manifest_controlled_vocabularies.xlsx

	A	B	C	D	E	F	G	H	I	J	K	L	M	N	O	P	Q	R	S	T	U	V	W	X	Y
1	Field	File_name	Sample_ID	Program	Sub-program	Lab	Species	Modality	Technique	Subspecimen_type	Data_type	File_type	Access	Checksum	Anatomical_site	Counts_pipeline	Read_aligner	Genome_build	Gene_set_release	BCDC_Project	BCDC_collection	CA_usage	CA_IC_id	CA_donor	CA_tissue_provider
2	Description - IMPORTANT: Delete this column AND this row before saving manifest file	A submission-unique file name only, with no directory path information	The unique identifier of the biological sample. For BICCN datasets, this should match the Sample ID in BCDC metadata	If you are unsure of the proper program designation, please contact NeMO	For the most part, this corresponds to a single grant. Contact NeMO to add additional terms	PI of the lab under which data was generated. Contact NeMO to add additional terms	Common name for the species of the sample	Name of data modality used to categorize data at a high level	Omics technique performed	Type of subspecimen analyzed	Indicates whether data is raw sequence or processed	Format of file, used for validation. If you are submitting a file type other than those listed here, please contact NeMO to prevent processing delays	Consented access level of data	An MD5 checksum must be provided for every file	Name of anatomical structure from which sample was obtained (Optional, ro be required for Q2 submission)	For Counts data only: Pipeline used for generation of counts results. See NeMO documentation for explanation of pipeline names, or contact NeMO to add new pipeline(s) to the list (Optional)	For Aligned data only: Tool or pipeline used to generate alignments. See NeMO documentation for explanation of pipeline names, or contact NeMO to add new pipeline(s) to the list (Optional)	For Aligned data only: Genome build of the reference used for alignment (Optional)	For Aligned data only: Release of the reference used for alignment (Optional)	For BICCN projects only: BCDC code for project that describes a given dataset; reflects grouping of data for reporting purposes (Recommended)	For BICCN projects only: BCDC code for collection within the project; reflects grouping of data for reporting purposes (Recommended)	For controlled access data only: consent group for data use (Optional)	For human data, include Institutional Certification form file name excluding ".pdf" extension (Optional)	For controlled access data only: Unique identifier of individual donor providing sample (Optional)	For controlled access data only: Lab or PI last name providing tissue (Optional)
3	Controlled vocabulary	NA	NA	biccc	AIBS Internal	adey	arctic_ground_squirrel	epigenome	10x Chromium 3' v2 sequencing	bulk	raw	bam	open	NA	NA	NA	NA	NA	NA	HumanM110xProj	HumanM110x	gru	NA	NA	NA
4				biccn	R01_adey	akbarian	armadillo	multimodal	10x Chromium 3' v3 sequencing	cellgroup	align	bed	controlled							HumanPSeqL23Proj	HumanPSeqL23_T	health_medical
5				other	RF1_adey	anderson	chimpanzee	spatial_transcriptome	ATAC-seq	cells	counts	bigbed	embargo							adey_sciMETv2	MacaqueM110X	disease-specific
6				test	RF1_fan	arlotta	common_tree_shrew	transcriptome	DIVA-seq	nuclei	other	bigwig								dulac_hyp_sn_10x_proj	MousePSeqVIS_T	other
