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).
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
GSM8341985	M	M	NA	Agree	0.04	5.50	0.00	27.64	7.57	54.55	SECOND_READ_TRANSCRIPTION_STRAND	AMBIGUOUS	0.620661	0.040441	0.028615	0.310283	50.41	26.17	23.05	391	LP2 (2026-09-30)	PASS	NonPolyA_perM 391 is between 350 and 700, outside the range of every calibration study; check the study methods
GSM8341986	M	M	NA	Agree	0.04	6.04	0.00	38.20	10.54	62.74	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.736647	0.05033	0.03143	0.181593	47.78	11.95	39.88	190	LP2 (2026-09-30)	PASS	NonPolyA_perM 190 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM8341987	M	M	NA	Agree	0.04	4.87	0.00	35.70	7.39	62.42	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.810507	0.037949	0.027002	0.124541	63.37	10.92	25.34	119	LP2 (2026-09-30)	PASS	NonPolyA_perM 119 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM8341988	M	M	NA	Agree	0.05	5.96	0.00	32.58	8.32	65.98	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.778324	0.040635	0.033371	0.147669	64.31	13.40	21.92	176	LP2 (2026-09-30)	PASS	NonPolyA_perM 176 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM8341989	M	M	NA	Agree	0.00	6.19	0.00	36.85	8.33	74.20	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.803533	0.040542	0.036292	0.119634	65.41	11.10	23.13	158	LP2 (2026-09-30)	PASS	NonPolyA_perM 158 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM8341990	M	M	NA	Agree	0.00	7.51	0.00	36.56	9.55	70.00	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.68153	0.051023	0.033953	0.233494	48.40	16.95	34.27	346	LP2 (2026-09-30)	PASS	NonPolyA_perM 346 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM8341991	M	M	NA	Agree	0.00	6.03	0.00	41.96	10.75	76.55	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.846571	0.040934	0.034978	0.077517	75.00	8.36	16.36	137	LP2 (2026-09-30)	PASS	NonPolyA_perM 137 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM8341992	M	M	NA	Agree	0.01	6.73	0.00	45.33	10.41	73.17	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.758758	0.057262	0.037668	0.146312	59.17	12.72	27.62	204	LP2 (2026-09-30)	PASS	NonPolyA_perM 204 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does