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). For 15 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
GSM7976453	F	F	NA	Agree	4.30	0.00	0.00	0.00	0.00	0.00	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.806111	0.060751	0.12716	0.005978	61.42	10.78	26.66	8175	LP2 (2026-09-30)	PASS	NonPolyA_perM 8175 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM7976454	F	F	NA	Agree	7.50	0.00	0.00	0.05	0.00	0.02	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.814939	0.063627	0.111209	0.010225	64.80	9.35	25.11	6440	LP2 (2026-09-30)	PASS	NonPolyA_perM 6440 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM7976455	F	F	NA	Agree	4.37	0.00	0.00	0.00	0.00	0.00	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.826924	0.048868	0.120827	0.00338	65.45	10.28	23.39	4548	LP2 (2026-09-30)	PASS	NonPolyA_perM 4548 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM7976456	F	F	NA	Agree	3.93	0.00	0.00	0.00	0.00	0.00	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.845334	0.047265	0.104834	0.002566	70.52	9.28	19.51	2650	LP2 (2026-09-30)	PASS	NonPolyA_perM 2650 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM7976457	F	F	NA	Agree	5.83	0.00	0.00	0.04	0.00	0.00	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.847173	0.049968	0.10036	0.002499	67.62	8.19	23.37	3555	LP2 (2026-09-30)	PASS	NonPolyA_perM 3555 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM7976458	F	F	NA	Agree	5.54	0.00	0.00	0.00	0.00	0.00	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.840182	0.049412	0.100956	0.00945	69.80	10.18	19.11	4570	LP2 (2026-09-30)	PASS	NonPolyA_perM 4570 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM7976459	F	F	NA	Agree	6.38	0.00	0.00	0.00	0.00	0.00	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.818486	0.062443	0.115196	0.003874	67.16	9.94	22.10	4013	LP2 (2026-09-30)	PASS	NonPolyA_perM 4013 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM7976460	F	F	NA	Agree	9.50	0.00	0.00	0.01	0.00	0.00	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.824357	0.073729	0.099252	0.002662	71.29	8.34	19.60	2661	LP2 (2026-09-30)	PASS	NonPolyA_perM 2661 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM7976461	F	F	NA	Agree	4.63	0.00	0.00	0.00	0.00	0.00	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.81754	0.058216	0.120489	0.003756	67.99	10.43	20.66	4321	LP2 (2026-09-30)	PASS	NonPolyA_perM 4321 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM7976462	F	F	NA	Agree	7.68	0.00	0.00	0.01	0.00	0.01	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.829246	0.062569	0.104899	0.003285	71.56	9.05	18.46	3695	LP2 (2026-09-30)	PASS	NonPolyA_perM 3695 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM7976463	F	F	NA	Agree	2.11	0.00	0.00	0.01	0.00	0.00	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.813523	0.046868	0.135377	0.004233	64.79	11.59	22.69	5820	LP2 (2026-09-30)	PASS	NonPolyA_perM 5820 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM7976464	F	F	NA	Agree	10.92	0.00	0.00	0.01	0.00	0.00	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.829254	0.065013	0.102511	0.003222	67.62	8.85	22.55	4409	LP2 (2026-09-30)	PASS	NonPolyA_perM 4409 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM7976465	F	F	NA	Agree	5.92	0.00	0.00	0.00	0.00	0.00	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.802623	0.069497	0.122442	0.005437	65.59	10.41	23.08	5376	LP2 (2026-09-30)	PASS	NonPolyA_perM 5376 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM7976466	M	M	NA	Agree	0.24	1.99	0.00	12.63	2.82	9.74	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.819642	0.061398	0.114379	0.00458	65.73	8.96	24.24	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
GSM7976467	M	M	NA	Agree	0.31	2.15	0.00	12.48	2.31	9.66	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.836774	0.054607	0.104869	0.00375	72.85	9.39	16.99	3191	LP2 (2026-09-30)	PASS	NonPolyA_perM 3191 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM7976468	M	M	NA	Agree	0.65	2.15	0.00	12.07	2.64	8.48	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.808135	0.08097	0.107113	0.003782	73.36	9.22	16.69	2910	LP2 (2026-09-30)	PASS	NonPolyA_perM 2910 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM7976469	M	M	NA	Agree	0.36	2.11	0.00	12.59	2.60	9.66	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.828592	0.055427	0.112841	