|
| Status |
Public on Oct 28, 2020 |
| Title |
Group1-Desc-Control-2 |
| Sample type |
SRA |
| |
|
| Source name |
Gut microbiome - Descending colon
|
| Organism |
mouse gut metagenome |
| Characteristics |
strain: C57BL/6
strain description: C57BL/6 Background; Cage A
treatment: Control
Sex: F
age: 3.4
sample code: XL310-2Dis_S250_L001_R1
|
| Treatment protocol |
To generate mice with induced O-glycan deficiency in either the ascending or descending colon, mutant or WT littermates were injected intraperitoneally with 0.5 mg tamoxifen (TM, or ~20 mg/kg, MP Bio-medicals) in an ethanol/sunflower seed oil mixture (1:9 (v/v)) daily for 5 consecutive days, and mice were analyzed for deletion 5 or 10 days post final TM treatment. The dosage of TM was determined after serial titrations and characterization of different TM dosages in different mutant models.
|
| Growth protocol |
To produce mice with induced deficiency of O-glycans specifically in colon, C1galt1-floxed (C1galt1f/f);C3GnT-/- females were crossed with previously generated C1galt1f/f;VillinCre-ERT2 (TM-IEC C1galt1f/f) mice on a C3GnT+/- background to generate C1galt1f/f;VillinCre-ERT2;C3GnT-/- (TM-DKO) and WT littermates. All mutant mice and WT littermates were on a C57BL/6J (BL/6) and 129/SvImJ (129/Sv) mixed background. Inbred WT mice (BL/6, Balb/c, and 129SvJ mice) were obtained from the Jackson Laboratory. Outbred WT CD1 mice and Swiss Webster (SW) mice and Sprague Dawley rat were bred in house. Animals were fed standard chow (PicoLab Rodent Diet 20; LabDiet 5053). Animals were housed in a specific pathogen free facility (SPF). All animal experiments were approved by the Institutional Animal Care and Use Committee of Oklahoma Medical Research Foundation.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA extraction and sequencing of the 16S ribosomal RNA gene was performed for mouse fecal samples as previously described (Tong et. al, PMID: 25367129). In brief, bacterial DNA was extracted using the ZymoBIOMICS DNA kit (cat#D4300) with bead beating.
The V4 region of the 16S gene was amplified and barcoded using 515f/806r primers then 250x2 bp sequencing was performed on an Illumina HiSeq 2500.
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
16S rDNA sequencing
Dis-Group1-Control_2
|
| Data processing |
Library strategy: 16S rNA sequencing
Data quality check was done on an Illumina SAV. Demultiplexing was performed with the Illumina Bcl2fastq2 v 2.17 program.
Raw data were processed using DADA2 in R and quality-filtered reads (~50862 reads per sample) were used to identify amplicon sequence variants (ASV), with taxonomy assigned based upon the Silva database.
Data in supplementary file ProDis_ASVcounts.txt was generated by the DADA2 pipeline: tab delimited file with 1) #OTU: nucleotide sequence of the exact amplicon sequence variant (ASV), 2) per-sample ASV counts, and 3) full phylogeny of the ASV (species level)
Genome_build: SILVA microbial database
Supplementary_files_format_and_content: Tab delimited: 1) #OTU: nucleotide sequence of the exact amplicon sequence variant (ASV), 2) per-sample ASV counts, and 3) full phylogeny of the ASV (species level)
|
| |
|
| Submission date |
Jun 25, 2019 |
| Last update date |
Oct 28, 2020 |
| Contact name |
David Casero |
| E-mail(s) |
dcasero@ucla.edu
|
| Phone |
3108250274
|
| Organization name |
UCLA
|
| Department |
Pathology and Laboratory Medicine
|
| Street address |
610 Charles Young Drive East
|
| City |
Los Angeles |
| State/province |
CA |
| ZIP/Postal code |
90095 |
| Country |
USA |
| |
|
| Platform ID |
GPL22735 |
| Series (2) |
| GSE133256 |
Ascending colon-derived mucin-type O-glycans form key mucus layers encapsulating microbiota in the colon (16S rNA-seq) |
| GSE133257 |
Ascending colon-derived mucin-type O-glycans form key mucus layers encapsulating microbiota in the colon |
|
| Relations |
| BioSample |
SAMN12130949 |
| SRA |
SRX6358986 |
