scRNA-seq and CITE-seq

PBMC scRNA-seq

scRNA-seq data from peripheral blood mononuclear cells (PBMCs) was generated on the 10x Genomics 3' scRNA-seq Platform (v3.1). For data collection and processing details, see the Cohorts and Experimental Methods sections.

Below, we provide labeled and annotated PBMC scRNA-seq data from our NDMM cohort and healthy controls from the Sound Life cohort. More information about the Sound Life cohort is available in the Dynamics of Immune Health and Age website.

All .h5ad files for this project contain sample and subject metadata, in addition to cell type labels and QC metrics. Click the header below for descriptions of these metadata:

Each file contains sample-level metadata, as well as cell-level cell type labels and QC metrics. The following values are stored in the .obs section of these .h5ad files as descriptions of observations:

Sample Identifiers
cohort.cohortGuid: A Globally Unique Identifier (GUID) of the Cohort the subject enrolled in for our study subject.subjectGuid: A GUID for the Subject
subject.subjectID: The Subject ID used in the figures and text of our article
sample.sampleKitGuid: A GUID for the Sample Kit, representing all material collected at a visit
specimen.specimenGuid: A GUID for the specific aliquot used for the experiment

Subject Metadata
subject.biologicalSex: The biological sex of the Subject
subject.birthYear: The Birth Year of the Subject
subject.ageAtFirstDraw:The Age of the Subject at their first on-study sample collection
subject.race:The self-reported Race of the Subject
subject.ethnicity:The self-reported Ethnicity of the subject
subject.cmv:The CMV Status of the subject, as determined by an HCMV assay (Negative or Positive)
subject.treatmentResponse: The treatment response recorded at End of Induction therapy
subject.fluVaccineResponse: The flu vaccine response category assigned to the subject based on post-ASCT flu vaccine timepoints (Responder or Non-Responder)

Sample Metadata
sample.visitName: The name of the study visit (i.e. time point)
sample.visitLabel: The abbreviated label for the study visit used in manuscript figures
sample.drawYear: The year of the study visit (e.g. 2021)
sample.subjectAgeAtDraw: The age of the Subject in years at the time of sample collection
sample.daysSinceFirstVisit: Number of days since the subject's initial visit

Process Identifiers
batch_id: A GUID for the batch of samples processed together (e.g. B039)
pool_id: A GUID for the pool of samples combined for Cell Hashing (e.g. B039-P1)
chip_id: A GUID for the 10x Genomics chip the cells were loaded into (e.g. B039-P1C2)
well_id: A GUID for the 10x Genomics well the cells were loaded into within the chip (e.g. B039-P1C2W4)
*barcodes: A GUID for the individual cell
original_barcodes: The original, sequence-based barcode generated by 10x Genomics Cell Ranger software
cell_name: A quasi-unique, memorable cell identifier generated using an adjective-adjective-animal structure

*used as the primary cell index in our .h5ad files

Cell QC Metrics
n_reads: Number of reads assigned to the cell barcode
n_umis: Number of Unique Molecular Identifiers (unique molecules) detected
n_genes: Number of genes with at least 1 UMI detected
total_counts_mito: Total number of reads that were assigned to mitochondrial genes
pct_counts_mito: Percent of reads that were assigned to mitochondrial genes
doublet_score: Doublet score assigned by Scrublet for doublet detection

Cell Labeling Results
AIFI_L1: Final broad class cell type label (9 types)
AIFI_L2: Final mid resolution cell type label (29 types)
AIFI_L3: Final high resolution cell type label (71 types)
AIFI_L2_label: Abbreviated mid resolution cell type label used in figures
AIFI_L3_label: Abbreviated high resolution cell type label used in figures

Visit Group .h5ad files

We are providing our scRNA-seq data in AnnData (.h5ad) format. For more details about AnnData, see the AnnData Documentation Page.

