title: Transcriptomic Profiling of Circulating Tumor Cells in Multiple Myeloma: A New Model to Understand Disease Dissemination II

summary:
The number of peripheral blood (PB) circulating tumor cells (CTCs) predicts risk of transformation in smoldering multiple myeloma (MM) and survival in active MM. Growing evidence suggests that as the tumor progresses and the microenvironment becomes hypoxic, clonal plasma cells (PCs) constantly invade new regions of the bone marrow (BM) through induced systemic recirculation. Of note, the frequency of CTCs is typically low and thus, it could be hypothesized that the dissemination of MM is made by few tumor cells with unique features that induce them to egress the BM and spread the disease through PB. This hypothesis has not been demonstrated because the molecular profile of CTCs in MM has not been investigated.
We used gene expression profiling (GEP) arrays to identify gene regulatory networks related to disease dissemination by comparing the molecular profile of CTCs with patient-matched BM clonal PCs.

overall_design: We used FACS and patient-specific aberrant phenotypes to isolate CTCs and BM clonal PCs of paired PB and BM samples from 24 newly-diagnosed MM, 9 relapses and 1 monoclonal gammopathy of undetermined significance.

first: Michal

last: Šimíček

first: Marco

last: Vicari

first: Lucie

last: Brozova

first: Leire

last: Burgos

first: Renata

last: Bezdekova

first: Diego

last: Alignani

first: Maria-Jose

last: Calasanz

first: Kateřina

last: Growková

first: Ludek

last: Pour

first: Rafel

last: Rios

first: Joaquin

last: Martinez-Lopez

first: Pamela

last: Millacoy

first: Luis

last: Palomera

last: del Orbe

first: Sonia

last: Garate

first: Laura

last: Blanco

first: Maria

last: Collantes

first: Patricia

last: Maiso


title: Distinction of junctional cancers of gastric and oesophageal origin (DJANGO), batch#2

status: Public on Mar 01 2019

city: Oxford

first: Jan

last: Bornschein

address: John Radcliffe Hospital, Headley Way

department: Translational Gastroenterology Unit

country: United Kingdom

institute: Oxford University

summary:
Aim of the study was the distinction of adeoncarcinomas at the gastroesophageal junction by their expression profile. Differential gene expression analysis between tumours of different Siewert type did not reveal relevant results.
Stratification into three intrinsic subgroups was done by an diagonal distribution model using the mclust package in R. Clinicopathological and demographic parameters showed a similar distribution within the subgroups.
Genes set ernichment analysis revealed different biological features for each subgroup that were also reflected by significant differences in the prognostic outcome for the patients, mainly overall survival and recurrence free survival.

overall_design:
n=60, 49 gastro-oesophageal adenocarcinoma samples, 11 non-cancer control samples. (11 of the 49 cancer samples were technical replicates of samples also used in batch#1).
adenocarcinoma samples: 35 GOJ (12 type 1, 13 type 2, 10 type 3), 6 distal body, 8 antrum.
non-cancer control samples: 4 duodenum, 3 gastric body, 4 gastric cardia (matched samples from 4 individual patients).

first: Lorenz

last: Wernisch

first: Richard

last: Newton

first: Juliane

last: Perner

last: Secrier

first: Shona

last: MacRae

first: Ahmad

last: Miremadi

first: Suraj

last: Menon

first: Matthew

last: Eldridge

first: Lawrence

last: Bower

last: O'Donovan

last: Turkington

first: Michael

last: Selgrad

first: Marino

last: Venerito

first: Simon

last: Tavaré

first: Peter

last: Malfertheiner

first: Rebecca

middle: C

last: Fitzgerald


title: Distinction of junctional cancers of gastric and oesophageal origin (DJANGO), batch#1

last: Bornschein

overall_design: n=72 gastro-oesophageal adenocarcinoma samples, 84 GOJ (24 type 1, 20 type 2, 14 type 3), 6 proximal body/fundus, 8 distal body.


title: Distinction of junctional cancers of gastric and oesophageal origin (DJANGO)

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

overall_design: Refer to individual Series


title: Small RNA sequencing of extracellular vesicles from MDA-MB-231 cells treated with PBS, docetaxel (DTX), or doxorubicin (DOXO)

status: Public on Mar 07 2019

city: Duarte

first: Xiwei

last: Wu

state: CA

address: 1500 E. Duarte Rd.

department: Computational and Quantitative Medicine

country: USA

institute: City of Hope National Medical Center

type: Non-coding RNA profiling by high throughput sequencing

summary: To identify the extracellular-vesicle-encapsulated miRNAs that are differentially secreted by the MDA-MB-231 metastatic breast cancer cells following treatment with chemotherapy drugs, we profiled the small RNAs (between 17 and 52 nt) isolated from extracellular vesicles by Illumina sequencing.  miRNAs that are significantly induced by chemotherapy drugs are identified.

overall_design: Extracellular vesicles were collected by ultracentrifugation of the conditioned medium of MDA-MB-231 cells that had been treated with docetaxel (DTX; 4 nM), doxorubicin (DOXO; 125 nM), or PBS for 48 h.  RNA was extracted using TRIZOL LS (Thermo Fisher Scientific), and subjected to library construction and Illumina sequencing.

first: Shizhen

middle: E

last: Wang


title: PfAP2-G ChIP-seq in committed schizonts, sexual rings, and stage I gametocytes

status: Public on Feb 11 2019

city: University Park

first: Manuel

last: Llinas

state: PA

address: Millennium Science Complex

department: Biochemistry and Molecular Biology

institute: Pennsylvania State University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: In the malaria parasite Plasmodium falciparum, the switch from asexual multiplication to sexual differentiation into gametocytes is essential for transmission to mosquitos. One of the key determinants of sexual commitment is the transcription factor PfAP2-G, which has been proposed to orchestrate this crucial cell fate decision by driving expression of gametocyte genes. We show conclusively that PfAP2-G is a transcriptional activator of gametocyte genes and identify the earliest known markers expressed during commitment. Remarkably, we also find that in sexually committed cells, PfAP2-G is associated with the promoters of genes important for red blood cell invasion and activates them through its interactions with a second transcription factor. We thus demonstrate an intriguing transcriptional link between the apparently opposing processes of red blood cell invasion and gametocytogenesis that is coordinated by the master regulator PfAP2-G. This finding has important implications for the development of new anti-malarial drugs that block the invasion of red blood cells by sexually committed cells, thereby preventing parasite transmission.

overall_design: ChIP was performed on the AP2-G-DD line (+Shld1) at schizont, ring, and stage I gametocyte stages using an antibody against HA. There are two biological replicates for each of the three stages, giving a total of six samples. The input material served as the control.

first: Gabrielle

middle: A

last: Josling

first: Jarrett

last: Venezia

first: Lindsey

last: Orchard

first: Timothy

middle: J

last: Russell

first: Heather

last: Painter

last: Llinás


title: Transcriptome analysis of antigen-specific T follicular helper (Tfh) cells and non-Tfh cells

city: Berlin

first: Pawel

last: Durek

address: Charitéplatz 1

country: Germany

institute: Deutsches Rheuma-Forschungszentrum

type: Expression profiling by high throughput sequencing

summary: To identify transcription factors critically involved in the Tfh cell transcriptional network, antigen-specific Tfh and non-Tfh cells from a day 8 immune response were analyzed by RNA-seq.

overall_design: Ovalbumin-specific T cells from OT-II TCR-transgenic mice were transferred into C57BL/6 recipients, which were immunized subcutaneously with nitrophenol coupled to ovalbumin. Eight days after immunization, transgenic T cells from pooled inguinal lymph nodes were sorted for a CD44hi CXCR5+ PD-1+ Tfh and CD44hi CXCR5- PD-1- non-Tfh cell phenotype for analysis by RNA-seq.

first: Annette

last: Lahmann

first: Julia

last: Kuhrau

first: Franziska

last: Fuhrmann

first: Frederik

last: Heinrich

first: Laura

last: Bauer

first: Mir-Farzin

last: Mashreghi

first: Andreas

last: Hutloff


title: Global identification of functional microRNA-mRNA interactions in Drosophila

city: New York

first: Hans-Hermann

last: Wessels

address: 101 Avenue of the Americas

institute: New York Genome Center

summary:
MicroRNAs (miRNAs) are key mediators of post-transcriptional gene expression silencing. So far, no comprehensive experimental annotation of functional miRNA target sites exists in Drosophila. To close this gap, we generated the first transcriptome-wide in vivo map of miRNA-mRNA interactions in Drosophila melanogaster, making use of single nucleotide resolution in Argonaute1 (AGO1) crosslinking and immunoprecipitation (CLIP) data.
Absolute quantification of cellular miRNA levels presents the miRNA pool in Drosophila cell lines to be more diverse than previously reported. Benchmarking two CLIP approaches, we identify a similar predictive potential to unambiguously assign thousands of miRNA-mRNA pairs from AGO1 interaction data at unprecedented depth, achieving higher signal-to-noise ratios than with computational methods alone. Quantitative RNA-Seq and sub-codon resolution ribosomal footprinting data upon AGO1 depletion enabled the determination of miRNA-mediated effects on target expression and translation. We thus provide the first comprehensive resource of miRNA target sites and their quantitative functional impact in Drosophila.

overall_design: 1) Endogenous AGO1 PARCLIP and HITSCLIP small RNA sequencing data of wt Drosophila S2 cells. 2) smallRNA-seq data of endogenously 5’phosphorylated small RNA species wt Drosophila S2 cells. 3) Stranded, single-end, rRNA-depleted RNA-seq data upon dsRNA-mediated knockdown of AGO1 and control treatments. 4) Matched ribosomal footprinting data upon dsRNA-mediated knockdown of AGO1 and control treatments.

first: Svetlana

last: Lebedeva

first: Antje

last: Hirsekorn

first: Ricardo

last: Wurmus

first: Altuna

last: Akalin

first: Neelanjan

last: Mukherjee

first: Uwe

last: Ohler


title: PfAP2-G target gene promoter mutants expression timecourse

status: Public on Feb 08 2019

first: Manuel

last: Llinas

state: Pennsylvania

address: Millennium Science Complex, Pollock Rd

institute: Penn State University

overall_design: Two lines were tested: AP2-G-DD and AP2-G-DD-ap2-g-mut. At 24 hpi, highly synchronous parasites were treated with Shld1 to stabilise the AP2-G-DD protein. RNA was collected from each culture in parallel at intervals of six hours for the next 66 hours, to give a total of 22 samples (11 for each line). Cy5-labelled cDNA generated from these samples was hybridized against a Cy3-labeled reference pool of 3D7 mixed staged parasites spiked with cDNA from the samples (to make up 50% of the new reference pool) on a two-color array.

first: Gabrielle

last: Josling

first: Jarrett

last: Venezia

first: Lindsey

last: Orchard

first: Timothy

last: Russell

last: Painter


title: An Open-Label Pilot Study to Evaluate the Efficacy of Tofacitinib in Moderate to Severe Patch Type Alopecia Areata, Totalis and Universalis

status: Public on Feb 28 2019

first: James

last: Chen

state: NEW YORK

address: 1130 St Nicholas Ave

department: Systems Biology

institute: Columbia University

summary: This study was an open-label, clinical trial to investigate tofacitinib 5 mg to 10 mg PO twice daily in the treatment of moderate/severe alopeica areata and to identify if gene expression of the scalp correlates with clinical response. Gene expression profiling was performed on scalp biopsies of alopecia areata patients taken at baseline and up to 24 weeks of treatment of tofacitinib. We applied both naïve and supervised clustering to this dataset in order to assess two features: the overall molecular effect of tofacitinib treatment on patient samples, and the concordant molecular response of the disease. The former was assessed by an unbiased, unsupervised differential expression analysis and the latter was measured by response to previously published gene expression signatures defining AA pathology. To ensure parity of the data, for this analysis we only included patient samples that had matched pre-treatment, Tx-00, and 24 weeks of treatment, Tx-24, samples. Gene expression profiles and Alopecia Areata Disease Activity Index (ALADIN) scores correlated with clinical response.

