title: Single-cell gene expression profiles of human retinal progenitor cells and photoreceptor precursors from deep full-length scRNA-seq.

status: Public on Jan 01 2023

city: Los Angeles

first: David

last: Cobrinik

address: 4546 Sunset Blvd

institute: Children's Hospital Los Angeles

summary: The human retina has unique features that are not all fully replicated in animal models. Several human-specific features center on cone photoreceptors such as a cone-rich fovea, three cone types, and the cone precursor’s proliferative response to RB1 loss. Prior droplet-based single cell RNA-sequencing (scRNA-seq) datasets have not clearly defined cone precursor developmental states or gene expression patterns.  To further elucidate photoreceptor developmental trajectories, we FACS-enriched cone and rod precursors and retinal progenitor cells from eighteen Fetal Week 13-19 retina and performed deep, full-length scRNA-seq. These data were used to evaluate post-mitotic photoreceptor precursor trajectories, accompanying gene expression changes, and cone-specific features that drive the cone precursor proliferative response.

overall_design: Retinal progenitor cells and photoreceptor precursors were FACS-enriched from dissociated human fetal retinae and single cells either directly sorted or collected by microfluidics isolation, followed by SMART-seq based scRNA-seq.

first: Dominic

middle: W

last: Shayler

first: Kevin

last: Stachalek

first: Sunhye

last: Lee

first: Mitali

last: Singh

first: Matthew

last: Thornton

first: Brendan

last: Grubbs

first: Hardeep

middle: P


title: Whole genome bisulfite sequencing of two/three-week-old Arabidopsis thaliana plants of the genotypes Col-0, nrpe1-11 and ros1-4.

status: Public on Nov 07 2022

city: Sheffield

first: Jurriaan

last: Ton

state: South Yorkshire

address: Western Bank

department: Animal and Plant Sciences

country: United Kingdom

institute: University of Sheffield

type: Methylation profiling by high throughput sequencing

summary: This study used the mutants nrpe1-11 and ros1-4 to assess the impact of RNA-directed DNA methylation (RdDM) and ROS1 on the Arabidopsis thaliana (ecotype Col-0) methylome.

overall_design: Genome-wide methylation profiles for the above ground tissue of 2/3-week-old plants of the genotypes Col-0, nrpe1-11 and ros1-4. A total of 12 Bisulfite-seq samples, 4 biological replicates per genotype.

first: Samuel

last: Wilkinson

first: Adam

last: Hannan Parker

first: Amos

last: Muench

first: Robert

middle: S

last: Wilson

first: Kourosh

last: Hooshmand

first: Michael

middle: A

last: Henderson

first: Emma

middle: K

last: Moffat

first: Pedro

last: Rocha

first: Helen

last: Hipperson

first: Joost

middle: H

last: Stassen

first: Ana

last: López Sánchez

first: Inge

last: Fomsgaard

first: Paal

last: Krokene

first: Melissa

last: Mageroy


title: Cancer-selective metabolic vulnerabilities in MYC-amplified medulloblastoma. [CRISPRseq]

status: Public on Nov 09 2022

city: Hamilton

first: Sheila

last: Singh

state: ON

address: 1280 Main Street West

department: Biochemistry and Biomedical Sciences

country: Canada

institute: McMaster University

summary: MYC-driven medulloblastoma (MB) is an aggressive pediatric brain tumor characterized by therapy resistance and disease recurrence. Here we integrated data from unbiased genetic screening and metabolomic profiling to identify multiple cancer-selective metabolic vulnerabilities in MYC-driven MB tumor cells, which are amenable to therapeutic targeting. Among these targets, dihydroorotate dehydrogenase (DHODH), an enzyme that catalyzes de novo pyrimidine biosynthesis, emerged as a favorable candidate for therapeutic targeting. Mechanistically, DHODH inhibition acts on-target leading to uridine metabolite scarcity and hyperlipidemia, accompanied by reduced protein O-GlcNAcylation and c-Myc degradation. Pyrimidine starvation evokes a metabolic stress response that leads to cell cycle arrest and apoptosis. We further show that an orally available small molecule DHODH inhibitor demonstrates potent mono-therapeutic efficacy against patient-derived MB xenografts in vivo. The reprogramming of pyrimidine metabolism in MYC-driven medulloblastoma represents an unappreciated therapeutic strategy and a potential new class of treatments with stronger cancer selectivity and fewer neurotoxic sequelae.

overall_design: A CRISPR-Cas9 screen on SU-MB002 cells was conducted using the TKOv3 CRISPR library.  Cells were transduced with the TKOv3 library at an MOI ~ 0.3, cells were selected with puromycin, and then cultured in Neurocult Complete media for 30 days.  gDNA was extracted from pelleted samples, guide sequences were amplified, and quantified by next-generation sequencing.

first: William

middle: D

last: Gwynne

first: Yujin

last: Suk

first: Stefan

last: Custers

first: Nicholas

last: Mikolajewicz

first: Jeremy

last: Chan

first: Zsolt

last: Zador

first: Shawn

last: Chafe

first: Kui

last: Zhai

first: Laura

last: Escudero

first: Cunjie

last: Zhang

first: Olga

last: Zaslaver

first: Chirayu

last: Chokshi

first: Muhammad

middle: V

last: Shaikh

first: David

last: Bakhshinyan

first: Ian

last: Burns

first: Iqra

last: Chaudhry

first: Omri

last: Nachmani

first: Daniel

last: Mobilio

middle: T

last: Maich

first: Patricia

last: Mero

first: Kevin

middle: R

last: Brown

first: Andrew

last: Quaile

first: Chitra

last: Venugopal

first: Jason

first: Rafael

last: Montenegro-Burke


title: The METTL3 RNA methyltransferase regulates androgen signalling in castrate resistant prostate cancer cells

status: Public on Nov 02 2022

city: Nottingham

first: Nigel

last: Mongan

address: University Park

department: Biodiscovery Institute

institute: University of Nottingham

type: Expression profiling by high throughput sequencing

summary: siRNAs targeting METTL3 used to deplete METTL3 in castrate resistant LNCaP:C42 and 22Rv1 prosate cancer cells and the effect on basal and androgen regulated gene expression and splicing determined.

overall_design: A pool of siRNAs were used to deplete METTL3 in castrate resistant but enzalutamide sensitive LNCaP:C42 and enzalutamide-resistant 22Rv1 prostate cancer cells and the effect on basal and androgen (R1881, 1nM) regulated gene expression and alternative splicing determined using RNA sequencing.

first: Daisy

middle: B

last: Haigh

first: Corinne

middle: L

last: Woodcock

first: Jennifer

last: Lothion-Roy

first: Anna

middle: E

last: Harris

first: Atara

last: Ntekim

first: Jenny

last: Persson

first: Brian

last: Robinson

first: Francesca

last: Khani

first: Kristian

last: Laursen

first: Lorraine

middle: J

last: Gudas

first: Michael

last: Toss

first: Emad

last: Rakha

first: Catrin

last: Rutland

first: Rupert

last: Fray

first: Jennie

middle: N

last: Jeyapalan


title: Foxp3-specific deletion of CREB generates Th2 biased ST-2 positive regulatory T-cells with enhanced IL-10 production and suppressive capacity

status: Public on Dec 01 2022

city: Aachen

first: Zhijian

last: Li

state: North Rhine-Westphal

address: Pauwelsstr. 19

country: Germany

institute: RWTH Aachen University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Regulatory T cells (Tregs) are gatekeepers of immune homeostasis and characterized by expression of Foxp3, which maintains Treg identity. The transcriptional activator CREB critically stabilizes Foxp3 expression in vitro. Here we demonstrate that in mice with a Foxp3-specific knockout of CREB, Tregs show a reduced Foxp3 expression in vivo, but surprisingly enhanced expression of IL-13, IL-10, ST-2 and CREM. This rendered such Tregs highly suppressive in vitro and prevents disease activity in Th1 models like T cell mediated transfer colitis in an IL-10 dependent way. On the other hand, type 2 B cell responses were enhanced resulting in high IgE levels and susceptibility towards experimental asthma. Our data suggest that CREB expression in Tregs is important for the balance between Th1 and Th2 responses by regulating ST-2 and IL-10.

overall_design: ATAC-seq profiles of  6-12 weeks old wild type (WT) and (Foxp3cre x CREB- flox) KO mice

first: Kim

last: Ohl

first: Judit

last: Hriczko

first: Saskia

last: Schulz

first: Thomas

last: Look

first: Tannaz

last: Goodarzi

first: Sudheendra

last: Hebbar Subramanyam

first: Tim

last: Clarner

first: Miriam

last: Scheld

first: Markus

last: Kipp

first: Eva

last: Verjans

first: Svenja

last: Böll

first: Ivan

last: Costa

first: Lin

last: Gan

first: Bernd

last: Denecke

first: Angela

last: Schippers

first: Stefan

last: Floess

first: Edgar

last: Schmitt

first: Tobias

last: Bopp

first: Rudi

last: Beyaert

first: Bart

last: Lambrecht

first: Martin

last: Zenke

first: Norbert

last: Wagner

first: Klaus

last: Tenbrock


title: Genome-wide maps of SP100A binding chromatin.

status: Public on Nov 10 2022

city: Guangzhou

first: hongchang

last: hongchang

state: guangdong

address: East Outer Ring Road, Guangzhou University City, Guangzhou

country: China

institute: Sun yat-sen university

summary: Sp100 protein has been previously reported to contain direct DNA binding domains or to interact with chromosomal proteins to regulate transcription of genes of both cellular and viral origin. Thus, investigation of how IFNβ shifted chromosomal association pattern of Sp100A may help to elucidate the biological function of this isoform in response to IFN. Herein this study, Cleavage Under Targets and Tagmentation (CUT&Tag) technique plus Illumina deep sequencing(deep-seq) was employed to analyze Sp100A associated host chromosomal regions in NT and IFNβ treated Sp100Aoe cells. The sample from HEp-2 cells served as negative control as it lacked Flag-Sp100A expression61. General chromosome association pattern profiling of Sp100A showed that the protein was preferentially associated with promoter region within -3kb to 3kb distance to the transcription start site (TSS) and was most frequently located within the transcription regulation area less than 1kb from the TSS, reinforcing its major role as a transcriptional regulator. Further in-depth comparison of the enrichment level of Sp100A in the promoter regions between NT and IFNβ groups revealed the following findings: I) IFN stimulation substantially changed the promoter region binding affinity of Sp100A on a huge group of targeted genes. Among the promoters with increased Sp100A association frequency in response to IFNβ, the top ones include promoters of ISGs such as OAS2P, DDX58P, IFI16P, MX2P and ISG15P . II) Comparison of the enrichment degree of Sp100A in the promoter regions of a set of experimentally confirmed antiviral ISGs, reviewed by Charles Rice in 2011, revealed an overall enrichment of Sp100A on these ISGs upon IFN signaling .Specifically, Sp100A was preferential assembled on promoters of OAS2, RIG-I (DDX58), IFI16, RSAD2 (Viperin), MX2, SLC15A3 and ISG15 with more than 5-fold higher enrichment in IFNβ group over NT group.

overall_design: Examination of Genome-wide maps of SP100A binding chromatin under IFNβ or Mock treated conditions.

