title: T46_RIF@0.03uM+1h_b10_3

description: Library name: T46x_RIF_D1_OTB.Transcriptomics_U_R3

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_INDIGO6OTB_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_INDIGO6OTB_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.

value: RIF, 0.03uM

value: 1 hour


title: Bone marrow derived dendritic cells, PBS for 6 hours, rep3

status: Public on Mar 19 2025

type: SRA

city: Gwangju

first: Sang-Pil

last: Choi

address: 86, Kimchi-ro, Nam-gu

country: South Korea

institute: World Institution of Kimchi

description:
Library name: BMDC_PBS_rep3
SRR32609698

library_source: transcriptomic

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

molecule: total RNA

organism: Mus musculus

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

tag: tissue

value: Bone marrow

tag: cell line

value: BMDCs

tag: cell type

value: Dendritic cells

tag: genotype

value: WT

tag: treatment

value: BMDC differentiation and PBS treatement

tag: batch


title: control cells, IL-1β treatment_1

city: Xi'an

first: Xue

last: Hao

address: Shanghua Road

country: China

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

molecule: polyA RNA

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: control

value: IL-1Beta treatment


title: HN878_Thp1Cells@Unknown+-1h_b13_1

city: Seattle

first: Ethan

last: Bustad

state: WA

address: 1900 Ninth Ave.

department: CGIDR

country: USA

institute: Seattle Children's Research Institute

description: Library name: KA_2_S12

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

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.

tag: strain

value: Bacteria

value: Wildtype

value: THP1 cells

tag: time

value: Unknown


title: control cells, IL-1β treatment_3


title: SRC_3KO_GFP_P1_S67

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: condition

tag: tumor status

value: Tumor bearing


title: Bone marrow derived dendritic cells, PBS for 6 hours, rep2

description:
Library name: BMDC_PBS_rep2
SRR32609697


title: HN878_IrradiatedMimic@Unknown+672h_b13_1

description: Library name: iMTB_28_S19

value: Irradiated Mtb

value: 672 hours


title: control cells, no treatment_2

value: no treatment


title: T46_RIF@0.03uM+1h_b10_2

description: Library name: T46x_RIF_D1_OTB.Transcriptomics_U_R2

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.

value: RIF, 0.03uM

value: 1 hour


title: T46_RIF@0.03uM+1h_b10_1

description: Library name: T46x_RIF_D1_OTB.Transcriptomics_U_R1


title: Bone marrow derived dendritic cells, PBS for 6 hours, rep1

description:
Library name: BMDC_PBS_rep1
SRR32609696

value: Bone marrow

value: BMDCs

value: Dendritic cells

value: WT


title: FOXP3cre_GFP_P1_S69

value: Control


title: RNA-seq_NPC, Grb10 SV40pA RNA truncation mutant, rep3

city: Miami

first: Danny

last: Reinberg

state: FL

address: 1501 NW 10th Avenue (C227)

department: John T. MacDonald Department of Human Genetics

institute: Miller School of Medicine and Sylvester Comprehensive Cancer Center

description:
Library name: RNAseq_NPC_Grb10_pA_rep3
NPC_Grb10_pA_rep3

data_processing:
RNA-seq fastq files were processed using the route “rna-star” and “rna-star-groups-dge” from the Slide-n-Seq (sns) pipeline: https://igordot.github.io/sns/
Assembly: mm10
Supplementary files format and content: tab-delimited text file that contains raw counts of mapped reads for each gene

source_name: E14 Grb10 pA

growth_protocol: E14Tga2 (ATCC, CRL-1821) mouse ESCs (E14) were cultured in N2B27 media [Advanced Dulbecco's modified eagle medium (DMEM)/F12:Neurobasal-A (1:1) medium (ThermoFisher Scientific 12634028 and 10888022, respectively), with 3% ESC-grade fetal bovine serum (v/v, Gemini 900-108), 1x N2 (ThermoFisher Scientific 17502-048), 1x B27 (Thermo Fisher 17504-044), 2 mM L-glutamine (Sigma G7513), 0.1 mg/mL Penicillin-Streptomycin (Sigma P0781), 0.1 mM β-mercaptoethanol (ThermoFisher Scientific 21985023)] supplemented with leukemia inhibitory factor (homemade), 3 μM CHIR99021 (Tocris 4423) and 1 μM PD0325901 (Sigma PZ0162) on 0.1% gelatin-coated (Millipore ES-006-B) plates at 37°C and 5% CO2.

extract_protocol:
RNA was purified using RNeasy Plus Mini Kit (Qiagen 74136).
rRNA was depleted from 1 ug starting total RNA using NEBNext rRNA Depletion Kit v2 (NEB E7405) following manufacturer’s instructions. cDNA was synthesized using NEBNext Ultra II RNA first strand synthesis module (NEB E7771) (with random hexamers) and NEBNext Ultra II Directional RNA second strand synthesis module (NEB E7550) following manufacturer’s instructions. Libraries were prepared using NEBNext Ultra II DNA Library prep kit for Illumina (E7645S) in conjunction with NEBNext Multiplex Oligos for Illumina (E7600S or E7335S) for barcoding.

treatment_protocol:
In vitro differentiation of ESCs to NPCs as follows: plates were coated overnight at 37°C with 10 ug/mL Laminin (R&D Systems 3446-005-01) in 1x Phosphate Buffered Saline (PBS). ESCs were dissociated with TrypLE Express (Gibco 12605-028). Cells were seeded on laminin-coated plates at a pre-titrated density of ~15,000/cm2. Cells were differentiated for 2 days in N2B27 media.
For CTCF rescue experiments, E14 - CTCF-AID2 degron; Dox inducible CTCF WT or ΔZF1 rescue cells were treated with 1 uM 5-Ph-IAA (Bio Academia 30-003) and 1 ug/mL doxycycline (Sigma D5207) for 24 hours and then harvested for downstream applications.

value: E14 Grb10 pA

value: neural progenitor cells


title: S5_FOxP3_Cre

value: Non-tumor bearing


title: SG1_RIF@0.03uM+1h_b10_2

description: Library name: SG1_RIF_D1_OTB.Transcriptomics_U_R2

value: Bacteria

value: Wildtype


title: SG1_RIF@0.03uM+1h_b10_3

description: Library name: SG1_RIF_D1_OTB.Transcriptomics_U_R3


title: control cells, no treatment_1

value: cartilage

value: primary chondrocytes

value: control


title: S4_Treg1_WT

source_name: Tregs

value: Tregs


title: scRNASeq Mouse Thymus: Wild type, P28, Bio Rep 2, Batch E

city: Nashville

first: Bryan

middle: Robert

last: Helm

state: Tennessee

address: 2525 West End Avenue, Suite 1100

department: Center for Quantitative Science

institute: Vanderbilt University Medical Center

library_source: transcriptomic single cell

data_processing:
FASTQ files were processed with Cellranger v 6.0.1 to derive filtered feature count matrices. Reads were aligned against mm10 and filtered feature matrices were used for downstream analysis.
Assembly: mm10
Supplementary files format and content: Default outputs from Cellranger: barcodes, features, and count matrices

source_name: Thymus

extract_protocol:
Thymus cells were extracted from perinatal mice (days 0, 3, 7, 10, 15, and 28) and FACS sorted to isolate TEC populations.
Single cell suspensions were processed in the University of Texas Genomic Sequencing and Analysis Facility. Briefly, cell suspensions were loaded on the Chromium Controller (10X Genomics) and processed for cDNA library generation following the manufacturer’s instructions for the Chromium NextGEM Single Cell 3’ Reagent Kit v3.1 (10X Genomics).

value: Thymus

value: Thymic Epithelial Cells

tag: age (days)


title: RNA-seq_NPC, Grb10 SV40pA RNA truncation mutant, rep1

description:
Library name: RNAseq_NPC_Grb10_pA_rep1
NPC_Grb10_pA_rep1


title: SG1_RIF@0.03uM+1h_b10_1

description: Library name: SG1_RIF_D1_OTB.Transcriptomics_U_R1

value: RIF, 0.03uM

value: 1 hour


title: scRNASeq Mouse Thymus: Wild type, P15, Bio Rep 1, Batch F


title: scRNASeq Mouse Thymus: Wild type, P28, Bio Rep 1, Batch C


title: RNA-seq_NPC, Podxl SV40pA RNA truncation mutant, rep3

description:
Library name: RNAseq_NPC_Podxl_pA_rep3
NPC_Podxl_pA_rep3

source_name: E14 Podxl pA

value: E14 Podxl pA


title: SA161_RIF@0.03uM+1h_b10_3

description: Library name: SA161_RIF_D1_OTB.Transcriptomics_U_R3


title: FOXP3cre_GFP_P2_S70

value: Tumor bearing


title: control cells, no treatment_3

value: no treatment


title: S2_SRC3KO_Tam1_GFP


title: S1_SRC3KO_Tam1_GFP


title: RNA-seq_NPC, Podxl SV40pA RNA truncation mutant, rep1

description:
Library name: RNAseq_NPC_Podxl_pA_rep1
NPC_Podxl_pA_rep1


title: scRNASeq Mouse Thymus: Wild type, P10, Bio Rep 2, Batch F

value: WT


title: SA161_RIF@0.03uM+1h_b10_2

description: Library name: SA161_RIF_D1_OTB.Transcriptomics_U_R2


title: scRNASeq Mouse Thymus: Wild type, P10, Bio Rep 1, Batch C


title: 44B4_Tobra_21D

city: Reykjavik

first: Thorarinn

last: Gudjonsson

address: Vatnsmyrarvegur 16

department: Faculty of Medicine

country: Iceland

institute: University of Iceland

data_processing:
Kallisto 0.48
Assembly: hsGRCh38
Supplementary files format and content: Kallisto 0.48 abundance file .h5 and .tsv

organism: Homo sapiens

growth_protocol: VA10 cells were expanded in BEGM media at monolayer before being seeded in DMEM supplemented with 10% FBS on Transwell filters. Cultures were then airlifted and maintained in DMEM + 2% Ultroser G for 21 days at 37C and 5%CO2.

extract_protocol:
RNA was harvested using TRIzol Reagent.
NextSeq2k : QIAGEN RNA sequencing Services

treatment_protocol: 35uM of macrolide ans aminoglycoside treatment was added at airlift and maintained for 21 days. Vehicle control received equal volume of DMSO.