overall_design: Gene expression analysis of 12 (6 T0 and 6 T24) scalp biopsies of alopecia areata patients and 6 control samples.

first: Ali

last: Jabbari

first: Freda

last: Sansaricq

first: Jane

last: Cerise

first: Avi

last: Bitterman

first: Grace

last: Ulerio

first: Julissa

last: Borbon

first: Raphael

last: Clynes

first: Angela

last: Christiano

first: Julian

last: Mackay-Wiggan


title: PfAP2-G DD +Shld1 vs. -Shld1 expression timecourse

overall_design: At 24 hpi, highly synchronous AP2-G-DD parasites were either treated with Shld1 to stabilise the AP2-G-DD protein or the vehicle control (ethanol). RNA was collected from both cultures in parallel at intervals of six hours for the next 66 hours, to give a total of 22 samples (11 for each condition). Cy5-labelled cDNA generated from these samples was hybridized against a Cy3-labeled reference pool of 3D7 mixed staged parasites spiked with cDNA from the samples (to make up 63% of the new reference pool) on a two-color array.

first: Heather

last: Llinás


title: Transcriptional changes associated with overexpression of TBX3 isoforms (TBX3iso1 and TBX3iso2) in the DCIS-like 21NT cell line

status: Public on Feb 07 2019

city: London

first: Alan

last: Tuck

address: 339 Windermere Rd

department: Pathology and Laboratory Medicine

country: Canada

institute: Western University

type: Genome binding/occupancy profiling by array


title: Hsa_circ_101555 functions as a competing endogenous RNA of miR-597-5p to promote colorectal cancer progression [Circular RNAs]

status: Public on Feb 06 2019

city: Soochow

first: Qiaoming

last: Zhi

address: No.188 Shizi Road

country: China

institute: Soochow university

summary: Circular RNAs (circRNAs) represent critical roles in the biology of various cancers. However, their expression patterns and biological functions in human colorectal cancer (CRC) remain largely unknown. The aim of this study was to explore circRNAs profiles in CRC and investigate key circRNAs involved in CRC tumourigenesis and progression.

overall_design: To detect the circRNAs expression profiles in 10 colrectal cancer (CRC) tissues and their corresponding normal-appearing tissues (NATs) by human circRNA expression profile chips and to identify the differentially expressed circRNAs between CRC and their corresponding NATs based on the chip data. In this way, this study provided the basis for identifying novel CRC biomarkers and further studying the roles and functions of differentially expressed circRNAs in CRC. The function of the differentially expressed circRNAs were analyzed by bioinformatic methods.

first: Daiwei

last: Wan

first: Ye

last: Han

first: Zhihua

last: Xu

first: Rui

last: Ren

first: Zhenlong

first: Dai


title: Hsa_circ_101555 functions as a competing endogenous RNA of miR-597-5p to promote colorectal cancer progression

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

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus


title: Hsa_circ_101555 functions as a competing endogenous RNA of miR-597-5p to promote colorectal cancer progression [lncRNA/mRNAs]

summary: Given the role of lncRNAs and mRNAs in tumor pathogenesis, we set out to identify transcripts that potentially drive colorectal tumorigenesis. In this study, we will use the microarray analysis to study the differences of the expression profiles of lncRNA and mRNA in colorectal cancer tissues, analyzing the differentially expressed genes by GO/KEGG enrichment, and predicting the new lncRNAs’ function.

overall_design: To detect the lncRNA/mRNA expression profiles in 10 colorectal cancer (CRC) tissues and their corresponding normal-appearing tissues (NATs) by human lncRNA/mRNA expression profile chips and to identify the differentially expressed lncRNA/mRNA between CRC and their corresponding NATs based on the chip data. In this way, this study provided the basis for identifying novel CRC biomarkers and further studying the roles and functions of differentially expressed lncRNA/mRNA in CRC. The function of the differentially expressed lncRNA/mRNA were analyzed by bioinformatic methods.

last: Chen


title: Hsa_circ_101555 functions as a competing endogenous RNA of miR-597-5p to promote colorectal cancer progression [microRNA]

summary: Using the highly sensitive miRCURYTM LNA Array, we screened 2081 microRNAs abundant 10 colorectal cancer (CRC) tissues and their corresponding normal-appearing tissues (NATs), and the function of differentially expressed microRNAs were analyzed by bioinformatics. The enrichment results indicated that these microRNAs perhaps participated in the occurrence and development process of colorectal cancer.

overall_design: In this study, ten cases of colrectal cancer (CRC) tissues and their corresponding normal-appearing tissues (NATs) were used to acquire the microRNA expression profiling. The function of the differentially expressed microRNA were analyzed by bioinformatic methods. Finally,compared with the NATs，the expression of 341 microRNAs were up regulated,and 95 microRNAS were down regulated in colorectal cancer.


title: Transcriptional changes associated with overexpression of TBX3 isoforms (TBX3iso1 and TBX3iso2) in the DCIS-like 21NT cell line (RNA-Seq)

summary:
Purpose: The acquisition of cellular invasiveness of breast epithelial cells and subsequent transition from ductal carcinoma in situ (DCIS) to invasive breast cancer is a critical step in breast cancer progression. Very little is known about the molecular dynamics governing this transition. We have previously shown that overexpression of the transcriptional regulator TBX3 in DCIS-like 21NT cells results in increased survival, growth, and invasiveness. In this study we explore the role of TBX3 in breast cancer progression pathways, focusing specifically on its involvement in the induction of EMT and the transition from DCIS to invasive mammary carcinoma.
Methods: Total mRNA was isolated from 21NT transfected cell lines. Sequencing was conducted using an Illumina HiSeq 2500 sequencer, comparing the resultant transcriptional profiles with overexpression of either TBX3 isoform (TBX3iso1 or TBX3iso2) as fold changes relative to the empty vector control. RNA-Seq data was integrated with ChIP-array data downstream to assess direct targets of TBX3 isoforms and relate it to the process of EMT. TBX3, SLUG and TWIST1 expression were assessed by immunohistochemistry in two independent early-stage (Stage 0 and Stage 1) breast cancer cohorts.
Results: An EMT-related transcriptional profile was observed with overexpression of TBX3iso1 and TBX3iso2. Using genome-wide bioinformatic approaches in conjunction with more conventional in vitro studies, we have identified SLUG and TWIST1 as downstream targets of TBX3 and have assessed their expression by immunohistochemistry in two different patient cohorts. Our findings suggest that TBX3 facilitates the process of early invasion in DCIS lesions by promoting the induction of EMT and tumor progression through the low-grade pathway. Finally, we propose a progression model in which SLUG is an important and necessary effector downstream of TBX3, leading to increased motility, invasiveness, and induction of key invasiveness-associated genes.
Conclusions: This is the only existing study which has conducted assessment of transcriptional changes associated with TBX3 isoforms (TBX3iso1 and TBX3iso2). Our published study has identified the transcriptional regulator TBX3 as an enabler of EMT in non-high grade, pre-invasive lesions of the breast, inducing SLUG and promoting the transition from in situ (DCIS) to invasive breast cancer.

overall_design: Examination of transcriptional changes with TBX3 isoform overexpression (3 total cell lines sequenced in duplicate; expressed as fold change relative to the empty vector control)

first: Milica

last: Krstic

first: Bart

last: Kolendowski

first: Matthew

last: Cecchini

first: Carl

middle: O

last: Postenka

first: Haider

middle: M

last: Hassan

first: Joseph

last: Andrews

first: Connor

middle: D

last: MacMillan

first: Karla

last: Williams

first: Hon

middle: S

last: Leong

first: Muriel

last: Brackstone

last: Torchia

first: Ann

middle: F

last: Chambers

middle: B


title: Expression data from parental and SLX4IP-depleted D2.OR cells

status: Public on Jan 27 2019

city: Cleveland

first: William

last: Schiemann

state: OH

address: 2103 Cornell Rd.

department: Case Comprehensive Cancer Center

institute: Case Western Reserve University

summary:
Loss of SLX4IP elicits the metastatic outgrowth of nonmetastatic breast cancer cells by activating Wnt signaling to induce telomere maintenance mechanism switching
We sought to assess genome-wide transcriptomic profiles governed by loss of SLX4IP expression in latent D2.OR breast cancer cells

overall_design: We propagated parental and SLX4IP-depleted D2.OR cells in 3D-culture for 7 days, at which point total RNA was isolated and subsequently subjected to Affymetrix GeneChip Mouse Gene 2.0 ST Array analysis. Arrays were peformed in triplicate for each cell line.

middle: P

first: Nathaniel

last: Robinson


title: Regulation of Macrophage Foam Cell Formation during Nitrogen Mustard (NM)-Induced Pulmonary Fibrosis by Lung Lipids

status: Public on Jan 25 2019

city: Gainesville

first: Ley

middle: Cody

last: Smith

state: FL

address: 2187 Mowry Rd

institute: University of Florida

summary: Nitrogen mustard (NM) is a vesicant known to target the lung, causing acute injury which progresses to fibrosis. Evidence suggests that activated macrophages contribute to the pathologic response to NM.  In these studies, we analyzed the role of lung lipids generated following NM exposure on macrophage activation and phenotype.  Treatment of rats with NM (0.125 mg/kg, i.t.) resulted in a time-related increase in enlarged vacuolated macrophages in the lung.  At 28 d post exposure, macrophages stained positively for Oil Red O, a marker of neutral lipids. This was correlated with an accumulation of oxidized phospholipids in lung macrophages and epithelial cells, and an increase in bronchoalveolar lavage fluid (BAL) phospholipids.  RNA-sequencing analysis revealed that lipid handling pathways under control of the transcription factors LXR, FXR and PPAR-ɣ were significantly altered following NM exposure. Whereas at 1-3 d post NM, FXR and the downstream oxidized low density lipoprotein receptor, Cd36, were increased, Lxr and the lipid extrusion pump targets, Abca1 and Abcg1 were reduced.  Treatment of naïve lung macrophages with lipid enriched fractions of BAL collected 3 d after NM resulted in upregulation of Nos2, Apoe and Ptgs2, markers of pro-inflammatory activation, while lipid-enriched BAL collected 28 d post NM upregulated expression of the anti-inflammatory markers, Il10, Cd163, and Cx3cr1, and induced the formation of lipid-laden foamy macrophages. These data suggest that NM-induced alterations in lipid handling and metabolism drive macrophage foam cell formation, potentially contributing to the development of pulmonary fibrosis.

overall_design: Alveolar macrophages were collected by gentile message from male wistar rats 1 d or 28 d after intratracheal exposure to NM and from rats intratracheally exposed to PBS. There were three biological replicates per exposure group.

