title: TMZ rep 2

city: Charlottesville

first: Matthew

last: Lazzara

state: VA

address: 345 Crispell Dr

institute: University of Virginia

description:
G816TMZ_S26
G816_RNA-seq_counts.csv

data_processing:
Illumina RNAExpress.App Version 1.1.0
Sequence reads were trimmed for adaptor sequence/low-quality sequence using IlluminaRNAExpress.TrimAdaptors
Cleaned up reads were aligned to human transcriptome version hg19 using STAR aligner version 2.5.3a
Read count extraction and normalization were performed using Starcount-M2Pass
Assembly: hg19_refseq
Supplementary files format and content: comma-separated values files including transcript counts for each sample

source_name: glioblastoma

growth_protocol: G816 cells were grown adherently on Matrigel basement membrane in Neurobasal medium with B27, N2,  L-glutamine, and penicillin/streptomycin, supplemented with 50 ng/mL EGF and FGFb.

extract_protocol:
RNA was extracted from cells using the RNeasy kit (Qiagen).
Library preparation was performed using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina.

treatment_protocol: Cells were treated with TGFβ+TNFα (both ligands at 10 ng/mL) or temozolomide (100 μM) every two days for four days.

value: glioblastoma

value: glioma-initiating

value: TMZ 4 days


title: TMZ rep 3

status: Public on Jan 10 2024

type: SRA

country: USA

description:
G816TMZ_S27
G816_RNA-seq_counts.csv

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

tag: tissue

tag: cell line

tag: cell type

tag: treatment


title: TMZ rep 1

description:
G816TMZ_S25
G816_RNA-seq_counts.csv


title: TB_22010_pre-plasma IgM

type: protein

city: Bronx

first: Jacqueline

middle: M.

last: Achkar

state: NY

address: 1300 Morris Park Ave

institute: Albert Einstein College of Medicine

description: IgM

hyb_protocol: Slides with 8 arrays on each were blocked with 3% BSA (GEMINi Bio-Products, standard grade) in PBS at 4°C overnight, washed with 0.1 % PBS-T, and then incubated with BALF (1:8) or plasma (1:100), diluted in 0.1% PBST with 3% BSA, for 4 hrs at 37°C. After washing, bound antibodies were detected by Cy3 Goat Anti-Human Serum IgA (Jackson ImmunoResearch Labs Cat# 109-165-011, RRID:AB 2337721) and Alexa 647 Goat Anti-Human IgG (Jackson ImmunoResearch Labs Cat# 109-605-008, RRID:AB_2337882. Slides were then washed with PBST, spun dry in a centrifuge, and scanned.

scan_protocol: The slides were scanned using the GenePix 4000 Microarray scanner system. Scanned images were analyzed with by the image-processing software G\enePix Pro 7.3.0.0 to analyze the images and measure the median pixel intensity (MPI).

data_processing: The median pixel intensity of each feature was background subtracted. A minimum value of pixel intensity (400) was determined by the median pixel intensity of the spots with low quality, which was determined by the software quality control score for each spot depending on signal-to-noise ratio and spot shape. The scanned images were visually inspected. The spots with obvious local artifacts were excluded from analysis. The array features were printed in triplicate. The final data were averaged from the triplicates.

label: Anti-human  IgM  DyLight™ 649

molecule: protein

organism: Macaca fascicularis

source_name: pre-plasma

label_protocol: Anti-human IgM (mu chain) (GOAT) Antibody DyLight™ 649 Conjugated - 609-143-007 (Rockland)

extract_protocol: Plasma was obtained from peripheral blood samples and the BAL procedure was performed as previously described via direct visualization of the airway and lavage of ~ 40 ml normal saline (0.9%). Animal protocols and procedures were approved by the University of Pittsburgh’s Institutional Animal Care and Use Committee before the collection of samples.

treatment_protocol: BALF dilted (1:8) or plasma diluted (1:100)

tag: infection states

value: Symtomatic uncontrolled Mtb infection/TB disease


title: TGFb+TNFa rep 3

description:
G816TT_S24
G816_RNA-seq_counts.csv

value: TGFβ+TNFα 4 days


title: TB_22010_pre-BALF IgM

description: IgM

source_name: pre-BALF


title: TB_21410_pre-plasma IgM

description: IgM


title: LTBI_9911_3mo-BALF IgG

description: IgG

hyb_protocol: Slides with 16 arrays on each were blocked SuperBlock (Thermo Fisher Scientific), then incubated with BALF (1:35) or plasma (1:100) diluted in phosphate buffered saline with 5% skim milk and 0.2% tween 20 (PBST) for 16 hrs at 4°C. After washing with 5% skim milk and 0.2% tween 20 (PBST) (3 x 5 min), slides were incubated with Cy3 Goat Anti-Human Serum IgA (Jackson ImmunoResearch Labs Cat# 109-165-011, RRID:AB_2337721) and Alexa 647 Goat Anti-Human IgG (Jackson ImmunoResearch Labs Cat# 109-605-008, RRID:AB_2337882; diluted at 1:200 in 5% skim milk and 0.2% tween 20 (PBST)) for 2 hrs at 4°C

scan_protocol: Slides were scanned at 635 nm and 535 nm with a Tecan PowerScanner, and images were quantified with the ArrayPro Analyzer Software (Media Cybernetics, Inc.).

data_processing: Spots were considered reactive if the ratio of the median fluorescent intensity (MFI) of the gene was greater than 1.4 x the median of negative control genes

label: Alexa 647 Goat Anti-Human IgG

value: Asymptomatic controlled Mtb infection


title: LTBI_9911_3mo-Plasma IgG

description: IgG

label_protocol: Alexa 647 Goat Anti-Human IgG (Jackson ImmunoResearch Labs Cat# 109-605-008, RRID:AB_2337882


title: LTBI_9911_6mo-BALF IgG

description: IgG


title: LTBI_9911_Pre-BALF IgG

description: IgG

source_name: Pre-BALF


title: TB_10208_3mo-BALF IgG

description: IgG

value: Symptomatic uncontrolled Mtb infection/TB disease


title: TB_10208_3mo-Plasma IgG

description: IgG


title: TGFb+TNFa rep 2

description:
G816TT_S23
G816_RNA-seq_counts.csv


title: LTBI_9911_Pre-Plasma IgG

description: IgG

source_name: Pre-Plasma


title: LTBI_9911_6mo-Plasma IgG

description: IgG


title: TB_10208_6mo-BALF IgG

description: IgG


title: TB_21410_early-plasma IgM

description: IgM

source_name: early-plasma


title: LTBI_9811_Pre-Plasma IgG

description: IgG


title: TB_21410_early-BALF IgM

description: IgM

source_name: early-BALF


title: Untreated rep 3

description:
G816Untr_S21
G816_RNA-seq_counts.csv

value: Untreated


title: TB_21410_pre-BALF IgM

description: IgM


title: Untreated rep 2

description:
G816Untr_S20
G816_RNA-seq_counts.csv


title: TB_20708_early-plasma IgM

description: IgM


title: TB_20708_pre-BALF IgM

description: IgM


title: Untreated rep 1

description:
G816Untr_S19
G816_RNA-seq_counts.csv


title: LTBI_9811_Pre-BALF IgG

description: IgG


title: TB_20708_early-BALF IgM

description: IgM


title: TB_21310_early-BALF IgM

description: IgM


title: TB_20708_pre-plasma IgM

description: IgM


title: TB_21310_early-plasma IgM

description: IgM


title: TB_21310_pre-plasma IgM

description: IgM


title: TB_21310_pre-BALF IgM

description: IgM


title: MEF-NT, Day 2, Biol Rep 4

city: Cambridge

first: Ming-Hsuan

last: Wen

address: Tennis Court Road

country: United Kingdom

institute: Wellcome/Cancer Research UK Gurdon Institute, University of Cambridge

data_processing:
Fasta files from M. musculus (mm10) and X. laevis (xla9.1) were concatenated one after the other in order to create a hybrid large mouse-Xenopus genome.
To distinguish the X. laevis chromosomes in the fasta file, they were renamed as ‘xla_chr’ instead of just ‘chr’.
Similarly, the gtf files containing the annotation of all transcripts from Mouse (mm10) and of all primary transcript from X. laevis (xla9.1) have been concatenated.
FastQ files were processed with cutadatp (version 1.9.1, options -q 10 -O 3) for adapter trimming.
Filtered reads were then aligned to the hybrid mouse-Xenopus genome with tophat (version v2.1.1).
Transcripts were assigned to gene and counted using htseq-count (HTSeq-0.5.4p3).
The M. musculus (mm10) was replaced with H. sapiens (hg38) in experiments with human cells transplanted into Xenopus oocytes.
Assembly: mm10
Assembly: hg38
Supplementary files format and content: exl files include TPM for each sample

organism: Mus musculus

source_name: embryonic fibroblasts

extract_protocol:
RNA was extracted by Qiagen Rneasy Mini Kit and BrUTP incorporated RNA was isolated via immunoprecipitation.
RNA-seq libraries were prepared by Ovation Single Cell RNA-seq System (NuGEN) and 10 ng of BrUTP incorporated RNA was used for each library.

value: embryonic fibroblasts


title: HP1cTKO RRBS

city: Berlin

first: Andrew

last: Newman

address: Charitéplatz 1

department: Institute for Cell and Neurobiology

country: Germany

institute: Charité Universitätsmedizin Berlin

description: For conditional KO, 4-OH Tamoxifen (SIGMA, #H7904; (Z)-4-Hydroxytamoxifen, ≥98% Z isomer, dissolved in ethanol) was added to medium to a final concentration of 800 nM.

library_source: genomic

data_processing:
RNAseq reads aligned using STAR with --outFilderMultimapNmax 100 --winAnchorMultimapNmax 100 --outSAmstrandField intronMotif and the gencode.vM16.basic.annotation.gtf. Count table across all samples was generated using TETranscripts
ChIPseq reads were trimmed using trimmomatic SE with LEADING:5, TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:30.  Trimmed reads were aligned using bowtie2 using default parameters. Bigwig files were created using deeptools' bamCoverage with --normalizeUsing RPGC --effectiveGenomeSize 2652783500 --extendReads 125
RRBS reads were trimmed using trim_galore --rrbs and aligned to the bisulfite genome using bismark with --bowtie1 -n 1 -l 45
Genome_build: GRCm38.p5
Supplementary_files_format_and_content: RNAseq counts, bigwig for ChIP-seq, coverage files for RRBS

molecule: genomic DNA

source_name: murine embryonic stem cells

growth_protocol: ESCs were cultured in D-MEM (Kohjin-bio, #16003550) with 20% fetal bovine serum (Sigma-Aldrich, #172012), MEM nonessential amino acids (GIBCO, #11140-050), L-glutamine (GIBCO, #25030-081), 2-mercaptoethanol (Sigma-Aldrich, #M1753), and LIF (in-house preparation) on mitomycin C-treated (Sigma-Aldrich, #M4287) primary MEF feeder layers

extract_protocol:
RNA was isolated using the Relia-prep RNA mini kit (Promega), for ChIP, lysates were clarified from sonicated nuclei and precipitated with an antibody. Genomic DNA for RRBS was isolated using the Allprep DNA/RNA mini kit (QIAGEN #80204) Bisulfite conversion was done by the EZ DNA Methylation Gold kit (Zymo Research, #D5005) with 50ng of DNA per sample.
RNAseq libraries were prepared with NEBNext Ultra RNA library prep kit for Illumina using 1ug of RNA per sample. ChIP multiplex libraries were prepared by NEBNext Ultra DNA library Prep kit for Illumina.

value: murine embryonic stem cells

tag: strain

tag: genotype

tag: chip antibody

value: 4-OHT tamoxifen treatment for 6 days


title: TB_18106_early-plasma IgM

description: IgM


title: endosperm, wild type, 16 days after pollination, rep2

city: Hefei

first: Di

last: Peng

address: Huangshan Road 443

country: China

institute: University of Science and Technology of China

data_processing:
The resulting clean reads were aligned to the B73 reference genome (Zm-B73-REFERENCE-NAM-5.0) using the HISAT2 program
Assembly: Zm-B73-REFERENCE-NAM-5.0
Supplementary files format and content: tab-delimited txt file include FPKM value for each sample

molecule: polyA RNA

organism: Zea mays

source_name: endosperm

extract_protocol:
Total RNA was extracted from maize endosperm using TRIzol reagent (Invitrogen). Kit for Illumina
Sequencing libraries were generated using VAHTSTM mRNA-seq V2 Library Prep Kit for Illumina.