value: bronchial epithelial

value: Tobra


title: SA161_RIF@0.03uM+1h_b10_1

description: Library name: SA161_RIF_D1_OTB.Transcriptomics_U_R1


title: 44B3_Tobra_21D


title: RNA-seq_NPC, Grb10 SV40pA RNA truncation mutant, rep2

description:
Library name: RNAseq_NPC_Grb10_pA_rep2
NPC_Grb10_pA_rep2

value: E14 Grb10 pA

value: neural progenitor cells


title: HN878_RIF@0.03uM+1h_b10_3

description: Library name: HN878_RIF_D1_OTB.Transcriptomics_U_R3

value: Bacteria

value: Wildtype


title: RNA-seq_NPC, E14 WT, rep3

description:
Library name: RNAseq_NPC_WT_E14_rep3
NPC_WT_E14_rep3


title: HN878_RIF@0.03uM+1h_b10_2

description: Library name: HN878_RIF_D1_OTB.Transcriptomics_U_R2


title: 44B1_Tobra_21D


title: scRNASeq Mouse Thymus: Wild type, P03, Bio Rep 2, Batch F


title: 22C4_Soli_21D

value: Soli


title: HN878_RIF@0.03uM+1h_b10_1

description: Library name: HN878_RIF_D1_OTB.Transcriptomics_U_R1


title: RNA-seq_NPC, Podxl SV40pA RNA truncation mutant, rep2

description:
Library name: RNAseq_NPC_Podxl_pA_rep2
NPC_Podxl_pA_rep2


title: RNA-seq_ESC, Grb10 SV40pA RNA truncation mutant, rep3

description:
Library name: RNAseq_ESC_Grb10_pA_rep3
ESC_Grb10_pA_rep3

value: embryonic stem cells


title: scRNASeq Mouse Thymus: Wild type, P03, Bio Rep 1, Batch D


title: 22C3_Soli_21D


title: 22C1_Soli_21D


title: H37Rv_RIF@0.03uM+1h_b10_3

description: Library name: H37Rv_RIF_D1_OTB.Transcriptomics_U_R3


title: RNA-seq_ESC, Grb10 SV40pA RNA truncation mutant, rep2

description:
Library name: RNAseq_ESC_Grb10_pA_rep2
ESC_Grb10_pA_rep2


title: scRNASeq Mouse Thymus: Wild type, P00, Bio Rep 2, Batch E


title: H37Rv_RIF@0.03uM+1h_b10_2

description: Library name: H37Rv_RIF_D1_OTB.Transcriptomics_U_R2


title: RNA-seq_ESC, Grb10 SV40pA RNA truncation mutant, rep1

description:
Library name: RNAseq_ESC_Grb10_pA_rep1
ESC_Grb10_pA_rep1


title: H37Rv_RIF@0.03uM+1h_b10_1

description: Library name: H37Rv_RIF_D1_OTB.Transcriptomics_U_R1


title: scRNASeq Mouse Thymus: Wild type, P00, Bio Rep 1, Batch D


title: 22B4_Roxi_21D

value: Roxi


title: scRNASeq Mouse Thymus: Wild type, P07, Bio Rep 2, Batch D

value: Thymus


title: RNA-seq_ESC, Podxl SV40pA RNA truncation mutant, rep3

description:
Library name: RNAseq_ESC_Podxl_pA_rep3
ESC_Podxl_pA_rep3


title: CDC1551_RIF@0.03uM+1h_b10_5

description: Library name: CDC1553_RIF_D1_OTB.Transcriptomics_U_R3


title: 22B3_Roxi_21D


title: scRNASeq Mouse Thymus: Wild type, P07, Bio Rep 1, Batch D

value: Thymic Epithelial Cells


title: + induction_IP

city: Xia men

first: luo

last: ya

address: Xiang'an South Road

institute: School of Life Sciences, Xiamen University

library_source: genomic

data_processing:
Raw reads containing adaptor sequences and those with ambiguous or low-quality bases at the beginning or end were trimmed using Trimmomatic(0.39).
The qualified reads from each sample were aligned to the assembled reference genome using BWA (0.7.17) with default parameters.
MACS2(V2.1.1) was used to call peaks with the pvaue ＜0.01 and annotated to the gene functional region.
Assembly: GRCm39
Supplementary files format and content: bigWig,narrowPeak

molecule: genomic DNA

source_name: stromal vascular fraction

growth_protocol: Cells were cultured in growth media containing high-glucose DMEM, 100 U/ml penicillin, 100 mg/ml streptomycin, and 10% FBS (Excell) at 37 °C in an atmosphere of 8% CO2.

extract_protocol:
For fixation, the cells were treated with 1% PFA at 37 °C for 15 minutes. To stop the fixation process, 0.125 M glycine was added and incubated for 5 minutes at room temperature. Following fixation, the cells were washed with cold PBS supplemented with 1 mM PMSF and lysed with ChIP SDS lysis buffer (50 mM Tris-HCl, pH 8.1, 10 mM EDTA, 1% SDS) containing protease inhibitor and phosphatase inhibitors for 15 minutes on ice. To achieve DNA fragmentation within the desired range of 200-800 base pairs, an ultrasonic processor (DIAGENODE) was used on ice.
Hieff NGS®MaxUp II DNA Library Prep Kit for Illumina® (YEASEN,Shanghai,China）was used for library preparations.

treatment_protocol: To investigate the genomic binding patterns of SOX4, we established a stable cell line of BAT SVF overexpressing 3XHA-SOX4 for ChIP-Seq assays. Subsequently, the cells were cultured until they reached 100% confluence and were then treated with PBS or adipogenic cocktail for 1 hr before being harvested.

value: BAT SVF

value: stromal vascular fraction

tag: chip antibody

value: HA (Abcam.#ab9110)

value: adipogenic differentiation


title: RNA-seq_ESC, Podxl SV40pA RNA truncation mutant, rep2

description:
Library name: RNAseq_ESC_Podxl_pA_rep2
ESC_Podxl_pA_rep2

value: E14 Podxl pA


title: + induction_INPUT


title: RNA-seq_NPC, E14 WT, rep1

description:
Library name: RNAseq_NPC_WT_E14_rep1
NPC_WT_E14_rep1


title: CDC1551_RIF@0.03uM+1h_b10_4

description: Library name: CDC1552_RIF_D1_OTB.Transcriptomics_U_R2

value: RIF, 0.03uM

value: 1 hour


title: RNA-seq_NPC, E14 WT, rep2

description:
Library name: RNAseq_NPC_WT_E14_rep2
NPC_WT_E14_rep2


title: 22A4_Ery_21D

value: bronchial epithelial

value: Ery


title: - induction_IP


title: T46_Untreated@0+0h_b10_3

description: Library name: T46x_RIF_D0_OTB.Transcriptomics_U_R3

value: Untreated

value: 0 hours


title: RNA-seq_ESC, Podxl SV40pA RNA truncation mutant, rep1

description:
Library name: RNAseq_ESC_Podxl_pA_rep1
ESC_Podxl_pA_rep1


title: 22A2_Ery_21D


title: RNA-seq_ESC, E14 WT, rep3

description:
Library name: RNAseq_ESC_WT_E14_rep3
ESC_WT_E14_rep3


title: - induction_INPUT


title: 22B2_Roxi_21D


title: Spheroids 1-1

city: Brussels

first: Gilbert

last: Vassart

address: Route de Lennik 808

department: IRIBHM

country: Belgium

institute: ULB

data_processing:
ATACseq paired-end reads of 50 bp were trimmed for adaptor sequences (using Trimmomatic).
ATAC-seq paired-end reads were then aligned to the mouse GRCm38 genome (using Bowtie2)
Mitochondrial reads and reads aligned to scaffolds and undefined chromosomes were excluded from downstream analysis.
Duplicated reads were removed by Picard tools.
Read start sites were adjusted to represent the center of the transposon binding event as described in Li et al., 2009.
Assembly: Peak calling was performed on each individual sample using Macs2.
Supplementary files format and content: CSV files containing the length of the peacks

source_name: Intestinal

growth_protocol: EDTA fraction of small intestine give rise to organoids which they can grow on medium containing ENR,but treating the remaning materials with Collagenase/ Dispase solution give rise to adult spheroids which they can grow in BCM.

extract_protocol:
Tissues were digested, sorted in 1ml PBS 3% FBS. Nuclei were isolated to proceed to transposase reaction (Illumina). DNA was purified using the MinElute purification kit.
DNA libraries were PCR amplified (NEBNext High-Fidelity 2x PCR Master Mix, New England Biolabs), indexed using primers described by Buenrostro et al. (2013), and double size selected (from 150 to 1200 bp) using AmpureXP magnetic beads (Beckman) following the manufacturer's recommendations. The multiplexed libraries were loaded on a NovaSeq 6000 (Illumina) using a S2 flow cell and paired-end sequences were produced using a 200 Cycle Kit.

value: Intestinal

value: Crypts

value: All intestinal epithelium

value: Lger5CreERT2 (HE) - Rosa26Tom (HE)

value: BCM medium


title: 22A1_Ery_21D


title: T46_Untreated@0+0h_b10_1

description: Library name: T46x_RIF_D0_OTB.Transcriptomics_U_R1

value: Bacteria

value: Wildtype


title: RNA-seq_ESC, E14 WT, rep2

description:
Library name: RNAseq_ESC_WT_E14_rep2
ESC_WT_E14_rep2

value: embryonic stem cells


title: T46_Untreated@0+0h_b10_2

description: Library name: T46x_RIF_D0_OTB.Transcriptomics_U_R2


title: SG1_Untreated@0+0h_b10_3

description: Library name: SG1_RIF_D0_OTB.Transcriptomics_U_R3


title: Organoids 2-2

value: ENR medium


title: RNA-seq_ESC, E14 WT, rep1

description:
Library name: RNAseq_ESC_WT_E14_rep1
ESC_WT_E14_rep1


title: 11C3_Clari_21D

value: Clari


title: NPC, Grb10 SV40pA RNA truncation mutant, rep2

description: Library name: NPC_Grb10_pA_rep2

data_processing:
Micro-C analysis was performed according to the pipeline described by Dovetail Genomics in https://micro-c.readthedocs.io/en/latest/index.html. Briefly, multiple pairs of fastq files (2 biological replicates per condition) were aligned to the mm10 reference genome using BWA-MEM split alignment. Pairtools was used for the next steps: identifying valid ligation events (pairs), removing PCR duplicates, generating and down-sampling the final pairs files. Pairs files were down-sampled such that all samples being compared together had equal number of valid pairs. The down-sampled pairs files were used for downstream analysis. Cool and mcool files were generated using cooler. Hic contact matrices were generated using Juicer Tools. Fithic2 was used to determine the contact counts of each pair-wise 5-kb bins, and calculate the likelihood of a contact to be significantly higher than expected for its genomic distance (q-value).
Assembly: mm10
Supplementary files format and content: pairs, cool, mcool, and hic of combined replicates; txt.gz file of FitHiC2 ouput
Library strategy: MicroC

extract_protocol:
Cells in a confluent 15 cm tissue culture plate (~30 million (M) cells) were dissociated with TrypLE Express and crosslinked with freshly made 3 mM ethylene glycol bis (EGS) in PBS (5 mL per 5M cells), incubated at room temperature for 45 minutes. Crosslinking reaction was quenched by adding Tris pH 7.5 to final 0.75 M concentration and incubated at room temperature for 5 minutes. EGS-crosslinked cells were washed twice with 0.5% BSA in PBS and subjected to the second crosslinking with 1% formaldehyde in PBS (5 mL per 5M cells), incubated at room temperature for 10 minutes. Crosslinking reaction was quenched again by adding Tris pH 7.5 to final 0.75 M concentration, incubated at room temperature for 5 minutes. Cells were washed twice with 0.5% BSA in PBS and aliquoted into 5M cells per 1.5 mL tube. Cell pellets were spun down, snap-frozen, and stored in −80°C. Crosslinked cells (5M in 1.5 mL tubes) were thawed on ice and permeabilized in cold Micro-C Buffer (MB) #1 (50mM NaCl, 10mM Tris pH 7.5, 5mM MgCl2, 1mM CaCl2, 0.2% NP-40, 1x Protease Inhibitor Cocktail) for 20 minutes on ice. Chromatin from permeabilized cells was digested by adding micrococcal nuclease (MNase) (NEB M0247SVIAL) at 1:100 dilution and incubated at 37°C for 10 minutes, shaking at 850 rpm. Dilution of MNase was pre-titrated such that chromatin is digested efficiently into nucleosome-sized fragments. Enzyme activity was stopped by adding EGTA to a final concentration of 4 mM and incubated at 65°C for 10 minutes. MNase-digested chromatin was washed twice with ice-cold MB #2 (50mM NaCl, 10mM Tris pH 7.5, 10mM MgCl2). Digested chromatin fragments were then subjected to 3’-dephosphorylation and 5’-phosphorylation by 0.5 U/uL T4 Polynucleotide Kinase in 1x NEBuffer 2.1 (NEB B6002S) with 2 mM ATP and 5 mM DTT, incubated for 15 minutes at 37°C with interval mixing. 3’-end-chewing was done by adding 0.5 U/uL DNA Polymerase I Klenow Fragment and incubating another 15 minutes in 37°C. Blunt-end reaction was triggered by adding biotin-dATP, biotin-dCTP, dGTP, and dTTP to a final concentration of 66 uM and incubated at 25°C for 45 minutes. The reaction was stopped by adding 30 mM EDTA final concentration and incubating at 65°C for 20 minutes. Chromatin was washed once with cold MB #3 (50mM Tris pH 7.5, 10mM MgCl2). Chromatin fragments with biotin-dNTPs were then ligated with 20 U/uL T4 DNA ligase (NEB M0202M), incubated at room temperature for at least 2.5 hours with slow rotation. Unligated ends containing biotin-dNTPs were then removed by 5 U/uL exonuclease III in 1x NEBuffer 1 (NEB B7001S), incubated at 37°C for 15 minutes. Chromatin was subjected to reverse crosslinking with 1 mg/mL Proteinase K (Sigma 3115879001), 1% SDS, and 100 ug/mL RNase A (ThermoFisher Scientific EN0531), incubated at 65°C overnight. DNA was extracted by adding 1x volume Phenol:Chloroform:Isoamyl Alcohol (25:24:1) solution (Thermofisher Scientific 15593049) and isolating aqueous phase after centrifugation. DNA was purified from the aqueous phase using a PCR purification kit (Zymo Research DCC-5 D4013) following manufacturer’s instructions. Separation of monomers and dimers was done by running purified DNA on 3% TBE agarose gel. 200-400 bp DNA was then extracted from the gel by Zymo Gel DNA recovery kit (Zymo Research D4008). DNA with biotin-dNTPs was captured by Dynabeads® MyOne Streptavidin C1 (ThermoFisher Scientific 65001).
Standard library preparation protocol including end-repair, A-tailing, and adaptor ligation was performed on beads with enzymes from NEBNext Ultra II DNA Library prep kit for Illumina (E7645S). NEBNext Multiplex Oligos for Illumina® (Dual Index Primers Set 1, E7600S) were used for barcoding. Sequencing library was amplified by Kapa HiFi PCR enzyme (KAPA KK2601).