first: Alessandro

last: Venosa

first: Debra

middle: L

last: Laskin

first: Ron

last: Hart


title: Regulation of sexual differentiation is linked to invasion in malaria parasites

first: Manuel

last: Llinas


title: Transcript analysis reveals a hypoxic inflammatory environment in human chronic otitis media with effusion

status: Public on Jan 24 2019

city: Midlothian

first: Michael

last: Cheeseman

address: Easter Bush

department: Developmental Biology

institute: Roslin Institute

summary: Chronic otitis media with effusion (COME) is the most common cause of childhood hearing loss in the developed world.  Underlying pathophysiology is not well understood, and in particular the factors that lead to the transition from acute to chronic inflammation.  Here we present the first genome-wide transcript analysis of white blood cells in the effusion of children with COME.  Analysis of microarray data for enriched pathways reveals upregulation of hypoxia pathways, which is confirmed using real-time PCR and determining VEGF protein titres.  Other pathways upregulated in both mucoid and serous effusions include Toll-like receptor signalling, complement, and RANK-RANKL.  Transcript analysis indicates serous fluids have CD4+ and CD8+ T-lymphocyte, and NK cell signatures. Overall, our findings suggest that inflammation and hypoxia pathways are important in the pathology of COME and targets for potential therapeutic intervention, and that mucoid and serous COME may represent different immunological responses.

overall_design: 23 samples from 11 patients, 6 mucoid ear effusion, 6 serous ear effusion, and 11 whole blood samples used as a control. Samples were processed in two batch of experiment, with no batch effect detected.

first: Mahmood

last: Bhutta

first: Jane

last: Lambie

first: Lindsey

last: Hobson

first: Hayley

last: Tyrer

first: Debbie

first: George

last: Nicholson

first: Sheena

last: Lee

first: Steve

last: Brown

first: Anagha

last: Joshi

first: Helen

first: Chiara

last: Piccinelli

first: Guillaume

last: Devailly

first: James

last: Ramsden

middle: T


title: PfAP2-G and PfAP2-I ChIP-seq in schizonts

summary: In the malaria parasite Plasmodium falciparum, the switch that occurs from asexual multiplication to sexual differentiation is essential for transmission to mosquitos. One of the key drivers of commitment to sexual development is the transcription factor AP2-G. Although it has been hypothesised that AP2-G orchestrates this crucial cell fate decision by driving expression of gametocyte genes, the molecular mechanisms by which this occurs remain unknown. We show conclusively that AP2-G is a transcriptional activator of gametocyte genes and identify the earliest target genes expressed during commitment. Remarkably, we also find that in committed cells AP2-G is associated with the promoters of genes important for red blood cell invasion and activates them through its interactions with another transcription factor. We thus demonstrate for the first time an intriguing transcriptional link between the apparently opposing processes of red blood cell invasion and gametocytogenesis. This suggests that committed schizonts may have a distinct invasion preference or pathway that is transcriptionally regulated by AP2-G.

overall_design: ChIP was performed on the AP2-G-DD::AP2-I-GFP line (+ Shld1) at the schizont stage using antibodies against GFP and HA. The input material served as the control. There are two biological replicates, giving a total of six samples.

first: Gabrielle

last: Josling

first: Jarrett

last: Venezia

last: Orchard

first: Timothy

last: Russell

first: Heather

last: Painter

last: Llinás


title: Defining the chromatin compaction state of all histone post-translational modifications

status: Public on Jan 22 2019

city: Philadelphia

first: Naomi

last: Goldman

address: 324 BRB II/III, 421 Curie Blvd

institute: University of Pennsylvania

summary: By performing metabolic incorporation of heavy labeled amino acids in cell culture, we estimated the turnover rates of histones decorated with different PTMs, and correlated this information with how “active” chromatin is where these PTMs reside.

overall_design: Examination of 5 different histone modifications in EL4 cells.

first: Simone

last: Sidoli

first: Mariana

last: Lopes

first: Peder

last: Lund

first: Maria

last: Fasolino

first: Mariel

last: Coradin

first: Natarajan

middle: V

last: Bhanu

first: Katarzyna

last: Kulej

first: Golnaz

last: Vahedi

first: Benjamin

last: Garcia


title: Characterization of RNA context tumor associated macrophages and related extracellular vesicles

city: guangzhou

first: fei

last: chen

address: yanjiangxi road

institute: sun yat-sen university

overall_design: Refer to individual Series


title: Characterization of RNA context tumor associated macrophages and related extracellular vesicles [small RNA-seq]

summary: Extracellular vesicles (EVs) are membrane vesicles released by all cell types and contain proteins and non-coding RNAs, which are transported into recipient cells to regulate their signal transduction and functions. Increasing evidence has demonstrated that EV shuttling is an effective means of bio-molecule transportation among various cell types in the tumor microenvironment, and thus plays a critical role in regulating cancer cell biology. Previous studies have shown that TAMs are an important source of extracellular vesicles and the extracellular vesicles released by TAMs can promote the invasiveness of breast cancer cells. In this study, we studied the differential expression of TAM EV and the donor cells.

overall_design: Examination of small RNA-seq in TAMs and TAM EV (mixture from 10 donors).

first: Erwei

last: Song

first: Fei

last: Chen


title: Characterization of RNA context tumor associated macrophages and related extracellular vesicles [RNA-seq]

overall_design: Examination of RNA-seq in TAMs and TAM EV (mixture from 10 donors).


title: Transmission of extracellular vesicle packaged lncRNA from TAMs to breast cancer cells


title: The mRNA and lncRNA profiles of breast cancer cells with or without TAMs coculture

summary: We compared the lncRNA expression profile of breast cancer cells with or without TAMs coculture in transwell system.

overall_design: A six chip study using total RNA recovered  from breast cancer cells with or without TAMs coculture, n=3.

first: Shicheng

last: Su


title: The mRNA and lncRNA profiles of the  extracellular vesicle from monocytes-derived macrophages (MDMs) and tumor associated macrophages (TAMs)

summary: We compared the lncRNA expression profile of  extracellular vesicle from MDMs and TAMs. TAMs were polarized by treating human monocytes-derived macrophages (MDMs) with the conditioned media of MDA-MB-231 cells.

overall_design: A six chip study using  extracellular vesicle-packaged RNA of MDMs and TAMs from 3 donors.


title: Transcriptomic analysis of the Trichoderma virens- Arabidopsis thaliana interaction

status: Public on Jan 18 2019

city: Hermosillo

first: Miguel

middle: Angel

last: Hernandez

state: Sonora

address: Carretera Gustavo Enrique Astiazarán Rosas No. 46

department: Coordinación de Tecnología de Alimentos de Origen Vegetal

country: Mexico

institute: Centro de Investigación en Alimentación y Desarrollo

summary:
Trichoderma spp. are filamentous fungi that colonize plant roots conferring beneficial effects to plants, indirectly through the induction of their defense systems or directly through the suppression of phytopathogens in the rhizosphere. Transcriptomic analyses of Trichoderma emerged as a powerful method for identifying the molecular events underlying the establishment of this beneficial relationship. Here, we focus on the transcriptomic response of Trichoderma virens during its interaction with Arabidopsis seedlings. The main response of T. virens to co-cultivation with Arabidopsis was the repression of gene expression. The biological processes of transport and metabolism of carbohydrates were downregulated, including a set of cell-wall-degrading enzymes putatively relevant for root-colonization. Repression of such genes reached their basal levels at later times of the interaction when genes belonging to the biological process of copper ion transport were induced, a necessary process providing copper as a cofactor for cell-wall degrading enzymes with auxiliary activities (AAs) class. RNA-Seq analysis showed the induction of a member of the SNF2 family of chromatin remodelers/helicase-related proteins, which was named IPA-1 (Increased Protection of Arabidopsis-1). Sequence analyses of IPA-1 showed as its closest relatives members of the Rad5/Rad16- and SNF2-subfamilies; however, it grouped into a different clade. Although deletion of ipa-1 in T. virens did not affect its growth, the antibiosis of Δipa-1 culture filtrates showed a diminished effect against Rhizoctonia solani but remained unaltered against Botrytis cinerea. Triggering of the plant defense genes in plants treated with Δipa-1 was higher, showing enhanced resistance against Pseudomonas syringae but not against B. cinerea as
compared to wild type.

overall_design: Twenty ten-day-old Arabidopsis seedlings grown on MS 1× plates were root inoculated with T. virens WT (wild-type), and mycelia were collected at 48, 72 and 96 hpi (hours post inoculation). T. virens growing in MS 1× plates were used as control. RNA total of three biological replicates was used to construct the RNA-seq libraries for each treatment.

first: Magnolia

last: Estrada-Rivera

last: Hernández-Oñate

first: Mitzuko

last: Dautt-Castro

first: Jose

last: Gallardo

first: Oscar

middle: G

last: Rebolledo-Prudencio

first: Catalina

last: Arenas-Huertero

first: Alfredo

last: Herrera-Estrella

first: Sergio

last: Casas-Flores


title: Gene expression data of human T cell isolated from PBMCs of healthy controls and atopic dermatitis patients.

status: Public on Jan 06 2019

city: Seoul

first: Kwang Hoon

last: Lee

address: 50-1, Yonsei-ro, Seodaemun-gu

department: Dermatology

country: South Korea

institute: Yonsei University College of Medicine

summary:
We identified zinc-alpha-2-glycoprotein (ZAG), a 41-kDa adipokine that regulates body weight, lipid, and mobilization, as a novel biomarker for AD. ZAG levels were consistently decreased in sera, T cells, and skin in human AD patients compared with healthy controls.
We used microarrays to obtain the data of expressions of ZAG in human T cell isolated from PBMCs of healthy controls and atopic dermatitis patients.

overall_design: Human PBMCs samples were obtained in accordance with a protocol approved by the Yonsei University College of Medicine Institutional Review Board (4-2013-0624).

first: Ji-Yeon

last: Noh

first: Jung

middle: U

last: Shin

first: Kwang-Hoon


title: The mRNA and lncRNA profiles of the monocytes-derived macrophages (MDMs) and tumor associated macrophages (TAMs)

summary: We compared the lncRNA expression profile of MDMs and TAMs. TAMs were polarized by treating human monocytes-derived macrophages (MDMs) with the conditioned media of MDA-MB-231 cells.

overall_design: A six chip study using total RNA recovered from MDMs and TAMs from 3 donors.


title: Transcriptome Analysis of Huh7 cells Infected with Adenovirus Overexpression GSTZ1 or PCK1

status: Public on Jan 02 2019

city: chongqing

first: tang

last: ni

address: yixueyuan Road NO.1

institute: Chongqing Medical University

summary: Purpose:To understand the change in cellular metabolism and function for the overxepression of GSTZ1 or PCK1 in hepatoma cells. Methods:Total RNAs of AdGFP- , AdGSTZ1-, or AdPCK1-infected Huh7 cells were extracted using TRIzol (Invitrogen), following the manufacturer’s instructions. RNA-seq and bioinformatic data analysis were performed by Shanghai Novel Bio Ltd. Briefly, strand-specific RNA-seq libraries were prepared using the Total RNA-seq (H/M/R) Library Prep Kit (Vazyme Biotech, Nanjing, China) and were sequenced on Ion Torrent Proton sequencing platform. Raw reads in FASTQ format were subjected to quality control using FastQC. RNA-seq reads were aligned to the reference genome using Bowtie. Uniquely mapped reads were used for further analysis. Gene expression levels are expressed as RPKM (reads per kilobase per million reads) and differences in gene expression were calculated with rSeq. Results:There were 498 genes differentially expressed in AdPCK1-infected Huh 7 cells,  513 genes differentially expressed in AdGSTZ1-infected Huh 7 cells compare to the GFP control group respectively (fold change >1.5 or < 0.667; FDR < 0.05).

