title: Gene expression profile of a FLT3-ITD acute myeloid leukemia cell line treated with FLT3 inhibitors for six and twelve hours

city: Cincinnati

first: Daniel

last: Starczynowski

state: Ohio

address: 3333 Burnet Ave

department: Experimental Hematology and Cancer Biology

institute: Cincinnati Children's Hospital Medical Center

summary: Adaptive resistance is an important mechanism of resistance to tyrokine kinase inhibitors in cancer. With this study we aimed to determine which signaling pathways may contribute to adaptive resistance by examining the mRNA profiles of FLT3-ITD AML cells treated with the FLT3 inhibitor, AC220. We also aimed to determine whether our novel inhibitor, NCGC1481, would inhibit the activation of these pathways. We concluded that AC220 induces activation of innate immune signaling and NCGC1481 prevents this activation.

overall_design: mRNA profiles of a FLT3-ITD AML cell line treated with AC220 or novel compound, NCGC1481, compared to DMSO control at 6 and 12 hours of treatment

first: Katelyn

last: Melgar

middle: T


title: Loss of Kat2a enhances transcriptional noise and depletes acute myeloid leukemia stem-like cells

status: Public on Feb 03 2020

city: Cambridge

first: Cristina

last: Pina

address: Long Road

department: Department of Haematology Cambridge Biomedical Campus NHS - Blood and Transplant

country: United Kingdom

institute: University of Cambridge

type: Genome binding/occupancy profiling by high throughput sequencing

type: Expression profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: RiboMeth-Seq analysis of purified U6 and U2 snRNAs

city: Regensburg

first: Gerhard

last: Lehmann

address: Universitaetsstrasse 31

department: Biochemistry 1

country: Germany

institute: University of Regensburg

summary: The La-related protein LARP7 has been mainly described as a component of the 7SK small nuclear ribonucleoprotein (snRNP) complex, which negatively regulates RNA polymerase II by sequestering the positive transcription elongation factor b (P-TEFb). In our studies, we discovered a novel, 7SK snRNP-independent function of LARP7. We show that LARP7 interacts with the U6 spliceosomal RNA as well as with the small nucleolar RNAs (snoRNAs) directing the 2'-O-methylations of U6. To investigate the relevance of this interaction, U6 or U2 snRNAs were purified from total RNA by pulldown of biotinylated antisense oligonucleotides and the occurence of 2’-O-methylations was investigated by RiboMeth-seq analysis. A comparison between U6 and U2 snRNA isolated from HEK293 wildtype or LARP7 knockout cell lines revealed that 2’-O-methylations of the U6 snRNA are specifically lost in the absence of LARP7. Alazami syndrome is a form of primary dwarfism associated with mutations in the LARP7 gene. RiboMeth-seq analyses performed with RNA isolated from blood samples of two Alazami patients or healthy parents as well as from B-lymphoblastoid cell lines (B-LCLs) derived from an Alazami patient and from a healthy parent confirmed the impact of mutant LARP7 protein variants on the 2’-O-methylation profile of the U6 snRNA.

overall_design: Three biological replicates were performed with the U6 snRNA purified from wildtype HEK293 cell and two biological replicates each from two independent HEK293 LARP7 knockout clones generated with the CRISPR/Cas9 system. 2’-O-methylations of the U2 snRNAs were analyzed from one sample derived from wildtype HEK293 cells and from two independent HEK293 LARP7 knockout clones (one sample each). HEK293 T-Rex LARP7 ko cell lines stably overexpressing FLAG/HA-tagged LARP7 wildtype or F44A mutants were assayed in two biological replicates each for U6 2’-O-methylations. U6 2’-O-methylations were also analyzed from material purified from human blood samples. Therefore, U6-snRNA originating from two siblings carrying homozygous loss-of-function mutations in the LARP7 gene and from both heterozygous parents was used for RiboMeth-Seq experiments. RiboMeth-Seq analyses of purified U6 snRNAs were also performed from total RNA extracted from two B-LCL cell lines originating either from a boy affected by the Alazami syndrome or from his non-affected father (two replicates each).

first: Daniele

last: Hasler

first: Norbert

last: Eichner

first: Erdmute

last: Kunstmann

first: Gunter

last: Meister


title: Identification of small RNAs interacting with FLAG/HA(FH)-tagged LARP7

summary: The La-related protein LARP7 has been mainly described as a component of the 7SK small nuclear ribonucleoprotein (snRNP) complex, which negatively regulates RNA polymerase II by sequestering the positive transcription elongation factor b (P-TEFb). In our studies, we discovered a novel, 7SK snRNP-independent function of LARP7. We show that LARP7 interacts with the U6 spliceosomal RNA as well as with the small nucleolar RNAs (snoRNAs) directing the 2'-O-methylations of U6. Importantly, in the absence of LARP7, significantly less 2'-O-methylations are deposited on U6 affecting splicing fidelity. Mutations in the LARP7 gene have been associated with the Alazami syndrome, a form of primordial dwarfism characterized by intellectual disability. We describe a novel loss-of-function mutation of LARP7 occurring in Alazami patients and detect reduced 2'-O-methylations of U6 in patient-derived samples. Thus, aberrant posttranscriptional RNA modifications of the spliceosomal U6 snRNA may contribute to the development of this severe disease.

overall_design: Identification of small RNAs interacting with stably expressed FH-tagged LARP7 by anti-FLAG immunoprecipitations, gel fractionation of the co-precipitated RNAs and sequencing of three distinct RNA bands.

first: Rajyalakshmi

last: Meduri

first: Utz

last: Fischer


title: Impact of homozygous loss-of-function mutations in the LARP7 gene on the pA+ transcriptome of a B-lymphoblastoid cell line (B-LCL)

summary: The La-related protein LARP7 has been mainly described as a component of the 7SK small nuclear ribonucleoprotein (snRNP) complex, which negatively regulates RNA polymerase II by sequestering the positive transcription elongation factor b (P-TEFb). In our studies, we discovered a novel, 7SK snRNP-independent function of LARP7. We show that LARP7 interacts with the U6 spliceosomal RNA as well as with the small nucleolar RNAs (snoRNAs) directing the 2'-O-methylations of U6. Importantly, in the absence of LARP7, significantly less 2'-O-methylations are deposited on U6 affecting splicing fidelity. Mutations in the LARP7 gene have been associated with the Alazami syndrome, a form of primary dwarfism characterized by intellectual disability. We describe a novel loss-of-function mutation of LARP7 occurring in Alazami patients and detect reduced 2'-O-methylations of U6 in patient-derived samples. Thus, aberrant posttranscriptional RNA modifications of the spliceosomal U6 snRNA may contribute to the development of this severe disease.

overall_design: Analysis of the impact of homozygous loss-of-function mutations in the LARP7 gene on the expression and the alternative splicing of pA+ RNA transcripts. Two replicates each of a B-LCL derived from a boy diagnosed for the Alazami syndrome and carrying an homozygous mutations in the LARP7 gene (cell line AAAS14, established from the donor at the age of 4 years) and a B-LCL derived from the healthy father, heterozygous for the LARP7 mutation (cell line  AASD72, established from the donor at the age of 46 years)

first: Maciej

last: Bak

first: Mihaela

last: Zavolan


title: Transcriptomic profiles reveal differences between the right and left ventricle (RV and LV) in both normoxia and hypoxia

city: La Jolla

first: Paul

middle: A

last: Insel

state: CA

address: 9500 Gilman Drive

department: Pharmacology

country: USA

institute: UC San Diego

summary: We performed RNA-seq to analyze gene expression in rat cardiac tissue from the left and right ventricle for animals in a) normoxia and b) exposed to hypoxia (10% O2) for 2 weeks

overall_design: Three biological replicates each in four groups a) Right Ventricle, Normoxia; b) Left Ventricle, Normoxia; c) Right Ventricle, Hypoxia; d) Left Ventricle, Hypoxia

first: Matthew

middle: W

last: Gorr

first: Krishna

last: Sriram


title: Widespread EJC footprints in the RNA degradome mark mRNA degradation before steady-state translation

status: Public on Feb 02 2020

city: Nankang

first: Ho-Ming

last: Chen

state: Taipei

address: No. 128, Sec. 2, Academia Road

department: Agricultural Biotechnology Research Center

country: Taiwan

institute: Academia Sinica

summary: Exon junction complexes (EJCs) are deposited to mRNAs during splicing and displaced from mRNAs by ribosomes in the pioneer round of translation. The understanding of EJC-bound mRNA degradation before steady-state translation has been limited to nonsense-mediated mRNA decay (NMD) due to a lack of suitable methodologies. Here, we show that RNA degradome data of Arabidopsis, rice, worm and human cells all exhibit a predominant accumulation of 5′ monophosphate (5′P) ends in the canonical EJC region. Inhibition of 5′-3′ exoribonuclease activity and overexpression of an EJC disassembly factor in Arabidopsis reduced the 5′P ends accumulating in the EJC region, supporting the notion that these 5′P ends are in vivo EJC footprints. Hundreds of Arabidopsis NMD targets possess evident EJC footprints, validating their degradation during the pioneer round of translation. In addition to premature termination codons, plant microRNAs can also direct the degradation of EJC-bound mRNAs. However, the production of EJC footprints from NMD but not microRNA targets is dependent on an NMD factor, SMG7. Together, our finding demonstrating in vivo EJC footprinting unravels the composition of the RNA degradome, and provides a new avenue for studying NMD and other mechanisms, such as microRNAs, targeting EJC-bound mRNAs for degradation before steady-state translation.

overall_design: Profiling 5' ends of RNA degradation intermediates in Arabidopsis thaliana by parallel analysis of RNA ends (PARE)

first: Wen-Chi

last: Lee

first: Bo-Han

last: Hou

first: Cheng-Yu

first: Shu-Ming

last: Tsao

first: Ping

last: Kao


title: Gene expression profiles of wild-type and PERK-deficient cells during activation of OXPHOS

city: Miyazaki City

first: Hideki

last: Nishitoh

state: Miyazaki Prefecture

address: 5200 Kihara, Kiyotake

department: Department of Medical Sciences

country: Japan

institute: University of Miyazaki

summary: Intracellular ATP is mainly produced by the glycolysis pathway in culture cells incubated with high-glucose medium, whereas ATP production is switched to the OXPHOS pathway by culturing with the no-glucose medium. To elucidate the potential function of PERK during activation of OXPHOS pathway, we perfomed RNA-sequencing analayais using wild-type and PERK-deficient HEK293 cells.

overall_design: Examination of gene expression in wild-type and PERK-deficient HEK293 cells during  activation of OXPHOS.

first: Hironori

last: Kato

first: Kousuke

last: Tanimoto


title: Human endothelial cell microRNA expression in high and low stiffness

city: New Haven

first: Stefania

last: Nicoli

state: CT

address: 300 George street

department: Internal Medicine

institute: Yale University

type: Non-coding RNA profiling by high throughput sequencing


title: Human endothelial cell microRNA expression in high and low stiffness [sRNA-seq]

summary: Purpose: Mechanical homeostasis is a crucial process for endothelial cell (EC) survival and functionality. Cells can sense environmental change and modify the expression of extracellular matrix, focal adhesion and cytoskeleton protein to maintain the correct mechanical homeostasis. In this study, we observed change in microRNA levels linked with mechanical response. ECs were seeded for 48 hour on PDMS 3 kPa and 30 kPa substrate coating with fibronectin to simulate "soft" and "stiff" substrate, then sRNA-seq was performed.

overall_design: Endothelial cells (ECs) were seeded for 48h on substrate at 3 and 30 kPa to approximate “soft” and “rigid” tissue, respectively. SRNA-seq was performed to establish the microRNA profile in the two conditions.

