title: LEDGF/p75 is Dispensable for Hematopoiesis but Essential for MLL-rearranged Leukemogenesis

city: Leuven

first: Jonas

last: Demeulemeester

state: Belgium

address: ON5 Herestraat 49

department: Center for Cancer Biology

country: Belgium

institute: VIB – KU Leuven

summary: Mixed-lineage leukemia (MLL) represents a genetically distinct and aggressive subset of human acute leukemia carrying chromosomal translocations of the MLL gene. These translocations result in oncogenic fusions that mediate aberrant recruitment of transcription machinery to MLL target genes. The N-terminus of MLL and MLL-fusions form a complex with Lens Epithelium-Derived Growth Factor (LEDGF/p75; encoded by the Psip1 gene) and MENIN. This complex contributes to the association of MLL and MLL-fusion multiprotein complexes with chromatin. Several studies have shown that both MENIN and LEDGF/p75 are required for efficient MLL fusion-mediated transformation and for the expression of downstream MLL-regulated genes like HOXA9 and MEIS1. In light of the development of a therapeutic strategy targeting this complex, understanding the function of LEDGF/p75 in normal hematopoiesis is crucial. We generated a conditional Psip1 knockout mouse model in the hematopoietic compartment and examined the effects of LEDGF/p75 depletion in postnatal hematopoiesis and the initiation of MLL leukemogenesis. Psip1 knockout mice were viable but showed several defects in hematopoiesis, reduced colony-forming activity in vitro, decreased expression of Hox genes in hematopoietic stem cells and decreased MLL occupancy at MLL target genes. Finally, in vitro and in vivo experiments showed that LEDGF/p75 is dispensable for steady state hematopoiesis but essential for the initiation of MLL-mediated leukemia. These data corroborate the MLL-LEDGF/p75 interaction as novel target for the treatment of MLL-rearranged leukemia.

overall_design: mRNA profiles of lineage depleted cells from bone marrow of PsipFl/Fl and PsipVav/Vav mice harvested after one round in a myeloid colony formation assay as generated by deep sequencing, in triplicate, using Illumina HiSeq 2500

first: Sara

last: El Ashkar

first: Jan

last: De Rijck


title: Anti-GBM mouse model protection effect by DDR1 inhibitors

status: Public on Sep 30 2017

city: Basel

first: Laura

last: Badi

address: Grenzacherstrasse

country: Switzerland

institute: Hoffmann La Roche LTD

summary: A total of 40 female mice 129/SV aged 3-6 months and weighting 18-25 g were used (Janvier, Le Genest-St-Isle, France). NTS was injected in mice (10 μl/gBW/day) during three consecutive days. The total number of mice was divided to five treatment groups as followed: 8 mice were injected with PBS and fed with vehicle, 8 mice were injected with NTS and fed with vehicle, 8 mice were injected with NTS and fed with low dose DDR1i, 8 mice were injected with NTS and fed with high dose DDR1i and 8 mice were injected with NTS and fed with Imatinib. All treatments were provided by oral gavage. Treatment was started one day [PM{1}] prior first injection of NTS or PBS. The average food intake was controlled by weighing the food every three days. Mice were found to consume about 4g/day/mouse [PM{2}] which was similar to all groups.

overall_design:
40 samples, 5 treatment groups
Please note that one sample was discarded due to poor quality.


title: CIC and ATXN1L knockout gene expression data

city: Vancouver

first: Derek

last: Wong

state: British Columbia

address: 675 W 10th Ave

department: Molecular Oncology

country: Canada

institute: University of British Columbia

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

overall_design: Refer to individual Series


title: Transcriptional response of bovine moncocyte-derived macrophages to infection with strains of Mycobacterium bovis and Mycobacterium avium subspecies paratuberculosis

city: Stirling

first: Iain

last: Gallagher

address: Room 4B133 Cottrell Building, University of Stirling, Airthrey Road

department: Faculty of Health Sciences and Sport

country: United Kingdom

institute: University of Stirling

type: Expression profiling by high throughput sequencing

summary: Mycobacterium bovis (M. bovis) and Mycobacterium avium subspecies paratuberculosis (MAP) are important pathogens of cattle, causing bovine tuberculosis and Johne’s disease respectively.  M. bovis and MAP infect residential macrophages in the lung and intestines respectively and subvert the macrophage biology to create a survival niche. To investigate this interaction we simultaneously studied the transcriptional response of bovine monocyte-derived macrophages to infection with two strains of M. bovis (AF2122/97 and G18) and two strains of MAP (C & L1).

overall_design: 120 samples were analysed in total; derived from six biological replicates (i.e. cells isolated from six cattle).  Cells were left uninfected (medium only controls) or infected with either a M. bovis strain (AF2122/97 or G18) or a MAP strain (C or L1).  Cells were harvested at 2, 6, 24 and 48h post infection.

first: Kirsty

last: Jensen

middle: J

first: Nicholas

last: Johnston

first: Michael

last: Welsh

first: Robin

last: Skuce

first: John

middle: L

last: Williams

first: Elizabeth

last: Glass


title: Integrative analysis of transcriptional and DNA methylation changes associated with PCB126 exposure in adult zebrafish (Danio rerio)

city: Woods Hole

first: Neelakanteswar

last: Aluru

state: MA

address: 45 Water Street

department: Biology

country: USA

institute: Woods Hole Oceanographic Institution

type: Methylation profiling by high throughput sequencing

summary: The aryl hydrocarbon receptor (AHR) is a ligand-activated transcription factor well known for mediating the toxicity of environmental chemicals such as polychlorinated biphenyls (PCBs) and polyaromatic hydrocarbons (PAHs). There is extensive knowledge on the range of target genes regulated by AHR ligands. However, there is limited information on the effect of AHR ligands on DNA methylation. The objective of this study is to investigate genome-wide changes in DNA methylation and gene expression patterns in response to PCB126 exposure. Adult zebrafish were exposed to 10 nM PCB126 for 24 hours (waterborne exposure) and were reared in clean water for 7 days before tissue sampling. DNA methylation and transcriptional changes in the liver and brain tissues were quantified by Reduced Representation Bisulfite Sequencing (RRBS) and RNAseq, respectively. RRBS analysis revealed DNA hypomethylation in response to PCB exposure in both liver and brain tissues. We observed 482 and 476 differentially methylated regions (DMRs) in the liver and brain tissues respectively. Most of the DMRs are located more than 20 kilobases upstream of the transcriptional start sites. RNAseq results from the liver revealed differential expression of genes related to xenobiotic metabolism, oxidative stress and carbohydrate metabolism in response to PCB exposure. In the brain, PCB exposure altered the expression of genes involved in myelination and glutamate signaling. Our results suggest that there is very little correlation between DNA methylation and gene expression patterns among the differentially expressed genes (DEGs). We are currently investigating the relationship between DMRs and DEGs.

overall_design: Two different tissues (Liver and brain) from PCB126 and DMSO-exposed zebrafish were analyzed for DNA methylation and gene expression using RRBS and RNAseq respectively. Four biological replicates per treatment were analyzed (n=4 individual fish).

first: Sibel

last: Karchner


title: CIC and ATXN1L knockout gene expression data [NHA]

summary: CIC has recently been implicated as a negative prognostic factor in multiple cancers. CIC and ATXN1L have been reported as interactors in several cellular contexts including development and disease state. To investigate the relationship between CIC and ATXN1L on a transcriptomic level, CIC-KO and ATXN1L-KO cell lines were generated. Gene expression profiling of CIC-KO and ATXN1L-KO cell lines was performed by microarray and differentially expressed genes were compared. We found a high degree of overlap in differentially expressed genes in CIC-KO and ATXN1L-KO suggesting loss of either interacting partner to lead to similar transcriptomic changes.

overall_design: The parental CIC/ATXN1L-WT NHA, two CIC-KO NHA derived (A2, H9) and one ATXN1L-KO NHA derived (B82) cell lines were generated using CRISPR/Cas9 genome editing technology. Gene expression profiling was performed in 3 biological triplicates for each cell line.

first: Kohl

last: Lounsbury

first: Amy

last: Lum

first: Veronique

last: LeBlanc

first: Suganthi

last: Chittaranjan

first: Marco

last: Marra

first: Stephen

last: Yip


title: CIC and ATXN1L knockout gene expression data [HEK]

overall_design: Three ATXN1L-WT HEK derived (parental HEK, and CRISPR controls N4, N8) and three ATXN1L-KO HEK derived (A10, A30, B21) cell lines were generated using CRISPR/Cas9 genome editing technology. Gene expression profiling was performed in 3 biological triplicates for each cell line.


title: Expression data from BeWo cells treated without or with PKA- or EPAC-selected cAMP analogs

city: Tokyo

first: Kazuya

last: Kusama

address: 1-1-1 Yayoi, Bunkyo-ku

country: Japan

institute: The University of Tokyo

summary:
Cyclic AMP activates two downstream factors, protein kinase A (PKA) and exchange protein directly activated by cAMP (EPAC) and both downstream signalings induce syncytialization, cell fusion and the production of hCG and progesterone.
We used microarray to identify novel transcription factors related to syncytialization in two cAMP signaling-stimulated BeWo cells.

overall_design: Human placenta choriocarcinoma cell line BeWo cells were treated without or with Epac- or PKA-selective cAMP analogs for 48 h, of which RNAs were extracted and subjected to Affymetrix microarrays.

first: Rulan

last: Bai

first: Kazuhiko

last: Imakawa


title: Gene expression profile of the RAG2 gene depletion on thymus of mouse

city: Seoul

first: Yun-Jung

last: Choi

address: 120 Neungdon-ro,Gwangjib-gu

department: Animal biotechnology

country: South Korea

institute: KONKUK University

summary: It contains a disruption of the recombination activating gene 2 (RAG2) and homozygoue mice exhibit total inability to initiate V(D)J rearrangement and fail to generate mature T or B lymphocytes. (https://www.taconic.com)

overall_design:
For comparison anaysis between species (RAG2 KO mouse and pig), We purchase RAG2 KO mouse from Taconic farms Inc. The comparison study of SCID mice and pigs as best hosts for xenogeneic tissue or cell grafts is poorly understood. Here, we sought to clarify different biological properties between mouse and pig by examining their function in lymphoid organs.
Please note that the superseries GSE97505 records represent the pig data

first: Jin-Hoi

last: Kim


title: Converting self-renewal in naïve pluripotency to naïve endoderm [I]

status: Public on Oct 01 2017

city: Copenhagen

first: Joshua

last: Brickman

address: 3B Blegdamsvej

country: Denmark

institute: DanStem

summary: A novel strategy to generate bipotent primitive endoderm cultures from murine embryonic stem cells in vitro.

overall_design: ESCs (ESC) were differentiated for 7-8 days in the presence of Activin/CHIRON/LIF (Diff). Differentiated cultures were passaged as nEnd, and several different passages are analysed here- passage 7-10 are defined as mid-passage (Mid), passage 14-15 are defined as late passage (Late). XEN cells were included as controls. In the case of nEnd cultures, each replicate is from a different experimental set of differentiatiations and passages. In all cases except for XEN, the double reporter line HRHnG was used.

