title: GDF11 3H treatment 2

description: Library name: Sample 5


title: mESC Tet1/2/3 TKO, PyBo, rep2

status: Public on Oct 21 2025

type: SRA

city: Mainz

first: Alexandr

last: Gopanenko

address: Ackermannweg 4

country: Germany

institute: Institute of Molecular Biology gGmbH (IMB)

description:
Library name: sample_8
total RNA, rRNA-depleted

library_source: transcriptomic

data_processing:
Raw read data were quality-assessed by FastQC (v.0.11.9, https://www.bioinformatics.babraham.ac.uk/projects/fastqc/). Alignment to the reference genome was performed using STAR (v. 2.7.10a) allowing soft-clipping with non-default parameters: --outFilterScoreMinOverLread 0.33, --outFilterMatchNminOverLread 0.33 and --outFilterMismatchNoverReadLmax 0.02, that ensure mapping of overlapping reads and allowed for up to 2% of mismatches. The reference (GRCm39.dna_sm.primary_assembly.fa) was taken from https://ftp.ensembl.org/pub/release-107 and the genome index was generated using M.mus.GRCm39.107.gtf for annotation and --sjdbOverhang 99 (read length - 1).
C-to-T events were identified using JACUSA2 (v.2.0.4) applying 2 conditions mode (call-2, PyBo/Mal vs mock), scanning only positions with coverage >5 reads (-c 5), minimum base quality > 20 (-q 20) and mapping quality > 20 (-m 20), taking into account rev-strand specificity of the libraries (P RF-FIRSTSTRAND) and using bam files with only uniquely mapped reads as an input. Shortly, to identify PyBo/Mal-induced C-to-T events for Tet1/2/3 or Alkbh1 CTRL samples, we applied the following filtering criteria for raw JACUSA2 output files: 1) JACUSA2 score >2, 2) C-to-T conversion level > 5% in each of 3 replicate of PyBo/Mal-treated sample, 3) ≥ 5 reads (average of 3 replicates) supporting mismatched T in PyBo/Mal-treated samples, and 4) C-to-T conversion level < 2% in each of 3 replicate of mock-treated samples, and less <5 reads (average of 3 replicates) supporting mismatched T in mock-treated samples. The C-to-T events that passed filtering were annotated with hiAnnotator (v. 1.34.0) using Mus_musculus.GRCm39.107.gtf as a gene model. In cases when the C-to-T site overlapped with multiple transcripts, we employed the following strategy to clarify the transcript annotation. Firstly, the gene with the correct orientation for the C-to-T site and the highest expression level was selected. Secondly, the transcript variant was selected with the following prioritization: (1) highest expression (2) marked as canonical and (3) the longest transcript variant. The transcript expression level was determined using kallisto (v. 0.44.0).
Assembly: GRCm39 (mm39)
Supplementary files format and content: bedGraph; shared C-to-T events observed in CTRL samples detected by PyBo-assisted RNA-seq

molecule: total RNA

organism: Mus musculus

source_name: mouse embryonic stem cells

growth_protocol: mESC clones were cultured on tissue culture plates coated with 0.1% gelatin solution in 2i medium (50% Neurobasal and 50% DMEM/F-12 medium, supplemented with 1x N2, 1x B27, 2 mM L-Glutamine, 1000 U/ml Leukemia inhibitory factor, 100 U/ml Pen-Strep, 1 µM PD0325901, 3 µM CHIR99021 and 50 µg/ml BSA) at 37 °C in 5% CO2 and 20% O2.

extract_protocol:
Total RNA was isolated from cultured cells using QIAzol Lysis Reagent (Qiagen) according to the manufacturer’s protocol followed by TURBO DNase (Invitrogen) treatment and another round of QIAzol purification.
Ribosomal RNA was depleted using the NEBNext rRNA Depletion Kit v2 (human/Mouse/Rat) (NEB) following the manufacturer’s protocol and purified using the RNA Clean & Concentrator kit (Zymo Research). For PyBo-seq, 200 ng of RNA was incubated in 900 mM pyridine borane in 600 mM sodium acetate (pH 5.2) at 37°C for 24 hours. For Mal-seq, 200 ng of RNA was incubated in 150 mM malononitrile in 1x TE buffer (pH 7.4) at 37°C for 24 hours. For mock treated samples, water was added instead of chemicals.
For PyBo-seq of ribosomal RNA, total RNA was chemically fragmented to 120-180 nt-long fragments and PyBo-treated as described above.
RNA library preparation was performed using the TruSeq Stranded mRNA Library Prep kit (20020594, Illumina), entering the protocol at the RNA fragmentation step and excluding the poly(A) enrichment. 10 ng RNA was used as starting amount. Libraries were size-selected for >100 bp fragments.
Library construction of rRNA was done with the NEXTFLEX Small RNA-Seq Kit V3 (Bioo Scientific) following Step A to Step G of Bioo Scientific`s standard protocol (V19.01) using the NEXTFLEX 3’ SR Adaptor and 5’ SR Adaptor. Step A (NEXTFLEX 3` 4N Adenylated Adapter Ligation) was performed overnight at 20°C and for step F (Bead Cleanup) the modified protocol was used to retain small RNAs. Libraries were prepared with a starting amount of 1.4 ng RNA and amplified in 21 PCR cycles. Libraries were size-selected for 18 – 362 nt insert size.

tag: cell type

value: mouse embryonic stem cells

tag: genotype

value: Tet1/2/3 TKO

tag: treatment


title: LK Gfi1-tdTomato intermediate Csf1r- cell 66

city: Cincinnati

first: Nathan

last: Salomonis

state: OH

address: 3333 Burnet Avenue

department: Biomedical Informatics

country: USA

institute: Cincinnati Children's Hospital

description:
LK.Gfi_int_Csf1r_neg.CD150-.66
Fluidigm C1

data_processing:
Data analyses were performed as in PMID: 32494068.
Assembly: mm10
Supplementary files format and content: RSEM transcript per million estimates text file

source_name: Bone Marrow

extract_protocol:
Fluidigm C1 captures were performed as described in PMID: 32494068.
Library preperation was performed as described in PMID: 32494068.
Library strategy was performed as described in PMID: 32494068.

tag: tissue

value: Bone Marrow

value: WT

tag: protocol

value: paired-end


title: mESC Tet1/2/3 CTRL, PyBo, rep2

description:
Library name: sample_2
total RNA, rRNA-depleted

value: Tet1/2/3 wildtype


title: p20169.s031_101_PT10018

city: Boston

first: Dan

last: Barouch

state: MA

address: 3 Blackfan Cir

department: CVVR

institute: Beth Israel Deaconess Medical Center

data_processing:
Transcript abundance estimates were calculated internal to the STAR aligner using the algorithm of htseq-count(2). DESeq2 was used for normalization(3), producing a normalized read count.
Assembly: GRCh38
Supplementary files format and content: airis_countMatrix.csv
Supplementary files format and content: raw count matrix

organism: Homo sapiens

source_name: Blood

extract_protocol:
PBMCs were lysed in 700 L of Trizol and then extracted using the miRNeasy Mini kit (Qiagen) with on-column DNase digestion. RNA quality was assessed using a TapeStation 4200 (Agilent) and then ten nanograms of total RNA was used as input for cDNA synthesis using the Clontech SMART-Seq v4 Ultra Low Input RNA kit (Takara Bio) according to the manufacturer’s instructions.
Amplified cDNA was fragmented and appended with dual-indexed barcodes using the Nextera XT DNA Library Preparation kit (Illumina). Libraries were validated by capillary electrophoresis on a TapeStation 4200 (Agilent), pooled at equimolar concentrations, and sequenced with PE100 reads on an Illumina NovaSeq 6000, yielding ~30 million reads per sample on average. Alignment was performed using STAR version 2.7.3a(1)and transcripts were annotated using a composite genome reference which included GRCh38 Ensembl release 100 and SARS-CoV-2 (GCF_009858895.2, ASM985889v3, MN985325.1).

value: Blood

tag: pasc severity

value: mild


title: Healthy scalp skin sample 1

city: San Francisco

first: Jarish

last: Cohen

state: CA

address: 513 Parnassus Ave, HSW12 Room 1201B

department: Dermatology

institute: University of California, San Francisco

description:
Library name: HSS1
9736 cells detected

library_source: transcriptomic single cell

data_processing:
Cellranger 7.0.0 was used to demultiplex and count samples.
Assembly: GRCh38-2020-A
Supplementary files format and content: Filtered feature barcode matrices

molecule: nuclear RNA

source_name: healthy human scalp skin specimen

extract_protocol:
Formalin fixed, paraffin embedded tissue was dissociated and single nuclei were isolated using the standard 10x Genomics FLEX assay protocol. Each sample was pooled with additional samples following barcoding. Samples were run within separate batches.
The 10x Genomics Single Cell Gene Expression FLEX protocol was used for probe hybiridization and library construction according to the manufacter's instructions.

value: healthy human scalp skin specimen

tag: batch


title: mESC Tet1/2/3 CTRL, PyBo, rep1

description:
Library name: sample_1
total RNA, rRNA-depleted


title: LK Gfi1-tdTomato intermediate Csf1r- cell 64

description:
LK.Gfi_int_Csf1r_neg.CD150-.64
Fluidigm C1


title: p20169.s030_100_PT121

value: severe


title: Cartilage MPRA K562 replicate 4

city: Cambridge

first: Terence

last: Capellini

address: 11 Divinity Avenue

department: Human Evolutionary Biology

institute: Harvard University

description: Library name: 290k_Cartilage_cDNA_K562_rep4

data_processing:
Read merging using NGmerge v0.3
Read counts per barcode using MPRAmatch pipeline (https://github.com/tewhey-lab/MPRASuite/tree/main)
forward and reverse read merging using BBMap fuse.sh pad=100
match barcodes to oligos using MPRAcount pipeline, modified to avoid an error due to “%sequence mismatch” threshold by setting the value for all sequences below the standard threshold (https://github.com/tewhey-lab/MPRASuite/tree/main)
Differential expression between oligos was determined using MPRAmodel (https://github.com/tewhey-lab/MPRASuite/tree/main)
Assembly: hg38
Supplementary files format and content: count table of barcodes oligo pairs in each replicate as output by MPRAcount, attributes table, and condition table, for processing via MPRAmodel (https://github.com/tewhey-lab/MPRASuite/tree/main)

source_name: GFP mRNA

growth_protocol: K562 cells were grown with RPMI 1640 Complete Medium supplemented with  + 10% FBS + 1% Penicillin-Streptomycin, TC28a2 and CHON002 cells were grown with DMEM Dulbecco's Modified Eagle Medium supplemented  + 10% FBS + 1% Penicillin-Streptomycin

extract_protocol:
Pellets were defrosted before the addition of RLT buffer containing 2M DTT (40ul for every 1ml of RLT buffer for >2x10^8 cells). Pellets were disrupted using a 10 mL syringe and 21-gauge needle before the addition of equal amounts of 70% ethanol. Samples were then processed using the Qiagen Maxi RNeasy and following the isolation procedure instructions. RNA was nano dropped and stored at -80˚C.
Half of the RNA sample was taken for MPRA clean up processing and library generation whilst saving the remaining half. Samples underwent a 1-hour DNase digest at 37˚C to remove any contaminating DNA, particularly coming from the plasmid. Following this biotagged GFP primer probes (CGCCGTAGGTGAAGGTGGTCACGAGGGTGGGCCAG/3BioTEG/, CCAGGATGTTGCCGTCCTCCTTGAAGTCGATGCCC/3BioTEG/, CCTCGATGTTGTGGCGGGTCTTGAAGTTCACCTTG/3BioTEG/) were adhered to the GFP sequence of mRNA products using formamide cross linking (2.5 hours at 65˚C). This was followed by hybridization of streptavidin magnetic DynabeadsTM (15 mins, rtp, on nutator) that bind to the BioTEG portion of the probes now bound to the mRNA products of interest. Dynabeads were made RNase free prior to use following provided protocols. mRNA bound to Dynabeads was then isolated using a magnet to remove beads from the rest of the RNA containing solution in clean up stages followed by elution in 25ul of RNAse free water at both 70˚C and then 80˚C. To remove any remaining plasmid DNA, a further 1-hour 37˚C digest was performed before RNA SPRI bead cleanup (standard isolation and elution protocols) and performing first strand synthesis and reverse transcription (ThermoFisher Scientific, 18080044). Following reverse transcription, DNA SPRI was performed to remove any remaining reagents and concentrations checked using qPCR analysis. If CT value was below 18, samples were amplified at 2 cycles above their CT value before attaching unique illumina P5 and P7 adapter pairs. At this stage, four plasmid replicates were included and prepared for sequencing to assess library diversity representation for downstream processing. Samples were then assessed for concentration before pooling to form an equimolar pool. The resulting pool was sequenced five times on an Illumina NovaSeq X 10B flowcell to a depth of >125 million reads per replicate.

treatment_protocol: 300-500 million cells per technical replicate were transfected at 200ug/ml (K562, T/C-28a2) and 300ug/ml (CHON-002) of plasmid library, using a MaxCyte ATx electroporation device. Preexisting electroporation protocols established by MaxCyte were used and optimized in our hands by FACS analysis using a control plasmid on the device for each cell line. R1000 cartridges were used at ~125 million cells per cartridge. Following electroporation, cells were allowed to rest for 25 minutes in proprietary MaxCyte Buffer in a 6-well plate at 37˚C. Cells were then plated in their respective media at a 50%-70% density. Cells were harvested 24 hours post-transfection, spun down and snap frozen on dry ice before storing at -80˚C. Five technical replicates were transfected per cell-line.

