title: RNA-seq expression profiling of stromal and epithelial cell subpopulations from human breast tissue

status: Public on Mar 19 2021

city: Parkville

first: Gordon

last: Smyth

state: Vic

address: 1G Royal Pde

department: Bioinformatics

country: Australia

institute: Walter and Eliza Hall Institute of Medical Research

summary: Human breast samples were obtained from eight women with pathologically normal breast tissue and from three women with BRCA2 mutations. Total RNA was extracted from sorted luminal progenitor (Lin?/CD29lo/CD24+), mature luminal (Lin?/CD29hi/CD24+), basal and stromal cell populations.

overall_design:
Mammary cell subpopulations were sorted from breast tissue from each of 11 individuals, three carrying BRCA2 mutations and eight with normal breast tissue. For one normal individual, tissue samples were obtained from both left and right breasts. Epithelial populations (basal, LP and ML) were sorted from all samples and, in  addition, stroma cells were sorted from 6 of the normal samples. All RNA sample were profiled by RNA-seq.

-------------------------------------
Submitter states " am unable to upload the raw sequence data files because of privacy concerns with human samples."

first: Yunshun

last: Chen

first: Bhupinder

last: Pal

first: Jane

last: Visvader


title: Direct profiling of genome-wide dCas9 and Cas9 specificity using ssDNA mapping (CasKAS)

status: Public on Apr 23 2021

city: Stanford

first: Georgi

middle: Kolev

last: Marinov

state: California

address: 279 Campus Drive West, Beckman Center, B-257A/259

department: Genetics

country: USA

institute: STANFORD UNIVERSITY

summary: Detecting and mitigating off-target activity is critical to the practical application of CRISPR-mediated genome and epigenome editing. While numerous methods have been developed to map genome-wide sgRNA specificity genome-wide, they are generally time-consuming and/or expensive, and not applicable to catalytically dead CRISPR enzymes. We have developed a rapid, inexpensive, and facile assay for identifying off-target CRISPR binding and cleavage by chemically mapping the unwound single-stranded DNA structures formed upon CRISPR binding (``CasKAS''). We demonstrate this method in both in vitro and in vivo contexts.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

middle: K

first: Samuel

middle: H

last: Kim

first: S

middle: T

last: Bagdatli

first: Alexandro

middle: E

last: Trevino

first: Josh

last: Tycko

first: Tong

last: Wu

first: Lacramioara

last: Bintu

first: Michael

middle: C

last: Bassik

first: Chuan

last: He

first: Anshul

last: Kundaje

first: William

middle: J

last: Greenleaf


title: Immunotherapy against amyloid beta is modulated by meningeal lymphatic function IV

status: Public on Mar 11 2021

city: Saint Louis

first: Jonathan

last: Kipnis

state: MO

address: 4515 McKinley Ave

department: Pathology and Immunology

institute: Washington University in Saint Louis

type: Expression profiling by high throughput sequencing

summary: A growing body of evidence points to passive immunotherapy as a promising therapeutic strategy against AD. Herein, we show that meningeal lymphatic vasculature becomes dysfunctional in AD transgenic mice and that manipulating meningeal lymphatic drainage affects the outcome of anti-Aβ immunotherapy.

overall_design: Brain tissue was isolated from 22-26 months old male APPswe mice, after intracisterna magna injections of 5 uL of AAV1-CMV-eGFP or AAV1-CMV-mVEGF-C (each at 1012 GC/μL) in combination with a series of weekly intraperitoneal injections of mIgG or mAducanumab antibodies (each at 40 mg/kg). The whole hippocampus was macrodissected from right brain hemisphere (in ice cold media) and snap frozen until total RNA extraction and purification. Each RNA sample sequenced in this experiment resulted from a single hippocampus (single mouse).

first: Sandro

last: Da Mesquita

first: Zachary

last: Papadopoulos

first: Taitea

last: Dykstra

first: Morgan

last: Wall

first: Fabiana

middle: G

last: Farias

first: Logan

last: Brase

first: Hong

last: Jiang

first: Chinnappa

middle: D

last: Kodira

first: Kalil

last: Alves de Lima

first: Jasmin

last: Herz

first: Antoine

last: Louveau

first: Dylan

last: Goldman

first: Andrea

middle: F

last: Salvador

first: Suna

last: Onengut-Gumuscu

first: Emily

last: Farber

first: Nisha

last: Dabhi

first: Tatiana

last: Kennedy

first: Mary

last: Milam

first: Wendy

last: Baker

first: Igor

last: Smirnov

first: Stephen

middle: S

last: Rich

first: David

middle: M

last: Holtzman

first: Carlos

last: Cruchaga

first: Oscar

last: Harari


title: Immunotherapy against amyloid beta is modulated by meningeal lymphatic function V

first: Jonathan

last: Kipnis

overall_design: Brain cells were isolated from 22-26 months old male APPswe mice, after intracisterna magna injections of 5 uL of AAV1-CMV-eGFP or AAV1-CMV-mVEGF-C (each at 1012 GC/μL) in combination with intraperitoneal injections of mIgG or mAducanumab antibodies (each at 40 mg/kg). Brain cell suspensions were obtained by enzymatic and mechanic digestion of right brain hemisphere tissue, stained for surface markers and enriched for specific populations (microglia/macrophages, blood endothelial cells and mural cells) by FACS sorting. Each individual sample used in this single cell RNA sequencing experiment resulted from brain cells pooled from 3 mice.

first: Sandro

last: Da Mesquita

first: Zachary

last: Papadopoulos

first: Taitea

last: Dykstra

first: Morgan

last: Wall

first: Fabiana

last: Farias

first: Logan

last: Brase

first: Hong

last: Jiang

first: Chinnappa

last: Kodira

last: Kipnnis


title: Single-cell analysis of chromatin silencing programs in development and tumor progression

status: Public on Apr 12 2021

city: Seattle

first: Jorja

last: Henikoff

state: WA

address: 1100 Fairview AV N, A1-162

department: Basic Sciences

institute: Fred Hutchinson Cancer Research Center

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Single-cell analysis has become a powerful approach for the molecular characterization of complex tissues. Methods for quantifying gene expression and chromatin accessibility2 of single cells are now well-established, but analysis of chromatin regions with specific histone modifications has been technically challenging.  Here, we adapt the recently published CUT&Tag method3 to scalable single-cell platforms to profile chromatin landscapes in single cells (scCUT&Tag) from complex tissues. We focus on profiling Polycomb Group (PcG) silenced regions marked by H3K27 trimethylation (H3K27me3) in single cells as an orthogonal approach to chromatin accessibility for identifying cell states. We show that scCUT&Tag profiling of H3K27me3 distinguishes cell types in human blood and allows the generation of cell-type-specific PcG landscapes from heterogeneous tissues. Furthermore, we use scCUT&Tag to profile H3K27me3 in a brain tumor patient before and after treatment, identifying cell types in the tumor microenvironment and heterogeneity in PcG activity in the primary sample and after treatment.

overall_design: We used Cleavage under targets and Tagmentation (Cut-and-Tag), a chromatin profiling strategy in which antibody-targeted controlled integration of DNA sequencing adapters produce libraries in nuclei. The resulting nuclei were isolated either by a microwell approach (Takara’s iCell8) or by a microfluidic approach (10x Genomic’s GEM) where unique barcodes are added, followed by paired-end sequencing.

first: Steven

first: Hatice

last: Kaya-Okur

first: Kami

last: Ahmad

last: Wu

first: Scott

middle: N

last: Furlan

first: Anoop

middle: P

last: Patel

first: A

middle: B

last: Mihalas


title: Promotion of Cholangiocarcinoma Growth by Diverse Cancer-associated Fibroblast Subpopulations

status: Public on Apr 28 2021

city: NEW YORK

first: Robert

last: Schwabe

state: NY

address: 1130 ST NICHOLAS AVE - ROOM 916B

department: Medicine

institute: Columbia University

summary: Here we analyzed mouse and human samples to characterize origin, subtypes, functions and cell-cell interactions of cancer-associated fibroblasts in cholangiocarcinoma, a highly desmoplastic tumor of the liver. Hepatic stellate cell-derived cancer-associated fibroblasts were isolated from two different models of murine intrahepatic cholangiocarcinoma, induced by overexpression of YAP+AKT or KRASG12D in combination with sg-p19, and compared by bulk RNA-sequencing to hepatic stellate cells from two models of liver fibrosis, induced by bile duct ligation or DDC diet. CAF-enriched fractions of from YAP+AKT or KRAS/sg-p19-induced intrahepatic cholangiocarcinoma, were analyzed by single-cell RNA sequencing. A cell suspension from human cholangiocarcinoma, containing all cell populations, was analyzed by single cell RNA-sequencing.

overall_design:
Bulk RNA sequencing was perfomed in 19 samples: 4 isolates of quiescent mouse hepatic stellate cells (HSC);  4 isolates of HSC from bile duct-ligated (BDL) mice, 4 HSC isolates  from mice treated with DDC diet, 4 isolates fo HSC-derived CAF from YAP/AKT-induced intrahepatic cholangiocarcinoma (ICC); 3 isolateds of HSC-derived CAF from KRAS/sg-p19 induced ICC.  Single cell RNA-sequencing was performed in 3 samples: one sample of CAF-enriched cells isolated from YAP/AKT-induced ICC; one sample of CAF-enriched cells isolated from KRAS/sg-p19-induced ICC; one sample containing all cell populations from a patient with hilar cholangiocarcinoma (CCA). Biliary liver fibrosis was induced in eight-week-old mice subjected to ligation of the common bile duct as previously described. Mice were euthanized 14 days after the surgery. As a second model of well-established cholestatic liver fibrosis, mice treated with diet containing 0.1% 3,5-diethoxycarbonyl-1,4-dihydrocollidine (DDC) for three weeks. For induction of ICC, plasmids were injected into six to seven week old mice by hydrodynamic tail vein injection at 20μg:5μg ratio of transposon to transposase-encoding plasmid (pT3-EF1α-HA-myr-AKT (mouse), pT3-EF1α-YapS127A (human) for YAP/AKT-induced ICC model) or 25μg:5μg ratio of transposon to transposase-encoding plasmid (pCaggs- KRASG12D transposon plasmid) and 10μg CRISPR/Cas9 sgRNA-p19 plasmid (KRAS/P19 model). Mouse HSC were isolated by in situ liver perfusion as previously described, the cells were further purified by FACS using endogenous retinoid fluorescence or by LRAT-Cre-induced TdTomato fluorescence. CAFs from Lrat-Cre+ TdTom+ Col1a1-GFP+ mice were isolated from tumors following the HSC protocol with few modifications. Before FACS sorting, cells were subjected to a separation gradient using Nycodenz 34%. CAF were sorted for Col1a1-induced GFP; HSC-derived CAFs were sorted by Col1a1-induced GFP and TdTomato double positive signal. All cell sorting was performed on a BD Aria II Cell Sorter, followed by RNA sequencing or scRNA sequencing. For bulk RNA sequencing, purified HSC and HSC-CAF freshly isolated and never cultured, RNA was extracted using the RNeasy Micro or Mini Kit (Qiagen) with on-column DNAse digestion accordingly to manufacturer instructions. RNA (RNA integrity number [RIN] >8, as determined by Bioanalyzer 2100, Agilent Technologies) was used to construct libraries using Illumina TruSeq RNA Preparation Kit according to the manufacturer’s instructions. For single cell RNA sequencing, freshly isolated cells from the YAP/AKT ICC sample were sorted for Col1a1-driven GFP.  To obtain a CAF-enriched sample still containing multiple cell populations for CellPhoneDB analysis, for the KRAS/p19 ICC sample we combined Col1a1-GFP+ cells (60%) with the entire cell population (40%) after sorting on a BD Aria II Cell Sorter. Tumor specimen from 1 CCA patient was freshly dissociated, minced to 2-4 mm sized pieces and subsequently digested to single cell suspension using Multi Tissue Human Tumor Dissociation Kit 1 (Miltenyi Biotec) and a gentleMACS OctoDissociator (Miltenyi Biotec) according to the manufacturer’s instructions. The dissociated samples were processed for scRNA sequencing.