first: Kathryn

middle: G

last: Anderson

middle: M


title: Gene expression profile of the RAG2 gene depletion on LN of mouse


title: Development of gene expression signatures of CTCF-expressing vs CTCF-depleted hepatocellular carcinoma cells

city: Hong Kong

first: Kwong Wai

last: CHOY

address: Hong Kong

department: O and G

country: Hong Kong

institute: CUHK

summary: To understand the functional role of CTCF in the oncogenesis of HCC, we constructed lentiviruses expressing control shRNA (shCont) or shRNA agains CTCF (shCTCF) and transduced them into PLC5 cells respectively. After 24 hours, cells were cultered in puromycin containing medium (5 ug) for another 24 hours. Cells were returned to normal medium for another 48 hours before total mRNAs were corrected for whole genome gene expression array analysis. Expression of FoxM1 gene from this signature was quantified in an independent set of RNA samples by real-time PCR, confirming differntial expression of this gene in shCTCF expressing cells.

overall_design: Gene expressions were measured in PLC5 cells transduced with lentivirues expressing non-targeting shRNA or shRNA against CTCF followed by growing in puromycin selection media for 24 hours.

first: C

middle: B

last: Ko

first: Bin

last: Zhang

first: Kwong

middle: W

last: Choy

first: Hoi

middle: K

last: Wong


title: RNA-SEQ analysis of postnatal Ret-positive (EGFP-labeled) nociceptive (NaV1.8 population) dorsal root ganglia L345 or L6S1 neurons.

city: Edinburgh

first: GUDMAP

last: Developers

address: Crewe Road

institute: IGMM MRC Human Genetics Unit

summary: The goal of this set is to build expression data using FACS isolated Ret-positive cells (postnatal) harvested from a RetFloxedEGFP reporter mouse crossed with NaV1.8Cre mice to enrich for Ret nociceptor population. To enrich for bladder projecting neurons L6S1 DRGs were FACS isolated. L3,4, 5 lumbar levels were also FACS isolated to aid in differential expression of Ret-nociceptor population from L6S1 and L345 spinal DRG levels. The series further includes these populations from males and females to uncover sex based differences.

overall_design: RNA was extracted from 3 month FACS isolated dorsal root ganglia dissected from RetFloxedEGFP (RET9 allele is floxed followed by conditional expression of EGFP: abbreviated 9CG) C57BL/6J mice (knocked-in Ret locus-heterozyotes, EGFP is expressed only after Cre-mediated excision from NaV1.8 cells: in DRGS, only small unmyelinated Ret expressing cells) and sequenced using Illumina Hiseq 2500 platform.

first: Eric

last: Tycksen

first: Masato

last: Hoshi

first: Judy

last: Golden

first: Amanda

last: Knoten

first: Sanjay

last: Jain


title: Gene expression profile of the RAG2 gene depletion on spleen of mouse


title: RNA-SEQ analysis of E18.5 ALL Ret-positive (EGFP-labeled) male or female dorsal root ganglia neurons.

summary: The goal of this set is to build expression data using FACS isolated Ret-positive cells harvested from a Ret-EGFP reporter mouse (embryonic day E18.5 male or female). These can be used as a time point in comparative analysis of ontogeny of genes expressed at various developmental time points.

overall_design: RNA was extracted from E18.5 FACS isolated dorsal root ganglia dissected from Ret-EGFP C57BL/6J mice (EGFP knocked-in Ret locus-heterozyotes) and sequenced using Illumina Hiseq 2500 platform. Refer to protocols on the GUDMAP website under Jain.


title: Molecular regulation mechanism of cold acclimation and cold tolerance in tea leaves

status: Public on Sep 29 2017

city: Hangzhou

first: Xinyuan

last: Hao

state: Zhejiang

address: No.9 Meiling South Road, Xihu District

country: China

institute: TRICAAS

summary: Recently, intensive global climate change has become a major factor impacting plant survival during the winter. Freezing cold temperatures during the winter and abnormal temperature fluctuations during the winter and early spring are the most harmful ambient factors threatening tea plant winter survival and currently cause marked economic losses in tea production. In this study, by simulating natural climate change, we established cold acclimation (CA) and rapid cold stress (after CA) conditions to comprehensively investigate the transcriptome changes involved in CA and rapid cold stress. Electrolyte leakage (EL) rate and expression profile clustering analyses confirmed that the experimental design was valid. Comparative transcription analysis identified many differentially expressed genes (DEGs) involved in both processes. Time course and pathway enrichment analyses further revealed the physiological changes that occur during the initial period of CA and the cell wall changes that occur throughout the entire CA process; these changes play crucial roles in increasing freezing tolerance during this process. Compared with CA, different cold response mechanisms were rapidly activated under cold stress; however, the subsequent accumulation of reactive oxygen species, which affect multiple aspects, caused by freezing cold could be the harshest factor impairing tea leaves. Moreover, we investigated 60 DEGs shared by both processes and highlighted the importance of KCSs, HXXXD-type acyl-transferase family proteins, NAC080, SWEETs and ENOs in the responses to various cold conditions. These results greatly improve our knowledge of cold response mechanisms in tea plants and provide meaningful information for functional studies investigating cold tolerance-related genes.

overall_design: Total of 8 biosamples including cold acclimation treatment and freezing cold treatment, triplication were applied. Therefore 24 microarray were used in this study.


title: HM450 analysis pregnancy anxiety

first: Stephan

last: Claes

address: Herestraat 49

department: Department of Neurosciences

institute: KU Leuven

type: Methylation profiling by genome tiling array

summary: DNA methylation profiling of low versus high pregnancy anxiety (22 versus 23 cord blood samples, respectively) using the Illumina Infinium HM450 array

overall_design:
Low (n = 22) and high (n = 23) pregnancy anxiety samples were selected from a study cohort of 80 mother-infant dyads, based on the lowest and highest scores on the Pregnancy Related Anxiety Questionnaire. Cord blood DNA samples were bisulfite treated and randomized across four Illumina HM450 BeadChips. One sample was replicated on each chip to account for batch effects.

Please note that four technical replicates were carried out for  PELS_08 sample and only the 'replicate 3' was included in further analyses.

first: Elise

last: Vangeel

first: Ehsan

last: Pishva

first: Titia

last: Hompes

first: Daniel

last: van den Hove

first: Karel

last: Allegaert

first: Kathleen

last: Freson

first: Benedetta

last: Izzi


title: Genome-wide analysis of transcription, H2A.Z, nucleosomes and HSF1 dynamics in response to temperature increase in Arabidopsis thaliana [RNA-Seq III]

city: Cambridge

first: Sandra

last: Cortijo

address: Bateman Street

institute: Sainsbury Laboratory, Cambridge University

summary: Plants are sessile organisms and therefore must sense and respond to changes of their surrounding conditions such as ambient temperature, which vary diurnally and seasonally. It is not yet clear how plants sense temperature and integrate this information into their development. We have previously shown that H2A.Z-nucleosomes are evicted in response to warmer temperatures. It is not clear however, whether the link between transcriptional responsiveness and changes in H2A.Z binding in context of temperature shifts is a global trend that can be seen throughout the genome, or the phenomenon is specific to a specialised set of temperature-responsive genes. In addition to the role of H2A.Z-nucleosome dynamics in the transcriptional response to temperature, it was shown that genes strongly misregulated in the h2a.z mutant are enriched for gene categories involved in response to multiple environmental cues. This suggests that H2A.Z could be implicated in the transcriptional response to various environmental inputs, raising the question: What brings the specificity of H2A.Z dynamics in response to temperature? To address this question we have profiled H2A.Z-nucleosome occupancy genome wide (using ChIP-seq) during a time course after temperature variation and compared its dynamics to transcriptional changes. We identified a fast, targeted and transient eviction of H2A.Z associated with transcriptional activation in response to temperature for a few hundreds genes. This eviction is associated with a reduction of the stability of the nucleosome. Moreover the genes with a fast H2A.Z eviction were strongly enriched in heat shock elements in their promoter and we observed a strong association between HSF1 binding and H2AZ eviction at warm temperature. These results highlight the importance of the interplay between transcription factors and chromatin to allow a controlled and dynamics response to temperature.

overall_design: RNA-seq were generated in duplicate for seedlings shifted to warm temperature

first: Phil

last: Wigge

first: Varodom

last: Charoensawan


title: Gene expression profile of the RAG2 gene depletion on spleen, thymus, and LN of mouse

first: Yun-Jung

last: Choi


title: RNA-SEQ analysis of E12.5 ALL Ret-positive (EGFP-labeled) FACSd dorsal root ganglia neurons

first: GUDMAP

last: Developers

summary: The goal of this set is to build expression data using FACS isolated Ret-positive cells harvested from a Ret-EGFP reporter mouse (embryonic day E12.5). These can be used as a time point in comparative analysis of ontogeny of genes expressed at various developmental time points.

overall_design: RNA was extracted from E12.5 FACS isolated dorsal root ganglia dissected from Ret-EGFP C57BL/6J mice (EGFP knocked-in Ret locus-heterozyotes) and sequenced using Illumina Hiseq 2500 platform. Refer to protocols on the GUDMAP website under Jain.

first: Eric

last: Tycksen

first: Masato

last: Hoshi


title: RNA-SEQ E18.5 Ret-positive (EGFP-labeled) Nav1.8 dorsal root ganglia neurons.

summary: The goal of this set is to build expression data using FACS isolated Ret-positiveNaV1.8 cells harvested from RetFloxedEGFP;NaV1.8Cre embryos (embryonic day E18.5 male or female). These can be used as a time point in comparative analysis of ontogeny of genes expressed at various developmental time points in Ret nociceptors.

overall_design: RNA was extracted from E18.5 FACS isolated dorsal root ganglia dissected from RetFloxedEGFP:NaV1.8Cre mice (EGFP conditionally expressed in Ret population that express Cre from the NaV1.8 locus) and sequenced using Illumina Hiseq 2500 platform. Refer to protocols on the GUDMAP website under Jain.

first: Judy

last: Golden

first: Amanda

last: Knoten

first: Sanjay

last: Jain


title: Whole transcriptome (gene expression and splice isoform changes) profiling using Affymetrix Human Transcriptome Array 2.0

status: Public on Sep 28 2017

city: New York

first: John

last: Blenis

state: NY

address: 413 East 69th Street

department: Meyer Cancer Center and Department of Pharmacology

institute: Weill Cornell Medicine

summary:
Transcriptome analysis of total RNA samples from human cell line (LAM 621-101, female)
Global gene and splice isoform expression profiling was performed to get a comprehensive view of transcriptome changes in human Lymphangioleiomyomatosis (LAM 621-101, female) cell line after inhibition of mTORC1 and SRPK2 proteins.

overall_design:
We analyzed Lymphangioleiomyomatosis cell line (LAM 621-101, female) after treatment of rapamycin or knockdown of SRPK2 using the Affymetrix Human Transcriptome Array 2.0 platform. Three biological replicates were performed. CEL files were processed by Affymetrix Expression Console Software 1.4.1. to generate CHP files for gene expression and splice isoform analyses.

