title: The helicase domain of Dicer ensures essential accuracy of miRNA biogenesis in mice

first: Filip

last: Horvat

address: Videnska 1083

institute: Institute of Molecular Genetics of the ASCR

summary: Dicer ribonucleases, which generate small RNAs for the RNA interference (RNAi) and microRNA (miRNA) pathways, often have an N-terminal DExD helicase subdomain (also called HEL1). In the mammalian Dicer, HEL1 inhibits RNAi while it appears unnecessary for miRNA biogenesis. To determine its functional significance, we genetically eliminated HEL1 from Dicer in mice. We observed embryonic growth retardation, defects in the cardiopulmonary system, and perinatal lethality. HEL1 suppresses biogenesis of mirtrons, a non-canonical low-abundant class of miRNAs, and is required for high-fidelity cleavage and strand selection during biogenesis of canonical miRNAs. The HEL1 domain itself is essential rather than its helicase activity, because mutations of critical catalytic amino acids do not affect mouse viability or fertility and have minimal impact on miRNA biogenesis. Therefore, HEL1 is a critical structural component of the mammalian Dicer, supporting its role of a conserved structural “mold” that ensures high-fidelity processing and adaptive evolution of mammalian miRNA precursors.

overall_design: Bulk small RNA-seq of 8 mouse E15.5 embryo samples:  - 3x WT  - 5x DicerX homozygotes

first: Petr

last: Svoboda

first: Radek

last: Malik

first: Eliska

last: Taborska


title: MYC Deregulation and PTEN Loss Model Tumor and Stromal Heterogeneity of Aggressive Triple-Negative Breast Cancer

status: Public on Oct 17 2022

city: Portland

first: Zinab

last: Doha

state: OR

address: 2730 S MOODY AVE

country: USA

institute: Oregon Health & Science University

type: Expression profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: DNA sequencing for Round 5 of the pHLA-A2 yeast display library selection for MA2 Fab

status: Public on Oct 09 2022

city: Stanford

first: Xinbo

last: Yang

state: CA

address: 279 Campus Drive

department: MCP

institute: Stanford University

overall_design: A TCR mimic antibody Fab fragment was selected on a HLA-A2 peptide library displayed on yeast for cross-reactivity check

first: K

middle: C

last: Garcia


title: Influenza virus transcription and progeny production are poorly correlated in single cells

status: Public on Oct 08 2022

city: Seattle

first: Jesse

last: Bloom

state: WA

address: 1100 Fairview Ave N, room B3-123

institute: Fred Hutchinson Cancer Center

summary: The ultimate success of a viral infection at the cellular level is determined by the number of progeny virions produced. However, most single-cell studies of infection quantify the expression of viral transcripts and proteins, rather than the amount of progeny virions released from infected cells. Here we overcome this limitation by simultaneously measuring transcription and progeny production from single influenza-virus-infected cells by embedding nucleotide barcodes in the viral genome. We find that viral transcription and progeny production are poorly correlated in single cells. The cells that transcribe the most viral mRNA do not produce the most viral progeny, and often represent aberrant infections that fail to express the influenza NS gene. However, only some of the discrepancy between transcription and progeny production can be explained by viral gene absence or mutations: there is also a wide range of progeny production among cells infected by complete unmutated virions. Overall, our results show that viral transcription is a relatively poor predictor of an infected cell’s contribution to the progeny population.

sample_organism: Influenza A virus (A/California/04/2009(H1N1))

overall_design: We performed single-cell RNA sequencing of influenza-infected cells. The influenza virus library we used contained nucleotide barcodes that linked the infected cell to the progeny it produced. We quantified the physical progeny produced by infected cells by sequencing viral barcodes from the supernatant. We quantified infectious progeny produced by sequencing viral barcodes from a new set of cells infected with the supernatant. We also sequenced the full-length viral transcripts in the single-cell cDNA library using long-read sequencing.

first: David

middle: J

last: Bacsik

first: Bernadeta

last: Dadonaite

first: Andrew

last: Butler

first: Allison

last: Greaney

first: Nicholas

middle: S

last: Heaton

middle: D


title: Epigenome analysis and Gene expression analysis of hESCs undergoing neuronal differentiation

status: Public on Oct 13 2022

city: Oslo

first: Ragnhild

last: Eskeland

address: Sognsvannsveien 9

department: Institute of Basic Medical Sciences

country: Norway

institute: University of Oslo

type: Methylation profiling by genome tiling array

type: Genome binding/occupancy profiling by high throughput sequencing

overall_design:
Refer to individual Series
GSE192854
GSE192855
GSE192856
GSE192857


title: Epigenome analysis of hESCs undergoing neuronal differentiation [methylation array]

summary: Genome wide DNA methylation profiling of human embryonic stem cells (hESCs) at day 0, and day 7, 13 and 20 of neuronal differentiation. The Illumina Infinium MethylationEPIC_v-1-0_B3 was used to obtain DNA methylation profiles accross approximately 850k CpGs in differentiating cells. Samples included 6 day 0 replicates, 6 day 7 replicates, 4 day 13 replicates and 6 day 20 replicates.

overall_design: Bisulphite converted DNA from the 22 samples were hybridised to the Illumina Infinium MethylationEPIC BeadChip

first: Mari

last: Spildrejorde

first: Athina

last: Samara

first: Martin

last: Falck

first: Ankush

last: Sharma

first: Magnus

last: Leithaug

first: Stefania

last: Modafferi

first: Kristina

last: Gervin

first: Robert

last: Lyle


title: Single-cell ATAC-seq analysis of hESCs undergoing neuronal differentiation [scATAC-seq]

summary: Genome-wide gene expression profiling of hESCs undergoing neuronal differentiation at four distinct time-points. hESCs are differentiated using a novel protocol, and day 0, 7, 13 and 20 were charachterized.

overall_design:
Genome wide gene expression profiling of (n= 19) samples from human embryonic stem cells (hESCs) at day 0 (n=5), and day 7(n = 6), 13 (n= 4) and 20 (n=4) of neuronal differentiation

**Raw data are not provided as they can not be shared due to the material transfer agreement**

**Please note that processed data files have been replaced on Dec 3, 2022, as the previous data were not in a usable form for certain tools***

first: Pål

middle: M

last: Bjørnstad


title: Gene expression analysis of hESCs undergoing neuronal differentiation [RNA-seq]

overall_design:
Genome wide gene expression profiling of (n= 19) samples from human embryonic stem cells (hESCs) at day 0 (n=5), and day 7(n = 6), 13 (n= 4) and 20 (n=4) of neuronal differentiation
**Raw data are not provided as they can not be shared due to the material transfer agreement**


title: Fetal origin of sex-bias brain aging [RNA-seq]

status: Public on Oct 12 2022

city: Columbia

first: Susanta

middle: K.

last: Behura

state: Missouri

address: 920 East Campus Drive

department: Division of Animal Sciences

institute: Univeristy of Missouri

summary: In this study, gene expression of brain from postnatal (day 5) and aging (week 70) mice (C57BL/6J) was profiled. The data was used to infer transcriptional network of genes associated with epigenetic clock and GnRHR pathway in the brain. The results of this study suggested that brain aging originated early-in life.

overall_design: RNA-seq of C57BL/6J mice (postnatal day 5 and week 70) brain.

first: Maliha

last: Islam

first: Monica

last: Strawn

middle: K


title: Single-nuclei RNA sequencing (snRNA-seq) uncovers trophoblast cell types and lineages in the mature bovine placenta

status: Public on Oct 05 2022

city: Pullman

first: Kimberly

last: Davenport

address: 100 Dairy Rd

department: Animal Science

institute: Washington State University

summary: Ruminants have a semi-invasive placenta, which possess highly vascularized placentomes formed by maternal endometrial caruncles and fetal placental cotyledons and required for fetal development to term. The synepitheliochorial placenta of cattle contains at least two trophoblast cell populations, including uninucleate (UNC) and binucleate (BNC) cells that are most abundant in the cotyledonary chorion of the placentomes. The interplacentomal placenta is more epitheliochorial in nature with the chorion developing specialized areolae over the openings of uterine glands. Of note, the cell types in the placenta and cellular and molecular mechanisms governing trophoblast differentiation and function are little understood in ruminants. To fill this knowledge gap, the cotyledonary and intercotyledonary areas of the mature day 195 bovine placenta were analyzed by single nuclei analysis. Single-nuclei RNA-seq analysis found substantial differences in cell type composition and transcriptional profiles between the two distinct regions of the placenta. Based on clustering and cell marker gene expression, five different trophoblast cell types were identified in the chorion, including proliferating and differentiating UNC and two different types of BNC in the cotyledon. Cell trajectory analyses provided a framework for understanding the differentiation of trophoblast UNC into BNC. The upstream transcription factor binding analysis of differentially expressed genes identified a candidate set of regulator factors and genes regulating trophoblast differentiation. This foundational information is useful to discover essential biological pathways underpinning the development and function of the bovine placenta.

overall_design: Nuclei were isolated and libraries prepared following the 10X Genomics platform protocols

first: M Sofia

last: Ortega

first: Hongyu

last: Liu

first: Eleanore

middle: V

last: O'Neil

last: Kelleher

first: Wesley

last: Warren

first: Thomas

middle: E

last: Spencer


title: RNAseq analysis of a Drosophila mitochondrial complex I deficiency model

status: Public on Oct 07 2022

city: London

first: Joseph

middle: M.

last: Bateman

state: (Click to Select US State)

address: Guy's campus

country: United Kingdom

institute: King's College London

summary: RNAseq was performed from Drosophila head tissue of a mitochondrial complex I deficiency model. The NDUFS1 homolog ND-75 was knocked down in Drosophila neurons using nSybGal4. Heads were collected from control of ND-75 knockdown flies and used for RNAseq analysis.

overall_design: nSybGal4 flies were crossed to either w[1118] control flies or ND-75 RNAi flies (HMS00853). Heads were collected from 20 progeny for each genotype with 4 biological replicates.

first: Lucy

last: Granat


title: The Northern Corn Leaf Blight Resistance Gene, Ht1, Encodes an NLR Immune Receptor

status: Public on Oct 03 2022

city: Johnston

first: Shawn

last: Thatcher

state: Iowa

address: South Drive

institute: Corteva Agriscience

summary: Northern corn leaf blight (NLB), caused by the fungal pathogen Exserohilum turcicum, results significant yield reductions in infected corn. The first major locus conferring resistance to E. turcicum race 0, Ht1, was identified over 50 years ago, but despite widespread deployment the underlying gene has remained unknown. We employed map-based cloning to identify the Ht1 causal gene, which was found to be a coiled-coil nucleotide-binding, leucine-rich repeat (NLR) gene, termed PH4GP-Ht1. Transgenic testing confirmed that addition of the native PH4GP-Ht1 sequence to the susceptible maize variety PH184C resulted in resistance to E. turcicum race 0. A survey of the maize NAM genomes revealed that susceptible Ht1 alleles had very low to no expression, but overexpression of the susceptible B73 allele did not result in resistant plants, indicating that relatively minor protein sequence variations may underlie the resistance phenotype. Modeling of the PH4GP-Ht1 protein indicated that it has structural homology to the Arabidopsis NLR resistance gene ZAR1, and likely forms a similar homo-pentamer structure following activation. RNA-seq data from an infection time course revealed that one week after inoculation there was a threefold reduction in fungal biomass and a dramatic increase in DEGs when comparing mock to inoculated PH4GP-Ht1 transgenic plants and null plants. These results demonstrate that the NLR PH4GP-Ht1 is the causal gene underlying the NLB resistance phenotype of Ht1.

