title: H3K4me3_CS_VC02


title: PA_LTi_rep2

status: Public on Sep 03 2021

type: SRA

city: Beijing

first: Chao

last: Zhong

address: 38 Xueyuan Rd , Haidian District

department: Institute of Systems Biomedicine

country: China

institute: Peking University

description:
P-2
Bulk RNA-Seq

library_source: transcriptomic

data_processing:
Illumina Casava1.8 software used for basecalling.
For bulk RNA-Seq, sequence reads were mapped to the mouse (mm10) genome with hisat2 (2.1.0) with default settings and we kept one hit if multiple reads were mapped to the same position for each RNA-Seq library. For each RNA-Seq sample, gene expression was quantified using featureCounts function in Subread package.
For single-cell RNA-Seq, the sequencing data were aligned and quantified using the BD Rhapsody WTA Local bioinformatics pipeline (version 1.9.1, BD) against the mouse GRCm39 reference genome.
Genome_build: mm10 (bulk RNA-Seq) / GRCm39 (single-cell RNA-Seq)
Supplementary_files_format_and_content: *.txt: Read count; plain text files; Columns from left to right denote ENSEMBL ID, chromosome, start, end, strand, exon length, number of read mapped to exons.

molecule: total RNA

organism: Mus musculus

source_name: LTi cultured in presence of palmitic acid

extract_protocol:
(WT/KO:PD-1-high/PD-1-neg): Single cell suspension were obtained from the colon lamina propria of C57BL/6 mice. For sorting huPD-1high LTi and huPD-1- LTi cells, cells were stained with relative antibodies followed by sorting on a BD Aria III cell sorter for "live Lineage-CD127+KLRG-1-c-Kit+CCR6+huPD-1high" and "live Lineage-CD127+KLRG-1-c-Kit+CCR6+huPD-1-" cells.(C-1, C-2, P-1, P-2): Single cell suspension were obtained from the small intestinal lamina propria of B6 mice. For sorting LTi cells, cells were stained with relative antibodies followed by sorting on a BD Aria III cell sorter for "live Lineage-CD127+KLRG-1-c-Kit+CCR6+"siLP-ILC: Single cell suspension were obtained from the small intestinal lamina propria of C57BL/6 mice. For sorting ILC, cells were stained with relative antibodies followed by sorting on a BD Aria III cell sorter for "live Lineage-CD127+“
Bulk RNA-Seq: The sorted LTi were collected in lysis buffer of the SMART-Seq HT Kit (Takara) followed with cDNA synthesis and amplification according to the manufacturer’s protocols. Sequencing libraries were generated using NEB Next Ultra DNA Prep Kit (New England Biolabs), according to the manufacturer’s instruction. Libraries were assessed using the Agilent 2100 Bioanalyzer system and sequenced by paired-end 150 base pair reads using the Illumina NovaSeq platform. single-cell RNA-Seq: Small intestine lamina propria lymphocytes were stained for ILC sorting (live lineage-CD127+) by FACSAria III Cell Sorter (BD Biosciences). The viability of sorted cells was assessed as >90%. Single cell capture and cDNA synthesis were performed on the BD Rhapsody Single-Cell Analysis System (BD), according to the manufacturer’s instruction. Then, the single-cell library was generated and sent to sequencing on Illumina NovaSeq platform.

treatment_protocol: (WT/KO:PD-1-high/PD-1-neg): Age-matched adult Pdcd1hu/+ mice and Pdcd1hu/- mice were administrated fed with 3% (w/v) DSS in their drinking water for 6 days, followed with recovery by DSS withdrawal for 1 day. (C-1, C-2, P-1, P-2): LTi were sorted from siLP of adult B6 mice. The sorted LTi were cultured in presence or absence of palmitic acid (100mM ) for 3 days.sc-siLP-ILC: ILC were sorted from siLP of adult B6 mice.

tag: strain

tag: isolate

value: isolated from small intestinal lamina propria lymphocytes

tag: in vivo treatment

tag: in vitro treatment

value: cultured in presence of palmitic acid


title: sc-siLP-ILC

description:
sc-siLP-ILC
Sc-RNA-Seq

source_name: small intestinal lamina propria ILC sorted from B6 mice


title: H3K27me3_CTL_HCTR13

city: Barcelona

first: Mar

last: Gonzalez-Ramirez

address: C/ Dr Aiguader 88

country: Spain

institute: Center for Genomic Regulation (CRG)

library_source: genomic

data_processing:
ChIP-seq analysis: Alignment: Sequence reads of the samples with spike-in were mapped to a synthetic genome containing the human and the fruit fly chromosomes (hg19+dm3) using BOWTIE (PubMed ID 19261174) with the option -m 1. Peak detection was performed with MACS (PubMed ID: 18798982). Peaks were reported in BED format. ChIP-seq genome-wide profiles with spike-in were normalized by the total number of fly reads of each sample.
RNA-seq analysis: Alignment: Sequence reads were mapped against the hg19 mouse genome assembly using TopHat (PubMed ID 22383036) with the option ‐g 1.
Genome_build: hg19
Supplementary_files_format_and_content: Files *.bedgraph.gz (BedGraph, genome-wide ChIP-seq/RNA-seq)

molecule: genomic DNA

organism: Homo sapiens

extract_protocol:
For RNAseq: RNA was extracted using RNeasy Lipid Tissue Mini kit (Qiagen).
For ChIPseq: ChIP experiments were carried out following a standard protocol in the lab (Morey et al., Cell Stem Cell 2013).
Libraries were prepared according to Illumina instructions.

treatment_protocol: Patients with  tumoral adenocortical Cushing Syndrome and control patients matched by BMI, sex, age and cardiometabolic features.

tag: tissue

value: visceral adipose tissue

tag: chip antibody

value: H3K27me3 (Millipore #07–449)

tag: status

value: CTL

tag: drosophila spike-in

value: YES


title: Ctr_LTi_rep2

description:
C-2
Bulk RNA-Seq

source_name: LTi cultured in absence of palmitic acid

value: cultured in absence of palmitic acid


title: RNA-Seq Pre-exposure prophylaxis sample 30, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library

city: Montreal

first: Erwin

last: Schurr

address: 1001 boulevard Decarie

country: Canada

institute: McGill University Health Centre

description:
Pre-exposure prophylaxis sample 30, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library
mRNA, poly-A selected
PrEP.AMP30.MTB.0_RNA_R1_quant.sf

data_processing:
Basecalling was done with Illumina Casava 1.8.2 and fastq files generated via bcl2fastq v2.18.
Fastq files were trimmed to remove leftover adaptor sequences and < phred 20 bases using cutadapt v2.6.
Read alignment was performed with STAR v2.7.3a and resulting alignments in transcriptomic coordinates was input to Salmon v1.1.0 for gene expression estimation.
Gene level estimated counts matrix was created in R v3.6.1, using tximport v1.12.3 with the option “lengthScaledTPM”.
Libray depth and compositional bias scaling factors were calculated via the function calcNormFactors from edgeR v3.26.8 and used by limma’s voom function (v3.40.6) to generate the normalized log2(CPM) expression matrix.
Genome_build: GRCh38.p13 (ENSEMBL v99)
Supplementary_files_format_and_content: tab-delimited text files including transcript estimated counts and TPM values for each sample.
Supplementary_files_format_and_content: tab-delimited matrix table with raw estimated gene counts for every gene and sample (lengthScaledTPM).
Supplementary_files_format_and_content: tab-delimited matrix table with normalized gene expression in log2 scale for tested genes (created with limma's voom function). Covariates not regressed out.

source_name: bronchoalveolar lavage

extract_protocol:
Cells were lysed with Trizol and kept at -80°C until extraction.  RNA isolation was performed with miRNeasy kit and RNA integrity (RIN) was assessed with the Agilent 2100 Bioanalyzer.
RNA libraries were prepared for sequencing using standard unstrand Illumina protocols (TruSeq RNA Library Preparation Kit v2, Set A ).

treatment_protocol: Bronchoalveolar lavage samples were filtered to remove macro contaminants and alveolar macrophages (AM) cells enrich via tube adhesion method. 1 x 106 AM cells were cultured with media (not challenged) or media + Mtb (challenged) for 20h.

tag: ethnicity

value: Caucasian

tag: Sex

value: M

tag: age

value: depression

tag: sexually transmitted infections

value: no

tag: quantiferon tb reagent

tag: cd4 count

tag: viral load

value: not detected

tag: prescription drugs

value: Truvada

tag: active ingredient

value: Emtricitabine, Tenofovir_DF

tag: art start year

tag: recreational drugs

tag: cigarette smoker

tag: bal sampling date

tag: mtb challenged

tag: rin

tag: average library size

tag: sequencing run

tag: lane


title: RNA-Seq Pre-exposure prophylaxis sample 31, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library

description:
Pre-exposure prophylaxis sample 31, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library
mRNA, poly-A selected
PrEP.AMP31.MTB.0_RNA_R1_quant.sf

tag: ethnicity

tag: Sex


title: RNA-Seq Pre-exposure prophylaxis sample 29, Alveolar macrophage, Mycobacterium tuberculosis challenged library

description:
Pre-exposure prophylaxis sample 29, Alveolar macrophage, Mycobacterium tuberculosis challenged library
mRNA, poly-A selected
PrEP.AMP29.MTB.1_RNA_R1_quant.sf

value: North african

tag: age

tag: sexually transmitted infections

value: chlamydia PCR+

value: yes

value: cannabis


title: H3K4me3_CS_H507

tag: tissue

tag: chip antibody

tag: status

value: CS

tag: drosophila spike-in


title: RNA-Seq Pre-exposure prophylaxis sample 30, Alveolar macrophage, Mycobacterium tuberculosis challenged library

description:
Pre-exposure prophylaxis sample 30, Alveolar macrophage, Mycobacterium tuberculosis challenged library
mRNA, poly-A selected
PrEP.AMP30.MTB.1_RNA_R1_quant.sf

tag: quantiferon tb reagent

tag: cd4 count

tag: viral load

tag: prescription drugs

tag: active ingredient

tag: art start year


title: Ctr_LTi_rep1

description:
C-1
Bulk RNA-Seq

tag: strain

tag: isolate

value: isolated from small intestinal lamina propria lymphocytes

tag: in vivo treatment

tag: in vitro treatment


title: PA_LTi_rep1

description:
P-1
Bulk RNA-Seq

value: cultured in presence of palmitic acid


title: Patient 1 Lung Scan 26689 A10 ROI 007

type: RNA

city: New York

first: Robert

last: Sebra

state: NY

address: One Gustave L. Levy Place

department: Genetics and Genomic Sciences

country: USA

institute: Icahn School of Medicine at Mount Sinai

description: Unstained 4μm-thick sections were cut from FFPE blocks from two patients and immunoflourescently labeled with PanCK, CD45, CD68 and DAPI. Twelve regions of interest (ROIs) per slide were selected for targeted spatial transcriptomics (GeoMx, Nanostring) with >1,600 cancer atlas transcripts and 10 additional SARS-CoV-2 genes.

hyb_protocol: Immunoflourecent tissue profiling was performed using PanCK (488) cytokeratin, CD45 (647) immune response, CD68 (568) macrophage inflammatory response, and DAPI DNA staining to enable selection of 12 regions of interest (ROIs) for targeted spatial transcriptomics using the commercial Nanostring GeoMx.

scan_protocol: Nanostring GeoMx Digital Spatial Profiling (DSP) Platform

data_processing:
Digital Count Coversion (DCC) files are generated by GeoMx NGS Pipeline. The pipeline processed reads for high quality with adapter removal resulting in trimmed reads, and the paired-end reads were merged and aligned. Then PCR duplicates were removed by matching on the Unique Molecular Index (UMI), resulting in deduplicated reads.
Biological Probe QC was performed  to exclude outlier probes.
QC was done in two steps, first Segment QC and then Biological Probe QC.  In segment QC, raw read threshold, percent aligned reads, sequence saturation and technical background were compared to an expected range to determine the overall quality of the data. We then performed Biological Probe QC to determine the thresholds for excluding outlier probes. Once all ROIs were processed, the raw counts were Q3 normalized against housekeeping genes by averaging to the geometric mean of the internal spike-in controls by which system variation was accounted for.
Normalization was done by Nanostring's software. The raw counts were Q3 normalized against housekeeping genes by averaging to the geometric mean of the internal spike-in controls.

source_name: Lung

label_protocol: The spatial transcriptomic panel included >1600 targeted cancer transcriptome atlas panel with 27 additional SARS-CoV-2 targets added (including ORF1ab and S protein)  to encompass a comprehensive detection of host immune and inflammatory response alongside direct SARS-CoV-2 infection genes.

extract_protocol: Unstained sections were freshly cut from FFPE blocks at 4µm-thickness onto positively charged slides, stored at 4ºC.

