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). For 2 samples processed before workflow 2.1, ComputedSex is the earlier curated call, kept after review where it differed from the rule above.
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
GSM7777631	M	M	NA	Agree	0.03	7.99	0.00	24.25	6.63	29.61	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.760137	0.196618	0.041935	0.00131	80.50	6.45	12.20	2785	LP2 (2026-09-30)	PASS	NonPolyA_perM 2785 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM7777632	M	M	NA	Agree	0.03	7.46	0.00	22.19	5.24	23.24	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.724679	0.20543	0.03488	0.035012	80.98	10.67	7.57	2440	LP2 (2026-09-30)	PASS	NonPolyA_perM 2440 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM7777633	M	M	NA	Agree	0.04	8.26	0.00	24.07	5.91	26.66	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.756462	0.198795	0.041943	0.0028	78.54	6.57	14.02	3355	LP2 (2026-09-30)	PASS	NonPolyA_perM 3355 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM7777634	M	M	NA	Agree	0.03	8.41	0.00	24.79	5.59	25.93	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.732766	0.209083	0.034013	0.024138	78.05	9.38	11.90	2502	LP2 (2026-09-30)	PASS	NonPolyA_perM 2502 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM7777635	M	M	NA	Agree	0.02	1.64	0.00	5.42	1.92	6.68	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.780215	0.144046	0.04897	0.02677	41.94	8.19	49.52	5315	LP2 (2026-09-30)	PASS	NonPolyA_perM 5315 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM7777636	M	M	NA	Agree	0.00	0.86	0.00	2.97	1.25	3.38	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.801112	0.11346	0.076243	0.009186	50.23	8.87	40.14	8287	LP2 (2026-09-30)	PASS	NonPolyA_perM 8287 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM7777637	M	M	NA	Agree	0.00	0.25	0.00	1.22	0.46	1.83	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.714326	0.099547	0.122436	0.063692	43.61	18.05	37.00	19773	LP2 (2026-09-30)	PASS	NonPolyA_perM 19773 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM7777638	M	M	NA	Agree	0.00	0.84	0.00	2.82	0.86	3.91	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.739705	0.095572	0.087181	0.077541	38.15	14.50	46.64	11676	LP2 (2026-09-30)	PASS	NonPolyA_perM 11676 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM7777639	M	M	NA	Agree	0.00	0.92	0.00	2.65	1.19	3.62	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.795415	0.082712	0.080327	0.041546	48.57	10.70	39.96	9894	LP2 (2026-09-30)	PASS	NonPolyA_perM 9894 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM7777640	M	M	NA	Agree	0.00	3.96	0.00	9.77	3.96	11.81	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.80072	0.142192	0.040313	0.016776	48.26	6.41	44.96	3267	LP2 (2026-09-30)	PASS	NonPolyA_perM 3267 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM7777641	M	M	NA	Agree	0.02	3.69	0.00	10.29	2.95	11.89	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.795708	0.142129	0.03952	0.022643	48.23	7.72	43.70	3221	LP2 (2026-09-30)	PASS	NonPolyA_perM 3221 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM7777642	M	M	NA	Agree	0.00	0.60	0.00	1.97	0.78	2.32	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.805503	0.071417	0.100998	0.022082	46.25	10.44	42.33	14722	LP2 (2026-09-30)	PASS	NonPolyA_perM 14722 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM7777643	M	M	NA	Agree	0.00	0.34	0.00	1.06	0.73	2.09	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.801913	0.073235	0.108131	0.016722	42.91	9.53	46.59	14587	LP2 (2026-09-30)	PASS	NonPolyA_perM 14587 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM7777644	M	M	NA	Agree	0.00	1.40	0.00	4.96	1.76	5.54	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.760019	0.12078	0.062107	0.057094	50.36	12.27	36.79	7051	LP2 (2026-09-30)	PASS	NonPolyA_perM 7051 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM7777645	