title: Zebra PS

city: 경상남도 양산시

first: Eun Jung

last: Kwon

state: 경상남도

address: Pusan National University, Yangsan,, Republic of Korea

institute: Pusan National University

description: 10X genomics

data_processing:
First, the quality and basic statistics of raw sequencing data were checked through FastQC. After the quality control process, sequencing data were processed through a Cell Ranger v6.0.0 (10X Genomics) count pipeline using zebrafish genome (GRCz11). The zebrafish genome and transcriptome information were downloaded from the Ensembl FTP server (release 104), and the index was constructed by processing with the Cell Ranger mkref pipeline. The cellranger count pipeline produces gene expression matrices containing the unique molecular identifier (UMI) counts per gene, per barcode. Also, clusters with expression profiles and information on differential gene expression were generated from the pipeline.
Downstream analysis was performed using Seurat (version 4.3.0) in R (version 4.2.2) to process data produced through 10x genomics.
Assembly: GRCz11
Supplementary files format and content: Three types of processed data files are provided: barcode.tsv, features.tsv, matrix.mtx

source_name: embryos

extract_protocol:
The samples were carefully resuspended in a cold, calcium- and magnesium-free solution containing 0.04% BSA/PBS. Cell counting was performed using the LUNA-FX7™ Automated Fluorescence Cell Counter (Logos Biosystems) with acridine orange (AO) and propidium iodide (PI) staining (Logos Biosystems, catalog number F23001). Following this, the cells were processed using the Dead Cells Removal Kit (Miltenyi Biotech, catalog number 130-090-101) and MS columns (Miltenyi Biotech, catalog number 130-042-201) in accordance with the manufacturer’s guidelines.
Following the guidelines of the 10x Chromium Single Cell 5’ v2 protocol (10x Genomics, document number CG000331), Single Cell RNA-seq libraries were generated using the 10x Chromium Controller and the Next Gem Single Cell 5’ Reagent v2 kits (10x Genomics, PN-1000244). In brief, the cell suspension (aiming for a recovery of 10,000 cells) was combined with the reverse transcription master mix and loaded along with Single Cell 5′ Gel Beads and Partitioning Oil into a Single Cell K Chip (10x Genomics, PN-1000286) to create single-cell Gel Bead-in-emulsion (GEM) droplets. Within these GEMs, RNA transcripts from single cells were uniquely barcoded and reverse-transcribed. After the GEM-RT reaction, where barcoded full-length cDNA was synthesized from mRNA, the barcoded cDNA molecules were enriched with PCR. For the preparation of the 5’ Gene Expression Library, the amplified cDNA underwent a series of steps, including enzymatic fragmentation, end-repair, A-tailing, adapter ligation, and index PCR.

value: embryos

tag: Stage

value: 120 hpf


title: KO 3

status: Public on Mar 19 2025

type: SRA

city: New York

first: Tyler

last: Lu

state: New York

address: 1300 York Avenue

country: USA

institute: Weill Cornell Medicine

library_source: transcriptomic

data_processing:
Sequencing reads in FASTQ format were aligned, and filtered feature-barcode matrices were generated for each sample using Cell Ranger (v.6.1.2). Using Seurat (55) cells were retained if they met the following criteria: less than 15% mitochondrial percentage, total counts below 10,000, and between 300 and 5,500 features. This approach was taken to exclude low-quality cells, lysed cells, and doublets. After normalization, 4,000 variable features were selected with the FindVariableFeatures function using the ‘vst’ method. FindNeighbors was then run after scaling using the first 20 principal components and a k.param of 15. Clustering was conducted using Seurat with a resolution of 0.2 and the default settings.
Assembly: GRCm38/mm10
Supplementary files format and content: ALL processed data files are in .h5 format

molecule: total RNA

organism: Mus musculus

source_name: Lung

extract_protocol:
To isolate lung LECs, mice carrying the Prox1-EGFP reporter (in which all LECs are labeled with GFP) were injected with AlexaFluor647-conjugated isolectin (Invitrogen) for intravital labeling of endothelial cells just prior to sacrifice, as previously described. The lungs were then digested using dispase/collagenase in HBSS to generate a single cell suspension for FACS, with additional staining using antibodies for CD31 (Biolegend  102418), lineage cocktail (Bioloegend 133311), and Epcam (Biolegend 118225). LECs were sorted using positive selection for isolectin, CD31, GFP, and negative gating for Epcam and Lineage markers.
10X Genomics Chromium Single-cell 3' Library RNA-Seq Assays

tag: tissue

value: Lung

tag: cell type

value: Lymphatic Endothelial Cells

tag: genotype

value: CLEC2 KO


title: CC39034032

city: Birmingham

first: Kaleen

middle: M

last: Lavin

state: Alabama

address: 908 20th Street South, Room 201-C

department: Medicine

institute: University of Alabama at Birmingham

data_processing:
FASTQs from different flow cells were combined for a given sample using NGmerge
alignment via TopHat
Assembly: ensembl Hg19
Supplementary files format and content: processed data are RPKM normalized read counts

molecule: polyA RNA

organism: Homo sapiens

source_name: skeletal muscle

extract_protocol:
TRIzol method. Homogenized samples were thawed on ice followed by the addition of 200µL of chloroform and thorough mixing, then a  5 min incubation at room temperature, followed by centrifugation for 15 min at 40ºC at 12000g.  The clear, aqueous top layer was collected and total RNA was precipitated by adding 100% cold ethanol to the extracted portion until a final concentration of 35% ethanol was achieved. Samples were then incubated for 30 minutes at 200C and centrifuged for 15 minutes at 40C at 16000g.  75% ethanol was used to wash the RNA pellet twice, and the RNA pellet was left to air-dry after which it was resuspended in 20µL of nuclease-free, ultra-pure diethlpyrocarbonate-treated water.
Libraries were created using a non-strand specific library of polyA RNA (Illumina TruSeq RNA Sample Prep Kit v2, Illumina, San Diego, CA)

value: skeletal muscle

tag: participant id

tag: diet

value: HiCarb

tag: timepoint

value: IP


title: sgNTC_OTI_2

type: RNA

city: Memphis

first: Hongbo

last: Chi

state: TN

address: 262 Danny Thomas Place

department: Immunology

institute: St Jude Children's Research Hospital

hyb_protocol: Labeled cDNA was included in a hybridization mix that was incubated on the Clariom S mouse array for 16 hours at 45◦c while rotating at 60 rpm.

scan_protocol: GeneChips were scanned using the AffymetrixGeneChip Scanner 3000 7G.

data_processing: Probe signals were quantile normalized and summarized by the RMA algorithm using the Affymetrix Expression Console software v1.1

label: biotin

source_name: B16-OVA-Cas9-sgNTC with OT-I CD8+ T cells treatment

label_protocol: High-quality RNA was processed using Thermo Fisher (Affymetrix) Whole Transcript (WT) Plus assay kit

growth_protocol: B16-OVA-Cas9-sgNTC/sgVdac2 tumor cells were cultured according to ATCC guideline.

extract_protocol: Total RNA samples were prepared according to the prototol of Rneasy Micro kit from Qiagen,

treatment_protocol: B16-OVA-Cas9-sgNTC/sgVdac2 tumor cells were co-cultured with  OT-I CD8+ T cells at E:T ratio of 0.5:1 for 24h, survived tumor cells were sorted after co-culture for RNA extraction.

tag: strain

value: B16-OVA-Cas9-sgNTC with OT-I CD8+T cell treatment


title: H37Rv_CFZ@3.2uM+16h_b7_3

city: Seattle

first: Ethan

last: Bustad

state: WA

address: 1900 Ninth Ave.

department: CGIDR

institute: Seattle Children's Research Institute

description: Library name: H37Rv_3_2uM_CFZ_T16_R3_S24_R1

data_processing:
Libraries were sequenced at the University of Washington Northwest Genomics Center with the Illumina NextSeq 500 High Output v2 kit (Illumina Inc., San Diego, CA). The sequencing run generated an average of 75 million base-pair paired-end raw read counts per library.
Read alignment and gene expression estimation was carried out using a custom processing pipeline in R that harnesses the Bowtie 2 utilities, which is publicly accessible at https://github.com/robertdouglasmorrison/DuffyTools, and https://github.com/robertdouglasmorrison/DuffyNGS.
TPM (transcripts per million) reads were calculated and used as the expression value reported in the second processed data file.
Assembly: Accession # AL123456.3 | Mycobacterium tuberculosis H37Rv complete genome
Supplementary files format and content: FrontiersInTb_INDIGO1Sherman_GEO_processed_reads.txt is a matrix of aligned read values representing the expression levels of each gene for each sample. Each row represents a different sample, and each column represents the expression of each gene. The first 6 columns give the metadata information associated with each sample.
Supplementary files format and content: FrontiersInTb_INDIGO1Sherman_GEO_processed_tpm.txt is a matrix of TPM values representing the expression levels of each gene for each sample. Each row represents a different sample, and each column represents the expression of each gene. The first 6 columns give the metadata information associated with each sample.

organism: Mycobacterium tuberculosis H37Rv

source_name: Bacteria

growth_protocol: Mycobacterium tuberculosis was routinely grown in Middlebrook 7H9 broth supplemented with 10% OADC and 0.05% Tyloxapol or 0.025% Tween80 (v/v) at 37°C on a rotary shaker.

extract_protocol:
Bacterial pellets suspended in TRIzol were transferred to a tube containing Lysing Matrix B (QBiogene) and vigorously shaken in a homogenizer. The mixture was centrifuged, and RNA was extracted from the supernatant with chloroform, followed by RNA precipitation by isopropanol and high-salt solution (0.8 M Na citrate, 1.2 M NaCl). Total RNA was purified using a RNeasy kit following the manufacturer’s recommendations (Qiagen). rRNA was depleted from samples using a custom-designed set of biotinylated oligonucleotides based on the method described in PMID: 32317317.
Illumina sequencing libraries were prepared using the NEBNext Ultra II RNA Library Prep kit for Illumina (New England Biolabs, Ipswich, MA) according to the manufacturer’s instructions, and using the AMPure XP reagent (Agencourt Bioscience Corporation, Beverly, MA) for size selection and cleanup of adaptor-ligated DNA. We used the NEBNext Multiplex Oligos for Illumina (Dual Index Primers Set 1) to barcode the libraries to enable sample multiplexing per sequencing run. The prepared libraries were quantified using the Kapa quantitative PCR (qPCR) quantification kit.

value: Bacteria

value: Wildtype

tag: treatment

value: CFZ, 3.2uM

tag: batch

tag: time

value: 16 hours


title: Zebra Control

country: South Korea

description: 10X genomics

organism: Danio rerio

value: Wild-type


title: KO 2


title: sgNTC_OTI_1


title: Day12_Treg_B16F10_SKO_control_03

city: Chicago

first: Benjamin

middle: D.

last: Singer

state: Illinois

address: 303 E. Superior St., Simpson Querrey 5th floor

institute: Northwestern University Feinberg School of Medicine

description:
Library name: Sample 25
Treg cells sorted at day 12 post-engraftment from subcutaneous B16-F10 melanoma tumors implanted on 12-15 week-old male Black 6 mice
RawCounts2.csv

data_processing:
Basecalls performed using Illumina RTA2 software.
bcl-convert/3.10.5 was used to convert bcl files to fastq files (default parameters).
FASTQ files were processed using the nf-core/RNA-seq pipeline1 v3.18 implemented in Nextflow v24.04.4 with Northwestern University Quest HPC (Genomic Nodes) configuration
csv files including raw counts values for each sample was generated by nf-core/RNA-seq pipeline1 v3.18 (--aligner star_salmon)
Assembly: GRCm38/mm10
Supplementary files format and content: csv files including raw counts values for each sample

source_name: Treg cells (Foxp3-YFP+)

extract_protocol:
RNA was extracted from FACSorted cells using the AllPrep DNA/RNA Micro Kit.
Next Ultra II RNA Kits (NEB)

value: Treg cells (Foxp3-YFP+)


title: CC39034031

value: Base


title: H37Rv_CFZ@3.2uM+16h_b7_2

description: Library name: H37Rv_3_2uM_CFZ_T16_R2_S23_R1


title: H37Rv_CFZ@3.2uM+16h_b7_1

description: Library name: H37Rv_3_2uM_CFZ_T16_R1_S22_R1


title: KO 1


title: Day12_Treg_B16F10_SKO_control_02

description:
Library name: Sample 24
Treg cells sorted at day 12 post-engraftment from subcutaneous B16-F10 melanoma tumors implanted on 12-15 week-old male Black 6 mice
RawCounts2.csv


title: Control 3

value: Control


title: CC39034029

value: LowCarb


title: Day12_Treg_B16F10_SKO_control_01

description:
Library name: Sample 23
Treg cells sorted at day 12 post-engraftment from subcutaneous B16-F10 melanoma tumors implanted on 12-15 week-old male Black 6 mice
RawCounts2.csv


title: Control 2


title: CC39034028


title: H37Rv_PA824@0.8uM+16h_b7_3

description: Library name: H37Rv_0_8uM_PA824_T16_R3_S30_R1


title: Day12_Treg_B16F10_DKO_control_06

description:
Library name: Sample 22
Treg cells sorted at day 12 post-engraftment from subcutaneous B16-F10 melanoma tumors implanted on 12-15 week-old male Black 6 mice
RawCounts2.csv


title: H37Rv_PA824@0.8uM+16h_b7_2

description: Library name: H37Rv_0_8uM_PA824_T16_R2_S29_R1


title: Control 1


title: WT_0h 1

growth_protocol: B16-OVA-Cas9-sgNTC/Vdac2 tumor cells were cultured according to ATCC guideline.