***Please note that the AJ064 raw data was not provided due to IRB protocol as it contains identiable personal sequencing data of this patient currently undergoing treatment.

first: Silvia

last: Affo

first: Ajay

last: Nair

first: Francesco

last: Brundu


title: Sex and cell-specific gene expression in corticolimbic brain regions associated with psychiatric disorders revealed by bulk and single-nuclei RNA sequencing

status: Public on Mar 10 2021

city: Verdun

first: Nicholas

last: O'Toole

state: QC

address: 6875 Boulevard Lasalle

country: Canada

institute: Douglas Mental Health University Institute

summary:
Background
There are sex-specific differences in the prevalence, symptomology and course of psychiatric
disorders. However, preclinical models have primarily used males, such that the molecular
mechanisms underlying sex-specific differences in psychiatric disorders are not well established.
Methods
In this study, we compared transcriptome-wide gene expression profiles in male and female rats
within the corticolimbic system, including the cingulate cortex, nucleus accumbens medial shell
(NAcS), ventral dentate gyrus and the basolateral amygdala (n=22-24 per group/region).
Findings
We found over 3,000 differentially expressed genes (DEGs) in the NAcS between males and
females. Of these DEGs in the NAcS, 303 showed sex-dependent conservation DEGs in humans and
were significantly enriched for gene ontology terms related to blood vessel morphogenesis and
regulation of cell migration. Single nuclei RNA sequencing in the NAcS of male and female rats
identified widespread sex-dependent expression, with genes upregulated in females showing a
notable enrichment for synaptic function. Female upregulated genes in Astrocytes, Drd3+MSNs
and Oligodendrocyte were also enriched in several psychiatric genome-wide association studies
(GWAS). Interpretation
Our data provide comprehensive evidence of sex- and cell-specific molecular profiles in the NAcS.
Importantly these differences associate with anxiety, bipolar disorder, schizophrenia, and cross-
disorder, suggesting an intrinsic molecular basis for sex-based differences in psychiatric disorders
that strongly implicates the NAcS.

overall_design: Single nucleus RNA sequencing of the Nucleus Accumbens shell in male and female rats.

last: O’Toole

first: Eamon

last: Fitzgerald

first: Tieyuan

last: Zhang


title: Self-reactivity shapes functional diversity of naive CD8+ T cells by co-opting tonic type I interferon [RNA-Seq_1]

status: Public on Jun 19 2021

city: Hwasun-eup, Hwasun-gun

first: Jae-Ho

last: Cho

state: Jeollanam-do

address: 264, Seoyang-ro

country: South Korea

institute: CHONNAM NATIONAL UNIVERSITY

summary: The strength of the T cell receptor interaction with self-ligands affects antigen-specific immune responses. However, the precise role, functional relationship, and underlying mechanisms have not been elucidated completely. Here, we demonstrate that naive CD8+ T cells with relatively high self-reactivity are phenotypically heterogeneous owing to varied responses to type I interferon (T1IFN), resulting in three distinct subsets, CD5loLy6C–, CD5hiLy6C–, and CD5hiLy6C+ cells. CD5hiLy6C+ cells differ from CD5loLy6C– and CD5hiLy6C– cells in their gene expression profiles and functional properties. Moreover, CD5hiLy6C+ cells demonstrate more extensive antigen-specific expansion upon viral infection, with enhanced differentiation into terminal effector cells and reduced memory cell generation. Such unique features of CD5hiLy6C+ cells are imprinted in a steady-state and observed even for those of monoclonal CD8+ T cell populations in a T1IFN dependent fashion. These findings demonstrate that self-reactivity shapes the functional diversity of naive CD8+ T cells by co-opting tonic T1IFN signaling.

overall_design: Gene profiles of 3 naive (CD44lo) CD8+ T cell subsets (CD5lo, CD5hi Ly6C-, and CD5hi Ly6C+)

first: Young-Jun

last: Ju

first: Sung-Woo

last: Lee


title: Resolving the graft ischemia-reperfusion injury during liver transplantation at the single cell resolution

status: Public on Apr 07 2021

city: Guangzhou

first: Zhiyong

last: Guo

state: Guangdong

address: 58. Zhongshan 2 Road, Guangzhou, China

country: China

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

summary: Ischemia-reperfusion injury (IRI) remains the major reason for impaired donor graft function and increased mortality post-liver transplantation. The mechanism of IRI involves multiple pathophysiological processes and numerous types of cells. However, a systematic and comprehensive single-cell transcriptional profile of intrahepatic cells during liver transplantation is still unclear. We performed a single-cell transcriptome analysis of 14,313 cells from liver tissues collected from pre-procurement, at the end of preservation and 2 h post-reperfusion. We made detailed annotations of mononuclear phagocyte, endothelial cell, NK/T, B and plasma cell clusters, and we described the dynamic changes of the transcriptome of these clusters during IRI and the interaction between mononuclear phagocyte clusters and other cell clusters. In addition, we found that TNFAIP3 interacting protein 3 (TNIP3), specifically and highly expressed in Kupffer cell clusters post-reperfusion, may have a protective effect on IRI. In summary, our study provides the first dynamic transcriptome map of intrahepatic cell clusters during liver transplantation at single-cell resolution.

overall_design: Single cell transcriptome detection of intrahepatic cells at 3 time points during liver transplantation

first: Linhe

last: Wang

first: Jie

last: Li

first: Shuai

last: He

first: Yang

last: Liu

first: Haitian

last: Chen

first: Shujiao

first: Meixian

last: Yin

first: DaWei

last: Zou

first: Jinghong

last: Xu

first: Shirui

first: Tao

last: Luo

first: Xinyu

last: Yu

first: Shunwei

last: Huang

first: Xiaoshun


title: miRNA profiling of Wild Type Wistar rat in postanatal retinal development

status: Public on Mar 24 2021

city: Pécs

first: Kovács-Valasek

last: Andrea

state: Baranya

address: Ifjusag utja 6

country: Hungary

institute: University of Pécs

type: Non-coding RNA profiling by high throughput sequencing

summary:
Purpose: to reveal the small RNA profile of postnatal retina in Wistar WU albino rat by Ion-Torrent PGM sequencing technology.
Methods : Wistar WU rats ranging in age from P1 to P21 were anesthetized by inhalation using Forane prior to sacrifice at the same hour to avoid circadian variation. Total RNA was extracted from the retinal tissues of various developmental stages using NucleoSpin miRNA kit (Macherey–Nagel, Düren, Germany) following manufacturer's instructions. The miRNA concentration was assessed using Qubit microRNA Assay Kit (ThermoFisher Scientific, MA, USA). The RNA integrity number (RIN), an algorithm for judging the integrity of RNA samples, were evaluated using Agilent 2100 Bioanalyzer (Agilent Technologies, USA) following the manufacturing instruction of the RNA 6000 Nano kit and RIN>7 was considered acceptable. MicroRNAs was also determined using the Agilent Small RNA Kit to have deeper view in the 10 to 40-nucleotide size range. Small RNA library construction from pooled retinal samples (N=3, in each age-group) were carried out according to the Ion Total RNA-Seq Kit v2 protocol (Revision E) with slight modification. Enzymatic reaction was performed in half reaction volume, while cleaning procedures were executed with the accurate final volume according to the protocol. The Ion 316 or 318 ™ Chip v2 was used for sequencing on the Ion Torrent PGM™ instrument according to the protocol of Ion PGM™ Hi-Q View Sequencing Kit. To assess reliability of miRNA workflow solution in 316 v2 chip, two independent P7 samples were assayed (biological replicates) and P21 sample were sequenced as technical replicates in every sequencing procedure. Some samples were also sequenced in 318 v2 chip (P3, P5, P10, P15 and P21) as biological replicate. Ion Torrent Suite Platform was used to trim the raw sequence data and remove any residual sequencing adapter fragments that remained on the 5′ or 3′ ends. Reads were mapped to the non-coding RNAs from ENSEMBL [Rnor_6.0 (GCA_000001895.4)] using TMAP algorithm. These aligned BAM (Binary Alignment Map) files were further processed in Galaxy Web-based platform (Afgan, 2018) via Cufflinks, Cuffmerge and Cuffdiff (Version 2.2.1.3) application (Trapnell, 2010). Further analysis and visualising of the datasets was carried out in R Studio Software environment. qRT–PCR validation was performed using TaqMan assays.

overall_design: Retinal miRNA profiles of Wistar WU rats ranging in age from P1 to P21 were generated using IonTorrent.

first: Robert

last: Gabriel

first: Andrea

last: Kovács-Valasek


title: Immunotherapy against amyloid beta is modulated by meningeal lymphatic function VI

first: Jonathan

last: Kipnis

overall_design: Brain cells were isolated from 4 months old male 5xFAD mice, after intracisterna magna injections of 5 uL of Visudyne (Vis., verteporfin for injection) alone, or followed by 5 steps of transcranial photoconversion (Vis./photo.), in combination with a series of weekly intraperitoneal injections of mIgG or mAducanumab antibodies (each at 40 mg/kg). Brain cell suspensions were obtained by enzymatic and mechanic digestion of right brain hemisphere tissue, stained for surface markers and enriched for specific populations (microglia/macrophages, blood endothelial cells and mural cells) by FACS sorting. Each individual sample used in this single cell RNA sequencing experiment resulted from brain cells pooled from 3 mice.

first: Sandro

last: Da Mesquita

first: Zachary

last: Papadopoulos

first: Taitea

last: Dykstra

first: Morgan

last: Wall

first: Fabiana

last: Farias

first: Logan

last: Brase

first: Hong

last: Jiang

first: Chinnappa

last: Kodira

first: Kalil

last: Alves de Lima

first: Jasmin

last: Herz

first: Antoine

last: Louveau

first: Dylan

last: Goldman

last: Salvador

first: Suna

last: Onengut-Gumuscu

first: Emily

last: Farber

first: Nisha

last: Dabhi

first: Tatiana

last: Kennedy

first: Mary

last: Milam

first: Wendy

last: Baker

first: Igor

last: Smirnov

first: Stephen

last: Rich

first: David

last: Holtzman

first: Carlos

last: Cruchaga

first: Oscar

last: Harari


title: Genome-wide maps of H3K27Ac occupancy on chromatin in mouse ovaries before and after hCG treatment.

status: Public on Jan 30 2021

city: Hangzhou

first: Yin-Li

last: Zhang

address: No. 3 Qingchun East Road, Jianggan District

institute: Sir Run Run Shaw Hospital, Zhejiang University School of Medicine

summary: Chromatin immunoprecipitation-based sequencing (ChIP-seq) of H3K27Ac was performed using mouse ovarian granulosa cells before and after ovulatory signal stimulation. We found genome-wide H3K27Ac was erased rapidly at 1h after hCG treatment, and new H3K27Ac was established at 4h after hCG treatment.

overall_design: H3K27Ac ChIP-seq  using  mouse ovaries at 0h, 1h and 4h after hCG treatment

first: Jiamin

last: Jin

first: Xiang

last: Li


title: Immunotherapy against amyloid beta is modulated by meningeal lymphatic function III

first: Jonathan

last: Kipnis

overall_design: Lymphatic endothelial cells (LECs) were isolated from the meninges of 20-24 months old male C57BL/6J mice, 4 weeks after intracisterna magna injection of 5 uL of AAV1-CMV-eGFP or AAV1-CMV-mVEGF-C (each at 1012 GC/μL). LECs were sorted by FACS directly into lysis buffer according to the following phenotype: Singlets DAPI-CD45-CD31+PDPN+. Each individual sample results from meningeal cells pooled from 10 mice.

