title: CRISPR/Cas9-mediated gene correction in newborn rabbits with hereditary tyrosinemia type I [DeepSeq2]

status: Public on Dec 31 2019

city: Guangzhou

first: Shixue

last: Gou

address: No. 190, Kaiyuan Avenue, Huangpu District, Guangzhou

institute: GUANGZHOU INSTITUTES OF BIOMEDICINE AND HEALTH,CHINESE ACADEMY OF SCIENCES

type: Genome variation profiling by high throughput sequencing

summary: Mutations in the metabolic enzyme fumarylacetoacetate hydrolase (FAH) cause hereditary tyrosinemia type I (HT1) in human. HT1 patients present acute and irreversible liver and kidney damage during infancy. CRISPR/Cas9-medated precise correction of disease-causing mutations in the liver of infant may provide a promising approach for the treatment of monogenetic liver metabolic disorders. However, to date, all previous precise gene therapy studies were conducted in adult HT1 rodent models (mice and rats), which are not able to recover irreversible pathological changes and result in less treatment effectiveness. In addition, rodent animals have very tiny livers comparing with that of humans, and HT1 rodent models do not authentically recapitulate some symptoms of human patients such as kidney damage. Therefore, to achieve the data which could be more translationable to medical practice of HT1 disease treatment by correcting gene mutation of hepatocytes, here, we chose a HT1 rabbit model, owning relatively large livers, and displaying liver and kidney damage as human patients, as the subject to test the gene therapy effectiveness starting from newborn stage. By delivery CRISPR/Cas9 system and donor templates to the livers by ear vein injection of adeno-associated virus (AAV), HT1 rabbits could be rescued the lethal phenotypes and were able to grow up to adult normally without NTBC treatment and give birth to offspring. In the livers of AAV-treated HT1 rabbits, both HDR-mediated and NHEJ-mediated gene corrections were occurred with the efficiencies ranged from 3.30% to 8.58%. Gene corrected HT1 rabbits showed normal structure and function of both livers and kidneys. This study in rabbits provides useful large-animal preclinical data to treat genetic metabolic disorders affecting the liver with gene therapy.

overall_design:
60 samples for High-throughput sequencing, including 10 sample as FA1# OT-2mis, 10 sample as FA2# OT-2mis#, 10 sample as FA3# OT-2mis#, 10 sample as WT1 OT-2mis, 10 sample as WT2 OT-2mis, and 10 sample as WT3 OT-2mis.
FA1# OT-2mis are the general designation of the 10 potential off-target sites (OTSs) with 2 bp mismatches for the gRNA we design in FA1#?FA1# is the serial numbers of an FAH mutation rabbits with CRISPR/Cas9-mediated gene correction.
FA2# OT-2mis are the general designation of the 10 potential off-target sites (OTSs) with 2 bp mismatches for the gRNA we design in FA2#?FA2# is the serial numbers of an FAH mutation rabbits with CRISPR/Cas9-mediated gene correction.
FA3# OT-2mis are the general designation of the 10 potential off-target sites (OTSs) with 2 bp mismatches for the gRNA we design in FA3#?FA3# is the serial numbers of an FAH mutation rabbits with CRISPR/Cas9-mediated gene correction.
WT1 OT-2mis are the general designation of the 10 potential off-target sites (OTSs) with 2 bp mismatches for the gRNA we design in the wildtype rabbits called WT1#.
WT2 OT-2mis are the general designation of the 10 potential off-target sites (OTSs) with 2 bp mismatches for the gRNA we design in the wildtype rabbits called WT2#.
WT3 OT-2mis are the general designation of the 10 potential off-target sites (OTSs) with 2 bp mismatches for the gRNA we design in the wildtype rabbits called WT3#.

last: Li

first: Jiaowei

first: Quanjun

last: Zhang

first: Jingke

last: Xie

first: Li

first: Qin

last: Jin

first: Ouyang

last: Zhen

first: Fangbing

first: Weikai

last: Ge

first: Hui

last: Shi

first: Yanhui

last: Liang

first: Huang

last: Xingyun

first: Zhenpeng

last: Zhuang

first: Xiaozhu

last: Zhao

first: Meng

last: Lian

first: Yinghua

last: Ye

first: Longquan

last: Quan

first: Han

last: Wu

first: Kepin

first: Liangxue

last: Lai


title: CRISPR/Cas9-mediated gene correction in newborn rabbits with hereditary tyrosinemia type I [DeepSeq1]

first: Shixue

last: Gou

country: China

overall_design:
18 samples for High-throughput sequencing, including 6 sample as FA1#, 6 sample as FA2#, and 6 sample as FA3#.
FA1 and FA2 are the serial numbers of two newborn FAH mutation rabbits with CRISPR/Cas9-mediated gene correction. Liver tissues in six positions of FA1 and FA2 were collected and numbered FA1#-L1-6 and FA2#-L1-6.

first: Jiaowei

last: Wang

first: Quanjun

first: Jingke

last: Chen


title: Two separate roles for the transcription coactivator SAGA and a set of genes redundantly regulated by TFIID and SAGA

status: Public on Jan 08 2020

city: Oklahoma City

first: Rafal

last: Donczew

state: OK

address: 825 NE 13th St

department: Cell Cycle and Cancer Biology

country: USA

institute: Oklahoma Medical Research Foundation

type: Expression profiling by high throughput sequencing

type: Genome binding/occupancy profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Major surgery induces acute changes in DNA methylation associated with immune response pathways

status: Public on Dec 24 2019

city: Exeter

first: Jonathan

last: Mill

address: Barrack Road

country: United Kingdom

institute: Complex Disease Epigenetics Group, University of Exeter Medical School

type: Methylation profiling by genome tiling array

summary: Using a longitudinal study design, we quantified DNA methylation across the genome in a cohort of 30 elderly patients (average age = 77.9 years (range 62-91)) undergoing major surgery (either elective colorectal surgery, elective hip replacement surgery, and emergency hip surgery following fracture). From each individual, detailed clinical blood measures were collected and DNA methylation was profiled using the Illumina Human Methylation 450 array (g450K arrayh) (Illumina Inc. San Diego, California) in DNA samples isolated from purified PBMCs collected at three time-points: i) immediately before surgery (baseline (BL)), ii) in the morning of post-operative day 1 (POD1) and iii) between post-operative day 4 and 7 (POD4/7) prior to discharge from hospital.

overall_design: Using a longitudinal study design, we quantified DNA methylation across the genome in a cohort of 30 elderly patients undergoing major surgery. DNA methylation was profiled using the Illumina Human Methylation 450 array.

first: Ryoichi

last: Sadahiro

first: Bridget

last: Knight

first: Ffion

last: James

first: Eilis

last: Hannon

first: John

last: Charity

first: Ian

middle: R

last: Daniels

first: Joe

last: Burrage

first: Olivia

last: Knox

first: Bethany

last: Crawford

first: Neil

middle: J

last: Smart


title: Transcriptome profiling of inflorescence stem tissues from Arabidopsis thaliana series 2

status: Public on Feb 10 2020

city: Heidelberg

first: Thomas

last: Greb

address: Im Neuenheimer Feld 360

department: Centre for Organismal Studies

country: Germany

institute: Heidelberg University

summary: We report the application of laser capture microdissection (LCM) for high resolution transcriptome profiling of the second internode of the Arabidopsis thaliana inflorescence stem. In this series, we used LCM to determine and compare the transcriptome profiles of the phloem cap, the pith, and the remaining vascular bundle area.

overall_design: mRNA profiles of the phloem cap, the pith and the remaining vascular bundle area in the Arabidopsis thaliana inflorescence stem was compared. 2 replicates for each sample type are provided.

first: Javier

last: Agusti

first: Virginie

last: Jouannet

first: Dongbo

last: Shi


title: 10x Genomics scRNA-seq from monocytes and macrophages

status: Public on Dec 20 2019

city: Boston

first: Nikolai

last: Slavov

state: MA

address: 360 Huntington Avenue

institute: Northeastern University

summary: The fate and physiology of individual cells are controlled by protein interactions. Yet, our ability to quantitatively analyze proteins in single cells has remained limited. To overcome this barrier, we developed SCoPE2. It lowers cost and hands-on time by introducing automated and miniaturized sample preparation while substantially increasing quantitative accuracy. These advances enabled us to analyze the emergence of cellular heterogeneity as homogeneous monocytes differentiated into macrophage-like cells in the absence of polarizing cytokines. SCoPE2 quantified over 2,700 proteins in 1,018 single monocytes and macrophages in ten days of instrument time, and the quantified proteins allowed us to discern single cells by cell type. Furthermore, the data uncovered a continuous gradient of proteome states for the macrophage-like cells, suggesting that macrophage heterogeneity may emerge even in the absence of polarizing cytokines. Parallel measurements of transcripts by 10x Genomics scRNA-seq suggest that SCoPE2 samples 20-fold more copies per gene, thus supporting quantification with improved count statistics. Joint analysis of the data indicated that most genes had similar responses at the protein and RNA levels, though the responses of hundreds of genes differed. Our methodology lays the foundation for automated and quantitative single-cell analysis of proteins by mass-spectrometry.

overall_design: Analysis of monocytes differentiating into macrophages


title: A MORC-driven transcriptional switch controls Toxoplasma developmental trajectories and sexual commitment

status: Public on Dec 21 2019

city: LA TRONCHE

first: Mohamed-ali

last: HAKIMI

state: Grenoble

address: Domaine de la Merci, Campus Santé

country: France

institute: CNRS

summary: Toxoplasma gondii has a complex life cycle that is typified by asexual development that takes place in vertebrates, and sexual reproduction, which occurs exclusively in felids and is therefore less studied. The developmental transitions rely on changes in the patterns of gene expression, and recent studies have assigned roles for chromatin shapers, including histone modifications, in establishing specific epigenetic programs for each given stage. Here, we identified the T. gondii microrchidia (MORC) protein as an upstream transcriptional repressor of sexual commitment. MORC, in a complex with Apetala 2 (AP2) transcription factors, was shown to recruit the histone deacetylase HDAC3, thereby impeding the accessibility of chromatin at the genes that are exclusively expressed during sexual stages. We found that MORC-depleted cells underwent marked transcriptional changes, resulting in the expression of a specific repertoire of genes, and revealing a shift from asexual proliferation to sexual differentiation. MORC acts as a master regulator that directs the hierarchical expression of secondary AP2 transcription factors, and these transcription factors potentially contribute to the unidirectionality of the life cycle. Thus, MORC plays a cardinal role in the T. gondii life cycle, and its conditional depletion offers a method to study the sexual development of the parasite in vitro, and is proposed as an alternative to the requirement of T. gondii infections in cats.

