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| Status |
Public on Dec 01, 2015 |
| Title |
250μM_SNP_Replicate |
| Sample type |
SRA |
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| Source name |
Plants 3 hours after treatment with 250μM SNP (replicate of sample 3)
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| Organism |
Gossypium hirsutum |
| Characteristics |
ecotype: CCRI10
tissue: cotyledon
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| Treatment protocol |
20 days after germination, plants with robust and consistent growth condition were irrigated with 100μM SNP, 250μM SNP, 10μM cPTIO respectively under continuous light.
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| Growth protocol |
Seeds of Gossypium hirsutum L. ecotype CCRI10 were cultured in a mix of sand and nutritional soil in a culture room under white fluorescent light (16h light/8h dark) with day/night temperatures of 30/22℃.
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA was extracted using the EASYspin Plant Total RNA Extraction Reagent (Aidlab, BeiJing, China) in accordance with the manufacturer’s instruction and stored at −70°C freezer. RNA samples with A260/A280 ≥ 1.8, A260/A230≥1.8, and RIN ≥6.5 were considered acceptable for library construction.
Poly(A)-containing mRNA was purified from six micrograms total RNA by oligo(dT) magnetic adsorption beads and cDNA was synthesized using oligo(dT) as primer. The bead-bound cDNA was firstly digested with restriction enzyme NlaⅢ, which recognizes and cuts off the CATG sites. The fragments apart from the 3' cDNA fragments connected to oligo(dT) beads were washed away and the Illumina adaptor 1 was ligated to the sticky 5' end of the digested bead-bound cDNA fragments. The 3′cDNA fragments attached to the oligo(dT) beads were subsequently digested with restriction enzyme MmeⅠ, which recognizes the junction of Illumina adaptor 1 and CATG site and cuts at 17bp downstream of the CATG site, producing tags with adaptor 1. After removing 3' fragments with magnetic beads precipitation, Illumina adaptor 2 was ligated to the 3' ends of tags, acquiring tags with different adaptors of both ends to form tag libraries. After linear PCR amplification, fragments were purified by PAGE Gel electrophoresis. The quantification and qualification of the sample libraries were controlled by Agilent 2100 Bioanaylzer and ABI StepOnePlus Real-Time PCR System.
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| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2000 |
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| Data processing |
the libraries were sequenced using Illumina HiSeq™ 2000, producing the raw data.
Clean tags were acquired from raw sequences after removing (1) 39 bp adaptor sequences, (2) empty reads, (3) low-quality tags with unknown sequences ‘‘N’’, (4) tags unequal to 21bp, and (5) tags with only one copy number.
All clean tags were mapped to the reference sequences and only 1bp mismatch was considered.
Unambiguous clean tags were obtained by filtering clean tags which mapped to multiple reference sequences.
The number of unambiguous clean tags for each gene was calculated and then normalized to TPM
Genome_build: we used an integrated reference gene database with 104,831 sequences for tag mapping. The unambiguous tags that can’t be mapped to reference genes were subsequently mapped to the D genome (Gossypium raimondii)
Supplementary_files_format_and_content: Text files include lengths and counts of each distinct reads.
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| Submission date |
Dec 27, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Juan Huang |
| E-mail(s) |
huang200669@163.com
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| Phone |
+86-03722525365
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| Organization name |
Northwest Agriculture & Forestry University
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| Department |
College of Agronomy
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| Street address |
NO. 3. WeiHui Road
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| City |
YangLing |
| State/province |
Shaanxi |
| ZIP/Postal code |
712100 |
| Country |
China |
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| Platform ID |
GPL16485 |
| Series (1) |
| GSE53674 |
Transcriptome profiling of Gossypium hirsutum in response to NO by high-throughput tag-sequencing |
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| Relations |
| BioSample |
SAMN02486613 |
| SRA |
SRX399579 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1298739_processed_data_250uM_SNP_Replicate.txt.gz |
1.8 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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