7				scorch	RF1_macosko	behrens	crab-eating_macaque	genome	Drop-seq	reconstructions		csv								dulac_pag_sn_10x_proj	adey_sciMETv2_human_cortex	NA
8					RF1_nowakowski	buenrostro	domestic_cat		mC-seq2			fastq								dulac_poa_dev_sn_10x_proj	dulac_hyp_sn_10xv2
9					RF1_regev	callaway	domestic_ferret		PATCH-Seq			mtx								ecker_hu_DNAseq_proj	dulac_pag_sn_10xv2
10					RF1_ren	cemba	green_monkey		SMART-seq v4			tsv								ecker_hu_sn_ATACseq_proj	dulac_poa_dev_sn_10x_RNAseq
11					RF1_roussos	cheng	human		Split-seq			H5								ecker_hu_sn_mCseq_proj	ecker_hu_DNAseq
12					RF1_tasic	dulac	macaque		mC-seq2, retrograde tracing			loom								ecker_sn_ATACseq_proj	ecker_hu_sn_ATACseq
13					RF1_tilgner	ecker	marmoset		PacBio long read sequencing			plink.bed								ecker_sn_mCseq_proj	ecker_hu_sn_mCseq
14					U01_akbarian	fox	mouse		SNARE-seq2;ATAC-seq			bim								ecker_sn_mCseq_retro_proj	ecker_sn_ATACseq
15					U01_devhu	ho	norway_rat		SNARE-seq2;RNAseq			fam								feng_multiome_proj	ecker_sn_mCseq
16					U01_ecker	kellis	opossum		sci-RNA-seq3											feng_sn_dropseq_proj	ecker_sn_mCseq_retro
17					U01_feng	kenny	owl_monkey		sci-ATAC-seq3											huang_dev_cx_proj	feng_multiome_ATACseq
18					U01_fox	kriegstein	pig		gwas											huang_macosko_sn_10xv3_proj	feng_multiome_RNAseq
19					U01_ho	lein	pig_tailed_macaque		Slide-seq											huang_pn_proj	feng_sn_10xv3
20					U01_kellis	linnarsson	rabbit		SHARE-seq											huang_sn_10v2_proj	feng_sn_dropseq
21					U01_kenny	macosko	rhesus_macaque		Oxford Nanopore long read sequencing											huang_sn_10v3_proj	huang_dev_cx_scATAC
22					U01_lein	macosko_regev	small-eared_galago		sciMETv2											human_cortex	huang_dev_cx_scRNA
23					U01_macosko	mansvelder	western_gorilla		10x Genomics Multiome											human_specialized_types_proj	huang_pn_bulk_SSv4
24					U01_rana	mccarroll	baboon		m3C-seq											human_variation	huang_pn_sn_10xv2
25					U01_sestan	mukamel	coyote		mC-seq3											kriegstein_sc_10x_proj	huang_pn_sn_10xv3
26					U01_snyder-mackler	nowakowski	squirrel_monkey		10x Chromium 3' v3.1 sequencing											kriegstein_sc_ATACseq_proj	huang_sn_10xv2
27					U01_tilgner	rana			sciATAC											kriegstein_sc_multiome_proj	huang_sn_10xv3
28					U01_zhangk	regev			10X Genomics Multiome;ATAC-seq											kriegstein_sn_10x_proj	human_cortex_SS4_Open_GRU
29					U01_zhangl	ren			10X Genomics Multiome;RNAseq											lein_L5_pseq_proj	human_cortex_SS4_counts
30					U19_cemba	roussos			Paired-tag;RNAseq											lein_evo_10x_proj	human_cortex_SS4_restricted_GRU
31					U19_huang	sestan			Paired-tag;DNAseq											lein_evo_Iso_Seq_proj	human_cortex_SS4_restricted_limited
32					U19_zeng	snyder-mackler			Tempo-seq											lein_human_pseq_proj	human_specialized_types
33					UM1_cheng	spudich			STARmap											lein_lgn_proj	human_variation_10X
34					UM1_spudich	tamas			10xFlex-NextGEM											lein_sn_10x	human_variation_wgs
35					mccarroll	tasic			10xFlex-GEMX											lein_sn_SSv4_proj	kriegstein_patchseq_tx
36					R01_Duan	tilgner			10xFlex-GEMXv2											lein_sn_hippocampus_proj	kriegstein_sc_10xv2
37					RF1_Mitra	tolias														macosko_bg_multiome_proj	kriegstein_sc_10xv3
38					RF1_Shepherd	zeng														macosko_bg_shareseq_proj	kriegstein_sc_ATACseq
39					U19_Deisseroth	zhang														macosko_bg_slideseq_proj	kriegstein_sc_multiome