overall_design: We report genome-wide H4K31me1, H4(K5-K8-12-K16)ac, MORC and HDAC3, profiles in Toxoplasma gondii using ChIP-seq in the context of MORC protein knock-down

first: Dayana

middle: C

last: Farhat

first: Christopher

last: Swale

first: Celine

last: Dard

first: Dominique

last: Cannella

first: Philippe

last: Ortet

first: Mohamed

last: Barakat

first: Fabien

last: Sindikubwabo

first: Lucid

last: Belmudes

first: Pieter-Jan

last: De Bock

first: Yohann

last: Couté

first: Alexandre

last: Bougdour

middle: A


city: La Tronche

state: Isère

address: Domaine de la Merci, Campus santé

department: Prevention and Therapy of Chronic diseases

institute: Centre de Recherche Inserm U1209 / CNRS UMR5309 / UGA

summary: Purpose: T. gondii has a complex life cycle typified by an asexual development taking place in vertebrate and a sexual reproduction occurring exclusively in felids and thereby is less studied. The developmental transitions rely on changes in gene expression patterns, and recent studies have assigned roles for chromatin shapers, including histone modifications, in establishing specific programs for a given stage. Here, we identified T. gondii microrchidia (MORC) protein as an upstream transcriptional repressor of sexual commitment. MORC, in partnership with Apetala (AP2) transcription factors, was shown to recruit the histone deacetylase HDAC3, thereby impeding the chromatin accessibility of the genes predestined to be exclusively expressed in sexual stages. As such, MORC-depleted cells underwent marked transcriptional changes, resulting in the expression of a specific repertoire of genes, thus revealing a shift from asexual proliferation to sexual differentiation. MORC acts as a master regulator that directs the hierarchical expression of secondary AP2 factors, with these latter potentially contributing to the unidirectionality of the life cycle. Thus, MORC plays a cardinal role in the T. gondii life cycle, and its conditional depletion offers a way to study the parasite’s sexual development in vitro, and proposes an alternative to the requirement of cat infections.

overall_design: Methods: RNA profiles were generated from HFF infected cells that were left untreated or treated with IAA (500 µM) or FR235222 (50 nM). Biological duplicates were performed for each condition. Total RNAs were extracted and purified using RNeasy Plus Mini Kit (Qiagen). RNA-sequencing was performed by GENEWIZ (South Plainfield, NJ, USA). The RNA quality was assessed using an Agilent RNA ScreenTape Analysis.  Illumina TruSEQ RNA library prep of selected polyA RNAs and sequencing reagents were used following the manufacturer's recommendations (Illumina, San Diego, CA, USA). The samples were paired-end multiplex sequenced (2 × 150 bp) on the Illumina Hiseq platform and generated at least 25 million reads for each sample. The RNA-Seq reads (FASTQ) were processed and analyzed using the Lasergene Genomics Suite version 15 (DNASTAR, Madison, WI, USA) using default parameters. The paired-end reads were uploaded onto the SeqMan NGen (version 15, DNASTAR. Madison, WI, USA) platform for reference-based assembly using the Toxoplasma Type II ME49 strain (ToxoDB-40, ME49 genome) as reference template. The ArrayStar module (version 15, DNASTAR. Madison, WI, USA) was used for normalization, differential gene expression and statistical analysis of uniquely mapped paired-end reads using the default parameters. The expression data quantification and normalization were calculated using the RPKM (Reads Per Kilobase of transcript per Million mapped reads) normalization method.

first: Céline

first: Mohamed-Ali

last: Hakimi


title: Effect of long-term corticosteroid treatment on microRNA and gene expression profiles in Chronic Obstructive Pulmonary Disease

city: Sydney

first: Alen

last: Faiz

state: NSW

address: 431 Glebe Point Rd

country: Australia

institute: Woolcock Institute of Medical Research

summary: To investigate whether expression of  microRNAs (miRNAs) are modulated by ICS treatment and whether this change in microRNA expression relates to improved clinical outcomes in COPD patients.

overall_design: The inclusion criteria for this study required participants to be steroid-naive or without inhaled corticosteroids (ICS) treatment for 6 months, current or ex-smokers with moderate-to-severe COPD. Patients included in this study were treated with 1) Placebo twice daily for 30 months; 2) fluticasone 500µg twice daily for 30 months; 3) fluticasone 500µg + salmeterol 50µg twice daily for 30 months. Bronchial biopsies for microRNA profiling were taken at baseline and 6- and 30-months.

first: Maarten

last: van den Berge


title: Vascular fate in misidentified pluripotent-derived blood-brain-barrier endothelial cells rescued by transcriptional reprogramming.

status: Public on Dec 25 2019

city: New York

first: Tyler

last: Lu

state: New York

address: 1300 York Avenue

institute: Weill Cornell Medicine

summary: A single-cell suspension was loaded into the Bio-Rad ddSEQ Single-Cell Isolator on which cells were isolated, lysed and barcoded in droplets. Droplets were then disrupted and cDNA was pooled for second strand synthesis. Libraries were generated with direct tagmentation followed by 3’ enrichment and sample indexing using Illumina Nextera library prep kit. Pooled libraries were sequenced on the Illumina NextSeq500 sequencer. Sequencing data were primarily analyzed using the SureCell RNA Single-Cell App in Illumina BaseSpace Sequence Hub.

overall_design: Cell samples were harvested from  in vitro culture conditions and sequenced using Illumina NextSeq500.

middle: M

first: Sean

last: Houghton

first: Shahin

last: Rafii

first: Dritan

last: Agalliu

first: David

last: Redmond

first: Raphael

last: Lis


title: FBXW4 acts as a protector of FOLFOX-based Chemotherapy in Metastatic Colorectal Cancer Identified by Co-expression network analysis

status: Public on Jan 28 2020

city: Fuzhou

first: Xingrong

state: China

address: 29 Xinquan Road

department: Colorectal surgery

institute: Fujian medical university union hospital

summary: To measure global gene expression in primary metastatic colorectal cancer patients who have undergone fluorouracil, leucovorin and oxaliplatin (FOLFOX) chemotherapy and screen valuable biomarkers to predict the effects of chemotherapy. Samples from primary metastatic colorectal cancer patients were collected. The effects of chemotherapy were evaluated.

overall_design: All patients underwent standard FOLFOX regimen chemotherapy in four cycles after signing the chemotherapy agreement; subsequently, they were evaluated in accordance with the Response Evaluation Criteria In Solid Tumors (RECIST).Each sample was collected immediately following resection. Each sample was stored in liquid nitrogen until total RNA extraction.

first: Yiyi

last: Zhang


title: Single Cell RNA-seq analysis of gene expression patterns of cells from stem-cell-derived-synthetic-blastocysts, called as 'ES-' or 'EPS-blastoids'.

status: Public on Nov 30 2019

city: Cambridge

first: Florian

last: Hollfelder

address: 80 tennis court road

institute: University of Cambridge

summary: To test the efficacy of stem cell lines to generate 'stem-cell-derived-synthetic blastocysts', we dissociated ES- (built by conventional embryonic stem cells and trophoblast stem cells) or EPS-blastoids (built by extended potential pluripotent stem cells and trophoblast stem cells) into single cells following 96h of culture for single-cell transcriptome analysis.

overall_design: Examination of gene expression patterns of cells was performed with the single-cell transcriptome analysis following 96h of culture. Single-cell transcriptome analysis was performed using an inDrops v3 barcoding scheme, and the data preprocessing was performed according to the Github inDrops analysis pipeline in order to generate count matrices (https://github.com/indrops/indrops). The transcriptomic analysis comprises three replicates of SB-EP, two replicates of SB-2iLif and one replicate of natural mouse embryo cells at E4.5.

first: Joachim

last: De Jonghe

first: Berna

last: Sozen

first: Andy

last: Cox

first: Magdalena

last: Zernicka-Goetz


title: Gene expression profiling in follicular lymphoma (FL) samples and paired transformed follicular lymphoma (tFL) (n=6 samples)

first: Sara

last: Parsa

state: NY

department: Cancer Biology and Genetics

institute: Memorial Sloan-Kettering Cancer Center

summary: Follicular lymphoma (FL)  is the second most common forms of B cell lymphoma that result from the expansion of germinal center (GC) B cells. Here, we aimed to find differential expression of genes between patient samples isolated from indoent FL or transformed and aggressive FL.

overall_design: Using RNA-seq we profiled human FL and paired tFL samples

first: Ana

last: Ortega-Molina

first: Wayne

last: Tam

first: Nicholas

last: Socci

first: Hans-Guido

last: Wendel


title: The serine hydroxymethyltransferase-2 (SHMT2) initiates lymphoma development through epigenetic tumor suppressor silencing.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: Modifiers and Mediators of Craniosynostosis Severity   Revealed by Differential Gene Expression

status: Public on Jan 15 2020

city: Rochester

first: Asha

last: Nair

address: 200 1ST ST SW

institute: Mayo Clinic

summary: Severity of craniosynostosis in humans varies widely even in patients with identical genetic mutations, and severity corresponds with morbidity. In this study we compared RNA sequencing data from cranial tissues of a severe form of Crouzon craniosynostosis syndrome (C57BL/6 FGFR2C342Y/+ mice) with those of a less severe form of Crouzon craniosynostosis (BALB/c FGFR2C342Y/+ mice) to identify genetic modifiers that influence craniosynostosis phenotype severity. Comparison of the mice revealed neonatal onset of coronal suture fusion in the form of suture obliteration in C57BL/6 mice (88% incidence, p<.001 between genotypes) in C57BL/6 mice. Coronal suture fusion in the form of point fusions across the suture occurred at approximately 4 weeks after birth, with less severe skull shape abnormalities, in BALB/c mice. Substantially fewer genes were differentially expressed in BALB/c FGFR2+/+ vs. FGFR2C342Y/+ mice (87 out of 15,893 expressed genes) than in C57BL/6 FGFR2C+/+ vs. FGFR2C342Y/+ mice (2,043 out of 19,097 expressed genes). Further investigation of the gene expression data revealed differential expression of coronal suture associated genes, eph/ephrin boundary genes, cell proliferation genes and osteoblast differentiation genes, among others. The most striking pattern in the data was the minimal change in gene expression seen in  BALB/c FGFR2+/+ vs. FGFR2C342Y/+ mice. Analysis of protein processing and lysosomal components support the hypothesis that the craniosynostosis phenotype is less severe in BALB/c mice because the mutant FGFR2C342Y protein is not expressed to the same extent as that seen in C57BL/6 mice. Together, these results suggest that a strategy aimed at increasing degradation of the mutant receptor could lead to diminished phenotype severity.

overall_design: Comparison of gene expression in cranial tissues of wild type and Crouzon FGFR2-C342Y/+ mutant mice on C57BL/6 vs. BALB/c genetic background strains

first: Amel

last: Dudakovic

first: HwaKyung

last: Nam

first: Andre

last: van Wijnen

middle: E

last: Hatch


title: Gene expression profiling in B220+ from normal spleen, VavPBcl2/vector and VavPBcl2/Myc lymphomas

summary: Follicular lymphoma (FL)  is the second most common forms of B cell lymphoma that result from the expansion of germinal center (GC) B cells. Here, we aimed to find differential expression of genes between noemal spleen, indoent FL (VavPBcl2/vector) and transformed and aggressive FL (VavPBcl2/MYC) in our mouse model.

overall_design: Using RNAseq we profiled murine purified B220+ cells from normal spleen (n=4), lymphomas transduced with empty vector (n=8) or Myc (n=8)

first: Ed

last: Reznik


title: Escalation in the host-pathogen arms race: a host resistance response corresponds to a heightened bacterial virulence response

status: Public on Dec 14 2019

city: Saint Louis

first: Rebecca

last: Bart

state: MO

address: 975 North Warson Road

institute: Donald Danforth Plant Science Center

summary: The zig-zag model of host-pathogen interaction describes the relative strength of defense response across a spectrum of pathogen-induced plant phenotypes. A stronger defense response results in increased resistance. Here, we investigate the strength of pathogen virulence during disease and place these findings in the context of the zig-zag model. Xanthomonas vasicola pv. holcicola (Xvh) causes sorghum bacterial leaf streak. Despite being widespread, this disease has not been described in detail at the molecular level. We divided diverse sorghum genotypes into three groups based on disease symptoms: water-soaked lesions, red lesions, and resistance. Bacterial growth assays confirmed that these three phenotypes represent a range of resistance and susceptibility. To simultaneously reveal defense and virulence responses across the spectrum of disease phenotypes, we performed dual RNA-seq on Xvh-infected sorghum. Consistent with the zig-zag model, the expression of plant defense-related genes was strongest in the resistance interaction. Surprisingly, bacterial virulence genes related to the type III secretion system (T3SS) and type III effectors (T3Es) were also most highly expressed in the resistance interaction. This expression pattern was observed at multiple time points within the sorghum-Xvh pathosystem. Further, a similar expression pattern was observed in Arabidopsis infected with Pseudomonas syringae for effector-triggered immunity via AvrRps4 but not AvrRpt2. Specific metabolites were able to repress the Xvh virulence response in vitro and in planta suggesting a possible signaling mechanism. Taken together, these findings reveal multiple permutations of the continually evolving host-pathogen arms race from the perspective of host defense and pathogen virulence responses.