treatment_protocol: Tumor cells were treated with mouse IFNg at 10ng/ml

value: no treatment


title: Day12_Treg_B16F10_DKO_control_05

description:
Library name: Sample 21
Treg cells sorted at day 12 post-engraftment from subcutaneous B16-F10 melanoma tumors implanted on 12-15 week-old male Black 6 mice
RawCounts2.csv


title: CC39034027


title: H37Rv_PA824@0.8uM+16h_b7_1

description: Library name: H37Rv_0_8uM_PA824_T16_R1_S28_R1


title: CC39034026


title: H37Rv_CFZ@0.8uM+16h_b7_3

description: Library name: H37Rv_0_8uM_CFZ_T16_R3_S21_R1

value: CFZ, 0.8uM


title: CC39034025


title: MCD.aDBI_10

city: PARIS

first: Guido

last: Kroemer

address: 15 rue de L'école de médecine

country: France

institute: Centre de Recherche des Cordeliers

data_processing:
Illumina Casava1.7 software used for basecalling
ShortRead, v1.52.0
STAR
Assembly: GRCm38
Supplementary files format and content: xlsx file with raw count follow by DESeq2 analysis

source_name: Liver

extract_protocol:
Total RNA from liver was purified with RNeasy Plus Mini Kitl following the manufacture instructions (Quiagen #74134). Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1,5 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Adult male mice (8 weeks old, C57BL/6) subjected to Regular Chow Diet (RCD) or Methionine and Choline Deficient Diet (MCD) (regime duration: 6 weeks) and injected with Isotype or monoclonal anti-ACBP/DBI (2 dose per week from week 4 to week 6)

value: Liver

tag: Sex

value: male

value: Methionine and Choline Deficient Diet (MCD, Safe #AIN-76)

tag: antibody

value: Monoclonal anti-ACBP/DBI (aDBI, Fred Hutch Cancer Center)


title: MCD.aDBI_9


title: CC39034030

value: skeletal muscle


title: Day12_Treg_B16F10_DKO_control_03

description:
Library name: Sample 19
Treg cells sorted at day 12 post-engraftment from subcutaneous B16-F10 melanoma tumors implanted on 12-15 week-old male Black 6 mice
RawCounts2.csv


title: Day12_Treg_B16F10_DKO_control_04

description:
Library name: Sample 20
Treg cells sorted at day 12 post-engraftment from subcutaneous B16-F10 melanoma tumors implanted on 12-15 week-old male Black 6 mice
RawCounts2.csv


title: H37Rv_CFZ@0.8uM+16h_b7_2

description: Library name: H37Rv_0_8uM_CFZ_T16_R2_S20_R1


title: MCD.aDBI_8


title: CC39020024

value: HiCarb


title: MCD.aDBI_7


title: H37Rv_CFZ@0.8uM+16h_b7_1

description: Library name: H37Rv_0_8uM_CFZ_T16_R1_S19_R1

value: Bacteria


title: H37Rv_PA824@0.2uM+16h_b7_3

description: Library name: H37Rv_0_2uM_PA824_T16_R3_S27_R1

value: Wildtype


title: Day12_Treg_B16F10_DKO_control_02

description:
Library name: Sample 18
Treg cells sorted at day 12 post-engraftment from subcutaneous B16-F10 melanoma tumors implanted on 12-15 week-old male Black 6 mice
RawCounts2.csv


title: Day12_Treg_B16F10_DKO_control_01

description:
Library name: Sample 17
Treg cells sorted at day 12 post-engraftment from subcutaneous B16-F10 melanoma tumors implanted on 12-15 week-old male Black 6 mice
RawCounts2.csv


title: CC39020022


title: H37Rv_PA824@0.2uM+16h_b7_2

description: Library name: H37Rv_0_2uM_PA824_T16_R2_S26_R1


title: MCD.aDBI_5


title: CC39020021


title: Day12_Treg_B16F10_DKO_08

description:
Library name: Sample 16
Treg cells sorted at day 12 post-engraftment from subcutaneous B16-F10 melanoma tumors implanted on 12-15 week-old male Black 6 mice
RawCounts2.csv


title: Day12_Treg_B16F10_DKO_07

description:
Library name: Sample 15
Treg cells sorted at day 12 post-engraftment from subcutaneous B16-F10 melanoma tumors implanted on 12-15 week-old male Black 6 mice
RawCounts2.csv


title: MCD.aDBI_4


title: H37Rv_PA824@0.2uM+16h_b7_1

description: Library name: H37Rv_0_2uM_PA824_T16_R1_S25_R1


title: H37Rv_CFZ@0.2uM+16h_b7_3

description: Library name: H37Rv_0_2uM_CFZ_T16_R3_S18_R1

value: CFZ, 0.2uM


title: CC39020020

value: IP


title: Day12_Treg_B16F10_DKO_06

description:
Library name: Sample 14
Treg cells sorted at day 12 post-engraftment from subcutaneous B16-F10 melanoma tumors implanted on 12-15 week-old male Black 6 mice
RawCounts2.csv


title: MCD.aDBI_3


title: Day12_Treg_B16F10_DKO_05

description:
Library name: Sample 13
Treg cells sorted at day 12 post-engraftment from subcutaneous B16-F10 melanoma tumors implanted on 12-15 week-old male Black 6 mice
RawCounts2.csv


title: H37Rv_CFZ@0.2uM+16h_b7_2

description: Library name: H37Rv_0_2uM_CFZ_T16_R2_S17_R1

value: 16 hours


title: MCD.aDBI_2


title: CC39020019


title: CC39020018


title: CC39020023


title: CC39020017


title: MCD.aDBI_1


title: Day12_Treg_B16F10_DKO_03

description:
Library name: Sample 11
Treg cells sorted at day 12 post-engraftment from subcutaneous B16-F10 melanoma tumors implanted on 12-15 week-old male Black 6 mice
RawCounts2.csv

value: Treg cells (Foxp3-YFP+)


title: MCD.aDBI_6


title: H37Rv_CFZ@0.2uM+16h_b7_1

description: Library name: H37Rv_0_2uM_CFZ_T16_R1_S16_R1


title: Day12_Treg_B16F10_DKO_04

description:
Library name: Sample 12
Treg cells sorted at day 12 post-engraftment from subcutaneous B16-F10 melanoma tumors implanted on 12-15 week-old male Black 6 mice
RawCounts2.csv


title: H37Rv_MXF@0.08uM+16h_b7_3

description: Library name: H37Rv_0_08uM_MOX_T16_R3_S15_R1

value: MXF, 0.08uM


title: Day12_Treg_B16F10_DKO_02

description:
Library name: Sample 10
Treg cells sorted at day 12 post-engraftment from subcutaneous B16-F10 melanoma tumors implanted on 12-15 week-old male Black 6 mice
RawCounts2.csv


title: H37Rv_MXF@0.08uM+16h_b7_2

description: Library name: H37Rv_0_08uM_MOX_T16_R2_S14_R1


title: MCD.Isotype_9

value: mouse IgG2a Isotype (Isotype, Bioxcell #BE0085)


title: H37Rv_MXF@0.08uM+16h_b7_1

description: Library name: H37Rv_0_08uM_MOX_T16_R1_S13_R1


title: MCD.Isotype_10


title: CC39020016

value: LowCarb

value: Base


title: Day12_Treg_B16F10_DKO_01

description:
Library name: Sample 9
Treg cells sorted at day 12 post-engraftment from subcutaneous B16-F10 melanoma tumors implanted on 12-15 week-old male Black 6 mice
RawCounts2.csv


title: CC39020014


title: MCD.Isotype_8


title: H37Rv_MXF@0.005uM+16h_b7_3

description: Library name: H37Rv__005uM_MOX_T16_R3_S9_R1


title: Day12_Treg_B16F10_a2SKO_04

description:
Library name: Sample 8
Treg cells sorted at day 12 post-engraftment from subcutaneous B16-F10 melanoma tumors implanted on 12-15 week-old male Black 6 mice
RawCounts2.csv


title: MCD.Isotype_7


title: CC39020013


title: H37Rv_MXF@0.005uM+16h_b7_2

description: Library name: H37Rv__005uM_MOX_T16_R2_S8_R1


title: MCD.Isotype_6


title: H37Rv_MXF@0.005uM+16h_b7_1

description: Library name: H37Rv__005uM_MOX_T16_R1_S7_R1


title: CC39020012


title: Day12_Treg_B16F10_a2SKO_02

description:
Library name: Sample 6
Treg cells sorted at day 12 post-engraftment from subcutaneous B16-F10 melanoma tumors implanted on 12-15 week-old male Black 6 mice
RawCounts2.csv


title: MCD.Isotype_5


title: CC39020011


title: Day12_Treg_B16F10_a2SKO_01

description:
Library name: Sample 5
Treg cells sorted at day 12 post-engraftment from subcutaneous B16-F10 melanoma tumors implanted on 12-15 week-old male Black 6 mice
RawCounts2.csv


title: H37Rv_MXF@0.02uM+16h_b7_2

description: Library name: H37Rv_0_02uM_MOX_T16_R3_S12_R1

value: MXF, 0.02uM


title: MCD.Isotype_4

value: Liver


title: H37Rv_MXF@0.02uM+16h_b7_1

description: Library name: H37Rv_0_02uM_MOX_T16_R2_S11_R1


title: CC39020015


title: MCD.Isotype_3

value: male


title: CC39020010


title: CC39020009


title: MCD.Isotype_2

value: Methionine and Choline Deficient Diet (MCD, Safe #AIN-76)


title: Day12_Treg_B16F10_a1SKO_03

description:
Library name: Sample 3
Treg cells sorted at day 12 post-engraftment from subcutaneous B16-F10 melanoma tumors implanted on 12-15 week-old male Black 6 mice
RawCounts2.csv


title: H37Rv_Untreated@0+16h_b6_2

description: Library name: Rv_T16_Set_B_R2

value: Untreated


title: Day12_Treg_B16F10_a1SKO_04

description:
Library name: Sample 4
Treg cells sorted at day 12 post-engraftment from subcutaneous B16-F10 melanoma tumors implanted on 12-15 week-old male Black 6 mice
RawCounts2.csv


title: MCD.Isotype_1


title: CC39020008

value: skeletal muscle


title: CC39020007


title: H37Rv_H2O@0+16h_b2_2

description: Library name: Rv_ND_T16_Set_B_H2O_R2_S24


title: Day12_Treg_B16F10_a2SKO_03

description:
Library name: Sample 7
Treg cells sorted at day 12 post-engraftment from subcutaneous B16-F10 melanoma tumors implanted on 12-15 week-old male Black 6 mice
RawCounts2.csv


title: RCD.aDBI_5

value: Regular chow diet (RCD, Safe #A04)

value: Monoclonal anti-ACBP/DBI (aDBI, Fred Hutch Cancer Center)


title: CC39020006


title: H37Rv_H2O@0+16h_b1_2

description: Library name: Rv_ND_T16_Set_B_H2O_R1_S23

value: Bacteria

value: Wildtype


title: RCD.aDBI_4


title: DEK_IP_2

city: Wuhan

first: Dong

last: Chen

state: Hubei

address: 388 GaoXin 2nd Road, East Lake Hi-Tech Development Zone

department: Center for Genome Analysis

country: China

institute: ABLife, Inc.

data_processing:
Illumina bcl2fastq software used for basecalling.
3' adapter (end1:AGATCGGAAGAGC;end2:AGATCGGAAGAGC) and low quality bases trimmed using FASTX-Toolkit (Version 0.0.13). the short reads less than 16nt were also dropped.
Reads were mapped using tophat2 --read-edit-dist 4 -N 4 --b2-N 1 -a 8 -m 0 -g 2 -p 12 --microexon-search --no-coverage-search --report-secondary-alignments. Uniq mapped reads were remained. while several mapped reads have the same start position and end position, only one is considered.
After reads were aligned onto the genome, we analysis the unique reads binding regions of DEK on genome were identified using “ABLIRC” strategy
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include peak information

growth_protocol: HeLa cells were first lysed in ice-cold lysis buffer (10 mM HEPES, pH 7.0, 100 mM KCl, 5 mM MgCl2, 0.5% NP-40, 10 mM DTT) with 200 U/ml RNase inhibitor (Promega) and a protease inhibitor (Roche) on ice for 5 min

extract_protocol:
The beads were washed 6 times with lysis buffer and then divided into two groups, one for RNA isolation from DEK-RNA complexes and another for the western blotting assay for DEK immunoprecipitation.The DEK-bound RNAs were isolated from the immunoprecipitate of monoclonal Flag antibody (Sigma), followed by the preparation of the Illumina Truseq pair-end libraries.
The reverse transcription was performed with RT primers harboring 3' adaptor sequence and random hexamer. The generated cDNAs were PCR-amplified and the 200-500 bp products were purified

treatment_protocol: The supernatant was pre-cleared with 100 μl of DynaBeads protein G (Life Technologies) at 4 °C for 30 min. The pre-cleared supernatant was incubated with DynaBeads protein G conjugated with monoclonal Flag antibody (Sigma) or Input at 4℃ for 30 min.

