastarrika

first: Stefan

last: Janssens

first: Elena

last: Iglesias

first: Gloria

last: Abizanda

first: Xabier

last: Martinez de Morentin

first: Christoph

last: Bock

first: Diego

last: Alignani

first: Gema

last: Medal

first: David

last: Gomez-Cabrero

first: Igor

last: Prudovsky

first: Yong

last: Ri-Jin

first: Sergey

last: Ryzhov

first: Haifeng

last: Yin

first: Beatriz

last: Pelacho

first: Volkhard

last: Lindner

last: Lara-Astiaso

first: Felipe

last: Prosper


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

last: Zhao

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

first: Wenhui

last: Qiao

first: Yuka

last: Martens

first: Yingxue

last: Ren


title: SIK2 maintains breast cancer stemness by phosphorylating  LRP6 and activating Wnt/β-catenin signaling

status: Public on Mar 24 2021

city: Chang Sha

first: zhuoxian

last: rong

state: Hu Nan

address: Xiangya road 87th

institute: central south universty

summary:
Purpose: Analysis of the regulatory network involved in SIK2 in breast cancer cells activated by the Wnt/β-catenin pathway.
Methods: mRNA profiles of BT549-shSIK2 and BT549-Scrambled group that Wnt3a treated for 2 hours were generated by deep sequencing,  using Illumina Novaseq platform. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.16.1). The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate . Genes with an adjusted P-value <0.05 found by DESeq2 were assigned as differentially expressed. Clusterprofiler software was used to perform GO function enrichment analysis and KEGG pathway enrichment analysis of the differential gene sets.
Results: We identified 1709 differential genes, of which 1147 were up-regulated and 562 were down-regulated. In GO enrichment analysis, the biological process is mainly in the cell ions homeostasis, the cell components are mainly enriched on the cell surface, and the molecular function is mainly in the transmembrane signaling receptor activity. KEGG analysis shows that differential genes are enriched in Axon guidance and Nicotinate and nicotinamide metabolism pathways.
Conclusion: Based on RNA-seq analysis, the regulatory network involved in SIK2 in breast cancer response to Wnt signaling is depicted.

first: Zhuoxian

last: Rong

first: Yuezhen

last: Deng

first: Xinxin

first: Lunquan

last: Sun


title: Genome-wide alterations of uracil distribution patterns

status: Public on Sep 20 2020

city: Budapest

first: Angela

last: Bekesi

address: Műegyetem rakpart 3.

department: Department of Applied Biotechnology and Food Science

country: Hungary

institute: Budapest University of Technology and Economics, Faculty of Chemical Technology and Biotechnology

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

overall_design: Refer to individual Series


title: Single cell RNA-seq analysis reveals the crucial role of Collagen triple helix repeat containing 1 (Cthrc1) cardiac fibroblasts for ventricular remodeling after myocardial infarction [ATAC-seq]

first: Silvia

last: Hernandez

overall_design: Time-course of study of cardiac fibroblasts after myocardial infarction. Samples include Healthy Myocardium (Control) and 7, 14, 30 days post-infarction. Cardiac fibroblasts were also selected (mEFSK4) from Cthrc1-KO mice 7 days post-infarction.

first: Adrian

last: Ruiz-Villalba

first: Juan

middle: P

last: Romero

first: Amaia

last: Vilas-Zornoza

first: Nikolaus

last: Fortelny

first: Laura

last: Castro

first: Patxi

last: San Martin-Uriz

first: Erika

last: Lorenzo-Vivas

first: Paula

last: Garcia-Olloqui

first: Marcel

last: Palacios

last: Gavira

first: Gorka

last: Bastarrika

first: Stefan

last: Janssens

first: Elena

last: Iglesias

first: Gloria

last: Abizanda

first: Xabier

last: Martinez de Morentin

first: Christoph

last: Bock

first: Diego

last: Alignani

first: Gema

last: Medal

first: David

last: Gomez-Cabrero

last: Prudovsky


title: Human Single Cell Transcriptional Profiling Identifies Epigenetically Altered PGE2 Pathway that Modulates Diabetic Macrophage Phenotype and Wound Repair

first: Lam

last: Tsoi

summary: single cell RNA-sequencing to profile the transcriptomes of lesional skin of diabetic patients at the cellular level.

