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| Status |
Public on Aug 15, 2017 |
| Title |
athb25 gDNA |
| Sample type |
SRA |
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| Source name |
athb25, seedlings
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| Organism |
Arabidopsis thaliana |
| Characteristics |
tissue: seedlings
genotype: athb25
developmental stage: two weeks old
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| Growth protocol |
Seeds were sown on MS media, statified at 4 C for 2-d before being transferred to long-day conditions at 22°C.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
QIAgen DNeasy extraction
Nextera DNA Library prep (Illumina)
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| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
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| Data processing |
Reads were trimmed with trimgalore (v0.4.2) with options --phred33 --paired --nextera
mapped with bowtie2 (2.2.29) [Langmead 2012] with option -X 1500 onto the TAIR10 genome with the pROK2 T-DNA sequence as a supplementary chromosome [Baulcombe 1986, Ülker 2008]
Read pairs with one read mapping to the T-DNA and its mate mapping to the genome were extracted from the SAM output with awk ‘($3 == “pROK2_T-DNA_only” && $7 != “=”)’, to identify T-DNA insertion sites.
Genome_build: TAIR10 + pROK2 T-DNA
Supplementary_files_format_and_content: filtered alignments for read pairs mapping across the T-DNA – genome junction.
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| Submission date |
Aug 01, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Quentin Gouil |
| Organization name |
Walter and Eliza Hall
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| Department |
Epigenetics and Development
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| Lab |
Ritchie lab
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| Street address |
1G Royal Parade
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| City |
Parkville |
| State/province |
VIC |
| ZIP/Postal code |
3052 |
| Country |
Australia |
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| Platform ID |
GPL19580 |
| Series (2) |
| GSE94459 |
methylC-seq, RNA-seq and sRNA-seq data over Arabidopsis thaliana germination |
| GSE102126 |
Whole-genome resequencing of T-DNA insertion lines |
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| Relations |
| BioSample |
SAMN07431849 |
| SRA |
SRX3052754 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2724498_athb25.T-DNA_pairs.sam.gz |
3.0 Kb |
(ftp)(http) |
SAM |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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