To reduce download size, normalized data are not provided. Normalization and log transformation can be performed using the scanpy package with:

scanpy.pp.normalize_total(adata, target_sum = 1e4)
scanpy.pp.log1p(adata)

Each file provided below contains a subset of the full > 5.6 million cell dataset. Sample counts, cell counts, and approximate file sizes are below:

File Name	N Subjects	N Samples	N Cells	File Size
MM_VRd_Treatment_Visits.h5ad	17	71	1,105,587	9.8 GB
MM_VRd_Flu_Vaccine_Visits.h5ad	15	81	1,194,809	11 GB
MM_VRd_COVID_Vaccine_Visits.h5ad	2	5	73,721	0.8 GB
Healthy_Flu_Vaccine_Year1_Visits.h5ad	33	102	1,695,860	27 GB
Healthy_Flu_Vaccine_Year2_Visits.h5ad	31	94	1,407,393	23 GB

NDMM PBMC scRNA-seq .h5ad files

File Name	Description	Download Link
Healthy_Flu_Vaccine_Year1_Visits.h5ad	Healthy control vaccine visit PBMC scRNA-seq
Healthy_Flu_Vaccine_Year2_Visits.h5ad	Healthy control vaccine visit PBMC scRNA-seq
NDMM_VRd_COVID_Vaccine_Visits.h5ad	NDMM COVID vaccine visit PBMC scRNA-seq
NDMM_VRd_Flu_Vaccine_Visits.h5ad	NDMM Flu vaccine visit PBMC scRNA-seq
NDMM_VRd_Treatment_Visits.h5ad	NDMM treatment visit PBMC scRNA-seq

BMMC CITE-seq

CITE-seq data, which includes both transcriptional and cell-surface epitope measurement, from bone marrow mononuclear cells (BMMCs) was generated on the 10x Genomics 3' scRNA-seq platform (v3.1).

BMMCs were stained with a custom panel of 59 oligo-conjugated antibodies (Antibody-Derived Tags; ADTs). Click the header below to view a list of the antibodies utilized for ADT staining:

All antibodies were obtained from BioLegend as TotalSeq anti-human ADTs. Catalog number and TotalSeq ID columns refer to BioLegend accessions.

