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For all control samples annotated as male, we multiply the RCs on chrX by two to make them comparable with female control samples.
Twelve samples annotated as laser capture micro-dissected (LCM) non-malignant fallopian tube epithelium without BRCA1 or BRCA2 mutations were selected.
We excluded probes which were not determined to be expressed significantly above background in 90% of samples; annotated as 'bad' quality according to detailed analysis of Illumina expression arrays (47) or overlapped SNPs which were validated in dbSNP version 131 and, if frequency information was available, not monomorphic in Europeans.
Close inspection of these 521 samples revealed that they included 3 samples that were in fact DNA-seq runs, 312 samples annotated as single-cell sequencing runs, 97 samples that specifically targeted the HLA region and 1 sample was a Geuvadis run [ 28] that did not cluster near the other Geuvadis samples.
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Contigs were annotated as above.
All sequences were annotated as above.
Here, we generated representative expression vectors for each stage of development as the mean of all samples annotated with a given developmental stage ontology category.
In two cases, the samples were annotated as male but clustered within the females; these are likely mis-annotations.
Two other upregulated genes in our constitutive samples are annotated as putative phenylcoumaran benzylic ether reductase.
To eliminate all other small non-coding RNAs, clean tags from each sample were annotated as tRNAs, rRNAs, scRNAs, snRNAs, and snoRNAs.
From these samples, 79 are annotated as Her2 and 36 as Her2.
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