first: Sandro

last: Da Mesquita

first: Zachary

last: Papadopoulos

first: Taitea

last: Dykstra

first: Morgan

last: Wall

first: Fabiana

last: Farias

first: Logan

last: Brase

first: Hong

last: Jiang

first: Chinnappa

last: Kodira

first: Kalil

last: Alves de Lima

first: Jasmin

last: Herz

last: Louveau

first: Andrea


title: Immunotherapy against amyloid beta is modulated by meningeal lymphatic function

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

overall_design: Refer to individual Series


title: H3K4me3 and H3K27ac ChIp-seq

status: Public on Dec 17 2020

city: Manchester

first: Michela

last: Garofalo

address: Alderley Park

country: United Kingdom

institute: CRUK Manchester Institute

summary: By integrating chromatin and transcriptome analyses of ChIp-seq and Cap Analysis of Gene Expression sequencing (CAGE-seq), we showed that the presence of an active promoter and an enhancer at the KIMAT1 and HIF1A-As2 promoter region.

overall_design: Examination of 2 different histone modifications in H1299 cells

first: Lei

last: Shi

first: Sudhakar

last: Sahoo

first: Hui-Sun

last: Leong


title: TP53 wild type cells are resistant to arsenic trioxide induced dynamic transcriptional changes

status: Public on Dec 31 2020

city: FuZhou

first: Haiwei

last: Wang

state: FuJian

address: Daoshan road 180

institute: Fujian Maternity and Child Health Hospital

summary: Previous and our results show that cells with mutant p53 are more sensitive to arsenic trioxide (ATO) induced cell growth inhibition. To explore the underling mechanisms, we conduct a detailed analysis of the globe transcriptional profiles of ATO regulated genes in breast, colon and lung cancer cells with different p53 status. We find p53 wild type cells are resistant to ATO induced globe dynamic transcriptional changes, thus resistant to ATO induced cell growth inhibition. P53 inhibitor PFTα releases p53 mediated transcriptional resistance and increases the sensitivity of ATO in p53 wild type tumor cells.

overall_design: Breast cancer SKBR3, MCF7, colon cancer SW620, HCT116 and lung cancer H1299, A549 cells were treated with ATO 5μM for 0, 6, 12, 24 and 36 hours. TP53 wild type MCF7, HCT116 and A549 cells were treated with the combination of ATO and TP53 inhibitor PFTα at 6h, 12h, 24h and 36 hours. Total RNA was collected and profiled to Affymetrix microarray.


title: Alternative splicing coupled mRNA decay shapes the temperature-dependent transcriptome

status: Public on Nov 01 2020

city: Berlin

first: Marco

last: Preussner

address: Takustrasse 6

country: Germany

institute: FU berlin

summary: Mammalian body temperature oscillates with the time of the day and is altered in diverse pathological conditions. We recently identified a body temperature-sensitive thermometer-like kinase, which alters SR protein phosphorylation and thereby globally controls alternative splicing (AS). AS can generate unproductive variants which are recognized and degraded by diverse mRNA decay pathways – including nonsense-mediated decay (NMD). Here we show extensive coupling of body temperature-controlled AS to mRNA decay, leading to global control of temperature-dependent gene expression (GE). Temperature-controlled, decay-inducing splicing events are evolutionarily conserved and pervasively found within RNA-binding proteins, including most SR proteins. AS-coupled poison exon inclusion is essential for rhythmic GE of SR proteins and has a global role in establishing temperature-dependent rhythmic GE profiles, both, in mammals under circadian body temperature cycles and in plants in response to ambient temperature changes. Together, these data identify body temperature-driven AS coupled mRNA decay as an evolutionary ancient, core clock-independent mechanism to generate rhythmic GE.

overall_design: Hepatocytes were pre-entrained to 34°C or 38°C for 12 hours. Cells were shifted and after 4 hours DMSO or CHX was added for 4 further hours; RNA was extracted and analyzed by RNA-Seq.

first: Florian

last: Heyd


title: DHX9 and NPM1 silencing RNA-seq

summary: In our study, we valided DHX9 and NPM1 interact with KIMAT1, whereas DHX9 also interacts with HIF1A-As2. DHX9 is a highly conserved DEAD-box protein expressed in the nucleus and the cytoplasm, involved in many processes including transcriptional activation, miRNA biogenesis and tumor cell maintenance. NPM1 is predominantly localized in the nucleoplasm, where it associates with active RNA polymerase II and transcriptionally activates genes involved in cancer. We silenced DHX9 and NPM1 and performed RNA-seq to examine the dysregulated genes by DHX9 and NPM1.

overall_design: siRNAs targeting control, DHX9 or NPM1 were tranfected in H1299 cells. Total RNAs were extracted after 48 hours of tranfection.


title: Immunotherapy against amyloid beta is modulated by meningeal lymphatic function I

first: Jonathan

last: Kipnis

overall_design: Lymphatic endothelial cells (LECs) were isolated from the meninges of male 5xFAD mice, or non-transgenic wild type age-matched littermates (WT), at the age of 6 months. LECs were sorted by FACS directly into lysis buffer according to the following phenotype: Singlets DAPI-CD45-CD31+PDPN+. Each individual sample results from meningeal cells pooled from 10 mice.

first: Sandro

last: Da Mesquita

first: Zachary

last: Papadopoulos

first: Antoine

first: Dylan

last: Goldman

last: Salvador

first: Suna

last: Onengut-Gumuscu

first: Emily

last: Farber

first: Nisha

last: Dabhi

first: Tatiana

last: Kennedy

first: Mary

last: Milam

first: Wendy

last: Baker

first: Igor

last: Smirnov

first: Stephen

last: Rich

first: David

last: Holtzman

first: Carlos

last: Cruchaga

first: Oscar

last: Harari


title: Insulin resistance rewires the metabolic gene program and glucose utilization in human white adipocytes

status: Public on Feb 28 2021

city: Kongens Lyngby

first: Julia

last: Villarroel

address: Kulsviervænget 41

country: Denmark

institute: University of Copenhagen

summary: The aim of this study is to define the molecular alterations occurring in human adipose tissue leading to its dysfunction. While obesity (defined by BMI>30) is strongly associated with insulin resistance and metabolic disorders, some individuals with obesity remain insulin sensitive. Therefore, in this study, we have considered a control group  (lean, insuln sensitive: BMI<25, HOMA-IR<2), a group with overweight/obesity but without insulin resistance (BMI>25, HOMA-IR<2) and a group with overweight and insulin resistance (BMI>25, HOMA-IR>3) to dissect the transcriptional changes in viscreal adipose tissue due to increased fat mass, and those associated with metabolic disorder.

overall_design: 16 samples of human omental fat. 5 x Lean Insuline Sensitive patients + 6 x Obese Insuline Sensitive patients + 5 x Obese Insuline Resistant

first: Marie

last: Isidor

first: Wentao

last: Dong

first: Rogelio

middle: I

last: Servin-Uribe

first: Ali

last: Alintas

first: Jorge

last: Ayala-Sumuano

first: Alfredo

last: Varela-Echavarría

first: Juleen

middle: R

last: Zierath

first: Gregory

last: Stephanopoulos

first: Yazmín

last: Macotela

first: Brice

last: Emanuelli


title: Immunotherapy against amyloid beta is modulated by meningeal lymphatic function II

first: Jonathan

last: Kipnis

overall_design: At the age of 4 months, male 5xFAD mice were subjected to an intracisterna magna injection of Visudyne (5 uL) alone (control), or injection of Visudyne (5 uL) followed by 5 steps of transcranial photoconversion using a 689-nm-wavelength non-thermal red light (to induce meningeal lymphatic vessel ablation). Injections were repeated 3 weeks later and mice were euthanized 3 weeks after the last injection. Microglia from the brain cortex were sorted by FACS based on the following phenotype: Singlets SYTOX-Ly6G-CD45+CD11b+. Each individual sample results from brain cortical cells pooled from 3 mice.

first: Sandro

last: Da Mesquita

first: Zachary

last: Papadopoulos

first: Taitea

last: Dykstra

first: Morgan

last: Wall

first: Fabiana

last: Farias

first: Logan

last: Brase

first: Hong

last: Jiang

first: Chinnappa

last: Kodira

first: Kalil

last: Alves de Lima

first: Jasmin

last: Herz

first: Antoine

last: Louveau

first: Dylan

last: Goldman

first: Andrea

last: Salvador

first: Suna

last: Onengut-Gumuscu

first: Emily

last: Farber

first: Nisha

last: Dabhi

first: Tatiana

last: Kennedy

first: Mary

last: Milam

first: Wendy

last: Baker


title: Early Stem Cell Aging in the Mature Brain

status: Public on Mar 03 2021

city: Los Angeles

first: Albina

address: 1425 San Pablo Street

department: Stem Cell and Regenerative Medicine

institute: University of Southern California

summary: Stem cell dysfunction drives many age-related disorders. Identifying mechanisms that initially compromise stem cell behavior represent early targets to enhance stem cell function later in life. Here, we pinpoint multiple factors that disrupt neural stem cell (NSC) behavior in the adult hippocampus. Clonal tracing showed that NSCs exhibit asynchronous depletion by identifying short-term (ST-NSC) and long-term NSCs (LT-NSCs). ST-NSC divide rapidly to generate neurons and deplete in the young brain. Meanwhile, multipotent LT-NSCs are maintained for months, but are pushed out of homeostasis by lengthening quiescence. Single cell transcriptome analysis of deep NSC quiescence revealed several hallmarks of molecular aging in the mature brain and identified tyrosine-protein kinase Abl1 as an NSC pro-aging factor. Treatment with the Abl-inhibitor Imatinib increased NSC proliferation without impairing NSC maintenance in the middle-aged brain. Our study indicates that hippocampal NSCs are particularly vulnerable to cellular aging, yet NSC function can be partially restored.

overall_design: single cell RNA-Sequencing of neural stem cells and immediate progeny derived from the dentate gyrus. 48 cells from 2 month old mice and 41 from 4.5 month old mice.

last: Ibrayeva

first: Maxwell

last: Bay

first: Elbert

last: Pu

first: David

last: Jörg

first: Lei

last: Peng

first: Heechul

last: Jun

first: Naibo

last: Zhang

first: Daniel

last: Aaron

first: Congrui

last: Lin

first: Galen

last: Resler

first: Axel

last: Hidalgo

first: Mi-Hyeon

last: Jang

first: Benjamin

last: Simons

first: Michael

middle: A

last: Bonaguidi


title: Enhancer analysis of HER2+ cell lines SKBR-3 (ER-) and BT474m1 (ER+) in response to lapatinib and JQ1 and analysis of FOXA1 chromatin binding in SKBR-3 cells in response to lapatinib and JQ1 and impact of FOXA1 knockdown on BRD4 and MED1

status: Public on Nov 03 2020

city: Indianapolis

first: Steven

last: Angus

state: IN

address: 1044 W Walnut St

department: Pediatrics

institute: Indiana University School of Medicine

summary: SKBR-3 and BT474m1 HER2+ breast cancer cell lines were treated with lapatinib, JQ1, or lapatinib and JQ1 or (for SKBR-3) treated with siRNA pools (non-targeting control or FOXA1) prior to drug treatment before being used for ChIPseq (BRD4, MED1, H3K27Ac, or FOXA1 (for SKBR-3))

overall_design: 36 experimental samples analyzed, 6 chromatin input control samples

first: Gary

middle: L

last: Johnson


title: Adaptive responses to targeted therapy in HER2-positive breast cancer (RNAseq) - TBCRC 036 / LCCC1214 / ClinicalTrials.gov Identifier: NCT01875666

status: Public on Nov 18 2020

summary: Inhibition of the HER2/ERBB2 receptor is a keystone to treating HER2-positive malignancies, particularly breast cancer, but a significant fraction of HER2-positive (HER2+) breast cancers recur or fail to respond. Anti-HER2 monoclonal antibodies, like trastuzumab or pertuzumab, and ATP active site inhibitors like lapatinib, commonly lack durability because of adaptive changes in the tumor leading to resistance. HER2+ cell line responses to inhibition with lapatinib were analyzed by RNAseq and ChIPseq to characterize transcriptional and epigenetic changes. Motif analysis of lapatinib-responsive genomic regions implicated the pioneer transcription factor FOXA1 as a mediator of adaptive responses. Lapatinib in combination with FOXA1 depletion led to dysregulation of enhancers, impaired adaptive upregulation of HER3, and decreased proliferation. HER2-directed therapy using clinically relevant drugs (trastuzumab with or without lapatinib or pertuzumab) in a 7-day clinical trial designed to examine early pharmacodynamic response to antibody-based anti-HER2 therapy showed reduced FOXA1 expression was coincident with decreased HER2 and HER3 levels, decreased proliferation gene signatures, and increased immune gene signatures. This highlights the importance of the immune response to anti-HER2 antibodies and suggests that inhibiting FOXA1-mediated adaptive responses in combination with HER2 targeting is a potential therapeutic strategy.

