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Sample GSM4215585 Query DataSets for GSM4215585
Status Public on Sep 01, 2020
Title Shoot apices, TFL1 Input Rep2 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 SAMN13546265
SRA SRX7353888

Supplementary file Size Download File type/resource
GSM4215585_TFLInput2.bw 96.4 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record
Processed data provided as supplementary file

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