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ERX2133330: Illumina HiSeq 2500 paired end sequencing; Scottish Blackface x Texel sheep transcriptome and gene expression atlas.
1 ILLUMINA (Illumina HiSeq 2500) run: 27M spots, 6.8G bases, 2.6Gb downloads

Design: RNA-Seq transcriptomic paired end experiment using polyA selection on an Illumina HiSeq 2500
Submitted by: The Roslin Institute
Study: RNA sequencing of tissues and cell types from Texel x Scottish Blackface sheep for transcriptome annotation and expression analysis.
show Abstracthide Abstract
Sheep are an important source of meat, milk and fibre globally. To support functional annotation of the sheep genome we have produced a high-resolution atlas of gene expression from a comprehensive set of tissues and cell types from Texel x Scottish Blackface crossbred individuals. RNA-Seq libraries were generated by Edinburgh Genomics from tissues and cells representing all the major organ systems from adult sheep and from several juvenile, neonatal and prenatal developmental time points. The dataset includes 352 medium depth (>25 million reads per sample) mRNA-Seq stranded libraries (125 base pairs paired-end) and 74 high depth (>100 million reads per sample) total RNA-Seq stranded libraries (125 base pairs paired-end). 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 emily.clark@roslin.ed.ac.uk or faang-dcc@ebi.ac.uk to enquire. The full guidelines can be found at http://www.faang.org/data-share-principle.
Sample: peripheral blood mononuclear cells from an adult male TxBF sheep
SAMEA6004918 • ERS2107357 • All experiments • All runs
Organism: mixed sample
Library:
Name: SHPM2PBMC
Instrument: Illumina HiSeq 2500
Strategy: RNA-Seq
Source: TRANSCRIPTOMIC
Selection: Oligo-dT
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: 251 days
experimental protocol: https://support.illumina.com/content/dam/illumina- (show full text...)(hide...)
https://support.illumina.com/content/dam/illumina-support/documents/documentation/chemistry_documentation/samplepreps_truseq/truseqstrandedmrna/truseq-stranded-mrna-sample-prep-guide-15031047-e.pdf
extraction protocol: ftp://ftp.faang.ebi.ac.uk/ftp/protocols/assays/ROS (show full text...)(hide...)
ftp://ftp.faang.ebi.ac.uk/ftp/protocols/assays/ROSLIN_SOP_Isolation_of_Total_RNA_from_Cells_Without_DNase_Treatment_20161116.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: -3.173114 decimal degrees
library preparation location latitude: 55.923953 decimal degrees
library preparation date: 2015-04 YYYY-MM
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: -3.173114 decimal degrees
sequencing location latitude: 55.923953 decimal degrees
sequencing date: not applicable
experiment target: polyA RNA
rna preparation 3' adapter ligation protocol: https://support.illumina.com/content/dam/illumina- (show full text...)(hide...)
https://support.illumina.com/content/dam/illumina-support/documents/documentation/chemistry_documentation/samplepreps_truseq/truseqstrandedmrna/truseq-stranded-mrna-sample-prep-guide-15031047-e.pdf
rna preparation 5' adapter ligation protocol: https://support.illumina.com/content/dam/illumina- (show full text...)(hide...)
https://support.illumina.com/content/dam/illumina-support/documents/documentation/chemistry_documentation/samplepreps_truseq/truseqstrandedmrna/truseq-stranded-mrna-sample-prep-guide-15031047-e.pdf
library generation pcr product isolation protocol: https://support.illumina.com/content/dam/illumina- (show full text...)(hide...)
https://support.illumina.com/content/dam/illumina-support/documents/documentation/chemistry_documentation/samplepreps_truseq/truseqstrandedmrna/truseq-stranded-mrna-sample-prep-guide-15031047-e.pdf
preparation reverse transcription protocol: https://support.illumina.com/content/dam/illumina- (show full text...)(hide...)
https://support.illumina.com/content/dam/illumina-support/documents/documentation/chemistry_documentation/samplepreps_truseq/truseqstrandedmrna/truseq-stranded-mrna-sample-prep-guide-15031047-e.pdf
library generation protocol: https://support.illumina.com/content/dam/illumina- (show full text...)(hide...)
https://support.illumina.com/content/dam/illumina-support/documents/documentation/chemistry_documentation/samplepreps_truseq/truseqstrandedmrna/truseq-stranded-mrna-sample-prep-guide-15031047-e.pdf
read strand: mate 2 sense
rna purity - 260:280 ratio: 2.03
rna purity - 260:230 ratio: 2.23
rna integrity number: 9.6
Runs: 1 run, 27M spots, 6.8G bases, 2.6Gb
Run# of Spots# of BasesSizePublished
ERR207433527,045,6906.8G2.6Gb2017-08-10

ID:
4376781

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