overall_design: NOTE: Due to incomplete permissions from participating institutions, we are unable to upload raw data at this time due to patient privacy concerns.


title: In-situ cell-type specific chromatin topologies in the brain revealed by genome architecture mapping

status: Public on Aug 27 2021

first: Alexander

last: Kukalev

address: Hannoversche Str., 28

department: Berlin Institute for Medical Systems Biology

institute: Max-Delbrueck Center for Molecular Medicine

summary: We report the application of genome architecture mapping in specific cell types in mouse brain. We generated cell-type specific chromatin contact maps in mouse dopaminergic neurons from the midbrain ventral tegmental area (VTA DN), pyramidal glutamatergic neurons from the cornus ammonis 1 region of the hippocampus (CA1 PGN), and non-neuronal post-mitotic oligodendrocytes from the somatosensory cortex (SSC_Olig). We explored cell-type specific chromatin topologies genome-wide at multiple genomic scales. Our data demonstrates that chromatin organization is cell type specific and reflects cell specialization at all genomic scales.

overall_design: Briefly, we isolated single thin tissue sections by ultrathin cryosectioning (approx. 220 nm) of the mouse brain region of interest, and selected specific cell-types using immunofluorescence with specific AB markers. Following cell identification, 3 nuclear sections (nuclear profiles; NPs) were captured by laser microdissection in individual PCR caps. We then extracted, amplified and sequenced the DNA from each PCR cap.

first: Warren

last: Winick-Ng

first: Izabela

last: Harabula

first: Mandy

last: Meijer

first: Leonid

last: Serebreni

first: Rieke

last: Kempfer

first: Mark

last: Ungless

first: Gonçalo

last: Castelo-Branco

first: Georg

last: Dechant

first: Ana

last: Pombo


title: Keystone genes for tooth development [microarray]

city: Helsinki

first: Jukka

last: Jernvall

address: P.O. Box 56 (Viikinkaari 9)

country: Finland

institute: University of Helsinki

summary:
The expression levels of developing mouse molar transcriptome were measured.
5 samples of both E13.5 and E14.5 of mouse developing molar tooth.

overall_design: expression profiling of molar 1 tooth germ from stages E13.5 or E14.5. 5 replicates at each developmental stage.

first: Outi

last: Hallikas

first: Rishi

last: Das Roy

first: Mona

last: Christensen

first: Elodie

last: Renvoisé

first: Ana-Marija

last: Sulic


title: An organelle-tethering mechanism couples flagellation to cell division in bacteria

status: Public on Feb 18 2021

city: Geneva 4

first: Patrick

middle: H.

last: Viollier

address: Rue Michel Servet 1

department: Dept.  Microbiology and Molecular Medicine

country: Switzerland

institute: University of Geneva, Faculty of Medicine / CMU

summary: In both free-living and pathogenic bacteria, problems in the synthesis and assembly of early flagellar components invariably lead to cell division defects. However, the mechanism that fine-tunes the cell division cycle with the flagellar biogenesis is poorly understood. Herein, we report the role of the conserved regulator MadA in coupling flagellar biogenesis to cell division in Caulobacter crescentus. We demonstrate that MadA is required to induce the flagellar specific type III export component FlhA to release and activate FliX, which in-turn is required to license the conserved σ54-activator, FlbD. In the absence of MadA, FliX is tethered to FlhA, inhibiting FlbD activation and crippling completion of flagellar biogenesis and cell division. Furthermore, we demonstrate that MadA exploits a divisome-stoichiometric to control cell division. We propose that MadA has a sentinel-type function that warrants progression of the flagellar biogenesis, and the cell division cycle, once early flagellar structures are properly assembled.

overall_design: Global transcriptome profiling (gene expression) by RNA-Seq in Caulobacter crescentus NA1000(WT), flbD::Tn and ΔmadA backgrounds.

first: Lokesh

last: Kumar

first: Manisha

last: Siwach

first: Saravanan

last: Palani

first: Gaël

last: Panis

first: Coralie

last: Fumeaux

first: Samada

last: Muraleedharan

middle: H

first: Sunish

middle: K

last: Radhakrishnan


title: MicroRNA-29 is an essential regulator of non-CG methylation during brain maturation

status: Public on Feb 14 2021

city: Boston

first: Jeremy

last: Simon

state: MA

address: 450 Brookline Ave

department: Department of Data Science

institute: Dana-Farber Cancer Institute

type: Methylation profiling by high throughput sequencing


title: Genes expression in intestinal GVHD

status: Public on Jan 28 2021

city: Suzhou

first: xiaoliang

last: yu

state: Jiangsu

address: Chongwen Road

institute: Suzhou Institute of Systems Medicine


title: KRAS drives lung cancer metastasis through lncRNA-mediated transcriptional and post-transcriptional regulation

first: Michela

last: Garofalo


title: A Hidradenitis Suppurativa Molecular Disease Signature Derived from Patient Samples by High-Throughput RNA Sequencing

city: Collegeville

first: Johannes

last: Freudenberg

state: Pennsylvania

address: 1250 S Collegeville Rd

department: Human Genetics

institute: GlaxoSmithKline

summary: Hidradenitis suppurativa is a common, debilitating inflammatory skin disease linked to immune dysregulation and abnormalities in follicular structure and function.  Few studies have characterized the transcriptomic profile of affected and unaffected skin. We established an RNA-Seq based hidradenitis suppurativa expression disease signature and found it largely concordant with an earlier microarray-based study. We confirmed known aspects of the underlying disease biology including known immune response pathways, differential regulation of antimicrobial peptides, and complement activation. We further characterize the extent of changes in the complement cascade in hidradenitis lesions and highlight a signature that implicates host response to bacteria in disease pathogenesis.

overall_design: Patient-derived RNA from lesional and matching perilesional skin biopsies were used to identify an expression-based hidradenitis suppurativa disease signature.

first: Zhi

last: Liu

first: Jennifer

last: Singh

first: Elizabeth

last: Thomas

first: Christopher

last: Traini

first: Deepak

last: Rajpal

first: Chris

last: Sayed


title: Determine the effects of METTL16 on global translation efficiency via ribosome profiling (Ribo-seq)

status: Public on Oct 28 2021

city: Monrovia

first: Jianjun

last: Chen

state: CA

department: Systems Biology

institute: Beckman Research Institute of City of Hope

summary: METTL16 is a member of methyltransferase like (METTL) family. Unlike well-studied METTL3 and METTL14, we found a much higher percentage of METTL16 is localized in the cytosol. The subcellular distribution holds the ability to potentiate translation efficiency. Via Far-western blotting and Co-Immunoprecipitation (Co-IP) assays, we have identified the direct interactions between METTL16 and eukaryotic initiation factor 3 (eIF3) a and b. Via cross-linking immunoprecipitation and qPCR (CLIP-qPCR), we have discovered the direct associations between METTL16 and rRNAs. The METTL16-eIF3a/b and METTL16-rRNAs interactions induce the binding between eIF3 and 18S rRNA, promote the formation of 43S preinitiation complex, and eventually expedite translation initiation, the rate-limiting step of translation. To determine the exact effects of METTL16 on translation efficiency, we performed ribosome profiling (Ribo-seq) with HEK293T upon CRISPR-Cas9-induced METTL16 knockout. To guarantee the repeatability and avoid any potential off-target effects, we included 3 distint sgRNAs against METTL16.

overall_design: The Cas9 single clone of HEK293T cells was infected with lentivirus sgRNAs against METTL16 and the cells were collected at 70-80% confluency after selection with blasticidin and puromycin for at least 1 week. The samples were subjected to ribosome profiling and both the input RNA and footprint RNAs were used for sequencing. Three sgRNAs against METTL16 groups and one sgNS group were included.

first: Rui

last: Su

first: Lei

last: Dong


title: The transcriptomic and physiological basis of desiccation stress response in natural European D. melanogaster populations

city: Barcelona

first: Gabriel

middle: Eduardo

last: Rech

address: Passeig Marítim de la Barceloneta 37-49

country: Spain

institute: Consejo Superior de Investigaciones Cientificas - Institute of Evolutionary Biology (CSIC-UPF)

summary: Climate change is one of the main factors shaping the distributions and biodiversity of organisms, among others by greatly altering water availability, thus exposing species and ecosystems to harsh desiccation conditions. Insects are specially threatened by these challenging dry environments, thanks to their small size and thus large surface area to volume ratio. Drosophila melanogaster is a great model to study the response of populations to rapidly changing conditions, because of its southern African origin and recent and fast worldwide spreading. Desiccation stress response is a complex and extensively studied trait, however the natural variation and underlying molecular and physiological mechanisms responsible for the tolerance in natural European D. melanogaster populations has never been studied. Here we subjected to desiccation stress 74 natural D. melanogaster European strains, belonging to five different climate zones. We found that the strains belonging to the cold semi-arid climates are more tolerant compared to the others, and that this tolerance can be explained by the combination of altitude and evaporation. The tolerant strains had a lower level of initial water content and lost less water during desiccation stress. We found that the reduction in the water loss happens through a decrease in the respiration rate in desiccation stress conditions, and by having a less permeable cuticle prior the stress exposure. The decreased rate of respiration in the tolerant strains is a consequence of the down-regulation of genes related to diverse metabolic processes. Moreover, we found that the genes related to response to stimulus and environmental sensing are up-regulated only in the tolerant strains. We also identified four transposable element insertions, which might be responsible for changes in gene expression. Overall, our study for the first time described the physiological and transcriptomic changes underlying the desiccation tolerance of natural European D. melanogaster strains, and generated a list of putative mutations shaping desiccation stress response.

overall_design: Six Drosophila melanogaster strains (three  tolerant to desiccation stress: ES_GIM_15_12 (GIM-012), ES_GIM_15_24 (GIM-024),ES_COR_15_23 (COR-023) and three sensitive to desiccation stress ES_TOM_15_8 (TOM-08), LUN_15_7 (LUN-07) and MUN_15_13 (MUN-013)) were chosen for RNA sequencing. For each of the six strains, three replicates were subjected to desiccation stress (treated samples) and other three acted as control. In treated conditions,  flies were placed in empty vials and between the cotton and the parafilm, three grams of silica gel (Merck) were placed, so they were starved and desiccated. Control vials were prepared similarly, except that it contained 1mL of 1% agar on the bottom of the vial to prevent desiccation. Agar in the tubes provides hydration but not food source for the control flies (Sinclair et al 2007).

first: Vivien

last: Horvath

first: Sara

last: Guirao-Rico

first: Judit

last: Salces-Ortiz

middle: E

first: Eugenio

last: Aprea

first: Mirco

last: Rodeghiero

first: Gianfranco

last: Anfora

first: Josefa

last: González


title: KIMAT1 and HIF1A-As2 silencing RNA-seq

first: Michela

last: Garofalo

summary: In our study, we valided the important oncogeneic roles of KIMAT1 and HIF1A-As2 in non-small cell lung cancer. We used custom designed GapmeRs to silence the KIMAT1 and HIF1A-As2 in H1299 and performed RNA-seq. 11389 and 7767 genes were regulated by KIMAT1 and HIF1A-As2, respectively.

