|
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 |