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Status |
Public on Jul 07, 2015 |
Title |
P60 Male F1i sample 1 |
Sample type |
SRA |
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Source name |
P60 Male F1i cerebellum
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Organism |
Mus musculus |
Characteristics |
strain: C57Bl/6JxCast/EiJ hybrid gender: male developmental stage: postnatal day 60 tissue: cerebellum
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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.
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Growth protocol |
F1 hybrids were generated by reciprocally crossing C57Bl/6J and Cast/EiJ mouse strains
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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
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 2000 |
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Description |
MF1i1_P60 processed data files: MF.A.P8.P60.allele.csv,F.X.P8.P60.allele.csv
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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
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Submission date |
Apr 03, 2015 |
Last update date |
May 15, 2019 |
Contact name |
Nimrod Daniel Rubinstein |
Organization name |
Harvard University
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Department |
Molecular and Cellular Biology
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Lab |
Dulac
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Street address |
16 Divinity Avenue
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City |
Cambridge |
State/province |
MA |
ZIP/Postal code |
02138 |
Country |
USA |
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Platform ID |
GPL13112 |
Series (1) |
GSE67556 |
Parent-of-Origin Allelic Expression in the Mouse Cerebellum |
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Relations |
BioSample |
SAMN03459490 |
SRA |
SRX978342 |
Supplementary data files not provided |
SRA Run Selector |
Raw data are available in SRA |
Processed data are available on Series record |
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