0.003141	72.75	10.54	15.87	2971	LP2 (2026-09-30)	PASS	NonPolyA_perM 2971 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM7976470	M	M	NA	Agree	0.28	2.22	0.00	13.55	2.78	9.96	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.823647	0.050128	0.123051	0.003174	61.89	10.08	26.98	6893	LP2 (2026-09-30)	PASS	NonPolyA_perM 6893 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM7976471	M	M	NA	Agree	0.12	2.86	0.00	16.45	3.91	13.56	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.839632	0.049863	0.107317	0.003188	61.31	8.54	29.14	5564	LP2 (2026-09-30)	PASS	NonPolyA_perM 5564 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM7976472	M	M	NA	Agree	0.32	2.60	0.00	14.28	3.18	11.44	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.83407	0.050381	0.111948	0.003601	61.36	9.03	28.58	6163	LP2 (2026-09-30)	PASS	NonPolyA_perM 6163 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM7976473	M	M	NA	Agree	0.17	1.70	0.00	11.03	2.52	9.05	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.817005	0.048123	0.13112	0.003752	64.56	11.37	23.02	6994	LP2 (2026-09-30)	PASS	NonPolyA_perM 6994 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM7976474	M	M	NA	Agree	0.66	3.32	0.00	18.28	3.93	14.59	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.81938	0.08081	0.097493	0.002317	72.02	7.49	19.53	3175	LP2 (2026-09-30)	PASS	NonPolyA_perM 3175 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM7976475	M	M	NA	Agree	0.41	2.30	0.00	14.03	3.22	10.17	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.821562	0.062681	0.111771	0.003986	67.82	9.28	22.02	4394	LP2 (2026-09-30)	PASS	NonPolyA_perM 4394 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM7976476	M	M	NA	Agree	0.26	1.98	0.00	10.16	2.23	8.97	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.817803	0.045976	0.132046	0.004176	70.79	12.23	16.01	4964	LP2 (2026-09-30)	PASS	NonPolyA_perM 4964 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM7976477	M	Undetermined	NA	Conflict	0.78	0.50	0.00	2.31	0.50	1.32	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.815222	0.068413	0.113471	0.002894	71.25	9.62	18.21	3606	LP2 (2026-09-30)	PASS	NonPolyA_perM 3606 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM7976478	M	M	NA	Agree	0.28	2.49	0.00	13.37	2.92	12.11	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.82184	0.057135	0.11835	0.002676	67.08	10.21	21.74	4587	LP2 (2026-09-30)	PASS	NonPolyA_perM 4587 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM7976479	M	M	NA	Agree	0.31	3.04	0.00	15.64	3.30	13.68	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.793158	0.0725	0.13087	0.003472	53.76	7.99	37.05	6219	LP2 (2026-09-30)	PASS	NonPolyA_perM 6219 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM7976480	M	M	NA	Agree	0.28	1.44	0.00	9.11	2.00	7.28	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.824344	0.045803	0.125872	0.003981	70.05	11.97	17.10	4870	LP2 (2026-09-30)	PASS	NonPolyA_perM 4870 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM7976481	M	M	NA	Agree	0.55	1.97	0.00	11.52	2.41	8.57	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.820288	0.063975	0.112543	0.003194	67.82	9.46	21.93	3291	LP2 (2026-09-30)	PASS	NonPolyA_perM 3291 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM7976482	F	F	NA	Agree	6.59	0.00	0.00	0.03	0.00	0.00	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.808264	0.068747	0.118036	0.004953	67.02	9.71	22.50	4506	LP2 (2026-09-30)	PASS	NonPolyA_perM 4506 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM7976483	F	F	NA	Agree	8.89	0.00	0.00	0.01	0.00	0.00	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.813554	0.070615	0.11038	0.00545	65.55	8.78	24.74	5246	LP2 (2026-09-30)	PASS	NonPolyA_perM 5246 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM7976484	F	F	NA	Agree	13.02	0.00	0.00	0.00	0.00	0.00	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.777714	0.100385	0.118012	0.003888	68.49	8.20	22.35	3664	LP2 (2026-09-30)	PASS	NonPolyA_perM 3664 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM7976485	F	F	NA	Agree	9.21	0.00	0.00	0.00	0.00	0.00	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.779409	0.093908	0.119018	0.007665	70.26	10.11	18.87	4242	LP2 (2026-09-30)	PASS	NonPolyA_perM 4242 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM7976486	F	F	NA	Agree	9.03	0.00	0.00	0.02	0.00	0.00	