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Sample GSM1649961

Query DataSets for GSM1649961

Status

Public on Jul 07, 2015

Title

P8 Female F1i sample 3

Sample type

SRA

Source name

P8 Female F1i cerebellum

Organism

Mus musculus

Characteristics

strain: C57Bl/6JxCast/EiJ hybrid
gender: female
developmental stage: postnatal day 8
tissue: cerebellum

Treatment protocol

Animals were kept in standard housing conditions at room temperature and on a reverse 12-h light/dark cycle. Food and water were available ad libitum.

Growth protocol

F1 hybrids were generated by reciprocally crossing C57Bl/6J and Cast/EiJ mouse strains

Extracted molecule

polyA RNA

Extraction protocol

RNA was isolated from tissues of interest using the Trizol reagent (Life Technologies) according to the manufacturer instructions and further purified using DNase I digestion and the RNeasy kit (Qiagen).
3ug of total RNA were used for preparing libraries according to the Illumina Tru-Seq RNA sample preparation protocol. Average fragment size of 250 bp was selected
Each RNA-seq library was sequenced on an individual HiSeq200 lane generating 59bp single-end reads

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina HiSeq 2000

Description

FF1i3_P8
processed data files: MF.A.P8.P60.allele.csv,F.X.P8.P60.allele.csv

Data processing

Quality and adapter trimming was performed using the Trim Galore utility (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore) with stringency level 3.
Each C57Bl/6J×Cast/EiJ hybrid RNA-seq sequenced library was mapped to the C57Bl/6J, Cast/EiJ diploid genome and transcriptome splice junctions using STAR RNA-seq aligner (Dobin et al., 2013) allowing a maximum of three mismatches.
Cutom code was used to transfor bam files from C57Bl/6J×Cast/EiJ genomic coordinates to C57Bl/6J×Cast/EiJ transcriptomic coordinates where reads not mapping to any transcript were removed.
Transcript expression levels were estimated using MMSEQ (Turro et al., 2011).
Trannscripts with considerable read-sharing were collapsed as described in the manuscript.
FPKM units were converted to TPM units and an the low expression cutoff was empirically determined as described in the manuscript
Genome_build: C57Bl/6J and Cast/EiJ single nucleotide polymorphisms and indels (obtained from the Mouse Genome Project: ftp://ftpmouse. sanger.ac.uk/REL-1303-SNPs_Indels-GRCm38) were incorporated into the Mus musculus GRCm38 reference genome sequence to obtain a C57Bl/6J, Cast/EiJ diploid genome.
Supplementary_files_format_and_content:

MF.A.P8.P60.allele.csv: A table which rows are autosomal transcript IDs and columns are for each sample: (1) MMSEQ's posterior mean of log(paternal TPM), (2) MMSEQ's posterior variance of log(paternal TPM), (3) MMSEQ's posterior mean of log(maternal TPM), (4) MMSEQ's posterior variance of log(maternal TPM), (5) MMSEQ's posterior mean of log(paternal TPM) - log(maternal TPM), (6) MMSEQ's posterior variance of log(paternal TPM) - log(maternal TPM)

F.X.P8.P60.allele.csv: A table which rows are X-linked transcript IDs and columns are for each female sample: (1) MMSEQ's posterior mean of log(paternal TPM), (2) MMSEQ's posterior variance of log(paternal TPM), (3) MMSEQ's posterior mean of log(maternal TPM), (4) MMSEQ's posterior variance of log(maternal TPM), (5) MMSEQ's posterior mean of log(paternal TPM) - log(maternal TPM), (6) MMSEQ's posterior variance of log(paternal TPM) - log(maternal TPM)

gencode.vM2.annotation.2wayconspseudos.knownGene.retro.fnRDB.C57.CAST.gtf.gz: A GTF file of the C57Bl/6k, Cast/Eij diploid transcriptome which was used to quantify expression from the F1 hybrids used in this study reference genome sequence to obtain a C57Bl/6J, Cast/EiJ diploid genome.

Supplementary_File_1.xlsx: An excel file which contains the results of inferring parentally biased expression for either both P8 and P60 age groups together or each age group separately, for autosomes, and X chromosome

Submission date

Apr 03, 2015

Last update date

May 15, 2019

Contact name

Nimrod Daniel Rubinstein

Organization name

Harvard University

Department

Molecular and Cellular Biology

Lab

Dulac