first: Albertomaria

last: Moro

first: Driscoll

last: Tristan

first: Dionna

last: Kasper


title: Human endothelial cell microRNA expression in high and low stiffness [RNA-seq]

summary: Purpose: Mechanical homeostasis is a crucial process for endothelial cell (EC) survival and functionality. Cells can sense environmental change and modify the expression of extracellular matrix, focal adhesion and cytoskeleton protein to maintain the correct mechanical homeostasis. In this study, we observed change in mRNA levels linked with mechanical response. ECs were seeded for 48 hour on PDMS 3 kPa and 30 kPa substrate coating with fibronectin to simulate "soft" and "stiff" substrate, then RNA-seq was performed.

overall_design: Endothelial cells (ECs) were seeded for 48h on substrate at 3 and 30 kPa to approximate “soft” and “rigid” tissue, respectively. RNA-seq was performed to establish the mRNA profile in the two conditions.


title: Ribosomes guide pachytene piRNA formation on long intergenic piRNA precursors

city: Rochester

first: Xin

last: Li

state: NY

address: 601 Elmwood Ave.

department: Biochemistry and biophysics

institute: University of Rochester Med Center

summary: PIWI-interacting RNAs (piRNAs) are a class of small non-coding RNAs essential for fertility. In adult mouse testes, most piRNAs are derived from long single-stranded RNAs lacking annotated open reading frames (ORFs). The mechanisms underlying how piRNA sequences are defined during the cleavages of piRNA precursors remain elusive. Here, we show that 80S ribosomes translate the 5′-proximal short ORFs (uORFs) of piRNA precursors. The MOV10L1/Armitage RNA helicase then facilitates the translocation of ribosomes into the uORF downstream regions (UDRs). The ribosome-bound UDRs are targeted by piRNA processing machinery, with the processed ribosome-protected regions becoming piRNAs. The dual modes of interaction between ribosomes and piRNA precursors underlie the distinct piRNA biogenesis requirements at uORFs and UDRs. Ribosomes also mediate piRNA processing in roosters and green lizards, implying that this mechanism is evolutionarily conserved in amniotes. Our results uncover a function for ribosomes on non-coding regions of RNAs and reveal the mechanisms underlying how piRNAs are defined.

sample_organism:
Mus musculus
Anolis carolinensis

platform_organism:
Mus musculus
Anolis carolinensis

overall_design: High-throughput sequencing data including RNAseq, small RNAseq, Ribo-seq and Degradome-seq of mouse and lizard testis.

middle: Z

first: Yu

middle: H

last: Sun


title: Transcriptomic profiling of MLL-r AML PDX cells treated with CDKI-73 and/or JQ1

city: Adelaide

first: Richard

last: D'Andrea

state: South Australia

address: Cancer Research Institute, Frome Road

department: Centre for Cancer Biology

country: Australia

institute: University of South Australia

overall_design:
RNA was extracted from MLL-r AML PDX cells treated with CDKI-73, JQ1, or a combination of aforemetioned compounds for 4 hours, and transcriptome was profiled using RNA-Seq
Cryopreserved MLL-r AML (AML-18) PDX cells were thawed and allowed to equilibrate for 3 hours prior to in vitro drug treatment with 250 nM CDKI-73, 1480 nM JQ1 the combination of both drugs or vehicle control (DMSO). After 4 hours, total RNA was extracted using TRIzol (Invitrogen) and purified using the RNeasy kit (Qiagen). Whole transcriptome libraries were prepared using the Illumina TruSeq Stranded Total RNA Sample Preparation Kit with Ribo-Zero Gold rRNA depletion. Sequencing was performed using the Illumina HiSEQ2500 platform as 100 bp single ended sequencing

first: Luke

last: Jones

first: Ka

middle: L


title: Gene expression profiles of control or PERK siRNA-transfected brown adipocyte during the differentiation

summary: The area of mitochondria in differentiated brown adipocytes is dramatically increased compared with that in brown pre-adipocytes. The ATP production is switched from the glycolysis pathway to the OXPHOS pathway during brown adipocyte differentiation. Endoplasmic reticulum (ER) is surrounded by mitochondria and the area of contact sites between mitochondria and the ER is increased. ER stress sensor PERK was phosphorylated during differentiation. To elucidate the mitochondria-ER crosstalk signaling mediated by PERK, RNA-sequencing analysis was performed using control siRNA- or PERK siRNA-transfected brown adipocytes.

overall_design: Examination of gene expression in control or PERK siRNA-transfected brown adipocyte during  the differentiation.


title: RNA-seq in putamen of Multiple system atrophy patients

status: Public on Feb 01 2020

city: Copenhagen NW

first: Rasmus

last: Rydbirk

state: Please Select

address: Nielsine Nielsens Vej 6B, stair 11B, 2nd Floor

department: Department of Neurology

country: Denmark

institute: Bispebjerg-Frederiksberg Hospital

summary: We performed RNA-seq on total RNA from tissue samples from putamen of the brain from Multiple system atrophy patients.

overall_design:
Total RNA was extracted from tissue samples from ten Multiple system atrophy patients. rRNA was depleted before sequencing. Samples were sequenced in duplicates, creating two paired-end experiments per sample.
contributor:  Bispebjerg Brain Bank

first: Tomasz

last: Brudek

first: Thomas

middle: M

last: Hyde

first: Bente

last: Pakkenberg

first: Susana

last: Aznar


title: Transcriptomic analysis of regulatory gene expression profiles by EIJ1 under Pst D3000 treatments

city: Guangzhou

first: Hailun

last: Liu

address: No.723, Xingke Road, Tianhe District

country: China

institute: Chinese Academy of Sciences

summary: To understand how the EIJ1 complex functions in plant innate immunity, a genome-wide transcriptomic analysis was carried out using 3-week-old of eij1-1 and Col plants under dip inoculated with Pst DC3000 (OD600 = 0.1) treatment. Basing on the criteria of 2-fold cutoff for the genes with 5% false discovery rate, we first identified the differentially expressed genes in eij1_P vs Col_P, which are referred to stress response and innate immune response. These data suggest that EIJ1 may be involved in plant immune response.

overall_design: Three-week-old of eij1-1 and Col plants were dip inoculated with Pst DC3000 (OD600 = 0.1). The treated leaves were collected at 24 hpi. RNA sequencing was performed by the Biomarker Technologies Corporation (Beijing, China) using an Illumina NovaSeq platform.

first: Xingliang

last: Hou


title: RNA-seq in putamen of Parkinson's disease patients

summary: We performed RNA-seq on total RNA from tissue samples from putamen of the brain from Parkinson's disease patients.

overall_design:
Total RNA was extracted from tissue samples from ten Parkinson's disease patients. rRNA was depleted before sequencing. Samples were sequenced in duplicates, creating two paired-end experiments per sample.
contributor: Harvard Brain Tissue Resource Center


title: RNA-seq to identify targets of integrin alpha2 in breast cancer

city: Chicago

first: Huiping

state: IL

address: 303 E Superior

institute: Northwestern University

summary: Knockdown of ITGA2 was done in MDA-MB-231 cells and RNA-seq results were compared to control cells.

overall_design:
RNA-seq analysis were done in triplicates of knockdown control and ITGA2 knockdown.
Submitted by: Nuseq Core facility of Northwestern


title: Statin regulated microRNAs in human umbilical vein endothelial cells

first: hyung

last: chun

address: 300 George St Room 770H

summary: Evaluation of microRNAs that are regulated by statin stimulation of endothelial cells

overall_design: Triplicates per group, subjected to: 1) DMSO (vehicle), 2) simvastatin (10 micromolar)

first: Hyung

middle: J

last: Chun


title: Next Generation Sequencing Analysis of CircRNAs/linear RNA in Isolated Renal Proximal Tubule tissues from Acute kidney injury mice

city: Chengdu

first: Wanxin

last: Tang

state: Sichuan

address: No.37, Guoxue alley, Department of nephrology, West China Hospital, Sichuan University,

summary: The goal of this study was to find the differentially expressed circRNAs/linear RNA in AKI mice model compared to normal mice. We established cisplatin-induced AKI mice models and then extracted RNAs from isolated renal tubular tissues for Next Generation Sequencing(NGS) at different time points during early stage of AKI. CircRNA library was constructed by NEB Next®Ultra™ small RNA Sample Library Prep Kit for Illumina®. NGS was performed by using Illumina HiSeq 2500 Genome Sequencers.The original image data file was transformed into Raw Data by Base Calling. Clean Data was obtained by removing reads that containing joints and more than 5% N (undetermined base information). Mapped Reads were obtained by sequence alignment between Clean Reads and reference genome sequenced using BWA software package. CIRI software was used to predict circRNAs. Finally, we identified 2162 circRNAs and our study  represents the first detailed analysis of AKI mice circRNA transcriptomes, which provide a framework for investigations of circRNAs expression profiles in AKI

overall_design: Examination of 8 proximal tubule tissues from 4 different time points.  Each time point has a biological duplication.

first: Dongmei

last: Zhang

first: Yiling

last: Cao

first: Zheng

last: Wang

first: Yongdi

last: Zuo


title: Transcription profiling of tomato plants overexpressing SlMYB14

city: Shanghai

first: zhenjun

last: li

address: Beidi rd 2901

institute: Shanghai academy of agricultural sciences

summary: In order to investigate the possible molecular mechanisms of SlMYB14 function in plant growth and stress responses, we employed the RNA-seq approach to identify the genes with altered expression levels in SlMYB14 transgenic plants.

overall_design: RNA-sequencing was carried out using two independent transgenic lines (OE5, OE7). Total RNA was isolated with Trizol reagent (Invitrogen, USA) from the aerial part of the one-week-old seedlings of 35Spro:SlMYB14 （OE5 and OE7）and Zhongshu 4 (ZS4) plants grown in parallel under unstressed conditions. Materials from 10 plants of each genotype were pooled for RNA isolation.

first: Zhenjun

last: Li

first: Quanhong

last: Yao


title: Analysis of DNA Methylation in Sperm, egg cell, fertilized zygote and preimplantation embryonic cells

city: guangzhou

first: yuling

last: huang

address: No. 250, Changgang East Road, Haizhu District, Guangzhou

institute: Center for Reproductive Medicine, Third Affiliated Hospital of Guangzhou Medical University

type: Methylation profiling by genome tiling array

summary: 10% of methylation sites in CpG islands. In this study, the genome-wide CpG islands of human sperm, oocyte and pre-implantation embryos were analyzed using the almost complete coverage of promoters and CpG islands (most methylation-producing regions) methylation microarray method (MeDIP-Chip). Dynamic changes in methylation of sub-regions to understand the dynamic pattern of CpG island and promoter methylation, possible regulatory mechanisms of this methylation dynamic change, and function during early embryonic development.

overall_design: This study showed that the methylation of whole-genome CpG islands in human pre-implantation embryos showed a unique dynamic pattern: after fertilization, the prokaryotic nucleus began to demethylate, and the 4cell phase of the whole genome CpG island had the lowest degree of methylation, and then gradually re-established. The methylation pattern was established; the ICM methylation level in the blastocyst stage was close to that of the oocyte, and the methylation level of TE was between the oocyte and the sperm; while the human and mammalian preimplantation embryos were in the whole genome. The lowest level of the level is in the ICM stage. There are three dramatic changes in the methylation of CpG islands in the pre-embryo of the genome at different developmental stages. The main stage of methylation erasure of CpG islands is 4cell phase, while the whole genome-wide erasure is in 2cell phase.

first: Yuling

last: Huang

first: Lei


title: Dysregulated RPB1 is a targetable master driver of overgrowth  in acute myeloid leukemia.

city: Hangzhou

first: Qingfeng

last: Yu

state: Zhejiang

address: No.88 Jiefang Road

department: Department of Hematology and Cancer Institute

institute: The Second Affiliated Hospital, Zhejiang University School of Medicine

summary: Dysregulated RPB1 is a critical oncogenic hub that drives overgrowth hijacking an array of oncogenic and anti-apoptosis factors.Targeting RPB1 leads to potent regression of human refractory AML in mouse models.