value: endosperm

value: wild type


title: endosperm, zmnac128 zmnac130, 16 days after pollination, rep1

value: zmnac128 zmnac130


title: endosperm, zmnac128 zmnac130, 16 days after pollination, rep2


title: endosperm, wild type, 16 days after pollination, rep1


title: wt RRBS

value: WT


title: LTBI_9811_6mo-BALF IgG

description: IgG


title: LTBI_9811_3mo-BALF IgG

description: IgG


title: LTBI_9811_6mo-Plasma IgG

description: IgG


title: LTBI_9811_3mo-Plasma IgG

description: IgG


title: LTBI_9808_6mo-Plasma IgG

description: IgG


title: HP1cTKO ESCs clone 20 H3K9me3 ChIP

value: Histone H3K9me3 antibody (mAb), Clone:MABI 0319


title: TB_17406_early-plasma IgM

description: IgM


title: TB_18106_early-BALF IgM

description: IgM


title: HP1cTKO ESCs clone 10 H3K9me3 ChIP


title: TB_17406_early-BALF IgM

description: IgM


title: SAMPLE 111 -Before challenge Male caLen Mouse 93

city: Athens

first: Daniel

middle: Roberto

last: Perez

state: GA

address: 953 College Station Road

institute: University of Georgia

description: Fig 9

hyb_protocol: Serum and BALF were diluted 1:100 in a protein array blocking buffer (GVS, Sanford,  ME, USA), supplemented with E. coli lysate (GenScript, Piscataway, NJ, USA) to a final  concentration of 10 mg/mL, and preincubated at room temperature (RT) for 30 min. Concurrently,  arrays were rehydrated in blocking buffer (without lysate) for 30 min. Blocking  buffer was removed, and arrays were probed with preincubated serum samples using  sealed chambers to prevent cross-contamination of samples between the pads. Arrays were  incubated overnight at 4  C with gentle agitation. They were then washed at RT three  times with Tris-buffered saline (TBS) containing 0.05% Tween 20 (T-TBS), biotin-conjugated  goat anti-mouse IgA and Biotin-conjugated anti-mouse IgG (Jackson Immuno Research  Laboratories, Inc., West Grove, PA, USA) were diluted 1:400 in blocking buffer and applied  to separate arrays for 1 h, RT with gentle agitation. Arrays were washed three times  with T-TBS, followed by incubation with streptavidin-conjugated Qdot655 (Thermo Fisher  Scientific, Waltham, MA, USA) diluted 1:200 in blocking buffer for 1 h, RT. Arrays were  washed three times with T-TBS and once with water. Arrays were air dried by centrifugation  at 500 g for 5 min. Images were acquired using the ArrayCAM imaging system from  Grace Bio-Labs (Bend, OR, USA). Spot and background intensities were measured using  an annotated grid (.gal) file. Mean fluorescence across antigens grouped by isotypes were  used for subsequent analysis. The different antigens were acquired from Sino biological  (Wayne, PA, USA).

scan_protocol: Images were acquired using the ArrayCAM imaging system from Grace Bio-Labs (Bend, OR) with gain and exposure times of 50 and 400-1000ms, respectively.

data_processing: Spot and background intensities were measured using an annotated grid (.gal) file.  Signal intensities (SI) for each antigen on the array were first background corrected by subtracting sample-specific T-PBS buffer signals from purified protein spot signals. For statistical analysis,   A one-way ANOVA was performed. A P value below 0.05 was considered significan. All data analyses and graphs were performed using GraphPad Prism software version 9 (GraphPad Software Inc., San Diego, CA, USA).

source_name: BALF

tag: vaccine regimen

value: prime

tag: vaccine

value: caLen

tag: time point

value: d20 dpi

tag: mouse id


title: HP1DKO aged hippocampus rep3

source_name: 13 month old hippocampus

value: 13 month old hippocampus

value: mixed C57BL/6/129

value: normal aging


title: wt ESCs clone 10 H3K9me3 ChIP


title: SAMPLE 110 -Prime-boost vac regime Male caLen Mouse 92

description: Fig 9

value: prime/boost

value: d14 dpb


title: LTBI_9808_6mo-BALF IgG

description: IgG

value: Asymptomatic controlled Mtb infection


title: LTBI_9808_2mo-Plasma IgG

description: IgG


title: SAMPLE 109 -Prime-boost vac regime Male caLen Mouse 91

description: Fig 9


title: LTBI_9808_2mo-BALF IgG

description: IgG


title: LTBI_9411_Pre-Plasma IgG

description: IgG


title: TB_17106_early-BALF IgM

description: IgM

value: Symtomatic uncontrolled Mtb infection/TB disease


title: TB_17106_early-plasma IgM

description: IgM


title: TB_10908_pre-plasma IgM

description: IgM


title: SAMPLE 108 -Before challenge Female caLen Mouse 82

description: Fig 9


title: SAMPLE 107 -Before challenge Female caLen Mouse 81

description: Fig 9


title: HP1DKO aged hippocampus rep2


title: SAMPLE 112 -Before challenge Male caLen Mouse 94

description: Fig 9


title: TB_10908_pre-BALF IgM

description: IgM


title: LTBI_9411_Pre-BALF IgG

description: IgG


title: HP1DKO aged hippocampus rep1


title: genomic DNA_DU145 cells_SAHA_rep1

type: genomic

city: Guangzhou

first: Xiong

last: Li

address: 19 Nonglinxia Road

institute: Guangdong Pharmaceutical University

description: SAMPLE 7

hyb_protocol: Bisulfite-converted DNA was analyzed on an Illumina Infinium MethylationEPIC(850K) BeadChip (Illumina).

scan_protocol: Illumina iSCAN was used to scan the chip to get the Idat files.

data_processing: R ChAMP package (version 2.12.4)

label: cy3, cy5

source_name: DU145 cells, SAHA, rep1

label_protocol: DNA was bisulfite treated using the Zymo Research EZ DNA methylaiton-Glod Kits (Zymo Research, Irvine, CA, USA) according to standard instructions

growth_protocol: DU145 prostate cancer cells were maintained in 1640 medium supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37℃

extract_protocol: Genomic DNA was extracted and purified from DU145 cell samples using Qiagen DNeasy Kit according to manufactor's instructions

treatment_protocol: Cells were maintained in 1640 medium supplemented with 10% FBS and 20μm H93 (DMSO dissolved), 500 nm SAHA (DMSO dissolved) or DMSO only for 6 days. The medium were changed everyday.

value: prostate cancer cells

value: SAHA 500nm

tag: time

value: Day 6


title: HP1gKO aged hippocampus rep3


title: LTBI_9411_6mo-Plasma IgG

description: IgG


title: genomic DNA_DU145 cells_H93_rep2

description: SAMPLE 5

source_name: DU145 cells, H93, rep2


title: SAMPLE 106 -Prime-boost vac regime Female caLen Mouse 80

description: Fig 9


title: LTBI_9411_6mo-BALF IgG

description: IgG


title: SAMPLE 105 -Prime-boost vac regime Female caLen Mouse 79

description: Fig 9


title: HP1gKO aged hippocampus rep1


title: genomic DNA_DU145 cells_H93_rep3

description: SAMPLE 6

source_name: DU145 cells, H93, rep3


title: TGFb+TNFa rep 1

description:
G816TT_S22
G816_RNA-seq_counts.csv

value: glioblastoma

value: glioma-initiating

value: TGFβ+TNFα 4 days


title: LTBI_9411_2mo-BALF IgG

description: IgG


title: LTBI_9311_Pre-Plasma IgG

description: IgG


title: TB_10908_early-plasma IgM

description: IgM


title: genomic DNA_DU145 cells_SAHA_rep3

description: SAMPLE 9

source_name: DU145 cells, SAHA, rep3

value: WT


title: LTBI_9311_Pre-BALF IgG

description: IgG


title: genomic DNA_DU145 cells_SAHA_rep2

description: SAMPLE 8

source_name: DU145 cells, SAHA, rep2


title: genomic DNA_DU145 cells_DMSO_rep1

description: SAMPLE 1

source_name: DU145 cells, DMSO, rep1

value: DMSO


title: genomic DNA_DU145 cells_H93_rep1

description: SAMPLE 4

source_name: DU145 cells, H93, rep1


title: SAMPLE 101 -Prime-boost vac regime Male RAM-IGIP Mouse 67

description: Fig 9

value: RAM-IGIP (H1N1)


title: HP1BKO aged hippocampus rep1


title: SAMPLE 102 -Prime-boost vac regime Male RAM-IGIP Mouse 68

description: Fig 9


title: HP1BKO aged hippocampus rep2


title: TB_10208_pre-plasma IgM

description: IgM

source_name: pre-plasma


title: TB_10908_early-BALF IgM

description: IgM


title: TB_10808_early-plasma IgM

description: IgM


title: TB_10808_early-BALF IgM

description: IgM


title: LTBI_9311_6mo-Plasma IgG

description: IgG


title: genomic DNA_DU145 cells_DMSO_rep3

description: SAMPLE 3

source_name: DU145 cells, DMSO, rep3


title: HP1gKO aged hippocampus rep2


title: SAMPLE 103 -Before challenge Male RAM-IGIP Mouse 69

description: Fig 9

value: prime

value: d20 dpi


title: TB_10208_early-plasma IgM

description: IgM


title: WT aged hippocampus rep2

value: 13 month old hippocampus

value: mixed C57BL/6/129


title: LTBI_9311_6mo-BALF IgG

description: IgG


title: SAMPLE 100 -Before challenge Female RAM-IGIP Mouse 58

description: Fig 9


title: WT aged hippocampus rep3

value: normal aging


title: SAMPLE 104 -Before challenge Male RAM-IGIP Mouse 70

description: Fig 9


title: TB_10208_pre-BALF IgM

description: IgM

source_name: pre-BALF


title: SAMPLE 99 -Before challenge Female RAM-IGIP Mouse 57

description: Fig 9


title: LTBI_9808_Pre-BALF IgG

description: IgG

source_name: Pre-BALF


title: WT aged hippocampus rep1


title: TB_10208_early-BALF IgM

description: IgM

source_name: early-BALF


title: LTBI_9411_2mo-Plasma IgG

description: IgG


title: LTBI_9911_pre-plasma IgM

description: IgM


title: LTBI_9311_2mo-Plasma IgG

description: IgG


title: HP1DKO young hippocampus rep3

source_name: 3 month old hippocampus

value: 3 month old hippocampus


title: HP1DKO young hippocampus rep4


title: HP1DKO young hippocampus rep2


title: LTBI_9911_pre-BALF IgM

description: IgM

value: Asymptomatic controlled Mtb infection


title: genomic DNA_DU145 cells_DMSO_rep2

description: SAMPLE 2

source_name: DU145 cells, DMSO, rep2


title: SAMPLE 98 -Prime-boost vac regime Female RAM-IGIP Mouse 56

description: Fig 9

value: prime/boost

value: d14 dpb


title: LTBI_9911_early-plasma IgM

description: IgM

source_name: early-plasma


title: LTBI_9911_early-BALF IgM

description: IgM


title: LTBI_9311_2mo-BALF IgG

description: IgG


title: HP1gKO young hippocampus rep3


title: LTBI_9811_pre-plasma IgM

description: IgM


title: LTBI_9208_Pre-Plasma IgG

description: IgG

source_name: Pre-Plasma


title: wt ESCs clone 20 H3K9me3 ChIP

source_name: murine embryonic stem cells

value: murine embryonic stem cells

value: Histone H3K9me3 antibody (mAb), Clone:MABI 0319


title: SAMPLE 95 -Before challenge Male RAM Mouse 45

description: Fig 9

source_name: BALF

value: RAM (H1N1)


title: LTBI_9811_pre-BALF IgM

description: IgM


title: LTBI_9208_2mo-Plasma IgG

description: IgG


title: SAMPLE 96 -Before challenge Male RAM Mouse 46

description: Fig 9


title: SAMPLE 97 -Prime-boost vac regime Female RAM-IGIP Mouse 55

description: Fig 9


title: HP1gKO young hippocampus rep2


title: LTBI_9208_2mo-BALF IgG

description: IgG


title: LTBI_9811_early-plasma IgM

description: IgM


title: SAMPLE 92 -Before challenge Female RAM Mouse 34

description: Fig 9


title: SAMPLE 94 -Prime-boost vac regime Male RAM Mouse 44

description: Fig 9


title: SAMPLE 93 -Prime-boost vac regime Male RAM Mouse 43

description: Fig 9


title: LTBI_9811_early-BALF IgM

description: IgM


title: LTBI_9808_pre-BALF IgM

description: IgM


title: LTBI_9808_early-BALF IgM

description: IgM


title: LTBI_9808_early-plasma IgM

description: IgM


title: HP1BKO young hippocampus rep2


title: HP1BKO young hippocampus rep3


title: SAMPLE 89 -Prime-boost vac regime Female RAM Mouse 31

description: Fig 9


title: HP1gKO young hippocampus rep1


title: HP1BKO young hippocampus rep1


title: WT young hippocampus rep4


title: SAMPLE 88 -Before challenge Male Mock Mouse 11

description: Fig 9

value: PBS


title: LTBI_9411_pre-plasma IgM

description: IgM


title: WT young hippocampus rep3


title: SAMPLE 86 -Before challenge Female Mock Mouse 5

description: Fig 9


title: SAMPLE 87 -Before challenge Male Mock Mouse 10

description: Fig 9


title: WT young hippocampus rep2


title: SAMPLE 90 -Prime-boost vac regime Female RAM Mouse 32

description: Fig 9


title: SAMPLE 91 -Before challenge Female RAM Mouse 33

description: Fig 9


title: LTBI_9411_pre-BALF IgM

description: IgM


title: LTBI_9208_6mo-BALF IgG

description: IgG


title: LTBI_6909_2mo-Plasma IgG

description: IgG


title: LTBI_9208_6mo-Plasma IgG

description: IgG


title: LTBI_6909_6mo-BALF IgG

description: IgG


title: LTBI_6909_6mo-Plasma IgG

description: IgG


title: LTBI_6909_Pre-Plasma IgG

description: IgG


title: LTBI_6909_Pre-BALF IgG

description: IgG


title: LTBI_9208_Pre-BALF IgG

description: IgG


title: LTBI_6909_2mo-BALF IgG

description: IgG


title: HP1DKO young hippocampus rep1


title: WT young hippocampus rep1


title: LTBI_6709_Pre-Plasma IgG

description: IgG


title: LTBI_6709_Pre-BALF IgG

description: IgG


title: LTBI_6709_6mo-Plasma IgG

description: IgG


title: 6742

type: RNA

city: Houston

first: Caleb

middle: A

last: Wood

state: TX

address: 1 Baylor Plaza

institute: Baylor College of Medicine

description: NanoString Neuroinflammation Probes

hyb_protocol: NanoString Neuroinflammation probes.