tag: cell line

value: HeLa

tag: genotype/variation

value: expressing vector with DEK-FLAG

tag: rip antibody

value: anti-FLAG (sigma, F7425)


title: H37Rv_DMSO@0+16h_b2_2

description: Library name: Rv_ND_T16_Set_B_DMSO_R2_S22

value: DMSO, 0

value: 16 hours


title: RCD.aDBI_3


title: DEK_IP_1


title: CC39020004

value: LowCarb


title: DEK_input_2


title: H37Rv_DMSO@0+16h_b1_2

description: Library name: Rv_ND_T16_Set_B_DMSO_R1_S21


title: CC39020003

value: HiCarb


title: H37Rv_Untreated@0+16h_b6_1

description: Library name: Rv_T16_Set_B_R1


title: H37Rv_NaOH@0+16h_b2_2

description: Library name: Rv_ND_T16_Set_B_0_5M_NaOH_R2_S26

value: NaOH, 0


title: Day12_Treg_B16F10_a1SKO_02

description:
Library name: Sample 2
Treg cells sorted at day 12 post-engraftment from subcutaneous B16-F10 melanoma tumors implanted on 12-15 week-old male Black 6 mice
RawCounts2.csv

value: Treg cells (Foxp3-YFP+)


title: DEK_input_1


title: RCD.aDBI_2

value: Liver

value: male


title: Day12_Treg_B16F10_a1SKO_01

description:
Library name: Sample 1
Treg cells sorted at day 12 post-engraftment from subcutaneous B16-F10 melanoma tumors implanted on 12-15 week-old male Black 6 mice
RawCounts2.csv


title: CC39020001

value: Base


title: RCD.aDBI_1


title: CC39020002

value: skeletal muscle

value: IP


title: RCD.Isotype_5

value: Regular chow diet (RCD, Safe #A04)

value: mouse IgG2a Isotype (Isotype, Bioxcell #BE0085)


title: H37Rv_NaOH@0+16h_b1_2

description: Library name: Rv_ND_T16_Set_B_0_5M_NaOH_R1_S25

value: Bacteria

value: Wildtype


title: HeLa_DEK_1

data_processing:
Illumina bcl2fastq software used for basecalling.
3' adapter (end1:AGATCGGAAGAGC;end2:AGATCGGAAGAGC) and low quality bases trimmed using FASTX-Toolkit (Version 0.0.13). the short reads less than 16nt were also dropped.
Reads were mapped using tophat2 --read-edit-dist 4 -N 4 --b2-N 1 -a 8 -m 0 -g 20 -p 16 --no-discordant. Uniq mapped reads were remained. while several mapped reads have the same start position and end position, only one is considered.
edgeR was used to the DEG analysis with FC>2  Pvalue <= 0.01 Qvalue <= 0.05
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include gene FPKM values for each Sample

source_name: HeLa_DEK overexpression

growth_protocol: HeLa cells were cultured under standard conditions with Dulbecco’s modified Eagle’s medium (DMEM) with 10% fetal bovine serum (FBS), 100 µg/mL streptomycin, and 100 U/mL penicillin.

extract_protocol:
Total RNA was extracted by the TRIZOL (Ambion) and was further purified with two phenol-chloroform treatments.The purified RNA was then treated with RQ1 DNase (RNase free) (Promega, Madison, WI, USA) and its quality and quantity were redetermined by measuring the absorbance at 260 nm/280 nm (A260/A280) using Smartspec Plus (BioRad, USA). The integrity of RNA was then verified by 1.5% agarose gel electrophoresis.
For each sample, 10μg of the total RNA was used for RNA-seq library preparation. Polyadenylated mRNAs were purified and concentrated with oligo(dT)-conjugated magnetic beads (Invitrogen, Carlsbad, CA, USA) before directional RNA-seq library preparation. The purified mRNAs were then iron fragmented at 95°C followed by end repair and 5' adaptor ligation. Then, reverse transcription was performed with RT primer harboring 3' adaptor sequence and randomized hexamer. The cDNAs were purified, amplified, and stored at -80°C until they were used for sequencing.  For high-throughput sequencing, the libraries were prepared following the manufacturer's instructions. Illumina HiSeq 4000 was used to collect data from 150-bp pair-end sequencing (ABlife Inc., Wuhan, China).

treatment_protocol: Plasmids transfection of HeLa cells was performed using lipofectAMINE 2000 (Invitrogen, Carlsbad, CA, USA) according to the manufacturer's protocol. Transfected cells were harvested after 48 h for q-PCR analysis.

value: HeLa

value: DEK overexpression


title: RCD.Isotype_4


title: H37Rv_H2O@0+16h_b2_1

description: Library name: Rv_ND_T16_Set_A_H2O_R2_S6


title: H37Rv_H2O@0+16h_b1_1

description: Library name: Rv_ND_T16_Set_A_H2O_R1_S5


title: RCD.Isotype_3


title: LLC1-Ddx54KD/anti-PD1_treatmet

city: Yuseong-gu

first: Jeong-Ryeol

last: Gong

state: Daejeon

address: 291, Daehak-ro

institute: KAIST

hyb_protocol: Probe hybridization was carried out overnight at 50°C using the commercially available 5K Xenium Mouse Gene Expression panel, targeting selected thalamic genes. Following hybridization, the slides underwent washing procedures to remove any non-bound probes. This was followed by a ligation step lasting 2 hours at 37°C, allowing the probes to specifically anneal to their corresponding mRNA targets. The probes were then enzymatically amplified through a rolling circle amplification PCR process for 2 hours at 37°C. After amplification, additional washing steps were performed, and quenching procedures were implemented to minimize background autofluorescence. Subsequently, a DAPI nuclear stain was applied to visualize cell nuclei. Finally, the prepared slide cassettes were loaded onto the Xenium Analyzer instrument for further analysis.

scan_protocol: Xenium In Situ Analyzer

data_processing: Data processed using Xenium Ranger software.

label: 5K murine probe set

tag: strain background

value: LLC1 cancer tissue in syngeneic mouse model


title: CC39020005


title: LLC1-WT/anti-PD1_treatmet


title: H37Rv_DMSO@0+16h_b2_1

description: Library name: Rv_ND_T16_Set_A_DMSO_R2_S4

value: DMSO, 0

value: 16 hours


title: RCD.Isotype_2


title: H37Rv_DMSO@0+16h_b1_1

description: Library name: Rv_ND_T16_Set_A_DMSO_R1_S3


title: APF_96h

city: Waltham

first: Yerbol

last: Kurmangaliyev

state: MA

address: 415 South Street, MS 029

department: Biology

institute: Brandeis University

description: Library name: APF_96h

library_source: transcriptomic single cell

data_processing:
Raw scRNA-seq reads were processed using Cell Ranger (10X Genomics, version: 7.1.0).
Biological replicates were demultiplexed based on a unique genotypes of wild-type DGRP chromosomes using demuxlet (version 2).
The scRNA-seq analysis was performed using Seurat package (5.0.1).
Assembly: dm6 (FlyBase 6.29)
Supplementary files format and content: Single-cell raw count matrix (TAB-separated file).
Supplementary files format and content: Single-cell metadata table (TAB-separated file).

organism: Drosophila melanogaster

source_name: sorted neurons

extract_protocol:
Dissected brains were enzymatically dissociated, and GFP+ cells were isolated using FACS.
Single-cell suspensions were used to generate scRNA-seq libraries using the 10X Genomics Chromium Next GEM Single Cell 3’-kit (v3.1) following the manufacturer’s protocol.

value: sorted neurons

value: LPLC2, LPLC1, LC4

tag: developmental stage

value: 96h APF


title: RCD.Isotype_1

tag: tissue

value: Liver


title: H37Rv_NaOH@0+16h_b2_1

description: Library name: Rv_ND_T16_Set_A_0_5M_NaOH_R2_S8

tag: cell type

value: NaOH, 0


title: LLC1-Ddx54KD/Isotype


title: APF_72h

description: Library name: APF_72h

value: 72h APF


title: LLC1-WT/Isotype


title: H37Rv_Untreated@0+0h_b2_2

description: Library name: Rv_ND_T0_Set_B_R2_S20

tag: genotype

value: Untreated

value: 0 hours


title: S3 leukemic MxCre;Ptpn11D61Y/+ - BM - LSK - 768

city: Freiburg

first: Senthilkumar

last: Ramamoorthy

address: Mathildenstraße 1

country: Germany

institute: UNIVERSITAETSKLINIKUM FREIBURG

description: RNA-seq of bone marrow LSK cells from S3 leukemic MxCre;Ptpn11D61Y/+ mouse - 768

data_processing:
The base calling was performed by using BCL2Fastq pipeline and bcl2fastq (version 2.20.0.422).
The quality of the RNA sequencing data was checked using the FastQC (v0.11.9) and RSeQC (v4.0.0) tools. The 100bp paired-end reads were trimmed using trimgalore (v0.6.5) and  mapped to the mouse reference genome (mm10) using the STAR aligner (2.5.3a). The log-transformed total count per million (CPM) was calculated for each gene and genes with values greater than 0 in at least two samples were included for further analysis. Differential gene expression was calculated by a linear modeling approach using functions available in the R package limma. For differential expression analysis, the functions lmfit, eBayes and contrast.fit available in limma were applied to the voom-transformed expression values.  A set of significant differentially expressed genes was selected with an adjusted p-value cut-off of 0.05 after applying the Benjamini-Hochberg correction for multiple testing.
The raw read counts obtained from STAR are provided.
Assembly: mouse (mm10)
Supplementary files format and content: txt
Supplementary files format and content: The raw read count

source_name: Bonemarrow

growth_protocol: Primary CD11b+ cells from BM and spleen were isolated by MACS/FACS and subjected to RNA isolation.

extract_protocol:
RNA was extracted using the RNeasy Micro Kit (Qiagen, #74104) according to the manufacturer's instructions.
The RNAseq library was generated using Illumina TrueSeq® Standard Library Prep Kit.

treatment_protocol: No treatment

value: Bonemarrow

value: LSK


title: HeLa_control_2

value: control plasmid


title: S3 leukemic MxCre;Ptpn11D61Y/+ - Spleen - CD11b+ - 640

description: RNA-seq of spleen CD11b+ cells from S3 leukemic MxCre;Ptpn11D61Y/+ mouse - 640

source_name: Spleen

value: Spleen


title: Lactating_ileum_rep4

city: London

first: Irene

last: Miguel-Aliaga

address: 1 Midland Rd

country: United Kingdom

institute: The Francis Crick Institute

description: Run 2

hyb_protocol: Standalone custom probes for 300 genes were hybridised for 20 hours overnight, followed by washing, ligation of the probe ends to the targeted RNAs generating circular DNA probes with high specificity. Rolling Circle Amplification was then used to generate hundreds of copies of the gene-specific barcode for each RNA binding event, resulting in a strong signal-to-noise ratio. Background fluorescence was then quenched chemically to mitigate tissue auto-fluorescence. The tissues sections were then stained with DAPI nuclear stain.

scan_protocol: Xenium slides were loaded onto the Xenium instrument for imaging and decoding image data to transcripts (Xenium software version 1.8.2.1)

data_processing: Cell segmentation and transcript assignment was directly performed on-instrument. The analysis was performed both using count matrices derived from the multimodal segmentation and from nuclei segmentation. The results from these analyses were highly consistent, with analogous cell populations identified in both. Cells with 0 counts were filtered from further analysis. The merged raw count matrix was normalised using the Seurat v_5.1.0 NormalizeData function. The dataset was subsampled to 500,000 cells using the Seurat v_5.1.0 SketchData function to ensure representation of rare populations. PCA was performed on all 300 genes and the top 30 PCs were selected for downstream dimensionality reduction using the UMAP algorithm and subjected to Louvain clustering at resolution 0.3. Cluster markers were identified using a Wilcoxon test, comparing each cluster to the union of all other clusters. Identified cluster labels were projected onto the full dataset using the Seurat v_5.1.0 ProjectData function. Epithelial clusters were identified based on the expression of known epithelial markers and by their colocalisation in reduced dimensions. Cells from these clusters were selected for further analysis. The sketched epithelial data was subjected to PCA (300 genes), dimensionality reduction using the UMAP algorithm and Louvain clustering at resolution 0.5 (30 PCs). Cluster markers were again identified using a Wilcoxon test, comparing each cluster to the union of all other clusters and cluster labels were projected onto the full dataset using the Seurat v_5.1.0 ProjectData function.  Of note, good mixing between samples from all slides can be seen on both the UMAP of the whole dataset and the epithelial UMAP, with no sample specific clusters observed, suggesting minimal batch effects. For all further analyses the full (rather than sketched) datasets were used.

source_name: Lactating (day 7) ileum

growth_protocol: Mice used in this study were maintained according to standard practices and all procedures were approved by Imperial College London and conformed to UK Home Office requirements (ASPA 1986) and the ARRIVE guidelines.

extract_protocol: 5 µm FFPE tissue sections were placed on Xenium slides, followed by deparaffinization and permeabilization to make the mRNA accessible.

