title: Blood,excercised,cell535,wk03rd_infec


title: ATAC_2h_washout_BRM014_rep2

status: Public on Jun 13 2024

type: SRA

city: Boston

first: Julia

middle: M

last: Rogers

state: Massachusetts

address: 45 Shattuck Street

department: BCMP

country: USA

institute: Harvard Medical School

description: merged_ATAC_single_2_washout_brm014.bedGraph.bw

library_source: genomic

data_processing:
Read pairs were trimmed to 100 base pairs using a custom script (trim_and_filter_PE.pl, https://doi.org/10.5281/zenodo.11222086), and reads with a minimum average quality score of 20 were kept. Adapter sequences were removed using cutadapt 1.1441. Reads were first mapped to the spike genome (dm6), using bowtie1.2.2 (-k1 -v2 -X1000 – allow-contain -- best parameters). Reads that did not map to the spike genome were mapped to the human genome (hg38), using bowtie1.2.245 (-k1 -v2 -X1000 – allow-contain -- best parameters). Samtools 1.943 was used to flag duplicate reads, which were then removed. A custom script, extract_fragments.pl, was used to filter and retain unique reads between 10 and 150 base pairs, which correspond to regions of open chromatin, and convert files into bedGraph format. Spike return rates were not significantly different between samples. To normalize samples, reads mapping to the -1 kb to +1 kb region around active promoters in this cell type were counted using the custom script makeheatmap with the “-b v -v t -s b” options. The number of these reads was used to calculate size factors using DESeq246. These size factors were scaled so the minimum was 1, and used to normalize bedGraphs with the custom script normalize_bedGraph.pl. Biological replicates (n=2) were merged using the script bedgraphs2stbedGraph.pl.
Assembly: hg38
Supplementary files format and content: bigwig files with replicates merged for each time point

molecule: genomic DNA

organism: Homo sapiens

growth_protocol: SC2 squamous cell carcinoma cells were cultured in keratinocyte media, consisting of: 3:1 DMEM:F12 + 10% Fetal Bovine Serum (Gemini Bio-Products 100-106) + 1X Penicillin-Streptomycin (ThermoFisher 15140163) + 1X Reagent Mix (see below) + 1 μM Compound E (EMD Millipore565790) gamma secretase inhibitor (GSI). 100X Reagent Mix was prepared in 3:1 DMEM:F12 media, containing 40 mg/mL Hydrocortisone (Sigma-Aldrich H0888), 500 ng/mL Insulin (Sigma-Aldrich I6634), 1mg/mL EGF (Sigma-Aldrich E9644), 0.84 mg/mL Cholera toxin (Sigma-Aldrich C9903), 500 mg/mL Transferrin (Sigma-Aldrich T2036), and 1.3 mg/mL Liothyronine (Sigma-Aldrich T6397). GSI was prepared as a 1 mM stock of Compound E in DMSO (Sigma-Aldrich 472301). Cells were split every 3-4 days, using 0.25% trypsin (VWR 45000-664) supplemented with 1 μM GSI. Cells were incubated in 0.25% trypsin at 37 ºC until cells began to slough off the plate, then were quenched with fresh media and replated. Cells were routinely tested for mycoplasma, and used for experiments within 1 month of thawing a fresh vial.

extract_protocol:
At the time point after washout or mock washout, cells were rinsed in PBS, and harvested using 0.25 % trypsin with GSI and/or BRM014 according to the sample, and quenched with SC2 media containing GSI and/or  BRM014. Cells were counted, and 100,000 cells were transferred to an Eppendorf tube, and combined with 10,000 fly spike-in cells. The spike-in S2 cells had been collected, resuspended in BAMBANKER cryopreservative media (VWR 101974-112), aliquoted, and stored at -80°C. All spike in aliquots for one experimental time course replicate were thawed and combined before beginning the time course. ATAC was performed according to the OmniATAC protocol. Briefly, cells were pelleted at 500 g for 5 min at 4°C, and supernatant was removed. The cell pellet was resuspended in 50 mL ATAC lysis buffer by pipetting up and down 3 times (Cold ATAC-Resuspension Buffer (10 mM Tris–HCl pH 7.5, 10 mM NaCl and 3 mM MgCl2) + 0.1 % NP40 (EMD Millipore 492018) + 0.1 % Tween-20 (EMD Millipore 655206) + 0.01 % digitonin (Promega G9441)). Up to 4 samples were processed at 1 time, and samples were staggered by 15 seconds. After exactly 3 min of lysis, 1 mL of ATAC wash buffer (Cold ATAC-Resuspension Buffer + 0.1 % Tween-20 (EMD Millipore655206)) was added to the tube. Nuclei were pelleted at 500 g for 10 min at 4°C, and supernatant was removed. Nuclei were resuspended in 50 mL of Transposition mix (1x TD buffer (Illumina 20334197), 3 mL Tn5 transposase (Illumina 20334197), 0.33x PBS, 0.01 % digitonin, 0.1 % Tween-20), and incubated at 37°C in a thermomixer at 1000 rpm for 30 minutes. The reactions were quenched with 250 mL of binding buffer from the MinElute PCR purification kit (Qiagen 28004) and purified using this kit.
The eluate was then used as the input for barcoding PCR, to add sequencing adapters and sequencing barcodes, as described in Grandi et al.. Both the qPCR and Qubit methods were used to quantify the libraries to determine the total number of PCR cycles, as described in the OmniATAC protocol. After the final PCR cycles, libraries were cleaned up with the MinElute PCR purification kit, quantified using the NEBNext Library Quant kit (New England Biolabs E7630), and pooled for sequencing. Libraries were sequenced paired end on a NovaSeq with an S1 single lane 100 cycle kit.

treatment_protocol: For all gamma secretase inhibitor (GSI) washouts, media was removed, cells were washed twice with media containing 0.1% DMSO instead of GSI, and replenished with media containing 0.1%  DMSO instead of GSI, for a total of three media changes. In the mock washouts, both the washing media and the replenishing media contained 1 μM GSI. For experiments with BRM014 (MedChem Express HY-119374), the replenishing media, but not the washout media, either contained 1µM BRM014 or 0.01% DMSO depending on the sample. The evening before the time course, cells were plated in 12 well dishes, at 125,000 cells / well in SC2 media with 1 µM GSI. For each time course, 14 samples were prepared: 0 hr mock washout + BRM014, 0 hr mock washout – BRM014, 1 hr washout + BRM014, 1 hr washout - BRM014, 1 hr mock washout + BRM014, 1 hr mock washout - BRM014, 2 hr washout + BRM014, 2 hr washout - BRM014, 2 hr mock washout + BRM014, 2 hr mock washout - BRM014, 4 hr washout + BRM014, 4 hr washout - BRM014, 4 hr mock washout + BRM014, 4 hr mock washout - BRM014. Replicates were performed on different days (n=2).

tag: cell line

tag: cell type

value: squamous cell carcinoma

tag: treatment

value: GSI washout


title: ATAC_2h_washout_DMSO_rep1

description: merged_ATAC_single_2_washout_dmso.bedGraph.bw


title: Blood,excercised,cell536,wk04th_infec

city: Sydney

first: Rowena

last: Bull

state: NSW

address: Wallace Wurth Building (C27)

country: Australia

institute: University of New South Wales

description: SMARTseq2 single cell RNA sequencing data from E2-specific memory B cells

library_source: transcriptomic single cell

data_processing:
The raw data was aligned with human genome to map the heavy and light chain genes which were further annotated using IgBlast software implemented in VDJPuzzle
Inhouse pipeline used to generate the matrix that was further processed using seurat and other packages for paired-end sequences
Assembly: Sequences were processed using VDJPuzzle for BCR data and inhouse pipelines for Gene expression analysis
Supplementary files format and content: barcodes.tsv
Supplementary files format and content: features.tsv
Supplementary files format and content: matrix.mtx

molecule: total RNA

source_name: Blood

extract_protocol:
Seven to ten million cryopreserved PBMCs were sorted for E2-specific B cells as described previously. S figure 4, in the article indicates the time points selected for flow analysis and transcriptomics/repertoire analysis. In brief, PBMCs were stained with an in-house developed rE2 cocktail tetramer (Gt1a [H77] and Gt3a [UKN3A13.6]) as well as anti-CD19, anti-CD20, anti-CD10, anti-CD38, anti-IgD, anti-IgG, anti-CD27,anti-CD21 and anti-CD95 antibodies, and single cell sorted using flow cytometry. Population phenotypes were analysed with FlowJo version 10 software (Tree Star Inc.) (See CTAT Table for antibody details and see S Figure 3 for gating strategy and how gates were set for CD95 positivity based on FMO).
E2+ B cells were sorted into single wells and single cell RNA sequencing was performed following the smartseq2 protocol as previously described. BCR sequences were reconstructed using VDJpuzzle 2.0. Identification of B cell clonotypes and SHM across infections was done using Immcantation framework.  Paired-end reads from Smart-seq2 were aligned with STAR (version 2.7.1a) using the GRCh38.p13 human reference genome. Transcripts per Million (TPM) were quantified using RSEM (version 1.2.28) using rsem-calculate-expression command on HPC clusters.

tag: tissue

value: Blood

value: human samples

value: Memory B cells

tag: genotype


title: ATAC_2h_GSI_DMSO_rep1

description: merged_ATAC_single_2_gsi_dmso.bedGraph.bw

value: mock washout


title: Blood,excercised,cell538,wk04th_infec


title: Blood,excercised,cell534,wk03rd_infec


title: ATAC_2h_GSI_BRM014_rep2

description: merged_ATAC_single_2_gsi_brm014.bedGraph.bw


title: ATAC_2h_GSI_DMSO_rep2


title: ATAC_2h_washout_BRM014_rep1


title: Blood,excercised,cell533,wk03rd_infec


title: Blood,excercised,cell532,wk03rd_infec


title: ATAC_4h_GSI_DMSO_rep2

description: merged_ATAC_single_4_gsi_dmso.bedGraph.bw


title: ATAC_1h_washout_DMSO_rep1

description: merged_ATAC_single_1_washout_dmso.bedGraph.bw


title: Blood,excercised,cell531,wk03rd_infec


title: ATAC_1h_washout_BRM014_rep2

description: merged_ATAC_single_1_washout_brm014.bedGraph.bw


title: Blood,excercised,cell529,wk03rd_infec


title: ATAC_1h_washout_BRM014_rep1


title: ATAC_1h_GSI_DMSO_rep2

description: merged_ATAC_single_1_gsi_dmso.bedGraph.bw


title: Blood,excercised,cell528,wk03rd_infec


title: Blood,excercised,cell527,wk03rd_infec


title: Blood,excercised,cell537,wk04th_infec


title: ATAC_1h_GSI_DMSO_rep1


title: Blood,excercised,cell526,wk03rd_infec


title: ATAC_1h_GSI_BRM014_rep2

description: merged_ATAC_single_1_gsi_brm014.bedGraph.bw


title: ATAC_1h_GSI_BRM014_rep1


title: ATAC_0h_GSI_DMSO_rep1

description: merged_ATAC_single_0_gsi_dmso.bedGraph.bw


title: Blood,excercised,cell523,wk03rd_infec


title: ATAC_0h_GSI_DMSO_rep2


title: ATAC_1h_washout_DMSO_rep2


title: Blood,excercised,cell525,wk03rd_infec


title: ATAC_2h_GSI_BRM014_rep1


title: Blood,excercised,cell520,wk03rd_infec


title: Blood,excercised,cell522,wk03rd_infec


title: Blood,excercised,cell524,wk03rd_infec


title: Sh-DDX41_2_411D

city: Cincinnati

first: Kwangmin

last: Choi

state: Ohio

address: 333 Burnet Avenue

department: Experimental Hematology & Cancer Biology

institute: Cincinnati Children's Hospital Medical Center

library_source: transcriptomic

data_processing:
The quality of paired reads were checked using FASTQC (v0.11.7)
Reads were aligned against human mm10 genome using HISAT2 (v2.0.5)
Each gene-level raw counts were calculated using featureCounts (v1.5.2)
Assembly: hg38
Supplementary files format and content: Tab-delimited text file, raw gene-count matrix

growth_protocol: MOLM13 cells are grown in RPMI medium containing 20% FBS and Pen/strep

extract_protocol:
RNA was isolated using the Quick-RNA Miniprep Kit (Zymo)
TruSeq Stranded mRNA library prep, follwing manufacturer protocol (Illumina)

treatment_protocol: MOLM13 cells are transduced by pLKO-GFP viruses produced in 293T cells by transfection with viral plasmid and lentiviral envelope plasmids. Cells were sorted on a Sony SH800 sorter on the fourth day post-tranduction.


