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| !Assay | ||
| seqspec_version: 0.3.0 | ||
| assay_id: HiRES | ||
| name: HiRES | ||
| doi: https://doi.org/10.1126/science.adg3797 | ||
| date: 08 June 2023 | ||
| description: Linking genome structures to functions by simultaneous single-cell Hi-C and RNA-seq | ||
| modalities: | ||
| - rna | ||
| - dna | ||
| lib_struct: Custom | ||
| library_protocol: Custom | ||
| library_kit: Illumina Truseq Dual Index | ||
| sequence_protocol: Illumina NovaSeq 6000 | ||
| sequence_kit: NovaSeq 6000 v1.5 | ||
| sequence_spec: [] | ||
| library_spec: | ||
| - !Region | ||
| parent_id: null | ||
| region_id: hic | ||
| region_type: dna | ||
| name: HiC | ||
| sequence_type: joined | ||
| sequence: AATGATACGGCGACCACCGAGATCTACACNNNNNNNNNNNNNNNNCGCGTCTGTCGTCGGCAGCGTCAGATGTGTATAAGAGACAGXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXCTGTCTCTTATACACATCTCCGAGCCCACGAGACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG | ||
| min_len: 153 | ||
| max_len: 1150 | ||
| onlist: null | ||
| regions: | ||
| - !Region | ||
| parent_id: hic | ||
| region_id: hic-illumina_p5 | ||
| region_type: illumina_p5 | ||
| name: Illumina P5 | ||
| sequence_type: fixed | ||
| sequence: AATGATACGGCGACCACCGAGATCTACAC | ||
| min_len: 29 | ||
| max_len: 29 | ||
| onlist: null | ||
| regions: null | ||
| - !Region | ||
| parent_id: hic | ||
| region_id: hic-index5 | ||
| region_type: barcode | ||
| name: Cell Barcode 1 | ||
| sequence_type: onlist | ||
| sequence: NNNNNNNNNNNNNNNN | ||
| min_len: 8 | ||
| max_len: 8 | ||
| onlist: !Onlist | ||
| file_id: atac_737K-arc-v1.txt.gz | ||
| filename: atac_737K-arc-v1.txt.gz | ||
| filetype: txt | ||
| filesize: 0 | ||
| url: https://teichlab.github.io/scg_lib_structs/data/10X-Genomics/atac_737K-arc-v1.txt.gz | ||
| urltype: https | ||
| md5: 0 | ||
| location: remote | ||
| regions: null | ||
| - !Region | ||
| parent_id: hic | ||
| region_id: hic-nextera_read1 | ||
| region_type: nextera_read1 | ||
| name: nextera_read1 | ||
| sequence_type: fixed | ||
| sequence: TCGTCGGCAGCGTCAGATGTGTATAAGAGACAG | ||
| min_len: 33 | ||
| max_len: 33 | ||
| onlist: null | ||
| regions: null | ||
| - !Region | ||
| parent_id: hic | ||
| region_id: hic-gDNA | ||
| region_type: gdna | ||
| name: gDNA | ||
| sequence_type: random | ||
| sequence: XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX | ||
| min_len: 1 | ||
| max_len: 1000 | ||
| onlist: null | ||
| regions: null | ||
| - !Region | ||
| parent_id: hic | ||
| region_id: hic-nextera_read2 | ||
| region_type: nextera_read2 | ||
| name: nextera_read2 | ||
| sequence_type: fixed | ||
| sequence: CTGTCTCTTATACACATCTCCGAGCCCACGAGAC | ||
| min_len: 34 | ||
| max_len: 34 | ||
| onlist: null | ||
| regions: null | ||
| - !Region | ||
| parent_id: hic | ||
| region_id: hic-index7 | ||
| region_type: barcode | ||
| name: HiC barcode 2 | ||
| sequence_type: onlist | ||
| sequence: NNNNNNNN | ||
| min_len: 8 | ||
| max_len: 8 | ||
| onlist: null | ||
| regions: null | ||
| - !Region | ||
| parent_id: hic | ||
| region_id: hic-illumina_p7 | ||
| region_type: illumina_p7 | ||
| name: Illumina P7 | ||
| sequence_type: fixed | ||
