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
GSM3723398	not_specified	M	NA	Conflict	1.57	18.66	0.00	36.16	14.61	48.50	FIRST_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.467743	0.411419	0.051372	0.069465	81.67	9.52	8.19	1120	LP2 (2026-09-30)	PASS	NonPolyA_perM 1120 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM3723399	not_specified	F	NA	Conflict	435.23	0.00	0.00	0.00	0.05	0.00	FIRST_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.459163	0.418832	0.049596	0.072409	82.01	9.72	7.63	1042	LP2 (2026-09-30)	PASS	NonPolyA_perM 1042 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM3723400	not_specified	M	NA	Conflict	1.88	21.03	0.00	42.53	16.88	49.37	FIRST_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.456827	0.418357	0.052892	0.071924	80.57	9.41	9.42	915	LP2 (2026-09-30)	PASS	NonPolyA_perM 915 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM3723401	not_specified	M	NA	Conflict	1.05	18.86	0.00	36.43	13.74	43.37	FIRST_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.473041	0.407998	0.051413	0.067548	80.84	9.14	9.39	963	LP2 (2026-09-30)	PASS	NonPolyA_perM 963 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM3723402	not_specified	F	NA	Conflict	380.89	0.00	0.00	0.00	0.00	0.00	FIRST_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.476209	0.404784	0.050862	0.068145	80.84	9.12	9.43	1102	LP2 (2026-09-30)	PASS	NonPolyA_perM 1102 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM3723403	not_specified	F	NA	Conflict	437.15	0.00	0.00	0.00	0.09	0.00	FIRST_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.471354	0.416323	0.051387	0.060935	81.80	8.40	9.22	1091	LP2 (2026-09-30)	PASS	NonPolyA_perM 1091 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM3723404	F	F	NA	Agree	98.10	0.00	0.00	0.00	0.00	0.00	FIRST_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.685363	0.264301	0.03686	0.013475	89.53	4.36	5.23	1242	LP2 (2026-09-30)	PASS	NonPolyA_perM 1242 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM3723405	F	F	NA	Agree	80.33	0.00	0.00	0.00	0.00	0.00	FIRST_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.725009	0.226639	0.03638	0.011971	90.69	4.24	4.31	1135	LP2 (2026-09-30)	PASS	NonPolyA_perM 1135 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM3723406	F	M	NA	Conflict	0.06	6.72	0.00	20.88	5.62	14.68	FIRST_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.748527	0.201949	0.036216	0.013308	90.60	3.82	4.92	938	LP2 (2026-09-30)	PASS	NonPolyA_perM 938 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM3723407	F	F	NA	Agree	79.61	0.04	0.00	0.00	0.00	0.00	FIRST_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.72798	0.227619	0.032191	0.01221	90.98	4.10	4.18	1094	LP2 (2026-09-30)	PASS	NonPolyA_perM 1094 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM3723408	F	F	NA	Agree	94.09	0.00	0.00	0.00	0.00	0.00	FIRST_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.717015	0.234271	0.035483	0.01323	90.28	4.04	4.83	1104	LP2 (2026-09-30)	PASS	NonPolyA_perM 1104 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM3723409	F	F	NA	Agree	91.26	0.00	0.00	0.00	0.00	0.00	FIRST_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.738838	0.21406	0.034742	0.012359	90.63	4.00	4.62	969	LP2 (2026-09-30)	PASS	NonPolyA_perM 969 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM3723410	F	F	NA	Agree	126.43	0.00	0.00	0.05	0.05	0.00	FIRST_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.63208	0.305024	0.042784	0.020113	86.18	5.29	7.42	1669	LP2 (2026-09-30)	PASS	NonPolyA_perM 1669 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM3723411	F	F	NA	Agree	89.83	0.00	0.00	0.00	0.00	0.00	FIRST_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.700962	0.244783	0.03654	0.017715	89.60	4.92	4.65	1181	LP2 (2026-09-30)	PASS	NonPolyA_perM 1181 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM3723412	F	F	NA	Agree	76.88	0.00	0.00	0.11	0.00	0.00	FIRST_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.761573	0.195015	0.031332	0.01208	90.25	3.40	5.70	781	LP2 (2026-09-30)	PASS	NonPolyA_perM 781 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM3723413	F	F	NA	Agree	87.80	0.00	0.00	0.00	0.00	0.00	FIRST_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.702849	0.245479	0.034809	0.016863	89.74	4.59	4.85	1195	LP2 (2026-09-30)	PASS	NonPolyA_perM 1195 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM3723414	M	M	NA	Agree	0.23	7.54	0.00	21.52	7.60	16.43	FIRST_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.714945	0.23295	0.038392	0.013712	90.23	4.01	5.06	882	LP2 (2026-09-30)	PASS	NonPolyA_perM 882 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM3723415	M	M	NA	Agree	0.13	8.31	0.00	25.61	7.22	17.44	FIRST_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.715672	0.234681	0.035501	0.014145	90.84	3.93	4.56	732	LP2 (2026-09-30)	PASS	NonPolyA_perM 732 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM3723416	M	M	NA	Agree	0.22	5.61	0.00	18.62	5.67	14.19	FIRST_READ_TRANSCRIPTION_STRAND	AMBIGUOUS	0.73097	0.201656	0.056557	0.010816	91.17	3.78	4.21	664	LP2 (2026-09-30)	PASS	NonPolyA_perM 664 is between 350 and 700, outside the range of every calibration study; check the study methods
GSM3723417	M	M	NA	Agree	1.59	7.57	0.00	20.58	5.84	13.76	FIRST_READ_TRANSCRIPTION_STRAND	AMBIGUOUS	0.67482	0.205831	0.11047	0.00888	90.06	3.80	4.78	683	LP2 (2026-09-30)	PASS	NonPolyA_perM 683 is between 350 and 700, outside the range of every calibration study; check the study methods
GSM3723418	M	M	NA	Agree	0.74	8.66	0.00	20.33	7.95	16.19	FIRST_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.458174	0.261714	0.273621	0.006492	86.37	4.53	6.09	879	LP2 (2026-09-30)	PASS	NonPolyA_perM 879 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM3723419	M	M	NA	Agree	0.25	8.72	0.00	22.75	7.58	13.80	FIRST_READ_TRANSCRIPTION_STRAND	AMBIGUOUS	0.747573	0.207234	0.032477	0.012716	91.23	3.67	4.40	676	LP2 (2026-09-30)	PASS	NonPolyA_perM 676 is between 350 and 700, outside the range of every calibration study; check the study methods
GSM3723420	M	M	NA	Agree	0.19	7.10	0.00	22.39	6.60	15.90	FIRST_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.668582	0.2328	0.084985	0.013633	88.98	4.51	5.38	785	LP2 (2026-09-30)	PASS	NonPolyA_perM 785 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM3723421	M	M	NA	Agree	0.06	6.78	0.00	23.44	8.03	13.61	FIRST_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.706194	0.244166	0.034172	0.015468	90.66	4.27	4.29	766	LP2 (2026-09-30)	PASS	NonPolyA_perM 766 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM3723422	M	M	NA	Agree	0.34	8.10	0.00	18.65	7.47	12.08	FIRST_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.475295	0.264831	0.249358	0.010515	86.47	5.12	5.43	1031	LP2 (2026-09-30)	PASS	NonPolyA_perM 1031 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM3723423	M	M	NA	Agree	0.17	6.06	0.00	23.41	7.04	15.89	FIRST_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.652003	0.240979	0.089416	0.017602	88.34	4.94	5.52	981	LP2 (2026-09-30)	PASS	NonPolyA_perM 981 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not