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
GSM3139725	F	F	NA	Agree	125.99	0.00	0.00	0.00	0.00	0.00	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.911714	0.048494	0.037482	0.002311	88.45	2.17	9.09	47	LP2 (2026-09-30)	PASS	NonPolyA_perM 47 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM3139726	F	F	NA	Agree	127.67	0.00	0.00	0.00	0.00	0.00	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.909348	0.049735	0.038169	0.002748	87.47	2.17	9.97	33	LP2 (2026-09-30)	PASS	NonPolyA_perM 33 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM3139727	F	F	NA	Agree	174.02	0.00	0.00	0.00	0.00	0.00	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.886184	0.07271	0.038159	0.002946	87.47	2.19	10.02	42	LP2 (2026-09-30)	PASS	NonPolyA_perM 42 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM3139728	F	F	NA	Agree	41.80	0.00	0.00	0.00	0.00	0.00	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.92775	0.030582	0.037272	0.004396	86.30	3.07	10.36	39	LP2 (2026-09-30)	PASS	NonPolyA_perM 39 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM3139729	F	F	NA	Agree	59.52	0.00	0.00	0.00	0.00	0.00	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.921932	0.037833	0.036555	0.003679	79.53	2.61	17.57	43	LP2 (2026-09-30)	PASS	NonPolyA_perM 43 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM3139730	F	F	NA	Agree	98.61	0.00	0.00	0.00	0.00	0.00	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.900459	0.05937	0.035404	0.004766	87.93	2.76	8.92	43	LP2 (2026-09-30)	PASS	NonPolyA_perM 43 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM3139731	F	F	NA	Agree	101.23	0.00	0.00	0.00	0.00	0.00	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.90956	0.048717	0.038267	0.003455	87.85	2.43	9.44	57	LP2 (2026-09-30)	PASS	NonPolyA_perM 57 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM3139732	F	F	NA	Agree	120.37	0.00	0.00	0.00	0.00	0.00	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.900678	0.05848	0.037416	0.003425	88.47	2.52	8.67	50	LP2 (2026-09-30)	PASS	NonPolyA_perM 50 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM3139733	F	F	NA	Agree	134.61	0.00	0.00	0.00	0.00	0.00	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.904589	0.055279	0.037103	0.003029	87.88	2.39	9.33	50	LP2 (2026-09-30)	PASS	NonPolyA_perM 50 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does