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 3 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
GSM1124036	not_specified	Undetermined	NA	Conflict	210.84	8.72	0.00	18.58	7.81	24.30	NONE	AMBIGUOUS	0.66435	0.274895	0.060752	0.000003	95.54	1.56	2.88	360	LP2 (2026-09-30)	PASS	NonPolyA_perM 360 is between 350 and 700, outside the range of every calibration study; check the study methods
GSM1124037	not_specified	Undetermined	NA	Conflict	147.57	9.04	0.00	19.59	8.00	23.89	NONE	POLYA	0.660225	0.279562	0.060203	0.000009	95.76	1.88	2.34	348	LP2 (2026-09-30)	PASS	NonPolyA_perM 348 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM1124038	not_specified	Undetermined	NA	Conflict	120.32	7.75	0.00	24.11	7.70	27.09	NONE	POLYA	0.679541	0.249173	0.071279	0.000007	96.18	1.28	2.52	294	LP2 (2026-09-30)	PASS	NonPolyA_perM 294 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM1124039	not_specified	Undetermined	NA	Conflict	107.94	6.55	0.00	17.73	6.99	19.26	NONE	POLYA	0.745411	0.190692	0.063894	0.000003	96.40	1.63	1.95	284	LP2 (2026-09-30)	PASS	NonPolyA_perM 284 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM1124040	not_specified	Undetermined	NA	Conflict	226.04	2.89	0.00	6.09	3.32	7.48	NONE	POLYA	0.66868	0.267465	0.063843	0.000011	96.19	1.23	2.56	311	LP2 (2026-09-30)	PASS	NonPolyA_perM 311 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM1124041	not_specified	Undetermined	NA	Conflict	232.52	6.61	0.00	23.55	7.11	18.27	NONE	POLYA	0.680373	0.226788	0.092837	0.000003	96.64	1.46	1.87	307	LP2 (2026-09-30)	PASS	NonPolyA_perM 307 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM1124042	not_specified	F	NA	Conflict	337.10	0.02	0.00	0.04	0.00	0.24	NONE	POLYA	0.666681	0.258392	0.074924	0.000003	97.10	0.94	1.93	288	LP2 (2026-09-30)	PASS	NonPolyA_perM 288 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM1124043	not_specified	F	NA	Conflict	275.05	0.00	0.00	0.06	0.00	0.00	NONE	POLYA	0.715952	0.211474	0.072569	0.000005	96.81	1.40	1.77	219	LP2 (2026-09-30)	PASS	NonPolyA_perM 219 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does