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 (2026-10-20) 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 5 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
GSM4753258	M	M	NA	Agree	0.01	4.66	0.00	21.69	9.31	44.82	NONE	POLYA	0.927233	0.035511	0.03526	0.001996	97.50	1.99	0.42	54	LP2 (2026-09-30)	PASS	NonPolyA_perM 54 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM4753259	M	M	NA	Agree	0.00	4.99	0.00	22.97	12.02	44.65	NONE	POLYA	0.927434	0.036132	0.035043	0.001391	97.67	1.83	0.42	47	LP2 (2026-09-30)	PASS	NonPolyA_perM 47 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM4753260	M	M	NA	Agree	0.01	6.24	0.00	23.09	11.63	58.02	NONE	POLYA	0.920994	0.040491	0.036896	0.001619	97.42	2.09	0.37	49	LP2 (2026-09-30)	PASS	NonPolyA_perM 49 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM4753261	M	M	NA	Agree	0.00	4.20	0.00	21.64	11.59	48.26	NONE	POLYA	0.903534	0.05918	0.036168	0.001118	97.31	2.11	0.47	88	LP2 (2026-09-30)	PASS	NonPolyA_perM 88 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM4753262	M	M	NA	Agree	0.00	3.97	0.00	20.76	12.50	49.72	NONE	POLYA	0.914088	0.044551	0.039961	0.001401	97.05	2.37	0.43	89	LP2 (2026-09-30)	PASS	NonPolyA_perM 89 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM4753263	M	M	NA	Agree	0.01	4.21	0.00	17.92	11.71	43.95	NONE	POLYA	0.90709	0.055963	0.036125	0.000822	97.48	2.03	0.38	77	LP2 (2026-09-30)	PASS	NonPolyA_perM 77 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM4753264	M	M	NA	Agree	0.00	3.38	0.00	18.29	9.62	39.73	NONE	POLYA	0.928133	0.033178	0.037396	0.001292	97.21	2.25	0.43	50	LP2 (2026-09-30)	PASS	NonPolyA_perM 50 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM4753265	M	M	NA	Agree	0.00	4.72	0.00	20.61	11.84	43.23	NONE	POLYA	0.92496	0.036102	0.037745	0.001193	97.45	1.99	0.45	58	LP2 (2026-09-30)	PASS	NonPolyA_perM 58 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM4753266	M	M	NA	Agree	0.00	4.33	0.00	14.48	9.54	44.03	NONE	POLYA	0.924101	0.034029	0.036524	0.005346	96.98	2.45	0.48	70	LP2 (2026-09-30)	PASS	NonPolyA_perM 70 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM4753267	M	M	NA	Agree	0.00	3.76	0.00	17.30	7.52	43.20	NONE	POLYA	0.92842	0.031465	0.034794	0.005321	96.42	3.11	0.36	41	LP2 (2026-09-30)	PASS	NonPolyA_perM 41 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM4753268	M	M	NA	Agree	0.00	2.55	0.00	11.74	5.85	33.25	NONE	POLYA	0.931939	0.02823	0.035096	0.004736	96.92	2.61	0.38	53	LP2 (2026-09-30)	PASS	NonPolyA_perM 53 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM4753269	M	M	NA	Agree	0.00	3.48	0.00	17.47	8.88	42.97	NONE	POLYA	0.92627	0.033001	0.038484	0.002245	96.80	2.64	0.42	77	LP2 (2026-09-30)	PASS	NonPolyA_perM 77 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM4753270	M	M	NA	Agree	0.00	0.54	0.00	2.28	1.42	15.81	NONE	POLYA	0.661977	0.010746	0.299164	0.028113	85.45	13.53	0.43	24	LP2 (2026-09-30)	PASS	NonPolyA_perM 24 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM4753271	M	M	NA	Agree	0.00	0.45	0.00	1.39	0.67	18.65	NONE	POLYA	0.656697	0.010547	0.299641	0.033114	88.01	10.89	0.38	41	LP2 (2026-09-30)	PASS	NonPolyA_perM 41 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM4753272	M	M	NA	Agree	0.01	0.28	0.00	1.06	0.38	15.31	NONE	POLYA	0.69528	0.011998	0.237225	0.055497	86.18	12.61	0.53	57	LP2 (2026-09-30)	PASS	NonPolyA_perM 57 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM4753273	M	M	NA	Agree	0.00	0.62	0.00	2.65	1.06	25.73	NONE	POLYA	0.740634	0.011749	0.207318	0.040299	88.46	10.57	0.41	60	LP2 (2026-09-30)	PASS	NonPolyA_perM 60 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM4753274	M	M	NA	Agree	0.00	0.17	0.00	0.74	0.25	14.98	NONE	POLYA	0.603983	0.009464	0.344873	0.04168	88.91	10.26	0.49	39	LP2 (2026-09-30)	PASS	NonPolyA_perM 39 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM4753275	M	M	NA	Agree	0.00	0.16	0.00	1.21	0.27	17.44	NONE	POLYA	0.691417	0.011619	0.245525	0.051439	87.03	10.76	0.45	55	LP2 (2026-09-30)	PASS	NonPolyA_perM 55 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM4753276	M	M	NA	Agree	0.00	0.37	0.00	1.33	0.64	15.19	NONE	POLYA	0.635215	0.007921	0.327923	0.02894	88.31	10.77	0.38	29	LP2 (2026-09-30)	PASS	NonPolyA_perM 29 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM4753277	M	M	NA	Agree	0.00	0.86	0.00	2.99	1.92	28.60	NONE	POLYA	0.726937	0.011029	0.234592	0.027441	88.90	10.11	0.38	33	LP2 (2026-09-30)	PASS	NonPolyA_perM 33 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM4753278	M	M	NA	Agree	0.00	0.61	0.00	2.41	1.49	19.73	NONE	POLYA	0.712764	0.010134	0.249919	0.027184	87.50	11.17	0.37	25	LP2 (2026-09-30)	PASS	NonPolyA_perM 25 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM4753279	M	M	NA	Agree	0.00	0.26	0.00	0.73	0.57	13.29	NONE	POLYA	0.628634	0.008419	0.3329	0.030047	87.43	11.56	0.44	32	LP2 (2026-09-30)	PASS	NonPolyA_perM 32 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM4753280	M	M	NA	Agree	0.00	0.26	0.00	1.47	0.68	19.61	NONE	POLYA	0.684515	0.009486	0.279562	0.026437	88.08	10.89	0.43	35	LP2 (2026-09-30)	PASS	NonPolyA_perM 35 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM4753281	M	M	NA	Agree	0.00	0.40	0.00	1.51	0.82	17.03	NONE	POLYA	0.670428	0.008885	0.296407	0.02428	86.77	12.14	0.40	58	LP2 (2026-09-30)	PASS	NonPolyA_perM 58 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does