title: PB04838-001 MM Post Induction 2-Cycles

description:
Library name: PB04838-001
H5 file contains RNA expression matrix

value: PBMC

value: Caucasian

value: MM Post Induction 2-Cycles


title: S34KO_12hr_TGF_3

status: Public on Jul 15 2026

type: SRA

city: Thiruvananthapuram

first: Karthik

last: Chandiran

state: Kerala

address: 3103, School of Biology, Indian Institute of Science Education and Research - Thiruvananthapuram, Maruthamala P.O., Vithura, Kerala 695551

department: Biology

country: India

institute: IISER-Thiruvananthapuram

description: Library name: Sample-30

library_source: transcriptomic

data_processing:
Sickle was used to perform quality control and trim the sequences when necessary with a minimum QC score of 25 and basepair length of 45 after trimming
Trimmed sequences were aligned to mm10 genome assembly using Hisat2
Using samtools aligned sequences were sorted and converted to BAM files
Assembly: mm39
Supplementary files format and content: counts

molecule: total RNA

organism: Mus musculus

source_name: spleen, lymph node

extract_protocol:
Total RNA was extracted using Rneasy mini plus kit (Qiagen)
RNA libraries for RNAseq were created using Illumina TruSeq Stranded mRNA library preparation kit. Illumina MiSeq Nano v2 Reagent kit for pooling check

tag: tissue

value: spleen, lymph node

tag: cell line

value: primary cells

tag: cell type

value: CD8 T

tag: genotype

tag: treatment


title: PB04837-001 MM Post Transplant 1 year

city: Seattle

first: Allen Institute

last: For Immunology

state: Washington

address: 615 Westlake Ave N, Seattle, WA

country: USA

institute: Allen Institute

description:
Library name: PB04837-001
H5 file contains RNA expression matrix

library_source: transcriptomic single cell

data_processing:
Multiplexed sequencing data were prepared using a preprocessing pipeline based on 10x Genomics CellRanger software (version 3.1.0; Released July 24, 2019), with the 10x Genomics GRCh38/hg38 Human Transcriptome Reference (refdata-cellranger-GRCh38-3.0.0; based on the GRCh38 genome reference and Ensembl v93 transcriptome annotations; Released Nov. 19, 2018) to generate cell x UMI count matrices for each Well.
To identify cells originating from each sample, we utilized software tools for HTO quantification and sample demultiplexing to generate separate HDF5-formatted files for each originating sample (as described in Swanson, et al. (2021); DOI: 10.1186/s12859-022-04620-2). This process also removes Cell Barcodes that contain HTOs from multiple samples (doublets or multiplets) or with no detectable sample label (no hash).
After demultiplexing, data from individual samples assembled across all hashed wells were given a first pass of cell type labels using Seurat label transfer with reference to the PBMC dataset provided by the Satija Lab (Stuart and Butler, et al. (2019); DOI: 10.1016/j.cell.2019.05.031) and provided online with the Seurat PBMC scATAC-seq vignette (v 3.0; Compiled June 6, 2019).
For analysis, high quality cells were selected based on the following cutoffs: <10% mitochondria reads, number of genes detected between 200 and 5000, RNA UMIs/cells between 1500 and 750000. After QC filtering, all remaining cells were clustered using a Scanpy (v1.9.6) workflow that consisted of normalization using scanpy.pp.normalize_total with the parameter target_sum = 1e4; log transformation using scanpy.pp.log1p; highly variable gene detection using scanpy.pp.highly_variable_genes; scaling of highly variable gene data using sc.pp.scale; Dimensionality reduction using scanpy.tl.pca with the parameter svd_solver = 'arpack'.
Supplementary files format and content: Ensembl GRCh38-3.0.0
Supplementary files format and content: h5 files, gene expression matrix

organism: Homo sapiens

source_name: Blood

extract_protocol:
PBMCs were removed from liquid nitrogen and rapidly thawed in a 37°C water bath. Cells were diluted dropwise into 40 mL AIM V media (Thermo Fisher Scientific) pre-warmed to 37°C. Cells were pelleted at 400 x g for 5–10 min at 4–10°C, resuspended in 5 mL cold AIM V media, and counted using a Cellometer Spectrum or Cellaca. After adding 30 mL cold AIM V media, cells were re-pelleted and resuspended to the appropriate concentrations for scRNAseq.
scRNAseq libraries were generated using a modified 10x genomics chromium 3′ single cell gene expression assay with Cell Hashing. Sample libraries were constructed across different batches, with the addition of a common healthy donor leukopak sample in each library as batch control. Libraries were sequenced on the Illumina Novaseq platform. Hashed 10x Genomics scRNA-seq data processing was carried out using BarWare (BMC Bioinformatics 2022, doi: 10.1186/s12859-022-04620-2) to generate sample-specific output files.

value: Blood

tag: subject id

tag: birth year

tag: Sex

value: Female

tag: race

tag: days since_first_visit

tag: visit

value: MM Post Transplant 1 year

tag: batch id

tag: sample bridging_control

value: FALSE


title: S34KO_12hr_TGF_2

description: Library name: Sample-29


title: 558M_PBMC_BCR

city: Houston

first: Sung Wook

last: Kang

state: TX

address: one plaza

department: Surgery

institute: Baylor college of medicine

description:
Library name: 558M_PBMC_BCR
FFPE

data_processing:
Sequencing reads were aligned to the mouse reference transcriptome (mm10) using the Cell Ranger multi pipeline (10x Genomics, v9.0.0) with default parameters. This pipeline enables the joint processing of gene expression and TCR V(D)J profiling data from the same cellular libraries, allowing for the simultaneous quantification of transcriptomic profiles and immune receptor sequences.
Assembly: mm10
Supplementary files format and content: filtered_feature_bc_matrix.h5 -> scRNA data
Supplementary files format and content: filtered_contig_annotations.csv -> immuno profiling results
Library strategy: BCR-seq

source_name: PBMC

extract_protocol:
Single-cell suspensions from each heart tissue and matched PBMC sample were loaded into separate wells of a Chromium Next GEM Chip N (10X Genomics, Cat# 2000418) to generate gel beads-in-emulsion (GEMs), each containing uniquely barcoded beads for downstream single-cell capture and indexing. Cell concentration was adjusted to approximately 700-2,000 cells/µL to target recovery of up to 20,000 cells per sample. Sequencing libraries for 5’ gene expression and T cell receptor (TCR) V(D)J profiling were prepared using the Chromium Next GEM Single Cell 5' HT Reagent Kits v2 (10X Genomics, Cat# 1000356), the Mouse Chromium Single Cell V(D)J Amplification Kits (10X Genomics, Cat#1000254) and the Library Construction Kit (10X Genomics, Cat# 1000190) according to the manufacturer’s instructions.
All libraries were sequenced on the Illumina NovaSeq 6000 system using paired-end reads with dual indexing 26 cycles for Read 1, 10 cycles for i7 Index, 10 cycles for i5 Index, and 90 cycles for Read 2), targeting 400 million reads per gene expression library and 100 million reads per TCR amplification library.


title: S34KO_12hr_TGF_1

description: Library name: Sample-28


title: PB04836-001 MM Pre-Treatment

description:
Library name: PB04836-001
H5 file contains RNA expression matrix

value: Male

value: MM Pre-Treatment


title: PB02730-002 MM CD38 6 weeks

description:
Library name: PB02730-002
H5 file contains RNA expression matrix

value: Asian

value: MM CD38 6 weeks


title: PB02724-002 MM CD38 4 weeks

description:
Library name: PB02724-002
H5 file contains RNA expression matrix

value: MM CD38 4 weeks


title: 558M_Heart_BCR

description:
Library name: 558M_Heart_BCR
FFPE


title: PB04835-001 MM Pre-Treatment

description:
Library name: PB04835-001
H5 file contains RNA expression matrix

value: African American


title: S34KO_12hr_NoTGF_4

description: Library name: Sample-27


title: PB04831-001 Flu Year 2 Day 90

description:
Library name: PB04831-001
H5 file contains RNA expression matrix

value: Flu Year 2 Day 90


title: S34KO_12hr_NoTGF_3

description: Library name: Sample-26


title: PB04828-001 MM Post Transplant 60 Days

description:
Library name: PB04828-001
H5 file contains RNA expression matrix

value: PBMC

value: MM Post Transplant 60 Days


title: S34KO_12hr_NoTGF_2

description: Library name: Sample-25


title: S34KO_12hr_NoTGF_1

description: Library name: Sample-24


title: S4KO_12hr_TGF_3

description: Library name: Sample-23


title: PB04811-002 MM Pre-Treatment

description:
Library name: PB04811-002
H5 file contains RNA expression matrix

value: Caucasian


title: PB04810-001 Flu Year 2 Day 90

description:
Library name: PB04810-001
H5 file contains RNA expression matrix


title: S4KO_12hr_TGF_2

description: Library name: Sample-22

value: spleen, lymph node


title: PB04809-001 Flu Year 2 Day 7

description:
Library name: PB04809-001
H5 file contains RNA expression matrix

value: Flu Year 2 Day 7


title: S4KO_12hr_TGF_1

description: Library name: Sample-21

value: primary cells

value: CD8 T


title: PB04807-001 Flu Year 2 Day 90

description:
Library name: PB04807-001
H5 file contains RNA expression matrix

value: Blood

value: Female


title: S4KO_12hr_NoTGF_3

description: Library name: Sample-20


title: PB04701-001 Flu Year 2 Day 0

description:
Library name: PB04701-001
H5 file contains RNA expression matrix

value: Flu Year 2 Day 0

value: FALSE


title: S4KO_12hr_NoTGF_2

description: Library name: Sample-19


title: PB04698-001 Flu Year 1 Day 90

description:
Library name: PB04698-001
H5 file contains RNA expression matrix

value: Flu Year 1 Day 90


title: PB04695-001 MM Post Transplant 60 Days

description:
Library name: PB04695-001
H5 file contains RNA expression matrix


title: S4KO_0hr_2

description: Library name: Sample-17


title: EomesKO_12hr_TGF_2

description: Library name: Sample-15

value: EomesKO


title: S4KO_0hr_1

description: Library name: Sample-16


title: PB04686-001 MM End Induction 1st Draw

description:
Library name: PB04686-001
H5 file contains RNA expression matrix

value: Male

value: MM End Induction 1st Draw


title: PB04689-002 MM Pre-Treatment

description:
Library name: PB04689-002
H5 file contains RNA expression matrix

value: MM Pre-Treatment


title: EomesKO_12hr_TGF_1

description: Library name: Sample-14


title: PB04682-001 Flu Year 2 Day 7

description:
Library name: PB04682-001
H5 file contains RNA expression matrix

value: Other


title: EomesKO_12hr_NoTGF_1

description: Library name: Sample-12


title: PB04680-001 Flu Year 2 Day 7

description:
Library name: PB04680-001
H5 file contains RNA expression matrix

value: PBMC


title: EomesKO_0hr_2

description: Library name: Sample-11


title: PB04679-001 Flu Year 1 Day 0

description:
Library name: PB04679-001
H5 file contains RNA expression matrix

value: Flu Year 1 Day 0


title: PB04677-002 Flu Year 1 Day 7

description:
Library name: PB04677-002
H5 file contains RNA expression matrix

value: Caucasian

value: Flu Year 1 Day 7


title: WT_12hr_TGF_3

description: Library name: Sample-9

value: spleen, lymph node

value: WT


title: PB04528-001 MM Post Transplant 1 year

description:
Library name: PB04528-001
H5 file contains RNA expression matrix

value: MM Post Transplant 1 year


title: WT_12hr_TGF_2

description: Library name: Sample-8

value: primary cells

value: CD8 T


title: PB02770-001 Flu Year 2 Day 7

description:
Library name: PB02770-001
H5 file contains RNA expression matrix

value: Blood

value: Flu Year 2 Day 7


title: WT_12hr_TGF_1

description: Library name: Sample-7


title: PB02768-001 Flu Year 1 Stand-Alone

description:
Library name: PB02768-001
H5 file contains RNA expression matrix

value: Flu Year 1 Stand-Alone

value: FALSE


title: WT_12hr_NoTGF_2

description: Library name: Sample-5


title: PB02767-001 Flu Year 1 Stand-Alone

description:
Library name: PB02767-001
H5 file contains RNA expression matrix

value: Female


title: PB02763-001 Flu Year 2 Stand-Alone

description:
Library name: PB02763-001
H5 file contains RNA expression matrix

value: Flu Year 2 Stand-Alone


title: WT_0hr_3

description: Library name: Sample-3


title: PB02762-001 Flu Year 2 Stand-Alone

description:
Library name: PB02762-001
H5 file contains RNA expression matrix

value: Male


title: PB02757-001 MM Pre-Treatment

description:
Library name: PB02757-001
H5 file contains RNA expression matrix

value: Other

value: MM Pre-Treatment


title: PB02752-001 MM Post Induction 2-Cycles

description:
Library name: PB02752-001
H5 file contains RNA expression matrix

value: PBMC

value: MM Post Induction 2-Cycles


title: PB02747-001 MM Post Induction 2-Cycles

description:
Library name: PB02747-001
H5 file contains RNA expression matrix

value: African American


title: t=48h, rep2

city: Ness Ziona

first: Inbar

last: Cohen Gihon

address: Reuven 24

department: Biochemistry

country: Israel

institute: Israel Institute For Biological Research

description: Library name: sample 20

data_processing:
Sequenced reads were trimmed using FastQC for data filtering, and trimmed reads were mapped via HISAT2 for read alignment, followed by featureCounts quantification and differential expression analysis using DESeq
Assembly: GRCm39
Supplementary files format and content: raw_counts.csv