Please note that each sample was analyzed for gene expression and re-analyzed for splice isoform expression. Therefore, the raw data CEL file linked to *[splice isoform analysis] sample is identical to that linked to the corresponding *[gene expression] sample record.

first: Gina

last: Lee


title: microRNA-21 deletion impairs regulatory T cell function

city: Charlottesville

first: Yong

last: Huang

state: VA

address: 1340 Jefferson Park Ave

department: Medicine

institute: University of Viginia

summary: Background:  It has been found that miR-21 is increased in colonic tissues and decreased in peripheral blood regulatory T cells (Tregs) of patients with ulcerative colitis (UC). We aimed to investigate the influence of miR-21 on Tregs function in intestinal inflammation. Methods: Various CD4+ T cell populations were flow-cytometry sorted from miR-21-/- mice and littermates (WT) utilization in T-cell transfer colitis model and suppression of T cell activation and proliferation by Tregs. Gene expression was microarray-profiled and validated by qPCR, ELISA and immunofluorescence. miR-21 mimic and inhibitor studies and a 3’-untranslated region of SOCS5 luciferase report assay were used to validate the effect of miR-21. Results: As compared to their littermates,  miR-21-/- mice have less Tregs in lymph nodes. miR-21-/- Tregs produced higher amount of SOCS5 and IFNγ, and lower amount of Jak3, Stat3, Stat5a, Foxp3, TGFβ1 and IL10. miR-21-/- Tregs reduced suppressive function in vitro and in vivo.  Functional assays indicated that miR-21 could directly suppress SOCS5 expression. Conclusions: Expression and function of miR-21 are cell-type- and context- dependent. miR-21 deficiency result in impaired SOCS-JAK-STAT pathway activity in Tregs. miR-21 play a positive role in Tregs differentiation and suppressive function.

overall_design: Various CD4+ T cell populations were isolated by flow-cytometry sorting from mesenteric lymph nodes of  Mir-21-/- mice (KO) and littermates (WT). Total RNAs were purified from these T cells for gene expression analysis. Gene expression profiles of the T cells were compared between Mir21-/- and WT to identify differentially expressed genes. Quantitative real-time qPT-PCR was used to validate the differential expression of genes.

first: Feng

last: Wu

first: Fengshi

last: Dong

middle: H

last: Kwon


title: NFATC2 knock-down on melanoma cell line A375

first: Sara

last: Aibar

department: Center for Brain & Disease Research

institute: VIB-KU Leuven

summary: RNA-seq on NFATC2 knock-down (siRNA) on melanoma cell line A375

overall_design: RNA-seq on the melanoma cell line A375 under two treatment conditions: NFATC2 siRNA and non-targeting control siRNA

first: Jasper

last: Wouters

first: Stein

last: Aerts


title: Cross-Platform single cell analysis of kidney development shows stromal cells express Gdnf

city: Cincinnati

first: Mike

last: Adam

state: Ohio

address: 240 Albert Sabin Way

department: CBDI

institute: Cincinnati Children's Hospital Research Foundation

summary: The developing kidney provides a useful model for study of the principles of organogenesis. In this report we use three independent platforms, Drop-seq, Chromium 10XGenomics and Fluidigm C1, to carry out single cell RNA-seq analysis of the E14.5 mouse kidney. Using the software AltAnalyze, in conjunction with the unsupervised approach ICGS, we were able to identify and confirm the presence of 16 distinct cell populations during this stage of active nephrogenesis.

overall_design: E14.5 mouse kidney cells were analyzed using three different single-cell rna-seq platforms: Drop-seq, Chromium 10X, and Fluidigm C1.

first: S

middle: S

last: Potter


title: Precise modulation of genome functions and live tracking of genome regions in CRISPR/dCas9 knockin mice

city: Beijing

first: Xueying

last: Mai

address: 7 Science Park Road ZGC Life Science Park

institute: National Institute of Biological Sciences, Beijing

summary: we demonstrated ex vivo and in vivo validation of dCas9 KI functions such as transcription

overall_design: live mRNA profiles of wild type (WT) and SunTag-dCas9 mice were generated by deep sequencing.Myod1 actived and control live mRNA profiles of SunTag-dCas9 mice were generated by deep sequencing.

first: Yu

last: Zhang


title: RNA-Seq analysis of 3 month old all Ret-positive (EGFP-labeled) dorsal root ganglia L345 or L6S1 neurons

first: GUDMAP

last: Developers

summary: The goal of this set is to build expression data using FACS isolated Ret-positive cells harvested from a Ret-EGFP reporter mouse (3 month old).  To enrich for bladder projecting neurons L6S1 DRGs were FACS isolated.  L3,4, 5 lumbar levels were also FACS isolated to aid in differential expression of Ret-positive populations from L6S1 and L345 and help enrich bladder Ret-positive neurons. The series further includes these populations from males and females to uncover sex based differences.

overall_design: RNA was extracted from 3 month FACS isolated dorsal root ganglia dissected from Ret-EGFP C57BL/6J mice (EGFP knocked-in Ret locus-heterozyotes) and sequenced using Illumina Hiseq 2500 platform.

first: Eric

last: Tycksen

last: Hoshi


title: FoxP3 scanning mutagenesis reveals functional variegation and mild mutations with atypical autoimmune phenotypes [nanostring]

city: Boston

first: CBDM

last: Lab

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

institute: Harvard Medical School

summary: Nanostring profiles of CD4+ T cells transduced with EV, WT or FoxP3 mutants

overall_design: DAPI-CD4+THY1.1high T cells were double sorted after 3 days of retroviral infection. Total RNA was prepared using RLT buffer followed by NanoString nCounter assay system manual

first: HoKeun

first: Christophe

last: Benoist

first: Diane

last: Mathis


title: Genome wide screen to identify HDAC5 association in the cultured striatal neurons

city: Charleston

first: Makoto

last: Taniguchi

state: SC

address: 173 Ashley Ave

institute: Medical University of South Carolina

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Purpose: using next generation sequencing, we identify the HDAC5 assocaited genomic region in the mouse cultured striatal neurons.

overall_design: We performed chromatin immunoprecipitation using anti-HDAC5 antibody or normal rabbit IgG as control with the mouse cultured striatal neurons stimulated with elevation of cAMP. The ChIP samples were subjected to the next generation sequencing.

first: Taniguchi

last: Makoto

first: Cowan

last: Christopher


title: FoxP3 scanning mutagenesis reveals functional variegation and mild mutations with atypical autoimmune phenotypes

type:
Expression profiling by array
Other

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

overall_design: Refer to individual Series


title: Genome-wide analysis of transcription, H2A.Z, nucleosomes and HSF1 dynamics in response to temperature increase in Arabidopsis thaliana

first: Sandra

last: Cortijo


title: Adaptation of iCLIP to plants determines the binding landscape of the clock-regulated RNA-binding protein AtGRP7

city: Bielefeld

first: Martin

last: Lewinski

address: Universitätsstraße 25

department: RNA Biology and Molecular Physiology

country: Germany

institute: Bielefeld University


title: FoxP3 scanning mutagenesis reveals functional variegation and mild mutations with atypical autoimmune phenotypes [microarray]

summary: Microarray profiles of M176, M354 and WT FoxP3 -transdued (in vitro) and -Treg from mice

overall_design: DAPI-CD4+Thy1.1high T cells for in vitro transduction or DAPI-CD4+CD25high Tregs were double sorted from treated mice. Total RNA was prepared using Trizol method followed by amplification and cDNA preparation. cDNA was hybridized to Affymetrix ST1.0 microarrays.

first: Ho-Keun

last: Kwon


title: Identification of AtGRP7 targets by iCLIP

summary: A key function for RNA-binding proteins in orchestrating plant development and environmental responses is well established. However, the lack of a genome-wide view on their in vivo binding targets and binding landscapes represents a gap in understanding the mode of action of plant RNA-binding proteins. Here, we adapt individual nucleotide resolution crosslinking immunoprecipitation (iCLIP) for genome-wide determining the binding repertoire of the circadian clock-regulated Arabidopsis thaliana glycine-rich RNA-binding protein AtGRP7. We have established iCLIP for plants to identify target transcripts of the RNA-binding protein AtGRP7. This paves the way to investigate the dynamics of posttranscriptional networks in response to exogenous and endogenous cues.

overall_design: AtGRP7 iCLIP

first: Katja

last: Meyer

first: Tino

last: Köster

first: Christine

last: Nolte

first: Claus

last: Weinholdt

first: Ivo

last: Grosse

first: Dorothee

last: Staiger


title: Division-induced DNA double strand breaks in the chromosome terminus region of Escherichia coli lacking RecBCD DNA repair enzyme

first: David

last: Leach

address: KIng's Building

institute: University of Edinburgh

summary: RecBCD protein complex is an important player of DSB repair in bacteria and bacteria that cannot repair DNA double-stranded breaks (DSB) have a low viability. Whole genome sequencing analyses showed a deficit in specific sequences of the chromosome terminus region in recB mutant cells, suggesting terminus DNA degradation during growth. We studied here the phenomenon of terminus DNA loss by 42 whole genome sequencing and microscopy analyses of exponentially growing bacteria. We tested all processes known to take place in the chromosome terminus region for a putative role in DNA loss: replication fork termination, dimer resolution, resolution of catenated chromosomes, and translocation of the chromosome arms in daughter cells during septum formation. None of the mutations that affect these processes prevents the phenomenon. However, we observed that terminus DNA loss is abolished in cells that cannot divide. We propose that in cells defective for RecBCD-mediated DSB repair the terminus region of the chromosome remains in the way of the growing septum during cell division, then septum closure triggers chromosome breakage and, in turn, DNA degradation.

overall_design: Comparison of RecA binding in the terminus region of Escherichia coli in LB and M9 media

first: Anurag

last: Sinha

first: Adeline

last: Durand

first: Jean-Michel

last: Desfontaines

first: Ielyzaveta

last: Iurchenko

first: Hélène

last: Auger

middle: R

first: François-Xavier

last: Barre

first: Bénédicte

last: Michel


title: Glucocorticoid-induced phosphorylation by CDK9 specifies the coactivator functions of transcriptional cofactor GRIP1 in macrophages

city: New york

first: Yurii

last: Chinenov

state: New York

address: 535 E 71 str, Hospital for Special Surgery

department: Research Division

institute: Hospital for special surgery

summary: Glucocorticoid Receptor (GR) suppresses inflammation by activating anti-inflammatory and repressing pro-inflammatory genes. GR-interacting protein (GRIP)1 of the p160 family has emerged as a unique GR corepressor in macrophages (MΦ), however, whether GRIP1 contributes to GR-activated transcription, and what dictates its context-specific coactivator vs. corepressor properties is unknown. We report that loss of GRIP1 in human and mouse MΦ attenuated GR-mediated induction of several anti-inflammatory targets, revealing a non-redundant function of GRIP1 in coactivation. Moreover, glucocorticoid treatment of quiescent MΦ globally directed GRIP1 toward GR-bound genomic sites dominated by classic palindromic GREs, suggesting its dedicated role as a GR coactivator. Further, GRIP1 N-terminal region was phosphorylated at a serine cluster by Cyclin-Dependent Kinase (CDK)9, which was recruited into GC-induced GR:GRIP1:CDK9 ternary complexes, producing distinct GRIP1 phospho-isoforms at different GREs even associated with the same gene. Functionally, phosphorylation potentiated GRIP1 coactivator properties by facilitating its recruitment and/or creating novel protein:protein interaction surfaces in a GRE-specific manner. Strikingly, GRIP1 function as a GR corepressor was phosphorylation-independent; consistently, no phospho-GRIP1 or CDK9 was detected at GR transrepression sites near pro-inflammatory genes. Thus, liganded GR in MΦ restricts actions of its own coregulator via CDK9-mediated phosphorylation to a subset of complexes driving anti-inflammatory gene transcription.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: 1. Analysis of Glucocorticoid receptor (NR3C1) cistromes in differentiated THP1 cells (human) and mouse bone marrow derived macrophages treated with dexamethasone in comparasion to untreated control, 2. Analysis of GRIP1 (Ncoa2) cistromes in differentiated THP1 cells (human) and mouse bone marrow derived macrophages treated with dexamethasone in comparasion to untreated control, 3) Analysis of phospho-S469 GRIP1(Ncoa2) cistrome in  differentiated THP1 cells (human) treated with dexamethasone in comparasion to untreated control

middle: A

last: Rollins

first: Maddalena

last: Coppo

first: Inez

last: Rogatsky


title: Gene Expression Profile of human hepatocellular carcinoma by RNA sequencing

city: Guangzhou

first: Jingping

last: Yun

state: Guangdong

address: 651 Dongfeng East Road

department: Pathology

institute: Sun Yat-sen University Cancer Center

summary: The aim of the present study was to investigate biomarkers in the malignant process of HCC by high throughput sequencing.