value: E14 Grb10 pA

value: neural progenitor cells


title: spia2

description: intestinal adult spheroids 2

data_processing:
The multiplexed libraries were loaded on a NovaSeq 6000 (Illumina) and sequences were produced using a 200 Cycles Kit. Approximately 25 million paired-ends reads were mapped against the mouse reference genome GRCm38 using STAR software to generate read alignments for each sample. Annotations Mus-musculus.GRCm38.90.gtf were acquired from ftp.Ensembl.org. After transcript assembling, gene-level counts were obtained using HTSeq.
Assembly: mm10
Supplementary files format and content: CSV files include RP20M values for each sample

growth_protocol: EDTA fraction of small intestine give rise to organoids which they can grow on medium containing ENR, Collagenase/ Dispase fraction give rise to adult spheroids when using the two layer protocol which we try to grow them in medium containing ENR, BCM and wnt3a

extract_protocol:
RNA was extracted using mirVana™ miRNA Isolation Kit (Invitrogen).
Indexed cDNA libraries were obtained using the TruSeq stranded mRNA LP (Illumina) following manufacturer’s recommendations.

tag: cell subtype

value: All intestinal epithelium cell type

value: SmaCre(HE)- Rosa26YFP(HE)

value: SatoENR (ENR)


title: 11C1_Clari_21D

value: bronchial epithelial


title: SG1_Untreated@0+0h_b10_2

description: Library name: SG1_RIF_D0_OTB.Transcriptomics_U_R2

value: Untreated

value: 0 hours


title: Spheroids in two layer, M33 CD Wnt3a

data_processing:
The multiplexed libraries were loaded on a NovaSeq 6000 (Illumina) and sequences were produced using a 200 Cycles Kit. Approximately 25 million paired-ends reads were mapped against the mouse reference genome GRCm38 using STAR software to generate read alignments for each sample. Annotations Mus-musculus.GRCm38.90.gtf were acquired from ftp.Ensembl.org. After transcript assembling, gene-level counts were obtained using HTSeq.
Assembly: mm10
Supplementary files format and content: csv files include RP20M values for each sample

value: Intestinal

value: Crypts

value: Vil1CreERT2 (HE)- Rosa26tom(HE)

value: first Wnt3a+ ENR and then transferred in ENR medium passage 3 day 5

tag: group

value: Spheroids in two layer


title: NPC, Grb10 SV40pA RNA truncation mutant, rep1

description: Library name: NPC_Grb10_pA_rep1


title: SA161_Untreated@0+0h_b10_3

description: Library name: SA161_RIF_D0_OTB.Transcriptomics_U_R3

value: Bacteria

value: Wildtype


title: NPC, Podxl SV40pA RNA truncation mutant, rep1

description: Library name: NPC_Podxl_pA_rep1

value: E14 Podxl pA


title: SA161_Untreated@0+0h_b10_2

description: Library name: SA161_RIF_D0_OTB.Transcriptomics_U_R2


title: 11B2_Azm_21D

value: Azm


title: spia1

description: intestinal adult spheroids 1


title: Spheroids in two layer, M31 CD Wnt3a

value: Vil1CreERT2 (HE)- Rosa26tom(WT)


title: Spheroids in two layer, F10 CD Wnt3a


title: Spheroids in two layer, M33 CD BCM

value: BCM medium passage 1 day 5


title: NPC, E14 WT, rep1

description: Library name: NPC_WT_E14_rep1

value: neural progenitor cells


title: SA161_Untreated@0+0h_b10_1

description: Library name: SA161_RIF_D0_OTB.Transcriptomics_U_R1


title: NPC, Podxl SV40pA RNA truncation mutant, rep2

description: Library name: NPC_Podxl_pA_rep2


title: 11C4_Clari_21D

value: Clari


title: HN878_Untreated@0+0h_b10_3

description: Library name: HN878_RIF_D0_OTB.Transcriptomics_U_R3


title: NPC, E14 WT, rep2

description: Library name: NPC_WT_E14_rep2


title: 11A4_Ctrl_21D

value: Ctrl


title: 11B4_Azm_21D

value: bronchial epithelial


title: SG1_Untreated@0+0h_b10_1

description: Library name: SG1_RIF_D0_OTB.Transcriptomics_U_R1

value: Untreated


title: Input, NPC, E14 WT, rep2

description: Library name: Input_NPC_WT_E14_rep2

data_processing:
Reads were aligned to the mouse reference genome mm10, using Bowtie2 with default parameters. Reads of quality score less than 30 were removed using samtools and PCR duplicates were removed using picard. Regions in mm10 genome blacklist was removed using bedtools to generate the final BAM files. The final BAM files for replicates of same condition were merged using samtools. Bigwig files were generated from individual sample replicate BAM files and merged BAM files using deeptools with parameters: --binSize 50 --normalizeUsing RPKM --ignoreDuplicates --ignoreForNormalization chrX --extendReads 250. narrowPeaks per sample replicate were generated using MACS2 with parameters -g mm -B -f BAMPE --keep-dup all -q 0.01.
Assembly: mm10
Supplementary files format and content: bigWig of individual sample replicates and merged replicates, narrowPeak for each sample replicate

extract_protocol:
Cells in a confluent 15 cm tissue culture plate washed once with PBS and fixed for 10 minutes with 1% formaldehyde in 15 mL fixation buffer (10 mM HEPES pH 7.5, 15 mM NaCl, 0.15 mM EDTA, 0.075 mM EGTA in DMEM). Formaldehyde was quenched with 125 mM glycine, incubated for 5 mins at room temperature. Cells were washed and scraped in PBS and transferred to 15 mL tubes. Nuclei were isolated using buffers supplemented with 1x protease inhibitor cocktail (Roche 11873580001) in the following order: 5 mL LB1 (20 mM Tris pH 7.5, 10 mM NaCl, 1 mM EDTA, 0.2% NP-40; 10 min on ice), 5 mL LB2 (20 mM Tris pH 7.5, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA; 10 min on ice), and 1.2 mL LB3 (20 mM Tris pH 7.5, 150 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 1% Triton X-100, 0.1% sodium deoxycholate, 0.1% SDS). Nuclei in LB3 were transferred to 15 mL Bioruptor Pico tubes (Diagenode C30010017) containing 800 mg sonication beads. Chromatin was fragmented in LB3 to an average size of 200-250 bp using a Bioruptor Pico (Diagenode). Insoluble material was pelleted by centrifuging at 15,000 g for 10 minutes in 4oC, and supernatant was kept. Supernatant containing sonicated chromatin were pre-cleared with 25 uL Protein G Dynabeads (Invitrogen 10004D), incubated rotating in 4oC for 1 hour. For each reaction, 2-4 ug antibody was incubated with 10 ul Protein G Dynabeads in LB3, rotating at 4oC for 3 hours. Antibody-bead complexes were added to 300 ug of pre-cleared chromatin and incubated rotating at 4oC overnight. 30 ug chromatin was used as input control. Beads were then washed 4 times with RIPA buffer (50 mM HEPES pH 7.5, 500 mM LiCl, 1 mM EDTA, 0.5% sodium deoxycholate, 1% NP-40) and washed once with TE50 buffer (10 mM Tris pH 8.0, 1 mM EDTA, 50 mM NaCl). The beads-bound chromatin was eluted in 125 uL elution buffer (50 mM Tris pH 8.0, 10 mM EDTA, 1% SDS), incubated at 65°C for 1 hour. Eluted chromatin was de-crosslinked by incubating overnight at 55°C, shaking 1000 rpm, with 0.6 mg/mL proteinase K and 0.1 mg/mL RNase A. 1x volume Phenol:Chloroform:Isoamyl Alcohol (25:24:1) solution was added to the elution and aqueous phase was isolated after centrifugation. DNA was purified from the aqueous phase using a PCR purification kit (Zymo Research DCC-5 D4013) following manufacturer’s instructions.
Libraries were prepared using NEBNext Ultra II DNA Library prep kit for Illumina (E7645S) following manufacturer’s instructions but using ½ volume for all the reactions. NEBNext Multiplex Oligos for Illumina® (Dual Index Primers Set 1, E7600S) were used for barcoding.


title: Spheroids in two layer, M31 CD BCM

value: All intestinal epithelium cell type


title: 11A3_Ctrl_21D


title: HN878_Untreated@0+0h_b10_2

description: Library name: HN878_RIF_D0_OTB.Transcriptomics_U_R2

value: 0 hours


title: 11B1_Azm_21D


title: HN878_Untreated@0+0h_b10_1

description: Library name: HN878_RIF_D0_OTB.Transcriptomics_U_R1


title: Spheroids in two layer, F10 CD BCM

value: Intestinal

value: Crypts


title: Input, NPC, E14 WT, rep1

description: Library name: Input_NPC_WT_E14_rep1


title: 11A2_Ctrl_21D


title: 04B4_Tobra_14D

value: Tobra


title: 04B2_Tobra_14D


title: Spheroids in two layer, M33 CD ENR

value: Vil1CreERT2 (HE)- Rosa26tom(HE)

value: Wnt3a+ ENR medium passage 1 day 5

value: Spheroids in two layer


title: Smc3 ChIP, NPC, Grb10 SV40pA RNA truncation mutant, rep2

description: Library name: Smc3_NPC_Grb10_pA_rep2

value: E14 Grb10 pA

value: Smc3 (Abcam ab9263)


title: H37Rv_Untreated@0+0h_b10_2

description: Library name: H37Rv_RIF_D0_OTB.Transcriptomics_U_R2

value: Bacteria

value: Wildtype


title: Smc3 ChIP, NPC, Grb10 SV40pA RNA truncation mutant, rep1

description: Library name: Smc3_NPC_Grb10_pA_rep1

value: neural progenitor cells


title: 04B1_Tobra_14D


title: Smc3 ChIP, NPC, Podxl SV40pA RNA truncation mutant, rep2

description: Library name: Smc3_NPC_Podxl_pA_rep2

value: E14 Podxl pA


title: H37Rv_Untreated@0+0h_b10_1

description: Library name: H37Rv_RIF_D0_OTB.Transcriptomics_U_R1


title: Smc3 ChIP, NPC, Podxl SV40pA RNA truncation mutant, rep1

description: Library name: Smc3_NPC_Podxl_pA_rep1


title: Organoids, M33 EDTA

value: ENR medium passage 1 day 5

value: Organoids


title: CDC1551_Untreated@0+0h_b10_2

description: Library name: CDC1552_RIF_D0_OTB.Transcriptomics_U_R2

value: Untreated


title: CDC1551_Untreated@0+0h_b10_3

description: Library name: CDC1553_RIF_D0_OTB.Transcriptomics_U_R3


title: 04A1_Ctrl_14D

value: bronchial epithelial

value: Ctrl


title: Spheroids in two layer, F10 CD ENR

value: Intestinal

value: All intestinal epithelium cell type

value: Vil1CreERT2 (HE)- Rosa26tom(WT)


