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Sample GSM561871 Query DataSets for GSM561871
Status Public on Jul 01, 2010
Title TSS_FWAF_logphase
Sample type SRA
Source name G. sulfurreducens PCA, grown in FWAF medium, mid-log phase
Organism Geobacter sulfurreducens PCA
Characteristics strain: PCA
genotype: wild type
condition: fresh water acetate-fumarate (FWAF) medium
Growth protocol G. sulfurreducens PCA strain was cultured in FWAF medium, under strictly anoxic conditions at 30°C, and harvested at mid-exponential phase.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted using Trizol (Invitrogen) and DNA was removed by DNase digestion. RNA quality and concentration was determined by analysis with a Thermo NanoDrop 1000.

RNA with 5’-monophosphate end was removed with 5’-phosphate-dependent exonuclease. The 5’-triphosphate end of primary RNA was then converted to 5’-monophosphate end with RNA 5’ polyphosphatase. 5’ sRNA adapter was ligated to the 5’ end of mRNA. cDNAs were then synthesized from the adapter-ligated mRNA using 3’-adapter. Fraction of the cDNA between 100 bp and 300 bp was then gel purified and PCR amplified.
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina Genome Analyzer II
Data processing Alignment: The data were aligned onto the G. sulfurreducens PCA genome (NC_002939.4) using the Mosaik Aligner (, hash size = 15, mismatch=0. These data are in the *bed files.

5' end: the 5' end of unique aligned reads were counted and considered as potential transcription start sites. These data are in the *wig files.
Submission date Jun 30, 2010
Last update date May 15, 2019
Contact name Bernhard Palsson
Phone 858-534-5668
Fax 858-822-3120
Organization name UCSD
Department Bioengineering
Lab Systems Biology Research Group
Street address 9500 Gilman Dr.
City La Jolla
State/province CA
ZIP/Postal code 92122
Country USA
Platform ID GPL10638
Series (2)
GSE22511 Genome-wide transcription start site determination of Geobacter sulfurreducens under multiple growth conditions
GSE22512 Analysis of Geobacter sulfurreducens under multiple growth conditions
SRA SRX023132
BioSample SAMN00016912

Supplementary file Size Download File type/resource
GSM561871_TSS_FWAF_logphase_aligned_unique.bed.gz 1.6 Mb (ftp)(http) BED
GSM561871_TSS_FWAF_logphase_aligned_unique.wig.gz 86.8 Kb (ftp)(http) WIG
SRA Run SelectorHelp
Processed data provided as supplementary file
Raw data are available in SRA

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