sample_organism:
Sorghum bicolor
Xanthomonas vasicola

platform_organism:
Sorghum bicolor
Xanthomonas vasicola

overall_design: Dual RNA-seq profiled in 7 combinations (21 samples) of Xanthomonas vasicola pv. holcicola (Xvh) and three sorghum genotypes. The fourth leaf of 14-day-old sorghum plants was syringe-inoculated with bacterial suspensions and a mock treatment. At 48 h after inoculation, the infected tissue areas in leaves were harvested. Total RNA was extracted, followed by ribosomal RNA depletion, cDNA library preparation, and RNA-sequencing. Bacteria were grown on plates containing NYGA medium were also analyzed. For the samples, three independent replicates were taken.

first: Qi

last: Wang

first: Nadia

last: Shakoor

first: Adam

last: Boyher

first: Kira

last: Veley

first: Jeffrey

last: Berry

first: Todd

last: Mockler

middle: S


title: Sonoselective Transfection of Cerebral Vasculature without Blood-Brain Barrier Disruption - Singel Cell RNA seq

status: Public on Dec 13 2019

city: Charlottesville

first: Alexander

last: Mathew

state: VA

address: 415 Lane Road

institute: University of Virginia

summary: Treatment of many pathologies of the brain could be improved markedly by the development of non-invasive therapeutic approaches that elicit robust, endothelial cell-selective, gene expression in specific brain regions that are targeted under MR image-guidance. While focused ultrasound (FUS) in conjunction with gas-filled microbubbles (MBs) has emerged as a non-invasive modality for MR image-guided gene delivery to the brain, it has been used exclusively to transiently disrupt the blood-brain barrier (BBB), which may induce a sterile inflammation response. Here, we introduce a new MR image-guided FUS method that elicits endothelial-selective transfection of the cerebral vasculature (i.e. “sonoselective” transfection), without opening the BBB. We first determined that activating circulating, cationic plasmid-bearing, MBs with pulsed low-pressure (0.1 MPa) 1.1 MHz FUS facilitates sonoselective gene delivery to the endothelium without MRI-detectable disruption of the BBB. The degree of endothelial selectivity varied inversely with the FUS pressure, with higher pressures (i.e. 0.3 MPa and 0.4 MPa FUS) consistently inducing BBB opening and extravascular transfection. Bulk RNA sequencing analyses revealed that the sonoselective low pressure regimen does not upregulate inflammatory or immune responses. Single cell RNA sequencing indicated that the transcriptome of sonoselectively transfected brain endothelium was unaffected by the treatment. The approach developed here permits targeted gene delivery to blood vessels and could be used to promote angiogenesis, release endothelial cell-secreted factors to stimulate nerve regrowth, or recruit neural stem cells.

overall_design: FACS was first used to isolate mRUBY+ cells from pooled brain tissue wherein mRUBY plasmid-bearing MBs were activated with FUS at 0.1, 0.2, and 0.4 MPa (n = 3 per group). Brain tissue from mice that received mRUBY plasmid-MB injection, but without FUS application, were used to generate the flow cytometry gating scheme. Single cell RNA sequencing was then performed on mRUBY+ cell populations from 0.1, 0.2, and 0.4 MPa treated mice, as well as from untreated mice.


title: Transcriptome signatures reveal candidate key genes in the whole blood of patients with lumbar disc prolapse

status: Public on Dec 03 2019

city: Chengdu

first: Yi

state: Sichuan

address: 132 West First Section First Ring Road

institute: Sichuan Provincial Orthopedic Hospital

summary: The present study aimed to investigate differentially expressed genes in whole blood obtained from patients with lumbar disc prolapse and healthy volunteers. A total of 8 patients with lumbar disc prolapse and 8 healthy volunteers were recruited. An Agilent SurePrint G3 human gene expression microarray 8x60 K was used to perform the microarray analyses.

overall_design: We recruited 8 patients with lumbar disc prolapse confirmed by magnetic resonance imaging, and 8 volunteers with no clinical evidence of low back pain or sciatica. Ten millilitres of fasting WB was collected from the left median cubital vein of each participant between 7:00 and 7:30 AM. All WB samples were incubated in a PAXgene Blood RNA tube (BD, USA) for less than 72 h at -20°C and then submitted to Shanghai Bohao Biotechnology Co., Ltd (Shanghai, China) for gene chip hybridization screening. The microarray experiments were performed using an Agilent SurePrint G3 human gene expression microarray 8 ╳ 60 K at Shanghai Biotechnology Co., Ltd (Shanghai, China) following the standard protocol of Agilent Technologies (CA, USA).

first: Wang

last: Yi


title: Massively Parallel Reporter Assay of human-specific substitutions in neurodevelopmental enhancers

status: Public on Nov 26 2019

city: New Haven

first: James

middle: Patrick

last: Noonan

state: CT

address: 333 Cedar Street

department: Genetics

institute: Yale University

summary: We performed a Massively Parallel Reporter Assay (MPRA) to screen >30,000 human-specific substitutions in ChIP-seq-identified Human Gain Enhancers (HGEs) and Human Accelerated Regions (HARs), highly conserved non-coding regions that show accelerated sequence evolution in humans. After comparing human and chimpanzee reference alleles, we used a second MPRA to deconvolute individual substitutions within differentially active enhancers from substitutions in the same fragment and from other variants (human segregating variants or chimpanzee-specific variants) to isolate their specific effects on enhancer activity.

sample_organism:
Pan troglodytes
Homo sapiens

platform_organism:
Pan troglodytes
Homo sapiens

overall_design: This submission contains data for two MPRA experiments. MPRA1 contains data for an inert library, a competent library, and four experimental replicates. MPRA2 contains data for an inert library and two experimental replicates. This submission also contains ATAC-seq data for hNSCs (three replicates).

first: Severin

last: Uebbing

first: Jake

last: Gockley

middle: P


title: Identification of microRNA-dependent gene regulatory networks driving human pancreatic endocrine cell differentiation [Islet ATAC-Seq]

status: Public on Nov 14 2019

city: La Jolla

first: Maike

last: Sander

state: CA

address: 2880 Torrey Pines Scenic Dr.

institute: UC San Diego

summary: MicroRNAs (miRNAs) are small non-coding RNA molecules that have the ability to drive cell lineage decisions by regulating the expression of hundreds of genes. Although evidence indicates that miRNAs have roles in pancreas development and endocrine cell function, the role of miRNAs in pancreatic endocrine cell differentiation has not been systematically explored. To address this, we performed genome-wide small RNA sequencing analysis in pancreatic progenitor cells differentiated in vitro from human embryonic stem cells and endocrine cells isolated from whole human islets. This analysis revealed miRNAs that increase in expression during endocrine cell differentiation. Employing gain-of-function experiments, we identified four miRNAs that can repress a large number of genes that are normally down-regulated during endocrine cell differentiation, including genes encoding transcription factors known to regulate endocrine cell development as well as cell cycle regulators. This knowledge about miRNA target genes in conjunction with HITS-CLIP data allowed us to construct an integrated miRNA-gene regulatory network of endocrine cell differentiation. Our integrated analysis indicates a key role for the identified miRNAs in establishing a transcriptional landscape that promotes the differentiation of pancreatic progenitor cells into endocrine cells.  This study not only sheds light on the mechanisms that underlie human endocrine cell differentiation, but also has important implications for devising improved protocols for producing replacement beta cells for diabetes cell therapy.

overall_design: ATAC-seq analysis of human Cadaveric islet cells

first: Allen

first: Kelly

last: Frazer


title: Responses tophytoalexins in the necrotrophic fungus Alternaria brassicicola

status: Public on Nov 15 2019

city: BEAUCOUZE

first: Sandra

last: Pelletier

address: 42, rue Georges Morel - BP 60057

institute: INRA

summary: To gain insights into the cellular mechanisms by which indolic phytoalexins exerts its toxicity and investigate the adaptive strategies used by the fungus, we analyzed fungal transcriptional responses to short-term exposure to brassinin and camalexin.

overall_design: Camalexin (50 µM) and brassinin (100 µM) treatments were compared to non-treated cultures at three time points (0.5 h, 2 h and 6 h). Three biological replicates were analyzed per comparison using the dye-switch method.

first: G

last: N’Guyen

first: T

last: Guillemette

first: P

last: Simoneau

first: S


title: Comparative Physiological, Metabolomic, and Transcriptomic Analyses Reveal Developmental Stage-Dependent Effects of Cluster Bagging on Phenolic Metabolism in Cabernet Sauvignon Grape Berries

status: Public on Nov 25 2019

city: Beijing

first: Run-Ze

last: Sun

address: No.20 Nanxincun, Xiangshan, Haidian District

department: Institute of Botany

institute: Chinese Academy of Sciences

summary: Light conditions significantly influence grape berry ripening and the accumulation of phenolic compounds, but the underlying molecular basis remains partially understood. Here, we applied integrated transcriptomics and pathway-level metabolomics analyses to investigate the effect of cluster bagging during various developmental stages on phenolic metabolism in Cabernet Sauvignon grapes. Bagging treatments had limited effects on berry quality attributes at harvest and did not consistently affect phenolic acid biosynthesis between seasons. Significantly elevated flavan-3-ol and flavonol contents were detected in re-exposed berries after bagging during early-developmental stages, while bagging after véraison markedly inhibited skin anthocyanin accumulation. Several anthocyanin derivatives and flavonol glycosides were identified as marker phenolic metabolites for distinguishing bagged and non-bagged grapes. Coordinated transcriptional changes in the light signaling components CRY2 and HY5/HYHs, transcription regulator MYBA1, and enzymes LAR, ANR, UFGT and FLS4, coincided well with light-responsive biosynthesis of the corresponding flavonoids. The activation of multiple hormone signaling pathways after both light exclusion and re-exposure treatments was inconsistent with the changes in phenolic accumulation, indicating a limited role of plant hormones in mediating light/darkness-regulated phenolic biosynthesis processes. Furthermore, gene-gene and gene-metabolite network analyses discovered that the light-responsive expression of genes encoding bHLH, MYB, WRKY, NAC, and MADS-box transcription factors, and proteins involved in genetic information processing and epigenetic regulation such as nucleosome assembly and histone acetylation, showed a high positive correlation with grape berry phenolic accumulation in response to different light regimes. Altogether, our findings provide novel insights into the understanding of berry phenolic biosynthesis under light/darkness and practical guidance for improving grape features.

overall_design: Grape Berries from T1 treatment (CBFH) at E-L 31, 35, 36, 37, and 38 stages, T8 treatment (CBV) at E-L 36, 37, and 38 stages, and the control group at E-L 29, 31, 35, 36, 37, and 38 stages during the 2012 growing season were selected to conduct the transcriptome profiling analysis based on the physiological and metabolic results. Each sample contain three biological replicates.

