title: Characterization of Staphylococcus epidermidis clinical and commensal isolates transcriptome upon interaction with human blood

city: Braga

first: Ângela

last: França

address: Campus de Gualtar

department: Biological Engineering

country: Portugal

institute: University of Minho

summary: The release of cells from S. epidermidis biofilms formed on medical devices has been associated with the onset of bloodstream infections, resulting in increased morbidity and mortality rates. This has to do, in part, with the difficulty to accurately diagnose S. epidermidis bloodstream infections. S. epidermidis is a ubiquitous commensal of human skin and mucosa and, thus, a positive blood culture does not always represent an infection, possibly being the result of contamination during blood collection. As such, there is a high demand to find markers that can help clinicians to distinguish infection (clinical isolates) from contamination (commensal strains). With that in mind, several studies comparing phenotypic or genetic characteristics of clinical and commensal isolates have been performed over the years. However, because S. epidermidis virulence factors seem to be the same that confer its fitness as a commensal, we hypothesized that the ability of S. epidermidis strains to adapt to the host environment may not depend on a specific phenotypic and/or genetic makeup, but rather on the regulation of gene transcription. Thus, using RNA-Sequencing (RNA-seq), we characterized the transcriptome of commensal and clinical isolates in the context of infection to try to uncover differences and, thus, identify markers that could be used for the diagnostics. Several markers with the potential to discriminate between both groups were highlighted. Nevertheless, when the results obtained were confirmed in a wider collection of clinical and commensal isolates the discriminatory power of the genes initially identified was lost. Although we cannot rule out that the characterization of a larger collection of isolates would identify potential candidates, our transcriptomic data was not able to confirm our initial hypothesis, evidencing S. epidermidis opportunistic nature.

overall_design: The transcriptome of the cells released from biofilms formed by three S. epidermidis clinical and three commensal isolates was characterized upon incubation with human blood for 2h at 37 oC and with agitation at 80 rpm. Each condition under test was analyzed once by RNA-seq, however, each sample analyzed was prepared by mixing total RNA from three independent assays.

first: Susana

last: Brás

first: Nuno

last: Cerca


title: The Keap1-Nrf2-Bach1 signaling mediates UBR7 negative regulation of HK2 to inhibit glycolysis and HCC tumorigenesis [RNA-seq]

status: Public on Dec 09 2022

city: Guangxi

first: Bo

last: Tang

address: 6 Shuangyong Road

country: China

institute: Guangxi Medical University

type: Expression profiling by high throughput sequencing

summary: We found that Keap1-Nrf2 signaling pathway mediates UBR7 to regulate HK2 expression through the modification of histone H2BK120 monoubiquitination, thereby inhibiting glycolysis and HCC tumorigenesis.

overall_design: The gene expression of  in wild-type and Alb-Cre;UBR7fl/fl mouse liver primary cells were detected were detected by RNA sequencing.

first: Liang

last: Zhao

first: Yang

last: Li

first: Hongliang

last: Dai


title: Gene expression microarray analysis on the dentate gyrus of forebrain-specific calcineurin knockout mice and control mice

city: Toyoake

first: Hideo

last: Hagihara

address: 1-98 Dengakugakubo, Kutsukake-cho

department: Institute for Comprehensive Medical Science

country: Japan

institute: Fujita Health University

summary: The gene expression patterns in the dentate gyrus of forebrain-specific calcineurin knockout mice and control mice were examined using Affymetrix GeneChip arrays.

overall_design: Dentate gyrus RNA isolated from forebrain-specific calcineurin knockout mice (n = 6) or control mice (n = 6)


title: Bulk RNA-sequencing of unsorted and PAX7::GFP-sorted ESC-derived myogenic progenitors

city: Baltimore

first: Emily

last: Lo

state: MD

address: 733 N Broadway

country: USA

institute: Johns Hopkins

summary: Tissue engineering strategies that combine human pluripotent stem cell-derived myogenic progenitors (hPDMs) with advanced biomaterials provide promising tools for engineering 3D skeletal muscle grafts to model tissue development in vitro and promote muscle regeneration in vivo. We recently demonstrated (i) the potential for obtaining large numbers of hPDMs using a combination of two small molecules and (ii) the application of electrospun fibrin microfiber bundles for functional skeletal muscle restoration following volumetric muscle loss. In this study, we demonstrate that the biophysical cues provided by the microfiber bundles can induce unsorted hPDMs to form multinucleated myotubes that express desmin and myosin heavy chain. To reduce the batch-to-batch variability of these samples, we tested a genetic PAX7 reporter line (PAX7::GFP) to sort for more homogenous populations of hPDMs. RNA sequencing and gene set enrichment analyses confirmed that PAX7::GFP-sorted hPDMs exhibited higher expression of myogenic genes while unsorted hPDMs demonstrated increased expression of genes associated with embryonic, neural crest, and fibroadipogenic progenitor lineages. We tested engineered skeletal muscle grafts derived from either PAX7::GFP-sorted or unsorted hPDMs within in vivo skeletal muscle defects. The unsorted hPDM-derived grafts also exhibited greater fibrosis and more proinflammatory responses. In contrast, the PAX7::GFP-sorted groups had moderately high vascular infiltration, more implanted cell association with embryonic myosin heavy chain (eMHC) regions, and greater CD206:CD86 ratios compared to unsorted hPDMs and acellular fibers suggesting they induced more pro-regenerative microenvironments. These findings demonstrated some promise for the use of PAX7::GFP-sorted hPDMS on fibrin microfiber bundles and provided some insights for improving the cell-biomaterial system to stimulate more robust in vivo skeletal muscle regeneration.

overall_design: 3 unsorted ESC-derived myogenic progenitors and 3 PAX7::GFP-sorted ESC-derived myogenic progenitors

first: Sarah

middle: M

last: Somers

first: Jordana

last: Gilbert-Honick

first: In

middle: Y

last: Choi

middle: K

first: HoTae

last: Lim

first: Hannah

last: Takasuka

first: Kathryn

middle: R

last: Wagner

first: Hai-Quan

last: Mao

first: Patrick

last: Cahan

first: Gabsang

last: Lee

first: Warren

middle: L

last: Grayson


title: Transcriptome sequencing in HL-60 induced neutrophils between the stimulation of AGEs and high-glucose

city: Shanghai

first: Yutian

last: Kang

state: Shanghai

address: 197 ruijin'er road, shanghai

department: Burn Institute

institute: Shanghai Jiao Tong University School of Medicine Affiliated Ruijin Hospital

summary: We report the high-throughput sequencing results in mammalian cell lines. Neutrophils were induced by HL-60 with 1umol/L ATRA(all-trans retinoid acid ) stimulation for 7days.  Neutrophils were then stimulated with 0.05ug/mL AGEs，30mmol/L D-glucose, AGEs+D-glucose and 0.05ug/mL BSA (control) for 24-hours, then mRNA profiles were extracted and tested using Illumina Hiseq 4000. This study provides a prospective work for the influence of AGEs and high-glucose in human neutrophils.

overall_design: Examination of the effection for 2 different stimulus in HL-60 induced neutrophils.

first: Shuliang

last: Lu

first: Jiaoyun

last: Dong

first: Ming

last: Tian


title: High dose isoleucine stabilizes nuclear PTEN to suppress the proliferation of lung cancer

status: Public on Dec 08 2022

city: Xi' an

first: Xuetong

last: Chen

address: Taibai road, No. 229

institute: Northwest University

summary:
To explore the potential mechanism of isoleucine anti-tumor, we performed transcriptome data analysis of LLC mouse tumor xenograft model.
We then performed gene expression profiling analysis using data obtained from RNA-seq of tumor tissues in two groups (Control & Isoleucine).

overall_design: Comparative gene expression profiling analysis of RNA-seq data for tumor tissue from mice treated with isoleucine or PBS.

first: Haiqing

last: Wang

first: Sen


title: Roerr et al CGH data

city: Seattle

first: Maitreya

middle: J.

last: Dunham

state: WA

address: Foege Building, S403B, Box 355065

department: Genome Sciences

institute: University of Washington

summary: Comparative genomic hybridization experiments comparing DNA from experimentally evolved yeast strains to DNA from a euploid control.

first: Celia

last: Payen

first: John

last: Matese


title: The Keap1-Nrf2-Bach1 signaling mediates UBR7 negative regulation of HK2 to inhibit glycolysis and HCC tumorigenesis

first: Bo

last: Tang

type: Genome binding/occupancy profiling by high throughput sequencing

overall_design: The promoter regions of genes that bind to H2BK120ub in wild-type and Alb; Cre-UBR7fl/fl mouse liver primary cells were detected by ChiP-seq.

first: Liang

last: Zhao

first: Yang

last: Li

first: Hongliang

last: Dai


title: The miR-497~195 cluster suppresses cell cycle regulators and in vivo leukemia growth in B-cell precursor Acute Lymphoblastic Leukemia [miRNA-seq]

city: Padova

first: Stefania

last: Bortoluzzi

address: via G. Colombo 3

department: Department of Molecular Medicine

country: Italy

institute: University of Padova

type: Non-coding RNA profiling by high throughput sequencing

summary: Despite considerable improvements in the treatment of B-cell precursor acute lymphoblastic leukemia (BCP-ALL), relapse is still associated with poor prognosis. We previously found that the risk for early relapse can be predicted by the rapid engraftment of patient-derived blasts transplanted into NOD/SCID mice. In search for the cellular and molecular profile associated with this phenotype, we investigated the expression of microRNAs (miRNAs) in different engraftment phenotypes and patient outcomes. We found miR-497~195 high expression in patient-derived xenograft samples with slow engraftment, derived from patients with favorable outcome. In contrast, epigenetic repression and low expression of these miRNAs was observed in rapidly engrafting samples, which were associated with early relapse. Overexpression of miR-497~195 in patient-derived cells suppressed in vivo engraftment of leukemia cells and considerably prolonged recipient survival by inhibition of regulators of cell cycle progression. As key factors for the entry in S phase were downregulated upon miR-497~195 overexpression, we identified CDK4/CCND3 mediated control of G1/S transition as a principal mechanism for miR-497~195 mediated suppression of leukemia progression in BCP-ALL. Thus, the association of the miR-497~195 cluster expression with outcome in BCP-ALL, and the importance of these miRNAs in counteracting the development of ALL in vivo indicate the relevance of the involved pathways as potential targets for therapeutic intervention.

