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| Status |
Public on Jun 10, 2022 |
| Title |
Aechmea_fasciata, IP494-1B-EIN3, biol rep2 |
| Sample type |
SRA |
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| Source name |
leaf
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| Organism |
Aechmea fasciata |
| Characteristics |
tissue: leaf
chip antibody: EIN3
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| 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.
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
IP494-1B-EIN3
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| 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
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| Submission date |
Jun 09, 2022 |
| Last update date |
Jun 10, 2022 |
| Contact name |
Jiabin Wang |
| E-mail(s) |
jiabinwangfuhu@sina.com
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| Phone |
+8689823300522
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| Organization name |
Chinese Academy of Tropical Agricultural Sciences
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| Street address |
Baodaoxincun
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| City |
Danzhou |
| State/province |
Hainan |
| ZIP/Postal code |
571737 |
| Country |
China |
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| Platform ID |
GPL32333 |
| Series (1) |
| GSE205799 |
Ethylene-induced flowering in Aechmea fasciata |
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| Relations |
| BioSample |
SAMN28948808 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM6229557_IP_Af_2.clean.uniq.rmdup.bedGraph.gz |
33.5 Mb |
(ftp)(http) |
BEDGRAPH |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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