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| Status |
Public on Jun 21, 2013 |
| Title |
M-P4h_r1_HiSeq |
| Sample type |
SRA |
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| Source name |
E. coli cells_M-P4h
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| Organism |
Escherichia coli |
| Characteristics |
strain: K12
substrain: MG1655
culture/growth condition: MOPS-P 4h
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using a RiboPureTM -Bacteria Kit (Ambion) following the manufacturer’s instructions. Once isolated, ~10μg total RNA was treated with 8 units DNase (Invitrogen) twice to remove genomic DNA.
To enrich mRNAs and other transcripts, majority of rRNAs were removed from the DNase-treated total RNA using a MICROBExpress kit (Ambion) following the manufacturer’s instructions.
For the Illumina GAII platform, the directional RNA-seq libraries were constructed by following an Illumina’s instruction using their Small RNA Sample Prep Kit with some modifications. For the HiSeq 2000 platform, the directional RNA-seq libraries were constructed using Illumina’s TruSeq Small RNA Sample Prep Kit.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
processed data file: M-P4h.plus.BigWig, M-P4h.minus.BigWig
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| Data processing |
Merge the replicates for each sample. For example, for sample HS15min, merge HS15min_r1.HiSeq.fastq.gz, HS15min_r2.HiSeq.fastq.gz and HS15min_r3.HiSeq.fastq.gz to one fastq file
Sequenced reads were trimmed for adaptor sequence, then mapped to E. coli K12 genome using bowtie v0.12.7 with parameters bowtie -t -v 3 -m 1 --best -S -p 2
Transform the mapped file format from sam to sorted bam which are later tranfered to bigWig, and separated by the strand (plus and minus).
Genome_build: Escherichia coli K12 str MG1655
Supplementary_files_format_and_content: BigWig files for whole-genome reads coverage (including number of mapped reads) for each sample. Each sample has two files, one for plus strand, and the other for minus strand. Therefore, there are 14 BigWig files for 7 samples.
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| Submission date |
Jun 20, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Zhengchang Su |
| E-mail(s) |
zcsu@uncc.edu
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| Phone |
704-687-7996
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| Organization name |
UNC Charlotte
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| Department |
Bioinformatics and Genomics
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| Lab |
Su Lab
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| Street address |
9201 University City Blvd
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| City |
Charlotte |
| State/province |
NC |
| ZIP/Postal code |
28223 |
| Country |
USA |
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| Platform ID |
GPL14548 |
| Series (1) |
| GSE48151 |
Directional RNA-seq reveals highly complex condition-dependent transcriptomes in E. coliK12 through accurate full-length transcripts assembling |
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| Relations |
| BioSample |
SAMN02209695 |
| SRA |
SRX312074 |
| Supplementary data files not provided |
SRA Run Selector |
| Processed data are available on Series record |
| Raw data are available in SRA |
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