overall_design: Human leukemia cells rapidly (N=6, short TTL) and slowly (N=7, long TTL) engrafting in NOD/SCID mice, from BCP-ALL pediatric patients

first: Elena

last: Boldrin

first: Enrico

last: Gaffo

first: Judith

last: Boer

first: Salih

last: Demir

first: Julia

last: Zinngrebe

first: Felix

last: Seyfried

first: Rainer

last: Claus

first: Christoph

last: Plass

first: Monique

middle: D

first: Klaus-Michael

last: Debatin

first: Geertruy

last: Kronnie

first: Lüder

middle: H

last: Meyer


title: Nonwoven-based gelatin/polycaprolactone membrane loaded with ERK inhibitor U0126 for treatment of tendon defects

status: Public on Dec 10 2022

city: Guangzhou

first: Liangliang

last: Xu

state: Yuexiu

address: Guangzhou

institute: Guangzhou University of Chinese Medicine

summary:
Background: Tendon is a major component of musculoskeletal system connecting the muscles to the bone. Tendon injuries are very common orthopedics problems leading to impeded motion. Up to now, there still lacks effective treatments for tendon diseases.
Methods: Tendon stem/progenitor cells (TSPCs) were isolated from the patellar tendons of SD rats. The expression levels of genes were evaluated by quantitative RT-PCR. Immunohistochemistry staining was performed to confirm the presence of tendon markers in tendon tissues. Bioinformatics analysis of data acquired by RNA-seq was used to find out the differentially expressed genes. Rat patellar tendon injury model was used to evaluate the effect of U0126 on tendon injury healing. Biomechanical testing was applied to evaluate the mechanical properties of newly formed tendon tissues.
Results: In this study, we have shown that ERK inhibitor U0126 rather PD98059 could effectively increase the expression of tendon-related genes and promote the tenogenesis of TSPCs in vitro. To explore the underlying mechanisms, RNA sequencing was performed to identify the molecular difference between U0126-treated and control TSPCs. The result showed that GDF6 was significantly increased by U0126, which is an important factor of the TGFβ superfamily regulating tendon development and tenogenesis. In addition, NBM (nonwoven-based gelatin/polycaprolactone membrane) which mimics the native microenvironment of the tendon tissue was used as an acellular scaffold to carry U0126. The results demonstrated that when NBM was used in combination with U0126, tendon healing was significantly promoted with better histological staining outcomes and mechanical properties.
Conclusion: Taken together, we have found U0126 promoted tenogenesis in TSPCs through activating GDF6, and NBM loaded with U0126 significantly promoted tendon defect healing, which provides a new treatment for tendon injury.

overall_design: mRNA profiles of TSPCs and U0126 treated TSPCs

first: Yonghui

last: Hou

first: Bingyu

last: Zhou

first: Ming

last: Ni


title: A preliminary study on the screening and mechanism of miRNA as a biomarker for patients with different progressive chronic obstructive pulmonary disease (COPD)

city: urumchi

first: siming

last: Tao

address: 116 Huanghe Road

institute: Xinjiang Uygur Autonomous Region Key Laboratory of Respiratory Physiology and Pathology

summary: In this study, a high-throughput sequencing technology was used to screen the differentially expressed miRNA in the patients with "fast" and "slow" progression of chronic obstructive pulmonary disease (COPD). Moreover, the possible mechanism, affecting the progression of COPD, was preliminarily analyzed based on the target genes of candidate miRNAs.

overall_design: From January 2018 to December 2019, a total of 240 patients diagnosed with stable COPD in the respiratory department at the Fourth Affiliated Hospital of Xinjiang Medical University, Xinjiang, China, were recruited for this study. Five patients from each of the "fast" progression, "slow" progression, and Normal group and four patients from the COPD group were selected. The peripheral blood samples were taken from the participants, followed by total RNA extraction and high throughput miRNA sequencing. The differentially expressed miRNAs among the different progressive COPD groups were identified using bioinformatics analysis. Then, the candidate miRNAs were externally verified. In addition, the target gene of this miRNA was identified and its effects on the cell activity, cell cycle, apoptosis, and other biological phenotypes of COPD were analyzed.

first: Siming

first: Chunyan

last: Liao

first: Fengsen

last: Li


title: microRNA counts from forebrain (ENCSR966UUJ)

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

institute: ENCODE DCC

summary:
Nanostring miRNA Array on embryonic 16.5 day mouse forebrain

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


title: microRNA counts from neural tube (ENCSR940THV)

summary:
Nanostring miRNA Array on embryonic 11.5 day (e11.5) mouse neural tube

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


title: microRNA counts from liver (ENCSR942IBI)

summary:
Nanostring miRNA Array on embryonic 11.5 day (e11.5) mouse liver

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


title: microRNA counts from heart left ventricle (ENCSR888ZAA)

summary:
Nanostring miRNA Array on human heart left ventricle

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


title: microRNA counts from GM23338 (ENCSR894GAC)

summary:
Nanostring miRNA Array on human induced pluripotent stem cell

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


title: microRNA counts from midbrain (ENCSR921CNU)

summary:
Nanostring miRNA Array on embryonic 14.5 day mouse midbrain

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


title: microRNA counts from adrenal gland (ENCSR895SFC)

summary:
Nanostring miRNA Array on human adrenal gland

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


title: microRNA counts from ovary (ENCSR854NNW)

summary:
Nanostring miRNA Array on human female gonad

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


title: microRNA counts from kidney (ENCSR853PWX)

summary:
Nanostring miRNA Array on embryonic 15.5 day mouse kidney

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


title: microRNA counts from forebrain (ENCSR866SQU)

summary:
Nanostring miRNA Array on embryonic 10.5 day mouse forebrain

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


title: microRNA counts from intestine (ENCSR888TKN)

summary:
Nanostring miRNA Array on embryonic 15.5 day mouse intestine

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


title: microRNA counts from testis (ENCSR882QTS)

summary:
Nanostring miRNA Array on human testis

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


title: microRNA counts from heart (ENCSR883USZ)

summary:
Nanostring miRNA Array on postnatal 0 day mouse heart

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


title: microRNA counts from liver (ENCSR888CKV)

summary:
Nanostring miRNA Array on embryonic 12.5 day mouse liver

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


title: microRNA counts from liver (ENCSR860OEN)

summary:
Nanostring miRNA Array on postnatal 0 day mouse liver

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


title: microRNA counts from thyroid gland (ENCSR869POD)

summary:
Nanostring miRNA Array on human thyroid gland

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


title: microRNA counts from embryonic facial prominence (ENCSR828SVM)

summary:
Nanostring miRNA Array on embryonic 15.5 day mouse embryonic facial prominence

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


title: microRNA counts from hindbrain (ENCSR821ZGZ)

summary:
Nanostring miRNA Array on embryonic 12.5 day mouse hindbrain

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


title: microRNA counts from intestine (ENCSR814KDR)

summary:
Nanostring miRNA Array on embryonic 16.5 day mouse intestine

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


title: microRNA counts from stomach (ENCSR805WTW)

summary:
Nanostring miRNA Array on embryonic 14.5 day mouse stomach

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


title: microRNA counts from heart (ENCSR823KMG)

summary:
Nanostring miRNA Array on embryonic 10.5 day mouse heart

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


title: microRNA counts from body of pancreas (ENCSR800WFS)

summary:
Nanostring miRNA Array on human pancreas

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


title: microRNA counts from myocyte (ENCSR782VMS)

summary:
Nanostring miRNA Array on human LHCN-M2 differentiated for 7 days

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


title: microRNA counts from hindbrain (ENCSR826DZM)

summary:
Nanostring miRNA Array on embryonic 15.5 day mouse hindbrain

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


title: microRNA counts from embryonic facial prominence (ENCSR822RRV)

summary:
Nanostring miRNA Array on embryonic 10.5 day mouse embryonic facial prominence

