title: Analytical kinetic model of native tandem promoters in E. coli

status: Public on Jan 17 2022

city: Tampere

first: Andre

middle: Sanches

last: Ribeiro

state: Pirkanmaa

address: Address:Arvo Ylpön katu 34

country: Finland

institute: Tampere University

summary: Tandem promoters are common in nature, but investigations on their dynamics have so far largely relied on synthetic constructs. Thus, their regulation and potentially unique dynamics remain unexplored. We first performed a comprehensive exploration of the conservation of genes regulated by these promoters in E. coli and the properties of their input transcription factors. We then measured protein and RNA levels expressed by 30 Escherichia coli tandem promoters, to establish an analytical model of the expression dynamics of genes controlled by such promoters. We show that start site occlusion and downstream RNAP occupancy can be realistically captured by a model with RNAP binding affinity, the time length of open complex formation, and the nucleotide distance between transcription start sites. This study contributes to a better understanding of the unique dynamics tandem promoters can bring to the dynamics of gene networks and will assist in their use in synthetic genetic circuits.

overall_design:
Examination of genome-wide responses over time
Genewiz (Germany)

first: Vatsala

last: Chauhan

first: Mohamed

last: Bahrudeen

first: Cristina

middle: D

last: Palma

first: Ines

middle: C

last: Baptista

first: Bilena

last: Almeida

first: Suchintak

last: Dash

first: Vinodh

last: Kandavalli


title: 16S rRNA gene sequence data  revealed effects of natural phenylethanoids on gut microbiota.

status: Public on Jan 24 2022

city: Tianjin

first: miaomiao

last: Jiang

address: 10 Poyanghu Road, West Area, Tuanbo New Town, Jinghai District, Tianjin

country: China

institute: Tianjin University of Traditional Chinese Medicine

summary: The aim of study is to evaluate whether salidroside (S), tyrosol (T) and hydroxytyrosol (H) which are dietary phenylethanoids of natural origins have an influence on reversing gut dysbiosis  induced by metabolic syndrome (MetS) mice. C57 BL/6J female mice induced by high fructose diet were established. All mice were adapted to the environment for 7 days with normal diet and sterile drinking water (DW), and randomly divided into 6 groups. Mice in the ND group are fed with ND and treated with normal saline. Other groups were fed with high fructose (HFru) by administration of normal saline, salidroside (S), tyrosol (T) or hydroxytyrosol (H) for 12 weeks by intragastric gavage. Fresh feces from each mouse were collected one days before the end of the experiment and temporarily placed in sterile tubules, and then snap-frozen in liquid nitrogen. Total DNA from stool bacteria was extracted using QIAamp DNA stool mini kit from Qiagen (Germantown, MD, USA) according to the manufacturer’s instructions. Illumina HiSeq sequencing analysis of the DNA samples.16S rRNA gene sequence data further revealed that S, T and H could enhance the diversity of gut microbiota. In general, the abundance of Shigella, Acinetobacter, Lactobacillus, Staphylococcus and Sporosarcina had changed significantly. These findings suggest that S, T and H probably suppress lipid accumulation and to hepatoprotective effect and improve intestinal microflora disorders to attenuate metabolic syndromes.

overall_design: The 16S rRNA gene sequences in stool bacteria of mice were detected in 5 different groups, with 6 samples in each group, namely control, model, salidroside (S), tyrosol (T) and hydroxytyrosol (H) group.

first: Miaomiao

first: Xiujun

last: Zhan

first: Mingshuai

last: He


title: Bidirectional genome-wide CRISPR screens reveal host factors regulating SARS-CoV-2, MERS-CoV and seasonal HCoVs

status: Public on Jan 20 2022

city: Cambridge

first: John

middle: G

last: Doench

state: MA

address: 75 Ames St.

department: Genetic Perturbation Platform

country: USA

institute: Broad Institute

summary: Several genome-wide CRISPR knockout screens have been conducted to identify host factors regulating SARS-CoV-2 replication, but the models used have often relied on overexpression of ACE2 receptor and didn’t express TMPRSS2 protease, known to be important for viral entry at the plasma membrane. Here, we conducted a meta-analysis of these screens and showed a high level of cell-type specificity of the identified hits, arguing for the necessity to pursue efforts to uncover the full landscape of SARS-CoV-2 regulators. We performed genome-wide, bidirectional CRISPR screens in Calu-3 lung epithelial cells, as well as knockout screens in Caco-2 intestinal cells. As well as identifying ACE2 and TMPRSS2 as top hits, our study reveals a series of so far unidentified and critical host-dependency factors, including the Adaptins AP1G1 and AP1B1 and the flippase ATP8B1. Additionally, new anti-SARS-CoV-2 proteins with potent activity, including several membrane-associated Mucins (MUC1, MUC4 and MUC21), IL6R and CD44 were identified . We further observed that these genes mostly acted at the critical step of viral entry, with the notable exception of ATP8B1, the knockout of which prevented late stages of viral replication. Exploring the pro- and anti-viral breadth of these genes using highly pathogenic MERS-CoV, seasonal HCoV-NL63 and -229E and influenza A virus, we reveal that some genes such as AP1G1 and ATP8B1 are general coronavirus cofactors. In contrast, Mucins recapitulated their known role as a general antiviral defense mechanism. These results demonstrate the value of considering multiple cell models and perturbational modalities for understanding SARS-CoV-2 replication and provide a list of potential new targets for therapeutic interventions.

overall_design: 37 samples analyzed, Control named:initial population, Selected population named: resistant population, replicates are included and mentioned below

first: Antoine

last: Rebendenne

first: Priyanka

last: Roy

first: Ana-Luiza

last: Valadao

first: Yenarae

last: Lee

first: Peter

last: DeWeirdt

first: Mudra

last: Hegde

first: Caroline

last: Goujon


title: Cap-independent translation and a precisely localized RNA sequence enable SARS-CoV-2 to control host translation and escape anti-viral response

city: Rehovot

first: Igor

last: Ulitsky

address: Hertzl St.

country: Israel

institute: Weizmann Institute of Science

type: Expression profiling by high throughput sequencing

summary: Translation of SARS-CoV-2-encoded mRNAs by the host ribosomes is essential for its  propagation. Following infection, the early expressed viral protein NSP1 binds the  ribosome, represseses translation and induces mRNA degradation, while the host elicits  anti-viral response. The mechanisms enabling viral mRNAs to escape this multifaceted  repression remain obscure. Here we show that expression of NSP1 leads to  destabilization of multi-exon cellular mRNAs, while intron-less transcripts, such as viral  mRNAs and anti-viral interferon genes, remain relatively stable. We identified a  conserved and precisely located cap-proximal RNA element devoid of guanosines that  confers resistance to NSP1-meidated translation inhibition. Importantly, the primary  sequence rather than the secondary structure is critical for protection. We further show  that the genomic 5’UTR of SARS-CoV-2 exhibits an IRES-like activity and promotes  expression of NSP1 in an eIF4E-independent and Torin-1 resistant manner. Upon  expression, NSP1 enhances cap-independent translation. However, the sub-genomic  5’UTRs are highly sensitive to eIF4E availability, rendering viral propagation partially  sensitive to Torin-1. The combined NSP1-mediated degradation of spliced mRNAs and  translation inhibition of single-exon genes, along with the unique features present in the  viral 5’UTRs, ensure robust expression of viral mRNAs. These features can be exploited  as potential therapeutic targets

overall_design: RNA-seq of a time course of ActD-treated HEK293 cells over-expressing GFP or SARS-CoV-2 NSP1 , in order to calculate transcript half-lives

first: Boris

last: Slobodin

first: Urmila

last: Sehrawat

first: Binyamin

last: Zuckerman

first: Rivka

last: Dikstein


title: Rapid redistribution and extensive cobinding of NANOG and GATA6 at shared regulatory elements underlie specification of divergent cell fates [reChIP]

status: Public on Jan 16 2022

city: Bethesda

first: Pedro

middle: P

last: Rocha

state: Maryland

address: 6 Center Drive Building 6B 2B220

department: NICHD

institute: National Institutes of Health

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Establishment of divergent cell types from a common progenitor requires transcription factors (TFs) to promote lineage-restricted transcriptional programs while suppressing alternative fates. In the mouse blastocyst, cells of the inner cell mass (ICM) coexpress NANOG and GATA6, two TFs that drive the bifurcation of these progenitors into either the epiblast (Epi) or the primitive endoderm (PrE), respectively. Here, using in vitro differentiation, we describe the molecular mechanisms of how GATA6 quickly induces the PrE fate while repressing the Epi lineage. GATA6 functions as a pioneer TF by inducing nucleosome repositioning at regulatory elements controlling PrE genes, making them accessible for deposition of active histone marks and leading to rewiring of chromatin interactions and ultimately transcriptional activation. GATA6 also binds most regulatory elements of Epi genes followed by eviction of the Epi-specific TFs NANOG and SOX2, loss of active histone marks, and reduction in chromatin accessibility that culminates in transcriptional repression. Unexpectedly, evicted NANOG and SOX2 transiently bind PrE regulatory elements occupied by GATA6. Our study shows that GATA6 binds and modulate the same regulatory elements as Epi TFs, a phenomenon we also validated in blastocysts. We propose that the ability of PrE and Epi-specific TFs to extensively bind and regulate the same gene networks contributes to ICM plasticity and allows rapid cell lineage specification by coordinating both activation and repression of divergent transcriptional programs.

overall_design: Mapping changes in Nanog binding during in vitro differentiation of mouse embryonic stem cells into primitive endoderm

first: Joyce

middle: J

last: Thompson


title: Expression analysis in Carm1 and Pax3 mutant embryos

city: Seattle

first: David

last: Beier

state: WA

address: 1900 9th Avenue

department: CDBRM

institute: Seattle Children's Research Institute

summary: We have found that Coactivator-associated Arginine Methyltransferase 1 (Carm1) mutant mice have highly penetrant heart defects. These are similar to those found in Pax3 mutant mice and PAX3 is a target of CARM1-mediated methylation. We analyzed gene expression at mid-gestation in both mutant lines.

overall_design: RNA was obtained from E12.5 Carm1 and Pax3 mutant embryos and sequenced by a commercial provider (Novogene).

middle: R

first: Andrew

last: Timms


title: Glioblastoma stem cells after treatment with HLM006474, S3I-201 or their combination.

status: Public on Jan 15 2022

city: Singapore

first: Roberto

last: Tirado-Magallanes

email: e0056363@nus.edu.sg, rtmag4@gmail.com

state: Singapore

address: 14 Medical Dr

country: Singapore

institute: Cancer Science Institute of Singapore

summary: Malignant gliomas, including glioblastoma (GBM), are uniformly lethal with inferior prognosis and lack of effective treatment. Although the H2AZ2 variant histone is overexpressed in diverse cancer types where it promotes cancer cell proliferation, there are no H2AZ2 inhibitors to-date for clinical intervention. Here, we explored approaches to pharmacologically target the H2AZ2-dependent pathways in GBM.

overall_design: RNA-seq from glioblastoma stem cell specimens (TS-543) following treatment with  DMSO, HLM006474, S3I-201 or combination of HLM006474 and  S3I-201.

first: Yoon

last: Jeehyun

first: Oleg

last: Grinchuk

first: Derrick

middle: S

last: Tong Ong


title: Histone variant H2AFV equips glioblastoma stem cells with transcriptional potency and efficient DNA damage response [ATAC-seq]

summary: Tumors are composed of cellular subpopulations with varying degree of proliferative and tumorigenic potential. Here, we identify inter- and intra-tumor heterogeneous expression of histone variant H2AFV in numerous cancer types, with high H2AFV expression correlating with cancer stem cells, poorly differentiated tumors and inferior patient survival. Depletion of H2AFV impairs proliferation, invasiveness, tumorigenicity and tumor initiating cell frequency of glioblastoma. Mechanistically, H2AFV regulates chromatin accessibility of both active and repressive complexes at the promoters and enhancers of genes: the former activates genes involved in cell proliferation/self-renewal and invasiveness while the latter suppresses cellular differentiation in cancer stem cells. Our studies uncover H2AFV as an important epigenetic determinant in cancer stem cell fate and a significant contributor of intratumor heterogeneity.