scan_protocol: Scanned in a NanoString nCounter.

data_processing: NanoString Neuroinflammation probes were scanned in a NanoString nCounter. The resulting data were exported and provided as a CSV file. Differential gene expression analysis was performed using the edgeR pipeline v3.38.4 (Robinson et. al., Bioinformatics, 2010). Counts were then normalized to library size using the ‘Upper Quartile’ method. Principle component analysis was first performed on normalized expression data to identify potential outlier samples. No samples were removed from downstream analysis. Counts were first normalized to remove variation using control genes in the RUVg function within RUVSeq v1.30.0 (Risso et. al., Nat. Biotechnol., 2010). Results were calculated via the “likelihood ratio testing’ parameter and Benjamin-Hochberg p-adjustment method. Genes with adjusted p-value < 0.05 and absolute value of logFC above 0.05 were considered statistically significant. Heatmaps was created using ‘pretty heatmap’ package in R v1.0.12. Heatmap for all DEGs was generated using log-transformed counts and scaled by row where colors represent row z-scores. Heatmap to compare logFC between dox + LPS vs untreated and LPS vs untreated was generated using logFC values; colors represent raw logFC values. Volcano plots were generated using the ‘Enhanced Volcano’ package in R v1.14.0 (Blighe et. al., EnhancedVolcano, 2018).  All genes were included in the analysis.

source_name: Brain cortex

label_protocol: RNA samples were hybridized with the NanoString nCounter Mouse Neuroinflammation panel and processed according to the NanoString manual MAN-10023-11.

growth_protocol: Mice were maintained in accordance with institutional and IACUC polices. Access to food and water was ad libitum.

extract_protocol: Total RNA was extracted from frozen cortical tissue using RNeasy Plus Micro Kit (#74034, Qiagen) following the manufacturer’s instructions. Brains were homogenized using the Bead Rupter Elite Bead Mill Homogenizer (#19-042E, OMNI International) in homogenization buffer from the RNeasy Plus Micro Kit with Reagent DX added at 1:200 dilution (#1011008, Qiagen) to reduce foaming. RNA quality and concentration were measured using a NanoDrop UV-vis spectrophotometer (#13-400-519, ThermoFisher).

treatment_protocol: See experimental groups listed under title, above

tag: Sex

value: male

value: Untreated

tag: mouse line

value: CamKIIα-TTA/tetO-APP102 x FVB

value: brain cortex

tag: age

value: 12 wks


title: SAMPLE 84 -Before challenge Male caLen Mouse 94

description: Fig 9

source_name: Serum

value: prime

value: caLen

value: d20 dpi


title: LTBI_6709_6mo-BALF IgG

description: IgG


title: LTBI_9311_pre-BALF IgM

description: IgM


title: SAMPLE 83 -Before challenge Male caLen Mouse 93

description: Fig 9


title: 5649

description: NanoString Neuroinflammation Probes

value: female

value: WT


title: LTBI_9311_early-plasma IgM

description: IgM

value: Asymptomatic controlled Mtb infection


title: LTBI_9208_pre-plasma IgM

description: IgM


title: LTBI_6709_2mo-BALF IgG

description: IgG


title: LTBI_6609_Pre-Plasma IgG

description: IgG


title: SAMPLE 82 -Prime-boost vac regime Male caLen Mouse 92

description: Fig 9

value: prime/boost


title: SAMPLE 81 -Prime-boost vac regime Male caLen Mouse 91

description: Fig 9

value: d14 dpb


title: SAMPLE 80 -Before challenge Female caLen Mouse 82

description: Fig 9


title: LTBI_9311_early-BALF IgM

description: IgM


title: SAMPLE 79 -Before challenge Female caLen Mouse 81

description: Fig 9


title: LTBI_6709_2mo-Plasma IgG

description: IgG


title: LTBI_9208_pre-BALF IgM

description: IgM


title: SAMPLE 78 -Prime-boost vac regime Female caLen Mouse 80

description: Fig 9


title: LTBI_6609_Pre-BALF IgG

description: IgG


title: LTBI_9411_early-BALF IgM

description: IgM


title: LTBI_9311_pre-plasma IgM

description: IgM


title: LTBI_9411_early-plasma IgM

description: IgM


title: LTBI_9208_early-plasma IgM

description: IgM


title: SAMPLE 85 -Before challenge Female Mock Mouse 4

description: Fig 9


title: 5635

description: NanoString Neuroinflammation Probes


title: LTBI_6609_6mo-Plasma IgG

description: IgG


title: LTBI_9208_early-BALF IgM

description: IgM


title: LTBI_6909_pre-plasma IgM

description: IgM


title: LTBI_6609_6mo-BALF IgG

description: IgG


title: LTBI_6609_2mo-Plasma IgG

description: IgG


title: SAMPLE 77 -Prime-boost vac regime Female caLen Mouse 79

description: Fig 9


title: LTBI_6909_early-plasma IgM

description: IgM


title: LTBI_6909_pre-BALF IgM

description: IgM


title: SAMPLE 73 -Prime-boost vac regime Male RAM-IGIP Mouse 67

description: Fig 9

value: RAM-IGIP (H1N1)


title: LTBI_6909_early-BALF IgM

description: IgM


title: SAMPLE 72 -Before challenge Female RAM-IGIP Mouse 58

description: Fig 9


title: SAMPLE 74 -Prime-boost vac regime Male RAM-IGIP Mouse 68

description: Fig 9


title: SAMPLE 75 -Before challenge Male RAM-IGIP Mouse 69

description: Fig 9


title: LTBI_6709_pre-plasma IgM

description: IgM


title: SAMPLE 76 -Before challenge Male RAM-IGIP Mouse 70

description: Fig 9


title: 1759

description: NanoString Neuroinflammation Probes


title: 1821

description: NanoString Neuroinflammation Probes


title: 1840

description: NanoString Neuroinflammation Probes


title: 1760

description: NanoString Neuroinflammation Probes


title: 1836

description: NanoString Neuroinflammation Probes


title: 1733

description: NanoString Neuroinflammation Probes

value: LPS


title: 1764

description: NanoString Neuroinflammation Probes


title: 1746

description: NanoString Neuroinflammation Probes


title: SAMPLE 70 -Prime-boost vac regime Female RAM-IGIP Mouse 56

description: Fig 9


title: SAMPLE 71 -Before challenge Female RAM-IGIP Mouse 57

description: Fig 9


title: LTBI_6709_early-plasma IgM

description: IgM


title: LTBI_6709_early-BALF IgM

description: IgM


title: 1861

description: NanoString Neuroinflammation Probes


title: 1977

description: NanoString Neuroinflammation Probes

value: Dox


title: 1770

description: NanoString Neuroinflammation Probes


title: 1439

description: NanoString Neuroinflammation Probes


title: 1732

description: NanoString Neuroinflammation Probes


title: LTBI_6709_pre-BALF IgM

description: IgM


title: SAMPLE 68 -Before challenge Male RAM Mouse 46

description: Fig 9

value: RAM (H1N1)


title: LTBI_6609_pre-plasma IgM

description: IgM


title: SAMPLE 69 -Prime-boost vac regime Female RAM-IGIP Mouse 55

description: Fig 9


title: SAMPLE 67 -Before challenge Male RAM Mouse 45

description: Fig 9


title: LTBI_6609_pre-BALF IgM

description: IgM


title: LTBI_6609_early-BALF IgM

description: IgM


title: LTBI_6509_pre-plasma IgM

description: IgM


title: SAMPLE 63 -Before challenge Female RAM Mouse 33

description: Fig 9


title: LTBI_6609_early-plasma IgM

description: IgM


title: SAMPLE 65 -Prime-boost vac regime Male RAM Mouse 43

description: Fig 9


title: SAMPLE 66 -Prime-boost vac regime Male RAM Mouse 44

description: Fig 9


title: SAMPLE 64 -Before challenge Female RAM Mouse 34

description: Fig 9


title: LTBI_6509_pre-BALF IgM

description: IgM


title: SAMPLE 62 -Prime-boost vac regime Female RAM Mouse 32

description: Fig 9


title: LTBI_6309_2mo-Plasma IgG

description: IgG


title: LTBI_6309_Pre-Plasma IgG

description: IgG


title: LTBI_6309_6mo-BALF IgG

description: IgG


title: LTBI_6309_2mo-BALF IgG

description: IgG


title: LTBI_6309_Pre-BALF IgG

description: IgG


title: 1743

description: NanoString Neuroinflammation Probes

value: Dox+LPS


title: 1427

description: NanoString Neuroinflammation Probes


title: 1756

description: NanoString Neuroinflammation Probes


title: 1854

description: NanoString Neuroinflammation Probes


title: 1766

description: NanoString Neuroinflammation Probes

value: male


title: 1765

description: NanoString Neuroinflammation Probes

value: CamKIIα-TTA/tetO-APP102 x FVB


title: LTBI_4808_Pre-BALF IgG

description: IgG


title: LTBI_6509_2mo-BALF IgG

description: IgG


title: LTBI_6509_Pre-Plasma IgG

description: IgG


title: LTBI_6509_2mo-Plasma IgG

description: IgG


title: LTBI_6509_6mo-Plasma IgG

description: IgG


title: LTBI_6609_2mo-BALF IgG

description: IgG


title: LTBI_6509_6mo-BALF IgG

description: IgG


title: LTBI_6509_Pre-BALF IgG

description: IgG


title: SAMPLE 61 -Prime-boost vac regime Female RAM Mouse 31

description: Fig 9


title: LTBI_4808_2mo-Plasma IgG

description: IgG


title: LTBI_6509_early-plasma IgM

description: IgM


title: CCD841_H3K18bu_CUTnTag_but2

city: Palo Alto

first: Michael

last: Nshanian

state: CA

institute: Stanford University

data_processing:
Basecalls were performed using bcl2fastq2 (v2.17.1) for HiSeq and Novaseq output.
CUTnTag reads were trimmed from 3' end using cutadapt (v 1.9.1) until the final base had a quality score > 30.
CUTnTag reads were aligned to the UCSC hg38 or mm10 genomes using Bowtie2 (v 2.3.1). Only uniquely mapped reads were retained with at most two mismatches.
To create CUTnTag coverage plots, the locations of the mapped reads were enormalized to reads per million and reformatted to .bigWig file format.
Peaks were called using MACS2 (2.1.0) with the significance cut-off q-value (FDR) <= 0.01.
Assembly: hg38, mm10
Supplementary files format and content: bam, narrowPeak

growth_protocol: EMEM media containing 10 % fetal bovine serum (FBS)/1 % Pen/Strep (PS). All cell lines were maintained at 37C in a humidified atmosphere containing 5 % CO2

extract_protocol:
CUT&Tag was performed using CUT&Tag-ITTM assay kits (Active Motif # 53160, 53170). ~500,000 viable nuclei (30 mg tissue) were used per reaction. Tissue samples were Dounced 20 times with a loose pestle and 10 times with a tight pestle. 5 μg of undiluted primary antibody was added to each sample for an overnight incubation at 4C with orbital mixing. 100 μL of 1:100 of Guinea Pig Anti-Rabbit secondary antibody was then added to each reaction and the samples were incubated on an orbital rotator for 60 min at RT. Assembled pA-Tn5 Transposomes were added to each sample and reactions were incubated on an orbital rotator for 60 min at RT. 125 μL of Tagmentation Buffer (5 mL Dig-300 buffer and 50 µL 1 M MgCl2) was added to each sample and reactions were incubated at 37C for 1 h. Nextera i5 and i7 indexing primers were used and final PCR reactions were purified using Zymo DNA Clean and Concentrator-5 Kit (cat # D4013).
Final PCR reactions were purified using Zymo DNA Clean and Concentrator-5 Kit (cat # D4013)
CUT&Tag-ITTM assay kits (Active Motif # 53160, 53170) and Hatice S. Kaya-Okur et al., (Nat Comm 2019)

treatment_protocol: Cells were treated with 1 mM Na Butyrate (NaBu) for 12-16 hrs followed by counting.