first: Qiu-Hong

last: Pan

first: Chang-Qing

last: Duan

first: Jun

last: Wang


status: Public on Jan 23 2020

city: Seoul

first: BYUNGJOO

last: PARK

address: 120, Neungdong-ro, Gwangjin-gu,

department: Infectious disease

country: South Korea

institute: College of Veterinary medicine, Konkuk University

summary: Purpose: We investigated the host immune response and the virus evasion mechanism in gnotobiotic pig infected with HuNoV by mRNA sequencing.

overall_design: We performed mRNA seguencing of the ileum tissue from gnotobiotic pigs inoculated with/without Enterobacter cloacae and Human norovirus GII after 3 days

first: Byung-joo

last: Park


title: Acquisition of a unique mesenchymal precursor-like blastema state underlies successful adult mammalian digit tip regeneration

city: Toronto

first: Freda

middle: D

last: Miller

state: Ontario

address: 686 Bay Street

department: Neurosciences and Mental Health

country: Canada

institute: The Hospital For Sick Children

summary: Here, we investigate the origin and nature of blastema cells that regenerate the adult murine digit tip. We show that Pdgfra-expressing mesenchymal cells in uninjured digits establish the regenerative blastema and are essential for regeneration. Single cell profiling shows that the mesenchymal blastema cells are distinct from both uninjured digit and embryonic limb/digit Pdgfra-positive cells. This unique blastema state is environmentally determined; dermal fibroblasts transplanted into the regenerative, but not non-regenerative, digit express blastema markers and contribute to bone regeneration. Moreover, lineage tracing with single cell profiling indicates that endogenous osteoblasts/osteocytes acquire a blastema mesenchymal transcriptional state and contribute to both dermis and bone regeneration. Thus, mammalian digit tip regeneration occurs via a distinct adult mechanism where the regenerative environment promotes acquisition of a unique blastema state that allows cells from tissues like bone to contribute to regeneration of other mesenchymal tissues such as the dermis.

overall_design: High-throughput single cell transcriptomic profiles of uninjured (dataset1 and duplicate dataset), regenerating (7, 10, 14, duplicate 14 dataset, 28, 56 days post amputation) and non-regenerative (10, duplicate 10 dataset, 14 days post amputation) digit tips of C57BL/6 and transgenic Dmp1CreERT2;TdTomato (Uninjured and 14 day post amputation) adult mice, together with embryonic limbs (E11)/digit tips (E14) or neonatal (P3) digit tips of C57BL/6 mice were generated by single cell RNA sequencing, using the 10X Genomics platform. Processed data for 16 datasets are included as indicated.

first: Mekayla

last: Storer

first: Neemat

last: Mahmud

first: Konstantina

last: Karamboulas

first: Michael

last: Borrett

first: Scott

last: Yuzwa

first: Alaura

last: Androschuk

middle: V

last: Sefton

first: David

last: Kaplan


title: Gene expression of murine long-lived bone marrow plasma cells ex vivo and plasma cells cultured for 3 days with ST2 stromal cells and the cytokine APRIL under physiological oxygen conditions.

status: Public on Dec 01 2019

city: Berlin

first: Pawel

last: Durek

address: Charitéplatz 1

institute: Deutsches Rheuma-Forschungszentrum

summary: We compared gene expression profiles of murine longlived bone marrow plasma cells isolated from immunized C57BL/6J in the memory phase with plasma cells co-cultured for 3 days with murine ST2 stromal cells in the presence of the cytokine APRIL under physiological oxygen conditions.

overall_design: C57BL/6J mice were primed with NP-CCG in incomplete Freud`s Adjuvants intraperitoneally. Mice were challenged twice after the prime with the same injection in cycles of 21 days. 30 days after the last boost, longlived plasma cells were magnetically isolated (Miltenyi Biotec, Germany) with a 2 step-protocol including depletion of B220 and CD49b expressing cells and subsequent positive enrichment of CD138high plasma cells. Plasma cells were directly processed for RNA preparation or cultured for 3 days in co-culture with murine ST2 stromal cells in the presence of the cytokine APRIL under physiological oxygen conditions. After culture, plasma cells were FACSorted using FACSAria II. Total RNA was extracted using the RNeasy Micro KIT (Quiagen) and hybridized to MG 430 2 GeneChips according to the whole-transcriptome pico KIT. The integrity of isolated RNA was assessed for each sample using an Agilent 2100 Bioanalyzer (Agilent, Waldbronn, Germany) and amount was checked with a NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE). Hybridization was performed in a Hybridization Oven 640, and chips were washed and stained in the Fluidics Station 400 (both Affymetrix). Finally, the arrays were scanned with a GeneChip Scanner 3000 using the GCOS software, version 1.4, both Affymetrix.

first: Stefanie

last: Hahne

first: Adriano

last: Taddeo

first: Georg

last: Petkau

first: Darya

last: Malko

first: Manja

last: Thiem

first: Cora

last: Klaeden

first: Rebecca

last: Cornelis

first: Koji

last: Tokoyoda

first: Francesco

last: Siracusa

first: Bimba

middle: F

last: Hoyer

first: Falk

last: Hiepe

first: Mir-Farzin

last: Mashregi

first: Hyun-Dong

last: Chang

first: Andreas

last: Radbruch


title: Differential gene expression profile of S100A4 null mouse lens

status: Public on Jan 19 2020

city: Chapel Hill

last: Corcoran

state: NC

address: 125 Mason Farm Rd

institute: University of North Carolina at Chapel Hill

summary: Whole lens transcriptome profiling by RNA-seq analysis was performed to investigate the role of S100A4 in lens architecture and function.  These studies yielded the intriguing discovery that absence of S100A4 in the lens results in robust induction of gene expression of S100A5, an olfactory sensory neuron specific protein, and of genes encoding various photoreceptor and Müller glial cell proteins

overall_design: Two biological repeats of wildtype and S100A4 null mouse lens samles (derived from one month-old mice and for each sample, 6-12 lenses were pooled) were evaluated for changes in gene expression by RNA-seq analysis

first: Rupalatha

last: Maddala

first: P

last: Rao


title: Identification of microRNA-dependent gene regulatory networks driving human pancreatic endocrine cell differentiation [Islet RNA-Seq]

first: Maike

last: Sander

overall_design: RNA-seq analysis of human cadaver islet

first: Allen

last: Wang

first: Kelly

last: Frazer


title: Identification of microRNA-dependent gene regulatory networks driving human pancreatic endocrine cell differentiation [H1 RNA-seq]

overall_design: RNA-seq analysis of H1 cells differentiated pancreatic progenitor stage cells.

first: Wen

last: Jin


title: Identification of microRNA-dependent gene regulatory networks driving human pancreatic endocrine cell differentiation [RNA-Seq III]

overall_design: RNA-seq analysis of H1 cells differentiated pancreatic progenitor stage cells


title: Identification of microRNA-dependent gene regulatory networks driving human pancreatic endocrine cell differentiation [small RNA-seq]

type: Non-coding RNA profiling by high throughput sequencing

overall_design: Small RNA-seq analysis of CyT49 cells differentiated pancreatic progenitor stage cells.

first: Ruiyu

last: Xie


title: Control of prostate tumour growth by the long non-coding RNA GHSROS

city: Woolloongabba

first: Inge

last: Seim

state: Queensland

address: 37 Kent St

institute: Queensland University of Technology

summary: We overexpressed the long non-coding RNA GHSROS in the metastatic prostate cancer cell line PC3.

overall_design: Examination of cultured PC3 prostate cancer cells expressing the long non-coding RNA GHSROS


title: Identification of microRNA-dependent gene regulatory networks driving human pancreatic endocrine cell differentiation [ATAC-seq]

overall_design: ATAC-seq analysis of CyT49 cells differentiated pancreatic progenitor stage cells.


title: Clonally expanded CD8 T cells patrol Alzheimer's cerebrospinal fluid [CSF]

status: Public on Nov 04 2019

city: Stanford

first: Olivia

last: Leventhal

state: California (CA)

address: 1201 Welch Road, rm p220

department: Neurology

institute: Stanford University

summary: Alzheimer’s disease (AD) is an age-related neurodegenerative disorder in which neuroinflammation plays a critical function. Recurring viral infections and loss of immune competence increase risk for developing AD, yet the cellular and molecular mechanisms driving these immune changes are unknown. Here we performed mass cytometry of peripheral blood mononuclear cells and detected an immunologic signature of AD characterized by increased numbers of CD8+ T effector memory CD45RA+ (TEMRA) cells. CD8+ TEMRA cells were negatively associated with cognition and single cell RNA sequencing revealed their cytotoxic effector function. Strikingly, we discovered identical, shared T cell receptors (TCRs) of clonally expanded CD8+ TEMRA cells in cerebrospinal fluid (CSF) of three AD patients. Deep TCR sequencing, machine learning, and peptide screens identified the HLA-B*08:01-restricted Epstein-Barr virus trans-activator protein BZLF1 as the cognate antigen of a novel AD CSF TCR . These results provide the first evidence of clonal, antigen-specific T  cells patrolling the intrathecal space of brains affected by age-related neurodegeneration

overall_design:
Examination of transcriptional profile of  cells from the cerbrospinal fluid of healthy and diseased patients.

AD = Alzheimer's disease
MCI = mild cognitive impairment
HC = healthy control

first: David

last: Gate


title: Gene Expression Profiles of Multiple Myeloma from the sorted SP/LC and CD138+ cells

status: Public on Oct 31 2019

city: Iowa City

first: Fenghuang

last: Zhan

state: IA

address: Newton rd. CBRB 3269

department: Department of Internal Medicine

institute: University of Iowa

summary:
Analysis of sorted SP/LC population and a CD138+ main population cells. Results provide insight into which gene is involed in the drug resistance and tumor growth enriches for cancer stem-like cells.
Keywords: multiple myeloma, cancer stem cell

overall_design: Side populations and CD138+ from MM patients were isolated by flow cytometry using Hoechst 33342 and CD138 antibody. The total RNA was isolated from these populations using the RNeasy RNA isolation kit (Qiagen). The RNA was then converted to cDNA and they were hybridized to the Human Genome U133Plus 2.0 GeneChip microarrays (Affymetrix). The data was normalized using the MAS5 algorithm of the Affymetrix expression console version1.1 software(Affymetrix). A comparison of transcriptional profiles was then performed in side population compared to the main population in myeloma.


title: Clonally expanded CD8 T cells patrol Alzheimer's cerebrospinal fluid [TCR-seq]

overall_design:
Examination of transcriptional profile of  cells from the cerbrospinal fluid of healthy and diseased patients.

AD = Alzheimer's disease
PD = Parkinson's disease
MCI = Mild cognitive impairment
HC = healthy control


title: Clonally expanded CD8 T cells patrol Alzheimer's cerebrospinal fluid [TEMRA]

overall_design:
Examination of transcriptional profile of TEMRA cells from the blood of healthy and diseased patients.