growth_protocol: RAW264.7 cells were mainained in DMEM supplemented with 10% Fetal bovine aserum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C. Jak1 KO cells were maintained in the sasme medium supplemented with 5ug/ml puromycin

extract_protocol:
RNA was harvested using Rneasy mini kit (Qiagen).
RNA libraries for RNA-seq were prepared using TrueSeq mRNA Prep kit (Illumina), following manufacturer’s protocols

treatment_protocol: Cells were seeded 24h post infection. 90% confluent cells were infected with LVS-GFP strain at MOI=2500 for 3h. Following 1h of 50ug/ml gentamicin to kill extracellular bacteria.after which  cells were maintaind with 2ug/ml gentamicin. cells were harvested for RNA extraction at 0,0.5,1.5,4,8,24,48h post infection

value: Macrophage

value: F. tularensis infection


title: t=48h, rep1

description: Library name: sample 19

value: WT


title: PB02740-001 Flu Year 1 Day 7

description:
Library name: PB02740-001
H5 file contains RNA expression matrix

value: Caucasian

value: Flu Year 1 Day 7


title: t=24h, rep3

description: Library name: sample 18


title: PB02738-001 Flu Year 2 Stand-Alone

description:
Library name: PB02738-001
H5 file contains RNA expression matrix

value: Blood


title: t=24h, rep2

description: Library name: sample 17


title: PB02737-001 Flu Year 2 Day 0

description:
Library name: PB02737-001
H5 file contains RNA expression matrix

value: Flu Year 2 Day 0


title: PB02735-002 Flu Year 2 Day 0

description:
Library name: PB02735-002
H5 file contains RNA expression matrix


title: t=8h, rep3

description: Library name: sample 15


title: PB02733-001 Flu Year 1 Day 0

description:
Library name: PB02733-001
H5 file contains RNA expression matrix

value: Flu Year 1 Day 0


title: t=8h, rep2

description: Library name: sample 14


title: t=8h, rep1

description: Library name: sample 13


title: PB02729-001 MM Post Transplant 60 Days

description:
Library name: PB02729-001
H5 file contains RNA expression matrix

value: MM Post Transplant 60 Days

value: FALSE


title: t=4h, rep1

description: Library name: sample 10


title: PB02681-001 MM Post Transplant 1 year

description:
Library name: PB02681-001
H5 file contains RNA expression matrix

value: Female

value: MM Post Transplant 1 year


title: PB02732-001 Flu Year 2 Stand-Alone

description:
Library name: PB02732-001
H5 file contains RNA expression matrix

value: Flu Year 2 Stand-Alone


title: t=1.5h, rep3

description: Library name: sample 9


title: PB02679-001 MM Post Transplant 1 year

description:
Library name: PB02679-001
H5 file contains RNA expression matrix


title: PB02091-01 Flu Year 1 Day 90

description:
Library name: PB02091-01
H5 file contains RNA expression matrix

value: Male

value: Other

value: Flu Year 1 Day 90


title: t=1.5h, rep1

description: Library name: sample 7


title: PB02087-01 MM Post Transplant 1 year

description:
Library name: PB02087-01
H5 file contains RNA expression matrix

value: PBMC


title: t=0.5h, rep3

description: Library name: sample 6

value: Macrophage


title: PB02085-01 Flu Year 1 Day 90

description:
Library name: PB02085-01
H5 file contains RNA expression matrix


title: t=1.5h, rep2

description: Library name: sample 8

value: F. tularensis infection


title: t=0.5h, rep2

description: Library name: sample 5

value: WT


title: S4KO_12hr_NoTGF_1

description: Library name: Sample-18

value: spleen, lymph node

value: primary cells

value: CD8 T


title: PB02084-01 Flu Year 2 Day 90

description:
Library name: PB02084-01
H5 file contains RNA expression matrix

value: Blood

value: Caucasian

value: Flu Year 2 Day 90


title: PB04694-001 Flu Year 2 Day 90

description:
Library name: PB04694-001
H5 file contains RNA expression matrix

value: FALSE


title: PB04693-001 Flu Year 1 Day 90

description:
Library name: PB04693-001
H5 file contains RNA expression matrix


title: EomesKO_12hr_NoTGF_2

description: Library name: Sample-13

value: EomesKO


title: t=0.5h, rep1

description: Library name: sample 4


title: single B. thetaiotaomicron cells at MEP from well D12

city: Wurzburg

first: Elise

last: Bornet

address: Josef-Schneider Strasse 2

country: Germany

institute: Helmholtz Insitute

description: Library name: D12

data_processing:
Sequence reads were trimmed for Nextera adapter and MATQ-Seq primers using bbmap. bbduk.sh -Xmx10g t=20
Trimmed reads were then mapped to the reference genome using bowtie2 version 2.3.4.1. bowtie2 -p 30
features were assigned using featureCounts.
Read counts extraction was performed using feature counts version 2.0.1
Assembly: GCF_000011065.1
Supplementary files format and content: tab delimited text file contains raw counts for each sample

organism: Bacteroides thetaiotaomicron

growth_protocol: B. thetaiotaomicron cells were grown in tryptone yeast glucose (TYG) media to mid-exponential phase (OD2), anaerobiaclly at 37 degrees.

extract_protocol:
MATQ-Seq and ribosomal RNA depletion with DASH. A single cell was sorted per well of a 96 well plate. Cells were lysed using mechanical sonication. cDNA librairies were obtained using the MATQ-Seq reverse transcription protocol. Ribosomal cDNA was depleted from the cDNA librairies using DASH, optimized for bacteroides thetaiotaomicron.
Library were constructed using the Nextera XT kit from Illumina

treatment_protocol: Fixed in 50% RNAlater

value: Fixed in 50% RNAlater

tag: batch


title: EomesKO_0hr_1

description: Library name: Sample-10


title: PB02081-01 Flu Year 1 Day 7

description:
Library name: PB02081-01
H5 file contains RNA expression matrix

value: Flu Year 1 Day 7


title: t=0, rep3

description: Library name: sample 3

value: mock


title: PB02080-01 MM Pre-Treatment

description:
Library name: PB02080-01
H5 file contains RNA expression matrix

value: Female

value: MM Pre-Treatment


title: t=0, rep2

description: Library name: sample 2


title: PB02771-001 MM Post Transplant 1 year

description:
Library name: PB02771-001
H5 file contains RNA expression matrix

value: PBMC

value: Male

value: Other

value: MM Post Transplant 1 year


title: WT_12hr_NoTGF_3

description: Library name: Sample-6

value: spleen, lymph node

value: WT


title: PB02078-01 Flu Year 1 Day 0

description:
Library name: PB02078-01
H5 file contains RNA expression matrix

value: Flu Year 1 Day 0


title: t=0, rep1

description: Library name: sample 1

value: Macrophage


title: WT_12hr_NoTGF_1

description: Library name: Sample-4

value: primary cells

value: CD8 T


title: PB02072-01 MM Post Transplant 90 Days

description:
Library name: PB02072-01
H5 file contains RNA expression matrix

value: Blood

value: MM Post Transplant 90 Days

value: FALSE


title: Liver, 12 weeks, replicate 4

city: Freiburg

first: Ahmad

last: Al Ajami

address: Breisacherstr. 153

department: Medical Faculty

institute: University of Freiburg

description: Library name: L_20

data_processing:
Read quality was assessed using FastQC v0.11.9. Raw paired-end reads were processed with cutadapt v4.2 to remove adapter sequences, poly-G artifacts, and low-quality bases. Reads were discarded if they contained more than two expected errors, more than 30% ambiguous bases, or were shorter than 20 nucleotides after trimming. Processed reads were aligned to the mouse reference genome GRCm39 from Ensembl release 113 using STAR v2.7.11b. Gene-level counts were generated using STAR with the option –quantMode GeneCounts.
Assembly: Mus musculus reference genome GRCm39, Ensembl release 113.
Supplementary files format and content: Tab-delimited text file containing raw counts (as generated by the STAR aligner).

molecule: polyA RNA

source_name: Liver

extract_protocol:
Mouse kidney, liver, and heart tissues collected from mice at 8, 10, or 12 weeks of age were homogenized on ice in RLT lysis buffer from the RNeasy Mini Kit (Qiagen, Hilden, Germany; Cat. No. 74104) using an IKA® T10 basic homogenizer at maximum speed for 30 s. Total RNA was extracted according to the manufacturer’s instructions. RNA concentration and purity were assessed using a NanoDrop™ spectrophotometer, and RNA integrity was assessed using the Agilent 2100 Bioanalyzer system.
High-quality total RNA samples were submitted to Novogene Bioinformatics Technology Co., Ltd. for library preparation and sequencing. RNA-seq libraries were constructed according to Novogene standard protocols and sequenced on an Illumina NovaSeq platform to generate approximately 30 million paired-end reads per sample with a read length of 2 × 150 bp.