first: Hongchang

last: Dong

first: Wencheng

last: Wu

first: Jingjing

last: Li

first: Yilei

last: Ma

first: Xiaomei

last: Deng

first: Deyin

last: Guo

first: Pei

last: Xu


title: Cancer-selective metabolic vulnerabilities in MYC-amplified medulloblastoma

first: Sheila

last: Singh

type: Methylation profiling by genome tiling array

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

overall_design: Refer to individual Series


title: Nanopore sequencing of estradiol and DMSO treated XVE:ROS1-YFP plants

first: Jurriaan

last: Ton

summary: Transgenic plants carrying an estradiol-inducible ROS1-YFP construct (XVE:ROS1-YFP) were subjected to long-read sequencing (Oxford Nanopore Technologies) to assess the global impacts of ROS1 activity on the methylome of Arabidopsis thaliana (ecotype Col-0).

overall_design: Genome-wide methylation frequency profiles for the above ground tissue of 20-day-old XVE:ROS1-YFP plants treated with β-Estradiol or a dimethyl sulfoxide (DMSO) control.

first: Samuel

last: Wilkinson

first: Adam

last: Parker

first: Amos

last: Muench

first: Robert

last: Wilson

first: Kourosh

last: Hooshmand

first: Michael

last: Henderson

first: Emma

last: Moffat

first: Pedro

last: Rocha

first: Helen

last: Hipperson

first: Joost

last: Stassen

first: Ana

last: López Sánchez

first: Inge

last: Fomsgaard

first: Paal

last: Krokene

first: Melissa

last: Mageroy


title: Chronic HIV-1 Tat action induces HLA-DR downregulation in B cells: a mechanism for lymphoma immune escape in people living with HIV

status: Public on Sep 04 2022

city: Villejuif

first: Anna

last: Schwager

state: Please Select

address: 39 114 Rue Edouard Vaillant

department: CNRS UMR9018

country: France

institute: Institut Gustave Roussy

summary: Despite the introduction of combined antiretroviral therapy (cART), people living with HIV (PLWH) still have an increased risk of EBV-associated B cell malignancies. In the HIV setting, B cell physiology is altered by co-existence with HIV-infected cells and the chronic action of secreted viral proteins, e.g. HIV-1 Tat that, once released, efficiently penetrates non-infected cells. Here we modeled a chronic action of HIV-1 Tat on B cells by ectopically expressing Tat or its mutant version TatC22G deprived of transactivation activity in two EBV-immortalized lymphoblastoid B cell lines. RNA-sequencing analysis revealed that Tat regulated the expression of hundreds of genes, including downregulation of a subset of genes related to MHC class II. Tat-induced transcriptional downregulation of HLA-DRB1, HLA-DRB5 genes was accompanied by a decrease in HLA-DR surface expression; this effect could be reproduced by co-cultivating B cells with Tat-expressing T cells. Notably, HLA-DRB1 expression in B cells was also decreased in PLWH. Chronic Tat presence decreased the NF-ᴋB pathway activity; this downregulated NF-ᴋB-dependent transcriptional targets, including MHC class II genes. Tat-induced HLA-DR downregulation in B cells also impaired EBV-specific CD4+ T cell response, which could contribute to the escape from immune surveillance and eventually promote B cell lymphomagenesis.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for B-cells (BLAS) expressing WT or mutated (C22G) Tat protein


title: Dual states of Bmi1-expressing intestinal stem cells drive epithelial development and  tissue regeneration

status: Public on Sep 09 2022

city: Portland

last: Wong

state: OR

address: 2720 S Moody Ave, Mailcode KCRB

country: USA

institute: Oregon Health & Science Universtiy

summary: We demonstrate that Bmi1-expressing cells represent the predominant epithelial ISC in early intestinal development and precede existence of the canonical Wnt-dependent Lgr5+ stem cell population. We reveal that early in development, Bmi1+ ISCs are highly proliferative, then transition to a slow-cycling state with the emergence of the Lgr5+ ISC. Combining single cell RNA-sequencing (scRNA-seq) with bulk population ATAC-seq (Assay for Transposase Accessible Chromatin sequencing) analyses, we identify that a non-canonical Wnt signaling pathway correlates with the temporal presence of the highly proliferative developmental Bmi1+ ISC population.

overall_design: Single Bmi1-expressing murine intestinal epithelial cells were FACS-isolated from embryos at various different ages or adult animals. scRNA-seq was performed using standard protocols.

first: Nicholas

last: Smith

first: Guanming

last: Wu

first: Sidharth

middle: k

last: Sengupta


title: scNMT-seq of the adult NSC lineage - MAB-seq

status: Public on Sep 16 2022

city: Heidelberg

last: Martin-Villalba

address: Im Neuenheimer Feld 280

department: Molecular Neurobiology

institute: German Cancer Research Center

summary: Stem cells in the adult brain are specialized astrocytes capable of generating neurons and glial cells. While neural stem cells (NSCs) and common astrocytes have clearly distinct functions, they share highly similar transcriptome profiles. How stemness is molecularly encoded is therefore unclear. Here we use single-cell NMT-seq to simultaneously characterize the transcriptome, DNA methylome and chromatin accessibility of astrocytes and the NSC lineage in the healthy and ischemic brain. Our data reveal distinct methylation profiles associated with either astrocyte or stem cell function. Stemness is conferred by methylation of astrocyte genes and demethylation of neurogenic genes that are expressed only later. Surprisingly, ischemic injury unlocks the stemness-methylome in common astrocytes enabling generation of neuroblasts. Furthermore, we show that oligodendrocytes employ Tet-mediated demethylation to regulate expression of myelin-related genes, many of which are abnormally methylated in multiple sclerosis. Overall, we show that DNA methylation is a promising target for regenerative medicine.

overall_design: Oligodendrocytes, neuroblasts and adult neural stem cells/astrocytes were isolated via flourescence-activated cell sorting (FACS) from the ventricular-subventricular zone. Each biological replicate consists of 10.000-20.000 cells from 12 pooled mice. Samples were subjected to MAB-seq in order to detect remnants of active demethylation via TET enzymes.

first: Lukas

last: Kremer

first: Santiago

last: Cerrizuela

first: Mohammad

last: Eid Al Shukairi

first: Tobias

last: Ellinger

first: Jannes

last: Straub

first: Sascha

last: Dehler

first: Aylin

last: Korkmaz

first: Dieter

last: Weichenhan

first: Christoph

last: Plass

first: Simon

last: Anders


title: Long-lasting memory of jasmonic acid-dependent immunity requires DNA demethylation and ARGONAUTE1

first: Jurriaan

last: Ton


title: scNMT-seq of pancreatic organoids - RNA

status: Public on Aug 12 2022

first: Ana

summary: Single-cell nucleosome, methylome and transcriptome (scNMT) sequencing is a recently developed method that allows multiomics profiling of single cells. In this scNMT protocol, we describe profiling of cells from mouse brain and pancreatic organoids, using liquid handling platforms to increase throughput from 96-well to 384-well plate format. Our approach miniaturizes reaction volumes and incorporates the latest Smart-seq3 protocol to obtain a higher number of detected genes and genomic DNA (gDNA) CpG sites per cell. We outline normalization steps to optimally distribute per-cell sequencing depth.

overall_design: Primary pancreatic acinar cells were isolated by digestive dissociation of pancreatic tissue and subsequent density gradient centrifugation. After cultivation as 3D matrigel embedded organoids for 9 days, the cells were harvested and subjected to the miniaturized scNMT-seq protocol.

first: Oguzhan

last: Kaya

first: Andrea

last: Sarvari

first: Jan

last: Brunken

first: Andrés

last: Sanz-Morejón


title: scNMT-seq of pancreatic organoids - DNA methylation and chromatin accessibility

overall_design:
Primary pancreatic acinar cells were isolated by digestive dissociation of pancreatic tissue and subsequent density gradient centrifugation. After cultivation as 3D matrigel embedded organoids for 9 days, the cells were harvested and subjected to the miniaturized scNMT-seq protocol.
The samples listed here represent the epigenomic portion of this multi-omic data set, i.e. DNA methylation and chromatin accessibility assessed with single-cell NOMe-seq.


title: Multi-omic analysis of cell-of-origin and epigenomic state in pediatric H3K27M gliomas (scRNA-Seq)

status: Public on Aug 05 2022

city: Montréal

first: Claudia

last: Kleinman

state: Québec

address: 3999 Côte Ste-Catherine Road

department: Human Genetics

institute: Lady Davis Institute for Medical Research

summary: Canonical (H3.1/H3.2) and noncanonical (H3.3) histone 3 K27M-mutant gliomas have unique spatiotemporal distributions, partner alterations, and molecular profiles. The contribution of the cell-of-origin to these differences has been challenging to uncouple from the oncogenic reprogramming induced by the mutation. Here, we perform an integrated analysis of 116 tumors, including single-cell transcriptome and chromatin accessibility, 3D chromatin architecture and epigenomic profiles, and show that K27M-mutant gliomas faithfully maintain chromatin configuration at developmental genes consistent with anatomically distinct oligodendrocyte-precursor-like cells (OPC). H3.3K27M thalamic gliomas map to prosomere 2-derived lineages. In turn, H3.1K27M ACVR1-mutant pontine gliomas uniformly mirror early ventral NKX6-1+/SHH-dependent brainstem OPCs, while H3.3K27M gliomas frequently resemble dorsal PAX3+/BMP-dependent progenitors. Our data suggest a context-specific vulnerability in H3.1K27M-mutant SHH-dependent ventral OPCs, which rely on acquisition of ACVR1 mutations to drive aberrant BMP signaling required for oncogenesis. The unifying action of K27M mutations is to restrict H3K27me3 at PRC2 landing sites, while other epigenetic changes are mainly contingent on the cell-of-origin chromatin state and cycling rate.

overall_design:
37 patient tumors analysed by scRNA-seq.
-------------------------------------------
Authors state "patient privacy concerns and have been deposited to EGA  instead"

first: Selin

last: Jessa

first: Abdulshakour

last: Mohammadnia

first: Ashot

last: Harutyunyan

first: Maud

last: Hulswit

first: Srinidhi

last: Varadharajan

first: Hussein

last: Lakkis

first: Nisha

last: Kabir

first: Zahedeh

last: Bashardanesh

first: Steven

last: Hébert

first: Damien

last: Faury

first: Maria

middle: C

last: Vladoiu

first: Samantha

last: Worme

first: Marie

last: Coutelier

first: Brian

last: Krug

first: Augusto

middle: F

last: Andrade

first: Manav

last: Pathania

last: Bajic

first: Alexander

middle: G

last: Weil

first: Benjamin

last: Ellezam

first: Jeffrey

last: Atkinson

first: Roy

last: Dudley

first: Jean-Pierre

last: Farmer

first: Sebastien

last: Perreault

last: Garcia

first: Valerie

last: Larouche

first: Mathieu

last: Blanchette

first: Livia

last: Garzia

first: Aparna

last: Bhaduri

first: Keith

last: Ligon

first: Pratiti

last: Bandopadhayay

first: Michael

last: Taylor

first: Stephen

last: Mack

first: Nada

last: Jabado


title: scNMT-seq of the adult NSC lineage - RNA

first: Ana

last: Martin-Villalba

overall_design: Astrocytes, oligodendrocytes, adult neural stem cells as well as their progeny were isolated via flourescence-activated cell sorting (FACS) from the ventricular-subventricular zone, striatum, and olfactory bulb. Each biological replicate (pA, pB, …) consists of one or more mice. Cells were subjected to scNMT-seq in order to quantify DNA methylation, chromatin accessibility, and gene expression at single cell resolution.

