Workflow: expression values from HPC RGD workflow (processed before workflow 2.1); computed sex, strand and library prep added by RGD attribute backfill 1.0 (2026-10-21) using the workflow 2.1 rules. Note: ComputedSex is called from sex-gene expression: R = (Xist TPM + 1) / (median TPM of Uty, Ddx3y, Kdm5d and Eif2s3y + 1); R >= 10 is called F, R <= 1 is called M, and other values, or samples where Xist and the Y-gene median are both below 1 TPM, are Undetermined. Females express Xist and males the Y-linked genes. Sry is reported but not used in the calculation. XYRatio (X:Y read coverage) is shown for reference only. Agreement compares ComputedSex with InputSex (submitted to GEO).
SampleID	InputSex	ComputedSex	XYRatio	Agreement	Xist	Uty	Sry	Ddx3y	Kdm5d	Eif2s3y	ComputedStrand	ComputedLibraryPrep	PctMRNA	PctIntronic	PctIntergenic	PctRibosomal	UniqPct	MultiPct	TooShortPct	NonPolyA_perM	LibraryPrepRule	LibraryPrepQC	LibraryPrepReason
GSM6523748	not_specified	M	NA	Conflict	0.03	9.22	0.00	29.41	15.55	49.23	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.549049	0.374708	0.073501	0.002742	85.36	2.94	10.25	1999	LP2 (2026-09-30)	PASS	NonPolyA_perM 1999 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM6523749	not_specified	M	NA	Conflict	0.10	9.22	0.00	26.59	17.52	53.23	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.563271	0.362324	0.071861	0.002544	85.28	2.77	10.55	1768	LP2 (2026-09-30)	PASS	NonPolyA_perM 1768 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM6523750	not_specified	M	NA	Conflict	0.05	8.86	0.00	28.27	15.56	51.56	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.558197	0.369009	0.069405	0.003389	84.27	2.73	11.68	1912	LP2 (2026-09-30)	PASS	NonPolyA_perM 1912 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM6523751	not_specified	M	NA	Conflict	0.05	8.43	0.00	28.83	17.03	54.32	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.558378	0.368182	0.071013	0.002426	86.42	2.73	9.48	1710	LP2 (2026-09-30)	PASS	NonPolyA_perM 1710 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM6523752	not_specified	M	NA	Conflict	0.11	8.40	0.00	29.48	16.44	57.94	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.578552	0.346975	0.071402	0.003071	84.42	2.72	11.50	1607	LP2 (2026-09-30)	PASS	NonPolyA_perM 1607 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM6523753	not_specified	M	NA	Conflict	0.11	8.28	0.00	31.34	17.03	57.09	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.564196	0.360653	0.072179	0.002972	84.44	2.84	11.30	1837	LP2 (2026-09-30)	PASS	NonPolyA_perM 1837 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not