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| Status |
Public on May 22, 2024 |
| Title |
ChIPseq of H3K4me3 in NC350 roots Rep2 |
| Sample type |
SRA |
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| Source name |
root tips
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| Organism |
Zea mays |
| Characteristics |
tissue: root tips
inbred line: NC350
genotype: WT
antibody: H3K4me3 (Millipore, 07-473)
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| Growth protocol |
For collecting immature ears, maize inbreds were grown in the CSHL Uplands Farm field in the summer until they reached the appropriate stage. The plants were collected from the field, and 5-10mm primary and secondary ear primordia were dissected in the lab then frozen in LN2 and stored at -80°C. TIL11 plants were grown in CSHL Upland Farm field from September to early October to promote floral transition by natural short day conditions. Immature TIL11 ears at an equivalent development stage (with inflorescence meristems, spikelet pair meristems, spikelet meristems and floral meristems) were collected under a dissecting microscope, frozen in LN2 stored at -80°C. For endosperm samples, ears of field-grown plants were sib-pollinated and collected 15 DAP. Endosperm was dissected in the lab, frozen in LN2 and stored in -80°C. For root tips samples, seeds were germinated on wet paper towels in a Pyrex dish kept in the incubator at 26°C in continuous darkness. After 5 days, 1-3 mm root tips were cut off with a razor blade on ice, frozen in LN2 and stored at -80°C. For coleoptilar nodes samples, seeds were germinated in flats in a long day (8h dark/16h light) growth chamber, 27°C day and 24°C night, and light at 130 μmoles at the top flat. After 5 days, seedlings were unearthed and 5 mm sections around coleoptilar nodes were dissected on ice, frozen in LN2 and stored at -80°C. For TFs ChIPseq, TU1A-YFP (Han, Jackson, and Martienssen 2012), and GT1-YFP (Whipple et al. 2011) transgenic lines were introgressed into the bd1;Tunicate (bd1;Tu) double mutant background, which produces highly proliferative ears, to generate large amounts of ear tissue.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
For histone ChIPseq, chromatin was extracted as previously described (Villar and Köhler 2010). Briefly, tissue was crosslinked with 1% formaldehyde, ground and sheared with Covaris ultrasonicator. Mixture of Dynabeads with proteins A and G (1:1) (Invitrogen) was used for the IP and DNA was purified using ChIP Clean-up and Concentrator kit (Zymo Research). For TFs ChIP-seq, chromatin was extracted as previously described (Xu et al. 2021).
Histone ChIPseq libraries were constructed using Ultra II DNA kit (NEB). TF ChIP-seq libraries were constructed with NEXTflex ChIPseq kit (PerkinElmer Applied Genomics)
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
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| Data processing |
Adapter trimming with cutadapt
Mapping to each respective genome with bowtie2 (parameters: --end-to-end --maxins 1500)
For Input, coverage tracks (bigwig) were created with deeptools bamCoverage
For IP, peaks were identified by calling peak with macs2 using the corresponding Input control. H3K4me1 broad peaks were called with parameter --broad, the other IPs narrow peaks were called with --call-summits.
For TF IP, tracks of log fold change enrichment of IP over Input were created with deeptools bamCompare (parameters: --scaleFactorsMethod "None" --normalizeUsing CPM --extendReads 300)
Assembly: B73 NAM; NC350 NAM; W22 v2; TIL11 v1.1
Supplementary files format and content: For Input: bigiwig file (coverage) for histone, logFC IP/Input for TFs.
Supplementary files format and content: For IP: list of identified peaks (macs2 narrowPeak or broadPeak format)
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| Submission date |
May 21, 2024 |
| Last update date |
May 23, 2024 |
| Contact name |
Jonathan Cahn |
| E-mail(s) |
[email protected]
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| Organization name |
CSHL
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| Street address |
1 Bungtown Rd
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| City |
Cold Spring Harbor |
| State/province |
NY |
| ZIP/Postal code |
11724 |
| Country |
USA |
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| Platform ID |
GPL20156 |
| Series (2) |
| GSE254486 |
MaizeCODE reveals bi-directionally expressed enhancers that harbor molecular signatures of maize domestication [ChIP-seq] |
| GSE254496 |
MaizeCODE reveals bi-directionally expressed enhancers that harbor molecular signatures of maize domestication |
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| Relations |
| BioSample |
SAMN41481774 |
| SRA |
SRX24641560 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM8285346_NC350_roots_H3K4me3_Rep2_peaks.narrowPeak.gz |
5.6 Mb |
(ftp)(http) |
NARROWPEAK |
SRA Run Selector |
| Raw data are available in SRA |
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