AD = Alzheimer's disease
MCI = mild cognitive impairment
HC = healthy control


title: Transcriptomic Analysis of Differentiating Primary Myoblasts treated or not with TGFB1 recombinant protein or ITD-1 compound.

status: Public on Oct 01 2019

city: Lyon

first: Fabien

last: Le Grand

address: 8 avenue Rockefeller

department: Melis

institute: Institut Neuromyogene

summary:
Transforming Growth Factor beta (TGFβ) signaling cascade plays a fundamental role during muscle development and regeneration. Previous reports proposed several roles for the TGFβ superfamily members and generally they are considered negative regulators of myogenic differentiation. However, the activation of this signaling pathway has been shown to be essential to obtain a correct muscle tissue repair process. Due to these contrasting results, we decided to investigate the role of TGFb cascade in muscle cells.
To identify the genetic networks regulated by TGFB signaling in muscle cells, we performed transcriptome analysis of differentiated primary myocytes, stimulated with either TGFB1 or ITD-1

overall_design: We cultured primary myoblasts at 30,000 cells per cm2 onto matrigel-coated plates. Once adherent, cells were incubated in differentiation medium (DMEM with 2% Horse serum and 1% penicillin/streptomycin) for 24 hours. At this point, myoblasts were treated with TGFB1 recombinat protein at a final concentration of 20ng/ml or ITD-1 compound at 5mM for 24 hours.

first: Francesco

last: Girardi


title: Single-cell RNA-seq reveals novel cell differentiation dynamics during human airway epithelium regeneration

status: Public on Sep 20 2019

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

institute: IPMC/CNRS

summary: The upper airway epithelium is mainly composed of 4 cell types: multiciliated, goblet, secretory and basal cells. It constitutes an efficient first line of defense of the respiratory tract against a large panel of inhaled substances. Upon injury, regeneration of this epithelium through proliferation and differentiation events can restore a proper mucociliary function. In chronic airway diseases, such as chronic obstructive pulmonary disease or asthma, the injured epithelium frequently displays defective repair leading to tissue remodeling, characterized by a loss of multiciliated cells and mucus hyper-secretion. This situation emphasizes the need to accurately delineate the drivers of differentiation dynamics and cell fate in human airway epithelium. We have used single cell transcriptomics to characterize the sequence of cellular and molecular processes taking place during human airway mucociliary epithelium regeneration in vitro. A comparison with single-cell data from fresh human and pig airway samples, and from in vitro mouse tracheal epithelial cells confirmed our findings in several distinct mammalian species. Single-cell RNA-seq in the airways provides novel insights in differentiation dynamics with the identification of alternative cell trajectories, novel cell subpopulations and by mapping the activation and repression of key signaling pathways.

sample_organism:
Homo sapiens
Sus scrofa
Mus musculus

platform_organism:
Homo sapiens
Sus scrofa
Mus musculus

overall_design: Single-cell RNA-seq of airway epithelial cells from various origins: human in vitro time course differentiation, human bronchial biopsy, human nasal brushing, human nasal turbinate, mouse in vitro differentiation and pig trachea

first: Sandra

last: Ruiz-Garcia

first: Marie

last: Deprez

first: K

first: A

last: Paquet

last: Cavard

first: I

last: Caballero

first: M

last: Arguel

first: S

last: Leroy

first: C

middle: H

last: Marquette

last: Barbry

first: L

last: Zaragosi


title: Identification of a unique subtype of lung squamous cell carcinoma defined by SOX2 and a neural differentiation factor BRN2 [ChIP-seq]

status: Public on Sep 17 2019

city: New York

first: Hideo

last: Watanabe

address: One Gustave L. Levy Place

department: Department of Medicine, Division of Pulmonary, Critical Care and Sleep Medicine

institute: Icahn School of Medicine at Mount Sinai

summary: Lineage-specific transcriptional regulators control differentiation states not only during normal development but also during cancer evolution. By investigating super-enhancer landscape of lung squamous cell carcinoma (LUSC), we identified a unique ‘neural’ subtype defined by Sox2 and a neural lineage factor Brn2. Robust protein-protein interaction and genomic co-occupancy of these factors indicated their transcriptional cooperation in this ‘neural’ LUSC in contrast to the cooperation of Sox2 and p63 in the classical LUSC. Introduction of p63 expression in the “neural’ LUSC invoked the classical LUSC lineage accompanied by Brn2 downregulation and increased activities of ErbB/Akt and MAPK-ERK pathways. Collectively, our data demonstrate a unique LUSC lineage featured by Sox2 cooperation with Brn2 instead of p63, for which distinct therapeutic approaches may be warranted.

overall_design: Genome-wide profiles of histone H3K27 acetylation, Sox2 binding, p63 binding and Brn2 binding in LUSC cell lines

first: Takashi

last: Sato


title: Identification of a unique subtype of lung squamous cell carcinoma defined by SOX2 and a neural differentiation factor BRN2

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

overall_design: Refer to individual Series


title: Perturbation of the metabolic phenotypes of vaccination by the gut microbiome in humans [phase II]

status: Public on Sep 05 2019

city: Palo Alto

first: Dmitri

last: Kazmin

address: 240 Pasteur Dr

department: Institute for Immunity, Transplantation and Infection

summary: We performed an experiment in humans, in which broad spectrum antibiotics were administered to healthy young adults, prior and subsequent to vaccination with the seasonal influenza vaccine. Transcriptional profiling of peripheral blood mononuclear cells was performed prior to the vaccination and as a time course following the vaccine administration.

overall_design: In a follow up to the previous study, a total of 11 study participants aged 18-45 received a trivalent influenza vaccine (TIV) on day 0. XXXXXXX subjects were randomized to a five-day oral broad-spectrum antibiotic regimen consisting of neomycin, vancomycin, and metronidazole between day -3 and day 1. Vaccine was administered at Day 0. Biologic samples were collected and analyses performed at regular intervals.

first: Thomas

last: Hagan

first: Mario

last: Cortese

first: Bali

last: Pulendran


title: Perturbation of the metabolic phenotypes of vaccination by the gut microbiome in humans [phase I]

overall_design: A total of 22 study participants aged 18-45 received a trivalent influenza vaccine (TIV) on day 0. Eleven subjects were randomized to a five-day oral broad-spectrum antibiotic regimen consisting of neomycin, vancomycin, and metronidazole between day -3 and day 1. Vaccine was administered at Day 0. Biologic samples were collected and analyses performed at regular intervals.


title: Perturbation of the metabolic phenotypes of vaccination by the gut microbiome in humans


title: Transcriptional characterization of mPFCs

status: Public on Aug 20 2019

first: Gregory

last: Putzel

address: 430 East 29th Street

department: Microbiology

institute: NYU Langone Health

summary: Medial prefrontal cortices (mPFCs) were dissected from the brain of control or antibiotic-treated 10 week old male mice, before or after fear conditioning and extinction learning for transcriptional analysis.

overall_design: Mouse mPFCs were dissected by referring to the Allen Brain Atlas. Coordinates relative to bregma are: 1.3 to 2.8 mm anterior, -1 to 1 mm lateral, and 0 to 1 mm ventral. RNA was extracted using Trizol (Invitrogen) and chloroform and further purified using the RNAeasy mini spin columns (Qiagen).

first: Coco

last: Chu

first: David

last: Artis


title: Identification of microRNA-dependent gene regulatory networks driving human pancreatic endocrine cell differentiation

first: Maike

last: Sander


title: Identification of early response genes to low-intensity pulsed ultrasound in bone marrow stromal cells

status: Public on Aug 19 2019

city: Toyama

first: Yoshiaki

last: Tabuchi

state: Toyama

address: 2630 Sugitani

department: Life Science Research Center

country: Japan

institute: University of Toyama

summary:
Low-intensity pulsed ultrasound (LIPUS) has been applied as a therapeutic adjunct to promote fracture healing. However, the detailed molecular mechanisms by which LIPUS promotes bone fracture healing have not yet been fully elucidated.
In the present study, the early response genes elicited by low-intensity pulsed ultrasound (LIPUS) in bone marrow stromal cells (BMSCs) were investigated using GeneChip® oligonucleotide microarrays.

overall_design: Mouse ST2 bone marrow stromal cells were used. The cells were cultured in RPMI 1640 medium supplemented with 10% fetal bovine serum at 37°C in humidified air with 5% CO2. The cells treated with LIPUS (25 mW/cm2 for 20 min), then cultured at 37°C for 0.5, 1 and 3 h. Total RNA samples were prepared from the cells, and quality of the RNA was analyzed using a Bioanalyzer 2100. Gene expression was analyzed by an Affymetrix GeneChip® system with a GeneChip Mouse Genome 430 2.0 array. Sample preparation for array hybridization was carried out as described in the manufacturer’s instructions.


title: Single-cell transcriptome analysis reveals differential nutrient absorption functions in human intestine

status: Public on Oct 21 2019

first: Ye-guang

last: Chen

address: Tsinghua Road, Medical Building

department: School of life science

institute: Tsinghua University

summary: 14537 epithelial cells from adult human ileum, colon and rectum are performed single-cell transcriptome analysis, cell types and signature genes are presented, so as new representative genes. Bases on the gene expression pattern, difference of cell types, signaling changes, absorption funciton, inmmunity and hormone activity are analyzed. In addition, species diversity is briefly performed by analysis of human and mouse ileum single-cell database.

overall_design: identify cell consititution and function difference of ileum, colon and rectum at single-cell level.

first: Yalong

last: Wang

first: Wanlu

last: Song

first: Jilian

first: Ting

first: Xiaochen

last: Xiong

first: Zhen

last: Qi

first: Wei

last: Fu

first: Xuerui

last: Yang

first: Ye-Guang


title: Gene expression analysis of human bronchial airway epithelial BEAS-2B cells stimulated by glucocorticoid, long-acting β2-adrenoceptor agonist or both combined.

status: Public on Aug 01 2019

city: Calgary

first: Robert

last: Newton

state: Alberta

address: 3330 Hospital Dr NW

department: Snyder Institute for Chronic Diseases

institute: University of Calgary

summary:
In asthma, the clinical efficacy of inhaled corticosteroids (ICSs) is enhanced by long-acting β2-adrenoceptor agonists (LABAs). ICSs, or more accurately, glucocorticoids, promote therapeutically-relevant changes in gene expression and this genomic effect can be enhanced by a LABA.
To investigate the gene expression changes by each condition, transcriptomic analysis was performed on RNA extracted from BEAS-2B cells treated with budesonide, formoterol, or both combined.

overall_design: BEAS-2B cells were either not treated or treated with budesonide, formoterol or both combined for 1, 2, 6 and 18 h. Four independent experimental determinations for each condition were analyzed, altogether, 64 arrays were hybridized.

first: Mahmoud

last: Mostafa

first: Christopher

last: Rider


title: Quantitative comparison between cellular mRNAs and exosomal mRNAs in human iPSC-derived motor neurons

status: Public on Jul 30 2019

city: Fujisawa

first: Kentaro

last: Otake

state: Kanagawa

address: 26-1, Muraoka-Higashi 2-Chome

department: Neuroscience Drug Discovery Unit

institute: Takeda Pharmaceutical Company Limited

summary: The order in the abundance of exosomal mRNAs was not the same with that of the source cellular mRNAs in human iPSC-derived motor neurons.

overall_design: The abundance of mRNAs in human iPSC-derived motor neurons and their exosomes were quantitatively compared by next-generation sequencing.

first: Keiko

last: Tominari

first: Osamu

last: Sano

first: Hidehisa

last: Iwata

first: Yoshihiko

last: Hirozane


title: Functional cooperation of glycine synthase-reductase pathway with Wood-Ljungdahl pathway for autotrophic growth of Clostridium drakei

city: Yuseong-gu

first: Yoseb

state: Daejeon

address: 291 Daehak-ro

institute: KAIST

summary: The Wood-Ljungdahl pathway in acetogens converts C1 compounds, such as CO2 and CO, into acetyl-CoA. Similarly, the glycine synthase pathway assimilates C1 compounds into glycine. Partial glycine synthase genes are widely conserved in the Wood-Ljungdahl pathway gene cluster but functional relationship between the pathways in autotrophic condition remains unknown. To comprehend, we assembled Clostridium drakei genome (5.7-Mbp) with intact glycine synthase pathway and constructed a genome-scale metabolic model, iSL836, predicting increased metabolic flux rates of the Wood-Ljungdahl pathway and the glycine synthase-reductase associated reactions under autotrophic conditions. Along with the observation of significant transcriptional activation of genes in the pathways, surprisingly, 13C-labeling experiments and enzyme activity assays confirmed the strain synthesizes glycine and converts into acetyl-phosphate. This study suggests the Wood-Ljungdahl and the glycine synthase-reductase pathways convert CO2 into acetyl-CoA and acetyl-phosphate, respectively. In our knowledge, this is the first report on co-utilization of the pathways under autotrophic growth in acetogen.

