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). For 1 sample 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
GSM8248834	F	F	NA	Agree	97.90	0.00	0.00	0.00	0.00	0.00	FIRST_READ_TRANSCRIPTION_STRAND	POLYA	0.886681	0.057002	0.048049	0.008269	72.85	3.07	23.64	67	LP2 (2026-09-30)	PASS	NonPolyA_perM 67 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM8248835	F	F	NA	Agree	64.00	0.00	0.00	0.00	0.00	0.00	FIRST_READ_TRANSCRIPTION_STRAND	POLYA	0.915368	0.03595	0.046418	0.002264	72.33	2.87	24.38	28	LP2 (2026-09-30)	PASS	NonPolyA_perM 28 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM8248836	F	F	NA	Agree	287.15	0.00	0.00	0.00	0.00	0.00	FIRST_READ_TRANSCRIPTION_STRAND	POLYA	0.841567	0.092685	0.057531	0.008218	72.57	3.88	22.81	97	LP2 (2026-09-30)	PASS	NonPolyA_perM 97 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM8248837	F	F	NA	Agree	136.88	0.00	0.00	0.00	0.00	0.00	FIRST_READ_TRANSCRIPTION_STRAND	POLYA	0.866152	0.077021	0.051538	0.005289	70.94	3.02	25.51	92	LP2 (2026-09-30)	PASS	NonPolyA_perM 92 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM8248838	F	F	NA	Agree	5.32	0.00	0.00	0.00	0.00	0.00	FIRST_READ_TRANSCRIPTION_STRAND	POLYA	0.867446	0.035677	0.048733	0.048143	71.52	7.58	19.96	59	LP2 (2026-09-30)	PASS	NonPolyA_perM 59 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does