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 3 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
GSM5370902	not_specified	Undetermined	NA	Conflict	519.31	23.11	0.00	36.10	13.85	26.12	NONE	POLYA	0.502923	0.442887	0.042715	0.011475	85.35	4.27	10.01	347	LP2 (2026-09-30)	PASS	NonPolyA_perM 347 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM5370903	not_specified	Undetermined	NA	Conflict	588.47	22.93	0.00	58.06	11.05	58.61	NONE	AMBIGUOUS	0.458255	0.477002	0.043421	0.021321	83.80	5.79	10.02	393	LP2 (2026-09-30)	PASS	NonPolyA_perM 393 is between 350 and 700, outside the range of every calibration study; check the study methods
GSM5370904	not_specified	Undetermined	NA	Conflict	131.74	18.54	0.00	54.37	9.14	69.36	NONE	POLYA	0.753111	0.179754	0.039325	0.027811	75.44	13.49	10.79	47	LP2 (2026-09-30)	PASS	NonPolyA_perM 47 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM5370905	not_specified	Undetermined	NA	Conflict	89.15	16.17	0.00	37.57	8.06	55.57	NONE	POLYA	0.762795	0.177508	0.031849	0.027849	75.90	12.84	11.09	37	LP2 (2026-09-30)	PASS	NonPolyA_perM 37 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM5370906	not_specified	Undetermined	NA	Conflict	230.37	34.69	0.00	45.94	10.26	118.85	NONE	POLYA	0.615634	0.327335	0.035603	0.021429	76.65	7.69	15.36	179	LP2 (2026-09-30)	PASS	NonPolyA_perM 179 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM5370907	not_specified	Undetermined	NA	Conflict	212.36	30.86	0.00	42.33	11.39	109.58	NONE	POLYA	0.603129	0.328222	0.035153	0.033497	77.72	9.79	12.17	187	LP2 (2026-09-30)	PASS	NonPolyA_perM 187 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM5370908	not_specified	Undetermined	NA	Conflict	66.56	11.86	0.00	19.14	5.38	64.80	NONE	POLYA	0.776949	0.148009	0.036472	0.038571	74.71	12.94	12.12	44	LP2 (2026-09-30)	PASS	NonPolyA_perM 44 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM5370909	not_specified	Undetermined	NA	Conflict	50.26	18.69	0.00	38.07	8.65	98.87	NONE	POLYA	0.780024	0.163433	0.032851	0.023692	72.89	12.08	14.80	48	LP2 (2026-09-30)	PASS	NonPolyA_perM 48 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM5370910	not_specified	Undetermined	NA	Conflict	201.76	25.38	0.00	46.02	11.02	107.60	NONE	POLYA	0.673913	0.245546	0.037989	0.042551	74.74	9.77	15.25	172	LP2 (2026-09-30)	PASS	NonPolyA_perM 172 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM5370911	not_specified	Undetermined	NA	Conflict	153.85	27.36	0.00	48.03	14.94	144.55	NONE	POLYA	0.672242	0.251406	0.038214	0.038138	77.08	9.25	13.42	185	LP2 (2026-09-30)	PASS	NonPolyA_perM 185 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM5370912	not_specified	Undetermined	NA	Conflict	100.27	13.01	0.00	21.55	5.47	68.77	NONE	POLYA	0.810959	0.123791	0.035757	0.029493	73.92	11.19	14.72	34	LP2 (2026-09-30)	PASS	NonPolyA_perM 34 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM5370913	not_specified	Undetermined	NA	Conflict	82.83	19.40	0.00	33.23	9.53	98.24	NONE	POLYA	0.815874	0.121315	0.037105	0.025705	74.61	9.97	15.23	30	LP2 (2026-09-30)	PASS	NonPolyA_perM 30 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM5370914	not_specified	Undetermined	NA	Conflict	203.57	25.33	0.00	52.63	12.73	108.60	NONE	POLYA	0.662088	0.262929	0.038391	0.036593	76.14	9.97	13.67	179	LP2 (2026-09-30)	PASS	NonPolyA_perM 179 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM5370915	not_specified	Undetermined	NA	Conflict	332.11	28.88	0.00	42.43	13.30	78.79	NONE	POLYA	0.630489	0.307054	0.036747	0.02571	75.23	8.34	16.21	193	LP2 (2026-09-30)	PASS	NonPolyA_perM 193 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM5370916	not_specified	Undetermined	NA	Conflict	154.83	5.34	0.00	10.78	3.05	35.85	NONE	POLYA	0.751176	0.183976	0.032697	0.032152	73.03	12.53	14.25	43	LP2 (2026-09-30)	PASS	NonPolyA_perM 43 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM5370917	not_specified	Undetermined	NA	Conflict	82.98	22.71	0.00	36.27	8.58	90.50	NONE	POLYA	0.774031	0.176726	0.031893	0.01735	73.94	10.97	14.93	55	LP2 (2026-09-30)	PASS	NonPolyA_perM 55 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does