title: Dose dependent expression of extracellular microRNAs in HCT116 colorectal cancer cells exposed to high dose rate ionizing radiation

status: Public on Sep 16 2021

city: Hirosaki

first: Satoru

last: Monzen

state: Aomori

address: Hon-cho 66-1

country: Japan

institute: Hirosaki University

summary: Biomarkers of tumour response to radiotherapy could help in optimising cancer treatment. In this study, we focus on identifying changes in extracellular miRNA as a biomarker of radiation-induced damage to human colorectal cancer cells. HCT116 cells were exposed to increasing doses of X-rays, and extracellular miRNAs were analysed by microarray. The results were correlated with frequencies of micronuclei. Fifty-nine miRNAs with positive correlation and four with negative correlation between dose (up to 6 Gy) and expression of extracellular miRNA were verified. In addition, for samples between 0 and 10 Gy, 12 miRNAs into those 59 miRNAs with positive correlation were verified. Of these, these miRNAs showed significantly positive correlation up to 10 Gy between micronucleus frequency and expression of extracellular miRNA. These results suggest that specific miRNAs could be cell damage markers and could serve as secreted radiotherapy response biomarkers for colorectal cancer; however, the results must be validated in serum samples collected from patients undergoing radiotherapy.

overall_design: Radiation induced extracellular micro RNA  expression in murine colon cancer cell (HCT116)  was measured at 72 hours after exposure to doses of 0, 6 and 10 Gy X-rays.  Four independent experiments were performed at each doses using different cell culture.

first: Tatsuya

last: Ueno


title: Glycolytic preconditioning in astrocytes mitigates trauma-induced neurodegeneration

status: Public on Aug 26 2021

city: Dallas

first: Peter

middle: M

last: Douglas

state: Texas

address: 6000 Harry Hines Blvd

department: Department of Molecular Biology

country: USA

institute: University of Texas Southwestern Medical Center at Dallas

type: Expression profiling by high throughput sequencing

summary: Reducing mitochondrial electron transport induces a Warburg-like shift to accommodate for the energetic burden caused by brain trauma and salvage dopaminergic neurons. This metabolic shift is evident in the transcriptional upregulation of key genes in the Pyruvate Dehydrogenase Complex and glycolytic pathway.

overall_design: 10 week old Surf1+/+ and Surf1-/- mice were subjected to closed-head traumatic brain injury. Brain RNA was harvested 2 hours post-injury and submitted for sequencing.

first: Rene

middle: S

last: Fonseca


title: CXCR4 drives lympho-myeloid fate of hematopoietic progenitors via mTOR and mitochondrial metabolic pathways

status: Public on Sep 02 2021

city: Toronto

first: Vincent

last: Rondeau

state: Ontario

address: 101 College Street

country: Canada

institute: University Health Network

summary: Hematopoietic stem and progenitor cells (HSPCs), including the multipotent progenitors (MPPs), are responsible for replenishing immune cells. They reside in bone marrow (BM) endosteal and (peri)-vascular niches, which provide all cellular and molecular components required for their lifelong maintenance and fate. Among them, the CXCL12 chemokine and one of its receptor, CXCR4, exert a dominant role in promoting HSPC retention and quiescence. These processes are deregulated in the WHIM Syndrome (WS), a rare immunodeficiency caused by inherited heterozygous autosomal gain-of-function CXCR4 mutations that affect homologous desensitization of the receptor. Clinically, WS is notably characterized by severe, chronic circulating lymphopenia whose mechanisms remain to be elucidated. Using a mouse model carrying a naturally occurring WS-linked Cxcr4 mutation, we explored the possibility that the lymphopenia in WS originates from defects at the MPP level in BM. The global strategy consists in performing high-throughput RNA-seq analyses of the different MPP subsets bearing or not the WS-linked Cxcr4 mutation to investigate the impact of the gain-of-Cxcr4-function on the molecular identity of MPP subsets.

overall_design: RNAseq data were generated from pools of 3 x 103 MPP1-4 sorted from the marrow fraction of WT and Cxcr41013-bearing mice.

first: Rondeau

last: Vincent

first: Balabanian

last: Karl

first: Mancini

last: Stéphane


title: Single-oocyte transcriptome analysis reveals aging-associated effects influenced by life stage and calorie restriction

status: Public on Aug 02 2021

city: Kobe

first: Tomoya

last: KITAJIMA

address: 2-2-3 Minatojima-minamimachi

department: Center for Biosystems Dynamics Research

institute: RIKEN

summary: Chromosome segregation errors in oocytes lead to the production of aneuploid eggs, which are the leading cause of pregnancy loss and of several congenital diseases such as Down syndrome. The frequency of chromosome segregation errors in oocytes increases with maternal age, especially at a late stage of reproductive life. How aging at various life stages affects oocytes differently remains poorly understood. In this study, we describe aging-associated changes in the transcriptome profile of mouse oocytes throughout reproductive life. Our single-oocyte comprehensive RNA sequencing using RamDA-seq revealed that oocytes undergo transcriptome changes at a late reproductive stage, whereas their surrounding cumulus cells exhibit transcriptome changes at an earlier stage. Calorie restriction, a paradigm that reportedly prevents aging-associated egg aneuploidy, promotes a transcriptome shift in oocytes with the up-regulation of genes involved in chromosome segregation. This shift is accompanied by the improved maintenance of chromosomal cohesin, the loss of which is a hallmark of oocyte aging and causes chromosome segregation errors. These findings have implications for understanding how oocytes undergo aging-associated functional decline throughout their reproductive life in a context-dependent manner.

overall_design: Single oocytes and their surrounding cumulus cells were analyzed for each age/diet class in two independent experiments: 2 months (Young), 4months, 9 months (Middle), 14 months (Old), 9 months (Calorie Restriction) with hyperovulation, and 2 months without hyperovulation.

first: Tappei

last: Mishina

first: Namine

last: Tabata

first: Tetsutaro

last: Hayashi

first: Mika

last: Yoshimura

first: Mana

last: Umeda

first: Masashi

last: Mori

first: Yayoi

last: Ikawa

first: Hiroshi

last: Hamada

first: Itoshi

last: Nikaido

last: Kitajima


title: The Distinct Immune Nature of the Fetal Inflammatory Response Syndrome Type I and Type II

status: Public on Aug 05 2021

city: Detroit

first: Adi

last: Tarca

state: MI

address: 3990 John R. St, 4 Brush South

institute: Wayne State University

summary: Umbilical cord blood samples from neonates with FIRS type I, FIRS type II, and without FIRS were profiled using paired-end Illumina RNAseq to evaluate transcriptomic changes associated with these syndromes.

overall_design: The study included umbilical cord blood from neonates diagnosed with FIRS type I (n = 11), FIRS type II (n = 6), or without FIRS (n = 22) born to women who underwent preterm labor with intact membranes.

first: Nardhy

last: Gomez-Lopez

first: Roberto

last: Romero

first: Bogdan

last: Done

middle: L


title: ABI1-based 7-gene expression signature predicts breast cancer metastasis and survival

status: Public on Aug 18 2021

city: Syracuse

first: Vladimir

middle: A

last: Kuznetsov

state: NY

address: 750 E Adams St

department: Urology / Biochemistry and Molecular Biology

institute: SUNY Upstate Medical University

summary: Collection of human breast cancer gene expressed measured by GPL2567. This subpopulation of breast cancer has gene expression and clinical data which were used for survival prediction analysis; resulting in emphasizing the ABI1-based 7-gene prognostic signature, as a prospective multi-gene expression clinical biomarker of breast cancer aggressiveness and metastasis, and therapeutic target.

overall_design: 295 breast cancer samples from human patients were taken. Gene expression was measured using the GPL2567 dual-channel microarray platform. Clinical data including lymph node and estrogen receptor (ER) status, disease free, metastasis, and overall survival times were measured. This dataset was used to develop a prognostic signature of metastatic breast cancer defined by our ABI1-based prognostic signature.

first: Andre

last: Grageda

first: Csaba

last: Papp

first: Leszek

last: Kotula


title: The human mitochondrial translatome promotes mitonuclear balance

status: Public on May 30 2021

city: Boston

first: Mary

middle: T

last: Couvillion

state: MA

address: 77 Avenue Louis Pasteur

department: Genetics

institute: Harvard Medical School

summary: Oxidative phosphorylation (OXPHOS) complexes consist of nuclear- and mitochondrial- encoded subunits, forcing cross-compartment synchronization of gene expression to achieve mitonuclear balance. To characterize how human cells coordinate OXPHOS gene expression, we establish a mitoribosome profiling approach that resolves features of the mitochondrial translatome, including the synthesis of a four amino acid mitopeptide. Strikingly, average mitochondrial and cytoplasmic synthesis rates correspond precisely across OXPHOS complexes. Coordinated mitochondrial and cytosolic synthesis does not require rapid feedback between the two translation systems. By contrast, we find that the Leigh syndrome gene, LRPPRC, maintains correlated mitochondrial and cytosolic translatomes. Our results lead to a model of human mitonuclear balance that requires tightly balanced cross-compartment protein synthesis, representing a vulnerability for cellular proteostasis.

overall_design: Mitochondrial ribosome profiling in 5 human cells types, as well as cytosolic ribosome profiling and RNA-seq in select cell types. Drug and genetic perturbations also included

first: Iliana

middle: C

last: Soto

first: Katja

last: Hansen

first: Stirling

last: Churchman


title: The mRNA and miRNA profiles from rats ventral prostate submitted to maternal low protein diet

status: Public on Jul 25 2021

city: Botucatu

first: Sérgio

middle: Alexandre Alcantara

last: Santos

state: São Paulo

address: Rua Professor Doutor Antonio 250 Celso Wagner Zanin

department: department of structural and functional biology

country: Brazil

institute: UNESP

type: Non-coding RNA profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: The miRNA profile from rats ventral prostate submitted to maternal low protein diet

summary:
Purpose: The goals of this study are to compare NGS-derived ventral prostate transcriptome profiling (RNA-seq) from control and offspring submitted to maternal low protein diet during gestation and lactational period, on postnatal day 21 and 540.
Methods: Ventral prostate microRNA profiles of 21- and 540-day-old control rats (CTR) and gestacional and lactacional low protein diet rats (GLLP) were generated by deep sequencing, in triplicate, using Illumina HiSeq-2500.

overall_design: Ventral prostate microRNA profiles of 21- and 540-day-old rat and (CTR) and gestational and lactational low protein diet rats (GLLP).

first: Luis

last: Justulin

first: Ana

last: Camargo

first: Ketlin

last: Colombelli

first: Flávia

middle: B

last: Constatntino

first: Sergio


title: Longitudinal Study of Transcriptomic Changes Occurring Over the Course of CHOP Treatment in Canine Lymphoma

status: Public on Jul 14 2021

first: Miles

last: Mee

address: 661 University Ave Suite 510

institute: Ontario Institute for Cancer Research

summary: The standard treatment for canine lymphoma (cL)  is the CHOP chemotherapy protocol. Most cL patients treated with CHOP initially achieve remission but the duration varies and the majority of dogs eventually relapse with a multidrug resistant phenotype. This study assesses changes in gene expression occurring in cL tumor cell populations over the course of CHOP treatment. We measured gene expression using RNA-Seq on 15 cL patient samples taken prior to treatment and again 6 weeks into treatment.

overall_design: Differential gene expression between canine lymphoma tumour samples from 15 dogs taken prior to treatment and 6 weeks into treatment.   There were no replicate or control samples.