value: Large intestine; colon, epithelial

value: 1 mM NaBu


title: CCD841_H4K12bu_CUTnTag_but1


title: CCD841_H4K12bu_CUTnTag_but2


title: CCD841_H3K18bu_CUTnTag_but1


title: 05162022_SW480_But3

data_processing:
The raw data were aligned to the human genome (hg38) by STAR v.2.5.4b (https://github.com/alexdobin/STAR).
The aligned transcripts were quantitated based on features in the GENCODE annotation database (hg38) by RSEM v.1.3.1 (http://deweylab.biostat.wisc.edu/rsem/).
Differentially expressed genes were detected and normalized using DESeq2 v.1.20.0 R package with a FDR-adjusted P-value cutoff of < 0.05 (https://bioconductor.org/packages/release/bioc/html/DESeq2.html).
Assembly: hg38
Supplementary files format and content: tab-delimited file includes raw counts for each sample
Supplementary files format and content: tab-delimited file includes RPKM values for each sample

extract_protocol:
RNA was extracted using the RNeasy Mini Kit (#74136, Qiagen).
Libraries were prepared using NEBNext Ultra II RNA library prep kit for Illumina (# E7770) and rRNA depletion kit (# E6310).

treatment_protocol: Cells were treated with 10 mM Na Propionate (NaPr) or 1 mM Na Butyrate (NaBu) for 12-16 hrs. followed by cell counting and library preparation.


title: LTBI_6309_early-BALF IgM

description: IgM


title: LTBI_6509_early-BALF IgM

description: IgM


title: 1738

description: NanoString Neuroinflammation Probes

value: brain cortex

value: 12 wks


title: LTBI_6309_pre-plasma IgM

description: IgM


title: LTBI_6309_pre-BALF IgM

description: IgM


title: 05162022_SW480_But2


title: LTBI_6309_early-plasma IgM

description: IgM


title: LTBI_23010_Pre-BALF IgG

description: IgG


title: LTBI_23010_2mo-Plasma IgG

description: IgG


title: LTBI_23010_Pre-Plasma IgG

description: IgG


title: LTBI_23010_pre-plasma IgM

description: IgM


title: LTBI_4808_2mo-BALF IgG

description: IgG


title: SAMPLE 58 -Before challenge Female Mock Mouse 5

description: Fig 9

value: prime

value: PBS

value: d20 dpi


title: 05162022_SW480_Cnt3

value: 0 mM NaBu


title: SAMPLE 60 -Before challenge Male Mock Mouse 11

description: Fig 9


title: LTBI_23010_pre-BALF IgM

description: IgM

value: Asymptomatic controlled Mtb infection


title: SAMPLE 59 -Before challenge Male Mock Mouse 10

description: Fig 9


title: LTBI_23010_early-plasma IgM

description: IgM


title: LTBI_23010_2mo-BALF IgG

description: IgG


title: LTBI_22810_Pre-Plasma IgG

description: IgG


title: 05162022_SW480_But1


title: LTBI_23010_early-BALF IgM

description: IgM


title: 05162022_SW480_Cnt1


title: LTBI_22810_2mo-Plasma IgG

description: IgG


title: 10222020_SW480_Prop3

value: 10 mM NaPr


title: SAMPLE 51 -Before challenge Female caLen Mouse 81

description: Fig. 8 and 9

value: caLen


title: SAMPLE 52 -Before challenge Female caLen Mouse 82

description: Fig. 8 and 9


title: 10222020_SW480_Prop2


title: LTBI_22810_pre-BALF IgM

description: IgM


title: SAMPLE 50 -Prime-boost vac regime Female caLen Mouse 80

description: Fig. 8 and 9

value: prime/boost

value: d14 dpb


title: 05162022_SW480_Cnt2


title: 10222020_SW480_Prop1


title: LTBI_22810_early-BALF IgM

description: IgM


title: 10222020_SW480_Cnt3

value: 0 mM NaPr


title: LTBI_22810_early-plasma IgM

description: IgM


title: LTBI_22710_3mo-Plasma IgG

description: IgG


title: SAMPLE 48 -Before challenge Male RAM-IGIP Mouse 70

description: Fig. 8 and 9

value: RAM-IGIP (H1N1)


title: LTBI_22710_3mo-BALF IgG

description: IgG


title: SAMPLE 49 -Prime-boost vac regime Female caLen Mouse 79

description: Fig. 8 and 9


title: LTBI_22810_Pre-BALF IgG

description: IgG


title: LTBI_22810_2mo-BALF IgG

description: IgG


title: LTBI_21910_Pre-BALF IgG

description: IgG


title: LTBI_21910_Pre-Plasma IgG

description: IgG


title: SAMPLE 55 -Before challenge Male caLen Mouse 93

description: Fig. 8 and 9


title: SAMPLE 56 -Before challenge Male caLen Mouse 94

description: Fig. 8 and 9


title: LTBI_22810_pre-plasma IgM

description: IgM


title: LTBI_22710_pre-plasma IgM

description: IgM


title: LTBI_21910_2mo-Plasma IgG

description: IgG


title: 10222020_SW480_Cnt2


title: SAMPLE 53 -Prime-boost vac regime Male caLen Mouse 91

description: Fig. 8 and 9


title: SAMPLE 46 -Prime-boost vac regime Male RAM-IGIP Mouse 68

description: Fig. 8 and 9


title: 10222020_SW480_Cnt1


title: LTBI_21910_2mo-BALF IgG

description: IgG


title: SAMPLE 57 -Before challenge Female Mock Mouse 4

description: Fig 9


title: SAMPLE 45 -Prime-boost vac regime Male RAM-IGIP Mouse 67

description: Fig. 8 and 9


title: LTBI_21810_Pre-Plasma IgG

description: IgG


title: LTBI_22710_early-BALF IgM

description: IgM


title: SAMPLE 54 -Prime-boost vac regime Male caLen Mouse 92

description: Fig. 8 and 9


title: SAMPLE 47 -Before challenge Male RAM-IGIP Mouse 69

description: Fig. 8 and 9


title: SAMPLE 44 -Before challenge Female RAM-IGIP Mouse 58

description: Fig. 8 and 9


title: LTBI_21910_pre-BALF IgM

description: IgM


title: LTBI_21810_Pre-BALF IgG

description: IgG


title: LTBI_21810_2mo-Plasma IgG

description: IgG


title: SAMPLE 43 -Before challenge Female RAM-IGIP Mouse 57

description: Fig. 8 and 9


title: LTBI_21910_pre-plasma IgM

description: IgM


title: SAMPLE 41 -Prime-boost vac regime Female RAM-IGIP Mouse 55

description: Fig. 8 and 9


title: SAMPLE 40 -Before challenge Male RAM Mouse 46

description: Fig. 8 and 9

value: RAM (H1N1)


title: LTBI_22710_early-plasma IgM

description: IgM


title: SAMPLE 39 -Before challenge Male RAM Mouse 45

description: Fig. 8 and 9


title: SAMPLE 38 -Prime-boost vac regime Male RAM Mouse 44

description: Fig. 8 and 9


title: SAMPLE 42 -Prime-boost vac regime Female RAM-IGIP Mouse 56

description: Fig. 8 and 9


title: LTBI_21710_2mo-Plasma IgG

description: IgG


title: LTBI_21710_Pre-BALF IgG

description: IgG


title: LTBI_21710_Pre-Plasma IgG

description: IgG


title: LTBI_21810_2mo-BALF IgG

description: IgG


title: LTBI_21710_2mo-BALF IgG

description: IgG


title: SAMPLE 37 -Prime-boost vac regime Male RAM Mouse 43

description: Fig. 8 and 9


title: LTBI_21610_Pre-Plasma IgG

description: IgG


title: SAMPLE 36 -Before challenge Female RAM Mouse 34

description: Fig. 8 and 9


title: SW480_but_cnt_3

data_processing:
Basecalls were performed using bcl2fastq2 (v2.17.1) for HiSeq and Novaseq output.
ATAC-seq reads were trimmed from 3' end using cutadapt (v 1.9.1) until the final base had a quality score > 30.
ATAC-seq reads were aligned to the UCSC hg38 or mm10 genomes using Bowtie2 (v 2.3.1). Only uniquely mapped reads were retained with at most two mismatches.
To create ATAC-seq coverage plots, the locations of the mapped reads were enormalized to reads per million and reformatted to .bigWig file format.
Peaks were called using MACS2 (2.1.0) with the significance cut-off q-value (FDR) <= 0.01.
Assembly: hg38, mm10
Supplementary files format and content: narrowPeak

growth_protocol: EMEM media (or RPMI for CT26) containing 10 % fetal bovine serum (FBS)/1 % Pen/Strep (PS). All cell lines were maintained at 37C in a humidified atmosphere containing 5 % CO2

extract_protocol:
ATAC-seq was performed using Omni-ATAC as described in Corces et al. (Nat. Methods 2017). 50,000 viable cells were pelleted and resuspended in ATAC-Resuspension Buffer. Cells were resuspended in transposition mix containing TD buffer and transposase (Illumina Tagmented DNA enzyme and buffer kit, Ref 20034210)
Final PCR reactions were purified using Zymo DNA Clean and Concentrator-5 Kit (cat # D4013)
Corces et al. (Nat. Methods 2017)

treatment_protocol: Cells were treated with 10 mM Na Propionate (NaPr) or 1 mM Na Butyrate (NaBu) for 12-16 hrs followed by counting.


title: LTBI_21810_early-BALF IgM

description: IgM


title: SW480_but_3


title: SW480_prop_3


title: LTBI_21710_pre-plasma IgM

description: IgM


title: LTBI_21810_early-plasma IgM

description: IgM


title: SW480_but_cnt_1


title: LTBI_21910_early-plasma IgM

description: IgM


title: LTBI_21810_pre-BALF IgM

description: IgM


title: SW480_prop_1


title: LTBI_21810_pre-plasma IgM

description: IgM


title: LTBI_21910_early-BALF IgM

description: IgM


title: SW480_but_1


title: SW480_but_2


title: SW480_but_cnt_2


title: SW480_prop_2


title: SW480_prop_cnt_3


title: LTBI_21610_Pre-BALF IgG

description: IgG


title: SAMPLE 35 -Before challenge Female RAM Mouse 33

description: Fig. 8 and 9


title: LTBI_21710_pre-BALF IgM

description: IgM


title: SAMPLE 34 -Prime-boost vac regime Female RAM Mouse 32

description: Fig. 8 and 9


title: SW480_prop_cnt_1


title: LTBI_21710_early-plasma IgM

description: IgM


title: SAMPLE 33 -Prime-boost vac regime Female RAM Mouse 31

description: Fig. 8 and 9


title: LTBI_21710_early-BALF IgM

description: IgM


title: SAMPLE 32 -Before challenge Male Mock Mouse 11

description: Fig. 8 and 9


title: SW480_prop_cnt_2


title: LTBI_21610_pre-BALF IgM

description: IgM


title: LTBI_21510_pre-plasma IgM

description: IgM


title: SAMPLE 29 -Before challenge Female Mock Mouse 4

description: Fig. 8 and 9


title: SAMPLE 30 -Before challenge Female Mock Mouse 5

description: Fig. 8 and 9


title: LTBI_21610_early-BALF IgM

description: IgM


title: SAMPLE 28 -Before challenge Male caLen Mouse 94

description: Fig. 8 and 9


title: SAMPLE 27 -Before challenge Male caLen Mouse 93

description: Fig. 8 and 9


title: SAMPLE 31 -Before challenge Male Mock Mouse 10

description: Fig. 8 and 9


title: LTBI_21510_pre-BALF IgM

description: IgM


title: SAMPLE 26 -Prime-boost vac regime Male caLen Mouse 92

description: Fig. 8 and 9


title: LTBI_21610_early-plasma IgM

description: IgM


title: LTBI_21610_pre-plasma IgM

description: IgM


title: SW480_H4K12bu_but_ChIP_1

data_processing:
Basecalls were performed using bcl2fastq (v2.17.1) for HiSeq and Novaseq output.
ChIP-seq reads were trimmed from 3' end using cutadapt (v 1.8.1) until the final base had a quality score > 30.
ChIP-seq reads were aligned to the UCSC hg38 genome using Bowtie2 (v 2.3.1). Only uniquely mapped reads were retained with at most two mismatches.
To create ChIP-seq coverage plots, the locations of the mapped reads were extended 150 bp to denote extended fragments, renormalized to reads per million and reformatted to .bigWig file format.
Peaks were called using MACS2 (2.1.0) with the significance cut-off q-value (FDR) <= 0.01.
Assembly: hg38
Supplementary files format and content: bam, narrowPeak

growth_protocol: EMEM media containing 10 % fetal bovine serum (FBS)/1 % Pen/Strep (PS). All cell lines were maintained at 37C in a humidified atmosphere containing 5 % CO2.

