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 (2026-10-21) 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). For 2 samples processed before workflow 2.1, ComputedSex is the earlier curated call, kept after review where it differed from the rule above.
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
GSM9198044	M	M	NA	Agree	0.02	11.53	0.00	43.60	11.00	54.36	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.848056	0.082665	0.0584	0.010879	94.06	3.30	2.48	70	LP2 (2026-09-30)	PASS	NonPolyA_perM 70 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM9198045	M	M	NA	Agree	0.05	13.74	0.00	51.25	15.55	52.65	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.843579	0.093366	0.051876	0.011178	92.39	3.33	4.06	67	LP2 (2026-09-30)	PASS	NonPolyA_perM 67 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM9198046	M	M	NA	Agree	0.08	16.21	0.00	52.76	16.18	41.04	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.756596	0.137827	0.054007	0.051571	85.21	6.92	7.60	192	LP2 (2026-09-30)	PASS	NonPolyA_perM 192 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM9198047	M	M	NA	Agree	0.01	11.50	0.00	46.83	10.75	52.58	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.871226	0.06936	0.046903	0.012512	92.99	3.53	3.26	58	LP2 (2026-09-30)	PASS	NonPolyA_perM 58 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM9198048	M	M	NA	Agree	0.22	12.62	0.00	45.00	14.01	55.96	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.859688	0.076676	0.051435	0.012201	91.81	3.54	4.43	40	LP2 (2026-09-30)	PASS	NonPolyA_perM 40 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM9198049	M	F	NA	Conflict	266.01	0.06	0.00	0.50	0.10	0.18	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.804449	0.131971	0.049996	0.013584	91.01	3.63	5.12	78	LP2 (2026-09-30)	PASS	NonPolyA_perM 78 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM9198050	M	M	NA	Agree	0.02	4.61	0.00	15.35	4.57	18.97	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.320433	0.0579	0.025875	0.595793	38.68	58.16	2.88	1245	LP2 (2026-09-30)	LOW_MAPPING	NonPolyA_perM 1245 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM9198051	M	M	NA	Agree	0.04	16.22	0.00	59.23	14.99	57.02	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.806337	0.114776	0.053101	0.025786	90.01	4.60	5.16	85	LP2 (2026-09-30)	PASS	NonPolyA_perM 85 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM9198052	M	F	NA	Conflict	210.77	0.10	0.00	0.48	0.12	0.36	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.840819	0.087067	0.047512	0.024602	91.34	4.71	3.71	104	LP2 (2026-09-30)	PASS	NonPolyA_perM 104 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM9198053	M	M	NA	Agree	0.05	14.24	0.00	50.14	13.61	59.22	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.850296	0.091185	0.04711	0.011409	92.56	3.55	3.63	76	LP2 (2026-09-30)	PASS	NonPolyA_perM 76 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM9198054	M	F	NA	Conflict	119.24	0.77	0.00	2.64	0.75	2.93	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.867386	0.059508	0.047568	0.025539	89.67	5.03	5.05	64	LP2 (2026-09-30)	PASS	NonPolyA_perM 64 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM9198055	M	F	NA	Conflict	284.59	0.09	0.00	0.17	0.02	0.29	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.838384	0.097942	0.048766	0.014908	91.27	3.74	4.74	68	LP2 (2026-09-30)	PASS	NonPolyA_perM 68 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM9198056	M	M	NA	Agree	0.12	14.52	0.00	50.76	14.12	56.46	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.836797	0.098259	0.047966	0.016978	91.42	4.02	4.31	83	LP2 (2026-09-30)	PASS	NonPolyA_perM 83 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM9198057	M	F	NA	Conflict	305.06	0.02	0.00	0.09	0.10	0.02	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.784338	0.142411	0.059273	0.013978	93.47	3.51	2.82	98	LP2 (2026-09-30)	PASS	NonPolyA_perM 98 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM9198058	M	F	NA	Conflict	303.89	0.02	0.00	0.04	0.00	0.03	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.826561	0.102043	0.060814	0.010582	92.91	3.18	3.73	68	LP2 (2026-09-30)	PASS	NonPolyA_perM 68 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM9198059	M	M	NA	Agree	0.25	13.77	0.00	51.56	14.65	54.16	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.812311	0.115142	0.058252	0.014295	92.90	3.59	3.28	71	LP2 (2026-09-30)	PASS	NonPolyA_perM 71 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM9198060	M	M	NA	Agree	0.35	11.28	0.00	42.23	12.27	49.81	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.859547	0.076258	0.051498	0.012696	92.29	3.70	3.80	59	LP2 (2026-09-30)	PASS	NonPolyA_perM 59 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM9198061	M	M	NA	Agree	2.03	10.89	0.00	46.67	12.22	56.14	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.819631	0.092687	0.059222	0.028461	90.71	4.94	4.14	97	LP2 (2026-09-30)	PASS	NonPolyA_perM 97 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM9198062	M	M	NA	Agree	1.09	12.61	0.00	47.49	14.20	55.82	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.802924	0.120552	0.054557	0.021967	89.91	4.43	5.43	86	LP2 (2026-09-30)	PASS	NonPolyA_perM 86 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM9198063	M	M	NA	Agree	0.03	12.00	0.00	43.63	12.71	54.50	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.813927	0.118632	0.053504	0.013937	93.48	3.64	2.69	75	LP2 (2026-09-30)	PASS	NonPolyA_perM 75 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM9198064	M	F	NA	Conflict	220.61	0.06	0.00	0.19	0.09	0.13	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.837425	