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). For 4 samples processed before workflow 2.1, ComputedSex is the earlier curated call, kept after review where it differed from the rule above.
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
GSM9135902	F	F	NA	Agree	8.18	0.00	0.00	0.00	0.00	0.00	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.901923	0.029669	0.06132	0.007088	93.75	4.41	1.42	12	LP2 (2026-09-30)	PASS	NonPolyA_perM 12 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM9135903	F	F	NA	Agree	26.34	0.00	0.00	0.00	0.00	0.00	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.903866	0.030536	0.060099	0.005499	94.27	3.99	1.34	14	LP2 (2026-09-30)	PASS	NonPolyA_perM 14 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM9135904	F	F	NA	Agree	19.51	0.00	0.00	0.00	0.00	0.00	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.906303	0.029599	0.059921	0.004177	94.37	3.89	1.35	17	LP2 (2026-09-30)	PASS	NonPolyA_perM 17 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM9135905	F	F	NA	Agree	10.52	0.00	0.00	0.00	0.00	0.00	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.90257	0.028577	0.060928	0.007925	93.84	4.41	1.34	12	LP2 (2026-09-30)	PASS	NonPolyA_perM 12 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM9135906	F	F	NA	Agree	27.63	0.00	0.00	0.00	0.00	0.00	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.904761	0.031034	0.059164	0.005041	94.29	3.95	1.38	16	LP2 (2026-09-30)	PASS	NonPolyA_perM 16 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM9135907	F	F	NA	Agree	0.20	0.00	0.00	0.00	0.00	0.00	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.895539	0.040016	0.060864	0.003581	94.29	3.94	1.37	32	LP2 (2026-09-30)	PASS	NonPolyA_perM 32 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM9135908	F	F	NA	Agree	89.06	0.00	0.00	0.00	0.00	0.00	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.893873	0.043938	0.059445	0.002744	94.58	3.68	1.34	30	LP2 (2026-09-30)	PASS	NonPolyA_perM 30 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM9135909	F	F	NA	Agree	25.34	0.00	0.00	0.00	0.00	0.00	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.900616	0.03301	0.061264	0.005111	93.97	4.19	1.44	18	LP2 (2026-09-30)	PASS	NonPolyA_perM 18 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM9135910	F	F	NA	Agree	15.26	0.00	0.00	0.00	0.00	0.00	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.907722	0.027126	0.059968	0.005185	94.32	3.99	1.31	8	LP2 (2026-09-30)	PASS	NonPolyA_perM 8 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM9135911	F	F	NA	Agree	20.07	0.00	0.00	0.00	0.00	0.00	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.90624	0.029598	0.060327	0.003836	94.30	3.97	1.34	17	LP2 (2026-09-30)	PASS	NonPolyA_perM 17 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM9135912	F	F	NA	Agree	12.88	0.00	0.00	0.00	0.00	0.00	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.903808	0.028318	0.061153	0.006721	93.89	4.27	1.44	13	LP2 (2026-09-30)	PASS	NonPolyA_perM 13 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM9135913	F	F	NA	Agree	15.05	0.00	0.00	0.00	0.00	0.00	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.90583	0.027211	0.060701	0.006257	94.15	4.13	1.34	11	LP2 (2026-09-30)	PASS	NonPolyA_perM 11 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM9135914	F	F	NA	Agree	35.54	0.00	0.00	0.00	0.00	0.00	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.906114	0.030722	0.05844	0.004724	94.33	3.93	1.34	17	LP2 (2026-09-30)	PASS	NonPolyA_perM 17 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM9135915	F	F	NA	Agree	37.09	0.00	0.00	0.00	0.00	0.00	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.902489	0.032354	0.059545	0.005613	94.24	4.03	1.35	18	LP2 (2026-09-30)	PASS	NonPolyA_perM 18 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM9135916	F	F	NA	Agree	57.08	0.00	0.00	0.00	0.00	0.00	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.895189	0.037052	0.059734	0.008025	93.90	4.31	1.38	25	LP2 (2026-09-30)	PASS	NonPolyA_perM 25 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM9135917	F	F	NA	Agree	12.16	0.00	0.00	0.00	0.00	0.00	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.908243	0.027521	0.058478	0.005758	94.42	3.99	1.19	12	LP2 (2026-09-30)	PASS	NonPolyA_perM 12 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM9135918	F	F	NA	Agree	16.65	0.00	0.00	0.00	0.00	0.00	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.904939	0.029722	0.059051	0.006288	94.18	4.13	1.27	15	LP2 (2026-09-30)	PASS	NonPolyA_perM 15 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM9135919	F	F	NA	Agree	12.38	0.00	0.00	0.00	0.00	0.00	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.907033	0.027949	0.059181	0.005838	94.26	4.11	1.22	10	LP2 (2026-09-30)	PASS	NonPolyA_perM 10 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM9135920	F	F	NA	Agree	12.34	0.00	0.00	0.00	0.00	0.00	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.905656	0.028185	0.059885	0.006274	94.16	4.13	1.30	15	LP2 (2026-09-30)	PASS	NonPolyA_perM 15 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM9135921	