overall_design: To reveal the biological basis of POLR2A dependency of AML cells, we performed genetic silence of POLR2A in a highly aggressive human AML cell line MOLM-13 using doxycycline (Dox)-inducible CRISPR/Cas9 mediated POLR2A knockout system, and examined the effects of POLR2A silence on proliferation and viability of MOLM-13 cells. The biological basis of POLR2A between the control and POLR2A-KO cells were generated by deep sequencing, using Illumina HiSeq 4000.

first: Jiwei


title: Impact of Tle1, Tle3, and Tle4 deficiency on hematopoietic stem cells (HSCs) [RNA-seq]

city: Xi'an

first: Xiaoke

last: Ma

state: Shaanxi

address: No.2 South TaiBai Road

institute: Xidian University

summary:
To compare the transcriptomes between control and Tle1/3/4-deficient HSCs
Tle co-repressors can co-opt a number of transcription factors to repress target gene expression. Due to gene duplication during evolution, there are 4 Tle genes in mammalian genome, and their functional redundancy has a major hurdle to understand their roles in hematopoietic stem cells (HSCs). Here we used Vav-Cre to ablate Tle1, 3, and 4 genes in HSCs, and performed RNA-seq to determine the impact of Tle deficiency on HSCs. To further define the regulatory mechanisms, we performed Tle3 ChIPseq on c-Kit+ hematopoietic progenitor cells. The data obtained collectively indicate a critical, intrinsic requirement for Tle corepressors in HSC self-renewal.

overall_design: Bone marrow cells were harvested from control or Tle1/3/4-deficient mice. For the latter, all three Tle genes were floxed, and Vav-Cre was used to excise the floxed genes in all hematopoietic cells including HSCs. Lin-cKit+Sca1+ CD150+CD48– HSCs were sort-purified for total RNA extraction.

first: Hai-Hui

last: Xue


title: Genome-wide maps of Tle3 binding in hematopoietic progenitor cells [ChIP-seq]

summary:
To determine Genome-wide Tle3 binding locations in c-Kit+ mouse bone marrow cells
Tle co-repressors can co-opt a number of transcription factors to repress target gene expression. Due to gene duplication during evolution, there are 4 Tle genes in mammalian genome, and their functional redundancy has a major hurdle to understand their roles in hematopoietic stem cells (HSCs). Here we used Vav-Cre to ablate Tle1, 3, and 4 genes in HSCs, and performed RNA-seq to determine the impact of Tle deficiency on HSCs. To further define the regulatory mechanisms, we performed Tle3 ChIPseq on c-Kit+ hematopoietic progenitor cells. The data obtained collectively indicate a critical, intrinsic requirement for Tle corepressors in HSC self-renewal.

overall_design: WT C57BL/6 mice at 8-10 weeks old were used to purify for lineage-negative, cKit-positive bone marrow cells, and the cells were used in ChIP-Seq analysis.


title: Genome-wide maps of Tle3 binding and Tle1/3/4 deficiency on hematopoietic stem cells

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

overall_design: Refer to individual Series


title: Nucleosome profiles in strains with different inter-NDR distances at HML

status: Public on Feb 06 2020

city: Berkeley

first: Daniel

middle: S

last: Saxton

address: 100 University Ave

department: MCB

institute: University of California Berkeley

summary: Heterochromatin is a complex structure comprised of nucleosome arrays that are bound by silencing factors. This composition suggests that certain configurations of nucleosome arrays are permissible for heterochromatic silencing. We tested this idea in S. cerevisiae by systematically altering the distance between heterochromatic Nucleosome Depleted Regions (NDRs), which is predicted to affect local nucleosome positioning by limiting how nucleosomes can be packed between NDRs. Consistent with this prediction, some inter-NDR distances led to poorly positioned nucleosome arrays within heterochromatin. Furthermore, these conditions that caused poor nucleosome positioning also led to defects in both heterochromatin stability and the ability of cells to generate and inherit a silenced transcriptional state. These findings strongly suggest that nucleosome positioning contributes to formation and maintenance of functional heterochromatin.

overall_design:
We report nucleosome positions by using native Mnase-seq. The results strongly suggest that inter-NDR (nucleosomal depleted region) distance affects nucleosome positioning at HML.
Genome-wide analysis of nucleosome positions in strains of interest, with a particular focus on nucleosome positioning at HML.

first: Jasper

last: Rine


title: Tissue responses to Shiga toxin in human intestinal organoids

city: Cincinnati

first: Alison

last: Weiss

address: 231 Albert Sabin Way

department: COM Molecular Genetics

institute: University of Cincinnati

summary: Intestinal tissue responses to protein synthesis inhibition by Shiga toxin are complex.  Organoid models allow for an unprecedented examination of human tissue responses to a deadly Shiga toxin.

overall_design: Comparison of RNA profile for gene upregulation and downregulation in organoids microinjected with PBS and Shiga toxin.

first: Suman

last: Pradhan


title: miR-335 overexpression effect on HUVEC gene expression

first: hyung

last: chun

summary: Evaluation of gene transcripts that are affected by miR-335 overexpression in HUVECs

overall_design: Duplicates per group, subjected to: 1) GFP-lentivirus overexpression, 2) miR-335 GFP lentivirus overexpression

first: Hyung

last: Chun


title: Peptides encoded by 5’ untranslated regions mediate pain sensitization

city: Richardson

first: Theodore

last: Price

state: TX

address: 800 W Campbell Rd.

institute: University of Texas at Dallas

summary: Nociceptors are neurons responsible for the detection of pain producing stimuli. Persistent changes in their activity, termed plasticity, benefit survival through injury avoidance and are regulated on a translational basis. Yet, the mRNAs whose translation facilitates plasticity are unknown. Here, we apply ribosome profiling to dorsal root ganglion and identify a small number of transcripts that are selectively translated in response to plasticity mediators. Among them are Arc and Fos, genes implicated in episodic learning in the brain. We demonstrate that the ribosomal S6 kinase 1 is responsible for their production in nociceptors. Blocking S6 driven translation also reduces pain associated behavioral responses in vivo. In addition to translation of coding regions of mRNA, we detect pervasive ribosome occupancy in 5’ untranslated regions. We find that peptides encoded by open reading frames in the 5’ untranslated regions of Calca and Egr2 increase neuronal excitability in vitro and are sufficient to induce pain-like behaviors in vivo. Together, our findings uncover new targets of translational control that drive changes in plasticity and suggest new mechanisms for targeted pain therapeutics that disrupt pain signaling.

overall_design: We applied ribosome profiling to DRG neurons in culture in response to NGF/IL-6 treatment

first: Paulino

last: Barragan-Iglesias

first: June

middle: B

last: de la Peña

first: Tzu-Fang

last: Lou

first: Andi

last: Wanghzou

first: Bryan

last: Black

first: Nikesh

last: Kunder

first: Salim

last: Megat

first: Jamie

middle: K

last: Moy

first: Pradyta

middle: R

last: Ray

first: Tarjani

last: Shukla

first: Joseph

last: Pancrazio

first: Zachary

last: Campbell


title: Circular RNA Expression is Suppressed by Androgen Receptor (AR) Regulated Adenosine DeAminase that act on RNA (ADAR1) in Human Hepatocellular Carcinoma

first: Cai

last: Xiujun

state: State...

address: #204b  Conant Road 204B

department: general surgery

institute: university of Zhejiang

summary: Hepatocellular carcinoma (HCC) is a heterogeneous malignancy as a result of complex genetic and epigenetic alterations. HCC is characterized by a clear gender disparity for which lacking a clear mechanistic understanding. By utilizing circular RNA (circRNA) microarray survey coupled with in vitro analysis, we analyzed the influence of androgen receptor (AR) on circRNA expression in HCC. Our results indicated that AR could suppress circRNA expression by up-regulating adenosine deaminase that act on RNA (ADAR1) p110 at a transcriptional level. Reporter assay further confirmed the role of AR as a transcriptional activator of ADAR1 expression. Furthermore, data collected from our center strongly suggest that ADAR1 expression can effectively predict HCC patients’ prognosis and an abnormal overexpression of ADAR1 is positively correlated with AR in HCC. In addition, we found CircARSP91 (hsa_circ_0085154), one of the circRNAs down-regulated by AR in an ADAR1-dependent manner, could inhibit HCC tumor growth both in vitro and in vivo. These findings highlight the fact that AR as a contributing factor for gender disparity in HCC can cause complex consequences though regulation of circRNA expression. Better understanding of roles of circRNA during HCC initiation and progression will be a key to develop novel HCC therapies.

overall_design:
[i] We detected the circular RNA expression profile of shAR-MHCC-97H (named as s97H.shAR) and shScr-MHCC-97H (named as s97H.PLKO). The stable transfected cells was established by using lenti-virus system. The knocking-down or overexpression efficiency was verified on both mRNA level and protein level.
[ii] We detected the circular RNA expression profile of oeAR-LO2 (named as LO2.AR) and vector-LO2 (named as LO2.PWPI). The stable transfected cells was established by using lenti-virus system. The knocking-down or overexpression efficiency was verified on both mRNA level and protein level.

first: Xiujun

last: Cai

first: Liang

last: Shi


title: Comparison of expression profiles of SCD::Keap1F/F and SCD::Keap1F/F::Tie1-Cre mouse pulmonary primary endothelial cells(MPPCECs)

city: Sendai

first: Masayuki

last: Yamamoto

address: 2-1 Seiryo-machi, Aoba-ku

department: Medical Biochemistry

institute: Tohoku University Graduate School of Medicine

summary: This experiment evaluate the expression level of Nrf2 genes transcript in mouse primary endothelial cells of  a pathology model mice of Sickle cell disease (SCD). Constitutive activation of Nrf2 in SCD suppresses inflammation and organ injury. In the present study we aim to assess the benefit of specific- cell Nrf2 activation in endothelial ceels exclusively.

overall_design: mRNA profiles of SCD::Keap1F/F and SCD::Keap1F/F::Tie1-Cre of MPPCECs  were generated by deep sequencing, in triplicate.

first: Nadine

last: Keleku-Lukwete

first: Suzuki

last: Mikiko

first: Harit

last: Panda

first: Akihito

last: Otsuki

first: Fumiki

last: Katsuoka

first: Ritsumi

last: Saitou

first: Daisuke

last: Saigusa

first: Akira

last: Uruno


title: Genome-wide distribution of H2AS40Gc in mouse embryonic stem cells.

city: Imabari-shi

first: Koji

last: Hayakawa

state: Ehime

address: 1-3 Ikoino-oka

department: Department of Toxicology, Faculty of Veterinary Medicine

institute: Okayama University of Science

summary: We report genome-wide distribution of O-GlcNAcylated H2A at serine 40 (H2AS40Gc) in mouse embryonic stem cells (mESCs, J1 line) cultured in 25 mM glucose (HG-mESCs) or 1 mM glucose (LG-mESCs) condition. We found that H2AS40Gc was mainly located at genic area, positively correlated with the gene expression both in HG- and LG-mESCs. Interestingly, H2AS40Gc localization was overlapped with H2AX, γH2AX and O-GlcNAc transferase (Ogt), and varied by extracellular glucose concentration. This study using ChIP-seq and RNA-seq analysis provides genomic distribution of newly O-GlcNAc histone modification in mESCs.

overall_design: ChIP-seq of H2AS40Gc and RNA-seq analysis in HG-mESCs and LG-mESCs.

first: Kunio

last: Shiota


title: Arabidopsis thaliana Wild-type vs. mutant (PcG)

city: Strasbourg

first: Wen-Hui

last: Shen

address: 12 rue du General Zimmer

country: France

institute: IBMP-CNRS

summary: Transcriptional profiling of Arabidopsis wild-type (Col0) control flower buds or seedlings with corresponding mutant flower buds or seedlings is performed using Aligent's Whole Arabidopsis Gene Expression Microarray (G2519F, V4, 4x44K).