overall_design: ATAC-seq from glioblastoma stem cell specimens (TS-543) following treatment either with non-targeting or targeting shRNA.

last: Ong

middle: T

last: Magallanes


title: Histone variant H2AFV expression defines functionally distinct cancer subpopulations [RNA-seq]

overall_design: RNA-seq from glioblastoma stem cell specimens (TS-543) following treatment either with non-targeting or targeting shRNA.


title: lncRNA CYTOR promotes aberrant glycolysis and mitochondrial respiration via HNRNPC-mediated ZEB1 stabilization in oral squamous cell carcinoma

status: Public on Jan 09 2022

city: Nanjing

first: Weiwen

last: Zhu

state: Jiangsu

address: Hanzhong Road 140#

department: Stomatology

institute: Nanjing Medical University

summary: Oral squamous cell carcinoma (OSCC), the most common malignancy of the oral and maxillofacial region, severely affects human health. However, current treatments for OSCC commonly show only a ~60% five-year survival rate of patients with distant metastases, indicating an urgent need for targeted treatments for patients with advanced metastases. Here, we report a survival-related long non-coding RNA, CYTOR, which is highly expressed in the lesions of oral cancer patients. We found that CYTOR can promote both migration and invasion in oral cancer cells as well as the epithelial-mesenchymal transition (EMT). RNA-sequencing of CYTOR-knockdown oral cancer cells revealed that CYTOR can regulate mitochondrial respiration and RNA splicing. Mechanistically, we found that nuclear-localized CYTOR interacts with HNRNPC, resulting in stabilization of ZEB1 mRNAs by inhibiting the nondegradative ubiquitination of HNRNPC. By synthesizing CYTOR-targeting small interfering RNAs (siRNAs) encapsulated in Nanoscale Metal Organic Frameworks (NMOFs), we demonstrate the targeted suppression of CYTOR to inhibit invasion and metastasis of oral cancer cells in a nude mouse model. Cumulatively, this study reveals the potential role of the CYTOR-HNRNPC-ZEB1 axis in regulating mitochondrial metabolism and glycolysis of oral cancer cells, and illustrates the effective use of lncRNA targeting in anti-metastatic cancer therapies.

overall_design:
For RNA-seq assays:
(1) Cal27 cells were transfected by CYTOR-sh and negative control (NC) sequence to knockdown (KD) CYTOR expression level, three NC transfected samples and three CYTOR-KD transfected samples were analyszed.
(2) Cal27 cells were transfected by HNRNPC-sh and negative control (NC) sequence to knockdown (KD) HNRNPC expression level, three NC transfected samples and three HNRNPC-KD transfected samples were analyszed.

For RIP-seq assay:
Cal27 cells were harvested by RIP lysis buffer, then the lysates were immunoprecipitated by 5μg anti-HNRNPC antibody. The purified input and HNRNPC-IP RNA samples were then subjected to RNA-seq analysis.


title: Single nucleus pituitary transcriptomic and epigenetic landscape reveals human stem cell heterogeneity with diverse regulatory mechanisms (snATAC-seq)

status: Public on Jan 10 2022

city: Los Angeles

first: Michel

middle: A

last: Zamojski

state: California

address: 8700 Beverly Boulevard

department: Regenerative Medicine Institute

institute: Cedars-Sinai Medical Center

overall_design: Single nucleus chromatin accessibility profiling of post-mortem human pituitaries by single nuclei ATAC-seq, using Illumina

first: Zidong

last: Zhang

first: Gregory

last: Smith

first: Thea

middle: L

last: Willis

first: Val

last: Yianni

first: Natalia

last: Mendelev

first: Hanna

last: Pincas

first: Nitish

last: Seenarine

first: Mary-Anne

last: Amper

first: Mital

last: Vasoya

first: Venugopalan

last: Nair

first: Judith

last: Turgeon

first: Daniel

last: Bernard

first: Olga

last: Troyanskaya

first: Cynthia

last: Andoniadou

first: Stuart

last: Sealfon

first: Frederique

last: Ruf-Zamojski


title: Single nucleus pituitary transcriptomic and epigenetic landscape reveals human stem cell heterogeneity with diverse regulatory mechanisms (snMultiome)

first: Michel

last: Zamojski

overall_design: Same-cell single nucleus transcriptome and chromatin accessibility profiling of post-mortem human pituitaries by single nuclei multiome, using Illumina


title: Single nucleus pituitary transcriptomic and epigenetic landscape reveals human stem cell heterogeneity with diverse regulatory mechanisms (snRNA-seq)

overall_design: Single nucleus transcriptome profiling of post-mortem human pituitaries by single nuclei GEM RNA-seq, using Illumina

first: Zidong

last: Zhang


title: Bioinformatic analysis of PD-1 checkpoint blockade response in severe influenza infection [RNA-Seq]

status: Public on Jan 06 2022

city: ningbo

first: huilin

last: Ou

address: xinning road

institute: lihuili hospital

summary: A BALB/c mouse model of severe influenza A/H1N1 infection was constructed, and whole-transcriptome sequencing of mice treated with PD-1 checkpoint blockade before severe A/PR8(H1N1) influenza infection and IgG2a isotype control before infection were performed.

first: Huilin


title: A mannose-sensing AraC-type transcriptional activator regulates intestinal colonization of Vibrio cholerae

status: Public on Jan 05 2022

city: Seoul

first: Yong-Joon

last: Cho

address: 1 Gwanak-ro, Gwanak-gu

country: South Korea

institute: Seoul National University

summary: In this study, we show that ManR (VC1825) activates the transcription of the mannose operon in M9 medium supplemented with fructose or mannose, and  when manR is impaired Vibrio cholerae cells fail to colonize the intestine and host survival is significantly prolonged in a fruit fly Drosophila melanogaster infection model. To identify other target genes of ManR, transcriptome analysis was performed in wild-type V. cholerae and manR mutant strains, , grown on M9 medium supplemented with glucose, fructose, or mannose.

sample_organism: Vibrio cholerae O1 biovar El Tor str. N16961

overall_design: Transcriptome profiles of WT V. cholerae and manR mutant cells grown on a single carbohydrate as a sole carbon source (glucose, fructose, mannose)

first: Hye-Young

last: Lee

first: Yeong-Jae

last: Seok


title: Enhanced CLIP-seq analysis of PTBP1 and IGF2BP2 binding targets

status: Public on Jan 02 2022

city: Beijing

first: Wei

last: Han

address: Dongdansantiao 5

institute: CAMS&PUMC

summary: To investigate the binding targets of PTBP1 (PTB) and IGF2BP2 (IMP2) in glioma cells, we carried out an unbiased analysis of transcripts bound by PTBP1 and IGF2BP2 using enhanced crosslinking immunoprecipitation followed by high-throughput sequencing (eCLIP) in A172 glioma cells. We repeated the eCLIP method twice in each experiment, and found that the ratio of PTBP1 and IGF2BP2 binding mRNAs overlap was very high.

overall_design: eCLIP studies were performed according to the published protocol (Eric L Van Nostrand et al., 2016). 2 × 107 A172 cells incubated for 3 hours with 500 μM 4-thiouridine (4SU, T4509, Sigma) were crosslinked with 2× 400 mJ/cm2 365 nm UV light, and snap frozen. Cells were then lysed by 1ml CLIP lysis buffer (50 mM Tris-HCl pH7.4, 100 mM Nacl, 1% NP-40, 0.1% SDS, 0.5% sodium deoxycholate) with temporary addition of 1 mM DTT (P2325, Gibco), 5.5 μl 200 × protease inhibitor cocktail Ⅲ (539134-1SET, Calbiochem/MercK) and 11 μl RNase inhibitor (N2515, Promega)  and treated with RNase I (AM2295, Invitrogen by Thermo Fisher Scientific) to fragment RNA. PTBP1 or IGF2BP2 antibody (RN011P/RN008P, MBL Beijing Biotech co., LTD) was then pre-coupled to Protein A Dynabeads(10002D, Invitrogen by Thermo Fisher Scientific), added to lysate, and incubated overnight at 4℃. Prior to immunoprecipitation, 2% of the sample was taken as the paired input sample. The remaining samples were ligated to the RNA adapter, washed and separated magnetically.


title: Itaconate is an inhibitor of TET DNA dioxygenases

city: Hangzhou

first: Li

last: Shen

state: Zhejiang Province

address: 866 Yuhangtang Road

institute: Life Sciences Institute, Zhejiang University

type: Methylation profiling by high throughput sequencing

summary: Immune-response gene 1 (IRG1) transcription is rapidly induced by pathogen infections and inflammatory conditions primarily in cells of myeloid lineage. Deletion of Irg1 in mice causes severe defects in response to bacterial and viral infection and rapid death. IRG1 encodes a mitochondrial metabolic enzyme, aconitate decarboxylase 1 (ACOD1), that catalyzes the decarboxylation of cis-aconitate, a tricarboxylic acid cycle intermediate, to produce the anti-inflammatory metabolite itaconic acid (ITA). ITA can inhibit SDH5, resulting in elevated levels of succinate and metabolic reprogramming, or alkylate protein cysteine residues to induce electrophilic stress response mediated by NRF2 and IκBζ. Here we show that ITA is an antagonist of α-ketoglutarate (α-KG) and a potent inhibitor of α-KG/Fe2+-dependent TET family of DNA dioxygenases. In vitro, ITA binds to TET2 and inhibits the catalytic activity of TET2 and, reciprocally, α-KG blocks ITA binding to and inhibition of TET2. In vivo, lipopolysaccharides (LPS) treatment, which induces IRG1 expression and causes the intracellular accumulation of ITA, inhibits TET activity in Irg1-WT, but not Irg1-KO macrophages. Moreover, TET2 is a major target of ITA function in suppressing LPS-induced genes. LPS stimulates p65 NF-κB/RelA to bind with and recruit TET2 to hydroxymethylate and activate the Nfkbiz gene, which encodes IκBζ. Our results thus identify a physiological metabolite inhibitor of TET enzymes and reveal a novel mechanism for the anti-inflammatory function of ITA through dampening TET2-mediated NF-κB signaling.

overall_design: 5hmC profiling of mouse BMDMs treated with or without octyl-ITA or with octyl-ITA pre-treatment of wildtype or IRG1_KO BMDMs also treated with LPS for 0, 4 or 12 hours.

first: Miao

last: Shi

first: Yezhang

last: Zhu


title: Dysfunctional ERG signaling drives pulmonary vascular aging and persistent fibrosis

status: Public on Dec 31 2021

city: Rochester

first: Aditya

last: Bhagwate

state: MN

address: 200 1st Street SW

institute: Mayo Clinic

summary: We identified the transcription factor ETS-related gene (ERG) as a putative orchestrator of lung capillary homeostasis and repair following injury, and whose function was dysregulated in aging. Single-cell RNA-seq of ERG deficient mouse lungs revealed transcriptional abnormalities and fibrogenic features, resembling those associated with aging and IPF, including reduced number of lung progenitor ECs, known as general capillary (gCap) ECs.

