|
| Status |
Public on Jun 24, 2022 |
| Title |
I_Col-0 IgG_ChIP-seq |
| Sample type |
SRA |
| |
|
| Source name |
de-etiolated seedling
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
t-dna mutant: Col-0
antibodies: mouse IgG (Jackson ImmunoResearch, 015-000-003)
|
| Treatment protocol |
no treatment
|
| Growth protocol |
Seedlings were grown on Linsmaier and Skoog medium supplemented with 1% sucrose, sample 12 is derived from flowers of soil-grown plants
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Kaufmann et al. 2010 DOI:10.1038/nprot.2009.244
Kaufmann et al. 2010 DOI:10.1038/nprot.2009.244
Libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
control
|
| Data processing |
base-calling using RTA 2.7.7
alignment using Bowtie2 2.1.0
bam file comparison using deepTools2.0/bamCompare
data extraction using bigWigAverageOverBed
ChIP-seq peak identification with SICER 1.1 with the following setting: redundancy threshold (1), window size (200), fragment size (100), effective genome fraction (0.8), gap size (600), FDR (0.01)
Genome_build: TAIR10
|
| |
|
| Submission date |
Jun 23, 2022 |
| Last update date |
Nov 29, 2022 |
| Contact name |
Joseph R Ecker |
| E-mail(s) |
ecker@salk.edu
|
| Phone |
8584534100
|
| Organization name |
HHMI-Salk-Institute
|
| Department |
Genomic Analysis Laboratory
|
| Lab |
Ecker lab
|
| Street address |
10010 North Torrey Pines Road
|
| City |
La Jolla |
| State/province |
CA |
| ZIP/Postal code |
92037 |
| Country |
USA |
| |
|
| Platform ID |
GPL21785 |
| Series (1) |
| GSE108401 |
The Complex Architecture of Transgene Insertions |
|
| Relations |
| BioSample |
SAMN29271677 |
| SRA |
SRX15855489 |