extract_protocol:
Cells were trypsinized and cross-linked with 1% formaldehyde (EMD Millipore) for 10 min at RT and quenched with 2 M glycine (Thermo Fisher Scientific) for 5 min at room temperature. Chromatin corresponding to 10 million cells for histone modifications was sheared with SFX250 Sonifier (Branson). The lysates were transferred to Diagenode tubes, sonicated 16 rounds of 30 seconds on 30 seconds off, vortexing every 4th round. Protein G beads (80uL) and lysates were washed with RIPA buffer and immunoprecipitated with antibodies targeting given Kacyl marks. 5 μg for each condition, at 4 °C overnight on a nutator. For the input sample, 200 μl of sheared nuclear lysate was removed and stored overnight at 4 °C.
ChIP-DNA and input was reverse crosslinked by incubating overnight at 65 °C in 1% SDS, 1x TE buffer. On the third day, ChIP-DNA was treated with RNase A (Qiagen) and Proteinase K (ThermoFisher Scientific) and then purified using Qiagen QIAquick purification columns. The ChIP-DNA samples were end repaired using End-It DNA End Repair Kit (Lucigen) and A-tailed using Klenow Fragment and dATP (New England Biolabs). Illumina TruSeq adapters (Illumina) were ligated and libraries size-selected (200 - 400 bp) by gel extraction before PCR amplification. The purified libraries were subjected to paired-end sequencing on the Illumina HiSeq 4000/Novaseq 6000 SP to obtain an average of approximately 30 - 35 million uniquely mapped reads for each sample


title: SW480_H4K12bu_but_ChIP_2


title: LTBI_21510_2mo-Plasma IgG

description: IgG


title: SW480_but_input


title: LTBI_21610_2mo-BALF IgG

description: IgG


title: LTBI_21610_2mo-Plasma IgG

description: IgG


title: LTBI_21510_Pre-Plasma IgG

description: IgG


title: SW480_H3K18ac_but_ChIP_2


title: SW480_H4K12ac_but_ChIP_1


title: LTBI_21510_Pre-BALF IgG

description: IgG


title: LTBI_21408_Pre-BALF IgG

description: IgG


title: LTBI_21408_2mo-Plasma IgG

description: IgG


title: LTBI_21510_2mo-BALF IgG

description: IgG


title: LTBI_21408_2mo-BALF IgG

description: IgG


title: LTBI_21510_early-plasma IgM

description: IgM


title: SAMPLE 25 -Prime-boost vac regime Male caLen Mouse 91

description: Fig. 8 and 9


title: LTBI_21510_early-BALF IgM

description: IgM


title: SAMPLE 24 -Before challenge Female caLen Mouse 82

description: Fig. 8 and 9


title: SW480_H3K18bu_but_ChIP_1


title: LTBI_21408_pre-BALF IgM

description: IgM


title: SAMPLE 23 -Before challenge Female caLen Mouse 81

description: Fig. 8 and 9


title: PIMP_4

first: Irina

last: Mohorianu

address: Puddicombe Way

department: Wellcome-MRC Cambridge Stem Cell Institute

institute: University of Cambridge

data_processing:
Quality checks were performed using FastQC (v0.12.1), summarised with MultiQC (v1.14). Reads were then subsampled. Alignment to the human reference genome (build GRCh38.p13) was performed using STAR (v2.7.10a) with default parameters. The counts of the aligned reads corresponding to exons were obtained using featureCounts program against the exon annotations obtained from the ensembl database (annotation file Homo_sapiens.GRCh38.101.gtf). MA plots, JSIs and PCA were performed as further quality checks.
The resulting expression values were normalised using quantile normalisation [Bolstad2003] and noise levels were assessed using noisyR count matrix approach [Moutsopoulos2021].
Differential expression analysis was performed using edgeR (v3.34.1) [Robinson2010] and DESeq2 1.32.0 [Love2014].
The visualisation, and community accessible overview were complied using bulkAnalyseR [Moutsopoulos2023].
Assembly: hg38 (GRCh38.p13)
Supplementary files format and content: count matrix containing raw gene expression
Supplementary files format and content: count matrix containing normalised and denoised gene expression

source_name: cells

growth_protocol: Human iPSCs-derived microglia (hiMG) were derived from human induced pluripotent stem cells (iPSCs). Human iPSCs were cultured in mTeSR1 (Stem Cell Technologies) on hESC-qualified Matrigel-coated plates (Corning). iPSCs were routinely passaged using accutase cell detachment solution (Stem Cell Technologies). Using an adapted protocol with minor modifications, microglia were differentiated from iPSCs via embryoid bodies (EBs) and primitive macrophage precursors (PMPs)86,87. iPSCs were dissociated to single cells with accutase cell detachment solution and plated at 10,000 cells per well in 96-well ultra-low attachment plates (Corning) in 100 μL of microglia embryoid body induction media (MEBIM) supplemented with the ROCK inhibitor StemMACS Y27632 (Miltenyi Biotec) prior to centrifugation at 300 x g for 3 min at room temperature (RT). Plated cells were then stored in a 5% CO2 incubator set to 37°C. EBs were cultured for 4 days with a half medium (i.e., 50 μL) exchange with MEBIM occurring after 2 days. When performing the half media change, small molecule concentrations were doubled to account for the media already present in the wells. After 4 days, 16 EBs were plated per well of tissue-culture treated 6-well plates in 3 mL of microglia differentiation medium A (MDM-A). From this point forward, 2 mL medium was exchanged every 5-6 days. When performing the two-thirds media change, small molecule concentrations were doubled to account for the media already present in the wells. After 14 days, PMPs were harvested from suspension during a media exchange. Harvested media was first filtered through a 40 μm nylon membrane then centrifuged at 500 x g for 5 min at RT. Pelleted cells were resuspended in an appropriate volume of microglia differentiation medium B (MDM-B) and a cell count performed using trypan blue (Thermo Fisher Scientific) exclusion. Cells were plated at a density of 180,000 – 200,000 cells/cm2 in 6-well plates in 1.5 mL of MDM-B. PMPs adhered to the uncoated tissue culture-treated plastic within 24 hrs. The maturation of the PMPs into microglia occurred over 14+ days, with half the medium exchanged every 3 days. When performing the half media change, small molecule concentrations were doubled to account for the media already present in the wells. All cytokines and growth factors were obtained from Peprotech. After a minimum of 14 days of maturation, microglia-like cells were incubated in 2 mL of accutase cell detachment solution for 20-30 min in a 5% CO2 incubator set to 37°C. After 20-30 min, any remaining attached cells were detached with gentle pipetting. Microglia-like cells were centrifuged at 500 x g for 5 min at RT. Pelleted cells were resuspended in an appropriate volume of MDM-B and a cell count performed using trypan blue exclusion. Cells were allowed to rest for 48 hrs prior to experiments being performed.

extract_protocol:
Qiagen RNeasy Kit
standard Illumina protocol

value: cells

value: human primitive macrophage precursors


title: SAMPLE 22 -Prime-boost vac regime Female caLen Mouse 80

description: Fig. 8 and 9


title: SW480_H3K18ac_but_ChIP_1

value: Large intestine; colon, epithelial

value: 1 mM NaBu


title: LTBI_21408_early-BALF IgM

description: IgM


title: SW480_H3K18bu_but_ChIP_2


title: SW480_H4K12ac_but_ChIP_2


title: LTBI_21408_early-plasma IgM

description: IgM


title: SAMPLE 21 -Prime-boost vac regime Female caLen Mouse 79

description: Fig. 8 and 9


title: PIMP_3


title: LTBI_21308_early-plasma IgM

description: IgM


title: PIMP_2


title: LTBI_21308_early-BALF IgM

description: IgM


title: LTBI_21308_pre-plasma IgM

description: IgM


title: LTBI_21308_pre-BALF IgM

description: IgM


title: LTBI_20808_pre-plasma IgM

description: IgM


title: LTBI_20808_pre-BALF IgM

description: IgM


title: SAMPLE 20 -Before challenge Male RAM-IGIP Mouse 70

description: Fig. 8 and 9


title: SAMPLE 17 -Prime-boost vac regime Male RAM-IGIP Mouse 67

description: Fig. 8 and 9


title: SAMPLE 15 -Before challenge Female RAM-IGIP Mouse 57

description: Fig. 8 and 9


title: MG_2

value: human induced microglia


title: PIMP_1


title: IPS_4

value: human induced pluripotent cells


title: MG_4


title: MG_3


title: SAMPLE 19 -Before challenge Male RAM-IGIP Mouse 69

description: Fig. 8 and 9

value: prime


title: SAMPLE 18 -Prime-boost vac regime Male RAM-IGIP Mouse 68

description: Fig. 8 and 9


title: SAMPLE 16 -Before challenge Female RAM-IGIP Mouse 58

description: Fig. 8 and 9

value: d20 dpi


title: MG_1


title: LTBI_20808_early-plasma IgM

description: IgM


title: LTBI_20808_3mo-Plasma IgG

description: IgG


title: LTBI_20808_6mo-Plasma IgG

description: IgG


title: LTBI_20808_6mo-BALF IgG

description: IgG


title: LTBI_20808_3mo-BALF IgG

description: IgG


title: LTBI_19808_2mo-Plasma IgG

description: IgG


title: LTBI_19808_5mo-Plasma IgG

description: IgG


title: LTBI_20808_Pre-BALF IgG

description: IgG


title: LTBI_20808_Pre-Plasma IgG

description: IgG


title: LTBI_19808_Pre-BALF IgG

description: IgG


title: SAMPLE 14 -Prime-boost vac regime Female RAM-IGIP Mouse 56

description: Fig. 8 and 9


title: IPS_3


title: LTBI_20808_early-BALF IgM

description: IgM


title: IPS_2


title: SAMPLE 13 -Prime-boost vac regime Female RAM-IGIP Mouse 55

description: Fig. 8 and 9


title: LTBI_19808_pre-plasma IgM

description: IgM


title: LTBI_17906_6mo-Plasma IgG

description: IgG


title: LTBI_19808_2mo-BALF IgG

description: IgG


title: LTBI_19808_5mo-BALF IgG

description: IgG


title: LTBI_19808_Pre-Plasma IgG

description: IgG


title: HPDE_GSK_3

city: Melbourne

first: Assam

last: El-Osta

address: 75 Commercial Road

country: Australia

institute: Baker Heart and Diabetes Institute

data_processing:
Raw FASTQ reads underwent quality (>20) and adapter trimming using skewer
Trimmed reads were mapped to human genome build GRCh38 (Ensembl) using STAR aligner (2.7.9a)
Aligned reads were sorted and duplicates marked with samtools
Unique tags aligning to genes (Ensembl 104 annotations) in sorted data were counted using Subread - FeatureCounts
Assembly: hg38
Supplementary files format and content: tab-separated-value file includes a feature~sample raw read counts matrix

source_name: Pancreatic cell line

growth_protocol: Exocrine tissue was isolated as a by-product of islet isolation by intraductal perfusion and digestion of the pancreas with collagenase AF-1,44 (SERVA/Nordmark, Germany), followed by purification using Ficoll density gradients.45  The acinar and ductal tissue obtained from high-density fractions were cultured in Miami Media 1A (Mediatech/Corning 98–021, USA) supplemented with 2.5% human serum albumin (Australian Red Cross, Melbourne, VIC, Australia), in a 37 °C, 5% CO2 incubator. Immortalized human derived pancreatic ductal epithelial cells were cultured at 37 °C in an atmosphere of 5% CO2 in complete Keratinocyte Serum-Free Media (supplemented with human recombinant EGF, Bovine Pituitary Extract and Antibiotic-Antimycotic [Gibco]).

extract_protocol:
Treated human ex vivo pancreatic cells and human pancreatic ductal epithelial cells were lysed using TRIzol reagent (Invitrogen), and Total RNA was extracted from the cells using RNeasy Kit (QIAGEN) including DNase treatment according to manufacturer protocol
Barcoded RNA-seq libraries were generated from ribosomal RNA depleted total RNA using the NEBNext® rRNA Depletion Kit (Human/Mouse/Rat) (New England Biolabs, Ipswich, MA) in conjunction with the NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® (New England Biolabs) using 1μg of input total RNA and following the manufacturer’s instructions for depletion and library construction

treatment_protocol: Human pancreatic exocrine cells were either left untreated or exposed to 10 μM GSK126 (S7061, SelleckChem) or 1 μM Tazemetostat (S7128, SelleckChem) at a density of 1 × 106 cells per well for 24 h. After the initial 24 h incubation, fresh Miami Media was added, and the cells were cultured for an additional 24 h with either 10 μΜ GSK126 or 1 μM Tazemetostat. All incubations occurred in Miami Media 1A (Mediatech/Corning 98-021, USA) supplemented with 2.5% human serum albumin (Australian Red Cross, Melbourne, VIC, Australia) in a cell culture incubator at 37 °C with 5% CO2 for a total of 48 h. HPDE cells were seeded on Day 0 and allowed to adhere for 24h before treatment on Day 1 (10 μΜ GSK126 or 1 μM Tazemetostat). Following a further 24h of culture, the second dose was delivered in fresh K-SFM.  All cells were harvested following a total of 48h incubation with EZH2 inhibitor or vehicle control (DMSO 0.001%).