overall_design: Profile of whole transcripts of Clostridium drakei generated by deep sequencing using Miseq

first: Jongoh

last: Shin

first: Sangrak

last: Jin

first: Gyu-Min

last: Lee

first: Jin-Soo

first: Seul-Gi

last: Kang

first: Jung-Kul

first: Dong-Rip

last: Kim

first: Eun-Yeol

first: Suhyung

last: Cho

first: Sun-Chang

first: Donghyuk

first: Byung-Kwan


title: C/EBPa mediates the growth inhibitory effect of progestins on breast cancer cells

status: Public on Jul 25 2019

city: Barcelona

first: Miguel

last: Beato

state: Barcelona

address: Dr. Aiguader, 88

department: Gene expression, stem cells and cancer

country: Spain

institute: CRG

summary: Steroid hormones are key gene regulators in breast cancer cells. While estrogens stimulate cell proliferation, progestins activate a single cell cycle followed by proliferation arrest. Here, we use biochemical and genome wide approaches to show that progestins achieve this effect via a functional crosstalk with C/EBPα. Using ChIP-seq, we identify around 1,000 sites where C/EBPα binding precedes and helps binding of Progesterone Receptor (PR) in response to hormone. These regions exhibit epigenetic marks of active enhancers and C/EBPα  maintains an open chromatin conformation that facilitates loading of ligand activated PR. Prior to hormone exposure, C/EBPα favors promoter-enhancer contacts that assure hormonal regulation of key genes involved in cell proliferation by facilitating binding of RAD21, YY1 and the Mediator complex. Knockdown of C/EBPα disrupts enhancer-promoter contacts and decreases the presence of these architectural proteins, highlighting its key role in 3D chromatin looping. Thus, C/EBPα  fulfills a previously unknown function as a potential growth modulator in hormone-dependent breast cancer.

overall_design: Examination of progesterone receptor, Topo2a and C/EBPa binding in T47D breast cancer cell line. Effect of Topo2a inhibition in hormone-dependent gene regulation.

first: A

last: Nacht

first: Roberto

last: Ferrari

first: Roser

last: Zaurin

first: Valentina

last: Scabia

first: José

last: Carbonell

first: Francois

last: Le Dily

first: Javier

last: Quilez

first: Alexandra

last: Leopoldi

first: Cathrin

last: Brisken

first: Guillermo

last: Vicent


title: Clonally expanded CD8 T cells patrol Alzheimer's cerebrospinal fluid

first: Olivia

last: Leventhal


title: Next-generation sequencing of rhesus macaques lung after treatment with a low-dose or clinical antenatal corticosteroid treatment

status: Public on Jun 21 2019

city: Miami

first: Augusto

last: Schmidt

state: FL

address: 1611 NW 12th ave

institute: University of Miami Miller School of Medicine

summary:
Purpose: Evaluate fetal lung maturation and transcriptome after clinical treatment with antenatal corticosteroids compared to an alternative treatment with a slow release low-dose formulation.

Methods: Lung mRNA profiles of rhesus macaques were generated by RNA sequencing. Reads that met quality thresholds were aligned to the rhesus macaque genome and number of reads per gene was counted.
RNA-sequencing of the hippocampus was done. Differential expression analysis was done using read counts.

Results: A relatively low dose of Beta-Ac increased lung compliance, surfactant concentration and relative airspace of the fetal lung equivalent to the clinical drug. By transcriptome analyses, the early suppression of genes associated with immune responses and the downregulation of genes associated with developmental pathways were less changed by Beta-Ac than the clinical drug.
There were no significant differences between Beta-Ac and control while the clinical drug suppressed maturational pathways including genes involved in neurogenesis, neuronal differentiation and stem cell fate commitment.

Conclusions: We report that low-dose betamethasone-acetate has decreased impact on lung transcriptome compared to the clinical treatment.

overall_design: Time-pregnant rhesus macaques were treated with [1] antenatal corticosteroids or placebo prior to delivery at 4-6h or 5 days after treatments [2] corticsteroid treatments or placebo 5 days prior to delivery.

first: Paranthaman

last: Kannan

first: Lisa

last: Miller

first: Yan

last: Xu

first: Jeffrey

last: Whitsett

first: Alan

last: Jobe


title: USP8 mutations determine genes’ expression profile of pituitary corticotroph adenomas, regardless of tumor functional status.

status: Public on Jun 20 2019

city: Warsaw

first: Mateusz

last: Bujko

address: Roentgena 5

department: Molecular Oncology Department

country: Poland

institute: Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology

summary: The aim of the study was to compare genes’ expression profiles of functioning and silent corticotroph adenomas to investigate possible biological mechanism of different hormone secretion . Since USP8 is the best know driver gene mutated in large proportion of ACTH-omas we intended to verify whether the mutation occurs in SCAs and how it affects transcriptomic profile.

overall_design: 20 samples were analyzed inclusding 8 silent corticotroph pituitary adenoma (SCA) samples and 12 functioning corticotroph pituitary adenoma (Cushing disease) samples. 2 of the SCA and 4 of the Cushing disease samples had mutated USP8 while the otheres were wild type.

first: Paulina

last: Kober

first: Joanna

last: Boresowicz

first: Agnieszka

last: Paziewska

first: Michalina

last: Dabrowska

first: Natalia

last: Rusetska

first: Agata

last: Piascik

first: Monika

last: Pekul

first: Jacek

last: Kunicki

first: Wieslaw

last: Bonicki

first: Grzegorz

last: Zielinski

first: Maria

last: Maksymowicz


title: MEF2C knock-down in Human Skeletal Myoblasts

status: Public on Jun 01 2019

city: Poznan

first: Michał

last: Szcześniak

address: Uniwersytetu Poznanskiego 6

department: Institute of Human Biology and Evolution

institute: Adam Mickiewicz University

summary: The main goal of this work was to determine the connection between MEF2C expression and its role in miRNA biogenesis in the differentiation of human skeletal muscle cells.In summary, our results demonstrated a significant role for MEF2C myogenic factor in sculpting the microtranscriptome during the differentiation of skeletal muscle cells.

overall_design: miRNAs libraries from HSkM cell treated with control siRNA (n=3) and siRNA against MEF2C (n=3) were generated by deep sequencing, in triplicate, using the  Illumina HiSeq 2000

first: Krzysztof

last: Sobczak

last: Piasecka

last: Sekrecki

middle: W


title: Radiation enhances melanoma response to immunotherapeutic and synergizes with benzodiazepines to promote improved anti-tumor activity

status: Public on May 21 2019

city: Cincinnati

first: Soma

last: Sengupta

state: OH

address: 3125 Eden Avenue

institute: University of Cincinnati

summary: The RNA-Seq data of 17 brain metastatic samples short-read sequences were aligned to the hg19 human reference genome using STAR (v 2.4.1a). featureCounts was used to count the reads of the mapped bam files. SAMseq was used to conduct differential expression analysis among the two treatment groups. SAMseq was utilized as it accounts for potential correlation in expression among genes and its permutation-based testing method was deemed more appropriate for a smaller sample size. After identifying the differentially expressed genes (FDR cut-off, 0.05), expression levels were normalized with the samr R package before being log2 transformed. This data was utilized to generate a heatmap with the patients sorted with supervised clustering based upon their immunotherapy/radiation groups and the gene dendrogram was created with Pearson’s Correlation Coefficient and with the Ward D2 linkage method. Differentially expressed genes (FDR<0.05[KD1] ) were subjected to pathway analysis using MetaCore.

overall_design: Differential expression analysis across two different patient groups based upon their timing of immunotherapy and radiation therapy.

first: Maxwell

last: Xu

first: Daniel

last: Krummel

first: Mohammad

last: Khan


title: Global gene networks in canine peripheral blood mononuclear cells infected with Mycobacterium avium subsp.hominissuis

status: Public on Jun 27 2019

city: Seoul

first: Suji

last: Kim

state: Gwanak-gu

address: 1, Gwanak-ro

department: Veterinary Medicine

institute: Seoul National University

summary: An opportunistic intracellular pathogen Mycobacterium avium subsp. hominissuis, a member of the nontuberculous mycobacteria (NTM) cluster, causes respiratory disease in immunosuppressed hosts. In particular, infected companion dogs are a potential role to transmit the agent to children or immunosuppressed people. The purpose of this study is to investigate a host-M. avium hominissuis interactome in canine PBMCs during the infection.

overall_design: Peripheral blood mononuclear cells were isolated from buffy coats of six healthy beagle dogs by density gradient centrifugation. PBMCs were stimulated in vitro with M. avium hominissuis strain 104. Total RNAs were extracted from the cells at 2h, 6h, 12h, and 24h after infection. The construction of library was performed using QuantSeq 3’mRNA-Seq Library Prep Kit. High-throughput sequencing was performed as single-end 75 sequencing using NextSeq 500.

first: Han-Sang

last: Yoo


title: Dissecting the single-cell transcriptome network underlying gastric premalignant lesions and early gastric cancer [10x genomics]

status: Public on Jul 20 2019

city: Beijing

first: Shao

last: Li

state: Beijing

address: Haidian district

summary: Intestinal-type gastric cancer is preceded by premalignant lesions including chronic atrophic gastritis and intestinal metaplasia. In this study, we performed a scRNA-seq survey of 56,440 cells from thirteen gastric antral mucosa biopsies from nine patients with Non-atrophic gastritis (NAG), CAG, IM or early gastric cancer (EGC), and constructed a single-cell transcriptome atlas for gastric premalignant and early-malignant lesions. The thirteen biopsies, including three wild superficial gastritis (NAG) ones, three CAG ones, six IM ones and one EGC , spanned the cascade from gastritis to early gastric cancer.For each biopsy, we isolated single cells without prior selection for cell types and utilized the 10x Chromium platform to generate RNA-seq data. After removing low-quality cells (Methods), a total of 32, 332 cells that passed the quality control were retained for subsequent analysis, which yielded a median of 1941 detected genes per cell.

overall_design: a scRNA-seq survey of 56,440 cells from thirteen gastric antral mucosa biopsies from nine patients with Non-atrophic gastritis (NAG), Chronic atrophic gastritis (CAG), Intestinal metaplasia (IM) or early gastric cancer (EGC), using 10X genomics.

first: Peng

last: Zhang


title: Genome-wide transcriptome analysis to identify genes involved in adventitious root formation of ramie (Boehmeria nivea L. Gaud) cutting

city: Changsha

first: Yongting

last: Yu

address: No 348, Xianjiahu West Rd.

