Metagenome in psoriasis vs healthy controls, San Francisco

To investigate the gut microbiome associated with psoriasis pathogenesis, we perform shotgun metagenomic analysis in 15 healthy subjects and 33 psoriasis patients. DNA was extracted from fecal samples with the modified cetyl trimethylammonium bromide (CTAB) method. The quality of the extracted DNA was assessed by gel electrophoresis and Quant-iT PicoGreen dsDNA Assay (Life Technologies) The extracted DNA was submitted to Vincent J. Coates Genomic Sequencing Laboratory at the California Institute for Quantitative Biosciences (www.qb3.berkeley.edu/gsl) for metagenomic library construction and sequencing. The metagenomic libraries were constructed using PrepX DNA library kit (Takara bio) and sequenced on HiSeq4000 (Illumina) for pair-end 150bp sequencing. Average of 22 million pair-end total reads were generated per sample. Reads were first mapped to human genome (GRCh38, GENCODE release 25) by bowtie2 (v2.2.8) to identified human DNA. The non-human reads were extracted and sorted by using samtool (v0.1.19). The resulting non-human reads are deposited.

Classified as human gut / stool shotgun DNA metagenome of adult by opus_adjudicated with confidence 0.80. Assay shotgun_dna.

• host run.host_tax_id · “9606”
• host study.description · “15 healthy subjects and 33 psoriasis patients”
• body site study.description · “DNA was extracted from fecal samples”
• life stage sample.attr.host_age · “29 (n=43/48)”

48 runs over 48 samples · mean 6.01 Gbp per run (median 5.65 Gbp, total 288.69 Gbp; 48 runs with a base count) · layout PAIRED 48 · platform ILLUMINA 48 · models Illumina HiSeq 4000 (48) · 90% of runs with a Sandpiper profile · first public 2021-07-04

Chang HW first · Yan D · Singh R · Bui A · Lee K · Truong A · Milush JM · Somsouk M · Liao W last · Argentini C first · Lugli GA · Tarracchini C · Fontana F · Mancabelli L · Viappiani A · Anzalone R · Angelini L · Alessandri G · Longhi G · Bianchi MG · Taurino G · Bussolati O · Milani C · van Sinderen D · Turroni F · Ventura M last · De Biase R · Bocchio F · De Conto F · Nouvenne A · Ticinesi A · Meschi T · Cecchi R · Wang X first · Sun J · Zhang X · Chen W · Cao J · Hu H last · Xie Y first · Lv G · Su D · Li M · Xu Q · Chen H · Cheng F · Dai D last

PRJNA634145.csv.gz (2.7 KB) · parquet (73.3 KB) — all 48 samples, every field with route and confidence · PRJNA634145_determinations.csv.gz (5.8 KB) — 609 evidence rows