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.802293	0.08589	0.10839	0.003427	69.87	6.85	22.33	3408	LP2 (2026-09-30)	PASS	NonPolyA_perM 3408 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM7976487	F	F	NA	Agree	8.14	0.00	0.00	0.00	0.00	0.00	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.813092	0.075586	0.107227	0.004095	68.93	8.44	21.70	4516	LP2 (2026-09-30)	PASS	NonPolyA_perM 4516 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM7976488	F	F	NA	Agree	7.24	0.00	0.00	0.01	0.00	0.00	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.818407	0.066006	0.111895	0.003693	71.11	9.14	18.90	4266	LP2 (2026-09-30)	PASS	NonPolyA_perM 4266 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM7976489	F	F	NA	Agree	11.53	0.01	0.00	0.01	0.00	0.02	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.81768	0.078617	0.099063	0.004641	77.26	8.68	13.31	3203	LP2 (2026-09-30)	PASS	NonPolyA_perM 3203 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM7976490	M	M	NA	Agree	0.55	2.03	0.00	11.10	2.67	11.20	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.808583	0.068982	0.115929	0.006506	65.02	9.41	24.68	5799	LP2 (2026-09-30)	PASS	NonPolyA_perM 5799 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM7976491	M	M	NA	Agree	0.35	1.60	0.00	9.77	2.25	9.48	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.821467	0.059903	0.112823	0.005807	67.07	9.33	22.91	4000	LP2 (2026-09-30)	PASS	NonPolyA_perM 4000 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM7976492	M	M	NA	Agree	0.66	1.85	0.00	9.68	2.24	10.68	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.79712	0.075656	0.119864	0.00736	72.43	9.99	16.84	3465	LP2 (2026-09-30)	PASS	NonPolyA_perM 3465 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM7976493	M	M	NA	Agree	0.43	1.41	0.00	9.87	1.86	8.41	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.812398	0.049182	0.132698	0.005722	61.51	10.74	26.88	6419	LP2 (2026-09-30)	PASS	NonPolyA_perM 6419 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM7976494	M	M	NA	Agree	0.80	1.64	0.00	10.80	2.33	8.82	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.805447	0.069291	0.119072	0.006189	64.45	9.38	25.29	5428	LP2 (2026-09-30)	PASS	NonPolyA_perM 5428 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM7976495	M	M	NA	Agree	0.68	1.34	0.00	7.82	1.90	8.13	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.822199	0.049788	0.123162	0.004851	73.64	11.36	14.29	4009	LP2 (2026-09-30)	PASS	NonPolyA_perM 4009 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM7976496	M	M	NA	Agree	0.60	1.42	0.00	9.45	2.69	10.77	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.822614	0.047952	0.123298	0.006136	61.55	9.61	28.07	6326	LP2 (2026-09-30)	PASS	NonPolyA_perM 6326 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM7976497	M	M	NA	Agree	0.55	1.74	0.00	10.78	2.66	11.25	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.808896	0.058782	0.128053	0.004269	65.93	10.72	22.47	6121	LP2 (2026-09-30)	PASS	NonPolyA_perM 6121 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM7976498	M	M	NA	Agree	0.50	1.84	0.00	9.68	2.60	10.70	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.802663	0.066615	0.123403	0.007319	62.52	10.13	26.25	7463	LP2 (2026-09-30)	PASS	NonPolyA_perM 7463 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM7976499	M	M	NA	Agree	0.31	1.22	0.00	7.93	1.82	8.11	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.788283	0.055768	0.147464	0.008485	67.33	13.57	18.08	7828	LP2 (2026-09-30)	PASS	NonPolyA_perM 7828 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM7976500	M	M	NA	Agree	0.82	1.94	0.00	10.53	2.80	11.03	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.804464	0.072116	0.119619	0.0038	67.65	9.71	21.80	5186	LP2 (2026-09-30)	PASS	NonPolyA_perM 5186 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM7976501	M	M	NA	Agree	0.73	1.87	0.00	10.69	2.62	10.02	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.812675	0.065503	0.116614	0.005208	70.28	9.99	18.85	4594	LP2 (2026-09-30)	PASS	NonPolyA_perM 4594 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM7976502	M	M	NA	Agree	0.35	2.73	0.00	16.66	3.88	14.23	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.829014	0.062666	0.104028	0.004292	63.73	8.07	27.17	5911	LP2 (2026-09-30)	PASS	NonPolyA_perM 5911 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not