40					U19_Svoboda	ndhlovu														macosko_mouse_slideseq_proj	kriegstein_sn_10xv2
41					u01_tasic	duan														mop_evo_tx_epi_pseq_proj	lein_L5_pseq_t
42						dougherty														nowakowski_evobc_proj	lein_evo_10x_arcticgroundsquirrel
43						bubak														nowakowski_pndev_10xv3_proj	lein_evo_10x_armadillo
44						deisseroth														sestan_sn_10x_proj	lein_evo_10x_cat
45																				snyder-mackler_macaque_proj	lein_evo_10x_chimp
46																				tasic_ATACseq_proj	lein_evo_10x_ferret
47																				tasic_sc_SSV4_proj	lein_evo_10x_galago
48																				tilgner_sc_10x_PB	lein_evo_10x_gorilla
49																				zeng_anderson_sc_10xv2_proj	lein_evo_10x_greenmonkey
50																				zeng_anderson_sc_10xv3_proj	lein_evo_10x_nemestrina
51																				zeng_sc_10x_proj	lein_evo_10x_opposum
52																				zeng_sc_SSv4_proj	lein_evo_10x_owlmonkey
53																				zeng_sn_10x_proj	lein_evo_10x_pig
54																				zeng_sn_SSv4_proj	lein_evo_10x_rabbit
55																				zeng_tolias_pseq_proj	lein_evo_10x_rat
56																				zhangK_snareseq	lein_evo_10x_rhesus
57																				zhangl_kz_omics_proj	lein_evo_10x_treeshrew
58																				ecker_hu_sn_m3Cseq_proj	lein_evo_10x_baboon
59																				adey_sciATAC	lein_evo_10x_coyote
60																				ren_pairedtag_proj	lein_evo_10x_squirrel_monkey
61																				shepherd_rnafish_proj	lein_evo_Iso_Seq_armadillo
62																				svoboda_Th_proj	lein_evo_Iso_Seq_green_monkey
63																				tasic_wb_proj	lein_evo_Iso_Seq_arctic_ground_squirrel
64																					lein_evo_Iso_Seq_nemestrina
65																					lein_evo_Iso_Seq_opossum
66																					lein_evo_Iso_Seq_squirrel_monkey
67																					lein_human_pseq_t
68																					lein_lein_pseq_tx
69																					lein_mansvelder_pseq_tx
70																					lein_sn_10xv2
71																					lein_sn_10xv3
72																					lein_sn_SSv4
73																					lein_sn_hippocampus
74																					lein_tamas_pseq_tx
75																					lgn_fascicularis
76																					lgn_human
77																					lgn_mouse
78																					lgn_nemestrina
79																					macosko_bg_multiome_atac_human
80																					macosko_bg_multiome_gex_human
81																					macosko_bg_multiome_atac_macaque
82																					macosko_bg_multiome_gex_macaque
83																					macosko_bg_shareseq_macaque
84																					macosko_bg_slideseq_human
85																					macosko_bg_slideseq_macaque
86																					macosko_mouse_slideseq_slideseqdataset
87																					mop_evo_pseq_hu_t
88																					mop_evo_pseq_t
89																					nowakowski_evobc
90																					nowakowski_pndev_10xv3
91																					sestan_sc_10xv2_nhp_dev
92																					sestan_sc_10xv3_nhp_dev
93																					sestan_sn_10xv3_human
94																					sestan_sn_10xv3_human_pfc
95																					sestan_sn_10xv3_nhp_adult
96																					sestan_sn_10xv3_nhp_adult_pfc
97																					sestan_sn_10xv3_pig
98																					snyder-mackler_macaque_scATAC
99																					snyder-mackler_macaque_scRNA
100																					tasic_ATACseq