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


title: microRNA counts from bipolar neuron (ENCSR765ZSI)

summary:
Nanostring miRNA Array on PGP human bipolar spindle neuron

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


title: microRNA counts from right lobe of liver (ENCSR776XYQ)

summary:
Nanostring miRNA Array on human right lobe of liver

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


title: microRNA counts from forebrain (ENCSR743UOB)

summary:
Nanostring miRNA Array on embryonic 15.5 day mouse forebrain

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


title: microRNA counts from neural tube (ENCSR702DUC)

summary:
Nanostring miRNA Array on embryonic 15.5 day mouse neural tube

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


title: microRNA counts from skeletal muscle tissue (ENCSR753HJF)

summary:
Nanostring miRNA Array on postnatal 0 day mouse skeletal muscle

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


title: microRNA counts from limb (ENCSR685QWR)

summary:
Nanostring miRNA Array on embryonic 10.5 day mouse limb

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


title: microRNA counts from forebrain (ENCSR669EWD)

summary:
Nanostring miRNA Array on embryonic 11.5 day (e11.5) mouse forebrain

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


title: microRNA counts from limb (ENCSR664WGP)

summary:
Nanostring miRNA Array on embryonic 15.5 day mouse limb

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


title: microRNA counts from heart (ENCSR652IDV)

summary:
Nanostring miRNA Array on embryonic 13.5 day mouse heart

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


title: microRNA counts from limb (ENCSR608HDW)

summary:
Nanostring miRNA Array on embryonic 13.5 day mouse limb

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


title: microRNA counts from limb (ENCSR606IHZ)

summary:
Nanostring miRNA Array on embryonic 11.5 day (e11.5) mouse limb

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


title: microRNA counts from gastrocnemius medialis (ENCSR655NLY)

summary:
Nanostring miRNA Array on human skeletal muscle tissue

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


title: microRNA counts from hindbrain (ENCSR598WZW)

summary:
Nanostring miRNA Array on embryonic 13.5 day mouse hindbrain

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


title: microRNA counts from kidney (ENCSR672TMZ)

summary:
Nanostring miRNA Array on embryonic 15.5 day mouse kidney

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


title: microRNA counts from smooth muscle cell (ENCSR625DUG)

summary:
Nanostring miRNA Array on SESCC human H9 derived smooth muscle

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


title: microRNA counts from neural progenitor cell (ENCSR624LFP)

summary:
Nanostring miRNA Array on human neural progenitor cell

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


title: microRNA counts from kidney (ENCSR596MKU)

summary:
Nanostring miRNA Array on postnatal 0 day mouse kidney

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


title: microRNA counts from heart (ENCSR590PHU)

summary:
Nanostring miRNA Array on embryonic 11.5 day (e11.5) mouse heart

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


title: microRNA counts from thyroid gland (ENCSR567SVD)

summary:
Nanostring miRNA Array on human thyroid gland

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


title: microRNA counts from forebrain (ENCSR776CGZ)

summary:
Nanostring miRNA Array on embryonic 13.5 day mouse forebrain

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


title: microRNA counts from hindbrain (ENCSR722SLO)

summary:
Nanostring miRNA Array on embryonic 10.5 day mouse hindbrain

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


title: microRNA counts from lower leg skin (ENCSR798NKG)

summary:
Nanostring miRNA Array on human lower leg skin

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


title: microRNA counts from kidney (ENCSR498PUG)

summary:
Nanostring miRNA Array on embryonic 16.5 day mouse kidney

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


title: microRNA counts from embryonic facial prominence (ENCSR506JCY)

summary:
Nanostring miRNA Array on embryonic 15.5 day mouse embryonic facial prominence

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


title: microRNA counts from liver (ENCSR495JDH)

summary:
Nanostring miRNA Array on embryonic 13.5 day mouse liver

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


title: microRNA counts from testis (ENCSR494FIS)

summary:
Nanostring miRNA Array on human testis

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


title: microRNA counts from prostate gland (ENCSR630JWA)

summary:
Nanostring miRNA Array on human prostate

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


title: microRNA counts from heart (ENCSR594ZQX)

summary:
Nanostring miRNA Array on embryonic 12.5 day mouse heart

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


title: microRNA counts from hindbrain (ENCSR392BBU)

summary:
Nanostring miRNA Array on embryonic 11.5 day (e11.5) mouse hindbrain

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


title: microRNA counts from limb (ENCSR552NEH)

summary:
Nanostring miRNA Array on embryonic 14.5 day mouse limb

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


title: microRNA counts from vagina (ENCSR591LEQ)

summary:
Nanostring miRNA Array on human vagina

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


title: microRNA counts from midbrain (ENCSR378DMT)

summary:
Nanostring miRNA Array on embryonic 11.5 day (e11.5) mouse midbrain

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


title: microRNA counts from body of pancreas (ENCSR538MBL)

summary:
Nanostring miRNA Array on human pancreas

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


title: microRNA counts from thymus (ENCSR523DJZ)

summary:
Nanostring miRNA Array on postnatal 0 day mouse thymus

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


title: microRNA counts from gastrocnemius medialis (ENCSR505IZZ)

summary:
Nanostring miRNA Array on human skeletal muscle tissue

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


title: microRNA counts from liver (ENCSR327VOK)

summary:
Nanostring miRNA Array on embryonic 16.5 day mouse liver

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


title: microRNA counts from stomach (ENCSR323GNP)

summary:
Nanostring miRNA Array on postnatal 0 day mouse stomach

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


title: microRNA counts from heart (ENCSR301FQU)

summary:
Nanostring miRNA Array on embryonic 15.5 day mouse heart

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


title: microRNA counts from liver (ENCSR283GCF)

summary:
Nanostring miRNA Array on embryonic 14.5 day mouse liver

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


title: microRNA counts from embryonic facial prominence (ENCSR489TWI)

summary:
Nanostring miRNA Array on embryonic 12.5 day mouse embryonic facial prominence

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


title: microRNA counts from hepatocyte (ENCSR448MNV)

summary:
Nanostring miRNA array on human hepatocyte derived from H9

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


title: microRNA counts from neural tube (ENCSR485BIK)

summary:
Nanostring miRNA Array on embryonic 12.5 day mouse neural tube

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


title: microRNA counts from lung (ENCSR277GWK)

summary:
Nanostring miRNA Array on embryonic 15.5 day mouse lung

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


title: microRNA counts from heart left ventricle (ENCSR425ZMS)

summary:
Nanostring miRNA Array on human heart left ventricle

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


title: microRNA counts from uterus (ENCSR486QHW)

summary:
Nanostring miRNA Array on human uterus

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


title: microRNA counts from hindbrain (ENCSR471YND)

summary:
Nanostring miRNA Array on postnatal 0 day mouse hindbrain

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


title: microRNA counts from forebrain (ENCSR392AII)

summary:
Nanostring miRNA Array on embryonic 14.5 day mouse forebrain

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


title: microRNA counts from adrenal gland (ENCSR381ADE)

summary:
Nanostring miRNA Array on human adrenal gland

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


title: microRNA counts from neural tube (ENCSR369ZII)

summary:
Nanostring miRNA Array on postnatal 0 day mouse neural tube

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


title: microRNA counts from midbrain (ENCSR340CTF)

summary:
Nanostring miRNA Array on embryonic 10.5 day mouse midbrain

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


title: microRNA counts from midbrain (ENCSR257PBL)

summary:
Nanostring miRNA Array on embryonic 12.5 day mouse midbrain

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


title: microRNA counts from midbrain (ENCSR247SSE)

summary:
Nanostring miRNA Array on embryonic 15.5 day mouse midbrain

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


title: microRNA counts from spleen (ENCSR332XWL)

summary:
Nanostring miRNA Array on postnatal 0 day mouse spleen

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


title: microRNA counts from midbrain (ENCSR347QCM)

summary:
Nanostring miRNA Array on embryonic 16.5 day mouse midbrain

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


title: microRNA counts from midbrain (ENCSR215OAK)

summary:
Nanostring miRNA Array on postnatal 0 day mouse midbrain

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


title: microRNA counts from prostate gland (ENCSR227VCK)

summary:
Nanostring miRNA Array on human prostate

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


title: microRNA counts from embryonic facial prominence (ENCSR207NKU)

summary:
Nanostring miRNA Array on embryonic 13.5 day mouse embryonic facial prominence

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


title: microRNA counts from stomach (ENCSR213NEM)

summary:
Nanostring miRNA Array on embryonic 16.5 day mouse stomach

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


title: microRNA counts from right atrium auricular region (ENCSR326JQW)

summary:
Nanostring miRNA Array on human right cardiac atrium

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


title: microRNA counts from forebrain (ENCSR184PQQ)

summary:
Nanostring miRNA Array on postnatal 0 day mouse forebrain

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


title: microRNA counts from embryonic facial prominence (ENCSR201KHF)

summary:
Nanostring miRNA Array on embryonic 11.5 day (e11.5) mouse embryonic facial prominence

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


title: microRNA counts from hindbrain (ENCSR269WSU)

summary:
Nanostring miRNA Array on embryonic 16.5 day mouse hindbrain

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


title: microRNA counts from intestine (ENCSR262WRN)

summary:
Nanostring miRNA Array on embryonic 15.5 day mouse intestine

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


title: microRNA counts from right atrium auricular region (ENCSR258UGT)


title: microRNA counts from lung (ENCSR137ZTO)

summary:
Nanostring miRNA Array on embryonic 16.5 day mouse lung

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


title: microRNA counts from neural tube (ENCSR132FJG)

summary:
Nanostring miRNA Array on embryonic 13.5 day mouse neural tube

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


title: microRNA counts from midbrain (ENCSR130SVF)

summary:
Nanostring miRNA Array on embryonic 13.5 day mouse midbrain

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


title: microRNA counts from vagina (ENCSR065OIA)

summary:
Nanostring miRNA Array on human vagina

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


title: microRNA counts from limb (ENCSR042BYK)

summary:
Nanostring miRNA Array on embryonic 12.5 day mouse limb

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


title: microRNA counts from intestine (ENCSR232JFQ)

summary:
Nanostring miRNA Array on postnatal 0 day mouse intestine

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


title: microRNA counts from lung (ENCSR100XAT)

summary:
Nanostring miRNA Array on embryonic 14.5 day mouse lung

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


title: microRNA counts from hindbrain (ENCSR083USL)

summary:
Nanostring miRNA Array on embryonic 14.5 day mouse hindbrain

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


title: microRNA counts from urinary bladder (ENCSR108YYU)

summary:
Nanostring miRNA Array on postnatal 0 day mouse bladder

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


title: microRNA counts from heart (ENCSR023TWU)

summary:
Nanostring miRNA Array on embryonic 14.5 day mouse heart

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


title: microRNA counts from liver (ENCSR035TGL)

summary:
Nanostring miRNA Array on embryonic 15.5 day mouse liver

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


title: microRNA counts from lower leg skin (ENCSR021JTM)