tag: scan id

tag: roi(lable)


title: Patient 1 Lung Scan 26689 A10 ROI 008


title: H3K27me3_CTL_H465

value: visceral adipose tissue

value: H3K27me3 (Millipore #07–449)

value: CTL


title: RNA-Seq Pre-exposure prophylaxis sample 28, Alveolar macrophage, Mycobacterium tuberculosis challenged library

description:
Pre-exposure prophylaxis sample 28, Alveolar macrophage, Mycobacterium tuberculosis challenged library
mRNA, poly-A selected
PrEP.AMP28.MTB.1_RNA_R1_quant.sf

tag: ethnicity

value: Caucasian

tag: Sex

tag: age

tag: sexually transmitted infections

tag: recreational drugs

tag: cigarette smoker

tag: bal sampling date

tag: mtb challenged

tag: rin

tag: average library size

tag: sequencing run

tag: lane


title: RNA-Seq Pre-exposure prophylaxis sample 29, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library

description:
Pre-exposure prophylaxis sample 29, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library
mRNA, poly-A selected
PrEP.AMP29.MTB.0_RNA_R1_quant.sf

value: M

tag: quantiferon tb reagent

tag: cd4 count

tag: viral load

tag: prescription drugs

tag: active ingredient

tag: art start year


title: H3K27me3_CTL_H425

tag: tissue

tag: chip antibody

tag: status

tag: drosophila spike-in

value: YES


title: Patient 1 Lung Scan 26689 A10 ROI 005

tag: scan id

tag: roi(lable)


title: Patient 1 Lung Scan 26689 A10 ROI 006


title: H3K27me3_CS_VC06


title: N2A_Neurite_GFP_Rep2

city: Aurora

first: Matthew

last: Taliaferro

state: CO

department: Biochemistry and Molecular Genetics

institute: University of Colorado Anschutz Medical Campus

data_processing:
Adapters were trimmed using Cutadapt
Reads were aligned using bowtie2
The number of unique UMIs per reference oligonucleotide was calcuated using https://github.com/TaliaferroLab/OligoPools/blob/master/analyzeresults/UMIsperOligo.py
Genome_build: mm10
Supplementary_files_format_and_content: txt files containing the number of unique umis for each oligonucleotide

source_name: Mouse Neuro2A cell line

growth_protocol: CAD cells were grown in DMEM/F12. N2A cells were grown in DMEM. Both were supplemented with 10% FBS. To differentiate cells, FBS was removed.

extract_protocol:
RNA was extract with Zymo Quick RNA microprep kits
Libraries were constructed using gene-specific RT-PCR

tag: reporter scaffold

value: GFP

tag: compartment

value: Neurite

tag: cell line


title: Patient 1 Lung Scan 26689 A10 ROI 004


title: Patient 1 Lung Scan 26689 A10 ROI 010


title: H3K27me3_CS_VC02


title: Patient 1 Lung Scan 26689 A10 ROI 009


title: N2A_Neurite_GFP_Rep3


title: N2A_Neurite_FF_Rep4

value: Firefly luciferase


title: H3K27me3_CS_H507


title: H3K27me3_CTL_HCTR10


title: N2A_Neurite_FF_Rep3


title: H3K27ac_CTL_HCTR13

value: H3K27ac (Millipore #07-360)


title: RNA-Seq Pre-exposure prophylaxis sample 27, Alveolar macrophage, Mycobacterium tuberculosis challenged library

description:
Pre-exposure prophylaxis sample 27, Alveolar macrophage, Mycobacterium tuberculosis challenged library
mRNA, poly-A selected
PrEP.AMP27.MTB.1_RNA_R1_quant.sf

tag: ethnicity

value: Hispanic

tag: Sex

tag: age

tag: sexually transmitted infections

value: chlamydia PCR+ and gonorrhea PCR+

value: no

value: not detected

value: Truvada

value: Emtricitabine, Tenofovir_DF

tag: recreational drugs

tag: cigarette smoker

tag: bal sampling date

tag: mtb challenged

tag: rin

tag: average library size

tag: sequencing run


title: RNA-Seq Pre-exposure prophylaxis sample 27, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library

description:
Pre-exposure prophylaxis sample 27, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library
mRNA, poly-A selected
PrEP.AMP27.MTB.0_RNA_R1_quant.sf

tag: quantiferon tb reagent

tag: cd4 count

tag: viral load

tag: prescription drugs

tag: active ingredient

tag: art start year

tag: lane


title: RNA-Seq Pre-exposure prophylaxis sample 26, Alveolar macrophage, Mycobacterium tuberculosis challenged library

description:
Pre-exposure prophylaxis sample 26, Alveolar macrophage, Mycobacterium tuberculosis challenged library
mRNA, poly-A selected
PrEP.AMP26.MTB.1_RNA_R1_quant.sf

tag: ethnicity

tag: Sex

value: Syphilis RPR+

value: cannabis

value: yes


title: N2A_Neurite_FF_Rep2

tag: reporter scaffold

tag: compartment

tag: cell line


title: H3K27ac_CTL_HCTR10

tag: tissue

value: visceral adipose tissue

tag: chip antibody

tag: status

value: CTL

tag: drosophila spike-in


title: N2A_Neurite_FF_Rep1


title: H3K27me3_CS_VC04

value: H3K27me3 (Millipore #07–449)

value: CS


title: RNA-Seq Pre-exposure prophylaxis sample 26, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library

description:
Pre-exposure prophylaxis sample 26, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library
mRNA, poly-A selected
PrEP.AMP26.MTB.0_RNA_R1_quant.sf

value: Caucasian

value: M

tag: age

tag: sexually transmitted infections

tag: recreational drugs

tag: cigarette smoker

tag: bal sampling date

tag: mtb challenged

tag: rin

tag: average library size

tag: sequencing run


title: Patient 1 Lung Scan 26689 A10 ROI 003

tag: scan id

tag: roi(lable)


title: RNA-Seq Pre-exposure prophylaxis sample 25, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library

description:
Pre-exposure prophylaxis sample 25, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library
mRNA, poly-A selected
PrEP.AMP25.MTB.0_RNA_R1_quant.sf

tag: ethnicity

tag: Sex

tag: quantiferon tb reagent

tag: cd4 count

tag: viral load

tag: prescription drugs

tag: active ingredient

tag: art start year

tag: lane


title: Patient 1 Lung Scan 26689 A10 ROI 002


title: RNA-Seq Pre-exposure prophylaxis sample 28, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library

description:
Pre-exposure prophylaxis sample 28, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library
mRNA, poly-A selected
PrEP.AMP28.MTB.0_RNA_R1_quant.sf

tag: age

tag: sexually transmitted infections

tag: recreational drugs

tag: cigarette smoker


title: Patient 2 Heart Scan 26688 A6 ROI 011

source_name: Heart


title: Patient 2 Heart Scan 26688 A6 ROI 012


title: N2A_Neurite_GFP_Rep1

tag: reporter scaffold

value: GFP

tag: compartment

value: Neurite

tag: cell line


title: H3K27ac_CTL_H425

tag: tissue

tag: chip antibody

value: H3K27ac (Millipore #07-360)

tag: status

tag: drosophila spike-in

value: YES


title: N2A_Soma_GFP_Rep3

value: Cell body


title: N2A_Soma_GFP_Rep4


title: H3K27ac_CTL_H465


title: N2A_Neurite_GFP_Rep4


title: RNA-Seq Pre-exposure prophylaxis sample 23, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library

description:
Pre-exposure prophylaxis sample 23, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library
mRNA, poly-A selected
PrEP.AMP23.MTB.0_RNA_R1_quant.sf

tag: ethnicity

tag: Sex

value: fibromyalgia

value: no

tag: quantiferon tb reagent

tag: cd4 count

value: not detected

tag: bal sampling date

tag: mtb challenged

tag: rin

tag: average library size

tag: sequencing run


title: Patient 1 Lung Scan 26689 A10 ROI 001

tag: scan id

tag: roi(lable)


title: Patient 2 Heart Scan 26688 A6 ROI 010


title: N2A_Soma_FF_Rep3

tag: reporter scaffold

value: Firefly luciferase

tag: compartment


title: Patient 2 Heart Scan 26688 A6 ROI 008


title: RNA-Seq Healthy control sample 21, Alveolar macrophage, Mycobacterium tuberculosis challenged library

description:
Healthy control sample 21, Alveolar macrophage, Mycobacterium tuberculosis challenged library
mRNA, poly-A selected
HC.AMC21.MTB.1_RNA_R1_quant.sf

tag: age

value: hypertension, type.2.diabetes

tag: sexually transmitted infections

tag: viral load

value: not tested

tag: prescription drugs

tag: active ingredient

tag: art start year

tag: recreational drugs

tag: cigarette smoker

tag: lane


title: RNA-Seq Healthy control sample 22, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library

description:
Healthy control sample 22, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library
mRNA, poly-A selected
HC.AMC22.MTB.0_RNA_R1_quant.sf

tag: ethnicity

tag: Sex

value: F

tag: quantiferon tb reagent

tag: cd4 count

value: cannabis

value: yes

tag: bal sampling date

tag: mtb challenged


title: H3K27ac_CS_VC04

tag: tissue

value: visceral adipose tissue

tag: chip antibody

tag: status

value: CS

tag: drosophila spike-in


title: Patient 2 Heart Scan 26688 A6 ROI 006

tag: scan id

tag: roi(lable)


title: RNA-Seq Pre-exposure prophylaxis sample 23, Alveolar macrophage, Mycobacterium tuberculosis challenged library

description:
Pre-exposure prophylaxis sample 23, Alveolar macrophage, Mycobacterium tuberculosis challenged library
mRNA, poly-A selected
PrEP.AMP23.MTB.1_RNA_R1_quant.sf

value: Caucasian

value: M

tag: age

tag: sexually transmitted infections

tag: viral load

tag: prescription drugs

value: Truvada

tag: active ingredient

value: Emtricitabine, Tenofovir_DF

tag: rin

tag: average library size

tag: sequencing run


title: RNA-Seq Pre-exposure prophylaxis sample 25, Alveolar macrophage, Mycobacterium tuberculosis challenged library

description:
Pre-exposure prophylaxis sample 25, Alveolar macrophage, Mycobacterium tuberculosis challenged library
mRNA, poly-A selected
PrEP.AMP25.MTB.1_RNA_R1_quant.sf

tag: ethnicity

tag: Sex

tag: quantiferon tb reagent

tag: cd4 count

tag: art start year

tag: recreational drugs

tag: cigarette smoker

tag: lane


title: RNAseq_CTL_HCTR13

tag: tissue

tag: status

value: CTL

tag: drosophila spike-in

value: NO


title: Patient 2 Heart Scan 26688 A6 ROI 005

tag: scan id

tag: roi(lable)


title: H3K27ac_CS_VC02

tag: chip antibody

value: H3K27ac (Millipore #07-360)

value: YES


title: N2A_Soma_GFP_Rep2

tag: reporter scaffold

value: GFP

tag: compartment

value: Cell body

tag: cell line


title: Patient 2 Heart Scan 26688 A6 ROI 009


title: Patient 2 Heart Scan 26688 A6 ROI 004


title: N2A_Soma_FF_Rep4

value: Firefly luciferase


title: H3K27ac_CS_VC06


title: H3K27ac_CS_H507


title: N2A_Soma_GFP_Rep1


title: RNA-Seq Healthy control sample 22, Alveolar macrophage, Mycobacterium tuberculosis challenged library

description:
Healthy control sample 22, Alveolar macrophage, Mycobacterium tuberculosis challenged library
mRNA, poly-A selected
HC.AMC22.MTB.1_RNA_R1_quant.sf

tag: ethnicity

tag: age

tag: sexually transmitted infections

value: no

tag: viral load

value: not tested

tag: prescription drugs

tag: active ingredient

tag: bal sampling date

tag: mtb challenged

tag: rin

tag: average library size

tag: sequencing run


title: RNAseq_CTL_HCTR10

tag: tissue

tag: status

tag: drosophila spike-in


title: Patient 2 Heart Scan 26688 A6 ROI 002

tag: scan id

tag: roi(lable)


title: Patient 2 Heart Scan 26688 A6 ROI 007


title: RNA-Seq Healthy control sample 20, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library

description:
Healthy control sample 20, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library
mRNA, poly-A selected
HC.AMC20.MTB.0_RNA_R1_quant.sf

value: Asian

tag: Sex

tag: quantiferon tb reagent

tag: cd4 count

tag: art start year

tag: recreational drugs

tag: cigarette smoker

tag: lane


title: RNAseq_CTL_HCTR7


title: N2A_Soma_FF_Rep2

tag: reporter scaffold

tag: compartment

tag: cell line


title: CAD_Neurite_GFP_Rep2

source_name: Mouse CAD cell line

value: Neurite

value: CAD


title: RNA-Seq Healthy control sample 19, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library

description:
Healthy control sample 19, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library
mRNA, poly-A selected
HC.AMC19.MTB.0_RNA_R1_quant.sf

tag: ethnicity

tag: age

tag: sexually transmitted infections

tag: viral load

tag: prescription drugs

tag: active ingredient

tag: bal sampling date

tag: mtb challenged

tag: rin

tag: average library size


title: RNA-Seq Healthy control sample 20, Alveolar macrophage, Mycobacterium tuberculosis challenged library

description:
Healthy control sample 20, Alveolar macrophage, Mycobacterium tuberculosis challenged library
mRNA, poly-A selected
HC.AMC20.MTB.1_RNA_R1_quant.sf

tag: Sex

tag: quantiferon tb reagent

tag: cd4 count

tag: art start year

value: yes

tag: sequencing run


title: Patient 2 Heart Scan 26688 A6 ROI 003

description: Unstained 4μm-thick sections were cut from FFPE blocks from two patients and immunoflourescently labeled with PanCK, CD45, CD68 and DAPI. Twelve regions of interest (ROIs) per slide were selected for targeted spatial transcriptomics (GeoMx, Nanostring) with >1,600 cancer atlas transcripts and 10 additional SARS-CoV-2 genes.