overall_design: RNA-seq quantification of maize plants inoculated with northern leaf blight


title: RNAseq expression libraries from Mycobacterium abscessus with deletion of the sRNA B11

city: Worcester

first: Scarlet

middle: Sara

last: Shell

state: Massachusetts

address: 60 Prescott St, WPI

department: Biology and Biotechnology

institute: Worcester Polytechnic Institute

summary: WT M. abscessus ATCC_19977 was used to construct a targeted deletion mutant lacking the sRNA B11 and a complemented version of the mutant with ectopic expression of B11 from its native promoter at the L5 site. The deletion mutant was also complemented with versions of B11 that lacked a single C from the first loop or had an extra C in the second loop. All strains were grown to log phase and the extracted RNA was used to perform expression profiling by RNAseq.

overall_design: Triplicate cultures were grown to mid-log phase in 7H9 supplemented with glycerol, Tween 80, and ADC. RNA was extracted from each cultured, subject to rRNA depletion, and used to contruct Illumina RNAseq libraries.

first: Daniel

last: Barkan

first: Michal

last: Bar-Oz

first: Maria

middle: N

last: Alonso

last: Martini


title: C-section delivery related high sensitivity to inflammation in mice is unchained by gut barrier-microbiota imbalances in the early life

status: Public on Oct 02 2022

city: Caldes de Montbui

first: Yuliaxis

last: Ramayo Caldas

state: Barcelona

address: Torre Marimon

country: Spain

institute: IRTA

summary: The main goal of this study is to decipher the role of CSD in the early-life gut microbiota-barrier alterations and its links with later-life risks of intestinal inflammation

overall_design: Total RNA was isolated from the colon samples using RNeasy Mini Kit, according to manufacturer's instructions. The RNA integrity was verified in Bioanalyzer 2100 with RNA 6000 Nano chips (Agilent Technologies). Only samples that have RNA. To identify the differential expressed genes between CSD and VD samples, we fit a linear model for each gene using the eBayes function from the limma R package, setting the sex and the delivery mode as fixed effects integrity >9 were used for the study.

first: Mélina

last: Gallopin

first: Rebeca

last: Martin-Rosique


title: The loss of Nudt15 thiopurine detoxification enhances direct DNA damage in hematopoietic stem cells (HSCs)

status: Public on Oct 04 2022

city: Otsu

first: Noriaki

last: Yamashita

state: Shiga

address: seta-tsukinowa

department: Department of Medicine

country: Japan

institute: Shiga University of Medical Science

summary: The kinetics of HSCs after 6-MP administration were examined by flow cytometry analysis, and genes differentially expressed between HSCs from Nudt15+/+ mice and HSCs from Nudt15R138C/R138C mice were identified by RNA-sequencing before the appearance of 6-MP-induced HSC damage.

overall_design: HSCs extracted from Nudt15+/+ and Nudt15R138C/R138C mice treated with 6-MP were analyzed by comparative gene expression profiling using RNA-seq.

first: Masahiro

last: Kawahara

first: Takayuki

last: Imai

first: Goichi

last: Tatsumi

first: Ai

last: Asai-Nishishita

first: Atsushi

last: Nishida

first: Akira

last: Andoh


title: Single-cell multi-omics analyses in the DILfrequency clinical trail samples

city: Oxford

first: Ricardo

middle: C.

last: Ferreira

address: Wellcome Trust Centre For Human Genetics, Roosevelt Drive

department: Wellcome Trust Centre for Human Genetics

institute: University of Oxford

summary: Despite early clinical success, the mechanisms of action of low-dose interleukin-2 (LD-IL-2) immunotherapy remain only partly understood. This dataset was generated using samples from the DILfrequency clinical trail, to examine the effects of interval administration of low-dose recombinant IL-2 (iLD-IL-2) using high-resolution, single-cell multi-omics.

overall_design: Thirteen adult T1D patients were recruited and treated with recombinant IL-2 every three days for a period of 30 days. For each participant, three longitudinal blood samples were taken on Day 0, Day 27 and Day 55, respectively. Selected immune cell subsets were isolated from each sample by Fluorescence-activated Cell Sorting (FACS), and analysed with BD Rhapsody single-cell sequencing platform using custom mRNA and AbSeq panels. All conclusions related to COVID-19 in the manuscript were made by comparing previously published data with the current dataset, which by itself contains no COVID-19 patients

first: Jia-Yuan

last: Zhang

first: Fiona

last: Hamey

first: Dominik

last: Trzupek

first: Marius

last: Mickunas

first: Mercede

last: Lee

first: Leila

last: Godfrey

first: Jennie

middle: H

last: Yang

first: Marcin

middle: L

last: Pekalski

first: Jane

last: Kennet

first: Frank

last: Waldron-Lynch

first: Mark

last: Evans

first: Timothy

middle: I

last: Tree

first: Linda

last: Wicker

first: John

middle: A

last: Todd


title: Skipper analysis of RNA-protein interactions highlights depletion of genetic variation in translation factor binding sites

city: La Jolla

first: Gene

middle: W

last: Yeo

address: 2880 Torrey Pines Scenic Dr

department: Cellular & Molecular Medicine

institute: University of California San Diego

summary: Technology for crosslinking and immunoprecipitation followed by sequencing (CLIP-seq) has identified the transcriptomic targets of hundreds of RNA-binding proteins in cells. To improve the power of existing and future CLIP-seq datasets, we introduce Skipper, an end-to-end workflow that converts unprocessed reads into annotated binding sites using an improved statistical framework. Compared to existing methods, Skipper on average calls 3.1-4.2 times more transcriptomic binding sites and sometimes >10 times more sites, providing deeper insight into post-transcriptional gene regulation. Skipper also calls binding to annotated repetitive elements and identifies bound elements for 99% of enhanced CLIP experiments. We perform nine translation factor enhanced CLIPs and apply Skipper to learn determinants of translation factor occupancy including transcript region, sequence, and subcellular localization. Furthermore, we observe depletion of genetic variation in occupied sites and nominate transcripts subject to selective constraint because of translation factor occupancy. Skipper offers fast, easy, customizable analysis of CLIP-seq data.

overall_design: eCLIP of ribosome proteins and EIFs in K562 cells, in duplicate

first: Evan

last: Boyle

first: Hsuan-Lin

last: Her

first: Jasmine

middle: R

last: Mueller

first: Grady

middle: G

last: Nguyen


title: An overlapped natural antisense lncRNA FCER1A-AS controls anaphylactic reaction by promoting FcεRIα expression

city: shanghai

first: ruoyu

last: tang

address: si ping road

country: China

institute: tongji university

summary: Functioned as α-subunit of the high-affinity immunoglobulin E receptor (FcεRIα), FcεRIα plays a central role in the pathogenesis of Ig-E-mediated allergy and other IgE-related disorders. FcεRIα is normally expressed only in limited spectrum of cells like basophils and mast cells, but the mechanism of controlling FcεRIα expression in these cells is less well understood. In this study, we found fully overlapped natural antisense transcript (NATs) of FcεRIα (FCER1A-AS) is co-expressed with cognate sense transcript (FCER1A-S) in IL-3 induced FcεRIα-expressing cells or in high FcεRIα-expressing cell line MC/9. When FCER1A-AS is selectively knocked down by CRISPR/RfxCas13d (CasRx) approach in MC/9, expression of mRNA and proteins of FCER1A-S is also markedly decreased. Furthermore, deficiency of FCER1A-AS along with lack of FCER1A-S expression is found in two different lines of gene-targeted mice in which FCER1A locus is disturbed at different sites. More importantly, the FCER1A-AS-deficient homozygous mice display similarly diminished anaphylactic reaction as FCER1A gene knockout mice. Thus, we uncovered in this investigation that the expression of FCER1A-S is positively regulated by co-expressed fully overlapped antisense transcript.

overall_design: RNA-seq in MC/9 cell line, IL-3 treated bone marrow cells, using Illumina Hiseq 4000 platform

first: Ruoyu

last: Tang

first: Xiao-ping

last: Chen


title: Transcriptomic data from cultured human fetal lung tip-derived organoids treated with MAPK inhibitors or AKT inhibitor

status: Public on Sep 30 2022

city: Cambridge

first: Shuyu

last: Liu

address: Tennis Court

department: The Gurdon Institute

institute: University of Cambridge

summary: Human fetal lung tip cells were purifed from developing human lungs at pseudoglandular in vitro cultured as organoids. Whole transcriptomic data for 3 organoid lines received different signalling inhibitors were profiled  by RNA seq.

overall_design: Human lung tip organoids of three conditions from three biological replicates

first: Emma

last: Rawlins


title: Apolipoprotein A1-Manipulated Cholesterol Efflux Subverts the Phagocytic Fragility of TAMs and Improves Oncolytic Viro-Immunotherapy in Glioblastoma [BMDMs RNA-seq]

city: Nanjing

first: Shiqun

last: Wang

state: Jiangsu

address: 22 Hankou Road

institute: Nanjing university

summary: We found that TAMs in the glioblatoma (GBM) tumor microenvironment are enriched for cholesterol and highly express ABCA1/G1. To investigate the biological effects of enhancing cholesterol efflux of TAMs in GBM, we constructed APOA1-overexpressing GL261 cell line. We harvested tumor tissue and sorted these TAMs by anti-mouse F4/80 magnetic beads 17 days after intracranial transplantation of GL261-APOA1 cell line and control cells in immunocompetent C57 mice. Samples were subjected to transcriptome sequencing.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for BMDMs treated with vehicle (CTRL, n=3), doxycycline (DOX, n=3), or 7-ketocholesterol (7K-Cho, n=3)

first: Wang

last: Shiqun

first: Zuo

last: Shuguang

first: Wu

last: Jingyi

first: Kong

last: Lingkai


title: Bifidobacterium longum subsp. infantis transcriptomes in response to various nitrogen sources

city: Amherst

first: David

last: Sela

address: 102 Holdsworth Way

department: Food Science

institute: University of Massachusetts Amherst

summary: The purpose of this project was to determine the whole transcriptome response of Bifidobacterium longum subsp. infantis to human milk urea compared to complex nitrogen and L-cysteine.

overall_design: RNA was isolted and sequenced from three strains of Bifidobacterium longum subsp. infantis grown on modified MRS supplemented with urea, complex nitrogen and L-cysteine as a primary nitrogen source. Biological duplicate was performed for each bacteria strain with each treatment.

first: Xiaomeng

last: You


title: Disseminative Recurrence Signature for hepatocellular carcinoma from non-alcoholic fatty liver disease

status: Public on Sep 29 2022

city: Dallas

first: Yujin

last: Hoshida

state: TX

address: 5323 Harry Hines Blvd

institute: University of Texas Southwestern Medical Center

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

overall_design: Refer to individual Series


title: Knockout of PP1 in Leishmania major reveals a critical role for protein phosphatase 1 during RNA polymerase II transcription termination

status: Public on Oct 01 2022

city: Athens

first: Haidong

last: Yan

state: Georgia

address: 220 Mark Twain Cir Apt D

institute: University of Georgia

summary: Base J is a modified DNA base that is enriched at RNA polymerase II termination sites. We previously identified a complex in Leishmania major and T. brucei composed of PNUTS, PP1, Wdr82 and a J-binding protein (JBP3). We show that deletion of PP1 in L. major leads to readthrough transcription and expression of downstream genes.

overall_design: The role of PP1in regulating transcription termination was investigated using inducible KO of PP1 in L. major. We used 6 RNA seq libraries to determine gene expression changes following the loss of PP1.

first: Robert

last: Sabatini

first: Rudo

last: Kieft

middle: J

last: Schmitz


title: DYRK2 gene transfer suppresses liver tumorigenesis

status: Public on Sep 24 2022

city: Nishi-Shimbashi

first: Hiroshi

last: Kamioka

state: Tokyo

department: Gastroenterology and Hepatology

institute: Jikei University School of Medicine

summary: We generated liver-specific Dyrk2 knockout mice mating Dyrk2 flox mice with Alb-cre mice and co-introduced SB13-transposase-, myrAkt-, Myc- and mutant Hras-expressing plasmids with either HA- or Dyrk2-expressing plasmid into the knockout mice by HTVi. Dyrk2-expressing suppressed tumorigenesis compared with HA-expressing.

