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Sample GSM1366275 Query DataSets for GSM1366275
Status Public on May 21, 2015
Title CTRL_100p_4
Sample type SRA
Source name Heart; Population
Organism Mus musculus
Characteristics strain: c57
developmental stage: Adult
tissue: Heart
cell type: Population
Extracted molecule polyA RNA
Extraction protocol Starting from bulk heart tissue total RNA from a C57/BL6 adult male mouse (Zyagen), five replicates were begun with 100 pg. of total RNA. All diluted replicates shared the same original mother tube. Each sample was individually amplified using three rounds of a linear in vitro-transcription-based method.
Samples were prepared for multiplexed paired-end sequencing using the Illumina Truseq stranded system according to manufacturer instructions.
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
Description 100pg_HRTms_5
Data processing genome_build: mm9
genome_build: rn5
Illumina Casava 1.8.1 and 1.8.2 software used for basecalling.
We trimmed reads for adapter and poly-A contamination using in-house software before aligning to the mouse genome and transcriptome using RNA-Seq Unified Mapper (versions 2.0.2_06 and 2.0.3_04) and mouse genome build mm9 (mouse) or to the rat genome using STAR and rat genome build rn5. We required three or less mismatches per 100 bases.
Using uniquely aligned reads to RefSeq annotations downloaded from UCSC genome browser, we assigned read counts to genes using HTSeq and htseq-count. Only exonic reads were counted, with overlap assigned using the intersection non-empty method.
Supplementary_files_format_and_content: tab-delimited text files include raw counts for each gene
Submission date Apr 09, 2014
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 GPL17021
Series (1)
GSE56638 Deep sequencing reveals cell-type specific patterns of single cell transcriptome variation
BioSample SAMN02725883
SRA SRX515410

Supplementary file Size Download File type/resource
GSM1366275_CTRL_100p_4_counts.txt.gz 89.3 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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