title: H37Rv_Untreated@0+0h_b10_3

description: Library name: H37Rv_RIF_D0_OTB.Transcriptomics_U_R3

value: 0 hours


title: 04A3_Ctrl_14D


title: Smc3 ChIP, NPC, E14 WT, rep2

description: Library name: Smc3_NPC_WT_E14_rep2


title: CDC1551_Untreated@0+0h_b10_1

description: Library name: CDC1551_RIF_D0_OTB.Transcriptomics_U_R1


title: Crypts-M11-WT

value: Crypts

value: Lgr5DTR (WT)

value: the crypts were isolated after EDTA treatment


title: Organoids, M31 EDTA 1


title: Smc3 ChIP, NPC, E14 WT, rep1

description: Library name: Smc3_NPC_WT_E14_rep1

value: Smc3 (Abcam ab9263)


title: 02C4_Soli_14D

value: Soli


title: Organoids, M31 EDTA 2


title: 02C3_Soli_14D


title: T46_RIF@0.03uM+8h_b10_2

description: Library name: T46_RIF_D8_OTB_drug_transcriptome_U_R2_S27_R1

value: Bacteria

value: Wildtype

value: RIF, 0.03uM

value: 8 hours


title: Crypts-M3-WT


title: Spheroids in two layer, M31 CD ENR

value: Wnt3a+ ENR medium passage 1 day 5

value: Spheroids in two layer


title: CTCF ChIP, NPC, Grb10 SV40pA RNA truncation mutant, rep1

description: Library name: CTCF_NPC_Grb10_pA_rep1

value: E14 Grb10 pA

value: neural progenitor cells

value: CTCF (Abcam ab70303)


title: T46_RIF@0.03uM+8h_b10_1

description: Library name: T46_RIF_D8_OTB_drug_transcriptome_U_R1_S26_R1


title: Crypts-M30-HE

value: Intestinal

value: All intestinal epithelium cell type

value: Lgr5DTR (HE)


title: CTCF ChIP, NPC, E14 WT, rep2

description: Library name: CTCF_NPC_WT_E14_rep2


title: SG1_RIF@0.03uM+1h_b10_6

description: Library name: SG1_RIF_D1_OTB_drug_transcriptome_U_R3_S18_R1

value: 1 hour


title: 02B4_Roxi_14D

value: bronchial epithelial

value: Roxi


title: 04A4_Ctrl_14D

value: Ctrl


title: 02B1_Roxi_14D


title: 02A3_Ery_14D

value: Ery


title: CTCF ChIP, NPC, Podxl SV40pA RNA truncation mutant, rep2

description: Library name: CTCF_NPC_Podxl_pA_rep2

value: E14 Podxl pA


title: SG1_RIF@0.03uM+8h_b10_2

description: Library name: SG1_RIF_D8_OTB_drug_transcriptome_U_R2_S31_R1

value: Bacteria

value: Wildtype


title: Crypts-M3-HE

value: Crypts

value: the crypts were isolated after EDTA treatment


title: CTCF ChIP, NPC, Podxl SV40pA RNA truncation mutant, rep1

description: Library name: CTCF_NPC_Podxl_pA_rep1


title: CTCF ChIP, NPC, E14 WT, rep1

description: Library name: CTCF_NPC_WT_E14_rep1


title: 02B2_Roxi_14D


title: SG1_RIF@0.03uM+8h_b10_3

description: Library name: SG1_RIF_D8_OTB_drug_transcriptome_U_R3_S32_R1

value: RIF, 0.03uM

value: 8 hours


title: Crypts-M13-HE


title: PlusMinus

description: 10X Genomics

data_processing:
The multiplexed libraries were loaded on a NovaSeq 6000 (Illumina) and sequences were produced using a 200 Cycles Kit. Approximately 25 million paired-ends reads were mapped against the mouse reference genome GRCm38 using STAR software to generate read alignments for each sample. Annotations Mus-musculus.GRCm38.90.gtf were acquired from ftp.Ensembl.org. After transcript assembling, gene-level counts were obtained using HTSeq.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

extract_protocol:
After removal of EDTA fraction, samples from 5 Vil-Cre (Heterozygotes,HE), Rosa26R-Tomato (HE) mice were treated with collagenase (0.132mg/ml) Dispase (0.66mg/ml) and DNase1 (0.05mg/ml) solution for 35 min at 37°C, washed 2 times with BCM-2mM EDTA solution with centrifugation at 500g for 2min in-between. The cell pellet was washed once with PBS-2%FBS (FACS solution) and centrifuged at 500g for 2min. The cells were then incubated with rat anti-mouse CD16/CD32 (blocking solution) at a final dilution of 1/50 (v:v) in FACS solution for 15 min. The APC rat anti-mouse CD31 (1/200), APC rat anti-mouse CD45 (1/500) and BV711 rat anti-mouse CD326 (Epcam,1/200) antibodies were added to blocking solution and incubated for 45 min on ice. After 3 washes with FACS solution, DAPI was added to mark the dead cells (1/2000) and the cells were sorted using the FACS Aria I cytometer (BD Biosciences). Twenty thousand Epcam-positive and Tomato-negative (PlusMinus) or Epcam-positive and Tomato-positive (PlusPlus) cells were collected for each animal. These cells were processed through the Chromium Next GEM Single Cell 3’ Reagent Kits v3.1 (10X Genomics) according to manufacturer’s recommendations and sequenced on Novaseq6000 (Illumina).
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics).

value: All intestinal epithelium

value: Vil1Cre (HE)- Rosa26tom(HE)

value: EDTA plus, Collagenase/ dispase treatment


title: Crypts-F4-WT

description:
This animal was removed beceause of the gender differences
MMA4-F4-WT.4

value: Intestinal

value: All intestinal epithelium cell type

value: Lgr5DTR (WT)


title: SG1_RIF@0.03uM+1h_b10_5

description: Library name: SG1_RIF_D1_OTB_drug_transcriptome_U_R2_S17_R1

value: 1 hour


title: cardiac tissues, GY4-6W

city: Beijing

first: Jiao

last: Fan

address: Fuxing road

institute: 301 hospital

data_processing:
RNA quality was examined using an Agilent 2100 Bioanalyzer.
Sequencing data were generated on an Illumina HiSeq platform with a 150-bp paired-end read length by Novogene.
Quality control of the RNA-seq data was performed using FastQC (v0.11.8).
The RNA-seq data was trimmed with Trim Galore (v0.6.1) using default parameters for pair-end data to remove both low-quality reads and adaptors.
The trimmed RNA-seq data were aligned to the Rattus norvegicus transcriptome with STAR (v2.5.0a) using default parameters.
Assembly: mm10
Supplementary files format and content: gene_count.txt

source_name: cardiac tissues

extract_protocol:
Total RNA samples of cardiac tissues from radiated mice and control mice were isolated using TRIzol reagent (Invitrogen) and treated with RNase-free DNase I (New England Biolabs, MA, USA), to remove any contaminating genomic DNA.
The RNA-seq library was prepared for sequencing using standard Illumina protocols.

value: cardiac tissues

value: WT

value: radiation


title: Input, NPC, CTCF-WT rescue, rep2

description: Library name: Input_NPC_WT_rep2

source_name: E14 CTCF-AID2 degron; Dox inducible CTCF-WT rescue

value: neural progenitor cell

value: 1 uM 5-Ph-IAA + 1 ug/mL Dox


title: CTCF ChIP, NPC, Grb10 SV40pA RNA truncation mutant, rep2

description: Library name: CTCF_NPC_Grb10_pA_rep2

value: E14 Grb10 pA

value: neural progenitor cells

value: CTCF (Abcam ab70303)


title: Input, NPC, CTCF-WT rescue, rep3

description: Library name: Input_NPC_WT_rep3

value: E14 CTCF-AID2 degron; Dox inducible CTCF-WT rescue


title: SA161_RIF@0.03uM+8h_b10_3

description: Library name: SA161_RIF_D8_OTB_drug_transcriptome_U_R3_S25_R1

value: Bacteria

value: Wildtype

value: RIF, 0.03uM

value: 8 hours


title: SG1_RIF@0.03uM+8h_b10_1

description: Library name: SG1_RIF_D8_OTB_drug_transcriptome_U_R1_S30_R1


title: 02C1_Soli_14D

value: bronchial epithelial

value: Soli


title: 02A4_Ery_14D

value: Ery


title: Input, NPC, CTCF-WT rescue, rep4

description: Library name: Input_NPC_WT_rep4


title: PlusPlus

description: 10X Genomics

value: Intestinal

value: Crypts

value: All intestinal epithelium

value: Vil1Cre (HE)- Rosa26tom(HE)

value: EDTA plus, Collagenase/ dispase treatment


title: cardiac tissues, GY3-6W

value: cardiac tissues

value: WT

value: radiation


title: SA161_RIF@0.03uM+8h_b10_2

description: Library name: SA161_RIF_D8_OTB_drug_transcriptome_U_R2_S24_R1


title: 01B4_Azm_14D

value: Azm


title: 01B3_Azm_14D


title: Input, NPC, CTCF-WT rescue, rep1

description: Library name: Input_NPC_WT_rep1

value: E14 CTCF-AID2 degron; Dox inducible CTCF-WT rescue

value: neural progenitor cell

value: 1 uM 5-Ph-IAA + 1 ug/mL Dox


title: SG1_RIF@0.03uM+1h_b10_4

description: Library name: SG1_RIF_D1_OTB_drug_transcriptome_U_R1_S16_R1

value: Bacteria

value: Wildtype

value: RIF, 0.03uM

value: 1 hour


title: SA161_RIF@0.03uM+8h_b10_1

description: Library name: SA161_RIF_D8_OTB_drug_transcriptome_U_R1_S23_R1

value: 8 hours


title: cardiac tissues, GY2-6W


title: 02A1_Ery_14D

value: bronchial epithelial

value: Ery


title: SA161_RIF@0.03uM+1h_b10_5

description: Library name: SA161_RIF_D1_OTB_drug_transcriptome_U_R2_S8_R1


title: 01A3_Clari_14D

value: Clari


title: Input, ESC, CTCF-WT rescue, rep3

description: Library name: Input_ESC_WT_rep3

value: embryonic stem cell


title: Input, ESC, CTCF-WT rescue, rep4

description: Library name: Input_ESC_WT_rep4


title: 01A4_Clari_14D


title: Input, ESC, CTCF-WT rescue, rep1

description: Library name: Input_ESC_WT_rep1

source_name: E14 - CTCF-AID2 degron; Dox inducible CTCF WT rescue


title: 01B2_Azm_14D


title: cardiac tissues, GY1-6W


title: SA161_RIF@0.03uM+1h_b10_4

description: Library name: SA161_RIF_D1_OTB_drug_transcriptome_U_R1_S7_R1


title: Input, ESC, CTCF-WT rescue, rep2

description: Library name: Input_ESC_WT_rep2


title: 01A1_Clari_14D


title: cardiac tissues, WT2-6W

value: control


title: HN878_RIF@0.03uM+8h_b10_2

description: Library name: HN878_RIF_D8_OTB_drug_transcriptome_U_R3_S29_R1


title: Smc3 ChIP, NPC, CTCF-ZF1 mutant rescue, rep2

description: Library name: Smc3_NPC_ZF1_rep2

source_name: E14 CTCF-AID2 degron; Dox inducible CTCF-ZF1 mutant rescue

value: Smc3 (Abcam ab9263)


