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
GSM4954072	not_specified	M	NA	Conflict	0.02	15.47	0.00	40.39	16.82	43.11	SECOND_READ_TRANSCRIPTION_STRAND	AMBIGUOUS	0.548767	0.4015	0.048318	0.001415	90.38	1.90	7.30	673	LP2 (2026-09-30)	PASS	NonPolyA_perM 673 is between 350 and 700, outside the range of every calibration study; check the study methods
GSM4954073	not_specified	M	NA	Conflict	0.05	13.30	0.00	41.36	14.68	42.85	SECOND_READ_TRANSCRIPTION_STRAND	AMBIGUOUS	0.511226	0.438714	0.04863	0.00143	93.25	1.74	4.63	659	LP2 (2026-09-30)	PASS	NonPolyA_perM 659 is between 350 and 700, outside the range of every calibration study; check the study methods
GSM4954074	not_specified	M	NA	Conflict	0.04	14.48	0.00	24.14	13.12	54.08	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.550774	0.385917	0.052694	0.010614	90.42	3.74	5.35	1117	LP2 (2026-09-30)	PASS	NonPolyA_perM 1117 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM4954075	not_specified	M	NA	Conflict	0.10	16.17	0.00	27.06	13.01	49.01	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.546239	0.386004	0.054881	0.012876	91.01	3.88	4.63	1064	LP2 (2026-09-30)	PASS	NonPolyA_perM 1064 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM4954076	not_specified	M	NA	Conflict	0.06	17.24	0.00	33.64	17.11	53.47	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.504881	0.431067	0.051314	0.012737	92.21	3.57	3.79	1017	LP2 (2026-09-30)	PASS	NonPolyA_perM 1017 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM4954077	not_specified	M	NA	Conflict	0.11	17.92	0.00	30.92	17.04	53.40	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.499605	0.43476	0.054324	0.01131	92.17	3.52	3.87	1036	LP2 (2026-09-30)	PASS	NonPolyA_perM 1036 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not