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ERX1886690: Illumina HiSeq 2500 paired end sequencing; Pig transcriptome annotation and gene expression atlas
6 ILLUMINA (Illumina HiSeq 2500) runs: 46.2M spots, 9.2G bases, 5.7Gb downloads

Submitted by: The Roslin Institute
Study: Pig transcriptome and gene expression atlas
show Abstracthide Abstract
RNA sequencing of pig tissues for transcritpome annotation and expression analysis. Tissue specific RNA-seq data was generated to support annotation of coding and non-coding genes and to measure tissue specific expression. This study is part of the FAANG project, promoting rapid prepublication of data to support the research community. These data are released under Fort Lauderdale principles, as confirmed in the Toronto Statement (Toronto International Data Release Workshop. Birney et al. 2009. Pre-publication data sharing. Nature 461:168-170). Any use of this dataset must abide by the FAANG data sharing principles. Data producers reserve the right to make the first publication of a global analysis of this data. If you are unsure if you are allowed to publish on this dataset, please contact alan.archibald@roslin.ed.ac.uk, lel.eory@roslin.ed.ac.uk and faang@iastate.edu to enquire. The full guidelines can be found at http://www.faang.org/data-share-principle”.
Sample: alveolar macrophages from a juvenile Duroc pig
SAMEA103886137 • ERS1793662 • All experiments • All runs
Organism: mixed sample
Library:
Name: 2023N060
Instrument: Illumina HiSeq 2500
Strategy: RNA-Seq
Source: TRANSCRIPTOMIC
Selection: Inverse rRNA
Layout: PAIRED
Construction protocol: TruSeq Stranded mRNA Sample Preparation Guide Revision E
Experiment attributes: (show all 24 attributes...) (hide...)
assay type: transcription profiling by high throughput sequenc (show full text...)(hide...)
transcription profiling by high throughput sequencing
sample storage: frozen, -150 freezer
sample storage processing: cryopreservation, other
sampling to preparation interval: 1 weeks
experimental protocol: http://support.illumina.com/content/dam/illumina-s (show full text...)(hide...)
http://support.illumina.com/content/dam/illumina-support/documents/documentation/chemistry_documentation/samplepreps_truseq/truseqstrandedtotalrna/truseq-stranded-total-rna-sample-prep-guide-15031048-e.pdf
extraction protocol: ftp://ftp.faang.ebi.ac.uk/ftp/protocols/samples/RO (show full text...)(hide...)
ftp://ftp.faang.ebi.ac.uk/ftp/protocols/samples/ROSLIN_SOP_Isolation_of_RNA_from_frozen_tissue_20161108.pdf
library preparation location: Edinburgh Genomics, The University of Edinburgh, E (show full text...)(hide...)
Edinburgh Genomics, The University of Edinburgh, EH9 3FL, Edinburgh, Scotland
library preparation location longitude: -3 decimal degrees
library preparation location latitude: 56 decimal degrees
library preparation date: 2013-10-15 YYYY-MM-DD
sequencing location: Edinburgh Genomics, The University of Edinburgh, E (show full text...)(hide...)
Edinburgh Genomics, The University of Edinburgh, EH9 3FL, Edinburgh, Scotland
sequencing location longitude: -3 decimal degrees
sequencing location latitude: 56 decimal degrees
sequencing date: not applicable
experiment target: total RNA
rna preparation 3' adapter ligation protocol: http://support.illumina.com/content/dam/illumina-s (show full text...)(hide...)
http://support.illumina.com/content/dam/illumina-support/documents/documentation/chemistry_documentation/samplepreps_truseq/truseqstrandedtotalrna/truseq-stranded-total-rna-sample-prep-guide-15031048-e.pdf
rna preparation 5' adapter ligation protocol: http://support.illumina.com/content/dam/illumina-s (show full text...)(hide...)
http://support.illumina.com/content/dam/illumina-support/documents/documentation/chemistry_documentation/samplepreps_truseq/truseqstrandedtotalrna/truseq-stranded-total-rna-sample-prep-guide-15031048-e.pdf
library generation pcr product isolation protocol: http://support.illumina.com/content/dam/illumina-s (show full text...)(hide...)
http://support.illumina.com/content/dam/illumina-support/documents/documentation/chemistry_documentation/samplepreps_truseq/truseqstrandedtotalrna/truseq-stranded-total-rna-sample-prep-guide-15031048-e.pdf
preparation reverse transcription protocol: http://support.illumina.com/content/dam/illumina-s (show full text...)(hide...)
http://support.illumina.com/content/dam/illumina-support/documents/documentation/chemistry_documentation/samplepreps_truseq/truseqstrandedtotalrna/truseq-stranded-total-rna-sample-prep-guide-15031048-e.pdf
library generation protocol: http://support.illumina.com/content/dam/illumina-s (show full text...)(hide...)
http://support.illumina.com/content/dam/illumina-support/documents/documentation/chemistry_documentation/samplepreps_truseq/truseqstrandedtotalrna/truseq-stranded-total-rna-sample-prep-guide-15031048-e.pdf
read strand: mate 2 sense
rna purity - 260:280 ratio: 1.98
rna purity - 260:230 ratio: 2.16
rna integrity number: 8.6
Runs: 6 runs, 46.2M spots, 9.2G bases, 5.7Gb
Run# of Spots# of BasesSizePublished
ERR182427117,181,8403.4G2Gb2017-02-21
ERR18243247,613,5071.5G956Mb2017-02-21
ERR18243257,644,8151.5G962.2Mb2017-02-21
ERR18243646,222,5651.2G839.4Mb2017-02-21
ERR18243656,263,2951.3G842.5Mb2017-02-21
ERR18243841,322,475264.5M168.8Mb2017-02-21

ID:
3732228

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