M	M	NA	Agree	0.02	7.73	0.00	31.61	6.02	28.69	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.782784	0.155397	0.03558	0.026239	49.64	7.43	42.61	2038	LP2 (2026-09-30)	PASS	NonPolyA_perM 2038 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM7777646	M	M	NA	Agree	0.02	3.62	0.00	11.86	2.90	12.30	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.777075	0.123908	0.048373	0.050644	48.41	9.93	41.10	6290	LP2 (2026-09-30)	PASS	NonPolyA_perM 6290 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM7777647	M	M	NA	Agree	0.01	4.57	0.00	12.68	3.73	11.83	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.783243	0.148183	0.053912	0.014663	55.37	7.01	37.04	6327	LP2 (2026-09-30)	PASS	NonPolyA_perM 6327 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM7777648	M	M	NA	Agree	0.00	1.98	0.00	6.33	1.97	6.83	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.696182	0.123393	0.052286	0.12814	39.31	17.69	42.28	8398	LP2 (2026-09-30)	PASS	NonPolyA_perM 8398 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM7777649	M	M	NA	Agree	0.01	3.42	0.00	8.51	2.80	8.88	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.746549	0.157887	0.043529	0.052035	48.91	10.84	39.62	5311	LP2 (2026-09-30)	PASS	NonPolyA_perM 5311 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM7777651	M	M	NA	Agree	0.01	3.06	0.00	8.18	3.01	9.26	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.760885	0.151677	0.045591	0.041848	51.00	10.62	37.76	4872	LP2 (2026-09-30)	PASS	NonPolyA_perM 4872 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM7777652	M	M	NA	Agree	0.00	4.08	0.00	15.18	3.04	15.58	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.769571	0.140482	0.040373	0.049573	47.66	10.15	41.80	3669	LP2 (2026-09-30)	PASS	NonPolyA_perM 3669 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM7777653	M	M	NA	Agree	0.01	3.50	0.00	10.85	3.05	10.80	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.778244	0.1438	0.046423	0.031533	57.30	9.55	32.59	4531	LP2 (2026-09-30)	PASS	NonPolyA_perM 4531 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM7777654	M	M	NA	Agree	0.00	0.69	0.00	3.12	0.76	3.47	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.591634	0.079091	0.052166	0.277109	28.58	29.63	41.07	9408	LP2 (2026-09-30)	PASS	NonPolyA_perM 9408 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM7777655	M	M	NA	Agree	0.00	2.52	0.00	6.51	2.33	7.73	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.795789	0.119156	0.070715	0.01434	49.48	7.53	42.30	7864	LP2 (2026-09-30)	PASS	NonPolyA_perM 7864 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM7777656	M	M	NA	Agree	0.04	6.93	0.00	22.68	4.92	22.96	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.69908	0.195813	0.03588	0.069227	75.01	13.84	10.40	2282	LP2 (2026-09-30)	PASS	NonPolyA_perM 2282 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM7777657	M	M	NA	Agree	0.04	8.30	0.00	25.33	6.03	27.29	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.713602	0.227523	0.041123	0.017751	76.25	8.72	14.18	2758	LP2 (2026-09-30)	PASS	NonPolyA_perM 2758 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM7777658	M	M	NA	Agree	0.05	7.49	0.00	22.66	5.44	23.33	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.591054	0.202187	0.026983	0.179775	65.91	23.05	10.50	1537	LP2 (2026-09-30)	PASS	NonPolyA_perM 1537 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM7777659	M	M	NA	Agree	0.03	5.68	0.00	18.08	4.37	18.38	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.672334	0.232173	0.040159	0.055333	76.81	13.38	8.93	3389	LP2 (2026-09-30)	PASS	NonPolyA_perM 3389 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM7777661	M	M	NA	Agree	0.05	6.21	0.00	24.30	6.32	22.36	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.74732	0.2024	0.046193	0.004088	52.86	4.31	42.40	3410	LP2 (2026-09-30)	PASS	NonPolyA_perM 3410 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not