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 (2026-10-16) 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
GSM3738621	M	M	NA	Agree	0.04	2.39	0.00	16.80	3.68	16.26	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.803159	0.055746	0.058572	0.082524	80.60	16.13	2.15	2439	LP2 (2026-09-30)	PASS	NonPolyA_perM 2439 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM3738622	M	M	NA	Agree	0.05	2.28	0.00	16.18	3.21	16.78	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.804459	0.068441	0.071148	0.055952	81.21	14.86	2.42	3780	LP2 (2026-09-30)	PASS	NonPolyA_perM 3780 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM3738623	M	M	NA	Agree	0.03	2.56	0.00	19.42	3.19	16.33	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.825663	0.046455	0.074725	0.053157	80.60	14.65	3.25	3044	LP2 (2026-09-30)	PASS	NonPolyA_perM 3044 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM3738624	M	M	NA	Agree	0.04	2.39	0.00	13.55	3.31	14.45	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.809924	0.061845	0.064159	0.064072	81.07	14.98	2.79	3311	LP2 (2026-09-30)	PASS	NonPolyA_perM 3311 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM3738625	M	M	NA	Agree	0.09	3.13	0.00	20.19	4.79	18.57	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.801073	0.090537	0.061444	0.046946	83.26	12.74	2.84	2764	LP2 (2026-09-30)	PASS	NonPolyA_perM 2764 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM3738626	M	M	NA	Agree	0.09	2.51	0.00	15.25	3.65	15.12	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.794329	0.07524	0.056152	0.074279	81.41	14.88	2.70	2444	LP2 (2026-09-30)	PASS	NonPolyA_perM 2444 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM3738627	M	M	NA	Agree	0.04	2.78	0.00	19.66	3.73	15.34	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.816069	0.060378	0.073027	0.050526	80.48	14.57	3.41	3011	LP2 (2026-09-30)	PASS	NonPolyA_perM 3011 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM3738628	M	M	NA	Agree	0.05	3.15	0.00	19.58	4.21	14.96	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.798713	0.080803	0.069094	0.051389	80.04	14.00	4.28	3288	LP2 (2026-09-30)	PASS	NonPolyA_perM 3288 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM3738629	M	M	NA	Agree	0.04	2.36	0.00	20.09	3.21	15.70	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.824986	0.051951	0.073006	0.050056	81.68	14.38	2.69	2778	LP2 (2026-09-30)	PASS	NonPolyA_perM 2778 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM3738630	M	M	NA	Agree	0.03	3.36	0.00	19.91	3.97	16.59	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.797275	0.095167	0.072455	0.035103	83.05	13.01	2.49	3100	LP2 (2026-09-30)	PASS	NonPolyA_perM 3100 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM3738631	M	M	NA	Agree	0.03	2.53	0.00	20.14	3.50	19.28	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.822937	0.055392	0.072323	0.049347	81.48	14.46	2.59	3101	LP2 (2026-09-30)	PASS	NonPolyA_perM 3101 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM3738632	M	M	NA	Agree	0.04	2.88	0.00	16.17	3.86	16.65	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.799216	0.071534	0.064654	0.064596	80.77	14.99	2.82	2932	LP2 (2026-09-30)	PASS	NonPolyA_perM 2932 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not