GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Sample GSM2724502 Query DataSets for GSM2724502
Status Public on Aug 15, 2017
Title smb gDNA
Sample type SRA
Source name smb, seedlings
Organism Arabidopsis thaliana
Characteristics tissue: seedlings
genotype: smb
developmental stage: two weeks old
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.
Extracted molecule genomic DNA
Extraction protocol QIAgen DNeasy extraction
Nextera DNA Library prep (Illumina)
Library strategy OTHER
Library source genomic
Library selection other
Instrument model Illumina NextSeq 500
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.
Submission date Aug 01, 2017
Last update date May 15, 2019
Contact name Quentin Gouil
Organization name Walter and Eliza Hall
Department Epigenetics and Development
Lab Ritchie lab
Street address 1G Royal Parade
City Parkville
State/province VIC
ZIP/Postal code 3052
Country Australia
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
BioSample SAMN07431845
SRA SRX3052758

Supplementary file Size Download File type/resource
GSM2724502_smb.T-DNA_pairs.sam.gz 6.2 Kb (ftp)(http) SAM
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap