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
GSM1039505	M	M	NA	Agree	1.16	1.96	0.00	22.82	6.21	38.04	NONE	POLYA	0.935387	0.022997	0.026368	0.015248	78.30	5.26	15.95	13	LP2 (2026-09-30)	PASS	NonPolyA_perM 13 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM1039506	M	M	NA	Agree	0.00	2.57	0.00	22.56	3.37	47.47	NONE	POLYA	0.930296	0.026211	0.02738	0.016113	78.34	4.50	16.89	19	LP2 (2026-09-30)	PASS	NonPolyA_perM 19 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM1039507	M	M	NA	Agree	0.00	2.62	0.00	26.04	4.90	37.63	NONE	POLYA	0.920939	0.024249	0.026401	0.028411	77.23	5.54	16.95	22	LP2 (2026-09-30)	PASS	NonPolyA_perM 22 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM1039508	both	F	NA	Conflict	156.80	0.00	0.00	0.04	0.06	0.08	NONE	POLYA	0.899599	0.040876	0.037872	0.021653	83.86	8.47	6.93	36	LP2 (2026-09-30)	PASS	NonPolyA_perM 36 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM1039509	both	Undetermined	NA	Conflict	71.03	3.26	0.00	16.77	5.60	32.19	NONE	POLYA	0.848759	0.069083	0.065666	0.016492	75.13	6.10	16.59	92	LP2 (2026-09-30)	PASS	NonPolyA_perM 92 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM1039510	both	F	NA	Conflict	297.37	0.00	0.00	0.00	0.00	0.00	NONE	POLYA	0.88519	0.069047	0.036628	0.009135	76.77	4.70	16.52	91	LP2 (2026-09-30)	PASS	NonPolyA_perM 91 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM1039511	M	M	NA	Agree	0.65	3.36	0.00	24.75	5.51	43.66	NONE	POLYA	0.926181	0.025888	0.028342	0.01959	83.24	6.04	10.21	16	LP2 (2026-09-30)	PASS	NonPolyA_perM 16 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM1039512	M	M	NA	Agree	0.00	4.03	0.00	24.15	5.26	49.52	NONE	POLYA	0.934398	0.025321	0.027589	0.012691	75.07	4.26	20.40	33	LP2 (2026-09-30)	PASS	NonPolyA_perM 33 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM1039513	M	M	NA	Agree	0.16	1.91	0.00	20.82	5.11	37.17	NONE	POLYA	0.93605	0.022735	0.023192	0.018023	73.01	5.07	20.04	17	LP2 (2026-09-30)	PASS	NonPolyA_perM 17 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does