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 1 sample 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
GSM9088135	F	F	NA	Agree	101.84	0.00	0.00	0.00	0.00	0.00	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.725309	0.075284	0.04509	0.154316	78.52	20.09	0.29	102	LP2 (2026-09-30)	PASS	NonPolyA_perM 102 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM9088136	F	F	NA	Agree	127.37	0.00	0.00	0.00	0.00	0.00	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.774753	0.08835	0.049304	0.087592	84.20	14.50	0.31	110	LP2 (2026-09-30)	PASS	NonPolyA_perM 110 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM9088137	F	F	NA	Agree	139.59	0.00	0.00	0.00	0.00	0.00	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.683362	0.10201	0.05021	0.164418	76.71	21.94	0.31	181	LP2 (2026-09-30)	PASS	NonPolyA_perM 181 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM9088138	F	F	NA	Agree	142.05	0.02	0.00	0.00	0.00	0.00	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.766658	0.103292	0.051293	0.078756	84.60	14.05	0.32	179	LP2 (2026-09-30)	PASS	NonPolyA_perM 179 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM9088139	F	F	NA	Agree	158.21	0.04	0.00	0.00	0.00	0.00	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.765475	0.108993	0.054058	0.071474	84.84	13.80	0.32	204	LP2 (2026-09-30)	PASS	NonPolyA_perM 204 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM9088140	F	F	NA	Agree	0.68	0.00	0.00	0.00	0.00	0.00	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.795375	0.106505	0.049667	0.048454	86.68	11.91	0.29	201	LP2 (2026-09-30)	PASS	NonPolyA_perM 201 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM9088141	F	F	NA	Agree	154.45	0.00	0.00	0.00	0.00	0.00	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.782165	0.111141	0.058015	0.04868	86.62	11.86	0.33	149	LP2 (2026-09-30)	PASS	NonPolyA_perM 149 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM9088142	F	F	NA	Agree	125.91	0.00	0.00	0.00	0.00	0.00	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.799247	0.101064	0.062447	0.037242	87.39	11.19	0.35	153	LP2 (2026-09-30)	PASS	NonPolyA_perM 153 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM9088143	F	F	NA	Agree	172.91	0.00	0.00	0.00	0.00	0.00	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.726278	0.114103	0.052137	0.107482	81.29	17.30	0.28	215	LP2 (2026-09-30)	PASS	NonPolyA_perM 215 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM9088144	F	F	NA	Agree	106.79	0.00	0.00	0.02	0.00	0.00	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.760318	0.09757	0.050867	0.091244	82.13	16.45	0.30	155	LP2 (2026-09-30)	PASS	NonPolyA_perM 155 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM9088145	F	F	NA	Agree	115.59	0.00	0.00	0.00	0.00	0.00	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.766069	0.103755	0.053349	0.076827	83.04	15.47	0.31	159	LP2 (2026-09-30)	PASS	NonPolyA_perM 159 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM9088146	F	F	NA	Agree	111.53	0.00	0.00	0.00	0.00	0.00	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.793219	0.093486	0.053177	0.060117	84.96	13.50	0.34	145	LP2 (2026-09-30)	PASS	NonPolyA_perM 145 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM9088147	F	F	NA	Agree	128.42	0.00	0.00	0.00	0.00	0.00	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.757819	0.105386	0.042224	0.094571	76.77	10.96	8.07	125	LP2 (2026-09-30)	PASS	NonPolyA_perM 125 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM9088148	F	F	NA	Agree	143.91	0.00	0.00	0.00	0.00	0.00	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.784669	0.099653	0.041737	0.073941	80.64	9.10	6.88	121	LP2 (2026-09-30)	PASS	NonPolyA_perM 121 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM9088149	F	F	NA	Agree	121.11	0.00	0.00	0.00	0.00	0.00	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.765356	0.097715	0.040821	0.096107	78.93	11.06	6.69	114	LP2 (2026-09-30)	PASS	NonPolyA_perM 114 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM9088150	F	F	NA	Agree	113.13	0.00	0.00	0.00	0.00	0.00	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.846175	0.087204	0.045656	0.020964	81.25	5.09	8.83	139	LP2 (2026-09-30)	PASS	NonPolyA_perM 139 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM9088151	F	F	NA	Agree	90.31	0.00	0.00	0.00	0.00	0.00	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.827487	0.086836	0.041111	0.044566	83.50	7.10	6.30	114	LP2 (2026-09-30)	PASS	NonPolyA_perM 114 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM9088152	F	F	NA	Agree	114.47	0.00	0.00	0.00	0.00	0.00	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.83785	0.088335	0.045011	0.028804	83.83	5.98	6.69	142	LP2 (2026-09-30)	PASS	NonPolyA_perM 142 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM9088153	F	F	NA	Agree	106.63	0.09	0.00	0.00	0.00	0.00	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.789788	0.104238	0.063476	0.042498	81.76	15.29	0.27	196	LP2 (2026-09-30)	PASS	NonPolyA_perM 196 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM9088154	F	F	NA	Agree	145.63	0.00	0.00	0.00	0.00	0.00	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.778058	0.11817	0.058992	0.04478	84.35	13.07	0.21	179	LP2 (2026-09-30)	PASS	NonPolyA_perM 179 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM9088155	F	F	NA	Agree	132.97	0.00	0.00	0.00	0.00	0.00	