value: Pancreatic cell line

value: HPDEC

value: Human Pancreatic Ductal Epithelial Cells

value: 1. GSK126 (10 μM) for 24hrs, 2. GSK126 (10 μM) for 24hrs, total treatment 48hours


title: HPDE_GSK_2


title: HPDE_EPZ_3

value: 1. Tazemetostat (EPZ 1 μM ) for 24hrs, 2.Tazemetostat (EPZ 1 μM ) for 24hrs, total treatment 48hours


title: LTBI_19808_pre-BALF IgM

description: IgM

value: Asymptomatic controlled Mtb infection


title: IPS_1


title: LTBI_19808_early-BALF IgM

description: IgM


title: LTBI_17906_early-BALF IgM

description: IgM


title: LTBI_19808_early-plasma IgM

description: IgM


title: HPDE_GSK_1


title: SAMPLE 10 -Prime-boost vac regime Male RAM Mouse 44

description: Fig. 8 and 9

value: prime/boost

value: d14 dpb


title: SAMPLE 11 -Before challenge Male RAM Mouse 45

description: Fig. 8 and 9

value: RAM (H1N1)


title: SAMPLE 9 -Prime-boost vac regime Male RAM Mouse 43

description: Fig. 8 and 9


title: LTBI_17906_early-plasma IgM

description: IgM


title: SAMPLE 12 -Before challenge Male RAM Mouse 46

description: Fig. 8 and 9


title: SAMPLE 8 -Before challenge Female RAM Mouse 34

description: Fig. 8 and 9


title: SAMPLE 7 -Before challenge Female RAM Mouse 33

description: Fig. 8 and 9


title: LTBI_17906_2mo-BALF IgG

description: IgG


title: LTBI_17806_6mo-Plasma IgG

description: IgG


title: LTBI_17806_6mo-BALF IgG

description: IgG


title: LTBI_17906_6mo-BALF IgG

description: IgG


title: LTBI_17906_2mo-Plasma IgG

description: IgG


title: HPDE_EPZ_2


title: LTBI_17806_early-plasma IgM

description: IgM


title: SAMPLE 6 -Prime-boost vac regime Female RAM Mouse 32

description: Fig. 8 and 9


title: HPDE_EPZ_1


title: HPDE_DMSO_3

value: 1. Vehicle (DMSO) for 24hrs, 2.Vehicle (DMSO) for 24hrs, total treatment 48hours


title: LTBI_17806_early-BALF IgM

description: IgM


title: HPDE_DMSO_1


title: HPDE_DMSO_2


title: HPAD_11_GSK

source_name: Pancreas

value: Pancreas

value: Human pancreatic exocrine cells


title: HPAD_11_EPZ


title: HPAD_11_DMSO


title: mouse liver tumor_WT [IP]

city: guangzhou

first: qiannan

last: ren

address: 651 DF ROAD

institute: SYSUCC

data_processing:
We used trim to cut off sequencing connectors and low-quality fragments of sequencing data. When implementing raw data Trimming, we use fastp software, and the steps of data processing are as follows:(1) reads with a mass value of less than 15 and more than 40% of the base number of the reads were deleted.(2) More than 6 reads with N base were removed.(3) reads with adapter were removed.(4) reads shorter than 50bp after pruning were discarded.
The comparison software we chose was BWA (Burrows Wheeler Aligner)
MACS2 software was used (threshold was pvalue< =0.005) Complete the peak calling analysis, and make statistics on the number, width and distribution of peaks, and screen out the genes related to peaks.
Supplementary files format and content: BAM
Supplementary files format and content: bigwig

organism: Mus

source_name: liver tissue

extract_protocol:
1% formaldehyde was used to fix cells for 10 minutes. Lysate cells, separate chromatin, and randomly cut chromatin by ultrasound or enzyme treatment
The library was constructed (including terminal repair, A addition, splicing, length screening, PCR amplification) and high-throughput sequencing was performed.

value: liver tissue

value: MALE

value: HA (CST CAT3724)


title: SAMPLE 5 -Prime-boost vac regime Female RAM Mouse 31

description: Fig. 8 and 9


title: LTBI_17006_early-BALF IgM

description: IgM


title: mouse liver tumor_WT [input]


title: RAPA_3

city: Rochester

first: Hani

last: Awad

address: 601 Elmwood Avenue

department: Biomedical Engineering

institute: University of Rochester

description: Donor 3: collagen hydrogel model of an injured tendons composed of human primary tenocytes (TCs) and tissue macrophages (tMɸ)

data_processing:
Raw reads generated from the Illumina basecalls were demultiplexed using bcl2fastq version 2.20.0.
Quality filtering and adapter removal are performed using FastP version 0.23.1 with the following parameters: "--length_required 35 --cut_front_window_size 1 --cut_front_mean_quality 13 --cut_front --cut_tail_window_size 1 --cut_tail_mean_quality 13 --cut_tail -y –r".1
Processed/cleaned reads were then mapped to the GRCm39/gencode M31 or GRCh38/genecode38 (Mouse OR Human) reference using STAR_2.7.9a with the following parameters: "—twopass Mode Basic --runMode alignReads --outSAMtype BAM Unsorted – outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical –outReadsUnmapped Fastx".2,3
Genelevel read quantification was derived using the subread-2.0.1 package (featureCounts) with a GTF annotation file (GRCm39/gencode M31 or GRCh38/gencode42) and the following parameters for stranded RNA libraries "-s 2 -t exon -g gene_name" OR "-s 0 -t exon -g gene_name" for un stranded libraries
Differential expression analysis was performed using DESeq2-1.34.0 with a P-value threshold of 0.05 within R version 3.5.1 (https://www.R-project.org/).
Assembly: GRCh38/genecode38 for Human Samples
Supplementary files format and content: Tab-delimited text file includes Raw counts for each sample

source_name: Tissue-on-a-Chip platform interfacing a vascular monolayer with a tendon tissue construct.

growth_protocol: The fully assembled quad culture hToC devices were cultured in serum-free xvivo-10 media from LONZA and 10 ng/ml of TGF-β1 introduced onto the tissue hydrogel compartment to induce fibrosis.

extract_protocol:
RNA was extracted using the Qiagen mini plus kit. 150 pg pf cDNA was used to generate sequencing libraries.
NexteraXT library preparation kit (Illumina, San Diego, CA) per manufacturer’s protocols.

treatment_protocol: 10 ng/ml of Rapamycin treatment was introduced into the vascular component of the fully assembled, TGFβ1-treated hToC devices and cultured for 24 hours.

value: HUVECs, Human Primary Tendon Fibroblasts, Human Primary Monocytes

value: Rapamycin


title: LTBI_17606_6mo-Plasma IgG

description: IgG


title: LTBI_17006_early-plasma IgM

description: IgM


title: LTBI_17606_early-plasma IgM

description: IgM


title: LTBI_17706_early-plasma IgM

description: IgM


title: LTBI_17706_early-BALF IgM

description: IgM


title: LTBI_17606_early-BALF IgM

description: IgM


title: LTBI_11108_pre-BALF IgM

description: IgM


title: SAMPLE 4 -Before challenge Male Mock Mouse 11

description: Fig. 8 and 9

value: prime

value: PBS

value: d20 dpi


title: LTBI_17606_2mo-Plasma IgG

description: IgG


title: SAMPLE 3 -Before challenge Male Mock Mouse 10

description: Fig. 8 and 9


title: mouse liver tumor_Q62L [IP]


title: LTBI_17706_2mo-Plasma IgG

description: IgG


title: LTBI_17806_2mo-Plasma IgG

description: IgG


title: LTBI_17706_6mo-Plasma IgG

description: IgG


title: LTBI_17806_2mo-BALF IgG

description: IgG


title: LTBI_17706_2mo-BALF IgG

description: IgG


title: LTBI_17706_6mo-BALF IgG

description: IgG


title: RAPA_2

value: Tissue-on-a-Chip platform interfacing a vascular monolayer with a tendon tissue construct.


title: LTBI_11108_early-plasma IgM

description: IgM


title: mouse liver tumor_Q62L [input]


title: RAPA_1


title: LTBI_11108_early-BALF IgM

description: IgM


title: mouse liver tumor_E81Q [IP]


title: SAMPLE 1 -Before challenge Female Mock Mouse 4

description: Fig. 8 and 9


title: EC_RAPA_3

description: Donor 3: vascular monolayer composed of human umbilical endothelial cells (ECs) and circulating Monocytes (cMɸ)


title: EC_RAPA_2


title: mouse liver tumor_E81Q [input]


title: LTBI_11008_pre-BALF IgM

description: IgM


title: mouse liver tumor_WT [RNA-seq]

data_processing:
Filter the raw data:these include the removal of reads with adapter, reads containing N(which means that base information cannot be determined), and low-quality reads(Qphred <=) The number of bases of 20 accounts for more than 50% of the total read length of reads).
Build an index of the reference genome using HISAT2 v2.0.5. The paired end clean reads were compared with the reference genome using HISAT2 v2.0.5
Supplementary files format and content: text file including the number of different genes between samples
Supplementary files format and content: text file including FPKM for each sample

extract_protocol:
Based on the structural characteristics of polyA tail in most mrnas of eukaryotes, the mRNA with polyA tail was enriched by Oligo(dT) magnetic beads
The initial RNA for library construction was total RNA, total amount > =1ug. Illumina's NEBNext® UltraTM was used to build the library RNA Library Prep Kit.
After the library is constructed, initial quantification is performed using Qubit2.0 Fluorometer, dilution of the library to 1.5ng/ul, and then the insert size of the library is tested using Agilent 2100 bioanalyzer.
After the library test is qualified, different libraries are carried out Illumina sequencing after pooling according to the requirements of effective concentration and target data volume, and then generated 150bp paired end reading. The basic principle of Sequencing is Sequencing by Synthesis.

value: primary hepatocytes

value: WT

tag: strain background

value: FVB/N


title: LTBI_11008_early-BALF IgM

description: IgM

data_processing: The median pixel intensity of each feature was background subtracted. A minimum value of pixel intensity (400) was determined by the median pixel intensity of the spots with low quality, which was determined by the software quality control score for each spot depending on signal-to-noise ratio and spot shape. The scanned images were visually inspected. The spots with obvious local artifacts were excluded from analysis. The array features were printed in triplicate. The final data were averaged from the triplicates.

value: Asymptomatic controlled Mtb infection


title: mouse liver tumor_Q62L [RNA-seq]

tag: tissue


title: SAMPLE 2 -Before challenge Female Mock Mouse 5

description: Fig. 8 and 9


title: LTBI_10708_pre-BALF IgM

description: IgM


title: LTBI_17606_6mo-BALF IgG

description: IgG

data_processing: Spots were considered reactive if the ratio of the median fluorescent intensity (MFI) of the gene was greater than 1.4 x the median of negative control genes


title: LTBI_11108_Pre-BALF IgG

description: IgG


title: LTBI_17006_6mo-BALF IgG

description: IgG


title: LTBI_17006_6mo-Plasma IgG

description: IgG


title: LTBI_17606_2mo-BALF IgG

description: IgG


title: LTBI_10708_early-plasma IgM

description: IgM


title: LTBI_17006_2mo-BALF IgG

description: IgG


title: LTBI_11108_Pre-Plasma IgG

description: IgG


title: Quad_pos_TGFb1_2

description: Collagen hydrogel model of an injured tendons composed of human primary tenocytes (TCs) and tissue macrophages (tMɸ)

growth_protocol: All cells were cultured in the hToC platform in xvivo-10 media from LONZA and 10 ng/ml of TGF-β1 introduced onto the tissue compartment. The culture was maintained for either 24 or 72-hours.

treatment_protocol: 10 ng/ml of Rapamycin treatment was introduced onto the vascular component and cultured for 24 hours.


title: Quad_pos_TGFb1_3


title: Quad_pos_TGFb1_1


title: EC_RAPA_1


title: LTBI_17006_2mo-Plasma IgG

description: IgG


title: Quad_neg_TGFb1_3


title: LTBI_11108_6mo-BALF IgG

description: IgG


title: LTBI_10708_early-BALF IgM

description: IgM


title: LTBI_11108_2mo-BALF IgG

description: IgG


title: 12_T3022_SARS-CoV-2 + IL-13

city: Seattle,

first: Stephanie

last: Osmond

state: WA

address: 1201 9th Ave

institute: Benaroya Research Institute

library_source: transcriptomic single cell

data_processing:
Base-calling was performed automatically with Illumina RTA (v. 1.18.66.3).
For each flowcell, libraries were demultiplexed using Cellranger mkfastq (v 6.1.1; All unambiguously demultiplexed reads for each sample were combined for downstream processing.
Reads were aligned to the genome, collapsed to UMIs, and counts per gene ID were estimated using 10X Cell Ranger count (v. 6.1.1).
Barcodes were called as cells or background using default settings in 10X Cell Ranger (v. 6.1.1).
Assembly: GRCh38
Supplementary files format and content: Sparse matrix HDF5 file with UMI counts per barcode per gene ID, and table of read characteristics for each UMI / barcode combination

source_name: Bronchial AEC

extract_protocol:
For scRNA-seq, bronchial AECs from a subset of the healthy nonsensitizedchildren (n 5 2) and children with allergic asthma (n 5 2) were differentiated ex vivo at an ALI to generate organotypic cultures by the same methods as already mentioned. Cultures were stimulated without or with IL-13 (10 ng/mL), with each medium change starting 1 week before and throughout SARS-CoV-2 infection
Cells were loaded onto a 10X Genomics GemCode Single-Cell Instrument per manufacturer instructions for nanodroplet single-cell capture, cell lysis, mRNA rtPCR, and cDNA barcoding within droplets.
NextSeq 10x chemistry

value: Bronchial AEC

tag: condition

value: SARS-CoV-2 + IL-13

tag: participant

value: Healthy


title: mouse liver tumor_E81Q [RNA-seq]