title: HN878_RIF@0.03uM+8h_b10_1

description: Library name: HN878_RIF_D8_OTB_drug_transcriptome_U_R1_S28_R1


title: 6d-#5-2

city: shanghai

first: zhenghui

last: hong

state: --- Select a state ---

address: dongchuan road NO.800

department: life of science

institute: shanghai jiaotong university

description: Riboseq

data_processing:
Raw reads containing more than 50% of low quality bases or 10% of N bases were removed and adapter sequences were trimmed by fastp software. Reads with lengths between 20-40 nt were subjected to further analysis. The reads mapped to rRNAs, transfer RNAs (tRNA), small nuclear RNAs (snRNA), small nucleolar RNAs (snoRNA), and miRNAs were removed by using the short reads alignment tool Bowtie2. The remaining reads were mapped to the TAIR10 Arabidopsis reference genome by using STAR software. Three-nucleotide periodicity was plotted using the riboWaltz R package96. Reads counts in the open reading frame of coding genes were calculated by RSEM software, and the FPKM was calculated. Differentially translated genes were identified by using DESeq2 software. Genes fulfilling the criteria of FDR < 0.05 and fold-change ≥ 2 were considered to be differentially translated and were subjected to GO enrichment analysis
Assembly: The  reads were mapped to the TAIR10 Arabidopsis reference genome by using STAR software
Supplementary files format and content: counts files included raw counts and FPKM for each sample
Library strategy: Ribo-seq

organism: Arabidopsis thaliana

source_name: whole seedlings

extract_protocol:
Six-day-old WT and #5 seedlings were snap freezing and ground with liquid nitrogen and then dissolved in 400 µL of lysis buffer (20 mM Tris·HCl, pH 7.4, 150 mM NaCl, 5 mM MgCl2, 1 mM DTT, 100 µg/ml cycloheximide, and 1% [v/v] Triton X-100). The samples were incubated on ice for 10 min, centrifugated at 20,000g for 10 min at 4 ℃. For footprint preparation, 10 µL of RNase I (NEB) and 6 µL of DNase I (NEB) were added to 400 µL of lysate and incubated for 45 min at room temperature with gentle mixing.
Illumina HiSeq 2500

value: whole seedlings

value: ClpD-overexpression in WT


title: cardiac tissues, WT1-6W

value: cardiac tissues

value: WT


title: Smc3 ChIP, NPC, CTCF-ZF1 mutant rescue, rep1

description: Library name: Smc3_NPC_ZF1_rep1

value: E14 CTCF-AID2 degron; Dox inducible CTCF-ZF1 mutant rescue

value: neural progenitor cell


title: 6d-#5-1

description: Riboseq


title: HN878_RIF@0.03uM+1h_b10_6

description: Library name: HN878_RIF_D1_OTB_drug_transcriptome_U_R3_S15_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_INDIGO6OTB_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_INDIGO6OTB_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.

value: Bacteria


title: cardiac tissues, GY3-1d

value: radiation


title: cardiac tissues, WT3-6W


title: HN878_RIF@0.03uM+1h_b10_4

description: Library name: HN878_RIF_D1_OTB_drug_transcriptome_U_R1_S13_R1

value: Wildtype

value: RIF, 0.03uM


title: 6d-WT-1

description: Riboseq

value: Wide type


title: cardiac tissues, WT4-6W


title: Smc3 ChIP, NPC, CTCF-WT rescue, rep2

description: Library name: Smc3_NPC_WT_rep2

value: E14 CTCF-AID2 degron; Dox inducible CTCF-WT rescue

value: 1 uM 5-Ph-IAA + 1 ug/mL Dox


title: Smc3 ChIP, NPC, CTCF-WT rescue, rep1

description: Library name: Smc3_NPC_WT_rep1


title: cardiac tissues, GY1-1d


title: #5-6d-1

description: RNAseq

data_processing:
Low-quality reads and the adapter sequences were filtered by fastp software (version 0.18.0). The reads mapped to ribosome RNA (rRNA) were identified by short reads alignment tool Bowtie2 (version 2.2.8) and removed. The clean reads were mapped to the TAIR10 Arabidopsis reference genome using HISAT2.2.489 and assembled by using StringTie v1.3.1 for each sample in a reference-based approach. For each transcription region, the FPKM (fragment per kilobase of transcript per million mapped reads) value was calculated by using RSEM software. Differential gene expression analysis was performed using DESeq2 software.
Assembly: The clean reads were mapped to the TAIR10 Arabidopsis reference genome using HISAT2.2.4
Supplementary files format and content: The RNAseq counts files included raw counts and FPKM for each sample

extract_protocol:
Six-d-old WT and #5 seedlings were collected and total RNA was extracted using Trizol reagent kit (Invitrogen) according to the manufacturer’s instruction.
The mRNA was enriched by using Oligo(dT) beads, fragmented, and cDNA was synthesized by using the NEBNext Ultra RNA Library Prep Kit for Illumina (NEB #7530, New England Biolabs). The purified double-strand cDNA fragments were end-repaired, A base added, and ligated to Illumina sequencing adapters. The ligation products were purified with the AMPure XP Beads (1.0X), subjected to size selection by agarose gel electrophoresis, and amplified by PCR. Sequencing was performed on an Illumina HiSeq 2500 platform performed by Gene Denovo Biotechnology Co.


title: Smc3 ChIP, ESC, CTCF-ZF1 mutant rescue, rep1

description: Library name: Smc3_ESC_ZF1_rep1


title: 6d-WT-2

description: Riboseq


title: HN878_RIF@0.03uM+1h_b10_5

description: Library name: HN878_RIF_D1_OTB_drug_transcriptome_U_R2_S14_R1

value: 1 hour


title: H37Rv_RIF@0.03uM+1h_b10_6

description: Library name: H37Rv_RIF_D1_OTB_drug_transcriptome_U_R3_S3_R1


title: H37Rv_RIF@0.03uM+8h_b10_1

description: Library name: H37Rv_RIF_D8_OTB_drug_transcriptome_U_R1_S19_R1

value: 8 hours


title: cardiac tissues, WT3-1d

value: control


title: WT-6d-2

description: rnaseq


title: cardiac tissues, WT1-1d


title: #5-6d-2

description: RNAseq


title: cardiac tissues, WT2-1d


title: Smc3 ChIP, ESC, CTCF-WT rescue, rep1

description: Library name: Smc3_ESC_WT_rep1

value: embryonic stem cell

value: Smc3 (Abcam ab9263)


title: Smc3 ChIP, ESC, CTCF-ZF1 mutant rescue, rep2

description: Library name: Smc3_ESC_ZF1_rep2


title: H37Rv_RIF@0.03uM+1h_b10_4

description: Library name: H37Rv_RIF_D1_OTB_drug_transcriptome_U_R1_S1_R1


title: cardiac tissues, GY2-1d


title: WT-6d-1

description: RNAseq

value: whole seedlings


title: Smc3 ChIP, ESC, CTCF-WT rescue, rep2

description: Library name: Smc3_ESC_WT_rep2


title: H37Rv_RIF@0.03uM+1h_b10_5

description: Library name: H37Rv_RIF_D1_OTB_drug_transcriptome_U_R2_S2_R1


title: Rad21 ChIP, NPC, CTCF-ZF1 mutant rescue, rep2

description: Library name: Rad21_NPC_ZF1_rep2

value: Rad21 (Abcam ab217678)


title: p53 YC replicate 3

city: Paris

first: Boris

last: BARDOT

address: 26 rue d'Ulm

country: France

institute: Institut Curie

description: total ribo-depleted RNA

data_processing:
Reads were mapped on mouse genome version GRCm38 with tophat version 2.1.1, with the following parameters : -g 1 -N 3 --read-edit-dist 3 -r 155 --mate-std-dev 80 –no-coverage-search --library-type fr-firststrand.
Only unique mapped reads were kept for further analysis.
Read counting was performed using featureCounts version 1.6.0 on the annotation gencode.vM18, with the following parameters : -F "GTF" -p -s 2 -O.
Assembly: GRCm38
Supplementary files format and content: Tab-delimited text files containing raw read counts for each gene

extract_protocol: RNA was depleted from ribosomal RNA, then converted into cDNA using a TruSeq Stranded Total Library preparation kit (Illumina).

treatment_protocol: Thymus were removed from 8 weeks-old mice, flash frozen on liquid nitrogen, and RNA was extracted using Nucleospin RNA II (Macherey-Nagel). The quality of RNA was checked with Bioanalyzer Agilent and RNAs with a RIN>6 retained for further analyzis

value: Thymus

value: C57BL6/J (> 5 backcrosses)

tag: Sex

value: male

tag: age

value: 8 weeks old


title: H37Rv_INH@3.6uM+1h_b10_3

description: Library name: H37Rv_IHN_D1_OTB_drug_transcriptome_U_R3_S35_R1

value: Bacteria

value: INH, 3.6uM


title: p53 YC replicate 2

description: total ribo-depleted RNA


title: HDFs, senescent cells 3

city: Athens

first: Eleni

last: Mavrogonatou

address: Patriarchou Grigoriou & Neapoleos

department: Institute of Biosciences and Applications

country: Greece

institute: NCSR "Demokritos"

data_processing:
FASTQ files were trimmed with Trim Galore (v.0.6.51) to remove low quality read ends using a Phred score of 20.
A two steps alignment procedure was applied. Pre-processed reads were aligned against the hg38 reference genome (Ensembl) with HISAT2 (v.2.2.1) and then the reads left unmapped were subjected to a second alignment round using BOWTIE2 (v.2.3.5.1) with the -local and -very-sensitive local switches turned on.
Downstream analysis of the resulting BAM files was performed with metaseqR2 R package (v.1.9.2).
Reads were summarized per gene and the returned gene count table was normalized using the Bioconductor package DESeq after removing genes having zero reads across all samples.
Post-normalization, gene counts were filtered for possible artifacts using default gene filtering options.
Assembly: human genome hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample.

source_name: human skin

growth_protocol: All cells were routinely cultured in Dulbecco’s Modified Eagle Medium (DMEM) supplemented with penicillin (100 U/mL)/streptomycin (100 mg/mL) (obtained from Biosera, Nuaillé, France) and 10% (v/v) FBS (from Gibco BRL, Invitrogen, Paisley, UK), were maintained in a humidified atmosphere of 5% CO2 at 37℃ and were subcultured when confluent using a trypsin/citrate (0.25%:0.30% w/v) solution. Cells were regularly tested to ensure their mycoplasma-free status.

extract_protocol:
Total RNA was extracted with Trizol reagent.
For library preparation, the 3′ mRNA-Seq Library Prep Kit Protocol for Ion Torrent (QuantSeq-LEXOGEN™, Vienna, Austria) was used according to the manufacturer’s instructions.

treatment_protocol:
For the induction of premature senescence, primary early-passage (young) HDFs were treated with γ-irradiation in a 60Co gamma source.
For UVB irradiation, confluent culture dishes were placed in the center of a UV box under a UVB lamp with an emission spectrum of 280-360 nm and a peak at 306 nm, after aspiration of the culture medium and its replacement by a thin layer of phosphate-buffered saline (PBS). Right after UVB irradiation, PBS was replaced by fresh culture medium supplemented with 10% (v/v) FBS and cells were further incubated at 37℃ for the selected time periods according to the experimental design. Cells were exposed to repeated doses of 35 mJ/cm2 twice per day for five consecutive days.