treatment_protocol: 7–10-week-old C57BL/6J wild-type mice were purchased from Charles River, UK. Mice were housed under specific-pathogen-free conditions on a 12h dark/light cycle at constant temperature (20–22°C) and humidity (45–50%). Experimental repeats were conducted at comparable times to minimise possible circadian effects. Age-matched groups of littermates were used for all experiments. For pregnancy and lactation experiments, pregnancy day 0 was defined by detection of a vaginal plug; lactation day 0 was defined by the birth of pups. For all experiments, pregnancy day 7 (D7) and lactation day 7 (D7) were used as time points for pregnancy and lactation, respectively.

tag: condition

value: Lactating (day 7)


title: S3 leukemic MxCre;Ptpn11D61Y/+ - BM - CD11b+ - 640

description: RNA-seq of bone marrow CD11b+ cells from S3 leukemic MxCre;Ptpn11D61Y/+ mouse - 640


title: S3 leukemic MxCre;Ptpn11D61Y/+ - Spleen - CD11b+ - 815

description: RNA-seq of spleen CD11b+ cells from S3 leukemic MxCre;Ptpn11D61Y/+ mouse - 815


title: Virgin_ileum_rep4

description: Run 2

source_name: Virgin ileum

value: Virgin


title: Mouse 23, AAV-Cas9-miR-124-g4, Cas9 negative nuclei

city: Marseille

first: Eduardo

last: Gascon

address: 27 boulevard Jean Moulin

department: Institut de Neurosciences de la Timone

institute: Aix-Marseille University, CNRS

description:
Library name: Sample 28
column name in raw_counts_HAneg.csv : X24_g4_HAneg

data_processing:
Raw sequencing data in FASTQ format were pre-processed using the GeneGlobe platform (https://geneglobe.qiagen.com/fr/analyze). This step included quality control, adapter trimming, and alignment to the mouse reference genome (Mus musculus GRCm38.101).
Assembly: Mus musculus GRCm38.101
Supplementary files format and content: tab-delimited csv files include raw counts for each sample

molecule: nuclear RNA

source_name: Motor cortex

extract_protocol:
After dissection, tissues were fixed with 1% PFA and conserved at -80°C. Nuclei were extracted at 4°C in a homogenization buffer using a Dounce homogenizer, and stained with Hoechst 33342 and an anti-HA-tag-alexa-647 antibody in staining buffer (PBS, RNase Inhibitor, 0.5% BSA and 0.1% Triton-X-100). HA-positive and HA-negative nuclei were sorted with a Cytoflex SRT (Beckman Coulter). Sorted nuclei were conserved at -80°C. Total RNA extraction was performed using Qiazol and chloroform phase separation followed by precipitation of RNA.
40 to 2000 pg of purified total RNA were used as starting material for the preparation of libraries using the QIAseq FastSelect RNA library kit (Qiagen, #334235)

treatment_protocol: Stereotactic injection of AAV-Cas9-miR-124-empty (left side) and AAV-Cas9-miR-124-g4 (right side)

value: Motor cortex

tag: cell sub-population

value: Cas9-HA-tag negative


title: Pregnant_ileum_rep4

description: Run 2

source_name: Pregnant (day 7) ileum

value: Pregnant (day 7)


title: H37Rv_Untreated@0+0h_b2_1

description: Library name: Rv_ND_T0_Set_A_R2_S2

value: Bacteria

value: Wildtype


title: Mouse 21, AAV-Cas9-miR-124-g4, Cas9 negative nuclei

description:
Library name: Sample 26
column name in raw_counts_HAneg.csv : X22_g4_HAneg


title: S3 leukemic MxCre;Ptpn11D61Y/+ - BM - CD11b+ - 815

description: RNA-seq of bone marrow CD11b+ cells from S3 leukemic MxCre;Ptpn11D61Y/+ mouse - 815


title: Lactating_ileum_rep3

description: Run 2


title: HeLa_control_1

value: HeLa


title: H37Rv_Untreated@0+0h_b1_2

description: Library name: Rv_ND_T0_Set_B_R1_S19


title: Mouse 22, AAV-Cas9-miR-124-g4, Cas9 negative nuclei

description:
Library name: Sample 27
column name in raw_counts_HAneg.csv : X23_g4_HAneg


title: H37Rv_Untreated@0+0h_b1_1

description: Library name: Rv_ND_T0_Set_A_R1_S1


title: Pregnant_ileum_rep3

description: Run 2


title: Mouse 20, AAV-Cas9-miR-124-g4, Cas9 negative nuclei

description:
Library name: Sample 25
column name in raw_counts_HAneg.csv : X20_g4_HAneg


title: HeLa_DEK_2

value: DEK overexpression


title: S3 leukemic MxCre;Ptpn11D61Y/+ - BM - LSK - 815

description: RNA-seq of bone marrow LSK cells from S3 leukemic MxCre;Ptpn11D61Y/+ mouse - 815


title: H37Rv_NaOH@0+16h_b1_1

description: Library name: Rv_ND_T16_Set_A_0_5M_NaOH_R1_S7

value: NaOH, 0

value: 16 hours


title: H37Rv_LVF+DMSO@4xMIC+16h_b2_2

description: Library name: Rv_4X_LVF_MIC_T16_DMSO_Set_B_R2_S36

value: LVF+DMSO, 4xMIC


title: APF_48h

description: Library name: APF_48h

value: sorted neurons

value: LPLC2, LPLC1, LC4

value: 48h APF


title: S3 leukemic MxCre;Ptpn11D61Y/+ - Spleen - CD11b+ - 540

description: RNA-seq of spleen CD11b+ cells from S3 leukemic MxCre;Ptpn11D61Y/+ mouse - 540


title: H37Rv_LVF+DMSO@4xMIC+16h_b1_2

description: Library name: Rv_4X_LVF_MIC_T16_DMSO_Set_B_R1_S35


title: Mouse 19, AAV-Cas9-miR-124-g4, Cas9 negative nuclei

description:
Library name: Sample 24
column name in raw_counts_HAneg.csv : X19_g4_HAneg


title: Lactating_ileum_rep2

description: Run 1


title: H37Rv_LVF+DMSO@4xMIC+16h_b2_1

description: Library name: Rv_4X_LVF_MIC_T16_DMSO_Set_A_R2_S18


title: S3 leukemic MxCre;Ptpn11D61Y/+ - BM - LSK - 540

description: RNA-seq of bone marrow LSK cells from S3 leukemic MxCre;Ptpn11D61Y/+ mouse - 540

value: Bonemarrow

value: LSK


title: Mouse 18, AAV-Cas9-miR-124-g4, Cas9 negative nuclei

description:
Library name: Sample 23
column name in raw_counts_HAneg.csv : X18_g4_HAneg


title: Virgin_ileum_rep2

description: Run 1


title: Pregnant_ileum_rep2

description: Run 1


title: Mouse 17, AAV-Cas9-miR-124-g4, Cas9 negative nuclei

description:
Library name: Sample 22
column name in raw_counts_HAneg.csv : X17_g4_HAneg


title: Control Ptpn11D61Y/+  - Spleen - CD11b+ - Rep2

description: RNA-seq of spleen CD11b+ cells from control Ptpn11D61Y/+ mouse - Rep2

value: Spleen


title: Mouse 22, AAV-Cas9-miR-124-empty, Cas9 negative nuclei

description:
Library name: Sample 20
column name in raw_counts_HAneg.csv : X23_empty_HAneg


title: Pregnant_ileum_rep1

description: Run 1


title: H37Rv_CPF+NaOH@12uM+16h_b2_2

description: Library name: Rv_4X_CPF_MIC_T16_0_5M_NaOH_Set_B_R2_S34

value: CPF+NaOH, 12uM


title: Control Ptpn11D61Y/+  - BM - CD11b+ - Rep2

description: RNA-seq of bone marrow CD11b+ cells from control Ptpn11D61Y/+ mouse - Rep2


title: Mouse 23, AAV-Cas9-miR-124-empty, Cas9 negative nuclei

description:
Library name: Sample 21
column name in raw_counts_HAneg.csv : X24_empty_HAneg

value: Motor cortex


title: Mouse 21, AAV-Cas9-miR-124-empty, Cas9 negative nuclei

description:
Library name: Sample 19
column name in raw_counts_HAneg.csv : X22_empty_HAneg

value: Cas9-HA-tag negative


title: S3 leukemic MxCre;Ptpn11D61Y/+ - BM - CD11b+ - 540

description: RNA-seq of bone marrow CD11b+ cells from S3 leukemic MxCre;Ptpn11D61Y/+ mouse - 540


title: Lactating_ileum_rep1

description: Run 1

value: Lactating (day 7)


title: H37Rv_CPF+NaOH@12uM+16h_b1_2

description: Library name: Rv_4X_CPF_MIC_T16_0_5M_NaOH_Set_B_R1_S33

value: Bacteria


title: H37Rv_CPF+NaOH@12uM+16h_b2_1

description: Library name: Rv_4X_CPF_MIC_T16_0_5M_NaOH_Set_A_R2_S16

value: Wildtype


title: Virgin_ileum_rep3

description: Run 2

value: Virgin


title: Mouse 20, AAV-Cas9-miR-124-empty, Cas9 negative nuclei

description:
Library name: Sample 18
column name in raw_counts_HAneg.csv : X20_empty_HAneg


title: Virgin_ileum_rep1

description: Run 1


title: Control Ptpn11D61Y/+  - Spleen - CD11b+ - Rep1

description: RNA-seq of spleen CD11b+ cells from control Ptpn11D61Y/+ mouse - Rep1


title: Mouse Brain w/ MES Organoid, Xenium In Situ Spatial Gene Expression

city: St. Louis

first: Jeffrey

middle: Robert

last: Millman

state: MO

address: 660 South Euclid

institute: Washington University in St. Louis

description: MES TXP

hyb_protocol: The slides were processed using the “Xenium Slides and Sample Prep Reagents” kit (PN-1000460, 10X Genomics), beginning with an incubation in a decrosslinking and permeabilization solution at 80°C for 30min.

scan_protocol: The Xenium slides were then processed according to the “Xenium In Situ Gene Expression” user guide (CG000582 Rev D, 10X Genomics) for the remaining slide preparation steps. The slides were incubated at 50°C for 17h with the pre-designed gene expression probe set, “Xenium Human Brain Gene Expression”. This was followed by a series of wash and enzymatic steps, including a 30min post-hybridization wash at 37°C, a 2h ligation at 37°C, and a 2h amplification step at 30°C. After additional washes, the slides were treated with an autofluorescence quencher and a stained with DAPI.

data_processing:
Data processed using Xenium Ranger software
genome build/assembly: GRCh38-2020-A
processed data files format and content: gzip compressed archive of CSV, JSON, TIFF, TSV, ZIP, OME, PARQUET

source_name: Whole brain section

label_protocol: Subsequently, the slides were stored overnight at room temperature with a desiccant for further drying. The following day, Xenium slides were processed following the “Xenium In Situ for FFPE-Deparaffinization and Decrosslinking” protocol (CG000580 Rev C, 10X Genomics). The Xenium slides were then assembled into Xenium cassettes (PN-1000566, 10X Genomics), which allow for the incubation of slides on the Xenium Thermocycler Adapter plate in a PCR machine with a closed lid for precise temperature control.

growth_protocol: Brain organoids were generated using the same protocol as described Lancaster et al. Nature Protocols 2014, with the exception that mTESR1 (Stem Cell Technologies) was used during embryoid body formation. After 1 month of in vitro differentiation, brain organoid were dissociated into cells and injected into the brain of seven-week-old female athymic nude mice.

extract_protocol: Sections were prepared according to the “Xenium In Situ for FFPE-Tissue Preparation Guide” (CG000578 Rev C, 10X Genomics) protocol. Briefly, 5µm sections were cut and carefully placed onto the Sample Area of a Xenium slide (PN-1000465). The slides were then placed in a drying rack at room temperature for 30min to remove excess water, followed by a 3h incubation at 42°C on a Xenium Thermocycler Adapter plate positioned in a thermocycler (BioRad).

treatment_protocol: Genetically engineered H1 hPSCs cell lines were generated by the Genome Engineering & Stem Cell Center at Washington University School of Medicine in St. Louis. Briefly, H1 hPSCs were transfected with Cas9 recombinant protein and synthetic single guide RNA to introduce a C>T mutation within the telomerase reverse transcriptase (TERT) gene promoter. The H1 TERT mutant cell line was then further to modified, by the same procedure, to introduce either a point mutation targeting the TP53 gene or knockouts mutations in the PTEN and NF1 genes.

