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| Status |
Public on Jul 05, 2013 |
| Title |
Tcf21MO-45 |
| Sample type |
SRA |
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| Source name |
Tcf21-depleted_hearts
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| Organism |
Xenopus laevis |
| Characteristics |
injected with: Tcf21-MO
genotype/variation: Tcf21-depleted
Stage: stage 44-45
tissue: 70-100 pooled hearts
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| Treatment protocol |
RNA from hearts was extracted using Trizol
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| Growth protocol |
Embryos were injected with MO at fertilization and maintained in 0.1xMBS between 16-23oC until stage 44-45
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
Hearts were dissected from anaethetized embryos, collected into Trizol on ice and flash frozen in liquid nitrogen until processed. Total RNA was harvested using Trizol reagent.1 ug of total RNA was used for the construction of polyA sequencing libraries.
Illumina mRNA Sequencing Sample Preparation Guide, September 2009 (Amin et al, in review)
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer II |
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| Description |
Sample 2
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| Data processing |
Image analysis and base calling was performed by the Sequencing Control Software (SCS) Real Time Analysis (RTA, v.2.6), ran on the Illumina Genome Analyzer control computer at UNC HTSF. Post-processing of the data was performed using the Illumina CASAVA pipeline software (v.1.7) using the default parameters.
Sequenced reads were mapped to a cDNA library from Xenbase (8,879 cDNA sequences annotated as RefSeq sequences, Feb 7th 2012) using default settings on bowtie2 v2.0.0.6 with parameters -x
Samtools v 0.1.18.0 was used to tabulate read counts from aligned reads, indexed from .bam file
Reads were normalized to total read counts and assessed for fold change in experimental Tcf21-depleted gene dataset compared to sibling controls.
Genome_build: Refseq cDNA library from Xenbase (Feb 2012, Taejoon Kwon, University of Austin at Texas, Marcotte lab) was used for read alignments in the absence of an annotated Xenopus laevis genome at the time
Supplementary_files_format_and_content: tab-delimited text files include normalized values for total read counts and fold change
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| Submission date |
Apr 04, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Panna Tandon |
| Organization name |
UNC at Chapel Hill
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| Street address |
220 Fordham Hall
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| City |
Chapel Hill |
| State/province |
NC |
| ZIP/Postal code |
27599 |
| Country |
USA |
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| Platform ID |
GPL9408 |
| Series (1) |
| GSE45786 |
Cardiac transcriptome of Tcf21-depleted Xenopus embryos |
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| Relations |
| SRA |
SRX260071 |
| BioSample |
SAMN01999086 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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