MAGE-TAB Version 1.1 Investigation Title RNA-seq of coding RNA from tissue samples of 122 human individuals representing 32 different tissues Experimental Design organism part comparison design Experimental Design Term Source REF EFO Experimental Design Term Accession Number EFO_0001750 Experimental Factor Name organism part Experimental Factor Type organism part Experimental Factor Term Source REF EFO Experimental Factor Term Accession Number EFO_0000635 Person Last Name Hallström Person First Name Björn Person Mid Initials M Person Email bjorn.hallstrom@gmail.com Person Phone Person Fax Person Affiliation Science for Life Laboratory, Royal Institute of Technology, Stockholm Person Address Person Roles data analyst;investigator;submitter Person Roles Term Source REF Person Roles Term Accession Number Quality Control Type Quality Control Term Source REF Quality Control Term Accession Number Replicate Type Replicate Term Source REF Replicate Term Accession Number Normalization Type Normalization Term Source REF Normalization Term Accession Number Date of Experiment 2014-05-04 Public Release Date 2015-01-14 PubMed ID 5613900 26694548 27699219 Publication DOI 10.1126/science.1260419 10.1371/journal.pone.0145301 None Publication Author List Uhlén M, Fagerberg L, Hallström BM, Lindskog C, Oksvold P, Mardinoglu A, Sivertsson Å, Kampf C, Sjöstedt E, Asplund A, Olsson I, Edlund K, Lundberg E, Navani S, Szigyarto CA, Odeberg J, Djureinovic D, Takanen JO, Hober S, Alm T, Edqvist PH, Berling H, Tegel H, Mulder J, Rockberg J, Nilsson P, Schwenk JM, Hamsten M, von Feilitzen K, Forsberg M, Persson L, Johansson F, Zwahlen M, von Heijne G, Nielsen J, Pontén F Habuka M, Fagerberg L, Hallström BM, Pontén F, Yamamoto T, Uhlen M. Djureinovic D, Hallström BM, Horie M, Mattsson JS, La Fleur L, Fagerberg L, Brunnström H, Lindskog C, Madjar K, Rahnenführer J, Ekman S, Ståhle E, Koyi H, Brandén E, Edlund K, Hengstler JG, Lambe M, Saito A, Botling J, Pontén F, Uhlén M, Micke P. Publication Title Proteomics. Tissue-based map of the human proteome The Urinary Bladder Transcriptome and Proteome Defined by Transcriptomics and Antibody-Based Profiling. Profiling cancer testis antigens in non-small-cell lung cancer. Publication Status in preparation Publication Status Term Source REF Publication Status Term Accession Number Experiment Description RNA-seq was performed of tissue samples from 122 human individuals representing 32 different tissues in order to study the human tissue transcriptome. This submission contains 27 new samples and the data from E-MTAB-1733. Protocol Name P-MTAB-33472 P-MTAB-33473 P-MTAB-40601 P-MTAB-40602 P-MTAB-40600 P-MTAB-33470 P-MTAB-33471 Protocol Type nucleic acid library construction protocol nucleic acid sequencing protocol nucleic acid library construction protocol nucleic acid extraction protocol nucleic acid sequencing protocol growth protocol nucleic acid extraction protocol Protocol Term Source REF EFO EFO EFO EFO EFO EFO EFO Protocol Term Accession Number EFO_0004184 EFO_0004170 EFO_0004184 EFO_0002944 EFO_0004170 EFO_0003789 EFO_0002944 Protocol Description Illumina Truseq RNA v2 Clustered on cBot and sequenced on Illumina HiSeq 2000/2500 according to manufacturers instructions. Libraries were constructed using the TruSeq v 2 kit, with poly-A-enrichment or with the TruSeq Stranded kit (see library strand annotation). The tissue was homogenized mechanically using a 3 mm steel grinding ball (VWR). Total RNA was extracted from cell lines and tissue samples using the RNeasy Mini Kit (Qiagen, Hilden, Germany) according to the manufacturers instructions. The extracted RNA samples were analyzed using either an Experion automated electrophoresis system (Bio-Rad Laboratories, Hercules, CA, USA) with the standard-sensitivity RNA chip or an Agilent 2100 Bioanalyzer system (Agilent Biotechnologies, Palo Alto, USA) with the RNA 6000 Nano Labchip Kit. Only samples of high-quality RNA (RNA Integrity Number 7.5) were used in the following mRNA sample preparation for sequencing. 2x100 bp paired end sequencing The use of human tissue samples was approved by the Uppsala Ethical Review Board (Reference #2011/473). Tissues samples, collected within the infrastructure of an established biobank, were embedded in Optimal Cutting Temperature (O.C.T.) compound and stored at -80C. A hematoxylin-eosin (HE) stained frozen section (4um) was prepared from each sample using a cryostat and the CryoJane Tape-Transfer System (Instrumedics, St. Louis, MO, USA). Each slide was examined by a pathologist to ensure proper tissue morphology. Three sections (10um) were cut from each frozen tissue block and collected into a tube for subsequent RNA extraction. The tissue was homogenized mechanically using a 3 mm steel grinding ball (VWR). Total RNA was extracted from cell lines and tissue samples using the RNeasy Mini Kit (Qiagen, Hilden, Germany) according to the manufacturers instructions. The extracted RNA samples were analyzed using either an Experion automated electrophoresis system (Bio-Rad Laboratories, Hercules, CA, USA) with the standard-sensitivity RNA chip or an Agilent 2100 Bioanalyzer system(Agilent Biotechnologies, Palo Alto, USA) with the RNA 6000 Nano Labchip Kit. Only samples of high-quality RNA (RNA Integrity Number 7.5) were used in the following mRNA sample preparation for sequencing. Protocol Parameters Protocol Hardware Illumina HiSeq 2000 Illumina HiSeq 2500 Protocol Software Protocol Contact Term Source Name EFO ArrayExpress Term Source File http://www.ebi.ac.uk/efo/ http://www.ebi.ac.uk/arrayexpress/ Term Source Version 2.38 SDRF File E-MTAB-2836.sdrf.txt Comment [Submitted Name] RNA-seq of coding RNA from tissue samples of 122 human individuals representing 32 different tissues. Comment [SecondaryAccession] ERP006650 Comment [SequenceDataURI] http://www.ebi.ac.uk/ena/data/view/ERR579122-ERR579155 Comment [AEExperimentType] RNA-seq of coding RNA Comment[ArrayExpressAccession] E-MTAB-2836