overall_design: Tumors and paired non-tumor tissues were collected from HCC patients during surgeries at Sun Yat-sen University Cancer Center. Samples were profiled separately using the Illumina HiSeq™ 2500 by MyGene Diagnostics Co., Ltd (Guangzhou, China).


title: GABPA ChIP-seq in human monocytic THP-1 cells

city: Kuopio

first: Carsten

last: Carlberg

address: Yliopistonranta 1D

department: Institute of Biomedicine

country: Finland

institute: University of Eastern Finland

summary: ChIP-seq for GABPA in THP-1 cells after stimulation with the the natural VDR ligand 1,25-dihydroxyvitamin D3 (1,25(OH)2D3)

overall_design: THP-1 cells were treated for 24 h with 100 nM 1,25(OH)2D3 or vehicle before ChIP assay

first: Sabine

last: Seuter

first: Antonio

last: Neme


title: Temporal Control of Mammalian Cortical Neurogenesis by m6A Methylation

city: Munich

first: Francisca

last: Rojas Ringeling

address: Feodor-Lynen-Straße 25, 81377

department: Biochemistry

institute: Ludwig Maximilian University of Munich

summary: N6-methyladenosine (m6A), installed by the Mettl3/Mettl14 methyltransferase complex, is the most prevalent internal mRNA modification. Whether m6A regulates mammalian brain development is unknown. Here we show that Mettl14 deletion in the embryonic mouse brain diminishes m6A levels, prolongs cell cycle of radial glia cells, and extends cortical neurogenesis into postnatal stages. Mettl3 knockdown also prolongs neural progenitor cell cycle and promotes radial glia cell maintenance. m6A-sequencing of the embryonic mouse cortex reveals enrichment of mRNAs related to transcription factors, cell cycle and neuron differentiation, and Mettl14 deletion attenuates their decay. Notably, Mettl14-/- radial glia cells precociously express neuronal proteins. Further analysis uncovers previously unappreciated transcriptional pre-patterning in cortical neural stem cells. Comparison of m6A-mRNA landscapes between mouse and human cortical neural progenitors identifies human-specific tagging of transcripts related to epigenetic regulation and brain disorder risk genes. Our study reveals an epitranscriptomic mechanism in heightened transcriptional coordination during mammalian cortical neurogenesis.

overall_design: m6A profiling of mouse developing brain (E13.5) (performed with 3 replicate pull-downs) and m6A profiling of human 47 day organoids (performed with 2 replicate pull-downs). In addition, there is m6A sequencing of PCW11 human brain cortex, performed with 3 replicate pull-downs


title: Single-cell sequencing reveals dissociation-induced gene expression in tissue subpopulations

city: Utrecht

first: Susanne C

middle: van den

last: Brink

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute

summary: In many gene expression studies, cells are extracted by tissue dissociation and Fluorescence-Activated Cell Sorting (FACS), but the effect of these protocols on cellular transcriptomes is not well characterized and often ignored. Here, we applied single-cell mRNA sequencing (scRNA-seq) to muscle stem cells, and unexpectedly found a subpopulation that is strongly affected by the widely-used dissociation protocol that we employed. One implication of this finding is that several published transcriptomics studies may need to be reinterpreted. Importantly, we detected similar subpopulations in other single-cell datasets, suggesting that cells from other tissues might be affected by this artefact as well.

sample_organism:
Danio rerio
Mus musculus

platform_organism:
Danio rerio
Mus musculus

overall_design:
Mouse satellite cells and zebrafish fin cells were extracted from Tibialis Anterior muscles of Pax7nGFP mice and wildtype zebrafish fins, respectively. For cell extraction, traditional (Supplementary Methods) dissociation protocols that combine mechanical and enzymatic dissociation were employed, and live cells were subsequently sorted into plates using FACS. Next, single-cell mRNA sequencing (CEL-Seq or SORT-Seq (robotized version of CEL-Seq2)) was applied, and data was analyzed with RaceID2 to identify clusters.
CEL-Seq samples: Manual CEL-Seq; Satellite cells (unstained); Male Pax7nGFP mice (5-7 months old); 1h collagenase-treated (default dissociation protocol); 96 cells per plate with 96 different barcodes (see "Cel-seq_barcodes_96.csv"); some primes numbers are bulk samples (see "BulkSamples_BarcodesAndNrOfCellsUsed_perCEL-Seq1-library"); Spike-ins included (see "ERCC92.fa"); No mitochondrial reads in count tables; Sequencing lanes not concatenated in fastq-files uploaded here; "Merged_CEL-Seq_AllMiceAndLibrariesMerged.csv"-file is count table with reads from all mice and libraries merged (Annotation of columns: Zx.y, where Z = mouse, x = library and y = cell barcode; bulk samples are not included any more in this file); See Supplementary Methods for details.
SORT-Seq 1h and 2h dissociated samples: Robotized CEL-Seq2; Satellite cells (unstained); Male Pax7nGFP mice (5-7 months old; 8 muscles from 4 mice); One plate of 1h (default dissociation protocol) and one plate of 2h collagenase-treated cells; 384 cells per plate with each of the 96 barcodes (see "Cel-seq_barcodes_96.csv") used 4 times per plate (therefore, each plate has 4 libraries); No bulk samples included; Spike-ins included (see "ERCC92.fa"); No mitochondrial reads in count table; In some wells, we sorted no cell (internal negative control; barcodes #95 and #96 were used for empty wells); Sequencing lanes not concatenated in fastq-files uploaded here; "Merged_SORT-Seq_DissociationTimecourse.csv"-file is count table were reads from all dissociation timepoints are merged (Annotation columns: DZhx_y, where Z = 1 or 2 hours collagenase-treated, x = library and y = cell barcode); See Supplementary Methods for details.
SORT-Seq MitoTracker stained samples (pilot and repeat): Robotized CEL-Seq2 samples; Satellite cells stained with MitoTracker; Female Pax7nGFP mice (1 4.7-months old mouse for pilot experiment; 3 6-months old mice for repeat experiment); 1h collagenase-treated (default dissociation protocol); 384 cells per plate with each of the 384 barcodes (see "Cel-seq_barcodes_384.csv") used 1 times per plate (therefore, each plate has 1 library); Note: pilot experiment has 263 cells (so plate was partly empty), repeat experiment done with 4 full plates; No bulk samples included; Spike-ins included (see "ERCC92.fa"); Mitochondrial reads (rows named "*__chrM") included in count tables (these were removed prior to RaceID2); In some wells, we sorted no cell (barcodes #357-#360 and #381-#384 were used for empty wells); Sequencing lanes concatenated in fastq-files uploaded here; No merged file was generated for pilot experiment (as only one library), "Merged_MitoTracker_Repeat.csv"-file is count table were reads from all plates of repeat experiment were merged (Annotation of columns: Plx_Welly, where x = plate number (1-4) and x = cell barcode); See Supplementary Methods for details.
SORT-Seq zebrafish fin samples: Robotized CEL-Seq2; Fin cells (unstained; all live cells); Wildtype zebrafish; Dissociated using default fin dissociation protocol (Supplementary Methods); 384 cells per plate with each of the 384 barcodes (see "Cel-seq_barcodes_384.csv") used 1 times per plate (therefore, each plate has 1 library); Note: only merged count table file ("fin_C_E_count_table.csv", Annotation columns: Xx.py.prim.finZ, where x = cell barcode, y = plate number and Z is fish (C or E)) and no individual library count table files were uploaded to GEO for zebrafish fin data; No bulk samples included; Spike-ins not included in merged count tables file; Mitochondrial reads not included in merged count tables file; In some wells, we sorted no cell (barcodes #357-#360 and #381-#384 were used for empty wells); Sequencing lanes concatenated in fastq-files uploaded here; See Supplementary Methods for details.

first: Susanne

middle: C

last: van den Brink

first: Fanny

last: Sage

first: Ábel

last: Vértesy

first: Bastiaan

last: Spanjaard

first: Josi

last: Peterson-Maduro

first: Chloé

last: Baron

first: Catherine

last: Robin

first: Alexander

last: van Oudenaarden


title: Expression data from glioblastoma derived sphere lines, adherent cell lines and their original glioblastoma tumor

status: Public on Sep 27 2017

city: Lausanne

first: Pierre

last: Bady

address: Quartier UNIL-Sorge

department: Swiss Institute of Bioinformatics

institute: CHUV / BCF / SIB

summary: Glioblastoma (GBM) derived sphere lines and adherent cell lines are an important tool for research in basic and translational neuro-oncology. Documentation of their genetic identity has become a requirement for scientific journals and grant applications to exclude cross-contamination and misidentification that lead to misinterpretation of results. Here, we report expression data for 26 samples including 4 GBM derived sphere lines (4 x 3 replicates), 2 GBM derived sphere lines passaged through intracranial  transplantation (2x 1), 2 adherent GBM derived cell lines (2 + 2 x 3 replicates), 4 corresponding glioblastoma tumors and 2 non-tumor brain tissues.

first: Davide

last: Sciuscio

first: Monika

middle: E

last: Hegi


title: ChIP sequencing

city: Shanghai

first: Meng-Meng

last: Ji

address: Ruijin No.2 Road

institute: Shanghai Ruijin Hospital

summary: ChIP sequencing for 4 samples..

overall_design: Examing the protein (H3K4me3)-DNA interaction sites


title: Treatment with Albumin (A)-Hydroxyoleic acid (HOA) complex restores sensorimotor function in rats with spinal cord injury: Efficacy and gene expression regulation

city: Toledo

first: Gerardo

last: Avila Martín

address: Finca La Peraleda s/n

department: Research Unit

country: Spain

institute: National Paraplejic Hospital

summary: Sensorimotor dysfunction following incomplete spinal cord injury (SCI) is often characterized by paralysis, spasticity and pain. Previously, we showed that intrathecal (i.t.) administration of the albumin-oleic acid (A-OA) complex in rats with SCI produced partial improvement of these symptoms and that oral 2-hydroxyoleic acid (HOA), a non-hydrolyzable OA analogue), was efficacious in the modulation and treatment of nociception and pain-related anxiety, respectively. Here we observed that intrathecal treatment with the complex albumin-HOA (A-HOA) every 3 days following T9 spinal contusion injury promoted significant recovery in locomotor function and marked an inhibition of TA noxious reflex activity (i.e., nociception) in Wistar rats. To investigate the mechanism of action of A-HOA, microarray analysis was carried out in the spinal cord lesion area. Representative genes involved in pain and neuroregeneration were selected to validate the changes observed in the microarray analysis by quantitative real-time RT-PCR. Comparison of the expression between healthy rats, SCI rats, and SCI treated with A-HOA rats revealed relevant changes in the expression of genes associated with neuronal morphogenesis and growth, neuronal survival, pain and inflammation. Thus, treatment with A-HOA not only induced a significant overexpression of growth and differentiation factor 10 (GDF10), tenascin C (TNC), aspirin (ASPN) and sushi-repeat-containing X-linked 2 (SRPX2), but also a significant reduction in the expression of prostaglandin E synthase (PTGES) and phospholipases A1 and A2 (PLA1/2). Currently, SCI has very important unmet clinical needs. A-HOA proved to downregulate genes involved in inflammation and upregulate genes involved in neuron growth, which balanced the important body response to medular lesion and allowed recovery from paralysis and pain.