tag: cell line

value: lymphoblast


title: Cartilage MPRA K562 replicate 5

description: Library name: 290k_Cartilage_cDNA_K562_rep5


title: p20169.s029_87_PT078

value: critical


title: Cartilage MPRA K562 replicate 3

description: Library name: 290k_Cartilage_cDNA_K562_rep3


title: LK Gfi1-tdTomato intermediate Csf1r- cell 63

description:
LK.Gfi_int_Csf1r_neg.CD150-.63
Fluidigm C1


title: In vitro glucocorticoid treated glucocorticoid receptor knockout tumor cells 2

city: Manchester

first: Santiago

last: Zelenay

address: Wilmslow Rd, Manchester M20 4BX

country: United Kingdom

institute: Cancer Research UK Manchester Institute

description:
Library name: 20967 GRKO CP 1µM 2
20967_3-22_CP_1uM_RNA_14-9-22_B_S31

data_processing:
Counts were filtered with minimum CPM of 0.5 in ≥3 samples and normalized using the EdgeR package of Bioconductor, and log2(CPM+1) values were used for generating heatmaps and downstream analysis. Enrichment of molecular pathways (MSigDB) was evaluated by Gene Set Enrichment Analysis (GSEA) and differential gene expression analysis was evaluated by DESeq2 using the respective GenePattern modules. DEGs were defined based on linear fold change ±1.5 and adjusted P value/false discovery rate <0.05. Unless specified, all modules and packages were run with default parameters.
Assembly: mm10
Supplementary files format and content: raw_counts.txt - raw RNA-Seq counts for each sample.

source_name: In-vitro-treated cells

extract_protocol:
Tumors were collected in PureZOL Reagent (BioRad) and stored at -80°C. For processing, tumors were dissociated with 5mm Stainless steel beads (Qiagen) using the TissueLyser II (QIAGEN). Total RNA was extracted using the Direct-zol RNA Mini Prep Kit (Zymo Research) following the manufacturer’s recommendations and included a DNase digestion step. RNA was quantified using a NanoDrop One (ThermoFisher) or a Bioanalyzer (Agilent Technologies) for RNA-seq. For qPCR, total RNA was extracted from cells using RLT lysis buffer (QIAGEN) and purified using RNeasy RNA isolation kit (QIAGEN). RNA was quantified using a NanoDrop One (ThermoFisher) and 2mg cDNA was synthesized by reverse transcription using High Capacity cDNA reverse transcription kit (Applied Biosystems).
For bulk RNA-seq, mRNA libraries were prepared using QuantSeq 3’ mRNA-Seq Library Prep Kit FWD with UDI (Lexogen) from 500 ng total RNA, quality checked by Fragment Analyzer, quantified by qPCR using the KAPA Library Quantification Kit for Illumina (Roche), and sequenced on the Illumina NovaSeq 6000. RNA-Seq reads were quality checked using MultiQC v1.4, which aggregated metrics from FastQC v 0.11.7 (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/), trimmed using Trim Galore version 0.6.5, and aligned in single-end mode to the mouse genome assembly (GRCm38.75) using the STAR aligner version 2.6.1d with default parameters. Mapped data were converted to gene level integer read counts (expression) using featureCounts and Ensemble GTF annotation (Mus_musculus.GRCm38.75.gtf).

value: In-vitro-treated cells

value: 20967 glucocorticoid receptor knockout

value: Melanoma (glucocorticoid receptor knockout)

value: Cell line generated from C57BL/6 Nras+LSL-G12D;Tyr::CreERT2+/o background; tumours grown in wild type C57BL/6 mice

value: Clobetasol propionate 10µM


title: p20169.s028_85_PT052


title: In vitro glucocorticoid treated glucocorticoid receptor knockout tumor cells 1

description:
Library name: 20967 GRKO CP 1µM 1
20967_3-22_CP_1uM_RNA_14-9-22_A_S21


title: Cartilage MPRA K562 replicate 2

description: Library name: 290k_Cartilage_cDNA_K562_rep2


title: p20169.s026_81_PT060


title: In vitro Control treated glucocorticoid receptor knockout tumor cells 3

description:
Library name: 20967 GRKO DMSO 3
20967_3-22_DMSO_RNA_14-9-22_C_S28

value: DMSO


title: Cartilage MPRA K562 replicate 1

description: Library name: 290k_Cartilage_cDNA_K562_rep1


title: p20169.s025_78_PT023


title: Healthy scalp skin sample 2

description:
Library name: HSS2
8595 cells detected


title: LK Gfi1-tdTomato intermediate Csf1r- cell 60

description:
LK.Gfi_int_Csf1r_neg.CD150-.60
Fluidigm C1


title: p20169.s024_76_PT094


title: Cartilage MPRA TC28a2 replicate 5

description: Library name: 290k_Cartilage_cDNA_TC28_rep5

value: chondrocyte


title: LK Gfi1-tdTomato intermediate Csf1r- cell 65

description:
LK.Gfi_int_Csf1r_neg.CD150-.65
Fluidigm C1

value: Bone Marrow


title: In vitro Control treated glucocorticoid receptor knockout tumor cells 1

description:
Library name: 20967 GRKO DMSO 1
20967_3-22_DMSO_RNA_14-9-22_A_S27


title: LK Gfi1-tdTomato intermediate Csf1r- cell 59

description:
LK.Gfi_int_Csf1r_neg.CD150-.59
Fluidigm C1

value: WT


title: In vitro Control treated glucocorticoid receptor knockout tumor cells 2

description:
Library name: 20967 GRKO DMSO 2
20967_3-22_DMSO_RNA_14-9-22_B_S30


title: In vitro glucocorticoid treated glucocorticoid receptor knockout tumor cells 3

description:
Library name: 20967 GRKO CP 1µM 3
20967_3-22_CP_1uM_RNA_14-9-22_C_S29


title: LK Gfi1-tdTomato intermediate Csf1r- cell 58

description:
LK.Gfi_int_Csf1r_neg.CD150-.58
Fluidigm C1

value: paired-end


title: Cartilage MPRA TC28a2 replicate 4

description: Library name: 290k_Cartilage_cDNA_TC28_rep4


title: Cartilage MPRA TC28a2 replicate 3

description: Library name: 290k_Cartilage_cDNA_TC28_rep3


title: In vitro glucocorticoid treated parental tumor cells 2

description:
Library name: 20967 parental CP 1µM 2
20967_O_CP_1uM_RNA_14-9-22_B_S24

value: Melanoma


title: p20169.s023_69_PT052

value: Blood


title: p20169.s021_60_PT116


title: LK Gfi1-tdTomato intermediate Csf1r- cell 62

description:
LK.Gfi_int_Csf1r_neg.CD150-.62
Fluidigm C1


title: In vitro glucocorticoid treated parental tumor cells 1

description:
Library name: 20967 parental CP 1µM 1
20967_O_CP_1uM_RNA_14-9-22_A_S22


title: Cartilage MPRA TC28a2 replicate 2

description: Library name: 290k_Cartilage_cDNA_TC28_rep2


title: p20169.s020_56_PT004


title: LK Gfi1-tdTomato intermediate Csf1r- cell 56

description:
LK.Gfi_int_Csf1r_neg.CD150-.56
Fluidigm C1


title: LK Gfi1-tdTomato intermediate Csf1r- cell 61

description:
LK.Gfi_int_Csf1r_neg.CD150-.61
Fluidigm C1


title: Cartilage MPRA TC28a2 replicate 1

description: Library name: 290k_Cartilage_cDNA_TC28_rep1


title: p20169.s018_51_PT020


title: LK Gfi1-tdTomato intermediate Csf1r- cell 55

description:
LK.Gfi_int_Csf1r_neg.CD150-.55
Fluidigm C1


title: In vitro Control treated parental tumor cells 2

description:
Library name: 20967 parental DMSO 2
20967_O_DMSO_RNA_14-9-22_B_S23


title: In vitro Control treated parental tumor cells 3

description:
Library name: 20967 parental DMSO 3
20967_O_DMSO_RNA_14-9-22_C_S25


title: p20169.s017_49_PT004


title: In vitro Control treated parental tumor cells 1

description:
Library name: 20967 parental DMSO 1
20967_O_DMSO_RNA_14-9-22_A_S26


title: Cartilage MPRA CHON002 replicate 4

description: Library name: 290k_Cartilage_cDNA_CHON_rep4


title: LK Gfi1-tdTomato intermediate Csf1r- cell 54

description:
LK.Gfi_int_Csf1r_neg.CD150-.54
Fluidigm C1


title: Cartilage MPRA CHON002 replicate 5

description: Library name: 290k_Cartilage_cDNA_CHON_rep5


title: p20169.s014_42_PT004


title: LK Gfi1-tdTomato intermediate Csf1r- cell 53

description:
LK.Gfi_int_Csf1r_neg.CD150-.53
Fluidigm C1


title: Cartilage MPRA CHON002 replicate 3

description: Library name: 290k_Cartilage_cDNA_CHON_rep3


title: p20169.s013_41_PT003


title: Glucocorticoid treated glucocorticoid receptor knockout (GRKO) tumor 5

description:
Library name: CE027 4.5 RNA
CE027_4-5_RNA_S3

source_name: Ex-vivo whole tumour

value: Ex-vivo whole tumour

value: Clobetasol propionate 0.05% ointment three times weekly topically


title: Cartilage MPRA CHON002 replicate 2

description: Library name: 290k_Cartilage_cDNA_CHON_rep2


title: Glucocorticoid treated glucocorticoid receptor knockout (GRKO) tumor 4

description:
Library name: CE027 4.4 RNA
CE027_4-4_RNA_S2


title: p20169.s012_37_PT089


title: LK Gfi1-tdTomato intermediate Csf1r- cell 57

description:
LK.Gfi_int_Csf1r_neg.CD150-.57
Fluidigm C1


title: LK Gfi1-tdTomato intermediate Csf1r- cell 51

description:
LK.Gfi_int_Csf1r_neg.CD150-.51
Fluidigm C1


title: Cartilage MPRA CHON002 replicate 1

description: Library name: 290k_Cartilage_cDNA_CHON_rep1


title: Glucocorticoid treated glucocorticoid receptor knockout (GRKO) tumor 3

description:
Library name: CE027 4.3 RNA
CE027_4-3_RNA_S4


title: p20169.s009_27_PT060

value: severe


title: Glucocorticoid treated glucocorticoid receptor knockout (GRKO) tumor 2

description:
Library name: CE027 4.2 RNA
CE027_4-2_RNA_S8


title: p20169.s008_23_PT004


title: LK Gfi1-tdTomato intermediate Csf1r- cell 50

description:
LK.Gfi_int_Csf1r_neg.CD150-.50
Fluidigm C1


title: human.PBMCs.CD8_HTGTS_TCR_seq_TcrJ_mix_rep3

city: Shanghai

first: Haiqiang

last: Dai

address: 320 Yue Yang Road

country: China

institute: Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell  Science

description: Library name: sample60

library_source: genomic

data_processing:
For Tcra and Tcrb gene rearrangement analysis, sequencing reads were aligned to the mm10 reference genome for mouse T cells and to the hg38 reference genome for human T cells. All duplicate junctions were retained in the analyses. To quantify the utilization level of V, D and J segments in TCR α and β gene rearrangements, we defined “on-target” sequences as the 40-bp regions flanking the recombination signal sequences (RSS) (RSS ± 40 bp). which were then used to determine the usage of V(D)J segments. To quantify TCR repertoires, we employed a pipeline called "HTGTSrep" to identify the productive and non-productive V(D)J rearrangements, as well as to analyze the motifs and length distribution of CDR3 regions.
Assembly: mm10;hg38
Supplementary files format and content: tlx

molecule: genomic DNA

extract_protocol:
Cells were collected and lysed in cell lysis buffer using proteinase K. Genomic DNA was later precipitated and dissolved in TE before shearing.
3-20 μg DNA was fragmented via sonication on Qsonic biorupter and subjected to linear PCR amplification with a biotinylated primer as following PCR conditions: 95°C 2 min; 95°C 30s; 58°C 30 s; 72°C 90 s; 80 cycles; 72°C 2 min. Primers were removed by VAHTS DNA Clean Beads (Vazyme, N411). The resulting single-strand biotinylated PCR products were collected via Dynabeads MyONE C1 streptavidin beads (ThermoFisher, 65002) and ligated to bridge adapters overnight in the presence of 15% PRG8000. Ligation were conducted following 25°C 60 min; 22°C 120 min; 16°C 9-12 h. Subsequently, i5-indexed bait-specific inner primers and i7-index adapter primers were added to adapter-ligated products by nested PCR. Excess primers were removed by VAHTS DNA Clean Beads (Vazyme, N411), and the purified PCR products were further tagged with Illumina sequencing adapter sequences. Libraries were size-selected by resolving PCR products on a 2% agarose gel, isolating fragments between 300-700 bp for mouse or human samples, with recovery performed via gel extraction. The HTGTS-TCR-seq libraries were sequenced on NovaXplus (Illumina) using 150-bp paired-end reads.