first: Brenda

last: Coomber


title: Plasma proteomics in preterm birth and normal pregnancy

status: Public on May 24 2021

first: Adi

last: Tarca

summary:
Maternal plasma samples collected longitudinally from pregnant women were profiled using SomaLogic aptamer-based assays in women with normal pregnancy and those who delivered preterm.
DiagnosisGA is the gestational age at diagnosis with any disease indicated by the Group variable, and it is set to NA for normal pregnancies. In the Group variable, sPTD stands for spontaneous preterm delivery, and PPROM for preterm premature rupture of membranes.
Additional longitudinal samples of the controls, including the two samples included herein, are also available and described in PMID: 28738067.

overall_design: Longitudinal study with both cases and controls being sampled at 17-22 and 27-33 weeks of gestation.

first: Roberto

last: Romero

first: Bogdan

first: Nardhy

last: Gomez-Lopez

first: Hassan

last: Sonia


title: The precursors of hematopoietic stem cells during mouse embryogenesis

status: Public on Jul 17 2021

city: Kumamoto

first: Saori

last: Morino-Koga

state: Kumamoto

address: 2-2-1 Honjo, Chuo-ku

department: Institute of Molecular Embryology and Genetics

institute: Kumamoto University

summary: Definitive hematopoietic stem cells (HSCs) bud off from the hemogenic endothelial cells (HEC) located in the dorsal aorta of the mouse embryo. The maturation of HSCs from HEC occurs through the precursor of HSCs (pre-HSCs) between embryonic day (E) 9.5 and E11.5. To clarify the differentiation process of pre-HSCs, we performed single-cell RNA-seq analysis of cells dissociated from the dorsal aorta and its surrounding tissues and the fetal liver at E10.5 and E11.5. We identified pre-HSCs population generated from an arterial marker-expressing cluster. Thus, our data might be useful to understand the differentiation process of pre-HSCs.

overall_design: Single-cell RNA-seq analyses of the dorsal aorta and its surrounding tissues and the fetal liver of E10.5 and E11.5 embryos.

first: Tomomasa

last: Yokomizo

first: Toshio

last: Suda

first: Minetaro

last: Ogawa


title: AURKA Inhibition Reprograms Metabolism dependent on PGC1α to Drive Synthetic Lethality with Fatty Acid Oxidation Inhibition in Glioblastoma

status: Public on Jun 17 2021

first: Boston University

last: Microarray and Sequencing Resource

address: 72 East Concord Street, E631

department: Microarray and Sequencing Resource

institute: Boston University

summary:
We described the metabolic alterations in glioblastoma model systems elicited by AURKA inhibition. By utilizing proteomic and transcriptomic analyses coupled with untargeted polar and nonpolar metabolite analysis by LC/MC, we found that AURKA inhibition leads to a profound reprogramming of tumor metabolism, which suppresses c-Myc protein levels and increases pro-survival PGC1α which in concert mediate a suppression of glycolysis and a concomitant activation of oxidative phosphorylation (OXPHOS) that is fueled by enhanced fatty acid oxidation (FAO). We targeted these metabolic aberrations with novel combination therapies involving clinical approved drugs in glioblastoma system both in vitro and in vivo.
We used microarrays to detail the global programme of gene expression underlying cellularisation and identified distinct classes of up-regulated and down-regulated genes in Alisertib resistant cells.

overall_design: GBM22 cells were chronically treated with Alisertib for 10 days. Then the cells were collected and mRNA was extracted.

first: Thi

last: Nguyen

first: Markus

last: Siegelin


title: Whole blood transcriptomics data in preterm birth and early preeclampsia

summary:
Maternal whole blood colected longitudinally were profiled using Affymetrix Human Transcriptome Arrays to evaluate prediction of gestational age in normal and complicated pregnancies and predict preterm birth.
LMP is the date at the last menstrual period. Oper_LMP is the date at the last menstrual period with eventual adjustment based on ultrasound determination. Gestational age (GA) (weeks) is defined as (Date at sample - Oper_LMP)/7.  For control pregnancies, SubGroup defines those with spontaneous labor at term (TL) as opposed with those delivered by cesarean section (TNL). Train is 1 if the sample was used in sub-challenge 1 in the training set as opposed to test set (0). D2 is 1 if the sample was used in the 2 interval prediction scenario, and if yes, it was assigned to the interval given by column D2Interval. D3 is 1 if the sample was used in the 3 interval prediction scenario, and if yes, it was assigned to the interval given by column D3Interval.  DiagnosisGA is the gestational age at diagnosis with any disease indicated by the Group variable, and it is set to NA for normal pregnancies.

overall_design: Longitudinal study

first: Gaurav

last: Bhatti


title: Animal study to validate effects of ACOT1 silencing in Non-alcoholic Fatty Liver Disease (NAFLD)

status: Public on May 25 2021

first: Marc

last: Angeli

address: 101 College street

department: Multi Organ Transplant

summary:
6-8-week-old male C57BL/6 were divided into 2 groups after 12 weeks on the HFD diet, and tail vein injections of an Adenoviral vector containing
Ad-GFP-U6-scramble-shRNA or Ad-GFP-U6-m-ACOT1-shRNA at 1x109 PFU were performed weekly for 6 weeks (Vector Biolabs)

overall_design: Using Adinoviral vectors to silence ACOT 1 in mice after a 16 weeks of High Fat, High Carbohydrate diet.

first: Mamatha

last: Bhat

first: Cristina

last: Baciu

first: Diogo

last: Pellegrina


title: Maternal whole blood transcriptomics to assess changes with gestational age in normal pregnancy II

first: Adi

summary:
Maternal whole blood colected longitudinally were profiled using Affymetrix Human Transcriptome Arrays .
This is a re-analysis of GSE121974, with additional metadata and different summarization of gene expression at ENTREZ ID level instead of Transcript Cluster as in the original submission.
LMP is the date at the last menstrual period. Oper_LMP is the date at the last menstrual period with eventual adjustment based on ultrasound determination. Gestational age (GA) (weeks) is defined as (Date at sample - Oper_LMP)/7. For control pregnancies, SubGroup defines those with spontaneous labor at term (TL) as opposed with those delivered by cesarean section (TNL). Train is 1 if the sample was used in sub-challenge 1 in the training set as opposed to test set (0). D2 is 1 if the sample was used in the 2 interval prediction scenario, and if yes, it was assigned to the interval given by column D2Interval. D3 is 1 if the sample was used in the 3 interval prediction scenario, and if yes, it was assigned to the interval given by column D3Interval.  DiagnosisGA is the gestational age at diagnosis with any disease indicated by the Group variable, and it is set to NA for normal pregnancies.

overall_design: Longitudinal study including 4 to 6 blood samples collected from each of the 49 women with a normal pregnancy.


title: Maternal whole blood transcriptomics to assess changes with gestational age in normal pregnancy I

summary:
Maternal whole blood colected longitudinally were profiled using Affymetrix Human Transcriptome Arrays to evaluate changes with gestational age and with labor in normal pregnancy.
This is a re-analysis of GSE113809, with additional metadata and different summarization of gene expression at ENTREZ ID level instead of Transcript Cluster as in the original submission.
LMP is the date at the last menstrual period. Oper_LMP is the date at the last menstrual period with eventual adjustment based on ultrasound determination. Gestational age (GA) (weeks) is defined as (Date at sample - Oper_LMP)/7. For control pregnancies, SubGroup defines those with spontaneous labor at term (TL) as opposed with those delivered by cesarean section (TNL). Train is 1 if the sample was used in sub-challenge 1 in the training set as opposed to test set (0). D2 is 1 if the sample was used in the 2 interval prediction scenario, and if yes, it was assigned to the interval given by column D2Interval. D3 is 1 if the sample was used in the 3 interval prediction scenario, and if yes, it was assigned to the interval given by column D3Interval.  DiagnosisGA is the gestational age at diagnosis with any disease indicated by the Group variable, and it is set to NA for normal pregnancies.

overall_design: The study included normal pregnancies with (n=8) and without (n=8) spontaneous labor at term.  Half of the women in each group had 3 longitudinal samples taken from 12.1-40.3 weeks of gestation, while the other half of women had only one sample taken at term before delivery, for a total of 32 samples.

first: Roberto


title: Animal study to validate effects of ACOT1 in Non-alcoholic Fatty Liver Disease (NAFLD)

status: Public on May 21 2021

summary:
6-8-week-old male C57BL/6 were divided into 2 groups after 12 weeks on the HFD diet, and tail vein injections of either an Adenoviral vector
(with Adenoviral type 5 backbone) containing Ad-GFP-m-ACOT1 or Ad-GFP at 1x109 PFU were performed weekly for 4 weeks

overall_design: Ad-GFP-m-ACOT1 or Ad-GFP


title: Myofibroblast transcriptome indicates SFRP2+ fibroblast progenitors in systemic sclerosis skin

status: Public on May 20 2021

city: Pittsburgh

first: Tracy

last: Tabib

state: PA

address: 200 Lothrop Street

department: Department of Medicine

institute: University of Pittsburgh

summary: Skin and lung fibrosis in systemic sclerosis (SSc) is driven by myofibroblasts, alpha-smooth muscle actin (SMA) expressing cells that produce matrix as well as increase tension on surrounding tissues. Myofibroblast progenitors have been described to arise from a variety of cell types in murine fibrosis models, but relatively modest insight is available as to their source and differentiation in fibrotic human diseases. We utilize single cell RNA-sequencing to examine the transcriptome changes that occur in fibroblasts in SSc skin and during myofibroblast differentiation. We show that dermal myofibroblasts arise from an SFRP2/DPP4-expressing progenitor fibroblast population. In SSc skin, fibroblasts undergo global changes in gene expression, including SFRP2-expressing fibroblasts, which globally upregulate expression of markers, such as PRSS23 and THBS1. However, only a fraction of SSc fibroblasts differentiate into myofibroblasts, as shown by expression of additional markers, such as SFRP4 and FNDC1. These results indicate that myofibroblasts derive from a specific fibroblast subpopulation in SSc skin, that their differentiation proceeds in two stages and that other fibroblast populations also shift transcriptomes in SSc skin, suggesting a cytokine driven process. The myofibroblast transcriptome implicates upstream transcription factors that should help further unravel the drivers of myofibroblast differentiation.

overall_design: Using droplet-based single cell RNA sequencing we analyzed 12 scleroderma (SSc) biopsy skin specimens against 10 healthy controls.  Clustering, pseudotime, and transcription factor inference analyses were performed and select marker gene were examined for coexpression using immunofluorescence.

first: Mengqi

last: Huang

first: Nina

last: Morse

first: Anna

last: Papazoglou

first: Rithika

last: Behera

first: Minxue

last: Jia

first: Melissa

last: Bulik

first: Daisy

middle: E

last: Monier

first: Panayiotis

middle: V

last: Benos

first: Wei

last: Chen

first: Robyn

last: Domsic

first: Robert

last: Lafyatis


title: Whole blood transcriptomics data in normal pregnancy, preterm birth and early preeclampsia

last: Tarca


title: Robust single-cell discovery of RNA targets of RNA binding proteins and ribosomes [tia1_eclip]

status: Public on May 09 2021

city: La Jolla

first: Gene

last: Yeo

state: CA

address: 2880 Torrey Pines Scenic Dr. Room 3805/Yeo Lab

institute: UCSD

summary: RNA binding proteins (RBPs) are critical regulators of gene expression and RNA processing that are required for gene function. Yet, the dynamics of RBP regulation in single cells is unknown. To address this gap in understanding, we developed STAMP (Surveying Targets by APOBEC Mediated Profiling), which efficiently detects RBP RNA interactions. STAMP does not rely on UV crosslinking or immunoprecipitation and, when coupled with single cell capture, can identify RBP and cell type specific RNA protein interactions for multiple RBPs and cell types in single pooled experiments. Pairing STAMP with long read sequencing also yields RBP target sites for full length isoforms. Finally, conducting STAMP using small ribosomal subunits (RiboSTAMP) allows analysis of transcriptome wide ribosome association in single cells. STAMP enables the study of RBP RNA interactomes and translational landscapes with unprecedented cellular resolution.