value: Whole brain section

tag: tissue type

value: Mouse Brain w/ MES Organoid


title: H37Rv_CPF+NaOH@12uM+16h_b1_1

description: Library name: Rv_4X_CPF_MIC_T16_0_5M_NaOH_Set_A_R1_S15

tag: strain

value: 16 hours


title: Mouse 19, AAV-Cas9-miR-124-empty, Cas9 negative nuclei

description:
Library name: Sample 17
column name in raw_counts_HAneg.csv : X19_empty_HAneg

tag: treatment


title: H37Rv_BDQ+DMSO@2uM+16h_b2_2

description: Library name: Rv_4X_BDQ_MIC_T16_DMSO_Set_B_R2_S32

value: BDQ+DMSO, 2uM

tag: batch


title: Mouse 18, AAV-Cas9-miR-124-empty, Cas9 negative nuclei

description:
Library name: Sample 16
column name in raw_counts_HAneg.csv : X18_empty_HAneg


title: MES Organoid, Xenium In Situ Spatial Gene Expression

description: MES Organoid

source_name: Whole brain organoid

value: Whole brain organoid

value: MES Organoid


title: Control Ptpn11D61Y/+  - BM - LSK - Rep1

description: RNA-seq of bone marrow LSK cells from control Ptpn11D61Y/+ mouse - Rep1


title: H37Rv_LVF+DMSO@4xMIC+16h_b1_1

description: Library name: Rv_4X_LVF_MIC_T16_DMSO_Set_A_R1_S17

value: LVF+DMSO, 4xMIC

tag: time


title: PRO Organoid, Xenium In Situ Spatial Gene Expression

description: PRO Organoid

value: PRO Organoid


title: H37Rv_BDQ+DMSO@2uM+16h_b2_1

description: Library name: Rv_4X_BDQ_MIC_T16_DMSO_Set_A_R2_S14


title: Mouse Brain w/ PRO Organoid, Xenium In Situ Spatial Gene Expression

description: PRO TXP

value: Mouse Brain w/ PRO Organoid


title: Control MxCre - Spleen - CD11b+ - Rep2

description: RNA-seq of spleen CD11b+ cells from control MxCre mouse - Rep2

value: Spleen

value: MxCre


title: Mouse 23, AAV-Cas9-miR-124-g4, Cas9 positive nuclei

description:
Library name: Sample 14
column name in raw_counts_Hapos.csv : X24_g4_Hapos

value: Motor cortex

value: Cas9-HA-tag positive


title: WT Organoid, Xenium In Situ Spatial Gene Expression

description: WT Organoid

value: WT Organoid


title: H37Rv_BDQ+DMSO@2uM+16h_b1_1

description: Library name: Rv_4X_BDQ_MIC_T16_DMSO_Set_A_R1_S13

value: Bacteria


title: H37Rv_BDQ+DMSO@2uM+16h_b1_2

description: Library name: Rv_4X_BDQ_MIC_T16_DMSO_Set_B_R1_S31

value: Wildtype


title: Mouse Brain w/ WT Organoid, Xenium In Situ Spatial Gene Expression

description: WT TXP

value: Mouse Brain w/ WT Organoid


title: Control MxCre - BM - CD11b+ - Rep2

description: RNA-seq of bone marrow CD11b+ cells from control MxCre mouse - Rep2

value: Bonemarrow


title: Mouse 22, AAV-Cas9-miR-124-g4, Cas9 positive nuclei

description:
Library name: Sample 13
column name in raw_counts_Hapos.csv : X23_g4_Hapos


title: Control MxCre - BM - LSK - Rep2

description: RNA-seq of bone marrow LSK cells from control MxCre mouse - Rep2

value: LSK


title: Control Ptpn11D61Y/+  - BM - LSK - Rep2

description: RNA-seq of bone marrow LSK cells from control Ptpn11D61Y/+ mouse - Rep2


title: Mouse 21, AAV-Cas9-miR-124-g4, Cas9 positive nuclei

description:
Library name: Sample 12
column name in raw_counts_Hapos.csv : X22_g4_Hapos


title: H37Rv_AMK+H2O@4xMIC+16h_b1_2

description: Library name: Rv_4X_AMK_MIC_T16_H2O_Set_B_R1_S29

value: AMK+H2O, 4xMIC

value: 16 hours


title: H37Rv_AMK+H2O@4xMIC+16h_b2_2

description: Library name: Rv_4X_AMK_MIC_T16_H2O_Set_B_R2_S30


title: NC210, normoxic (6-months post-hypercapnia) control female

city: Nutley

first: Andy

last: Madrid

state: NJ

address: 111 Ideation Way

institute: Hackensack Meridian Health

description:
Library name: NC210
Processed data includes bed files of estimated methylation levels with columns as: chromosome, position of CpG (+), position CpG (-), methylation level, number of methylated reads, number of unmethylated reads

library_source: genomic

data_processing:
Raw reads were assessed for quality using FastQC. Reads were trimmed, aligned to the mm10 version of the mouse genome, deduplicated, and methylation levels extracted using the gemBS pipeline. CpGs were collapsed across top and bottom strands using bismark
Assembly: mm10
Supplementary files format and content: Bed-like file. Processed data includes bed files of estimated methylation levels with columns as: chromosome, position of CpG (+), position CpG (-), methylation level, number of methylated reads, number of unmethylated reads

molecule: genomic DNA

extract_protocol:
After specified timepoints, animals were euthanized. Then leg skin was dissected with tweezers and muscles exposed and under real time magnification using an illuminated magnifier (Omano, China) muscles were dissected individually, cutting first the distal tendon, and gently removing the entire muscle using dissecting scissors (Roboz RS-5840). After the proximal tendon was severed, the muscle was put in contact with a gauze under magnification to eliminate remaining blood, fat, and if needed also remaining tendon using scissors. Muscle was then weighed using an analytical balance (Sartorius Entris, Germany). Mass determination was performed on the tibialis anterior (TA), extensor digitorum longus (EDL), and soleus muscles.
DNA was isolated from muscle samples using the GeneJET Genomic DNA Purification Kit (Thermo Scientific, K0721) catalogue #) following manufacturer’s protocols. DNA concentration was determined using a Qubit fluorometer (Thermo Fisher Scientific) and quality was assessed by agarose gel electrophoresis. Two hundred nanograms of high molecular weight genomic DNA was sent to the University of Illinois at Urbana-Champaign Roy J. Carver Biotechnology Center for DNA sequence library construction, using the NEBNext Enzymatic Methyl-seq (EM-seq™) kit (New England Biolabs, #E7120L), and whole genome sequencing on a Next-Generation sequencer (Illumina NovaSeq X).

value: skeletal muscle

tag: Sex

value: female

value: WT

value: normoxic, 44 weeks aged

tag: age

value: 44 weeks


title: Control MxCre - Spleen - CD11b+ - Rep1

description: RNA-seq of spleen CD11b+ cells from control MxCre mouse - Rep1

value: Spleen


title: H37Rv_AMK+H2O@4xMIC+16h_b2_1

description: Library name: Rv_4X_AMK_MIC_T16_H2O_Set_A_R2_S12


title: Mouse 19, AAV-Cas9-miR-124-g4, Cas9 positive nuclei

description:
Library name: Sample 10
column name in raw_counts_Hapos.csv : X19_g4_Hapos


title: Control Ptpn11D61Y/+  - BM - CD11b+ - Rep1

description: RNA-seq of bone marrow CD11b+ cells from control Ptpn11D61Y/+ mouse - Rep1


title: NC209, normoxic (6-months post-hypercapnia) control female

description:
Library name: NC209
Processed data includes bed files of estimated methylation levels with columns as: chromosome, position of CpG (+), position CpG (-), methylation level, number of methylated reads, number of unmethylated reads


title: NC208, normoxic (6-months post-hypercapnia) control female

description:
Library name: NC208
Processed data includes bed files of estimated methylation levels with columns as: chromosome, position of CpG (+), position CpG (-), methylation level, number of methylated reads, number of unmethylated reads


title: Control MxCre - BM - LSK - Rep1

description: RNA-seq of bone marrow LSK cells from control MxCre mouse - Rep1

value: MxCre


title: Mouse 17, AAV-Cas9-miR-124-empty, Cas9 negative nuclei

description:
Library name: Sample 15
column name in raw_counts_HAneg.csv : X17_empty_HAneg

value: Motor cortex

value: Cas9-HA-tag negative


title: Mouse 18, AAV-Cas9-miR-124-g4, Cas9 positive nuclei

description:
Library name: Sample 9
column name in raw_counts_Hapos.csv : X18_g4_Hapos

value: Cas9-HA-tag positive


title: 6F_CBL_3_12448_F

first: Bic

last: MSKCC

state: NY

address: 1275 York Ave.

institute: Memorial SLoan-Kettering Cancer Center

data_processing:
CutAdapt version cutadapt-1.6 was used to trim and filter reads. Adapters were trimmed with minimum overlap of 10 bases and reads of less than half original read length were filtered out.
STAR version STAR-STAR_2.5.0a was run using the 2-pass method. First pass was run with the following parameters: --outFilterIntronMotifs RemoveNoncanonicalUnannotated --outSAMattributes All --outSAMunmapped Within. Genome database was then generated using the minimum read length of half desired read length and second pass was run against the new genome file with the same parameters as pass 1.
Expression count matrix was computed using HTSeq version HTSeq-0.5.3. Parameters set were: -m intersection-strict -s reverse -t exon
Assembly: mm10 + human genes: CBL,KRAS,PTPN11,RIT1
Supplementary files format and content: tab delimited file containing raw counts for each sample

source_name: primary cell line

growth_protocol: Mouse primary CSF-1 dependent macrophages are immortalized with the SV-U19-5 retrovirus. They were cultured in RPMI 1640 medium with Glutamax (Gibco), 10 % heat-inactivated fetal bovine serum (FBS, EMD Millipore) and 100 ng/mL recombinant CSF-1. Growth medium was renewed every second day. When confluency reached 80%, cells were passaged by cell scraping and plated at 5 X 104 cells/ cm2 in tissue culture treated plates. For collection for RNA sequencing, cells were plated one day prior at 5 X 104 cells/ cm2 in medium containing 10 ng/mL CSF-1 for lines expressing wild-type (WT) and mutant CBL, RIT1 and KRAS proteins and 100 ng/mL CSF-1 for lines expressing WT and mutant PTPN11

extract_protocol:
Total RNA was extracted using RNeasy Mini kit (Qiagen), following the manufacturer’s instructions
PolyA selection and TruSeq library preparation according to instructions provided by Illumina (TruSeq Stranded mRNA LT Kit, Illumina), with 8 cycles of PCR.

tag: cell line

value: primary cell line

value: macrophages

value: CBL WT


title: NC207, normoxic (6-months post-hypercapnia) control female

description:
Library name: NC207
Processed data includes bed files of estimated methylation levels with columns as: chromosome, position of CpG (+), position CpG (-), methylation level, number of methylated reads, number of unmethylated reads


title: Mouse 17, AAV-Cas9-miR-124-g4, Cas9 positive nuclei

description:
Library name: Sample 8
column name in raw_counts_Hapos.csv : X17_g4_Hapos


title: H37Rv + Empty Plasmid, Day 12, Culture H6

description: Library name: EmptyPlasmid_D12_H6_R2

data_processing:
Libraries were sequenced at the University of Washington Northwest Genomics Center with the Illumina NextSeq 500 High Output v2 kit (Illumina Inc., San Diego, CA). The sequencing run generated an average of 75 million base-pair paired-end raw read counts per library.
Read alignment and gene expression estimation was carried out using a custom processing pipeline in R that harnesses the Bowtie 2 utilities, which is publicly accessible at https://github.com/robertdouglasmorrison/DuffyTools, and https://github.com/robertdouglasmorrison/DuffyNGS.
TPM reads were calculated and used as the expression value reported in the second processed data file.
Assembly: Accession # AL123456.3 | Mycobacterium tuberculosis H37Rv complete genome
Supplementary files format and content: FrontiersInTb_Hypoxia_GEO_processed_reads.txt is a matrix of aligned read values representing the expression levels of each gene for each sample. Each row represents a different sample, and each column represents the expression of each gene. The first 5 columns give the metadata information associated with each sample.
Supplementary files format and content: FrontiersInTb_Hypoxia_GEO_processed_tpm.txt is a matrix of TPM values representing the expression levels of each gene for each sample. Each row represents a different sample, and each column represents the expression of each gene. The first 5 columns give the metadata information associated with each sample.

growth_protocol: Wildtype H37Rv (ATCC 27294) transformed with a control anhydrotetracycline (ATc)-inducible expression vector (H37Rv::pEXCF-empty, which does not induce recombinant gene expression) were cultured under in Middlebrook 7H9 with the oleic acid, bovine albumin, dextrose, and catalase (OADC) supplement (Difco) and with 0.05% Tween 80 at 37°C. H37Rv::pEXCF-empty was grown with the addition of 50 µg/mL hygromycin B to maintain the plasmid.

extract_protocol:
Bacterial pellets suspended in TRIzol were transferred to a tube containing Lysing Matrix B (QBiogene) and vigorously shaken in a homogenizer. The mixture was centrifuged, and RNA was extracted from the supernatant with chloroform, followed by RNA precipitation by isopropanol and high-salt solution (0.8 M Na citrate, 1.2 M NaCl). Total RNA was purified using a RNeasy kit following the manufacturer’s recommendations (Qiagen). rRNA was depleted from samples using the RiboZero rRNA removal (bacteria) magnetic kit (Illumina Inc., San Diego, CA).
Illumina sequencing libraries were prepared using the NEBNext Ultra RNA Library Prep kit for Illumina (New England Biolabs, Ipswich, MA) according to the manufacturer’s instructions, and using the AMPure XP reagent (Agencourt Bioscience Corporation, Beverly, MA) for size selection and cleanup of adaptor-ligated DNA. We used the NEBNext Multiplex Oligos for Illumina (Dual Index Primers Set 1) to barcode the libraries to enable sample multiplexing per sequencing run. The prepared libraries were quantified using the Kapa quantitative PCR (qPCR) quantification kit.

