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 (2026-10-22) 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
GSM3754029	M	M	NA	Agree	0.17	8.31	0.00	17.01	9.74	42.00	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.601954	0.324775	0.060401	0.01287	91.97	4.50	3.14	835	LP2 (2026-09-30)	PASS	NonPolyA_perM 835 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM3754030	M	M	NA	Agree	0.20	8.79	0.00	16.36	9.46	43.14	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.607712	0.315851	0.060923	0.015514	91.66	4.72	3.20	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
GSM3754031	M	M	NA	Agree	0.24	10.16	0.00	20.09	11.08	45.25	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.590239	0.326829	0.061064	0.021868	91.32	5.08	3.16	887	LP2 (2026-09-30)	PASS	NonPolyA_perM 887 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM3754032	M	M	NA	Agree	0.20	8.58	0.00	16.58	8.17	50.36	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.674357	0.257854	0.058856	0.008933	91.81	4.20	3.57	815	LP2 (2026-09-30)	PASS	NonPolyA_perM 815 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM3754033	M	M	NA	Agree	0.16	9.20	0.00	15.20	9.33	54.86	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.646694	0.285887	0.060517	0.006902	92.32	3.92	3.34	712	LP2 (2026-09-30)	PASS	NonPolyA_perM 712 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM3754034	M	M	NA	Agree	0.35	12.96	0.12	21.59	11.42	49.06	SECOND_READ_TRANSCRIPTION_STRAND	AMBIGUOUS	0.584533	0.350826	0.05719	0.007452	92.81	3.36	3.42	582	LP2 (2026-09-30)	PASS	NonPolyA_perM 582 is between 350 and 700, outside the range of every calibration study; check the study methods