overall_design: Crosslinking and immunoprecipitation of TIA1 bound RNA and sequencing from 2 technical replicates.

first: Kris

last: Brannan

first: Brian

last: Yee

first: Isaac

last: Chaim

first: Dan

last: Lorenz

first: Ryan

last: Marina

first: Assael

last: Madrigal

first: Kevin

last: Dong

first: Eric

last: Kofman

first: Pratibha

last: Jagannatha

middle: W


title: Robust single-cell discovery of RNA targets of RNA binding proteins and ribosomes [STAMP_pacbio]

summary: RNA binding proteins (RBPs) are critical regulators of gene expression and RNA processing that are required for gene function. Yet, the dynamics of RBP regulation in single cells is unknown. To address this gap in understanding, we developed STAMP (Surveying Targets by APOBEC Mediated Profiling), which efficiently detects RBP-RNA interactions. STAMP does not rely on UV-crosslinking or immunoprecipitation and, when coupled with single-cell capture, can identify RBP- and cell type-specific RNA-protein interactions for multiple RBPs and cell types in single, pooled experiments. Pairing STAMP with long-read sequencing yields RBP target sites in an isoform-specific manner. Finally, Ribo-STAMP leverages small ribosomal subunits to measure transcriptome-wide ribosome association in single cells. STAMP enables the study of RBP-RNA interactomes and translational landscapes with unprecedented cellular resolution.

overall_design: strategy for immunoprecipitation-free detection of protein-RNA interactions by fusion of RNA binding proteins and ribosomal subunits to the C-to-U RNA editing enzyme APOBEC1 and quantification of interaction-driven edits by sequencing, to allow interaction detection on long-read and single-cell platforms

middle: R


title: Robust single-cell discovery of RNA targets of RNA binding proteins and ribosomes [STAMP_new_eclip]

overall_design: Crosslinking and immunoprecipitation of APOBEC, SLBP, TIA1, and RBFOX2 bound RNA and sequencing from 2 technical replicates.


title: Robust single-cell discovery of RNA targets of RNA binding proteins and ribosomes [scRNA-seq]

overall_design: Cells expressing RBP-APOBEC1 fusions for C-to-U editing of RBP target-RNAs were processed through the Chromium Single Cell Gene Expression Solution using the Chromium Single Cell 3’ Gel Bead, Chip, 3’ Library and 3’ Feature Barcode Library Kits v3 (10X Genomics) as per the manufacturer’s protocol. The following fusion expressions were processed for a target of 10,000 cells/ experiment: transient transfection of control- and RBFOX2-APOBEC1 (STAMP) in HEK293T and separately in neural progenitor cells (NPC), independent stable inductions of control- and RBFOX2:TIA1-STAMP (cell mixture, capture sequence barcoded), and RPS2-STAMP.


title: Regulation of TLR8-activated gene expression in human neutrophils

status: Public on May 07 2021

city: Verona

first: Francisco

middle: Miguel Angel

last: Bianchetto-Aguilera

state: VR

address: Strade le Grazie, 8

country: Italy

institute: University of Verona

type: Genome binding/occupancy profiling by high throughput sequencing


title: Robust single-cell discovery of RNA targets of RNA binding proteins and ribosomes [NP]

overall_design: This data was generated using a strategy for immunoprecipitation-free detection of protein-RNA interactions by fusion of RNA binding proteins and ribosomal subunits to the C-to-U RNA editing enzyme APOBEC1 and quantification of interaction-driven edits by sequencing, to allow interaction detection on long-read and single-cell platforms.


title: Robust single-cell discovery of RNA targets of RNA binding proteins and ribosomes

summary: RNA binding proteins (RBPs) are critical regulators of gene expression and RNA processing that are required for gene function. Yet, the dynamics of RBP regulation in single cells is unknown. To address this gap in understanding, we developed STAMP (Surveying Targets by APOBEC Mediated Profiling), which efficiently detects RBP-RNA interactions. STAMP does not rely on UV-crosslinking or immunoprecipitation and, when coupled with single-cell capture, can identify RBP- and cell type-specific RNA-protein interactions for multiple RBPs and cell types in single-pooled experiments. Pairing STAMP with long-read sequencing also yields RBP target sites for full-length isoforms. Finally, conducting STAMP using small ribosomal subunits (Ribo-STAMP) allows analysis of transcriptome-wide ribosome association in single cells. STAMP enables the study of RBP-RNA interactomes and translational landscapes with unprecedented cellular resolution.

overall_design: Refer to individual Series


title: Regulation of TLR8-activated gene expression in human neutrophils [RNA-seq neutrophils & monocytes]

summary: The transcription factors that regulate gene expression in stimulated neutrophils are poorly characterized. Herein, we found that the genomic distribution of the myeloid lineage determining transcription factors PU.1 and C/EBPβ, as well as that of the histone modification H3K27Ac, which marks active chromatin, significantly change in human neutrophils treated with R848, a ligand of TLR8.

overall_design: Examination of histone modification, transcription factor binding and transcriptome in human neutrophils and granulocytic-differentiated HL-60 cell line

first: Nicola

last: Tamassia

first: Gioacchino

last: Natoli

first: Marco

last: Cassatella


title: Regulation of TLR8-activated gene expression in human neutrophils  [RNA-seq HL-60]


title: Mapping the genetic architecture of human traits to cell types in the kidney identifies mechanisms of disease and potential treatments [RNA-seq]

city: Philadelphia

first: Xin

last: Sheng

institute: University of Pennsylvania

summary: The functional interpretation of GWAS remains challenging due to the cell-type dependent influences of genetic variants. Here, we generated comprehensive maps of expression quantitative trait loci (eQTL) for 659 microdissected human kidney samples and identified cell-type eQTLs by mapping interactions between cell type abundance and genotype. By partitioning heritability using stratified LD-score regression to integrate GWAS with scRNA-seq and snATAC-seq data, we prioritized proximal tubules in kidney function and endothelial cells and distal tubule segments in blood pressure pathogenesis. Bayesian colocalization analysis nominated more than 200 genes for kidney function and hypertension. Our study clarifies the mechanism of commonly used antihypertensive and renal protective drugs and identifies drug repurposing opportunities for kidney disease.

overall_design: RNA-seq data for human tubule and glomerular samples

first: Ziyuan

last: Ma

first: Matthew

middle: J

last: Seasock

first: Katalin

last: Susztak


title: Regulation of TLR8-activated gene expression in human neutrophils [ChIP-seq]


title: Robust single-cell discovery of RNA targets of RNA binding proteins and ribosomes [RNA-seq]

first: Gene

last: Yeo

overall_design: strategy for immunoprecipitation-free detection of protein-RNA interactions by fusion of RNA binding proteins and ribosomal subunits to the C-to-U RNA edtiing enzyme APOBEC1 and quantification of interaction-driven edits by sequencing, to allow interaction detection on long-read and single-cell platforms

first: Kris

last: Brannan


title: Adult rat ventral tegmental area single-nucleus RNA-seq dataset for "An atlas of transcriptionally defined cell populations in the rat ventral tegmental area"

status: Public on Mar 31 2021

city: Birmingham

first: Jeremy

middle: Jason

last: Day

state: AL

address: 1825 University Blvd

department: Neurobiology

institute: UAB

summary: This dataset contains single-nucleus RNA sequencing results from adult rat brain (ventral tegmenal area, or VTA). The goal of this experiment was to define the transcriptional landscapes of distinct cell types in the VTA. Single-cell sequencing was carried out with nuclei suspensions (sorted using flow cytometry) using the 10X Genomics Chromium single cell sequencing platform.

overall_design: This experiment contains 4 biological samples, each of which combined tissue collected from 3 animals of the same sex. Samples were adult rat VTA microdissections isolated from male and female rats. Tissue was lysed to allow for nuclei collection via centrifugation. FACS-sorted nuclei were subject to 10X Genomics GEM generation and barcoding, GEM-RT cleanup and cDNA amplication, and library construction using a Chromium Single Cell 3ʹ Reagent Kit (v3 chemistry). Libraries underwent directional, paired-end PolyA+ RNA-seq on an Illumina Next-seq 500. Each sample has multiple raw fastq files, corresponding to different sequencing lanes (e.g., L001, L002, etc) and different reads (e.g., R1, R2). Additional index files are also provided for each sample and each lane (I1).

first: Robert

last: Phillps

first: Jennifer

last: Tuscher

first: Samantha

last: Black

first: Lara

last: Ianov


title: Systematic discovery and perturbation of regulatory genes in human T cells reveals the architecture of immune networks [CRISPR]

status: Public on Apr 26 2021

city: San Francisco

first: Alexander

last: Marson

address: 1650 Owens St

institute: Gladstone-UCSF Institute of Genomic Immunology

summary: Complex gene regulatory networks ensure that important genes are expressed at precise levels. When gene expression within these networks is sufficiently perturbed it can lead to disease. To understand how gene expression disruptions percolate through a network, we must first map the connections between regulatory genes and their downstream targets. However, it has been challenging to identify the upstream regulators for genes of interest. Here we develop a system for systematic discovery of upstream regulators of critical immune factors – IL2RA, IL-2, and CTLA4 – in primary human T cells. Then, CRISPR perturbations coupled with RNA-Seq, and ATAC-Seq, allowed us to map the full network of these regulators’ target genes and enhancers. These regulators form highly interconnected networks with extensive feedback loops. Furthermore, this network is highly enriched for autoimmune-associated disease variants and genes. These results provide insight into how autoimmune associated disease genes are regulated in T cells as well as broader principles about the structure of human gene regulatory networks.

overall_design: Pooled CRISPR screen followed by FACS to sort CD25 (IL2RA), IL-2, and CTLA4 high or low expressing cells.

first: Jacob

last: Freimer

first: Oren

last: Shaked

first: Sahin

last: Naqvi

first: Nasa

last: Sinnott-Armstrong

first: Arwa

last: Kathiria

first: Amy

middle: F

last: Chen

first: Jessica

last: Cortez

first: William

last: Greenleaf

first: Jonathan

middle: K

last: Pritchard


title: The transcriptome of rabbit conjunctiva in dry eye disease: Large-scale changes and similarity to the human dry eye

status: Public on Mar 30 2021

city: STONY BROOK

first: Adam

last: Master

state: NEW YORK

address: 101 Nicolls Road, Sciences Center

department: Department of Preventive Medicine

institute: The State University of New York in Stony Brook

summary:
Rabbit Dry Eye Diesease model induced with 3 weekly injections of Concanavalin A into the periorbital lacrimal glands Male Dutch-Belted rabbits.
The pathophysiology of dry eye disease (DED) remains largely unknown, accounting in part for the lack of successful treatments.  The transcriptome of full-thickness’s conjunctival tissue from rabbits with DED and from normal controls was determined using microarrays.  DED induced large-scale changes in gene transcription involving 5,184 genes (22% of the total). Differentially expressed genes could be segregated into: functional modules and clusters; altered pathways; functionally linked genes; and groups of individual genes of known or suspected pathophysiological relevance to DED. A common feature of these subgroups is the breadth and magnitude of the changes that encompass ocular immunology and essentially all aspects of cell biology.  Prominent changes concerned innate and adaptive immune responses; ocular surface inflammation; at least 25 significantly altered signaling pathways; a large number of chemokines; cell cycle; and apoptosis.  Comparison of our findings to the limited extant transcriptomic data from DED patients associated with either Sjogren’s syndrome or non-Sjogren’s etiologies revealed a significant correlation between human and rabbit DED transcriptomes.  Our data, establishing the large-scale transcriptomic changes of DED and their potential similarity to the human, underscore the enormous complexity of DED; establish a robust animal model of DED; will help expand our understanding of its pathophysiology; and could guide the development of successful therapeutic strategies.