first: Frank

last: Davis

first: Katherine

last: Gallagher


title: Single Cell Analysis Reveals NUPR1 Promotes Docetaxel Resistance in Prostate Cancer

status: Public on Sep 01 2020

first: Evan

middle: T

last: Keller

address: 2800 Plymouth Rd

summary: The majority of prostate cancer (PCa) patients treated with docetaxel develop resistance to it.  In order to better understand the mechanism behind the acquisition of resistance, we conducted single cell total RNA sequencing (sctotal RNA-seq) of docetaxel sensitive and resistant variants of DU145 and PC3 PCa cell lines.  Overall, sensitive and resistant cells clustered separately.  However, for both cell lines we identified rare sensitive cells that clustered with the resistant cells indicating resistant cells pre-exist in the sensitive population.  Differential gene expression analysis between resistant and sensitive cells revealed 182 differentially expressed genes common to both PCa cell lines.  A subset of these genes gave a gene expression profile in the resistant-like sensitive cells similar to the resistant cells.  Exploration for functional gene pathways identified 218 common pathways between the two cell lines.  Protein ubiquitination was the most differentially regulated pathway and was enriched in the resistant cells.  Transcriptional regulator analysis identified potential 321 regulators across both cell lines.  One of the top regulators identified was nuclear protein 1 (NUPR1).  In contrast to the single cell analysis, bulk analysis of the cells did not reveal NUPR1 as a promising candidate.  Knockdown and overexpression of NUPR1 in the PCa cells demonstrated that NUPR1 confers docetaxel resistance in both cell lines.  Collectively, these data demonstrate the utility of sctotal RNA-seq to identify regulators of drug resistance.  Furthermore, NUPR1 was identified as a mediator of PCa drug resistance, which provides the rationale to explore NUPR1 and its target genes to for reversal of docetaxel resistance.

overall_design: Single cell sequencing of DU145 and PC3 sensitive and docetaxel resistant cell lines

first: Patricia

last: Schnepp

first: Greg

last: Shelley

first: Nicole

last: Wakim

first: Hui

last: Jiang

first: Atsushi

last: Mizokami


title: Transcriptional dynamics of ricin-induced ARDS

status: Public on Nov 17 2020

city: Beijing

first: Duo

last: Su

address: Street Dongdajie

institute: Beijing Institute of Microbiology and Epidemiology

summary: We report the presence of pathologic states of epithelial, mesenchymal and vascular endothelial cells and molecular programs involved in immunopathological progression. We also report the transcriptionally functional diversity of neutrophils and identify a previously undetected neutrophil subset undergoing transdifferentiated process. Cell–cell interaction analysis reveal vascular mural cells as potential crosstalk hubs in pulmonary communication network.

overall_design: Examination of dynamic transcriptional signatures of lung structural and immune populations during the early stages of ARDS

first: Huiying

last: Yang

first: Dongsheng

last: Zhou


title: Comparison of the expression profiles of 630E strain and a sig54 mutant after 6h of growth

status: Public on Aug 28 2020

city: Paris

first: Marc

last: Monot

address: 28 rue du docteur roux

institute: Institut Pasteur

summary: Transcriptional profiling of C. difficile 630E strain vs. a sig54 mutant after 6h of growth in TY.

overall_design: Two-conditions experiments, 630E strain 6h vs. sig54 mutant 6h, 4 biological replicates for each condition.