overall_design: Total RNAs from Dyrk2-expressed HCC in 3 Dyrk2 LKO mice were compared with Total RNAs from HA-expressed HCC in 3 Dyrk2 LKO mice.

first: Satomi

last: Yogosawa

first: Tsunekazu

last: Oikawa

first: Kiyotsugu

last: Yoshida


title: Variation in histone configurations correlates with gene expression across nine inbred strains of mice

status: Public on Sep 25 2022

city: Bar Harbor

first: Petko

last: Petkov

state: ME

address: 600 Main St

institute: The Jackson Laboratory

type: Methylation profiling by high throughput sequencing


title: The 3D enhancer network of the developing T cell genome is controlled by SATB1 [RNA-seq]

status: Public on Sep 23 2022

city: Tampa

first: Tomas

last: Zelenka

state: Florida

address: 12902 Magnolia Drive

department: Immunology

institute: H. Lee Moffitt Cancer Center & Research Institute

summary: Mechanisms of tissue-specific gene expression regulation, particularly via spatial coordination of gene promoters and their regulatory elements are poorly understood. Here we investigated the 3D genome organization of developing murine T cells. We identified a tissue-specific genome organizer SATB1 as a factor enriched at the anchors of promoter-enhancer chromatin loops. To unravel its functions in T cells, we generated Satb1fl/flCd4-Cre+ (Satb1 cKO) conditional knockout animals. Satb1 cKO animals suffer from severe autoimmunity so we sought to investigate a potential link between the autoimmunity and putatively deregulated nuclear architecture caused by SATB1 depletion.  This series of RNA-Seq experiments is a part of SuperSeries including also ATAC-Seq, Hi-C and HiChIP experiments to fully understand the deregulation of Satb1 cKO thymocytes and to unravel the roles of SATB1 in T cell chromatin organization. RNA-Seq experiments supported the repressive nature of Satb1 cKO nuclear environment and together with the other datasets it showed that SATB1 functions primarily as an activator. SATB1 mediates promoter-enhancer chromatin loops affecting a number of master regulator genes whose deregulation in knockout animals may comprise a cell-intrinsic mechanism of the autoimmunity. Our findings indicate a possible existence of a special class of genome organizers controlling tissue and/or time-specific transcriptional programs via spatial chromatin arrangements that are complementary to the function of conventional and ubiquitously expressed genome organizers.

overall_design: Three biological replicates from each wild type and conditional knockout Satb1fl/flCd4-Cre+ mice were analyzed. Total RNA was isolated from thymocytes and depleted from ribosomal RNA. Strand-specific total RNA libraries were created and sequenced.

first: Antonios

last: Klonizakis

first: Charalampos

last: Spilianakis


title: RNAseq of CD14 T cells from female Rheumatoid arthritis patients [NeumRA_CD14]

status: Public on Sep 27 2022

city: Gothenburg

first: Maria

last: Bokarewa

state: VG

address: Guldhedagatan 10A

department: Rheumatology and Inflammation Research

country: Sweden

institute: Gothenburg University

summary: RNAseq of CD14 cells from 60 female RA patients activated with LPS for 2 hours. Patients were collected crossectionally from the Rheumatology clinic during 2019-2020. Age md 64, range 23-76 years, Disease duration md 10, range 1-45 years.

overall_design: 60 women with  rheumatoid arthritis, CD4 cells  from human PBMC isolated by positive selection on Easysep (cat. #17858), stimulated with LPS (Sigma Aldrich L2880, 5ug/ml) for 2h

first: Karin

middle: M

last: Andersson

first: Malin

middle: C

last: Erlandsson

first: Nina

last: Oparina

first: Eric

last: Malmhäll-Bah


title: Dynamic gene expression in Schwann cell for regulating myelination

status: Public on Sep 21 2022

city: Nantong

first: Yun

last: Gu

address: 19 Qixiu Road

department: Jiangsu Key Laboratory of Neuroregeneration

institute: Nantong University

summary: To obtain the dynamic gene expression of myelinating Schwann cells, we have employed gene expression profiling microarray as a discovery platform to analyze the gene expression of Schwann cells in different stages of myelination in an DRG neuron and SC co-culture myelinating model. Rat Schwann cells and dorsal root ganglion (DRG) neurons were cocultured and induced myelination in DMEM medium containing 15% FBS, 50 ng/ml NGF and 50 μg/ml L-ascorbic acid for 21d.  During the co-cultivation, myelinating SCs at different stages dissected by Laser microdissection (LMD) in myelination model (i.e. co-culture 1d, 3d, 7d, 14d, 21d), the Schwann cells without co-culture as control samples (i.e. co-culture 0d).  The results from Euclidean distance matrix, principal component analysis, and hierarchical clustering indicated that 2 nodal transitions in temporal gene expressions could segregate 3 distinct transcriptional phases within the period of DRG/SC co-culture 21 days. The 3 phases were designated as “premyelination”, “myelination”, and “mature phase”, respectively, by referring to morphological observation of post co-culture changes and gene ontology (GO) analysis.

overall_design: Dynamic gene expression of myelinating Schwann cells were measured at co-culture 0d, 1d, 3d, 7d, 14d, 21d.  Three independent experiments were performed at each time using different donors for each experiment.

last: GU

first: Gang

last: Chen


title: The 3D enhancer network of the developing T cell genome is shaped by SATB1

status: Public on Sep 22 2022

summary: Mechanisms of tissue-specific gene expression regulation via 3D genome organization are poorly understood. Here we uncover the regulatory chromatin network of developing T cells and identify SATB1, a tissue-specific genome organizer, enriched at the anchors of promoter-enhancer loops. We have generated a T-cell specific Satb1 conditional knockout mouse which allows us to infer the molecular mechanisms responsible for the deregulation of its immune system. H3K27ac HiChIP and Hi-C experiments indicate that SATB1-dependent promoter-enhancer loops regulate expression of master regulator genes (such as Bcl6), the T cell receptor locus and adhesion molecule genes, collectively being critical for cell lineage specification and immune system homeostasis. SATB1-dependent regulatory chromatin loops represent a more refined layer of genome organization built upon a high-order scaffold provided by CTCF and other factors. Overall, our findings unravel the function of a tissue-specific factor that controls transcription programs, via spatial chromatin arrangements complementary to the chromatin structure imposed by ubiquitously expressed genome organizers.

overall_design: This SuperSeries is composed of the SubSeries listed below. Please, refer to individual SubSeries.


title: Identification and characterization of sugar regulated promoters in Chaetomium thermophilum

status: Public on Sep 26 2022

city: Heidelberg

first: Ed

last: Hurt

address: Im Neuenheimer Feld 328

country: Germany

institute: BZH

summary: The thermophilic fungus Chaetomium thermophilum has been successfully used in the past for biochemical and high resolution structural studies of protein complexes, but subsequent functional analysis of these assemblies were hindered due to the lack of genetic tools in this thermophile, which are typically amenable in several other mesophilic eukaryotic model organisms, in particular the yeast Saccharomycers cerevisiae. Hence, we aimed to develop a regulatable gene-expression system in C. thermophilum, which might facilitate such in vivo studies, based on what we know about the galactose-inducible GAL promoter in yeast. To identify sugar-regulatable promoters in C. thermophilum, we performed comparative xylose- versus glucose-dependent gene expression studies, which uncovered a number of enzymes induced by xylose but repressed by glucose. Subsequently, we cloned the promoters of the two most stringently regulated genes, the xylosidase-like gene (XYL) and xylitol dehydrogenase (XDH), obtained from this genome-wide analysis in front of the thermostable YFP (yellow fluorescent protein) reporter. In this way, we could demonstrate xylose-dependent YFP expression by either western blotting or life cell imaging fluorescence microscopy. Prompted by these results, we finally expressed a well-characterized dominant-negative ribosome assembly factor mutant, rsa4 E117>D, under the control of the XDH promoter, which allowed us to induce a nuclear export defect of the pre-60S subunit when C. thermophilum cells were grown in xylose but not glucose containing medium. Altogether, our study recognized xylose-regulatable promoters in Chaetomium thermophilum, which may foster functional studies of genes of interest in this thermophilic eukaryotic model organism.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for Chaetomium thermophilum cells exposed to glucose (G) or xylose (X) as sole carbon source in comparison to a carbon depleted refernece medium (R).

first: Sven

last: Reislöhner

first: Geza

last: Schermann

first: Max

last: Kilian

first: Daniela

last: S Muñoz

first: Christian

last: Zimmerli

first: Nikola

last: Kellner

first: Jochen

last: Baßler

first: Michael

last: Brunner


title: RNA-seq Files : The Hypoxia Response Pathway Promotes PEP Carboxykinase And Gluconeogenesis In C. elegans

status: Public on Sep 19 2022

city: Piscataway

first: Christopher

last: Rongo

state: NJ

address: 190 Frelinghuysen Road, #163

department: Waksman Institute

institute: Rutgers University

summary: RNA was isolated from L4 stage animals for the following genotypes: N2, hif-1(ia4), egl-9(sa307), hif-1(ia4);egl-9(sa307) grown at 20C. Total RNA was isolated and used to prepare libraries using the Illumina Truseq with polyA selection. Libraries were sequenced across two lanes on an Illumina HiSeq2000 (GeneWiz) or an Illumina HiSeq 2500 in Rapid Run Mode (RUCDR).

overall_design: Developmentally synchronized animals were obtained by hypochlorite treatment of gravid adults and embryos hatched overnight for 15-17 hours in M9.  Starvation-arrested L1s were plated on NGM plates and grown at 20°C until L4 stage. Total RNA was isolated from animals using Trizol (Invitrogen) combined with Bead Beater lysis in four biological replicates for each genotype. An mRNA library (single-end, 50-bp reads) was prepared for each sample/replicate using Illumina Truseq with PolyA selection (Genewiz or RUCDR).  Libraries were sequenced across two lanes on an Illumina HiSeq2000 (GeneWiz) or an Illumina HiSeq 2500 in Rapid Run Mode (RUCDR).

first: Mehul

last: Vora

first: Stephanie

last: Pyonteck


title: Propionibacterium freudenreichii MJ2 inhibits RANKL-induced osteoclast differentiation and ameliorates rheumatoid arthritis in collagen-induced arthritis model

status: Public on Sep 18 2022

city: seoul

first: jiah

last: yeom

address: Anamro 145

country: South Korea

institute: Korea university

summary: Osteoclast differentiation is crucial for bone absorption and osteoclast is involved in bone destruction in rheumatoid arthritis. The aim of this study was to investigate the inhibitory effect of MJ2 on osteoclast differentiation and to elucidate its mechanism. Murine macrophage cell line, Raw 264.7 cells and collagen-induced arthritis mouse model were used for in vitro and in vivo study, respectively. MJ2-treated cells significantly inhibited osteoclast differentiation and decreased arthritic score. Surface proteins (SP) extracted from MJ2 also showed inhibitory effect on osteoclast differentiation by upregulating lipocalin 2 (lcn2) expression. Specifically, heat shock protein 60 (hsp60) in SP was revealed as an active component of MJ2. Hsp60 inhibited binding of receptor activator of nuclear factor-κB ligand (RANKL) to receptor activator of nuclear factor κB (RANK). In conclusion, MJ2 inhibited osteoclast formation and differentiation through lcn2 and RANKL-binding property and the effective component of MJ2 might be hsp60 present in surface layer.

