|
| Status |
Public on May 01, 2019 |
| Title |
Lethal_paternal_excess_3 [RNA-Seq] |
| Sample type |
SRA |
| |
|
| Source name |
Endosperm
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
genotype: Ler female x 4N Col male
developmental stage: 7 days after pollination
|
| Treatment protocol |
no treatment
|
| Growth protocol |
Plants were grown in a growth-chamber with 16-hour days at ~21 C. Flowers were emasculated 2 days before pollination. Seeds were dissected at seven DAP
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Seeds from crosses between multiple individuals were hand-dissected and total embryo or endosperm RNA isolated using the Ambion RNAqueous Micro Kit.
DNase I-treated RNA (Invitrogen, Life Technologies Corporation, Carlsbad, CA) was used to prepare mRNA-seq libraries using the SMARTerUltralowPOLYA kit at the Whitehead Institute's Genome Technology Core.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
mRNA-seq
|
| Data processing |
Sequence data were filtered for quality with “ trim_galore -q 25 --phred64 --fastqc --length 20 --stringency 5”.
Filtered reads were aligned to the TAIR10 genome using “tophat -i 30 -I 3000 --solexa1.3-quals -p 5 -g 5 --segment-mismatches 1 --segment-length 18 --b2-very-sensitive”
CUFFDIFF with default settings and the ARAPORT11 genome annotation to calculate changes in gene expression and their statistical significance.
We used a custom script (https://github.com/clp90/imprinting_analysis/tree/master/helper_scripts) to identify allele specific reads.
To assess TE transcript levels, we aligned our reads to the REPBASE consensus sequence (Jurka et al., 2005) using “ bowtie -v 2 -m 3 --best --strata -p 5 --phred64” and summed reads mapping to each TE family. META1, ATHILA6A and ATGP8 were precluded from further analyses because of mapping artifacts. Differential expression was identified using DEGSEQ.
Genome_build: TAIR10
Supplementary_files_format_and_content: Cuffdiff output with details of differential expression
Supplementary_files_format_and_content: Allele specific differences in expression between balanced, lethal and viable paternal excess endosperm
Supplementary_files_format_and_content: TE expression differences
|
| |
|
| Submission date |
Feb 22, 2019 |
| Last update date |
May 01, 2019 |
| Contact name |
satyaki P Rajavasireddy |
| E-mail(s) |
satyaki@wi.mit.edu
|
| Phone |
6072290279
|
| Organization name |
Whitehead Institute for Biomedical Research
|
| Lab |
Gehring Lab
|
| Street address |
455 Main Street
|
| City |
Cambridge |
| State/province |
Massachusetts |
| ZIP/Postal code |
02142 |
| Country |
USA |
| |
|
| Platform ID |
GPL17639 |
| Series (2) |
| GSE126931 |
Paternally-acting canonical RNA-directed DNA methylation pathway genes sensitizes Arabidopsis endosperm to paternal dosage [RNA-Seq] |
| GSE126932 |
Paternally-acting canonical RNA-directed DNA methylation pathway genes sensitizes Arabidopsis endosperm to paternal dosage |
|
| Relations |
| BioSample |
SAMN10987537 |
| SRA |
SRX5408234 |