value: Liver

tag: age

value: 12 weeks


title: PB02071-01 Flu Year 1 Day 7

description:
Library name: PB02071-01
H5 file contains RNA expression matrix

value: Flu Year 1 Day 7


title: Liver, 12 weeks, replicate 3

description: Library name: L_19


title: PB02070-01 MM Post Induction 2-Cycles

description:
Library name: PB02070-01
H5 file contains RNA expression matrix

value: Female

value: Caucasian

value: MM Post Induction 2-Cycles


title: WT_0hr_2

description: Library name: Sample-2


title: Liver, 12 weeks, replicate 2

description: Library name: L_18


title: WT_0hr_1

description: Library name: Sample-1


title: PB02070-03 MM Post Induction 2-Cycles

description:
Library name: PB02070-03
H5 file contains RNA expression matrix

value: PBMC


title: Liver, 12 weeks, replicate 1

description: Library name: L_17


title: PB02069-01 Flu Year 1 Day 0

description:
Library name: PB02069-01
H5 file contains RNA expression matrix

value: Male

value: Other


title: PB02068-03 MM Post Induction 2-Cycles

description:
Library name: PB02068-03
H5 file contains RNA expression matrix


title: Liver, 10 weeks, replicate 4

description: Library name: L_12

value: WT

value: 10 weeks


title: Liver, 10 weeks, replicate 3

description: Library name: L_11


title: PB02067-01 Flu Year 2 Day 7

description:
Library name: PB02067-01
H5 file contains RNA expression matrix

value: Flu Year 2 Day 7


title: Liver, 10 weeks, replicate 2

description: Library name: L_10


title: PB02065-01 Flu Year 1 Day 7

description:
Library name: PB02065-01
H5 file contains RNA expression matrix


title: Liver, 10 weeks, replicate 1

description: Library name: L_9


title: PB02064-01 Flu Year 2 Day 7

description:
Library name: PB02064-01
H5 file contains RNA expression matrix


title: Liver, 8 weeks, replicate 4

description: Library name: L_4

value: 8 weeks


title: PB02063-01 Flu Year 2 Day 7

description:
Library name: PB02063-01
H5 file contains RNA expression matrix


title: PB02062-01 Flu Year 2 Day 0

description:
Library name: PB02062-01
H5 file contains RNA expression matrix

value: Flu Year 2 Day 0


title: Liver, 8 weeks, replicate 3

description: Library name: L_3


title: Liver, 8 weeks, replicate 2

description: Library name: L_2


title: PB02061-01 Flu Year 1 Stand-Alone

description:
Library name: PB02061-01
H5 file contains RNA expression matrix

value: Blood

value: Flu Year 1 Stand-Alone


title: PB02060-01 Flu Year 1 Day 0

description:
Library name: PB02060-01
H5 file contains RNA expression matrix

value: Flu Year 1 Day 0

value: FALSE


title: PB02059-01 Flu Year 2 Day 0

description:
Library name: PB02059-01
H5 file contains RNA expression matrix


title: Kidney, 12 weeks, replicate 4

description: Library name: K_20

source_name: Kidney

value: Kidney

value: 12 weeks


title: Kidney, 12 weeks, replicate 3

description: Library name: K_19


title: PB02057-01 Flu Year 2 Day 0

description:
Library name: PB02057-01
H5 file contains RNA expression matrix


title: Kidney, 12 weeks, replicate 2

description: Library name: K_18


title: PB02056-01 Flu Year 2 Stand-Alone

description:
Library name: PB02056-01
H5 file contains RNA expression matrix

value: Flu Year 2 Stand-Alone


title: PB02055-01 Flu Year 1 Stand-Alone

description:
Library name: PB02055-01
H5 file contains RNA expression matrix

value: Female

value: Caucasian


title: Kidney, 10 weeks, replicate 4

description: Library name: K_12


title: PB02054-01 Flu Year 1 Stand-Alone

description:
Library name: PB02054-01
H5 file contains RNA expression matrix

value: PBMC


title: PB02053-01 Flu Year 2 Stand-Alone

description:
Library name: PB02053-01
H5 file contains RNA expression matrix

value: Male


title: Kidney, 12 weeks, replicate 1

description: Library name: K_17


title: Kidney, 10 weeks, replicate 2

description: Library name: K_10


title: PB02052-01 MM End Induction 1st Draw

description:
Library name: PB02052-01
H5 file contains RNA expression matrix

value: MM End Induction 1st Draw


title: Kidney, 10 weeks, replicate 1

description: Library name: K_9

value: WT


title: PB02051-01 Flu Year 1 Stand-Alone

description:
Library name: PB02051-01
H5 file contains RNA expression matrix


title: Kidney, 8 weeks, replicate 4

description: Library name: K_4


title: PB02049-01 Flu Year 2 Stand-Alone

description:
Library name: PB02049-01
H5 file contains RNA expression matrix


title: PB02047-01 MM Pre-Treatment

description:
Library name: PB02047-01
H5 file contains RNA expression matrix

value: MM Pre-Treatment


title: Kidney, 8 weeks, replicate 3

description: Library name: K_3


title: Kidney, 8 weeks, replicate 2

description: Library name: K_2


title: Kidney, 8 weeks, replicate 1

description: Library name: K_1


title: PB01360-01 MM End Induction 1st Draw

description:
Library name: PB01360-01
H5 file contains RNA expression matrix

value: Other


title: PB01358-01 MM Post Induction 2-Cycles

description:
Library name: PB01358-01
H5 file contains RNA expression matrix

value: MM Post Induction 2-Cycles


title: PB01356-01 Flu Year 1 Day 90

description:
Library name: PB01356-01
H5 file contains RNA expression matrix

value: Flu Year 1 Day 90


title: Heart, 12 weeks, replicate 3

description: Library name: H_19

source_name: Heart

value: Heart


title: Heart, 12 weeks, replicate 2

description: Library name: H_18


title: Heart, 12 weeks, replicate 1

description: Library name: H_17


title: PB01350-01 COVID-19 Visit 7 Pre-transplant

description:
Library name: PB01350-01
H5 file contains RNA expression matrix

value: Blood

value: COVID-19 Visit 7 Pre-transplant


title: PB01348-01 MM Pre-Treatment

description:
Library name: PB01348-01
H5 file contains RNA expression matrix

value: FALSE


title: PB01339-01 COVID-19 Visit 6 Pre-transplant

description:
Library name: PB01339-01
H5 file contains RNA expression matrix

value: COVID-19 Visit 6 Pre-transplant


title: Heart, 10 weeks, replicate 3

description: Library name: H_11

value: 10 weeks


title: Heart, 10 weeks, replicate 2

description: Library name: H_10


title: PB01335-01 MM Post Transplant 60 Days

description:
Library name: PB01335-01
H5 file contains RNA expression matrix

value: MM Post Transplant 60 Days


title: Heart, 10 weeks, replicate 1

description: Library name: H_9


title: PB01334-01 MM Post Induction 2-Cycles

description:
Library name: PB01334-01
H5 file contains RNA expression matrix


title: Heart, 8 weeks, replicate 4

description: Library name: H_4

value: 8 weeks


title: PB01331-01 COVID-19 Visit 5 Pre-transplant

description:
Library name: PB01331-01
H5 file contains RNA expression matrix

value: Caucasian

value: COVID-19 Visit 5 Pre-transplant


title: Heart, 8 weeks, replicate 3

description: Library name: H_3


title: PB01327-01 Flu Year 1 Day 0

description:
Library name: PB01327-01
H5 file contains RNA expression matrix

value: PBMC

value: Male

value: Flu Year 1 Day 0


title: Heart, 8 weeks, replicate 2

description: Library name: H_2

value: WT


title: PB01326-01 Flu Year 1 Day 7

description:
Library name: PB01326-01
H5 file contains RNA expression matrix

value: Flu Year 1 Day 7


title: Heart, 8 weeks, replicate 1

description: Library name: H_1


title: PB01325-01 MM Post Transplant 60 Days

description:
Library name: PB01325-01
H5 file contains RNA expression matrix

value: Female


title: TAM_KD_Rep3

city: Paris

first: Fiorella

last: Grandi

address: 105 Bld d'Hopital

department: Centre de Recherche de Myologie

country: France

institute: Sorbonne Universite

description:
Library name: KD_6G
Mbnl KD_10W_3

data_processing:
Aligment to mm10, deseq2 analysis for differential gene expression
Assembly: mm10
Supplementary files format and content: raw counts

source_name: muscle

extract_protocol:
RNA was extracted from muscle tissue after 10 week of AAV injection.
Libraries were made with illumina RNA sequencing kit.

value: muscle

value: tibialis anterior

value: KD


title: TAM_KD_Rep2

description:
Library name: KD_5G
Mbnl KD_10W_2


title: PB01323-01 Flu Year 1 Day 0

description:
Library name: PB01323-01
H5 file contains RNA expression matrix

value: Blood


title: TAM_KD_Rep1

description:
Library name: KD_4G
Mbnl KD_10W_1


title: PB01321-01 Flu Year 1 Day 7

description:
Library name: PB01321-01
H5 file contains RNA expression matrix

value: FALSE


title: TAM_CTL_Rep3

description:
Library name: Control_6D
CTRL_10W_3

value: Control


title: PB01319-01 Flu Year 1 Day 0

description:
Library name: PB01319-01
H5 file contains RNA expression matrix


title: PB01318-03 Flu Year 1 Stand-Alone

description:
Library name: PB01318-03
H5 file contains RNA expression matrix

value: Flu Year 1 Stand-Alone


title: PB01318-01 Flu Year 1 Stand-Alone

description:
Library name: PB01318-01
H5 file contains RNA expression matrix


title: TAM_CTL_Rep1

description:
Library name: Control_4D
CTRL_10W_1


title: snMuscle_TAM_MBNLKD_DTA_Rep2

description: Library name: DTA75

data_processing:
Fastq files were processed using 10x Genomic's CellRanger Pipeline
barcode, matrix and feature files were imported into Seurat for downstream analysis and cell annotation.
Assembly: mm10
Supplementary files format and content: h5 files contain the output from CellRanger.

molecule: nuclear RNA

extract_protocol:
nuclei were extracted using a a dounce homogenizer as in Grandi 2022 Nature Protocols
Libraries were made following the 10x 3' Gex manual with no modifications. 11 PCR cycles were performed.

value: MBNL1 and 2 knockdown


title: single B. thetaiotaomicron cells at MEP from well H4

description: Library name: H4

value: Fixed in 50% RNAlater


title: PB01317-02 MM Post Induction 2-Cycles

description:
Library name: PB01317-02
H5 file contains RNA expression matrix

value: Caucasian

value: MM Post Induction 2-Cycles


title: PB01351-01 Flu Year 1 Day 90

description:
Library name: PB01351-01
H5 file contains RNA expression matrix

value: PBMC

value: Flu Year 1 Day 90


title: Heart, 12 weeks, replicate 4

description: Library name: H_20

value: Heart

value: 12 weeks


title: snMuscle_TAM_MBNLKD_DTA_Rep1

description: Library name: DTA57


title: snMuscle_TAM_MBLKD_CTL_Rep2

description: Library name: CTL76


title: PB01316-01 MM Pre-Treatment

description:
Library name: PB01316-01
H5 file contains RNA expression matrix

value: Male

value: Other

value: MM Pre-Treatment


title: Heart, 10 weeks, replicate 4

description: Library name: H_12

value: WT

value: 10 weeks


title: PB01316-03 MM Pre-Treatment

description:
Library name: PB01316-03
H5 file contains RNA expression matrix

value: Blood


title: snMuscle_TAM_MBLKD_CTL_Rep1

description: Library name: CTL55

value: muscle

value: tibialis anterior


title: PB00250-01 Flu Year 1 Stand-Alone

description:
Library name: PB00250-01
H5 file contains RNA expression matrix

value: Female

value: Flu Year 1 Stand-Alone

value: FALSE


title: S48_EXP2161RNA18_WT_IgG_3

city: Tampa

first: Youngchul

last: Kim

address: 12902 Magnolia Dr

institute: H. Lee Moffitt Cancer Center

description: Library name: S48_EXP2161RNA18_WT_IgG_3

data_processing:
read adapters were detected using BBMerge (v37.02) and subsequently removed with cutadapt (v1.8.1)
Processed raw reads were then aligned to mouse genome mm10 using STAR (v2.7.7a)
Gene-level expression was estimated as read count  using RSEM (v1.3.0) and GENCODE gene model vM21
Supplementary files format and content: tab-delimited text file include raw count for each sample

source_name: Fresh tumor tissue

growth_protocol: C57BL/6J and iNOS KO mice were obtained from Jackson Laboratories (Bar Harbor, ME) at 4 weeks of age and housed for 2 weeks under institutional IACUC approval. B16-D5 cells were injected subcutaneously into the flank of mice 8 days before treatment (day -8) to allow tumors to establish. Day 0 marks the initiation of therapy.

extract_protocol:
Fresh tumor tissue was processed for total RNA extraction using the RNeasy Blood & Tissue Kit (Qiagen, Germantown, MD) per the manufacturer’s instructions. RNA was quantified with the Qubit Fluorometer (ThermoFisher Scientific, Waltham, MA) and assessed for quality using the Agilent TapeStation 4200 (Agilent Technologies, Santa Clara, CA).
Samples were prepared for RNA sequencing with the NuGEN Universal Mouse RNA-Seq Library Preparation Kit with NuQuant (Tecan Genomics, Redwood City, CA). Using 100 ng of RNA, cDNA and strand-specific libraries were generated following the manufacturer’s protocol. Quality control included TapeStation size assessment and quantification via the Kapa Library Quantification Kit (Roche, Wilmington, MA).

treatment_protocol: Mice were randomly assigned to three groups: control (no treatment), IgG-treated (#BE0089, BioXCell, Lebanon, NH), and anti-PD-1-treated (#BE0146, BioXCell, Lebanon, NH). Treatments (250 µg/200 µL PBS) were administered on Days 0 and 3.

