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).
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
GSM1717069	M	M	NA	Agree	0.04	2.93	0.00	13.58	4.37	34.03	NONE	POLYA	0.946216	0.021466	0.028294	0.004024	95.29	3.36	1.03	39	LP2 (2026-09-30)	PASS	NonPolyA_perM 39 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM1717070	M	M	NA	Agree	0.04	1.35	0.00	6.00	1.37	19.51	NONE	POLYA	0.958857	0.018274	0.020987	0.001882	94.93	3.25	1.60	33	LP2 (2026-09-30)	PASS	NonPolyA_perM 33 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM1717071	M	M	NA	Agree	0.06	1.20	0.00	9.21	3.21	22.71	NONE	POLYA	0.958588	0.018021	0.020261	0.003131	95.62	3.20	0.94	12	LP2 (2026-09-30)	PASS	NonPolyA_perM 12 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does