Rabbit Lung_DH_TO_Control

Experiment ID:ERP010078
Technology:RNA-Seq
Description:Investigation into the effects of Congenital Diaphragmatic Hernia (CDH) and subsequent treatment with tracheal occlusion (TO) on the pulmonary transcriptome. A diaphragm defect was created by surgical means in fetal rabbits. The surgical creation of diaphragmatic hernia (DH) allows for direct analysis of changes in pulmonary gene expression due to pulmonary hypoplasia, without the need for gene knockdown (as for KO mice) or use of teratogens (such as nitrofen). The subsequent treatment with tracheal occlusion (TO) was also investigated to determine the changes in gene expression due to forced lung growth in the prenatal phase. RNA-Seq analysis was performed on left lung samples from fetal rabbits. Samples were generated and analysed for DH (n=4), TO (n=6), and control lungs (n=4)
Source:ERP010078 SRA

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Library ID
Identifier of the RNA-Seq library
Anat. entity ID
ID of the anatomical localization of the sample
Anat. entity name
Name of the anatomical localization of the sample
Anat. entity author annotation
Free text annotation of anatomical localization of the sample as provided by authors
Stage ID
ID of the developmental and life stage of the sample
Stage name
Name of the developmental and life stage of the sample
Stage author annotation
Free text annotation of the developmental and life stage of the sample as provided by authors
Sex
Annotation of the sex of the sample
Strain
Annotation of the strain of the sample
Time
Free text annotation of the time of sampling as provided by authors
Time unit
Unit for the time of sampling as provided by authors
Species
Physiological status
Physiological status of the organism at time of sampling
Technology
Sequencing platform
Sequenced transcript part
Possible values are: full length, all parts of the transcript are sequenced; 3': only the 3' end of the transcript is sequenced; 5': only the 5' end of the transcript is sequenced.
Fragmentation
Size of the RNA fragmentation
Run sequencing type
Paired-end or single-read run
Total read count
Total number of reads for the library.
Mapped read count
Number of reads that could be mapped to the transcriptome.
Total UMI count
Total number of individual RNA molecules (UMI) for the annotated sample. Only applicable for libraries producing UMIs.
Mapped UMI count
Number of UMIs that could be mapped to the transcriptome. Only applicable for libraries producing UMIs.
Distinct rank count
When performing a fractional ranking of the genes in the annotated sample, based on their expression level, number of distinct ranks observed, to have a value of the power for distinguishing expression levels. Used as a weight to compute a weighted mean rank accross samples for each gene and compute expression scores in Bgee.
Max rank
When performing a fractional ranking of the genes in the annotated sample, based on their expression level, maximum rank attained in the sample. Used to normalize ranks accross samples and compute expression scores in Bgee.
Link to processed expression values
See the processed expression value results for this assay
ERX921841UBERON:0002168 left lungleft lungUBERON:0000068 embryo stagegestational age: 30 dayNANANANAOryctolagus cuniculusNAIlluminaIllumina HiSeq 2000FULL_LENGTH50single145255248324011001621618667Browse results
ERX921845UBERON:0002168 left lungleft lungUBERON:0000068 embryo stagegestational age: 30 dayNANANANAOryctolagus cuniculusNAIlluminaIllumina HiSeq 2000FULL_LENGTH50single97642775772619001587618475Browse results
ERX921848UBERON:0002168 left lungleft lungUBERON:0000068 embryo stagegestational age: 30 dayNANANANAOryctolagus cuniculusNAIlluminaIllumina HiSeq 2000FULL_LENGTH50single2203185412844765001679318970.5Browse results
ERX921851UBERON:0002168 left lungleft lungUBERON:0000068 embryo stagegestational age: 30 dayNANANANAOryctolagus cuniculusNAIlluminaIllumina HiSeq 2000FULL_LENGTH50single141893708110008001627318683Browse results