title: ATAC_0h_GSI_BRM014_rep2

description: merged_ATAC_single_0_gsi_brm014.bedGraph.bw


title: Blood,excercised,cell521,wk03rd_infec


title: Sh-DDX41_2_411B


title: Blood,excercised,cell530,wk03rd_infec


title: Blood,excercised,cell517,wk03rd_infec


title: ATAC_0h_GSI_BRM014_rep1


title: Sh-DDX41_2_411A


title: Blood,excercised,cell518,wk03rd_infec


title: Sh-DDX41_1_409B


title: Sh-DDX41_1_409A


title: Blood,excercised,cell514,wk03rd_infec


title: Sh-DDX41_1_409D


title: Blood,excercised,cell516,wk03rd_infec


title: Blood,excercised,cell515,wk03rd_infec


title: sh-Control_38D

value: sh-Control


title: Blood,excercised,cell513,wk03rd_infec


title: Blood,excercised,cell519,wk03rd_infec


title: Blood,excercised,cell511,wk03rd_infec


title: sh-Control_38B


title: Blood,excercised,cell512,wk03rd_infec


title: KI_4

first: William

middle: T.

last: Pu

state: Ma

address: 300 Longwood Ave

department: Cardiology

institute: Boston Children's Hospital

data_processing:
Raw reads were trimmed using Trim Galore (https://github.com/FelixKrueger/TrimGalore). Clean reads were aligned to the human genome (hg38) using STAR (Version 2.7.10). To calculate gene expression values, the FPKM (Fragments Per Kilobase Million) values were calculated by Cufflinks (version 2.1.1). Principle component analyses were performed by the “prcomp” function of R. For differential expression analysis, read count tables were generated using HTSeq (Version 0.6.1), which were used for differential gene expression analysis using the R DEseq2 package. Differentially expressed genes were defined as genes with count>5, Log2FoldChange>1, and PAdj<0.05.
Assembly: human genome (hg38)
Supplementary files format and content: CSV

source_name: iPSC

extract_protocol:
RNeasy Plus mini kit (Qiagen, #74134)
stranded RNA-seq

value: iPSC

value: iPSC-Cardiomyocyte

value: PBS


title: Blood,excercised,cell510,wk03rd_infec


title: Blood,excercised,cell506,wk03rd_infec


title: Blood,excercised,cell509,wk03rd_infec


title: Blood,excercised,cell504,wk03rd_infec


title: Sh-Control_38A


title: ASO4_1

description: WTC, ASO4 treated

value: WT


title: ASOcontrol_2

description: WTC, ASOcontrol treated

value: ASO control


title: Blood,excercised,cell508,wk03rd_infec


title: KI_1


title: ASOcontrol_1

description: WTC, ASOcontrol treated


title: Blood,excercised,cell505,wk03rd_infec


title: ASO4_4

description: WTC, ASO4 treated


title: ASOcontrol_4

description: WTC, ASOcontrol treated


title: Blood,excercised,cell502,wk03rd_infec


title: Blood,excercised,cell503,wk03rd_infec


title: KI_3


title: Blood,excercised,cell501,wk03rd_infec


title: ASO3_3

description: WTC, ASO3 treated


title: Blood,excercised,cell507,wk03rd_infec


title: ASO3_4

description: WTC, ASO3 treated


title: Blood,excercised,cell500,wk03rd_infec


title: Blood,excercised,cell498,wk03rd_infec


title: ASO3_2

description: WTC, ASO3 treated


title: ASO1_4

description: WTC, ASO1 treated


title: ASO4_2

description: WTC, ASO4 treated


title: Blood,excercised,cell499,wk03rd_infec


title: ASO1_3

description: WTC, ASO1 treated


title: Blood,excercised,cell497,wk03rd_infec


title: ASO1_1

description: WTC, ASO1 treated


title: Non-treated_3

description: WTC, non-treated


title: Blood,excercised,cell495,wk03rd_infec


title: Non-treated_1

description: WTC, non-treated


title: Blood,excercised,cell492,wk03rd_infec


title: Blood,excercised,cell493,wk03rd_infec


title: OF054

city: New York

first: Osama

last: Al Dalahmah

state: NY

address: 622 West 168th Street

department: Pathology & Cell Biology

institute: Columbia University Irving Medical Center

description: 10X Genomics

data_processing:
Alignment was done using the CellRanger pipeline (10X Genomics) to GRCh38.p12 (refdata-cellrangerGRCh38–1.2.0 file provided by 10x Genomics).
Count matrices were generated from BAM files using default parameters of the DropEst pipeline.
Filtering low quality cells: we first used the combined quality calls from the CellRanger algorithm as well as the DropEst algorithm. This allowed us to retain more high quality nuclei than either algorithm alone. Data 562  QC was done using the scater package 48. Nuclei with percent exonic reads from all reads in the range of less 75% were included. Nuclei with percent mitochondrial reads aligning to mitochondria genes of more than 14% were excluded. Genes were filtered by keeping features with > 10 counts per row in at least in 31 cells. A temporary count slot was created by decontaminating the counts from ambient RNA by calling decontX() function in R . These counts were used for downstream clustering, but not differential gene expression analysis.
to correct for sequencing and technical batches, we utilized Liger and SeuratWrappers for Seurat. Briefly, Seurat objects containing raw reads were normalized in Seurat by calling NormalizeData() on the combined object. Variable features were then detected by calling FindVariableFeatures(). We then scaled the data by calling ScaleData(object, split.by = "Batch", do.center = FALSE). Next, we called RunOptimizeALS(object, k = 20, lambda = 5, split.by = "Batch") and RunQuantileAlignSNF(object, split.by = "Batch").
Normalization of counts was done using the SCTrasform function in Seurat, accounting for mitochondrial reads and batch
Assembly: GRCh38
Supplementary files format and content: .csv files of matrix that are gzipped

source_name: Cingulate

extract_protocol:
The tissue was homogenized in a Dounce homogenizer with 12–15 strokes of the loose pestle and 12–15 strokes of the tight pestle on ice in a Triton X-100 based, sucrose containing buffer. The suspension from each sample was filtered through a BD Falcon tubes with a cell strainer caps (Becton Dickinson, cat. no. 352235), washed, re-filtered, washed, followed by a cleanup step using iodixanol gradient centrifugation. The nuclear pellet was then re-suspended in 1% BSA in 545 nuclease-free PBS (containing RNAse inhibitors) and titrated to 600-1200 nuclei/μl.
Nuclear suspensions were processed by the Chromium Controller (10x Genomics) using single Cell 3′ Reagent Kit v2 or v3 (Chromium Single Cell 3′ Library & Gel Bead Kit v2/v3, catalog number PN-1000075; Chromium Single Cell A Chip Kit, 48 runs, catalog number: 120236; 10x Genomics). Sequencing and alignment: Sequencing of the snRNAseq libraries was done on Illumina NOVAseq 6000 platformV4 150 bp paired end reads.
snRNA (single-nuclei RNA sequencing)

value: Cingulate

tag: Sex

value: Female

tag: grade

tag: batch


title: Blood,excercised,cell496,wk03rd_infec


title: Blood,excercised,cell491,wk03rd_infec


title: Blood,excercised,cell489,wk03rd_infec


title: OF052

description: 10X Genomics

source_name: Accumbens

value: Accumbens


title: OF053

description: 10X Genomics

value: Male

value: Control


title: Blood,excercised,cell488,wk03rd_infec


title: Blood,excercised,cell490,wk03rd_infec


title: OF049

description: 10X Genomics

source_name: Caudate

value: Caudate


title: OF055

description: 10X Genomics


title: Blood,excercised,cell486,wk03rd_infec


title: Blood,excercised,cell487,wk03rd_infec


title: OF048

description: 10X Genomics


title: OF051

description: 10X Genomics


title: Blood,excercised,cell484,wk03rd_infec


title: OF047

description: 10X Genomics


title: Blood,excercised,cell485,wk03rd_infec


title: Non-treated_4

description: WTC, non-treated


title: OF046

description: 10X Genomics

value: HDJ


title: Blood,excercised,cell483,wk03rd_infec

value: Blood


title: Blood,excercised,cell494,wk03rd_infec

value: human samples


title: OF045

description: 10X Genomics


title: Blood,excercised,cell482,wk03rd_infec

value: Memory B cells


title: OF044

description: 10X Genomics


title: Blood,excercised,cell481,wk03rd_infec


title: OF043

description: 10X Genomics


title: OF050

description: 10X Genomics


title: OF042

description: 10X Genomics


title: Blood,excercised,cell480,wk03rd_infec


title: Blood,excercised,cell478,wk03rd_infec


title: Blood,excercised,cell479,wk03rd_infec


title: OF036

description: 10X Genomics


title: Blood,excercised,cell475,wk03rd_infec


title: OF041

description: 10X Genomics


title: Blood,excercised,cell476,wk03rd_infec


title: Blood,excercised,cell473,wk03rd_infec


title: OF037

description: 10X Genomics


title: OF035

description: 10X Genomics


title: OF040

description: 10X Genomics


title: Blood,excercised,cell474,wk03rd_infec


title: Blood,excercised,cell472,wk03rd_infec


title: Blood,excercised,cell471,wk03rd_infec


title: OF038

description: 10X Genomics


title: OF039

description: 10X Genomics


title: OF033

description: 10X Genomics


title: OF034

description: 10X Genomics


title: Blood,excercised,cell470,wk03rd_infec


title: OF032

description: 10X Genomics


title: Blood,excercised,cell477,wk03rd_infec


title: OF028

description: 10X Genomics


title: OF029

description: 10X Genomics


title: Blood,excercised,cell469,wk03rd_infec


title: OF030

description: 10X Genomics


title: OF027

description: 10X Genomics


title: Blood,excercised,cell468,wk03rd_infec


title: OF025

description: 10X Genomics


title: OF026

description: 10X Genomics


title: Blood,excercised,cell466,wk03rd_infec


title: Blood,excercised,cell467,wk03rd_infec


title: OF022

description: 10X Genomics


title: Blood,excercised,cell464,wk03rd_infec


title: OF023

description: 10X Genomics


title: Blood,excercised,cell463,wk03rd_infec


title: Blood,excercised,cell457,wk03rd_infec


title: Blood,excercised,cell461,wk03rd_infec


title: H5286Cin

description: 10X Genomics


title: Blood,excercised,cell462,wk03rd_infec


title: Blood,excercised,cell455,wk03rd_infec


title: Blood,excercised,cell460,wk03rd_infec


title: Blood,excercised,cell458,wk03rd_infec


title: H5263Cin

description: 10X Genomics


title: Blood,excercised,cell456,wk03rd_infec


title: C5596Cin

description: 10X Genomics


title: Blood,excercised,cell454,wk03rd_infec


title: C5700Cin

description: 10X Genomics


title: H5608Cin

description: 10X Genomics


title: Blood,excercised,cell465,wk03rd_infec


title: Blood,excercised,cell452,81M


title: OF019

description: 10X Genomics


title: H5109Cin

description: 10X Genomics


title: Blood,excercised,cell453,81M


title: H4161Cin

description: 10X Genomics


title: OF020

description: 10X Genomics


title: H5608Cd

description: 10X Genomics


title: Blood,excercised,cell450,81M


title: Blood,excercised,cell449,81M


title: Blood,excercised,cell459,wk03rd_infec


title: H5109Cd

description: 10X Genomics


title: C4812Cd

description: 10X Genomics


title: Blood,excercised,cell448,81M


title: Blood,excercised,cell447,81M


title: H5263Cd

description: 10X Genomics


title: Blood,excercised,cell451,81M


title: Blood,excercised,cell446,81M


title: C5227Cd

description: 10X Genomics


title: C5227Cin

description: 10X Genomics


title: Blood,excercised,cell445,81M


title: Blood,excercised,cell444,81M


title: H4161Cd

description: 10X Genomics


title: Blood,excercised,cell442,81M


title: H5109A

description: 10X Genomics


title: Blood,excercised,cell443,81M


title: C5227A

description: 10X Genomics


title: H4161A

description: 10X Genomics


title: Blood,excercised,cell440,81M


title: H5575Cd

description: 10X Genomics


title: 5596Cd

description: 10X Genomics


title: Blood,excercised,cell441,81M


title: H5493Cd

description: 10X Genomics


title: Blood,excercised,cell439,81M


title: Blood,excercised,cell437,81M


title: H5575A

description: 10X Genomics


title: C5700Cd

description: 10X Genomics


title: Blood,excercised,cell434,81M


title: H5493A

description: 10X Genomics


title: C5700A

description: 10X Genomics


title: Blood,excercised,cell436,81M


title: C5596A

description: 10X Genomics


title: H5608A

description: 10X Genomics


title: Blood,excercised,cell432,81M


title: 5493Cin

description: 10X Genomics


title: Blood,excercised,cell431,81M


title: H5263A

description: 10X Genomics


title: Blood,excercised,cell433,81M


title: 5382Cin

description: 10X Genomics


title: 5575Cin

description: 10X Genomics


title: HMC3P2A-3

data_processing:
Raw reads were aligned to the reference (GRCh38.92) using STAR78.
Count matrices were generated from the BAM files using featureCount with default options.
Differential gene expression analysis was performed in EdgeR using the glmQLFit method79. Gene set enrichment analysis was performed in enrichR80 and/or gprofiler281, 82.
Assembly: GRCh38 Ensemble 91
Supplementary files format and content: .csv files

source_name: Microglia cell lines (HMC3)

growth_protocol: HMC3 cells (ATCC cat#CRL-3304) were seeded in 24 well-plate at 5X10^4 each well in 0.5ml culture medium (DMEM with 10% FBS medium) and cultured overnight

extract_protocol:
Total RNA was extracted from frozen brain tissue samples using an automated Qiagen platform (QiaSymphony). RIN values were measured on an Agilent Bioanalyzer. All samples had RIN values > 7.
The samples were processed using an Illumina® Stranded mRNA Prep kit and were sequenced on an Illumina NOVASEQ 6000 sequencer to produce stranded 100-base pair paired end libraries at 20 million read depth per sample. For RNAseq of microglial cultures, the samples were processed using an Illumina TruSeq Stranded total RNA kit and sequenced on an Illumina NextSeq sequencer at a read depth of 10 million reads per sample.