summary:
Nanostring miRNA Array on human lower leg skin

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


title: microRNA counts from stomach (ENCSR006GDO)

summary:
Nanostring miRNA Array on embryonic 15.5 day mouse stomach

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


title: microRNA counts from uterus (ENCSR101DVP)

summary:
Nanostring miRNA Array on human uterus

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


title: microRNA counts from heart (ENCSR037NRU)

summary:
Nanostring miRNA Array on embryonic 16.5 day mouse heart

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


title: microRNA counts from forebrain (ENCSR002TKA)

summary:
Nanostring miRNA Array on embryonic 12.5 day mouse forebrain

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


title: microRNA counts from lung (ENCSR025YVG)

summary:
Nanostring miRNA Array on postnatal 0 day mouse lung

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


title: Effect of overexpression of VIM-AS1 on gene expression in LNCaP cells

city: Xi'an

first: Shengjia

last: Shi

address: No.169 Changle Road

department: Department of Immunology

institute: Air Force Medical University

summary:
Purpose: To detect the diffirential expressed genes in LNCaP cells transfected with VIM-AS1 overexression vetor and control pcDNA3.1 vector
Method: Transcriptome sequencing was sued to detect the diffirential expressed genes in LNCaP cells transfected with VIM-AS1 overexression vetor and control pcDNA3.1 vector
Results :We performed transcriptome sequencing to identify the target genes in VIM-AS1 overexpressed LNCaP cells and normal control. 67 genes were found statistically up-regulated more than two-fold and 187 genes were found statistically down-regulated more than two-fold in VIM-AS1 overexpressed LNCaP cells
Conclusion:Our study represents the first detailed analyasis of transcriptomes in LNCaP cells with VIM-AS1 overexpression and control cells.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for LNCaP cells transfected with VIM-AS1 overexression vetor and control pcDNA3.1 vector

first: Donghui

last: Han

first: Rui

last: Zhang

first: Angang

last: Yang


title: microRNA counts from neural tube (ENCSR184JSL)

summary:
Nanostring miRNA Array on embryonic 14.5 day mouse neural tube

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


title: Proteomic and Genomic Profiling of Plasma Exosomes from Ankylosing Spondylitis Patients

city: Toronto

first: Fataneh

last: Tavasolian

state: Ontario

address: 60 leonard Ave

country: Canada

institute: Krembil Research institute

summary: Recent advances in knowledge of the biology of Ankylosing Spondylitis (AS) using innovative genetic and biomarker approaches offer the opportunity to address current challenges in AS diagnosis and management. Altered expression of microRNAs (miRNAs) may contribute to immune dysregulation and play a significant role in the onset and persistence of inflammation in AS. The capacity of exosomes to transport miRNAs between cells, thereby inducing phenotypic alterations in recipient cells has been the subject of considerable attention in recent years. This study reports the first comprehensive  miRNA profiling of plasma-derived exosomes utilizing Gene Ontology (GO) annotation and pathway analysis.

overall_design: Plasma samples from AS patients and healthy controls (HC) were isolated via ultracentrifuge and subjected to extracellular vesicle (EV) flow cytometry analysis to characterize exosome surface markers by a multiplex immunocapture assay. Cytokine profiling of plasma-derived exosomes and cell culture supernatant was performed. Next-generation sequencing was used to identify miRNA populations in exosomes enriched from plasma fractions.

first: Starlee

last: Lively

first: Chiara

last: Pastrello

first: Michael

last: Tang

first: Melissa

last: Lim

first: Addison

last: Pacheco

first: Zoya

last: Qaiyum

first: Enoch

last: Yau

first: Igor

last: Jurisica

first: Mohit

last: Kapoor

first: Robert

last: Inman


title: Anti-HIV-1 CAR-T cells armed with autogenic broadly neutralizing antibody and follicle-homing receptor CXCR5 ar effective against different HIV-1 clades and reduce viral reservoir in HIV-1-infected individuals

city: 上海

first: Zhu

last: YouWei

address: 130 Dong'an Road

department: Institutes of Biomedical Sciences

institute: Fudan university

summary: Chimeric antigen receptor T (CAR-T) cells, long proposed for HIV-1 treatment, has yet to achieve desirable therapeutic efficacy. In our study, M10 CAR-T cells were used for treating 18 HIV-1 patients via a regimen combining two M10 infusions and repeat chidamide stimulation for HIV reservoir activation. Consequently, 74.3% of M10 infusions resulted in significant suppression of viral rebound (averaging 77.4% decline), with 10 patients showing persistently reduced cell-associated HIV-1 RNA levels (averaging > 1.15 log10) over the 150-day observation period. To evaluate the genetic change, the PCR products were sequenced on a PacBio sequel platform by Genewiz (Genewiz, Suzhou, China) in 10 HIV patients treated by M10 CAR-T immunotherapy and 2 controls only applied with HAART therapy. High-throughput sequencing of partial pol gene and env gene amplified from whole blood samples at baseline or final visit.The results demonstrated that several participants showed a genetic shift in the composition of viral reservoir populations after treatment. Additionally, in some participants, the remaining proviruses showed reduced overall diversity in the virus pol gene. The results also reveal the selective pressure mainly targeted the env gene. This comprehensive survey supported the potential of M10 CAR-T cells as a new, safe, and effective therapeutic option toward HIV-1 eradication in AIDS patients.

overall_design:
M10 CAR-T cells were used for treating 18 HIV-1 patients via a regimen combining two M10 infusions and repeat chidamide stimulation for HIV reservoir activation.To evaluate the genetic change, the PCR products were sequenced on a PacBio sequel platform by Genewiz (Genewiz, Suzhou, China) in 10 HIV patients treated by M10 CAR-T immunotherapy and 2 controls only applied with HAART therapy.
Please note that the *.target.fa.gz contains 10nt of upstream and downstream of HIV protease/ reverse transcriptase (PR/RT) region extracted from the sequencing data . The files were included in the records as the study focuses on the diversity and genetic distance of this region in the sequencing analysis section, and to help other readers to reproduce the original data.

first: Yunyu

last: Mao

first: Jianqing

last: Xu


title: Macrophage-CITED2 and inflammatory gene expression

city: Cleveland

first: Ernest

last: Chan

state: OH

address: 10900 Euclid Ave, Robbins E211

department: PQHS

institute: CWRU

summary: CITED2 is a member of the CBP/p300-interacting transactivator with Glu/Asp-rich carboxy-terminal domain family of transcriptional regulators and is exclusively localized in the nucleus. Previous studies have demonstrated that CITED2 plays an important role in cellular development and differentiation. Experimental murine studies have shown that Cited2 mutation or deficiency results in congenital heart and neural crest defects, impairment in the development of lung, liver, placenta, and adrenal tissue, and perturbation in the left-right patterning of the body axis. Previous studies have also show that CITED2 is predominantly expressed in murine and human macrophages. Myeloid-specific CITED2 deficient mice are highly susceptible to lipopolysaccharide (LPS)-induced endotoxic shock syndrome, zymosan-induced lung inflammation, and experimental atherogenesis. Mechanistically,  CITED2 in cooperation with PPARγ promotes anti-inflammatory gene expression while suppressing NFκB, HIF1α, STAT1, and IRF1 signaling to attenuate pro-inflammatory gene expression in macrophages.

overall_design: The bone marrow derived macrophges were obtained from Lyz2cre and Lyz2cre:CITED2Fl/Fl mice (n=3). Total RNA samples derived from these BMDMs were subjected to RNAseq analyses.

first: Ganapati

last: Mahabeleshwar

first: E


title: Cancer Cells Resistant to Immune Checkpoint Blockade Acquire Interferon-Associated Epigenetic Memory to Sustain T Cell Dysfunction (CUTNRUN)

city: Philadelphia

first: Kathryn

last: Tsai

state: PA

address: 421 Curie Blvd

department: Radiation Oncology

institute: University of Pennsylvania

summary:
We show that across human and/or mouse tumors immune dysfunction is associated with cancer cells acquiring epigenetic features of inflammatory memory.
Here, inflammatory memory domains, many of which are initiated by chronic IFNG, are established by STAT1 and IRF3 and link H3K4me1-marked chromatin accessibility to increased expression of a subset of IFN-stimulated genes (ISGs).

overall_design: CUTNRUN

first: Bihui

first: Jingya

last: Qiu


title: Cancer Cells Resistant to Immune Checkpoint Blockade Acquire Interferon-Associated Epigenetic Memory to Sustain T Cell Dysfunction

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

overall_design: Refer to individual Series


title: Cancer Cells Resistant to Immune Checkpoint Blockade Acquire Interferon-Associated Epigenetic Memory to Sustain T Cell Dysfunction (ATAC-Seq I)

overall_design: ATAC-Seq


title: DNA Promoter Hypermethylation of Melanocyte Lineage Genes Determines Melanoma Phenotype

city: Lund

first: Martin

last: Lauss

address: Barngatan 2B

department: Dept of Oncology

country: Sweden

institute: Lund University

summary: Cellular stress contributes to the capacity of melanoma cells to undergo phenotype switching into highly migratory and drug tolerant dedifferentiated states. Such dedifferentiated melanoma cell states are marked by loss of melanocyte specific gene expression and increase of mesenchymal markers. Two crucial transcription factors, MITF and SOX10, important in melanoma development and progression have been implicated in this process. In this study we describe that loss of MITF is associated with a distinct transcriptional program, MITF promoter hypermethylation and poor patient survival in metastatic melanoma. From a comprehensive collection of melanoma cell lines, we observed that MITF methylated cultures were subdivided in two distinct subtypes. Examining mRNA levels of neural crest associated genes we found that one subtype had lost the expression of several lineage genes including SOX10. Intriguingly, SOX10 loss was associated with SOX10 gene promoter hypermethylation and distinct phenotypic and metastatic properties. Depletion of SOX10 in MITF methylated melanoma cells using CRISPR/Cas9 confirmed these findings. In conclusion, this study describes the significance of melanoma state and the underlying functional properties explaining the aggressiveness of such states.