first: Lukas

middle: P

last: Kremer

first: Santiago

last: Cerrizuela

first: Mohammad

last: Eid Al Shukairi

first: Tobias

last: Ellinger

first: Jannes

last: Straub

first: Sascha

last: Dehler

first: Aylin

last: Korkmaz

first: Dieter

last: Weichenhan

first: Christoph

last: Plass

first: Simon

last: Anders


title: scNMT-seq of the adult NSC lineage - DNA methylation and chromatin accessibility


title: NGS analysis of T-ALL cell lines treated with mTORC1 inhibitor

status: Public on Feb 23 2023

city: pADOVA

first: Loredana

last: Urso

address: gattamelata 64

department: DISCOG

country: Italy

institute: Università degli studi di Padova

summary: We recentlly showed that everolimus, a mTORC1 inhibitor increases reactive oxygen species (ROS) levels, decreases the levels of NADPH and of glucose-6-phosphate dehydrogenase (G6PD), the rate-limiting enzyme of the pentose phosphate pathway (PPP), and induces apoptosis of T-ALL cells.

overall_design: Jurkat, TALL-1 and CEM cells lines were treated with 10 μM everolimus or drug vehicle after for 24 hours. Then we collected cells and extracted the RNA to perform the RNASEq analysis.

first: Alberto

last: Corradin

first: Micol

last: Silic-Benussi

first: Vincenzo

last: Ciminale


title: Multi-omic analysis by single-cell sequencing of epigenomic state in pediatric H3K27M gliomas

status: Public on Aug 04 2022

first: Claudia

last: Kleinman


title: Interactions with Commensal or Non-commensal Streptococci Alter Streptococcus mutans Transcriptome and Behaviors

status: Public on Aug 03 2022

city: Columbus

first: Justin

middle: Ray

last: Kaspar

state: OH

address: 305 W 12th Ave

department: Biosciences

institute: The Ohio State University

summary:
RNA-Seq was used to compare the transcriptome of Streptococcus mutans UA159 during growth alone in monoculture, in coculture with Streptococcus gordonii DL1, Streptococcus sanguinis SK36 or Streptococcus oralis 34, and in a quadculture containing all four species. Individual cultures of commensal species Streptococcus gordonii DL1, Streptococcus sanguinis SK36 and Streptococcus oralis 34 were sequenced as well. This revealed a common transcriptome pattern in S. mutans when grown in mixed-species culture, indepenedent of the species identity that S. mutans was cultured with. Additionally, transcriptome changes in the commensal species could also be determined when undergoing competition from S. mutans.

RNA-Seq was used to compare the transcriptome of Streptococcus mutans UA159 during growth alone in monoculture or in coculture with Streptococcus sobrinus NIDR 6715, Lactobacillus casei ATCC 4646 or Corynebacterium matruchotii ATCC 14266. These data were compared to previous coculture and quadculture RNA-Seq data with commensal streptococci (GSE209925). These data confirmed a common transcriptome pattern in S. mutans when grown in mixed-species culture with commensal streptococci that is not present with non-commensal streptococci, indepenedent of the species identity that S. mutans was cultured with.

sample_organism:
Streptococcus gordonii
Streptococcus oralis
Streptococcus sanguinis
Streptococcus mutans
Streptococcus sobrinus
Lacticaseibacillus casei
Corynebacterium matruchotii
Streptococcus mutans UA159

overall_design:
All four Streptococcus species were grown to mid-exponential log phase (OD600 nm ~ 0.4) in TYG growth medium (20 mM glucose concentration). After dilution, species were either grown alone (monoculture), in combination with Streptococcus mutans (coculture), or in a quadculture that contained all four species growing together. All cultures were harvested at mid-exponential log phase for comparison of gene expression across conditions.

GSM6407694-96, GSM6407715-17, GSM6620246-54:
All bacteria were grown to mid-exponential log phase (OD600 nm ~ 0.4) in TYG growth medium (20 mM glucose concentration). After dilution, species were either grown alone (monoculture) or in combination with Streptococcus mutans (coculture). All cultures were harvested at mid-exponential log phase for comparison of gene expression across conditions.
Streptococcus mutans Non-normalized Read Counts - Degust Input.csv


title: Single nucleus multiomics identifies ZEB1 and MAFB as candidate regulators of Alzheimer’s disease-specific cis regulatory elements [Multi-omics]

status: Public on Jan 09 2023

city: Huntsville

first: Lindsay

last: Rizzardi

state: AL

address: 601 Genome Way

institute: HudsonAlpha Institute for Biotechnology

summary: Cell type-specific transcriptional differences between brain tissues from donors with Alzheimer’s Disease (AD) and unaffected controls have been well-documented, but few studies have rigorously interrogated the regulatory mechanisms responsible for these alterations. We performed single nucleus multiomics (snRNA-seq + snATAC-seq) on 105,332 nuclei isolated from cortical tissues from 7 AD and 8 unaffected donors to identify candidate cis-regulatory elements (CREs) involved in AD-associated transcriptional changes. We detected 319,861 significant correlations, or links, between gene expression and cell-type specific transposase accessible regions that are enriched for active CREs. Among these, 40,831 were unique to AD tissues. Validation experiments confirmed the activity of many regions, including several candidate regulators of APP expression. We identified ZEB1 and MAFB as transcription factors playing important roles in AD-specific gene regulation in neurons and microglia, respe  ctively. Microglial links were globally enriched for heritability of AD risk and previously identified active regulatory regions.

overall_design: We performed single nucleus multiomics (snRNA+snATAC) on postmortem DLPFC tissues from 7 AD and 8 unaffected donors.

first: Ashlyn

last: Anderson

first: Jacob

last: Loupe


title: The role of aV Integrin in regulating macrophage phenotype and function during cardiac remodeling after myocardial infarction

status: Public on Dec 31 2022

city: Bronx

first: Silvia

last: Hernandez

state: New York

address: 1300 Morris Park Avenue

department: Medicine-Cardiology

institute: Albert Einstein College of Medicine

summary: Macrophages infiltrate the infarcted heart and play a critical role in repair, remodeling and fibrosis. Macrophages sense changes in the extracellular matrix (ECM) environment through Integrins, thus activating signaling pathways that regulate their function. Our data show that av integrin is highly expressed in isolated bone marrow macrophages and is markedly upregulated in response to TGF-β, a growth factor known to be activated in the infarcted heart. Accordingly, we hypothesize that aV integrin induction in infarct macrophages may regulate macrophage phenotype, function and response to key macrophage-activating signals following MI.

overall_design: In order to study the role of integrin aV in mmacrophages in vitro, we isolated bone marrow macrophages from WT mice and grow them  in fibronectic coated and normal culture dishes, and treated them with a anti-integrin αV neutralizing antibody and its control (IgG).

first: Ruoshui

last: Li

first: Bijun

last: Chen

first: Anis

last: Hanna

first: Claudio

last: Humeres

first: Jun

first: Nikolaos

last: Frangogiannis


title: EIF2AK1-mediated signaling drives SF3B1 mutation-induced arrest in terminal erythroid differentiation in myelodysplastic syndrome with ringed sideroblasts

status: Public on Jul 30 2022

first: Feiyang

last: Ma

state: CA

address: 610, Charles Young Dr East, TLSB 3000C

department: Molecular Biology Institute

institute: UCLA

summary: SF3B1 mutations, which occur in 20% of patients with myelodysplastic syndromes (MDS), are the hallmarks of a specific MDS subtype, MDS with ringed sideroblasts (MDS-RS), which is characterized by the accumulation of erythroid precursors in the bone marrow.

overall_design:
Single cell ATAC sequencing and single cell RNA sequencing on Lin-CD34+ cells and mononuclear cells from primary SF3B1-mutant MDS-RS samples

UPDATE: [Aug-11-2025] The cell type for Sample GSM5678325 was corrected from "Lin-CD34+" to "bone marrow mononuclear cells".

first: Vera

last: Adema

first: Simona

last: Colla


title: RNA structure landscape of S. cerevisiae introns

status: Public on Jul 28 2022

city: PALO ALTO

first: Rhiju

last: Das

address: 279 Campus Dr, B419 Beckman Center

institute: Stanford University

summary: Pre-mRNA secondary structures are hypothesized to play widespread roles in regulating RNA processing pathways, but these structures have been difficult to visualize in vivo. Here, we characterize S. cerevisiae pre-mRNA structures through transcriptome-wide dimethyl sulfate (DMS) probing, enriching for low-abundance pre-mRNA through splicing inhibition. These data enable evaluation of structures from phylogenetic and mutational studies as well as identification of new structures across 161 introns. We find widespread formation of “zipper stems” between the 5’ splice site and branch point, “downstream stems” between the branch point and the 3’ splice site, and previously uncharacterized long stems that distinguish pre-mRNA from spliced mRNA. Multi-dimensional chemical mapping reveals that intron structures can form in vitro without the presence of binding partners, and structure ensemble prediction suggests that these structures appear in introns across the Saccharomyces genus. We develop the functional assay VARS-seq to characterize variants of RNA structure in high-throughput and we apply the method on 135 sets of stems across 7 introns, finding that some structured elements can increase spliced mRNA levels despite being distal from canonical splice sites. Unexpectedly, other structures including zipper stems can increase retained intron levels. This transcriptome-wide inference of intron RNA structures suggests new ideas and model systems for understanding how pre-mRNA folding influences gene expression.

overall_design: 1. RNA structure probing after splicing inhibition in yeast: RNA was treated with DMS and reverse transcription with TGIRT (DMS-MaPseq) for samples and controls. The samples include: two replicates of DMS treatment after splicing inhibition (one replicate with 3 lanes of sequencing, and another with one lane), one sample for DMS treatment without splicing inhibition, and one sample for a no-modification control with splicing inhibition. 2. Splicing measurements for intron variant library: Intron structure variant libraries were integrated into the S. cerevisiae genome in their native gene context. Splicing levels were measured with RNA-sequencing, and gDNA sequencing was used to identify intron variants by pairing randomized barcodes to intron sequences.