tag: cell type


title: 16_T3015-0_SARS-CoV-2 + IL-13

tag: treatment


title: LTBI_10408_pre-plasma IgM

description: IgM

source_name: pre-plasma

tag: infection states


title: LTBI_11008_Pre-BALF IgG

description: IgG

source_name: Pre-BALF


title: Quad_neg_TGFb1_2


title: Quad_neg_TGFb1_1


title: LTBI_11008_6mo-BALF IgG

description: IgG


title: 15_T3015-0_SARS-CoV-2 Alone

value: SARS-CoV-2 Alone


title: EC_Quad_pos_TGFb1_2

description: Vascular monolayer composed of human umbilical endothelial cells (ECs) and circulating Monocytes (cMɸ)


title: 28_T187_SARS-CoV-2 + IL-13

value: Asthma


title: 24_T170_SARS-CoV-2 + IL-13


title: EC_Quad_pos_TGFb1_3


title: 27_T187_SARS-CoV-2 Alone


title: LTBI_10211_pre-plasma IgM

description: IgM


title: LTBI_10408_early-BALF IgM

description: IgM

source_name: early-BALF


title: 11_T3022_SARS-CoV-2 Alone


title: LTBI_11008_2mo-BALF IgG

description: IgG


title: LTBI_10408_early-plasma IgM

description: IgM


title: LTBI_10708_Pre-BALF IgG

description: IgG


title: 23_T170_SARS-CoV-2 Alone


title: LTBI_10708_Pre-Plasma IgG

description: IgG


title: EC_Quad_neg_TGFb1_3


title: EC_Quad_pos_TGFb1_1


title: LTBI_10708_2mo-Plasma IgG

description: IgG


title: EC_Quad_neg_TGFb1_2


title: EC_Quad_neg_TGFb1_1


title: LTBI_10708_2mo-BALF IgG

description: IgG


title: LTBI_10408_pre-BALF IgM

description: IgM

source_name: pre-BALF


title: LTBI_10211_early-BALF IgM

description: IgM


title: LTBI_10211_early-plasma IgM

description: IgM


title: LTBI_10708_pre-plasma IgM

description: IgM


title: LTBI_10111_pre-plasma IgM

description: IgM


title: EC_CTRL_3


title: LTBI_10111_pre-BALF IgM

description: IgM


title: EC_CTRL_1


title: EC_CTRL_2


title: CTRL_3


title: LTBI_10211_pre-BALF IgM

description: IgM


title: LTBI_10111_early-plasma IgM

description: IgM


title: LTBI_10111_early-BALF IgM

description: IgM


title: CTRL_2


title: LTBI_10408_Pre-Plasma IgG

description: IgG


title: LTBI_10011_pre-BALF IgM

description: IgM


title: CTRL_1


title: Tiss24hrctrI2

description: Donor 2: collagen hydrogel model of an injured tendons composed of human primary tenocytes (TCs) and tissue macrophages (tMɸ)


title: LTBI_10011_early-plasma IgM

description: IgM


title: LTBI_10408_6mo-Plasma IgG

description: IgG


title: LTBI_10408_2mo-Plasma IgG

description: IgG


title: LTBI_10408_2mo-BALF IgG

description: IgG


title: LTBI_10408_Pre-BALF IgG

description: IgG


title: LTBI_10211_Pre-BALF IgG

description: IgG


title: LTBI_10211_Pre-Plasma IgG

description: IgG


title: LTBI_10011_early-BALF IgM

description: IgM


title: Tiss24hrctrI1


title: Yeast-kcs1, Low Nitrogen, 20 hr, rep 3

city: ANN ARBOR

first: Anuj

last: Kumar

state: MI

address: 1105 N. University Avenue, BSB Room 3210

department: MCDB

institute: University of Michigan

data_processing:
Quality control: 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 1 containing poly-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content of the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reads mapping to the reference genome: 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.
Novel transcripts prediction: The mapped reads of each sample were assembled by StringTie (v1.3.3b) in a reference-based approach. StringTie uses a novel network flow algorithm as well as an optional de novo assembly step to assemble and quantify full length transcripts representing multiple splice variants for each gene locus.
Quantification of gene expression level: featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. The 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: Differential expression analysis of two conditions/groups (three biological replicates per condition) was performed using the DESeq2 R package (1.20.0). DESeq2 provide statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate . Genes with an adjusted P-value <=0.05. found by DESeq2 were assigned as differentially expressed.
Assembly: Saccharomyces Genome Database (2014). Strain: S288C. RefSeq:GCF_000146045.2
Supplementary files format and content: Txt file indicating expression read counts for all genes identified by sequencing. Columns indicate read counts for the indicated gene (row) in the respective sample.
Supplementary files format and content: Txt file summarizing transcript expression levels as fragments per kilobase of transcript per million reads mapped; the data account for sequencing depth and feature length.

organism: Saccharomyces cerevisiae

source_name: yeast cell

extract_protocol:
RNA was isolated from frozen cell pellets using the RiboPure Yeast Kit (Thermo Fisher Scientific). RNA samples were treated with DNase, and RNA concentrations were determined using the NanoDrop microvolume spectrophotometer. RNA quality control, sequencing, and analysis was performed by Novogene (CA, USA). RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
Libraries were prepared for sequencing as follows. Total RNA was used as input material for the RNA sample preparations. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

tag: strain

value: yeast cell

tag: genotype


title: RAPA3


title: LTBI_10408_6mo-BALF IgG

description: IgG

extract_protocol: Plasma was obtained from peripheral blood samples and the BAL procedure was performed as previously described via direct visualization of the airway and lavage of ~ 40 ml normal saline (0.9%). Animal protocols and procedures were approved by the University of Pittsburgh’s Institutional Animal Care and Use Committee before the collection of samples.


title: Yeast-kcs1, Low Nitrogen, 20 hr, rep 2


title: RAPA2


title: LTBI_10211_6mo-Plasma IgG

description: IgG


title: LTBI_10011_pre-plasma IgM

description: IgM


title: RAPA1


title: Yeast-WT KCS1, Low Nitrogen, 20 hr, rep 3


title: Yeast-WT KCS1, Low Nitrogen, 20 hr, rep 2


title: Yeast-WT KCS1, Low Nitrogen, 20 hr, rep 1


title: EC24hrCTRL2

description: Donor 2: vascular monolayer composed of human umbilical endothelial cells (ECs) and circulating Monocytes (cMɸ)


title: EC24hrCTRL1


title: LTBI_10211_6mo-BALF IgG

description: IgG


title: LTBI_10211_3mo-BALF IgG

description: IgG


title: LTBI_10211_3mo-Plasma IgG

description: IgG


title: m_BP1_wt

city: Hamburg

first: Marco

last: Er Lukowiak

address: Bernhard-Nocht-Straße 74

institute: Bernhard-Nocht-Institute for tropical medicine

description: blood.csv

data_processing:
Nextflow RNAseq v3.8 pipeline
using star_salmon
Star results are further processed using DESeq2
Assembly: GRCm38
Supplementary files format and content: VST transformed data matrix

source_name: blood

extract_protocol:
Neutrophil granulocytes from bone marrow were isolated using a Neutrophil Isolation Kit, blood neutrophils were isolated by FACS-sorting
Library preparation was performed by using a QIAseq FX DNA Library Kit

value: blood

value: m


title: C2C12 myotubes_50 µg/mL STEE-treated_6 hours_rep1

city: Tsukuba

first: Kengo

last: Iwata

state: Ibaraki

address: 1-1-1 Tennodai

department: Alliance for Research on the Mediterranean and North Africa (ARENA)

country: Japan

institute: University of Tsukuba / Nippo., Co., Ltd.

description: Cells were exposed to serum-free Opti-MEM (Gibco) in which the extracts were dissolved.

hyb_protocol: Labeled strands were hybridized to probes on Clariom S Mouse assay chip for 16 hours at 45 °C with constant rotation in GeneChip™ Hybridization Oven 645.

scan_protocol: The hybridized chip was washed and stained on the GeneChip™ Fluidics Station 450, and then scanned on the GeneChip™ Scanner 3000.

data_processing:
CHP files (the gene-level information) was obtained from CEL files (the probe intensity) using robust multichip analysis (RMA) summarization algorithm in Expression Console software. Subsequent data processing was carried out in Transcriptome Analysis Console (TAC) 4.0 software. Two mRNA biological samples of each group were provided for the analysis.
Signal intensities for all samples (average of the duplicates) and comparative data ('STEE30 vs Control' and 'STEE50 vs Control' fold change) generated using TAC software can be found in the additional sheets.

label: biotin

source_name: C2C12 myotubes, 50 µg/mL STEE-treated, 6 hours.

label_protocol: RNAs were reverse transcribed and biotinylated with GeneChip™ WT PLUS Reagent Kit (ThermoFisher Scientific), according to the manufacturer’s instructions.

growth_protocol: Mouse skeletal muscle-derived C2C12 myoblast (ATCC) were cultured at 37°C under 5% CO2 in DMEM supplemented with 10% FBS (Gibco) and 1% anti-bacterial penicillin/streptomycin (PS). To induce differentiation, the growth medium was replaced with a differentiation medium composed of DMEM supplemented with 2% horse serum (Gibco) and 1% PS when cells reached about 90% confluence.

extract_protocol: Total RNAs were isolated from the cells with RNeasy plus mini kit (Qiagen).

treatment_protocol: After differentiation for 6 days, C2C12 myotubes were treated with the extract dissolved in serum-free Opti-MEM (Gibco) for 6 hours.

tag: cell line

value: skeletal muscle

value: myotubes

value: differentiated from myoblast

value: 6-days differentiation

value: 50 ug/mL STEE-treated, 6 hours.


title: LTBI_10111_6mo-Plasma IgG

description: IgG


title: LTBI_10111_Pre-BALF IgG

description: IgG


title: LTBI_10111_6mo-BALF IgG

description: IgG


title: w_BP3_ALA

description: blood.csv

value: f

value: ALA


title: EC_RAPA1

value: Tissue-on-a-Chip platform interfacing a vascular monolayer with a tendon tissue construct.

value: HUVECs, Human Primary Tendon Fibroblasts, Human Primary Monocytes

value: Rapamycin


title: Yeast-kcs1, Low Nitrogen, 20 hr, rep 1


title: w_BP2_ALA

description: blood.csv


title: LTBI_10111_3mo-Plasma IgG

description: IgG

value: Asymptomatic controlled Mtb infection


title: 24HR_CTRL_2_QUAD_PLUS_TGF_24HR_TRT_09_02_22

description: Donor 1: collagen hydrogel model of an injured tendons composed of human primary tenocytes (TCs) and tissue macrophages (tMɸ)


title: LTBI_10111_3mo-BALF IgG

description: IgG


title: EC24hrCTRL3


title: C2C12 myotubes_50 µg/mL STEE-treated_6 hours_rep2


title: w_BP1_ALA

description: blood.csv


title: C2C12 myotubes_untreated_rep2

description: Timeline for RNA extraction is the same as for the extract treatment group.

source_name: C2C12 myotubes, untreated.

value: untreated.


title: C2C12 myotubes_untreated_rep1


title: m_BP4_ALA

description: blood.csv


title: LTBI_10111_Pre-Plasma IgG

description: IgG

source_name: Pre-Plasma


title: EC_RAPA2


title: 24HR_CTRL_1_QUAD_PLUS_TGF_24HR_TRT_09_02_22


title: LTBI_10011_Pre-Plasma IgG

description: IgG


title: Line#2, Tam-inducible, Input [ChIP-seq]

city: Brookline

first: Ramesh

last: Shivdasani

state: Massachusetts

address: SM1052, Smith10, 450 Brookline Ave

department: Medical Oncology

institute: DFCI

data_processing:
ChIP-seq reads were trimmed cutadapt verion 1.14
ChIP-seq reads were aligned to the UCSC hg19 genome using Bowtie2 version 2.3.5.
To create ChIP-seq coverage plots, the locations of the mapped ChIP-seq reads were extended to 150 bp to represent sequenced fragments, renormalized (to reads per million, rpm) and reformatted in the bigWig file format.
bigWig files were generated using deeptools bamCoverage using reads per genomic content normalization, with 10bp windows, smoothed over 30bp
Assembly: hg19
Supplementary files format and content: bigWig

growth_protocol: DMEM, 20 % F12K, 20% FBS, 10% R-Spondin-2 conditioned medium, 10 mM nicotinamide, 100µg/ml Primocin, 1 μM A8301, 5 μg/ml  insulin, 10 μM Y-27632, 1 μM DMH1, 50 ng/ml EGF and 2 μM T3. Cells were cultured at 37oC at 7.5% CO2.

