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).
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
GSM5534956	F	F	NA	Agree	162.09	0.00	0.00	0.00	0.00	0.00	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.849752	0.096478	0.045099	0.00867	81.96	2.32	15.50	91	LP2 (2026-09-30)	PASS	NonPolyA_perM 91 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM5534957	F	F	NA	Agree	46.24	0.00	0.00	0.00	0.00	0.00	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.849504	0.061406	0.043934	0.045156	78.35	5.91	15.53	66	LP2 (2026-09-30)	PASS	NonPolyA_perM 66 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM5534958	F	F	NA	Agree	155.96	0.00	0.00	0.00	0.00	0.00	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.853352	0.090011	0.046853	0.009784	82.19	2.40	15.18	86	LP2 (2026-09-30)	PASS	NonPolyA_perM 86 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM5534959	F	F	NA	Agree	117.40	0.00	0.00	0.00	0.00	0.00	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.865855	0.076626	0.044004	0.013515	84.05	2.81	12.91	84	LP2 (2026-09-30)	PASS	NonPolyA_perM 84 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM5534960	F	F	NA	Agree	42.83	0.00	0.00	0.00	0.00	0.00	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.888651	0.055578	0.045379	0.010393	84.01	2.83	12.93	87	LP2 (2026-09-30)	PASS	NonPolyA_perM 87 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM5534961	F	F	NA	Agree	31.79	0.00	0.00	0.00	0.00	0.00	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.898172	0.048293	0.043071	0.010464	84.34	2.78	12.67	66	LP2 (2026-09-30)	PASS	NonPolyA_perM 66 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does