Fwd: Samples for RNAseq-E.D Vagelis Harokopos Fri, Feb 12, 2021 at 12:20 PM To: Martin Reczko Cc: Pantelis Hatzis , Vagelis Rinotas , Eleni Douni , Αnthi Kolokotroni Dear Martin, Could you please proceed with the analysis of Dr Dounis lab, Mouse 3'RNAseq samples. All the information can be found in the attachments Thank you Vaggelis ---------- Forwarded message --------- From: Αnthi Kolokotroni Date: Thu, Feb 11, 2021 at 5:03 PM Subject: Samples for RNAseq-E.D To: Vagelis Harokopos , Pantelis Hatzis Cc: Vagelis Rinotas , Eleni Douni Καλησπέρα σας, Επισυνάπτω το αρχείο με τα στοιχεία των δειγμάτων RNA . Για οποιαδήποτε περαιτέρω πληροφορία ή διευκρίνιση, με ενημερώνετε. Κολοκοτρώνη Ανθή -- Kolokotroni Anthi MSc, PhD student Institute of Immunology, Douni Lab Biomedical Sciences Research Center "Al. Fleming" 34 Fleming Street 16672 Vari-Greece Tel: +30(210)9656310 ext. 205 -- Vaggelis Harokopos, PhD ------------------------------------------------------------------------- Genomics Facility BSRC Al. Fleming 34 Fleming str • Vari • Athens • 16672 • Greece T +30 210 9656310, int. 221 harokopos@fleming.gr • genomics@fleming.gr www.fleming.gr/facilities/genomics Principal Investigator: Eleni Douni Scientist Name: Anthi Kolokotroni Experiment Name: Mammary gene expression analysis e-mail: douni@fleming.gr, kolokotroni@fleming.gr, rinotas@fleming.gr Department: Bioinnovation Address: Click here to enter text. Tel: 2109656310-205 or 150 Fax: Click here to enter text. Sequencing Type: 3'RNAseq *DNAseq/Other: Please specify (i.e. Fragment DNA, ChIPseq, Peptides, PCR products) Brief Experiment Description & Comments Gene expression analysis from mammary tissue between TgRANKL/RANKLtles/tles and TgRANKL/RANKLtles/tles +Denosumab mice at the age of 6 months , after MPA/DMBA administration (4 female TgRANKL/RANKLtles/tles and 4 female TgRANKL/RANKLtles/tles +Denosumab biological replicants) RANKL/RANKLtles/tles is a humanized model that overexpress human RANKL transgene and non functional mouse RANKL. Condition 1: TgRANKL/RANKLtles/tles control group, Condition 2: TgRANKL/RANKLtles/tles Denosumbab treated group Barcode Name Sample Bases >=Q20 Bases Reads Mean Read Length Groups ION463 IonXpress_012 ED3R12_1001 460,725,033 354,622,646 3,326,911 138 bp Cond1 IonXpress_013 ED3R13_1012 1,610,313,375 1,217,908,919 11,158,486 144 bp Cond2 IonXpress_014 ED3R14_1013 1,164,594,080 887,994,898 8,179,719 142 bp Cond2 IonXpress_015 ED3R15_1020 460,225,012 352,806,074 3,424,808 134 bp Cond2 IonXpress_016 ED3R16_1030 778,552,860 593,540,491 5,647,769 137 bp Cond2 ION464 IonXpress_009 ED3R9_961 570,696,589 432,075,104 3,912,573 145 bp Cond1 IonXpress_010 ED3R10_993 538,743,187 408,201,997 3,889,095 138 bp Cond1 IonXpress_011 ED3R11_999 791,443,792 605,374,344 5,533,762 143 bp Cond1 #@ Dear all, at http://genomics-lab.fleming.gr/fleming/EDlab/run464/metaseqR2_run464 you will find the metaseqR2 [1] differential gene expression analysis using the contrast Cond1_vs_Cond2 (note the used naming convention: in A_vs_B, A is the reference). In the "Results" section, there are links to download the diff. expr. results after the "DEG table", "Download the whole result list for Cond1_vs_Cond2." 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. (2015)