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Sample GSM1170037 Query DataSets for GSM1170037
Status Public on Jun 21, 2013
Title M-P4h_r1_HiSeq
Sample type SRA
 
Source name E. coli cells_M-P4h
Organism Escherichia coli
Characteristics strain: K12
substrain: MG1655
culture/growth condition: MOPS-P 4h
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.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
 
Description processed data file: M-P4h.plus.BigWig, M-P4h.minus.BigWig
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.
 
Submission date Jun 20, 2013
Last update date May 15, 2019
Contact name Zhengchang Su
E-mail(s) zcsu@uncc.edu
Phone 704-687-7996
Organization name UNC Charlotte
Department Bioinformatics and Genomics
Lab Su Lab
Street address 9201 University City Blvd
City Charlotte
State/province NC
ZIP/Postal code 28223
Country USA
 
Platform ID GPL14548
Series (1)
GSE48151 Directional RNA-seq reveals highly complex condition-dependent transcriptomes in E. coliK12 through accurate full-length transcripts assembling
Relations
BioSample SAMN02209695
SRA SRX312074

Supplementary data files not provided
SRA Run SelectorHelp
Processed data are available on Series record
Raw data are available in SRA

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