value: PBMCs CD8+ T cells


title: LK Gfi1-tdTomato intermediate Csf1r- cell 49

description:
LK.Gfi_int_Csf1r_neg.CD150-.49
Fluidigm C1


title: p20169.s007_22_PT050


title: Glucocorticoid treated glucocorticoid receptor knockout (GRKO) tumor 1

description:
Library name: CE027 4.1 RNA
CE027_4-1_RNA_S18


title: Control treated glucocorticoid receptor knockout (GRKO) tumor 5

description:
Library name: CE027 3.5 RNA
CE027_3-5_RNA_S15

value: Control


title: human.PBMCs.CD8_HTGTS_TCR_seq_TcrJ_mix_rep2

description: Library name: sample59


title: p20169.s006_19_PT050


title: Control treated glucocorticoid receptor knockout (GRKO) tumor 4

description:
Library name: CE027 3.4 RNA
CE027_3-4_RNA_S20


title: LK Gfi1-tdTomato intermediate Csf1r- cell 47

description:
LK.Gfi_int_Csf1r_neg.CD150-.47
Fluidigm C1


title: LK Gfi1-tdTomato intermediate Csf1r- cell 52

description:
LK.Gfi_int_Csf1r_neg.CD150-.52
Fluidigm C1


title: human.PBMCs.CD4_HTGTS_TCR_seq_TcrJ_mix_rep3

description: Library name: sample57

value: PBMCs CD4+ T cells


title: p20169.s005_18_PT030

value: moderate


title: LK Gfi1-tdTomato intermediate Csf1r- cell 46

description:
LK.Gfi_int_Csf1r_neg.CD150-.46
Fluidigm C1


title: Control treated glucocorticoid receptor knockout (GRKO) tumor 3

description:
Library name: CE027 3.3 RNA
CE027_3-3_RNA_S10

value: 20967 glucocorticoid receptor knockout

value: Melanoma (glucocorticoid receptor knockout)


title: LK Gfi1-tdTomato intermediate Csf1r- cell 45

description:
LK.Gfi_int_Csf1r_neg.CD150-.45
Fluidigm C1


title: p20169.s004_14_PT032

value: critical


title: Control treated glucocorticoid receptor knockout (GRKO) tumor 2

description:
Library name: CE027 3.2 RNA
CE027_3-2_RNA_S7

value: Cell line generated from C57BL/6 Nras+LSL-G12D;Tyr::CreERT2+/o background; tumours grown in wild type C57BL/6 mice


title: p20169.s003_12_PT023


title: LK Gfi1-tdTomato intermediate Csf1r- cell 44

description:
LK.Gfi_int_Csf1r_neg.CD150-.44
Fluidigm C1


title: human.PBMCs.CD4_HTGTS_TCR_seq_TcrJ_mix_rep1

description: Library name: sample55


title: BI4328.97.97PASC

description:
Library name: BI4328.97.97PASC
AdditionalSamples.rawCounts.csv
AdditionalSamples.logNormalizedCounts.csv

data_processing:
FastQC (version v0.11.8) was applied to check the quality of raw reads. Trimmomatic (version v0.38) was applied to cut adaptors and trim low-quality bases with default setting. STAR Aligner version 2.7.1a was used to align the reads. Picard tools (version 2.20.4) was applied to mark duplicates of mapping. The StringTie version 2.0.4 was used to assemble the RNA-Seq alignments into potential transcripts. The featureCounts (version 1.6.0)/HTSeq was used to count mapped reads for genomic features such as genes, exons, promoter, gene bodies, genomic bins and chromosomal locations. The De-Seq2 (version 1.14.1) was used to do the differential analysis. The Gene Ontology Analysis was done using ClusterProfiler package in R.
Assembly: Genome Reference Consortium Human Build 38 patch release 14 (GRCh38.p14), SARS-CoV-2 Reference Genome (RefBank Accession: GCF_009858895.2)
Supplementary files format and content: AdditionalSamples.rawCounts.csv: raw read count matrix
Supplementary files format and content: AdditionalSamples.logNormalizedCounts.csv: log-normalized read count matrix

source_name: Whole blood

extract_protocol:
RNA extraction was performed using RNeasy Plus Mini Kit (Qiagen) following the manufacturer’s protocol. Isolated RNA sample quality was assessed by High Sensitivity RNA Tapestation (Agilent Technologies Inc., California, USA) and quantified by AccuBlue® Broad Range RNA Quantitation assay (Biotium, California, USA). Paramagnetic beads coupled with oligo d(T)25 are combined with total RNA to isolate poly(A)+ transcripts based on NEBNext® Poly(A) mRNA Magnetic Isolation Module manual (New England BioLabs Inc., Massachusetts, USA).
Prior to first strand synthesis, samples are randomly primed (5´ d(N6) 3´ [N=A,C,G,T]) and fragmented based on manufacturer’s recommendations. The first strand is synthesized with the Protoscript II Reverse Transcriptase with a longer extension period, approximately 30 minutes at 42⁰C. All remaining steps for library construction were used according to the NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina® (New England BioLabs Inc., Massachusetts, USA). Final libraries quantity was assessed by Qubit 2.0 (ThermoFisher, Massachusetts, USA) and quality was assessed by TapeStation HSD1000 ScreenTape (Agilent Technologies Inc., California, USA). Average final library size was about 450bp with an insert size of about 300bp. Illumina® 8-nt dual-indices were used. Equimolar pooling of libraries was performed based on QC values and sequenced on an Illumina® NovaSeq X Plus 10B (Illumina, California, USA) with a read length configuration of 150 PE for 40M PE reads per sample (20M in each direction).

value: Whole blood

tag: current long_covid_status

value: PASC

tag: time of_blood_draw


title: Control treated glucocorticoid receptor knockout (GRKO) tumor 1

description:
Library name: CE027 3.1 RNA
CE027_3-1_RNA_S12


title: human.PBMCs.CD4_HTGTS_TCR_seq_TcrJ_mix_rep2

description: Library name: sample56

value: WT


title: p20169.s002_8_PT052


title: p20169.s001_1_PT023


title: Glucocorticoid treated parental tumor 5

description:
Library name: CE027 2.5 RNA
CE027_2-5_RNA_S19


title: LK Gfi1-tdTomato intermediate Csf1r- cell 42

description:
LK.Gfi_int_Csf1r_neg.CD150-.42
Fluidigm C1

value: Bone Marrow

value: paired-end


title: BI4327.15.15PASC

description:
Library name: BI4327.15.15PASC
AdditionalSamples.rawCounts.csv
AdditionalSamples.logNormalizedCounts.csv

value: Acute


title: LK Gfi1-tdTomato intermediate Csf1r- cell 48

description:
LK.Gfi_int_Csf1r_neg.CD150-.48
Fluidigm C1


title: Glucocorticoid treated parental tumor 4

description:
Library name: CE027 2.4 RNA
CE027_2-4_RNA_S5

value: Ex-vivo whole tumour

value: Melanoma


title: LK Gfi1-tdTomato intermediate Csf1r- cell 41

description:
LK.Gfi_int_Csf1r_neg.CD150-.41
Fluidigm C1


title: BI4326.79.79PASC

description:
Library name: BI4326.79.79PASC
AdditionalSamples.rawCounts.csv
AdditionalSamples.logNormalizedCounts.csv


title: Helicon4, 100mpk, 48hr,rep5 [SH7084_SA91298_S4]

first: YaGuang

last: Si

address: 30 Acorn Park Dr

institute: Fogpharma

data_processing:
Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.39
The trimmed reads were mapped to the Homo sapiens GRCh38 reference genome available on ENSEMBL using the STAR aligner v.2.7.7a
Host reads were removed with XenofilteR
Unique gene hit counts were calculated by using featureCounts from the R Subread package v.2.4.2
Read filtering, normalization, and differential expression analysis with respect to biological variation was performed with the edgeR package v.4.0.2 in R
Assembly: GRCh38
Supplementary files format and content: CPM from EdgeR for all samples in EXCEL format

molecule: polyA RNA

extract_protocol:
RNA extraction was performed using NEBNext Ultra II Directional RNA Library Prep Kit following manufacture's instructions (New England BioLabs, Ipswich, MA)
library preparation and sequencing were performed by Fulgent Gentetics (Houston, TX) with TruSeq stranded mRNA library kit on Novaseq S4 Platform with PolyA enrichment.

value: Colorectal adenocarcinoma

tag: dose

tag: time

tag: replicate


title: Glucocorticoid treated parental tumor 3

description:
Library name: CE027 2.3 RNA
CE027_2-3_RNA_S17

value: Clobetasol propionate 0.05% ointment three times weekly topically


title: BI4326.376.376PASC

description:
Library name: BI4326.376.376PASC
AdditionalSamples.rawCounts.csv
AdditionalSamples.logNormalizedCounts.csv


title: human.PBMCs.CD8_HTGTS_TCR_seq_TcrJ_mix_rep1

description: Library name: sample58

value: Blood

value: PBMCs CD8+ T cells


title: Helicon4, 100mpk, 48hr,rep4 [SH7083_SA91293_S55]


title: LK Gfi1-tdTomato intermediate Csf1r- cell 40

description:
LK.Gfi_int_Csf1r_neg.CD150-.40
Fluidigm C1


title: Glucocorticoid treated parental tumor 2

description:
Library name: CE027 2.2 RNA
CE027_2-2_RNA_S16


title: BI4326.27.27PASC

description:
Library name: BI4326.27.27PASC
AdditionalSamples.rawCounts.csv
AdditionalSamples.logNormalizedCounts.csv


title: LK Gfi1-tdTomato intermediate Csf1r- cell 39

description:
LK.Gfi_int_Csf1r_neg.CD150-.39
Fluidigm C1


title: Helicon4, 100mpk, 48hr,rep2 [SH7083_SA91290_S52]


title: Glucocorticoid treated parental tumor 1

description:
Library name: CE027 2.1 RNA
CE027_2-1_RNA_S13


title: BI4326.170.170PASC

description:
Library name: BI4326.170.170PASC
AdditionalSamples.rawCounts.csv
AdditionalSamples.logNormalizedCounts.csv


title: LK Gfi1-tdTomato intermediate Csf1r- cell 38

description:
LK.Gfi_int_Csf1r_neg.CD150-.38
Fluidigm C1


title: LK Gfi1-tdTomato intermediate Csf1r- cell 43

description:
LK.Gfi_int_Csf1r_neg.CD150-.43
Fluidigm C1


title: Helicon4, 100mpk, 48hr,rep1 [SH7083_SA91289_S51]


title: BI4323.95.95PASC

description:
Library name: BI4323.95.95PASC
AdditionalSamples.rawCounts.csv
AdditionalSamples.logNormalizedCounts.csv


title: BI4323.386.386PASC

description:
Library name: BI4323.386.386PASC
AdditionalSamples.rawCounts.csv
AdditionalSamples.logNormalizedCounts.csv


title: Gr4, rep8 [C22013016LR01_Gr4_620330]

data_processing:
Quality evaluation of reads was performed with FastQC v.11.9.
Low quality reads were filtered with Fastp v.22.0
Mouse reads were removed with Xenome v1.1.1
Samples with at least 15 million human reads were mapped with STAR v2.4.2a to the human genome, GRCh38.d1
Unique gene hit counts were calculated by using featureCounts from the R Subread package v.2.4.2
Read filtering, normalization, and differential expression analysis with respect to biological variation was performed with the edgeR package v.4.0.2 in R
Assembly: GRCh38.d1
Supplementary files format and content: CPM from EdgeR for all samples in EXCEL format

source_name: Patient derived xenograft

extract_protocol:
Total RNA was extracted from the 10 mg tissues after grinding by Homogenizer (Scientz) using using TRIzol® Reagent (Invitrogen) and RNeasy MinElute Cleanup Kit (Qiagen) according to the manufacturer's instructions in Mingma Technologies Co., Ltd at Shanghai. Then the integrity of the total RNA was determined by 4200 Bioanalyser (Agilent) and quantified using the NanoDrop ( Thermo Scientific). About 500 ng high-quality RNA sample (OD260/280=1.9~2.0, RIN≥8) was used to construct sequencing library.
RNA purification, reverse transcription, library construction and sequencing were performed in Sequanta Technologies Co., Ltd at Shanghai according to the manufacturer's instructions. The mRNA-focused sequencing libraries from total RNA were prepared using Illumina TruSeq Stranded mRNA Library Prep kit. PolyA mRNA was purified from total RNA using oligo-dT-attached magnetic beads and then fragmented by fragmentation buffer. Taking these short fragments as templates, first strand cDNA was synthesized using reverse transcriptase and random primers. Then in the process of second strand cDNA synthesis, RNA template was removed and a replacement strand, incorporating dUTP in place of dTTP to generate ds cDNA, was synthesized. The incorporation of dUTP quenches the second strand during amplification, because the polymerase does not incorporate past this nucleotide. AMPure XP (Beckmen) beads were then used to purify the ds cDNA from the reaction mix. Next, the ds cDNA was subjected to end-repair, phosphorylation and 'A' base addition according to Illumina's library construction protocol. In the following process, Illumina sequencing adapters were added to both size of the ds cDNA fragments. After PCR amplification for DNA enrichment, the AMPure XP Beads were used to clean up the target fragments of 200–300 bp.
After library construction, Qubit 3.0 fluorometer dsDNA HS Assay (Thermo Fisher Scientific) was used to quantify concentration of the resulting sequencing libraries, while the size distribution was analyzed using Agilent BioAnalyzer (Agilent). Sequencing was performed using an Illumina systems Novaseq 6000 following Illumina-provided protocols for 2x150 paired-end sequencing in Sequanta Technologies Co., Ltd.

tag: host

value: mouse

value: Patient derived xenograft

tag: disease

value: 2d post-2nd dose


title: MultiLin-Gata1-mCherry negative CD150+ cell 92

description:
Oct23_x_x_002_Cell_92
Fluidigm C1


title: Control treated parental tumor 3

description:
Library name: CE027 1.3 RNA
CE027_1-3_RNA_S6

value: Control


title: Gr4, rep7 [C22013015LR01_Gr4_620307]


title: MultiLin-Gata1-mCherry negative CD150+ cell 91

description:
Oct23_x_x_002_Cell_91
Fluidigm C1


title: BI4322.224.Recovered

description:
Library name: BI4322.224.Recovered
AdditionalSamples.rawCounts.csv
AdditionalSamples.logNormalizedCounts.csv

value: Recovered


title: Control treated parental tumor 2

description:
Library name: CE027 1.2 RNA
CE027_1-2_RNA_S9

value: Cell line generated from C57BL/6 Nras+LSL-G12D;Tyr::CreERT2+/o background; tumours grown in wild type C57BL/6 mice


title: MultiLin-Gata1-mCherry negative CD150+ cell 90

description:
Oct23_x_x_002_Cell_90
Fluidigm C1


title: Control treated parental tumor 1

description:
Library name: CE027 1.1 RNA
CE027_1-1_RNA_S1


title: Gr4, rep5 [C22013013LR01_Gr4_620278]


title: BI4320.371.Recovered

description:
Library name: BI4320.371.Recovered
AdditionalSamples.rawCounts.csv
AdditionalSamples.logNormalizedCounts.csv

value: Whole blood


title: Gr4, rep4 [C22013012LR01_Gr4_620325]


title: MultiLin-Gata1-mCherry negative CD150+ cell 89

description:
Oct23_x_x_002_Cell_89
Fluidigm C1

value: WT


title: BI4320.181.Recovered

description:
Library name: BI4320.181.Recovered
AdditionalSamples.rawCounts.csv
AdditionalSamples.logNormalizedCounts.csv


title: cFb_Old_MI_rep3

city: Bucharest

first: Evelyn-Gabriela

last: Nastase-Rusu

state: Romania

address: B.P. Hasdeu St

country: Romania

institute: The Institute of Cellular Biology and Pathology "Nicolae Simionescu"