value: human skin

value: primary normal human dermal fibroblasts

value: ionizing radiation


title: Rad21 ChIP, NPC, CTCF-ZF1 mutant rescue, rep1

description: Library name: Rad21_NPC_ZF1_rep1

value: E14 CTCF-AID2 degron; Dox inducible CTCF-ZF1 mutant rescue

value: neural progenitor cell

value: 1 uM 5-Ph-IAA + 1 ug/mL Dox


title: HDFs, senescent cells 2


title: p53 YC replicate 1

description: total ribo-depleted RNA


title: H37Rv_INH@3.6uM+1h_b10_2

description: Library name: H37Rv_IHN_D1_OTB_drug_transcriptome_U_R2_S34_R1

value: Wildtype

value: 1 hour


title: H37Rv_INH@3.6uM+1h_b10_1

description: Library name: H37Rv_IHN_D1_OTB_drug_transcriptome_U_R1_S33_R1


title: HDFs, senescent cells 1


title: p53 KO replicate 3

description: total ribo-depleted RNA


title: Rad21 ChIP, NPC, CTCF-WT rescue, rep2

description: Library name: Rad21_NPC_WT_rep2

value: E14 CTCF-AID2 degron; Dox inducible CTCF-WT rescue


title: Rad21 ChIP, NPC, CTCF-WT rescue, rep1

description: Library name: Rad21_NPC_WT_rep1


title: HDFs, UVB-resistant cells 2

value: UVB


title: HDFs, UVB-resistant cells 3


title: p53 KO replicate 2

description: total ribo-depleted RNA


title: CDC1551_RIF@0.03uM+8h_b10_3

description: Library name: CDC1551_RIF_D8_OTB_drug_transcriptome_U_R3_S22_R1

value: RIF, 0.03uM

value: 8 hours


title: p53 KO replicate 1

description: total ribo-depleted RNA

value: Thymus

value: C57BL6/J (> 5 backcrosses)


title: CDC1551_RIF@0.03uM+8h_b10_2

description: Library name: CDC1551_RIF_D8_OTB_drug_transcriptome_U_R2_S21_R1


title: Rad21 ChIP, ESC, CTCF-ZF1 mutant rescue, rep1

description: Library name: Rad21_ESC_ZF1_rep1

value: embryonic stem cell

value: Rad21 (Abcam ab217678)


title: CDC1551_RIF@0.03uM+8h_b10_1

description: Library name: CDC1551_RIF_D8_OTB_drug_transcriptome_U_R1_S20_R1

value: Bacteria


title: Rad21 ChIP, ESC, CTCF-WT rescue, rep2

description: Library name: Rad21_ESC_WT_rep2


title: p53 WT replicate 2

description: total ribo-depleted RNA

value: male

value: 8 weeks old


title: p53 WT replicate 3

description: total ribo-depleted RNA


title: CDC1551_RIF@0.03uM+1h_b10_3

description: Library name: CDC1551_RIF_D1_OTB_drug_transcriptome_U_R3_S6_R1


title: HDFs, young cells 3

value: human skin

value: primary normal human dermal fibroblasts

value: control


title: Rad21 ChIP, ESC, CTCF-WT rescue, rep1

description: Library name: Rad21_ESC_WT_rep1

value: 1 uM 5-Ph-IAA + 1 ug/mL Dox


title: CDC1551_RIF@0.03uM+1h_b10_2

description: Library name: CDC1551_RIF_D1_OTB_drug_transcriptome_U_R2_S5_R1

value: Wildtype


title: HDFs, young cells 2


title: p53 WT replicate 1

description: total ribo-depleted RNA


title: CDC1551_RIF@0.03uM+1h_b10_1

description: Library name: CDC1551_RIF_D1_OTB_drug_transcriptome_U_R1_S4_R1

value: 1 hour


title: CTCF ChIP, NPC, CTCF-ZF1 mutant rescue, rep4

description: Library name: CTCF_NPC_ZF1_rep4

value: E14 CTCF-AID2 degron; Dox inducible CTCF-ZF1 mutant rescue

value: neural progenitor cell

value: CTCF (Abcam ab70303)


title: HDFs, young cells 1


title: CTCF ChIP, NPC, CTCF-ZF1 mutant rescue, rep3

description: Library name: CTCF_NPC_ZF1_rep3


title: CDC1551_INH@3.6uM+1h_b10_1

description: Library name: CDC1551_IHN_D1_OTB_drug_transcriptome_U_R1_S36_R1

value: INH, 3.6uM


title: db/db female

city: Davis

first: Saivageethi

last: Nuthikattu

state: CA

address: 550 Hutchison Dr

department: Internal Medicine, Cardiovascular division

institute: University of California Davis

description:
Parse Biosciences
These raw fastq files of sublibrary 2 and 6 contain uniquely barcoded cells from all eight samples (3,4,9,10,6,12,18, and 24). Samples and processed files details are provided in the sample manifest file.

data_processing:
Each sublibrary contains uniquely barcoded cells from all samples.  Raw sequencing data for sub library-2 and sub library-6 were preprocessed and combined using Parse Biosciences’ split-pipe pipeline (v0.9.6p). Expression matrices were imported into Seurat for downstream analyses.
Assembly: GRCm39
Supplementary files format and content: text

source_name: left hippocampus

extract_protocol:
Wild type (C57BL/6J) and db/db female mice were fed a standard purified diet AIN-93M, for 8 wks. Mice were sacrificed at 18 weeks of age and hippocampus was dissected from left hemisphere and then stored at -80 degree celcius. Hippocampal nuclei was isolated and fixed using Parse biosciences nuclei isolation and fixation protocol.
Barcoded single cell libraries were prepared from fixed single cell suspensions using Evercode Whole Transcriptome Mega kit (Parse Biosciences) following the manufacturer’s instructions.  Individual transcriptomes from all samples were uniquely labeled by passing fixed nuclei through four rounds of barcoding. In each round, pooled cells are randomly distributed into different wells, and transcripts are labeled with well-specific barcodes. Using next-generation sequencing, cells from individual samples are identified using the first well (first barcode) placement. Each sublibrary contains uniquely barcoded cells from all samples.  At the end of library prep, cells are distributed into 16 different sublibraries. The cDNA and library fragment size distribution were verified on a Bioanalyzer 2100 and TapeStation, respectively. The libraries were quantified by fluorometry on a Qubit instrument and by qPCR with a Kapa Library Quant kit prior to sequencing. The libraries were sequenced with paired-end 100 bp reads.  The sequencing generated approximately 35,000 reads per cell.
single nuclei RNA sequencing

value: left hippocampus

value: 4.5 months

value: All hippocampal cells

value: female

value: db/db


title: Rad21 ChIP, ESC, CTCF-ZF1 mutant rescue, rep2

description: Library name: Rad21_ESC_ZF1_rep2

value: embryonic stem cell

value: Rad21 (Abcam ab217678)


title: F3 (RNA-seq)

city: Chicago

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
Align with STAR v2.5.2
Generated count matrix using HTSeq v0.13.5
Normalization w/ DESeq2 v1.37
Assembly: mm10
Supplementary files format and content: Tab-delimited text file includes normalized counts for each sample

source_name: Primary Cells

extract_protocol:
RNA was extracted using RNeasy Mini Kit [Qiagen, #74104]
Libraries were prepared from 1ug of sample RNA using KAPA RNA HyperPrep Kit with RiboErase (HMR) [Roche, # 08098131702]

value: Primary Cells

value: Skeletal Muscle Fibroblasts

value: Aromhum mice

value: Fulvestrant (100nM)

value: 48 hrs


title: DDX54_KD_PD1

city: Yuseong-gu

first: Jeong-Ryeol

last: Gong

state: Daejeon

address: 291, Daehak-ro

institute: KAIST

description: 10x genomics

data_processing:
We processed single cell RNA seq data using CellRanger version 2.1.0 using default parameters.
We aligned data to the mm10 reference genome.
Assembly: mm10
Supplementary files format and content: h5 format files

source_name: Xenograft mass

extract_protocol:
After euthanizing the LLC1 xenograft mouse model, single cells were obtained from the mouse cancer tissues. From this population, CD45-positive immune cells were separated using Aria Fusion (Becton Dickinson) flow cytometry.
10x genomics libraries ( chemistry version 2, 5 prime seq)

value: Xenograft mass


title: HDFs, UVB-resistant cells 1

value: human skin

value: primary normal human dermal fibroblasts

value: UVB


title: WT_DDX54_PD1

description: 10x genomics


title: T46_INH@3.6uM+1h_b10_1

description: Library name: T46_INH_D1_OTB_drug_transcriptome_U_R2_S24_R1.fastq.gz

source_name: Bacteria

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.

value: Bacteria

value: Wildtype

value: INH, 3.6uM

value: 1 hour


title: SG1_INH@3.6uM+1h_b10_1

description: Library name: SG1_INH_D1_OTB_drug_transcriptome_U_R2_S29_R1.fastq.gz


title: CTCF ChIP, NPC, CTCF-ZF1 mutant rescue, rep2

description: Library name: CTCF_NPC_ZF1_rep2

value: E14 CTCF-AID2 degron; Dox inducible CTCF-ZF1 mutant rescue

value: neural progenitor cell

value: 1 uM 5-Ph-IAA + 1 ug/mL Dox

value: CTCF (Abcam ab70303)


title: CTCF ChIP, NPC, CTCF-WT rescue, rep4

description: Library name: CTCF_NPC_WT_rep4

value: E14 CTCF-AID2 degron; Dox inducible CTCF-WT rescue


title: F2 (RNA-seq)

value: Primary Cells

value: Skeletal Muscle Fibroblasts


title: CTCF ChIP, NPC, CTCF-ZF1 mutant rescue, rep1

description: Library name: CTCF_NPC_ZF1_rep1


title: F1 (RNA-seq)

value: Aromhum mice

value: Fulvestrant (100nM)


title: EF3 (RNA-seq)

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

value: 48 hrs


title: DDX54_KD_CTRL

description: 10x genomics

value: Xenograft mass

value: CTRL


title: WT_DDX54_CTRL

description: 10x genomics


title: CTCF ChIP, NPC, CTCF-WT rescue, rep3

description: Library name: CTCF_NPC_WT_rep3


title: SOX4-MKO 2

data_processing:
FPKM values for each sample were calculated using Cufflinks version 2.1.1.Differential gene expression analysis was carried out using the Cuffdiff package.
Assembly: mm10
Supplementary files format and content: tab-delimited text files includeRPKM values for each Sample

source_name: Brown adipose tissue (BAT)

growth_protocol: 15-week-old male mice were housed at colony cages under specific conditions: temperature maintained at 22-24 °C, humidity at 50-60%, and a 12-hour light/dark cycle starting at 7:00 am.

extract_protocol:
Total RNA was isolated using RNeasy Mini Kit (Qiagen) following the manufacturer’s protocol. DNase I in column digestion was included to ensure the RNA quality.
RNA library preparation was performed by using Stranded mRNA-seq Lib Prep Kit for Illumina (Cat. RK20301; ABclonal). Paired-end sequencing was performed with Illumina HiSeq platform.

treatment_protocol: For RNA-Seq, BAT tissues were isolated from 15-week-old male Sox4-MKO mice and control littermate mice  (n = 2 mice per genotype).