tag: scan id

tag: roi(lable)


title: RNAseq_CTL_H465

tag: tissue

value: visceral adipose tissue

tag: status

tag: drosophila spike-in


title: CAD_Neurite_GFP_Rep1

tag: reporter scaffold

tag: compartment

tag: cell line


title: RNA-Seq Healthy control sample 21, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library

description:
Healthy control sample 21, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library
mRNA, poly-A selected
HC.AMC21.MTB.0_RNA_R1_quant.sf

tag: ethnicity

value: Caucasian

value: M

tag: age

value: hypertension, type.2.diabetes

tag: sexually transmitted infections

tag: viral load

tag: prescription drugs

tag: active ingredient

tag: recreational drugs

tag: cigarette smoker

tag: bal sampling date

tag: lane


title: Patient 2 Lymph node Scan 26688 A24 ROI 011

source_name: Lymph node

tag: scan id

tag: roi(lable)


title: RNA-Seq Healthy control sample 18, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library

description:
Healthy control sample 18, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library
mRNA, poly-A selected
HC.AMC18.MTB.0_RNA_R1_quant.sf

tag: Sex

tag: quantiferon tb reagent

tag: cd4 count

tag: art start year

tag: mtb challenged

tag: rin

tag: average library size

tag: sequencing run


title: Patient 2 Lymph node Scan 26688 A24 ROI 012


title: N2A_Soma_FF_Rep1

tag: reporter scaffold

tag: compartment

tag: cell line


title: RNA-Seq Healthy control sample 16, Alveolar macrophage, Mycobacterium tuberculosis challenged library

description:
Healthy control sample 16, Alveolar macrophage, Mycobacterium tuberculosis challenged library
mRNA, poly-A selected
HC.AMC16.MTB.1_RNA_R1_quant.sf

tag: ethnicity

value: F

tag: age

tag: sexually transmitted infections

tag: viral load

tag: prescription drugs

tag: active ingredient

tag: recreational drugs


title: CAD_Neurite_GFP_Rep4


title: CAD_Neurite_GFP_Rep3


title: RNAseq_CTL_H517

tag: tissue

tag: status

value: CTL

tag: drosophila spike-in

value: NO


title: Patient 2 Heart Scan 26688 A6 ROI 001

tag: scan id

tag: roi(lable)


title: RNAseq_CTL_HCTR11


title: CAD_Neurite_FF_Rep4


title: CAD_Soma_GFP_Rep4


title: RNA-Seq Healthy control sample 18, Alveolar macrophage, Mycobacterium tuberculosis challenged library

description:
Healthy control sample 18, Alveolar macrophage, Mycobacterium tuberculosis challenged library
mRNA, poly-A selected
HC.AMC18.MTB.1_RNA_R1_quant.sf

tag: Sex

tag: quantiferon tb reagent

tag: cd4 count

tag: art start year

tag: cigarette smoker

tag: bal sampling date

tag: mtb challenged

tag: rin

tag: average library size

tag: lane


title: Patient 2 Lymph node Scan 26688 A24 ROI 007


title: RNA-Seq Healthy control sample 19, Alveolar macrophage, Mycobacterium tuberculosis challenged library

description:
Healthy control sample 19, Alveolar macrophage, Mycobacterium tuberculosis challenged library
mRNA, poly-A selected
HC.AMC19.MTB.1_RNA_R1_quant.sf

tag: ethnicity

tag: age

tag: sexually transmitted infections

tag: viral load

tag: prescription drugs

tag: active ingredient

tag: sequencing run


title: RNAseq_CTL_H446

tag: tissue

tag: status

tag: drosophila spike-in


title: Patient 2 Lymph node Scan 26688 A24 ROI 010

tag: scan id

tag: roi(lable)


title: RNA-Seq Healthy control sample 14, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library

description:
Healthy control sample 14, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library
mRNA, poly-A selected
HC.AMC14.MTB.0_RNA_R1_quant.sf

tag: Sex

tag: quantiferon tb reagent

tag: cd4 count

tag: art start year

tag: recreational drugs

tag: cigarette smoker

tag: bal sampling date


title: RNA-Seq Healthy control sample 16, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library

description:
Healthy control sample 16, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library
mRNA, poly-A selected
HC.AMC16.MTB.0_RNA_R1_quant.sf

tag: ethnicity

tag: age

tag: sexually transmitted infections

tag: mtb challenged

tag: rin

tag: average library size

tag: lane


title: RNAseq_CTL_H460

tag: tissue

tag: status

tag: drosophila spike-in


title: RNAseq_CTL_H438


title: Patient 2 Lymph node Scan 26688 A24 ROI 005

tag: scan id

tag: roi(lable)


title: RNAseq_CTL_H434


title: RNAseq_CS_HVC06

value: CS


title: CAD_Neurite_FF_Rep1

tag: reporter scaffold

tag: compartment

tag: cell line


title: Patient 2 Lymph node Scan 26688 A24 ROI 008


title: CAD_Soma_GFP_Rep1

value: GFP


title: Patient 2 Lymph node Scan 26688 A24 ROI 009


title: CAD_Neurite_FF_Rep3


title: CAD_Neurite_FF_Rep2


title: RNAseq_CTL_H425


title: RNAseq_CTL_H437


title: RNA-Seq Healthy control sample 13, Alveolar macrophage, Mycobacterium tuberculosis challenged library

description:
Healthy control sample 13, Alveolar macrophage, Mycobacterium tuberculosis challenged library
mRNA, poly-A selected
HC.AMC13.MTB.1_RNA_R1_quant.sf

tag: Sex

tag: quantiferon tb reagent

tag: cd4 count

tag: viral load

tag: prescription drugs

tag: active ingredient

tag: art start year

tag: recreational drugs

tag: cigarette smoker

tag: sequencing run


title: Patient 2 Lymph node Scan 26688 A24 ROI 006


title: RNA-Seq Healthy control sample 14, Alveolar macrophage, Mycobacterium tuberculosis challenged library

description:
Healthy control sample 14, Alveolar macrophage, Mycobacterium tuberculosis challenged library
mRNA, poly-A selected
HC.AMC14.MTB.1_RNA_R1_quant.sf

tag: ethnicity

tag: age

tag: sexually transmitted infections

tag: bal sampling date

tag: mtb challenged

tag: rin

tag: average library size

tag: lane


title: RNA-Seq Healthy control sample 15, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library

description:
Healthy control sample 15, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library
mRNA, poly-A selected
HC.AMC15.MTB.0_RNA_R1_quant.sf

tag: Sex

tag: quantiferon tb reagent


title: RNAseq_CS_HVC09

tag: tissue

tag: status

tag: drosophila spike-in


title: RNA-Seq Healthy control sample 12, Alveolar macrophage, Mycobacterium tuberculosis challenged library

description:
Healthy control sample 12, Alveolar macrophage, Mycobacterium tuberculosis challenged library
mRNA, poly-A selected
HC.AMC12.MTB.1_RNA_R1_quant.sf

tag: cd4 count

tag: viral load

tag: prescription drugs

tag: active ingredient

tag: art start year


title: RNA-Seq Healthy control sample 12, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library

description:
Healthy control sample 12, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library
mRNA, poly-A selected
HC.AMC12.MTB.0_RNA_R1_quant.sf

tag: ethnicity

tag: age

tag: recreational drugs

tag: cigarette smoker

tag: sequencing run


title: CAD_Soma_FF_Rep2

tag: reporter scaffold

tag: compartment

value: Cell body

tag: cell line


title: CAD_Soma_GFP_Rep2


title: RNAseq_CS_H507


title: CAD_Soma_GFP_Rep3


title: RNA-Seq Healthy control sample 15, Alveolar macrophage, Mycobacterium tuberculosis challenged library

description:
Healthy control sample 15, Alveolar macrophage, Mycobacterium tuberculosis challenged library
mRNA, poly-A selected
HC.AMC15.MTB.1_RNA_R1_quant.sf

tag: Sex

tag: sexually transmitted infections

tag: quantiferon tb reagent

tag: bal sampling date

tag: mtb challenged

tag: rin

tag: average library size

tag: lane


title: RNA-Seq Healthy control sample 13, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library

description:
Healthy control sample 13, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library
mRNA, poly-A selected
HC.AMC13.MTB.0_RNA_R1_quant.sf

tag: cd4 count

tag: viral load

tag: prescription drugs

tag: active ingredient

tag: art start year


title: RNAseq_CS_HVC05

tag: tissue

tag: status

tag: drosophila spike-in


title: CAD_Soma_FF_Rep3

tag: reporter scaffold

value: Firefly luciferase

tag: compartment

tag: cell line


title: RNA-Seq Healthy control sample 10, Alveolar macrophage, Mycobacterium tuberculosis challenged library

description:
Healthy control sample 10, Alveolar macrophage, Mycobacterium tuberculosis challenged library
mRNA, poly-A selected
HC.AMC10.MTB.1_RNA_R1_quant.sf

tag: ethnicity

tag: Sex

tag: age

tag: sexually transmitted infections

value: no

tag: quantiferon tb reagent

tag: recreational drugs

tag: cigarette smoker

tag: sequencing run


title: RNAseq_CS_HVC04


title: CAD_Soma_FF_Rep4


title: Patient 2 Lymph node Scan 26688 A2 ROI 009

tag: scan id

tag: roi(lable)


title: Patient 2 Lymph node Scan 26688 A2 ROI 010


title: Sensitivity_FACT_H3K27ac_10Knuclei_rep1_mm10

city: Uppsala

first: xingqi

last: chen

address: Uppsala Biomedical Center C10:2, Husargatan 3

department: IGP

country: Sweden

institute: Uppsala University

data_processing:
Library strategy: FACT-seq
Adaptors were trimmed.
All reads were aligned to hg38/mm10 using bowtie2 with the following parameters "--end-to-end --very-sensitive -I 10 -X 700"
The aligned BAM files were sorted and filtered with alignment quality of >Q2 using samtools v.1.9.
The bigwig files were generated from BAM files using deeptools with the parameters "bamCoverage –normalizeUsing CPM".
H3K27me3 peaks were called using SICER with following parameters ‘gap size = 600 bp and window size = 200 bp’.
H3K27ac peaks were called using SICER with following parameters ‘gap size = 400 bp and window size = 200 bp.
Genome_build: hg38 and mm10
Supplementary_files_format_and_content: bigwig and peaks.txt files

source_name: Mouse kidney 8 weeks

growth_protocol: GM12878 cells were grown in RPMI 1640 (Gibco, 31870-025), 2 mM L-glutamine (Gibco, 25030-024), 15% fetal bovine serum (Gibco, 10270-106) and 1% Pen/Strep (Gibco, 15140-122).

extract_protocol:
RNA is synthesized after in vitro transcription from tagmented DNA. And cDNA is synthesized after reverse transcription.
dsDNA was tagmented with Tn5, then PCR is performed using primers with barcode.

treatment_protocol: Samples were fixed with 4% paraformaldehyde overnight, and then washed with phosphate-buffered saline (PBS) and kept in 70% ethanol for paraffin embedding.

tag: strain

value: FVBN

value: kidney

tag: treatment

value: FFPE


title: Patient 2 Lymph node Scan 26688 A24 ROI 003


title: Patient 2 Lymph node Scan 26688 A24 ROI 001


title: CAD_Soma_FF_Rep1

value: CAD


title: Sensitivity_FACT_H3K27ac_10Knuclei_rep2_mm10

tag: tissue


title: Patient 2 Lymph node Scan 26688 A24 ROI 004


title: Patient 2 Lymph node Scan 26688 A2 ROI 012


title: Patient 2 Lymph node Scan 26688 A24 ROI 002


title: RNA-Seq Healthy control sample 11, Alveolar macrophage, Mycobacterium tuberculosis challenged library

description:
Healthy control sample 11, Alveolar macrophage, Mycobacterium tuberculosis challenged library
mRNA, poly-A selected
HC.AMC11.MTB.1_RNA_R1_quant.sf

tag: cd4 count

tag: viral load

value: not tested

tag: prescription drugs

tag: active ingredient

tag: art start year

tag: bal sampling date

tag: mtb challenged

value: yes

tag: rin

tag: average library size

tag: lane


title: Sensitivity_FACT_H3K27ac_1000nuclei_rep1_mm10


title: RNA-Seq Healthy control sample 10, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library

description:
Healthy control sample 10, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library
mRNA, poly-A selected
HC.AMC10.MTB.0_RNA_R1_quant.sf

tag: ethnicity

value: Caucasian

tag: Sex

tag: age

tag: sexually transmitted infections

tag: quantiferon tb reagent

tag: recreational drugs

tag: cigarette smoker


title: RNA-Seq Healthy control sample 11, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library

description:
Healthy control sample 11, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library
mRNA, poly-A selected
HC.AMC11.MTB.0_RNA_R1_quant.sf

value: M

tag: cd4 count

tag: sequencing run


title: Patient 2 Lymph node Scan 26688 A2 ROI 011

description: Unstained 4μm-thick sections were cut from FFPE blocks from two patients and immunoflourescently labeled with PanCK, CD45, CD68 and DAPI. Twelve regions of interest (ROIs) per slide were selected for targeted spatial transcriptomics (GeoMx, Nanostring) with >1,600 cancer atlas transcripts and 10 additional SARS-CoV-2 genes.

