|
| Status |
Public on Sep 01, 2020 |
| Title |
Shoot apices, TFL1B input ChIP-Seq |
| Sample type |
SRA |
| |
|
| Source name |
42-day old short-day-grown shoot apices
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
ecotype: Col-0
transgenics: gTFL1_GFP
genotype: WT
tissue: shoot apices
chip antibody: none
|
| Treatment protocol |
No Treatment
|
| Growth protocol |
Plants were grown in short days (8hr light, 16 hr dark ) for 42 days with a light intensity of 120 μMol/m2s
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
ChIP assay was performed according to Yamaguchi et al., 2014. N. Yamaguchi et al., PROTOCOLS: Chromatin Immunoprecipitation from Arabidopsis Tissues. Arabidopsis Book 12, e0170 (2014).
DNA libraries were generated using the ThruPLEX DNA-seq kit (RUBICON GENOMICS, cat. R400406) and quantified by the NEBNext Library Quant Kit (cat. E7630L). Equal amounts of DNA were pooled from each library with different dual indexing primers and sequenced on a Next seq
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
all_input_merged.bigwig
|
| Data processing |
Base-calling was performed automatically in Illumina BaseSpace
Trimmed sequencing reads were aligned to the Arabidopsis thaliana genome using Bowtie2 v2.3.1 with the `--no-unal` parameter and further processed as per ENCODE guidelines (Landt et al 2012)
For narrowPeak files, significant peaks were identified using MACS2 2.1.1 callpeak on ChIP samples relative to relevant control ChIPs performed in non epitope containing plants using 224 bp read extension and summit q-value ≤ 10^-10.
For bigwig files, reads were extended to 224 bp using bedtools v.2.26.0, normalized to 10 million reads mapped per million reads sequenced (10RPM) and coverage was averaged using bedtools.
Genome_build: TAIR10
Supplementary_files_format_and_content:
bigwig normalized to 10RPKM for single replicates
bigwig normalized to 10RPKM for the mean of three replicates for each sample
bigwig normalized to 10RPKM for the mean of three replicates for each sample after subtracting the relevant background sample
bed file (narrowPeak format) containing peaks called by MACS v2.1.0.20151222 filtered by Q-value < 1e-10
|
| |
|
| Submission date |
Dec 12, 2019 |
| Last update date |
Sep 02, 2020 |
| Contact name |
Doris Wagner |
| E-mail(s) |
wagnerdo@sas.upenn.edu
|
| Phone |
2158980483
|
| Organization name |
University of Pennsylvania
|
| Department |
Department of Biology
|
| Lab |
Wagner Lab
|
| Street address |
103G Carolyn Lynch Laboratory
|
| City |
Philadelphia |
| State/province |
PA |
| ZIP/Postal code |
19104 |
| Country |
USA |
| |
|
| Platform ID |
GPL19580 |
| Series (2) |
| GSE129532 |
Florigen family chromatin recruitment, competition and targets [ChIP-Seq] |
| GSE141894 |
Florigen family chromatin recruitment, competition and targets |
|
| Relations |
| BioSample |
SAMN13546264 |
| SRA |
SRX7353889 |