first: Ramya

last: Rangan

first: Rui

last: Huang

first: Oarteze

last: Hunter

first: Phillip

last: Pham

first: Manuel

last: Ares Jr


title: Predicting seasonal influenza vaccine response using systemic gene expression profiling

status: Public on Jul 11 2022

city: Bethesda

first: Megan

last: Hockman

state: MD

address: 50 South Drive

department: NIAID

institute: National Institutes of Health

summary: Seasonal influenza is a primary public health burden in the USA and globally.  Annual vaccination programs are designed on the basis of circulating influenza viral strains. However,  the effectiveness of the seasonal influenza vaccine is highly variable between seasons and among individuals.  A number of factors are known to influence vaccination effectiveness including age, sex, and comorbidities.  Here, we sought to determine whether whole blood gene expression profiling prior to vaccination is informative about pre-existing immunological status and the immunological response to vaccine.  We performed whole transcriptome analysis using RNA sequencing (RNAseq) of whole blood samples obtained prior to vaccination from participants enrolled in an annual influenza vaccine trial.  Serological status prior to vaccination and 28 days following vaccination were assessed using the hemagglutination inhibition assay (HAI) to define baseline immune status and the response to vaccination.  We find evidence that genes with immunological functions are increased in expression in individuals with higher pre-existing immunity and in those individuals who mount a greater response to vaccination.  Using a random forest model we find that this set of genes can be used to predict vaccine response with a performance similar to a model that incorporates physiological and prior vaccination status alone.   Our study shows that increased expression of immunological genes, possibly reflecting greater plasmablast cell populations, prior to vaccination is associated with an enhanced response to vaccine.  Furthermore, in the absence of demographic and physiological information gene expression signatures are informative about the likely response of an individual to seasonal influenza vaccination.

overall_design: Comparative gene expression profiling of humans prior to influenza vaccination

first: David

last: Gresham

first: Christian

last: Forst

first: Matthew

last: Chung

first: Lauren

last: Lashua

first: Emily

last: Adney

first: Michael

last: Carlock

first: Ted

last: Ross

first: Elodie

last: Ghedin

first: Mohammed

last: Khalfan


title: Linking genome structures to functions during lineage specification by simultaneous single-cell Hi-C and RNA-seq  simultaneous single-cell Hi-C and RNA-seq

status: Public on Jan 31 2023

city: Beijing

first: Menghan

last: Liu

address: Yiheyuan Road

institute: Peking University

summary: Remarkable progress has been made recently in single-cell chromosome conformation capture technologies. However, a method that allows simultaneous profiling of chromatin architecture and gene expression has not been reported. Here we developed an assay named Hi-C and RNA-seq employed simultaneously (HiRES) and performed it on thousands of single cells from developing mouse embryos. Single-cell 3D genome structures, despite being heavily determined by the cell cycle and developmental stages, gradually diverged in a cell-type-specific manner as development progressed. We further developed a computational pipeline to identify and link differential chromatin interactions to their relevant genes based on covariation of interaction strength and transcription activity. By comparing the pseudo temporal dynamics of chromatin interactions with gene expression, we found a widespread chromatin rewiring that occurred prior to transcription activation. Our results demonstrate that the establishment of specific chromatin interactions are tightly related to transcriptional control and cell functions during lineage specification.

overall_design: Using Hi-C and RNA-seq to analyze single cells from mouse embryos and mouse brains.

first: Zhiyuan

first: Yujie

last: Chen

first: Qimin

last: Xia


title: Consumption of fishmeal from salmon by-products increased the accumulation of cholesterol in liver of mice

status: Public on Jul 01 2022

city: OSLO

first: Knut

middle: Tomas

last: Dalen

state: OSLO

address: Sognsvannsveien 9

department: Department of Nutriton

country: Norway

institute: University of Oslo

summary:
Purpose: By-products from farmed fish contain large amounts of proteins and may be used for human consumption. The purpose of this study was to investigate cardiometabolic effects and metabolic tolerance in mice consuming fishmeal from salmon by-products, salmon filet or beef.

Methods: Female C57BL/6J mice were fed chow, as a healthy reference group, or a high-fat diet for 10 weeks to induce obesity and glucose intolerance. Obese mice were subsequently given isocaloric diets containing 50% of the dietary protein from salmon fishmeal, salmon filet or beef for 10 weeks. Mice were subjected to metabolic phenotyping, which included measurements of body composition, energy metabolism in metabolic cages and glucose tolerance. Lipid content and markers of hepatic toxicity were determined in plasma and liver. Hepatic gene and protein expression was determined with RNA sequencing and immunoblotting.

Results: Mice fed fishmeal, salmon filet or beef had similar food intake, energy consumption, body weight gain, adiposity, glucose tolerance and circulating levels of lipids and hepatic toxicity markers, such as p-ALT and p-AST. Fishmeal increased hepatic cholesterol levels by 35-36% as compared to salmon filet (p = 0.0001) and beef (p = 0.005). This was accompanied by repressed expression of genes involved in steroid and cholesterol metabolism and reduced levels of circulating Pcsk9.

Conclusion: Salmon fishmeal was well tolerated, but increased hepatic cholesterol content. The high cholesterol content in fishmeal may be responsible for the effects on hepatic cholesterol metabolism. Before introducing fishmeal from salmon by-products as a dietary component, it may be advantageous to reduce the cholesterol content in fishmeal.

overall_design: Female 8-week old C57BL/6J mice were fed chow or a high fat. The high-fat fed mice were then given controlled, isocaloric diets where 50% of the dietary protein was from fishmeal from salmon by-products, salmon filet or beef for 10 weeks

first: Marit

last: Hjorth

first: Atanaska

last: Doncheva


title: Genome-wide molecular effects of the neuropsychiatric 16p11 CNVs in an iPSC-iN neuronal model

city: Thousand Oaks

first: Xianglong

last: Zhang

address: One Amgen Center Dr.

department: Department of Cardiometabolic Disorders

institute: Amgen Inc.

summary: Copy number variants (CNVs), either deletions or duplications, at the 16p11.2 locus in the human genome are known to increase the risk for autism spectrum disorders (ASD), schizophrenia, and for several other developmental conditions. Here, we investigate the global effects on gene expression and DNA methylation using a 16p11.2 CNV patient-derived induced pluripotent stem cell (iPSC) to induced neuron (iN) cell model system. This approach revealed genome-wide alterations to both gene expression and to DNA methylation patterns and also yielded specific leads on genes potentially contributing to some of the known 16p11.2 patient phenotypes. Specifically, PCSK9 is identified as a possible contributing factor in the development of facial abnormalities, as well as the reciprocal head circumference and body mass index (BMI) phenotypes seen in the deletion and duplication patients. Additionally, the protocadherin (PCDH) gene family is found to have significantly altered methylation patterns in the CNV patient samples.

overall_design: Investigated tissue specific gene expression patterns in induced neurons derived from induced pluripotent stem cells (iPSCs) from patients with 16p11.2 deletion and duplication.

first: Thomas

last: Ward

first: Louis

last: Leung

first: Bo

last: Zhou

first: Rebecca

last: Harper

first: Kristin

last: Muench

first: Arineh

last: Khechaduri

first: Steve

last: Ho

first: Carol

last: Charlton

first: Melanie

last: Plastini

first: Marcus

first: Reenal

last: Pattni

first: Yiling

last: Huang

first: Ricardo

last: Dolmetsch

first: Joachim

last: Hallmayer

first: Phillippe

last: Mourrain

first: Theo

last: Palmer

first: Alexander

last: Urban


title: Expression data from kidney biopsies of patients with chronic liver disease

status: Public on Jun 12 2022

city: Tucson

first: Nathan

last: Cherrington

state: Arizona

address: 1703 E. Mabel Street

department: Pharmacology & Toxicology

institute: University of Arizona

summary: Identification of increased complement component expression in the kidneys of patients with defined chronic liver disease etiology will allow future mechanistic studies of liver-associated renal injury. This study demonstrates the urgency for further investigation of renal function relative to inflammatory liver diseases.

overall_design: Renal biopsies from patients with chronic liver disease underwent RNA extraction and hybridization on Affymetrix microarrays to obtain global transcriptional profiles for hypothesis driving experiments

first: Kayla

last: Frost


title: Expression profiling of Normal colonic epilthelial RNA and colorectal cancer cell lines RNA

status: Public on Jun 01 2022

city: Houston

first: Ganiraju

last: Manyam

state: TX

address: 1515 Holcombe Blvd

institute: UT MD Anderson Cancer Center

summary: Colorectal cancer cell line expression microarray

overall_design: Expression Microarray in six in vitro grown colorectal cancer cell lines (SW480, SW620 & KM12C, KM12SM, KM12L4A, HCT116)

first: Apurva

middle: M

last: Hegde

first: Jennifer

last: Carter

first: Subrata

last: Sen


title: CGH profiling of Normal male/female DNA and colorectal cancer cell lines

type: Genome variation profiling by genome tiling array

summary: Colorectal cancer cell line aCGH, in reference to normal genomic DNA

overall_design: Microarray Comparative Genomic Hybridization in six in vitro grown colorectal cancer cell lines (SW480, SW620 & KM12C, KM12SM, KM12L4A, HCT116)


title: Next Generation Sequencing of Newly excysted juveniles, Juveniles and Adult Fasciola hepatica

status: Public on May 31 2022

city: Ultimo

first: Alison

last: Ricafrente

state: New South Wales

address: 15 Broadway

department: School of Life Sciences

country: Australia

institute: University of Technology Sydney

type: Non-coding RNA profiling by high throughput sequencing

summary:
Purpose: The miRnome of the liver fluke, Fasciola hepatica, has historically been assembled with limited omic's resources using specific life stages. The goals of this study is to quanity the known and published miRNAs and determine novel miRNAs across three intra-mammlian life stages.
Methods: Total RNA was extracted from newly ecysted juveniles 24h post excystment, juveniles at 21d post infection in rats and adult worms during hepatic infection in sheep. Total RNA of each sample was prepared for miRNA sequencing library. Sequenced reads were cleaned and quanitified for F. hepatica mature miRNAs from miRBase version 21 and published miRNAs from Ricafrente et al 2021 using Bowtie tool. Cleaned reads were additionally analysed for novel miRNAs using MiRDeep2 tool in conjunction with the F. hepatica genome and mature miRNAs from F. hepatica, S. japonicum, S. mansoni and C.elegans. Known/published and novel miRNA read counts were normalised to CPM.
Results:  Of all miRNAs known/published and novel, 124 miRNAs now make up the F. hepatica miRnome. Each life stage exhibited a unique miRNA profile, from which NEJs were the most differentially expressed compared to juveniles and adult.
Conclusions:  Our study is the first to comparatively assess the miRNA profiles of the intrammalian life stages of F.hepatica simultaneously, from which the miRnome has now been expanded from 77 to 124.

overall_design: miRNA profiles of Fasciola hepatica life stages; newly excysted juveniles 24h, juveniles 21d and adult

first: Sheila

last: Donnelly

first: Nham

last: Tran


title: Leptin receptor marks and targets the hair follicle mesenchymal niche

status: Public on May 16 2022

city: Irvine

first: Maksim

last: Plikus

state: California

address: 845 Health Sciences Road

department: Developmental and Cell Biology

institute: University of California, Irvine

summary: We report the single-cell transcriptomes of whole, unsorted backskin skin cells isolated from P46 Lepr-Cre;mTmG;Smo and Lepr-Cre;mTmG;Smo+/- female mice and sorted Lepr-expressing, GFP-positive cells isolated from backskin of P50 Lepr-Cre;mTmG female mice

overall_design: Examination and comparison of gene expression and cell-cell signaling of whole, unsorted dorsal skin cells from P46 Lepr-Cre;mTmG;Smo and Lepr-Cre;mTmG;Smo+/- female mice; and examination of gene expression of sorted Lepr-expressing, GFP-positive cells from backskin of P50 Lepr-Cre;mTmG female mice.