treatment_protocol: 100ng/mL ATc was added one day prior to onset of hypoxia. Strains were cultured in oxygen-limited conditions (1% aerobic O2 tension) for 7 days, followed by reaeration on day 7-12, initiated by transferring cultures into continuously rolled bottles with 5:1 head space ratio. Bacterial survival and growth were enumerated by plating for CFU on Middlebrook 7H10 solid media plates.

value: Bacteria

value: Empty Plasmid

value: Reaeration

value: Day 12


title: 6F_CBL_2_12448_F


title: NC206, normoxic (6-months post-hypercapnia) control female

description:
Library name: NC206
Processed data includes bed files of estimated methylation levels with columns as: chromosome, position of CpG (+), position CpG (-), methylation level, number of methylated reads, number of unmethylated reads

value: skeletal muscle


title: H37Rv + Empty Plasmid, Day 12, Culture H5

description: Library name: EmptyPlasmid_D12_H5_R1


title: Mouse 23, AAV-Cas9-miR-124-empty, Cas9 positive nuclei

description:
Library name: Sample 7
column name in raw_counts_Hapos.csv : X24_empty_Hapos


title: Mouse 22, AAV-Cas9-miR-124-empty, Cas9 positive nuclei

description:
Library name: Sample 6
column name in raw_counts_Hapos.csv : X23_empty_Hapos


title: NC205, normoxic (acute) control female

description:
Library name: NC205
Processed data includes bed files of estimated methylation levels with columns as: chromosome, position of CpG (+), position CpG (-), methylation level, number of methylated reads, number of unmethylated reads

value: female

value: normoxic, 20 weeks aged

value: 20 weeks


title: H37Rv + Empty Plasmid, Day 11, Culture TC6, Rep 3

description: Library name: EmptyPlasmid_D11_TC6_R3

value: Day 11


title: H37Rv + Empty Plasmid, Day 11, Culture TC6, Rep 1

description: Library name: EmptyPlasmid_D11_TC6_R1


title: NC204, normoxic (acute) control female

description:
Library name: NC204
Processed data includes bed files of estimated methylation levels with columns as: chromosome, position of CpG (+), position CpG (-), methylation level, number of methylated reads, number of unmethylated reads

value: WT


title: Mouse 20, AAV-Cas9-miR-124-g4, Cas9 positive nuclei

description:
Library name: Sample 11
column name in raw_counts_Hapos.csv : X20_g4_Hapos


title: 4G_KRAS_2

value: KRAS WT


title: H37Rv + Empty Plasmid, Day 11, Culture H7

description: Library name: EmptyPlasmid_D11_H7_R3


title: Mouse 21, AAV-Cas9-miR-124-empty, Cas9 positive nuclei

description:
Library name: Sample 5
column name in raw_counts_Hapos.csv : X22_empty_Hapos

value: Motor cortex


title: NC203, normoxic (acute) control female

description:
Library name: NC203
Processed data includes bed files of estimated methylation levels with columns as: chromosome, position of CpG (+), position CpG (-), methylation level, number of methylated reads, number of unmethylated reads


title: Control MxCre - BM - CD11b+ - Rep1

description: RNA-seq of bone marrow CD11b+ cells from control MxCre mouse - Rep1

value: Bonemarrow

value: MxCre


title: 4G_KRAS_1

value: primary cell line


title: NC202, normoxic (acute) control female

description:
Library name: NC202
Processed data includes bed files of estimated methylation levels with columns as: chromosome, position of CpG (+), position CpG (-), methylation level, number of methylated reads, number of unmethylated reads


title: Mouse 20, AAV-Cas9-miR-124-empty, Cas9 positive nuclei

description:
Library name: Sample 4
column name in raw_counts_Hapos.csv : X20_empty_Hapos

value: Cas9-HA-tag positive


title: H37Rv_AMK+H2O@4xMIC+16h_b1_1

description: Library name: Rv_4X_AMK_MIC_T16_H2O_Set_A_R1_S11

value: Wildtype

value: AMK+H2O, 4xMIC

value: 16 hours


title: Mouse 19, AAV-Cas9-miR-124-empty, Cas9 positive nuclei

description:
Library name: Sample 3
column name in raw_counts_Hapos.csv : X19_empty_Hapos


title: H37Rv + Empty Plasmid, Day 11, Culture H6

description: Library name: EmptyPlasmid_D11_H6_R2

value: Bacteria

value: Empty Plasmid

value: Reaeration


title: 30_R420Q_3

value: macrophages

value: R420Q WT


title: NC201, normoxic (acute) control female

description:
Library name: NC201
Processed data includes bed files of estimated methylation levels with columns as: chromosome, position of CpG (+), position CpG (-), methylation level, number of methylated reads, number of unmethylated reads

value: skeletal muscle

value: female

value: normoxic, 20 weeks aged

value: 20 weeks


title: 6F_CBL_1_12448_F

value: CBL WT


title: H37Rv + Empty Plasmid, Day 11, Culture H5

description: Library name: EmptyPlasmid_D11_H5_R1

value: Day 11


title: 4G_KRAS_3

value: KRAS WT


title: Mouse 18, AAV-Cas9-miR-124-empty, Cas9 positive nuclei

description:
Library name: Sample 2
column name in raw_counts_Hapos.csv : X18_empty_Hapos

value: Motor cortex


title: 30_R420Q_2

value: primary cell line


title: Mouse 17, AAV-Cas9-miR-124-empty, Cas9 positive nuclei

description:
Library name: Sample 1
column name in raw_counts_Hapos.csv : X17_empty_Hapos

value: Cas9-HA-tag positive


title: H37Rv + Empty Plasmid, Day 10, Culture TC6, Rep 3

description: Library name: EmptyPlasmid_D10_TC6_R3

value: Day 10


title: NC110, normoxic (6-months post-hypercapnia) control male

description:
Library name: NC110
Processed data includes bed files of estimated methylation levels with columns as: chromosome, position of CpG (+), position CpG (-), methylation level, number of methylated reads, number of unmethylated reads

value: male

value: WT

value: normoxic, 44 weeks aged

value: 44 weeks


title: H37Rv + Empty Plasmid, Day 10, Culture TC6, Rep 1

description: Library name: EmptyPlasmid_D10_TC6_R1

value: Bacteria

value: Empty Plasmid

value: Reaeration


title: NC108, normoxic (6-months post-hypercapnia) control male

description:
Library name: NC108
Processed data includes bed files of estimated methylation levels with columns as: chromosome, position of CpG (+), position CpG (-), methylation level, number of methylated reads, number of unmethylated reads

value: skeletal muscle


title: H37Rv + Empty Plasmid, Day 10, Culture H7

description: Library name: EmptyPlasmid_D10_H7_R3


title: 21_KRAS_A59G_1

value: macrophages


title: Treg_B16F10_control_04, RRBS

description: Treg cells sorted at day 15 post-engraftment from subcutaneous B16-F10 melanoma tumors implanted on 12-15 week-old male Black 6 mice

data_processing:
Basecalls performed using Illumina RTA2 software.
Indexed samples were demultiplexed to fastq files with bcl-convert v3.10.5.
Reads were  trimmed of 10 base pairs from the 5’ end with TrimGalore! v0.4.3 to remove primer and adapter sequences.
Sequence alignment to the GRCm38/mm10 reference genome and methylation extraction ignoring 1 base at the 3’ end (after reviewing the M-bias plots) were performed with Bismark v0.16.3.
Assembly: GRCm38/mm10
Supplementary files format and content: Bismark tab-delimited "coverage" files for cytosines in CpG context with the following columns: <chromosome> <start position> <end position> <methylation percentage> <count methylated> <count unmethylated>

extract_protocol:
Genomic DNA was extracted from FACSorted cells using the AllPrep DNA/RNA Micro Kit.
Genomic DNA was quantified with a Qubit 3.0 instrument. Genomic DNA was then digested with the restriction endonuclease MspI (New England BioLabs). Resulting fragments underwent size selection for fragments ~100-250-bp in length using SPRI beads (MagBio Genomics) and subsequent bisulfite conversion using the EZ DNA Methylation-Lightning Kit (Zymo Research) per the manufacturer’s protocol. Bisulfite conversion efficiency averaged 99.5% as estimated by the measured percent of unmethylated CpGs in λ-bacteriophage DNA (New England BioLabs N3013S) added at a 1:200 ratio to each sample. Libraries for Illumina-based sequencing were prepared with the Pico Methyl-Seq Library Prep Kit (Zymo Research) using Illumina TruSeq DNA methylation barcodes. Libraries were run on a High Sensitivity chip using an Agilent TapeStation 4200 to assess size distribution and overall quality of the amplified library. Fluorometric quantitation and TapeStation size distribution estimates permitted equimolar pooling, and six pooled libraries per run were sequenced on an Illumina NextSeq 500 instrument using the NextSeq 500/550 V2 High Output reagent kit (1 x 75 cycles).

value: B16 melanoma tumor

value: Treg


title: Treg_B16F10_KO_01, RRBS


title: 21_KRAS_A59G_2


title: H37Rv + Empty Plasmid, Day 10, Culture H5

description: Library name: EmptyPlasmid_D10_H5_R1


title: Treg_B16F10_control_03, RRBS


title: NC106, normoxic (6-months post-hypercapnia) control male

description:
Library name: NC106
Processed data includes bed files of estimated methylation levels with columns as: chromosome, position of CpG (+), position CpG (-), methylation level, number of methylated reads, number of unmethylated reads


title: 16E_PTPN11_T73I_3


title: H37Rv + Empty Plasmid, Day 9, Culture TC6, Rep 3

description: Library name: EmptyPlasmid_D9_TC6_R3

value: Day 9


title: 16E_PTPN11_T73I_2


title: NC105, normoxic (acute) control male

description:
Library name: NC105
Processed data includes bed files of estimated methylation levels with columns as: chromosome, position of CpG (+), position CpG (-), methylation level, number of methylated reads, number of unmethylated reads

value: normoxic, 20 weeks aged

value: 20 weeks


title: Treg_B16F10_control_02, RRBS


title: NC104, normoxic (acute) control male

description:
Library name: NC104
Processed data includes bed files of estimated methylation levels with columns as: chromosome, position of CpG (+), position CpG (-), methylation level, number of methylated reads, number of unmethylated reads


title: 30_R420Q_1

value: primary cell line

value: R420Q WT


title: 16E_PTPN11_T73I_1


title: Treg_B16F10_control_01, RRBS


title: NC109, normoxic (6-months post-hypercapnia) control male

description:
Library name: NC109
Processed data includes bed files of estimated methylation levels with columns as: chromosome, position of CpG (+), position CpG (-), methylation level, number of methylated reads, number of unmethylated reads


title: NC103, normoxic (acute) control male

description:
Library name: NC103
Processed data includes bed files of estimated methylation levels with columns as: chromosome, position of CpG (+), position CpG (-), methylation level, number of methylated reads, number of unmethylated reads


title: Treg_B16F10_KO_02, RRBS


title: 21_KRAS_A59G_3


title: H37Rv + Empty Plasmid, Day 9, Culture TC6, Rep 1

description: Library name: EmptyPlasmid_D9_TC6_R1


title: SplenocyteTreg_homeostasis_KO_03, RRBS

description: Splenic Treg cells from 12-15 week-old male Black 6 mice

value: spleen


title: NC102, normoxic (acute) control male

description:
Library name: NC102
Processed data includes bed files of estimated methylation levels with columns as: chromosome, position of CpG (+), position CpG (-), methylation level, number of methylated reads, number of unmethylated reads

value: male


title: NC107, normoxic (6-months post-hypercapnia) control male

description:
Library name: NC107
Processed data includes bed files of estimated methylation levels with columns as: chromosome, position of CpG (+), position CpG (-), methylation level, number of methylated reads, number of unmethylated reads

value: WT


title: H37Rv + Empty Plasmid, Day 9, Culture H7

description: Library name: EmptyPlasmid_D9_H7_R3


title: 15E_PTPN11_3

value: PTPN11 WT


title: H37Rv + Empty Plasmid, Day 10, Culture H6

description: Library name: EmptyPlasmid_D10_H6_R2

value: Day 10


title: H37Rv + Empty Plasmid, Day 9, Culture H6

description: Library name: EmptyPlasmid_D9_H6_R2

value: Bacteria


title: SplenocyteTreg_homeostasis_KO_02, RRBS


title: H37Rv + Empty Plasmid, Day 9, Culture H5

description: Library name: EmptyPlasmid_D9_H5_R1

value: Empty Plasmid


title: NC101, normoxic (acute) control male

description:
Library name: NC101
Processed data includes bed files of estimated methylation levels with columns as: chromosome, position of CpG (+), position CpG (-), methylation level, number of methylated reads, number of unmethylated reads


title: 15E_PTPN11_1


title: SplenocyteTreg_homeostasis_KO_01, RRBS


title: HC210, 6-months post-hypercapnia female

description:
Library name: HC210
Processed data includes bed files of estimated methylation levels with columns as: chromosome, position of CpG (+), position CpG (-), methylation level, number of methylated reads, number of unmethylated reads