overall_design: 3 samples in triplicate, total 9 samples; negative control, MJ treated group, and SF treated group in raw 264.7 cell

first: S

last: Ma

first: J

last: Yeom

first: Y

last: Lim


title: Gene therapy using genome-edited human iPS cell-derived neural stem cells overcomes refractory course of invasive glioma stem cells

status: Public on Sep 16 2022

city: Stanford

first: Kent

last: Imaizumi

address: 318 Campus Drive

institute: Stanford University

summary: Spatiotemporal analyses using brain slice culture and brain clearing demonstrated that human induced pluripotent stem cell-derived neural stem cells (iPSC-NSCs) possess higher tumor-trophic migratory capacity than fetal NSCs, adipose tissue and bone marrow derived mesenchymal stem cells (MSCs). NSCs expressing prodrug converting enzyme fusion gene exhibited strong anti-tumor effect for glioma stem cell in vivo models. The present research concepts may become a platform of cell-based gene therapy for glioma.

overall_design: In vitro-cultured iPSC-NSCs, fetal NSCs, MSCs,  glioma cell lines, glioma stem cell lines were analyzed for RNA-seq.

first: Ryota

last: Tamura

first: Masahiro

last: Toda


title: Systematic analysis of circadian gene expression mediated by epigenetic modification and 3D genome organization in Rice [ChIP-Seq]

status: Public on Sep 15 2022

city: Wuhan

first: guoting

last: chen

address: 1 Shizishan Street, Hongshan District

institute: National Key Laboratory of Crop Genetic Improvement

summary: Plants are extremely sensitive to and can re-output rhythm by light signals during photoperiod cues. The circadian transcriptome and epigenetically modified rice genome exhibited distinct circadian behavioural outputs under three light signals during the photoperiod.By comparing and analysing the output circadian genes under different light signals, we detected that constant light (LL) shortens the day-night cycle, while constant night (DD) suppresses the oscillation amplitude. The circadian changing lncRNAs at the genome-wide level that were temporally correlated with oscillating genes at proximal loci and accompanied by synchronised circadian oscillations of H3K9ac modifications. We used the Assay for Transposase Accessible Chromatin with sequencing (ATAC-seq) to profile the open chromatin regions and transcription factor (TF) footprints in rice at six time points (ZT0, ZT4, ZT8, ZT12, ZT16, and ZT20). The regulation of circadian gene expression occurs, not through temporal regulation of chromatin opening but through time-dependent binding of transcription factors in cis-regulatory elements. We mapped the 4D genome architecture of rice by employing BL-Hi-C, to capture oscillating chromatin interactions at ZT8 and ZT20. Circadian genes within the same peak phases of expression were preferentially coordinated transcription with non-circadian genes. Circadian genes at the ZT8 circadian phase tended to be enriched in ZT8-speific spatial clusters to orchestrate gene expression. Our findings contribute significantly to a more comprehensive understanding of the molecular interactions within the oscillator, and with clock-controlled pathways in rice.

overall_design: Circadian oscillations of H3K9ac modification at six time points (ZT0, ZT4, ZT8, ZT12, ZT16, and ZT20) under LL, LD, and DD conditions.

first: Ying

last: Zhang

first: Guoting

last: Chen


title: The Hypoxia Response Pathway Promotes PEP Carboxykinase And Gluconeogenesis In C. elegans


title: Systematic analysis of circadian gene expression mediated by epigenetic modification and 3D genome organization in Rice [RNA-Seq]

overall_design: Circadian gene expression analysis of RNA-seq data at six time points (ZT0, ZT4, ZT8, ZT12, ZT16, and ZT20) under LL, LD, and DD conditions.


title: Systematic analysis of circadian gene expression mediated by epigenetic modification and 3D genome organization in Rice [ATAC-Seq]

overall_design: Timing specificity of transcription factors binding may underlie circadian gene expression in rice


title: Systematic analysis of circadian gene expression mediated by epigenetic modification and 3D genome organization in Rice


title: The 3D enhancer network of the developing T cell genome is controlled by SATB1 [Hi-C]

first: Tomas

last: Zelenka

summary: Mechanisms of tissue-specific gene expression regulation, particularly via spatial coordination of gene promoters and their regulatory elements are poorly understood. Here we investigated the 3D genome organization of developing murine T cells. We identified a tissue-specific genome organizer SATB1 as a factor enriched at the anchors of promoter-enhancer chromatin loops. To unravel its functions in T cells, we generated Satb1fl/flCd4-Cre+ (Satb1 cKO) conditional knockout animals. Satb1 cKO animals suffer from severe autoimmunity so we sought to investigate a potential link between the autoimmunity and putatively deregulated nuclear architecture caused by SATB1 depletion.  This series of Hi-C and HiChIP experiments is a part of SuperSeries including also RNA-Seq and ATAC-Seq experiments to fully understand the deregulation of Satb1 cKO thymocytes and to unravel the roles of SATB1 in T cell chromatin organization. Utilizing the HiChIP data, we compared SATB1 and CTCF-mediated chromatin loops, revealing that SATB1 builds a more refined layer of genome organization upon the CTCF scaffold. Moreover, H3K27ac HiChIP and Hi-C experiments in WT and Satb1 cKO thymocytes helped us to assess the functional impact of SATB1 and its underlying genome-wide regulome. SATB1 primarily mediates promoter-enhancer loops affecting a number of master regulator genes whose deregulation in knockout animals may comprise a cell-intrinsic mechanism of the autoimmunity. Our findings indicate a possible existence of a special class of genome organizers controlling tissue and/or time-specific transcriptional programs via spatial chromatin arrangements that are complementary to the function of conventional ubiquitously expressed genome organizers.

overall_design: Two biological replicates for each sample were used. We performed SATB1 HiChIP, CTCF HiChIP (both only in WT) and H3K27ac HiChIP in WT and Satb1fl/flCd4-Cre+ murine thymocytes. Moreover, we performed Hi-C experiments in WT and Satb1fl/flCd4-Cre+ murine thymocytes. All interaction matrices are provided as well as processed HiChIP loops and binding sites of the targeted factors derived from the HiChIP datasets. For SATB1 binding site identification, we used a different HiChIP dataset from an unsuccessful HiChIP experiment with high proportion of Dangling End Pairs (rep3, rep4), which is more suitable for SATB1 peak calling.

first: Antonios

last: Klonizakis

first: Charalampos

last: Spilianakis


title: Systematic analysis of circadian gene expression mediated by epigenetic modification and 3D genome organization in Rice [Hi-C]

overall_design: Circadian oscillations of genes are synchronized with the dynamics of chromatin 3D organization


title: Establishment and characterization of patient-derived xenograft from leptomeningeal spread of a rare pediatric anaplastic pleomorphic xanthoastrocytoma (PXA) bearing a CDC42SE2-BRAF fusion.

status: Public on Sep 14 2022

city: indianapolis

first: nur

middle: p

last: Damayanti

state: Indiana

address: 980 w walnut st, R3/C343

institute: IUSM

summary:
To establish and to characterize patient derived preclinical model of rare pediatric glioma, anaplastic pleomorphic xanthoastrocytoma. The model was derived from tumor found at leptomeningeal spread site.
we perform multi omics analysis including in this file is RNA seq to asses molecular fidelity of the patient derived model ( xenograft and xenoline) compared to original tumor from patient.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for xenograft passage 1  (PDX1281) and 2 (PDX1282), xenoline (X128), normal human astrocyte and patient tumor (Pttumor)

first: Nur

middle: P


title: Worksite-based intensive lifestyle therapy has profound cardiometabolic benefits in people with obesity and type 2 diabetes

status: Public on Sep 08 2022

city: Izumo

first: Jun

last: Yoshino

state: Shimane

address: 89-1 Enya-cho

institute: Faculty of Medicine, Shimane University

summary: Weight loss and physical activity are the cornerstones of therapy for type 2 diabetes. However, providing an effective lifestyle intervention is difficult because of limited availability of reliable programs, patient inconvenience, and cost. A worksite setting provides a unique opportunity for lifestyle therapy because it reduces these barriers. We conducted an 8-month randomized controlled trial in persons with obesity and diabetes to determine the therapeutic effects and potential mechanisms of intensive-lifestyle-therapy (energy restriction and supervised exercise training) conducted at the worksite. Intensive-lifestyle-therapy resulted in marked (17%) weight loss, associated with beneficial changes in body composition, cardiorespiratory fitness, muscle strength, glycemic control, β-cell function and insulin sensitivity in the liver, adipose tissue, and skeletal muscle, despite a decrease in diabetes medication use. These beneficial effects were associated with changes in skeletal muscle (increased metabolite content and expression of genes involved in NAD biosynthesis, sirtuin signaling, and mitochondrial biogenesis and function), adipose tissue (decreased expression of genes involved in extracellular matrix remodeling), and a major plasma mediator of insulin resistance (decreased plasma PAI-1). These findings demonstrate that effective intensive-lifestyle-therapy can be implemented at the worksite, and has profound therapeutic, clinical, physiological, and cellular effects in people with obesity and type 2 diabetes.

overall_design: In this study, we evaluated the effects of standard care (SC) and intensive lifestyle therapy (ILT) treatments on gene expression profiling in skeletal muscle and subcutaneous adipose tissue obtained from people with obesity and type 2 diabetes.

first: Mihoko

first: Gordon

last: Smith

first: Richard

last: Stein

first: Dominic

last: Reeds

first: Bruce

last: Patterson

first: Bettina

last: Mittendorfer

first: Samuel

last: Klein


title: DksA acts as a transcriptional switch in stress and virulence in Acinetobacter baumannii

status: Public on Sep 13 2022

city: Würzburg

first: Lars

last: Barquist

state: Bayern

address: Josef-Schneider-Straße 2 / Bau D15

institute: Helmholtz Institute for RNA-based Infection Research

summary: Ability to redirect limiting cellular resources accurately is key to bacteria for surviving in harsh environments that they often encounter during their lifetime.  DksA, a transcriptional initiating factor, plays critical roles in regulating stress responses and antibiotic tolerance. Acinetobacter baumannii has become a major healthcare threat and responsible for both nosocomial and community acquired deadly infections worldwide. Yet, little is known about the role of DksA in A. baumannii. Here we describe a highly pleiotropic nature of DksA that it helps redirect the key metabolic pathways associated with the respiration, energy production, protein biosynthesis. Inhibition of ribosomal RNAs, ATP production by DksA is detrimental to bacteria under bacteriostatic stresses such as copper and trimethoprim. By contrast, it is required for survival in stresses that generate reactive-oxygen species such as zinc and gentamycin. Bacteria lacking DksA exhibit increase sensitivity to human serum, promote biofilm formation and capsule production. Not only does DksA show diverse phenotypes in vitro, but it also impacted on virulence in a niche specific manner during in vivo Galleria mellonella and murine infections. Our data collectively provides the detailed insight into the role of DksA in stress protection and virulence in A. baumannii and layout a roadmap for similar findings in other clinically important pathogens.

overall_design: Examination of mRNA profiles of A. baumannii wild-type and its dksA knockout mutant under copper or zinc stress stimulations.

first: Ram

last: Maharjan

first: Amy

last: Cain

first: Bart

last: Eijkelkamp


title: A single-cell transcriptome atlas of the zebrafish telencephalon

status: Public on Sep 02 2022

city: Worcester

first: Summer

last: Thyme

state: MA

address: 364 Plantation St

institute: UMass Chan Medical School

summary: Wild-type zebrafish telencephalon single-cell RNA-sequencing from 6 dpf, 15 dpf, and adult.

overall_design: 10x libraries of single cell transcriptomes

first: Shristi

last: Pandey


title: RNA sequencing of tumor tissues from 12 glioblastoma patients

status: Public on Sep 01 2022

city: Jinan

first: Gang

last: Li

state: Shandong

address: 107 Wenhua Xi Road

department: Neurosurgery

institute: Qilu Hospital of Shandong University

summary: We performed RNA sequencing on tumor samples from 12 glioblastoma patients to compare differences in gene expression between tumors

overall_design: Comparative gene expression profiling analysis of RNA-seq data for 12 glioblastoma tissues

first: Hao

last: Xue


title: Purification and SmartSeq2 single cell RNA-sequencing of patient human skeletal stem cells

city: Sacramento

first: Thomas

last: Ambrosi

state: California

address: 2700 Stockton Blvd

institute: UC Davis

summary: We have used SmartSeq2 to sequence single human skeletal stem cells (SSCs) freshly purified via FACS of tissue derived from a patient undergoing spinal fusion surgery to demonstrate this application.

