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Sample GSM1202315 Query DataSets for GSM1202315
Status Public on Oct 15, 2013
Title RN0014
Sample type SRA
 
Source name rat_hippocampus dendrite
Organism Rattus norvegicus
Characteristics strain: Sprague-Dawley
age: Embryonic 18D
tissue: Hippocampus Dendrite
amplification: 3x aRNA
Extracted molecule total RNA
Extraction protocol single cells and dendrites were harvested by mechanical isolation, RNA was extracted using the freeze/thaw method, and aRNA amplified
RNA libraries were prepared for sequencing using standard Illumina protocols
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina Genome Analyzer II
 
Description processed data file: CIRTs_RnDend.txt
Data processing For dendrite and soma samples Illumina Casave 1.3 software for base-calling
For BAT and cardiomyocyte samples Illumina Casave 1.8.1 software for base-calling
Sequenced reads were trimmed for adaptor sequence, then mapped to mm9 whole genome (for mouse samples) and rn4 whole genome for rat samples using RUM 2.0.3_04 pipeline for the dendritic ans soma sample, RUM 1.09 for BAT samples and RUM 1.11 for cardiomyocytes with default parameters
Reads mapping the intronic regions of genes by paired-end alignment were counted
Genome_build: mm9 for mouse and rn4 for rat
Supplementary_files_format_and_content: tab-delimited text file containing the processed putative cytoplasmically retained intronic contig coordinates along with the #reads mapping to each
 
Submission date Aug 06, 2013
Last update date May 15, 2019
Contact name Junhyong Kim
Organization name University of Pennsylvania
Department Biology
Lab Junhyong Kim
Street address 433 S University Avenue
City Philadelphia
State/province PA
ZIP/Postal code 19104
Country USA
 
Platform ID GPL10287
Series (1)
GSE49592 Subcellular RNA Sequencing Reveals Broad Presence of Cytoplasmic Intron-sequence Retaining Transcripts in Mouse and Rat Neurons.
Relations
BioSample SAMN02303481
SRA SRX331977

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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