This webpage is created for sharing the datasets of the CRISPR and cas gene study of the Human Microbiome Project (HMP1-II) samples and consists of spacer and repeat sequences (hmp1-II-crispr-spacers.tar.gz, hmp1-II-crispr-repeats.tar.gz) recovered from the whole genome shotgun samples using a read-based approach (Crass, Skennerton et al, 2013). The functional and taxonomic spacer annotation was obtained by aligning the spacer content to the sample’s metagenome and the UniRef90 collection (hmp1-II-crispr-spacers-annotation.tar.gz).
We further provide the UniRef90 profiling of the 2,355 metagenomes of the HMP1-II collection which was used as the basis of the Cas1-Cas12 analysis (Files hmp1-II_uniref90.tar.gz and hmp1-II_uniref90_cas.tar.gz). We used a custom HUMAnN2 database to subet relevant protein families (humann2_cas_mapping.tar.gz).
This dataset is also available at Mendeley Data via doi 10.17632/bsmmy8pwrt.1
CRISPR elements
| Dataset | MD5 | Description |
|---|---|---|
| hmp1-II-crispr-spacers-annotation.tar.gz | 710c6dca143017c58acf3f98f7877736 |
annotated spacer set |
| hmp1-II-crispr-spacers.tar.gz | 104b51c91063161a7d4a5bfc30e4bc3d |
CRISPR spacers |
| hmp1-II-crispr-repeats.tar.gz | a2893a93321792f9ec7fd569f1973ab5 |
CRISPR repeats |
| mapping_assembly.tar.gz | 035b3cbd5ebee9498f9588f72f3a0ecd |
Annotation of 1,630,590 spacers based on mapping to the sample’s assembly |
Cas profile
| Dataset | MD5 | Description |
|---|---|---|
| hmp1-II_uniref90.tar.gz | 9459f63518cfa9c9cd71332d1a70ca2b |
Global UniRef90 Profile generated with the HMP Unified Metabolic Analysis Network (HUMAnN2) and normalized for gene length and sequencing depth |
| humann2_cas_mapping.tar.gz | 7e75d603475d63cd08e05ae2478c4d8a |
Cas table of UniRef90 families used to subset the global UniRef90 Profile for Cas analysis |
| hmp1-II_uniref90_cas.tar.gz | ccd7e242dd80e50c17a10e2b9bd54e5e |
Filtered UniRef90 abundance profile for relevant Cas1 - Cas12 gene families (normalized for gene length and sequencing depth) |
If you find this data useful, please cite our paper
Philipp C. Münch, PC,Franzosa EA, Stecher B, McHardy AC* and Huttenhower C*. Natural CRISPR systems and targets in the human microbiome, Cell Host & Microbe (in Revision)
- these authors share senior authorship