value: Fresh tumor tissue

tag: disease

value: melanoma

value: Ctrl

tag: timepoint


title: PB00246-01 MM End Induction 1st Draw

description:
Library name: PB00246-01
H5 file contains RNA expression matrix

tag: tissue

value: PBMC

value: Caucasian

value: MM End Induction 1st Draw


title: S47_EXP2161RNA17_WT_IgG_2

description: Library name: S47_EXP2161RNA17_WT_IgG_2


title: PB00244-01 MM Post Induction 2-Cycles

description:
Library name: PB00244-01
H5 file contains RNA expression matrix

value: MM Post Induction 2-Cycles


title: S46_EXP2161RNA16_WT_IgG_1

description: Library name: S46_EXP2161RNA16_WT_IgG_1


title: PB00241-01 MM Post Induction 2-Cycles

description:
Library name: PB00241-01
H5 file contains RNA expression matrix


title: S45_EXP2161RNA15_WT_aPD1_4

description: Library name: S45_EXP2161RNA15_WT_aPD1_4


title: PB00240-01 MM Post Transplant 60 Days

description:
Library name: PB00240-01
H5 file contains RNA expression matrix

value: MM Post Transplant 60 Days


title: S44_EXP2161RNA14_WT_aPD1_3

description: Library name: S44_EXP2161RNA14_WT_aPD1_3


title: PB00235-01 MM End Induction 1st Draw

description:
Library name: PB00235-01
H5 file contains RNA expression matrix

value: Male


title: single B. thetaiotaomicron cells at MEP from well D4

description: Library name: D4

value: WT

value: Fixed in 50% RNAlater


title: S43_EXP2161RNA13_WT_aPD1_2

description: Library name: S43_EXP2161RNA13_WT_aPD1_2


title: PB00139-01 MM Pre-Treatment

description:
Library name: PB00139-01
H5 file contains RNA expression matrix

value: Blood

value: MM Pre-Treatment


title: PB00138-01 MM Post Induction 2-Cycles

description:
Library name: PB00138-01
H5 file contains RNA expression matrix


title: S42_EXP2161RNA12_WT_Ctrl_3

description: Library name: S42_EXP2161RNA12_WT_Ctrl_3

value: IgG


title: S41_EXP2161RNA11_WT_Ctrl_2

description: Library name: S41_EXP2161RNA11_WT_Ctrl_2


title: PB01324-01 MM Post Transplant 90 Days

description:
Library name: PB01324-01
H5 file contains RNA expression matrix

value: MM Post Transplant 90 Days


title: PB00137-01 MM Post Induction 2-Cycles

description:
Library name: PB00137-01
H5 file contains RNA expression matrix


title: S40_EXP2161RNA10_WT_Ctrl_1

description: Library name: S40_EXP2161RNA10_WT_Ctrl_1


title: PB00136-01 MM Pre-Treatment

description:
Library name: PB00136-01
H5 file contains RNA expression matrix


title: S39_EXP2161RNA9_KO_IgG_3

description: Library name: S39_EXP2161RNA9_KO_IgG_3


title: PB00134-01 MM Pre-Treatment

description:
Library name: PB00134-01
H5 file contains RNA expression matrix


title: S38_EXP2161RNA8_KO_IgG_2

description: Library name: S38_EXP2161RNA8_KO_IgG_2


title: PB06445-006 MM Post Transplant 2 year

description:
Library name: PB06445-006
H5 file contains RNA expression matrix

value: MM Post Transplant 2 year


title: PB06435-001 MM Post Transplant 60 Days

description:
Library name: PB06435-001
H5 file contains RNA expression matrix

value: FALSE


title: S36_EXP2161RNA6_KO_aPD1_3

description: Library name: S36_EXP2161RNA6_KO_aPD1_3

value: Fresh tumor tissue


title: S37_EXP2161RNA7_KO_IgG_1

description: Library name: S37_EXP2161RNA7_KO_IgG_1

value: melanoma


title: S35_EXP2161RNA5_KO_aPD1_2

description: Library name: S35_EXP2161RNA5_KO_aPD1_2


title: PB06430-008 Flu Year 1 Day 0

description:
Library name: PB06430-008
H5 file contains RNA expression matrix

value: Other

value: Flu Year 1 Day 0


title: PB06427-003 Flu Year 1 Day 90

description:
Library name: PB06427-003
H5 file contains RNA expression matrix

value: PBMC

value: Female

value: Caucasian

value: Flu Year 1 Day 90


title: TAM_CTL_Rep2

description:
Library name: Control_5D
CTRL_10W_2

value: muscle

value: tibialis anterior

value: Control


title: S34_EXP2161RNA4_KO_aPD1_1

description: Library name: S34_EXP2161RNA4_KO_aPD1_1

value: WT


title: PB06426-003 Flu Year 2 Day 7

description:
Library name: PB06426-003
H5 file contains RNA expression matrix

value: Blood

value: Flu Year 2 Day 7


title: PB06424-006 Flu Year 2 Day 0

description:
Library name: PB06424-006
H5 file contains RNA expression matrix

value: Flu Year 2 Day 0


title: S33_EXP2161RNA3_KO_Ctrl_4

description: Library name: S33_EXP2161RNA3_KO_Ctrl_4


title: S32_EXP2161RNA2_KO_Ctrl_2

description: Library name: S32_EXP2161RNA2_KO_Ctrl_2


title: PB06423-003 Flu Year 2 Day 0

description:
Library name: PB06423-003
H5 file contains RNA expression matrix

value: Male


title: PB06422-004 Flu Year 2 Stand-Alone

description:
Library name: PB06422-004
H5 file contains RNA expression matrix

value: Flu Year 2 Stand-Alone

value: FALSE


title: S31_EXP2161RNA1_KO_Ctrl_1

description: Library name: S31_EXP2161RNA1_KO_Ctrl_1

value: Fresh tumor tissue

value: melanoma


title: PB06420-002 Flu Year 2 Stand-Alone

description:
Library name: PB06420-002
H5 file contains RNA expression matrix


title: S29_EXP2128RNA29_IgG_D3_3

description: Library name: S29_EXP2128RNA29_IgG_D3_3


title: PB05148-001 Flu Year 1 Day 7

description:
Library name: PB05148-001
H5 file contains RNA expression matrix

value: African American

value: Flu Year 1 Day 7


title: S30_EXP2128RNA30_IgG_D3_5

description: Library name: S30_EXP2128RNA30_IgG_D3_5


title: S28_EXP2128RNA28_IgG_D3_2

description: Library name: S28_EXP2128RNA28_IgG_D3_2

value: Ctrl


title: PB05119-006 MM Post Transplant 2 year

description:
Library name: PB05119-006
H5 file contains RNA expression matrix

value: PBMC

value: Other

value: MM Post Transplant 2 year


title: PB05008-002 MM Post Transplant 2 year

description:
Library name: PB05008-002
H5 file contains RNA expression matrix

value: Female

value: Caucasian


title: S27_EXP2128RNA27_aPD1D3_5

description: Library name: S27_EXP2128RNA27_aPD1D3_5

value: WT


title: S26_EXP2128RNA26_aPD1D3_4

description: Library name: S26_EXP2128RNA26_aPD1D3_4


title: PB05007-001 MM Post Transplant 1 year

description:
Library name: PB05007-001
H5 file contains RNA expression matrix

value: Blood

value: MM Post Transplant 1 year


title: PB05006-002 MM Post Transplant 1 year

description:
Library name: PB05006-002
H5 file contains RNA expression matrix


title: S25_EXP2128RNA25_aPD1D3_3

description: Library name: S25_EXP2128RNA25_aPD1D3_3


title: S23_EXP2128RNA23_Ctrl_D3_2

description: Library name: S23_EXP2128RNA23_Ctrl_D3_2


title: PB04840-008 MM End Induction 1st Draw

description:
Library name: PB04840-008
H5 file contains RNA expression matrix

value: MM End Induction 1st Draw


title: S22_EXP2128RNA22_Ctrl_D3_1

description: Library name: S22_EXP2128RNA22_Ctrl_D3_1

value: IgG


title: S24_EXP2128RNA24_Ctrl_D3_4

description: Library name: S24_EXP2128RNA24_Ctrl_D3_4


title: PB04842-008 MM Post Transplant 60 Days

description:
Library name: PB04842-008
H5 file contains RNA expression matrix

value: Male

value: MM Post Transplant 60 Days


title: PB04825-008 MM Post Induction 2-Cycles

description:
Library name: PB04825-008
H5 file contains RNA expression matrix

value: MM Post Induction 2-Cycles

value: FALSE


title: PB04824-001 MM End Induction 1st Draw

description:
Library name: PB04824-001
H5 file contains RNA expression matrix


title: S21_EXP2128RNA21_IgG_D1_6

description: Library name: S21_EXP2128RNA21_IgG_D1_6

value: Fresh tumor tissue

value: melanoma


title: PB04700-006 Flu Year 2 Day 0

description:
Library name: PB04700-006
H5 file contains RNA expression matrix

value: Flu Year 2 Day 0


title: S17_EXP2128RNA17_aPD1_D1_4

description: Library name: S17_EXP2128RNA17_aPD1_D1_4


title: S18_EXP2128RNA18_aPD1_D1_5

description: Library name: S18_EXP2128RNA18_aPD1_D1_5


title: S16_EXP2128RNA16_aPD1_D1_2

description: Library name: S16_EXP2128RNA16_aPD1_D1_2


title: S19_EXP2128RNA19_IgG_D1_2

description: Library name: S19_EXP2128RNA19_IgG_D1_2


title: PB04697-007 Flu Year 2 Day 90

description:
Library name: PB04697-007
H5 file contains RNA expression matrix

value: PBMC

value: Flu Year 2 Day 90


title: PB04696-007 Flu Year 2 Day 90

description:
Library name: PB04696-007
H5 file contains RNA expression matrix


title: S20_EXP2128RNA20_IgG_D1_4

description: Library name: S20_EXP2128RNA20_IgG_D1_4


title: PB04692-006 MM Post Transplant 2 year

description:
Library name: PB04692-006
H5 file contains RNA expression matrix

value: MM Post Transplant 2 year


title: Liver, 8 weeks, replicate 1

description: Library name: L_1

value: Liver

value: 8 weeks


title: PB04685-001-002 MM End Induction 1st Draw

description:
Library name: PB04685-001-002
H5 file contains RNA expression matrix

value: Female

value: Other


title: S15_EXP2128RNA15_Ctrl_D1_6

description: Library name: S15_EXP2128RNA15_Ctrl_D1_6

value: WT


title: PB04684-004 Flu Year 1 Day 0

description:
Library name: PB04684-004
H5 file contains RNA expression matrix

value: Blood

value: Caucasian

value: Flu Year 1 Day 0


title: S14_EXP2128RNA14_Ctrl_D1_3

description: Library name: S14_EXP2128RNA14_Ctrl_D1_3


title: PB04683-007 Flu Year 2 Day 7

description:
Library name: PB04683-007
H5 file contains RNA expression matrix

value: Flu Year 2 Day 7


title: S13_EXP2128RNA13_Ctrl_D1_1

description: Library name: S13_EXP2128RNA13_Ctrl_D1_1


title: PB04681-008 Flu Year 2 Day 0

description:
Library name: PB04681-008
H5 file contains RNA expression matrix


title: S12_EXP2128RNA12_IgG_D0_6

description: Library name: S12_EXP2128RNA12_IgG_D0_6


title: PB04532-002 MM Post Transplant 2 year

description:
Library name: PB04532-002
H5 file contains RNA expression matrix


title: S11_EXP2128RNA11_IgG_D0_2

description: Library name: S11_EXP2128RNA11_IgG_D0_2


title: PB04615-004 Flu Year 2 Stand-Alone

description:
Library name: PB04615-004
H5 file contains RNA expression matrix

value: Flu Year 2 Stand-Alone


title: S10_EXP2128RNA10_IgG_D0_1

description: Library name: S10_EXP2128RNA10_IgG_D0_1

value: Ctrl


title: Kidney, 10 weeks, replicate 3

description: Library name: K_11

value: Kidney

value: 10 weeks


title: PB04531-001 MM Post Transplant 1 year

description:
Library name: PB04531-001
H5 file contains RNA expression matrix

value: Male

value: MM Post Transplant 1 year

value: FALSE


title: S09_EXP2128RNA9_aPD1_D0_5

description: Library name: S09_EXP2128RNA9_aPD1_D0_5

value: Fresh tumor tissue

value: melanoma


title: PB04527-001 MM Post Transplant 1 year

description:
Library name: PB04527-001
H5 file contains RNA expression matrix

value: PBMC


title: S08_EXP2128RNA8_aPD1_D0_3

description: Library name: S08_EXP2128RNA8_aPD1_D0_3


title: PB02772-001-003 MM End Induction 1st Draw

description:
Library name: PB02772-001-003
H5 file contains RNA expression matrix

value: Female

value: MM End Induction 1st Draw


title: S07_EXP2128RNA7_aPD1_D0_1

description: Library name: S07_EXP2128RNA7_aPD1_D0_1

value: WT


title: S06_EXP2128RNA6_Ctrl_D0_4

description: Library name: S06_EXP2128RNA6_Ctrl_D0_4


title: PB02745-002 MM Post Transplant 60 Days

description:
Library name: PB02745-002
H5 file contains RNA expression matrix

value: Blood

value: MM Post Transplant 60 Days


title: PB02750-001-002 MM Post Induction 2-Cycles

description:
Library name: PB02750-001-002
H5 file contains RNA expression matrix

value: Caucasian

value: MM Post Induction 2-Cycles


title: S05_EXP2128RNA5_Ctrl_D0_2

description: Library name: S05_EXP2128RNA5_Ctrl_D0_2


title: PB02728-001 MM Pre-Treatment

description:
Library name: PB02728-001
H5 file contains RNA expression matrix

value: MM Pre-Treatment


title: S04_EXP2128RNA4_Ctrl_D0_1

description: Library name: S04_EXP2128RNA4_Ctrl_D0_1

value: Ctrl


title: S03_EXP2128RNA3_Ctrl_0hrs_3

description: Library name: S03_EXP2128RNA3_Ctrl_0hrs_3


title: PB02739-001-004 MM Post Induction 2-Cycles

description:
Library name: PB02739-001-004
H5 file contains RNA expression matrix

value: Other


title: PB02726-003 MM Pre-Treatment

description:
Library name: PB02726-003
H5 file contains RNA expression matrix


title: S02_EXP2128RNA2_Ctrl_0hrs_2

description: Library name: S02_EXP2128RNA2_Ctrl_0hrs_2


title: S20_EXP2128RNA1_Ctrl_0hrs_1

description: Library name: S20_EXP2128RNA1_Ctrl_0hrs_1


title: PB02709-001-003 MM Pre-Treatment

description:
Library name: PB02709-001-003
H5 file contains RNA expression matrix

value: African American


title: PB02697-001 MM End Induction 1st Draw

description:
Library name: PB02697-001
H5 file contains RNA expression matrix


title: PB02695-005 Flu Year 1 Day 90

description:
Library name: PB02695-005
H5 file contains RNA expression matrix

value: Male

value: Flu Year 1 Day 90


title: PB02691-004 MM Post Transplant 1 year

description:
Library name: PB02691-004
H5 file contains RNA expression matrix

value: MM Post Transplant 1 year

value: FALSE


title: Hindlimb_WT_E135_LaminB1_Rep2

city: Utrecht

first: Jop

last: Kind

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute

description: Library name: LaminB1_ab16048_mm10_WT_HL_Rep2

library_source: genomic

data_processing:
Adapters were trimmed with Trim Galore (v0.6.4) using --paired --nextera.
Trimmed reads were aligned to mm10 with Bowtie2 (v2.3.5.1) (ref) using --local --very-sensitive-local --no-mixed --no-discordant --phred33 -I 10 -X 2000.
Aligned reads were filtered for properly paired reads with MAPQ ≥ 20 using samtools (v1.10) view -f 2 -q 20, sorted, and stripped of ENCODE blacklisted regions (ref) with bedtools (v2.29.2) intersect -v.
Coverage tracks were generated with deepTools2 (v3.4.1) at 10 bp bin size with read extension and CPM normalisation, ignoring chrX and chrY.
Coverage tracks were quantile-normalised within each antibody using normalize.quantiles.use.target from the preprocessCore R package, with the first sample of each set as the target distribution. Normalised values were then scaled to their 99.99th percentile and clipped to a maximum of 1.
Assembly: mm10
Supplementary files format and content: bw
Library strategy: CUT&Tag

molecule: genomic DNA

source_name: Hindlimb

growth_protocol: Embryos were isolated from the uteri of pregnant mothers between 8.5 and 13.5 days after the plug date. Embryos were dissected on ice in HBBS (for 8.5-day embryos) or PBS (for 9.5-13.5-day embryos), and staged based on morphology, size, and/or somite number.Samples were processed to create single cell suspensions differently depending on stage. Whole E8.5 embryos were pooled by precise somite number and transferred for tissue dissociation in 200 μl TrypLE Express (Gibco,12604013; Gibco) at 37 °C and triturated by pipetting at 10-20 minutes intervals for a total of 40 minutes. By contrast, tissues from E9.5 to E13.5 embryos were microdissected and pooled as needed. Tissues were then dissociated with Trypsin-EDTA (Thermo Fisher, 25300096; Thermo Fisher) and trituration by pipetting at 37°C at 2-3 minute intervals until no visible clumps remained (~5-15 minutes). Digestion was immediately halted by addition of 10% FCS/PBS. Following dissociation, all samples were cleared of  cell clumps by filtration (40 μm, Flowmi Cell Strainer, Scienceware) and then pelleted by centrifugation at 300 g for 5 minutes at 4°C. Cells were resuspended in 1:1 ratio of F1 [40% FCS/60% DMEM] and F2 solution [20%DMSO/40%FCS/40% DMEM] and cryopreserved.