overall_design: Affymetrix GeneChip™ Rabbit Gene 1.0 ST Arrays (ThermoFisher Scientific) were used to analyze transcriptome changes in rabbit conjunctival tissues. Two experimental groups: ConA vs. Naive of rabbit conjunctival tissues were compared in triplicate. To obtain enough RNA, samples from 3 independent animals (6 eye tissues) were pulled for each microarray.

first: Apostolos

last: Kontzias

first: Liqun

last: Huang

first: Wei

first: Anna

last: Tsioulias

first: Samaneh

last: Zarabi

first: Michael

last: Wolek

first: Brian

middle: M

last: Wollocko

last: Honkanen

first: Basil

last: Rigas


title: Analysis of changes in circular RNA expression in human dilated cardiomyopathy

status: Public on Mar 10 2021

city: shanghai

first: Zhenhao

last: Lin

address: shanghaixuhui

country: China

institute: Fudan University

summary: Circular RNAs (circRNAs) have been reported to play important roles in various cardiovascular diseases. However, their expression profile in human dilated cardiomyopathy (DCM) has not been fully elucidated. In our study, heart samples from DCM patients and healthy controls were used to identify circRNAs by  high-throughput sequencing. A total of 9585 circRNAs were identified in the DCM and control groups. To assess the differentially expressed circRNAs, the criteria were set as a fold change of ≥ 2 or ≤ 0.5 and a P value of < 0.05. Compared with circRNAs in the control group, 298 dysregulated circRNAs were identified in patients with DCM, of which 231 were upregulated and 85 were downregulated.  In conclusion, our study evaluated cardiac circRNA expression in DCM by high-throughput sequencing and provide a foundation for future studies of circRNAs in DCM.

overall_design: CircRNA expression profiles of dilated cardiomyopathy patients and healthy controls were generated by  high-throughput sequencing


title: Systematic discovery and perturbation of regulatory genes in human T cells reveals the architecture of immune networks [RNA-Seq]

first: Alexander

last: Marson

overall_design: RNA-Seq of CD4+CD25- human T cells after CRISPR KO of 24 genes or AAVS1 controls

first: Jacob

last: Freimer

first: Oren

last: Shaked

first: Sahin

last: Naqvi


title: Systematic discovery and perturbation of regulatory genes in human T cells reveals the architecture of immune networks

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


title: Human chorionic gonadotropin modulates the transcriptome of the myometrium and cervix in late gestation

status: Public on Mar 05 2021

first: Adi

last: Tarca

summary: Murine myometrium and cervix samples were profiled using paired-end Illumina RNA-seq to evaluate transcriptomic changes in these tissues associated with the systemic administration of hCG.

overall_design: The study included myometrial and cervical samples from mice intraperitoneally administrated with human chorionic gonadotropin (n = 10) or PBS (n = 10), for a total of 40 samples.

first: Nardhy

last: Gomez-Lopez

first: Roberto

last: Romero


title: Systematic discovery and perturbation of regulatory genes in human T cells reveals the architecture of immune networks [ATAC-Seq]

overall_design: ATAC-Seq of CD4+CD25- human T cells after CRISPR KO of 24 genes or AAVS1 controls

first: Nasa

last: Sinnott-Armstrong

first: Arwa

last: Kathiria

first: Amy

last: Chen

first: Jessica

last: Cortez

first: William

last: Greenleaf

first: Jonathan

last: Pritchard


title: Systematic discovery and perturbation of regulatory genes in human T cells reveals the architecture of immune networks [Amplicon]

overall_design: Amplicon sequencing to detect insertion/deletions at CRISPR guide RNA target sites.


title: Human hepatocyte PNPLA3 148M exacerbates rapid non-alcoholic fatty liver disease development in chimeric mice

status: Public on Feb 13 2021

city: New York

first: Mohammad

last: Kabbani

address: 1230 York Ave, Box 64

institute: The Rockefeller University

summary: We report how human hepatocytes with PNPLA3 148I and 148M variants (rs738409) engrafted in the livers of chimeric mice respond to different durations of hypercaloric western style diet (WD).  To determine how WD affected human and mouse gene expression we performed RNA-sequencing (RNA-seq) on livers from fasting mice.

overall_design: Liver transcriptomic profile of 6hrs fasting human liver chimeric mice engrafted with either a 148I or 148M human hepatocyte donor after different durations of WD or chow.

first: Eleftherios

last: Michailidis

first: Sandra

last: Steensels

first: Clifton

last: Fulmer

first: Joseph

last: Luna

first: Jérémie

last: Le Pen

first: Matteo

last: Tardelli

first: Brandon

last: Razooky

first: Inna

last: Ricardo-Lax

first: Chenhui

last: Zou

first: Briana

last: Zeck

first: Ansgar

last: Stenzel

first: Corrine

last: Quirk

first: Lander

last: Foquet

first: Alison

last: Ashbrook

last: Schneider

first: Serkan

last: Belkaya

first: Gadi

last: Lalazar

first: Yupu

last: Liang

first: Meredith

last: Pittman

first: Lindsey

last: Devisscher

first: Hiroshi

last: Suemizu

first: Neil

last: Theise

first: Luis

last: Chiriboga

first: David

last: Cohen

first: Robert

last: Copenhaver

first: Markus

last: Grompe

first: Philip

last: Meuleman

first: Baran

last: Ersoy

first: Charles

last: Rice

first: Ype

last: de Jong


title: A genetic map of the murine dorsal vagal complex and its role in obesity

status: Public on Feb 12 2021

city: Copenhagen

first: Tune

middle: Hannes

last: Pers

address: Blegdamsvej 3B

department: Novo Nordisk Foundation Center for Basic Metabolic Research

country: Denmark

institute: University of Copenhagen


title: A genetic map of the murine dorsal vagal complex and its role in obesity [bulk RNA-seq]

summary: The brainstem dorsal vagal complex (DVC) is known to regulate energy balance and is the target of appetite suppressing hormones, such as glucagon-like peptide-1 (GLP-1). Here we provide a comprehensive genetic map of the DVC and identify neuronal populations that control feeding. Combining bulk and single-nucleus gene expression and chromatin profiling of DVC cells, we reveal 25 neuronal populations with unique transcriptional and chromatin accessibility landscapes and peptide receptor expression profiles. GLP-1 receptor (GLP-1R) agonist administration induces gene expression alterations specific to two distinct sets of Glp1r neurons – one population in the area postrema (AP) and one in the nucleus of the solitary tract (NTS) that also expresses calcitonin receptor (Calcr). Transcripts and regions of accessible chromatin linked to obesity-associated genetic variants are enriched in AP and NTS neurons that express Glp1r and/or Calcr, and activation of several of these neuronal populations decreases feeding in rodents. Thus, DVC neuronal populations associated with obesity predisposition suppress feeding and may represent targets for therapy of obesity.

overall_design: Bulk RNA-sequencing

first: Mette

middle: Q

last: Ludwig

first: Martin

middle: G

last: Myers Jr

middle: H


title: RNA sequencing reveals distinct immune responses in the chorioamniotic membranes of women with preterm labor and microbial or sterile intra-amniotic inflammation

status: Public on Feb 01 2021

first: Adi

last: Tarca

address: 3990 John R. St, 4 Brush South

institute: Wayne State University

summary: Chorioamniotic membrane samples were profiled using paired-end Illumina RNAseq to evaluate transcriptomic changes in these tissues associated with the inflammatory status of the amniotic cavity.

overall_design: The study included women with intact membranes who underwent spontaneous preterm labor and birth without intra-amniotic inflammation (PTL, n = 12), with sterile intra-amniotic inflammation (PTL_SIAI, n = 17), and with intra-amniotic infection (PTL_IAI, n = 11).

first: Nardhy

last: Gomez-Lopez

first: Roberto

last: Romero

middle: L

first: Chaur-Dong

last: Hsu


title: A genetic map of the murine dorsal vagal complex and its role in obesity [single-cell RNA-seq and ATAC-seq]

overall_design: single-nucleus RNA- and ATAC-sequencing


title: Global gene regulation by RNA-binding protein NrdA in Aspergillus luchuensis mut. kawachii

status: Public on Jan 08 2021

city: Kagoshima

first: Taiki

last: Futagami

address: Korimoto 1-21-24

department: Department of Agriculture

institute: Kagoshima University

summary: We report that the RNA-binding protein NrdA has a significant role on the global mRNA expression in the white koji fungus, Aspergillus luchuensis mut. kawachii. We constructed the nrdA conditional expression strain using the Tet-On system in A. kawachii. Downregulation of nrdA caused severe growth defect, indicating that NrdA is essential for proliferation of A. kawachii. Parallel RNA-seq and RNA immunoprecipitation (RIP)-seq analysis identified potential NrdA-interacted transcripts, corresponding to 32% of predicted protein coding genes of A. kawachii. Subsequent gene ontology analysis suggested that overexpression of NrdA affects a variety of metabolic activity including secondary metabolite production.

overall_design: Examination of functional role of RNA-binding protein NrdA in the white koji fungus

first: Kazuki

last: Mori

first: Chihiro

last: Kadooka


title: Macrophage training to Borrelia burgdorferi governs cardiac inflammation in the mammalian host

status: Public on Jan 21 2021

city: Derio

first: Jose

middle: Luis

last: Lavin

state: Bizkaia

address: Parque Tecnológico de Bizkaia Building 502, Floor 0

country: Spain

institute: CIC bioGUNE

overall_design: Refer to individual Series


title: scRNA-sequencing reveals new enteric nervous system roles for GDNF, NRTN, and TBX3

status: Public on Jan 01 2021

first: Michael

last: Gonzalez

state: Pennsylvania

address: 3535 Market St

department: Translational Medicine and Human Genetics

summary: Bowel function requires coordinated activity of many enteric neuron subtypes. Clear definition of subtype-specific gene expression may facilitate molecular diagnoses for bowel motility disorders. Using adult mouse colon RNAseq data from 635 myenteric neurons and 707 E17.5 neurons, we defined seven adult myenteric neuron subtypes, eight E17.5 neuron subtypes and hundreds of differentially-expressed genes. Manually dissected human colon myenteric plexus yielded data from 48 neurons, 3798 glia, 5568 smooth muscle, 377 interstitial cells, and 2153 macrophages. Immunohistochemistry demonstrated differential protein abundance for BNC2, PBX3, RBFOX1, TBX2, and TBX3 in enteric neuron subtypes. Conditional Tbx3 loss reduced NOS1-expressing myenteric neurons. Differential Gfra1 and Gfra2 expression coupled with calcium imaging revealed that GDNF and neurturin acutely and differentially regulate activity of ~50% of myenteric neurons with distinct effects on smooth muscle contractions. This insight into enteric nervous system biology provides a foundation for future studies of bowel motility disorders.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: 20 scRNAseq datasets were analyzed: (1) 3 single-nucleus seq runs from mouse distal colon, (2) 16 single nucleus seq samples from human, (3) 1 single cell seq from E17.5 mouse whole bowel

first: Christina

last: Wright

first: Sabine

last: Schneider

first: Kristen

last: Smith-Edwards

first: Fernanda

last: Mafra

first: Anita

last: Leembruggen

first: Deepika

last: Kothakapa

first: Jessica

middle: B

last: Anderson

first: Beth

middle: A

last: Maguire

first: Tao

last: Gao

first: Tricia

last: Missall

first: Marthe

last: Howard

first: Joel

middle: C

last: Bornstein

first: Brian

last: Davis

first: Robert

middle: O

last: Heuckeroth


title: Tamoxifen treatment as a therapeutic approach in a murine model of X-linked myotubular myopathy (Mtm1-/y)

status: Public on Dec 15 2020

city: ILLKIRCH

first: Jocelyn

last: Laporte

address: 1, rue Laurent Fries

country: France

institute: IGBMC

summary: In this study, we performed RNA sequencing on tibialis anterior muscle of male mice of 7 weeks of age. WT and Mtm1 deficient (Mtm1-/y) mice as well as tamoxifen-treated WT and tamoxifen-treated Mtm1-/y mice were sequenced.