overall_design: mRNA profiles of AdGFP1, AdGSTZ1- or AdPCK1-infected  Huh 7 cells were generated by deep sequencing in triplicate, using Ion Torrent Proton sequencing platform.

first: Ni

last: Tang

first: Ailong

last: Huang

first: Kai

last: Wang

first: Lin

last: Tuo

first: Jin

last: Xiang

first: Yi

last: Yang

first: Fan

first: Li

last: Liang

first: Jingjing

last: Li


title: Gene expression data from healthy controls and atopic dermatitis patients skin

summary:
We identified zinc-alpha-2-glycoprotein (ZAG), a 41-kDa adipokine that regulates body weight, lipid, and mobilization, as a novel biomarker for AD. ZAG levels were consistently decreased in sera, T cells, and skin in human AD patients compared with healthy controls.
We used microarrays to obtain the data of expressions of ZAG between human healthy controls and atopic patients skin.

overall_design: Human skin samples were obtained in accordance with a protocol approved by the Yonsei University College of Medicine Institutional Review Board (4-2013-0624).


title: Methylomic Analysis reveals Epigenetic Pattern of SH2B1 in Chinese Monozygotic Twins Discordant for Autism Spectrum Disorder [Methylation 450K]

status: Public on Dec 31 2018

city: Washington

first: Zhenzhi

state: DC

address: 3900 reservoir rd nw

institute: Georgetown University

type: Methylation profiling by genome tiling array

summary: Autism spectrum disorder(ASD) is a complex neurodevelopmental disorder. Aberrant DNA methylation has been observed in ASD but the mechanisms remain largely unknown. Here, we employed discordant monozygotic twins to investigate the contribution of DNA methylation to ASD etiology. Genome-wide DNA methylation analysis was performed using samples obtained from five pairs of ASD-discordant monozygotic twins, which revealed a total of 2397 differentially methylated genes. Further, such gene list was annotated with Kyoto Encyclopedia of Genes and Genomes and demonstrated predominant activation of neurotrophin signaling pathway in ASD-discordant monozygotic twins. The methylation of SH2B1 gene was further confirmed in the ASD-discordant, ASD-concordant monozygotic twins, and a set of 30 pairs of sporadic case-control by bisulfite-pyrosequencing. The results showed that there was a greater DNA methylation difference in ASD-discordant monozygotic twins than ASD-concordant monozygotic twins. Further, verification of the Chr.16:28856743 of SH2B1 showed significant differences in DNA methylation between case and control. These results suggest abnormal methylation of SH2B1 is associated with ASD etiology. Our data suggest that it might be worthwhile to further explore the functions of SH2B1 and related genes of neurotrophin signaling pathway in ASD.

overall_design: Whole blood samples were obtained from five monozygotic twin paris with discordant ASD. Samples from two twin pairs underwent Reduced representation bisulfite sequencing (RRBS) and three twin pairs underwent Infinium 450K to determine methylation level.

first: Shuang

first: Yihan

first: Haixin

first: Xiaolei

first: Xuelai

last: Zhan

first: Yan

first: Xiaodan

first: Zhaomin

last: Gao

first: Min

last: Zhang

first: Jia

first: Lili

last: Fan

first: Wei

last: Xia

first: Lijie

last: Wu


title: Methylomic Analysis reveals Epigenetic Pattern of SH2B1 in Chinese Monozygotic Twins Discordant for Autism Spectrum Disorder [Bisulfite-seq]

type: Methylation profiling by high throughput sequencing


title: Mus musculus intestinal epithelial MODE-K cells incubated with Heligmosomoides bakeri secreted extracellular vesicles (EVs)

city: Edinburgh

first: José

middle: Roberto

last: Bermúdez-Barrientos

state: Lothian

address: Charlotte Auerbach Rd

department: Institute of Immunology & Infection

institute: The University of Edinburgh

summary: Small RNAs are emerging as important molecules for cross-species communication. Thanks to available and affordable sequencing technologies it is now possible to sequence small RNAs (sRNA-Seq) present in samples of interacting organisms. A first step when analyzing sRNA-Seq of two interacting species is to determine which sequences are being produced by which organism. Due to their small size (18-30), small RNAs could easily map to both host and parasite genomes. Here we produced data for Mus musculus intestinal epithelial cells treated with Extracellular Vesicles (EV) produced by the parasitic nematode Heligmosomoides bakeri.

sample_organism:
Mus musculus
Heligmosomoides polygyrus bakeri

overall_design: MODE-K cells were incubated with H. bakeri vesicles for 4 and 24 hours, cells were washed with PBS buffer before small RNA sequencing, three biological replicates were generated for each condition. Sequencing was performed on an Illumina HiSeq high output v4

first: Jose

middle: R

last: Bermudez-Barrientos

first: Obed

last: Ramirez-Sanchez

first: Franklin

middle: W

last: Chow

first: Amy

middle: H

last: Buck

first: Cei

last: Abreu-Goodger


title: Methylomic Analysis reveals Epigenetic Pattern of SH2B1 in Chinese Monozygotic Twins Discordant for Autism Spectrum Disorder

first: Zhenzhi

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


title: Single cell sequencing of stromal vascular fraction (SVF) under B3-adrenergic agonist stimulation and mature adipocytes under cold exposure and B3-adrenergic agonist stimulation

status: Public on Oct 17 2019

city: Los Angeles

first: Douglas

last: Arneson

address: 2000 Terasaki Life Sciences Bldg 610 Charles E Young Drive East

department: Integrative Biology and Physiology

institute: UCLA

summary: A single cell suspension was generated from B3-adrenergic agonist (CL; 1 mg/kg/day) for 4 days and saline mouse SVF, and single-cell mRNAseq libraries were generated with Drop-Seq. A single cell suspension was generated from mouse mature adipocyte nuclei under the following conditions: RT, 24hrs @ 4 °C , 48hrs @ 4 °C, 4days @ 4 °C and B3-adrenergic agonist (CL; 1 mg/kg/day) and single-cell mRNAseq libraries were generated with 10X genomics.

overall_design: Drop-Seq was performed on two separate days using the same age (10 week) and strain (C57BL/6) mice. 10X Genomics single cell sequencing was performed on three separate days using the same age (10 week) and two groups of C57BL/6 mice: C57BL/6 Il10rαF/F and C57BL/6 AdIL10RαKO.

first: P

last: Tontonoz

last: Rajbhandari

first: D


title: Cold priming and triggering of Arabidopsis accessions

status: Public on Jan 31 2019

city: Potsdam

first: Ellen

last: Zuther

address: Am Muehlenberg 1

department: Transcript Profiling

institute: MPI of Molecular Plant Physiology

summary: Plants from temperate regions can be primed by exposure to low, non-freezing temperatures resulting in improved freezing tolerance. Whereas the molecular and metabolic basis of cold priming has been investigated in detail, hardly anything is known about memory of a previous cold event under warm conditions and a following low temperature triggering event. We show that three days of cold priming at 4°C, a seven-day lag phase at 20°C and a triggering treatment of 4°C improved the freezing tolerance of Arabidopsis Col-0 and other accessions compared to plants that were not primed before. Transcripts, metabolites and lipids as possible molecular determinants of this increase in freezing tolerance were investigated in Arabidopsis accessions Col-0 and N14 after priming, memory phase and triggering by Illumina-based RNA-Seq, GC-MS metabolite profiling and UPLC FT-MS-based lipidomics. Comparing primed and triggered with only triggered samples 93 and 128 unique differentially expressed genes could be identified in Col-0 and N14, together with three and six significantly changed lipids and one metabolite in N14. Possible functions of these candidates will be discussed. This work identified for the first time molecular and metabolic changes accompanying cold stress memory and triggering by a second cold stress.

overall_design: 6 different conditions were analyzed, control - 28 day old plants (C28), primed (3 days at 4oC) plants (C28P3), primed plants after a memory phase (7 days at 20oC) (C28P3L7), primed and triggered plants (another 3 days at 4oC) (C28P3L7T3) and a developmental control - 35 day old plants (C35) and a primed developmental control (C35P3), 3 independent biological experiments were performed, 2 Arabidopsis accessions were investigated (Col-0 and N14), altogether 36 RNA Seq samples

first: Stephanie

last: Schaarschmidt

first: Axel

last: Fischer

first: Majken

last: Pagter

first: Dirk

last: Walther

first: Heike

last: Sprenger

middle: K

last: Hincha


title: Reversal of human regulatory T cell suppression throgh TLR8 signaling

status: Public on Dec 30 2018

city: St. Louis

first: Guangyong

last: Peng

state: MO

address: 1100 S Grand Blvd.

department: Internal Medicine

institute: Saint Louis University

summary: Analyses of gene alterations of human Treg cells treated with or without TLR8 ligand using the Illumina whole-genome Human HT-12 BeadChips. The study will provide important information for the molecular signature changes during the reversal of human Treg suppression mediated by activation of TLR8 signaling.

overall_design: Human naturally occurring Treg cells were isolated from PBMCs of healthy donors and treated with or without Poly-G3 for 0 and 24 hours. Total RNA was purified from Poly-G3 treated and untreated human Treg cells, and transcriptome analyses of Treg cells were performed using the Illumina whole-genome Human HT-12 BeadChips.

first: Peng

last: Guangyong


title: Characterization of microRNA-493-5p targets in liver cell lines

status: Public on Dec 05 2018

city: Wako

first: Luc

last: Gailhouste

state: Saitama

address: 408 Main Research Building, 2-1 Hirosawa

department: Cluster for Pioneering Research

country: Japan

institute: RIKEN

summary: Numerous studies have described the critical role played by microRNAs (miRNAs) in cancer progression and the potential of these small non-coding RNAs for diagnostic or therapeutic applications. However, the mechanisms responsible for the altered expression of miRNAs in malignant cells remain poorly understood. Herein, via epigenetic unmasking, we identified a group of miRNAs located in the imprinted delta like non-canonical Notch ligand 1 (DLK1)-maternally expressed 3 (MEG3) locus that were repressed in hepatic tumor cells. Notably, miR-493-5p epigenetic silencing was correlated with hypermethylation of the MEG3-differentially regulated region (DMR) in liver cancer cell lines and tumor tissues from patients. Experimental rescue of miR-493-5p promoted an anti-cancer response by hindering hepatocellular carcinoma (HCC) cell growth in vitro and tumor progression in vivo. We found that miR-493-5p mediated part of its tumor-suppressor activity by abrogating overexpression of insulin-like growth factor 2 (IGF2) and the IGF2-derived intronic oncomir miR-483-3p in HCC cells characterized by IGF2 loss of imprinting (LOI). In summary, this study describes an unknown miRNA-dependent regulatory mechanism between two distinct imprinted loci and a possible therapeutic window for liver cancer patients exhibiting IGF2-miR-483 LOI and amplification.

overall_design: To identify miR-493-5p targets, Hep3B and HepG2 cells were transfected using miR-493-5p and negative control miRNA mimics.