extract_protocol:
Cells were thawed at 37°C and immediately washed twice with warm ESCs media by centrifugation at 400 g for 10 minutes at RT. Pipetting was performed as gently as possible to ensure cell viability. Subsequently, cells were transferred on ice and washed twice with cold 0.04%BSA/PBS by centrifugation at 400 g for 10 minutes at 4°C. After final wash, the pellet was thoroughly resuspended in the NE1 buffer and incubated on ice for 10 minutes, then spun down at 500 g for 10 minutes at 4°C. Subsequently, nuclei were resuspended in Wash buffer and quantified using a haemocytometer. 100 thousand nuclei from E13.5 limb and ESCs samples, and 10 thousand nuclei from E8.5-E9.5 samples, per reaction were used.
NGS libraries were generated by amplifying the CUT&Tag DNA fragments with barcoded i5 and i7 primers as described previously with minor modifications (PMID: 34932975). Briefly, following PCR 1x volume of Ampure XP beads (Beckman Coulter) were mixed with the NGS libraries and incubated at RT for 10 min. After magnetic separation, the beads were washed three times on the magnet with 80% ethanol and the libraries were eluted with Tris-HCl, pH 8.0. The quality of the purified NGS libraries was assessed with the D5000 tapestation electrophoresis (Agilent Technologies).

value: Hindlimb

tag: developmental stage

tag: antibody


title: Hindlimb_WT_E135_LaminB1_Rep1

description: Library name: LaminB1_ab16048_mm10_WT_HL_Rep1

tag: genotype


title: PB02686-005 MM Post Transplant 60 Days

description:
Library name: PB02686-005
H5 file contains RNA expression matrix

tag: cell type

value: PBMC


title: ESCs_WT_LaminB1_Rep2

description: Library name: LaminB1_ab16048_mm10_NE_ESCs_Rep2

source_name: ESCs

value: ESCs


title: ESCs_WT_LaminB1_Rep1

description: Library name: LaminB1_ab16048_mm10_NE_ESCs_Rep1


title: PB02094-03 MM End Induction 1st Draw

description:
Library name: PB02094-03
H5 file contains RNA expression matrix

tag: subject id

value: MM End Induction 1st Draw


title: Forelimb_WT_E9_LaminB1_Rep4

description: Library name: LaminB1_ab16048_mm10_E95S_Rep4

source_name: Forelimb

value: Forelimb

value: WT


title: PB02088-03 Flu Year 2 Day 90

description:
Library name: PB02088-03
H5 file contains RNA expression matrix

value: Blood

tag: birth year

value: Flu Year 2 Day 90


title: Forelimb_WT_E9_LaminB1_Rep3

description: Library name: LaminB1_ab16048_mm10_E95S_Rep3


title: PB02082-04 Flu Year 1 Day 90

description:
Library name: PB02082-04
H5 file contains RNA expression matrix

tag: Sex

value: Female

value: Caucasian


title: Forelimb_WT_E9_LaminB1_Rep2

description: Library name: LaminB1_ab16048_mm10_E95S_Rep2


title: PB02076-06 Flu Year 1 Day 7

description:
Library name: PB02076-06
H5 file contains RNA expression matrix

tag: race

value: Flu Year 1 Day 7


title: Forelimb_WT_E9_LaminB1_Rep1

description: Library name: LaminB1_ab16048_mm10_E95S_Rep1


title: Forelimb_WT_E95_LaminB1_Rep4

description: Library name: LaminB1_ab16048_mm10_E95L_Rep4


title: PB02073-03 Flu Year 1 Stand-Alone

description:
Library name: PB02073-03
H5 file contains RNA expression matrix

tag: days since_first_visit

value: Flu Year 1 Stand-Alone


title: PB02079-01 MM Post Transplant 60 Days

description:
Library name: PB02079-01
H5 file contains RNA expression matrix

tag: visit

value: MM Post Transplant 60 Days


title: PB02068-06 MM Post Induction 2-Cycles

description:
Library name: PB02068-06
H5 file contains RNA expression matrix

value: Male

value: MM Post Induction 2-Cycles

tag: batch id


title: Forelimb_WT_E95_LaminB1_Rep3

description: Library name: LaminB1_ab16048_mm10_E95L_Rep3


title: Forelimb_WT_E95_LaminB1_Rep1

description: Library name: LaminB1_ab16048_mm10_E95L_Rep1


title: Forelimb_WT_E95_LaminB1_Rep2

description: Library name: LaminB1_ab16048_mm10_E95L_Rep2


title: PB02066-01 Flu Year 1 Day 0

description:
Library name: PB02066-01
H5 file contains RNA expression matrix

value: Flu Year 1 Day 0

tag: sample bridging_control


title: PB02050-07 MM Pre-Treatment

description:
Library name: PB02050-07
H5 file contains RNA expression matrix

value: MM Pre-Treatment

value: FALSE


title: Whole_embryo_WT_E85_LaminB1_Rep4

description: Library name: LaminB1_ab16048_mm10_E85_Rep4

source_name: Whole embryo

value: Whole embryo


title: PB01364-08 MM End Induction 1st Draw

description:
Library name: PB01364-08
H5 file contains RNA expression matrix

value: PBMC


title: Whole_embryo_WT_E85_LaminB1_Rep3

description: Library name: LaminB1_ab16048_mm10_E85_Rep3


title: PB01357-08 MM End Induction 1st Draw

description:
Library name: PB01357-08
H5 file contains RNA expression matrix

value: MM End Induction 1st Draw


title: Whole_embryo_WT_E85_LaminB1_Rep2

description: Library name: LaminB1_ab16048_mm10_E85_Rep2


title: PB01329-03 COVID-19 Visit 4 Pre-transplant

description:
Library name: PB01329-03
H5 file contains RNA expression matrix

value: COVID-19 Visit 4 Pre-transplant


title: PB01333-01 MM Post Induction 2-Cycles

description:
Library name: PB01333-01
H5 file contains RNA expression matrix


title: Whole_embryo_WT_E85_LaminB1_Rep1

description: Library name: LaminB1_ab16048_mm10_E85_Rep1

value: WT


title: Hindlimb_DeltaBor_E135_LaminB1_Rep2

description: Library name: LaminB1_ab16048_mm10_DeltaBor_HL_Rep2

value: Hindlimb


title: PB01328-01 Flu Year 1 Day 7

description:
Library name: PB01328-01
H5 file contains RNA expression matrix

value: Blood


title: Hindlimb_DeltaBor_E135_LaminB1_Rep1

description: Library name: LaminB1_ab16048_mm10_DeltaBor_HL_Rep1


title: PB01322-12 MM Post Transplant 60 Days

description:
Library name: PB01322-12
H5 file contains RNA expression matrix

value: Female


title: Hindlimb_WT_E135_IgG_Rep4

description: Library name: IgG_Isotope_CS5415S_mm10_WT_HL_Rep4

value: IgG


title: PB01315-07 MM Pre-Treatment

description:
Library name: PB01315-07
H5 file contains RNA expression matrix

value: Caucasian


title: Hindlimb_WT_E135_IgG_Rep3

description: Library name: IgG_Isotope_CS5415S_mm10_WT_HL_Rep3


title: PB00251-02 MM Post Transplant 60 Days

description:
Library name: PB00251-02
H5 file contains RNA expression matrix


title: Hindlimb_WT_E135_IgG_Rep2

description: Library name: IgG_Isotope_CS5415S_mm10_WT_HL_Rep2


title: PB00249-02 MM End Induction 1st Draw

description:
Library name: PB00249-02
H5 file contains RNA expression matrix


title: Hindlimb_WT_E135_IgG_Rep1

description: Library name: IgG_Isotope_CS5415S_mm10_WT_HL_Rep1


title: PB00248-03 MM End Induction 1st Draw

description:
Library name: PB00248-03
H5 file contains RNA expression matrix

value: Other


title: ESCs_WT_IgG_Rep4

description: Library name: IgG_Isotope_CS5415S_mm10_NE_ESCs_Rep4

value: ESCs


title: PB00247-01 MM Pre-Treatment

description:
Library name: PB00247-01
H5 file contains RNA expression matrix


title: PB00245-01 MM End Induction 1st Draw

description:
Library name: PB00245-01
H5 file contains RNA expression matrix


title: PB00243-05 MM Post Induction 2-Cycles

description:
Library name: PB00243-05
H5 file contains RNA expression matrix

value: Male


title: ESCs_WT_IgG_Rep2

description: Library name: IgG_Isotope_CS5415S_mm10_NE_ESCs_Rep2


title: ESCs_WT_IgG_Rep3

description: Library name: IgG_Isotope_CS5415S_mm10_NE_ESCs_Rep3


title: PB00242-01-02 MM Post Induction 2-Cycles

description:
Library name: PB00242-01-02
H5 file contains RNA expression matrix

value: MM Post Induction 2-Cycles


title: ESCs_WT_IgG_Rep1

description: Library name: IgG_Isotope_CS5415S_mm10_NE_ESCs_Rep1


title: Forelimb_WT_E9_IgG_Rep4

description: Library name: IgG_Isotope_CS5415S_mm10_E95S_Rep4

value: Forelimb


title: PB00239-02 MM Pre-Treatment

description:
Library name: PB00239-02
H5 file contains RNA expression matrix

value: MM Pre-Treatment


title: Forelimb_WT_E9_IgG_Rep3

description: Library name: IgG_Isotope_CS5415S_mm10_E95S_Rep3


title: PB00238-02 MM End Induction 1st Draw

description:
Library name: PB00238-02
H5 file contains RNA expression matrix

value: FALSE


title: PB00237-11 MM Pre-Treatment

description:
Library name: PB00237-11
H5 file contains RNA expression matrix


title: Forelimb_WT_E9_IgG_Rep2

description: Library name: IgG_Isotope_CS5415S_mm10_E95S_Rep2


title: Forelimb_WT_E9_IgG_Rep1

description: Library name: IgG_Isotope_CS5415S_mm10_E95S_Rep1


title: PB00236-12 MM Post Induction 2-Cycles

description:
Library name: PB00236-12
H5 file contains RNA expression matrix


title: Forelimb_WT_E95_IgG_Rep4

description: Library name: IgG_Isotope_CS5415S_mm10_E95L_Rep4


title: PB00234-01-01 MM Pre-Treatment

description:
Library name: PB00234-01-01
H5 file contains RNA expression matrix


title: Forelimb_WT_E95_IgG_Rep3

description: Library name: IgG_Isotope_CS5415S_mm10_E95L_Rep3


title: Forelimb_WT_E95_IgG_Rep2

description: Library name: IgG_Isotope_CS5415S_mm10_E95L_Rep2


title: PB00233-01 MM Pre-Treatment

description:
Library name: PB00233-01
H5 file contains RNA expression matrix


title: PB00133-12 MM Pre-Treatment

description:
Library name: PB00133-12
H5 file contains RNA expression matrix


title: Forelimb_WT_E95_IgG_Rep1

description: Library name: IgG_Isotope_CS5415S_mm10_E95L_Rep1


title: PB00132-03 MM Pre-Treatment

description:
Library name: PB00132-03
H5 file contains RNA expression matrix


title: Whole_embryo_WT_E85_IgG_Rep4

description: Library name: IgG_Isotope_CS5415S_mm10_E85_Rep4

value: Whole embryo


title: PB00135-01 MM Post Induction 2-Cycles

description:
Library name: PB00135-01
H5 file contains RNA expression matrix

value: PBMC


title: Whole_embryo_WT_E85_IgG_Rep3

description: Library name: IgG_Isotope_CS5415S_mm10_E85_Rep3


title: PB06425-001 MM Post Transplant 1 year

description:
Library name: PB06425-001
H5 file contains RNA expression matrix

value: African American

value: MM Post Transplant 1 year


title: Whole_embryo_WT_E85_IgG_Rep2

description: Library name: IgG_Isotope_CS5415S_mm10_E85_Rep2

value: WT


title: BMC04999-001 MM Stand-Alone Collection

description:
Library name: BMC04999-001
H5 file contains RNA expression matrix, tsv contains ADT cell surface protein capture