treatment_protocol: co-culture with control, CLU overexpressing, or MT3 overexpressing astrocytes in a transwell assay. The astrocytes were seeded in the upper chamber of a 24 well-plate 0.4um polycarbonate membrane inserts (costar cat#3413) pre-coated with Poly L-Lysine, at 5X10^4 cells per insert in 0.1ml of astrocyte growth medium (Sciencell™) 3 hours before transferring the insert to the wells containing the microglia. The two cell types were co-cultured for 24hrs before the astrocyte inserts were removed for collecting microglial RNA for RNAseq

value: Microglia cell lines (HMC3)


title: HMC3P2A-2


title: Blood,excercised,cell438,81M


title: Blood,excercised,cell427,81M


title: Blood,excercised,cell426,81M


title: HMC3P2A-1


title: Blood,excercised,cell425,81M


title: Blood,excercised,cell435,81M


title: HMC3MT3-3


title: HMC3MT3-2


title: Blood,excercised,cell424,81M


title: 5404Cin

description: 10X Genomics


title: Blood,excercised,cell423,81M


title: Blood,excercised,cell422,81M


title: Blood,excercised,cell421,81M


title: Blood,excercised,cell430,81M


title: HMC3HA-3


title: HMC3DMSO-4


title: Blood,excercised,cell429,81M


title: HMC3HA-2


title: HMC3DMSO-1


title: Blood,excercised,cell420,81M


title: Blood,excercised,cell418,81M


title: HMC3DMSO-2


title: HMC3DMSO-3


title: Blood,excercised,cell417,81M


title: Blood,excercised,cell416,81M


title: HMC3CLU-3


title: Blood,excercised,cell415,81M


title: Blood,excercised,cell428,81M


title: HMC3CLU-2


title: HMC3CLU-1


title: Blood,excercised,cell414,81M


title: Blood,excercised,cell413,81M


title: OF052


title: HMC3MT3-1


title: Blood,excercised,cell412,81M


title: OF051


title: Blood,excercised,cell419,81M


title: OF050

value: J


title: Blood,excercised,cell411,81M


title: OF049


title: Blood,excercised,cell410,81M


title: Blood,excercised,cell409,81M


title: OF047


title: OF048


title: OF046


title: Blood,excercised,cell408,81M


title: OF044


title: Blood,excercised,cell404,81M


title: Blood,excercised,cell407,81M


title: Blood,excercised,cell403,81M


title: OF043


title: Blood,excercised,cell401,81M


title: OF041


title: OF045


title: Blood,excercised,cell402,81M


title: OF040


title: Blood,excercised,cell400,81M


title: Blood,excercised,cell398,81M


title: OF039


title: Blood,excercised,cell399,81M


title: OF037


title: OF038


title: OF042


title: Blood,excercised,cell397,81M


title: Blood,excercised,cell396,81M


title: Blood,excercised,cell405,81M


title: Blood,excercised,cell395,81M


title: OF036


title: OF035


title: Blood,excercised,cell406,81M


title: OF034


title: Blood,excercised,cell392,81M


title: Blood,excercised,cell394,81M


title: Blood,excercised,cell393,81M


title: OF031


title: Blood,excercised,cell391,81M


title: Blood,excercised,cell390,81M


title: OF029


title: OF030


title: OF032


title: OF028


title: Blood,excercised,cell388,81M


title: OF027


title: Blood,excercised,cell389,81M


title: Blood,excercised,cell387,81M


title: OF025


title: Blood,excercised,cell386,48M


title: OF024


title: OF023


title: OF026


title: Blood,excercised,cell385,48M


title: Blood,excercised,cell383,48M


title: Blood,excercised,cell384,48M


title: Blood,excercised,cell382,48M


title: OF022


title: Blood,excercised,cell380,48M


title: Blood,excercised,cell381,48M


title: OF019


title: Blood,excercised,cell379,48M


title: H5301_Cing


title: C5382_Cing


title: OF021


title: Blood,excercised,cell377,48M


title: Blood,excercised,cell375,48M


title: Blood,excercised,cell376,48M


title: OF033


title: C4518_Cing


title: H5575_Caud


title: Blood,excercised,cell374,48M


title: H5575_Cing


title: Blood,excercised,cell373,48M


title: C180_Cing


title: Blood,excercised,cell370,48M


title: Blood,excercised,cell372,48M


title: H5493_Cing


title: Blood,excercised,cell371,48M


title: H5300_Cing


title: C98_Cing


title: Blood,excercised,cell368,48M


title: H3859_Cing


title: OF020


title: C4812_Cing


title: Blood,excercised,cell378,48M


title: Blood,excercised,cell369,48M


title: Blood,excercised,cell367,48M


title: C5404_Cing


title: Blood,excercised,cell366,48M


title: C5832_Caud


title: Blood,excercised,cell365,48M


title: Blood,excercised,cell362,48M


title: Blood,excercised,cell364,48M


title: C5700_Caud


title: Blood,excercised,cell361,48M


title: C5700_Accum


title: Blood,excercised,cell363,48M


title: H5608-Cing


title: Blood,excercised,cell359,48M


title: C5596_Cing


title: Blood,excercised,cell358,wk24


title: H5608_Accum


title: C5596_Caud


title: Blood,excercised,cell357,wk24


title: H4929_Cing


title: Blood,excercised,cell356,wk24


title: H5575_Accum


title: C5700_Cing


title: Blood,excercised,cell353,wk24


title: Blood,excercised,cell354,wk24


title: Blood,excercised,cell355,wk24


title: H5493_Caud


title: Blood,excercised,cell360,48M


title: H5493_Accum


title: H5608_Caud


title: H5263_Cing


title: Blood,excercised,cell352,wk24


title: Blood,excercised,cell350,wk24


title: H5263_Caud


title: Blood,excercised,cell349,wk24


title: C5227_Accum


title: Blood,excercised,cell351,wk24


title: C5596_Accum


title: H5263_Accum


title: Blood,excercised,cell346,wk24


title: C5227_Caud


title: C5227_Cing


title: H5109_Caud


title: H5109_Cing


title: H5109_Accum


title: Blood,excercised,cell344,wk24


title: C4915_Cing


title: Blood,excercised,cell345,wk24


title: Blood,excercised,cell347,wk24


title: Blood,excercised,cell343,wk24


title: C4915_Caud


title: Blood,excercised,cell340,wk24


title: H4161_Cing


title: Blood,excercised,cell342,wk24


title: C4915_Accum


title: Blood,excercised,cell341,wk24


title: Blood,excercised,cell339,wk24


title: C4812_Caud


title: Blood,excercised,cell337,wk24


title: Blood,excercised,cell338,wk24


title: H4161_Caud


title: Blood,excercised,cell348,wk24


title: CD8_40_14

city: Munich

first: David

last: Effinger

address: Marchioninistraße 15

department: Department of Anaesthesiology

country: Germany

institute: LMU University Hospital

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
The mapped reads of each sample were assembled by StringTie (v1.3.3b) (Mihaela Pertea.et al. 2015) in a reference-based approach.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2R package (1.20.0).
Assembly: Reference genome: Homo Sapiens(GRCh38/hg38)
Supplementary files format and content: txt files with raw counts CD4 T cells at T14 CTRL vs Keto
Supplementary files format and content: txt files with raw counts CD4 T cells at T1 CTRL vs Keto
Supplementary files format and content: txt files with raw counts CD8 T cells at T14 CTRL vs Keto
Supplementary files format and content: txt files with raw counts CD8 T cells at T1 CTRL vs Keto

source_name: immune cell

extract_protocol:
Peripheral blood mononuclear cells (PBMC) were obtained by HIsopaque-1077-based density centrifugation (Sigma-Aldrich, St. Louis, MO,USA). CD4 and CD8 T-cell isolation from PBMC was performed via microbead-based separation (CD4 MicroBeads, human, # 130-045-10; CD8 MicroBeads, human # 130-045-201; Miltenyi Biotec, Bergisch Gladbach,Germany) via an AutoMACSPro Separator according to the manufacturer's protocol (# 130-092-545, Miltenyi Biotec, Bergisch Gladbach, Germany).T cells were lysed in QIAzol Lysis Reagent and isolated using the miRNeasy Mini Kit (50) according to the manufacturer's protocol.
Messenger RNAwas purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNAwas synthesized using random hexamer primers,followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non-directional library. For the non-directional library, it was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. For the directional library, it was ready after end repair, A-tailing, adapter ligation, size selection,USER enzyme digestion, amplification, and purification. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries will be pooled and sequenced on Illumina platforms, according to effective library concentration and data amount.