overall_design: The study is composed of 4 groups of mice: WT, Mtm1-/y, WT Tamox and Mtm1-/y Tamox. Each group was composed of triplicates or quadruplicates. The comparison of transcriptome profiles across the different genotypes was assessed in this study.

first: S

last: Djeddi

first: D

last: Reiss

first: A

last: Menuet

last: Freismuth

last: Djerroud

first: R

last: Gomez-Oca

middle: S

last: Sosson

first: C

last: Kretz

first: L

last: Negroni

last: Keime

first: O

last: Dorchies

first: J

last: Thompson


title: Single-cell RNA sequencing of human iPSC-derived cells

status: Public on Mar 02 2021

city: Shenzhen

first: Minglin

last: Ou

address: No.1017, Dongmen North Road, Luohu District

department: Clinical Medical Research Center of The Second Clinical Medical College

institute: Jinan University

summary: We directly reprogramed two human iPS cell lines to cardiac cells and collected four groups of samples at four time points (day 0, day 2, day 4, and day 10) during cardiac differentiation for Single-cell RNA sequencing.

overall_design: The four groups of samples, which were collected at four time points during cardiac differentiation, were loaded on a 10X Chromium instrument (10X Genomics) and used for single-cell RNA sequencing according to manufacturer’s protocol. The SRA Study accession was SRP194999, and BioProject accession was PRJNA541018.

first: Yong

last: Dai


title: Multi-omics comparisons of different forms of centronuclear myopathies and the effects of several therapeutic strategies


title: TRANSCRIPTOMIC PROFILING ACROSS THE SPECTRUM OF NON-ALCOHOLIC FATTY LIVER DISEASE

status: Public on Dec 03 2020

city: Newcastle

first: Simon

last: Cockell

address: Framlington Place

country: United Kingdom

institute: Newcastle University

summary:
The pathophysiological mechanisms that drive non-alcoholic fatty liver disease (NAFLD) progression remain poorly understood. This multicenter study characterized the transcriptional changes that occur as liver disease progresses.
216 snap frozen liver biopsies, comprising 206 NAFLD cases with different fibrosis stages and 10 controls were studied. Samples underwent high-throughput RNA sequencing.
This study provides novel insights into transcriptional changes during liver disease evolution and progression as well as proof of principle that transcriptomic changes reveal potentially tractable biomarkers for NAFLD fibrosis.

overall_design: 216 snap-frozen biopsies were processed for RNA sequencing on the Illumina NextSeq 500 system.

first: Quentin

last: Anstee

first: Ann

last: Daly

first: Olivier

last: Govaere


title: Genetic downregulation of Dnm2 as a therapeutic approach in a murine model of X-linked myotubular myopathy (Mtm1-/y)

last: Laporte

summary: In this study, we performed RNA sequencing on tibialis anterior muscle of male mice. WT and Mtm1 deficient (Mtm1-/y) mice as well as on Dnm2+/- mice and on Mtm1-/y mice crossed with Dnm2+/- (Mtm1-/yDnm2+/-) were sequenced. A longitudinal follow up was established by sequencing all the genotypes at E18.5, 2w and 7w.

overall_design: The study is composed of 4 groups of mice: WT, Mtm1-/y, Dnm2+/- and Mtm1-/yDnm2+/-, for each age. Each group was composed from 2 to 5 replicates. The comparison of transcriptome profiles across different ages and different genotypes was assessed in this study.

last: Djeddi

last: Reiss


title: Abi1 gene dose study in PyVT breast tumors

status: Public on Dec 08 2020

city: Syracuse

first: Vladimir

last: Kuznetsov

address: 750 E Adams St

institute: SUNY Upstate Medical University

summary: To execute RNA-Seq analysis of PyMT breast tumors studied in animals with and heterozygous and homozygous states of Abi1 gene

overall_design: 64 total samples were analyzed: PyMT-positive animals, with wild-type Abi1 or homozygous or heterozygous Abi1 loss. Multiple sections from each tumor were analyzed in this cohort.

first: Angelina

last: Regua

first: Andre

last: Grageda

first: Csaba

last: Papp

first: Leszek

last: Kotula


title: Dnm2 downregulation by antisense oligonucleotide (ASO1) injections rescue a murine model of recessive centronuclear myopathy (Bin1mck-/-)

first: Jocelyn

summary: In this study, we performed RNA sequencing on tibialis anterior muscle of male mice. WT (injected with PBS) and Bin1mck-/- (injected with PBS) mice as well as ASO1 injected Bin1mck-/- mice and ASO1 injected WT mice were sequenced at 7 weeks of age. ASO1 targets specifically Dnm2 ARN.

overall_design: The study is composed of 4 groups of mice: WT PBS, Bin1mck-/- PBS, WT ASO1 and Bin1mck-/- ASO1. Each group was composed of quadruplicates. The comparison of transcriptome profiles across the different genotypes was assessed in this study.

first: S

first: D

first: A

last: Menuet

last: Freismuth

last: Djerroud

last: Gomez-Oca

last: Sosson

last: Kretz

last: Negroni

last: Keime


title: DNA methylation profiles of F1 mice sperm of the control group and arsenic group II

city: Tsukuba

first: Keiko

last: Nohara

address: 16-2 Onogawa

department: Center for Health and Environmental Risk Research

institute: National Institute for Environmental Studies

type: Methylation profiling by high throughput sequencing

summary: Pregnant C3H mice were given tap water (control group) and tap water containing 85 ppm sodium arsenite from gestational day 8 to 18 (arsenic group), respectively. The DNA methylomes of sperm of F1 mice were investigated by RRBS method. The results showed that gestational arsenic exposure increased hypomethylated cytosines in active retrotransposon subfamilies. The present study has indicated environmental impacts on sperm DNA methylome establishment.

overall_design: Five DNA samples of purified sperm were prepared from F1 mice (17-19 weeks of age) born to the control dams and gestationally arsenite exposed dams, respectively, and subjected to RRBS analysis.


title: DNA methylation profiles of F1 mice sperm of the control group and arsenic group

summary: Pregnant C3H mice were given tap water (control group) and tap water containing 85 ppm sodium arsenite from gestational day 8 to 18 (arsenic group), respectively. The DNA methylomes of sperm of F1 mice were investigated by RRBS method. The results showed that gestational arsenic exposure increased hypomethylated cytosines in the F1 sperm genome. The present study has indicated environmental impacts on sperm DNA methylome establishment.

overall_design: Five DNA samples of sperm were prepared from F1 mice (15- 17 weeks of age) born to the control dams and gestationally arsenite exposed dams, respectively, and subjected to RRBS analysis.


title: Dnm2 downregulation by antisense oligonucleotide (ASO1) injections rescue a murine model of autosomal dominant centronuclear myopathy (Dnm2SL/+)

last: Laporte

summary: In this study, we performed RNA sequencing on tibialis anterior muscle of male mice. WT (injected with ASO control) and Dnm2SL/+ (injected with ASO control) mice as well as ASO1 injected Dnm2SL/+ mice and ASO1 injected WT mice were sequenced at 7w of age. ASO1 targets specifically Dnm2 ARN.

overall_design:
The study is composed of 4 groups of mice: WT ASO Control, Dnm2SL/+ ASO Control, WT ASO1 and Dnm2SL/+ ASO1. Each group was composed from 3 to 6 replicates. The comparison of transcriptome profiles across the different genotypes was assessed in this study.

UPDATE: [07-01-2024] The title and treatment of GSM4859606 were corrected. The labels of the raw gene counts matrix were corrected.

first: R

first: C

first: L

first: O

last: Dorchies

first: J

last: Thompson


title: Genetic surexpression of human BIN1 as a therapeutic approach in a murine model of X-linked myotubular myopathy (Mtm1-/y)

summary: In this study, we performed RNA sequencing on tibialis anterior muscle of male mice at 7 weeks of age. WT and Mtm1 deficient (Mtm1-/y) mice were sequenced. The rescued mice, Mtm1-/y mice crossed with TgBIN1 mice (Mmt1-/yTgBIN1) and the associated control mice TgBIN1 were also sequenced.

overall_design: The study is composed of 4 groups of mice: WT, Mtm1-/y, TgBIN1 and Mtm1-/yTgBIN1. Each group was composed from triplicates to quadruplicates. The comparison of transcriptome profiles across the different genotypes was assessed in this study.

last: Djeddi

last: Reiss


title: Next Generation Sequencing Facilitates Quantitative Analysis of Renca and B16 Murine Cancer Line Transcriptomes

status: Public on Nov 25 2020

city: Cambridge

first: Kathleen

middle: Brosnahan

last: Yates

address: 75 Ames Street

department: Cancer Program

institute: Broad Institute of MIT and Harvard

summary: Renca, a murine renal cell carcinoma, and B16F10, a murine melanoma, were transcriptionally profiled in a study designed to accompany an in vivo CRISPR screen to identify novel immunotherapy dependencies.

overall_design: RNA sequencing libraries were generated from in vitro cultures of Renca and B16 cells.

first: Robert

middle: T

last: Manguso

first: Juan

last: Dubrot

first: Sarah

last: Lane-Reticker


title: Comprehensive analysis of metastatic gastric cancer tumor cells using Single-cell RNA-seq

status: Public on Dec 06 2020

city: Shanghai

first: Sibo

last: Zhu

state: China

address: songhulu 2005

summary: Gastric cancer (GC) is a leading cause of cancer-induced mortality with poor prognosis with metastasis. However, the mechanism of gastric carcinoma lymph node metastasis remains unknown due to traditional bulk-leveled approaches mask roles of subpopulations. To answer questions from the gastric carcinoma intratumoral perspective in the metastasis, we performed single-cell level analysis on three gastric cancer patients with primary cancer and paired metastatic lymph node cancer tissues using scRNA-seq. Results showed distinct carcinoma profiles from each patient, and diverse microenvironmental subsets were shared by a different patient. Clustering data showed significant intratumoral heterogeneity. Results also revealed a subgroup of cells bridging the metastatic group and primary group, implying the transition state of cancer during the metastatic process. In the present study we obtained a more comprehensive picture over gastric cancer lymph node metastasis, and we discovered some GC lymph node metastasis marker genes (ERBB2, CLDN11 and CDK12), as well as potential gastric cancer evolutionary driving genes (FOS and JUN), which provide a basis for the treatment of heterogeneity.

first: Bin

last: Wang

first: Yingyi

last: Zhang

first: Tao

last: Qing

first: Kaichen

last: Xing

first: Jie

last: Li

first: Timing

last: Zhen

first: Xianbao

last: Zhan


title: AIB1D4 role in early breast cancer progression

status: Public on Nov 08 2020

city: Washington

first: Ghada

last: Sharif

state: DC

address: 3970 Reservoir Rd NW NRB E311

institute: Georgetown University

summary: We report the role of AIB1D4 in early stage breast cancer progression. Using CRISPR editing, we generated isogeneic cell lines that only express  AIB1D4 and not full length AIB1 then extracted RNA for sequencing from cell lines and mamary fat pad xenografts in SCID/Beige mice. Data was aligned to Hg19 with STAR and processed with EdgeR.

overall_design:
Examination of RNA-seq of 4 cell lines in triplicate and three pooled tumor xenografts (MCFDCIS alone, MCFDCIS-D4 and MCFDCIS + MCFDCIS-D4) in triplicate.