overall_design: ERG fl/fl and CDH5-CreER(T): ERG fl/fl mice were injected with 5 injections of 0.5 mg tamoxifen daily. Ninty days after tamoxifen injections, whole lungs were isolated and digested using the Miltenyi Biotec Lung Dissociation Kit to create a single cell suspsensions used  for single cell sequencing

first: Giovanni

last: Ligresti

first: Tho

middle: X

last: Pham


title: Bioinformatic analysis of PD-1 checkpoint blockade response in severe influenza infection [miRNA-Seq]

type: Non-coding RNA profiling by high throughput sequencing

overall_design: whole-transcriptome sequencing of mice treated with PD-1 checkpoint blockade before severe A/PR8(H1N1) influenza infection and IgG2a isotype control before infection were performed.


title: ChIP-Seq of RNAP in E. coli DY330

status: Public on Jan 01 2022

first: Dmitry

last: Sutormin

address: 401 Terry Ave N

institute: Institute for Systems Biology

summary: Distribution of RNAP beta' subunit (RpoC) on genomic sites was studied for exponentially growing Escherichia coli using ChIP-Seq.

overall_design: DNA crosslinked with TAP-tagged RpoC was purified and sequenced from E. coli DY330 culture growing in LB medium (exponenrial phase, OD600=0.6). Cultures were crosslinked with 1% formaldehyde. Total DNA purified from a de-crosslinked cells lysate served as a Mock control.

first: Sergei

last: Borukhov


title: Bioinformatic analysis of PD-1 checkpoint blockade response in severe influenza infection

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

overall_design: Refer to individual Series


title: RNA-seq analysis of conventionally raised zebrafish larvae compared to germ-free zebrafish larvae and germ-free larvae treated with zebrafish metabolites.

city: Guelph

first: Terry

last: Van Raay

state: ON

address: 474-570 Gordon St

department: Molecular and Cellular Biology

country: Canada

institute: University of Guelph

summary: Here, we explore the impact of rearing zebrafish embryos in the absence of microbes on early neural development as well as investigate whether any potential changes can be rescued with treatment of metabolites derived from the zebrafish gut microbiota. RNA was extracted from a pool of five heads for each treatment at long-pec stage (2 days post fertilization) and sequenced at a depth of 80-100 million reads per sample. We identified 361 genes significantly down regulated in GF embryos compared to conventionally raised embryos via RNA-Seq analysis. Of these, 42 were rescued with the treatment of zebrafish gut-derived metabolites to GF embryos. Gene ontology analysis revealed that these genes are involved in prominent neurodevelopmental pathways including transcriptional regulation and Wnt signalling.

first: Victoria

last: Rea

first: Terence


title: Genome-wide strand-specific mapping of cleavage sites induced by topoisomerase I in E. coli

summary: Cleavage sites induced by the EcTopoI G116S M320V topoisomerase mutant were identified in E. coli genome with a single-nucleotide resolution using Topo-Seq.

overall_design: Expression of EcTopoI G116S M320V strepII-tagged mutant (“intrinsically-poisoned” mutant known to form stable covalent complexes with DNA) was transiently (30 min) induced from a plasmid. Covalent complexes with DNA were enriched by immunoprecipitation and obtained DNA fragments were sequenced. Non-induced samples and samples without immunoprecipitation step served as controls. 3 biological replicates were processed and sequenced.


title: Genome-wide strand-specific R-loops mapping in E. coli DY330 using DRIP-Seq

summary: Distribution of R-loops on genomic sites was studied for exponentially growing Escherichia coli in different conditions using strand-specific DRIP-Seq with S9.6 antibodies.

overall_design: Total nucleic acids were extracted from E. coli DY330 culture growing in LB medium (exponenrial phase, OD600=0.6). Cultures were either untreated (i), or treated with 100 mkg/ml rifampicin for 20 min (ii, Rif), or EcTopoI 14-kDa CTD was overexpressed from pCA25 plasmid for 60 min (iii, CTD), or EcTopoI 14-kDa CTD was overexpressed from pCA25 plasmid for 60 min and then 100 mkg/ml rifampicin was added for 20 min (iv, CTD/Rif). R-loops were enriched with S9.6 antibodies and prepared for sequencing using Accel-NGS 1S kit. Sample treated with RNAse HI before enrichment with the antibodies served as a control. For each condition 3 biological replicates were processed and sequenced.

first: Alina

last: Galivondzhyan


title: Single nucleus pituitary transcriptomic and epigenetic landscape reveals human stem cell heterogeneity with diverse regulatory mechanisms

first: Michel

last: Zamojski


title: Modeling Focal Cortical Dysplasia (FCD) using cortical organoids

city: Campinas

first: Simoni

last: Avansini

state: Sao Paulo

address: Tessalia Vieira Camargo Street,126

department: Translacional Medicine

country: Brazil

institute: University of Campinas

summary:
We generated cortical organoids from four FCD patients. To generate cortical organoids, we used induced pluriplotent stem cells (iPSCs) obtained from skin biopsy from these FCD selected patients and healthy controls. We extrated RNA samples from the cortical organoids to do customized panel of gene expression.
Gene expression using NanoString Human Neuropathology Panel from four FCD patients and four controls

overall_design: We studied four FCD patients and four controls.

middle: H


title: Hematopoietic-mesenchymal signal regulates properties of mesenchymal stem cells

city: Tokyo

first: Sanshiro

last: Kanazawa

address: 7-3-1, Hongo, Bunkyo-ku

department: Oral and Maxillofacial Surgery

country: Japan

institute: The University of Tokyo Hospital

summary:
It is well known that the properties of hematopoietic stem cells (HSCs) such as their ability to self-renew, and multipotency are maintained through interactions with mesenchymal cells. Meanwhile, the identification of cells that are the key component of niche remains a subject of dispute. Mesenchymal stem cells (MSCs) are one of the niche component cells, MSCs are one of the niche component cells which provide stemness signal to HSCs, while it is also hypothesized that there is also a counterpart signal from hematopoiesistic cells to mesenchymeal cells, as HSCs also constitute core stem cells niche for MSCs. Although mesenchymal stem cells (MSCs) have also been studied intensively, the signals involved in the maintenance of their properties have not attracted much attentions.
We used microarrays to detail the global programme of gene expression underlying HSC-MSC interaction and identified distinct classes of regulated genes during this process.

overall_design: MSCs were selected at cocultured with HSC for RNA extraction and hybridization on Affymetrix microarrays. We sought to obtain homogeneous populations of MSCs in order to increase the temporal resolution of expression profiles. To that end, we FACS-sorted MSCs according to transduce sufficient signals at day 6 in cocultured.

first: Atsuhiko

last: Hikita


title: A single-cell map of dynamic chromatin landscapes of immune cells in renal cell carcinoma

city: Tarrytown

first: Qingqing

last: Wang

state: NY

address: 777 Old Saw Mill River Road

institute: Regeneron Pharmaceuticals


title: A single-cell map of dynamic chromatin landscapes of immune cells in renal cell carcinoma (scATAC-Seq)

summary: A complete chart of the chromatin regulatory elements of immune cells in patients with cancer and their dynamic behavior is necessary to understand the developmental fates and to guide therapeutic strategies. Here, we map, at the single-cell level, the chromatin landscape of immune cells from blood, normal adjacent kidney, and malignant tissue from patients with early-stage clear cell renal cell carcinoma (ccRCC). Specifically in T cells, we catalogue the various cell states dictated by tissue- and developmental stage-specific chromatin accessibility patterns and we infer key chromatin regulators of these states. In the CD8+ T cells progression to dysfunction, we observe an extensive rewiring of the regulatory networks. Unexpectedly, we find that among the transcription factors that orchestrate the path to dysfunction, NFkB, a transcription factor with an established prosurvival role during TCR-mediated activation, is associated with a proapoptotic program in late stages of dysfunction in ccRCC infiltrating CD8+ T cells. Importantly, the epigenomic profiling can stratify RCC patients based on a NFkB-driven proapoptotic signature which was also validated at the gene expression and protein level. Our study provides a rich resource for understanding the functional states and regulatory dynamics of immune cells in RCC.

overall_design: We used scATAC-seq to profile the epigenetic landscape of human immune cells from blood, normal adjacent kidney, and malignant tissues from early stage clear cell renal cell carcinoma patients at baseline. We also performed scRNA-seq for transcriptomic profiling of these sample cells.

first: Nikos

last: Kourtis

first: Bei


title: Single nuclei ATAC-seq (10X Genomics Chromium) of MGE, CGE, LGE and cortical regions from mouse embryonic forebrain

first: Timothy

last: Petros

state: MD

address: 35 Convent Drive Building 35A, Room 3B-1002

institute: NIH

summary: While comparative genetic analysis has been performed between distinct regions of the embryonic forebrain, a comprehensive characterization of differential epigenomic organization has not been performed. We collected single-cell chromatin accessibility profiles from four distinct neurogenic regions of the embryonic mouse forebrain using single nuclei ATAC-Seq (snATAC-Seq). We identified thousands of differentially accessible peaks, many restricted to distinct progenitor cell types or brain regions. We integrated snATAC-Seq and single cell transcriptome data to characterize changes of chromatin accessibility at enhancers and promoters that were tightly coupled to transcript abundance. Multi-modal integration of histone modifications (CUT&Tag and CUT&RUN), promoter-enhancer interactions (Capture-C) and high-order chromatin structure (Hi-C) extended these initial observations. This dataset reveals a diverse chromatin landscape with region-specific regulatory mechanisms and genomic interactions in distinct neurogenic regions of the embryonic mouse brain and represents an extensive public resource of a ‘ground truth’ epigenomic landscape at this critical stage of neurogenesis.

overall_design: MGE, CGE, LGE and cortical regions from E12.5 or E14.5 mouse embryos. 2 replicates per region.

first: C

last: Rhodes

first: A

last: Mitra


title: Mouse neurogenesis


title: Distinct functions of three chromatin remodelers in activator binding and preinitiation complex assembly

status: Public on Dec 29 2021

first: Alan

last: Hinnebusch

address: 6 Center Drive, 6/230

institute: NIH, NICHD

summary: ATP-dependent chromatin remodelers (CRs), including SWI/SNF, RSC and Ino80C in budding yeast, are thought to stimulate transcription by repositioning or evicting promoter nucleosomes. The relative importance of these CRs in stimulating activator binding and recruitment of TATA-binding protein (TBP) to promoters is incompletely understood. Examining mutants depleted of the catalytic subunits of these CRs, we determined that RSC and Ino80C stimulate binding of transcription factor Gcn4 to nucleosome-depleted regions, or linkers between genic nucleosomes, at multiple target genes activated by Gcn4 in amino acid-starved cells, frequently by evicting nucleosomes from the Gcn4 binding motifs.  At some genes, SWI/SNF functionally complements RSC, while opposing RSC at others to limit Gcn4 binding. The CRs in turn are recruited by Gcn4 to establish positive or negative feedback loops that control Gcn4 binding.  The three CRs also cooperate to enhance TBP recruitment, again involving nucleosome depletion, at both Gcn4 target genes and highly expressed ribosomal protein genes, whereas only RSC and Ino80C act broadly throughout the genome to enhance this key step in preinitiation complex assembly. Our findings illuminate functional cooperation among multiple CRs in regulating activator binding and promoter activation.

overall_design: Formaldehyde-fixed and sonicated DNA fragments were immunopurified and subjected to paired-end sequencing.

first: Yashpal

last: Rawal

first: Hongfang

last: Qiu


title: ChIP-Seq of topoisomerase I in E. coli DY330

first: Dmitry

last: Sutormin

summary: Distribution of topoisomerase I (EcTopoI) on genomic sites was studied for exponentially growing Escherichia coli in different conditions using ChIP-Seq.