overall_design: Flower buds of wild-type Col0 control _vs_ Flower buds of mutant Atring1ab, lhp1 or clf ; 7-day-old seedlings of wild-type Col0 control _vs_ 7-day-old seedlings of mutant Atring1ab. Two or three biological replicates: 2 or 3 control, 2 or 3 mutant, independently grown and harvested. One replicate per array.

first: Anne

last: Molitor

first: Donghong

last: Chen


title: Local inhibition of protein phosphatase 1 by NUAK1 promotes spliceosome assembly and reveals a MYC-sensitive feedback control of transcriptional elongation

city: Wuerzburg

first: Martin

last: Eilers

address: Am Hubland

department: Chair for Biochemistry and Molecular Biology

institute: University of Wuerzburg

summary: Deregulated expression of MYC induces a dependence on the NUAK1 kinase, but the molecular mechanisms underlying this dependence have not been fully clarified. Here we show that NUAK1 is a predominantly nuclear protein that associates with a network of nuclear protein phosphatase 1 (PP1) interactors and that PNUTS, a nuclear regulatory subunit of PP1, is phosphorylated by NUAK1. Both NUAK1 and PNUTS associate with the splicing machinery. Inhibition of NUAK1 abolishes chromatin association of PNUTS, reduces spliceosome activity and suppresses nascent RNA synthesis. Activation of MYC does not bypass the requirement for NUAK1 for spliceosome activity, but significantly attenuates transcription inhibition. Consequently, NUAK1 inhibition in MYC-transformed cells induces global accumulation of RNAPII both at the pause-site and at the first exon/intron boundary, but does not increase mRNA synthesis. We suggest that NUAK1 inhibition in the presence of deregulated MYC traps non-productive RNAPII due to the absence of correctly assembled spliceosomes.

overall_design: 4sU-, mRNA- and RNAPII- or PNUTS-ChIP-seq after inhibition of NUAK1 in U2OS cells.

first: Giacomo

last: Cossa

first: Isabelle

last: Roeschert

first: Florian

last: Prinz

first: Apoorva

last: Baluapuri

first: Raphael

last: Vidal

first: Christina

last: Schülein-Völk

first: Yun-Chien

last: Chang

first: Carsten

middle: P

last: Ade

first: Guido

last: Mastrobuoni

first: Cyrille

last: Girard

first: Lars

last: Wortmann

first: Susanne

last: Walz

first: Reinhard

last: Lührmann

first: Stefan

last: Kempa

first: Bernhard

last: Kuster

first: Elmar

last: Wolf

first: Dominik

last: Mumberg


title: Integrated analysis of miRNA-mRNA interactions reveals novel target pathways in hypertension-induced cardiac remodeling (mRNA-seq dataset)

status: Public on Jan 31 2020

city: Fuzhou

first: Jun

last: Peng

state: Fujian

address: 1 Qiuyang Road, Minhou Shangjie

department: Academy of Integrative Medicine

institute: Fujian University of Traditional Chinese Medicine

summary: The goals of the study are to compare differently expressed genes in heart tissues of hypertensive rats (spontaneously Hypertension Rats, SHR) with age-matched control rats (wistar Rats, WKY),  identify new targets to reverse hypertension induced cardiac remodeling  and idetify the targets of Traditional Chinese Medicine QDG.

overall_design: RNA sequencing was performed with heart tissue of  NS or QDG treated SHRs and WKY Rats (n = 6 for each group) to identify the differently expressed genes and related pathway.

first: Jianfeng

last: Chu

first: Xiangyan

last: Wu

first: Aling

last: Shen

first: Ying

last: Cheng

first: Zhiqing

first: Meizhu


title: Integrated analysis of miRNA-mRNA interactions reveals novel target pathways in hypertension-induced cardiac remodeling (miRNA-seq dataset)

summary: The goals of the study are to compare differently expressed genes in heart tissues of hypertensive rats (spoutaneously Hypertension Rats, SHR) with age-matched control rats (wistar Rats, WKY),  identify new targets to reverse hypertension induced cardiac remodeling  and idetify the targets of Traditional Chinese Medicine QDG.


title: Integrated analysis of miRNA-mRNA interactions reveals novel target pathways in hypertension-induced cardiac remodeling


title: MNase-seq analysis in human breast cancer cells

city: RTP

first: Takashi

last: Shimbo

address: 111 TW Alexander Dr.

institute: NIH/NIEHS

summary: Nucleosomes are the most basic units of chromatin and are regulators of genome integrity and gene expression.  The fundamental mechanism how nucleosomes are dynamically regulated is one of the main questions in chromatin organization; most of the study has, however, focused on its positioning.  Here we performed HiLo-MNase-seq, which involves limit and partial digestion of chromatin by micrococcal nuclease (MNase) to identify the positioning of nucleosome array along with the kinetics of MNase digestion.  We identified a subset of unique nucleosomes with fast digestion kinetics at the transcription factor binding sites that have been characterized as nucleosome depleted regions (NDRs).  By inhibiting RNA polymerase II, we also showed that those nucleosomes changed its sensitivity to MNase in a context-dependent manner. These findings implicated a self-reinforcing regulatory network involving nucleosomes, Pol II, and transcription factors for fine-tuning of gene expression.

overall_design: MNase-seq experiment was performed in human breast cancer cells, MCF-7. Two biological replicates were prepared.

first: Grimm

last: Sara

first: Paul

last: Wade


title: Profiling of alternative transcription start sites and alternative polyadenylation sites in Xenopus tropicalis

city: Pullman

first: Zhihua

last: Jiang

state: WA

address: Veterinary and Biomedical Research Building, Room 151

department: Animal Science

institute: Washington State University

summary: We have developed both WTSS-seq (whole transcriptome start site sequencing) and WTTS-seq (whole transcriptome termini site sequencing) methods to capture either 5’- or 3’-ends of transcripts. HATT-seq (head and tail tag sequencing) is still under development, which can be used to capture both 5’- and 3’ ends of each transcript simultaneously.  Iso-seq was used to produce full-length transcripts, which can be used to validate both alternative transcription start sites and alternative polyadenylation sites. CAGE-seq was used to confirm alternative transcription start sites only.

overall_design: A total of 14 WTSS-seq libraries were constructed using six individual adult males, six individual adult females and an RNA pool with three adult females (repeated twice). One CAGE-seq library was prepared with the three adult female pool using service provided by DNAFORM Precision Gene Technologies, Yokohama, Japan. The same three-female pool was used to develop one HATT-seq library. The same six individual males and six individual females were also used to profile 3’-ends of transcripts using WTTS-seq for a total of 12 libraries.  One embryo pool was formed using total RNA collected from two families at stage 6, 8, 11, 15 and 28. As well, an adult pool was prepared from three male and three female adults.  The embryo and adult pools were used to construct a total of one Iso-seq libraries.  In brief, this submission involved 30 libraries in total.

first: Xiang

last: Zhou

first: Yangzi

last: Zhang

first: Jennifer

last: Michal

first: Lujiang

last: Qu


title: The G-protein coupled receptor GPR8 regulates secondary metabolism and mating associated chemical communication in Trichoderma reesei

city: Vienna

first: Monika

last: Schmoll

address: Djerassiplatz 1

department: Centre of Microbiology and Environmental Systems Science

country: Austria

institute: University of Vienna

summary: GPR8 exerts a light dependent function on secondary metabolism, which is in part mediated by YPR2 and the function of SOR7

overall_design: Strains of this study were grown on Mandels Andreotti Minimal Medium with 1 % w/v microcrystalline cellulose as  carbon source in constant light or constant darkness.

first: Wolfgang

last: Hinterdobler

first: Alberto

last: Monroy

first: Sabrina

last: Beier


title: Whole-transcriptome sequencing of A549 cells and cisplatin-resistance A549/DPP cells

city: Huai'an

first: Jie

state: Jiangsu

address: Huaihai South Road

department: Department of Respiratory Diseases

institute: the Affiliated Huai’an Hospital of Xuzhou Medical University

summary: The aim of this study was to investigate the molecular mechanisms underlying cisplatin 14 (DDP) resistance in non-small cell lung cancer (NSCLC) cells by constructing a competing 15 endogenous RNA (ceRNA) network.

overall_design: The gene expression profiles of human lung adenocarcinoma DDP-resistant cell line (A549/DDP) and its progenitor (A549) were comparatively evaluated by whole-transcriptome sequencing. The differentially expressed genes (DEGs) were subjected to KEGG pathway analysis. The expression levels of mRNAs involved in several pathways associated with conferring DDP resistance to tumor cells were evaluated. The ceRNA network was constructed based on the mRNA expression levels and the sequencing data of miRNA and lncRNA. Several ceRNA regulatory relationships were validated

first: Yufeng

last: Wan


title: DNA methylation data from 13 ATRT tumor samples

city: Heidelberg

first: Martin

last: Sill

address: Im Neuenheimer Feld 280

department: Division of Pediatric Neurooncology

institute: DKFZ

summary: The samples deposited here are part of the ATRT consensus cohort as published in Ho et al. ("Molecular subgrouping of Atypical Teratoid/Rhabdoid Tumors (ATRT) - a reinvestigation and current consensus") and have so far not been included in any publication.

overall_design: 13 ATRT samples were selected for DNA extraction and hybridization on Illumina DNA methylation arrays to determine their molecular subtype.

first: Pascal

last: Johann

first: Ben

last: Ho

first: Yura

last: Grabovska

first: Marcel

last: Kool

first: Daniel

last: Williamson

first: Annie

last: Huang


title: DNA methylation data from 153 ATRT tumor samples

summary: Clinical and molecular risk factors were analyzed in a large cohort of patients with Atypical Teratoid Rhabdoid Tumors (ATRT) recruited to the European Rhabdoid Regsitry (EU-RHAB) and data were validated in a second independent cohort of ATRT patients.

overall_design: 153 ATRT samples were selected for DNA extraction and hybridization on Illumina DNA methylation arrays to determine their molecular subtype.

first: Michael

last: Frühwald

last: Hasselblatt


title: Neutrophil dysregulation is pathogenic in idiopathic inflammatory myopathies

city: Bethesda

first: Iago

last: Pinal-Fernandez

state: MARYLAND

address: 50 South Drive, Room 1142, Building 50, MSC 8024

department: NIAMS

institute: NIH

summary: We report the RNAseq gene expression levels of in the muscle biopsies of 39 subjects with adult dermatomyositis (DM) and 20 normal muscle specimens (NT)

overall_design: Cross-sectional study analyzing the RNA expression levels of dermatomyositis and normal muscle biopsies.

first: Andrew

last: Mammen


title: Transcriptional profiling of HCC515 lung cells with dox-inducible KEAP1 knockdown and/or STK11 re-addition, under different metabolic tstress conditions

city: South San Francisco

first: Anneleen

last: Daemen

state: CA

address: 1 DNA Way

institute: GENENTECH, INC.

summary:
HCC515 lung cells with dox-inducible KEAP1 knockdown and/or STK11 re-addition, under two different metabolic stress conditions, baseline vs. suspension, were transcriptionally profiled to investigate whether KEAP1 knockdown can rescue metabolic defects in STK11-null cancer cells and how the regulation of the transcriptome by KEAP1 knockdown is affected by STK11 status and different metabolic stress conditions.
In lung adenocarcinoma (LUAD), stabilization of the transcription factor NRF2 through genomic alterations in KEAP1 and NFE2L2 occurs in roughly a quarter of patients, often in the context of STK11 tumor suppressor loss. In this study, we demonstrate that NRF2 activation in the context of concurrent KRAS mutation and STK11 loss promotes aggressive LUAD tumor behavior in both human and mouse preclinical models. This phenotype is associated with metabolic rewiring and rescue by NRF2 of redox stress, high in STK11 null tumors. Applying a novel, pan-lung cancer, diagnostic NRF2 activation gene expression signature that is independent of frequently co-occurring mutations, we dissect the independent contributions of the three most frequent genetic events in human LUAD (NRF2 activation, STK11 loss and KRAS mutations) on patient prognosis and clinical responses in a dataset of second-line LUAD patients treated with immunotherapy or chemotherapy (OAK trial). Our findings underscore that both individual effects and epistatic relationships among oncogenic and tumor suppressor pathways influence tumor biology, immune contexture and patient clinical outcomes. Our work also highlights the value of lung cancer disease sub-classification based on genetic and expression profiling as part of patient clinical management.

