ena-STUDY-IMPERIAL COLLEGE-19-12-2017-10:53:00:451-76
Metagenomic reads for the microbiota of premature infant faecal samples
24 faecal samples from premature infants (12 from babies who developed NEC, 12 from control infants), a negative control (no faeces) and a technical replicate underwent a DNA extraction process which enriched for microbial DNA. Briefly, DNA extractions were performed with 200 mg of faeces and the process included selective lysis of eukaryotic cells and degradation of eukaryotic DNA, followed by bead-beating to extract bacterial DNA prior to purification. The DNA was fragmented using the NEBNext dsDNA fragmentase kit (NEB), and shotgun libraries prepared using the KAPA HyperPrep kit (KAPA Biosystems). Ligated libraries were PCR amplified with the number of cycles being dependant on starting material (between two and eight cycles). The library was normalised, pooled and diluted to 1.6pM prior to loading on an Illumina NextSeq 500 system. Paired end sequencing was performed using a v2 300 cycle high output reagent kit (Illumina).  Sample Key: N1 SAMEA104443118 N2 SAMEA104443120 N3 SAMEA104443105 N4 SAMEA104443122 N5 SAMEA104443106 N6 SAMEA104443124 N7 SAMEA104443126 N8 SAMEA104443108 N9 SAMEA104443127 N10 SAMEA104443110 N11 SAMEA104443112 N12 SAMEA104443115 C1 SAMEA104443119 C2 SAMEA104443121 C3 SAMEA104443123 C4 SAMEA104443125 C5 SAMEA104443107 C6 SAMEA104443128 C7 SAMEA104443129 C8 SAMEA104443109 C9 SAMEA104443111 C10 SAMEA104443113 C11 SAMEA104443114 C12 SAMEA104443117 C12R SAMEA104443116 Negative SAMEA104443104
24 faecal samples from premature infants (12 from babies who developed NEC, 12 from control infants), a negative control (no faeces) and a technical replicate underwent a DNA extraction process which enriched for microbial DNA. Briefly, DNA extractions were performed with 200 mg of faeces and the process included selective lysis of eukaryotic cells and degradation of eukaryotic DNA, followed by bead-beating to extract bacterial DNA prior to purification. The DNA was fragmented using the NEBNext dsDNA fragmentase kit (NEB), and shotgun libraries prepared using the KAPA HyperPrep kit (KAPA Biosystems). Ligated libraries were PCR amplified with the number of cycles being dependant on starting material (between two and eight cycles). The library was normalised, pooled and diluted to 1.6pM prior to loading on an Illumina NextSeq 500 system. Paired end sequencing was performed using a v2 300 cycle high output reagent kit (Illumina).  Sample Key: N1 SAMEA104443118 N2 SAMEA104443120 N3 SAMEA104443105 N4 SAMEA104443122 N5 SAMEA104443106 N6 SAMEA104443124 N7 SAMEA104443126 N8 SAMEA104443108 N9 SAMEA104443127 N10 SAMEA104443110 N11 SAMEA104443112 N12 SAMEA104443115 C1 SAMEA104443119 C2 SAMEA104443121 C3 SAMEA104443123 C4 SAMEA104443125 C5 SAMEA104443107 C6 SAMEA104443128 C7 SAMEA104443129 C8 SAMEA104443109 C9 SAMEA104443111 C10 SAMEA104443113 C11 SAMEA104443114 C12 SAMEA104443117 C12R SAMEA104443116 Negative SAMEA104443104