overall_design: DNA crosslinked with SPA-tagged EcTopoI was purified and sequenced from E. coli DY330 culture growing in LB medium (exponential phase, OD600=0.6). Cultures were either crosslinked with 1% formaldehyde untreated (i), or treated with 100 mkg/ml rifampicin for 20 min before crosslinking (ii, Rif), or EcTopoI 14-kDa CTD was overexpressed from pCA25 plasmid for 60 min before crosslinking (iii, CTD), or EcTopoI 14-kDa CTD was overexpressed from pCA25 plasmid for 60 min and then 100 mkg/ml rifampicin was added for 20 min before crosslinking (iv, CTD/Rif).  Total DNA purified from a de-crosslinked cells lysate served as a Mock control. For each condition 3 biological replicates were processed and sequenced.


title: HOTAIRM1 knockdown microarray

status: Public on Dec 26 2021

first: Wei

last: Han

type:
Expression profiling by array
Non-coding RNA profiling by array

summary: To investigate the target genes of HOTAIRM1 in glioma cells, we conducted a lncRNA + mRNA expression microarray analysis to identify novel HOTAIRM1 regulating genes. Three glioma cell lines U87MG, T98G and A172 stably knockdown HOTAIRM1 were used as the experiments models. We conservatively established a minimum of 2-fold difference between shHOTAIRM1 (knockdown HOTAIRM1) and shNT (control group), and identified 10 up-regulated and 22 down-regulated genes that met the threshold in all cell lines.

overall_design: Total RNAs from ～106 shNT-U87MG, shHOTAIRM1-U87MG, shNT-T98G, shHOTAIRM1-T98G, shNT-A172 and shHOTAIRM1-A172 cells were extracted using TRIzol reagent (Invitrogen, USA). The RNA integrity was measured at an Agilent Bioanalyzer 2100 instrument (Agilent Technologies, Santa Clara, CA, USA). The qualified total RNA was further purified by using a NucleoSpin RNA clean-up kit (740.948.250, Macherey-Nagel). cRNA was synthesized and then cDNA was reverse transcribed and purified with Nucleospin Extract Ⅱ (740.609.250, Macherey-Nagel). The labelled cDNA was used for hybridization on the Genechip Agilent Human lncRNA 4 × 180 K array (Agilent Technologies). The slides were scanned in an Agilent Microarray Scanner (Agilent Technologies) under the default settings in CapitalBio Corporation. Quantile algorithm (Gene Spring Software 11.0, Agilent Technologies) was used for the raw data normalization.


title: Prognostic classifier to identify intermediate and high-risk clear-cell renal cell carcinoma patients at higher risk for tumor progression

city: Barcelona

first: Juanjo

last: Lozano

address: C/ Rosselló 153

department: Plataforma de Bioinformatica

country: Spain

institute: CIBEREHD

summary:
Background. Current clinicopathological factors are not accurate enough to predict tumor progression in intermediate/high-risk clear cell renal cell carcinoma (ccRCC).
Objective: To develop a prognostic classifier for intermediate/high-risk ccRCC based on gene expression and histopathological prognostic factors.
Design, setting and participants: Retrospective, multicenter study including 84 intermediate/high-risk ccRCC patients who underwent surgery. Global gene expression patterns were analyzed in 13 tissue samples from progressive and non-progressive ccRCC using Illumina Hi-seq 2000 kit. Expression levels of 22 selected genes were assessed by nCounter Analysis in an independent series of 71 ccRCC. A combined genetic-clinicopathological classifier for predicting tumor progression was developed.
Outcomes measurements and statistical analysis: Logistic regression analysis was used to identify independent prognostic factors.
Results and Limitations: A total of 1202 genes were found differentially expressed between progressive and non-progressive intermediate/high-risk ccRCC. In the independent cohort, 7 genes remained significant differentially expressed between the groups. Expression of HS6ST2, pT stage, tumor size and ISUP grade were found independent prognostic factors for tumor progression (p<0.05). A risk score generated using these variables was able to distinguish a subset of patients at higher-risk of progression (HR 7,27; p<0,001), improving the individual discriminative performance of each of these variables on their own.
Conclusions: A novel prognostic algorithm based on genetic and clinicopathological factors was successfully developed. This model may aid physicians to select high-risk patients for further adjuvant target therapy or immune therapy.

overall_design:
Patient summary
In this report we identified biomarkers for tumor progression from tissue samples of intermediate/high-risk ccRCC. Using the molecular findings and the clinical data, we developed an improved prognostic model which could help to provide better individualized management recommendations.

first: Fiorella

last: Roldan Chavez

first: Lourdes

last: Mengual Brichs

first: Laura

last: Izquierdo Reyes


title: AGAP2-AS1 as prognostic biomarker in low-risk clear cell renal cell carcinoma patients with progressing disease

city: Bergen

first: Philipp

last: Strauss

address: Haukeland Universitetssykehus Laboratoriebygget, 7. etg. Heis øst

country: Norway

institute: University of Bergen

summary:
Purpose:  Clear cell renal cell carcinoma (ccRCC) is the most common renal cancer. Thirty percent of patients with localized ccRCC develop metastases during follow-up. Although current scoring methods correctly identify patients at low progression risk, a small subgroup still experiences metastatization. We therefore aimed to identify ccRCC progression biomarkers in “low-risk” patients, potentially eligible for adjuvant treatments.

Methods: We performed next-generation sequencing of RNA from formalin-fixed samples obtained at initial surgery from 8 “low-risk” patients with progressing tumours and 16 patients with similar Leibovich score, tumour stage and size, creatinine levels and surgical treatment, not progressing to recurrence with metastasis. Key results were confirmed with qPCR, immunohistochemistry and in external data.

Results: Principal component analysis indicates that systematic transcriptomic differences are detectable at the time of initial surgery. 1167 genes, related to cancer and immune-related pathways, were differentially expressed between progressors and non-progressors. Search for a classifier revealed that overexpression of AGAP2-AS1, an antisense long non-coding RNA, alone, correctly classified 23 of 24 samples without requiring larger gene panels. AGAP2-AS1 gene overexpression was confirmed by qPCR (p <0.05) and correlated with shorter progression-free survival (p: <0.0005). Immunohistochemistry confirmed upregulation at the protein level of AGAP2.

Conclusion: AGAP2-AS1 may represent a novel biomarker identifying high risk patients currently classified as “low risk” at the time of surgery.

overall_design:
Next-generation sequencing of RNA from formalin-fixed samples obtained at initial surgery from 8 “low-risk” patients with progressing tumours and 16 patients with similar Leibovich score, tumour stage and size, creatinine levels and surgical treatment, not progressing to recurrence with metastasis. Key results were confirmed with qPCR, immunohistochemistry and in external data.

*** Raw data is to be made available through dbGaP (controlled access) due to patient privacy concerns****

first: Sigrid

last: Nakken

first: Øystein

last: Eikrem

first: Hans-Peter

last: Marti

first: Christian

last: Beisland

first: Leif

last: Bostad

first: Andreas

last: Scherer

first: Arnar

last: Flatberg

first: Vidar

last: Beisvag

first: Jessica

last: Furriol


title: A single-cell map of dynamic chromatin landscapes of immune cells in renal cell carcinoma (scRNA-Seq and TCR-Seq)

first: Qingqing

last: Wang

overall_design: We used single cell RNA-seq (5' RNA expression sequencing)  and TCR-sequencing (VDJ sequencing)  of human immune cells from blood, normal adjacent kidney, and malignant tissues from early stage clear cell renal cell carcinoma patients at baseline. The VDJ region sequencing is included in the 5' RNA expression sequencing as in 10x Genomics Chromium protocols

first: Nikos

last: Kourtis

first: Bei


title: Single cell RNA-seq (10X Genomics Chromium) of MGE, CGE, LGE and cortical regions from mouse embryonic forebrain

first: Timothy

last: Petros

overall_design: MGE, CGE, LGE and cortical regions from E12.5 mouse embryos.

first: C

last: Rhodes

first: A

last: Mitra

first: D

last: Lee


title: Differentially expressed genes in pancreatic cancer cell with erastin and vitamin C treatment

status: Public on Dec 24 2021

city: Zhengjiang

first: Yawen

last: Liu

address: Xuefu Road 301

institute: Jiangsu University

summary: We use RNA Sequencing to analyze the potential molecular mechanisms in human pancreatic cancer cell line BxPC3 cells after erastin and vitamin C treatment for 48h.

overall_design: Examination of 4 different treatments in human pancreatic cancer cells.

first: Pu

last: Huang


title: Defining the cell surface proteomic landscape of multiple myeloma reveals immunotherapeutic strategies and biomarkers of drug resistance

status: Public on Dec 10 2021

city: Stanford

first: Ian

middle: Daniel

last: Ferguson

state: CA

address: 265 Campus Dr

department: Cancer Biology PhD program

institute: Stanford University

summary: The myeloma cell surface proteome (“surfaceome”) not only determines tumor interaction with the microenvironment but serves as an emerging arena for therapeutic development. Here, we use glycoprotein capture proteomics to first define surface markers most-enriched on myeloma when compared to B-cell malignancy models, revealing unexpected biological signatures unique to malignant plasma cells. We next integrate our proteomic dataset with existing transcriptome databases, nominating CCR10 and TXNDC11 as possible monotherapeutic targets and CD48 as a promising co-target for increasing avidity of BCMA-directed cellular therapies. We further identify potential biomarkers of resistance to proteasome inhibitors and lenalidomide including changes in CD53, EVI2B, CD10, and CD33. Comparison of short-term treatment with chronic resistance delineates large differences in surface proteome profile under each type of drug exposure. Finally, we develop a miniaturized version of the surface proteomics protocol and present the first surface proteomic profile of a primary plasma cell sample. Our dataset provides a unique resource to advance the biological, therapeutic, and diagnostic understanding of myeloma.

overall_design: Data uploaded here: RNA sequencing data for wild type myeloma cell lines and one B-lymphoblastoid cell line along with proteasome-inhibitor (bortezomib and carfilzomib) resistant comparitors.

first: Arun

last: Wiita


title: Comprehensive Analysis of the Testis from Wild-Type and Alkbh5- Knockout Mice Using Single-Cell RNA Sequencing

status: Public on Dec 09 2021

city: nantong

first: hong

last: shihao

address: 19 Qixiu Road

institute: Nantong university

summary: The RNA demethylase ALKBH5 is regarded as the “eraser” in N6-methyladenosine (m6A) modification. ALKBH5 deficiency has been reported to cause male infertility in mice; however, the mechanisms that confer disruption of spermatogenesis are not completely clear. In this study, we profiled testis samples from wild-type (WT) and Alkbh5 knockout (KO) mice by single-cell RNA sequencing (scRNA-seq). We obtained scRNA-seq data of 5596 and 6816 testis cells from a WT and KO mouse, respectively. Genetic profile differences between the groups were detected at different germ cell development stages, from the development of spermatogonia to sperm cells, as well as in macrophages, Sertoli cells, and Leydig cells. We further focused on differentially expressed genes related to spermatogenesis in germ cells and somatic cells (Sertoli cells and Leydig cells), and identified their functions and associated pathways by gene ontology enrichment analysis, such as chromatin-related functional pathways and Dnah8 gene, This study providing the first scRNA-seq profiles of the testes of ALKBH5-deficient mice highlights that ALKBH5 is an important transcription factor for germ cell development and spermatogenesis with new molecular mechanistic insight. These findings can provide the basis for further research into the causes and treatment of male infertility.

overall_design: comprehensive analyses of single-cell RNA-seq data revealed differences between wild-type (WT) and Alkbh5 knockout (KO) mice.