overall_design: SmartSeq2 single cell RNA sequencing of 96 flow cytometrically purified single human skeletal stem cells from patient tissue derived during spinal fusion surgery.

first: Charles

middle: K

last: Chan

first: Malachia

middle: Y

last: Hoover


title: Phosphatidylinositol-Specific Phospholipase C can inhibit the proliferation of and suppress the phagocytosis of Müller cells via modulating PI3K/AKT signaling pathway

city: wenzhou

first: Bianjin

last: Sun

state: zhejiang

address: No. 270 Xueyuan West Road, Lucheng District

institute: School of Ophthalmology and Optometry and Eye Hospital, School of Biomedical Engineering, Wenzhou Medical University

summary: Transcriptome analysis showed that the PI-PLC protein is closely related to phagocytosis by tissue cells

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: We then performed gene expression profiling analysis using data obtained from RNA-seq of eyeball organization from C57/B6 mouse and human muller cell

first: Shudan

last: Lin

first: Mengmeng

last: Zheng

first: Beijia


title: Gene Expressions in OCCC using Nanostring analysis

status: Public on Sep 05 2022

city: Beijing

first: Min

last: Yin

address: Dongcheng

institute: Peking Union Medical College Hospital

summary: Gene expression of OCC according to chemotherapeutic response was analyzed using Nanostring nCounter PanCancer Pathway Panel.

overall_design: All 24 OCCC patients were divided into chemosensitive (12 cases) and chemoresistant (12 cases) groups and difference of gene expression between the groups was analyzed using customized 770 gene NanoString Panel.

first: Huimei

last: Zhou


title: Investigation of head and neck squamous carcinoma (HNSCC) spatial transcriptome evolution

status: Public on Aug 29 2022

city: Taipei

first: Chih-Hung

last: Chung

address: No.155, Sec.2, Linong Street, Taipei, 112 Taiwan (ROC)

department: Institute of Clinical Medicine

country: Taiwan

institute: National Yang Ming Chiao Tung University

summary: We collected matched pairs of primary tumor (invasive front and intra-tumor region), metastatic region and adjacent normal tissue from head and neck squamous cell carcinoma patients at the Taipei Veterans General Hospital (TVGH) for RNA sequencing analysis.

overall_design: RNA Sequencing of HNSCC pateint tumor in different part

first: Muh-Hwa

last: Yang

first: Shyh-Kuan

last: Tai


title: ChIP-Seq Files : The Hypoxia Response Pathway Promotes PEP Carboxykinase And Gluconeogenesis In C. elegans

first: Christopher

last: Rongo

summary: To identify genes directly regulated by HIF-1, we performed ChIP-seq on L4-stage egl-9(sa307); hif-1(ia4); odIs131[hif-1::gfp] animals, which have activated HIF-1 under aerobic conditions, using anti-GFP antibodies to precipitate DNA bound by HIF-1::GFP followed by high-throughput sequencing to identify peaks of reads corresponding to HIF-1 binding sites

overall_design: ChIP-seq on OR3349 (odIS131[hif-1::gfp) control animals and OR3350 (egl-9(sa307); hif-1(ia4); odIs131[hif-1::gfp]) under 21% O2, NGM media with OP50-1 as food

first: Mehul

last: Vora

first: Stephanie

last: Pyonteck

first: Valerie

last: Reinke


title: Immune microenvironment and molecular mechanism of oral lichen planus [Single cell RNA-Seq]

status: Public on Aug 24 2022

city: Chengdu

first: Hao

last: Xu

state: China

address: No.17 section3 renmin south road, chengdu

institute: Sichuan university

summary: Oral lichen planus (OLP) is a chronic inflammatory disease with various clinical subtypes. Recurrent erosion of OLP brings great physical and mental pain to patients without clear pathogenesis. Herein, this study is the first to utilize single-cell RNA sequencing combined with spatial transcriptome and bulk RNA-seq to explore the tissual microenvironments of patients within normal oral mucosa, non-erosive OLP (ENOLP) and erosive OLP (EOLP).

overall_design: We utilized five OLP samples and one normal oral mucosa donated from a volunteer to perform scRNA-seq analysis to comprehensively and accurately characterize the tissue microenvironment between normal and OLP, to deeply explore the immune mechanism of OLP erosion. Next, we utilized two OLP samples to perform spatial transcriptome analysis to reconfirm the immune mechanism of OLP erosion combined with spatial location of cell types. Finally, we established a clinical cohort of 40 participants followed up for 1 year and performed RNA-seq with these 40 samples to support the above results.

first: Qianhui

last: Shang

first: Qianming

last: Chen


title: The Translation Initiation Factor Homolog, eif4e1c, Regulates Cardiomyocyte Metabolism and Proliferation During Heart Regeneration.

status: Public on Aug 25 2022

city: Columbus

first: Joseph

middle: Aaron

last: Goldman

state: Ohio

address: 119 Rightmire Hall, 1060 Carmack Road

department: Biological Chemistry and Pharmacology

institute: The Ohio State University

summary: The eIF4E family of translation initiation factors bind 5’ methylated caps and act as the limiting-step for mRNA translation. The canonical eIF4E1A is required for cell viability, yet other related families exist and are all utilized in specific contexts or tissues. Here, we describe a new family called Eif4e1c that is ancestral to the canonical eIF4E1A in vertebrates, and for which we find roles during heart development and regeneration in zebrafish. The Eif4e1c family is present in all aquatic vertebrates but has been lost in all terrestrial species. A core group of amino acids shared over 500 million years of evolution from ray-finned fish to sharks forms an evolutionarily conserved binding interface along the surface of the protein, suggesting Eif4e1c functions in a novel pathway.  Deletion of eif4e1c in zebrafish caused growth deficits and impaired survival in juveniles. Mutants surviving to adulthood had fewer cardiomyocytes, while also showing reduced proliferative responses to cardiac injury. Ribosome profiling of mutant hearts demonstrated changes in translation efficiency of mRNA for genes known to regulate cardiomyocyte proliferation. Although eif4e1c is expressed in many tissues and is the predominant cap-binding initiation homolog in embryos, its disruption had most notable impact on the heart and at juvenile stages.  Our findings reveal context-dependent requirements for translation initiation regulators during heart regeneration.

overall_design: Ribosome profiling of adult uninjured eif4e1c zebrafish mutant hearts and adult uninjured EK zebrafish (wildtype) hearts.

first: Anupama

last: Rao

first: Frank

last: Tedeschi

first: Eckhard

last: Jankowsky


title: BET inhibition targets ABC-DLBCL constitutive B-cell receptor signaling through PAX5

city: Waltham

first: Derek

middle: B

last: Oien

address: 35 Gatehouse Dr

institute: AstraZeneca

summary: B-cell receptor (BCR) signaling is essential for the diffuse large B-cell lymphoma (DLBCL) subtype that originates from activated B-cells (ABC). ABC-DLBCL cells are sensitive to Bruton tyrosine kinase intervention. However, ABC-DLBCL patients had overall response rates of 33-37% for Bruton tyrosine kinase inhibitors, suggesting the evaluation of combination-based treatment for improved efficacy. We investigated the efficacy and mechanism of AZD5153 combined with the Bruton tyrosine kinase inhibitor acalabrutinib in ABC-DLBCL preclinical models. AZD5153 is a bivalent BET inhibitor that simultaneously engages the two bromodomains of BRD4. Adding AZD5153 to acalabrutinib demonstrated a combination benefit in ABC-DLBCL cell lines and PDX models. Differential expression analyses in treated tumors identified significant alterations of BCR, PAX5, RELB/alternative NFκB, and toll-like receptor/interferon signaling. PAX5 is a transcription factor for BCR signaling genes and may be critical to the perpetually active BCR signaling in ABC-DLBCL. We demonstrate that AZD5153 decreases PAX5 expression, while acalabrutinib disruption to BCR signaling inhibits PAX5 activation. Furthermore, several interferons were decreased by AZD5153 and acalabrutinib in tumors. Adding IFNß1 to cells in vitro restored PAX5 activation. Our results demonstrate AZD5153 enhances the efficacy of acalabrutinib through PAX5 and BCR mechanisms that are critical for ABC-DLBCL.

overall_design: Xenograft tumors from TMD8 and LY6934 mouse models after dosing with AZD5153 and acalabrutinib were excised and snap frozen in liquid nitrogen. Treatments were A) TMD8 (4 hours): vehicle (0.5% hydroxymethylcellulose, 0.1% Tween80), 0.72 mg/kg AZD5153 QD, 20 mg/kg acalabrutinib BID, or 0.72 mg/kg AZD5153 QD + 20 mg/kg acalabrutinib BID, and B) LY6934 (25 days): vehicle (0.5% hydroxymethylcellulose, 0.1% Tween80) or 0.5 mg/kg AZD5153 QD + 20 mg/kg acalabrutinib BID. Tumor tissue was lysed and RNA was extracted using RNeasy kit (Qiagen, Hildren, Germany) according to manufacturer’s instructions. RNA concentration was quantified using the Qubit fluorometer (ThermoFisher, Waltham, MA). 15 RNA samples were sent to Novogene for library preparation and human RNA sequencing.

first: Samantha

last: Sharma

first: Maureen

last: Hattersley

first: Michelle

last: DuPont

first: Steven

last: Criscione

first: Laura

last: Prickett

first: Anne

middle: U

last: Goeppert

first: Lisa

last: Drew

first: Yi

last: Yao

first: Jingwen

last: Zhang

first: Ho

last: Chan


title: Differentially expressed SE-lncRNAs in lung adenocarcinoma

city: Nanjing

first: Feng

last: Jiang

state: Jiangsu

address: Baiziting 42

institute: Jiangsu Institute of Cancer Research

summary: Background: Lung adenocarcinoma (LUAD) is the leading cause of deaths worldwide, and metastasis accounts for the vast majority of cancer-related deaths. Driver mutations play important roles in treatment decision making for LUAD patients, while the complicated metastatic progress cannot be explained by genetic aberrations alone. Epigenomic reprogramming is particularly notable as an important signature of the metastasis transition. However, long noncoding RNAs (lncRNAs) hijacked by super-enhancer (SE), vital regulatory elements in epigenome, remain elusive in the progression of metastasis.  Methods: SE associated lncRNAs microarray was utilized to identified the dysregulated lncRNAs related to metastasis. ChIP-seq, Hi-C data analysis and luciferase reporter assay were utilized to confirm LINC01977 was hijacked by SE. In vitro and in vivo assays were applied to elucidate effects of LINC01977 on the malignancy of LUAD.  Results: In this study, we identified that LINC01977, a cancer-testis lncRNA, was up-regulated in tumor, which was driven by a …kb-long SE upstream of LINC01977 and sensitive to BRD4 inhibitor. LINC01977-antisense oligonucleotides (ASO) dramatically suppresses proliferation and invasion both in vitro and in vivo. Mechanically, LINC01977 promotes phosphorylation of SMAD3 to facilitate its nuclear retention, and it also act as a scaffold to cooperate the interaction between SMAD3 and CBP/P300, the transcriptional co-activators, to regulate the downstream target gene ZEB1. Interestingly, SMAD3 also positively regulated LINC09177 transcription by binding the promoter and active elements of its SE, which was medicated by canonical TGF-β signaling secreted by M2-like tumor-associated macrophages (TAM2). We also revealed that the expression of LINC01977 was positively correlated with TAM2 infiltration especially in early stage. Additionally, stage I LUAD patients with high LIN01977 expression predicated a shorter progression-free survival (PFS).  Conclusions: LINC01977 promotes the malignant progression of LUAD through facilitating the interaction between SMAD3 and CBP/P300. The upregulation of LINC01977 was medicated by super-enhancer and TAM2 infiltration, dependent on canonical TGF-β signaling. LINC01977 could be a valuable therapeutic target especially for early stage patients.