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated using a E220 focused-ultrasonicator (Covaris).
ChIP-seq libraries were prepared using the KAPA HTP Library Preparation Kit complemented with NEXTflex DNA Barcodes from Bioo Scientific. 10 ng of DNA was used as starting material for input and ip samples. Libraries were amplified using 13 cycles on the thermocycler. Post amplification libraries were size selected at 250-450bp in length using Agencourt AMPure XP beads from Beckman Coulter. Libraries were validated using the Agilent High Sensitivity DNA Kit.

value: Neurog3 Tam-inducible Ileal intestinal stem cells

tag: chip antibody


title: Line#2, Tam-inducible, Day3, H3K27ac [ChIP-seq]

value: H3K27ac (ActiveMotif, #39135)


title: RAPA_2_QUAD_PLUS_TGF_24HR_TRT_09_02_22


title: C2C12 myotubes_30 µg/mL STEE-treated_6 hours_rep2

source_name: C2C12 myotubes, 30 µg/mL STEE-treated, 6 hours.

value: 30 ug/mL STEE-treated, 6 hours.


title: Line#2, Tam-inducible, Day1, H3K27ac [ChIP-seq]


title: Line#2, Tam-inducible, Day0, H3K27ac [ChIP-seq]


title: LTBI_10011_Pre-BALF IgG

first: Jacqueline

last: Achkar

institute: Albert Einstein College of Medicine

description: IgG


title: m_BP3_ALA

description: blood.csv

value: blood


title: Line#1, Dox-inducible, Day8, RNA rep2

data_processing:
sequence reads were mapped to hg19 using STAR aligner
Read count extraction were performed using STAR aligner v2.6.0c
Assembly: hg19
Supplementary files format and content: tab-delimited text files include STAR raw counts for each Sample

growth_protocol: DMEM, 20% F12K, 20% FBS, 10% R-Spondin-2 conditioned medium, 10 mM nicotinamide, 100µg/ml Primocin, 1 μM A8301, 5 μg/ml  insulin, 10 μM Y-27632, 1 μM DMH1, 50 ng/ml EGF and 2 μM T3. Cells were cultured at 37oC at 7.5% CO2.

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 2µg of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared by Novogene Corporation Inc.

treatment_protocol:
Enteroendocrine differentiation was induced by transient treatment of ISCs (designated day 0, D0) for 48 h with 1µM tamoxifen or 1µg/ml doxycycline.
After 2 days diffrentiated cells were then cultured  with culture media deprived of EGF

value: Neurog3 Dox-inducible Ileal intestinal stem cells

value: TetO-Neurog; PGK-rtTA-BlastR

value: 1µg/ml Dox for initial 48 h

value: Day 8


title: RAPA_1_QUAD_TGF_24HR_TRT_09_02_22


title: m_BP2_ALA

description: blood.csv

value: m


title: Degenerative_Y8445_D2

city: Columbus

first: Maciej

last: Pietrzak

state: OH

address: 1800 Cannon Drive, 340C Lincoln Tower

department: Department of Biomedical Informatics College of Medicine

institute: Ohio State University

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Cartilage endplate

growth_protocol: Human primary CEP cells (p1) were cultured in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
After culture, cells were rinsed with 1X PBS and released using trypsin-EDTA (0.25%) (ThermoFisher).  Cells were filtered using a 70um cell strained (VWR), rinsed three times using 1X PBS supplemented with 0.04% w/v BSA, then re-suspended in 1X PBS supplemented with w/v 0.04% BSA at a concentration of 700-1200 cells/uL according to 10X Genomics instructions.
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics). Briefly, CEP cells were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

treatment_protocol: "Healthy" CEP cells were isolated from healthy IVDs (Thompson Grade <= 2) and "degenerative" CEP cells were isolated from degenerative IVDs (Thompson Grade >= 4).

value: Cartilage endplate

value: Primary cells

value: Cartilage endplate cell

value: WT

value: Disease


title: LTBI_10011_6mo-BALF IgG

city: Bronx

address: 1300 Morris Park Ave

description: IgG


title: m_BP1_ALA

description: blood.csv

value: ALA


title: Line#1, Dox-inducible, Day8, RNA rep1


title: w_BP4_wt

description: blood.csv

value: f


title: Line#1, Dox-inducible, Day4, RNA rep2

value: Day 4


title: Healthy_Y8444_H1

description: 10x Genomics

value: Healthy


title: w_BP3_wt

description: blood.csv


title: Line#1, Dox-inducible, Day4, RNA rep1


title: Line#1, Dox-inducible, Day3, RNA rep2

value: Day 3


title: w_BP2_wt

description: blood.csv


title: w_BP1_wt

description: blood.csv


title: LTBI_10011_3mo-BALF IgG

description: IgG

value: Asymptomatic controlled Mtb infection


title: LTBI_10011_6mo-Plasma IgG

description: IgG


title: TB_9711_Pre-Plasma IgA

description: IgA

label: Cy3 Goat Anti-Human Serum IgA

label_protocol: Cy3 Goat Anti-Human Serum IgA (Jackson ImmunoResearch Labs Cat# 109-165-011, RRID:AB 2337721)

value: Symptomatic uncontrolled Mtb infection/TB disease


title: Line#1, Dox-inducible, Day3, RNA rep1

value: Neurog3 Dox-inducible Ileal intestinal stem cells


title: TB_9711_Pre-BALF IgA

description: IgA


title: Hu19

description: Bulk RNA-seq

data_processing:
RNA-Seq reads were first mapped to the human genome GRCh38 using Hierarchical Indexing for Spliced Alignment of Transcripts (HISAT2)
Raw read counts for each gene were quantified by using featureCounts software.
RNA-seq counts were obtained by using GENCODE v.27 Gene Transfer Format (GTF) file as a transcript reference (GENCODE annotation).
Supplementary files format and content: tab-delimited text file includes RPM values for each Sample

growth_protocol: Human primary CEP cells (p1/p2) were cultured in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
At the end of culture, cells were collected in Trizol and RNA was harvested using a PureLink RNA Mini kit (Thermo Fisher).
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

tag: group


title: m_BP3_wt

description: blood.csv

value: blood


title: Hu17

description: Bulk RNA-seq


title: m_BP4_wt

description: blood.csv


title: LTBI_10011_3mo-Plasma IgG

description: IgG


title: Hu23

description: Bulk RNA-seq


title: Hu21

description: Bulk RNA-seq


title: Hu16

description: Bulk RNA-seq


title: m_BP2_wt

description: blood.csv


title: Line#1, Dox-inducible, Day2, RNA rep2

value: TetO-Neurog; PGK-rtTA-BlastR

value: 1µg/ml Dox for initial 48 h

value: Day 2


title: TB_9711_6mo-Plasma IgA

description: IgA


title: Line#1, Dox-inducible, Day1, RNA rep2

value: 1µg/ml Dox for initial 24 h

value: Day 1


title: Hu18

description: Bulk RNA-seq

value: Cartilage endplate

value: Primary cells

value: Cartilage endplate cell


title: Line#1, Dox-inducible, Day2, RNA rep1


title: sample19, f, bone marrow, ALA

description: bonemarrow.csv

source_name: bone marrow

value: bone marrow

value: ALA


title: TB_9711_3mo-Plasma IgA

description: IgA


title: TB_9711_6mo-BALF IgA

description: IgA


title: Line#1, Dox-inducible, Day1, RNA rep1


title: TB_9611_Pre-Plasma IgA

description: IgA


title: C2C12 myotubes_30 µg/mL STEE-treated_6 hours_rep1

value: skeletal muscle

value: myotubes

value: differentiated from myoblast

value: 6-days differentiation

value: 30 ug/mL STEE-treated, 6 hours.


title: Hu12

description: Bulk RNA-seq

value: WT

value: Healthy


title: TB_9711_3mo-BALF IgA

description: IgA

value: Symptomatic uncontrolled Mtb infection/TB disease


title: Hu15

description: Bulk RNA-seq

value: Disease


title: sample18, f, bone marrow, ALA

description: bonemarrow.csv

value: f


title: sample17, f, bone marrow, ALA

description: bonemarrow.csv


title: Line#1, Dox-inducible, Day0, RNA rep2

value: Neurog3 Dox-inducible Ileal intestinal stem cells

value: TetO-Neurog; PGK-rtTA-BlastR

value: No treatment

value: Day 0


title: sample16, f, bone marrow, ALA

description: bonemarrow.csv


title: Line#2, Tam-inducible, Day8, RNA rep2

value: Neurog3 Tam-inducible Ileal intestinal stem cells

value: 1µM Tam for initial 48 h

value: Day 8


title: sample15, f, bone marrow, ALA

description: bonemarrow.csv

value: bone marrow

value: ALA


title: Line#2, D6 HES6-KO, tam-inducible, Multiome-seq, RNA

description: 3' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript

data_processing:
Pre-processing of sequencing results to generate count matrices (gene expression and ATAC barcode counts) was performed using the 10x genomics Cell Ranger ARC pipeline aligning to the hg19 genome build.
Assembly: hg19
Supplementary files format and content: 10x Genomics output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz

source_name: Ileum

extract_protocol:
Stem cells / Differentiated EECs were dissociated using 1x TrypLE Exprress at 37 °C for 10 min. Cells were washed and re-suspended in PBS and stained with a Viability Dye, washed and resuspended in FACS buffer (HBSS without Ca+2, Mg+2 and phenol red, 0.9% Glucose, 10 mM HEPES, 500 ppm N-acetyl L-cystein, 10µM Y27632,  2% FBS). Alive cells were sorted using a FACS (BD Aria) according to the presence or absence of mCherry signal. Cells were washed and resuspended in PBS. Nuclei were extracted and resuspended in PBS supplemented with 0.04% w/v BSA.
Library was prepared using Chromium Next GEM Single Cell Multiome ATAC + Gene Expression protocol (10x Genomics). Cellular mRNA and ATAC sites were reverse-transcribed and indexed with a shared cellular barcode. Indexed cDNAs were then pooled and amplified by PCR according to the Chromium Next GEM Single Cell Multiome ATAC + Gene Expression protocol (10x Genomics) and with specific primers amplifying the ATAC sites. SPRI bead size selection was performed in order to separate both the mRNA-derived cDNA (>300bp) and the ATAC sites (>180bp). For the mRNA derived cDNA and ATAC library preparation, we further proceeded according to the manufacturer’s instructions for Next GEM Single Cell Multiome ATAC + Gene Expression protocol (10x Genomics).

value: Ileum

value: D6 HES6-KO, tam-inducible

tag: library type

value: mRNA


title: Line#2, Tam-inducible, Day8, RNA rep1

tag: time


title: Line#2, D3 HES6-KO, tam-inducible, Multiome-seq, RNA

value: D3 HES6-KO, tam-inducible


title: Line#2, Tam-inducible, Day4, RNA rep2

value: Day 4


title: sample13, m, bone marrow, ALA

description: bonemarrow.csv

tag: Sex

value: m


title: sample14, m, bone marrow, ALA

description: bonemarrow.csv


title: Line#2, D6 NEUROD1-TAD-KO, tam-inducible, Multiome-seq, RNA

value: D6 NEUROD1-TAD-KO, tam-inducible


title: sample12, m, bone marrow, ALA

description: bonemarrow.csv


title: sample11, m, bone marrow, ALA

description: bonemarrow.csv


title: Line#1, Dox-inducible, Day0, RNA rep1


title: Line#2, D6 NEUROD1-DBD-KO, tam-inducible, Multiome-seq, RNA

value: D6 NEUROD1-DBD-KO, tam-inducible


title: sample8, f, bone marrow, WT

description: bonemarrow.csv

value: f

value: WT


title: TB_9611_3mo-Plasma IgA

description: IgA

value: Symptomatic uncontrolled Mtb infection/TB disease


title: TB_9511_Pre-BALF IgA

description: IgA


title: TB_9511_6mo-BALF IgA

description: IgA


title: TB_9511_6mo-Plasma IgA

description: IgA


title: TB_9611_3mo-BALF IgA

description: IgA


title: TB_9511_Pre-Plasma IgA

description: IgA


title: sample6, f, bone marrow, WT

description: bonemarrow.csv


title: TB_9511_3mo-BALF IgA

description: IgA


title: TB_7009_Pre-Plasma IgA

description: IgA


title: TB_7009_Pre-BALF IgA

description: IgA


title: TB_9511_3mo-Plasma IgA

description: IgA


title: TB_9611_Pre-BALF IgA

description: IgA


title: TB_7009_6mo-Plasma IgA

description: IgA


title: sample5, f, bone marrow, WT

description: bonemarrow.csv


title: Line#2, D3 ASCL1-KO, tam-inducible, Multiome-seq, RNA

value: D3 ASCL1-KO, tam-inducible


title: Line#2, Tam-inducible, Day1, RNA rep2

value: Neurog3 Tam-inducible Ileal intestinal stem cells

value: 1µM Tam for initial 24 h

value: Day 1


title: Line#2, Tam-inducible, Day3, RNA rep2

value: 1µM Tam for initial 48 h

value: Day 3


title: Line#2, Tam-inducible, Day2, RNA rep2

value: Day 2


title: Line#2, Tam-inducible, Day4, RNA rep1


title: sample10, m, bone marrow, ALA

description: bonemarrow.csv

value: bone marrow

value: ALA


title: Line#2, Tam-inducible, Day1, RNA rep1


title: Line#2, Tam-inducible, Day3, RNA rep1


title: sample4, m, bone marrow, WT

description: bonemarrow.csv


title: sample7, f, bone marrow, WT

description: bonemarrow.csv


title: Line#2, Tam-inducible, Day0, RNA rep1

value: No treatment

value: Day 0


title: Line#2, Tam-inducible, Day2, RNA rep1


title: Line#2, D6 ASCL1-KO, tam-inducible, Multiome-seq, RNA

value: Ileum

value: D6 ASCL1-KO, tam-inducible

value: mRNA


title: sample3, m, bone marrow, WT

description: bonemarrow.csv

value: m


title: Line#2, D6 scrambled, tam-inducible, Multiome-seq, RNA, rep2

value: D6 scrambled, tam-inducible