data_processing:
According to Novogene methods: Raw data (raw reads) of FASTQ format were firstly processed through fastp. In this step, clean data (clean reads) were obtained by removing reads containing adapter and poly-N sequences and reads with low quality from raw data (the error rate of a single base should be lower than 1%. In some special cases, the maximum error rate of a single base should not be greater than 6%)
According to Novogene methods:Reference genome and gene model annotation files were downloaded from genome website browser (NCBI/UCSC/Ensembl) directly. Paired-end clean reads were mapped to the reference genome using HISAT2 software. HISAT2 uses a large set of small GFM indexes that collectively cover the whole genome. These small indexes (called local indexes), combined with several alignment strategies, enable rapid and accurate alignment of sequencing reads. The StringTie v1.3.3
According to Novogene methods:FeatureCountsv1.5.0-p3 was used to count the read numbers mapped of each gene, including known and novel genes. And then FPKM of each gene was calculated.
Assembly: GRCm39/mm39
Supplementary files format and content: tab-delimitated text file includes raw count for all the sample
Supplementary files format and content: tab-delimitated text file includes FPKM values for all  sample

source_name: heart

growth_protocol: C57BL/6J mice (from Jackson Laboratory) - bred in the animal facility of the Institute of Cellular Biology and Pathology, Bucharest, Romania (specific pathogen free conditions, controlled environment of 12/12 hours light/dark cycle, 21°C, 55% to 60% humidity, with chow and water ad libitum). A cohort of female and male naturally aging mice was established by maintaining the animals in the aforementioned conditions. The animals were sacrificed by heart removal after being anesthetized to surgical level with a cocktail of Ketamine:Xylazine (100:10 mg/kg b.w.). Primary mouse cardiac fibroblasts were isolated as follows: the heart was digested in 0.1% Trypsin and 100 µg/mL Collagenase type I (Sigma) in HBSS (0.137 M NaCl, 5.4 mM KCl, 0.25 mM Na2HPO4, 0.44 mM KH2PO4, 1.3 mM CaCl2, 1 mM MgSO4, 4.2 mM NaHCO3), in a water bath, at 37°C, under constant stirring, in multiple 5-min fractions. The resulting single cell suspension was centrifugated at 400 g for 5 minutes at 4°C. The resulting pellet was resuspended in 10 mL of fibroblast culture medium containing DMEM/F12 supplemented with 10% FBS, 1% Penicillin-Streptomycin-Amphotericin B, 1X L-Glutamine, 10 ng/µL FGF, 10 µg/mL Insulin, divided on two 60 mm × 15 mm Petri dishes and cultured in a humidified atmosphere with 5% CO2 at 37°C. The medium was freshened after the first 24 hours and the next two days. At day 5 we collected the cells for subsequent analyzes.

extract_protocol:
Total RNA was extracted from PBS-washed cell pellets using miRNeasy Mini Kit (Qiagen). The samples were homogenized in 1 mL Qiazol (Qiagen) using a vortex, followed by incubation at room temperature for 5 minutes. Chloroform was added to the lysates followed by cooled centrifugation at 12,000 g for 15 minutes at 4°C. Exactly 650 µL of the upper aqueous phase was mixed with 750 µL ethanol and RNA was precipitated on a miRNeasy mini column followed by automated washing with RPE and RWT buffer in a Qiacube liquid handling robot. Finally, total RNA was eluted in 30 µL nuclease free water. Total RNA integrity was checked using the RNA 6000 Nano Assay (Agilent, CA), as well as spectrophotometric RNA quantification (Nanodrop). All samples showed RIN values between 9.4 to 10, except for one sample with a RIN of 6.6.
library construction and sequencing was done by Novogene

treatment_protocol: Myocardial infarction was induced in young and old mice by left anterior descending (LAD) coronary artery ligation. Briefly, anesthetized (ketamine: 100 mg/kg, xylazine: 20 mg/kg) and orotracheally intubated mice underwent thoracotomy in the fourth left intercostal space, and the LAD was permanently ligated with a 7-0 silk suture approximately 2 mm below its emergence from the left atrium. Prior and after surgery, mice were subcutaneously injected with buprenorphine (100 µg/kg) for analgesia. For the group receiving MSC therapy, 5 µl cell suspension containing 5 x 105 cells in PBS was injected into the ventricular wall, below the ligature site, immediately after LCA ligation. Age-matched sham-infarcted animals, which underwent the same surgical intervention without the tightening of the suture, were used as controls.

value: heart

tag: strain

value: Primary cardiac fibroblasts

value: wild-type

tag: age group

value: old

tag: age (months)

tag: surgery

value: MI

tag: cell isolation_time

value: 7 days post-surgery_intervention

tag: time in_culture

value: 5 days


title: Control treated parental tumor 5

description:
Library name: CE027 1.5 RNA
CE027_1-5_RNA_S11

tag: tissue

value: Ex-vivo whole tumour

tag: cell type

value: Melanoma

tag: genotype

tag: treatment


title: BI4320.102.Recovered

description:
Library name: BI4320.102.Recovered
AdditionalSamples.rawCounts.csv
AdditionalSamples.logNormalizedCounts.csv

tag: current long_covid_status


title: MultiLin-Gata1-mCherry negative CD150+ cell 93

description:
Oct23_x_x_002_Cell_93
Fluidigm C1

value: Bone Marrow

tag: protocol

value: paired-end


title: MultiLin-Gata1-mCherry negative CD150+ cell 88

description:
Oct23_x_x_002_Cell_88
Fluidigm C1


title: Control treated parental tumor 4

description:
Library name: CE027 1.4 RNA
CE027_1-4_RNA_S14

tag: cell line


title: MultiLin-Gata1-mCherry negative CD150+ cell 87

description:
Oct23_x_x_002_Cell_87
Fluidigm C1


title: Gr4, rep3 [C22013011LR01_Gr4_620242]

value: mouse

value: Patient derived xenograft

value: Colorectal adenocarcinoma

tag: dose

tag: time

value: 2d post-2nd dose


title: BI4316.177.Recovered

description:
Library name: BI4316.177.Recovered
AdditionalSamples.rawCounts.csv
AdditionalSamples.logNormalizedCounts.csv

value: Whole blood

value: Recovered

tag: time of_blood_draw


title: Gr4, rep2 [C22013010LR01_Gr4_620231]

tag: host

tag: disease

tag: replicate


title: BI4323.187.187PASC

description:
Library name: BI4323.187.187PASC
AdditionalSamples.rawCounts.csv
AdditionalSamples.logNormalizedCounts.csv

value: PASC


title: MultiLin-Gata1-mCherry negative CD150+ cell 86

description:
Oct23_x_x_002_Cell_86
Fluidigm C1

value: WT


title: cFb_Old_MI_rep2

value: heart

tag: strain

value: Primary cardiac fibroblasts

value: wild-type

tag: age group

tag: age (months)


title: cFb_Old_sham-MI_rep2

value: old

tag: surgery

value: Sham-MI

tag: cell isolation_time

value: 7 days post-surgery_intervention

tag: time in_culture


title: Gr4, rep1 [C22013009LR01_Gr4_620223]

tag: tissue


title: Gr4, rep6 [C22013014LR01_Gr4_620282]

tag: treatment


title: BI4312.828.Recovered

description:
Library name: BI4312.828.Recovered
AdditionalSamples.rawCounts.csv
AdditionalSamples.logNormalizedCounts.csv

tag: current long_covid_status


title: cFb_Old_MI_rep1

tag: cell type

tag: genotype

value: MI

value: 5 days


title: MultiLin-Gata1-mCherry negative CD150+ cell 85

description:
Oct23_x_x_002_Cell_85
Fluidigm C1

value: Bone Marrow

tag: protocol

value: paired-end


title: cFb_Old_sham-MI_rep1


title: MultiLin-Gata1-mCherry negative CD150+ cell 84

description:
Oct23_x_x_002_Cell_84
Fluidigm C1


title: cFb_Young_MI+MSC_rep5

value: young

value: MI+mesenchymal_stem_cells (MSC)


title: BI4312.437.Recovered

description:
Library name: BI4312.437.Recovered
AdditionalSamples.rawCounts.csv
AdditionalSamples.logNormalizedCounts.csv


title: Gr3, rep6 [C22013007LR01_Gr3_620305]

value: mouse

value: Patient derived xenograft

value: Colorectal adenocarcinoma

tag: dose

tag: time

value: 2d post-2nd dose


title: cFb_Young_MI+MSC_rep4


title: Gr3, rep5 [C22013006LR01_Gr3_620288]

tag: host


title: MultiLin-Gata1-mCherry negative CD150+ cell 83

description:
Oct23_x_x_002_Cell_83
Fluidigm C1

value: WT


title: BI4312.190.Recovered

description:
Library name: BI4312.190.Recovered
AdditionalSamples.rawCounts.csv
AdditionalSamples.logNormalizedCounts.csv

value: Whole blood

value: Recovered

tag: time of_blood_draw


title: MultiLin-Gata1-mCherry negative CD150+ cell 82

description:
Oct23_x_x_002_Cell_82
Fluidigm C1


title: cFb_Young_MI+MSC_rep3

value: heart

value: Primary cardiac fibroblasts

value: wild-type


title: BI4311.761.971PASC

description:
Library name: BI4311.761.971PASC
AdditionalSamples.rawCounts.csv
AdditionalSamples.logNormalizedCounts.csv

value: PASC


title: Gr3, rep4 [C22013004LR01_Gr3_620265]

tag: disease

tag: replicate


title: MultiLin-Gata1-mCherry negative CD150+ cell 81

description:
Oct23_x_x_002_Cell_81
Fluidigm C1


title: BI4311.359.569PASC

description:
Library name: BI4311.359.569PASC
AdditionalSamples.rawCounts.csv
AdditionalSamples.logNormalizedCounts.csv


title: Gr3, rep3 [C22013003LR01_Gr3_620262]


title: MultiLin-Gata1-mCherry negative CD150+ cell 80

description:
Oct23_x_x_002_Cell_80
Fluidigm C1


title: BI4311.30.240PASC

description:
Library name: BI4311.30.240PASC
AdditionalSamples.rawCounts.csv
AdditionalSamples.logNormalizedCounts.csv

value: Acute


title: Gr3, rep2 [C22013002LR01_Gr3_620260]


title: Gr3, rep7 [C22013008LR01_Gr3_620326]


title: Gr3, rep1 [C22013001LR01_Gr3_620204]


title: BI4312.450.Recovered

description:
Library name: BI4312.450.Recovered
AdditionalSamples.rawCounts.csv
AdditionalSamples.logNormalizedCounts.csv


title: BI4311.166.376PASC

description:
Library name: BI4311.166.376PASC
AdditionalSamples.rawCounts.csv
AdditionalSamples.logNormalizedCounts.csv


title: MultiLin-Gata1-mCherry negative CD150+ cell 78

description:
Oct23_x_x_002_Cell_78
Fluidigm C1


title: cFb_Young_MI+MSC_rep1

tag: strain

tag: age group

value: 7 days post-surgery_intervention

value: 5 days


title: MultiLin-Gata1-mCherry negative CD150+ cell 79

description:
Oct23_x_x_002_Cell_79
Fluidigm C1

value: Bone Marrow

value: paired-end


title: Gr2, rep8 [C22013000LR01_Gr2_620320]


title: BI4310.332.PASC

description:
Library name: BI4310.332.PASC
AdditionalSamples.rawCounts.csv
AdditionalSamples.logNormalizedCounts.csv


title: MultiLin-Gata1-mCherry negative CD150+ cell 77

description:
Oct23_x_x_002_Cell_77
Fluidigm C1


title: BI4310.277.1050PASC

description:
Library name: BI4310.277.1050PASC
AdditionalSamples.rawCounts.csv
AdditionalSamples.logNormalizedCounts.csv


title: cFb_Young_MI_rep3

value: young

tag: age (months)

tag: surgery

value: MI


title: Gr2, rep7 [C22012999LR01_Gr2_620290]

value: mouse

value: Patient derived xenograft


title: MultiLin-Gata1-mCherry negative CD150+ cell 76

description:
Oct23_x_x_002_Cell_76
Fluidigm C1


title: BI4310.200.973PASC

description:
Library name: BI4310.200.973PASC
AdditionalSamples.rawCounts.csv
AdditionalSamples.logNormalizedCounts.csv


title: cFb_Young_MI_rep2

tag: cell isolation_time

tag: time in_culture


title: cFb_Young_MI+MSC_rep2

tag: tissue

value: MI+mesenchymal_stem_cells (MSC)


title: cFb_Young_MI_rep1


title: MultiLin-Gata1-mCherry negative CD150+ cell 75

description:
Oct23_x_x_002_Cell_75
Fluidigm C1

value: WT

tag: treatment


title: Gr2, rep5 [C22012997LR01_Gr2_620283]

value: Colorectal adenocarcinoma

value: 2d post-2nd dose


title: BI4310.189.400PASC

description:
Library name: BI4310.189.400PASC
AdditionalSamples.rawCounts.csv
AdditionalSamples.logNormalizedCounts.csv

value: Whole blood

tag: current long_covid_status


title: Gr2, rep6 [C22012998LR01_Gr2_620289]


title: MultiLin-Gata1-mCherry negative CD150+ cell 74

description:
Oct23_x_x_002_Cell_74
Fluidigm C1

tag: cell type

tag: genotype


title: cFb_Young_sham-MI_rep5

value: heart

value: Primary cardiac fibroblasts

value: Sham-MI


title: cFb_Young_MI_rep4

value: wild-type


title: BI4307.363.Recovered

description:
Library name: BI4307.363.Recovered
AdditionalSamples.rawCounts.csv
AdditionalSamples.logNormalizedCounts.csv

value: Recovered


title: cFb_Young_MI_rep5

value: 7 days post-surgery_intervention

value: 5 days


title: Gr2, rep4 [C22012996LR01_Gr2_620254]

tag: dose


title: MultiLin-Gata1-mCherry negative CD150+ cell 73

description:
Oct23_x_x_002_Cell_73
Fluidigm C1

value: Bone Marrow

tag: protocol

value: paired-end


title: MultiLin-Gata1-mCherry negative CD150+ cell 72

description:
Oct23_x_x_002_Cell_72
Fluidigm C1


title: cFb_Young_sham-MI_rep3

value: young


title: Gr2, rep3 [C22012995LR01_Gr2_620253]