first: Thomas

last: Dubois


title: Single cell RNA-seq analysis reveals the crucial role of Collagen triple helix repeat containing 1 (Cthrc1) cardiac fibroblasts for ventricular remodeling after myocardial infarction

first: Silvia

last: Hernandez

sample_organism:
Homo sapiens
Sus scrofa
Mus musculus

platform_organism:
Homo sapiens
Sus scrofa
Mus musculus


title: Visceral adipose tissue macrophage subsets

status: Public on Aug 07 2020

city: Pittsburgh

first: Partha

last: Dutta

state: PA

address: 200 Lothrop Street

institute: University of Pittsburgh

summary: We identified two different subsets of macrophages in visceral adipose tissue. These two subsets were transcriptomically different. We observed that C3CR1-low CCR2-low macrophages are transcriptomically different after myocardial infarction (MI).

overall_design: We sorted CX3CR1-high CCR2-high and CX3CR1-low and CCR2-low macrophages from visceral adipose tissue and blood monocytes from mice in the steady state, and CX3CR1-low and CCR2-low macrophages from visceral adipose tissue of mice with MI or sham surgery directly in RNA extraction buffer (Applied Biosystems Pico Pure Kit for mRNA extraction) and performed RNA-seq analysis.


title: HuR-dependent gene expression in brown adipose tissue

status: Public on Jul 22 2020

city: Columbus

first: Michael

last: Tranter

state: OH

address: 2255 Kenny Road

department: Molecular Medicine and Therapeutics

institute: The Ohio State University

summary: We utilized adipocyte-specific deletion of HuR followed by RNA-seq of total BAT mRNA to identify HuR-dependent gene expression within BAT

overall_design: RNA-seq from BAT from Adipocyte-specific HuR deletion and littermate controls


title: Genome-wide mapping of active RNA polymerases using precision nuclear run-on (PRO-seq) during female mouse ES differentiation

status: Public on Jun 25 2020

city: Boston

first: Eric

last: Aeby

state: Massachusetts

address: 185 Cambridge Street

department: Department of Molecular Biology and Department of Genetics

institute: Howard Hughes Medical Institute, Massachusetts General HospitalMassachusetts General Hospital, Harvard Medical School

summary: We analyzed the effect of developmental differentiation on nascent transcripts population in female mouse embryonic stem cells.

overall_design: Hybrid female mouse ES cells carrying a deletion of Tsix promoter on the mus allele were followed during differentiation

first: Hungoo

last: Lee

first: Jeannie


title: Whole transcriptome analysis for kidney aging in mice [non-coding RNA]

status: Public on Jul 11 2020

city: Xi’an

first: Fan

middle: Fan

last: Gao

state: Shaanxi

address: West Yanta Road 277

department: Dialysis Department of Nephrology Hospital

institute: the First Affiliated Hospital of Xi’an Jiaotong University

summary: The goals of this study are to explore the differential expression of non-coding RNAs in mice kideny during aging

overall_design: The non-coding RNA expression of  3-month-old, 12-month-old and 24-month-old C57BL/6 mice kidney  was performed using RNA-sequencing.

first: Hongli

first: Lei

last: Chen

first: Fanfan


title: Single cell RNA-seq analysis reveals the crucial role of Collagen triple helix repeat containing 1 (Cthrc1) cardiac fibroblasts for ventricular remodeling after myocardial infarction [RNA-seq]

first: Adrian

last: Ruiz-Villalba

first: Juan

last: Romero

first: Amaia

last: Vilas-Zornoza

first: Nikolaus

last: Fortelny

first: Laura

last: Castro

first: Patxi

last: San Martin-Uriz

first: Erika

last: Lorenzo-Vivas

first: Paula

last: Garcia-Olloqui

first: Marcel

last: Palacios

last: Gavira

first: Gorka

last: Bastarrika

first: Stefan

last: Janssens

first: Elena

last: Iglesias

first: Gloria

last: Abizanda

first: Xabier

last: Martinez de Morentin

first: Christoph

last: Bock

first: Diego

last: Alignani

first: Gema

last: Medal

first: David

last: Gomez-Cabrero

first: Igor

last: Prudovsky

first: Yong

last: Ri-Jin

first: Sergey

last: Ryzhov

first: Haifeng

last: Yin

first: Beatriz

last: Pelacho

first: Volkhard

last: Lindner

last: Lara-Astiaso

first: Felipe

last: Prosper


title: Whole transcriptome analysis for kidney aging in mice [miRNA-seq]