overall_design: HCC515 stable cells (KEAP1-wildtype, STK11-null) were plated in 10% Tet-Free FBS media. Cells were stably transfected with a dox-inducible control vector (LUCshRNA), KEAP1shRNA knockdown, or STK11shRNA re-addition. The +dox treated cells were transfected with KEAP1shRNA, STK11shRNA + KEAP1shRNA, STK11shRNA + LUCshRNA, or LUCshRNA. The -dox treated cells were transfected with the LUCshRNA or KEAP1shRNA. All +dox treated cells were grown in media (baseline or suspension) with 0.2ug/ml doxycycline and maintained for a total of 7 days. At day 7 of dox induction, cells were harvested for RNA preparation. The cells without dox (the -dox cells) were also split in a similar manner without exposure to 0.2ug/ml dox. RNA-seq data were generated for the 4 +dox treated cells and the 2 -dox treated cells in duplicate, separately for baseline and suspension media (n=2x12, 24 samples).

first: Georgia

last: Hatzivassiliou


title: Expression data of cultured MCF10A cells transduced with MYB or MYB-NFIB expression vectors

city: Gothenburg

first: Mattias

last: Andersson

address: Medicinaregatan 1F

department: Sahlgrenska Cancer Center

country: Sweden

institute: University of Gothenburg

summary: This experiment investigates differences between control cells (empty vector) and cells with MYB or MYB-NFIB (M14N9) overexpression using MSCV vectors

overall_design: A total of 9 samples are analyzed of which 3 are control samples

first: Göran

last: Stenman


title: Expression analysis of C. elegans wild-type N2, eat-2, acs-20 and eat-2; acs-20 mutants

city: Nanjing

first: Lina

last: Zou

address: 12 Xue-Fu Road, Pukou District , Nanjing, Jiangsu

department: Model Animal Research Center

institute: Nanjing University

summary: Investigation of whole genome gene expression level changes in C. elegans eat-2, acs-20 and eat-2; acs-20 mutant compared to the wild-type N2 strain.

overall_design: RNA-Seq analysis of C. elegans wild-type N2 (3 replicates), eat-2 mutant (3 replicates), acs-20 mutant (3 replicates) and eat-2; acs-20 double mutant (3 replicates).

first: Di

last: Chen


title: The acute effects of growth hormone in adipose tissue involve suppression of anti-lipolytic signals

city: Aarhus

first: Kasper

last: Thorsen

address: Brendstrupgaardsvej

institute: Aarhus University Hospital

summary: Human subjects (n=9) underwent acute intravenous exposure to GH vs. saline on separate occasions with measurement of serum FFA for 2 h, and GH signaling and gene expression (gene array and PCR)

overall_design: Human, cross-over design. 18 samples.

first: Niels

last: Jessen

first: Katrine

last: Høyer


title: Transcriptional signatures of progressive neuropathology in tau and amyloid mouse models

city: Exeter

first: Jonathan

last: Mill

address: RILD Building, RD&E Hospital, Barrack Rd

institute: University of Exeter Medical School

summary: Using highly-parallel RNA-sequencing on samples from rTg4510 and J20 mice (n = 121 mice), collected at four different time points, we profiled transcriptional changes in the entorhinal cortex paralleling the progression of Alzheimer's disease-associated pathology.

overall_design: Highly parallel RNA-seq of the entorhinal cortex at four time points in transgenic (rTg4510 and J20) and wild type littermate control mice (n=121)

first: Isabel

last: Castanho


title: DREAM regulates gene expression and Ca2+ mobilization in sperm cells

city: Cantoblanco

first: Juan

middle: Carlos

last: Oliveros

state: Madrid

address: Darwin 3

country: Spain

institute: CNB, CSIC

summary: Calcium influx is a critical event in mammalian fertilization, but the molecular mechanisms that govern the calcium dynamics in spermatozoa in response to physiological stimuli are still poorly understood. In the present work we analyze the role of the Ca2+-dependent transcriptional repressor DREAM (downstream regulatory element antagonist modulator) in spermatozoa using a transgenic mouse line that express a dominant constitutively active DREAM mutant. Genome-wide expression analysis of transgenic mice showed that DREAM modulates gene expression throughout the maturation process of sperm from spermatogonia to mature spermatozoa.

overall_design: We used Affymetrix microarrays (GeneChip Mouse Genome 430 2.0) to compare global gene expression in wild type (WT) versus transgenic testis cells. For each type of sample three hybridizations were carried-out (independent biological replicates).

first: Marcos

last: Rivas

first: Diego

last: Villar

first: Miriam

last: Pérez

first: Paz

last: González

first: Raúl

last: Fernández

first: Belén

last: Pintado

first: Alfonso

last: Gutiérrez-Adan

first: Jose

last: Naranjo

first: Britt

last: Mellström


title: Transcriptome analyses of Colletotrichum orbiculare during appressorium formation in planta

city: Kanazawa

first: Takumi

last: Nishiuchi

address: 13-1 Takaramachi

institute: Kanazawa University

summary: To elucidate the involvement of MOR (morphogenesis-related NDR kinase network) pathway in regulation of genes that are specifically expressed during appressorium development in planta, transcriptome analyses at the stage of appressorium formation (4 hours post inoculation) and in planta were performed and revealed that MOR is responsible for the expression of a subset of the plant signal induced genes with potential roles in pathogenicity.

overall_design: We collected samples from germinating conidia incubated on cucumber cotyledons (in planta) for 4 h of the MTF4-OX or mtf4Δ strains. Four replicates were performed for each experiment.

first: Sayo

last: Kodama

first: Yasuyuki

last: Kubo


title: Transcriptional regulation of tDNA in H9 ESCs

city: Birmingham

first: keith

middle: e

last: giles

state: AL

address: 1825 University Blvd/ SHEL 706

department: Biochemistry & Molecular Genetics/ Stem Cell Institute

institute: University of Alabama at Birmingham

summary: The localization of Pol III, TFIIIB, and TFIIIC in untreated H9 ESCs and after 48 hours of 50ng/mL Activin A treatment was determined by ChIP-seq.

sample_organism:
Homo sapiens
Mus musculus

overall_design: 3 replicates of H9 ESCs and 2 replictates of Activin A treated (endoderm)

first: Keith

middle: E

last: Giles

first: Jessica

last: Woolnough


title: Differential genomic-methylation profile of EOL-1 cells transduced with WT/mutant-DNMT3A

city: TauYau

first: Yun-Shien

last: Lee

state: Taiwan

address: TauYau

department: Dept. Biotechnology

institute: Ming Chuan Univ

summary:
DNA methyltransferase 3A (DNMT3A) gene is mutated in various myeloid neoplasms including acute myeloid leukemia (AML), especially at the Arg882 and associated with inferior outcomes. Here we wished to perform the differential genomic-methylation profile in EOL-1 cells over-expressed with DNMT3A-Arg882Cys(R882C) and DNMT3A-Ser714Cys (S714C) mutations including DNMT3A-WT and vector.
Results: Differential genomic-methylation assess identified both hypo- and hypermethylation features in different regions throughout the whole genome of DNMT3A mutants-transduced EOL-1 cells.

overall_design: DNA methyltransferase 3A (DNMT3A) gene is mutated in various myeloid neoplasms including acute myeloid leukemia (AML), especially at the Arg882 and associated with inferior outcomes. Despite the current progress of functional role of DNMT3A mutations, the molecular pathogenesis of myeloid malignancies remains poorly understood. The mechanisms of AML transformation and functional role of DNMT3A mutations through its target genes in the leukemogenesis remain to be explored. Here we wished to perform the differential genomic-methylation profile in EOL-1 cells over-expressed with DNMT3A-Arg882Cys(R882C) and DNMT3A-Ser714Cys (S714C) mutations including DNMT3A-WT and vector using Illumia MethylationEPIC BeadChip microarray.

first: Rabindranath

last: Bera

first: Lee-Yung

last: Shih

first: Ming-Chun

last: Chiu

first: Ying-Jung

last: Huang

first: Der-Cherng

last: Liang


title: Thyroid hormone inhibits hepatocellular carcinoma progression via induction of differentiation and metabolic reprogramming

city: CAGLIARI

first: AMEDEO

last: COLUMBANO

address: VIA PORVELL 4

department: DIPARTIMENTO DI SCIENZE BIOMEDICHE

country: Italy

institute: UNIVERSITA' DEGLI STUDI DI CAGLIARI

summary: T3 induces a global shift of the expression profile of KRT-19+ lesions towards that of fully differentiated hepatocytes

overall_design: 8 controls, 10 CK-19-negative preneoplastic nodules, 10 CK-19-positive preneoplastic nodule, 10  CK-19-positive preneoplastic nodule +T3 2 d,10  CK-19-positive preneoplastic nodule +T3 4 d.

first: Pia

last: Sulas


title: Transcriptomic modifications associated to protective effect of Pedro-Ximenez must on p,p´- DDE-induced liver injury in aged Mus spretus mice

city: Cordoba

first: Nieves

last: Abril

state: Not Applicable

address: Campus Rabanales, edificio C6, 2ª planta

institute: University of Córdoba

summary: The increase of aged population makes it necessary to find effective prevention and treatment procedures to help the elderly to enjoy a healthy and long life. The organochlorine compound p,p´-DDE (1,1-dichloro-2,2-bis(p-chlorophenyl) ethylene) is a DDT metabolic byproduct that generates great concern because its deleterious effects on both human and environment health. It is an endocrine disruptor agent and causes alterations in immune response, reproductive system, development, nervous system and endocrine homeostasis. Nutritional interventions may improve health and prolong life. A transcriptional study was carried on in order to analyze the biological responses caused by p,p´-DDE exposure in the liver of aged Mus spretus mice. Data showed that the elderly are especially sensitive to the toxicity of environmental contaminants. This work also evaluated the possible hepatoprotective effect of including sun-dried Pedro Ximenez must in the diet when p,p´-DDE exposure happens simultaneously. Our results showed that this dietary intervention controls the hepatic metabolism of carbohydrates and lipids through restoring bile acid homeostasis, improving the overall health in the elderly.

overall_design: Twenty-month Mus spretus (inbred SPRET/EiJ strain) were fed for 60 days with Teklad diet supplemented with p,p'-DDE (450 mg/kg) dissolved in corn oil. PXM exposed group (four mice) was fed the same diet but also received water with Pedro Ximenez must (85 mg/L of total polyphenols and 31 g/L of 1:1 glucose/fructose). Control group (four mice) was fed only with Teklad diet and corn oil.

first: Noelia

last: Morales-Prieto


title: Paradoxical CD4 decline on ART: a novel, rare and perplexing immunologic outcome

city: Hamilton

first: Craig

last: Martens

state: MT

address: 903 S. 4th St

department: DIR

institute: NIAID

summary: The goal of antiretroviral therapy (ART) is to suppress HIV-1-replication and reconstitute CD4-T-cells. Here, we report on HIV-infected individuals, who had a paradoxical decline in CD4-T-cells despite ART-mediated suppression of plasma HIV-1 load (plHIV-1). We defined such immunological outcome as extreme immune decline (EXID).

overall_design: RNA-Seq of patient derived PBMC, 5 replicates of 5 different conditions.

