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| Status |
Public on May 21, 2015 |
| Title |
CRD_7 |
| Sample type |
SRA |
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| Source name |
Heart; Cardiomyocyte
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| Organism |
Mus musculus |
| Characteristics |
strain: AG-Geminin
developmental stage: embryonic day 14.5
tissue: Heart
cell type: Cardiomyocyte
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| 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.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
G29
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| 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
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| Submission date |
Apr 09, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Junhyong Kim |
| Organization name |
University of Pennsylvania
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| Department |
Biology
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| Lab |
Junhyong Kim
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| Street address |
433 S University Avenue
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| City |
Philadelphia |
| State/province |
PA |
| ZIP/Postal code |
19104 |
| Country |
USA |
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| Platform ID |
GPL13112 |
| Series (1) |
| GSE56638 |
Deep sequencing reveals cell-type specific patterns of single cell transcriptome variation |
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| Relations |
| BioSample |
SAMN02725924 |
| SRA |
SRX515335 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1366200_CRD_7_counts.txt.gz |
82.5 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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