overall_design: In the study presented here, we obtained tumor tissues with matched adjacent tissues from 5 patients who underwent radical surgery without neoadjuvant chemotherapy and who were diagnosed with LUAD at the Jiangsu Cancer Hospital (Nanjing, China). Each patient contains complete clinical and pathological information. Super Enhancer lncRNA Microarrays from ArrayStar Co. were conducted for each tissue and acquired expression profiles of a total of 7753 unique LncRNAs with regulated by super-enhancers, potentially. In all, we obtained differential super-enhancers-related LncRNAs expression between tumor tissues and adjacent tissues.

first: Lin

last: Xu

first: Gaochao

last: Dong

first: Te


title: Early postoperative treatment versus initial observation in CNS WHO grade 2 and 3 oligodendroglioma: clinical outcomes and DNA methylation patterns

status: Public on Aug 22 2022

city: Wien

first: Gerwin

last: Heller

address: Währinger Gürtel 18-20

department: Medicine I

country: Austria

institute: Medical University of Vienna

summary: In the past decades, ample evidence has shown that combined radio-chemotherapy is superior  to either radiotherapy or chemotherapy alone in oligodendroglioma. However, the survival  benefit comes at the cost of immediate and long-term toxicities. Therefore, deferring  postoperative therapy until progression may be a valid option to delay treatment-related side  effects. Still, systematic data and reliable predictive biomarkers are limited. In this large  retrospective series of oligodendroglioma cases, we could show that early postoperative  treatment is not associated with improved PFS and OS while correcting for baseline differences  between both groups. In addition, we performed whole-genome DNA methylation analyses and  observed a predictive role of certain methylation patterns independent from MGMT promoter  methylation status, extent of resection and CNS WHO grade. The results of this real-life study  may serve as a benchmark for future trial planning in oligodendroglioma, and further studies  should evaluate the predictive value of DNA methylation profiles.

overall_design: Compare DNA methylation pattern between patients who received adjuvant treatment. Patients were stratified into  PFS above (Benefit) or  below (No_benefit) the median of all patients receiving early postoperative treatment.

first: Anna

last: Bergmeister-Berghoff

first: Maximilian

last: Mair


title: RANK ligand converts the NCoR/HDAC3 co-repressor to a PGC1β- and RNA-dependent co-activator of osteoclast gene expression [ATAC-seq]

city: La Jolla

first: Christopher

last: Glass

state: CA

address: 9500 Gilman Dr

department: CMM

institute: University of California, San Diego

summary:
To investigate the enhancer/promoter activity in the regulation of osteoclast differentiation, we used bone marrow cells treated with or without RANKL.
We then analyzed open chromatin regions obtained from ATAC-seq data.

overall_design: ATAC peak-associated H3K27ac analysis for active enhancer/promoter regions

first: Yohei

last: Abe

first: Eric

last: Kofman

first: Maria

last: Almeida

first: Zhengyu

last: Ouyang

first: Filipa

last: Ponte

first: Jasmine

last: Mueller

first: Nathanael

last: Spann

first: Jason

middle: S

last: Seidman

first: Joshua

middle: D

last: Stender

first: Havilah

last: Taylor

first: Weiwei

last: Fan

first: Verena

last: Link

first: Isidoro

last: Cobo

first: Johannes

last: Schlachetzki

first: Takao

last: Hamakubo

first: Kristen

last: Jepsen

first: Juro

last: Sakai

first: Michael

last: Downes

first: Ronald

last: Evans

first: Gene

last: Yeo

first: Stavros

last: Manolagas

last: Rosenfeld


title: RANK ligand converts the NCoR/HDAC3 co-repressor to a PGC1β- and RNA-dependent co-activator of osteoclast gene expression [eCLIP-seq]

first: Christopher

last: Glass

summary:
To investigate the cooperative function NCoR/HDAC3/PGC1β complex in the regulation of osteoclast differentiation, we used NCoR KO or PGC1β KO bone marrow cells and non-coding RNA Dancr/Rnu12 siRNA knockdown bone marrow cells or RAW 264.7 cells.
We selected Dancr and Rnu12 as non-coding RNAs to knockdown based on results from an eCLIP essay.

overall_design: eCLIP-seq with PGC1B-specific antibody in mouse osteoclasts

first: Yohei

last: Abe

first: Eric

last: Kofman

first: Maria

last: Almeida

first: Zhengyu

last: Ouyang

first: Filipa

last: Ponte

last: Mueller


title: RANK ligand converts the NCoR/HDAC3 co-repressor to a PGC1β- and RNA-dependent co-activator of osteoclast gene expression [ChIP-seq]

summary:
To investigate the genomic localization of NCoR/HDAC3/PGC1β complex and the enhancer/promoter activity in the regulation of osteoclast differentiation, we used NCoR KO or PGC1β KO bone marrow cells, non-coding RNA Dancr/Rnu12 siRNA knockdown bone marrow cells and FLAG-tagged PGC1β RNA recognition motif deletion mutant expressed RAW 264.7 cells.
We then performed chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for H3K27ac, NCoR, HDAC3, PGC1β, p65, Fosl2, PU.1 and FLAG-tag.

overall_design: Genomic localization of NCoR/HDAC3/PGC1β and transcription factors with H3K27 acetylation depending on RANK signal

first: Jasmine

first: Nathanael

last: Spann

first: Jason

last: Seidman

first: Joshua

last: Stender

first: Havilah

last: Taylor

first: Weiwei

last: Fan

last: Link

last: Cobo


title: RANK ligand converts the NCoR/HDAC3 co-repressor to a PGC1β- and RNA-dependent co-activator of osteoclast gene expression

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

overall_design: Refer to individual Series


title: FAM122A is required for mesendodermal and cardiac differentiation of embryonic stem cells [ChIP-seq]

status: Public on Aug 18 2022

city: Shanghai

first: Yunsheng

last: Yang

address: Chong-Qing South Road

institute: Shanghai Jiao Tong University

summary: Mesendodermal specification and cardiac differentiation are key issues for developmental biology and heart regeneration medicine. Previously, we demonstrated that FAM122A, a highly conserved house-keeping gene, is an endogenous inhibitor of protein phosphatase 2A (PP2A) and participates in multi facet physiological and pathological processes, however, the in vivo function of FAM122A is largely unknown. In this study, we found that Fam122 deletion results in embryonic lethality with severe defects of cardiovascular developments and significantly attenuates the cardiac functions in conditional cardiac-specific knockout mice. More importantly, Fam122a deficiency impairs mesendodermal specification and cardiac differentiation from mouse embryonic stem cells, but not influences the pluripotent identity. Mechanical investigation shows that the impaired differentiation potential is caused through the dysregulation of histone modification and Wnt and Hippo signaling pathways by modulating PP2A activity. These findings suggest that FAM122A is a novel and critical regulator in mesendodermal specification and cardiac differentiation. This not only significantly extends our understanding the regulatory network of mesendodermal/cardiac differentiation, but also establishes a previously uncharacterized connection between PP2A and mesendodermal specification.

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for the histone modifications H3K4me3, H3K27me3 and H3K27ac in Ctrl and Fam122a KO mESCs at different stage.

first: Yun-Sheng

first: Ying

last: Huang


title: Mouse feeder-free alveolar organoids treated by bleomycin

status: Public on Aug 21 2022

city: Hamamatsu

first: Yasunori

last: Enomoto

state: Shizuoka

address: 1-20-1 Handayama

department: Department of Regenerative and Infectious Pathology

institute: Hamamatsu University School of Medicine

summary: To investigate the direct effect of bleomycin on alveolar epithelium, feeder-free mouse alveolar organoids were treated by bleomycin (100μM) for 48 hours in vitro and then analyzed.

overall_design:
Alveolar organoids were made from primary alveolar epithelial cell type 2 (GFP+ in FACS) isolated from tamoxifen-treated Sftpc-creERT2; Rosa26-mTmG mice (male, 9wks).
Comparative gene expression profiling analysis of RNA-seq data between bleomycin-treated and untreated mouse alveolar organoids.


title: FAM122A is required for mesendodermal and cardiac differentiation of embryonic stem cells


title: The changes of Chromatin Accessibiliy Triggered by Unilateral Nephrectomy [ATAC-seq]

status: Public on Aug 14 2022

city: Bethesda

first: Hiroaki

last: Kikuchi

state: MD

address: 10 CENTER DR

department: Epithelial Systems Biology Laboratory, Systems Biology Center

institute: NHLBI

summary:
Purpose: Experiments were done in mice undergoing unilateral nephrectomy (UNx) and sham nephrectomy. At specific time points (24 hours and 72 hours) after surgery, the earliest first portion of the kidney proximal tubule (PT-S1)  and the cortical collecting duct (CCD) were manually micro-dissected and utilized for transcriptomic analysis by single-tubule small sample RNA-Seq and single-tubule ATAC seq.
Methods: We carried out ATAC-sequencing in microdissected ealiest portion of proximal tubules (PT-S1) from mice with or without (sham) unilateral nephrectomy (UNx). Each group (Sham or UNx) has 3 biological replicates.
Results and conclusion: ATAC-seq peaks in microdissected PT-S1 revealed a predominance of binding site motifs corresponding to PPARα.

overall_design: The transposed DNA fragments from microdissected proximal tubules were generated and sequenced using Illumina Novaseq 6000.

first: Kavee

last: Limbutara

first: Jung

last: Hyun Jun

first: Chen

last: Lihe

first: Benjamin

last: Carter

first: Chung-Lin

last: Chou

first: Chin-Rang

first: Mark

last: Knepper


title: Chromatin jets define the properties of cohesin-driven in vivo loop extrusion

status: Public on Aug 15 2022

city: London

first: Ya

last: Guo

address: Faculty of Medicine, Imperial College, Hammersmith Hospital Campus

department: Epigenetics section

institute: MRC London Institute of Medical Sciences

summary: Complex genomes show intricate organization in three-dimensional (3D) nuclear space. Current models posit that cohesin extrudes loops to form self-interacting domains delimited by the DNA binding protein CTCF. Here, we describe and quantitatively characterize cohesin-propelled, jet-like chromatin contacts as landmarks of loop extrusion in quiescent mammalian lymphocytes. Experimental observations and polymer simulations indicate that narrow origins of loop extrusion favor jet formation. Unless constrained by CTCF, jets propagate symmetrically for 1-2 Mb, providing an estimate for the range of in vivo loop extrusion. Asymmetric CTCF binding deflects the angle of jet propagation as experimental evidence that cohesin-mediated loop extrusion can switch from bi- to unidirectional and is controlled independently in both directions. These data offer new insights into the physiological behavior of in vivo cohesin-mediated loop extrusion and further our understanding of the principles that underlie genome organization.

overall_design:
Chromatin contact profiles in wild type, CD4 Cre Ctcf lox/lox and CD4 Cre Rad21 lox/lox Ctcf lox/lox immature CD4+ CD8+ double positive thymocytes were generated by in situ Hi-C, complemented by ChIP-seq of
CTCF, Rad21, and H3K27ac.

first: Matthias

last: Merkenschlager


title: FAM122A is required for mesendodermal and cardiac differentiation of embryonic stem cells [RNA-seq]

overall_design: Comparative gene expression profiling analysis of RNA-seq data for Ctrl and Fam122a KO mESCs at different stage.