overall_design: GapmeRs targeting control or lncRNAs were tranfected in H1299 cells. Total RNAs were extracted after 48 hours of tranfection.

last: Shi

first: Sudhakar

last: Sahoo

first: Hui-Sun

last: Leong


title: KRAS WT and G12D overexpression RNA-seq

summary: KRAS is an important oncogene in cancer. Long noncoding RNAs (lncRNAs) have been characterized to be involved in various types of cancer. In this study, we investigated the functions of KRAS-responsive lncRNAs in cancer. We perfomed the RNA-seq to examine the lncRNA expression after overexpession of KRAS WT and G12D in H1299 cells.

overall_design: KRAS WT, G12D or empty vector was tranfected in H1299 cells. Total RNAs were extracted after 48 hours of tranfection.


title: Adaptive responses of the HER2+ SKBR-3 and BT474m1 cell lines to lapatinib and JQ1

status: Public on Oct 26 2020

first: Steven

last: Angus

summary: SKBR-3 or BT474m1 HER2+ breast cancer cells were treated with either DMSO, 300nM lapatinib, 300nM JQ1, or lapatinib and JQ1 in combination for 48h.

overall_design: 8 experimental samples

first: Gary

last: Johnson


title: FOXA1-dependent responses of the HER2+ SKBR-3 cell line to lapatinib

summary: SKBR-3 HER2+ breast cancer cells were treated with 25 nM Dharmacon siGENOME non-targeting (NT) siRNA control pool or siRNA pool targeting FOXA1 for 48h, then treated with either DMSO or 300nM lapatinib for 24h.

overall_design: 12 experimental samples


title: Identification of BBOX1 as a Therapeutic Target in Triple-Negative Breast Cancer

status: Public on Dec 02 2020

first: Jeremy

last: Simon

summary: Triple-negative breast cancer (TNBC) is an aggressive and highly lethal disease. Because of its heterogeneity and lack of hormone receptors or HER2 expression, targeted therapy is limited. Here, by performing a functional siRNA screening for 2-OG–dependent enzymes, we identified gamma-butyrobetaine hydroxylase 1 (BBOX1) as an essential gene for TNBC tumorigenesis. BBOX1 depletion inhibits TNBC cell growth while not affecting normal breast cells. Mechanistically, BBOX1 binds with the calcium channel inositol-1,4,5-trisphosphate receptor type 3 (IP3R3) in an enzymatic-dependent manner and prevents its ubiquitination and proteasomal degradation. BBOX1 depletion suppresses IP3R3-mediated endoplasmic reticulum calcium release, therefore impairing calcium-dependent energy-generating processes including mitochondrial respiration and mTORC1-mediated glycolysis, which leads to apoptosis and impaired cell-cycle progression in TNBC cells. Therapeutically, genetic depletion or pharmacologic inhibition of BBOX1 inhibits TNBC tumor growth in vitro and in vivo. Our study highlights the importance of targeting the previously uncharacterized BBOX1–IP3R3–calcium oncogenic signaling axis in TNBC.

overall_design: RNA-seq of MDA-MB-468 cells treated with shRNA to BBOX1 or scrambled control

first: Qing

last: Zhang


title: Gene expression profiling of rice mature leaves in response to elevated CO2

status: Public on Oct 10 2020

city: Sendai

first: Yonghyun

last: Kim

state: Miyagi

address: Aramaki, Aoba-ku

department: Graduate School of Agricultural Science

country: Japan

institute: Tohoku University

summary: Elevated CO2 (eCO2) condition has influence on developing leaf growth of rice (Oryza sativa cv. Nipponbare), specifically lower than P4 (plastochron number) stage, resulting in decrease in leaf size compared with that grown at ambient CO2 (aCO2). In this case, decrease in leaf size seems to be one of acclimation process at CO2 replete environment despite of the fact that number of tiller increase during CO2 replete periods; however, it is not yet elucidated which endogenous signal play a precise role in depression of developing leaf growth in those process. In this context, to elucidate precise signal interaction between mature and developing leaf of rice at eCO2 environment, we profiled gene expressions of mature rice leaf blade (P6) using oligo DNA microarray 4X44K RAP-DB (Agilent Technologies, Santa clara, CA).

overall_design: eCO2 induced gene expression in rice leaf blade at eCO2 was measured at 7 h and 13.5 h after elevated CO2 treatment on daytime. Three independent experiments were performed at each time (7 and 13.5 h) using different samples

first: Mitsue

last: Miyao


title: Keystone genes for tooth development [Rat RNA-Seq]

first: Jukka

last: Jernvall

summary:
The expression levels of developing rat molar transcriptome were measured.
5 samples each from  embryonic day 15.5, and 17.5 of rat developing molar tooth.

overall_design: Wild type tooth germs were dissected from embryonic stages corresponding to E15.5 and E17.5 molar development. We used DA/HanRj rats.

first: Outi

last: Hallikas

first: Rishi

last: Das

first: Mona

last: Christensen

first: Elodie

last: Renvoisé

first: Ana-Marija

last: Sulic


title: Keystone genes for tooth development [single-cell RNA-seq]

summary:
Single cell RNAseq of E14.5 mouse molar
Analysis of gene expression in single cell of mouse E14.5 molar

overall_design: 4 molar teeth from embryonic day 14.5 mouse were analyzed in single cell RNAseq.

last: Das Roy


title: An unorthodox flagellin paralog integrates cell cycle and flagellar assembly cues for flagellin translation (RNA-seq)

status: Public on Oct 27 2020

first: Patrick

last: Viollier

summary: How cellular checkpoints couple the orderly assembly of macromolecular machines with cell cycle progression is poorly understood. The alpha-proteobacterium Caulobacter crescentus assembles a single polar flagellum during each cell cycle. We discovered that expression of multiple flagellin transcripts is licensed by a translational checkpoint responsive to a dual input signal: a secretion-competent hook-basal-body (HBB) structure and a surge in the FlaF secretion chaperone during cytokinesis, instructed by the cell cycle circuitry. We find that the unorthodox FljJ flagellin, one of six flagellin paralogs, acts as checkpoint linchpin, binding both FlaF and the FlbT translational regulator. FljJ recruits FlbT to inhibit translation at the 5’ untranslated region in other flagellin transcripts before HBB assembly. Once FlaF is synthesized and stabilized, it directs FljJ secretion through the HBB, thereby separating FlbT from its co-activator and relieving translational inhibition. The FlbT/FlaF pair is wide-spread and functional properties are conserved in alpha-proteobacteria, including pathogens.

overall_design: Global transcriptome profiling (gene expression) by RNA-Seq in Caulobacter crescentus WT and ΔflaF backgrounds.

first: Silvia

last: Ardissone

first: Nicolas

last: Kint

first: Bianca

last: Petrignani

first: Gaël

last: Panis


title: An unorthodox flagellin paralog integrates cell cycle and flagellar assembly cues for flagellin translation (Tn-seq)

overall_design: Genome-wide transposon mutagenesis coupled with deep-sequencing  (Tn-Seq) of Caulobacter crescentus NA1000 (WT) and ΔtipF pSA607 mutant.


title: An unorthodox flagellin paralog integrates cell cycle and flagellar assembly cues for flagellin translation

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

sample_organism:
Caulobacter vibrioides
Caulobacter vibrioides NA1000

overall_design: Refer to individual Series


title: Effects of PAK4 knockdown on gene expression in glioblastoma-associated endothelial cells

status: Public on Sep 13 2020

city: Philadelphia

first: Yi

last: Fan

state: PA

address: 3400 Civic Center Blvd, SCTR 8-168

department: Radiation Oncology

institute: University of Pennsylvania

summary: PAK4 was knocked down in human glioblastoma (GBM)-associated endothelial cells (ECs) using CRISPR-Cas9/gRNA. RNA was isolated and analyzed by RNAseq. The effects of PAK4 knockout on gene expression were determined.

overall_design: ECs were isolated from GBM tumors and transduced with the lentivirus expressing PAK4 sgRNA or control sgRNA, followed by cell selection by incubation with medium containing 2 µg/ml puromycin. RNA was isolated and analyzed by RNAseq.

first: Wenjuan

last: Ma

first: Duo


title: Identification of genome-wide binding sites of Psi, Myc and Pol and gene expression following Psi or Myc knockdown in Drosophila larval wing tissue

status: Public on Jun 30 2020

city: Canberra

first: Olga

last: Zaytseva

state: ACT

address: 131 Garran Road

institute: John Curtin School of Medical Research


title: Persistent activation of mRNA translation by transient Hsp90 inhibition

status: Public on Aug 11 2020

city: Berkeley

first: Timothy

middle: J

last: Eisen

state: CALIFORNIA

address: Stanley Hall

institute: UC Berkeley

summary: The heat shock protein 90 (Hsp90) chaperone functions as a protein-folding buffer and plays a unique role promoting the evolution of new heritable traits. To better understand how Hsp90 can affect mRNA translation we screened more than 1600 factors involved in mRNA regulation for physical interactions with Hsp90 in human cells. The mRNA binding protein CPEB2 strongly binds Hsp90 via its prion domain. In a yeast model, transient inhibition of Hsp90 resulted in persistent activation of a CPEB translation reporter even in the absence of exogenous CPEB that persisted for 30 generations after the inhibitor was removed. Ribosomal profiling revealed that some endogenous yeast mRNAs, including HAC1, show a persistent change in translation efficiency following transient Hsp90 inhibition. Thus, transient loss of Hsp90 function can promote a non-genetic inheritance of a translational state affecting specific mRNAs, introducing a new mechanism by which Hsp90 can promote phenotypic variation.

overall_design: Ribosome-profiling data examining heat shock and Hsp90 inhibition in yeast.

first: Peter

last: Tsvetkov

first: Sven

last: Heinrich

first: Zarina

last: Brune

first: Erinc

last: Hallacli

first: Greg

last: Newby

first: Can

last: Kayatekin

first: David

last: Pincus

first: Susan

last: Lindquist


title: Identification of genome-wide binding sites of Psi, Myc and Pol in Drosophila imaginal wing discs using Targeted DamID

summary: Targeted DamID was performed to identify binding targets of P-element somatic inhinitor (Psi), Myc and RNA Polymerase (using the RpII18 subunit common to all 3 polymerases). Scalloped(sd)-GAL4 was used to restrict expression to the wing disc.

overall_design: Dam methylase fusion constructs under the control of UAS were expressed for 24 hours using the scalloped-GAL4 driver in the background of temperature-sensitive GAL80. 3 replicates each of Psi-Dam, Myc-Dam and Pol-Dam were normalised to the corresponding Dam-only control.

first: Owen

last: Marshall

first: Leonie

last: Quinn


title: Selective 40S footprinting reveals that scanning ribosomes remain cap-tethered in human cells

status: Public on Jun 25 2020

city: Heidelberg

first: Jonathan

last: Bohlen

address: Im Neuenheimer Feld 581

institute: DKFZ

summary: Translation regulation occurs largely during initiation. Currently, translation initiation can be studied in vitro, but these systems lack features present in vivo and on endogenous mRNAs. Here we develop selective 40S footprinting for visualizing initiating 40S ribosomes on endogenous mRNAs in vivo. It pinpoints where on an mRNA initiation factors join the ribosome to act, and where they leave. We discover that in human cells most scanning ribosomes remain attached to the 5’ cap. Consequently, only one ribosome scans a 5’UTR at a time, and 5’UTR length affects translation efficiency. We discover that eIF3B, eIF4G1 and eIF4E remain on translating 80S ribosomes with a decay half-length of ~12 codons. Hence ribosomes retain these initiation factors while translating short upstream Open Reading Frames (uORFs), providing an explanation for how ribosomes can re-initiate translation after uORFs in humans. This method will be of use for studying translation initiation mechanisms in vivo.