first: Yingzi

last: Liu

first: Christian

last: Guerrero-Juarez

first: Qing

last: Nie


title: Comparative Characterization of 3D Chromatin Organization in Triple-Negative Breast Cancers [Hi-C]

status: Public on May 06 2022

city: Daejeon

first: Taemook

last: Kim

address: 291 Daehak-ro, Yuseong-gu

department: Biological sciences

country: South Korea

institute: Korea Advanced Institute of Science and Technology

summary: Triple-negative breast cancer (TNBC) is malignant cancer with a high risk of recurrence. To date, the underlying 3D chromatin organizations of TNBC have remained unclear. Here, using in situ Hi-C, we characterized the 3D chromatin organizations in cells representing five distinct subtypes of breast cancer (including TNBC) and TNBC tissues, compared to normal cells/tissues. We found that the global and local 3D architectures are severely disrupted in TNBC cells. Importantly, we detected CTCF-dependent TNBC-susceptible loss/gain of 3D chromatin organizations and found that these changes were strongly associated with perturbed chromatin accessibility and transcriptional dysregulations. Although some discrepancies exist between TNBC cell lines and tissues, we observed that perturbed local 3D architectures found in TNBC cells are partially conserved in TNBC tissues. Furthermore, we discovered distinct tissue-specific chromatin loops by comparing normal and TNBC tissues. Collectively, our findings provide important features of 3D chromatin organization in TNBC.

overall_design:
For Hi-C experiment (cell lines) : Human mammary epithelial cell (HMEC, as a control) and the cell line of 5 breast cancer subtypes, The cell lines were performed the biological replicates. For Hi-C experiment (Tissues) : Five Contralateral breast normal tissue, three triple negative breast cancer (IDC) tissues.
Please note that each processed data was generated from all replicates and is linked to the corresponding rep1 sample records.

first: Sungwook

last: Han

first: Yujin

last: Chun

first: Hyeokjun

last: Yang

first: Hyesung

last: Min

first: Sook Young

last: Jeon

first: Jang-il

first: Hyeong-Gon

last: Moon

first: Daeyoup

last: Lee


title: Comparative Characterization of 3D Chromatin Organization in Triple-Negative Breast Cancers

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

overall_design: Refer to individual Series


title: Systemic circulating microRNA landscape in Lynch syndrome

status: Public on Apr 25 2022

city: Jyväskylä

first: Tero

last: Sievänen

address: Rautpohjankatu 8

country: Finland

institute: University of Jyväskylä

summary:
Purpose:  Lynch syndrome (LS) is a hereditary cancer syndrome. Systemic circulating microRNA expression levels (c-miRnome) in LS carriers have not been characterized previously. This exploratory study characterized the systemic c-miRnomes of LS carriers with or without cancer and compared it to c-miRnomes of sporadic rectal cancer patients and healthy controls.
Methods: Blood serum samples of Lynch syndrome carriers without (n=81) or with (n=13) cancer, sporadic rectal cancer patients (n=24) and healthy controls (n=37) were sequenced with NextSeq500. FastQC was used for quality controls. High quality samples with Phred score >25 were selected for downstream analysis. FastX-toolkit was used for trimming and filtering. Mapping of the reads to miRbase (v.22) was conducted with Bowtie with v-mode and best strata parameters for single-end data. Only the uniquely mapped reads were selected for differential expression (DE) analysis. Dimension reduction analysis was conducted with t-SNE. Target gene prediction and pathway analysis was performed with mirWalk and validated with COSMIC-database.
Results: An average of 3.2M reads pers sample was achieved. We identified a pool of 228 c-miRs common to all study groups that was used to setup the design matrix for DE analysis. We identified a c-miRnome of 40 DE c-miRs that discern healthy LS carriers from healthy controls but could not distinguish them from cancer patients with or without LS. Our results suggested that hereditary and sporadic carcinogenesis share common biological pathways and alterations in these pathways generate a c-miR response, which can be used to track oncogenic stress at cancer-free state in LS.
Conclusion: Our results show that c-miRs hold diagnostic and predictive potential in molecular profiling of human cancers.

overall_design: Healthy LS carriers (n=81), LS carriers with cancer (n=13), sporadic rectal cancer patients (n=24) and healthy, non-LS controls (n=37)

first: Tia-Marje

last: Korhonen

first: Tiina

last: Jokela

first: Maarit

last: Ahtiainen

first: Laura

last: Lahtinen

first: Teijo

last: Kuopio

first: Anna

last: Lepistö

first: Elina

last: Sillanpää

first: Jukka-Pekka

last: Mecklin

first: Toni

last: Seppälä

first: Eija

middle: K

last: Laakkonen


title: Ad26.COV2.S Prevents SARS-CoV-2 Induced Pathways of Inflammation and Thrombosis in Hamsters

status: Public on Mar 26 2022

city: Boston

first: Dan

last: Barouch

state: MA

address: 3 Blackfan Cir

department: CVVR

institute: Beth Israel Deaconess Medical Center

summary: Syrian golden hamsters exhibit features of severe disease after SARS-CoV-2 challenge and are therefore useful models of COVID-19 pathogenesis and prevention with vaccines. Recent studies have shown that SARS-CoV-2 infection stimulates type I interferon, myeloid, and inflammatory signatures similar to human disease, and that weight loss can be prevented with vaccines. However, the impact of vaccination on transcriptional programs associated with COVID-19 pathogenesis and protective adaptive immune responses is unknown. Here we show that SARS-CoV-2 challenge in hamsters stimulates myeloid and inflammatory programs as well as signatures of complement and thrombosis associated with human COVID-19. Notably, single-dose immunization with Ad26.COV2.S, an adenovirus serotype 26 vector (Ad26)-based vaccine expressing a stabilized SARS-CoV-2 spike protein, prevents the upregulation of these pathways such that the gene expression profiles of vaccinated hamsters are comparable to uninfected animals. Furthermore, we validated the protective efficacy of the Ad26.COV2.S against proinflammatory pathways and coagulation cascade in rhesus macaques by proteomics. Finally, we show that Ad26.COV2.S vaccination induces T and B cell signatures that correlate with binding and neutralizing antibody responses. These data provide further insights into the mechanisms of Ad26.COV2.S based protection against severe COVID-19 in hamsters.

overall_design: In-depth analyses of bulk RNA-Seq transcriptomic profiling of lung tissues at day 4 post-SARS-CoV-2 WA1 challenge from Ad26.COV2.S vaccinated and sham unvaccinated hamsters.

first: Malika

last: Aid

first: Samuel

last: Vidal

first: Cesar

last: Piedra-Mora

first: Sarah

last: Ducat

first: Chi

last: Chan

first: Stephen

last: Bondoc

first: Alessandro

last: Colarusso

first: Carly

last: Starke

first: Michael

last: Nekorchuk

first: Kathleen

last: Busman-Sahay

first: Jacob

middle: D

last: Estes

first: Amanda

last: Martinot

middle: H


title: Single-cell triple-omics uncovers DNA methylation as key feature of stemness in the healthy and ischemic adult brain

status: Public on Aug 12 2022

city: Heidelberg

first: Ana

last: Martin-Villalba

address: Im Neuenheimer Feld 280

institute: German Cancer Research Center


title: Transcriptomic measurement of Escherichia coli under aerobic and microaerobic conditions

status: Public on Mar 15 2022

city: Taipei

first: Gan-Guang

last: Liou

state: Taiwan

address: Institute of Molecular Biology, Academia Sinica., 128 Sec. 2, Academia Rd, Nankang,

country: Taiwan

summary: A total of 4388/4385 genes' transcripts (under aerobic/microaerobic condition, respectively) were identified. Among them, 105 and 71 transcripts were confidently determined to be up- or down-regulated by more than 4 folds with false discovery rate (FDR) p value more than 1, respectively. Additionally, 49 known regulatory non-coding small RNAs (sRNAs) were detected, and 18 sRNAs were differentially abundant (more than 1.5 fold-change). Functional characterizations were revealed that the major differential expression genes were involved in (i) acid response/cation homeostasis (ex: gadAXW, and hdeAB-yhiD operons), (ii) cell adhesion/biofilm formation (ex; fimAICDFGH, and csgDEFG operons), (iii) electron transportation (ex: cydAB, and nrdHIEF operons), (iv) ion transporter (ex: efeU, and efeOB operons), (v) Iron-sulfur cluster assembly (ex: iscRSUA and sufABCDSE operons), and (vi) the undoubtable anaerobic respiration/fermentation (ex: hyaABCDEF and hybOABCDEFG operons) & aerobic respiration (ex: sdhDAB and sucABCDSE operons).

overall_design: To compare the NGS-derived transcriptome profiles (RNA-seq data) of Escherichia coli under aerobic and microaerobic growth conditions

first: Sue

last: Lin-Chao


title: A homologous or variant booster vaccine after Ad26.COV2.S immunization enhances SARS-CoV-2-specific immune responses in rhesus macaques

status: Public on Feb 10 2022

summary: Ad26.COV2.S has demonstrated durability and clinical efficacy against symptomatic COVID-19 in humans. In this study, we report the correlates of durability of humoral and cellular immune responses in 20 rhesus macaques immunized with single-shot Ad26.COV2.S and the immunogenicity of a booster shot at 8 to 10 months after the initial immunization. Ad26.COV2.S elicited durable binding and neutralizing antibodies as well as memory B cells and long-lived bone marrow plasma cells. Innate immune responses and bone marrow plasma cell responses correlated with durable antibody responses. After Ad26.COV2.S boost immunization, binding and neutralizing antibody responses against multiple SARS-CoV-2 variants increased 31- to 69-fold and 23- to 43-fold, respectively, compared with preboost concentrations. Antigen-specific B cell and T cell responses also increased substantially after the boost immunization. Boosting with a modified Ad26.COV2.S.351 vaccine expressing the SARS-CoV-2 spike protein from the beta variant led to largely comparable responses with slightly higher beta- and omicron-specific humoral immune responses. These data demonstrate that a late boost with Ad26.COV2.S or Ad26.COV2.S.351 resulted in a marked increase in humoral and cellular immune responses that were highly cross-reactive across multiple SARS-CoV-2 variants in rhesus macaques.

overall_design: Twenty-four outbred Indian-origin adult male and female rhesus macaques (Macaca mulatta) aged 4 to 22 years were randomly allocated to groups. Sample size and age criteria were determined on the basis of the results of previous nonhuman primate studies. All animals were housed at BIOQUAL Inc. Animals were immunized with 10^11 vp (n = 10) or 5 × 10^10 vp (n = 10) Ad26.COV2.S and were followed for either 230 or 315 days. Four unvaccinated animals were used as controls. The vaccinated animals were then boosted with 5 × 10^10 vp Ad26.COV2.S (n = 10) or Ad26.COV2.S.351 (n = 10). Half of the animals in each original dose group were immunized by each booster vaccine. All immunologic studies were performed blinded. No data points were omitted from analysis. Animal studies were conducted in compliance with all relevant local, state, and federal regulations and were approved by the BIOQUAL Institutional Animal Care and Use Committee.

first: Xuan

last: He


title: Whole transcriptome profiling of Japanese  nonalcoholic fatty liver disease cohort.