value: female

value: hypercapnia, 44 weeks aged

value: 44 weeks


title: 8H_CBL_C404Y_3

value: macrophages


title: H37Rv + Empty Plasmid, Day 8, Culture TC6, Rep3

description: Library name: EmptyPlasmid_D8_TC6_R3

value: Reaeration

value: Day 8


title: SplenocyteTreg_homeostasis_control_03, RRBS

value: Treg


title: HC209, 6-months post-hypercapnia female

description:
Library name: HC209
Processed data includes bed files of estimated methylation levels with columns as: chromosome, position of CpG (+), position CpG (-), methylation level, number of methylated reads, number of unmethylated reads

value: skeletal muscle


title: 8H_CBL_C404Y_2

value: primary cell line


title: SplenocyteTreg_homeostasis_control_02, RRBS


title: H37Rv + Empty Plasmid, Day 8, Culture TC6, Rep 1

description: Library name: EmptyPlasmid_D8_TC6_R1


title: HC208, 6-months post-hypercapnia female

description:
Library name: HC208
Processed data includes bed files of estimated methylation levels with columns as: chromosome, position of CpG (+), position CpG (-), methylation level, number of methylated reads, number of unmethylated reads


title: H37Rv + Empty Plasmid, Day 8, Culture H7

description: Library name: EmptyPlasmid_D8_H7_R3


title: SplenocyteTreg_homeostasis_control_01, RRBS


title: 8H_CBL_C404Y_1


title: 7G_CBL_C384Y_3


title: 15E_PTPN11_2


title: H37Rv + Empty Plasmid, Day 8, Culture H6

description: Library name: EmptyPlasmid_D8_H6_R2


title: HC206, 6-months post-hypercapnia female

description:
Library name: HC206
Processed data includes bed files of estimated methylation levels with columns as: chromosome, position of CpG (+), position CpG (-), methylation level, number of methylated reads, number of unmethylated reads


title: H37Rv + Empty Plasmid, Day 8, Culture H5

description: Library name: EmptyPlasmid_D8_H5_R1


title: 7G_CBL_C384Y_2


title: HC207, 6-months post-hypercapnia female

description:
Library name: HC207
Processed data includes bed files of estimated methylation levels with columns as: chromosome, position of CpG (+), position CpG (-), methylation level, number of methylated reads, number of unmethylated reads


title: Day15_Treg_B16F10_KO_03, RNA-seq

data_processing:
Basecalls performed using Illumina RTA2 software.
bcl2fastq v2.20 was used to convert bcl files to fastq files (default parameters).
FASTQ files were processed using the nf-core/RNA-seq pipeline1 v3.9 implemented in Nextflow v23.04.2 with Northwestern University Quest HPC (Genomic Nodes) configuration
csv file including raw counts values for each sample was generated by nf-core/RNA-seq pipeline1 v3.9 (--aligner star_salmon)
Assembly: GRCm38/mm10
Supplementary files format and content: csv file including raw counts values for each sample

value: B16 melanoma tumor


title: Day15_Treg_B16F10_KO_02, RNA-seq


title: H37Rv + Empty Plasmid, Day 7, Culture TC6, Rep 3

description: Library name: EmptyPlasmid_D7_TC6_R3

value: Hypoxia

value: Day 7


title: Day15_Treg_B16F10_KO_01, RNA-seq


title: 7G_CBL_C384Y_1


title: HC205, acute hypercapnia female

description:
Library name: HC205
Processed data includes bed files of estimated methylation levels with columns as: chromosome, position of CpG (+), position CpG (-), methylation level, number of methylated reads, number of unmethylated reads

value: WT

value: hypercapnia, 20 weeks aged

value: 20 weeks


title: Day15_Treg_B16F10_control_05, RNA-seq


title: HC204, acute hypercapnia female

description:
Library name: HC204
Processed data includes bed files of estimated methylation levels with columns as: chromosome, position of CpG (+), position CpG (-), methylation level, number of methylated reads, number of unmethylated reads


title: 6F_CBL_3_12448_D

value: CBL WT


title: HC203, acute hypercapnia female

description:
Library name: HC203
Processed data includes bed files of estimated methylation levels with columns as: chromosome, position of CpG (+), position CpG (-), methylation level, number of methylated reads, number of unmethylated reads


title: H37Rv + Empty Plasmid, Day 7, Culture H7

description: Library name: EmptyPlasmid_D7_H7_R3

value: Bacteria

value: Empty Plasmid


title: H37Rv + Empty Plasmid, Day 7, Culture TC6, Rep 1

description: Library name: EmptyPlasmid_D7_TC6_R1


title: 6F_CBL_2_12448_D


title: Day15_Treg_B16F10_control_04, RNA-seq

description: Treg cells sorted at day 15 post-engraftment from subcutaneous B16-F10 melanoma tumors implanted on 12-15 week-old male Black 6 mice


title: H37Rv + Empty Plasmid, Day 7, Culture H5

description: Library name: EmptyPlasmid_D7_H5_R1


title: H37Rv + Empty Plasmid, Day 7, Culture H6

description: Library name: EmptyPlasmid_D7_H6_R2


title: 6F_CBL_1_12448_D


title: Day15_Treg_B16F10_control_03, RNA-seq


title: HC201, acute hypercapnia female

description:
Library name: HC201
Processed data includes bed files of estimated methylation levels with columns as: chromosome, position of CpG (+), position CpG (-), methylation level, number of methylated reads, number of unmethylated reads

value: female


title: HC202, acute hypercapnia female

description:
Library name: HC202
Processed data includes bed files of estimated methylation levels with columns as: chromosome, position of CpG (+), position CpG (-), methylation level, number of methylated reads, number of unmethylated reads


title: Day15_Treg_B16F10_control_02, RNA-seq


title: H37Rv + Empty Plasmid, Day 4, Culture TC6

description: Library name: EmptyPlasmid_D4_TC6_R1

value: Day 4


title: Day15_Treg_B16F10_control_01, RNA-seq


title: HC110, 6-months post-hypercapnia male

description:
Library name: HC110
Processed data includes bed files of estimated methylation levels with columns as: chromosome, position of CpG (+), position CpG (-), methylation level, number of methylated reads, number of unmethylated reads

value: male

value: hypercapnia, 44 weeks aged

value: 44 weeks


title: SplenocyteTreg_homeostasis_KO_04, RNA-seq

value: spleen

value: Treg


title: 14E_RIT1_M107V_3

value: primary cell line

value: macrophages


title: HC109, 6-months post-hypercapnia male

description:
Library name: HC109
Processed data includes bed files of estimated methylation levels with columns as: chromosome, position of CpG (+), position CpG (-), methylation level, number of methylated reads, number of unmethylated reads

value: skeletal muscle


title: H37Rv + Empty Plasmid, Day 4, Culture H7

description: Library name: EmptyPlasmid_D4_H7_R3

value: Hypoxia


title: 14E_RIT1_M107V_1


title: 14E_RIT1_M107V_2


title: HC108, 6-months post-hypercapnia male

description:
Library name: HC108
Processed data includes bed files of estimated methylation levels with columns as: chromosome, position of CpG (+), position CpG (-), methylation level, number of methylated reads, number of unmethylated reads

value: WT


title: 13E_RIT1_F99C_3


title: H37Rv + Empty Plasmid, Day 4, Culture H6

description: Library name: EmptyPlasmid_D4_H6_R2


title: H37Rv + Empty Plasmid, Day 4, Culture H5

description: Library name: EmptyPlasmid_D4_H5_R1


title: SplenocyteTreg_homeostasis_KO_02, RNA-seq

description: Splenic Treg cells from 12-15 week-old male Black 6 mice


title: H37Rv + Empty Plasmid, Day 2, Culture TC6

description: Library name: EmptyPlasmid_D2_TC6_R1

value: Day 2


title: SplenocyteTreg_homeostasis_KO_01, RNA-seq


title: HC107, 6-months post-hypercapnia male

description:
Library name: HC107
Processed data includes bed files of estimated methylation levels with columns as: chromosome, position of CpG (+), position CpG (-), methylation level, number of methylated reads, number of unmethylated reads


title: 13E_RIT1_F99C_1


title: HC105, acute hypercapnia male

description:
Library name: HC105
Processed data includes bed files of estimated methylation levels with columns as: chromosome, position of CpG (+), position CpG (-), methylation level, number of methylated reads, number of unmethylated reads

value: hypercapnia, 20 weeks aged

value: 20 weeks


title: 12E_RIT1_3

value: RIT1 WT


title: HC104, acute hypercapnia male

description:
Library name: HC104
Processed data includes bed files of estimated methylation levels with columns as: chromosome, position of CpG (+), position CpG (-), methylation level, number of methylated reads, number of unmethylated reads


title: SplenocyteTreg_homeostasis_control_04, RNA-seq


title: HC103, acute hypercapnia male

description:
Library name: HC103
Processed data includes bed files of estimated methylation levels with columns as: chromosome, position of CpG (+), position CpG (-), methylation level, number of methylated reads, number of unmethylated reads


title: 13E_RIT1_F99C_2


title: H37Rv + Empty Plasmid, Day 2, Culture H6

description: Library name: EmptyPlasmid_D2_H6_R2

value: Bacteria

value: Empty Plasmid


title: 12E_RIT1_2


title: SplenocyteTreg_homeostasis_control_02, RNA-seq


title: 12E_RIT1_1


title: HC102, acute hypercapnia male

description:
Library name: HC102
Processed data includes bed files of estimated methylation levels with columns as: chromosome, position of CpG (+), position CpG (-), methylation level, number of methylated reads, number of unmethylated reads


title: SplenocyteTreg_homeostasis_KO_03, RNA-seq


title: H37Rv + Empty Plasmid, Day 0, Culture TC6

description: Library name: EmptyPlasmid_D0_TC6_R1

value: Control

value: Day 0


title: SplenocyteTreg_homeostasis_control_01, RNA-seq


title: H37Rv + Empty Plasmid, Day 2, Culture H5

description: Library name: EmptyPlasmid_D2_H5_R1


title: H37Rv + Empty Plasmid, Day 0, Culture H7

description: Library name: EmptyPlasmid_D0_H7_R3


title: 11H_CBL_I383M_3


title: HC101, acute hypercapnia male

description:
Library name: HC101
Processed data includes bed files of estimated methylation levels with columns as: chromosome, position of CpG (+), position CpG (-), methylation level, number of methylated reads, number of unmethylated reads

value: male


title: 11H_CBL_I383M_2


title: Input (ChIP-seq)

first: Serdar

last: Bulun

state: IL

address: 250 East Superior Street, Suite 03-2303

department: Department of Obstetrics and Gynecology

institute: Feinberg School of Medicine at Northwestern University

data_processing:
Trim adaptors with trimmomatic v0.39
Aligned with bowtie2 v2.2.71
Remove duplicates with Picard v2.21.4
Peak calling with MACS v2.2.71
Assembly: mm10
Supplementary files format and content: narrowPeak files for each sample

source_name: Primary Cells

extract_protocol:
Cells were fixed in formaldehyde for 15 minutes at room temperature. Processing and library preparation was performed by Active Motif Services. 30ug of chromatin was used with 4ug of ERα antibody [Millipore Sigma, #06–935].
Illumina DNA Prep kit was used and performed by Active Motif Services

value: Primary Cells

value: Skeletal Muscle Fibroblasts

value: Aromhum mice

tag: chip antibody

value: Input sample

value: 1 hr


title: A205, aged female

description:
Library name: A205
Processed data includes bed files of estimated methylation levels with columns as: chromosome, position of CpG (+), position CpG (-), methylation level, number of methylated reads, number of unmethylated reads

source_name: skeletal muscle

value: skeletal muscle

value: female

value: 72 weeks aged

value: 72 weeks


title: 11H_CBL_I383M_1

value: primary cell line

value: macrophages


title: H37Rv + Empty Plasmid, Day 0, Culture H5

description: Library name: EmptyPlasmid_D0_H5_R1


title: A204, aged female

description:
Library name: A204
Processed data includes bed files of estimated methylation levels with columns as: chromosome, position of CpG (+), position CpG (-), methylation level, number of methylated reads, number of unmethylated reads

value: WT


title: H37Rv + Empty Plasmid, Day 0, Culture H6

description: Library name: EmptyPlasmid_D0_H6_R2

value: Bacteria


title: F3 (ChIP-seq)

value: ERα ChIP antibody (Millipore Sigma #06-935)

value: Fulvestrant (100nM)


title: H37Rv + Empty Plasmid, Day 2, Culture H7

description: Library name: EmptyPlasmid_D2_H7_R3

value: Empty Plasmid

value: Hypoxia

value: Day 2


title: 10H_CBL_C416S_3


title: SplenocyteTreg_homeostasis_control_03, RNA-seq

value: spleen

value: Treg


title: F2 (ChIP-seq)

value: Primary Cells

value: Skeletal Muscle Fibroblasts

value: Aromhum mice


title: A203, aged female

description:
Library name: A203
Processed data includes bed files of estimated methylation levels with columns as: chromosome, position of CpG (+), position CpG (-), methylation level, number of methylated reads, number of unmethylated reads

value: skeletal muscle

value: female


title: F1 (ChIP-seq)

value: 1 hr


title: HN878_Stearic Acid@Unknown+1344h_b13_1

description: Library name: Stearic_acid_42_S17

data_processing:
Libraries were sequenced at the University of Washington Northwest Genomics Center with the Illumina NextSeq 500 High Output v2 kit (Illumina Inc., San Diego, CA). The sequencing run generated an average of 75 million base-pair paired-end raw read counts per library.
Read alignment and gene expression estimation was carried out using a custom processing pipeline in R that harnesses the Bowtie 2 utilities, which is publicly accessible at https://github.com/robertdouglasmorrison/DuffyTools, and https://github.com/robertdouglasmorrison/DuffyNGS.
TPM (transcripts per million) reads were calculated and used as the expression value reported in the second processed data file.
Assembly: Accession # AL123456.3 | Mycobacterium tuberculosis H37Rv complete genome
Supplementary files format and content: FrontiersInTb_INDIGO7Mark_GEO_processed_reads.txt is a matrix of aligned read values representing the expression levels of each gene for each sample. Each row represents a different sample, and each column represents the expression of each gene. The first 6 columns give the metadata information associated with each sample.
Supplementary files format and content: FrontiersInTb_INDIGO7Mark_GEO_processed_tpm.txt is a matrix of TPM values representing the expression levels of each gene for each sample. Each row represents a different sample, and each column represents the expression of each gene. The first 6 columns give the metadata information associated with each sample.

