Marker gene sequencing of environmental sample - SRA

SRX22902467: Marker gene sequencing of environmental sample
1 ILLUMINA (Illumina MiSeq) run: 224,233 spots, 112.6M bases, 52.7Mb downloads

Design: The v4-v5 hypervariable regions of the bacterial SSU rRNA gene were amplified using degenerate primers. The primers were 518F (CCAGCAGCYGCGGTAAN) and 926R (CCGTCAATTCNTTTRAGT CCGTCAATTTCTTTGAGT CCGTCTATTCCTTTGANT). Amplification was done with fusion primers containing the 16S-only sequences fused to Illumina adapters. The forward primers included a 5 nt multiplexing barcode and the reverse a 6 nt index. We generated PCR amplicons in triplicate 33 uL reaction volumes with an amplification cocktail containing 0.67 U SuperFi Taq Polymerase (Invitrogen, Carlsbad, CA), 1X enzyme buffer (includes MgCl2), 200 uM dNTP PurePeak DNA polymerase mix (ThermoFisher), and 0.3 uM of each primer. We added approximately 10-25 ng template DNA to each PCR and ran a no-template control for each primer pair. Amplification conditions were: initial 94C, 3 minute denaturation step; 30 cycles of 94C for 30s, 57C for 45s, and 72C for 60s; final 2 minute extension at 72C. The triplicate PCR reactions were pooled after amplification, visualized with the negative controls on a Caliper LabChipGX or Agilent TapeStation 4200, and purified using Ampure followed by PicoGreen quantitation and Ampure size selection.

Submitted by: Marine Biological Laboratory

Study: Deep Subsurface Targeted Locus (Loci)

PRJNA268940 • SRP050383 • All experiments • All runs

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This project targets deep microbial ecosystems of three significant, mostly unexplored (for microbiology) North American geological provinces: the Basin and Range, Black Hills, and Canadian Shield. In addition to their value for the exploration of novel deep habitats, these samples also allow us to address the following questions: (1) Is everything truly everywhere? (2) How does one recognize indigenous deep life? and (3) Is it possible via existing excavations to sample below the lower biosphere limit?

Sample: Novel Terrestrial Deep Subsurface Habitats of the North American Basin and Range, Black Hills, and Canadian Shield

SAMN03246968 • SRS775463 • All experiments • All runs

Organism: aquatic metagenome

Library:

Name: U12N_10_tunnel_Bv4v5

Instrument: Illumina MiSeq

Strategy: AMPLICON

Source: METAGENOMIC

Selection: PCR

Layout: PAIRED

Runs: 1 run, 224,233 spots, 112.6M bases, 52.7Mb

Run	# of Spots	# of Bases	Size	Published
SRR27223829	224,233	112.6M	52.7Mb	2023-12-15

ID:: 30963306

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