title: Stromal-epithelial interaction via soluble factors in prostate carcinoma cell lines

city: Essen

first: Bettina

last: Budeus

address: Virchowstrasse 173

department: Institute for Cell Biology

institute: University Hospital Essen

summary: Cell-cell communication is an important process in healthy tissue but also gains enhanced attention regarding pathological tissue. To date, the tumor microenvironment is gradually brought into focus when studying tumorigenesis. In the prostate gland, stromal and epithelial cells greatly interact to maintain homeostasis or tissue integrity. This study focuses on an indirect communication via soluble factors. For this approach, the prostate carcinoma cell line LNCaP and the stromal primary cells p21 were co-cultured without direct contact and RNA was isolated at defined time points (one, three and seven days). RNA sequencing finally revealed a time-depending differential expression profile.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for co-cultured LNCaP and p21 cells interacting via soluble factors for one, three and seven days. Co-cultures with the same cell line were used as controls.

first: Elena

last: Czyrnik

first: René

last: Scholtysik

first: Gunther

last: Wennemuth


title: A twin UGUA motif directs the balance between gene isoforms through CFIm and the mTORC1 signaling pathway

status: Public on Aug 11 2022

city: Pittsburgh

first: Hun-Way

last: Hwang

state: PA

address: 3550 Terrace Street

department: Department of Pathology

institute: University of Pittsburgh

summary: To identify APA changes in Tsc1-cKO mice, cTag-PAPERCLIP was performed on pAAV-Camk2a-iCre injected Tsc1-WT and Tsc1-floxed cTag-PABP mice. To identify CPSF6-dependent PAS, PAPERCLIP was performed on shCPSF6-BE2C cells with/without doxycycline treatment.

overall_design: cTag-PAPERCLIP and PAPERCLIP library construction was performed as previously described (Hwang et al., Neuron 2017; Kunisky et al., Cell Rep 2021) and the libraries were sequenced on Illumina NextSeq

first: R. Samuel

last: Herron

first: Alexander

last: Kunisky

first: Jessica

last: Madden

first: Vivian

middle: I

last: Anyaeche

first: May

middle: Z

last: Maung


title: Effect of knockdown SHMT2 on gene expression in LX2 cells.

city: nanjing

first: Gao

last: yanjie

address: 163 Xianlin Road, Qixia District

department: School of life science

institute: Nanjing University

summary: We  performed gene expression profiling analysis using data obtained from RNA-seq of 2 treatment cells

overall_design: Comparative gene expression profiling analysis of RNA-seq data for knockdown SHMT2 and control LX2 cells

first: Yanjie

last: Gao


title: Targeted protein degradation reveals Pol II heterogeneity and functional diversity [ChAR-Seq]

status: Public on Aug 09 2022

first: Xiong

last: Ji

address: Haidian District, Beijing Summer Palace Road No. 5

department: School of Life Sciences

institute: Peking University

summary: RNA polymerase II (Pol II) subunits are thought to be involved in various transcription-associated processes, but it is unclear whether they play different regulatory roles in modulating gene expression. Here, we performed nascent and mature transcript sequencing after the acute degradation of 12 mammalian Pol II subunits and profiled their genomic binding sites and protein interactomes to dissect their molecular functions. We found that Pol II subunits contribute differently to Pol II cellular localization and transcription process and preferentially regulate RNA processing (such as RNA splicing and 3’ end maturation). Genes sensitive to the depletion of different Pol II subunits tend to be involved in diverse biological functions and show different RNA half-lives. Sequences, associated protein factors, and RNA structures are correlated with Pol II subunit-mediated differential gene expression. These findings collectively suggest that the heterogeneity of Pol II and different genes appear to depend on some of the subunits.

overall_design: We performed PRO-seq, ChAR-seq, RNA-seq, and ChIP-seq to investigate the roles of various specialized subunits in transcription and post-transcriptional regulation. The V6.5 mouse ES (mES) cell line was used for all the high-throughput analyses. Degron mES cells were pretreated with 1 μg/ml Doxycycline for 12h to induce TIR1 expression, and treated with or without 500 μM IAA for different hours refer to individual Series. For PRO-seq, ChAR-seq, and RNA-seq, the Drosophila S2 cells were used as the spike-in cells, and for ChIP-seq, the ZBTB11-GFP expressing cells were used as the spike-in cells.

first: Yuanjun

last: Li

first: Jie

last: Huang


title: Effect of deletion of von-Hippel-Lindau (VHL) in the proximal tubule in diabetic kidney disease

status: Public on Aug 08 2022

city: Kiel

first: Eileen

last: Dahlke

state: Schleswig-Holstein

address: Otto-Hahn-Platz 8

department: Anatomisches Institut

institute: Christian-Albrechts-Universität Kiel

summary: To establish the role of proximal tubular hypoxia in diabetic kidney disease, we use a mouse line with a specific deletion of von-Hippel-Lindau (VHL) in the proximal tubule and treat them with streptozotocin (STZ) to induce a type I diabetes mellitus. 10 weeks after induction of diabetes mellitus samples were collected.

overall_design: We then performed gene expression profiling analysis using data obtained from RNA-seq of control mice and proximal tubular-specific VHL-deletion mice with and without STZ-treatment (induction of diabetes mellitus).

first: Madlen

last: Kunke

first: Luis

last: Rodriguez

first: Joana

last: Bernardes

first: Robert

last: Häsler

first: Franziska

last: Theilig


title: Microarray gene expression data from MCF-7 and MPiFR cells

status: Public on Aug 05 2022

city: Odense M

first: Carla

last: Alves

address: Fioniavej 36, 2. sal

country: Denmark

institute: SDU

summary:
The PI3K inhibitor (PI3Ki) alpelisib in combination with fulvestrant is currently FDA approved for the treatment of advanced ER+ breast cancer following progression on endocrine therapy. It is unclear which treatment strategy is beneficial following progression on the combination of PI3Ki and fulvestrant, and therefore, identification of novel therapeutic targets is needed.
We used microarrays to detail the global programme of gene expression in cells resistant to the combination of PI3Ki and fulvestrant (MPiFR). The parental sensitive cell line, MCF-7, was used for comparison. The gene expression analysis revealed a significant number of genes altered in the MPiFR cells vs. MCF-7 cells. We found a significant upregulation of cell cycle-related genes, particularly CDK6, CDK2, and cyclin E1 and E2 in MPiFR vs. MCF-7 cells.

overall_design: The combined PI3Ki, alpelisib, and fulvestrant- resistant cell line is derived from MCF-7 and was established through long-term treatment with fulvestrant and increasing concentrations of PI3Ki. Total RNA from MCF-7 and MPiFR cells was extracted and arrayed separately in Human Transcriptome Array 2.0 (HTA, Affymetrix).

middle: L

first: Karimi

last: Leena


title: RANK ligand converts the NCoR/HDAC3 co-repressor to a PGC1β- and RNA-dependent co-activator of osteoclast gene expression [RNA-seq]

first: Christopher

last: Glass

summary:
To investigate the cooperative function NCoR/HDAC3/PGC1β complex in the regulation of osteoclast differentiation, we used NCoR KO or PGC1β KO bone marrow cells and non-coding RNA Dancr/Rnu12 siRNA knockdown bone marrow cells or RAW 264.7 cells.
We then performed gene expression profiling analysis using data obtained from RNA-seq.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for bone marrow cells treated with or without RANKL

first: Yohei

last: Abe

first: Eric

middle: R

last: Kofman

first: Maria

last: Almeida

first: Zhengyu

last: Ouyang

first: Filipa

last: Ponte

first: Jasmine

last: Mueller

first: Nathanael

last: Spann

first: Jason

last: Seidman

first: Joshua

last: Stender

first: Havilah

last: Taylor

first: Weiwei

last: Fan

first: Verena

last: Link

first: Isidoro

last: Cobo

first: Johannes

last: Schlachetzki

first: Takao

last: Hamakubo

first: Kristen

last: Jepsen

first: Juro

last: Sakai

first: Michael

last: Downes

first: Ronald

last: Evans

first: Gene

middle: W

last: Yeo

first: Stavros

last: Manolagas

last: Rosenfeld


title: Transcriptome Changes of Microdissected Kidney Tubules triggered by Unilateral Nephrectomy [RNA-seq]

first: Hiroaki

last: Kikuchi

summary:
Purpose: Experiments were done in mice undergoing unilateral nephrectomy (UNx) and sham nephrectomy. At specific time points (24 hours and 72 hours) after surgery, the earliest first portion of the kidney proximal tubule (PT-S1)  and the cortical collecting duct (CCD) were manually micro-dissected and utilized for transcriptomic analysis by single-tubule small sample RNA-Seq.
Methods: We carried out RNA-sequencing in microdissected ealiest portion of proximal tubules (PT-S1) or cortical collecting duct (CCD) from mice with or without (sham) unilateral nephrectomy (UNx). Each group (Sham or UNx) has 3-5 biological replicates.
Results and conclusion: RNA-Seq in microdissected PT-S1 at 24 hours showed that peroxisome proliferator-activated receptor alpha (PPARα) target genes were strongly upregulated. RNA-Seq in microdissected PT-S1 at 72 hours showed that cell cycle related genes were strongly upregulated. RNA-Seq in microdissected CCD at both 24 hours and 72 hours showed that cell cycle related genes were strongly upregulated.

overall_design: cDNAs from microdissected proximal tubules and cortical collecting ducts were generated and sequenced using Illumina Novaseq 6000.

first: Kavee

last: Limbutara

first: Jung

last: Hyun Jun

first: Chen

last: Lihe

first: Benjamin

last: Carter

first: Chung-Lin

last: Chou

first: Chin-Rang

last: Yang

first: Mark

middle: A

last: Knepper


title: BLIMP1 and NR4A3 Transcription Factors Reciprocally Regulate Antitumor CAR T-cell Stemness and Exhaustion [RNA-Seq]

status: Public on Aug 04 2022

city: Philadelphia

first: Inyoung

last: Jung

address: SPE, 9-304, 3400 Civic Center Blvd, Bldg. 421

institute: University of Pennsylvania

summary: Chimeric antigen receptor (CAR) T-cells have not induced meaningful clinical responses in solid tumor indications. Loss of T-cell stemness, poor expansion capacity and exhaustion during prolonged tumor antigen exposure are major causes of CAR T-cell therapeutic resistance. scRNA-sequencing analysis of CAR T-cells from a first-in-human trial in metastatic prostate cancer identified two distinct and independently validated cell states associated with antitumor potency or lack of efficacy. Low levels of the PRDM1 gene encoding the BLIMP1 transcription factor defined highly potent TCF7+CD8+ CAR T-cells, while enrichment of TIM3+CD8+ T-cells with elevated PRDM1 expression predicted poor outcome. PRDM1 single knockout promoted TCF7-dependent CAR T-cell stemness and proliferation resulting in marginally enhanced leukemia control. However, in the setting of PRDM1 deficiency, a negative epigenetic feedback program of NFAT-driven T-cell dysfunction characterized by compensatory upregulation of NR4A3 and multiple other genes encoding exhaustion-related transcription factors hampered effector function in solid tumors. PRDM1 and NR4A3 combined ablation skewed CAR T-cell phenotypes away from TIM3+CD8+ and toward TCF7+CD8+ to counter exhaustion of tumor-infiltrating CAR T-cells and improve in vivo antitumor responses, effects that were not achieved with BLIMP1 or NR4A3 single disruption alone. These data reveal a novel molecular targeting strategy to enrich stem-like CAR T-cells resistant to exhaustion and underscore dual inhibition of PRDM1/NR4A3 expression or activity as a promising approach to advance adoptive cell immuno-oncotherapy.

overall_design: On day 0, 5, and 20 of the CAR T-cell restimlation assay,  before stimulation and after the fourth tumor challenge respectively, CD8+ CAR T-cells were isolated and total mRNA was extracted. Gene expression was examined by paired-end RNA-seq of AAVS and PRDM1 knockout CD8+ PSMA CAR T-cells with two technical repeats across two biological replicates.