overall_design: We use four different animals for each experimental group which were extracted and processed separately

last: Avila-Martín

first: Manuel

last: Mata-Roig

first: Iriana

last: Galán-Arriero

first: Julian

last: Taylor

first: Xavier

last: Busquets

first: Pablo

middle: V

last: Escribá


title: FIBP maintains colorectal cancer cells stemness via demethylation of stemness genes

first: Lu

last: Lu

address: No.12,Airport Road,Baiyun District

institute: Guangzhou University of Chinese Medicine

summary: To validate how FIBP influences stemness, we obtained the genome-wide methylation in HCT116-CSCs by an Illumina HumanMethylation450 BeadChip.

overall_design: Examination of genome-wide DNA methylation in 3 cell types (Vector, FIBP_knockdown, FIBP/GSK3b_knockdown)

first: Wen-Bo

last: Niu


title: Whole Transcriptomic Analysis of Trichostatin A or Grape Seed Extract treated SK-MEL-3 melanoma cells.

city: Tallahassee

first: Elizabeth

last: Mazzio

state: Florida

address: 1515 MLK Blvd

department: College of Pharmacy & Pharmaceutical Science

institute: Florida Agricultural & Mechanical University

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

platform_organism:
Homo sapiens
synthetic construct


title: Predictive analysis of long non-coding RNA expression profiles in tumor and normal tissues from glioblastoma patients

city: Zhengzhou

first: Jianjun

last: Gu

address: No.7 Weiwulu

institute: Henan Provincial People's Hospital

summary: We compared lncRNA expression data in tumor tissues from 9 patients and 3 healthy tissues by using an HlncOA 1.0 array. Data show that 185 lncRNAs, including 90 upregulated and 95 downregulated lncRNA transcripts, were significantly dysregulated in glioblastoma tissues. Then, 8 dysregulated lncRNAs were validated in another 50 samples of specimens using quantitative real-time polymerase chain reaction assays（qRT-PCR）. We predicted lncRNA-miRNA-mRNA networks by co-expressing lncRNA and mRNA with altered miRNA. Bioinformatic analysis was used to predict possible pathways in which these networks might be involved. Finally, we analyzed interactions between validated lncRNAs and their potential cancer-related miRNA targets to identify the potential roles of lncRNAs in glioblastomas.

overall_design: We hypothesized that lncRNAs are involved in the pathogenesis of glioblastomas, so we compared lncRNA expression data in tumor tissues from 9 patients and 3 healthy tissues by using an HlncOA 1.0 array. Data show that 185 lncRNAs, including 90 upregulated and 95 downregulated lncRNA transcripts, were significantly dysregulated in glioblastoma tissues. Then, 8 dysregulated lncRNAs were validated in another 50 samples of specimens using quantitative real-time polymerase chain reaction assays（qRT-PCR）. We predicted lncRNA-miRNA-mRNA networks by co-expressing lncRNA and mRNA with altered miRNA.


title: Whole miRNA transcriptome profiling of Trichostatin A and Grape Seed Extract treated SK-MEL-3 human melanoma cells.

summary: In this study, over 1400 compounds were initially screened for capacity to inhibit the kinetic enzyme activity of nuclear HDACs isolated from SK-MEL-3 cells. From these findings we evaluate miRNA whole transcriptome changes that occur at a 24 hour time point in SK-ME-3 cells in the presence of a known HDAC inhibitor (Trichostatin A) (1uM) or a natural product HDAC inhibitor Grapeseed Extract (120ug/ml), both tested at sub-lethal concentrations relative to untreated controls. Microarrays were acquired using miRNA 4.1 Human Arrays (Affymetrix, Thermo-Fisher Scientific).

first: Kara

middle: F

last: Soliman


title: Microarray whole transcriptome profiling of Trichostatin A and Grape Seed Extract in SK-MEL-3 melanoma cells.

summary: In this study, we initially screened over 1400 natural products for capacity to inhibit the kinetic enzyme activity of nuclear HDACs isolated from SK-MEL-3 cells. From these findings we evaluate whole transcriptome changes that occur at a 24 hour time point in SK-ME-3 cells in the presence of a known HDAC inhibitor (Trichostatin A) (1uM) or a natural product HDAC inhibitor Grapeseed Extract (120ug/ml), both tested at sub-lethal concentrations relative to untreated controls. Microarrays were acquired for mRNAs and long intergenic non-coding RNA transcripts using the GeneChip™ Human 2.1ST ARRAY by Affymetrix Inc


title: Deletion of MtrA inhibits cellular development of Streptomyces coelicolor and alters expression of developmental regulatory genes

city: Jinan

first: Guangxiang

last: Cao

address: 18877 jingshi Road

institute: Shandong Academy of Medical Sciences

summary: The developmental life cycle of Streptomyces species includes aerial hyphae formation and spore maturation, two distinct developmental processes that are controlled, respectively, by two families of developmental regulatory genes, bld and whi. In this study, we show that the response regulator MtrA (SCO3013) is critical for normal development of aerial hyphae in S. coelicolor and related species. ΔmtrA, a deletion mutant of the response regulator gene mtrA, exhibited the bald phenotype typical of bld mutants defective in aerial mycelium formation, with formation either much delayed or absent depending on the culture medium. Transcriptional analysis indicated that MtrA activates multiple genes involved in formation of aerial mycelium, including chp, rdl, and ram genes, as well as developmental regulatory genes of the bld and whi families. However, the major regulatory gene bldD showed enhanced expression in ΔmtrA, suggesting it is repressed by MtrA. EMSAs indicated that MtrA binds upstream of several genes with altered expression in ΔmtrA, including bldD and whiI, and sequences similar to the consensus binding sequence for MtrA of another actinomycete, Mycobacterium tuberculosis, were found in the bound sites. A loosely conserved recognition sequence containing two short, direct repeats was identified for MtrA of S. coelicolor and was validated using mutational analysis. MtrA homologues are widely distributed among Streptomyces species, and as with S. coelicolor, deletion of the mtrA homologues sve_2757 from S. venezuelae and sli_3357 from S. lividans resulted in conditional bald morphology. Our study suggests a critical and conserved role for MtrA in Streptomyces development.

overall_design: mRNA profiles of Streptomyces wild-type and ΔMtrA mutant strains were generated by deep sequencing

first: Xiuhua

last: Pang

first: Peipei

last: Zhang


title: MCPyV ST activates Max target genes by recruiting TRRAP/EP400 complex

first: Jingwei

last: Cheng

address: 450 Brookline Ave

department: Medical Oncology

institute: Dana-Farber Cancer Institute


title: Histone Deacetylase inhibitor, LBH589, has antitumor effects on undifferentiated pleomorphic sarcoma cells via the downregulation of FOSL1

city: Kagoshima

first: Yoshinobu

last: Saito

address: 8-35-1, Sakuragaoka

institute: Kagoshima University

summary: Background  Epigenetic mutations are involved in oncogenesis and therefore their regulator Histone deacetylaces (HDACs) can be a therapeutic target. In this study, we investigated the anticancer effect and mechanism of pan-HDAC inhibitor, LBH589, against undifferentiated pleomorphic sarcoma (UPS).   Method  To elucidate the molecular target, we performed RNA microarray for UPS cells after treated LBH589. Data were validated by RT-PCR and Westernblot.  Result  We found that LBH589 decrease the expression of Fos-like 1 (FOSL1) gene in four UPS cell lines. Knockdown of FOSL1 by RNA interference inhibited cell proliferation and conversely, overexpression increased cell proliferative capacity. Furthermore, we showed that knockdown of FOSL1 cause elevation of p21 expression in UPS cells.  Conclusion  FOSL1 codes the FRA-1 protein and forms activator protein-1 (AP-1) complexes in collaboration with members of the JUN family to drive gene transcription. FOSL1 is overexpressed in several malignant tumors and considered to be a poor prognostic factor. In this study, we showed that the antitumor effect by HDAC inhibitor is partly due to down regulation of FOSL1.

overall_design: Human undifferentiated pleomorphic sarcoma cell line, GBS-1,  was treated with LBH589 and change of gene expression was measured at 0, 12, and 24 hours.  One independent sample were examined at each time.

first: Takao

last: Setoguhi


title: Bone Marrow Derived Macrophages, NSCLC cell lines, and Kras G12D Lung Tumors Treated with Epigenetic Agents

city: Baltimore

first: Michael

middle: Jonathan

last: Topper

state: MD

address: 1650 Orleans St., Suite 530

department: Oncology

institute: Johns Hopkins University

summary:
Transcriptional profiling of Aza+ITF-2357 treated bone marrow derived macrophages vs. Mock treated bone marrow derived macrophages. Aim was to elucidate the effects of epigentic drug treatment on in vitro cultured macrophages and to compare these data to in vivo treated macrophage populations.
Transcriptional profiling of  NSCLC cell lines treated with epigenetic agents
Transcriptional profiling of  immune populations in the lung Kras G12D tumor micronevironment treated with combination epigenetic therapy
Transcriptional profiling of  lung Kras G12D tumors treated with combination epigenetic therapy

overall_design:
Two color array representation of two-condition experiment Aza+ITF-2357 treated bone marrow derived macrophages vs. Mock treated bone marrow derived macrophages. Data are single array representation of 3 pooled bone marrow derived macrophage replicates for each condition.
Two-condition experiment,  Mock vs. MS-275, Mock vs. ITF-2357, Mock vs. Azacitidine, Mock vs. Azacitidine+MS-275, Mock vs. Azacitidine+ITF-2357
Two-condition experiment: Mock vs. 0.5mg/kg Azacitidine + 2.0mg/kg ITF-2357. Populations assayed in this experiment: Macrophages- CD45+, CD11b+, F4/80+; T lymphocytes: CD45+, CD3+, CD8+
Two-condition experiment,  Mock vs. 0.5mg/kg Azacitidine + 2.0mg/kg ITF-2357


title: Expression data from retinoic acid-induced differentiation of human embryonic stem cells (hESCs)

city: New Haven

first: Natalia

last: Ivanova

state: CT

address: 10 Amistad Street, Room 220

department: Genetics

institute: Yale University

summary:
Human embryonic stem cells (hESCs) display a unique ability to self-renew in culture while retaining the potential to form the full repertoire of cell types found in the body. A complex molecular network underlies the maintenance of this pluripotent state.
We used microarrays to identify genes that are highly expressed in pluripotent hESCs, but are consequently down-regulated upon differentiation in the presence of retinoic acid.

overall_design: H1 hESCs in mTeSR media were differentiated in 5 μM retinoic acid. RNA samples were collected at daily timepoints (days 0 to 10 of differentiation) for hybridization on Affymetrix microarrays. Undifferentiated HUES8 and H9 hESC lines were maintained in mTeSR media and anaylzed for control and comparison purposes.

first: Zheng

last: Wang


title: Alteration of gene expression by AIMP3 depletion in mouse embryonic stem cells

city: Goyang-si, Gyeonggi-do

first: Sun Mi

last: Kim

address: Ilsan-ro 323

institute: National Cancer Center

summary: To elucidate the regulatory mechanisms of AIMP3 for the pluripotency and differentiation in mESCs, we performed a microarray analysis in control and AIMP3-depleted mESCs. Compared to control, 1,279 genes were significantly up or down-regulated (1.5 fold, p<0.05) in AIMP3-depleted cells. Through analysis with DAVID bioinformatics online tolls, the p53 signaling pathway was found to be activated in AIMP3-depleted cells. Alterations of p53 signaling pathway-related genes were confirmed by real-time PCR.

