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| Status |
Public on Aug 29, 2013 |
| Title |
pHerd30T-LL37 CK+ anaerobic |
| Sample type |
SRA |
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| Source name |
E.coli Top 10
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| Organism |
Escherichia coli |
| Characteristics |
strain: E.coli Top 10
genotype/variation: no LL37 expression (control)
growth condition: anaerobic
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| Treatment protocol |
Total RNA was isolated with TRIzol (invitrogen, Carlsbad, CA) according to the manufacture's instruction. DNA was removed from RNA extracts with RNase-free DNase I (New England Biolabs, Beverly, MA, USA) by incubation at 37°C for 30 min. The quality of total RNA was assessed by using 2100 Bioanalyzer (Agilent, Santa Clara, USA) and also checked by agarose gel electrophoresis. rRNAs was subsquently removed from the total mRNA following the instruction of the Ribo-Zero rRNATM Removal kit (Epicentre, Madison, WI, USA).
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| Growth protocol |
37C in LB medium under aerobic and anaerobic condition
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| Extracted molecule |
total RNA |
| Extraction protocol |
mRNA of prokaryotes is enriched just by removing rRNAs from the total RNA. Adding the fragmentation buffer, the mRNA is interrupted to short fragments (about 200 bp), then the first strand cDNA is synthesized by random hexamer-primer using the mRNA fragments as templates. Buffer, dNTPs, RNase H and DNA polymerase I are added to sythsize the second strand. The double strand cDNA is purified with QiaQuick PCR extraction kit and washed with EB buffer for end repair and single nucleotide A (adenine) addition.
sequencing adaptors are ligated to the fragments. The required fragments is purified by agrose gel electrophoresis and enriched by PCR amplification. The library products are ready for sequencing analysis via Illumina HiSeq™ 2000.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
Sample 3
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| Data processing |
The original image data is transfered into sequence data by base calling
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to DH10B gene using CLC Genomics Workbench, default parameters
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using CLC Genomics Workbench, default parameters
Genome_build: GI:170079663/NC_010473
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample
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| Submission date |
Aug 28, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
WEI LIU |
| E-mail(s) |
biolwei@sina.com.cn
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| Organization name |
ZAAS
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| Street address |
198 SHIQIAO ROAD
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| City |
HANGZHOU |
| ZIP/Postal code |
310021 |
| Country |
China |
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| Platform ID |
GPL14548 |
| Series (1) |
| GSE43408 |
Quantitative Different Analysis of antimicrobial peptide LL37 expressed in E.coli Top 10 under aerobic and anaerobic condition. |
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| Relations |
| BioSample |
SAMN02336959 |
| SRA |
SRX340778 |
| 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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