tag: host

value: mouse

tag: time


title: cFb_Young_sham-MI_rep4


title: Gr2, rep2 [C22012994LR01_Gr2_620222]

value: Patient derived xenograft

tag: disease


title: BI4307.210.Recovered

description:
Library name: BI4307.210.Recovered
AdditionalSamples.rawCounts.csv
AdditionalSamples.logNormalizedCounts.csv

tag: time of_blood_draw


title: MultiLin-Gata1-mCherry negative CD150+ cell 71

description:
Oct23_x_x_002_Cell_71
Fluidigm C1


title: BI4306.186.Recovered

description:
Library name: BI4306.186.Recovered
AdditionalSamples.rawCounts.csv
AdditionalSamples.logNormalizedCounts.csv


title: BI4306.104.Recovered

description:
Library name: BI4306.104.Recovered
AdditionalSamples.rawCounts.csv
AdditionalSamples.logNormalizedCounts.csv


title: cFb_Young_sham-MI_rep2

tag: strain


title: MultiLin-Gata1-mCherry negative CD150+ cell 70

description:
Oct23_x_x_002_Cell_70
Fluidigm C1


title: Gr1, rep8 [C22012992LR01_Gr1_620308]

value: vehicle

tag: replicate


title: BI4305.363.Recovered

description:
Library name: BI4305.363.Recovered
AdditionalSamples.rawCounts.csv
AdditionalSamples.logNormalizedCounts.csv


title: Gr1, rep7 [C22012991LR01_Gr1_620298]


title: Gr1, rep6 [C22012990LR01_Gr1_620270]


title: MultiLin-Gata1-mCherry negative CD150+ cell 68

description:
Oct23_x_x_002_Cell_68
Fluidigm C1

value: WT


title: BI4305.210.Recoveredoriginal

description:
Library name: BI4305.210.Recoveredoriginal
AdditionalSamples.rawCounts.csv
AdditionalSamples.logNormalizedCounts.csv


title: cFb_Young_rep4

tag: age group

tag: age (months)

value: 0 days post-surgery_intervention


title: BI4305.210.Recoveredreplacement

description:
Library name: BI4305.210.Recoveredreplacement
AdditionalSamples.rawCounts.csv
AdditionalSamples.logNormalizedCounts.csv


title: MultiLin-Gata1-mCherry negative CD150+ cell 67

description:
Oct23_x_x_002_Cell_67
Fluidigm C1


title: Gr1, rep5 [C22012989LR01_Gr1_620243]

value: Colorectal adenocarcinoma

value: 2d post-2nd dose


title: BI4305.192.Recovered

description:
Library name: BI4305.192.Recovered
AdditionalSamples.rawCounts.csv
AdditionalSamples.logNormalizedCounts.csv

value: Whole blood


title: cFb_Young_rep2

value: heart

value: Primary cardiac fibroblasts

tag: surgery

tag: cell isolation_time


title: Gr1, rep4 [C22012988LR01_Gr1_620239]

tag: tissue


title: cFb_Young_rep3

value: wild-type

tag: time in_culture


title: BI4305.105.Recovered

description:
Library name: BI4305.105.Recovered
AdditionalSamples.rawCounts.csv
AdditionalSamples.logNormalizedCounts.csv

tag: current long_covid_status

value: Recovered


title: cFb_Young_rep1

tag: cell type


title: BI4303.361.Recovered

description:
Library name: BI4303.361.Recovered
AdditionalSamples.rawCounts.csv
AdditionalSamples.logNormalizedCounts.csv


title: MultiLin-Gata1-mCherry negative CD150+ cell 65

description:
Oct23_x_x_002_Cell_65
Fluidigm C1

tag: genotype

tag: treatment


title: Gr1, rep3 [C22012987LR01_Gr1_620233]


title: FACS-scRNA_Set5_Port_2 HTO

description:
10X Chromium 3′ v3.1
FACS-scRNA-seq Validation - Index Sort Gates

library_source: other

data_processing:
Cells were multiplexed using HTOs to distinguish CITE-Seq ADT concentration or cell population. HTO barcode count matrices were obtained through the multimodal analysis workflow in Cell Ranger, prior to normalization (counts per ten thousand (CPTT)). Cell barcodes with > 30% of normalized reads assigned to multiple HTOs were annotated as doublets, with confident singlet assigned to cells with >40% of normalized reads assigned to a single HTO (HTO processing module of AltAnalyze). Cells were further filtered based on the 7 mouse/rat isotype control antibodies counts (Source code) and performed quality control filtering in Seurat V4 by nFeature_RNA>500 & nCount_RNA >1000 & percent.mt<25. This QC step filtered 393,748 cells to 315,792 high-quality single cells in the initial titration dataset and 90,889 to 72,198 cells in the final titrated CITE-Seq dataset.All Cell Ranger produced count matrices underwent ambient RNA exclusion using the software SoupX with a contamination fraction of 15% and quality control filtering by HTO. Ambient corrected transcriptome counts and associated ADTs counts were supplied as input to the software TotalVI to obtain normalized and denoised ADT counts. The Honeycomb HIVE CLX capture system (discountinued, Honeycomb Biotechnologies, Inc) was applied using the manufacturer’s instructions to the following populations: CD117-enriched bone marrow, sorted cells from basophil/mast enriched gates, and those from eosinophil enriched gates. Briefly, 30,000 cells of each population were loaded per HIVE by centrifugation and processed immediately without freezing. Libraries were quality checked and then pooled for sequencing on a Novaseq 6000 SP flow cells for PE50 using customized sequencing and indexing primers. Cells were called based UMI per cell knee plot and gene count matrix was generated by aligning to mm10-v2 for downstreatm analysis.
Assembly: mm10
Supplementary files format and content: .h5 Cell Ranger filtered sparse matrix files

molecule: other

extract_protocol:
CITE-seq was performed with 3 different ADT panel configurations: (1) a customized 65-plex cocktail, (2) a prototype 200-plex cocktail for antibody titration (cat number), and (3) a titrated 110-plex cocktail (cat number). Each configuration used TotalSeq-A antibodies purchased from BioLegend (Supplmentary Table X). The 65-plex cocktail was comprised of known hematopoietic stem and progenitor markers as an initial test of the technology, using CD117-enriched mouse bone marrow as input and applying antibodies at the concentrations recommended by BioLegend. The 200-plex cocktail was provided as a lyophilized mix, uniform for each TotalSeq antibody, which was rehydrated at 8x concentration and subsequently diluted to five concentrations: 4x, 2x, 1x, 0.5x, and 0.25x. 1x concentration was determined based on the performance of ADTs in the 65-plex panel or according manufacturer’s recommendation. Five sorted populations were profiled with the 200-plex panel to comprehensively represent rare cell populations in the marrow: total bone marrow cells, CD117-enriched bone marrow cells, FACS sorted HSC/MPP cells (Lin- CD117+ Sca1+ and exclusive of CD48+ CD150-), FACS sorted Multi-Lin cells (Lin- CD117+ CD34+ CD16/32+/low CD115- CD11b- Ly6C- CD150-), and FACS sorted CD127+ (Lymphoid) cells. An unique HTO antibody was added to denote each titration concentration. Same cell population stained with different titration concentrations were pooled together after washing seperately. For the titrated 110-plex panel, a customized lyophilized cocktail was created by BioLegend using selected concentrations from the 200-plex titration experiment. The titrated cocktail was applied to the same five populations except for total bone marrow cells. In addition, each sorted cell population from various gates were stained with an unique HTO, washed and pooled. In each experiment, cells were washed on Laminar Wash MINI or HT2000 System (Curiox Biosystems Inc) with the following settings: 25 cycles, flow rate of 10uL/s, initial volume of 55uL. Pooled cells were captured by 10X Chromium X 3’ version 3.1 kit (1000268, 10X Genomics). TEA-seq was performed on the same groups of cells profiled by CITE-seq following it’s published (reference eLIFE TEA-seq paper) protocol with minor modifications: (1) using a digitonin concentration of 0.025% based on optimization results, (2) the addition of protector RNAse inhibitor (Roche 3335402001) in perm, wash and tagmentation buffers. (3) 80ul instead of 160ul supernant from cDNA amplifications were used to purify pre-amplified ADT. Briefly, 100,000 to 250,000 leftover cells from CITE-seq experiment were permeablized in digitonin perm buffer, washed and then processed as nuclei according to 10X Multiome (1000283, 10X Gemonics) protocol.
Library prep was performed according to protocols with minor modifications such as reduced PCR cycles for ADT and HTO library amplifications. We found pre-PCR ADT/HTO in our libraries were abundant enough that we generally reduced 2 cycles (ADT: 10-12 cycles, HTO: 9-10 cycles). Final transcriptome, ADT and HTO libraries were quantified and analyzed by Qubit dsDNA HS (1000268, Invitrogen), High Sensitivity DNA kit (5067-4626, Agilent Technologies) on 2100 bioanalyzer (G2939BA, Agilent Technologies) and KAPA HiFi library quantification kit (KK4824, Roche).
Dual-indexed transcriptome libraries were pooled and sequenced across multiple Illumina Novaseq 6000 S4 or X plus flow cells (Illumina) with PE150+10+10 or PE100+10+10 settings. Single indexed ADT and HTO libraries were pooled and sequenced on Illumina S2 flow cells with PE50+8 setting or with transcriptome libraries. BCL files were demultiplexed into fastq files for CellRanger input. “AT” was added to the end of RPI-x ADT i7 index (6bp) to match D70X_long HTO index (8bp). HTO and ADT FASTQ files were supplied as 3P feature barcode together with transcriptome FASTQ files into Cell Ranger V6.1.2 count pipeline. Transcriptome was mapped to mm10-v2 reference genomes for downstream analysis and visualization.

value: FACS-sorted hashed Lineages

tag: protocol

value: scRNA-Seq

tag: molecule type

value: HTO


title: cFb_Young_sham-MI_rep1

value: Sham-MI

value: 7 days post-surgery_intervention

value: 5 days


title: Gr2, rep1 [C22012993LR01_Gr2_620211]

tag: host

value: mouse

value: Patient derived xenograft

tag: dose

tag: time


title: MultiLin-Gata1-mCherry negative CD150+ cell 64

description:
Oct23_x_x_002_Cell_64
Fluidigm C1

value: Bone Marrow

value: WT

value: paired-end


title: Gr1, rep2 [C22012986LR01_Gr1_620232]

tag: disease

value: Colorectal adenocarcinoma

value: vehicle

value: 2d post-2nd dose


title: MultiLin-Gata1-mCherry negative CD150+ cell 69

description:
Oct23_x_x_002_Cell_69
Fluidigm C1


title: MultiLin-Gata1-mCherry negative CD150+ cell 63

description:
Oct23_x_x_002_Cell_63
Fluidigm C1


title: FACS-scRNA_Set5_Port_2 RNA

value: RNA


title: BI4303.101.Recovered

description:
Library name: BI4303.101.Recovered
AdditionalSamples.rawCounts.csv
AdditionalSamples.logNormalizedCounts.csv

value: Whole blood

tag: time of_blood_draw


title: BI4301.388.Recovered

description:
Library name: BI4301.388.Recovered
AdditionalSamples.rawCounts.csv
AdditionalSamples.logNormalizedCounts.csv

value: Recovered


title: MultiLin-Gata1-mCherry negative CD150+ cell 61

description:
Oct23_x_x_002_Cell_61
Fluidigm C1


title: FACS-scRNA_Set5_Port_1 RNA

value: FACS-sorted hashed Lineages


title: FACS-scRNA_Set5_Port_1 HTO

value: scRNA-Seq


title: p22179-s086_635870-27-Jul-2020

data_processing:
Alignment was performed using STAR version 2.7.3a and transcripts were annotated using a composite genome reference which included GRCh38 patch 14, and SARS-CoV-2 (GCF_009858895.2,ASM985889v3,MN985325.1).
Transcript abundance estimates were calculated internal to the STAR aligner using the algorithm of htseq-count.
DESeq2 was used for normalization, producing a normalized read count.
Assembly: Genome Reference Consortium Human Build 38 patch release 14 (GRCh38.p14), SARS-CoV-2 Reference Genome (RefBank Accession: GCF_009858895.2)
Supplementary files format and content: PASC.ProcessedData.CountMatrix.Human.csv (read count matrix)

source_name: PBMC

extract_protocol:
PBMCs were lysed in 700 mL of Trizol and then extracted using the miRNeasy Mini kit (Qiagen) with on-column DNase digestion.
RNA quality was assessed using a TapeStation 4200 (Agilent) and then ten nanograms of total RNA was used as input for cDNA synthesis using the Clontech SMART-Seq v4 Ultra Low Input RNA kit (Takara Bio) according to the manufacturer’s instructions. Amplified cDNA was fragmented and appended with dual-indexed barcodes using the Nextera XT DNA Library Preparation kit (Illumina).
Libraries were validated by capillary electrophoresis on a TapeStation 4200 (Agilent), pooled at equimolar concentrations, and sequenced with PE100 reads on an Illumina NovaSeq 6000, yielding ~30 million reads per sample on average.