F	F	NA	Agree	75.21	0.00	0.00	0.00	0.00	0.00	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.896898	0.041893	0.058188	0.003021	94.70	3.63	1.28	27	LP2 (2026-09-30)	PASS	NonPolyA_perM 27 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM9135922	F	F	NA	Agree	31.63	0.00	0.00	0.00	0.00	0.00	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.90317	0.031058	0.058844	0.006927	94.25	4.08	1.30	20	LP2 (2026-09-30)	PASS	NonPolyA_perM 20 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM9135923	F	F	NA	Agree	36.15	0.00	0.00	0.00	0.00	0.00	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.902582	0.034074	0.058605	0.004739	94.44	3.89	1.28	17	LP2 (2026-09-30)	PASS	NonPolyA_perM 17 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM9135924	F	F	NA	Agree	56.74	0.00	0.00	0.00	0.00	0.00	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.894262	0.040605	0.059907	0.005225	94.39	3.94	1.28	22	LP2 (2026-09-30)	PASS	NonPolyA_perM 22 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM9135925	F	F	NA	Agree	9.23	0.00	0.00	0.00	0.00	0.00	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.908193	0.026841	0.060439	0.004527	94.15	4.01	1.43	13	LP2 (2026-09-30)	PASS	NonPolyA_perM 13 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM9135926	F	F	NA	Agree	22.90	0.00	0.00	0.00	0.00	0.00	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.908404	0.028998	0.058684	0.003914	94.25	3.84	1.52	17	LP2 (2026-09-30)	PASS	NonPolyA_perM 17 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM9135927	F	F	NA	Agree	16.34	0.00	0.00	0.00	0.00	0.00	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.908195	0.027401	0.059762	0.004642	94.21	4.02	1.39	16	LP2 (2026-09-30)	PASS	NonPolyA_perM 16 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM9135928	F	F	NA	Agree	10.47	0.00	0.00	0.00	0.00	0.00	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.906765	0.027778	0.060042	0.005415	94.10	4.08	1.44	14	LP2 (2026-09-30)	PASS	NonPolyA_perM 14 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM9135929	F	F	NA	Agree	39.46	0.00	0.00	0.00	0.00	0.00	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.904866	0.032475	0.059279	0.00338	94.41	3.78	1.42	21	LP2 (2026-09-30)	PASS	NonPolyA_perM 21 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM9135930	F	F	NA	Agree	30.63	0.00	0.00	0.00	0.00	0.00	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.905241	0.031294	0.057968	0.005497	94.03	4.04	1.51	15	LP2 (2026-09-30)	PASS	NonPolyA_perM 15 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM9135931	F	F	NA	Agree	21.19	0.00	0.00	0.00	0.00	0.00	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.906127	0.029618	0.05991	0.004345	94.12	3.99	1.50	11	LP2 (2026-09-30)	PASS	NonPolyA_perM 11 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM9135932	F	F	NA	Agree	0.21	0.00	0.00	0.00	0.00	0.00	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.890004	0.043571	0.059103	0.007322	93.77	4.28	1.49	30	LP2 (2026-09-30)	PASS	NonPolyA_perM 30 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM9135933	F	F	NA	Agree	7.88	0.00	0.00	0.00	0.00	0.00	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.796135	0.025746	0.052723	0.125396	83.40	15.01	1.21	15	LP2 (2026-09-30)	PASS	NonPolyA_perM 15 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM9135934	F	F	NA	Agree	21.01	0.00	0.00	0.00	0.00	0.00	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.909132	0.028703	0.05828	0.003884	94.48	3.86	1.26	10	LP2 (2026-09-30)	PASS	NonPolyA_perM 10 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM9135935	F	F	NA	Agree	11.11	0.00	0.00	0.00	0.00	0.00	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.909452	0.027486	0.058367	0.004695	94.29	4.00	1.30	14	LP2 (2026-09-30)	PASS	NonPolyA_perM 14 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM9135936	F	F	NA	Agree	20.77	0.00	0.00	0.00	0.00	0.00	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.908666	0.028464	0.058914	0.003956	94.52	3.86	1.23	12	LP2 (2026-09-30)	PASS	NonPolyA_perM 12 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM9135937	F	F	NA	Agree	45.62	0.00	0.00	0.00	0.00	0.00	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.906855	0.032277	0.057756	0.003112	94.58	3.75	1.26	18	LP2 (2026-09-30)	PASS	NonPolyA_perM 18 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM9135938	F	F	NA	Agree	27.98	0.00	0.00	0.00	0.00	0.00	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.907734	0.029537	0.058036	0.004693	94.34	3.96	1.30	12	LP2 (2026-09-30)	PASS	NonPolyA_perM 12 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM9135939	F	F	NA	Agree	31.61	0.00	0.00	0.00	0.00	0.00	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.907812	0.02987	0.0584	0.003917	94.31	3.88	1.42	15	LP2 (2026-09-30)	PASS	NonPolyA_perM 15 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM9135940	F	F	NA	Agree	46.69	0.00	0.00	0.00	0.00	0.00	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.893092	0.035772	0.059246	0.01189	93.70	4.62	1.31	24	LP2 (2026-09-30)	PASS	NonPolyA_perM 24 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does