overall_design: Alterations of gene expression by AIMP3 depletion were measured at 4 days after exposure to 2 μM tamoxifen (4-OHT) in AIMP3f/f;cre-ERT2 mouse embryonic stem cells.

first: Sun

first: Ho

last: Lee


title: Learning the regulatory grammar of yeast 5' untranslated regions from a large library of random sequences

city: Seattle

first: Georg

last: Seelig

state: Washington

address: 185 Stevens Way, Paul Allen Center - Room AE100R, Box 352500

department: Department of Electrical Engineering

institute: University of Washington

summary:
Our ability to predict protein expression from DNA sequence alone remains poor, reflecting our limited understanding of cis-regulatory grammar and hampering the design of engineered genes for synthetic biology applications. Here, we generate a model that predicts the translational efficiency of the 5’ untranslated region (UTR) of mRNAs in the yeast Saccharomyces cerevisiae. We constructed a library of half a million 50-nucleotide- long random 5’ UTRs and assayed their activity in a massively parallel growth selection experiment. The resulting data allow us to quantify the impact on translation of Kozak sequence composition, upstream open reading frames (uORFs) and secondary structure. We trained a convolutional neural network (CNN) on the random library and showed that it performs well at predicting the translational efficiency of both a held-out set of the random 5’ UTRs as well as native S. cerevisiae 5’ UTRs. The model additionally was used to computationally evolve highly translating 5’ UTRs. We confirmed experimentally that the great majority of the evolved sequences lead to higher translation rates than the starting sequences, demonstrating the predictive power of this model.
The sequences were assayed in the context of a constant promoter and downstream coding sequence. Cell growth was used as a proxy for protein expression. Growth was measured by determining the ratio of sequence counts before and after growth selection.

overall_design: We assayed three libraries, a library of random sequences, a library of sequences derived from the native 5' untranslated regions of Saccharomyces cerevisiae and a library of sequences that we created using our convolutional neural network model. All sequences are less than or equal to 50 nucleotides long.

first: Josh

last: Cuperus

first: Benjamin

last: Groves

first: Anna

last: Kuchina

first: Alexander

last: Rosenberg

first: Nebojsa

last: Jojic

first: Stanely

last: Fields


title: Identify and characterize the circular RNAs expressed in in the half-smooth tongue sole (Cynoglossus semilaevis)

city: Yantai

first: yeying

last: sun

address: No.346 Guanhai road

institute: Binzhou Medical Univeristy

summary: Half-smooth tongue sole (Cynoglossus semilaevis) is a commercially valuable flatfish, ranking among the most valuable fishes in the coastal areas of China. It has an asymmetric body shape with lateralization of the eyes to the same side during metamorphosis as same as the other flatfish species. However, little is known about the function and profile of circRNAs in the half-smooth tongue sole. In this study,a total of 2730 circRNAs were identified from in the fish by deep RNA-sequencing technique.

overall_design: Gonad, liver, spleen, heart, kidney, gill, muscle, and brain tissues were collected individually. To determine the expression profiles of circRNAs in half-smooth tongue sole, total RNA was isolated from the different tissues to form tissue pool. Three micrograms of RNA per sample were used as the input material for the RNA sample preparations. The expression profiles of circRNAs  were determined by genome-wide large-scale next-generation deep sequencing by using the Illumina platforms.

first: Yeying

last: Sun

first: Rongrong

last: Liu


title: The human lncRNA LINC-PINT inhibits tumor cell migration through a highly conserved sequence element

city: Pamplona

first: Maite

last: Huarte

state: Navarra

address: c/ Avd Pio XII, 55

institute: Centro de Investigación Médica Aplicada

summary: It is now obvious that the majority of cellular transcripts do not code for proteins, and a significant subset of them are long noncoding RNAs (lncRNAs). Many lncRNAs show aberrant expression in cancer, and some of them have been linked to cellular transformation. However, the underlying mechanisms remain poorly understood. Here we characterize the function of the p53-regulated human lncRNA LINC-PINT in cancer. We found that LINC-PINT acts as tumor suppressor lncRNA. Its expression is downregulated in multiple types of cancer and correlates with good prognosis in lung adenocarcinoma. LINC-PINT inhibits the migration capacity and invasive phenotype of cancer cells in vitro and in vivo, and it does so by repressing a proinvasion gene signature in a PRC2-dependent manner. By applying cross-species conservation analysis combined with functional experimental validations we found that the function of LINC-PINT is highly dependent on a short sequence conserved across mammals, sequence that mediates the interaction with PRC2. We propose that LINC-PINT may function as a molecular exchanger that provides PRC2 to active gene promoters for their silencing, mechanisms that could be shared by other PRC2-interacting lncRNAs.

overall_design: We analyzed gene expression in colon adenocarcinoma HCT116 cell line vs LINC-PINT overexpressing HCT116  using the Affymetrix Human Gene 2.0 ST platform. Three techinical replicates were performed per condition.

first: Oskar

last: Marín-Béjar

first: Aina

last: Mas

first: Jovanna

last: González

first: Dannys

middle: J

last: Martínez-Herrera

first: Xabier

last: Morales

first: Mikel

last: Galduroz

first: Alejandro

last: Athie

first: Ivan

last: Raimondi

first: Elena

last: Grossi

first: Ana

last: Rouzaut

first: Igor

last: Ulitsky


title: RNA-sequencing of MHC-cycD2 transgenic mice after Transverse Aortic Constriction and Aortocaval Shunt surgery

city: Goettingen

first: Sara

last: Khadjeh

address: Robert-Koch-Str. 42a

department: Clinic for Cardiology and Pneumology

institute: University Medical Center Göttingen

summary: Expression profiling by high throughput sequencing of mice overexpressing cyclin D2 compared to WT control, and of TG mice after pressure and volume overload

overall_design: Examination of 4 Groups of mice: WT (n=5), MHC-cycD2 sham (n=5), MHC-cycD2 TAC (n=3), MHC-cycD2 Shunt (n=5) and 4 comparisons: GroupIcontrolWT_vs_GroupIicontrolsham, GroupIicontrolsham_vs_GroupIIITreatmentTAC, GroupIicontrolsham_vs_GroupIVTreatmentShunt, GroupIIITreatmentTAC_vs_GroupIVTreatmentShunt

first: Karl

last: Toischer


title: Genome-wide identification and prediction of long non-coding RNAs in the half-smooth tongue sole (Cynoglossus semilaevis)

first: yeying

last: sun

summary: Half-smooth tongue sole (Cynoglossus semilaevis) is a commercially valuable flatfish, ranking among the most valuable fishes in the coastal areas of China. It has an asymmetric body shape with lateralization of the eyes to the same side during metamorphosis as same as the other flatfish species. However, little is known about the function and profile of lncRNAs in the half-smooth tongue sole. In this study, we carry out a genome-wide review of lncRNAs in the fish by using large-scale deep sequencing.

overall_design: Gonad, liver, spleen, heart, kidney, gill, muscle, and brain tissues were collected individually. To determine the expression profiles of lncRNAs in half-smooth tongue sole, total RNA was isolated from the different tissues to form tissue pool. Three micrograms of RNA per sample were used as the input material for the RNA sample preparations. The expression profiles of lncRNAs and mRNAs were determined by genome-wide large-scale next-generation deep sequencing by using the Illumina platforms.

first: Xiangwen

last: Xia


title: Discovery and mechanistic characterization of A-485, a potent p300/CBP catalytic inhibitor

city: North Chicago

first: Xin

last: Lu

state: IL

address: 1 North Waukegan Rd

department: Oncology Discovery

institute: Abbvie

summary: The dynamic and reversible acetylation of proteins catalyzed by histone acetyltransferases (HATs) and histone deacetylases (HDACs) was discovered more than 2 decades ago and the enzymatic function of these enzymes are established as a major epigenetic regulatory mechanism of gene transcription.  Thus, these epigenetic modifiers are involved in multiple diseases and represent attractive targets for therapeutic intervention.  While HDAC inhibitors have been developed and approved by the FDA to treat certain cancers, progress on the development of drug-like HAT inhibitors has lagged. The HAT paralogs p300 and CBP (here called p300/CBP) are key transcriptional co-activators that are essential for a multitude of cellular processes and also implicated in human pathological conditions, including cancer.  Current p300/CBP HAT domain inhibitors including natural products and bisubstrate analogs such as Lys-CoA either lack potency and selectivity or suffer from poor cellular permeability.  C646 is widely utilized as a tool to inhibit p300/CBP HAT activity, but its off-target activity and reactivity may limit its cellular specificity.  Here, we describe A-485 as a potent, selective and drug-like p300/CBP catalytic inhibitor.  We show the first high resolution (1.95Å) co-crystal structure of a pharmacologically active small molecule (A-485) bound to the catalytic active site of p300 HAT domain and demonstrate that A-485 is an acetyl-CoA competitive inhibitor of p300/CBP.  A-485 selectively inhibited proliferation across lineage-specific tumor types, including several hematological malignancies and androgen receptor-positive prostate cancer.  A-485 robustly inhibited the androgen receptor transcriptional program in both androgen sensitive and castrate resistant prostate cancer and inhibited tumor growth in a castration resistant xenograft model.  These results demonstrate the feasibility of selectively drugging the catalytic activity of histone acetyltransferases, provide the framework for delineating the enzymatic functions of HATs, and pave the way for the development of novel therapeutics targeting HAT activity.

overall_design: This study contains 2 biological replicates for each of 11 samples for 22 total samples. Samples 1 and 2 are unstimulated controls for LnCaP-FGC cells, and samples 13 and 14 are unstimulated controls for 22Rv1 cells.

first: Kenneth

middle: D

last: Bromberg

first: Paul

last: Hessler

first: Tamar

last: Uziel


title: Transcriptional reprogramming of human CD4 T cells transitioning from active to memory state

first: Liang

last: Shan

address: 300 Cedar Street

department: Immunobiology

summary: The latent reservoir for HIV-1 in resting memory CD4+ T cells is the major barrier to curing HIV-1 infection. Studies of HIV-1 latency have focused on regulation of viral gene expression in cells in which latent infection is established. However, it remains unclear how infection initially becomes latent. Here we described a unique set of properties of CD4+ T cells undergoing effector-to-memory transition including temporary up-regulation of CCR5 expression and rapid down-regulation of cellular gene transcription. These cells allowed completion of steps in the HIV-1 life cycle through integration, but suppressed HIV-1 gene transcription, thus allowing the establishment of latency. CD4+ T cells in this stage were substantially more permissive for HIV-1 latent infection than other CD4+ T cells. Establishment of latent HIV-1 infection in CD4+ T could be inhibited by viral-specific CD8+ T cells, a result with implications for elimination of latent HIV-1 infection by T cell-based vaccines.

overall_design: CD4+ T cells from three donors at 5 different treatment time points.

first: Robert

last: Siliciano


title: Differential Expression of MicroRNAs Among Cell Populations in the Regenerating Adult Mouse Olfactory Epithelium

status: Public on Sep 26 2017

city: Miami

first: Lina

last: Shehadeh

state: FL

department: Medicine

institute: University of Miami

overall_design: Progenitor cells were purified from methimazole-lesioned olfactory epithelium based on c-Kit expression, and miRNA expression was assayed in c-Kit (+) and c-Kit (-) cell populations. N=3 mice/samples per group.

