Saved in:
| Main Author: | |
|---|---|
| Format: | Recurso digital |
| Language: | |
| Published: |
Zenodo
2025
|
| Online Access: | https://doi.org/10.5281/zenodo.17964272 |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
| _version_ | 1866902116138745856 |
|---|---|
| author | Grandchamp, Anna |
| author_facet | Grandchamp, Anna |
| contents | <p>DESwoMAN was used with Strategy 1 and Strategy 2 with human genome as query. <br>For Strategy 1, The genome of Homo sapiens (human): GRCh38.p14 was downloaded from NCBI RefSeq (O’Leary et al., 2016) database and used as query genome. As target, we used mammalian outgroup species and downloaded the reference genomes ofPan Paniscus (Bonobo) : NCBI RefSeq assembly GCF_029289425.2. Gorilla gorilla (Gorilla) NCBI RefSeq assembly GCF_029281585.2. Pan Troglodytes (Chimpanzee) NCBI RefSeq assembly GCF_028858775.2. Macaca mulatta (macaque) NCBI RefSeq assembly GCF_003339765.1. Mus musculus (mouse) NCBI RefSeq assembly GCF_000001635.27. Pongo Pygmaeus (Orangutan) NCBI RefSeq assembly GCF_028885625.2. For each genome, mammal brain RNA-seq data (Brawand et al., 2011) were downloaded in NCBI Sequence Read Archive (Leinonen et al., 2010), where author produced 131 high-quality polyadenylated RNA-seq libraries of mammals. We used : Homo sapiens}: brain (ID hsa br F 1 SRR306838), Mus musculus : brain (ID mmu br F 1 SRR306757), Gorilla gorilla brain (ID ggo br M 1 SRR306801), Pongo Pygmaeus bain (ID ppy br F 1 SRR306791), Macaca mulatta brain (ID mml br F 1 SRR306777), Pan Troglodytes (ID ptr br F 1 SRR306811) and Pan Paniscus brain (ID ppa br F 1 SRR306826). <br>For Strategy 2, 5 human RNA-seq data were selected from : brain (ID hsa br F 1 SRR306838), cerebellum (ID hsa cb F 1 SRR306844), heart (ID hsa ht F 1 SRR306847), kidney (ID hsa kd F 1 SRR306851) and testis (ID hsa ts M 1 SRR306857). </p> <p> </p> <p>O’Leary, N. A., Wright, M. W., Brister, J. R., Ciufo, S., Haddad, D., McVeigh, R., Rajput, B., Robbertse,503<br>B., Smith-White, B., Ako-Adjei, D., et al. Reference sequence (refseq) database at ncbi: current status,504<br>taxonomic expansion, and functional annotation. Nucleic acids research, 44(D1):D733–D745, 2016.</p> <p> </p> <p>Brawand, D., Soumillon, M., Necsulea, A., Julien, P., Csárdi, G., Harrigan, P., Weier, M., Liechti, A., Aximu-439<br>Petri, A., Kircher, M., et al. The evolution of gene expression levels in mammalian organs. Nature, 478440<br>(7369):343–348, 2011.</p> <p> </p> <p>Leinonen, R., Sugawara, H., Shumway, M., and Collaboration, I. N. S. D. The sequence read archive. Nucleic485<br>acids research, 39(suppl_1):D19–D21, 2010.</p> |
| format | Recurso digital |
| id | zenodo_https___doi_org_10_5281_zenodo_17964272 |
| institution | Zenodo |
| language | |
| publishDate | 2025 |
| publisher | Zenodo |
| record_format | zenodo |
| spellingShingle | DESwoMAN supp files Grandchamp, Anna <p>DESwoMAN was used with Strategy 1 and Strategy 2 with human genome as query. <br>For Strategy 1, The genome of Homo sapiens (human): GRCh38.p14 was downloaded from NCBI RefSeq (O’Leary et al., 2016) database and used as query genome. As target, we used mammalian outgroup species and downloaded the reference genomes ofPan Paniscus (Bonobo) : NCBI RefSeq assembly GCF_029289425.2. Gorilla gorilla (Gorilla) NCBI RefSeq assembly GCF_029281585.2. Pan Troglodytes (Chimpanzee) NCBI RefSeq assembly GCF_028858775.2. Macaca mulatta (macaque) NCBI RefSeq assembly GCF_003339765.1. Mus musculus (mouse) NCBI RefSeq assembly GCF_000001635.27. Pongo Pygmaeus (Orangutan) NCBI RefSeq assembly GCF_028885625.2. For each genome, mammal brain RNA-seq data (Brawand et al., 2011) were downloaded in NCBI Sequence Read Archive (Leinonen et al., 2010), where author produced 131 high-quality polyadenylated RNA-seq libraries of mammals. We used : Homo sapiens}: brain (ID hsa br F 1 SRR306838), Mus musculus : brain (ID mmu br F 1 SRR306757), Gorilla gorilla brain (ID ggo br M 1 SRR306801), Pongo Pygmaeus bain (ID ppy br F 1 SRR306791), Macaca mulatta brain (ID mml br F 1 SRR306777), Pan Troglodytes (ID ptr br F 1 SRR306811) and Pan Paniscus brain (ID ppa br F 1 SRR306826). <br>For Strategy 2, 5 human RNA-seq data were selected from : brain (ID hsa br F 1 SRR306838), cerebellum (ID hsa cb F 1 SRR306844), heart (ID hsa ht F 1 SRR306847), kidney (ID hsa kd F 1 SRR306851) and testis (ID hsa ts M 1 SRR306857). </p> <p> </p> <p>O’Leary, N. A., Wright, M. W., Brister, J. R., Ciufo, S., Haddad, D., McVeigh, R., Rajput, B., Robbertse,503<br>B., Smith-White, B., Ako-Adjei, D., et al. Reference sequence (refseq) database at ncbi: current status,504<br>taxonomic expansion, and functional annotation. Nucleic acids research, 44(D1):D733–D745, 2016.</p> <p> </p> <p>Brawand, D., Soumillon, M., Necsulea, A., Julien, P., Csárdi, G., Harrigan, P., Weier, M., Liechti, A., Aximu-439<br>Petri, A., Kircher, M., et al. The evolution of gene expression levels in mammalian organs. Nature, 478440<br>(7369):343–348, 2011.</p> <p> </p> <p>Leinonen, R., Sugawara, H., Shumway, M., and Collaboration, I. N. S. D. The sequence read archive. Nucleic485<br>acids research, 39(suppl_1):D19–D21, 2010.</p> |
| title | DESwoMAN supp files |
| url | https://doi.org/10.5281/zenodo.17964272 |