http://genomics-lab.fleming.gr/fleming/Stathopoulos/lung/www/GSR1-FULA1.bam http://genomics-lab.fleming.gr/fleming/Stathopoulos/lung/www/R_2015_05_14_12_15_30_user_ION-184-DrStathopoulos_150514_NKRNAseq_GSR1-4.GSR1-FULA1.IonXpressRNA_004.fastq Dear Mario, at http://genomics-lab.fleming.gr/fleming/Stathopoulos/lung/wwwFELA you'll find the bam files for the FELA samples: GSR15-FELA1.bam.sorted.bam GSR16-FELA12.bam.sorted.bam The samples and the number of reads obtained are: GSR15-FELA1 30830171 GSR16-FELA12 36263111 I'll add the diff. exp. analysis. Best wishes, Martin /data/images/proton2/run359/wwwFELA/ So in total, we will have data on FULA cells (n=3), BULA cells (n=2), BELA cells (n=2), FELA cells (n =2), CULA cells (n=1), and benign tracheal cells (n=2, one from each FVB and BALB/c strains, samples FVB Trachea IonXpressRNA_015 and Balb/c IonXpressRNA_014_rawlib.basecaller). I) Each of the five different tumor cell categories compared with benign samples by unpaired student's t-test and a cutoff of 2. the.contrasts.1 <- c( "Benign_vs_FELA" ) the.path="/data/images/proton/StathopoulosLab/lung/www" metaseqr( sample.list=file.path(the.path,"targetsFELA.txt"), contrast=the.contrasts.1, annotation="download", org="mm10", refdb="refseq", normalization="deseq", statistics="deseq", fig.format=c("png","pdf"), export.where=file.path(the.path,"metaseqr_StathopoulosLab_lung"), restrict.cores=0.5, qc.plots=c( "mds","biodetection","countsbio","saturation","readnoise","filtered", "correl","pairwise","boxplot","gcbias","lengthbias","meandiff", "meanvar","biodist","volcano","deheatmap" ), exon.filters=NULL, gene.filters=list( length=list( length=500 ), avg.reads=list( average.per.bp=100, quantile=0.25 ), expression=list( median=TRUE, mean=FALSE, quantile=NA, known=NA, custom=NA ), biotype=get.defaults("biotype.filter","hg19") ), pcut=0.05, export.what=c("annotation","p.value","adj.p.value","fold.change", "counts","flags"), export.scale=c("log2","rpgm"), export.values="normalized", export.counts.table=TRUE, report.top=0.05 ) II) A comparison by strain, ie, FULA and FELA cells (n=5) compared with BULA and BELA cells (n=4) of all genes and of only the genes emerging from I. III) A comparison by carcinogen, ie, FULA and BULA and CULA cells (n=6) compared with FELA and BELA cells (n=4) of all genes and of only the genes emerging from I. #@ 17072017 Fela cell line seq, Kpm files index Martin Reczko Mon, Jul 17, 2017 at 8:09 PM To: "Pepe, Mario" Cc: Vagelis Harokopos , "Georgios Stathopoulos, Dr." Dear Mario, at http://genomics-lab.fleming.gr/fleming/Stathopoulos/run326tracks you will find sorted bam and bai files for the samples. The commands to produce this are like: samtools sort GSR14_KPM4.bam GSR14_KPM4.sorted samtools index GSR14_KPM4.sorted.bam Being 'at the end' of the pipeline, can't help you concerning the Fela samples. Best wishes, Martin #@ Dear Dr the analysis of your RNAseq experiment has finished. The samples and the number of reads obtained are: GSR1-FULA1 32542150 GSR4-BULA1 35829804 GSR5-BULA2 24400838 GSR6-BELA1 24942622 GSR2-FULA1 31266132 GSR7-BELA2 36593470 GSR3-FULA3 29280708 GSR8-FUBtrachea 46944053 GSR9-mTECsBalbc 46238995 GSR10-P53FllFl 23824156 At http://genomics-lab.fleming.gr/cgi-bin/hgTracks?db=mm10&hubUrl=http://genomics-lab.fleming.gr/fleming/Stathopoulos/lung/www/hub.txt you will find tracks for all samples integrated in our UCSC genome browser mirror. These tracks are sampled to smallest library (GSR10-P53FllFl with 23824156 reads). At http://genomics-lab.fleming.gr/fleming/Stathopoulos/lung/www/metaseqr_StathopoulosLab_lung/index.html