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
GSM4257204	F	F	NA	Agree	415.95	0.00	0.00	0.05	0.00	0.00	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.498215	0.431816	0.05696	0.013009	74.81	3.03	21.46	1384	LP2 (2026-09-30)	PASS	NonPolyA_perM 1384 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM4257205	F	F	NA	Agree	439.20	0.00	0.00	0.00	0.00	0.10	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.483434	0.435794	0.075699	0.005072	73.61	2.40	23.16	1134	LP2 (2026-09-30)	PASS	NonPolyA_perM 1134 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM4257206	F	F	NA	Agree	418.68	0.00	0.00	0.00	0.00	0.00	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.505577	0.425613	0.061651	0.007159	75.27	2.51	21.46	1379	LP2 (2026-09-30)	PASS	NonPolyA_perM 1379 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM4257207	F	F	NA	Agree	337.00	0.00	0.00	0.08	0.00	0.05	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.537084	0.395453	0.060928	0.006534	74.67	2.78	21.74	1380	LP2 (2026-09-30)	PASS	NonPolyA_perM 1380 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM4257208	F	F	NA	Agree	362.25	0.00	0.00	0.05	0.07	0.15	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.510273	0.415478	0.066662	0.007586	72.89	2.79	23.54	1421	LP2 (2026-09-30)	PASS	NonPolyA_perM 1421 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM4257209	F	F	NA	Agree	293.55	0.00	0.00	0.00	0.03	0.06	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.543584	0.380842	0.06118	0.014395	72.86	3.27	23.13	1397	LP2 (2026-09-30)	PASS	NonPolyA_perM 1397 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not