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 (2026-10-16) 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
GSM3295005	M	M	NA	Agree	0.04	0.62	0.00	4.93	3.65	16.07	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.809932	0.065476	0.022144	0.102448	70.94	12.07	16.67	80	LP2 (2026-09-30)	PASS	NonPolyA_perM 80 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM3295006	M	M	NA	Agree	0.02	0.21	0.00	1.86	2.37	12.84	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.88983	0.051199	0.025354	0.033617	71.80	6.49	21.29	65	LP2 (2026-09-30)	PASS	NonPolyA_perM 65 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM3295007	M	M	NA	Agree	0.02	0.55	0.00	5.99	3.69	18.92	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.867591	0.056304	0.022286	0.053819	75.32	7.80	16.56	64	LP2 (2026-09-30)	PASS	NonPolyA_perM 64 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM3295008	M	M	NA	Agree	0.02	0.63	0.00	4.42	2.90	15.05	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.889518	0.050979	0.021918	0.037585	74.97	6.08	18.64	57	LP2 (2026-09-30)	PASS	NonPolyA_perM 57 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does