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
GSM4743066	F	F	NA	Agree	59.66	0.00	0.00	0.00	0.00	0.00	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.701287	0.225738	0.064838	0.008137	84.44	6.34	8.04	2973	LP2 (2026-09-30)	PASS	NonPolyA_perM 2973 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM4743067	F	F	NA	Agree	54.32	0.00	0.00	0.00	0.00	0.00	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.686482	0.232096	0.071848	0.009574	83.29	7.09	8.38	3202	LP2 (2026-09-30)	PASS	NonPolyA_perM 3202 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM4743068	F	F	NA	Agree	28.67	0.00	0.00	0.00	0.00	0.00	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.77221	0.158702	0.060818	0.00827	83.33	6.58	9.01	2527	LP2 (2026-09-30)	PASS	NonPolyA_perM 2527 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM4743069	F	F	NA	Agree	23.26	0.00	0.00	0.00	0.00	0.00	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.768933	0.154972	0.066408	0.009687	82.43	7.47	8.95	2726	LP2 (2026-09-30)	PASS	NonPolyA_perM 2726 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM4743070	F	F	NA	Agree	26.67	0.00	0.00	0.00	0.00	0.00	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.758618	0.168459	0.062813	0.01011	83.55	7.03	8.30	2698	LP2 (2026-09-30)	PASS	NonPolyA_perM 2698 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM4743071	F	F	NA	Agree	46.79	0.00	0.00	0.00	0.00	0.00	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.697767	0.227034	0.065888	0.009311	83.39	6.55	8.81	3348	LP2 (2026-09-30)	PASS	NonPolyA_perM 3348 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM4743072	F	F	NA	Agree	40.79	0.00	0.00	0.00	0.00	0.00	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.757003	0.177671	0.05496	0.010366	84.31	6.03	8.70	2271	LP2 (2026-09-30)	PASS	NonPolyA_perM 2271 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM4743073	F	F	NA	Agree	47.98	0.00	0.00	0.00	0.00	0.00	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.752895	0.18703	0.051132	0.008943	84.15	5.56	9.29	2155	LP2 (2026-09-30)	PASS	NonPolyA_perM 2155 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM4743074	F	F	NA	Agree	41.35	0.00	0.00	0.00	0.00	0.00	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.749139	0.184917	0.055707	0.010237	84.67	6.12	8.17	2449	LP2 (2026-09-30)	PASS	NonPolyA_perM 2449 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM4743075	F	F	NA	Agree	43.62	0.00	0.00	0.00	0.00	0.00	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.753182	0.179714	0.056303	0.010802	83.06	6.27	9.59	2835	LP2 (2026-09-30)	PASS	NonPolyA_perM 2835 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM4743076	F	F	NA	Agree	47.29	0.00	0.00	0.00	0.00	0.00	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.749782	0.183134	0.05325	0.013834	83.07	6.12	9.84	2250	LP2 (2026-09-30)	PASS	NonPolyA_perM 2250 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM4743077	F	F	NA	Agree	44.16	0.00	0.00	0.00	0.00	0.00	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.752101	0.176637	0.053987	0.017275	82.01	6.61	10.41	2203	LP2 (2026-09-30)	PASS	NonPolyA_perM 2203 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM4743078	F	F	NA	Agree	38.25	0.00	0.00	0.00	0.00	0.00	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.752594	0.177262	0.060787	0.009357	82.37	6.58	9.93	2730	LP2 (2026-09-30)	PASS	NonPolyA_perM 2730 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM4743079	F	F	NA	Agree	56.50	0.00	0.00	0.00	0.00	0.00	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.71056	0.215399	0.061755	0.012287	83.06	6.54	9.21	2746	LP2 (2026-09-30)	PASS	NonPolyA_perM 2746 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM4743080	F	F	NA	Agree	47.20	0.00	0.00	0.00	0.00	0.00	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.741363	0.190411	0.056424	0.011801	83.54	6.44	8.97	2521	LP2 (2026-09-30)	PASS	NonPolyA_perM 2521 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM4743081	F	F	NA	Agree	33.24	0.00	0.00	0.00	0.00	0.00	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.762775	0.162825	0.059323	0.015076	83.15	7.19	8.65	2150	LP2 (2026-09-30)	PASS	NonPolyA_perM 2150 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM4743082	F	F	NA	Agree	47.87	0.00	0.00	0.00	0.00	0.00	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.748266	0.180085	0.059964	0.011684	83.61	6.79	8.43	3472	LP2 (2026-09-30)	PASS	NonPolyA_perM 3472 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM4743083	F	F	NA	Agree	44.00	0.00	0.00	0.00	0.00	0.00	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.744628	0.180965	0.059464	0.014942	83.09	6.93	8.88	3519	LP2 (2026-09-30)	PASS	NonPolyA_perM 3519 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM4743084	F	F	NA	Agree	33.93	0.00	0.00	0.00	0.00	0.00	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.756374	0.172209	0.052077	0.01934	82.59	6.69	9.77	2009	LP2 (2026-09-30)	PASS	NonPolyA_perM 2009 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM4743085	F	F	NA	Agree	38.70	0.00	0.00	0.00	0.00	0.00	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.76058	0.174457	0.055229	0.009734	84.20	6.08	8.78	2059	LP2 (2026-09-30)	PASS	NonPolyA_perM 2059 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM4743086	F	F	NA	Agree	33.20	0.00	0.00	0.00	0.00	0.00	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.764675	0.158074	0.066249	0.011003	82.87	7.44	8.58	2316	LP2 (2026-09-30)	PASS	NonPolyA_perM 2316 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM4743087	F	F	NA	Agree	27.62	0.00	0.00	0.00	0.00	0.00	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.775366	0.158602	0.056162	0.00987	84.52	6.31	8.19	1949	LP2 (2026-09-30)	PASS	NonPolyA_perM 1949 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM4743088	F	F	NA	Agree	26.89	0.00	0.00	0.00	0.00	0.00	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.770087	0.163171	0.057787	0.008956	84.20	6.47	8.29	2273	LP2 (2026-09-30)	PASS	NonPolyA_perM 2273 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM4743089	F	F	NA	Agree	29.02	0.00	0.00	0.00	0.00	0.00	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.775774	0.165882	0.05059	0.007754	86.57	5.83	6.71	1419	LP2 (2026-09-30)	PASS	NonPolyA_perM 1419 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not