first: Andrea

last: Lisco

first: Chun-Shu

last: Wong

first: Silvia

last: Lage

first: Itsik

last: Levy

first: Jason

last: Brophy

first: Jeffrey

last: Lennox

first: Maura

last: Manion

first: Megan

last: Anderson

first: Yolanda

last: Mejia

first: Christopher

last: Grivas

first: Harry

last: Mystakelis

first: Peter

last: Burbelo

first: Ainhoa

last: Perez-Diez

first: Adam

last: Rupert

first: Sarah

last: Anzick

first: Caryn

last: Morse

first: Shanna

last: Chan

first: Claire

last: Deleage

first: Irini

last: Sereti


title: Redefining synchronous colorectal cancer on the basis of clonality

city: Salamanca

first: Juan Luis

last: Garcia

state: Salamanca

address: Campus Miguel de Unamuno

institute: Centro de Investigación del Cáncer IBMCC-CIC

summary:
Background: Synchronous colorectal cancer (SCRC) is not widely studied, and one of its most striking aspects the possible clonal origin of at least a part of the cases.
Materials and methods: We studied 104 paired-SCRCs of 52 consecutive patients without hereditary forms of CRC. We used a Single-Nucleotide Polymorphism array to characterize the genomic profiles, and subsequently used a statistical application to define them according to clonality within the same individual; the results were confirmed by next generation sequencing of the main CRC-related genes. We categorized the ensuing groups according to colon location, trying to find differential phenotypes with clinical implications.
Results: The SCRC Monoclonal group (M) (19 cases) was divided into Monosegmental (MM) and Pancolonic (MP) groups. The MM subgroup consisted of 10 cases (19% of the total), while the MP group contained 9 cases (17%). The SCRC Polyclonal group (P) (33 cases) was also divided into Monosegmental (PM) and Pancolonic (PP) groups: 19 cases were PM (37%), showing preference for location in the left colon (17 cases, 89%), whereas 14 cases were PP (27%). Correlations with clinical features were mainly related to prognosis and familial cancer history. The MM group showed a high rate of mucinous tumors (37.5%), had the lowest mean number of tumors and associated polyps, and the worst prognosis. The MP group included the youngest age at diagnosis and the largest mean-number of associated polyps, had comparatively intermediate mean number of tumors, and showed the best prognosis and a familial cancer component. The PM group seemed to be a “frontier” group. Finally, the PP group also exhibited a mucin component, with the highest mean-number of tumors (4.6) compared with the mean-number of polyps (7.7), had a poor prognosis and consisted of sporadic cases.
Conclusions: The statistical application we employed seems to define clonality more accurately in SCRC, and this, together with the tumor locations, helped us to configure a classification with prognostic and clinical value. These categories may serve as a starting point to analyze more selectively the molecular basis of SCRC and its relationship with environmental factors.

overall_design: A total of 53 individuals diagnosed with Synchronous colorectal cancer (SCRC) were consecutively collected from January 2006 at the 12 de Octubre University Hospital (Madrid). We defined a CRC as SCRC when 2 or more histologically distinct colorectal tumors were identified in the same patient at the same time or in a period less than six month after the first diagnosis.

first: José

last: Perea

first: Juan

last: García

first: Luis

last: Corchete

first: Eva

last: Lumbreras

first: María

last: Arriba

first: Daniel

last: Rueda

first: Sandra

last: Tapial

first: Jessica

last: Pérez

first: Victoria

last: Vieiro

last: Rodríguez

first: Lorena

last: Brandáriz

first: Mariano

last: García-Arranz

first: Damián

last: García-Olmo

first: Ajay

last: Goel

first: Miguel

last: Urioste

first: Rogelio

last: González-Sarmiento


title: Protection of SH-SY5Y cells against 6-OHDA by 3,4-dihydroxybenzalacetone (DBL) and caffeic acid phenethyl ester (CAPE)

first: Takumi

last: Nishiuchi

summary: 3,4-dihydroxybenzalacetone (DBL) and Caffeic acid phenethyl ester (CAPE) are both catechol-containing phenylpropanoid derivatives. In the present study, we compared the neuroprotective characteristics of these compounds and other phenylpropanoid derivatives against Parkinson’s disease-related neurotoxin 6-hydroxydopamine (6-OHDA). Pretreatment of human SH-SY5Y neuroblastoma cells with DBL or CAPE, but not with other compounds, prevented 6-OHDA-induced cell death, with marked effects observed for CAPE. To identify the mechanism, we compared gene expression profiles induced by these compounds in SH-SY5Y cells.

overall_design: Two sets of samples, derived from DBL-treated, CAPE-treated, or control (without treatment) cells, were prepared. Genes upregulated more than two fold by each compound were analyzed.

first: Osamu

last: Hori


title: Study on the circular RNA expression profile of articular chondrocytes in an IL-1β-induced mouse model of osteoarthritis

city: shanghai

first: zhibin

last: zhou

address: 415 Fengyang Road

department: orthopedics

institute: changzheng hospital

summary: Circular RNA expression profiling by high-throughput sequencing

overall_design: Circular RNA expression profiling of primary mouse articular chondrocyte treated with interleukin-1β.In this study, we have attempted to explore the effects of interleukin-1β on circular RNA expression alteration and have identified numerous  circular RNAs which are involved in osteoarthritis pathogenesis.

first: Zhibin

last: Zhou

first: Lei

last: Zhu


title: Multi-omics profiling for individualized precision wellness [blood (PBMCs) RNA-seq]

city: East Lansing

first: George

last: Mias

address: 775 Woodlot Drive, Rm1319

department: Biochemistry and Molecular Biology

institute: Michigan State University

summary: The investigation includes findings from our clinical trial, monitoring individualized response to pneumococcal vaccination, where we have carried out integrative profiling on peripheral blood mononuclear cells (PBMCs) and saliva pre and post vaccination in a single individual. This is to our knowledge the most extensive saliva-centered omics dataset on an individual, covering 100 timepoints over the course of one year. The time span covers a healthy period as well as comprehensive monitoring of innate and adaptive immune responses following pneumococcal vaccination. Protein and RNA from saliva and PBMCs were produced at each timepoint (100 timepoints for saliva, 25 for PBMCs), and mass spectrometry proteomics and RNA-sequencing were carried out for all samples in non-targeted comprehensive profiling.    Specifically, a single individual (male, 38) was profiled over multiple timepoints during healthy periods, as well as post treatment with pneumococcal vaccine (PPSV23). Initially pre-immunization samples, including a 24 hour period with hourly sampling (samples P1052515H07-P1052615H08), were collected to provide a comparative baseline. A subsequent 24-hour time course was performed, with again hourly samples taken pre and post vaccination (P1060715H07-P1060815H06). The PPSV23 pneumococcal vaccine was admistered inbetween timepoints at approximately 10.30am, prior to datapoint P1060715H11. Following the vaccination, and after the 24 hour monitoring, daily samples were taken for about a month (up to sample P1070715H08), to capture innate and adaptive responses in saliva. Two more weekly samples followed, with then monthly sample till the end of the investigation. Concurrently, weekly or monthly PBMC samples were taken.    Omics sample analysis includes: RNA-sequencing of total RNA in saliva and PBMCs. small RNA sequencing in saliva. Proteomics in saliva and PBMCs. small RNA from extracellular vesicles in saliva.    Note on sample naming: The sample identifier/name P1MMDDYYHhh corresponds to: patient index:P1, date MMDDYY and hour hh preceded by H using 24hour enumeration. Overall the study produced 100 timepoints for saliva in the span of a year, as well as 30 PBMC samples.

overall_design: Peripheral Blood Mononuclear Cell (PBMC) RNA-sequencing summary: Examination of gene expression dynamics in a single individual in PBMCs over multiple timepoints. 25 weekly/monthly samples follow the changes in expression in 1 individual over the span of 1 year. The timepoints include pre and post vaccination response, for pneumococcal vaccine (PPSV23).

middle: I

first: Lavida

last: Brooks

first: Vikas

last: Singh


title: Gene expression profile of cancer stem cells (CSCs) isolated from wild type (WT) and Sfrp1-/- mice skin squamous cell carcinoma (SCC)

status: Public on Jan 30 2020

city: Navi Mumbai

first: SANJEEV

last: WAGHMARE

state: MAHARASHTRA

address: Sector 22, Kharghar

department: STEM CELL BIOLOGY GROUP

country: India

institute: ACTREC, TATA MEMORIAL CENTRE

summary:
Sfrp1 is a Wnt inhibitor that is down regulated in various human cancers such as acute myeloid leukaemia, hepatocellular carcinoma, pancreatic, ovarian and breast cancer etc. Our study has shown that the loss of Sfrp1 in mouse skin leads to early tumor initiation with induced skin chemical carcinogenesis. Further, CSCs isolated from the Sfrp1-/- tumors showed increased in vivo tumorigenic potential with enhanced tumor propagating cell (TPC) frequency when injected into NOD/SCID mice.
Hence, in order to understand the molecular mechanism involved in CSC regulation in the absence of sfrp1, we have performed microarray analysis on CSCs isolated from mice skin SCC. The data showed upregulation of genes involved in the regulation of tumor aggressiveness, metastasis and stemness in Sfrp1-/- CSCs as compared to WT CSCs. Our study has provided significant contribution to the existing knowledge of Sfrp1 by showing the uncharted role of Sfrp1 in tumor initiation and CSC regulation.

overall_design: To understand the molecular mechanism in CSC regulation, we have performed genome wide expression profile of CSCs from Sfrp1-/- SCC and WT SCC. Using well defined skin CSC markers (Lin-/ Epcam+/ α6-integrin+/CD34+) the CSCs were FACS sorted and RNA was extracted. The cDNA was prepared, labelled and hybridization was performed by loading onto GeneChip® MTA 1.0 array (Affymetrix, USA).

first: Sanjeev

last: Waghmare


title: mature piRNAs and piRNA-Likes expression profile in human bronchial epithelial (HBE) and squamous cell carcinoma (SCC) cells

city: Baltimore

first: Theresa

last: Hodges

state: MD

address: 801 W. Baltimore Street

department: Institute for Genome Sciences

institute: University of Maryland Baltimore

summary: we profiled small RNAs binding to phosphorylated Serine (p-Ser), Threonine (p-Thr) and Tyrosine (p-Tyr) residues of proteins in human lung bronchial epithelial (HBE) and lung squamous cell carcinoma (SCC) cells. A total of 1986 unique p-Proteins interacted piRNAs and piRNA-Likes were called.

overall_design: Immunoprecipitated small RNA were purified from normal Human Bronchial Epithelial (HBE), and Squamous Cell Carcinoma (SCC) cells for preparation of high-throughput sequencing libraries.

first: Yuping

last: Mei

first: Li

last: Mao


title: Comparative transcriptome analysis of cadmium responses in Lolium multiflorum

city: Harbin

first: Junchao

last: Zhao

state: HeiLongjiang

address: 600 Changjiang Road

institute: The Northeast Agricultural University

summary: Heavy metal cadmium (Cd) affects seriously crop growth, quality and yield, and has potential threats to human safety. We found the difference of two ryegrasses (Lolium multiflorum Lam.), a high-Cd tolerance (LmHC) and a low-Cd tolerance (LmLC) cultivars , in response to cadmium stress. The germination rate, plant growth, and fresh weight of LmHC were much better than that of LmLC. So we use RNA sequencing to investigate the differentially expressed genes(DEGs) about cadmium response between LmHC and LmLC. Real-time quantitative PCR analysis showed that the same DEGs of LmLC and LmHC had obviously difference expression level under Cd treatment. It was suggestion that differential expression of DEGs might be involved in regulating Cd tolerance, accumulation and translocation.These results will be helpful for understanding the underlying molecular mechanism in Cd toxicity and provide references for improving the ecological environment through genetic improvement.