value: immune cell

value: CD8 T cell

value: Keto


title: H4161_Accum


title: CD8_39_14


title: CD8_39_1


title: Blood,excercised,cell331,wk24


title: Blood,excercised,cell336,wk24


title: CD8_40_1


title: Blood,excercised,cell330,wk24


title: Blood,excercised,cell334,wk24


title: Blood,excercised,cell329,wk24


title: Blood,excercised,cell335,wk24


title: Blood,excercised,cell328,wk0-3rd-infec


title: CD8_38_14

value: CTRL


title: CD8_37_1


title: CD8_36_1


title: Blood,excercised,cell333,wk24


title: Blood,excercised,cell327,wk0-3rd-infec


title: Blood,excercised,cell332,wk24


title: CD8_35_14


title: CD8_37_14


title: Blood,excercised,cell325,wk0-3rd-infec


title: Blood,excercised,cell324,wk0-3rd-infec


title: Blood,excercised,cell323,wk0-3rd-infec


title: CD8_35_1


title: Blood,excercised,cell321,wk0-3rd-infec


title: CD8_34_1


title: Blood,excercised,cell322,wk0-3rd-infec


title: CD8_33_14


title: CD8_33_1


title: Blood,excercised,cell326,wk0-3rd-infec


title: CD8_31_14


title: CD8_38_1


title: CD8_36_14


title: Blood,excercised,cell320,wk0-3rd-infec


title: Blood,excercised,cell319,wk0-3rd-infec


title: CD8_31_1


title: Blood,excercised,cell318,wk0-3rd-infec


title: CD8_30_14


title: CD8_30_1


title: Blood,excercised,cell317,wk0-3rd-infec


title: CD8_29_14


title: Blood,excercised,cell315,wk0-3rd-infec


title: Blood,excercised,cell314,wk0-3rd-infec


title: CD8_26_1


title: CD8_29_1


title: CD8_34_14


title: Blood,excercised,cell316,wk0-3rd-infec


title: CD8_25_1


title: Blood,excercised,cell312,wk0-3rd-infec


title: Blood,excercised,cell313,wk0-3rd-infec


title: CD8_26_14


title: CD8_25_14


title: Blood,excercised,cell311,wk0-3rd-infec


title: Blood,excercised,cell310,wk0-3rd-infec


title: Blood,excercised,cell309,wk0-3rd-infec


title: CD8_19_1


title: CD8_20_1


title: Blood,excercised,cell308,wk0-3rd-infec


title: CD8_16_1


title: Blood,excercised,cell306,wk0-3rd-infec


title: CD8_16_14


title: Blood,excercised,cell305,wk0-3rd-infec


title: CD8_19_14


title: CD8_15_14


title: CD8_15_1


title: Blood,excercised,cell304,wk0-3rd-infec


title: CD8_20_14


title: CD8_13_14


title: Blood,excercised,cell303,wk0-3rd-infec


title: Blood,excercised,cell302,wk0-3rd-infec


title: Blood,excercised,cell301,wk0-3rd-infec


title: CD8_12_1


title: Blood,excercised,cell299,wk0-3rd-infec


title: Blood,excercised,cell298,wk0-3rd-infec


title: Blood,excercised,cell297,wk0-3rd-infec


title: CD8_8_14


title: Blood,excercised,cell300,wk0-3rd-infec


title: CD8_10_1


title: CD8_8_1


title: CD8_13_1


title: Blood,excercised,cell296,wk0-3rd-infec


title: CD8_10_14


title: Blood,excercised,cell307,wk0-3rd-infec


title: Blood,excercised,cell294,wk0-3rd-infec


title: CD8_5_1


title: Blood,excercised,cell293,wk0-3rd-infec


title: CD8_4_14


title: CD8_4_1


title: CD8_3_14


title: Blood,excercised,cell292,wk0-3rd-infec


title: CD8_12_14


title: Blood,excercised,cell289,wk0-3rd-infec


title: Blood,excercised,cell290,wk0-3rd-infec


title: Blood,excercised,cell291,wk0-3rd-infec


title: Blood,excercised,cell287,wk0-3rd-infec


title: CD8_1_14


title: CD8_1_1


title: CD4_40_14

value: CD4 T cell


title: Blood,excercised,cell284,66M


title: CD8_5_14


title: CD4_39_14


title: CD4_39_1


title: Blood,excercised,cell283,66M


title: Blood,excercised,cell285,66M


title: CD4_40_1


title: Blood,excercised,cell281,66M


title: CD4_37_14


title: Blood,excercised,cell280,66M


title: Blood,excercised,cell282,66M


title: CD8_3_1


title: CD4_38_14


title: CD4_38_1


title: Blood,excercised,cell279,66M


title: Blood,excercised,cell277,66M


title: CD4_36_1


title: CD4_35_14


title: CD4_36_14


title: CD4_37_1


title: Blood,excercised,cell276,66M


title: Blood,excercised,cell275,66M


title: CD4_34_14


title: Blood,excercised,cell274,66M


title: CD4 35 T1


title: Blood,excercised,cell286,66M


title: Blood,excercised,cell288,wk0-3rd-infec


title: CD4_34_1


title: CD4_33_14


title: Blood,excercised,cell273,66M


title: Blood,excercised,cell271,66M


title: CD4_33_1


title: Blood,excercised,cell270,66M


title: CD4_31_1


title: Blood,excercised,cell269,66M


title: CD4_30_14


title: CD4_30_1


title: Blood,excercised,cell278,66M


title: CD4_29_14


title: Blood,excercised,cell268,66M


title: Blood,excercised,cell266,66M


title: Blood,excercised,cell267,66M


title: CD4_29_1


title: Blood,excercised,cell265,66M


title: CD4_26_14


title: CD4_25_14


title: CD4_25_1


title: CD4_20_14


title: Blood,excercised,cell261,66M


title: Blood,excercised,cell263,66M


title: Blood,excercised,cell272,66M


title: CD4_20_1


title: CD4_31_14


title: Blood,excercised,cell259,66M


title: CD4_19_1


title: Blood,excercised,cell258,66M


title: Blood,excercised,cell257,66M


title: CD4_16_14


title: CD4_16_1


title: Blood,excercised,cell256,66M


title: Blood,excercised,cell255,66M


title: Blood,excercised,cell254,66M


title: CD4_26_1


title: Blood,excercised,cell264,66M


title: CD4_13_14


title: CD4_15_1


title: Blood,excercised,cell262,66M


title: Blood,excercised,cell252,66M


title: Blood,excercised,cell253,66M


title: CD4_13_1


title: CD4_12_14


title: CD4_12_1


title: Blood,excercised,cell260,66M


title: CD4_19_14


title: CD4_10_1


title: Blood,excercised,cell248,66M


title: Blood,excercised,cell247,66M


title: Blood,excercised,cell249,66M


title: CD4_8_1


title: Blood,excercised,cell246,66M


title: CD4_8_14


title: CD4_5_14


title: Blood,excercised,cell244,54M


title: Blood,excercised,cell245,54M


title: Blood,excercised,cell251,66M


title: Blood,excercised,cell243,54M


title: Blood,excercised,cell242,54M


title: CD4_4_1


title: CD4_3_14


title: CD4_10_14


title: Blood,excercised,cell241,54M


title: CD4_4_14


title: Blood,excercised,cell240,54M


title: Blood,excercised,cell239,54M


title: CD4_1_14


title: CD4_3_1


title: Blood,excercised,cell238,54M


title: CD4_1_1


title: Blood,excercised,cell250,66M


title: Blood,excercised,cell237,54M


title: Blood,excercised,cell236,54M


title: MeOH_HEK293T_Buffer_only_replicate3

city: La Jolla

first: Brian

last: Yee

state: CA

address: 9500 Gilman Dr

department: Health

institute: UCSD

data_processing:
remove adapter with Cutadapt
align to hg38 using STAR 2.4.0 (Homo sapiens) or mm10 using STAR 2.5.2 (Mus musculus)
SAILOR analysis to call C-to-U edits and keep only sites with score >0.5 and edit fraction <80%
FLARE analysis to call C-to-U edit clusters
Intersect the edit clusters from 3 replicates, which yields "*confident_peaks.bed"
Subtract STAMP confident clusters to Buffer only control, which yields "*cleaned_confident_peaks.bed"
Assembly: hg38
Assembly: mm10
Supplementary files format and content: SAILOR step yields bed file: *0.5Score0.8Fraction.fastqTr.sorted.STARUnmapped.out.sorted.STARAligned.out.sorted.bam.combined.readfiltered.formatted.varfiltered.snpfiltered.ranked.bed
Supplementary files format and content: FLARE step yields .tsv file: "*merged_sorted_peaks.fdr_0.1.d_15.scored.tsv"
Supplementary files format and content: Intersection step yields .bed file:  "*confident_peaks.bed"
Supplementary files format and content: Subtraction step yields .bed file:  "*cleaned_confident_peaks.bed"

source_name: Kidney

extract_protocol:
Direct-zol RNA Miniprep Kits, Zymo Research (Cat # R2052)
Ilumina TruSeq Stranded mRNA Library Prep (Cat #  20020594)

value: Kidney

value: immortalized cell line

tag: replicate


title: Blood,excercised,cell235,54M


title: MeOH_HEK293T_Buffer_only_replicate2


title: CD4_5_1


title: MeOH_HEK293T_Buffer_only_replicate1


title: MeOH_HEK293T_TDP43_replicate3


title: MeOH_HEK293T_Enzyme_only_replicate1


title: Blood,excercised,cell232,54M


title: Blood,excercised,cell234,54M


title: Blood,excercised,cell229,54M


title: Blood,excercised,cell228,54M


title: Blood,excercised,cell233,54M


title: MeOH_HEK293T_TDP43_replicate2


title: Blood,excercised,cell230,54M


title: MeOH_HEK293T_Enzyme_only_replicate2


title: MeOH_HEK293T_Enzyme_only_replicate3


title: MeOH_HEK293T_TDP43_replicate1


title: Blood,excercised,cell224,54M


title: MeOH_HEK293T_RBFOX2_replicate2


title: Blood,excercised,cell227,54M


title: PFA_HEK293T_Buffer_Only_replicate2


title: MeOH_HEK293T_RBFOX2_replicate1


title: Blood,excercised,cell226,54M


title: Blood,excercised,cell231,54M


title: Blood,excercised,cell225,54M


title: PFA_HEK293T_Buffer_Only_replicate3


title: Blood,excercised,cell222,54M


title: Blood,excercised,cell223,54M


title: PFA_HEK293T_Buffer_Only_replicate1


title: Blood,excercised,cell221,54M


title: PFA_HEK293T_Enzyme_Only_replicate3


title: PFA_HEK293T_Enzyme_Only_replicate2


title: MeOH_HEK293T_RBFOX2_replicate3


title: Blood,excercised,cell295,wk0-3rd-infec


title: CD4_15_14


title: Blood,excercised,cell216,54M


title: Blood,excercised,cell220,54M


title: Blood,excercised,cell215,54M


title: PFA_HEK293T_TDP43_STAMP_replicate1


title: PFA_HEK293T_RBFOX2_STAMP_replicate3


title: Blood,excercised,cell218,54M


title: PFA_HEK293T_TDP43_STAMP_replicate3


title: MEL1_S6_2-IP

first: Hui

last: Pan

address: 1 Joslin Place

department: Bioinformatics and Biostatistics Core

institute: Joslin Diabetes Center

data_processing:
The reads were mapped and counted in 50-bp bins of each gene.
Peak calling, peak merging, and read counting in merged peaks were using the R package MeRIPtools (Zhang et al. 2020).
Supplementary files format and content: CSV

extract_protocol:
H1 and MEL1 hESCs were differentiated to Stage 3 (S3), Stage 4 (S4) and Stage 6 (S6) as reported previously (Kahraman et al. Nat Metab. 2022).
Total RNA was isolated by TRIzol reagent and mRNAs were purified by dynabeads mRNA purification kit.

value: hESCs

tag: clone

tag: type

value: ip


title: Blood,excercised,cell217,54M


title: MEL1_S4_2-IP


title: Blood,excercised,cell214,54M


title: Blood,excercised,cell212,54M


title: Blood,excercised,cell208,54M


title: PFA_HEK293T_RBFOX2_STAMP_replicate2


title: Blood,excercised,cell213,54M


title: MEL1_S4_1-IP


title: MEL1_S0_2-IP


title: MEL1_S3_1-IP


title: Blood,excercised,cell207,54M


title: Blood,excercised,cell206,54M


title: MEL1_S6_1-IP


title: Blood,excercised,cell210,54M


title: PFA_HEK293T_RBFOX2_STAMP_replicate1


title: Blood,excercised,cell211,54M


title: Blood,excercised,cell209,54M


title: Blood,excercised,cell219,54M


title: PFA_HEK293T_Enzyme_Only_replicate1


title: PFA_HEK293T_TDP43_STAMP_replicate2


title: MEL1_S3_2-IP


title: MEL1_S4_2-input

value: input


title: MEL1_S6_2-input


title: Blood,excercised,cell203,54M


title: Blood,excercised,cell205,54M


title: Blood,excercised,cell201,54M


title: MEL1_S0_2-input


title: MEL1_S6_1-input


title: Blood,excercised,cell200,54M


title: MEL1_S4_1-input


title: Blood,excercised,cell197,54M


title: MEL1_S0_1-IP


title: Blood,excercised,cell196,54M


title: Blood,excercised,cell199,54M


title: MEL1_S0_1-input


title: H1_S6_2-IP


title: Blood,excercised,cell198,54M


title: Blood,excercised,cell195,54M


title: H1_S4_1-IP


title: Blood,excercised,cell194,54M


title: Blood,excercised,cell193,54M


title: H1_S4_2-IP


title: H1_S3_2-IP


title: H1_S3_1-IP


title: Blood,excercised,cell192,54M


title: MEL1_S3_2-input


title: Blood,excercised,cell204,54M


title: Blood,excercised,cell202,54M


title: Blood,excercised,cell191,54M


title: MEL1_S3_1-input


title: H1_S0_1-IP


title: H1_S0_2-IP


title: Blood,excercised,cell190,54M


title: Blood,excercised,cell189,54M


title: H1_S6_1-input


title: Blood,excercised,cell188,54M


title: H1_S4_1-input


title: Blood,excercised,cell186,54M


title: H1_S4_2-input


title: H1_S3_2-input


title: Blood,excercised,cell187,54M


title: H1_S6_1-IP


title: Blood,excercised,cell184,54M


title: H1_S0_2-input


title: H1_S0_1-input


title: H1_S3_1-input


title: Blood,excercised,cell182,54M


title: H1_S6_2-input


title: Blood,excercised,cell181,54M


title: H1_scr_b_Dox_P

data_processing:
The reads were trimmed for adapters and filtered by sequencing Phred quality (>= Q15) using fastp.
The gene count table was generated by aligning reads to the human transcriptome (Ensembl version 102) using kallisto and converting transcript counts to gene counts using tximport.
Supplementary files format and content: CSV

extract_protocol:
FACS-sorted cells were washed with DPBS and lysed in TRIzol for RNA isolation using RNeasy Micro Kit (Qiagen) according to the manufacturer's instructions.
RNA libraries were prepared using SMARTer Stranded Total RNA-Seq kit v2 (Takara).

value: beta-like

tag: RNAi

value: iScramble

value: Doxycycline


title: Blood,excercised,cell183,54M

value: Blood

value: human samples


title: H1_scr_a_Dox_P


title: Blood,excercised,cell179,54M

value: Memory B cells


title: Blood,excercised,cell180,54M


title: H1_KD2_c_Dox_P


title: Blood,excercised,cell178,54M


title: H1_KD2_c_Dox_N

value: Control


title: Blood,excercised,cell177,54M


title: H1_KD2_b_Dox_P


title: H1_KD2_a_Dox_P


title: Blood,excercised,cell175,54M


title: Blood,excercised,cell176,54M


title: H1_KD2_b_Dox_N


title: Blood,excercised,cell185,54M


title: Blood,excercised,cell171,54M


title: Blood,excercised,cell172,54M


title: Blood,excercised,cell173,54M


title: scBCR, adult male, subject P11, bone marrow, year 1 day-90, replicate 2

city: New Haven

first: Steven

last: Kleinstein

state: Ct

address: 300 George St.

