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 10 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
GSM8554936	M	M	NA	Agree	0.17	1.36	0.00	9.47	3.46	8.53	FIRST_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.711279	0.091426	0.083084	0.114211	74.57	18.18	6.12	3417	LP2 (2026-09-30)	PASS	NonPolyA_perM 3417 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM8554937	M	M	NA	Agree	0.06	1.17	0.00	5.72	2.32	6.32	FIRST_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.667917	0.087594	0.116744	0.127746	70.72	23.69	4.43	4238	LP2 (2026-09-30)	PASS	NonPolyA_perM 4238 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM8554938	M	M	NA	Agree	0.03	0.79	0.00	4.71	1.42	5.25	FIRST_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.690883	0.06628	0.126036	0.116801	70.01	24.33	4.53	4322	LP2 (2026-09-30)	PASS	NonPolyA_perM 4322 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM8554939	M	M	NA	Agree	0.07	0.59	0.00	4.95	1.74	5.52	FIRST_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.689719	0.061608	0.130125	0.118548	69.53	24.78	4.48	4653	LP2 (2026-09-30)	PASS	NonPolyA_perM 4653 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM8554940	M	M	NA	Agree	0.05	0.48	0.00	4.48	1.80	5.50	FIRST_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.69522	0.057811	0.13292	0.114049	69.43	24.53	4.88	4207	LP2 (2026-09-30)	PASS	NonPolyA_perM 4207 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM8554941	F	F	NA	Agree	4.74	0.00	0.00	0.01	0.02	0.14	FIRST_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.69836	0.062557	0.121327	0.117756	69.28	23.54	6.05	3864	LP2 (2026-09-30)	PASS	NonPolyA_perM 3864 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM8554942	F	F	NA	Agree	5.55	0.00	0.00	0.00	0.00	0.00	FIRST_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.692216	0.05939	0.117203	0.131191	69.26	24.35	5.28	3655	LP2 (2026-09-30)	PASS	NonPolyA_perM 3655 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM8554943	F	F	NA	Agree	4.51	0.00	0.00	0.00	0.00	0.00	FIRST_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.689941	0.056573	0.115313	0.138173	68.80	25.07	5.08	4116	LP2 (2026-09-30)	PASS	NonPolyA_perM 4116 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM8554944	F	F	NA	Agree	5.21	0.00	0.00	0.00	0.00	0.02	FIRST_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.729677	0.059921	0.128588	0.081815	71.93	20.54	6.29	3810	LP2 (2026-09-30)	PASS	NonPolyA_perM 3810 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM8554945	F	F	NA	Agree	4.25	0.01	0.00	0.00	0.00	0.00	FIRST_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.709373	0.059612	0.13146	0.099555	71.36	22.83	4.57	4183	LP2 (2026-09-30)	PASS	NonPolyA_perM 4183 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM8554946	M	M	NA	Agree	0.06	0.84	0.00	5.50	2.24	5.98	FIRST_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.706577	0.064337	0.124454	0.104632	71.27	22.55	5.03	4405	LP2 (2026-09-30)	PASS	NonPolyA_perM 4405 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM8554947	M	M	NA	Agree	0.05	0.54	0.00	5.10	1.59	5.56	FIRST_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.703559	0.069342	0.132647	0.094452	71.57	22.34	4.89	4046	LP2 (2026-09-30)	PASS	NonPolyA_perM 4046 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM8554948	M	M	NA	Agree	0.08	0.42	0.00	4.16	1.83	5.47	FIRST_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.715351	0.060127	0.13517	0.089351	70.93	22.60	5.25	3935	LP2 (2026-09-30)	PASS	NonPolyA_perM 3935 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM8554949	M	M	NA	Agree	0.10	1.31	0.00	8.36	2.97	9.78	FIRST_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.758373	0.062074	0.098307	0.081245	76.53	17.26	5.37	2307	LP2 (2026-09-30)	PASS	NonPolyA_perM 2307 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM8554950	M	M	NA	Agree	0.07	0.74	0.00	6.10	2.46	6.84	FIRST_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.727809	0.06314	0.118253	0.090799	73.39	20.25	5.24	3392	LP2 (2026-09-30)	PASS	NonPolyA_perM 3392 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM8554951	F	F	NA	Agree	5.32	0.00	0.00	0.06	0.01	0.00	FIRST_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.72167	0.054833	0.131294	0.092203	71.83	22.30	4.70	4130	LP2 (2026-09-30)	PASS	NonPolyA_perM 4130 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM8554952	F	F	NA	Agree	4.66	0.00	0.00	0.01	0.02	0.00	FIRST_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.735037	0.057023	0.115599	0.092341	72.46	20.34	5.84	4545	LP2 (2026-09-30)	PASS	NonPolyA_perM 4545 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM8554953	F	F	NA	Agree	6.78	0.00	0.00	0.00	0.00	0.02	FIRST_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.7191	0.06008	0.11703	0.10379	71.68	21.51	5.46	4543	LP2 (2026-09-30)	PASS	NonPolyA_perM 4543 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM8554954	F	F	NA	Agree	5.49	0.00	0.00	0.02	0.00	0.00	FIRST_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.720729	0.057582	0.113728	0.107961	71.77	21.54	5.40	4236	LP2 (2026-09-30)	PASS	NonPolyA_perM 4236 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not
GSM8554955	F	F	NA	Agree	0.58	0.05	0.00	0.03	0.01	0.08	FIRST_READ_TRANSCRIPTION_STRAND	RRNA_DEPLETED	0.717849	0.056947	0.123255	0.101949	71.12	22.24	5.31	3876	LP2 (2026-09-30)	PASS	NonPolyA_perM 3876 >= 700: non-polyadenylated small RNAs retained, as rRNA depletion does and oligo-dT selection does not