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| Status |
Public on Dec 01, 2017 |
| Title |
Vegetative biol. rep. 3 |
| Sample type |
SRA |
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| Source name |
Vegetative
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| Organism |
Azospirillum brasilense |
| Characteristics |
strain: sp7
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNA extraction via acid phenol:cholorform and precipitated with 2mM LiCl and 100% ETOH; RNA cleaned with RNAeasy Qiagen Clean up Kit
cDNA prepared from Bacterial Scripting Complete Kit (Illumina)
RNA-seq; Illumina NextSeq on High Output 75 cycle
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| Description |
GSF1390-B3_S12
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| Data processing |
Quality Control: reads were trimmed with Trimmomatic on a sliding window of 5:25, minimum read length of 40bp
Aligned with Bowtie2 to A. brasilense sp7 genome; NCBI assembly GCF_001315025.1
Gene counts quantified with HTSeq
Differential gene expression analysized with DESeq2 in R
Genome_build: ASM131501v1
Supplementary_files_format_and_content: Excel files include gene number and associatd KEGG identification with the basemean, log2fold change of vegetative expression over cyst expression, p-value of change, and false discovert rate adjusted p-value.
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| Submission date |
Sep 25, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Elizabeth Ann Malinich |
| E-mail(s) |
eczerwin@umail.iu.edu
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| Organization name |
Indiana University
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| Department |
Biology
|
| Lab |
Carl Bauer
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| Street address |
212 S Hawthorne Dr Rm313
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| City |
Bloomington |
| State/province |
IN |
| ZIP/Postal code |
47401 |
| Country |
USA |
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| Platform ID |
GPL24043 |
| Series (1) |
| GSE104188 |
Transcriptome profile of vegetative and cyst cells states of Azospirillum brasilense sp7 |
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| Relations |
| BioSample |
SAMN07692738 |
| SRA |
SRX3210815 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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