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). For 2 samples processed before workflow 2.1, ComputedSex is the earlier curated call, kept after review where it differed from the rule above.
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
GSM4981856	not_specified	Undetermined	NA	Conflict	73.83	0.81	0.00	2.30	1.68	5.47	NONE	RRNA_DEPLETED	0.776916	0.115958	0.091838	0.015287	73.84	8.23	17.05	1038	LP2 (2026-09-30)	PASS	NonPolyA_perM 1038 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM4981857	not_specified	Undetermined	NA	Conflict	37.90	1.32	0.00	5.84	3.46	11.60	NONE	RRNA_DEPLETED	0.773569	0.121932	0.092554	0.011945	75.60	7.32	16.21	1204	LP2 (2026-09-30)	PASS	NonPolyA_perM 1204 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM4981858	not_specified	Undetermined	NA	Conflict	33.29	1.78	0.00	7.08	3.63	12.32	NONE	RRNA_DEPLETED	0.784954	0.108345	0.095324	0.011376	75.50	7.70	15.88	1188	LP2 (2026-09-30)	PASS	NonPolyA_perM 1188 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM4981859	not_specified	Undetermined	NA	Conflict	47.84	1.31	0.00	5.98	3.59	16.78	NONE	RRNA_DEPLETED	0.766898	0.134218	0.088909	0.009976	77.33	7.11	14.65	1076	LP2 (2026-09-30)	PASS	NonPolyA_perM 1076 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM4981860	not_specified	Undetermined	NA	Conflict	32.20	1.90	0.00	5.52	3.27	15.32	NONE	RRNA_DEPLETED	0.796925	0.107093	0.085761	0.010221	75.45	6.02	17.65	701	LP2 (2026-09-30)	PASS	NonPolyA_perM 701 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM4981861	not_specified	Undetermined	NA	Conflict	32.38	2.32	0.00	7.00	3.40	16.02	NONE	AMBIGUOUS	0.802108	0.103447	0.083805	0.01064	76.13	5.71	17.42	676	LP2 (2026-09-30)	PASS	NonPolyA_perM 676 is between 350 and 700, outside the range of every calibration study; check the study methods
GSM4981862	not_specified	Undetermined	NA	Conflict	46.22	1.74	0.00	4.50	2.40	10.53	NONE	RRNA_DEPLETED	0.791952	0.119415	0.081846	0.006786	77.12	5.27	16.85	715	LP2 (2026-09-30)	PASS	NonPolyA_perM 715 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM4981863	not_specified	Undetermined	NA	Conflict	38.04	2.66	0.00	7.14	4.25	17.05	NONE	RRNA_DEPLETED	0.778681	0.125392	0.08449	0.011437	74.77	6.05	18.30	807	LP2 (2026-09-30)	PASS	NonPolyA_perM 807 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not