0.092946	0.0559	0.013729	92.58	3.57	3.64	70	LP2 (2026-09-30)	PASS	NonPolyA_perM 70 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM9198065	M	F	NA	Conflict	160.77	0.51	0.00	1.78	0.56	1.44	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.846782	0.082451	0.054886	0.015881	92.59	3.85	3.35	53	LP2 (2026-09-30)	PASS	NonPolyA_perM 53 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM9198066	M	F	NA	Conflict	331.20	0.50	0.00	1.47	0.34	1.31	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.782816	0.148707	0.05738	0.011097	92.59	3.18	4.01	108	LP2 (2026-09-30)	PASS	NonPolyA_perM 108 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM9198067	M	M	NA	Agree	1.87	8.85	0.00	37.57	11.74	52.39	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.86871	0.056951	0.054155	0.020184	91.07	4.62	4.12	40	LP2 (2026-09-30)	PASS	NonPolyA_perM 40 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM9198068	M	M	NA	Agree	19.17	12.41	0.00	47.74	14.53	50.08	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.810131	0.119371	0.05231	0.018188	90.70	4.11	4.96	66	LP2 (2026-09-30)	PASS	NonPolyA_perM 66 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM9198069	M	F	NA	Conflict	345.06	0.41	0.00	1.61	0.48	1.39	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.779838	0.151025	0.057835	0.011302	92.36	3.16	4.24	110	LP2 (2026-09-30)	PASS	NonPolyA_perM 110 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM9198070	M	M	NA	Agree	7.08	13.45	0.00	52.55	14.05	55.21	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.807455	0.131926	0.047876	0.012743	93.55	3.59	2.62	103	LP2 (2026-09-30)	PASS	NonPolyA_perM 103 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM9198071	M	F	NA	Conflict	312.16	0.00	0.00	0.04	0.00	0.02	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.838946	0.094819	0.052529	0.013705	92.64	3.49	3.66	73	LP2 (2026-09-30)	PASS	NonPolyA_perM 73 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM9198072	M	M	NA	Agree	0.33	15.27	0.00	55.16	14.51	54.93	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.782968	0.13547	0.0519	0.029662	91.40	5.09	3.25	123	LP2 (2026-09-30)	PASS	NonPolyA_perM 123 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM9198073	M	M	NA	Agree	0.07	13.53	0.00	49.93	11.53	61.49	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.868004	0.072881	0.044079	0.015037	92.09	4.01	3.64	63	LP2 (2026-09-30)	PASS	NonPolyA_perM 63 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM9198074	M	F	NA	Conflict	289.76	0.78	0.00	2.86	0.76	2.98	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.798045	0.118885	0.051835	0.031235	89.69	5.33	4.71	126	LP2 (2026-09-30)	PASS	NonPolyA_perM 126 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM9198075	M	M	NA	Agree	0.89	18.34	0.00	53.66	15.11	57.83	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.765584	0.158722	0.054447	0.021247	91.25	4.07	4.43	118	LP2 (2026-09-30)	PASS	NonPolyA_perM 118 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM9198076	M	F	NA	Conflict	433.07	0.09	0.00	0.37	0.09	0.32	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.809192	0.128291	0.049564	0.012953	93.80	3.49	2.47	90	LP2 (2026-09-30)	PASS	NonPolyA_perM 90 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM9198077	M	F	NA	Conflict	1.26	0.00	0.00	0.02	0.01	0.00	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.833953	0.101016	0.047087	0.017945	92.45	4.03	3.27	86	LP2 (2026-09-30)	PASS	NonPolyA_perM 86 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM9198078	M	M	NA	Agree	3.63	15.87	0.00	55.66	16.63	56.50	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.769163	0.162242	0.053076	0.015519	92.52	3.64	3.60	116	LP2 (2026-09-30)	PASS	NonPolyA_perM 116 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM9198079	M	F	NA	Conflict	221.35	0.09	0.00	0.29	0.05	0.31	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.860855	0.080388	0.045604	0.013153	91.59	3.88	4.28	61	LP2 (2026-09-30)	PASS	NonPolyA_perM 61 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM9198080	M	F	NA	Conflict	189.61	0.41	0.00	1.97	0.60	3.13	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.87073	0.061205	0.042202	0.025864	90.12	5.23	4.42	78	LP2 (2026-09-30)	PASS	NonPolyA_perM 78 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM9198081	M	M	NA	Agree	0.69	15.03	0.00	53.09	17.01	56.28	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.808198	0.11693	0.051901	0.022972	91.08	4.48	4.20	76	LP2 (2026-09-30)	PASS	NonPolyA_perM 76 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM9198082	M	M	NA	Agree	0.08	16.52	0.00	59.09	15.47	51.95	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.794466	0.137339	0.056637	0.011559	92.39	3.23	4.18	93	LP2 (2026-09-30)	PASS	NonPolyA_perM 93 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM9198083	M	F	NA	Conflict	332.73	0.02	0.00	0.03	0.01	0.00	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.804312	0.120753	0.060991	0.013944	92.69	3.43	3.68	75	LP2 (2026-09-30)	PASS	NonPolyA_perM 75 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM9198084	M	M	NA	Agree	0.40	15.50	0.00	55.64	15.01	57.56	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.758452	0.157736	0.053558	0.030255	90.18	5.07	4.49	126	LP2 (2026-09-30)	PASS	NonPolyA_perM 126 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM9198085	M	F	NA	Conflict	1.38	0.00	0.00	0.03	0.00	0.02	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.814007	0.115206	0.048929	0.021857	91.61	4.36	3.79	81	LP2 (2026-09-30)	PASS	NonPolyA_perM 81 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does