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 (2026-10-20) 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
GSM4708524	F	F	NA	Agree	66.70	0.00	0.00	0.02	0.00	0.00	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.660619	0.239973	0.080152	0.019256	83.67	7.05	6.49	5477	LP2 (2026-09-30)	PASS	NonPolyA_perM 5477 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM4708525	F	F	NA	Agree	48.72	0.00	0.00	0.00	0.00	0.03	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.636354	0.267603	0.081346	0.014697	85.06	6.57	5.52	4608	LP2 (2026-09-30)	PASS	NonPolyA_perM 4608 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM4708526	F	F	NA	Agree	40.47	0.00	0.00	0.01	0.00	0.00	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.676141	0.208313	0.09045	0.025096	80.63	9.47	6.27	5442	LP2 (2026-09-30)	PASS	NonPolyA_perM 5442 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM4708527	F	F	NA	Agree	49.86	0.00	0.00	0.00	0.00	0.00	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.665007	0.192166	0.078123	0.064704	78.33	12.20	6.40	4868	LP2 (2026-09-30)	PASS	NonPolyA_perM 4868 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM4708528	F	F	NA	Agree	31.69	0.00	0.00	0.00	0.00	0.00	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.752303	0.140514	0.08931	0.017874	80.81	9.21	6.21	4730	LP2 (2026-09-30)	PASS	NonPolyA_perM 4730 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM4708529	F	F	NA	Agree	43.43	0.00	0.00	0.00	0.00	0.00	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.635681	0.264031	0.084032	0.016255	83.63	7.03	6.32	4717	LP2 (2026-09-30)	PASS	NonPolyA_perM 4717 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM4708530	F	F	NA	Agree	48.30	0.00	0.00	0.02	0.00	0.00	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.578297	0.325254	0.08472	0.011729	85.39	6.14	5.26	4231	LP2 (2026-09-30)	PASS	NonPolyA_perM 4231 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM4708531	F	F	NA	Agree	30.27	0.00	0.00	0.00	0.00	0.00	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.689692	0.198561	0.089752	0.021994	80.18	8.79	7.35	4967	LP2 (2026-09-30)	PASS	NonPolyA_perM 4967 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM4708532	F	F	NA	Agree	68.34	0.00	0.00	0.00	0.00	0.00	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.623376	0.274705	0.078226	0.023693	83.36	7.98	5.48	4501	LP2 (2026-09-30)	PASS	NonPolyA_perM 4501 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM4708533	F	F	NA	Agree	31.95	0.00	0.00	0.01	0.00	0.00	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.644797	0.158352	0.077646	0.119205	72.30	16.81	7.89	4291	LP2 (2026-09-30)	PASS	NonPolyA_perM 4291 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM4708534	F	F	NA	Agree	38.86	0.00	0.00	0.00	0.00	0.00	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.666833	0.22091	0.088216	0.024041	81.68	8.78	5.99	6628	LP2 (2026-09-30)	PASS	NonPolyA_perM 6628 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM4708535	F	F	NA	Agree	32.36	0.00	0.00	0.00	0.00	0.00	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.634407	0.256958	0.091613	0.017022	82.83	8.06	5.46	5897	LP2 (2026-09-30)	PASS	NonPolyA_perM 5897 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM4708536	F	F	NA	Agree	20.97	0.00	0.00	0.00	0.00	0.00	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.647431	0.145322	0.089573	0.117674	70.60	17.88	7.83	6270	LP2 (2026-09-30)	PASS	NonPolyA_perM 6270 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM4708537	F	F	NA	Agree	38.55	0.00	0.00	0.02	0.00	0.00	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.701655	0.196677	0.088193	0.013475	81.86	8.58	5.84	5308	LP2 (2026-09-30)	PASS	NonPolyA_perM 5308 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM4708538	F	F	NA	Agree	38.70	0.00	0.00	0.00	0.00	0.00	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.672535	0.223111	0.08711	0.017245	81.89	8.53	6.05	4933	LP2 (2026-09-30)	PASS	NonPolyA_perM 4933 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM4708539	F	F	NA	Agree	60.99	0.00	0.00	0.00	0.00	0.00	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.566318	0.260349	0.072271	0.101062	75.27	14.32	7.74	5441	LP2 (2026-09-30)	PASS	NonPolyA_perM 5441 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM4708540	F	F	NA	Agree	47.90	0.00	0.00	0.00	0.00	0.00	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.639049	0.256367	0.083458	0.021126	82.36	8.11	6.47	5552	LP2 (2026-09-30)	PASS	NonPolyA_perM 5552 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM4708541	F	F	NA	Agree	36.63	0.00	0.00	0.00	0.00	0.00	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.633126	0.227197	0.085579	0.054098	78.71	11.41	6.67	4499	LP2 (2026-09-30)	PASS	NonPolyA_perM 4499 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM4708542	F	F	NA	Agree	80.04	0.00	0.00	0.00	0.00	0.00	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.610908	0.292734	0.080694	0.015665	83.47	7.44	5.91	4359	LP2 (2026-09-30)	PASS	NonPolyA_perM 4359 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM4708543	F	F	NA	Agree	37.31	0.00	0.00	0.00	0.00	0.00	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.754351	0.14104	0.084299	0.02031	80.94	8.97	6.77	4661	LP2 (2026-09-30)	PASS	NonPolyA_perM 4661 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not