first: Shihao

last: Hong

first: Xiaozhong

last: Shen

first: Chunhai

last: Luo

first: Fei

last: Sun


title: Transcriptional profile of Smad4-deficient CTLs is similar to TRM

status: Public on Dec 22 2021

city: Farmington

first: Linda

last: Cauley

state: CT

address: 263 Farmington Ave

department: Immunology

institute: UConn Health

summary: Transforming growth factor β (TGFβ) is a morphogenic protein that augments antiviral immunity by altering the functional properties of pathogen-specific memory CD8 T cells. During infection, TGFβ inhibits formation of effector (TEFF) and circulating memory CD8 T cells, while encouraging tissue-resident memory CD8 T cells (TRM) to settle in peripheral tissues. SMAD proteins are signaling intermediates that are used by members of the TGF cytokine family to modify gene expression. Using RNA-sequencing we determined that SMAD4 altered the transcriptional profile of antiviral CTLs during respiratory infection. Our data show that SMAD4 and TGFβ use alternate signaling pathways to cooperatively regulate a collection of genes that determine whether pathogen-specific memory CD8 T cells localize in peripheral or lymphoid tissues. During infection, SMAD4 acts independently of TGF to inhibit TRM development, while inducing genes that support formation of circulating memory CD8 T cells. The genes that are modulated by SMAD4 include several homing receptors (CD103, KLRG1 and CD62L) and transcription factors (Hobit and EOMES) that support memory formation.

overall_design: mRNA expression analysis of 2 samples: WT & Smad4 deficient Early Effector CD8 T cells. D6 X31 infection Early effector subset (KLRG1lo, CD127lo, CD103lo)

first: Yinghong

last: Hu

first: Karthik

last: Chandiran


title: Small non-coding RNA organ expression atlas

status: Public on Dec 19 2021

city: Saarbrücken

first: Tobias

last: Fehlmann

address: Campus E2 1

country: Germany

institute: Saarland University

summary: We sequenced 188 tissue samples comprising 35 organ types retrieved from six humans. To demonstrate evolutionary conservation we sequenced in addition 58 samples from 6 tissues of mice.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: sncRNA-seq of 188 human tissue samples and 58 mouse tissue samples.

first: Nicole

last: Ludwig

first: Andreas

last: Keller

first: Laura

last: Gröger


title: Polypyrimidine Tract Binding Protein 1 regulates the activation of mouse CD8 T cells

city: Cambridge

first: Louise

last: Matheson

address: Babraham Research Campus

department: Laboratory of Lymphocyte Signalling and Development

country: United Kingdom

institute: The Babraham Institute

summary: We show that the RNA-binding protein Polypyrimidine Tract Binding Protein 1 (PTBP1) is dispensable for the development of naïve mouse CD8 T cells, but is necessary for the optimal expansion and production of effector molecules by antigen-specific CD8 T cells in vivo.  PTBP1 has an essential role in regulating the early events following activation of the naïve CD8 T cell leading to IL-2 and TNF production. It is also required to protect activated CD8 T cells from apoptosis. PTBP1 controls alternative splicing of over 400 genes in naïve CD8 T cells in addition to regulating the abundance of ~200 mRNAs. PTBP1 is required for the nuclear accumulation of c-Fos, NFATc2 and NFATc3, but not NFATc1. This selective effect on NFAT proteins correlates with PTBP1-promoted expression of the shorter Ab1 isoform and exon 13 skipped Ab2 isoform of the catalytic A-sububit of calcineurin phosphatse. These findings reveal a crucial role for PTBP1 in regulating CD8 T cell activation.

overall_design: Short-read Illumina mRNA-seq libraries were generated from naïve and activated CD8 T cells from control and PTBP1 conditional knockout mice, with four biological replicates per condition. The corresponding replicates for naïve and activated samples for a given genotype were from the same mouse. Long-read ONT cDNA-PCR libraries were also generated from the same RNA samples as the Illumina libraries, except that the fourth replicate for activated cells was omitted. PTBP1 iCLIP libraries were prepared from activated CD8 T cells, with four biological replicates in control cells, and two biological replicates in PTBP1 conditional knockout cells as a negative control.

first: Elisa

last: Monzon-Casanova

first: Vanessa

last: D'Angeli

first: Özge

last: Gizlenci

first: Martin

last: Turner


title: microRNA sequencing of human placentae and matched maternal plasma from 6-23 weeks of gestation

status: Public on Dec 23 2021

city: Adelaide

first: James

last: Breen

state: SA

address: 108 North Terrace (Ground Floor)

department: John Curtin School of Medical Research

country: Australia

institute: Australian National University

summary: microRNAs are increasingly seen as important regulators of placental development and opportunistic biomarker targets. We generated miRNA profiles using 96 placentas from presumed normal pregnancies, across early gestation, in combination with matched profiles from maternal plasma. We identified 637 miRNAs with expression in 86 samples (after removing poor quality samples), showing a clear gestational age gradient and identified 374 differentially expressed (DE) miRNAs across a gestational cut-off of 6-10 weeks’ and 11-23 weeks’. We see a clear gestational age group bias in miRNA clusters C19MC, C14MC, miR-17~92 and paralogs, regions that also include many DE miRNAs. Proportional change in expression of placenta-specific miRNA clusters was reflected in maternal plasma, with C19MC miRNAs miR-516b-5p and 517a-3p showing potential as a biomarkers. Chorionic villous samples across early gestation display differential miRNA profiles, particularly in the expression of highly placenta-specific miRNA clusters, and at the presumed introduction of oxygenated maternal blood into the placenta. Data presented here comprise a clinically important reference set for studying early placenta development and enabling development of minimally invasive methods for monitoring placental health.

overall_design: smallRNA-seq analysis of placenta tissues and matched maternal plasma between 6-23+6 weeks of gestation

first: Melanie

last: Smith

first: Katherine

last: Pillman

first: Dale

last: McAninch

first: Tanja

last: Jankovic-Karasoulos

first: Qianhui

last: Wan

first: K

last: Bogias

first: Dylan

last: McCullough

first: Tina

last: Bianco-Miotto

first: Claire

last: Roberts


title: Identification of Smad2 and Smad3 specific binding sites in a breast cancer cell line model

status: Public on Dec 08 2021

city: Singapore

first: Wee Kiat Jeremy

last: Ng

address: 20 College Road

institute: Singapore General Hospital

summary: We identify Smad2 and Smad3 specific binding site in a breast cancer breast cell model MDA-MB-231 using LAP-tag GFP fusion proteins under the control of endogenous regulatory elements. Stable cell lines were generated via transfection with a BAC followed by antibiotics selection. We show that LAP-fused SMad2/3 can be used to recapitulate native TGFB signaling. Smad2/Smad3 specific binding sites were identified by ChIP-seq against GFP before and after TGFB treatment. Genomic DNA was sequenced via single end sequencing on Illumina HiSeq

overall_design: Chromatin immunoprecipitation against GFP in fusion protein before and after TGFB treatment

first: Esther

last: Ong

first: Jeremy

middle: W

first: Greg

last: Tucker-Kellogg


title: Machine Learning Models Predict the Primary Sites of Head and Neck Squamous Cell Carcinoma Metastases Based on DNA Methylation

city: Berlin

first: Maximilian

last: Leitheiser

address: Charitéplatz 1

department: Institute of Pathology

institute: Charité - University Hospital Berlin

type: Methylation profiling by genome tiling array

summary: In head and neck squamous cell cancers (HNSCs) that present as metastases with an unknown primary (HNSC-CUPs), the identification of a primary tumor improves therapy options and increases patient survival. However, the currently available diagnostic methods are laborious and do not offer a sufficient detection rate. Predictive machine learning models based on DNA methylation profiles have recently emerged as a promising technique for tumor classification. We applied this technique to HNSC to develop a tool that can improve the diagnostic workup for HNSC-CUPs. On a reference cohort of 405 primary HNSC samples, we developed four classifiers based on different machine learning models (random forest (RF), neural network (NN), elastic net penalized logistic regression (LOGREG), support vector machine (SVM)) that predict the primary site of HNSC tumors from their DNA methylation profile. The classifiers achieved high classification accuracies (RF=83%, NN=88%, LOGREG=SVM=89%) on an independent cohort of 64 HNSC metastases. Further, the NN, LOGREG, and SVM models significantly outperformed p16 status as a marker for an origin in the oropharynx. In conclusion, the DNA methylation profiles of HNSC metastases are characteristic for their primary sites and the classifiers developed in this study, which are made available to the scientific community, can provide valuable information to guide the diagnostic workup of HNSC-CUP.

overall_design: The DNA methylation of 49 samples of head and neck squamous cell cancers from cervical lymph nodes metastases were analyzed using the Illumina Infinium MethylationEPIC BeadChip. The primary tumor was located in the oral cavity for 22 cases, in the oropharynx for 17 cases, in the hypopharynx for 3 cases, and in the larynx for 7 cases.

first: David

last: Capper

first: Philipp

last: Seegerer

first: Annika

last: Lehmann

first: Ulrich

last: Schüller

first: Klaus-Robert

last: Müller

first: Frederick

last: Klauschen

last: Jurmeister

first: Michael

last: Bockmayr


title: Gene expression profiling on heads of Drosophila chromodomain helicase DNA binding protein 1 (CHD1) deletion mutants

status: Public on Dec 07 2021

city: Innsbruck

first: Ingo

last: Bauer

state: Tirol

address: Innrain 80-82

department: Institute of Molecular Biology

country: Austria

institute: Medical University of Innsbruck

summary: CHD1 is a conserved ATP-dependent chromatin remodeling factor with roles in transcriptional regulation and chromatin assembly. Here we show that deletion of Chd1 causes multiple behavioral and metabolic defects. In particular, it diminishes food-intake and results in shortened lifespan of mutant flies. These phenotypes can be rescued by brain-specific expression of Chd1 via the elav promoter. Consistently, neuron-specific expression of Chd1 rescues the wide-spread transcriptional dysregulation observed in the absence of CHD1.

overall_design: RNA was prepared from heads of 10 day-old Drosophila females for RNA-seq analysis. Three genoytypes were used (Chd1-deficient, Chd1-rescued, elavGal4>UAS-Chd1)

first: Ines

last: Schoberleitner

first: Alexandra

last: Lusser


title: Targeting the mRNA endonuclease CPSF73 inhibits breast cancer cell migration and invasion

status: Public on Dec 05 2021

city: Boston

first: Huiyun

last: Liu

state: Massachusetts

address: 150 Harrison Avenue, Jaharis building, Room 401A

institute: Tufts university school of medicine

summary: Cleavage by the endonuclease CPSF73 and polyadenylation of nascent RNA is an essential step in co-transcriptional mRNA maturation, and abnormal poly(A) site choices have been associated with human diseases, including cancer. Recent work has surprisingly identified CPSF73 as a promising drug target for inhibiting the growth of specific cancers. However, our understanding of the regulation of CPSF73 is still at an early stage. Here, we report that a HECT-like E3 ligase, UBE3D, participates in stabilizing CPFS73 protein by preventing its ubiquitin-mediated degradation by the proteasome. Depletion of UBE3D in both non-cancer cells and cancer cells leads to CPSF73 downregulation, a pre-mRNA cleavage defect and dysregulated gene expression. UBE3D dysfunction or chemical inactivation of CPFS73 inhibited migration and invasion as well as stem cell renewal phenotypes in vitro in triple negative breast cancer cells. Our findings indicate that targeting the pre-mRNA processing nuclease CPSF73 has potential for breast cancer therapy.

overall_design: Analysis of gene expression changes and readthrough transcripts in UBE3D depleted human cells

first: Daniel

last: Heller-Trulli

last: Moore


title: Gene expression profile of azacitidine- and decitabine- resistant HTLV-1-infected cell lines

status: Public on Nov 30 2021

city: Saga

first: Tatsuro

last: Watanabe

state: Saga

address: 5-1-1 Nabeshima, Saga

institute: Saga University

summary: We generated azacitidine (AZA)- and decitabine (DAC)-resistant (AZA-R and DAC-R, respectively) cells from drug-sensitive ATL cell lines TL-Om1 and MT-2 via long-term drug exposure. To identify molecular mechanisms responsible for acquired resistance, we performed transcriptome analysis using Clariom S microarray.