overall_design: Selective and total 40S and 80S footprinting was carried out on HeLa and NIH3T3 cells. Selective datasets were produced for factors eIF3B, eIF4E, eIF2S1 and eIF4G1.

first: Aurelio

last: Teleman


title: RNA-Seq of brain metastatic breast cancer cell lines after knockout of lipid metabolism genes using CRISPR/Cas9 gene editing

status: Public on Jun 26 2020

city: Cambridge

first: Xin

last: Jin

address: 415 Main Street

institute: Broad Institute of MIT and Harvard

summary: Brain metastasis is one of the lethal causes of breast cancer. Here we identified an altered lipid metabolism state to be associated with brain metastatic potential of breast cancer cell lines. To investigate the mechanism, we knocked out genes mediating this altered state and examined transcriptomic changes. The results revealed that these genes confer cells a state with increased lipid and cholesterol biosynthesis and that resembles the lipid metabolite state seen in the brain. These findings revealed an unappreciated machinery that cancer cells adopt for their increased adaptability to the brain microenvironment.

overall_design: CRISPR/Cas9-expressing versions of the cell lines were infected with guides targeting sterol regulatory element-binding protein 1 (SREBF1), SREBP cleavage-activating protein (SCAP), phosphomevalonate kinase (PMVK) or non-targeting controls. Knock-out and wild-type cells were profiled with RNA-Seq. Profiling was performed for four brain metastatic breast cell lines including MDAMB231, HCC1806, HCC1954, and JIMT1.


title: Development of gene expression signatures for glioblastoma stem-like cells infected with oncolytic virus

status: Public on Jul 29 2020

city: Warsaw

first: Klaudia

last: Kiel

address: Adolfa Pawińskiego 5

country: Poland

institute: Mossakowski Medical Research Centre Polish Academy of Sciences

summary: To further develop gene expression approach, we have employed whole genome microarray expression profiling as a discovery platform to identify genes with the potential to identify oncolytic virus (OV) infection effect in different subpopulations of glioblastoma stem-like cells (G cells). Cells were transfected with either control or OV. OV affects gene expression patterns in cell subtype specific pattern.

overall_design:
Two-conditions experiment, G cells mock vs. OV. Biological replicates: 6

The Sample data tables were updated on May 19, 2023.

first: Agnieszka

last: Bronisz

first: Jakub

last: Godlewski


title: Analysis of human stroke brain tissue resected during decompressive craniectomy or stroke-ectomy surgery

city: Albuquerque

first: Tamara

last: Roitbak

address: 1 University of New Mexico

institute: University of New Mexico

summary:
Purpose: Signaling pathways mediated by microRNAs (miRNAs) represent one of the mechanisms that regulate stroke progression and recovery. The goal of this study is to investigate miRNA expression signatures in freshly removed human stroke brain tissue.
Methods: Human brain samples (5 stroke and 3 non-stroke samples) obtained at 48-72 hours after stroke onset during craniectomy and stroke-ectomy, were subjected to histopathological and immunofluorescence microscopy analyses. NGS sequencing was performed by Qiagen company and analyses were carried out using QIAseq miRNA Quantification workflow and RNA-seq Analysis tools within CLC Genomics Workbench (version 20.0.2). Reads were normalized for expression analysis using trimmed mean of M-values method (TMM). miRNA profiling was performed using the EdgeR in Bioconductor package. Whole transcriptome RNA-sequencing Analysis: The unmapped reads from the NGS miRNA analysis were extracted, deduplicated and mapped to the genome. Gene expressions were calculated by counting number of reads mapping to the annotated gene loci. Human miR-155 Targets RT2 Profiler PCR Array (Qiagen) was performed using 3 RNA samples per stroke and control groups. The PCR Array Data analysis was performed using an automated PCR Analysis Web Portal and GeneGlobe Data Analysis (Qiagen).
Results: Human stroke brain tissue was characterized by classic ischemic changes, including significant neuronal and vascular damage, and prominent edema. The absence of monocytes and notable neutrophil infiltration indicated the early stage of leukocyte response to ischemia. miRNA NGS analysis detected 36 miRNAs with significantly aberrant expression in stroke tissue, as compared to non-stroke samples. Of these miRNAs, 19 were previously identified in stroke patient blood and CSF, while dysregulation of 16 miRNAs was newly detected in this study. Bioinformatics pathway enrichment analysis demonstrated a strong association of the identified miRNAs with stroke-related biological processes and signaling pathways
Conclusions: Dysregulated miRNAs detected in our study could be regarded as potential candidates for biomarkers and/or targets for therapeutic intervention. The obtained data will serve for better understanding of the molecular basis of stroke and provide valuable information for the future functional studies in the experimental models of stroke.

overall_design: microRNA profiles of human brain tissue samples from 5 stroke and 3 non-stroke samples

first: Andrew

last: Carlson

first: William

last: McKay

first: Jeremy

last: Edwards

first: Radha

last: Swaminathan

first: Karen

last: SantaCruz

first: Ron

last: Mims

first: Howard

last: Tonas


title: Detection of genomic G-quadruplexes in living cells using a small artificial protein

status: Public on Oct 13 2020

city: Beijing

first: Zheng

last: Tan

address: 1 Beichen West Road, Chaoyang District

institute: Institute of Zoology, Chinese Academy of Sciences

summary: G-quadruplex (G4) structures formed by guanine-rich nucleic acids are implicated in essential physiological and pathological processes and serve as important drug targets. The genome-wide detection of G4s in living cells is important for exploring the functional role of G4s but has not yet been achieved due to the lack of a suitable G4 probe. Here we report an artificial 6.7 kDa G4 probe (G4P) protein that binds G4s with high affinity and specificity. We used it to capture G4s in living human, mouse, and chicken cells with the ChIP-Seq technique, yielding genome-wide landscape as well as details on the positions, frequencies, and sequence identities of G4 formation in these cells. Our results indicate that transcription is accompanied by a robust formation of G4s in genes. In human cells, we detected up to >123,000 G4P peaks, of which >1/3 had a fold increase of ≥5 and were present in >60% promoters and ~70% genes. Being much smaller than a scFv antibody (27 kDa) or even a nanobody (12-15 kDa), we expect that the G4P may find diverse applications in biology, medicine, and molecular devices as a G4 affinity agent.

sample_organism:
Gallus gallus
Homo sapiens
Mus musculus

platform_organism:
Gallus gallus
Homo sapiens
Mus musculus

overall_design: We engineered a divalent G-quadruplex (G4) probe (G4P) protein that binds to the two terminal G-quartets of a G4 with high affinity and specificity through a synergy of two independent binding activities. G4-ChIP technique was developed by expressing the G4P to capture the formation of G4s in live animal cells to reveal the locations, magnitudes, and sequence identities of G4s genome-wide.

first: Ke-wei

last: Zheng

first: Jia-yu

last: Zhang

first: Yi-de

last: He

first: Jia-yuan

last: Gong

first: Cui-jiao

last: Wen

first: Juan-nan

last: Chen

first: Yu-hua

last: Hao

first: Yong

last: Zhao


title: Total RNA-Seq in TRAF4-overexpressing castration-resistant xenograft tumors and the control castration-responsive tumors

status: Public on Jul 15 2020

city: Houston

first: Huan

last: Meng

state: Texas

address: One Baylor Plaza BCM 130

department: Department of Molecular & Cellular Biology

institute: Baylor College of Medicine

summary: We reported the tumor total gene expression TRAF4-overexpressing castration-resistant xenograft tumors and the control castration-responsive tumors

overall_design: TRAF4 overexpressing or control LNCaP cells were injected into NOD/SCID mice subcutaneously. When tumors reach approximately 1cm in diameter, mice were were anesthetized using isoflourane and surgically castrated using standard surgical technique. For in vivo studies, 5-to 6-week-old male SCID mice (The Jackson Laboratory) were used for experimental castrate resistant prostate cancer study.


title: RNA-sequencing following Psi or Myc knockdown in Drosophila larval wing tissue

first: Olga

last: Zaytseva

summary: RNA-seq analysis of gene expression changes following the depletion of P-element somatic inhibitor (Psi) or Myc via RNAi in wing discs of mid-third instar larvae, compared with control. Differential splicing analysis was also performed on the Psi RNAi dataset.

overall_design: Expression was performed using the tubulin-GAL4 driver in the background of temperature-sensitive GAL80, restricting RNAi knockdown to 3 days prior to collection. Larval wing discs were collected in lots of 20; 60 wings were pooled for each replicate before RNA extraction and sequencing. Samples were performed in triplicate; for analysis either Psi RNAi or Myc RNAi were compared to control

first: Leonie

last: Quinn

first: Maurits

last: Evers


title: Adaptive Gene Profiling of Mycobacterium Tuberculosis during Sub-lethal Kanamycin Exposure

status: Public on Jul 06 2020

city: Wuhan

first: Habib

last: Zeshan

state: Hubei

address: shizishan street No.1

department: College of veterinary medicine

institute: Huazhong Agricultural University

summary:
Objectives: Mtb adaptation is the major threat to affective disease control.The objective of this study was to identify major contributors participating in Mtb adaptation process during sub-lethal drug exposure through next generation sequencing
Methods: The sequence reads that passed quality filters were analyzed through Tophat-2  and HT-Seq after being unified with housekeeping genes expression level.Adaptation analysis was performed through classifying genes expression in count table by K-Means clustering algorithm and find interested genes pattern
Results: Genes responsible for lipid metabolism strongly repressed while involved in virulence and information pathways up regulated under sub-lethal kanamycin stress.Moreover an adaptive network comprise of Ra1750,Ra3160,Ra3161,Ra2492 and Ra3893 identified in kanamycin treated Mtb
Conclusions: Mtb has a complex regulatory inter-connected gene network supporting its survival under diverse environmental conditions.

overall_design: H37Ra were cultured under sub-lethal kanamycin exposure along with untreated sample as control for 72 hours. Half of the bacteria were sub-cultured under same conditions and remaining were subjected for RNA Seq to compare adaptive gene profile of treated samples with control.

first: Zeshan

last: Habib

first: Weize

last: Xu


title: Whole blood transcriptional responses of very preterm infants during late-onset sepsis

status: Public on Jun 03 2020

city: Burnaby

first: Amy

last: Lee

state: BC

address: 8888 University Drive

department: Molecular Biology and Biochemistry

institute: Simon Fraser University

summary: Host immune responses during late-onset sepsis (LOS) in very preterm infants are poorly characterised due to a complex and dynamic pathophysiology and challenges in working with small available blood volumes. We present here an unbiased transcriptomic analysis of whole peripheral blood from very preterm infants at the time of LOS. RNA-Seq was performed on peripheral blood samples (6 – 29 days postnatal age) taken at the time of suspected LOS from very preterm infants <30 weeks gestational age. Infants were classified based on blood culture positivity and elevated C-reactive protein concentrations as having confirmed LOS (n=5), possible LOS (n=4) or no LOS (n=9). Bioinformatics and statistical analyses performed included pathway over-representation and protein-protein interaction network analyses. Plasma cytokine immunoassays were performed to validate differentially expressed cytokine pathways.The blood leukocyte transcriptional responses of infants with confirmed LOS differed significantly from infants without LOS (1,317 differentially expressed genes). However, infants with possible LOS could not be distinguished from infants with no LOS or confirmed LOS. Transcriptional alterations associated with LOS included genes involved in pathogen recognition (mainly TLR pathways), cytokine signalling (both pro-inflammatory and inhibitory responses), immune and haematological regulation (including cell death pathways), and metabolism (altered cholesterol biosynthesis). At the transcriptional-level cytokine responses during LOS were characterised by over-representation of IFN-α/β, IFN-γ, IL-1 and IL-6 signalling pathways and up-regulation of genes for inflammatory responses. Infants with confirmed LOS had significantly higher levels of IL-1α and IL-6 in their plasma. Blood responses in very preterm infants with LOS are characterised by altered host immune responses that appear to reflect unbalanced immuno-metabolic homeostasis.