tag: scan id

tag: roi(lable)


title: Sensitivity_FACT_H3K27ac_1000nuclei_rep2_mm10

tag: strain

tag: tissue

tag: treatment


title: Sensitivity_FACT_H3K27ac_4000nuclei_rep2_mm10


title: Patient 2 Lymph node Scan 26688 A2 ROI 008


title: Patient 2 Lymph node Scan 26688 A2 ROI 007


title: Patient 2 Lymph node Scan 26688 A2 ROI 006


title: RNA-Seq Healthy control sample 9, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library

description:
Healthy control sample 9, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library
mRNA, poly-A selected
HC.AMC9.MTB.0_RNA_R1_quant.sf

tag: viral load

tag: prescription drugs

tag: active ingredient

tag: art start year

value: cannabis

tag: bal sampling date

tag: mtb challenged

tag: rin


title: RNA-Seq Healthy control sample 8, Alveolar macrophage, Mycobacterium tuberculosis challenged library

description:
Healthy control sample 8, Alveolar macrophage, Mycobacterium tuberculosis challenged library
mRNA, poly-A selected
HC.AMC8.MTB.1_RNA_R1_quant.sf

tag: ethnicity

tag: Sex

tag: age

tag: sexually transmitted infections

tag: quantiferon tb reagent

tag: average library size

tag: lane


title: RNA-Seq Healthy control sample 9, Alveolar macrophage, Mycobacterium tuberculosis challenged library

description:
Healthy control sample 9, Alveolar macrophage, Mycobacterium tuberculosis challenged library
mRNA, poly-A selected
HC.AMC9.MTB.1_RNA_R1_quant.sf

tag: cd4 count

tag: recreational drugs

tag: cigarette smoker

tag: sequencing run


title: Mouse_H3K4me1_CUT_Tag_frozen_rep2_mm10

data_processing:
Library strategy: CUT&Tag
Adaptors were trimmed.
All reads were aligned to hg38/mm10 using bowtie2 with the following parameters "--end-to-end --very-sensitive -I 10 -X 700"
The aligned BAM files were sorted and filtered with alignment quality of >Q2 using samtools v.1.9.
The bigwig files were generated from BAM files using deeptools with the parameters "bamCoverage –normalizeUsing CPM".
H3K27me3 peaks were called using SICER with following parameters ‘gap size = 600 bp and window size = 200 bp’.
H3K27ac peaks were called using SICER with following parameters ‘gap size = 400 bp and window size = 200 bp.
Genome_build: hg38 and mm10
Supplementary_files_format_and_content: bigwig and peaks.txt files

tag: strain

tag: tissue

tag: treatment

value: Frozen


title: RNA-Seq Healthy control sample 8, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library

description:
Healthy control sample 8, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library
mRNA, poly-A selected
HC.AMC8.MTB.0_RNA_R1_quant.sf

tag: viral load

tag: prescription drugs

tag: active ingredient

tag: art start year

tag: bal sampling date


title: Macrophages, Sp rep. 1

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

country: France

institute: IPMC/CNRS

description: MPI macrophages stimulated with heat-killed S. pneumoniae MOI 30 for 18h

data_processing:
AB Small RNA pipeline v5.0 matching, normalization to 1.000.000 miRNAs count in each sample
STAR aligner
FeatureCount gene couting
Genome_build: mm10
Supplementary_files_format_and_content: featurecounts.txt: tab-delimited text file with gene couting using featureCount

source_name: Macrophages

growth_protocol: Cells were cultured in RPMI GlutaMAX 10% of FBS and 1% of Penicillin and Streptomycin with 30ng/mL of murine GM-CSF. Passage was done every 3 days.

extract_protocol:
Total RNA from cellular lysate was extracted using the NucleoSpin® RNA kit (Macherey‑Nagel, Hoerdt, Germany).
Libraries were generated from 1µg of total RNA using Truseq Stranded mRNA kit (Illumina). Libraries were then quantified with KAPA library quantification kit (Kapa biosystems) and pooled. 4nM of this pool were loaded on a Nextseq 500 high output flowcell and sequenced on a NextSeq 500 platform (Illumina) with 2×75bp paired-end chemistry.

treatment_protocol: Cells were treated with sodium acetate 30mM for 1h and then stimulated with heat-killed S. pneumoniae MOI of 30 for 18h

tag: mouse strain

tag: cell type

value: Macrophages originated from fetal liver (Max Planck Institute cells - MPI)

value: Stimulation with S. pneumoniae


title: RNA-Seq Healthy control sample 7, Alveolar macrophage, Mycobacterium tuberculosis challenged library

description:
Healthy control sample 7, Alveolar macrophage, Mycobacterium tuberculosis challenged library
mRNA, poly-A selected
HC.AMC7.MTB.1_RNA_R1_quant.sf

tag: ethnicity

tag: Sex

tag: age

value: hypertension, diabetes, gout

tag: sexually transmitted infections

tag: quantiferon tb reagent

tag: mtb challenged

tag: rin


title: Sensitivity_FACT_H3K27ac_4000nuclei_rep1_mm10

tag: strain


title: Macrophages, Sp rep. 3


title: RNAseq_CS_HVC02

tag: tissue

value: visceral adipose tissue

tag: status

value: CS

tag: drosophila spike-in

value: NO


title: Macrophages, SpA rep. 2

description: MPI macrophages pre-treated with acetate 30mM for 1h, then stimulated with heat-killed S. pneumoniae MOI 30 for 18h

tag: treatment

value: Acetate treatment + Stimulation with S. pneumoniae


title: Macrophages, SpA rep. 3


title: Macrophages, SpA rep. 1


title: Mouse_FACT_H3K4me1_rep2_mm10

value: FVBN


title: BAT_01: BAT_control_rep1

city: guangzhou

first: zhipeng

last: zou

state: guangdong

address: tonghe road

department: Cell Biology

institute: southern medical university

hyb_protocol: Each slide was hybridized with 600 ng Cy3-labeled cRNA using Gene Expression Hybridization Kit (Cat.# 5188-5242, Agilent technologies), After 17 hours hybridization, slides were washed in staining dishes (Cat.# 121, Thermo Shandon) with Gene Expression Wash Buffer Kit(Cat.# 5188-5327, Agilent technologies), following the manufacturer’s instructions.

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat#G2565CA, Agilent technologies) with default settings, Dye channel: Green, Scan resolution=3μm, PMT 100%, 20bit.

data_processing: Data were extracted with Feature Extraction software 10.7 (Agilent technologies). Raw data were normalized by Quantile algorithm, limma packages in R.

source_name: 1-month male mice

label_protocol: Total RNA was amplified and labeled by Low Input Quick Amp Labeling Kit, One-Color (Cat.# 5190-2305, Agilent technologies), following the manufacturer’s instructions. Labeled cRNA were purified by RNeasy mini kit (Cat.# 74106, QIAGEN).

growth_protocol: Mice lacking Rheb in the adipocyte lineage were generated by mating RhebFL/FL mice with fabp4-Cre conditional knockout mice.

extract_protocol: Total RNA was extracted with Trizol following the manufacturer’s instructions.

tag: genotype

value: control littermates

value: brown adipose tissue

tag: gender

value: male


title: 2012364_Mouse-5 OR Mouse-3 Tumor J35+70

city: Paris

first: Pierre

last: de la Grange

address: 29, rue du Faubourg Saint-Jacques

department: Paris Biotech Santé

institute: GenoSplice technology

description: Tumor from PBC mouse after cholangitis induction and ectopic CCA growth

data_processing:
Library strategy: TCR-seq
barcode/feature matrices with cellranger v5.0.0 count
clonotye data with cellrange v5.0.0 vdj
Genome_build: mm10
Supplementary_files_format_and_content: cellrange count filtered output and cellranger vdj filtered contig annotation

extract_protocol:
Blood was drawn 7 days before and 34 days after PBC induction. One hundred five days after cholangitis induction (equivalent to 70 days after the engraftment of the CCA cells), blood, liver and the CCA tumor were collected from a PBC mouse. A soft red blood cell lysis protocol was used to preserved cell fitness and viability. Briefly, 500µL of PBS was added onto blood, followed by 3.5mL of sterile water. After mixing, 400µL of PBS 10x was included before centrifugation. Cells were resuspended in PBS containing 0.5% BSA and 5mM EDTA. Liver preparation. Perfused livers were cut into small pieces and transferred to GentleMACSTM C tubes (Miltenyi Biotech) containing 3mL of CO2 independent medium. After mechanical dissociation using GentleMACSTM Octo Dissociator (Miltenyi Biotech), the cell suspension was transferred into 50mL tubes for extensive washing. Finally, the cell pellet was resuspended in PBS containing 0.5% BSA and 5mM EDTA. Tumor preparation. Tumors were cut into small pieces and placed into GentleMACSTM C Tubes. Then, a cocktail of tissue-dissociating enzymes resuspended in 2.35mL of RPMI medium was added (Mouse tumor dissociation kit, Miltenyi Biotech). GentleMACSTM C Tubes containing the tissue were placed and incubated at 37°C onto a GentleMACSTM Octo Dissociator equipped with heaters (Miltenyi Biotech) for dissociation to occur. Next, cells were filtered through a 100µm cell strainer and washed twice in PBS. Finally, the cell pellet was resuspended in PBS containing 0,5% BSA and 5mM EDTA. T cell sorting. CD4+ and CD8+ T cells from blood, liver and tumor were sort-purified in a two-step procedure in which T cells were initially enriched in CD3+ cells using MoJoSortTM mouse negative selection kit (BioLegend). Then, CD3+ cells were stained with a cocktail of antibodies targeting CD11c, Ly6C, Ly6G, CD19, F4/80, NK1.1 (all in FITC for Lineage negative exclusion), CD45, CD8, and CD4, together with DAPI, then sorted using BD FACSAria III as DAPI-, Lineage-, CD45+, CD4+ or CD8+ cells. After sorting, cells were counted, then CD4+ and CD8+ cells were mixed at 1:1 ratio. Final concentration was adjusted to 800 cells/µL (400 CD4+:400 CD8+ cells/µL)
scRNA-seq was performed on the 1:1 CD4+:CD8+ T cell mixture prepared from blood, tumor or liver. A total of 10000 cells per tissue were loaded onto the NextGEM 10x chip (10x Genomics). The RNA capture, barcoding, cDNA amplification and library were performed according the manufacturer’s recommendations (CG00207_Chronium NextGEM SingleCellV(D)J v1.1 user guide). 10x libraries were sequenced on NovaSeq (Illumina) SP (for TCR-seq) or S1 (for gene expression).

treatment_protocol: Autoimmune primary biliary cholangitis (PBC) was induced in a C57Bl/6 mice as described before: Chang et al., 2014; Wakabayashi et al., 2008. Briefly, mice were immunized with 100 µg of 2-octynoic acid BSA conjugate (2OA-BSA) intraperitoneally (i.p.) in a mix of PBS and complete Freund’s adjuvant (CFA, Sigma-Aldrich) at day 0 and were reboosted at days 14 and 28 with 2OA-BSA and incomplete Freund’s Adjuvant (IFA, Sigma Aldrich). Concomitantly with the two first injections of 2OA-BSA, mice were also injected intravenously (i.v.) with 2 μg of α-galactosylceramide (α-GalCer, Abcam) in PBS.   Thirty-five days after the beginning of cholangitis induction, 3x10^6 SB1-JP4 cells (murine cholangiocarcinoma cells) were resuspended in 100 µL of PBS and injected subcutaneously, under anesthesia with 2.5% isoflurane, in the right flank of C57Bl/6 mice.