institute: Institute of Bast Fiber Crops, Chinese Academy of Agricultural Science

summary: Two ramie cultivars, Zhongzhu no 2(Z2) and Huazhu no 4 (H4), showed constructing adventitious root formation (ARF) rate. Comparative transcriptome analysis was performed to study gene expression profiles in Z2 and H4 ramie during adventitious root formation. Illumina sequencing yielded a total of 92,794,556,688 bases data, and about 301.47 M and 313.06 M raw reads for Z2 and H4 plants, respectively. After quality control, every library obtained over 43 million reads, which is enough for the quantitative analysis of gene expression. Using Trinity software, these clean reads were first assembled into 121,492 transcripts, finally into 66,881 unigenes with an average length of 1144.25 bp. About 148.74 M and 138.72 M clean reads of H4 and Z2 were mapped to reference genes via Bowtie, respectively. The ratio of mapped clean reads for eight libraries ranged from 74.47% to 75.38% (average: 74.8%). By comparing gene expression levels in Tm and CK ramie stems, we identified 772 DEGs in H4 plants during RPF, including 7220 up-regulated and 8154 down-regulated DEGs. We identified 1256 DEGs in Z2 plants during RPF, which included 779 up-regulated and 447 down-regulated DEGs. We also identified 1919 DEGs between Z2 and H4 plants. There were 1147 (731 up-regulate and 416 down-regulated) DEGs uniquely in Z2, and 603 (202 up-regulate and 461 down-regulated) DEGs uniquely in H4 plants. The two genotypes shared 109 DEGs, which indicates some common pathways during ARF.

overall_design: Stem samples of water cultured (tm) and untreated (ck) ramie were RNA-Seq sequenced to study differentially expressed genes.

first: Bing

last: Guo

first: Aiguo

last: Zhu


title: Formaldehyde-fixed RNA-Immunoprecipitation (fRIP for heterogenous ribonucleoprotein K (hnRNP K)

status: Public on May 01 2019

city: Houston

first: Vrutant

last: Shah

state: TX

address: 1515 Holcombe Blvd #1000

department: EMC

institute: UT MD Anderson Cancer Center

summary: fRIP experiments were performed in OCI-AML3 cells to identify transcripts that bind to hnRNP K.

overall_design: fRIP experiments were performed in OCI-AML3 cells in triplicate as described in using a modified version of the protocol described in PMID: 26883116. Input and hnRNP K immunoprecipitation samples (IP) were sequenced.

first: Prerna

last: Malaney

first: Xiaorui

first: Sean

last: Post


title: Human pluripotency is initiated and preserved by a unique subset of founder cells [microarray]

status: Public on Apr 11 2019

city: Hamilton

first: Mickie

last: Bhatia

address: 1200 Main Street West

department: Stem Cell and Cancer Research Institute (SCC-RI)

institute: McMaster University

summary: The assembly of organized colonies is the earliest manifestation in the derivation or induction of pluripotency in vitro. However, the necessity and origin of this assemblance is unknown. Here, we identify human pluripotent founder cells (hPFCs) that initiate as well as preserve and establish pluripotent stem cell (PSC) cultures. PFCs are marked by N-cadherin expression (NCAD+) and reside exclusively at the colony boundary of primate PSCs. As demonstrated by functional analysis, hPFCs harbor the clonogenic capacity of PSC cultures and emerge prior to commitment events or phenotypes associated with pluripotent reprogramming. Comparative single cell analysis with pre and post implantation primate embryos revealed hPFCs share hallmark properties with primitive endoderm (PrE) and can be regulated by non-canonical Wnt signaling. Uniquely informed by primate embryo organization in vivo, our study defines a subset of founder cells critical to the establishment pluripotent state.

overall_design: Gene-expression profiles of FACS-isolated H9 hESC subsets (NCAD+, NCAD-:SSEA3+, and NCAD-:SSEA3-) by microarray (Affymetrix Human Gene 1.0 ST Array). The FACS-isolation and total RNA extraction were repeated three times independently.

first: Mio

last: Nakanishi


title: Differentially expressed genes in livers and abdominal fats between normal- and high-fat diet-fed dwarf broilers

status: Public on Apr 16 2019

city: Guangzhou

first: Wen

last: Luo

state: Guangdong

address: Wushan

institute: South China Agricultural University

summary: To investigate genes involved in abdominal fat deposition and fat metabolism of broilers with dw gene, we used highthroughput sequencing to detect the differentially expressed genes in livers and abdominal fats of dwarf broilers which were fed with a normal diet and a high-fat diet, respectively. The broilers began to fed with a normal or a high-fat diet in 1-week-old. After 7 weeks, the broilers were be executed and the livers and abdominal fats were used to extracted total RNAs. Finally, the total RNAs were be sequenced used BGISEQ-500 platform.

overall_design: Our aim was to investigate the differentially expressed genes in broilers that were fed with normal diet or high-fat diet.

first: Jiahui

last: Chen


title: Inhalation exposure of hexanal in rats (DNA methylation)

status: Public on Apr 05 2019

first: Yoon

last: Cho

address: hwarang-ro 14

institute: KIST

summary: To further development of insight into the mechanism of toxicity, it is important to employ whole genome microarray expression profiling to identify and characterize DNA methylation profiles as a discovery platform relevant for toxicologic mechanisms of hexanal. DNA methylation have prominent epigenetic role in regulation of gene expression, cell cycle control, apoptosis, cancer development and proliferation-related processes. However, few reports have described the effect of hexanal on DNA methylation expression profiles using animal model. In this respect, we studied the expression profiles of DNA methylation in hexanal-exposed in rats by DNA methylation microarray analysis.

overall_design: To evaluate the DNA methylation expression in lung tissue of rats after exposure of hexanal, Fischer-344 rats were inhaled to three concentrations (600, 1000, 1500 mg/m3) for 5 weeks. DNA methylation expression analysis was conducted using custom-designed 400K methylation microarray (Agilent Technologies, USA).

first: Jae-Chun

last: Ryu


title: RNA sequencing to compare gene expession in control and PF228-treated hepatic stellate cells

status: Public on Apr 15 2019

city: Austin

first: Ningling

last: Kang

state: MN

address: 801 16th AVE NE

department: Hormel Institute

institute: University of Minnesota

summary: Primary human hepatic stellate cells (HSCs) isolated from healthy donors were purchased from ScienCell Research Laboratories.  They were preincubated with or without PF228 and stimulated with TGFbeta1 (5 ng/ml) for 24 hours.  Cells were collected for RNA isolation and RNA sequencing.  The goal of this study was to identify genes transcriptionally regulated by TGFbeta1 and FAK.

overall_design: There were 4 groups of cells based upon the following treatments:  DMSO, DMSO+TGFbeta1, PF228, PF228+TGFbeta1. Each group had 3 repeats, so 12 RNA samples were sent to UMN Genomic Center for RNA sequencing.  The RNA samples were converted to Illumina sequencing libraries by using Illumina’s Truseq Stranded mRNA Sample Preparation Kit.  Truseq libraries were then subjected to cluster by using Illumina cBot instrument and sequencing was done by using HiSeq2500.


title: An inter-chromosomal transcription hub activates the unfolded protein response in plasma cells

status: Public on Apr 10 2019

city: La Jolla

first: Kees

last: Murre

state: CALIFORNIA

address: 9500 gilman drive, NSB 5114A

department: Biology

institute: UCSD

summary: Previous studies have indicated that the transcription signature of antibody-secreting cells is closely associated with the induction of the unfolded protein response pathway (UPR). Here we have used genome-wide and single cell analyses to examine the folding patterns of plasma cell genomes. We found that plasma cells adopt a cartwheel configuration and undergo large-scale changes in chromatin folding at genomic regions associated with a plasma cell specific transcription signature. During plasma cell differentiation, Blimp1 assembles into an inter-chromosomal transcription hub with genes associated with the UPR, biosynthesis of the endoplasmic reticulum (ER) as well as a cluster of genes linked with Alzheimer’s disease. We suggest that the assembly of the Blimp1-UPR-ER transcription hub permits the coordinate activation of a wide spectrum of genes that collectively establish plasma cell identity.

overall_design: ATAC-Seq, RNA-Seq, ChIP-Seq and TCC

first: Alexandra

last: Bortnick

first: Zhaoren

last: He

first: Cornelis


title: Human pluripotency is initiated and preserved by a unique subset of founder cells [single-cell RNA-sequencing]

state: Ontario

summary: The assembly of organized colonies is the earliest manifestation in the derivation or induction of pluripotency in vitro. However, the necessity and origin of this assemblance is unknown. Here, we identify human pluripotent founder cells (hPFCs) that initiate as well as preserve and establish pluripotent stem cell (PSC) cultures. PFCs are marked by N-cadherin expression (NCAD+) and reside exclusively at the colony boundary of primate PSCs. Functional analysis demonstrated hPFCs harbor the clonogenic capacity of PSC cultures, and emerge prior to commitment events or phenotypes associated with pluripotent reprogramming. Comparative single cell analysis with pre- and post-implantation primate embryos revealed hPFCs share hallmark properties with primitive endoderm (PrE) and can be regulated by non-canonical Wnt signaling. Uniquely informed by primate embryo organization in vivo, our study defines a subset of founder cells uniquely involved in the establishment pluripotent state.

overall_design: Droplet-based single-cell RNA-sequencing of bulk- and NCAD-positive hESCs. Two lines of hESCs (H1 and H9) were loaded to the Chromium Controller as mixtures and then computationally segregated based on coverage of the sex chromosomes after sequencing and alignment.

last: NAKANISHI

last: BHATIA


title: Physiological and molecular dissection of daily variance in exercise capacity

status: Public on Apr 07 2019

city: Rehovot

first: Jonathan

middle: Aryeh

last: Sobel

address: Benoziyo Building for Biological Sciences, room 277S, Weizmann Institute of Science

department: Biomolecular Sciences

country: Israel

institute: Weizmann Institute of science

summary: Physical performance relies on the concerted action of myriad responses, many of which are under circadian clock control. Little is known, however, regarding the time-dependent effect on exercise performance at the molecular level. We found that both mice and humans exhibit day-time variance in exercise capacity between the early and late part of their active phase. The day-time variance in mice was dependent on exercise intensity and relied on the circadian clock proteins PER1/2. High throughput gene expression and metabolic profiling of skeletal muscle revealed metabolic pathways that are differently activated upon exercise in a day-time dependent manner. Remarkably, we discovered that ZMP, an endogenous AMPK activator, is induced by exercise in a time-dependent manner to regulate key steps in glycolytic and fatty acid oxidation pathways and potentially enhance exercise capacity. Overall, we propose that time of the day is a major modifier of exercise capacity and associated metabolic pathways.

overall_design: basal, high intensity and moderate intensity runnig protocol at ZT14 and ZT22 in gastrocnemius muscle in C57B6 mice

first: Saar

last: Ezagouri

first: Ziv

last: Zwighaft

first: Gad

last: Asher


title: Vitamin E inhibits abdominal fat deposition through distinct lipid metabolism-related pathways in broilers

status: Public on Apr 01 2019

city: Longyan

first: Yanfa

last: Sun

state: Fujian

address: Dongxiao North Road No. 1, Xinluo District

department: College of Life Science

institute: Longyan University

summary: We report the pathway and key genes were identified between control and vitamin E added through RNA sequencing.

overall_design: Examination of 3 VS 3 abdominal fat tissue of control and added 50 mg vitamin E


title: SPIB promotes anoikis resistance via elevated autolysosomal process in lung cancer cells [ChIP-seq]

status: Public on Mar 11 2019

city: Tianjin

first: Zhenyi

last: Ma

address: 22 Qixiangtai Road

department: Biochemistry and Molecular Biology

institute: Tianjin Medical University

summary: Anoikis (detachment-induced cell death) is a specific type of programmed cell death which occurs in response to the loss of the correct extracellular matrix connections. Anoikis resistance is an important mechanism in cancer invasiveness and metastatic behavior. Autophagy, on the other hand, involves the degradation of damaged organelles and the recycling of misfolded proteins and intracellular components. However, the intersection of these two cellular responses in lung cancer cells has not been extensively studied. Here, we identified that upon matrix deprivation, the lymphocyte lineage-specific Ets transcription factor SPIB was activated and directly enhanced SNAP47 transcription in certain lung cancer cells. Loss of attachment-induced autophagy significantly increased anoikis resistance by SPIB activation. Consistent with this function, SPIB depletion by short hairpin RNA abrogated SNAP47 transcriptional activation upon matrix deprivation. Therefore, these data delineate an important role of SPIB in autophagy-mediated anoikis resistance in lung cancer cells. Accordingly, these findings suggest that manipulating SPIB-regulated pathways in vivo and evaluating the impact of anoikis resistance warrant further investigation.