overall_design: Gene epxression profiles of DAC-R and AZA-R cells were compared with their parental cells. Total RNA was extracted from each cell line cultured in normal growth condition and gene expressions were compared among three groups; parent, DAC-R and AZA-R.

first: N

last: Yoshida

first: T

first: Y

last: Yamamoto

first: H

last: Ureshino

first: K

last: Kamachi

last: Kurahashi

last: Fukuda-Kurahashi

first: S

last: Kimura


title: CDC-like Kinase 4 Deficiency Contributes to Pathological Cardiac  Hypertrophy by Modulating NEXN Phosphorylation

status: Public on Nov 23 2021

city: Shanghai

first: Jian

last: Huang

address: No. 150 Jimo Road

department: Department of Cardiology

institute: Shanghai East Hospital, Tongji University School of Medicine

summary: To investigate how sustained NEXN phosphorylation ameliorated the pathological phenotype in Clk4-cKO mice. We performed microarray analysis in the Clk4-cKO  myocardium treated with AAV NEXN-S437E, wherein AAV NEXN-WT served as a control.

overall_design: Clk4-cKO myocardium treated with AAV NEXN-S437E, wherein AAV NEXN-WT served as a control. n = 3 animals for each group.

first: Yi-han

last: Chen


title: Differential expression of mRNA, lncRNA and circRNA in esophageal squamous cell carcinoma by genome-wide sequencing

status: Public on Dec 01 2021

city: Nanjing

first: Sachin

last: Mulmi Shrestha

address: Dingjiaqiao Street-87

department: Gastroenterology

institute: Southeast University

summary: Altogether 12 tissue specimens were collected from Esophageal squamous cell carcinoma patients (4 normal tissues,  4 cancer adjacent tissue, 4 cancer tissue). Tissue samples were kept in RNA Later solution and preserved in liquid nitrogen. Then, tissue samples were further processed to extract mRNA,lnc RNA and circRNA profile

overall_design: RNA profiles of  test and control samples of the collected tissue samples were generated by deep sequencing, using Illumina HiSeq 4000.

first: Lihua

last: Ren

first: Xin

last: Fang

first: Hui

last: Ye

first: Ruihua

last: Shi


title: RNA-expression analysis on smooth muscle cells of diabetic donors after empagliflozin treatment

status: Public on Nov 27 2021

city: Hannover

first: Lena

middle: Marie

last: Bode

address: Carl-Neuberg-Str. 1

department: Dept. of Cardiology and Angiology

institute: Hannover Medical School

summary:
Purpose: We report vascular effects of empagliflozin stimulation.
Results: Gene set enrichment analysis of RNA-Seq showed negative regulation of vascular smooth muscle cell proliferation. Gene set overlapped by the vasoactive peptide apelin, being upregulated by empagliflozin treatment.

overall_design: Comparison of RNA expression in human diabetic smooth muscle cells stimulated with fetal calf serum or empagliflozin.

first: Jochen

last: Dutzmann

middle: M


title: Effect of HKDC1 ablation on hepatocellular carcinoma proliferation

status: Public on Nov 21 2021

city: Chicago

first: Md. Wasim

last: Khan

state: IL

address: 835 S Wolcott Ave

department: Medicine

institute: University of Illinois at Chicago

summary: Hepatocellular carcinoma (HCC) is a leading cause of death from cancer malignancies. Recently, a putative fifth hexokinase, hexokinase domain containing 1 (HKDC1), was shown to have significant overexpression in HCC compared to healthy tissue. Using a combination of in vitro and in vivo tools, we examined the role of HKDC1 in HCC development and progression. Importantly, HKDC1 ablation stops HCC development and progression via action by promoting metabolic reprogramming and a shift of glucose flux away from the TCA cycle.  HKDC1 ablation leads to mitochondrial dysfunction resulting in less cellular energy which cannot be compensated by enhanced glucose uptake. Moreover, we show that the interaction of HKDC1 with the mitochondria is essential for its role in HCC progression, and without this mitochondrial interaction mitochondrial dysfunction occurs. HKDC1 is highly expressed in HCC cells, but only to a minimal degree in hepatocytes under normal conditions therefore targeting HKDC1, specifically its interaction with the mitochondria, reveals a highly selective approach to target cancer cells in HCC.

overall_design: mRNA samples from Hpeg2 cells either expressing an Empty vector (EV) or sgRNA against HKDC1 (KO) was extracted for RNA-seq.

first: M

first: Brian

last: Layden


first: Huiyun

last: Liu

department: Development, Molecular & Chemical Biology

first: Daniel

last: Heller-Trulli

first: Claire

last: Moore


title: Reversal of lineage plasticity in RB1/TP53-deleted prostate cancer through FGFR and Janus kinase inhibition

status: Public on Nov 07 2021

city: New York

first: Dana

last: Pe'er

address: 417 E 68th St

institute: Memorial Sloan Kettering Cancer Center

summary: The inherent plasticity of tumor cells provides a mechanism of resistance to many molecularly targeted therapies, exemplified by adeno-to-neuroendocrine lineage transitions seen in prostate and lung cancer. Here we investigate the root cause of this lineage plasticity in a primary murine prostate organoid model that mirrors the lineage transition seen in patients. These cells lose luminal identity within weeks following deletion of Trp53 and Rb1, ultimately acquiring an Ar-negative, Syp+ phenotype after orthotopic in vivo transplantation. Single-cell transcriptomic analysis revealed progressive mixing of luminal-basal lineage features after tumor suppressor gene deletion, accompanied by activation of Jak/Stat and Fgfr pathway signaling and interferon-a and -g gene expression programs prior to any morphologic changes. Genetic or pharmacologic inhibition of Jak1/2 in combination with FGFR blockade restored luminal differentiation and sensitivity to antiandrogen therapy in models with residual AR expression. Collectively, we show lineage plasticity initiates quickly as a largely cell-autonomous process and, through newly developed computational approaches, identify a pharmacological strategy that restores lineage identity using clinical grade inhibitors.

overall_design:
Six prostate organoid samples:
Wild-type prostate organoid isolated from TP53 loxP/loxP and RB1 loxP/loxP mice and cultured under standard organoid conditions with dihydrotestosterone (DHT) exposure
Prostate organoid at 2 weeks following cre mediated RB1 and TP53 deletion and cultured under standard organoid conditions with dihydrotestosterone (DHT) exposure
Prostate organoid at 4 weeks following cre mediated RB1 and TP53 deletion and cultured under standard organoid conditions with dihydrotestosterone (DHT) exposure
Prostate organoid at 8 weeks following cre mediated RB1 and TP53 deletion and cultured under standard organoid conditions with dihydrotestosterone (DHT) exposure
Prostate organoid at 4 weeks following cre mediated RB1 and TP53 deletion and cultured under standard organoid conditions withre enzalutamide (ENZ) exposure
Prostate organoid at 8 weeks following cre mediated RB1 and TP53 deletion and cultured under standard organoid conditions withre enzalutamide (ENZ) exposure

first: Charles

last: Sawyers

first: Joseph

last: Chan

first: Wouter

last: Karthaus


title: 16S V3-V4 -based microbial profiling of matched healthy and inflamed ileal mucosa from patients affected by Crohn’s disease

status: Public on Nov 22 2021

city: Firenze

first: Matteo

last: Ramazzotti

address: viale Morgagni 50

department: Experimental and Clinical Biomedical Sciences

country: Italy

institute: University of Florence

summary: Crohn’s Disease (CD) pathogenesis is still unclear. Disorders in the mucosal immunoregulation and its crosstalk with the microbiota may represent an important component in tissue injury. We aimed to characterize the molecular immune response distribution within the ileal layers ( mucosa, submucosa and serosa) and to evaluate the correlated microbiota in pathological/healthy settings comparing first surgery/relapse clinical conditions.

overall_design: 10 matched pairs of paraffin-embedded ileal tissue specimens was extracted and 16S rDNA amplicons (V3-V4 region)

first: Amedeo

last: Amedei


title: RNA sequencing analysis of CopY-deficient Streptococcus agalactiae during Zn stress

city: Gold Coast

first: Glen

last: Ulett

state: QLD

address: Parklands Drive

department: School of Medical Science

institute: Griffith University

summary: Total RNA was isolated from mid-log phase Streptococcus agalactiae cells deficient in CopY (∆copY strain GU2857), grown in Todd-Hewitt broth (THB) medium supplemented with 0.25 mM Zn and sequenced using Illumina NextSeq500.

overall_design: Four biological replicate cultures of S. agalactiae deficient in CopY (∆copY strain GU2857) were grown in THB + 0.25 mM Zn.


title: Single-cell gene expression of anti-viral CD4  T cells in Bcl6 and Blimp1 deficient conditions

status: Public on Nov 05 2021

first: Thomas

last: Ciucci

summary: Single-cell gene expression of effector CD4+ T cells  WT,  Bcl6-deficient , Blimp1-deficient or Bcl6 Blimp1-deficient was determined by scRNAseq after LCMV Armstrong infection

overall_design: Mixed bone marrow chimera made of  WT,  Bcl6-deficient , Blimp1-deficient or Bcl6 Blimp1-deficient cells were infected with LCMV Armstrong. 7 days post-infection GP66+ CD4+ T cells were sorted and gene expression was determined by scRNAseq

first: Remy

last: Bosselut


title: RNA-sequencing data of CMT-93 cells exposed to LPS and/or garlic extract

status: Public on Nov 02 2021

city: Frederiksberg C

first: Andrew

last: Williams

state: --- Select One ---

address: Dyrlægevej 100

country: Denmark

institute: University of Copenhagen

summary: We show here the transcriptional response in CMT-93 intestinal epithelial cells treated with Trichuris muris antigen and/or a garlic extract (40% PTSO-PTS).

overall_design: RNA was obtained from cells (triplicates) of control, T. mruis antigens, PTSO-PTS, and T. muris + PTSO-PTS


title: Downregulation of HDAC9 by β-hydroxybutyrate suppresses vascular calcification in chronic kidney disease

status: Public on Nov 01 2021

city: Guangzhou

first: Zirong

last: Lan

address: 253 Industrial Avenue

institute: Zhujiang Hospital, Southern Medical University

summary: In this study, we report the protective effect of β-hydroxybutyrate (BHB) on vascular calcification in chronic kidney disease (CKD). To further investigate the mechanism underpinning the protective effect of BHB on vascular calcification, we performed high-throughput RNA-seq to identify the target gene of BHB. Our data demonstrate that BHB supplementation inhibits vascular calcification in CKD via targeting HDAC9.

overall_design: Human vascular smooth muscle cells were cultured in calcifying medium (CM) in the presence or absence of β-hydroxybutyrate (BHB). RNA-seq was performed to determine the downstream target of BHB.