overall_design:
RNA sequencing was performed to investigate the differentially expressed genes about cadmium transporter between Lolium multiflorum High Cadmium (LmHC) and Lolium multiflorum Low Cadmium (LmLC).
mRNA profiles of two Lolium multiflorum with cadmium treatment 0h and 24h were generated by deep sequencing. The sequence reads that passed quality filters were analyzed at the transcript.

first: Aimin

first: Kun

last: Qiao


title: Genome Wide Analysis of Gene Expression Changes in Skin from Patients with Type 2 Diabetes

city: Austin

first: Aaron

last: Baker

address: 1 University Station

institute: University Of Texas At Austin

summary: We investigated genome wide changes in gene expression in skin between patients with type 2 diabetes and non-diabetic patients using next generation sequencing. We compared the gene expression in skin samples taken from 27 patients (13 with type 2 diabetes and 14 non-diabetic).

overall_design: mRNA profiles of the skin of type 2 diabetic and non-diabetic patients were generated by Illumina Hi Seq 4000.

first: Eri

last: Takematsu

first: Adrianne

last: Spencer

first: Jeff

last: Auster

first: Po-Chih

last: Chen

first: Annette

last: Graham

first: Patricia

last: Martin


title: Increased neural progenitor proliferation in a hiPSC model of autism induces replication stress-associated genome instability [GRO-seq]

city: La Jolla

first: Meiyan

last: Wang

address: 10010 N. Torrey Pines Road

institute: The Salk Institute for biological studies

summary:
The association between macrocephaly and autism spectrum disorder (ASD)
suggests that the mechanisms underlying excessive neural growth could contribute to ASD pathogenesis. Consistently, neural progenitor cells (NPCs) derived from induced pluripotent stem cells (iPSCs) of ASD individuals with early developmental brain enlargement are inherently more proliferative than control NPCs. Here, we show that hiPSC-derived NPCs from ASD individuals with macrocephaly display an altered DNA replication program and increased DNA damage. When compared to the control NPCs, high throughput genome-wide translocation sequencing (HTGTS) demonstrates that ASD-derived NPCs harbored elevated DNA double-strand breaks in replication stress-susceptible genes, some of which are associated with ASD pathogenesis. Our results provide a mechanism linking hyperproliferation of NPCs with the pathogenesis of ASD by disrupting long neural genes involved in cell-cell adhesion and migration.

overall_design: We applied GRO-seq to investigate gene expression level in human neural progenitor cells.


title: RNA-seq analysis of transcriptomic changes in HS2 enhancer perturbed cells

city: Memphis

first: Jian

last: Xu

state: Tennessee

address: 262 Danny Thomas Place, MS 345

department: Pathology

institute: St. Jude Children's Research Hospital

summary: Tissue-specific gene expression requires coordinated control of gene-proximal and distal cis-regulatory elements (CREs), yet functional analysis of putative gene-distal CREs such as enhancers remains challenging. Here we describe enhanced CRISPR/dCas9-based epigenetic editing systems, enCRISPRa and enCRISPRi, for multiplexed analysis of enhancer function in situ and in vivo. Using dual effector proteins capable of re-writing enhancer-associated chromatin modifications, we show that enCRISPRa and enCRISPRi modulate gene transcription by remodeling local epigenetic landscapes at sgRNA-targeted enhancers and associated genes. Comparing with existing methods, our systems display more robust and specific perturbations of gene transcription with minimal off-targets. Allele-specific targeting of enCRISPRa to oncogenic TAL1 super-enhancer modulates TAL1 expression and cancer progression in xenotransplants. Furthermore, multiplexed perturbations of lineage-specific enhancers in an enCRISPRi knock-in mouse establish in vivo evidence for lineage-restricted requirement of developmentally regulated enhancers during hematopoietic lineage specification. Hence, enhanced CRSIPR epigenetic editing provides opportunities for interrogating enhancer function in development and disease.

overall_design: RNA-seq was performed to determine the transcriptomic changes in HS2 enhancer perturbed cells

first: Kailong

last: Li

first: Yuxuan

last: Liu


title: ATAC-Seq of Xenopus tail regeneration

city: Stanford

first: Jessica

middle: Kay

last: Chang

address: 300 Pasteur Drive, Alway Building M311

department: Genetics

institute: Stanford University

summary: Mammals possess limited regeneration capabilities, where the few examples of scarless healing tend to be restricted to early development. In light of this, it is of great interest to study animals that can faithfully regrow complete appendages, and uncover the biological properties that facilitate this process. Xenopus tropicalis tadpoles are excellent vertebrate models of regeneration, as they rapidly recover lost tails within just one week post amputation. Though we have some understanding of what pathways are required for tail regeneration, we have yet to systematically chronicle the regulatory events that coordinate this specialized response to injury. Here, we highlight a striking phenomenon in Xenopus regeneration, whereby nuclei within the fin epithelium of an amputated tail change shape in a dramatic and stereotyped manner during regeneration. We assess chromatin accessibility dynamics through ATAC-Seq of nine time points of regeneration, and find that large scale changes in chromatin state are highly correlated to changes in nuclear shape. To identify critical regulators of these chromatin dynamics, we describe and apply a machine learning method, PFBoost, which integrates information from motifs underlying dynamically accessible ATAC-Seq peaks and differentially expressed transcription factors from time-matched RNA-Seq data to predict chromatin state. To functionally evaluate PFBoost-predicted regeneration regulators, we developed an inducible CRISPRi system utilizing the FKBP derived destabilizing domain, and knockdown expression of these regulators during the early hours of regeneration. With this methodology, we identified and describe two novel regulators of regeneration, spib and chd8. We provide not only an abundant resource for chromatin dynamics in tail regeneration, but also chronicle an intriguing mechanism of regeneration regulation in the form of nuclear shape change and coordinate changes in chromatin state.

overall_design:
Profiling of chromatin accessibility across nine time points in tadpole tail regeneration; sequenced in duplicate via Illumina HiSeq and NextSeq.

Please note that each *combined_reps.bw file was generated from both replicates and is linked to the corresponding 'rep1' sample records.

first: Andrea

last: Wills

first: Julie

middle: C


title: ChIP-seq analysis of cas9, HA, H3K4me, H3K4me2, H3K9me3, H3K27ac, CTCF, GATA1 and TAL1 in HS2 enhancer perturbed K562 cells or other leukemia cell lines

overall_design: ChIP-seq was performed to determine the chromatin occupancy of Cas9, HA, H3K4me, H3K4me2, H3K9me3, H3K27ac, H3K27me3, CTCF, GATA1 and TAL1 in HS2 enhancer perturbed K562 cells or other leukemia cell lines


title: Massively parallel Cas13d screens reveal principles for guide RNA design

city: New York

first: Hans-Hermann

last: Wessels

address: 101 Avenue of the Americas

institute: New York Genome Center

summary: Type VI CRISPR enzymes are RNA-targeting proteins with nuclease activity that enable specific and robust target gene knockdown without altering the genome. To define rules for the design of Cas13d guide RNAs, we conducted massively parallel screens targeting messenger RNAs of a green fluorescent protein transgene, and CD46, CD55 and CD71 cell-surface proteins in human cells. In total, we measured the activity of 24,460 gRNAs with and without mismatches relative to the target sequences. Knockdown efficacy is driven by gRNA-specific features and target site context. Single mismatches generally reduce knockdown to a modest degree, but spacer nucleotides 15–21 are largely intolerant of target site mismatches. We developed a computational model to identify optimal gRNAs and confirm their generalizability testing 3,979 guides targeting mRNAs of 48 endogenous genes. We show that Cas13 can be used in forward transcriptomic pooled screens and, using our model, predict optimized Cas13 gRNAs for all protein-coding transcripts in the human genome.

overall_design: Evaluation of RfxCas13d guide RNAs. Pooled CRISPR screen.

first: Alejandro

last: Méndez-Mancilla

first: Xinyi

last: Guo

first: Mateusz

last: Legut

first: Zharko

last: Daniloski

first: Neville

last: Sanjana


title: ATAC-seq analysis of Jurkat leukemia cell lines

overall_design: ATAC-seq was performed to determine the chromatin accessibility in leukemia cell lines


title: Genome-wide in vivo CNS Screening Identifies Genes that Modify CNS Neuronal Survival and mHTT Toxicity

city: Cambridge

first: Myriam

last: Heiman

state: Massachusetts

address: 77 Massachusetts Ave., Bldg 46-4285

department: Brain and Cognitive Sciences

institute: Massachusetts Institute of Technology

summary: Unbiased in vivo genome-wide genetic screening is a powerful approach to elucidate new molecular mechanisms, but such screening has not been possible to perform in the mammalian central nervous system (CNS).  Here we report the results of the first genome-wide genetic screens in the CNS using both shRNA and CRISPR libraries.  Our screens identify many classes of CNS neuronal essential genes, and demonstrate that CNS neurons are particularly sensitive not only to perturbations to synaptic processes, but also autophagy, proteostasis, mRNA processing, and mitochondrial function.  These results reveal a molecular logic for the common implication of these pathways across multiple neurodegenerative diseases.  To further identify disease-relevant genetic modifiers, we applied our screening approach to two mouse models of Huntington’s disease (HD).  Top mutant Huntingtin toxicity modifier genes included several Nme genes and several genes involved in methylation-dependent chromatin silencing and dopamine signaling, results that reveal new HD therapeutic target pathways.

overall_design: Single-cell profiling of Nme1 overexpressing spiny projection neurons in R62 mouse model of HD

first: Sergio

last: Pineda


title: Increased neural progenitor proliferation in a hiPSC model of autism induces replication stress-associated genome instability [HTGTS]

overall_design: We applied LAM-HTGTS to map DNA double-strand breaks in human neural progenitor cells.


title: Increased neural progenitor proliferation in a hiPSC model of autism induces replication stress-associated genome instability

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

overall_design: Refer to individual Series


title: Expression profiling of PBMCs from patients with systemic lupus erythematosus

status: Public on Jan 29 2020

city: Nanjing

first: Weiwei

last: Chen

address: Department of Rheumatology and Immunology

institute: Nanjing Drum Tower Hospital

summary: Aberrant gene expression analysis between peripheral blood mononuclear cells (PBMCs) samples from healthy controls (HC) and patients with systemic lupus erythmatosus (SLE) were identified using Affymetrix gene arrays

overall_design: Peripheral blood mononuclear cell (PBMCs) from healthy controls (HC) and systemic lupus erythematosus (SLE) were isolated and total RNA was extracted for Affymetrix gene microarray analysis.

first: W


title: Tissue-specific structurome changes in the RNA structurome mediate salt salinity response in Arabidopsis

city: University Park

first: Zhao

last: SU

state: PA

address: 354 N. Frear

department: Biology

institute: The Penn State University

summary: We employed Structure-seq2 method to probe RNA structure genome-wide in Arabidopsis shoot and root tissue separately and investigate the effect of salt stress on the RNA structurome in vivo.

