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 (2026-10-20) 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
GSM4284833	not_specified	Undetermined	NA	Conflict	13.42	4.11	0.00	18.27	4.68	32.21	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.787691	0.134684	0.074483	0.003142	82.52	7.92	7.89	3731	LP2 (2026-09-30)	PASS	NonPolyA_perM 3731 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM4284834	not_specified	M	NA	Conflict	5.62	6.10	0.00	22.15	5.89	43.72	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.670093	0.2344	0.092055	0.003453	81.75	9.52	6.70	7089	LP2 (2026-09-30)	PASS	NonPolyA_perM 7089 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM4284835	not_specified	Undetermined	NA	Conflict	11.17	4.37	0.00	15.93	4.81	33.20	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.667651	0.236966	0.092103	0.00328	81.37	9.41	7.05	7301	LP2 (2026-09-30)	PASS	NonPolyA_perM 7301 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM4284836	not_specified	Undetermined	NA	Conflict	39.33	1.80	0.00	5.79	1.53	10.45	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.717485	0.177728	0.100633	0.004155	78.58	9.82	9.47	6659	LP2 (2026-09-30)	PASS	NonPolyA_perM 6659 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM4284837	not_specified	Undetermined	NA	Conflict	41.31	5.46	0.00	17.73	5.43	33.44	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.62464	0.298572	0.073225	0.003563	84.03	6.63	7.54	5898	LP2 (2026-09-30)	PASS	NonPolyA_perM 5898 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM4284838	not_specified	M	NA	Conflict	7.89	6.62	0.00	27.40	7.68	52.06	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.647273	0.268746	0.081266	0.002716	79.84	7.59	10.52	6623	LP2 (2026-09-30)	PASS	NonPolyA_perM 6623 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not