value: PBMC

tag: gender

value: Female

tag: ethnicity

value: Not Hispanic or Latino

tag: age

tag: vaccine product

value: unknown

tag: gcid

tag: subject id

tag: timepoint

tag: pasc status

value: PASC


title: MultiLin-Gata1-mCherry negative CD150+ cell 62

description:
Oct23_x_x_002_Cell_62
Fluidigm C1

tag: tissue

tag: cell type

tag: genotype


title: MultiLin-Gata1-mCherry negative CD150+ cell 66

description:
Oct23_x_x_002_Cell_66
Fluidigm C1

tag: treatment

tag: protocol


title: MultiLin-Gata1-mCherry negative CD150+ cell 60

description:
Oct23_x_x_002_Cell_60
Fluidigm C1


title: cFb_Young_rep5

value: heart

tag: strain

value: Primary cardiac fibroblasts

value: wild-type

tag: age group

value: young

tag: age (months)

tag: surgery

tag: cell isolation_time

value: 0 days post-surgery_intervention

tag: time in_culture

value: 5 days


title: CellTag_Sca-_2 RNA

description:
10X Chromium 3′ v3.1
CellTag

value: Bone Marrow

value: Sca-

value: WT

tag: molecule type


title: BI4300.954.Recovered

description:
Library name: BI4300.954.Recovered
AdditionalSamples.rawCounts.csv
AdditionalSamples.logNormalizedCounts.csv

value: Whole blood

tag: current long_covid_status

value: Recovered

tag: time of_blood_draw


title: BI4301.197.Recovered

description:
Library name: BI4301.197.Recovered
AdditionalSamples.rawCounts.csv
AdditionalSamples.logNormalizedCounts.csv


title: p22179-s085_635870-04-Dec-2020

tag: gender

tag: ethnicity

tag: age

tag: vaccine product

tag: gcid

tag: subject id


title: p22179-s084_627934-26-Mar-2021

tag: cell type

value: Male

value: Moderna

tag: timepoint

tag: pasc status


title: BI4303.192.Recovered

description:
Library name: BI4303.192.Recovered
AdditionalSamples.rawCounts.csv
AdditionalSamples.logNormalizedCounts.csv

tag: tissue


title: BI4300.376.Recovered

description:
Library name: BI4300.376.Recovered
AdditionalSamples.rawCounts.csv
AdditionalSamples.logNormalizedCounts.csv


title: CellTag_Sca-_1 RNA

description:
10X Chromium 3′ v3.1
CellTag

tag: genotype

tag: treatment

tag: protocol

value: scRNA-Seq

value: RNA


title: MultiLin-Gata1-mCherry negative CD150+ cell 59

description:
Oct23_x_x_002_Cell_59
Fluidigm C1

value: paired-end


title: MultiLin-Gata1-mCherry negative CD150+ cell 58

description:
Oct23_x_x_002_Cell_58
Fluidigm C1


title: CellTag_Sca+_2 RNA

description:
10X Chromium 3′ v3.1
CellTag

value: Sca+


title: p22179-s083_627934-09-Sep-2020

value: PBMC

value: Not Hispanic or Latino

value: PASC


title: Gr1, rep1 [C22012985LR01_Gr1_620210]

tag: host

value: mouse

value: Patient derived xenograft

tag: disease

value: Colorectal adenocarcinoma

value: vehicle

tag: time

value: 2d post-2nd dose

tag: replicate


title: p22179-s082_627934-14-Oct-2020

tag: gender


title: CellTag_Sca+_1 RNA

description:
10X Chromium 3′ v3.1
CellTag

value: Bone Marrow

value: WT

tag: molecule type


title: MultiLin-Gata1-mCherry negative CD150+ cell 56

description:
Oct23_x_x_002_Cell_56
Fluidigm C1


title: BI4103.732.732PASC

description:
Library name: BI4103.732.732PASC
AdditionalSamples.rawCounts.csv
AdditionalSamples.logNormalizedCounts.csv

value: Whole blood

tag: current long_covid_status

tag: time of_blood_draw


title: MultiLin-Gata1-mCherry negative CD150+ cell 57

description:
Oct23_x_x_002_Cell_57
Fluidigm C1


title: FACS-scRNA_Set4 HTO

description:
10X Chromium 3′ v3.1
FACS-scRNA-seq Validation - MultiLin Targeted

value: FACS-sorted hashed Lineages

value: HTO


title: p22179-s080_245742-25-Aug-2021

value: Female

tag: ethnicity

tag: age

tag: vaccine product

value: Pfizer

tag: gcid


title: BI4103.455.455PASC

description:
Library name: BI4103.455.455PASC
AdditionalSamples.rawCounts.csv
AdditionalSamples.logNormalizedCounts.csv


title: FACS-scRNA_Set4 RNA

tag: cell type

value: scRNA-Seq

value: RNA


title: p22179-s081_627934-09-Jul-2020

value: PBMC

value: Male

value: Moderna

tag: subject id

tag: timepoint

tag: pasc status


title: p22179-s079_245742-18-Nov-2021

value: Not Hispanic or Latino

value: PASC


title: BI4300.103.Recovered

description:
Library name: BI4300.103.Recovered
AdditionalSamples.rawCounts.csv
AdditionalSamples.logNormalizedCounts.csv

tag: tissue

value: Recovered


title: MultiLin-Gata1-mCherry negative CD150+ cell 54

description:
Oct23_x_x_002_Cell_54
Fluidigm C1

tag: genotype

tag: treatment

tag: protocol

value: paired-end


title: MultiLin-Gata1-mCherry negative CD150+ cell 55

description:
Oct23_x_x_002_Cell_55
Fluidigm C1


title: FACS-scRNA_Set3 HTO

description:
10X Chromium 3′ v3.1
FACS-scRNA-seq Validation - Pronk et al


title: p22179-s078_245742-12-May-2021


title: BI4036.359.Recovered

description:
Library name: BI4036.359.Recovered
AdditionalSamples.rawCounts.csv
AdditionalSamples.logNormalizedCounts.csv


title: BI4103.195.195PASC

description:
Library name: BI4103.195.195PASC
AdditionalSamples.rawCounts.csv
AdditionalSamples.logNormalizedCounts.csv


title: FACS-scRNA_Set3 RNA


title: BI4036.191.Recovered

description:
Library name: BI4036.191.Recovered
AdditionalSamples.rawCounts.csv
AdditionalSamples.logNormalizedCounts.csv


title: p22179-s077_973285-24-Aug-2020

value: unknown


title: MultiLin-Gata1-mCherry negative CD150+ cell 52

description:
Oct23_x_x_002_Cell_52
Fluidigm C1

value: Bone Marrow


title: p22179-s076_973285-27-Jul-2020


title: MultiLin-Gata1-mCherry negative CD150+ cell 53

description:
Oct23_x_x_002_Cell_53
Fluidigm C1

value: WT


title: BI4035.352.Recovered

description:
Library name: BI4035.352.Recovered
AdditionalSamples.rawCounts.csv
AdditionalSamples.logNormalizedCounts.csv

value: Whole blood


title: BI4036.112.Recovered

description:
Library name: BI4036.112.Recovered
AdditionalSamples.rawCounts.csv
AdditionalSamples.logNormalizedCounts.csv


title: p22179-s075_973285-21-May-2020


title: FACS-scRNA_Set2_Port_2 RNA

description:
10X Chromium 3′ v3.1
FACS-scRNA-seq Validation - Specified States 2

value: FACS-sorted hashed Lineages


title: FACS-scRNA_Set2_Port_1 HTO

value: HTO


title: p22179-s074_961867-13-Jan-2021

value: Female


title: MultiLin-Gata1-mCherry negative CD150+ cell 49

description:
Oct23_x_x_002_Cell_49
Fluidigm C1


title: BI4035.177.Recovered

description:
Library name: BI4035.177.Recovered
AdditionalSamples.rawCounts.csv
AdditionalSamples.logNormalizedCounts.csv


title: MultiLin-Gata1-mCherry negative CD150+ cell 51

description:
Oct23_x_x_002_Cell_51
Fluidigm C1


title: FACS-scRNA_Set2_Port_1 RNA


title: MultiLin-Gata1-mCherry negative CD150+ cell 48

description:
Oct23_x_x_002_Cell_48
Fluidigm C1


title: BI4035.100.Recovered

description:
Library name: BI4035.100.Recovered
AdditionalSamples.rawCounts.csv
AdditionalSamples.logNormalizedCounts.csv


title: MultiLin-Gata1-mCherry negative CD150+ cell 50

description:
Oct23_x_x_002_Cell_50
Fluidigm C1


title: FACS-scRNA_Set1_Port_3 HTO

description:
10X Chromium 3′ v3.1
FACS-scRNA-seq Validation - Specified States


title: BI4033.98.98PASC

description:
Library name: BI4033.98.98PASC
AdditionalSamples.rawCounts.csv
AdditionalSamples.logNormalizedCounts.csv


title: MultiLin-Gata1-mCherry negative CD150+ cell 47

description:
Oct23_x_x_002_Cell_47
Fluidigm C1


title: BI4033.175.175PASC

description:
Library name: BI4033.175.175PASC
AdditionalSamples.rawCounts.csv
AdditionalSamples.logNormalizedCounts.csv


title: p22179-s071_830593-15-Oct-2020

value: NOPASC


title: FACS-scRNA_Set1_Port_3 RNA

value: scRNA-Seq


title: FACS-scRNA_Set2_Port_2 HTO


title: MultiLin-Gata1-mCherry negative CD150+ cell 46

description:
Oct23_x_x_002_Cell_46
Fluidigm C1


title: BI4032.168.Recovered

description:
Library name: BI4032.168.Recovered
AdditionalSamples.rawCounts.csv
AdditionalSamples.logNormalizedCounts.csv


title: p22179-s070_830593-13-Apr-2020


title: MultiLin-Gata1-mCherry negative CD150+ cell 45

description:
Oct23_x_x_002_Cell_45
Fluidigm C1


title: FACS-scRNA_Set1_Port_2 RNA

value: RNA


title: BI4030.762.Recovered

description:
Library name: BI4030.762.Recovered
AdditionalSamples.rawCounts.csv
AdditionalSamples.logNormalizedCounts.csv


title: MultiLin-Gata1-mCherry negative CD150+ cell 44

description:
Oct23_x_x_002_Cell_44
Fluidigm C1


title: FACS-scRNA_Set1_Port_1 HTO


title: BI4030.379.Recovered

description:
Library name: BI4030.379.Recovered
AdditionalSamples.rawCounts.csv
AdditionalSamples.logNormalizedCounts.csv


title: MultiLin-Gata1-mCherry intermediate-high cell 9

description:
Oct23_x_x_001_Cell_9
Fluidigm C1


title: p22179-s073_857858-05-Nov-2020

value: PBMC

value: Pfizer


title: FACS-scRNA_Set1_Port_1 RNA


title: CITE_Titrated_112_Kit+_3 ADT

description:
10X Chromium 3′ v3.1
Final Product CITE-seq - 112 ADT Panel

data_processing:
*library strategy: CITE-seq
Cells were multiplexed using HTOs to distinguish CITE-Seq ADT concentration or cell population. HTO barcode count matrices were obtained through the multimodal analysis workflow in Cell Ranger, prior to normalization (counts per ten thousand (CPTT)). Cell barcodes with > 30% of normalized reads assigned to multiple HTOs were annotated as doublets, with confident singlet assigned to cells with >40% of normalized reads assigned to a single HTO (HTO processing module of AltAnalyze). Cells were further filtered based on the 7 mouse/rat isotype control antibodies counts (Source code) and performed quality control filtering in Seurat V4 by nFeature_RNA>500 & nCount_RNA >1000 & percent.mt<25. This QC step filtered 393,748 cells to 315,792 high-quality single cells in the initial titration dataset and 90,889 to 72,198 cells in the final titrated CITE-Seq dataset.All Cell Ranger produced count matrices underwent ambient RNA exclusion using the software SoupX with a contamination fraction of 15% and quality control filtering by HTO. Ambient corrected transcriptome counts and associated ADTs counts were supplied as input to the software TotalVI to obtain normalized and denoised ADT counts. The Honeycomb HIVE CLX capture system (discountinued, Honeycomb Biotechnologies, Inc) was applied using the manufacturer’s instructions to the following populations: CD117-enriched bone marrow, sorted cells from basophil/mast enriched gates, and those from eosinophil enriched gates. Briefly, 30,000 cells of each population were loaded per HIVE by centrifugation and processed immediately without freezing. Libraries were quality checked and then pooled for sequencing on a Novaseq 6000 SP flow cells for PE50 using customized sequencing and indexing primers. Cells were called based UMI per cell knee plot and gene count matrix was generated by aligning to mm10-v2 for downstreatm analysis.
Assembly: mm10
Supplementary files format and content: .h5 Cell Ranger filtered sparse matrix files

tag: adt cocktail

value: Titrated Mix 112-ADT

value: CITE-Seq

value: ADT


title: FACS-scRNA_Set1_Port_2 HTO


title: BI4030.101.Recovered

description:
Library name: BI4030.101.Recovered
AdditionalSamples.rawCounts.csv
AdditionalSamples.logNormalizedCounts.csv

value: Recovered


title: p22179-s066_775987-27-Oct-2020

tag: gender

value: Not Hispanic or Latino

value: Moderna

value: PASC


title: p22179-s072_857858-28-Jul-2020


title: BI4028.86.86PASC

description:
Library name: BI4028.86.86PASC
AdditionalSamples.rawCounts.csv
AdditionalSamples.logNormalizedCounts.csv


title: p22179-s069_783259-26-Oct-2020


title: p22179-s065_775987-24-Jul-2020


title: MultiLin-Gata1-mCherry intermediate-high cell 43

description:
Oct23_x_x_001_Cell_43
Fluidigm C1

value: Bone Marrow

value: WT

value: paired-end


title: MultiLin-Gata1-mCherry intermediate-high cell 5

description:
Oct23_x_x_001_Cell_5
Fluidigm C1


title: CITE_Titrated_112_Kit+_2 ADT

tag: molecule type


title: CITE_Titrated_112_Kit+_3 RNA


title: BI4028.146.146PASC

description:
Library name: BI4028.146.146PASC
AdditionalSamples.rawCounts.csv
AdditionalSamples.logNormalizedCounts.csv

value: Whole blood

tag: current long_covid_status


title: MultiLin-Gata1-mCherry intermediate-high cell 42

description:
Oct23_x_x_001_Cell_42
Fluidigm C1


title: BI4027.840.840PASC

description:
Library name: BI4027.840.840PASC
AdditionalSamples.rawCounts.csv
AdditionalSamples.logNormalizedCounts.csv

tag: time of_blood_draw


title: BI4030.169.Recovered

description:
Library name: BI4030.169.Recovered
AdditionalSamples.rawCounts.csv
AdditionalSamples.logNormalizedCounts.csv


