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 (2026-10-22) 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
GSM5516759	M	M	NA	Agree	0.91	19.44	0.00	22.03	22.47	24.24	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.420616	0.397906	0.072835	0.108642	45.30	9.92	43.94	6483	LP2 (2026-09-30)	PASS	NonPolyA_perM 6483 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM5516760	M	M	NA	Agree	0.57	18.34	0.00	18.95	22.15	33.95	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.431251	0.416976	0.084698	0.067074	45.82	7.19	45.95	8525	LP2 (2026-09-30)	PASS	NonPolyA_perM 8525 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM5516762	M	M	NA	Agree	0.52	17.38	0.00	26.47	20.72	26.17	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.422259	0.395171	0.073837	0.108733	46.57	10.26	42.38	6499	LP2 (2026-09-30)	PASS	NonPolyA_perM 6499 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM5516764	M	M	NA	Agree	0.28	15.60	0.00	26.37	17.87	20.93	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.489579	0.268158	0.078559	0.163704	42.75	14.49	41.67	7687	LP2 (2026-09-30)	PASS	NonPolyA_perM 7687 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not