first: L

first: T

last: Ochiya


title: RB tumor suppressor promotes cancer immunity through downregulating PD-L1 expression

status: Public on Nov 19 2018

city: San Antonio

first: Zhenqing

last: Ye

state: TX

address: 8403 Floyd Curl Dr

department: 6Department of Population Health Sciences

institute: UT Health San Antonio

summary: Aberrant expression of immune checkpoint protein programmed death ligand-1 (PD-L1) promotes immune tolerance in cancer. RB is a tumor suppressor known to regulate the cell cycle, DNA damage response, and differentiation. Here, we demonstrate transient knockdown or homozygous deletion of RB markedly induces PD-L1 mRNA expression. RB binds to NFκB protein p65 and serine-249/threonine-252 (S249/T252) phosphorylation of RB is important for its interaction with p65 and suppression of PD-L1 expression. RNA-seq analysis identifies a subset of NFκB pathway genes including PD-L1 are selectively upregulated by RB knockdown. S249/T252-phosphorylated RB inversely correlates with PD-L1 expression in patient samples. Expression of a RB-derived S249/T252 phospho-mimicking peptide blocks radiation-induced PD-L1 expression and increases the anti-cancer efficacy of radiation in mice. Our findings reveal a previously unappreciated tumor suppressor function of hyperphosphorylated RB in inhibition of NFκB activity and PD-L1 expression, suggesting this regulatory module can be exploited to overcome cancer immune evasion.

overall_design: Examination of RNA expression in PC-3 cells  knocked down endogenous RB or treated cells with the CDK4/6 inhibitor palbociclib

first: Jin

last: Xin

first: Ye

last: Zhenqing

first: Wang

last: Liguo

first: Huang

last: haojie


title: Transcription-dependent control of stem cell self-renewal and differentiation by the splicing factor U2AF1

status: Public on Dec 03 2018

city: Montpellier

first: Laurent

last: MANCHON

address: 1919 Route de Mende

country: France

institute: CNRS

summary:
Purpose: Here we describe the modulation of a gene expression program involved in cell fate.
Methods: We depleted U2AF1 in human induced pluripotent stem cells (hiPSCs) to the level found in differentiated cells using an inducible shRNA system, followed by high-throughput RNAseq, revealing a gene expression program involved in cell fate determination.
Results: Approximately 85% of the total raw reads were mapped to the human genome sequence (GRCh37), giving an average of 200 million human reads per sample for total RNA and 15 million human reads per sample for small RNA libraries.
Conclusions: Our results show that transcriptional control of gene expression in hiPSCs can be set by the CSF U2AF1, establishing a direct link between transcription and AS during cell fate determination.

overall_design: hiPSCs were differentiated into the three germ layers following the described protocol in the study (Gifford et al., 2013).

first: Abdelhamid

middle: M

last: Laaref

last: Manchon

first: Jamal

last: Tazi


title: KAP1 targets actively transcribed genomic loci to exert pleomorphic effects on RNA Polymerase II- and III-mediated expression

status: Public on Nov 16 2018

city: Barcelona

first: Evarist

middle: Planet

last: Letschert

state: Spain

address: C/ Baldiri Reixac 10

department: Biostatistics

country: Spain

institute: IRB Barcelona

overall_design: Refer to individual Series


title: KAP1 targets actively transcribed genomic loci to exert pleomorphic effects on RNA Polymerase II- and III-mediated expression [RNA-Seq, small RNA-Seq]

summary: KAP1 (KRAB-associated protein 1) is best known as a co-repressor responsible for inducing heterochromatin formation notably at transposable elements. However, it has also been observed to bind the transcription start site of actively expressed genes. To address this paradox, we characterized the protein interactome of KAP1 in human embryonic stem cells and in the K562 erythro-leukemia cell line. We found that the regulator can associate with a wide range of nucleic acid binding proteins, nucleosome remodelers, chromatin modifiers and other transcription modulators. We further determined that KAP1 is recruited not only at actively transcribed polymerase II promoters, but also at genetic units driven by polymerase III, for instance tRNA genes. While KAP1 depletion induced a mild downregulation of these genes, at PolII-transcribed units it resulted in pleomorphic effects, whether expression of these genes was normally constitutive or inducible, consistent with the breadth of possible KAP1 interactors

overall_design: RNA-sequencing analysis of Hepa 1.6 WT and Kap1 knock-down cells. Small RNA-sequencing analysis of Hepa 1.6 WT and Kap1 knock-down cells, and of primary murine hepatocytes WT and Kap1 knock-out.

first: Annamaria

last: Kauzlaric

last: Planet


title: KAP1 targets actively transcribed genomic loci to exert pleomorphic effects on RNA Polymerase II- and III-mediated expression [ChIP-Seq]

overall_design: ChIP-sequencing analysis of histone marks (H3K9me3, H3K4me1, H3K27ac) and RNA Polymerases II and III in Hepa 1.6 murine hepatoma cell line


title: RNA-Sequencing data of Varicella Zoster Virus (VZV)-infected human dermal fibroblasts (HDF)

status: Public on Oct 18 2018

first: Ok Sarah

last: Shin

address: 148, Gurodongro, Gurogu

institute: Korea Univ.

summary: RNA profiles of HDF infected with various VZV strains were generated by High-throughput sequencing using Illumina Hi-seq 2500

overall_design: Investigation of host immune response differences in response to infection with clinical VZV and vaccine VZV.

first: Ok

middle: S

first: Soo-jin

last: Oh


title: microRNA expression profiles for DLD-1 cells with circLONP2 overexpression

status: Public on Oct 27 2018

city: Guangzhou

first: han

last: kai

state: Guangdong

address: Dongfeng Road East

institute: Sun Yat-sen university cancer center

summary: We have employed microRNA microarray expression profiling as a discovery platform to identify the specific microRNAs that were regulated by circLONP2.

overall_design: Human colorectal carcinoma cell line DLD-1 were transfected with circLONP2 overexpressing plasmid or negative control, and microRNA microarray were applied.

first: Han

last: Kai


title: Metabolic labeling of RNAs uncovers hidden features and dynamics of the Arabidopsis thaliana transcriptome

status: Public on Oct 31 2018

city: Oldenburg

first: Sascha

last: Laubinger

address: Carl-von-Ossietzky-Str. 9-11

institute: University of Oldenburg


title: Comparative analysis of gene expression profile of pre-defined niches within demyelinated white matter in rats

status: Public on Sep 14 2018

city: Gdansk

first: Jakub

last: Mieczkowski

address: Debinki 12

country: Poland

institute: Medical University of Gdansk

summary: Microenviromental niche characterization by comparative transcriptome profiling. The hypothesis tested in the present study was that unique properties of the perivascular niche within remyelinating white matter would create microenvironment that favor the alternative differentiation of oligodendrocyte precursor cells.

overall_design: Total RNA obtained from laser capture isolated discrete areas of cereberal wnite matter at 6 and 10 days after demyeliantion.

first: Justyna

last: Ulanska

first: Malgorzata

last: Zawadzka


title: A chromatin integration labeling method enables lower-input epigenomic profiling

status: Public on Oct 09 2018

city: Fukuoka

first: Yasuyuki

last: Ohkawa

address: 3-1-1 Maidashi

institute: Medical Institute of Bioregulation

summary: We established a novel epigenomic profiling method ChIL-seq which does not employ immunoprecipitation, but instead exploits immunostaining.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: We performed ChIL-seq on C2C12, NIH3T3, K562, MCF-7 and MDA-MB-231 cells with various cell numbers (1, 100, 1k, 10k and 100k cells) against various histone modifications and transcription factors, as well as H3K4me3 ChIP-seq for C2C12, MCF-7 and MDA-MB-231.

first: Jumpei

last: Nogami

first: Kazumitsu

last: Maehara

first: Akihito

last: Harada


title: Proteogenomic landscape of medulloblastoma subgroups [SNP]

status: Public on Sep 09 2018

city: Orsay

first: Olivier

last: Ayrault

address: Institut Curie / CNRS UMR 3347 / INSERM U1021 Bldg. 110 – Centre Universitaire

institute: Institut Curie

type:
Genome variation profiling by SNP array
SNP genotyping by SNP array

summary: Extensive high-throughput sequencing led to the characterization of four main medulloblastoma subgroups. However, to date these analyses have not attained a global comprehension of their dynamic network complexity. Wishing to get a comprehensive view of all medulloblastoma subgroups, we employed a proteomic analysis to integrate accurate protein activity. In this study we present the first analysis regrouping genomic and methylation status, whole-transcriptome sequencing and quantitative proteomics. First, our proteomic analysis clarified medulloblastoma subgroup identity. Second, analysis of proteome and phosphoproteome highlighted disregulated signalling pathways that have not been predicted by transcriptomic analysis. Altogether, combined multi-scale analyses of medulloblastoma have allowed us to identify and prioritize novel molecular drivers involved in human medulloblastoma.

overall_design: 38 human medulloblastoma samples were profiled on Illumina Infinium OncoArray-500k v1.0

first: Antoine

last: Forget

first: Marc

last: Remke

first: Daniel

last: Picard

first: Michael

last: Taylor


title: The pancreatic cancer stem cell marker CD44v6 affects transcription, translation and signaling: consequences on exosome composition and delivery

status: Public on Sep 20 2018

city: Heidelberg

first: Jan

last: Provaznik

state: Baden-Wuerttemberg

address: Meyerhofstr. 1

department: Genomics Core Facility

institute: EMBL Heidelberg

summary:
In cells recovery in wt, claudin7knockdown and  palmitoylation site mutated claudin7 rescue was compared to elaborate the impact of claudin7 and palmitoylation site mutated claudin7 on miRNA recovery 2. In exosomes recovery in wt, claudin7knockdown and palmitoylation site mutated claudin7 rescue was compared to elaborate the impact of claudin7 and palmitoylation site mutated claudin7 in cells on the transport into exosomes during exosome biogenesis and the step of intraluminal vesicle loading.
The comparison of the miRNA and proteins in cells allowed to judge on the impact of claudin7- and palmitoylation site mutated claudin7-related miRNA on protein recovery.
The comparison of the miRNA and proteins in exosomes allowed to judge on the impact of claudin7- and palmitoylation site mutated claudin7-recruited miRNA on protein silencing in exosomes.
The comparison between the impact of claudin7 and palmitoylation site mutated claudin7 on miRNA and proteins in cells versus exosomes allowed to judge on linked versus independent recruitment of miRNA and proteins and the impact of claudin7 on the recruitment of the mRNA processing machinery into exosomes.

overall_design: miRNA was analyzed in cells and exosomes of the rat pancreatic adenocarcinoma ASML wt, ASML-claudin7knockdown and ASML-claudin7kd cells rescued with claudin7 with a mutated palmitoylation site. miRNA analyses were compared with proteome analysis of the cell listed above.

first: Hanxue

last: Sun

first: Sanyukta

last: Rana

first: Zhe

last: Wang

first: Kun

last: Zhao

first: Martina

last: Schnölzer

first: Thilo

last: Hackert

first: Qingjie

last: Lv

first: Margot

last: Zöller


title: Transcriptome alterations of murine brown adipose tissue during cold exposure

status: Public on Sep 05 2018

city: Freising

first: Tobias

last: Fromme

address: Gregor-Mendel-Str. 2

department: Molecular Nutritional Medicine

institute: Technical University of Munich

summary: We analyzed coding transcript abundance in interscapular brown adipose tissue of mice acclimated to room temperature or 5°C (6h, 24h or 48h).

overall_design: We sequenced total RNA from interscapular brown fat from 13 male C57BL/6J mice exposed to room temperature (n=4) or 5°C for 6h (n=3), 24h (n=3) or 48h (n=3).

first: Stefanie

middle: F

last: Maurer

first: Martin

last: Klingenspor


title: RNA-seq analysis regarding adrenal gland contribution in mouse steroid synthesis

status: Public on Sep 03 2018

city: Turku

first: Matti

last: Poutanen

address: Kiinamyllynkatu 10

department: Institute of Biomedicine

country: Finland

institute: University of Turku

summary: The adrenal glands of mice are derived from an experiment with two study groups: Intact and orchiectomised (ORX) mice.