overall_design:
RNAseq of 86 melanoma cell lines and three cultures of human epidermal melanocytes.
The authors state "due to Swedish law, the patient consent, and the risk that the sequencing data contains personally-identifiable information and hereditary mutations, we cannot deposit the short sequencing read data in a repository."

first: Katja

last: Harbst

first: Göran

last: Jönsson


title: Cancer Cells Resistant to Immune Checkpoint Blockade Acquire Interferon-Associated Epigenetic Memory to Sustain T Cell Dysfunction (ATAC-Seq II)


title: Elongation factor-specific capture of RNA polymerase II complexes

city: London

first: Richard

middle: James

last: Mitter

state: LONDON

address: 1 Midland Road

department: Bioinformatics & Biostatistics

country: United Kingdom

institute: The Francis Crick Institute

summary: Transcription of protein-coding genes is regulated by dynamic association of co-factors with RNA polymerase II (RNAPII). The function of these factors and their relationship with RNAPII is often poorly understood. Here, we present an approach for elongation factor-specific mNET capture (EMCAP) of RNA polymerase II complexes for sequencing and mass spectrometry analysis, for investigating the function of such RNAPII regulatory proteins. As proof of principle, we apply EMCAP to the RNAPII-associated proteins SCAF4 and SCAF8, which share an essential role as mRNA anti-terminators but have individual roles at the 3’end of genes. Mass spectrometry analysis shows that both SCAF4 and SCAF8 are part of RNAPII elongation complexes containing 3’end processing factors but depleted of splicing components. Importantly, the EMCAP-seq profiles of SCAF4- and SCAF8-RNAPII complexes reflect their function as mRNA-anti-terminators and their competing functions at the end of genes where they prevent or promote transcriptional readthrough.

overall_design: Comparison of mammalian native transcript elongation (mNET) capture of RNA polymerase II complexes associated with SCAF4 and SCAF8 in HEK293 cells.

first: Lea

last: Gregersen

first: Jesper

middle: Q

last: Svejstrup


title: Unique expression profile for type-I, -II, and -III IFNs regarding epithelial reorganization in primary epithelial cells

city: Munich

first: Anna

last: Erb

address: Biedersteinerstr 29

department: Zentrum für Allergie und Umwelt

country: Germany

institute: Klinikum Rechts der Isar

summary: We provide evidence that the type-I, -II and -III IFNs induced differentially expressed genes associated with inflammation and epithelial remodeling. Besides their overlapping induced interferon stimulated genes, all IFN family members enhanced the antiviral host intrinsic defence mechanisms by increasing epithelial integrity.

overall_design: Primary differentiated organotypic 3D air-liquid interphase cultures were incubated with IFNa (300 IU/ml), IFNb (100 IU/ml), IFNg (200IU/ml), IFNL1 (100 ng/ml), IFNL3 (100 ng/ml)

first: A

first: U

last: Zissler

first: M

last: Oelsner

last: Chaker

first: C

last: Schmidt

last: Jakwerth


title: Single cell RNA-sequencing reveals distinct cardiac-derived stromal cell subpopulations

city: Atlanta

first: Michael

last: Davis

state: GA

address: 2015 Uppergate Dr

institute: Emory University

summary: Comparison of neonate- vs. child-derived cardiac c-kit+ stromal cell (CSC) from congenital heart disease patients

overall_design: single cell RNA sequencing

first: Jessica

last: Hoffman

first: Arun

last: Jayaraman

first: Micahel

middle: E


title: SALL4 Occupany in mESCs by Cut & Run

city: Minneapolis

first: Micah

last: Gearhart

state: MN

address: 6-160 Jackson Hall, 321 Church St.

department: Genetics, Cell Biology and Development

institute: University of Minnesota

summary: High confidence SALL4 targets were identified in mESCs by performing Cut&Run on SALL4 Flox/Flox and SALL4 -/- cells.  We validated a commercially available antibody that specifically recognizes SALL4 protein.

overall_design: SALL4 and IgG Cut & Run experiments in SALL4 Flox/Flox aand SALL4 -/- mESC cells, in duplicate.

first: Yasuhiko

last: Kawakami


title: Transcriptome analysis reveals that jasmonic acid biosynthesis and signaling is associated with the biosynthesis of asperosaponin VI in Dipsacus asperoides

city: Guiyang

first: Jiao

last: Xu

address: Dongqing South Road, Huaxi District

institute: Guizhou University of traditonal Chinese Medicine

summary: In present study, Transcriptome analysis revealed  unique differentially expressed genes (DEGs). including  transcription factors (TFs), during root development in D. asperoides. In addition, α-linolenic acid metabolism, jasmonic acid (JA) biosynthesis, JA signal transduction, sesquiterpenoid and triterpenoid biosynthesis, and terpenoid backbone biosynthesis were prominently enriched.

overall_design: The roots of one-leaf stage (L1), two-leaf stage (L2), and plants that had been growing for 7 months (M7)


title: Gene expression of differentiated human induced pluripotent stem cells

city: Boston

first: Johan

last: Spetz

state: MA

address: HSPH2, Room 229, 655 Huntington Ave.

department: JBL Center for Radiation Sciences

institute: Harvard School of Public Health

summary: Gene expression of Human DiPS 1016 SeVA iPSCs and hiPSCs-differentiated into endothelial, vascular smooth muscle or white adipose tissue cells.

overall_design: RNA was extracted from Human DiPS 1016 SeVA iPSCs and hiPSCs-differentiated into endothelial, vascular smooth muscle or white adipose tissue cells using the QIAcube and the RNeasy Plus Mini Kit (QIAGEN). RNA quality was ascertained with the TapeStation (Agilent), and only samples with a RIN>9.0 value were used for sequencing. Sequencing libraries were made with the PrepX DNA library kit (Takara bio) using the Apollo system (Takara bio). Quality control for the libraries was performed using the KAPA library quantification kit (Roche) and the TapeStation (Agilent). Sequencing libraries were barcoded, pooled and sequenced on a HiSeq 2500 (Illumina) with single-end 150bp reads. Sequencing output was de-multiplexed, barcodes removed, trimmed for quality, and FastQC was run on all files for quality control. Reads were aligned to human genome assembly GRCh38 using STAR76.

first: Mary

last: Florido

first: Cameron

middle: S

last: Fraser

first: Xingping

last: Qin

first: Stacey

middle: J

last: Yu

first: Rumani

last: Singh

first: Max

last: Friesen

first: Chad

middle: A

last: Cowan

first: Lee

last: Rubin

first: Joe

last: Salem

first: Javid

last: Moslehi

first: Kristopher

last: Sarosiek


title: scRNA-Seq datasets profiling peripheral leukocyte response when co-cultured with fibroblasts isolated from reindeer back skin or antler velvet.

city: Calgary

first: Jeff

last: Biernaskie

state: Alberta

address: 3330 Hospital Drive NW

department: Comparative Biology and Experimental Medicine

institute: University of Calgary

summary: In adult mammals, skin wound healing has evolved to favor rapid repair through the formation of fibrotic scar. These dermal scars are dysfunctional and may lead to chronic disfigurement and disability, yet the biologic mechanisms that drive fibrosis and prevent tissue regeneration remain unknown. Here, we report that reindeer (Rangifer tarandus) antler velvet exhibits regenerative wound healing, whereas identical full-thickness injury in dorsal back skin of the same animal forms fibrotic scar. This regenerative capacity is retained even following ectopic transplantation of velvet to a scar-forming site, demonstrating that this latent regenerative capacity is innate to velvet cells and independent of local factors derived from the growing antler. Single cell RNA-sequencing of uninjured skin revealed a marked divergence in resting fibroblast transcriptional states and immunomodulatory function. Uninjured velvet fibroblast shared a striking resemblance with human fetal fibroblasts whereas uninjured back skin fibroblasts exhibited an overrepresentation of pro-inflammatory genes resembling adult human fibroblasts. Identical skin injury resulted in site-specific fibroblast polarization; back fibroblasts exacerbated the inflammatory response, whereas velvet fibroblasts adopted an immunosuppressive state and reverted back to a regeneration-competent ground state. Consequently, velvet wounds exhibited an accelerated adoption of anti-inflammatory immune states and an expedited resolution of immune response. This study demonstrates reindeer as a novel comparative mammalian model to study both adult skin regeneration (velvet) and scar formation (back skin) within the same animal. Our study underscores the importance of fibroblast heterogeneity in shaping local immune cell functions that ultimately polarize wound healing outcomes. Purposeful, acute modulation of fibroblast-mediated immune signaling represents an important therapeutic avenue to mitigate scar and improve wound healing.