department: Pathology

institute: Yale University

data_processing:
Bulk BCR: Demultiplexed pair-end reads were preprocessed using pRESTO v.0.5.7. Initial germline V(D)J gene annotation was  performed using IgBLAST v1.9.0. IgBLAST output was processed using  Change-O v0.4.0.
scBCR: Demultiplexed pair-end FASTQ reads were preprocessed using the “cellranger vdj” command from 10 × Genomics’ Cell Ranger v.3.1.0 for alignment against the GRCh38 human reference v.3.1.0 (refdata-cellranger-vdj-GRCh38-alts-ensembl-3.1.0). Initial germline V(D)J gene annotation was performed as described for bulk sequencing BCR reads
Processed BCR sequences from bulk sequencing and single-cell sequencing (Extended Data Table 4), were combined with monoclonal antibody sequences for further analysis.
Combined BCR sequences were called for genotyping using the function findNovelAlleles() and inferGenotype() from TIgGER v.0.2.11 ([MH5] ). Individual genotypes, including novel V gene alleles missing from IMGT/ GENE-DB, were computationally inferred and used to finalize V(D)J annotations.
Assembly: GRCh38
Supplementary files format and content: tar.gz: compressed archive of 10X Genomics Cell Ranger output files.
Supplementary files format and content: tsv: AIRR-seq rearrangement format

molecule: polyA RNA

source_name: bone marrow

extract_protocol:
PBMCs were isolated from blood. Fine-needle aspiration was performed on axillary lymph nodes. RNA was purified from whole PBMCs and sorted PBs from participants using the RNeasy Micro Kit (Qiagen).
Bulk BCR: Reverse transcription, unique molecular identifier (UMI) barcoding, cDNA amplification, and Illumina linker addition to B cell heavy chain transcripts were performed using the human NEBNext Immune Sequencing Kit (NEB) according to the manufacturer’s instructions.  scBCR libraries were prepared as recommended by the 10× Genomics Chromium Single Cell V(D)J Reagent Kit (v1 Chemistry) user guide, with appropriate modifications to the PCR cycles based on the calculated cDNA concentration

tag: isolate

tag: age

value: bone marrow

value: plasma cells


title: scBCR, adult male, subject P11, bone marrow, year 1 day-90, replicate 1


title: Blood,excercised,cell170,54M


title: scBCR, adult male, subject P11, bone marrow, year 1 day-35, replicate 1


title: LAM Donor Region 1

city: Iowa City

first: Amy

middle: Leanne

last: Ryan

state: IA

address: 51 Newton Road

department: Anatomy and Cell Biology

institute: The University of Iowa

description: FFPE Spatial Transcriptome Sequencing

data_processing:
Raw Sewuencing data were processed using the 10x Gemonics SpaceRanger pipeline to generate FASTQ files
Sequences were aligned to GRCh38 genome to gene expression count using Space Ranger's default settings
Gene expression level of Refseq coding genes were quantified using Space Ranger's default settings
Assembly: GRCh38
Supplementary files format and content: filt_feat_bc_matrix.h5: list of gene IDs
Supplementary files format and content: aligned_fluicicials.jpg: aligned fluidicials of the tissue image
Supplementary files format and content: detected_tissue_image.jpg: image of the tissue and spots
Supplementary files format and content: scalefactors_json.json.jpg: scale factors in json format
Supplementary files format and content: tissue_hires_image.png: hi-res image of the tissue
Supplementary files format and content: tissue_lowres_image.png: low-res image of the tissue
Supplementary files format and content: tissue_positions_list.csv: list of spatial barcodes and the coordinates ospecifying spots
Library strategy: Spatial Transcriptomics

source_name: Lung Distal Tissue from LAM Patient

growth_protocol: Donor lung tissue from end-stage LAM patient

extract_protocol:
10µm sections were cut using a microtome
Spatial Transcriptome sequencing libraries were prepared with 10x Genomic Visium Spatial Gene Expression Slides & reagent kit according to the manufacturers instructions

treatment_protocol: Paraffin embedded blocks from LAM patient lung tissue were prepared from formalin fixed end-stage lung tissue following standard proceedures. Two independent reqions of the tissue block were selected for Spatial Transcriptomics

value: Lung Distal Tissue

tag: disease

value: LAM Patient

value: All Lung Cell Types

value: Unknown


title: LAM Donor Region 2

description: FFPE Spatial Transcriptome Sequencing


title: scBCR, adult male, subject P11, bone marrow, year 1 day-180, replicate 1


title: Blood,excercised,cell168,54M


title: scBCR, adult male, subject P11, bone marrow, year 1 day-180, replicate 2


title: Blood,excercised,cell165,54M


title: scBCR, adult male, subject P11, bone marrow, year 1 day-35, replicate 2


title: scBCR, adult male, subject P11, bone marrow, year 1 day-0, replicate 2


title: Blood,excercised,cell164,54M


title: scBCR, adult male, subject P11, bone marrow, year 1 day-0, replicate 1


title: scBCR, adult male, subject P05, bone marrow, year 2 day-90, replicate 1


title: Blood,excercised,cell166,54M


title: Blood,excercised,cell163,54M


title: Blood,excercised,cell174,54M


title: scBCR, adult male, subject P05, bone marrow, year 2 day-28, replicate 1


title: Blood,excercised,cell162,54M


title: scBCR, adult male, subject P05, bone marrow, year 2 day-0, replicate 2


title: Blood,excercised,cell161,54M


title: Blood,excercised,cell160,54M


title: scBCR, adult male, subject P05, bone marrow, year 2 day-0, replicate 1


title: Blood,excercised,cell169,54M


title: Blood,excercised,cell167,54M


title: scBCR, adult male, subject P05, bone marrow, year 1 day-90, replicate 2


title: Blood,excercised,cell159,54M


title: scBCR, adult male, subject P05, bone marrow, year 1 day-90, replicate 1


title: Blood,excercised,cell158,54M


title: scBCR, adult male, subject P05, bone marrow, year 1 day-28, replicate 1


title: scBCR, adult male, subject P05, bone marrow, year 1 day-180, replicate 2


title: scBCR, adult male, subject P05, bone marrow, year 1 day-0, replicate 1


title: scBCR, adult male, subject P05, bone marrow, year 1 day-28, replicate 2


title: Blood,excercised,cell156,42M


title: Blood,excercised,cell157,54M


title: Blood,excercised,cell152,42M


title: scBCR, adult male, subject P05, bone marrow, year 1 day-0, replicate 2


title: Blood,excercised,cell155,42M


title: scBCR, adult male, subject P05, bone marrow, year 1 day-180, replicate 1


title: scBCR, adult male, subject P04, bone marrow, year 1 day-28, replicate 2


title: Blood,excercised,cell153,42M


title: Blood,excercised,cell151,42M


title: Blood,excercised,cell154,42M


title: Blood,excercised,cell149,42M


title: Blood,excercised,cell150,42M


title: scBCR, adult male, subject P04, bone marrow, year 1 day-28, replicate 1


title: scBCR, adult male, subject P04, bone marrow, year 1 day-180, replicate 2


title: Blood,excercised,cell147,42M


title: scBCR, adult male, subject P04, bone marrow, year 1 day-180, replicate 1


title: Blood,excercised,cell148,42M


title: scBCR, adult male, subject P04, bone marrow, year 1 day-0, replicate 2


title: Blood,excercised,cell145,42M


title: scBCR, adult male, subject P04, bone marrow, year 2 day-0, replicate 2


title: scBCR, adult male, subject P04, bone marrow, year 2 day-0, replicate 1


title: Blood,excercised,cell144,42M


title: scBCR, adult male, subject P04, bone marrow, year 1 day-0, replicate 1


title: P11 adult male, bone marrow, year 1 day-90, replicate 1

description:
adult male, bone marrow, year 1 day-90, replicate 1
P11_BMPC_d90_1_Y1

data_processing: Base calls were converted to fastq sequences and demultiplexed using the cellranger v3.1.0 mkfastq function.  Demultiplexed pair-end FASTQ reads were first preprocessed on a by-sample basis using the ‘cellranger count’ command from 10× Genomics’ Cell Ranger v.3.1.0 for alignment against the GRCh38 human reference v.3.0.0 (refdata-cellranger-GRCh38- 3.0.0). The feature biotypes were retrieved using biomaRt v.2.42.0 ([MH8] ) from Ensembl release 93 ([MH9] ).  Additional quality control was performed as follows. (1) To remove presumably lysed cells, cells with mitochondrial content greater than 15% of all transcripts were removed. (2) To remove likely doublets, cells with more than 7,000 features were removed. (3) Genes that were expressed in less than 5 cells in any sample and cells with detectable expression of fewer than 400 genes were removed.  Gene expression analysis of CellRanger output was performed using Seurat v.4.0.3.1.1  Assembly: GRCh38  Supplementary files format and content: tar.gz: compressed archive of 10X Genomics Cell Ranger output files.  Supplementary files format and content: Rds: Seurat analyses saved as R objects

extract_protocol: PBMCs were isolated using Vacutainer CPT tubes (BD); the remaining red blood cells were lysed with ammonium chloride lysis buffer (Lonza). Cells were immediately used or cryopreserved in 10% dimethylsulfoxide (DMSO) in FBS. A qualified physician’s assistant performed ultrasound guided fine needle aspirate (FNA) of axillary lymph nodes under the supervision of a radiologist. Lymph node dimensions and cortical thickness were measured prior to each FNA. Six passes were made using 25-gauge needles, which were flushed with 3 ml of RPMI 1640 supplemented with 10% FBS and 100 U/ml penicillin/streptomycin, followed by three 1 ml rinses. Red blood cells were lysed with ammonium chloride lysis buffer. Cells were washed twice with PBS supplemented with 2% FBS and 2 mM EDTA and immediately used or cryopreserved in 10% DMSO in FBS.  Libraries were prepared using 10x Genomics' Chromium Next GEM single cell 5' gene expression workflow.


title: Blood,excercised,cell143,42M


title: Blood,excercised,cell142,42M


title: Blood,excercised,cell141,42M


title: P11 adult male, bone marrow, year 1 day-35, replicate 1

description:
adult male, bone marrow, year 1 day-35, replicate 1
P11_BMPC_d35_1_Y1


title: P11 adult male, bone marrow, year 1 day-180, replicate 1

description:
adult male, bone marrow, year 1 day-180, replicate 1
P11_BMPC_d180_1_Y1


title: P11 adult male, bone marrow, year 1 day-35, replicate 2

description:
adult male, bone marrow, year 1 day-35, replicate 2
P11_BMPC_d35_2_Y1


title: Blood,excercised,cell138,42M


title: Blood,excercised,cell139,42M


title: Blood,excercised,cell140,42M


title: P11 adult male, bone marrow, year 1 day-0, replicate 2

description:
adult male, bone marrow, year 1 day-0, replicate 2
P11_BMPC_d0_2_Y1


title: P05 adult male, bone marrow, year 2 day-90, replicate 1

description:
adult male, bone marrow, year 2 day-90, replicate 1
P05_BMPC_d90_1_Y2


title: Blood,excercised,cell146,42M


title: P11 adult male, bone marrow, year 1 day-0, replicate 1

description:
adult male, bone marrow, year 1 day-0, replicate 1
P11_BMPC_d0_1_Y1


title: Blood,excercised,cell135,42M

description: SMARTseq2 single cell RNA sequencing data from E2-specific memory B cells


title: Blood,excercised,cell136,42M


title: P11 adult male, bone marrow, year 1 day-180, replicate 2

description:
adult male, bone marrow, year 1 day-180, replicate 2
P11_BMPC_d180_2_Y1


title: P05 adult male, bone marrow, year 2 day-28, replicate 1

description:
adult male, bone marrow, year 2 day-28, replicate 1
P05_BMPC_d28_1_Y2


title: Blood,excercised,cell133,42M


title: Blood,excercised,cell131,42M


title: P11 adult male, bone marrow, year 1 day-90, replicate 2

description:
adult male, bone marrow, year 1 day-90, replicate 2
P11_BMPC_d90_2_Y1


title: Blood,excercised,cell132,42M


title: P05 adult male, bone marrow, year 2 day-0, replicate 1

description:
adult male, bone marrow, year 2 day-0, replicate 1
P05_BMPC_d0_1_Y2


title: P05 adult male, bone marrow, year 1 day-90, replicate 2

description:
adult male, bone marrow, year 1 day-90, replicate 2
P05_BMPC_d90_2_Y1


title: P05 adult male, bone marrow, year 1 day-90, replicate 1

description:
adult male, bone marrow, year 1 day-90, replicate 1
P05_BMPC_d90_1_Y1


title: Blood,excercised,cell137,42M


title: Blood,excercised,cell134,42M


title: P05 adult male, bone marrow, year 1 day-28, replicate 2

description:
adult male, bone marrow, year 1 day-28, replicate 2
P05_BMPC_d28_2_Y1


title: P05 adult male, bone marrow, year 1 day-28, replicate 1

description:
adult male, bone marrow, year 1 day-28, replicate 1
P05_BMPC_d28_1_Y1


title: Blood,excercised,cell130,42M


title: Blood,excercised,cell128,42M


title: Blood,excercised,cell129,42M


title: Blood,excercised,cell124,42M


title: P05 adult male, bone marrow, year 1 day-180, replicate 1

description:
adult male, bone marrow, year 1 day-180, replicate 1
P05_BMPC_d180_1_Y1


title: P05 adult male, bone marrow, year 1 day-180, replicate 2

description:
adult male, bone marrow, year 1 day-180, replicate 2
P05_BMPC_d180_2_Y1


title: Blood,excercised,cell127,42M


title: P04 adult male, bone marrow, year 1 day-28, replicate 1

description:
adult male, bone marrow, year 1 day-28, replicate 1
P04_BMPC_d28_1_Y1


title: Blood,excercised,cell122,42M


title: P05 adult male, bone marrow, year 1 day-0, replicate 1

description:
adult male, bone marrow, year 1 day-0, replicate 1
P05_BMPC_d0_1_Y1


title: Blood,excercised,cell126,42M


title: P05 adult male, bone marrow, year 2 day-0, replicate 2

description:
adult male, bone marrow, year 2 day-0, replicate 2
P05_BMPC_d0_2_Y2


title: P04 adult male, bone marrow, year 1 day-28, replicate 2

description:
adult male, bone marrow, year 1 day-28, replicate 2
P04_BMPC_d28_2_Y1


