|
| Status |
Public on Nov 12, 2020 |
| Title |
HiC_replicate1 |
| Sample type |
SRA |
| |
|
| Source name |
Leaf tissue
|
| Organism |
Zea mays |
| Characteristics |
genotype: B73
tissue: leaf
development stage: v04
|
| Growth protocol |
Plants were grown under normal light and temperature conditions in a static greenhouse and tissue was collected when plants reached the v04 stage.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Leaf tissue was collected and grinded before storage at -80C. Lysates were recovered according to the Dovetail Hi-C Library Preparation Kit protocol. Since tissues had previously been grinded (in liquid nitrogen) before long-term storage at -80°C, 2ml 1X PBS and 81μl 37% formaldehyde were added directly to 250mg of frozen and grinded tissue in a 15-ml tube then incubated at room temperature for 15min, prior to completing the protocol.
Libraries were constructed with the Dovetail Hi-C Library preparation Kit (Dovetail), according to the manufacturer’s instructions, including protocol modifications recommended by Dovetail for plant tissue.
|
| |
|
| Library strategy |
Hi-C |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
Reports for all chromosomes except Chr0. HITADs file contains hierarchical TADs produced by runHIC followed by the hitad pipeline; default parameters. HIC file contains interaction matrices produced by Juicer from Juicer Tools 1.9.9 as inter.hic. HiC_replicate1-merged_loops.bedpe contains loops called by HICCUPS from Juicer Tools 1.9.9 based on HiC_replicate1-inter.hic.
|
| Data processing |
Illumina CASAVA 1.8 software was used for basecalling.
Following quality score-based trimming , reads with adapter sequences or of low quality were removed.
Filtered reads were processed using the Juicer package versions 1.9.9 and 1.14.08, for replicates 1 and 2, respectively.
Hierarchical TADs were called for both Hi-C replicates using HiTAD from the TADLib package. Default parameters were used. The related runHiC pipeline was run for each replicate, also with defaults, to generate the .cool files needed for HiTAD analysis.
Chromatin loops were detected using the HICCUPS software package from the Juicer package versions 1.9.9 and 1.14.08, for replicates 1 and 2, respectively.
Genome_build: Zea_mays.AGPv4
Supplementary_files_format_and_content: Hi-C interaction matrices (.hic" files) containing paired-end Hi-C reads
|
| |
|
| Submission date |
Nov 11, 2020 |
| Last update date |
Nov 12, 2020 |
| Contact name |
John Anthony Crow |
| E-mail(s) |
johna.crow@corteva.com
|
| Organization name |
Corteva Agriscience
|
| Department |
Applied Science and Technology
|
| Lab |
Genomics Technologies
|
| Street address |
7000 NW 62nd Ave
|
| City |
Johnston |
| State/province |
Iowa |
| ZIP/Postal code |
50131 |
| Country |
USA |
| |
|
| Platform ID |
GPL29401 |
| Series (1) |
| GSE161294 |
Co-location of chromatin loop anchors with the gene transcription machinery in maize. |
|
| Relations |
| BioSample |
SAMN15573781 |
| SRA |
SRX8766952 |