value: CCA tumor

value: Wild type

value: 2-octynoic acid BSA conjugate + alpha-galactosylceramide

tag: day of collection

tag: protocol

value: single-cell TCRalphaBeta


title: BAT_02: BAT_rhebAD KO_rep1

value: littermates with rheb knockout in adipocytes


title: Patient 2 Lymph node Scan 26688 A2 ROI 004

tag: scan id

tag: roi(lable)


title: 2012385_Mouse-5 OR Mouse-3 Tumor J35+70

data_processing:
barcode/feature matrices with cellranger v5.0.0 count
clonotye data with cellrange v5.0.0 vdj
Genome_build: mm10
Supplementary_files_format_and_content: cellrange count filtered output and cellranger vdj filtered contig annotation

source_name: Tumor from PBC mouse after cholangitis induction and ectopic CCA growth

value: single-cell mRNA


title: RNA-Seq Healthy control sample 7, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library

description:
Healthy control sample 7, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library
mRNA, poly-A selected
HC.AMC7.MTB.0_RNA_R1_quant.sf

tag: ethnicity

value: Caucasian

tag: Sex

value: M

value: no

tag: cd4 count

tag: viral load

value: not tested

tag: prescription drugs

tag: active ingredient

tag: art start year

tag: recreational drugs

tag: cigarette smoker

tag: bal sampling date

tag: average library size

tag: sequencing run

tag: lane


title: Mouse_FACT_H3K4me1_rep1_mm10

tag: strain

tag: tissue

value: kidney

tag: treatment

value: FFPE


title: Patient 2 Lymph node Scan 26688 A2 ROI 003

tag: scan id

tag: roi(lable)


title: Patient 2 Lymph node Scan 26688 A2 ROI 002


title: RNA-Seq Healthy control sample 2, Alveolar macrophage, Mycobacterium tuberculosis challenged library

description:
Healthy control sample 2, Alveolar macrophage, Mycobacterium tuberculosis challenged library
mRNA, poly-A selected
HC.AMC2.MTB.1_RNA_R1_quant.sf

tag: ethnicity

tag: Sex

tag: age

tag: sexually transmitted infections

tag: quantiferon tb reagent

value: cannabis

value: yes

tag: mtb challenged

tag: rin


title: Patient 2 Lymph node Scan 26688 A2 ROI 001


title: Mouse_H3K4me1_CUT_Tag_frozen_rep1_mm10

value: FVBN

value: Frozen


title: Macrophages, Sp rep. 2

tag: mouse strain

tag: cell type

value: Macrophages originated from fetal liver (Max Planck Institute cells - MPI)

value: Stimulation with S. pneumoniae


title: RNA-Seq Healthy control sample 2, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library

description:
Healthy control sample 2, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library
mRNA, poly-A selected
HC.AMC2.MTB.0_RNA_R1_quant.sf

tag: cd4 count

tag: viral load

tag: prescription drugs

tag: active ingredient

tag: art start year

tag: recreational drugs

tag: cigarette smoker

tag: bal sampling date

tag: average library size


title: Mouse_H3K36me3_CUT_Tag_frozen_rep2_mm10

tag: strain

tag: tissue

tag: treatment


title: FACT_H3K36me3_65C_01SDS_SD_rep2_mm10


title: Patient 2 Lung Scan 26688 A19 ROI 011

tag: scan id

tag: roi(lable)


title: Patient 2 Lung Scan 26688 A19 ROI 009


title: 2012385_Mouse-4 OR Mouse-3 Liver J35+70

description: Liver from PBC mouse after cholangitis induction and ectopic CCA growth

value: Liver

tag: genotype

value: Wild type

tag: day of collection

tag: protocol


title: ATAC-Seq Person living with HIV sample 26, Alveolar macrophage, Mycobacterium tuberculosis challenged library

description:
Person living with HIV sample 26, Alveolar macrophage, Mycobacterium tuberculosis challenged library
Tn5 transposase

data_processing:
Fastq files were trimmed to remove  nextera adaptors  and < phred 10 using cutadapt v2.6 with TrimGalore v0.6.5
Reads were  aligned to both human (hg38) and Mtb (H37rv) genomes using BWA v0.7.17 default parameters. PICARD v2.18.9 was used to mark duplicates and to assess the fragment length distribution. Reads aligning to the mitochondrial genome were removed with samtools v1.9
alignmentSieve v3.3.2 was used to: (i) select unique paired-end reads using the --samFlagExclude 1804; (ii) remove ENCODE hg38 blacklisted regions; and (iii) to extract fragments between 40 – 2000bp in length
Peaks were called with MACS2 v2.2.6 callpeak was used with --call-summits in BAMPE mode. The summit of each peak was extended 250bp in both directions resulting in fixed-width peaks of exactly 501bp. Fiixed-width peaks overlapping in at least two samples were merged with bedtools v2.26
featureCounts v1.6.3 was used to count the number of unique fragments  overlapping the targeted regions.
Libray depth and was calculated via calcNormFactors in edgeR v3.26.8 and used by limma’s voom function (v3.40.6) to generate the normalized log2(CPM) expression matrix.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files including the number of fragmentes overlaping assessed peaks for each sample.
Supplementary_files_format_and_content: tab-delimited matrix table with normalized peak quantification in log2 scale for every sample. Covariates not regressed out.

extract_protocol:
Cells were lysed with Trizol and kept at -80°C until extraction.  For ATAC-seq, 50,000 cell were  isolated and incubated with Tn5 transposase for DNA tagmentation.  The fragment length distribution was assessed with the Agilent 2100 Bioanalyzer.
ATACseq libraries were prepared for sequencing using standard paired end sequencing.

tag: ethnicity

tag: Sex

tag: age

tag: sexually transmitted infections

tag: quantiferon tb reagent

tag: cd4 count

value: Atripla

value: Emtricitabine, Tenofovir_DF, Efavirenz

tag: mtb challenged

tag: average tagmented library size

tag: fragments in clean bam

tag: sequencing run

tag: lane


title: ATAC-Seq Person living with HIV sample 27, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library

description:
Person living with HIV sample 27, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library
Tn5 transposase

tag: prescription drugs

value: Descovy, Isentress

tag: active ingredient

tag: art start year

tag: recreational drugs

tag: cigarette smoker

tag: bal sampling date


title: Patient 2 Lymph node Scan 26688 A2 ROI 005

tag: scan id

tag: roi(lable)


title: ATAC-Seq Person living with HIV sample 27, Alveolar macrophage, Mycobacterium tuberculosis challenged library

description:
Person living with HIV sample 27, Alveolar macrophage, Mycobacterium tuberculosis challenged library
Tn5 transposase

tag: ethnicity

value: Caucasian

tag: Sex

tag: age


title: FACT_H3K36me3_65C_01SDS_SD_rep1_mm10

tag: strain

tag: tissue

tag: treatment


title: Patient 2 Lung Scan 26688 A19 ROI 010


title: 2012364_Mouse-4 OR Mouse-3 Liver J35+70

source_name: Liver from PBC mouse after cholangitis induction and ectopic CCA growth

tag: genotype

value: 2-octynoic acid BSA conjugate + alpha-galactosylceramide

tag: day of collection

tag: protocol

value: single-cell TCRalphaBeta


title: 2011751_Mouse-3 OR Mouse-3 Blood J0

description: Blood from PBC mouse before cholangitis induction

value: Blood


title: Mouse_H3K36me3_CUT_Tag_frozen_rep1_mm10

value: kidney


title: PGC1a_CTD_AP_rep2

city: Basel

first: Joaquín

last: Pérez-Schindler

address: Klingelbergstrasse 50 / 70

department: Biozentrum

country: Switzerland

institute: University of Basel

data_processing:
Single-end sequencing was performed using the Illumina NextSeq 500 and control software version 2.2.0.4.
Analyzed on the Galaxy platform (https://usegalaxy.eu/). Reads were trimmed with Trim Galore! (Galaxy version 0.4.3.1) and quality was assessed using FastQC (Galaxy version 0.72+galaxy1). Reads were aligned to the mm10 version of the mouse genome using STAR (Galaxy version 2.7.2b) and duplicated reads were removed with MarkDuplicates (Galaxy version 2.18.2.2). Next, we used MACS2 callpeak (Galaxy version, #2.1.1.20160309.6) for peak calling, while ChIPseeker (Galaxy version, #1.18.0+galaxy1) was used to annotate peaks.
Genome_build: mm10
Supplementary_files_format_and_content: One excel (xlsx) file containing annotated peaks and 2 bigwig files with normalized alignment of reads from BAM files.

source_name: C2C12 skeletal muscle cells

growth_protocol: C2C12 myoblasts were grown in Dulbecco's modified Eagle's medium (DMEM) supplemented with 10% fetal bovine serum (growth medium). To induce differentiation, growth medium of about 90% confluent myoblasts was changed to DMEM supplemented with 2% horse serum (differentiation medium). Experiments using C2C12 myotubes were performed after 4 days of differentiation. Cells were maintained at 37°C, 95% O2 and 5% CO2.

extract_protocol:
Cells were collected in TRI Reagent (Sigma #T9424), following which RNA was purified using Direct-zol™ RNA MiniPrep (Zymo Research, #R2050). Next, 5 µg of RNA were used for input or affinity purification with recombinant CTD of mouse PGC-1alpha (US Biological Life Sciences, #156296), following which bound RNA was purified with Direct-zol™ RNA MiniPrep kit.
Purified RNA from input and affinity purification samples was used to prepare libraries with Stranded Total RNA Prep with Ribo-Zero Plus kit (Illumina, # 20040525).
RNA-seq (in vitro AP-seq)

treatment_protocol: Cells were transduced with HA-Flag-PGC-1alpha FL adenovirus at multiplicity of infection 3. Adenoviruses were prepared in the corresponding medium and cells were transduced for 4 h. Next, cells were washed once with phosphate buffered saline (PBS) and, then, incubated in adenovirus-free medium for a total of 48 h.

tag: cell line

value: C2C12 skeletal muscle cells

tag: differentiation state

value: C2C12 myotubes

value: PGC1a full length overexpression

tag: protein for affinity purification


title: ATAC-Seq Person living with HIV sample 26, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library

description:
Person living with HIV sample 26, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library
Tn5 transposase

value: M

tag: sexually transmitted infections

value: no

tag: quantiferon tb reagent

tag: cd4 count

tag: prescription drugs

tag: active ingredient

tag: art start year

tag: recreational drugs

tag: mtb challenged

tag: average tagmented library size

tag: fragments in clean bam

tag: sequencing run

tag: lane


title: FACT_H3K36me3_65C_01SDS_rep2_mm10

tag: strain

value: FVBN

tag: tissue

tag: treatment

value: FFPE


title: Patient 2 Lung Scan 26688 A19 ROI 008

description: Unstained 4μm-thick sections were cut from FFPE blocks from two patients and immunoflourescently labeled with PanCK, CD45, CD68 and DAPI. Twelve regions of interest (ROIs) per slide were selected for targeted spatial transcriptomics (GeoMx, Nanostring) with >1,600 cancer atlas transcripts and 10 additional SARS-CoV-2 genes.

tag: scan id

tag: roi(lable)


title: FACT_H3K36me3_65C_01SDS_rep1_mm10


title: Patient 2 Lung Scan 26688 A19 ROI 012


title: ATAC-Seq Person living with HIV sample 25, Alveolar macrophage, Mycobacterium tuberculosis challenged library

description:
Person living with HIV sample 25, Alveolar macrophage, Mycobacterium tuberculosis challenged library
Tn5 transposase

tag: ethnicity

tag: Sex

tag: age

tag: sexually transmitted infections

tag: cigarette smoker

tag: bal sampling date

value: yes


title: Mouse_H3K27me3_CUT_Tag_Frozen_rep2_mm10

value: Frozen


title: ATAC-Seq Person living with HIV sample 25, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library

description:
Person living with HIV sample 25, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library
Tn5 transposase

tag: quantiferon tb reagent

tag: cd4 count

tag: prescription drugs

value: Atripla

tag: active ingredient

tag: art start year

tag: recreational drugs


title: Patient 2 Lung Scan 26688 A19 ROI 007


title: Patient 2 Lung Scan 26688 A19 ROI 006


title: Mouse_H3K27me3_CUT_Tag_Frozen_rep1_mm10

tag: strain


title: Patient 2 Lung Scan 26688 A19 ROI 005


title: PGC1a_CTD_AP_rep1

tag: cell line

tag: differentiation state

tag: genotype

tag: protein for affinity purification

value: CTD of mouse PGC-1alpha (US Biological Life Sciences, #156296)


title: 2012364_Mouse-2 OR Mouse-3 Blood J35+70

description: Blood from PBC mouse after cholangitis induction and ectopic CCA growth

tag: tissue

value: Wild type

tag: treatment

tag: day of collection

tag: protocol


title: Input_rep1


title: Mouse_H3K27me3_FACT_with_KM65C01SDS01SD-rep2_mm10


title: ATAC-Seq Person living with HIV sample 21, Alveolar macrophage, Mycobacterium tuberculosis challenged library

description:
Person living with HIV sample 21, Alveolar macrophage, Mycobacterium tuberculosis challenged library
Tn5 transposase

tag: ethnicity

value: Caucasian

tag: Sex

tag: age

tag: sexually transmitted infections

value: Truvada, Tivicay

value: cannabis

tag: cigarette smoker

tag: mtb challenged

tag: average tagmented library size

tag: fragments in clean bam

tag: sequencing run

tag: lane


title: ATAC-Seq Person living with HIV sample 23, Alveolar macrophage, Mycobacterium tuberculosis challenged library

description:
Person living with HIV sample 23, Alveolar macrophage, Mycobacterium tuberculosis challenged library
Tn5 transposase

tag: quantiferon tb reagent

tag: cd4 count

tag: prescription drugs

value: Genvoya

tag: active ingredient

value: Emtricitabine, Tenofovir_AF, Cobicistat, Elvitegravir

tag: art start year

tag: recreational drugs

tag: bal sampling date


title: Patient 2 Lung Scan 26688 A19 ROI 004

tag: scan id

tag: roi(lable)


title: Serpin.NT.SCI119_07_S7

city: Suita

first: Takashi

last: Shimbo

state: Osaka

address: 2-2 Yamadaoka

country: Japan

institute: Osaka university

description:
processed data file: serpin.count_table.tsv
processed data file: serpin.metadata.tsv

data_processing:
The barcoded sequence was corrected by an edit distance < 2.
The corrected reads were processed using Drop-seq_tools-1.12 (https://github.com/broadinstitute/Drop-seq).
The Drop-seq_tools’ DigitalExpression output was filtered using the numbers of reads, transcripts and genes as well as the percentage of mitochondrial genes for each cell.
The alignment was done with STAR (v2.5b).
Genome_build: ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE63nnn/GSE63472/suppl/GSE63472_mm10_reference_metadata.tar.gz
Supplementary_files_format_and_content: count_table.tsv contains digital gene expression for every sample.
Supplementary_files_format_and_content: metadata.tsv contains various annotation, e.g. sample names, time point, treatment, etc.

