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 (2026-10-20) 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
GSM3421768	not_specified	M	NA	Conflict	0.03	3.93	0.00	14.08	10.74	85.12	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.91176	0.026832	0.038593	0.022815	91.06	6.62	2.00	50	LP2 (2026-09-30)	PASS	NonPolyA_perM 50 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM3421769	not_specified	M	NA	Conflict	0.04	4.41	0.00	18.52	13.83	97.12	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.89674	0.037132	0.038761	0.027367	91.13	6.81	1.72	64	LP2 (2026-09-30)	PASS	NonPolyA_perM 64 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM3421770	not_specified	M	NA	Conflict	0.01	4.43	0.00	16.74	10.17	99.03	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.904901	0.024847	0.038813	0.031439	90.49	7.58	1.65	53	LP2 (2026-09-30)	PASS	NonPolyA_perM 53 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM3421771	not_specified	M	NA	Conflict	0.02	3.52	0.00	12.45	8.37	90.11	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.904991	0.020179	0.037945	0.036885	90.14	8.02	1.55	48	LP2 (2026-09-30)	PASS	NonPolyA_perM 48 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM3421772	not_specified	M	NA	Conflict	0.00	2.41	0.00	15.97	7.68	76.58	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.884068	0.038294	0.042503	0.035134	90.44	7.45	1.75	96	LP2 (2026-09-30)	PASS	NonPolyA_perM 96 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM3421773	not_specified	M	NA	Conflict	0.00	1.99	0.00	12.33	6.78	69.80	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.880081	0.028193	0.039915	0.051811	88.54	9.36	1.79	86	LP2 (2026-09-30)	PASS	NonPolyA_perM 86 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM3421774	not_specified	M	NA	Conflict	0.00	2.07	0.00	12.01	7.14	74.93	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.895933	0.029073	0.042811	0.032183	90.56	7.54	1.56	81	LP2 (2026-09-30)	PASS	NonPolyA_perM 81 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM3421775	not_specified	M	NA	Conflict	0.07	2.90	0.00	19.10	7.94	86.96	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.889347	0.037658	0.044564	0.028431	83.99	6.64	9.06	86	LP2 (2026-09-30)	PASS	NonPolyA_perM 86 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM3421776	not_specified	F	NA	Conflict	68.65	0.01	0.00	0.06	0.02	0.22	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.859801	0.057714	0.044764	0.037721	89.07	7.57	3.01	97	LP2 (2026-09-30)	PASS	NonPolyA_perM 97 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM3421777	not_specified	M	NA	Conflict	0.00	4.41	0.00	13.29	8.66	98.75	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.920974	0.021484	0.037771	0.01977	90.67	7.38	1.41	70	LP2 (2026-09-30)	PASS	NonPolyA_perM 70 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM3421778	not_specified	M	NA	Conflict	0.02	6.23	0.00	19.54	12.09	103.14	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.906242	0.026519	0.039985	0.027253	89.56	7.97	1.70	83	LP2 (2026-09-30)	PASS	NonPolyA_perM 83 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM3421779	not_specified	M	NA	Conflict	0.01	6.14	0.00	18.18	10.26	105.77	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.913963	0.025172	0.038588	0.022277	89.76	7.52	1.98	83	LP2 (2026-09-30)	PASS	NonPolyA_perM 83 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM3421780	not_specified	M	NA	Conflict	0.01	4.69	0.00	13.71	10.11	113.40	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.932646	0.021861	0.03682	0.008673	91.82	6.37	1.30	78	LP2 (2026-09-30)	PASS	NonPolyA_perM 78 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM3421781	not_specified	M	NA	Conflict	0.01	4.29	0.00	14.41	9.20	105.37	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.92689	0.021461	0.036583	0.015067	91.12	6.97	1.41	86	LP2 (2026-09-30)	PASS	NonPolyA_perM 86 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM3421782	not_specified	M	NA	Conflict	0.00	4.34	0.00	15.01	10.59	112.08	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.918685	0.02142	0.036846	0.023049	90.43	7.75	1.30	91	LP2 (2026-09-30)	PASS	NonPolyA_perM 91 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM3421783	not_specified	Undetermined	NA	Conflict	5.69	0.00	0.00	0.00	0.00	0.00	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.920754	0.017178	0.041002	0.021065	90.08	7.57	1.83	31	LP2 (2026-09-30)	PASS	NonPolyA_perM 31 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does