|
| Status |
Public on May 29, 2019 |
| Title |
brain.Se0.1.rep3 |
| Sample type |
SRA |
| |
|
| Source name |
Mouse fed with 0.1 ppm dietary Se for 5 weeks
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57Bl/6J
gender: male
pathology: No gross pathology observed
tissue: Mouse whole brain
|
| Treatment protocol |
Eight-weeks old C57BL/6J male mice were fed with diet supplemented with either 0, 0.1, 0.4 or 2.25 ppm for five weeks
|
| Growth protocol |
Normal chow until the Se diet was fed
|
| Extracted molecule |
total RNA |
| Extraction protocol |
TRIzol® Reagent (Thermo Fisher Scientific)
TruSeq Stranded Total RNA Kit (Illumina; RS-122-2201)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Samples were pooled and sequenced on one HiSeq run using Illumina TruSeq Stranded Total RNA Kit RS-122-2201.
Basecalling was performed by RTA (version 1.18.64).
Demultiplexing and FASTQ generation was performed using bcl2fastq (version 2.17) allowing 1 mismatch.
Reads were filtered with a base call quality >94% of bases with Q30 and and above.
Trimming of adapters and low-quality bases was performed using Trimmomatic (version 0.33).
First pass alignment of reads to the mm10 reference genome was performed using STAR (version 2.5.2b) with parameters: STAR --genomeDir /path/to/genomeDir --outFilterIntronMotifs RemoveNoncanonicalUnannotated --outSAMstrandField None --outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.3 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --clip3pAdapterSeq - --readFilesIn /path/to/read1.fastq.gz /path/to/read2.fastq.gz --readFilesCommand zcat --runThreadN 32 --outFileNamePrefix <prefix> --outSAMtype BAM Unsorted
Second pass alignment of reads to the mm10 reference genome was performed using STAR (version 2.5.2b) with parameters: STAR --genomeDir /path/to/genomeDir --outFilterIntronMotifs RemoveNoncanonicalUnannotated --outSAMstrandField None --outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.3 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --clip3pAdapterSeq - --readFilesIn /path/to/read1.fastq.gz /path/to/read2.fastq.gz --readFilesCommand zcat --runThreadN 32 --outFileNamePrefix <prefix> --outSAMunmapped Within --outWigType None --outWigStrand Stranded --sjdbFileChrStartEnd /path/to/sjdbFile.txt --sjdbGTFfile /path/to/annotations.gtf --limitSjdbInsertNsj 4000000 --quantMode TranscriptomeSAM GeneCounts --outSAMtype BAM SortedByCoordinate
Gene-level expression quantificiation and library size normalization in counts-per-million was performed using RSEM (version 1.3.0).
Quantile-normalization and differential expression was performed using limma-voom (version 3.34.5).
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files are limma-voom normalized differential expression output.
|
| |
|
| Submission date |
Apr 01, 2019 |
| Last update date |
May 29, 2019 |
| Contact name |
Sun Hee Yim |
| E-mail(s) |
shyim@rics.bwh.harvard.edu
|
| Phone |
6176510330
|
| Organization name |
BWH/Harvard Medical School
|
| Department |
Medicine
|
| Lab |
Genetics
|
| Street address |
77 Ave Louis Pasteur, RM435
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02115 |
| Country |
USA |
| |
|
| Platform ID |
GPL17021 |
| Series (1) |
| GSE129138 |
Selenium Deficiency is Associated with Pro-Longevity Mechanisms |
|
| Relations |
| BioSample |
SAMN11309377 |
| SRA |
SRX5620707 |