data_processing:
Multiplexed sequencing data were prepared using a preprocessing pipeline based on 10x Genomics CellRanger software (version 3.1.0; Released July 24, 2019), with the 10x Genomics GRCh38/hg38 Human Transcriptome Reference (refdata-cellranger-GRCh38-3.0.0; based on the GRCh38 genome reference and Ensembl v93 transcriptome annotations; Released Nov. 19, 2018) to generate cell x UMI count matrices for each Well.
To identify cells originating from each sample, we utilized software tools for HTO quantification and sample demultiplexing to generate separate HDF5-formatted files for each originating sample (as described in Swanson, et al. (2021); DOI: 10.1186/s12859-022-04620-2). This process also removes Cell Barcodes that contain HTOs from multiple samples (doublets or multiplets) or with no detectable sample label (no hash).
After demultiplexing, data from individual samples assembled across all hashed wells were given a first pass of cell type labels using Seurat label transfer with reference to the PBMC dataset provided by the Satija Lab (Stuart and Butler, et al. (2019); DOI: 10.1016/j.cell.2019.05.031) and provided online with the Seurat PBMC scATAC-seq vignette (v 3.0; Compiled June 6, 2019).
For analysis, high quality cells were selected based on the following cutoffs: <10% mitochondria reads, number of genes detected between 200 and 5000, RNA UMIs/cells between 1500 and 750000. After QC filtering, all remaining cells were clustered using a Scanpy (v1.9.6) workflow that consisted of normalization using scanpy.pp.normalize_total with the parameter target_sum = 1e4; log transformation using scanpy.pp.log1p; highly variable gene detection using scanpy.pp.highly_variable_genes; scaling of highly variable gene data using sc.pp.scale; Dimensionality reduction using scanpy.tl.pca with the parameter svd_solver = 'arpack'.
Supplementary files format and content: Ensembl GRCh38-3.0.0
Supplementary files format and content: h5 files, gene expression matrix
Library strategy: CITE-seq

source_name: Bone Marrow

extract_protocol:
BMMCs were removed from liquid nitrogen and rapidly thawed in a 37°C water bath. Cells were diluted dropwise into 40 mL AIM V media (Thermo Fisher Scientific) pre-warmed to 37°C. Cells were pelleted at 400 x g for 5–10 min at 4–10°C, resuspended in 5 mL cold AIM V media, and counted using a Cellometer Spectrum or Cellaca automatic cell counter.  Individual samples are hashtagged with unique oligo barcodes and stained with an antibody dependent tag (ADT) panel and pooled. Pools are stained with a viability dye (FSV510) and sorted for live cells using BD Aria Cell Sorter. Live cells are then collected and diluted to appropriate concentrations for 3' CITEseq.
scRNAseq libraries were generated using a modified 10x genomics chromium 3′ single cell gene expression assay with Cell Hashing. Sample libraries were constructed across different batches, with the addition of a common healthy donor leukopak sample in each library as batch control. Libraries were sequenced on the Illumina Novaseq platform. Hashed 10x Genomics scRNA-seq data processing was carried out using BarWare (BMC Bioinformatics 2022, doi: 10.1186/s12859-022-04620-2) to generate sample-specific output files.

value: Bone Marrow

value: BMMC

value: MM Stand-Alone Collection


title: Whole_embryo_WT_E85_IgG_Rep1

description: Library name: IgG_Isotope_CS5415S_mm10_E85_Rep1

value: IgG


title: BMC05003-003 MM CD38 Progression

description:
Library name: BMC05003-003
H5 file contains RNA expression matrix, tsv contains ADT cell surface protein capture

value: Caucasian

value: MM CD38 Progression


title: BMC05000-005 MM CD38 Progression

description:
Library name: BMC05000-005
H5 file contains RNA expression matrix, tsv contains ADT cell surface protein capture

value: Female


title: Hindlimb_DeltaBor_E135_IgG_Rep3

description: Library name: IgG_Isotope_CS5415S_mm10_DeltaBor_HL_Rep3

value: Hindlimb

value: DeltaBor


title: Hindlimb_DeltaBor_E135_IgG_Rep4

description: Library name: IgG_Isotope_CS5415S_mm10_DeltaBor_HL_Rep4


title: BMC04997-004 MM CD38 8 weeks

description:
Library name: BMC04997-004
H5 file contains RNA expression matrix, tsv contains ADT cell surface protein capture

value: Male

value: MM CD38 8 weeks


title: BMC04438-006 MM CD38 8 weeks

description:
Library name: BMC04438-006
H5 file contains RNA expression matrix, tsv contains ADT cell surface protein capture

value: FALSE


title: Hindlimb_DeltaBor_E135_IgG_Rep2

description: Library name: IgG_Isotope_CS5415S_mm10_DeltaBor_HL_Rep2


title: BMC04433-002 MM CD38 Progression

description:
Library name: BMC04433-002
H5 file contains RNA expression matrix, tsv contains ADT cell surface protein capture


title: Hindlimb_DeltaBor_E135_IgG_Rep1

description: Library name: IgG_Isotope_CS5415S_mm10_DeltaBor_HL_Rep1


title: Hindlimb_WT_E135_H3K9me3_Rep2

description: Library name: H3K9me3_AM39161_mm10_WT_HL_Rep2


title: BMC04432-005 MM CD38 Pre-treatment

description:
Library name: BMC04432-005
H5 file contains RNA expression matrix, tsv contains ADT cell surface protein capture

value: MM CD38 Pre-treatment


title: BMC04430-007 MM CD38 8 weeks

description:
Library name: BMC04430-007
H5 file contains RNA expression matrix, tsv contains ADT cell surface protein capture


title: Hindlimb_WT_E135_H3K9me3_Rep1

description: Library name: H3K9me3_AM39161_mm10_WT_HL_Rep1


title: Hindlimb_DeltaBor_E135_H3K9me3_Rep2

description: Library name: H3K9me3_AM39161_mm10_DeltaBor_HL_Rep2


title: BMC04429-001 MM CD38 8 weeks

description:
Library name: BMC04429-001
H5 file contains RNA expression matrix, tsv contains ADT cell surface protein capture


title: Hindlimb_DeltaBor_E135_H3K9me3_Rep1

description: Library name: H3K9me3_AM39161_mm10_DeltaBor_HL_Rep1


title: BMC02616-008 MM CD38 Pre-treatment

description:
Library name: BMC02616-008
H5 file contains RNA expression matrix, tsv contains ADT cell surface protein capture


title: Hindlimb_WT_E135_H3K9me2_Rep4

description: Library name: H3K9me2_ab1220_mm10_WT_HL_Rep4


title: BMC02615-007 MM CD38 8 weeks

description:
Library name: BMC02615-007
H5 file contains RNA expression matrix, tsv contains ADT cell surface protein capture


title: Hindlimb_WT_E135_H3K9me2_Rep3

description: Library name: H3K9me2_ab1220_mm10_WT_HL_Rep3


title: BMC02614-001 MM CD38 Pre-treatment

description:
Library name: BMC02614-001
H5 file contains RNA expression matrix, tsv contains ADT cell surface protein capture

value: Other


title: Hindlimb_WT_E135_H3K9me2_Rep2

description: Library name: H3K9me2_ab1220_mm10_WT_HL_Rep2


title: BMC02610-001 MM CD38 Pre-treatment

description:
Library name: BMC02610-001
H5 file contains RNA expression matrix, tsv contains ADT cell surface protein capture

value: Asian


title: Hindlimb_WT_E135_H3K9me2_Rep1

description: Library name: H3K9me2_ab1220_mm10_WT_HL_Rep1


title: Hindlimb_DeltaBor_E135_H3K9me2_Rep4

description: Library name: H3K9me2_ab1220_mm10_DeltaBor_HL_Rep4


title: BMC02608-002 MM CD38 Pre-treatment

description:
Library name: BMC02608-002
H5 file contains RNA expression matrix, tsv contains ADT cell surface protein capture


title: Hindlimb_DeltaBor_E135_H3K9me2_Rep3

description: Library name: H3K9me2_ab1220_mm10_DeltaBor_HL_Rep3


title: BMC02607-005 MM CD38 8 weeks

description:
Library name: BMC02607-005
H5 file contains RNA expression matrix, tsv contains ADT cell surface protein capture


title: BMC02609-010 MM CD38 Pre-treatment

description:
Library name: BMC02609-010
H5 file contains RNA expression matrix, tsv contains ADT cell surface protein capture


title: BMC02606-004 MM CD38 Pre-treatment

description:
Library name: BMC02606-004
H5 file contains RNA expression matrix, tsv contains ADT cell surface protein capture


title: BMC04749-02-001 MM Post Transplant 1 year

description:
Library name: BMC04749-02-001
H5 file contains RNA expression matrix, tsv contains ADT cell surface protein capture

value: MM Post Transplant 1 year


title: Hindlimb_DeltaBor_E135_H3K9me2_Rep2

description: Library name: H3K9me2_ab1220_mm10_DeltaBor_HL_Rep2


title: Hindlimb_DeltaBor_E135_H3K9me2_Rep1

description: Library name: H3K9me2_ab1220_mm10_DeltaBor_HL_Rep1


title: Hindlimb_WT_E135_H3K27me3_Rep2

description: Library name: H3K27me3_CS9733_mm10_WT_HL_Rep2

value: WT


title: BMC02612-01 MM Pre-Treatment

description:
Library name: BMC02612-01
H5 file contains RNA expression matrix, tsv contains ADT cell surface protein capture

value: Bone Marrow

value: MM Pre-Treatment


title: Hindlimb_WT_E135_H3K27me3_Rep1

description: Library name: H3K27me3_CS9733_mm10_WT_HL_Rep1


title: BMC02419-01 MM Pre-Treatment

description:
Library name: BMC02419-01
H5 file contains RNA expression matrix, tsv contains ADT cell surface protein capture

value: BMMC


title: Hindlimb_DeltaBor_E135_H3K27me3_Rep2

description: Library name: H3K27me3_CS9733_mm10_DeltaBor_HL_Rep2


title: BMC06488-001 MM Post Transplant 90 Days

description:
Library name: BMC06488-001
H5 file contains RNA expression matrix, tsv contains ADT cell surface protein capture

value: MM Post Transplant 90 Days


title: Hindlimb_DeltaBor_E135_H3K27me3_Rep1

description: Library name: H3K27me3_CS9733_mm10_DeltaBor_HL_Rep1


title: BMC06487-009 MM Post Transplant 2 year

description:
Library name: BMC06487-009
H5 file contains RNA expression matrix, tsv contains ADT cell surface protein capture

value: Caucasian

value: MM Post Transplant 2 year


title: BMC06486-009 MM Post Transplant 2 year

description:
Library name: BMC06486-009
H5 file contains RNA expression matrix, tsv contains ADT cell surface protein capture

value: Female


title: Hindlimb_WT_E135_H3K27ac_Rep2

description: Library name: H3K27ac_AM39685_mm10_WT_HL_Rep2

value: Hindlimb


title: Hindlimb_WT_E135_H3K27ac_Rep1

description: Library name: H3K27ac_AM39685_mm10_WT_HL_Rep1


title: BMC06485-002 MM End Induction 1st Draw

description:
Library name: BMC06485-002
H5 file contains RNA expression matrix, tsv contains ADT cell surface protein capture

value: MM End Induction 1st Draw


title: Hindlimb_DeltaBor_E135_H3K27ac_Rep2

description: Library name: H3K27ac_AM39685_mm10_DeltaBor_HL_Rep2

value: DeltaBor


title: BMC06483-001 MM Post Transplant 1 year

description:
Library name: BMC06483-001
H5 file contains RNA expression matrix, tsv contains ADT cell surface protein capture

value: Male

value: African American


title: Hindlimb_DeltaBor_E135_H3K27ac_Rep1

description: Library name: H3K27ac_AM39685_mm10_DeltaBor_HL_Rep1


title: BMC05004-009 MM Post Transplant 90 Days

description:
Library name: BMC05004-009
H5 file contains RNA expression matrix, tsv contains ADT cell surface protein capture

value: FALSE


title: BMC05002-003 MM Pre-Treatment

description:
Library name: BMC05002-003
H5 file contains RNA expression matrix, tsv contains ADT cell surface protein capture


title: Normal male mouse 3 ATAC

city: Kansas City

first: Kaela

middle: Margaret

last: Varberg

state: MO

address: 2401 Gillham Road; CMRI 7902.19

department: Pediatrics

institute: Children's Mercy

description: Library name: 10x_mousebrain_RA2_M1_scmxATAC

library_source: genomic single cell

data_processing:
Fastq files were processed using cellranger-arc count pipeline
cellranger-arc counts QCed, normalized via SCTransform, and merged to create joint RNA/ATAC dataset using Seurat/Signac software
Cells annotated with cell type via label transfer using the 2023 mouse brain atlas provided by the Allen Institute
RNA and ATAC data used to construct regulatory TF networks using IReNA software
Assembly: mm10

source_name: Brain

growth_protocol: C57BL/6 mouse pups were exposed to hyperoxia (85% O₂) or room air from postnatal days 1–14. The prefrontal cortices were dissected on postnatal day 14.

extract_protocol:
Nucleus were isolated from 40-50 mg of flash-frozen mouse brain tissue using the Chromium Nucleus Isolation Kit with RNase Inhibitor (PN-1000494, 10x Genomics, Pleasanton, CA, USA) according to the manufacturer’s protocol, with a final nucleus resuspension volume of 100 µL.
Single-nucleus partitioning was performed using a Chromium Controller (10x Genomics). snATAC-seq and GEX libraries were prepared using the Chromium Next GEM Single Nucleus Multiome ATAC + Gene Expression Reagent Bundle (PN-1000283, 10x Genomics) following the manufacturer’s protocol, and libraries were sequenced on a NovaSeq 6000 Xp (Illumina, San Diego, CA, USA).