overall_design: Whole blood was collected 3 days post-wound from venous blood supply into EDTA tubes. Blood was spun at 300g for 10 mins and plasma was removed and stored at -80oC. Buffy coat was collected, and red blood cells were lysed with ACK buffer (1:10 ACK to blood cells) for 5 minutes and then spun at 300g for 5min and then supernatant.  To liberate fibroblasts from reindeer back skin and velvet, either a 12mm circular biopsy punches (velvet) or an elliptical skin excision (back skin) was collected and dissociated to single cells by mincing the skin into 1–2 mm pieces using a pair of scalpels. Minced tissue was first submerged in dispase (2 mg/ml at 37°C for 10 minutes, Stem Cell Technologies) to remove epidermis and then in collagenase type IV (2 mg/ml at 37 for 1-3 hours with mechanical trituration at set intervals, Sigma) to digest the dermal extracellular matrix. Dissociated cell suspensions were passed through 100μm and then 70μm cell strainers, centrifuged at 1200rpm for 6 minutes to pellet the liberated cells, and resuspended in complete fibroblast culture media (DMEM + 10%FBS, 5mL of L-glutamine, penicillin-streptomycin). Fibroblasts were expanded for three days in a 37 °C 5% CO2 tissue culture incubator prior to initiating co-culture with circulating immune cells. Following co-culture incubation, immune cells cells were resuspended in 2% BSA in PBS at a final concentration prior to loading into the 10X controller. All samples were processed according to 10X Genomics ChromiumTM Single Cell 3’ Reagent Guidelines NextGEM Chemistry as per the manufacturer’s protocol. In brief, cells were partitioned into Gel Bead-In-EMulsions (GEMs) using 10xTM GemCodeTM Technology. This process lysed cells and enabled barcoded reverse transcription of RNA, generating full-length cDNA from poly-adenylated mRNA. DynaBeads® MyOneTM Silane magnetic beads were used to remove leftover biochemical reagents, then cDNA was amplified by PCR. Quality control size gating was used to select cDNA amplicon size prior to library construction. Read 1 primer sequences were added to cDNA during GEM incubation. D11 primers, D12 and C12  primers, i7 sample index, and Read 2 primer sequences were added during library construction. Quality control and cDNA quantification was performed using DTape station 1000. Sequencing was performed using Illumina NovaSeq with an S2 flow cell.

first: Sarthak

last: Sinha

first: Holly

last: Sparks

first: Hayley

last: Robbins

first: Kevin

last: Gowing

first: Arzina

last: Jaffer

first: Rohit

last: Arora

first: Sam

last: Raredon

first: Leslie

last: Cao

first: Scott

last: Swanson

first: Peng

last: Jiang

first: Olivia

last: Hee

first: Hanna

last: Pope

first: Elodie

last: Labit

first: Matt

last: Workentine

first: Laura

last: Niklason

first: Nicole

last: Rosin

first: Greg

last: Muench

first: Ron

last: Stewart

first: John

last: Matyas

first: Robert

last: McCorkell


title: Single-cell profiling of ectopic velvet grafts transplanted onto non-regenerative backskin to assess whether regenerative propensity is intrinsic to reindeer velvet

first: Jeff

last: Biernaskie

summary: We have previously described the reindeer antler velvet as a highly unique mammalian model of adult skin regeneration as wounds on backskin form a raised, contractile scar devoid of appendages or pigment, whereas identical wounds in antler velvet exhibit scar-less regeneration. To ask whether regenerative capacity is inherent to cells within the velvet (and not due to factors derived from the antler environment), we transplanted full thickness velvet skin grafts onto dorsal backskin. This scRNA-Seq sample profiles cells within the ectopic velvet graft to assess their molecular resemblance to regenerative velvet or non-regenerative dorsal backskin.

overall_design: To examine if the ability to regenerate skin is intrinsic to antler velvet, we performed autologous grafting to relocate a full thickness antler velvet graft to a non-regenerative location on the animal’s back. As is expected following full-thickness skin grafting, grafts were observed to slough the epidermis and reveal the unpigmented dermal tissue to be well-integrated into the graft bed. Four weeks after grafting, the animals were again anesthetized and staples/sutures removed. The graft was then harvested with an 8mm biopsy punch to remove a full thickness piece of skin. To investigate whether ectopic velvet grafts retained regenerative function, we isolated single-cells from the 8mm biopsy punch and processed according to 10X Genomics Chromium Single Cell 3’ Reagent Guidelines v3 Chemistry as per the manufacturer’s protocol. In brief, single cells were sorted based on forward versus side scatter gating into 0.1% BSA–PBS and partitioned into Gel Bead-In-EMulsions (GEMs) using 10x GemCodeTM Technology. Next-Generation Sequencing was performed using the Illumina NovaSeq S2 Flow cells. All raw FASTQs were aligned to the bovine (Bos taurus) reference genome generated using cellranger mkref pipeline. The resulting gene barcode matrix was processed using Seurat (v3.1.1) R toolkit.

first: Sarthak

last: Sinha

first: Holly

last: Sparks

last: McCorkel


title: NIK/MAP3K14 in hepatocytes orchestrates NASH to hepatocellular carcinoma progression via JAK2/STAT5 inhibition

city: Baltimore

first: Supriyo

last: De

state: Maryland

address: 251 Bayview Blvd

department: Laboratory of Genetics and Genomics

institute: NIA-IRP, NIH

summary: Nonalcoholic fatty liver disease (NAFLD) ranges from steatosis to nonalcoholic steatohepatitis (NASH), that often progresses to hepatocellular carcinoma (HCC) through a largely undefined mechanism. NASH and HCC both depend on inflammatory signaling whose master regulator is the NFκB transcription factor family, activated by canonical and non-canonical pathways. Here, we investigated non-canonical NFκB-inducing kinase (NIK/MAP3K14) in metabolic NASH, NASH to HCC transition as well as in DEN-induced HCC. We revealed that hepatocyte-specific NIK deficiency (NIKLKO) ameliorated metabolic NASH complications and reduced hepatocarcinogenesis however, independent of its role in NFB pathway. Instead, hepatic NIK attenuated hepatoprotective JAK2/STAT5 signaling that is a prerequisite for NASH and NASH to HCC progression in mice and humans. Our data suggest NIK-mediated inhibitory JAK2 phosphorylation at serine 633 that might be amenable for future therapeutic interventions in patients.

overall_design: Five non-tumor and five tumor biopsy samples were obtained and their transcriptional profiles compared.

first: Anna

last: Vesting

first: Alexander

last: Jais

first: Paul

last: Klemm

first: Lukas

last: Steuernagel

first: Peter

last: Wienand

first: Morten

last: Fog-Tonnesen

first: Henning

last: Hvid

first: Anna-Lena

first: Christian

last: Kukat

first: Hendrik

last: Nolte

first: Theodoros

last: Georgomanolis

first: Janine

last: Pasparakis

first: Manolis

first: Andreas

last: Schmidt

first: Marcus

last: Krüger

first: Marc

last: Supprian

first: Ari

last: Waisman

first: Beate

last: Straub

first: Nathanael

last: Raschzok

first: Michel

last: Bernier

last: Birkenfeld

first: Nadine

last: Hövelmeyer

first: Jens

middle: C

last: Brüning

first: F

middle: T

last: Wunderlich


title: PML nuclear bodies form a regulatory hub via liquid-liquid phase separation for TRIM33 control of Lefty1/2 genes in mouse embryonic stem cells [RNA-seq]

city: Beijing

first: Hongyao

last: Sun

address: Tsinghua street

institute: Tsinghua university

summary: TRIM33 is a chromatin reader required for nodal signaling during mesendoderm differentiation, although differences in its function between mouse embryonic stem cells (mESCs) and differentiated mesendoderm cells are unknown. Here, we found that TRIM33 co-condenses with PML nuclear bodies (NBs) via liquid-liquid phase separation specifically in mESCs to mediate nodal signaling-directed transcription of Lefty1/2. Our findings show that TRIM33 puncta formation depends on the presence of PML NBs. TurboID proximity labeling further revealed that PML NBs recruit distinct sets of client proteins in NaAsO2-treated, untreated mESCs, and differentiated cells. TRIM33 and PML co-regulate Lefty1/2 expression, while PML NBs directly associate with the Lefty1/2 loci and  regulate a gene cluster that includes Lefty1/2 loci specifically in mESCs. Moreover, TRIM33 association with chromatin depends on PML NBs. Thus, PML NBs serve as a hub for transcriptional regulation of Lefty1/2 by TRIM33 and other pluripotency factors in mESCs.

overall_design: ESCs were cultured on gelatin coated plates with 15% serum ESC culture medium. mESCs untreated/treated with sodium arsenite treated (200 μM), activin A (50 ng/ml) or SB431542 (10 μM)  for 2h were harvested for RNA-seq

first: Yutong

last: Chen

first: Kun

last: Yan

first: Yanqiu

last: Shao

first: Qiangfeng

last: Zhang

first: Yi

last: Lin

first: Qiaoran

last: Xi


title: Recruitment of TRIM33 to cell-context specific PML nuclear bodies regulates Nodal signaling in mESCs

summary: TRIM33 is a chromatin reader required for mesendoderm differentiation upon activation of Nodal signaling. But, its role in mESCs is still elusive. Here, we found that TRIM33 co-localizes with promyelocytic leukemia nuclear bodies (PML NBs) specifically in mESCs to mediate Nodal signaling-directed transcription of Lefty1/2. We showed that TRIM33 puncta formation in mESCs depends on PML and specific assembly of PML NBs. Moreover, TRIM33 and PML co-regulate Lefty1/2 expression in mESCs. In addition, both PML and mESCs-specific PML NBs are required for TRIM33 recruitment at Lefty1/2 loci. Remarkably, PML NBs directly associate with the Lefty1/2 loci in mESCs. Finally, a TurboID proximity labeling experiment confirmed that TRIM33 is highly enriched in the mESCs-specific PML NBs. Thus, our study provides the mechanistic insight about TRIM33 condensate in regulating Nodal signaling-directed transcription in mESCs, it also reveals that PML NBs recruit distinct sets of client proteins in cell context dependent manner.

overall_design: ChIP was performed as previously described (Wang et al., 2017; Xi et al., 2011). CUT&TAG was performed with Hieff NGS Fast Tagment DNA Library Prep Kit for Illumina kit as manufacture protocol described. Illumina sequencing was performed after ChIP or CUT&TAG experiment.


