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). For 16 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
GSM8374951	F	F	NA	Agree	0.59	0.00	0.00	0.00	0.00	0.00	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.684043	0.070928	0.100487	0.144542	66.57	24.17	5.13	15589	LP2 (2026-09-30)	PASS	NonPolyA_perM 15589 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM8374952	F	F	NA	Agree	0.78	0.00	0.00	0.00	0.00	0.00	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.656532	0.078848	0.099866	0.164755	64.17	26.75	4.93	17335	LP2 (2026-09-30)	PASS	NonPolyA_perM 17335 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM8374953	F	F	NA	Agree	0.79	0.00	0.00	0.00	0.00	0.00	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.707377	0.083655	0.097797	0.111171	68.12	20.57	7.25	14802	LP2 (2026-09-30)	PASS	NonPolyA_perM 14802 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM8374954	F	F	NA	Agree	1.13	0.00	0.00	0.00	0.00	0.00	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.687821	0.089158	0.098726	0.124295	67.89	21.95	6.17	15009	LP2 (2026-09-30)	PASS	NonPolyA_perM 15009 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM8374955	F	F	NA	Agree	0.52	0.00	0.00	0.00	0.00	0.00	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.695793	0.071062	0.093771	0.139374	67.66	23.83	2.14	11706	LP2 (2026-09-30)	PASS	NonPolyA_perM 11706 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM8374956	F	F	NA	Agree	1.33	0.00	0.00	0.00	0.00	0.00	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.649635	0.104523	0.098088	0.147754	63.41	23.75	6.40	14487	LP2 (2026-09-30)	PASS	NonPolyA_perM 14487 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM8374957	F	F	NA	Agree	2.07	0.00	0.00	0.00	0.00	0.00	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.617226	0.12465	0.105665	0.15246	64.55	24.74	6.23	15176	LP2 (2026-09-30)	PASS	NonPolyA_perM 15176 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM8374958	F	F	NA	Agree	1.51	0.00	0.00	0.00	0.00	0.00	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.641503	0.10802	0.099472	0.151005	65.47	24.41	5.73	15071	LP2 (2026-09-30)	PASS	NonPolyA_perM 15071 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM8374959	F	F	NA	Agree	0.80	0.00	0.00	0.00	0.00	0.00	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.63674	0.079962	0.109822	0.173476	60.44	27.56	3.88	13915	LP2 (2026-09-30)	PASS	NonPolyA_perM 13915 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM8374960	F	F	NA	Agree	0.63	0.00	0.00	0.00	0.00	0.00	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.65756	0.075917	0.107282	0.159241	62.14	26.89	5.82	18106	LP2 (2026-09-30)	PASS	NonPolyA_perM 18106 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM8374961	F	F	NA	Agree	0.52	0.00	0.00	0.00	0.00	0.00	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.605928	0.075299	0.12585	0.192923	55.34	32.55	6.38	26359	LP2 (2026-09-30)	PASS	NonPolyA_perM 26359 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM8374962	F	F	NA	Agree	0.83	0.00	0.00	0.00	0.00	0.00	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.648448	0.078551	0.118142	0.15486	60.11	28.15	6.28	18999	LP2 (2026-09-30)	PASS	NonPolyA_perM 18999 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM8374963	F	F	NA	Agree	0.96	0.00	0.00	0.00	0.00	0.00	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.640224	0.069474	0.10369	0.186611	59.35	28.57	6.56	17393	LP2 (2026-09-30)	PASS	NonPolyA_perM 17393 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM8374964	F	F	NA	Agree	0.95	0.00	0.00	0.00	0.00	0.00	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.662868	0.060416	0.141329	0.135388	55.53	30.97	5.06	22813	LP2 (2026-09-30)	PASS	NonPolyA_perM 22813 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM8374965	F	F	NA	Agree	1.24	0.00	0.00	0.00	0.00	0.00	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.669782	0.06219	0.12833	0.139697	58.25	30.28	5.26	22067	LP2 (2026-09-30)	PASS	NonPolyA_perM 22067 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM8374966	F	F	NA	Agree	1.45	0.00	0.00	0.00	0.00	0.00	SECOND_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.621894	0.065386	0.129155	0.183565	55.48	32.01	6.09	25617	LP2 (2026-09-30)	PASS	NonPolyA_perM 25617 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not