title: P04 adult male, bone marrow, year 1 day-180, replicate 2

description:
adult male, bone marrow, year 1 day-180, replicate 2
P04_BMPC_d180_2_Y1


title: Blood,excercised,cell123,42M


title: P04 adult male, bone marrow, year 1 day-180, replicate 1

description:
adult male, bone marrow, year 1 day-180, replicate 1
P04_BMPC_d180_1_Y1


title: Blood,excercised,cell119,42M

description: SMARTseq2 single cell RNA sequencing data from E2-specific memory B cells


title: P04 adult male, bone marrow, year 2 day-0, replicate 2

description:
adult male, bone marrow, year 2 day-0, replicate 2
P04_BMPC_d0_2_Y2


title: Blood,excercised,cell121,42M


title: Blood,excercised,cell120,42M


title: P04 adult male, bone marrow, year 2 day-0, replicate 1

description:
adult male, bone marrow, year 2 day-0, replicate 1
P04_BMPC_d0_1_Y2


title: P04 adult male, bone marrow, year 1 day-0, replicate 2

description:
adult male, bone marrow, year 1 day-0, replicate 2
P04_BMPC_d0_2_Y1


title: Blood,excercised,cell118,42M


title: Blood,excercised,cell117,42M


title: Blood,excercised,cell116,42M


title: Blood,excercised,cell115,42M


title: P04 adult male, bone marrow, year 1 day-0, replicate 1

description:
adult male, bone marrow, year 1 day-0, replicate 1
P04_BMPC_d0_1_Y1


title: P05 adult male, bone marrow, year 1 day-0, replicate 2

description:
adult male, bone marrow, year 1 day-0, replicate 2
P05_BMPC_d0_2_Y1


title: scBCR, adult male, subject P11, PBMC ASC, year 2 day-6, replicate 1

source_name: PBMC

value: PBMC

value: male


title: scBCR, adult male, subject P11, PBMC ASC, year 1 day-6, replicate 1


title: scBCR, adult male, subject P11, PBMC enriched for IgD B cells, year 2 day-90, replicate 1


title: scBCR, adult male, subject P11, PBMC enriched for IgD B cells, year 2 day-35, replicate 1


title: Blood,excercised,cell113,42M


title: Blood,excercised,cell125,42M


title: Blood,excercised,cell111,42M


title: Blood,excercised,cell110,42M


title: scBCR, adult male, subject P11, PBMC enriched for IgD B cells, year 1 day-0, replicate 1


title: Blood,excercised,cell108,42M


title: scBCR, adult male, subject P11, PBMC enriched for IgD B cells, year 1 day-35, replicate 1


title: scBCR, adult male, subject P11, PBMC enriched for IgD B cells, year 2 day-0, replicate 1


title: scBCR, adult male, subject P05, PBMC enriched for IgD B cells, year 2 day-6, replicate 1


title: Blood,excercised,cell112,42M


title: scBCR, adult male, subject P05, PBMC, year 1 day-180, replicate 2


title: Blood,excercised,cell107,42M


title: scBCR, adult male, subject P05, PBMC, year 1 day-90, replicate 2


title: scBCR, adult male, subject P05, PBMC, year 1 day-120, replicate 1


title: Blood,excercised,cell109,42M


title: Blood,excercised,cell105,42M


title: scBCR, adult male, subject P05, PBMC, year 1 day-90, replicate 1


title: Blood,excercised,cell103,42M


title: scBCR, adult male, subject P05, PBMC, year 1 day-60, replicate 1


title: Blood,excercised,cell114,42M


title: Blood,excercised,cell102,42M


title: Blood,excercised,cell101,42M


title: scBCR, adult male, subject P05, PBMC, year 1 day-28, replicate 1


title: Blood,excercised,cell100,42M


title: scBCR, adult male, subject P05, PBMC, year 1 day-28, replicate 2


title: Blood,excercised,cell99 ,42M


title: scBCR, adult male, subject P05, PBMC, year 1 day-12, replicate 1


title: Blood,excercised,cell98 ,42M


title: scBCR, adult male, subject P05, PBMC, year 1 day-5, replicate 2


title: Blood,excercised,cell106,42M


title: scBCR, adult male, subject P11, PBMC enriched for IgD B cells, year 1 day-120, replicate 1


title: scBCR, adult male, subject P05, PBMC, year 1 day-5, replicate 1


title: scBCR, adult male, subject P05, PBMC, year 1 day-0, replicate 1


title: Blood,excercised,cell93 ,wk0


title: Blood,excercised,cell96 ,42M


title: Blood,excercised,cell104,42M


title: Blood,excercised,cell94 ,wk0


title: scBCR, adult male, subject P05, PBMC enriched for IgD B cells, year 1 day-180, replicate 1


title: scBCR, adult male, subject P05, PBMC enriched for IgD B cells, year 1 day-90, replicate 1


title: scBCR, adult male, subject P05, PBMC enriched for IgD B cells, year 1 day-120, replicate 1


title: Blood,excercised,cell92 ,wk0


title: Blood,excercised,cell91 ,wk0


title: scBCR, adult male, subject P05, PBMC enriched for IgD B cells, year 2 day-90, replicate 1


title: scBCR, adult male, subject P05, PBMC enriched for IgD B cells, year 1 day-60, replicate 1


title: scBCR, adult male, subject P05, PBMC enriched for IgD B cells, year 2 day-60, replicate 1


title: Blood,excercised,cell90 ,wk0


title: scBCR, adult male, subject P05, PBMC, year 1 day-12, replicate 2


title: Blood,excercised,cell89 ,wk0


title: Blood,excercised,cell88 ,wk0


title: Blood,excercised,cell95 ,wk0


title: scBCR, adult male, subject P05, PBMC enriched for IgD B cells, year 2 day-28, replicate 1


title: scBCR, adult male, subject P05, PBMC, year 1 day-0, replicate 2


title: scBCR, adult male, subject P05, PBMC enriched for IgD B cells, year 1 day-28, replicate 1


title: scBCR, adult male, subject P05, PBMC enriched for IgD B cells, year 2 day-13, replicate 1


title: Blood,excercised,cell86 ,wk0


title: Blood,excercised,cell97 ,42M


title: Blood,excercised,cell84 ,wk0


title: scBCR, adult male, subject P05, PBMC enriched for IgD B cells, year 1 day-5, replicate 1


title: scBCR, adult male, subject P05, PBMC enriched for IgD B cells, year 1 day-12, replicate 1


title: Blood,excercised,cell83 ,wk0


title: Blood,excercised,cell85 ,wk0


title: Blood,excercised,cell82 ,wk0


title: scBCR, adult male, subject P05, PBMC enriched for IgD B cells, year 2 day-0, replicate 1


title: Blood,excercised,cell79 ,wk0


title: Blood,excercised,cell87 ,wk0


title: Blood,excercised,cell80 ,wk0


title: Blood,excercised,cell81 ,wk0


title: scBCR, adult male, subject P05, Lymph Node, year 1 day-90, replicate 1

source_name: Lymph Node

value: Lymph Node


title: scBCR, adult male, subject P05, Lymph Node, year 1 day-90, replicate 2


title: Blood,excercised,cell78 ,wk0


title: Blood,excercised,cell76 ,wk0


title: scBCR, adult male, subject P05, Lymph Node, year 2 day-120, replicate 3


title: Blood,excercised,cell75 ,wk0


title: scBCR, adult male, subject P05, Lymph Node, year 2 day-120, replicate 1


title: Blood,excercised,cell74 ,wk0


title: scBCR, adult male, subject P05, Lymph Node, year 2 day-120, replicate 2


title: scBCR, adult male, subject P05, Lymph Node, year 2 day-60, replicate 3


title: Blood,excercised,cell73 ,wk0


title: scBCR, adult male, subject P05, Lymph Node, year 2 day-60, replicate 1


title: Blood,excercised,cell70 ,wk0


title: Blood,excercised,cell69 ,wk0


title: scBCR, adult male, subject P05, Lymph Node, year 1 day-60, replicate 2


title: Blood,excercised,cell71 ,wk0


title: scBCR, adult male, subject P05, PBMC enriched for IgD B cells, year 1 day-0, replicate 1


title: Blood,excercised,cell72 ,wk0


title: Blood,excercised,cell68 ,wk0


title: scBCR, adult male, subject P05, Lymph Node, year 2 day-28, replicate 3


title: scBCR, adult male, subject P05, Lymph Node, year 1 day-180, replicate 2


title: scBCR, adult male, subject P05, Lymph Node, year 2 day-120, replicate 4


title: Blood,excercised,cell77 ,wk0


title: Blood,excercised,cell67 ,wk0


title: Blood,excercised,cell66 ,wk0


title: Blood,excercised,cell64 ,wk0


title: scBCR, adult male, subject P05, Lymph Node, year 1 day-28, replicate 3


title: scBCR, adult male, subject P05, Lymph Node, year 2 day-28, replicate 2


title: scBCR, adult male, subject P05, Lymph Node, year 2 day-28, replicate 1


title: Blood,excercised,cell65 ,wk0


title: Blood,excercised,cell63 ,wk0


title: Blood,excercised,cell62 ,wk0


title: scBCR, adult male, subject P05, Lymph Node, year 1 day-12, replicate 3


title: Blood,excercised,cell59 ,wk0


title: Blood,excercised,cell61 ,wk0


title: scBCR, adult male, subject P05, Lymph Node, year 1 day-28, replicate 1


title: scBCR, adult male, subject P05, Lymph Node, year 2 day-60, replicate 2


title: scBCR, adult male, subject P05, Lymph Node, year 1 day-28, replicate 2


title: Blood,excercised,cell60 ,wk0


title: scBCR, adult male, subject P05, Lymph Node, year 2 day-7, replicate 2


title: scBCR, adult male, subject P05, Lymph Node, year 2 day-7, replicate 3


title: scBCR, adult male, subject P05, Lymph Node, year 1 day-12, replicate 2


title: Blood,excercised,cell57 ,wk0


title: Blood,excercised,cell56 ,wk0


title: Blood,excercised,cell55 ,wk0


title: scBCR, adult male, subject P05, Lymph Node, year 1 day-5, replicate 2


title: scBCR, adult male, subject P05, Lymph Node, year 2 day-7, replicate 1


title: scBCR, adult male, subject P05, Lymph Node, year 1 day-12, replicate 1


title: scBCR, adult male, subject P05, Lymph Node, year 1 day-180, replicate 1


title: Blood,excercised,cell53 ,wk0


title: Blood,excercised,cell58 ,wk0


title: scBCR, adult male, subject P05, Lymph Node, year 1 day-5, replicate 1


title: Blood,excercised,cell54 ,wk0


title: Blood,excercised,cell51 ,wk0


title: scBCR, adult male, subject P05, Lymph Node, year 2 day-0, replicate 3


title: Larv gypsy3 insertion HiC Repli2res

city: Montpellier

first: Bernd

last: Schuettengruber

address: 141, rue de la cardonille

country: France

institute: Institute de Génétique Humaine

description:
gypsy3_4
resequenced sample gypsy3_2

data_processing:
Hi-C data was processed using the schic2 pipeline (https://github.com/tanaylab/schic2). In brief, raw sequencing reads were mapped independently to the reference genome using Bowtie2 in local alignment mode. The uniquely mapped (MAPQ > 36) reads were translated into a pair of fragment-ends (fends) by associating each read with its downstream fend. PCR duplicates and reads mapping to the same restriction fragment were excluded.
Assembly: dm6
Supplementary files format and content: Each processed file represent pairwise information of the observed genome contacts in the form of a "misha" (https://github.com/tanaylab/misha) database entry and can be further analyzed using the "shaman" pipeline (https://github.com/tanaylab/shaman).