source_name: Colon

extract_protocol: RNA-seq library was constructed using modified Smart-seq2 method.

treatment_protocol: For time course study, mice were treated with 1.5%DSS for 6 days (Day0 to Day6) then switched to drinking water until Day15. For treatment study, 6 shots of murine recombinant Serpina3n or PBS was intravenously injected (20 μg/kg per day) from Day0 to Day5.

tag: tissue

value: Colon

tag: treatment


title: Serpin.NT.SCI119_10_S10


title: Serpin.NT.SCI119_09_S9


title: Serpin.NT.SCI119_08_S8


title: Input_rep2

tag: cell line

value: C2C12 skeletal muscle cells

tag: differentiation state

value: C2C12 myotubes

tag: genotype

tag: protein for affinity purification


title: Patient 2 Lung Scan 26688 A19 ROI 002


title: ATAC-Seq Person living with HIV sample 21, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library

description:
Person living with HIV sample 21, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library
Tn5 transposase

tag: ethnicity

tag: Sex

value: M

tag: age

tag: sexually transmitted infections

tag: cigarette smoker

tag: mtb challenged

tag: average tagmented library size

tag: fragments in clean bam

tag: sequencing run


title: ATAC-Seq Person living with HIV sample 23, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library

description:
Person living with HIV sample 23, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library
Tn5 transposase

value: no

tag: quantiferon tb reagent

tag: cd4 count

tag: prescription drugs

tag: active ingredient

tag: art start year

tag: recreational drugs

tag: bal sampling date

tag: lane


title: 2011753_Mouse-3J40 OR Mouse-3 Blood J35

description: Blood from PBC mouse after cholangitis induction

tag: tissue

value: Blood

tag: strain

tag: genotype

tag: treatment

value: 2-octynoic acid BSA conjugate + alpha-galactosylceramide

tag: day of collection

tag: protocol

value: single-cell TCRalphaBeta


title: ATAC-Seq Person living with HIV sample 20, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library

description:
Person living with HIV sample 20, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library
Tn5 transposase

tag: ethnicity

tag: Sex

tag: age

tag: sexually transmitted infections

value: Truvada, Tybost, Prezista

value: Emtricitabine, Tenofovir_DF, Cobiscistat, Darunavir

tag: cigarette smoker

tag: mtb challenged

tag: average tagmented library size


title: Mouse_H3K27me3_FACT_with_KM01SDS65C-rep2_mm10

value: FVBN

value: kidney

value: FFPE


title: Patient 2 Lung Scan 26688 A19 ROI 001

tag: scan id

tag: roi(lable)


title: ATAC-Seq Person living with HIV sample 19, Alveolar macrophage, Mycobacterium tuberculosis challenged library

description:
Person living with HIV sample 19, Alveolar macrophage, Mycobacterium tuberculosis challenged library
Tn5 transposase

value: Caucasian

tag: quantiferon tb reagent

tag: cd4 count

tag: prescription drugs

value: Triumeq

tag: active ingredient

value: Abacavir, Dolutegravir, Lamivudine

tag: art start year

tag: recreational drugs

tag: bal sampling date

value: yes

tag: fragments in clean bam

tag: sequencing run


title: Mouse_H3K27me3_FACT_with_KM65C01SDS01SD-rep1_mm10

tag: strain

tag: tissue

tag: treatment


title: Mouse_H3K27me3_FACT_with_KM03SDS50C-rep1_mm10


title: Mouse_H3K27me3_FACT_with_KM03SDS50C-rep2_mm10


title: ATAC-Seq Person living with HIV sample 20, Alveolar macrophage, Mycobacterium tuberculosis challenged library

description:
Person living with HIV sample 20, Alveolar macrophage, Mycobacterium tuberculosis challenged library
Tn5 transposase

tag: ethnicity

tag: Sex

tag: age

tag: sexually transmitted infections

value: cannabis

tag: cigarette smoker

tag: lane


title: ATAC-Seq Person living with HIV sample 19, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library

description:
Person living with HIV sample 19, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library
Tn5 transposase

tag: quantiferon tb reagent

tag: cd4 count

tag: mtb challenged

tag: average tagmented library size


title: ATAC-Seq Person living with HIV sample 17, Alveolar macrophage, Mycobacterium tuberculosis challenged library

description:
Person living with HIV sample 17, Alveolar macrophage, Mycobacterium tuberculosis challenged library
Tn5 transposase

tag: prescription drugs

value: Viread, Tivicay, Edurant

tag: active ingredient

value: Tenofovir_DF, Dolutegravir, Rilpivirine

tag: art start year

tag: recreational drugs


title: Patient 2 Spleen Scan 26688 A11 ROI 011

source_name: Spleen

tag: scan id

tag: roi(lable)


title: Serpin.NT.SCI119_06_S6

tag: tissue

value: Colon

tag: treatment


title: Serpin.NT.SCI119_05_S5


title: Patient 2 Lung Scan 26688 A19 ROI 003


title: Mouse_H3K27ac_Frozen_CUT_Tag_ac-rep1_mm10

tag: strain

value: Frozen


title: Mouse_H3K27me3_FACT_with_KM01SDS65C-rep1_mm10


title: Patient 2 Spleen Scan 26688 A11 ROI 009


title: Serpin.NT.SCI119_02_S2


title: ATAC-Seq Person living with HIV sample 15, Alveolar macrophage, Mycobacterium tuberculosis challenged library

description:
Person living with HIV sample 15, Alveolar macrophage, Mycobacterium tuberculosis challenged library
Tn5 transposase

tag: ethnicity

tag: Sex

value: M

tag: age

value: HIV x 2003

value: no

tag: bal sampling date

tag: fragments in clean bam

tag: sequencing run


title: Patient 2 Spleen Scan 26688 A11 ROI 010


title: Serpin.NT.SCI119_04_S4


title: Serpin.NT.SCI119_01_S1


title: Mouse_H3K27ac_FFPE_FACT_rep2_mm10


title: Patient 2 Spleen Scan 26688 A11 ROI 007


title: Patient 2 Spleen Scan 26688 A11 ROI 012


title: Patient 2 Spleen Scan 26688 A11 ROI 006


title: Mouse_H3K27me3_FACT_with_KM01SDS50C-rep1_mm10


title: ATAC-Seq Person living with HIV sample 14, Alveolar macrophage, Mycobacterium tuberculosis challenged library

description:
Person living with HIV sample 14, Alveolar macrophage, Mycobacterium tuberculosis challenged library
Tn5 transposase

tag: sexually transmitted infections

tag: quantiferon tb reagent

tag: cd4 count

value: Kivexa, Reyataz, Norvir

value: Abacavir, Lamivudine, Atazanavir, Ritonavir

tag: cigarette smoker

tag: mtb challenged

tag: lane


title: Serpin.IBD+Serpin.SCI121_07_S7


title: Patient 2 Spleen Scan 26688 A11 ROI 008

description: Unstained 4μm-thick sections were cut from FFPE blocks from two patients and immunoflourescently labeled with PanCK, CD45, CD68 and DAPI. Twelve regions of interest (ROIs) per slide were selected for targeted spatial transcriptomics (GeoMx, Nanostring) with >1,600 cancer atlas transcripts and 10 additional SARS-CoV-2 genes.

tag: scan id


title: Mouse_H3K27ac_FFPE_FACT_rep1_mm10

value: FVBN


title: Mouse_H3K27ac_Frozen_CUT_Tag_ac-rep2_mm10

value: kidney


title: Serpin.NT.SCI119_03_S3


title: ATAC-Seq Person living with HIV sample 17, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library

description:
Person living with HIV sample 17, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library
Tn5 transposase

tag: prescription drugs

tag: active ingredient

tag: art start year

tag: recreational drugs

tag: average tagmented library size


title: ATAC-Seq Person living with HIV sample 15, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library

description:
Person living with HIV sample 15, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library
Tn5 transposase

tag: ethnicity

tag: Sex


title: Mouse_H3K27me3_FACT_with_KM01SDS50C-rep2_mm10

tag: strain

tag: tissue

tag: treatment

value: FFPE


title: ATAC-Seq Person living with HIV sample 14, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library

description:
Person living with HIV sample 14, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library
Tn5 transposase

value: Caucasian

tag: age

tag: sexually transmitted infections

tag: bal sampling date

tag: fragments in clean bam

tag: sequencing run


title: Patient 2 Spleen Scan 26688 A11 ROI 005

tag: roi(lable)


title: Mouse_H3K27ac_FACT_without_retrieval_rep2_mm10


title: ATAC-Seq Person living with HIV sample 13, Alveolar macrophage, Mycobacterium tuberculosis challenged library

description:
Person living with HIV sample 13, Alveolar macrophage, Mycobacterium tuberculosis challenged library
Tn5 transposase

value: F

tag: quantiferon tb reagent

tag: cd4 count

value: Complera, Reyataz, Isentress

value: Emtricitabine, Tenofovir_DF, Rilpivirine, Atazanavir, Raltegravir

tag: cigarette smoker

tag: mtb challenged

tag: lane


title: Serpin.IBD+Serpin.SCI121_08_S8


title: Mouse_H3K27ac_FACT_without_retrieval_rep1_mm10


title: Serpin.IBD+Serpin.SCI121_06_S6


title: Patient 2 Spleen Scan 26688 A11 ROI 004

tag: scan id


title: Serpin.IBD+Serpin.SCI121_05_S5


title: Patient 2 Spleen Scan 26688 A11 ROI 001


title: Patient 2 Spleen Scan 26688 A11 ROI 002


title: ATAC-Seq Person living with HIV sample 13, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library

description:
Person living with HIV sample 13, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library
Tn5 transposase

tag: ethnicity

tag: prescription drugs

tag: active ingredient

tag: art start year

tag: recreational drugs

value: cannabis

value: yes

tag: average tagmented library size


title: 201022_antiCD3_RAPO [RAPO-201022]

city: Seoul

first: Mi-La

last: Cho

address: 222,Banpo-daero, Seocho-gu

country: South Korea

institute: The Catholic University of Korea

data_processing:
Illumina bcl2fastq2-v2.20.0 software used for basecalling.
Trimmomatic program is used to remove adapter sequences and bases with base quality lower than three from the ends. Also using sliding window method, bases of reads that does not qualify for window size 4, and mean quality 15 are trimmed. Afterwards, reads with length shorter than 36bp are dropped to produce trimmed data.
Sequenced reads were mapped to GRCh38 whole genome by using HISAT2 version 2.1.0 with parameter -p 20 -dta --rna-strandness RF --novel-splicesite-outfile -x -1 -2
Fragment Per Kilobase of exon per Megabase of library size (FPKM) were calculated by using StringTie version 2.1.3b, with parameter --rf -p 20 -l -o -G -A -C -e
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

molecule: polyA RNA

source_name: cell from Human

growth_protocol: RA patient-derived peripheral mononuclear cells were routinely by 10% RPMI media.

extract_protocol:
RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: RA PBMCs treatment with B. longum RAPO in the presence of  anti CD3 0.5ug/mL for 48hrs. (5x10^5/6well)

tag: subject status

value: Rheumatoid Arthritis patient

tag: age

value: post natal day 21

tag: cell type

value: PBMC

tag: treatment


title: Cochlear SCs (Ikzf2 and Atoh1)-P60-42 [Nascent HCs-16]

first: Zhiyong

last: Liu

address: 7 Science Park Road ZGC Life Science Park

institute: National Institute of Biological Sciences, Beijing

data_processing:
FastQC (v0.11.9) and Trimmomatic (v0.39) were used for quality control.
eads were mapped to the mouse reference genome (mm10) with high quality, using Hisat2 (v2.1.0) with default parameters.
Transcript Per Million (TPM) were calculated by StringTie  (v1.3.5) with default parameters.
Raw counts were calculated by HTSeq (v0.10.0) software
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Cochlear supporting cells with ectopic Atoh1 and Ikzf2

extract_protocol:
Cochlear duct was carefully dissected out and digested by enzymes, wild type adult OHCs and SCs as well as SCs with ectopic Atoh1 and Ikzf2 that were genetically labelled by Tdtomato were manually picked, followed by cDNA generation and amplication via smartseq HT kit (Cat#: 634437, Takara ).
RNA libraries were prepared by tagmentation Kit (Cat#: TD503, Vazyme).

