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
GSM4585993	M	M	NA	Agree	0.02	0.51	0.00	1.63	3.87	11.97	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.923062	0.023364	0.03595	0.017624	87.64	3.94	8.13	40	LP2 (2026-09-30)	PASS	NonPolyA_perM 40 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM4585994	M	M	NA	Agree	0.00	0.71	0.00	1.40	4.20	10.53	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.910096	0.019895	0.033909	0.0361	87.99	5.36	6.43	34	LP2 (2026-09-30)	PASS	NonPolyA_perM 34 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM4585995	M	M	NA	Agree	0.00	1.13	0.00	2.85	4.84	15.70	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.912614	0.032484	0.035742	0.019159	88.87	3.96	6.89	28	LP2 (2026-09-30)	PASS	NonPolyA_perM 28 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM4585996	M	M	NA	Agree	0.00	1.09	0.00	2.87	4.38	15.04	SECOND_READ_TRANSCRIPTION_STRAND	AMBIGUOUS	0.78028	0.016113	0.031849	0.171758	75.46	17.81	6.46	413	LP2 (2026-09-30)	PASS	NonPolyA_perM 413 is between 350 and 700, outside the range of every calibration study; check the study methods
GSM4585997	M	M	NA	Agree	0.00	1.03	0.00	2.71	4.25	18.31	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.907229	0.02287	0.035249	0.034652	87.32	5.68	6.70	39	LP2 (2026-09-30)	PASS	NonPolyA_perM 39 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM4585998	M	M	NA	Agree	0.00	0.65	0.00	2.07	4.34	12.04	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.900215	0.017122	0.031559	0.051104	87.39	6.88	5.46	34	LP2 (2026-09-30)	PASS	NonPolyA_perM 34 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM4585999	M	M	NA	Agree	0.01	1.63	0.00	7.85	5.91	27.79	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.865261	0.054657	0.041547	0.038534	86.61	5.86	7.29	88	LP2 (2026-09-30)	PASS	NonPolyA_perM 88 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM4586000	M	M	NA	Agree	0.02	1.65	0.00	3.91	5.59	23.51	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.890379	0.031863	0.039842	0.037915	87.31	5.92	6.51	47	LP2 (2026-09-30)	PASS	NonPolyA_perM 47 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM4586001	M	M	NA	Agree	0.01	1.45	0.00	3.45	4.71	17.59	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.902056	0.024209	0.037056	0.036679	86.22	5.59	7.96	48	LP2 (2026-09-30)	PASS	NonPolyA_perM 48 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM4586002	M	M	NA	Agree	0.01	0.48	0.00	1.78	2.73	11.57	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.907885	0.027376	0.035029	0.029711	88.86	4.98	5.90	54	LP2 (2026-09-30)	PASS	NonPolyA_perM 54 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM4586003	M	M	NA	Agree	0.01	0.67	0.00	2.10	2.78	13.54	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.9084	0.028534	0.033587	0.029479	88.91	5.02	5.84	42	LP2 (2026-09-30)	PASS	NonPolyA_perM 42 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM4586004	M	M	NA	Agree	0.01	0.76	0.00	1.95	3.97	10.40	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.910564	0.01649	0.033539	0.039408	88.15	5.91	5.63	26	LP2 (2026-09-30)	PASS	NonPolyA_perM 26 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM4586005	M	M	NA	Agree	0.01	1.63	0.00	4.49	5.52	19.55	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.901327	0.025694	0.037823	0.035156	84.75	5.41	9.60	41	LP2 (2026-09-30)	PASS	NonPolyA_perM 41 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM4586006	M	M	NA	Agree	0.01	2.02	0.00	7.07	6.98	25.05	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.863202	0.052062	0.04064	0.044096	85.24	6.33	8.16	63	LP2 (2026-09-30)	PASS	NonPolyA_perM 63 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM4586007	M	M	NA	Agree	0.03	1.51	0.00	5.24	6.04	27.92	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.84814	0.072946	0.041387	0.037527	87.09	5.81	6.79	79	LP2 (2026-09-30)	PASS	NonPolyA_perM 79 