status: Public on Apr 05 2022

city: Tokyo

first: Hayato

last: Nakagawa

address: 7-3-1 Hongo Bunkyo-ku

country: Japan

institute: The University of Tokyo

summary: Nonalcoholic steatohepatitis (NASH) is a severe form of nonalcoholic fatty liver disease (NAFLD) that is characterized by hepatic steatosis, inflammation, hepatocellular injury, and fibrosis, which lead to progressed cirrhosis and hepatocellular carcinoma. Despite its increasing prevalence on a global scale, the pathogenesis of NASH progression is not well understood. To elucidate the underlying mechanisms of NASH progression, we conducted transcriptome analyses of Japanese NAFLD cohort in our facility.

overall_design: 94 biopsy proven NAFLD patients were studied. The liver biopsy samples underwent high-throughput RNA sequencing and we compared relative gene expression levels across these samples.

first: Yuki

last: Matsushita

first: Satoshi

last: Kawamura

first: Naoto

last: Fujiwara


title: Interleukin-10 regulates reservoir establishment and persistence in antiretroviral therapy-treated, SIV-infected macaques

status: Public on Feb 09 2022

first: Dan

last: Barouch

summary: Interleukin (IL)-10 is an immunosuppressive cytokine that signals through STAT3 to regulate T follicular helper cell (TFH) differentiation and germinal center formation, which we propose acts as a determinant of HIV/SIV persistence. In SIV-infected macaques, levels of IL-10 in plasma and lymph node (LN) are induced by infection and not normalized with ART. During chronic infection, plasma IL-10 and transcriptomic signatures of IL-10 signaling were significantly correlated with the cell-associated SIV-DNA content within LN CD4+ memory subsets, including TFH, and predicted the frequency of CD4+ TFH and their cell-associated SIV-DNA content during ART, respectively. Notably, in ART-treated RMs, cells harboring SIV-DNA by DNAscope were preferentially found in the LN B-cell follicle in close proximity to IL-10. Finally, we demonstrate that the in vivo neutralization of soluble IL-10 in ART-treated, SIV-infected macaques significantly reduces B cell follicle maintenance and, by extension, cellular sites of viral persistence, including LN TFH and memory CD4+ T-cells expressing PD-1 and CTLA-4. Thus, these data support a role for IL-10 in maintaining a pool of target cells in lymphoid tissue that serve as a niche for viral persistence. Targeting IL-10 signaling to impair CD4+ T-cell survival and improve antiviral immune responses may represent a novel approach to limit viral persistence in ART-suppressed people living with HIV.

overall_design: Evaluation of the safety and bioactivity of IL-10 neutralization in SIV-infected rhesus macaques receiving short-term ART.

first: Justin

last: Harper

first: Susan

last: Ribeiro

first: Malika

last: Aid

first: Claire

last: Deleage

first: Luca

last: Micci

first: Maria

last: Pino

first: Barbara

last: Cervasi

first: Gopalan

last: Raghunathan

first: Eric

last: Rimmer

first: Gulesi

last: Ayanoglu

first: Guoxin

last: Wu

first: Neeta

last: Shenvi

first: Richard

last: Barnard

first: Gregory

last: Prete

first: Steven

last: Bosinger

first: Kirk

last: Easley

first: Bonnie

last: Howell

last: Gorman

first: Daria

last: Hazuda

first: Rafick-Pierre

last: Sekaly

first: Mirko

last: Paiardini


title: Towards an Understanding of the Pathomechanisms of Uterine Fibroids

status: Public on May 01 2022

city: Oxford

first: Adam

last: Cribbs

address: Windmill Road, Oxford, OX3 7LD, UK

institute: University of Oxford

summary: Uterine fibroids (UFs) are benign tumours affecting up to 80% of women of reproductive age. Although mutations in MED12 or HMGA2 account for the majority of UF occurrence, the processes by which these lead to UFs remain poorly understood. Here we present a comprehensive systems biology study, merging clinical, genetic, transcriptomic and proteomic information to better understand the patho-mechanisms underlying UF.

overall_design: Tissues from uterine fibroid patients were collected from 137 donors undergoing hysterectomy, myomectomy or TCRF at the John Radcliffe Hospital, Oxford, in accordance with guidelines under the ENDOX study (09/H0604/58). This study was supported by a grant within the Oxford-Bayer collaboration.

first: Chen-Yi

middle: Y

last: Wang

first: Martin

last: Philpott


title: Time-Resolved Gene Expression Analysis Monitors the Regulation of Inflammatory Mediators and Attenuation of Adaptive Immune Response by Vitamin D

status: Public on Jan 22 2022

city: Kuopio

first: Andrea

last: Hanel

address: Yliopistonranta 1E, POB 1627

department: Institute of Biomedicine

institute: University of Eastern Finland

summary: In this study, we focused on the time-course of transcriptional changes in freshly isolated human PBMCs 4, 8, 24 and 48 h after onset of stimulation with the active vitamin D metabolite 1α,25-dihydroxyvitamin D3 (1,25(OH)2D3) compared to vehicle (0.1% EtOH).

overall_design: PBMCs of a healthy male donor were isolated within one hour after peripheral blood collection and exposed for 4, 8, 24 or 48 h to either 10 nM 1α,25-dihydroxyvitamin D3 or solvent (0.1% EtOH). All experiments were performed in three repeats. Total RNA was extracted and subjected to RNA-seq analysis.

first: Carsten

last: Carlberg


title: The integrated stress response protects microtubule dynamics to recover from proteotoxic stress

status: Public on Jul 15 2022

city: New York

first: Douglas

last: Barrows

state: NY

address: 1230 York Ave

institute: Rockefeller University

summary: By performing ribosome profiling on squamous cell carcinoma stem cells (either control or S51A mutant) we found that the ISR translationally regulates a network of centrosomal proteins to help cellular recovery upon proteotoxic stress.

overall_design:
Ribosome profiling and total RNA sequencing were performed on control and S51A cells either vehicle-treated or treated with the proteosome inhibitor bortezomib for 4.5h

UPDATE: [Aug-19-2025] The titles, source names, and characteristics for the following Samples were swapped:
GSM5823982 <--> GSM5823986
GSM5823983 <--> GSM5823987
GSM5823984 <--> GSM5823988
GSM5823985 <--> GSM5823989
GSM5823998 <--> GSM5824002
GSM5823999 <--> GSM5824003
GSM5824000 <--> GSM5824004
GSM5824001 <--> GSM5824005
The raw data and processed data associated with each GSMxxx did not change.

first: Brian

last: Hurwitz

first: Nicola

last: Guzzi

first: Thomas

last: Carroll

first: Elaine

last: Fuchs


title: Analysis of mRNA-derived siRNAs in mutants of mRNA maturation and surveillance pathways in Arabidopsis thaliana

status: Public on Feb 02 2022

city: Warsaw

first: Michal

last: Krzyszton

address: Pawinskiego 5a

country: Poland

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

summary:
Defects in RNA maturation and RNA decay factors may generate substrates for the RNA interference machinery. This phenomenon was observed in plants where mutations in some RNA-related factors lead to the production of RNA-quality control small interfering RNAs and several mutants show enhanced silencing of reporter transgenes. To assess the potential of RNAi activation on endogenous transcripts, we sequenced small RNAs from a set of Arabidopsis thaliana mutants with defects in various RNA metabolism pathways. We observed a global production of siRNAs caused by inefficient pre-mRNA cleavage and polyadenylation leading to read-through transcription into downstream antisense genes. In addition, in the lsm1a lsm1b double mutant, we identified NIA1, SMXL5, and several miRNA-targeted mRNAs as producing siRNAs, a group of transcripts suggested being especially sensitive to deficiencies in RNA metabolism. However, in most cases, RNA metabolism perturbations do not lead to the widespread production of siRNA derived from mRNA molecules. This observation is contrary to multiple studies based on reporter transgenes and suggests that only a very high accumulation of defective mRNA species caused by specific mutations or substantial RNA processing defects trigger RNAi pathways.

Founded by National Science Centre Grant, Poland (UMO-2013/08/M/NZ1/00931, UMO-2018/29/B/NZ3/01980).

overall_design: Small RNA profiles of ahg2-1, ccr4a, pab2 pab4, upf1-5, upf3-1, lsm1a lsm1b, ncb4, cstf64-2, fy-2 and rsr1-2 mutant plants with Col-0 wild type plants (three biological replicates) in three experimental sets. Set 1: Col0_1, lsm1a lsm1b, ncb4, upf1-5 and upf3-1. Set 2: Col0_2, ahg2-1, ccr4a, pab2 pab4,  fy-2 and rsr1-2. Small RNA-seq data for Col-0 plants matching cstf64-2 mutant from set 3 are part of the earlier submission: GSE99600. Samples for small RNA-seq in GSE99600 submission and cstf64-2 small RNA-seq in this experiment were prepared in parallel from plants grown at the same time.

first: Joanna

last: Kufel


title: JAK3/TEC and TYK2/JAK1 inhibitors demonstrate significant improvement in scalp alopecia areata biomarkers

status: Public on Jan 25 2022

first: Ana

last: Pavel

address: One Gustave L. Levy Place

department: Dermatology

institute: Icahn School of Medicine at Mount Sinai

summary: We present the biopsy sub-study results from the first randomized, placebo-controlled clinical trial in patients with alopecia areata (AA) with ≥50% scalp hair loss and ≤7 years since the last AA episode. In this sub-study, we evaluated the molecular responses to PF-06651600, an oral inhibitor of JAK3 and the tyrosine kinase expressed in hepatocellular carcinoma (TEC) kinase family, and PF-06700841, an oral TYK2/JAK1 inhibitor, versus placebo in nonlesional and lesional scalp biopsies of biopsy samples from patients with AA.

overall_design: This is a novel design, phase 2a, multicenter study that evaluates the efficacy, safety, and tolerability of PF-06651600 and PF-06700841 versus placebo in patients with AA. The biopsy sub-study took place during the randomized, double-blind initial 24 weeks of the trial. 46 patients were included in the biopsy sub-study as follows: PF-06651600 (n=18), PF-06700841 (n=16), and placebo (n=12).

first: Emma

last: Guttman-Yassky

middle: B

first: Aisleen

last: Diaz

first: Ning

last: Zhang

first: Ester

last: Del Duca

first: Yeriel

last: Estrada

first: Brett

last: King

first: Anindita

last: Banerjee

first: Christopher

last: Banfield

first: Ann

last: Cox

first: Dowty

last: Martin

first: Karen

last: Page

first: Michael

last: Vincent

first: Weidong

first: Zhu

last: Linda

first: Elena

last: Peeva


title: Mechanical Tension Mobilizes Lgr6+ Epidermal Stem Cells to Drive Skin Growth (II)

status: Public on Dec 30 2021

city: baltimore

first: Yingchao

last: Xue

address: 1500 orleans st, room 216

institute: johns hopkins university

summary: Uniquely among mammalian organs, skin is capable of dramatic size change in adults, yet the mechanisms underlying this striking capacity are unclear. Here, we utilize a system of controlled tissue expansion in mice to uncover cellular and molecular determinants of skin growth. Through machine learning-guided three-dimensional tissue reconstruction, we capture morphometric changes in growing skin. We find that most growth is driven by the proliferation of the epidermis in response to mechanical tension, with more limited changes in dermal and subdermal compartments. Epidermal growth is achieved through preferential activation and differentiation of not Lgr5+, but instead Lgr6+ stem cells of the interfollicular epidermis, driven in part by the Hippo pathway. By single-cell RNA sequencing, we uncover further changes in mechanosensitive and metabolic pathways underlying growth control in the skin. These studies point to therapeutic strategies to enhance skin growth and establish a platform for understanding organ size dynamics in adult mammals.