you will find the metaseqR [1] differential gene expression analysis using the contrasts "Benign_vs_FULA", "Benign_vs_BULA", "Benign_vs_BELA", "Benign_vs_CULA". At http://genomics-lab.fleming.gr/fleming/Stathopoulos/lung/www/metaseqr_StathopoulosLab_lung_strain/index.html you will find the metaseqR differential gene expression analysis using the contrast "BULAandBELA_vs_FULA". At http://genomics-lab.fleming.gr/fleming/Stathopoulos/lung/www/metaseqr_StathopoulosLab_lung_carcinogen./index.html you will find the metaseqR differential gene expression analysis using the contrast "FULAandBULAandCULA_vs_BELA". Note the used naming convention for reporting differential expression: in A_vs_B, A is always the reference. The differential gene expression analysis can be downloaded in each report in the section "Results", "Download the whole result list for "... If you select significantly deregulated genes, please use the column J = FDR_edger and select genes with FDR_edger <= 0.05 . FDR_edger is the p-vaule adjusted for multiple testing. With best regards, Martin Reczko [1] Moulos P and Hatzis P “Systematic integration of RNA-Seq statistical algorithms for accurate detection of differential gene expression patterns.” Nucl. Acids Res. (2014) doi: 10.1093/nar/gku1273 http://nar.oxfordjournals.org/content/early/2014/12/01/nar.gku1273.abstract. #@ From: Pepe, Mario [mailto:mario.pepe@helmholtz-muenchen.de] Sent: Friday, March 17, 2017 1:20 PM To: Vagelis Harokopos Cc: Georgios Stathopoulos Subject: RNAseq Lung AdenoCarcinoma cell lines Dear Dr Harokopos I am Mario Pepe, PhD student in Stathopoulos´s lab. I write to your attention to kindly ask some informations. The last time that DR Stathopoulos write to you, it was about to ask to analyze our LA samples for the differential gene expression. The samples involved were: FULA 1 IonXpressRNA_004 BULA 1 IonXpressRNA_011 BULA 2 IonXpressRNA_012 BELA 1 IonXpressRNA_013 FULA 2 IonXpressRNA_006 BELA 2 IonXpressRNA_014 FULA 3 IonXpressRNA_010 FVB Trachea IonXpressRNA_015 CULA IonXpress_016 Balb/c IonXpressRNA_014_rawlib.basecaller. I would ask if you have any news about it. Also DR Stathopoulos would knows about the sequencing status og the cell line FELA1 and FELA2. Thanks for your time and your attention. I look forward for your reply Best Regards Mario Pepe Helmholtz Zentrum München Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH) Ingolstädter Landstr. 1 85764 Neuherberg www.helmholtz-muenchen.de Aufsichtsratsvorsitzende: MinDir'in Bärbel Brumme-Bothe Geschäftsführer: Prof. Dr. Günther Wess, Heinrich Baßler, Dr. Alfons Enhsen Registergericht: Amtsgericht München HRB 6466 USt-IdNr: DE 129521671 #@ Stathopoulos, Georgios, Dr. Mon, Feb 13, 2017 at 3:47 PM To: harokopos , Martin Reczko Cc: "Pepe, Mario" , Nikolaos Kanellakis Dear Vaggelis and Martin, We would be grateful if you could also analyze in a similar way you looked at our mesothelioma cell lines, also our lung adenocarcinoma cell lines. We would be very much interested in their gene expression profile compared with tracheal epithelial cells. The samples already sequenced are: FULA 1 IonXpressRNA_004 run184/R_2015_05_14_12_15_30_user_ION-184-DrStathopoulos_150514_NKRNAseq_GSR1-4.GSR1-FULA1.IonXpressRNA_004.fastq BULA 1 IonXpressRNA_011 run184/R_2015_05_14_12_15_30_user_ION-184-DrStathopoulos_150514_NKRNAseq_GSR1-4.GSR4-BULA1.IonXpressRNA_011.fastq BULA 2 IonXpressRNA_012 run185/R_2015_05_15_12_20_11_user_ION-185-DrStathopoulos_150515_NKRNAseq_GSR5-6.GSR5-BULA2.IonXpressRNA_012.fastq