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
GSM3139535	not_specified	F	NA	Conflict	73.38	0.00	0.00	0.00	0.00	0.00	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.179534	0.146479	0.033051	0.640937	28.97	57.68	12.96	8215	LP2 (2026-09-30)	LOW_MAPPING	NonPolyA_perM 8215 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM3139536	not_specified	F	NA	Conflict	55.81	0.00	0.00	0.00	0.00	0.00	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.33836	0.238732	0.07471	0.348198	50.96	37.80	10.44	7561	LP2 (2026-09-30)	PASS	NonPolyA_perM 7561 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM3139537	not_specified	F	NA	Conflict	119.56	0.00	0.00	0.00	0.00	0.00	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.476287	0.379399	0.078547	0.065767	79.90	13.06	6.10	9828	LP2 (2026-09-30)	PASS	NonPolyA_perM 9828 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM3139538	not_specified	M	NA	Conflict	0.91	11.88	0.00	24.59	12.25	24.58	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.422449	0.30844	0.060566	0.208545	66.02	25.94	7.20	6209	LP2 (2026-09-30)	PASS	NonPolyA_perM 6209 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM3139539	not_specified	Undetermined	NA	Conflict	1.34	0.00	0.00	0.00	0.00	0.00	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.357921	0.311087	0.051654	0.279339	61.28	30.05	7.89	7866	LP2 (2026-09-30)	PASS	NonPolyA_perM 7866 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM3139540	not_specified	F	NA	Conflict	71.05	0.00	0.00	0.00	0.00	0.20	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.1611	0.125024	0.026293	0.687582	25.39	60.62	13.62	6820	LP2 (2026-09-30)	LOW_MAPPING	NonPolyA_perM 6820 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM3139541	not_specified	F	NA	Conflict	61.72	0.00	0.00	0.00	0.00	0.00	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.324268	0.226911	0.060843	0.387978	44.72	36.39	18.29	10617	LP2 (2026-09-30)	LOW_MAPPING	NonPolyA_perM 10617 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM3139542	not_specified	F	NA	Conflict	92.95	0.00	0.00	0.00	0.00	0.00	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.379359	0.312538	0.062359	0.245745	61.76	28.78	8.45	11936	LP2 (2026-09-30)	PASS	NonPolyA_perM 11936 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM3139543	not_specified	F	NA	Conflict	120.79	0.00	0.00	0.00	0.05	0.00	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.41406	0.386939	0.07212	0.12688	74.67	18.49	5.81	12494	LP2 (2026-09-30)	PASS	NonPolyA_perM 12494 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM3139544	not_specified	F	NA	Conflict	71.93	0.00	0.00	0.00	0.00	0.00	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.470123	0.335759	0.082895	0.111223	73.23	18.86	6.63	16201	LP2 (2026-09-30)	PASS	NonPolyA_perM 16201 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM3139545	not_specified	M	NA	Conflict	0.72	8.60	0.00	13.05	9.29	21.88	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.502226	0.297789	0.079491	0.120494	73.30	19.93	5.74	14766	LP2 (2026-09-30)	PASS	NonPolyA_perM 14766 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM3139546	not_specified	M	NA	Conflict	1.07	9.65	0.00	17.79	13.15	19.83	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.492359	0.362166	0.072358	0.073117	79.92	14.56	4.45	11489	LP2 (2026-09-30)	PASS	NonPolyA_perM 11489 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not