overall_design: This experiment totally includes 10 samples from mice. We take skin samples from expanded mouse and non-expanded control mice, at four different time points, along with two non-surgery mice skin samples with different hair cycle. The time points including PI-0, PI-7, PI-14, PI-21. PI- means days post-fully injection of the expander. The Telogen is the rest stage of hair cycle, the Anagen is the growth stage of hair cycle. RNA were extracted from whole skin tissue, and subjected for microarray analysis.

first: Chenyi

last: Lyu

first: Sashank

last: Reddy

first: Luis

last: Garza


title: Translational application of pharmacogenomics for refractory lung cancer

status: Public on Jan 03 2022

city: Goyang-si

first: namhee

last: yu

state: Gyeonggi-do

address: 323, Ilsan-ro, Ilsandong-gu

institute: National cancer center

summary: Patient-derived cells (PDC) recapitulate the characteristics of lung cancer and its therapeutic response. We collected cancer cells of patients to receive various chemotherapy and performed integrative analysis for pharmachogenomics.

overall_design: To identify the genomics characteristics, RNA-Seq and target-seq dataset was collected from lung cancer PDC of refractory patients. Drug response screening was performed from matched samples, and susceptibilities according to gene expression and variants were tested.

first: Ji-Youn

last: Han

first: Charny

last: Park

first: Sunshin

last: Kim

first: Sung-Ho

last: Gho

first: Namhee

last: Yu

first: Youngjoo

last: Lee

first: Eun

last: Kang


title: Single-cell transcriptome profiling reveals nucleus pulposus heterogeneity and immunity during degeneration progression

status: Public on Dec 26 2021

city: Sydney

first: Ji

last: Tu

email: ji.tu@unsw.edu.au, ji.tu@outlook.com

state: NSW

address: High St, Kensington

institute: University of New South Wales

summary: We performed single cell RNA-seq of nuclear pulposus tissues across 8 individuals with progressive degeneration grades on BD Rhapsody system.

overall_design: All users of the GSE165722 dataset MUST acknowledge and cite the associated article: Tu et al., Advanced Science (Weinh), 2022.

first: Jun

last: Zou


title: RNA-seq of nine canine prostate cancer cell lines reveals diverse therapeutic target signatures

status: Public on Feb 08 2022

city: Graz

first: Leila

last: Taher

address: Stremayrgasse 16/I

country: Austria

institute: Graz University of Technology

summary:
Background: Canine prostate adenocarcinoma (PAC) and transitional cell carcinoma (TCC) are typically characterized by metastasis and chemoresistance. Cell lines are important model systems for developing new therapeutic strategies. However, as they adapt to culturing conditions and undergo clonal selection, they can diverge from the tissue from which they were originally derived. Therefore, a comprehensive characterization of cell lines and their original tissues is paramount.
Methods: This study compared the transcriptomes of nine canine cell lines derived from PAC, PAC metastasis and TCC to their respective original primary tumor or metastasis tissues. Special interests were laid on cell culture-related differences, epithelial to mesenchymal transition (EMT), the prostate and bladder cancer pathways, therapeutic targets in the PI3K-AKT signaling pathway and genes correlated with chemoresistance towards doxorubicin and carboplatin.
Results: Independent analyses for PAC, PAC metastasis and TCC revealed 1,743, 3,941 and 463 genes, respectively, differentially expressed in the cell lines relative to their original tissues (DEGs). While genes associated with tumor microenvironment were mostly downregulated in the cell lines, patient-specific EMT features were conserved. Furthermore, examination of the prostate and bladder cancer pathways revealed extensive concordance between cell lines and tissues. Interestingly, all cell lines preserved downstream PI3K-AKT signaling, but each featured a unique therapeutic target signature. Additionally, resistance towards doxorubicin was associated with G2/M cell cycle transition and cell membrane biosynthesis, while carboplatin resistance correlated with histone, m- and tRNA processing.
Conclusions: Comparative whole-transcriptome profiling of cell lines and their original tissues identifies models with conserved therapeutic target expression. Moreover, it is useful for selecting suitable negative controls, i.e., cell lines lacking therapeutic target expression, increasing the transfer efficiency from in vitro to primary neoplasias for new therapeutic protocols. In summary, the dataset presented here constitutes a rich resource for canine prostate and bladder cancer research.

overall_design: Characterization of nine canine prostate cancer cell lines, compared with original tumor tissues

first: Eva-Maria

last: Packeiser

first: Weibo

last: Kong

first: Mathias

last: Ernst

first: Julia

last: Beck

first: Mario

last: Hewicker-Trautwein

first: Bertram

last: Brenig

first: Ekkehard

last: Schütz

first: Hugo

last: Murua Escobar

first: Ingo

last: Nolte


title: Detection Novel miRNA/mRNA Potentially Involved in Renal Proximal Tubular Epithelial Cells under DM Using Next-Generation Sequencing and Bioinformatic Approaches

status: Public on Jan 10 2022

city: Kaohsiung

first: Yi-Chun

last: Tsai

address: No.100 , Tzyou 1st Road

institute: Kaohsiung Medical University

summary: MicroRNAs/mRNAs are hypothesized to play critical roles in the regulation of DM-induced proximal tubular injury. The aim of this study is to explore novel microRNAs and mRNA differentially expressed in RPTECs of a normal individual and a DM patient.

overall_design: Next-generation sequencing for small RNA/mRNA of RPTECs with normal individual and DM

first: Mei-Chuan

last: Kuo

first: Ya-Ling

last: Hsu


title: Mechanical Tension Mobilizes Lgr6+ Epidermal Stem Cells to Drive Skin Growth

first: Yingchao

last: Xue

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

overall_design: Refer to individual Series


title: Comprehensive molecular and clinical characterization of NUP98 fusions in pediatric acute myeloid leukemia

status: Public on Dec 15 2021

city: Seattle

first: Soheil

last: Meshinchi

state: Washington

address: 1100 Fairview Ave N.

department: Clinical Research Division

institute: Fred Hutchinson Cancer Research Center

summary: Genome wide DNA methylation profiling of pediatric acute myeloid leukemia (AML) from diagnostic and relapsed specimens.

overall_design: Bisulphite converted DNA from primary pediatric AML  samples were hybridised to the Illumina Infinium HumanMethylationEPIC BeadChip.

first: Rhonda

last: Ries

first: Jason

last: Farrar

first: Tim

last: Triche Jr.


title: ChIA-PET from BJ (ENCSR956IXE)

status: Public on Nov 04 2021

city: Stanford

first: ENCODE

last: DCC

address: 300 Pasteur Dr

institute: ENCODE DCC

summary:
RNAPII ChIA-PET in BJ

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


title: ChIA-PET from activated CD4-positive, alpha-beta T cell (ENCSR733XLQ)

summary:
RNAPII ChIA-PET in CD4_Activated_Day7

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


title: ChIA-PET from activated CD8-positive, alpha-beta T cell (ENCSR982KEM)

summary:
RNAPII ChIA-PET in CD8_Activated_Day2

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


title: RNAseq of bladder cancer samples from Xiangya hospital

status: Public on Nov 13 2021

city: Changsha

first: Hu

last: Jiao

address: No.87 Xiangya Road, Changsha, Hunan

institute: Xiangya hospital，Central South University

summary: 57 cancer tissues and 13 normal tissues

overall_design:
RNA-seq of bladder cancer and normal bladder tissue.

>>>Submitter states that raw data are not available due to patient privacy concerns<<<

first: Xiongbing

last: Zu


title: ChIA-PET from activated CD4 positive, naive alpha-beta T cell (ENCSR731OFF)

summary:
CTCF ChIA-PET in Naive_CD4_Activated_Day2

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


title: ChIA-PET from CD4-positive naive resting alpha-beta T cell (ENCSR763OCG)

summary:
RNAPII ChIA-PET in Naive_CD4_Resting

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


title: ChIA-PET from activated CD4-positive, alpha-beta memory T cell (ENCSR877ZRR)

summary:
RNAPII ChIA-PET in Memory_CD4_Activated_Day2

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


title: ChIA-PET from CD4-positive, alpha-beta T cell (ENCSR448ZLA)

summary:
RNAPII ChIA-PET in CD4_Resting

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


title: ChIA-PET from activated CD4 positive, naive alpha-beta T cell (ENCSR446MTI)

summary:
RNAPII ChIA-PET in Naive_CD4_Activated_Day7

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


title: ChIA-PET from CD4-positive, alpha-beta memory T cell (ENCSR569TBN)

summary:
RNAPII ChIA-PET in Memory_CD4_Resting

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


title: AmpliSeq Illumina sequencing in male wild-type (Srgn+/+) and serglycin-deficient (Srgn-/-) mice show that serglycin regulates the immune profile of adipose tissue inflammation

status: Public on Dec 11 2021

city: OSLO

first: Knut

last: Dalen

address: Sognsvannsveien 9

institute: University of Oslo

summary:
Purpose: We here hypothesized that serglycin may have an impact on obese inflammation. To address this, we subjected Srgn+/+ and Srgn-/- male mice to an eight-week high fat/high sucrose diet, followed by an analysis of the effects of serglycin-deficiency on adipose tissue transcriptome.
Methods: Ampliseq sequencing was performed on an Ion S5™ XL Sequencer. Total RNA was isolated from eWAT (n=5) using the Direct-zol RNA MiniPrep column kit (The Epigenetics Company, Irvine, CA). cDNA libraries were prepared and amplified with the Ion AmpliSeq™ Transcriptome Mouse Gene Expression Kit (Life Technologies, Carlsbad, CA), following the manufacturer`s instructions. Sequencing was performed on an Ion S5™ XL Sequencer (Thermo Scientific, Waltham, MA). Data had read lengths with average between 98 and 110 bp and high mapping (95% of aligned bases). The expression values were generated by using software Torrent Suite™ (version 5.10.1).
Results: The absence of serglycin caused reduced expression of numerous genes linked to inflammatory pathways.
Conclusions: This study identifies a role for serglycin, in particular the macrophages, in regulating the immune response in adipose inflammation.

overall_design: mRNA profiles of epidydimal white adipose tissue of male  Srgn+/+ (n=5) and Srgn-/- (n=5) mice fed a high sucrose/high fat diet for eight weeks.

first: Atanaska

last: Doncheva

first: Gunnar

last: Pejler


title: ChIA-PET from RWPE1 (ENCSR617FPZ)

summary:
RNAPII ChIA-PET with RWPE1 cell

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


title: ChIA-PET from activated CD4 positive, naive alpha-beta T cell (ENCSR550JJT)

summary:
CTCF ChIA-PET in Naive_CD4_Activated_Day7

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


title: ChIA-PET from activated CD8-positive, alpha-beta memory T cell (ENCSR697ZHG)

summary:
CTCF ChIA-PET in Memory_CD8_Activated_Day2

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


title: ChIA-PET from activated CD8-positive, alpha-beta T cell (ENCSR531UMR)

summary:
CTCF ChIA-PET in CD8_Activated_Day7

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


title: Gene expression analysis of effects of Met on BMDMs co-cultured with COM-TECs.