first: Fan

last: Gao

summary: The goals of this study are to explore the differential expression of non-coding RNAs in mice kidne during aging

first: Hongli

last: Jiang

first: Lei

last: Chen

first: Fanfan


title: Analysis of the coding and non-coding RNA temporal transcriptome of developing seeds in sunflower

status: Public on Jun 05 2020

city: Harbin

first: Jian

last: Wang

address: 600 Changjiang Road

institute: Northeast Agricultural University


title: Systematic identification of Circular RNAs in pre-ovulatory ovarian follicles of goats

status: Public on Jul 03 2020

city: Wuhan

first: Hu

last: Tao

state: Hubei

address: Shizishan street

institute: Hubei Academy of Agricultural Sciences

summary: We deep sequenced and analyzed circRNA using deep RNA sequencing (RNA-seq) in pre-ovulatory follicle samples of Macheng black goats and Boer goats. We analyzed the RNA-seq data with 301 million reads and 288 million reads,  and reveal the expression profiles of circRNAs and predicted 13,950 circRNAs. 827 circRNA host genes, mostly related to transferase activity and metabolic process. Twenty-four circRNAs were upregulated and 13 were downregulated in the pre-ovulatory follicles of the Boer group compared to their expression in the Macheng group.

overall_design: Examination of circRNAs expression profile in pre-ovulatory follicle samples of Macheng black goats and Boer goats

first: Mingxin


title: Analysis of the coding and non-coding RNA temporal transcriptome of developing seeds in sunflower [ncRNA-seq]

status: Public on Jun 02 2020

summary: miRNA-sequencing of seeds in three developmental stages was performed to reveals gene regulation in relation to oil and fatty acid accumulation in sunflower

overall_design: miRNA-sequencing profiles of seeds of high oleic acid L-1-OL-1 were generated by deep sequencing at 7-, 22- and 37 day.

first: Yan

last: Liu

first: Fei

last: Zhou


title: Caulobacter crescentus mRNA half-lives by rifampicin transcription shutoff

status: Public on Sep 04 2020

city: Bloomington

first: Jared

middle: Michael

last: Schrader

state: IN

address: 212 S Hawthorne Dr

department: Biology

institute: Indiana University

summary: mRNA half-life profiling in the bacterium Caulobacter crescentus was preformed by shutting of transcription with the antibiotic rifampicin, and following mRNA abundance at 1, 2, 4, 8, and 15 minutes post rifampicin.  All RNA measurements were performed on cells grown to mid-log in M2G minimal growth medium.  Two biological replicates time coursees were collected from independent starter cultures.

overall_design: Total RNA samples were collected just prior to rifampicin addition, and after 1, 2, 4, 8, or 15 minutes incubation with 100ug/mL rifampicin.  Each total RNA sample was depleted of rRNA using the ribozero kit (Illumina) for gram negative bacteria, and subjected to total RNA-seq libraries as in (Ingolia et al. Science 2009).  RNA was left in each sample as an internal control for stable RNA.  Resulting DNA libraries  were pooled, and sequenced in a Hiseq 2500 (U. Texas - Austin).

first: Nadra

last: Al-Husini


title: Single cell human melanocytes

status: Public on May 29 2020

city: Salt Lake City

first: Robert

middle: L

last: Judson-Torres

state: Utah

address: 2000 Circle of Hope

department: Dermatology

institute: Huntsman Cancer Institute at the University of Utah

summary: We report single cell transcriptomes from human skin samples that have been enriched for melanocytes using FACS. This work revealed anatomical site-specific melanocyte expression programs. In addition, by surveying melanocytes at different stages of development, we identified development-associated expression programs that are reflected in the dedifferentiation of melanomas.

