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
GSM4289045	M	M	NA	Agree	0.15	2.53	0.00	6.87	1.76	15.34	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.736341	0.176338	0.08646	0.000862	93.12	3.46	1.68	1728	LP2 (2026-09-30)	PASS	NonPolyA_perM 1728 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM4289046	M	M	NA	Agree	0.25	2.44	0.00	5.96	1.13	19.38	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.740031	0.174789	0.084834	0.000346	91.51	3.03	3.62	1365	LP2 (2026-09-30)	PASS	NonPolyA_perM 1365 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM4289047	M	M	NA	Agree	0.15	1.86	0.00	5.86	1.22	13.46	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.770555	0.14852	0.080252	0.000672	92.08	3.20	2.99	1766	LP2 (2026-09-30)	PASS	NonPolyA_perM 1766 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM4289048	M	M	NA	Agree	0.24	2.02	0.00	5.72	0.90	15.44	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.735393	0.174562	0.089469	0.000575	91.23	3.60	3.16	2463	LP2 (2026-09-30)	PASS	NonPolyA_perM 2463 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM4289049	M	M	NA	Agree	0.28	2.20	0.00	6.00	1.00	16.91	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.723281	0.186284	0.089832	0.000604	93.04	3.20	1.74	1685	LP2 (2026-09-30)	PASS	NonPolyA_perM 1685 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM4289050	M	M	NA	Agree	0.32	2.51	0.00	5.59	0.95	17.40	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.709915	0.197708	0.091809	0.000568	93.28	3.12	1.62	1668	LP2 (2026-09-30)	PASS	NonPolyA_perM 1668 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM4289051	M	M	NA	Agree	0.37	2.71	0.00	6.42	1.35	19.93	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.686901	0.214268	0.098254	0.000577	91.87	3.30	2.88	1603	LP2 (2026-09-30)	PASS	NonPolyA_perM 1603 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM4289052	M	M	NA	Agree	0.31	2.47	0.00	5.54	1.27	16.63	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.684374	0.216203	0.098871	0.000552	93.12	3.25	1.67	1387	LP2 (2026-09-30)	PASS	NonPolyA_perM 1387 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM4289053	M	M	NA	Agree	0.18	2.42	0.00	5.63	1.00	15.53	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.701194	0.201702	0.096385	0.000719	91.46	3.47	3.15	2028	LP2 (2026-09-30)	PASS	NonPolyA_perM 2028 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM4289054	M	M	NA	Agree	0.24	3.07	0.00	7.62	1.74	19.05	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.673331	0.228292	0.097733	0.000644	91.92	3.15	2.89	1432	LP2 (2026-09-30)	PASS	NonPolyA_perM 1432 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM4289055	M	M	NA	Agree	0.25	2.30	0.00	5.30	0.82	16.35	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.703131	0.200378	0.095858	0.000633	91.54	3.37	3.09	1726	LP2 (2026-09-30)	PASS	NonPolyA_perM 1726 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM4289056	M	M	NA	Agree	0.29	2.39	0.00	5.43	1.29	16.61	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.645033	0.248353	0.105951	0.000662	91.37	3.17	3.28	1229	LP2 (2026-09-30)	PASS	NonPolyA_perM 1229 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not