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
GSM2635756	not_specified	M	NA	Conflict	0.09	4.92	0.00	38.16	14.28	61.20	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.836979	0.112211	0.035739	0.015072	90.77	4.93	3.43	137	LP2 (2026-09-30)	PASS	NonPolyA_perM 137 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM2635757	not_specified	M	NA	Conflict	0.04	6.42	0.00	42.03	14.57	62.58	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.826243	0.117061	0.035812	0.020884	89.71	5.22	3.98	140	LP2 (2026-09-30)	PASS	NonPolyA_perM 140 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM2635758	not_specified	M	NA	Conflict	0.04	5.15	0.00	34.63	14.10	47.59	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.829922	0.11793	0.035588	0.01656	90.70	4.96	3.30	130	LP2 (2026-09-30)	PASS	NonPolyA_perM 130 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM2635759	not_specified	M	NA	Conflict	0.16	4.85	0.00	28.80	16.54	33.24	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.800743	0.15282	0.033967	0.01247	91.87	4.45	2.95	140	LP2 (2026-09-30)	PASS	NonPolyA_perM 140 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM2635760	not_specified	M	NA	Conflict	0.14	4.39	0.00	35.89	19.16	29.47	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.800902	0.157272	0.034571	0.007256	92.85	3.61	2.79	137	LP2 (2026-09-30)	PASS	NonPolyA_perM 137 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM2635761	not_specified	M	NA	Conflict	0.09	4.97	0.00	29.02	19.41	28.68	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.795632	0.15811	0.035767	0.010491	91.24	4.11	3.68	173	LP2 (2026-09-30)	PASS	NonPolyA_perM 173 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does