overall_design: RNA-seq analysis of intact (n = 5) and ORX (n = 6) samples

first: Riikka

last: Huhtaniemi


title: Germline Dependent Gene Expression Changes in the Adult Head of Drosophila melanogaster Females

status: Public on Sep 01 2018

city: Tallahassee

first: Michelle

last: Arbeitman

address: 1115 West Call Street

department: Department of Biomedical Sciences

institute: Florida State University

summary: To gain insight into the molecular underpinnings of the post-mating response that depend on the germline, we independently assess the contribution of the female germline and the male germline on gene expression changes in head tissues of females using RNA-seq.

overall_design: mRNA profiles of head tissues in virgin and mated (1 and 3 days post-mating) females that either have or are lacking a germline and females mated to males that either have or are lacking a germline. Samples were generated in triplicate and sequenced on an Illumina Genome Analyzer IIx.

middle: N

first: Nicole

last: Newell

first: Surjyendu

last: Ray


title: Active site of cyanobacterial RNA polymerase compensates for the absence of proofreading factors [Synechoscystis sp]

status: Public on Aug 15 2018

city: Newcastle upon Tyne

first: Katherine

last: James

address: Urban Sciences Building

department: School of Computing

institute: Newcastle University

summary: We found that cyanobacterial RNA polymerase possesses very efficient intrinsic proofreading ability. This ability allows model species of cyanobacteria, Synechocystis sp PCC 6803 to keep in vivo level of transcriptional mistakes close to that of E.coli.

overall_design: Sequencing of total RNA prepared from exponentially grown cells

first: Yulia

last: Yuzenkova


title: Active site of cyanobacterial RNA polymerase compensates for the absence of proofreading factors

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

sample_organism:
Synechocystis sp. PCC 6803
Escherichia coli K-12


title: MicroRNAs Regulated by Eicosapentaenoic Acid (EPA) in Brown, Subcutaneous, and visceral Adipose Tissue of Diet-Induced Obese Mice

status: Public on Dec 26 2018

city: Lubbock

first: Naima

last: Moustaid-Moussa

address: 1301 Akron Street

department: Nutritional Sciences & Obesity Research Institute

institute: Texas Tech University

summary: To understand differences in microRNA (miRNA) signatures between two different diets with and without EPA in brown, subcutaneous, and viscerl tissue from C57BL/6 mice to understand mechanistic insight regarding their contribution to metabolic disorders in obesity.  We performed small RNA-sequencing of brown, subcutaneous adipose from high fat diet (45% kcal from fat) and high fat diet supplemented with EPA (45% Kcal from fat, 6.75% EPA).  Using the Gunaratne Next Generation pipeline (published in Creighton et al. 2009) miRNA expression profiles were identified. Counts of each unique read were normalized to total usable reads, and had 40 counts added. We mapped about 13.8 million sequence reads per sample to the Mus musculus genome (build mm 10). AS a total 1251 miRNAs were identified in three adipose tissue and out of which in bown adipose tissue 15 showd differential expression between BF-HF and BF-EPA .IN subcutaneous adipose tissue 3 miRNAs showed differntial expression between SUB-HF and SUB-EPA. EPA  differentially regulate specific miRNAs expression in brown, subcutaneous, and visceral adipose tissue.

overall_design: Method : We performed small RNA-sequencing of brown, subcutaneous adipose from high fat diet (45% kcal from fat) and high fat diet supplemented with EPA (45% Kcal from fat, 6.75% EPA). Results:Using the Gunaratne Next Generation pipeline (published in Creighton et al. 2009) miRNA expression profiles were identified. Counts of each unique read were normalized to total usable reads, and had 40 counts added. We mapped about 13.8 million sequence reads per sample to the Mus musculus genome (build mm 10). AS a total 1251 miRNAs were identified in three adipose tissue and out of which in bown adipose tissue 15 showd differential expression between BF-HF and BF-EPA .IN subcutaneous adipose tissue 3 miRNAs showed differntial expression between SUB-HF and SUB-EPA. Conclusion : EPA  differentially regulate specific miRNAs expression in brown, subcutaneous, and visceral adipose tissue

first: Mandana

last: Pahlavani

first: Nadeeja

last: Wijayatunga

first: Kameswara

last: Kottapalli

first: Prathibha

first: Latha

last: Ramalingam

first: Preethi

last: Gunaratne

first: Cristian

last: Coarfa

first: Nishan

last: Kalupahana


title: Purification of GFRα1+ and GFRα1- spermatogonial stem cells reveals a niche-dependent mechanism for fate determination

status: Public on Dec 01 2018

city: Stanford

first: Steven

middle: E

last: Artandi

address: CCSR Room 1150, 259 Campus Drive

department: Hematology

institute: Stanford University

summary: Undifferentiated spermatogonia comprise a pool of stem cells and progenitor cells that show heterogeneous expression of markers, including the cell surface receptor GFRα1. Technical challenges in isolation of GFRα1+ versus GFRα1- undifferentiated spermatogonia have precluded the comparative molecular characterization of these subpopulations and their functional evaluation as stem cells. Here, we develop a method to purify these subpopulations by FACS and show that GFRα1+ and GFRα1- undifferentiated spermatogonia both demonstrate elevated transplantation activity while differing principally in receptor tyrosine kinase signaling and cell cycle. We identify the cell surface molecule MCAM as differentially expressed in these populations and show that antibodies to MCAM allow isolation of highly enriched populations of GFRα1+ and GFRα1- spermatogonia from adult, wild-type mice. In germ cell culture, GFRα1- cells upregulate MCAM expression in response to GDNF/FGF stimulation. In transplanted hosts, GFRα1- spermatogonia yield GFRα1+ spermatogonia and restore spermatogenesis, albeit at lower rates than their GFRα1+ counterparts. Together, these data provide support for a model of a stem cell pool in which the GFRα1+ and GFRα1- cells are closely related, but show key cell-intrinsic differences and can interconvert between the two states based, in part, on access to niche factors.

overall_design: RNA-Seq transcriptional analysis of three stem cell and progenitor populations isolated from the testis of adult Tert-Tomato reporter mice and gonocytes isolated from day 6 (P6) neonates.

first: Alina

last: Garbuzov

first: Matthew

last: Pech

first: Meena

last: Sukhwani

first: Kazuteru

last: Hasegawa

first: Ruixuan

middle: J

last: Zhang

first: Kyle

last: Orwig


title: Active site of cyanobacterial RNA polymerase compensates for the absence of proofreading factors [Ecoli]

first: Katherine

last: James

first: Yulia


title: Kindlin -2 is Essential for Preserving Integrity of the Developing Heart and Preventing Ventricular Rupture

status: Public on Dec 04 2018

city: La Jolla

first: Yongxin

last: Mu

address: 9500 Gilman Drive

department: medicine

institute: University of California SD

summary: Using RNA sequencing we compared the transcriptome change between control and kindlin2 knockout heart samples

overall_design: Three control or kindlin2 knockout hearts at embryonic day 10.5 were subjected to sequencing

first: Zhiyuan

first: Ju

last: Chen


title: Nociceptor translational profiling reveals the RagA-mTORC1 network as a critical generator of neuropathic pain

status: Public on Aug 01 2018

city: Richardson

first: Theodore

middle: John

last: Price

address: 800 W Campbell Rd

department: Behavioral and Brain Sciences

institute: The University of Texas at Dallas

summary: Pain sensing neurons, nociceptors, are key drivers of neuropathic pain. We used translating ribosome  affinity purification (trap) to comprehensively characterize up- and down-regulated mRNA  translation in Scn10a-positive nociceptors in chemotherapy-induced neuropathic pain. We provide  evidence that an underlying mechanism driving these changes in gene expression is a sustained  mTORC1 activation driven by MNK1-eIF4E signaling. RagA, a GTPase controlling mTORC1 activity, is  identified as a novel target of MNK1-eIF4E signaling, demonstrating a new link between these distinct  signaling pathways. Neuropathic pain and RagA translation are strongly attenuated by genetic  ablation of eIF4E phosphorylation, MNK1 elimination or treatment with the MNK inhibitor eFT508. We  reveal a novel translational circuit for the genesis of neuropathic pain with important implications for  next generation neuropathic pain therapeutics.

overall_design:
Examination of paired unbiased mRNA profile and mRNA profile based on eGFP + L10a (RPL10A) pulldown (TRAP assay) for normal mouse DRG (4 assays / replicates) and DRG from CIPN (Paclitaxel) model mouse (5 assays, 2 pooled to make 4 replicates)
Associated NIH grants: R01NS065926 (TJP), R01NS098826 (TJP and GD), R01CA200263 (PMD) and R01NS100788 (ZTC)

first: Zachary

last: Campbell

first: Gregory

last: Dussor

first: Kevin

last: Webster

first: Nahum

last: Sonenberg

first: Arkady

last: Khoutursky

first: Patrick

last: Dougherty

first: Salim

last: Megat

first: Pradipta

last: Ray

first: Jamie

last: Moy

first: Tzu-Fang

last: Lou

first: Paulino

last: Barragan-Iglesias

first: Yan

last: Li

first: Grishma

last: Pradhan

first: Andi

last: Wangzhou

first: Ayesha

last: Ahmad

first: Robert

middle: Y

last: North


title: Microbiota Depletion Impairs Adaptive Thermogenesis of Both Brown and Beige Adipose Tissue

status: Public on Nov 01 2018

city: Dallas

first: Li

address: 5323 Harry Hines Boulevard

institute: UT Southwestern Medical Center

summary: Comparsion of gene expression in scWAT/pgVAT of Ctrl, ABX and SZ-ABX mice.

overall_design: Mice were maintained under specific-pathogen-free facility (SPF) in 12h:12h day and night cycles at 23 ± 1oC and fed standard chow diet (20% Protein, 70% Carbohydrate and 10% Fat, #D12450B, Research Diet, America). Mice were provided with autoclaved drinking water. Antibiotic treatment started in 8-9 weeks old animals for 3-4 weeks.

first: L

first: B

first: J

last: Speakman


title: A genomic study of the contribution of DNA methylation to regulatory evolution in primates

status: Public on Sep 25 2018

city: Chicago

first: Lauren

middle: Elizabeth

last: Blake

state: Illinois

address: 920 E. 58th Street, CLSC 317

department: Human Genetics

institute: University of Chicago

summary: A long-standing hypothesis is that changes in gene regulation play an important role in adaptive evolution, notably in primates. Yet, in spite of the evidence accumulated in the past decade that regulatory changes contribute to many species-specific adaptations, we still know remarkably little about the mechanisms of regulatory evolu tion. In this study we focused on DNA methylation, an epigenetic mechanism whose contribution to the evolution of gene expression remains unclear. To interrogate the methylation status of the vast majority of cytosines in the genome, we performed whole-genome bisulfite conversion followed by high-throughput sequencing across 4 tissues (heart, kidney, liver and lung) in 3 primate species (human, chimpanzee and macaque). In parallel, we collected gene expression profiles using RNA-seq from the same tissue samples, allowing us to perform a high resolution scan for genes and pathways whose regulation evolved under natural selection. We integrated these datasets to characterize better the genome features whose methylation status leads to expression changes, and we developed a statistical model to quantify the proportion of variation in gene expression levels across tissues and species.