title: p22179-s063_730342-13-Jul-2020

value: Male

tag: ethnicity


title: p22179-s067_775987-05-Feb-2021

value: Female

tag: age


title: CITE_Titrated_112_Kit+_2 RNA


title: MultiLin-Gata1-mCherry intermediate-high cell 41

description:
Oct23_x_x_001_Cell_41
Fluidigm C1


title: CITE_Titrated_112_Kit+_1 ADT


title: p22179-s068_783259-09-Jul-2020

tag: vaccine product


title: MultiLin-Gata1-mCherry intermediate-high cell 40

description:
Oct23_x_x_001_Cell_40
Fluidigm C1


title: MultiLin-Gata1-mCherry intermediate-high cell 7

description:
Oct23_x_x_001_Cell_7
Fluidigm C1


title: BI4027.194.194PASC

description:
Library name: BI4027.194.194PASC
AdditionalSamples.rawCounts.csv
AdditionalSamples.logNormalizedCounts.csv


title: CITE_Titrated_112_Kit+_1 RNA


title: p22179-s061_711280-12-Nov-2020

tag: gcid


title: MultiLin-Gata1-mCherry intermediate-high cell 4

description:
Oct23_x_x_001_Cell_4
Fluidigm C1

tag: cell type


title: CITE_Titrated_112_CD127+ ADT


title: BI4027.104.104PASC

description:
Library name: BI4027.104.104PASC
AdditionalSamples.rawCounts.csv
AdditionalSamples.logNormalizedCounts.csv


title: p22179-s064_740210-12-Nov-2020

tag: subject id


title: MultiLin-Gata1-mCherry intermediate-high cell 39

description:
Oct23_x_x_001_Cell_39
Fluidigm C1


title: CITE_Titrated_112_HSC-MPP ADT

value: Lin- Sca+ Cd117+


title: BI4021.833.833PASC

description:
Library name: BI4021.833.833PASC
AdditionalSamples.rawCounts.csv
AdditionalSamples.logNormalizedCounts.csv


title: CITE_Titrated_112_CD127+ RNA

value: RNA


title: MultiLin-Gata1-mCherry intermediate-high cell 38

description:
Oct23_x_x_001_Cell_38
Fluidigm C1


title: MultiLin-Gata1-mCherry intermediate-high cell 37

description:
Oct23_x_x_001_Cell_37
Fluidigm C1


title: p22179-s059_711280-08-May-2020

value: PBMC

tag: timepoint


title: p22179-s058_675218-06-Nov-2020

tag: pasc status


title: BI4021.1678.1678PASC

description:
Library name: BI4021.1678.1678PASC
AdditionalSamples.rawCounts.csv
AdditionalSamples.logNormalizedCounts.csv

tag: tissue


title: CITE_Titrated_112_HSC-MPP RNA

tag: genotype


title: BI4021.1100.1100PASC

description:
Library name: BI4021.1100.1100PASC
AdditionalSamples.rawCounts.csv
AdditionalSamples.logNormalizedCounts.csv


title: p22179-s057_675218-05-Aug-2020


title: MultiLin-Gata1-mCherry intermediate-high cell 36

description:
Oct23_x_x_001_Cell_36
Fluidigm C1

tag: treatment


title: BI4021.1009.1009PASC

description:
Library name: BI4021.1009.1009PASC
AdditionalSamples.rawCounts.csv
AdditionalSamples.logNormalizedCounts.csv


title: CITE_Titrated_112_MultiLin_2 ADT

tag: protocol


title: p22179-s062_730342-07-Dec-2020


title: MultiLin-Gata1-mCherry intermediate-high cell 35

description:
Oct23_x_x_001_Cell_35
Fluidigm C1


title: p22179-s056_642537-18-Feb-2021


title: BI4027.746.746PASC

description:
Library name: BI4027.746.746PASC
AdditionalSamples.rawCounts.csv
AdditionalSamples.logNormalizedCounts.csv


title: CITE_Titrated_112_MultiLin_2 RNA

tag: adt cocktail


title: p22179-s055_642537-25-Mar-2021

tag: gender


title: MultiLin-Gata1-mCherry intermediate-high cell 34

description:
Oct23_x_x_001_Cell_34
Fluidigm C1


title: BI4019.907.Recovered

description:
Library name: BI4019.907.Recovered
AdditionalSamples.rawCounts.csv
AdditionalSamples.logNormalizedCounts.csv


title: p22179-s060_711280-22-Oct-2020

value: Pfizer


title: p22179-s054_642537-21-Dec-2020


title: MultiLin-Gata1-mCherry intermediate-high cell 33

description:
Oct23_x_x_001_Cell_33
Fluidigm C1


title: CITE_Titrated_112_MultiLin_1 RNA

value: Titrated Mix 112-ADT

tag: molecule type


title: BI4017.360.Recovered

description:
Library name: BI4017.360.Recovered
AdditionalSamples.rawCounts.csv
AdditionalSamples.logNormalizedCounts.csv

tag: current long_covid_status


title: MultiLin-Gata1-mCherry intermediate-high cell 32

description:
Oct23_x_x_001_Cell_32
Fluidigm C1


title: CITE_Titration_TotalBM ADT

description:
10X Chromium 3′ v3.1
Titration - 195 ADT Panel

value: Total Marrow

value: 5-fold Titration 195-ADT

value: CITE-Seq


title: BI4019.189.Recovered

description:
Library name: BI4019.189.Recovered
AdditionalSamples.rawCounts.csv
AdditionalSamples.logNormalizedCounts.csv

value: Recovered

tag: time of_blood_draw


title: CITE_Titration_TotalBM HTO

value: HTO


title: p22179-s052_615993-20-Jul-2020

tag: ethnicity

value: Not Hispanic or Latino

value: none listed in Epic

value: PASC


title: BI4017.182.Recovered

description:
Library name: BI4017.182.Recovered
AdditionalSamples.rawCounts.csv
AdditionalSamples.logNormalizedCounts.csv


title: p22179-s051_602232-29-Oct-2020

tag: age


title: p22179-s053_615993-19-Oct-2020

tag: vaccine product


title: MultiLin-Gata1-mCherry intermediate-high cell 31

description:
Oct23_x_x_001_Cell_31
Fluidigm C1

value: Bone Marrow

value: WT

value: paired-end


title: BI4014.463.Recovered

description:
Library name: BI4014.463.Recovered
AdditionalSamples.rawCounts.csv
AdditionalSamples.logNormalizedCounts.csv

value: Whole blood


title: MultiLin-Gata1-mCherry intermediate-high cell 29

description:
Oct23_x_x_001_Cell_29
Fluidigm C1


title: p22179-s050_602232-20-Jul-2020

value: Female

tag: gcid


title: CITE_Titration_TotalBM RNA

tag: cell type

value: RNA


title: p22179-s049_601096-14-Dec-2020

value: PBMC

value: unknown

tag: subject id

value: NOPASC


title: MultiLin-Gata1-mCherry intermediate-high cell 30

description:
Oct23_x_x_001_Cell_30
Fluidigm C1


title: CITE_Titration_CD127+ HTO


title: BI4014.190.Recovered

description:
Library name: BI4014.190.Recovered
AdditionalSamples.rawCounts.csv
AdditionalSamples.logNormalizedCounts.csv


title: MultiLin-Gata1-mCherry intermediate-high cell 27

description:
Oct23_x_x_001_Cell_27
Fluidigm C1


title: BI4014.105.Recovered

description:
Library name: BI4014.105.Recovered
AdditionalSamples.rawCounts.csv
AdditionalSamples.logNormalizedCounts.csv


title: CITE_Titrated_112_MultiLin_1 ADT

description:
10X Chromium 3′ v3.1
Final Product CITE-seq - 112 ADT Panel

value: Titrated Mix 112-ADT

value: ADT


title: BI4019.462.Recovered

description:
Library name: BI4019.462.Recovered
AdditionalSamples.rawCounts.csv
AdditionalSamples.logNormalizedCounts.csv


title: p22179-s048_599658-16-Nov-2020

value: Moderna

tag: timepoint


title: MultiLin-Gata1-mCherry intermediate-high cell 26

description:
Oct23_x_x_001_Cell_26
Fluidigm C1


title: p22179-s047_599658-21-Sep-2020

tag: pasc status


title: BI4012.27.605PASC

description:
Library name: BI4012.27.605PASC
AdditionalSamples.rawCounts.csv
AdditionalSamples.logNormalizedCounts.csv

tag: tissue

value: Acute


title: CITE_Titration_CD127+ RNA

tag: genotype

value: 5-fold Titration 195-ADT

value: CITE-Seq


title: MultiLin-Gata1-mCherry intermediate-high cell 24

description:
Oct23_x_x_001_Cell_24
Fluidigm C1

tag: treatment


title: CITE_Titration_MultiLin HTO

tag: protocol

value: HTO


title: BI4012.174.415PASC

description:
Library name: BI4012.174.415PASC
AdditionalSamples.rawCounts.csv
AdditionalSamples.logNormalizedCounts.csv

value: PASC


title: MultiLin-Gata1-mCherry intermediate-high cell 23

description:
Oct23_x_x_001_Cell_23
Fluidigm C1

value: Bone Marrow


title: CITE_Titration_MultiLin ADT

value: WT

tag: adt cocktail


title: p22179-s046_592571-22-Apr-2021

tag: gender

value: Not Hispanic or Latino

value: Pfizer


title: p22179-s045_592571-25-Nov-2020

value: Female


title: BI4012.143.721PASC

description:
Library name: BI4012.143.721PASC
AdditionalSamples.rawCounts.csv
AdditionalSamples.logNormalizedCounts.csv

value: Whole blood


title: MultiLin-Gata1-mCherry intermediate-high cell 22

description:
Oct23_x_x_001_Cell_22
Fluidigm C1

value: paired-end


title: CITE_Titration_MultiLin RNA

tag: molecule type

value: RNA


title: p22179-s044_592571-07-Aug-2020

value: PBMC


title: MultiLin-Gata1-mCherry intermediate-high cell 21

description:
Oct23_x_x_001_Cell_21
Fluidigm C1


title: BI4010.297.1097PASC

description:
Library name: BI4010.297.1097PASC
AdditionalSamples.rawCounts.csv
AdditionalSamples.logNormalizedCounts.csv

tag: current long_covid_status


title: BI4008.727.1087PASC

description:
Library name: BI4008.727.1087PASC
AdditionalSamples.rawCounts.csv
AdditionalSamples.logNormalizedCounts.csv

tag: time of_blood_draw


title: CITE_Titration_CD127+ ADT


title: CITE_Titration_HSC-MPP HTO

value: Lin- Sca+ Cd117+


title: p22179-s043_592571-28-Apr-2020

tag: ethnicity


title: BI4008.363.723PASC

description:
Library name: BI4008.363.723PASC
AdditionalSamples.rawCounts.csv
AdditionalSamples.logNormalizedCounts.csv


title: p22179-s041_588063-24-Nov-2020

tag: age

value: unknown


title: CITE_Titration_HSC-MPP RNA


title: CITE_Titration_HSC-MPP ADT

value: ADT


title: MultiLin-Gata1-mCherry intermediate-high cell 19

description:
Oct23_x_x_001_Cell_19
Fluidigm C1


title: CITE_Titration_Kit+ HTO


title: p22179-s040_588063-15-Sep-2020

tag: vaccine product


title: p22179-s042_588063-26-Feb-2021

tag: gcid


title: CITE_Titration_Kit+ ADT

tag: cell type


title: BI4007.734.734PASC

description:
Library name: BI4007.734.734PASC
AdditionalSamples.rawCounts.csv
AdditionalSamples.logNormalizedCounts.csv


title: MultiLin-Gata1-mCherry intermediate-high cell 18

description:
Oct23_x_x_001_Cell_18
Fluidigm C1


title: MultiLin-Gata1-mCherry intermediate-high cell 17

description:
Oct23_x_x_001_Cell_17
Fluidigm C1


title: BI4010.748.748PASC

description:
Library name: BI4010.748.748PASC
AdditionalSamples.rawCounts.csv
AdditionalSamples.logNormalizedCounts.csv


title: CITE_Titration_Kit+ RNA


title: BI4007.487.487PASC

description:
Library name: BI4007.487.487PASC
AdditionalSamples.rawCounts.csv
AdditionalSamples.logNormalizedCounts.csv


title: MultiLin-Gata1-mCherry intermediate-high cell 20

description:
Oct23_x_x_001_Cell_20
Fluidigm C1


title: MultiLin-Gata1-mCherry intermediate-high cell 15

description:
Oct23_x_x_001_Cell_15
Fluidigm C1


title: BI4007.1125.1125PASC

description:
Library name: BI4007.1125.1125PASC
AdditionalSamples.rawCounts.csv
AdditionalSamples.logNormalizedCounts.csv


title: p22179-s037_578305-15-Dec-2020

value: Male

tag: subject id


title: CITE_195_CD127+ ADT

description:
10X Chromium 3′ v3.1
Universal Mix v1.0 - 195 ADT Panel

value: Universal PBMC Mix 195-ADT


title: p22179-s036_548367-10-Dec-2020

value: Moderna

tag: timepoint


title: MultiLin-Gata1-mCherry intermediate-high cell 13

description:
Oct23_x_x_001_Cell_13
Fluidigm C1


title: BI4006.870.1117PASC

description:
Library name: BI4006.870.1117PASC
AdditionalSamples.rawCounts.csv
AdditionalSamples.logNormalizedCounts.csv


title: CITE_195_CD127+ RNA

value: CITE-Seq


title: MultiLin-Gata1-mCherry intermediate-high cell 2

description:
Oct23_x_x_001_Cell_2
Fluidigm C1


title: BI4006.467.714PASC

description:
Library name: BI4006.467.714PASC
AdditionalSamples.rawCounts.csv
AdditionalSamples.logNormalizedCounts.csv

value: PASC


title: CITE_195_MultiLin ADT

value: Bone Marrow


title: BI4002.373.373PASC

description:
Library name: BI4002.373.373PASC
AdditionalSamples.rawCounts.csv
AdditionalSamples.logNormalizedCounts.csv


title: MultiLin-Gata1-mCherry intermediate-high cell 11

description:
Oct23_x_x_001_Cell_11
Fluidigm C1

value: WT


title: BI4008.112.472PASC

description:
Library name: BI4008.112.472PASC
AdditionalSamples.rawCounts.csv
AdditionalSamples.logNormalizedCounts.csv


