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| Status |
Public on Feb 23, 2024 |
| Title |
shRNAseq in TIL11 ears Rep1B |
| Sample type |
SRA |
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| Source name |
immature ears
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| Organism |
Zea mays subsp. parviglumis |
| Characteristics |
tissue: immature ears
inbred line: TIL11
genotype: WT
developmental stage: 5-10 mm
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| Growth protocol |
For collecting immature ears, TIL11 plants were grown in the CSHL Uplands Farm field from September to early October to promoter 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 pollen samples, plants were grown in a short day (8h light/16h dark) walk-in chamber to promote floral transition. Fresh pollen was harvested, frozen in LN2 and stored at -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.
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted with Direct-zol RNA Miniprep Kit (Zymo Reserach).
RNAseq libraries were constructed from 1ug of total RNA with TruSeq Stranded Total RNA LT Kit, including RiboZero Plant depletion and oligo(dT) and random probes for cDNA synthesis. RAMPAGE libraries were constructed from 5ug total RNA following published protocol (Batut and Gingeras 2013) using RiboMinus Plant depletion. shRNAseq libraries were constructed from 5ug of total RNA using TruSeq Small RNA protocol after RiboMinus Plant depletion and size selection of 100 to 205nt with BluePippin (Sage Science).
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| Library strategy |
ncRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina NextSeq 500 |
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| Description |
TIL11_ears_shRNA_Rep1_results.txt
TIL11_ears_shRNAseq_Rep1B
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| Data processing |
Adapter trimming with cutadapt
For RNAseq and RAMPAGE: mapping to TIL11 v1.1 genome with STAR (parameters: --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.04 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outFilterMultimapNmax 20 --quantMode GeneCounts).
For RAMPAGE only, TSS were identified by calling peak with macs2 using the corresponding RNAseq control.
For shRNA, trimmed fastq files were depleted of snoRNAs, rRNAs and tRNAs by mapping to these structural RNAs from zea mays with bowtie2, and the leftover reads were mapped to TIL11 v1.1 with ShortStack (--mmap u --dicermin 20 --dicermax 24 --bowtie_m all --mismatches 1 --foldsize 1000 --pad 250)
Assembly: TIL11 v1.1
Supplementary files format and content: For RNAseq: count table on all TIL11 v1.1 genes for each sample (combined ReadsPerGene.out.tab files from STAR)
Supplementary files format and content: For RAMPAGeE: list of identified TSS (macs2 narrowPeak format)
Supplementary files format and content: For shRNA: table of identified clusters (ShortStack Results file)
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| Submission date |
Jan 29, 2024 |
| Last update date |
Feb 23, 2024 |
| Contact name |
Jonathan Cahn |
| E-mail(s) |
cahnjonathan@gmail.com
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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 |
GPL34141 |
| Series (2) |
| GSE254490 |
MaizeCODE reveals bi-directionally expressed enhancers that harbor molecular signatures of maize domestication |
| GSE254496 |
MaizeCODE reveals bi-directionally expressed enhancers that harbor molecular signatures of maize domestication |
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| Relations |
| BioSample |
SAMN12897279 |
| SRA |
SRX6936198 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
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