| sequence: ATCTCGTATGCCGTCTTCTGCTTG | ||
| min_len: 24 | ||
| max_len: 24 | ||
| onlist: null | ||
| regions: null | ||
| - !Region | ||
| parent_id: null | ||
| region_id: rna | ||
| region_type: rna | ||
| name: RNA | ||
| sequence_type: joined | ||
| sequence: AATGATACGGCGACCACCGAGATCTACACNNNNNNNNNNNNNNNNCGCGTCTGTCGTCGGCAGCGTCAGATGTGTATAAGAGACAGXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXCTGTCTCTTATACACATCTCCGAGCCCACGAGACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG | ||
| min_len: 153 | ||
| max_len: 1150 | ||
| onlist: null | ||
| regions: | ||
| - !Region | ||
| parent_id: rna | ||
| region_id: rna-illumina_p5 | ||
| region_type: illumina_p5 | ||
| name: Illumina P5 | ||
| sequence_type: fixed | ||
| sequence: AATGATACGGCGACCACCGAGATCTACAC | ||
| min_len: 29 | ||
| max_len: 29 | ||
| onlist: null | ||
| regions: null | ||
| - !Region | ||
| parent_id: rna | ||
| region_id: rna-index5 | ||
| region_type: barcode | ||
| name: Cell Barcode 1 | ||
| sequence_type: onlist | ||
| sequence: NNNNNNNNNNNNNNNN | ||
| min_len: 8 | ||
| max_len: 8 | ||
| onlist: !Onlist | ||
| file_id: index5.txt | ||
| filename: index5.txt | ||
| filetype: txt | ||
| filesize: 0 | ||
| url: index5.txt | ||
| urltype: local | ||
| md5: 0 | ||
| location: local | ||
| regions: null | ||
| - !Region | ||
| parent_id: rna | ||
| region_id: rna-nextera_read1 | ||
| region_type: nextera_read1 | ||
| name: nextera_read1 | ||
| sequence_type: fixed | ||
| sequence: TCGTCGGCAGCGTCAGATGTGTATAAGAGACAG | ||
| min_len: 33 | ||
| max_len: 33 | ||
| onlist: null | ||
| regions: null | ||
| - !Region | ||
| parent_id: rna | ||
| region_id: rna-gDNA | ||
| region_type: cdna | ||
| name: cDNA | ||
| sequence_type: random | ||
| sequence: XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX | ||
| min_len: 1 | ||
| max_len: 1000 | ||
| onlist: null | ||
| regions: null | ||
| - !Region | ||
| parent_id: rna | ||
| region_id: rna-umi | ||
| region_type: umi | ||
| name: RNA UMI | ||
| sequence_type: random | ||
| sequence: XXXXXXXX | ||
| min_len: 8 | ||
| max_len: 8 | ||
| onlist: null | ||
| regions: null | ||
| - !Region | ||
| parent_id: rna | ||
| region_id: rna-linker | ||
| region_type: linker | ||
| name: rna-linker | ||
| sequence_type: fixed | ||
| sequence: CATTGCGCAATACTACCTCAACC | ||
| min_len: 23 | ||
| max_len: 23 | ||
| onlist: null | ||
| regions: null | ||
| - !Region | ||
| parent_id: rna | ||
| region_id: rna-nextera_read2 | ||
| region_type: nextera_read2 | ||
| name: nextera_read2 | ||
| sequence_type: fixed | ||
| sequence: CTGTCTCTTATACACATCTCCGAGCCCACGAGAC | ||
| min_len: 34 | ||
| max_len: 34 | ||
| onlist: null | ||
| regions: null | ||
| - !Region | ||
| parent_id: rna | ||
| region_id: rna-index7 | ||
| region_type: barcode | ||
| name: RNA barcode 2 | ||
| sequence_type: onlist | ||
| sequence: NNNNNNNN | ||
| min_len: 8 | ||
| max_len: 8 | ||
| onlist: null | ||
| regions: null | ||
| - !Region | ||
| parent_id: rna | ||
| region_id: rna-illumina_p7 | ||
| region_type: illumina_p7 | ||
| name: Illumina P7 | ||
| sequence_type: fixed | ||
| sequence: ATCTCGTATGCCGTCTTCTGCTTG | ||
| min_len: 24 | ||
| max_len: 24 | ||
| onlist: null | ||
| regions: null |