tag: strain

value: post natal day 60

tag: genotype

tag: tissue

value: Cochlea

value: Cochlear supporting cells


title: Cochlear SCs (Ikzf2 and Atoh1)-P60-41 [Nascent HCs-15]


title: ATAC-Seq Person living with HIV sample 11, Alveolar macrophage, Mycobacterium tuberculosis challenged library

description:
Person living with HIV sample 11, Alveolar macrophage, Mycobacterium tuberculosis challenged library
Tn5 transposase

tag: Sex

value: M

tag: sexually transmitted infections

value: no

tag: quantiferon tb reagent

tag: cd4 count

value: Complera

tag: cigarette smoker

tag: bal sampling date

tag: fragments in clean bam

tag: sequencing run


title: Patient 2 Spleen Scan 26688 A11 ROI 003

tag: scan id

tag: roi(lable)


title: 201016_antiCD3_RAPO [RAPO-201016]

tag: subject status


title: ATAC-Seq Person living with HIV sample 10, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library

description:
Person living with HIV sample 10, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library
Tn5 transposase

tag: ethnicity

tag: age

tag: prescription drugs

value: Intelence, Prezista, Tivicay, Norvir

tag: active ingredient

value: Etravirine, Darunavir, Dolutegravir, Ritonavir

tag: art start year

tag: recreational drugs

tag: mtb challenged

tag: average tagmented library size

tag: lane


title: Cochlear SCs (Ikzf2 and Atoh1)-P60-40 [SCs failing to become HC-15]

tag: strain

tag: genotype

tag: tissue

tag: cell type


title: ATAC-Seq Person living with HIV sample 11, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library

description:
Person living with HIV sample 11, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library
Tn5 transposase

value: Caucasian

tag: Sex

tag: sexually transmitted infections

tag: quantiferon tb reagent

tag: cd4 count

tag: cigarette smoker

tag: bal sampling date

tag: fragments in clean bam

tag: sequencing run


title: ATAC-Seq Person living with HIV sample 9, Alveolar macrophage, Mycobacterium tuberculosis challenged library

description:
Person living with HIV sample 9, Alveolar macrophage, Mycobacterium tuberculosis challenged library
Tn5 transposase

tag: ethnicity

tag: age

tag: prescription drugs

value: Truvada, Isentress

tag: active ingredient

tag: art start year


title: Cochlear SCs (Ikzf2 and Atoh1)-P60-39 [Nascent HCs-14]

tag: strain


title: Serpin.IBD+Serpin.SCI121_02_S2

description:
processed data file: serpin.count_table.tsv
processed data file: serpin.metadata.tsv

value: Colon

tag: treatment


title: 201022_antiCD3_Vehicle [VeCD31-201022]

tag: subject status


title: Serpin.IBD+Serpin.SCI121_04_S4

tag: tissue


title: Serpin.IBD+PBS.SCI120_10_S10

value: PBS


title: Serpin.IBD+PBS.SCI120_09_S9


title: 201016_antiCD3_Vehicle [CD3-201016]

tag: cell type


title: GM_CUT_Tag_H3K27me3_rep2_hg38

value: B cell


title: Serpin.IBD+Serpin.SCI121_01_S1


title: Cochlear SCs (Ikzf2 and Atoh1)-P60-36 [Nascent HCs-11]

tag: genotype


title: Cochlear SCs (Ikzf2 and Atoh1)-P60-38 [Nascent HCs-13]


title: ATAC-Seq Person living with HIV sample 5, Alveolar macrophage, Mycobacterium tuberculosis challenged library

description:
Person living with HIV sample 5, Alveolar macrophage, Mycobacterium tuberculosis challenged library
Tn5 transposase

tag: Sex

tag: sexually transmitted infections

tag: quantiferon tb reagent

value: Truvada

value: Emtricitabine, Tenofovir_DF

tag: recreational drugs

tag: mtb challenged

value: yes

tag: average tagmented library size

tag: lane


title: Serpin.IBD+PBS.SCI120_08_S8


title: GM_CUT_Tag_H3K27me3_rep1_hg38


title: ATAC-Seq Person living with HIV sample 10, Alveolar macrophage, Mycobacterium tuberculosis challenged library

description:
Person living with HIV sample 10, Alveolar macrophage, Mycobacterium tuberculosis challenged library
Tn5 transposase

tag: ethnicity

tag: age

tag: cd4 count

tag: cigarette smoker

tag: bal sampling date

tag: fragments in clean bam

tag: sequencing run


title: ATAC-Seq Person living with HIV sample 9, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library

description:
Person living with HIV sample 9, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library
Tn5 transposase

tag: prescription drugs

tag: active ingredient

tag: art start year

value: cannabis


title: Serpin.IBD+Serpin.SCI121_03_S3

tag: tissue

tag: treatment


title: Cochlear SCs (Ikzf2 and Atoh1)-P60-35 [Nascent HCs-10]

tag: strain

value: post natal day 60

tag: genotype

tag: cell type


title: Cochlear SCs (Ikzf2 and Atoh1)-P60-34 [SCs failing to become HC-14]

value: Cochlea


title: Cochlear SCs (Ikzf2 and Atoh1)-P60-37 [Nascent HCs-12]

value: Cochlear supporting cells


title: GM_FACT_H3K27me3_rep2_hg38


title: GM_FACT_H3K27me3_rep1_hg38


title: Cochlear SCs (Ikzf2 and Atoh1)-P60-33 [SCs failing to become HC-13]


title: ATAC-Seq Person living with HIV sample 5, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library

description:
Person living with HIV sample 5, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library
Tn5 transposase

tag: Sex

value: M

tag: sexually transmitted infections

tag: quantiferon tb reagent

tag: recreational drugs

tag: mtb challenged

tag: average tagmented library size


title: Serpin.IBD+PBS.SCI120_06_S6


title: Serpin.IBD+PBS.SCI120_05_S5


title: GBM2-FACT-H3K27ac-rep2_hg38

source_name: glioblastoma

value: brain

value: FFPE


title: GBM2-FACT-H3K27ac-rep1_hg38


title: ATAC-Seq Person living with HIV sample 3, Alveolar macrophage, Mycobacterium tuberculosis challenged library

description:
Person living with HIV sample 3, Alveolar macrophage, Mycobacterium tuberculosis challenged library
Tn5 transposase

source_name: bronchoalveolar lavage

tag: ethnicity

tag: age

value: no

tag: cd4 count

tag: cigarette smoker

tag: bal sampling date

tag: lane


title: Serpin.IBD+PBS.SCI120_07_S7

tag: tissue


title: Serpin.IBD+PBS.SCI120_04_S4

tag: treatment


title: Cochlear SCs (Ikzf2 and Atoh1)-P60-32 [Nascent HCs-9]

tag: strain


title: Serpin.IBD+PBS.SCI120_03_S3


title: Cochlear SCs (Ikzf2 and Atoh1)-P60-31 [SCs failing to become HC-12]

tag: genotype


title: Cochlear SCs (Ikzf2 and Atoh1)-P60-30 [SCs failing to become HC-11]

tag: cell type


title: GBM4-FACT-H3K27ac-rep2_hg38


title: Serpin.IBD+PBS.SCI120_02_S2


title: Cochlear SCs (Ikzf2 and Atoh1)-P60-29 [SCs failing to become HC-10]


title: ATAC-Seq Person living with HIV sample 4, Alveolar macrophage, Mycobacterium tuberculosis challenged library

description:
Person living with HIV sample 4, Alveolar macrophage, Mycobacterium tuberculosis challenged library
Tn5 transposase

tag: Sex

tag: prescription drugs

value: Biktarvy

tag: active ingredient

tag: art start year

tag: fragments in clean bam

tag: sequencing run


title: ATAC-Seq Person living with HIV sample 4, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library

description:
Person living with HIV sample 4, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library
Tn5 transposase

tag: ethnicity

value: Caucasian

tag: sexually transmitted infections

tag: quantiferon tb reagent

tag: recreational drugs

tag: mtb challenged

tag: average tagmented library size


title: ATAC-Seq Pre-exposure prophylaxis sample 37, Alveolar macrophage, Mycobacterium tuberculosis challenged library

description:
Pre-exposure prophylaxis sample 37, Alveolar macrophage, Mycobacterium tuberculosis challenged library
Tn5 transposase

tag: age

tag: cd4 count

tag: cigarette smoker

tag: bal sampling date

tag: lane


title: GBM4-FACT-H3K27ac-rep1_hg38

tag: tissue

tag: treatment


title: ATAC-Seq Person living with HIV sample 3, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library

description:
Person living with HIV sample 3, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library
Tn5 transposase

tag: Sex

tag: prescription drugs

value: Truvada, Isentress

tag: active ingredient


title: Serpin.IBD+PBS.SCI120_01_S1

value: Colon


title: GBM1-FACT-H3K27ac-rep2_hg38


title: GBM1-FACT-H3K27ac-rep1_hg38


title: ATAC-Seq Pre-exposure prophylaxis sample 37, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library

description:
Pre-exposure prophylaxis sample 37, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library
Tn5 transposase

tag: art start year

tag: fragments in clean bam

tag: sequencing run


title: Cochlear SCs (Ikzf2 and Atoh1)-P60-27 [SCs failing to become HC-8]

tag: strain

tag: genotype

tag: cell type


title: Cochlear SCs (Ikzf2 and Atoh1)-P60-28 [SCs failing to become HC-9]


title: Time Course IBD.DAY15.SCI133_20_S20

description:
processed data file: tc_ibd.count_table.tsv
processed data file: tc_ibd.metadata.tsv

value: DSS

tag: time point

value: Day 15


title: ATAC-Seq Pre-exposure prophylaxis sample 36, Alveolar macrophage, Mycobacterium tuberculosis challenged library

description:
Pre-exposure prophylaxis sample 36, Alveolar macrophage, Mycobacterium tuberculosis challenged library
Tn5 transposase

tag: ethnicity

tag: age

tag: sexually transmitted infections

value: gonorrhea PCR+

tag: quantiferon tb reagent

value: Truvada

tag: recreational drugs

value: ketamine

tag: mtb challenged

tag: average tagmented library size


title: Time Course IBD.DAY15.SCI133_19_S19

tag: tissue

tag: treatment


title: GBM3-FACT-H3K27ac-rep2_hg38


title: Cochlear SCs (Ikzf2 and Atoh1)-P60-26 [SCs failing to become HC-7]


title: GBM3-FACT-H3K27ac-rep1_hg38


title: Time Course IBD.DAY15.SCI133_17_S17


title: Time Course IBD.DAY15.SCI133_18_S18


title: ATAC-Seq Pre-exposure prophylaxis sample 35, Alveolar macrophage, Mycobacterium tuberculosis challenged library

description:
Pre-exposure prophylaxis sample 35, Alveolar macrophage, Mycobacterium tuberculosis challenged library
Tn5 transposase

tag: Sex

value: Chlamydia â€“ 2018

tag: cd4 count

tag: prescription drugs

tag: active ingredient

value: Emtricitabine, Tenofovir_DF

value: cocaine

tag: cigarette smoker

value: yes

tag: bal sampling date

tag: lane


title: Cochlear SCs (Ikzf2 and Atoh1)-P60-24 [SCs failing to become HC-5]

tag: strain

value: post natal day 60

tag: genotype

value: Cochlea

tag: cell type

value: Cochlear supporting cells


title: ATAC-Seq Pre-exposure prophylaxis sample 35, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library

description:
Pre-exposure prophylaxis sample 35, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library
Tn5 transposase

tag: ethnicity

value: M

tag: age

tag: sexually transmitted infections

value: no

tag: art start year

tag: fragments in clean bam

tag: sequencing run


title: FACT_seq_HCRC-H3K27ac.rep2_hg38

source_name: colon

tag: tissue

value: colon

tag: treatment

value: FFPE


title: Time Course IBD.DAY15.SCI133_16_S16

value: Colon

tag: time point


title: FACT_seq_HCRC-H3K27ac.rep1_hg38


title: Cochlear SCs (Ikzf2 and Atoh1)-P60-22 [Nascent HCs-7]


title: ATAC-Seq Pre-exposure prophylaxis sample 34, Alveolar macrophage, Mycobacterium tuberculosis challenged library

description:
Pre-exposure prophylaxis sample 34, Alveolar macrophage, Mycobacterium tuberculosis challenged library
Tn5 transposase

value: Asian

tag: Sex

value: Chlamydia â€“ 2017

tag: quantiferon tb reagent

tag: cd4 count

tag: prescription drugs

tag: recreational drugs

tag: mtb challenged

tag: average tagmented library size


title: GM-CUT_Tag-H3K27ac-rep2_hg38

value: B cell


title: Cochlear SCs (Ikzf2 and Atoh1)-P60-23 [Nascent HCs-8]

tag: strain

tag: genotype

tag: cell type


title: Time Course IBD.DAY15.SCI133_15_S15

value: DSS

value: Day 15


title: ATAC-Seq Pre-exposure prophylaxis sample 36, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library

description:
Pre-exposure prophylaxis sample 36, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library
Tn5 transposase

tag: ethnicity

value: Caucasian

tag: age

tag: sexually transmitted infections

value: gonorrhea PCR+

value: Truvada

tag: active ingredient

value: ketamine

tag: cigarette smoker

tag: bal sampling date

tag: lane


title: Time Course IBD.DAY15.SCI133_14_S14

tag: tissue

tag: treatment

tag: time point


title: GM-CUT_Tag-H3K27ac-rep1_hg38


title: Cochlear SCs (Ikzf2 and Atoh1)-P60-21 [Nascent HCs-6]