title: p22179-s035_524853-18-May-2021

value: Not Hispanic or Latino

tag: pasc status

value: NOPASC


title: MultiLin-Gata1-mCherry intermediate-high cell 12

description:
Oct23_x_x_001_Cell_12
Fluidigm C1

tag: tissue


title: CITE_195_MultiLin RNA

tag: genotype


title: p22179-s039_578305-02-Sep-2020

value: Pfizer


title: BI4002.174.174PASC

description:
Library name: BI4002.174.174PASC
AdditionalSamples.rawCounts.csv
AdditionalSamples.logNormalizedCounts.csv

value: Whole blood


title: p22179-s034_485912-22-Sep-2020

value: Female


title: MultiLin-Gata1-mCherry intermediate-high cell 10

description:
Oct23_x_x_001_Cell_10
Fluidigm C1

tag: treatment

value: paired-end


title: p22179-s033_485912-07-Dec-2020

value: PBMC


title: CITE_195_HSC-MPP RNA

value: Lin- Sca+ Cd117+

tag: protocol

value: RNA


title: p22179-s038_578305-01-Jul-2020


title: p22179-s032_450560-02-Nov-2020

value: unknown


title: CITE_195_HSC-MPP ADT

tag: adt cocktail

value: ADT


title: MultiLin-Gata1-mCherry intermediate-high cell 14

description:
Oct23_x_x_001_Cell_14
Fluidigm C1


title: MultiLin-Gata1-mCherry intermediate-high cell 1

description:
Oct23_x_x_001_Cell_1
Fluidigm C1


title: BI4002.103.103PASC

description:
Library name: BI4002.103.103PASC
AdditionalSamples.rawCounts.csv
AdditionalSamples.logNormalizedCounts.csv


title: p22179-s031_440795-11-Aug-2020

tag: gender


title: cKit+CD127+ cell 96

description:
Il7r.Cd117.Cell_96
Fluidigm C1

value: cKit+CD127+ cell


title: CITE_195_Kit+_2 RNA

value: Universal PBMC Mix 195-ADT

tag: molecule type


title: BI4001.919.1328PASC

description:
Library name: BI4001.919.1328PASC
AdditionalSamples.rawCounts.csv
AdditionalSamples.logNormalizedCounts.csv

tag: current long_covid_status


title: cKit+CD127+ cell 95

description:
Il7r.Cd117.Cell_95
Fluidigm C1


title: p22179-s030_440795-28-Sep-2020


title: BI4001.321.730PASC

description:
Library name: BI4001.321.730PASC
AdditionalSamples.rawCounts.csv
AdditionalSamples.logNormalizedCounts.csv

tag: time of_blood_draw


title: CITE_195_Kit+_1 ADT

value: CITE-Seq


title: cKit+CD127+ cell 93

description:
Il7r.Cd117.Cell_93
Fluidigm C1


title: p22179-s029_440795-09-Jul-2020

tag: ethnicity

value: PASC


title: CITE_195_Kit+_1 RNA

value: Bone Marrow


title: BI4001.1060.1469PASC

description:
Library name: BI4001.1060.1469PASC
AdditionalSamples.rawCounts.csv
AdditionalSamples.logNormalizedCounts.csv


title: cKit+CD127+ cell 92

description:
Il7r.Cd117.Cell_92
Fluidigm C1

value: WT


title: CITE_60_ADT_Kit+ ADT

description:
10X Chromium 3′ v3.0
Initial CITE-seq - 60 ADT Panel

value: Manual Titrated 60-ADT


title: p22179-s028_440795-08-Jan-2021

value: Not Hispanic or Latino

tag: age


title: BI376.561.Recovered

description:
Library name: BI376.561.Recovered
AdditionalSamples.rawCounts.csv
AdditionalSamples.logNormalizedCounts.csv

value: Recovered


title: cKit+CD127+ cell 90

description:
Il7r.Cd117.Cell_90
Fluidigm C1


title: CITE_60_ADT_Kit+ RNA


title: cKit+CD127+ cell 91

description:
Il7r.Cd117.Cell_91
Fluidigm C1


title: CITE_195_Kit+_2 ADT


title: BI376.368.Recovered

description:
Library name: BI376.368.Recovered
AdditionalSamples.rawCounts.csv
AdditionalSamples.logNormalizedCounts.csv

value: Whole blood


title: TEA_MultiLin_2 ATAC

description:
10X Chromium 3′ v3.1
TEA-seq
TEA_MultiLin_2.h5

tag: sampe type

value: ATAC

value: Titrated Mix 112-ADT

value: TEA-Seq


title: BI338.163.Recovered

description:
Library name: BI338.163.Recovered
AdditionalSamples.rawCounts.csv
AdditionalSamples.logNormalizedCounts.csv


title: p22179-s026_315570-06-May-2020

value: PBMC

value: Male

tag: vaccine product

tag: gcid

value: NOPASC


title: p22179-s025_310418-26-Jan-2021

tag: cell type

value: Female

value: Moderna

tag: subject id


title: cKit+CD127+ cell 89

description:
Il7r.Cd117.Cell_89
Fluidigm C1

value: cKit+CD127+ cell

value: paired-end


title: TEA_MultiLin_2 ADT

value: ADT


title: BI4001.688.1097PASC

description:
Library name: BI4001.688.1097PASC
AdditionalSamples.rawCounts.csv
AdditionalSamples.logNormalizedCounts.csv

value: PASC


title: BI338.100.Recovered

description:
Library name: BI338.100.Recovered
AdditionalSamples.rawCounts.csv
AdditionalSamples.logNormalizedCounts.csv


title: p22179-s024_310418-14-Aug-2020

tag: timepoint

tag: pasc status


title: TEA_MultiLin_2 RNA

tag: tissue

value: Bone Marrow

value: RNA

tag: genotype

value: WT


title: BI1419.610.Recovered

description:
Library name: BI1419.610.Recovered
AdditionalSamples.rawCounts.csv
AdditionalSamples.logNormalizedCounts.csv

value: Recovered


title: p22179-s023_310418-18-Sep-2020

value: Not Hispanic or Latino


title: TEA_MultiLin_1 ATAC

description:
10X Chromium 3′ v3.1
TEA-seq
TEA_MultiLin_1.h5

value: ATAC

tag: treatment

tag: protocol


title: BI1419.140.Recovered

description:
Library name: BI1419.140.Recovered
AdditionalSamples.rawCounts.csv
AdditionalSamples.logNormalizedCounts.csv

value: Whole blood


title: cKit+CD127+ cell 87

description:
Il7r.Cd117.Cell_87
Fluidigm C1


title: cKit+CD127+ cell 86

description:
Il7r.Cd117.Cell_86
Fluidigm C1


title: TEA_MultiLin_1 ADT

tag: adt cocktail

value: Titrated Mix 112-ADT

value: TEA-Seq


title: p22179-s022_261527-09-Jul-2020

value: PBMC

tag: gender


title: 181121_cochlea_8D

first: Erin

middle: Elizabeth

last: Duffy

address: 200 Longwood Ave, Goldenson 405

department: Neurobiology

institute: Harvard Medical School

description: Library name: 181121_cochlea_8D

data_processing:
All experiments were sequenced on the NextSeq 500 (Illumina). Seventy-five bp paired-endreads were obtained for all datasets. ATAC-seq experiments were sequenced to a minimumdepth of 20 million reads. All samples were aligned to the mm10 genome using default parameters for the Subreadalignment software (subread-1.4.6-p3) (3) after quality trimming with Trimmomatic v0.33(4) with the following command: java -jar trimmomatic-0.33.jar SE -threads 1 -phred33 [FASTQ_FILE] ILLUMINACLIP:[ADAPTER_FILE]:2:30:10 LEADING:5TRAILING:5 SLIDINGWINDOW:4:20 MINLEN:45. Nextera adapters were specified for ATAC-seq data.
Putative cochlear GREs (regions of ATAC-seq enrichment) were identified as described previously. Briefly, peaks were determined using MACS2 (v 2.1.0) parameters -p 1e- 5–nolambda – keep-dup all – slocal 10000, as previously described 29 . Peaks from individual sample replicates were intersected to find only reproducible regions of enrichment. Blacklist regions were removed as previously described. To identify sites with enriched ATAC-seq signal (peaks), we applied the IDR pipeline using the MACS2 peak calling algorithm 60 with the following parameters: –nomodel –extsize 200 –keep-dup all. An IDR threshold of 0.01 was used for self- consistency, true replicate, and pooled-consistency analyses. The ‘optThresh’ cutoff was then used to obtain a final set of high-confidence, reproducible ATAC-seq peaks for each sample.
Assembly: mm10

source_name: COCHLEA

extract_protocol:
Neonatal (P2, n=3; P5, n=3; P8, n=4) CD1 mice were sacrificed and cochleas were dissected bilaterally as described above. All tissue from each animal was combined and dounced 10 times in 5 ml of HB buffer (0.25 M sucrose, 25 mM KCl, 5 mM MgCl 2 , 20 mM Tricine-KOH pH 7.8, 1 mM DTT, 0.15 mM spermine, 0.5 mM spermidine, DTT 1 mM [Sigma], one-half Roche proteinase inhibitor tablet) in a 7-ml Dounce homogenizer with tight pestle, then supplemented with IGEPAL CA-630 to final concentration of 0.3%, and finally dounced an additional five times with the tight pestle. Nuclei were filtered through a 40-μm strainer and gently combined 1:1 with 50% iodixanol. Nuclei were then underlaid with a gradient of 1 ml 40% iodixanol and 1 ml 30% iodixanol and centrifuged at 10,000g for 19 minutes using the no brake setting. Purified nuclei (0.8 ml) were then collected from the 30/40% interface. A 20-μl aliquot was taken for visual inspection and cell counting, with typical yield of ~100,000-200,000 cochlear nuclei per animal.
ATAC-seq (assay for transposase accessible chromatin with sequencing) was performed using the OMNI-ATAC protocol 58 immediately following the nuclear isolation steps described above. Nuclei (50,000) were pelleted at 500 g for 10 minutes at 4°C in a fixed angle centrifuge and resuspended in 50 μl transposition buffer (prepared from Illumina kit components TD buffer and 100 nM transposase, as well as 0.01% digitonin, 0.1% Tween-20) via careful pipetting. Transposition occurred at 37°C in a thermomixer at 1000 rpm for 30 minutes before resuspension in 250 μl of DNA binding buffer (Zymo DNA Clean and Concentrator Kit) and reaction cleanup per manufacture instructions, with final elution volume of 21 μl in elution buffer. Samples were amplified following NEBNext High-Fidelity 2X PCR Master Mix manufacturer protocols (NEB) in a total reaction volume of 50 μl (1.25 μM each of i5 and i7 sequencing primers) at 72°C for 5 minutes, 98°C for 30 seconds, (98°C for 10 seconds, 63°C for 30 seconds, and 72°C for 1 minute) x10 cycles. PCR samples were re-purified following the Zymo manufacturer protocol and eluted into 21 μl of elution buffer. Size selection was performed via agarose gel (150-1000 bp) followed by Qiagen MinElute gel extraction according to the manufacturer’s instructions, with two serial 10 μl elution steps. Sequencing (75-bp paired-end) was performed on an Illumina NextSeq500.

value: COCHLEA

tag: post-natal age_(days)


title: p22179-s027_315570-20-Aug-2020

value: Male

value: unknown

value: NOPASC


title: cKit+CD127+ cell 85

description:
Il7r.Cd117.Cell_85
Fluidigm C1

value: cKit+CD127+ cell

value: paired-end


title: p22179-s021_261527-07-Aug-2020

value: Female

value: Moderna

value: PASC


title: TEA_MultiLin_1 RNA

value: Bone Marrow

value: RNA

value: WT


title: cKit+CD127+ cell 84

description:
Il7r.Cd117.Cell_84
Fluidigm C1


title: 181121_cochlea_8B

description: Library name: 181121_cochlea_8B


title: TEA_HSC-MPP_2 ATAC

description:
10X Chromium 3′ v3.1
TEA-seq
TEA_HSC-MPP_2.h5

value: ATAC

value: Lin- Sca+ Cd117+


title: 181121_cochlea_8C

description: Library name: 181121_cochlea_8C


title: p22179-s020_251227-06-Nov-2020

value: Not Hispanic or Latino


title: TEA_HSC-MPP_2 ADT

value: ADT

value: Titrated Mix 112-ADT

value: TEA-Seq


title: p22179-s019_251227-06-Aug-2020

value: PBMC


title: cKit+CD127+ cell 88

description:
Il7r.Cd117.Cell_88
Fluidigm C1


title: cKit+CD127+ cell 83

description:
Il7r.Cd117.Cell_83
Fluidigm C1


title: p22179-s018_251227-04-May-2020


title: cKit+CD127+ cell 82

description:
Il7r.Cd117.Cell_82
Fluidigm C1


title: 181121_cochlea_8A

description: Library name: 181121_cochlea_8A

value: COCHLEA


title: TEA_HSC-MPP_2 RNA


title: cKit+CD127+ cell 81

description:
Il7r.Cd117.Cell_81
Fluidigm C1


title: 181121_cochlea_5D

description: Library name: 181121_cochlea_5D


title: 181121_cochlea_5C

description: Library name: 181121_cochlea_5C


title: TEA_HSC-MPP_1 ATAC

description:
10X Chromium 3′ v3.1
TEA-seq
TEA_HSC-MPP_1.h5


title: p22179-s016_243818-18-May-2020

value: Pfizer


title: TEA_HSC-MPP_1 ADT


title: 181121_cochlea_5B

description: Library name: 181121_cochlea_5B


title: 181121_cochlea_2D

description: Library name: 181121_cochlea_2D


title: p22179-s015_227438-07-Jul-2021


title: cKit+CD127+ cell 79

description:
Il7r.Cd117.Cell_79
Fluidigm C1

value: cKit+CD127+ cell


title: TEA_HSC-MPP_1 RNA


title: cKit+CD127+ cell 78

description:
Il7r.Cd117.Cell_78
Fluidigm C1

value: paired-end


title: p22179-s014_227438-12-Nov-2021

value: Female