value: Brown adipose tissue (BAT)

value: Brown adipose tissue adipocytes


title: EF2 (RNA-seq)


title: CTCF ChIP, NPC, CTCF-WT rescue, rep2

description: Library name: CTCF_NPC_WT_rep2


title: SA161_INH@3.6uM+1h_b10_1

description: Library name: SA161_INH_D1_OTB_drug_transcriptome_U_R2_S23_R1.fastq.gz

value: Bacteria

value: Wildtype

value: INH, 3.6uM


title: SA161_INH@3.6uM+8h_b10_1

description: Library name: SA161_IHN_D8_OTB_drug_transcriptome_U_R2_S36_R1.fastq.gz

value: 8 hours


title: SOX4-MKO 1


title: EF1 (RNA-seq)


title: HN878_INH@3.6uM+1h_b10_3

description: Library name: HN878_INH_D1_OTB_drug_transcriptome_U_R3_S28_R1.fastq.gz

value: 1 hour


title: CTCF ChIP, NPC, CTCF-WT rescue, rep1

description: Library name: CTCF_NPC_WT_rep1

value: neural progenitor cell

value: 1 uM 5-Ph-IAA + 1 ug/mL Dox

value: CTCF (Abcam ab70303)


title: SOX4FF2

value: WT


title: E3 (RNA-seq)

value: Primary Cells

value: Skeletal Muscle Fibroblasts

value: Aromhum mice

value: Estrogen (10nM)


title: T46_INH@3.6uM+1h_b10_2

description: Library name: T46_INH_D1_OTB_drug_transcriptome_U_R3_S25_R1.fastq.gz


title: HN878_INH@3.6uM+1h_b10_2

description: Library name: HN878_INH_D1_OTB_drug_transcriptome_U_R2_S27_R1.fastq.gz


title: SOX4FF1


title: E2 (RNA-seq)

value: 48 hrs


title: HN878_INH@3.6uM+1h_b10_1

description: Library name: HN878_INH_D1_OTB_drug_transcriptome_U_R1_S26_R1.fastq.gz


title: CTCF ChIP, ESC, CTCF-ZF1 mutant rescue, rep3

description: Library name: CTCF_ESC_ZF1_rep3

value: E14 CTCF-AID2 degron; Dox inducible CTCF-ZF1 mutant rescue

value: embryonic stem cell


title: E1 (RNA-seq)


title: H37Rv_INH@3.6uM+8h_b10_3

description: Library name: H37Rv_INH_D8_OTB_drug_transcriptome_U_R3_S32_R1.fastq.gz


title: CTCF ChIP, ESC, CTCF-ZF1 mutant rescue, rep2

description: Library name: CTCF_ESC_ZF1_rep2


title: V3 (RNA-seq)

value: Veh (Ethanol, DMSO)


title: JURKAT, day7, unsorted, rep2

city: Salt Lake City

first: Birgit

last: Knoechel

address: 2000 Circle of Hope

institute: HCI

data_processing:
Sequencing reads were processed using the 'count_spaces_genome.py’ script of the Zhang lab (https://github.com/fengzhanglab/Screening_Protocols_manuscript/)
Assembly: NA
Supplementary files format and content: *._readcount.txt: tab-delimited text file with read counts per sgRNA
Library strategy: CRISPR screen

source_name: Jurkat

growth_protocol: RPMI1640, 10% fetal bovine serum, 25mM HEPES, 55nM B-mercapthoethanol, 1% pen/strep, 1% glutamine,  1% NEAA, 1% Sodium pyruvate at 37C and 5% CO2

extract_protocol:
Cells were lysed in buffer ATL (Qiagen) and decrosslinked overnight at 56C. gDNA was purified using QIAamp DNA Blood Midi Kit (Qiagen).
sgRNA fragments in gDNA were amplified in 2 PCR reactions with a maximum of 35 cycles in total using NEBNext® High-Fidelity 2X PCR Master Mix. Sample barcodes with a stagger region were added in the second PCR. Libraries were gel extracted and purified using Agencourt AMPure XP beads (Beckman Coulter) validated using the Agilent High Sensitivity DNA kit.

value: Jurkat

value: T cell acute lymphoblastic leukemia


title: JURKAT, day7, Galectin9 high20, rep2


title: V2 (RNA-seq)


title: CTCF ChIP, ESC, CTCF-ZF1 mutant rescue, rep1

description: Library name: CTCF_ESC_ZF1_rep1


title: JURKAT, day7, Galectin9 low20, rep2


title: H37Rv_INH@3.6uM+8h_b10_1

description: Library name: H37Rv_INH_D8_OTB_drug_transcriptome_U_R1_S30_R1.fastq.gz

value: Bacteria

value: Wildtype

value: INH, 3.6uM


title: V1 (RNA-seq)


title: CTCF ChIP, ESC, CTCF-WT rescue, rep3

description: Library name: CTCF_ESC_WT_rep3

value: E14 CTCF-AID2 degron; Dox inducible CTCF-WT rescue


title: CTCF ChIP, ESC, CTCF-WT rescue, rep4

description: Library name: CTCF_ESC_WT_rep4

value: 1 uM 5-Ph-IAA + 1 ug/mL Dox


title: JURKAT, day7, unsorted, rep1


title: F3 (ATAC-seq)

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

extract_protocol:
Cell pellets were processed according to manufacturer’s instructions - ATAC-Seq Kit (Active Motif, # 53150)
ATAC-Seq Kit (Active Motif, # 53150)

value: Fulvestrant (100nM)

value: 1 hr


title: JURKAT, day7, Galectin9 low20, rep1


title: CDC1551_INH@3.6uM+8h_b10_3

description: Library name: CDC1551_INH_D8_OTB_drug_transcriptome_U_R3_S35_R1.fastq.gz

value: 8 hours


title: JURKAT, day7, Galectin9 high20, rep1


title: CTCF ChIP, ESC, CTCF-WT rescue, rep2

description: Library name: CTCF_ESC_WT_rep2

value: CTCF (Abcam ab70303)


title: F2 (ATAC-seq)

value: Primary Cells

value: Skeletal Muscle Fibroblasts

value: Aromhum mice


title: CTCF ChIP, ESC, CTCF-ZF1 mutant rescue, rep4

description: Library name: CTCF_ESC_ZF1_rep4

value: E14 CTCF-AID2 degron; Dox inducible CTCF-ZF1 mutant rescue


title: CTCF ChIP, ESC, CTCF-WT rescue, rep1

description: Library name: CTCF_ESC_WT_rep1

value: embryonic stem cell


title: F1 (ATAC-seq)


title: CDC1551_INH@3.6uM+8h_b10_1

description: Library name: CDC1551_INH_D8_OTB_drug_transcriptome_U_R1_S33_R1.fastq.gz


title: HPB-ALL, H3K27ac, HiChIP

data_processing:
Sequencing reads were processed by HiC-Pro 2.10.0 alligned to reference genome hg19 with default settings.
HiChIP matrices and bam files were generated using HiCExplorer 3.4.1.
Normalized bigwigs were generated by bamCoverage from deeptools 3.0.2.
HiChIP-seq peaks were called by HiCHIP-Peaks 0.1.2 and HiChIP loops by the hichipper 0.7.7. algorithm
Assembly: hg19
Supplementary files format and content: bam and matrix files (HiC explorer 3.4.1)
Supplementary files format and content: bigwig (bamCoverage from deeptools 3.0.2)
Supplementary files format and content: links (hichipper 0.7.7)
Library strategy: HiChIP-seq

source_name: HPB-ALL

extract_protocol:
Cells were fixed with 1% formaldehyde for 15 min at RT with rotation. After quenching and cell lysis, chromatin was digested using MBol restriction enzyme. Overhangs were filled with biotin-dATP, dCTP, dGTP, dTTP and ligated with T4 DNA ligase followed by sonication using a Covaris S220 Sonicator.
Immunoprecipitated DNA was captured by biotin pull-down, transposed with Tn5 and amplified. Post amplification libraries were purified using Agencourt AMPure XP beads (Beckman Coulter) and validated using the Agilent High Sensitivity DNA kit.

value: HPB-ALL


title: H37Rv_INH@3.6uM+8h_b10_2

description: Library name: H37Rv_INH_D8_OTB_drug_transcriptome_U_R2_S31_R1.fastq.gz


title: Loucy, H3K27ac, HiChIP

source_name: Loucy

value: Loucy


title: CDC1551_INH@3.6uM+1h_b10_3

description: Library name: CDC1551_INH_D1_OTB_drug_transcriptome_U_R3_S21_R1.fastq.gz

value: 1 hour


title: KOSBR

city: New York

first: David

last: Redmond

state: New York

address: 1300 York Avenue

institute: Weill Cornell Medicine

description: 10X Genomics

data_processing:
Sequencing data from the Illumina NovaSeq were aligned to mouse mm10 in CellRanger v5.0.1.
Assembly: mm10
Supplementary files format and content: HDF5 file

source_name: Proximal Colon

extract_protocol:
The tissue samples were incubated in 20mM EDTA-PBS while rocking in a cold room for 90 minutes. Every 30 minutes, the tubes containing the intestinal tissues were shaken vigorously for one minute to collect dissociated epithelial fractions. After 90 minutes, the three collections from each tissue were combined and dissociated into single cells using TrypLE for one minute at 37°C.The single-cell suspensions in FACS buffer (containing 1% glucose, 10mM HEPES, 10μM Y-27632, 1mM N-acetyl-L-cysteine, and 2% FBS in DPBS) were passed through a 40μm filter. The cells were then stained with anti-mouse CD326 (EpCam, Key Resources Table). Live EpCam+ epithelial cells were sorted using a Symphony S6 II cell sorter in FACS buffer.
For each sample, 10,000 cells were loaded into each channel of the Chromium Controller cartridge to produce droplets. Beads-in-emulsion (GEMs) were transferred, and GEM reverse transcription (GEM-RT) was performed in droplets via PCR incubation. After the post-GEM-RT reaction, first-strand cDNA was purified. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size. TruSeq Read 1 (read 1 primer sequence) was added during GEM incubation. A sample index and TruSeq Read 2 (read 2 primer sequence) were added through end-repair, A-tailing, adaptor ligation, and PCR. The final libraries were assessed using an Agilent Technology 2100 Bioanalyzer and sequenced on an Illumina NovaSeq sequencer.

value: Proximal Colon

value: Epithelial cells

value: Corn oil


title: Jurkat, H3K27ac, HiChIP

value: Jurkat

value: T cell acute lymphoblastic leukemia


title: EF2 (ATAC-seq)

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


title: H37Rv_Untreated@0+-1h_b3_9

description: Library name: Untreat_R3_S30

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_INDIGO2PPIs_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_INDIGO2PPIs_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.

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: 16 hours


title: EF3 (ATAC-seq)

value: Primary Cells

value: Skeletal Muscle Fibroblasts

value: 1 hr


title: EF1 (ATAC-seq)

value: Aromhum mice


title: H37Rv_Untreated@0+-1h_b3_8

description: Library name: Untreat_R2_S29


title: Retina_OIR-Norm_P18_rep3

first: Frederic

last: Blond

address: 17 rue Moreau

institute: Institut de la Vision

data_processing:
After sequencing, fastq files were aligned to the Mus musculus reference genome from Ensembl (Ensembl 105, December 2021) using STAR (version 2.7.9a) with the option “- -quantMode GeneCounts” to extract the raw counts for each gene, and all count files were concatenated into a single file.
The count file and a descriptive sample file were loaded into our in-house R Shiny application “EyeDVseq” for analysis: the genes with a total count below 10 across samples were filtered out and the differential gene expression analysis was performed using the version 1.40.2 DESeq integrated into EyeDVseq, comparing OIR-Norm as control and OIR-CIH as the condition.
The resulting gene list was then filtered, with |Log2(Fold Change)| > 0.5 and pAdj-values < 0.05 being considered significant.
Assembly: GRCm38 Ensembl release 105
Supplementary files format and content: Comma-separated file including raw counts for all Samples
Supplementary files format and content: Comma-separated file containing all Samples metadata

source_name: retina

growth_protocol: In an adaptation of the widely used OIR model (13) C57BL/6J mice at postnatal (PN) day 8 (PN8) were exposed, with their mothers, for 5 days to hyperoxic conditions (75% O2), inducing vaso-obliteration and subsequent capillary loss of the central retinal vasculature (13). At PN13, mice were returned to room-air conditions which induces extensive neovascularization in all experimental mice with maximum effects on PN18.

extract_protocol:
Fresh eyes (3 eyes from the OIR-Norm group, 3 eyes from the OIR-CIH group, all at PN18) were dissected on ice to isolate retinas immediately after enucleation. Retinal RNA was extracted using the NuceloSpin RNA kit (Macherey-Nagel) according to the Midi protocol in the manufacturer's instructions. RNA quality was confirmed using a Bioanalyzer RNA Analysis kit (Agilent).
RNA sequencing libraries were prepared from 250 ng total RNA using the TruSeq Stranded mRNA Library Prep kit (Illumina)

treatment_protocol: CIH was induced in C57BL6/J mice using a Hycon0520 simulator that can oscillate the cage O2 concentration extremely quickly. For 10 hours during the daytime (corresponding to the mouse sleep period) CIH experimental animals were exposed daily to 266 cycles of a 135s program of oscillating O2 concentration as follows: decrease of 20.95% O2 to 5% O2 in 45s, 5% O2 for 30s, increase to 20.95% O2 in 15s, 45s of 20.95% O2 (adapted from Xu et al.). Control animals were exposed to the same flow (and noise) of gasses, without affecting O2 concentrations.