value: Brain

tag: strain

tag: treatment

value: control


title: Normal male mouse 3 GEX

description: Library name: 10x_mousebrain_RA2_M1_scmxGEX


title: Normal male mouse 2 ATAC

description: Library name: 10x_mousebrain_RA1_M_scmxATAC


title: BMC04996-003 MM Post Transplant 90 Days

description:
Library name: BMC04996-003
H5 file contains RNA expression matrix, tsv contains ADT cell surface protein capture

value: Other


title: BMC04998-003 MM Post Transplant 2 year

description:
Library name: BMC04998-003
H5 file contains RNA expression matrix, tsv contains ADT cell surface protein capture


title: BMC04995-001 MM End Induction 1st Draw

description:
Library name: BMC04995-001
H5 file contains RNA expression matrix, tsv contains ADT cell surface protein capture


title: Normal male mouse 2 GEX

description: Library name: 10x_mousebrain_RA1_M_scmxGEX


title: Normal male mouse 1 ATAC

description: Library name: 10x_mousebrain_RA_M_scmxATAC


title: BMC04994-003 MM Post Transplant 2 year

description:
Library name: BMC04994-003
H5 file contains RNA expression matrix, tsv contains ADT cell surface protein capture


title: BMC04970-001 MM End Induction 1st Draw

description:
Library name: BMC04970-001
H5 file contains RNA expression matrix, tsv contains ADT cell surface protein capture


title: Hyperoxia male mouse 3 ATAC

description: Library name: 10x_mousebrain_O2-2_M3_scmxATAC

value: hyperoxia


title: BMC04969-009 MM Post Transplant 1 year

description:
Library name: BMC04969-009
H5 file contains RNA expression matrix, tsv contains ADT cell surface protein capture

value: Bone Marrow

value: MM Post Transplant 1 year


title: BMC04968-007 MM Pre-Treatment

description:
Library name: BMC04968-007
H5 file contains RNA expression matrix, tsv contains ADT cell surface protein capture

value: BMMC

value: MM Pre-Treatment


title: Hyperoxia male mouse 2 ATAC

description: Library name: 10x_mousebrain_O2-2_M2_scmxATAC


title: Hyperoxia male mouse 3 GEX

description: Library name: 10x_mousebrain_O2-2_M3_scmxGEX


title: BMC04966-004 MM Pre-Treatment

description:
Library name: BMC04966-004
H5 file contains RNA expression matrix, tsv contains ADT cell surface protein capture


title: Hyperoxia male mouse 2 GEX

description: Library name: 10x_mousebrain_O2-2_M2_scmxGEX


title: BMC04967-003 MM Post Transplant 2 year

description:
Library name: BMC04967-003
H5 file contains RNA expression matrix, tsv contains ADT cell surface protein capture

value: Caucasian


title: BMC04964-006 MM Post Transplant 90 Days

description:
Library name: BMC04964-006
H5 file contains RNA expression matrix, tsv contains ADT cell surface protein capture

value: MM Post Transplant 90 Days


title: Hyperoxia male mouse 1 ATAC

description: Library name: 10x_mousebrain_O2-1_M4_scmxATAC


title: BMC04963-008 MM End Induction 1st Draw

description:
Library name: BMC04963-008
H5 file contains RNA expression matrix, tsv contains ADT cell surface protein capture


title: Hyperoxia male mouse 1 GEX

description: Library name: 10x_mousebrain_O2-1_M4_scmxGEX


title: Normal female mouse 3 ATAC

description: Library name: 10x_mousebrain_RA-1_F4_scmxATAC


title: BMC04962-006 MM Pre-Treatment

description:
Library name: BMC04962-006
H5 file contains RNA expression matrix, tsv contains ADT cell surface protein capture


title: Normal female mouse 3 GEX

description: Library name: 10x_mousebrain_RA-1_F4_scmxGEX


title: BMC04961-009 MM Post Transplant 90 Days

description:
Library name: BMC04961-009
H5 file contains RNA expression matrix, tsv contains ADT cell surface protein capture

value: Female


title: BMC04757-010 MM Post Transplant 2 year

description:
Library name: BMC04757-010
H5 file contains RNA expression matrix, tsv contains ADT cell surface protein capture

value: MM Post Transplant 2 year


title: Normal female mouse 2 ATAC

description: Library name: 10x_mousebrain_RA-1_F3_scmxATAC


title: BMC04756-010 MM Post Transplant 1 year

description:
Library name: BMC04756-010
H5 file contains RNA expression matrix, tsv contains ADT cell surface protein capture


title: Normal female mouse 2 GEX

description: Library name: 10x_mousebrain_RA-1_F3_scmxGEX


title: Normal female mouse 1 ATAC

description: Library name: 10x_mousebrain_RA-1_F1_scmxATAC


title: BMC04755-001 MM Post Transplant 1 year

description:
Library name: BMC04755-001
H5 file contains RNA expression matrix, tsv contains ADT cell surface protein capture


title: Normal female mouse 1 GEX

description: Library name: 10x_mousebrain_RA-1_F1_scmxGEX


title: BMC04754-010 MM Post Transplant 2 year

description:
Library name: BMC04754-010
H5 file contains RNA expression matrix, tsv contains ADT cell surface protein capture


title: Hyperoxia female mouse 3 ATAC

description: Library name: 10x_mousebrain_O2-2_F2_scmxATAC


title: BMC04753-009 MM Post Transplant 1 year

description:
Library name: BMC04753-009
H5 file contains RNA expression matrix, tsv contains ADT cell surface protein capture


title: Hyperoxia female mouse 3 GEX

description: Library name: 10x_mousebrain_O2-2_F2_scmxGEX


title: BMC04752-008 MM Post Transplant 1 year

description:
Library name: BMC04752-008
H5 file contains RNA expression matrix, tsv contains ADT cell surface protein capture


title: Hyperoxia female mouse 2 ATAC

description: Library name: 10x_mousebrain_O2-1_F2_scmxATAC


title: Hyperoxia female mouse 2 GEX

description: Library name: 10x_mousebrain_O2-1_F2_scmxGEX


title: BMC04751-003 MM Post Transplant 1 year

description:
Library name: BMC04751-003
H5 file contains RNA expression matrix, tsv contains ADT cell surface protein capture


title: BMC04750-005 MM Post Transplant 1 year

description:
Library name: BMC04750-005
H5 file contains RNA expression matrix, tsv contains ADT cell surface protein capture


title: Hyperoxia female mouse 1 ATAC

description: Library name: 10x_mousebrain_O2-1_F1_scmxATAC


title: BMC04748-006 MM Post Transplant 1 year

description:
Library name: BMC04748-006
H5 file contains RNA expression matrix, tsv contains ADT cell surface protein capture


title: Hyperoxia female mouse 1 GEX

description: Library name: 10x_mousebrain_O2-1_F1_scmxGEX


title: BMC04707-003 MM Pre-Treatment

description:
Library name: BMC04707-003
H5 file contains RNA expression matrix, tsv contains ADT cell surface protein capture


title: BMC04437-005 MM End Induction 1st Draw

description:
Library name: BMC04437-005
H5 file contains RNA expression matrix, tsv contains ADT cell surface protein capture

value: MM End Induction 1st Draw


title: TQ6,Ctrl-CAR-T,replicate 3

city: Guangzhou, China

first: Xiaoyun

last: Luo

state: Guangdong

address: No. 9 XingDaoHuanBei Road, Guangzhou International Bio Island, Guangzhou 510005, Guangdong Province, China

country: China

institute: Guangzhou National Laboratory

description:
Library name: Sample 12
10x Genomics

data_processing:
Raw reads were processed using Cell Ranger (10x Genomics v7.1.0) for demultiplexing, alignment to the reference genome(GRCm38), barcode assignment, and UMI counting. Gene expression matrices and TCR clonotype information were generated using the Cell Ranger count and vdj pipelines, respectively. Downstream analyses including quality control, normalization, dimensionality reduction, clustering, and visualization were performed using Seurat(v4.3.0) in R(v4.1.2).
Assembly: GRCm38
Supplementary files format and content: Processed data files include filtered gene expression matrices, and TCR clonotype annotation files generated by the Cell Ranger vdj pipeline.
Library strategy: TCR-Seq

source_name: CD45+ cells

extract_protocol:
Fresh tissues were immediately used to prepare their single cell suspension. Briefly, the collected fresh tissue was washed by DPBS (PBS without calcium and magnesium) and carefully chopped into small pieces. Enzymatic digestion was performed with collagenase I (2 mg/mL), collagenase II (2 mg/mL), collagenase IV (2 mg/mL) and dispase (0.2 mg/mL) under 37 °C for 15-25 minutes. The digested solution was transferred to a centrifuge tube through a 40 μm stainless nylon mesh (Greiner Bio-OneGmbH, Germany). The filtrate was immediately centrifuged at 500 g for 5 min, and discarded the supernatant slowly. The cell sediment was resuspended and lysis with RBC Lysis buffer on ice for 5 min to remove red blood cells, and then washed with DPBS at 400 g for 5 min twice. Cell concentration and viability were determined on a Cellometer Auto 2000 (nexcelom, USA) after AO/PI staining. Immediately after dissociation, cells were resuspended in FACS buffer (5% FBS in PBS) and Fc-blocked for 10 min. This was followed by a wash and staining with anti-CD45 PE (BioLegend; San Diego, CA) for 30 min in sorting buffer (0.1% BSA in PBS) at 4 °C. After washing, viable CD45+  cells were sorted using the BDFACSAria Ⅲ. Subsequently, the cells were washed twice and re-suspended in a sorting buffer. A cell number and viability count were performed on a Cellometer Auto 2000 using the ViaStain™ AOPI Staining Solution (Nexcelom Bioscience LLC, Lawrence, MA, USA) immediately prior to scRNAseq.
Library was performed according to the manufacter's instructions (single cell 5' v2 protocol, 10x Genomics). Briefly, single-cell suspensions were resuspended in the master mix andloaded together with partitioning oil and gel beads into the chip to generate the gelbead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in everysingle GEM was retrotranscripted to cDNA, which contains an llumina R1 primersequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooledbarcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR andthe apropiated sized fragments were selected with SPRIselect reagent forsubsequent library construction. During the library construction llumina R2 primersequence, paired-end constructs with P5 and P7 sequences and a sample indexwere added.

treatment_protocol: C57BL/6J mice were inoculated subcutaneously with 1 × 10⁶ MC38-Trop2 tumor cells (n = 3 / group). At 14 d, 1×106 Ctrl-CAR-T or 3P7-CAR-T cells were injected intravenously without CY pretreatment. On day 21, tumor-infiltrating lymphocytes were harvested, and live CD45⁺ FVS700⁻ cells isolated from the tumors were sorted and subjected to single‑cell RNA sequencing and TCR sequencing seqanalysis.

tag: cell line

value: CD45+ cells

value: Primary cells

value: WT

value: Ctrl-CAR-T

tag: age

value: 8 weeks old

tag: host stain


title: BMC04436-007 MM End Induction 1st Draw

description:
Library name: BMC04436-007
H5 file contains RNA expression matrix, tsv contains ADT cell surface protein capture

tag: tissue

value: FALSE


title: TQ5,Ctrl-CAR-T,replicate 2

description:
Library name: Sample 11
10x Genomics


title: TQ4,Ctrl-CAR-T,replicate 1

description:
Library name: Sample 10
10x Genomics


title: TQ3,3P7-CAR-T,replicate 3

description:
Library name: Sample 9
10x Genomics


title: BMC04435-009 MM End Induction 1st Draw

description:
Library name: BMC04435-009
H5 file contains RNA expression matrix, tsv contains ADT cell surface protein capture


title: BMC04431-002 MM Pre-Treatment

description:
Library name: BMC04431-002
H5 file contains RNA expression matrix, tsv contains ADT cell surface protein capture

value: Male

value: Other


title: BMC04434-007 MM Post Transplant 1 year

description:
Library name: BMC04434-007
H5 file contains RNA expression matrix, tsv contains ADT cell surface protein capture

value: Bone Marrow


title: TQ1,3P7-CAR-T,replicate 1

description:
Library name: Sample 7
10x Genomics


title: TQ2,3P7-CAR-T,replicate 2

description:
Library name: Sample 8
10x Genomics


title: BMC02620-002 MM Post Transplant 90 Days

description:
Library name: BMC02620-002
H5 file contains RNA expression matrix, tsv contains ADT cell surface protein capture


title: CQH6,Ctrl-CAR-T,replicate 3

description:
Library name: Sample 6
10x Genomics

data_processing:
Raw reads were processed using Cell Ranger (10x Genomics v7.1.0) for demultiplexing, alignment to the reference genome(GRCm38), barcode assignment, and UMI counting. Gene expression matrices and TCR clonotype information were generated using the Cell Ranger count and vdj pipelines, respectively. Downstream analyses including quality control, normalization, dimensionality reduction, clustering, and visualization were performed using Seurat(v4.3.0) in R(v4.1.2).
Assembly: GRCm38
Supplementary files format and content: Processed data files include filtered gene expression matrices, and TCR clonotype annotation files generated by the Cell Ranger vdj pipeline.


