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Sample GSM6229554 Query DataSets for GSM6229554
Status Public on Jun 10, 2022
Title Aechmea_fasciata, IN_494_1B, biol_rep2
Sample type SRA
 
Source name leaf
Organism Aechmea fasciata
Characteristics tissue: leaf
chip antibody: none
Extracted molecule genomic DNA
Extraction protocol Cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated using a E220 focused-ultrasonicator (Covaris).
Libraries were prepared using a library preparation kit (New England Biolabs) according to the manufacturer’s instructions.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 2000
 
Description IN_494_1B
Data processing Basecalls were performed using bcl2fastq2 (v2.20).
ChIP-seq reads were trimmed from 3' end until the final base had a quality score > 30, using Trimmomatic v0.36, discarding reads left with < 20 bp.
ChIP-seq reads were aligned to the genome of Aechmea fasciata. Only uniquely mapping reads with at most two mismatches were retained.
To create ChIP-seq coverage plots, the locations of the mapped ChIP-seq reads were extended to 150 bp to represent sequenced fragments, renormalized (to reads per million, rpm) and reformatted in the bigWig file format.
Peaks were called using MACS v 2.1.1.20160309 with the significance cut-off q-value <=0.01.
Assembly: The genome of Aechmea fasciata.
Supplementary files format and content: bedGraph files
 
Submission date Jun 09, 2022
Last update date Jun 10, 2022
Contact name Jiabin Wang
E-mail(s) jiabinwangfuhu@sina.com
Phone +8689823300522
Organization name Chinese Academy of Tropical Agricultural Sciences
Street address Baodaoxincun
City Danzhou
State/province Hainan
ZIP/Postal code 571737
Country China
 
Platform ID GPL32333
Series (1)
GSE205799 Ethylene-induced flowering in Aechmea fasciata
Relations
BioSample SAMN28948811

Supplementary file Size Download File type/resource
GSM6229554_In_Af_2.clean.uniq.rmdup.bedGraph.gz 55.5 Mb (ftp)(http) BEDGRAPH
Raw data are available in SRA
Processed data provided as supplementary file

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