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
GSM4561574	F	F	NA	Agree	49.85	0.00	0.00	0.00	0.00	0.00	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.502432	0.403421	0.083537	0.010611	78.68	5.25	15.17	2602	LP2 (2026-09-30)	PASS	NonPolyA_perM 2602 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM4561575	F	F	NA	Agree	48.45	0.00	0.00	0.00	0.00	0.00	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.493554	0.418759	0.086973	0.000714	76.32	4.78	17.96	2823	LP2 (2026-09-30)	PASS	NonPolyA_perM 2823 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM4561576	F	F	NA	Agree	56.48	0.00	0.00	0.00	0.00	0.00	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.505514	0.410052	0.083864	0.00057	79.25	4.51	15.29	2271	LP2 (2026-09-30)	PASS	NonPolyA_perM 2271 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM4561577	F	F	NA	Agree	34.80	0.00	0.00	0.00	0.00	0.00	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.540356	0.364181	0.094647	0.000816	75.97	6.35	16.87	3183	LP2 (2026-09-30)	PASS	NonPolyA_perM 3183 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM4561578	F	F	NA	Agree	52.72	0.00	0.00	0.00	0.00	0.00	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.50944	0.405114	0.084782	0.000664	78.62	4.66	15.79	2485	LP2 (2026-09-30)	PASS	NonPolyA_perM 2485 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM4561579	F	F	NA	Agree	34.56	0.00	0.00	0.00	0.00	0.00	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.518228	0.382113	0.099027	0.000631	74.52	6.25	18.23	3828	LP2 (2026-09-30)	PASS	NonPolyA_perM 3828 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM4561580	F	F	NA	Agree	90.96	0.00	0.00	0.00	0.00	0.00	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.521395	0.407889	0.069963	0.000753	77.65	2.95	18.62	1059	LP2 (2026-09-30)	PASS	NonPolyA_perM 1059 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM4561581	F	F	NA	Agree	44.81	0.00	0.00	0.00	0.00	0.00	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.498685	0.409134	0.091485	0.000697	75.54	4.89	18.67	2766	LP2 (2026-09-30)	PASS	NonPolyA_perM 2766 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM4561582	M	M	NA	Agree	0.03	26.20	0.00	125.85	24.86	109.37	SECOND_READ_TRANSCRIPTION_STRAND	AMBIGUOUS	0.559631	0.382577	0.05752	0.000271	93.28	3.98	0.89	640	LP2 (2026-09-30)	PASS	NonPolyA_perM 640 is between 350 and 700, outside the range of every calibration study; check the study methods
GSM4561583	M	M	NA	Agree	0.11	26.67	0.00	98.10	26.71	71.69	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.505883	0.43009	0.063658	0.000369	92.83	3.64	0.86	984	LP2 (2026-09-30)	PASS	NonPolyA_perM 984 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM4561584	M	M	NA	Agree	0.24	30.13	0.00	131.02	31.26	77.57	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.489032	0.44364	0.066923	0.000405	93.29	3.58	0.87	995	LP2 (2026-09-30)	PASS	NonPolyA_perM 995 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM4561585	M	M	NA	Agree	0.16	33.84	0.00	144.68	36.29	89.26	SECOND_READ_TRANSCRIPTION_STRAND	AMBIGUOUS	0.497864	0.43601	0.064327	0.001799	93.99	3.29	0.75	687	LP2 (2026-09-30)	PASS	NonPolyA_perM 687 is between 350 and 700, outside the range of every calibration study; check the study methods
GSM4561586	M	M	NA	Agree	0.22	29.73	0.00	148.76	33.92	85.92	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.502536	0.432334	0.064893	0.000236	93.83	3.37	0.74	837	LP2 (2026-09-30)	PASS	NonPolyA_perM 837 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM4561587	M	M	NA	Agree	0.14	26.46	0.00	117.07	29.86	78.33	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.504578	0.429938	0.065213	0.000271	93.30	3.63	0.78	876	LP2 (2026-09-30)	PASS	NonPolyA_perM 876 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM4561588	M	M	NA	Agree	0.09	41.64	0.00	160.21	35.03	99.87	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.510839	0.425314	0.063663	0.000184	94.01	3.36	0.78	812	LP2 (2026-09-30)	PASS	NonPolyA_perM 812 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM4561589	M	M	NA	Agree	0.14	24.91	0.00	122.64	27.17	81.07	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.53157	0.405664	0.062434	0.000332	92.09	3.52	1.86	888	LP2 (2026-09-30)	PASS	NonPolyA_perM 888 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not