title: BMC02619-003 MM End Induction 1st Draw

description:
Library name: BMC02619-003
H5 file contains RNA expression matrix, tsv contains ADT cell surface protein capture


title: CQH5,Ctrl-CAR-T,replicate 2

description:
Library name: Sample 5
10x Genomics


title: BMC02617-002 MM Post Transplant 90 Days

description:
Library name: BMC02617-002
H5 file contains RNA expression matrix, tsv contains ADT cell surface protein capture


title: CQH4,Ctrl-CAR-T,replicate 1

description:
Library name: Sample 4
10x Genomics


title: BMC02618-008 MM Post Transplant 90 Days

description:
Library name: BMC02618-008
H5 file contains RNA expression matrix, tsv contains ADT cell surface protein capture


title: BMC02613-010 MM Pre-Treatment

description:
Library name: BMC02613-010
H5 file contains RNA expression matrix, tsv contains ADT cell surface protein capture


title: CQH3,3P7-CAR-T,replicate 3

description:
Library name: Sample 3
10x Genomics


title: CQH2,3P7-CAR-T,replicate 2

description:
Library name: Sample 2
10x Genomics


title: BMC02611-009 MM Pre-Treatment

description:
Library name: BMC02611-009
H5 file contains RNA expression matrix, tsv contains ADT cell surface protein capture

value: African American


title: BMC02605-005 MM End Induction 1st Draw

description:
Library name: BMC02605-005
H5 file contains RNA expression matrix, tsv contains ADT cell surface protein capture

value: BMMC


title: CQH1,3P7-CAR-T,replicate 1

description:
Library name: Sample 1
10x Genomics


title: BMC02603-006 MM Pre-Treatment

description:
Library name: BMC02603-006
H5 file contains RNA expression matrix, tsv contains ADT cell surface protein capture

value: MM Pre-Treatment


title: BALB CRS  Group No.13

city: Saga city

first: Taiga

last: Kurihara

state: Saga (佐賀県)

address: 5-1-1 Nabeshima

country: Japan

institute: Saga University

description: Library name: BALB CRS 13

data_processing:
Raw reads with low quality and adapter sequences were removed using Cutadapt v.2.9.
Raw FASTQ files were processed for transcript quantification using Salmon. Transcript-level abundance estimates were summarized into gene-level expression matrices for downstream analyses.
Assembly: GRCm38
Supplementary files format and content: Processed data files are tab-delimited text files containing gene-level normalized expression values generated from Salmon quantification.

source_name: medial prefrontal cortex

growth_protocol: Mice were housed under standard laboratory conditions (24°C, 40–60% humidity, 12-h light/dark cycle) with food and water available ad libitum. Mice were acclimated for 1 week before experiments. Mice aged 9–10 weeks were used for RNA-seq experiments.

extract_protocol:
After completion of behavioral testing, mice were sacrificed and medial prefrontal cortex (mPFC) tissue was collected using a 1.5-mm tissue punch from coronal brain sections (+2.0 to +1.5 mm from bregma). Total RNA was extracted using TRIzol reagent (Thermo Fisher Scientific) according to the manufacturer’s instructions.
Libraries were prepared using the TruSeq Stranded mRNA Library Preparation Kit (Illumina) according to the manufacturer’s protocol. Sequencing was performed on an Illumina NovaSeq 6000 platform with paired-end 150 bp reads to achieve a coverage of approximately 6 Gb per sample.

treatment_protocol: Mice were assigned to control or chronic restraint stress (CRS) groups. CRS mice were restrained in their home cages using polyethylene restrainers for 6 h per day for 21 consecutive days. Control mice were handled similarly without restraint stress.

value: medial prefrontal cortex

value: BALB/cCrSlc

value: CRS


title: BALB CRS  Group No.15

description: Library name: BALB CRS 15


title: Normal male mouse 1 GEX

description: Library name: 10x_mousebrain_RA_M_scmxGEX

value: Brain

value: control


title: BMC02601-003 MM Post Transplant 90 Days

description:
Library name: BMC02601-003
H5 file contains RNA expression matrix, tsv contains ADT cell surface protein capture

value: Caucasian

value: MM Post Transplant 90 Days


title: BALB Control  Group No.10

description: Library name: BALB Control 10

value: Control


title: BMC02600-006 MM End Induction 1st Draw

description:
Library name: BMC02600-006
H5 file contains RNA expression matrix, tsv contains ADT cell surface protein capture

value: MM End Induction 1st Draw


title: BALB CRS  Group No.12

description: Library name: BALB CRS 12


title: BMC02599-003 MM Post Transplant 90 Days

description:
Library name: BMC02599-003
H5 file contains RNA expression matrix, tsv contains ADT cell surface protein capture

value: Female


title: BALB Control  Group No.9

description: Library name: BALB Control 9


title: BMC02596-008 MM Post Transplant 90 Days

description:
Library name: BMC02596-008
H5 file contains RNA expression matrix, tsv contains ADT cell surface protein capture

value: FALSE


title: BMC02597-003 MM End Induction 1st Draw

description:
Library name: BMC02597-003
H5 file contains RNA expression matrix, tsv contains ADT cell surface protein capture

value: Male


title: BALB Control  Group No.5

description: Library name: BALB Control 5


title: B6 CRS Group No.14

description: Library name: B6 CRS 14


title: BMC02595-009 MM End Induction 1st Draw

description:
Library name: BMC02595-009
H5 file contains RNA expression matrix, tsv contains ADT cell surface protein capture


title: B6 CRS Group No.13

description: Library name: B6 CRS 13


title: BMC02594-006 MM Pre-Treatment

description:
Library name: BMC02594-006
H5 file contains RNA expression matrix, tsv contains ADT cell surface protein capture


title: B6 CRS Group No.12

description: Library name: B6 CRS 12


title: BMC02441-003 MM Pre-Treatment

description:
Library name: BMC02441-003
H5 file contains RNA expression matrix, tsv contains ADT cell surface protein capture


title: B6 Control  Group No.9

description: Library name: B6 Control 9


title: BMC02439-004 MM Pre-Treatment

description:
Library name: BMC02439-004
H5 file contains RNA expression matrix, tsv contains ADT cell surface protein capture


title: B6 Control  Group No.3

description: Library name: B6 Control 3


title: BMC02438-002 MM End Induction 1st Draw

description:
Library name: BMC02438-002
H5 file contains RNA expression matrix, tsv contains ADT cell surface protein capture

value: Other


title: B6 Control  Group No.2

description: Library name: B6 Control 2


title: BMC02437-002 MM Pre-Treatment

description:
Library name: BMC02437-002
H5 file contains RNA expression matrix, tsv contains ADT cell surface protein capture

value: Bone Marrow


title: BMC02436-003 MM Pre-Treatment

description:
Library name: BMC02436-003
H5 file contains RNA expression matrix, tsv contains ADT cell surface protein capture


title: 4T1 cells, P3FI-90, rep2

city: Jinan

first: Wenhao

last: Li

address: Wenhua Xi Road No. 107

institute: Qilu Hospital of Shandong University

description:
Library name: Sample 5
Column name in readout count.txt: P3FI90_2

data_processing:
The raw image data files obtained from high-throughput sequencing are converted into raw sequencing data through CASAVA base calling analysis.
Reads were discarded if they were shorter than 100 bp after adaptor and low-quality base trimming, contained more than 10 N bases, or had over 40% of bases with a quality score <= 30 in a single-end read.
Clean reads were aligned to the reference genome using Hisat2, which provided the alignment positions on the genome or genes, along with sequence features specific to each sample.
Following aligment, the read counts for each gene were quantified based on genomic coordinates.
StringTie was employed to estimate gene expression levels, and the expression values were normalized using FPKM.
Assembly: GRCm39
Supplementary files format and content: xlsx files include FPKM values for each sample
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

growth_protocol: 4T1 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37°C.

extract_protocol:
Total RNA was harvested using TRIzol reagent (Invitrogen).
Transcriptome libraries were prepared using the Illumina mRNA–Seq Sample Preparation Kit. The libraries were qualified and quantified using an Agilent 2100 bioanalyzer and then sequenced on the Illumina Novaseq 6000 platform.

treatment_protocol: 4T1 cells were treated with DMSO or P3FI-90 (10 μM) for 24 h.

value: mouse mammary gland epithelial cancer cell


title: BMC02435-002 MM Post Transplant 90 Days

description:
Library name: BMC02435-002
H5 file contains RNA expression matrix, tsv contains ADT cell surface protein capture

value: BMMC


title: 4T1 cells, P3FI-90, rep3

description:
Library name: Sample 6
Column name in readout count.txt: P3FI90_3


title: 4T1 cells, P3FI-90, rep1

description:
Library name: Sample 4
Column name in readout count.txt: P3FI90_1


title: BMC02434-001 MM Pre-Treatment

description:
Library name: BMC02434-001
H5 file contains RNA expression matrix, tsv contains ADT cell surface protein capture

value: MM Pre-Treatment


title: BMC02433-002 MM End Induction 1st Draw

description:
Library name: BMC02433-002
H5 file contains RNA expression matrix, tsv contains ADT cell surface protein capture


title: 4T1 cells, DMSO, rep3

description:
Library name: Sample 3
Column name in readout count.txt: DMSO_3

value: DMSO


title: 4T1 cells, DMSO, rep2

description:
Library name: Sample 2
Column name in readout count.txt: DMSO_2


title: BMC02432-002 MM Pre-Treatment

description:
Library name: BMC02432-002
H5 file contains RNA expression matrix, tsv contains ADT cell surface protein capture


title: 4T1 cells, DMSO, rep1

description:
Library name: Sample 1
Column name in readout count.txt: DMSO_1


title: BMC02431-002 MM Post Transplant 90 Days

description:
Library name: BMC02431-002
H5 file contains RNA expression matrix, tsv contains ADT cell surface protein capture


title: SHAM,DAY3,SAMPLE2

city: guangzhou

first: Fanning

last: Zeng

address: Nanshitou Street, Haizhu District

department: Department of Anesthesiology

institute: Zhujiang hospital, Southern Medical University

description: Library name: SHAM,DAY3,SAMPLE2

data_processing:
Raw gene expression matrices generated per sample using CellRanger were imported into R (version 4.0.0) and converted to a Seurat object using the Seurat R package (version 4.1.0)41. Dead cells and doublets were removed. The first, the total number of UMIs and genes, and percentage of UMIs derived from mitochondrial genome for each cell were counted. Then, Cells which had over 15% UMIs derived from mitochondrial genome were discarded. Next, the upper bound was calculated as mean plus two standard deviation (SD) and the lower bound as mean minus two SD for both the total UMIs and genes, respectively. Finally, Cells with total UMIs or genes outside of the upper and lower bounds were removed.
Assembly: Mouse mm10
Supplementary files format and content: Tab-separated values files and matrix fles

source_name: hippocampus

extract_protocol:
After successful establishment of the SNI model, mice were randomly selected for tissue sampling. The whole fresh hippocampus tissues were placed in sterile petri dishes and rinsed with 10 mL of 4 °C pre-chilled DPBS, repeated 1-2 times to remove residual tissue protection solution. The rinsed tissues were placed in a new petri dish. After adding type II collagenase working solution, the tissues were cut into small pieces of about 1-2 mm3. The cut tissues were transferred to a 50 mL centrifuge tube containing 5 mL of digestion solution and placed in a 37 °C water bath for shaking and digestion. After digestion, the digest was filtered through a pre-wetted 70 μm cell sieve. Thereafter, the filtrate was collected into a new 50 mL centrifuge tube. After washing with 10 mL of DPBS containing 2% FBS, the filtrate was collected into the same centrifuge tube. Following centrifugation at 900 g for 30 min at room temperature, the supernatant was discarded. The pellet was added to 5 mL of DPBS containing 2% FBS, and the cells were resuspended by gentle pipetting and mixing. After centrifugation and the supernatant discarded, 3 mL of pre-chilled red blood cell lysate was added to the cell pellet and incubated at room temperature for 3 min. After discarding the supernatant, the pellet was added to 5 mL of pre-chilled DPBS containing 2% FBS. The cell suspension was stained by trypan blue and was counted using Countess® II Cell Counting. If the cell viability was more than 80%, 10× Genomics sample processing was carried out.
The prepared cell suspension, 10× barcode gel magnetic beads and oil were added to different chambers of Chromium Chip B respectively, and Gel Beads-Emulsion (GEM) was formed through the microfluidic cross system. The GEM was transferred to the PCR machine for reverse transcription, with 30 nt oligo-dT reverse transcription primers on the gel magnetic beads. The poly-A RNA in cells was reverse transcribed into first strand cDNA with barcode and unique molecular identifiers (UMI) information. After magnetic bead purification of first-strand cDNA, the cDNA was amplified by RT-PCR. Afterwards, amplified cDNA was digested and fragmented, and the optimal fragment was screened with magnetic beads. The cDNA library containing P5 and P7 adapters was prepared by end-repairing, adding A, and connecting Read 2 sequencing primers with adapters. Following purification, the concentration of cDNA was measured using Qubit and fragment size was measured using Agilent 2100.The libraries were sequenced on Novaseq 6000.

value: hippocampus

value: ALL CELL

value: SHAM


title: BMC02430-003 MM Pre-Treatment

description:
Library name: BMC02430-003
H5 file contains RNA expression matrix, tsv contains ADT cell surface protein capture


title: SHAM,DAY7,SAMPLE1

description: Library name: SHAM,DAY7,SAMPLE1


title: BMC02429-001 MM Post Transplant 90 Days

description:
Library name: BMC02429-001
H5 file contains RNA expression matrix, tsv contains ADT cell surface protein capture


title: SNI,DAY21,SAMPLE3

description: Library name: SNI,DAY21,SAMPLE3

value: SNI


title: SNI,DAY21,SAMPLE2

description: Library name: SNI,DAY21,SAMPLE2