overall_design: For each structure-seq library, ~40 hydroponically grown Arabidopsis plants were used, which were dissected into shoot and root tissues. For the +DMS shoot sample, forty excised shoots from control or NaCl treatment were immersed in 20 mL DMS reaction buffer (40 mM HEPES (pH 7.5), 100 mM KCl, and 0.5 mM MgCl2) in a 50 mL conical centrifuge tube. Then 150 µl DMS (D186309, Sigma-Aldrich) was immediately added to the solution to a final concentration of 0.75% (~75 mM) for 5 min of DMS treatment, after which dithiothreitol (DTT) at a final concentration of 0.5 M was supplied to quench DMS in the reaction for 2 min followed by two washes with deionized water before immediate drying and freezing in liquid nitrogen. The −DMS sample was processed through the same procedure by placing materials in the DMS buffer for 20 min but without addition of DMS. Three independent biological replicates were prepared for both control and NaCl-treated shoot libraries, and for both −DMS and +DMS libraries, for a total of three −Salt−DMS libraries, three −Salt+DMS libraries, three +Salt−DMS libraries, and three +Salt+DMS libraries. All procedures for generation of root Structure-seq libraries were identical as for shoot library preparation, except that the initial material was the root tissue from forty plants each of control or NaCl treatment. Frozen samples were subjected to RNA extraction using the NucleoSpin RNA Plant kit (Cat# 740949, Macherey-Nagel, Germany) following the manufacturer’s protocol. Then the Structure-seq libraries were prepared according to the Structure-seq2 protocol, and starting with 300 ng total RNA. In total, 24 Structure-seq libraries were generated. Library DNA size distribution and consistency between biological replicates was assessed by Agilent 2100 Bioanalyzer (Agilent Technologies). After qPCR to quantify the library molarity, a pool of all libraries at equal molarity was made, and libraries were subjected to next-generation sequencing on an Illumina HiSeq 2500 at the Genomics Core Facility of the Penn State University to generate 150 nt single-end reads.

last: Su

first: David

last: Tack

first: Yunqing

last: Yu

first: Philip

last: Bevilacqua

first: Sarah

last: Assmann


title: DNA methylation analysis of mouse embryonic fibroblasts (MEFs) and Thymidine treatment-induced MEFs (induced cells).

status: Public on Jan 28 2020

city: Beijing

first: Benyu

last: Liu

state: Beijing

address: 15, Datun Road, Chaoyang district

department: The CAS key Laboratory of Infection and Immunity, Institute of Biophysics

institute: Institute of Biophysics, CAS

summary: Investigation of DNA methlation changing in  thymidine treatment-induced MEFs. Mouse embryonic fibroblasts (MEFs) were obtained at E14.5 embryos and supplied with Dulbecco’s modified Eagle’s medium (DMEM) (Invitrogen) with 15% FBS, 100 μg/ml streptomycin and 100 U/ml penicillin. Potential hematopoietic progenitor cells (CD45+CD41+CD31+c-Kit+) were negatively selected with Biotin labeled anti-CD45, anti-CD31, anti-CD41 and anti-c-Kit antibodies by magnetic beads. Hereafter, treated MEFs are referred to as 4neg MEFs for initiation of induction. 4neg MEFs were seeded on mitomycin (MMC)-treated MEFs as feeder cells and cultured in DMEM with 15% FBS, 100  μg/ml streptomycin, 100 U/ml penicillin, 2 mM L-glutamine, 0.1 mM non-essential amino acids and 100 μM thymidine as induction medium for 2 days followed with analysis

overall_design: DNA was purified from MEFs in the absence or presence of thymidine for 2 days. DNA samples were sheared into 200-1000 bp fragments by Bioruptor sonicator (Diagenode). Sonicated genomic DNA was immunoprecipitated by anti-5-methylcytosine antibody (Diagenode) followed by purification using Qiagen MinElute columns. The purified DNA was quantified using a nanodrop ND-1000, labeled by the NimbleGen Dual-Color DNA labeling Kit and array hybridized according to the manufacturer’s protocol (Nimblegene Systems, Inc., Madison, WI, USA).

first: Buqing

last: Ye


title: PAF1 Drives Pancreatic Cancer Oncogenesis by Promoting Stemness via PHF5A/DDX3 Sub-complex

city: Omaha

first: Saswati

last: Karmakar

state: NE

address: 42nd st & Emile

institute: UNMC


title: Pulmonary Eosinophilic Granulomatosis with Polyangiitis has IgG4 Plasma Cells and Immunoregulatory Features

city: Salt Lake City

first: Edwin

last: Lin

address: 50 N medical dr

institute: University of Utah

summary:
The pathologic findings and immunologic mechanisms in eosinophilic granulomatosis with polyangiitis (EGPA) are poorly understood. To characterize pulmonary EGPA’s mechanisms, we examined EGPA paraffin-embedded lung biopsies by immunostaining, RNA sequencing, and reverse transcriptase PCR, compared to normal lung.
EGPA lung infiltrates had eosinophils, alveolar macrophages, B and T cells, plasma cells, basophils, and mast cells. Mast cell degranulation was sparse. PhosphoSMAD2 immunostaining suggests TGFβ activity.
Using both immunostaining and RNA-sequencing, showed significant increases for both type 2 related genes (CD209, TNFSF14 (induces TGFβ and IL-13)), immunoregulatory genes (FOXP3, CYP27B1 (makes calcitriol), ALOX15 and particularly IGHG4). Regulatory T cells and IgG4 plasma cells with IgG4-containing presumed immune complexes coating macrophages, were strikingly abundant relative to controls. HPGD (metabolizes prostaglandins and other eicosanoids) was substantially decreased. RNA studies also showed increased contents of collagen transcripts, IL13, CCL18, and CCL13.
These findings suggest a novel mechanism involving alveolar macrophages, activated by ALOX15-eicosanoid products, making chemokines CCL18 and CCL13 and thus inducing a mixed type 2 plus immunoregulatory immune response. This infiltrate resembles the immune response to an invasive parasite rather than the IgE / mast cell degranulation response to luminal parasites or in asthma and other classic allergies. These findings also suggest new potential treatment targets for EGPA.

overall_design: RNA seq of EGPA versus control

first: Fred

last: Clayton


title: NAT8L mRNA oxidation is linked to neurodegeneration in multiple sclerosis

city: Kent

first: Soumitra

last: Basu

state: Ohio

address: 203 WilIiams Hall

department: Chemistry and Biochemistry

institute: Kent State University

summary: RNA oxidation has been implicated in neurodegeneration, but the underlying mechanism for such effects is unclear. Recently, we demonstrated extensive RNA oxidation within the neurons in multiple sclerosis (MS) brain. In this report we identified selectively oxidized mRNAs in neuronal cells that pertained to neuropathological pathways. N-acetyl aspartate transferase 8 like (NAT8L) mRNA is one such transcript, whose translated product enzymatically synthesizes N-acetyl aspartic acid (NAA), a neuronal metabolite essential for myelin synthesis. We reasoned that impediment of translation of an oxidized NAT8L mRNA will result in reduction in its cognate protein, thus lowering NAA level. This assertion is directly supported by our studies on a model cellular system, an MS animal model and postmortem human MS brain. Reduced NAA level in the brain could hamper myelin synthesis causing neuronal damage, which results in MS neurodegeneration. Overall, this work provides a framework for mechanistic understanding of the link between RNA oxidation and neurodegenerative diseases.

overall_design: mRNA profiles of human neuroblastoma (SH-SY5Y) cells in oxidized (SNP treated) and non-oxidized (untreated) states were generated by deep sequencing, in duplicate, using Illumina Hiseq platform.

first: Chattopadhyay

last: Ansuman


title: High-dose ascorbic acid synergizes with anti-PD1 in a lymphoma mouse model

status: Public on Jan 27 2020

city: Bronx

first: Amit

last: Verma

state: NY

address: 1300 Morris Park Ave

department: Medicine

institute: Albert Einstein College of Medicine

summary: Major efforts are underway to identify agents that can potentiate effects of immune checkpoint inhibition. Here, we show that ascorbic acid (AA) treatment caused genome wide demethylation and enhanced expression of endogenous retroviral elements in lymphoma cells. AA also increased 5-hydroxymethylcytosine (5hmC) levels of CD8+ T cells and enhanced their cytotoxic activity in a lymphoma co-culture system. High-dose AA treatment synergized with anti-PD1 therapy in a syngeneic lymphoma mouse model, resulting in marked inhibition of tumor growth compared with either agent alone. Analysis of the intra-tumoral epigenome revealed increased 5hmC with AA treatment, consistent with in vitro findings. Analysis of the tumor immune microenvironment revealed that AA strikingly increased intra-tumoral infiltration of CD8+ T cells and macrophages, suggesting enhanced tumor immune recognition. The combination treatment markedly enhanced intra-tumoral infiltration of macrophages and CD8+ T lymphocytes, granzyme B production by cytotoxic cells (cytotoxic T cells and Natural Killer cells), and IL-12 production by antigen presenting cells compared with single agent anti-PD1. These data indicate that AA potentiates anti-PD1 checkpoint inhibition through synergistic mechanisms. The study provides compelling rationale for testing combinations of AA and anti-PD1 agents in lymphoma patients as well as in pre-clinical models of other malignancies.

overall_design: We studied cytosine methylation patterns in 2 control and 2 AA-treated Ly1 [b-cell lymphoma] cells.

first: Kith

last: Pradhan

first: Niraj

last: Shenoy


title: PAF1 Drives Pancreatic Cancer Oncogenesis by Promoting Stemness via PHF5A/DDX3 Sub-complex (RNA-seq)

summary: In this study, we established that PAF1 is critical for pancreatic tumorigenesis, and CSC-driven tumor maintenance because depletion of PAF1 resulted in significantly less tumor burden and reduction in CSC populations.

overall_design: SW1990 side population control and PAF1 CRISPR KD cells were subjected to RNA sequencing

first: Surinder

last: Batra


title: Single-Cell Transcriptomic Atlas of Primate Ovarian Aging

city: Shanghai

first: Yuxuan

last: Zheng

address: 825 Zhangheng Rd.

institute: Fudan University

summary: Molecular mechanisms of ovarian aging and female age-related fertility decline remain unclear. We surveyed the single-cell transcriptomic landscape of ovaries from young and aged non-human primates (NHPs) and identified seven ovarian cell types with distinct gene expression signatures, including oocyte and six types of ovarian somatic cells. In-depth dissection of gene expression dynamics of oocytes revealed four subtypes at sequential and stepwise developmental stages. Further analysis of cell type-specific aging-associated transcriptional changes uncovered the disturbance of antioxidant signaling specific to early-stage oocytes and granulosa cells, indicative of oxidative damage as a crucial factor in ovarian functional decline with age. Additionally, inactivated antioxidative pathways, increased reactive oxygen species and apoptosis were observed in granulosa cells from aged women. This study provides comprehensive understanding of the cell type-specific mechanisms underlying primate ovarian aging at single-cell resolution, revealing new diagnostic biomarkers and potential therapeutic targets for age-related human ovarian disorders.

sample_organism:
Macaca fascicularis
Homo sapiens

platform_organism:
Macaca fascicularis
Homo sapiens

overall_design:
We collected ~3,500 single cells from the ovary of 4 young (YF1, YF2, YF3 and YF4) and 4 aged monkeys (OF1, OF2, OF3 and OF4) and performed single-cell RNA-seq sequencing.
We have also collected IDH1- and NDUFB10-knockdown KGN cells (a human granulosa cell line) (samples labelled with 'IDH1' or 'NDUFB10'), and KGN cells transfected with negative control duplex (samples labelled with 'NC'). These three types were cultured with or without H2O2 treatment:  H2O2-treated group (samples labelled with 'H2O2') and untreated group (samples labelled with 'B').

first: Si

last: Wang

first: Jingyi

last: Li

first: Yang

first: Weiqi

last: Zhang

first: Moshi

last: Song

first: Zunpeng

first: Zheying

last: Min

first: Huifang

last: Hu

first: Ying

last: Jing

first: Xiaojuan

last: He

first: Liang

last: Sun

first: Lifang

last: Ma

first: Concepcion

last: Rodriguez Esteban

first: Piu

last: Chan

first: Jie

last: Qiao

first: Qi

last: Zhou

first: Juan

last: Izpisua Belmonte

first: Jing

last: Qu

first: Fuchou

last: Tang

first: Guang-Hui


title: High-dose Ascorbic acid synergizes with anti-PD1 in a Lymphoma mouse model

first: Amit

last: Verma

overall_design: We studied HERV expression patterns in 2 control and 2 AA-treated Ly1[b-cell lymphoma] cells, using RNA sequencing data.

first: Niraj

last: Shenoy

first: Kith

last: Pradhan