organism: Drosophila melanogaster

source_name: larval imaginal leg discs

growth_protocol: Drosophila Melanogaste flies gtown at 20°C on, standard medium

extract_protocol:
HiC was performed according the protocol of the EpiTect Hi-C Kit from Quiagen
Libraries were preapred according the protocol of the EpiTect Hi-C Kit from Quiagen

value: larval imaginal leg discs

value: insertion gypsy


title: scBCR, adult male, subject P05, Lymph Node, year 1 day-60, replicate 1


title: Larv gypsy3 insertion HiC Repli2


title: Blood,excercised,cell49 ,wk0


title: Blood,excercised,cell50 ,wk0


title: Larv gypsy3 insertion HiC Repli1


title: Blood,excercised,cell48 ,wk0


title: scBCR, adult male, subject P05, Lymph Node, year 2 day-0, replicate 1


title: Blood,excercised,cell46 ,78M


title: Larv gypsy2 insertion HiC Repli3


title: scBCR, adult male, subject P05, Lymph Node, year 2 day-0, replicate 2


title: RBFOX2.WB_rep1_INPUT

data_processing:
Data was processed using the eCLIP pipeline and available at: http://github.com/yeolab/eclip
Unique Molecular Identifiers (UMIs) were extracted from raw sequencing reads with umi_tools extract
Post-umi-extracted reads were trimmed for adapter sequences and barcode sequences (eCLIP samples) using cutadapt.
Trimmed reads were mapped against RepBase with STAR to remove reads mapping to repetitive sequences (--outFilterMultimapNmax 30 --alignEndsType EndToEnd --outFilterMultimapScoreRange 1 --outSAMmode Full --outFilterType BySJout --outSAMtype BAM Unsorted --outFilterScoreMin 10 --outReadsUnmapped Fastx --outSAMattributes All)
Remaining reads were mapped to the appropriate genome build (mm10) using STAR aligner (--outFilterMultimapNmax 1 --alignEndsType EndToEnd --outFilterMultimapScoreRange 1 --outSAMmode Full --outFilterType BySJout --outSAMtype BAM Unsorted --outFilterScoreMin 10 --outReadsUnmapped Fastx --outSAMattributes All)
Uniquely mapped reads were removed of PCR duplicates with umi_tools
Peak clusters were identified with CLIPper, available at: https://github.com/YeoLab/clipper
Clusters enriched over corresponding size-matched input (SMInput) were identified using a custom Perl script, available in the main eCLIP repository as: overlap_peakfi_with_bam.pl
Overlapping enriched clusters (peaks) were merged with a custom perl script, available in the main eCLIP repository as: compress_l2foldenrpeakfi_for_replicate_overlapping_bedformat.pl
Assembly: mm10
Supplementary files format and content: bigwigs contain RPM-normalized read densities of uniquely-mapped reads
Supplementary files format and content: BED files contain CLIPper peak clusters. Columns 4 and 5 describe the -log10(p-value) and log2(fold) enrichment IP over corresponding SMInput.

organism: Mus musculus

source_name: Whole Brain

growth_protocol: Mouse NPCs were cultured in DMEM/F12 media with 1x B27 and 1x penicillin/streptomycin in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Cells were lysed and and sonicated in eCLIP lysis buffer, and RNA was fragmented using RNase I (Ambion) and UPF1:RNA complexes were immunoprecipitated with UPF1-specific antibody (A301-902A)
RNA was reverse transcripted with Superscript III, and adaptor was ligated with T4 RNA Ligase 1, then libraries were constructed with Q5 High-Fidelity 2x Master Mix (NEB)

treatment_protocol: 4 µl Ctrl or iCRE lentivirus were added to 500 µl medium with 4 µg/ml protamine sulfate pwe well for treatemtn of 400k NPCs per well in a 12-well plate

value: Whole Brain


title: Blood,excercised,cell47 ,78M


title: Blood,excercised,cell45 ,78M


title: Larv gypsy2 insertion HiC Repli1


title: scBCR, adult male, subject P04, PBMC, year 2 day-7


title: scBCR, adult male, subject P05, Lymph Node, year 1 day-0, replicate 2


title: Blood,excercised,cell43 ,78M


title: Blood,excercised,cell52 ,wk0


title: Larv gypsy3 insertion HiC Repli1res

description:
gypsy3_3
resequenced sample gypsy3_1


title: Blood,excercised,cell44 ,78M


title: Larv gypsy1 insertion HiC Repli3


title: scBCR, adult male, subject P04, PBMC, year 1 day-5


title: MDMs, Normoxia_day2_rep3

city: Cambridge

first: Niek

last: Wit

state: Not US or Canada

address: Puddicombe Way

department: Department of Medicine

country: United Kingdom

institute: University of Cambridge

data_processing:
Quality trimming, to remove adapter sequences and check for low quality base calling, was performed with TrimGalore
Transcript quantification was performed using Salmon
Differential transcript analysis was performed with DESeq2
Assembly: Gencode Human Release 35 (GRCh38.p13)
Supplementary files format and content: Salmon quant files that contain TPM values for each transcript

source_name: Monocyto-derived macrophages

growth_protocol: Monocyte derived macrophages were maintained in RPMI supplemented with 10% Human AB serum.

extract_protocol:
Total RNA was extracted from MDM using the RNeasy Plus minikit.
RNASequencing libraries were generated using the SMARTer Stranded Total RNA-Seq v2 - Pico Input Mammalian kit (Takara).

treatment_protocol: Hypoxic cell culture was performed in a Whitley H35 Hypoxystation at 37 °C, 5% CO2, 1 % O2and 94% N2.

value: Monocyto-derived macrophages

tag: individual

value: Healthy donor 3

value: Normoxia


title: MDMs, Normoxia_day2_rep2

value: Healthy donor 2


title: scBCR, adult male, subject P04, PBMC enriched for IgD B cells, year 1 day-120


title: Blood,excercised,cell42 ,78M

value: Blood

value: human samples

value: Memory B cells


title: Larv gypsy1 insertion HiC Repli2


title: Blood,excercised,cell41 ,78M


title: Larv gypsy2 insertion HiC Repli2


title: MDMs, Normoxia_day2_rep1

value: Healthy donor 1


title: scBCR, adult male, subject P04, PBMC enriched for IgD B cells, year 2 day-90


title: scBCR, adult male, subject P04, PBMC enriched for IgD B cells, year 2 day-14


title: Blood,excercised,cell40 ,78M


title: Blood,excercised,cell39 ,78M


title: Larv gypsy1 insertion HiC Repli1


title: scBCR, adult male, subject P05, Lymph Node, year 1 day-0, replicate 1


title: MDMs, Hypoxia_day2_rep2

value: Hypoxia


title: Larv RE deletion HiC Repli2

description: delta RE2

value: deletion ring enhancer


title: scBCR, adult male, subject P04, PBMC enriched for IgD B cells, year 1 day-12


title: MDMs, Hypoxia_day2_rep3


title: pupe WT Repl3

description: pupe delta WT3

source_name: pupal imaginal leg discs

value: pupal imaginal leg discs

value: Wild type


title: scBCR, adult male, subject P04, PBMC enriched for IgD B cells, year 2 day-0

value: PBMC

value: male


title: MDMs, Hypoxia_day2_rep1


title: Blood,excercised,cell38 ,78M


title: RBFOX2.WB_rep1_IP


title: Blood,excercised,cell37 ,78M


title: 10ng/mL TGFB1 treated A375 Replicate 3

first: Leonard

last: Zon

state: MA

address: 1 Blackfan Circle

department: Oncology/Hematology

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using cutadapt, then mapped to Ensembl GRCh38 whole genome using tophat 2.1
Transcript abundance were calculated with Htseq-count
Assembly: GRCh38
Supplementary files format and content: raw count file

source_name: A375 Cells

growth_protocol: A375 were grown in filter sterilized DMEM, 10% FBS, 1% PenStrep, 1% Glutamine at 37°C

extract_protocol:
RNA was collected from adherent cells using the Qiagen RNeasy Plus Mini Kit (Qiagen #74134).
One microgram of RNA was ribodepleted using NEBNext rRNA Depletion Kit (NEB #E6310). Ribodepleted RNA was fragmented, reverse transcribed, and library prepped (NEB #E7530, NEB #E7335).

treatment_protocol: Cells were starved for 2 hours then treated with 10ng/mL TGFB1 ligand or 4mM HCl containing 1mg/mL BSA vehicle control for 2 hours.

value: A375 Cells


title: pupe WT Repl2

description: pupe delta WT2


title: scBCR, adult male, subject P04, PBMC enriched for IgD B cells, year 1 day-0


title: Blood,excercised,cell36 ,78M

source_name: Blood


title: pupe WT Repl1

description: pupe delta WT1


title: 10ng/mL TGFB1 treated A375 Replicate 2


title: Larv RE deletion HiC Repli1

description: delta RE1

value: larval imaginal leg discs


title: Blood,excercised,cell35 ,78M


title: Blood,excercised,cell34 ,78M


title: Larv WT HiC Repli3

description: delta WT3


title: scBCR, adult male, subject P04, Lymph Node, year 1 day-120, replicate 1

value: Lymph Node


title: scBCR, adult male, subject P04, Lymph Node, year 1 day-120, replicate 2


title: Larv WT HiC Repli2

description: delta WT2


title: 10ng/mL TGFB1 treated A375 Replicate 1


title: Vehicle Control treated A375 Replicate 3

value: Vehicle


title: Blood,excercised,cell33 ,78M


title: Larv WT HiC Repli1

description: delta WT1


title: scBCR, adult male, subject P04, Lymph Node, year 2 day-90, replicate 1


title: Vehicle Control treated A375 Replicate 2


title: Blood,excercised,cell32 ,78M


title: Vehicle Control treated A375 Replicate 1


title: TGFB1 stimulated A375 JUNB 11.18.20

data_processing:
ChIP-Seq aligned to GRCh38 with Bowtie with max mismatch 2bp
peaks were called using MACS 2.0 with the following setting: q-value 0.05
Assembly: GRCh38
Supplementary files format and content: narrowPeak Bed files from MACS 2.0 output

growth_protocol: A375s were grown in filter sterilized DMEM, 10% FBS, 1% PenStrep, 1% Glutamine at 37°C

extract_protocol:
A375 cells were fixed directly in 15cm plates with 11% formaldehyde and collected by scraping. Approximately 100,000,000 cells were used per condition. Cells were lysed using lysis buffers with protease inhibitors (Roche #05056489001) and sonicated such that fragmented chromatin was 200-300bp long. Optimal chromatin length was confirmed by gel electrophoresis. Prior to antibody addition, 50µL chromatin was collected for input sample. The remaining sonicated chromatin was incubated overnight at 4°C with 10µg antibody attached to Dynabeads (Invitrogen #10004D). Samples (including inputs) were washed with wash buffers and eluted for 6 hours at 70°C, treated with RNaseA (Sigma #R4642) and ProteinaseK (Life Technologies #AM2546), and purified using Zymo ChIP DNA Concentrator kit (Genesee Scientific #11-379C).
Libraries were end repaired (VWR #ER81050), polyA tailed (Invitrogen #18252-015, NEB #M0212L), adaptor ligated (NEB #E7335), size selected using Ampure XP beads (Beckman Coulter #A63881, Life Technologies #12027), and PCR amplified (NEB #M0531).

treatment_protocol: Cells were starved for 2 hours. Treated with 10ng/mL TGFB1 ligand or 4mM HCl containing 1mg/mL BSA vehicle control for 2 hours.

tag: chip antibody

value: JUNB


title: scBCR, adult male, subject P04, Lymph Node, year 2 day-90, replicate 2


title: Blood,excercised,cell31 ,78M

data_processing:
The raw data was aligned with human genome to map the heavy and light chain genes which were further annotated using IgBlast software implemented in VDJPuzzle
Inhouse pipeline used to generate the matrix that was further processed using seurat and other packages for paired-end sequences
Assembly: Sequences were processed using VDJPuzzle for BCR data and inhouse pipelines for Gene expression analysis
Supplementary files format and content: barcodes.tsv
Supplementary files format and content: features.tsv
Supplementary files format and content: matrix.mtx

extract_protocol:
Seven to ten million cryopreserved PBMCs were sorted for E2-specific B cells as described previously. S figure 4, in the article indicates the time points selected for flow analysis and transcriptomics/repertoire analysis. In brief, PBMCs were stained with an in-house developed rE2 cocktail tetramer (Gt1a [H77] and Gt3a [UKN3A13.6]) as well as anti-CD19, anti-CD20, anti-CD10, anti-CD38, anti-IgD, anti-IgG, anti-CD27,anti-CD21 and anti-CD95 antibodies, and single cell sorted using flow cytometry. Population phenotypes were analysed with FlowJo version 10 software (Tree Star Inc.) (See CTAT Table for antibody details and see S Figure 3 for gating strategy and how gates were set for CD95 positivity based on FMO).
E2+ B cells were sorted into single wells and single cell RNA sequencing was performed following the smartseq2 protocol as previously described. BCR sequences were reconstructed using VDJpuzzle 2.0. Identification of B cell clonotypes and SHM across infections was done using Immcantation framework.  Paired-end reads from Smart-seq2 were aligned with STAR (version 2.7.1a) using the GRCh38.p13 human reference genome. Transcripts per Million (TPM) were quantified using RSEM (version 1.2.28) using rsem-calculate-expression command on HPC clusters.