first: Jianyun

last: Yan


title: Single-cell transcriptome analysis reveals mesenchymal stem cells in cavernous hemangioma

status: Public on Nov 17 2021

city: Tianjin

first: Shan

last: Gao

address: No 94, weijin road

institute: Nankai University

summary:
A cavernous hemangioma, well-known as vascular malformation, is present at birth, grows proportionately with the child, and does not undergo regression. Although a cavernous hemangioma has well-defined histopathological characteristics, its origin and formation remain unknown. In the present study, we characterized the cellular heterogeneity of cavernous hemangioma using single-cell RNA sequencing (scRNA-seq). The main contribution of the present study is the discovery of mesenchymal stem cells (MSCs) that cause cavernous hemangioma formation and may be abnormally or incompletely differentiated from epiblast stem cells. EGFR inhibitors are the potential drugs to treat cavernous hemangiomas.
Other new findings include the responsive ACKR1 positive endothelial cell (ACKR1+EC) and BTNL9 positive endothelial cell (BTNL9+EC) and the BTNL9-caused checkpoint blockade enhanced by the CXCL12-CXCR4 signalling. The activated CD8+T and NK cells may highly express CCL5 for their infiltration in cavernous hemangiomas, independent on the tumor cell-derived CCL5-IFNG-CXCL9 pathway. The plasmacytoid dendritic cells (pDCs) function for anti-tumour as CD8+T cells in cavernous hemangiomas. The oxidised low-density lipoprotein (oxLDL) and scavenger receptors (SRs) may play an important role in the immune responses in the tumour microenvironment of cavernous hemangiomas. Notably, we propose that oxLDL induces the oxLDL-OLR1-NLRP3 pathway in M1-like macrophages via the over-expression of OLR1, whereas oxLDL induces the oxLDL-SRs-C1q pathway in M2-like macrophages via the over-expression of many SRs (LILRB5, etc) except OLR1. The highly expressed EREG in M1-like macrophages and the highly expressed EGFR in MSCs may cause MSC proliferation and the tumour progression.
The present study revealed the origin of cavernous hemangiomas and reported the marker genes, cell types and molecular mechanisms, which are associated with the origin, formation, progression, diagnosis or therapy of cavernous hemangiomas. Our discoveries facilitate the development of gold standards for molecular diagnosis and effective drugs for treatment, and enrich the fundamental knowledge in the research field of immune, cancer and even cell biology.

overall_design: The lesion was obtained as tumour tissue from a 6-year-old patient diagnosed with cavernous hemangioma. Using tissue in the center of the lesion, scRNA-seq libraries (10x Genomics, USA) were constructed and sequenced to produce ~163 Gbp of raw data. After data cleaning and quality control, a total of 10,784 cells and 22,023 genes were identified to produce a 22,010×10,784 matrix and an 13×10,784 matrix, representing the expression levels of nuclear and mitochondrial genes, respectively.

first: Jinsong

last: Shi


title: In vivo lentiviral vector gene therapy to cure hereditary tyrosinemia type 1 and prevent  development of precancerous and cancerous lesions

status: Public on Nov 20 2021

city: Rochester

middle: Benjamin

last: Lillegard

address: 200 First St. SW

department: Surgery

institute: The Mayo Clinic

summary: Conventional therapy for hereditary tyrosinemia type-1 (HT1) with 2-(2-nitro-4-  trifluoromethylbenzoyl)-1,3-cyclohexanedione (NTBC) delays and in some cases fails to prevent  disease progression to liver fibrosis, liver failure, and activation of tumorigenic pathways. Here  we demonstrate for the first time a cure of HT1 by direct, in vivo administration of a therapeutic  lentiviral vector targeting the expression of a human fumarylacetoacetate hydrolase (FAH)  transgene in the porcine model of HT1. This therapy was well tolerated and provided stable  long-term expression of FAH in pigs with HT1. Genomic integration displayed a benign profile,  with subsequent fibrosis and tumorigenicity gene expression patterns similar to wild-type  animals as compared to NTBC-treated or diseased untreated animals. Indeed, the phenotypic and  genomic data following in vivo lentiviral vector administration demonstrate comparative  superiority over other therapies including ex vivo cell therapy and therefore support clinical  application of this approach.

overall_design:
23 samples were analyzed. WT animal RNA expression profiles were compared to animals treated with the standard of care for HT1: NTBC, as well as LV-FAH gene therapy, and the negative control, which was cycled on and off the standard of care NTBC.  Samples were also analyzed for integration profiles of LV-FAH from various tissues in the LV-FAH treated animals.

****Please note that raw data for the '282 NTBC RNA-Seq', '266 RNA-seq (RLI)' samples are unavailable and thus are not included in the records****

first: Clara

last: Nicolas

first: Caitlin

last: VanLith

first: Kari

last: Allen

first: Raymond

last: Hickey

first: Zeji

last: Du

first: Lori

last: Hillin

first: Rebekah

last: Guthman

first: William

last: Cao

first: Benjamin

last: Haugo

first: Aditya

last: Bhagwate

last: O'Brien

first: Jean-Pierre

last: Kocher

first: Robert

last: Kaiser

first: Stephen

last: Russell

middle: B


title: RNA-sequencing data of caecum tissue of mice infected with helminths and administered garlic extract

first: Andrew

last: Williams

summary: We show here the transcriptional response in caecum tissue of mice infected with Trichuris muris for 35 days and given either garlic extract treatment or control treatment.

overall_design: RNA was obtained from caecum tissue at necrospy following 35 days of T. muris infection.


title: Transcriptional Changes when TGF-beta type II receptor is deleted

status: Public on Nov 06 2021

city: St. Louis

first: Leslie

middle: Stuart

last: Gewin

state: MO

address: 660 S Euclid Ave, McDonnell Science Building, Rm 718

department: Medicine (Nephrology)

institute: Washington University in St. Louis

summary: We looked at transcriptional changes in immortalized IMCD (inner medullary collecting duct cells) derived from Tgfbr2floxed mice, described in detail in manuscript PMID: 20576806

overall_design:
There were a total of 4 samples: 2 in serum replete media and 2 in serum depleted media and in each condition we used IMCD cells either with the TGF-beta receptor intact (floxed) or treated with Cre and deleted
*** RAW DATA NOT AVAILABLE (Submitter statement: "sequencing was done in 2014 by the Vanderbilt University Core and the FASTQ files are not saved.") ***

first: Gewin

last: Leslie

first: Violich

last: Ivo


title: RNA-sequencing data of macrophages exposed to LPS and/or garlic extract

summary: We show here the transcriptional response in RAW 264.7 macrophages treated with LPS and/or a garlic extract (PTSO)

overall_design: RNA was obtained from cells (triplicates) of control, LPS, PSTO, and LPS + PSTO.


title: Expression data from hepatocyte-like cells (HLCs) differentiated from human induced pluripotent stem cells (iPSCs)

status: Public on Nov 03 2021

city: Laurel

first: Xiugong

last: Gao

address: 8301 Muirkirk Rd

department: HFP/OLOAS/OCT/DT

institute: US FDA

summary: We devised two hepatocyte differentiation methods, namely Method 1 (M1) and Method 2 (M2), through modifying existing well-known hepatocyte differentiation strategies, and compared the resultant cells phenotypically, functionally and transcriptomically at different stages of hepatocyte differentiation.        !Series_summary =We used microarrays to compare the global gene expression of the HLCs differentiated using the two methods, M1 and M2.

overall_design: HLCs were collected at day 17 (D17) and day 21 (D21) for RNA extraction and hybridization on Affymetrix microarrays. Primary human hepatocytes (PHHs) were also included in the study for comparison.

first: Rong

last: Li


title: Setdb1 regulates Cohesin at H3K9me3-independent topological domains [Hi-C]

status: Public on Nov 16 2021

city: Singapore

first: Yingying

last: Zeng

state: --- Select a state ---

address: 61 Biopolis Drive

institute: Institute of Molecular and Cell Biology

summary:
Hi-C experiments were performed on E14 cells knocked down with shEV, shSetdb1, and shSmc1a.
Please note that the GSM6037819 - GSM6037836 samples were generated with higher resolution to supplement the previous data (GSM5689250-GSM5689252) with low resolution.

overall_design: Hi-C experiments on E14 mESCs

first: T

last: Warrier

first: C

last: El Farran

first: H

first: Y

last: Loh


title: Cancer cells are sensitive to wild-type IDH1 inhibition under nutrient limitation

city: Cleveland

first: Ata

last: Abbas

state: OH

address: 10900 Euclid Ave

department: Division of Hematology & Oncology

institute: Case Western Reserve University

summary: Pancreatic cancer cells alter their metabolism to survive cancer-associated stress. For example, cancer cells must adapt to steep nutrient gradients that characterize the natural tumor microenvironment. In the absence of adaptive strategies, harsh metabolic conditions promote free radicals and impair energy production in tumor cells. Towards this end, wild-type isocitrate dehydrogenase 1 (IDH1) activity is a metabolic requirement for cancer cells living in a harsh metabolic milieu. The cytosolic enzyme interconverts isocitrate and α-ketoglutarate (αKG) and uses NADP(H) as a cofactor. We show that under low nutrient conditions, the enzymatic reaction favors oxidative decarboxylation to yield NADPH and αKG. Metabolic studies showed that the IDH1 products directly support an antioxidant defense and mitochondrial function in stressed cancer cells. Genetic IDH1 suppression reduced pancreatic cancer cells' growth in vitro under low nutrient conditions and in mouse models of pancreatic cancer. Thus, intrinsic tumor microenvironment conditions sensitized wild-type IDH1 to FDA-approved AG-120 (ivosidenib) and revealed the drug to be a potent single-agent therapeutic in cell culture and diverse in vivo cancer models. This work identified a potentially new repertoire of safe cancer therapies, including a clinically available compound, to treat multiple wild-type IDH1 cancers, including pancreatic cancer.

overall_design: MiaPaCa-2 cells under low glucose for 48 hours (2.5 mM glucose) compared with control (25 mM glucose). Three independent biological replicates were used.

first: Ali

last: Vaziri-Gohar

first: Jordan

last: Winter


title: RNA-seq analysis of mRNA profiles in the livers of Mettl3 flox/flox and hepatocyte-specific Mettl3 knockout (HKO) mice

status: Public on Oct 29 2021

city: Harbin

first: Zheng

last: Chen

state: Heilongjiang

address: 92 Xidazhijie  Harbin Institute of Technology

institute: Harbin Institute of Technology

summary:
Purpose: The goal of this study is to compare transcriptome profilings of liver from Mettl3 flox/flox and hepatocyte-specific Mettl3 knockout (HKO) mice.
Methods: Total RNA was extracted using Tripure Isolation Reagent (Roche, Mannheim, Germany) from livers of Mettl3 flox/flox and HKO mice at 8 weeks old. mRNA profiles were generated by deep sequencing using an Illumina HiSeq X Ten platform. Paired-end clean reads were aligned to the mouse reference genome(Ensemble_GRCm38.90) with Hisat2 (version 2.0.4), and the aligned reads were used to quantify mRNA expression by using HTSeq (version 0.9.1).
Conclusion: The hepatic mRNA profiles in Mettl3 flox/flox and HKO mice were characterized.

overall_design: RNA samples were pooled from livers of METTL3 HKO and Mettl3 flox/flox mice (n=4 for each group). mRNA profiles of HKO and Mettl3 flox/flox livers were generated by deep sequencing, in a single test, using Illumina HiSeq X Ten platform.

first: Xinzhi


title: Transcriptome Profiling of Ginsenoside Metabolites to Identify Estrogen Receptor Alpha Activity

status: Public on Oct 26 2021

city: Yokohama

first: mami

last: kikegawa

state: Kanagawa

address: 601 Matanocho Totsuka-ku

department: Kampo Medicine

institute: Yokohama University of Pharmacy

summary: 20(S)-Protopanaxadiol (PPD) and 20(S)-Protopanaxatriol (PPT) are major metabolites of ginseng in humans and are considered to have estrogenic activity in cellular bioassays. In this study, we conducted in silico analyses to determine whether PPD and PPT interact with estrogen receptor alpha (ERα) and compared them with ERα agonists, partial agonists, and antagonists to identify their ERα activity.

overall_design: mRNA profiles　of 4 kinds conpound exposed  in MCF-7 cells.