UPDATE: [Jan-17-2025] The titles of Samples GSM4135857-GSM4135859 were swapped with the titles of Samples GSM4135860-GSM4135862.

first: Anna

last: Riegel


title: Induction of adult cardiomyocyte renewal by Klf1

status: Public on Oct 31 2020

city: Darlinghurst

first: David

middle: Thomas

last: Humphreys

address: 405 Liverpool Street

department: Genome core

country: Australia

institute: Victor Chang Cardiac Research Institute

summary: In highly regenerative animals, cardiac regeneration occurs innately through cardiomyocyte dedifferentiation and proliferation, although the regenerative mechanisms remain unclear. This project contains processed data sets that were used to identify that klf1, a Kruppel-like transcription factor essential for red blood cell development, is also necessary and sufficient in the myocardium for the induction of cardiomyocyte dedifferentiation and proliferation in adult zebrafish hearts. Raw data has been deposited to  PRJNA551130

overall_design: RNASeq, ATAC Seq, whole genome bisulphite sequencing and chip seq on either WT or klf1 overexpressing zebrafish hearts.

first: Masahito

last: Ogawa

first: Fan-Suo

last: Geng

first: Kotaro

last: Sugimoto

first: Ozren

last: Bogdanovic

first: Kazu

last: Kikuchi


title: RNA-seq of mouse glioma tumors with or without ASCL1

status: Public on Nov 05 2020

city: Dallas

first: Jane

middle: E

last: Johnson

state: TX

address: 5323 Harry Hines Blvd

department: Neuroscience

institute: UT Southwestern Medical Center

summary: Tamoxifen was administered to Glast-CreER;Nf1-flox/flox;Tp53-flox/flox or Glast-CreER;Ascl1-flox/flox;Nf1-flox/flox;Tp53-flox/flox at E14.5 to induce tumors in the brain

overall_design: Tumors were dissected for RNA-extraction from mice exhibiting neurological symptoms such as epilepsy and abnormal motor coordination

first: Tou

middle: Y

last: Vue

first: Rahul

last: Kollipara


title: ASCL1 ChIP-seq of patient-derived-xenograft (PDX) GBM lines and RNA-seq of mouse glioma tumors

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


title: Single-cell transcriptomic sampling of regenerating mouse muscle tissue

status: Public on Oct 14 2020

city: Ithaca

middle: William

last: McKellar

address: 237 Tower Rd

department: Biomedical Engineering

institute: Cornell University

summary: We report a series of single-cell transcriptomic datasets of regenerating mouse muscle tissue generated with the 10x Genomics Chromium v3 platform.

overall_design: The overall objective of the study was to generate a high-resolution transcriptomic reference of the distinct cell populations in the mouse muscle at different timepoints after notexin-injury.

first: Benjamin

middle: D

last: Cosgrove

first: Andrea

middle: J

last: De Micheli

middle: W


title: Deletion of Mediator 1 suppresses TGFb signaling leading to changes in epidermal lineages and regeneration

status: Public on Sep 02 2020

city: San Francisco

first: Yuko

last: Oda

address: 111N-MB 360 1700 Owens St, Suite 360

department: Endocrine Research

institute: VA Medical Center UCSF

summary: Epidermal lineages and injury induced regeneration are controlled by transcriptional programs coordinating cellular signaling and epigenetic regulators, but the mechanism remains unclear. Previous studies showed that conditional deletion of the transcriptional coactivator Mediator 1 (Med1) changes epidermal lineages and accelerates wound re-epithelialization. Here, we studied a molecular mechanism by which Med1 facilitates these processes, in particular, by focusing on TGFb signaling through genome wide transcriptome analysis.  The expression of the TGF ligands (Tgfb1/b2) and their downstream target genes is decreased in both normal and wounded Med1 null skin. Med1 silencing in cultured keratinocytes likewise reduces the expression of the ligands (TGFb1/b2) and diminishes activity of TGFb signaling as shown by decreased p-Smad2/3. Silencing Med1 increases keratinocyte proliferation and migration in vitro. Epigenetic studies using chromatin immuno-precipitation and next generation DNA sequencing reveals that Med1 regulates transcription of TGFb components by forming large clusters of enhancers called super-enhancers at the regulatory regions of the TGFb ligand and SMAD3 genes. These results demonstrate that Med1 is required for the maintenance of the TGFb  signaling pathway. Finally, we show that pharmacological inhibition of TGFb signaling enhances epidermal lineages and accelerates wound re-epithelialization in skin similar to that seen in the Med1 null mice, providing new insights into epidermal regeneration.

overall_design: Identification of super-enhancers by Med1 with  CTCF and active histone modification (H3K27ac) in primary epidermal keratinocytes.

first: Mark

last: Meyer

first: Daniel

last: Bikle

first: Wesley

last: Pike


title: Genome-wide alterations of uracil distribution patterns

status: Public on Sep 20 2020

city: Budapest

first: Angela

last: Bekesi

address: Műegyetem rakpart 3.

department: Department of Applied Biotechnology and Food Science

country: Hungary

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

overall_design: Refer to individual Series


title: ASCL1 ChIP-seq of patient-derived-xenograft (PDX) GBM lines

summary: R548 and R738 PDX-GBMs were grown orthotopically in the brains of NOD-SCID mice

overall_design: Tumors were dissected for ChIP-seq experiments

middle: K

first: Robert

middle: M

last: Bachoo


title: A single-cell method to map higher-order 3D genome organization in thousands of individual cells reveals structural heterogeneity in mouse ES cells

status: Public on Aug 12 2020

city: Pasadena

first: Mary

middle: Villanueva

last: Arrastia

address: 1200 E California Blvd

department: Chemistry and Chemical Engineering

institute: California Institute of Technology

summary: In eukaryotes, the nucleus is organized into a three dimensional structure consisting of both local interactions such as those between enhancers and promoters, and long-range higher-order structures such as nuclear bodies. This organization is central to many aspects of nuclear function, including DNA replication, transcription, and cell cycle progression. Nuclear structure intrinsically occurs within single cells; however, measuring such a broad spectrum of 3D DNA interactions on a genome-wide scale and at the single cell level has been a great challenge. To address this, we developed single-cell split-pool recognition of interactions by tag extension (scSPRITE), a new method that enables measurements of genome-wide maps of 3D DNA structure in thousands of individual nuclei. scSPRITE maximizes the number of DNA contacts detected per cell enabling high-resolution genome structure maps within each cells and is easy-to-use and cost-effective. scSPRITE accurately detects chromosome territories, active and inactive compartments, topologically associating domains (TADs), and higher-order structures within single cells. In addition, scSPRITE measures cell-to-cell heterogeneity in genome structure at different levels of resolution and shows that TADs are dynamic units of genome organization that can vary between different cells within a population. scSPRITE will improve our understanding of nuclear architecture and its relationship to nuclear function within an individual nucleus from complex cell types and tissues containing a diverse population of cells.

overall_design: scSPRITE was designed to study higher-order 3D DNA organization at the level of single cells. We applied this method to study mouse ES cells, and genome organization was analyzed in 1000 single cells.     Ensemble and single cell cluster files are provided. Additionally, 1000 single cell heatmaps (at 1Mb and 40kb resolution) are provided in the supplemental files. The single cell maps contain both weighted and unweighted files. In the unweighted files, each bin (whether 1Mb or 40kb) in the single cell heatmaps reflect the number of clusters containing a contact in that bin. The weighted files are weighted by the size of the cluster.

middle: V

first: Joanna

last: Jachowicz

first: Noah

last: Ollikainen

first: Matthew

last: Curtis

first: Charlotte

last: Lai

first: Sofia

last: Quinodoz

first: David

last: Selck

first: Mitchell

last: Guttman

first: Rustem

middle: F

last: Ismagilov


title: Methylation and accessibility profiling of GM12878, MCF-10A, MCF-7, and MDA-MB-231 using nanopore sequencing

status: Public on Aug 07 2020

city: Baltimore

first: Isac

last: Lee

state: MD

address: 3400 N. Charles St.

institute: Johns Hopkins University

summary: Probing epigenetic features on long molecules of DNA has tremendous potential to advance our understanding of the phased epigenome. In this study, we evaluate CpG methylation and chromatin accessibility simultaneously on long strands of DNA using GpC methyltransferase to exogenously label open chromatin, coupled with nanopore sequencing technology. We performed nanopore sequencing of Nucleosome Occupancy and Methylome (nanoNOMe) on four human cell lines (GM12878, MCF-10A, MCF-7, MDA-MB-231), and demonstrate the ability to directly measure methylation and chromatin accessibility in genomic features such as structural variations and repetitive elements. The long single-molecule resolution allows footprinting of protein and nucleosome binding and determining the combinatorial promoter epigenetic state on individual molecules. Long-read sequencing makes it possible to robustly assign reads to haplotypes, enabling allele-specific epigenetic analysis across the genome. We use existing SNV data on GM12878 to present the first fully phased human Probing epigenetic features on long molecules of DNA has tremendous potential to advance our understanding of the phased epigenome. We evaluate CpG methylation and chromatin accessibility simultaneously on long strands of DNA using GpC methyltransferase to exogenously label open chromatin, coupled with nanopore sequencing technology. We performed nanopore sequencing of Nucleosome Occupancy and Methylome (nanoNOMe) on four human cell lines (GM12878, MCF-10A, MCF-7, MDA-MB-231), and demonstrate the ability to directly measure methylation and chromatin accessibility in genomic features such as structural variations and repetitive elements. The long single-molecule resolution allows footprinting of protein and nucleosome binding and determining the combinatorial promoter epigenetic state on individual molecules. Long-read sequencing makes it possible to robustly assign reads to haplotypes, enabling allele-specific epigenetic analysis across the genome. We use existing SNV data on GM12878 to present the first fully phased human epigenome, consisting of chromosome-level allele-specific profiles of CpG methylation and chromatin accessibility.mosome-level allele-specific profiles of CpG methylation and chromatin accessibility.

overall_design: We examined genome-wide DNA methylation and chromatin accessibility using nanoNOMe in GM12878, MCF-10A, MCF-7, and MDA-MB-231 cell lines.

first: Roham

last: Razaghi

first: Timothy

last: Gilpatrick

first: Michael

last: Molnar

first: Ariel

last: Gershman

first: Norah

last: Sadowski

first: Fritz

last: Sedlazeck

first: Kasper

last: Hansen

first: Jared

last: Simpson

first: Winston

last: Timp


title: circRNome of human pluripotent stem cells

status: Public on Jul 07 2020

city: Milan

first: Mario

last: Barilani

address: Via F. Sforza 35

institute: Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico

summary: Induction of pluripotency in somatic cells needs the full activation of the pluripotency gene regulatory network (PGRN). The core transcription factors of the PGRN establish a  crosstalk with specific micro RNA (miRNA) families to sustain the pluripotent program and govern cell fate decisions. Very recently, circular RNA (circRNA) have been proposed as novel players in the regulation of this molecular circuitry. Herein, we successfully generated human induced pluripotent stem cells (hiPSC) by zero-footprint reprogramming of cord blood mesenchymal stem cells. The hiPSC were extensively characterized for stemness and tri-lineage differentiation potential compared to human embryonic stem cells and parental unreprogrammed cells to assess complete acquisition of the pluripotent identity. High-throughput array-based molecular analyses of messenger RNA (mRNA) (631 genes), miRNA (754 miRNA) and, for the first time, circRNA (13,617 circRNA) were performed to address the role of circRNA in the PGRN. As a result, a circRNA-guided map of miRNA and mRNA associated to naïve and primed pluripotent identity is provided.

