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
GSM8009657	M	M	NA	Agree	0.08	5.53	0.00	17.77	11.22	44.03	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.593837	0.291042	0.09018	0.024941	73.55	6.99	17.82	6039	LP2 (2026-09-30)	PASS	NonPolyA_perM 6039 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM8009658	M	F	NA	Conflict	124.69	0.00	0.00	0.00	0.00	0.00	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.548798	0.336755	0.087864	0.026582	74.53	6.65	17.39	5207	LP2 (2026-09-30)	PASS	NonPolyA_perM 5207 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM8009659	M	F	NA	Conflict	89.44	0.00	0.00	0.00	0.00	0.00	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.555055	0.328498	0.087111	0.029336	73.96	7.82	16.86	5277	LP2 (2026-09-30)	PASS	NonPolyA_perM 5277 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM8009660	M	F	NA	Conflict	88.05	0.00	0.00	0.00	0.00	0.00	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.604049	0.278606	0.084263	0.033082	76.45	8.21	14.28	5447	LP2 (2026-09-30)	PASS	NonPolyA_perM 5447 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM8009661	M	F	NA	Conflict	71.75	0.00	0.00	0.00	0.00	0.00	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.635554	0.26655	0.091646	0.00625	80.56	5.52	12.78	4058	LP2 (2026-09-30)	PASS	NonPolyA_perM 4058 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM8009662	M	M	NA	Agree	0.05	5.31	0.00	18.86	9.11	46.86	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.679655	0.204498	0.094382	0.021465	76.56	8.31	14.02	4943	LP2 (2026-09-30)	PASS	NonPolyA_perM 4943 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM8009663	M	F	NA	Conflict	62.42	0.00	0.00	0.00	0.00	0.00	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.664181	0.225205	0.090695	0.019919	77.44	7.56	13.74	4637	LP2 (2026-09-30)	PASS	NonPolyA_perM 4637 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM8009664	M	F	NA	Conflict	88.01	0.00	0.00	0.00	0.00	0.00	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.629426	0.283392	0.080957	0.006224	81.44	5.06	12.32	3607	LP2 (2026-09-30)	PASS	NonPolyA_perM 3607 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM8009665	M	M	NA	Agree	0.02	12.16	0.00	65.49	13.51	128.72	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.909433	0.051102	0.037763	0.001701	93.60	1.80	4.46	50	LP2 (2026-09-30)	PASS	NonPolyA_perM 50 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM8009666	M	F	NA	Conflict	146.45	0.00	0.00	0.00	0.00	0.00	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.902668	0.056386	0.039003	0.001943	93.52	1.71	4.63	64	LP2 (2026-09-30)	PASS	NonPolyA_perM 64 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM8009667	M	F	NA	Conflict	151.28	0.00	0.00	0.00	0.00	0.00	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.895957	0.062243	0.04067	0.00113	93.48	1.64	4.73	73	LP2 (2026-09-30)	PASS	NonPolyA_perM 73 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM8009668	M	F	NA	Conflict	135.79	0.00	0.00	0.00	0.00	0.00	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.91088	0.049352	0.037633	0.002135	93.29	1.76	4.83	58	LP2 (2026-09-30)	PASS	NonPolyA_perM 58 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM8009669	M	F	NA	Conflict	125.63	0.00	0.00	0.00	0.00	0.00	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.894011	0.062369	0.041828	0.001792	93.26	1.72	4.86	67	LP2 (2026-09-30)	PASS	NonPolyA_perM 67 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM8009670	M	M	NA	Agree	0.01	9.96	0.00	59.83	14.15	115.82	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.903415	0.051414	0.042206	0.002966	93.32	1.90	4.63	68	LP2 (2026-09-30)	PASS	NonPolyA_perM 68 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM8009671	M	F	NA	Conflict	160.60	0.00	0.00	0.00	0.03	0.11	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.89393	0.061876	0.041949	0.002245	93.50	1.67	4.68	61	LP2 (2026-09-30)	PASS	NonPolyA_perM 61 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM8009672	M	F	NA	Conflict	121.79	0.00	0.00	0.00	0.00	0.00	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.925054	0.042625	0.031623	0.000698	90.76	1.45	7.67	34	LP2 (2026-09-30)	PASS	NonPolyA_perM 34 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM8009687	M	M	NA	Agree	6.22	14.83	0.00	34.42	19.23	58.39	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.520157	0.405009	0.072201	0.002632	83.07	2.99	13.25	885	LP2 (2026-09-30)	PASS	NonPolyA_perM 885 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM8009688	M	F	NA	Conflict	242.95	0.00	0.00	0.00	0.00	0.32	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.47533	0.4518	0.070191	0.002679	82.90	2.99	13.37	930	LP2 (2026-09-30)	PASS	NonPolyA_perM 930 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM8009689	M	F	NA	Conflict	243.45	0.00	0.00	0.04	0.00	0.00	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.470089	0.456868	0.069616	0.003427	82.40	3.02	13.87	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
GSM8009690	M	F	NA	Conflict	266.02	2.10	0.00	3.63	2.32	7.13	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.471974	0.457341	0.069164	0.001521	82.60	2.70	13.96	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
GSM8009691	M	Undetermined	NA	Conflict	37.15	13.81	0.00	27.92	20.54	50.24	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.44892	0.479419	0.069551	0.002111	80.97	2.94	15.34	982	LP2 (2026-09-30)	PASS	NonPolyA_perM 982 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM8009692	M	Undetermined	NA	Conflict	29.51	15.79	0.00	35.07	18.61	49.16	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.471194	0.456991	0.069557	0.002258	82.11	2.71	14.44	834	LP2 (2026-09-30)	PASS	NonPolyA_perM 834 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM8009693	M	M	NA	Agree	0.03	13.44	0.00	34.01	17.40	57.03	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.507792	0.416354	0.072711	0.003144	82.91	3.01	13.36	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
GSM8009694	M	M	NA	Agree	0.04	12.62	0.00	33.80	18.57	50.58	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.500256	0.424776	0.071967	0.003001	84.48	3.21	11.61	853	LP2 (2026-09-30)	PASS	NonPolyA_perM 853 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM8009695	M	M	NA	Agree	16.76	10.43	0.00	26.94	15.35	44.83	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.549053	0.375659	0.073035	0.002253	82.62	3.23	13.46	883	LP2 (2026-09-30)	PASS	NonPolyA_perM 883 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM8009696	M	F	NA	Conflict	148.25	1.37	0.00	3.68	1.63	6.21	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.544647	0.37451	0.07685	0.003994	84.33	3.64	11.34	1025	LP2 (2026-09-30)	PASS	NonPolyA_perM 1025 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM8009697	M	F	NA	Conflict	116.03	2.50	0.00	6.36	3.30	10.70	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.561944	0.356849	0.075203	0.006003	84.36	3.81	11.16	893	LP2 (2026-09-30)	PASS	NonPolyA_perM 893 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM8009698	M	F	NA	Conflict	243.85	0.61	0.00	1.60	1.15	2.13	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.496636	0.423515	0.07546	0.004389	81.77	3.11	14.39	841	LP2 (2026-09-30)	PASS	NonPolyA_perM 841 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not