first: Mami

last: Kikegawa

first: Hideko

last: Sone


title: ATAC-seq of liver samples in Mettl3 flox/flox and hepatocyte-specific Mettl3 knockout (HKO) mice

summary:
Purpose: The goal of this study is to determine whether hepatic deletion of Mettl3 affects chromatin accessibility.
Methods: Liver samples were pooled from livers of Mettl3 HKO and Mettl3 flox/flox mice (n=4 for each group). Nuclei was extracted from liver samples, and the nuclei pellet was resuspended in the Tn5 transposase reaction mix. The transposition reaction was incubated at 37°C for 30 min. Equimolar Adapter1 and Adatper 2 were added after transposition, PCR was then performed to amplify the library. After the PCR reaction, libraries were purified with the AMPure beads and library quality was assessed with Qubit. The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumina) according to the manufactuer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina NovaSeq 6000 platform and 150 bp paired-end reads were generated. ATAC-seq analysis was performed using a standard protocol.
Results: The hepatic chromatin accessibility in Mettl3 flox/flox and HKO mice were characterized.


title: RNA-seq and ATAC-seq of liver samples in Mettl3 flox/flox and hepatocyte-specific Mettl3 knockout (HKO) mice

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

overall_design: Refer to individual Series


title: RNA-seq in HCT116 cell lines

status: Public on Oct 24 2021

city: Zhengzhou

first: Zhuoyu

last: Gu

address: Jianshe East Road

institute: The First Affiliated Hospital, Zhengzhou University

summary:
Purpose: The goals of this study are to invsetigate the primary biological process of hnRNPK.
Methods: Briefly, samples (HCT116 cells transfected with control or hnRNPK shRNA) were used to extract total RNAs for quality control and RNA-seq loading samples. RNA-seq was performed as DGE on an Illumia HiSeq platform and 50 bp paired-end reads were generated (BGI Co. Ltd.).
Results: Regulation of transcription by RNA polymerase II was identified as the primary biological process according to the gene ontology (GO) analysis. Regulation of transcription by RNA polymerase II and translation by ribosome were identified as the primary biological processes according to the gene set enrichment analysis (GSEA).
Conclusions: RNA-seq in HCT116 cell lines revealed that hnRNPK mainly regulated cellular transcription and translation.

overall_design: mRNA profiles of HCT116  hnRNPK shNC cells and HCT116 hnRNPK knockdown cells


title: N1-methylpseudouridine found within COVID-19 mRNA vaccines produces faithful protein products

status: Public on Oct 25 2021

city: St Louis

first: Hani

last: Zaher

address: 1 Brookings Drive

department: Biology

summary: Given the interest in the COVID mRNA vaccines, we sought to investigate how the RNA modification N1-methylpseudouridine (and its related modification, pseudouridine) is read by ribosomes and reverse transcriptases. By looking at reverse transcriptase data, we can gain information on how the modification affects duplex stability, which may have important consequences for the tRNA-mRNA interactions found in the ribosome.

overall_design: Deep sequencing of cDNA generated by reverse transcribing synthetic RNA containing no modifications, a single uridine to pseudouridine substitution, or a single uridine to N1-methylpseudouridine substitution. The RNA was transcribed using both M-MLV and AMV.

first: Kyusik

middle: Q

last: Kim

first: Bhagyashri

middle: D

last: Burgute

first: Shin-Cheng

last: Tzeng

first: Crystal

last: Jing

first: Courtney

last: Jungers

first: Junya

last: Zhang

first: Liewei

last: Yan

first: Richard

last: Vierstra

first: Sergej

last: Djuranovic

first: Bradley

last: Evans


title: Maternal SMCHD1 controls both imprinted Xist expression and imprinted X chromosome inactivation

city: Heidelberg

first: Quentin

last: Gouil

state: VIC

address: Studley Road

institute: Olivia Newton-John Cancer Research Institute

summary: Embryonic development is dependent on the maternal supply of proteins through the oocyte, including factors setting up the adequate epigenetic patterning of the zygotic genome.   We previously reported that one such factor is the epigenetic repressor SMCHD1, whose maternal supply controls autosomal imprinted expression in mouse preimplantation embryos and mid-gestation placenta. In mouse preimplantation embryos, X chromosome inactivation is also an imprinted process. Combining genomics and imaging, we show that maternal SMCHD1 is required not only for the imprinted expression of Xist in preimplantation embryos, but also for the efficient silencing of the inactive X in both the preimplantation embryo and mid-gestation placenta.  These results expand the role of SMCHD1 in enforcing the silencing of Polycomb targets. The inability of zygotic SMCHD1 to fully restore imprinted X inactivation further points to maternal SMCHD1's role in setting up the appropriate chromatin environment during preimplantation development, a critical window of epigenetic remodelling.

overall_design: methylome and transcriptome analysis of mouse embryos with maternal deletions of Smchd1

first: Iromi

last: Wanigasuriya

first: Marnie

middle: E

last: Blewitt


title: Profiling of mRNA transcriptomic changes using RNA-seq in postmortem nucleus accumbens of subjects with alcohol use disorder

status: Public on Oct 13 2021

city: Boston

first: Huiping

address: 72 East Concord Street

department: Psychiatry

institute: Boston University School of Medicine

summary:
Purpose: The goal of this study to examine mRNA transcriptomic changes in reward-related brain regions of subjects with alcohol use disorder.
Methods: Total RNAs were extracted from postmortem nucleus accumbens of 12 AUD and 12 control subjects. rRNA depletion RNA sequencing was performed and the sequence reads were processed using the bulk RNA-seq processing pipeline Pipeliner workflow (Federico et al. Front Genet 2019; 10, 614). AUD-associated mRNA transcriptomic changes were analyzed by the Limma-Voom method.
Results: Differentially expressed mRNAs (absolute FC>2.0 & P<0.05) were identified in postmortem nucleus accumbens of subjects with alcohol use disorder (AUD).
Chronic alcohol consumption may alter mRNA transcriptome profiles in reward-related brain regions, resulting in alcohol-induced neuroadaptations.

overall_design: Cases and controls were matched by race, sex, age, etc.

first: Zhang

last: Huiping


title: Profiling of mRNA transcriptomic changes using RNA-seq in postmortem ventral tegmental area (VTA) of subjects with alcohol use disorder

summary:
Purpose: The goal of this study to examine mRNA transcriptomic changes in reward-related brain regions of subjects with alcohol use disorder.
Methods: Total RNAs were extracted from postmortem ventral tegmental area of 12 AUD and 12 control subjects. rRNA depletion RNA sequencing was performed and the sequence reads were processed using the bulk RNA-seq processing pipeline Pipeliner workflow (Federico et al. Front Genet 2019; 10, 614). AUD-associated mRNA transcriptomic changes were analyzed by the Limma-Voom method.
Results: Differentially expressed mRNAs (absolute FC>2.0 & P<0.05) were identified in postmortem ventral tegmental area of subjects with alcohol use disorder (AUD).
Chronic alcohol consumption may alter mRNA transcriptome profiles in reward-related brain regions, resulting in alcohol-induced neuroadaptations.


title: Modular, Cascade-like Transcriptional Program of Regeneration in Stentor

status: Public on Oct 20 2021

city: San Francisco

first: Wallace

last: Marshall

institute: UCSF

summary: The giant ciliate Stentor coeruleus is a classical model system for studying regeneration and morphogenesis at the level of a single cell. The anterior of the cell is marked by an array of cilia, known as the oral apparatus, which can be induced to shed and regenerate in a series of reproducible morphological steps, previously shown to require transcription. If a cell is cut in half, each half will regenerate an intact cell, including a new oral apparatus in the posterior half. We used RNAseq to assay the dynamic changes in Stentor’s transcriptome during regeneration, after both oral apparatus shedding and bisection, allowing us to identify distinct temporal waves of gene expression. By comparing transcriptional profiles of different regeneration events in the same species, we were able to classify regeneration genes into groups based on their potential role for regeneration in distinct cell regeneration paradigms, and provides new insight into how a single cell can coordinate complex morphogenetic pathways to regenerate missing structures.

overall_design: RNA-seq time series of regeneration paradigms in Stentor: 1. sucrose-shocked-induced OA regeneration (10 timepoints, 4 replicates) 2. sucrose-shocked-induced OA regeneration in the presence of cycloheximide ( 5 timepoints, 3 replicates) or in the presence of DMSO (5 timepoints, 3 replicates) 3. bisected cells (anterior and posterior fragments both assayed -- 6 timepoints 3 replicates)

first: Pranidhi

last: Sood

first: Athena

last: Lin

first: Rebecca

last: McGillivary


title: Genome-wide PBMCs Profiling Reveals Early Detection of Immunothrombotic Dysregulation in COVID-19 based on Blood Routine Test: A Multi-Center Retrospective Study of 1219 Patients

status: Public on Oct 06 2021

first: zhaoming

last: Zhou

address: 1023-1063 shatai South Road, Baiyun District, Guangzhou

institute: School of Public Health,Southern Medical University

summary: The present study aimed to develop algorithms for early identification of patients who are at risk of being involved in abnormal immunothrombosis, enabling prompt interventions and averted progression of disease.

overall_design:
RNA-Seq profiling of peripheral blood mononuclear cells (PBMCs) derived from patients with COVID-19 as well as multi-omics data integrative of plasma and cytology levels were studied. A multi-center cohort of 1219 patients was utilized to validate the transcriptional findings and model constructions.
In our research, RNA-Seq profiling of peripheral blood mononuclear cells (PBMCs) derived from 40 patients with or without COVID-19 was analyzed. In the meanwhile, multi-omics data integrative of plasma and cytology levels were studied.
After the transcriptome analysis and multi-omics analysis, clinical laboratory examination results from a multi-center cohort of 1219 patients were utilized to validate the transcriptional findings and for the prognostic model constructions.

first: Zhaoming

first: Cheng


title: The novel peptide ScrA acts through the SaeRS two component system to regulate virulence gene expression in Staphylococcus aureus

status: Public on Oct 01 2021

city: Athens

first: Ronan

middle: Kevin

last: Carroll

state: OHIO

address: 107 Irvine Hall

department: Biological Sciences

institute: Ohio University

summary: Staphylococcus aureus is a Gram-positive opportunistic pathogen, which is carried by approximately 30 % of the population at any time. In addition to being a commensal S. aureus can cause an array of infections, ranging from mild skin and soft tissue infections to life threatening endocarditis and septicemia. S. aureus encodes a variety of virulence factors that facilitate its pathogenic lifestyle. Genes encoding these virulence factors are under tight control by a complex regulatory network, which includes, sigma factors, sRNAs, and protein-based systems, such as Two-Component Systems (TCS). Previous work in our lab demonstrated that overexpression of the sRNA tsr37 leads to an increase in cellular aggregation in the absence of host serum. We determined that the clumping phenotype was dependent on a previously unannotated 88 amino acid protein encoded within the tsr37 sRNA transcript (which we named ScrA for S. aureus clumping regulator A).  In addition to increased clumping, overexpression of ScrA also leads to increased biofilm formation. To investigate the mechanism of action of ScrA we performed mass spectrometry proteomics and RNA-sequencing in the ScrA overexpressing strain. A variety of virulence factors, including several surface adhesins were upregulated while several proteases were downregulated. Moreover, results showed a significant upregulation of the SaeRS two component system, suggesting that ScrA is influencing SaeRS activity. We go on to demonstrate that overexpression of ScrA in a saeR mutant abrogates the clumping/biofilm phenotypes confirming that ScrA functions via the Sae system. Finally, we identified the ArlRS TCS as a potential positive regulator of scrA expression. Collectively our results show that ScrA is an activator of the SaeRS system and suggests that ScrA may act as an intermediary between the ArlRS and SaeRS systems.

overall_design: Six data sets in total.  Three biological replicates from wild type S. aureus cells containing the pMK4 empty vector, and three biological replicates from the wild type overproducing scrAB

first: Marcus

last: Wittekind

first: Andrew

last: Frey

first: Paul

last: Briaud

last: Wiemels

first: Lindsey

middle: N

last: Shaw

middle: K