overall_design: One sample (human cord blood mesenchymal stem cells reprogrammed to pluripotency) to be compared with GSE122178 (reference of unreprogrammed human cord blood mesenchymal stem cells)

first: Alessandro

last: Cherubini


title: Amniotic fluid transcriptome: a glimpse into fetal development and placental cellular dynamics during normal pregnancy

status: Public on Jul 03 2020

city: Detroit

first: Adi

last: Tarca

address: 3990 John R. St, 4 Brush South

institute: Wayne State University

summary: Amniotic fluid was colelcted during midtrimester from 30 women and at term gestation from 68 women. Cell free RNA was profiled by HTA 2.0 arrays to study the effect of gestational age and other relevant convariates on gene expression and splicing during normal pregnancy.

overall_design: Cross-sectional

middle: L

first: Roberto

last: Romero

first: Bogdan

last: Done

first: Nardhy

last: Gomez-Lopez

first: Sonia

last: Hassan


title: Single cell mapping of breast tumor stroma reveals dynamically evolving compositions of cancer-associated fibroblasts along tumor progression

status: Public on Jun 29 2020

city: Rehovot

first: Ido

last: Amit

address: 234 Herzl st.

department: Immunology

country: Israel

institute: Weizmann Institute of Science


title: Single cell mapping of breast tumor stroma reveals dynamically evolving compositions of cancer-associated fibroblasts along tumor progression (scRNA-seq dataset)

summary: Tumors are complex ecosystems, in which malignant and non-malignant cells engage in continuous interactions. Cancer associated fibroblasts (CAFs) are the most abundant non-malignant cells in the majority of carcinomas. The wide range of activities that CAFs perform suggests a dynamic and heterogeneous composition, yet tumor infiltrating CAF subpopulations remain poorly characterized. Here we used single-cell RNA sequencing, index sorting and bulk RNA sequencing to map CAFs at various stages of tumor progression and metastasis.

overall_design: BALB/c female mice were orthotopically injected with 4T1-luc cells into the mammary pat pad. Tumors were harvested two weeks or four weeks following the injection. Mammary tissue was harvested from naïve mice (normal mammary fat pad), and lung metastases were harvested five weeks after the injection. The tissues were then dissociated and single-cell sorted for MARS-sequencing, using the follwing gating strategy to select for stromal cells: PI- /Ter119-/ CD45-/ EpCAM-.

first: Gil

last: Friedman

first: Eyal

last: David

first: Chamutal

last: Bornstein

first: Amir

last: Giladi

first: Ruth

last: Scherz-Shouval


title: Single cell mapping of breast tumor stroma reveals dynamically evolving compositions of cancer-associated fibroblasts along tumor progression (bulk RNA-seq dataset)

summary: Tumors are complex ecosystems, in which malignant and non-malignant cells engage in continuous interactions. Cancer associated fibroblasts (CAFs) are the most abundant non-malignant cells in the majority of carcinomas. The wide range of activities that CAFs perform suggests a dynamic and heterogeneous composition, yet tumor infiltrating CAF subpopulations remain poorly characterized. Here we used single cell RNA sequencing and index sorting to map CAFs at various stages of tumor progression and metastasis.


title: The early local and systemic Type I interferon responses to ultraviolet B light exposure are cGAS dependent.

status: Public on Apr 13 2020

city: Minneapolis

first: Michael

last: Gale

state: Minnesota

address: 689 23rd Ave SE

department: Microbiology and Immunology

institute: University of Minnesota

summary: Most systemic lupus erythematosus (SLE) patients are photosensitive and ultraviolet B light (UVB) exposure worsens cutaneous disease and precipitates systemic flares of disease. The pathogenic link between skin disease and systemic exacerbations in SLE remains elusive. In an acute model of UVB-triggered inflammation, we observed that a single UV exposure triggered a striking IFN-I signature not only in the skin, but also in the blood and kidneys. The early IFN-I signature was significantly higher in female compared to male mice. The early IFN-I response in the skin was almost entirely, and in the blood partly, dependent on the presence of cGAS, as was skin inflammatory cell infiltration. Inhibition of cGAMP hydrolysis augmented the UVB-triggered IFN-I response. UVB skin exposure leads to cGAS-activation and both local and systemic IFN-I signature and could contribute to acute flares of disease in susceptible subjects such as patients with SLE.

overall_design: We compared skin tissue biopsies in healthy subjects prior to UV (0hr) and after UV exposure (6 and 24hr).

first: Sladjana

last: Skopelja-Gardner

first: Jie

last: An

first: Keith

middle: B

last: Elkon

first: Richard

middle: R

last: Green

last: Gale Jr


title: Adult nucleus accumbens single-nucleus RNA-seq dataset for "A dopamine-induced coordinated gene expression program regulates neuronal function and cocaine response"

status: Public on Jun 24 2020

city: Birmingham

first: Jeremy

middle: Jason

last: Day

address: 1825 University Blvd

institute: UAB

summary: This dataset contains single-nucleus RNA sequencing results from adult rat brain (nucleus accumbens) and serves as the basis for characterization of transcriptional response to cocaine (20mg/kg, intraperitoneal injection). The goal of this experiment was to define the transcriptional response to cocaine across distinct cell types in the nucleus accumbens. Single-cell sequencing was carried out on FACS-sorted nuclei isolated from these experiments using the 10X Genomics Chromium single cell sequencing platform.

overall_design: This experiment contains 4 biological samples. Samples were adult rat nucelus accumbens brain tissue isolated from rats 1hr after treatment with either saline or cocaine. Tissue was lysed to allow for nuclei collection via centrifugation. FACS-sorted nuclei were subject to 10X Genomics GEM generation and barcoding, GEM-RT cleanup and cDNA amplication, and library construction using a Chromium Single Cell 3ʹ Reagent Kit (v3 chemistry). Libraries underwent directional, paired-end PolyA+ RNA-seq on an Illumina Next-seq 500. Each sample has multiple raw fastq files, corresponding to different sequencing lanes (e.g., L001, L002, etc) and different reads (e.g., R1, R2). Additional index files are also provided for each sample and each lane (I1).

first: Robert

middle: A

last: Phillps

first: Corey

middle: G

last: Duke

first: Jennifer

last: Tuscher

first: Morgan

last: Zipperly

first: Lara

last: Ianov


title: Gene expression of unperturbed young and aged mouse bladders

status: Public on Apr 30 2020

city: St. Louis

first: Indira

middle: U

last: Mysorekar

state: MO

address: 425 S. Euclid Ave, OB/GYN, BJCIH 10th Floor, Attn: Mysorekar Lab

department: OB/GYN

institute: Washington University in St. Louis School of Medicine

summary: Aging has multifaceted effects on the immune system, but how aging affects tissue-specific immunity is not well-defined. Bladder diseases characterized by chronic inflammation are highly prevalent in older women, but mechanisms by which aging promotes these pathologies remain unknown. Tissue transcriptomics of unperturbed, young, and aged bladders identified a highly altered immune landscape as a fundamental feature of the aging female bladder. Detailed mapping of immune cells using single cell RNA- sequencing revealed novel subsets of macrophages and dendritic cells and unique changes to the immune repertoire in the aged bladder. B and T cells are highly enriched in aged bladders and spontaneously form organized bladder tertiary lymphoid tissues (bTLTs).

overall_design: 4 young (3 mo) and 4 aged (18 mo) C57BL6J mouse bladders

first: Marianne

last: Ligon


title: Genome-wide alterations of uracil distribution patterns in human DNA upon chemotherapeutic treatments

first: Angela

last: Bekesi

summary:
We report a new immunoprecipitation-coupled sequencing (DIP-Seq) application termed U-DNA-Seq, where a tailored and catalytically inactive uracil-DNA glycosylase (UNG) was used as uracil-DNA sensor to immunoprecipitate uracil containing genomic DNA fragments.
Genomic uracil was profiled in drug-treated (5-fluoro-2'-deoxyuridine (5FdUR) or raltitrexed (RTX)) or non-treated (NT) HCT116 cells expressing the UNG inhibitor (UGI). The same experiments were also performed in the mismatch repair proficient version of the HCT116 cells (HCT116MMR), where chromosome 3 is reinserted to restore functional MMR (PMID: 8044777). Moreover, wild-type HCT116 or K562 cells were also measured. We found that regions of uracil enrichment in this assay were rather broad as compared to the sharp peaks typical in ChIP-seq. Therefore, we applied an approach alternative to the conventional peak calling. Namely, we calculated genome scaled coverage tracks and log2 ratio tracks of the enriched versus the input samples using deepTools package (bamCoverage and bigwigCompare tools, respectively) to provide a more appropriate description of uracil-enriched genomic regions. Interval (bed) files were also derived from these log2 ratio tracks to be able to screen large datasets for colocalizing features with them. For wider context of the study, see the related publication.

overall_design:
Genomic uracil patterns were determined in drug-treated (5FdUR or RTX) HCT116 cells that are either deficient (HCT116) or proficient in mismatch repair (HCT116MMR) and stably express the UNG inhibitor protein, UGI (samples are as follows: 5FdUR_UGI_HCT116, RTX_UGI_HCT116, 5FdUR_UGI_HCT116MMR, RTX_UGI_HCT116MMR). These were compared to the non-treated UGI-expressing (NT_UGI_HCT116 and NT_UGI_HCT116MMR), as well as to the wild-type HCT116 (WT_HCT116) and K562 (WT_K562) cells. In case of both HCT116 and HCT116MMR samples two independent biological replicates were measured (rep1 and rep2), while in case of K562, only one experiment was done.
Genomic DNA was isolated from each sample and fragmented to approximately 300 bp fragments by sonication (“input” samples (son)). A part of the input sample was incubated with FLAG-tagged uracil-DNA sensor, which was finally precipitated by anti-FLAG beads, resulting in the “enriched U-DNA” sample (IP). Control U-DNA-IP experiments (ctr) were also done using sensor-free beads in 5FdUR treated and non-treated HCT116. Input, U-DNA enriched, and control samples were sequenced by Illumina paired-end reads (PE) 100 bp in a HiSeq 4000 or by PE 150 bp in a Novaseq 6000 platform. Reads were filtered and aligned to the reference human genome (GRCh38.d1.vd1, (https://gdc.cancer.gov/about-data/data-harmonization-and-generation/gdc-reference-files)). Here we provide the following processed files for each pair of samples: 1) log2 ratio (enriched versus input) tracks for individual replicates as well as for merged data (log2.bw); 2) interval files of uracil enriched regions derived from the log2 ratio tracks (region.bed). Regarding the control experiments, log2 ratio (enriched corrected with scaled control versus input) tracks are provided as processed data. For details see the Supplementary Material of the related publication.

first: Hajnalka

last: Pálinkás

first: Angéla

last: Békési

first: Lőrinc

last: Pongor

first: Eszter

last: Holub

first: Gábor

last: Papp

first: Carolina

last: Gemma

first: Simak

last: Ali

first: Balázs

last: Győrffy

first: Beáta

last: Vértessy


title: Regulatory T Cells Play a Central Role in a Subset of Idiopathic Preterm Birth and Adverse Neonatal Outcomes

status: Public on Jun 04 2020

first: Adi

last: Tarca

state: MI

summary: Regulatory T cells (Tregs) have been exhaustively investigated during early pregnancy; however, their role later in gestation is poorly understood. Herein, we report that functional Tregs are reduced at the maternal-fetal interface in a subset of women with idiopathic preterm labor/birth (PTB), which is accompanied by a concomitant increase in Tc17 cells. In mice, depletion of functional Tregs during late gestation induced PTB and adverse neonatal outcomes, which were rescued by the adoptive transfer of such cells. Treg depletion did not alter obstetrical parameters in the mother; yet, it increased susceptibility to endotoxin-induced PTB. The mechanisms whereby the loss of Tregs induces adverse perinatal outcomes involved tissue-specific immune responses and mild systemic maternal inflammation together with dysregulation of developmental and cellular processes in the placenta, in the absence of intra-amniotic inflammation. These findings provide mechanistic evidence supporting a central role for Tregs in the pathophysiology of idiopathic PTB and adverse neonatal outcomes.