title: Age-associated downregulation of glutamate and GABA neurotransmission-related gene expression in the rostral ventrolateral medulla of male Fischer 344 rats

status: Public on Dec 07 2022

city: El Paso

first: Sivasai

last: Balivada

state: Texas

address: 4th floor, Bioscience research building

institute: University of Texas at El Paso

summary: The rostral ventrolateral medulla (RVLM), a part of the medullary reticular formation, plays a major role in several physiological responses, including cardiovascular and sympathetic nervous system functions. Although aging causes disturbances in the responses of these physiological systems, RVLM involvement in these age-related changes is not clear. Previous work using high-throughput gene expression analysis of the RVLM in aged animals suggested that chemical neurotransmission-related genes might be downregulated with advancing age. Since the RVLM function involves a balance of inhibitory and excitatory inputs, which is largely mediated by gamma-aminobutyric acid (GABA) and excitatory amino acid (EAA) neurotransmission, we hypothesized that aging is associated with altered excitatory and/or inhibitory neurotransmission-related gene expression in the RVLM. To test this hypothesis, we micropunched an RVLM-containing area from young (3–5 months), middle-aged (12–14 months), and aged (22–26 months) Fischer 344 male rats. RNA purified from these micropunches was analyzed using GABA and Glutamate RT2 Profiler PCR arrays (n= 8–10). In addition, the expression of selected genes was validated at the RNA level using TaqMan® based- qPCR and at the protein level using western blotting. All the genes that displayed significant differential expression (1.5-fold, p < .05, FDR < .05) were identified to be downregulated in the RVLM of aged and middle-aged rats compared to young rats. Among the downregulated genes, the percentage of glutamate neurotransmission-related genes was higher than GABA neurotransmission-related genes. Solute carrier family 1 member 6 (Slc1a6) gene showed the highest fold downregulation at the RNA level in the RVLM of aged compared to young rats, and its protein product, Excitatory amino acid transporter 4 (EAAT4), showed a downregulatory trend in the RVLM of aged and middle-aged rats. These results suggest that molecular constituents of both GABA and glutamate neurotransmission might be altered in the RVLM of aged and middle-aged rats, and the changes in glutamate neurotransmission might be more prominent. Investigating age-associated anatomical and functional changes in RVLM GABA and glutamate neurotransmission might provide a foundation for understanding the effects of aging on physiological function.

overall_design: Rostral ventrolateral medulla (RVLM) containing lower brainstem area was micropunched from young (3–5 months, 304 ± 7 g, n=8), middle-aged (12–14 months, 425 ±  8 g, n=8), and aged (22–26 months, 432 ± 11 g, n=8) male Fischer 344 rats. RNA collected from these tissue punches was analyzed using Rat GABA & Glutamate RT2 Profiler PCR arrays (Qiagen, Inc., GeneGlobe ID PARN-152Z).

first: Geronimo

middle: P

last: Tapia

first: Hitesh

middle: N

last: Pawar

first: Arshad

last: Khan

first: Michael

last: Kenney


title: Transcriptome analysis of Control and STAT3 knockdown in HepG2 cell lines

city: Wuhan

first: zhang

last: Cheng

address: Huangjiahu

institute: Wuhan University of Science and Technology

summary: To investigate the effect of STAT3 knockdown on transcription, we constructed control and STAT3 knockdown HepG2 cell lines by shRNA. We then performed gene expression profiling using data obtained from RNA-seq.

overall_design: Gene expression differential display.

first: Zhang


title: Cancer Cells Resistant to Immune Checkpoint Blockade Acquire Interferon-Associated Epigenetic Memory to Sustain T Cell Dysfunction (RNA-Seq)

first: Kathryn

last: Tsai

overall_design: RNA-Seq

first: Bihui

last: Xu

first: Jingya

last: Qiu


title: Cytokines in the ApoE-/- mice atherosclerotic plaque

first: Xianda

address: No. 49, Huayuan Bei Road, Haidian District

department: Institute of Vascular Medicine

institute: Peking University Third Hospital

summary: To identify the dynamic changes of cytokines in the ApoE-/- mice atherosclerotic plaque, heart, and serum upon β-adrenergic stimulation (isoproterenol, 5 mg/kg body weight) at 0.5hrs, 1hrs, 3hrs and 24hrs using mouse cytokine antibody arrays.

overall_design: 45 samples. Male ApoE knockout mice (8 weeks of age, C57BL/6J background) fed a high fat diet containing 40 kcal% fat and 1.25% cholesterol (D12108C, Reaserch Diets, USA) for 2 weeks. Carotid collar placement was performed 2 weeks later to induce carotid artery plaque. After carotid collar placement and high-fat feeding for 3 months, mice were subcutaneously injected with a single dose of ISO (Sigma-Aldrich, St. Louis, MO, USA; 5 mg/kg body weight, as determined effective by dose-response preliminary experiments) or saline (10 mL/kg body weight).There are 9 groups: vehicle group, mice were subcutaneous injected with a single dose of saline (10 ml/kg body weight), ISO groups, mice were subcutaneous injected with a single dose of isoproterenol (5 mg/kg body weight) after 0.5hrs, 1hrs, 3hrs and 24hrs (vessel, heart and plasma groups by different pionts)

first: Han

last: Xiao


title: Transcriptomics of colorectal cancer in Siriraj cohort, Thailand (NanoString)

city: Bangkok-noi

first: Chandhanarat

last: Chandhanayingyong

state: Bangkok

address: 2 Wanglang road

department: Orthopaedic Surgery

country: Thailand

institute: Mahidol University

summary: To investigate the transcriptomes in colorectal cancer patients, who were diagnosed and treated at Siriraj Hospital, Thailand, we performed gene expression profiling analysis using data obtained from RNA-seq and Nanostring platforms.

overall_design: Total RNA was extracted from primary colorectal cancer tissues for comparative gene expression profiling analysis using RNA-seq and Nanostring platforms and then classifying consensus molecular subtypes.

first: Vitoon

last: Chinswangwatanakul

first: Pariyada

last: Tanjak

first: Amphun

last: Chaiboonchoe


title: PML nuclear bodies form a regulatory hub via liquid-liquid phase separation for TRIM33 control of Lefty1/2 genes in mouse embryonic stem cells [CHIP-seq]

first: Hongyao

last: Sun

overall_design: TRIM33-ChIP-seq using GFP-trap experiments profiling TRIM33 chromatin association in GFP-TRIM33 mESCs. PML, SMAD2/3 and H3K27ac ChIP-seq using cut&tag method experiments profiling PML, SMAD2/3 and H3K27ac chromatin association in PML-KO or WT mESCs.

first: Yutong

last: Chen

first: Kun

last: Yan

first: Yanqiu

last: Shao

first: Qiangfeng

last: Zhang

first: Yi

first: Qiaoran


title: NR5A2 bridges zygotic genome activation to lineage segregation in early mouse development

first: Bofeng

last: Liu

address: Haidian District

department: School of Life Science

institute: Tsinghua University

summary: After fertilization, zygotic genome activation (ZGA) enables the conversion of two terminally differentiated gametes to a totipotent embryo. Zygotes further give rise to the pluripotent embryonic lineages and extraembryonic trophectoderm after the first lineage commitment. While much is learned for pluripotency regulation, how ZGA is connected to the pluripotency commitment in early embryos remains unclear. Here, we investigated the role of nuclear receptor (NR) family TFs in mouse pre-implantation embryos, whose motifs are highly enriched in accessible chromatin at the 2-cell (2C) to 8-cell (8C) stages. We found NR5A2 is required for the early development, as both knockdown and knockout of Nr5a2 led to morula arrest. 4-8C activated genes (mid-preimplantation activation), including key pluripotency marker genes (i.e. Nanog, Pou5f1, and Tdgf1) and trophectoderm genes (i.e. Klf5, Elf3, and Gata3). Genome-wide chromatin binding and RNA-seq analyses showed NR5A2 bound and regulated the 4-8C genes, including both ICM and TE genes in 2C and 8C embryos , indicating its roles in bipotency program. Interestingly, NR5A2 occupied sites predominantly reside in accessible B1 elements where its motif is embedded at the 2-8C stage. Taken together, these data demonstrate the role of NR5A2 as a key regulator that bridges ZGA to lineage segregation.

overall_design: CUT&RUN, RNA-seq, and ATAC-seq were applied on mouse pre-implantation embryos and cell lines.

first: Fangnong

last: Lai

first: Lijia

last: Li

first: Xiaoyu

last: Hu

first: Wei

last: Xie


title: Comprehensive Transcriptome Analysis of Different Skin Colors to Evaluate Genes Related to the Formation of Pigment in Celestial Goldfish

first: Bo

address: No. 2 Yuanmingyuan West Road, College Animal Science & Technology, China Agriculture University, Beijing

institute: China Agricultural University

summary: the current study paints a thorough transcriptome profiles of different skin color groups (white, yellow and brown) in celestial goldfish, and several candidate genes were selected as important functional genes involved in the color variation

overall_design: In this study, high-throughput RNA sequencing was carried out on the back skin tissues of celestial goldfish with different skin colors(brown,yellow and white).

first: Rongni

first: Ran

last: Cui

first: Xin


title: Gene expression profile at single cell level of the cerebral cortex at different sleep need

city: Tsukuba

first: Kanako

last: Iwasaki

state: Ibaraki

address: Tennodai 1-1-1

institute: WPI-IIIS, University of Tsukuba

summary: Gene expression profile varies along with sleep/wake behavior. We used single nucleus RNA sequencing (snRNA-seq) to analyze differentially expressed genes depending on sleep need.

overall_design: The primary motor cortex of ad lib sleep slept or sleep deprived mice, and the same brain region locally administrated with AAV expressing wild-type or gein-of-function-mutated SIK3 were analyzed using snRNA-seq.