status: Public on Dec 29 2021

city: Wuhan

first: Haoran

last: Liu

state: Hubei

address: Jiefang avenue 1095

department: Urology

institute: Tongji Hospital

summary: Microarray analysis was used to assess the expression levels of mRNAs in bone marrow-derived macrophages (BMDMs) pretreated with metformin (Met) or PBS and co-cultured with renal tubular epithelial cells (TECs) or COM-TECs (NC vs. COM, COM vs. COM + Met).BMDMs and TECs were isolated from wild-type (WT) C57BL/6J mice. To developed a BMDM-COM-stimulated TECs co-culture system, BMDMs were plated in the upper chamber of 6-well Transwell plates with a pore size of 0.4 μm (Corning, USA), while TECs were plated in the lower chamber. In the COM and COM + Met groups, TECs were treated with COM (100 μg/mL) for 24 h and BMDMs were treated with Met (5.0mM) for 24 h.

overall_design: mRNA expression profile in BMDMs treated with Met or PBS and co-cultured with TECs or COM-TECs.

first: Xiangyang

last: Yao

first: Chen

last: Duan

first: Tao

last: Ye

first: Xiaoqi

last: Yang

first: Peng

last: Lv

first: Bo

last: Li

first: Zhangqun

first: Hua

last: Xu


title: ChIA-PET from activated CD8-positive, alpha-beta T cell (ENCSR408MRB)

summary:
CTCF ChIA-PET in CD8_Activated_Day2

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


title: ChIA-PET from B cell (ENCSR536ZNI)

summary:
CTCF ChIA-PET in B_Cell

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


title: ChIA-PET from activated CD4 positive, naive alpha-beta T cell (ENCSR402NAQ)

summary:
RNAPII ChIA-PET in Naive_CD4_Activated_Day2

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


title: ChIA-PET from activated CD4-positive, alpha-beta memory T cell (ENCSR291RCO)

summary:
CTCF ChIA-PET in Memory_CD4_Activated_Day7

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


title: ChIA-PET from activated B cell (ENCSR494NNF)

summary:
CTCF ChIA-PET in B_Cell_Activated

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


title: ChIA-PET from activated CD4-positive, alpha-beta T cell (ENCSR314TNQ)

summary:
RNAPII ChIA-PET in CD4_Activated_Day2

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


title: ChIA-PET from CD4-positive, alpha-beta memory T cell (ENCSR106INW)

summary:
CTCF ChIA-PET in Memory_CD4_Resting

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


title: ChIA-PET from activated CD8-positive, alpha-beta memory T cell (ENCSR378IUJ)

summary:
CTCF ChIA-PET in Memory_CD8_Activated_Day7

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


title: ChIA-PET from activated CD4-positive, alpha-beta T cell (ENCSR093CTT)

summary:
CTCF ChIA-PET in CD4_Activated_Day2

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


title: ChIA-PET from CD8-positive, alpha-beta memory T cell (ENCSR187PXW)

summary:
CTCF ChIA-PET in Memory_CD8_Resting

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


title: ChIA-PET from CD8-positive, alpha-beta T cell (ENCSR185VQH)

summary:
RNAPII ChIA-PET in CD8_Resting

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


title: ChIA-PET from CD4-positive, alpha-beta T cell (ENCSR345UIQ)

summary:
CTCF ChIA-PET in CD4_Resting

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


title: ChIA-PET from B cell (ENCSR172WWJ)

summary:
RNAPII ChIA-PET in B_Cell

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


title: ChIA-PET from CD8-positive, alpha-beta T cell (ENCSR180GEY)

summary:
CTCF ChIA-PET in CD8_Resting

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


title: ChIA-PET from activated CD4-positive, alpha-beta memory T cell (ENCSR159PXF)

summary:
RNAPII ChIA-PET in Memory_CD4_Activated_Day7

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


title: ChIA-PET from activated CD4-positive, alpha-beta T cell (ENCSR962FFY)

summary:
CTCF ChIA-PET in CD4_Activated_Day7

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


title: ChIA-PET from CD8-positive, alpha-beta memory T cell (ENCSR149TQU)

summary:
RNAPII ChIA-PET in Memory_CD8_Resting

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


title: ChIA-PET from common myeloid progenitor, CD34-positive (ENCSR421NGZ)

summary:
CTCF ChIA-PET in CD34_HSC

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


title: ChIA-PET from activated CD8-positive, alpha-beta T cell (ENCSR217TFN)

summary:
RNAPII ChIA-PET in CD8_Activated_Day7

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


title: ChIA-PET from CD4-positive naive resting alpha-beta T cell (ENCSR120LMS)

summary:
CTCF ChIA-PET in Naive_CD4_Resting

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


title: ChIA-PET from activated CD8-positive, naive alpha-beta T cell (ENCSR114QCL)

summary:
RNAPII ChIA-PET in Naive_CD8_Activated_Day7

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


title: ChIA-PET from activated B cell (ENCSR096ZPB)

summary:
RNAPII ChIA-PET in B_Cell_Activated

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


title: Human kidney organoid scRNA-seq (from study: Genome-wide screening in human kidney organoids identifies novel aspects of nephrogenesis)

status: Public on Aug 10 2021

city: Basel

first: Rosemarie

last: Ungricht

address: Fabrikstrasse 22

department: DAx

country: Switzerland

institute: Novartis Institute for BioMedical Research

summary: Human iPSC-derived kidney organoids used for genome-wide CRISPR screening were profiled using scRNA-seq to characterize the maturation state at day 21, 28 and 35. Unsupervised clustering attributed cell types to segmented epithelium, podocytes and stroma and revealed stable cell type identity over time with a fibrotic signature in the stroma.

overall_design: The 10x Genomics platform was used to profile kidney organoid single cells.

first: Laure

last: Guibbal

first: Marie

last: Lasbennes

first: Vanessa

last: Orsini

first: Martin

last: Beibel

first: Annick

last: Waldt

first: Rachel

last: Cuttat

first: Walter

last: Carbone

first: Anne

last: Basler

first: Guglielmo

last: Roma

first: Florian

last: Nigsch

first: Jan

last: Tchorz

first: Dominic

last: Hoepfner

first: Philipp

middle: S

last: Hoppe


title: ChIA-PET from HepG2 (ENCSR857MYZ)

status: Public on Jun 15 2021

first: ENCODE

last: DCC

summary:
RNAPII ChIA-PET with HepG2 cell

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


title: ChIA-PET from GM10248 (ENCSR825RKJ)

summary:
RNAPII ChIA-PET with GM10248 cell

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


title: ChIA-PET from K562 (ENCSR880DSH)

summary:
RNAPII ChIA-PET in K562

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


title: Differences in fetal longissimus muscle gene expression between low and high maternal nutrition

status: Public on Sep 29 2021

city: Tsukuba

first: Susumu

last: Muroya

state: Ibaraki

address: Ikenodai 2

department: Animal Products Research Division

institute: NARO Institute of Livestock and Grassland Science

summary: To investigate the impact of maternal nutrient restriction on skleletal muscle gene expression, we profiled gene expression in longissimus muscle of  Japanese Black fetal calves in high and low nutrient condition of pregnant maternal cows .

overall_design: Japanese Black cows were fed with 60% (low-nutrition (LN) group, n=4) or 120% (high-nutrition (HN) group, n=4) of overall nutritional requirement during gestation. The fetal longissimus muscles were obtained at 8.5-mo post-conception of the maternal cows. The microarray-based gene expression was analyzed using the pooled total RNA samples for each of the nutritional treatment group.


title: RNA binding proteins in cancer spliceome

status: Public on Sep 17 2021

first: Dong

last: Chen

address: 388 GaoXin 2nd Road, East Lake Hi-Tech Development Zone

department: Center for Genome Analysis

institute: ABLife, Inc.

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

overall_design:
There are 5 sets of data in this study, as follows:

(1) 50 pairs of transcriptomes from 50 patients covering 9 types of cancer
(2) H3K36me3 ChIP-seq data from HeLa cells with the normal PTB expression and with shRNA knockdown of PTB. 4 pairs (input as controls)
(3) PTB ChIP-seq data from HeLa cells with the normal PTB expression. 2 pairs (input as controls)
(4) 9 transcriptomes of control HeLa cells and those treated with anti-PTB and anti-PKM2 oligos
(5) 9 transcriptomes of control tumor tissues from control, and those treated with anti-PTB and anti-PKM2 oligos


title: ChIA-PET from HEK293T (ENCSR676KCF)

summary:
CTCF ChIA-PET in HEK293T

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


title: ChIA-PET from common myeloid progenitor, CD34-positive (ENCSR065MBZ)

summary:
RNAPII ChIA-PET in CD34_HSC

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


title: ChIA-PET from CD8-positive naive resting alpha-beta T cell (ENCSR064OTE)

summary:
RNAPII ChIA-PET in Naive_CD8_Resting

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


title: ChIA-PET from activated CD8-positive, alpha-beta memory T cell (ENCSR041UPG)

summary:
RNAPII ChIA-PET in Memory_CD8_Activated_Day2

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


title: The influence of sex and age on the lens injury response

status: Public on Jul 10 2021

city: Newark

first: Melinda

middle: K.

last: Duncan

state: DE

address: 327 Wolf Hall

department: Biological Sciences

institute: University of Delaware

summary:
The purpose of this study was to investigate/characterize age- and sex-dependent changes in transcriptomic profile in a mouse model of cataract surgery that mimics human cataract surgery. This surgery involves the removal of lens fiber cells (LFC) leaving behind the lens capsule and associated lens epithelial cells (LEC). The lens capsule and associated remnant LECs were harvested either following cataract surgery (0 hour) or 24 hours later. Fiber cells were collected at the time of surgery, equivalent to 0 hour, and analyzed separately from epithelial cells.
For samples from LEC, each biological replicate is a pool of 5 lens capsules from 5 independent mice.
For samples from LFC, each biological replicate is a pool of 2 fiber cell masses from two independent mice.
Mice were either 24 months old (Aged), or 3 months old (Young).

overall_design: A total of 24 biological replicates were sequenced, with 2 male and 2 female biological replicates per experimental condition.

first: Adam

last: Faranda

first: Mahbubbul

last: Shihan

first: Yan

last: Wang


title: ChIA-PET from activated CD4-positive, alpha-beta memory T cell (ENCSR154MAJ)

summary:
CTCF ChIA-PET in Memory_CD4_Activated_Day2

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


title: ChIA-PET from A549 (ENCSR911ZMB)

summary:
CTCF ChIA-PET in A549

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


title: ChIA-PET from GM10248 (ENCSR627XQX)

summary:
CTCF ChIA-PET with GM10248 cell

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


title: ChIA-PET from AG04449 (ENCSR720WRW)

summary:
RNAPII ChIA-PET in AG04449

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


title: ChIA-PET from MCF 10A (ENCSR499JGQ)

summary:
RNAPII ChIA-PET with MCF10A cell

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


title: ChIA-PET from BJ (ENCSR573PZV)

summary:
CTCF ChIA-PET in BJ

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