first: Bradley

last: Goldstein


title: Anti-mycobacterial activity correlates with altered DNA methylation pattern in immune cells from BCG-vaccinated subjects

city: Linköping

first: Jyotirmoy

last: Das

address: Sandbäcksgatan 7

department: Medical Microbiology

country: Sweden

institute: Linkoping University

summary: The reason for the largely variable protective effect against TB of the vaccine Bacille Calmette-Guerin (BCG) is not understood. In this study, we investigated whether epigenetic mechanisms are involved in the response of immune cells to the BCG vaccine. We isolated peripheral blood mononuclear cells (PBMCs) from BCG-vaccinated subjects and performed global DNA methylation analysis in combination with functional assays representative of innate immunity against Mycobacterium tuberculosis  infection. Enhanced containment of replication was observed in monocyte-derived macrophages from a sub-group of BCG-vaccinated individuals (identified as ‘responders’). A stable and robust differential DNA methylation pattern in response to BCG could be observed in PBMCs isolated from the responders but not from the non-responders. Gene ontology analysis revealed that promoters with altered DNA methylation pattern were strongly enriched among genes belonging to immune pathways in responders, however no enrichments could be observed in the non-responders. Our findings suggest that BCG-induced epigenetic reprogramming of immune cell function can enhance anti-mycobacterial immunity. Understanding why BCG induces this responses in responders but not in nnon-responders could provide clues to improvement of TB vaccine efficacy.

overall_design: 8 Sample DNAs were isolated from NK cells and the aPBMCs using QiAmp DNA isolation kit. DNA concentrations were measured by Qubit fluorometer. DNA samples were bisulphite converted, amplified, fragmented and hybridized to an Illumina Infinium Human Methylation 450K Bead Chip and scanned

first: Deepti

last: Verma

first: Venkata

last: Prasa

first: Johanna

last: Raffestseder

first: Mihaela

last: Martis

first: Ratnesh

last: Mehta

first: Mihai

last: Netea

first: Maria

last: Lerm


title: Unintended side effects of transformation are very rare

city: Saint Louis

first: Ezekiel

last: Maier

state: MO

address: 4515 McKinley Ave

department: Computer Science

institute: Washington University in Saint Louis

summary: Received wisdom in the field of fungal biology holds that the process of editing a genome by transformation and homologous recombination is inherently mutagenic. However, that belief is based only on circumstantial evidence. We provide the first direct measurement of the effects of transformation on the genome by sequencing the genomes of 29 transformants and 30 untransformed controls to high coverage. Contrary to the received wisdom, our results show that transformation of DNA flanked by long targeting sequences, followed by homologous recombination and selection on a drug marker, is extremely safe. Gene deletion may select for a few mutations that occur after transformation, but even then we found fewer than two point mutations per gene deletion strain. We also tested these strains for changes in gene expression and found only a few genes that were consistently differentially expressed between wild types and strains with a drug resistance marker inserted. As part of this process, we provide the first published genome sequence of the commonly used laboratory strain Cryptococcus neoformans var. grubii strain KN99.

overall_design: A total of 39 expression profiles were generated by RNA-seq analysis of wildtype and neutral transformant cells grown in capsule inducing conditions for 90 minutes. Raw sequencing data has already been submitted to the Short Read Archive under SRA study SRP107007 and BioProject PRJNA384617

first: Ryan

middle: Z

last: Friedman

first: Stacey

last: Gish

first: Holly

last: Brown

first: Lindsey

last: Brier

first: Nicole

last: Howard

first: Tamara

middle: L

last: Doering

first: Michael

last: Brent


title: BPIFA1 Regulates Interferon-Mediated Lung Neutrophil Recruitment During Acute Inflammation

first: Clemente

last: Britto

address: 300 Cedar St TAC S419

summary: BPIFA1 (BPI-fold containing group A member 1) is an airway host-protective protein with immunomodulatory properties that binds to LPS and is regulated by infectious and inflammatory signals. Differential expression of BPIFA1 has been widely reported in lung disease, yet the biological significance of this observation is unclear. We sought to understand the role of BPIFA1 fluctuations in modulating lung inflammation. We treated WT and bpifa1-/- mice with intranasal LPS and performed transcriptomic analyses to determine the immune effects of BPIFA1 deficiency. Transcriptomic analysis revealed a signature of 379 genes that differentiated bpifa1-/- mice from WT. During acute lung inflammation, the most strongly downregulated innate immunity genes in bpifa1-/- mice were cxcl9 and cxcl10. This was consistent with significantly decreased expression of IFN-g, IFN-l and downstream IFN-stimulated genes (ISG) and IFN-regulatory factors (IRF) important for innate immune responses.

overall_design: BPIFA1-/- and WT controls were treated with 5 micrograms of intranasal LPS and gene expression analysis was performed at 0, 8, and 24 hours. Controls received intranasal PBS. Groups: WT at 0 hours (n=6), bpifa1-/- at 0 hours (n=6), WT at 8 hours (n=6), bpifa1-/- at 0 hours (n=5), WT at 24 hours (n=5), bpifa1-/- at 0 hours (n=5)

first: Naiqian

last: Niu

first: Sara

last: Khanal

first: Jose

last: Herazo-Maya

first: Luai

last: Huleihel

first: Lokesh

last: Sharma

first: Naftali

last: Kaminski

first: Charles

last: Dela Cruz

first: Lauren

last: Cohn


title: Expression of genes in hepatic progenitor-like cells derived from human iPS cells, and cultured progenitor cells

city: Isehara

first: Akihide

last: Kamiya

state: Kanagawa

address: 143 Shimokasuya

institute: Tokai University

summary: To analyze stem/progenitor cell function, we purified hepatic progenitor-like cells in human iPS cell culture stimulated with cytokines.

overall_design: Gene expression in primary CD13+CD133+ cells derived from human iPS cell culture. In addition, cultured progenitor cells were also analyzed.


title: Transcriptional and Chromatin Dynamics of Muscle Regneration after Severe Trauma

city: Lexington

first: Darrell

middle: Orlyn

last: Ricke

state: MA

address: 244 Wood Street

department: Group 48 Bioengineering Systems & Technology

institute: MIT Lincoln Laboratory

type: Non-coding RNA profiling by high throughput sequencing

summary: Following injury, adult skeletal muscle undergoes a well-coordinated sequence of molecular and physiological events to promote repair and regeneration. However, a thorough understanding of the in vivo epigenomic and transcriptional mechanisms that control these reparative events is lacking. To address this, we monitored the in vivo dynamics of three histone modifications and coding and noncoding RNA expression throughout the regenerative process in a mouse model of traumatic muscle injury. We first illustrate how both coding and noncoding RNAs in tissues and sorted satellite cells are modified and regulated during various stages after trauma. Next, we use chromatin immunoprecipitation followed by sequencing to evaluate the chromatin state of cis-regulatory elements (promoters and enhancers) and view how these elements evolve and influence various muscle repair and regeneration transcriptional programs. These results provide a comprehensive view of the central factors that regulate muscle regeneration and underscore the multiple levels through which both transcriptional and epigenetic patterns are regulated to enact appropriate repair and regeneration.

overall_design:
ChIP-Seq time course of muscle injury healing with controls
RNA-Seq time course of muscle satellite cells following injury healing
miRNA-seq time course of muscle satellite cells following injury healing

middle: O

first: Anna

last: Shcherbina

first: Carlos

last: Aguilar


title: Comparative genomics analysis of Aspergillus glaucus CCHA provides insights into the adaptation of stress response

city: Tianjin

first: Jingen

last: Li

address: Xiqi Dao 32, Tianjin Airport Economic Area

institute: Tianjin institute of industrial biotechnology,Chinses Academy of Sciences

summary: Aspergillus display an amazing level of diversity in physiologies, and environments that they occupy. Strategies for coping with diverse environmental stresses have evolved in different Aspergillus species. Therefore, Aspergillus are considered to be good models for investigating the adaptation and response to many natural and anthropogenic environmental stressors. Recent genome sequencing projects in several Aspergillus have provided insights into the molecular and genetic mechanisms underlying their responses to some environmental stressors. However, to better clarify the conserved and differentiated features of the adaptive response to specific stresses and to trace the evolutionary process of environmental adaptation and response in Aspergillus, insight from more Aspergillus species with different evolutionary positions, such as A. glaucus, and thus offer a large number of models of adaptation and response to various environmental stresses. Here, we report a high-quality reference genome assembly of A. glaucus CCHA from the surface of wild vegetation around saltern of Jilin, China, based on sequence data from whole-genome shotgun (WGS) sequencing platforms of Illumina solexa technologies. This assembly contains 106 scaffolds ( >1 Kb; N50 = ~0.795 Mb), has a length of ~28.9 Mb and covers ~97% of the predicted genome size (~120 Mb). Together with the data analyses from comprehensive transcriptomic surveys and comparative genomic analyses, we aim to obtain new insights into molecular mechanisms of the adaptation to living at high salt in the saltern

overall_design: RNA was extracted from cultures of Aspergillus glaucus CCHA growing in medium supplemented with NaCl on different concentration.

first: Chaoguang

last: Tian


title: Gene expression profiles of mouse embryonic fibroblasts (MEFs), induced cardiomyocytes (iCMs) and heart.

city: Kamakura

first: Satoshi

last: Kondo

address: Tebiro 6-10-1

department: New Projects Development Division

institute: Toray Industries,Inc.

summary:
Global gene expression patterns of the iCMs shift from a MEF state toward a cardiac-like phenotype by Gata4/Mef2c/Tbx5 (GMT) or GMT/Hand2 (GHMT) transduction at 2 and 4 weeks after transduction (2W, 4W).
Hand2 upregulated a panel of cardiac genes and suppressed cell cylce genes during cardiac reprogramming.

overall_design: MEFs were used for negative control, mouse heart tissue for positive control. Gene expression profiles were compared among MEFs, iCMs and heart.

first: Tomohiko

last: Umei

first: Masaki

last: Ieda


title: Short-term in vitro culture of rat fetal testes with all-trans retinoic acid

city: Providence

first: Daniel

middle: James

last: Spade

state: RI

address: Box G-E5

department: Pathology and Laboratory Medicine

institute: Brown University

summary:
Analysis of gene expression and alternate splicing effects of retinoic acid treatment on gestational day 15 rat fetal testes in whole testis culture
Retinoic acid exposure in cultured fetal testis has previously been demonstrated to have significant effects on the histology of the fetal testis in multiple species, as well as to alter the meiotic states of germ cells. However, previous experiments have not analyzed the mechanisms by which retinoic acid exposure leads to altered tubulogenesis and loss of seminiferous cord structure. This experiment demonstrated that retinoic acid exposure activated signaling pathways that promote the ovary development program and oppose normal testis development in mid-gestational rat fetal testes.

overall_design: Testes were isolated from rats on gestational day 15. A paired design was used in which a single testis from each of six rat fetuses was cultured in 10^-6 M all-trans retinoic acid (ATRA), while the contralateral testis was cultured in vehicle (DMSO) media. After 24 h culture, total RNA was isolated, and gene expression and alternate splicing were analyzed using the Affymetrix Clariom D Rat assay.

first: Christoph

last: Schorl

first: Edward

last: Dere

first: Susan

last: Hall

first: Kim

last: Boekelheide


title: Mining novel candidate imprinted genes using genome-wide methylation screening and literature review

city: São Paulo

first: Ana

last: Krepischi

state: São Paulo

address: Rua do Matão, 277

country: Brazil

institute: University of São Paulo

summary: Large-scale transcriptome and methylome data analyses obtained by high-throughput technologies have been enabling the identification of novel imprinted genes. We investigated genome-wide DNA methylation patterns in multiple human tissues, using a high-resolution microarray to uncover hemimethylated CpGs located in promoters overlapping CpG islands, aiming to identify novel candidate imprinted genes. Using our approach, we recovered ~30% of the known human imprinted genes, further 168 candidates were identified, 61 of which with at least three hemimethylated CpGs shared by more than two tissue types. Thirty-four of these candidate genes are members of the protocadherins cluster on 5q31.3; in mice, protocadherin genes have non-imprinted monoallelic randomic expression, which might be the case in humans. Among the remaining 27 genes, ZNF331 was recently validated as an imprinted gene, and six of them have been reported as candidates, supporting our prediction. Five candidates (CCDC166, ARC, PLEC, TONSL and VPS28) map to 8q24.3, and might constitute a novel imprinted cluster. Additionally, we performed a comprehensive compilation of known human and mice imprinted genes from literature and databases, and a comparison among high-throughput imprinting studies in humans. The screening for hemimethylated CpGs shared by multiple human tissues, together with the extensive review, appears as a useful approach to reveal candidate imprinted genes.

