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Sample GSM1020675 Query DataSets for GSM1020675
Status Public on Dec 21, 2012
Title rat_b_brain
Sample type SRA
 
Source name rat_brain
Organism Rattus norvegicus
Characteristics strain: BN/SsNHsd
tissue: brain
Treatment protocol RNALater
Growth protocol standard lab/farm conditions
Extracted molecule total RNA
Extraction protocol Animals were sacrificed with no input from the authors (i.e. each group/facility utilized their standard method). Tissues samples were isolated from each organ, placed into an appropriate volume of RNALater, and incubated at 4C overnight. Each sample was then homogenized in a bead-mill in a phenol/chlorofom solution and RNA was isolated by and treated with DNAse on a Qiagen miRNEasy column.
Strand-specific libraries were generated using the standard RNA-Seq protocol / dUTP method, with the “second-day” done on the Beckman-Coulter SPRIworks machine. Briefly, before second-strand synthesis, samples are precipitated first and the second strand is made using a dNTP solution that replaces dTTP with dUTP. Before the final PCR step, libraries are treated with an enzyme that removes dUTP from dsDNA.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
 
Description Sample 37
Data processing Base-calling: Illumina Real Time Analysis, scoring metric v1.5
Long-read (76-108bp libraries) were mapped with TopHat v1.1.4 with the following additional parameters: --no-novel-indels, -r [inner length], --segment-length 20, --solexa-1.3-quals, --coverage-search -g [species.gtf]
junctions from all long read (76-108bp libraries) were combined and all libraries were mapped by TopHat v1.1.4 with the following parameters: --no-novel-indels, -r [inner length], --segment-length 20, --solexa-1.3-quals, --coverage-search, -j [species_junction_file.bed] -g [species.gtf]
Cufflinks v1.0.2 was run on the long read libraries with the following parameters: --min-isoform-fraction 0.00, --pre-mrna-fraction 0.00, -g [species.gtf], --max-intron-length 100000, -u, -b [genome.fa], --library-type ff-firststrand
Transcripts from libraries within a species were combined with CuffCompare v1.0.2 with the following parameters: -r [species.gtf]
Cufflinks v1.0.2 was run on all libraries with the following parameters: --min-isoform-fraction 0.05, --pre-mrna-fraction 0.10, -G [combined_species.gtf from above], --max-intron-length 100000, -u, -b [genome.fa], --library-type ff-firststrand
Transcripts from libraries from each individual were combined with CuffCompare v1.0.2 with the following parameters: -r [combined_species.gtf]
Genome_build: mouse: mm9, rat: rn4, cow: bt4, chicken: gg3, rhesus: rhemac2, human: hg19
Supplementary_files_format_and_content: mapped reads
 
Submission date Oct 17, 2012
Last update date May 15, 2019
Contact name Jason Merkin
E-mail(s) jmerkin@mit.edu, jjmerkin@gmail.com
Organization name MIT
Department Biology
Lab Burge
Street address 31 Ames St
City Cambridge
State/province MA
ZIP/Postal code 02142
Country USA
 
Platform ID GPL14844
Series (1)
GSE41637 Evolutionary dynamics of gene and isoform regulation in mammalian tissues
Relations
SRA SRX196299
BioSample SAMN01766849

Supplementary file Size Download File type/resource
GSM1020675_rat_b_brain.transcripts.gtf.gz 38.9 Mb (ftp)(http) GTF
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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