{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Amelie Baud"],"organism":["Mus musculus"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-5276"],"description":["This experiment was carried out to determine whether social genetic effects (also called indirect genetic effects) contribute to variation in gene expression. That is to say, are differences in gene expression attributable to genetic differences in cage mates?  The block factor refers to the order of mouse sacrificing within each cage."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Sequencing - All libraries were multiplexed in one 85-plex and sequenced in 5 HiSeq 2500 rapid runs to obtain paired-end, 51 bp reads.","Library Construction - Libraries were prepared according to the dUTP strand-specific protocol.","Sample Treatment - Mice were co-housed with a single cage mate from either the C57BL6/J or DBA/2J strain from weaning (3 weeks old) to sacrifice (11 weeks old).","Nucleic Acid Extraction - Total RNA was extracted using a Qiagen Qiacube and RNeasy mini kit according to the manufacturers protocols and was loaded on a 96-well plate, 17 with samples randomly allocated to wells, for shipment to the sequencing centre."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Data Transformation - High quality alignments were selected using the following criteria: both reads of the pair had to uniquely map to the same chromosome and within 2.3 Mb of each other (length of the longest gene). Expression levels were quantified at the gene level using HTSeq (version 0.6.1), considering high quality alignments only and UCSC annotations (GRCm38/mm10).","Sequence Alignment - We used SNPs and indels identified in D2 (Sanger Mouse Project, files mgp.v3.snps.rsIDdbSNPv137.vcf and mgp.v3.indels.rsIDdbSNPv137.vcf, both on GRCm38) to construct a D2 genome and the corresponding gene annotation file using the software SeqNature (version 1.2). Reads were aligned using Tophat (Tophat2 version 2.0.11, Bowtie version 2.2.2.0, and Samtools version 0.1.19.0), considering either the B6 genome (GRCm38) or the D2 genome."],"omics_type":["Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["Illumina HiSeq 2500"],"study_type":["RNA-seq of coding RNA"],"species":["Mus musculus"],"pubmed_title":["Genetic variation in the social environment contributes to health and disease"],"pubmed_authors":["Amelie Baud","Amelie Baud, Megan K. Mulligan, Francesco Paolo Casale, Jesse F. Ingels, Casey J. Bohl, Jacques Callebert, Jean-Marie Launay, Jon Krohn, Andres Legarra, Robert W. Williams, Oliver Stegle"],"additional_accession":[]},"is_claimable":false,"name":"RNA-seq of prefrontal cortex samples from 11-week old C57BL6/J and DBA/2J mice housed either with a mouse of the same strain or a mouse of the other strain","description":"This experiment was carried out to determine whether social genetic effects (also called indirect genetic effects) contribute to variation in gene expression. That is to say, are differences in gene expression attributable to genetic differences in cage mates?  The block factor refers to the order of mouse sacrificing within each cage.","dates":{"release":"2016-12-07T00:00:00Z","modification":"2022-01-31T19:25:02.986Z","creation":"2022-01-31T19:25:02.986Z"},"accession":"E-MTAB-5276","cross_references":{"ENA":["ERP020466"],"EFO":["EFO_0002944","EFO_0004170","EFO_0004917","EFO_0003816","EFO_0003738","EFO_0003969","EFO_0004184"]}}