overall_design: RNAseq was used to survey the molecular processes dysregulated in the placenta upon Treg depletion [n=5 per group, Partial Treg-depleted (25 μg/kg)  Foxp3DTR dams, Total Treg-depleted (50 μg/kg)  Foxp3DTR dams, and non-Treg-depleted (PBS) controls]

first: Nardhy

last: Gomez-Lopez

first: Bogdan

last: Done

first: Gaurav

last: Bhatti


title: Distinct and redundant roles of nuclear RNA exosome targeting complexes

status: Public on Feb 06 2020

city: Aarhus C

first: Manfred

last: Schmid

address: CF Møllers Alle bldg 1130

department: Molecular Biology and Genetics

institute: Aarhus University

summary: Degradation of transcripts in mammalian nuclei is primarily facilitated by the RNA exosome. To obtain substrate specificity, the exosome is aided by adaptors; in the nucleoplasm, the Nuclear EXosome Targeting (NEXT) complex and the PolyA (pA) eXsome Targeting (PAXT) connection. However, how exact targeting is achieved remains enigmatic. Employing high-resolution 3’end sequencing of both steady state and newly produced pA+ and pA- RNA, we demonstrate that NEXT substrates arise from heterogenous and predominantly pA- 3’ends often covering kb-wide genomic regions. In contrast, PAXT targets harbor well-defined pA+ 3’ends defined by canonical pA site usage. Irrespective this clear division, NEXT and PAXT act redundantly in two ways: i) Regional redundancy: The majority of exosome-targeted transcription units produce both NEXT- and PAXT-sensitive RNA isoforms; and ii) Isoform redundancy: The PAXT connection ensures the fail-safe decay of post-transcriptionally polyadenylated NEXT targets. In conjunction, this provides for the efficient nuclear removal of superfluous RNA.

overall_design: RNA 3'end seq of total and early (10min 4sU labelled) pA+ and pA+ + pA- RNA 3' ends after knock-down of exosome co-factors in HeLa cells .

first: Guifen

last: Wu

first: Leonor

last: Rib

first: Patrik

last: Polak

first: Nicola

last: Meola

first: Albin

last: Sandelin

first: Torben

middle: H

last: Jensen


title: RNA-seq in human RPE1-hTERT cells

status: Public on Feb 29 2020

city: Amsterdam

first: Fred

last: van Leeuwen

address: Plesmanlaan 121

department: Gene Regulation

country: Netherlands

institute: Netherlands Cancer Institute

summary: Gene expression was profiled in unperturbed RPE1-hTERT cells by RNA-seq.

overall_design: RNA-seq in RPE1-hTERT cells


title: Single-cell transcriptomic atlas of the mouse regenerating muscle tissue

status: Public on Jan 11 2020

first: Andrea

last: De Micheli

state: NY

address: 161 Weill Hall

summary: We report a series of single-cell transcriptomic datasets of the mouse regenerating muscle tissue produced using the Chromium 10X technology.

overall_design: The overall objective of the study was to generate a transcriptomic atlas of the distinct cell populations in the mouse muscle at different timepoints post notexin-injury using single-cell RNA-sequencing.

first: Benjamin

last: Cosgrove

first: Lauren

last: Walter


title: CxxC Finger Protein 1-mediated Histone H3 Lysine-4 Trimethylation is Essential for Proper Meiotic Crossover Formation in Mice

status: Public on Mar 11 2020

city: Hangzhou

first: Li

last: Shen

state: Zhejiang Province

address: 866 Yuhangtang Road

institute: Life Sciences Institute, Zhejiang University

summary: CXXC finger protein 1 (Cfp1) is a DNA-binding component of the SETD1 methyltransferase complex, targets SETD1A/B to most CpG islands (CpGI), and mediates the generation of H3K4me3. Deficiency of CFP1 in mice leads to pre-implantation lethality. Previous data suggest an indispensable role of CFP1 in germ cell development and meiosis. However, it remains unclear if CFP1-mediated H3K4 trimethylation is also required for the earliest stages of meiosis in both male and female germ cells. Here, we revealed that Cxxc1 deletion caused a decrease of H3K4me3 levels in spermatocytes after the zygotene stage, impaired double strand breaks (DSBs) repairing, and crossover formation in meiotic prophase. As the results, Cxxc1-deleted spermatocytes failed to complete meiosis and were arrested at the meiosis II. ChIP-seq results revealed that H3K4me3  globally descreased at transcriptional start sites in Cxxc1-null spermatocytes at the leptotene/zygotene and pathytene stages.RNA-seq at different stages revealed an earlier expression of genes within the spermatogenesis pathway in Cxxc1-null spermatocytes. These results  indicated that CFP1 is required for H3K4me3 accumulation at the gene promoters of male germ cells and play a key role in regulating programed gene expression that is essential for spermatogenesis.

overall_design: We examined H3K4me3 and transcriptomes in WT and  Cxxc1-null spermatocytes at different stages.


title: Determination of Sox10-regulated genes in the oligodendroglial precursor cell line OLN93

status: Public on Dec 15 2019

city: Erlangen

first: Michael

last: Wegner

state: Bavaria

address: Fahrstr. 17

department: Institut of Biochemistry

country: Germany

summary: To determine Sox10-regulated genes in the oligodendroglial precursor cell line OLN93, CRISPR/Cas9-mediated genome editing was performed to inactivate Sox10. For CRISPR/Cas9-mediated Sox10 inactivation, two guide sequences (5’-GCTGCGAGCCAGCCCAGGGCC-3’ for clone A and 5’-GTTGCCCAATTCGCCG GGCCC-3’ for clone B) were separately cloned into pX330. Oln93 cells were co-transfected with pEGFP-N1 and the pX330 plasmids that express the respective guide RNA and SpCas9. Transfected GFP-positive cells were enriched by fluorescence activated cell-sorting and seeded at single cell density in 96-well plates. Homogeneously GFP-expressing clones were analysed for loss of Sox10 protein by immunocytochemistry. Clones without Sox10 protein were obtained with both guide RNAs. Sox10 inactivation was confirmed by Sanger sequencing of the Sox10 gene. RNA was isolated from one clone A and one clone B as well as two independent RNA samples of wildtype OLN93 cells and submitted to RNA-seq.

overall_design: mRNA profiles of control (ctrl) and genome-edited Sox10-deficient (Sox10ko) OLN93 cells were generated using Illumina HiSeq 2500 platform.

first: Matthias

last: Weider

first: Franziska

last: Fröb


title: Phenotypic and Transcriptomic Characterization of ElyC-Defective Escherichia coli Under Optimal and Stress-inducing Temperatures

status: Public on Mar 20 2020

city: Montreal

first: Fardin

last: Ghobakhlou

state: QC

address: Pavillon Roger-Gaudry, S-640  2900 Boulevard Edouard-Montpetit,  Montréal, QC

department: Microbiology , Infectiology and Immunology

institute: University of Montreal

summary: The bacterial cell envelope is a primary defense mechanism, protecting cells from environmental and intrinsic stressors and ensuring homeostasis. Understanding the molecular pathways involved in envelope biology is critical for both basic and translational research. Peptidoglycan (PG), a key structural component of the envelope, protects bacteria from mechanical and osmotic stress, and maintains cell shape and integrity. We previously identified the Escherichia coli ElyC protein, which contains a conserved domain of unknown function, as essential for envelope integrity at low temperatures. ElyC is required for PG assembly at 21°C and for lipid carrier metabolism in the membrane-associated biosynthesis of PG and other envelope polysaccharides. In ElyC-defective cells at 21°C, PG assembly is blocked, leading to cell lysis. The physiological role of ElyC at 37°C remained unexplored. We performed phenotypic characterization and transcriptomic profiling of ΔelyC mutant cells grown at 37°C and 21°C, compared to wild-type cells. Although ΔelyC mutants grow similarly to wild-type cells at 37°C, they exhibit altered morphology. PG quantification revealed significant inhibition of PG biosynthesis in the absence of ElyC at 37°C. Moreover, these cells show increased sensitivity to PG-targeting β-lactam antibiotics. RNA-Seq analysis revealed that the loss of ElyC leads to a defective cellular envelope at 21°C, whereas at 37°C, the response is more moderate. While PG defects in ElyC-deficient cells are lethal at 21°C, these cells retain sufficient PG integrity at 37°C to survive. However, they are morphologically defective, under envelope stress, and more sensitive to antibiotics. Our findings highlight ElyC’s critical role in the metabolic regulation of PG biosynthesis at both optimal and suboptimal temperatures. These results underscore the importance of ElyC in maintaining cell envelope integrity and its potential as a target for antibiotic development.

overall_design: We performed phenotypic and transcriptomic analyses on E. coli wild-type strain MG1655 (rph1 ilvG rfb-50) and its derivative elyC::frt (EM9), grown at 21°C and 37°C to early-log phase (OD600 of 0.30-0.35). The mRNA profiles of the wild-type and mutant strains were generated through deep sequencing, performed in triplicate, using the Illumina HiSeq2000 platform in 75-nucleotide paired-end mode.

first: Imène

last: Kouidmi

first: Laura

last: Alvarez

first: Catherine

last: Paradis-Bleau

first: Felipe

last: Cava


title: Maternal whole blood expression changes with gestational age in normal pregnancy by Human Transcriptome Arrays

status: Public on Dec 17 2019

first: Adi

last: Tarca

summary: Maternal plasama colected longitudinally were profiled using Affymetrix Human Transcriptome Arrays to evaluate changes with gestational age.

overall_design: Longitudinal study including 4 to 6 blood samples collected from each of the 49 women with a normal pregnancy.

first: A

first: R

last: Romero

first: G

last: Bhatti

first: N

last: Gomez-Lopez

first: H

last: Sonia


title: Alzheimer’s disease DNA (hydroxy)methylome in the brain and blood: OXT methylation as a preclinical marker.

status: Public on Dec 09 2019

city: Göttingen

first: Roy

last: Lardenoije

address: Robert-Koch-Str. 40

institute: University Medical Center Göttingen

summary: The present study investigated the DNA methylome and hydroxymethylome, as well as unmodified cytosine in relation to Alzheimer’s disease (AD). We identified epigenetic differences between AD patients and age-matched controls in the middle temporal gyrus, in genomic regions associated with genes such as OXT, ACSL1, RHBDF2, C3, and MIR9-3HG. Interestingly, we found that OXT methylation in the blood of aged, non-demented individuals is also associated with conversion to AD dementia. The current GEO submission concerns the middle temporal gyrus Illumina HumanHT-12 V4.0 expression dataset of this study that was used to look at the correlation between the detected epigenetic changes and gene expression.

overall_design: Total RNA obtained from 78 frozen MTG samples hybridized to the Illumina HumanHT-12 v4 BeadChip.

first: Daniël

last: van den Hove

first: Diego

last: Mastroeni


title: Distinct immune responses to type I and III interferons are regulated by interferon regulatory factor 1

status: Public on Sep 30 2019

first: Michael

last: Gale

summary: Type I and III interferons (IFNs) are critical antiviral molecules thought to activate similar signaling cascades resulting in the induction of shared downstream IFN-stimulated genes. This study reveals an unappreciated fundamental difference in the signal transduction downstream of type I and type III IFNs that has broad implications for their functionalities during infection and inflammation.

overall_design: RNA-seq profiling was performed on immortalized human hepatocytes PH5CH8 cells either as controls or IRF1 KO cells stimulated with different interferon treatments.

first: Adriana

last: Forero

first: Snehal

last: Ozarkar

first: Chia

last: Lee

first: Lomon

last: So

first: Richard

last: Green

first: Ram

last: Savan

last: Gale Jr.