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Sample GSM1366197 Query DataSets for GSM1366197
Status Public on May 21, 2015
Title CRD_4
Sample type SRA
Source name Heart; Cardiomyocyte
Organism Mus musculus
Characteristics strain: AG-Geminin
developmental stage: embryonic day 14.5
tissue: Heart
cell type: Cardiomyocyte
Extracted molecule polyA RNA
Extraction protocol Ventricular cardiomyocytes were isolated from E14.5 transgenic mice expressing the green S/G2/M fluorescent ubiquitination-based cell cycle indicator, “Fucci” (A. Sakaue-Sawano et al., Visualizing spatiotemporal dynamics of multicellular cell-cycle progression. Cell 132, 487–498 (2008)), using a modified protocol of the neomyts cardiomyocyte isolation kit (Cellutron Life Technologies). The dissociated cell suspensions were resuspended in 500μl of PBS supplemented with 5% FBS solution and sorted by flow cytometryon a FACSAria instrument operating at low pressure (20 psi) using a 100μm nozzle. Samples were sorted individually into 96-well plates containing RT buffer for linear in vitro-transcription T7-based antisense RNA (aRNA) amplification. Collected samples were 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 system according to manufacturer instructions.
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
Description N24
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 GPL13112
Series (1)
GSE56638 Deep sequencing reveals cell-type specific patterns of single cell transcriptome variation
BioSample SAMN02725923
SRA SRX515332

Supplementary file Size Download File type/resource
GSM1366197_CRD_4_counts.txt.gz 83.4 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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