first: In-Young

first: Vivek

last: Narayan

first: Sierra

last: McDonald

first: Andrew

middle: J

last: Rech

first: Robert

last: Bartoszek

first: Gwanui

last: Hong

first: Mega

middle: M

last: Davis

first: Jun

last: Xu

first: Alina

last: Boesteanu

first: Julie

last: Barber-Rontenberg

first: Gabriela

last: Plesa

first: Simon

middle: F

last: Lacey

last: Jadlowsky

first: Donald

last: Siegel

first: Dana

last: Hammill

first: Park

last: Cho-Park

first: Shelley

last: Berger

first: Naomi

last: Haas

first: Joseph

last: Fraietta


title: BLIMP1 and NR4A3 Transcription Factors Reciprocally Regulate Antitumor CAR T-cell Stemness and Exhaustion [ATAC-Seq]

first: Inyoung

last: Jung

overall_design: CD8+ CAR T-cells were isolated from the manufactured PSMA CAR T-cells. Chromatin accessibility across the genome was determined by ATAC sequencing of AAVS1 and PRDM1 knockout CD8+ PSMA CAR T-cells with two technical repeats across two biological replicates.

first: In-Young

first: Vivek

last: Narayan

last: McDonald

middle: C


title: The transcriptomic response of bovine uterine tissue is altered in response to sperm from high and low fertility bulls

status: Public on Aug 01 2022

city: Dunsany

first: Paul

last: Cormican

address: Grange

department: Bioscience

country: Ireland

institute: Teagasc

summary: The aim of this study was to profile the transcriptome and perform histological analysis of the bovine uterus in response to sperm from high fertility (HF) and low fertility (LF) bulls

overall_design: Post-mortem uterine biopsies and uterine explants were collected from nulliparous heifers after a fixed time artificial insemination (AI) to a synchronized estrus with frozen-thawed semen from 5 HF and 5 LF bulls. Uterine biopsies were also collected from control (CTRL) heifers which were not inseminated. Differential gene expression in these tissues was assessed using RNA-Seq.


title: YOUNG BLOOD-DERIVED PLATELET FACTORS ATTENUATE INFLAMMATION AND RESCUE COGNITION IN AGING

city: San Francisco

first: Karishma

middle: Joanne Bhatia

last: Pratt

address: 513 Parnassus Ave, Med. Sci. Bldg S1364

department: Anatomy

institute: UCSF

summary: Platelet-derived factors in young blood decrease neuroinflammation and enhance cognitive function in the aged hippocampus.

overall_design: CITE-sequencing analysis of immune cells isolated from the spleen of aged mice treated with Platelet Factor 4 (aged PF4) or saline control (aged control), or young saline treated control mice (young control).

first: Adam

last: Schroer

first: Juliana

last: Sucharov Costa

first: Saul

last: Villeda


title: BLIMP1 and NR4A3 Transcription Factors Reciprocally Regulate Antitumor CAR T-cell Stemness and Exhaustion

overall_design: Refer to individual Series


title: Deep sequencing data from PAM screen of Pa83 type IV-A CRISPR-Cas system

status: Public on Aug 19 2022

city: Logan

first: Olive

last: Redman

state: UT

address: 0300 Old Main Hill

department: Chemistry and Biochemistry

institute: Utah State University

summary: In this work the favorable PAM sequences for a type IV-A CRISPR-Cas system were determined

overall_design: E. coli containing a recombinant type IV-A CRISPR-Cas immune system from P. aeruginosa were challenged against a plasmid library consisting of a complementary target flanked by a randomized protospacer-adjacent motif (PAM) sequence. E coli containing a nonfunctioning recombinant system without a CRISPR were also challenged with the PAM library as a control. Both the targeting and control experiments were done in biological triplicate, and the plasmid from the surviving cells was then purified and the target sequence extracted with PCR. Sequence counts for each PAM were then calculated from the resulting Illumina seq data, and a depletion score for each PAM was calculated.

first: Aaron

last: Thomas

first: Ryan

last: Jackson


title: STING affects gene expression

status: Public on Aug 10 2022

city: Wuhan

first: Junjie

last: Zhang

state: Hubei

address: Donghu Road, No. 115

department: Medical Research Institute

institute: Wuhan University

summary: RNAseq of control and Sting-/- L929 cells to compare gene expression change

overall_design: RNA was extracted from control and Sting-/- L929 cells and RNA-seq was performed. Three replicates are included for each samples.

first: Liting

first: Jun

last: Xie


title: Half-life estimation in the cyanobacterium Synechocystis sp. PCC 6803 Transcriptome wide during iron starvation

status: Public on Jul 30 2022

city: Freiburg im Breisgau

first: Loubna

last: Youssar

state: Baden-Wurttemberg

address: Schänzlestraße 1

institute: University of Freiburg

summary: Cyanobacteria, photoautotrophic prokaryotes, contribute significantly to the global photosynthesis and require large amounts of the essential micronutrient iron in order to maintain their Fe-rich photosynthetic apparatus. Here we use the model organism Synechocystis sp. PCC 6803 (later referred to Synechocystis) in both, standard and iron stress conditions, to study transcription and post-transcription regulation in iron deprivation. Although iron is one of the most abundant metals on earth, it is not soluble under aerobic conditions. Thus Synechocystis had to find ways to overcome iron deficiency. At the same time, however, free intracellular iron needs to be kept at permissive levels, as it becomes toxic under aerobic conditions by producing reactive oxygen species. For these reasons, complex regulatory networks have evolved to tightly control intracellular iron concentrations, ensuring its essential function yet avoiding cellular damage (Pierre Cornelis et al). In a previous study, we investigated iron deprivation in Synechocystis using customised amplification library for the analysis of global gene expression in the unicellular cyanobacterium (Hernández-Prieto et al, 2012; Georg et al, 2017),(Georg et al, 2017) but it is still little known about RNA stability in this organism. We now extend this study through a transcriptome wide half-life analysis in Synechocystis grown under standard and iron-limiting conditions using oligonucleotide microarrays that detect both protein-coding and non-coding transcripts (ncRNA). We used the antibiotic Rifampicin to stop the transcription. Samples were taken at time points 0 min (before the addition of rifampicin) and in a time series of 2 min, 4 min, 8 min, 16 min, 32 min and 64 min after its addition.

overall_design: Three and two biological replicates were used for standard and iron stress condition respectively. Half-life was estimated for each condition.

first: Jens

last: Georg

first: Wolfgang

last: Hess

first: Gergana

last: Kostova

first: Walja

last: Wanney


title: Recruitment of ETS1 to activated accessible regions promotes cilia genes transcriptional program in ciliopathy [RNA-seq]

status: Public on Jul 28 2022

city: Zhanjiang

first: Yun-Miao

last: Guo

address: 236 Yuanzhu Road

department: Zhanjiang Institute of Clinical Medicine

institute: Central People's Hospital of Zhanjiang

summary: Defects in cilia genes that is critical in cilia formation and function can cause complicated ciliopathy syndromes involving multiple organs and tissues; however, the underlying regulatory mechanisms of cilia gene networks in ciliopathy are largely unknown. Here, we define the genome-wide redistribution of chromatin accessibilities and extensive divergence of cilia genes expression programs happened in ciliopathy. Mechanistically, the distinct ciliopathy-activated accessible regions (CAAs) are characterized to positively regulate robust changes of flanking cilia genes, which are a key transcriptional feature of cilia required for the response to developmental signals. Moreover, the single transcriptional factors, ETS1, can be recruited to CAAs thus prominently reconstructing chromatin accessibility in ciliopathy. CAAs collapse driven by ETS1 suppression subsequently cause defective cilia formation and impaired developmental signal transduction, which eventually develops ciliopathy phenotypes of short fins and pericardium edema in larval fishes. Therefore, our results depicted a dynamic landscape of chromatin accessibility in ciliopathy, and uncover an insightful role of ETS1 in controlling global cilia genes transcriptional program by reprogramming widespread chromatin state.

overall_design: gene expression profiling analysis of RNA-seq data

first: Dong-Hui

first: Yi-Ting

last: Guan


title: Recruitment of ETS1 to activated accessible regions promotes cilia genes transcriptional program in ciliopathy

type: Genome variation profiling by high throughput sequencing

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


title: Effect of sgRNA-mediated disruption of GLUT1 on gene expression on c-Kit+ MLL::AF9 leukemia cells

city: Lund

first: Marcus

last: Järås

address: Universitetssjukhuset

department: Clinical Genetics

institute: Lund University

summary: Acute myeloid leukemia (AML) is initiated and propagated by leukemia stem cells (LSCs), a self-renewing population of leukemia cells. Here we performed an in vivo CRISPR screen and identified the facilitated glucose transporter type 1 (GLUT1) as a critical metabolic dependency for murine MLL::AF9 LSCs. GLUT1 disruption by genetic ablation or by pharmacological inhibition with BAY-876 led to suppression of leukemia progression and improved survival in an MLL::AF9 mouse model of AML. Glut1 inhibition further resulted in glycolytic suppression, decreased levels of tricarboxylic cycle intermediates, and elevated levels of amino acids. These changes in metabolic profile coincided with increased autophagic activity and differentiation of AML cells. Notably, dual inhibition of GLUT1 and oxidative phosphorylation exhibited synergistic anti-leukemic effects in human AML cells. Collectively, these findings increase our understanding of how murine LSCs are metabolically regulated and highlight GLUT1 inhibition as a promising therapeutic adjuvant approach in AML.

overall_design: Mouse MLL-AF9 leukemia cells were transduced with control or Glut1 sgRNAs. Cells were collected 3 days post transduction and RNA sequencing was performed on FACS sorted GFP+ cells. Total number of samples - 12. Replicates - Control_sgRNA - 4, Glut1_sgRNA_1 - 4, Glut1_sgRNA_2 - 4.

first: Maria

last: Rodriguez Zabala


title: Recruitment of ETS1 to activated accessible regions promotes cilia genes transcriptional program in ciliopathy [ATAC-seq]

overall_design: Chromatin accessibility analysis of ATAC-Seq data


title: Escort Cells scRNA-seq

status: Public on Jul 27 2022

city: Hangzhou

first: Zhi

last: Dong

state: Zhejiang

address: 866 Yuhangtang Rd, Hangzhou

institute: Zhejiang University

summary: Drosophila ovarian Follicle Stem Cells (FSC) present an excellent paradigm for understanding how a community of active stem cells maintained by population asymmetry is regulated. Here we describe single-cell RNA sequencing studies of a pre-sorted population of cells that include FSCs and the neighboring cell types, Escort Cells (ECs) and Follicle Cells (FCs), which they support. Cell-type assignment relies on anterior-posterior (AP) location within the germarium. We clarify the previously determined location of FSCs and use spatially targeted lineage studies as further confirmation. The scRNA profiles among four clusters are consistent with an AP progression from anterior ECs through posterior ECs and then FSCs, to early FCs. Several genes with graded profiles from ECs to FCs are highlighted as candidate effectors of the inverse gradients of the two principal signaling pathways, Wnt and JAK-STAT, that guide FSC differentiation and division.

overall_design: GFP positive cells from C587-GAL4 / yw; UAS-CD8-RFP/+ ovaries were sorted via Fluorescence-activated cell sorting (FACS). The sorted cells were loaded on a Chromium Single cell Controller (10 X Genomics) using the Chromium Single-cell 3’ Library & Gel Bead kit v3 according to manufacturer’s directions.

first: Lan

last: Pang

first: Zhiguo

last: Liu

first: Yifeng

last: Sheng

first: Xavier

last: Thibault

first: Amy

last: Reilein

first: Daniel

last: Kalderon

first: Jianhua

last: Huang