|
| Status |
Public on Aug 09, 2024 |
| Title |
Heart Tsu1xCol0 biological rep 2 |
| Sample type |
SRA |
| |
|
| Source name |
Embryo
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
tissue: embryo
Stage: Heart
female parent strain: Tsu-1
male parent strain: Col-0
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Embryos were manually isolated as in Xiang et al., 2011. Embryos were washed by moving them away form the maternal tissues to a corner of the petri dish and then pipetted along with <5uL intro another petri dish containing 50 mL of the isolating solution.
RNA was extracted using the RNAqueous-Micro kit (Ambion, Catalog# 1927). The mRNA amplification was conducted according to the protocol provided in the MessageAmp aRNA kit (Ambion, Catalog# 1750). Illumina mRNA-seq libraries were prepared using the TruSeq RNA kit (Ver 1, rev A).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer II |
| |
|
| Description |
he.TC.BR2
processed data file:
total.reads.tsv
parental.contributions.tsv
|
| Data processing |
Diploid genome and annotations were generated using the variants called with freebayes v1.0.0 (Garrison and Marth, 2012) from raw Tsu-1 sequencing data (Warthmann et al., 2008), TAIR10 assembly and Araport 11 annotation. Variants were filtered to have a minimum phred quality of 20 and a maximum of 0.05 normalized likelihood of being heterozygous
Reads were aligned agains generated diploid genome using STAR V 2.7.0d (Dobin et al., 2013) with parameters: --outFilterMultimapNmax 1 --outFilterMultimapScoreRange 0 --alignIntronMax 900 --alignMatesGapMax 900, for allele-specific expression. For total expression, with parameters: --alignIntronMax 900 --alignMatesGapMax 900 --twopassMode Basic
Reads aligned to variants inside annotated genes were counted using featurecounts V 1.6.0 (Liao et al., 2014) with flags: -p -O –fraction, for allele-specific expression. For total expression with flags: -p -M -O –fraction.
Differential expression analysis was performed using the likelihood ratio test impremented in edgeR (Robinson et al., 2010) on the counts for each accession; the normalization factors and library sizes were calculated using the total variant counts per gene (adding counts for each parent)
Genome_build: TAIR 10
Supplementary_files_format_and_content: Tab-delimited file containing either total read count per gene; or estimated maternal fraction and BH-adjusted P values, calculated by edgeR, and reads aligned to variants added across technical and biological replicates.
|
| |
|
| Submission date |
Jun 10, 2019 |
| Last update date |
Aug 09, 2024 |
| Contact name |
Charles Stewart Gillmor |
| E-mail(s) |
stewart.gillmor@cinvestav.mx
|
| Phone |
+52014621663013
|
| Organization name |
CINVESTAV
|
| Department |
LANGEBIO
|
| Lab |
Genetica y epigenetica de semillas
|
| Street address |
Libramiento Norte Carretera Leon Km 9.6
|
| City |
Irapuato |
| State/province |
Guanajuato |
| ZIP/Postal code |
36821 |
| Country |
Mexico |
| |
|
| Platform ID |
GPL9302 |
| Series (1) |
| GSE132449 |
Epigenetic marks correlated with differential parental genome contributions to plant zygotic transcriptomes |
|
| Relations |
| BioSample |
SAMN12001422 |
| SRA |
SRX6028146 |