overall_design: Genome-wide DNA methylation data were generated from 67 samples from different normal human tissues (leukocyte, brain frontal cortex, liver, breast, melanocyte and chorionic villus), using the HM450K platform (Illumina). It was applied an approach to uncover hemimethylated CpGs located in promoters overlapping CpG islands common to all tissues, aiming to identify novel candidate imprinted genes.

first: Adriano

last: Bonaldi

first: André

middle: Y

last: Kashiwabara

first: Érica

last: Araújo

first: Lygia

last: Pereira

first: Alexandre

last: Paschoal

first: Mayra

middle: B

last: Andozia

first: Darine

last: Villela

first: Maria

middle: P

last: Rivas

first: Claudia

middle: K

last: Suemoto

last: Pasqualucci

first: Lea

middle: T

last: Grinberg

first: Helena

last: Brentani

first: Silvya

last: Maria-Engler

first: Dirce

middle: M

last: Carraro

first: Angela

last: Vianna-Morgante

first: Carla

last: Rosenberg

first: Luciana

last: Vasques


title: The comparsion of gene expression in ALVAC- and Ad5-infected human monocyte-derived dendritic cells

city: Galveston

first: Fengliang

last: Liu

state: Texas

address: 301 University Blvd

department: Microbiology and Immunlogy

institute: The University of Texas Medical Branch

summary: Analysis of the effects of different vaccine viral vectors on gene expression in human monocyte-derived dendritic cells (MDDCs), which were generated from isolated monocytes from 3 different donors. The goal in this study was to find the difference of gene expression in human MDDCs upon ALVAC and Ad5 vrial vectors infection.

overall_design: RNA was isolated from ALVAC- and Ad5-infected human monocyte-derived dendritic cells, which were generated from monocytes isolated from 3 different donors, at 24 hours post-infection

first: Haitao

last: Hu


title: Comparative gene expression analyses reveal distinct molecular signature between differentially reprogrammed cardiomyocytes

city: Birmingham

first: Yang

last: Zhou

state: AL

address: 1825 University Blvd

department: Department of Biomedical Engineering

institute: University of Alabama at Birmingham

summary: Cardiomyocytes derived from induced pluripotent stem cells (iPSC-CMs) or directly reprogrammed from non-myocytes (induced cardiomyocytes, iCMs) are promising sources for heart regeneration or disease modeling. However, the similarities and differences between iPSC-CM and iCM are still unknown. Here we performed transcriptome analyses of beating iPSC-CMs and iCMs generated from cardiac fibroblasts (CFs) of the same origin. Although both iPSC-CMs and iCMs establish CM-like molecular features globally, iPSC-CMs exhibit a relatively hyperdynamic epigenetic status while iCMs exhibit maturation status that more resemble adult CMs. Based on gene expression of metabolic enzymes, iPSC-CMs primarily employ glycolysis while iCMs utilize fatty acid oxidation as the main pathway. Importantly, iPSC-CMs and iCMs exhibit different cell cycle status, alteration of which influenced their maturation. Therefore, our study provides a foundation for understanding the pros and cons of different reprogramming approaches.

overall_design: To dissect the similarities and differences of gene expression profiles between reprogrammed cardiomyocytes (CMs), we generated contractile CMs by iPSC differentiation and direct reprogramming from neonatal cardiac fibroblasts (neoCFs) of the same origin. We collected two independent iPSC line-derived beating CMs and iCMs in duplicate for microarray analysis and also included duplicate of primary neoCFs and neoCMs isolated from transgenic pups as controls. Additionally, we harvested reprogrammed cells at different time points (D0, D3, D5, D7, D10 and D14) during early iCM reprogramming. Microarray was performed on Agilent mouse 8x60K GE 1color platform.

first: Li

last: Wang

first: Ziqing

first: Sahar

last: Alimohamadi

first: Chaoying

last: Yin

first: Jiandong

last: Qian


title: Nutritional effects by beta-carotene in liver in males and females of control wildtype mice versus BCMO knockout mice

city: Wageningen

first: Evert

middle: M.

last: van Schothorst

address: De Elst 1

institute: Wageningen University

summary: Molecular mechanisms triggered by high dietary beta-carotene (BC) intake in liver are largely unknown. We performed microarray gene expression analysis on liver tissue of BC supplemented beta-carotene 15,150-monooxygenase 1 knockout (Bcmo1-/-) mice, which are—like humans—able to accumulate BC. This was compared with litter mates being wild-type (Bcmo1+/+) mice, and we analysed both males and females, as we previously showed that in lung tissue we observed opposite gene regulation between males and females (Van Helden et al., CMLS 2011).

overall_design: The experimental setup has been described previously for females and males (Van Helden et al., CMLS 2010 and Carcinogenesis, 2011, resp.). Twelve female (fe) and 12 male (ma) B6129SF1 (Bcmo1+/+) and 12 female and 12 male B6;129S-Bcmo1tm1dnp (Bcmo1-/-) mice were used for the dietary intervention, which was conducted in accordance with the German animal protection laws by the guidelines of the local veterinary authorities. During the breeding and weaning periods of the mice, mothers were maintained on KLIBA 3430 chow containing 14,000 IU vitamin A/kg diet (Provima Kliba AG, Kaiseraugst, Switzerland). Five-week-old female and male Bcmo1+/+ and Bcmo1-/- mice were caged in groups containing two to four siblings per group and were maintained under environmentally controlled conditions (temperature 24 C, 12 h/12 h light/dark cycle). Mice had ad libitum access to feed and water. Basic feed consisted of the pelletized diet D12450B (Research Diets Inc, USA) with a fat content of 10%. The diet was modified to contain 1,500 IU vitamin A/kg of diet, which is a vitamin A-sufficient diet, and the control diet (control) was supplemented with water-soluble vehicle beadlets (DSM Nutritional Products Ltd., Basel, Switzerland) containing DL-alpha-tocopherol and ascorbyl palmitate as stabilizers, as well as carriers such as gelatin, corn oil, sucrose and starch. The BC diet (BC) was supplemented with identical water-soluble beadlets containing BC (DSM Nutritional Products Ltd., Basel, Switzerland) to generate 150 mg BC/kg diet. Beadlets were added by the manufacturer before low temperature pelletting. Feed pellets were color marked and stored at 4 C in the dark. After 14 weeks of dietary intervention, mice were killed after isoflurane and ketamin anesthesia and blood and liver tissue isolated. Livers were rinsed in phosphate-buffered saline (PBS) and snap frozen in liquid nitrogen, and subsequently stored at -80 C. Transcriptomic analyses were performed using Agilent whole genome 4x44K gene expression arrays according to the manufacturer's procedure.

first: Yvonne

last: van Helden

first: Jaap

last: Keijer

first: Suzanne

last: Hessel

first: Annelies

last: Bunschoten

first: Johannes

last: Von Lintig

first: George

last: Lietz


title: UBE3A-mediated regulation of imprinted genes and epigenome-wide marks in human neurons

city: Davis

first: Simon

middle: Jesse

last: Lopez

state: CA

address: One Shields Ave

department: MMI

institute: UC Davis

summary: The dysregulation of genes in neurodevelopmental disorders that lead to social and cognitive phenotypes is a complex, multilayered process involving both genetics and epigenetics. Parent-of-origin effects of deletion and duplication of the 15q11-q13 locus leading to Angelman, Prader-Willi, and Dup15q syndromes are due to imprinted genes, including UBE3A, which is maternally expressed exclusively in neurons. UBE3A encodes a ubiquitin E3 ligase protein with multiple downstream targets, including RING1B, which in turn monoubiquitinates histone variant H2A.Z. To understand the impact of neuronal UBE3A levels on epigenome-wide marks of DNA methylation, histone variant H2A.Z positioning, active H3K4me3 promoter marks, and gene expression, we took a multi-layered genomics approach. We performed an siRNA knockdown of UBE3A in two human neuroblastoma cell lines, including parental SH-SY5Y and the SH(15M) model of Dup15q. Genes differentially methylated across cells with differing UBE3A levels were enriched for functions in gene regulation, DNA binding, and brain morphology. Importantly, we found that altering UBE3A levels had a profound epigenetic effect on the methylation levels of up to half of known imprinted genes. Genes with differential H2A.Z peaks in SH(15M) compared to SH-SY5Y were enriched for ubiquitin and protease functions and associated with autism, hypoactivity, and energy expenditure. Together, these results support a genome-wide epigenetic consequence of altered UBE3A levels in neurons and suggest that UBE3A regulates an imprinted gene network involving DNA methylation patterning and H2A.Z deposition.

overall_design: triplicate siRNA knockdowns of UBE3A (siUBE3A) or control (siCTL) in a human neuronal cell line (SH-SY5Y) and a chromosome duplication model of Dup15q syndrome (SH(15M)). From these cell cultures, we isolated DNA for WGBS, RNA for RNA-seq, and chromatin for ChIP-seq of one histone mark of active promoters (H3K4me3) and one histone variant (H2A.Z) of active promoters and poised genes.

first: S


title: Two distinct myeloid subsets at the term human fetal-maternal interface

city: St. Louis

first: Marco

last: Colonna

state: Missouri

address: 509 S Euclid Ave

department: Pathology and Immunology

institute: Washington University in St. Louis

summary: The subsets of immune cells within the human placenta are incompletely described. We used microarray to determine the transcriptional differences between two myeloid subsets in the term human placenta.

overall_design:
Human myeloid cells from the normal human term placenta were sorted to high purity for RNA extraction and hybridization on Affymetrix microarrays.

This series contains re-analyzed samples from GSE78896: GSM2080659 - GSM2080662.

first: Marina

last: Cella

first: M

last: Robinette


title: Nutritional effects by beta-carotene versus control in lung, inguinal white adipose tissue, and liver in males and females of control wildtype mice versus BCMO/BCO1 knockout mice

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

overall_design: Refer to individual Series


title: IMM_IL-17RC_KO mice_exp1

status: Public on Sep 25 2017

city: Cleveland

first: Junjie

last: Zhao

state: Ohio

address: 9500 Euclid Avenue, NE4256

department: Immunology

institute: Cleveland Clinic Lerner Research Institute

summary: This study identifies a novel mechanism linking IL-17A with colon tissue repair and tumor development. Abrogation of IL-17A signaling mice attenuated tissue repair of DSS-induced damage in colon epithelium and markedly reduced tumor development in AOM/DSS model of colitis-associated cancer. The goal of these studies is to identify genes associated with IL-17RC deficiency during AOM-DSS induced tumorigenesis

overall_design: Wild-type and IL-17RC KO mice were subjected to AOM-DSS induced tumorigenic protocol. Treated/untreated mice were sacrificed and their colons resected for total RNA at different time points during the AOM-DSS treatment.

first: Julie

last: Carman

first: Wen-Pin

last: Yang

first: Jun

last: Zhu

first: Jarod

last: Zepp