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 (2026-10-21) 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
GSM4290698	not_specified	M	NA	Conflict	0.02	2.57	0.00	8.90	3.44	12.87	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.694602	0.164521	0.065318	0.075559	82.89	13.01	3.74	1299	LP2 (2026-09-30)	PASS	NonPolyA_perM 1299 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM4290699	not_specified	M	NA	Conflict	0.03	4.67	0.00	12.46	4.76	17.41	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.66104	0.240025	0.055596	0.043338	87.36	8.54	3.78	789	LP2 (2026-09-30)	PASS	NonPolyA_perM 789 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM4290700	not_specified	M	NA	Conflict	0.01	4.79	0.00	12.62	4.66	15.91	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.684355	0.216966	0.05342	0.045259	86.35	9.08	4.25	858	LP2 (2026-09-30)	PASS	NonPolyA_perM 858 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM4290701	not_specified	M	NA	Conflict	0.01	4.27	0.00	13.33	4.73	17.46	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.685244	0.200903	0.055779	0.058075	84.71	10.63	4.31	975	LP2 (2026-09-30)	PASS	NonPolyA_perM 975 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM4290702	not_specified	M	NA	Conflict	0.00	2.15	0.00	8.42	3.42	11.32	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.619362	0.174922	0.074371	0.131345	74.42	19.37	5.77	1913	LP2 (2026-09-30)	PASS	NonPolyA_perM 1913 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM4290703	not_specified	M	NA	Conflict	0.02	4.07	0.00	10.37	3.99	14.84	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.687395	0.191065	0.058808	0.062732	84.40	11.32	3.94	1055	LP2 (2026-09-30)	PASS	NonPolyA_perM 1055 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM4290704	not_specified	M	NA	Conflict	0.01	4.17	0.00	11.24	4.50	17.40	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.686885	0.221895	0.052227	0.038993	86.26	8.99	4.43	792	LP2 (2026-09-30)	PASS	NonPolyA_perM 792 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM4290705	not_specified	M	NA	Conflict	0.03	4.22	0.00	12.38	4.65	19.51	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.705705	0.210289	0.048892	0.035115	86.36	8.31	4.99	708	LP2 (2026-09-30)	PASS	NonPolyA_perM 708 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM4290706	not_specified	M	NA	Conflict	0.02	4.23	0.00	13.13	3.94	19.02	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.697484	0.210914	0.050646	0.040957	86.85	9.05	3.78	801	LP2 (2026-09-30)	PASS	NonPolyA_perM 801 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM4290707	not_specified	M	NA	Conflict	0.01	4.62	0.00	15.50	4.31	19.64	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.723301	0.19648	0.047494	0.032724	87.46	9.46	2.65	831	LP2 (2026-09-30)	PASS	NonPolyA_perM 831 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM4290708	not_specified	M	NA	Conflict	0.01	3.07	0.00	10.39	4.04	15.45	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.693869	0.186838	0.055046	0.064248	83.36	12.04	4.25	1042	LP2 (2026-09-30)	PASS	NonPolyA_perM 1042 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM4290709	not_specified	M	NA	Conflict	0.00	3.40	0.00	11.73	3.76	17.26	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.708753	0.186324	0.052989	0.051934	84.42	10.56	4.67	912	LP2 (2026-09-30)	PASS	NonPolyA_perM 912 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM4290710	not_specified	M	NA	Conflict	0.03	4.41	0.00	12.65	4.44	19.67	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.694045	0.216508	0.050615	0.038831	86.61	8.77	4.26	784	LP2 (2026-09-30)	PASS	NonPolyA_perM 784 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM4290711	not_specified	M	NA	Conflict	0.02	3.95	0.00	12.97	4.51	17.78	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.683053	0.221008	0.051652	0.044286	86.25	9.09	4.31	854	LP2 (2026-09-30)	PASS	NonPolyA_perM 854 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM4290712	not_specified	M	NA	Conflict	0.00	3.68	0.00	12.12	4.45	14.59	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.674025	0.198431	0.058441	0.069102	82.48	13.25	3.95	1135	LP2 (2026-09-30)	PASS	NonPolyA_perM 1135 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM4290713	not_specified	M	NA	Conflict	0.06	4.17	0.00	12.31	4.52	17.30	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.638122	0.247912	0.060699	0.053267	83.53	10.99	5.08	1085	LP2 (2026-09-30)	PASS	NonPolyA_perM 1085 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM4290714	not_specified	M	NA	Conflict	0.02	2.65	0.00	9.78	3.73	14.86	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.672222	0.188408	0.058633	0.080737	81.16	14.09	4.39	1152	LP2 (2026-09-30)	PASS	NonPolyA_perM 1152 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM4290715	not_specified	M	NA	Conflict	0.02	3.17	0.00	9.52	3.75	15.09	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.685391	0.183598	0.058712	0.0723	82.61	13.22	3.85	1032	LP2 (2026-09-30)	PASS	NonPolyA_perM 1032 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not