overall_design: ChIP was performed in SPIB overexpressed H1703 cells under attached and suspended condition. Samples including Attached-input, Attached-ChIPSeq, Suspended-input and Suspended-ChIPSeq

first: Hua

last: Zhang


title: SPIB promotes anoikis resistance via elevated autolysosomal process in lung cancer cells [RNA-seq]

overall_design: mRNA profiles of attached H1703 control,attached H1703 SPIB-KD，ECM detached H1703 control,ECM detached H1703 SPIB-KD. There are two biological repeats in each group.


title: RNA-seq following knockdown of a sex determing gene in house fly

status: Public on Feb 19 2019

first: Richard

last: Meisel

address: 3455 Cullen Blvd

department: Biology and Biochemistry

institute: University of Houston

summary: We injected double-stranded RNA (dsRNA) into house fly embryos to knock down transformer (Md-tra), creating sex-reversed males that do not carry a Y chromosome. We also injected dsRNA trageting GFP as a sham treatment. We used RNA-seq to compare gene expression in the sex-reversed males with genotypic (normal) females (injected with dsRNA targeting GFP) and two types of genotypic (normal) males (injected with dsRNA targeting Md-tra or GFP). The expression profiles of sex-reversed males were similar to normal males. In contrast, about two thousand genes are differentially expressed between sex-reversed males and normal females, a similar magnitude as between normal males and females.

overall_design: Four different genotype by treatment combinations were assayed: 1. genotypic males treated with dsRNA targeting Md-tra; 2. genotypic males treated with dsRNA targeting GFP; 3. genotypic females treated with dsRNA targeting Md-tra (sex-reversed males); 4. genotypic females with dsRNA targeting GFP. For each genotype by treatment combination, expression was measured in both head and abdomen. Three biological replicates of each genotype by treatment and tissue were assayed.

first: Jae

last: Son

first: Danie

last: l Bopp


title: Differentially expressed genes in livers and abdominal fats between normal- and high-fat diet-fed chickens

status: Public on Mar 16 2019

first: Wen

last: Luo

summary: To investigate genes involved in abdominal fat deposition and fat metabolism of broilers, we used highthroughput sequencing to detect the differentially expressed genes in livers and abdominal fats of broilers which were fed with a normal diet and a high-fat diet, respectively. The broilers began to fed with a normal or a high-fat diet in 1-week-old. After 7 weeks, the broilers were be executed and the livers and abdominal fats were used to extracted total RNAs. Finally, the total RNAs were be sequenced used BGISEQ-500 platform.

first: Xiquan


title: Long non-coding RNA expression profile associated with malignant progression of oral submucous fibrosis

status: Public on Feb 13 2019

city: Shenzhen

first: Giles

last: Hu

address: Dapeng

institute: YJY

summary: Oral submucous fibrosis (OSF) as one of the malignant disorders endures a series of histopathological stages to invasive oral squamous cell carcinoma (OSCC) eventually. The role of long non-coding RNA (lncRNA) expression in OSF malignant progression is still poorly understood. Genome-wide lncRNA expression profiling of normal mucous, OSF and OSCC tissues was performed by RNA sequencing. Bioinformatic methods were applied for differential lncRNA analysis and functional enrichment analysis. Quantitative-RT-PCR was used to verify identified lncRNAs.21 novel transcripts were differentially expressed among all three stages during OSF progression with varied expression levels. Our study firstly comprehensively elucidated lncRNAs expression profile of the process of OSCC premalignant lesion to OSCC.

overall_design: 18 samples for RNA-seq

first: Shanghui

last: Zhou

first: Yun

last: Zhu

first: Zhijing

first: Dahe

first: Feng

last: Guo

first: Xinchun

last: Jian

first: Chenping


title: Single-cell RNA-seq of Drosophila melanogaster male and female late third instar larval gonads

status: Public on Feb 01 2019

city: Bethesda

first: Justin

middle: Matthew

last: Fear

state: MD

address: 50 South Drive

department: LCDB

institute: NIDDK, NIH

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

overall_design: Refer to individual Series


title: Bi-directional interaction between mesenchymal stem cells and transit amplifying cells in mesenchymal tissue homeostasis

status: Public on Jan 30 2019

city: Los Angeles

first: junjun

last: jing

address: 2250 Alcazar Street

institute: Center for Craniofacial Molecular Biology, University of Southern California


title: Bi-directional interaction between mesenchymal stem cells and transit amplifying cells in mesenchymal tissue homeostasis [MSCTAC]

summary: We sequenced mouse incisor mRNA from one-month-old Gli1-CreER;tdT and Axin2-CreER;tdT mice to compare their gene expression profile

overall_design: mRNA from Axin2+ and Gli1+ cells from one-month-old Gli1-CreER;tdT and Axin2-CreER;tdT mice incisors were generated for RNA sequencing

first: Junjun

last: Jing

first: Jifan

last: Feng


title: yylncT acts as a gatekeeper of the mesodermal transcriptional program by local modulation of DNMT3B [mouse]

status: Public on Jan 29 2019

city: Aachen

first: Chao-Chung

last: Kuo

state: NRW

address: Pauwelsstrasse 30

department: IZKF Genomics Facility

institute: RWTH Aachen University Hospital

summary:
Bidirectional transcription is a prevalent feature of eukaryotic promoters. The goal of this study is to identify novel divergent long-coding RNAs during differentiation of human ES to cardiomyocytes.
Methods: Paired end RNA-Seq was performed on the tissue obtained from the cardiogenic region of the indicated  embroynic stages of  mice. Following stages of mouse development were used:- E8,E8.5,E9.5 and E14.,
Results: Using an optimized data analysis workflow, we mapped about ~70 million sequence reads per sample to the mouse  genome (build mm10).
Conclusions: Our study represents the detailed analysis of the genome wide identification of divergent long-coding RNA generated by paired end RNA-seq technology. Our results show that NGS offers a comprehensive and more accurate quantitative and qualitative evaluation of long-non coding RNA content within a cell. We conclude that RNA-seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biological functions.

overall_design: We have used 4 different time-point (all in triplicates), covering the key stages of in vivo cardiac development in mice embryos. It includes E8, E8.5, E9.5 and E14.

first: Leo

last: Kurian

first: Stefan

last: Frank


title: Single-cell RNA-seq of Drosophila melanogaster male late third instar larval gonads

summary: The male larval gonad is a complex tissue made up of multiple cell types including germ cells and somatic cells. It is also a key developmental stage with the germline undergoing spermatogenesis. The diversity of cell types and transcriptional regulation of the developing gonad has only been broadly described. In order to get single cell resolution, we profiled late third instar larval testes of a reference Drosophila melanogaster genotype, w[1118] using single-cell RNA-Seq (scRNA-Seq). We identified and annotated 9 cell types including 4 stages of the germ cell lineage, and provide transcriptional profiles for each cell type.

overall_design: We generated late third instar larval testes scRNA-Seq profiles in biological quadruplicate pools on the 10X Chromium System (10X Genomics, Pleasanton, CA) with the v2 chemistry. We sequenced (Read1=26 bp, Read2=98 bp and Readi7=8 bp) on a Illumina HiSeq 2500 (Illumina, San Diego, CA).

first: Sharvani

last: Mahadevaraju

first: Brian

last: Oliver


title: Mammalian Hbs1L deficiency causes Pelota depletion and is associated with a unique phenotype

status: Public on Jan 15 2019

city: Boston

first: Pankaj

last: Agrawal

address: 300 Longwood ave

institute: Boston Children's Hospital

summary: Hbs1 has been established as a central component of the cell’s translational quality control pathways in both yeast and prokaryotic models; however, the functional characteristics of its human ortholog (Hbs1L) have not been well-defined.  We recently reported a novel human phenotype resulting from a mutation in the critical coding region of the HBS1L gene characterized by facial dysmorphism, severe growth restriction, axial hypotonia, global developmental delay and retinal pigmentary deposits.  Here we further characterize downstream effects of the human HBS1L mutation. HBS1L has three transcripts in humans, and RT-PCR demonstrated reduced mRNA levels corresponding with transcripts V1 and V2 whereas V3 expression was unchanged. Western blot analyses revealed HBS1L protein was absent in proband samples. Additionally, polysome profiling revealed an abnormal aggregation of 80S monosomes in patient cells under baseline conditions.  RNASeq data corresponded to the patient phenotype, with biological process analysis showing skeletal system development and sensory development genes being most altered between patient and controls.  Ribosomal sequencing demonstrated an increased translation efficiency of ribosomal RNA in Hbs1L-deficient fibroblasts, suggesting that there may be a compensatory increase in ribosome translation to accommodate the increased 80S monosome peak. Furthermore, lack of Hbs1L caused depletion of Pelota protein in both patient cells and mouse tissues, while PELO mRNA levels were unaffected. Inhibition of proteasomal function partially restored Pelota expression in human Hbs1L-deficient cells. We also describe a mouse model harboring a knockdown mutation in the murine Hbs1l gene that shared several of the phenotypic elements observed in the Hbs1L-deficient human including facial dysmorphism, growth restriction and retinal deposits. The Hbs1lKO mice similarly demonstrate diminished Pelota levels that were rescued by proteasome inhibition.

overall_design: 12 physical samples of cell cultures (patient and 2 healthy individuals as controls, 2-6 replicates per individual). Ribo-seq and mRNA-seq libraries prepared from the same samples (matched within sample)

first: Amy

last: O’Connell

first: Maxim

last: Gerashchenko

first: Marie-Francoise

last: O'Donohue

first: Samantha

last: Rosen

first: Eric

last: Huntzinger

first: Diane

last: Gleeson

first: Antonella

last: Galli

first: Edward

last: Ryder

first: Siqi

last: Cao

first: Quinn

last: Murphy

first: Shideh

last: Kazarounian

first: Sarah

middle: U

last: Morton

first: Klaus

last: Schmitz-Abe

first: Vadim

middle: N

last: Gladyshev

first: Pierre-Emmanuel

last: Gleizes

first: Bertrand

last: Seraphin

middle: B


title: Transcriptomic responses to hypoxia in endometrial stromal fibroblasts and decidual stromal cells

status: Public on Jan 01 2019

city: West Haven

first: Kalle

middle: T

last: Rytkönen

state: CT

address: 840 West Campus Drive

department: EEB, Systems Biology institute

institute: Yale University

summary: We sequenced mRNA from hypoxia treated endometrial stromal fibroblasts and decidual stromal cells in order to better understand endometrial hypoxia responses

overall_design: We sequenced mRNA from hypoxia treated (1% O2 , 24 hours) endometrial stromal fibroblasts (2 biological replicates) and decidual stromal cells (2 biological replicates) and compared these to the corresponding normoxic samples that were made available earlier (GSM1556296, GSM1556297, GSM1556298, GSM1556299)


title: yylncT acts as a gatekeeper of the mesodermal transcriptional program by local modulation of DNMT3B

city: Cologne

first: Leo

last: Kurian

state: I am not in the U.S. or Canada

address: Kurian lab,Center for Molecular Medicine, Robert-Koch-Str. 21

department: Center for Molecular Medicine

institute: University of Cologne Germany