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.788466	0.112973	0.060697	0.037863	84.25	13.42	0.17	165	LP2 (2026-09-30)	PASS	NonPolyA_perM 165 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM9088156	F	F	NA	Agree	131.24	0.00	0.00	0.00	0.00	0.00	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.771927	0.103821	0.055748	0.068505	81.83	15.69	0.20	176	LP2 (2026-09-30)	PASS	NonPolyA_perM 176 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM9088157	F	F	NA	Agree	111.58	0.00	0.00	0.00	0.00	0.00	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.820388	0.097398	0.063161	0.019053	85.75	11.50	0.32	158	LP2 (2026-09-30)	PASS	NonPolyA_perM 158 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM9088158	F	F	NA	Agree	144.34	0.02	0.00	0.00	0.00	0.00	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.797856	0.11514	0.061458	0.025547	85.70	12.00	0.23	219	LP2 (2026-09-30)	PASS	NonPolyA_perM 219 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM9088159	F	F	NA	Agree	145.23	0.00	0.00	0.02	0.00	0.00	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.836035	0.091903	0.054063	0.018	86.93	10.82	0.19	112	LP2 (2026-09-30)	PASS	NonPolyA_perM 112 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM9088160	F	F	NA	Agree	118.47	0.00	0.00	0.00	0.00	0.00	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.805284	0.098018	0.056025	0.040673	83.83	13.71	0.33	140	LP2 (2026-09-30)	PASS	NonPolyA_perM 140 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM9088161	F	F	NA	Agree	194.51	0.00	0.00	0.00	0.12	0.00	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.404757	0.286729	0.307302	0.001212	82.76	6.15	6.49	234	LP2 (2026-09-30)	PASS	NonPolyA_perM 234 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM9088162	F	F	NA	Agree	191.04	0.00	0.00	0.00	0.01	0.00	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.769663	0.135777	0.080117	0.014443	85.08	8.08	4.09	218	LP2 (2026-09-30)	PASS	NonPolyA_perM 218 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM9088163	F	F	NA	Agree	162.64	0.01	0.00	0.00	0.00	0.00	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.743493	0.145643	0.101478	0.009386	84.95	7.21	4.72	180	LP2 (2026-09-30)	PASS	NonPolyA_perM 180 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM9088164	F	F	NA	Agree	171.02	0.00	0.00	0.00	0.00	0.00	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.772358	0.13725	0.081893	0.008499	86.17	7.69	3.51	241	LP2 (2026-09-30)	PASS	NonPolyA_perM 241 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM9088165	F	F	NA	Agree	203.95	0.00	0.00	0.00	0.00	0.00	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.786032	0.122264	0.068942	0.022762	85.49	8.62	3.32	149	LP2 (2026-09-30)	PASS	NonPolyA_perM 149 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM9088166	F	F	NA	Agree	273.47	0.00	0.00	0.00	0.00	0.00	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.770416	0.138327	0.078448	0.01281	85.72	7.37	4.20	161	LP2 (2026-09-30)	PASS	NonPolyA_perM 161 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM9088167	F	F	NA	Agree	252.85	0.00	0.00	0.00	0.00	0.00	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.777148	0.132835	0.084518	0.0055	86.14	6.47	4.94	128	LP2 (2026-09-30)	PASS	NonPolyA_perM 128 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM9088168	F	F	NA	Agree	221.44	0.05	0.00	0.00	0.02	0.00	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.570299	0.208448	0.220345	0.000908	74.87	7.01	13.31	145	LP2 (2026-09-30)	PASS	NonPolyA_perM 145 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM9088169	F	F	NA	Agree	192.20	0.01	0.00	0.00	0.00	0.00	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.770036	0.128154	0.06767	0.03414	84.04	9.29	4.11	167	LP2 (2026-09-30)	PASS	NonPolyA_perM 167 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM9088170	F	F	NA	Agree	107.39	0.01	0.00	0.00	0.00	0.12	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.748593	0.129944	0.10459	0.016873	81.05	5.96	11.90	153	LP2 (2026-09-30)	PASS	NonPolyA_perM 153 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM9088171	F	F	NA	Agree	20.37	0.03	0.00	0.02	0.00	0.04	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.731056	0.131246	0.112438	0.025259	76.48	6.08	16.23	121	LP2 (2026-09-30)	PASS	NonPolyA_perM 121 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM9088172	F	F	NA	Agree	127.72	0.00	0.00	0.00	0.00	0.00	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.742316	0.135586	0.087727	0.034371	79.40	6.21	13.31	206	LP2 (2026-09-30)	PASS	NonPolyA_perM 206 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM9088173	F	F	NA	Agree	177.80	0.01	0.00	0.00	0.00	0.00	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.806129	0.117245	0.052405	0.024221	87.26	6.52	5.47	193	LP2 (2026-09-30)	PASS	NonPolyA_perM 193 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM9088174	F	F	NA	Agree	142.32	0.00	0.00	0.00	0.00	0.00	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.807863	0.111738	0.056696	0.023703	86.08	7.21	5.93	260	LP2 (2026-09-30)	PASS	NonPolyA_perM 260 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does
GSM9088175	F	F	NA	Agree	158.28	0.00	0.00	0.00	0.00	0.00	SECOND_READ_TRANSCRIPTION_STRAND	POLYA	0.811916	0.117403	0.051109	0.019572	87.24	6.18	5.85	223	LP2 (2026-09-30)	PASS	NonPolyA_perM 223 <= 350: non-polyadenylated small RNAs removed, as oligo-dT (polyA) selection does