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
GSM8714990	M	M	NA	Agree	0.00	7.06	0.00	51.97	19.36	50.91	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.894847	0.057472	0.042204	0.005477	95.55	2.36	1.83	71	LP2 (2026-09-30)	PASS	NonPolyA_perM 71 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM8714991	M	M	NA	Agree	0.12	7.71	0.00	46.75	16.42	57.91	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.85529	0.095196	0.043799	0.005715	95.15	2.51	2.02	119	LP2 (2026-09-30)	PASS	NonPolyA_perM 119 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM8714992	M	M	NA	Agree	0.12	7.70	0.00	53.06	20.78	67.15	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.851205	0.095046	0.045644	0.008105	94.85	2.68	2.15	116	LP2 (2026-09-30)	PASS	NonPolyA_perM 116 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM8714993	M	M	NA	Agree	0.04	8.56	0.00	50.81	21.83	55.86	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.866136	0.082885	0.046246	0.004733	95.44	2.32	1.92	113	LP2 (2026-09-30)	PASS	NonPolyA_perM 113 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does