value: retina

value: wt

value: Control


title: HPB-ALL, WCE (for H3K27ac)

data_processing:
Nextflow ChIP-seq pipeline 1.0.0. was used with default settings to analyze ChIP-sequencing data. Sequencing reads were aligned to the hg19 genome.
Assembly: hg19
Supplementary files format and content: bigWig, narrowPeak (IRF1/TFAP4 ChIP only), broadPeak (H3K27ac ChIP only)

extract_protocol:
Cells were fixed with 1% formaldehyde for 15 min at RT with rotation. After quenching and cell lysis, chromatin was sonicated using a Covaris S220 Sonicator
ChIP-seq libraries were prepared using the End-It DNA End-Repair Kit (Lucigen), Klenow enzyme (3’-5’ exo 5U/ul, NEB) for A-tailing and Quick Ligation Kit (NEB) for adapter ligation. Libraries were amplified (PFU Ultra II HS (Agilent)) using 14 cycles on the thermocycler. Post amplification libraries were purified using Agencourt AMPure XP beads (Beckman Coulter) and validated using the Agilent High Sensitivity DNA kit.

value: HPB-ALL


title: E3 (ATAC-seq)

value: Estrogen (10nM)


title: Retina_OIR-Norm_P18_rep2


title: CCRF-CEM, H3K27ac, HiChIP

source_name: CCRF-CEM

value: CCRF-CEM


title: CDC1551_INH@3.6uM+8h_b10_2

first: Ethan

last: Bustad

address: 1900 Ninth Ave.

institute: Seattle Children's Research Institute

description: Library name: CDC1551_INH_D8_OTB_drug_transcriptome_U_R2_S34_R1.fastq.gz

value: INH, 3.6uM

value: 8 hours


title: Retina_OIR-Norm_P18_rep1


title: HPB-ALL, H3K27ac, ChIP

value: T cell acute lymphoblastic leukemia

value: H3K27ac (Abcam, ab4729)


title: E2 (ATAC-seq)


title: H37Rv_Untreated@0+-1h_b3_7

description: Library name: Untreat_R1_S28

value: Bacteria

value: Wildtype


title: Retina_OIR-CIH_P18_rep3

value: CIH


title: H37Rv_Untreated@0+-1h_b3_6

description: Library name: U3_S7

value: Untreated

value: 16 hours


title: Loucy, WCE

value: Loucy


title: E1 (ATAC-seq)

value: Primary Cells

value: Skeletal Muscle Fibroblasts

value: Aromhum mice

value: 1 hr


title: Retina_OIR-CIH_P18_rep2

value: retina

value: wt


title: SBR

description: 10X Genomics

value: Proximal Colon

value: Epithelial cells

value: TAM


title: Loucy, TFAP4, ChIP

value: T cell acute lymphoblastic leukemia

value: TFAP4 (Sigma Aldrich, HPA001912)


title: H37Rv_Untreated@0+-1h_b3_5

description: Library name: U2_S4

value: Bacteria


title: V3 (ATAC-seq)

value: Veh (Ethanol, DMSO)


title: CDC1551_INH@3.6uM+1h_b10_2

description: Library name: CDC1551_INH_D1_OTB_drug_transcriptome_U_R2_S20_R1.fastq.gz

value: Wildtype

value: INH, 3.6uM

value: 1 hour


title: Retina_OIR-CIH_P18_rep1

value: CIH


title: Loucy, IRF1, ChIP

value: Loucy

value: IRF1 (Cell Signaling, 8478)


title: H37Rv_Untreated@0+-1h_b3_4

description: Library name: U1_S1

value: Untreated

value: 16 hours


title: V2 (ATAC-seq)

value: Primary Cells

value: Skeletal Muscle Fibroblasts

value: Aromhum mice

value: 1 hr


title: H37Rv_OMP@400uM+-1h_b3_3

description: Library name: O3_S9

value: OMP, 400uM


title: KOPT-K1, WCE

value: T cell acute lymphoblastic leukemia


title: H37Rv_OMP@400uM+-1h_b3_2

description: Library name: O2_S6


title: V1 (ATAC-seq)


title: KOPT-K1, TFAP4, ChIP

value: TFAP4 (Sigma Aldrich, HPA001912)


title: tumor, reta wd, mouse 236, rep6

first: Matthew

middle: A

last: Cottam

state: TN

address: 2301 Vanderbilt Place

department: Surgical Sciences

description:
Library name: S000005-42057-002
Treatment switched from RETA (30 nmol/Kg) to Veh (water), two weeks after starting RETA treatment

data_processing:
Reads from RNAseq data were quality controlled and aligned using the nf-core/RNAseq pipeline.
Aligned transcript counts were imported into R v4.2.2 using Tximport v1.32.0. Low capture genes with less than ten total counts summed across all samples were removed.
Assembly: GRCm39
Supplementary files format and content: Normalized_counts_all-samples.csv contains normalized counts of aligned reads using Deseq2.

source_name: KPCY pancreatic cancer tumor

growth_protocol: The UTHSC Animal Care and Use Committee (IACUC) approved all protocols and methods following protocol #24-0504.0. All animals in the study were kept on a 12 hr light/dark cycle and fed 60 kcal% from high-fat diet (D12492i, Research Diets Inc.). KPCY 2838 mouse pancreatic cancer cell line was acquired from Kerafast® (Shirley, MA). KPCY cells were cultured in DMEM (Cat. No. 11965092, Gibco, Waltham, MA) supplemented with 1% penicillin-streptomycin (Cat. No. SV30010, HyClone™, Cytiva, Marlborough, MA), 1% GlutaMAX (Cat. No. 35050061, Gibco, Waltham, MA), and 10% FBS (Cat. No. 26140-087 Gibco, Waltham, MA) per instructions from Kerafast® for subcutaneous injections in N = 36 male obese C57BL/6J mice (21 weeks old). Two x 10^5 KPCY 2838 cells in sterile PBS were injected subcutaneously in the right flank. Mice were palpated at injection sites every three days for one week after injecting the cells, after which the tumors were measured every other day using a digital caliper.

extract_protocol:
At the beginning of the treatment, mice were randomly segregated into three groups that included vehicle (water, N = 10), RETA (30 nmol/Kg, N = 12), or RETA-withdrawal (switched from 30 nmol/Kg RETA to water after stabilized weight loss, N = 14). Tumor size was calculated using the formula (width^2 × length/2). Body weights were recorded every day. Mice were sacrificed at endpoint and tumors were excised, weighed, and snap-frozen in liquid nitrogen. Tumor RNA seq analysis was performed for a subset of mice from each treatment group.
mRNA-seq libraries for the Illumina platform were generated and sequenced at Azenta using the Illumina HiSeq 2 × 150 bp configuration following the manufacturer’s protocol. ~30 million paired-end reads per sample.

value: KPCY pancreatic cancer tumor

value: KPCY

value: KPCY 2838 pancreatic cancer cells

value: RETA withdrawal


title: tumor, reta wd, mouse 233, rep5

description:
Library name: S000005-42054-002
Treatment switched from RETA (30 nmol/Kg) to Veh (water), two weeks after starting RETA treatment

treatment_protocol: At the beginning of the treatment, mice were randomly segregated into three groups that included vehicle (water, N = 10), RETA (30 nmol/Kg, N = 12), or RETA-withdrawal (switched from 30 nmol/Kg RETA to water after stabilized weight loss, N = 14). Tumor size was calculated using the formula (width^2 × length/2). Body weights were recorded every day. Mice were sacrificed at endpoint and tumors were excised, weighed, and snap-frozen in liquid nitrogen. Tumor RNA seq analysis was performed for a subset of mice from each treatment group.


title: KOPT-K1, IRF1, ChIP


title: H37Rv_LAN@200uM+-1h_b3_3

description: Library name: L3_S8

value: Bacteria

value: Wildtype

value: LAN, 200uM


title: H37Rv_OMP@400uM+-1h_b3_1

description: Library name: O1_S3


title: tumor, reta wd, mouse 231, rep4

description:
Library name: S000005-42052-002
Treatment switched from RETA (30 nmol/Kg) to Veh (water), two weeks after starting RETA treatment


title: H37Rv_LAN@200uM+-1h_b3_2

description: Library name: L2_S5


title: Jurkat, TFAP4, ChIP

value: Jurkat


title: H37Rv_LAN@200uM+-1h_b3_1

description: Library name: L1_S2


title: Jurkat, IRF1, ChIP

value: IRF1 (Cell Signaling, 8478)


title: tumor, reta wd, mouse 221, rep3

description:
Library name: S000005-42043-002
Treatment switched from RETA (30 nmol/Kg) to Veh (water), two weeks after starting RETA treatment


title: HPB-ALL, WCE

value: HPB-ALL


title: tumor, reta wd, mouse 210, rep1

description:
Library name: S000005-42034-002
Treatment switched from RETA (30 nmol/Kg) to Veh (water), two weeks after starting RETA treatment


title: tumor, reta wd, mouse 212, rep2

description:
Library name: S000005-42036-002
Treatment switched from RETA (30 nmol/Kg) to Veh (water), two weeks after starting RETA treatment


title: H37Rv_VER@80uM+-1h_b3_3

description: Library name: CV80_S26

value: VER, 80uM

value: 16 hours


title: HPB-ALL, TFAP4, ChIP


title: Jurkat, WCE


title: tumor, reta, mouse 218, rep4

description:
Library name: S000005-42041-002
Treated subcutaneously with 100 uL 30 nmol/Kg RETA (prepared in water) every other day

value: RETA


title: HPB-ALL, IRF1, ChIP


title: DND-41, WCE


title: tumor, reta, mouse 214, rep3

description:
Library name: S000005-42038-002
Treated subcutaneously with 100 uL 30 nmol/Kg RETA (prepared in water) every other day


title: VDAC2KO_IFNg1

type: RNA

city: Memphis

first: Hongbo

last: Chi

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 human 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: VDAC2 KO LOVO tumor cells with IFNg treatment

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

growth_protocol: Cells were cultured with EMEM medium ( 10% FBS).

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

treatment_protocol: WT and VDAC2 KO LOVO tumor cells were left untreated or treated with IFNg treatment (10ng/ml) for 48 hours.

value: LOVO tumor cells


title: H37Rv_RAB@200uM+-1h_b3_3

city: Seattle

description: Library name: CR200_S22

value: RAB, 200uM


title: DND-41, TFAP4, ChIP

value: T cell acute lymphoblastic leukemia


title: tumor, reta, mouse 213, rep2

description:
Library name: S000005-42037-002
Treated subcutaneously with 100 uL 30 nmol/Kg RETA (prepared in water) every other day


title: VDAC2KO_IFNg2


title: H37Rv_PAN@800uM+-1h_b3_3

description: Library name: CP800_S24

value: PAN, 800uM


title: VDAC2KO_IFNg3


title: VDAC2KO1

source_name: VDAC2 KO LOVO tumor cells without IFNg treatment


title: WT3

source_name: WT LOVO tumor cells without IFNg treatment


title: VDAC2KO3


title: WT_IFNg1

source_name: WT LOVO tumor cells with IFNg treatment


title: WT_IFNg2


title: WT_IFNg3


title: DND-41, IRF1, ChIP


title: H37Rv_Untreated@0+-1h_b3_3

description: Library name: CUNT_S27

value: Untreated


title: tumor, reta, mouse 209, rep5

description:
Library name: S000005-42033-002
Treated subcutaneously with 100 uL 30 nmol/Kg RETA (prepared in water) every other day

value: KPCY pancreatic cancer tumor

value: KPCY


title: H37Rv_VER@80uM+-1h_b3_2

description: Library name: BV80_S20


title: tumor, reta, mouse 206, rep1

description:
Library name: S000005-42031-002
Treated subcutaneously with 100 uL 30 nmol/Kg RETA (prepared in water) every other day

value: KPCY 2838 pancreatic cancer cells


title: WT2