| Alias |
Interfold |
| Description |
The proximal murine colon contains mucosal folds that are known to be associated with morphologically distinct microbes. To identify these microbes, we utilized the technique of laser capture microdissection to sample microbes associated with these folds (interfold region) and within the central lumen (digesta region). Tag pyrosequencing of 16S rRNA genes was used to compare microbial populations between interfold and digesta samples. |
| Host (scientific name) |
Mus musculus |
| INSDC center alias |
WUSTL |
| INSDC center name |
Washington University School of Medicine, St. Louis, MO. USA |
| INSDC first public |
2010-11-10T00:00:12Z |
| INSDC last update |
2018-03-09T09:52:15Z |
| INSDC status |
public |
| SRA accession |
ERS013679 |
| Sample Name |
ERS013679 |
| Title |
mouse gut metagenome |
| age |
8 weeks |
| amount or size of sample collected |
1 LCM cap per mouse (3 mice) |
| assembly |
Ribosomal Database Project (RDP) (Cole et al 2009, Wang et al 2007). High-quality reads of at least 310 bases were aligned using the INFERNAL aligner (Nawrocki et al 2009) at the RDP. |
| body habitat |
colon |
| body site |
mucosa |
| collection date |
2009-10-19 |
| diet |
Standard irradiated chow diet (PicoLab Rodent Chow 20, Purina Mills) and water ad libitum. |
| environment |
Proximal murine colon; Mucosa |
| environmental package |
host associated |
| experimental factor |
The proximal murine colon contains mucosal folds that are known to be associated with morphologically distinct microbes. To identify these microbes, we utilized the technique of laser capture microdissection to sample microbes associated with these folds (interfold region) and within the central lumen (digesta region). Tag pyrosequencing of 16S rRNA genes was used to compare microbial populations between interfold and digesta samples. |
| geographic location (country) |
USA:Washington |
| geographic location (latitude and longitude) |
38.638231 N 90.264076 W |
| height or length |
not recorded |
| host color |
black |
| host subject id |
N1, N2, N3 |
| host taxid |
10090 |
| investigation type |
miens-survey |
| library reads sequenced |
29563 |
| life stage |
adult |
| nucleic acid amplification |
Hamady M, Walker JJ, Harris JK, Gold NJ, Knight R (2008). Error-correcting barcoded primers for pyrosequencing hundreds of samples in multiplex. Nat Methods 5: 235-237 |
| nucleic acid extraction |
QIAamp DNA Micro Kit (Qiagen, Valencia, CA). After DNA extraction samples from the Interfold-region were pooled for sequence analysis |
| pcr conditions |
initial denaturation:95°C_2 min; 95°C_20 sec; 52°C_20 sec; 65°C_1 min; 30 cycles |
| pcr primers |
27F: 5'-AGAGTTTGATCCTGGCTCAG-3’; 338R: 5'-TGCTGCCTCCCGTAGGAGT-3’ |
| pooling of DNA extracts (if done) |
1 LCM sample from 3 individual mice were pooled after DNA extraction, 4 replicate PCR reactions from that DNA sample were also pooled prior to sequencing |
| project name |
16s rRNA-pyrosequencing-mouse colon |
| sample collection device or method |
Laser capture microdissection (LCM) |
| sample storage duration |
3 days |
| sample storage location |
Freezer #5 TSS |
| sample storage temperature |
-20 |
| sequence quality check |
Tags, primers and low quality sequences were removed using the GL FLX software hosted at the Ribosomal Database Project (RDP) (Cole et al 2009, Wang et al 2007). |
| sequencing method |
pyrosequencing; GS-FLX Titanium |
| sex |
female |
| target gene |
16S rRNA gene, V1 and V2 region |