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
GSM2689747	not_specified	M	NA	Conflict	0.01	1.66	0.00	5.50	2.64	11.89	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.624643	0.166398	0.191243	0.017716	76.37	17.88	4.92	31288	LP2 (2026-09-30)	PASS	NonPolyA_perM 31288 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM2689748	not_specified	M	NA	Conflict	0.01	1.22	0.00	4.10	1.28	8.25	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.656291	0.09235	0.212267	0.039092	70.90	24.95	3.57	28150	LP2 (2026-09-30)	PASS	NonPolyA_perM 28150 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM2689749	not_specified	M	NA	Conflict	0.03	1.99	0.00	6.81	3.02	13.79	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.556249	0.1944	0.232399	0.016952	79.30	14.60	4.81	25112	LP2 (2026-09-30)	PASS	NonPolyA_perM 25112 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM2689750	not_specified	M	NA	Conflict	0.01	1.51	0.00	5.10	1.60	9.60	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.688521	0.10619	0.17979	0.025498	76.68	19.52	3.28	19081	LP2 (2026-09-30)	PASS	NonPolyA_perM 19081 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM2689751	not_specified	M	NA	Conflict	0.02	1.91	0.00	7.08	2.82	13.68	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.610539	0.18101	0.192203	0.016249	78.58	16.37	4.17	27497	LP2 (2026-09-30)	PASS	NonPolyA_perM 27497 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM2689752	not_specified	M	NA	Conflict	0.01	1.54	0.00	4.91	1.64	7.77	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.615427	0.173165	0.18402	0.027389	76.22	19.76	3.44	19667	LP2 (2026-09-30)	PASS	NonPolyA_perM 19667 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not