sample_organism:
Macaca mulatta
Pan troglodytes
Homo sapiens

overall_design: We extracted RNA and genomic DNA followed by high-throughput sequencing across 4 tissues (heart, kidney, liver and lung) in 4 individuals per primate species (human, chimpanzee and macaque).

first: Julien

last: Roux

first: Irene

last: Hernando-Herraez

first: Chiaowen

last: Hsiao

first: Nicholas

last: Banovich

first: Raquel

last: Garcia Perez

first: Claudia

last: Chavarria

first: Amy

last: Mitrano

first: Jonathan

last: Pritchard

first: Tomas

last: Marques-Bonet

first: Yoav

last: Gilad


title: Epigenetic-scale comparison of human iPSCs from menstrual blood cells generated by retrovirus, Sendai virus or episomal vectors

status: Public on Jul 12 2018

city: Setagaya-ku

first: Akihiro

last: Umezawa

state: Tokyo

department: Center for Regenerative Medicine

institute: National Center for Child Health and Development

summary: Human induced pluripotent stem cells (iPSCs) are established by introducing several reprogramming factors, such as OCT3/4, SOX2, KLF4, c-MYC. Because of their pluripotency and immortality, iPSCs are considered to be a powerful tool for regenerative medicine. To date, iPSCs have been established all over the world by various gene delivery methods. All methods induced high-quality iPSCs, but epigenetic analysis of abnormalities derived from differences in the gene delivery methods has not yet been performed. Here, we generated genetically matched human iPSCs from menstrual blood cells by using three kinds of vectors, i.e., retrovirus, Sendai virus, and episomal vectors, and compared genome-wide DNA methylation profiles among them. Although comparison of aberrant methylation revealed that iPSCs generated by Sendai virus vector have lowest number of aberrant methylation sites among the three vectors, the iPSCs generated by non-integrating methods did not show vector-specific aberrant methylation. However, the differences between the iPSC lines were determined to be the number of random aberrant hyper-methylated regions compared with embryonic stem cells. These random aberrant hyper-methylations might be a cause of the differences in the properties of each of the iPSC lines.

overall_design:
we generated genetically matched human iPSCs from menstrual blood cells by using three kinds of vectors, i.e., retrovirus, Sendai virus, and episomal vectors, and compared genome-wide DNA methylation profiles among them.
Bisulphite converted DNA were hybridised to the Illumina Infinium Human Methylation450K Beadchip

first: Koichiro

last: Nishino

first: Yoshikazu

last: Arai

first: Ken

last: Takasawa

first: Masashi

last: Toyoda

first: Mayu

last: Yamazaki-Inoue

first: Tohru

last: Sugawara

first: Hidenori

last: Akutsu

last: Nishimura

first: Manami

last: Ohtaka

first: Mahito

last: Nakanishi


title: A GENETIC, GENOMIC, AND COMPUTATIONAL RESOURCE FOR EXPLORING NEURAL CIRCUIT FUNCTION

status: Public on Aug 05 2018

city: Bethesda

first: Fred

middle: P.

last: Davis

state: MD

address: 9000 Rockville Pike

department: NIAMS

institute: NIH

summary: The anatomy of many neural circuits is being characterized with increasing resolution, but their molecular properties remain mostly unknown. Here, we characterize gene expression patterns in distinct neural cell types of the Drosophila visual system using genetic lines to access individual cell types, the TAPIN-seq method to measure their transcriptomes, and a probabilistic method to interpret these measurements. We used these tools to build a resource of high-resolution transcriptomes for 100 driver lines covering 67 cell types. Combining these transcriptomes with recently reported connectomes helps characterize how information is transmitted and processed across a range of scales, from individual synapses to circuit pathways. We describe examples that include identifying neurotransmitters, including cases of co-release, generating functional hypotheses based on receptor expression, as well as identifying strong commonalities between different cell types.

overall_design: 266 RNA-seq samples including 242 nuclear RNA-seq libraries prepared from specific cell types using INTACT/TAPIN, 8 samples dissected from the optic lobe, and 16 control libraries to characterize the INTACT/TAPIN protocols.

middle: P

first: Aljoscha

last: Nern

first: Serge

last: Picard

first: Michael

middle: B

last: Reiser

first: Gerald

last: Rubin

first: Sean

last: Eddy

first: Gilbert

middle: L

last: Henry


title: Adjusting for batch effects in DNA methylation microarray data, a lesson learned

status: Public on Jul 01 2018

city: Vancouver

first: Wendy

last: Robinson

state: BC

address: 950 W 28th Ave

department: Medical Genetics

institute: University of British Columbia

summary: It is well known, but frequently overlooked, that low- and high-throughput molecular data may contain batch effects, i.e., systematic technical variation. Confounding of experimental batches with the variable(s) of interest is especially concerning, as a batch effect may then be interpreted as a biologically significant finding. An integral step towards reducing false discovery in molecular data analysis includes inspection for batch effects and application of computational tools to reduce this signal if present. In a 30-sample pilot Illumina Infinium HumanMethylation450 (450k array) experiment, we identified two sources of batch effects: array row and chip. Here, we demonstrate two approaches taken to process the 450k data in which an R function, ComBat, was applied to adjust for this non-biological signal. In the “initial analysis”, the application of ComBat to an unbalanced study design resulted in 9,683 and 19,192 significant (FDR<0.05) DNA methylation differences, despite none present prior to correction. Suspicious of this dramatic change, a “revised processing” included changes to our analysis as well as a greater number of samples, and successfully reduced batch effects without introducing false signal. Our work supports conclusions made by an article previously published in this journal: though the ultimate antidote to batch effects is thoughtful study design, every DNA methylation microarray analysis should inspect, assess and, if necessary, adjust for batch effects. The analysis experience presented here can serve as a reminder to the broader community to establish research questions a priori, ensure that they match with study design and encourage communication between technicians and analysts.

overall_design: Full details of this analysis can be found in PMID:XXXXX. 450k data was generated from 30 human placentas randomly distributed within a larger batch of 84 samples run across seven chips. This design maximized cost-effectiveness by allowing several subsets of the 84 samples to be analyzed to address separate research questions. For initial processing, we extracted the data relating only to the 30-sample pilot study (these samples are labelled as initial_processing in the characterisitcs: processing group column). A standard step in our quality control assessment, principal component analysis (PCA), suggested the presence of batch effects (i.e., technical – as opposed to biological – sources of data variation (Leek et al., 2010)) relating to how the samples were dispersed across 450k chips (see details below). We employed ComBat (Leek et al.), an empirical Bayes approach implemented in the R software environment (R Core Team, 2014), to regress out batch effects in the pilot data. After this correction was applied however, we found 9,683 and 19,192 differentially methylated sites (FDR <0.05) in association with our biological variable of interest, while none had been found prior to correction. We were suspicious of this dramatic change and conducted a new analysis utilizing more samples. 29 other placental samples from within the 84-sample batch were included in the revised analysis (samples labelled as revised_processing in the characteristics: processing group column2), to increase the pre-processing sample size from 30 to 59, with a better distribution of samples across chips and rows. This larger group also allowed for the inclusion of a technical replicate to better monitor data processing (PM72r). The Matrix processed values included are those of the 59 samples in the revised analysis. The 30 pilot samples (initial_processing in the characterisitcs: processing group column) were then selected out of the larger group of 59 samples to adress biological questions. A description of the biological analysis can be found in PMID:XXXX.

first: E

last: Price


title: Differences in expression profiling and biomarkers between histological colorectal carcinomas subsets from the serrated pathway

status: Public on Jun 27 2018

city: Valencia

first: Francisco

middle: García

last: García

address: Eduardo Primo Yúfera, 3

department: Bionformatics & Biostatistics Unit

institute: CIPF

summary: Despite recent different molecular classifications for colorectal cancer (CRC) have been proposed, CRCs are currently diagnosed based their histology [Hamilton] and just a few biomarkers are used to determine the most suitable treatment. It is for this reason important to correlate molecular profiling with histological features. This issue is especially critical in the serrated pathway for colorectal carcinogenesis since it is not as clearly discerned as the conventional adenoma-carcinoma. Furthermore, making the immune surveillance awake against tumor is now considered as a breakthrough in cancer treatment and the serrated pathological pathway comprises two CRC subtypes with typical weak (SAC) and abundant (hMSI-H) immune responses. Therefore, it is crucial to characterize the biology of these tumors since no previous studies have compared their molecular signatures.

overall_design: In this study, we used gene expression arrays to investigate differences between two experimental classes for carcinomas: serrated and high-level of microsatellite instability.

first: José

last: García-Solano

first: M

middle: C

last: Turpin

last: García-García

first: Daniel

last: Torres-Moreno

first: Ana

last: Conesa

first: Pablo

last: Conesa-Zamora


title: RNA-seq transcriptional profiling in sciatic nerves from wildtype and Pmp22 transgenic rats during perinatal development

status: Public on Jun 19 2018

city: Tübingen

first: Vikas

last: Bansal

state: BW

address: Otfried Müller Strasse 23

institute: German Center for Neurodegenerative Diseases (DZNE)-Tübingen

summary: The goal of this study was to identify deregulated genes in Schwann cells of Pmp22 transgenic rats in comparison to wildtype rats. Three timepoints in the course of peripheral nerve myelination were chosen (embryonic day [E] 21, perinatal day [P]6  and P18) in order to reveal mechanistic insight into  early pathological processes of Charcot-Marie-Tooth disease 1A (CMT1A).

overall_design: Three perinatal timepoints were chosen (E21, P6, P18) in order to cover the course of peripheral nerve myelination. The sciatic nerves of wildtype and Pmp22 transgenic rats were collected in four biological replicates per timepoint and genotype.

first: Robert

last: Fledrich

first: Stefan

last: Bonn

middle: W

last: Sereda

first: Ruth

last: Stassart


title: Transcriptome analysis of paired luminal breast tumor and para-carcinoma tissues

status: Public on Jun 01 2018

city: Shanghai

first: Wei

last: Sun

address: Dongan Road 270

department: Department of Musculoskeletal Surgery

institute: Fudan University Shanghai Cancer Center

summary: With stringent filtering criteria (fold change>2, p<0.001 and False Discovery Rate (FDR) <0.01), we identified 133 lncRNAs and 370 mRNAs that were the most highly differentially expressed. Of all the lncRNAs, 61 were upregulated, and 72 were downregulated.

overall_design: Twenty one paired luminal breast tumor (ER+) and para-carcinoma RNA samples extracted from fresh frozen tissues were analyzed  using the Affymetrix Human Transcriptome 2.0 Arrays. Array data was processed by Partak genomic suite software.

first: Xiaoen

last: Xu

first: Yizhou

last: Jiang

first: Xi

last: Jin

first: Ping

last: Zhou

first: Yirong

last: Liu

first: Zhiming

last: Shao


title: Cecal mRNA expression in Collaborative Cross Breeding Population

city: Bar Harbor

first: Jason

middle: A

last: Bubier

state: ME

address: 600 Main St

institute: The Jackson Laboratory

summary: The data was used for eQTL analysis of cecum gene expression in the Collaborative Cross Breeding Population.

overall_design:
Total RNA islated from the cecum of the collaborative cross breeding population.
**RAW DATA was not provided due to the Oak Ridge National Laboratory shut down of the mouse program**

first: Elissa

last: Chesler


title: transcriptome expression profiling of cisplatin chemoresistance 5-8F cells

status: Public on Aug 01 2019

city: Guangzhou

first: Jian

last: Zhang

address: 78 Hengzhigang Road, Guangzhou

institute: Affiliated Cancer Hospital & Institute of Guangzhou Medical University

summary: Radiotherapy and adjuvant cisplatin (DDP) chemotherapy are standard administrations applied in the treatment of NPC. However, molecular change and functions of DDP chemo-resistance in nasopharyngeal carcinoma are still poorly understood.

