Arctic char log read counts
Read counts from RNA-sequencing experiment in Arctic char (Prokkola et al.). Rows correspond to genes and columns correspond to samples. Reads can be downloaded from NCBI SRA (accession SRP068854). The used reference is available at DDBJ/EMBL/GenBank under the accession GEKT00000000. The trimmed PE...
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Online Access: | https://dx.doi.org/10.6084/m9.figshare.5662489 https://figshare.com/articles/Arctic_char_log_read_counts/5662489 |
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ftdatacite:10.6084/m9.figshare.5662489 2023-05-15T14:53:57+02:00 Arctic char log read counts Prokkola, Jenni 2017 https://dx.doi.org/10.6084/m9.figshare.5662489 https://figshare.com/articles/Arctic_char_log_read_counts/5662489 unknown figshare Creative Commons Attribution 4.0 International https://creativecommons.org/licenses/by/4.0/legalcode cc-by-4.0 CC-BY 60806 Animal Physiological Ecology FOS Biological sciences 60408 Genomics dataset Dataset 2017 ftdatacite https://doi.org/10.6084/m9.figshare.5662489 2021-11-05T12:55:41Z Read counts from RNA-sequencing experiment in Arctic char (Prokkola et al.). Rows correspond to genes and columns correspond to samples. Reads can be downloaded from NCBI SRA (accession SRP068854). The used reference is available at DDBJ/EMBL/GenBank under the accession GEKT00000000. The trimmed PE reads from all samples were aligned against the assembly using Bowtie2, ignoring discordant and mixed alignments and allowing a maximum of 40 multiple alignments per read. Read counts per cluster were obtained using Corset (Davidson and Oshlack 2014). Clusters that were expressed with >1 counts per million reads (cpm) in at least 3 samples across all 18 samples were included in the analysis. Data were normalized for library sizes in Studio using edgeR package TMM-normalization (Robinson and Oshlack 2010) and normalized log counts of reads per million mapped reads in each sample exported. Dataset Arctic DataCite Metadata Store (German National Library of Science and Technology) Arctic Davidson ENVELOPE(-44.766,-44.766,-60.766,-60.766) |
institution |
Open Polar |
collection |
DataCite Metadata Store (German National Library of Science and Technology) |
op_collection_id |
ftdatacite |
language |
unknown |
topic |
60806 Animal Physiological Ecology FOS Biological sciences 60408 Genomics |
spellingShingle |
60806 Animal Physiological Ecology FOS Biological sciences 60408 Genomics Prokkola, Jenni Arctic char log read counts |
topic_facet |
60806 Animal Physiological Ecology FOS Biological sciences 60408 Genomics |
description |
Read counts from RNA-sequencing experiment in Arctic char (Prokkola et al.). Rows correspond to genes and columns correspond to samples. Reads can be downloaded from NCBI SRA (accession SRP068854). The used reference is available at DDBJ/EMBL/GenBank under the accession GEKT00000000. The trimmed PE reads from all samples were aligned against the assembly using Bowtie2, ignoring discordant and mixed alignments and allowing a maximum of 40 multiple alignments per read. Read counts per cluster were obtained using Corset (Davidson and Oshlack 2014). Clusters that were expressed with >1 counts per million reads (cpm) in at least 3 samples across all 18 samples were included in the analysis. Data were normalized for library sizes in Studio using edgeR package TMM-normalization (Robinson and Oshlack 2010) and normalized log counts of reads per million mapped reads in each sample exported. |
format |
Dataset |
author |
Prokkola, Jenni |
author_facet |
Prokkola, Jenni |
author_sort |
Prokkola, Jenni |
title |
Arctic char log read counts |
title_short |
Arctic char log read counts |
title_full |
Arctic char log read counts |
title_fullStr |
Arctic char log read counts |
title_full_unstemmed |
Arctic char log read counts |
title_sort |
arctic char log read counts |
publisher |
figshare |
publishDate |
2017 |
url |
https://dx.doi.org/10.6084/m9.figshare.5662489 https://figshare.com/articles/Arctic_char_log_read_counts/5662489 |
long_lat |
ENVELOPE(-44.766,-44.766,-60.766,-60.766) |
geographic |
Arctic Davidson |
geographic_facet |
Arctic Davidson |
genre |
Arctic |
genre_facet |
Arctic |
op_rights |
Creative Commons Attribution 4.0 International https://creativecommons.org/licenses/by/4.0/legalcode cc-by-4.0 |
op_rightsnorm |
CC-BY |
op_doi |
https://doi.org/10.6084/m9.figshare.5662489 |
_version_ |
1766325640739422208 |