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
GSM5680704	not_specified	F	NA	Conflict	246.42	3.42	0.00	16.79	7.49	22.58	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.86161	0.094639	0.037287	0.006464	93.74	3.95	1.94	188	LP2 (2026-09-30)	PASS	NonPolyA_perM 188 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM5680705	not_specified	Undetermined	NA	Conflict	218.18	6.89	0.00	35.97	16.00	42.79	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.848643	0.10358	0.039315	0.008462	93.61	4.10	1.87	192	LP2 (2026-09-30)	PASS	NonPolyA_perM 192 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM5680706	not_specified	F	NA	Conflict	212.02	3.41	0.00	18.91	6.57	19.84	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.863217	0.093668	0.037096	0.006019	93.34	4.25	2.08	176	LP2 (2026-09-30)	PASS	NonPolyA_perM 176 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM5680707	not_specified	F	NA	Conflict	101.04	0.05	0.00	0.00	0.00	0.00	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.89882	0.068074	0.029601	0.003504	93.79	4.11	1.66	110	LP2 (2026-09-30)	PASS	NonPolyA_perM 110 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM5680708	not_specified	F	NA	Conflict	99.10	0.05	0.00	0.00	0.00	0.00	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.898316	0.069009	0.029077	0.003598	93.67	4.02	1.91	117	LP2 (2026-09-30)	PASS	NonPolyA_perM 117 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM5680709	not_specified	F	NA	Conflict	95.09	0.00	0.00	0.00	0.00	0.00	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.902374	0.066138	0.028495	0.002993	94.26	4.09	1.23	104	LP2 (2026-09-30)	PASS	NonPolyA_perM 104 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does