organism: Mycobacterium tuberculosis

value: Wildtype

value: Stearic acid

value: 1344 hours


title: 10H_CBL_C416S_2

value: primary cell line

value: macrophages


title: A202, aged female

description:
Library name: A202
Processed data includes bed files of estimated methylation levels with columns as: chromosome, position of CpG (+), position CpG (-), methylation level, number of methylated reads, number of unmethylated reads

value: WT

value: 72 weeks aged

value: 72 weeks


title: HN878_Stearic Acid@Unknown+672h_b13_1

description: Library name: Stearic_acid_28_S16

value: Bacteria

value: 672 hours


title: EF3 (ChIP-seq)

value: ERα ChIP antibody (Millipore Sigma #06-935)

value: Estrogen (10nM) + Fulvestrant (100nM)


title: HN878_Stearic Acid@Unknown+336h_b13_1

description: Library name: Stearic_acid_14_S30

value: 336 hours


title: EF2 (ChIP-seq)

value: Primary Cells

value: Skeletal Muscle Fibroblasts

value: Aromhum mice


title: Zbtb20-cKO cells, IL-1β treatment_3

city: Xi'an

first: Xue

last: Hao

address: Shanghua Road

institute: Xi'an Honghui Hospital

data_processing:
Hisat2 (v2.0.5)
Paired-end 150-bp clean reads were aligned to the Mus Musculus (GRCm38/mm10) reference genome using Hisat2 (v2.0.5).
The differentially expressed genes (DEGs) were identified using the DESeq2 R package (1.20.0) with padj < 0.05.
Assembly: GRCm38/mm10
Supplementary files format and content: excel file includes count values for each sample

source_name: cartilage

growth_protocol: To isolated primary chondrocytes, rib cartilage was dissected from P0-P3 wildtype or Zbtb20f/f pups and digested with collagenase D (Roche) solution as described previously. The purified primary chondrocytes were resuspended with low-glucose DMEM (Gibco) supplemented with 10% fetal bovine serum (Gibco), 50 U/mL penicillin and 0.05 mg/mL streptomycin as a monolayer under sterile conditions at 37 °C under 5% CO2. Only the first passage cells were used for experiments.

extract_protocol:
The chondrocytes treated by 1ng/mL IL-1β or not were harvested and lysed in TRIzol reagent (Invitrogen). The purified mRNA was quantified and qualified using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
cDNA library was prepared using NEBNext® Ultra™ RNA Library Prep Kit for Illumina®

treatment_protocol: The chondrocytes were treated with 1ng/mL recombinant murine IL-1β (211-11B; PEPROTECH) for 48h to induce in vitro inflammation response.

value: cartilage

value: primary chondrocytes

value: IL-1Beta treatment


title: 10H_CBL_C416S_1


title: A105, aged male

description:
Library name: A105
Processed data includes bed files of estimated methylation levels with columns as: chromosome, position of CpG (+), position CpG (-), methylation level, number of methylated reads, number of unmethylated reads

value: skeletal muscle

value: male


title: HN878_Stearic Acid@Unknown+0h_b13_1

description: Library name: Stearic_acid_0_S29

source_name: Bacteria

value: Wildtype

value: Stearic acid

value: 0 hours


title: EF1 (ChIP-seq)

value: 1 hr


title: Zbtb20-cKO cells, IL-1β treatment_2


title: E3 (ChIP-seq)

value: Estrogen (10nM)


title: A104, aged male

description:
Library name: A104
Processed data includes bed files of estimated methylation levels with columns as: chromosome, position of CpG (+), position CpG (-), methylation level, number of methylated reads, number of unmethylated reads

value: WT

value: 72 weeks aged

value: 72 weeks


title: A103, aged male

description:
Library name: A103
Processed data includes bed files of estimated methylation levels with columns as: chromosome, position of CpG (+), position CpG (-), methylation level, number of methylated reads, number of unmethylated reads


title: Zbtb20-cKO cells, IL-1β treatment_1


title: HN878_Thp1Cells@Unknown+-1h_b13_2

description: Library name: KA_3_S13

value: Bacteria

value: THP1 cells

value: Unknown


title: E2 (ChIP-seq)

value: Primary Cells

value: Skeletal Muscle Fibroblasts

value: Aromhum mice

value: ERα ChIP antibody (Millipore Sigma #06-935)


title: Zbtb20-cKO cells, no treatment_3

value: cartilage

value: primary chondrocytes

value: no treatment


title: A102, aged male

description:
Library name: A102
Processed data includes bed files of estimated methylation levels with columns as: chromosome, position of CpG (+), position CpG (-), methylation level, number of methylated reads, number of unmethylated reads

value: skeletal muscle

value: male


title: E1 (ChIP-seq)

value: 1 hr


title: HN878_IrradiatedMimic@Unknown+1344h_b13_1

description: Library name: iMTB_42_S20

value: Wildtype

value: Irradiated Mtb

value: 1344 hours


title: Zbtb20-cKO cells, no treatment_1


title: V3 (ChIP-seq)

value: Veh (Ethanol, DMSO)


title: A101, aged male

description:
Library name: A101
Processed data includes bed files of estimated methylation levels with columns as: chromosome, position of CpG (+), position CpG (-), methylation level, number of methylated reads, number of unmethylated reads

value: WT

value: 72 weeks aged

value: 72 weeks


title: HC106, 6-months post-hypercapnia male

description:
Library name: HC106
Processed data includes bed files of estimated methylation levels with columns as: chromosome, position of CpG (+), position CpG (-), methylation level, number of methylated reads, number of unmethylated reads

value: hypercapnia, 44 weeks aged

value: 44 weeks


title: HN878_IrradiatedMimic@Unknown+0h_b13_1

description: Library name: iMTB_0_S31

value: Bacteria

value: 0 hours


title: Zbtb20-cKO cells, no treatment_2

value: cartilage


title: Bone marrow derived dendritic cells, Latilactobacillus sakei Wikim0185 (cell to bacteria ratio 1:5) for 6 hours,rep3

city: Gwangju

first: Sang-Pil

last: Choi

address: 86, Kimchi-ro, Nam-gu

institute: World Institution of Kimchi

description:
Library name: BMDC_Wikim0185_rep3
SRR32609701

data_processing:
Trimmomatic v0.38 was used to remove adapter sequences and trim bases with poor base quality.
The cleaned reads were aligned to the Mus musculus (mm10) using HISAT v2.1.0
The reference genome sequence and gene annotation data were downloaded from NCBI Genome assembly and NCBI RefSeq database respectively. Aligned data (SAM file format) were sorted and indexed using SAMtools v 1.9.
the transcripts were assembled and quantified using StringTie v2.1.3b
Gene-level and Transcript-level quantification were calculated as raw read count, FPKM (Fragments Per Kilobase of transcript per Million mapped reads) and TPM (Transcripts Per Million).
Assembly: mm10
Supplementary files format and content: text file includes raw counts for each Sample
Supplementary files format and content: text files include FPKM values for each Sample

source_name: Bone marrow

growth_protocol: the femora and tibiae of 8-week-old female BALB/c mice were isolated, rinsed in PBS, and crushed with a mortar to release BM cells. BM cells (2 × 10⁶) were seeded into petri dishes containing 10 mL of complete RPMI-1640 medium supplemented with 10% (v/v) fetal bovine serum, 100 U/mL penicillin, 100 µg/mL streptomycin, and 50 µM β-mercaptoethanol (Gibco Thermo Fisher Scientific, MA, USA), in the presence of 20 ng/mL murine granulocyte-macrophage colony-stimulating factor (GM-CSF; PeproTech, NJ, USA). On day 3, 10 mL of fresh complete RPMI-1640 containing 20 ng/mL murine GM-CSF was added to the culture. On day 6, 10 mL of the medium was replaced with fresh complete RPMI-1640 containing 20 ng/mL murine GM-CSF. On day 8, BMDCs were collected

extract_protocol:
Total RNA was purified from BMDCs using Trizol reagent (Thermo Fisher Scientific, USA) according to the manufacturer’s instructions.
The RNA isolated from each sample was used to construct sequencing libraries with the SMARTer Universal Low Input RNA Kit for Sequencing, following the manufacturer's protocol.

treatment_protocol: BMDCs co-cultured with PBS or Wikim0185 (cell to bacteria ratio, 1:5) for 6 h

value: Bone marrow

value: BMDCs

value: Dendritic cells

value: BMDC differentiation and Wikim0185 treatement


title: A201, aged female

description:
Library name: A201
Processed data includes bed files of estimated methylation levels with columns as: chromosome, position of CpG (+), position CpG (-), methylation level, number of methylated reads, number of unmethylated reads

value: skeletal muscle

value: female


title: V2 (ChIP-seq)

value: Primary Cells

value: Skeletal Muscle Fibroblasts

value: Aromhum mice

value: ERα ChIP antibody (Millipore Sigma #06-935)

value: 1 hr


title: Bone marrow derived dendritic cells, Latilactobacillus sakei Wikim0185 (cell to bacteria ratio 1:5) for 6 hours, rep2

description:
Library name: BMDC_Wikim0185_rep2
SRR32609700

value: WT


title: Bone marrow derived dendritic cells, Latilactobacillus sakei Wikim0185 (cell to bacteria ratio 1:5) for 6 hours, rep1

description:
Library name: BMDC_Wikim0185_rep1
SRR32609699


title: control cells, IL-1β treatment_2

value: primary chondrocytes

value: control

value: IL-1Beta treatment


title: V1 (ChIP-seq)

value: Veh (Ethanol, DMSO)


title: HN878_Untreated@0+-1h_b13_1

description: Library name: HN878_R1_1Probe

extract_protocol:
Bacterial pellets suspended in TRIzol were transferred to a tube containing Lysing Matrix B (QBiogene) and vigorously shaken in a homogenizer. The mixture was centrifuged, and RNA was extracted from the supernatant with chloroform, followed by RNA precipitation by isopropanol and high-salt solution (0.8 M Na citrate, 1.2 M NaCl). Total RNA was purified using a RNeasy kit following the manufacturer’s recommendations (Qiagen). rRNA was depleted from samples using a custom-designed set of biotinylated oligonucleotides based on the method described in PMID: 32317317.
Illumina sequencing libraries were prepared using the NEBNext Ultra II RNA Library Prep kit for Illumina (New England Biolabs, Ipswich, MA) according to the manufacturer’s instructions, and using the AMPure XP reagent (Agencourt Bioscience Corporation, Beverly, MA) for size selection and cleanup of adaptor-ligated DNA. We used the NEBNext Multiplex Oligos for Illumina (Dual Index Primers Set 1) to barcode the libraries to enable sample multiplexing per sequencing run. The prepared libraries were quantified using the Kapa quantitative PCR (qPCR) quantification kit.

value: Bacteria

value: Wildtype

value: Untreated

value: 0 hours


title: HN878_Untreated@0+-1h_b13_2

description: Library name: HN878_R2_1Probe


title: SRC_3KO_GFP_P2_S68

city: Houston

first: Prashi

last: Jain

state: TX

address: 1 Baylor Plaza

department: Molecular and Cellular Biology

institute: Baylor college of Medicine

data_processing:
The data quality was assessed using FastQC and low quality basepairs were removed using TrimGalore.
After trimming samples were aligned to mm10 using STAR
Features were quantified using featureCounts and the Gencode gene model
Differential gene expression was inferred after RUVSeq normalization using EdgeR; significance was achieved for fold change exceeding 1.5x and FDR-adjusted q-value<0.05
Assembly: mm10
Supplementary files format and content: Gene expression as read counts for all samples.

source_name: Tregs GFP+

extract_protocol:
Tregs were isolated from the spleens of SRC-3KO and WT animals and sorted for GFP. Total RNA was isolated from GFP+ Tregs using Qiagen micro RNAesy plus kit. Quality control of isolated RNA samples was checked using Agilent Bioanalyzer. Takera SMART-Seq v4 kit was used to generate the low throughput sequencing libraries.
RNA libraries were prepared using Takara Bio SMART-seq v4 plus by manufacturer recommended protocol.

value: Tregs

tag: tumor status

value: Tumor bearing