overall_design: Examination of blood leukocyte transcriptional responses of 5 infants with confirmed LOS, 4 infants with possible LOS and 9 infants with no LOS.

first: Sherrianne

last: Ng

first: Tobias

last: Strunk

first: Erin

last: Gill

first: Reza

last: Falsafi

first: Julie

last: Hibbert

first: Robert

middle: W

last: Hancock

first: Andrew

last: Currie


title: USP37 Promotes Deubiquitination of HIF2a in Kidney Cancer

status: Public on May 27 2020

city: Boston

first: Jeremy

last: Simon

institute: Dana-Farber Cancer Institute

summary: Clear cell renal cell carcinoma (ccRCC) is characterized by a loss of tumor suppressor Von Hippel Lindau (VHL) function, which leads to accumulation of hypoxia inducible factor  (including HIF1 and HIF2). HIF2 was previously reported to be one of the major oncogenic drivers in ccRCC, however its therapeutic targeting remains challenging. Here we performed a deubiquitinase (DUB) cDNA library binding screen and discovered that USP37 is a DUB that binds HIF2 and promotes HIF2 deubiquitination. As a result, USP37 promotes HIF2 protein stability in an enzymatically dependent manner and depletion of USP37 leads to HIF2 downregulation in ccRCC. Functionally, USP37 depletion causes decreased cell proliferation measured by MTS, 2-D colony formation as well as 3-D anchorage independent growth. USP37 is also essential for maintaining kidney tumorigenesis in an orthotopic xenograft model and its depletion leads to decreased primary kidney tumorigenesis and spontaneous lung metastasis. Our results suggest that USP37 is a potential new therapeutic target in ccRCC.

overall_design: RNA-seq of 786-O cells treated with sgRNA to HIF2a or USP37, or scrambled control

first: Qing

last: Zhang


title: Nascent RNA sequencing (PRO-seq) after adipogenesis induction of 3T3-L1 cells

status: Public on May 13 2020

city: Farmington

first: Michael

middle: Joseph

last: Guertin

state: CT

address: 400 Farmington Ave

department: Center for Cell Analysis and Modeling

institute: University of Connecticut

summary: These experiments identify the early and terminal changes in nascent RNA that results from treating cells with 0.25 U/mL Insulin, 250 nM dexamethasone, and 0.5 mM 3-isobutyl-1-methylxanthine

overall_design: Cells were treated with this differentiation cocktail for 20 min, 40 min, 60 min, 2 hr, 3 hr, 4hr, and 6 days in triplicate


title: RNA-Seq of multiplexed metastasis xenogfrates of barcoded cell line pools

first: Xin

last: Jin

summary: Large-scale metastasis research has been infeasible as the use of in vivo hosts precluded the scale of such experiments. Here we introduce a barcoding strategy coupled with deep sequencing that is capable of determining the metastatic abilities of human cancer cell lines in murine xenografts at scale. We developed a RNA-Seq based readout method and an analysis framework that co-capture the cell lines that metastasize to the target organs and their averaged transcriptomes in different in vivo microenvironment. We applied the approach to a cohort of basal-like breast cell lines and revealed their diverse metastatic patterns, a heterogeneity as seen in patients. Expression analysis revealed organ-specific transcriptional states and differential pathway activities in metastases from one site to another.

overall_design:
Individual breast cancer cell lines were labeled with unique barcodes, and barcoded cell lines were pooled at equal ratio, and cell line pools were injected into the left-ventricle of NSG mice. Animals were sacrificed 5 weeks after injection, and organs including brain, lung, liver, kidney, bone were harvested. Organs were dissociated to single cell suspensions, subjected to mouse stroma depletion, and sorting for GFP+ cancer cells. Sorted metastatic cells from different organs were then used for low-input RNA-Seq.

The pilot pool contains MDAMB231_BREAST, HCC1954_BREAST, BT549_BREAST, CAL851_BREAST
The g1 pool contains BT549_BREAST, HDQP1_BREAST, JIMT1_BREAST, MDAMB157_BREAST, MDAMB436_BREAST, HCC1806_BREAST, HMC18_BREAST, MDAMB468_BREAST, DU4475_BREAST.
The g2 pool contains CAL851_BREAST, HCC1143_BREAST, HCC70_BREAST, HCC1395_BREAST, HCC1187_BREAST, HCC38_BREAST, HCC1569_BREAST, HCC1937_BREAST, BT20_BREAST, HCC1599_BREAST.

Please note that [1] average count data was generated for some replicate samples (e.g.  'pilot.S5962' data column contains averag data over pilot.59, pilot.60, pilot.61, pilot.62) and thus total 144 processed data columns are provided for total 154 samples [2] For mapping and gene counting per se, standard parameters from the software packages were used, and code will be made available upon request as stated in the manuscript.


title: 17β-estradiol regulates the release of exosomes via miR-1495p and hnRNPA2/B1 in ER+ breast cancer cells

status: Public on Mar 01 2020

first: George

last: Calin

state: TX

address: 1881 East Road

department: Experimental Therapeutics

institute: MD Anderson Cancer Center

summary:
We analyzed RNA from 2 breast cancer cell lines (MDA-MB-231 (MM231) and MCF7)  and exosomes derived from them
We used Affymetrix miRNA-3 array to determine the miRNA profile  to find out whether miRs content in exosomes and expression levels were different after 17β-estradiol .

overall_design: Here, we performed a global profiling of differentially expressed miRNAs in breast cancer cell lines

first: Barbara

last: Pardini


title: Glyceollin transcription factor GmMYB29A2 is a regulator of soybean resistance to Phytophthora sojae

status: Public on Jun 10 2020

city: Morgantown

first: Nik

last: Kovinich

state: WV

address: 1194 Evansdale Drive

department: Plant and Soil Sciences

institute: West Virginia University

summary: RNA-seq was conducted on hairy roots of Williams 82 (W82) and imbibing seeds of Harosoy 63 (H63) upon treatment with the P. sojae wall glucan elicitor (WGE) at the times of maximum glyceollin biosynthesis.

overall_design: Imbibed seeds of H63 and Hairy roots of W82 were treated with WGE or H2O (mock) and at the time of maximum glyceollin accumulation after treatment (48 h and 24 h, respectively), total RNA was extracted for RNA-seq. WGE samples were compared to the mock to identify upregulated genes, then these were searched for common genes among the two tissue types.

first: N


title: Unique and Shared Roles for Histone H3K36 Methylation States in Transcription Regulation Functions

status: Public on Apr 29 2020

address: 450 Brookline Ave

summary: Set2 co-transcriptionally methylates lysine 36 of histone H3 (H3K36), producing mono-, di-, and trimethylation (H3K36me1/2/3). These modifications recruit or repel chromatin effector proteins important for transcriptional fidelity, mRNA splicing, and DNA repair. However, it was not known whether the different methylation states of H3K36 have distinct biological functions. Here, we use engineered forms of Set2 that produce different lysine methylation states to identify unique and shared functions for H3K36 modifications. Although H3K36me1/2 and H3K36me3 are functionally redundant in many SET2 deletion phenotypes, we found that H3K36me3 has a unique function related to Bur1 kinase activity and FACT (facilitates chromatin transcription) complex function. Further, during nutrient stress, either H3K36me1/2 or H3K36me3 represses high levels of histone acetylation and cryptic transcription that arises from within genes. Our findings uncover the potential for the regulation of diverse chromatin functions by different H3K36 methylation states.

overall_design: RNA-seq of five yeast Set2 models, two timepoints following nutrient stress (0, 60min), in biological triplicate

first: Julia

middle: V

last: DiFiore

first: Brian

middle: D

last: Strahl


title: The zinc finger domains in U2AF26 and U2AF35 have diverse functionalities including a role in controlling translation

status: Public on May 01 2020

city: Berlin

first: Marco

last: Preussner

address: Takustrasse 6

institute: FU berlin

summary: Recent work has associated point mutations in both zinc fingers (ZnF) of the spliceosome component U2AF35 with malignant transformation. However, surprisingly little is known about the functionality of the U2AF35 ZnF domains in general. Here we have analyzed key functionalities of the ZnF domains of mammalian U2AF35 and its paralog U2AF26. Both ZnFs are required for splicing regulation, whereas only ZnF2 controls protein stability and contributes to the interaction with U2AF65. These features are confirmed in a naturally occurring splice variant of U2AF26 lacking ZnF2, that is strongly induced upon activation of primary mouse T cells and localized in the cytoplasm. Using Ribo-Seq in a model T cell line we provide evidence for a role of U2AF26 in activating cytoplasmic steps in gene expression, notably translation. Consistently, an MS2 tethering assay shows that cytoplasmic U2AF26/35 increase translation when localized to the 5’UTR of a model mRNA. This regulation is partially dependent on ZnF1 thus providing a connection between a core splicing factor, the ZnF domains and the regulation of translation. Altogether, our work reveals unexpected functions of U2AF26/35 and their ZnF domains, thereby contributing to a better understanding of their role and regulation in mammalian cells.

overall_design: EL4 cells, either control or stabely overexpressing a U2af26 variant localizing to the cytoplasm, were investigated via ribosome profiling. In parallel total RNA was sequenced to normalize for changes in gene expression levels.

first: Florian

last: Heyd


title: Transcriptome profiles in E. coli under a prolonged starvation environment

status: Public on Apr 24 2020

city: Tsukuba

first: Sotaro

last: Takano

state: Ibaraki

address: Central 6-10, Higashi 1-1-1

department: Bioproduction

institute: National Institute of Advanced Industrial Science and Technology

summary: How microorganisms resist nutrient-deficiency is important for understanding the pervasive prosperity of microbes in severe nutrient conditions. In laboratory culture, E. coli can survive for a long period of time under starvation, denoted as long-term stationary phase (LSP). Although physiology of those viable cells is of great interest, their genome-wide response has not yet been fully understood. In this study, we employed high-density oligonucleotide array to investigate the transcriptional profile of the cells exposed with supernatant of LSP culture. We compared the expression profiles of LSP to those of exponentially and short-term stationary phase, and revealed that the cellular physiology in the LSP environment is primarily represented by up-regulation of transporter genes and down-regulation of biosynthesis genes, which is similar to those in the short-term stationary phase. Our analysis further detected the differentially expressed functional gene categories between short- and long-term stationary phase, in terms of increasing the expressions of some stress-response genes and repressing the translational genes expressions, suggesting more survival/maintenance weighted metabolism in LSP. We also found the population-density-susceptible expression profiles in the LSP condition, which is also informative to understand the survival mechanism in long-term starvation.