BELA 1 IonXpressRNA_013 run185/R_2015_05_15_12_20_11_user_ION-185-DrStathopoulos_150515_NKRNAseq_GSR5-6.GSR6-BELA1.IonXpressRNA_013.fastq FULA 2 IonXpressRNA_006 run186/R_2015_05_21_11_36_50_user_ION-186-DrStathopoulos_150521_NKRNAseq_GSR2-7.GSR2-FULA1.IonXpressRNA_006.fastq BELA 2 IonXpressRNA_014 run186/R_2015_05_21_11_36_50_user_ION-186-DrStathopoulos_150521_NKRNAseq_GSR2-7.GSR7-BELA2.IonXpressRNA_014.fastq FULA 3 IonXpressRNA_010 run187/R_2015_05_22_13_04_56_user_ION-187-DrStathopoulos_150522_NKRNAseq_GSR3-8.GSR3-FULA3.IonXpressRNA_010.fastq FVB Trachea IonXpressRNA_015 run187/R_2015_05_22_13_04_56_user_ION-187-DrStathopoulos_150522_NKRNAseq_GSR3-8.GSR8-FUBtrachea.IonXpressRNA_015.fastq CULA IonXpress_016 run277/R_2016_03_08_13_22_40_user_IONAS-277-ITlab_DrStath_160308_ChIP-RNA_ITC112-113_GSR10.GSR10-P53FllFl.IonXpress_016.fastq Balb/c IonXpressRNA_014_rawlib.basecaller run268/R_2016_01_29_13_01_36_user_IONAS-268-GSR9_GSkP4-5_GKLex1-4_160129.GSR9-mTECsBalbc.IonXpressRNA_014.fastq The samples pending are FELA1 and FELA2. So in total, we will have data on FULA cells (n=3), BULA cells (n=2), BELA cells (n=2), FELA cells (n =2), CULA cells (n=1), and benign tracheal cells (n=2, one from each FVB and BALB/c strains, samples FVB Trachea IonXpressRNA_015 and Balb/c IonXpressRNA_014_rawlib.basecaller). The names of these cell lines have 4 parts: The first letter indicates the mouse strain of origin (C, C57BL/6; F, FVB; B, Balb/c), the second the carcinogen used (U, urethane; E, DEN), LA denotes lung adenocarcinoma, and the number their series of derivation from different mice. The comparisons of gene expression we want to do are: I) Each of the five different tumor cell categories compared with benign samples by unpaired student's t-test and a cutoff of 2. II) A comparison by strain, ie, FULA and FELA cells (n=5) compared with BULA and BELA cells (n=4) of all genes and of only the genes emerging from I. III) A comparison by carcinogen, ie, FULA and BULA and CULA cells (n=6) compared with FELA and BELA cells (n=4) of all genes and of only the genes emerging from I. Let me know where we stand with FELA sequencing and whether these analyses are doable. Thanks in advance, G Georgios T. Stathopoulos, MD PhD Research Group Leader, Lung Carcinogenesis Comprehensive Pneumology Center (CPC) and Institute for Lung Biology and Disease (iLBD) Ludwig-Maximilians-Universität, Asklepios Fachkliniken München-Gauting und Helmholtz Zentrum München A member of the German Center for Lung Research (Deutsche Zentrum für Lungenforschung, DZL) Max-Lebsche-Platz 31, 81377 München [T] +49 (89) 3187 4846 [F] +49 (89) 3187 4661 [E] stathopoulos@helmholtz-muenchen.de [U] http://www.helmholtz-muenchen.de/ilbd From: "harokopos" To: "Anthi Krontira" Cc: "Stathopoulos, Georgios, Dr." , "Georgios Stathopoulos" , "Martin Reczko" Sent: Friday, January 13, 2017 4:17:32 PM Subject: RE: RNAa απο εργ Γ.ΣΤΑΘΟΠΟΥΛΟΥ ΠΑΤΡΑ Αγαπητή Ανθή, Παρακάτω σου στέλνω συνημμένα όλα τα link που μου έστειλε o βιοπληροφορικός μας, Marn Reczko, όπου θα βρεις τα raw data, την ανάλυση και τα tracks των τελευταίων RNAseq σας. at http://genomics-lab.fleming.gr/fleming/Stathopoulos/run326/ (credentials: User name: Stathopoulos Password: StathopoulosLab) are the bam files for runs 325 and 326: GSR11_wt1.bam GSR12_KPM1.bam GSR13_KPM3.bam GSR14_KPM4.bam and the QC-reports: Auto_user_IONAS-325-DrStath_161220_RNAseq_GSR11-12_425.pdf Auto_user_IONAS-326-DrStath_161220_RNAseq_GSR13-14_426.pdf At http://genomics-lab.fleming.gr/fleming/Stathopoulos/run326/metaseqr_WT_vs_KPM/index.html