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 (2026-10-21) 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
GSM5835139	F	F	NA	Agree	56.35	0.00	0.00	0.00	0.00	0.00	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.754963	0.11173	0.096339	0.036967	86.19	11.03	2.33	3320	LP2 (2026-09-30)	PASS	NonPolyA_perM 3320 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM5835140	F	F	NA	Agree	135.75	0.00	0.00	0.00	0.00	0.00	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.673812	0.221364	0.09156	0.013263	90.42	6.59	2.49	2518	LP2 (2026-09-30)	PASS	NonPolyA_perM 2518 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM5835141	F	F	NA	Agree	137.55	0.00	0.00	0.00	0.00	0.00	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.648055	0.232545	0.095431	0.023969	88.51	8.29	2.63	2892	LP2 (2026-09-30)	PASS	NonPolyA_perM 2892 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM5835142	F	F	NA	Agree	118.64	0.00	0.00	0.00	0.00	0.00	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.662591	0.227155	0.092732	0.017522	89.27	7.73	2.45	2374	LP2 (2026-09-30)	PASS	NonPolyA_perM 2374 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM5835143	F	F	NA	Agree	140.26	0.00	0.00	0.00	0.00	0.00	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.712822	0.196335	0.083395	0.007448	91.01	5.88	2.57	2227	LP2 (2026-09-30)	PASS	NonPolyA_perM 2227 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM5835144	F	F	NA	Agree	104.26	0.00	0.00	0.00	0.00	0.00	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.67051	0.19873	0.098006	0.032754	86.88	9.74	2.80	5049	LP2 (2026-09-30)	PASS	NonPolyA_perM 5049 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM5835145	F	F	NA	Agree	103.33	0.00	0.00	0.00	0.00	0.00	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.605019	0.270659	0.101445	0.022878	87.43	9.08	2.88	5932	LP2 (2026-09-30)	PASS	NonPolyA_perM 5932 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM5835146	F	F	NA	Agree	89.04	0.00	0.00	0.00	0.00	0.00	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.712988	0.157554	0.097616	0.031842	86.77	10.16	2.52	5366	LP2 (2026-09-30)	PASS	NonPolyA_perM 5366 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM5835147	F	F	NA	Agree	81.17	0.00	0.00	0.00	0.00	0.00	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.727398	0.152527	0.102754	0.017322	89.42	8.16	1.98	2297	LP2 (2026-09-30)	PASS	NonPolyA_perM 2297 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM5835148	F	F	NA	Agree	107.57	0.00	0.00	0.00	0.00	0.00	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.690555	0.193182	0.098683	0.01758	88.74	8.65	2.15	2566	LP2 (2026-09-30)	PASS	NonPolyA_perM 2566 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM5835149	F	F	NA	Agree	81.64	0.00	0.00	0.00	0.00	0.00	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.739763	0.134773	0.102173	0.023291	88.45	8.73	2.34	2590	LP2 (2026-09-30)	PASS	NonPolyA_perM 2590 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM5835150	F	F	NA	Agree	89.66	0.00	0.00	0.00	0.00	0.00	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.70438	0.174719	0.096811	0.02409	88.52	8.61	2.37	2578	LP2 (2026-09-30)	PASS	NonPolyA_perM 2578 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not