tag: cell line


title: Blood,excercised,cell30 ,78M

tag: cell type


title: scBCR, adult male, subject P04, Lymph Node, year 2 day-60, replicate 2


title: TGFB1 stimulated A375 ATF3 11.18.20

tag: treatment


title: scBCR, adult male, subject P04, Lymph Node, year 2 day-14, replicate 2

tag: tissue


title: Blood,excercised,cell29 ,78M

tag: genotype


title: Vehicle Control treated ZMEL1 Replicate 3

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using cutadapt, then mapped to Ensembl GRCz11 whole genome using tophat 2.1
Transcript abundance were calculated with Htseq-count
Assembly: GRCz11
Supplementary files format and content: raw count file

organism: Danio rerio

source_name: ZMEL1 Cells

growth_protocol: ZMEL1 were grown in filter sterilized DMEM, 10% FBS, 1% PenStrep, 1% Glutamine at 28°C

value: ZMEL1 Cells


title: Blood,excercised,cell28 ,78M


title: scBCR, adult male, subject P04, Lymph Node, year 2 day-14, replicate 1

tag: Sex


title: Vehicle Control A375 ATF3 11.18.20


title: Blood,excercised,cell27 ,78M


title: Vehicle Control treated ZMEL1 Replicate 2


title: Vehicle Control treated ZMEL1 Replicate 1


title: Blood,excercised,cell26 ,78M


title: TGFB1 stimulated A375 Input 11.18.20


title: scBCR, adult male, subject P04, Lymph Node, year 1 day-12, replicate 1


title: scBCR, adult male, subject P04, Lymph Node, year 1 day-5, replicate 2


title: 10ng/mL TGFB1 treated ZMEL1 Replicate 3


title: TGFB1 stimulated A375 MITF 7.17.18

value: MITF


title: scBCR, adult male, subject P04, Lymph Node, year 1 day-5, replicate 1


title: scBCR, adult male, subject P04, Lymph Node, year 1 day-12, replicate 2


title: 10ng/mL TGFB1 treated ZMEL1 Replicate 1


title: Vehicle Control A375 MITF 7.17.18


title: scBCR, adult male, subject P04, Lymph Node, year 2 day-0, replicate 2


title: Blood,excercised,cell24 ,78M

value: Blood


title: Blood,excercised,cell25 ,78M

value: human samples


title: scBCR, adult male, subject P04, Lymph Node, year 2 day-60, replicate 1


title: CsA

city: Saint Louis

first: Li

last: Ding

state: MO

address: 660 S. Euclid Avenue

institute: Washington University in St. Louis

description: 10X Genomics

data_processing:
cellranger-6.1.1
Assembly: mm10-2020-A
Supplementary files format and content: gene expression matrices and raw data

source_name: skin graft

extract_protocol:
CD45+ cells harvested from skin grafts
10x 3'v3 protocol for downstream library prep and construction

value: skin graft

value: CD45+ sorted cells

value: C57BL/6 (B6; H-2b) and BALB/c (H-2d)

value: CsA


title: DMSO

description: 10X Genomics

value: DMSO


title: Bari_plus_CsA

description: 10X Genomics

value: Bari Plus CsA


title: Vehicle Control A375 JUNB 11.18.20


title: 10ng/mL TGFB1 treated ZMEL1 Replicate 2


title: Blood,excercised,cell23 ,78M

value: Memory B cells


title: TGFB1 stimulated A375 INPUT 7.17.18


title: scBCR, adult male, subject P04, Lymph Node, year 2 day-0, replicate 1

value: male


title: Blood,excercised,cell22 ,78M


title: Vehicle Control A375 INPUT 7.17.18

value: A375 Cells


title: Blood,excercised,cell21 ,78M


title: Vehicle Control A375 Input 11.18.20


title: scBCR, adult male, subject P04, Lymph Node, year 1 day-0, replicate 2


title: Syngeneic_Control

description: 10X Genomics

value: Control


title: scBCR, adult male, subject P04, lymph node, year 1 day-0, replicate 1

value: Lymph Node


title: OVE26_CD45+Immune_7M

first: Zeguo

last: Sun

address: 1468 Madison Avenue

institute: Ichan School of Medicine at Mount Sinai

description: OVE26 mouse at 7 months old

data_processing:
The 10X Libraries were sequenced on the Illumina NovaSeq6000 sequencer with pair-end reads (28 bp for read 1 and 91 bp for read 2). The sequencing data were primarily analyzed by the 10X cellranger pipeline (v3.0.2) in two steps. In the first step, cellranger mkfastq demultiplexed samples and generated fastq files; and in the second step, cellranger count aligned fastq files to the 10X pre-built mouse reference (mm10)  and extracted gene expression UMI counts matrix.
We filtered cells with less than 300 or more than 5000 genes detected, and cells with mitochondria gene content greater than 20%, and used the remaining cells for downstream analysis.
Assembly: mm10
Supplementary files format and content: gene-cell expression matrix of raw read counts in xls file format

source_name: Kidney CD45+ cells

growth_protocol: Diabetic OVE26 mice (FVB(Cg)-Tg(Cryaa-Tag, Ins2-CALM1)26Ove/PneJ) in FVB background were obtained from The Jackson Laboratory. Bodyweight and fasting blood glucose levels were monitored biweekly by glucometer readings. DM was conﬁrmed by fasting blood glucose level 300 mg/dl. The age-and sex-matched WT littermates served as non-diabetic controls.

extract_protocol:
CD45+ enriched immune cell fraction: Briefly, minced kidney were digested in the digestion buffer for 20 minutes at 37°C, passed through a 70-micron cell strainer, and collected by centrifugation. Cells were resuspended in blocking solution (PBS without calcium and magnesium containing 0.04% BSA and Fc blocking solution) and incubated for 30 minutes on ice. Cells were then washed with PBS with 0.04% BSA and incubated for 30 minutes at room temperature with the PE rat anti-mouse CD45 (1:200, catalog no. 12–0451, 30-F11; eBioscience). After washing, the cell suspension was sieved through a 40-micron cell strainer and centrifuged at 4°C. Cells were also stained with viability dye (DAPI). Samples were sorted using a BD FACS Aria II.
Sequencing libraries were constructed according to 10x standard protocol by following the steps cDNA fragmentation, end repair and A-tailing, size selection by SPRIselect beads (Beckman Coulter), adaptor ligation, sample index PCR amplification, and repeat SPRIselect beads size selection. The final constructed single-cell libraries were sequenced by Illumina Novaseq machine with total reads per cell targeted for a minimum of 30,000.

value: kidney

value: CD45+ Immune cells

value: 7 months


title: Blood,excercised,cell20 ,78M


title: TGFB1 stimulated A375 Smad2/3 6.11.18


title: adult male, PBMC ASC year 2 day-6, replicate 1

data_processing:
Base calls were converted to fastq sequences and demultiplexed using the cellranger v3.1.0 mkfastq function.
Demultiplexed pair-end FASTQ reads were first preprocessed on a by-sample basis using the ‘cellranger count’ command from 10× Genomics’ Cell Ranger v.3.1.0 for alignment against the GRCh38 human reference v.3.0.0 (refdata-cellranger-GRCh38- 3.0.0). The feature biotypes were retrieved using biomaRt v.2.42.0 ([MH8] ) from Ensembl release 93 ([MH9] ).
Additional quality control was performed as follows. (1) To remove presumably lysed cells, cells with mitochondrial content greater than 15% of all transcripts were removed. (2) To remove likely doublets, cells with more than 7,000 features were removed. (3) Genes that were expressed in less than 5 cells in any sample and cells with detectable expression of fewer than 400 genes were removed.
Gene expression analysis of CellRanger output was performed using Seurat v.4.0.3.1.1
Assembly: GRCh38
Supplementary files format and content: tar.gz: compressed archive of 10X Genomics Cell Ranger output files.
Supplementary files format and content: Rds: Seurat analyses saved as R objects

extract_protocol:
PBMCs were isolated using Vacutainer CPT tubes (BD); the remaining red blood cells were lysed with ammonium chloride lysis buffer (Lonza). Cells were immediately used or cryopreserved in 10% dimethylsulfoxide (DMSO) in FBS.   A qualified physician’s assistant performed ultrasound guided fine needle aspirate (FNA) of axillary lymph nodes under the supervision of a radiologist. Lymph node dimensions and cortical thickness were measured prior to each FNA. Six passes were made using 25-gauge needles, which were flushed with 3 ml of RPMI 1640 supplemented with 10% FBS and 100 U/ml penicillin/streptomycin, followed by three 1 ml rinses. Red blood cells were lysed with ammonium chloride lysis buffer. Cells were washed twice with PBS supplemented with 2% FBS and 2 mM EDTA and immediately used or cryopreserved in 10% DMSO in FBS.
Libraries were prepared using 10x Genomics' Chromium Next GEM single cell 5' gene expression workflow.

value: PBMC


title: Blood,excercised,cell19 ,78M

value: Blood


title: WT_CD45+Immune_7M

description: Wild type mouse at 7 months old

value: WT


title: TGFB1 stimulated A375 H3K27ac 6.11.18


title: Bari

description: 10X Genomics

value: skin graft

value: Bari


title: adult male, PBMC ASC year 1 day-6, replicate 1


title: Blood,excercised,cell18 ,78M

value: human samples


title: Vehicle Control A375 Smad2/3 6.11.18

value: Vehicle


title: adult male, PBMC enriched for IgD B cell, year 2 day-90, replicate 1


title: Vehicle Control A375 H3K27ac 6.11.18


title: 3' GEX library of 5 GFP positive mice

city: Farmington

middle: F

last: Flynn

state: CT

address: 10 Discovery Drive

institute: The Jackson Laboratory

description: 10x Genomics

data_processing:
Illumina base call files for all libraries were converted to FASTQs using bcl2fastq v2.20.0.422 and FASTQ files associated with the gene expression libraries were aligned to the GRCm38 reference assembly with vM23 annotations from GENCODE (10x Genomics mm10 reference 2020-A) using the version 6.1.2 Cell Ranger multi pipeline (10x Genomics).  The FASTQ files associated with the hashtag libraries were processed with the CITE-seq-Count v1.4.5 which populates a cell-barcode by hashtag matrix file which produces a cell-by-hashtag digital count matrix for each hashtag library. De-multiplexing was also done using the Cell Ranger multi pipeline with the MULTIseqDemux algorithm. Downstream analysis was performed using the Seurat R toolkit (version 4.2.0)26. Cells were further excluded from downstream analysis if they did not meet the following criteria: (1) more than 300 genes detected per cell; (2) less than 20% mitochondrial transcripts; (3) less than 1% hemoglobin transcripts. After quality control filtering, 11,530 and 11,699 cells remained in the GFPhigh and non-GFPhigh groups, respectively. The gene expression matrices were normalized by the total UMI counts in each cell, multiplied by 10,000, log-transformed, and the top 2,000 most variable genes were selected using the variance stabilizing transformation method. The two groups were then integrated using the standard workflow in Seurat toolkit, which resulted in an integrated gene expression matrix. Using the integrated matrix, the mean expression of each gene in the cells was scaled to 0, and a linear dimensional reduction (principal component analysis, PCA) was performed on the scaled data. To cluster the cells, the first 40 PCs were used to construct a K-nearest neighbor (KNN) graph. The clusters were identified through the Louvain algorithm on the KNN graph. The resolution parameter was set as 0.2, which resulted in 16 cell clusters comprising 10 different cell types. The single cells were visualized in a 2D UMAP embedding that was computed from the KNN graph. To define the cell clusters, marker genes, which (1) detected at a minimum of 25% of cells in the cluster and (2) the mean expression in the cluster compared to all other cells is higher than 0.25 (log scale), were generated by the FindAllMarkers function using Wilcoxon Rank Sum test under the ‘‘RNA’’ assay.
Assembly: mm10
Supplementary files format and content: Seurat rds file
Supplementary files format and content: GFP_pos_neg_fat_All.rds

source_name: Stromal vascular fraction (SVF) from Epididymal white adipose tissue in female p21-Cre/+; +/+ mice

extract_protocol:
SVF cells were isolated from 5 25-30 months old female P mice. Cells from each donor were labelled with cell hashing antibodies (TotalSeq-A anti-mouse Hashtag, BioLegend) according to the manufacturer’s protocol. Cells were then washed, and resuspended in 0.04% BSA/PBS. Labelled cells from each donor were pooled at equal proportions, then immediately sorted on a BD FACSAria Fusion cell sorter (BD Biosciences) for viable GFPhigh and non-GFPhigh cell populations. Cells from wildtype mice were used as GFP background for gating and sorting. Cell viability was assessed on a Countess II automated cell counter (Thermo Fisher Scientific). Up to 12,000 cells were loaded onto one lane of a 10X Chromium X. Single cell capture, barcoding and library preparation were performed using the 10X Chromium platform version 3.1 chemistry according to the manufacturer’s protocol (CG000388). cDNA and libraries were checked for quality on Agilent 4200 TapeStation (Agilent Technologies, Santa Clara, CA) and Qubit Fluorometer (Thermo Fisher Scientific), quantified by KAPA qPCR. Library was sequenced on an Illumina NovaSeq 6000 S4 v1.5 200 cycle flow cell lane, targeting 6,000 barcoded cells with an average sequencing depth of 50,000 reads per cell.
10X Chromium platform version 3.1 chemistry according to the manufacturer’s protocol (CG000388)

tag: stain

value: female

value: 25-30 month

value: SVF cells were sorted on a BD FACSAria Fusion cell sorter (BD Biosciences) for viable GFPhigh (GFP_pos) and non-GFPhigh (GFP_neg) cell populations.


title: Blood,excercised,cell17 ,78M

value: Memory B cells


title: HTO library of 5 GFP positive mice

description: 10x Genomics

value: Stromal vascular fraction (SVF) from Epididymal white adipose tissue in female p21-Cre/+; +/+ mice


title: adult male, PBMC enriched for IgD B cell, year 2 day-35, replicate 1

value: male


title: Blood,excercised,cell16 ,78M


title: 3' GEX library of 5 GFP negative mice

description: 10x Genomics


title: Vehicle Control A375 INPUT 6.11.18

value: A375 Cells


title: HTO library of 5 GFP negative mice

description: 10x Genomics


title: Blood,excercised,cell15 ,78M