overall_design: Single cell RNA-seq of human skin from multiple sites and ages

first: Daniel

middle: D

last: Le

first: Rachel

last: Belote

first: Spyros

last: Darmanis


title: Analysis of the coding and non-coding RNA temporal transcriptome of developing seeds in sunflower [RNA-seq]

summary: RNA-sequencing (lncRNA,mRNA and circRNA) of seeds in three developmental stages was performed to reveals gene regulation in relation to oil and fatty acid accumulation in sunflower

overall_design: RNA-sequencing (lncRNA,mRNA and circRNA) profiles of seeds of high oleic acid L-1-OL-1 were generated by deep sequencing at 7-, 22- and 37 day.


title: Whole transcriptome analysis for kidney aging in mice


title: Next Generation Sequencing of miRNome of G-CSF treated huCD34+ HSPCs

status: Public on Jan 12 2020

city: Leipzig

first: Gerhard

last: Behre

address: Johannisallee 32A

department: Division of Hematology and Oncology

institute: Leipzig University Hospital

summary: MicroRNAs (miRNAs) are a class of small non coding RNAs (ncRNAs) with 19-25 nucleotides in length, which can inhibit the translation or induce the destabilization and/or degradation of their mRNA targets, usually by binding in an incomplete manner to the 3`untranslated region (3`UTR) of their respective targets. We were interested in miRNAs that are regulated during G-CSF induced myeloid differentiation.

overall_design: Examination of miRNA expression patterns upon G-CSF administration on huCD34+ HSPCs. NGS was performed out of 3 independent experiments.

first: Jens-Uwe

last: Hartmann


title: Mechanisms of heat-induced transcriptional memory profiled in mouse embryonic fibroblasts (MEFs).

status: Public on Mar 04 2020

city: Stockholm

first: Anniina

last: Vihervaara

address: Tomtebodavägen 23A

department: Gene Technology

institute: KTH Royal Institute of Technology

summary: Precision run-on sequencing (PRO-seq) of nascent RNA synthesis across the mouse genome. The PRO-seq data was generated from MEFs that were either unconditioned (unC) or preconditioned with a single 1h heat shock exposure, followed by a 48-h recovery (preC).The unconditioned and preconditioned cells were subjected to a single heat shock, during which the the kinetics of nascent transcription response was monitored.

overall_design:
Genome-wide nascent transcription profiles mapped in MEFs in non-strss conditions, upon 1h heat shock and 4h recovery from heat shock. Additionally, MEFs were either unconditioned or preconditioned with a single heat shock exposure, and the kinetics of transriptional response to heat shock monitored with PRO-seq upon 0', 12.5', 25' and 40' additional heat shock exposure.

Please note that [1] the Normalized_*.bigWig processed data was generated from all replicates combined and is linked to the corresponding replicate 1 sample records (i.e.*BR1, *BR1a samples) [2] the Normalized_PROseq_MEF_uC_12HS_BRs_*Strand.bigWig processed data was generated from GSM1843440 (GSE71708) raw data (5' adapter sequence: TGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC) and is linked as Series supplementary files.

first: Dig

middle: B

last: Mahat

first: John

last: Lis


title: DCP1A knockout: transcriptome-wide characterization

first: Eric

last: Aeby

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


title: scRNA-seq of the developing human retina

status: Public on May 07 2020

city: St. Louis

first: Brian

middle: Stewart

last: Clark

state: Missouri

address: 660 S Euclid Ave; Campus Box #8096

department: Ophthalmology and Visual Sciences

institute: Washington University

summary: Time-series of single-cell RNA-sequencing performed on stem cell derived retinal organoids or post-mortem tissue from the developing and adult retina

overall_design: 10x Genomics V2 single-cell RNA-sequencing

first: Seth

last: Blackshaw

first: James

last: Handa

first: Rod

last: Bremner

first: Donald

last: Zack