overall_design: In total 23 samples; 5 different condtions (late-log in M63 glucose, short-term stationary phase in M63 glucose, glucose straved in M63, and long-term stationary phase in M63 glucose)

first: Yoshie

last: Yama

first: Hiromi

last: Takahashi

first: Saburo

last: Tsuru


title: Integrative and quantitative analysis reveals proper CtrA-dependent cell cycle regulation in the absence of the DivJ/PleC asymmetry module in the stalked budding bacterium Hyphomonas neptunium

status: Public on Mar 29 2020

city: Geneva 4

first: Patrick

last: Viollier

address: Rue Michel Servet 1

institute: University of Geneva, Faculty of Medicine / CMU

summary: Alphaproteobacteria stand out for their complex cell cycles, which are often regulated by the DivJ/PleC-DivK-DivL-CckA-ChpT-CtrA pathway. DivJ and PleC set up the polarity of the cell, thereby eventually leading to differential activation of the DNA-binding response regulator CtrA in the two nascent daughter cells. CtrA regulates replication and transcription of many genes, thereby ensuring that processes such as motility and cell division take place at the appropriate cell cycle stage. The cell cycle of the stalked budding alphaproteobacterium Hyphomonas neptunium culminates in an asymmetric cell division at the stalk-bud junction. Here, we investigate the role of the pathway from DivJ and PleC down to CtrA in this recently established model organism. Even though DivJ and PleC are localized to opposite poles, suggesting they are involved in polarity establishment inH. neptunium, DivJ, PleC and the other components of the upstream pathway (DivK and PleD) are not essential for cell cycle regulation. In contrast, the downstream part of the pathway starting from DivL is essential and involved in the regulation of important functions such as replication inhibition, cell division and motility, as shown by the identification of the (direct) regulon of CtrA. The overlap between the regulons of DivJ and PleC, DivK and CtrA is only partial, demonstrating that additional factors feeding into the pathway must be present in H. neptunium. Furthermore, unlike in other alphaproteobacteria, the regulation of CtrA throughout the cell cycle does not take place at the level of CtrA abundance in H. neptunium. All in all, the DivL-CckA-ChpT-CtrA pathway plays an essential role in the regulation of the complicated cell cycle ofH. neptunium, but several proteins feeding into CtrA remain undiscovered. The in-depth analysis of CtrA regulation in this stalked budding organism leads to hypotheses that might also hold in well-established model organisms such as Caulobacter crescentus.

overall_design: Examination of CtrA and GcrA whole genome binding/occupency (ChIP-Seq) in WT Hyphomonas neptunium LE670 (ATCC15444).

first: Oliver

last: Leicht

first: Muriel

middle: C

last: van Teeseling

first: Gaël

last: Panis

first: Céline

last: Reif

first: Heiko

last: Wendt

first: Martin

last: Thanbichler


title: Genome-wide Screening Identifies SFMBT1 as an Oncogenic Driver in Cancer with VHL Loss

status: Public on Feb 04 2020

first: Jeremy

last: Simon

summary: von Hippel-Lindau (VHL) is a critical tumor suppres- sor in clear cell renal cell carcinomas (ccRCCs). It is important to identify additional therapeutic targets in ccRCC downstream of VHL loss besides hypox- ia-inducible factor 2a (HIF2a). By performing a genome-wide screen, we identified Scm-like with four malignant brain tumor domains 1 (SFMBT1) as a candidate pVHL target. SFMBT1 was considered to be a transcriptional repressor but its role in cancer remains unclear. ccRCC patients with VHL loss-of- function mutations displayed elevated SFMBT1 pro- tein levels. SFMBT1 hydroxylation on Proline residue 651 by EglN1 mediated its ubiquitination and degra- dation governed by pVHL. Depletion of SFMBT1 abolished ccRCC cell proliferation in vitro and in- hibited orthotopic tumor growth in vivo. Integrated analyses of ChIP-seq, RNA-seq, and patient prog- nosis identified sphingosine kinase 1 (SPHK1) as a key SFMBT1 target gene contributing to its onco- genic phenotype. Therefore, the pVHL-SFMBT1- SPHK1 axis serves as a potential therapeutic avenue for ccRCC

overall_design: ChIP-seq for SFMBT1 and input control. RNA-seq for two independent siRNA against SFMBT1, as well as scrambled control, each performed in triplicate.

middle: M

first: Qing

last: Zhang


title: Integrative and quantitative view of the CtrA regulatory network in a stalked budding bacterium

city: Marburg

address: Hans-Meerwein-Strasse 4

department: Biology

institute: Philipps-Universität Marburg

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

overall_design: Refer to individual Series


title: Molecular architecture of the DNA-binding sites of the P-loop ATPases MipZ and ParA from Caulobacter crescentus

status: Public on Mar 20 2020

summary: The spatiotemporal regulation of chromosome segregation and cell division in Caulobacter crescentus is mediated by two related P-loop ATPases, ParA and MipZ. Both of these proteins share the ability to form dynamic concentration gradients that control the positioning of regulatory targets within the cell. Their proper localization relies on their nucleotide-dependent cycling between a monomeric and a dimeric state, driven by interaction with the chromosome partitioning protein ParB, and on the ability of the dimeric species to associate non-specifically with the nucleoid. In this study, we use a combination of genetic screening, biochemical analysis and hydrogen-deuterium exchange mass spectrometry to identify the residues mediating the interaction of MipZ with DNA. Our results show that the DNA-binding activity of MipZ relies on a series of positively charged and hydrophobic residues lining both sides of the dimer interface. MipZ thus appears to associate with DNA in a sequence-independent manner through electrostatic interactions with the DNA phosphate backbone. In support of this hypothesis, chromatin immuno-precipitation analyses did not reveal any specific target sites in vivo. When extending our analysis to ParA, we found that the architectures of the MipZ and ParA DNA-binding sites are markedly different, although their relative positions on the dimer surface and their mode of DNA binding are conserved. Importantly, bioinformatic analysis suggests that the same principles apply to other members of the P-loop ATPase family. ParA-like ATPases thus share common mechanistic features, although their modes of action have diverged considerably during the course of evolution.

overall_design: Examination of MipZ whole genome binding/occupancy (ChIP-Seq) in Caulobacter crescentus

first: Yacine

last: Refes

first: Binbin

last: He

first: Laura

last: Corrales-Guerrero

first: Wieland

last: Steinchen

first: Gert

last: Bange


title: Molecular Mechanisms and Targets of the Cholehepatic Drug, NorUrsodeoxycholic Acid

status: Public on Feb 11 2020

city: Atlanta

first: Paul

last: Dawson

state: GA

address: 1760 Haygood Drive

department: Division of Pediatric GI/Hepatology

institute: Emory University

summary: RNA-seq has been applied to compare the liver gene differentiation between WT mice fed with Chow and norUDCA containing diet. We aimed to determine the transporter for norUDCA absorption and circulation.

overall_design: Examine liver gene expression between WT mice fed with Chow and norUDCA containing diet.

first: Jianing

last: Li


title: The conserved transcriptional regulator CdnL is required for metabolic homeostasis and morphogenesis in Caulobacter

status: Public on Jan 11 2020

summary: Bacterial growth and division require regulated synthesis of the macromolecules used to expand and replicate components of the cell. Transcription of housekeeping genes required for metabolic homeostasis and cell proliferation is guided by the sigma factor σ70. The conserved CarD-like transcriptional regulator, CdnL, associates with promoter regions where σ70 localizes and stabilizes the open promoter complex. However, the contributions of CdnL to metabolic homeostasis and bacterial physiology are not well understood. Here, we show that Caulobacter crescentus cells lacking CdnL have severe morphological and growth defects. Specifically, ∆cdnL cells grow slowly in both rich and defined media, and are wider, more curved, and have shorter stalks than WT cells. These defects arise from transcriptional downregulation of most major classes of biosynthetic genes, leading to significant decreases in the levels of critical metabolites, including pyruvate, -ketoglutarate, ATP, NAD+, UDP-N-acetyl-glucosamine, lipid II, and purine and pyrimidine precursors. Notably, we find that ∆cdnL cells are glutamate auxotrophs, and ∆cdnL is synthetic lethal with other genetic perturbations that limit glutamate synthesis and lipid II production. Our findings implicate CdnL as a direct and indirect regulator of genes required for metabolic homeostasis that impacts morphogenesis through availability of lipid II and other metabolites.

overall_design: Examination of CdnL and RpoD whole genome binding/occupancy (ChIP-Seq) in WT Caulobacter crescentus

first: Selamawit

last: Woldemeskel

first: Allison

last: Daitch

last: Alvarez

first: Rilee

last: Zeinert

first: Diego

last: Gonzalez

first: Erika

last: Smith

first: Justine

last: Collier

first: Peter

last: Chien

first: Felipe

last: Cava

first: Erin

last: Goley


title: Endometrial cancer cell line with acquired resistance to medroxyprogesterone acetate

status: Public on Dec 31 2019

city: Jinan

first: Jie

last: Jiang

address: Department of Obstetrics and Gynecology, Qi Lu Hospital, No.107 Wenhua Road, Jinan250012, Shandong, China

department: Department of Obstetrics and Gynecology

institute: Qi Lu Hospital, Shandong University

summary: To investigate progestin resistance in endometrial cancer ,we examined the changes in gene expression before and after development of acquired MPA resistance. Results provide insight into molecular mechanisms of acquired resistance to MPA in endometrial cancer.

overall_design: Ishikawa and IshikawaPR cells were used for microarrays. IshikawaPR cell were newly established in our laboratory from Ishikawa cell as an acquired MPA resistant subline, which were established in the stimulation and selection of MPA for almost 10 months.

first: Wenzhi

first: Chunping

last: Qiu


title: ATAC-seq profiling of open chromatin in PLC-PRF cells

status: Public on Dec 13 2019

city: Tianjin

first: Heng

last: Zhang

address: 38 Rd.Tongyan

institute: Nankai University

summary: Epithelial–mesenchymal transition (EMT) is an important mechanism of metastasis and malignant progression of hepatocellular carcinoma (HCC). However, the transcriptional regulation mechanism of EMT remains poorly understood. Some transcriptional co-activators can form phase-separated condensates at super-enhancers that compartmentalize and concentrate the transcription apparatus to drive robust gene expression. Here, we demonstrate that Twist1 and YY1, interact with p300 and form phase-separated local high-concentration interaction hubs at super-enhancers of miRNA-9 and activate its expression to induce EMT and promote the malignant evolution of HCC. Phase separation disrupted by metformin perturbs Twist–YY1 condensates, thereby inhibiting EMT.   To explore how the Twist1 complex regulates miR-9 expression by binding SE region, we performed Twist1 ChIP-seq combined with H3K4me3, H3K4me1, H3K27ac, DNAse, p300, and YY1 ChIP-seq data to detect the SEs of miR-9. After metformin treatment, the peak of Twist1/YY1 on miR-9 SE decreased. Metformin specifically affects the binding of Twist1/YY1 to the miR-9 SE region.  1,6-hexanediol, as an aliphatic alcohol, can weaken hydrophobic interactions and inhibit liquid–liquid phase separation by disrupting hydrophobic interactions. In order to prove Twist1/YY1 interaction at these sites requires phase separation, we detect the accessibility of miR-9 SE regions in 1,6-hexanediol-treated cells. The result showed a general decrease in the accessibility of miR-9 super-enhancer regions in 1,6-hexanediol-treated cells and Twist1 / YY1 combines the SE region of miR-9 in the form of phase separation.

overall_design: The assay for transposase-accessible chromatin combined with high-throughput sequencing (ATAC-seq)  to  detect the accessibility of miR-9 super-enhancer regions in 1,6-hexanediol-treated cells.

first: Jing

last: Meng

first: Xiaorui

last: Wang


title: Long non-coding RNA and mRNA transcriptomic profiles after ischemia-reperfusion injury in rat spinal cord.

status: Public on Dec 08 2019

city: shanghai

first: zhibin

last: zhou

address: 415 Fengyang Road

department: orthopedics

institute: changzheng hospital

summary: With the aim of exploring expression profiles and biological functions of long non-coding RNA (lncRNA) and mRNAs after ischemia-reperfusion injury (SCII), differentially expressed lncRNAs (DElncRNAs) and mRNAs (DEmRNAs) in rat spinal cords were identified following SCII through high-throughput RNA sequencing. In total, 1455 lncRNAs and 6707 mRNAs were observed to be differentially expressed (FC ≥1.5 and P <0.05) after SCII, including 761 up-regulated and 694 down-regulated lncRNAs and, 3772 up-regulated and 2935 down-regulated mRNAs.

overall_design: LncRNA and mRNAs profiles of rat spinal cord in ischemia-reperfusion injury were generated by deep sequencing.

first: Zhibin

last: Zhou

first: Lei

last: Zhu


title: ChipSeq of Twist1 and YY1 in PLC-PRF-5 cells

overall_design: ChipSeq of Twist1 and YY1 under metformin treatment in HCC cells