Target	Clone	Titer	TotalSeq ID	Catalog Number	RRID
CD1a	HI149	1.0	A0402	300133	AB_2783146
CD1c	L161	0.2	A0160	331539	AB_2734326
CD2	TS1/8	0.02	A0367	309229	AB_2783172
CD3	UCHT1	0.075	A0034	300475	AB_2734246
CD4	RPA-T4	0.1	A0072	300563	AB_2734247
CD7	CD7-6B7	0.1	A0066	343123	AB_2734345
CD8	SK1	0.02	A0046	344751	AB_2734351
CD10	HI10a	0.75	A0062	312231	AB_2734286
CD11b	ICRF44	0.05	A0161	301353	AB_2734249
CD11c	S-HCL-3	0.1	A0053	371519	AB_2749971
CD13	WM15	0.2	A0364	301729	AB_2783151
CD14	M5E2	0.1	A0081	301855	AB_2734254
CD16	3G8	0.1	A0083	302061	AB_2734255
CD19	HIB19	0.1	A0050	302259	AB_2734256
CD20	2H7	0.05	A0100	302359	AB_2749984
CD22	S-HCL-1	0.2	A0393	363514	AB_2734404
CD24	ML5	0.5	A0180	311137	AB_2750374
CD25	BC96	0.08	A0085	302643	AB_2734258
CD27	O323	0.1	A0154	302847	AB_2750000
CD33	P67.6	0.2	A0052	366629	AB_2734409
CD34	581	0.4	A0054	343537	AB_2749972
CD36	5-271	0.02	A0407	336225	AB_2800892
CD38	HB-7	0.01	A0410	356635	AB_2800967
CD39	A1	0.1	A0176	328233	AB_2750005
CD40	5C3	0.5	A0031	334346	AB_2749968
CD41	HIP8	0.1	A0353	303737	AB_2783162
CD45RA	HI100	0.125	A0063	304157	AB_2734267
CD47	CC2C6	0.2	A0026	323129	AB_2734305
CD56 (NCAM)	5.1H11	0.1	A0047	362557	AB_2749970
CD64	10.1	0.1	A0162	305037	AB_2750366
CD66b	6/40c	0.25	A0166	392905	AB_2750372
CD69	FN50	0.75	A0146	310947	AB_2749997
CD71	CY1G4	0.1	A0394	334123	AB_2800884
CD80	2D10	1.0	A0005	305239	AB_2749958
CD84	CD84.1.21	0.75	A0872	326011	AB_2814189
CD86	IT2.2	0.05	A0006	305443	AB_2734273
CD88	S5/1	1.0	A1046	344321	AB_2888875
CD94	DX22	0.2	A0867	305521	AB_2814142
CD117 (c-kit)	104D2	0.75	A0061	313241	AB_2734287
CD123	6H6	0.1	A0064	306037	AB_2749977
CD127 (IL-7Rα)	A019D5	0.125	A0390	351352	AB_2734366
CD141 (Thrombomodulin)	M80	0.75	A0163	344121	AB_2783229
CD163	GHI/61	0.75	A0358	333635	AB_2750343
CD172a (SIRPα)	15-414	0.5	A0408	372109	AB_2783285
CD192 (CCR2)	K036C2	1.0	A0242	357229	AB_2750501
CD195 (CCR5)	J418F1	0.5	A0141	359135	AB_2749994
CD206 (MMR)	15-2	1.0	A0205	321143	AB_2750010
CD226 (DNAM-1)	GHI/61	0.75	A0805	333635	AB_2750343
CD269 (BCMA)	19F2	2.0	A0056	357521	AB_2749974
CD274 (B7-H1, PD-L1)	29E.2A3	1.0	A0007	329743	AB_2749959
CD279 (PD-1)	EH12.2H7	2.0	A0088	329955	AB_2734322
CD304 (Neuropilin-1)	12C2	0.5	A0406	354525	AB_2783261
CD314 (NKG2D)	1D11	0.75	A0165	320835	AB_2734298
CD319 (CRACC)	162.1	1.0	A0830	331821	AB_2800872
CX3CR1	K0124E1	1.0	A0179	355709	AB_2832698
HLA-DR	L243	0.2	A0159	307659	AB_2750001
IgD	IA6-2	0.05	A0384	348243	AB_2783238
IgG Fc	M1310G05	1.0	A0375	410725	AB_2783329
IgM	MHM-88	0.1	A0136	314541	AB_2749992

Subject Group .h5ad files

We are providing our scRNA-seq data in AnnData (.h5ad) format. For more details about AnnData, see the AnnData Documentation Page.

To reduce download size, normalized data are not provided. Normalization and log transformation can be performed using the scanpy package with:

scanpy.pp.normalize_total(adata, target_sum = 1e4)
scanpy.pp.log1p(adata)

Antibody-dervided tags (ADT) for a custom panel of 59 targets are provided as a table of counts of ADT-derived UMIs for each antibody per cell. These counts are stored in the adata.obsm['adt_counts'] slot.

As for PBMC data, the .h5ad files for this project contain sample and subject metadata. Click the header below for descriptions of these metadata fields:

*used as the primary cell index in our .h5ad files

Cell Labeling Results
BMMC_L1: Final broad class cell type label (7 types)
BMMC_L2: Final mid resolution cell type label (39 types)
BMMC_L3: Final high resolution cell type label (64 types)
BMMC_L2_label: Abbreviated mid resolution cell type label used in figures
BMMC_L3_label: Abbreviated high resolution cell type label used in figures

The .h5ad files provided below are separated into two groups, from NDMM patients or from the 10 healthy control subjects for BMMCs:

File Name	N Subjects	N Samples	N Cells	File Size
MM_VRd_BMMC_Visits.h5ad	17	59	1,102,669	30 GB
Healthy_BMMC_Visits.h5ad	10	10	69,296	1.2 GB

NDMM BMMC CITE-seq .h5ad files

File Name	Description	Download Link
Healthy_BMMC_Visits.h5ad	Bone Marrow CITE-seq from Healthy controls
NDMM_VRd_BMMC_Visits.h5ad	Bone Marrow CITE-seq from MM patients