first: Staci

last: Kim

first: Noriko

last: Hotta-Hirashima

first: Fuyuki

last: Asano

first: Tomohiro

last: Kitazono

first: Shinya

last: Nakata

first: Nodoka

last: Asama

first: Haruna

last: Komiya

first: Hiromasa

last: Funato

first: Masashi

last: Yanagisawa


title: Anthocyanin-rich extract from black beans exert anti-diabetic effects in rats through multi-genomic mode of action in adipose tissue

city: Kannapolis

first: Dragan

last: Milenkovic

state: NC

address: 600 Laureate Way

department: Department of Food Bioprocessing & Nutrition Sciences

institute: North Carolina State University

summary:
The aim of this study was to investigate multi-genomic effects of BB consumption and identify regulatory networks potentially mediating T2DM on AT
Male Wistar diabetic rats consumed an anthocyanin-rich black bean extract for 5 weeks. Global gene expression from AT, including protein coding and non-coding RNA profiles was determined using RNAseq. Biological function analyses were performed using integrated bioinformatic tools.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for adipose tissue of rat: healthy, diabetic and diabetic+bean extract

first: Karla

last: Damián-Medina


title: Comparative transcriptome analysis reveals the Sclerotinia sclerotiorum resistance mechanism in sunflower

city: Shenyang

first: Mingzhu

last: Zhao

state: Liaoning

address: Dongling Roat

department: Institute of Crop Research

institute: Liaoning Academy of Agricultural Sciences

summary:
Background: Sclerotinia sclerotiorum is one of the most severe fungus diseases in many important crops including sunflower (Helianthus annuus) worldwide. Breeding the resistant varieties are the best strategy to control S. sclerotiorum, however, the molecular regulatory mechanisms of sunflower in response to S. sclerotiorum remain poorly understood.
Methods: We performed a leaf transcriptomic analysis to understand the differential defense response to S. sclerotiorum in a disease resistant (DR) genotype and a disease susceptible (DS) genotype of sunflower 24 h post-inoculation.
Results: A total of 7439 and 10151 differentially expressed genes (DEGs) were identified in DR and DS genotypes, respectively suggesting that the former is less affected by S. sclerotiorum infection. Pathway analysis revealed that response to S. sclerotiorum was mostly enriched in the DEGs that are involved in the cell wall, redox homeostasis, immune response, protein kinase activity, hormone, transcription factor activities as well as secondary metabolism. The magnitude of expression changes in a set of genes encoding expansins, pectate lyase activities, antioxidant activity and ethylene following S. sclerotiorum infection likely contributed to the different resistance levels of these two genotypes. One gene encoding effector receptor NLR revealing significant opposite expression pattern between DR and DS genotypes along with three hub-genes CDPK9, MAPK5, CML23 by protein-protein interaction (PPI) network analysis were considered as the most possible candidate genes.
Conclusion: Our results provide in-depth insights into the molecular mechanisms associated with sunflower defense responses against S. sclerotiorum that will be of great utility in Sclerotinia-resistance breeding.

first: Jingang

last: Liu


title: Role of pericytes in the development of cerebral cavernous malformations

city: Harbin

first: zifeng

last: dai

state: Heilongjiang province

address: 23 Youzheng Street, Nangang District

department: Neurosurgery

institute: First Affiliated Hospital of Harbin Medical University

summary: Cerebral cavernous malformation (CCM) is caused by loss-of-function mutations in CCM1, CCM2, or CCM3 genes of endothelial cells. It is characterized by pericyte deficiency. However, the role of pericytes in CCMs remains poorly understood. Our study showed that pericytes in Cdh5CreERT2; Ccm1fl/fl (Ccm1ECKO) mice were high expression of PDGFRβ. The inhibition of pericyte function by CP-673451 aggravated the CCM lesion development. RNA-seq analysis revealed the molecular traits of pericytes, such as highly expressed ECM-related genes, especially Fn1. Furthermore, KLF4 coupled with phosphorylated SMAD3 promoted the transcription of fibronectin in pericytes of CCM lesions. RGDS peptide, an inhibitor of fibronectin, decreased the lesion area in the cerebella and retinas of Ccm1ECKO mice. Also, human CCM lesions had abundant fibronectin deposition, and pSMAD3- and KLF4-positive pericytes. The current data demonstrated that pericytes are essential for CCM lesion development, and fibronectin intervention may provide a novel target for therapeutic intervention in such patients.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for pericytes purified from Ccm1fl/fl mice and Cdh5Cre/+ERT2;Ccm1fl/fl mice treated by 4-hydroxy-tamoxifen. Three independent biological replicates were used for the analysis.

first: Z

middle: F

last: Dai

first: C

middle: B

last: Shi


title: The relationship between the aberrant long non-coding RNA-mediated competitive endogenous RNA network and Alzheimer's disease pathogenesis

first: Zhongdi

last: Cai

state: Beijing

address: Institute of Medicinal Biotechnology, No.2 Tiantan Xili, Dongcheng District, Beijing

institute: Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College

summary: In this research, we investigated the abnormal expression of lncRNA and established lncRNA-associated ceRNA regulatory networks composed of potential therapeutic targets in AD based on RNA sequencing (RNA-seq) analysis and experimental verification. RNA-seq was performed in the cerebral cortex and hippocampus of 5×FAD mice of AD to systematically investigate altered lncRNA-associated ceRNA regulatory network, along with qualitative analyses for key differentially expressed lncRNAs, miRNAs, and mRNAs involved. The results showed that 7 lncRNAs were significantly altered in the cortex and hippocampus of 5×FAD mice compared with WT mice. The potential functions of differentially expressed genes were highly correlated with learning and memory activities and the pathogenesis of AD. Furthermore, lncRNA Xist and highly correlated miRNAs and mRNAs were identified as key mediators of pathophysiological processes in AD. Our findings illustrated the AD-derived lncRNA-mediated ceRNA network, accompanied by aberrant expression involved in the pathological gene networks, which may contribute to understanding the pathological mechanism of AD and provide potential therapeutic targets for drug development.

overall_design: Three 7-month-old 5 × FAD mice of C57BL/6J genetic background and their non-transgenic mice (WT mice) of the same month of age  were grouped. Each group consisted of two females and one male (n = 3 per group). The cerebral cortex and hippocampus were taken from each mouse, for a total of 12 samples.

first: Li

last: Zeng

first: Mimin

first: Kaiyue

first: Ting

last: Sun

first: Zhuorong

last: Li

first: Rui


title: Ethanol withdrawal-induced adaptations in prefrontal corticotropin releasing factor receptor1-expressing neurons regulate anxiety and conditioned rewarding effects of ethanol

city: La Jolla

first: Alain

last: Domissy

state: CA

address: 10550 North Torrey Pines Road

department: Immunology

institute: The Scripps Research Institute

summary: Corticotropin-releasing factor and its cognate type-1 receptor, a prominent brain stress system, is implicated in anxiety and alcohol use disorder (AUD). We tested the hypothesis that medial prefrontal cortex CRF1-expressing (mPFCCRF1+) neurons comprise a distinct population that exhibits neuroadaptations following withdrawal from chronic ethanol that underlie AUD- related behavior. We found that mPFCCRF1+ neurons comprise a glutamatergic population with distinct electrophysiological properties and regulate anxiety and conditioned rewarding effects of ethanol. To gain mechanistic insight into these electrophysiological adaptations, we sequenced the transcriptome of mPFCCRF1+ neurons and found that withdrawal leads to an increase in colony-stimulating factor 1 (CSF1) in this population. We found that selective overexpression of CSF1 in mPFCCRF1+ neurons is sufficient to decrease glutamate transmission, heighten anxiety, and abolish ethanol reinforcement, providing mechanistic insight into the observed mPFCCRF1+ synaptic adaptations in withdrawal that drive these behavioral phenotypes. Together, these findings highlight mPFCCRF1+ neurons as a critical site of enduring adaptations that may contribute to the persistent vulnerability to ethanol misuse in abstinence, and CSF1 as a novel target for therapeutic intervention for withdrawal-related negative affect.

overall_design: rnaseq assay for 11 mice, 5 control and 6 ethanol treated animals.

first: Reesha

last: Patel

first: Dayne

middle: R

last: Mayfield

first: Marisa

last: Roberto


title: IkappaBzeta Controls IL-17-triggered Gene Expression Program in Intestinal Epithelial Cells that Prevents Expansion of SFB and Attenuates Autoimmune Disorders [ATAC-Seq]

city: Ota-ku

first: Soh

last: Yamazaki

state: Tokyo

address: 5-21-16 Omorinishi

department: Biohemistry

institute: Toho University School of Medicine

summary: Control of gut microbes is crucial for not only local defense in the intestine but also proper systemic immune responses.  Although intestinal epithelial cells (IECs) play important roles in cytokine-mediated control of enterobacteria, the underlying mechanisms are not fully understood.  Here we show that deletion of IkappaBzeta in IECs in mice leads to dysbiosis with marked expansion of segmented filamentous bacteria (SFB), thereby enhancing Th17 cell development and exacerbating autoimmune inflammatory diseases.  Mechanistically, the IkappaBzeta deficiency results in Paneth cell loss and impaired expression of IL-17-inducible genes involved in IgA production.  The Paneth cell loss is caused by aberrant activation of IFN-gamma signaling and a failure of IL-17-mediated recovery from IFN-gamma-induced damage.  Thus, the IL-17R–IkappaBzeta axis in IECs contributes to the maintenance of intestinal homeostasis by serving as a key component in a regulatory loop consisting of the gut microbiota and immune cells

overall_design: The jejuna of Nfkbizfl/flVil1-Cre and control mice were analyzed by ATAC-seq analysis.

first: Hiroyasu

last: Nakano