value: post natal day 60


title: ATAC-Seq Pre-exposure prophylaxis sample 33, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library

description:
Pre-exposure prophylaxis sample 33, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library
Tn5 transposase

tag: Sex

value: depression

tag: quantiferon tb reagent

tag: cd4 count

tag: prescription drugs

value: Truvada, Remeron

value: Emtricitabine, Tenofovir_DF

tag: art start year

value: speed

tag: fragments in clean bam

tag: sequencing run


title: ATAC-Seq Pre-exposure prophylaxis sample 33, Alveolar macrophage, Mycobacterium tuberculosis challenged library

description:
Pre-exposure prophylaxis sample 33, Alveolar macrophage, Mycobacterium tuberculosis challenged library
Tn5 transposase

tag: ethnicity

value: M

value: no

tag: recreational drugs

tag: mtb challenged

value: yes

tag: average tagmented library size


title: GM-FACT-H3K27ac-rep2_hg38


title: Time Course IBD.DAY15.SCI133_12_S12

value: Colon


title: Cochlear SCs (Ikzf2 and Atoh1)-P60-19 [Nascent HCs-4]

tag: strain

tag: age

tag: genotype

value: Cochlea

tag: cell type

value: Cochlear supporting cells


title: Cochlear SCs (Ikzf2 and Atoh1)-P60-20 [Nascent HCs-5]

tag: tissue


title: Cochlear SCs (Ikzf2 and Atoh1)-P60-25 [SCs failing to become HC-6]


title: Time Course IBD.DAY15.SCI133_13_S13

tag: treatment

value: DSS

tag: time point


title: ATAC-Seq Pre-exposure prophylaxis sample 32, Alveolar macrophage, Mycobacterium tuberculosis challenged library

description:
Pre-exposure prophylaxis sample 32, Alveolar macrophage, Mycobacterium tuberculosis challenged library
Tn5 transposase

tag: Sex

tag: sexually transmitted infections

tag: quantiferon tb reagent

tag: active ingredient

tag: cigarette smoker

tag: bal sampling date

tag: lane


title: ATAC-Seq Pre-exposure prophylaxis sample 32, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library

description:
Pre-exposure prophylaxis sample 32, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library
Tn5 transposase

tag: ethnicity

tag: cd4 count

tag: prescription drugs

tag: art start year

tag: recreational drugs

tag: fragments in clean bam

tag: sequencing run


title: L11_rep2

description: LiverL11_rep2_EKDL190133819-1a-AK11820-AK14824_HM55FDSXX_L2

data_processing:
Adaptor sequences were trimmed from fastq file
All data were mapped to the hg19 reference genome using bowtie2 using the parameter --very-sensitive
PCR and optical duplicates were removed using Picard v.1.119
The bam file were filtered for alignment quality of >Q10, . Reads mapping to mitochondria were removed
peaks were called using MACS2 with q = 0.01
Genome_build: hg19
Supplementary_files_format_and_content: bigwig and peaks

source_name: Liver

growth_protocol: Frozen liver tissues samples (n=11) were obtained from the human tissue lab,a biobank for multi-organ donors funded by the excellence of diabetes research in Sweden (EXODIAB), following the Uppsala Regional Ethics Committee approval.3 samples were harvested from donor diagnosed with T2D (HbA1c≥6.5%) and 8 from control donors characterized by normoglycemia (CTRL). Suspension of single nuclei was prepared for each sample using the gentleMACS dissociator (Miltenyi) program E. ~5 mg of frozen liver tissue was transferred into a gentleMACS C-tube with 10 ml of 0,250 M Sucrose solution. The homogenate was filtered using 100 µm MACS SmartStrainers and the volume adjusted to 15 ml with the Sucrose solution. The homogenate was then centrifuged at 600 x g at 4 C in an Eppendorf 5810R Centrifuge and the supernatant was discarded. The nuclei in the pellet were resuspended in 1 ml of PBS with 0,04% BSA and filtered using a 30 µm MACS SmartStrainers. The nuclei suspension was evaluated for purity and concentration using the Countess™ II Automated Cell Counter (Thermo Scientific) via staining with trypan blue.

extract_protocol:
All the libraries are ATAC procol, DNA was purified with MiniElution kit
The ATAC library construction was done with standard ATAC-seq protocol.

treatment_protocol: there is no treaemnt for the cells

tag: donor status

value: donor diagnosed with T2D

tag: tissue

value: Liver


title: Time Course IBD.DAY12.SCI133_10_S10

tag: treatment

tag: time point

value: Day 12


title: Cochlear SCs (Ikzf2 and Atoh1)-P60-16 [SCs failing to become HC-2]

tag: strain

tag: age

tag: genotype

tag: cell type


title: L11_rep1

description: LiverL11_rep1_EKDL190133819-1a-AK1972-AK14824_HM55FDSXX_L2


title: ATAC-Seq Pre-exposure prophylaxis sample 34, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library

description:
Pre-exposure prophylaxis sample 34, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library
Tn5 transposase

value: Asian

tag: Sex

tag: sexually transmitted infections

value: Chlamydia â€“ 2017

tag: quantiferon tb reagent

value: Truvada

tag: active ingredient

tag: cigarette smoker

tag: bal sampling date

tag: mtb challenged

tag: average tagmented library size


title: Cochlear SCs (Ikzf2 and Atoh1)-P60-17 [SCs failing to become HC-3]

value: post natal day 60


title: Cochlear SCs (Ikzf2 and Atoh1)-P60-18 [SCs failing to become HC-4]


title: Time Course IBD.DAY12.SCI133_09_S9


title: ATAC-Seq Pre-exposure prophylaxis sample 31, Alveolar macrophage, Mycobacterium tuberculosis challenged library

description:
Pre-exposure prophylaxis sample 31, Alveolar macrophage, Mycobacterium tuberculosis challenged library
Tn5 transposase

tag: ethnicity

value: Caucasian

tag: cd4 count

tag: prescription drugs

tag: art start year

tag: recreational drugs

tag: fragments in clean bam

tag: sequencing run

tag: lane


title: Cochlear SCs (Ikzf2 and Atoh1)-P60-15 [Nascent HCs-3]

tag: strain

tag: age

tag: genotype

tag: tissue

tag: cell type


title: GM-FACT-H3K27ac-rep1_hg38

value: B cell


title: ATAC-Seq Pre-exposure prophylaxis sample 31, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library

description:
Pre-exposure prophylaxis sample 31, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library
Tn5 transposase

tag: Sex

tag: sexually transmitted infections

tag: quantiferon tb reagent

tag: active ingredient

value: Emtricitabine, Tenofovir_DF

tag: cigarette smoker


title: Cochlear SCs (Ikzf2 and Atoh1)-P60-14 [SCs failing to become HC-1]


title: Time Course IBD.DAY12.SCI133_07_S7

tag: treatment

tag: time point


title: Time Course IBD.DAY12.SCI133_08_S8


title: Time Course IBD.DAY15.SCI133_11_S11

value: Day 15


title: ATAC-Seq Pre-exposure prophylaxis sample 29, Alveolar macrophage, Mycobacterium tuberculosis challenged library

description:
Pre-exposure prophylaxis sample 29, Alveolar macrophage, Mycobacterium tuberculosis challenged library
Tn5 transposase

tag: ethnicity

value: North african

value: M

value: chlamydia PCR+

tag: cd4 count

tag: prescription drugs

tag: art start year

value: cannabis

tag: bal sampling date

tag: mtb challenged

tag: average tagmented library size


title: L9_rep1

description: LiverL9rep1_EKDL190133819-1a-AK1554-AK17204_HM55FDSXX_L2

tag: donor status


title: Time Course IBD.DAY12.SCI133_05_S5

description:
processed data file: tc_ibd.count_table.tsv
processed data file: tc_ibd.metadata.tsv

tag: tissue

value: Colon


title: ATAC-Seq Pre-exposure prophylaxis sample 29, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library

description:
Pre-exposure prophylaxis sample 29, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library
Tn5 transposase

tag: age

value: yes

tag: recreational drugs

value: no

tag: fragments in clean bam

tag: sequencing run

tag: lane


title: L9_rep2

description: LiverL9rep2_EKDL190133819-1a-AK1569-AK17204_HM55FDSXX_L2

value: donor diagnosed with T2D

value: Liver


title: L8_rep2

description: LiverL8_rep2_EKDL190133819-1a-AK1750-AK17202_HM55FDSXX_L2

value: control donors characterized by normoglycemia


title: Cochlear SCs (Ikzf2 and Atoh1)-P60-12 [Nascent HCs-2]

tag: strain

tag: genotype

value: Cochlea

tag: cell type

value: Cochlear supporting cells


title: Time Course IBD.DAY12.SCI133_06_S6

tag: treatment

value: DSS

tag: time point

value: Day 12


title: ATAC-Seq Pre-exposure prophylaxis sample 28, Alveolar macrophage, Mycobacterium tuberculosis challenged library

description:
Pre-exposure prophylaxis sample 28, Alveolar macrophage, Mycobacterium tuberculosis challenged library
Tn5 transposase

tag: ethnicity

value: Caucasian

tag: Sex

tag: sexually transmitted infections

tag: quantiferon tb reagent

tag: cd4 count

tag: prescription drugs

value: Truvada

tag: active ingredient

tag: cigarette smoker


title: Time Course IBD.DAY12.SCI133_04_S4

tag: tissue


title: ATAC-Seq Pre-exposure prophylaxis sample 28, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library

description:
Pre-exposure prophylaxis sample 28, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library
Tn5 transposase

tag: age

value: Emtricitabine, Tenofovir_DF

tag: art start year

tag: recreational drugs

tag: bal sampling date

tag: mtb challenged

tag: average tagmented library size

tag: fragments in clean bam


title: Cochlear SCs (Ikzf2 and Atoh1)-P60-11 [OHC like cells-10]

tag: strain

value: post natal day 60

tag: genotype

tag: cell type


title: L10_rep2

description: LiverL10_rep2_EKDL190133819-1a-7UDI1214-AK17202_HM55FDSXX_L2

tag: donor status


title: L10_rep1

description: LiverL10_rep1_EKDL190133819-1a-AK1576-AK17202_HM55FDSXX_L2


title: Time Course IBD.DAY12.SCI133_03_S3

tag: treatment

tag: time point


title: L7_rep2

description: LiverL7_rep2_EKDL190133819-1a-AK16533-AK13180_HM55FDSXX_L2


title: ATAC-Seq Pre-exposure prophylaxis sample 27, Alveolar macrophage, Mycobacterium tuberculosis challenged library

description:
Pre-exposure prophylaxis sample 27, Alveolar macrophage, Mycobacterium tuberculosis challenged library
Tn5 transposase

tag: ethnicity

value: Hispanic

tag: Sex

value: M

tag: sexually transmitted infections

value: chlamydia PCR+ and gonorrhea PCR+

tag: quantiferon tb reagent

tag: cd4 count

tag: prescription drugs

tag: sequencing run

tag: lane


title: Cochlear SCs (Ikzf2 and Atoh1)-P60-13 [OHC like cells-11]

tag: age

tag: tissue


title: Cochlear SCs (Ikzf2 and Atoh1)-P60-9 [OHC like cells-8]


title: L7_rep1

description: LiverL7_rep1_EKDL190133819-1a-AK1575-AK13180_HM55FDSXX_L2


title: Cochlear SCs (Ikzf2 and Atoh1)-P60-8 [OHC like cells-7]


title: Cochlear SCs (Ikzf2 and Atoh1)-P60-10 [OHC like cells-9]


title: Time Course IBD.DAY12.SCI133_02_S2

value: Colon


title: ATAC-Seq Healthy control sample 22, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library

description:
Healthy control sample 22, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library
Tn5 transposase

value: F

tag: active ingredient

tag: art start year

tag: recreational drugs

value: cannabis

tag: cigarette smoker

value: yes

tag: bal sampling date

tag: mtb challenged

tag: average tagmented library size

tag: fragments in clean bam


title: ATAC-Seq Healthy control sample 22, Alveolar macrophage, Mycobacterium tuberculosis challenged library

description:
Healthy control sample 22, Alveolar macrophage, Mycobacterium tuberculosis challenged library
Tn5 transposase

tag: ethnicity

tag: Sex

value: no


title: Time Course IBD.DAY09.SCI132_20_S20

tag: treatment

tag: time point

value: Day 9


title: Time Course IBD.DAY09.SCI132_19_S19


title: L5_rep2

description: LiverL5_rep2_EKDL190133819-1a-AK16808-AK14824_HM55FDSXX_L2

tag: donor status

value: control donors characterized by normoglycemia

value: Liver


title: L6_rep2

description: LiverL6_rep2_EKDL190133819-1a-AK16539-AK14824_HM55FDSXX_L2


title: Cochlear SCs (Ikzf2 and Atoh1)-P60-7 [Nascent HCs-1]

tag: strain

tag: genotype

value: Cochlea

tag: cell type

value: Cochlear supporting cells