WGS of Franconibacter sp. isolated from oil contaminated soil - SRA

SRX14706932: WGS of Franconibacter sp. isolated from oil contaminated soil
1 ILLUMINA (NextSeq 500) run: 3.5M spots, 1G bases, 438.2Mb downloads

Design: The paired-end sequencing library was prepared from the QC passed genomic DNA samples using illumina TruSeq Nano DNA Library Prep Kit. Briefly, approximately 200 ng of DNA was fragmented by Covaris M220 to generate a mean fragment distribution of 350bp. Covaris shearing generates dsDNA fragments with 3' or 5' overhangs. The fragments were then subjected to end-repair. This process converts the overhangs resulting from fragmentation into blunt ends using End Repair Mix. The 3' to 5' exonuclease activity of this mix removes the 3' overhangs and the 5' to 3' polymerase activity fills in the 5' overhangs followed by adapter ligation to the fragments. This strategy ensures a low rate of chimera (concatenated template) formation. The ligated products were size selected using AMPure XP beads. The size-selected products were PCR amplified with the index primer as described in the kit protocol indexing adapters were ligated to the ends of the DNA fragments, preparing them for hybridization onto a flow cell. The PCR enriched library was analyzed on 4200 Tape Station system (Agilent Technologies) using high sensitivity D1000 Screen tape as per manufacturer instructions.

Submitted by: Indian Institute of Technology Delhi

Study: Franconibacter sp. IITDAS19 Genome sequencing and assembly

PRJNA821685 • SRP367132 • All experiments • All runs

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Franconibacter sp. strain IITDAS19 was isolated from the oil-contaminated soilsample from Assam oil fields, India. The bacterium is Gram-negative and belongsto the family of Enterobacteriaceae. Recently, we have shown that the bacteriumproduces a potent biosurfactant Rhamnolipid, which resulted in enhanced oilrecovery in simulated sand column experiments. However, the genes responsiblefor the biosynthesis of rhamnolipid have not been identified in this bacterium.Whole-genome sequencing was performed to find the catabolic and anabolicactivities of the bacterium.

Sample: Franconibacter sp. isolated from oil-contaminated soil

SAMN27121214 • SRS12469698 • All experiments • All runs

Organism: Franconibacter sp. IITDAS19

Library:

Name: IITDAS19

Instrument: NextSeq 500

Strategy: WGS

Source: GENOMIC

Selection: RANDOM

Layout: PAIRED

Runs: 1 run, 3.5M spots, 1G bases, 438.2Mb

Run	# of Spots	# of Bases	Size	Published
SRR18577966	3,487,110	1G	438.2Mb	2022-04-08

ID:: 21046414

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