overall_design: Three independent cell-culture replicates from the total population of 5-8F and stable cisplatin chemoresistance 5-8F (5-8F/DDP) cell lines were used to generate total RNA. Total RNA was extracted using Trizol.

first: Yawei

last: Yuan


title: RNA transcriptome sequencing analysis of AGS cells transfected with MFAP2 shRNA or control shRNA

status: Public on May 23 2018

city: Wuhan

first: Lianlian

last: Wu

state: Hubei

address: Jiefang Road 238

department: Department of Gastroenterology, Renmin Hospital of Wuhan University

institute: Wuhan University

summary: An RNA transcriptome sequencing analysis was performed in AGS cells that were transfected with MFAP2 shRNA or control shRNA.

overall_design: mRNA profiles of AGS cells transfected with MFAP2 shRNA or control shRNA.

first: Honggang

last: Yu

first: Qianshan

last: Ding


title: Global hypomethylation mediated changes regulate constitutive PD-L1 expression in melanoma

status: Public on May 24 2018

city: Dunedin

first: Aniruddha

last: Chatterjee

state: Otago

address: 270 Great king Street

department: Pathology

country: New Zealand

institute: University of Otago

overall_design: Refer to individual Series


title: Transcriptomic comparison between human epidermis and human sebaceous glands

status: Public on Apr 30 2018

city: Sophia Antipolis

first: CORINNE

last: MENIGOT

address: 2400 route des colles

institute: GALDERMA R & D

summary: Analysis of gene expression profiling of human epidermis and sebaceous glands. Skin samples were obtained from 5 healthy individuals undergoing plastic surgery

overall_design: Total of 10 chips. 5 healthy volunteers : 1 biopsy per patient

first: Johannes

last: Voegel


title: Transcriptomic profiling of the PhzIR quorum sensing, Gac- and PtrA- regulons of Pseudomonas chlororaphis PA23

status: Public on May 26 2018

city: Winnipeg

first: Teresa

middle: R

last: de Kievit

state: Manitoba

address: 45 Chancellor's Circle

department: Microbiology

institute: University of Manitoba

summary: The biocontrol agent Pseudomonas chlororaphis PA23 protects canola (Brassica napus) against infection by the necrotrophic fungus Sclerotinia sclerotiorum. Production of PA23 secondary metabolites is governed by a complex regulatory pathway that includes the GacA/GacS two component system, the PhzI/PhzR quorum-sensing system, and a novel LysR-type transcriptional regulator, called PtrA. Through RNA-sequencing, transcriptomic profiles of PA23-WT, two quorum sensing-deficient strains, PA23-AHL and PA23-phzR, and regulatory mutants PA23-gacA, PA23-gacS and PA23-ptrA were generated allowing elucidation of the PhzRI, Gac and PtrA regulons of P. chlororaphis PA23.

overall_design: a total of 18 samples: 6 strains: Pseudomonas chlororaphis PA23 Wildtype (control), gacA-, gacS-, ptrA-, phzR- and AHL- deficient strains with 3 biological replicates per strain

first: Nidhi

last: Shah

first: Michael

middle: G

last: Becker

first: Mark

last: Belmonte

first: Dilantha

last: Fernando

last: deKievit


title: Long-acting immune responses including plasma cells and alteration of sebaceous glands cause atrophic scar formation in acne patients

summary: Background: Possible outcomes of acne lesions are atrophic scars which may cause serious physical and psychological distress. Current treatments of post-acne scarring remain difficult and often require invasive procedures. Pathophysiological studies on acne scaring investigated only the first week of papule life.  Objectives: Study the pathophysiology of atrophic acne scar formation to identify molecular and cellular pathways that can lead to new therapies for the prevention of acne scarring.    Methods: Large-scale gene expression profiling of uninvolved acne skin and acne papules of 48 hours and 3 weeks of age, respectively, of both, scar-prone (SP) and non-scar-prone (NSP) patients was performed. Immunohistochemistry techniques were applied to confirm transcriptomics results on the protein and cellular level.  Results: Gene expression and immunohistochemistry analyses showed a very similar immune response in 48 hours-old papules in SP and NSP populations characterized by elevated numbers of T cells, neutrophils and macrophages. However, only in SP patients the immune response persisted in 3 week-old papules, and was characterized by an important infiltrate of B cells. Transient down-modulation of genes related to lipid metabolism was observed in 48 hours-old papules in NSP patients, followed by normalization of gene expression levels after 3 weeks.  In contrast, in SP patients a drastic reduction of lipid metabolizing enzymes was observed in 3 week-old papules, suggesting irreversible modifications. The affected lipid metabolism genes were found preferentially expressed in human sebaceous glands, pointing to a destruction of sebaceous gland structures after 3 weeks of inflammatory remodelling in SP acne patients.

overall_design: Total of 54 chips. 18  Non-scar-prone and Scar-prone patients : 3 biospies per patient: 1 in non-lesional skin (Back), 1 on papule less than 48 H old (Back), 1 on skin with papule of  21 days old (Back).


title: Expression data from MDA-MB-231 breast cancer cells

status: Public on Apr 21 2018

city: Edmonton

first: Marnie

last: Newell

state: AB

address: 4-031 LKS Bldg, University of Alberta

department: Nutrition

institute: University of Alberta

summary:
MDA-MB-231 breast cancer cells were treated with docosahexaenoic acid with or without doxorubicin chemotherapy
Microarrays were used to detail changes in gene expression in the treatments

overall_design: MDA-MB-231 breast cancer cells were treated for 48h with 60uM docosahexaenoic acid  followed by 24 h with 60uM DHA with or without 4.1x10-7 M doxorubicin chemotherapy whereupon RNA was extracted and hybridized on Affymetrix microarrays.

first: Catherine

last: Field


title: Reprogrammed marrow adipocytes: an unexpected role in the genesis of myeloma-induced bone disease

status: Public on Apr 18 2018

city: Houston

first: Jing

last: Yang

state: Texas

address: 7455 Fannin

institute: MD Anderson Cancer Center

summary: Multiple myeloma is characterized by osteolytic lesions caused by osteoclast-mediated bone resorption and reduced bone formation. A unique feature of myeloma is a failure of bone healing following successful treatment. Identification of increased adipocyte numbers in marrow of successfully treated patients led us to demonstrate that normal marrow adipocytes, when co-cultured with myeloma cells, are reprogrammed and produce adipokines that activate osteoclastogenesis and suppress osteoblastogenesis. These adipocytes have reduced expression of peroxisome proliferator-activated receptor γ (PPARγ) mediated by recruitment of polycomb-repressive complex 2 (PRC2) via specificity protein 1, which modifies PPARγ promoter methylation at trimethyl lysine-27 histone H3. We confirmed the importance of PPARγ methylation by demonstrating that adipocyte-specific knockout of EZH2, a member of the PRC2, prevents adipocyte reprogramming and reverses bone changes in vivo. These results define a heretofore unrecognized role for adipocytes in genesis of myeloma-associated bone disease and that reversal of adipocyte reprogramming has therapeutic implications.

overall_design: Normal adipocytes (nADs) isolated from normal bone marrow samples (n = 6) and the marrow of myeloma patients in complete remission (CR Pt; n = 12), Then total RNA was extracted and used for comparison by gene expression profiling.

first: Huan

last: Liu

first: Jin

last: He

first: Su

last: Koh

first: Yuping

last: Zhong

first: Zhiqiang

last: Wang

first: Yujin

first: Zongwei

last: Li

first: Bjorn

middle: T

last: Tam

first: Pei

last: Lin

first: Ken

middle: H

last: Young

first: Min

last: Xiao

first: Behrang

last: Amini

last: Starbuck

first: Hans

last: Lee

first: Nora

middle: M

last: Navone

first: Richard

last: Davis

first: Qiang

last: Tong

first: P

last: Bergsagel

last: Hou

first: Qing

last: Yi

first: Robert

middle: Z

last: Orlowski

middle: F

last: Gagel


title: Transcriptional Modulation of Human Endogenous Retroviruses in Primary CD4+ T Cells Following Vorinostat Treatment

status: Public on May 01 2018

city: Cambridge

first: Cory

middle: Haley

last: White

state: MA

address: 320 Bent St

department: DAGS

institute: Merck

summary:
Purpose: In an HIV cure setting, Vorinostat may provide the “shock” capable of flushing HIV out of the persistent reservoir, while antiretroviral therapy is used to prevent new infections.  However, this drug may modulate the expression of human endogenous retroviruses (HERVs).  This study demonstrates significant modulation of HERVs and suggests that they should be considered as off-target effects of this drug treatment.
Methods: Peripheral blood mononuclear cells were collected from 4 healthy donors.  Naive CD4 T cells were isolated and utilized to assess HERV dysregulation after treatment with Vorinostat.  Cells were collected for study and exposed to a dose of Vorinostat (10uM dose over a 24 hour period).  After this, RNA was extracted from cells and their untreated paired counterparts for deep sequencing by Expression Analysis. Sequence reads that passed quality filters were mapped to the HERVd reference database using Bowtie and counted using HTSeq.  Any HERV which did not achieve at least 1 count per million mapped and counted reads in at least 4 samples was discarded.  Differential expression was performed upon the filtered dataset with edgeR and using TMM normalization.
Results: Using an custom built data analysis pipeline, ~100 million reads per sample were mapped to the HERVd reference database and identified 10784 distinct dysregulated elements Bowtie/HTSeq workflow. Differential expression analysis was performed between vorinostat treated and untreated conditions which demonstrated 2102 dysregulated HERV elements with 1007 downregulated and 1095 upregulated (FDR < 0.05) with EdgeR.  Results were further subset with a log2FC ± 3 which resulted in 451 upregulated and 363 downregulated HERV elements from 81 and 82 distinct families respectively.  HERV elements from the LTR12 family were by far the most dramatically upregulated in family frequency and fold change magnitude.  Further confirmation with droplet digital PCR confirmed upregulation of LTR12 elements and demonstrated an exponential dose response curve with HERV expression found at even moderate doses (334nM) of vorinostat treatment.
Conclusions: This study represents the first detailed analysis of HERV dysregulation following vorinostat treatment using the untargeted approach of total RNA-Seq.  These results demonstrate that vorinostat dysregulates multiple HERV families with a propensity to upregulate members of the LTR12 HERV family.  This study also provides a methodology to analyze HERV dysregulation in future treatments with vorinostat or other drugs by providing a mechanism to choose primer and probe sets which will properly represent HERV dysregulation as expression across an HERV is not uniform or continuous.  Finally, this work suggests that HERV dysregulation by vorinostat treatment should be considered an off-target effect of this drug and HERV elements, such as LTR12, should be monitored as biomarkers during shock and kill clinical trials with HDAC inhibitors and that trial subjects should be screened to explore further HIV:HERV interactions.

overall_design: Profiles of 4 healthy donors in 2 conditions (8 paired total samples) were generated with deep sequencing by Expression Analysis.

first: Nadejda

last: Beliakova-Bethell

first: Steven

last: Lada

first: Michael

middle: S

last: Breen

first: Gkikas

last: Magiorkinis

first: Douglas

middle: D

last: Richman

first: John

last: Frater

first: Christopher

last: Woelk