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM4586008	M	M	NA	Agree	0.00	0.52	0.00	1.43	2.91	7.52	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.890753	0.015973	0.031229	0.062045	86.66	7.47	5.62	31	LP2 (2026-09-30)	PASS	NonPolyA_perM 31 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM4586009	M	M	NA	Agree	0.00	0.85	0.00	1.59	3.47	10.71	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.92354	0.015498	0.033636	0.027327	88.86	4.60	6.25	21	LP2 (2026-09-30)	PASS	NonPolyA_perM 21 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM4586010	M	M	NA	Agree	0.00	0.78	0.00	1.65	3.39	11.89	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.928382	0.015964	0.031549	0.024105	89.03	4.56	6.08	29	LP2 (2026-09-30)	PASS	NonPolyA_perM 29 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM4586011	M	M	NA	Agree	0.02	0.92	0.00	4.21	2.33	12.93	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.869149	0.03915	0.039494	0.052207	85.06	7.55	7.07	84	LP2 (2026-09-30)	PASS	NonPolyA_perM 84 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM4586012	M	M	NA	Agree	0.00	0.43	0.00	1.44	3.17	7.19	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.881144	0.018073	0.033611	0.067172	84.61	8.44	6.74	31	LP2 (2026-09-30)	PASS	NonPolyA_perM 31 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM4586013	M	M	NA	Agree	0.00	0.62	0.00	2.66	3.98	12.79	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.896289	0.026205	0.038736	0.038769	87.06	5.96	6.73	57	LP2 (2026-09-30)	PASS	NonPolyA_perM 57 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM4586014	M	M	NA	Agree	0.01	0.61	0.00	1.97	3.02	12.95	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.876506	0.03715	0.035792	0.050552	83.52	6.69	9.54	65	LP2 (2026-09-30)	PASS	NonPolyA_perM 65 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM4586015	M	M	NA	Agree	0.01	0.67	0.00	2.08	3.17	12.12	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.897369	0.022674	0.035076	0.044881	85.87	6.58	7.31	59	LP2 (2026-09-30)	PASS	NonPolyA_perM 59 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM4586016	M	M	NA	Agree	0.00	0.67	0.00	2.58	3.47	13.12	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.900288	0.016266	0.034455	0.048991	86.11	6.82	6.74	27	LP2 (2026-09-30)	PASS	NonPolyA_perM 27 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM4586017	M	M	NA	Agree	0.01	1.01	0.00	3.02	5.56	18.10	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.900439	0.019674	0.037641	0.042246	84.99	5.87	8.94	42	LP2 (2026-09-30)	PASS	NonPolyA_perM 42 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM4586018	M	M	NA	Agree	0.03	1.76	0.00	5.69	7.44	26.72	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.880936	0.044109	0.041143	0.033812	86.11	5.40	8.27	74	LP2 (2026-09-30)	PASS	NonPolyA_perM 74 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM4586019	M	M	NA	Agree	0.05	1.60	0.00	6.31	6.36	27.23	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.819901	0.066015	0.040462	0.073623	82.72	9.24	7.78	83	LP2 (2026-09-30)	PASS	NonPolyA_perM 83 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM4586020	M	M	NA	Agree	0.01	0.80	0.00	2.61	3.90	18.61	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.895777	0.027817	0.037511	0.038895	87.71	5.93	6.13	46	LP2 (2026-09-30)	PASS	NonPolyA_perM 46 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM4586021	M	M	NA	Agree	0.02	0.93	0.00	3.22	4.47	17.45	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.908356	0.029241	0.036591	0.025813	89.14	4.69	5.93	42	LP2 (2026-09-30)	PASS	NonPolyA_perM 42 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM4586022	M	M	NA	Agree	0.00	0.79	0.00	1.86	3.69	16.15	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.861796	0.020236	0.030707	0.087261	83.14	10.10	6.56	104	LP2 (2026-09-30)	PASS	NonPolyA_perM 104 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does